Quantitative Biology

Authors and titles for June 2020

[251] arXiv:2006.16006 [pdf, other]

Title: New forms of structure in ecosystems revealed with the Kuramoto model

John Vandermeer, Zachary Hajian-Forooshani, Nicholas Medina, Ivette Perfecto

Comments: 18 pages, 5 figures

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

[252] arXiv:2006.16189 [pdf, other]

Title: DOME: Recommendations for supervised machine learning validation in biology

Ian Walsh, Dmytro Fishman, Dario Garcia-Gasulla, Tiina Titma, Gianluca Pollastri, The ELIXIR Machine Learning focus group, Jen Harrow, Fotis E. Psomopoulos, Silvio C.E. Tosatto

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

[253] arXiv:2006.16203 [pdf, other]

Title: How does the extracellular matrix affect the rigidity of an embedded spheroid?

Amanda Parker, M. Cristina Marchetti, M. Lisa Manning, J. M. Schwarz

Comments: Main text: 5 pages, 3 figures. Supplementary Material: 13 pages, 14 figures

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

[254] arXiv:2006.16204 [pdf, other]

Title: Coloured noise time series as appropriate models for environmental variation in artificial evolutionary systems

Matt Grove, James M. Borg, Fiona Polack

Comments: 8 pages, 4 figures, 2020 conference on Artificial Life

Subjects: Populations and Evolution (q-bio.PE); Neural and Evolutionary Computing (cs.NE); Physics and Society (physics.soc-ph)

[255] arXiv:2006.16326 [pdf, other]

Title: Impact of contamination factors on the COVID-19 evolution in Senegal

Vieux Medoune Ndiaye, Serigne Omar Sarr, Babacar Mbaye Ndiaye

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

[256] arXiv:2006.16379 [pdf, other]

Title: Optimized lockdown strategies for curbing the spread of COVID-19: A South African case study

Laurentz E. Olivier, Stefan Botha, Ian K. Craig

Comments: 11 pages, 7 figures, 4 tables

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

[257] arXiv:2006.16486 [pdf, other]

Title: Modeling tau transport in the axon initial segment

Ivan A. Kuznetsov, Andrey V. Kuznetsov

Comments: final accepted version

Journal-ref: Mathematical Biosciences, vol. 329, article # 108468, 2020

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

[258] arXiv:2006.16487 [pdf, other]

Title: On the derivation of the renewal equation from an age-dependent branching process: an epidemic modelling perspective

Swapnil Mishra, Tresnia Berah, Thomas A. Mellan, H. Juliette T. Unwin, Michaela A Vollmer, Kris V Parag, Axel Gandy, Seth Flaxman, Samir Bhatt

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

[259] arXiv:2006.16525 [pdf, other]

Title: Hunting Co-operation in the Middle Predator in Three Species Food Chain Model

Nishchal Sapkota, Rimsha Bhatta, Phillip Dabney, Zhifu Xie

Journal-ref: 2019 Proceedings of LA/MS Section of Mathematical Association of America

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

[260] arXiv:2006.16630 [pdf, other]

Title: Computing extracellular electric potentials from neuronal simulations

Torbjørn V. Ness, Geir Halnes, Solveig Næss, Klas H. Pettersen, Gaute T. Einevoll

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

[261] arXiv:2006.16648 [pdf, other]

Title: Associations between finger tapping, gait and fall risk with application to fall risk assessment

Jian Ma

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

[262] arXiv:2006.16676 [pdf, other]

Title: Experimental visually-guided investigation of sub-structures in three-dimensional Turing-like patterns

Martin Skrodzki, Ulrich Reitebuch, Eric Zimmermann

Journal-ref: Exploratory Papers of Automata 2021, https://hal.archives-ouvertes.fr/hal-03270664

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

[263] arXiv:2006.16735 [pdf, other]

Title: Inferring epistasis from genomic data with comparable mutation and outcrossing rate

Hong-Li Zeng, Eugenio Mauri, Vito Dichio, Simona Cocco, Remi Monasson, Erik Aurell

Comments: 16 pages, 9 figures. Substantial revision from second version, previous suggestions and comments gratefully acknowledged

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

[264] arXiv:2006.16787 [pdf, other]

Title: Optimal surface topography for cell adhesion is driven by cell membrane mechanics

Matej Daniel, Kristina Eleršič Filipič, Eva Filová, Jaroslav Fojt

Subjects: Cell Behavior (q-bio.CB); Biological Physics (physics.bio-ph)

[265] arXiv:2006.16791 [pdf, other]

Title: Local Causal Structure Learning and its Discovery Between Type 2 Diabetes and Bone Mineral Density

Wei Wang, Gangqiang Hu, Bo Yuan, Shandong Ye, Chao Chen, YaYun Cui, Xi Zhang, Liting Qian

