references.bib

@article{abrams-pompe_role_2020,
  title = {The {{Role}} of {{Magnetic Resonance Imaging}} and {{Positron Emission Tomography}}/{{Computed Tomography}} in the {{Primary Staging}} of {{Newly Diagnosed Prostate Cancer}}: {{A Systematic Review}} of the {{Literature}}},
  author = {{Abrams-Pompe}, Raisa S. and Fanti, Stefano and Schoots, Ivo G. and Moore, Caroline M. and Turkbey, Baris and Vickers, Andrew J. and Walz, Jochen and Steuber, Thomas and Eastham, James A.},
  year = {2020},
  month = dec,
  journal = {European Urology Oncology},
  issn = {2588-9311},
  doi = {10.1016/j.euo.2020.11.002},
  abstract = {Context Management of newly diagnosed prostate cancer (PCa) is guided in part by accurate clinical staging. The role of imaging, including magnetic resonance imaging (MRI) and positron emission tomography/computed tomography (PET/CT), in initial staging remains controversial. Objective To systematically review the studies of MRI and/or PET/CT in the staging of newly diagnosed PCa with respect to tumor (T), nodal (N), and metastatic (M) staging (TNM staging). Evidence acquisition We performed a systematic review of the literature using MEDLINE and Web of Science databases between 2012 and 2020 following the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) statement guidelines. Evidence synthesis A total of 139 studies (83 on T, 47 on N, and 24 on M status) were included. Ninety-nine (71\%) were retrospective, 39 (28\%) were prospective, and one was a randomized controlled trial (RCT). Most studies on T staging examined MRI, while PET/CT was used primarily for N and M staging. Sensitivity for the detection of extraprostatic extension, seminal vesicle invasion, or lymph node invasion ranged widely. When imaging was incorporated into existing risk tools, gain in accuracy was observed in some studies, although these findings have not been replicated. For M staging, most favorable results were reported for prostate-specific membrane antigen (PSMA) PET/CT, which demonstrated significantly better performance than conventional imaging. Conclusions A variety of studies on modern imaging techniques for TNM staging in newly diagnosed PCa exist. For T and N staging, reported sensitivity of imaging modalities such as MRI or PET/CT varied widely due to data heterogeneity, small sample size, and low event rates resulting in large confidence intervals and a high level of uncertainty. Therefore, uniformity in data presentation and standardization on this topic are needed. The most promising technique for M staging, which was evaluated recently in an RCT, is PSMA-PET/CT. Patient summary We performed a systematic review of currently available imaging modalities to stage newly diagnosed prostate cancer. With respect to local tumor and lymph node assessment, performance of imaging ranged widely. However, prostate-specific membrane antigen positron emission tomography/computed tomography showed favorable results for the detection of distant metastases.},
  keywords = {Extraprostatic extension,Imaging,Lymph node metastases,Magnetic resonance imaging,Metastases,Positron emission tomography,Prostate cancer,Prostate-specific membrane antigen positron emission tomography/computed tomography,Staging},
  file = {C:\Users\roman\OneDrive\Documents\Library\Abrams-Pompe et al_2020_The Role of Magnetic Resonance Imaging and Positron Emission.pdf}
}

@article{al-mamgani_contralateral_2017,
  title = {Contralateral Regional Recurrence after Elective Unilateral Neck Irradiation in Oropharyngeal Carcinoma: {{A}} Literature-Based Critical Review},
  shorttitle = {Contralateral Regional Recurrence after Elective Unilateral Neck Irradiation in Oropharyngeal Carcinoma},
  author = {{Al-Mamgani}, Abrahim and {van Werkhoven}, Erik and Navran, Arash and Karakullukcu, Baris and {Hamming-Vrieze}, Olga and Machiels, Melanie and {van der Velden}, Lilly-Ann and Vogel, Wouter V. and Klop, W. Martin},
  year = {2017},
  month = sep,
  journal = {Cancer Treatment Reviews},
  volume = {59},
  pages = {102--108},
  issn = {0305-7372},
  doi = {10.1016/j.ctrv.2017.07.004},
  urldate = {2022-07-01},
  abstract = {Background The head and neck region has rich regional lymphatic network, with a theoretical risk on contralateral metastasis from oropharyngeal cancer (OPC). There is a long-standing convention to irradiate the great majority of these tumors electively to both sides of the neck to reduce the risk of contralateral regional failure (cRF), but this can induce significant toxicity. We aimed to identify patient groups where elective contralateral irradiation may safely be omitted. Methods PubMed and EMBASE were searched for original full-text articles in English with a combination of search terms related to the end points: cRF in OPC primarily treated by radiotherapy only to the ipsilateral neck and identifying predictive factors for increased incidence of cRF. The data from the identified studies were pooled, the incidence of cRF was calculated and the correlation with different predictive factors was investigated. Results Eleven full-text articles met the inclusion criteria. In these studies, 1116 patients were treated to the ipsilateral neck alone. The mean incidence of cRF was 2.42\% (range 0{\textendash}5.9\%, 95\% CI 1.6{\textendash}3.5\%). The incidence of cRF correlated only with T-stage (p=0.008), and involvement of midline (p=0.001). However, the significant correlation with T-stage can be explained by the very low incidence of cRF among T1 (0.77\%), and disappeared when the incidence of cRF was compared between T2, T3,and T4 (p=0.344). Conclusion The incidence of cRF in patients with OPC is very low, with involvement of midline providing the most significant prognosticator. These results call for trials on unilateral elective irradiation in selected groups.},
  langid = {english},
  keywords = {Contralateral failure,Contralateral regional recurrence,Elective irradiation,Oropharyngeal cancer,Unilateral neck irradiation},
  file = {C:\Users\roman\Zotero\storage\NS4YUGLN\S0305737217301093.html}
}

@article{aldridge_group_2019,
  title = {Group {{Testing}}: {{An Information Theory Perspective}}},
  shorttitle = {Group {{Testing}}},
  author = {Aldridge, Matthew and Johnson, Oliver and Scarlett, Jonathan},
  year = {2019},
  journal = {Foundations and Trends{\textregistered} in Communications and Information Theory},
  volume = {15},
  number = {3-4},
  eprint = {1902.06002},
  pages = {196--392},
  issn = {1567-2190, 1567-2328},
  doi = {10.1561/0100000099},
  urldate = {2022-02-01},
  abstract = {The group testing problem concerns discovering a small number of defective items within a large population by performing tests on pools of items. A test is positive if the pool contains at least one defective, and negative if it contains no defectives. This is a sparse inference problem with a combinatorial flavour, with applications in medical testing, biology, telecommunications, information technology, data science, and more. In this monograph, we survey recent developments in the group testing problem from an information-theoretic perspective. We cover several related developments: efficient algorithms with practical storage and computation requirements, achievability bounds for optimal decoding methods, and algorithm-independent converse bounds. We assess the theoretical guarantees not only in terms of scaling laws, but also in terms of the constant factors, leading to the notion of the \{{\textbackslash}em rate\} of group testing, indicating the amount of information learned per test. Considering both noiseless and noisy settings, we identify several regimes where existing algorithms are provably optimal or near-optimal, as well as regimes where there remains greater potential for improvement. In addition, we survey results concerning a number of variations on the standard group testing problem, including partial recovery criteria, adaptive algorithms with a limited number of stages, constrained test designs, and sublinear-time algorithms.},
  archiveprefix = {arxiv},
  keywords = {Computer Science - Discrete Mathematics,Computer Science - Information Theory,Mathematics - Probability,Mathematics - Statistics Theory},
  file = {C\:\\Users\\roman\\OneDrive\\Desktop\\aldridge_group_2019-zotero.md;C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Aldridge et al_2019_Group Testing.pdf;C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Aldridge et al_2019_Group Testing2.pdf;C\:\\Users\\roman\\Zotero\\storage\\DXERFHPD\\1902.html}
}

@book{ang_radiotherapy_2011,
  title = {Radiotherapy for {{Head}} and {{Neck Cancers}}: {{Indications}} and {{Techniques}}},
  author = {Ang, K K and Garden, A S},
  year = {2011},
  publisher = {{Williams \& Wilkins}}
}

@article{aponte_introduction_2022,
  title = {An Introduction to Thermodynamic Integration and Application to Dynamic Causal Models},
  author = {Aponte, Eduardo A. and Yao, Yu and Raman, Sudhir and Fr{\"a}ssle, Stefan and Heinzle, Jakob and Penny, Will D. and Stephan, Klaas E.},
  year = {2022},
  month = feb,
  journal = {Cognitive Neurodynamics},
  volume = {16},
  number = {1},
  pages = {1--15},
  issn = {1871-4080, 1871-4099},
  doi = {10.1007/s11571-021-09696-9},
  urldate = {2022-08-03},
  abstract = {In generative modeling of neuroimaging data, such as dynamic causal modeling (DCM), one typically considers several alternative models, either to determine the most plausible explanation for observed data (Bayesian model selection) or to account for model uncertainty (Bayesian model averaging). Both procedures rest on estimates of the model evidence, a principled trade-off between model accuracy and complexity. In the context of DCM, the log evidence is usually approximated using variational Bayes. Although this approach is highly efficient, it makes distributional assumptions and is vulnerable to local extrema. This paper introduces the use of thermodynamic integration (TI) for Bayesian model selection and averaging in the context of DCM. TI is based on Markov chain Monte Carlo sampling which is asymptotically exact but orders of magnitude slower than variational Bayes. In this paper, we explain the theoretical foundations of TI, covering key concepts such as the free energy and its origins in statistical physics. Our aim is to convey an in-depth understanding of the method starting from its historical origin in statistical physics. In addition, we demonstrate the practical application of TI via a series of examples which serve to guide the user in applying this method. Furthermore, these examples demonstrate that, given an efficient implementation and hardware capable of parallel processing, the challenge of high computational demand can be overcome successfully. The TI implementation presented in this paper is freely available as part of the open source software TAPAS.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Aponte et al_2022_An introduction to thermodynamic integration and application to dynamic causal.pdf}
}

@article{attenberger_stellenwert_nodate,
  title = {{Stellenwert und qualitative Voraussetzungen der Magnetresonanztomografie (MRT) f{\"u}r die Therapieplanung beim~Rektumkarzinom {\textendash} Interdisziplin{\"a}re Empfehlungen der AIO, ARO, ACO und der Deutschen R{\"o}ntgengesellschaft}},
  author = {Attenberger, Ulrike Irmgard and Clasen, Stephan and Ghadimi, Michael and Grosse, Ulrich and Antoch, Gerald and Schreyer, Andreas G. and Wessling, Johannes and Hausmann, Daniel and Piso, Pompiliu and Plodeck, Verena and Stintzing, Sebastian and R{\"o}del, Claus Michael and Hofheinz, Ralf Dieter},
  year = {1},
  journal = {R{\"o}Fo},
  number = {EFirst},
  publisher = {{Thieme. All rights reserved.}},
  issn = {1438-9029},
  doi = {10.1055/a-1299-1807},
  urldate = {2021-02-04},
  abstract = {Abstract Due to its excellent intrinsic soft tissue contrast, magnetic resonance imaging allows excellent visualization and anatomical separation of therapy-relevant risk structures such as the mesorectal fascia, local lymph nodes, and vascular structures in patients with rectal carcinoma. This makes magnetic resonance imaging (MRI) a valuable evaluation method for further therapeutic stratification. In particular, MRI is indispensable for the decision to refrain from neoadjuvant therapy and to choose a primary surgical approach. In addition to the oncologically generally relevant T-, N-, and M-criteria, two further parameters are included: the extramural vascular infiltration and the circumferential resection margin. Due to the significant impact of MRI on further therapeutic decision-making, standardized MR image quality is considered essential. Key Points: \hspace{0.6em} Magnetic resonance imaging is a valuable evaluation method for further therapeutic stratification. Critical anatomic landmarks for evaluation are circumferential resection margins. Citation Format Attenberger UI, Clasen S, Ghadimi M et{$\mkern1mu$}al. Importance and Qualitative Requirements of Magnetic Resonance Imaging for Therapy Planning in Rectal Cancer {\textendash} Interdisciplinary Recommendations of AIO, ARO, ACO and the German Radiological Society. Fortschr R{\"o}ntgenstr 2020; DOI: 10.1055/a-1299-1807 Zusammenfassung Die Magnetresonanztomografie (MRT) erlaubt aufgrund ihres ausgezeichneten intrinsischen Weichteilkontrastes bei Patienten mit Rektumkarzinom eine hervorragende Darstellung und anatomische Separation therapierelevanter Risikostrukturen wie der mesorektalen Faszie, lokaler Lymphknoten und benachbarter Organe. Dies macht die MRT zu einer wertvollen Bewertungsmethode f{\"u}r die therapeutische Stratifizierung. Insbesondere ist die MRT unverzichtbar f{\"u}r die Entscheidung f{\"u}r den Verzicht auf eine neoadjuvante Therapie und die Wahl eines prim{\"a}r operativen Vorgehens. Neben den onkologisch allgemein relevanten T-, N- und M-Kriterien finden 2~weitere Parameter Eingang: die extramurale Gef{\"a}{\ss}infiltration und der zirkumferenzielle Resektionsrand. Aufgrund des wesentlichen Einflusses des MRTs auf die therapeutische Entscheidungsfindung ist eine fl{\"a}chendeckende, standardisierte Bildqualit{\"a}t essenziell. Kernaussagen: \hspace{0.6em} Die MRT ist eine wertvolle Bewertungsmethode f{\"u}r die weitere therapeutische Stratifizierung des Rektumkarzinoms. Wesentliche Kriterien f{\"u}r die therapeutische Stratifizierung sind: mesorektale Faszie (MRF), Lymphknotensituation, extramurale Gef{\"a}{\ss}infiltration. Zitierweise Attenberger UI, Clasen S, Ghadimi M et{$\mkern1mu$}al. Importance and Qualitative Requirements of Magnetic Resonance Imaging for Therapy Planning in Rectal Cancer {\textendash} Interdisciplinary Recommendations of AIO, ARO, ACO and the German Radiological Society. Fortschr R{\"o}ntgenstr 2020; DOI: 10.1055/a-1299-1807},
  langid = {ngerman},
  keywords = {CRM,MRI,rectal cancer,therapeutic stratification},
  file = {C:\Users\roman\OneDrive\Documents\Library\Attenberger et al_0000_Stellenwert und qualitative Voraussetzungen der Magnetresonanztomografie (MRT).pdf}
}

@article{avanzini_cancer_2019,
  title = {Cancer Recurrence Times from a Branching Process Model},
  author = {Avanzini, Stefano and Antal, Tibor},
  year = {2019},
  month = nov,
  journal = {PLOS Computational Biology},
  volume = {15},
  number = {11},
  pages = {e1007423},
  publisher = {{Public Library of Science}},
  doi = {10.1371/journal.pcbi.1007423},
  abstract = {Author summary The majority of cancer related deaths are due to the development of secondary tumors called metastases. However, the dynamics of metastases establishment and growth and their relation with the primary tumor evolution are still not clear. A standard treatment starts with the resection of the primary tumor. At this time metastases may have already formed and still be too small to be detected. The presence of only undetectable metastases poses a challenge for deciding on the follow-up therapy. These small metastases could grow to a detectable size{\textemdash}thus leading to a recurrence of the disease{\textemdash}some time after surgery. We are interested in this time until cancer relapse. We present a mathematical model of metastases formation using tools from probability theory and estimate the model parameters for five different cancer types. Our predictions for the probability of visible metastases present at surgery and the mean time to relapse when no visible metastases are found at surgery are both in agreement with clinical data.},
  file = {C:\Users\roman\OneDrive\Documents\Library\Avanzini_Antal_2019_Cancer recurrence times from a branching process model.pdf}
}

@article{bahig_vocal-cord_2021,
  title = {Vocal-Cord {{Only}} vs. {{Complete Laryngeal}} Radiation ({{VOCAL}}): A Randomized Multicentric {{Bayesian}} Phase {{II}} Trial},
  shorttitle = {Vocal-Cord {{Only}} vs. {{Complete Laryngeal}} Radiation ({{VOCAL}})},
  author = {Bahig, Houda and Rosenthal, David I. and {Nguyen-Tan}, F{\'e}lix-Phuc and Fuller, David C. and Yuan, Ying and Hutcheson, Katherine A. and Christopoulos, Apostolos and Nichols, Anthony C. and Fung, Kevin and Ballivy, Olivier and Filion, Edith and Ng, Sweet Ping and Lambert, Louise and Dorth, Jennifer and Hu, Kenneth S. and Palma, David},
  year = {2021},
  month = apr,
  journal = {BMC Cancer},
  volume = {21},
  number = {1},
  pages = {446},
  issn = {1471-2407},
  doi = {10.1186/s12885-021-08195-8},
  urldate = {2023-07-20},
  abstract = {Radiotherapy, along with laser surgery, is considered a standard treatment option for patients with early glottic squamous cell cancer (SCC). Historically, patients have received complete larynx radiotherapy (CL-RT) due to fear of swallowing and respiratory laryngeal motion and this remains the standard approach in many academic institutions. Local control (LC) rates with CL-RT have been excellent, however this treatment can carry significant toxicities include adverse voice and swallowing outcomes, along with increased long-term risk of cerebrovascular morbidity. A recent retrospective study reported improved voice quality and similar local control outcomes with focused vocal cord radiotherapy (VC-RT) compared to CL-RT. There is currently no prospective evidence on the safety of VC-RT. The primary objective of this Bayesian Phase II trial is to compare the LC of VC-RT to that of CL-RT in patients with T1N0 glottic SCC.},
  keywords = {Glottic cancer,Larynx,Local control,Radiotherapy,Vocal cord},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Bahig et al_2021_Vocal-cord Only vs.pdf;C\:\\Users\\roman\\Zotero\\storage\\X8YLTWC4\\s12885-021-08195-8.html}
}

@article{bassioni_risk_2012,
  title = {Risk {{Assessment}} of {{Using Aluminum Foil}} in {{Food Preparation}}},
  author = {Bassioni, Ghada and Mohammed, Fathia S and Zubaidy, Essam Al and Kobrsi, Issam},
  year = {2012},
  journal = {Int. J. Electrochem. Sci.},
  volume = {7},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Bassioni et al_2012_Risk Assessment of Using Aluminum Foil in Food Preparation.pdf}
}

@article{bataini_natural_1985,
  title = {Natural History of Neck Disease in Patients with Squamous Cell Carcinoma of Oropharynx and Pharyngolarynx},
  author = {Bataini, J and {Others}},
  year = {1985},
  journal = {Radiother. Oncol.},
  volume = {3},
  pages = {245--255},
  doi = {10.1016/S0167-8140(85)80033-5}
}

@article{batth_practical_2014,
  title = {Practical Considerations in Reducing Swallowing Dysfunction Following Concurrent Chemoradiotherapy with Intensity-Modulated Radiotherapy for Head and Neck Cancer},
  author = {Batth, S S and Caudell, J J and Chen, A M},
  year = {2014},
  journal = {Head Neck},
  volume = {36},
  pages = {291--298},
  doi = {10.1002/hed.23246}
}

@article{bauwens_prevalence_2021,
  title = {Prevalence and Distribution of Cervical Lymph Node Metastases in {{HPV-positive}} and {{HPV-negative}} Oropharyngeal Squamous Cell Carcinoma},
  author = {Bauwens, Laurence and Baltres, Aline and Fiani, Danny-Joe and Zrounba, Philippe and Buiret, Guillaume and Fleury, Bertrand and Benzerdjeb, Nazim and Gr{\'e}goire, Vincent},
  year = {2021},
  month = apr,
  journal = {Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology},
  volume = {157},
  pages = {122--129},
  issn = {1879-0887},
  doi = {10.1016/j.radonc.2021.01.028},
  abstract = {OBJECTIVE: In oropharyngeal squamous cell carcinoma (OP-SCC), the prevalence and distribution of clinical and pathological lymph node metastasis in the neck have been extensively reported. It served as the basis for consensus recommendations on the selection of the lymph node levels in the neck requiring a treatment. The objective of the study is to compare the prevalence and distribution of neck node metastases in HPV+ and HPV- OP-SCC from a large series of patients with OP-SCC who underwent a cervical lymph-node dissection (LND) as part of their treatment. METHODS: The study concentrated on OP-SCC patients treated by various neck node dissection (LND) procedures from January 2014 to December 2018 in 3 French institutions. Patients with prior head and neck cancer, prior neck surgery, the use of induction chemotherapy, or patients with carcinoma of unknown primary were excluded. HPV-status was assessed by p16 immunohistochemistry. For each patient, the clinical and the pathological nodal status, as well as the distribution of the positive nodes in each neck level (from Ia to V) were reported. RESULTS: Two-hundred and sixty-three patients were included (126 p16-negative (p16-), and 137 p16-positive (p16+). The rate of clinical positive node (cN+) reached 54\% and 88.3\% in the p16- and p16+ groups, respectively (p~{$<~$}0.001); the corresponding rate of pathological positive node (pN+) reached 61.9\% and 91.2\%, respectively (p~{$<~$}0.001). Regarding the clinical lymph node distribution, in p16+ patients, more positive nodes were observed in the ipsilateral level IV (p~=~0.003), and less positive nodes were observed in the contralateral levels III and IV (p~=~0.003 and p~=~0.045, respectively). Regarding the pathologic lymph node distribution in the ipsilateral neck, in the cN0 patients, no significant difference was observed between p16- and p16+ patients (p~=~0.33 to 1); in the cN+ patients, the nodes were distributed in levels Ib, II, III, IV and V without differences between the p16- and the p16+ patients. In the contralateral neck of p16- patients, nodes metastases were mainly observed in levels II, III and IV, whereas for the p16+ patients, positive nodes were only observed in level II (p~=~0.03). CONCLUSION: This study demonstrated the higher prevalence of cN+ and pN+ in p16+ OP-SCC patients, but without meaningful difference in the distribution of the lymph node drainage between p16- and p16+ OP-SCC. It indicates that no difference should be made between p16- and p16+ patients regarding the extend of neck treatment.},
  langid = {english},
  pmid = {33545255},
  keywords = {head \& neck,Head and Neck Neoplasms,Human Papillomavirus (HPV),Humans,Lymph node metastases,Lymph Nodes,Lymphatic Metastasis,Neck dissection,Oropharyngeal Neoplasms,Oropharynx,p16,Papillomavirus Infections,Prevalence,Radiotherapy,Retrospective Studies,Squamous Cell Carcinoma of Head and Neck},
  file = {C:\Users\roman\OneDrive\Documents\Library\Bauwens et al_2021_Prevalence and distribution of cervical lymph node metastases in HPV-positive.pdf}
}

@article{benson_markov_2006,
  title = {A {{Markov}} Model Approach to Predicting Regional Tumor Spread in the Lymphatic System of the Head and Neck},
  author = {Benson, Noah and Whipple, Mark and Kalet, Ira J},
  year = {2006},
  journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium},
  pages = {31--35},
  issn = {1942-597X},
  abstract = {Radiation planning for cancer therapy is becoming more and more dependent on the prediction of microscopic tumor spread to regional lymph nodes for its success. It is known that microscopic spread tends to follow established lymphatic drainage pathways in the head and neck based on the location of the primary tumor. In this paper,we propose a novel model for the prediction of regional lymphatic involvement of head and neck squamous cell carcinoma based on primary tumor location and T-stage. The proposed model operates from first anatomical principles and basic stochastic techniques, and is validated against surgical data.},
  langid = {english},
  keywords = {Lymphatic Metastasis,Markov Chains},
  file = {C:\Users\roman\OneDrive\Documents\Library\Benson et al_2006_A Markov model approach to predicting regional tumor spread in the lymphatic.pdf}
}

@article{bertsch_rheology_2019,
  title = {Rheology of {{Swiss Cheese Fondue}}},
  author = {Bertsch, Pascal and Savorani, Laura and Fischer, Peter},
  year = {2019},
  month = jan,
  journal = {ACS Omega},
  volume = {4},
  number = {1},
  pages = {1103--1109},
  issn = {2470-1343},
  doi = {10.1021/acsomega.8b02424},
  urldate = {2022-11-23},
  abstract = {, Cheese fondue is a popular Swiss dish prepared by melting cheese under the addition of wine, starch, and seasoning. The flow behavior or rheology of fondue is crucial for mouthfeel, flavor release, and the tendency of fondue to cling to the bread. Fondue is a complex multiphase system whose rheology is determined by the interactions of its colloidal ingredients. We establish cheese fondue as a water-continuous system with dispersed fat droplets, charged caseins, and starch granules. Irreversible phase separation, a common issue in fondue preparation, may be prevented by addition of a critical minimum starch concentration. Fondue was found to be a shear-thinning yield stress fluid, which is desirable for mouthfeel and facilitates fondue to cling to the bread for consumption. Fondue showed a viscoelastic stress response around the gel point (G{${'}$} {$\approx$} G{${''}$}), which is proposed as crucial for the balance of orally perceived gumminess (G{${'}$}) and liquidity (G{${''}$}). Ethanol addition and lowering pH toward the isoelectric point of casein, as associated with wine addition, decrease fondue viscosity due to a decrease in casein micelle size. Below the isoelectric point of casein, fondue is unstable and phase separates, potentially impeding fondue digestion. Thus, fondue rheology is governed by the complex colloidal interactions within its ingredients, and ultimately determines fondue eating experience.},
  pmcid = {PMC6648832},
  pmid = {31459386},
  file = {C:\Users\roman\OneDrive\Documents\Library\Bertsch et al_2019_Rheology of Swiss Cheese Fondue.pdf}
}

@book{beyzadeoglu_radiation_2015,
  title = {Radiation {{Therapy}} for {{Head}} and {{Neck Cancers}}: A {{Case-Based Review}}},
  author = {Beyzadeoglu, M and Ozyigit, G and Selek, U},
  year = {2015},
  publisher = {{Springer}}
}

@article{bhat_derivation_2010,
  title = {On the {{Derivation}} of the {{Bayesian Information Criterion}}},
  author = {Bhat, Harish and Kumar, Nitesh},
  year = {2010},
  month = jan,
  abstract = {We present a careful derivation of the Bayesian Inference Criterion (BIC) for model selection. The BIC is viewed here as an approximation to the Bayes Factor. One of the main ingredients in the approximation, the use of Laplace's method for approximating integrals, is explained well in the literature. Our derivation sheds light on this and other steps in the derivation, such as the use of a flat prior and the invocation of the weak law of large numbers, that are not often discussed in detail.},
  file = {C\:\\Users\\roman\\OneDrive\\Desktop\\bhat_derivation_2010-zotero.md;C\:\\Users\\roman\\OneDrive\\Desktop\\bhat_derivation_2010.md;C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Bhat_Kumar_2010_On the Derivation of the Bayesian Information Criterion2.pdf}
}

@article{bhattacharya_lymph_2021-2,
  title = {Lymph Node Extracapsular Extension as a Marker of Aggressive Phenotype: {{Classification}}, Prognosis and Associated Molecular Biomarkers},
  shorttitle = {Lymph Node Extracapsular Extension as a Marker of Aggressive Phenotype},
  author = {Bhattacharya, Priyanka and Mukherjee, Rajarshi},
  year = {2021},
  month = apr,
  journal = {European Journal of Surgical Oncology},
  volume = {47},
  number = {4},
  pages = {721--731},
  issn = {0748-7983},
  doi = {10.1016/j.ejso.2020.09.005},
  urldate = {2023-03-10},
  abstract = {Lymph node extracapsular extension, also termed extranodal extension or extracapsular spread (ECS) from lymph nodes, is a key characteristic of aggressive phenotype in cancer, carrying a major impact on prognosis. Controversy exists with regards the classification of ECS by different histopathological assessment methods published in the literature. Whilst much focus has been placed on ECS in the setting of head and neck cancer, numerous studies also highlight its significance in a range of other malignancies, including a wide range of gastrointestinal malignancies. Prognostically, the presence of ECS broadly negatively impacts on disease recurrence and survival, with a greater range of studies now demonstrating how the nature and extent of ECS influences disease outcomes. Molecular techniques such as DNA sequencing and immunohistochemistry have identified molecular biomarkers associated with ECS. Knowledge of these biomarkers will help guide future broader studies. Technological advancements resulting from the recent -omics revolution and utilising an early, wide-ranging, and integrated approach, provide the prospect of improved identification of biomarkers associated with aggressive phenotype. These approaches may validate existing putative biomarkers or identify novel independent prognostic and predictive biomarkers, facilitating a future personalized medicine approach.},
  langid = {english},
  keywords = {Biomarker,Cancer,Extracapsular spread,Lymph node,Metastasis},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Bhattacharya_Mukherjee_2021_Lymph node extracapsular extension as a marker of aggressive phenotype.pdf;C\:\\Users\\roman\\Zotero\\storage\\HPUSU86S\\S0748798320307757.html}
}

@article{biau_selection_2019,
  title = {Selection of Lymph Node Target Volumes for Definitive Head and Neck Radiation Therapy: A 2019 {{Update}}},
  author = {Biau, Julian and Lapeyre, Michel and Troussier, Idriss and Budach, Wilfried and Giralt, Jordi and Grau, Cai and Kazmierska, Joanna and Langendijk, Johannes A. and Ozsahin, Mahmut and O'Sullivan, Brian and Bourhis, Jean and Gr{\'e}goire, Vincent},
  year = {2019},
  month = may,
  journal = {Radiotherapy and Oncology},
  volume = {134},
  pages = {1--9},
  publisher = {{Elsevier}},
  issn = {0167-8140},
  doi = {10.1016/j.radonc.2019.01.018},
  urldate = {2021-02-08},
  keywords = {guideline},
  file = {C:\Users\roman\OneDrive\Documents\Library\Biau et al_2019_Selection of lymph node target volumes for definitive head and neck radiation.pdf}
}

@article{binder_adaptive_1997,
  title = {Adaptive Probabilistic Networks with Hidden Variables},
  author = {Binder, J and {Others}},
  year = {1997},
  journal = {Mach. Learn.},
  volume = {29},
  pages = {213--244},
  doi = {10.1023/A:1007421730016}
}

@book{bishop_pattern_2006,
  title = {Pattern Recognition and Machine Learning},
  author = {Bishop, Christopher M.},
  year = {2006},
  series = {Information Science and Statistics},
  publisher = {{Springer}},
  address = {{New York}},
  isbn = {978-0-387-31073-2},
  langid = {english},
  lccn = {Q327 .B52 2006},
  keywords = {Machine learning,Pattern perception},
  file = {C:\Users\roman\OneDrive\Documents\Library\Bishop_2006_Pattern recognition and machine learning.pdf}
}

@article{bissiri_general_2016,
  title = {A General Framework for Updating Belief Distributions},
  author = {Bissiri, P. G. and Holmes, C. C. and Walker, S. G.},
  year = {2016},
  month = nov,
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume = {78},
  number = {5},
  pages = {1103--1130},
  issn = {13697412},
  doi = {10.1111/rssb.12158},
  urldate = {2022-08-03},
  abstract = {We propose a framework for general Bayesian inference. We argue that a valid update of a prior belief distribution to a posterior can be made for parameters which are connected to observations through a loss function rather than the traditional likelihood function, which is recovered as a special case. Modern application areas make it increasingly challenging for Bayesians to attempt to model the true data-generating mechanism. For instance, when the object of interest is low dimensional, such as a mean or median, it is cumbersome to have to achieve this via a complete model for the whole data distribution. More importantly, there are settings where the parameter of interest does not directly index a family of density functions and thus the Bayesian approach to learning about such parameters is currently regarded as problematic. Our framework uses loss functions to connect information in the data to functionals of interest. The updating of beliefs then follows from a decision theoretic approach involving cumulative loss functions. Importantly, the procedure coincides with Bayesian updating when a true likelihood is known yet provides coherent subjective inference in much more general settings. Connections to other inference frameworks are highlighted.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Bissiri et al_2016_A general framework for updating belief distributions.pdf}
}

@article{blackburn_whole_2014,
  title = {Whole {{Body}} and {{Local Muscle Vibration Reduce Artificially Induced Quadriceps Arthrogenic Inhibition}}},
  author = {Blackburn, J. Troy and Pamukoff, Derek N. and Sakr, Mark and Vaughan, Aaron J. and Berkoff, David J.},
  year = {2014},
  month = nov,
  journal = {Archives of Physical Medicine and Rehabilitation},
  volume = {95},
  number = {11},
  pages = {2021--2028},
  issn = {0003-9993},
  doi = {10.1016/j.apmr.2014.07.393},
  urldate = {2021-11-08},
  abstract = {Objective To evaluate the effects of whole body vibration (WBV) and local muscle vibration (LMV) on quadriceps function after experimental knee effusion (ie, simulated pathology). Design Randomized controlled trial. Setting Research laboratory. Participants Healthy volunteers (N=43) were randomized to WBV (n=14), LMV (n=16), or control (n=13) groups. Interventions Saline was injected into the knee to induce quadriceps arthrogenic muscle inhibition (AMI). All groups then performed isometric squats while being exposed to WBV, LMV, or no vibration (control). Main Outcome Measures Quadriceps function was assessed at baseline, immediately after effusion, and immediately and 5 minutes after each intervention (WBV, LMV, control) via voluntary peak torque (VPT) and the central activation ratio (CAR) during maximal isometric knee extension on a multifunction dynamometer. Results The CAR improved in the WBV (11.4\%, P=.021) and LMV (7.3\%, P{$<$}.001) groups immediately postintervention, but they did not improve in the control group. Similarly, VPT increased by 16.5\% (P=.021) in the WBV group and 23\% (P=.078) in the LMV group immediately postintervention, but it did not increase in the control group. The magnitudes of improvements in the CAR and VPT did not differ between the WBV and LMV groups. Conclusions Quadriceps AMI is a common complication following knee pathology that produces quadriceps dysfunction and increases the risk of posttraumatic osteoarthritis. Quadriceps strengthening after knee pathology is often ineffective because of AMI. WBV and LMV improve quadriceps function equivocally after simulated knee pathology, effectively minimizing quadriceps AMI. Therefore, these stimuli may be used to enhance quadriceps strengthening, therefore improving the efficacy of rehabilitation and reducing the risk of osteoarthritis.},
  langid = {english},
  keywords = {Anterior cruciate ligament,Knee,Osteoarthritis,Quadriceps muscle,Rehabilitation,Vibration},
  file = {C:\Users\roman\OneDrive\Documents\Library\Blackburn et al_2014_Whole Body and Local Muscle Vibration Reduce Artificially Induced Quadriceps.pdf}
}

@article{blackwelder_proving_1982,
  title = {``{{Proving}} the Null Hypothesis'' in Clinical Trials},
  author = {Blackwelder, William C.},
  year = {1982},
  month = dec,
  journal = {Controlled Clinical Trials},
  volume = {3},
  number = {4},
  pages = {345--353},
  issn = {0197-2456},
  doi = {10.1016/0197-2456(82)90024-1},
  urldate = {2023-07-04},
  abstract = {When designing a clinical trial to show whether a new or experimental therapy is as effective as a standard therapy (but not necessarily more effective), the usual null hypothesis of equality is inappropriate and leads to logical difficulties. Since therapies cannot be shown to be literally equivalent, the appropriate null hypothesis is that the standard therapy is more effective than the experimental therapy by at least some specified amount. The problem is presented in terms of a trial in which the outcome of interest is dichotomous; test statistics, confidence intervals, and sample size calculations are discussed. The required sample size may be larger for either null hypothesis formulation than for the other, depending on the specific assumptions made. Reporting results in terms of confidence intervals is especially useful for this type of trial.},
  langid = {english},
  keywords = {confidence interval,design,null hypothesis,sample size},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Blackwelder_1982_“Proving the null hypothesis” in clinical trials.pdf;C\:\\Users\\roman\\Zotero\\storage\\MCLZWUHU\\0197245682900241.html}
}

@article{bradley_rank_1952,
  title = {Rank {{Analysis}} of {{Incomplete Block Designs}}: {{I}}. {{The Method}} of {{Paired Comparisons}}},
  shorttitle = {Rank {{Analysis}} of {{Incomplete Block Designs}}},
  author = {Bradley, Ralph Allan and Terry, Milton E.},
  year = {1952},
  journal = {Biometrika},
  volume = {39},
  number = {3/4},
  eprint = {2334029},
  eprinttype = {jstor},
  pages = {324--345},
  publisher = {{[Oxford University Press, Biometrika Trust]}},
  issn = {0006-3444},
  doi = {10.2307/2334029},
  urldate = {2022-08-17},
  file = {C:\Users\roman\OneDrive\Documents\Library\Bradley_Terry_1952_Rank Analysis of Incomplete Block Designs.pdf}
}

@techreport{bratman_-escalation_nodate,
  type = {Clinical {{Trial}}},
  title = {De-{{Escalation Radiotherapy}} in {{Patients With Low-Risk HPV-Related Oropharyngeal Squamous Cell Carcinoma}}},
  shorttitle = {{{EVADER}}},
  author = {Bratman, Scott},
  number = {NCT03822897},
  address = {{Toronto, Canada}},
  institution = {{Princess Margaret Cancer Centre}},
  urldate = {2022-10-25},
  abstract = {The purpose of this study is to find out whether radiotherapy to some of the lymph node areas can be safely omitted to decrease side effects without increasing the risk of the tumour coming back. The standard or usual treatment for this disease includes radiotherapy or radiotherapy combined with chemotherapy or antibody therapy. These treatments are highly effective at curing most patients with HPV-related cancer of the oropharynx, but short and long-term side effects from treatment can be significant.}
}

@article{bratman_cctg_2020,
  title = {{{CCTG HN}}.10: {{A}} Phase {{II}} Single-Arm Trial of Elective Volume Adjusted de-Escalation Radiotherapy ({{EVADER}}) in Patients with Low-Risk {{HPV-related}} Oropharyngeal Squamous Cell Carcinoma ({{NCT03822897}}).},
  shorttitle = {{{CCTG HN}}.10},
  author = {Bratman, Scott Victor and Berthelet, Eric and Butler, James B. and {de Almeida}, John R and Karam, Irene and Metser, Ur and Olson, Robert Anton and Pochini, Craig and Waldron, John and Yu, Eugene and McNiven, Andrea and Cheung, Winson Y. and Gaudet, Marc and Hunter, Sarah and Chen, Bingshu E. and Parulekar, Wendy R.},
  year = {2020},
  month = may,
  journal = {Journal of Clinical Oncology},
  volume = {38},
  number = {15\_suppl},
  pages = {TPS6592-TPS6592},
  publisher = {{Wolters Kluwer}},
  issn = {0732-183X},
  doi = {10.1200/JCO.2020.38.15_suppl.TPS6592},
  urldate = {2022-07-01},
  abstract = {TPS6592 Background: Treatment for HPV positive(+) oropharyngeal squamous cell carcinoma (OSCC) is highly effective but associated with significant short and long term treatment related morbidity. We hypothesize that decreasing the regions of elective nodal irradiation (ENI) in the neck will lead to less toxicity and better quality of life/functional outcomes while maintaining high disease control rates in patients with favourable prognosis HPV+ OSCC. Methods: HN.10 is a Canadian Cancer Trials Group phase II trial with a primary objective to evaluate the efficacy of primary definitive radiotherapy (RT) or chemoradiotherapy (CRT) utilizing volume reduced ENI as measured by 2-year event-free survival (EFS) in patients with low-risk HPV+ OPSCC. Secondary objectives include to evaluate overall survival, local control, regional control, locoregional control, out-of-field regional control, distant metastasis free survival, early and late toxicities of treatment, subjective swallowing functions, quality of life, utilization of healthcare resources, work productivity, and prognostic biomarkers. An imaging and biospecimen bank will be compiled as part of trial conduct. Key eligibility criteria include: pathologically proven diagnosis of HPV+ OPSCC; HPV association determined locally by either p16 immunohistochemistry or direct detection of HPV DNA sequences (e.g. by PCR or in situ hybridization) performed on a core needle or surgical biopsy specimen of the primary tumour or involved cervical lymph node; clinical stage T1-3 N0-1 M0 (UICC/AJCC 8th Ed.); fit for radiotherapy +/-chemoradiotherapy. Statistical Design: The primary endpoint is 2-year EFS. Assuming 2-year EFS to be 91\% (Ha) for low-risk HPV-related OPSCC with standard treatment, and that the experimental treatment will be considered as ineffective if the 2-year EFS is {$\leq$} 85\% (H0), with one-sided alpha of 0.1, a sample size of 100 patients will have 80\% power to detect a 6\% difference of 2-year EFS. With 3 years of accrual and 2 years of follow-up, the total duration of this study will be 5 years. A total of 304.7 person-years of follow-up is needed for the final analysis. The null hypothesis (H0) will be rejected when the observed survival rate is 88.85\% or higher (i.e. if there are 18 or fewer EFS events observed). Conduct to Date: Study activation February 20, 2019. Enrollment as of January 29 2020: 23. Clinical trial information: NCT03822897.},
  keywords = {2,261-137-440,261-137-7270,261-265,283-147-7027-9452,283-6695,3,38092-22180,4,613-135-2563-5094,7}
}

@article{bray_global_2018,
  title = {Global Cancer Statistics 2018: {{GLOBOCAN}} Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries},
  shorttitle = {Global Cancer Statistics 2018},
  author = {Bray, Freddie and Ferlay, Jacques and Soerjomataram, Isabelle and Siegel, Rebecca L. and Torre, Lindsey A. and Jemal, Ahmedin},
  year = {2018},
  journal = {CA: A Cancer Journal for Clinicians},
  volume = {68},
  number = {6},
  pages = {394--424},
  issn = {1542-4863},
  doi = {10.3322/caac.21492},
  urldate = {2022-10-06},
  abstract = {This article provides a status report on the global burden of cancer worldwide using the GLOBOCAN 2018 estimates of cancer incidence and mortality produced by the International Agency for Research on Cancer, with a focus on geographic variability across 20 world regions. There will be an estimated 18.1 million new cancer cases (17.0 million excluding nonmelanoma skin cancer) and 9.6 million cancer deaths (9.5 million excluding nonmelanoma skin cancer) in 2018. In both sexes combined, lung cancer is the most commonly diagnosed cancer (11.6\% of the total cases) and the leading cause of cancer death (18.4\% of the total cancer deaths), closely followed by female breast cancer (11.6\%), prostate cancer (7.1\%), and colorectal cancer (6.1\%) for incidence and colorectal cancer (9.2\%), stomach cancer (8.2\%), and liver cancer (8.2\%) for mortality. Lung cancer is the most frequent cancer and the leading cause of cancer death among males, followed by prostate and colorectal cancer (for incidence) and liver and stomach cancer (for mortality). Among females, breast cancer is the most commonly diagnosed cancer and the leading cause of cancer death, followed by colorectal and lung cancer (for incidence), and vice versa (for mortality); cervical cancer ranks fourth for both incidence and mortality. The most frequently diagnosed cancer and the leading cause of cancer death, however, substantially vary across countries and within each country depending on the degree of economic development and associated social and life style factors. It is noteworthy that high-quality cancer registry data, the basis for planning and implementing evidence-based cancer control programs, are not available in most low- and middle-income countries. The Global Initiative for Cancer Registry Development is an international partnership that supports better estimation, as well as the collection and use of local data, to prioritize and evaluate national cancer control efforts. CA: A Cancer Journal for Clinicians 2018;0:1-31. {\textcopyright} 2018 American Cancer Society},
  langid = {english},
  keywords = {cancer,epidemiology,incidence,survival},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Bray et al_2018_Global cancer statistics 2018.pdf;C\:\\Users\\roman\\Zotero\\storage\\4MDCS7Z9\\caac.html}
}

@article{breiner_refolding_2019,
  title = {Refolding and {\emph{in Vitro}} Characterization of Human Papillomavirus 16 Minor Capsid Protein {{L2}}},
  author = {Breiner, Bastian and Preuss, Laura and Roos, Nora and Conrady, Marcel and Lilie, Hauke and Iftner, Thomas and Simon, Claudia},
  year = {2019},
  month = apr,
  journal = {Biological Chemistry},
  volume = {400},
  number = {4},
  pages = {513--522},
  issn = {1437-4315, 1431-6730},
  doi = {10.1515/hsz-2018-0311},
  urldate = {2022-02-07},
  abstract = {The minor capsid protein L2 of papillomaviruses exhibits multiple functions during viral entry including membrane interaction. Information on the protein is scarce, because of its high tendency of aggregation. We determined suitable conditions to produce a functional human papillomavirus (HPV) 16 L2 protein and thereby provide the opportunity for extensive in vitro analysis with respect to structural and biochemical information on L2 proteins and mechanistic details in viral entry. We produced the L2 protein of high-risk HPV 16 in Escherichia coli as inclusion bodies and purified the protein under denaturing conditions. A successive buffer screen resulted in suitable conditions for the biophysical characterization of 16L2. Analytical ultracentrifugation of the refolded protein showed a homogenous monomeric species. Furthermore, refolded 16L2 shows secondary structure elements. The N-terminal region including the proposed transmembrane region of 16L2 shows alpha-helical characteristics. However, overall 16L2 appears largely unstructured. Refolded 16L2 is capable of binding to DNA indicating that the putative DNA-binding regions are accessible in refolded 16L2. Further the refolded protein interacts with liposomal membranes presumably via the proposed transmembrane region at neutral pH without structural changes. This indicates that 16L2 can initially interact with membranes via pre-existing structural features.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Breiner et al_2019_Refolding and iin vitro-i characterization of human papillomavirus 16 minor.pdf}
}

@book{brierley_tnm_2017,
  title = {{{TNM}} Classification of Malignant Tumours},
  editor = {Brierley, James and Gospodarowicz, M. K. and Wittekind, Ch},
  year = {2017},
  edition = {Eighth edition},
  publisher = {{John Wiley \& Sons, Inc}},
  address = {{Chichester, West Sussex, UK ; Hoboken, NJ}},
  isbn = {978-1-119-26357-9},
  lccn = {RC258},
  keywords = {classification,Neoplasms}
}

