id stringlengths 9 13 | submitter stringlengths 4 48 | authors stringlengths 4 9.62k | title stringlengths 4 343 | comments stringlengths 2 480 ⌀ | journal-ref stringlengths 9 309 ⌀ | doi stringlengths 12 138 ⌀ | report-no stringclasses 277
values | categories stringlengths 8 87 | license stringclasses 9
values | orig_abstract stringlengths 27 3.76k | versions listlengths 1 15 | update_date stringlengths 10 10 | authors_parsed listlengths 1 147 | abstract stringlengths 24 3.75k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2011.11639 | Cristina Postigo | Maria Vittoria Barbieri, Luis Simon Monllor-Alcaraz, Cristina Postigo,
Miren Lopez de Alda | Improved fully automated method for the determination of medium to
highly polar pesticides in surface and groundwater and application in two
distinct agriculture-impacted areas | Published in Science of the Total Environment | Science of The Total Environment Volume 745, 25 November 2020,
140650 | 10.1016/j.scitotenv.2020.140650 | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Water is an essential resource for all living organisms. The continuous and
increasing use of pesticides in agricultural and urban activities results in
the pollution of water resources and represents an environmental risk. To
control and reduce pesticide pollution, reliable multi-residue methods for the
detection of... | [
{
"created": "Mon, 23 Nov 2020 17:47:30 GMT",
"version": "v1"
}
] | 2020-11-25 | [
[
"Barbieri",
"Maria Vittoria",
""
],
[
"Monllor-Alcaraz",
"Luis Simon",
""
],
[
"Postigo",
"Cristina",
""
],
[
"de Alda",
"Miren Lopez",
""
]
] | Water is an essential resource for all living organisms. The continuous and increasing use of pesticides in agricultural and urban activities results in the pollution of water resources and represents an environmental risk. To control and reduce pesticide pollution, reliable multi-residue methods for the detection of t... |
1309.0547 | Ian Dworkin | Christopher H. Chandler, Sudarshan Chari, David Tack and Ian Dworkin | Causes and Consequences of genetic background effects illuminated by
integrative genomic analysis | Accepted in Genetics | Genetics 2014 196(4):1321-1336 | 10.1534/genetics.113.159426 | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The phenotypic consequences of individual mutations are modulated by the wild
type genetic background in which they occur.Although such background dependence
is widely observed, we do not know whether general patterns across species and
traits exist, nor about the mechanisms underlying it. We also lack knowledge on
h... | [
{
"created": "Mon, 2 Sep 2013 21:12:14 GMT",
"version": "v1"
},
{
"created": "Thu, 23 Jan 2014 20:12:22 GMT",
"version": "v2"
},
{
"created": "Sat, 1 Feb 2014 16:04:28 GMT",
"version": "v3"
}
] | 2014-06-04 | [
[
"Chandler",
"Christopher H.",
""
],
[
"Chari",
"Sudarshan",
""
],
[
"Tack",
"David",
""
],
[
"Dworkin",
"Ian",
""
]
] | The phenotypic consequences of individual mutations are modulated by the wild type genetic background in which they occur.Although such background dependence is widely observed, we do not know whether general patterns across species and traits exist, nor about the mechanisms underlying it. We also lack knowledge on how... |
2303.05513 | Parsaoran Hutapea | Christopher M. Altenderfer, Frank N. Chang, Parsaoran Hutapea | Development of Pipetting Devices to Separate Protein Complexes | 6 pages, 2 figures, Discovery to Commercialization Conference, The
Nanotechnology Institute, October 2009, The Chemical Heritage Foundation,
Philadelphia, PA | null | null | null | q-bio.OT physics.flu-dyn | http://creativecommons.org/publicdomain/zero/1.0/ | The objective of this project is to develop an automated device used to spot
protein samples on a hydrophobic membrane to be used for the patented
electrophoresis method developed by Chang and Yonan in 2008 [1]. This novel
method performs electrophoresis directly on hydrophobic blot membranes as
opposed to the previo... | [
{
"created": "Tue, 6 Dec 2022 15:44:29 GMT",
"version": "v1"
}
] | 2023-03-13 | [
[
"Altenderfer",
"Christopher M.",
""
],
[
"Chang",
"Frank N.",
""
],
[
"Hutapea",
"Parsaoran",
""
]
] | The objective of this project is to develop an automated device used to spot protein samples on a hydrophobic membrane to be used for the patented electrophoresis method developed by Chang and Yonan in 2008 [1]. This novel method performs electrophoresis directly on hydrophobic blot membranes as opposed to the previous... |
1705.09132 | Milad Mozafari | Milad Mozafari, Saeed Reza Kheradpisheh, Timoth\'ee Masquelier, Abbas
Nowzari-Dalini, Mohammad Ganjtabesh | First-spike based visual categorization using reward-modulated STDP | supplementary materials are added, Caltech face/motorbike
demonstration figure is updated, some parts of the main manuscript are moved
to the supplementary materials, additional network analysis and performance
comparison with deep nets are added | Mozafari, Milad, et al. "First-Spike-Based Visual Categorization
Using Reward-Modulated STDP". IEEE Transactions on Neural Networks and
Learning Systems (2018). DOI: https://doi.org/10.1109/TNNLS.2018.2826721 | 10.1109/TNNLS.2018.2826721 | null | q-bio.NC cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reinforcement learning (RL) has recently regained popularity, with major
achievements such as beating the European game of Go champion. Here, for the
first time, we show that RL can be used efficiently to train a spiking neural
network (SNN) to perform object recognition in natural images without using an
external cl... | [
{
"created": "Thu, 25 May 2017 11:38:16 GMT",
"version": "v1"
},
{
"created": "Tue, 2 Jan 2018 11:31:48 GMT",
"version": "v2"
},
{
"created": "Tue, 10 Jul 2018 12:20:52 GMT",
"version": "v3"
}
] | 2018-07-11 | [
[
"Mozafari",
"Milad",
""
],
[
"Kheradpisheh",
"Saeed Reza",
""
],
[
"Masquelier",
"Timothée",
""
],
[
"Nowzari-Dalini",
"Abbas",
""
],
[
"Ganjtabesh",
"Mohammad",
""
]
] | Reinforcement learning (RL) has recently regained popularity, with major achievements such as beating the European game of Go champion. Here, for the first time, we show that RL can be used efficiently to train a spiking neural network (SNN) to perform object recognition in natural images without using an external clas... |
q-bio/0411028 | Manuel Middendorf | Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund,
Christina Leslie | Predicting Genetic Regulatory Response Using Classification | 8 pages, 4 figures, presented at Twelfth International Conference on
Intelligent Systems for Molecular Biology (ISMB 2004), supplemental website:
http://www.cs.columbia.edu/compbio/geneclass | Proceedings of the Twelfth International Conference on Intelligent
Systems for Molecular Biology (ISMB 2004), Bioinformatics 20 Suppl 1,
I232-I240, 2004 | null | null | q-bio.QM | null | We present a novel classification-based method for learning to predict gene
regulatory response. Our approach is motivated by the hypothesis that in simple
organisms such as Saccharomyces cerevisiae, we can learn a decision rule for
predicting whether a gene is up- or down-regulated in a particular experiment
based o... | [
{
"created": "Fri, 12 Nov 2004 20:39:45 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Middendorf",
"Manuel",
""
],
[
"Kundaje",
"Anshul",
""
],
[
"Wiggins",
"Chris",
""
],
[
"Freund",
"Yoav",
""
],
[
"Leslie",
"Christina",
""
]
] | We present a novel classification-based method for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as Saccharomyces cerevisiae, we can learn a decision rule for predicting whether a gene is up- or down-regulated in a particular experiment based on ... |
0804.4804 | Tamar Friedlander | Tamar Friedlander and Naama Brenner | From cellular properties to population asymptotics in the Population
Balance Equation | Exact solution of Eq. 9 is added | PRL 101, 018104 (2008) | 10.1103/PhysRevLett.101.018104 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Proliferating cell populations at steady state growth often exhibit broad
protein distributions with exponential tails. The sources of this variation and
its universality are of much theoretical interest. Here we address the problem
by asymptotic analysis of the Population Balance Equation. We show that the
steady st... | [
{
"created": "Wed, 30 Apr 2008 12:06:25 GMT",
"version": "v1"
},
{
"created": "Mon, 2 Jun 2008 13:32:47 GMT",
"version": "v2"
},
{
"created": "Thu, 24 Jul 2008 10:03:03 GMT",
"version": "v3"
}
] | 2008-07-24 | [
[
"Friedlander",
"Tamar",
""
],
[
"Brenner",
"Naama",
""
]
] | Proliferating cell populations at steady state growth often exhibit broad protein distributions with exponential tails. The sources of this variation and its universality are of much theoretical interest. Here we address the problem by asymptotic analysis of the Population Balance Equation. We show that the steady stat... |
0704.0357 | Gergely J Sz\"oll\H{o}si | Gergely J Szollosi and Imre Derenyi | Evolutionary games on minimally structured populations | Supporting information available as EPAPS Document No.
E-PLEEE8-78-144809 at http://ftp.aip.org/epaps/phys_rev_e/E-PLEEE8-78-144809/ | PHYSICAL REVIEW E 78, 031919 (2008) | 10.1103/PhysRevE.78.031919 | null | q-bio.PE q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Population structure induced by both spatial embedding and more general
networks of interaction, such as model social networks, have been shown to have
a fundamental effect on the dynamics and outcome of evolutionary games. These
effects have, however, proved to be sensitive to the details of the underlying
topology ... | [
{
"created": "Tue, 3 Apr 2007 11:02:47 GMT",
"version": "v1"
},
{
"created": "Fri, 13 Apr 2007 15:49:13 GMT",
"version": "v2"
},
{
"created": "Wed, 15 Oct 2008 11:29:30 GMT",
"version": "v3"
}
] | 2009-11-13 | [
[
"Szollosi",
"Gergely J",
""
],
[
"Derenyi",
"Imre",
""
]
] | Population structure induced by both spatial embedding and more general networks of interaction, such as model social networks, have been shown to have a fundamental effect on the dynamics and outcome of evolutionary games. These effects have, however, proved to be sensitive to the details of the underlying topology an... |
2212.01191 | Fabian Gr\"unewald | Peter C. Kroon, Fabian Gr\"unewald, Jonathan Barnoud, Marco van
Tilburg, Paulo C. T. Souza, Tsjerk A. Wassenaar, Siewert-Jan Marrink | Martinize2 and Vermouth: Unified Framework for Topology Generation | corresponding authors: F. Gr\"unewald f.grunewald[at]rug.nl; S. J.
Marrink s.j.marrink[at]rug.nl; changes made in v2: new benchmark test-case;
data availability statement; language corrections; changes made in v3:
additional test cases for non-protein molecules; updated explanation of the
graph matching algorit... | null | null | null | q-bio.QM cond-mat.other cs.CE | http://creativecommons.org/licenses/by/4.0/ | Ongoing advances in force field and computer hardware development enable the
use of molecular dynamics (MD) to simulate increasingly complex systems with
the ultimate goal of reaching cellular complexity. At the same time, rational
design by high-throughput (HT) simulations is another forefront of MD. In these
areas,... | [
{
"created": "Tue, 29 Nov 2022 11:23:42 GMT",
"version": "v1"
},
{
"created": "Fri, 30 Jun 2023 12:44:38 GMT",
"version": "v2"
},
{
"created": "Tue, 9 Apr 2024 09:49:09 GMT",
"version": "v3"
}
] | 2024-04-10 | [
[
"Kroon",
"Peter C.",
""
],
[
"Grünewald",
"Fabian",
""
],
[
"Barnoud",
"Jonathan",
""
],
[
"van Tilburg",
"Marco",
""
],
[
"Souza",
"Paulo C. T.",
""
],
[
"Wassenaar",
"Tsjerk A.",
""
],
[
"Marrink",
"Siewert-J... | Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design by high-throughput (HT) simulations is another forefront of MD. In these areas, t... |
1604.02553 | P. Gaspard | Pierre Gaspard | Kinetics and thermodynamics of exonuclease-deficient DNA polymerases | Physical Review E (2016) | Phys. Rev. E 93, 042419 (2016) | 10.1103/PhysRevE.93.042419 | null | q-bio.SC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A kinetic theory is developed for exonuclease-deficient DNA polymerases,
based on the experimental observation that the rates depend not only on the
newly incorporated nucleotide, but also on the previous one, leading to the
growth of Markovian DNA sequences from a Bernoullian template. The dependences
on nucleotide ... | [
{
"created": "Sat, 9 Apr 2016 12:20:36 GMT",
"version": "v1"
}
] | 2018-01-04 | [
[
"Gaspard",
"Pierre",
""
]
] | A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of Markovian DNA sequences from a Bernoullian template. The dependences on nucleotide co... |
1801.03843 | Francesc Rossell\'o | Tom\'as M. Coronado, Arnau Mir, Francesc Rossell\'o | The probabilities of trees and cladograms under Ford's $\alpha$-model | 9 pages | The Scientific World Journal Vol. 2018, Article ID 1916094, 7
pages | 10.1155/2018/1916094 | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We give correct explicit formulas for the probabilities of rooted binary
trees and cladograms under Ford's $\alpha$-model.
