Quantitative Biology

Authors and titles for May 2020

[1] arXiv:2005.00004 [pdf, other]

Title: Massive viral replication and cytopathic effects in early COVID-19 pneumonia

L. Schifanella, J.L. Anderson, M. Galli, M. Corbellino, A. Lai, G. Wieking, B. Grzywacz, N.R. Klatt, A.T. Haase, T.W. Schacker

Comments: 19 pages, 4 figures, 3 extended data figures

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

[2] arXiv:2005.00049 [pdf, other]

Title: Heterogeneous social interactions and the COVID-19 lockdown outcome in a multi-group SEIR model

Jean Dolbeault, Gabriel Turinici

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

[3] arXiv:2005.00082 [pdf, other]

Title: Software for Microscopy Workshop White Paper

Raghav Chhetri, Stephan Preibisch, Nico Stuurman

Comments: 10 pages

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

[4] arXiv:2005.00106 [pdf, other]

Title: Effects of weather and policy intervention on COVID-19 infection in Ghana

Wahab Abdul Iddrisu, Peter Appiahene, Justice A. Kessie

Comments: 14 pages, 5 figures, 3 tables

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

[5] arXiv:2005.00389 [pdf, other]

Title: Random tags can sustain high heterophily levels

Julien Flaig, Nicolas Houy

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

[6] arXiv:2005.00394 [pdf, other]

Title: Bacterial pathways for the biosynthesis of ubiquinone

Sophie Saphia Abby, Katayoun Kazemzadeh, Charles Vragniau, Ludovic Pelosi, Fabien Pierrel

Subjects: Biomolecules (q-bio.BM)

[7] arXiv:2005.00401 [pdf, other]

Title: A continuous-time state-space model for rapid quality-control of Argos locations from animal-borne tags

Ian D. Jonsen, Toby A. Patterson, Daniel P. Costa, Philip D. Doherty, Brendan J. Godley, W. James Grecian, Christophe Guinet, Xavier Hoenner, Sarah S. Kienle, Patrick W. Robison, Stephen C. Votier, Matthew J. Witt, Mark A. Hindell, Robert G. Harcourt, Clive R. McMahon

Comments: 25 pages, 10 figures

Journal-ref: Mov Ecol 8, 31 (2020)

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

[8] arXiv:2005.00435 [pdf, other]

Title: Protein-protein modelling using cryo-EM restraints

Mikael Trellet, Gydo van Zundert, Alexandre M.J.J. Bonvin

Comments: 28 pages including 7 figures

Journal-ref: In: Structural Bioinformatics. Methods in Molecular Biology, vol 2112. Humana, New York, NY, (2020)

Subjects: Biomolecules (q-bio.BM)

[9] arXiv:2005.00469 [pdf, other]

Title: Manifold learning for brain connectivity

Félix Renard, Christian Heinrich, Marine Bouthillon, Maleka Schenck, Francis Schneider, Stéphane Kremer, Sophie Achard

Comments: submitted

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

[10] arXiv:2005.00495 [pdf, other]

Title: Inferring the effective fraction of the population infected with Covid-19 from the behaviour of Lombardy, Madrid and London relative to the remainder of Italy, Spain and England

Robert S Thorne

Comments: 19 pages. 6 this http URL updated article considers the possibility of variable susceptibility to infection. The analysis remains unaltered but the interpretation of the results is extended. The overall conclusions are largely unaltered

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

[11] arXiv:2005.00573 [pdf, other]

Title: Modeling COVID-19 in Cape Verde Islands -- An application of SIR model

Adilson Silva

Comments: 23 pages, 8 figures and 6 tables

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

[12] arXiv:2005.00608 [pdf, other]

Title: Characterizing spreading dynamics of subsampled systems with non-stationary external input

Jorge de Heuvel (1), Jens Wilting (1), Moritz Becker (1 and 2), Viola Priesemann (1), Johannes Zierenberg (1) ((1) Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany, (2) Department of Computational Neuroscience, Third Institute of Physics - Biophysics, Georg-August-University, Göttingen, Germany)

Journal-ref: Phys. Rev. E 102, 040301 (2020)

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

[13] arXiv:2005.00750 [pdf, other]

Title: Simulations of the spread of COVID-19 and control policies in Tunisia

Slimane Ben Miled, Amira Kebir

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

[14] arXiv:2005.00805 [pdf, other]

Title: Fighting seizures with seizures: diffusion and stability in neural systems

Erik D. Fagerholm, Chayanin Tangwiriyasakul, Karl J. Friston, Inês R. Violante, Steven Williams, David W. Carmichael, Suejen Perani, Federico E. Turkheimer, Rosalyn J. Moran, Robert Leech, Mark P. Richardson

