Quantitative Biology

Authors and titles for May 2020

[101] arXiv:2005.04796 [pdf, other]

Title: Metabolic heat in microbial conflict and cooperation

Steven A. Frank

Comments: V3: Added new figure, more references, some editing. V2: Add several key references, comments about heat diffusion as single-cell scale

Journal-ref: Frontiers in Ecology and Evolution 8:275 (2020)

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

[102] arXiv:2005.04877 [pdf, other]

Title: The Biophysical Micro-Environment's Influence on Cell Fate Decisions During Macrophage Activation and Somatic Cell Reprogramming

Zachary Reitz

Comments: PhD thesis (2019)

Subjects: Cell Behavior (q-bio.CB); Genomics (q-bio.GN); Molecular Networks (q-bio.MN)

[103] arXiv:2005.04937 [pdf, other]

Title: Using statistics and mathematical modelling to understand infectious disease outbreaks: COVID-19 as an example

Christopher E. Overton, Helena B. Stage, Shazaad Ahmad, Jacob Curran-Sebastian, Paul Dark, Rajenki Das, Elizabeth Fearon, Timothy Felton, Martyn Fyles, Nick Gent, Ian Hall, Thomas House, Hugo Lewkowicz, Xiaoxi Pang, Lorenzo Pellis, Robert Sawko, Andrew Ustianowski, Bindu Vekaria, Luke Webb

Journal-ref: Infectious Disease Modelling, Volume 5 (2020), 409-441

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

[104] arXiv:2005.05015 [pdf, other]

Title: GLN -- a method to reveal unique properties of lasso type topology in proteins

Wanda Niemyska, Kenneth C. Millett, Joanna I. Sulkowska

Comments: 25 pages, 8 figures, submitted to the journal and waiting for reviews, having Supplementary Material

Subjects: Biomolecules (q-bio.BM)

[105] arXiv:2005.05053 [pdf, other]

Title: Low-Rank Nonlinear Decoding of $\mu$-ECoG from the Primary Auditory Cortex

Melikasadat Emami, Mojtaba Sahraee-Ardakan, Parthe Pandit, Alyson K. Fletcher, Sundeep Rangan, Michael Trumpis, Brinnae Bent, Chia-Han Chiang, Jonathan Viventi

Comments: 4 pages, 3 figures

Subjects: Neurons and Cognition (q-bio.NC); Machine Learning (cs.LG); Neural and Evolutionary Computing (cs.NE); Signal Processing (eess.SP); Machine Learning (stat.ML)

[106] arXiv:2005.05163 [pdf, other]

Title: Computable Phenotypes of Patient Acuity in the Intensive Care Unit

Yuanfang Ren (1) (2), Jeremy Balch (3), Kenneth L. Abbott (3), Tyler J. Loftus (1) (3), Benjamin Shickel (1) (2), Parisa Rashidi (1) (4), Azra Bihorac (1) (2), Tezcan Ozrazgat-Baslanti (1) (2) ((1) Intelligent Clinical Care Center (IC3), University of Florida, Gainesville, FL, USA, (2) Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA, (3) Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA, (4) J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL)

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

[107] arXiv:2005.05249 [pdf, other]

Title: COVID-19 mitigation strategies and overview on results from relevant studies in Europe

Philipp Heider

Comments: Not up-to-date anymore

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

[108] arXiv:2005.05295 [pdf, other]

Title: Exact Parallelization of the Stochastic Simulation Algorithm for Scalable Simulation of Large Biochemical Networks

Arthur P. Goldberg (1), David R. Jefferson (2), John A. P. Sekar (1), Jonathan R. Karr (1) ((1) Icahn Institute for Data Science and Genomic Technology, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, (2) Lawrence Livermore National Laboratory)

Comments: 21 pages, 4 figures; 2020-05-20 submission: updated authors, affiliations, emails, acknowledgments and layout

Subjects: Molecular Networks (q-bio.MN); Distributed, Parallel, and Cluster Computing (cs.DC); Data Structures and Algorithms (cs.DS); Quantitative Methods (q-bio.QM)

[109] arXiv:2005.05320 [pdf, other]

Title: Simulating the spread of COVID-19 via spatially-resolved susceptible-exposed-infected-recovered-deceased (SEIRD) model with heterogeneous diffusion

Alex Viguerie, Guillermo Lorenzo, Ferdinando Auricchio, Davide Baroli, Thomas J.R. Hughes, Alessia Patton, Alessandro Reali, Thomas E. Yankeelov, Alessandro Veneziani

Comments: 7 pages, 3 figures

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

[110] arXiv:2005.05403 [pdf, other]