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

[266] arXiv:2006.16928 [pdf, other]

Title: Using A Partial Differential Equation with Google Mobility Data to Predict COVID-19 in Arizona

Haiyan Wang, Nao Yamamoto

Journal-ref: Mathematical Biosciences and Engineering, 2020, 17(5): 4891-4904

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

[267] arXiv:2006.16955 [pdf, other]

Title: We Should at Least Be Able to Design Molecules That Dock Well

Tobiasz Cieplinski, Tomasz Danel, Sabina Podlewska, Stanislaw Jastrzebski

Comments: Published in Journal of Chemical Information and Modeling

Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG); Machine Learning (stat.ML)

[268] arXiv:2006.00018 (cross-list from physics.bio-ph) [pdf, other]

Title: Stability of gene regulatory networks

Yipei Guo, Ariel Amir

Comments: 14 pages, 6 figures

Subjects: Biological Physics (physics.bio-ph); Disordered Systems and Neural Networks (cond-mat.dis-nn); Molecular Networks (q-bio.MN)

[269] arXiv:2006.00067 (cross-list from cs.CV) [pdf, other]

Title: Automated Measurements of Key Morphological Features of Human Embryos for IVF

Brian D. Leahy, Won-Dong Jang, Helen Y. Yang, Robbert Struyven, Donglai Wei, Zhe Sun, Kylie R. Lee, Charlotte Royston, Liz Cam, Yael Kalma, Foad Azem, Dalit Ben-Yosef, Hanspeter Pfister, Daniel Needleman

Comments: to be presented at MICCAI 2020

Subjects: Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Other Quantitative Biology (q-bio.OT)

[270] arXiv:2006.00085 (cross-list from physics.soc-ph) [pdf, other]

Title: Mortality containment vs. economics opening: optimal policies in a SEIARD model

Andrea Aspri, Elena Beretta, Alberto Gandolfi, Etienne Wasmer

Subjects: Physics and Society (physics.soc-ph); General Economics (econ.GN); Optimization and Control (math.OC); Populations and Evolution (q-bio.PE)

[271] arXiv:2006.00122 (cross-list from physics.bio-ph) [pdf, other]

Title: Stick-Slip model for actin-driven cell protrusions, cell polarisation and crawling

Pierre Sens

Comments: 12 pages, 5 figures

Subjects: Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)

[272] arXiv:2006.00129 (cross-list from cond-mat.soft) [pdf, other]

Title: Theory and Simulations of condensin mediated loop extrusion in DNA

Ryota Takaki, Atreya Dey, Guang Shi, Dave Thirumalai

Subjects: Soft Condensed Matter (cond-mat.soft); Genomics (q-bio.GN)

[273] arXiv:2006.00343 (cross-list from econ.EM) [pdf, other]

Title: Statistical Decision Properties of Imprecise Trials Assessing COVID-19 Drugs

Charles F. Manski, Aleksey Tetenov

Comments: 28 pages, 4 tables

Subjects: Econometrics (econ.EM); Quantitative Methods (q-bio.QM); Methodology (stat.ME)

[274] arXiv:2006.00523 (cross-list from physics.soc-ph) [pdf, other]

Title: The Effects of Stringent Interventions for Coronavirus Pandemic

Ting Tian (1), Wenxiang Luo (1), Yukang Jiang (1), Minqiong Chen (1), Canhong Wen (2), Wenliang Pan (1), Xueqin Wang (2) ((1) School of Mathematics, Sun Yat-sen University, (2) School of Management, University of Science and Technology of China)

Comments: 29 pages, 6 figures, Ting Tian, Wenxiang Luo and Yukang Jiang contributed equally to this article

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

[275] arXiv:2006.00531 (cross-list from econ.EM) [pdf, other]

Title: Lockdown Strategies, Mobility Patterns and COVID-19

Nikos Askitas, Konstantinos Tatsiramos, Bertrand Verheyden

Journal-ref: Nature Journal: Scientific Reports 2021

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

[276] arXiv:2006.00564 (cross-list from math.DS) [pdf, other]

Title: Hamiltonian structure of compartmental epidemiological models

Angel Ballesteros, Alfonso Blasco, Ivan Gutierrez-Sagredo

Comments: Minor misprints corrected

Journal-ref: Physica D: Nonlinear Phenomena 413 (2020) 132656

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

[277] arXiv:2006.00674 (cross-list from cs.DL) [pdf, other]

Title: Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCov literature

Milad Haghani, Michiel C. J. Bliemer

Journal-ref: Scientometrics (2020)

Subjects: Digital Libraries (cs.DL); Information Retrieval (cs.IR); Physics and Society (physics.soc-ph); Other Quantitative Biology (q-bio.OT)