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

[15] arXiv:2005.00913 [pdf, other]

Title: Square Root Laws in Structured Fisheries

Jerzy Filar, Sabrina Streipert

Comments: 7 figures, 9 pages main text, 6 pages supplementary material

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

[16] arXiv:2005.00921 [pdf, other]

Title: An Epidemic Model SIPHERD and its application for prediction of the spread of COVID-19 infection for India and USA

Ashutosh Mahajan, Ravi Solanki, A.S. Namitha

Comments: 6 pages, 11 figures

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

[17] arXiv:2005.01001 [pdf, other]

Title: Spatiotemporal dynamics in demography-sensitive disease transmission: COVID-19 spread in NY as a case study

Joydeep Munshi, Indranil Roy, Ganesh Balasubramanian

Comments: 14 pages, 6 figures

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

[18] arXiv:2005.01042 [pdf, other]

Title: Transcriptional landscape of SARS-CoV-2 infection dismantles pathogenic pathways activated by the virus, proposes unique sex-specific differences and predicts tailored therapeutic strategies

Paolo Fagone, Rosella Ciurleo, Salvo Danilo Lombardo, Carmelo Iacobello, Concetta Ilenia Palermo, Yehuda Shoenfeld, Klaus Bendtzen, Placido Bramanti, Ferdinando Nicoletti

Subjects: Cell Behavior (q-bio.CB)

[19] arXiv:2005.01149 [pdf, other]

Title: Effective lockdown and role of hospital-based COVID-19 transmission in some Indian states: An outbreak risk analysis

Tridip Sardar, Sourav Rana

Comments: 45 pages

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

[20] arXiv:2005.01200 [pdf, other]

Title: Evolution of chemotactic hitchhiking

Gurdip Uppal, Weiyi Hu, Dervis Can Vural

Comments: 10 pages, 5 figures

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

[21] arXiv:2005.01356 [pdf, other]

Title: A single psychotomimetic dose of ketamine decreases thalamocortical spindles and delta oscillations in the sedated rat

Didier Pinault (FMTS)

Comments: Schizophrenia Research, Elsevier, In press

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

[22] arXiv:2005.01375 [pdf, other]

Title: Synthesis and characterization of novel benzimidazole embedded 1,3,5-trisubstituted pyrazolines as antimicrobial agents

Gopal Krishna Padhy, Jagadeesh Panda, Ajaya Kumar Behera

Comments: 9 Pages,2 figures, 1 table

Journal-ref: J. Med. Chem. 51 (2008) 5243, Pharma Chem. 8 (2016) 425, RSC Adv. 6 (2016) 8303, Int. J. Mol. Sci. 13 (2012)16472, J. Chem. Res. 40 (2016) 228

Subjects: Biomolecules (q-bio.BM)

[23] arXiv:2005.01377 [pdf, other]

Title: A Bayesian traction force microscopy method with automated denoising in a user-friendly software package

Yunfei Huang, Gerhard Gompper, Benedikt Sabass

Subjects: Cell Behavior (q-bio.CB); Soft Condensed Matter (cond-mat.soft)

[24] arXiv:2005.01434 [pdf, other]

Title: Modeling the Epidemic Outbreak and Dynamics of COVID-19 in Croatia

Ante Lojić Kapetanović, Dragan Poljak

Comments: 5 pages, 6 figures, to appear in the Proceedings of the SpliTech2020 conference

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

[25] arXiv:2005.01436 [pdf, other]

Title: Metamorphic Proteins in light of the Anfinsen Dogma

Jorge A. Vila

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

[26] arXiv:2005.01491 [pdf, other]

Title: Transcriptional profiling reveals fundamental differences in iPS-derived progenitors of endothelial cells (PECs) versus adult circulating EPCs

Elmira Jalilian, William Raimes

Subjects: Cell Behavior (q-bio.CB); Populations and Evolution (q-bio.PE)

[27] arXiv:2005.01549 [pdf, other]

Title: Computational modelling in single-cell cancer genomics: methods and future directions

Allen W Zhang, Kieran R Campbell

Comments: Review article; 10 pages, 1 figure, 2 tables

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

[28] arXiv:2005.01579 [pdf, other]

Title: SARS-CoV-2 mortality in blacks and temperature-sensitivity to an angiotensin-2 receptor blocker

Donald R. Forsdyke

Comments: Pages: 20. Words: 5739. Figures: 3. References: 72. Updated references and text

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

[29] arXiv:2005.01625 [pdf, other]

Title: Adapt or perish: Evolutionary rescue in a gradually deteriorating environment

Loïc Marrec, Anne-Florence Bitbol

Comments: 36 pages, 18 figures

Journal-ref: Genetics 216, 573-583 (2020)

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

[30] arXiv:2005.01628 [pdf, other]

Title: Gene-Environment Interaction in the Era of Precision Medicine -- Fix the Potholes or Start Building a New Road?

