Quantitative Biology

Authors and titles for January 2020

[101] arXiv:2001.07841 [pdf, other]

Title: Simultaneous Localization and Parameter Estimation for Single Particle Tracking via Sigma Points based EM

Ye Lin, Sean B. Andersson

Comments: Accepted by 58th Conference on Decision and Control (CDC)

Subjects: Biomolecules (q-bio.BM); Optimization and Control (math.OC)

[102] arXiv:2001.07844 [pdf, other]

Title: NJst and ASTRID are not statistically consistent under a random model of missing data

John A. Rhodes, Michael G. Nute, Tandy Warnow

Comments: 6 pages, no figures, provides counterexample to theorem (the first and corresponding author are both co-authors on this paper)

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

[103] arXiv:2001.08028 [pdf, other]

Title: Neural dynamics under active inference: plausibility and efficiency of information processing

Lancelot Da Costa, Thomas Parr, Biswa Sengupta, Karl Friston

Comments: 12 pages, 3 figures

Journal-ref: Entropy 2021

Subjects: Neurons and Cognition (q-bio.NC); Populations and Evolution (q-bio.PE)

[104] arXiv:2001.08101 [pdf, other]

Title: Stability of a non-local kinetic model for cell migration with density dependent orientation bias

Nadia Loy, Luigi Preziosi

Subjects: Cell Behavior (q-bio.CB); Adaptation and Self-Organizing Systems (nlin.AO)

[105] arXiv:2001.08264 [pdf, other]

Title: Heart rate variability code: Does it exist and can we hack it?

Martin G. Frasch

Journal-ref: Bioengineering 2023

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

[106] arXiv:2001.08285 [pdf, other]

Title: The kinetic space of multistationarity in dual phosphorylation

E. Feliu, N. Kaihnsa, T. de Wolff, O. Yürük

Subjects: Molecular Networks (q-bio.MN); Algebraic Geometry (math.AG); Dynamical Systems (math.DS)

[107] arXiv:2001.08332 [pdf, other]

Title: Nonlinear control in the nematode C. elegans

Megan Morrison, Charles Fieseler, J. Nathan Kutz

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

[108] arXiv:2001.08346 [pdf, other]

Title: Unsupervised learning of control signals and their encodings in $\textit{C. elegans}$ whole-brain recordings

Charles Fieseler, Manuel Zimmer, J. Nathan Kutz

Comments: 10 pages, 5 figures

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

[109] arXiv:2001.08349 [pdf, other]

Title: Investigating naturalistic hand movements by behavior mining in long-term video and neural recordings

Satpreet H. Singh, Steven M. Peterson, Rajesh P. N. Rao, Bingni W. Brunton

Subjects: Neurons and Cognition (q-bio.NC); Computer Vision and Pattern Recognition (cs.CV); Image and Video Processing (eess.IV)

[110] arXiv:2001.08369 [pdf, other]

Title: Modeling state-transition dynamics in resting-state brain signals by the hidden Markov and Gaussian mixture models

Takahiro Ezaki, Yu Himeno, Takamitsu Watanabe, Naoki Masuda

Comments: Sample code is available at this https URL

Journal-ref: Eur. J. Neurosci. 54:5404-5416 (2021)

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

[111] arXiv:2001.08570 [pdf, other]

Title: Deep learning-based prediction of response to HER2-targeted neoadjuvant chemotherapy from pre-treatment dynamic breast MRI: A multi-institutional validation study

Nathaniel Braman, Mohammed El Adoui, Manasa Vulchi, Paulette Turk, Maryam Etesami, Pingfu Fu, Kaustav Bera, Stylianos Drisis, Vinay Varadan, Donna Plecha, Mohammed Benjelloun, Jame Abraham, Anant Madabhushi

Comments: Braman and El Adoui contributed equally to this work. 33 pages, 3 figures in main text

Subjects: Quantitative Methods (q-bio.QM); Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Image and Video Processing (eess.IV); Applications (stat.AP); Machine Learning (stat.ML)

[112] arXiv:2001.08717 [pdf, other]

Title: Finer Metagenomic Reconstruction via Biodiversity Optimization

Simon Foucart, David Koslicki

Subjects: Genomics (q-bio.GN); Optimization and Control (math.OC)

[113] arXiv:2001.08808 [pdf, other]

Title: Intensity Discriminability of Electrocutaneous and Intraneural Stimulation Pulse Frequency in Intact Individuals and Amputees

Jacob A. George, Mark R. Brinton, Paul C. Colgan, Garrison K. Colvin, Sliman J. Bensmaia, Gregory A. Clark

Comments: IEEE EMBC 2020

Subjects: Neurons and Cognition (q-bio.NC); Robotics (cs.RO)

[114] arXiv:2001.08924 [pdf, other]

Title: Radiomics and artificial intelligence analysis of CT data for the identification of prognostic features in multiple myeloma

