Quantitative Biology

Authors and titles for October 2020

[51] arXiv:2010.03642 [pdf, other]

Title: Parkland Trauma Index of Mortality (PTIM): Real-time Predictive Model for PolyTrauma Patients

Adam J. Starr, Manjula Julka, Arun Nethi, John D. Watkins, Ryan W. Fairchild, Michael W. Cripps, Dustin Rinehart, Hayden N. Box

Comments: 8 pages, 5 figures

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG)

[52] arXiv:2010.03951 [pdf, other]

Title: MolDesigner: Interactive Design of Efficacious Drugs with Deep Learning

Kexin Huang, Tianfan Fu, Dawood Khan, Ali Abid, Ali Abdalla, Abubakar Abid, Lucas M. Glass, Marinka Zitnik, Cao Xiao, Jimeng Sun

Comments: NeurIPS 2020 Demonstration Track

Subjects: Quantitative Methods (q-bio.QM); Human-Computer Interaction (cs.HC); Machine Learning (cs.LG)

[53] arXiv:2010.04115 [pdf, other]

Title: Modeling the spread of COVID-19 pandemic in Morocco

Houssine Zine, El Mehdi Lotfi, Marouane Mahrouf, Adnane Boukhouima, Yassine Aqachmar, Khalid Hattaf, Delfim F. M. Torres, Noura Yousfi

Comments: This is a preprint of a paper whose final and definite form is published in 'Analysis of Infectious Disease Problems (Covid-19) and Their Global Impact', Springer Nature Singapore Pte Ltd. First submitted 18/April/2020; revised 22/Sept/2020; accepted 08/Oct/2020

Subjects: Populations and Evolution (q-bio.PE)

[54] arXiv:2010.04123 [pdf, other]

Title: Statistical complexity is maximized close to criticality in cortical dynamics

Nastaran Lotfi, Thaís Feliciano, Leandro A. A. Aguiar, Thais Priscila Lima Silva, Tawan T. A. Carvalho, Osvaldo A. Rosso, Mauro Copelli, Fernanda S. Matias, Pedro V. Carelli

Comments: 8 pages, 6 figures

Journal-ref: Phys. Rev. E 103, 012415 (2021)

Subjects: Neurons and Cognition (q-bio.NC)

[55] arXiv:2010.04247 [pdf, other]

Title: Entropic Causal Inference for Neurological Applications

Jeremie Fish, Alexander DeWitt, Abd AlRahman R. AlMomani, Paul J. Laurienti, Erik Bollt

Subjects: Neurons and Cognition (q-bio.NC); Dynamical Systems (math.DS)

[56] arXiv:2010.04269 [pdf, other]

Title: Music to My Ears: Neural modularity and flexibility differ in response to real-world music stimuli

Melia E. Bonomo, Anthony K. Brandt, J. Todd Frazier, Christof Karmonik

Comments: 23 pages, 5 figures

Subjects: Neurons and Cognition (q-bio.NC)

[57] arXiv:2010.04325 [pdf, other]

Title: Minimal Specifications for Non-Human Primate MRI: Challenges in Standardizing and Harmonizing Data Collection

Joonas A. Autio, Qi Zhu, Xiaolian Li, Matthew F. Glasser, Caspar M. Schwiedrzik, Damien A. Fair, Jan Zimmermann, Essa Yacoub, Ravi S. Menon, David C. Van Essen, Takuya Hayashi, Brian Russ, Wim Vanduffel

Subjects: Neurons and Cognition (q-bio.NC)

[58] arXiv:2010.04346 [pdf, other]

Title: State and parameter estimation from exact partial state observation in stochastic reaction networks

Muruhan Rathinam, Mingkai Yu

Subjects: Molecular Networks (q-bio.MN); Probability (math.PR)

[59] arXiv:2010.04378 [pdf, other]

Title: An alternative delayed population growth difference equation model

Sabrina H. Streipert, Gail S. K. Wolkowicz

Comments: 11 pages, 3 figures, Appendix: 13 pages

Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS)

[60] arXiv:2010.04530 [pdf, other]

Title: Evaluation of the Topological Agreement of Network Alignments

Concettina Guerra, Pietro Hiram Guzzi

Subjects: Molecular Networks (q-bio.MN)

