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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1212.1909 | Luay Nakhleh | Yun Yu and Luay Nakhleh | Fast Algorithms for Reconciliation under Hybridization and Incomplete
Lineage Sorting | null | null | null | null | q-bio.PE cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reconciling a gene tree with a species tree is an important task that reveals
much about the evolution of genes, genomes, and species, as well as about the
molecular function of genes. A wide array of computational tools have been
devised for this task under certain evolutionary events such as hybridization,
gene dup... | [
{
"created": "Sun, 9 Dec 2012 18:12:55 GMT",
"version": "v1"
}
] | 2012-12-11 | [
[
"Yu",
"Yun",
""
],
[
"Nakhleh",
"Luay",
""
]
] | Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised for this task under certain evolutionary events such as hybridization, gene dupli... |
2405.04550 | Cole Gawin | Cole Gawin | Exploring a Cognitive Architecture for Learning Arithmetic Equations | 16 pages, 6 figures, 2 tables | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | The acquisition and performance of arithmetic skills and basic operations
such as addition, subtraction, multiplication, and division are essential for
daily functioning, and reflect complex cognitive processes. This paper explores
the cognitive mechanisms powering arithmetic learning, presenting a
neurobiologically ... | [
{
"created": "Sun, 5 May 2024 18:42:00 GMT",
"version": "v1"
}
] | 2024-05-09 | [
[
"Gawin",
"Cole",
""
]
] | The acquisition and performance of arithmetic skills and basic operations such as addition, subtraction, multiplication, and division are essential for daily functioning, and reflect complex cognitive processes. This paper explores the cognitive mechanisms powering arithmetic learning, presenting a neurobiologically pl... |
q-bio/0609033 | Deok-Sun Lee | Deok-Sun Lee, Heiko Rieger | Comparative study of the transcriptional regulatory networks of E. coli
and yeast: Structural characteristics leading to marginal dynamic stability | 7 pages, 5 figures | null | null | null | q-bio.MN | null | Dynamical properties of the transcriptional regulatory network of {\it
Escherichia coli} and {\it Saccharomyces cerevisiae} are studied within the
framework of random Boolean functions. The dynamical response of these networks
to a single point mutation is characterized by the number of mutated elements
as a function... | [
{
"created": "Fri, 22 Sep 2006 20:09:44 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Lee",
"Deok-Sun",
""
],
[
"Rieger",
"Heiko",
""
]
] | Dynamical properties of the transcriptional regulatory network of {\it Escherichia coli} and {\it Saccharomyces cerevisiae} are studied within the framework of random Boolean functions. The dynamical response of these networks to a single point mutation is characterized by the number of mutated elements as a function o... |
q-bio/0602002 | Thilo Gross | Ralf Steuer, Thilo Gross, Joachim Selbig and Bernd Blasius | Structural Kinetic Modeling of Metabolic Networks | 14 pages, 8 figures (color) | PNAS 103(32), 11868-11873, 2006. | 10.1073/pnas.0600013103 | null | q-bio.MN q-bio.CB | null | To develop and investigate detailed mathematical models of cellular metabolic
processes is one of the primary challenges in systems biology. However, despite
considerable advance in the topological analysis of metabolic networks,
explicit kinetic modeling based on differential equations is still often
severely hamper... | [
{
"created": "Wed, 1 Feb 2006 08:59:17 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Steuer",
"Ralf",
""
],
[
"Gross",
"Thilo",
""
],
[
"Selbig",
"Joachim",
""
],
[
"Blasius",
"Bernd",
""
]
] | To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit kinetic modeling based on differential equations is still often severely hampered... |
2302.09217 | Yunyi Shen | Hongliang Bu and Yunyi Shen | Identify local limiting factors of species distribution using min-linear
logistic regression | null | null | null | null | q-bio.QM stat.AP | http://creativecommons.org/licenses/by-sa/4.0/ | Logistic regression is a commonly used building block in ecological modeling,
but its additive structure among environmental predictors often assumes
compensatory relationships between predictors, which can lead to problematic
results. In reality, the distribution of species is often determined by the
least-favored f... | [
{
"created": "Sat, 18 Feb 2023 02:55:28 GMT",
"version": "v1"
}
] | 2023-02-21 | [
[
"Bu",
"Hongliang",
""
],
[
"Shen",
"Yunyi",
""
]
] | Logistic regression is a commonly used building block in ecological modeling, but its additive structure among environmental predictors often assumes compensatory relationships between predictors, which can lead to problematic results. In reality, the distribution of species is often determined by the least-favored fac... |
2104.09188 | Claudius Gros | Claudius Gros | A devil's advocate view on 'self-organized' brain criticality | null | Journal of Physics: Complexity 2, 031001 (2021) | 10.1088/2632-072X/abfa0f | null | q-bio.NC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stationarity of the constituents of the body and of its functionalities is a
basic requirement for life, being equivalent to survival in first place.
Assuming that the resting state activity of the brain serves essential
functionalities, stationarity entails that the dynamics of the brain needs to
be regulated on a t... | [
{
"created": "Mon, 19 Apr 2021 10:21:53 GMT",
"version": "v1"
}
] | 2021-05-14 | [
[
"Gros",
"Claudius",
""
]
] | Stationarity of the constituents of the body and of its functionalities is a basic requirement for life, being equivalent to survival in first place. Assuming that the resting state activity of the brain serves essential functionalities, stationarity entails that the dynamics of the brain needs to be regulated on a tim... |
1905.08518 | Christian Jelsch | L. Dettori, Christian Jelsch (CRM2), Y. Guiavarc'h, S. Delaunay
(LSGC), X. Framboisier (LSGC), I. Chevalot (LSGC), C. Humeau (LIBio) | Molecular rules for selectivity in lipase-catalysed acylation of lysine | null | Process Biochemistry, Elsevier, 2018, 74, pp.50-60 | 10.1016/j.procbio.2018.07.021 | null | q-bio.QM physics.chem-ph q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The selectivity of L-lysine acylation by lauric acid catalysed by Candida
antarctica lipase B (CALB) was investigated combining experimental and
theoretical methodologies. Experiments showed the near-exclusive acylation of
lysine $\epsilon$-amino group; only traces of product resulting from the
acylation of lysine $\... | [
{
"created": "Tue, 21 May 2019 09:43:58 GMT",
"version": "v1"
}
] | 2019-05-22 | [
[
"Dettori",
"L.",
"",
"CRM2"
],
[
"Jelsch",
"Christian",
"",
"CRM2"
],
[
"Guiavarc'h",
"Y.",
"",
"LSGC"
],
[
"Delaunay",
"S.",
"",
"LSGC"
],
[
"Framboisier",
"X.",
"",
"LSGC"
],
[
"Chevalot",
"I.",
"",
... | The selectivity of L-lysine acylation by lauric acid catalysed by Candida antarctica lipase B (CALB) was investigated combining experimental and theoretical methodologies. Experiments showed the near-exclusive acylation of lysine $\epsilon$-amino group; only traces of product resulting from the acylation of lysine $\al... |
1601.02240 | Chaitanya A. Athale | Chaitanya A. Athale | Effect of Replication Fork Dynamics on Escherichia coli Cell Size | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The variability in cell size of an isogenic population of Escherichia coli
has been widely reported in experiment. The probability density function (PDF)
of cell lengths has been variously described by exponential and lognormal
functions. While temperature, population density and growth rate have all been
shown to af... | [
{
"created": "Sun, 10 Jan 2016 17:56:36 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Jan 2016 13:05:11 GMT",
"version": "v2"
},
{
"created": "Thu, 13 Apr 2017 09:44:13 GMT",
"version": "v3"
},
{
"created": "Mon, 20 May 2019 07:32:35 GMT",
"version": "v4"
}
] | 2019-05-21 | [
[
"Athale",
"Chaitanya A.",
""
]
] | The variability in cell size of an isogenic population of Escherichia coli has been widely reported in experiment. The probability density function (PDF) of cell lengths has been variously described by exponential and lognormal functions. While temperature, population density and growth rate have all been shown to affe... |
q-bio/0406051 | Ha Youn Lee | Ha Youn Lee and Mehran Kardar | Statistics of lines of natural images and implications for visual
detection | null | null | null | null | q-bio.NC cond-mat.soft | null | As borders between different regions, lines are an important element of
natural images. Already at the level of the mammalian primary visual cortex
(V1), neurons respond best to lines of a given orientation. We reduce a set of
images to linear segments and analyze their statistical properties. In
particular, appropri... | [
{
"created": "Tue, 29 Jun 2004 15:42:28 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Lee",
"Ha Youn",
""
],
[
"Kardar",
"Mehran",
""
]
] | As borders between different regions, lines are an important element of natural images. Already at the level of the mammalian primary visual cortex (V1), neurons respond best to lines of a given orientation. We reduce a set of images to linear segments and analyze their statistical properties. In particular, appropriat... |
1005.3204 | Sergei Nechaev | V.A. Avetisov, S.K. Nechaev, A.B. Shkarin | On the motifs distribution in random hierarchical networks | 7 pages, 5 figures | null | 10.1016/j.physa.2010.09.016 | null | q-bio.QM cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The distribution of motifs in random hierarchical networks defined by
nonsymmetric random block--hierarchical adjacency matrices, is constructed for
the first time. According to the classification of U. Alon et al of network
superfamilies by their motifs distributions, our artificial directed random
hierarchical netw... | [
{
"created": "Tue, 18 May 2010 13:57:26 GMT",
"version": "v1"
}
] | 2015-05-19 | [
[
"Avetisov",
"V. A.",
""
],
[
"Nechaev",
"S. K.",
""
],
[
"Shkarin",
"A. B.",
""
]
] | The distribution of motifs in random hierarchical networks defined by nonsymmetric random block--hierarchical adjacency matrices, is constructed for the first time. According to the classification of U. Alon et al of network superfamilies by their motifs distributions, our artificial directed random hierarchical networ... |
1412.6225 | Angelo Rosa Dr | Manon Valet, Angelo Rosa | Viscoelasticity of model interphase chromosomes | 10 pages, 6 figures, accepted for publication in Journal of Chemical
Physics | J. Chem. Phys. 141, 245101 (2014) | 10.1063/1.4903996 | null | q-bio.BM cond-mat.soft physics.bio-ph q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigated the viscoelastic response of model interphase chromosomes by
tracking the three-dimensional motion of hundreds of dispersed Brownian
particles of sizes ranging from the thickness of the chromatin fiber up to
slightly above the mesh size of the chromatin solution. In agreement with
previous computation... | [
{
"created": "Fri, 19 Dec 2014 06:01:42 GMT",
"version": "v1"
}
] | 2015-01-06 | [
[
"Valet",
"Manon",
""
],
[
"Rosa",
"Angelo",
""
]
] | We investigated the viscoelastic response of model interphase chromosomes by tracking the three-dimensional motion of hundreds of dispersed Brownian particles of sizes ranging from the thickness of the chromatin fiber up to slightly above the mesh size of the chromatin solution. In agreement with previous computational... |
2206.06583 | Fajie Yuan | Mingyang Hu, Fajie Yuan, Kevin K. Yang, Fusong Ju, Jin Su, Hui Wang,
Fei Yang, Qiuyang Ding | Exploring evolution-aware & -free protein language models as protein
function predictors | null | null | null | null | q-bio.QM cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Large-scale Protein Language Models (PLMs) have improved performance in
protein prediction tasks, ranging from 3D structure prediction to various
function predictions. In particular, AlphaFold, a ground-breaking AI system,
could potentially reshape structural biology. However, the utility of the PLM
module in AlphaFo... | [
{
"created": "Tue, 14 Jun 2022 03:56:10 GMT",
"version": "v1"
},
{
"created": "Sun, 16 Oct 2022 10:00:24 GMT",
"version": "v2"
}
] | 2022-10-18 | [
[
"Hu",
"Mingyang",
""
],
[
"Yuan",
"Fajie",
""
],
[
"Yang",
"Kevin K.",
""
],
[
"Ju",
"Fusong",
""
],
[
"Su",
"Jin",
""
],
[
"Wang",
"Hui",
""
],
[
"Yang",
"Fei",
""
],
[
"Ding",
"Qiuyang",
"... | Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI system, could potentially reshape structural biology. However, the utility of the PLM module in AlphaFold... |
1911.02601 | Joaquin Goni | Enrico Amico, Kausar Abbas, Duy Anh Duong-Tran, Uttara Tipnis,
Meenusree Rajapandian, Evgeny Chumin, Mario Ventresca, Jaroslaw Harezlak,
Joaqu\'in Go\~ni | Towards an information theoretical description of communication in brain
networks | 28 pages; 4 figures; 1 table; 2 supplementary figures; 2
supplementary tables | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modeling communication dynamics in the brain is a key challenge in network
neuroscience. We present here a framework that combines two measurements for
any system where different communication processes are taking place on top of a
fixed structural topology: Path Processing Score (PPS) estimates how much the
brain si... | [
{
"created": "Wed, 6 Nov 2019 19:18:17 GMT",
"version": "v1"
},
{
"created": "Fri, 2 Oct 2020 19:21:35 GMT",
"version": "v2"
}
] | 2020-10-06 | [
[
"Amico",
"Enrico",
""
],
[
"Abbas",
"Kausar",
""
],
[
"Duong-Tran",
"Duy Anh",
""
],
[
"Tipnis",
"Uttara",
""
],
[
"Rajapandian",
"Meenusree",
""
],
[
"Chumin",
"Evgeny",
""
],
[
"Ventresca",
"Mario",
""
... | Modeling communication dynamics in the brain is a key challenge in network neuroscience. We present here a framework that combines two measurements for any system where different communication processes are taking place on top of a fixed structural topology: Path Processing Score (PPS) estimates how much the brain sign... |
2112.07775 | Tobiloba Adejumo | Tobiloba Adejumo, Tae-Hoon Kim, David Le, Taeyoon Son, Guangying Ma,
Xincheng Yao | Depth-resolved vascular profile features for artery-vein classification
in OCT and OCT angiography of human retina | 11 pages, 4 figures | null | 10.1364/BOE.450913 | null | q-bio.TO eess.IV | http://creativecommons.org/licenses/by/4.0/ | This study is to characterize reflectance profiles of retinal blood vessels
in optical coherence tomography (OCT), and to validate these vascular features
to guide artery-vein classification in OCT angiography (OCTA) of human retina.
Depth-resolved OCT reveals unique features of retinal arteries and veins.