| [
{
"created": "Thu, 11 Jan 2018 16:07:53 GMT",
"version": "v1"
}
] | 2019-03-29 | [
[
"Coronado",
"Tomás M.",
""
],
[
"Mir",
"Arnau",
""
],
[
"Rosselló",
"Francesc",
""
]
] | We give correct explicit formulas for the probabilities of rooted binary trees and cladograms under Ford's $\alpha$-model. |
2303.00163 | Stefanie I. Becker | Stefanie I. Becker, Zachary Hamblin-Frohman, Hongfeng Xia and Zeguo
Qiu | Tuning to non-veridical features in attention and perceptual
decision-making | 33 pages (double-spaced), 6 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | When searching for a lost item, we tune attention to the known properties of
the object. Previously, it was believed that attention is tuned to the
veridical attributes of the search target (e.g., orange), or an attribute that
is slightly shifted away from irrelevant features towards a value that can more
optimally d... | [
{
"created": "Wed, 1 Mar 2023 01:32:00 GMT",
"version": "v1"
}
] | 2023-03-02 | [
[
"Becker",
"Stefanie I.",
""
],
[
"Hamblin-Frohman",
"Zachary",
""
],
[
"Xia",
"Hongfeng",
""
],
[
"Qiu",
"Zeguo",
""
]
] | When searching for a lost item, we tune attention to the known properties of the object. Previously, it was believed that attention is tuned to the veridical attributes of the search target (e.g., orange), or an attribute that is slightly shifted away from irrelevant features towards a value that can more optimally dis... |
2310.02300 | J. C. Phillips | J. C. Phillips | Why and How Did the COVID Pandemic End Abruptly? | 5 pages, 1 figure | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Phase transition theory, implemented quantitatively by thermodynamic scaling,
has explained the evolution of Coronavirus extremely high contagiousness caused
by a few key mutations from CoV2003 to CoV2019 identified among hundreds, as
well as the later 2021 evolution to Omicron caused by 30 mutations. It also
showed ... | [
{
"created": "Tue, 3 Oct 2023 14:39:35 GMT",
"version": "v1"
}
] | 2023-10-05 | [
[
"Phillips",
"J. C.",
""
]
] | Phase transition theory, implemented quantitatively by thermodynamic scaling, has explained the evolution of Coronavirus extremely high contagiousness caused by a few key mutations from CoV2003 to CoV2019 identified among hundreds, as well as the later 2021 evolution to Omicron caused by 30 mutations. It also showed th... |
1803.04364 | Sheraz Khan | Sheraz Khan, Javeria Hashmi, Fahimeh Mamashli, Konstantinos Michmizos,
Manfred Kitzbichler, Hari Bharadwaj, Yousra Bekhti, Santosh Ganesan, Keri A
Garel, Susan Whitfield-Gabrieli, Randy Gollub, Jian Kong, Lucia M Vaina,
Kunjan Rana, Steven Stufflebeam, Matti Hamalainen, and Tal Kenet | Maturation Trajectories of Cortical Resting-State Networks Depend on the
Mediating Frequency Band | null | null | null | null | q-bio.NC cs.DM stat.ML | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The functional significance of resting state networks and their abnormal
manifestations in psychiatric disorders are firmly established, as is the
importance of the cortical rhythms in mediating these networks. Resting state
networks are known to undergo substantial reorganization from childhood to
adulthood, but whe... | [
{
"created": "Tue, 13 Feb 2018 01:04:40 GMT",
"version": "v1"
}
] | 2018-03-13 | [
[
"Khan",
"Sheraz",
""
],
[
"Hashmi",
"Javeria",
""
],
[
"Mamashli",
"Fahimeh",
""
],
[
"Michmizos",
"Konstantinos",
""
],
[
"Kitzbichler",
"Manfred",
""
],
[
"Bharadwaj",
"Hari",
""
],
[
"Bekhti",
"Yousra",
... | The functional significance of resting state networks and their abnormal manifestations in psychiatric disorders are firmly established, as is the importance of the cortical rhythms in mediating these networks. Resting state networks are known to undergo substantial reorganization from childhood to adulthood, but wheth... |
1906.11039 | Nadia Loy | Nadia Loy and Luigi Preziosi | Kinetic models with non-local sensing determining cell polarization and
speed according to independent cues | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cells move by run and tumble, a kind of dynamics in which the cell alternates
runs over straight lines and re-orientations. This erratic motion may be
influenced by external factors, like chemicals, nutrients, the extra-cellular
matrix, in the sense that the cell measures the external field and elaborates
the signal ... | [
{
"created": "Mon, 17 Jun 2019 16:15:30 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Jun 2019 06:43:59 GMT",
"version": "v2"
},
{
"created": "Mon, 1 Jul 2019 14:06:31 GMT",
"version": "v3"
}
] | 2019-07-02 | [
[
"Loy",
"Nadia",
""
],
[
"Preziosi",
"Luigi",
""
]
] | Cells move by run and tumble, a kind of dynamics in which the cell alternates runs over straight lines and re-orientations. This erratic motion may be influenced by external factors, like chemicals, nutrients, the extra-cellular matrix, in the sense that the cell measures the external field and elaborates the signal ev... |
2309.15397 | C.C. Alan Fung | Huilin Zhao and Sungchil Yang and Chi Chung Alan Fung | Short-Term Postsynaptic Plasticity Facilitates Predictive Tracking in
Continuous Attractors | 29 pages, 9 figures | null | null | null | q-bio.NC cond-mat.dis-nn | http://creativecommons.org/licenses/by/4.0/ | The N-methyl-D-aspartate receptor (NMDAR) is a crucial component of synaptic
transmission, and its dysfunction is implicated in many neurological diseases
and psychiatric conditions. NMDAR-based short-term postsynaptic plasticity
(STPP) is a newly discovered postsynaptic response facilitation mechanism. Our
group has... | [
{
"created": "Wed, 27 Sep 2023 04:40:51 GMT",
"version": "v1"
}
] | 2023-09-28 | [
[
"Zhao",
"Huilin",
""
],
[
"Yang",
"Sungchil",
""
],
[
"Fung",
"Chi Chung Alan",
""
]
] | The N-methyl-D-aspartate receptor (NMDAR) is a crucial component of synaptic transmission, and its dysfunction is implicated in many neurological diseases and psychiatric conditions. NMDAR-based short-term postsynaptic plasticity (STPP) is a newly discovered postsynaptic response facilitation mechanism. Our group has s... |
1205.1912 | Jan Urban | Jan Urban | Blank measurement based time-alignment in LC-MS | Urban J., Hrouzek P., Van\v{e}k J., Kopeck\'y J., \v{S}tys D.,
Time-Alignment in HPLC-MS based on blank measurement, 36th International
symposium on High-Performance Liquid Phase separations and Related
Techniques, Budapest, Hungary, 2011. Urban J., Hrouzek P., Van\v{e}k J.,
Kopeck\'y J., \v{S}tys D., Blank mea... | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Here are presenting the blank based time-alignment (BBTA) as a strong
analytical approach for treatment of non-linear shift in time occurring in
HPLC-MS data. Need of such tool in recent large dataset produced by analytical
chemistry and so-called omics studies is evident. Proposed approach is based on
measurement an... | [
{
"created": "Wed, 9 May 2012 08:51:38 GMT",
"version": "v1"
}
] | 2016-11-11 | [
[
"Urban",
"Jan",
""
]
] | Here are presenting the blank based time-alignment (BBTA) as a strong analytical approach for treatment of non-linear shift in time occurring in HPLC-MS data. Need of such tool in recent large dataset produced by analytical chemistry and so-called omics studies is evident. Proposed approach is based on measurement and ... |
1809.06997 | Shou-Wen Wang | Shou-Wen Wang, Lei-Han Tang | Emergence of collective oscillations in adaptive cells | 11 pages and 6 figures for the main text. 18 pages and 14 figures for
supplementary | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Collective oscillation of cells in a population has been reported under
diverse biological contexts and with vastly different molecular constructs.
Could there be common principles similar to those that govern spontaneous
oscillation in mechanical or electrical systems? Here, we answer this question
in the affirmativ... | [
{
"created": "Wed, 19 Sep 2018 03:30:04 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Sep 2018 16:20:40 GMT",
"version": "v2"
},
{
"created": "Fri, 5 Jul 2019 16:01:26 GMT",
"version": "v3"
}
] | 2019-07-08 | [
[
"Wang",
"Shou-Wen",
""
],
[
"Tang",
"Lei-Han",
""
]
] | Collective oscillation of cells in a population has been reported under diverse biological contexts and with vastly different molecular constructs. Could there be common principles similar to those that govern spontaneous oscillation in mechanical or electrical systems? Here, we answer this question in the affirmative ... |
1008.0717 | Tsvi Tlusty | Arbel D. Tadmor, Tsvi Tlusty | A Coarse-Grained Biophysical Model of E. coli and Its Application to
Perturbation of the rRNA Operon Copy Number | null | PLoS Comput Biol. 2008 May 2;4(4):e1000038 | 10.1371/journal.pcbi.1000038 | null | q-bio.MN physics.bio-ph q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a biophysical model of Escherichia coli that predicts growth rate
and an effective cellular composition from an effective, coarse-grained
representation of its genome. We assume that E. coli is in a state of balanced
exponential steadystate growth, growing in a temporally and spatially constant
environment... | [
{
"created": "Wed, 4 Aug 2010 08:47:56 GMT",
"version": "v1"
}
] | 2010-08-05 | [
[
"Tadmor",
"Arbel D.",
""
],
[
"Tlusty",
"Tsvi",
""
]
] | We propose a biophysical model of Escherichia coli that predicts growth rate and an effective cellular composition from an effective, coarse-grained representation of its genome. We assume that E. coli is in a state of balanced exponential steadystate growth, growing in a temporally and spatially constant environment, ... |
q-bio/0502003 | Anastasia Anishchenko | A. Anishchenko (1), E. Bienenstock (1), A. Treves (2) ((1) Brown
University, (2) SISSA) | Autoassociative Memory Retrieval and Spontaneous Activity Bumps in
Small-World Networks of Integrate-and-Fire Neurons | 25 pages, 7 figures; submitted to Neural Computation | null | null | null | q-bio.NC | null | Qualitatively, some real networks in the brain could be characterized as
'small worlds', in the sense that the structure of their connections is
intermediate between the extremes of an orderly geometric arrangement and of a
geometry-independent random mesh. Small worlds can be defined more precisely in
terms of their... | [
{
"created": "Fri, 4 Feb 2005 03:05:49 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Anishchenko",
"A.",
""
],
[
"Bienenstock",
"E.",
""
],
[
"Treves",
"A.",
""
]
] | Qualitatively, some real networks in the brain could be characterized as 'small worlds', in the sense that the structure of their connections is intermediate between the extremes of an orderly geometric arrangement and of a geometry-independent random mesh. Small worlds can be defined more precisely in terms of their m... |
2402.09163 | Emma Kun | P\'eter Ozsv\'art, Emma Kun | Cosmic radiation drives quasi-periodic changes in the diversity of
siliceous marine microplankton | 13 Pages, 2 Figures. Submitted to Astrobiology. Comments welcome | null | null | null | q-bio.PE astro-ph.EP astro-ph.GA astro-ph.HE physics.ao-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Radiolarians are significant contributors to the oceanic primary productivity
and the global silica cycle in the last 500 Myr. Their diversity throughout the
Phanerozoic shows periodic fluctuations. We identify a possible abiotic
candidate for driving these patterns which seems to potentially influence
radiolarian di... | [
{
"created": "Wed, 14 Feb 2024 13:27:31 GMT",
"version": "v1"
}
] | 2024-02-15 | [
[
"Ozsvárt",
"Péter",
""
],
[
"Kun",
"Emma",
""
]
] | Radiolarians are significant contributors to the oceanic primary productivity and the global silica cycle in the last 500 Myr. Their diversity throughout the Phanerozoic shows periodic fluctuations. We identify a possible abiotic candidate for driving these patterns which seems to potentially influence radiolarian dive... |
2103.06562 | Renaud Jolivet | Dmytro Grytskyy and Renaud B. Jolivet | A learning rule balancing energy consumption and information
maximization in a feed-forward neuronal network | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Information measures are often used to assess the efficacy of neural
networks, and learning rules can be derived through optimization procedures on
such measures. In biological neural networks, computation is restricted by the
amount of available resources. Considering energy restrictions, it is thus
reasonable to ba... | [
{
"created": "Thu, 11 Mar 2021 09:41:53 GMT",
"version": "v1"
}
] | 2021-03-12 | [
[
"Grytskyy",
"Dmytro",
""
],
[
"Jolivet",
"Renaud B.",
""
]
] | Information measures are often used to assess the efficacy of neural networks, and learning rules can be derived through optimization procedures on such measures. In biological neural networks, computation is restricted by the amount of available resources. Considering energy restrictions, it is thus reasonable to bala... |
1205.1322 | Alex Skvortsov | P. Katauskis, P. Skakauskas, A. Skvortsov | The receptor-toxin-antibody interaction: Mathematical model and
numerical simulation | 6 pages, 7 figures | null | null | null | q-bio.CB | http://creativecommons.org/licenses/publicdomain/ | A reaction-diffusion model of receptor-toxin-antibody (RTA) interaction is
studied numerically. The protective properties of an antibody against a given
toxin are evaluated for a spherical cell placed into a toxin-antibody solution.
The selection of parameters for numerical simulation approximately corresponds
to the... | [
{
"created": "Mon, 7 May 2012 08:49:47 GMT",
"version": "v1"
},
{
"created": "Tue, 5 Jun 2012 07:44:52 GMT",
"version": "v2"
}
] | 2012-06-06 | [
[
"Katauskis",
"P.",
""
],
[
"Skakauskas",
"P.",
""
],
[
"Skvortsov",
"A.",
""
]
] | A reaction-diffusion model of receptor-toxin-antibody (RTA) interaction is studied numerically. The protective properties of an antibody against a given toxin are evaluated for a spherical cell placed into a toxin-antibody solution. The selection of parameters for numerical simulation approximately corresponds to the p... |
1309.2622 | Liane Gabora | Liane Gabora | Five clarifications about cultural evolution | 23 pages. arXiv admin note: substantial text overlap with
arXiv:1206.4386 | Journal of Cognition and Culture, 11, 61-83 (2011) | 10.1163/156853711X568699 | null | q-bio.PE q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper reviews and clarifies five misunderstandings about cultural
evolution identified by Henrich, Boyd, and Richerson (2008). First, cultural
representations are neither discrete nor continuous; they are distributed
across neurons that respond to microfeatures. This enables associations to be
made, and cultural... | [
{
"created": "Tue, 10 Sep 2013 19:31:05 GMT",
"version": "v1"
},
{
"created": "Sun, 30 Jun 2019 02:17:23 GMT",
"version": "v2"
}
] | 2019-07-02 | [
[
"Gabora",
"Liane",
""
]
] | This paper reviews and clarifies five misunderstandings about cultural evolution identified by Henrich, Boyd, and Richerson (2008). First, cultural representations are neither discrete nor continuous; they are distributed across neurons that respond to microfeatures. This enables associations to be made, and cultural c... |
2310.13806 | Brian Hutchinson | Sarah Coffland and Katie Christensen and Filip Jagodzinski and Brian
Hutchinson | RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep
Learning | Presented at Computational Structural Bioinformatics Workshop 2023 | Proceedings of the 14th ACM International Conference on
Bioinformatics, Computational Biology, and Health Informatics. ACM BCB 2023 | 10.1145/3584371.3612951 | null | q-bio.BM cs.AI cs.LG q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An amino acid insertion or deletion, or InDel, can have profound and varying
functional impacts on a protein's structure. InDel mutations in the
transmembrane conductor regulator protein for example give rise to cystic
fibrosis. Unfortunately performing InDel mutations on physical proteins and
studying their effects ... | [
{
"created": "Fri, 20 Oct 2023 20:36:13 GMT",
"version": "v1"
}
] | 2023-10-24 | [
[
"Coffland",
"Sarah",
""
],
[
"Christensen",
"Katie",
""
],
[
"Jagodzinski",
"Filip",
""
],
[
"Hutchinson",
"Brian",
""
]
] | An amino acid insertion or deletion, or InDel, can have profound and varying functional impacts on a protein's structure. InDel mutations in the transmembrane conductor regulator protein for example give rise to cystic fibrosis. Unfortunately performing InDel mutations on physical proteins and studying their effects is... |
2002.00363 | Jos\'e A. Cuesta | Susanna Manrubia, Jos\'e A. Cuesta, Jacobo Aguirre, Sebastian E.
