Quantitative Biology

Authors and titles for May 2020

[201] arXiv:2005.09190 [pdf, other]

Title: Transient behaviour towards the stable limit cycle in the Selkov model of Glycolysis: A physiological disorder

Tanmay Das, Muktish Acharyya

Comments: 8 oages Latex and 5 eps figures

Journal-ref: Physica A 567 (2021) 125684

Subjects: Quantitative Methods (q-bio.QM); Soft Condensed Matter (cond-mat.soft); Adaptation and Self-Organizing Systems (nlin.AO); Biological Physics (physics.bio-ph)

[202] arXiv:2005.09390 [pdf, other]

Title: Control Strategy Identification via Trap Spaces in Boolean Networks

Laura Cifuentes Fontanals, Elisa Tonello, Heike Siebert

Comments: 16 pages, 2 figures

Journal-ref: Proceedings Computational Methods in Systems Biology (CMSB) 2020, Springer International Publisher

Subjects: Molecular Networks (q-bio.MN)

[203] arXiv:2005.09421 [pdf, other]

Title: Diffusivity Estimation for Activator-Inhibitor Models: Theory and Application to Intracellular Dynamics of the Actin Cytoskeleton

Gregor Pasemann, Sven Flemming, Sergio Alonso, Carsten Beta, Wilhelm Stannat

Journal-ref: J Nonlinear Sci 31, 59 (2021)

Subjects: Quantitative Methods (q-bio.QM); Dynamical Systems (math.DS); Numerical Analysis (math.NA); Methodology (stat.ME)

[204] arXiv:2005.09426 [pdf, other]

Title: Mathematical model of COVID-19 intervention scenarios for Sao Paulo- Brazil

Osmar Pinto Neto, Jose Clark Reis, Ana Carolina Brisola Brizzi, Gustavo Jose Zambrano, Joabe Marcos de Souza, Wellington Amorim Pedroso, Rodrigo Cunha de Mello Pedreiro, Bruno de Matos Brizzi, Ellysson Oliveira Abinader, Deanna M. Kennedy, Renato Amaro Zangaro

Comments: 24 pages, 4 figures, 1 table

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

[205] arXiv:2005.09431 [pdf, other]

Title: Probabilistic Optically-Selective Single-molecule Imaging Based Localization Encoded (POSSIBLE) Microscopy for Ultra-superresolution Imaging

Partha Pratim Mondal

Comments: 9 pages

Subjects: Quantitative Methods (q-bio.QM); Image and Video Processing (eess.IV); Applied Physics (physics.app-ph); Biological Physics (physics.bio-ph)

[206] arXiv:2005.09475 [pdf, other]

Title: Forecasting Covid-19 dynamics in Brazil: a data driven approach

Igor G. Pereira, Joris M. Guerin, Andouglas G. Silva Junior, Cosimo Distante, Gabriel S. Garcia, Luiz M. G. Gonçalves

Comments: First version submitted to Chaos, Solitons and Fractals, 41 pages, complementary material at this http URL

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

[207] arXiv:2005.09537 [pdf, other]

Title: Simulation of laser induced retinal thermal injuries for non-uniform irradiance profiles and their evaluation according to the laser safety standard

Sebastian Kotzur, Siegfried Wahl, Annette Frederiksen

Journal-ref: Proc. SPIE 11363, Tissue Optics and Photonics (2020)

Subjects: Tissues and Organs (q-bio.TO); Optics (physics.optics)

[208] arXiv:2005.09572 [pdf, other]

Title: Ensemble Transfer Learning for the Prediction of Anti-Cancer Drug Response

Yitan Zhu, Thomas Brettin, Yvonne A. Evrard, Alexander Partin, Fangfang Xia, Maulik Shukla, Hyunseung Yoo, James H. Doroshow, Rick Stevens

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

[209] arXiv:2005.09592 [pdf, other]

Title: Minimal models of invasion and clonal selection in cancer

Chay Paterson

Subjects: Populations and Evolution (q-bio.PE); Soft Condensed Matter (cond-mat.soft); Tissues and Organs (q-bio.TO)

[210] arXiv:2005.09598 [pdf, other]

Title: Animal social networks: an introduction for complex systems scientists

Josefine Bohr Brask, Samuel Ellis, Darren P Croft

Comments: 15 pages, 2 figures

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

[211] arXiv:2005.09622 [pdf, other]

Title: Learning Equations from Biological Data with Limited Time Samples

John T. Nardini, John H. Lagergren, Andrea Hawkins-Daarud, Lee Curtin, Bethan Morris, Erica M. Rutter, Kristin R. Swanson, Kevin B. Flores

Subjects: Quantitative Methods (q-bio.QM)

[212] arXiv:2005.09625 [pdf, other]

Title: Inference, prediction and optimization of non-pharmaceutical interventions using compartment models: the PyRoss library