Retinal ar... | [
{
"created": "Tue, 14 Dec 2021 22:49:46 GMT",
"version": "v1"
},
{
"created": "Sun, 6 Feb 2022 18:39:06 GMT",
"version": "v2"
}
] | 2022-02-08 | [
[
"Adejumo",
"Tobiloba",
""
],
[
"Kim",
"Tae-Hoon",
""
],
[
"Le",
"David",
""
],
[
"Son",
"Taeyoon",
""
],
[
"Ma",
"Guangying",
""
],
[
"Yao",
"Xincheng",
""
]
] | This study is to characterize reflectance profiles of retinal blood vessels in optical coherence tomography (OCT), and to validate these vascular features to guide artery-vein classification in OCT angiography (OCTA) of human retina. Depth-resolved OCT reveals unique features of retinal arteries and veins. Retinal arte... |
2206.15459 | Axel Brandenburg | Axel Brandenburg | Quadratic growth during the COVID-19 pandemic: merging hotspots and
reinfections | 11 pages, 10 figures, 1 table | J. Phys. A: Math. Theor. 56, 044002 (2023) | 10.1088/1751-8121/acb743 | NORDITA-2022-043 | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The existence of an exponential growth phase during early stages of a
pandemic is often taken for granted. However, for the 2019 novel coronavirus
epidemic, the early exponential phase lasted only for about six days, while the
quadratic growth prevailed for forty days until it spread to other countries
and continued,... | [
{
"created": "Thu, 30 Jun 2022 17:53:08 GMT",
"version": "v1"
},
{
"created": "Fri, 30 Dec 2022 11:17:16 GMT",
"version": "v2"
}
] | 2023-02-14 | [
[
"Brandenburg",
"Axel",
""
]
] | The existence of an exponential growth phase during early stages of a pandemic is often taken for granted. However, for the 2019 novel coronavirus epidemic, the early exponential phase lasted only for about six days, while the quadratic growth prevailed for forty days until it spread to other countries and continued, a... |
2007.10458 | Chowdhury Rahman | Ruhul Amin, Chowdhury Rafeed Rahman, Md. Sadrul Islam Toaha and
Swakkhar Shatabda | i6mA-CNN: a convolution based computational approach towards
identification of DNA N6-methyladenine sites in rice genome | null | null | 10.1101/2020.07.08.194308 | null | q-bio.GN cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | DNA N6-methylation (6mA) in Adenine nucleotide is a post replication
modification and is responsible for many biological functions. Experimental
methods for genome wide 6mA site detection is an expensive and manual labour
intensive process. Automated and accurate computational methods can help to
identify 6mA sites i... | [
{
"created": "Mon, 20 Jul 2020 20:37:01 GMT",
"version": "v1"
},
{
"created": "Tue, 11 Aug 2020 11:05:22 GMT",
"version": "v2"
}
] | 2020-08-12 | [
[
"Amin",
"Ruhul",
""
],
[
"Rahman",
"Chowdhury Rafeed",
""
],
[
"Toaha",
"Md. Sadrul Islam",
""
],
[
"Shatabda",
"Swakkhar",
""
]
] | DNA N6-methylation (6mA) in Adenine nucleotide is a post replication modification and is responsible for many biological functions. Experimental methods for genome wide 6mA site detection is an expensive and manual labour intensive process. Automated and accurate computational methods can help to identify 6mA sites in ... |
1103.5488 | Jorge Ramirez | Jorge M Ramirez | Population persistence under advection-diffusion in river networks | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An integro-differential equation on a tree graph is used to model the
evolution and spatial distribution of a population of organisms in a river
network. Individual organisms become mobile at a constant rate, and disperse
according to an advection-diffusion process with coefficients that are constant
on the edges of ... | [
{
"created": "Mon, 28 Mar 2011 21:07:47 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Mar 2011 21:35:21 GMT",
"version": "v2"
}
] | 2011-04-01 | [
[
"Ramirez",
"Jorge M",
""
]
] | An integro-differential equation on a tree graph is used to model the evolution and spatial distribution of a population of organisms in a river network. Individual organisms become mobile at a constant rate, and disperse according to an advection-diffusion process with coefficients that are constant on the edges of th... |
1105.4425 | Andrea Markelz | J.Y. Chen, D.K. George, Yunfen He, J.R.Knab and A. G. Markelz | Functional State Dependence of Picosecond Protein Dynamics | 4 main pages, 3 figures, 1 table, 2 supplemental tables | null | null | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We examine temperature dependent picosecond dynamics as a function of
structure and function for lysozyme and cytochrome c using temperature
dependent terahertz permittivity measurements. A double Arrhenius temperature
dependence with activation energies E1 ~ 0.1 kJ/mol and E2 ~10 kJ/mol fits the
native state respons... | [
{
"created": "Mon, 23 May 2011 08:01:45 GMT",
"version": "v1"
}
] | 2011-05-24 | [
[
"Chen",
"J. Y.",
""
],
[
"George",
"D. K.",
""
],
[
"He",
"Yunfen",
""
],
[
"Knab",
"J. R.",
""
],
[
"Markelz",
"A. G.",
""
]
] | We examine temperature dependent picosecond dynamics as a function of structure and function for lysozyme and cytochrome c using temperature dependent terahertz permittivity measurements. A double Arrhenius temperature dependence with activation energies E1 ~ 0.1 kJ/mol and E2 ~10 kJ/mol fits the native state response.... |
0709.1195 | Emmanuel Tannenbaum | Emmanuel Tannenbaum | Selective advantage for sexual reproduction with random haploid fusion | 11 pages, 1 figure, submitted to Physical Review E (additional 4
figures included in Phys. Rev. E submission) | null | null | null | q-bio.PE q-bio.CB | null | This paper develops a simplified set of models describing asexual and sexual
replication in unicel- lular diploid organisms. The models assume organisms
whose genomes consist of two chromosomes, where each chromosome is assumed to
be functional if it is equal to some master sequence $ \sigma_0 $, and
non-functional o... | [
{
"created": "Sat, 8 Sep 2007 09:52:35 GMT",
"version": "v1"
}
] | 2007-09-11 | [
[
"Tannenbaum",
"Emmanuel",
""
]
] | This paper develops a simplified set of models describing asexual and sexual replication in unicel- lular diploid organisms. The models assume organisms whose genomes consist of two chromosomes, where each chromosome is assumed to be functional if it is equal to some master sequence $ \sigma_0 $, and non-functional oth... |
2401.10972 | Paula Mercurio | Paula Mercurio and Di Liu | Clustering Molecular Energy Landscapes by Adaptive Network Embedding | 19 pages, 10 figures | null | null | null | q-bio.BM cond-mat.stat-mech cs.LG | http://creativecommons.org/licenses/by/4.0/ | In order to efficiently explore the chemical space of all possible small
molecules, a common approach is to compress the dimension of the system to
facilitate downstream machine learning tasks. Towards this end, we present a
data driven approach for clustering potential energy landscapes of molecular
structures by ap... | [
{
"created": "Fri, 19 Jan 2024 17:12:07 GMT",
"version": "v1"
}
] | 2024-01-23 | [
[
"Mercurio",
"Paula",
""
],
[
"Liu",
"Di",
""
]
] | In order to efficiently explore the chemical space of all possible small molecules, a common approach is to compress the dimension of the system to facilitate downstream machine learning tasks. Towards this end, we present a data driven approach for clustering potential energy landscapes of molecular structures by appl... |
1710.05914 | Davide Nardone | Davide Nardone, Angelo Ciaramella, Mariangela Cerreta, Salvatore
Pulcrano, Gian Carlo Bellenchi, Giuseppe Manco, Ferdinando Febbraio | SELYMATRA: Web Application for the analysis of mass spectra | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Surface Enhanced Laser Desorption/Ionization-Time Of Flight Mass Spectrometry
(SELDI-TOF MS) is a variant of the MALDI. It is uses in many cases especially
for the analysis of protein profiling and for preliminary screening tasks of
complex sample aimed for the searching of biomarker. Unfortunately, these
analysis ar... | [
{
"created": "Sun, 15 Oct 2017 16:05:43 GMT",
"version": "v1"
}
] | 2017-10-18 | [
[
"Nardone",
"Davide",
""
],
[
"Ciaramella",
"Angelo",
""
],
[
"Cerreta",
"Mariangela",
""
],
[
"Pulcrano",
"Salvatore",
""
],
[
"Bellenchi",
"Gian Carlo",
""
],
[
"Manco",
"Giuseppe",
""
],
[
"Febbraio",
"Ferdin... | Surface Enhanced Laser Desorption/Ionization-Time Of Flight Mass Spectrometry (SELDI-TOF MS) is a variant of the MALDI. It is uses in many cases especially for the analysis of protein profiling and for preliminary screening tasks of complex sample aimed for the searching of biomarker. Unfortunately, these analysis are ... |
2102.04260 | Delfim F. M. Torres | Marouane Mahrouf, Adnane Boukhouima, Houssine Zine, El Mehdi Lotfi,
Delfim F. M. Torres, Noura Yousfi | Modeling and Forecasting of COVID-19 Spreading by Delayed Stochastic
Differential Equations | This is a preprint of a paper whose final and definite form is
published, open access, by 'Axioms' (ISSN: 2075-1680). Submitted Axioms: 2
Dec 2020; Revised: 20 and 31 Jan 2021; correction to proofs: 4 Feb 2021 | Axioms 10 (2021), no. 1, Art. 18, 16 pp | 10.3390/axioms10010018 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The novel coronavirus disease (COVID-19) pneumonia has posed a great threat
to the world recent months by causing many deaths and enormous economic damage
worldwide. The first case of COVID-19 in Morocco was reported on 2 March 2020,
and the number of reported cases has increased day by day. In this work, we
extend t... | [
{
"created": "Thu, 4 Feb 2021 19:15:32 GMT",
"version": "v1"
}
] | 2021-02-10 | [
[
"Mahrouf",
"Marouane",
""
],
[
"Boukhouima",
"Adnane",
""
],
[
"Zine",
"Houssine",
""
],
[
"Lotfi",
"El Mehdi",
""
],
[
"Torres",
"Delfim F. M.",
""
],
[
"Yousfi",
"Noura",
""
]
] | The novel coronavirus disease (COVID-19) pneumonia has posed a great threat to the world recent months by causing many deaths and enormous economic damage worldwide. The first case of COVID-19 in Morocco was reported on 2 March 2020, and the number of reported cases has increased day by day. In this work, we extend the... |
1006.2923 | Christian Guill | Christian Guill, Barbara Drossel, Wolfram Just, and Eddy Carmack | A three-species model explaining cyclic dominance of pacific salmon | 7 pages, 5 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The four-year oscillations of the number of spawning sockeye salmon
(Oncorhynchus nerka) that return to their native stream within the Fraser River
basin in Canada are a striking example of population oscillations. The period
of the oscillation corresponds to the dominant generation time of these fish.
Various - not ... | [
{
"created": "Tue, 15 Jun 2010 08:40:28 GMT",
"version": "v1"
}
] | 2010-06-16 | [
[
"Guill",
"Christian",
""
],
[
"Drossel",
"Barbara",
""
],
[
"Just",
"Wolfram",
""
],
[
"Carmack",
"Eddy",
""
]
] | The four-year oscillations of the number of spawning sockeye salmon (Oncorhynchus nerka) that return to their native stream within the Fraser River basin in Canada are a striking example of population oscillations. The period of the oscillation corresponds to the dominant generation time of these fish. Various - not fu... |
1411.5624 | Jian-Zhou Zhu | Kun Gao, HongGuang Sun, Jian-Zhou Zhu | Disorder and Power-law Tails of DNA Sequence Self-Alignment
Concentrations in Molecular Evolution | a figure for the introductory discussion removed; less lengthy | null | null | null | q-bio.PE physics.bio-ph q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The self-alignment concentrations, $c(x)$, as functions of the length, $x$,
of the identically matching maximal segments in the genomes of a variety of
species, typically present power-law tails extending to the largest scales,
i.e., $c(x) \propto x^{\alpha}$, with similar or apparently different negative
$\alpha$s (... | [
{
"created": "Thu, 20 Nov 2014 17:49:54 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Nov 2014 11:44:07 GMT",
"version": "v2"
},
{
"created": "Sat, 20 Dec 2014 02:50:39 GMT",
"version": "v3"
}
] | 2014-12-23 | [
[
"Gao",
"Kun",
""
],
[
"Sun",
"HongGuang",
""
],
[
"Zhu",
"Jian-Zhou",
""
]
] | The self-alignment concentrations, $c(x)$, as functions of the length, $x$, of the identically matching maximal segments in the genomes of a variety of species, typically present power-law tails extending to the largest scales, i.e., $c(x) \propto x^{\alpha}$, with similar or apparently different negative $\alpha$s ($<... |
q-bio/0312006 | Thomas Down | Thomas A. Down and Tim J. P. Hubbard | Relevance Vector Machines for classifying points and regions in
biological sequences | 16 pages, 3 figures | null | null | null | q-bio.GN | null | The Relevance Vector Machine (RVM) is a recently developed machine learning
framework capable of building simple models from large sets of candidate
features. Here, we describe a protocol for using the RVM to explore very large
numbers of candidate features, and a family of models which apply the power of
the RVM to ... | [
{
"created": "Thu, 4 Dec 2003 11:55:20 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Down",
"Thomas A.",
""
],
[
"Hubbard",
"Tim J. P.",
""
]
] | The Relevance Vector Machine (RVM) is a recently developed machine learning framework capable of building simple models from large sets of candidate features. Here, we describe a protocol for using the RVM to explore very large numbers of candidate features, and a family of models which apply the power of the RVM to cl... |
1807.03784 | Dirson Jian Li | Dirson Jian Li | Observations and perspectives on the diversification of genomes | 43 pages, 10 figures | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Rich information on the prebiotic evolution is still stored in contemporary
genomic data. The statistical mechanism at the sequence level may play a
significant role in the prebiotic evolution. Based on statistical analysis of
genome sequences, it has been observed that there is a close relationship
between the evolu... | [
{
"created": "Tue, 10 Jul 2018 17:20:33 GMT",
"version": "v1"
}
] | 2018-07-12 | [
[
"Li",
"Dirson Jian",
""
]
] | Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome sequences, it has been observed that there is a close relationship between the evoluti... |
q-bio/0612014 | Vladislav Volman | Vladislav Volman, Eshel Ben-Jacob, Herbert Levine | The astrocyte as a gatekeeper of synaptic information transfer | 31 pages, 8 figures | null | null | null | q-bio.NC | null | We present a simple biophysical model for the coupling between synaptic
transmission and the local calcium concentration on an enveloping astrocytic
domain. This interaction enables the astrocyte to modulate the information flow
from presynaptic to postsynaptic cells in a manner dependent on previous
activity at this... | [
{
"created": "Thu, 7 Dec 2006 22:39:33 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Volman",
"Vladislav",
""
],
[
"Ben-Jacob",
"Eshel",
""
],
[
"Levine",
"Herbert",
""
]
] | We present a simple biophysical model for the coupling between synaptic transmission and the local calcium concentration on an enveloping astrocytic domain. This interaction enables the astrocyte to modulate the information flow from presynaptic to postsynaptic cells in a manner dependent on previous activity at this a... |
2402.16615 | Gregory Reeves | Sharva V. Hiremath, Etika Goyal, Gregory T. Reeves, Cranos M. Williams | FRAP analysis Measuring biophysical kinetic parameters using image
analysis | 10 pages, 10 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Understanding transcription factor dynamics is crucial for unraveling the
regulatory mechanisms of gene expression that underpin cellular function and
development. Measurements of transcription factor subcellular movements are
essential for developing predictive models of gene expression. However,
obtaining these qua... | [
{
"created": "Fri, 23 Feb 2024 17:57:32 GMT",
"version": "v1"
},
{
"created": "Tue, 16 Jul 2024 20:38:38 GMT",
"version": "v2"
}
] | 2024-07-18 | [
[
"Hiremath",
"Sharva V.",
""
],
[
"Goyal",
"Etika",
""
],
[
"Reeves",
"Gregory T.",
""
],
[
"Williams",
"Cranos M.",
""
]
] | Understanding transcription factor dynamics is crucial for unraveling the regulatory mechanisms of gene expression that underpin cellular function and development. Measurements of transcription factor subcellular movements are essential for developing predictive models of gene expression. However, obtaining these quant... |
1911.12253 | Paul Samuel Ignacio | Paul Samuel Ignacio, David Uminsky, Christopher Dunstan, Esteban
Escobar, Luke Trujillo | Classification of Single-lead Electrocardiograms: TDA Informed Machine
Learning | \c{opyright} 2019 IEEE. Personal use of this material is permitted.