Ahnert, Lee Altenberg, Alejandro V. Cano, Pablo Catal\'an, Ramon
Diaz-Uriarte, Santiago F. Elena, Juan Antonio Garc\'ia-Mart\'in, Paulien
Hogeweg, Bhavin S. Khatri, Joachim Krug, Ard A. Louis, Nora S. Martin, Joshua
L. Payne, Matthew J. Tarnowski,... | From genotypes to organisms: State-of-the-art and perspectives of a
cornerstone in evolutionary dynamics | 111 pages, 11 figures uses elsarticle latex class | Physics of Life Reviews 38, 55-106 (2021) | 10.1016/j.plrev.2021.03.004 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding how genotypes map onto phenotypes, fitness, and eventually
organisms is arguably the next major missing piece in a fully predictive theory
of evolution. We refer to this generally as the problem of the
genotype-phenotype map. Though we are still far from achieving a complete
picture of these relationshi... | [
{
"created": "Sun, 2 Feb 2020 11:12:01 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Jul 2020 17:35:29 GMT",
"version": "v2"
},
{
"created": "Wed, 17 Mar 2021 15:11:45 GMT",
"version": "v3"
}
] | 2022-05-20 | [
[
"Manrubia",
"Susanna",
""
],
[
"Cuesta",
"José A.",
""
],
[
"Aguirre",
"Jacobo",
""
],
[
"Ahnert",
"Sebastian E.",
""
],
[
"Altenberg",
"Lee",
""
],
[
"Cano",
"Alejandro V.",
""
],
[
"Catalán",
"Pablo",
""
... | Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships... |
2011.04892 | Peixiao Wang | Peixiao Wang, Tao Hu, Hongqiang Liu and Xinyan Zhu | Exploring the impact of under-reported cases on the COVID-19
spatiotemporal distribution using healthcare worker infection data | null | Cities, 2022 | 10.1016/j.cities.2022.103593 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | A timely understanding of the spatiotemporal pattern and development trend of
COVID-19 is critical for timely prevention and control. However, the
under-reporting of cases is widespread in fields associated with public health.
It is also possible to draw biased inferences and formulate inappropriate
prevention and co... | [
{
"created": "Tue, 10 Nov 2020 04:48:49 GMT",
"version": "v1"
},
{
"created": "Thu, 26 Nov 2020 03:10:18 GMT",
"version": "v2"
},
{
"created": "Mon, 30 Nov 2020 14:06:54 GMT",
"version": "v3"
},
{
"created": "Sun, 13 Dec 2020 14:13:25 GMT",
"version": "v4"
},
{
"c... | 2024-01-15 | [
[
"Wang",
"Peixiao",
""
],
[
"Hu",
"Tao",
""
],
[
"Liu",
"Hongqiang",
""
],
[
"Zhu",
"Xinyan",
""
]
] | A timely understanding of the spatiotemporal pattern and development trend of COVID-19 is critical for timely prevention and control. However, the under-reporting of cases is widespread in fields associated with public health. It is also possible to draw biased inferences and formulate inappropriate prevention and cont... |
1701.03448 | Johannes M\"uller | Johannes M\"uller, Karin M\"unch, Bendix Koopmann, Eva Stadler, Louisa
Roselius, Dieter Jahn, Richard M\"unch | Plasmid segregation and accumulation | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The segregation of plasmids in a bacterial population is investigated.
Hereby, a dynamical model is formulated in terms of a size-structured
population using a hyperbolic partial differential equation incorporating
non-local terms (the fragmentation equation). For a large class of parameter
functions this PDE can be ... | [
{
"created": "Thu, 12 Jan 2017 18:35:23 GMT",
"version": "v1"
}
] | 2017-01-13 | [
[
"Müller",
"Johannes",
""
],
[
"Münch",
"Karin",
""
],
[
"Koopmann",
"Bendix",
""
],
[
"Stadler",
"Eva",
""
],
[
"Roselius",
"Louisa",
""
],
[
"Jahn",
"Dieter",
""
],
[
"Münch",
"Richard",
""
]
] | The segregation of plasmids in a bacterial population is investigated. Hereby, a dynamical model is formulated in terms of a size-structured population using a hyperbolic partial differential equation incorporating non-local terms (the fragmentation equation). For a large class of parameter functions this PDE can be re... |
1501.00019 | Peter Waddell | Peter J. Waddell | Extended Distance-based Phylogenetic Analyses Applied to 3D Homo Fossil
Skull Evolution | 42 pages, 18 figures | null | null | null | q-bio.PE q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This article shows how 3D geometric morphometric data can be analyzed using
newly developed distance-based evolutionary tree inference methods, with
extensions to planar graphs. Application of these methods to 3D representations
of the skullcap (calvaria) of 13 diverse skulls in the genus Homo, ranging from
Homo erec... | [
{
"created": "Tue, 30 Dec 2014 21:05:27 GMT",
"version": "v1"
}
] | 2015-01-05 | [
[
"Waddell",
"Peter J.",
""
]
] | This article shows how 3D geometric morphometric data can be analyzed using newly developed distance-based evolutionary tree inference methods, with extensions to planar graphs. Application of these methods to 3D representations of the skullcap (calvaria) of 13 diverse skulls in the genus Homo, ranging from Homo erectu... |
1405.3946 | Hatef Sadeghi | Hatef Sadeghi, S. Bailey and Colin J. Lambert | Silicene-based DNA Nucleobase Sensing | null | Appl. Phys. Lett. 104, 103104 (2014) | 10.1063/1.4868123 | null | q-bio.QM cond-mat.mes-hall cond-mat.mtrl-sci physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a DNA sequencing scheme based on silicene nanopores. Using first
principles theory, we compute the electrical properties of such pores in the
absence and presence of nucleobases. Within a two-terminal geometry, we analyze
the current-voltage relation in the presence of nucleobases with various
orientations... | [
{
"created": "Tue, 13 May 2014 11:21:49 GMT",
"version": "v1"
}
] | 2014-05-16 | [
[
"Sadeghi",
"Hatef",
""
],
[
"Bailey",
"S.",
""
],
[
"Lambert",
"Colin J.",
""
]
] | We propose a DNA sequencing scheme based on silicene nanopores. Using first principles theory, we compute the electrical properties of such pores in the absence and presence of nucleobases. Within a two-terminal geometry, we analyze the current-voltage relation in the presence of nucleobases with various orientations. ... |
1605.01155 | Lincong Wang | Lincong Wang | The contributions of surface charge and geometry to protein-solvent
interaction | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To better understand protein-solvent interaction we have analyzed a variety
of physical and geometrical properties of the solvent-excluded surfaces (SESs)
over a large set of soluble proteins with crystal structures. We discover that
all have net negative surface charges and permanent electric dipoles. Moreover
both ... | [
{
"created": "Wed, 4 May 2016 06:34:11 GMT",
"version": "v1"
}
] | 2016-05-05 | [
[
"Wang",
"Lincong",
""
]
] | To better understand protein-solvent interaction we have analyzed a variety of physical and geometrical properties of the solvent-excluded surfaces (SESs) over a large set of soluble proteins with crystal structures. We discover that all have net negative surface charges and permanent electric dipoles. Moreover both SE... |
1012.0985 | Andree-Aimee Toucas | Jean Geringer, Laurent Navarro, Bernard Forest | Influence of proteins from physiological solutions on the
electrochemical behaviour of the Ti-6Al-4V alloy: reproducibility and
time-frequency dependence. ---- Influence de la teneur en prot\'eines de
solutions physiologiques sur le comportement \'electrochimique du Ti-6Al-4V :
reproductibilit\'e et repr\'esent... | null | Mat\'eriaux & Techniques 98, 1 (2010) 59-68 | 10.1051/mattech/2010020 | JG-M\&T-98-1 | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The electrochemical behaviour of the biomedical and metallic alloys,
especially in the orthopaedic implants fields, raises many questions. This
study is dedicated for studying the Ti-6Al-4V alloy, by electrochemical
impedance spectroscopy, EIS, in various physiological media,: Ringer solution,
phosphate buffered solu... | [
{
"created": "Sun, 5 Dec 2010 10:33:52 GMT",
"version": "v1"
}
] | 2020-07-17 | [
[
"Geringer",
"Jean",
""
],
[
"Navarro",
"Laurent",
""
],
[
"Forest",
"Bernard",
""
]
] | The electrochemical behaviour of the biomedical and metallic alloys, especially in the orthopaedic implants fields, raises many questions. This study is dedicated for studying the Ti-6Al-4V alloy, by electrochemical impedance spectroscopy, EIS, in various physiological media,: Ringer solution, phosphate buffered soluti... |
1903.11373 | Dalit Engelhardt | Dalit Engelhardt | Dynamic Control of Stochastic Evolution: A Deep Reinforcement Learning
Approach to Adaptively Targeting Emergent Drug Resistance | null | Journal of Machine Learning Research 21(203): 1-30, 2020 | null | null | q-bio.PE cs.LG q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The challenge in controlling stochastic systems in which low-probability
events can set the system on catastrophic trajectories is to develop a robust
ability to respond to such events without significantly compromising the
optimality of the baseline control policy. This paper presents CelluDose, a
stochastic simulat... | [
{
"created": "Wed, 27 Mar 2019 12:25:48 GMT",
"version": "v1"
},
{
"created": "Thu, 15 Oct 2020 22:21:53 GMT",
"version": "v2"
}
] | 2020-10-28 | [
[
"Engelhardt",
"Dalit",
""
]
] | The challenge in controlling stochastic systems in which low-probability events can set the system on catastrophic trajectories is to develop a robust ability to respond to such events without significantly compromising the optimality of the baseline control policy. This paper presents CelluDose, a stochastic simulatio... |
1211.0646 | Alex Robson | Alex Robson, Kevin Burrage, Mark Leake | Inferring diffusion in single live cells at the single molecule level | combined ms (1-37 pages, 8 figures) and SI (38-55, 3 figures) | null | 10.1098/rstb.2012.0029 | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The movement of molecules inside living cells is a fundamental feature of
biological processes. The ability to both observe and analyse the details of
molecular diffusion in vivo at the single molecule and single cell level can
add significant insight into understanding molecular architectures of diffusing
molecules ... | [
{
"created": "Sat, 3 Nov 2012 22:43:52 GMT",
"version": "v1"
}
] | 2012-11-21 | [
[
"Robson",
"Alex",
""
],
[
"Burrage",
"Kevin",
""
],
[
"Leake",
"Mark",
""
]
] | The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single molecule and single cell level can add significant insight into understanding molecular architectures of diffusing molecules an... |
1904.03531 | Sliman Bensmaia | Elizaveta V. Okorokova, James M. Goodman, Nicholas G. Hatsopoulos and
Sliman J. Bensmaia | Decoding hand kinematics from population responses in sensorimotor
cortex during grasping | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The hand, a complex effector comprising dozens of degrees of freedom of
movement, endows us with the ability to flexibly, precisely, and effortlessly
interact with objects. The neural signals associated with dexterous hand
movements in primary motor cortex (M1) and somatosensory cortex (SC) have
received comparativel... | [
{
"created": "Sat, 6 Apr 2019 21:05:30 GMT",
"version": "v1"
},
{
"created": "Thu, 20 Jun 2019 03:58:50 GMT",
"version": "v2"
}
] | 2019-06-21 | [
[
"Okorokova",
"Elizaveta V.",
""
],
[
"Goodman",
"James M.",
""
],
[
"Hatsopoulos",
"Nicholas G.",
""
],
[
"Bensmaia",
"Sliman J.",
""
]
] | The hand, a complex effector comprising dozens of degrees of freedom of movement, endows us with the ability to flexibly, precisely, and effortlessly interact with objects. The neural signals associated with dexterous hand movements in primary motor cortex (M1) and somatosensory cortex (SC) have received comparatively ... |
1209.3802 | Adel Dayarian | Adel Dayarian and Anirvan M. Sengupta | Titration and hysteresis in epigenetic chromatin silencing | null | 2013 Phys. Biol. 10 036005 | 10.1088/1478-3975/10/3/036005 | NSF-KITP-12-172 | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Epigenetic mechanisms of silencing via heritable chromatin modifications play
a major role in gene regulation and cell fate specification. We consider a
model of epigenetic chromatin silencing in budding yeast and study the
bifurcation diagram and characterize the bistable and the monostable regimes.
The main focus o... | [
{
"created": "Mon, 17 Sep 2012 21:38:47 GMT",
"version": "v1"
},
{
"created": "Mon, 24 Sep 2012 20:25:40 GMT",
"version": "v2"
},
{
"created": "Fri, 15 Feb 2013 00:32:25 GMT",
"version": "v3"
}
] | 2013-04-24 | [
[
"Dayarian",
"Adel",
""
],
[
"Sengupta",
"Anirvan M.",
""
]
] | Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation diagram and characterize the bistable and the monostable regimes. The main focus of ... |
1607.01010 | Evelyn Tang | Evelyn Tang, Chad Giusti, Graham Baum, Shi Gu, Eli Pollock, Ari E.
Kahn, David Roalf, Tyler M. Moore, Kosha Ruparel, Ruben C. Gur, Raquel E.
