Quantitative Biology

Authors and titles for April 2020

[101] arXiv:2004.04222 [pdf, other]

Title: Centralized and decentralized isolation strategies and their impact on the COVID-19 pandemic dynamics

Alexandru Topirceanu, Mihai Udrescu, Radu Marculescu

Comments: 18 pages, 13 figures

Subjects: Populations and Evolution (q-bio.PE); Multiagent Systems (cs.MA); Social and Information Networks (cs.SI); Physics and Society (physics.soc-ph)

[102] arXiv:2004.04271 [pdf, other]

Title: Simple Formulas for a Two-Tier Strategy to Flatten the Curve

Michael Nikolaou

Comments: 6 pages 7 figures arXiv:2003.12055v1 [q-bio.PE] 26 Mar 2020

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

[103] arXiv:2004.04281 [pdf, other]

Title: A comparative analysis for SARS-CoV-2

Goksel Misirli

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

[104] arXiv:2004.04299 [pdf, other]

Title: Quartet-Based Inference Methods are Statistically Consistent Under the Unified Duplication-Loss-Coalescence Model

Alexey Markin, Oliver Eulenstein

Subjects: Populations and Evolution (q-bio.PE); Probability (math.PR)

[105] arXiv:2004.04387 [pdf, other]

Title: Is the epidemic spread related to GDP? Visualizing the distribution of COVID-19 in Chinese Mainland

Yi Zhang (1,3), Hanwen Tian (1), Yinglong Zhang (2), Yiping Chen (3) ((1) College of Geography and Environmental Science, Northwest Normal University, China, (2) Zhejiang Provincial Institute of Communications Planning, Design & Research Co., Ltd., China, (3) Institute of Earth Environment, Chinese Academy of Sciences, China)

Comments: 7 pages, 1 figure

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

[106] arXiv:2004.04463 [pdf, other]

Title: Dynamic causal modelling of COVID-19

Karl J. Friston, Thomas Parr, Peter Zeidman, Adeel Razi, Guillaume Flandin, Jean Daunizeau, Oliver J. Hulme, Alexander J. Billig, Vladimir Litvak, Rosalyn J. Moran, Cathy J. Price, Christian Lambert

Comments: Technical report: 40 pages, 13 figures and 2 tables

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

[107] arXiv:2004.04470 [pdf, other]

Title: Fluctuation relations and fitness landscapes of growing cell populations

Arthur Genthon, David Lacoste

Journal-ref: Sci Rep 10, 11889 (2020)

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

[108] arXiv:2004.04472 [pdf, other]

Title: Hysteresis in anesthesia and recovery: Experimental observation and dynamical mechanism

Chun-Wang Su, Liang Zheng, You-Jun Li, Hai-Jun Zhou, Jue Wang, Zi-Gang Huang, Ying-Cheng Lai

Subjects: Neurons and Cognition (q-bio.NC); Biological Physics (physics.bio-ph)

[109] arXiv:2004.04474 [pdf, other]

Title: Towards in-silico robotic post-stroke rehabilitation for mice

Lorenzo Vannucci, Maria Pasquini, Cristina Spalletti, Matteo Caleo, Silvestro Micera, Cecilia Laschi, Egidio Falotico

Comments: 7 pages, 9 figures. To be published in the 2019 IEEE International Conference on Cyborg and Bionic Systems

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

[110] arXiv:2004.04529 [pdf, other]

Title: Scenario analysis of non-pharmaceutical interventions on global COVID-19 transmissions

Xiaohui Chen, Ziyi Qiu

Comments: published in Covid Economics: Vetted and Real-Time Papers, Centre for Economic Policy Research (CEPR)

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

[111] arXiv:2004.04567 [pdf, other]

Title: The pandemic of viruses with a long incubation phase in the small world

P.A. Golovinski

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

[112] arXiv:2004.04583 [pdf, other]

Title: Comparison of different exit scenarios from the lock-down for COVID-19 epidemic in the UK and assessing uncertainty of the predictions

Anatoly Zhigljavsky, Roger Whitaker, Ivan Fesenko, Kobi Kremnizer, Jack Noonan

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

[113] arXiv:2004.04604 [pdf, other]

