Quantitative Biology

Authors and titles for January 2020

[1] arXiv:2001.00091 [pdf, other]

Title: Hemoglobin Non-equilibrium Oxygen Dissociation Curve

Rosella Scrima, Sabino Fugetto, Nazzareno Capitanio, Domenico L. Gatti

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

[2] arXiv:2001.00114 [pdf, other]

Title: Expertise and Task Pressure in fNIRS-based brain Connectomes

F. Deligianni, H. Singh, H.N. Modi, S. Jahani, M. Yucel, A. Darzi, D.R. Leff, G.Z. Yang

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

[3] arXiv:2001.00122 [pdf, other]

Title: Entropic Decision Making

Adnan Rebei

Comments: 84 pages, 22 figures

Subjects: Neurons and Cognition (q-bio.NC); General Economics (econ.GN)

[4] arXiv:2001.00192 [pdf, other]

Title: A Quantized Representation of Probability in the Brain

James Tee, Desmond P. Taylor

Comments: 12 pages, 23 figures, 6 tables. arXiv admin note: substantial text overlap with arXiv:1805.01631

Journal-ref: IEEE Transactions on Molecular, Biological and Multi-Scale Communications (30 October 2019)

Subjects: Neurons and Cognition (q-bio.NC); Information Theory (cs.IT)

[5] arXiv:2001.00209 [pdf, other]

Title: Phenotypic Performance of Kambro Crossbreeds of Female Broiler Cobb 500 and Male Pelung Blirik Hitam

I Wayan Swarautama Mahardhika, Budi Setiadi Daryono

Comments: PDF, 15 pages, 3 figures, 4 tables, original research paper

Journal-ref: Buletin Veteriner Udayana (2019) Volume 11 No. 2: 188-202

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

[6] arXiv:2001.00316 [pdf, other]

Title: Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis

Ruijin Wu, Rahul Prabhu, Aysegul Ozkan, Meera Sitharam

Subjects: Biomolecules (q-bio.BM)

[7] arXiv:2001.00492 [pdf, other]

Title: The Effect of Treatment-Related Deaths and "Sticky" Diagnoses on Recorded Prostate Cancer Mortality

H. Gilbert Welch, Michael J. Barry, William C Black, Yunjie Song, Elliott S. Fisher

Comments: 20 pages, 5 figures

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

[8] arXiv:2001.00628 [pdf, other]

Title: Deterministic and Stochastic Research of Cubic Population Model with Harvesting

Özgür Gültekin, Çağatay Eskin, Esra Yazıcıoğlu

Comments: 18 pages, 33 figures

Journal-ref: Fluctuation and Noise Letters, Vol. 20, No. 03, 2150023 (2021)

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

[9] arXiv:2001.00641 [pdf, other]

Title: AI and Medicine

Mihai Nadin

Comments: 53 pages, 4 figures

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

[10] arXiv:2001.00837 [pdf, other]

Title: The double dealing of cyclin D1

Guergana Tchakarska (GPMCND), Brigitte Sola (GPMCND)

Journal-ref: Cell Cycle, Taylor & Francis, 2010, pp.1-16

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

[11] arXiv:2001.00874 [pdf, other]

Title: Drug delivery in tumors is enhanced by bacterial proteolytic activity in a size and binding affinity dependent manner -A mechanistic understanding

Hiroaki Shirai, Kosuke Tsukada

Comments: 50 pages, 10 figures, 2 tables

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

[12] arXiv:2001.00958 [pdf, other]

Title: From Best Hits to Best Matches

Peter F. Stadler, Manuela Geiß, David Schaller, Alitzel López Sánchez, Marcos E. González, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernández Rosales

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

[13] arXiv:2001.01006 [pdf, other]

Title: Review of Single-cell RNA-seq Data Clustering for Cell Type Identification and Characterization

Shixiong Zhang, Xiangtao Li, Qiuzhen Lin, Ka-Chun Wong

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

[14] arXiv:2001.01109 [pdf, other]

Title: Natural intelligence and anthropic reasoning

P Slijepcevic

Comments: 44 pages, 2 tables, 6 figures

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

[15] arXiv:2001.01161 [pdf, other]

Title: Using physical features of protein core packing to distinguish real proteins from decoys

Alex T. Grigas, Zhe Mei, John D. Treado, Zachary A. Levine, Lynne Regan, Corey S. O'Hern