@book{brierley_tnm_2021,
  title = {{{TNM}} Atlas: Illustrated Guide to the {{TNM}} Classification of Malignant Tumours},
  shorttitle = {{{TNM}} Atlas},
  editor = {Brierley, James and Asamura, Hisao and van Eycken, Elisabeth and Rous, Brian and {Union for International Cancer Control}},
  year = {2021},
  edition = {7. edition},
  publisher = {{Wiley-Blackwell}},
  address = {{Hoboken, NJ}},
  abstract = {"Introductory Notes The following sites are included: Lip, oral cavity, Pharynx: oropharynx, nasopharynx, hypopharynx, Larynx: supraglottis, glottis, subglottis, Nasal cavity and paranasal sinuses, Malignant melanoma of upper aerodigestive tract, Major salivary glands, Thyroid gland. Carcinomas arising in the minor salivary glands of the upper aerodigestive tract are classified according to the rules for tumours of their anatomic site of origin, e.g., oral cavity"--},
  isbn = {978-1-119-26384-5},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Brierley et al_2021_TNM atlas.pdf}
}

@article{bugshan_oral_2020,
  title = {Oral Squamous Cell Carcinoma: Metastasis, Potentially Associated Malignant Disorders, Etiology and Recent Advancements in Diagnosis},
  shorttitle = {Oral Squamous Cell Carcinoma},
  author = {Bugshan, Amr and Farooq, Imran},
  year = {2020},
  month = apr,
  journal = {F1000Research},
  volume = {9},
  pages = {229},
  issn = {2046-1402},
  doi = {10.12688/f1000research.22941.1},
  urldate = {2022-10-17},
  abstract = {Oral squamous cell carcinoma (OSCC) is a commonly occurring head and neck cancer. It has a high prevalence in certain parts of the world, and is associated with a high mortality rate. In this review, we describe metastasis related to OSCC, and disorders that could lead to OSCC with common etiological factors. In addition, a brief account of the diagnosis of OSCC and role of salivary biomarkers in its early detection has also been highlighted. Google Scholar and PubMed search engines were searched with keywords including ``oral squamous cell carcinoma'', ``OSCC'', ``oral cancer'', ``potentially malignant disorders in oral cavity'', ``etiological factors of OSCC'',~ ``diagnosis of OSCC'', and ``salivary biomarkers and OSCC'' to gather the literature for this review. The review concludes that OSCC has the potential for regional as well as distant metastasis, and many potentially malignant diseases can transform into OSCC with the help of various etiological factors. Diagnosis of OSCC involves traditional biopsy, but salivary biomarkers could also be utilized for early recognition.},
  pmcid = {PMC7194458},
  pmid = {32399208},
  file = {C:\Users\roman\OneDrive\Documents\Library\Bugshan_Farooq_2020_Oral squamous cell carcinoma.pdf}
}

@article{byers_frequency_1997,
  title = {Frequency and Therapeutic Implications of 'skip Metastases' in the Neck from Squamous Carcinoma of the Oral Tongue},
  author = {Byers, R.M. and Weber, R.S. and Andrews, T. and McGill, D. and Kare, R. and Wolf, P.},
  year = {1997},
  journal = {Head and Neck},
  volume = {19},
  number = {1},
  pages = {14--19},
  publisher = {{John Wiley and Sons Inc.}},
  issn = {01486403 (ISSN)},
  doi = {10.1002/(sici)1097-0347(199701)19:1<14::aid-hed3>3.0.co;2-y},
  langid = {english}
}

@article{calderazzo_decision-theoretic_2022,
  title = {A Decision-Theoretic Approach to {{Bayesian}} Clinical Trial Design and Evaluation of Robustness to Prior-Data Conflict},
  author = {Calderazzo, Silvia and Wiesenfarth, Manuel and {Kopp-Schneider}, Annette},
  year = {2022},
  month = jan,
  journal = {Biostatistics},
  volume = {23},
  number = {1},
  pages = {328--344},
  issn = {1465-4644},
  doi = {10.1093/biostatistics/kxaa027},
  urldate = {2023-08-16},
  abstract = {Bayesian clinical trials allow taking advantage of relevant external information through the elicitation of prior distributions, which influence Bayesian posterior parameter estimates and test decisions. However, incorporation of historical information can have harmful consequences on the trial's frequentist (conditional) operating characteristics in case of inconsistency between prior information and the newly collected data. A compromise between meaningful incorporation of historical information and strict control of frequentist error rates is therefore often sought. Our aim is thus to review and investigate the rationale and consequences of different approaches to relaxing strict frequentist control of error rates from a Bayesian decision-theoretic viewpoint. In particular, we define an integrated risk which incorporates losses arising from testing, estimation, and sampling. A weighted combination of the integrated risk addends arising from testing and estimation allows moving smoothly between these two targets. Furthermore, we explore different possible elicitations of the test error costs, leading to test decisions based either on posterior probabilities, or solely on Bayes factors. Sensitivity analyses are performed following the convention which makes a distinction between the prior of the data-generating process, and the analysis prior adopted to fit the data. Simulation in the case of normal and binomial outcomes and an application to a one-arm proof-of-concept trial, exemplify how such analysis can be conducted to explore sensitivity of the integrated risk, the operating characteristics, and the optimal sample size, to prior-data conflict. Robust analysis prior specifications, which gradually discount potentially conflicting prior information, are also included for comparison. Guidance with respect to cost elicitation, particularly in the context of a Phase II proof-of-concept trial, is provided.},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Calderazzo et al_2022_A decision-theoretic approach to Bayesian clinical trial design and evaluation.pdf;C\:\\Users\\roman\\Zotero\\storage\\V9QAEKQS\\5879225.html}
}

@article{candela_patterns_1990,
  title = {Patterns of Cervical Node Metastases from Squamous Carcinoma of the Oropharynx and Hypopharynx},
  author = {Candela, Frank C. and Kothari, Kiran and Shah, Jatin P.},
  year = {1990},
  month = may,
  journal = {Head \& Neck},
  volume = {12},
  number = {3},
  pages = {197--203},
  publisher = {{John Wiley \& Sons, Ltd}},
  issn = {1043-3074},
  doi = {10.1002/hed.2880120302},
  urldate = {2021-02-08},
  abstract = {Abstract A retrospective review of 333 previously untreated patients from 1965 to 1986, with primary squamous cell carcinoma of the oropharynx or hypopharynx, was undertaken to ascertain the prevalence of neck node metastases by neck level. The 333 patients underwent 344 classical radical neck dissections. Patients were grouped by clinical neck status at the time of neck dissection: elective dissection in the NO neck (N = 71), and immediate therapeutic dissection in the N+ neck (N = 259). Detailed analysis was performed for each group based on the specific primary site. This revealed a predominance of neck node metastases in levels II, III, and IV for both oropharyngeal and hypopharyngeal primaries. Isolated ?skip? metastases outside of levels II, III, or IV occurred in only 1 patient (0.3\%). Otherwise, level I or V involvement was always associated with nodal metastases at other levels (ie, N2 disease). These data support the trend toward selective limited neck dissection (anterior modified) in NO patients. Furthermore, they provide the foundation for planning of future prospective trials to assess the efficacy of modifications in the extent of neck dissection for carcinomas of the oropharynx or hypopharynx.},
  keywords = {patterns},
  file = {C:\Users\roman\OneDrive\Documents\Library\Candela et al_1990_Patterns of cervical node metastases from squamous carcinoma of the oropharynx.pdf}
}

@article{carr_lymphatic_1983,
  title = {Lymphatic Metastasis},
  author = {Carr, Ian},
  year = {1983},
  month = sep,
  journal = {Cancer and Metastasis Reviews},
  volume = {2},
  number = {3},
  pages = {307--317},
  issn = {1573-7233},
  doi = {10.1007/BF00048483},
  urldate = {2023-03-10},
  abstract = {Lymphatic metastasis is an important mechanism in the spread of human cancer. During its course, tumor cells first penetrate the basement of membrane of the epithelium, in which they arise, and then the underlying connective tissue, carried partly by hydrostatic pressure. They enter the lymphatic partly by active movement, pass up the lymphatic trunk; they then settle and proliferate in the subcapsular sinus, penetrate its endothelium and proliferate and destroy the node. There are varied forms of immune response in the node and in human nodes often a complex fibrous and vascular response. The degree of lymphocytic response may be important for prognosis. The nodal reaction may be stimulated by release of antigens from the tumor.},
  langid = {english},
  keywords = {footpad-lymph-node mode of lymphatic metastasis,lymphatic metastasis,lymphography,tumor cell heterogeneity},
  file = {C:\Users\roman\OneDrive\Documents\Library\Carr_1983_Lymphatic metastasis.pdf}
}

@article{celeux_computational_2000,
  title = {Computational and {{Inferential Difficulties}} with {{Mixture Posterior Distributions}}},
  author = {Celeux, Gilles and Hurn, Merrilee and Robert, Christian P.},
  year = {2000},
  month = sep,
  journal = {Journal of the American Statistical Association},
  volume = {95},
  number = {451},
  pages = {957--970},
  publisher = {{Taylor \& Francis}},
  issn = {0162-1459},
  doi = {10.1080/01621459.2000.10474285},
  urldate = {2023-09-07},
  abstract = {This article deals with both exploration and interpretation problems related to posterior distributions for mixture models. The specification of mixture posterior distributions means that the presence of k! modes is known immediately. Standard Markov chain Monte Carlo (MCMC) techniques usually have difficulties with well-separated modes such as occur here; the MCMC sampler stays within a neighborhood of a local mode and fails to visit other equally important modes. We show that exploration of these modes can be imposed using tempered transitions. However, if the prior distribution does not distinguish between the different components, then the posterior mixture distribution is symmetric and standard estimators such as posterior means cannot be used. We propose alternatives for Bayesian inference for permutation invariant posteriors, including a clustering device and alternative appropriate loss functions.},
  keywords = {Classification,Label switching,Loss functions,Markov chain Monte Carlo,Nonidentifiability,Simulated tempering},
  file = {C:\Users\roman\OneDrive\Documents\Library\Celeux et al_2000_Computational and Inferential Difficulties with Mixture Posterior Distributions.pdf}
}

@article{chadwick_molecular_1973,
  title = {A Molecular Theory of Cell Survival},
  author = {Chadwick, K. H. and Leenhouts, H. P.},
  year = {1973},
  month = jan,
  journal = {Physics in Medicine \& Biology},
  volume = {18},
  number = {1},
  pages = {78},
  issn = {0031-9155},
  doi = {10.1088/0031-9155/18/1/007},
  urldate = {2023-03-21},
  abstract = {A theory is presented to explain the effect of radiation on cell survival.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Chadwick_Leenhouts_1973_A molecular theory of cell survival.pdf}
}

@article{chao_determination_2002,
  title = {Determination and Delineation of Nodal Target Volumes for Head-and-Neck Cancer Based on Patterns of Failure in Patients Receiving Definitive and Postoperative {{IMRT}}},
  author = {Chao, K.S.Clifford and Wippold, Franz J and Ozyigit, Gokhan and Tran, Binh N and Dempsey, James F},
  year = {2002},
  month = aug,
  journal = {International Journal of Radiation Oncology*Biology*Physics},
  volume = {53},
  number = {5},
  pages = {1174--1184},
  issn = {0360-3016},
  doi = {10.1016/S0360-3016(02)02881-X},
  abstract = {Purpose: We present the guidelines for target volume determination and delineation of head-and-neck lymph nodes based on the analysis of the patterns of nodal failure in patients treated with intensity-modulated radiotherapy (IMRT). Methods and Materials: Data pertaining to the natural course of nodal metastasis for each head-and-neck cancer subsite were reviewed. A system was established to provide guidance for nodal target volume determination and delineation. Following these guidelines, 126 patients (52 definitive, 74 postoperative) were treated between February 1997 and December 2000 with IMRT for head-and-neck cancer. The median follow-up was 26 months (range 12{\textendash}55), and the patterns of nodal failure were analyzed. Results: These guidelines define the nodal target volume based on the location of the primary tumor and the probability of microscopic metastasis to the ipsilateral and contralateral (Level I{\textendash}V) nodal regions. Following these guidelines, persistent or recurrent nodal disease was found in 6 (12\%) of 52 patients receiving definitive IMRT, and 7 (9\%) of 74 patients receiving postoperative IMRT had failure in the nodal region. Conclusion: On the basis of our clinical experience in implementing inverse-planning IMRT for head-and-neck cancer, we present guidelines using a simplified, but clinically relevant, method for nodal target volume determination and delineation. The intention was to provide a foundation that enables different institutions to exchange clinical experiences in head-and-neck IMRT. These guidelines will be subject to future refinement when the clinical experience in head-and-neck IMRT advances.},
  keywords = {guideline,Head-and-neck cancer,Imaging-based,IMRT,Target definition},
  file = {C\:\\Users\\roman\\OneDrive\\Foam\\references\\chao_determination_2002-zotero.md;C\:\\Users\\roman\\OneDrive\\Foam\\references\\chao_determination_2002.md}
}

@article{chen_adaptive_2008,
  title = {Adaptive Fractionation Therapy: {{II}}. {{Biological}} Effective Dose},
  shorttitle = {Adaptive Fractionation Therapy},
  author = {Chen, Mingli and Lu, Weiguo and Chen, Quan and Ruchala, Kenneth and Olivera, Gustavo},
  year = {2008},
  month = sep,
  journal = {Physics in Medicine and Biology},
  volume = {53},
  number = {19},
  pages = {5513--5525},
  publisher = {{IOP Publishing}},
  issn = {0031-9155},
  doi = {10.1088/0031-9155/53/19/016},
  urldate = {2022-07-26},
  abstract = {Radiation therapy is fractionized to differentiate the cell killing between the tumor and organ at risk (OAR). Conventionally, fractionation is done by dividing the total dose into equal fraction sizes. However, as the relative positions (configurations) between OAR and the tumor vary from fractions to fractions, intuitively, we want to use a larger fraction size when OAR and the tumor are far apart and a smaller fraction size when OAR and the tumor are close to each other. Adaptive fractionation accounts for variations of configurations between OAR and the tumor. In part I of this series, the adaptation minimizes the OAR (physical) dose and maintains the total tumor (physical) dose. In this work, instead, the adaptation is based on the biological effective dose (BED). Unlike the linear programming approach in part I, we build a fraction size lookup table using mathematical induction. The lookup table essentially describes the fraction size as a function of the remaining tumor BED, the OAR/tumor dose ratio and the remaining number of fractions. The lookup table is calculated by maximizing the expected survival of OAR and preserving the tumor cell kill. Immediately before the treatment of each fraction, the OAR-tumor configuration and thus the dose ratio can be obtained from the daily setup image, and then the fraction size can be determined by the lookup table. Extensive simulations demonstrate the effectiveness of our method compared with the conventional fractionation method.},
  langid = {english}
}

@book{cheung_handbook_2015,
  title = {Handbook of Food Chemistry},
  editor = {Cheung, Peter C. K. and Mehta, Bhavbhuti M.},
  year = {2015},
  series = {Springer Reference},
  publisher = {{Springer}},
  address = {{Berlin Heidelberg}},
  isbn = {978-3-642-36604-8 978-3-642-36606-2},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Cheung_Mehta_2015_Handbook of food chemistry2.pdf}
}

@article{chronowski_unilateral_2012,
  title = {Unilateral Radiotherapy for the Treatment of Tonsil Cancer},
  author = {Chronowski, Gregory M. and Garden, Adam S. and Morrison, William H. and Frank, Steven J. and Schwartz, David L. and Shah, Shalin J. and Beadle, Beth M. and Gunn, G. Brandon and Kupferman, Michael E. and Ang, Kian K. and Rosenthal, David I.},
  year = {2012},
  month = may,
  journal = {International Journal of Radiation Oncology, Biology, Physics},
  volume = {83},
  number = {1},
  pages = {204--209},
  issn = {1879-355X},
  doi = {10.1016/j.ijrobp.2011.06.1975},
  abstract = {PURPOSE: To assess, through a retrospective review, clinical outcomes of patients with squamous cell carcinoma of the tonsil treated at the M. D. Anderson Cancer Center with unilateral radiotherapy techniques that irradiate the involved tonsil region and ipsilateral neck only. METHODS AND MATERIALS: Of 901 patients with newly diagnosed squamous cell carcinoma of the tonsil treated with radiotherapy at our institution, we identified 102 that were treated using unilateral radiotherapy techniques. All patients had their primary site of disease restricted to the tonsillar fossa or anterior pillar, with {$<$}1 cm involvement of the soft palate. Patients had TX (n = 17 patients), T1 (n = 52), or T2 (n = 33) disease, with Nx (n = 3), N0 (n = 33), N1 (n = 23), N2a (n = 21), or N2b (n = 22) neck disease. RESULTS: Sixty-one patients (60\%) underwent diagnostic tonsillectomy before radiotherapy. Twenty-seven patients (26\%) underwent excision of a cervical lymph node or neck dissection before radiotherapy. Median follow-up for surviving patients was 38 months. Locoregional control at the primary site and ipsilateral neck was 100\%. Two patients experienced contralateral nodal recurrence (2\%). The 5-year overall survival and disease-free survival rates were 95\% and 96\%, respectively. The 5-year freedom from contralateral nodal recurrence rate was 96\%. Nine patients required feeding tubes during therapy. Of the 2 patients with contralateral recurrence, 1 experienced an isolated neck recurrence and was salvaged with contralateral neck dissection only and remains alive and free of disease. The other patient presented with a contralateral base of tongue tumor and involved cervical lymph node, which may have represented a second primary tumor, and died of disease. CONCLUSIONS: Unilateral radiotherapy for patients with TX-T2, N0-N2b primary tonsil carcinoma results in high rates of disease control, with low rates of contralateral nodal failure and a low incidence of acute toxicity requiring gastrostomy.},
  langid = {english},
  pmid = {22019242},
  keywords = {{Carcinoma, Squamous Cell},Female,Humans,Lymph Node Excision,Male,Middle Aged,{Neoplasm Recurrence, Local},Neoplasm Staging,Radiography,Radiotherapy,{Radiotherapy, Intensity-Modulated},Retrospective Studies,Salvage Therapy,Survival Analysis,Survival Rate,Tonsillar Neoplasms,Tonsillectomy}
}

@article{chung_pattern_2016,
  title = {Pattern of Lymph Node Metastasis in Hypopharyngeal Squamous Cell Carcinoma and Indications for Level {{VI}} Lymph Node Dissection},
  author = {Chung, Eun-Jae and Kim, Go-Woon and Cho, Bum-Ki and Park, Hae Sang and Rho, Young-Soo},
  year = {2016},
  journal = {Head \& neck},
  volume = {38},
  number = {S1},
  pages = {E1969--E1973},
  publisher = {{Wiley Online Library}},
  keywords = {patterns},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Chung et al_2016_Pattern of lymph node metastasis in hypopharyngeal squamous cell carcinoma and.pdf;C\:\\Users\\roman\\OneDrive\\Foam\\references\\@chung_pattern_2016.md;C\:\\Users\\roman\\Zotero\\storage\\S4VMXGB3\\hed.html}
}

@article{clayman_role_2001,
  title = {The {{Role}} of {{Neck Dissection After Chemoradiotherapy}} for {{Oropharyngeal Cancer With Advanced Nodal Disease}}},
  author = {Clayman, Gary L. and Johnson II, Chad Jeffery and Morrison, William and Ginsberg, Lawrence and Lippman, Scott M.},
  year = {2001},
  month = feb,
  journal = {Archives of Otolaryngology{\textendash}Head \& Neck Surgery},
  volume = {127},
  number = {2},
  pages = {135--139},
  issn = {0886-4470},
  doi = {10.1001/archotol.127.2.135},
  urldate = {2023-03-13},
  abstract = {To analyze and compare the effectiveness of sequential platinum-based chemotherapy and radiotherapy with and without selective neck dissection in patients with N2a and greater stage node-positive squamous cell carcinoma of the oropharynx.Nonrandomized controlled trial.Tertiary referral center.Sixty-six patients with squamous cell carcinoma of the oropharynx staged N2a or greater.Platinum-based induction chemotherapy followed by definitive radiation therapy; and selective neck dissections 6 to 10 weeks following the completion of radiation therapy in patients with radiographic evidence suggesting residual neck disease.Locoregional recurrence and disease-free survival.Of 66 patients, 24 (36\%) had complete responses in the primary local tumor (oropharynx) and regional disease (neck nodes), as assessed clinically and radiographically. These patients had lower rates of locoregional recurrence than did patients showing no or partial responses, but the differences were not significant (P\&gt;.05). Of 18 patients undergoing neck dissection, 10 (56\%) had pathological evidence of residual tumor. Patients showing a complete response of regional and neck disease had significantly improved disease-specific and overall survival (P = .01 for both) compared with patients showing no or partial responses of their neck disease. Patients with no or partial responses who underwent neck dissections had significantly improved overall survival compared with similar patients who did not undergo neck dissections (P = .002).Even in patients with bulky nodal disease, a complete response in the neck to sequential chemotherapy and radiotherapy may indicate that neck surgery is not necessary for good locoregional control and improved disease-free survival. Neck dissection is recommended for patients with no or partial radiographic responses.Arch Otolaryngol Head Neck Surg. 2001;127:135-139--{$>$}},
  file = {C:\Users\roman\Zotero\storage\CTVLRQKK\482178.html}
}

@article{cluett_immersion_2018,
  title = {Immersion in Water during Labour and Birth},
  author = {Cluett, Elizabeth R. and Burns, Ethel and Cuthbert, Anna},
  year = {2018},
  journal = {Cochrane Database of Systematic Reviews},
  number = {5},
  publisher = {{John Wiley \& Sons, Ltd}},
  issn = {1465-1858},
  doi = {10.1002/14651858.CD000111.pub4},
  urldate = {2023-02-27},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Cluett et al_2018_Immersion in water during labour and birth.pdf}
}

@article{contreras_eliminating_2019,
  title = {Eliminating {{Postoperative Radiation}} to the {{Pathologically Node-Negative Neck}}: {{Long-Term Results}} of a {{Prospective Phase II Study}}},
  shorttitle = {Eliminating {{Postoperative Radiation}} to the {{Pathologically Node-Negative Neck}}},
  author = {Contreras, Jessika A. and Spencer, Christopher and DeWees, Todd and Haughey, Bruce and Henke, Lauren E. and Chin, Re-I and Paniello, Randal and Rich, Jason and Jackson, Ryan and Oppelt, Peter and Pipkorn, Patrik and Zevallos, Jose and Chernock, Rebecca and Nussenbaum, Brian and Daly, Mackenzie and Gay, Hiram and Adkins, Douglas and Thorstad, Wade},
  year = {2019},
  month = oct,
  journal = {Journal of Clinical Oncology},
  volume = {37},
  number = {28},
  pages = {2548--2555},
  publisher = {{Wolters Kluwer}},
  issn = {0732-183X},
  doi = {10.1200/JCO.19.00186},
  urldate = {2022-07-05},
  abstract = {PURPOSE The volume treated with postoperative radiation therapy (PORT) is a mediator of toxicity, and reduced volumes result in improved quality of life (QOL). In this phase II trial, treatment volumes were reduced by omitting PORT to the pathologically negative (PN0) neck in patients with primary head and neck squamous cell carcinoma. METHODS Patients with head and neck squamous cell carcinoma who underwent surgical resection and neck dissection with a PN0 neck and high-risk features mandating PORT to the primary and/or involved neck were eligible. The primary end point was greater than 90\% disease control in the unirradiated neck. QOL was evaluated using the MD Anderson Dysphagia Inventory and the University of Michigan patient-reported xerostomia questionnaire. RESULTS Seventy-three patients were enrolled, and 72 were evaluable. Median age was 56 years (range, 31 to 81 years); 58 patients were male, and 47 (65\%) had a smoking history. Sites included oral cavity (n = 14), oropharynx (n = 37), hypopharynx (n = 4), larynx (n = 16), and unknown primary tumor (n = 1). According to the American Joint Committee on Cancer Staging Manual (7th edition), 67 patients (93\%) had stage III/IV disease, and 71\% of tumors involved or crossed midline. No patient had contralateral neck PORT. In 17 patients (24\%), only the primary site was treated. At a median follow-up of 53 months, two patients experienced treatment failure of the PN0 unirradiated neck; they also experienced treatment failure locally. Unirradiated neck control was 97\% (95\% CI, 93.4\% to 100.0\%). Five-year rates of local control, regional control, progression-free survival, and overall survival were 84\%, 93\%, 60\%, and 64\%, respectively. QOL measures were not significantly different from baseline at 12 and 24 months post-PORT (P {$>$} .05). CONCLUSION Eliminating PORT to the PN0 neck resulted in excellent control rates in the unirradiated neck without long-term adverse effects on global QOL.},
  file = {C:\Users\roman\OneDrive\Documents\Library\Contreras et al_2019_Eliminating Postoperative Radiation to the Pathologically Node-Negative Neck.pdf}
}

@article{custer_effects_2017,
  title = {The {{Effects}} of {{Local Vibration}} on {{Balance}}, {{Power}}, and {{Self-Reported Pain After Exercise}}},
  author = {Custer, Lisa and Peer, Kimberly S. and Miller, Lauren},
  year = {2017},
  month = may,
  journal = {Journal of Sport Rehabilitation},
  volume = {26},
  number = {3},
  pages = {193--201},
  publisher = {{Human Kinetics, Inc.}},
  issn = {1543-3072, 1056-6716},
  doi = {10.1123/jsr.2015-0125},
  urldate = {2021-11-08},
  abstract = {Context: Muscle fatigue and acute muscle soreness occur after exercise. Application of a local vibration intervention may reduce the consequences of fatigue and soreness. Objective: To examine the effects of a local vibration intervention after a bout of exercise on balance, power, and self-reported pain. Design: Single-blind crossover study. Setting: Laboratory. Participants: 19 healthy, moderately active subjects. Interventions: After a 30-min bout of full-body exercise, subjects received either an active or a sham vibration intervention. The active vibration intervention was performed bilaterally over the muscle bellies of the triceps surae, quadriceps, hamstrings, and gluteals. At least 1 wk later, subjects repeated the bout, receiving the other vibration intervention. Main Outcome Measures: Static balance, dynamic balance, power, and self-reported pain were measured at baseline, after the vibration intervention, and 24 h postexercise. Results: After the bout of exercise, subjects had reduced static and dynamic balance and increased self-reported pain regardless of vibration intervention. There were no differences between outcome measures between the active and sham vibration conditions. Conclusions: The local vibration intervention did not affect balance, power, or self-reported pain.},
  chapter = {Journal of Sport Rehabilitation},
  langid = {american},
  file = {C:\Users\roman\Zotero\storage\TDG7CWA5\article-p193.html}
}

@book{darwiche_modeling_2009,
  title = {Modeling and {{Reasoning}} with {{Bayesian Networks}}},
  author = {Darwiche, A},
  year = {2009},
  publisher = {{Cambridge University Press}}
}

@article{de_bondt_detection_2007,
  title = {Detection of Lymph Node Metastases in Head and Neck Cancer: A Meta-Analysis Comparing {{US}}, {{USgFNAC}}, {{CT}} and {{MR}} Imaging},
  author = {De Bondt, R and {Others}},
  year = {2007},
  journal = {Eur. J. Radiol.},
  volume = {64},
  pages = {266--272},
  doi = {10.1016/j.ejrad.2007.02.037},
  file = {C:\Users\roman\OneDrive\Documents\Library\De Bondt_Others_2007_Detection of lymph node metastases in head and neck cancer.pdf}
}

@article{de_silva_model_2018,
  title = {A Model to Predict Nodal Metastasis in Patients with Oral Squamous Cell Carcinoma},
  author = {De Silva, R. K. and Siriwardena, B. S. M. S. and Samaranayaka, A. and Abeyasinghe, W. A. M. U. L. and Tilakaratne, W. M.},
  year = {2018},
  month = aug,
  journal = {PLoS ONE},
  volume = {13},
  number = {8},
  pages = {e0201755},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0201755},
  urldate = {2022-10-17},
  abstract = {Difficulty in precise decision making on necessity of surgery is a major problem when managing oral squamous cell carcinomas (OSCCs) with clinically negative neck. Therefore, use of clinical and histopathological parameters in combination would be important to improve patient management. The main objective is to develop a model that predicts the presence of nodal metastasis in patients with OSCC.623 patients faced neck dissections with buccal mucosal or tongue squamous cell carcinoma (SCC) were selected from patients' records. Demographic data, clinical information, nodal status, Depth of invasion (DOI) and pattern of invasion (POI) were recorded. The parameters which showed a significant association with nodal metastasis were used to develop a multivariable predictive model (PM). Univariate logistic regression was used to estimate the strengths of those associations in terms of odds ratios (OR). This showed statistically significant associations between status of the nodal metastasis and each of the following 4 histopathological parameters individually: size of the tumour (T), site, POI, and DOI. Specifically, OR of nodal metastasis for tongue cancers relative to buccal mucosal cancers was 1.89, P-value {$<$} 0.001. Similarly, ORs for POI type 3 and 4 relative to type 2 were 1.99 and 5.83 respectively. A similar relationship was found with tumour size; ORs for T2, T3, and T4 compared to T1 were 2.79, 8.27 and 8.75 respectively. These four histopathological parameters were then used to develop a predictive model for nodal metastasis. This model showed that probability of nodal metastasis is higher among tongue cancers with increasing POI, with increasing T, and with larger depths while other characteristics remained unchanged. The proposed model provides a way of using combinations of histopathological parameters to identify patients with higher risks of nodal metastasis for surgical management.},
  pmcid = {PMC6084951},
  pmid = {30091996},
  file = {C:\Users\roman\OneDrive\Documents\Library\De Silva et al_2018_A model to predict nodal metastasis in patients with oral squamous cell.pdf}
}

@article{de_veij_mestdagh_incidence_2019,
  title = {Incidence of Contralateral Regional Failure in the Electively Irradiated Contralateral Neck of Patients with Head and Neck Squamous Cell Carcinoma},
  author = {{de Veij Mestdagh}, Pieter D. and {van Werkhoven}, Eric and Navran, Arash and {de Boer}, Jan Paul and Schreuder, Willem H. and Vogel, Wouter V. and {Al-Mamgani}, Abrahim},
  year = {2019},
  month = apr,
  journal = {Clinical and Translational Radiation Oncology},
  volume = {17},
  pages = {7--13},
  issn = {2405-6308},
  doi = {10.1016/j.ctro.2019.04.015},
  urldate = {2022-09-21},
  abstract = {{\textbullet}               Contralateral regional failure still occurs after bilateral nodal irradiation.                                         {\textbullet}               No significant predictive factors were identified for contralateral regional failure.                                         {\textbullet}               Overall survival did not differ between patients with ipsi- or contralateral failure.},
  pmcid = {PMC6488558},
  pmid = {31061901},
  file = {C:\Users\roman\OneDrive\Documents\Library\de Veij Mestdagh et al_2019_Incidence of contralateral regional failure in the electively irradiated.pdf}
}

@article{de_veij_mestdagh_spectct-guided_2020,
  title = {{{SPECT}}/{{CT-guided}} Elective Nodal Irradiation for Head and Neck Cancer Is Oncologically Safe and Less Toxic: {{A}} Potentially Practice-Changing Approach},
  shorttitle = {{{SPECT}}/{{CT-guided}} Elective Nodal Irradiation for Head and Neck Cancer Is Oncologically Safe and Less Toxic},
  author = {{de Veij Mestdagh}, Pieter D. and Walraven, Iris and Vogel, Wouter V. and Schreuder, Willem H. and {van Werkhoven}, Erik and Carbaat, Casper and Donswijk, Maarten L. and {van den Brekel}, Michiel W.M. and {Al-Mamgani}, Abrahim},
  year = {2020},
  month = jun,
  journal = {Radiotherapy and Oncology},
  volume = {147},
  pages = {56--63},
  issn = {01678140},
  doi = {10.1016/j.radonc.2020.03.012},
  urldate = {2021-09-01},
  abstract = {Background and purpose: Bilateral elective nodal irradiation (ENI) remains the standard treatment for head and neck squamous cell carcinoma (HNSCC). Unilateral ENI could reduce treatment toxicity and improve health-related quality-of-life (HRQOL). This prospective proof-of-principle trial (NCT02572661) investigated the feasibility, safety and clinical benefits of SPECT/CT-guided ENI of the node-negative contralateral neck. Materials and methods: Patients with lateralized T1-3N0-2bM0 HNSCC of the oropharynx, oral cavity, larynx and hypopharynx underwent SPECT/CT after peritumoral 99mTc-nanocolloid injection. Patients without contralateral lymph drainage received ipsilateral ENI only. If lymph drainage to only one contralateral hot spot was visible, ENI to the contralateral neck would be limited to only the level containing the hot spot. The primary endpoint was the incidence of contralateral regional failure (CRF) at 2 years. Toxicity and HRQOL were compared with a 1:1 matched historical cohort that received standard bilateral ENI (B-ENI) with identical planning and treatment techniques. Results: Fifty patients were treated with SPECT/CT-guided ENI. After a median follow-up of 33 months (range 18{\textendash}45), CRF was observed in one patient (2\%; 95\% confidence interval: 0{\textendash}6\%). Compared to the matched B-ENI group, patients treated with SPECT/CT-guided ENI had significantly lower incidences of grade !2 dysphagia (54\% vs. 82\%; p {$<$} 0.001), tube feeding (10\% vs. 50\%; p {$<$} 0.001) and late grade !2 xerostomia (9\% vs. 54\%; p {$<$} 0.001). Significant and clinically relevant HRQOL benefits of SPECT/CTguided ENI were observed on the EORTC QLQ-C30 summary score, and QLQ-HN35 swallowing and dry mouth subscales. Conclusion: SPECT/CT-guided ENI is associated with a low risk of contralateral regional failure. Compared to B-ENI, SPECT/CT-guided ENI significantly reduces dysphagia, feeding tube placement, and late xerostomia and improves HRQOL.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\de Veij Mestdagh et al_2020_SPECT-CT-guided elective nodal irradiation for head and neck cancer is.pdf}
}

@article{dempster_maximum_1977,
  title = {Maximum {{Likelihood}} from {{Incomplete Data}} via the {{EM Algorithm}}},
  author = {Dempster, A. P. and Laird, N. M. and Rubin, D. B.},
  year = {1977},
  journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
  volume = {39},
  number = {1},
  eprint = {2984875},
  eprinttype = {jstor},
  pages = {1--38},
  publisher = {{[Royal Statistical Society, Wiley]}},
  issn = {0035-9246},
  urldate = {2022-10-17},
  abstract = {A broadly applicable algorithm for computing maximum likelihood estimates from incomplete data is presented at various levels of generality. Theory showing the monotone behaviour of the likelihood and convergence of the algorithm is derived. Many examples are sketched, including missing value situations, applications to grouped, censored or truncated data, finite mixture models, variance component estimation, hyperparameter estimation, iteratively reweighted least squares and factor analysis.},
  file = {C:\Users\roman\OneDrive\Documents\Library\Dempster et al_1977_Maximum Likelihood from Incomplete Data via the EM Algorithm.pdf}
}

@techreport{diez_canonical_2006,
  title = {Canonical Probabilistic Models for Knowledge Engineering},
  author = {D{\i}ez, F J and Druzdzel, M J},
  year = {2006},
  institution = {{UNED, Madrid, Spain}}
}

@article{dogan_assessment_2018,
  title = {Assessment of {{Online Adaptive MR-Guided SBRT}} of {{Liver Cancers}}},
  author = {Dogan, N. and Simpson, G. and Asher, D. and Padgett, K.R. and Portelance, L.},
  year = {2018},
  month = nov,
  journal = {International Journal of Radiation Oncology*Biology*Physics},
  volume = {102},
  number = {3},
  pages = {e52},
  issn = {03603016},
  doi = {10.1016/j.ijrobp.2018.07.470},
  urldate = {2022-02-07},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Dogan et al_2018_Assessment of Online Adaptive MR-Guided SBRT of Liver Cancers.pdf}
}

@article{doi:10.1080/01621459.1995.10476572,
  title = {Bayes Factors},
  author = {Kass, Robert E. and {Adrian E. Raftery}},
  year = {1995},
  journal = {Journal of the American Statistical Association},
  volume = {90},
  number = {430},
  eprint = {https://www.tandfonline.com/doi/pdf/10.1080/01621459.1995.10476572},
  pages = {773--795},
  publisher = {{Taylor \& Francis}},
  doi = {10.1080/01621459.1995.10476572},
  abstract = {Abstract In a 1935 paper and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is one-half. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P-values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this article we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology, and psychology. We emphasize the following points: {\textbullet} From Jeffreys' Bayesian viewpoint, the purpose of hypothesis testing is to evaluate the evidence in favor of a scientific theory. {\textbullet} Bayes factors offer a way of evaluating evidence in favor of a null hypothesis. {\textbullet} Bayes factors provide a way of incorporating external information into the evaluation of evidence about a hypothesis. {\textbullet} Bayes factors are very general and do not require alternative models to be nested. {\textbullet} Several techniques are available for computing Bayes factors, including asymptotic approximations that are easy to compute using the output from standard packages that maximize likelihoods. {\textbullet} In ``nonstandard'' statistical models that do not satisfy common regularity conditions, it can be technically simpler to calculate Bayes factors than to derive non-Bayesian significance tests. {\textbullet} The Schwarz criterion (or BIC) gives a rough approximation to the logarithm of the Bayes factor, which is easy to use and does not require evaluation of prior distributions. {\textbullet} When one is interested in estimation or prediction, Bayes factors may be converted to weights to be attached to various models so that a composite estimate or prediction may be obtained that takes account of structural or model uncertainty. {\textbullet} Algorithms have been proposed that allow model uncertainty to be taken into account when the class of models initially considered is very large. {\textbullet} Bayes factors are useful for guiding an evolutionary model-building process. {\textbullet} It is important, and feasible, to assess the sensitivity of conclusions to the prior distributions used.},
  file = {C:\Users\roman\OneDrive\Documents\Library\Kass_Adrian E. Raftery_1995_Bayes factors.pdf}
}

@techreport{eby_python_2010,
  type = {{{PEP}}},
  title = {Python {{Web Server Gateway Interface}} v1.0.1},
  author = {Eby, P. J.},
  year = {2010},
  number = {3333}
}

@article{edlow_7_2019,
  title = {7 {{Tesla MRI}} of the Ex Vivo Human Brain at 100 Micron Resolution},
  author = {Edlow, Brian L. and Mareyam, Azma and Horn, Andreas and Polimeni, Jonathan R. and Witzel, Thomas and Tisdall, M. Dylan and Augustinack, Jean C. and Stockmann, Jason P. and Diamond, Bram R. and Stevens, Allison and Tirrell, Lee S. and Folkerth, Rebecca D. and Wald, Lawrence L. and Fischl, Bruce and {van der Kouwe}, Andre},
  year = {2019},
  month = oct,
  journal = {Scientific Data},
  volume = {6},
  number = {1},
  pages = {244},
  publisher = {{Nature Publishing Group}},
  issn = {2052-4463},
  doi = {10.1038/s41597-019-0254-8},
  urldate = {2022-10-11},
  abstract = {We present an ultra-high resolution MRI dataset of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. After fixation in 10\% formalin, the specimen was imaged on a 7 Tesla MRI scanner at 100\,{\textmu}m isotropic resolution using a custom-built 31-channel receive array coil. Single-echo multi-flip Fast Low-Angle SHot (FLASH) data were acquired over 100\,hours of scan time (25\,hours per flip angle), allowing derivation of synthesized FLASH volumes. This dataset provides an unprecedented view of the three-dimensional neuroanatomy of the human brain. To optimize the utility of this resource, we warped the dataset into standard stereotactic space. We now distribute the dataset in both native space and stereotactic space to the academic community via multiple platforms. We envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance understanding of human brain anatomy in health and disease.},
  copyright = {2019 The Author(s)},
  langid = {english},
  keywords = {Brain,Brain imaging,Brain injuries,Magnetic resonance imaging},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Edlow et al_2019_7 Tesla MRI of the ex vivo human brain at 100 micron resolution.pdf;C\:\\Users\\roman\\Zotero\\storage\\WV7N8TRZ\\s41597-019-0254-8.html}
}

@article{eisbruch_intensity-modulated_2002,
  title = {Intensity-Modulated Radiation Therapy for Head and Neck Cancer: {{Emphasis}} on the Selection and Delineation of the Targets},
  author = {Eisbruch, Avraham and Foote, Robert L. and O'Sullivan, Brian and Beitler, Jonathan J. and Vikram, Bhadrasain},
  year = {2002},
  month = jul,
  journal = {Seminars in Radiation Oncology},
  volume = {12},
  number = {3},
  pages = {238--249},
  issn = {1053-4296},
  doi = {10.1053/srao.2002.32435},
  abstract = {The head and neck contain many critical, noninvolved structures in close vicinity to the targets. The tightly conformal doses produced by intensity-modulated radiation therapy (IMRT), and the lack of internal organ motion in the head and neck, provide the potential for organ sparing and improved tumor irradiation. Many studies of treatment planning for head and neck cancer have demonstrated the dosimetric superiority of IMRT over conventional techniques in these respects. The initial results of clinical studies demonstrate reduced xerostomia. They suggest an improvement in tumor control, which needs to be verified in larger studies and longer follow-up. Critical issues for successful outcome of head and neck IMRT are accurate selection of the neck lymph nodes that require adjuvant treatment, and accurate delineation on the planning computed tomography (CT) of the lymph-node bearing areas and subclinical disease adjoining the gross tumor. This review emphasizes these topics and provides some guidelines. Copyright 2002, Elsevier Science (USA). All rights reserved.},
  keywords = {guideline}
}

@article{ferlay_estimating_2019,
  title = {Estimating the Global Cancer Incidence and Mortality in 2018: {{GLOBOCAN}} Sources and Methods},
  shorttitle = {Estimating the Global Cancer Incidence and Mortality in 2018},
  author = {Ferlay, J. and Colombet, M. and Soerjomataram, I. and Mathers, C. and Parkin, D.m. and Pi{\~n}eros, M. and Znaor, A. and Bray, F.},
  year = {2019},
  journal = {International Journal of Cancer},
  volume = {144},
  number = {8},
  pages = {1941--1953},
  issn = {1097-0215},
  doi = {10.1002/ijc.31937},
  urldate = {2022-10-06},
  abstract = {Estimates of the worldwide incidence and mortality from 36 cancers and for all cancers combined for the year 2018 are now available in the GLOBOCAN 2018 database, compiled and disseminated by the International Agency for Research on Cancer (IARC). This paper reviews the sources and methods used in compiling the cancer statistics in 185 countries. The validity of the national estimates depends upon the representativeness of the source information, and to take into account possible sources of bias, uncertainty intervals are now provided for the estimated sex- and site-specific all-ages number of new cancer cases and cancer deaths. We briefly describe the key results globally and by world region. There were an estimated 18.1 million (95\% UI: 17.5{\textendash}18.7 million) new cases of cancer (17 million excluding non-melanoma skin cancer) and 9.6 million (95\% UI: 9.3{\textendash}9.8 million) deaths from cancer (9.5 million excluding non-melanoma skin cancer) worldwide in 2018.},
  langid = {english},
  keywords = {cancer,global estimates,GLOBOCAN,incidence,mortality},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Ferlay et al_2019_Estimating the global cancer incidence and mortality in 2018.pdf;C\:\\Users\\roman\\Zotero\\storage\\4YVC6RLD\\ijc.html}
}

@article{ferlito_elective_2009,
  title = {Elective Management of the Neck in Oral Cavity Squamous Carcinoma: Current Concepts Supported by Prospective Studies},
  shorttitle = {Elective Management of the Neck in Oral Cavity Squamous Carcinoma},
  author = {Ferlito, Alfio and Silver, Carl E. and Rinaldo, Alessandra},
  year = {2009},
  month = jan,
  journal = {British Journal of Oral and Maxillofacial Surgery},
  volume = {47},
  number = {1},
  pages = {5--9},
  issn = {02664356},
  doi = {10.1016/j.bjoms.2008.06.001},
  urldate = {2021-02-10},
  abstract = {The incidence of occult cervical metastasis in oral cavity cancer, even in early stages, is significant, necessitating elective treatment of the neck in a majority of cases. There is no method of imaging or other examination that will detect microscopic foci of metastatic disease in cervical lymph nodes. Immunohistochemical and molecular analysis of neck specimens reveals the incidence of occult metastases to be higher than revealed by light microscopy with ordinary hematoxylin and eosin staining. The neck may be treated electively by surgery or irradiation. Surgery has the advantage of permitting pathological staging of the neck, avoiding unnecessary radiation treatment and indicating cases where adjuvant therapy should be employed. As oral cavity cancer rarely metastasizes to level V, a radical or modified radical neck dissection of all five node levels is not necessary. Selective dissection of levels I{\textendash}III (``supraomohyoid neck dissection'') is the usual procedure of choice for elective dissection of the neck. Most of the relatively small number of isolated metastasis to level IV are from primary tumours of the tongue, which are known to produce ``skip'' metastases. Thus an ``extended supraomohyoid neck dissection'' of levels I{\textendash}IV is recommended by some authors for elective treatment of the neck in tongue cancer. A number of recent prospective multi-institutional studies have demonstrated that sublevel IIB is rarely involved with isolated metastasis from oral cavity primary tumours, except from some tongue cancers. Thus it is justifiable to omit dissection of sublevel IIB in elective treatment of most cases of oral cavity cancer. Bilateral neck dissection should be performed in elective treatment of tumours involving midline structures, and in patients with ipsilateral neck metastasis.},
  langid = {english},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Ferlito et al_2009_Elective management of the neck in oral cavity squamous carcinoma.pdf;C\:\\Users\\roman\\OneDrive\\Foam\\references\\@ferlito_elective_2009.md}
}