Title: A Review on Brain Mechanisms for Language Acquisition and Comprehension

Kailsah Nath Tripathi, Anand Bihari, Sudhakar Tripathi, R. B. Mishra

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

[111] arXiv:2005.05437 [pdf, other]

Title: End-to-End Automatic Sleep Stage Classification Using Spectral-Temporal Sleep Features

Hyeong-Jin Kim, Minji Lee, Seong-Whan Lee

Subjects: Neurons and Cognition (q-bio.NC); Signal Processing (eess.SP)

[112] arXiv:2005.05549 [pdf, other]

Title: Staggered Release Policies for COVID-19 Control: Costs and Benefits of Sequentially Relaxing Restrictions by Age

Henry Zhao, Zhilan Feng, Carlos Castillo-Chavez, Simon A. Levin

Comments: 22 pages (including Appendix), 10 figures

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

[113] arXiv:2005.05572 [pdf, other]

Title: Spike-Triggered Descent

Michael Kummer, Arunava Banerjee

Subjects: Neurons and Cognition (q-bio.NC); Neural and Evolutionary Computing (cs.NE)

[114] arXiv:2005.05595 [pdf, other]

Title: On nonlinear pest/vector control via the Sterile Insect Technique: impact of residual fertility

Maria Soledad Aronna (FGV), Yves Dumont (UMR AMAP)

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

[115] arXiv:2005.05596 [pdf, other]

Title: Optimal responsiveness and collective oscillations emerging from the heterogeneity of inhibitory neurons

Matteo di Volo, Alain Destexhe

Journal-ref: Scientific reports 2021

Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn)

[116] arXiv:2005.05606 [pdf, other]

Title: SkeleDock: A Web Application for Scaffold Docking in PlayMolecule

Alejandro Varela-Rial, Maciej Majewski, Alberto Cuzzolin, Gerard Martínez-Rosell, Gianni De Fabritiis

Subjects: Quantitative Methods (q-bio.QM); Biomolecules (q-bio.BM)

[117] arXiv:2005.05653 [pdf, other]

Title: The Intermittent Nature of Leaf Growth Fields

S. Armon, M. Moshe, E. Sharon

Comments: 20 pages, 4 figures, 4 sections of supplementary material -with one supplementary figure

Subjects: Tissues and Organs (q-bio.TO)

[118] arXiv:2005.05654 [pdf, other]

Title: On the usefulness of a minimalistic model to study tree-grass biomass distributions along biogeographic gradients in the savanna biome

Ivric Valaire Yatat Djeumen, Yves Dumont (UMR AMAP), Anna Doizy, P. Couteron (UMR AMAP)

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

[119] arXiv:2005.05656 [pdf, other]

Title: Life's mechanism

Simon Pierce

Comments: 9 pages

Subjects: Other Quantitative Biology (q-bio.OT)

[120] arXiv:2005.05784 [pdf, other]

Title: A Graph Gaussian Embedding Method for Predicting Alzheimer's Disease Progression with MEG Brain Networks

Mengjia Xu, David Lopez Sanz, Pilar Garces, Fernando Maestu, Quanzheng Li, Dimitrios Pantazis

Subjects: Neurons and Cognition (q-bio.NC); Machine Learning (cs.LG); Signal Processing (eess.SP); Machine Learning (stat.ML)

[121] arXiv:2005.05787 [pdf, other]

Title: Early Biomarkers and Intervention Programs for the Infant Exposed to Prenatal Stress

Marta C. Antonelli, Martin G. Frasch, Mercedes Rumi, Ritika Sharma, Peter Zimmermann, Maria Sol Molinet, Silvia M. Lobmaier

Comments: 18 pages-Review

Journal-ref: Curr Neuropharmacol 2021

Subjects: Quantitative Methods (q-bio.QM); Neurons and Cognition (q-bio.NC)

[122] arXiv:2005.05819 [pdf, other]

Title: Towards a Scientific Method for Dynamical Systems

Vincent Wang

Comments: 32 pages, 53 figures, extended version of submission to ACT2020 proceedings

Subjects: Quantitative Methods (q-bio.QM); Category Theory (math.CT); Molecular Networks (q-bio.MN)

[123] arXiv:2005.05858 [pdf, other]

Title: Understanding the principles of pattern formation driven by Notch signaling by integrating experiments and theoretical models

Federico Bocci, Jose Nelson Onuchic, Mohit Kumar Jolly

Subjects: Molecular Networks (q-bio.MN); Tissues and Organs (q-bio.TO)

[124] arXiv:2005.06032 [pdf, other]