R. Adhikari, Austen Bolitho, Fernando Caballero, Michael E. Cates, Jakub Dolezal, Timothy Ekeh, Jules Guioth, Robert L. Jack, Julian Kappler, Lukas Kikuchi, Hideki Kobayashi, Yuting I. Li, Joseph D. Peterson, Patrick Pietzonka, Benjamin Remez, Paul B. Rohrbach, Rajesh Singh, Günther Turk

Comments: Code and updates at this https URL 75 pages, 14 figures, and 1 table

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

[213] arXiv:2005.09630 [pdf, other]

Title: A systems biology approach to COVID-19 progression in a population

Magdalena Djordjevic, Andjela Rodic, Igor Salom, Dusan Zigic, Ognjen Milicevic, Bojana Ilic, Marko Djordjevic

Comments: 16 pages, 5 figures, 1 table. Advances in Protein Chemistry and Structural Biology (in press, 2021)

Journal-ref: Adv Protein Chem Struct Biol . 2021;127:291-314

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

[214] arXiv:2005.09687 [pdf, other]

Title: Deep learning approaches for neural decoding: from CNNs to LSTMs and spikes to fMRI

Jesse A. Livezey, Joshua I. Glaser

Comments: 22 pages, 3 figures

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

[215] arXiv:2005.09786 [pdf, other]

Title: Optimal quarantine strategies for the COVID-19 pandemic in a population with a discrete age structure

João A. M. Gondim, Larissa Machado

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

[216] arXiv:2005.09805 [pdf, other]

Title: Molecular Characterization of Ebselen Binding Activity to SARS-CoV-2 Main Protease

Cintia A. Menendez, Fabian Bylehn, Gustavo R. Perez-Lemus, Walter Alvarado, Juan J. de Pablo

Comments: 10 pages, 5 figures

Subjects: Biomolecules (q-bio.BM); Biological Physics (physics.bio-ph)

[217] arXiv:2005.09890 [pdf, other]

Title: Interactive exploration of population scale pharmacoepidemiology datasets

Tengel Ekrem Skar, Einar Holsbø, Kristian Svendsen, Lars Ailo Bongo

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

[218] arXiv:2005.09936 [pdf, other]

Title: Leveraging Insight from Centuries of Outbreak Preparedness to Improve Modern Planning Efforts

Nina H. Fefferman, Sharon DeWitte, Stephanie S. Johnson, Eric T. Lofgren

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

[219] arXiv:2005.09975 [pdf, other]

Title: A new formulation of compartmental epidemic modelling for arbitrary distributions of incubation and removal times

P. Hernández, C. Pena, A. Ramos, J.J. Gómez-Cadenas

Comments: 21 pages, 11 figures. v2 matches published version: improved presentation (including title, abstract and references), results and conclusions unchanged

Journal-ref: PLoS ONE 16(2): e0244107 (2021)

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

[220] arXiv:2005.10028 [pdf, other]

Title: Repositioning of 8565 existing drugs for COVID-19

Kaifu Gao, Duc Duy Nguyen, Jiahui Chen, Rui Wang, Guo-Wei Wei

Comments: 20 pages, 6 figures and 6 tables

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

[221] arXiv:2005.10055 [pdf, other]

Title: Blocking of the CD80/86 axis as a therapeutic approach to prevent progression to more severe forms of COVID-19

Antonio Julià, Irene Bonafonte, Antonio Gómez, María López-Lasanta, Mireia López-Corbeto, Sergio H. Martínez-Mateu, Jordi Lladós, Iván Rodríguez-Nunez, Richard M. Myers, Sara Marsal

Comments: 23 pages, 8 figures, 1 Table, Supplementary data (3 supplementary figures and 3 supplementary Tables)

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

[222] arXiv:2005.10223 [pdf, other]

Title: Quantifying socioeconomic activities and weather effects on the global spread of COVID-19 epidemic

Xinyi Shen (1), Chenkai Cai (1 and 2), Hui Li (3) ((1) Department of Civil and Environmental Engineering, University of Connecticut, (2) College of Hydrology and Water Resources, Hohai University, (3) Department of Finance, University of Connecticut)

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

[223] arXiv:2005.10227 [pdf, other]

Title: Hemogram Data as a Tool for Decision-making in COVID-19 Management: Applications to Resource Scarcity Scenarios

Eduardo Avila, Marcio Dorn, Clarice Sampaio Alho, Alessandro Kahmann

Comments: 14 pages, 5 figures, 2 tables, Tool Available at: this http URL

Subjects: Other Quantitative Biology (q-bio.OT); Machine Learning (cs.LG)

[224] arXiv:2005.10248 [pdf, other]

Title: Statistical Issues and Recommendations for Clinical Trials Conducted During the COVID-19 Pandemic