@article{finazzi_role_2019,
  title = {Role of {{On-Table Plan Adaptation}} in {{MR-Guided Ablative Radiation Therapy}} for {{Central Lung Tumors}}},
  author = {Finazzi, Tobias and Palacios, Miguel A. and Spoelstra, Femke O.B. and Haasbeek, Cornelis J.A. and Bruynzeel, Anna M.E. and Slotman, Ben J. and Lagerwaard, Frank J. and Senan, Suresh},
  year = {2019},
  month = jul,
  journal = {International Journal of Radiation Oncology*Biology*Physics},
  volume = {104},
  number = {4},
  pages = {933--941},
  issn = {03603016},
  doi = {10.1016/j.ijrobp.2019.03.035},
  urldate = {2022-02-07},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Finazzi et al_2019_Role of On-Table Plan Adaptation in MR-Guided Ablative Radiation Therapy for.pdf}
}

@article{fisher_design_1936,
  title = {The {{Design}} of {{Experiments}}},
  author = {Fisher, Ronald A.},
  year = {1936},
  month = feb,
  journal = {Nature},
  volume = {137},
  number = {3459},
  pages = {252--254},
  publisher = {{Nature Publishing Group}},
  issn = {1476-4687},
  doi = {10.1038/137252a0},
  urldate = {2023-07-04},
  abstract = {READERS of ``Statistical Methods for Research Workers'' will welcome Prof. Fisher's new book, which is partly devoted to a development of the logical ideas underlying the earlier volume and partly to an extension of the application of these ideas. At one time it was fashionable to say that Nature would only reply to one question at a time; the author, however, believes that her responses to a well thought out questionnaire will be more satisfactory.},
  copyright = {1936 Springer Nature Limited},
  langid = {english},
  keywords = {Humanities and Social Sciences,multidisciplinary,Science},
  file = {C:\Users\roman\OneDrive\Documents\Library\Fisher_1936_The Design of Experiments.pdf}
}

@misc{fong_marginal_2019,
  title = {On the Marginal Likelihood and Cross-Validation},
  author = {Fong, Edwin and Holmes, Chris},
  year = {2019},
  month = sep,
  number = {arXiv:1905.08737},
  eprint = {1905.08737},
  primaryclass = {stat},
  publisher = {{arXiv}},
  doi = {10.48550/arXiv.1905.08737},
  urldate = {2022-08-02},
  abstract = {In Bayesian statistics, the marginal likelihood, also known as the evidence, is used to evaluate model fit as it quantifies the joint probability of the data under the prior. In contrast, non-Bayesian models are typically compared using cross-validation on held-out data, either through \$k\$-fold partitioning or leave-\$p\$-out subsampling. We show that the marginal likelihood is formally equivalent to exhaustive leave-\$p\$-out cross-validation averaged over all values of \$p\$ and all held-out test sets when using the log posterior predictive probability as the scoring rule. Moreover, the log posterior predictive is the only coherent scoring rule under data exchangeability. This offers new insight into the marginal likelihood and cross-validation and highlights the potential sensitivity of the marginal likelihood to the choice of the prior. We suggest an alternative approach using cumulative cross-validation following a preparatory training phase. Our work has connections to prequential analysis and intrinsic Bayes factors but is motivated through a different course.},
  archiveprefix = {arxiv},
  keywords = {Statistics - Machine Learning,Statistics - Methodology},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Fong_Holmes_2019_On the marginal likelihood and cross-validation.pdf;C\:\\Users\\roman\\Zotero\\storage\\S8PGYZJA\\1905.html}
}

@article{foreman-mackey_cornerpy_2016,
  title = {Corner.Py: {{Scatterplot}} Matrices in {{Python}}},
  author = {{Foreman-Mackey}, Daniel},
  year = {2016},
  journal = {Journal of Open Source Software},
  volume = {1},
  number = {2},
  pages = {24},
  publisher = {{The Open Journal}},
  doi = {10.21105/joss.00024},
  file = {C:\Users\roman\OneDrive\Documents\Library\Foreman-Mackey_2016_corner.pdf}
}

@article{foreman-mackey_emcee_2013,
  title = {Emcee: {{The MCMC Hammer}}},
  author = {{Foreman-Mackey}, Daniel and Hogg, David W. and Lang, Dustin and Goodman, Jonathan},
  year = {2013},
  month = mar,
  journal = {{\textbackslash}pasp},
  volume = {125},
  number = {925},
  pages = {306},
  doi = {10.1086/670067},
  keywords = {Astrophysics - Instrumentation and Methods for Astrophysics,Physics - Computational Physics,Statistics - Computation},
  file = {C:\Users\roman\OneDrive\Documents\Library\Foreman-Mackey et al_2013_emcee.pdf}
}

@book{franceschetti_comparison_2022,
  title = {Comparison of {{Different Graphs}} in {{Hidden Markov Models Describing Lymphatic Spread}} of {{Head}} and {{Neck Cancer}}},
  author = {Franceschetti, Luca},
  year = {2022},
  month = aug,
  abstract = {The use of hidden Markov models (HMM) allows to describe the progression of cancer from the primary tumor to various lymph node levels (LNLs) for head and neck squamous cell carcinomas (HNSCCs). Thus far the choice of lymphatic channels to describe the spread of the cancer cells has been mostly anatomically motivated. This work uses a data-driven approach to compare different choices of edges in the graph of the model. The logarithm of the marginal likelihood and the associated Bayes factor are adopted as the means for this comparison. In addition, the probability of metastases in different LNLs according to the HMM graph is compared with the prevalence in the data set. This is to further investigate the importance of individual connections. The results indicate that the anatomically motivated graph describes the data comparatively well due to the important connection between LNL II and I. Further improvement is suggested by introducing a link between LNL III and V.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Franceschetti_2022_Comparison of Different Graphs in Hidden Markov Models Describing Lymphatic.pdf}
}

@misc{friel_estimating_2011,
  title = {Estimating the Evidence -- a Review},
  author = {Friel, Nial and Wyse, Jason},
  year = {2011},
  month = nov,
  number = {arXiv:1111.1957},
  eprint = {1111.1957},
  primaryclass = {stat},
  publisher = {{arXiv}},
  urldate = {2022-08-30},
  abstract = {The model evidence is a vital quantity in the comparison of statistical models under the Bayesian paradigm. This paper presents a review of commonly used methods. We outline some guidelines and offer some practical advice. The reviewed methods are compared for two examples; non-nested Gaussian linear regression and covariate subset selection in logistic regression.},
  archiveprefix = {arxiv},
  keywords = {Statistics - Methodology},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Friel_Wyse_2011_Estimating the evidence -- a review.pdf;C\:\\Users\\roman\\Zotero\\storage\\HLJHQPN4\\1111.html}
}

@book{fritz_international_2000,
  title = {International Classification of Diseases for Oncology: {{ICD-O}}},
  shorttitle = {International Classification of Diseases for Oncology},
  editor = {Fritz, April G.},
  year = {2000},
  edition = {3rd ed},
  publisher = {{World Health Organization}},
  address = {{Geneva}},
  abstract = {Includes sections for coding both topography and morphology of tumors. Lists new morphology code numbers, new morphology terms and synonyms, and terms changed to malignant},
  isbn = {978-92-4-154534-1},
  lccn = {RC258 .I44 2000},
  keywords = {classification,Classification,Neoplasms,Tumors},
  annotation = {OCLC: ocm45716980},
  file = {C:\Users\roman\OneDrive\Documents\Library\Fritz_2000_International classification of diseases for oncology.pdf}
}

@article{galan_nasonet_2002,
  title = {{{NasoNet}}, Modeling the Spread of Nasopharyngeal Cancer with Networks of Probabilistic Events in Discrete Time},
  author = {Galan, S F and {Others}},
  year = {2002},
  journal = {Artif. Intell. Med.},
  volume = {25},
  pages = {247--264},
  doi = {10.1016/S0933-3657(02)00027-1}
}

@book{gelman_bayesian_2015,
  title = {Bayesian {{Data Analysis}}},
  author = {Gelman, Andrew and Carlin, John B. and Stern, Hal S. and Dunson, David B. and Vehtari, Aki and Rubin, Donald B.},
  year = {2015},
  month = jul,
  edition = {3},
  publisher = {{Chapman and Hall/CRC}},
  address = {{New York}},
  doi = {10.1201/b16018},
  abstract = {Winner of the 2016 De Groot Prize from the International Society for Bayesian AnalysisNow in its third edition, this classic book is widely considered the leading text on Bayesian methods, lauded for its accessible, practical approach to analyzing data and solving research problems. Bayesian Data Analysis, Third Edition continues to take an applied},
  isbn = {978-0-429-11307-9},
  file = {C:\Users\roman\OneDrive\Documents\Library\Gelman et al_2015_Bayesian Data Analysis.pdf}
}

@article{gelman_simulating_1998,
  title = {Simulating {{Normalizing Constants}}: {{From Importance Sampling}} to {{Bridge Sampling}} to {{Path Sampling}}},
  shorttitle = {Simulating {{Normalizing Constants}}},
  author = {Gelman, Andrew and Meng, Xiao-Li},
  year = {1998},
  journal = {Statistical Science},
  volume = {13},
  number = {2},
  eprint = {2676756},
  eprinttype = {jstor},
  pages = {163--185},
  publisher = {{Institute of Mathematical Statistics}},
  issn = {0883-4237},
  urldate = {2022-08-03},
  abstract = {Computing (ratios of) normalizing constants of probability models is a fundamental computational problem for many statistical and scientific studies. Monte Carlo simulation is an effective technique, especially with complex and high-dimensional models. This paper aims to bring to the attention of general statistical audiences of some effective methods originating from theoretical physics and at the same time to explore these methods from a more statistical perspective, through establishing theoretical connections and illustrating their uses with statistical problems. We show that the acceptance ratio method and thermodynamic integration are natural generalizations of importance sampling, which is most familiar to statistical audiences. The former generalizes importance sampling through the use of a single "bridge" density and is thus a case of bridge sampling in the sense of Meng and Wong. Thermodynamic integration, which is also known in the numerical analysis literature as Ogata's method for high-dimensional integration, corresponds to the use of infinitely many and continuously connected bridges (and thus a "path"). Our path sampling formulation offers more flexibility and thus potential efficiency to thermodynamic integration, and the search of optimal paths turns out to have close connections with the Jeffreys prior density and the Rao and Hellinger distances between two densities. We provide an informative theoretical example as well as two empirical examples (involving 17- to 70-dimensional integrations) to illustrate the potential and implementation of path sampling. We also discuss some open problems.},
  file = {C:\Users\roman\OneDrive\Documents\Library\Gelman_Meng_1998_Simulating Normalizing Constants.pdf}
}

@article{geweke_interpretation_2007-1,
  title = {Interpretation and Inference in Mixture Models: {{Simple MCMC}} Works},
  shorttitle = {Interpretation and Inference in Mixture Models},
  author = {Geweke, John},
  year = {2007},
  month = apr,
  journal = {Computational Statistics \& Data Analysis},
  volume = {51},
  number = {7},
  pages = {3529--3550},
  issn = {0167-9473},
  doi = {10.1016/j.csda.2006.11.026},
  urldate = {2023-09-07},
  abstract = {The mixture model likelihood function is invariant with respect to permutation of the components of the mixture. If functions of interest are permutation sensitive, as in classification applications, then interpretation of the likelihood function requires valid inequality constraints and a very large sample may be required to resolve ambiguities. If functions of interest are permutation invariant, as in prediction applications, then there are no such problems of interpretation. Contrary to assessments in some recent publications, simple and widely used Markov chain Monte Carlo (MCMC) algorithms with data augmentation reliably recover the entire posterior distribution.},
  keywords = {Bayesian,Classification,Labeling},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Geweke_2007_Interpretation and inference in mixture models.pdf;C\:\\Users\\roman\\Zotero\\storage\\JCY2DHCU\\S0167947306004506.html}
}

@article{goel_clinical_2017,
  title = {Clinical {{Practice}} in {{PET}}/{{CT}} for the {{Management}} of {{Head}} and {{Neck Squamous Cell Cancer}}},
  author = {Goel, Reema and Moore, William and Sumer, Baran and Khan, Saad and Sher, David and Subramaniam, Rathan M.},
  year = {2017},
  month = aug,
  journal = {American Journal of Roentgenology},
  volume = {209},
  number = {2},
  pages = {289--303},
  issn = {0361-803X, 1546-3141},
  doi = {10.2214/AJR.17.18301},
  urldate = {2022-07-01},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Goel et al_2017_Clinical Practice in PET-CT for the Management of Head and Neck Squamous Cell.pdf}
}

@inproceedings{goggans_using_2004,
  title = {Using {{Thermodynamic Integration}} to {{Calculate}} the {{Posterior Probability}} in {{Bayesian Model Selection Problems}}},
  booktitle = {{{AIP Conference Proceedings}}},
  author = {Goggans, Paul M.},
  year = {2004},
  volume = {707},
  pages = {59--66},
  publisher = {{AIP}},
  address = {{Jackson Hole, Wyoming (USA)}},
  issn = {0094243X},
  doi = {10.1063/1.1751356},
  urldate = {2022-08-03},
  abstract = {This paper gives an algorithm for calculating posterior probabilities using thermodynamic integration. The thermodynamic integration calculations are accomplished by annealing an ensemble of Markov chains with an adaptive schedule. The algorithm includes a method for determining ``good'' starting positions for the chains at each new value of the annealing parameter.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Goggans_2004_Using Thermodynamic Integration to Calculate the Posterior Probability in.pdf}
}

@article{goodman_ensemble_2010,
  title = {Ensemble {{Samplers}} with Affine {{Invariance}}},
  author = {Goodman, Jonathan and Weare, Jonathan},
  year = {2010},
  journal = {Communications in Applied Mathematics and Computational Science},
  volume = {5},
  number = {1},
  issn = {1559-3940},
  doi = {10.2140/camcos.2010.5.65},
  abstract = {We propose a family of Markov chain Monte Carlo methods whose performance is unaffected by affine tranformations of space. These algorithms are easy to construct and require little or no additional computational overhead. They should be particularly useful for sampling badly scaled distributions. Computational tests show that the affine invariant methods can be significantly faster than standard MCMC methods on highly skewed distributions.},
  file = {C:\Users\roman\OneDrive\Documents\Library\Goodman_Weare_2010_Ensemble Samplers with affine Invariance.pdf}
}

@article{grandjean_developmental_2019,
  title = {Developmental Fluoride Neurotoxicity: An Updated Review},
  shorttitle = {Developmental Fluoride Neurotoxicity},
  author = {Grandjean, Philippe},
  year = {2019},
  month = dec,
  journal = {Environmental Health},
  volume = {18},
  number = {1},
  pages = {110},
  issn = {1476-069X},
  doi = {10.1186/s12940-019-0551-x},
  urldate = {2023-12-15},
  abstract = {After the discovery of fluoride as a caries-preventing agent in the mid-twentieth century, fluoridation of community water has become a widespread intervention, sometimes hailed as a mainstay of modern public health. However, this practice results in elevated fluoride intake and has become controversial for two reasons. First, topical fluoride application in the oral cavity appears to be a more direct and appropriate means of preventing caries. Second, systemic fluoride uptake is suspected of causing adverse effects, in particular neurotoxicity during early development. The latter is supported by experimental neurotoxicity findings and toxicokinetic evidence of fluoride passing into the brain.},
  keywords = {Cognitive disorder,Dental caries,Drinking water,Fluoridation,Fluoride poisoning,Intellectual disability,Neurotoxic disorder,Prenatal exposure delayed effects},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Grandjean_2019_Developmental fluoride neurotoxicity.pdf;C\:\\Users\\roman\\Zotero\\storage\\NKQBAJH6\\s12940-019-0551-x.html}
}

@article{gregoire_ct-based_2003,
  title = {{{CT-based}} Delineation of Lymph Node Levels and Related {{CTVs}} in the Node-Negative Neck: {{DAHANCA}}, {{EORTC}}, {{GORTEC}}, {{NCIC}},{{RTOG}} Consensus Guidelines},
  author = {Gr{\'e}goire, Vincent and Levendag, Peter and Ang, Kian K. and Bernier, Jacques and Braaksma, Marijel and Budach, Volker and Chao, Cliff and Coche, Emmanuel and Cooper, Jay S. and Cosnard, Guy and Eisbruch, Avraham and {El-Sayed}, Samy and Emami, Bahman and Grau, Cai and Hamoir, Marc and Lee, Nancy and Maingon, Philippe and Muller, Karin and Reychler, Herv{\'e}},
  year = {2003},
  month = dec,
  journal = {Radiotherapy and Oncology},
  volume = {69},
  number = {3},
  pages = {227--236},
  issn = {0167-8140},
  doi = {10.1016/j.radonc.2003.09.011},
  abstract = {Background and purpose: The appropriate application of 3-D CRT and IMRT for HNSCC requires a standardization of the procedures for the delineation of the target volumes. Over the past few years, two proposals{\textemdash}the so-called Brussels guidelines from Gr{\'e}goire et al., and the so-called Rotterdam guidelines from Nowak et al.{\textemdash}emerged from the literature for the delineation of the neck node levels. Detailed examination of these proposals however revealed some important discrepancies. Materials and methods: Within this framework, the Brussels and Rotterdam groups decided to review their guidelines and derive a common set of recommendations for delineation of neck node levels. This proposal was then discussed with representatives of major cooperative groups in Europe (DAHANCA, EORTC, GORTEC) and in North America (NCIC, RTOG), which, after some additional refinements, have endorsed them. The objective of the present article is to present the consensus guidelines for the delineation of the node levels in the node-negative neck. Results and conclusions: First a short discussion of the discrepancies between the previous Brussels and the Rotterdam guidelines is presented. The general philosophy of the consensus guidelines and the methodology used to resolve the various discrepancies are then described. The consensus proposal is then presented and representative CTVs that are consistent with these guidelines are illustrated on CT sections. Last, the limitations of the consensus guidelines are discussed and some concerns about the direct applications of these guidelines to the node-positive neck and the post-operative neck are described.},
  keywords = {guideline,Head and neck,Node levels,Radiotherapy},
  file = {C:\Users\roman\OneDrive\Documents\Library\Grégoire et al_2003_CT-based delineation of lymph node levels and related CTVs in the node-negative.pdf}
}

@article{gregoire_delineation_2014,
  title = {Delineation of the Neck Node Levels for Head and Neck Tumors: {{A}} 2013 Update. {{DAHANCA}}, {{EORTC}}, {{HKNPCSG}}, {{NCIC CTG}}, {{NCRI}}, {{RTOG}}, {{TROG}} Consensus Guidelines},
  author = {Gr{\'e}goire, Vincent and Ang, Kian and Budach, Wilfried and Grau, Cai and Hamoir, Marc and Langendijk, Johannes A. and Lee, Anne and Le, Quynh-Thu and Maingon, Philippe and Nutting, Chris and O'Sullivan, Brian and Porceddu, Sandro V. and Lengele, Benoit},
  year = {2014},
  month = jan,
  journal = {Radiotherapy and Oncology},
  volume = {110},
  number = {1},
  pages = {172--181},
  issn = {0167-8140},
  doi = {10.1016/j.radonc.2013.10.010},
  abstract = {In 2003, a panel of experts published a set of consensus guidelines for the delineation of the neck node levels in node negative patients (Radiother Oncol, 69: 227{\textendash}36, 2003). In 2006, these guidelines were extended to include the characteristics of the node positive and the post-operative neck (Radiother Oncol, 79: 15{\textendash}20, 2006). These guidelines did not fully address all nodal regions and some of the anatomic descriptions were ambiguous, thereby limiting consistent use of the recommendations. In this framework, a task force comprising opinion leaders in the field of head and neck radiation oncology from European, Asian, Australia/New Zealand and North American clinical research organizations was formed to review and update the previously published guidelines on nodal level delineation. Based on the nomenclature proposed by the American Head and Neck Society and the American Academy of Otolaryngology-Head and Neck Surgery, and in alignment with the TNM atlas for lymph nodes in the neck, 10 node groups (some being divided into several levels) were defined with a concise description of their main anatomic boundaries, the normal structures juxtaposed to these nodes, and the main tumor sites at risk for harboring metastases in those levels. Emphasis was placed on those levels not adequately considered previously (or not addressed at all); these included the lower neck (e.g. supraclavicular nodes), the scalp (e.g. retroauricular and occipital nodes), and the face (e.g. buccal and parotid nodes). Lastly, peculiarities pertaining to the node-positive and the post-operative clinical scenarios were also discussed. In conclusion, implementation of these guidelines in the daily practice of radiation oncology should contribute to the reduction of treatment variations from clinician to clinician and facilitate the conduct of multi-institutional clinical trials.},
  keywords = {guideline,Head and neck tumors,IMRT,Lymph node levels,Neck nodes,Worldwide consensus},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Grégoire et al_2014_Delineation of the neck node levels for head and neck tumors.pdf;C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Grégoire et al_2014_Delineation of the neck node levels for head and neck tumors2.pdf}
}

@article{gregoire_delineation_2018,
  title = {Delineation of the Primary Tumour Clinical Target Volumes ({{CTV-P}}) in Laryngeal, Hypopharyngeal, Oropharyngeal and Oral Cavity Squamous Cell Carcinoma: {{AIRO}}, {{CACA}}, {{DAHANCA}}, {{EORTC}}, {{GEORCC}}, {{GORTEC}}, {{HKNPCSG}}, {{HNCIG}}, {{IAG-KHT}}, {{LPRHHT}}, {{NCIC CTG}}, {{NCRI}}, {{NRG Oncology}}, {{PHNS}}, {{SBRT}}, {{SOMERA}}, {{SRO}}, {{SSHNO}}, {{TROG}} Consensus Guidelines},
  author = {Gr{\'e}goire, V and {Others}},
  year = {2018},
  journal = {Radiother. Oncol.},
  volume = {126},
  pages = {3--24},
  doi = {10.1016/j.radonc.2017.10.016},
  file = {C:\Users\roman\OneDrive\Documents\Library\Grégoire_Others_2018_Delineation of the primary tumour clinical target volumes (CTV-P) in laryngeal,.pdf}
}

@article{gregoire_proposal_2006,
  title = {Proposal for the Delineation of the Nodal {{CTV}} in the Node-Positive and the Post-Operative Neck},
  author = {Gr{\'e}goire, Vincent and Eisbruch, Avraham and Hamoir, Marc and Levendag, Peter},
  year = {2006},
  month = apr,
  journal = {Radiotherapy and Oncology},
  volume = {79},
  number = {1},
  pages = {15--20},
  issn = {0167-8140},
  doi = {10.1016/j.radonc.2006.03.009},
  abstract = {Background and purpose In 2003, a panel of experts published a set of consensus guidelines regarding the delineation of the neck node levels (Radiother Oncol, 2003; 69: 227{\textendash}36). These recommendations were applicable for the node-negative and the N1-neck, but were found too restrictive for the node-positive and the post-operative neck. Patients and methods In this framework, using the previous recommendations as a backbone, new guidelines have been proposed taking into account the specificities of the node-positive and the post-operative neck. Results Inclusion of the retrostyloid space cranially and the supra-clavicular fossa caudally is proposed in case of neck nodes (defined radiologically or on the surgical specimen) located in levels II, and IV or Vb, respectively. When extra-capsular rupture is suspected (on imaging) or demonstrated on the pathological specimen, adjacent muscles should also be included in the CTV. For node(s) located at the boundary between contiguous levels (e.g. levels II and Ib), these two levels should be delineated. In the post-operative setting, the entire `surgical bed' should be included. Last, the retropharyngeal space should be delineated in case of positive neck from pharyngeal tumors. Conclusions The objective of the manuscript is to give a comprehensive description of the new set of guidelines for CTV delineation in the node-positive neck and the post-operative neck, with a complementary atlas of the new anatomical structures to be included.},
  keywords = {CTV,guideline,Head neck,Node levels,Radiotherapy}
}

@article{gregoire_selection_2000,
  title = {Selection and Delineation of Lymph Node Target Volumes in Head and Neck Conformal Radiotherapy. {{Proposal}} for Standardizing Terminology and Procedure Based on the Surgical Experience},
  author = {Gr{\'e}goire, V and {Others}},
  year = {2000},
  journal = {Radiother. Oncol.},
  volume = {56},
  pages = {135--150},
  doi = {10.1016/S0167-8140(00)00202-4},
  keywords = {Computed tomography,Conformal radiotherapy,guideline,Head and neck tumor,Magnetic resonance imaging,Node level},
  file = {C:\Users\roman\OneDrive\Documents\Library\Grégoire_Others_2000_Selection and delineation of lymph node target volumes in head and neck.pdf}
}

@article{gregoire_selection_2000-1,
  title = {Selection and Delineation of Lymph Node Target Volumes in Head and Neck Conformal Radiotherapy. {{Proposal}} for Standardizing Terminology and Procedure Based on the Surgical Experience},
  author = {Gr{\'e}goire, Vincent and Coche, Emmanuel and Cosnard, Guy and Hamoir, Marc and Reychler, Herv{\'e}},
  year = {2000},
  month = aug,
  journal = {Radiotherapy and Oncology},
  volume = {56},
  number = {2},
  pages = {135--150},
  issn = {0167-8140},
  doi = {10.1016/S0167-8140(00)00202-4},
  urldate = {2023-10-25},
  abstract = {The increasing use of 3D treatment planning in head and neck radiation oncology has created an urgent need for new guidelines for the selection and the delineation of the neck node areas to be included in the clinical target volume. Surgical literature has provided us with valuable information on the extent of pathological nodal involvement in the neck as a function of the primary tumor site. In addition, few clinical series have also reported information on radiological nodal involvement in those areas not commonly included in radical neck dissection. Taking all these data together, guidelines for the selection of the node levels to be irradiated for the major head and neck sites could be proposed. To fill the missing link between these guidelines and the 3D treatment planning, recommendations for the delineation of these node levels (levels I{\textendash}VI and retropharyngeal) on CT (or MRI) slices have been proposed using the guidelines outlined by the Committee for Head and Neck Surgery and Oncology of the American Academy for Otolarynology-Head and Neck Surgery. These guidelines were adapted to take into account specific radiological landmarks more easily identified on CT or MRI slices than in the operating field.},
  keywords = {Computed tomography,Conformal radiotherapy,Head and neck tumor,Magnetic resonance imaging,Node level},
  file = {C\:\\Users\\roman\\Zotero\\storage\\HBCU9JR2\\Grégoire et al_2000_Selection and delineation of lymph node target volumes in head and neck.pdf;C\:\\Users\\roman\\Zotero\\storage\\M8S4JMXB\\S0167814000002024.html}
}

@book{grosu_target_2015,
  title = {Target {{Volume Definition}} in {{Radiation Oncology}}},
  author = {Grosu, A L A C N},
  year = {2015},
  publisher = {{Springer}}
}

@article{hagberg_exploring_2008,
  title = {Exploring {{Network Structure}}, {{Dynamics}}, and {{Function}} Using {{NetworkX}}},
  author = {Hagberg, Aric A and Schult, Daniel A and Swart, Pieter J},
  year = {2008},
  pages = {5},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Hagberg et al_2008_Exploring Network Structure, Dynamics, and Function using NetworkX.pdf}
}

@article{haimes_integrating_2007,
  title = {Integrating {{Bayes}}' {{Theorem}} with {{Dynamic Programming}} for {{Optimal Intelligence Collection}}},
  author = {Haimes, Yacov Y. and Yan, Zhenyu and Horowitz, Barry M.},
  year = {2007},
  journal = {Military Operations Research},
  volume = {12},
  number = {4},
  eprint = {43941086},
  eprinttype = {jstor},
  pages = {17--31},
  publisher = {{Military Operations Research Society}},
  issn = {1082-5983},
  urldate = {2021-05-31},
  abstract = {Bayes' theorem provides a theoretical foundation upon which to quantitatively update the credibility of prior information through new evidence. The method of analysis presented in this paper is based on the recognition that the construction of posterior probabilities on the basis of new intelligence (knowledge), which can be repeated again and again, is harmonious with Bellman's principle of optimality in dynamic programming. Furthermore, because of the compatibility between Bayes' formula for posterior probabilities and Bellman's recursive equation in dynamic programming, the two can be embedded into one integrated formulation to optimize sequential investments in different aspects of intelligence gathering and analysis. The integration for intelligence investments is developed in this paper including a set of example problems to demonstrate the methodology.},
  file = {C:\Users\roman\OneDrive\Documents\Library\Haimes et al_2007_Integrating Bayes' Theorem with Dynamic Programming for Optimal Intelligence.pdf}
}

@article{heckerman_toward_1992,
  title = {Toward Normative Expert Systems: {{Part I The Pathfinder}} Project},
  author = {Heckerman, D and Horvitz, E and Nathwani, B},
  year = {1992},
  journal = {Methods Inf. Med.},
  volume = {31},
  pages = {90--105},
  doi = {10.1055/s-0038-1634867}
}

@article{heckerman_toward_1992-1,
  title = {Toward Normative Expert Systems Part {{II Probability-based}} Representations for Efficient Knowledge Acquisition and Inference},
  author = {Heckerman, D and Nathwani, B N},
  year = {1992},
  journal = {Methods Inf. Med.},
  volume = {31},
  pages = {106--116},
  doi = {10.1055/s-0038-1634868}
}

@article{hennessey_human_2009,
  title = {Human {{Papillomavirus}} and {{Head}} and {{Neck Squamous Cell Carcinoma}}},
  author = {Hennessey, P.T. and Westra, W.H. and Califano, J.A.},
  year = {2009},
  month = apr,
  journal = {Journal of Dental Research},
  volume = {88},
  number = {4},
  pages = {300--306},
  issn = {0022-0345},
  doi = {10.1177/0022034509333371},
  urldate = {2022-10-06},
  abstract = {Over the past 20 years, high-risk human papillomavirus (HPV) infection has been established as a risk factor for developing head and neck squamous cell carcinoma, independent of tobacco and alcohol use. In particular, HPV is strongly associated with the development of oropharyngeal cancer and a small minority of oral cavity cancers. In this review, we summarize what is currently known about the biology of HPV, the mechanisms by which it effects malignant transformation, and the potential impact of HPV status on the clinical management of persons with head and neck cancer.},
  pmcid = {PMC3317947},
  pmid = {19407148},
  file = {C:\Users\roman\OneDrive\Documents\Library\Hennessey et al_2009_Human Papillomavirus and Head and Neck Squamous Cell Carcinoma.pdf}
}

@article{ho_decision_2014,
  title = {Decision Making in the Management of Recurrent Head and Neck Cancer},
  author = {Ho, Allen S. and Kraus, Dennis H. and Ganly, Ian and Lee, Nancy Y. and Shah, Jatin P. and Morris, Luc G. T.},
  year = {2014},
  journal = {Head \& Neck},
  volume = {36},
  number = {1},
  pages = {144--151},
  issn = {1097-0347},
  doi = {10.1002/hed.23227},
  urldate = {2024-01-12},
  abstract = {Despite substantial improvements in head and neck squamous cell carcinoma (HNSCC) treatment, the major obstacle to long-term survival remains disease recurrence. Salvage options are often limited due to prior therapy and the escalated morbidity of retreatment. The costs of treatment must be measured against the anticipated quality and quantity of life recovered, even with resectable disease. This review surveys the recurrent HNSCC literature to better guide decision making. Across multiple studies, negative prognostic factors include impaired performance status, advanced recurrent stage, brief disease-free interval, previous chemotherapy, and nonlaryngeal sites of recurrence. When possible, surgical salvage remains the principal option for durable disease control, quality of life preservation, and cure. Nonsurgical therapies have also demonstrated measurable improvements in locoregional control. Interpretation of salvage literature must be tempered by recognition of significant selection bias. The decision for salvage therapy must be individualized, with management that involves well-informed patients resulting in the best outcomes. {\textcopyright} 2013 Wiley Periodicals, Inc. Head Neck 36: 144{\textendash}151, 2014},
  langid = {english},
  keywords = {cancer recurrence,head and neck cancer,quality of life,reirradiation,salvage surgery},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Ho et al_2014_Decision making in the management of recurrent head and neck cancer.pdf;C\:\\Users\\roman\\Zotero\\storage\\NR6DWA6V\\hed.html}
}

@article{ho_patterns_2012,
  title = {Patterns of Regional Lymph Node Metastasis of Nasopharyngeal Carcinoma: {{A}} Meta-Analysis of Clinical Evidence},
  shorttitle = {Patterns of Regional Lymph Node Metastasis of Nasopharyngeal Carcinoma},
  author = {Ho, Francis CH and Tham, Ivan WK and Earnest, Arul and Lee, Khai Mun and Lu, Jiade J},
  year = {2012},
  month = dec,
  journal = {BMC Cancer},
  volume = {12},
  number = {1},
  pages = {98},
  issn = {1471-2407},
  doi = {10.1186/1471-2407-12-98},
  urldate = {2021-02-10},
  abstract = {Background: The characteristics of cervical lymphatic metastasis in nasopharyngeal carcinoma (NPC) are not completely understood. As such, radiotherapy to the entire lymphatic of the neck bilaterally has been empirically practiced even in early stage disease, although not supported by clinical evidence. We studied the pattern and probability of nodal metastasis through a meta-analysis of published evidences, with an aim to establish an evidence-based guideline for selecting and delineation of clinical target volume of neck lymphatics for conformation radiation for NPC. Methods: A literature search yielded an initial 411 original articles, and 13 studies with 2920 NPC cases staged via MRI were included in this analysis. The occurrence of nodal metastasis was calculated and analyzed according to the respective regional nodal levels. Results: 85\% of NPC cases presented with lymphadenopathy. The most commonly involved regions include retropharyngeal (69\%) and level II lymph nodes (70\%). The overall probability of levels III, IV, and V nodal involvement are 45\%, 11\%, and 27\%, respectively. Low-risk node groups included the supraclavicular, levels IA/IB and VI nodes, and parotid nodes with involvement rates at 3\%, 0\%, 3\%, 0\%, and 1\%, respectively. Nodal metastases followed an orderly pattern and the probability of ``skip'' metastasis between levels varied between 0.5-7.9\%. Conclusions: Lymph node metastasis in NPC follows a predictable and orderly pattern. The rarity of metastasis in certain nodal groups and ``skip'' metastasis suggest that reduced treatment volume is feasible in conformal radiotherapy for NPC.},
  langid = {english},
  keywords = {patterns},
  file = {C:\Users\roman\OneDrive\Documents\Library\Ho et al_2012_Patterns of regional lymph node metastasis of nasopharyngeal carcinoma.pdf}
}

@article{hoang_evaluation_2013,
  title = {Evaluation of Cervical Lymph Nodes in Head and Neck Cancer with {{CT}} and {{MRI}}: Tips, Traps, and a Systematic Approach},
  author = {Hoang, J K and {Others}},
  year = {2013},
  journal = {Am. J. Roentgenol.},
  volume = {200},
  pages = {W17-W25},
  doi = {10.2214/AJR.12.8960}
}

@inproceedings{hoffmann_detailed_2021,
  title = {Detailed Analysis of Lymphatic Progression Patterns for Oropharyngeal Squamous Cell Carcinoma},
  booktitle = {{{ESTRO}}},
  author = {Hoffmann, Jean-Marc and Pouymayou, Bertrand and Ludwig, Roman and Guckenberger, Matthias and Balermpas, Panagiotis and Unkelbach, Jan},
  year = {2021},
  pages = {25},
  address = {{Madrid}},
  urldate = {2022-10-25},
  abstract = {Purpose/Objective: Head \& neck squamous cell carcinomas (HNSCC) spread lymphatically through the neck and form metastases in regional lymph nodes. While the general directions of spread are understood and the prevalence of lymph node level (LNL) involvement has been reported, the details of lymphatic progression patterns are insufficiently quantified. Purpose of this study is to investigate, how the risk of metastases in a given level depends on whether or not upstream levels harbour metastases, how much the risk increases for late versus early T-stage, and if progression patterns differ between HPV positive versus negative tumors. Quantifying these dependencies may eventually lead to more personalized definition of the elective nodal CTV and tailored radiotherapy treatments. Materials/Methods: To address these questions, we retrospectively analysed all  patients with newly diagnosed oropharyngeal HNSCC treated at our institution between 2013 and 2019, resulting in a dataset of 287 patients. For all patients, involvement of LNLs I-IIV was recorded together with T-stage, midline extension, HPV status, smoking status, and primary tumor subsite. Using common criteria , LNL involvement was assessed individually based on available modalities (PET, MR, CT, FNA). To analyse the complex dataset, a graphical user interface linked to an SQL database was developed, which allows querying the number of patients with a certain combination of co-involved LNLs and tumor characteristics (Figure 1). Results: Table 1 reports the number of patients in whom a particular combination of LNLs was involved to highlighted selected findings: 1) Ipsilateral level IV was involved in 27\% of patients in whom level II and III were involved, but only in 2\% of patients in whom level II but not III is involved. 2) Prevalence of involvement of ipsilateral levels II, III, IV, V was 79\%, 34\%, 7\%, 3\% for early T-stage patients (T1/T2) and 85\%, 50\%, 17\%, 9\% for late T-stage (T3/T4), quantifying increasing involvement with T-stage especially for the more downstream levels.   3) Contralateral levels II, III, IV were involved in 41\%, 19\%, 4\% for tumors with midline extension and 12\%, 3\%, 2\% for tumors without midline extension.  4) The dataset provided no indication that LNL involvement is different for HPV positive vs negative tumors. 5 ) Ipsilateral level VII was involved in 10\% of all patients and in 14\% and 6\% of patients with primary tumors in the tonsil and the base of tongue, respectively. Conclusions: Detailed reporting and quantification of LNL involvement in HNSCC depending on involvement of upstream LNLs, T-stage, primary tumor subsite, midline extension, and potential other risk factors may allow for further personalization of CTV-N definition and reduced toxicity in the future. An example is identification of patients with minimal risk of level IV involvement to allow save exclusion of level IV from the CTV-N.}
}

@article{huang_re-evaluation_2017,
  title = {Re-Evaluation of {{Ipsilateral Radiation}} for {{T1-T2N0-N2b Tonsil Carcinoma}} at the {{Princess Margaret Hospital}} in the {{Human Papillomavirus Era}}, 25~{{Years Later}}},
  author = {Huang, Shao Hui and Waldron, John and Bratman, Scott V. and Su, Jie and Kim, John and Bayley, Andrew and Cho, John and Giuliani, Meredith and Hope, Andrew and Ringash, Jolie and Hansen, Aaron and {de Almeida}, John R. and Goldstein, David and {Perez-Ordonez}, Bayardo and Weinreb, Ilan and Tong, Li and Xu, Wei and O'Sullivan, Brian},
  year = {2017},
  month = may,
  journal = {International Journal of Radiation Oncology*Biology*Physics},
  volume = {98},
  number = {1},
  pages = {159--169},
  issn = {0360-3016},
  doi = {10.1016/j.ijrobp.2017.01.018},
  urldate = {2022-10-20},
  abstract = {Purpose To report the outcome of ipsilateral radiation therapy (RT) in human papillomavirus (HPV)-positive (HPV+) patients and HPV-negative (HPV-) patients with T1-T2N0-N2b tonsillar cancer treated 25~years after our initial historical cohort. Methods and Materials Patients with T1-T2N0-N2b tonsillar cancer who received ipsilateral RT or bilateral RT between 1999 and 2014 were reviewed. Overall survival (OS), local control (LC), regional control (RC), and grade 3 to 4 late toxicity (LT) were compared between ipsilateral RT and bilateral RT within HPV+ and HPV- patients, separately. Results HPV status was ascertained in 379/427 (88\%) consecutive patients (ipsilateral RT: 62 HPV+, 34 HPV-; bilateral RT: 240 HPV+ 240, 41 HPV-). The proportion of ipsilateral RT by N category for HPV+ and HPV- patients were as follows: N0: 24/37 (65\%) versus 28/48 (74\%); N1: 21/49 (43\%) versus 4/9 (44\%); N2a: 10/39 (26\%) versus 1/4 (25\%); and N2b: 7/177 (4\%) versus 1/24 (4\%), respectively. Of the patients receiving ipsilateral RT, 94/96 (98\%) were treated with RT alone. The median follow-up time was 5.03~years. The respective 5-year rates of OS, LC, RC, and LT were similar between ipsilateral RT and bilateral RT for the HPV+~patients (OS: 89\% vs 87\%, P=.55; LC: 97\% vs 98\%, P=.65; RC: 98\% vs 97\%, P=.27; LT: 17\% vs 12\%, P=.83) and HPV- patients (OS: 63\% vs 48\%, P=.27; LC: 90\% vs 80\%, P=.19; RC: 94\% vs 83\%, P=.14; LT: 15\% vs 22\%, P=.36). Of the 96 patients receiving ipsilateral RT, contralateral neck failure (CNF) occurred in 1/52 HPV+~patients and 1/34 HPV- patients. The 5-year CNF rates were 2\% (95\% CI: 1-9) (HPV+: 2\% [0-14]; HPV-: 3\% [0-21], P=.66). Five local failures (2 HPV+; 3 HPV-) and no distant failures were seen. The 5-year rates of LC, RC, and LT were 97\% versus 90\% (P=.24), 98\% versus 94\% (P=.25), and 18\% versus 15\% (P=.75) for the HPV+ and HPV- cohorts, respectively. Osteoradionecrosis occurred in 9 patients: 6/47 (13\%) treated with conventional RT and 3/49 (6\%) with intensity modulated RT (P=.32). Conclusion Ipsilateral radiation to selected patients with T1-T2N0-N2b tonsillar cancer results in equally excellent outcomes regardless of tumor HPV status.},
  langid = {english},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Huang et al_2017_Re-evaluation of Ipsilateral Radiation for T1-T2N0-N2b Tonsil Carcinoma at the.pdf;C\:\\Users\\roman\\Zotero\\storage\\DZDTR4E5\\S0360301617300226.html;C\:\\Users\\roman\\Zotero\\storage\\FCGE9IJA\\fulltext.html}
}

@misc{hudson_pydoctor_2022,
  title = {Pydoctor},
  author = {Hudson, Michael and Armstrong, Christopher and Lange, Jonathan},
  year = {2022}
}

@techreport{ICRU_prescribing_1993,
  title = {Prescribing, Recording, and Reporting Photon Beam Therapy},
  author = {{International Commission on Radiation Units and Measurements}},
  year = {1993},
  number = {50},
  institution = {{International Commission on Radiation Units and Measurements}},
  abstract = {This Report seeks to promote the use of a common language for specifying and reporting the doses in radiation therapy, as well as the volumes in which they are prescribed. Report 50 completely supersedes and updates ICRU Report 29 (published in 1978). The different volumes, which need to be identified prior to any radiotherapy, are first defined: the gross tumour volume, and the clinical target volume and the planning target volume (PTV). The two first ones are purely oncological concepts, the third one takes into account the movement of the patient and the inaccuracies due to patient-beam positioning, and related to the therapy equipment. Examples are given on how to identify these volumes from x-ray films and CT sections. Three classes of organs at risk are also defined. A substantial part of the report is devoted to the different ways of describing the dose variation throughout the PTV and identifying the high-dose or low-dose regions. External photon beam irradiation only is considered in Report 50. As a general rule for reporting, it is recommended to identify a Reference Point where the dose can be determined accurately and can be considered to be representative of the dose distribution throughout the PTV. The dose at the point (the ICRU Reference Point) should always be reported as well as the maximum and minimum doses in the PTV. The situation is more complex when two or more PTV's are identified: general recommendations are given. Three important appendices are added to the Report in order to help the reader apply the ICRU recommendations. Appendix I provides a list of the minimum requirements for documentation and for reporting the irradiation techniques. An anatomical code describing the different volumes is proposed. Appendix II contains 5 examples which illustrate, in detail, how to use the ICRU recommendations in practical clinical situations (tumour of the bronchus, breast, prostate, floor of the mouth and thigh). Appendix III discusses the relative merits of the ICRU Reference Point compared to the minimum and the mean doses at the PTV for reporting a therapeutic irradiation.}
}

@article{iyizoba-ebozue_retropharyngeal_2020,
  title = {Retropharyngeal {{Lymph Node Involvement}} in {{Oropharyngeal Carcinoma}}: {{Impact}} upon {{Risk}} of {{Distant Metastases}} and {{Survival Outcomes}}},
  shorttitle = {Retropharyngeal {{Lymph Node Involvement}} in {{Oropharyngeal Carcinoma}}},
  author = {{Iyizoba-Ebozue}, Zsuzsanna and Murray, Louise J. and Arunsingh, Moses and Dyker, Karen E. and Vaidyanathan, Sriram and Scarsbrook, Andrew F. and Prestwich, Robin J. D.},
  year = {2020},
  month = jan,
  journal = {Cancers},
  volume = {12},
  number = {1},
  pages = {83},
  publisher = {{Multidisciplinary Digital Publishing Institute}},
  doi = {10.3390/cancers12010083},
  urldate = {2021-11-22},
  abstract = {The influence of retropharyngeal lymph node (RPLN) involvement on prognosis in oropharyngeal carcinoma remains poorly defined. The aim of this study was to assess the impact of RPLN involvement upon outcomes. A single-centre retrospective analysis of 402 patients with oropharyngeal carcinoma treated nonsurgically between 2010 and 2017 was performed. All had a baseline 2-[fluorine-18]-fluoro-2-deoxy-d-glucose (FDG) PET-CT and contrast-enhanced MRI and/or CT. RPLN status was determined by radiology review of cases with reported abnormal RPLN. Multivariate backwards logistic regression was used to examine impact on outcomes of factors. Abnormal RPLNs were identified in 40/402 (10\%) of patients. Median follow up was 42.9 months. RPLN involvement was associated with inferior 3 year outcomes for overall survival (OS) (67.1\% vs. 79.1\%, p = 0.006) and distant metastases-free survival (DMFS) (73.9\% versus 88.0\%, p = 0.011), with no significant difference in local control (81.6\% vs. 87.7\%, p = 0.154) or regional control (80.7\% vs. 85.4\%, p = 0.252). On multivariate analysis abnormal RPLN, no concurrent chemotherapy and ongoing smoking were associated with inferior DMFS and OS, while advanced T stage was also associated with inferior OS. In summary, RPLN involvement, present in 10\% of patients, was an independent prognostic factor for the development of distant disease failure translating into inferior OS. These findings need confirmation in future studies.},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  langid = {english},
  keywords = {chemotherapy,distant metastases,lymph node,oropharynx cancer,radiotherapy,retropharyngeal,survival},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Iyizoba-Ebozue et al_2020_Retropharyngeal Lymph Node Involvement in Oropharyngeal Carcinoma.pdf;C\:\\Users\\roman\\Zotero\\storage\\QGJ7YA9W\\htm.html}
}