[61] arXiv:2010.04574 [pdf, other]

Title: The risk for a new COVID-19 wave -- and how it depends on $R_0$, the current immunity level and current restrictions

Tom Britton, Pieter Trapman, Frank Ball

Subjects: Populations and Evolution (q-bio.PE); Physics and Society (physics.soc-ph)

[62] arXiv:2010.04864 [pdf, other]

Title: A clustering-based biased Monte Carlo approach to protein titration curve prediction

Arun V. Sathanur, Nathan A. Baker

Subjects: Biomolecules (q-bio.BM)

[63] arXiv:2010.04942 [pdf, other]

Title: Contact Tracing & Super-Spreaders in the Branching-Process Model

Johannes Müller, Volker Hösel

Subjects: Populations and Evolution (q-bio.PE); Physics and Society (physics.soc-ph)

[64] arXiv:2010.05079 [pdf, other]

Title: Nowcasting of COVID-19 confirmed cases: Foundations, trends, and challenges

Tanujit Chakraborty, Indrajit Ghosh, Tirna Mahajan, Tejasvi Arora

Subjects: Populations and Evolution (q-bio.PE); Applications (stat.AP)

[65] arXiv:2010.05116 [pdf, other]

Title: Application and Extension of Mean-Field Theory such as SIR to Discuss the Non-Mean Field Problem of COVID-19

Hiroshi Isshiki, Masao Namiki

Comments: 19 pages, 21 figures, 1 table

Subjects: Populations and Evolution (q-bio.PE); Physics and Society (physics.soc-ph)

[66] arXiv:2010.05307 [pdf, other]

Title: Evolution of cooperation and consistent personalities in public goods games

Mohammad Salahshour

Comments: 30 pages, 12 figures

Journal-ref: Sci Rep 11, 23708 (2021)

Subjects: Populations and Evolution (q-bio.PE); Biological Physics (physics.bio-ph)

[67] arXiv:2010.05411 [pdf, other]

Title: Deep Learning Prediction of Adverse Drug Reactions Using Open TG-GATEs and FAERS Databases

Attayeb Mohsen, Lokesh P. Tripathi, Kenji Mizuguchi

Subjects: Genomics (q-bio.GN)

[68] arXiv:2010.05656 [pdf, other]

Title: Modeling Mito-nuclear Compatibility and its Role in Species Identification

Debora Princepe, Marcus A.M. de Aguiar

Comments: 27 pages, 6 figures

Journal-ref: Systematic Biology 70(1) pp.133-144, 2021

Subjects: Populations and Evolution (q-bio.PE); Genomics (q-bio.GN)

[69] arXiv:2010.05672 [pdf, other]

Title: Non-genetic variability: survival strategy or nuisance?

Ethan Levien, Jiseon Min, Jane Kondev, Ariel Amir

Subjects: Populations and Evolution (q-bio.PE)

[70] arXiv:2010.05850 [pdf, other]

Title: The foreshadow of a second wave: An analysis of current COVID-19 fatalities in Germany

Matthias Linden, Jonas Dehning, Sebastian B. Mohr, Jan Mohring, Michael Meyer-Hermann, Iris Pigeot, Anita Schöbel, Viola Priesemann

Comments: eine deutsche Übersetzung ist beigefügt

Subjects: Populations and Evolution (q-bio.PE); Physics and Society (physics.soc-ph)

[71] arXiv:2010.05897 [pdf, other]

Title: Stability of Imbalanced Triangles in Gene Regulatory Networks of Cancerous and Normal Cells

Abbas Karimi Rizi, Mina Zamani, Amirhossein Shirazi, G. Reza Jafari, János Kertész

Comments: 10 pages, 2 figures

Subjects: Molecular Networks (q-bio.MN); Biological Physics (physics.bio-ph)

[72] arXiv:2010.05950 [pdf, other]

Title: Breaking unidirectional invasions jeopardizes biodiversity in spatial May-Leonard systems

D. Bazeia, B.F. de Oliveira, J.V.O. Silva, A. Szolnoki

Comments: 9 pages, 6 figures

Journal-ref: Chaos, Solitons & Fractals Volume 141, December 2020, 110356

Subjects: Populations and Evolution (q-bio.PE); Statistical Mechanics (cond-mat.stat-mech); Pattern Formation and Solitons (nlin.PS); Physics and Society (physics.soc-ph)