R. Daniel Meyer, Bohdana Ratitch, Marcel Wolbers, Olga Marchenko, Hui Quan, Daniel Li, Chrissie Fletcher, Xin Li, David Wright, Yue Shentu, Stefan Englert, Wei Shen, Jyotirmoy Dey, Thomas Liu, Ming Zhou, Norman Bohidar, Peng-Liang Zhao, Michael Hale

Comments: Accepted for publication in Statistics in Biopharmaceutical Research. 40 pages

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

[225] arXiv:2005.10311 [pdf, other]

Title: Repeat Contacts and the Spread of Disease: An Agent Model with Compartmental Solution

Peter Cotton

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

[226] arXiv:2005.10332 [pdf, other]

Title: Evolutionary entropy and the Second Law of Thermodynamics

Lloyd Demetrius, Christian Wolf

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

[227] arXiv:2005.10428 [pdf, other]

Title: The Role of Energy Cost on Accuracy, Sensitivity, Specificity, Speed and Adaptation of T Cell Foreign and Self Recognition

Gyubaek Shin (1), Jin Wang (1 and 2) ((1) Department of Chemistry, SUNY Stony Brook, NY, USA, (2) Department of Physics and Astronomy, SUNY Stony Brook, NY, USA)

Comments: 13 pages, 14 figures

Subjects: Molecular Networks (q-bio.MN)

[228] arXiv:2005.10517 [pdf, other]

Title: Generalized half-center oscillators with short-term synaptic plasticity

Valentina Baruzzi, Matteo Lodi, Marco Storace, Andrey Shilnikov

Journal-ref: Phys. Rev. E 102, 032406 (2020)

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

[229] arXiv:2005.10598 [pdf, other]

Title: Fast and Accurate Langevin Simulations of Stochastic Hodgkin-Huxley Dynamics

Shusen Pu, Peter J. Thomas

Comments: 55 pages, 9 figures

Subjects: Neurons and Cognition (q-bio.NC); Numerical Analysis (math.NA)

[230] arXiv:2005.10644 [pdf, other]

Title: A Minimal-Input Multilayer Perceptron for Predicting Drug-Drug Interactions Without Knowledge of Drug Structure

Alun Stokes, William Hum, Jonathan Zaslavsky

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

[231] arXiv:2005.10739 [pdf, other]

Title: Assessing the Precision and Recall of msTALI as Applied to an Active-Site Study on Fold Families

Devaun McFarland (1), Homayoun Valafar (1) ((1) University of South Carolina)

Comments: 8 pages, 3 figures, 5 tables. This is an extended version of a similar abridged or short version used in conference

Subjects: Quantitative Methods (q-bio.QM); Computational Engineering, Finance, and Science (cs.CE)

[232] arXiv:2005.10746 [pdf, other]

Title: Tissue failure propagation as mediated by circulatory flow

Gurdip Uppal, Gokhan Bahcecioglu, Pinar Zorlutuna, Dervis Can Vural

Comments: 10 pages, 5 figures

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

[233] arXiv:2005.10797 [pdf, other]

Title: An Optimal Predictive Control Strategy for COVID-19 (SARS-CoV-2) Social Distancing Policies in Brazil

Marcelo Menezes Morato, Saulo Benchimol Bastos, Daniel Oliveira Cajueiro, Julio Elias Normey-Rico

Comments: 30 pages, 9 Figures, Preprint submitted to Annual Reviews in Control

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

[234] arXiv:2005.10831 [pdf, other]

Title: Repurpose Open Data to Discover Therapeutics for COVID-19 using Deep Learning

Xiangxiang Zeng, Xiang Song, Tengfei Ma, Xiaoqin Pan, Yadi Zhou, Yuan Hou, Zheng Zhang, George Karypis, Feixiong Cheng

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

[235] arXiv:2005.10951 [pdf, other]

Title: A machine learning approach to using Quality-of-Life patient scores in guiding prostate radiation therapy dosing

Zhijian Yang, Daniel Olszewski, Chujun He, Giulia Pintea, Jun Lian, Tom Chou, Ronald Chen, Blerta Shtylla

Subjects: Quantitative Methods (q-bio.QM); Tissues and Organs (q-bio.TO)

[236] arXiv:2005.11082 [pdf, other]

Title: Tractometry-based Anomaly Detection for Single-subject White Matter Analysis

Maxime Chamberland, Sila Genc, Erika P. Raven, Greg D. Parker, Adam Cunningham, Joanne Doherty, Marianne van den Bree, Chantal M. W. Tax, Derek K. Jones

Comments: Medical Imaging with Deep Learning (MIDL2020) Conference Short Paper

Journal-ref: Medical Imaging with Deep Learning 2020

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

[237] arXiv:2005.11085 [pdf, other]