Permission from IEEE must be obtained for all other uses, in any current or
future media, including reprinting/republishing this material for advertising
or promotional purposes, creating new collective works, for resale or
redistribution to se... | null | null | null | q-bio.QM cs.LG eess.SP math.AT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Atrial Fibrillation is a heart condition characterized by erratic heart
rhythms caused by chaotic propagation of electrical impulses in the atria,
leading to numerous health complications. State-of-the-art models employ
complex algorithms that extract expert-informed features to improve diagnosis.
In this note, we de... | [
{
"created": "Mon, 25 Nov 2019 05:20:48 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Nov 2019 02:12:48 GMT",
"version": "v2"
}
] | 2019-12-02 | [
[
"Ignacio",
"Paul Samuel",
""
],
[
"Uminsky",
"David",
""
],
[
"Dunstan",
"Christopher",
""
],
[
"Escobar",
"Esteban",
""
],
[
"Trujillo",
"Luke",
""
]
] | Atrial Fibrillation is a heart condition characterized by erratic heart rhythms caused by chaotic propagation of electrical impulses in the atria, leading to numerous health complications. State-of-the-art models employ complex algorithms that extract expert-informed features to improve diagnosis. In this note, we demo... |
0902.2708 | Maria Barbi | Vincent Dahirel, Fabien Paillusson, Marie Jardat, Maria Barbi,
Jean-Marc Victor | Non-specific DNA-protein interaction: Why proteins can diffuse along DNA | 4 pages, 4 figures, submitted to PRL | null | 10.1103/PhysRevLett.102.228101 | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The structure of DNA Binding Proteins enables a strong interaction with their
specific target site on DNA. However, recent single molecule experiment
reported that proteins can diffuse on DNA. This suggests that the interactions
between proteins and DNA play a role during the target search even far from the
specific ... | [
{
"created": "Mon, 16 Feb 2009 15:31:56 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Dahirel",
"Vincent",
""
],
[
"Paillusson",
"Fabien",
""
],
[
"Jardat",
"Marie",
""
],
[
"Barbi",
"Maria",
""
],
[
"Victor",
"Jean-Marc",
""
]
] | The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between proteins and DNA play a role during the target search even far from the specific si... |
1602.01743 | Jing Yang | Jing Yang, Christopher A. Penfold, Murray R. Grant, Magnus Rattray | Inferring the perturbation time from biological time course data | 63 pages, 20 figures, paper submitted to Bioinformatics | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Time course data are often used to study the changes to a biological process
after perturbation. Statistical methods have been developed to determine
whether such a perturbation induces changes over time, e.g. comparing a
perturbed and unperturbed time course dataset to uncover differences. However,
existing methods ... | [
{
"created": "Thu, 4 Feb 2016 16:55:36 GMT",
"version": "v1"
}
] | 2016-02-05 | [
[
"Yang",
"Jing",
""
],
[
"Penfold",
"Christopher A.",
""
],
[
"Grant",
"Murray R.",
""
],
[
"Rattray",
"Magnus",
""
]
] | Time course data are often used to study the changes to a biological process after perturbation. Statistical methods have been developed to determine whether such a perturbation induces changes over time, e.g. comparing a perturbed and unperturbed time course dataset to uncover differences. However, existing methods do... |
1812.03406 | Breno de Oliveira Ferraz | D. Bazeia, B.F. de Oliveira, A. Szolnoki | Phase transitions in dependence of apex predator decaying ratio in a
cyclic dominant system | version to appear in EPL. 7 pages, 7 figures | EPL 124 (2018) 68001 | 10.1209/0295-5075/124/68001 | null | q-bio.PE cond-mat.stat-mech physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cyclic dominant systems, like rock-paper-scissors game, are frequently used
to explain biodiversity in nature, where mobility, reproduction and
intransitive competition are on stage to provide the coexistence of
competitors. A significantly new situation emerges if we introduce an apex
predator who can superior all m... | [
{
"created": "Sat, 8 Dec 2018 23:50:39 GMT",
"version": "v1"
}
] | 2019-01-08 | [
[
"Bazeia",
"D.",
""
],
[
"de Oliveira",
"B. F.",
""
],
[
"Szolnoki",
"A.",
""
]
] | Cyclic dominant systems, like rock-paper-scissors game, are frequently used to explain biodiversity in nature, where mobility, reproduction and intransitive competition are on stage to provide the coexistence of competitors. A significantly new situation emerges if we introduce an apex predator who can superior all mem... |
1911.04329 | \'Alvaro Garc\'ia L\'opez | Irina Bashkirtseva, Lev Ryashko, \'Alvaro G. L\'opez, Jesus M. Seoane,
Miguel A. F. Sanju\'an | Tumor stabilization induced by T-cell recruitment fluctuations | null | null | 10.1142/S0218127420501795 | null | q-bio.OT nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The influence of random fluctuations on the recruitment of effector cells
towards a tumor is studied by means of a stochastic mathematical model.
Aggressively growing tumors are confronted against varying intensities of the
cell-mediated immune response for which chaotic and periodic oscillations
coexist together wit... | [
{
"created": "Thu, 7 Nov 2019 13:37:16 GMT",
"version": "v1"
},
{
"created": "Fri, 24 Jan 2020 11:02:39 GMT",
"version": "v2"
}
] | 2020-10-28 | [
[
"Bashkirtseva",
"Irina",
""
],
[
"Ryashko",
"Lev",
""
],
[
"López",
"Álvaro G.",
""
],
[
"Seoane",
"Jesus M.",
""
],
[
"Sanjuán",
"Miguel A. F.",
""
]
] | The influence of random fluctuations on the recruitment of effector cells towards a tumor is studied by means of a stochastic mathematical model. Aggressively growing tumors are confronted against varying intensities of the cell-mediated immune response for which chaotic and periodic oscillations coexist together with ... |
2005.12852 | Monjoy Saha | Monjoy Saha, Amit Kumar Ray, Swapan Kumar Basu | 3D CA model of tumor-induced angiogenesis | International Conference on Modeling and Simulation of Diffusive
Processes and Applications, 2012, Page 170-174 | null | null | null | q-bio.OT cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tumor-induced angiogenesis is the formation of new sprouts from preexisting
nearby parent blood vessels. Computationally, tumor-induced angiogenesis can be
modeled using cellular automata (CA), partial differential equations, etc. In
this present study, a realistic physiological approach has been made to model
the pr... | [
{
"created": "Mon, 25 May 2020 03:50:24 GMT",
"version": "v1"
}
] | 2020-05-27 | [
[
"Saha",
"Monjoy",
""
],
[
"Ray",
"Amit Kumar",
""
],
[
"Basu",
"Swapan Kumar",
""
]
] | Tumor-induced angiogenesis is the formation of new sprouts from preexisting nearby parent blood vessels. Computationally, tumor-induced angiogenesis can be modeled using cellular automata (CA), partial differential equations, etc. In this present study, a realistic physiological approach has been made to model the proc... |
2311.13901 | Ute Rogner | Chantal B\'ecourt (IC UM3 (UMR 8104 / U1016)), Sandrine Luce (IC UM3
(UMR 8104 / U1016)), Ute C Rogner (IC UM3 (UMR 8104 / U1016)), Christian
Boitard (IC UM3 (UMR 8104 / U1016)) | Differential action of TIGIT on islet and peripheral nerve autoimmunity
in the NOD mouse | Raw data and statistical analysis can be obtained from the
corresponding author | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We previously demonstrated that the abrogation of the ICOS pathway prevents
type 1 diabetes development in the Non Obese Diabetic (NOD) mouse, but results
in a CD4+ T-cell dependent autoimmune neuromyopathy in aged mice. Pancreatic
islet infiltrates in conventional NOD mice and neuromuscular infiltrates in
Icosl-/- N... | [
{
"created": "Thu, 23 Nov 2023 10:33:22 GMT",
"version": "v1"
}
] | 2023-11-27 | [
[
"Bécourt",
"Chantal",
"",
"IC UM3"
],
[
"Luce",
"Sandrine",
"",
"IC UM3"
],
[
"Rogner",
"Ute C",
"",
"IC UM3"
],
[
"Boitard",
"Christian",
"",
"IC UM3"
]
] | We previously demonstrated that the abrogation of the ICOS pathway prevents type 1 diabetes development in the Non Obese Diabetic (NOD) mouse, but results in a CD4+ T-cell dependent autoimmune neuromyopathy in aged mice. Pancreatic islet infiltrates in conventional NOD mice and neuromuscular infiltrates in Icosl-/- NOD... |
1306.3825 | Jacek Tyburczyk | Zdzislaw Burda, Jennifer Kornelsen, Maciej A. Nowak, Bartosz Porebski,
Uta Sboto-Frankenstein, Boguslaw Tomanek, Jacek Tyburczyk | Collective Correlations of Brodmann Areas fMRI Study with RMT-Denoising | null | null | 10.5506/APhysPolB.44.1243 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study collective behavior of Brodmann regions of human cerebral cortex
using functional Magnetic Resonance Imaging (fMRI) and Random Matrix Theory
(RMT). The raw fMRI data is mapped onto the cortex regions corresponding to the
Brodmann areas with the aid of the Talairach coordinates. Principal Component
Analysis (... | [
{
"created": "Mon, 17 Jun 2013 12:01:13 GMT",
"version": "v1"
}
] | 2015-06-16 | [
[
"Burda",
"Zdzislaw",
""
],
[
"Kornelsen",
"Jennifer",
""
],
[
"Nowak",
"Maciej A.",
""
],
[
"Porebski",
"Bartosz",
""
],
[
"Sboto-Frankenstein",
"Uta",
""
],
[
"Tomanek",
"Boguslaw",
""
],
[
"Tyburczyk",
"Jacek... | We study collective behavior of Brodmann regions of human cerebral cortex using functional Magnetic Resonance Imaging (fMRI) and Random Matrix Theory (RMT). The raw fMRI data is mapped onto the cortex regions corresponding to the Brodmann areas with the aid of the Talairach coordinates. Principal Component Analysis (PC... |
1607.04435 | Jose A. Cuesta | Jos\'e A. Cuesta and Susanna Manrubia | Enumerating secondary structures and structural moieties for circular
RNAs | 18 pages, 2 figures, requires svjour3.cls | Journal of Theoretical Biology 419, 375-382 (2017) | 10.1016/j.jtbi.2017.02.024 | null | q-bio.PE physics.bio-ph q-bio.BM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A quantitative characterization of the relationship between molecular
sequence and structure is essential to improve our understanding of how
function emerges. This particular genotype-phenotype map has been often studied
in the context of RNA sequences, with the folded configurations standing as a
proxy for the phen... | [
{
"created": "Fri, 15 Jul 2016 09:50:02 GMT",
"version": "v1"
},
{
"created": "Mon, 20 Feb 2017 18:04:11 GMT",
"version": "v2"
}
] | 2017-04-20 | [
[
"Cuesta",
"José A.",
""
],
[
"Manrubia",
"Susanna",
""
]
] | A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of RNA sequences, with the folded configurations standing as a proxy for the phenot... |
2105.01358 | Apoorv Kishore | Apoorv Kishore, Vivek Saraswat, Udayan Ganguly | Simplified Klinokinesis using Spiking Neural Networks for
Resource-Constrained Navigation on the Neuromorphic Processor Loihi | null | null | null | null | q-bio.NC cs.NE cs.SY eess.SY | http://creativecommons.org/licenses/by/4.0/ | C. elegans shows chemotaxis using klinokinesis where the worm senses the
concentration based on a single concentration sensor to compute the
concentration gradient to perform foraging through gradient ascent/descent
towards the target concentration followed by contour tracking. The biomimetic
implementation requires ... | [
{
"created": "Tue, 4 May 2021 08:26:46 GMT",
"version": "v1"
}
] | 2021-05-05 | [
[
"Kishore",
"Apoorv",
""
],
[
"Saraswat",
"Vivek",
""
],
[
"Ganguly",
"Udayan",
""
]
] | C. elegans shows chemotaxis using klinokinesis where the worm senses the concentration based on a single concentration sensor to compute the concentration gradient to perform foraging through gradient ascent/descent towards the target concentration followed by contour tracking. The biomimetic implementation requires co... |
1705.04942 | Adam Mahdi | Adam Mahdi, Dragana Nikolic, Anthony A. Birch, Mette S. Olufsen,
Ronney B. Panerai, David M. Simpson, Stephen J. Payne | Increased blood pressure variability upon standing up improves
reproducibility of cerebral autoregulation indices | 4 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dynamic cerebral autoregulation, that is the transient response of cerebral
blood flow to changes in arterial blood pressure, is currently assessed using a
variety of different time series methods and data collection protocols. In the
continuing absence of a gold standard for the study of cerebral autoregulation
it i... | [
{
"created": "Sun, 14 May 2017 09:57:04 GMT",
"version": "v1"
}
] | 2017-05-16 | [
[
"Mahdi",
"Adam",
""
],
[
"Nikolic",
"Dragana",
""
],
[
"Birch",
"Anthony A.",
""
],
[
"Olufsen",
"Mette S.",
""
],
[
"Panerai",
"Ronney B.",
""
],
[
"Simpson",
"David M.",
""
],
[
"Payne",
"Stephen J.",
""
... | Dynamic cerebral autoregulation, that is the transient response of cerebral blood flow to changes in arterial blood pressure, is currently assessed using a variety of different time series methods and data collection protocols. In the continuing absence of a gold standard for the study of cerebral autoregulation it is ... |
2302.06403 | Xu Ji | Xu Ji, Eric Elmoznino, George Deane, Axel Constant, Guillaume Dumas,
Guillaume Lajoie, Jonathan Simon, Yoshua Bengio | Sources of Richness and Ineffability for Phenomenally Conscious States | null | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Conscious states (states that there is something it is like to be in) seem
both rich or full of detail, and ineffable or hard to fully describe or recall.