Gur, Theodore D. Satterthwaite and Danielle S. Bassett | Developmental increases in white matter network controllability support
a growing diversity of brain dynamics | In press at Nature Communications | Nature Communications, 1252 (2017) | 10.1038/s41467-017-01254-4 | null | q-bio.NC cond-mat.dis-nn nlin.CD q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As the human brain develops, it increasingly supports coordinated control of
neural activity. The mechanism by which white matter evolves to support this
coordination is not well understood. We use a network representation of
diffusion imaging data from 882 youth ages 8 to 22 to show that white matter
connectivity be... | [
{
"created": "Mon, 4 Jul 2016 20:00:00 GMT",
"version": "v1"
},
{
"created": "Tue, 1 Nov 2016 04:03:51 GMT",
"version": "v2"
},
{
"created": "Mon, 2 Oct 2017 20:34:39 GMT",
"version": "v3"
}
] | 2017-11-02 | [
[
"Tang",
"Evelyn",
""
],
[
"Giusti",
"Chad",
""
],
[
"Baum",
"Graham",
""
],
[
"Gu",
"Shi",
""
],
[
"Pollock",
"Eli",
""
],
[
"Kahn",
"Ari E.",
""
],
[
"Roalf",
"David",
""
],
[
"Moore",
"Tyler M... | As the human brain develops, it increasingly supports coordinated control of neural activity. The mechanism by which white matter evolves to support this coordination is not well understood. We use a network representation of diffusion imaging data from 882 youth ages 8 to 22 to show that white matter connectivity beco... |
2312.03338 | Daniel Str\"ombom | Daniel Str\"ombom, Autumn Sands, Jason M. Graham, Amanda Crocker,
Cameron Cloud, Grace Tulevech, Kelly Ward | Modeling human activity-related spread of the spotted lanternfly
(Lycorma delicatula) in the US | 14 pages, 5 figures, 2 tables | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The spotted lanternfly (Lycorma delicatula) has recently spread from its
native range to several other countries and forecasts predict that it may
become a global invasive pest. In particular, since its confirmed presence in
the United States in 2014 it has established itself as a major invasive pest in
the Mid-Atlan... | [
{
"created": "Wed, 6 Dec 2023 08:20:59 GMT",
"version": "v1"
}
] | 2023-12-07 | [
[
"Strömbom",
"Daniel",
""
],
[
"Sands",
"Autumn",
""
],
[
"Graham",
"Jason M.",
""
],
[
"Crocker",
"Amanda",
""
],
[
"Cloud",
"Cameron",
""
],
[
"Tulevech",
"Grace",
""
],
[
"Ward",
"Kelly",
""
]
] | The spotted lanternfly (Lycorma delicatula) has recently spread from its native range to several other countries and forecasts predict that it may become a global invasive pest. In particular, since its confirmed presence in the United States in 2014 it has established itself as a major invasive pest in the Mid-Atlanti... |
1602.07100 | Koen Haak | Koen V. Haak, Andre F. Marquand, Christian F. Beckmann | Connectopic mapping with resting-state fMRI | null | null | 10.1016/j.neuroimage.2017.06.075 | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Brain regions are often topographically connected: nearby locations within
one brain area connect with nearby locations in another area. Mapping these
connection topographies, or 'connectopies' in short, is crucial for
understanding how information is processed in the brain. Here, we propose
principled, fully data-dr... | [
{
"created": "Tue, 23 Feb 2016 09:35:34 GMT",
"version": "v1"
},
{
"created": "Mon, 17 Jul 2017 09:39:28 GMT",
"version": "v2"
}
] | 2017-07-18 | [
[
"Haak",
"Koen V.",
""
],
[
"Marquand",
"Andre F.",
""
],
[
"Beckmann",
"Christian F.",
""
]
] | Brain regions are often topographically connected: nearby locations within one brain area connect with nearby locations in another area. Mapping these connection topographies, or 'connectopies' in short, is crucial for understanding how information is processed in the brain. Here, we propose principled, fully data-driv... |
1401.3254 | Marcelo Sobottka | Marcelo Sobottka and Andrew G. Hart | A model capturing novel strand symmetries in bacterial DNA | This is a pre-copy-editing, author-produced preprint of an article
accepted for publication in Biochemical and Biophysical Research
Communications. The definitive publisher-authenticated version is available
online at: http://dx.doi.org/10.1016/j.bbrc.2011.06.072 or
http://www.sciencedirect.com/science/article/... | Biochemical and Biophysical Research Communications, Volume 410,
Issue 4, 15 July 2011, Pages 823-828, ISSN 0006-291X | 10.1016/j.bbrc.2011.06.072 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chargaff's second parity rule for short oligonucleotides states that the
frequency of any short nucleotide sequence on a strand is approximately equal
to the frequency of its reverse complement on the same strand. Recent studies
have shown that, with the exception of organellar DNA, this parity rule
generally holds f... | [
{
"created": "Tue, 14 Jan 2014 16:57:24 GMT",
"version": "v1"
}
] | 2014-01-15 | [
[
"Sobottka",
"Marcelo",
""
],
[
"Hart",
"Andrew G.",
""
]
] | Chargaff's second parity rule for short oligonucleotides states that the frequency of any short nucleotide sequence on a strand is approximately equal to the frequency of its reverse complement on the same strand. Recent studies have shown that, with the exception of organellar DNA, this parity rule generally holds for... |
2108.00813 | Reza Sameni | Jorge Oliveira, Francesco Renna, Paulo Dias Costa, Marcelo Nogueira,
Cristina Oliveira, Carlos Ferreira, Alipio Jorge, Sandra Mattos, Thamine
Hatem, Thiago Tavares, Andoni Elola, Ali Bahrami Rad, Reza Sameni, Gari D
Clifford, Miguel T. Coimbra | The CirCor DigiScope Dataset: From Murmur Detection to Murmur
Classification | 12 pages, 6 tables, 8 figures, in IEEE Journal of Biomedical and
Health Informatics | null | 10.1109/JBHI.2021.3137048 | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cardiac auscultation is one of the most cost-effective techniques used to
detect and identify many heart conditions. Computer-assisted decision systems
based on auscultation can support physicians in their decisions. Unfortunately,
the application of such systems in clinical trials is still minimal since most
of them... | [
{
"created": "Mon, 2 Aug 2021 12:30:40 GMT",
"version": "v1"
},
{
"created": "Fri, 24 Dec 2021 07:53:12 GMT",
"version": "v2"
}
] | 2021-12-28 | [
[
"Oliveira",
"Jorge",
""
],
[
"Renna",
"Francesco",
""
],
[
"Costa",
"Paulo Dias",
""
],
[
"Nogueira",
"Marcelo",
""
],
[
"Oliveira",
"Cristina",
""
],
[
"Ferreira",
"Carlos",
""
],
[
"Jorge",
"Alipio",
""
... | Cardiac auscultation is one of the most cost-effective techniques used to detect and identify many heart conditions. Computer-assisted decision systems based on auscultation can support physicians in their decisions. Unfortunately, the application of such systems in clinical trials is still minimal since most of them o... |
q-bio/0309026 | Matthew Wiener | Ethan D. Gershon, Matthew C. Wiener, Peter E. Latham, and Barry J.
Richmond | Coding Strategies in Monkey V1 and Inferior Temporal Cortices | 25 pages, 8 figures. Originally submitted to the neuro-sys archive
which was never publicly announced (was 9804001) | J. Neurophsysiol. 79: 1135-1144, 1998 | null | null | q-bio.NC | null | We would like to know whether the statistics of neuronal responses vary
across cortical areas. We examined stimulus-elicited spike count response
distributions in V1 and IT cortices of awake monkeys. In both areas the
distribution of spike counts for each stimulus was well-described by a
Gaussian, with the log of the... | [
{
"created": "Thu, 9 Apr 1998 21:25:33 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Gershon",
"Ethan D.",
""
],
[
"Wiener",
"Matthew C.",
""
],
[
"Latham",
"Peter E.",
""
],
[
"Richmond",
"Barry J.",
""
]
] | We would like to know whether the statistics of neuronal responses vary across cortical areas. We examined stimulus-elicited spike count response distributions in V1 and IT cortices of awake monkeys. In both areas the distribution of spike counts for each stimulus was well-described by a Gaussian, with the log of the v... |
2308.16772 | Srdjan Ostojic | Srdjan Ostojic and Stefano Fusi | The computational role of structure in neural activity and connectivity | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One major challenge of neuroscience is finding interesting structures in a
seemingly disorganized neural activity. Often these structures have
computational implications that help to understand the functional role of a
particular brain area. Here we outline a unified approach to characterize these
structures by inspe... | [
{
"created": "Thu, 31 Aug 2023 14:49:49 GMT",
"version": "v1"
}
] | 2023-09-01 | [
[
"Ostojic",
"Srdjan",
""
],
[
"Fusi",
"Stefano",
""
]
] | One major challenge of neuroscience is finding interesting structures in a seemingly disorganized neural activity. Often these structures have computational implications that help to understand the functional role of a particular brain area. Here we outline a unified approach to characterize these structures by inspect... |
1508.05159 | Ivo Siekmann | Ivo Siekmann and Horst Malchow | Competition of residents and invaders in a variable environment:
Response to enemies and dangerous noise | 24 pages, 18 figures, submitted to Mathematical Modelling of Natural
Phenomena | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The possible control of competitive invasion by infection of the invader and
multiplicative noise is studied. The basic model is the Lotka-Volterra
competition system with emergent carrying capacities. Several stationary
solutions of the non-infected and infected system are identified as well as
parameter ranges of b... | [
{
"created": "Fri, 21 Aug 2015 01:20:34 GMT",
"version": "v1"
}
] | 2015-08-24 | [
[
"Siekmann",
"Ivo",
""
],
[
"Malchow",
"Horst",
""
]
] | The possible control of competitive invasion by infection of the invader and multiplicative noise is studied. The basic model is the Lotka-Volterra competition system with emergent carrying capacities. Several stationary solutions of the non-infected and infected system are identified as well as parameter ranges of bis... |
1503.01909 | Petter Holme | Petter Holme | Shadows of the SIS immortality transition in small networks | Bug fixes from the first version | Phys. Rev. E 92, (2015) 012804 | 10.1103/PhysRevE.92.012804 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Much of the research on the behavior of the SIS model on networks has
concerned the infinite size limit; in particular the phase transition between a
state where outbreaks can reach a finite fraction of the population, and a
state where only a finite number would be infected. For finite networks, there
is also a dyna... | [
{
"created": "Fri, 6 Mar 2015 11:00:08 GMT",
"version": "v1"
},
{
"created": "Wed, 13 May 2015 06:04:23 GMT",
"version": "v2"
}
] | 2015-07-13 | [
[
"Holme",
"Petter",
""
]
] | Much of the research on the behavior of the SIS model on networks has concerned the infinite size limit; in particular the phase transition between a state where outbreaks can reach a finite fraction of the population, and a state where only a finite number would be infected. For finite networks, there is also a dynami... |
2306.06298 | Tandy Warnow | Tandy Warnow, Steven N. Evans, and Luay Nakhleh | Progress on Constructing Phylogenetic Networks for Languages | 16 pages, 2 figures | null | null | null | q-bio.PE stat.AP | http://creativecommons.org/licenses/by/4.0/ | In 2006, Warnow, Evans, Ringe, and Nakhleh proposed a stochastic model
(hereafter, the WERN 2006 model) of multi-state linguistic character evolution
that allowed for homoplasy and borrowing. They proved that if there is no
borrowing between languages and homoplastic states are known in advance, then
the phylogenetic... | [
{
"created": "Fri, 9 Jun 2023 23:27:21 GMT",
"version": "v1"
},
{
"created": "Mon, 9 Oct 2023 19:06:56 GMT",
"version": "v2"
}
] | 2023-10-11 | [
[
"Warnow",
"Tandy",
""
],
[
"Evans",
"Steven N.",
""
],
[
"Nakhleh",
"Luay",
""
]
] | In 2006, Warnow, Evans, Ringe, and Nakhleh proposed a stochastic model (hereafter, the WERN 2006 model) of multi-state linguistic character evolution that allowed for homoplasy and borrowing. They proved that if there is no borrowing between languages and homoplastic states are known in advance, then the phylogenetic t... |
2008.07797 | Mike Steel Prof. | Andrew Francis, Daniel H. Huson and Mike Steel | Normalising phylogenetic networks | 18 pages, 5 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Rooted phylogenetic networks provide a way to describe species' relationships
when evolution departs from the simple model of a tree. However, networks
inferred from genomic data can be highly tangled, making it difficult to
discern the main reticulation signals present. In this paper, we describe a
natural way to tr... | [
{
"created": "Tue, 18 Aug 2020 08:24:03 GMT",
"version": "v1"
},
{
"created": "Fri, 28 May 2021 03:50:31 GMT",
"version": "v2"
}
] | 2021-05-31 | [
[
"Francis",
"Andrew",
""
],
[
"Huson",
"Daniel H.",
""
],
[
"Steel",
"Mike",
""
]
] | Rooted phylogenetic networks provide a way to describe species' relationships when evolution departs from the simple model of a tree. However, networks inferred from genomic data can be highly tangled, making it difficult to discern the main reticulation signals present. In this paper, we describe a natural way to tran... |
2111.04167 | Jeremie Unterberger M | J. Unterberger | Exact computation of growth-rate fluctuations in random environment | 17 pages | null | null | null | q-bio.PE cond-mat.stat-mech math.PR | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We consider a general class of Markovian models describing the growth in a
randomly fluctuating environment of a clonal biological population having
several phenotypes related by stochastic switching. Phenotypes differ e.g. by
the level of gene expression for a population of bacteria. The time-averaged
growth rate of... | [
{
"created": "Sun, 7 Nov 2021 19:58:43 GMT",
"version": "v1"
},
{
"created": "Sun, 23 Jan 2022 20:35:26 GMT",
"version": "v2"
}
] | 2022-01-25 | [
[
"Unterberger",
"J.",
""
]
] | We consider a general class of Markovian models describing the growth in a randomly fluctuating environment of a clonal biological population having several phenotypes related by stochastic switching. Phenotypes differ e.g. by the level of gene expression for a population of bacteria. The time-averaged growth rate of t... |
2009.13775 | Maryam Ghoojaei | Maryam Ghoojaei, Reza Shirkoohi, Mojtaba Saffari, Amirnader
Emamirazavi, Mehrdad Hashemi | Foot-print of Claudin and Occludin Transcriptome in Colorectal Cancer | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background and Purpose: Colorectal cancer as a leading cause of mortality
worldwide, can be regarded as a relatively common and fatal disease with
increasing incidence over recent years. Colorectal cancer is characterized by
uncontrolled growth of abnormal cells occurring in different parts of the
colon. About 90% of... | [
{
"created": "Tue, 29 Sep 2020 04:20:52 GMT",
"version": "v1"
}
] | 2020-09-30 | [
[
"Ghoojaei",
"Maryam",
""
],
[
"Shirkoohi",
"Reza",
""
],
[
"Saffari",
"Mojtaba",
""
],
[
"Emamirazavi",
"Amirnader",
""
],
[
"Hashemi",
"Mehrdad",
""
]
] | Background and Purpose: Colorectal cancer as a leading cause of mortality worldwide, can be regarded as a relatively common and fatal disease with increasing incidence over recent years. Colorectal cancer is characterized by uncontrolled growth of abnormal cells occurring in different parts of the colon. About 90% of d... |
1501.04015 | Thomas R. Sokolowski | Thomas R. Sokolowski and Ga\v{s}per Tka\v{c}ik | Optimizing information flow in small genetic networks. IV. Spatial
coupling | 17 pages, 8 figures (incl. 3 supporting figures) | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We typically think of cells as responding to external signals independently
by regulating their gene expression levels, yet they often locally exchange
information and coordinate. Can such spatial coupling be of benefit for
conveying signals subject to gene regulatory noise? Here we extend our
information-theoretic f... | [
{
"created": "Fri, 16 Jan 2015 15:32:02 GMT",
"version": "v1"
}
] | 2015-01-19 | [
[
"Sokolowski",
"Thomas R.",
""
],
[
"Tkačik",
"Gašper",
""
]
] | We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic fra... |
2305.16241 | Alessandro Grecucci Prof | Bianca Monachesi, Alessandro Grecucci, Parisa Ahmadi Ghomroudi, Irene
Messina | Understanding the neural architecture of emotion regulation by comparing
two different strategies: A meta-analytic approach | 32 pages, 3 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | In the emotion regulation literature, the amount of neuroimaging studies on
cognitive reappraisal led the impression that the same top-down,
control-related neural mechanisms characterize all emotion regulation
strategies. However, top-down processes may coexist with more bottom-up and
emotion-focused processes that ... | [
{
"created": "Thu, 25 May 2023 16:52:15 GMT",
"version": "v1"
}
] | 2023-05-26 | [
[
"Monachesi",
"Bianca",
""
],
[
"Grecucci",
"Alessandro",
""
],
[
"Ghomroudi",
"Parisa Ahmadi",
""
],
[
"Messina",
"Irene",
""
]
] | In the emotion regulation literature, the amount of neuroimaging studies on cognitive reappraisal led the impression that the same top-down, control-related neural mechanisms characterize all emotion regulation strategies. However, top-down processes may coexist with more bottom-up and emotion-focused processes that pa... |
0707.3716 | Lorenzo Farina | Maria Concetta Palumbo, Lorenzo Farina, Alberto De Santis, Alessandro
Giuliani, Alfredo Colosimo, Giorgio Morelli and Ida Ruberti | Post-transcriptional Regulation Drives Temporal Compartmentalization of
the Yeast Metabolic Cycle | 13 pages, 4 figures, 1 table | null | null | null | q-bio.CB q-bio.BM | null | The maintainance of a stable periodicity during the yeast metabolic cycle
involving approximately half of the genome requires a very strict and efficient
control of gene expression. For this reason, the metabolic cycle is a very good
candidate for testing the role of a class of post-transcriptional regulators,
the so... | [
{
"created": "Wed, 25 Jul 2007 12:21:28 GMT",
"version": "v1"
}
] | 2007-07-26 | [
[
"Palumbo",
"Maria Concetta",
""
],
[
"Farina",
"Lorenzo",
""
],
[
"De Santis",
"Alberto",
""
],
[
"Giuliani",
"Alessandro",
""
],
[
"Colosimo",
"Alfredo",
""
],
[
"Morelli",
"Giorgio",
""
],
[
"Ruberti",
"Ida",... | The maintainance of a stable periodicity during the yeast metabolic cycle involving approximately half of the genome requires a very strict and efficient control of gene expression. For this reason, the metabolic cycle is a very good candidate for testing the role of a class of post-transcriptional regulators, the so c... |
1504.03145 | Johan Elf | Mats Wallden, David Fange, \"Ozden Baltekin, Johan Elf | Fluctuations in growth rates determine the generation time and size
distributions of E. coli cells | null | null | null | null | q-bio.QM q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Isogenic Escherichia coli growing exponentially in a constant environment
display large variation in growth-rates, division-sizes and generation-times.
