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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2407.18494 | Yiduo Chen | Yi-Duo Chen, Jian-Yue Guan, Zhi-Xi Wu (Lanzhou Center for Theoretical
Physics, Key Laboratory of Theoretical Physics of Gansu Province, and Key
Laboratory of Quantum Theory and Applications of MoE, Lanzhou University,
Lanzhou, China and Institute of Computational Physics and Complex Systems,
Lanzhou University,... | Coevolutionary game dynamics with localized environmental resource
feedback | null | null | null | null | q-bio.PE nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dynamic environments shape diverse dynamics in evolutionary game systems. We
introduce spatial heterogeneity of resources into the Prisoner's Dilemma Game
model to explore the co-evolution of individuals' strategies and environmental
resources. The adequacy of resources significantly affects the survival
competitiven... | [
{
"created": "Fri, 26 Jul 2024 03:56:09 GMT",
"version": "v1"
}
] | 2024-07-29 | [
[
"Chen",
"Yi-Duo",
"",
"Lanzhou Center for Theoretical\n Physics, Key Laboratory of Theoretical Physics of Gansu Province, and Key\n Laboratory of Quantum Theory and Applications of MoE, Lanzhou University,\n Lanzhou, China and Institute of Computational Physics and Complex Systems,\n Lanzhou U... | Dynamic environments shape diverse dynamics in evolutionary game systems. We introduce spatial heterogeneity of resources into the Prisoner's Dilemma Game model to explore the co-evolution of individuals' strategies and environmental resources. The adequacy of resources significantly affects the survival competitivenes... |
1808.03642 | Alexandre De Brevern | Sneha Vishwanath (Molecular Biophysics Unit), Alexandre De Brevern
(BIGR), Narayanaswamy Srinivasan | Same but not alike: Structure, flexibility and energetics of domains in
multi-domain proteins are influenced by the presence of other domains | null | PLoS Computational Biology, Public Library of Science, 2018, 14
(2), pp.e1006008 | 10.1371/journal.pcbi.1006008 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The majority of the proteins encoded in the genomes of eukaryotes contain
more than one domain. Reasons for high prevalence of multi-domain proteins in
various organisms have been attributed to higher stability and functional and
folding advantages over single-domain proteins. Despite these advantages, many
proteins ... | [
{
"created": "Fri, 10 Aug 2018 07:01:29 GMT",
"version": "v1"
}
] | 2018-08-14 | [
[
"Vishwanath",
"Sneha",
"",
"Molecular Biophysics Unit"
],
[
"De Brevern",
"Alexandre",
"",
"BIGR"
],
[
"Srinivasan",
"Narayanaswamy",
""
]
] | The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins ar... |
1908.10897 | Andrew Eckford | Gregory R. Hessler, Andrew W. Eckford, and Peter J. Thomas | Linear Noise Approximation of Intensity-Driven Signal Transduction
Channels | Accepted for publication at the 2019 IEEE Global Communications
Conference (GLOBECOM) | null | null | null | q-bio.QM cs.IT math.IT q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biochemical signal transduction, a form of molecular communication, can be
modeled using graphical Markov channels with input-modulated transition rates.
Such channel models are strongly non-Gaussian. In this paper we use a linear
noise approximation to construct a novel class of Gaussian additive white noise
channel... | [
{
"created": "Wed, 28 Aug 2019 18:24:57 GMT",
"version": "v1"
}
] | 2019-08-30 | [
[
"Hessler",
"Gregory R.",
""
],
[
"Eckford",
"Andrew W.",
""
],
[
"Thomas",
"Peter J.",
""
]
] | Biochemical signal transduction, a form of molecular communication, can be modeled using graphical Markov channels with input-modulated transition rates. Such channel models are strongly non-Gaussian. In this paper we use a linear noise approximation to construct a novel class of Gaussian additive white noise channels ... |
1802.01328 | Marcus Krantz | Jesper Romers, Sebastian Thieme, Ulrike M\"unzner and Marcus Krantz | Using rxncon to develop rule based models | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a protocol for building, validating and simulating models of
signal transduction networks. These networks are challenging modelling targets
due to the combinatorial complexity and sparse data, which have made it a major
challenge even to formalise the current knowledge. To address this, the
community has d... | [
{
"created": "Mon, 5 Feb 2018 10:18:44 GMT",
"version": "v1"
}
] | 2018-02-06 | [
[
"Romers",
"Jesper",
""
],
[
"Thieme",
"Sebastian",
""
],
[
"Münzner",
"Ulrike",
""
],
[
"Krantz",
"Marcus",
""
]
] | We present a protocol for building, validating and simulating models of signal transduction networks. These networks are challenging modelling targets due to the combinatorial complexity and sparse data, which have made it a major challenge even to formalise the current knowledge. To address this, the community has dev... |
2201.11215 | Olusola Odeyomi | Olusola Odeyomi, and Gergely Zaruba | Predicting Succinylation Sites in Proteins with Improved Deep Learning
Architecture | null | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Post-translational modifications (PTMs) in proteins occur after the process
of translation. PTMs account for many cellular processes such as
deoxyribonucleic acid (DNA) repair, cell signaling and cell death. One of the
recent PTMs is succinylation. Succinylation modifies lysine residue from $-1$
to $+1$. Locating suc... | [
{
"created": "Mon, 27 Dec 2021 16:15:34 GMT",
"version": "v1"
}
] | 2022-01-28 | [
[
"Odeyomi",
"Olusola",
""
],
[
"Zaruba",
"Gergely",
""
]
] | Post-translational modifications (PTMs) in proteins occur after the process of translation. PTMs account for many cellular processes such as deoxyribonucleic acid (DNA) repair, cell signaling and cell death. One of the recent PTMs is succinylation. Succinylation modifies lysine residue from $-1$ to $+1$. Locating succi... |
2106.03276 | Zhou Fang | Zhou Fang, Ankit Gupta, Mustafa Khammash | Stochastic filtering for multiscale stochastic reaction networks based
on hybrid approximations | 8 figures, 33 pages. Accepted to the Journal of Computational Physics | null | 10.1016/j.jcp.2022.111441 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the past few decades, the development of fluorescent technologies and
microscopic techniques has greatly improved scientists' ability to observe
real-time single-cell activities. In this paper, we consider the filtering
problem associate with these advanced technologies, i.e., how to estimate
latent dynamic states... | [
{
"created": "Sun, 6 Jun 2021 23:28:44 GMT",
"version": "v1"
},
{
"created": "Sat, 9 Jul 2022 20:38:38 GMT",
"version": "v2"
}
] | 2022-07-27 | [
[
"Fang",
"Zhou",
""
],
[
"Gupta",
"Ankit",
""
],
[
"Khammash",
"Mustafa",
""
]
] | In the past few decades, the development of fluorescent technologies and microscopic techniques has greatly improved scientists' ability to observe real-time single-cell activities. In this paper, we consider the filtering problem associate with these advanced technologies, i.e., how to estimate latent dynamic states o... |
1602.02945 | Adeel Razi | Adeel Razi and Karl Friston | The connected brain: Causality, models and intrinsic dynamics | 52 pages, Feature Article, Accepted, IEEE Signal Processing Magazine | null | 10.1109/MSP.2015.2482121 | null | q-bio.NC math.DS stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, there have been several concerted international efforts - the BRAIN
initiative, European Human Brain Project and the Human Connectome Project, to
name a few - that hope to revolutionize our understanding of the connected
brain. Over the past two decades, functional neuroimaging has emerged as the
predominan... | [
{
"created": "Tue, 9 Feb 2016 11:54:38 GMT",
"version": "v1"
}
] | 2016-02-10 | [
[
"Razi",
"Adeel",
""
