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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2310.00067 | Diego Ferreiro | Ignacio E. S\'anchez, Ezequiel A. Galpern, Diego U. Ferreiro | Solvent constraints for biopolymer folding and evolution in
extraterrestrial environments | 25 pages, 6 figures | null | null | null | q-bio.BM astro-ph.EP | http://creativecommons.org/licenses/by-nc-sa/4.0/ | We propose that spontaneous folding and molecular evolution of biopolymers
are two universal aspects that must concur for life to happen. These aspects
are fundamentally related to the chemical composition of biopolymers and
crucially depend on the solvent in which they are embedded. We show that
molecular informatio... | [
{
"created": "Fri, 29 Sep 2023 18:18:18 GMT",
"version": "v1"
}
] | 2023-10-03 | [
[
"Sánchez",
"Ignacio E.",
""
],
[
"Galpern",
"Ezequiel A.",
""
],
[
"Ferreiro",
"Diego U.",
""
]
] | We propose that spontaneous folding and molecular evolution of biopolymers are two universal aspects that must concur for life to happen. These aspects are fundamentally related to the chemical composition of biopolymers and crucially depend on the solvent in which they are embedded. We show that molecular information ... |
2208.07653 | R. C. Penner | Robert Penner | Protein Geometry, Function and Mutation | 18 pages, 4 figures | null | null | null | q-bio.BM math.GT | http://creativecommons.org/licenses/by-nc-nd/4.0/ | This survey for mathematicians summarizes several works by the author on
protein geometry and protein function with applications to viral glycoproteins
in general and the spike glycoprotein of the SARS-CoV-2 virus in particular.
Background biology and biophysics are sketched. This body of work culminates in
a postula... | [
{
"created": "Tue, 16 Aug 2022 10:27:00 GMT",
"version": "v1"
},
{
"created": "Thu, 18 Aug 2022 09:31:22 GMT",
"version": "v2"
}
] | 2022-08-19 | [
[
"Penner",
"Robert",
""
]
] | This survey for mathematicians summarizes several works by the author on protein geometry and protein function with applications to viral glycoproteins in general and the spike glycoprotein of the SARS-CoV-2 virus in particular. Background biology and biophysics are sketched. This body of work culminates in a postulate... |
1302.2710 | Ryan Hernandez | M. Cyrus Maher, Lawrence H. Uricchio, Dara G. Torgerson, Ryan D.
Hernandez | Population Genetics of Rare Variants and Complex Diseases | 36 pages, 7 figures | Hum Hered 2012;74:118-128 | 10.1159/000346826 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Identifying drivers of complex traits from the noisy signals of genetic
variation obtained from high throughput genome sequencing technologies is a
central challenge faced by human geneticists today. We hypothesize that the
variants involved in complex diseases are likely to exhibit non-neutral
evolutionary signature... | [
{
"created": "Tue, 12 Feb 2013 06:16:04 GMT",
"version": "v1"
}
] | 2013-06-18 | [
[
"Maher",
"M. Cyrus",
""
],
[
"Uricchio",
"Lawrence H.",
""
],
[
"Torgerson",
"Dara G.",
""
],
[
"Hernandez",
"Ryan D.",
""
]
] | Identifying drivers of complex traits from the noisy signals of genetic variation obtained from high throughput genome sequencing technologies is a central challenge faced by human geneticists today. We hypothesize that the variants involved in complex diseases are likely to exhibit non-neutral evolutionary signatures.... |
1311.6864 | Eftychios A. Pnevmatikakis | Eftychios A. Pnevmatikakis, Josh Merel, Ari Pakman, Liam Paninski | Bayesian spike inference from calcium imaging data | null | null | null | null | q-bio.NC q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present efficient Bayesian methods for extracting neuronal spiking
information from calcium imaging data. The goal of our methods is to sample
from the posterior distribution of spike trains and model parameters (baseline
concentration, spike amplitude etc) given noisy calcium imaging data. We
present discrete tim... | [
{
"created": "Wed, 27 Nov 2013 03:59:13 GMT",
"version": "v1"
}
] | 2013-11-28 | [
[
"Pnevmatikakis",
"Eftychios A.",
""
],
[
"Merel",
"Josh",
""
],
[
"Pakman",
"Ari",
""
],
[
"Paninski",
"Liam",
""
]
] | We present efficient Bayesian methods for extracting neuronal spiking information from calcium imaging data. The goal of our methods is to sample from the posterior distribution of spike trains and model parameters (baseline concentration, spike amplitude etc) given noisy calcium imaging data. We present discrete time ... |
2311.00392 | Cornelis Klop | Cornelis Klop, Ruud Schreurs, Guido A De Jong, Edwin TM Klinkenberg,
Valeria Vespasiano, Naomi L Rood, Valerie G Niehe, Vidija Soerdjbalie-Maikoe,
Alexia Van Goethem, Bernadette S De Bakker, Thomas JJ Maal, Jitske W Nolte,
Alfred G Becking | An open-source, three-dimensional growth model of the mandible | null | null | 10.1016/j.compbiomed.2024.108455 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The available reference data for the mandible and mandibular growth consists
primarily of two-dimensional linear or angular measurements. The aim of this
study was to create the first open-source, three-dimensional statistical shape
model of the mandible that spans the complete growth period. Computed
tomography scan... | [
{
"created": "Wed, 1 Nov 2023 09:38:05 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Nov 2023 08:50:43 GMT",
"version": "v2"
}
] | 2024-04-17 | [
[
"Klop",
"Cornelis",
""
],
[
"Schreurs",
"Ruud",
""
],
[
"De Jong",
"Guido A",
""
],
[
"Klinkenberg",
"Edwin TM",
""
],
[
"Vespasiano",
"Valeria",
""
],
[
"Rood",
"Naomi L",
""
],
[
"Niehe",
"Valerie G",
""
... | The available reference data for the mandible and mandibular growth consists primarily of two-dimensional linear or angular measurements. The aim of this study was to create the first open-source, three-dimensional statistical shape model of the mandible that spans the complete growth period. Computed tomography scans ... |
1609.01790 | Danielle Bassett | Marcelo G. Mattar and Danielle S. Bassett | Brain Network Architecture: Implications for Human Learning | 9 pages, 5 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Human learning is a complex phenomenon that requires adaptive processes
across a range of temporal and spacial scales. While our understanding of those
processes at single scales has increased exponentially over the last few years,
a mechanistic understanding of the entire phenomenon has remained elusive. We
propose ... | [
{
"created": "Wed, 7 Sep 2016 00:22:40 GMT",
"version": "v1"
}
] | 2016-09-08 | [
[
"Mattar",
"Marcelo G.",
""
],
[
"Bassett",
"Danielle S.",
""
]
] | Human learning is a complex phenomenon that requires adaptive processes across a range of temporal and spacial scales. While our understanding of those processes at single scales has increased exponentially over the last few years, a mechanistic understanding of the entire phenomenon has remained elusive. We propose th... |
2304.07615 | David D. Reid | Zily Burstein, David D. Reid, Peter J. Thomas, and Jack D. Cowan | Pattern Forming Mechanisms of Color Vision | 21 pages, 15 figures | null | 10.1162/netn_a_00294 | null | q-bio.NC physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | While our understanding of the way single neurons process chromatic stimuli
in the early visual pathway has advanced significantly in recent years, we do
not yet know how these cells interact to form stable representations of hue.
Drawing on physiological studies, we offer a dynamical model of how the primary
visual ... | [
{
"created": "Sat, 15 Apr 2023 18:51:57 GMT",
"version": "v1"
}
] | 2023-04-18 | [
[
"Burstein",
"Zily",
""
],
[
"Reid",
"David D.",
""
],
[
"Thomas",
"Peter J.",
""
],
[
"Cowan",
"Jack D.",
""
]
] | While our understanding of the way single neurons process chromatic stimuli in the early visual pathway has advanced significantly in recent years, we do not yet know how these cells interact to form stable representations of hue. Drawing on physiological studies, we offer a dynamical model of how the primary visual co... |
1511.00964 | Markus Goldhacker | Markus Goldhacker, Ana Maria Tom\'e, Mark W. Greenlee, Elmar W. Lang | Frequency-resolved dynamic functional connectivity and scale-invariant
connectivity-state behavior | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Investigating temporal variability of functional connectivity is an emerging
field in connectomics. Entering dynamic functional connectivity by applying
sliding window techniques on resting-state fMRI (rs-fMRI) time courses emerged
from this topic. We introduce frequency-resolved dynamic functional
connectivity (frdF... | [
{
"created": "Tue, 3 Nov 2015 16:11:58 GMT",
"version": "v1"
}
] | 2015-11-04 | [
[
"Goldhacker",
"Markus",
""
],
[
"Tomé",
"Ana Maria",
""
],
[
"Greenlee",
"Mark W.",
""
],
[
"Lang",
"Elmar W.",
""
]
] | Investigating temporal variability of functional connectivity is an emerging field in connectomics. Entering dynamic functional connectivity by applying sliding window techniques on resting-state fMRI (rs-fMRI) time courses emerged from this topic. We introduce frequency-resolved dynamic functional connectivity (frdFC)... |
2301.00673 | Jean-Luc Boulnois | Jean-Luc Boulnois | Predator-Prey Linear Coupling with Hybrid Species | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The classical two-species non-linear Predator-Prey system, often used in
population dynamics modeling, is expressed in terms of a single positive
coupling parameter $\lambda$. Based on standard logarithmic transformations, we
derive a novel $\lambda$-\textit{invariant} Hamiltonian resulting in two
coupled first-order... | [
{
"created": "Thu, 29 Dec 2022 16:28:14 GMT",
"version": "v1"
}
] | 2023-01-03 | [
[
"Boulnois",
"Jean-Luc",
""
]
] | The classical two-species non-linear Predator-Prey system, often used in population dynamics modeling, is expressed in terms of a single positive coupling parameter $\lambda$. Based on standard logarithmic transformations, we derive a novel $\lambda$-\textit{invariant} Hamiltonian resulting in two coupled first-order O... |
1010.2105 | Philipp Altrock | Bin Wu, Philipp M. Altrock, Long Wang and Arne Traulsen | Universality of weak selection | 12 pages, 3 figures, accepted for publication in Physical Review E | Physical Review E 82, 046106 (2010) | 10.1103/PhysRevE.82.046106 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Weak selection, which means a phenotype is slightly advantageous over
another, is an important limiting case in evolutionary biology. Recently it has
been introduced into evolutionary game theory. In evolutionary game dynamics,
the probability to be imitated or to reproduce depends on the performance in a
game. The i... | [
{
"created": "Mon, 11 Oct 2010 13:51:44 GMT",
"version": "v1"
}
] | 2010-10-15 | [
[
"Wu",
"Bin",
""
],
[
"Altrock",
"Philipp M.",
""
],
[
"Wang",
"Long",
""
],
[
"Traulsen",
"Arne",
""
]
] | Weak selection, which means a phenotype is slightly advantageous over another, is an important limiting case in evolutionary biology. Recently it has been introduced into evolutionary game theory. In evolutionary game dynamics, the probability to be imitated or to reproduce depends on the performance in a game. The inf... |
1309.7546 | Liaofu Luo | Liaofu Luo | A Quantum Model on Chemically-Physically Induced Pluripotency in Stem
Cells | 3 figures and related discussions added in the revision, results
unchanged | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A quantum model on the chemically and physically induced pluripotency in stem
cells is proposed. Based on the conformational Hamiltonian and the idea of slow
variables (molecular torsions) slaving fast ones the conversion from the
differentiate state to pluripotent state is defined as the quantum transition
between c... | [
{
"created": "Sun, 29 Sep 2013 07:07:32 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Apr 2014 07:20:25 GMT",
"version": "v2"
},
{
"created": "Wed, 31 Dec 2014 02:51:30 GMT",
"version": "v3"
},
{
"created": "Mon, 5 Jan 2015 06:58:24 GMT",
"version": "v4"
},
{
"cre... | 2015-01-07 | [
[
"Luo",
"Liaofu",
""
]
] | A quantum model on the chemically and physically induced pluripotency in stem cells is proposed. Based on the conformational Hamiltonian and the idea of slow variables (molecular torsions) slaving fast ones the conversion from the differentiate state to pluripotent state is defined as the quantum transition between con... |
2105.01428 | Vito Dichio | Vito Dichio, Hong-Li Zeng and Erik Aurell | Statistical Genetics in and out of Quasi-Linkage Equilibrium (Extended) | 58 pages, 13 figures | 2023 Rep. Prog. Phys. 86 052601 | 10.1088/1361-6633/acc5fa | null | q-bio.PE cond-mat.dis-nn physics.bio-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | This review is about statistical genetics, an interdisciplinary topic between
statistical physics and population biology. The focus is on the phase of
quasi-linkage equilibrium (QLE). Our goals here are to clarify under which
conditions the QLE phase can be expected to hold in population biology and how
the stability... | [
{
"created": "Tue, 4 May 2021 11:34:27 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Mar 2022 15:06:39 GMT",
"version": "v2"
},
{
"created": "Thu, 10 Mar 2022 09:26:29 GMT",
"version": "v3"
},
{
"created": "Fri, 30 Sep 2022 14:10:34 GMT",
"version": "v4"
},
{
"cre... | 2023-04-07 | [
[
"Dichio",
"Vito",
""
],
[
"Zeng",
"Hong-Li",
""
],
[
"Aurell",
"Erik",
""
]
] | This review is about statistical genetics, an interdisciplinary topic between statistical physics and population biology. The focus is on the phase of quasi-linkage equilibrium (QLE). Our goals here are to clarify under which conditions the QLE phase can be expected to hold in population biology and how the stability o... |
1104.4524 | Jinzhi Lei JL | Jinzhi Lei | Stochastic Modeling in Systems Biology | 25 pages, 4 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many cellular behaviors are regulated by gene regulation networks, kinetics
of which is one of the main subjects in the study of systems biology. Because
of the low number molecules in these reacting systems, stochastic effects are
significant. In recent years, stochasticity in modeling the kinetics of gene
regulatio... | [
{
"created": "Sat, 23 Apr 2011 01:41:18 GMT",
"version": "v1"
}
] | 2011-04-26 | [
[
"Lei",
"Jinzhi",
""
]
] | Many cellular behaviors are regulated by gene regulation networks, kinetics of which is one of the main subjects in the study of systems biology. Because of the low number molecules in these reacting systems, stochastic effects are significant. In recent years, stochasticity in modeling the kinetics of gene regulation ... |
1510.04107 | F. Cecconi | Patrizio Ansalone and Mauro Chinappi and Lamberto Rondoni and Fabio