[73] arXiv:2010.06063 [pdf, other]

Title: Bayesian Weighted Triplet and Quartet Methods for Species Tree Inference

Andrew Richards, Laura Kubatko

Subjects: Populations and Evolution (q-bio.PE); Methodology (stat.ME)

[74] arXiv:2010.06066 [pdf, other]

Title: Quenching to fix metastable states in models of prebiotic chemistry

Qianyi Sheng, Ben Intoy, J.W. Halley

Comments: 13 pages, 13 figures

Journal-ref: Phys. Rev. E 102, 062412 (2020)

Subjects: Populations and Evolution (q-bio.PE); Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)

[75] arXiv:2010.06072 [pdf, other]

Title: Multi-Level Group Testing with Application to One-Shot Pooled COVID-19 Tests

Amit Solomon, Alejandro Cohen, Nir Shlezinger, Yonina C. Eldar, Muriel Médard

Subjects: Quantitative Methods (q-bio.QM); Applications (stat.AP)

[76] arXiv:2010.06078 [pdf, other]

Title: Interoception Underlies The Therapeutic Effects of Mindfulness Meditation for Post-Traumatic Stress Disorder: A Randomized Clinical Trial

Seung Suk Kang, Ph.D., Scott R. Sponheim, Ph.D., Kelvin O. Lim, M.D

Comments: 17 pages, 5 figures, 1 table

Subjects: Neurons and Cognition (q-bio.NC)

[77] arXiv:2010.06225 [pdf, other]

Title: Transcranial Bipolar Direct Current Stimulation of the Frontoparietal Cortex Reduces Ketamine-Induced Oscillopathies: A Pilot Study in the Sedated Rat

Caroline Lahogue (NCPS, FMTS, UNISTRA), Didier Pinault (NCPS, FMTS, UNISTRA)

Subjects: Neurons and Cognition (q-bio.NC)

[78] arXiv:2010.06245 [pdf, other]

Title: Automation of Hemocompatibility Analysis Using Image Segmentation and a Random Forest

Johanna C. Clauser, Judith Maas, Jutta Arens, Thomas Schmitz-Rode, Ulrich Steinseifer, Benjamin Berkels

Subjects: Quantitative Methods (q-bio.QM); Computer Vision and Pattern Recognition (cs.CV)

[79] arXiv:2010.06357 [pdf, other]

Title: Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies

Jiahui Chen, Kaifu Gao, Rui Wang, Guowei Wei

Comments: 28 pages, 17 figures

Subjects: Biomolecules (q-bio.BM)

[80] arXiv:2010.06409 [pdf, other]

Title: Counting, grafting and evolving binary trees

Thomas Wiehe

Comments: to appear in: Probabilistic Structures in Evolution, E.~Baake and A.~Wakolbinger (eds.), EMS Publishing House, Zurich

Journal-ref: Probabilistic Structures in Evolution (E. Baake and A. Wakolbinger, eds.), EMS Press, Berlin, 2021, pp. 427-450

Subjects: Populations and Evolution (q-bio.PE)

[81] arXiv:2010.06415 [pdf, other]

Title: Exact $p$-values for global network alignments via combinatorial analysis of shared GO terms (Subtitle: REFANGO: Rigorous Evaluation of Functional Alignments of Networks using Gene Ontology)

Wayne B. Hayes

Comments: 22 pages, 3 figures, 4 tables

Subjects: Molecular Networks (q-bio.MN); Discrete Mathematics (cs.DM)

[82] arXiv:2010.06423 [pdf, other]

Title: A comprehensive protocol for manual segmentation of the human claustrum and its sub-regions using high-resolution MRI

Seung Suk Kang, Joseph Bodenheimer, Tracey Butler

Comments: 15 pages, 6 figures

Subjects: Quantitative Methods (q-bio.QM); Image and Video Processing (eess.IV)

[83] arXiv:2010.06456 [pdf, other]

Title: Population-based Optimization for Kinetic Parameter Identification in Glycolytic Pathway in Saccharomyces cerevisiae

Ewelina Weglarz-Tomczak, Jakub M. Tomczak, Agoston E. Eiben, Stanley Brul

Comments: Code at this https URL

Subjects: Biomolecules (q-bio.BM); Neural and Evolutionary Computing (cs.NE)