],
[
"Friston",
"Karl",
""
]
] | Recently, there have been several concerted international efforts - the BRAIN initiative, European Human Brain Project and the Human Connectome Project, to name a few - that hope to revolutionize our understanding of the connected brain. Over the past two decades, functional neuroimaging has emerged as the predominant ... |
2010.13478 | Yong-Joon Song | Yong Joon Song, Dong Jin Ji, Hye In Seo, Gyu Bum Han, and Dong Ho Cho | Pairwise heuristic sequence alignment algorithm based on deep
reinforcement learning | 20pages, 9figures | null | null | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Various methods have been developed to analyze the association between
organisms and their genomic sequences. Among them, sequence alignment is the
most frequently used for comparative analysis of biological genomes. However,
the traditional sequence alignment method is considerably complicated in
proportion to the s... | [
{
"created": "Mon, 26 Oct 2020 10:49:12 GMT",
"version": "v1"
}
] | 2020-10-27 | [
[
"Song",
"Yong Joon",
""
],
[
"Ji",
"Dong Jin",
""
],
[
"Seo",
"Hye In",
""
],
[
"Han",
"Gyu Bum",
""
],
[
"Cho",
"Dong Ho",
""
]
] | Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the traditional sequence alignment method is considerably complicated in proportion to the seq... |
2002.07327 | Soha Hassoun | Gian Marco Visani, Michael C. Hughes, Soha Hassoun | Enzyme promiscuity prediction using hierarchy-informed multi-label
classification | Presented as a poster at the 2019 Machine Learning for Computational
Biology Symposium, Vancouver, CA Accepted for publication, Bioinformatics,
Jan 22, 2021 | null | null | null | q-bio.CB cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | As experimental efforts are costly and time consuming, computational
characterization of enzyme capabilities is an attractive alternative. We
present and evaluate several machine-learning models to predict which of 983
distinct enzymes, as defined via the Enzyme Commission, EC, numbers, are likely
to interact with a ... | [
{
"created": "Tue, 18 Feb 2020 01:39:24 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Jan 2021 03:01:52 GMT",
"version": "v2"
}
] | 2021-01-27 | [
[
"Visani",
"Gian Marco",
""
],
[
"Hughes",
"Michael C.",
""
],
[
"Hassoun",
"Soha",
""
]
] | As experimental efforts are costly and time consuming, computational characterization of enzyme capabilities is an attractive alternative. We present and evaluate several machine-learning models to predict which of 983 distinct enzymes, as defined via the Enzyme Commission, EC, numbers, are likely to interact with a gi... |
2010.16027 | Aditi Krishnapriyan | Nicolas Swenson, Aditi S. Krishnapriyan, Aydin Buluc, Dmitriy Morozov,
and Katherine Yelick | PersGNN: Applying Topological Data Analysis and Geometric Deep Learning
to Structure-Based Protein Function Prediction | The first two authors contributed equally to this work | null | null | null | q-bio.BM cs.LG math.AT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding protein structure-function relationships is a key challenge in
computational biology, with applications across the biotechnology and
pharmaceutical industries. While it is known that protein structure directly
impacts protein function, many functional prediction tasks use only protein
sequence. In this ... | [
{
"created": "Fri, 30 Oct 2020 02:24:35 GMT",
"version": "v1"
}
] | 2020-11-02 | [
[
"Swenson",
"Nicolas",
""
],
[
"Krishnapriyan",
"Aditi S.",
""
],
[
"Buluc",
"Aydin",
""
],
[
"Morozov",
"Dmitriy",
""
],
[
"Yelick",
"Katherine",
""
]
] | Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein function, many functional prediction tasks use only protein sequence. In this wo... |
1209.0813 | Matthias Steinruecken | Matthias Steinr\"ucken, Matthias Birkner, Jochen Blath | Analysis of DNA sequence variation within marine species using
Beta-coalescents | 15 pages, 16 figures | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We apply recently developed inference methods based on general coalescent
processes to DNA sequence data obtained from various marine species. Several of
these species are believed to exhibit so-called shallow gene genealogies,
potentially due to extreme reproductive behaviour, e.g. via Hedgecock's
"reproduction swee... | [
{
"created": "Tue, 4 Sep 2012 22:00:08 GMT",
"version": "v1"
},
{
"created": "Sun, 4 Nov 2012 23:23:35 GMT",
"version": "v2"
}
] | 2012-11-06 | [
[
"Steinrücken",
"Matthias",
""
],
[
"Birkner",
"Matthias",
""
],
[
"Blath",
"Jochen",
""
]
] | We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially due to extreme reproductive behaviour, e.g. via Hedgecock's "reproduction sweeps... |
1810.04589 | Thierry Mora | Martin Carballo-Pacheco, Jonathan Desponds, Tatyana Gavrilchenko,
Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora | Receptor crosstalk improves concentration sensing of multiple ligands | null | Phys. Rev. E 99, 022423 (2019) | 10.1103/PhysRevE.99.022423 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cells need to reliably sense external ligand concentrations to achieve
various biological functions such as chemotaxis or signaling. The molecular
recognition of ligands by surface receptors is degenerate in many systems
leading to crosstalk between different receptors. Crosstalk is often thought of
as a deviation fr... | [
{
"created": "Wed, 10 Oct 2018 15:28:10 GMT",
"version": "v1"
}
] | 2019-03-06 | [
[
"Carballo-Pacheco",
"Martin",
""
],
[
"Desponds",
"Jonathan",
""
],
[
"Gavrilchenko",
"Tatyana",
""
],
[
"Mayer",
"Andreas",
""
],
[
"Prizak",
"Roshan",
""
],
[
"Reddy",
"Gautam",
""
],
[
"Nemenman",
"Ilya",
... | Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems leading to crosstalk between different receptors. Crosstalk is often thought of as a deviation from... |
1810.00387 | Lei Zhou | Lei Zhou, Bin Wu, Jinming Du, Long Wang | Aspiration dynamics generate robust predictions in structured
populations | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Evolutionary game dynamics in structured populations are strongly affected by
updating rules. Previous studies usually focus on imitation-based rules, which
rely on payoff information of social peers. Recent behavioral experiments
suggest that whether individuals use such social information for strategy
updating may ... | [
{
"created": "Sun, 30 Sep 2018 14:30:43 GMT",
"version": "v1"
}
] | 2018-10-02 | [
[
"Zhou",
"Lei",
""
],
[
"Wu",
"Bin",
""
],
[
"Du",
"Jinming",
""
],
[
"Wang",
"Long",
""
]
] | Evolutionary game dynamics in structured populations are strongly affected by updating rules. Previous studies usually focus on imitation-based rules, which rely on payoff information of social peers. Recent behavioral experiments suggest that whether individuals use such social information for strategy updating may be... |
2307.15462 | Guy Ropars | Albert Le Floch and Guy Ropars | Hebbian control of fixations in a dyslexic reader | 8 pages, 6 figures | null | null | null | q-bio.NC physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | During reading, dyslexic readers exhibit more and longer fixations than
normal readers. However, there is no significant difference when dyslexic and
control readers perform only visual tasks on a string of letters, showing the
importance of cognitive processes in reading. This linguistic and cognitive
processing dem... | [
{
"created": "Fri, 28 Jul 2023 10:27:54 GMT",
"version": "v1"
}
] | 2023-07-31 | [
[
"Floch",
"Albert Le",
""
],
[
"Ropars",
"Guy",
""
]
] | During reading, dyslexic readers exhibit more and longer fixations than normal readers. However, there is no significant difference when dyslexic and control readers perform only visual tasks on a string of letters, showing the importance of cognitive processes in reading. This linguistic and cognitive processing deman... |