[278] arXiv:2006.00986 (cross-list from cs.LG) [pdf, other]

Title: Semi-Supervised Hierarchical Drug Embedding in Hyperbolic Space

Ke Yu, Shyam Visweswaran, Kayhan Batmanghelich

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

[279] arXiv:2006.00999 (cross-list from cs.CL) [pdf, other]

Title: A Neural Network Model of Lexical Competition during Infant Spoken Word Recognition

Mihaela Duta, Kim Plunkett

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

[280] arXiv:2006.01054 (cross-list from physics.soc-ph) [pdf, other]

Title: Effects of Population Co-location Reduction on Cross-county Transmission Risk of COVID-19 in the United States

Chao Fan, Sanghyeon Lee, Yang Yang, Bora Oztekin, Qingchun Li, Ali Mostafavi

Comments: 12 pages, 7 figures

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

[281] arXiv:2006.01061 (cross-list from stat.ML) [pdf, other]

Title: Reinforcement learning and Bayesian data assimilation for model-informed precision dosing in oncology

Corinna Maier, Niklas Hartung, Charlotte Kloft, Wilhelm Huisinga, Jana de Wiljes

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

[282] arXiv:2006.01249 (cross-list from math.OC) [pdf, other]

Title: Controlling Propagation of epidemics via mean-field control

Wonjun Lee, Siting Liu, Hamidou Tembine, Wuchen Li, Stanley Osher

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

[283] arXiv:2006.01511 (cross-list from physics.bio-ph) [pdf, other]

Title: Study of iron complexes in visceral organs and brain from a ${}^57$Fe enriched $\beta$-thalassaemia mouse model via M\"ossbauer Spectroscopy

G. Charitou, Ch. Tsertos (Dept. of Physics, Univ. of Cyprus), Y. Parpottas (Frederick University, Cyprus), M. Kleanthous, C. Lederer, M. Phylactides (Dept. of Molecular Genetics Thalassaemia, Cyprus Institute of Neurology and Genetics, Cyprus)

Comments: Preprint, 18 pages including 2 tables and 13 figures;Accepted by Journal of Molecular Structure

Subjects: Biological Physics (physics.bio-ph); Medical Physics (physics.med-ph); Tissues and Organs (q-bio.TO)

[284] arXiv:2006.01532 (cross-list from physics.bio-ph) [pdf, other]

Title: Optimal elasticity of biological networks

Henrik Ronellenfitsch

Comments: 5 pages, 4 figures, supplemental material

Journal-ref: Phys. Rev. Lett. 126, 038101 (2021)

Subjects: Biological Physics (physics.bio-ph); Materials Science (cond-mat.mtrl-sci); Soft Condensed Matter (cond-mat.soft); Tissues and Organs (q-bio.TO)

[285] arXiv:2006.01575 (cross-list from cond-mat.soft) [pdf, other]

Title: Quantifying material properties of cell monolayers by analyzing integer topological defects

Carles Blanch-Mercader, Pau Guillamat, Aurélien Roux, Karsten Kruse

Comments: 5 pages, 4 figures

Journal-ref: Phys. Rev. Lett. 126, 028101 (2021)

Subjects: Soft Condensed Matter (cond-mat.soft); Materials Science (cond-mat.mtrl-sci); Tissues and Organs (q-bio.TO)

[286] arXiv:2006.01725 (cross-list from cond-mat.soft) [pdf, other]

Title: Integer topological defects of cell monolayers -- mechanics and flows

Carles Blanch-Mercader, Pau Guillamat, Aurélien Roux, Karsten Kruse

Comments: 41 pages, 11 figures

Journal-ref: Phys. Rev. E 103, 012405 (2021)

Subjects: Soft Condensed Matter (cond-mat.soft); Materials Science (cond-mat.mtrl-sci); Tissues and Organs (q-bio.TO)

[287] arXiv:2006.01743 (cross-list from math.OC) [pdf, other]

Title: Data-Driven Infectious Disease Control with Uncertain Resources

Ceyda Yaba Best, Amin Khademi, Burak Eksioglu

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

[288] arXiv:2006.01748 (cross-list from physics.med-ph) [pdf, other]

Title: GPU-based parallel simulations of the Gatenby-Gawlinski model with anisotropic, heterogeneous acid diffusion

Corrado Mascia, Donato Pera, Chiara Simeoni

Comments: 9 pages, 3 figures, 2 tables

Subjects: Medical Physics (physics.med-ph); Analysis of PDEs (math.AP); Numerical Analysis (math.NA); Quantitative Methods (q-bio.QM)

[289] arXiv:2006.01764 (cross-list from physics.soc-ph) [pdf, other]