Daniela Schenonea, Rita Lai, Michele Cea, Federica Rossi, Lorenzo Torri, Bianca Bignotti, Giulia Succio, Stefano Gualco, Alessio Conte, Alida Dominietto, Anna Maria Massone, Michele Piana, Cristina Campi, Francesco Frassoni, Gianmario Sambuceti, Alberto Stefano Tagliafico

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

[115] arXiv:2001.08945 [pdf, other]

Title: Investigation of the cellular response to bone fractures: evidence for flexoelectricity

Raquel Núñez-Toldrà, Fabian Vasquez-Sancho, Nathalie Barroca, Gustau Catalan

Journal-ref: Scientific Reports volume 10, Article number: 254 (2020)

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

[116] arXiv:2001.09016 [pdf, other]

Title: TADPOLE Challenge: Accurate Alzheimer's disease prediction through crowdsourced forecasting of future data

Razvan V. Marinescu, Neil P. Oxtoby, Alexandra L. Young, Esther E. Bron, Arthur W. Toga, Michael W. Weiner, Frederik Barkhof, Nick C. Fox, Polina Golland, Stefan Klein, Daniel C. Alexander

Comments: 10 pages, 1 figure, 4 tables. arXiv admin note: substantial text overlap with arXiv:1805.03909

Journal-ref: MICCAI Multimodal Brain Image Analysis Workshop, 2019

Subjects: Populations and Evolution (q-bio.PE); Image and Video Processing (eess.IV); Applications (stat.AP)

[117] arXiv:2001.09400 [pdf, other]

Title: Fast library-driven approach for implementation of the voxel spread function technique for correcting magnetic field inhomogeneity artifacts

Jie Wen, Feiyan Zeng, Dmitriy Yablonskiy, Alexander Sukstansky, Ying Liu, Bin Cai, Yong Zhang, Weifu Lv

Comments: 14 pages, 5 figures

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

[118] arXiv:2001.09411 [pdf, other]

Title: Insight into the Unwrapping of the Dinucleosome

Fatemeh Khodabandeh, Hashem Fatemi, Farshid Mohammad-Rafiee1

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

[119] arXiv:2001.09481 [pdf, other]

Title: A Network Science Approach to Driver Gene Detection In Human Regulatory Network Using Genes Influence Evaluation

Mostafa Akhavan Safar, Babak Teimourpour, Mehrdad Kargari

Journal-ref: Journal of Biomedical Informatics,2020,103661,ISSN 1532-0464

Subjects: Molecular Networks (q-bio.MN)

[120] arXiv:2001.09600 [pdf, other]

Title: Metastable attractors explain the variable timing of stable behavioral action sequences

Stefano Recanatesi, Ulises Pereira, Masayoshi Murakami, Zachary Mainen, Luca Mazzucato

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

[121] arXiv:2001.09857 [pdf, other]

Title: An optimized pipeline for functional connectivity analysis in the rat brain

Yujian Diao, Ting Yin, Rolf Gruetter, Ileana O. Jelescu

Comments: 25 pages, 11 figures

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

[122] arXiv:2001.09928 [pdf, other]

Title: Unitary recordings in freely-moving pulse weakly electric fish suggest spike timing encoding of electrosensory signals

Alejo Rodríguez-Cattáneo, Ana Carolina Pereira, Pedro Aguilera, Angel Caputi

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

[123] arXiv:2001.09936 [pdf, other]

Title: On the anti-cancer effect of cold atmospheric plasma and the possible role of catalase-dependent apoptotic pathways

Charlotta Bengtson, Annemie Bogaerts

Journal-ref: Cells 2020, 9, 2330

Subjects: Molecular Networks (q-bio.MN)

[124] arXiv:2001.10035 [pdf, other]

Title: A Python based automated tracking routine for myosin II filaments

Lewis Mosby, Marco Polin, Darius V. Köster

Comments: 14 pages, 5 figures

Subjects: Subcellular Processes (q-bio.SC); Biological Physics (physics.bio-ph); Quantitative Methods (q-bio.QM)

[125] arXiv:2001.10351 [pdf, other]

Title: Unexpected parameter ranges of the 2009 A(H1N1) epidemic for Istanbul and the Netherlands

Ali Demirci, Ayse Peker Dobie, Ayse Humeyra Bilge, Semra Ahmetolan

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

[126] arXiv:2001.10414 [pdf, other]

Title: Predicting the Impact of Electric Field Stimulation in a Detailed Computational Model of Cortical Tissue

Frances Hutchings, Christopher Thornton, Chencheng Zhang, Yujiang Wang, Marcus Kaiser

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

[127] arXiv:2001.10437 [pdf, other]

Title: Differentiation of neural-type cells on multi-scale ordered collagen-silica bionanocomposites