José M. Álvarez-Castro

Comments: 12 pages with two figres (with two panels each) and two tables

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

[31] arXiv:2005.01696 [pdf, other]

Title: Customised fragment libraries for ab initio protein structure prediction using a structural alphabet

Surbhi Dhingra, Ramanathan Sowdhamini, Yves-Henri Sanejouand, Frédéric Cadet, Bernard Offmann

Comments: 18 pages, 7 figures, 2 Tables, 2 Supplementary Figures, 2 Supplementary Tables

Subjects: Quantitative Methods (q-bio.QM)

[32] arXiv:2005.01714 [pdf, other]

Title: Antimicrobial Peptide Prediction Using Ensemble Learning Algorithm

Neda Zarayeneh, Zahra Hanifeloo

Comments: It has been accepted to the ICBCB 2020 conference

Journal-ref: ICBCB 2020 conference

Subjects: Quantitative Methods (q-bio.QM)

[33] arXiv:2005.01798 [pdf, other]

Title: Automated Detection of Rest Disruptions in Critically Ill Patients

Vasundhra Iyengar, Azra Bihorac, Parisa Rashidi

Journal-ref: 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Montreal, QC, Canada, 2020, pp. 5450-5454

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Image and Video Processing (eess.IV); Machine Learning (stat.ML)

[34] arXiv:2005.01804 [pdf, other]

Title: Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models

Ngan Nguyen, Ondrej Strnad, Tobias Klein, Deng Luo, Ruwayda Alharbi, Peter Wonka, Martina Maritan, Peter Mindek, Ludovic Autin, David S. Goodsell, Ivan Viola

Subjects: Quantitative Methods (q-bio.QM)

[35] arXiv:2005.01820 [pdf, other]

Title: Fractional-order SEIQRDP model for simulating the dynamics of COVID-19 epidemic

Mohamed Bahloul, Abderrazak Chahid, Taous Meriem Laleg-Kirati

Comments: 11 Pages, 4 figures

Subjects: Populations and Evolution (q-bio.PE); Systems and Control (eess.SY)

[36] arXiv:2005.01838 [pdf, other]

Title: Gene drive dynamics in natural populations: The importance of density-dependence, space and sex

Sumit Dhole, Alun L Lloyd, Fred Gould

Journal-ref: Annual Review of Ecology Evolution and Systematics. Vol. 51, 2020

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

[37] arXiv:2005.01887 [pdf, other]

Title: Pain relief devoid of opioid side effects following central action of a silylated neurotensin analog

Pascal Tétreault, Élie Besserer-Offroy, Rebecca L. Brouillette, Adeline René, Alexandre Murza, Roberto Fanelli, Karyn Kirby, Alexandre J. Parent, Isabelle Dubuc, Nicolas Beaudet, Jérôme Côté, Jean-Michel Longpré, Jean Martinez, Florine Cavelier, Philippe Sarret

Comments: This is the post-print (accepted) version of the following article: Tétreault P, et al. (2020), Eur J Pharmacol. doi: https://doi.org/10.1016/j.ejphar.2020.173174, which has been accepted and published in final form at this https URL

Journal-ref: Eur J Pharmacol, 173174 (2020)

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

[38] arXiv:2005.01914 [pdf, other]

Title: Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization

Juan M. Escorcia-Rodríguez (1), Andreas Tauch (2), Julio A. Freyre-González (1) ((1) Regulatory Systems Biology Research Group, Laboratory of Systems and Synthetic Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, (2) Centrum für Biotechnologie (CeBiTec), Universität Bielefeld)

Comments: 25 pages, 6 figures, 11 pages supplementary information

Journal-ref: Computational and Structural Biotechnology Journal 18:1228-1237 (2020)

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

[39] arXiv:2005.01944 [pdf, other]

Title: Minimal epidemic model considering external infected injection and governmental quarantine policies: Application to COVID-19 pandemic

L. A. Rodríguez Palomino, Adrián A. Budini

Comments: 8 pages, 4 figures

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

[40] arXiv:2005.01955 [pdf, other]

Title: Motor protein transport along inhomogeneous microtubules

Shawn D. Ryan, Zachary McCarthy, Mykhailo Potomkin

Subjects: Subcellular Processes (q-bio.SC); Soft Condensed Matter (cond-mat.soft); Analysis of PDEs (math.AP)