2004.11626 | Yubo Huang | Yubo Huang and Weidong Zhang | Comprehensive Investigation and Isolation have Effectively Suppressed
the Spread of COVID-19 | The draft is the first vision | null | 10.1016/j.chaos.2020.110041 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The outbreak of COVID-19 since Dec. 2019 has caused severe life and economic
damage worldwide, many countries are trapped by medical resource constraints or
absence of targeted therapeutics, and therefore the implement of systemic
policies to block this pandemic should be prioritized. Based on the
transmission mechan... | [
{
"created": "Fri, 24 Apr 2020 09:52:58 GMT",
"version": "v1"
}
] | 2020-07-15 | [
[
"Huang",
"Yubo",
""
],
[
"Zhang",
"Weidong",
""
]
] | The outbreak of COVID-19 since Dec. 2019 has caused severe life and economic damage worldwide, many countries are trapped by medical resource constraints or absence of targeted therapeutics, and therefore the implement of systemic policies to block this pandemic should be prioritized. Based on the transmission mechanis... |
1408.3028 | Olivier Marre | Olivier Marre, Vicente Botella-Soler, Kristina D. Simmons, Thierry
Mora, Ga\v{s}per Tka\v{c}ik, Michael J. Berry II | High accuracy decoding of dynamical motion from a large retinal
population | 23 pages, 7 figures | null | 10.1371/journal.pcbi.1004304 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motion tracking is a challenge the visual system has to solve by reading out
the retinal population. Here we recorded a large population of ganglion cells
in a dense patch of salamander and guinea pig retinas while displaying a bar
moving diffusively. We show that the bar position can be reconstructed from
retinal ac... | [
{
"created": "Wed, 13 Aug 2014 15:25:15 GMT",
"version": "v1"
}
] | 2016-02-17 | [
[
"Marre",
"Olivier",
""
],
[
"Botella-Soler",
"Vicente",
""
],
[
"Simmons",
"Kristina D.",
""
],
[
"Mora",
"Thierry",
""
],
[
"Tkačik",
"Gašper",
""
],
[
"Berry",
"Michael J.",
"II"
]
] | Motion tracking is a challenge the visual system has to solve by reading out the retinal population. Here we recorded a large population of ganglion cells in a dense patch of salamander and guinea pig retinas while displaying a bar moving diffusively. We show that the bar position can be reconstructed from retinal acti... |
1304.4766 | Yongchao Liu | Yongchao Liu, Bernt Popp and Bertil Schmidt | High-speed and accurate color-space short-read alignment with CUSHAW2 | 2 pages,1 table | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Summary: We present an extension of CUSHAW2 for fast and accurate alignments
of SOLiD color-space short-reads. Our extension introduces a double-seeding
approach to improve mapping sensitivity, by combining maximal exact match seeds
and variable-length seeds derived from local alignments. We have compared the
perform... | [
{
"created": "Wed, 17 Apr 2013 11:06:33 GMT",
"version": "v1"
}
] | 2013-04-18 | [
[
"Liu",
"Yongchao",
""
],
[
"Popp",
"Bernt",
""
],
[
"Schmidt",
"Bertil",
""
]
] | Summary: We present an extension of CUSHAW2 for fast and accurate alignments of SOLiD color-space short-reads. Our extension introduces a double-seeding approach to improve mapping sensitivity, by combining maximal exact match seeds and variable-length seeds derived from local alignments. We have compared the performan... |
2007.03246 | Oleksandr Oliynyk | Anna Larsson, Soodabeh Majdi, Alexander Oleinick (PASTEUR), Irina Svir
(PASTEUR), Johan Dunevall, Christian Amatore (PASTEUR), Andrew Ewing | Intracellular Electrochemical Nanomeasurements Reveal that Exocytosis of
Molecules at Living Neurons is Subquantal and Complex | null | Angewandte Chemie International Edition, Wiley-VCH Verlag, 2020,
59 (17), pp.6711-6714 | 10.1002/anie.201914564 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Since the early work of Bernard Katz, the process of cellular chemical
communication via exocytosis, quantal release, has been considered to be all or
none. Recent evidence has shown exocytosis to be partial or 'subquantal' at
single-cell model systems, but there is a need to understand this at
communicating nerve ce... | [
{
"created": "Tue, 7 Jul 2020 07:31:35 GMT",
"version": "v1"
}
] | 2020-07-08 | [
[
"Larsson",
"Anna",
"",
"PASTEUR"
],
[
"Majdi",
"Soodabeh",
"",
"PASTEUR"
],
[
"Oleinick",
"Alexander",
"",
"PASTEUR"
],
[
"Svir",
"Irina",
"",
"PASTEUR"
],
[
"Dunevall",
"Johan",
"",
"PASTEUR"
],
[
"Amatore",
... | Since the early work of Bernard Katz, the process of cellular chemical communication via exocytosis, quantal release, has been considered to be all or none. Recent evidence has shown exocytosis to be partial or 'subquantal' at single-cell model systems, but there is a need to understand this at communicating nerve cell... |
0802.0029 | Ryo Kanada | Ryo Kanada, Fumiko Takagi, Macoto Kikuchi | Structural Fluctuations of Microtubule Binding Site of KIF1A in
Different Nucleotide States | 14 pages, 7 figures | null | null | null | q-bio.BM | null | How molecular motors like Kinesin regulates the affinity to the rail protein
in the process of ATP hydrolysis remains to be uncovered. To understand the
regulation mechanism, we investigate the structural fluctuation of KIF1A in
different nucleotide states that are realized in the ATP hydrolysis process by
molecular ... | [
{
"created": "Thu, 31 Jan 2008 23:42:57 GMT",
"version": "v1"
}
] | 2008-02-04 | [
[
"Kanada",
"Ryo",
""
],
[
"Takagi",
"Fumiko",
""
],
[
"Kikuchi",
"Macoto",
""
]
] | How molecular motors like Kinesin regulates the affinity to the rail protein in the process of ATP hydrolysis remains to be uncovered. To understand the regulation mechanism, we investigate the structural fluctuation of KIF1A in different nucleotide states that are realized in the ATP hydrolysis process by molecular dy... |
1708.03263 | Giovanni Petri | Giovanni Petri, Sebastian Musslick, Biswadip Dey, Kayhan Ozcimder,
David Turner, Nesreen K. Ahmed, Theodore Willke and Jonathan D. Cohen | Topological limits to parallel processing capability of network
architectures | version 4. Added SIs, 33 pages total, 4 figures + 14 figures in SI,
major edits to text | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ability to learn new tasks and generalize performance to others is one of
the most remarkable characteristics of the human brain and of recent AI
systems. The ability to perform multiple tasks simultaneously is also a
signature characteristic of large-scale parallel architectures, that is evident
in the human bra... | [
{
"created": "Thu, 10 Aug 2017 15:37:29 GMT",
"version": "v1"
},
{
"created": "Wed, 16 Aug 2017 09:12:46 GMT",
"version": "v2"
},
{
"created": "Wed, 18 Mar 2020 21:11:16 GMT",
"version": "v3"
},
{
"created": "Tue, 10 Nov 2020 18:03:26 GMT",
"version": "v4"
}
] | 2020-11-11 | [
[
"Petri",
"Giovanni",
""
],
[
"Musslick",
"Sebastian",
""
],
[
"Dey",
"Biswadip",
""
],
[
"Ozcimder",
"Kayhan",
""
],
[
"Turner",
"David",
""
],
[
"Ahmed",
"Nesreen K.",
""
],
[
"Willke",
"Theodore",
""
],... | The ability to learn new tasks and generalize performance to others is one of the most remarkable characteristics of the human brain and of recent AI systems. The ability to perform multiple tasks simultaneously is also a signature characteristic of large-scale parallel architectures, that is evident in the human brain... |
1102.4570 | Matjaz Perc | Zhen Wang, Aleksandra Murks, Wen-Bo Du, Zhi-Hai Rong, Matjaz Perc | Coveting thy neighbors fitness as a means to resolve social dilemmas | 10 two-column pages, 5 figures; accepted for publication in Journal
of Theoretical Biology | J. Theor. Biol. 277 (2011) 19-26 | 10.1016/j.jtbi.2011.02.016 | null | q-bio.PE cs.SI physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In spatial evolutionary games the fitness of each individual is traditionally
determined by the payoffs it obtains upon playing the game with its neighbors.
