Quantitative Biology

Authors and titles for Apr 2019

[1]  arXiv:1904.00088 [pdf, other]

Title: Physical constraints on accuracy and persistence during breast cancer cell chemotaxis

Authors: Julien Varennes, Hye-ran Moon, Soutick Saha, Andrew Mugler, Bumsoo Han

Subjects: Cell Behavior (q-bio.CB)

[2]  arXiv:1904.00099 [pdf, other]

Title: Random matrix analysis of Ca$^{2+}$ signals in $β$-cell collectives

Authors: Dean Korošak, Marjan Slak Rupnik

Subjects: Cell Behavior (q-bio.CB); Statistical Mechanics (cond-mat.stat-mech)

[3]  arXiv:1904.00117 [pdf, other]

Title: Estimation of cell lineage trees by maximum-likelihood phylogenetics

Authors: Jean Feng, William S DeWitt III, Aaron McKenna, Noah Simon, Amy Willis, Frederick A Matsen IV

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

[4]  arXiv:1904.00214 [pdf, other]

Title: Serostatus Testing & Dengue Vaccine Cost-Benefit Thresholds

Authors: Carl A. B. Pearson, Kaja M. Abbas, Samuel Clifford, Stefan Flasche, Thomas J. Hladish

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

[5]  arXiv:1904.00232 [pdf, ps, other]

Title: Unifying Modular and Core-Periphery Structure in Functional Brain Networks over Development

Authors: Shi Gu, Cedric Huchuan Xia, Rastko Ciric, Tyler M. Moore, Ruben C. Gur, Raquel E. Gur, Theodore D. Satterthwaite, Danielle S. Bassett

Subjects: Quantitative Methods (q-bio.QM)

[6]  arXiv:1904.00353 [pdf, ps, other]

Title: Long-range temporal correlation in Auditory Brainstem Responses to Spoken Syllable /da/

Authors: Marjan Mozaffarilegha, S. M. S. Movahed

Comments: 27 pages, 8 figures and one table

Journal-ref: Scientific Reports, volume 9, Article number: 1751 (2019)

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

[7]  arXiv:1904.00431 [pdf, other]

Title: Do Deep Neural Networks Model Nonlinear Compositionality in the Neural Representation of Human-Object Interactions?

Authors: Aditi Jha, Sumeet Agarwal

Comments: 4 pages, 2 figures; presented at CCN 2019

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

[8]  arXiv:1904.00445 [pdf, other]

Title: The KiTS19 Challenge Data: 300 Kidney Tumor Cases with Clinical Context, CT Semantic Segmentations, and Surgical Outcomes

Authors: Nicholas Heller, Niranjan Sathianathen, Arveen Kalapara, Edward Walczak, Keenan Moore, Heather Kaluzniak, Joel Rosenberg, Paul Blake, Zachary Rengel, Makinna Oestreich, Joshua Dean, Michael Tradewell, Aneri Shah, Resha Tejpaul, Zachary Edgerton, Matthew Peterson, Shaneabbas Raza, Subodh Regmi, Nikolaos Papanikolopoulos, Christopher Weight

Comments: 13 pages, 2 figures

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

[9]  arXiv:1904.00662 [pdf, ps, other]

Title: Unbiased on-lattice domain growth

Authors: Cameron A. Smith, Cécile Mailler, Christian A. Yates

Comments: 23 pages, 10 figures

Journal-ref: Phys. Rev. E 100, 063307 (2019)

Subjects: Quantitative Methods (q-bio.QM)

[10]  arXiv:1904.00825 [pdf, other]

Title: Simple unity among the fundamental equations of science

Authors: Steven A. Frank

Comments: arXiv admin note: text overlap with arXiv:1810.09262

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

[11]  arXiv:1904.00874 [pdf, other]

Title: Far-ranging generalist top predators enhance the stability of meta-foodwebs

Authors: Andreas Brechtel, Thilo Gross, Barbara Drossel

Journal-ref: Scientific Reportsvolume 9, Article number: 12268 (2019)

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

[12]  arXiv:1904.00919 [pdf, ps, other]

Title: A Deterministic Method to Calculate the AIS Trauma Score from a Finite Element Organ Trauma Model (OTM)

Authors: C. Bastien, C. Neal-Sturgess, J. Christensen, L. Wen

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

[13]  arXiv:1904.00986 [pdf, ps, other]