@book{jeffreys_theory_1998,
  title = {The {{Theory}} of {{Probability}}},
  author = {Jeffreys, Harold},
  year = {1998},
  month = aug,
  publisher = {{OUP Oxford}},
  abstract = {Another title in the reissued Oxford Classic Texts in the Physical Sciences series, Jeffrey's Theory of Probability, first published in 1939, was the first to develop a fundamental theory of scientific inference based on the ideas of Bayesian statistics. His ideas were way ahead of their time and it is only in the past ten years that the subject of Bayes' factors has been significantly developed and extended. Until recently the two schools of statistics (Bayesian and Frequentist) were distinctly different and set apart. Recent work (aided by increased computer power and availability) has changed all that and today's graduate students and researchers all require an understanding of Bayesian ideas. This book is their starting point.},
  googlebooks = {vh9Act9rtzQC},
  isbn = {978-0-19-158967-6},
  langid = {english},
  keywords = {Mathematics / Applied,Mathematics / Discrete Mathematics,Mathematics / Probability \& Statistics / General,Science / Physics / General}
}

@article{jensen_imaging_2021,
  title = {Imaging for {{Target Delineation}} in {{Head}} and {{Neck Cancer Radiotherapy}}},
  author = {Jensen, Kenneth and {Al-Farra}, Gina and Dejanovic, Danijela and Eriksen, Jesper G. and Loft, Annika and Hansen, Christian R. and Pameijer, Frank A. and Zukauskaite, Ruta and Grau, Cai},
  year = {2021},
  month = jan,
  journal = {Seminars in Nuclear Medicine},
  series = {Imaging {{Options}} for {{Head}} and {{Neck Cancer}}},
  volume = {51},
  number = {1},
  pages = {59--67},
  issn = {0001-2998},
  doi = {10.1053/j.semnuclmed.2020.07.010},
  urldate = {2022-07-01},
  abstract = {The definition of tumor involved volumes in patients with head and neck cancer poses great challenges with the increasing use of highly conformal radiotherapy techniques eg, volumetric modulated arc therapy and intensity modulated proton therapy. The risk of underdosing the tumor might increase unless great care is taken in the process. The information gained from imaging is increasing with both PET and MRI becoming readily available for the definition of targets. The information gained from these techniques is indeed multidimensional as one often acquire data on eg, metabolism, diffusion, and hypoxia together with anatomical and structural information. Nevertheless, much work remains to fully exploit the available information on a patient-specific level. Multimodality target definition in radiotherapy is a chain of processes that must be individually scrutinized, optimized and quality assured. Any uncertainties or errors in image acquisition, reconstruction, interpretation, and delineation are systematic errors and hence will potentially have a detrimental effect on the entire radiotherapy treatment and hence; the chance of cure or the risk of unnecessary side effects. Common guidelines and procedures create a common minimum standard and ground for evaluation and development. In Denmark, the treatment of head and neck cancer is organized within the multidisciplinary Danish Head and Neck Cancer Group (DAHANCA). The radiotherapy quality assurance group of DAHANCA organized a workshop in January 2020 with participants from oncology, radiology, and nuclear medicine from all centers in Denmark, treating patients with head and neck cancer. The participants agreed on a national guideline on imaging for target delineation in head and neck cancer radiotherapy, which has been approved by the DAHANCA group. The guidelines are available in the Supplementary. The use of multimodality imaging is being recommended for the planning of all radical treatments with a macroscopic tumor. 2-[18F]FDG-PET/CT should be available, preferable in the treatment position. The recommended MRI sequences are T1, T2 with and without fat suppression, and T1 with contrast enhancement, preferable in the treatment position. The interpretation of clinical information, including thorough physical examination as well as imaging, should be done in a multidisciplinary setting with an oncologist, radiologist, and nuclear medicine specialist.},
  langid = {english}
}

@inproceedings{jensen_notitle_1994,
  booktitle = {From {{Influence Diagrams}} to {{Junction Trees Uncertainty Proc}}. 1994},
  author = {Jensen, F and Jensen, F V and Dittmer, S L},
  year = {1994},
  pages = {367--373},
  publisher = {{Elsevier}}
}

@book{jerrum_approximation_1996,
  title = {Approximation {{Algorithms}} for {{NP-hard Problems}}},
  author = {Jerrum, M and Sinclair, A J A A F N-H P},
  year = {1996},
  publisher = {{PWS Publishing}}
}

@article{jiao_radiation-induced_2022,
  title = {Radiation-Induced {{Cell Death}} and {{Its Mechanisms}}},
  author = {Jiao, Yunfei and Cao, Fangyu and Liu, Hu},
  year = {2022},
  month = nov,
  journal = {Health Physics},
  volume = {123},
  number = {5},
  pages = {376--386},
  issn = {0017-9078},
  doi = {10.1097/HP.0000000000001601},
  urldate = {2023-03-21},
  abstract = {With rapid technical advances, ionizing radiation has been put into wider application in ordinary living, with the worst cytological effect on the human body being cell death. Moreover, according to the Nomenclature Committee on Cell Death, the method of radiation-induced cell death, usually classified as interphase and proliferative death, undergoes more detailed classifications oriented by its molecular mechanism. Elaborating its mode and molecular mechanism is crucial for the protection and treatment of radiation injury, as well as the radiotherapy and recovery of tumors. Varying with the changes of the radiation dose and the environment, the diverse targets and pathways of ionizing radiation result in various cell deaths. This review focuses on classifications of radiation-induced cell death and its molecular mechanism. We also examine the main characteristics of ionizing radiation-induced cell death. The modes of radiation-induced cell death can be classified as apoptosis, necrosis, autophagy-dependent cell death, pyroptosis, ferroptosis, immunogenic cell death, and non-lethal processes. Once the dose is high enough, radiation effects mostly appear as destructiveness (``destructiveness'' is used to describe a situation in which cells do not have the opportunity to undergo a routine death process, in which case high-dose radiation works like a physical attack). This breaks up or even shatters cells, making it difficult to find responses of the cell itself. Due to diversities concerning cell phenotypes, phases of cell cycle, radiation dose, and even cellular subregions, various methods of cell death occur, which are difficult to identify and classify. Additionally, the existence of common initial activation and signaling molecules among all kinds of cell deaths, as well as sophisticated crossways in cellular molecules, makes it more laborious to distinguish and classify various cell deaths.},
  pmcid = {PMC9512240},
  pmid = {36069830},
  file = {C:\Users\roman\OneDrive\Documents\Library\Jiao et al_2022_Radiation-induced Cell Death and Its Mechanisms.pdf}
}

@article{johnson_head_2020,
  title = {Head and Neck Squamous Cell Carcinoma},
  author = {Johnson, Daniel E. and Burtness, Barbara and Leemans, C. Ren{\'e} and Lui, Vivian Wai Yan and Bauman, Julie E. and Grandis, Jennifer R.},
  year = {2020},
  month = nov,
  journal = {Nature Reviews Disease Primers},
  volume = {6},
  number = {1},
  pages = {1--22},
  publisher = {{Nature Publishing Group}},
  issn = {2056-676X},
  doi = {10.1038/s41572-020-00224-3},
  urldate = {2022-10-07},
  abstract = {Most head and neck cancers are derived from the mucosal epithelium in the oral cavity, pharynx and larynx and are known collectively as head and neck squamous cell carcinoma (HNSCC). Oral cavity and larynx cancers are generally associated with tobacco consumption, alcohol abuse or both, whereas pharynx cancers are increasingly attributed to infection with human papillomavirus (HPV), primarily HPV-16. Thus, HNSCC can be separated into HPV-negative and HPV-positive HNSCC. Despite evidence of histological progression from cellular atypia through various degrees of dysplasia, ultimately leading to invasive HNSCC, most patients are diagnosed with late-stage HNSCC without a clinically evident antecedent pre-malignant lesion. Traditional staging of HNSCC using the tumour{\textendash}node{\textendash}metastasis system has been supplemented by the 2017 AJCC/UICC staging system, which incorporates additional information relevant to HPV-positive disease. Treatment is generally multimodal, consisting of surgery followed by chemoradiotherapy (CRT) for oral cavity cancers and primary CRT for pharynx and larynx cancers. The EGFR monoclonal antibody cetuximab is generally used in combination with radiation in HPV-negative HNSCC where comorbidities prevent the use of cytotoxic chemotherapy. The FDA approved the immune checkpoint inhibitors pembrolizumab and nivolumab for treatment of recurrent or metastatic HNSCC and pembrolizumab as primary treatment for unresectable disease. Elucidation of the molecular genetic landscape of HNSCC over the past decade has revealed new opportunities for therapeutic intervention. Ongoing efforts aim to integrate our understanding of HNSCC biology and immunobiology to identify predictive biomarkers that will enable delivery of the most effective, least-toxic therapies.},
  copyright = {2020 Springer Nature Limited},
  langid = {english},
  keywords = {Cancer genetics,Head and neck cancer},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Johnson et al_2020_Head and neck squamous cell carcinoma.pdf;C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Johnson et al_2020_Head and neck squamous cell carcinoma2.pdf;C\:\\Users\\roman\\Zotero\\storage\\APSHYD26\\s41572-020-00224-3.html}
}

@article{jones_level_1994,
  title = {The {{Level}} of {{Cervical Lymph Node Metastases}}: {{Their Prognostic Relevance}} and {{Relationship}} with {{Head}} and {{Neck Squamous Carcinoma Primary Sites}}},
  shorttitle = {The {{Level}} of {{Cervical Lymph Node Metastases}}},
  author = {Jones, A. S. and Roland, N. J. and Field, J. K. and Phillips, D. E.},
  year = {1994},
  journal = {Clinical Otolaryngology \& Allied Sciences},
  volume = {19},
  number = {1},
  pages = {63--69},
  issn = {1365-2273},
  doi = {10.1111/j.1365-2273.1994.tb01150.x},
  urldate = {2021-02-10},
  abstract = {It would seem logical that patients with nodal metastases low in the neck would fare less well than patients with disease high in the neck. The penultimate UICC classification suggested that neck node level was important although there was no mention of this in the most recent classification. In addition, patients with carcinomas at the various sites would be expected to have different patterns of nodal involvement. Of 3419 patients with head and neck squamous carcinoma on the Liverpool University Head and Neck Unit database, 947 had neck node metastases. The neck node levels were coded as (I)sub-mandibular, (II) above the thyroid notch, (III) below the thyroid notch and (IV) supra-clavicular/posterior triangle nodes. Levels II and III contained the deep jugular chain. The relationship between node level and site and sub-site and survival were analysed with particular emphasis on multivariate methods. The 5-year survival for the whole group was 51\% and survival fell with decreasing node level (I-IV) being 37\% for sub-mandibular nodes, 32\% for deep cervical nodes and 25\% for lower deep cervical nodes. The 18-month survival for supra-clavicular and posterior triangle nodes was 21\%. The difference in survival was significant (x23= 24.42, P {$<$} 0.001). Multivariate analysis confirmed that as the level of the nodes fell from the sub-mandibular refion to the supra-clavicular region the prognosis worsened (estimate = -0.3378, P = 0.0003). Level II (upper deep cervical) nodes were the most commonly involved with regards to all primary sites and formed 69\% of all neck node metastases. Over three quarters of laryngeal oropharyngeal and hypopharyngeal metastases went ot this level whereas only 47\% of oral cancers did. Most of the remainder of these latter lesions metastasized to level I (42\%). These findings were confirmed by multiple logistic regression. When studying survival for lymph node level with regard to site all sites had a reducing prognosis with decrasing node level except for larynx. Multiple linear regression showed an association between decreasing node level and increasing N-stage (P = 0.001) with increasing T-stage (P = 0.0014) and as the site moved from the mouth to the larynx (P = 0.0047). The present data support the view that neck node level is important as regards prognosis for most sites in the head and neck. The data confirm the clinical view that deep cervical nodes are most frequently affected by head and neck cancer with level IV nodes being unusual and clinically tending to herald a non head and neck tumour and that level III nodes are relatively uncommon. This is surprising as one would expect at least a proportion of laryngeal carcinomas and quite a high proportion of lhypopharyngeal carcinomas to metastasize to this region.},
  langid = {english},
  keywords = {head and neck squamous carcinoma,multivariate analysis,neck node level,neck node metastases},
  file = {C:\Users\roman\Zotero\storage\N3RJ6MWD\j.1365-2273.1994.tb01150.html}
}

@article{jung_development_2017,
  title = {Development of a {{Novel Markov Chain Model}} for the {{Prediction}} of {{Head}} and {{Neck Squamous Cell Carcinoma Dissemination}}},
  author = {Jung, Hyunggu and Law, Anthony and Grunblatt, Eli and Wang, Lucy L. and Kusano, Aaron and Mejino, Jose L. V. and Whipple, Mark E.},
  year = {2017},
  month = feb,
  journal = {AMIA Annual Symposium Proceedings},
  volume = {2016},
  pages = {1832--1839},
  issn = {1942-597X},
  urldate = {2023-03-27},
  abstract = {Prediction of microscopic tumor spread to regional lymph nodes can assist in radiation planning for cancer treatment. However, it is still challenging to predict tumor spread. In this paper, we present a unique approach to modeling how tumor cells disseminate to form regional metastases. This involves leveraging well established knowledge resources and commonly held notions of how cancer spreads. Using patient data, we utilized our approach to create a model of metastasis for the subset of head and neck squamous cell carcinoma that arises in the mucosa of the lateral tongue. The model was created using a training set extracted from the clinical records of 50 patients with tumors of this type who presented to the University of Washington head and tumor board over a three and half year period. The test sets consist of four case series drawn from the literature.},
  pmcid = {PMC5333213},
  pmid = {28269942},
  file = {C:\Users\roman\OneDrive\Documents\Library\Jung et al_2017_Development of a Novel Markov Chain Model for the Prediction of Head and Neck.pdf}
}

@article{karel_limitations_1997,
  title = {Limitations of Sensitivity, Specificity, Likelihood Ratio, and Bayes' Theorem in Assessing Diagnostic Probabilities: A Clinical Example},
  author = {Karel, G M M and {Others}},
  year = {1997},
  journal = {Epidemiology},
  volume = {8},
  pages = {12--17},
  doi = {10.1097/00001648-199701000-00002}
}

@article{kelly_upfront_2018,
  title = {Upfront Surgery versus Definitive Chemoradiotherapy in Patients with Human {{Papillomavirus-associated}} Oropharyngeal Squamous Cell Cancer},
  author = {Kelly, Jacqueline R. and Park, Henry S. and An, Yi and Yarbrough, Wendell G. and Contessa, Joseph N. and Decker, Roy and Mehra, Saral and Judson, Benjamin L. and Burtness, Barbara and Husain, Zain},
  year = {2018},
  month = apr,
  journal = {Oral Oncology},
  volume = {79},
  pages = {64--70},
  issn = {13688375},
  doi = {10.1016/j.oraloncology.2018.02.017},
  urldate = {2022-09-24},
  abstract = {Objectives: Currently, human papillomavirus-associated oropharyngeal squamous cell carcinoma (HPV-A OPC) is managed with either primary surgery or definitive chemoradiotherapy (CRT), despite the lack of supporting randomized prospective data. We therefore assessed the outcomes of each treatment strategy using the National Cancer Database (NCDB). Methods: The NCDB was used to identify patients diagnosed with cT1 N2a-2b or cT2 N1-2b HPV-A OPC from 2010 to 2013 who underwent treatment with primary surgery or CRT. Demographic and clinicopathologic predictors of treatment were analyzed by the chi-square test and logistic regression. Overall survival (OS) was evaluated using multivariable Cox proportional hazard regression, Kaplan-Meier, log-rank test, and propensity score-matched analysis. Results: We identified 3063 patients; 1576 (51.5\%) received CRT and 1487 (48.5\%) underwent primary surgery. Median follow up was 32 months. 972 (65.4\%) surgical patients received adjuvant CRT. On multivariable Cox regression, 3-year OS was comparable between surgery and CRT (hazard ratio [HR] 1.08, 95\% confidence interval [CI] 0.83{\textendash}1.41, P = 0.58). Inferior OS was significantly associated with increasing clinical T and N stage, older age, and non-private insurance. Propensity score-matching yielded a 2526 patient cohort and redemonstrated similar OS (HR, 1.09; 95\% CI 0.81{\textendash}1.47; P = 0.55). Comparable outcomes persisted in a subset analysis of patients with margin-negative resection, with 3-year OS 90.8\% in CRT patients vs. 93.6\% in surgery patients (log-rank P = 0.27). Conclusions: Upfront surgery and CRT yielded comparable 3-year OS outcomes in this cohort. In this national sample, 65.4\% of surgical patients received trimodal therapy with adjuvant CRT, highlighting the need for improved patient selection for primary surgery.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Kelly et al_2018_Upfront surgery versus definitive chemoradiotherapy in patients with human.pdf}
}

@article{kjems_elective_2016,
  title = {Elective {{Nodal Irradiation}} and {{Patterns}} of {{Failure}} in {{Head}} and {{Neck Cancer After Primary Radiation Therapy}}},
  author = {Kjems, Julie and Gothelf, Anita B. and H{\aa}kansson, Katrin and Specht, Lena and Kristensen, Claus A. and Friborg, Jeppe},
  year = {2016},
  month = mar,
  journal = {International Journal of Radiation Oncology*Biology*Physics},
  volume = {94},
  number = {4},
  pages = {775--782},
  issn = {0360-3016},
  doi = {10.1016/j.ijrobp.2015.12.380},
  urldate = {2023-07-03},
  abstract = {Purpose The delineation of elective clinical target volumes in head and neck cancer (HNC) is important; however, the extent of lymph node levels necessary to include is debated. A comprehensive analysis of recurrence patterns in a large cohort of patients with HNC was performed, with an emphasis on recurrence in the retropharyngeal region and level IB. Methods and Materials From 2005 to 2012, 942 patients with oropharyngeal, hypopharyngeal, laryngeal or oral cavity carcinomas were curatively treated with primary radiation therapy. The median follow-up period was 34~months, and 77\% of the patients underwent intensity modulated radiation therapy. The retropharyngeal region was only routinely included in cases of involvement of the posterior pharynx wall and level IB only in cases of involvement of the oral cavity. In patients with regional recurrence, the anatomic site of the recurrence was assessed from the surgical descriptions or computed tomography scans and compared with the original radiation treatment plan (available from 2007 onward). The p16 status was available for 282 oropharynx carcinoma cases, with 65\% p16-positive. Results Of the 942 patients, 376 (40\%) developed recurrences: 228 (24.2\%) local, 123 (13.1\%) regional, and 109 (11.6\%) distant. In 700 patients with available treatment plans, retropharyngeal and level IB recurrence was observed in 2 and 7 patients, respectively. Eight patients (1.1\%) had recurrence in a lymph node level not included in their primary treatment plan. For oropharynx carcinoma, the locoregional control rate (90\% vs 70\%) but not distant control rate (92\% vs 87\%), was significantly better in the p16-positive than in the p16-negative patients. Although fewer recurrences developed in the p16-positive group, patients with recurrence of p16-positive tumors were more likely to develop recurrence in distant sites. Conclusions Retropharyngeal or level IB recurrence after primary HNC radiation therapy is rare. Thus, inclusion of these regions in the elective treatment volumes should be limited to patients with involvement of the posterior pharyngeal wall or oral cavity.},
  langid = {english},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Kjems et al_2016_Elective Nodal Irradiation and Patterns of Failure in Head and Neck Cancer.pdf;C\:\\Users\\roman\\Zotero\\storage\\BGJYTWIG\\S0360301615272641.html}
}

@incollection{krause_fdg_2013,
  title = {{{FDG PET}} and {{PET}}/{{CT}}},
  booktitle = {Molecular {{Imaging}} in {{Oncology}}},
  author = {Krause, Berud J. and Schwarzenb{\"o}ck, Sarah and Souvatzoglou, Michael},
  editor = {Schober, Otmar and Riemann, Burkhard},
  year = {2013},
  series = {Recent {{Results}} in {{Cancer Research}}},
  pages = {351--369},
  publisher = {{Springer}},
  address = {{Berlin, Heidelberg}},
  doi = {10.1007/978-3-642-10853-2_12},
  urldate = {2022-10-18},
  abstract = {Molecular imaging with positron emission tomography (PET) using tumour-seeking radiopharmaceuticals has gained wide acceptance in oncology with many clinical applications. The hybrid imaging modality PET/CT allows assessing molecular as well as morphologic information at the same time. Therefore, PET/CT represents an efficient tool for whole body staging and re-staging within one imaging modality. In oncology the glucose analogue 18F-fluorodeoxyglucose (FDG) is the most widely used PET and PET/CT radiopharmaceutical in clinical routine. FDG PET and PET/CT have been used for staging and re-staging tumour patients in numerous studies. This chapter will discuss the use and the main indications of FDG PET and PET/CT in oncology with special emphasis on lung cancer, oesophageal cancer, colorectal cancer, head and neck cancer, lymphoma and breast cancer (among other tumour entities). A review of the current literature will be given with respect to primary diagnosis, staging and diagnosis of recurrent disease (local, lymph node and distant metastases). Besides its integral role in diagnosis, staging and re-staging of disease in oncology, there is increasing evidence that FDG PET and PET/CT can significantly contribute to therapy response assessment possibly influencing therapeutic management and treatment planning, to therapy tumour control and prediction of prognosis in oncologic patients, which will also be discussed in this chapter.},
  isbn = {978-3-642-10853-2},
  langid = {english},
  keywords = {Invasive Lobular Carcinoma,Oesophageal Cancer,Positron Emission Tomography,Standardize Uptake Value,Testicular Germ Cell Tumor},
  file = {C:\Users\roman\OneDrive\Documents\Library\Krause et al_2013_FDG PET and PET-CT.pdf}
}

@article{kyzas_18f-fluorodeoxyglucose_2008,
  title = {{{18F-fluorodeoxyglucose}} Positron Emission Tomography to Evaluate Cervical Node Metastases in Patients with Head and Neck Squamous Cell Carcinoma: A Meta-Analysis},
  author = {Kyzas, P A and {Others}},
  year = {2008},
  journal = {J. Natl Cancer Inst.},
  volume = {100},
  pages = {712--720},
  doi = {10.1093/jnci/djn125},
  file = {C:\Users\roman\OneDrive\Documents\Library\Kyzas_Others_2008_18F-fluorodeoxyglucose positron emission tomography to evaluate cervical node.pdf}
}

@book{lacave_knowledge_2003,
  title = {Knowledge {{Acquisition}} in {{PROSTANET}}{\textemdash}{{A Bayesian Network}} for {{Diagnosing Prostate Cancer}}},
  author = {Lacave, C and D{\'i}ez, F J},
  year = {2003},
  publisher = {{Springer}}
}

@book{lam_bayesian_nodate,
  title = {Bayesian {{Optimization}} with a {{Finite Budget}}: {{An Approximate Dynamic Programming Approach}}},
  shorttitle = {Bayesian {{Optimization}} with a {{Finite Budget}}},
  author = {Lam, Remi R. and Willcox, Karen E. and Wolpert, David H.},
  abstract = {Abstract We consider the problem of optimizing an expensive objective function when a finite budget of total evaluations is prescribed. In that context, the optimal solution strategy for Bayesian optimization can be formulated as a dynamic programming instance. This results in a complex problem with uncountable, dimension-increasing state space and an uncountable control space. We show how to approximate the solution of this dynamic programming problem using rollout, and propose rollout heuristics specifically designed for the Bayesian optimization setting. We present numerical experiments showing that the resulting algorithm for optimization with a finite budget outperforms several popular Bayesian optimization algorithms.},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Lam et al_Bayesian Optimization with a Finite Budget.pdf;C\:\\Users\\roman\\Zotero\\storage\\55BHE4MA\\summary.html}
}

@misc{lavrov_phylogenetic_2023,
  type = {Lecture Script},
  title = {Phylogenetic Trees},
  author = {Lavrov, Dennis},
  year = {2023},
  address = {{Iowa State University}},
  urldate = {2023-02-26},
  langid = {english},
  file = {C\:\\Users\\roman\\OneDrive\\Foam\\references\\@lavrov_phylogenetic_2023.md;C\:\\Users\\roman\\Zotero\\storage\\MU73SH3U\\01-phylogenetic_trees.pdf}
}

@inproceedings{law_infra-red_2019,
  title = {An {{Infra-red Reflecting Optical Coating}} for {{Solar Cover Glass}}},
  booktitle = {2019 {{IEEE}} 46th {{Photovoltaic Specialists Conference}} ({{PVSC}})},
  author = {Law, Adam M and Kaminski, Piotr M and Isherwood, Patrick J M and Michael Walls, John},
  year = {2019},
  month = jun,
  pages = {1913--1918},
  publisher = {{IEEE}},
  address = {{Chicago, IL, USA}},
  doi = {10.1109/PVSC40753.2019.8981269},
  urldate = {2022-06-16},
  abstract = {A major problem with silicon solar cells is that they lose efficiency with increased operating temperature, at a rate of about 0.5\% per 1{$\smwhtcircle$}C increase. This causes a significant reduction in power output, particularly in hot climates. A solution in the form of an optical coating is presented, which reflects infrared (IR) radiation to limit the module temperature increase. The optical coating is also anti-reflecting (AR) in the visible wavelength range, increasing the amount of light reaching the cell absorber. Modelling results show that the weighted average reflection (WAR) is reduced to 1.22\% in the wavelength range associated with the band gap of silicon. The optical coating then reflects up to 70\% of the infra-red. Although the model presented is based on silicon, the coating design can be modified to work with other photovoltaic technologies. The coating design uses only 4 layers and can be deposited using conventional high throughput magnetron sputtering systems already familiar to glass manufacturers. Preliminary work on optimising the coating deposition parameters is also presented here alongside modelling results. Deployment of the infra-red reflecting optical coating on solar cover glass represents a potential breakthrough in solar technology and will result in a significant increase in the power output of photovoltaic modules.},
  isbn = {978-1-72810-494-2},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Law et al_2019_An Infra-red Reflecting Optical Coating for Solar Cover Glass.pdf}
}

@article{lengele_anatomical_2007,
  title = {Anatomical Bases for the Radiological Delineation of Lymph Node Areas. {{Major}} Collecting Trunks, Head and Neck},
  author = {Lengel{\'e}, Beno{\^i}t and Hamoir, Marc and Scalliet, Pierre and Gr{\'e}goire, Vincent},
  year = {2007},
  month = oct,
  journal = {Radiotherapy and Oncology},
  volume = {85},
  number = {1},
  pages = {146--155},
  issn = {01678140},
  doi = {10.1016/j.radonc.2007.02.009},
  urldate = {2022-02-23},
  abstract = {Cancer spreads locally through direct infiltration into soft tissues or at distance by invading vascular structures, then migrating through the lymphatic or blood flow. Although cancer cells carried in the blood can end in virtually any corner of the body, lymphatic migration is usually stepwise, through successive nodal stops, which can temporarily delay further progression. In radiotherapy, irradiation of lymphatic paths relevant to the localisation of the primary has been common practice for decades. Similarly, excision of cancer is often completed by lymphatic dissection.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Lengelé et al_2007_Anatomical bases for the radiological delineation of lymph node areas.pdf}
}

@article{lim_distributions_2006,
  title = {Distributions of {{Cervical Lymph Node Metastases}} in {{Oropharyngeal Carcinoma}}: {{Therapeutic Implications}} for the {{N0 Neck}}:},
  shorttitle = {Distributions of {{Cervical Lymph Node Metastases}} in {{Oropharyngeal Carcinoma}}},
  author = {Lim, Young Chang and Koo, Bon Seok and Lee, Jin Seok and Lim, Jae-Yol and Choi, Eun Chang},
  year = {2006},
  month = jul,
  journal = {The Laryngoscope},
  volume = {116},
  number = {7},
  pages = {1148--1152},
  issn = {0023-852X},
  doi = {10.1097/01.mlg.0000217543.40027.1d},
  urldate = {2022-09-24},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Lim et al_2006_Distributions of Cervical Lymph Node Metastases in Oropharyngeal Carcinoma.pdf}
}

@article{lindberg_distribution_1972,
  title = {Distribution of Cervical Lymph Node Metastases from Squamous Cell Carcinoma of the Upper Respiratory and Digestive Tracts},
  author = {Lindberg, Robert},
  year = {1972},
  month = jun,
  journal = {Cancer},
  volume = {29},
  number = {6},
  pages = {1446--1449},
  publisher = {{John Wiley \& Sons, Ltd}},
  issn = {0008-543X},
  doi = {10.1002/1097-0142(197206)29:6<1446::AID-CNCR2820290604>3.0.CO;2-C},
  urldate = {2021-02-08},
  abstract = {Abstract The records of 2,044 patients with previously untreated squamous cell carcinomas of the head and neck were reviewed in order to define the incidence and topographical distribution of lymph node metastasis on admission. The common regions of metastasis are presented for each of the seven individual head and neck sites selected for study. Knowledge of the preferred areas of spread and those that are almost never involved allows the design of more adequate plans to manage the individual lesions.},
  keywords = {patterns},
  file = {C:\Users\roman\OneDrive\Documents\Library\Lindberg_1972_Distribution of cervical lymph node metastases from squamous cell carcinoma of.pdf}
}

@article{liu_magnetic_2006,
  title = {Magnetic Resonance Imaging of Retropharyngeal Lymph Node Metastasis in Nasopharyngeal Carcinoma: {{Patterns}} of Spread},
  shorttitle = {Magnetic Resonance Imaging of Retropharyngeal Lymph Node Metastasis in Nasopharyngeal Carcinoma},
  author = {Liu, Li-Zhi and Zhang, Guo-Yi and Xie, Chuang-Miao and Liu, Xue-Wen and Cui, Chun-Yan and Li, Li},
  year = {2006},
  month = nov,
  journal = {International Journal of Radiation Oncology*Biology*Physics},
  volume = {66},
  number = {3},
  pages = {721--730},
  issn = {03603016},
  doi = {10.1016/j.ijrobp.2006.05.054},
  urldate = {2021-02-10},
  abstract = {Purpose: To investigate the incidence, distribution, and spread pattern of retropharyngeal lymph node (RLN) involvement in patients with nasopharyngeal carcinoma (NPC) by using magnetic resonance imaging (MRI). Methods and Materials: The MR images of 275 patients with newly diagnosed NPC were reviewed retrospectively. Nodes were classified as metastatic based on size criteria, the presence of nodal necrosis, and extracapsular spread. Results: Retropharyngeal lymph node involvement was detected in 175 (63.6\%) patients. Metastatic RLNs were seen at the following levels: occipital bone, 24 (9.6\%) nodes; C1, 157 (62.5\%) nodes; C1/2, 40 (15.9\%) nodes; C2, 27 (10.8\%) nodes; C2/3, 1 (0.4\%) node; and C3, 2 (0.8\%) nodes. The incidence of RLN involvement was equal to the incidence of cervical lymph node involvement (81.4\% vs. 81.4\%) in 215 patients with nodal metastases. A significantly higher incidence of metastatic RLNs was observed in the presence of oropharynx, prestyloid parapharyngeal space, post-styloid parapharyngeal space, longus colli muscle, medial pterygoid muscle, levator muscle of velum palatini, tensor muscle of velum palatini, Level II node, Level III node, and Level V node involvement. A significantly lower incidence of metastatic RLNs was found in T1, N0, and Stage I disease. Conversely, no significant difference in the incidence of metastatic RLNs was observed between T1, 2, and, 3; N2 and N3; or Stage II, III, and IV disease. Conclusions: There is an orderly decrease in the incidence of metastatic lateral RLNs from the C1 to C3 level. Metastatic RLNs associate well with involvement of certain structures in early stage primary tumors and lymph node metastases of the upper jugular chain (Level II, Level III nodes) and the posterior triangle (Level V nodes). Both RLNs and cervical Level II nodes appear to be the first-echelon nodes in NPC. {\textcopyright} 2006 Elsevier Inc.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Liu et al_2006_Magnetic resonance imaging of retropharyngeal lymph node metastasis in.pdf}
}

@inproceedings{lokhava_fast_2019,
  title = {Fast and Secure Global Payments with {{Stellar}}},
  booktitle = {Proceedings of the 27th {{ACM Symposium}} on {{Operating Systems Principles}}},
  author = {Lokhava, Marta and Losa, Giuliano and Mazi{\`e}res, David and Hoare, Graydon and Barry, Nicolas and Gafni, Eli and Jove, Jonathan and Malinowsky, Rafa{\l} and McCaleb, Jed},
  year = {2019},
  month = oct,
  pages = {80--96},
  publisher = {{ACM}},
  address = {{Huntsville Ontario Canada}},
  doi = {10.1145/3341301.3359636},
  urldate = {2021-11-16},
  abstract = {International payments are slow and expensive, in part because of multi-hop payment routing through heterogeneous banking systems. Stellar is a new global payment network that can directly transfer digital money anywhere in the world in seconds. The key innovation is a secure transaction mechanism across untrusted intermediaries, using a new Byzantine agreement protocol called SCP. With SCP, each institution specifies other institutions with which to remain in agreement; through the global interconnectedness of the financial system, the whole network then agrees on atomic transactions spanning arbitrary institutions, with no solvency or exchange-rate risk from intermediary asset issuers or market makers. We present SCP's model, protocol, and formal verification; describe the Stellar payment network; and finally evaluate Stellar empirically through benchmarks and our experience with several years of production use.},
  isbn = {978-1-4503-6873-5},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Lokhava et al_2019_Fast and secure global payments with Stellar.pdf}
}

@article{lothian_safe_2009,
  title = {Safe, {{Healthy Birth}}: {{What Every Pregnant Woman Needs}} to {{Know}}},
  shorttitle = {Safe, {{Healthy Birth}}},
  author = {Lothian, Judith A.},
  year = {2009},
  journal = {The Journal of Perinatal Education},
  volume = {18},
  number = {3},
  pages = {48--54},
  issn = {1058-1243},
  doi = {10.1624/105812409X461225},
  urldate = {2023-01-06},
  abstract = {In spite of technology and medical science's ability to manage complex health problems, the current maternity care environment has increased risks for healthy women and their babies. It comes as a surprise to most women that standard maternity care does not reflect best scientific evidence. In this column, evidence-based maternity care practices are discussed with an emphasis on the practices that increase safety for mother and baby, and what pregnant women need to know in order to have safe, healthy births is described.},
  pmcid = {PMC2730905},
  pmid = {19750214},
  file = {C:\Users\roman\OneDrive\Documents\Library\Lothian_2009_Safe, Healthy Birth.pdf}
}

@article{lu_adaptive_2008,
  title = {Adaptive Fractionation Therapy: {{I}}. {{Basic}} Concept and Strategy},
  shorttitle = {Adaptive Fractionation Therapy},
  author = {Lu, Weiguo and Chen, Mingli and Chen, Quan and Ruchala, Kenneth and Olivera, Gustavo},
  year = {2008},
  month = sep,
  journal = {Physics in Medicine and Biology},
  volume = {53},
  number = {19},
  pages = {5495--5511},
  publisher = {{IOP Publishing}},
  issn = {0031-9155},
  doi = {10.1088/0031-9155/53/19/015},
  urldate = {2022-07-26},
  abstract = {Radiotherapy is fractionized to increase the therapeutic ratio. Fractionation in conventional treatment is determined as part of the prescription, and a fixed fraction size is used for the whole course of treatment. Due to patients' day-to-day variations on the relative distance between the tumor and the organs at risk (OAR), a better therapeutic ratio may be attained by using an adaptive fraction size. Intuitively, we want to use a larger fraction size when OAR and the tumor are far apart and a smaller fraction size when OAR and the tumor are close to each other. The concept and strategies of adaptive fractionation therapy (AFT) are introduced in this paper. AFT is an on-line adaptive technique that utilizes the variations of internal structures to get optimal OAR sparing. Changes of internal structures are classified as different configurations according to their feasibility to the radiation delivery. A priori knowledge is used to describe the probability distribution of these configurations. On-line processes include identifying the configuration via daily image guidance and optimizing the current fraction size. The optimization is modeled as a dynamic linear programming problem so that at the end of the treatment course, the tumor receives the same planned dose while OAR receives less dose than the regular fractionation delivery. Extensive simulations, which include thousands of treatment courses with each course consisting of 40 fractions, are used to test the efficiency and robustness of the presented technique. The gains of OAR sparing depend on the variations on configurations and the bounds of the fraction size. The larger the variations and the looser the bounds are, the larger the gains will be. Compared to the conventional fractionation technique with 2 Gy/fraction in 40 fractions, for a 20\% variation on tumor{\textendash}OAR configurations and [1 Gy, 3 Gy] fraction size bounds, the cumulative OAR dose with adaptive fractionation is 3{\textendash}8 Gy, or 7{\textendash}20\% less than that of the regular fractionation, while maintaining the same cumulative tumor dose as prescribed.},
  langid = {english}
}

@article{ludwig_dataset_2022,
  title = {A Dataset on Patient-Individual Lymph Node Involvement in Oropharyngeal Squamous Cell Carcinoma},
  author = {Ludwig, Roman and Hoffmann, Jean-Marc and Pouymayou, Bertrand and Morand, Gr{\'e}goire and D{\"a}ppen, Martina Broglie and Guckenberger, Matthias and Gr{\'e}goire, Vincent and Balermpas, Panagiotis and Unkelbach, Jan},
  year = {2022},
  month = aug,
  journal = {Data in Brief},
  volume = {43},
  pages = {108345},
  issn = {2352-3409},
  doi = {10.1016/j.dib.2022.108345},
  urldate = {2022-10-25},
  abstract = {Dataset We provide a dataset on lymph node level (LNL) involvement in 287 patients with newly diagnosed oropharyngeal squamous cell carcinoma (OPSCC). For each patient, ipsilateral and contralateral LNL involvement for levels I to VII is reported together with clinicopathological factors including TNM-stage, primary tumor subsite, tumor lateralization, HPV status, sex, age, smoking status, and primary treatment. LNL involvement was assessed individually based on available diagnostic modalities (PET, MRI, CT, fine needle aspiration) by reviewing pathology and radiology reports together with the radiological images. The data is shared as a CSV-table with rows of patients and columns of patient/tumor-specific information and the involvement of individual LNL based on the respective diagnostic modalities. Reuse potential Patterns of lymphatic progression have never been reported on a patient-individual basis in as much detail as provided in this dataset. The data can be used to build quantitative models for lymphatic tumor progression to estimate the probability of occult metastases in LNLs. This may in turn allow for further personalization of the elective clinical target volume definition in radiotherapy and the extent of neck dissection for surgically treated patients. The data can be pooled with other data to build large multi-institutional datasets on lymphatic metastatic progression in the future. Co-submission This paper supports the original scientific article by Roman Ludwig, Jean-Marc Hoffmann, Bertrand Pouymayou, Gr{\'e}goire Morand, Martina Broglie D{\"a}ppen, Matthias Guckenberger, Vincent Gr{\'e}goire, Panagiotis Balermpas, Jan Unkelbach, ``Detailed patient-individual reporting of lymph node involvement in oropharyngeal squamous cell carcinoma with an online interface'', Radiotherapy \& Oncology [1]},
  langid = {english},
  keywords = {head \& neck squamous cell carcinoma,Head \& neck squamous cell carcinoma,interface,Interface,lymphatic involvement,Lymphatic involvement,oropharynx,Oropharynx,patterns of progression,Patterns of progression,placeholder},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Ludwig et al_2022_A dataset on patient-individual lymph node involvement in oropharyngeal.pdf;C\:\\Users\\roman\\Zotero\\storage\\CQXT9BSN\\S2352340922005479.html}
}

@article{ludwig_detailed_2022,
  title = {Detailed Patient-Individual Reporting of Lymph Node Involvement in Oropharyngeal Squamous Cell Carcinoma with an Online Interface},
  author = {Ludwig, Roman and Hoffmann, Jean-Marc and Pouymayou, Bertrand and D{\"a}ppen, Martina Broglie and Morand, Gr{\'e}goire and Guckenberger, Matthias and Gr{\'e}goire, Vincent and Balermpas, Panagiotis and Unkelbach, Jan},
  year = {2022},
  month = apr,
  journal = {Radiotherapy and Oncology},
  volume = {169},
  pages = {1--7},
  issn = {0167-8140},
  doi = {10.1016/j.radonc.2022.01.035},
  urldate = {2022-10-25},
  abstract = {Purpose/Objective Whereas the prevalence of lymph node level (LNL) involvement in head \& neck squamous cell carcinomas (HNSCC) has been reported, the details of lymphatic progression patterns are insufficiently quantified. In this study, we investigate how the risk of metastases in each LNL depends on the involvement of upstream LNLs, T-category, HPV status and other risk factors. Materials/Methods We retrospectively analyzed patients with newly diagnosed oropharyngeal squamous cell carcinoma (OPSCC) treated at a single institution, resulting in a dataset of 287 patients. For all patients, involvement of LNLs I-VII was recorded individually based on available diagnostic modalities (PET, MRI, CT, FNA) together with clinicopathological factors. To analyze the dataset, a web-based graphical user interface (GUI) was developed, which allows querying the number of patients with a certain combination of co-involved LNLs and tumor characteristics. Results The full dataset and GUI is part of the publication. Selected findings are: Ipsilateral level IV was involved in 27\% of patients with level II and III involvement, but only in 2\% of patients with level II but not III involvement. Prevalence of involvement of ipsilateral levels II, III, IV, V was 79\%, 34\%, 7\%, 3\% for early T-category patients (T1/T2) and 85\%, 50\%, 17\%, 9\% for late T-category (T3/T4), quantifying increasing involvement with T-category. Contralateral levels II, III, IV were involved in 41\%, 19\%, 4\% and 12\%, 3\%, 2\% for tumors with and without midline extension, respectively. T-stage dependence of LNL involvement was more pronounced in HPV negative than positive tumors, but overall involvement was similar. Ipsilateral level VII was involved in 14\% and 6\% of patients with primary tumors in the tonsil and the base of tongue, respectively. Conclusions Detailed quantification of LNL involvement in HNSCC depending on involvement of upstream LNLs and clinicopathological factors may allow for further personalization of CTV-N definition in the future.},
  langid = {english},
  keywords = {Head \& neck squamous cell carcinoma,Interface,Lymphatic involvement,Oropharynx,Patterns of progression,placeholder},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Ludwig et al_2022_Detailed patient-individual reporting of lymph node involvement in.pdf;C\:\\Users\\roman\\Zotero\\storage\\YT83U74R\\fulltext.html;C\:\\Users\\roman\\Zotero\\storage\\ZSYGGWZ6\\2021.12.01.html}
}

@inproceedings{ludwig_dynamic_2021,
  title = {A Dynamic Model for Lymphatic Progression of Cancer through the Head \& Neck},
  booktitle = {{{ESTRO}}},
  author = {Ludwig, Roman and Pouymayou, Bertrand and Balermpas, Panagiotis and Unkelbach, Jan},
  year = {2021},
  pages = {75},
  address = {{Madrid}},
  urldate = {2022-10-25},
  abstract = {Purpose/Objective: Currently, elective CTV definition in head \& neck cancer is mostly based on the empiric prevalence of lymph node involvement for a given primary tumor location. However, an individual patient's risk of harboring microscopic metastases in each lymph node level (LNL) varies depending on their T-stage and findings of macroscopic metastases in LNLs through imaging. We propose a probabilistic model for lymphatic metastatic spread that can quantify this risk of microscopic involvement based on the individual patient's state of cancer progression, which may allow for personalized CTV-N definition. Material/Methods: A patient's state of disease is modelled via one hidden binary random variable for each LNL, which indicates if the LNL harbors tumor including occult metastases. This hidden state of a LNL is connected via sensitivity and specificity to an observed binary random variable that indicates if metastases are seen on imaging. Over one-time step, tumor cells may spread from the primary tumor to an LNL, or between LNLs, with some probability rate. Formally, this is described by a hidden Markov model (HMM). The directed arcs of the HMM's graph reflect the direction of lymph flow and spread probability rates are learned from a dataset of patients in whom involvement of each LNL was reported (Figure 1). T-stage can be incorporated into the model by assuming that on average late T-stage tumors had more time to progress than early T-stage tumors. We demonstrate the HMM model for ipsilateral spread of oropharyngeal head \& neck squamous cell carcinoma, trained via MCMC sampling using a dataset reconstructed from [2], and under the assumption that the portion of N0 patients is 30\% for early T-stage patients and 20\% for late T-stage. Results: Figure 2 shows the risk of occult metastases in LNL III and IV depending on T-stage and whether the upstream LNLs II and III harbor macroscopic metastases. For early T-stage, the expected risk for microscopic involvement of LNL III rises from 4.8 {$\pm$} 1.0 \% for N0 patients to 10.2 {$\pm$} 1.8 \% when macroscopic metastases in LNL II are observed. For late T-stage and macroscopic metastases in LNL II, the risk increases further to 13.7 {$\pm$}2.8 \% (figure 2a). Analogous findings are observed for level IV (figure 2b). Conclusions: HMMs provide a statistical framework to model the spread of lymphatic metastases. It allows us to estimate the risk of microscopic involvement of LNLs depending on T-stage and location of macroscopic metastases. But larger datasets of detailed involvement patterns, rather than reports of only prevalence, are needed before the model may inform guidelines for CTV-N definition.}
}