Title: Networks beyond pairwise interactions: structure and dynamics

Federico Battiston, Giulia Cencetti, Iacopo Iacopini, Vito Latora, Maxime Lucas, Alice Patania, Jean-Gabriel Young, Giovanni Petri

Comments: Accepted for publication in Physics Reports. 109 pages, 47 figures

Journal-ref: Physics Reports 874, 1 (2020)

Subjects: Physics and Society (physics.soc-ph); Disordered Systems and Neural Networks (cond-mat.dis-nn); Social and Information Networks (cs.SI); Adaptation and Self-Organizing Systems (nlin.AO); Neurons and Cognition (q-bio.NC)

[290] arXiv:2006.01878 (cross-list from physics.soc-ph) [pdf, other]

Title: Strategy dependent learning activity in cyclic dominant systems

Attila Szolnoki, Xiaojie Chen

Comments: 9 two-column pages, 7 figures, accepted for publication in Chaos, Solitons and Fractals

Journal-ref: Chaos, Solitons and Fractals 138 (2020) 109935

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

[291] arXiv:2006.01924 (cross-list from stat.ME) [pdf, other]

Title: Eigenvectors from Eigenvalues Sparse Principal Component Analysis (EESPCA)

H. Robert Frost

Subjects: Methodology (stat.ME); Quantitative Methods (q-bio.QM)

[292] arXiv:2006.01965 (cross-list from physics.soc-ph) [pdf, other]

Title: Disease and information spreading at different speeds in multiplex networks

Fátima Velásquez-Rojas, Paulo Cesar Ventura, Colm Connaughton, Yamir Moreno, Francisco A. Rodrigues, Federico Vazquez

Comments: 9 pages, 6 figures

Journal-ref: Phys. Rev. E 102, 022312 (2020)

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

[293] arXiv:2006.02035 (cross-list from physics.med-ph) [pdf, other]

Title: Non-invasive quantitative imaging of selective microstructure-sizes with magnetic resonance

Milena Capiglioni, Analia Zwick, Pablo Jimenez, Gonzalo A. Alvarez

Comments: 9 pages, 5 figures

Journal-ref: Phys. Rev. Applied 15, 014045 (2021)

Subjects: Medical Physics (physics.med-ph); Applied Physics (physics.app-ph); Quantitative Methods (q-bio.QM); Quantum Physics (quant-ph)

[294] arXiv:2006.02241 (cross-list from cs.SI) [pdf, other]

Title: Unlinking super-linkers: the topology of epidemic response (Covid-19)

Shishir Nagaraja

Comments: 16 pages, 4 figures

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

[295] arXiv:2006.02272 (cross-list from math.PR) [pdf, other]

Title: Identifiability of Stochastically Modelled Reaction Networks

German Enciso, Radek Erban, Jinsu Kim

Comments: 22 pages, 4 figures

Journal-ref: Eur. J. Appl. Math 32 (2021) 865-887

Subjects: Probability (math.PR); Molecular Networks (q-bio.MN)

[296] arXiv:2006.02275 (cross-list from cond-mat.soft) [pdf, other]

Title: From Hi-C Contact Map to Three-dimensional Organization of Interphase Human Chromosomes

Guang Shi, D. Thirumalai

Journal-ref: Phys. Rev. X 11, 011051 (2021)

Subjects: Soft Condensed Matter (cond-mat.soft); Biomolecules (q-bio.BM); Genomics (q-bio.GN); Quantitative Methods (q-bio.QM)

[297] arXiv:2006.02304 (cross-list from eess.SY) [pdf, other]

Title: A Dynamics-based Approach for the Target Control of Boolean Networks

Cui Su, Jun Pang

Subjects: Systems and Control (eess.SY); Molecular Networks (q-bio.MN)

[298] arXiv:2006.02427 (cross-list from nlin.CD) [pdf, other]

Title: Lyapunov spectra of chaotic recurrent neural networks

Rainer Engelken, Fred Wolf, L.F. Abbott

Subjects: Chaotic Dynamics (nlin.CD); Neurons and Cognition (q-bio.NC)

[299] arXiv:2006.02483 (cross-list from stat.AP) [pdf, other]

Title: Time Series Methods and Ensemble Models to Nowcast Dengue at the State Level in Brazil

Katherine Kempfert, Kaitlyn Martinez, Amir Siraj, Jessica Conrad, Geoffrey Fairchild, Amanda Ziemann, Nidhi Parikh, David Osthus, Nicholas Generous, Sara Del Valle, Carrie Manore

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

[300] arXiv:2006.02507 (cross-list from physics.soc-ph) [pdf, other]

Title: Mathematical Models for Describing and Predicting the COVID-19 Pandemic Crisis

P. H. P. Cintra, M. F. Citeli, F. N. Fontinele

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