The problem of ineffability, in particular, is a longstanding issue in
philosophy that partly motivates the explanatory gap: the belief that
consciousness cannot b... | [
{
"created": "Mon, 13 Feb 2023 14:41:04 GMT",
"version": "v1"
},
{
"created": "Wed, 1 Mar 2023 19:38:55 GMT",
"version": "v2"
},
{
"created": "Mon, 13 Mar 2023 01:06:34 GMT",
"version": "v3"
},
{
"created": "Fri, 17 Mar 2023 03:44:36 GMT",
"version": "v4"
},
{
"cr... | 2023-06-22 | [
[
"Ji",
"Xu",
""
],
[
"Elmoznino",
"Eric",
""
],
[
"Deane",
"George",
""
],
[
"Constant",
"Axel",
""
],
[
"Dumas",
"Guillaume",
""
],
[
"Lajoie",
"Guillaume",
""
],
[
"Simon",
"Jonathan",
""
],
[
"Ben... | Conscious states (states that there is something it is like to be in) seem both rich or full of detail, and ineffable or hard to fully describe or recall. The problem of ineffability, in particular, is a longstanding issue in philosophy that partly motivates the explanatory gap: the belief that consciousness cannot be ... |
1404.5725 | Ying Zhang | Ying Zhang | Application of signal processing techniques in the assessment of
clinical risks in preterm infants | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Preterm infants with very low birth weight suffer from a high risk of
intra-ventricular hemorrhage(IVH) and other serious diseases. To improve the
clinical risk assessment of preterm infants and develop potential clinically
makers for the adverse outcome, the first part of the paper develops the
frequency spectral an... | [
{
"created": "Wed, 23 Apr 2014 07:18:51 GMT",
"version": "v1"
}
] | 2014-04-24 | [
[
"Zhang",
"Ying",
""
]
] | Preterm infants with very low birth weight suffer from a high risk of intra-ventricular hemorrhage(IVH) and other serious diseases. To improve the clinical risk assessment of preterm infants and develop potential clinically makers for the adverse outcome, the first part of the paper develops the frequency spectral anal... |
2402.01942 | Michael Levet | Lora Bailey, Heather Smith Blake, Garner Cochran, Nathan Fox, Michael
Levet, Reem Mahmoud, Inne Singgih, Grace Stadnyk, Alexander Wiedemann | Pairwise Rearrangement is Fixed-Parameter Tractable in the Single
Cut-and-Join Model | Full version of paper to appear in SWAT 2024; arXiv admin note: text
overlap with arXiv:2305.01851 | null | null | null | q-bio.GN cs.DS math.CO | http://creativecommons.org/licenses/by/4.0/ | Genome rearrangement is a common model for molecular evolution. In this
paper, we consider the Pairwise Rearrangement problem, which takes as input two
genomes and asks for the number of minimum-length sequences of permissible
operations transforming the first genome into the second. In the Single
Cut-and-Join model ... | [
{
"created": "Fri, 2 Feb 2024 22:36:21 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Mar 2024 20:44:21 GMT",
"version": "v2"
},
{
"created": "Tue, 23 Apr 2024 20:42:28 GMT",
"version": "v3"
}
] | 2024-04-25 | [
[
"Bailey",
"Lora",
""
],
[
"Blake",
"Heather Smith",
""
],
[
"Cochran",
"Garner",
""
],
[
"Fox",
"Nathan",
""
],
[
"Levet",
"Michael",
""
],
[
"Mahmoud",
"Reem",
""
],
[
"Singgih",
"Inne",
""
],
[
"S... | Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations transforming the first genome into the second. In the Single Cut-and-Join model (B... |
2303.00904 | Hanbin Lee | Hanbin Lee, Moo Hyuk Lee | Disentangling Linkage and Population Structure in Association Mapping | 11 pages, 1 figure | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Genome-wide association study (GWAS) tests single nucleotide polymorphism
(SNP) markers across the genome to localize the underlying causal variant of a
trait. Because causal variants are seldom observed directly, a surrogate model
based on genotyped markers are widely considered. Although many methods
estimating the... | [
{
"created": "Thu, 2 Mar 2023 01:54:02 GMT",
"version": "v1"
}
] | 2023-03-03 | [
[
"Lee",
"Hanbin",
""
],
[
"Lee",
"Moo Hyuk",
""
]
] | Genome-wide association study (GWAS) tests single nucleotide polymorphism (SNP) markers across the genome to localize the underlying causal variant of a trait. Because causal variants are seldom observed directly, a surrogate model based on genotyped markers are widely considered. Although many methods estimating the p... |
1811.12490 | Derek Curtis | Derek John Curtis, Pauline Holbrook, Sarah Bew, Lynne Ford, Penny
Butler | Functional change in children with cerebral palsy | 14 pages, 5 tables | null | null | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Introduction There is increasing focus on the association between trunk
control and functional abilities in children with cerebral palsy (CP). The
purpose of this study was to determine the extent of functional change in
children with CP who participated in specific trunk and head postural control
training combined w... | [
{
"created": "Fri, 9 Nov 2018 13:56:23 GMT",
"version": "v1"
}
] | 2018-12-03 | [
[
"Curtis",
"Derek John",
""
],
[
"Holbrook",
"Pauline",
""
],
[
"Bew",
"Sarah",
""
],
[
"Ford",
"Lynne",
""
],
[
"Butler",
"Penny",
""
]
] | Introduction There is increasing focus on the association between trunk control and functional abilities in children with cerebral palsy (CP). The purpose of this study was to determine the extent of functional change in children with CP who participated in specific trunk and head postural control training combined wit... |
1611.01692 | Raul Isea | Raul Isea, Rafael Mayo-Garcia and Silvia Restrepo | Reverse vaccinology in Plasmodium falciparum 3D7 | 7 pages, 2 tables | J Immunol Tech Infect Dis (2016) 5:3 | null | null | q-bio.GN q-bio.PE | http://creativecommons.org/publicdomain/zero/1.0/ | A timely immunization can be effective against certain diseases and can save
thousands of lives. However, for some diseases it has been difficult, so far,
to develop an efficient vaccine. Malaria, a tropical disease caused by a
parasite of the genus Plasmodium, is one example. Bioinformatics has opened the
way to new... | [
{
"created": "Sat, 5 Nov 2016 19:44:21 GMT",
"version": "v1"
}
] | 2016-11-08 | [
[
"Isea",
"Raul",
""
],
[
"Mayo-Garcia",
"Rafael",
""
],
[
"Restrepo",
"Silvia",
""
]
] | A timely immunization can be effective against certain diseases and can save thousands of lives. However, for some diseases it has been difficult, so far, to develop an efficient vaccine. Malaria, a tropical disease caused by a parasite of the genus Plasmodium, is one example. Bioinformatics has opened the way to new l... |
1509.08322 | Simon Tanaka Mr. | Simon Tanaka | Technical Report: Modelling Multiple Cell Types with Partial
Differential Equations | technical report, 4 pages | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Partial differential equations are a convenient way to describe reaction-
advection-diffusion processes of signalling models. If only one cell type is
present, and tissue dynamics can be neglected, the equations can be solved
directly. However, in case of multiple cell types it is not always straight
forward to integ... | [
{
"created": "Mon, 28 Sep 2015 13:59:14 GMT",
"version": "v1"
}
] | 2015-09-29 | [
[
"Tanaka",
"Simon",
""
]
] | Partial differential equations are a convenient way to describe reaction- advection-diffusion processes of signalling models. If only one cell type is present, and tissue dynamics can be neglected, the equations can be solved directly. However, in case of multiple cell types it is not always straight forward to integra... |
2405.06072 | Miriam Furst | Asaf Zorea, Miriam Furst | Contribution of Coincidence Detection to Speech Segregation in Noisy
Environments | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | This study introduces a biologically-inspired model designed to examine the
role of coincidence detection cells in speech segregation tasks. The model
consists of three stages: a time-domain cochlear model that generates
instantaneous rates of auditory nerve fibers, coincidence detection cells that
amplify neural act... | [
{
"created": "Thu, 9 May 2024 19:43:19 GMT",
"version": "v1"
}
] | 2024-05-13 | [
[
"Zorea",
"Asaf",
""
],
[
"Furst",
"Miriam",
""
]
] | This study introduces a biologically-inspired model designed to examine the role of coincidence detection cells in speech segregation tasks. The model consists of three stages: a time-domain cochlear model that generates instantaneous rates of auditory nerve fibers, coincidence detection cells that amplify neural activ... |
2011.11717 | Onofrio M. Marag\`o | Laura Natali, Saga Helgadottir, Onofrio M. Marago, and Giovanni Volpe | Improving epidemic testing and containment strategies using machine
learning | 11 pages, 4 figures | null | null | null | q-bio.PE cs.LG physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | Containment of epidemic outbreaks entails great societal and economic costs.
Cost-effective containment strategies rely on efficiently identifying infected
individuals, making the best possible use of the available testing resources.