It is unclear how these seemingly random cell cycles can be reconciled with the
precise regulation required under conditions where the generation time is
shorter than... | [
{
"created": "Mon, 13 Apr 2015 11:53:44 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Oct 2015 18:04:57 GMT",
"version": "v2"
}
] | 2015-10-14 | [
[
"Wallden",
"Mats",
""
],
[
"Fange",
"David",
""
],
[
"Baltekin",
"Özden",
""
],
[
"Elf",
"Johan",
""
]
] | Isogenic Escherichia coli growing exponentially in a constant environment display large variation in growth-rates, division-sizes and generation-times. It is unclear how these seemingly random cell cycles can be reconciled with the precise regulation required under conditions where the generation time is shorter than t... |
1608.08498 | Rudolf Hanel Ass Prof Dr | Rudolf Hanel | Systemic stability, cell differentiation, and evolution - A dynamical
systems perspective | 8 pages 4 figures | null | null | null | q-bio.CB q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Species or population that proliferate faster than others become dominant in
numbers. Catalysis allows catalytic sets within a molecular reaction network to
dominate the non catalytic parts of the network by processing most of the
available substrate. As a consequence one may consider a 'catalytic fitness' of
sets of... | [
{
"created": "Tue, 30 Aug 2016 15:23:02 GMT",
"version": "v1"
}
] | 2016-08-31 | [
[
"Hanel",
"Rudolf",
""
]
] | Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available substrate. As a consequence one may consider a 'catalytic fitness' of sets of m... |
1209.1412 | Renato Vicente | Roberto H. Schonmann, Robert Boyd and Renato Vicente | The Taylor-Frank method cannot be applied to some biologically
important, continuous fitness functions | 9 pages, 1 figure | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Taylor-Frank method for making kin selection models when fitness is a
nonlinear function of a continuous phenotype requires this function to be
differentiable. This assumption sometimes fails for biologically important
fitness functions, for instance in microbial data and the theory of repeated
n-person games, ev... | [
{
"created": "Thu, 6 Sep 2012 21:15:41 GMT",
"version": "v1"
}
] | 2012-09-10 | [
[
"Schonmann",
"Roberto H.",
""
],
[
"Boyd",
"Robert",
""
],
[
"Vicente",
"Renato",
""
]
] | The Taylor-Frank method for making kin selection models when fitness is a nonlinear function of a continuous phenotype requires this function to be differentiable. This assumption sometimes fails for biologically important fitness functions, for instance in microbial data and the theory of repeated n-person games, even... |
2104.14189 | Jan Kierfeld | Matthias Schmidt, Jan Kierfeld | Chemomechanical simulation of microtubule dynamics with explicit lateral
bond dynamics | 37 pages + 14 figures + supplementary material | Front. Phys. 9:673875 (2021) | 10.3389/fphy.2021.673875 | null | q-bio.SC q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce and parameterize a chemomechanical model of microtubule dynamics
on the dimer level, which is based on the allosteric tubulin model and includes
attachment, detachment and hydrolysis of tubulin dimers as well as stretching
of lateral bonds, bending at longitudinal junctions, and the possibility of
latera... | [
{
"created": "Thu, 29 Apr 2021 08:17:45 GMT",
"version": "v1"
}
] | 2021-08-31 | [
[
"Schmidt",
"Matthias",
""
],
[
"Kierfeld",
"Jan",
""
]
] | We introduce and parameterize a chemomechanical model of microtubule dynamics on the dimer level, which is based on the allosteric tubulin model and includes attachment, detachment and hydrolysis of tubulin dimers as well as stretching of lateral bonds, bending at longitudinal junctions, and the possibility of lateral ... |
2008.08814 | Hessameddin Akhlaghpour | Hessameddin Akhlaghpour | An RNA-Based Theory of Natural Universal Computation | 66 pages total (25 pages main text excluding reference section), 7
figures, appendices in the same document | Journal of Theoretical Biology Volume 537, 21 March 2022, 110984 | 10.1016/j.jtbi.2021.110984 | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Life is confronted with computation problems in a variety of domains
including animal behavior, single-cell behavior, and embryonic development. Yet
we currently do not know of a naturally existing biological system that is
capable of universal computation, i.e., Turing-equivalent in scope. Generic
finite-dimensional... | [
{
"created": "Thu, 20 Aug 2020 07:38:13 GMT",
"version": "v1"
},
{
"created": "Tue, 6 Oct 2020 18:19:35 GMT",
"version": "v2"
},
{
"created": "Tue, 24 Aug 2021 00:12:18 GMT",
"version": "v3"
},
{
"created": "Sun, 12 Dec 2021 18:31:35 GMT",
"version": "v4"
}
] | 2022-03-10 | [
[
"Akhlaghpour",
"Hessameddin",
""
]
] | Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of universal computation, i.e., Turing-equivalent in scope. Generic finite-dimensional d... |
1501.07448 | Igor Goychuk | Igor Goychuk and Andriy Goychuk | Stochastic Wilson-Cowan models of neuronal network dynamics with memory
and delay | null | New Journal of Physics, vol. 17, 045029 (2015) | 10.1088/1367-2630/17/4/045029 | null | q-bio.NC cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a simple Markovian class of the stochastic Wilson-Cowan type
models of neuronal network dynamics, which incorporates stochastic delay caused
by the existence of a refractory period of neurons. From the point of view of
the dynamics of the individual elements, we are dealing with a network of
non-Markovian... | [
{
"created": "Thu, 29 Jan 2015 13:26:14 GMT",
"version": "v1"
}
] | 2015-05-01 | [
[
"Goychuk",
"Igor",
""
],
[
"Goychuk",
"Andriy",
""
]
] | We consider a simple Markovian class of the stochastic Wilson-Cowan type models of neuronal network dynamics, which incorporates stochastic delay caused by the existence of a refractory period of neurons. From the point of view of the dynamics of the individual elements, we are dealing with a network of non-Markovian s... |
2103.12481 | Mar\'ia Vallet-Regi | C. Heras, J. Jimenez Holguin, A. L. Doadrio, M. Vallet-Regi, S.
Sanchez-Salcedo, A. J. Salinas | Multifunctional antibiotic- and zinc-containing mesoporous bioactive
glass scaffolds to fight bone infection | 27 pages, 11 figures | Acta Biomaterialia 114, 395-406 (2020) | 10.1016/j.actbio.2020.07.044 | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Bone regeneration is a clinical challenge that requires multiple approaches.
Sometimes, it also includes the development of new osteogenic and antibacterial
biomaterials to treat the occurrence of possible infection processes derived
from surgery. This study evaluates the antibacterial properties of
meso-macroporous ... | [
{
"created": "Tue, 23 Mar 2021 12:12:15 GMT",
"version": "v1"
}
] | 2021-03-24 | [
[
"Heras",
"C.",
""
],
[
"Holguin",
"J. Jimenez",
""
],
[
"Doadrio",
"A. L.",
""
],
[
"Vallet-Regi",
"M.",
""
],
[
"Sanchez-Salcedo",
"S.",
""
],
[
"Salinas",
"A. J.",
""
]
] | Bone regeneration is a clinical challenge that requires multiple approaches. Sometimes, it also includes the development of new osteogenic and antibacterial biomaterials to treat the occurrence of possible infection processes derived from surgery. This study evaluates the antibacterial properties of meso-macroporous sc... |
1711.05141 | Andrei Olypher | Andrei Olifer | Generating behavioral acts of predetermined apparent complexity | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Behavior of natural and artificial agents consists of behavioral episodes or
acts. This study introduces a quantitative measure of behavioral acts -- their
apparent complexity. The measure is based on the concept of the Kolmogorov
complexity. It is an apparent measure because it is determined solely by the
readings o... | [
{
"created": "Tue, 14 Nov 2017 15:29:52 GMT",
"version": "v1"
}
] | 2017-11-15 | [
[
"Olifer",
"Andrei",
""
]
] | Behavior of natural and artificial agents consists of behavioral episodes or acts. This study introduces a quantitative measure of behavioral acts -- their apparent complexity. The measure is based on the concept of the Kolmogorov complexity. It is an apparent measure because it is determined solely by the readings of ... |
1709.06489 | Louis Lello | Louis Lello, Steven G. Avery, Laurent Tellier, Ana Vazquez, Gustavo de
los Campos, Stephen D.H. Hsu | Accurate Genomic Prediction Of Human Height | 17 pages, 10 figures | null | null | null | q-bio.GN cs.LG q-bio.QM stat.ML | http://creativecommons.org/licenses/by-nc-sa/4.0/ | We construct genomic predictors for heritable and extremely complex human
quantitative traits (height, heel bone density, and educational attainment)
using modern methods in high dimensional statistics (i.e., machine learning).