@inproceedings{ludwig_hidden_2020,
  title = {A {{Hidden Markov}} Model for Lymphatic Tumour Progression},
  booktitle = {{{SASRO}}},
  author = {Ludwig, Roman and Pouymayou, Bertrand and Balermpas, Panagiotis and Unkelbach, Jan},
  year = {2020},
  month = sep
}

@article{ludwig_hidden_2021,
  title = {A Hidden {{Markov}} Model for Lymphatic Tumor Progression in the Head and Neck},
  author = {Ludwig, Roman and Pouymayou, Bertrand and Balermpas, Panagiotis and Unkelbach, Jan},
  year = {2021},
  month = dec,
  journal = {Scientific Reports},
  volume = {11},
  number = {1},
  pages = {12261},
  issn = {2045-2322},
  doi = {10.1038/s41598-021-91544-1},
  urldate = {2021-09-27},
  abstract = {Currently, elective clinical target volume (CTV-N) definition for head and neck squamous cell carcinoma (HNSCC) is mostly based on the prevalence of nodal involvement for a given tumor location. In this work, we propose a probabilistic model for lymphatic metastatic spread that can quantify the risk of microscopic involvement in lymph node levels (LNL) given the location of macroscopic metastases and T-category. This may allow for further personalized CTV-N definition based on an individual patient's state of disease. We model the patient's state of metastatic lymphatic progression as a collection of hidden binary random variables that indicate the involvement of LNLs. In addition, each LNL is associated with observed binary random variables that indicate whether macroscopic metastases are detected. A hidden Markov model (HMM) is used to compute the probabilities of transitions between states over time. The underlying graph of the HMM represents the anatomy of the lymphatic drainage system. Learning of the transition probabilities is done via Markov chain Monte Carlo sampling and is based on a dataset of HNSCC patients in whom involvement of individual LNLs was reported. The model is demonstrated for ipsilateral metastatic spread in oropharyngeal HNSCC patients. We demonstrate the model's capability to quantify the risk of microscopic involvement in levels III and IV, depending on whether macroscopic metastases are observed in the upstream levels II and III, and depending on T-category. In conclusion, the statistical model of lymphatic progression may inform future, more personalized, guidelines on which LNL to include in the elective CTV. However, larger multi-institutional datasets for model parameter learning are required for that.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Ludwig et al_2021_A hidden Markov model for lymphatic tumor progression in the head and neck.pdf}
}

@misc{ludwig_lydata_2021,
  title = {{{lyDATA}}},
  author = {Ludwig, Roman and Hoffmann, Jean-Marc and Pouymayou, Bertrand and Morand, Gr{\'e}goire and Broglie D{\"a}ppen, Martina and Guckenberger, Matthias and Gr{\'e}goire, Vincent and Balermpas, Panagiotis and Unkelbach, Jan},
  year = {2021},
  month = nov,
  urldate = {2022-01-12},
  abstract = {Repository for storing datasets that report detailed lymphatic progression patterns of head \& neck cancer patients.},
  copyright = {MIT}
}

@misc{ludwig_lydata_2022,
  title = {{{lyDATA}}: 2021 {{CLB Oropharynx}}},
  shorttitle = {{{lyDATA}}},
  author = {Ludwig, Roman and Bauwens, Laurence and Baltres, Aline and Fiani, Danny-Joe and Zrounba, Philippe and Buiret, Guillaume and Fleury, Bertrand and Benzerdjeb, Nazim and Gr{\'e}goire, Vincent and Unkelbach, Jan},
  year = {2022},
  month = aug,
  publisher = {{Zenodo}},
  doi = {10.5281/ZENODO.10204085},
  urldate = {2023-11-30},
  abstract = {This data contains the detailed patterns of lymphatic progression of 263 patients with squamous cell carcinomas (SCCs) in the oropharynx, treated at the Centre L{\'e}on B{\'e}rard (CLB) between 2014 and 2018.},
  copyright = {Creative Commons Attribution Share Alike 4.0 International},
  keywords = {head \&amp; neck cancer,lymphatic spread,metastases,oropharynx,squamous cell carcinoma}
}

@misc{ludwig_lydata_2023,
  title = {{{lyDATA}}: 2021 {{USZ Oropharynx}}},
  shorttitle = {{{lyDATA}}},
  author = {Ludwig, Roman and Hoffmann, Jean-Marc and Pouymayou, Bertrand and Morand, Gr{\'e}goire and Broglie D{\"a}ppen, Martina and Guckenberger, Matthias and Gr{\'e}goire, Vincent and Balermpas, Panagiotis and Unkelbach, Jan},
  year = {2023},
  month = nov,
  publisher = {{Zenodo}},
  doi = {10.5281/ZENODO.5833835},
  urldate = {2023-11-30},
  abstract = {Dataset: We provide a dataset on lymph node level (LNL) involvement in 287 patients with newly diagnosed oropharyngeal squamous cell carcinoma (OPSCC). For each patient, ipsilateral and contralateral LNL involvement for levels I to VII is reported together with clinicopathological factors including TNM-stage, primary tumor subsite, tumor lateralization, HPV status, sex, age, smoking status, and primary treatment. LNL involvement was assessed individually based on available diagnostic modalities (PET, MRI, CT, fine needle aspiration) by reviewing pathology and radiology reports together with the radiological images. The data is shared as a CSV-table with rows of patients and columns of patient/tumor-specific information and the involvement of individual LNL based on the respective diagnostic modalities. Reuse potential: Patterns of lymphatic progression have never been reported on a patient-individual basis in as much detail as provided in this dataset. The data can be used to build quantitative models for lymphatic tumor progression to estimate the probability of occult metastases in LNLs. This may in turn allow for further personalization of the elective clinical target volume definition in radiotherapy and the extent of neck dissection for surgically treated patients. The data can be pooled with other data to build large multi-institutional datasets on lymphatic metastatic progression in the future.},
  copyright = {Creative Commons Attribution Share Alike 4.0 International},
  langid = {english},
  keywords = {head \&amp; neck cancer,lymphatic involvement,metastases,oropharynx,patterns of progression,squamous cell carcinoma,web interface}
}

@misc{ludwig_lydata_2023-1,
  title = {{{lyDATA}}: 2023 {{ISB Multisite}}},
  shorttitle = {{{lyDATA}}},
  author = {Ludwig, Roman and Werlen, Sandrine and Eli{\c c}in, Olgun and Dettmer, Matthias and Giger, Roland and Schubert, Adrian and Unkelbach, Jan},
  year = {2023},
  month = nov,
  publisher = {{Zenodo}},
  doi = {10.5281/ZENODO.10210423},
  urldate = {2023-11-30},
  abstract = {This contains data about clinically and pathologically diagnosed lymphatic patterns of progression from 332 patients treated at the Inselspital Bern between 2001 and 2018.},
  copyright = {Creative Commons Attribution 4.0 International}
}

@misc{ludwig_lydata_2023-2,
  title = {{{lyDATA}}: 2023 {{CLB Multisite}}},
  shorttitle = {{{lyDATA}}},
  author = {Ludwig, Roman and Barbatei, Dorothea and Zrounba, Philippe and Gr{\'e}goire, Vincent and Unkelbach, Jan},
  year = {2023},
  month = nov,
  publisher = {{Zenodo}},
  doi = {10.5281/ZENODO.10210361},
  urldate = {2023-11-30},
  abstract = {This cohort contains the pathology report data on lymphatic involvement in 373 patients with head and neck cancer, diagnosed and treated with neck dissection at the Centre L{\'e}on B{\'e}rard between 2001 and 2018.},
  copyright = {Creative Commons Attribution Share Alike 4.0 International}
}

@misc{ludwig_lyprox_2023,
  title = {{{LyProX}}},
  author = {Ludwig, Roman},
  year = {2023},
  month = may,
  address = {{Zurich, Switzerland}},
  urldate = {2023-05-31},
  abstract = {Web app for exploring patterns and correlations in the lymph node level involvements of head \& neck cancer patients.},
  copyright = {MIT},
  keywords = {cancer,django,head-and-neck,lymph-nodes,metastases,python,radiation-oncology,web-app}
}

@misc{ludwig_lyscripts_2023,
  title = {Lyscripts},
  author = {Ludwig, Roman},
  year = {2023},
  month = apr,
  address = {{Zurich, Switzerland}},
  urldate = {2023-05-31},
  abstract = {Scripts that are used in the pipelines of the lynference repository and to clean the raw data in the lyDATA repository.},
  copyright = {MIT},
  keywords = {cli,machine-learning,python,scripts}
}

@misc{ludwig_modelling_2023,
  title = {Modelling the {{Lymphatic Metastatic Progression Pathways}} of {{OPSCC}} from {{Multi-Institutional Datasets}}},
  author = {Ludwig, Roman and Schubert, Adrian and Barbatei, Dorothea and Bauwens, Lauence and Hoffmann, Jean-Marc and Werlen, Sandrine and Elicin, Olgun and Dettmer, Matthias and Zrounba, Philippe and Pouymayou, Bertrand and Balermpas, Panagiotis and Gr{\'e}goire, Vincent and Giger, Roland and Unkelbach, Jan},
  year = {2023},
  month = dec,
  journal = {arXiv.org},
  urldate = {2024-01-08},
  abstract = {The elective clinical target volume (CTV-N) in oropharyngeal squamous cell carcinoma (OPSCC) is currently based mostly on the prevalence of lymph node metastases in different lymph node levels (LNLs) for a given primary tumor location. We present a probabilistic model for ipsilateral lymphatic spread that can quantify the microscopic nodal involvement risk based on an individual patient's T-category and clinical involvement of LNLs at diagnosis. We extend a previously published hidden Markov model (HMM), which models the LNLs (I, II, III, IV, V, and VII) as hidden binary random variables (RVs). Each represents a patient's true state of lymphatic involvement. Clinical involvement at diagnosis represents the observed binary RVs linked to the true state via sensitivity and specificity. The primary tumor and the hidden RVs are connected in a graph. Each edge represents the conditional probability of metastatic spread per abstract time-step, given disease at the edge's starting node. To learn these probabilities, we draw Markov chain Monte Carlo samples from the likelihood of a dataset (686 OPSCC patients) from three institutions. We compute the model evidence using thermodynamic integration for different graphs to determine which describes the data best. The graph maximizing the model evidence connects the tumor to each LNL and the LNLs I through V in order. It predicts the risk of occult disease in level IV is below 5\% if level III is clinically negative, and that the risk of occult disease in level V is below 5\% except for advanced T-category (T3 and T4) patients with clinical involvement of levels II, III, and IV. The provided statistical model of nodal involvement in OPSCC patients trained on multi-institutional data may guide the design of clinical trials on volume-deescalated treatment of OPSCC and contribute to more personal guidelines on elective nodal treatment.},
  howpublished = {https://arxiv.org/abs/2312.11270v3},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Ludwig et al_2023_Modelling the Lymphatic Metastatic Progression Pathways of OPSCC from.pdf}
}

@article{ludwig_multi-centric_2023,
  title = {A Multi-Centric Dataset on Patient-Individual Pathological Lymph Node Involvement in Head and Neck Squamous Cell Carcinoma},
  author = {Ludwig, Roman and Schubert, Adrian and Barbatei, Dorothea and Bauwens, Laurence and Werlen, Sandrine and Elicin, Olgun and Dettmer, Matthias and Zrounba, Philippe and Balermpas, Panagiotis and Pouymayou, Bertrand and Gr{\'e}goire, Vincent and Giger, Roland and Unkelbach, Jan},
  year = {2023},
  month = dec,
  journal = {Data in Brief},
  pages = {110020},
  issn = {2352-3409},
  doi = {10.1016/j.dib.2023.110020},
  urldate = {2023-12-29},
  abstract = {Dataset We provide a dataset on lymph node metastases in 968 patients with newly diagnosed head and neck squamous cell carcinoma (HNSCC). All patients received neck dissection and we report the number of metastatic versus investigated lymph nodes per lymph node level (LNL) for every individual patient. Additionally, clinicopathological factors including T-category, primary tumor subsite (ICD-O-3 code), age, and sex are reported for all patients. The data is provided as three datasets: Dataset 1 contains 373 HNSCC patients treated at Centre L{\'e}on B{\'e}rard (CLB), France, with primary tumor location in the oral cavity, oropharynx, hypopharynx, and larynx. Dataset 2 contains 332 HNSCC patients treated at the Inselspital, Bern University Hospital (ISB), Switzerland with primary tumor location in the oral cavity, oropharynx, hypopharynx, and larynx. For these patients, additional information is provided including lateralization of the primary tumor, size and location of the largest metastases, and clinical involvement based on computed tomography (CT), magnetic resonance imaging (MRI), and/or 18FDG-positron emission tomography (PET/CT) imaging. Dataset 3 consists of 263 oropharyngeal SCC patients underlying a previous publication by Bauwens et al [1], which were treated at CLB. For these patients, additional information including HPV status, lateralization of the primary tumor and clinically diagnosed lymph node involvement is provided. Reuse Potential : The data may be used to quantify the probability of occult lymph node metastases in each LNL, depending on an individual patient's characteristics of the primary tumor and the location of clinically diagnosed lymph node metastases. As such, the data may contribute to further personalize the elective treatment of the neck for HNSCC patients, i.e. definition of the elective clinical target volume (CTV-N) in radiotherapy (RT) and the extent of neck dissection (ND) in surgery. There exists only one similar publicly available dataset that reports clinical involvement per LNL in 287 oropharyngeal SCC patients [2]. The data presented in this article substantially extends the available data, it additionally includes pathologically assessed involvement per LNL, and it provides data for multiple subsites in the head and neck region.},
  keywords = {graphical user interface,head and neck squamous cell carcinoma,lymph node involvement,neck dissection,patterns of progression},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Ludwig et al_2023_A multi-centric dataset on patient-individual pathological lymph node2.pdf;C\:\\Users\\roman\\Zotero\\storage\\FBF922DM\\S2352340923010478.html}
}

@inproceedings{ludwig_personalized_2022,
  title = {Personalized Elective Clinical Target Volume Definition in Head \& Neck Cancer},
  booktitle = {{{ICHNO}}/{{ECHNO}}},
  author = {Ludwig, Roman and Pouymayou, Bertrand and Hoffmann, Jean-Marc and Guckenberger, Matthias and Bauwens, Laurence and Gr{\'e}goire, Vincent and Balermpas, Panagiotis and Unkelbach, Jan},
  year = {2022},
  pages = {21},
  address = {{Brussels}},
  urldate = {2022-10-25},
  abstract = {Purpose/Objective: Head \& neck squamous cell carcinomas (HNSCC) spread lymphatically through the neck and form metastases in regional lymph nodes. Modern imaging techniques such as FDG-PET/CT can visualize sufficiently large metastases but fail to detect small occult metastases. Therefore, large parts of the neck are electively irradiated as part of the nodal clinical target volume (CTV-N). Here, we report on activities within a newly formed ESTRO working group that aims at developing computational methods to support CTV definition. The goal of this specific project is to improve quantification of the risk of occult disease in lymph node levels (LNL), considering the individual patient's state of tumor progression. Materials/Methods: Quantification of the risk of occult metastases relies on three main components. (1) detailed datasets of lymphatic progression patterns that report, on a patient-by-patient basis, the location of lymph node metastases together with primary tumor characteristics such as location, T-category, midsagittal plane extension, and HPV status; (2) sensitivity and specificity of diagnostic modalities to detect lymph node metastases, obtained from comparing pathological and clinical lymph node involvement; and (3) a statistical model that quantitatively describes lymphatic metastatic progression and the diagnostic process. Results: To address (1), we developed a web-based platform to host, visualize, and share datasets of lymphatic progression patterns, currently containing two datasets of 287 and 263 oropharyngeal  HNSCC patients from independent institutions. Figure 1 illustrates the use of the platform. To address (3), we develop a probabilistic model of metastatic progression based on Hidden Markov Models (Figure 2, upper panel). In this model, each LNL is represented by a hidden binary random variable that indicates if a LNL truly harbors tumor including occult metastases. Each LNL is further associated with a binary observed state, which indicates if the LNL harbors visible macroscopic metastases. Hidden microscopic state and observed macroscopic state are linked via (2), sensitivity and specificity. The parameters of the model are the probabilities for the primary tumor to spread to a LNL and the probabilities to spread from upstream to downstream LNL along the lymphatic drainage, which are learned from (1), datasets of lymph node level involvement. Estimating the risk of occult metastases for a newly diagnosed patient corresponds to calculating marginals of the joint probability distribution of LNL involvement conditioned on the patient's diagnose (Figure 2, bottom panel). Conclusions: Quantification of the probability of occult metastases in LNLs considering the individual patient's primary tumor characteristics and the visible state of nodal progression may allow for personalized volume de-escalation strategies to reduce treatment toxicity. To achieve this, larger multi-institutional training datasets are being collected.}
}

@inproceedings{ludwig_predicting_2022,
  title = {Predicting  Bilateral Involvement in Head \& Neck Cancer Using an Interpretable Probabilistic Model},
  booktitle = {{{ESTRO}}},
  author = {Ludwig, Roman and Pouymayou, Bertrand and Hoffmann, Jean-Marc and Balermpas, Panagiotis and Unkelbach, Jan},
  year = {2022},
  pages = {764},
  address = {{Copenhagen}},
  urldate = {2022-10-25},
  abstract = {Purpose/Objective: In current clinical practice, the elective clinical target volume (CTV-N) for oropharyngeal head \& neck squamous cell carcinoma (OHNSCC) is defined using prevalence-based guidelines [1], which recommend extensive bilateral neck irradiation for most patients. However, the actual patient-specific risk of harboring microscopic metastases in the contralateral neck remains insufficiently quantified. We propose a probabilistic and interpretable model for predicting the personalized risk of involvement in lymph node levels (LNLs) of both sides of the neck depending on T-stage, location of macroscopic metastases, and the primary tumor's lateralization.   This may identify additional patients in whom contralateral neck irradiation can be avoided or reduced, possibly reducing toxicity. Materials/Methods: We extracted the lymphatic patterns of progression for 287 OHNSCC patients treated at our institution. The data can be visualized at www.lyprox.org. This was used to train the hidden Markov model (HMM) for predicting nodal involvement we developed and published recently [2]. For this work, the model in [2] was extended to contralateral spread while treating mid-sagittal plane extension of the primary tumor as risk factor. It models the LNLs as binary random variables connected in a directed graph (Figure 1). The edges of the graph represent the lymphatic drainage pathways, which are associated with probabilities of metastatic spread per abstract time step. These are the parameters of the HMM that are learned from the dataset of 287 patients. Results: Figure 2a) shows the predicted risk of microscopic metastases in contralateral LNL II depending on T-category, the extent of CT-observed macroscopic metastases, and midline extension as a risk factor. This risk is low (0.5 {$\pm$} 0.3 \%) for patients with early T-category (T1 \& T2) tumors not extending over the midline with no clinically involved LNLs. However, it is significantly higher when the tumor is not lateralized, and we observe ipsilateral LNL II to be metastatic (7.2 {$\pm$} 1.9 \%). It further increases for late T-category (8.3 {$\pm$} 2 \%) and once more when the ipsilateral LNLs II, III and IV are clinically involved (10.3 {$\pm$} 2.6 \%). Figure 2b) shows the risk predicted for involvement in contralateral LNL III depending on the upstream level II.  Conclusion: An HMM as probabilistic framework proves to be both flexible to expand and suitable for predicting the risk of microscopic involvement in a personalized manner. We can specify a patient by T-category, observed macroscopic involvement and the primary tumor's midline extension to compute their risk for harboring microscopic metastases in any LNL recorded in the training cohort. Multi-institutional detailed datasets are however needed to validate the model's accuracy.}
}

@misc{luger_mapping_2021,
  title = {Mapping Stellar Surfaces {{III}}: {{An Efficient}}, {{Scalable}}, and {{Open-Source Doppler Imaging Model}}},
  shorttitle = {Mapping Stellar Surfaces {{III}}},
  author = {Luger, Rodrigo and Bedell, Megan and {Foreman-Mackey}, Daniel and Crossfield, Ian J. M. and Zhao, Lily L. and Hogg, David W.},
  year = {2021},
  month = oct,
  number = {arXiv:2110.06271},
  eprint = {2110.06271},
  primaryclass = {astro-ph},
  publisher = {{arXiv}},
  doi = {10.48550/arXiv.2110.06271},
  urldate = {2022-11-28},
  abstract = {The study of stellar surfaces can reveal information about the chemical composition, interior structure, and magnetic properties of stars. It is also critical to the detection and characterization of extrasolar planets, in particular those targeted in extreme precision radial velocity (EPRV) searches, which must contend with stellar variability that is often orders of magnitude stronger than the planetary signal. One of the most successful methods to map the surfaces of stars is Doppler imaging, in which the presence of inhomogeneities is inferred from subtle line shape changes in high resolution stellar spectra. In this paper, we present a novel, efficient, and closed-form solution to the problem of Doppler imaging of stellar surfaces. Our model explicitly allows for incomplete knowledge of the local (rest frame) stellar spectrum, allowing one to learn differences from spectral templates while simultaneously mapping the stellar surface. It therefore works on blended lines, regions of the spectrum where line formation mechanisms are not well understood, or stars whose spots have intrinsically different spectra from the rest of the photosphere. We implement the model within the open source starry framework, making it fast, differentiable, and easy to use in both optimization and posterior inference settings. As a proof-of-concept, we use our model to infer the surface map of the brown dwarf WISE 1049-5319B, finding close agreement with the solution of Crossfield et al. (2014). We also discuss Doppler imaging in the context of EPRV studies and describe an interpretable spectral-temporal Gaussian process for stellar spectral variability that we expect will be important for EPRV exoplanet searches.},
  archiveprefix = {arxiv},
  keywords = {Astrophysics - Earth and Planetary Astrophysics,Astrophysics - Instrumentation and Methods for Astrophysics,Astrophysics - Solar and Stellar Astrophysics},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Luger et al_2021_Mapping stellar surfaces III.pdf;C\:\\Users\\roman\\Zotero\\storage\\SQMZIU4V\\2110.html}
}

@article{mackay_information_nodate,
  title = {Information {{Theory}}, {{Inference}}, and {{Learning Algorithms}}},
  author = {MacKay, David J C},
  pages = {640},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\MacKay_Information Theory, Inference, and Learning Algorithms.pdf}
}

@book{marieb_human_1995,
  title = {Human Anatomy and Physiology},
  author = {Marieb, Elaine Nicpon},
  year = {1995},
  edition = {3rd ed},
  publisher = {{Benjamin/Cummings}},
  address = {{Redwood City, Calif.}},
  isbn = {978-0-8053-4281-9},
  langid = {english},
  annotation = {OCLC: 30778360}
}

@article{marur_head_2016,
  title = {Head and {{Neck Squamous Cell Carcinoma}}: {{Update}} on {{Epidemiology}}, {{Diagnosis}}, and {{Treatment}}},
  shorttitle = {Head and {{Neck Squamous Cell Carcinoma}}},
  author = {Marur, Shanthi and Forastiere, Arlene A.},
  year = {2016},
  month = mar,
  journal = {Mayo Clinic Proceedings},
  volume = {91},
  number = {3},
  pages = {386--396},
  issn = {0025-6196},
  doi = {10.1016/j.mayocp.2015.12.017},
  urldate = {2023-03-10},
  abstract = {Squamous cell carcinoma arises from multiple anatomic subsites in the head and neck region. The risk factors for development of cancers of the oral cavity, oropharynx, hypopharynx, and larynx include tobacco exposure and alcohol dependence, and infection with oncogenic viruses is associated with cancers developing in the nasopharynx, palatine, and lingual tonsils of the oropharynx. The incidence of human papillomavirus{\textendash}associated oropharyngeal cancer is increasing in developed countries, and by 2020, the annual incidence could surpass that of cervical cancer. The treatment for early-stage squamous cell cancers of the head and neck is generally single modality, either surgery or radiotherapy. The treatment for locally advanced head and neck cancers is multimodal, with either surgery followed by adjuvant radiation or chemoradiation as indicated by pathologic features or definitive chemoradiation. For recurrent disease that is not amenable to a salvage local or regional approach and for metastatic disease, chemotherapy with or without a biological agent is indicated. To date, molecular testing has not influenced treatment selection in head and neck cancer. This review will focus on the changing epidemiology, advances in diagnosis, and treatment options for squamous cell cancers of the head and neck, along with data on risk stratification specific to oropharyngeal cancer, and will highlight the direction of current trials.},
  langid = {english},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Marur_Forastiere_2016_Head and Neck Squamous Cell Carcinoma.pdf;C\:\\Users\\roman\\Zotero\\storage\\JNS3BK7K\\S002561961501006X.html}
}

@article{matt_dna_2016,
  title = {The {{DNA}} Damage-Induced Cell Death Response: A Roadmap to Kill Cancer Cells},
  shorttitle = {The {{DNA}} Damage-Induced Cell Death Response},
  author = {Matt, Sonja and Hofmann, Thomas G.},
  year = {2016},
  month = aug,
  journal = {Cellular and Molecular Life Sciences},
  volume = {73},
  number = {15},
  pages = {2829--2850},
  issn = {1420-9071},
  doi = {10.1007/s00018-016-2130-4},
  urldate = {2023-03-13},
  abstract = {Upon massive DNA damage cells fail to undergo productive DNA repair and trigger the cell death response. Resistance to cell death is linked to cellular transformation and carcinogenesis as well as radio- and chemoresistance, making the underlying signaling pathways a promising target for therapeutic intervention. Diverse DNA damage-induced cell death pathways are operative in mammalian cells and finally culminate in the induction of programmed cell death via activation of apoptosis or necroptosis. These signaling routes affect nuclear, mitochondria- and plasma membrane-associated key molecules to activate the apoptotic or necroptotic response. In this review, we highlight the main signaling pathways, molecular players and mechanisms guiding the DNA damage-induced cell death response.},
  langid = {english},
  keywords = {Adriamycin,ATM,ATR,Axin,BAX,c-Abl,Cancer therapy,Caspase 2,Chk1,Chk2,Doxorubicin,FOXO3,HIPK2,Hippo pathway,Ionizing radiation,MLKL,p53,p53 Serine 46,p73,PIDD,Pin1,PML,PUMA,RIPK1,RIPK3,SUMO,XAF1,Yap1},
  file = {C:\Users\roman\OneDrive\Documents\Library\Matt_Hofmann_2016_The DNA damage-induced cell death response.pdf}
}

@article{maxwell_extracapsular_2013,
  title = {Extracapsular Spread in Head and Neck Carcinoma: {{Impact}} of Site and Human Papillomavirus Status},
  shorttitle = {Extracapsular Spread in Head and Neck Carcinoma},
  author = {Maxwell, Jessica H. and Ferris, Robert L. and Gooding, William and Cunningham, Diana and Mehta, Vikas and Kim, Seungwon and Myers, Eugene N. and Johnson, Jonas and Chiosea, Simion},
  year = {2013},
  journal = {Cancer},
  volume = {119},
  number = {18},
  pages = {3302--3308},
  issn = {1097-0142},
  doi = {10.1002/cncr.28169},
  urldate = {2023-03-23},
  abstract = {BACKGROUND Extracapsular spread (ECS) in cervical lymph node metastases from head and neck squamous cell carcinoma (SCC) is regarded as an adverse prognostic factor and is often used to select patients who may benefit from adjuvant therapy. The prognostic value of ECS was evaluated for patients with oropharyngeal SCC (OPC; with known p16/human papillomavirus [HPV] status) and for patients with SCC of the oral cavity (OCC). METHODS Disease-specific survival (DSS) was assessed among SCC patients with cervical lymph node metastases (n = 347, including 133 patients with OPC and 214 patients with OCC). All patients were treated surgically between 1983 and 2009. ECS status was determined by pathologists at the time of initial pathologic evaluation and confirmed for this study. HPV status of patients with OPC was determined via immunohistochemistry for p16 and in situ hybridization. RESULTS Among OCC patients, ECS was a significant, independent factor influencing DSS. For OCC patients with ECS, 3-year DSS was 45\% (95\% confidence interval [CI], 36\%-56\%); for those without ECS, 3-year DSS was 71\% (95\% CI, 62\%-81\%; P = .0018). The effect of ECS was independent of the number of positive lymph nodes as well as other clinical, pathologic, and treatment variables. Of the 133 OPC patients, 76 (57\%) were p16-positive and 57 (43\%) were p16-negative. ECS status did not correlate with DSS among p16-positive or p16-negative OPC patients. CONCLUSION ECS was not associated with worse DSS in p16-positive or p16-negative OPC patients. Adverse prognostic value of ECS in OCC patients was confirmed. Cancer 2013;119:3302{\textendash}8. {\textcopyright} 2013 American Cancer Society.},
  langid = {english},
  keywords = {Extracapsular spread,HPV,oral cavity,oropharynx,p16,squamous cell carcinoma},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Maxwell et al_2013_Extracapsular spread in head and neck carcinoma.pdf;C\:\\Users\\roman\\Zotero\\storage\\9M2MKFP4\\cncr.html}
}

@article{mayinger_benefit_2021,
  title = {Benefit of Replanning in {{MR-guided}} Online Adaptive Radiation Therapy in the Treatment of Liver Metastasis},
  author = {Mayinger, Michael and Ludwig, Roman and Christ, Sebastian M. and Dal Bello, Riccardo and Ryu, Alex and Weitkamp, Nienke and Pavic, Matea and Garcia Sch{\"u}ler, Helena and Wilke, Lotte and Guckenberger, Matthias and Unkelbach, Jan and {Tanadini-Lang}, Stephanie and Andratschke, Nicolaus},
  year = {2021},
  month = may,
  journal = {Radiation Oncology (London, England)},
  volume = {16},
  number = {1},
  pages = {84},
  issn = {1748-717X},
  doi = {10.1186/s13014-021-01813-6},
  abstract = {PURPOSE: To assess the effects of daily adaptive MR-guided replanning in stereotactic body radiation therapy (SBRT) of liver metastases based on a patient individual longitudinal dosimetric analysis. METHODS: Fifteen patients assigned to SBRT for oligometastatic liver metastases underwent daily MR-guided target localization and on-table treatment plan re-optimization. Gross tumor volume (GTV) and organs at risk (OARs) were adapted to the anatomy-of-the-day. A reoptimized plan (RP) and a rigidly shifted baseline plan (sBP) without re-optimization were generated for each fraction. After extraction of DVH parameters for GTV, planning target volume (PTV), and OARs (stomach, duodenum, bowel, liver, heart) plans were compared on a per-patient basis. RESULTS: Median pre-treatment GTV and PTV were 14.9~cc (interquartile range (IQR): 7.7-32.9) and 62.7~cc (IQR: 42.4-105.5) respectively. SBRT with RP improved PTV coverage (V100\%) for 47/75 of the fractions and reduced doses to the most proximal OARs (D1cc, Dmean) in 33/75 fractions compared to sBP. RP significantly improved PTV coverage (V100\%) for metastases within close proximity to an OAR by 4.0\% ({$\leq$}\,0.2~cm distance from the edge of the PTV to the edge of the OAR; n\,=\,7; p\,=\,0.01), but only by 0.2\% for metastases farther away from OAR ({$>$}\,2~cm distance; n\,=\,7; p\,=\,0.37). No acute grade 3 treatment-related toxicities were observed. CONCLUSIONS: MR-guided online replanning SBRT improved target coverage and OAR sparing for liver metastases with a distance from the edge of the PTV to the nearest luminal OAR\,{$<$}\,2~cm. Only marginal improvements in target coverage were observed for target distant to critical OARs, indicating that these patients do not benefit from daily adaptive replanning.},
  langid = {english},
  pmcid = {PMC8097956},
  pmid = {33947429},
  keywords = {Adult,Female,Humans,Liver Neoplasms,Longitudinal Studies,Magnetic Resonance Imaging,Male,Middle Aged,Neoplasms,Organs at Risk,Prognosis,Radiosurgery,Radiotherapy Dosage,{Radiotherapy Planning, Computer-Assisted},{Radiotherapy, Intensity-Modulated},Retrospective Studies},
  file = {C:\Users\roman\OneDrive\Documents\Library\Mayinger et al_2021_Benefit of replanning in MR-guided online adaptive radiation therapy in the.pdf}
}

@inproceedings{mayinger_benefit_2022,
  title = {Benefit of Replanning in {{MR-guided}} Online Adaptive Radiation Therapy in Liver Metastasis Treatment},
  booktitle = {{{ESTRO}}},
  author = {Mayinger, Michael and Ludwig, Roman and Christ, Sebastian M. and Dal Bello, Riccardo and Ryu, Alex and Weitkamp, Nienke and Pavic, Matea and Garcia Sch{\"u}ler, Helena and Wilke, Lotte and Guckenberger, Matthias and Unkelbach, Jan and {Tanadini-Lang}, Stephanie and Andratschke, Nicolaus},
  year = {2022},
  pages = {58},
  address = {{Copenhagen}},
  urldate = {2022-10-25},
  abstract = {Purpose/Objective: To assess the effects of daily adaptive MR-guided replanning in stereotactic body radiation therapy (SBRT) of liver metastases based on a patient individual longitudinal dosimetric analysis. Materials/Methods: Fifteen patients assigned to SBRT for oligometastatic liver metastases underwent daily MR-guided target localization and on-table treatment plan re-optimization. A Monte Carlo algorithm based, intensity-modulated RT (IMRT) step and shoot treatment plan, referred to as ``baseline plan (BP)'' was calculated, using a grid spacing of 0.2 cm (Figure 1 A). Gross tumor volume (GTV) and organs at risk (OARs) were adapted to the anatomy-of-the-day. A rigidly shifted baseline plan (sBP; Figure 1 B) without re-optimization a reoptimized plan (RP; Figure 1 C) were generated for each fraction. After extraction of DVH parameters for GTV, planning target volume (PTV), and OARs (stomach, duodenum, bowel, liver, heart) plans were compared on a per-patient basis. Results: Median pre-treatment GTV and PTV were 14.9 cc (interquartile range (IQR): 7.7-32.9) and 62.7 cc (IQR: 42.4-105.5) respectively. SBRT with RP improved PTV coverage (V100\%) for 47/75 of the fractions and reduced doses to the most proximal OARs (D1cc, Dmean) in 33/75 fractions compared to sBP. RP significantly improved PTV coverage (V100\%) for metastases within close proximity to an OAR by 4.0\% ({$\leq$} 0.2 cm distance from the edge of the PTV to the edge of the OAR; n = 7; p = 0.01; Figure 2), but only by 0.2\% for metastases farther away from OAR ({$>$} 2 cm distance; n = 7; p = 0.37). No acute grade 3 treatment-related toxicities were observed. Conclusion: MR-guided online replanning SBRT improved target coverage and OAR sparing for liver metastases with a distance from the edge of the PTV to the nearest luminal OAR {$<$} 2 cm. Only marginal improvements in target coverage were observed for target distant to critical OARs, indicating that these patients do not benefit from daily adaptive replanning.}
}

@misc{mccool_apache_nodate,
  title = {Apache {{HTTP}} Server},
  author = {McCool, Robert},
  copyright = {Apache-2.0},
  howpublished = {The Apache Software Foundation}
}

@article{mclachlan_finite_2019,
  title = {Finite {{Mixture Models}}},
  author = {McLachlan, Geoffrey J. and Lee, Sharon X. and Rathnayake, Suren I.},
  year = {2019},
  journal = {Annual Review of Statistics and Its Application},
  volume = {6},
  number = {1},
  pages = {355--378},
  doi = {10.1146/annurev-statistics-031017-100325},
  urldate = {2024-01-15},
  abstract = {The important role of finite mixture models in the statistical analysis of data is underscored by the ever-increasing rate at which articles on mixture applications appear in the statistical and general scientific literature. The aim of this article is to provide an up-to-date account of the theory and methodological developments underlying the applications of finite mixture models. Because of their flexibility, mixture models are being increasingly exploited as a convenient, semiparametric way in which to model unknown distributional shapes. This is in addition to their obvious applications where there is group-structure in the data or where the aim is to explore the data for such structure, as in a cluster analysis. It has now been three decades since the publication of the monograph by McLachlan \& Basford (1988) with an emphasis on the potential usefulness of mixture models for inference and clustering. Since then, mixture models have attracted the interest of many researchers and have found many new and interesting fields of application. Thus, the literature on mixture models has expanded enormously, and as a consequence, the bibliography here can only provide selected coverage.},
  keywords = {EM algorithm,mixture proportions,mixtures of factor analyzers,model-based clustering,normal and t-mixture distributions},
  file = {C:\Users\roman\OneDrive\Documents\Library\McLachlan et al_2019_Finite Mixture Models.pdf}
}

@article{mermod_extracapsular_2016-1,
  title = {Extracapsular Spread in Head and Neck Squamous Cell Carcinoma: {{A}} Systematic Review and Meta-Analysis},
  shorttitle = {Extracapsular Spread in Head and Neck Squamous Cell Carcinoma},
  author = {Mermod, Maxime and Tolstonog, Genrich and Simon, Christian and Monnier, Yan},
  year = {2016},
  month = nov,
  journal = {Oral Oncology},
  volume = {62},
  pages = {60--71},
  issn = {1368-8375},
  doi = {10.1016/j.oraloncology.2016.10.003},
  urldate = {2023-03-10},
  abstract = {Extracapsular spread (ECS) is one of the most important prognostic factors in head and neck squamous cell carcinoma (HNSCC). However, despite its major clinical relevance, there are still a number of important remaining issues regarding this condition. Indeed, standardized diagnostic and grading criteria of ECS are still lacking. The imaging modality of choice for its diagnosis is a matter of debate. Current research looking at the identification of specific biomarkers is ongoing. Recent findings demonstrate a direct correlation between the level of extension of ECS and a poor prognosis. Accumulating data show that ECS does not carry the same adverse features in human papilloma virus (HPV)-positive oropharyngeal squamous cell carcinoma (OPSCC). New treatment strategies based on these factors are currently considered to investigate the possibility of diminishing the toxicity of chemo-radiotherapy while maintaining similar outcomes. The goal of this article was to provide a systematic review of the literature covering all the issues related to ECS. As an additional component of the review, meta-analyses were performed on relevant aspects of ECS for which previous quantitative data were outdated or not available. The results of these meta-analyses confirm the negative impact of ECS on loco-regional recurrence and distant metastasis. They also demonstrate the absence of a negative impact of ECS in HPV-positive OPSCC.},
  langid = {english},
  keywords = {Extracapsular spread,Extranodal spread,Head and neck squamous cell carcinoma,HPV,Lymph node metastasis,Meta-analysis,Perinodal spread,Systematic review,Transcapsular spread},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Mermod et al_2016_Extracapsular spread in head and neck squamous cell carcinoma.pdf;C\:\\Users\\roman\\Zotero\\storage\\QHB6RBSJ\\S1368837516301798.html}
}

@article{metropolis_equation_1953,
  title = {Equation of {{State Calculations}} by {{Fast Computing Machines}}},
  author = {Metropolis, Nicholas and Rosenbluth, Arianna W. and Rosenbluth, Marshall N. and Teller, Augusta H. and Teller, Edward},
  year = {1953},
  month = jun,
  journal = {The Journal of Chemical Physics},
  volume = {21},
  number = {6},
  pages = {1087--1092},
  publisher = {{American Institute of Physics}},
  issn = {0021-9606},
  doi = {10.1063/1.1699114},
  urldate = {2022-10-18}
}

@book{meyer_personlichkeit_2020,
  title = {{Pers{\"o}nlichkeit und Selbststeuerung der Generation Z: Ein Leitfaden f{\"u}r Bildungstr{\"a}ger und die mittelst{\"a}ndische Unternehmenspraxis}},
  shorttitle = {{Pers{\"o}nlichkeit und Selbststeuerung der Generation Z}},
  author = {Meyer, Karin},
  year = {2020},
  series = {{essentials}},
  publisher = {{Springer Fachmedien Wiesbaden}},
  address = {{Wiesbaden}},
  doi = {10.1007/978-3-658-32603-6},
  urldate = {2022-09-16},
  isbn = {978-3-658-32602-9 978-3-658-32603-6},
  langid = {ngerman},
  file = {C:\Users\roman\OneDrive\Documents\Library\Meyer_2020_Persönlichkeit und Selbststeuerung der Generation Z.pdf}
}

@article{moons_limitations_1997,
  title = {Limitations of {{Sensitivity}}, {{Specificity}}, {{Likelihood Ratio}}, and {{Bayes}}' {{Theorem}} in {{Assessing Diagnostic Probabilities}}: {{A Clinical Example}}},
  shorttitle = {Limitations of {{Sensitivity}}, {{Specificity}}, {{Likelihood Ratio}}, and {{Bayes}}' {{Theorem}} in {{Assessing Diagnostic Probabilities}}},
  author = {Moons, Karel G. M. and {van Es}, Gerrit-Anne and Deckers, Jaap W. and Habbema, J. Dik F. and Grobbee, Diederick E.},
  year = {1997},
  journal = {Epidemiology},
  volume = {8},
  number = {1},
  eprint = {3702416},
  eprinttype = {jstor},
  pages = {12--17},
  publisher = {{Lippincott Williams \& Wilkins}},
  issn = {1044-3983},
  urldate = {2021-06-09},
  abstract = {We evaluated the extent to which the sensitivity, specificity, and likelihood ratio of the exercise test to diagnose coronary artery disease vary across subgroups of a certain patient population. Among 295 patients suspected of coronary artery disease, as independently determined by coronary angiography, we assessed variation in sensitivity and specificity according to patient history, physical examination, exercise test results, and disease severity in 207 patients with and 88 patients without coronary artery disease, respectively. The sensitivity varied substantially according to sex (women 30\% and men 64\%), systolic blood pressure at baseline (53\% to 65\%), expected workload (50\% to 64\%), systolic blood pressure at peak exercise (50\% to 67\%), relative workload (33\% to 66\%), and number of diseased vessels (39\% to 77\%). The specificity varied across subgroups of sex (men 89\% and women 97\%) and relative workload (85\% to 98\%). The likelihood ratio varied (3.8 to 17.0) across the same patient subgroups, as did the sensitivity. As each population tends to be heterogeneous with respect to patient characteristics, no single level of these parameters can be given that is adequate for all subgroups. Use of these parameters as a basis for calculating diagnostic probabilities in individual patients using Bayes' theorem has serious limitations.},
  file = {C:\Users\roman\OneDrive\Documents\Library\Moons et al_1997_Limitations of Sensitivity, Specificity, Likelihood Ratio, and Bayes' Theorem.pdf}
}

@article{muehlemann_tutorial_2023,
  title = {A {{Tutorial}} on {{Modern Bayesian Methods}} in {{Clinical Trials}}},
  author = {Muehlemann, Natalia and Zhou, Tianjian and Mukherjee, Rajat and Hossain, Munshi Imran and Roychoudhury, Satrajit and {Russek-Cohen}, Estelle},
  year = {2023},
  month = may,
  journal = {Therapeutic Innovation \& Regulatory Science},
  volume = {57},
  number = {3},
  pages = {402--416},
  issn = {2168-4804},
  doi = {10.1007/s43441-023-00515-3},
  urldate = {2023-07-07},
  abstract = {Clinical trials continue to be the gold standard for evaluating new medical technologies. New advancements in modern computation power have led to increasing interest in Bayesian methods. Despite the multiple benefits of Bayesian approaches, application to clinical trials has been limited. Based on insights from the survey of clinical researchers in drug development conducted by the Drug Information Association Bayesian Scientific Working Group (DIA BSWG), insufficient knowledge of Bayesian approaches was ranked as the most important perceived barrier to implementing Bayesian methods. Results of the same survey indicate that clinical researchers may find the interpretation of results from a Bayesian analysis to be more useful than conventional interpretations. In this article, we illustrate key concepts tied to Bayesian methods, starting with familiar concepts widely used in clinical practice before advancing in complexity, and use practical illustrations from clinical development.},
  langid = {english},
  keywords = {Bayesian methods,Bayesian statistics,Clinical development,Clinical trials,Drug development},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Muehlemann et al_2023_A Tutorial on Modern Bayesian Methods in Clinical Trials.pdf;C\:\\Users\\roman\\Zotero\\storage\\JWNCMS3Y\\Muehlemann et al. - 2023 - A Tutorial on Modern Bayesian Methods in Clinical .pdf}
}

@article{mukherji_cervical_2001,
  title = {Cervical Nodal Metastases in Squamous Cell Carcinoma of the Head and Neck: {{What}} to Expect},
  author = {Mukherji, S.K. and Armao, D. and Joshi, V.M.},
  year = {2001},
  journal = {Head and Neck},
  volume = {23},
  number = {11},
  pages = {995--1005},
  issn = {10433074 (ISSN)},
  doi = {10.1002/hed.1144},
  langid = {english}
}

@article{murphy_bayes_2001,
  title = {The Bayes Net Toolbox for Matlab},
  author = {Murphy, K},
  year = {2001},
  journal = {Comput. Sci. Stat.},
  volume = {33},
  pages = {1024--1034}
}

