Quantitative Biology

Authors and titles for March 2020

[201] arXiv:2003.11859 [pdf, other]

Title: Thalamo-cortical spiking model of incremental learning combining perception, context and NREM-sleep-mediated noise-resilience

Bruno Golosio, Chiara De Luca, Cristiano Capone, Elena Pastorelli, Giovanni Stegel, Gianmarco Tiddia, Giulia De Bonis, Pier Stanislao Paolucci

Journal-ref: PLOS Computational Biology 17(6): e1009045 (2021)

Subjects: Neurons and Cognition (q-bio.NC); Distributed, Parallel, and Cluster Computing (cs.DC)

[202] arXiv:2003.11860 [pdf, other]

Title: Epidemics, the Ising-model and percolation theory: a comprehensive review focussed on Covid-19

Isys F. Mello, Lucas Squillante, Gabriel O. Gomes, Antonio C. Seridonio, M. de Souza

Comments: 33 pages, 10 figures, 2 tables (new sections and new figs. were added, review paper with new aspects of epidemics)

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

[203] arXiv:2003.11864 [pdf, other]

Title: Information and Communication Theoretical Understanding and Treatment of Spinal Cord Injuries: State-of-the-art and Research Challenges

Ozgur B. Akan, Hamideh Ramezani, Meltem Civas, Oktay Cetinkaya, Bilgesu A. Bilgin, Naveed A. Abbasi

Comments: IEEE Reviews in Biomedical Engineering

Subjects: Neurons and Cognition (q-bio.NC); Emerging Technologies (cs.ET)

[204] arXiv:2003.11920 [pdf, other]

Title: A simple Stochastic SIR model for COVID 19 Infection Dynamics for Karnataka: Learning from Europe

Ashutosh Simha, R. Venkatesha Prasad, Sujay Narayana

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

[205] arXiv:2003.11961 [pdf, other]

Title: PROSPECT-PRO for estimating content of nitrogen-containing leaf proteins and other carbon-based constituents

Jean-Baptiste Féret, Katja Berger, Florian de Boissieu, Zbyněk Malenovský

Comments: 47 pages, 8 figures Submitted to Remote Sensing of Environment, March, 20th, 2020

Subjects: Quantitative Methods (q-bio.QM)

[206] arXiv:2003.11975 [pdf, other]

Title: Purim: a rapid method with reduced cost for massive detection of CoVid-19

Benjamin Isac Fargion, Daniele Fargion, Pier Giorgio De Sanctis Lucentini, Emanuele Habib

Comments: 7 pages, 7 figures

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

[207] arXiv:2003.12017 [pdf, other]

Title: Prediction of number of cases expected and estimation of the final size of coronavirus epidemic in India using the logistic model and genetic algorithm

Ganesh Kumar M, Soman K.P, Gopalakrishnan E.A, Vijay Krishna Menon, Sowmya V

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

[208] arXiv:2003.12028 [pdf, other]

Title: Quantitative assessment of the role of undocumented infection in the 2019 novel coronavirus (COVID-19) pandemic

Yong-Shang Long, Zheng-Meng Zhai, Li-Lei Han, Jie Kang, Yi-Lin Li, Zhao-Hua Lin, Lang Zeng, Da-Yu Wu, Chang-Qing Hao, Ming Tang, Zonghua Liu, Ying-Cheng Lai

Comments: 20 pages, 7 figures

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

[209] arXiv:2003.12032 [pdf, other]

Title: Why case fatality ratios can be misleading: individual- and population-based mortality estimates and factors influencing them

Lucas Böttcher, Mingtao Xia, Tom Chou

Comments: 17 pp, 6 figures + Supplementary Information

Journal-ref: Physical Biology 17(6), 2020

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

[210] arXiv:2003.12055 [pdf, other]

Title: Age-structured impact of social distancing on the COVID-19 epidemic in India

Rajesh Singh, R. Adhikari

Comments: Code and updates at this https URL. 9 pages, 5 figures, and 2 tables

Subjects: Populations and Evolution (q-bio.PE); Statistical Mechanics (cond-mat.stat-mech)

[211] arXiv:2003.12068 [pdf, other]

Title: Modelling Recovered Cases and Death Probabilities for the COVID-19 Outbreak

Robert Schaback

Comments: 6 figures

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

[212] arXiv:2003.12089 [pdf, other]

Title: Population dynamics of Varroa mite and honeybee: Effects of parasitism with age structure and seasonality

Komi Messan, Marisabel Rodriguez Messan, Jun Chen, Gloria DeGrandi-Hoffman, Yun Kang