Comments: 7 pages, 5 figures

Journal-ref: Protein Science 29 (2020) 1931

Subjects: Biomolecules (q-bio.BM); Soft Condensed Matter (cond-mat.soft)

[16] arXiv:2001.01717 [pdf, other]

Title: Macromolecule Classification Based on the Amino-acid Sequence

Faisal Ghaffar, Sarwar Khan, Gaddisa O., Chen Yu-jhen

Comments: Another version of paper is present on arXiv. See arXiv:1907.03532

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

[17] arXiv:2001.01852 [pdf, other]

Title: Impact of network assortativity on epidemic and vaccination behaviour

Sheryl L. Chang, Mahendra Piraveenan, Mikhail Prokopenko

Comments: 17 pages, 13 figures

Journal-ref: chaos, solitons & fractals,140:110143, 2020

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

[18] arXiv:2001.02132 [pdf, other]

Title: Mitochondria in higher plants possess H2 evolving activity which is closely related to complex I

Xin Zhang, Zhao Zhang, Yanan Wei, Muhan Li, Pengxiang Zhao, Yao Mawulikplimi Adzavon, Mengyu Liu, Xiaokang Zhang, Fei Xie, Andong Wang, Jihong Sun, Yunlong Shao, Xiayan Wang, Xuejun Sun, Xuemei Ma (Corresponding author)

Subjects: Biomolecules (q-bio.BM)

[19] arXiv:2001.02173 [pdf, other]

Title: Inferring genetic fitness from genomic data

Hong-Li Zeng, Erik Aurell

Journal-ref: Phys. Rev. E 101, 052409 (2020)

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

[20] arXiv:2001.02201 [pdf, other]

Title: On-the-fly Prediction of Protein Hydration Densities and Free Energies using Deep Learning

Ahmadreza Ghanbarpour, Amr H. Mahmoud, Markus A. Lill

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

[21] arXiv:2001.02287 [pdf, other]

Title: A unified energy optimality criterion predicts human navigation paths and speeds

Geoffrey L. Brown, Nidhi Seethapathi, Manoj Srinivasan

Journal-ref: Proceedings of the National Academy of Sciences 118.29 (2021)

Subjects: Neurons and Cognition (q-bio.NC); Adaptation and Self-Organizing Systems (nlin.AO)

[22] arXiv:2001.02371 [pdf, other]

Title: Dynamics of a non-autonomous system with age-structured growth and harvesting of prey and mutually interfering predator with reliance on alternative food

N. S. N. V. K. Vyshnavi Devi, Debaldev Jana, M. Lakshmanan

Subjects: Populations and Evolution (q-bio.PE); Chaotic Dynamics (nlin.CD)

[23] arXiv:2001.02436 [pdf, other]

Title: EoN (Epidemics on Networks): a fast, flexible Python package for simulation, analytic approximation, and analysis of epidemics on networks

Joel C. Miller, Tony TIng

Comments: This paper is available in a shorter form without examples at this https URL

Journal-ref: Journal of Open Source Software, 4(44), 1731 (2019)

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

[24] arXiv:2001.02441 [pdf, other]

Title: Small protein number effects in stochastic models of autoregulated bursty gene expression

Chen Jia, Ramon Grima

Comments: 30 pages, 10 figures

Subjects: Subcellular Processes (q-bio.SC)

[25] arXiv:2001.02533 [pdf, other]

Title: An ecological framework for the analysis of prebiotic chemical reaction networks and their dynamical behavior

Zhen Peng, Alex Plum, Praful Gagrani, David A. Baum

Subjects: Populations and Evolution (q-bio.PE); Molecular Networks (q-bio.MN)

[26] arXiv:2001.02738 [pdf, other]

Title: Liquid-liquid microphase separation leads to formation of membraneless organelles

Srivastav Ranganathan, Eugene Shakhnovich

Subjects: Biomolecules (q-bio.BM); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)

[27] arXiv:2001.02744 [pdf, other]

Title: Contribution of high risk groups' unmet needs may be underestimated in epidemic models without risk turnover: a mechanistic modelling analysis

Jesse Knight, Stefan D. Baral, Sheree Schwartz, Linwei Wang, Huiting Ma, Katherine Young, Harry Hausler, Sharmistha Mishra

Comments: 33 pages, 20 figures, code: this https URL

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

[28] arXiv:2001.02843 [pdf, other]

Title: Population variability in the generation and thymic selection of T-cell repertoires