Cecconi | Driven diffusion against electrostatic or effective energy barrier
across Alpha-Hemolysin | RevTeX 4-1, 11 pages, 6 pdf figures, J. Chem. Phys. 2015 in press | null | null | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze the translocation of a charged particle across an Alpha-Hemolysin
(aHL) pore in the framework of a driven diffusion over an extended energy
barrier generated by the electrical charges of the aHL. A one-dimensional
electrostatic potential is extracted from the full 3D solution of the Poisson's
equation. We ... | [
{
"created": "Wed, 14 Oct 2015 14:14:59 GMT",
"version": "v1"
}
] | 2015-10-15 | [
[
"Ansalone",
"Patrizio",
""
],
[
"Chinappi",
"Mauro",
""
],
[
"Rondoni",
"Lamberto",
""
],
[
"Cecconi",
"Fabio",
""
]
] | We analyze the translocation of a charged particle across an Alpha-Hemolysin (aHL) pore in the framework of a driven diffusion over an extended energy barrier generated by the electrical charges of the aHL. A one-dimensional electrostatic potential is extracted from the full 3D solution of the Poisson's equation. We ch... |
1206.0094 | Peter Csermely | David M. Gyurko, Csaba Soti, Attila Stetak and Peter Csermely | System level mechanisms of adaptation, learning, memory formation and
evolvability: the role of chaperone and other networks | 19 pages, 2 Figures, 1 Table, 173 references | Current Protein and Peptide Science (2014) 15: 171-188 | 10.2174/1389203715666140331110522 | null | q-bio.MN physics.bio-ph q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During the last decade, network approaches became a powerful tool to describe
protein structure and dynamics. Here, we describe first the protein structure
networks of molecular chaperones, then characterize chaperone containing
sub-networks of interactomes called as chaperone-networks or chaperomes. We
review the ro... | [
{
"created": "Fri, 1 Jun 2012 06:34:03 GMT",
"version": "v1"
},
{
"created": "Sun, 9 Jun 2013 15:16:38 GMT",
"version": "v2"
},
{
"created": "Fri, 25 Apr 2014 10:32:43 GMT",
"version": "v3"
}
] | 2014-04-28 | [
[
"Gyurko",
"David M.",
""
],
[
"Soti",
"Csaba",
""
],
[
"Stetak",
"Attila",
""
],
[
"Csermely",
"Peter",
""
]
] | During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here, we describe first the protein structure networks of molecular chaperones, then characterize chaperone containing sub-networks of interactomes called as chaperone-networks or chaperomes. We review the role... |
1901.02478 | Andrew Jaegle | Andrew Jaegle, Vahid Mehrpour, Nicole Rust | Visual novelty, curiosity, and intrinsic reward in machine learning and
the brain | 13 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A strong preference for novelty emerges in infancy and is prevalent across
the animal kingdom. When incorporated into reinforcement-based machine learning
algorithms, visual novelty can act as an intrinsic reward signal that vastly
increases the efficiency of exploration and expedites learning, particularly in
situat... | [
{
"created": "Tue, 8 Jan 2019 19:34:44 GMT",
"version": "v1"
}
] | 2019-01-10 | [
[
"Jaegle",
"Andrew",
""
],
[
"Mehrpour",
"Vahid",
""
],
[
"Rust",
"Nicole",
""
]
] | A strong preference for novelty emerges in infancy and is prevalent across the animal kingdom. When incorporated into reinforcement-based machine learning algorithms, visual novelty can act as an intrinsic reward signal that vastly increases the efficiency of exploration and expedites learning, particularly in situatio... |
1810.07263 | Jie Liang | Anna Terebus, Chun Liu, and Jie Liang | Discrete Flux and Velocity Fields of Probability and Their Global Maps
in Reaction Systems | 21 pages, 5 figures | null | 10.1063/1.5050808 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stochasticity plays important roles in reaction systems. Vector fields of
probability flux and velocity characterize time-varying and steady-state
properties of these systems, including high probability paths, barriers,
checkpoints among different stable regions, as well as mechanisms of dynamic
switching among them.... | [
{
"created": "Tue, 16 Oct 2018 20:38:59 GMT",
"version": "v1"
}
] | 2018-12-05 | [
[
"Terebus",
"Anna",
""
],
[
"Liu",
"Chun",
""
],
[
"Liang",
"Jie",
""
]
] | Stochasticity plays important roles in reaction systems. Vector fields of probability flux and velocity characterize time-varying and steady-state properties of these systems, including high probability paths, barriers, checkpoints among different stable regions, as well as mechanisms of dynamic switching among them. H... |
0811.3510 | Noa Sela | Noa Sela, Britta Mersch, Nurit Gal-Mark, Galit Lev-Maor, Agnes Hotz-
Wagenblatt, Gil Ast | Comparative analysis of transposed element insertion within human and
mouse genomes reveals Alu's unique role in shaping the human transcriptome | null | Genome Biology 2007, 8:R127 | 10.1186/gb-2007-8-6-r127 | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Transposed elements (TEs) have a substantial impact on mammalian
evolution and are involved in numerous genetic diseases. We compared the impact
of TEs on the human transcriptome and the mouse transcriptome. Results: We
compiled a dataset of all TEs in the human and mouse genomes, identifying
3,932,058 an... | [
{
"created": "Fri, 21 Nov 2008 10:51:29 GMT",
"version": "v1"
}
] | 2008-11-24 | [
[
"Sela",
"Noa",
""
],
[
"Mersch",
"Britta",
""
],
[
"Gal-Mark",
"Nurit",
""
],
[
"Lev-Maor",
"Galit",
""
],
[
"Wagenblatt",
"Agnes Hotz-",
""
],
[
"Ast",
"Gil",
""
]
] | Background: Transposed elements (TEs) have a substantial impact on mammalian evolution and are involved in numerous genetic diseases. We compared the impact of TEs on the human transcriptome and the mouse transcriptome. Results: We compiled a dataset of all TEs in the human and mouse genomes, identifying 3,932,058 and ... |
1402.4896 | Daniel Balick | Ron Do, Daniel Balick, Heng Li, Ivan Adzhubei, Shamil Sunyaev and
David Reich | No evidence that natural selection has been less effective at removing
deleterious mutations in Europeans than in West Africans | 53 pages (22 page manuscript and 31 supplemental information) | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Non-African populations have experienced major bottlenecks in the time since
their split from West Africans, which has led to the hypothesis that natural
selection to remove weakly deleterious mutations may have been less effective
in non-Africans. To directly test this hypothesis, we measure the per-genome
accumulat... | [
{
"created": "Thu, 20 Feb 2014 05:24:11 GMT",
"version": "v1"
}
] | 2014-02-21 | [
[
"Do",
"Ron",
""
],
[
"Balick",
"Daniel",
""
],
[
"Li",
"Heng",
""
],
[
"Adzhubei",
"Ivan",
""
],
[
"Sunyaev",
"Shamil",
""
],
[
"Reich",
"David",
""
]
] | Non-African populations have experienced major bottlenecks in the time since their split from West Africans, which has led to the hypothesis that natural selection to remove weakly deleterious mutations may have been less effective in non-Africans. To directly test this hypothesis, we measure the per-genome accumulatio... |
1303.0673 | James Degnan | Sha Zhu, James H Degnan, Bjarki Eldon | Hybrid-Lambda: simulation of multiple merger and Kingman gene
genealogies in species networks and species trees | 5 pages, 1 figure | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Hybrid-Lambda is a software package that simulates gene trees under Kingman
or two Lambda-coalescent processes within species networks or species trees. It
is written in C++, and re- leased under GNU General Public License (GPL)
version 3. Users can modify and make new dis- tribution under the terms of this
license. ... | [
{
"created": "Mon, 4 Mar 2013 11:20:37 GMT",
"version": "v1"
}
] | 2013-03-05 | [
[
"Zhu",
"Sha",
""
],
[
"Degnan",
"James H",
""
],
[
"Eldon",
"Bjarki",
""
]
] | Hybrid-Lambda is a software package that simulates gene trees under Kingman or two Lambda-coalescent processes within species networks or species trees. It is written in C++, and re- leased under GNU General Public License (GPL) version 3. Users can modify and make new dis- tribution under the terms of this license. Fo... |
1706.00603 | Ahmad Mheich | Ahmad Mheich, Mahmoud Hassan, Fabrice Wendling | Classification of meaningful and meaningless visual objects: a graph
similarity approach | 4 pages, 2 figures, ICABME 2017 conference | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Cognition involves dynamic reconfiguration of functional brain networks at
sub-second time scale. A precise tracking of these reconfigurations to
categorize visual objects remains elusive. Here, we use dense
electroencephalography (EEG) data recorded during naming meaningful (tools,
animals) and scrambled objects fro... | [
{
"created": "Fri, 2 Jun 2017 09:25:28 GMT",
"version": "v1"
}
] | 2017-06-05 | [
[
"Mheich",
"Ahmad",
""
],
[
"Hassan",
"Mahmoud",
""
],
[
"Wendling",
"Fabrice",
""
]
] | Cognition involves dynamic reconfiguration of functional brain networks at sub-second time scale. A precise tracking of these reconfigurations to categorize visual objects remains elusive. Here, we use dense electroencephalography (EEG) data recorded during naming meaningful (tools, animals) and scrambled objects from ... |
1711.07164 | Lucas Valdez D. | L. D. Valdez, G. J. Sibona, C. A. Condat | Impact of rainfall on Aedes aegypti populations | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Aedes aegypti is the main vector of multiple diseases, such as Dengue, Zika,
and Chikungunya. Due to modifications in weather patterns, its geographical
range is continuously evolving. Temperature is a key factor for its expansion
into regions with cool winters, but rainfall can also have a strong impact on
the colon... | [
{
"created": "Mon, 20 Nov 2017 06:04:07 GMT",
"version": "v1"
}
] | 2017-11-21 | [
[
"Valdez",
"L. D.",
""
],
[
"Sibona",
"G. J.",
""
],
[
"Condat",
"C. A.",
""
]
] | Aedes aegypti is the main vector of multiple diseases, such as Dengue, Zika, and Chikungunya. Due to modifications in weather patterns, its geographical range is continuously evolving. Temperature is a key factor for its expansion into regions with cool winters, but rainfall can also have a strong impact on the coloniz... |
1508.05991 | Tatiana Tatarinova | Tatiana V. Tatarinova, Inna Lysnyansky, Yuri V. Nikolsky, and
Alexander Bolshoy | The mysterious orphans of Mycoplasmataceae | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: The length of a protein sequence is largely determined by its
function, i.e. each functional group is associated with an optimal size.
However, comparative genomics revealed that proteins length may be affected by
additional factors. In 2002 it was shown that in bacterium Escherichia coli and
the archaeon... | [
{
"created": "Mon, 24 Aug 2015 22:50:42 GMT",
"version": "v1"
}
] | 2015-08-26 | [
[
"Tatarinova",
"Tatiana V.",
""
],
[
"Lysnyansky",
"Inna",
""
],
[
"Nikolsky",
"Yuri V.",
""
],
[
"Bolshoy",
"Alexander",
""
]
] | Background: The length of a protein sequence is largely determined by its function, i.e. each functional group is associated with an optimal size. However, comparative genomics revealed that proteins length may be affected by additional factors. In 2002 it was shown that in bacterium Escherichia coli and the archaeon A... |
q-bio/0403016 | Ping Ao | X.-M. Zhu, L. Yin, L. Hood, and P. Ao | Robustness, Stability and Efficiency of Phage lambda Gene Regulatory
Network: Dynamical Structure Analysis | 31 pages | null | null | null | q-bio.MN cond-mat.stat-mech nlin.AO | null | Based on our physical and biological studies we have recently developed a
mathematical framework for the analysis of nonlnear dynamics. We call this
framework the dynamical structure analysis. It has four dynamical elements:
potential landscape, transverse matrix, descendant matrix, and stochastic
drive. In particula... | [
{
"created": "Mon, 15 Mar 2004 03:19:12 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Zhu",
"X. -M.",
""
],
[
"Yin",
"L.",
""
],
[
"Hood",
"L.",
""
],
[
"Ao",
"P.",
""
]
] | Based on our physical and biological studies we have recently developed a mathematical framework for the analysis of nonlnear dynamics. We call this framework the dynamical structure analysis. It has four dynamical elements: potential landscape, transverse matrix, descendant matrix, and stochastic drive. In particular,... |
2211.02358 | Alison Hale Ph.D. | Alison C Hale and Christopher P Jewell | An approach for benchmarking the numerical solutions of stochastic
compartmental models | 21 pages 3 figures | null | null | null | q-bio.PE stat.AP | http://creativecommons.org/licenses/by-nc-nd/4.0/ | An approach is introduced for comparing the estimated states of stochastic
compartmental models for an epidemic or biological process with analytically
obtained solutions from the corresponding system of ordinary differential
equations (ODEs). Positive integer valued samples from a stochastic model are
generated nume... | [
{
"created": "Fri, 4 Nov 2022 10:32:48 GMT",
"version": "v1"
},
{
"created": "Thu, 29 Jun 2023 10:14:49 GMT",
"version": "v2"
}
] | 2023-06-30 | [
[
"Hale",
"Alison C",
""
],
[
"Jewell",
"Christopher P",
""
]
] | An approach is introduced for comparing the estimated states of stochastic compartmental models for an epidemic or biological process with analytically obtained solutions from the corresponding system of ordinary differential equations (ODEs). Positive integer valued samples from a stochastic model are generated numeri... |
1206.1571 | Ramon Grima | R. Grima, D. R. Schmidt, T. J. Newman | Steady-state fluctuations of a genetic feedback loop: an exact solution | 31 pages, 3 figures. Accepted for publication in the Journal of
Chemical Physics (2012) | null | 10.1063/1.4736721 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genetic feedback loops in cells break detailed balance and involve
bimolecular reactions; hence exact solutions revealing the nature of the
stochastic fluctuations in these loops are lacking. We here consider the master
equation for a gene regulatory feedback loop: a gene produces protein which
then binds to the prom... | [
{
"created": "Thu, 7 Jun 2012 18:32:20 GMT",
"version": "v1"
},
{
"created": "Wed, 27 Jun 2012 21:19:48 GMT",
"version": "v2"
}
] | 2015-06-05 | [
[
"Grima",
"R.",
""
],
[
"Schmidt",
"D. R.",
""
],
[
"Newman",
"T. J.",
""
]
] | Genetic feedback loops in cells break detailed balance and involve bimolecular reactions; hence exact solutions revealing the nature of the stochastic fluctuations in these loops are lacking. We here consider the master equation for a gene regulatory feedback loop: a gene produces protein which then binds to the promot... |
1304.2054 | Mircea Andrecut Dr | M. Andrecut | Monte-Carlo Simulation of a Multi-Dimensional Switch-Like Model of Stem
Cell Differentiation | 16 pages, 4 figures | Theory and Applications of Monte Carlo Simulations, ed. Charles J.