Therefore, quickly identifying the optimal testing strategy is of critical
importanc... | [
{
"created": "Mon, 23 Nov 2020 20:46:01 GMT",
"version": "v1"
}
] | 2020-12-01 | [
[
"Natali",
"Laura",
""
],
[
"Helgadottir",
"Saga",
""
],
[
"Marago",
"Onofrio M.",
""
],
[
"Volpe",
"Giovanni",
""
]
] | Containment of epidemic outbreaks entails great societal and economic costs. Cost-effective containment strategies rely on efficiently identifying infected individuals, making the best possible use of the available testing resources. Therefore, quickly identifying the optimal testing strategy is of critical importance.... |
2408.00367 | Stephanie Hicks | Boyi Guo, Wodan Ling, Sang Ho Kwon, Pratibha Panwar, Shila Ghazanfar,
Keri Martinowich, Stephanie C. Hicks | Integrating spatially-resolved transcriptomics data across tissues and
individuals: challenges and opportunities | 16 pages, 2 figures | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Advances in spatially-resolved transcriptomics (SRT) technologies have
propelled the development of new computational analysis methods to unlock
biological insights. As the cost of generating these data decreases, these
technologies provide an exciting opportunity to create large-scale atlases that
integrate SRT data... | [
{
"created": "Thu, 1 Aug 2024 08:16:22 GMT",
"version": "v1"
}
] | 2024-08-02 | [
[
"Guo",
"Boyi",
""
],
[
"Ling",
"Wodan",
""
],
[
"Kwon",
"Sang Ho",
""
],
[
"Panwar",
"Pratibha",
""
],
[
"Ghazanfar",
"Shila",
""
],
[
"Martinowich",
"Keri",
""
],
[
"Hicks",
"Stephanie C.",
""
]
] | Advances in spatially-resolved transcriptomics (SRT) technologies have propelled the development of new computational analysis methods to unlock biological insights. As the cost of generating these data decreases, these technologies provide an exciting opportunity to create large-scale atlases that integrate SRT data a... |
1602.00723 | Dario Riccardo Valenzano | Arian \v{S}ajina, Dario Riccardo Valenzano | An In Silico Model to Simulate the Evolution of Biological Aging | 11 pages and 7 figures, written using the AIP distribution for REVTeX
4, Version 4.1 of REVTeX; corresponding author (D.R.V.) email:
dvalenzano@age.mpg.de | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biological aging is characterized by an age-dependent increase in the
probability of death and by a decrease in the reproductive capacity. Individual
age-dependent rates of survival and reproduction have a strong impact on
population dynamics, and the genetic elements determining survival and
reproduction are under d... | [
{
"created": "Mon, 1 Feb 2016 21:54:43 GMT",
"version": "v1"
}
] | 2016-02-03 | [
[
"Šajina",
"Arian",
""
],
[
"Valenzano",
"Dario Riccardo",
""
]
] | Biological aging is characterized by an age-dependent increase in the probability of death and by a decrease in the reproductive capacity. Individual age-dependent rates of survival and reproduction have a strong impact on population dynamics, and the genetic elements determining survival and reproduction are under dif... |
1605.06207 | Bernal Morera MSc | Bernal Morera | Mitochondrial genealogy of Maria Mercedes Cairol Antunez, footprint of
recent immigration to Costa Rica / La genealogia mitocondrial de Maria
Mercedes Cairol Antunez, huella de la inmigracion reciente a Costa Rica | 4 pages, 1 figure, 1 table, in Spanish | Boletin ASOGEHInforma 6(2): 11-14. 2012 | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The technological advances in Genetics have given rise to the science of
Molecular Genealogy, by giving us the opportunity to approach the study of
pedigrees from a new perspective, examining alive people at the same time than
collating records from their ancestors. A four generations matrilineal
genealogy is present... | [
{
"created": "Fri, 20 May 2016 03:55:18 GMT",
"version": "v1"
}
] | 2016-05-23 | [
[
"Morera",
"Bernal",
""
]
] | The technological advances in Genetics have given rise to the science of Molecular Genealogy, by giving us the opportunity to approach the study of pedigrees from a new perspective, examining alive people at the same time than collating records from their ancestors. A four generations matrilineal genealogy is presented... |
1606.05802 | Amy Gilson | Amy I. Gilson, Ahmee Marshall-Christensen, Jeong-Mo Choi, and Eugene
I. Shakhnovich | The role of evolutionary selection in the dynamics of protein structure
evolution | null | null | 10.1016/j.bpj.2017.02.029 | null | q-bio.PE q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Emergence of new protein structures has proved difficult to trace in nature
and engineer in the laboratory. However, one aspect of structure evolution has
proved immensely helpful for determining the three-dimensional structure of
proteins from their sequences: in the vast majority of cases, proteins that
share more ... | [
{
"created": "Sat, 18 Jun 2016 20:34:08 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Oct 2016 17:26:45 GMT",
"version": "v2"
}
] | 2017-05-24 | [
[
"Gilson",
"Amy I.",
""
],
[
"Marshall-Christensen",
"Ahmee",
""
],
[
"Choi",
"Jeong-Mo",
""
],
[
"Shakhnovich",
"Eugene I.",
""
]
] | Emergence of new protein structures has proved difficult to trace in nature and engineer in the laboratory. However, one aspect of structure evolution has proved immensely helpful for determining the three-dimensional structure of proteins from their sequences: in the vast majority of cases, proteins that share more th... |
q-bio/0607041 | Blas Echebarria | Blas Echebarria, Alain Karma | Amplitude equation approach to spatiotemporal dynamics of cardiac
alternans | 55 pages, 13 figures, to appear in Phys. Rev. E | null | 10.1103/PhysRevE.76.051911 | null | q-bio.TO nlin.PS | null | Amplitude equations are derived that describe the spatiotemporal dynamics of
cardiac alternans during periodic pacing of one- and two-dimensional
homogeneous tissue and one-dimensional anatomical reentry in a ring of
homogeneous tissue. These equations provide a simple physical understanding of
arrhythmogenic pattern... | [
{
"created": "Sun, 23 Jul 2006 15:27:19 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Oct 2007 13:43:35 GMT",
"version": "v2"
}
] | 2009-11-13 | [
[
"Echebarria",
"Blas",
""
],
[
"Karma",
"Alain",
""
]
] | Amplitude equations are derived that describe the spatiotemporal dynamics of cardiac alternans during periodic pacing of one- and two-dimensional homogeneous tissue and one-dimensional anatomical reentry in a ring of homogeneous tissue. These equations provide a simple physical understanding of arrhythmogenic patterns ... |
1707.08990 | Yi-Hsuan Lin | Yi-Hsuan Lin, Jacob P. Brady, Julie D. Forman-Kay, Hue Sun Chan | Charge Pattern Matching as a "Fuzzy" Mode of Molecular Recognition for
the Functional Phase Separations of Intrinsically Disordered Proteins | Accepted for publication in New Journal of Physics (IOP) for the
"Focus On Phase Transitions in Cells" Special Issue; 37 pages, 11 figures | New J. Phys. 19, 115003 (2017) | 10.1088/1367-2630/aa9369 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biologically functional liquid-liquid phase separation of intrinsically
disordered proteins (IDPs) is driven by interactions encoded by their amino
acid sequences. Little is currently known about the molecular recognition
mechanisms for distributing different IDP sequences into various cellular
membraneless compartme... | [
{
"created": "Thu, 27 Jul 2017 18:28:04 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Oct 2017 00:53:26 GMT",
"version": "v2"
}
] | 2017-11-15 | [
[
"Lin",
"Yi-Hsuan",
""
],
[
"Brady",
"Jacob P.",
""
],
[
"Forman-Kay",
"Julie D.",
""
],
[
"Chan",
"Hue Sun",
""
]
] | Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is currently known about the molecular recognition mechanisms for distributing different IDP sequences into various cellular membraneless compartment... |
2307.03757 | Adam Shephard | Adam J Shephard, Raja Muhammad Saad Bashir, Hanya Mahmood, Mostafa
Jahanifar, Fayyaz Minhas, Shan E Ahmed Raza, Kris D McCombe, Stephanie G
Craig, Jacqueline James, Jill Brooks, Paul Nankivell, Hisham Mehanna, Syed
Ali Khurram, Nasir M Rajpoot | A Fully Automated and Explainable Algorithm for the Prediction of
Malignant Transformation in Oral Epithelial Dysplasia | null | null | null | null | q-bio.QM cs.CV eess.IV | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Oral epithelial dysplasia (OED) is a premalignant histopathological diagnosis
given to lesions of the oral cavity. Its grading suffers from significant
inter-/intra- observer variability, and does not reliably predict malignancy
progression, potentially leading to suboptimal treatment decisions. To address
this, we d... | [
{
"created": "Thu, 6 Jul 2023 19:11:00 GMT",
"version": "v1"
}
] | 2023-07-11 | [
[
"Shephard",
"Adam J",
""
],
[
"Bashir",
"Raja Muhammad Saad",
""
],
[
"Mahmood",
"Hanya",
""
],
[
"Jahanifar",
"Mostafa",
""
],
[
"Minhas",
"Fayyaz",
""
],
[
"Raza",
"Shan E Ahmed",
""
],
[
"McCombe",
"Kris D",... | Oral epithelial dysplasia (OED) is a premalignant histopathological diagnosis given to lesions of the oral cavity. Its grading suffers from significant inter-/intra- observer variability, and does not reliably predict malignancy progression, potentially leading to suboptimal treatment decisions. To address this, we dev... |
1903.10323 | Kim Henriksen | Maja R. Radojcic, Christian S. Thudium, Kim Henriksen, Keith Tan, Rolf
Karlsten, Amanda Dudley, Iain Chessell, Morten A. Karsdal, Anne-Christine
Bay-Jensen, Michel D. Crema, Ali Guermazi | Biomarker of extracellular matrix remodelling C1M and proinflammatory
cytokine IL-6 are related to synovitis and pain in end-stage knee
osteoarthritis patients | 19 pages, 2 figures, 5 tables and 2 supplementary figures | Pain. 2017 Jul;158(7):1254-1263 | 10.1097/j.pain.0000000000000908 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Little is known about local and systemic biomarkers in relation to synovitis
and pain in end-stage osteoarthritis (OA) patients. We investigated the
associations between the novel extracellular matrix biomarker, C1M, and local
and systemic interleukin 6 (IL-6) with synovitis and pain. Serum C1M, plasma
and synovial f... | [
{
"created": "Wed, 20 Mar 2019 07:18:32 GMT",
"version": "v1"
}
] | 2019-03-26 | [
[
"Radojcic",
"Maja R.",
""
],
[
"Thudium",
"Christian S.",
""
],
[
"Henriksen",
"Kim",
""
],
[
"Tan",
"Keith",
""
],
[
"Karlsten",
"Rolf",
""
],
[
"Dudley",
"Amanda",
""
],
[
"Chessell",
"Iain",
""
],
[
... | Little is known about local and systemic biomarkers in relation to synovitis and pain in end-stage osteoarthritis (OA) patients. We investigated the associations between the novel extracellular matrix biomarker, C1M, and local and systemic interleukin 6 (IL-6) with synovitis and pain. Serum C1M, plasma and synovial flu... |
1305.4622 | Jacob Scott | Jacob G. Scott, Philip Gerlee, David Basanta, Alexander G. Fletcher,
Philip K. Maini and Alexander RA Anderson | Mathematical modeling of the metastatic process | 24 pages, 6 figures, Review | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mathematical modeling in cancer has been growing in popularity and impact
since its inception in 1932. The first theoretical mathematical modeling in
cancer research was focused on understanding tumor growth laws and has grown to
include the competition between healthy and normal tissue, carcinogenesis,
therapy and m... | [
{
"created": "Mon, 20 May 2013 19:54:03 GMT",
"version": "v1"
},
{
"created": "Tue, 21 May 2013 14:02:52 GMT",
"version": "v2"
}
] | 2013-05-22 | [
[
"Scott",
"Jacob G.",
""
],
[
"Gerlee",
"Philip",
""
],
[
"Basanta",
"David",
""
],
[
"Fletcher",
"Alexander G.",
""
],
[
"Maini",
"Philip K.",
""
],
[
"Anderson",
"Alexander RA",
""
]
] | Mathematical modeling in cancer has been growing in popularity and impact since its inception in 1932. The first theoretical mathematical modeling in cancer research was focused on understanding tumor growth laws and has grown to include the competition between healthy and normal tissue, carcinogenesis, therapy and met... |
1509.01957 | Jos\'e Halloy | A. Gribovskiy, F. Mondada, J.L. Deneubourg, L. Cazenille, N. Bredeche,
J. Halloy | Automated Analysis of Behavioural Variability and Filial Imprinting of
Chicks (G. gallus), using Autonomous Robots | 17 pages, 17 figures, 2 tables | null | null | null | q-bio.QM cs.LG cs.RO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inter-individual variability has various impacts in animal social behaviour.
This implies that not only collective behaviours have to be studied but also
the behavioural variability of each member composing the groups. To understand
those effects on group behaviour, we develop a quantitative methodology based
on auto... | [
{
"created": "Mon, 7 Sep 2015 09:22:43 GMT",
"version": "v1"
}
] | 2016-01-28 | [
[
"Gribovskiy",
"A.",
""
],
[
"Mondada",
"F.",
""
],
[
"Deneubourg",
"J. L.",
""
],
[
"Cazenille",
"L.",
""
],
[
"Bredeche",
"N.",
""
],
[
"Halloy",
"J.",
""
]
] | Inter-individual variability has various impacts in animal social behaviour. This implies that not only collective behaviours have to be studied but also the behavioural variability of each member composing the groups. To understand those effects on group behaviour, we develop a quantitative methodology based on automa... |
q-bio/0508023 | Eli Ben-Naim | E. Ben-Naim, P.L. Krapivsky | Rank Statistics in Biological Evolution | 4 pages, 3 figures | J. Stat. Mech. L10002 (2005) | 10.1088/1742-5468/2005/10/L10002 | null | q-bio.PE cond-mat.stat-mech math.PR q-bio.GN | null | We present a statistical analysis of biological evolution processes.
Specifically, we study the stochastic replication-mutation-death model where
the population of a species may grow or shrink by birth or death, respectively,
and additionally, mutations lead to the creation of new species. We rank the
various species... | [
{
"created": "Thu, 18 Aug 2005 04:52:50 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Ben-Naim",
"E.",
""
],
[
"Krapivsky",
"P. L.",
""
]
] | We present a statistical analysis of biological evolution processes. Specifically, we study the stochastic replication-mutation-death model where the population of a species may grow or shrink by birth or death, respectively, and additionally, mutations lead to the creation of new species. We rank the various species b... |
1012.3957 | Leonid Perlovsky | Leonid Perlovsky | Free Will and Advances in Cognitive Science | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Free will is fundamental to morality, intuition of self, and normal
functioning of the society. However, science does not provide a clear logical
foundation for this idea. This paper considers the fundamental scientific
argument against free will, called reductionism, and explains the reasons for
choosing dualism aga... | [
{
"created": "Fri, 17 Dec 2010 18:37:54 GMT",
"version": "v1"
}
] | 2010-12-20 | [
[
"Perlovsky",
"Leonid",
""
]
] | Free will is fundamental to morality, intuition of self, and normal functioning of the society. However, science does not provide a clear logical foundation for this idea. This paper considers the fundamental scientific argument against free will, called reductionism, and explains the reasons for choosing dualism again... |
1705.05919 | Maxat Kulmanov | Maxat Kulmanov, Mohammed Asif Khan and Robert Hoehndorf | DeepGO: Predicting protein functions from sequence and interactions
using a deep ontology-aware classifier | null | null | 10.1093/bioinformatics/btx624 | null | q-bio.GN cs.LG q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A large number of protein sequences are becoming available through the
application of novel high-throughput sequencing technologies. Experimental
functional characterization of these proteins is time-consuming and expensive,
and is often only done rigorously for few selected model organisms.
Computational function pr... | [
{
"created": "Mon, 15 May 2017 06:04:08 GMT",
"version": "v1"
}
] | 2017-09-28 | [
[
"Kulmanov",
"Maxat",
""
],
[
"Khan",
"Mohammed Asif",
""
],
[
"Hoehndorf",
"Robert",
""
]
] | A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often only done rigorously for few selected model organisms. Computational function pred... |
2308.03563 | Konstantin Sorokin | Konstantin Sorokin, Andrey Zaitsew, Aleksandr Levin, German Magai,
Maxim Beketov, Vladimir Sotskov | Global cognitive graph properties dynamics of hippocampal formation | 12 pages, 6 figures, paper for DAMDID 2023 Conference | null | null | null | q-bio.NC cs.IR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the present study we have used a set of methods and metrics to build a
graph of relative neural connections in a hippocampus of a rodent. A set of
graphs was built on top of time-sequenced data and analyzed in terms of
dynamics of a connection genesis. The analysis has shown that during the
process of a rodent exp... | [
{
"created": "Mon, 7 Aug 2023 13:15:33 GMT",
"version": "v1"
}
] | 2023-08-08 | [
[
"Sorokin",
"Konstantin",
""
],
[
"Zaitsew",
"Andrey",
""
],
[
"Levin",
"Aleksandr",
""
],
[
"Magai",
"German",
""
],
[
"Beketov",
"Maxim",
""
],
[
"Sotskov",
"Vladimir",
""
]
] | In the present study we have used a set of methods and metrics to build a graph of relative neural connections in a hippocampus of a rodent. A set of graphs was built on top of time-sequenced data and analyzed in terms of dynamics of a connection genesis. The analysis has shown that during the process of a rodent explo... |
0909.1370 | Conrad Burden | Sylvain Foret, Susan R. Wilson, Conrad J. Burden | Characterising the D2 statistic: word matches in biological sequences | 23 pages, 3 figures | null | null | null | q-bio.QM q-bio.GN stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Word matches are often used in sequence comparison methods, either as a
measure of sequence similarity or in the first search steps of algorithms such
as BLAST or BLAT. The D2 statistic is the number of matches of words of k
letters between two sequences. Recent advances have been made in the
characterisation of this... | [
{
"created": "Tue, 8 Sep 2009 01:46:58 GMT",
"version": "v1"
}
] | 2009-09-09 | [
[
"Foret",
"Sylvain",
""
],
[
"Wilson",
"Susan R.",
""
],
[
"Burden",
"Conrad J.",
""
]
] | Word matches are often used in sequence comparison methods, either as a measure of sequence similarity or in the first search steps of algorithms such as BLAST or BLAT. The D2 statistic is the number of matches of words of k letters between two sequences. Recent advances have been made in the characterisation of this s... |
2303.04898 | Daniel Friedman | Karl Friston, Daniel Ari Friedman, Axel Constant, V. Bleu Knight,
Thomas Parr, John O. Campbell | A variational synthesis of evolutionary and developmental dynamics | null | null | 10.3390/e25070964 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | This paper introduces a variational formulation of natural selection, paying
special attention to the nature of "things" and the way that different "kinds"
of "things" are individuated from - and influence - each other. We use the
Bayesian mechanics of particular partitions to understand how slow phylogenetic
process... | [
{
"created": "Wed, 8 Mar 2023 21:30:28 GMT",
"version": "v1"
}
] | 2023-07-05 | [
[
"Friston",
"Karl",
""
],
[
"Friedman",
"Daniel Ari",
""
],
[
"Constant",
"Axel",
""
],
[
"Knight",
"V. Bleu",
""
],
[
"Parr",
"Thomas",
""
],
[
"Campbell",
"John O.",
""
]
] | This paper introduces a variational formulation of natural selection, paying special attention to the nature of "things" and the way that different "kinds" of "things" are individuated from - and influence - each other. We use the Bayesian mechanics of particular partitions to understand how slow phylogenetic processes... |
2011.08088 | Mark Humphries | Mark D Humphries | Strong and weak principles of neural dimension reduction | 27 pages, 5 figures | null | 10.51628/001c.24619 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | If spikes are the medium, what is the message? Answering that question is
driving the development of large-scale, single neuron resolution recordings
from behaving animals, on the scale of thousands of neurons. But these data are
inherently high-dimensional, with as many dimensions as neurons - so how do we
make sens... | [
{
"created": "Mon, 16 Nov 2020 16:39:56 GMT",
"version": "v1"
},
{
"created": "Thu, 18 Mar 2021 17:22:03 GMT",
"version": "v2"
},
{
"created": "Mon, 24 May 2021 10:51:20 GMT",
"version": "v3"
},
{
"created": "Fri, 24 Feb 2023 15:06:18 GMT",
"version": "v4"
}
] | 2023-02-27 | [
[
"Humphries",
"Mark D",
""
]
] | If spikes are the medium, what is the message? Answering that question is driving the development of large-scale, single neuron resolution recordings from behaving animals, on the scale of thousands of neurons. But these data are inherently high-dimensional, with as many dimensions as neurons - so how do we make sense ... |
1411.0075 | Fabio Dercole | Fabio Dercole | The ecology of asexual pairwise interactions: A generalized law of mass
action | Submitted to Journal of Mathematical Biology on Feb. 3, 2014 | null | null | null | q-bio.PE math.DS nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A general procedure to formulate asexual (unstructured, deterministic)
population dynamical models resulting from individual pairwise interactions is
proposed. Individuals are characterized by a continuous strategy that
represents all their behavioral, morphological, and functional traits.