Nicolas Debons, Dounia Dems (LCMCP-MATBIO), Christophe Hélary, Sylvain Le Grill, Lise Picaut, Flore Renaud (LGBC), Nicolas Delsuc (UPMC), Marie-Claire Schanne-Klein (LOB), Thibaud Coradin (MATBIO), Carole Aimé (LCMCP, PASTEUR)

Journal-ref: Biomaterials Science, Royal Society of Chemistry (RSC), 2020

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

[128] arXiv:2001.10530 [pdf, other]

Title: Preliminary prediction of the basic reproduction number of the Wuhan novel coronavirus 2019-nCoV

Tao Zhou, Quanhui Liu, Zimo Yang, Jingyi Liao, Kexin Yang, Wei Bai, Xin Lü, Wei Zhang

Comments: 8 pages, 1 table and 1 figure

Journal-ref: Journal of Evidence Based Medicine (2020) 1

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

[129] arXiv:2001.10531 [pdf, other]

Title: Reduction in respiratory mortality not associated with influenza in Russia: effect of the introduction of pneumococcal vaccination (PCV13), or improvement in care?

Edward Goldstein

Comments: arXiv admin note: text overlap with arXiv:1911.13244

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

[130] arXiv:2001.10535 [pdf, other]

Title: Bridging the Gap Between Consciousness and Matter: Recurrent Out-of-Body Projection of Visual Awareness Revealed by the Law of Non-Identity

Jinsong Meng

Comments: 20 pages, 9 figures, and 1 table. Comments: 21 pages, 9 figures, and 1 table: typos corrected, references added, a figure moved from the supplementary part to the main text, typesetting changed from double columns to one column. Comments: 28 pages, 10 figures, and 1 table: style changed to APA, title changed, typos corrected, references added, a figure added

Journal-ref: Integrative Psychological and Behavioral Science,Volume 57 Issue 2, June 2023

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

[131] arXiv:2001.10573 [pdf, other]

Title: Study of dose-dependent combination immunotherapy using engineered T cells and IL-2 in cervical cancer

Heyrim Cho, Zuping Wang, Doron Levy

Comments: 8 pages, 7 figures

Subjects: Populations and Evolution (q-bio.PE); Tissues and Organs (q-bio.TO)

[132] arXiv:2001.10614 [pdf, other]

Title: An integrated in vitro in silico approach for silver nanoparticle dosimetry in cell cultures

Daniele Poli1, Giorgio Mattei, Nadia Ucciferri, Arti Ahluwalia

Comments: 20 pages, including Supplementary Materials

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

[133] arXiv:2001.10811 [pdf, other]

Title: Late Neandertals in Central Italy. High-resolution chronicles from Grotta dei Santi (Monte Argentario, Tuscany)

Adriana Moroni, Giovanni Boschian, Jacopo Crezzini, Guido Montanari-Canini, Giulia Marciani, Giulia Capecchi, Simona Arrighi, Daniele Aureli, Claudio Berto, Margherita Freguglia, Astolfo Araujo, Sem Scaramucci, Jean Jacques Hublin, Tobias Lauer, Stefano Benazzi, Fabio Parenti, Marzia Bonato, Stefano Ricci, Sahra Talamo, Aldo G. Segre, Francesco Boschin, Vincenzo Spagnolo

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

[134] arXiv:2001.10954 [pdf, other]

Title: Reducing complexity and unidentifiability when modelling human atrial cells

C. Houston, B. Marchand, L. Engelbert, C. D. Cantwell

Comments: 15 pages, 6 figures, submitted to Philosophical Transactions A

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

[135] arXiv:2001.11080 [pdf, other]

Title: Signatures of brain criticality unveiled by maximum entropy analysis across cortical states

Nastaran Lotfi, Antonio J. Fontenele, Thaís Feliciano, Leandro A. A. Aguiar, Nivaldo A. P. de Vasconcelos, Carina Soares-Cunha, Bárbara Coimbra, Ana João Rodrigues, Nuno Sousa, Mauro Copelli, Pedro V. Carelli

Journal-ref: Phys. Rev. E 102, 012408 (2020)

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

[136] arXiv:2001.11125 [pdf, other]

Title: Testing biological network motif significance with exponential random graph models

Alex Stivala, Alessandro Lomi

Comments: Major revision after reviewer comments. Includes supplementary tables and figures

Journal-ref: Applied Network Science (2021) 6:91

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

[137] arXiv:2001.11432 [pdf, other]

Title: Modeling bursting in neuronal networks using facilitation-depression and afterhyperpolarization

Lou Zonca, David Holcman

Comments: 8 figs

Journal-ref: Communications in Nonlinear Science and Numerical Simulation Volume 94, March 2021, 105555

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

[138] arXiv:2001.11437 [pdf, other]