Mode, Intech, 2011, ISBN: 978-953-307-427-6 | 10.5772/15474 | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The process controlling the diferentiation of stem, or progenitor, cells into
one specific functional direction is called lineage specification. An important
characteristic of this process is the multi-lineage priming, which requires the
simultaneous expression of lineage-specific genes. Prior to commitment to a
cert... | [
{
"created": "Sun, 7 Apr 2013 20:06:25 GMT",
"version": "v1"
}
] | 2013-04-09 | [
[
"Andrecut",
"M.",
""
]
] | The process controlling the diferentiation of stem, or progenitor, cells into one specific functional direction is called lineage specification. An important characteristic of this process is the multi-lineage priming, which requires the simultaneous expression of lineage-specific genes. Prior to commitment to a certai... |
2303.00068 | Kirsty Y. Wan | Karen Grace Bondoc-Naumovitz, Hannah Laeverenz-Schlogelhofer, Rebecca
N. Poon, Alexander K. Boggon, Samuel A. Bentley, Dario Cortese, Kirsty Y. Wan | Methods and measures for investigating microscale motility | 24 pages, 2 figures | null | 10.1093/icb/icad075 | null | q-bio.CB physics.bio-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Motility is an essential factor for an organism's survival and
diversification. With the advent of novel single-cell technologies, analytical
frameworks and theoretical methods, we can begin to probe the complex lives of
microscopic motile organisms and answer the intertwining biological and
physical questions of how... | [
{
"created": "Tue, 28 Feb 2023 20:11:16 GMT",
"version": "v1"
}
] | 2023-09-01 | [
[
"Bondoc-Naumovitz",
"Karen Grace",
""
],
[
"Laeverenz-Schlogelhofer",
"Hannah",
""
],
[
"Poon",
"Rebecca N.",
""
],
[
"Boggon",
"Alexander K.",
""
],
[
"Bentley",
"Samuel A.",
""
],
[
"Cortese",
"Dario",
""
],
[
"W... | Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile organisms and answer the intertwining biological and physical questions of how t... |
2210.16099 | Elvin Lo | Elvin Lo and Pin-Yu Chen | An Empirical Evaluation of Zeroth-Order Optimization Methods on
AI-driven Molecule Optimization | 15 pages, 4 figures | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Molecule optimization is an important problem in chemical discovery and has
been approached using many techniques, including generative modeling,
reinforcement learning, genetic algorithms, and much more. Recent work has also
applied zeroth-order (ZO) optimization, a subset of gradient-free optimization
that solves p... | [
{
"created": "Thu, 27 Oct 2022 01:58:10 GMT",
"version": "v1"
}
] | 2022-10-31 | [
[
"Lo",
"Elvin",
""
],
[
"Chen",
"Pin-Yu",
""
]
] | Molecule optimization is an important problem in chemical discovery and has been approached using many techniques, including generative modeling, reinforcement learning, genetic algorithms, and much more. Recent work has also applied zeroth-order (ZO) optimization, a subset of gradient-free optimization that solves pro... |
1305.1231 | Susan Khor | Susan Khor | Optimality of Moore neighborhoods in protein contact maps | null | null | null | null | q-bio.MN q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A protein contact map is a binary symmetric adjacency matrix capturing the
distance relationship between atoms of a protein. Each cell (i, j) of a protein
contact map states whether the atoms (nodes) i and j are within some Euclidean
distance from each other. We examined the radius one Moore neighborhood
surrounding ... | [
{
"created": "Mon, 6 May 2013 16:00:41 GMT",
"version": "v1"
}
] | 2013-05-07 | [
[
"Khor",
"Susan",
""
]
] | A protein contact map is a binary symmetric adjacency matrix capturing the distance relationship between atoms of a protein. Each cell (i, j) of a protein contact map states whether the atoms (nodes) i and j are within some Euclidean distance from each other. We examined the radius one Moore neighborhood surrounding ea... |
1505.01143 | Vicente M. Reyes Ph.D. | Vicente M. Reyes | Structure-Based Function Prediction of Functionally Unannotated
Structures in the PDB: Prediction of ATP, GTP, Sialic Acid, Retinoic Acid and
Heme-bound and -Unbound (Free) Nitric Oxide Protein Binding Sites | 33 pages total (12 pages text; 21 pages figures and tables); 2
figures; 6 tables (all multi-panel); 7200 words in text; 7274 words incl. in
figures and tables | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Due to increased activity in high-throughput structural genomics efforts
around the globe, there has been an accumulation of experimental protein 3D
structures lacking functional annotation, thus creating a need for
structure-based protein function assignment methods. Computational prediction
of ligand binding sites ... | [
{
"created": "Sat, 28 Feb 2015 04:17:34 GMT",
"version": "v1"
}
] | 2015-05-06 | [
[
"Reyes",
"Vicente M.",
""
]
] | Due to increased activity in high-throughput structural genomics efforts around the globe, there has been an accumulation of experimental protein 3D structures lacking functional annotation, thus creating a need for structure-based protein function assignment methods. Computational prediction of ligand binding sites (L... |
1604.03250 | Robert Patro | Avi Srivastava, Hirak Sarkar, Laraib Malik, Rob Patro | Accurate, Fast and Lightweight Clustering of de novo Transcriptomes
using Fragment Equivalence Classes | paper accepted at the RECOMB-Seq 2016 | null | null | null | q-bio.GN cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: De novo transcriptome assembly of non-model organisms is the
first major step for many RNA-seq analysis tasks. Current methods for de novo
assembly often report a large number of contiguous sequences (contigs), which
may be fractured and incomplete sequences instead of full-length transcripts.
Dealing wit... | [
{
"created": "Tue, 12 Apr 2016 05:23:37 GMT",
"version": "v1"
}
] | 2016-04-13 | [
[
"Srivastava",
"Avi",
""
],
[
"Sarkar",
"Hirak",
""
],
[
"Malik",
"Laraib",
""
],
[
"Patro",
"Rob",
""
]
] | Motivation: De novo transcriptome assembly of non-model organisms is the first major step for many RNA-seq analysis tasks. Current methods for de novo assembly often report a large number of contiguous sequences (contigs), which may be fractured and incomplete sequences instead of full-length transcripts. Dealing with ... |
2404.17981 | Fernanda Matias | \'Icaro Rodolfo Soares Coelho Da Paz, Pedro F. A. Silva, Helena
Bordini de Lucas, S\'ergio H. A. Lira, Osvaldo A. Rosso, Fernanda Selingardi
Matias | A symbolic information approach applied to human intracranial data to
characterize and distinguish different congnitive processes | null | null | null | null | q-bio.NC physics.bio-ph physics.comp-ph physics.data-an | http://creativecommons.org/licenses/by/4.0/ | How the human brain processes information during different cognitive tasks is
one of the greatest questions in contemporary neuroscience. Understanding the
statistical properties of brain signals during specific activities is one
promising way to address this question. Here we analyze freely available data
from impla... | [
{
"created": "Sat, 27 Apr 2024 18:52:58 GMT",
"version": "v1"
}
] | 2024-04-30 | [
[
"Da Paz",
"Ícaro Rodolfo Soares Coelho",
""
],
[
"Silva",
"Pedro F. A.",
""
],
[
"de Lucas",
"Helena Bordini",
""
],
[
"Lira",
"Sérgio H. A.",
""
],
[
"Rosso",
"Osvaldo A.",
""
],
[
"Matias",
"Fernanda Selingardi",
""
]
... | How the human brain processes information during different cognitive tasks is one of the greatest questions in contemporary neuroscience. Understanding the statistical properties of brain signals during specific activities is one promising way to address this question. Here we analyze freely available data from implant... |
1307.6583 | Jason Graham | Jason M Graham | A Measure of Control for Secondary Cytokine-Induced Injury of Articular
Cartilage: A Computational Study | null | null | null | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In previous works, the author and collaborators establish a mathematical
model for injury response in articular cartilage. In this paper we use
mathematical software and computational techniques, applied to an existing
model to explore in more detail how the behavior of cartilage cells is
influenced by several of, wh... | [
{
"created": "Wed, 24 Jul 2013 21:03:23 GMT",
"version": "v1"
}
] | 2013-07-26 | [
[
"Graham",
"Jason M",
""
]
] | In previous works, the author and collaborators establish a mathematical model for injury response in articular cartilage. In this paper we use mathematical software and computational techniques, applied to an existing model to explore in more detail how the behavior of cartilage cells is influenced by several of, what... |
0903.1753 | Ginestra Bianconi | Ginestra Bianconi, Luca Ferretti and Silvio Franz | Non-neutral theory of biodiversity | 4 pages, 3 figure | Europhys. Lett. 87, 28001 (2009) | 10.1209/0295-5075/87/28001 | null | q-bio.PE cond-mat.dis-nn cond-mat.stat-mech q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a non-neutral stochastic model for the dynamics taking place in a
meta-community ecosystems in presence of migration. The model provides a
framework for describing the emergence of multiple ecological scenarios and
behaves in two extreme limits either as the unified neutral theory of
biodiversity or as the... | [
{
"created": "Tue, 10 Mar 2009 12:49:43 GMT",
"version": "v1"
},
{
"created": "Fri, 16 Oct 2009 13:51:53 GMT",
"version": "v2"
}
] | 2015-05-13 | [
[
"Bianconi",
"Ginestra",
""
],
[
"Ferretti",
"Luca",
""
],
[
"Franz",
"Silvio",
""
]
] | We present a non-neutral stochastic model for the dynamics taking place in a meta-community ecosystems in presence of migration. The model provides a framework for describing the emergence of multiple ecological scenarios and behaves in two extreme limits either as the unified neutral theory of biodiversity or as the B... |
1211.4210 | Oscar Franz\'en | Oscar Franz\'en | Genome and transcriptome studies of the protozoan parasites Trypanosoma
cruzi and Giardia intestinalis | PhD thesis, Karolinska Institutet, November 2012 | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Trypanosoma cruzi and Giardia intestinalis are two human pathogens and
protozoan parasites responsible for the diseases Chagas disease and giardiasis,
respectively. Both diseases cause suffering and illness in several million
individuals. The former disease occurs primarily in South America and Central
America, and t... | [
{
"created": "Sun, 18 Nov 2012 11:36:07 GMT",
"version": "v1"
}
] | 2012-11-20 | [
[
"Franzén",
"Oscar",
""
]
] | Trypanosoma cruzi and Giardia intestinalis are two human pathogens and protozoan parasites responsible for the diseases Chagas disease and giardiasis, respectively. Both diseases cause suffering and illness in several million individuals. The former disease occurs primarily in South America and Central America, and the... |
2012.05744 | Yu Yao | Yu Yao and Klaas E. Stephan | Markov chain Monte Carlo methods for hierarchical clustering of dynamic
causal models | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we address technical difficulties that arise when applying
Markov chain Monte Carlo (MCMC) to hierarchical models designed to perform
clustering in the space of latent parameters of subject-wise generative models.
Specifically, we focus on the case where the subject-wise generative model is a
dynamic c... | [
{
"created": "Thu, 10 Dec 2020 15:26:12 GMT",
"version": "v1"
},
{
"created": "Mon, 14 Dec 2020 16:19:55 GMT",
"version": "v2"
}
] | 2020-12-15 | [
[
"Yao",
"Yu",
""
],
[
"Stephan",
"Klaas E.",
""
]
] | In this paper, we address technical difficulties that arise when applying Markov chain Monte Carlo (MCMC) to hierarchical models designed to perform clustering in the space of latent parameters of subject-wise generative models. Specifically, we focus on the case where the subject-wise generative model is a dynamic cau... |
1710.03366 | Bilal Khan | Bilal Khan, Ian Duncan, Mohamad Saad, Daniel Schaefer, Ashly Jordan,
Daniel Smith, Alan Neaigus, Don Des Jarlais, Holly Hagan, Kirk Dombrowski | Combination interventions for Hepatitis C and Cirrhosis reduction among
people who inject drugs: An agent-based, networked population simulation
experiment | null | null | 10.1371/journal.pone.0206356 | null | q-bio.PE cs.SI physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Hepatitis C virus (HCV) infection is endemic in people who inject drugs
(PWID), with prevalence estimates above 60 percent for PWID in the United
States. Previous modeling studies suggest that direct acting antiviral (DAA)
treatment can lower overall prevalence in this population, but treatment is
often delayed until... | [
{
"created": "Tue, 10 Oct 2017 00:56:02 GMT",
"version": "v1"
}
] | 2019-03-06 | [
[
"Khan",
"Bilal",
""
],
[
"Duncan",
"Ian",
""
],
[
"Saad",
"Mohamad",
""
],
[
"Schaefer",
"Daniel",
""
],
[
"Jordan",
"Ashly",
""
],
[
"Smith",
"Daniel",
""
],
[
"Neaigus",
"Alan",
""
],
[
"Jarlais",... | Hepatitis C virus (HCV) infection is endemic in people who inject drugs (PWID), with prevalence estimates above 60 percent for PWID in the United States. Previous modeling studies suggest that direct acting antiviral (DAA) treatment can lower overall prevalence in this population, but treatment is often delayed until t... |
2012.08755 | Sarah Fay | Sarah C. Fay, Dalton J. Jones, Munther A. Dahleh, A. E. Hosoi | Simple control for complex pandemics | null | null | null | null | q-bio.PE math.PR physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The COVID-19 pandemic began over two years ago, yet schools, businesses, and
other organizations are still struggling to keep the risk of disease outbreak
low while returning to (near) normal functionality. Observations from these
past years suggest that this goal can be achieved through the right balance of
mitigati... | [
{
"created": "Wed, 16 Dec 2020 06:10:05 GMT",
"version": "v1"
},
{
"created": "Tue, 2 Feb 2021 14:35:11 GMT",
"version": "v2"
},
{
"created": "Mon, 31 Jan 2022 02:22:15 GMT",
"version": "v3"
}
] | 2022-02-02 | [
[
"Fay",
"Sarah C.",
""
],
[
"Jones",
"Dalton J.",
""
],
[
"Dahleh",
"Munther A.",
""
],
[
"Hosoi",
"A. E.",
""
]
] | The COVID-19 pandemic began over two years ago, yet schools, businesses, and other organizations are still struggling to keep the risk of disease outbreak low while returning to (near) normal functionality. Observations from these past years suggest that this goal can be achieved through the right balance of mitigation... |
1209.4017 | Leonid Perlovsky | Leonid Perlovsky, Arnaud Cabanac, Marie-Claude Bonniot-Cabanac, Michel
Cabanac | Mozart Effect, Cognitive Dissonance, and the Pleasure of Music | 11 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Mozart effect refers to scientific data on short-term improvement on
certain mental tasks after listening to Mozart, and also to its popularized
version that listening to Mozart makes you smarter (Tomatis, 1991; Wikipedia,
2012). Does Mozart effect point to a fundamental cognitive function of music?