Zachary Sethna (1), Giulio Isacchini (2 and 3), Thomas Dupic (2), Thierry Mora (2), Aleksandra M. Walczak (2), Yuval Elhanati (1) ((1) Memorial Sloan Kettering Cancer (1) Laboratoire de physique de l'École Normale Supérieur, (3) Max Planck Institute for Dynamics and Self-organization)

Comments: 13 pages, 7 figure, 2 tables

Journal-ref: PLoS Computational Biology 16(12) e1008394 (2020)

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

[29] arXiv:2001.02844 [pdf, other]

Title: Real-time nanodiamond thermometry probing in-vivo thermogenic responses

Masazumi Fujiwara, Simo Sun, Alexander Dohms, Yushi Nishimura, Ken Suto, Yuka Takezawa, Keisuke Oshimi, Li Zhao, Nikola Sadzak, Yumi Umehara, Yoshio Teki, Naoki Komatsu, Oliver Benson, Yutaka Shikano, Eriko Kage-Nakadai

Comments: 9 + 10 pages, 4 + 11 figures, our submission is jointly with the paper arXiv:2001.02664

Journal-ref: Science Advances 6, eaba9636 (2020)

Subjects: Quantitative Methods (q-bio.QM); Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Biological Physics (physics.bio-ph); Quantum Physics (quant-ph)

[30] arXiv:2001.02868 [pdf, other]

Title: Dynamical phase separation on rhythmogenic neuronal networks

Mihai Bibireata, Valentin M. Slepukhin, Alex J. Levine

Comments: 14 pages, 15 figures

Journal-ref: Phys. Rev. E 101, 062307 (2020)

Subjects: Neurons and Cognition (q-bio.NC); Adaptation and Self-Organizing Systems (nlin.AO); Biological Physics (physics.bio-ph)

[31] arXiv:2001.03019 [pdf, other]

Title: Inflammatory Bowel Disease Biomarkers of Human Gut Microbiota Selected via Ensemble Feature Selection Methods

Hilal Hacilar, O.Ufuk Nalbantoglu, Oya Aran, Burcu Bakir-Gungor

Comments: 9 pages, 10 figures

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

[32] arXiv:2001.03059 [pdf, other]

Title: Interplay between reproduction and age selective harvesting delays of a single population non-autonomous system

N. S. N. V. K. Vyshnavi Devi, Debaldev Jana, M. Lakshmanan

Subjects: Populations and Evolution (q-bio.PE); Chaotic Dynamics (nlin.CD)

[33] arXiv:2001.03088 [pdf, other]

Title: An Investigation of Minimum Data Requirement for Successful Structure Determination of Pf2048.1 with REDCRAFT

Casey A. Cole, Daniela Ishimaru, Mirko Hennig, Homayoun Valafar

Comments: 8 pages. BioComp 2015

Subjects: Biomolecules (q-bio.BM)

[34] arXiv:2001.03092 [pdf, other]

Title: De Novo Assembly of Uca minax Transcriptome from Next Generation Sequencing

Hanin Omar, Casey A. Cole, Arjang Fahim, Giuliana Gusmaroli, Stephen Borgianini, Homayoun Valafar

Comments: 8 pages. BioComp 2015

Subjects: Genomics (q-bio.GN)

[35] arXiv:2001.03119 [pdf, other]

Title: Bone tools, ornaments and other unusual objects during the Middle to Upper Palaeolithic transition in Italy

Simona Arrighi, Adriana Moroni, Laura Tassoni, Francesco Boschin, Federica Badino, Eugenio Bortolini, Paolo Boscato, Jacopo Crezzini, Carla Figus, Manuela Forte, Federico Lugli, Giulia Marciani, Gregorio Oxilia, Fabio Negrino, Julien Riel-Salvatore, Matteo Romandini, Enza Elena Spinapolice, Marco Peresani, Annamaria Ronchitelli, Stefano Benazzi

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

[36] arXiv:2001.03207 [pdf, other]

Title: Split Optimization for Protein/Ligand Binding Models

Brian Davis, Kevin Mcloughlin, Jonathan Allen, Sally Ellingson

Subjects: Biomolecules (q-bio.BM)

[37] arXiv:2001.03260 [pdf, other]

Title: Supporting supervised learning in fungal Biosynthetic Gene Cluster discovery: new benchmark datasets