@article{murray_distributed_nodate,
  title = {Distributed {{Markov}} Chain {{Monte Carlo}}},
  author = {Murray, Lawrence},
  pages = {4},
  abstract = {We consider the design of Markov chain Monte Carlo (MCMC) methods for large-scale, distributed, heterogeneous compute facilities, with a focus on synthesising sample sets across multiple runs performed in parallel. While theory suggests that many independent Markov chains may be run and their samples pooled, the well-known practical problem of quasi-ergodicity, or poor mixing, frustrates this otherwise simple approach. Furthermore, without some mechanism for hastening the convergence of individual chains, overall speedup from parallelism is limited by the portion of each chain to be discarded as burn-in. Existing multiple-chain methods, such as parallel tempering and population MCMC, use a synchronous exchange of samples to expedite convergence. This work instead proposes mixing in an additional independent proposal, representing some hitherto best estimate or summary of the posterior, and cooperatively adapting this across chains. Such adaptation can be asynchronous, increases the ensemble's robustness to quasi-ergodic behaviour in constituent chains, and may improve overall tolerance to fault.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Murray_Distributed Markov chain Monte Carlo.pdf}
}

@article{murthy_prostate-only_2021,
  title = {Prostate-{{Only Versus Whole-Pelvic Radiation Therapy}} in {{High-Risk}} and {{Very High-Risk Prostate Cancer}} ({{POP-RT}}): {{Outcomes From Phase III Randomized Controlled Trial}}},
  author = {Murthy, Vedang and Maitre, Priyamvada and Kannan, Sadhana and Panigrahi, Gitanjali and Krishnatry, Rahul and Bakshi, Ganesh and Prakash, Gagan and Pal, Mahendra and Menon, Santosh and Phurailatpam, Reena and Mokal, Smruti and Chaurasiya, Dipika and Popat, Palak and Sable, Nilesh and Agarwal, Archi and Rangarajan, Venkatesh and Joshi, Amit and Noronha, Vanita and Prabhash, Kumar and Mahantshetty, Umesh},
  year = {2021},
  month = jan,
  journal = {Journal of Clinical Oncology},
  pages = {JCO.20.03282},
  publisher = {{Wolters Kluwer}},
  issn = {0732-183X},
  doi = {10.1200/JCO.20.03282},
  urldate = {2021-02-08},
  abstract = {PURPOSEWe report the clinical outcomes of a randomized trial comparing prophylactic whole-pelvic nodal radiotherapy to prostate-only radiotherapy (PORT) in high-risk prostate cancer.METHODSThis phase III, single center, randomized controlled trial enrolled eligible patients undergoing radical radiotherapy for node-negative prostate adenocarcinoma, with estimated nodal risk {$\geq$} 20\%. Randomization was 1:1 to PORT (68 Gy/25\# to prostate) or whole-pelvic radiotherapy (WPRT, 68 Gy/25\# to prostate, 50 Gy/25\# to pelvic nodes, including common iliac) using computerized stratified block randomization, stratified by Gleason score, type of androgen deprivation, prostate-specific antigen at diagnosis, and prior transurethral resection of the prostate. All patients received image-guided, intensity-modulated radiotherapy and minimum 2 years of androgen deprivation therapy. The primary end point was 5-year biochemical failure-free survival (BFFS), and secondary end points were disease-free survival (DFS) and overall survival (OS).RESULTSFrom November 2011 to August 2017, a total of 224 patients were randomly assigned (PORT = 114, WPRT = 110). At a median follow-up of 68 months, 36 biochemical failures (PORT = 25, WPRT = 7) and 24 deaths (PORT = 13, WPRT = 11) were recorded. Five-year BFFS was 95.0\% (95\% CI, 88.4 to 97.9) with WPRT versus 81.2\% (95\% CI, 71.6 to 87.8) with PORT, with an unadjusted hazard ratio (HR) of 0.23 (95\% CI, 0.10 to 0.52; P {$<$} .0001). WPRT also showed higher 5-year DFS (89.5\% v 77.2\%; HR, 0.40; 95\% CI, 0.22 to 0.73; P = .002), but 5-year OS did not appear to differ (92.5\% v 90.8\%; HR, 0.92; 95\% CI, 0.41 to 2.05; P = .83). Distant metastasis-free survival was also higher with WPRT (95.9\% v 89.2\%; HR, 0.35; 95\% CI, 0.15 to 0.82; P = .01). Benefit in BFFS and DFS was maintained across prognostic subgroups.CONCLUSIONProphylactic pelvic irradiation for high-risk, locally advanced prostate cancer improved BFFS and DFS as compared with PORT, but OS did not appear to differ.}
}

@article{muzaffar_recent_2021,
  title = {Recent {{Advances}} and {{Future Directions}} in {{Clinical Management}} of {{Head}} and {{Neck Squamous Cell Carcinoma}}},
  author = {Muzaffar, Jameel and Bari, Shahla and Kirtane, Kedar and Chung, Christine H.},
  year = {2021},
  month = jan,
  journal = {Cancers},
  volume = {13},
  number = {2},
  pages = {338},
  issn = {2072-6694},
  doi = {10.3390/cancers13020338},
  urldate = {2022-09-24},
  abstract = {Simple Summary Even with recent advances, there are urgent needs for novel therapies to improve overall survival and decrease toxicities in the management of head and neck squamous cell carcinoma (HNSCC). This article reviews historical data to provide a context and highlights recent data in understanding of epidemiology and pathophysiology and supporting changes in treatments of HNSCC, particularly in patients with recurrent and/or metastatic disease. For use of immune checkpoint modulators such as programmed cell death protein 1 (PD-1) inhibitors, potential predictive biomarkers of clinical benefits are also summarized. In addition, this article reviews currently ongoing clinical trials and provides a perspective on future research directions. Abstract Head and neck squamous cell carcinoma (HNSCC) is the most common cancer arising in the head and neck region. The most common risk factors are smoking, excessive drinking, and human papillomavirus (HPV) infection. While the overall incidence of smoking is decreasing, the incidence of HPV-related HNSCC is increasing in the United States and Western Europe, which led to a shift in understanding of the pathophysiology, treatment, and prognosis of this disease. The outcomes for non-metastatic HNSCC remains very encouraging and continues to improve. Advances in radiation technology and techniques, better organ preserving surgical options, and multidisciplinary treatment modalities have improved cure rates for locally advanced HNSCC patients. The treatment of metastatic disease, however, remains an area of need. The advancement of immune checkpoint inhibitors has provided significantly better outcomes, but only a small proportion of patients obtain benefits. Most recurrent and/or metastatic HNSCC patients continue to have poor survival. This has led to the vigorous investigation of new biomarkers and biomarker-based therapies. Novel therapeutic options including adaptive cellular therapy and therapeutic vaccines are also on the horizon. In this review, we highlight the latest advances in the field of HNSCC and the future direction of research.},
  pmcid = {PMC7831487},
  pmid = {33477635},
  file = {C:\Users\roman\OneDrive\Documents\Library\Muzaffar et al_2021_Recent Advances and Future Directions in Clinical Management of Head and Neck.pdf}
}

@article{nelson_run_2013,
  title = {{{RUN DMC}}: {{AN EFFICIENT}}, {{PARALLEL CODE FOR ANALYZING RADIAL VELOCITY OBSERVATIONS USING}} {{{\emph{N}}}} -{{BODY INTEGRATIONS AND DIFFERENTIAL EVOLUTION MARKOV CHAIN MONTE CARLO}}},
  shorttitle = {{{RUN DMC}}},
  author = {Nelson, Benjamin and Ford, Eric B. and Payne, Matthew J.},
  year = {2013},
  month = dec,
  journal = {The Astrophysical Journal Supplement Series},
  volume = {210},
  number = {1},
  pages = {11},
  issn = {0067-0049, 1538-4365},
  doi = {10.1088/0067-0049/210/1/11},
  urldate = {2022-09-02},
  abstract = {In the 20+ years of Doppler observations of stars, scientists have uncovered a diverse population of extrasolar multi-planet systems. A common technique for characterizing the orbital elements of these planets is the Markov Chain Monte Carlo (MCMC), using a Keplerian model with random walk proposals and paired with the Metropolis{\textendash}Hastings algorithm. For approximately a couple of dozen planetary systems with Doppler observations, there are strong planet{\textendash}planet interactions due to the system being in or near a mean-motion resonance (MMR). An N-body model is often required to accurately describe these systems. Further computational difficulties arise from exploring a high-dimensional parameter space ({$\sim$}7 {\texttimes} number of planets) that can have complex parameter correlations, particularly for systems near a MMR. To surmount these challenges, we introduce a differential evolution MCMC (DEMCMC) algorithm applied to radial velocity data while incorporating self-consistent N-body integrations. Our Radial velocity Using N-body DEMCMC (RUN DMC) algorithm improves upon the random walk proposal distribution of the traditional MCMC by using an ensemble of Markov chains to adaptively improve the proposal distribution. RUN DMC can sample more efficiently from high-dimensional parameter spaces that have strong correlations between model parameters. We describe the methodology behind the algorithm, along with results of tests for accuracy and performance. We find that most algorithm parameters have a modest effect on the rate of convergence. However, the size of the ensemble can have a strong effect on performance. We show that the optimal choice depends on the number of planets in a system, as well as the computer architecture used and the resulting extent of parallelization. While the exact choices of optimal algorithm parameters will inevitably vary due to the details of individual planetary systems (e.g., number of planets, number of observations, orbital periods, and signal-to-noise of each planet), we offer recommendations for choosing the DEMCMC algorithm's algorithmic parameters that result in excellent performance for a wide variety of planetary systems.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Nelson et al_2013_RUN DMC.pdf}
}

@book{nielsen_bayesian_2009,
  title = {Bayesian {{Networks}} and {{Decision Graphs}}},
  author = {Nielsen, T D and Jensen, F V},
  year = {2009},
  publisher = {{Springer}}
}

@misc{noauthor_creating_nodate,
  title = {Creating {{Models}}},
  journal = {Django documentation},
  urldate = {2022-09-29},
  howpublished = {https://docs.djangoproject.com/en/4.1/intro/tutorial02/\#creating-models},
  file = {C:\Users\roman\Zotero\storage\XP7BNRFV\creating_models.html}
}

@misc{noauthor_data_2022,
  title = {Data {{Version Control}}},
  shorttitle = {{{DVC}}},
  year = {2022},
  month = oct,
  address = {{San Francisco}},
  copyright = {Apache-2.0},
  howpublished = {Iterative, Inc}
}

@misc{noauthor_django_2022,
  title = {Django},
  year = {2022},
  address = {{Lawrence, Kansas}},
  howpublished = {Django Software Foundation}
}

@misc{noauthor_final_nodate,
  title = {Final {{Report Summary}} - {{ARTFORCE}} ({{Adaptive}} and Innovative {{Radiation Treatment FOR}} Improving {{Cancer}} Patients Treatment {{outcomE}}) | {{FP7}} | {{CORDIS}} | {{European Commission}}},
  urldate = {2023-02-10},
  howpublished = {https://cordis.europa.eu/project/id/257144/reporting},
  file = {C:\Users\roman\Zotero\storage\2RGEBTMJ\reporting.html}
}

@misc{noauthor_font_2022,
  title = {Font {{Awesome Free}}},
  year = {2022},
  address = {{Delaware}},
  copyright = {CC BY 4.0},
  howpublished = {Fonticons, Inc.}
}

@book{noauthor_generatingfunctionology_1994,
  title = {Generatingfunctionology},
  year = {1994},
  edition = {2nd ed},
  publisher = {{Academic Press}},
  address = {{Boston}},
  abstract = {This is the Second Edition of the highly successful introduction to the use of generating functions and series in combinatorial mathematics. This new edition includes several new areas of application, including the cycle index of the symmetric group, permutations and square roots, counting polyominoes, and exact covering sequences. An appendix on using the computer algebra programs MAPLE(r) and Mathematica(r) to generate functions is also included. The book provides a clear, unified introduction to the basic enumerative applications of generating functions, and includes exercises and solutions, many new, at the end of each chapter},
  isbn = {978-0-08-057151-5},
  langid = {english},
  lccn = {515.55},
  file = {C:\Users\roman\OneDrive\Documents\Library\1994_Generatingfunctionology.pdf}
}

@article{noauthor_guidelines_2000,
  title = {{{GUIDELINES FOR ICDO-3 IMPLEMENTATION}}},
  year = {2000},
  pages = {53},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\2000_GUIDELINES FOR ICDO-3 IMPLEMENTATION.pdf}
}

@misc{noauthor_inkscape_2022,
  title = {Inkscape},
  year = {2022},
  copyright = {GPL-2.0},
  howpublished = {The Inkscape Project}
}

@article{norwood_ranking_2004,
  title = {Ranking {{Crop Yield Models Using Out-of-Sample Likelihood Functions}}},
  author = {Norwood, Bailey and Roberts, Matthew C. and Lusk, Jayson L.},
  year = {2004},
  journal = {American Journal of Agricultural Economics},
  volume = {86},
  number = {4},
  eprint = {4492790},
  eprinttype = {jstor},
  pages = {1032--1043},
  publisher = {{[Agricultural \& Applied Economics Association, Oxford University Press]}},
  issn = {0002-9092},
  urldate = {2021-09-23},
  abstract = {There has been considerable debate regarding which probability distribution best represents crop yields. This study ranks six yield densities based on their out-of-sample forecasting performance. The forecasting ability for each density was ranked according to its likelihood function value when observed at out-of-sample observations. Results show that a semiparametric model offered by Goodwin and Ker best forecasts county average yields.},
  keywords = {likelihood,model validation},
  file = {C:\Users\roman\OneDrive\Documents\Library\Norwood et al_2004_Ranking Crop Yield Models Using Out-of-Sample Likelihood Functions.pdf}
}

@article{nuraini_tumor_2019,
  title = {Tumor {{Control Probability}} ({{TCP}}) and {{Normal Tissue Complication Probability}} ({{NTCP}}) with {{Consideration}} of {{Cell Biological Effect}}},
  author = {Nuraini, Rany and Widita, Rena},
  year = {2019},
  month = aug,
  journal = {Journal of Physics: Conference Series},
  volume = {1245},
  pages = {012092},
  doi = {10.1088/1742-6596/1245/1/012092},
  abstract = {In radiotherapy, Tumor Control Probability (TCP) is a parameter used to calculate the percentage of tumor killing, while its effect on normal tissue damage describe by Normal Tissue Complication Probability (NTCP). Both TCP and NTCP depend on fractionation and cell biological effects such as repopulation, repair, redistribution and re-oxygenation. It also depends on the statistical distribution model used. One model that can review the biological effects of cells is the Poisson model. In this research, we modified the Poisson model by considering the four biological effects mentioned above on TCP and only the effect of repair on NTCP. The objective of this research is to investigate the most dominant effect that influences TCP value and the effect of repair on NTCP. The results show that the effect of repair and repopulation cause tumor cells cannot be erased completely while the effects of resenitization (re-oxygenation and redistribution) can facilitate tumor cells to die. It can be seen that the most dominant biological effect is the repair effect on the tumor. This effect can be minimized by reducing the length of dose delivery time. Furthermore, the repair effect on normal tissue can reduce the value of NTCP about 9\% compared with other models. By using the ISO-NTCP curve we also get the spinal cord repair time after 15 hours.},
  file = {C:\Users\roman\OneDrive\Documents\Library\Nuraini_Widita_2019_Tumor Control Probability (TCP) and Normal Tissue Complication Probability.pdf}
}

@article{ohtani_structure_2008,
  title = {Structure and Function of Rat Lymph Nodes},
  author = {Ohtani, Osamu and Ohtani, Yuko},
  year = {2008},
  journal = {Archives of Histology and Cytology},
  volume = {71},
  number = {2},
  pages = {69--76},
  issn = {0914-9465, 1349-1717},
  doi = {10.1679/aohc.71.69},
  urldate = {2022-10-10},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Ohtani_Ohtani_2008_Structure and function of rat lymph nodes.pdf}
}

@article{oliver_rediscovery_2002,
  title = {The Rediscovery of the Lymphatic System: Old and New Insights into the Development and Biological Function of the Lymphatic Vasculature},
  shorttitle = {The Rediscovery of the Lymphatic System},
  author = {Oliver, Guillermo and Detmar, Michael},
  year = {2002},
  month = jan,
  journal = {Genes \& Development},
  volume = {16},
  number = {7},
  pages = {773--783},
  publisher = {{Cold Spring Harbor Lab}},
  issn = {0890-9369, 1549-5477},
  doi = {10.1101/gad.975002},
  urldate = {2022-10-07},
  abstract = {A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields},
  langid = {english},
  pmid = {11937485},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Oliver_Detmar_2002_The rediscovery of the lymphatic system.pdf;C\:\\Users\\roman\\Zotero\\storage\\HNBQFANP\\773.html}
}

@article{osullivan_benefits_2001,
  title = {The Benefits and Pitfalls of Ipsilateral Radiotherapy in Carcinoma of the Tonsillar Region},
  author = {O'Sullivan, B. and Warde, P. and Grice, B. and Goh, C. and Payne, D. and Liu, F.-F. and Waldron, J. and Bayley, A. and Irish, J. and Gullane, P. and Cummings, B.},
  year = {2001},
  month = oct,
  journal = {International Journal of Radiation Oncology, Biology, Physics},
  volume = {51},
  number = {2},
  pages = {332--343},
  publisher = {{Elsevier}},
  issn = {0360-3016},
  doi = {10.1016/S0360-3016(01)01613-3},
  urldate = {2022-07-05},
  langid = {english},
  pmid = {11567806},
  keywords = {Contralateral failure,Lymph nodes,Radiation therapy,Tonsillar carcinoma},
  file = {C:\Users\roman\Zotero\storage\J4S4CMSL\fulltext.html}
}

@misc{ottinger_rules_1997,
  title = {Rules for {{Variable}} and {{Class Naming}}},
  author = {Ottinger, Tim},
  year = {1997},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Ottinger_1997_Rules for Variable and Class Naming.pdf}
}

@article{overgaard_improving_2017,
  title = {Improving Radiotherapy of Squamous Cell Carcinoma of the Head and Neck ({{HNSCC}}) through a Continuous Process of Biological Based Clinical Trials{\textemdash}a 40-Year Experience from the {{Danish Head}} and {{Neck Cancer Group}}{\textemdash}{{DAHANCA}}},
  author = {Overgaard, J},
  year = {2017},
  journal = {Eur. J. Cancer},
  volume = {72},
  pages = {S102},
  doi = {10.1016/S0959-8049(17)30416-1}
}

@article{padgett_feasibility_2018,
  title = {Feasibility of {{Adaptive MR-guided Stereotactic Body Radiotherapy}} ({{SBRT}}) of {{Lung Tumors}}},
  author = {Padgett, Kyle R and Simpson, Garrett N and Llorente, Ricardo and Samuels, Michael A and Dogan, Nesrin},
  year = {2018},
  month = apr,
  journal = {Cureus},
  issn = {2168-8184},
  doi = {10.7759/cureus.2423},
  urldate = {2022-02-07},
  abstract = {Online adaptive radiotherapy (ART) with frequent imaging has the potential to improve dosimetric accuracy by accounting for anatomical and functional changes during the course of radiotherapy. Presented are three interesting cases that provide an assessment of online adaptive magnetic resonance-guided radiotherapy (MRgRT) for lung stereotactic body radiotherapy (SBRT).},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Padgett et al_2018_Feasibility of Adaptive MR-guided Stereotactic Body Radiotherapy (SBRT) of Lung.pdf}
}

@article{park_diagnostic_2020,
  title = {Diagnostic {{Accuracy}} and {{Confidence}} of [{{18F}}] {{FDG PET}}/{{MRI}} in Comparison with {{PET}} or {{MRI}} Alone in {{Head}} and {{Neck Cancer}}},
  author = {Park, Jisang and Pak, Kyoungjune and Yun, Tae Jin and Lee, Eun Kyoung and Ryoo, Inseon and Lee, Ji Ye and Hwang, Inpyeong and Yoo, Roh-Eul and Kang, Koung Mi and Choi, Seung Hong and Sohn, Chul-Ho and Cheon, Gi Jeong and Kim, Ji-hoon},
  year = {2020},
  month = jun,
  journal = {Scientific Reports},
  volume = {10},
  number = {1},
  pages = {9490},
  publisher = {{Nature Publishing Group}},
  issn = {2045-2322},
  doi = {10.1038/s41598-020-66506-8},
  urldate = {2022-07-01},
  abstract = {The usefulness of PET/MRI in head and neck malignancy has not been fully elucidated. The purpose of our study was to evaluate the diagnostic accuracy and confidence of PET/MRI in comparison with PET or MRI alone. This study included 73 consecutive patients who underwent [18F] FDG PET/MRI in head and neck under the suspicion of malignancy. A neuroradiologist and a nuclear medicine specialist reviewed MRI and PET images, respectively and independently, followed by a consensus review of PET/MRI one month later. For 134 lesions, accuracy and confidence were compared among PET, MRI, and PET/MRI. For lesion base, PET/MRI had a sensitivity of 85.7\%, a specificity of 89.1\%, a PPV of 89.6\%, a negative predictive value of 85.1\%, and an accuracy of 87.3\%. AUCs of PET/MRI per lesion (0.926) and per patient (0.934) for diagnosing malignancy were higher than PET (0.847 and 0.747, respectively) or MRI (0.836 and 0.798, respectively) alone (P\,{$<$}\,0.05). More than 80\% of the cases (111/134) showed diagnostic concordance between PET and MRI. PPV of PET/MRI was higher in malignant concordant cases (93.2\%, 55/59) than in discordant cases (62.5\%, 5/8) (p\,=\,0.040). Confident scoring rate in malignant concordant cases was higher on PET/MRI (96.6\%, 57/59) than on MRI (76.3\%, 45/59) (p\,=\,0.003). In conclusion, compared with PET or MRI alone, PET/MRI presents better diagnostic performance in accuracy and confidence for diagnosis of malignancy. PET/MRI is useful in patients with head and neck cancer.},
  copyright = {2020 The Author(s)},
  langid = {english},
  keywords = {Cancer imaging,Head and neck cancer,Oral cancer detection},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Park et al_2020_Diagnostic Accuracy and Confidence of [18F] FDG PET-MRI in comparison with PET.pdf;C\:\\Users\\roman\\Zotero\\storage\\5BNC68QF\\s41598-020-66506-8.html}
}

@book{pearl_probabilistic_1988,
  title = {Probabilistic {{Inference}} in {{Intelligent Systems}}},
  author = {Pearl, J},
  year = {1988},
  publisher = {{Morgan Kaufmann}}
}

@article{peltanova_effect_2019,
  title = {Effect of Tumor Microenvironment on Pathogenesis of the Head and Neck Squamous Cell Carcinoma: A Systematic Review},
  shorttitle = {Effect of Tumor Microenvironment on Pathogenesis of the Head and Neck Squamous Cell Carcinoma},
  author = {Peltanova, Barbora and Raudenska, Martina and Masarik, Michal},
  year = {2019},
  month = mar,
  journal = {Molecular Cancer},
  volume = {18},
  pages = {63},
  issn = {1476-4598},
  doi = {10.1186/s12943-019-0983-5},
  urldate = {2022-10-07},
  abstract = {The tumor microenvironment (TME) is comprised of many different cell populations, such as cancer-associated fibroblasts and various infiltrating immune cells, and non-cell components of extracellular matrix. These crucial parts of the surrounding stroma can function as both positive and negative regulators of all hallmarks of cancer development, including evasion of apoptosis, induction of angiogenesis, deregulation of the energy metabolism, resistance to the immune detection and destruction, and activation of invasion and metastasis. This review represents a summary of recent studies focusing on describing these effects of microenvironment on initiation and progression of the head and neck squamous cell carcinoma, focusing on oral squamous cell carcinoma, since it is becoming clear that an investigation of differences in stromal composition of the head and neck squamous cell carcinoma microenvironment and their impact on cancer development and progression may help better understand the mechanisms behind different responses to therapy and help define possible targets for clinical intervention.},
  pmcid = {PMC6441173},
  pmid = {30927923},
  file = {C:\Users\roman\OneDrive\Documents\Library\Peltanova et al_2019_Effect of tumor microenvironment on pathogenesis of the head and neck squamous.pdf}
}

@inproceedings{perez_haas_adaptive_2021,
  title = {Adaptive Fractionation at the {{MR-Linac}}},
  booktitle = {{{SASRO}}},
  author = {P{\'e}rez Haas, Yoel and Ludwig, Roman and Dal Bello, Riccardo and {Tanadini-Lang}, Stephanie and Unkelbach, Jan},
  year = {2021},
  month = sep,
  address = {{Rorschach, Switzerland}}
}

@unpublished{perez_haas_adaptive_2022,
  title = {Adaptive {{Fractionation}} at the {{MR-Linac}}},
  author = {P{\'e}rez Haas, Yoel and Ludwig, Roman and Dal Bello, Riccardo and {Tanadini-Lang}, Stephanie and Unkelbach, Jan},
  year = {2022},
  month = apr,
  address = {{Zurich, Switzerland}},
  abstract = {Objective: Inter-fraction motion of tumors and OARs can be visualized using MR-guidance. Whereas standard treatments aim to deliver the same dose in each fraction, adaptive fractionation (AF) is an approach to exploit inter-fraction motion by increasing the dose on days when the distance of tumor and OAR is large and decreasing the dose on unfavorable days. We develop an algorithm for AF and evaluate the concept for patients with abdominal tumors previously treated on the MR-Linac in 5 fractions. Approach: Given daily adapted treatment plans, inter-fractional changes are quantified by sparing factors \${\textbackslash}delta\_t\$. The key problem of AF is to decide on the dose to deliver in fraction \$t\$, given \${\textbackslash}delta\_t\$ and the dose delivered in previous fractions, but with unknown future sparing factors. Optimal doses are computed with a dynamic programming algorithm that assumes a normal distribution over \${\textbackslash}delta\$ with mean and variance estimated from previously observed patient-specific \${\textbackslash}delta\_t\$s. The computed doses maximize the expected tumor BED\$\_\{10\}\$ while staying below a maximum BED\$\_3\$ in the OAR. To evaluate the algorithm, 16 MR-Linac patients were retrospectively analyzed in whom tumor dose was compromised due to proximity of bowel, stomach, or duodenum. AF was compared to a reference treatment which delivers 6 Gy to the OAR in each fraction to reach exactly the 90 Gy BED\$\_3\$ constraint. Main Results: In 14 out of the 16 patients, AF increased the tumor BED\$\_\{10\}\$ compared to the reference treatment. However, in 11 of these 14 patients, the increase in BED\$\_\{10\}\$ was below 1 Gy, while two patients had an increase of more than 10 Gy BED\$\_\{10\}\$. One patient with an inferior plan had a decrease of 5.2 BED\$\_\{10\}\$. All extreme results were associated with large sparing factor variation. Significance: On average, AF provided only a small increase in tumor BED. However, AF may yield substantial benefits for individual patients with large variations in the geometry.},
  langid = {english}
}

@inproceedings{perez_haas_adaptive_2022-1,
  title = {Adaptive Fractionation at the {{MR-Linac}} Based on a Dynamic Programming Approach},
  booktitle = {{{ESTRO}}},
  author = {P{\'e}rez Haas, Yoel and Ludwig, Roman and Dal Bello, Riccardo and Wenhong, Lan and {Tanadini-Lang}, Stephanie and Unkelbach, Jan},
  year = {2022},
  pages = {836},
  address = {{Copenhagen}},
  urldate = {2022-10-25},
  abstract = {Purpose or Objective: Inter-fraction motion of tumors and dose-limiting OARs can be visualized using MR guidance. Whereas standard treatments deliver the same dose in each fraction, adaptive fractionation (AF) is an approach to exploit inter-fraction motion by increasing the dose on days when the distance of tumor and OAR is large and decreasing the dose on unfavorable days. We develop an algorithm for AF and evaluate the concept for former patients treated at the MR-Linac for abdominal tumors in 5 fractions. Materials and Methods: Given daily MR scans and adaptive treatment plans, inter-fractional changes in fraction t are quantified by sparing factors {$\delta$}t, which are defined as the ratio of dose delivered to the OAR (D1cc) and the tumor (D95\%). The key problem of AF is to decide on the dose to deliver in fraction t, given today's {$\delta$} and the dose delivered in previous fractions, but with unknown future {$\delta$}s. This problem can be formulated as a Markov decision problem and solved with a dynamic programming algorithm. The algorithm assumes a normal distribution over {$\delta$} with mean and variance estimated from previously observed patient specific {$\delta$}s and a population based prior for the variance. Based on the distribution, the algorithm computes optimal doses that maximize the expected tumor BED10 while staying below the maximum BED3 of 90 Gy in the OAR (30 Gy in 5 fractions). To evaluate the algorithm, 10 MR-Linac patients were exported in whom tumor dose was compromised due to proximity of bowel, stomach, duodenum or heart. Moreover, 1000 synthetic patients with similar {$\delta$} distribution have been sampled. AF was compared to a standard plan which delivers 6 Gy to the OAR in each fraction to reach exactly the 90 Gy BED3 constraint. Results: In 7 of the 10 patients, AF was equal or increased the tumor BED10, on average by 0.72 Gy (1.2\%). Figure 1 shows the 's and the respective doses based on AF for all patients. The biggest increase of 13.1 Gy (18.4\%) was achieved for patient 2 with {$\delta$}=[0.88,0.8,0.58,0.86,0.77] where AF delivered tumor doses of [4.4,8.7,17,0.9,2.1] and thereby exploited the low {$\delta$} in fraction 3. Figure 2a) illustrates the optimal policy for fraction 3, i.e. optimal dose to deliver as a function of {$\delta$}. For the 1000 generated patients, 84.1\% of plans were equal or superior to the standard plan with a mean improvement of 1.01 Gy (1.5\%) BED10. A distribution of the differences is shown in Figure 2b). With the most extreme plans having a benefit of up to 12 Gy BED10. Conclusion: On average, AF provided only a small increase in tumor BED. However, AF may yield substantial benefits for individual patients with large variations in the geometry.}
}

@article{pfister_head_2014,
  title = {Head and {{Neck Cancers}}, {{Version}} 2.2014},
  author = {Pfister, David G. and Spencer, Sharon and Brizel, David M. and Burtness, Barbara and Busse, Paul M. and Caudell, Jimmy J. and Cmelak, Anthony J. and Colevas, A. Dimitrios and Dunphy, Frank and Eisele, David W. and Gilbert, Jill and Gillison, Maura L. and Haddad, Robert I. and Haughey, Bruce H. and Hicks, Wesley L. and Hitchcock, Ying J. and Jimeno, Antonio and Kies, Merrill S. and Lydiatt, William M. and Maghami, Ellie and Martins, Renato and McCaffrey, Thomas and Mell, Loren K. and Mittal, Bharat B. and Pinto, Harlan A. and Ridge, John A. and Rodriguez, Cristina P. and Samant, Sandeep and Schuller, David E. and Shah, Jatin P. and Weber, Randal S. and Wolf, Gregory T. and Worden, Frank and Yom, Sue S. and McMillian, Nicole R. and Hughes, Miranda},
  year = {2014},
  month = oct,
  journal = {Journal of the National Comprehensive Cancer Network},
  volume = {12},
  number = {10},
  pages = {1454--1487},
  publisher = {{Harborside Press, LLC}},
  issn = {1540-1405, 1540-1413},
  doi = {10.6004/jnccn.2014.0142},
  urldate = {2022-09-24},
  abstract = {This selection from the NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Head and Neck Cancers focuses on glottic laryngeal cancer, which is the most common type of laryngeal cancer and has an excellent cure rate. The lymphatic drainage of the glottis is sparse, and early stage primaries rarely spread to regional nodes. Because hoarseness is an early symptom, most glottic laryngeal cancer is early stage at diagnosis. Updates to these guidelines for 2014 include revisions to ``Principles of Radiation Therapy'' for each site and ``Principles of Surgery,'' and the addition of a new section on ``Principles of Dental Evaluation and Management.''},
  chapter = {Journal of the National Comprehensive Cancer Network},
  langid = {american},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Pfister et al_2014_Head and Neck Cancers, Version 2.pdf;C\:\\Users\\roman\\Zotero\\storage\\9JU445E5\\article-p1454.html}
}

@article{pillsbury_iii_rationale_1997,
  title = {A {{Rationale}} for {{Therapy}} of the {{N0 Neck}}},
  author = {Pillsbury III, Harold C. and Clark, Madison},
  year = {1997},
  journal = {The Laryngoscope},
  volume = {107},
  number = {10},
  pages = {1294--1315},
  issn = {1531-4995},
  doi = {10.1097/00005537-199710000-00004},
  urldate = {2022-10-11},
  langid = {english},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Pillsbury III_Clark_1997_A Rationale for Therapy of the N0 Neck.pdf;C\:\\Users\\roman\\Zotero\\storage\\FWE4ZX58\\00005537-199710000-00004.html}
}

@article{pitman_rationale_2000,
  title = {Rationale for Elective Neck Dissection},
  author = {Pitman, Karen T.},
  year = {2000},
  month = jan,
  journal = {American Journal of Otolaryngology},
  volume = {21},
  number = {1},
  pages = {31--37},
  issn = {0196-0709},
  doi = {10.1016/S0196-0709(00)80121-0},
  urldate = {2022-10-11},
  abstract = {The objective of this study was to investigate the correlation between magnetic resonance imaging (MRI) characteristics of cervical lymph nodes and the pathologically confirmed status of cervical lymph node metastasis (LNM) in oral squamous cell carcinoma (OSCC) and to provide imaging evaluation parameters for the clinical diagnosis of cervical lymph node status in OSCC. In a retrospective analysis, 79 patients who were first pathologically diagnosed with OSCC were included. The MRI-derived imaging parameters of the cervical lymph nodes were evaluated and the pathological status of lymph nodes in neck dissection specimens was reviewed. The relationship between the imaging parameters and cervical LNM was analyzed. The MRI-derived imaging parameters of 4419 lymph nodes were evaluated, and the pathological status of 2463 lymph nodes was reviewed. The MRI-derived shortest axial diameter (SAD) and unclear boundary of the cervical lymph node were significantly related to LNM. The cutoff value of SAD that enabled identification of LNM was 3.6 mm, and it was 4.2 and 4.1 mm for the prediction of overall survival and disease-specific survival, respectively. The MRI-derived parameters SAD and unclear boundary of the cervical lymph node correlated with LNM in OSCC. MRI-derived SAD larger than 3 mm warrants simultaneous neck dissection at initial surgery. To explore the effects of elective neck irradiation (ENI) in clinically node-negative (cN0) sinonasal adenoid cystic carcinoma (SNACC). Between January 2000 and December 2016, 60 patients with cN0 sinonasal adenoid cystic carcinoma receiving surgery combined with radiotherapy were analyzed retrospectively, there were 39 received ENI (ENI group) and 21 with no ENI (non-ENI group). Propensity score matching (PSM) was performed to balance clinical factors and match patients. Kaplan-Meier method and Cox proportional hazard model were used to evaluate the impact of ENI on regional relapse risk and survival outcomes. The median follow-up time for our cohort was 82.0 months (12.4{\textendash}190.7 months). Four patients (6.7\%) developed neck nodal relapses, with a median time to progression of 38.8 months. Among them, two patients in ENI group but failed out-field. After PSM, 21 patients were matched in each group. The 7-year regional relapse-free survival (RRFS), distant metastasis free survival (DMFS), progression-free survival (PFS), and overall survival (OS) between ENI group and non-ENI group were 85.4\% vs 73.3\% (p = 0.845), 65.2\% vs 65.6\% (p = 0.548), 68.3\% vs 66.2\% (p = 0.425), and 87.3\% vs 84.0\% (p = 0.953). Multivariate Cox analysis showed ENI was not an independent prognostic factor associated with RRFS, DMFS, PFS and OS. Our findings firstly demonstrated the omission of elective neck irradiation in the management of cN0 sinonasal adenoid cystic carcinoma might be safe without compromising disease control and should be further investigated. We evaluated the relationships between depth of invasion (DOI) of tongue cancer, as measured with preoperative T1- and T2-weighted magnetic resonance imaging (MRI) and postoperative histopathologic (Path) specimens, with cervical lymph node metastasis (CLNM) and tumor stage. We also calculated the correlation of MRI and Path DOI measurements. This retrospective study included 101 patients who had squamous cell carcinoma of the tongue and were treated surgically. Two observers measured DOI on all 3 modalities. DOI thresholds for predicting CLNM with high diagnostic efficacy were 6.99 mm and 8.32 mm for MRI and 5 mm for Path. DOI values from all modalities were significantly different for tumors with and without CLNM (P {$<$} .01) and for the 4 TNM stages (P {$\leq$} .05), with increasing values corresponding to advancement in tumor stage. Addition of DOI changed the T level of many tumors based on the new TNM (tumor{\textendash}node{\textendash}metastasis) classification. The correlation coefficient between DOI calculated on each MRI sequence and Path was 0.90. MRI-derived DOI accurately reflected the subsequent metastatic status and degree of progression of tumor stages, with a strong positive correlation to Path values, and may be considered a predictor of tumor stage and CLNM. Elective neck dissection (END) versus observation remains controversial for cT1N0M0 oral cavity squamous cell carcinoma (OSCC). The aim of this study was to determine whether neck dissection is indicated for cT1N0M0 OSCC versus observation when considering oral cavity subsites and depth of invasion (DOI) as predictors. A multicenter, ambispective cohort study of patients with cT1N0M0 OSCC treated at the University of Michigan and Beijing Stomatological Hospital from August 1998 to July 2017 with a follow-up end date of July 2019 was performed. Patients were excluded if follow-up was less than 2 years and no neck disease had occurred or if the final pathologic analysis resulted in upstaging to T2 using American Joint Committee on Cancer criteria, eighth edition. A total of 283 patients met the criteria. The main outcome parameter was the 2-year neck metastatic rate. The total 2-year lymph node metastatic rate was 11.3\%. Overall neck metastatic rates escalated consistently according to DOI: less than 2 mm, 2.1\%; 2 to 3 mm, 9.4\%; 3 to 4 mm, 15.2\%; and 4 to 5 mm, 24.6\%. On univariate Cox regression analysis, DOI greater than 3 mm, tumor grade, and perineural invasion were statistically significant indicators of 2-year neck metastasis. On multivariate analysis, only DOI and tumor grade remained. On multivariate analysis of 2-year survival, no factors were independent predictors. Our proposed treatment strategy for END based both on statistically significant results for DOI and on review of the raw data using a 20\% cutoff analysis showed cutoffs of 2 mm for the tongue (18.2\%), 3 mm for the floor of the mouth (40.0\%) and upper gingiva (20\%), and 4 mm for the lower gingiva (33.3\%) and no cutoff for the hard palate (0.0\%). The watch-and-wait approach remains a reasonable approach in selected patients with cT1N0M0 OSCC. Decision making for END in T1N0M0 patients should minimally consider tumor grade, DOI, and oral cavity subsite. To determine the effects of nodal yield on survival in early stage oral cavity squamous cell carcinoma (OCSCC) in the context of primary tumor depth of invasion (DOI). Patients with early-stage clinically node-negative OCSCC who underwent upfront surgery at the primary site were identified using the National Cancer Database between 2004 and 2015. There were 3384 patients with {$<$}4 mm DOI and 1387 patients with {$\geq$}4 mm DOI identified. Management of the neck included observation (40\%), END with {$<$}18 nodes harvested {$\pm$} postoperative radiation (ND {$<$} 18, 16\%), and END with {$\geq$}18 nodes harvest {$\pm$} postoperative radiation (ND {$\geq$} 18, 44\%). When adjusted for relevant covariates, ND {$\geq$} 18 demonstrated statistically significant improvements in overall survival for both DOI {$<$} 4 mm and {$\geq$}4 mm (DOI {$<$} 4 mm: HR 0.67, 95\%CI 0.54{\textendash}0.85; DOI {$\geq$} 4 mm: HR 0.47, 95\%CI 0.34{\textendash}0.64). However, ND {$<$} 18 showed no significant difference from observation of the neck regardless of DOI (DOI {$<$} 4 mm: HR 0.82, 95\%CI 0.63{\textendash}1.07; DOI {$\geq$} 4 mm: HR 0.72, 95\%CI 0.51{\textendash}1.03). Of patients undergoing END, the most significant factors associated with obtaining a nodal yield of 18 or more were age less than 40 years (HR 2.58, 95\%CI 1.84{\textendash}3.63) and treatment at an academic facility (HR 2.47, 95\%CI 2.06{\textendash}2.96). END with 18 or more nodes is associated with improved survival outcomes in patients with early stage OCSCC regardless of DOI. END with less than 18 nodes, however, does not appear significantly different than observation of the neck alone. Achieving a lymph node yield of 18 or more is multifactorial and includes both patient and provider factors. In 1994 a decision analysis, based on the literature and utility ratings for outcome by a panel of experienced head and neck physicians, was presented which showed a threshold probability of occult metastases of 20\% to recommend elective treatment of the neck. It was stated that recommendations for the management of the cN0 neck are not immutable and should be reconfigured to determine the optimal management based on different sets of underlying assumptions. Although much has changed and is published in the almost 25 years after its publication, up to date this figure is still mentioned in the context of decisions on treatment of the clinically negative (cN0) neck. Therefore, we critically reviewed the developments in diagnostics and therapy and modeling approaches in the context of decisions on treatment of the cN0 neck. However, the results of studies on treatment of the cN0 neck cannot be translated to other settings due to significant differences in relevant variables such as population, culture, diagnostic work-up, follow-up, costs, institutional preferences and other factors. Moreover, patients may have personal preferences and may weigh oncologic outcomes versus morbidity and quality of life differently. Therefore, instead of trying to establish ``the'' best strategy for the cN0 neck or ``the'' optimal cut-off point for elective neck treatment, the approach to optimize the management of the cN0 neck would be to develop and implement models and decision support systems that can serve to optimize choices depending on individual, institutional, population and other relevant variables.},
  langid = {english},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Pitman_2000_Rationale for elective neck dissection.pdf;C\:\\Users\\roman\\Zotero\\storage\\XGM7H789\\S0196070900801210.html}
}

@article{poortmans_internal_2020,
  title = {Internal Mammary and Medial Supraclavicular Lymph Node Chain Irradiation in Stage {{I}}{\textendash}{{III}} Breast Cancer ({{EORTC}} 22922/10925): 15-Year Results of a Randomised, Phase 3 Trial},
  author = {Poortmans, Philip M and Weltens, Caroline and Fortpied, Catherine and Kirkove, Carine and {Peignaux-Casasnovas}, Karine and Budach, Volker and {van der Leij}, Femke and Vonk, Ernest and Weidner, Nicola and Rivera, Sofia and {van Tienhoven}, Geertjan and Fourquet, Alain and Noel, Georges and Valli, Mariacarla and Guckenberger, Matthias and Koiter, Eveline and Racadot, Severine and {Abdah-Bortnyak}, Roxolyana and Van Limbergen, Erik F and Engelen, Antoine and De Brouwer, Peter and Struikmans, Henk and Bartelink, Harry},
  year = {2020},
  month = dec,
  journal = {The Lancet Oncology},
  volume = {21},
  number = {12},
  pages = {1602--1610},
  publisher = {{Elsevier}},
  issn = {1470-2045},
  doi = {10.1016/S1470-2045(20)30472-1},
  urldate = {2021-02-08}
}

@book{pourret_bayesian_2005,
  title = {Bayesian {{Networks}}: A {{Practical Guide}} to {{Applications}}},
  author = {Pourret, O and Na{\"i}m, P and Marcot, B},
  year = {2005},
  publisher = {{Wiley}}
}

@article{pouymayou_analysis_2019,
  title = {Analysis of Lymphatic Metastasis and Progression Patterns for Clinical Target Volume ({{CTV}}) Definition in Head and Neck Squamous Cell Carcinoma ({{HNSCC}})},
  author = {Pouymayou, B. and Koechli, C. and Balermpas, P. and Guckenberger, M. and Unkelbach, J.},
  year = {2019},
  month = oct,
  journal = {Acta Oncologica},
  volume = {58},
  number = {10},
  pages = {1519--1522},
  publisher = {{Taylor \& Francis}},
  issn = {0284-186X},
  doi = {10.1080/0284186X.2019.1643919},
  urldate = {2022-10-14},
  pmid = {31364898},
  file = {C:\Users\roman\OneDrive\Documents\Library\Pouymayou et al_2019_Analysis of lymphatic metastasis and progression patterns for clinical target.pdf}
}

@article{pouymayou_bayesian_2019,
  title = {A {{Bayesian}} Network Model of Lymphatic Tumor Progression for Personalized Elective {{CTV}} Definition in Head and Neck Cancers},
  author = {Pouymayou, Bertrand and Balermpas, Panagiotis and Riesterer, Oliver and Guckenberger, Matthias and Unkelbach, Jan},
  year = {2019},
  month = aug,
  journal = {Physics in Medicine \& Biology},
  volume = {64},
  number = {16},
  pages = {165003},
  publisher = {{IOP Publishing}},
  issn = {1361-6560},
  doi = {10.1088/1361-6560/ab2a18},
  abstract = {Many tumors including head and neck squamous cell carcinoma (HNSCC) spread along the lymphatic network. Current imaging modalities can only detect sufficiently large metastases. Therefore, adjacent lymph node levels (LNL) are irradiated electively since they may harbor microscopic tumors. We apply Bayesian Networks (BN) to model lymphatic tumor progression. The model can subsequently be used to personalize the risk estimation of microscopic lymph node metastases in newly diagnosed patients based on their distribution of macroscopic metastases. A BN is a graphical representation of a joint probability distribution. We represent LNLs by binary random variables corresponding to the BN nodes. Each LNL is associated with a hidden microscopic state and an observed macroscopic state (e.g. 18F-FDG-PET/CT imaging). The primary tumor is represented by network input nodes. We demonstrate the concept for early T-stage oropharyngeal carcinomas and their spread to ipsilateral lymph node levels (LNL) Ib to IV. We show that the BN parameters can be efficiently learnt by merging pathology findings on microscopic tumor progression (which is limited to a few published studies) and imaging data on macroscopic tumor progression such as CT and 18F-FDG-PET (which are widely available in clinical practice). The trained network can be used to quantify how the distribution of macroscopic metastases impacts the probability of microscopic involvement of the remaining LNLs. The analysis suggests that the risk of microscopic involvement of level IV exceeds 5\% only if level III harbors metastases. Excluding level IV from the elective CTV for other patients would reduce the integral dose delivered to the patient and potentially reduce acute and late side effects.},
  file = {C:\Users\roman\OneDrive\Documents\Library\Pouymayou et al_2019_A Bayesian network model of lymphatic tumor progression for personalized.pdf}
}