Replication tests show that these predictors capture, respectively, $\sim$40,
20, and 9 pe... | [
{
"created": "Tue, 19 Sep 2017 15:32:37 GMT",
"version": "v1"
}
] | 2017-09-20 | [
[
"Lello",
"Louis",
""
],
[
"Avery",
"Steven G.",
""
],
[
"Tellier",
"Laurent",
""
],
[
"Vazquez",
"Ana",
""
],
[
"Campos",
"Gustavo de los",
""
],
[
"Hsu",
"Stephen D. H.",
""
]
] | We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication tests show that these predictors capture, respectively, $\sim$40, 20, and 9 perc... |
2106.13565 | Tancredi Caruso | Tancredi Caruso, Giulio Virginio Clemente, Matthias C Rillig, Diego
Garlaschelli | Fluctuating ecological networks: a synthesis of maximum-entropy
approaches for pattern detection and process inference | submitted | Methods in Ecology and Evolution, 00, 1-12 (2022) | 10.1111/2041-210X.13985 | null | q-bio.QM cond-mat.dis-nn physics.data-an | http://creativecommons.org/licenses/by/4.0/ | Ecological networks such as plant-pollinator systems and food webs vary in
space and time. This variability includes fluctuations in global network
properties such as total number and intensity of interactions but also in the
local properties of individual nodes such as the number and intensity of
species-level inter... | [
{
"created": "Fri, 25 Jun 2021 11:23:59 GMT",
"version": "v1"
},
{
"created": "Fri, 11 Mar 2022 09:03:31 GMT",
"version": "v2"
}
] | 2022-12-23 | [
[
"Caruso",
"Tancredi",
""
],
[
"Clemente",
"Giulio Virginio",
""
],
[
"Rillig",
"Matthias C",
""
],
[
"Garlaschelli",
"Diego",
""
]
] | Ecological networks such as plant-pollinator systems and food webs vary in space and time. This variability includes fluctuations in global network properties such as total number and intensity of interactions but also in the local properties of individual nodes such as the number and intensity of species-level interac... |
1706.05702 | Jeyashree Krishnan | Jeyashree Krishnan, PierGianLuca Porta Mana, Moritz Helias, Markus
Diesmann, Edoardo Di Napoli | Perfect spike detection via time reversal | 9 figures, Preliminary results in proceedings of the Bernstein
Conference 2016 | null | 10.3389/fninf.2017.00075 | null | q-bio.NC math.DG physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spiking neuronal networks are usually simulated with three main simulation
schemes: the classical time-driven and event-driven schemes, and the more
recent hybrid scheme. All three schemes evolve the state of a neuron through a
series of checkpoints: equally spaced in the first scheme and determined
neuron-wise by sp... | [
{
"created": "Sun, 18 Jun 2017 19:13:26 GMT",
"version": "v1"
}
] | 2018-01-24 | [
[
"Krishnan",
"Jeyashree",
""
],
[
"Mana",
"PierGianLuca Porta",
""
],
[
"Helias",
"Moritz",
""
],
[
"Diesmann",
"Markus",
""
],
[
"Di Napoli",
"Edoardo",
""
]
] | Spiking neuronal networks are usually simulated with three main simulation schemes: the classical time-driven and event-driven schemes, and the more recent hybrid scheme. All three schemes evolve the state of a neuron through a series of checkpoints: equally spaced in the first scheme and determined neuron-wise by spik... |
1512.06305 | Anca Radulescu | Anca Radulescu, Joanna Herron | Ebola impact and quarantine in a network model | 16 pages, 8 figures | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Much effort has been directed towards using mathematical models to understand
and predict contagious disease, in particular Ebola outbreaks. Classical SIR
(susceptible-infected-recovered) compartmental models capture well the dynamics
of the outbreak in certain communities, and accurately describe the differences
bet... | [
{
"created": "Sun, 20 Dec 2015 01:53:36 GMT",
"version": "v1"
}
] | 2015-12-22 | [
[
"Radulescu",
"Anca",
""
],
[
"Herron",
"Joanna",
""
]
] | Much effort has been directed towards using mathematical models to understand and predict contagious disease, in particular Ebola outbreaks. Classical SIR (susceptible-infected-recovered) compartmental models capture well the dynamics of the outbreak in certain communities, and accurately describe the differences betwe... |
1510.07371 | Lior Pachter | Lorian Schaeffer, Harold Pimentel, Nicolas Bray, P\'all Melsted and
Lior Pachter | Pseudoalignment for metagenomic read assignment | Replaced accidentally duplicated figure with correct version; fixed
some issues with figure generation and labeling; fixed problem with some
missing genomes from database; added link to GitHub repo containing analysis
code; included assessment of aggregate sensitivity and precision; clarified
assessment metrics... | null | null | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We explore connections between metagenomic read assignment and the
quantification of transcripts from RNA-Seq data. In particular, we show that
the recent idea of pseudoalignment introduced in the RNA-Seq context is
suitable in the metagenomics setting. When coupled with the
Expectation-Maximization (EM) algorithm, r... | [
{
"created": "Mon, 26 Oct 2015 05:58:58 GMT",
"version": "v1"
},
{
"created": "Tue, 1 Dec 2015 14:14:44 GMT",
"version": "v2"
}
] | 2015-12-02 | [
[
"Schaeffer",
"Lorian",
""
],
[
"Pimentel",
"Harold",
""
],
[
"Bray",
"Nicolas",
""
],
[
"Melsted",
"Páll",
""
],
[
"Pachter",
"Lior",
""
]
] | We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data. In particular, we show that the recent idea of pseudoalignment introduced in the RNA-Seq context is suitable in the metagenomics setting. When coupled with the Expectation-Maximization (EM) algorithm, rea... |
1712.05372 | Fr\'ed\'erique Robin | Fr\'ed\'erique Cl\'ement, Fr\'ed\'erique Robin and Romain Yvinec | Analysis and calibration of a linear model for structured cell
populations with unidirectional motion : Application to the morphogenesis of
ovarian follicles | null | null | null | null | q-bio.PE math.AP math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze a multi-type age dependent model for cell populations subject to
unidirectional motion, in both a stochastic and deterministic framework. Cells
are distributed into successive layers; they may divide and move irreversibly
from one layer to the next. We adapt results on the large-time convergence of
PDE sys... | [
{
"created": "Thu, 14 Dec 2017 18:06:44 GMT",
"version": "v1"
}
] | 2017-12-15 | [
[
"Clément",
"Frédérique",
""
],
[
"Robin",
"Frédérique",
""
],
[
"Yvinec",
"Romain",
""
]
] | We analyze a multi-type age dependent model for cell populations subject to unidirectional motion, in both a stochastic and deterministic framework. Cells are distributed into successive layers; they may divide and move irreversibly from one layer to the next. We adapt results on the large-time convergence of PDE syste... |
q-bio/0310001 | Rodrick Wallace | Rodrick Wallace | Comorbidity and Anticomorbidity: Autocognitive developmental disorders
of structured psychosocial stress | 18 pages, 2 figures | null | null | null | q-bio.NC q-bio.TO | null | We examine interacting cognitive modules of human biology which, in the
asymptotic limit of long sequences of responses, define the output of an
appropriate 'dual' information source. Applying a 'necessary condition'
communication theory formalism roughly similar to that of Dretske, but focused
entirely on long seque... | [
{
"created": "Wed, 1 Oct 2003 17:11:11 GMT",
"version": "v1"
},
{
"created": "Thu, 23 Oct 2003 16:58:40 GMT",
"version": "v2"
},
{
"created": "Fri, 12 Dec 2003 16:15:20 GMT",
"version": "v3"
}
] | 2007-05-23 | [
[
"Wallace",
"Rodrick",
""
]
] | We examine interacting cognitive modules of human biology which, in the asymptotic limit of long sequences of responses, define the output of an appropriate 'dual' information source. Applying a 'necessary condition' communication theory formalism roughly similar to that of Dretske, but focused entirely on long sequenc... |
0804.0696 | Heng Lian | Heng Lian | Inference of genetic networks from time course expression data using
functional regression with lasso penalty | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Statistical inference of genetic regulatory networks is essential for
understanding temporal interactions of regulatory elements inside the cells.
For inferences of large networks, identification of network structure is
typical achieved under the assumption of sparsity of the networks.
When the number of time point... | [
{
"created": "Fri, 4 Apr 2008 11:11:01 GMT",
"version": "v1"
},
{
"created": "Sat, 5 Apr 2008 06:59:27 GMT",
"version": "v2"
}
] | 2008-04-07 | [
[
"Lian",
"Heng",
""
]
] | Statistical inference of genetic regulatory networks is essential for understanding temporal interactions of regulatory elements inside the cells. For inferences of large networks, identification of network structure is typical achieved under the assumption of sparsity of the networks. When the number of time points in... |
2206.12747 | Khaled Mohammed Saifuddin | Khaled Mohammed Saifuddin, Briana Bumgardner, Farhan Tanvir, Esra
Akbas | HyGNN: Drug-Drug Interaction Prediction via Hypergraph Neural Network | Some new experiments have been added. One more dataset has been
considered. Theoretical part has been updated too | null | null | null | q-bio.QM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Drug-Drug Interactions (DDIs) may hamper the functionalities of drugs, and in
the worst scenario, they may lead to adverse drug reactions (ADRs). Predicting
all DDIs is a challenging and critical problem. Most existing computational
models integrate drug-centric information from different sources and leverage
them as... | [
{
"created": "Sat, 25 Jun 2022 22:48:27 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Jul 2022 06:31:25 GMT",
"version": "v2"
},
{
"created": "Fri, 15 Jul 2022 10:14:45 GMT",
"version": "v3"
},
{
"created": "Tue, 18 Apr 2023 09:57:00 GMT",
"version": "v4"
}
] | 2023-04-19 | [
[
"Saifuddin",
"Khaled Mohammed",
""
],
[
"Bumgardner",
"Briana",
""
],
[
"Tanvir",
"Farhan",
""
],
[
"Akbas",
"Esra",
""
]
] | Drug-Drug Interactions (DDIs) may hamper the functionalities of drugs, and in the worst scenario, they may lead to adverse drug reactions (ADRs). Predicting all DDIs is a challenging and critical problem. Most existing computational models integrate drug-centric information from different sources and leverage them as f... |
2202.07751 | Gabriel Ocker | Gabriel Koch Ocker | Dynamics of stochastic integrate-and-fire networks | A previous version of this article, now retracted
(https://journals.aps.org/prx/abstract/10.1103/ PhysRevX.12.041007),
contained errors described in the retraction notice
(https://journals.aps.org/prx/ abstract/10.1103/PhysRevX.13.029904). These
errors have been corrected in the current article, which was re-re... | null | null | null | q-bio.NC cond-mat.dis-nn | http://creativecommons.org/licenses/by/4.0/ | The neural dynamics generating sensory, motor, and cognitive functions are
commonly understood through field theories for neural population activity.
Classic neural field theories are derived from highly simplified models of
individual neurons, while biological neurons are highly complex cells.
Integrate-and-fire neu... | [
{
"created": "Tue, 15 Feb 2022 22:05:07 GMT",
"version": "v1"
},
{
"created": "Wed, 20 Jul 2022 18:49:50 GMT",
"version": "v2"
},
{
"created": "Fri, 29 Jul 2022 16:39:27 GMT",
"version": "v3"
},
{
"created": "Thu, 16 Feb 2023 19:00:39 GMT",
"version": "v4"
},
{
"c... | 2023-11-21 | [
[
"Ocker",
"Gabriel Koch",
""
]
] | The neural dynamics generating sensory, motor, and cognitive functions are commonly understood through field theories for neural population activity. Classic neural field theories are derived from highly simplified models of individual neurons, while biological neurons are highly complex cells. Integrate-and-fire neuro... |
1911.01202 | Michael Plank | Michael J Plank | Asymptotic expansion approximation for spatial structure arising from
directionally biased movement | null | Physica A: Statistical Mechanics and its Applications (2019) | 10.1016/j.physa.2019.123290 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spatial structure can arise in spatial point process models via a range of
mechanisms, including neighbour-dependent directionally biased movement. This
spatial structure is neglected by mean-field models, but can have important
effects on population dynamics. Spatial moment dynamics are one way to obtain a
determini... | [
{
"created": "Tue, 22 Oct 2019 03:07:58 GMT",
"version": "v1"
},
{
"created": "Tue, 5 Nov 2019 01:54:51 GMT",
"version": "v2"
}
] | 2019-11-06 | [
[
"Plank",
"Michael J",
""
]
] | Spatial structure can arise in spatial point process models via a range of mechanisms, including neighbour-dependent directionally biased movement. This spatial structure is neglected by mean-field models, but can have important effects on population dynamics. Spatial moment dynamics are one way to obtain a determinist... |
1903.06375 | Seong Jun Park | Seong Jun Park | Exploiting product molecule number to consider reaction rate fluctuation
in elementary reactions | null | null | 10.1063/5.0091597 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In many chemical reactions, reaction rate fluctuation is inevitable. Reaction
rates are different whenever chemical reaction occurs due to their dependence
on the number of reaction events or the product number. As such, understanding
the impact of rate fluctuation on product number counting statistics is of the
utmo... | [
{
"created": "Fri, 15 Mar 2019 05:53:42 GMT",
"version": "v1"
},
{
"created": "Mon, 18 Mar 2019 09:48:40 GMT",
"version": "v2"
}
] | 2024-06-19 | [
[
"Park",
"Seong Jun",
""
]
] | In many chemical reactions, reaction rate fluctuation is inevitable. Reaction rates are different whenever chemical reaction occurs due to their dependence on the number of reaction events or the product number. As such, understanding the impact of rate fluctuation on product number counting statistics is of the utmost... |
2402.00077 | Yuan Chen | Yuan Chen, Ronglai Shen, Xiwen Feng, Katherine Panageas | Unlocking the Power of Multi-institutional Data: Integrating and
Harmonizing Genomic Data Across Institutions | null | null | null | null | q-bio.GN cs.LG stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cancer is a complex disease driven by genomic alterations, and tumor
sequencing is becoming a mainstay of clinical care for cancer patients. The
emergence of multi-institution sequencing data presents a powerful resource for
learning real-world evidence to enhance precision oncology. GENIE BPC, led by
the American As... | [
{
"created": "Tue, 30 Jan 2024 23:25:05 GMT",
"version": "v1"
}
] | 2024-02-02 | [
[
"Chen",
"Yuan",
""
],
[
"Shen",
"Ronglai",
""
],
[
"Feng",
"Xiwen",
""
],
[
"Panageas",
"Katherine",
""
]
] | Cancer is a complex disease driven by genomic alterations, and tumor sequencing is becoming a mainstay of clinical care for cancer patients. The emergence of multi-institution sequencing data presents a powerful resource for learning real-world evidence to enhance precision oncology. GENIE BPC, led by the American Asso... |
q-bio/0607012 | Michael Deem | Jeong-Man Park and Michael W. Deem | Schwinger Boson Formulation and Solution of the Crow-Kimura and Eigen
Models of Quasispecies Theory | 37 pages; 4 figures; to appear in J. Stat. Phys | null | 10.1007/s10955-006-9190-z | null | q-bio.PE cond-mat.stat-mech | null | We express the Crow-Kimura and Eigen models of quasispecies theory in a
functional integral representation. We formulate the spin coherent state
functional integrals using the Schwinger Boson method. In this formulation, we
are able to deduce the long-time behavior of these models for arbitrary
replication and degrad... | [
{
"created": "Mon, 10 Jul 2006 00:16:41 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Park",
"Jeong-Man",
""
],
[
"Deem",
"Michael W.",
""
]
] | We express the Crow-Kimura and Eigen models of quasispecies theory in a functional integral representation. We formulate the spin coherent state functional integrals using the Schwinger Boson method. In this formulation, we are able to deduce the long-time behavior of these models for arbitrary replication and degradat... |
0801.3963 | Ines Samengo | Germ\'an Mato and In\'es Samengo | Type I and type II neuron models are selectively driven by differential
stimulus features | 25 pages and 9 figures. To appear in Neural Computation | null | null | null | q-bio.NC | null | Neurons in the nervous system exhibit an outstanding variety of morphological
and physiological properties. However, close to threshold, this remarkable
richness may be grouped succinctly into two basic types of excitability, often
referred to as type I and type II. The dynamical traits of these two neuron
types have... | [
{
"created": "Fri, 25 Jan 2008 15:58:52 GMT",
"version": "v1"
}
] | 2008-01-28 | [
[
"Mato",
"Germán",
""
],
[
"Samengo",
"Inés",
""
]
] | Neurons in the nervous system exhibit an outstanding variety of morphological and physiological properties. However, close to threshold, this remarkable richness may be grouped succinctly into two basic types of excitability, often referred to as type I and type II. The dynamical traits of these two neuron types have b... |
1312.3445 | Namiko Mitarai | Filippo Botta and Namiko Mitarai | Disturbance accelerates the transition from low- to high- diversity
state in a model ecosystem | 8 pages, 8 figures. Typos corrected | Phys. Rev. E vol 89, 022704 (2014) | 10.1103/PhysRevE.89.022704 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The effect of disturbance on a model ecosystem of sessile and mutually
competitive species [Mathiesen et al. Phys. Rev. Lett. 107, 188101 (2011);
Mitarai et al. Phys. Rev. E 86, 011929 (2012) ] is studied. The disturbance
stochastically removes individuals from the system, and the created empty sites
are re-colonized... | [
{
"created": "Thu, 12 Dec 2013 11:12:45 GMT",
"version": "v1"
},
{
"created": "Mon, 17 Feb 2014 15:13:34 GMT",
"version": "v2"
}
] | 2015-06-18 | [
[
"Botta",
"Filippo",
""
],
[
"Mitarai",
"Namiko",
""
]
] | The effect of disturbance on a model ecosystem of sessile and mutually competitive species [Mathiesen et al. Phys. Rev. Lett. 107, 188101 (2011); Mitarai et al. Phys. Rev. E 86, 011929 (2012) ] is studied. The disturbance stochastically removes individuals from the system, and the created empty sites are re-colonized b... |
1610.07406 | Seung Ki Baek | Su Do Yi, Seung Ki Baek, and Jung-Kyoo Choi | Combination with anti-tit-for-tat remedies problems of tit-for-tat | 21 pages, 3 figures | J. Theor. Biol. 412, 1 (2017) | 10.1016/j.jtbi.2016.09.017 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One of the most important questions in game theory concerns how mutual
cooperation can be achieved and maintained in a social dilemma. In Axelrod's
tournaments of the iterated prisoner's dilemma, Tit-for-Tat (TFT) demonstrated
the role of reciprocity in the emergence of cooperation. However, the stability
of TFT does... | [
{
"created": "Mon, 24 Oct 2016 13:39:44 GMT",
"version": "v1"
}
] | 2016-10-25 | [
[
"Yi",
"Su Do",
""
],
[
"Baek",
"Seung Ki",
""
],
[
"Choi",
"Jung-Kyoo",
""
]
] | One of the most important questions in game theory concerns how mutual cooperation can be achieved and maintained in a social dilemma. In Axelrod's tournaments of the iterated prisoner's dilemma, Tit-for-Tat (TFT) demonstrated the role of reciprocity in the emergence of cooperation. However, the stability of TFT does n... |
1409.1801 | Stephen Plaza | Stephen M. Plaza, Toufiq Parag, Gary B. Huang, Donald J. Olbris,
Mathew A. Saunders, Patricia K. Rivlin | Annotating Synapses in Large EM Datasets | null | null | null | null | q-bio.QM cs.CV q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reconstructing neuronal circuits at the level of synapses is a central
problem in neuroscience and becoming a focus of the emerging field of
connectomics. To date, electron microscopy (EM) is the most proven technique
for identifying and quantifying synaptic connections. As advances in EM make
acquiring larger datase... | [
{
"created": "Fri, 5 Sep 2014 13:52:47 GMT",
"version": "v1"
},
{
"created": "Thu, 4 Dec 2014 16:18:01 GMT",
"version": "v2"
}
] | 2014-12-05 | [
[
"Plaza",
"Stephen M.",
""
],
[
"Parag",
"Toufiq",
""
],
[
"Huang",
"Gary B.",
""
],
[
"Olbris",
"Donald J.",
""
],
[
"Saunders",
"Mathew A.",
""
],
[
"Rivlin",
"Patricia K.",
""
]
] | Reconstructing neuronal circuits at the level of synapses is a central problem in neuroscience and becoming a focus of the emerging field of connectomics. To date, electron microscopy (EM) is the most proven technique for identifying and quantifying synaptic connections. As advances in EM make acquiring larger datasets... |
q-bio/0511028 | Guillermo Abramson | G. Abramson, L. Giuggioli, V. M. Kenkre, J. W. Dragoo, R. R.