Would such an... | [
{
"created": "Sat, 15 Sep 2012 16:24:33 GMT",
"version": "v1"
}
] | 2012-09-19 | [
[
"Perlovsky",
"Leonid",
""
],
[
"Cabanac",
"Arnaud",
""
],
[
"Bonniot-Cabanac",
"Marie-Claude",
""
],
[
"Cabanac",
"Michel",
""
]
] | The Mozart effect refers to scientific data on short-term improvement on certain mental tasks after listening to Mozart, and also to its popularized version that listening to Mozart makes you smarter (Tomatis, 1991; Wikipedia, 2012). Does Mozart effect point to a fundamental cognitive function of music? Would such an e... |
2311.04953 | Aram Mohammed | Aram Akram Mohammed, Rasul Rafiq Aziz, Faraydwn Karim Ahmad, Ibrahim
Maaroof Noori and Tariq Abubakr Ahmad | Rooting capacity of hardwood cuttings of some fruit trees in relation to
cutting pattern | null | null | 10.26682/ajuod.2020.23.1.1 | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Study two cut patterns in hardwood cuttings of (Cydonia oblonga), (Punica
granatum) and (Ficus carica). The cuttings have been cut either straight with
different internode stub lengths [0 (just onto the basal node as control), 0.5,
1.0, 2.0 or 3.0 cm below the basal node], or slant with 45 degree angle for
each lengt... | [
{
"created": "Wed, 8 Nov 2023 17:13:18 GMT",
"version": "v1"
}
] | 2023-11-10 | [
[
"Mohammed",
"Aram Akram",
""
],
[
"Aziz",
"Rasul Rafiq",
""
],
[
"Ahmad",
"Faraydwn Karim",
""
],
[
"Noori",
"Ibrahim Maaroof",
""
],
[
"Ahmad",
"Tariq Abubakr",
""
]
] | Study two cut patterns in hardwood cuttings of (Cydonia oblonga), (Punica granatum) and (Ficus carica). The cuttings have been cut either straight with different internode stub lengths [0 (just onto the basal node as control), 0.5, 1.0, 2.0 or 3.0 cm below the basal node], or slant with 45 degree angle for each length ... |
2209.06944 | Iordanka Panayotova | Iordanka Panayotova, John Herrmann, Nathan Kolling | Bioeconomic analysis of harvesting within a predator-prey system: A case
study in the Chesapeake Bay fisheries | 39 pages, 16 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Sustainable use of biological resources is very important as over
exploitation on the long run may lead to stock depletion, which in turn may
threaten biodiversity. The Chesapeake Bay is an extremely complex ecosystem,
and sustainable harvesting of its fisheries is essential both for the
ecosystem's biodiversity and ... | [
{
"created": "Wed, 14 Sep 2022 21:29:41 GMT",
"version": "v1"
},
{
"created": "Thu, 12 Jan 2023 16:46:16 GMT",
"version": "v2"
}
] | 2023-01-13 | [
[
"Panayotova",
"Iordanka",
""
],
[
"Herrmann",
"John",
""
],
[
"Kolling",
"Nathan",
""
]
] | Sustainable use of biological resources is very important as over exploitation on the long run may lead to stock depletion, which in turn may threaten biodiversity. The Chesapeake Bay is an extremely complex ecosystem, and sustainable harvesting of its fisheries is essential both for the ecosystem's biodiversity and ec... |
1510.08372 | Haidong Dong | Haidong Dong, Yiyi Yan, Roxana S. Dronca, and Svetomir N. Markovic | T cell equation as a conceptual model of T cell responses for maximizing
the efficacy of cancer immunotherapy | 5 pages | SOJ Immunol 5(1):1-5, 2017 | 10.15226/2372-0948/4/1/00155 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Following antigen stimulation, the net outcomes of a T cell response are
shaped by integrated signals from both positive co-stimulatory and negative
regulatory molecules. Recently, the blockade of negative regulatory molecules
(i.e. immune checkpoint signals) demonstrates therapeutic effects in treatment
of human can... | [
{
"created": "Wed, 28 Oct 2015 16:36:04 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Sep 2017 02:15:04 GMT",
"version": "v2"
},
{
"created": "Sat, 16 Sep 2017 16:10:32 GMT",
"version": "v3"
}
] | 2017-09-19 | [
[
"Dong",
"Haidong",
""
],
[
"Yan",
"Yiyi",
""
],
[
"Dronca",
"Roxana S.",
""
],
[
"Markovic",
"Svetomir N.",
""
]
] | Following antigen stimulation, the net outcomes of a T cell response are shaped by integrated signals from both positive co-stimulatory and negative regulatory molecules. Recently, the blockade of negative regulatory molecules (i.e. immune checkpoint signals) demonstrates therapeutic effects in treatment of human cance... |
2209.12821 | Gerardo Chowell | Gerardo Chowell, Sushma Dahal, Yuganthi R. Liyanage, Amna Tariq,
Necibe Tuncer | Structural identifiability analysis of epidemic models based on
differential equations: A tutorial-based primer | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | The successful application of epidemic models hinges on our ability to
estimate model parameters from limited observations reliably. An
often-overlooked step before estimating model parameters consists of ensuring
that the model parameters are structurally identifiable from the observed
states of the system. In this ... | [
{
"created": "Mon, 26 Sep 2022 16:28:32 GMT",
"version": "v1"
},
{
"created": "Thu, 17 Aug 2023 16:04:45 GMT",
"version": "v2"
},
{
"created": "Wed, 27 Sep 2023 20:33:50 GMT",
"version": "v3"
}
] | 2023-09-29 | [
[
"Chowell",
"Gerardo",
""
],
[
"Dahal",
"Sushma",
""
],
[
"Liyanage",
"Yuganthi R.",
""
],
[
"Tariq",
"Amna",
""
],
[
"Tuncer",
"Necibe",
""
]
] | The successful application of epidemic models hinges on our ability to estimate model parameters from limited observations reliably. An often-overlooked step before estimating model parameters consists of ensuring that the model parameters are structurally identifiable from the observed states of the system. In this tu... |
1608.07259 | Anne Shiu | Mitchell Eithun and Anne Shiu | An All-Encompassing Global Convergence Result for Processive Multisite
Phosphorylation Systems | 23 pages; updated to be consistent with version 2 of arXiv:1606.09480 | null | null | null | q-bio.MN math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phosphorylation, the enzyme-mediated addition of a phosphate group to a
molecule, is a ubiquitous chemical mechanism in biology. Multisite
phosphorylation, the addition of phosphate groups to multiple sites of a single
molecule, may be distributive or processive. Distributive systems can be
bistable, while processive... | [
{
"created": "Thu, 25 Aug 2016 19:20:36 GMT",
"version": "v1"
},
{
"created": "Thu, 13 Apr 2017 14:08:52 GMT",
"version": "v2"
},
{
"created": "Fri, 2 Jun 2017 21:00:46 GMT",
"version": "v3"
}
] | 2017-06-06 | [
[
"Eithun",
"Mitchell",
""
],
[
"Shiu",
"Anne",
""
]
] | Phosphorylation, the enzyme-mediated addition of a phosphate group to a molecule, is a ubiquitous chemical mechanism in biology. Multisite phosphorylation, the addition of phosphate groups to multiple sites of a single molecule, may be distributive or processive. Distributive systems can be bistable, while processive s... |
1509.05986 | R.K. Brojen Singh | Soibam Shyamchand Singh, Khundrakpam Budhachandra Singh, Romana
Ishrat, B. Indrajit Sharma and R.K. Brojen Singh | Scaling in topological properties of brain networks | null | null | null | null | q-bio.NC physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The organization in brain networks shows highly modular features with weak
inter-modular interaction. The topology of the networks involves emergence of
modules and sub-modules at different levels of constitution governed by fractal
laws. The modular organization, in terms of modular mass, inter-modular, and
intra-mo... | [
{
"created": "Sun, 20 Sep 2015 09:33:50 GMT",
"version": "v1"
}
] | 2015-09-22 | [
[
"Singh",
"Soibam Shyamchand",
""
],
[
"Singh",
"Khundrakpam Budhachandra",
""
],
[
"Ishrat",
"Romana",
""
],
[
"Sharma",
"B. Indrajit",
""
],
[
"Singh",
"R. K. Brojen",
""
]
] | The organization in brain networks shows highly modular features with weak inter-modular interaction. The topology of the networks involves emergence of modules and sub-modules at different levels of constitution governed by fractal laws. The modular organization, in terms of modular mass, inter-modular, and intra-modu... |
q-bio/0511017 | Eytan Domany | Uri Einav, Yuval Tabach, Gad Getz, Assif Yitzhaky, Ugur Ozbek, Ninette
Amariglio, Shai Izraeli, Gideon Rechavi and Eytan Domany | Gene expression analysis reveals a strong signature of an interferon
induced pathway in childhood lymphoblastic leukemia as well as in breast and
ovarian cancer | null | Oncogene vol 24 p 6367 (2005) | null | null | q-bio.GN q-bio.MN | null | On the basis of epidemiological studies, infection was suggested to play a
role in the etiology of human cancer. While for some cancers such a role was
indeed demonstrated, there is no direct biological support for the role of
viral pathogens in the pathogenesis of childhood leukemia. Using a novel
bioinformatic tool... | [
{
"created": "Mon, 14 Nov 2005 19:03:21 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Einav",
"Uri",
""
],
[
"Tabach",
"Yuval",
""
],
[
"Getz",
"Gad",
""
],
[
"Yitzhaky",
"Assif",
""
],
[
"Ozbek",
"Ugur",
""
],
[
"Amariglio",
"Ninette",
""
],
[
"Izraeli",
"Shai",
""
],
[
"Rechavi",
... | On the basis of epidemiological studies, infection was suggested to play a role in the etiology of human cancer. While for some cancers such a role was indeed demonstrated, there is no direct biological support for the role of viral pathogens in the pathogenesis of childhood leukemia. Using a novel bioinformatic tool, ... |
2202.10849 | Birgitta Dresp-Langley | Birgitta Dresp-Langley | Brain representation of perceptual stimuli at different levels of
awareness | arXiv admin note: text overlap with arXiv:1805.09176 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This article questions the widespread assumption that there are brain
representations that will always remain unconscious in the sense of being
inaccessible to individual awareness under any circumstances. This implies that
some part of the knowledge generated by the brain is once and for always
excluded from conscio... | [
{
"created": "Tue, 22 Feb 2022 12:23:28 GMT",
"version": "v1"
}
] | 2022-02-23 | [
[
"Dresp-Langley",
"Birgitta",
""
]
] | This article questions the widespread assumption that there are brain representations that will always remain unconscious in the sense of being inaccessible to individual awareness under any circumstances. This implies that some part of the knowledge generated by the brain is once and for always excluded from conscious... |
1305.5650 | Dmitri Volchenkov | Dimitri Volchenkov, Jonathan Helbach, Marko Tscherepanow, Sina
K\"uhnel | Exploration-exploitation trade-off features a saltatory search behaviour | J. R. Soc. Interface, 2013 | null | null | null | q-bio.OT physics.soc-ph q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Searching experiments conducted in different virtual environments over a
gender balanced group of people revealed a gender irrelevant scale-free spread
of searching activity on large spatiotemporal scales. We have suggested and
solved analytically a simple statistical model of the coherent-noise type
describing the e... | [
{
"created": "Fri, 24 May 2013 08:38:11 GMT",
"version": "v1"
}
] | 2013-05-27 | [
[
"Volchenkov",
"Dimitri",
""
],
[
"Helbach",
"Jonathan",
""
],
[
"Tscherepanow",
"Marko",
""
],
[
"Kühnel",
"Sina",
""
]
] | Searching experiments conducted in different virtual environments over a gender balanced group of people revealed a gender irrelevant scale-free spread of searching activity on large spatiotemporal scales. We have suggested and solved analytically a simple statistical model of the coherent-noise type describing the exp... |
2311.07624 | Wensi Hu | Wensi Hu, Quan-Xing Liu, Bo Wang, Nuo Xu, Lijuan Cui, Chi Xu | Disordered hyperuniformity signals functioning and resilience of
self-organized vegetation patterns | 34 pages, 6 figures; Supplementary Materials, 19 pages, 10 figures, 2
tables | null | null | null | q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In harsh environments, organisms may self-organize into spatially patterned
systems in various ways. So far, studies of ecosystem spatial self-organization
have primarily focused on apparent orders reflected by regular patterns.