@article{pouymayou_pv-0315_2019,
  title = {{{PV-0315 A}} Risk Assessment Method Including Credible Intervals for Lymphatic Metastatic Spread for {{HNSCC}}},
  author = {Pouymayou, B and {Others}},
  year = {2019},
  journal = {Radiother. Oncol.},
  volume = {133},
  pages = {S163},
  doi = {10.1016/S0167-8140(19)30735-2},
  file = {C:\Users\roman\OneDrive\Documents\Library\Pouymayou_Others_2019_PV-0315 A risk assessment method including credible intervals for lymphatic.pdf}
}

@article{presnell_-and-out--sample_nodate,
  title = {The {{In-and-Out-of-Sample}} ({{IOS}}) {{Likelihood Ratio Test}} for {{Model Misspecification}}},
  author = {Presnell, Brett and Boos, Dennis D},
  pages = {29},
  abstract = {A new test of model misspecification, based on the ratio of in-sample and out-ofsample likelihoods, is proposed. The test is broadly applicable, and in simple problems approximates well known, intuitive methods. Using jackknife influence curve approximations, it is shown that the test statistic can be viewed asymptotically as a multiplicative contrast between two estimates of the information matrix that are equal under correct model specification. This approximation is used to show that the statistic is asymptotically normally distributed, though it is suggested that p-values be computed using the parametric bootstrap. The resulting methodology is demonstrated with a variety of examples and simulations involving both discrete and continuous data.},
  langid = {english},
  keywords = {cross-fold,validation},
  file = {C:\Users\roman\OneDrive\Documents\Library\Presnell_Boos_The In-and-Out-of-Sample (IOS) Likelihood Ratio Test for Model Misspecification.pdf}
}

@misc{preston-werner_semantic_nodate,
  title = {Semantic {{Versioning}} 2.0.0},
  author = {{Preston-Werner}, Tom},
  journal = {Semantic Versioning},
  urldate = {2022-10-04},
  abstract = {Semantic Versioning spec and website},
  copyright = {CC BY 3.0},
  howpublished = {https://semver.org/},
  langid = {english},
  file = {C:\Users\roman\Zotero\storage\SNZ4DY2K\semver.org.html}
}

@article{rackley_unilateral_2017,
  title = {Unilateral Radiotherapy for Surgically Resected Lateralized Squamous Cell Carcinoma of the Tonsil: {{Unilateral}} Radiotherapy in Tonsillar Cancer},
  shorttitle = {Unilateral Radiotherapy for Surgically Resected Lateralized Squamous Cell Carcinoma of the Tonsil},
  author = {Rackley, Thomas Paul and Namelo, Wanangwa Clara and Palaniappan, Nachi and Cole, Naomi and Owens, David M. J. and Evans, Mererid},
  year = {2017},
  month = jan,
  journal = {Head \& Neck},
  volume = {39},
  number = {1},
  pages = {17--23},
  issn = {10433074},
  doi = {10.1002/hed.24541},
  urldate = {2022-09-21},
  abstract = {Background. The purpose of this study was to determine the rate of contralateral neck recurrence after surgery and unilateral neck radiotherapy, for lateralized tonsillar cancers with ipsilateral neck disease, in order to inform future clinical trial protocols for this disease.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Rackley et al_2017_Unilateral radiotherapy for surgically resected lateralized squamous cell.pdf}
}

@article{ragin_survival_2007,
  title = {Survival of Squamous Cell Carcinoma of the Head and Neck in Relation to Human Papillomavirus Infection: {{Review}} and Meta-Analysis},
  shorttitle = {Survival of Squamous Cell Carcinoma of the Head and Neck in Relation to Human Papillomavirus Infection},
  author = {Ragin, Camille C. R. and Taioli, Emanuela},
  year = {2007},
  journal = {International Journal of Cancer},
  volume = {121},
  number = {8},
  pages = {1813--1820},
  issn = {1097-0215},
  doi = {10.1002/ijc.22851},
  urldate = {2022-10-18},
  abstract = {Human papillomavirus (HPV) has been associated with head and neck squamous cell carcinomas (HNSCC), especially of the oropharynx, with highest distribution in the tonsils. HPV infection has been associated with improved outcome, although not all the studies show consistent results. The reason for this is not clear. We reviewed all published articles and conducted a meta-analysis on the overall relationship between HPV infection and overall survival (OS) and disease-free survival (DFS) in HNSCC. Patients with HPV-positive HNSCC had a lower risk of dying (meta HR: 0.85, 95\% CI: 0.7{\textendash}1.0), and a lower risk of recurrence (meta HR: 0.62, 95\%CI: 0.5{\textendash}0.8) than HPV-negative HNSCC patients. Site-specific analyses show that patients with HPV-positive oropharyngeal tumours had a 28\% reduced risk of death (meta HR: 0.72, 95\%CI: 0.5{\textendash}1.0) in comparison to patients with HPV-negative oropharyngeal tumours. Similar observations were made for DFS (meta HR: 0.51, 95\% CI: 0.4{\textendash}0.7). There was no difference in OS between HPV-positive and negative non-oropharyngeal patients. The observed improved OS and DFS for HPV-positive HNSCC patients is specific to the oropharynx; these tumours may have a distinct etiology from those tumours in non-oropharyngeal sites. {\textcopyright} 2007 Wiley-Liss, Inc.},
  langid = {english},
  keywords = {disease-free survival,head and neck cancer,HPV,overall survival},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Ragin_Taioli_2007_Survival of squamous cell carcinoma of the head and neck in relation to human.pdf;C\:\\Users\\roman\\Zotero\\storage\\2IADXK96\\ijc.html}
}

@article{ramakrishnan_dynamic_2012,
  title = {A {{Dynamic Programming Approach}} to {{Adaptive Fractionation}}},
  author = {Ramakrishnan, Jagdish and Craft, David and Bortfeld, Thomas and Tsitsiklis, John N.},
  year = {2012},
  month = mar,
  journal = {Physics in Medicine and Biology},
  volume = {57},
  number = {5},
  eprint = {1109.4524},
  pages = {1203--1216},
  issn = {0031-9155, 1361-6560},
  doi = {10.1088/0031-9155/55/5/1203},
  urldate = {2021-06-11},
  abstract = {We conduct a theoretical study of various solution methods for the adaptive fractionation problem. The two messages of this paper are: (i) dynamic programming (DP) is a useful framework for adaptive radiation therapy, particularly adaptive fractionation, because it allows us to assess how close to optimal different methods are, and (ii) heuristic methods proposed in this paper are near-optimal, and therefore, can be used to evaluate the best possible benefit of using an adaptive fraction size. The essence of adaptive fractionation is to increase the fraction size when the tumor and organ-at-risk (OAR) are far apart (a "favorable" anatomy) and to decrease the fraction size when they are close together. Given that a fixed prescribed dose must be delivered to the tumor over the course of the treatment, such an approach results in a lower cumulative dose to the OAR when compared to that resulting from standard fractionation. We first establish a benchmark by using the DP algorithm to solve the problem exactly. In this case, we characterize the structure of an optimal policy, which provides guidance for our choice of heuristics. We develop two intuitive, numerically near-optimal heuristic policies, which could be used for more complex, high-dimensional problems. Furthermore, one of the heuristics requires only a statistic of the motion probability distribution, making it a reasonable method for use in a realistic setting. Numerically, we find that the amount of decrease in dose to the OAR can vary significantly (5 - 85\%) depending on the amount of motion in the anatomy, the number of fractions, and the range of fraction sizes allowed. In general, the decrease in dose to the OAR is more pronounced when: (i) we have a high probability of large tumor-OAR distances, (ii) we use many fractions (as in a hyper-fractionated setting), and (iii) we allow large daily fraction size deviations.},
  archiveprefix = {arxiv},
  keywords = {Physics - Medical Physics},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Ramakrishnan et al_2012_A Dynamic Programming Approach to Adaptive Fractionation.pdf;C\:\\Users\\roman\\Zotero\\storage\\2TPVRZ9V\\1109.html}
}

@book{rasmussen_gaussian_2006,
  title = {Gaussian Processes for Machine Learning},
  author = {Rasmussen, Carl Edward and Williams, Christopher K. I.},
  year = {2006},
  series = {Adaptive Computation and Machine Learning},
  publisher = {{MIT Press}},
  address = {{Cambridge, Mass}},
  isbn = {978-0-262-18253-9},
  langid = {english},
  lccn = {QA274.4 .R37 2006},
  keywords = {Data processing,Gaussian processes,Machine learning,Mathematical models},
  annotation = {OCLC: ocm61285753},
  file = {C:\Users\roman\OneDrive\Documents\Library\Rasmussen_Williams_2006_Gaussian processes for machine learning.pdf}
}

@article{razfar_incidence_2009,
  title = {Incidence and Patterns of Regional Metastasis in Early Oral Squamous Cell Cancers: {{Feasibility}} of Submandibular Gland Preservation},
  shorttitle = {Incidence and Patterns of Regional Metastasis in Early Oral Squamous Cell Cancers},
  author = {Razfar, Ali and Walvekar, Rohan R. and Melkane, Antoine and Johnson, Jonas T. and Myers, Eugene N.},
  year = {2009},
  month = dec,
  journal = {Head \& Neck},
  volume = {31},
  number = {12},
  pages = {1619--1623},
  issn = {10433074, 10970347},
  doi = {10.1002/hed.21129},
  urldate = {2021-02-10},
  abstract = {Methods. This was a retrospective study of 261 patients with OSCC treated primarily with surgery at a tertiary medical center. One hundred thirty-two early-stage (T1-2, N0) OSCCs were further analyzed. Results. The mean age was 59 years with male-to-female sex ratio of 1.4:1. Two hundred sixty-one neck dissections were performed with SMG removal in 253 patients. One patient with an advanced floor of mouth cancer had obvious infiltration of the SMG. Only 2.5\% (3 of 116) patients with early-stage OSCC had level I metastasis; none had SMG metastases. Conclusion. SMG preservation in early cancers (T1-2, N0) of the oral cavity should be feasible unless there is evidence of direct invasion of the gland or close proximity of the cancer to it. VC 2009 Wiley Periodicals, Inc. Head Neck 31: 1619{\textendash}1623, 2009},
  langid = {english},
  keywords = {patterns},
  file = {C:\Users\roman\OneDrive\Documents\Library\Razfar et al_2009_Incidence and patterns of regional metastasis in early oral squamous cell.pdf}
}

@article{rieder_bayesian_1975,
  title = {Bayesian {{Dynamic Programming}}},
  author = {Rieder, Ulrich},
  year = {1975},
  journal = {Advances in Applied Probability},
  volume = {7},
  number = {2},
  eprint = {1426080},
  eprinttype = {jstor},
  pages = {330--348},
  publisher = {{Applied Probability Trust}},
  issn = {0001-8678},
  doi = {10.2307/1426080},
  urldate = {2021-06-01},
  abstract = {We consider a non-stationary Bayesian dynamic decision model with general state, action and parameter spaces. It is shown that this model can be reduced to a non-Markovian (resp. Markovian) decision model with completely known transition probabilities. Under rather weak convergence assumptions on the expected total rewards some general results are presented concerning the restriction on deterministic generalized Markov policies, the criteria of optimality and the existence of Bayes policies. These facts are based on the above transformations and on results of Hindererand Sch{\"a}l.},
  file = {C:\Users\roman\OneDrive\Documents\Library\Rieder_1975_Bayesian Dynamic Programming.pdf}
}

@article{robbins_neck_2002,
  title = {Neck {{Dissection Classification Update}}: {{Revisions Proposed}} by the {{American Head}} and {{Neck Society}} and the {{American Academy}} of {{Otolaryngology}}{\textendash}{{Head}} and {{Neck Surgery}}},
  author = {Robbins, K. Thomas and Clayman, Garry and Levine, Paul A. and Medina, Jesus and Sessions, Roy and Shaha, Ashok and Som, Peter and Wolf, Gregory T. and {and the Committee for Head {and} Neck Surgery {and} Oncology}, American Academy of Otolaryngology{\textendash}Head {and} Neck Surgery},
  year = {2002},
  month = jul,
  journal = {Archives of Otolaryngology{\textendash}Head \& Neck Surgery},
  volume = {128},
  number = {7},
  pages = {751--758},
  issn = {0886-4470},
  doi = {10.1001/archotol.128.7.751},
  urldate = {2021-08-02},
  abstract = {Since the first description of the radical neck dissection by George Crile almost a century ago, many variations and modifications of the procedure have been added. These include the functional neck dissection, the modified radical neck dissection, and various selective neck dissections. In response to the need for an organized approach in describing these operations, the Committee for Head and Neck Surgery and Oncology of the American Academy of Otolaryngology{\textendash}Head and Neck Surgery (AAO-HNS) in 1988 initiated an effort to develop a standardized classification system for neck dissection (Table 1). During this process, input was obtained from the Education Committee of the American Society for Head and Neck Surgery (ASHNS) and its Council. The final product, endorsed by the ASHNS and the AAO-HNS, was published in the ARCHIVES and as a monograph by the AAO-HNS in 1991.},
  file = {C:\Users\roman\OneDrive\Foam\references\@robbins_neck_2002.md}
}

@article{robbins_standardizing_1991,
  title = {Standardizing {{Neck Dissection Terminology}}: {{Official Report}} of the {{Academy}}'s {{Committee}} for {{Head}} and {{Neck Surgery}} and {{Oncology}}},
  author = {Robbins, K. Thomas and Medina, Jesus E. and Wolfe, Gregory T. and Levine, Paul A. and Sessions, Roy B. and Pruet, Charles W.},
  year = {1991},
  month = jun,
  journal = {Archives of Otolaryngology{\textendash}Head \& Neck Surgery},
  volume = {117},
  number = {6},
  pages = {601--605},
  issn = {0886-4470},
  doi = {10.1001/archotol.1991.01870180037007},
  urldate = {2021-08-02},
  abstract = {{\textbullet} The emergence of the multitude of modified techniques for neck dissection procedure has resulted in a nomenclature system that is nonuniform. To eliminate potential misinterpretation, overlap, and lack of standardization, the Academy's Committee for Head and Neck Surgery and Oncology, with input from the Education Committee of the American Society of Head and Neck Surgery, has developed a classification system for these procedures. This has now been adopted by the American Academy of Otolaryngology{\textemdash}Head and Neck Surgery. The classification is based on the following concepts: (1) radical neck dissection is the fundamental procedure with which all other neck dissections are compared, (2) modified radical neck dissection denotes preservation of one or more nonlymphatic structure(s), (3) selective neck dissection denotes preservation of one or more group(s) of lymph nodes, and (4) extended radical neck dissection denotes removal of one or more additional lymphatic and/or nonlymphatic structure(s). Adherence to the principles of this classification system to describe neck dissection techniques should provide an improved method of communication. Furthermore, the system provides a rational framework on which subsequent terminology can be added.(Arch Otolaryngol Head Neck Surg. 1991;117:601-605)},
  file = {C:\Users\roman\Zotero\storage\VZTVVMUR\619715.html}
}

@article{rohde_18f-fluoro-deoxy-glucose-positron_2014,
  title = {{{18F-fluoro-deoxy-glucose-positron}} Emission Tomography/Computed Tomography in Diagnosis of Head and Neck Squamous Cell Carcinoma: {{A}} Systematic Review and Meta-Analysis},
  shorttitle = {{{18F-fluoro-deoxy-glucose-positron}} Emission Tomography/Computed Tomography in Diagnosis of Head and Neck Squamous Cell Carcinoma},
  author = {Rohde, Max and Dyrvig, Anne-Kirstine and Johansen, J{\o}rgen and S{\o}rensen, Jens A. and Gerke, Oke and Nielsen, Anne L. and {H{\o}ilund-Carlsen}, Poul Flemming and Godballe, Christian},
  year = {2014},
  month = sep,
  journal = {European Journal of Cancer},
  volume = {50},
  number = {13},
  pages = {2271--2279},
  issn = {0959-8049},
  doi = {10.1016/j.ejca.2014.05.015},
  urldate = {2022-07-01},
  abstract = {18F-fluoro-deoxy-glucose-positron emission tomography/computed tomography-scan (PET/CT) is used increasingly for detection of cancer. Precise diagnostic assessment of tumour extension in head and neck squamous cell carcinoma (HNSCC) is of critical importance for ensuring that patients receive proper treatment. Preliminary studies have shown divergent results of PET/CT in diagnosis and staging of HNSCC. The aims of this study were (1) to systematically review and meta-analyse published data about the diagnostic accuracy of PET/CT for diagnosing patients with HNSCC and (2) to compare the diagnostic accuracy of PET/CT with that of standard conventional imaging (SCI). Methods A systematic literature search in the PubMed, Embase and Cochrane databases on publications of PET/CT diagnostics of HNSCC from January 2005 to July 2013 was carried out. All retrieved studies were reviewed and qualitatively analysed. Along with the calculated pooled sensitivity and specificity of PET/CT and SCI, bubble- and summary receiver operating characteristics (SROC) plots were created. Findings Two meta-analyses of diagnostic accuracy were conducted. The first, on PET/CT, included 987 patients distributed across nine studies. The second, on SCI, included 517 patients participating in a total of six studies among those comparing PET/CT to SCI. The meta-analyses showed a pooled sensitivity of 89.3\% (95\% confidence interval [95\% CI]: 83.4{\textendash}93.2\%) and specificity of 89.5\% (95\% CI: 82.9{\textendash}93.7\%) for PET/CT and correspondingly, a pooled sensitivity and specificity of 71.6\% (95\% CI: 44.3{\textendash}88.9\%) and 78.0\% (95\%CI: 30.2{\textendash}96.7\%) for SCI. A graphical comparison to SCI showed a clear difference in favour of PET/CT. Interpretation PET/CT is highly accurate in diagnosing patients suffering from HNSCC},
  langid = {english},
  keywords = {Biopsy,CT,HNSCC,Meta-analysis,MRI,PET/CT},
  file = {C:\Users\roman\Zotero\storage\8SKBCNW7\S0959804914006832.html}
}

@article{rose_deterministic_1998,
  title = {Deterministic Annealing for Clustering, Compression, Classification, Regression, and Related Optimization Problems},
  author = {Rose, K.},
  year = {1998},
  month = nov,
  journal = {Proceedings of the IEEE},
  volume = {86},
  number = {11},
  pages = {2210--2239},
  issn = {1558-2256},
  doi = {10.1109/5.726788},
  abstract = {The deterministic annealing approach to clustering and its extensions has demonstrated substantial performance improvement over standard supervised and unsupervised learning methods in a variety of important applications including compression, estimation, pattern recognition and classification, and statistical regression. The application-specific cost is minimized subject to a constraint on the randomness of the solution, which is gradually lowered. We emphasize the intuition gained from analogy to statistical physics. Alternatively the method is derived within rate-distortion theory, where the annealing process is equivalent to computation of Shannon's rate-distortion function, and the annealing temperature is inversely proportional to the slope of the curve. The basic algorithm is extended by incorporating structural constraints to allow optimization of numerous popular structures including vector quantizers, decision trees, multilayer perceptrons, radial basis functions, and mixtures of experts.},
  keywords = {Annealing,Constraint optimization,Costs,Decision trees,Multilayer perceptrons,Pattern recognition,Physics,Rate-distortion,Temperature,Unsupervised learning},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Rose_1998_Deterministic annealing for clustering, compression, classification,.pdf;C\:\\Users\\roman\\Zotero\\storage\\QCDLFLY4\\726788.html}
}

@article{rosenberg_multi-institutional_2019,
  title = {A {{Multi-Institutional Experience}} of {{MR-Guided Liver Stereotactic Body Radiation Therapy}}},
  author = {Rosenberg, Stephen A. and Henke, Lauren E. and Shaverdian, Narek and Mittauer, Kathryn and Wojcieszynski, Andrzej P. and Hullett, Craig R. and Kamrava, Mitchell and Lamb, James and Cao, Minsong and Green, Olga L. and Kashani, Rojano and Paliwal, Bhudatt and Bayouth, John and Harari, Paul M. and Olsen, Jeffrey R. and Lee, Percy and Parikh, Parag J. and Bassetti, Michael},
  year = {2019},
  month = jan,
  journal = {Advances in Radiation Oncology},
  volume = {4},
  number = {1},
  pages = {142--149},
  issn = {24521094},
  doi = {10.1016/j.adro.2018.08.005},
  urldate = {2022-02-07},
  abstract = {Purpose: Daily magnetic resonance (MR)eguided radiation has the potential to improve stereotactic body radiation therapy (SBRT) for tumors of the liver. Magnetic resonance imaging (MRI) introduces unique variables that are untested clinically: electron return effect, MRI geometric distortion, MRI to radiation therapy isocenter uncertainty, multileaf collimator position error, and uncertainties with voxel size and tracking. All could lead to increased toxicity and/or local recurrences with SBRT. In this multi-institutional study, we hypothesized that direct visualization provided by MR guidance could allow the use of small treatment volumes to spare normal tissues while maintaining clinical outcomes despite the aforementioned uncertainties in MR-guided treatment.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Rosenberg et al_2019_A Multi-Institutional Experience of MR-Guided Liver Stereotactic Body Radiation.pdf}
}

@book{russell_artificial_2010,
  title = {Artificial Intelligence: A Modern Approach},
  shorttitle = {Artificial Intelligence},
  author = {Russell, Stuart J. and Norvig, Peter and Davis, Ernest},
  year = {2010},
  series = {Prentice {{Hall}} Series in Artificial Intelligence},
  edition = {3rd ed},
  publisher = {{Prentice Hall}},
  address = {{Upper Saddle River}},
  isbn = {978-0-13-604259-4},
  lccn = {Q335 .R86 2010},
  keywords = {Artificial intelligence}
}

@article{sanguineti_defining_2009,
  title = {Defining the Risk of Involvement for Each Neck Nodal Level in Patients with Early {{T-stage}} Node-Positive Oropharyngeal Carcinoma},
  author = {Sanguineti, G and {Others}},
  year = {2009},
  journal = {Int. J. Radiat. Oncol. Biol. Phys.},
  volume = {74},
  pages = {1356--1364},
  doi = {10.1016/j.ijrobp.2008.10.018},
  file = {C:\Users\roman\OneDrive\Documents\Library\Sanguineti_Others_2009_Defining the risk of involvement for each neck nodal level in patients with.pdf}
}

@article{schwarz_estimating_1978,
  title = {Estimating the {{Dimension}} of a {{Model}}},
  author = {Schwarz, Gideon},
  year = {1978},
  month = mar,
  journal = {The Annals of Statistics},
  volume = {6},
  number = {2},
  pages = {461--464},
  publisher = {{Institute of Mathematical Statistics}},
  issn = {0090-5364, 2168-8966},
  doi = {10.1214/aos/1176344136},
  urldate = {2022-09-03},
  abstract = {The problem of selecting one of a number of models of different dimensions is treated by finding its Bayes solution, and evaluating the leading terms of its asymptotic expansion. These terms are a valid large-sample criterion beyond the Bayesian context, since they do not depend on the a priori distribution.},
  keywords = {62F99,62J99,Akaike information criterion,asymptotics,dimension},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Schwarz_1978_Estimating the Dimension of a Model.pdf;C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Schwarz_1978_Estimating the Dimension of a Model2.pdf;C\:\\Users\\roman\\Zotero\\storage\\IRU98W26\\1176344136.html}
}

@book{segaran_programming_2007,
  title = {Programming Collective Intelligence: Building Smart Web 2.0 Applications},
  shorttitle = {Programming Collective Intelligence},
  author = {Segaran, Toby},
  year = {2007},
  edition = {1st ed},
  publisher = {{O'Reilly}},
  address = {{Beijing ; Sebastapol [CA]}},
  isbn = {978-0-596-52932-1},
  lccn = {T58.5 .S43 2007},
  keywords = {Information technology,Internet programming,Social aspects},
  annotation = {OCLC: ocn166886837},
  file = {C:\Users\roman\OneDrive\Documents\Library\Segaran_2007_Programming collective intelligence.pdf}
}

@article{shah_patterns_1990,
  title = {The Patterns of Cervical Lymph Node Metastases from Squamous Carcinoma of the Oral Cavity},
  author = {Shah, Jatin P. and Candela, Frank C. and Poddar, Anil K.},
  year = {1990},
  journal = {Cancer},
  volume = {66},
  number = {1},
  pages = {109--113},
  issn = {1097-0142},
  doi = {10.1002/1097-0142(19900701)66:1<109::AID-CNCR2820660120>3.0.CO;2-A},
  urldate = {2021-02-10},
  abstract = {A retrospective review of the records of 501 previously untreated patients from January 1, 1965 through December 31, 1986 with squamous cell carcinoma of the oral cavity was undertaken to ascertain the prevalence of ipsilateral neck node metastases (NM) by neck level. The 501 patients underwent 516 radical neck dissections. Patients were grouped by clinical neck status at the time of neck dissection: elective dissection (ED) in the NO neck, immediate therapeutic dissection (ITD) in the N+ neck, and subsequent therapeutic dissection (STD) in the neck observed which converted clinically to N+. Pathologically identified NM occurred 34\% of the time in ED, 69\% in ITD and 90\% in STD. The sensitivity, specificity, and overall accuracy of the clinical exam was 70\%, 65\%, and 68\%, respectively. Detailed analysis was performed for each group based on the primary site. This revealed a prevalence of NM in level IV of 3\% (five of 167) for ED versus 17\% (49/ 296) for ITD + STD (P {$<$} 0.001). Tongue, retromolar trigone, and cheek did not have NM in level V in any group. The prevalence of NM in level V for floor of mouth or gum primaries was {$<$} 1\% (one of 109) in ED versus 6\% (ten of 167) in ITD + STD (P {$<$} 0.03). These data support the trend toward selective limited neck dissection in both NO and N+ patients. Further, they provide the foundation for planning of future prospective trials to assess the efficacy of modifications in the extent of neck dissection.},
  langid = {english},
  keywords = {patterns},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Shah et al_1990_The patterns of cervical lymph node metastases from squamous carcinoma of the.pdf;C\:\\Users\\roman\\Zotero\\storage\\2ZXKIFJ5\\1097-0142(19900701)661109AID-CNCR28206601203.0.html}
}

@article{sher_prospective_2021,
  title = {Prospective {{Phase}} 2 {{Study}} of {{Radiation Therapy Dose}} and {{Volume De-escalation}} for {{Elective Neck Treatment}} of {{Oropharyngeal}} and {{Laryngeal Cancer}}},
  author = {Sher, David J. and Pham, Nhat-Long and Shah, Jennifer L. and Sen, Neilayan and Williams, Kimberly A. and Subramaniam, Rathan M. and Moore, William and Chorley, Regina and Ahn, Chul and Khan, Saad M.},
  year = {2021},
  month = mar,
  journal = {International Journal of Radiation Oncology*Biology*Physics},
  volume = {109},
  number = {4},
  pages = {932--940},
  issn = {0360-3016},
  doi = {10.1016/j.ijrobp.2020.09.063},
  urldate = {2023-08-28},
  abstract = {Purpose The required elective nodal dose and volumes for head and neck intensity modulated radiation therapy have largely been extrapolated from conventional radiation therapy fields. In this prospective, dual-center, phase 2 study, we investigated the efficacy and tolerability of reduced elective nodal volume and dose in oropharyngeal and laryngeal squamous cell carcinoma. Methods and Materials Patients with newly diagnosed squamous cell carcinoma of the oropharynx and larynx were eligible for enrollment. Each lymph node was characterized as involved or suspicious based on imaging criteria. For oropharynx cancer, only involved and immediately adjacent stations were treated to 40 Gy in 20 fractions. In larynx patients, at least bilateral levels II and III were treated to 40 Gy, with level IV treated only if level III was involved. Involved and suspicious nodes were then boosted with 30 Gy and 24 Gy in 15 fractions, respectively. Concurrent chemotherapy was required for stage T3N0-1 and IVA/B patients. The primary endpoint of the study was solitary elective volume recurrence, with secondary endpoints including patterns of failure and patient-reported outcomes. Results A total of 72 (51 oropharynx, 21 larynx) patients completed treatment on this trial from January 2017 through November 2018. The stages at presentations were 5, 17, and 50 stage I-II, III, and IV, respectively, with 90\% treated with chemoradiation therapy. At a median follow-up of 24.7 months for surviving patients, there have been no solitary elective nodal recurrences. Seven patients developed a nodal recurrence, 5 of which were in-field and 2 were elective with synchronous in-field recurrence. Patient-reported outcomes assessment at 1 year showed superior or equivalent outcomes compared with baseline, except for saliva and taste measures. Conclusions The results of this trial suggest that elective dose and volume reduction is oncologically sound for oropharyngeal and laryngeal cancer treated with intensity modulated radiation therapy, with promising quality-of-life outcomes.},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Sher et al_2021_Prospective Phase 2 Study of Radiation Therapy Dose and Volume De-escalation.pdf;C\:\\Users\\roman\\Zotero\\storage\\QM79CD78\\S0360301620344461.html}
}

@article{sia_molecular_2020,
  title = {Molecular {{Mechanisms}} of {{Radiation-Induced Cancer Cell Death}}: {{A Primer}}},
  shorttitle = {Molecular {{Mechanisms}} of {{Radiation-Induced Cancer Cell Death}}},
  author = {Sia, Joseph and Szmyd, Radoslaw and Hau, Eric and Gee, Harriet E.},
  year = {2020},
  journal = {Frontiers in Cell and Developmental Biology},
  volume = {8},
  issn = {2296-634X},
  urldate = {2023-03-21},
  abstract = {Radiation therapy (RT) is responsible for at least 40\% of cancer cures, however treatment resistance remains a clinical problem. There have been recent advances in understanding the molecular mechanisms of radiation-induced cell death. The type of cell death after radiation depends on a number of factors including cell type, radiation dose and quality, oxygen tension, TP53 status, DNA repair capacity, cell cycle phase at time of radiation exposure, and the microenvironment. Mitotic catastrophe (a pathway preceding cell death that happens in mitosis or as a consequence of aberrant mitotic progression) is the primary context of radiation-induced cell death in solid cancers, although in a small subset of cancers such as haematopoietic malignancies, radiation results in immediate interphase apoptosis, occurring within hours after exposure. There is intense therapeutic interest in using stereotactic ablative body radiotherapy (SABR), a precise, high-dose form of RT given in a small number of fractions, to prime the immune system for cancer cell killing, but the optimal radiation dose and fractionation remain unclear. Additionally, promising novel radiosensitisers targeting the cell cycle and DNA repair pathways are being trialled. In the context of the increasing use of SABR and such novel agents in the clinic, we provide an updated primer on the major types of radiation-induced cell death, focussing on their molecular mechanisms, factors affecting their initiation, and their implications on immunogenicity.},
  keywords = {cell death},
  file = {C:\Users\roman\OneDrive\Documents\Library\Sia et al_2020_Molecular Mechanisms of Radiation-Induced Cancer Cell Death.pdf}
}

@article{skinner_superstition_1992,
  title = {"{{Superstition}}" in the Pigeon},
  author = {Skinner, B. F.},
  year = {1992},
  journal = {Journal of Experimental Psychology: General},
  volume = {121},
  pages = {273--274},
  publisher = {{American Psychological Association}},
  address = {{US}},
  issn = {1939-2222},
  doi = {10.1037/0096-3445.121.3.273},
  abstract = {(This reprinted article originally appeared in the Journal of Experimental Psychology, 1948, Vol 38, 168{\textendash}272. The following abstract of the original article appeared in PA, Vol 22:4299.) A pigeon is brought to a stable state of hunger by reducing it to 75\% of its weight when well fed. It is put into an experimental cage for a few minutes each day. A food hopper attached to the cage may be swung into place so that the pigeon can eat from it. A solenoid and a timing relay hold the hopper in place for 5 sec at each reinforcement. If a clock is now arranged to present the food hopper at regular intervals with no reference whatsoever to the bird's behavior, operant conditioning usually takes place. The bird tends to learn whatever response it is making when the hopper appears. The response may be extinguished and reconditioned. The experiment might be said to demonstrate a sort of superstition. The bird behaves as if there were a causal relation between its behavior and the presentation of food, although such a relation is lacking. (PsycINFO Database Record (c) 2016 APA, all rights reserved)},
  keywords = {Animal Feeding Behavior,Operant Conditioning,Pigeons},
  file = {C:\Users\roman\Zotero\storage\IW3QRUVT\doiLanding.html}
}

@article{snyder_petct_2021,
  title = {{{PET}}/{{CT Poorly Predicts AJCC}} 8th {{Edition Pathologic Staging}} in {{HPV-Related Oropharyngeal Cancer}}},
  author = {Snyder, Vusala and Goyal, Lindsey K. and Bowers, Eve M. R. and Kubik, Mark and Kim, Seungwon and Ferris, Robert L. and Johnson, Jonas T. and Duvvuri, Umamaheswar and Gooding, William E. and Branstetter, Barton F. and Rath, Tanya J. and Sridharan, Shaum S.},
  year = {2021},
  month = jan,
  journal = {The Laryngoscope},
  volume = {n/a},
  number = {n/a},
  publisher = {{John Wiley \& Sons, Ltd}},
  issn = {0023-852X},
  doi = {10.1002/lary.29366},
  urldate = {2021-02-04},
  abstract = {Objective The American Joint Committee on Cancer (AJCC) 8th edition introduced distinct clinical and pathological staging paradigms for human papilloma virus positive (HPV+) oropharyngeal squamous cell carcinoma (OPSCC). Treatment planning for OPSCC often utilizes positron emission tomography/computed tomography (PET/CT) to assess clinical stage. We hypothesize that PET/CT will accurately predict final pathologic AJCC 8th edition staging in patients with HPV+ OPSCC. Methods All patients with primary HPV+ OPSCC with preoperative PET/CT who underwent transoral robotic surgery and neck dissection between 2011 and 2017 were identified. Data were collected via chart review. Two neuroradiologists performed blinded re-evaluation of all scans. Primary tumor size and cervical nodal disease characteristics were recorded and TNM staging was extrapolated. Cohen's kappa statistic was used to assess interrater reliability. Test for symmetry was performed to analyze discordance between radiologic and pathologic staging. Results Forty-nine patients met inclusion criteria. Interrater reliability was substantial between radiologists for nodal (N) and overall staging (OS) (? = 0.715 and 0.715). Radiologist A review resulted in identical OS for 67\% of patients, overstaging for 31\%, and understaging for 2\%. Radiologist B review resulted in 61\% identical OS, 39\% overstaging, and 0\% understaging. In misclassified cases, the test of symmetry shows strong bias toward overstaging N stage and OS (P?},
  keywords = {AJCC 8th edition,head and neck cancer staging,HPV+ oropharyngeal squamous cell carcinoma,human papilloma virus}
}

@book{sobin_tnm_2009,
  title = {{{TNM}} Classification of Malignant Tumours},
  author = {Sobin, L. H. and Gospodarowicz, M. K. and Wittekind, Ch},
  year = {2009},
  edition = {7th ed},
  publisher = {{Wiley-Blackwell}},
  address = {{Chichester, West Sussex, UK}},
  abstract = {TNM Classification of Malignant Tumours, 7th Edition provides the latest, internationally agreed-upon standards to describe and categorize cancer stages and progression. Published in affiliation with the International Union Against Cancer (UICC), this authoritative guide contains important updated organ-specific classifications that oncologists and other professionals who manage patients with cancer need to accurately classify tumours for staging, prognosis and treatment. The major alterations addressed in the 7th Edition concern carcinomas of the oesophag},
  isbn = {978-1-4443-5896-4},
  langid = {english},
  annotation = {OCLC: 1162077122}
}

@incollection{sokal_monte_1997,
  title = {Monte {{Carlo Methods}} in {{Statistical Mechanics}}: {{Foundations}} and {{New Algorithms}}},
  shorttitle = {Monte {{Carlo Methods}} in {{Statistical Mechanics}}},
  booktitle = {Functional {{Integration}}: {{Basics}} and {{Applications}}},
  author = {Sokal, A.},
  editor = {{DeWitt-Morette}, Cecile and Cartier, Pierre and Folacci, Antoine},
  year = {1997},
  series = {{{NATO ASI Series}}},
  pages = {131--192},
  publisher = {{Springer US}},
  address = {{Boston, MA}},
  doi = {10.1007/978-1-4899-0319-8_6},
  urldate = {2022-10-24},
  abstract = {These notes are an updated version of lectures given at the Cours de Troisi{\`e}me Cycle de la Physique en Suisse Romande (Lausanne, Switzerland) in June 1989. We thank the Troisi{\`e}me Cycle de la Physique en Suisse Romande and Professor Michel Droz for kindly giving permission to reprint these notes.},
  isbn = {978-1-4899-0319-8},
  langid = {english},
  keywords = {Autocorrelation Time,Coarse Grid,Ising Model,Monte Carlo Algorithm,Multigrid Method}
}

@article{souron_acute_2017,
  title = {Acute and Chronic Neuromuscular Adaptations to Local Vibration Training},
  author = {Souron, Robin and Besson, Thibault and Millet, Guillaume Y. and Lapole, Thomas},
  year = {2017},
  month = oct,
  journal = {European Journal of Applied Physiology},
  volume = {117},
  number = {10},
  pages = {1939--1964},
  issn = {1439-6327},
  doi = {10.1007/s00421-017-3688-8},
  urldate = {2021-11-08},
  abstract = {Vibratory stimuli are thought to have the potential to promote neural and/or muscular (re)conditioning. This has been well described for whole-body vibration (WBV), which is commonly used as a training method to improve strength and/or functional abilities. Yet, this technique may present some limitations, especially in clinical settings where patients are unable to maintain an active position during the vibration exposure. Thus, a local vibration (LV) technique, which consists of applying portable vibrators directly over the tendon or muscle belly without active contribution from the participant, may present an alternative to WBV. The purpose of this narrative review is (1) to provide a comprehensive overview of the literature related to the acute and chronic neuromuscular changes associated with LV, and (2) to show that LV training may be an innovative and efficient alternative method to the `classic' training programs, including in the context of muscle deconditioning prevention or rehabilitation. An acute LV application (one bout of 20{\textendash}60~min) may be considered as a significant neuromuscular workload, as demonstrated by an impairment of force generating capacity and LV-induced neural changes. Accordingly, it has been reported that a training period of LV is efficient in improving muscular performance over a wide range of training (duration, number of session) and vibration (frequency, amplitude, site of application) parameters. The functional improvements are principally triggered by adaptations within the central nervous system. A model illustrating the current research on LV-induced adaptations is provided.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Souron et al_2017_Acute and chronic neuromuscular adaptations to local vibration training.pdf}
}

@article{souron_eight_2017,
  title = {Eight Weeks of Local Vibration Training Increases Dorsiflexor Muscle Cortical Voluntary Activation},
  author = {Souron, Robin and Farabet, Adrien and F{\'e}asson, L{\'e}onard and Belli, Alain and Millet, Guillaume Y. and Lapole, Thomas},
  year = {2017},
  month = jun,
  journal = {Journal of Applied Physiology},
  volume = {122},
  number = {6},
  pages = {1504--1515},
  publisher = {{American Physiological Society}},
  issn = {8750-7587},
  doi = {10.1152/japplphysiol.00793.2016},
  urldate = {2021-11-08},
  abstract = {The aim of this study was to evaluate the effects of an 8-wk local vibration training (LVT) program on functional and corticospinal properties of dorsiflexor muscles. Forty-four young subjects were allocated to a training (VIB, n = 22) or control (CON, n = 22) group. The VIB group performed twenty-four 1-h sessions (3 sessions/wk) of 100-Hz vibration applied to the right tibialis anterior. Both legs were tested in each group before training (PRE), after 4 (MID) and 8 (POST) wk of training, and 2 wk after training (POST2W). Maximal voluntary contraction (MVC) torque was assessed, and transcranial magnetic stimulation (TMS) was used to evaluate cortical voluntary activation (VATMS), motor evoked potential (MEP), cortical silent period (CSP), and input-output curve parameters. MVC was significantly increased for VIB at MID for right and left legs [+7.4\% (P = 0.001) and +6.2\% (P {$<$} 0.01), respectively] and remained significantly greater than PRE at POST [+12.0\% (P {$<$} 0.001) and +10.1\% (P {$<$} 0.001), respectively]. VATMS was significantly increased for right and left legs at MID [+4.4\% (P {$<$} 0.01) and +4.7\% (P {$<$} 0.01), respectively] and at POST [+4.9\% (P = 0.001) and +6.2\% (P = 0.001), respectively]. These parameters remained enhanced in both legs at POST2W. MEP and CSP recorded during MVC and input-output curve parameters did not change at any time point for either leg. Despite no changes in excitability or inhibition being observed, LVT seems to be a promising method to improve strength through an increase of maximal voluntary activation, i.e., neural adaptations. Local vibration may thus be further considered for clinical or aging populations. NEW \& NOTEWORTHY The effects of a local vibration training program on cortical voluntary activation measured with transcranial magnetic stimulation were assessed for the first time in dorsiflexors, a functionally important muscle group. We observed that training increased maximal voluntary strength likely because of the strong and repeated activation of Ia spindle afferents during vibration training that led to changes in the cortico-motoneuronal pathway, as demonstrated by the increase in cortical voluntary activation.},
  keywords = {Boltzmann modeling,cortical voluntary activation,corticospinal excitability and inhibition,local vibration,transcranial magnetic stimulation},
  file = {C:\Users\roman\OneDrive\Documents\Library\Souron et al_2017_Eight weeks of local vibration training increases dorsiflexor muscle cortical.pdf}
}

@article{strohl_petct_2021,
  title = {{{PET}}/{{CT}} in {{Surgical Planning}} for {{Head}} and {{Neck Cancer}}},
  author = {Strohl, Madeleine P. and Ha, Patrick K. and Flavell, Robert R. and Yom, Sue S.},
  year = {2021},
  month = jan,
  journal = {Imaging Options for Head and Neck Cancer},
  volume = {51},
  number = {1},
  pages = {50--58},
  issn = {0001-2998},
  doi = {10.1053/j.semnuclmed.2020.07.009},
  abstract = {Fluorine-18 (18F)-fluorodeoxyglucose (FDG) positron emission tomography fused with computed tomography (PET/CT) is a valuable tool in surgical planning for head and neck squamous cell carcinoma (HNSCC). If performed prior to biopsy or other surgical intervention, FDG-PET/CT has high sensitivity for the detection of the primary site in patients with cervical lymph node metastases from unknown primary origin and can be used to direct the surgical workup. FDG-PET/CT is superior to CT alone for detection of nodal metastases outside the expected pattern or distant metastases or second primary cancers and can greatly affect determination of appropriate management including surgical eligibility. Prior to the advent of PET/CT, many patients undergoing (chemo)radiation-based therapy had planned post-treatment neck dissection; FDG-PET/CT now has a proven role in the evaluation of recurrent or persistent disease amenable to salvage surgery and enables safe avoidance of planned postradiation neck dissection with a high negative predictive value. Specifically for this important application, two standardized reporting metrics may be used in the head and neck anatomic region: the ``Hopkins criteria'' and the ``Neck Imaging Reporting and Data System''; both systems produce a formalized evaluation and recommendation based on PET/CT findings. The role of PET/CT as a replacement for elective neck dissection or examination under anesthesia remains controversial but deserves further study. FDG-PET/CT has a wide-ranging impact on the surgical management of patients with HNSCC and should be used routinely in patients with unknown primary nodal disease and those presenting with advanced-stage cancers at initial staging and to assess treatment response.}
}

@book{sutton_reinforcement_2018,
  title = {Reinforcement Learning: An Introduction},
  shorttitle = {Reinforcement Learning},
  author = {Sutton, Richard S. and Barto, Andrew G.},
  year = {2018},
  series = {Adaptive Computation and Machine Learning Series},
  edition = {Second edition},
  publisher = {{The MIT Press}},
  address = {{Cambridge, Massachusetts}},
  abstract = {"Reinforcement learning, one of the most active research areas in artificial intelligence, is a computational approach to learning whereby an agent tries to maximize the total amount of reward it receives while interacting with a complex, uncertain environment. In Reinforcement Learning, Richard Sutton and Andrew Barto provide a clear and simple account of the field's key ideas and algorithms."--},
  isbn = {978-0-262-03924-6},
  langid = {english},
  lccn = {Q325.6 .R45 2018},
  keywords = {Reinforcement learning},
  file = {C:\Users\roman\OneDrive\Documents\Library\Sutton_Barto_2018_Reinforcement learning2.pdf}
}