Title: Theoretical guidelines for editing ecological communities

Vu AT Nguyen, Dervis Can Vural

Comments: 10 pages, 8 figures

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

[139] arXiv:2001.11502 [pdf, other]

Title: Retrieving the structure of probabilistic sequences of auditory stimuli from EEG data

Noslen Hernández, Aline Duarte, Guilherme Ost, Ricardo Fraiman, Antonio Galves, Claudia D. Vargas

Comments: 16 pages, 7 figures

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

[140] arXiv:2001.11547 [pdf, other]

Title: HistomicsML2.0: Fast interactive machine learning for whole slide imaging data

Sanghoon Lee, Mohamed Amgad, Deepak R. Chittajallu, Matt McCormick, Brian P Pollack, Habiba Elfandy, Hagar Hussein, David A Gutman, Lee AD Cooper

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

[141] arXiv:2001.11582 [pdf, other]

Title: Sensitivity and specificity of a Bayesian single trial analysis for time varying neural signals

Jeff T. Mohl, Valeria C. Caruso, Surya T. Tokdar, Jennifer M. Groh

Comments: Accepted for publication in Neurons, Behavior, Data analysis, and Theory

Journal-ref: Neurons, Behavior, Data Analysis, and Theory, 2020

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

[142] arXiv:2001.11589 [pdf, other]

Title: Computational Fluid Dynamic Simulations In a Model of a Carotid Bifurcation Under Steady Flow Conditions

Nurullah Arslan, Kazim Besirli, Gurcan Comert, Omer F Beyca

Comments: 4 Pages, 7 figures, 4th International Advanced Technologies Symposium September 28 30, 2005, Konya, Turkey

Subjects: Tissues and Organs (q-bio.TO); Fluid Dynamics (physics.flu-dyn)

[143] arXiv:2001.11641 [pdf, other]

Title: Mathematical model for autoregulated miRNA biogenesis

Dimpal A Nyayanit, Chetan J Gadgil

Subjects: Molecular Networks (q-bio.MN)

[144] arXiv:2001.11679 [pdf, other]

Title: Learning of signaling networks: molecular mechanisms

Péter Csermely, Nina Kunsic, Péter Mendik, Márk Kerestély, Teodóra Faragó, Dániel V. Veres, Péter Tompa

Comments: cover story of the 2020 April issue of Trends in Biochemical Sciences

Journal-ref: Trends in Biochemical Sciences (2020) 45, 284-294

Subjects: Molecular Networks (q-bio.MN); Neural and Evolutionary Computing (cs.NE); Adaptation and Self-Organizing Systems (nlin.AO); Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)

[145] arXiv:2001.11789 [pdf, other]

Title: DeepHIPS: A novel Deep Learning based Hippocampus Subfield Segmentation method

Jose V. Manjon, Jose E. Romero, Pierrick Coupe

Comments: (19 pages, 2 figures)

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

[146] arXiv:2001.11972 [pdf, other]

Title: Data-driven biological network alignment that uses topological, sequence, and functional information

Shawn Gu, Tijana Milenkovic

Subjects: Molecular Networks (q-bio.MN)

[147] arXiv:2001.00224 (cross-list from nlin.PS) [pdf, other]

Title: Patterns, localized structures and fronts in a reduced model of clonal plant growth

Daniel Ruiz-Reynes, Luis Martin, Emilio Hernandez-Garcia, Edgar Knobloch, Damia Gomila

Comments: 14 pages, 18 figures. To appear in Physica D

Journal-ref: Physica D 414, 132723 (2020)

Subjects: Pattern Formation and Solitons (nlin.PS); Populations and Evolution (q-bio.PE)

[148] arXiv:2001.00258 (cross-list from eess.IV) [pdf, other]

Title: A Generalized Deep Learning Framework for Whole-Slide Image Segmentation and Analysis

Mahendra Khened, Avinash Kori, Haran Rajkumar, Balaji Srinivasan, Ganapathy Krishnamurthi

Subjects: Image and Video Processing (eess.IV); Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Tissues and Organs (q-bio.TO)

[149] arXiv:2001.00286 (cross-list from math.AP) [pdf, other]

Title: Non-Local Cell Adhesion Models: Steady States and Bifurcations

Andreas Buttenschön, Thomas Hillen

Comments: 130 pages

Subjects: Analysis of PDEs (math.AP); Cell Behavior (q-bio.CB)

[150] arXiv:2001.00370 (cross-list from math.NA) [pdf, other]

Title: Stability analysis for a new model of multispecies convection-diffusion-reaction in poroelastic tissue

Luis Miguel de Oliveira Vilaca, Bryan Gomez-Vargas, Sarvesh Kumar, Ricardo Ruiz-Baier, Nitesh Verma

Journal-ref: Applied Mathematical Modelling, 84, 425-446, 2020

Subjects: Numerical Analysis (math.NA); Quantitative Methods (q-bio.QM)