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

[213] arXiv:2003.12128 [pdf, other]

Title: Going in circles is the way forward: the role of recurrence in visual inference

Ruben S. van Bergen, Nikolaus Kriegeskorte

Subjects: Neurons and Cognition (q-bio.NC); Computer Vision and Pattern Recognition (cs.CV)

[214] arXiv:2003.12150 [pdf, other]

Title: Modeling the early evolution of the COVID-19 in Brazil: results from a Susceptible-Infectious-Quarantined-Recovered (SIQR) model

Nuno Crokidakis

Comments: 8 pages, 2 figures, updated version (v2, with a different title) will appear in IJMPC

Journal-ref: Int. J. Mod. Phys. C 31, 2050135 (2020)

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

[215] arXiv:2003.12191 [pdf, other]

Title: Distant sequence similarity between hepcidin and the novel coronavirus spike glycoprotein: a potential hint at the possibility of local iron dysregulation in COVID-19

Sepehr Ehsani

Comments: 21 pages, 1 table, 2 figures; updated main text, references and Figure 2

Journal-ref: Biol. Direct 15 (2020) 19

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

[216] arXiv:2003.12233 [pdf, other]

Title: PDE models of adder mechanisms in cellular proliferation

Mingtao Xia, Chris D. Greenman, Tom Chou

Comments: 23 pages, 8 figures

Subjects: Cell Behavior (q-bio.CB); Analysis of PDEs (math.AP)

[217] arXiv:2003.12400 [pdf, other]

Title: Metabolic graphs, LIFE method and the modeling of drug action on Mycobacterium tuberculosis

Sean T. McQuade, Nathaniel J. Merrill, Benedetto Piccoli

Comments: 22 pages, 8 figures (4pdf,4tikz)

Subjects: Molecular Networks (q-bio.MN)

[218] arXiv:2003.12417 [pdf, other]

Title: Temperature dependence of COVID-19 transmission

Alessio Notari

Comments: 5 pages, 5 figures. Updated with improved analysis, leading to higher significance. Analysis with extended dataset added

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

[219] arXiv:2003.12441 [pdf, other]

Title: Synchronized Pivots

J. C. Phillips

Comments: 15 pages, 5 figures

Subjects: Biomolecules (q-bio.BM); Molecular Networks (q-bio.MN)

[220] arXiv:2003.12454 [pdf, other]

Title: A Machine Learning alternative to placebo-controlled clinical trials upon new diseases: A primer

Ezequiel Alvarez (ICAS, Argentina), Federico Lamagna (CAB, Argentina), Manuel Szewc (ICAS, Argentina)

Comments: Work originally aimed for COVID-19 outbreak. All scripts are open source in this http URL

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

[221] arXiv:2003.12457 [pdf, other]

Title: How macroscopic laws describe complex dynamics: asymptomatic population and CoviD-19 spreading

D.Lanteri, D.Carco', P.Castorina

Journal-ref: International Journal of Modern Physics CVol. 31, No. 08, 2050112 (2020)

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

[222] arXiv:2003.12493 [pdf, other]

Title: Morphogen-regulated contact-mediated signaling between cells can drive the transitions underlying body segmentation in vertebrates

Chandrashekar Kuyyamudi, Shakti N. Menon, Sitabhra Sinha

Comments: 10 pages, 5 figures + 13 pages Supplementary Information

Journal-ref: Phys. Biol. 19, 016001 (2021)

Subjects: Tissues and Organs (q-bio.TO); Pattern Formation and Solitons (nlin.PS); Biological Physics (physics.bio-ph)

[223] arXiv:2003.12667 [pdf, other]

Title: On the Evolution of Covid-19 in Italy: a Follow up Note

Giuseppe Dattoli, Emanuele Di Palma, Silvia Licciardi, Elio Sabia

Comments: 10 pages, 28 figures

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

[224] arXiv:2003.12670 [pdf, other]

Title: Objective Multi-variable Classification and Inference of Biological Neuronal Networks

Michael Taynnan Barros, Harun Siljak, Peter Mullen, Constantinos Papadias, Jari Hyttinen, Nicola Marchetti

Subjects: Neurons and Cognition (q-bio.NC); Other Computer Science (cs.OH)

[225] arXiv:2003.12773 [pdf, other]

Title: Knowledge synthesis from 100 million biomedical documents augments the deep expression profiling of coronavirus receptors