Since defection yields the highest individual benefits, the outlook for
cooperators is gloomy. While network reciprocity promotes collaborative
efforts, chances ... | [
{
"created": "Tue, 22 Feb 2011 18:00:55 GMT",
"version": "v1"
}
] | 2011-04-04 | [
[
"Wang",
"Zhen",
""
],
[
"Murks",
"Aleksandra",
""
],
[
"Du",
"Wen-Bo",
""
],
[
"Rong",
"Zhi-Hai",
""
],
[
"Perc",
"Matjaz",
""
]
] | In spatial evolutionary games the fitness of each individual is traditionally determined by the payoffs it obtains upon playing the game with its neighbors. Since defection yields the highest individual benefits, the outlook for cooperators is gloomy. While network reciprocity promotes collaborative efforts, chances of... |
2303.11994 | Qiang Li | Qiang Li, Shujian Yu, Kristoffer H Madsen, Vince D Calhoun, Armin
Iraji | Higher-order Organization in the Human Brain from Matrix-Based R\'enyi's
Entropy | 5 pages, 3 figures; Accepted to Data Science and Learning Workshop:
Unraveling the Brain. A satellite workshop of ICASSP 2023 | 2023 IEEE International Conference on Acoustics, Speech, and
Signal Processing Workshops (ICASSPW) | 10.1109/ICASSPW59220.2023.10193346 | null | q-bio.NC cs.IT math.IT math.ST stat.TH | http://creativecommons.org/licenses/by/4.0/ | Pairwise metrics are often employed to estimate statistical dependencies
between brain regions, however they do not capture higher-order information
interactions. It is critical to explore higher-order interactions that go
beyond paired brain areas in order to better understand information processing
in the human bra... | [
{
"created": "Tue, 21 Mar 2023 16:23:51 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Apr 2023 15:17:46 GMT",
"version": "v2"
}
] | 2023-08-04 | [
[
"Li",
"Qiang",
""
],
[
"Yu",
"Shujian",
""
],
[
"Madsen",
"Kristoffer H",
""
],
[
"Calhoun",
"Vince D",
""
],
[
"Iraji",
"Armin",
""
]
] | Pairwise metrics are often employed to estimate statistical dependencies between brain regions, however they do not capture higher-order information interactions. It is critical to explore higher-order interactions that go beyond paired brain areas in order to better understand information processing in the human brain... |
1910.14490 | Julien Marlet | Jos\'e Bras Cachinho, Maud Fran\c{c}ois, Karl Stefic (MAVIVH - U1259
Inserm - CHRU Tours), Julien Marlet (MAVIVH - U1259 Inserm - CHRU Tours) | Positive HBs antigen in the absence of hepatitis B virus infection | in French | Annales de Biologie Clinique, John Libbey Eurotext, 2019, 77 (5),
pp.543-548 | 10.1684/abc.2019.1483 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | French recommendations for the screening of hepatitis B virus (HBV) infection
were updated in 2019 with the association of three markers: HBs Ag, anti-HBs Ab
and anti-HBc Ab. These three markers allow identification of infected patients,
vaccinated patients and patients who have been in contact with HBV. A positive
H... | [
{
"created": "Thu, 31 Oct 2019 14:29:24 GMT",
"version": "v1"
}
] | 2019-11-01 | [
[
"Cachinho",
"José Bras",
"",
"MAVIVH - U1259\n Inserm - CHRU Tours"
],
[
"François",
"Maud",
"",
"MAVIVH - U1259\n Inserm - CHRU Tours"
],
[
"Stefic",
"Karl",
"",
"MAVIVH - U1259\n Inserm - CHRU Tours"
],
[
"Marlet",
"Julien",
"",
"MAV... | French recommendations for the screening of hepatitis B virus (HBV) infection were updated in 2019 with the association of three markers: HBs Ag, anti-HBs Ab and anti-HBc Ab. These three markers allow identification of infected patients, vaccinated patients and patients who have been in contact with HBV. A positive HBs... |
1803.10579 | Alan D. Rendall | Pia Brechmann, Alan D. Rendall | Dynamics of the Selkov oscillator | null | null | null | null | q-bio.SC math.DS physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A classical example of a mathematical model for oscillations in a biological
system is the Selkov oscillator, which is a simple description of glycolysis.
It is a system of two ordinary differential equations which, when expressed in
dimensionless variables, depends on two parameters. Surprisingly it appears
that no ... | [
{
"created": "Wed, 28 Mar 2018 13:17:09 GMT",
"version": "v1"
}
] | 2018-03-29 | [
[
"Brechmann",
"Pia",
""
],
[
"Rendall",
"Alan D.",
""
]
] | A classical example of a mathematical model for oscillations in a biological system is the Selkov oscillator, which is a simple description of glycolysis. It is a system of two ordinary differential equations which, when expressed in dimensionless variables, depends on two parameters. Surprisingly it appears that no co... |
q-bio/0608020 | Lei-Han Tang | Sheng Hui and Lei-Han Tang | Ground state and glass transition of the RNA secondary structure | null | null | 10.1140/epjb/e2006-00347-x | null | q-bio.BM cond-mat.dis-nn | null | RNA molecules form a sequence-specific self-pairing pattern at low
temperatures. We analyze this problem using a random pairing energy model as
well as a random sequence model that includes a base stacking energy in favor
of helix propagation. The free energy cost for separating a chain into two
equal halves offers a... | [
{
"created": "Wed, 9 Aug 2006 22:47:35 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Hui",
"Sheng",
""
],
[
"Tang",
"Lei-Han",
""
]
] | RNA molecules form a sequence-specific self-pairing pattern at low temperatures. We analyze this problem using a random pairing energy model as well as a random sequence model that includes a base stacking energy in favor of helix propagation. The free energy cost for separating a chain into two equal halves offers a q... |
1509.03734 | Adam Kleczkowski | Adam Kleczkowski, Ciaran Ellis, Dave Goulson, Nick Hanley | Ecological-economic modelling of interactions between wild and
commercial bees and pesticide use | Working paper | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The decline in extent of wild pollinators in recent years has been partly
associated with changing farm practices and in particular with increasing
pesticide use. In this paper we combine ecological modelling with economic
analysis of a single farm output under the as- sumption that both pollination
and pest control ... | [
{
"created": "Sat, 12 Sep 2015 12:17:49 GMT",
"version": "v1"
}
] | 2015-09-15 | [
[
"Kleczkowski",
"Adam",
""
],
[
"Ellis",
"Ciaran",
""
],
[
"Goulson",
"Dave",
""
],
[
"Hanley",
"Nick",
""
]
] | The decline in extent of wild pollinators in recent years has been partly associated with changing farm practices and in particular with increasing pesticide use. In this paper we combine ecological modelling with economic analysis of a single farm output under the as- sumption that both pollination and pest control ar... |
2401.08805 | Carles Falc\'o | Carles Falc\'o, Daniel J. Cohen, Jos\'e A. Carrillo, Ruth E. Baker | Quantifying cell cycle regulation by tissue crowding | null | null | null | null | q-bio.QM physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | The spatiotemporal coordination and regulation of cell proliferation is
fundamental in many aspects of development and tissue maintenance. Cells have
the ability to adapt their division rates in response to mechanical
constraints, yet we do not fully understand how cell proliferation regulation
impacts cell migration... | [
{
"created": "Tue, 16 Jan 2024 20:01:59 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Feb 2024 15:51:26 GMT",
"version": "v2"
},
{
"created": "Wed, 24 Apr 2024 10:50:44 GMT",
"version": "v3"
}
] | 2024-04-25 | [
[
"Falcó",
"Carles",
""
],
[
"Cohen",
"Daniel J.",
""
],
[
"Carrillo",
"José A.",
""
],
[
"Baker",
"Ruth E.",
""
]
] | The spatiotemporal coordination and regulation of cell proliferation is fundamental in many aspects of development and tissue maintenance. Cells have the ability to adapt their division rates in response to mechanical constraints, yet we do not fully understand how cell proliferation regulation impacts cell migration p... |
2202.05468 | Shigehiro Yasui | Shigehiro Yasui, Yutaka Hatakeyama, Yoshiyasu Okuhara | Criticality in stochastic SIR model for infectious diseases | 15 pages, 1 figure | null | null | null | q-bio.PE cond-mat.stat-mech physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | We discuss the criticality in the stochastic SIR model for infectious
diseases. We adopt the path-integral formalism for the propagation of
infections among susceptible, infectious, and removed individuals, and perform
the perturbative and nonperturbative analyses to evaluate the critical value of
the basic reproduct... | [
{
"created": "Fri, 11 Feb 2022 06:03:40 GMT",
"version": "v1"
}
] | 2022-02-14 | [
[
"Yasui",
"Shigehiro",
""
],
[
"Hatakeyama",
"Yutaka",
""
],
[
"Okuhara",
"Yoshiyasu",
""
]
] | We discuss the criticality in the stochastic SIR model for infectious diseases. We adopt the path-integral formalism for the propagation of infections among susceptible, infectious, and removed individuals, and perform the perturbative and nonperturbative analyses to evaluate the critical value of the basic reproductio... |
1011.6048 | Jose Vilar | Jose M. G. Vilar | Noisy-threshold control of cell death | Supplementary information available at
http://www.biomedcentral.com/1752-0509/4/152 | BMC Systems Biology 4, 152 (2010) | null | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cellular responses to death-promoting stimuli typically proceed through a
differentiated multistage process, involving a lag phase, extensive death, and
potential adaptation. Deregulation of this chain of events is at the root of
many diseases. Improper adaptation is particularly important because it allows
cell sub-... | [
{
"created": "Sun, 28 Nov 2010 15:00:06 GMT",
"version": "v1"
}
] | 2010-12-03 | [
[
"Vilar",
"Jose M. G.",
""
]
] | Cellular responses to death-promoting stimuli typically proceed through a differentiated multistage process, involving a lag phase, extensive death, and potential adaptation. Deregulation of this chain of events is at the root of many diseases. Improper adaptation is particularly important because it allows cell sub-po... |
2307.10246 | Subba Reddy Oota | Subba Reddy Oota, Zijiao Chen, Manish Gupta, Raju S. Bapi, Gael
Jobard, Frederic Alexandre, Xavier Hinaut | Deep Neural Networks and Brain Alignment: Brain Encoding and Decoding
(Survey) | 47 pages, 23 figures | null | null | null | q-bio.NC cs.AI cs.CL cs.CV cs.HC cs.LG | http://creativecommons.org/licenses/by/4.0/ | Can we obtain insights about the brain using AI models? How is the
information in deep learning models related to brain recordings? Can we improve
AI models with the help of brain recordings? Such questions can be tackled by
studying brain recordings like functional magnetic resonance imaging (fMRI). As
a first step,... | [
{
"created": "Mon, 17 Jul 2023 06:54:36 GMT",
"version": "v1"
},
{
"created": "Mon, 8 Jul 2024 13:44:56 GMT",
"version": "v2"
}
] | 2024-07-09 | [
[
"Oota",
"Subba Reddy",
""
],
[
"Chen",
"Zijiao",
""
],
[
"Gupta",
"Manish",
""
],
[
"Bapi",
"Raju S.",
""
],
[
"Jobard",
"Gael",
""
],
[
"Alexandre",
"Frederic",
""
],
[
"Hinaut",
"Xavier",
""
]
] | Can we obtain insights about the brain using AI models? How is the information in deep learning models related to brain recordings? Can we improve AI models with the help of brain recordings? Such questions can be tackled by studying brain recordings like functional magnetic resonance imaging (fMRI). As a first step, t... |
1908.07209 | Jianxing Hu Mr | Yibo Li, Jianxing Hu, Yanxing Wang, Jielong Zhou, Liangren Zhang and
Zhenming Liu | DeepScaffold: a comprehensive tool for scaffold-based de novo drug
discovery using deep learning | Updates to this version 1. Add supporting information (aux.pdf) 2.