Populations group conspecif... | [
{
"created": "Sat, 1 Nov 2014 06:36:10 GMT",
"version": "v1"
}
] | 2014-11-04 | [
[
"Dercole",
"Fabio",
""
]
] | A general procedure to formulate asexual (unstructured, deterministic) population dynamical models resulting from individual pairwise interactions is proposed. Individuals are characterized by a continuous strategy that represents all their behavioral, morphological, and functional traits. Populations group conspecific... |
2208.08127 | Sakuntala Chatterjee | Shobhan Dev Mandal and Sakuntala Chatterjee | Effect of switching time scale of receptor activity on chemotactic
performance of Escherichia coli | null | Indian Journal of Physics, Special Issue: Physical Views of
Cellular processes, Volume 96, Issue 9, Pages 2619-2627 (2022) | 10.1007/s12648-021-02259-y | null | q-bio.CB physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | In the chemotactic motion of Escherichia coli, the switching of transmembrane
chemoreceptors between active and inactive states is one of the most important
steps of the signaling pathway. We study the effect of this switching
time-scale on the chemotactic performance of the cell. We quantify performance
by the chemo... | [
{
"created": "Wed, 17 Aug 2022 07:46:07 GMT",
"version": "v1"
}
] | 2022-08-18 | [
[
"Mandal",
"Shobhan Dev",
""
],
[
"Chatterjee",
"Sakuntala",
""
]
] | In the chemotactic motion of Escherichia coli, the switching of transmembrane chemoreceptors between active and inactive states is one of the most important steps of the signaling pathway. We study the effect of this switching time-scale on the chemotactic performance of the cell. We quantify performance by the chemota... |
1209.6513 | Mina Zarei | Mina Zarei, Bianca Sclavi, Marco Cosentino Lagomarsino | Gene silencing and large-scale domain structure of the E. coli genome | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA
loops, and form oligomeric structures connected to repression of gene
expression. Motivated by the link between chromosome organization, protein
binding and gene expression, we analyzed publicly available genomic data sets
of various origins,... | [
{
"created": "Fri, 28 Sep 2012 13:27:20 GMT",
"version": "v1"
}
] | 2012-10-01 | [
[
"Zarei",
"Mina",
""
],
[
"Sclavi",
"Bianca",
""
],
[
"Lagomarsino",
"Marco Cosentino",
""
]
] | The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression. Motivated by the link between chromosome organization, protein binding and gene expression, we analyzed publicly available genomic data sets of various origins, f... |
2012.09562 | Anastasia Ignatieva | Anastasia Ignatieva, Rune B. Lyngs\o, Paul A. Jenkins, Jotun Hein | KwARG: Parsimonious reconstruction of ancestral recombination graphs
with recurrent mutation | 18 pages, 12 figures; accepted for publication in Bioinformatics | null | 10.1093/bioinformatics/btab351 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The reconstruction of possible histories given a sample of genetic data in
the presence of recombination and recurrent mutation is a challenging problem,
but can provide key insights into the evolution of a population. We present
KwARG, which implements a parsimony-based greedy heuristic algorithm for
finding plausib... | [
{
"created": "Thu, 17 Dec 2020 13:19:39 GMT",
"version": "v1"
},
{
"created": "Thu, 13 May 2021 15:47:15 GMT",
"version": "v2"
}
] | 2021-05-14 | [
[
"Ignatieva",
"Anastasia",
""
],
[
"Lyngsø",
"Rune B.",
""
],
[
"Jenkins",
"Paul A.",
""
],
[
"Hein",
"Jotun",
""
]
] | The reconstruction of possible histories given a sample of genetic data in the presence of recombination and recurrent mutation is a challenging problem, but can provide key insights into the evolution of a population. We present KwARG, which implements a parsimony-based greedy heuristic algorithm for finding plausible... |
2111.14961 | David Bryant | Jandre Snyman and Colin Fox and David Bryant | Parsimony and the rank of a flattening matrix | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The standard models of sequence evolution on a tree determine probabilities
for every character or site pattern. A flattening is an arrangement of these
probabilities into a matrix, with rows corresponding to all possible site
patterns for one set $A$ of taxa and columns corresponding to all site patterns
for another... | [
{
"created": "Mon, 29 Nov 2021 21:13:21 GMT",
"version": "v1"
},
{
"created": "Fri, 3 Dec 2021 02:03:25 GMT",
"version": "v2"
},
{
"created": "Thu, 9 Dec 2021 01:37:47 GMT",
"version": "v3"
}
] | 2021-12-10 | [
[
"Snyman",
"Jandre",
""
],
[
"Fox",
"Colin",
""
],
[
"Bryant",
"David",
""
]
] | The standard models of sequence evolution on a tree determine probabilities for every character or site pattern. A flattening is an arrangement of these probabilities into a matrix, with rows corresponding to all possible site patterns for one set $A$ of taxa and columns corresponding to all site patterns for another s... |
2007.02169 | Joe Klobusicky | Joseph J. Klobusicky and John Fricks and Peter R. Kramer | Effective behavior of cooperative and nonidentical molecular motors | 73 pages, 4 Figures | null | null | null | q-bio.SC math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Analytical formulas for effective drift, diffusivity, run times, and run
lengths are derived for an intracellular transport system consisting of a cargo
attached to two cooperative but not identical molecular motors (for example,
kinesin-1 and kinesin-2) which can each attach and detach from a microtubule.
The dynami... | [
{
"created": "Sat, 4 Jul 2020 19:24:24 GMT",
"version": "v1"
},
{
"created": "Mon, 31 Aug 2020 18:47:07 GMT",
"version": "v2"
},
{
"created": "Thu, 21 Jan 2021 16:15:52 GMT",
"version": "v3"
}
] | 2021-01-22 | [
[
"Klobusicky",
"Joseph J.",
""
],
[
"Fricks",
"John",
""
],
[
"Kramer",
"Peter R.",
""
]
] | Analytical formulas for effective drift, diffusivity, run times, and run lengths are derived for an intracellular transport system consisting of a cargo attached to two cooperative but not identical molecular motors (for example, kinesin-1 and kinesin-2) which can each attach and detach from a microtubule. The dynamics... |
1212.1696 | Priya Moorjani | Priya Moorjani, Nick Patterson, Po-Ru Loh, Mark Lipson, P\'eter
Kisfali, Bela I Melegh, Michael Bonin, \v{L}udev\'it K\'ada\v{s}i, Olaf
Rie{\ss}, Bonnie Berger, David Reich, B\'ela Melegh | Reconstructing Roma history from genome-wide data | null | null | 10.1371/journal.pone.0058633 | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Roma people, living throughout Europe, are a diverse population linked by
the Romani language and culture. Previous linguistic and genetic studies have
suggested that the Roma migrated into Europe from South Asia about 1000-1500
years ago. Genetic inferences about Roma history have mostly focused on the Y
chromos... | [
{
"created": "Fri, 7 Dec 2012 19:59:41 GMT",
"version": "v1"
}
] | 2015-06-12 | [
[
"Moorjani",
"Priya",
""
],
[
"Patterson",
"Nick",
""
],
[
"Loh",
"Po-Ru",
""
],
[
"Lipson",
"Mark",
""
],
[
"Kisfali",
"Péter",
""
],
[
"Melegh",
"Bela I",
""
],
[
"Bonin",
"Michael",
""
],
[
"Kádaš... | The Roma people, living throughout Europe, are a diverse population linked by the Romani language and culture. Previous linguistic and genetic studies have suggested that the Roma migrated into Europe from South Asia about 1000-1500 years ago. Genetic inferences about Roma history have mostly focused on the Y chromosom... |
1210.0050 | Rohan Maddamsetti | Rohan Maddamsetti, Philip J. Hatcher, St\'ephane Cruveiller, Claudine
M\'edigue, Jeffrey E. Barrick, Richard E. Lenski | Horizontal gene transfer may explain variation in {\theta}s | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Martincorena et al. estimated synonymous diversity ({\theta}s = 2N{\mu})
across 2,930 orthologous gene alignments from 34 Escherichia coli genomes, and
found substantial variation among genes in the density of synonymous
polymorphisms. They argue that this pattern reflects variation in the mutation
rate per nucleotid... | [
{
"created": "Fri, 28 Sep 2012 22:14:55 GMT",
"version": "v1"
}
] | 2012-10-02 | [
[
"Maddamsetti",
"Rohan",
""
],
[
"Hatcher",
"Philip J.",
""
],
[
"Cruveiller",
"Stéphane",
""
],
[
"Médigue",
"Claudine",
""
],
[
"Barrick",
"Jeffrey E.",
""
],
[
"Lenski",
"Richard E.",
""
]
] | Martincorena et al. estimated synonymous diversity ({\theta}s = 2N{\mu}) across 2,930 orthologous gene alignments from 34 Escherichia coli genomes, and found substantial variation among genes in the density of synonymous polymorphisms. They argue that this pattern reflects variation in the mutation rate per nucleotide ... |
1301.2440 | Namiko Mitarai | Namiko Mitarai, Uri Alon, and Mogens H. Jensen | Entrainment of noise-induced and limit cycle oscillators under weak
noise | 27 pages in preprint style, 12 figues, 2 table | Chaos 23, 023125 (2013) | 10.1063/1.4808253 | null | q-bio.QM nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Theoretical models that describe oscillations in biological systems are often
either a limit cycle oscillator, where the deterministic nonlinear dynamics
gives sustained periodic oscillations, or a noise-induced oscillator, where a
fixed point is linearly stable with complex eigenvalues and addition of noise
gives os... | [
{
"created": "Fri, 11 Jan 2013 10:01:49 GMT",
"version": "v1"
},
{
"created": "Fri, 17 May 2013 01:52:31 GMT",
"version": "v2"
}
] | 2015-01-20 | [
[
"Mitarai",
"Namiko",
""
],
[
"Alon",
"Uri",
""
],
[
"Jensen",
"Mogens H.",
""
]
] | Theoretical models that describe oscillations in biological systems are often either a limit cycle oscillator, where the deterministic nonlinear dynamics gives sustained periodic oscillations, or a noise-induced oscillator, where a fixed point is linearly stable with complex eigenvalues and addition of noise gives osci... |
1004.3138 | Adri\'an L\'opez Garc\'ia de Lomana | Adri\'an L\'opez Garc\'ia de Lomana, Qasim K. Beg, G. de Fabritiis and
Jordi Vill\`a-Freixa | Statistical Analysis of Global Connectivity and Activity Distributions
in Cellular Networks | 17 pages, 1 figure, accepted for publication in Journal of
Computational Biology | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Various molecular interaction networks have been claimed to follow power-law
decay for their global connectivity distribution. It has been proposed that
there may be underlying generative models that explain this heavy-tailed
behavior by self-reinforcement processes such as classical or hierarchical
scale-free networ... | [
{
"created": "Mon, 19 Apr 2010 09:34:02 GMT",
"version": "v1"
}
] | 2010-04-20 | [
[
"de Lomana",
"Adrián López García",
""
],
[
"Beg",
"Qasim K.",
""
],
[
"de Fabritiis",
"G.",
""
],
[
"Villà-Freixa",
"Jordi",
""
]
] | Various molecular interaction networks have been claimed to follow power-law decay for their global connectivity distribution. It has been proposed that there may be underlying generative models that explain this heavy-tailed behavior by self-reinforcement processes such as classical or hierarchical scale-free network ... |
q-bio/0607010 | Franco Bagnoli | Luca Sguanci, Pietro Lio', Franco Bagnoli | The influence of risk perception in epidemics: a cellular agent model | null | Lecture Notes in Computer Science. vol. 4173, pp. 321-329 (2006) | 10.1007/11861201_38 | null | q-bio.PE | null | Our work stems from the consideration that the spreading of a disease is
modulated by the individual's perception of the infected neighborhood and
his/her strategy to avoid being infected as well. We introduced a general
``cellular agent'' model that accounts for a hetereogeneous and variable
network of connections. ... | [
{
"created": "Thu, 6 Jul 2006 13:50:21 GMT",
"version": "v1"
}
] | 2008-01-20 | [
[
"Sguanci",
"Luca",
""
],
[
"Lio'",
"Pietro",
""
],
[
"Bagnoli",
"Franco",
""
]
] | Our work stems from the consideration that the spreading of a disease is modulated by the individual's perception of the infected neighborhood and his/her strategy to avoid being infected as well. We introduced a general ``cellular agent'' model that accounts for a hetereogeneous and variable network of connections. Th... |
0802.0209 | Corey S. O'Hern | Gregg Lois, Jerzy Blawzdziewicz, and Corey S. O'Hern | Reliable protein folding on non-funneled energy landscapes: the free
energy reaction path | 13 pages, 9 figures | Biophys. J. 95, 2692 (2008) | 10.1529/biophysj.108.133132 | null | q-bio.BM | null | A theoretical framework is developed to study the dynamics of protein
folding. The key insight is that the search for the native protein conformation
is influenced by the rate r at which external parameters, such as temperature,
chemical denaturant or pH, are adjusted to induce folding. A theory based on
this insight... | [
{
"created": "Fri, 1 Feb 2008 21:55:57 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Lois",
"Gregg",
""
],
[
"Blawzdziewicz",
"Jerzy",
""
],
[
"O'Hern",
"Corey S.",
""
]
] | A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical denaturant or pH, are adjusted to induce folding. A theory based on this insight p... |
2206.14947 | Alexandra Rekesh | Tekin Gunasar, Alexandra Rekesh, Atul Nair, Penelope King, Anastasiya
Markova, Jiaqi Zhang, and Isabel Tate | Decision Forest Based EMG Signal Classification with Low Volume Dataset
Augmented with Random Variance Gaussian Noise | null | null | null | null | q-bio.NC cs.LG eess.SP stat.ML | http://creativecommons.org/licenses/by/4.0/ | Electromyography signals can be used as training data by machine learning
models to classify various gestures. We seek to produce a model that can
classify six different hand gestures with a limited number of samples that
generalizes well to a wider audience while comparing the effect of our feature
extraction result... | [
{
"created": "Wed, 29 Jun 2022 23:22:18 GMT",
"version": "v1"
}
] | 2022-07-01 | [
[
"Gunasar",
"Tekin",
""
],
[
"Rekesh",
"Alexandra",
""
],
[
"Nair",
"Atul",
""
],
[
"King",
"Penelope",
""
],
[
"Markova",
"Anastasiya",
""
],
[
"Zhang",
"Jiaqi",
""
],
[
"Tate",
"Isabel",
""
]
] | Electromyography signals can be used as training data by machine learning models to classify various gestures. We seek to produce a model that can classify six different hand gestures with a limited number of samples that generalizes well to a wider audience while comparing the effect of our feature extraction results ... |
2104.08280 | \'Elie Besserer-Offroy Ph.D. | M\'elanie Vivancos, Roberto Fanelli, \'Elie Besserer-Offroy, Sabrina
Beaulieu, Magali Chartier, Martin Resua-Rojas, Christine E. Mona, Santo
Previti, Emmanuelle R\'emond, Jean-Michel Longpr\'e, Florine Cavelier,
Philippe Sarret | Metabolically Stable Neurotensin Analogs Exert Potent and Long-Acting
Analgesia Without Hypothermia | This is the post-print (accepted) version of the following article:
Vivancos M, et al. (2021), Behav Brain Res. doi: 10.1016/j.bbr.2021.113189,
which has been accepted and published in final form at
https://www.sciencedirect.com/science/article/pii/S0166432821000772 | Behavioural Brain Research, 405:113189 (2021) | 10.1016/j.bbr.2021.113189 | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The endogenous tridecapeptide neurotensin (NT) has emerged as an important
inhibitory modulator of pain transmission, exerting its analgesic action
through the activation of the G protein-coupled receptors, NTS1 and NTS2.