Title: Efficiency of Covid-19 Mobile Contact Tracing Containment by Measuring Time Dependent Doubling Time

Antonio Bianconi, Augusto Marcelli, Gaetano Campi, Andrea Perali

Comments: 20 pages, 4 figures, 2 table

Journal-ref: Phys. Biol. 17 065006 (2020)

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

[114] arXiv:2004.04614 [pdf, other]

Title: Using random testing to manage a safe exit from the COVID-19 lockdown

Markus Müller, Peter M. Derlet, Christopher Mudry, Gabriel Aeppli

Comments: 18 pages, 6 figures, 2 appendices. Phys. Biol. (2020)

Subjects: Populations and Evolution (q-bio.PE); Other Condensed Matter (cond-mat.other); Statistical Mechanics (cond-mat.stat-mech); Medical Physics (physics.med-ph)

[115] arXiv:2004.04649 [pdf, other]

Title: A Mathematical Model of Local and Global Attention in Natural Scene Viewing

Noa Malem-Shinitski, Manfred Opper, Sebastian Reich, Lisa Schwetlick, Stefan A. Seelig, Ralf Engbert

Comments: 24 pages, 10 figures

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

[116] arXiv:2004.04675 [pdf, other]

Title: Deterministic Models in Epidemiology: From Modeling to Implementation

Aresh Dadlani, Richard O. Afolabi, Hyoyoung Jung, Khosrow Sohraby, Kiseon Kim

Comments: Tutorial

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

[117] arXiv:2004.04732 [pdf, other]

Title: Transparent Covid-19 prediction

Christoph Bandt

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

[118] arXiv:2004.04735 [pdf, other]

Title: A time-dependent SEIR model to analyse the evolution of the SARS-CoV-2 epidemic outbreak in Portugal

Pedro Teles

Comments: 7 figures. arXiv admin note: text overlap with arXiv:2003.10047

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

[119] arXiv:2004.04741 [pdf, other]

Title: The challenges of modeling and forecasting the spread of COVID-19

Andrea L. Bertozzi, Elisa Franco, George Mohler, Martin B. Short, Daniel Sledge

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

[120] arXiv:2004.04768 [pdf, other]

Title: Towards Better Opioid Antagonists Using Deep Reinforcement Learning

Jianyuan Deng, Zhibo Yang, Yao Li, Dimitris Samaras, Fusheng Wang

Comments: 10 pages, 7 figures

Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Computation and Language (cs.CL); Machine Learning (cs.LG)

[121] arXiv:2004.04819 [pdf, other]

Title: Some fractal thoughts about the COVID-19 infection outbreak

Massimo Materassi

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

[122] arXiv:2004.04874 [pdf, other]

Title: Implications of the virus-encoded miRNA and host miRNA in the pathogenicity of SARS-CoV-2

Zhi Liu, Jianwei Wang, Yuyu Xu, Mengchen Guo, Kai Mi, Rui Xu, Yang Pei, Qiangkun Zhang, Xiaoting Luan, Zhibin Hu, Xingyin Liu#

Comments: 24 pages,7 figures and 2 supplementary figures

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

[123] arXiv:2004.04903 [pdf, other]

Title: Scale invariance of cell size fluctuations in starving bacteria

Takuro Shimaya, Reiko Okura, Yuichi Wakamoto, Kazumasa A. Takeuchi

Comments: 15+23 pages, 5+11 figures and 2 tables

Journal-ref: Communications Physics 4, 238 (2021)

Subjects: Cell Behavior (q-bio.CB); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph)

[124] arXiv:2004.04935 [pdf, other]

Title: A single-cell RNA expression map of coronavirus receptors and associated factors in developing human embryos

Stacy Colaco, Karisma Chhabria, Domdatt Singh, Anshul Bhide, Neha Singh, Abhishek Singh, Atahar Husein, Anuradha Mishra, Richa Sharma, Nancy Ashary, Deepak Modi

Comments: 33 pages, 6 main figures, 3 main table, 2 supplementary figure

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

[125] arXiv:2004.04950 [pdf, other]