However, self-organized ecosystems may also have cryptic orders that can be
unveiled only... | [
{
"created": "Mon, 13 Nov 2023 08:03:09 GMT",
"version": "v1"
}
] | 2023-11-15 | [
[
"Hu",
"Wensi",
""
],
[
"Liu",
"Quan-Xing",
""
],
[
"Wang",
"Bo",
""
],
[
"Xu",
"Nuo",
""
],
[
"Cui",
"Lijuan",
""
],
[
"Xu",
"Chi",
""
]
] | In harsh environments, organisms may self-organize into spatially patterned systems in various ways. So far, studies of ecosystem spatial self-organization have primarily focused on apparent orders reflected by regular patterns. However, self-organized ecosystems may also have cryptic orders that can be unveiled only t... |
2010.03642 | Arun Nethi | Adam J. Starr, Manjula Julka, Arun Nethi, John D. Watkins, Ryan W.
Fairchild, Michael W. Cripps, Dustin Rinehart, and Hayden N. Box | Parkland Trauma Index of Mortality (PTIM): Real-time Predictive Model
for PolyTrauma Patients | 8 pages, 5 figures | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Vital signs and laboratory values are routinely used to guide clinical
decision-making for polytrauma patients, such as the decision to use damage
control techniques versus early definitive fracture fixation. Prior
multivariate models have tried to predict mortality risk, but due to several
limitations like one-time ... | [
{
"created": "Wed, 7 Oct 2020 20:34:03 GMT",
"version": "v1"
}
] | 2020-10-09 | [
[
"Starr",
"Adam J.",
""
],
[
"Julka",
"Manjula",
""
],
[
"Nethi",
"Arun",
""
],
[
"Watkins",
"John D.",
""
],
[
"Fairchild",
"Ryan W.",
""
],
[
"Cripps",
"Michael W.",
""
],
[
"Rinehart",
"Dustin",
""
],
... | Vital signs and laboratory values are routinely used to guide clinical decision-making for polytrauma patients, such as the decision to use damage control techniques versus early definitive fracture fixation. Prior multivariate models have tried to predict mortality risk, but due to several limitations like one-time pr... |
q-bio/0502017 | Marco Cosentino Lagomarsino | M. Cosentino Lagomarsino, P. Jona, B. Bassetti | The large-scale logico-chemical structure of a transcriptional
regulation network | null | null | null | null | q-bio.MN cond-mat.dis-nn | null | Identity, response to external stimuli, and spatial architecture of a living
system are central topics of molecular biology. Presently, they are largely
seen as a result of the interplay between a gene repertoire and the regulatory
machinery of the cell. At the transcriptional level, the cis-regulatory regions
establ... | [
{
"created": "Tue, 15 Feb 2005 23:45:37 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Lagomarsino",
"M. Cosentino",
""
],
[
"Jona",
"P.",
""
],
[
"Bassetti",
"B.",
""
]
] | Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory machinery of the cell. At the transcriptional level, the cis-regulatory regions establis... |
q-bio/0701045 | Lucilla de Arcangelis | G.L. Pellegrini, L. de Arcangelis, H.J. Herrmann, C. Perrone-Capano | Modelling the brain as a n Apollonian network | 9 pages, 10 figures | null | null | null | q-bio.NC | null | Networks of living neurons exhibit an avalanche mode of activity,
experimentally found in organotypic cultures. Moreover, experimental studies of
morphology indicate that neurons develop a network of small-world-like
connections, with the possibility of very high connectivity degree. Here we
study a recent model base... | [
{
"created": "Sat, 27 Jan 2007 00:17:13 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Pellegrini",
"G. L.",
""
],
[
"de Arcangelis",
"L.",
""
],
[
"Herrmann",
"H. J.",
""
],
[
"Perrone-Capano",
"C.",
""
]
] | Networks of living neurons exhibit an avalanche mode of activity, experimentally found in organotypic cultures. Moreover, experimental studies of morphology indicate that neurons develop a network of small-world-like connections, with the possibility of very high connectivity degree. Here we study a recent model based ... |
1802.09627 | Tito Arecchi | F.Tito Arecchi | Cognition and Reality | 18 pages; submitted to "Substantia" | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We discuss the two moments of human cognition, namely, apprehension (A),
whereby a coherent perception emerges from the recruitment of neuronal groups,
and judgment(B),that entails the comparison of two apprehensions acquired at
different times, coded in a suitable language and retrieved by memory. (B)
entails self-c... | [
{
"created": "Wed, 27 Dec 2017 09:39:38 GMT",
"version": "v1"
}
] | 2018-02-28 | [
[
"Arecchi",
"F. Tito",
""
]
] | We discuss the two moments of human cognition, namely, apprehension (A), whereby a coherent perception emerges from the recruitment of neuronal groups, and judgment(B),that entails the comparison of two apprehensions acquired at different times, coded in a suitable language and retrieved by memory. (B) entails self-con... |
1509.05802 | Daniel Barth | Krista M. Rodgers, F. Edward Dudek and Daniel S. Barth | Lack of appropriate controls leads to mistaking absence seizures for
post-traumatic epilepsy | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Here we provide a thorough discussion of a rebuttal by D'Ambrosio et al to a
study conducted by Rodgers et al. (Rodgers KM, Dudek FE, Barth DS (2015)
Progressive, Seizure-Like, Spike- Wave Discharges Are Common in Both Injured
and Uninjured Sprague-Dawley Rats: Implications for the Fluid Percussion Injury
Model of Po... | [
{
"created": "Fri, 18 Sep 2015 21:35:38 GMT",
"version": "v1"
}
] | 2015-09-22 | [
[
"Rodgers",
"Krista M.",
""
],
[
"Dudek",
"F. Edward",
""
],
[
"Barth",
"Daniel S.",
""
]
] | Here we provide a thorough discussion of a rebuttal by D'Ambrosio et al to a study conducted by Rodgers et al. (Rodgers KM, Dudek FE, Barth DS (2015) Progressive, Seizure-Like, Spike- Wave Discharges Are Common in Both Injured and Uninjured Sprague-Dawley Rats: Implications for the Fluid Percussion Injury Model of Post... |
2002.12883 | Michael Guertin | Kizhakke Mattada Sathyan, Thomas G. Scott, and Michael J. Guertin | The ARF-AID system: Methods that preserve endogenous protein levels and
facilitate rapidly inducible protein degradation | 43 pages, 8 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | The ARF-AID (Auxin Response Factor-Auxin Inducible Degron) system is a
re-engineered auxin-inducible protein degradation system. Inducible degron
systems are widely used to specifically and rapidly deplete proteins of
interest in cell lines and organisms. An advantage of inducible degradation is
that the biological s... | [
{
"created": "Fri, 28 Feb 2020 17:32:09 GMT",
"version": "v1"
}
] | 2020-03-02 | [
[
"Sathyan",
"Kizhakke Mattada",
""
],
[
"Scott",
"Thomas G.",
""
],
[
"Guertin",
"Michael J.",
""
]
] | The ARF-AID (Auxin Response Factor-Auxin Inducible Degron) system is a re-engineered auxin-inducible protein degradation system. Inducible degron systems are widely used to specifically and rapidly deplete proteins of interest in cell lines and organisms. An advantage of inducible degradation is that the biological sys... |
1903.10334 | Jon Borresen | Jon Borresen and Killian O'Brien | An Upper Bound on the Number of Discrete States Possible for the Human
Brain | 10 Pages, 5 Figures | null | null | null | q-bio.NC | http://creativecommons.org/publicdomain/zero/1.0/ | Human brains are arguably the most complex entities known. Composed of
billions of neurons, connected via a highly detailed structure where the
underlying method by which functionality occurs is still debated. Here we
consider one theory for neural coding, synchronization coding, which gives rise
to the highest possi... | [
{
"created": "Mon, 18 Mar 2019 11:47:11 GMT",
"version": "v1"
}
] | 2019-03-26 | [
[
"Borresen",
"Jon",
""
],
[
"O'Brien",
"Killian",
""
]
] | Human brains are arguably the most complex entities known. Composed of billions of neurons, connected via a highly detailed structure where the underlying method by which functionality occurs is still debated. Here we consider one theory for neural coding, synchronization coding, which gives rise to the highest possibl... |
2003.08447 | Rishikesh Magar | Rishikesh Magar, Prakarsh Yadav, Amir Barati Farimani | Potential Neutralizing Antibodies Discovered for Novel Corona Virus
Using Machine Learning | We have computationally predicted the neutralizing candidates against
COVID -19 using machine learning techniques. The main paper is 25 pages(4
figures) and Supporting information is 10 pages(5 figures) | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The fast and untraceable virus mutations take lives of thousands of people
before the immune system can produce the inhibitory antibody. Recent outbreak
of novel coronavirus infected and killed thousands of people in the world.
Rapid methods in finding peptides or antibody sequences that can inhibit the
viral epitope... | [
{
"created": "Wed, 18 Mar 2020 19:23:32 GMT",
"version": "v1"
}
] | 2020-03-20 | [
[
"Magar",
"Rishikesh",
""
],
[
"Yadav",
"Prakarsh",
""
],
[
"Farimani",
"Amir Barati",
""
]
] | The fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody. Recent outbreak of novel coronavirus infected and killed thousands of people in the world. Rapid methods in finding peptides or antibody sequences that can inhibit the viral epitopes ... |
1309.4287 | Javier Orlandi G | Javier G. Orlandi, Olav Stetter, Jordi Soriano, Theo Geisel and Demian
Battaglia | Transfer Entropy reconstruction and labeling of neuronal connections
from simulated calcium imaging | 24 pages, 4 figures | null | 10.1371/journal.pone.0098842 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neuronal dynamics are fundamentally constrained by the underlying structural
network architecture, yet much of the details of this synaptic connectivity are
still unknown even in neuronal cultures in vitro. Here we extend a previous
approach based on information theory, the Generalized Transfer Entropy, to the
recons... | [
{
"created": "Tue, 17 Sep 2013 12:49:08 GMT",
"version": "v1"
},
{
"created": "Tue, 6 May 2014 15:59:36 GMT",
"version": "v2"
}
] | 2017-02-08 | [
[
"Orlandi",
"Javier G.",
""
],
[
"Stetter",
"Olav",
""
],
[
"Soriano",
"Jordi",
""
],
[
"Geisel",
"Theo",
""
],
[
"Battaglia",
"Demian",
""
]
] | Neuronal dynamics are fundamentally constrained by the underlying structural network architecture, yet much of the details of this synaptic connectivity are still unknown even in neuronal cultures in vitro. Here we extend a previous approach based on information theory, the Generalized Transfer Entropy, to the reconstr... |
2004.08288 | \'Angel Gustavo Cervantes P\'erez | Ugo Avila-Ponce de Le\'on, \'Angel G. C. P\'erez, Eric Avila-Vales | A data driven analysis and forecast of an SEIARD epidemic model for
COVID-19 in Mexico | 13 pages, 8 figures | Big Data and Information Analytics, Vol. 5, No. 1 (2020) 14-28 | 10.3934/bdia.2020002 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose an SEIARD mathematical model to investigate the current outbreak
of coronavirus disease (COVID-19) in Mexico. We conduct a detailed analysis of
this model and demonstrate its application using publicly reported data. We
calculate the basic reproduction number ($R_0$) via the next-generation matrix
method, ... | [
{
"created": "Thu, 16 Apr 2020 09:26:53 GMT",
"version": "v1"
}
] | 2021-02-23 | [
[
"de León",
"Ugo Avila-Ponce",
""
],
[
"Pérez",
"Ángel G. C.",
""
],
[
"Avila-Vales",
"Eric",
""
]
] | We propose an SEIARD mathematical model to investigate the current outbreak of coronavirus disease (COVID-19) in Mexico. We conduct a detailed analysis of this model and demonstrate its application using publicly reported data. We calculate the basic reproduction number ($R_0$) via the next-generation matrix method, an... |
1203.4721 | Tommi Aho | Tommi Aho (1), Juha Kesseli (1), Olli Yli-Harja (1) and Stuart A.
Kauffman (1,2) ((1) Department of Signal Processing, Tampere University of
Technology, Finland, (2) Complex Systems Center, University of Vermont,
U.S.A) | Growth efficiency as a cellular objective in Eschericia coli | 18 pages, 5 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The identification of cellular objectives is one of the central topics in the
research of microbial metabolic networks. In particular, the information about
a cellular objective is needed in flux balance analysis which is a commonly
used constrained-based metabolic network analysis method for the prediction of
cellul... | [
{
"created": "Wed, 21 Mar 2012 12:31:13 GMT",
"version": "v1"
}
] | 2012-03-22 | [
[
"Aho",
"Tommi",
""
],
[
"Kesseli",
"Juha",
""
],
[
"Yli-Harja",
"Olli",
""
],
[
"Kauffman",
"Stuart A.",
""
]
] | The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used constrained-based metabolic network analysis method for the prediction of cellular... |
2211.06426 | Zsolt Vizi PhD | Evans Kiptoo Korir and Zsolt Vizi | Clustering of countries based on the associated social contact patterns
in epidemiological modelling | null | null | null | null | q-bio.QM cs.LG physics.soc-ph q-bio.PE stat.AP stat.ME | http://creativecommons.org/licenses/by/4.0/ | Mathematical models have been used to understand the spread patterns of
infectious diseases such as Coronavirus Disease 2019 (COVID-19). The
transmission component of the models can be modelled in an age-dependent manner
via introducing contact matrix for the population, which describes the contact
rates between the ... | [
{
"created": "Tue, 8 Nov 2022 10:59:14 GMT",
"version": "v1"
}
] | 2022-11-15 | [
[
"Korir",
"Evans Kiptoo",
""
],
[
"Vizi",
"Zsolt",
""
]
] | Mathematical models have been used to understand the spread patterns of infectious diseases such as Coronavirus Disease 2019 (COVID-19). The transmission component of the models can be modelled in an age-dependent manner via introducing contact matrix for the population, which describes the contact rates between the ag... |
1210.6444 | Marc Robinson-Rechavi | Barbara Piasecka, Pawel Lichocki, Sebastien Moretti, Sven Bergmann,
Marc Robinson-Rechavi | The hourglass and the early conservation models - co-existing
evolutionary patterns in vertebrate development | null | null | null | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Developmental constraints have been postulated to limit the space of feasible
phenotypes and thus shape animal evolution. These constraints have been
suggested to be the strongest during either early or mid-embryogenesis, which
corresponds to the early conservation model or the hourglass model,
respectively. Conflict... | [
{
"created": "Wed, 24 Oct 2012 07:22:42 GMT",
"version": "v1"
},
{
"created": "Wed, 13 Mar 2013 08:28:58 GMT",
"version": "v2"
}
] | 2013-03-14 | [
[
"Piasecka",
"Barbara",
""
],
[
"Lichocki",
"Pawel",
""
],
[
"Moretti",
"Sebastien",
""
],
[
"Bergmann",
"Sven",
""
],
[
"Robinson-Rechavi",
"Marc",
""
]
] | Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These constraints have been suggested to be the strongest during either early or mid-embryogenesis, which corresponds to the early conservation model or the hourglass model, respectively. Conflictin... |
1902.10950 | Francesco Maria Sabatini Dr | F.M. Sabatini, R.B. de Andrade, Y. Paillet, P. Odor, C. Bouget, T.