Whereas both NT receptors mediate the analgesic effects of NT, NTS1 activation
also produces hyp... | [
{
"created": "Fri, 16 Apr 2021 23:18:14 GMT",
"version": "v1"
}
] | 2021-04-20 | [
[
"Vivancos",
"Mélanie",
""
],
[
"Fanelli",
"Roberto",
""
],
[
"Besserer-Offroy",
"Élie",
""
],
[
"Beaulieu",
"Sabrina",
""
],
[
"Chartier",
"Magali",
""
],
[
"Resua-Rojas",
"Martin",
""
],
[
"Mona",
"Christine E... | The endogenous tridecapeptide neurotensin (NT) has emerged as an important inhibitory modulator of pain transmission, exerting its analgesic action through the activation of the G protein-coupled receptors, NTS1 and NTS2. Whereas both NT receptors mediate the analgesic effects of NT, NTS1 activation also produces hypot... |
1501.01860 | Simon R. Schultz | Simon R. Schultz, Robin A. A. Ince and Stefano Panzeri | Applications of Information Theory to Analysis of Neural Data | 8 pages, 2 figures | Encyclopedia of Computational Neuroscience 2014, pp 1-6 | 10.1007/978-1-4614-7320-6_280-1 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Information theory is a practical and theoretical framework developed for the
study of communication over noisy channels. Its probabilistic basis and
capacity to relate statistical structure to function make it ideally suited for
studying information flow in the nervous system. It has a number of useful
properties: i... | [
{
"created": "Thu, 8 Jan 2015 14:16:02 GMT",
"version": "v1"
}
] | 2015-01-09 | [
[
"Schultz",
"Simon R.",
""
],
[
"Ince",
"Robin A. A.",
""
],
[
"Panzeri",
"Stefano",
""
]
] | Information theory is a practical and theoretical framework developed for the study of communication over noisy channels. Its probabilistic basis and capacity to relate statistical structure to function make it ideally suited for studying information flow in the nervous system. It has a number of useful properties: it ... |
2210.06069 | Yangtian Zhang | Yangtian Zhang, Huiyu Cai, Chence Shi, Bozitao Zhong, Jian Tang | E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking | International Conference on Learning Representations (ICLR 2023) | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | In silico prediction of the ligand binding pose to a given protein target is
a crucial but challenging task in drug discovery. This work focuses on blind
flexible selfdocking, where we aim to predict the positions, orientations and
conformations of docked molecules. Traditional physics-based methods usually
suffer fr... | [
{
"created": "Wed, 12 Oct 2022 10:25:54 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Jun 2023 10:05:06 GMT",
"version": "v2"
}
] | 2023-06-02 | [
[
"Zhang",
"Yangtian",
""
],
[
"Cai",
"Huiyu",
""
],
[
"Shi",
"Chence",
""
],
[
"Zhong",
"Bozitao",
""
],
[
"Tang",
"Jian",
""
]
] | In silico prediction of the ligand binding pose to a given protein target is a crucial but challenging task in drug discovery. This work focuses on blind flexible selfdocking, where we aim to predict the positions, orientations and conformations of docked molecules. Traditional physics-based methods usually suffer from... |
2402.15181 | Diwakar Shukla | Joseph D. Clark, Xuenan Mi, Douglas A. Mitchell, and Diwakar Shukla | Substrate Prediction for RiPP Biosynthetic Enzymes via Masked Language
Modeling and Transfer Learning | null | null | null | null | q-bio.QM q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Ribosomally synthesized and post-translationally modified peptide (RiPP)
biosynthetic enzymes often exhibit promiscuous substrate preferences that
cannot be reduced to simple rules. Large language models are promising tools
for predicting such peptide fitness landscapes. However, state-of-the-art
protein language mod... | [
{
"created": "Fri, 23 Feb 2024 08:23:26 GMT",
"version": "v1"
}
] | 2024-02-26 | [
[
"Clark",
"Joseph D.",
""
],
[
"Mi",
"Xuenan",
""
],
[
"Mitchell",
"Douglas A.",
""
],
[
"Shukla",
"Diwakar",
""
]
] | Ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic enzymes often exhibit promiscuous substrate preferences that cannot be reduced to simple rules. Large language models are promising tools for predicting such peptide fitness landscapes. However, state-of-the-art protein language model... |
0705.2105 | Erik Volz | Erik Volz and Lauren Ancel Meyers | SIR epidemics in dynamic contact networks | 20 pages, 4 figures. Submitted to Proc. Roy. Soc. B | null | null | null | q-bio.PE q-bio.QM | null | Contact patterns in populations fundamentally influence the spread of
infectious diseases. Current mathematical methods for epidemiological
forecasting on networks largely assume that contacts between individuals are
fixed, at least for the duration of an outbreak. In reality, contact patterns
may be quite fluid, wit... | [
{
"created": "Tue, 15 May 2007 09:40:40 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Volz",
"Erik",
""
],
[
"Meyers",
"Lauren Ancel",
""
]
] | Contact patterns in populations fundamentally influence the spread of infectious diseases. Current mathematical methods for epidemiological forecasting on networks largely assume that contacts between individuals are fixed, at least for the duration of an outbreak. In reality, contact patterns may be quite fluid, with ... |
1904.01208 | Genki Ichinose | Azumi Mamiya and Genki Ichinose | Strategies that enforce linear payoff relationships under observation
errors in Repeated Prisoner's Dilemma game | 19 pages, 3 figures | Journal of Theoretical Biology 477, 63-76 (2019) | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The theory of repeated games analyzes the long-term relationship of
interacting players and mathematically reveals the condition of how cooperation
is achieved, which is not achieved in a one-shot game. In the repeated
prisoner's dilemma (RPD) game with no errors, zero-determinant (ZD) strategies
allow a player to un... | [
{
"created": "Tue, 2 Apr 2019 04:30:14 GMT",
"version": "v1"
},
{
"created": "Wed, 19 Jun 2019 01:15:36 GMT",
"version": "v2"
}
] | 2019-06-20 | [
[
"Mamiya",
"Azumi",
""
],
[
"Ichinose",
"Genki",
""
]
] | The theory of repeated games analyzes the long-term relationship of interacting players and mathematically reveals the condition of how cooperation is achieved, which is not achieved in a one-shot game. In the repeated prisoner's dilemma (RPD) game with no errors, zero-determinant (ZD) strategies allow a player to unil... |
1610.07212 | Alexander Pimenov | Alexander Pimenov | Positive steady state in multi-species models of real food webs | 11 pages, 3 tables | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Real food web data available in the literature presents us with the relations
between various species, sizes of these species, metabolic types of the species
and other useful information, which allows us to define parameters for the
mathematical dynamical models of these food webs, and perform theoretical
studies of ... | [
{
"created": "Sun, 23 Oct 2016 18:37:39 GMT",
"version": "v1"
}
] | 2016-10-25 | [
[
"Pimenov",
"Alexander",
""
]
] | Real food web data available in the literature presents us with the relations between various species, sizes of these species, metabolic types of the species and other useful information, which allows us to define parameters for the mathematical dynamical models of these food webs, and perform theoretical studies of th... |
1812.00625 | Gestionnaire Hal-Upmc | Kevin Fidelin (ICM, INSERM, CNRS, UPMC), Lydia Djenoune (ICM, INSERM,
CNRS, UPMC, MNHN), Caleb Stokes (ICM, INSERM, CNRS, UPMC), Andrew Prendergast
(ICM, INSERM, CNRS, UPMC), Johanna G\'omez (ICM, INSERM, CNRS, UPMC), Audrey
Baradel (ICM, INSERM, CNRS, UPMC), Filippo Del\^A bene (UPMC), Claire Wyart
(ICM, INSER... | State-Dependent Modulation of Locomotion by GABAergic Spinal Sensory
Neurons | null | Current Biology - CB, Elsevier, 2015, 25 (23), pp.3035-3047 | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The cerebrospinal fluid (CSF) constitutes an interface through which chemical
cues can reach and modulate the activity of neurons located at the epithelial
boundary within the entire nervous system. Here, we investigate the role and
functional connectivity of a class of GABAergic sensory neurons contacting the
CSF in... | [
{
"created": "Mon, 3 Dec 2018 09:35:14 GMT",
"version": "v1"
}
] | 2018-12-04 | [
[
"Fidelin",
"Kevin",
"",
"ICM, INSERM, CNRS, UPMC"
],
[
"Djenoune",
"Lydia",
"",
"ICM, INSERM,\n CNRS, UPMC, MNHN"
],
[
"Stokes",
"Caleb",
"",
"ICM, INSERM, CNRS, UPMC"
],
[
"Prendergast",
"Andrew",
"",
"ICM, INSERM, CNRS, UPMC"
],
[
... | The cerebrospinal fluid (CSF) constitutes an interface through which chemical cues can reach and modulate the activity of neurons located at the epithelial boundary within the entire nervous system. Here, we investigate the role and functional connectivity of a class of GABAergic sensory neurons contacting the CSF in t... |
1005.5536 | Peter Pfaffelhuber | Greg Ewing, Joachim Hermisson, Peter Pfaffelhuber, Johannes Rudolf | Selective sweeps for recessive alleles and for other modes of dominance | Published in the Journal of Mathematical Biology. The final
publication is available at http://www.springerlink.com | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A selective sweep describes the reduction of linked genetic variation due to
strong positive selection. If s is the fitness advantage of a homozygote for
the beneficial allele and h its dominance coefficient, it is usually assumed
that h=1/2, i.e. the beneficial allele is co-dominant. We complement existing
theory fo... | [
{
"created": "Sun, 30 May 2010 14:39:26 GMT",
"version": "v1"
},
{
"created": "Tue, 2 Nov 2010 10:55:48 GMT",
"version": "v2"
}
] | 2010-11-03 | [
[
"Ewing",
"Greg",
""
],
[
"Hermisson",
"Joachim",
""
],
[
"Pfaffelhuber",
"Peter",
""
],
[
"Rudolf",
"Johannes",
""
]
] | A selective sweep describes the reduction of linked genetic variation due to strong positive selection. If s is the fitness advantage of a homozygote for the beneficial allele and h its dominance coefficient, it is usually assumed that h=1/2, i.e. the beneficial allele is co-dominant. We complement existing theory for ... |
1302.7102 | Zuo-Bing Wu | Zuo-Bing Wu | Periodic correlation structures in bacterial and archaeal complete
genomes | 23 pages, 6 figures, 2 tables | Current Bioinformatics, Vol. 8(2), 267-274 (2013) | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The periodic transference of nucleotide strings in bacterial and archaeal
complete genomes is investigated by using the metric representation and the
recurrence plot method. The generated periodic correlation structures exhibit
four kinds of fundamental transferring characteristics: a single increasing
period, severa... | [
{
"created": "Thu, 28 Feb 2013 07:20:52 GMT",
"version": "v1"
}
] | 2013-03-01 | [
[
"Wu",
"Zuo-Bing",
""
]
] | The periodic transference of nucleotide strings in bacterial and archaeal complete genomes is investigated by using the metric representation and the recurrence plot method. The generated periodic correlation structures exhibit four kinds of fundamental transferring characteristics: a single increasing period, several ... |
2208.04852 | Artur M Schweidtmann | Jan G. Rittig, Qinghe Gao, Manuel Dahmen, Alexander Mitsos, Artur M.