Improvements to Section 2.2 3. Resolve grammar issues | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ultimate goal of drug design is to find novel compounds with desirable
pharmacological properties. Designing molecules retaining particular scaffolds
as the core structures of the molecules is one of the efficient ways to obtain
potential drug candidates with desirable properties. We proposed a
scaffold-based mol... | [
{
"created": "Tue, 20 Aug 2019 08:04:00 GMT",
"version": "v1"
},
{
"created": "Wed, 21 Aug 2019 14:25:05 GMT",
"version": "v2"
},
{
"created": "Fri, 23 Aug 2019 01:35:27 GMT",
"version": "v3"
},
{
"created": "Thu, 5 Sep 2019 00:47:25 GMT",
"version": "v4"
}
] | 2019-09-06 | [
[
"Li",
"Yibo",
""
],
[
"Hu",
"Jianxing",
""
],
[
"Wang",
"Yanxing",
""
],
[
"Zhou",
"Jielong",
""
],
[
"Zhang",
"Liangren",
""
],
[
"Liu",
"Zhenming",
""
]
] | The ultimate goal of drug design is to find novel compounds with desirable pharmacological properties. Designing molecules retaining particular scaffolds as the core structures of the molecules is one of the efficient ways to obtain potential drug candidates with desirable properties. We proposed a scaffold-based molec... |
2109.01172 | Fernando da Costa | Pedro R.S. Antunes, Fernando P. da Costa, Jo\~ao T. Pinto, Rafael
Sasportes | Modelling silicosis: dynamics of a model with piecewise constant rate
coefficients | 28 pages, 7 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the dynamics about equilibria of an infinite dimension
coagulation-fragmentation-death model for the silicosis disease mechanism
introduced recently by da Costa, Drmota, and Grinfeld [Modelling silicosis:
structure of equilibria, Euro. J. Appl. Math., 31 (6), (2020) 950-967] in the
case where the rate coeffi... | [
{
"created": "Thu, 2 Sep 2021 18:39:25 GMT",
"version": "v1"
}
] | 2021-09-06 | [
[
"Antunes",
"Pedro R. S.",
""
],
[
"da Costa",
"Fernando P.",
""
],
[
"Pinto",
"João T.",
""
],
[
"Sasportes",
"Rafael",
""
]
] | We study the dynamics about equilibria of an infinite dimension coagulation-fragmentation-death model for the silicosis disease mechanism introduced recently by da Costa, Drmota, and Grinfeld [Modelling silicosis: structure of equilibria, Euro. J. Appl. Math., 31 (6), (2020) 950-967] in the case where the rate coeffici... |
2003.12493 | Sitabhra Sinha | Chandrashekar Kuyyamudi, Shakti N. Menon and Sitabhra Sinha | Morphogen-regulated contact-mediated signaling between cells can drive
the transitions underlying body segmentation in vertebrates | 10 pages, 5 figures + 13 pages Supplementary Information | Phys. Biol. 19, 016001 (2021) | 10.1088/1478-3975/ac31a3 | null | q-bio.TO nlin.PS physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a unified mechanism that reproduces the sequence of dynamical
transitions observed during somitogenesis, the process of body segmentation
during embryonic development, that is invariant across all vertebrate species.
This is achieved by combining inter-cellular interactions mediated via
receptor-ligand cou... | [
{
"created": "Fri, 27 Mar 2020 15:55:30 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Sep 2021 18:39:53 GMT",
"version": "v2"
}
] | 2024-06-11 | [
[
"Kuyyamudi",
"Chandrashekar",
""
],
[
"Menon",
"Shakti N.",
""
],
[
"Sinha",
"Sitabhra",
""
]
] | We propose a unified mechanism that reproduces the sequence of dynamical transitions observed during somitogenesis, the process of body segmentation during embryonic development, that is invariant across all vertebrate species. This is achieved by combining inter-cellular interactions mediated via receptor-ligand coupl... |
2310.08613 | Teddy Lazebnik Dr. | Teddy Lazebnik, Orr Spiegel | Individual Variation Affects Outbreak Magnitude and Predictability in an
Extended Multi-Pathogen SIR Model of Pigeons Vising Dairy Farms | null | null | null | null | q-bio.PE cs.CE cs.IR cs.MA | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Zoonotic disease transmission between animals and humans is a growing risk
and the agricultural context acts as a likely point of transition, with
individual heterogeneity acting as an important contributor. Thus,
understanding the dynamics of disease spread in the wildlife-livestock
interface is crucial for mitigati... | [
{
"created": "Thu, 12 Oct 2023 06:26:20 GMT",
"version": "v1"
}
] | 2023-10-16 | [
[
"Lazebnik",
"Teddy",
""
],
[
"Spiegel",
"Orr",
""
]
] | Zoonotic disease transmission between animals and humans is a growing risk and the agricultural context acts as a likely point of transition, with individual heterogeneity acting as an important contributor. Thus, understanding the dynamics of disease spread in the wildlife-livestock interface is crucial for mitigating... |
2405.12645 | Yuanhong Tang | Yuanhong Tang, Shanshan Jia, Tiejun Huang, Zhaofei Yu, Jian K. Liu | Implementing feature binding through dendritic networks of a single
neuron | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A single neuron receives an extensive array of synaptic inputs through its
dendrites, raising the fundamental question of how these inputs undergo
integration and summation, culminating in the initiation of spikes in the soma.