Parmenter, C. A. Parmenter, T. L. Yates | Diffusion and Home Range Parameters for Rodents: Peromyscus maniculatus
in New Mexico | The published paper in Ecol. Complexity has an old version of Figure
6. Here we have put the correct version of Figure 6 | Ecological Complexity 3 (2006) 64-70 | 10.1016/j.ecocom.2005.07.001 | null | q-bio.PE | null | We analyze data from a long term field project in New Mexico, consisting of
repeated sessions of mark-recaptures of Peromyscus maniculatus (Rodentia:
Muridae), the host and reservoir of Sin Nombre Virus (Bunyaviridae:
Hantavirus). The displacements of the recaptured animals provide a means to
study their movement fro... | [
{
"created": "Wed, 16 Nov 2005 12:28:38 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Mar 2006 17:47:13 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Abramson",
"G.",
""
],
[
"Giuggioli",
"L.",
""
],
[
"Kenkre",
"V. M.",
""
],
[
"Dragoo",
"J. W.",
""
],
[
"Parmenter",
"R. R.",
""
],
[
"Parmenter",
"C. A.",
""
],
[
"Yates",
"T. L.",
""
]
] | We analyze data from a long term field project in New Mexico, consisting of repeated sessions of mark-recaptures of Peromyscus maniculatus (Rodentia: Muridae), the host and reservoir of Sin Nombre Virus (Bunyaviridae: Hantavirus). The displacements of the recaptured animals provide a means to study their movement from ... |
q-bio/0312042 | Anders Irb\"ack | Anders Irb\"ack, Fredrik Sjunnesson | Folding thermodynamics of three beta-sheet peptides: A model study | 17 pages, 7 figures, to appear in Proteins | Proteins 56 (2004) 110-116 | null | LU TP 03-40 | q-bio.BM cond-mat.soft | null | We study the folding thermodynamics of a beta-hairpin and two three-stranded
beta-sheet peptides using a simplified sequence-based all-atom model, in which
folding is driven mainly by backbone hydrogen bonding and effective hydrophobic
attraction. The native populations obtained for these three sequences are in
good ... | [
{
"created": "Tue, 30 Dec 2003 20:54:37 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Irbäck",
"Anders",
""
],
[
"Sjunnesson",
"Fredrik",
""
]
] | We study the folding thermodynamics of a beta-hairpin and two three-stranded beta-sheet peptides using a simplified sequence-based all-atom model, in which folding is driven mainly by backbone hydrogen bonding and effective hydrophobic attraction. The native populations obtained for these three sequences are in good ag... |
2009.06577 | Guilherme Innocentini | Guilherme C.P. Innocentini and Arran Hodgkinson and Fernando Antoneli
and Arnaud Debussche and Ovidiu Radulescu | Push-forward method for piecewise deterministic biochemical simulations | arXiv admin note: text overlap with arXiv:1905.00235 | Theoretical Computer Science Volume 893, 21 November 2021, Pages
17-40 | 10.1016/j.tcs.2021.05.025 | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A biochemical network can be simulated by a set of ordinary differential
equations (ODE) under well stirred reactor conditions, for large numbers of
molecules, and frequent reactions. This is no longer a robust representation
when some molecular species are in small numbers and reactions changing them
are infrequent.... | [
{
"created": "Mon, 14 Sep 2020 17:38:15 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Feb 2021 18:22:30 GMT",
"version": "v2"
}
] | 2021-12-17 | [
[
"Innocentini",
"Guilherme C. P.",
""
],
[
"Hodgkinson",
"Arran",
""
],
[
"Antoneli",
"Fernando",
""
],
[
"Debussche",
"Arnaud",
""
],
[
"Radulescu",
"Ovidiu",
""
]
] | A biochemical network can be simulated by a set of ordinary differential equations (ODE) under well stirred reactor conditions, for large numbers of molecules, and frequent reactions. This is no longer a robust representation when some molecular species are in small numbers and reactions changing them are infrequent. I... |
1412.7695 | German Mi\~no Dr | Germ\'an A. Mi\~no-Galaz | Allosteric Communication Pathways and Thermal Rectification in PDZ-2
Protein: A Computational Study | 29 pages, 8 Figures. All Results Unchanged. Changed Title. Improved
Grammar. Added references. Corrected typos. Elimination of the "Knocking"
argument for Asp5-Lys91 Interaction in Results and in Discussion sections | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Allosteric communication in proteins is a central and yet unsolved problem of
structural biochemistry. Previous findings, from computational biology (Ota and
Agard, 2005), have proposed that heat diffuses in a protein through cognate
protein allosteric pathways. This work studied heat diffusion in the well-known
PDZ-... | [
{
"created": "Wed, 24 Dec 2014 15:51:08 GMT",
"version": "v1"
},
{
"created": "Sat, 7 Mar 2015 08:34:58 GMT",
"version": "v2"
}
] | 2015-03-10 | [
[
"Miño-Galaz",
"Germán A.",
""
]
] | Allosteric communication in proteins is a central and yet unsolved problem of structural biochemistry. Previous findings, from computational biology (Ota and Agard, 2005), have proposed that heat diffuses in a protein through cognate protein allosteric pathways. This work studied heat diffusion in the well-known PDZ-2 ... |
1211.5730 | Claus O. Wilke | Stephanie J. Spielman and Claus O. Wilke | Membrane environment imposes unique selection pressures on transmembrane
domains of G protein-coupled receptors | 19 pages, 4 figures, to appear in J. Mol. Evol | null | null | null | q-bio.GN q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have investigated the influence of the plasma membrane environment on the
molecular evolution of G protein-coupled receptors (GPCRs), the largest
receptor family in Metazoa. In particular, we have analyzed the site-specific
rate variation across the two primary structural partitions, transmembrane (TM)
and extrame... | [
{
"created": "Sun, 25 Nov 2012 05:49:47 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Dec 2012 22:15:02 GMT",
"version": "v2"
}
] | 2013-01-01 | [
[
"Spielman",
"Stephanie J.",
""
],
[
"Wilke",
"Claus O.",
""
]
] | We have investigated the influence of the plasma membrane environment on the molecular evolution of G protein-coupled receptors (GPCRs), the largest receptor family in Metazoa. In particular, we have analyzed the site-specific rate variation across the two primary structural partitions, transmembrane (TM) and extramemb... |
2405.04248 | Evie Malaia | Michelle McCleod, Sean Borneman, Evie Malaia | Neurocomputational Phenotypes in Female and Male Autistic Individuals | 10 pages, 2 figures, 4 tables. Submitted to Journal of Science and
Health, University of Alabama | null | null | null | q-bio.NC nlin.CD | http://creativecommons.org/licenses/by/4.0/ | Autism Spectrum Disorder (ASD) is characterized by an altered phenotype in
social interaction and communication. Additionally, autism typically manifests
differently in females as opposed to males: a phenomenon that has likely led to
long-term problems in diagnostics of autism in females. These sex-based
differences ... | [
{
"created": "Tue, 7 May 2024 12:06:12 GMT",
"version": "v1"
}
] | 2024-05-08 | [
[
"McCleod",
"Michelle",
""
],
[
"Borneman",
"Sean",
""
],
[
"Malaia",
"Evie",
""
]
] | Autism Spectrum Disorder (ASD) is characterized by an altered phenotype in social interaction and communication. Additionally, autism typically manifests differently in females as opposed to males: a phenomenon that has likely led to long-term problems in diagnostics of autism in females. These sex-based differences in... |
2007.06975 | Francesco Di Lauro Mr | Francesco Di Lauro, Luc Berthouze, Matthew D. Dorey, Joel C. Miller,
Istv\'an Z. Kiss | The impact of network properties and mixing on control measures and
disease-induced herd immunity in epidemic models: a mean-field model
perspective | 25 pages, 9 figures, 1 Table | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The contact structure of a population plays an important role in transmission
of infection. Many ``structured models'' capture aspects of the contact
structure through an underlying network or a mixing matrix. An important
observation in such models, is that once a fraction $1-1/\mathcal{R}_0$ has
been infected, the ... | [
{
"created": "Tue, 14 Jul 2020 11:26:31 GMT",
"version": "v1"
}
] | 2020-07-15 | [
[
"Di Lauro",
"Francesco",
""
],
[
"Berthouze",
"Luc",
""
],
[
"Dorey",
"Matthew D.",
""
],
[
"Miller",
"Joel C.",
""
],
[
"Kiss",
"István Z.",
""
]
] | The contact structure of a population plays an important role in transmission of infection. Many ``structured models'' capture aspects of the contact structure through an underlying network or a mixing matrix. An important observation in such models, is that once a fraction $1-1/\mathcal{R}_0$ has been infected, the re... |
1107.2879 | Mariano Beguerisse D\'iaz | Mariano Beguerisse-Diaz, Baojun Wang, Radhika Desikan, Mauricio
Barahona | Squeeze-and-Breathe Evolutionary Monte Carlo Optimisation with Local
Search Acceleration and its application to parameter fitting | 15 Pages, 3 Figures, 6 Tables; Availability: Matlab code available
from the authors upon request | null | null | null | q-bio.QM cs.SY math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Estimating parameters from data is a key stage of the modelling
process, particularly in biological systems where many parameters need to be
estimated from sparse and noisy data sets. Over the years, a variety of
heuristics have been proposed to solve this complex optimisation problem, with
good results i... | [
{
"created": "Thu, 14 Jul 2011 17:52:39 GMT",
"version": "v1"
},
{
"created": "Sun, 23 Oct 2011 15:10:58 GMT",
"version": "v2"
},
{
"created": "Fri, 4 Nov 2011 17:08:36 GMT",
"version": "v3"
}
] | 2011-11-07 | [
[
"Beguerisse-Diaz",
"Mariano",
""
],
[
"Wang",
"Baojun",
""
],
[
"Desikan",
"Radhika",
""
],
[
"Barahona",
"Mauricio",
""
]
] | Motivation: Estimating parameters from data is a key stage of the modelling process, particularly in biological systems where many parameters need to be estimated from sparse and noisy data sets. Over the years, a variety of heuristics have been proposed to solve this complex optimisation problem, with good results in ... |
2309.03194 | James Malkin Mr | James Malkin, Cian O'Donnell, Conor Houghton, Laurence Aitchison | Signatures of Bayesian inference emerge from energy efficient synapses | 29 pages, 11 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Biological synaptic transmission is unreliable, and this unreliability likely
degrades neural circuit performance. While there are biophysical mechanisms
that can increase reliability, for instance by increasing vesicle release
probability, these mechanisms cost energy. We examined four such mechanisms
along with the... | [
{
"created": "Wed, 6 Sep 2023 17:57:07 GMT",
"version": "v1"
},
{
"created": "Sat, 23 Mar 2024 01:42:32 GMT",
"version": "v2"
},
{
"created": "Fri, 21 Jun 2024 09:14:57 GMT",
"version": "v3"
},
{
"created": "Mon, 1 Jul 2024 11:30:59 GMT",
"version": "v4"
}
] | 2024-07-02 | [
[
"Malkin",
"James",
""
],
[
"O'Donnell",
"Cian",
""
],
[
"Houghton",
"Conor",
""
],
[
"Aitchison",
"Laurence",
""
]
] | Biological synaptic transmission is unreliable, and this unreliability likely degrades neural circuit performance. While there are biophysical mechanisms that can increase reliability, for instance by increasing vesicle release probability, these mechanisms cost energy. We examined four such mechanisms along with the a... |
1705.07856 | James O'Dwyer | James P. O'Dwyer and Stephen J. Cornell | Cross-scale ecological theory sheds light on the maintenance of
biodiversity | 31 pages 3 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One of the first successes of neutral ecology was to predict
realistically-broad distributions of rare and abundant species. However, it has
remained an outstanding theoretical challenge to describe how this distribution
of abundances changes with spatial scale, and this gap has hampered attempts to
use observed spec... | [
{
"created": "Mon, 22 May 2017 17:00:42 GMT",
"version": "v1"
},
{
"created": "Wed, 7 Jun 2017 17:09:52 GMT",
"version": "v2"
},
{
"created": "Mon, 16 Jul 2018 19:48:48 GMT",
"version": "v3"
}
] | 2018-07-18 | [
[
"O'Dwyer",
"James P.",
""
],
[
"Cornell",
"Stephen J.",
""
]
] | One of the first successes of neutral ecology was to predict realistically-broad distributions of rare and abundant species. However, it has remained an outstanding theoretical challenge to describe how this distribution of abundances changes with spatial scale, and this gap has hampered attempts to use observed specie... |
1604.02399 | Matthew Tudor | Tracey Filzen, Peter Kutchukian, Jeffrey Hermes, Jing Li, Matthew
Tudor | Representing high throughput expression profiles via perturbation
barcodes reveals compound targets | 19 pages, 3 figures, 2 tables, 2 supplementary figures | null | 10.1371/journal.pcbi.1005335 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | High throughput mRNA expression profiling can be used to characterize the
response of cell culture models to perturbations such as pharmacologic
modulators and genetic perturbations. As profiling campaigns expand in scope,
it is important to homogenize, summarize, and analyze the resulting data in a
manner that captu... | [
{
"created": "Fri, 8 Apr 2016 16:53:19 GMT",
"version": "v1"
}
] | 2017-04-12 | [
[
"Filzen",
"Tracey",
""
],
[
"Kutchukian",
"Peter",
""
],
[
"Hermes",
"Jeffrey",
""
],
[
"Li",
"Jing",
""
],
[
"Tudor",
"Matthew",
""
]
] | High throughput mRNA expression profiling can be used to characterize the response of cell culture models to perturbations such as pharmacologic modulators and genetic perturbations. As profiling campaigns expand in scope, it is important to homogenize, summarize, and analyze the resulting data in a manner that capture... |
2102.10994 | Yurui Ming | Yurui Ming | Coherence of Working Memory Study Between Deep Neural Network and
Neurophysiology | null | null | null | null | q-bio.NC cs.LG cs.NE eess.SP | http://creativecommons.org/licenses/by/4.0/ | The auto feature extraction capability of deep neural networks (DNN) endows
them the potentiality for analysing complicated electroencephalogram (EEG) data
captured from brain functionality research. This work investigates the
potential coherent correspondence between the region-of-interest (ROI) for DNN
to explore, ... | [
{
"created": "Sat, 6 Feb 2021 09:09:57 GMT",
"version": "v1"
}
] | 2021-02-23 | [
[
"Ming",
"Yurui",
""
]
] | The auto feature extraction capability of deep neural networks (DNN) endows them the potentiality for analysing complicated electroencephalogram (EEG) data captured from brain functionality research. This work investigates the potential coherent correspondence between the region-of-interest (ROI) for DNN to explore, an... |
1901.09975 | Farouk Nathoo | Yunlong Nie, Eugene Opoku, Laila Yasmin, Yin Song, Jie Wang, Sidi Wu,
Vanessa Scarapicchia, Jodie Gawryluk, Liangliang Wang, Jiguo Cao, Farouk S.