Schweidtmann | Graph neural networks for the prediction of molecular structure-property
relationships | null | Machine Learning and Hybrid Modelling for Reaction Engineering,
Royal Society of Chemistry, ISBN 978-1-83916-563-4, 159-181, 2023 | 10.1039/BK9781837670178-00159 | null | q-bio.BM cs.LG math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular property prediction is of crucial importance in many disciplines
such as drug discovery, molecular biology, or material and process design. The
frequently employed quantitative structure-property/activity relationships
(QSPRs/QSARs) characterize molecules by descriptors which are then mapped to
the properti... | [
{
"created": "Mon, 25 Jul 2022 11:30:44 GMT",
"version": "v1"
}
] | 2024-01-17 | [
[
"Rittig",
"Jan G.",
""
],
[
"Gao",
"Qinghe",
""
],
[
"Dahmen",
"Manuel",
""
],
[
"Mitsos",
"Alexander",
""
],
[
"Schweidtmann",
"Artur M.",
""
]
] | Molecular property prediction is of crucial importance in many disciplines such as drug discovery, molecular biology, or material and process design. The frequently employed quantitative structure-property/activity relationships (QSPRs/QSARs) characterize molecules by descriptors which are then mapped to the properties... |
q-bio/0408016 | Michael Deem | Enrique T. Munoz and Michael W. Deem | Epitope analysis for influenza vaccine design | 20 pages, 3 figures, to appear in Vaccine | null | null | null | q-bio.BM q-bio.QM | null | Until now, design of the annual influenza vaccine has relied on phylogenetic
or whole-sequence comparisons of the viral coat proteins hemagglutinin and
neuraminidase, with vaccine effectiveness assumed to correlate monotonically to
the vaccine-influenza sequence difference. We use a theory from statistical
mechanics ... | [
{
"created": "Mon, 23 Aug 2004 22:11:05 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Munoz",
"Enrique T.",
""
],
[
"Deem",
"Michael W.",
""
]
] | Until now, design of the annual influenza vaccine has relied on phylogenetic or whole-sequence comparisons of the viral coat proteins hemagglutinin and neuraminidase, with vaccine effectiveness assumed to correlate monotonically to the vaccine-influenza sequence difference. We use a theory from statistical mechanics to... |
2104.08237 | Johanna Vielhaben | Johanna Vielhaben, Markus Wenzel, Eva Weicken, Nils Strodthoff | Predicting the Binding of SARS-CoV-2 Peptides to the Major
Histocompatibility Complex with Recurrent Neural Networks | Accepted at ICLR 2021 Workshop: Machine Learning for Preventing and
Combating Pandemics; code available at https://github.com/nstrodt/USMPep | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Predicting the binding of viral peptides to the major histocompatibility
complex with machine learning can potentially extend the computational
immunology toolkit for vaccine development, and serve as a key component in the
fight against a pandemic. In this work, we adapt and extend USMPep, a recently
proposed, conce... | [
{
"created": "Fri, 16 Apr 2021 17:16:35 GMT",
"version": "v1"
}
] | 2021-04-19 | [
[
"Vielhaben",
"Johanna",
""
],
[
"Wenzel",
"Markus",
""
],
[
"Weicken",
"Eva",
""
],
[
"Strodthoff",
"Nils",
""
]
] | Predicting the binding of viral peptides to the major histocompatibility complex with machine learning can potentially extend the computational immunology toolkit for vaccine development, and serve as a key component in the fight against a pandemic. In this work, we adapt and extend USMPep, a recently proposed, concept... |
1504.03343 | Apoorvagiri Lnu | Apoorvagiri, M.S. Nagananda | Quantization of mental stress using various physiological markers | 16 pages,11 Figures, 2 Tables; can also be found at PeerJ PrePrints
3:e1250 2015, page 1-16 | null | 10.7287/peerj.preprints.777v3 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The aim of this study is to quantize mental stress by integrating different
physiological markers like reaction time, photoplethysmograph (PPG), heart rate
variability (HRV) and subjective markers like questionnaire. The study included
10 subjects of age between 22 and 26 years. Study materials included the
results o... | [
{
"created": "Thu, 5 Feb 2015 19:19:30 GMT",
"version": "v1"
},
{
"created": "Fri, 1 May 2015 03:30:45 GMT",
"version": "v2"
}
] | 2015-05-04 | [
[
"Apoorvagiri",
"",
""
],
[
"Nagananda",
"M. S.",
""
]
] | The aim of this study is to quantize mental stress by integrating different physiological markers like reaction time, photoplethysmograph (PPG), heart rate variability (HRV) and subjective markers like questionnaire. The study included 10 subjects of age between 22 and 26 years. Study materials included the results of ... |
2110.13830 | Farshad Rafiei | Farshad Rafiei and Dobromir Rahnev | Does TMS increase BOLD activity at the site of stimulation? | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Transcranial magnetic stimulation (TMS) is widely used for understanding
brain function in neurologically intact subjects and for the treatment of
various disorders. However, the precise neurophysiological effects of TMS at
the site of stimulation remain poorly understood. The local effects of TMS can
be studied usin... | [
{
"created": "Tue, 26 Oct 2021 16:24:23 GMT",
"version": "v1"
}
] | 2021-10-27 | [
[
"Rafiei",
"Farshad",
""
],
[
"Rahnev",
"Dobromir",
""
]
] | Transcranial magnetic stimulation (TMS) is widely used for understanding brain function in neurologically intact subjects and for the treatment of various disorders. However, the precise neurophysiological effects of TMS at the site of stimulation remain poorly understood. The local effects of TMS can be studied using ... |
1408.6583 | Chiu Man Ho | Chiu Man Ho, Stephen D.H. Hsu | Determination of Nonlinear Genetic Architecture using Compressed Sensing | 20 pages, 8 figures. arXiv admin note: text overlap with
arXiv:1408.3421 | GigaScience 4: 44 (2015) | null | null | q-bio.GN stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a statistical method that can reconstruct nonlinear genetic
models (i.e., including epistasis, or gene-gene interactions) from
phenotype-genotype (GWAS) data. The computational and data resource
requirements are similar to those necessary for reconstruction of linear
genetic models (or identification of ... | [
{
"created": "Wed, 27 Aug 2014 22:32:50 GMT",
"version": "v1"
},
{
"created": "Sun, 19 Jul 2015 21:33:35 GMT",
"version": "v2"
}
] | 2015-09-29 | [
[
"Ho",
"Chiu Man",
""
],
[
"Hsu",
"Stephen D. H.",
""
]
] | We introduce a statistical method that can reconstruct nonlinear genetic models (i.e., including epistasis, or gene-gene interactions) from phenotype-genotype (GWAS) data. The computational and data resource requirements are similar to those necessary for reconstruction of linear genetic models (or identification of ge... |
0809.0773 | Mukhtar Ullah Mr. | Mukhtar Ullah, Olaf Wolkenhauer | Investigating the two-moment characterisation of subcellular biochemical
networks | 32 pages, 10 figures | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While ordinary differential equations (ODEs) form the conceptual framework
for modelling many cellular processes, specific situations demand stochastic
models to capture the influence of noise. The most common formulation of
stochastic models for biochemical networks is the chemical master equation
(CME). While stoch... | [
{
"created": "Thu, 4 Sep 2008 08:54:09 GMT",
"version": "v1"
},
{
"created": "Tue, 3 Feb 2009 12:03:38 GMT",
"version": "v2"
},
{
"created": "Thu, 2 Apr 2009 10:56:46 GMT",
"version": "v3"
}
] | 2009-04-02 | [
[
"Ullah",
"Mukhtar",
""
],
[
"Wolkenhauer",
"Olaf",
""
]
] | While ordinary differential equations (ODEs) form the conceptual framework for modelling many cellular processes, specific situations demand stochastic models to capture the influence of noise. The most common formulation of stochastic models for biochemical networks is the chemical master equation (CME). While stochas... |
1010.2508 | Wilfred Kepseu | Wilfred D. Kepseu, Paul Woafo and H. Sakaguchi | Intercellular spiral waves of calcium in a two dimensional network of
cells | 12 pages, 9 figures | null | null | null | q-bio.MN physics.bio-ph q-bio.BM q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is shown, by means of numerical simulations, that intercellular spiral
waves of calcium can be initiated in a network of coupled cells as a result of
a de-synchronization between Ca2+ oscillations in two domains. No artificial
heterogeneities need to be imposed to the system for spontaneous formation of
spiral wav... | [
{
"created": "Tue, 12 Oct 2010 20:29:04 GMT",
"version": "v1"
}
] | 2010-10-14 | [
[
"Kepseu",
"Wilfred D.",
""
],
[
"Woafo",
"Paul",
""
],
[
"Sakaguchi",
"H.",
""
]
] | It is shown, by means of numerical simulations, that intercellular spiral waves of calcium can be initiated in a network of coupled cells as a result of a de-synchronization between Ca2+ oscillations in two domains. No artificial heterogeneities need to be imposed to the system for spontaneous formation of spiral waves... |
2404.02789 | Giovanni Bussi | Giovanni Bussi, Massimiliano Bonomi, Paraskevi Gkeka, Michael Sattler,
Hashim M. Al-Hashimi, Pascal Auffinger, Maria Duca, Yann Foricher, Danny
Incarnato, Alisha N. Jones, Serdal Kirmizialtin, Miroslav Krepl, Modesto
Orozco, Giulia Palermo, Samuela Pasquali, Lo\"ic Salmon, Harald Schwalbe,
Eric Westhof, Martin ... | RNA Dynamics from Experimental and Computational Approaches | null | null | null | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ribonucleic acids (RNA) are unique in that they can store genetic
information, replicate and perform catalysis. Importantly, RNA molecules are
highly dynamic, and thus determining the ensemble of conformations that they
populate is crucial not only to elucidate their biological functions, but also
for their potential... | [
{
"created": "Wed, 3 Apr 2024 14:56:41 GMT",
"version": "v1"
}
] | 2024-04-04 | [
[
"Bussi",
"Giovanni",
""
],
[
"Bonomi",
"Massimiliano",
""
],
[
"Gkeka",
"Paraskevi",
""
],
[
"Sattler",
"Michael",
""
],
[
"Al-Hashimi",
"Hashim M.",
""
],
[
"Auffinger",
"Pascal",
""
],
[
"Duca",
"Maria",
... | Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining the ensemble of conformations that they populate is crucial not only to elucidate their biological functions, but also for their potential u... |
2110.06228 | Reinhard Schumacher | Robert A. Mason, Reinhard A. Schumacher, and Marcel A. Just | The Neuroscience of Advanced Scientific Concepts | 12 pages, 6 figures, open access publication | npj Science of Learning, 6, 29 (2021) | 10.1038/s41539-021-00107-6 | null | q-bio.NC physics.ed-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cognitive neuroscience methods can identify the fMRI-measured neural
representation of familiar individual concepts, such as apple, and decompose
them into meaningful neural and semantic components. This approach was applied
here to determine the neural representations and underlying dimensions of
representation of f... | [
{
"created": "Tue, 12 Oct 2021 18:00:03 GMT",
"version": "v1"
}
] | 2021-10-15 | [
[
"Mason",
"Robert A.",
""
],
[
"Schumacher",
"Reinhard A.",
""
],
[
"Just",
"Marcel A.",
""
]
] | Cognitive neuroscience methods can identify the fMRI-measured neural representation of familiar individual concepts, such as apple, and decompose them into meaningful neural and semantic components. This approach was applied here to determine the neural representations and underlying dimensions of representation of far... |
1208.2247 | Alessandro Daducci | Alessandro Daducci, Dimitri Van De Ville, Jean-Philippe Thiran, Yves
Wiaux | Sparse regularization for fiber ODF reconstruction: from the
suboptimality of $\ell_2$ and $\ell_1$ priors to $\ell_0$ | 26 pages, 9 figures | null | null | null | q-bio.QM physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Diffusion MRI is a well established imaging modality providing a powerful way
to probe the structure of the white matter non-invasively. Despite its
potential, the intrinsic long scan times of these sequences have hampered their
use in clinical practice. For this reason, a large variety of methods have been
recently ... | [
{
"created": "Fri, 10 Aug 2012 18:44:28 GMT",
"version": "v1"
},
{
"created": "Thu, 11 Jul 2013 10:50:12 GMT",
"version": "v2"
},
{
"created": "Sat, 28 Dec 2013 12:38:21 GMT",
"version": "v3"
}
] | 2013-12-31 | [
[
"Daducci",
"Alessandro",
""
],
[
"Van De Ville",
"Dimitri",
""
],
[
"Thiran",
"Jean-Philippe",
""
],
[
"Wiaux",
"Yves",
""
]
] | Diffusion MRI is a well established imaging modality providing a powerful way to probe the structure of the white matter non-invasively. Despite its potential, the intrinsic long scan times of these sequences have hampered their use in clinical practice. For this reason, a large variety of methods have been recently pr... |
1008.5072 | Cornelis Storm | Elisabeth M. Huisman, Claus Heussinger, Cornelis Storm, Gerard T.
Barkema | Semiflexible Filamentous Composites | Phys. Rev. Lett, to appear (4 pages, 2 figures) | null | 10.1103/PhysRevLett.105.118101 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inspired by the ubiquity of composite filamentous networks in nature we
investigate models of biopolymer networks that consist of interconnected floppy
and stiff filaments. Numerical simulations carried out in three dimensions
allow us to explore the microscopic partitioning of stresses and strains
between the stiff ... | [
{
"created": "Mon, 30 Aug 2010 12:54:58 GMT",
"version": "v1"
}
] | 2015-05-19 | [
[
"Huisman",
"Elisabeth M.",
""
],
[
"Heussinger",
"Claus",
""
],
[
"Storm",
"Cornelis",
""
],
[
"Barkema",
"Gerard T.",
""
]
] | Inspired by the ubiquity of composite filamentous networks in nature we investigate models of biopolymer networks that consist of interconnected floppy and stiff filaments. Numerical simulations carried out in three dimensions allow us to explore the microscopic partitioning of stresses and strains between the stiff an... |
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