Campagnaro, F. Gosselin, P. Janssen, W. Mattioli, J. Nascimbene, T. Sitzia,
T. Kuemmerle, S. Burrascano | Trade-offs between carbon stocks and biodiversity in European temperate
forests | Pre-review Version 2018, 07\23 + Supplementary information 43 Pages,
5 figures + 9 supplementary Figures | Global Change Biology 25(2):536-548 (2019) | 10.1111/gcb.14503 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Policies to mitigate climate change and biodiversity loss often assume that
protecting carbon-rich forests provides co-benefits in terms of biodiversity,
due to the spatial congruence of carbon stocks and biodiversity at
biogeographic scales. However, it remains unclear whether this holds at the
scales relevant for m... | [
{
"created": "Thu, 28 Feb 2019 08:50:11 GMT",
"version": "v1"
}
] | 2019-03-01 | [
[
"Sabatini",
"F. M.",
""
],
[
"de Andrade",
"R. B.",
""
],
[
"Paillet",
"Y.",
""
],
[
"Odor",
"P.",
""
],
[
"Bouget",
"C.",
""
],
[
"Campagnaro",
"T.",
""
],
[
"Gosselin",
"F.",
""
],
[
"Janssen",
... | Policies to mitigate climate change and biodiversity loss often assume that protecting carbon-rich forests provides co-benefits in terms of biodiversity, due to the spatial congruence of carbon stocks and biodiversity at biogeographic scales. However, it remains unclear whether this holds at the scales relevant for man... |
2211.07360 | Ajitesh Srivastava | James Orme-Rogers and Ajitesh Srivastava | Spatio-Temporal Attention in Multi-Granular Brain Chronnectomes for
Detection of Autism Spectrum Disorder | 6 pages, 2 figures | null | null | null | q-bio.NC cs.CV cs.LG | http://creativecommons.org/licenses/by/4.0/ | The traditional methods for detecting autism spectrum disorder (ASD) are
expensive, subjective, and time-consuming, often taking years for a diagnosis,
with many children growing well into adolescence and even adulthood before
finally confirming the disorder. Recently, graph-based learning techniques have
demonstrate... | [
{
"created": "Sun, 30 Oct 2022 01:43:17 GMT",
"version": "v1"
}
] | 2022-11-15 | [
[
"Orme-Rogers",
"James",
""
],
[
"Srivastava",
"Ajitesh",
""
]
] | The traditional methods for detecting autism spectrum disorder (ASD) are expensive, subjective, and time-consuming, often taking years for a diagnosis, with many children growing well into adolescence and even adulthood before finally confirming the disorder. Recently, graph-based learning techniques have demonstrated ... |
1907.02116 | Paria Mehrani | Paria Mehrani, Andrei Mouraviev, and John K. Tsotsos | Multiplicative modulations in hue-selective cells enhance unique hue
representation | null | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | There is still much to understand about the color processing mechanisms in
the brain and the transformation from cone-opponent representations to
perceptual hues. Moreover, it is unclear which areas(s) in the brain represent
unique hues. We propose a hierarchical model inspired by the neuronal
mechanisms in the brain... | [
{
"created": "Wed, 3 Jul 2019 19:57:33 GMT",
"version": "v1"
}
] | 2019-07-05 | [
[
"Mehrani",
"Paria",
""
],
[
"Mouraviev",
"Andrei",
""
],
[
"Tsotsos",
"John K.",
""
]
] | There is still much to understand about the color processing mechanisms in the brain and the transformation from cone-opponent representations to perceptual hues. Moreover, it is unclear which areas(s) in the brain represent unique hues. We propose a hierarchical model inspired by the neuronal mechanisms in the brain f... |
1211.0301 | Amelie Banc | M.-N. Labour (ICGICMMM, MMDN), Am\'elie Banc (L2C), Audrey Tourrette
(ICGICMMM), Fr\'ed\'erique Cunin (ICGICMMM), Jean-Michel Verdier (MMDN),
Jean-Marie Devoisselle (ICGICMMM), Anne Marcilhac (MMDN), Emmanuel Belamie
(ICGICMMM) | Thick collagen-based 3D matrices including growth factors to induce
neurite outgrowth | null | Acta Biomaterialia 8, 9 (2012) 3302-3312 | 10.1016/j.actbio.2012.05.015 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Designing synthetic microenvironments for cellular investigations is a very
active area of research at the crossroads of cell biology and materials
science. The present work describes the design and functionalization of a
three-dimensional (3D) culture support dedicated to the study of neurite
outgrowth from neural c... | [
{
"created": "Thu, 1 Nov 2012 20:29:27 GMT",
"version": "v1"
}
] | 2012-11-05 | [
[
"Labour",
"M. -N.",
"",
"ICGICMMM, MMDN"
],
[
"Banc",
"Amélie",
"",
"L2C"
],
[
"Tourrette",
"Audrey",
"",
"ICGICMMM"
],
[
"Cunin",
"Frédérique",
"",
"ICGICMMM"
],
[
"Verdier",
"Jean-Michel",
"",
"MMDN"
],
[
"De... | Designing synthetic microenvironments for cellular investigations is a very active area of research at the crossroads of cell biology and materials science. The present work describes the design and functionalization of a three-dimensional (3D) culture support dedicated to the study of neurite outgrowth from neural cel... |
0807.1803 | Kunihiko Kaneko | Kunihiko Kaneko and Chikara Furusawa | Consistency Principle in Biological Dynamical Systems | As a proceeding paper for European Confernce on Complex Systems | Theory Biosci. (2008) 127; 195-204 | null | null | q-bio.CB cond-mat.stat-mech nlin.AO q-bio.PE q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a principle of consistency between different hierarchical levels
of biological systems. Given a consistency between molecule replication and
cell reproduction, universal statistical laws on cellular chemical abundances
are derived and confirmed experimentally. They include a power law distribution
of gene ... | [
{
"created": "Fri, 11 Jul 2008 09:24:20 GMT",
"version": "v1"
}
] | 2008-07-21 | [
[
"Kaneko",
"Kunihiko",
""
],
[
"Furusawa",
"Chikara",
""
]
] | We propose a principle of consistency between different hierarchical levels of biological systems. Given a consistency between molecule replication and cell reproduction, universal statistical laws on cellular chemical abundances are derived and confirmed experimentally. They include a power law distribution of gene ex... |
1201.2033 | Michel Bellis | Michel Bellis | Mapping of Affymetrix probe sets to groups of transcripts using
transcriptional networks | 8 pages, 4 figures, 4tables. Formated version. Submitted to
Bioinformatics | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Usefulness of analysis derived from Affymetrix microarrays
depends largely upon the reliability of files describing the correspondence
between probe sets, genes and transcripts. In particular, in case a gene is
targeted by two probe sets, one must be able to assess if the corresponding
signals measure a g... | [
{
"created": "Tue, 10 Jan 2012 11:57:24 GMT",
"version": "v1"
},
{
"created": "Fri, 13 Jan 2012 15:40:56 GMT",
"version": "v2"
}
] | 2012-01-16 | [
[
"Bellis",
"Michel",
""
]
] | Motivation: Usefulness of analysis derived from Affymetrix microarrays depends largely upon the reliability of files describing the correspondence between probe sets, genes and transcripts. In particular, in case a gene is targeted by two probe sets, one must be able to assess if the corresponding signals measure a gro... |
2012.09930 | Linli Shi | Linli Shi (1), Ying Jiang (2), Fernando R. Fernandez (2,5,6), Lu Lan
(3), Guo Chen (3), Heng-ye Man (4,5), John A. White (2,5,6), Ji-Xin Cheng
(2,3), Chen Yang (1, 3) ((1) Department of Chemistry, Boston University,
Boston, USA, (2) Department of Biomedical Engineering, Boston University,
Boston, USA, (3) Depar... | Non-genetic acoustic stimulation of single neurons by a tapered fiber
optoacoustic emitter | 25 pages, 5 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As an emerging technology, transcranial focused ultrasound has been
demonstrated to successfully evoke motor responses in mice, rabbits, and
sensory/motor responses in humans. Yet, the spatial resolution of ultrasound
does not allow for high-precision stimulation. Here, we developed a tapered
fiber optoacoustic emitt... | [
{
"created": "Thu, 17 Dec 2020 20:50:19 GMT",
"version": "v1"
}
] | 2020-12-21 | [
[
"Shi",
"Linli",
""
],
[
"Jiang",
"Ying",
""
],
[
"Fernandez",
"Fernando R.",
""
],
[
"Lan",
"Lu",
""
],
[
"Chen",
"Guo",
""
],
[
"Man",
"Heng-ye",
""
],
[
"White",
"John A.",
""
],
[
"Cheng",
"J... | As an emerging technology, transcranial focused ultrasound has been demonstrated to successfully evoke motor responses in mice, rabbits, and sensory/motor responses in humans. Yet, the spatial resolution of ultrasound does not allow for high-precision stimulation. Here, we developed a tapered fiber optoacoustic emitter... |
2308.01918 | Raul Isea | Raul Isea | A General Approach to Modeling Covid-19 | 19 paqges, 3 figure | Journal Model Based Research (2023) Vol 2(2): 1 -19 | 10.14302/issn.2643-2811.jmbr-23-4556 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The present work shows that it is possible to analytically solve a general
model to explain the transmission dynamics of SARS-CoV-2. First, the
within-host model is described, and later a between-host model, where the
coupling between them is the viral load of SARS-CoV-2. The within-host model
describes the equations... | [
{
"created": "Tue, 11 Jul 2023 22:23:21 GMT",
"version": "v1"
}
] | 2023-08-07 | [
[
"Isea",
"Raul",
""
]
] | The present work shows that it is possible to analytically solve a general model to explain the transmission dynamics of SARS-CoV-2. First, the within-host model is described, and later a between-host model, where the coupling between them is the viral load of SARS-CoV-2. The within-host model describes the equations i... |
1207.2018 | Alexey Mazur K | Alexey K. Mazur | The torque transfer coefficient in DNA under torsional stress | 5 pages, 4 figures. To appear in Phys. Rev. E | null | 10.1103/PhysRevE.86.011914 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent years, significant progress in understanding the properties of
supercoiled DNA has been obtained due to nanotechniques that made stretching
and twisting of single molecules possible. Quantitative interpretation of such
experiments requires accurate knowledge of torques inside manipulated DNA. This
paper arg... | [
{
"created": "Mon, 9 Jul 2012 12:06:28 GMT",
"version": "v1"
}
] | 2015-06-05 | [
[
"Mazur",
"Alexey K.",
""
]
] | In recent years, significant progress in understanding the properties of supercoiled DNA has been obtained due to nanotechniques that made stretching and twisting of single molecules possible. Quantitative interpretation of such experiments requires accurate knowledge of torques inside manipulated DNA. This paper argue... |
2309.02665 | Xiaohuan Xia | Xiaohuan Xia (1), Andrei A. Klishin (1), Jennifer Stiso (1),
Christopher W. Lynn (2, 3), Ari E. Kahn (4), Lorenzo Caciagli (1), and Dani
S. Bassett (1 and 5) ((1) Department of Bioengineering, University of
Pennsylvania, (2) Joseph Henry Laboratories of Physics, Princeton University,
(3) Initiative for the Theo... | Human Learning of Hierarchical Graphs | 22 pages, 10 figures, 1 table | null | null | null | q-bio.NC cond-mat.stat-mech physics.bio-ph physics.soc-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Humans are constantly exposed to sequences of events in the environment.
Those sequences frequently evince statistical regularities, such as the
probabilities with which one event transitions to another. Collectively,
inter-event transition probabilities can be modeled as a graph or network. Many
real-world networks ... | [
{
"created": "Wed, 6 Sep 2023 02:22:17 GMT",
"version": "v1"
}
] | 2023-09-07 | [
[
"Xia",
"Xiaohuan",
"",
"1 and 5"
],
[
"Klishin",
"Andrei A.",
"",
"1 and 5"
],
[
"Stiso",
"Jennifer",
"",
"1 and 5"
],
[
"Lynn",
"Christopher W.",
"",
"1 and 5"
],
[
"Kahn",
"Ari E.",
"",
"1 and 5"
],
[
"Caciag... | Humans are constantly exposed to sequences of events in the environment. Those sequences frequently evince statistical regularities, such as the probabilities with which one event transitions to another. Collectively, inter-event transition probabilities can be modeled as a graph or network. Many real-world networks ar... |
2011.08703 | Chrisyen Damanik | Chrisyen Damanik, Sumiati Sinaga, Kiki Hardiansyah | Effectiveness Of Sesame Oil For The Prevention Of Pressure Ulcer In
Patients With Bed Rest Undergoing Hospitalization | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Pressure Ulcer is one of the most problems in patients with bed rest.
Reposition and skin care are deterrent against the incidence of pressure ulcer.