Hayda Almeida, Adrian Tsang, Abdoulaye Baniré Diallo

Comments: Accepted to Machine Learning and Artificial Intelligence in Bioinformatics and Medical Informatics (MABM2019) at IEEE BIBM 2019

Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG); Machine Learning (stat.ML)

[38] arXiv:2001.03397 [pdf, other]

Title: External noise removed from magnetoencephalographic signal using Independent Component Analyses of reference channels

Jeff Hanna, Cora Kim, Nadia Müller-Voggel

Comments: Accepted for publication in Journal of Neuroscience Methods

Subjects: Neurons and Cognition (q-bio.NC); Signal Processing (eess.SP)

[39] arXiv:2001.03560 [pdf, other]

Title: Biophysical models of cis-regulation as interpretable neural networks

Ammar Tareen, Justin B. Kinney

Comments: Presented at the 14th conference on Machine Learning in Computational Biology (MLCB 2019), Vancouver, Canada. Revised to add a link to code and to correct a typo in the King-Altman diagrams shown in Figure 3

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

[40] arXiv:2001.03561 [pdf, other]

Title: Non-Canonical GC Base Pairs and Mechanochemical Cleavage of DNA

Denis A. Semyonov, Yury D. Nechipurenko

Comments: 10 pages, 4 figures

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

[41] arXiv:2001.03567 [pdf, other]

Title: The use of biophysical approaches to understand ciliary beating

Pietro Cicuta

Comments: a review of 11 pages, Submitted to Biochemical Society Transactions

Subjects: Tissues and Organs (q-bio.TO); Soft Condensed Matter (cond-mat.soft); Adaptation and Self-Organizing Systems (nlin.AO); Medical Physics (physics.med-ph)

[42] arXiv:2001.03614 [pdf, other]

Title: Paradoxical Results of Long-Term Potentiation explained by Voltage-based Plasticity Rule

Claire Meissner-Bernard, Matthias Tsai, Laureline Logiaco, Wulfram Gerstner

Journal-ref: Front. Synaptic Neurosci. (2020) 12:585539

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

[43] arXiv:2001.03656 [pdf, other]

Title: Temporal patterns of dispersal-induced synchronization in population dynamics

Sungwoo Ahn, Leonid L Rubchinsky

Journal-ref: J Theor Biol 490:110159, 2020

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

[44] arXiv:2001.03693 [pdf, other]

Title: A Raspberry Pi-based, RFID-equipped birdfeeder for the remote monitoring of wild bird populations

Mason Youngblood

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

[45] arXiv:2001.03761 [pdf, other]

Title: Recurrence Quantification Analysis of Dynamic Brain Networks

Marinho A. Lopes, Jiaxiang Zhang, Dominik Krzemiński, Khalid Hamandi, Qi Chen, Lorenzo Livi, Naoki Masuda

Comments: 77 pages, 11 figures; note: the acknowledgments section is the most complete in this arxiv version (compared to the published version in EJN)

Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn)

[46] arXiv:2001.03781 [pdf, other]

Title: BioMETA: A multiple specification parameter estimation system for stochastic biochemical models

Arfeen Khalid

Subjects: Quantitative Methods (q-bio.QM); Molecular Networks (q-bio.MN)

[47] arXiv:2001.03848 [pdf, other]

Title: Cytoskeleton polarity is essential in determining orientational order in basal bodies of multi-ciliated cells

Toshinori Namba (1), Shuji Ishihara (1,2) ((1) Graduate School of Arts and Sciences, The University of Tokyo, (2) Universal Biology Institute, The University of Tokyo)

Comments: 30 pages, 8 figures (including Supporting Information), 2 tables

Journal-ref: PLoS Comput Biol 16(2): e1007649 (2020)

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

[48] arXiv:2001.03911 [pdf, other]

Title: Diverse genetic origins of medieval steppe nomad conquerors -- a response to Mikheyev et al. (2019)

Eran Elhaik

Comments: 13 pages, 2 figures

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

[49] arXiv:2001.03926 [pdf, other]

Title: Invasion rate versus diversity in population dynamics with catastrophes

Akiva Bruno Melka, Navit Dori, Yoram Louzoun

Comments: 5 pages, 4 figures

Journal-ref: Phys. Rev. Lett. 124, 158301 (2020)

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

[50] arXiv:2001.03965 [pdf, other]

Title: Sensitivity analysis methods in the biomedical sciences

George Qian, Adam Mahdi

Comments: 7 figures

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