[41] arXiv:2005.02071 [pdf, other]

Title: Automatic Tracking of the Muscle Tendon Junction in Healthy and Impaired Subjects using Deep Learning

Christoph Leitner, Robert Jarolim, Andreas Konrad, Annika Kruse, Markus Tilp, Jörg Schröttner, Christian Baumgartner

Comments: Accepted version to be published in 2020, 42nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Montreal, Canada

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

[42] arXiv:2005.02182 [pdf, other]

Title: Opportunities for multiscale computational modelling of serotonergic drug effects in Alzheimer's disease

Alok Joshi, Da-Hui Wang, Steven Watterson, Paula L. McClean, Chandan K. Behera, Trevor Sharp, KongFatt Wong-Lin

Comments: Accepted manuscript in Neuropharmacology

Subjects: Subcellular Processes (q-bio.SC); Molecular Networks (q-bio.MN); Neurons and Cognition (q-bio.NC)

[43] arXiv:2005.02188 [pdf, other]

Title: Mutations on COVID-19 diagnostic targets

Rui Wang, Yuta Hozumi, Changchuan Yin, Guo-Wei Wei

Comments: 3 tables and 6 pages, and 48 tables in the Supporting Material

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

[44] arXiv:2005.02211 [pdf, other]

Title: Recurrent Neural Network Learning of Performance and Intrinsic Population Dynamics from Sparse Neural Data

Alessandro Salatiello, Martin A. Giese

Journal-ref: Artificial Neural Networks and Machine Learning - ICANN 2020. ICANN 2020. Lecture Notes in Computer Science, vol 12396. Springer, Cham.:874-86

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

[45] arXiv:2005.02214 [pdf, other]

Title: Computational neurology: Computational modeling approaches in dementia

KongFatt Wong-Lin, Jose M. Sanchez-Bornot, Niamh McCombe, Daman Kaur, Paula L. McClean, Xin Zou, Vahab Youssofzadeh, Xuemei Ding, Magda Bucholc, Su Yang, Girijesh Prasad, Damien Coyle, Liam P. Maguire, Haiying Wang, Hui Wang, Nadim A.A. Atiya, Alok Joshi

Comments: Accepted manuscript as a book chapter in Systems Medicine: Integrative, Qualitative and Computational Approaches. Wolkenhauer, O. (ed.). Elsevier Inc

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

[46] arXiv:2005.02251 [pdf, other]

Title: Raccoons vs Demons: multiclass labeled P300 dataset

V. Goncharenko, R. Grigoryan, A. Samokhina

Subjects: Neurons and Cognition (q-bio.NC); Human-Computer Interaction (cs.HC); Machine Learning (cs.LG); Machine Learning (stat.ML)

[47] arXiv:2005.02261 [pdf, other]

Title: Crucial Inflammatory Mediators and Efficacy of Drug Interventions in Pneumonia Inflated COVID-19: An Invivo Mathematical Modelling Study

Bishal Chhetri, D. K. K. Vamsi, Vijay M. Bhagat, Ananth V. S., Bhanu Prakash, Roshan Mandale, Swapna Muthusamy, Carani B Sanjeevi

Comments: 50 pages, 37 figures

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

[48] arXiv:2005.02271 [pdf, other]

Title: Estimating the number of available states for normal and tumor tissues in gene expression space

Augusto Gonzalez, Frank Quintela, Dario A. Leon, Maria Luisa Bringas Vega, Pedro Valdes Sosa

Journal-ref: Biophysical Reports Volume 2, Issue 2, 8 June 2022, 100053

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

[49] arXiv:2005.02289 [pdf, other]

Title: In Silico Trial to test COVID-19 candidate vaccines: a case study with UISS platform

Giulia Russo, Marzio Pennisi, Marco Viceconti, Francesco Pappalardo

Comments: 8 pages, 7 figures

Subjects: Quantitative Methods (q-bio.QM); Multiagent Systems (cs.MA); Populations and Evolution (q-bio.PE); Tissues and Organs (q-bio.TO)

[50] arXiv:2005.02294 [pdf, other]

Title: Using posterior predictive distributions to analyse epidemic models: COVID-19 in Mexico City

Ramsés H. Mena, Jorge X. Velasco-Hernandez, Natalia B. Mantilla-Beniers, Gabriel A. Carranco-Sapiéns, Luis Benet, Denis Boyer, Isaac Pérez Castillo

Comments: 6 pages, 9 figures. The draft has been rewritten and the SI has been included as an ancillary file. The calibration of the model has been redone using the updated public data on May 7th

Journal-ref: Physical Biology 17 (2020), 065001

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