Title: COVID-19: The unreasonable effectiveness of simple models

Timoteo Carletti, Duccio Fanelli, Francesco Piazza

Comments: main paper + supplementary material

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

[238] arXiv:2005.11088 [pdf, other]

Title: Drug repurposing prediction for COVID-19 using probabilistic networks and crowdsourced curation

David J. Skelton, Aoesha Alsobhe, Elisa Anastasi, Christian Atallah, Jasmine E. Bird, Bradley Brown, Dwayne Didon, Phoenix Gater, Katherine James, David D. Lennon Jr, James McLaughlin, Pollyanna E. J. Moreland, Matthew Pocock, Caroline J. Whitaker, Anil Wipat

Comments: 30 pages, 5 figures, 2 tables + 1 additional table in supporting material

Subjects: Molecular Networks (q-bio.MN)

[239] arXiv:2005.11182 [pdf, other]

Title: Predicting the evolution of the COVID-19 epidemic with the A-SIR model: Lombardy, Italy and S\~ao Paulo state, Brazil

Armando G. M. Neves, Gustavo Guerrero

Comments: 33 pages, 14 figures

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

[240] arXiv:2005.11186 [pdf, other]

Title: EEG source localization analysis in epileptic children during a visual working-memory task

Evangelos Galaris, Ioannis Gallos, Ivan Myatchin, Lieven Lagae, Constantinos Siettos

Journal-ref: International Journal of Numerical Methods in Biomedical Engineering, 36:e3404, 2020

Subjects: Neurons and Cognition (q-bio.NC); Numerical Analysis (math.NA)

[241] arXiv:2005.11201 [pdf, other]

Title: Poverty levels, societal and individual heterogeneities explain the SARS-CoV-2 pandemic growth in Latin America

José Miguel Ponciano, Juan Adolfo Ponciano, Juan Pablo Gómez, Robert D. Holt, Jason K. Blackburn

Comments: 22 pages, 5 figures, Supplementary Material not uploaded

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

[242] arXiv:2005.11254 [pdf, other]

Title: Virtual Screening of Plant Metabolites against Main protease, RNA-dependent RNA polymerase and Spike protein of SARS-CoV-2: Therapeutics option of COVID-19

Md Sorwer Alam Parvez, Kazi Faizul Azim, Abdus Shukur Imran, Topu Raihan, Aklima Begum, Tasfia Saiyara Shammi, Sabbir Howlader, Farhana Rumzum Bhuiyan, Mahmudul Hasan

Comments: 29 pages, 5 figures

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

[243] arXiv:2005.11255 [pdf, other]

Title: Edge-effects dominate copying thermodynamics for finite-length molecular oligomers

Jenny Marie Poulton, Thomas Edward Ouldridge

Subjects: Subcellular Processes (q-bio.SC); Statistical Mechanics (cond-mat.stat-mech); Molecular Networks (q-bio.MN)

[244] arXiv:2005.11257 [pdf, other]

Title: Epidemiologically and Socio-economically Optimal Policies via Bayesian Optimization

Amit Chandak, Debojyoti Dey, Bhaskar Mukhoty, Purushottam Kar

Comments: Keywords: COVID-19, Optimal Policy, Lock-down, Epidemiology, Bayesian Optimization Code available at this https URL

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

[245] arXiv:2005.11277 [pdf, other]

Title: Infections and Identified Cases of COVID-19 from Random Testing Data

Allen Caldwell, Vasyl Hafych, Oliver SChulz, Lolian Shtembari

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

[246] arXiv:2005.11278 [pdf, other]

Title: The Impact of Response Measures on COVID-19-Related Hospitalization and Death Rates in Germany and Switzerland

Martin Huber, Henrika Langen

Comments: Evaluation of lockdown measures in Germany and Switzerland aimed at containing the COVID-19 epidemic

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

[247] arXiv:2005.11279 [pdf, other]

Title: An efficient explicit approach for predicting the Covid-19 spreading with undetected infectious: The case of Cameroon

Eric Ngondiep

Comments: 26 pages, 11 figures, 11 tables

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

[248] arXiv:2005.11343 [pdf, other]

Title: Mathematical analysis and potential therapeutic implications of a novel HIV-1 model of basal and activated transcription in T-cells and macrophages

Tin Phan, Catherine DeMarino, Fatah Kashanchi, Yang Kuang, Daniel M. Anderson, Maria Emelianenko

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

[249] arXiv:2005.11420 [pdf, other]

Title: Epidemic analysis of COVID-19 in Brazil by a generalized SEIR model

Suzete Afonso, Juarez Azevedo, Mariana Pinheiro

Comments: 12 pages, 10 figures

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

[250] arXiv:2005.11433 [pdf, other]

Title: Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts

Antti Lankinen, Ismael Mullor Ruiz, Thomas E. Ouldridge

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