Title: Impact of intervention on the spread of COVID-19 in India: A model based study

Abhishek Senapati, Sourav Rana, Tamalendu Das, Joydev Chattopadhyay

Comments: 25 pages, 10 figures. this https URL

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

[126] arXiv:2004.05060 [pdf, other]

Title: Estimating required 'lockdown' cycles before immunity to SARS-CoV-2: Model-based analyses of susceptible population sizes, 'S0', in seven European countries including the UK and Ireland

Rosalyn J. Moran, Erik D. Fagerholm, Maell Cullen, Jean Daunizeau, Mark P. Richardson, Steven Williams, Federico Turkheimer, Rob Leech, Karl J. Friston

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

[127] arXiv:2004.05069 [pdf, other]

Title: Beyond Rescorla-Wagner: the ups and downs of learning

Gianluca Calcagni, Justin A. Harris, Ricardo Pellón

Comments: 39 pages, 11 figures, 8 tables. v2: discussion improved, figures added, some parts shortened, conclusions unchanged, matches published version

Journal-ref: Comput. Brain Behav. (2021)

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

[128] arXiv:2004.05104 [pdf, other]

Title: Performance of weak species in the simplest generalization of the rock-paper-scissors model to four species

P.P. Avelino, B.F. de Oliveira, R.S. Trintin

Comments: 7 pages, 6 figures. arXiv admin note: text overlap with arXiv:1907.11280

Journal-ref: Phys. Rev. E 101, 062312 (2020)

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

[129] arXiv:2004.05129 [pdf, other]

Title: Dynamics of Vesicles Driven Into Closed Constrictions by Molecular Motors

Youngmin Park, Thomas G. Fai

Comments: 34 pages, 9 figures

Journal-ref: Bull. Math. Biol. 82, 141 (2020)

Subjects: Cell Behavior (q-bio.CB); Subcellular Processes (q-bio.SC)

[130] arXiv:2004.05256 [pdf, other]

Title: Deciphering the Protein Motion of S1 Subunit in SARS-CoV-2 Spike Glycoprotein Through Integrated Computational Methods

Hao Tian, Peng Tao

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

[131] arXiv:2004.05373 [pdf, other]

Title: A critique of the Covid-19 analysis for India by Singh and Adhikari

Abhishek Dhar

Comments: 9 pages

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

[132] arXiv:2004.05466 [pdf, other]

Title: Improving Baseline Subtraction for Increased Sensitivity of Quantitative PCR Measurements

Paul N. Patrone, Anthony J. Kearsley, Erica L. Romsos, Peter M. Vallone

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph); Data Analysis, Statistics and Probability (physics.data-an); Instrumentation and Detectors (physics.ins-det)

[133] arXiv:2004.05467 [pdf, other]

Title: Stochasticity-induced stabilization in ecology and evolution: a new synthesis

Antony Dean, Nadav M. Shnerb

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

[134] arXiv:2004.05513 [pdf, other]

Title: Limited containment options of COVID-19 outbreak revealed by regional agent-based simulations for South Africa

Andreas Bossert, Moritz Kersting, Marc Timme, Malte Schröder, Azza Feki, Justin Coetzee, Jan Schlüter

Comments: including 3 Figures and Supplementary Material

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

[135] arXiv:2004.05635 [pdf, other]

Title: A Spatial Markov Chain Cellular Automata Model for the Spread of Viruses

Fred Vermolen

Comments: 13 pages, 10 figures

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

[136] arXiv:2004.05639 [pdf, other]

Title: Robust predictive model for Carriers, Infections and Recoveries (CIR): first update for CoVid-19 in Spain

Efren M.Benavides

Comments: 9 pages, 4 figures

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

[137] arXiv:2004.05715 [pdf, other]

Title: Modeling the transmission of new coronavirus in S\~ao Paulo State, Brazil -- Assessing epidemiological impacts of isolating young and elder persons

Hyun Mo Yang, Luis Pedro Lombardi Junior, Ariana Campos Yang

Comments: 33 pages, 25 figures

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

[138] arXiv:2004.05726 [pdf, other]

Title: Linear rather than exponential decay: a mathematical model and underlying mechanisms