[84] arXiv:2010.06468 [pdf, other]

Title: Estimating COVID-19 cases and outbreaks on-stream through phone-calls

Ezequiel Alvarez, Daniela Obando, Sebastian Crespo, Enio Garcia, Nicolas Kreplak, Franco Marsico

Comments: 16 pages, 8 figs. Includes details on the Villa Azul outbreak in Argentina

Subjects: Populations and Evolution (q-bio.PE); Machine Learning (cs.LG); Machine Learning (stat.ML)

[85] arXiv:2010.06477 [pdf, other]

Title: 3DMolNet: A Generative Network for Molecular Structures

Vitali Nesterov, Mario Wieser, Volker Roth

Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)

[86] arXiv:2010.06683 [pdf, other]

Title: Medial Injury/Dysfunction Induced Granulation Tissue Repair is the Pathogenesis of Atherosclerosis

Xinggang Wang, Aijun Sun, Junbo Ge

Comments: 27 pages,8 figures

Subjects: Tissues and Organs (q-bio.TO); Fluid Dynamics (physics.flu-dyn)

[87] arXiv:2010.06995 [pdf, other]

Title: A Pathologist-Annotated Dataset for Validating Artificial Intelligence: A Project Description and Pilot Study

Sarah N Dudgeon (1), Si Wen (1), Matthew G Hanna (2), Rajarsi Gupta (3), Mohamed Amgad (4), Manasi Sheth (5), Hetal Marble (6), Richard Huang (6), Markus D Herrmann (7), Clifford H. Szu (8), Darick Tong (8), Bruce Werness (8), Evan Szu (8), Denis Larsimont (9), Anant Madabhushi (10), Evangelos Hytopoulos (11), Weijie Chen (1), Rajendra Singh (12), Steven N. Hart (13), Joel Saltz (3), Roberto Salgado (14), Brandon D Gallas (1) ((1) United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Imaging Diagnostics & Software Reliability, White Oak, MD, (2) Memorial Sloan Kettering Cancer Center, New York, NY, (3) Stony Brook Medicine Dept of Biomedical Informatics, Stony Brook, NY, (4) Department of Pathology, Northwestern University, Rubloff Building, Chicago Illinois, (5) United States Food and Drug Administration, Center for Devices and Radiological Health, Office of Product Quality and Evaluation, Office of Clinical Evidence and Analysis, Division of Biostatistics, White Oak, MD, (6) Massachusetts General Hospital/Harvard Medical School, Boston, MA, (7) Computational Pathology, Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, (8) Arrive Origin, San Francisco, CA, (9) Department of Pathology, Institut Jules Bordet, Brussels, Belgium, (10) Case Western Reserve University, Cleveland, OH, (11) iRhythm Technologies Inc., San Francisco, CA, (12) Northwell health and Zucker School of Medicine, New York, NY, (13) Department of Health Sciences Research, Mayo Clinic, Rochester MN, (14) Division of Research, Peter Mac Callum Cancer Centre, Melbourne, Australia, Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium)

Comments: 26 pages, 4 figures, 2 tables Submitted to the Journal of Pathology Informatics Project web page: this https URL

Subjects: Quantitative Methods (q-bio.QM); Image and Video Processing (eess.IV)

[88] arXiv:2010.07000 [pdf, other]

Title: Analytical parameter estimation of the SIR epidemic model. Applications to the COVID-19 pandemic

Dimiter Prodanov

Comments: 17 pages; 5 figures

Journal-ref: Entropy (Basel). 2020 Dec 31;23(1):E59. PMID: 33396355

Subjects: Populations and Evolution (q-bio.PE); Numerical Analysis (math.NA); Physics and Society (physics.soc-ph)

[89] arXiv:2010.07006 [pdf, other]

Title: Combining detection and reconstruction of correlational and quasi-periodic motifs in viral genomic sequences with transitional genome mapping: Application to COVID-19

Vladimr R. Chechetkin, Vasily V. Lobzin

Comments: 22 pages, 4 figures

Journal-ref: Journal of Integrated OMICS, 2021, v.11(1) p.5-11

Subjects: Quantitative Methods (q-bio.QM); Genomics (q-bio.GN)