Experimental and computational investigations have revealed various modes of
integration op... | [
{
"created": "Tue, 21 May 2024 09:55:51 GMT",
"version": "v1"
}
] | 2024-05-22 | [
[
"Tang",
"Yuanhong",
""
],
[
"Jia",
"Shanshan",
""
],
[
"Huang",
"Tiejun",
""
],
[
"Yu",
"Zhaofei",
""
],
[
"Liu",
"Jian K.",
""
]
] | A single neuron receives an extensive array of synaptic inputs through its dendrites, raising the fundamental question of how these inputs undergo integration and summation, culminating in the initiation of spikes in the soma. Experimental and computational investigations have revealed various modes of integration oper... |
q-bio/0402001 | Eli Ben-Naim | E. Ben-Naim, P.L. Krapivsky | Size of Outbreaks Near the Epidemic Threshold | 4 pages, 5 figures | Phys. Rev. E 69, 050901R (2004) | 10.1103/PhysRevE.69.050901 | null | q-bio.PE cond-mat.stat-mech math.PR | null | The spread of infectious diseases near the epidemic threshold is
investigated. Scaling laws for the size and the duration of outbreaks
originating from a single infected individual in a large susceptible population
are obtained. The maximal size of an outbreak n_* scales as N^{2/3} with N the
population size. This sc... | [
{
"created": "Sun, 1 Feb 2004 00:10:53 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Ben-Naim",
"E.",
""
],
[
"Krapivsky",
"P. L.",
""
]
] | The spread of infectious diseases near the epidemic threshold is investigated. Scaling laws for the size and the duration of outbreaks originating from a single infected individual in a large susceptible population are obtained. The maximal size of an outbreak n_* scales as N^{2/3} with N the population size. This scal... |
1811.00948 | Casper Beentjes | Casper Beentjes and Ruth Baker | Uniformisation techniques for stochastic simulation of chemical reaction
networks | null | J. Chem. Phys. 150, 154107 (2019) | 10.1063/1.5081043 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This work considers the method of uniformisation for continuous-time Markov
chains in the context of chemical reaction networks. Previous work in the
literature has shown that uniformisation can be beneficial in the context of
time-inhomogeneous models, such as chemical reaction networks incorporating
extrinsic noise... | [
{
"created": "Fri, 2 Nov 2018 15:57:03 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Apr 2019 07:49:18 GMT",
"version": "v2"
}
] | 2019-04-18 | [
[
"Beentjes",
"Casper",
""
],
[
"Baker",
"Ruth",
""
]
] | This work considers the method of uniformisation for continuous-time Markov chains in the context of chemical reaction networks. Previous work in the literature has shown that uniformisation can be beneficial in the context of time-inhomogeneous models, such as chemical reaction networks incorporating extrinsic noise. ... |
1305.3507 | Sungroh Yoon | Hanjoo Kim, Pablo Cordero, Rhiju Das, Sungroh Yoon | HiTRACE-Web: an online tool for robust analysis of high-throughput
capillary electrophoresis | null | null | 10.1093/nar/gkt501 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To facilitate the analysis of large-scale high-throughput capillary
electrophoresis data, we previously proposed a suite of efficient analysis
software named HiTRACE (High Throughput Robust Analysis of Capillary
Electrophoresis). HiTRACE has been used extensively for quantitating data from
RNA and DNA structure mappi... | [
{
"created": "Wed, 15 May 2013 14:51:59 GMT",
"version": "v1"
},
{
"created": "Tue, 21 May 2013 10:39:12 GMT",
"version": "v2"
}
] | 2015-02-10 | [
[
"Kim",
"Hanjoo",
""
],
[
"Cordero",
"Pablo",
""
],
[
"Das",
"Rhiju",
""
],
[
"Yoon",
"Sungroh",
""
]
] | To facilitate the analysis of large-scale high-throughput capillary electrophoresis data, we previously proposed a suite of efficient analysis software named HiTRACE (High Throughput Robust Analysis of Capillary Electrophoresis). HiTRACE has been used extensively for quantitating data from RNA and DNA structure mapping... |
2011.04252 | Michael Stumpf | Anissa Guillemin and Michael P.H. Stumpf | Non-equilibrium statistical physics, transitory epigenetic landscapes,
and cell fate decision dynamics | 14 pages, 3 Figures; Review (for Mathematical Biosciences and
Bioengineering) | null | null | null | q-bio.CB | http://creativecommons.org/licenses/by-sa/4.0/ | Statistical physics provides a useful perspective for the analysis of many
complex systems; it allows us to relate microscopic fluctuations to macroscopic
observations. Developmental biology, but also cell biology more generally, are
examples where apparently robust behaviour emerges from highly complex and
stochasti... | [
{
"created": "Mon, 9 Nov 2020 08:56:33 GMT",
"version": "v1"
}
] | 2020-11-10 | [
[
"Guillemin",
"Anissa",
""
],
[
"Stumpf",
"Michael P. H.",
""
]
] | Statistical physics provides a useful perspective for the analysis of many complex systems; it allows us to relate microscopic fluctuations to macroscopic observations. Developmental biology, but also cell biology more generally, are examples where apparently robust behaviour emerges from highly complex and stochastic ... |
2003.13655 | Gian Tartaglia | Andrea Vandelli, Michele Monti, Edoardo Milanetti, Riccardo Delli
Ponti and Gian Gaetano Tartaglia | Structural analysis of SARS-CoV-2 and prediction of the human
interactome | 30 pages, 4 figures | null | null | null | q-bio.BM q-bio.GN q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Specific elements of viral genomes regulate interactions within host cells.
Here, we calculated the secondary structure content of >2500 coronaviruses and
computed >100000 human protein interactions with severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2). We found that the 3 and 5 prime ends are
the most st... | [
{
"created": "Mon, 30 Mar 2020 17:41:26 GMT",
"version": "v1"
},
{
"created": "Fri, 3 Apr 2020 20:34:53 GMT",
"version": "v2"
},
{
"created": "Sun, 12 Apr 2020 14:30:28 GMT",
"version": "v3"
},
{
"created": "Wed, 29 Apr 2020 07:35:01 GMT",
"version": "v4"
}
] | 2020-04-30 | [
[
"Vandelli",
"Andrea",
""
],
[
"Monti",
"Michele",
""
],
[
"Milanetti",
"Edoardo",
""
],
[
"Ponti",
"Riccardo Delli",
""
],
[
"Tartaglia",
"Gian Gaetano",
""
]
] | Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2500 coronaviruses and computed >100000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We found that the 3 and 5 prime ends are the most stru... |
1604.02099 | Yoo Ah Kim | Yoo-Ah Kim, Sanna Madan, and Teresa M. Przytycka | WeSME: Uncovering Mutual Exclusivity of Cancer Drivers and Beyond | Paper accepted at RECOMB-CCB 2016 | null | null | null | q-bio.QM cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mutual exclusivity is a widely recognized property of many cancer drivers.
Knowledge about these relationships can provide important insights into cancer
drivers, cancer-driving pathways, and cancer subtypes. It can also be used to
predict new functional interactions between cancer driving genes and uncover
novel can... | [
{
"created": "Thu, 7 Apr 2016 18:18:21 GMT",
"version": "v1"
}
] | 2016-04-08 | [
[
"Kim",
"Yoo-Ah",
""
],
[
"Madan",
"Sanna",
""
],
[
"Przytycka",
"Teresa M.",
""
]
] | Mutual exclusivity is a widely recognized property of many cancer drivers. Knowledge about these relationships can provide important insights into cancer drivers, cancer-driving pathways, and cancer subtypes. It can also be used to predict new functional interactions between cancer driving genes and uncover novel cance... |
1509.04559 | Mohammad Soltani | Mohammad Soltani, Cesar Augusto Vargas-Garcia, Duarte Antunes,
Abhyudai Singh | Decomposing variability in protein levels from noisy expression, genome
duplication and partitioning errors during cell-divisions | 40 pages, 10 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inside individual cells, expression of genes is inherently stochastic and
manifests as cell-to-cell variability or noise in protein copy numbers. Since
proteins half-lives can be comparable to the cell-cycle length, randomness in
cell-division times generates additional intercellular variability in protein
levels. Mo... | [
{
"created": "Sat, 5 Sep 2015 22:15:36 GMT",
"version": "v1"
},
{
"created": "Fri, 2 Oct 2015 20:26:35 GMT",
"version": "v2"
}
] | 2015-10-06 | [
[
"Soltani",
"Mohammad",
""
],
[
"Vargas-Garcia",