Irina Kareva, Georgy Karev

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

[139] arXiv:2004.05730 [pdf, other]

Title: Estimation of time-varying reproduction numbers underlying epidemiological processes: a new statistical tool for the COVID-19 pandemic

Hyokyoung G. Hong, Yi Li

Comments: 16 pages, 4 figures

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

[140] arXiv:2004.05759 [pdf, other]

Title: Low-Cost and High-Throughput Testing of COVID-19 Viruses and Antibodies via Compressed Sensing: System Concepts and Computational Experiments

Jirong Yi, Raghu Mudumbai, Weiyu Xu

Comments: 11 pages

Subjects: Quantitative Methods (q-bio.QM); Information Theory (cs.IT); Signal Processing (eess.SP); Biomolecules (q-bio.BM)

[141] arXiv:2004.05778 [pdf, other]

Title: A simple statistical physics model for the epidemic with incubation period

David B. Saakian

Comments: 5 pages, 1 figure

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

[142] arXiv:2004.05895 [pdf, other]

Title: What did we learn from forty years of research on semantic interference? A Bayesian metaanalysis

A. Bürki, S. Elbuy, S. Madec, S. Vasishth

Subjects: Neurons and Cognition (q-bio.NC); Applications (stat.AP)

[143] arXiv:2004.06021 [pdf, other]

Title: Momentum managing epidemic spread and Bessel functions

Ivan Cherednik

Comments: 54 pages, 29 figures, v5: the two-phase formula for the spread was added covering practically the whole periods of Covid-19 in many countries; v6: the second waves were considered, editing; v7: some data refreshed, Journal reference added

Journal-ref: Chaos, Solitons & Fractals, Volume 139, October 2020, 110234

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

[144] arXiv:2004.06029 [pdf, other]

Title: Non-genetic inheritance restraint of cell-to-cell variation

Harsh Vashistha, Maryam Kohram, Hanna Salman

Subjects: Cell Behavior (q-bio.CB)

[145] arXiv:2004.06033 [pdf, other]

Title: The test-negative design with additional population controls: a practical approach to rapidly obtain information on the causes of the SARS-CoV-2 epidemic

Jan P Vandenbroucke, Elizabeth B Brickley, Christina M J E Vandenbroucke-Grauls, Neil Pearce

Comments: 13 pages, 1 figure, Appendices 9 pages. PMID: 32841988

Journal-ref: Epidemiology: November 2020 - Volume 31 - Issue 6 - p 836-843

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

[146] arXiv:2004.06107 [pdf, other]

Title: Analyzing the spatial distribution of acute coronary syndrome cases using synthesized data on arterial hypertension prevalence

Vasiliy N. Leonenko

Comments: Accepted for publication in the ICCS 2020 proceedings (Springer Lecture Notes in Computer Science series)

Subjects: Quantitative Methods (q-bio.QM)

[147] arXiv:2004.06111 [pdf, other]

Title: Open Data Resources for Fighting COVID-19

Teodoro Alamo, Daniel G. Reina, Martina Mammarella, Alberto Abella

Comments: 30 pages Minor improvements

Subjects: Other Quantitative Biology (q-bio.OT); Machine Learning (stat.ML)

[148] arXiv:2004.06220 [pdf, other]

Title: Embedded model discrepancy: A case study of Zika modeling

Rebecca E. Morrison, Americo Cunha Jr

Comments: 9 pages, 7 figures

Journal-ref: Chaos (2020)

Subjects: Populations and Evolution (q-bio.PE); Computational Engineering, Finance, and Science (cs.CE)

[149] arXiv:2004.06291 [pdf, other]

Title: Modeling, state estimation, and optimal control for the US COVID-19 outbreak

Calvin Tsay, Fernando Lejarza, Mark A. Stadtherr, Michael Baldea

Comments: Updated with available data through April 16, 2020

Journal-ref: Scientific Reports (2020) 10:10711

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

[150] arXiv:2004.06311 [pdf, other]

Title: Public Health Policy: COVID-19 Epidemic and SEIR Model with Asymptomatic Viral Carriers

Weijie Pang

Comments: 17 pages, 10 figures

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