Objective: This study aimed to analyze the effectiveness of sesame oil for the
prevention of pressure ulcer in patients with bed rest undergoing
hospitalization. Method... | [
{
"created": "Mon, 16 Nov 2020 14:45:14 GMT",
"version": "v1"
}
] | 2020-11-18 | [
[
"Damanik",
"Chrisyen",
""
],
[
"Sinaga",
"Sumiati",
""
],
[
"Hardiansyah",
"Kiki",
""
]
] | Pressure Ulcer is one of the most problems in patients with bed rest. Reposition and skin care are deterrent against the incidence of pressure ulcer. Objective: This study aimed to analyze the effectiveness of sesame oil for the prevention of pressure ulcer in patients with bed rest undergoing hospitalization. Method: ... |
1308.3172 | Botond Sipos | Botond Sipos, Greg Slodkowicz, Tim Massingham and Nick Goldman | Realistic simulations reveal extensive sample-specificity of RNA-seq
biases | Analysis pipeline and results at http://bit.ly/rlsim-pl | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/3.0/ | In line with the importance of RNA-seq, the bioinformatics community has
produced numerous data analysis tools incorporating methods to correct
sample-specific biases. However, few advanced simulation tools exist to enable
benchmarking of competing correction methods. We introduce the first framework
to reproduce the... | [
{
"created": "Wed, 14 Aug 2013 16:26:29 GMT",
"version": "v1"
}
] | 2013-08-15 | [
[
"Sipos",
"Botond",
""
],
[
"Slodkowicz",
"Greg",
""
],
[
"Massingham",
"Tim",
""
],
[
"Goldman",
"Nick",
""
]
] | In line with the importance of RNA-seq, the bioinformatics community has produced numerous data analysis tools incorporating methods to correct sample-specific biases. However, few advanced simulation tools exist to enable benchmarking of competing correction methods. We introduce the first framework to reproduce the p... |
2007.07154 | Hagai B. Perets | Hagai B. Perets and Ruth Perets | A preceding low-virulence strain pandemic inducing immunity against
COVID-19 | Comments are welcome | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Countries highly exposed to incoming traffic from China were expected to be
at the highest risk of COVID-19 spread. However, COVID-19 case numbers
(infection levels) are negatively correlated with incoming traffic-level.
Moreover, infection levels are positively correlated with population-size,
while the latter shoul... | [
{
"created": "Tue, 14 Jul 2020 16:13:43 GMT",
"version": "v1"
}
] | 2020-07-15 | [
[
"Perets",
"Hagai B.",
""
],
[
"Perets",
"Ruth",
""
]
] | Countries highly exposed to incoming traffic from China were expected to be at the highest risk of COVID-19 spread. However, COVID-19 case numbers (infection levels) are negatively correlated with incoming traffic-level. Moreover, infection levels are positively correlated with population-size, while the latter should ... |
1905.00574 | Mohammad Qasaimeh | Roaa Alnemari, Pavithra Sukumar, Muhammedin Deliorman, and Mohammad A.
Qasaimeh | Paper-based cell cryopreservation | null | null | null | null | q-bio.TO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The continuous development of simple and practical cell cryopreservation
methods is of great importance to a variety of sectors, especially when
considering the efficient short- and long-term storage of cells and their
transportation. Although the overall success of such methods has been increased
in recent years, th... | [
{
"created": "Thu, 2 May 2019 05:09:55 GMT",
"version": "v1"
}
] | 2019-05-03 | [
[
"Alnemari",
"Roaa",
""
],
[
"Sukumar",
"Pavithra",
""
],
[
"Deliorman",
"Muhammedin",
""
],
[
"Qasaimeh",
"Mohammad A.",
""
]
] | The continuous development of simple and practical cell cryopreservation methods is of great importance to a variety of sectors, especially when considering the efficient short- and long-term storage of cells and their transportation. Although the overall success of such methods has been increased in recent years, ther... |
1005.2372 | Andrew Black | Andrew J Black and Alan J McKane | Stochastic amplification in an epidemic model with seasonal forcing | Updated with revisions and two new appendices | J. Theor. Biol., 267, 85-94, (2010) | 10.1016/j.jtbi.2010.08.014 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the stochastic susceptible-infected-recovered (SIR) model with
time-dependent forcing using analytic techniques which allow us to disentangle
the interaction of stochasticity and external forcing. The model is formulated
as a continuous time Markov process, which is decomposed into a deterministic
dynamics t... | [
{
"created": "Thu, 13 May 2010 16:44:41 GMT",
"version": "v1"
},
{
"created": "Wed, 4 Aug 2010 10:56:59 GMT",
"version": "v2"
}
] | 2010-11-23 | [
[
"Black",
"Andrew J",
""
],
[
"McKane",
"Alan J",
""
]
] | We study the stochastic susceptible-infected-recovered (SIR) model with time-dependent forcing using analytic techniques which allow us to disentangle the interaction of stochasticity and external forcing. The model is formulated as a continuous time Markov process, which is decomposed into a deterministic dynamics tog... |
2201.04778 | Jiayu Shang | Jiayu Shang and Xubo Tang and Ruocheng Guo and Yanni Sun | Accurate identification of bacteriophages from metagenomic data using
Transformer | 15 phages, 11 figures | Briefings in Bioinformatics, Volume 23, Issue 4, July 2022,
bbac258 | 10.1093/bib/bbac258 | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Motivation: Bacteriophages are viruses infecting bacteria. Being key players
in microbial communities, they can regulate the composition/function of
microbiome by infecting their bacterial hosts and mediating gene transfer.
Recently, metagenomic sequencing, which can sequence all genetic materials from
various microb... | [
{
"created": "Thu, 13 Jan 2022 03:32:04 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Aug 2022 02:50:00 GMT",
"version": "v2"
}
] | 2022-08-15 | [
[
"Shang",
"Jiayu",
""
],
[
"Tang",
"Xubo",
""
],
[
"Guo",
"Ruocheng",
""
],
[
"Sun",
"Yanni",
""
]
] | Motivation: Bacteriophages are viruses infecting bacteria. Being key players in microbial communities, they can regulate the composition/function of microbiome by infecting their bacterial hosts and mediating gene transfer. Recently, metagenomic sequencing, which can sequence all genetic materials from various microbio... |
2202.04324 | Florent Meyniel | Edgar Y Walker, Stephan Pohl, Rachel N Denison, David L Barack,
Jennifer Lee, Ned Block, Wei Ji Ma, Florent Meyniel | Studying the neural representations of uncertainty | 23 pages, 3 figures. Nature Neuroscience (2023) | null | 10.1038/s41593-023-01444-y | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The study of the brain's representations of uncertainty is a central topic in
neuroscience. Unlike most quantities of which the neural representation is
studied, uncertainty is a property of an observer's beliefs about the world,
which poses specific methodological challenges. We analyze how the literature
on the neu... | [
{
"created": "Wed, 9 Feb 2022 08:13:36 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Aug 2022 14:47:41 GMT",
"version": "v2"
},
{
"created": "Thu, 15 Dec 2022 14:05:10 GMT",
"version": "v3"
},
{
"created": "Wed, 11 Oct 2023 07:46:37 GMT",
"version": "v4"
}
] | 2023-10-12 | [
[
"Walker",
"Edgar Y",
""
],
[
"Pohl",
"Stephan",
""
],
[
"Denison",
"Rachel N",
""
],
[
"Barack",
"David L",
""
],
[
"Lee",
"Jennifer",
""
],
[
"Block",
"Ned",
""
],
[
"Ma",
"Wei Ji",
""
],
[
"Meynie... | The study of the brain's representations of uncertainty is a central topic in neuroscience. Unlike most quantities of which the neural representation is studied, uncertainty is a property of an observer's beliefs about the world, which poses specific methodological challenges. We analyze how the literature on the neura... |
2108.04992 | Maxim Lavrentovich | Adam S. Bryant and Maxim O. Lavrentovich | Survival in Branching Cellular Populations | 23 pages, 10 figures, minor corrections and clarifications | Theor. Popul. Biol. 144 (2022) 13-23 | 10.1016/j.tpb.2022.01.005 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze evolutionary dynamics in a confluent, branching cellular
population, such as in a growing duct, vasculature, or in a branching microbial
colony. We focus on the coarse-grained features of the evolution and build a
statistical model that captures the essential features of the dynamics. Using
simulations and... | [
{
"created": "Wed, 11 Aug 2021 02:32:00 GMT",
"version": "v1"
},
{
"created": "Sun, 13 Feb 2022 06:52:29 GMT",
"version": "v2"
}
] | 2022-02-15 | [
[
"Bryant",
"Adam S.",
""
],
[
"Lavrentovich",
"Maxim O.",
""
]
] | We analyze evolutionary dynamics in a confluent, branching cellular population, such as in a growing duct, vasculature, or in a branching microbial colony. We focus on the coarse-grained features of the evolution and build a statistical model that captures the essential features of the dynamics. Using simulations and a... |
2111.10656 | Aleksei Shpilman | Natalia Zenkova, Ekaterina Sedykh, Tatiana Shugaeva, Vladislav
Strashko, Timofei Ermak, Aleksei Shpilman | Simple End-to-end Deep Learning Model for CDR-H3 Loop Structure
Prediction | NeurIPS 2021 Machine Learning for Structural Biology Workshop | null | null | null | q-bio.BM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Predicting a structure of an antibody from its sequence is important since it
allows for a better design process of synthetic antibodies that play a vital
role in the health industry. Most of the structure of an antibody is
conservative. The most variable and hard-to-predict part is the third
complementarity-determin... | [
{
"created": "Sat, 20 Nov 2021 18:55:09 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Dec 2021 14:40:58 GMT",
"version": "v2"
}
] | 2021-12-23 | [
[
"Zenkova",
"Natalia",
""
],
[
"Sedykh",
"Ekaterina",
""
],
[
"Shugaeva",
"Tatiana",
""
],
[
"Strashko",
"Vladislav",
""
],
[
"Ermak",
"Timofei",
""
],
[
"Shpilman",
"Aleksei",
""
]
] | Predicting a structure of an antibody from its sequence is important since it allows for a better design process of synthetic antibodies that play a vital role in the health industry. Most of the structure of an antibody is conservative. The most variable and hard-to-predict part is the third complementarity-determinin... |
2403.07664 | Lingyu Li | Lingyu Li, Chunbo Li | Enabling self-identification in intelligent agent: insights from
computational psychoanalysis | 18 pages, 3 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Building upon prior framework of computational Lacanian psychoanalysis with
the theory of active inference, this paper aims to further explore the concept
of self-identification and its potential applications. Beginning with two
classic paradigms in psychology, mirror self-recognition and rubber hand
illusion, we sug... | [
{
"created": "Tue, 12 Mar 2024 13:54:25 GMT",
"version": "v1"
}
] | 2024-03-13 | [
[
"Li",
"Lingyu",
""
],
[
"Li",
"Chunbo",
""
]
] | Building upon prior framework of computational Lacanian psychoanalysis with the theory of active inference, this paper aims to further explore the concept of self-identification and its potential applications. Beginning with two classic paradigms in psychology, mirror self-recognition and rubber hand illusion, we sugge... |
1809.10681 | Zexian Zeng | Zexian Zeng, Andy Vo, Chengsheng Mao, Susan E Clare, Seema A Khan,
Yuan Luo | Cancer classification and pathway discovery using non-negative matrix
factorization | 8 pages, 5 figures, conference | null | null | null | q-bio.GN cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Extracting genetic information from a full range of sequencing data is
important for understanding diseases. We propose a novel method to effectively
explore the landscape of genetic mutations and aggregate them to predict cancer
type. We used multinomial logistic regression, nonsmooth non-negative matrix
factorizati... | [
{
"created": "Thu, 27 Sep 2018 13:22:11 GMT",
"version": "v1"
},
{
"created": "Mon, 8 Oct 2018 19:56:24 GMT",
"version": "v2"
}
] | 2018-10-10 | [
[
"Zeng",
"Zexian",
""
],
[
"Vo",
"Andy",
""
],
[
"Mao",
"Chengsheng",
""
],
[
"Clare",
"Susan E",
""
],
[
"Khan",
"Seema A",
""
],
[
"Luo",
"Yuan",
""
]
] | Extracting genetic information from a full range of sequencing data is important for understanding diseases. We propose a novel method to effectively explore the landscape of genetic mutations and aggregate them to predict cancer type. We used multinomial logistic regression, nonsmooth non-negative matrix factorization... |
q-bio/0406012 | Ted Theodosopoulos | Patricia Theodosopoulos and Ted Theodosopoulos | A computational study of the statistical mechanics of antibody-antigen
conformations | 12 pages, 5 figures | null | null | null | q-bio.QM q-bio.BM q-bio.PE | null | We describe the representation of the chemical affinity between the
antigen-combining site of the immunoglobulin molecule and the antigen molecule
as the probability of the two molecules existing in a bound state. Our model is
based on the identification of shape attractors in the configuration space for
the joint an... | [
{
"created": "Fri, 4 Jun 2004 01:51:12 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Theodosopoulos",
"Patricia",
""
],
[
"Theodosopoulos",
"Ted",
""
]
] | We describe the representation of the chemical affinity between the antigen-combining site of the immunoglobulin molecule and the antigen molecule as the probability of the two molecules existing in a bound state. Our model is based on the identification of shape attractors in the configuration space for the joint anti... |
1112.3046 | Steven Frank | Steven A. Frank | Evolutionary foundations of cooperation and group cohesion | null | Games, Groups, and the Global Good (2009), Springer, 3-40 | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In biology, the evolution of increasingly cooperative groups has shaped the
history of life. Genes collaborate in the control of cells; cells efficiently
divide tasks to produce cohesive multicellular individuals; individual members
of insect colonies cooperate in integrated societies. Biological cooperation
provides... | [
{
"created": "Tue, 13 Dec 2011 21:13:22 GMT",
"version": "v1"
}
] | 2011-12-15 | [
[
"Frank",
"Steven A.",
""
]
] | In biology, the evolution of increasingly cooperative groups has shaped the history of life. Genes collaborate in the control of cells; cells efficiently divide tasks to produce cohesive multicellular individuals; individual members of insect colonies cooperate in integrated societies. Biological cooperation provides a... |
1305.0306 | Frederick Matsen IV | Connor O. McCoy and Frederick A. Matsen IV | Abundance-weighted phylogenetic diversity measures distinguish microbial
community states and are robust to sampling depth | Submitted to PeerJ | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In microbial ecology studies, the most commonly used ways of investigating
alpha (within-sample) diversity are either to apply count-only measures such as
Simpson's index to Operational Taxonomic Unit (OTU) groupings, or to use
classical phylogenetic diversity (PD), which is not abundance-weighted.