Title: Kaplan-Meier type survival curves for COVID-19: a health data based decision-making tool

J.M. Calabuig, L.M. García-Raffi, A. García-Valiente, E.A. Sánchez-Pérez

Comments: 12 pages, 6 figures

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

[125] arXiv:2005.06137 [pdf, other]

Title: Metapopulation network models for understanding, predicting and managing the coronavirus disease COVID-19

Daniela Calvetti, Alexander Hoover, Johnie Rose, Erkki Somersalo

Comments: 21 pages, 15 figures

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

[126] arXiv:2005.06180 [pdf, other]

Title: The impact of undetected cases on tracking epidemics: the case of COVID-19

Andrea De Simone, Marco Piangerelli

Comments: 23 Pages, 10 Figures

Journal-ref: Chaos, Solitons & Fractals, Volume 140, 2020, 110167

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

[127] arXiv:2005.06199 [pdf, other]

Title: In silico comparison of spike protein-ACE2 binding affinities across species; significance for the possible origin of the SARS-CoV-2 virus

Sakshi Piplani, Puneet Kumar Singh, David A. Winkler, Nikolai Petrovsky

Comments: Paper and supplementary data combined in one single pdf file

Journal-ref: Scientific Reports. 2021 Jun 24;11(1):13063. PMID: 34168168

Subjects: Biomolecules (q-bio.BM); Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)

[128] arXiv:2005.06239 [pdf, other]

Title: Classification of particle trajectories in living cells: machine learning versus statistical testing hypothesis for fractional anomalous diffusion

Joanna Janczura, Patrycja Kowalek, Hanna Loch-Olszewska, Janusz Szwabiński, Aleksander Weron

Comments: 32 pages, 5 figures

Journal-ref: Phys. Rev. E 102, 032402 (2020)

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph)

[129] arXiv:2005.06248 [pdf, other]

Title: Informed recruitment or the importance of taking stock

Meritxell Genovart, Daniel Oro, Remi Choquet, Roger Pradel

Comments: 10 pages, 1 figure

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

[130] arXiv:2005.06269 [pdf, other]

Title: On Kalman-Bucy filters, linear quadratic control and active inference

Manuel Baltieri, Christopher L. Buckley

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

[131] arXiv:2005.06286 [pdf, other]

Title: Dynamics of the COVID-19 pandemic in India

Subhas Khajanchi, Kankan Sarkar, Jayanta Mondal

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

[132] arXiv:2005.06297 [pdf, other]

Title: A numerical simulation of the COVID-19 epidemic in Argentina using the SEIR model

Juan E. Santos, Jose' M. Carcione, Gabriela B. Savioli, Patricia M. Gauzellino, Alejandro Ravecca, Alfredo Moras

Comments: arXiv admin note: substantial text overlap with arXiv:2004.03575

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

[133] arXiv:2005.06336 [pdf, other]

Title: Degradation of 2-mercaptobenzothizaole in microbial electrolysis cells: intermediates, toxicity, and microbial communities

M. Isabel San-Martin, Adrian Escapaa, Raul M. Alonso, Moises Canle, Antonio Moran

Journal-ref: published on Science of The Total Environment, 2020

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

[134] arXiv:2005.06504 [pdf, other]

Title: Alchemical Transformations for Concerted Hydration Free Energy Estimation with Explicit Solvation

Sheenam Khuttan, Solmaz Azimi, Joe Z. Wu, Emilio Gallicchio

Subjects: Quantitative Methods (q-bio.QM)

[135] arXiv:2005.06526 [pdf, other]

Title: COVID-19 pandemic control: balancing detection policy and lockdown intervention under ICU sustainability

Arthur Charpentier, Romuald Elie, Mathieu Laurière, Viet Chi Tran

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

[136] arXiv:2005.06539 [pdf, other]

Title: High fidelity epigenetic inheritance: Information theoretic model predicts $k$-threshold filling of histone modifications post replication

Nithya Ramakrishnan, Sibi Raj B Pillai, Ranjith Padinhateeri

Comments: 11 pages, 6 figures

Subjects: Genomics (q-bio.GN)

[137] arXiv:2005.06541 [pdf, other]

Title: Immunological determinants of clinical outcomes in COVID-19: A quantitative perspective

Elizabeth Krieger, Nicole Vissichelli, Stefan Leichtle, Markos Kashioris, Roy Sabo, Don Brophy, Xiang-Yang Wang, Pamela Kimbal, Michael Neale, Myrna G. Serrano, Gregory A. Buck, Catherine Roberts, Rehan Qayyum, Daniel Nixon, Steven Grossman, Amir A. Toor