"Cesar Augusto",
""
],
[
"Antunes",
"Duarte",
""
],
[
"Singh",
"Abhyudai",
""
]
] | Inside individual cells, expression of genes is inherently stochastic and manifests as cell-to-cell variability or noise in protein copy numbers. Since proteins half-lives can be comparable to the cell-cycle length, randomness in cell-division times generates additional intercellular variability in protein levels. More... |
1912.10251 | Chowdhury Rahman | Ruhul Amin, Chowdhury Rafeed Rahman, Md. Habibur Rahman Sifat, Md
Nazmul Khan Liton, Md. Moshiur Rahman, Swakkhar Shatabda and Sajid Ahmed | iPromoter-BnCNN: a Novel Branched CNN Based Predictor for Identifying
and Classifying Sigma Promoters | null | null | 10.1093/bioinformatics/btaa609 | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Promoter is a short region of DNA which is responsible for initiating
transcription of specific genes. Development of computational tools for
automatic identification of promoters is in high demand. According to the
difference of functions, promoters can be of different types. Promoters may
have both intra and inter ... | [
{
"created": "Sat, 21 Dec 2019 11:59:38 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Dec 2019 06:51:47 GMT",
"version": "v2"
},
{
"created": "Fri, 10 Jan 2020 01:20:09 GMT",
"version": "v3"
},
{
"created": "Tue, 16 Jun 2020 20:44:32 GMT",
"version": "v4"
}
] | 2020-07-06 | [
[
"Amin",
"Ruhul",
""
],
[
"Rahman",
"Chowdhury Rafeed",
""
],
[
"Sifat",
"Md. Habibur Rahman",
""
],
[
"Liton",
"Md Nazmul Khan",
""
],
[
"Rahman",
"Md. Moshiur",
""
],
[
"Shatabda",
"Swakkhar",
""
],
[
"Ahmed",
... | Promoter is a short region of DNA which is responsible for initiating transcription of specific genes. Development of computational tools for automatic identification of promoters is in high demand. According to the difference of functions, promoters can be of different types. Promoters may have both intra and inter cl... |
1512.01389 | Gerardo Chowell | C\'ecile Viboud, Lone Simonsen, Gerardo Chowell | A generalized-growth model to characterize the early ascending phase of
infectious disease outbreaks | 31 pages, 9 Figures, 1 Supp. Figure, 1 Table, final accepted version
(in press), Epidemics - The Journal on Infectious Disease Dynamics, 2016 | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A better characterization of the early growth dynamics of an epidemic is
needed to dissect the important drivers of disease transmission. We introduce a
2-parameter generalized-growth model to characterize the ascending phase of an
outbreak and capture epidemic profiles ranging from sub-exponential to
exponential gro... | [
{
"created": "Fri, 4 Dec 2015 12:36:10 GMT",
"version": "v1"
},
{
"created": "Fri, 15 Jan 2016 16:46:56 GMT",
"version": "v2"
}
] | 2016-01-18 | [
[
"Viboud",
"Cécile",
""
],
[
"Simonsen",
"Lone",
""
],
[
"Chowell",
"Gerardo",
""
]
] | A better characterization of the early growth dynamics of an epidemic is needed to dissect the important drivers of disease transmission. We introduce a 2-parameter generalized-growth model to characterize the ascending phase of an outbreak and capture epidemic profiles ranging from sub-exponential to exponential growt... |
2112.09806 | Jeremi K. Ochab | Dante R. Chialvo and Ignacio Cifre and Jeremi K. Ochab | Untangling the brain web: from the early days of complex functional
networks to the non-linear dynamical directed functional connectivity
measures | null | null | null | null | q-bio.NC nlin.AO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Already two decades passed since the first applications of graph theory to
brain neuroimaging. Since that early description, the characterization of the
brain as a very large interacting complex network has evolved in several
directions. In this brief review we discuss our contributions to this topic and
discuss some... | [
{
"created": "Fri, 17 Dec 2021 23:42:54 GMT",
"version": "v1"
}
] | 2021-12-21 | [
[
"Chialvo",
"Dante R.",
""
],
[
"Cifre",
"Ignacio",
""
],
[
"Ochab",
"Jeremi K.",
""
]
] | Already two decades passed since the first applications of graph theory to brain neuroimaging. Since that early description, the characterization of the brain as a very large interacting complex network has evolved in several directions. In this brief review we discuss our contributions to this topic and discuss some p... |
1101.1836 | Ahmad Khoureich Ka | Ahmad Khoureich Ka (IRMAR) | ECG beats classification using waveform similarity and RR interval | 4 pages | null | null | null | q-bio.QM physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper present an electrocardiogram (ECG) beat classification method
based on waveform similarity and RR interval. The purpose of the method is to
classify six types of heart beats (normal beat, atrial premature beat, paced
beat, premature ventricular beat, left bundle branch block beat and right
bundle branch bl... | [
{
"created": "Mon, 10 Jan 2011 15:03:05 GMT",
"version": "v1"
}
] | 2011-01-11 | [
[
"Ka",
"Ahmad Khoureich",
"",
"IRMAR"
]
] | This paper present an electrocardiogram (ECG) beat classification method based on waveform similarity and RR interval. The purpose of the method is to classify six types of heart beats (normal beat, atrial premature beat, paced beat, premature ventricular beat, left bundle branch block beat and right bundle branch bloc... |
1909.02664 | Babak Ravandi | Babak Ravandi and Arash Ravandi | Network-Based Approach for Modeling and Analyzing Coronary Angiography | null | null | 10.1007/978-3-030-40943-2_15 | null | q-bio.QM physics.data-an q-bio.TO stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Significant intra-observer and inter-observer variability in the
interpretation of coronary angiograms are reported. This variability is in part
due to the common practices that rely on performing visual inspections by
specialists (e.g., the thickness of coronaries). Quantitative Coronary
Angiography (QCA) approaches... | [
{
"created": "Thu, 5 Sep 2019 22:50:35 GMT",
"version": "v1"
}
] | 2020-02-27 | [
[
"Ravandi",
"Babak",
""
],
[
"Ravandi",
"Arash",
""
]
] | Significant intra-observer and inter-observer variability in the interpretation of coronary angiograms are reported. This variability is in part due to the common practices that rely on performing visual inspections by specialists (e.g., the thickness of coronaries). Quantitative Coronary Angiography (QCA) approaches a... |
2005.01579 | Donald Forsdyke Dr. | Donald R. Forsdyke | SARS-CoV-2 mortality in blacks and temperature-sensitivity to an
angiotensin-2 receptor blocker | Pages: 20. Words: 5739. Figures: 3. References: 72. Updated
references and text | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Tropical climates provoke adaptations in skin pigmentation and in mechanisms
controlling the volume, salt-content and pressure of body fluids. For many
whose distant ancestors moved to temperate climes, these adaptations proved
harmful: pigmentation decreased by natural selection and susceptibility to
hypertension em... | [
{
"created": "Thu, 30 Apr 2020 16:53:26 GMT",
"version": "v1"
},
{
"created": "Wed, 6 May 2020 15:58:25 GMT",
"version": "v2"
},
{
"created": "Sun, 24 May 2020 14:46:09 GMT",
"version": "v3"
},
{
"created": "Sat, 13 Jun 2020 15:10:49 GMT",
"version": "v4"
},
{
"cr... | 2020-08-07 | [
[
"Forsdyke",
"Donald R.",
""
]
] | Tropical climates provoke adaptations in skin pigmentation and in mechanisms controlling the volume, salt-content and pressure of body fluids. For many whose distant ancestors moved to temperate climes, these adaptations proved harmful: pigmentation decreased by natural selection and susceptibility to hypertension emer... |
0810.5434 | Laurent Noe | Mihkail Roytberg (IMPB-RAS), Anna Gambin, Laurent No\'e (LIFL, INRIA
Lille - Nord Europe), Slawomir Lasota, Eugenia Furletova (IMPB-RAS), Ewa
Szczurek (MPI), Gregory Kucherov (LIFL, INRIA Lille - Nord Europe) | Efficient seeding techniques for protein similarity search | null | BIRD - ALBIO 13 (2008) | 10.1007/978-3-540-70600-7 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We apply the concept of subset seeds proposed in [1] to similarity search in
protein sequences. The main question studied is the design of efficient seed
alphabets to construct seeds with optimal sensitivity/selectivity trade-offs.