[90] arXiv:2010.07071 [pdf, other]

Title: Exact neural mass model for synaptic-based working memory

Halgurd Taher, Alessandro Torcini, Simona Olmi

Comments: 47 pages, 14 figures

Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Dynamical Systems (math.DS); Adaptation and Self-Organizing Systems (nlin.AO); Biological Physics (physics.bio-ph)

[91] arXiv:2010.07143 [pdf, other]

Title: A Graph Neural Network Framework for Causal Inference in Brain Networks

Simon Wein, Wilhelm Malloni, Ana Maria Tomé, Sebastian M. Frank, Gina-Isabelle Henze, Stefan Wüst, Mark W. Greenlee, Elmar W. Lang

Subjects: Neurons and Cognition (q-bio.NC); Machine Learning (cs.LG)

[92] arXiv:2010.07162 [pdf, other]

Title: Deep brain stimulation for movement disorder treatment: Exploring frequency-dependent efficacy in a computational network model

Konstantinos Spiliotis, Jens Starke, Denise Franz, Angelika Richter, Rüdiger Köhling

Comments: 40 pages, 16 figures

Subjects: Neurons and Cognition (q-bio.NC); Dynamical Systems (math.DS)

[93] arXiv:2010.07326 [pdf, other]

Title: Collective defense of honeybee colonies: experimental results and theoretical modeling

Andrea López-Incera, Morgane Nouvian, Katja Ried, Thomas Müller, Hans J. Briegel

Journal-ref: BMC Biol 19, 106 (2021)

Subjects: Populations and Evolution (q-bio.PE); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)

[94] arXiv:2010.07399 [pdf, other]

Title: Nanopores -- a Versatile Tool to Study Protein Dynamics

Sonja Schmid, Cees Dekker

Comments: 20 pages, 6 figures, review article

Subjects: Quantitative Methods (q-bio.QM)

[95] arXiv:2010.07417 [pdf, other]

Title: Comparison between instrumental variable and mediation-based methods for reconstructing causal gene networks in yeast

Adriaan-Alexander Ludl, Tom Michoel

Journal-ref: Molecular Omics, 2021,17, 241-251

Subjects: Molecular Networks (q-bio.MN); Genomics (q-bio.GN); Applications (stat.AP)

[96] arXiv:2010.07437 [pdf, other]

Title: Tracking Results and Utilization of Artificial Intelligence (tru-AI) in Radiology: Early-Stage COVID-19 Pandemic Observations

Axel Wismüller, Larry Stockmaster

Comments: 9 pages, 1 figure, 1 table

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Populations and Evolution (q-bio.PE)

[97] arXiv:2010.07455 [pdf, other]

Title: Advances to tackle backbone flexibility in protein docking

Ameya Harmalkar, Jeffrey J. Gray

Subjects: Biomolecules (q-bio.BM)

[98] arXiv:2010.07473 [pdf, other]

Title: Modeling Microglia Activation and Inflammation-Based Neuroprotectant Strategies During Ischemic Stroke

Sara Amato, Andrea Arnold

Comments: 21 pages, 5 figures

Journal-ref: Bulletin of Mathematical Biology 83 (2021) 72

Subjects: Cell Behavior (q-bio.CB)

[99] arXiv:2010.07506 [pdf, other]

Title: EIC (Expert Information Criterion) not AIC: the cautious biologist's guide to model selection

Zachary M. Laubach, Eleanor J. Murray, Kim L. Hoke, Rebecca J. Safran, Wei Perng

Comments: Word count: 6791 Tables: 1 (Box 1) Figures: 9 References: 57

Subjects: Quantitative Methods (q-bio.QM)

[100] arXiv:2010.07826 [pdf, other]

Title: Mass Flow Analysis of SARS-CoV-2 for quantified COVID-19 Risk Analysis

Gjalt Huppes, Ruben Huele

Comments: 18 pages. 5 figures and 3 tables, included in the text body. Paper under review in the Journal of Industrial Ecology. Keywords: SARS-CoV-2; COVID-19; Virion Mass Balance; Routes to Exposure; Epidemic; Pandemic; Ventilation Rate; Risk Analysis

Subjects: Quantitative Methods (q-bio.QM); General Economics (econ.GN)