@article{takes_staging_2004,
  title = {Staging of the Neck in Patients with Head and Neck Squamous Cell Cancer: {{Imaging}} Techniques and Biomarkers},
  shorttitle = {Staging of the Neck in Patients with Head and Neck Squamous Cell Cancer},
  author = {Takes, Robert P},
  year = {2004},
  month = aug,
  journal = {Oral Oncology},
  volume = {40},
  number = {7},
  pages = {656--667},
  issn = {1368-8375},
  doi = {10.1016/j.oraloncology.2003.11.001},
  urldate = {2022-10-07},
  abstract = {Regional metastasis is an important factor in the treatment and prognosis of head and neck cancer patients. Current treatment strategies rely on staging based on the still limited accuracy of imaging techniques to detect regional metastases. If more certainty about the nodal status could be attained, treatment strategies concerning the neck could be better adjusted to the individual patient. The continuing improvement of established imaging techniques and the introduction of new imaging modalities will add to better staging. Moreover, the additional use of biomarkers studied on a protein, RNA or DNA level may provide even better information about the chance of occult nodal metastasis in head and neck cancer patients.},
  langid = {english},
  keywords = {Diagnostic imaging,Genetic markers,Head and neck neoplasms,Lymphatic metastasis,Neck dissection},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Takes_2004_Staging of the neck in patients with head and neck squamous cell cancer.pdf;C\:\\Users\\roman\\OneDrive\\Foam\\references\\@takes_staging_2004.md;C\:\\Users\\roman\\OneDrive\\Foam\\references\\@takes_staging_2004.md;C\:\\Users\\roman\\OneDrive\\Foam\\references\\chao_determination_2002.md;C\:\\Users\\roman\\OneDrive\\Foam\\references\\todo.md;C\:\\Users\\roman\\Zotero\\storage\\FKH623HB\\S1368837503002367.html}
}

@article{ter_braak_differential_2008,
  title = {Differential {{Evolution Markov Chain}} with Snooker Updater and Fewer Chains},
  author = {{ter Braak}, Cajo J. F. and Vrugt, Jasper A.},
  year = {2008},
  month = dec,
  journal = {Statistics and Computing},
  volume = {18},
  number = {4},
  pages = {435--446},
  issn = {0960-3174, 1573-1375},
  doi = {10.1007/s11222-008-9104-9},
  urldate = {2022-09-02},
  abstract = {Differential Evolution Markov Chain (DE-MC) is an adaptive MCMC algorithm, in which multiple chains are run in parallel. Standard DE-MC requires at least N = 2d chains to be run in parallel, where d is the dimensionality of the posterior. This paper extends DE-MC with a snooker updater and shows by simulation and real examples that DEMC can work for d up to 50{\textendash}100 with fewer parallel chains (e.g. N = 3) by exploiting information from their past by generating jumps from differences of pairs of past states. This approach extends the practical applicability of DE-MC and is shown to be about 5{\textendash}26 times more efficient than the optimal Normal random walk Metropolis sampler for the 97.5\% point of a variable from a 25{\textendash}50 dimensional Student t3 distribution. In a nonlinear mixed effects model example the approach outperformed a block-updater geared to the specific features of the model.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\ter Braak_Vrugt_2008_Differential Evolution Markov Chain with snooker updater and fewer chains.pdf}
}

@misc{thomas_bulma_2021,
  title = {Bulma},
  author = {Thomas, Jeremy},
  year = {2021},
  copyright = {MIT}
}

@misc{torvalds_git_2022,
  title = {Git},
  author = {Torvalds, Linus},
  year = {2022},
  copyright = {GPL-2.0}
}

@article{turchin_disentangling_2022,
  title = {Disentangling the Evolutionary Drivers of Social Complexity: {{A}} Comprehensive Test of Hypotheses},
  shorttitle = {Disentangling the Evolutionary Drivers of Social Complexity},
  author = {Turchin, Peter and Whitehouse, Harvey and Gavrilets, Sergey and Hoyer, Daniel and Fran{\c c}ois, Pieter and Bennett, James S. and Feeney, Kevin C. and Peregrine, Peter and Feinman, Gary and Korotayev, Andrey and Kradin, Nikolay and Levine, Jill and Reddish, Jenny and Cioni, Enrico and Wacziarg, Romain and {Mendel-Gleason}, Gavin and Benam, Majid},
  year = {2022},
  month = jun,
  journal = {Science Advances},
  volume = {8},
  number = {25},
  pages = {eabn3517},
  publisher = {{American Association for the Advancement of Science}},
  doi = {10.1126/sciadv.abn3517},
  urldate = {2023-05-05},
  abstract = {During the Holocene, the scale and complexity of human societies increased markedly. Generations of scholars have proposed different theories explaining this expansion, which range from broadly functionalist explanations, focusing on the provision of public goods, to conflict theories, emphasizing the role of class struggle or warfare. To quantitatively test these theories, we develop a general dynamical model based on the theoretical framework of cultural macroevolution. Using this model and Seshat: Global History Databank, we test 17 potential predictor variables proxying mechanisms suggested by major theories of sociopolitical complexity (and {$>$}100,000 combinations of these predictors). The best-supported model indicates a strong causal role played by a combination of increasing agricultural productivity and invention/adoption of military technologies (most notably, iron weapons and cavalry in the first millennium BCE).},
  file = {C:\Users\roman\OneDrive\Documents\Library\Turchin et al_2022_Disentangling the evolutionary drivers of social complexity.pdf}
}

@article{unkelbach_inclusion_2004,
  title = {Inclusion of Organ Movements in {{IMRT}} Treatment Planning via Inverse Planning Based on Probability Distributions},
  author = {Unkelbach, J and Oelfke, U},
  year = {2004},
  month = sep,
  journal = {Physics in Medicine and Biology},
  volume = {49},
  number = {17},
  pages = {4005--4029},
  issn = {0031-9155, 1361-6560},
  doi = {10.1088/0031-9155/49/17/013},
  urldate = {2021-06-14},
  abstract = {In this paper, we investigate an off-line strategy to incorporate inter-fraction organ motion in IMRT treatment planning. It was suggested that inverse planning could be based on a probability distribution of patient geometries instead of a single snap shot. However, this concept is connected to two intrinsic problems: first, this probability distribution has to be estimated from only a few images; and second, the distribution is only sparsely sampled over the treatment course due to a finite number of fractions. In the current work, we develop new concepts of inverse planning which account for these two problems.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Unkelbach_Oelfke_2004_Inclusion of organ movements in IMRT treatment planning via inverse planning.pdf}
}

@article{unkelbach_role_2020,
  title = {The Role of Computational Methods for Automating and Improving Clinical Target Volume Definition},
  author = {Unkelbach, Jan and Bortfeld, Thomas and Cardenas, Carlos E. and Gregoire, Vincent and Hager, Wille and Heijmen, Ben and Jeraj, Robert and Korreman, Stine S. and Ludwig, Roman and Pouymayou, Bertrand and Shusharina, Nadya and S{\"o}derberg, Jonas and {Toma-Dasu}, Iuliana and Troost, Esther G. C. and Vasquez Osorio, Eliana},
  year = {2020},
  month = dec,
  journal = {Radiotherapy and Oncology},
  series = {Physics {{Special Issue}}: {{ESTRO Physics Research Workshops}} on {{Science}} in {{Development}}},
  volume = {153},
  pages = {15--25},
  issn = {0167-8140},
  doi = {10.1016/j.radonc.2020.10.002},
  urldate = {2023-03-13},
  abstract = {Treatment planning in radiotherapy distinguishes three target volume concepts: the gross tumor volume (GTV), the clinical target volume (CTV), and the planning target volume (PTV). Over time, GTV definition and PTV margins have improved through the development of novel imaging techniques and better image guidance, respectively. CTV definition is sometimes considered the weakest element in the planning process. CTV definition is particularly complex since the extension of microscopic disease cannot be seen using currently available in-vivo imaging techniques. Instead, CTV definition has to incorporate knowledge of the patterns of tumor progression. While CTV delineation has largely been considered the domain of radiation oncologists, this paper, arising from a 2019 ESTRO Physics research workshop, discusses the contributions that medical physics and computer science can make by developing computational methods to support CTV definition. First, we overview the role of image segmentation algorithms, which may in part automate CTV delineation through segmentation of lymph node stations or normal tissues representing anatomical boundaries of microscopic tumor progression. The recent success of deep convolutional neural networks has also enabled learning entire CTV delineations from examples. Second, we discuss the use of mathematical models of tumor progression for CTV definition, using as example the application of glioma growth models to facilitate GTV-to-CTV expansion for glioblastoma that is consistent with neuroanatomy. We further consider statistical machine learning models to quantify lymphatic metastatic progression of tumors, which may eventually improve elective CTV definition. Lastly, we discuss approaches to incorporate uncertainty in CTV definition into treatment plan optimization as well as general limitations of the CTV concept in the case of infiltrating tumors without natural boundaries.},
  langid = {english},
  keywords = {Automatic image segmentation,Clinical target volume,Computational tumor growth models},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Unkelbach et al_2020_The role of computational methods for automating and improving clinical target.pdf;C\:\\Users\\roman\\Zotero\\storage\\X5ESXGRT\\S0167814020308380.html}
}

@article{van_allen_quantifying_2008,
  title = {Quantifying the Uncertainty of a Belief Net Response: {{Bayesian}} Error-Bars for Belief Net Inference},
  author = {Van Allen, T and {Others}},
  year = {2008},
  journal = {Artif. Intell.},
  volume = {172},
  pages = {483--513},
  doi = {10.1016/j.artint.2007.09.004}
}

@article{van_den_bosch_18f-fdg-petct-based_2020,
  title = {{{18F-FDG-PET}}/{{CT-based}} Treatment Planning for Definitive (Chemo)Radiotherapy in Patients with Head and Neck Squamous Cell Carcinoma Improves Regional Control and Survival},
  author = {{van den Bosch}, Sven and Doornaert, Patricia A.H. and Dijkema, Tim and Zwijnenburg, Ellen M. and Verhoef, Lia C.G. and Hoeben, Bianca A.W. and Kasperts, Nicolien and Smid, Ernst J. and Terhaard, Chris H.J. and Kaanders, Johannes H.A.M.},
  year = {2020},
  month = jan,
  journal = {Radiotherapy and Oncology},
  volume = {142},
  pages = {107--114},
  issn = {0167-8140},
  doi = {10.1016/j.radonc.2019.07.025},
  abstract = {Background and purpose Multimodality imaging including 18F-FDG-PET has improved the detection threshold of nodal metastases in head and neck squamous cell carcinoma (HNSCC). The aim of this retrospective analysis is to investigate the impact of FDG-PET/CT-based nodal target volume definition (FDG-PET/CT-based NTV) on radiotherapy outcomes, compared to conventional CT-based nodal target volume definition (CT-based NTV). Materials and methods Six-hundred-thirty-three patients treated for HNSCC with definitive (chemo)radiotherapy using IMRT/VMAT techniques between 2008 and 2017 were analyzed. FDG-PET/CT-based NTV was performed in 46\% of the patients. The median follow-up was 31\,months. Diagnostic imaging depicting the regional recurrence was co-registered with the initial CT-scan to reconstruct the exact site of the recurrence. Multivariate Cox regression analysis was performed to identify variables associated with radiotherapy outcome. Results FDG-PET/CT-based NTV improved control of disease in the CTVelective-nodal (HR: 0.33, p\,=\,0.026), overall regional control (HR: 0.62, p\,=\,0.027) and overall survival (HR: 0.71, p\,=\,0.033) compared to CT-based NTV. The risk for recurrence in the CTVelective-nodal was increased in case of synchronous local recurrence of the primary tumor (HR: 12.4, p\,{$<$}\,0.001). Conclusion FDG-PET/CT-based NTV significantly improved control of disease in the CTVelective-nodal, overall regional control and overall survival compared to CT-based NTV. A significant proportion of CTVelective-nodal recurrences are potentially new nodal manifestations from a synchronous local recurrent primary tumor. These results support the concept of target volume transformation and give an indication of the potential of FDG-PET to guide gradual radiotherapy dose de-escalation in elective neck treatment in HNSCC.},
  keywords = {Elective irradiation,FDG-PET,Head and neck cancer,Nodal target volume definition,Radiotherapy,Target volume transformation},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\van den Bosch et al_2020_18F-FDG-PET-CT-based treatment planning for definitive (chemo)radiotherapy in.pdf;C\:\\Users\\roman\\OneDrive\\Foam\\references\\@van_den_bosch_18f-fdg-petct-based_2020.md}
}

@article{van_dijk_head_2023,
  title = {Head and Neck Cancer Predictive Risk Estimator to Determine Control and Therapeutic Outcomes of Radiotherapy ({{HNC-PREDICTOR}}): Development, International Multi-Institutional Validation, and Web Implementation of Clinic-Ready Model-Based Risk Stratification for Head and Neck Cancer},
  shorttitle = {Head and Neck Cancer Predictive Risk Estimator to Determine Control and Therapeutic Outcomes of Radiotherapy ({{HNC-PREDICTOR}})},
  author = {{van Dijk}, Lisanne V. and Mohamed, Abdallah Sr and Ahmed, Sara and Nipu, Nafiul and Marai, G. Elisabeta and Wahid, Kareem and Sijtsema, Nanna M. and Gunn, Brandon and Garden, Adam S. and Moreno, Amy and Hope, Andrew J. and Langendijk, Johannes A. and Fuller, Clifton D.},
  year = {2023},
  month = jan,
  journal = {European Journal of Cancer (Oxford, England: 1990)},
  volume = {178},
  pages = {150--161},
  issn = {1879-0852},
  doi = {10.1016/j.ejca.2022.10.011},
  abstract = {BACKGROUND: Personalised radiotherapy can improve treatment outcomes of patients with head and neck cancer (HNC), where currently a 'one-dose-fits-all' approach is the standard. The aim was to establish individualised outcome prediction based on multi-institutional international 'big-data' to facilitate risk-based stratification of patients with HNC. METHODS: The data of 4611 HNC radiotherapy patients from three academic cancer centres were split into four cohorts: a training (n~=~2241), independent test (n~=~786), and external validation cohorts 1 (n~=~1087) and 2 (n~=~497). Tumour- and patient-related clinical variables were considered in a machine learning pipeline to predict overall survival (primary end-point) and local and regional tumour control (secondary end-points); serially, imaging features were considered for optional model improvement. Finally, patients were stratified into high-, intermediate-, and low-risk groups. RESULTS: Performance score, AJCC8thstage, pack-years, and Age were identified as predictors for overall survival, demonstrating good performance in both the training cohort (c-index~=~0.72 [95\% CI, 0.66-0.77]) and in all three validation cohorts (c-indices: 0.76 [0.69-0.83], 0.73 [0.68-0.77], and 0.75 [0.68-0.80]). Excellent stratification of patients with HNC into high, intermediate, and low mortality risk was achieved; with 5-year overall survival rates of 17-46\% for the high-risk group compared to 92-98\% for the low-risk group. The addition of morphological image feature further improved the performance (c-index~=~0.73 [0.64-0.81]). These models are integrated in a clinic-ready interactive web interface: https://uic-evl.github.io/hnc-predictor/ CONCLUSIONS: Robust model-based prediction was able to stratify patients with HNC in distinct high, intermediate, and low mortality risk groups. This can effectively be capitalised for personalised radiotherapy, e.g., for tumour radiation dose escalation/de-escalation.},
  langid = {english},
  pmcid = {PMC9853413},
  pmid = {36442460},
  keywords = {Decision support tool,Head and neck cancer,Head and Neck Neoplasms,Humans,Image biomarkers,Machine learning,Overall survival,Prognosis,Risk Assessment,Risk Factors,Treatment Outcome},
  file = {C:\Users\roman\Zotero\storage\UEI7W7R9\van Dijk et al_2023_Head and neck cancer predictive risk estimator to determine control and.pdf}
}

@article{vanderplas_python_nodate,
  title = {Python {{Data Science Handbook}}},
  author = {VanderPlas, Jake},
  pages = {548},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\VanderPlas_Python Data Science Handbook.pdf}
}

@article{vauterin_patterns_2006,
  title = {{{PATTERNS OF LYMPH NODE SPREAD OF CUTANEOUS SQUAMOUS CELL CARCINOMA OF THE HEAD AND NECK}}},
  author = {Vauterin, Tom J and Veness, Michael J and Morgan, Garry J and Poulsen, Michael G and O'Brien, Christopher J},
  year = {2006},
  pages = {7},
  abstract = {Background. Among patients with cutaneous squamous cell carcinoma (SCC) of the head and neck, recent studies have shown that those with involvement of the parotid gland also have a high incidence of neck node involvement. Treatment of the neck by either surgery or radiotherapy is therefore recommended among patients with parotid SCC, even if clinical examination is negative. The aim of this study was first to analyze patterns of metastatic spread in the parotid and cervical lymph nodes and then to correlate the pattern of involved nodes with the primary cutaneous site in order to guide the appropriate extent of surgery, should neck dissection be used to treat the neck in patients with parotid SCC.},
  langid = {english},
  keywords = {patterns},
  file = {C:\Users\roman\OneDrive\Documents\Library\Vauterin et al_2006_PATTERNS OF LYMPH NODE SPREAD OF CUTANEOUS SQUAMOUS CELL CARCINOMA OF THE HEAD.pdf}
}

@article{vitale_mitotic_2011,
  title = {Mitotic Catastrophe: A Mechanism for Avoiding Genomic Instability},
  shorttitle = {Mitotic Catastrophe},
  author = {Vitale, Ilio and Galluzzi, Lorenzo and Castedo, Maria and Kroemer, Guido},
  year = {2011},
  month = jun,
  journal = {Nature Reviews Molecular Cell Biology},
  volume = {12},
  number = {6},
  pages = {385--392},
  publisher = {{Nature Publishing Group}},
  issn = {1471-0080},
  doi = {10.1038/nrm3115},
  urldate = {2023-03-10},
  abstract = {The improper distribution of chromosomes during mitosis can contribute to malignant transformation. Higher eukaryotes have developed strategies for eliminating mitosis-incompetent cells, one of which is mitotic catastrophe. From a functional perspective, mitotic catastrophe can be defined as an oncosuppressive mechanism that precedes (and is distinct from) apoptosis, necrosis or senescence.},
  copyright = {2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  langid = {english},
  keywords = {Cancer,Cell death,Chromosomes,Genomic instability,Mechanisms of disease,Mitosis}
}

@article{vogel_prostate-specific_2022,
  title = {Prostate-Specific {{Membrane Antigen Positron Emission Tomography}}/{{Computed Tomography}}{\textendash}Based {{Lymph Node Atlas}} for {{Salvage Radiotherapy}} in {{Patients}} with {{Recurrent Prostate Cancer}}: {{A Validation}} of the {{New NRG Oncology}} 2020 Guideline},
  shorttitle = {Prostate-Specific {{Membrane Antigen Positron Emission Tomography}}/{{Computed Tomography}}{\textendash}Based {{Lymph Node Atlas}} for {{Salvage Radiotherapy}} in {{Patients}} with {{Recurrent Prostate Cancer}}},
  author = {Vogel, Marco M. E. and D{\"u}sberg, Mathias and St{\"o}hrer, Lucia and Dewes, Sabrina and Sage, Eva K. and Borm, Kai J. and Gschwend, J{\"u}rgen E. and Eiber, Matthias and Combs, Stephanie E. and Schiller, Kilian},
  year = {2022},
  month = dec,
  journal = {European Urology Oncology},
  volume = {5},
  number = {6},
  pages = {668--676},
  issn = {2588-9311},
  doi = {10.1016/j.euo.2022.09.006},
  urldate = {2023-03-31},
  abstract = {Background Approximately 20{\textendash}40\% of patients with prostate cancer (PC) who undergo radical prostatectomy (RP) experience relapse, with the majority of these cases developing pelvic lymph node (LN) metastases. Taking new data from the prostate-specific membrane antigen (PSMA) positron emission tomography (PET) era into account, the Radiation Therapy Oncology Group (RTOG) 2009 contouring guideline for the pelvic LNs from 2009 was updated by the NRG Oncology group in 2020 (NRG 2020). Objective To evaluate and validate the updated NRG 2020 guideline with our established LN atlas. Design, setting, and participants We screened 1653 PSMA PET/computed tomography (CT) data sets for patients with biochemical relapse who underwent a PET scan between November 2012 and November 2017. After screening, we developed an LN atlas using data from 233 patients. Outcome measurements and statistical analysis We evaluated LN overlap (OL) with the RTOG 2009 and NRG 2020 contouring guidelines. OL was defined as within ({$>$}90\%), partly within (10{\textendash}90\%), or outside ({$<$}10\%). Results and limitations In comparison to the RTOG 2009 guideline, 403 (52\%), 134 (17\%), and 241 (31\%) of the LNs were not, were partly, or were fully covered within the overall group, respectively. By contrast, using the NRG 2020 guideline, 302 (39\%), 190 (24\%), and 286 (37\%) of the LNs were not, were partly, or were fully covered, respectively (p~{$<~$}0.001). Limitations include the retrospective design with missing data and no histopathological confirmation of the PET results. Conclusions The updated NRG 2020 contouring guideline improves coverage of the pelvic LNs in patients undergoing salvage radiation therapy. However, PET/CT should be considered whenever possible to ensure coverage of untypical LN spread. Patient summary We compared the 2009 and 2020 guidelines on the radiation area for the pelvis for patients with recurrent prostate cancer that has spread to lymph nodes. The newer guideline provides better coverage of pelvic lymph nodes than the older one and is useful in planning radiation therapy. However, a scan of the pelvis using the newest technique should be considered for individual patients to ensure coverage of untypical lymph nodes.},
  langid = {english},
  keywords = {Contouring guideline,Irradiation,NRG Oncology,Pelvic lymph node,Prostate cancer,Prostate-specific membrane antigen positron emission tomography,Radiation Therapy Oncology Group,Radiotherapy},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Vogel et al_2022_Prostate-specific Membrane Antigen Positron Emission Tomography-Computed.pdf;C\:\\Users\\roman\\Zotero\\storage\\J4UBLIRV\\S2588931122001705.html}
}

@article{vorwerk_guidelines_2011,
  title = {Guidelines for Delineation of Lymphatic Clinical Target Volumes for High Conformal Radiotherapy: Head and Neck Region},
  author = {Vorwerk, Hilke and Hess, Clemens F.},
  year = {2011},
  month = aug,
  journal = {Radiation Oncology},
  volume = {6},
  number = {1},
  pages = {97},
  issn = {1748-717X},
  doi = {10.1186/1748-717X-6-97},
  abstract = {The success of radiotherapy depends on the accurate delineation of the clinical target volume. The delineation of the lymph node regions has most impact, especially for tumors in the head and neck region. The purpose of this article was the development an atlas for the delineation of the clinical target volume for patients, who should receive radiotherapy for a tumor of the head and neck region. Literature was reviewed for localisations of the adjacent lymph node regions and their lymph drain in dependence of the tumor entity. On this basis the lymph node regions were contoured on transversal CT slices. The probability for involvement was reviewed and a recommendation for the delineation of the CTV was generated.},
  keywords = {guideline}
}

@article{weiss_use_1997,
  title = {Use of Decision Analysis in Planning a Management Strategy for the Stage {{NO}} Neck},
  author = {Weiss, M H and Harrison, L B and Isaacs, R S},
  year = {1997},
  journal = {Arch. Otolaryngol. Head Neck Surg.},
  volume = {120},
  pages = {699--702},
  doi = {10.1001/archotol.1994.01880310005001}
}

@article{weissmann_deep_2023,
  title = {Deep {{Learning}} and {{Registration-Based Mapping}} for {{Analyzing}} the {{Distribution}} of {{Nodal Metastases}} in {{Head}} and {{Neck Cancer Cohorts}}: {{Informing Optimal Radiotherapy Target Volume Design}}},
  shorttitle = {Deep {{Learning}} and {{Registration-Based Mapping}} for {{Analyzing}} the {{Distribution}} of {{Nodal Metastases}} in {{Head}} and {{Neck Cancer Cohorts}}},
  author = {Weissmann, Thomas and Mansoorian, Sina and May, Matthias Stefan and Lettmaier, Sebastian and H{\"o}fler, Daniel and Deloch, Lisa and Speer, Stefan and Balk, Matthias and Frey, Benjamin and Gaipl, Udo S. and Bert, Christoph and Distel, Luitpold Valentin and Walter, Franziska and Belka, Claus and Semrau, Sabine and Iro, Heinrich and Fietkau, Rainer and Huang, Yixing and Putz, Florian},
  year = {2023},
  month = jan,
  journal = {Cancers},
  volume = {15},
  number = {18},
  pages = {4620},
  publisher = {{Multidisciplinary Digital Publishing Institute}},
  issn = {2072-6694},
  doi = {10.3390/cancers15184620},
  urldate = {2023-10-18},
  abstract = {We introduce a deep-learning- and a registration-based method for automatically analyzing the spatial distribution of nodal metastases (LNs) in head and neck (H/N) cancer cohorts to inform radiotherapy (RT) target volume design. The two methods are evaluated in a cohort of 193 H/N patients/planning CTs with a total of 449 LNs. In the deep learning method, a previously developed nnU-Net 3D/2D ensemble model is used to autosegment 20 H/N levels, with each LN subsequently being algorithmically assigned to the closest-level autosegmentation. In the nonrigid-registration-based mapping method, LNs are mapped into a calculated template CT representing the cohort-average patient anatomy, and kernel density estimation is employed to estimate the underlying average 3D-LN probability distribution allowing for analysis and visualization without prespecified level definitions. Multireader assessment by three radio-oncologists with majority voting was used to evaluate the deep learning method and obtain the ground-truth distribution. For the mapping technique, the proportion of LNs predicted by the 3D probability distribution for each level was calculated and compared to the deep learning and ground-truth distributions. As determined by a multireader review with majority voting, the deep learning method correctly categorized all 449 LNs to their respective levels. Level 2 showed the highest LN involvement (59.0\%). The level involvement predicted by the mapping technique was consistent with the ground-truth distribution (p for difference 0.915). Application of the proposed methods to multicenter cohorts with selected H/N tumor subtypes for informing optimal RT target volume design is promising.},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  langid = {english},
  keywords = {artificial intelligence,atlas,autosegmentation,deep learning,head and neck cancer,lymph node level classification,mapping,nodal metastasis,radiotherapy,target volume design},
  file = {C:\Users\roman\Zotero\storage\LGRQ579S\Weissmann et al_2023_Deep Learning and Registration-Based Mapping for Analyzing the Distribution of.pdf}
}

@article{willard-mack_normal_2006,
  title = {Normal {{Structure}}, {{Function}}, and {{Histology}} of {{Lymph Nodes}}},
  author = {{Willard-Mack}, Cynthia L.},
  year = {2006},
  month = aug,
  journal = {Toxicologic Pathology},
  volume = {34},
  number = {5},
  pages = {409--424},
  publisher = {{SAGE Publications Inc}},
  issn = {0192-6233},
  doi = {10.1080/01926230600867727},
  urldate = {2022-10-10},
  abstract = {Lymph nodes are traditionally regarded as having three compartments, the cortex, paracortex and medulla. B and T cells home to separate areas within these compartments, interact with antigen presenting cells, and undergo clonal expansion. This paper provides structural and functional details about how the lymph node brings lymphocytes and antigen presenting cells together. The concept of the lymphoid lobule as the basic functional and anatomic unit of the lymph node is developed and utilized to provide a framework for understanding lymph node pathobiology. Understanding the histomorphologic features of the lymphoid lobule and the role of the reticular meshwork scaffolding of the lymph node and how these related to the cortex, paracortex and medulla provides a unique approach to understanding lymph node structure and function.},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Willard-Mack_2006_Normal Structure, Function, and Histology of Lymph Nodes.pdf}
}

@article{wissmann_pathways_2006,
  title = {Pathways {{Targeting Tumor Lymphangiogenesis}}},
  author = {Wissmann, Christoph and Detmar, Michael},
  year = {2006},
  month = dec,
  journal = {Clinical Cancer Research},
  volume = {12},
  number = {23},
  pages = {6865--6868},
  issn = {1078-0432},
  doi = {10.1158/1078-0432.CCR-06-1800},
  urldate = {2022-10-07},
  abstract = {Tumor metastasis to sentinel lymph nodes represents the first step of tumor dissemination in most human cancers and serves as a major prognostic indicator for disease progression. Recent studies have revealed that tumors can actively induce the formation of lymphatic vessels, and that tumor lymphangiogenesis is correlated with lymph node metastasis in experimental cancer models and in several types of human cancers. Metastatic tumor cells may continue to promote lymphatic vessel growth even after their metastasis to sentinel lymph nodes, likely promoting further cancer spread. Vascular endothelial growth factor-C (VEGF-C) and VEGF-D were the first specific lymphangiogenesis factors identified, acting predominantly via VEGF receptor-3 (VEGFR-3) that is expressed by lymphatic endothelial cells, and a large number of clinical studies have shown a correlation between tumor expression of VEGF-C or VEGF-D and lymph node metastasis. VEGFR-3 activation promotes lymphatic endothelial cell proliferation, migration, and survival via the extracellular signal-regulated kinase 1/2, the phosphatidylinositol 3-kinase/AKT, and the c-Jun NH2-terminal kinase 1/2 pathways. Additional tumor lymphangiogenesis factors have been recently identified, including VEGF-A. Importantly, blockade of the VEGFR-3 pathway by specific antibodies, by soluble receptor constructs, and by small molecule kinase inhibitors efficiently inhibits experimental tumor lymphangiogenesis and metastasis and might also represent a novel therapeutic avenue for the treatment of human cancers.},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Wissmann_Detmar_2006_Pathways Targeting Tumor Lymphangiogenesis.pdf;C\:\\Users\\roman\\Zotero\\storage\\DLIFVYX5\\Pathways-Targeting-Tumor-Lymphangiogenesis.html}
}

@article{wong_cancers_2014,
  title = {Cancers of the Lung, Head and Neck on the Rise: Perspectives on the Genotoxicity of Air Pollution},
  shorttitle = {Cancers of the Lung, Head and Neck on the Rise},
  author = {Wong, Ian Chi Kei and Ng, Yuen-Keng and Lui, Vivian Wai Yan},
  year = {2014},
  month = oct,
  journal = {Chinese Journal of Cancer},
  volume = {33},
  number = {10},
  pages = {476--480},
  issn = {1000-467X},
  doi = {10.5732/cjc.014.10093},
  urldate = {2022-10-06},
  abstract = {Outdoor air pollution has been recently classified as a class I human carcinogen by the World Health Organization (WHO). Cumulative evidence from across the globe shows that polluted air is associated with increased risk of lung, head and neck, and nasopharyngeal cancers{\textemdash}all of which affect the upper aerodigestive tract. Importantly, these cancers have been previously linked to smoking. In this article, we review epidemiologic and experimental evidence of the genotoxic and mutagenic effects of air pollution on DNA, purportedly a key mechanism for cancer development. The alarming increase in cancers of the upper aerodigestive tract in Asia suggests a need to focus government efforts and research on reducing air pollution, promoting clean energy, and investigating the carcinogenic effects of air pollution on humans.},
  pmcid = {PMC4198750},
  pmid = {25011457},
  file = {C:\Users\roman\OneDrive\Documents\Library\Wong et al_2014_Cancers of the lung, head and neck on the rise.pdf}
}

@article{woolgar_histological_1999,
  title = {Histological Distribution of Cervical Lymph Node Metastases from Intraoral/Oropharyngeal Squamous Cell Carcinomas},
  author = {Woolgar, J.A.},
  year = {1999},
  month = jun,
  journal = {British Journal of Oral and Maxillofacial Surgery},
  volume = {37},
  number = {3},
  pages = {175--180},
  issn = {0266-4356},
  doi = {10.1054/bjom.1999.0036},
  abstract = {SUMMARY. The histological frequency and distribution of cervical lymph node metastases was studied in 326 neck dissections from 253 patients with an intraoral/oropharyngeal squamous cell carcinoma. Metastasis was evident in 118 patients (47\%) and 18 had bilateral metastasis. For primary sites other than the tongue, metastasis developed initially in a node(s) in the first drainage group (level I or II) with progressive involvement of neighbouring nodes (`overflow'). Simultaneous bilateral metastases were seen in some tumours of the floor of mouth, tongue and oropharynx which involved the midline. An erratic distribution of metastases suggestive of `fast-tracking' (skip lesions and peppering) was only seen in tongue tumours. The pattern of metastatic spread indicates that level IV nodes must be included in staging and therapeutic neck dissections in tongue cancer. Metastasis to `accessory' lymph nodes (lingual, buccal) occurs infrequently but may explain some `local' recurrences.},
  keywords = {patterns},
  file = {C:\Users\roman\OneDrive\Documents\Library\Woolgar_1999_Histological distribution of cervical lymph node metastases from.pdf}
}

@article{woolgar_topography_2007,
  title = {The Topography of Cervical Lymph Node Metastases Revisited: The Histological Findings in 526 Sides of Neck Dissection from 439 Previously Untreated Patients},
  author = {Woolgar, J.A.},
  year = {2007},
  month = mar,
  journal = {International journal of oral and maxillofacial surgery},
  volume = {36},
  number = {3},
  pages = {219--225},
  issn = {0901-5027},
  doi = {10.1016/j.ijom.2006.10.014},
  abstract = {The pathological reports, minimum datasets and topographical plots of the neck dissections from 439 cases of oral and oropharyngeal cancer reported by a single pathologist following a standard protocol were analysed. Metastasis was evident in 47\% of patients including bilateral metastases in 6\%, extracapsular spread in 29\% and matting in 7\%. The extent of metastasis (both volume and distribution) was greatest in tumours of the oropharynx followed by lateral tongue, ventral tongue and floor of mouth. The typical 'inverted-cone pattern' was seen in 67\% of patients with metastasis. A single micrometastasis was seen in 14\%, skip lesions in 10\% and involvement of 'other' nodal groups in 4\%. Contralateral neck metastases (0.4\%), peppering (2\%), flushing of lymph node sinuses (1\%) and all nodes positive (0.4\%) accounted for the remaining 'aberrant' patterns. Skip lesions were seen in tumours at all sites other than retromolar.},
  langid = {english},
  keywords = {patterns},
  file = {C:\Users\roman\OneDrive\Documents\Library\Woolgar_2007_The topography of cervical lymph node metastases revisited.pdf}
}

@book{world_health_organization_international_2004,
  title = {International Statistical Classification of Diseases and Related Health Problems},
  editor = {World Health Organization},
  year = {2004},
  edition = {10th revision, 2nd edition},
  publisher = {{World Health Organization}},
  address = {{Geneva}},
  isbn = {978-92-4-154649-2 978-92-4-154653-9 978-92-4-154654-6},
  langid = {english},
  lccn = {RB115 .I6 2004},
  keywords = {Nosology},
  file = {C:\Users\roman\OneDrive\Documents\Library\World Health Organization_2004_International statistical classification of diseases and related health problems.pdf}
}

@article{wynne_what_2006,
  title = {What Are {{Animals}}? {{Why Anthropomorphism}} Is {{Still Not}} a {{Scientific Approach}} to {{Behavior}}},
  shorttitle = {What Are {{Animals}}?},
  author = {Wynne, Clive D. L.},
  year = {2006},
  journal = {Comparative Cognition \& Behavior Reviews},
  volume = {2},
  issn = {19114745},
  doi = {10.3819/ccbr.2008.20008},
  urldate = {2022-12-28},
  langid = {english},
  file = {C:\Users\roman\OneDrive\Documents\Library\Wynne_2006_What are Animals.pdf}
}

@article{xing_relation_2016,
  title = {Relation between the Level of Lymph Node Metastasis and Survival in Locally Advanced Head and Neck Squamous Cell Carcinoma},
  author = {Xing, Yan and Zhang, Jianjun and Lin, Heather and Gold, Kathryn A. and Sturgis, Erich M. and Garden, Adam S. and Lee, J. Jack and William Jr, William N.},
  year = {2016},
  journal = {Cancer},
  volume = {122},
  number = {4},
  pages = {534--545},
  issn = {1097-0142},
  doi = {10.1002/cncr.29780},
  urldate = {2023-03-10},
  abstract = {BACKGROUND The current head and neck squamous cell carcinoma (HNSCC) staging system may not capture the full prognostic implications of regional lymph node involvement. This study investigated the impact of the level of lymph node metastasis (LNM) on survival. METHODS The Surveillance, Epidemiology, and End Results registry was queried for oral cavity (OC), oropharynx (OP), larynx (LAR), and hypopharynx (HP) HNSCC. A multivariate Cox proportional hazards model was used to evaluate whether the level of LNM was an independent prognostic factor. Site-specific recursive-partitioning analysis was performed to classify patients into different risk groups. RESULTS In all, 14,499 patients, including OC (n = 2463), OP (n = 8567), LAR (n = 2332), and HP patients (n = 1137), were analyzed. Both the American Joint Committee on Cancer (AJCC) N classification and the level of LNM showed significant effects on overall survival (OS) in patients with OC, OP, or LAR HNSCC but not in patients with HP HNSCC. In patients with N2 disease, the AJCC subclassification (N2a, N2b, or N2c) was significantly associated with the OS of patients with OP and LAR HNSCC but not with the OS of patients with OC or HP HNSCC, whereas the level of LNM (primary, secondary, or tertiary) was significantly associated with the OS of patients with OC, OP, and LAR HNSCC but not HP HNSCC. With recursive-partitioning analysis, a simple, primary site{\textendash}specific prognostic tool integrating the AJCC T and N classifications and the level of LNM was designed, and it could be easily used by health care providers in clinic. CONCLUSIONS The level of LNM is an independent prognostic factor for patients with locally advanced HNSCC and could add to the prognostic value of AJCC T and N classifications in patients with locally advanced HNSCC. Cancer 2016;122:534{\textendash}545. {\textcopyright} 2015 American Cancer Society.},
  langid = {english},
  keywords = {and End Results (SEER),Epidemiology,head and neck neoplasms,lymph nodes,metastasis,squamous cell cancer,Surveillance,survival,TNM},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Xing et al_2016_Relation between the level of lymph node metastasis and survival in locally.pdf;C\:\\Users\\roman\\Zotero\\storage\\U79E4TUZ\\cncr.html}
}

@inproceedings{zagorecki_probabilistic_2006,
  title = {Probabilistic {{Independence}} of {{Causal Influences}}.},
  author = {Zagorecki, Adam and Druzdzel, Marek},
  year = {2006},
  month = jan,
  pages = {325--332},
  abstract = {One practical problem with building large scale Bayesian network models is an expo- nential growth of the number of numerical parameters in conditional probability tables. Obtaining large number of probabilities from domain experts is too expensive and too time demanding in practice. A widely accepted solution to this problem is the assumption of independence of causal influences (ICI) which allows for parametric models that define conditional probability distributions using only a number of parameters that is linear in the number of causes. ICI models, such as the noisy-OR and the noisy-AND gates, have been widely used by practitioners. In this paper we propose PICI, probabilistic ICI, an extension of the ICI assumption that leads to more expressive parametric models. We provide examples of three PICI models and demonstrate how they can cope with a com- bination of positive and negative influences, something that is hard for noisy-OR and noisy-AND gates.},
  file = {C:\Users\roman\OneDrive\Documents\Library\Zagorecki_Druzdzel_2006_Probabilistic Independence of Causal Influences.pdf}
}

@article{zhang_mapping_2020,
  title = {Mapping the Spreading Routes of Lymphatic Metastases in Human Colorectal Cancer},
  author = {Zhang, Chong and Zhang, Lin and Xu, Tianlei and Xue, Ruidong and Yu, Liang and Zhu, Yuelu and Wu, Yunlong and Zhang, Qingqing and Li, Dongdong and Shen, Shuohao and Tan, Dongfeng and Bai, Fan and Zhang, Haizeng},
  year = {2020},
  month = apr,
  journal = {Nature Communications},
  volume = {11},
  number = {1},
  pages = {1993},
  publisher = {{Nature Publishing Group}},
  issn = {2041-1723},
  doi = {10.1038/s41467-020-15886-6},
  urldate = {2022-07-26},
  abstract = {Lymphatic metastases are closely associated with tumor relapse and reduced survival in colorectal cancer (CRC). How tumor cells disseminate within the lymphatic network remains largely unknown. Here, we analyze the subclonal structure of 94 tumor samples, covering the primary tumors, lymph node metastases (LNMs), and liver metastases from 10 CRC patients. We portray a high-resolution lymphatic metastatic map for CRC by dividing LNMs into paracolic, intermediate, and central subgroups. Among the 61 metastatic routes identified, 38 (62.3\%) are initiated from the primary tumors, 22 (36.1\%) from LNMs, and 1 from liver metastasis (1.6\%). In 5 patients, we find 6 LNMs that reseed 2 or more LNMs. We summarize 3 diverse modes of metastasis in CRC and show that skip spreading of tumor cells within the lymphatic network is common. Our study sheds light on the complicated metastatic pattern in CRC and has great clinical implications.},
  copyright = {2020 The Author(s)},
  langid = {english},
  keywords = {Cancer genomics,Gastrointestinal cancer,Metastasis},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Zhang et al_2020_Mapping the spreading routes of lymphatic metastases in human colorectal cancer.pdf;C\:\\Users\\roman\\Zotero\\storage\\4Y98YSHK\\s41467-020-15886-6.html}
}

@article{zhou_bayesian_2014,
  title = {Bayesian Network Approach to Multinomial Parameter Learning Using Data and Expert Judgments},
  author = {Zhou, Y and Fenton, N and Neil, M},
  year = {2014},
  journal = {Int. J. Approx. Reason.},
  volume = {55},
  pages = {1252--1268},
  doi = {10.1016/j.ijar.2014.02.008}
}

@article{zhou_bop2_2017,
  title = {{{BOP2}}: {{Bayesian}} Optimal Design for Phase {{II}} Clinical Trials with Simple and Complex Endpoints},
  shorttitle = {{{BOP2}}},
  author = {Zhou, Heng and Lee, J. Jack and Yuan, Ying},
  year = {2017},
  journal = {Statistics in Medicine},
  volume = {36},
  number = {21},
  pages = {3302--3314},
  issn = {1097-0258},
  doi = {10.1002/sim.7338},
  urldate = {2023-07-21},
  abstract = {We propose a flexible Bayesian optimal phase II (BOP2) design that is capable of handling simple (e.g., binary) and complicated (e.g., ordinal, nested, and co-primary) endpoints under a unified framework. We use a Dirichlet-multinomial model to accommodate different types of endpoints. At each interim, the go/no-go decision is made by evaluating a set of posterior probabilities of the events of interest, which is optimized to maximize power or minimize the number of patients under the null hypothesis. Unlike other existing Bayesian designs, the BOP2 design explicitly controls the type I error rate, thereby bridging the gap between Bayesian designs and frequentist designs. In addition, the stopping boundary of the BOP2 design can be enumerated prior to the onset of the trial. These features make the BOP2 design accessible to a wide range of users and regulatory agencies and particularly easy to implement in practice. Simulation studies show that the BOP2 design has favorable operating characteristics with higher power and lower risk of incorrectly terminating the trial than some existing Bayesian phase II designs. The software to implement the BOP2 design is freely available at www.trialdesign.org. Copyright {\textcopyright} 2017 John Wiley \& Sons, Ltd.},
  langid = {english},
  keywords = {Bayesian adaptive design,co-primary endpoints,early stopping,immunotherapy,ordinal endpoint},
  file = {C\:\\Users\\roman\\OneDrive\\Documents\\Library\\Zhou et al_2017_BOP2.pdf;C\:\\Users\\roman\\Zotero\\storage\\ZMLZV9K7\\sim.html}
}

@phdthesis{zora231470,
  title = {Modelling Lymphatic Metastatic Progression in Head and Neck Cancer},
  author = {Ludwig, Roman},
  year = {2023},
  address = {{Zurich}},
  abstract = {Head and neck squamous cell carcinomas (HNSCCs) are often treated using radiotherapy. Because this type of cancer frequently spreads to regional lymph nodes, parts of the lymphatic system are irradiated alongside the primary tumor. Macroscopic nodal metastasis, visible on imaging modalities such as computed tomography, is always included in the target volume of radiotherapy. Additionally, clinicians electively irradiate lymph node levels (LNLs) when their estimated risk to harbor microscopic disease exceeds a given threshold. Currently, this risk estimate is based on the overall prevalence of metastatic involvement in a given LNL as reported in the literature. However, few published studies on lymphatic metastatic progression patterns investigate how the probability of involvement of LNLs depends on the involvement of other levels and clinicopathological factors such as T-category, which is of crucial importance to create more personalized elective target volumes. This work makes three related contributions to address this problem: 1) We extracted a dataset of patients diagnosed with oropharyngeal SCC at the University Hospital Zurich (USZ). This dataset details the observed involvement per LNL and diagnostic modality together with tumor characteristics including subsite, T-category, lateralization and HPV status. It is thereby the most detailed dataset on patterns of lymphatic progression to date. 2) In addition to sharing the full dataset freely with the research community, we developed an intuitive web page named LyProX. The interface on this web page allows researchers to visually and interactively explore the data extracted at the USZ, as well as another dataset that was kindly provided to us by Vincent Gr{\'e}goire in response to our efforts. 3) Lastly, we have developed a hidden Markov model (HMM) that predicts the risk of microscopic disease, given an individual patient's clinical diagnosis. It builds on a previous probabilistic model using Bayesian networks (BNs) for the involvement of ipsilateral LNLs I, II, III, and IV, but extends it to naturally include T-category as diagnostic variable. Using Bayesian model comparison, the HMM framework is extended to include the LNLs I, II, III, IV, V, and VII in both the ipsi- and the contralateral side of the neck, accounting for the primary tumor's extension over the mid-sagittal plane as risk factor for contralateral nodal involvement. Ultimately, we train the HMM with the available data and demonstrate how the resulting predictions may be used to quantitatively predict the personalized risk of occult disease. We find that our model supports a reduction of electively irradiated nodal volumes, especially in the contralateral neck. As such, our model may support the design of future clinical trials on volume-deescalated radiotherapy of HNSCC.},
  langid = {english},
  school = {University of Zurich},
  keywords = {elective CTV definition,head and neck cancer,hidden Markov model,metastasis,radiotherapy},
  file = {C:\Users\roman\OneDrive\Documents\Library\Ludwig_2023_Modelling lymphatic metastatic progression in head and neck cancer2.pdf}
}