Comments: 36 pages, 1 table, 5 figures

Subjects: Cell Behavior (q-bio.CB)

[138] arXiv:2005.06552 [pdf, other]

Title: Regional analysis of COVID-19 in France from fit of hospital data with different evolutionary models

Gary A. Mamon (Institut d'Astrophysique de Paris (UMR 7095: CNRS & Sorbonne Université))

Comments: 21 pages. Comments welcome. This version 4 has a different title in the PDF to match that of arXiv, and a retouch of the last sentence of the last section and of the Acknowledgements

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

[139] arXiv:2005.06712 [pdf, other]

Title: Comparative Roles of Charge, $\pi$ and Hydrophobic Interactions in Sequence-Dependent Phase Separation of Intrinsically Disordered Proteins

Suman Das, Yi-Hsuan Lin, Robert M. Vernon, Julie D. Forman-Kay, Hue Sun Chan

Comments: 65 pages (main text and supporting information), 7 main-text figures, 7 supporting figures, 1 supporting table, 135 references; accepted for publication in the Proceedings of the National Academy of Sciences, U.S.A

Journal-ref: Proc. Natl. Acad. Sci. U.S.A. 117, 28795-28805 (2020)

Subjects: Biomolecules (q-bio.BM); Soft Condensed Matter (cond-mat.soft)

[140] arXiv:2005.06742 [pdf, other]

Title: Global analysis of the COVID-19 pandemic using simple epidemiological models

J.E. Amaro, J. Dudouet, J.N. Orce

Comments: 12 pages, 13 figures

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

[141] arXiv:2005.06755 [pdf, other]

Title: Merging 1D and 3D genomic information: Challenges in modelling and validation

Alessandra Merlotti, Angelo Rosa, Daniel Remondini

Comments: This review article contains 15 pages and 12 figures. It is part of a series of invited contribution for the Special Issue "Transcriptional Profiles and Regulatory Gene Networks" (June 2020) published in the journal "Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms"

Journal-ref: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms Volume 1863, Issue 6, June 2020, 194415

Subjects: Genomics (q-bio.GN); Biological Physics (physics.bio-ph)

[142] arXiv:2005.06758 [pdf, other]

Title: Mean-Field Game Analysis of SIR Model with Social Distancing

Samuel Cho

Comments: 17 pages, 8 figures

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

[143] arXiv:2005.06767 [pdf, other]

Title: A Conjectural Experiment to Observe the Effect of Conditional locked-down in an Epidemic

M.E. Hoque, S.K. Das

Comments: 9 pages (including references), 1 diagrams and 5 figures

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

[144] arXiv:2005.06776 [pdf, other]

Title: Group testing as a strategy for the epidemiologic monitoring of COVID-19

Vincent Brault, Bastien Mallein, Jean-Francois Rupprecht

Comments: 21 pages, 14 figures

Subjects: Quantitative Methods (q-bio.QM); Physics and Society (physics.soc-ph); Applications (stat.AP); Methodology (stat.ME)

[145] arXiv:2005.06777 [pdf, other]

Title: Power-law distribution in Burst-suppression on electroencephalogram of dogs

Chika Koyama, Taichi Haruna, Satoshi Hagihira, Kazuto Yamashita

Comments: 18 pages, 2 figures, 3 tables

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

[146] arXiv:2005.06933 [pdf, other]

Title: Emerging Polynomial Growth Trends in COVID-19 Pandemic Data and Their Reconciliation with Compartment Based Models

Katarina Bodova, Richard Kollar

Comments: 27 pages, 11 figures, 4 tables

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

[147] arXiv:2005.06938 [pdf, other]

Title: Neural Synchronization of Music Large-Scale Form

Lenz Hartmann, Rolf Bader

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

[148] arXiv:2005.07071 [pdf, other]

Title: Modeling and forecasting of the COVID-19 pandemic in India

Kankan Sarkar, Subhas Khajanchi

Comments: 30 pages, 12 figures

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

[149] arXiv:2005.07108 [pdf, other]

Title: Effective Model of Loop Extrusion Predicts Chromosomal Domains

M. Crippa, Y. Zhan, G. Tiana

Journal-ref: Phys. Rev. E 102, 032414 (2020)

Subjects: Biomolecules (q-bio.BM)

[150] arXiv:2005.07121 [pdf, other]

Title: Using Bayesian Optimization to Accelerate Virtual Screening for the Discovery of Therapeutics Appropriate for Repurposing for COVID-19

Edward O. Pyzer-Knapp

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