Although alpha div... | [
{
"created": "Wed, 1 May 2013 22:30:30 GMT",
"version": "v1"
}
] | 2013-05-03 | [
[
"McCoy",
"Connor O.",
""
],
[
"Matsen",
"Frederick A.",
"IV"
]
] | In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply count-only measures such as Simpson's index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity (PD), which is not abundance-weighted. Although alpha diver... |
2303.06183 | Sarah Kaakai | Daphn\'e Giorgi, Sarah Kaakai, Vincent Lemaire | Efficient simulation of individual-based population models: the R
Package IBMPopSim | null | null | null | null | q-bio.PE cs.MS math.PR | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The R Package IBMPopSim aims to simulate the random evolution of
heterogeneous populations using stochastic Individual-Based Models (IBMs).
The package enables users to simulate population evolution, in which
individuals are characterized by their age and some characteristics, and the
population is modified by diff... | [
{
"created": "Fri, 10 Mar 2023 19:31:50 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Feb 2024 14:56:53 GMT",
"version": "v2"
}
] | 2024-02-28 | [
[
"Giorgi",
"Daphné",
""
],
[
"Kaakai",
"Sarah",
""
],
[
"Lemaire",
"Vincent",
""
]
] | The R Package IBMPopSim aims to simulate the random evolution of heterogeneous populations using stochastic Individual-Based Models (IBMs). The package enables users to simulate population evolution, in which individuals are characterized by their age and some characteristics, and the population is modified by differen... |
2209.06603 | James Blachly | Charles Thomas Gregory and James S. Blachly | Typesafe Coordinate Systems in High-Throughput Sequencing Applications | 14 pages, 3 figures. Code available at
https://github.com/blachlylab/typesafe-coordinates | null | null | null | q-bio.GN cs.LO cs.PL | http://creativecommons.org/licenses/by-nc-sa/4.0/ | High-throughput sequencing file formats and tools encode coordinate intervals
with respect to a reference sequence in at least four distinct, incompatible
ways. Integrating data from and moving data between different formats has the
potential to introduce subtle off-by-one errors. Here, we introduce the notion
of typ... | [
{
"created": "Wed, 14 Sep 2022 12:41:52 GMT",
"version": "v1"
}
] | 2022-09-15 | [
[
"Gregory",
"Charles Thomas",
""
],
[
"Blachly",
"James S.",
""
]
] | High-throughput sequencing file formats and tools encode coordinate intervals with respect to a reference sequence in at least four distinct, incompatible ways. Integrating data from and moving data between different formats has the potential to introduce subtle off-by-one errors. Here, we introduce the notion of types... |
1604.03071 | Anton Korobeynikov | Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov and Pavel Pevzner | metaSPAdes: a new versatile de novo metagenomics assembler | null | null | null | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While metagenomics has emerged as a technology of choice for analyzing
bacterial populations, assembly of metagenomic data remains difficult thus
stifling biological discoveries. metaSPAdes is a new assembler that addresses
the challenge of metagenome analysis and capitalizes on computational ideas
that proved to be ... | [
{
"created": "Mon, 11 Apr 2016 19:09:22 GMT",
"version": "v1"
},
{
"created": "Mon, 1 Aug 2016 15:32:16 GMT",
"version": "v2"
}
] | 2016-08-02 | [
[
"Nurk",
"Sergey",
""
],
[
"Meleshko",
"Dmitry",
""
],
[
"Korobeynikov",
"Anton",
""
],
[
"Pevzner",
"Pavel",
""
]
] | While metagenomics has emerged as a technology of choice for analyzing bacterial populations, assembly of metagenomic data remains difficult thus stifling biological discoveries. metaSPAdes is a new assembler that addresses the challenge of metagenome analysis and capitalizes on computational ideas that proved to be us... |
2311.04545 | Eiji Yamamoto | Eiji Yamamoto and Keehyoung Joo and Jooyoung Lee and Mark S. P. Sansom
and Masato Yasui | Molecular mechanism of anion permeation through aquaporin 6 | null | null | null | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Aquaporins (AQPs) are recognized as transmembrane water channels that
facilitate selective water permeation through their monomeric pores. Among the
AQP family, AQP6 has a unique characteristic as an anion channel, which is
allosterically controlled by pH conditions and is eliminated by a single amino
acid mutation. ... | [
{
"created": "Wed, 8 Nov 2023 09:23:44 GMT",
"version": "v1"
}
] | 2023-11-09 | [
[
"Yamamoto",
"Eiji",
""
],
[
"Joo",
"Keehyoung",
""
],
[
"Lee",
"Jooyoung",
""
],
[
"Sansom",
"Mark S. P.",
""
],
[
"Yasui",
"Masato",
""
]
] | Aquaporins (AQPs) are recognized as transmembrane water channels that facilitate selective water permeation through their monomeric pores. Among the AQP family, AQP6 has a unique characteristic as an anion channel, which is allosterically controlled by pH conditions and is eliminated by a single amino acid mutation. Ho... |
2312.12916 | Matthias Borgstede | Matthias Borgstede | A generalized Price equation for fuzzy set-mappings | 9 pages | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The Price equation provides a formal account of selection building on a
right-total mapping between two classes of individuals, that is usually
interpreted as a parent-offspring relation. This paper presents a new
formulation of the Price equation in terms of fuzzy set-mappings to account for
structures where the tar... | [
{
"created": "Wed, 20 Dec 2023 10:52:54 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Jan 2024 14:24:26 GMT",
"version": "v2"
}
] | 2024-01-04 | [
[
"Borgstede",
"Matthias",
""
]
] | The Price equation provides a formal account of selection building on a right-total mapping between two classes of individuals, that is usually interpreted as a parent-offspring relation. This paper presents a new formulation of the Price equation in terms of fuzzy set-mappings to account for structures where the targe... |
q-bio/0412028 | Osvaldo Zagordi | O. Zagordi, J. R. Lobry | Forcing reversibility in the no strand-bias substitution model allows
for the theoretical and practical identifiability of its 5 parameters from
pairwise DNA sequence comparisons | 12 pages, 4 figures, corrected typos | Gene, Volume 347 (2) 175-182 (2005) | 10.1016/j.gene.2004.12.019 | null | q-bio.PE | null | Because of the base pairing rules in DNA, some mutations experienced by a
portion of DNA during its evolution result in the same substitution, as we can
only observe differences in coupled nucleotides. Then, in the absence of a bias
between the two DNA strands, a model with at most 6 different parameters
instead of 1... | [
{
"created": "Wed, 15 Dec 2004 18:15:33 GMT",
"version": "v1"
},
{
"created": "Thu, 16 Dec 2004 11:00:31 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Zagordi",
"O.",
""
],
[
"Lobry",
"J. R.",
""
]
] | Because of the base pairing rules in DNA, some mutations experienced by a portion of DNA during its evolution result in the same substitution, as we can only observe differences in coupled nucleotides. Then, in the absence of a bias between the two DNA strands, a model with at most 6 different parameters instead of 12 ... |
1806.09532 | Joos Behncke | Joos Behncke, Robin Tibor Schirrmeister, Martin V\"olker, Ji\v{r}\'i
Hammer, Petr Marusi\v{c}, Andreas Schulze-Bonhage, Wolfram Burgard, Tonio
Ball | Cross-paradigm pretraining of convolutional networks improves
intracranial EEG decoding | null | null | null | null | q-bio.NC cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When it comes to the classification of brain signals in real-life
applications, the training and the prediction data are often described by
different distributions. Furthermore, diverse data sets, e.g., recorded from
various subjects or tasks, can even exhibit distinct feature spaces. The fact
that data that have to ... | [
{
"created": "Wed, 20 Jun 2018 11:34:36 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Jul 2018 10:18:28 GMT",
"version": "v2"
}
] | 2018-07-23 | [
[
"Behncke",
"Joos",
""
],
[
"Schirrmeister",
"Robin Tibor",
""
],
[
"Völker",
"Martin",
""
],
[
"Hammer",
"Jiří",
""
],
[
"Marusič",
"Petr",
""
],
[
"Schulze-Bonhage",
"Andreas",
""
],
[
"Burgard",
"Wolfram",
... | When it comes to the classification of brain signals in real-life applications, the training and the prediction data are often described by different distributions. Furthermore, diverse data sets, e.g., recorded from various subjects or tasks, can even exhibit distinct feature spaces. The fact that data that have to be... |
1609.09202 | Sutapa Mukherji | Sutapa Mukherji | Transcriptional and translational regulation in Arc protein network of
Escherichia coli's stress response | 16 pages, 9 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, there has been a lot of effort in understanding sRNA mediated
regulation of gene expression and how this mode of regulation differs from
transcriptional regulation.In E.coli, in the presence of oxidative stress, the
synthesis of sigma^s is regulated through an interesting mechanism involving
both transcript... | [
{
"created": "Thu, 29 Sep 2016 04:49:58 GMT",
"version": "v1"
}
] | 2016-09-30 | [
[
"Mukherji",
"Sutapa",
""
]
] | Recently, there has been a lot of effort in understanding sRNA mediated regulation of gene expression and how this mode of regulation differs from transcriptional regulation.In E.coli, in the presence of oxidative stress, the synthesis of sigma^s is regulated through an interesting mechanism involving both transcriptio... |
1109.4498 | Ronan M.T. Fleming Dr | Ronan M.T. Fleming and Ines Thiele | Mass conserved elementary kinetics is sufficient for the existence of a
non-equilibrium steady state concentration | 11 pages, 2 figures (v2 is now placed in proper context of the
excellent 1962 paper by James Wei entitled "Axiomatic treatment of chemical
reaction systems". In addition, section 4, on "Utility of steady state
existence theorem" has been expanded.) | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Living systems are forced away from thermodynamic equilibrium by exchange of
mass and energy with their environment. In order to model a biochemical
reaction network in a non-equilibrium state one requires a mathematical
formulation to mimic this forcing. We provide a general formulation to force an
arbitrary large k... | [
{
"created": "Wed, 21 Sep 2011 10:31:29 GMT",
"version": "v1"
},
{
"created": "Sat, 18 Feb 2012 00:07:48 GMT",
"version": "v2"
}
] | 2012-02-21 | [
[
"Fleming",
"Ronan M. T.",
""
],
[
"Thiele",
"Ines",
""
]
] | Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to mimic this forcing. We provide a general formulation to force an arbitrary large kin... |
0807.4860 | Peter Csermely | Zoltan Spiro, Istvan A. Kovacs and Peter Csermely | Drug-therapy networks and the predictions of novel drug targets | This is an extended version of the Journal of Biology paper
containing 2 Figures, 1 Table and 44 references | Journal of Biology 2008, 7:20 | 10.1186/jbiol81 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, a number of drug-therapy, disease, drug, and drug-target networks
have been introduced. Here we suggest novel methods for network-based
prediction of novel drug targets and for improvement of drug efficiency by
analysing the effects of drugs on the robustness of cellular networks.
| [
{
"created": "Wed, 30 Jul 2008 13:28:27 GMT",
"version": "v1"
}
] | 2008-07-31 | [
[
"Spiro",
"Zoltan",
""
],
[
"Kovacs",
"Istvan A.",
""
],
[
"Csermely",
"Peter",
""
]
] | Recently, a number of drug-therapy, disease, drug, and drug-target networks have been introduced. Here we suggest novel methods for network-based prediction of novel drug targets and for improvement of drug efficiency by analysing the effects of drugs on the robustness of cellular networks. |
1511.04027 | Diego Chowell | Diego Chowell, Muntaser Safan, and Carlos Castillo-Chavez | Modeling the case of early detection of Ebola virus disease | null | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The most recent Ebola outbreak in West Africa highlighted critical weaknesses
in the medical infrastructure of the affected countries, including effective
diagnostics tools, sufficient isolation wards, and enough medical personnel.
Here, we develop and analyze a mathematical model to assess the impact of early
diagno... | [
{
"created": "Fri, 6 Nov 2015 23:18:32 GMT",
"version": "v1"
}
] | 2015-11-13 | [
[
"Chowell",
"Diego",
""
],
[
"Safan",
"Muntaser",
""
],
[
"Castillo-Chavez",
"Carlos",
""
]
] | The most recent Ebola outbreak in West Africa highlighted critical weaknesses in the medical infrastructure of the affected countries, including effective diagnostics tools, sufficient isolation wards, and enough medical personnel. Here, we develop and analyze a mathematical model to assess the impact of early diagnosi... |
q-bio/0502007 | Axel G. Rossberg | A. G. Rossberg, H. Matsuda, T. Amemiya, K. Itoh | Some Properties of the Speciation Model for Food-Web Structure -
Mechanisms for Degree Distributions and Intervality | 23 pages, 6 figures, minor rewrites | null | null | null | q-bio.PE q-bio.MN | null | We present a mathematical analysis of the speciation model for food-web
structure, which had in previous work been shown to yield a good description of
empirical data of food-web topology. The degree distributions of the network
are derived. Properties of the speciation model are compared to those of other
models tha... | [
{
"created": "Tue, 8 Feb 2005 05:05:17 GMT",
"version": "v1"
},
{
"created": "Thu, 2 Jun 2005 04:34:02 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Rossberg",
"A. G.",
""
],
[
"Matsuda",
"H.",
""
],
[
"Amemiya",
"T.",
""
],
[
"Itoh",
"K.",
""
]
] | We present a mathematical analysis of the speciation model for food-web structure, which had in previous work been shown to yield a good description of empirical data of food-web topology. The degree distributions of the network are derived. Properties of the speciation model are compared to those of other models that ... |
1303.5569 | Daniel Zerbino | Daniel R. Zerbino, Tracy Ballinger, Benedict Paten, Glenn Hickey and
David Haussler | Representing and decomposing genomic structural variants as balanced
integer flows on sequence graphs | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The study of genomic variation has provided key insights into the functional
role of mutations. Predominantly, studies have focused on single nucleotide
variants (SNV), which are relatively easy to detect and can be described with
rich mathematical models. However, it has been observed that genomes are highly
plastic... | [
{
"created": "Fri, 22 Mar 2013 10:10:41 GMT",
"version": "v1"
},
{
"created": "Thu, 3 Sep 2015 09:56:40 GMT",
"version": "v2"
}
] | 2015-09-04 | [
[
"Zerbino",
"Daniel R.",
""
],
[
"Ballinger",
"Tracy",
""
],
[
"Paten",
"Benedict",
""
],
[
"Hickey",
"Glenn",
""
],
[
"Haussler",
"David",
""
]
] | The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich mathematical models. However, it has been observed that genomes are highly plastic, ... |
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