AJ Venkatakrishnan, Arjun Puranik, Akash Anand, David Zemmour, Xiang Yao, Xiaoying Wu, Ramakrishna Chilaka, Dariusz K. Murakowski, Kristopher Standish, Bharathwaj Raghunathan, Tyler Wagner, Enrique Garcia-Rivera, Hugo Solomon, Abhinav Garg, Rakesh Barve, Anuli Anyanwu-Ofili, Najat Khan, Venky Soundararajan

Comments: 5 figures

Subjects: Genomics (q-bio.GN); Information Retrieval (cs.IR); Biomolecules (q-bio.BM); Tissues and Organs (q-bio.TO)

[226] arXiv:2003.12781 [pdf, other]

Title: A phenomenological approach to COVID-19 spread in a population

Anantanarayanan Thyagaraja

Comments: 12 pages, 5 figures

Subjects: Populations and Evolution (q-bio.PE); Adaptation and Self-Organizing Systems (nlin.AO)

[227] arXiv:2003.12886 [pdf, other]

Title: SARS-CoV-2 (COVID-19) by the numbers

Yinon M. Bar-On, Avi I. Flamholz, Rob Phillips, Ron Milo

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

[228] arXiv:2003.12928 [pdf, other]

Title: tACS Facilitates Flickering Driving by Boosting Steady-State Visual Evoked Potentials

Bingchuan Liu, Xinyi Yan, Xiaogang Chen, Yijun Wang, Xiaorong Gao

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

[229] arXiv:2003.12936 [pdf, other]

Title: The C-SHIFT algorithm for normalizing covariances

Evgenia Chunikhina, Paul Logan, Yevgeniy Kovchegov, Anatoly Yambartsev, Debashis Mondal, Andrey Morgun

Subjects: Genomics (q-bio.GN); Quantitative Methods (q-bio.QM); Applications (stat.AP); Methodology (stat.ME)

[230] arXiv:2003.12954 [pdf, other]

Title: Navigation and control of outcomes in a generalized Lotka-Volterra model of the microbiome

Eric W. Jones, Parker Shankin-Clarke, Jean M. Carlson

Comments: 24 pages, 10 figures

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

[231] arXiv:2003.13071 [pdf, other]

Title: Adjoint-based Data Assimilation of an Epidemiology Model for the Covid-19 Pandemic in 2020

Jörn Lothar Sesterhenn

Subjects: Populations and Evolution (q-bio.PE); Numerical Analysis (math.NA); Optimization and Control (math.OC)

[232] arXiv:2003.13149 [pdf, other]

Title: SOS: Online probability estimation and generation of T and B cell receptors

Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra M. Walczak, Thierry Mora

Journal-ref: Bioinformatics, Volume 36, Issue 16, 15 August 2020, Pages 4510--4512

Subjects: Genomics (q-bio.GN)

[233] arXiv:2003.13221 [pdf, other]

Title: Planning as Inference in Epidemiological Models

Frank Wood, Andrew Warrington, Saeid Naderiparizi, Christian Weilbach, Vaden Masrani, William Harvey, Adam Scibior, Boyan Beronov, John Grefenstette, Duncan Campbell, Ali Nasseri

Comments: Revisions

Journal-ref: Front Artif Intell. 2021; 4: 550603

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

[234] arXiv:2003.13282 [pdf, other]

Title: Accelerated infection testing at scale: a proposal for inference with single test on multiple patients

Tarun Jain, Bijendra Nath Jain

Comments: 8 pages

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

[235] arXiv:2003.13473 [pdf, other]

Title: Modern alleles in archaic human Y chromosomes support origin of modern human paternal lineages in Asia rather than Africa

Hongyao Chen, Shi Huang

Comments: 14 pages, 2 figures, 2 tables

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

[236] arXiv:2003.13540 [pdf, other]

Title: Dynamics of the COVID-1 -- Comparison between the Theoretical Predictions and the Real Data, and Predictions about Returning to Normal Life

Giorgio Sonnino, Pasquale Nardone

Comments: 34 pages, 19 figures, 6 tables

Journal-ref: Annals of Clinical and Medical Case Reports. 2020; 4(9): 1-21 - ISSN 2639-8109

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

[237] arXiv:2003.13543 [pdf, other]

Title: Glucose availability but not changes in pancreatic hormones sensitizes hepatic AMPK activity during nutritional transition in rodents

Camille Huet (IC UM3), Nadia Boudaba (IC UM3), Bruno Guigas, Benoit Viollet (IC UM3), Marc Foretz (IC UM3)

Comments: Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology, 2020

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

[238] arXiv:2003.13547 [pdf, other]

Title: Sex Differences in Severity and Mortality Among Patients With COVID-19: Evidence from Pooled Literature Analysis and Insights from Integrated Bioinformatic Analysis