Nathoo | Spectral Dynamic Causal Modelling of Resting-State fMRI: Relating
Effective Brain Connectivity in the Default Mode Network to Genetics | null | null | null | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We conduct an imaging genetics study to explore how effective brain
connectivity in the default mode network (DMN) may be related to genetics
within the context of Alzheimer's disease and mild cognitive impairment. We
develop an analysis of longitudinal resting-state functional magnetic resonance
imaging (rs-fMRI) an... | [
{
"created": "Mon, 28 Jan 2019 19:58:32 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Jan 2019 21:14:29 GMT",
"version": "v2"
},
{
"created": "Sat, 4 May 2019 03:33:14 GMT",
"version": "v3"
},
{
"created": "Wed, 8 May 2019 18:39:55 GMT",
"version": "v4"
},
{
"cre... | 2020-06-03 | [
[
"Nie",
"Yunlong",
""
],
[
"Opoku",
"Eugene",
""
],
[
"Yasmin",
"Laila",
""
],
[
"Song",
"Yin",
""
],
[
"Wang",
"Jie",
""
],
[
"Wu",
"Sidi",
""
],
[
"Scarapicchia",
"Vanessa",
""
],
[
"Gawryluk",
... | We conduct an imaging genetics study to explore how effective brain connectivity in the default mode network (DMN) may be related to genetics within the context of Alzheimer's disease and mild cognitive impairment. We develop an analysis of longitudinal resting-state functional magnetic resonance imaging (rs-fMRI) and ... |
2006.03915 | Damian Knopoff | Nicola Bellomo, Richard Bingham, Mark A.J. Chaplain, Giovanni Dosi,
Guido Forni, Damian A. Knopoff, John Lowengrub, Reidun Twarock and Maria
Enrica Virgillito | A multi-scale model of virus pandemic: Heterogeneous interactive
entities in a globally connected world | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper is devoted to the multidisciplinary modelling of a pandemic
initiated by an aggressive virus, specifically the so-called
\textit{SARS--CoV--2 Severe Acute Respiratory Syndrome, corona virus n.2}. The
study is developed within a multiscale framework accounting for the interaction
of different spatial scales... | [
{
"created": "Sat, 6 Jun 2020 16:45:59 GMT",
"version": "v1"
}
] | 2020-06-09 | [
[
"Bellomo",
"Nicola",
""
],
[
"Bingham",
"Richard",
""
],
[
"Chaplain",
"Mark A. J.",
""
],
[
"Dosi",
"Giovanni",
""
],
[
"Forni",
"Guido",
""
],
[
"Knopoff",
"Damian A.",
""
],
[
"Lowengrub",
"John",
""
]... | This paper is devoted to the multidisciplinary modelling of a pandemic initiated by an aggressive virus, specifically the so-called \textit{SARS--CoV--2 Severe Acute Respiratory Syndrome, corona virus n.2}. The study is developed within a multiscale framework accounting for the interaction of different spatial scales, ... |
1905.05030 | Daniele Proverbio | Daniele Proverbio and Marco Maggiora | Dynamical strategies for obstacle avoidance during Dictyostelium
discoideum aggregation: a Multi-agent system model | null | null | null | null | q-bio.CB nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chemotaxis, the movement of an organism in response to chemical stimuli, is a
typical feature of many microbiological systems. In particular, the social
amoeba \textit{Disctyostelium discoideum} is widely used as a model organism,
but it is not still clear how it behaves in heterogeneous environments. A few
models fo... | [
{
"created": "Mon, 13 May 2019 13:35:27 GMT",
"version": "v1"
},
{
"created": "Tue, 14 May 2019 07:03:58 GMT",
"version": "v2"
},
{
"created": "Mon, 16 Dec 2019 08:37:49 GMT",
"version": "v3"
}
] | 2019-12-17 | [
[
"Proverbio",
"Daniele",
""
],
[
"Maggiora",
"Marco",
""
]
] | Chemotaxis, the movement of an organism in response to chemical stimuli, is a typical feature of many microbiological systems. In particular, the social amoeba \textit{Disctyostelium discoideum} is widely used as a model organism, but it is not still clear how it behaves in heterogeneous environments. A few models focu... |
2008.05612 | Steph Owen MPhys | S. Owen | GPU accelerated enumeration and exploration of HP model
genotype-phenotype maps for protein folding | 25 pages, 20 figures | null | null | null | q-bio.BM physics.bio-ph q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Evolution can be broadly described in terms of mutations of the genotype and
the subsequent selection of the phenotype. The full enumeration of a given
genotype-phenotype (GP) map is therefore a powerful technique in examining
evolutionary landscapes. However, because the number of genotypes typically
grows exponenti... | [
{
"created": "Sat, 1 Aug 2020 22:59:48 GMT",
"version": "v1"
},
{
"created": "Fri, 27 Nov 2020 16:16:18 GMT",
"version": "v2"
}
] | 2020-11-30 | [
[
"Owen",
"S.",
""
]
] | Evolution can be broadly described in terms of mutations of the genotype and the subsequent selection of the phenotype. The full enumeration of a given genotype-phenotype (GP) map is therefore a powerful technique in examining evolutionary landscapes. However, because the number of genotypes typically grows exponential... |
1307.3329 | Ryan Solava | Ryan W. Solava and Tijana Milenkovi\'c | Revealing missing parts of the interactome | 16 pages, 3 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein interaction networks (PINs) are often used to "learn" new biological
function from their topology. Since current PINs are noisy, their computational
de-noising via link prediction (LP) could improve the learning accuracy. LP
uses the existing PIN topology to predict missing and spurious links. Many of
existin... | [
{
"created": "Fri, 12 Jul 2013 05:25:07 GMT",
"version": "v1"
}
] | 2013-07-15 | [
[
"Solava",
"Ryan W.",
""
],
[
"Milenković",
"Tijana",
""
]
] | Protein interaction networks (PINs) are often used to "learn" new biological function from their topology. Since current PINs are noisy, their computational de-noising via link prediction (LP) could improve the learning accuracy. LP uses the existing PIN topology to predict missing and spurious links. Many of existing ... |
1309.2382 | Benjamin Torben-Nielsen | Willem A.M. Wybo, Klaus M. Stiefel, Benjamin Torben-Nielsen | The Green's function formalism as a bridge between single and
multi-compartmental modeling | 16 pages, 2 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neurons are spatially extended structures that receive and process inputs on
their dendrites. It is generally accepted that neuronal computations arise from
the active integration of synaptic inputs along a dendrite between the input
location and the location of spike generation in the axon initial segment.
However, ... | [
{
"created": "Tue, 10 Sep 2013 06:10:42 GMT",
"version": "v1"
}
] | 2013-09-11 | [
[
"Wybo",
"Willem A. M.",
""
],
[
"Stiefel",
"Klaus M.",
""
],
[
"Torben-Nielsen",
"Benjamin",
""
]
] | Neurons are spatially extended structures that receive and process inputs on their dendrites. It is generally accepted that neuronal computations arise from the active integration of synaptic inputs along a dendrite between the input location and the location of spike generation in the axon initial segment. However, ma... |
q-bio/0408027 | Morten Kloster | Morten Kloster | Analysis of evolution through competitive selection | 12 pages, 10 figures | null | 10.1103/PhysRevLett.95.168701 | null | q-bio.PE physics.bio-ph | null | Recent studies of in vitro evolution of DNA via protein binding indicate that
the evolution behavior is qualitatively different in different parameter
regimes. I here present a general theory that is valid for a wide range of
parameters, and which reproduces and extends previous results. Specifically,
the mean-field ... | [
{
"created": "Mon, 30 Aug 2004 21:07:49 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Kloster",
"Morten",
""
]
] | Recent studies of in vitro evolution of DNA via protein binding indicate that the evolution behavior is qualitatively different in different parameter regimes. I here present a general theory that is valid for a wide range of parameters, and which reproduces and extends previous results. Specifically, the mean-field th... |
2006.05665 | Benjamin Ambrosio | Benjamin Ambrosio, M.A. Aziz-Alaoui | On a coupled time-dependent SIR models fitting with New York and
New-Jersey states COVID-19 data | null | null | 10.20944/preprints202006.0068.v1 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This article describes a simple Susceptible Infected Recovered (SIR) model
fitting with COVID-19 data for the month of march 2020 in New York (NY) state.
The model is a classical SIR, but is non-autonomous; the rate of susceptible
people becoming infected is adjusted over time in order to fit the available
data. The ... | [
{
"created": "Wed, 10 Jun 2020 05:45:44 GMT",
"version": "v1"
}
] | 2020-06-11 | [
[
"Ambrosio",
"Benjamin",
""
],
[
"Aziz-Alaoui",
"M. A.",
""
]
] | This article describes a simple Susceptible Infected Recovered (SIR) model fitting with COVID-19 data for the month of march 2020 in New York (NY) state. The model is a classical SIR, but is non-autonomous; the rate of susceptible people becoming infected is adjusted over time in order to fit the available data. The de... |
2206.04989 | Gopikrishnan Chirappurathu Remesan | Gopikrishnan C. Remesan and Jennifer A Flegg and Helen M Byrne | Two-phase model of compressive stress induced on a surrounding
hyperelastic medium by an expanding tumour | 26 pages, 7 figures | null | null | null | q-bio.TO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | \emph{In vitro} experiments in which tumour cells are seeded in a gelatinous
medium, or hydrogel, show how mechanical interactions between tumour cells and
the tissue in which they are embedded, together with local levels of an
externally-supplied, diffusible nutrient (e.g., oxygen), affect the tumour's
growth dynami... | [
{
"created": "Fri, 10 Jun 2022 10:52:00 GMT",
"version": "v1"
}
] | 2022-06-13 | [
[
"Remesan",
"Gopikrishnan C.",
""
],
[
"Flegg",
"Jennifer A",
""
],
[
"Byrne",
"Helen M",
""
]
] | \emph{In vitro} experiments in which tumour cells are seeded in a gelatinous medium, or hydrogel, show how mechanical interactions between tumour cells and the tissue in which they are embedded, together with local levels of an externally-supplied, diffusible nutrient (e.g., oxygen), affect the tumour's growth dynamics... |
1206.0858 | Jin Yang | Jin Yang and John E. Pearson | Origins of concentration dependence of waiting times for single-molecule
fluorescence binding | 11 pages, 4 figures; J. Chem. Phys., 137, 2012 | null | 10.1063/1.4729947 | null | q-bio.QM physics.bio-ph q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Binary fluorescence time series obtained from single-molecule imaging
experiments can be used to infer protein binding kinetics, in particular,
association and dissociation rate constants from waiting time statistics of
fluorescence intensity changes. In many cases, rate constants inferred from
fluorescence time seri... | [
{
"created": "Tue, 5 Jun 2012 09:40:15 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Jun 2012 13:46:16 GMT",
"version": "v2"
}
] | 2012-06-15 | [
[
"Yang",
"Jin",
""
],
[
"Pearson",
"John E.",
""
]
] | Binary fluorescence time series obtained from single-molecule imaging experiments can be used to infer protein binding kinetics, in particular, association and dissociation rate constants from waiting time statistics of fluorescence intensity changes. In many cases, rate constants inferred from fluorescence time series... |
1310.3185 | Filipe Tostevin | Alexander Buchner, Filipe Tostevin, Florian Hinzpeter, Ulrich Gerland | Optimization of collective enzyme activity via spatial localization | 12 pages, 9 figures + 5 pages supplementary material | J. Chem. Phys. 139, 135101 (2013) | 10.1063/1.4823504 | null | q-bio.SC q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The spatial organization of enzymes often plays a crucial role in the
functionality and efficiency of enzymatic pathways. To fully understand the
design and operation of enzymatic pathways, it is therefore crucial to
understand how the relative arrangement of enzymes affects pathway function.
Here we investigate the ... | [
{
"created": "Fri, 11 Oct 2013 16:15:30 GMT",
"version": "v1"
}
] | 2015-06-17 | [
[
"Buchner",
"Alexander",
""
],
[
"Tostevin",
"Filipe",
""
],
[
"Hinzpeter",
"Florian",
""
],
[
"Gerland",
"Ulrich",
""
]
] | The spatial organization of enzymes often plays a crucial role in the functionality and efficiency of enzymatic pathways. To fully understand the design and operation of enzymatic pathways, it is therefore crucial to understand how the relative arrangement of enzymes affects pathway function. Here we investigate the ef... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.