Title: A simple method for detecting chaos in nature

Authors: Daniel Toker, Friedrich T. Sommer, Mark D'Esposito

Subjects: Quantitative Methods (q-bio.QM); Chaotic Dynamics (nlin.CD)

[14]  arXiv:1904.00997 [pdf, ps, other]

Title: Quantitative phase microscopy spatial signatures of cancer cells

Authors: Darina Roitshtain, Lauren Wolbromsky, Evgeny Bal, Hayit Greenspan, Lisa L. Satterwhite, Natan T. Shaked

Journal-ref: Cytometry A. 2017 May;91(5):482-493

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

[15]  arXiv:1904.01096 [pdf, ps, other]

Title: Digging Deeper: Methodologies for High-Content Phenotyping and Knowledge-Abstraction in C. elegans

Authors: Nan Xu, Dhaval S. Patel, Hang Lu

Subjects: Quantitative Methods (q-bio.QM)

[16]  arXiv:1904.01166 [pdf, ps, other]

Title: The Configuration of the Perivascular System Transporting Macromolecules in the CNS (PREPRINT)

Authors: Beata Durcanova, Janine Appleton, Nyshidha Gurijala, Vasily Belov, Pilar Giffenig, Elisabeth Moeller, Matthew Hogan, Fredella Lee, Mikhail Papisov

Comments: 16 pages, 6 figures, 61 references

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

[17]  arXiv:1904.01208 [pdf, other]

Title: Strategies that enforce linear payoff relationships under observation errors in Repeated Prisoner's Dilemma game

Authors: Azumi Mamiya, Genki Ichinose

Comments: 19 pages, 3 figures

Journal-ref: Journal of Theoretical Biology 477, 63-76 (2019)

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

[18]  arXiv:1904.01235 [pdf, other]

Title: BPPart and BPMax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model

Authors: Ali Ebrahimpour-Boroojeny, Sanjay Rajopadhye, Hamidreza Chitsaz

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

[19]  arXiv:1904.01485 [pdf, other]

Title: Alternative Scoring Method of Pleurisy in Slaughtered Pigs: Preliminary Investigations

Authors: Giuseppe Marruchella, Michael Odintzov Vaintrub, Andrea Di Provvido, Elena Farina, Giorgio Fragassi, Giorgio Vignola

Comments: Proceedings of SIPAS, 2018

Journal-ref: SIPAS, 2018, 375-380

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

[20]  arXiv:1904.01637 [pdf, other]

Title: Learning Clinical Outcomes from Heterogeneous Genomic Data Sources

Authors: Safoora Yousefi, Amirreza Shaban, Mohamed Amgad, Ramraj Chandradevan, Lee A. D. Cooper

Subjects: Quantitative Methods (q-bio.QM); Genomics (q-bio.GN)

[21]  arXiv:1904.01655 [pdf, ps, other]

Title: A frame semantic overview of NLP-based information extraction for cancer-related EHR notes

Authors: Surabhi Datta, Elmer V Bernstam, Kirk Roberts

Comments: 2 figures, 4 tables

Subjects: Quantitative Methods (q-bio.QM); Computation and Language (cs.CL)

[22]  arXiv:1904.01847 [pdf, other]

Title: How the Avidity of Polymerase Binding to the -35/-10 Promoter Sites Affects Gene Expression

Authors: Tal Einav, Rob Phillips

Subjects: Subcellular Processes (q-bio.SC)

[23]  arXiv:1904.01862 [pdf, ps, other]

Title: Respiratory sympathetic modulation is augmented in chronic kidney disease

Authors: Manash Saha, Clément Menuet (INMED - INSERM U1249), Qi-Jian Sun, Peter Burke (NeuRA), Cara Hildreth, Andrew Allen, Jacqueline Phillips

Journal-ref: Respiratory Physiology and Neurobiology, Elsevier, In press

Subjects: Neurons and Cognition (q-bio.NC); Tissues and Organs (q-bio.TO)

[24]  arXiv:1904.01903 [pdf, ps, other]

Title: PyRod -- Tracing Water Molecules in Molecular Dynamics Simulations

Authors: David Schaller, Szymon Pach, Gerhard Wolber

Journal-ref: J.Chem.Inf.Model. (2019) 2818-2829

Subjects: Biomolecules (q-bio.BM)

[25]  arXiv:1904.01988 [pdf, other]

Title: Path mutual information for a class of biochemical reaction networks

Authors: Lorenzo Duso, Christoph Zechner

Comments: 6 pages, 2 figures

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