Xiyi Wei, Yu-Tian Xiao, Jian Wang, Rui Chen, Wei Zhang, Yue Yang, Daojun Lv, Chao Qin, Di Gu, Bo Zhang, Weidong Chen, Jianquan Hou, Ninghong Song, Guohua Zeng, Shancheng Ren

Comments: 43 pages, 5 figures, 4 tables, 6 supplementary figures, 4 supplementary tables

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

[239] arXiv:2003.13571 [pdf, other]

Title: Solvable delay model for epidemic spreading: the case of Covid-19 in Italy

Luca Dell'Anna

Comments: 11 pages, 6 figures, to appear in Scientific Reports

Journal-ref: Sci. Rep. 10, 15763 (2020)

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

[240] arXiv:2003.13634 [pdf, other]

Title: Stochastic single-particle based simulations of cellular signaling embedded into computational models of cellular morphology

Thorsten Prüstel, Martin Meier-Schellersheim

Comments: 26 pages, 7 figures

Subjects: Quantitative Methods (q-bio.QM)

[241] arXiv:2003.13655 [pdf, other]

Title: Structural analysis of SARS-CoV-2 and prediction of the human interactome

Andrea Vandelli, Michele Monti, Edoardo Milanetti, Riccardo Delli Ponti, Gian Gaetano Tartaglia

Comments: 30 pages, 4 figures

Subjects: Biomolecules (q-bio.BM); Genomics (q-bio.GN); Molecular Networks (q-bio.MN)

[242] arXiv:2003.13665 [pdf, other]

Title: Genomics-guided molecular maps of coronavirus targets in human cells: a path toward the repurposing of existing drugs to mitigate the pandemic

Gennadi Glinsky

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

[243] arXiv:2003.13747 [pdf, other]

Title: The D model for deaths by COVID-19

J. E. Amaro

Comments: 7 pages, 4 figures

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

[244] arXiv:2003.13754 [pdf, other]

Title: Autonomous discovery in the chemical sciences part I: Progress

Connor W. Coley, Natalie S. Eyke, Klavs F. Jensen

Comments: Revised version available at https://doi.org/10.1002/anie.201909987

Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Robotics (cs.RO); Applications (stat.AP); Machine Learning (stat.ML)

[245] arXiv:2003.13755 [pdf, other]

Title: Autonomous discovery in the chemical sciences part II: Outlook

Connor W. Coley, Natalie S. Eyke, Klavs F. Jensen

Comments: Revised version available at https://doi.org/10.1002/anie.201909989

Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Robotics (cs.RO); Applications (stat.AP); Machine Learning (stat.ML)

[246] arXiv:2003.13825 [pdf, other]

Title: On the role of theory and modeling in neuroscience

Daniel Levenstein, Veronica A. Alvarez, Asohan Amarasingham, Habiba Azab, Zhe Sage Chen, Richard C. Gerkin, Andrea Hasenstaub, Ramakrishnan Iyer, Renaud B. Jolivet, Sarah Marzen, Joseph D. Monaco, Astrid A. Prinz, Salma Quraishi, Fidel Santamaria, Sabyasachi Shivkumar, Matthew F. Singh, Roger Traub, Horacio G. Rotstein, Farzan Nadim, A. David Redish

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

[247] arXiv:2003.13890 [pdf, other]

Title: Robust predictive model for Carriers, Infections and Recoveries (CIR): predicting death rates for CoVid-19 in Spain

Efren M. Benavides

Comments: 11 pages, 2 figures; spelling and typos corrected

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

[248] arXiv:2003.13901 [pdf, other]

Title: COVID-19 infection and recovery in various countries: Modeling the dynamics and evaluating the non-pharmaceutical mitigation scenarios

Yong Zhang, Xiangnan Yu, HongGuang Sun, Geoffrey R. Tick, Wei Wei, Bin Jin

Comments: 29 pages, 8 figures

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

[249] arXiv:2003.13932 [pdf, other]

Title: COVID-19: A model for studying the evolution of contamination in Brazil

Rodrigo A. Schulz, Carlos H. Coimbra-Araújo, Samuel W. S. Costiche

Comments: 18 pages, 4 figures; corrected references and parameters

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

[250] arXiv:2003.13967 [pdf, other]

Title: Effects of social distancing and isolation on epidemic spreading: a dynamical density functional theory model

Michael te Vrugt, Jens Bickmann, Raphael Wittkowski

Comments: 9 pages, 3 figures

Journal-ref: Nature Communications 11, 5576 (2020)

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