We propose several different design methods and use them to construct several
alphabet... | [
{
"created": "Thu, 30 Oct 2008 07:41:00 GMT",
"version": "v1"
}
] | 2008-10-31 | [
[
"Roytberg",
"Mihkail",
"",
"IMPB-RAS"
],
[
"Gambin",
"Anna",
"",
"LIFL, INRIA\n Lille - Nord Europe"
],
[
"Noé",
"Laurent",
"",
"LIFL, INRIA\n Lille - Nord Europe"
],
[
"Lasota",
"Slawomir",
"",
"IMPB-RAS"
],
[
"Furletova",
... | We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We propose several different design methods and use them to construct several alphabets.... |
2109.12100 | Jiahui Chen | Jiahui Chen, Weihua Geng, Guo-Wei Wei | MLIMC: Machine learning-based implicit-solvent Monte Carlo | null | null | 10.1063/1674-0068/cjcp2109150 | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Monte Carlo (MC) methods are important computational tools for molecular
structure optimizations and predictions. When solvent effects are explicitly
considered, MC methods become very expensive due to the large degree of freedom
associated with the water molecules and mobile ions. Alternatively
implicit-solvent MC c... | [
{
"created": "Fri, 24 Sep 2021 17:47:07 GMT",
"version": "v1"
}
] | 2022-02-09 | [
[
"Chen",
"Jiahui",
""
],
[
"Geng",
"Weihua",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Monte Carlo (MC) methods are important computational tools for molecular structure optimizations and predictions. When solvent effects are explicitly considered, MC methods become very expensive due to the large degree of freedom associated with the water molecules and mobile ions. Alternatively implicit-solvent MC can... |
1403.7072 | Jack Dekker | Milton J. Haar and Jack Dekker | Weedy Adaptation in Setaria spp.: VII. Seed Germination Heteroblasty in
Setaria faberi | 19 pages, 5 figures, 4 tables | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The dormancy status of S. faberi seed at abscission was assessed with
reference to tiller and panicle development. Seed from a single genetic line
were grown under field, greenhouse and controlled environment growth chamber
conditions. At abscission, a small fraction (<10%) of S. faberi seed germinated
under favorabl... | [
{
"created": "Thu, 27 Mar 2014 15:13:21 GMT",
"version": "v1"
}
] | 2014-03-28 | [
[
"Haar",
"Milton J.",
""
],
[
"Dekker",
"Jack",
""
]
] | The dormancy status of S. faberi seed at abscission was assessed with reference to tiller and panicle development. Seed from a single genetic line were grown under field, greenhouse and controlled environment growth chamber conditions. At abscission, a small fraction (<10%) of S. faberi seed germinated under favorable ... |
1407.5590 | Petko Bogdanov | Petko Bogdanov, Nazli Dereli, Danielle S. Bassett, Scott T. Grafton,
Ambuj K. Singh | Learning about Learning: Human Brain Sub-Network Biomarkers in fMRI Data | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has become increasingly popular to study the brain as a network due to the
realization that functionality cannot be explained exclusively by independent
activation of specialized regions. Instead, across a large spectrum of
behaviors, function arises due to the dynamic interactions between brain
regions. The exist... | [
{
"created": "Mon, 21 Jul 2014 18:23:58 GMT",
"version": "v1"
}
] | 2014-07-22 | [
[
"Bogdanov",
"Petko",
""
],
[
"Dereli",
"Nazli",
""
],
[
"Bassett",
"Danielle S.",
""
],
[
"Grafton",
"Scott T.",
""
],
[
"Singh",
"Ambuj K.",
""
]
] | It has become increasingly popular to study the brain as a network due to the realization that functionality cannot be explained exclusively by independent activation of specialized regions. Instead, across a large spectrum of behaviors, function arises due to the dynamic interactions between brain regions. The existin... |
1811.03910 | Niladri Sarkar | Niladri Sarkar, Jacques Prost, Frank J\"ulicher | Field induced cell proliferation and death in a thick epithelium | 18 pages, 12 figures | null | null | null | q-bio.CB cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the dynamics of a thick polar epithelium subjected to the action of
both an electric and a flow field in a planar geometry. We develop a
generalized continuum hydrodynamic description and describe the tissue as a two
component fluid system. The cells and the interstitial fluid are the two
components and we k... | [
{
"created": "Fri, 9 Nov 2018 14:12:02 GMT",
"version": "v1"
}
] | 2018-11-12 | [
[
"Sarkar",
"Niladri",
""
],
[
"Prost",
"Jacques",
""
],
[
"Jülicher",
"Frank",
""
]
] | We study the dynamics of a thick polar epithelium subjected to the action of both an electric and a flow field in a planar geometry. We develop a generalized continuum hydrodynamic description and describe the tissue as a two component fluid system. The cells and the interstitial fluid are the two components and we kee... |
1506.02394 | Ulrich S. Schwarz | Ulrich S. Schwarz and Jerome R.D. Soine (Heidelberg University) | Traction force microscopy on soft elastic substrates: a guide to recent
computational advances | Revtex, 29 pages, 3 PDF figures, 2 tables. BBA - Molecular Cell
Research, online since 27 May 2015, special issue on mechanobiology | null | 10.1016/j.bbamcr.2015.05.028 | null | q-bio.QM cond-mat.soft q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The measurement of cellular traction forces on soft elastic substrates has
become a standard tool for many labs working on mechanobiology. Here we review
the basic principles and different variants of this approach. In general, the
extraction of the substrate displacement field from image data and the
reconstruction ... | [
{
"created": "Mon, 8 Jun 2015 08:24:24 GMT",
"version": "v1"
}
] | 2015-06-09 | [
[
"Schwarz",
"Ulrich S.",
"",
"Heidelberg University"
],
[
"Soine",
"Jerome R. D.",
"",
"Heidelberg University"
]
] | The measurement of cellular traction forces on soft elastic substrates has become a standard tool for many labs working on mechanobiology. Here we review the basic principles and different variants of this approach. In general, the extraction of the substrate displacement field from image data and the reconstruction pr... |
q-bio/0310027 | Ayse Erzan | Duygu Balcan, Ayse Erzan | Random model for RNA interference yields scale free network | 9 pages, 13 figures, submitted to Midterm Conference COSIN on
``Growing Networks and Graphs in Statistical Physics, Finance, Biology and
Social Systems'', Rome, 1-5 September 2003 | null | 10.1140/epjb/e2004-00055-7 | null | q-bio.GN | null | We introduce a random bit-string model of post-transcriptional genetic
regulation based on sequence matching. The model spontaneously yields a scale
free network with power law scaling with $ \gamma=-1$ and also exhibits
log-periodic behaviour. The in-degree distribution is much narrower, and
exhibits a pronounced pe... | [
{
"created": "Tue, 21 Oct 2003 14:39:58 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Balcan",
"Duygu",
""
],
[
"Erzan",
"Ayse",
""
]
] | We introduce a random bit-string model of post-transcriptional genetic regulation based on sequence matching. The model spontaneously yields a scale free network with power law scaling with $ \gamma=-1$ and also exhibits log-periodic behaviour. The in-degree distribution is much narrower, and exhibits a pronounced peak... |
2212.05617 | Michael Grinfeld | Bingzhang Chen and Michael Grinfeld | Decomposition of the Leinster-Cobbold Diversity Index | 10 pages, 1 figure | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The Leinster and Cobbold diversity index possesses a number of merits; in
particular, it generalises many existing indices and defines an effective
number. We present a scheme to quantify the contribution of richness, evenness,
and taxonomic similarity to this index. Compared to the work of van Dam (2019),
our approa... | [
{
"created": "Sun, 11 Dec 2022 22:20:46 GMT",
"version": "v1"
}
] | 2022-12-13 | [
[
"Chen",
"Bingzhang",
""
],
[
"Grinfeld",
"Michael",
""
]
] | The Leinster and Cobbold diversity index possesses a number of merits; in particular, it generalises many existing indices and defines an effective number. We present a scheme to quantify the contribution of richness, evenness, and taxonomic similarity to this index. Compared to the work of van Dam (2019), our approach... |
2312.11743 | Gurdip Uppal | Gurdip Uppal, Dervis Can Vural | On the possibility of engineering social evolution in microfluidic
environments | 16 pages, 5 figures | null | null | null | q-bio.PE cond-mat.soft | http://creativecommons.org/licenses/by/4.0/ | Many species of microbes cooperate by producing public goods from which they
collectively benefit. However, these populations are under the risk of being
taken over by cheating mutants that do not contribute to the pool of public
goods. Here we present theoretical findings that address how the social
evolution of mic... | [
{
"created": "Mon, 18 Dec 2023 22:57:07 GMT",
"version": "v1"
}
] | 2023-12-20 | [
[
"Uppal",
"Gurdip",
""
],
[
"Vural",
"Dervis Can",
""
]
] | Many species of microbes cooperate by producing public goods from which they collectively benefit. However, these populations are under the risk of being taken over by cheating mutants that do not contribute to the pool of public goods. Here we present theoretical findings that address how the social evolution of micro... |
2111.04740 | Nadia Brancati | Nadia Brancati, Anna Maria Anniciello, Pushpak Pati, Daniel Riccio,
Giosu\`e Scognamiglio, Guillaume Jaume, Giuseppe De Pietro, Maurizio Di
Bonito, Antonio Foncubierta, Gerardo Botti, Maria Gabrani, Florinda Feroce,
and Maria Frucci | BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images | 10 pages, 3 figures, 8 tables, 30 references | null | null | null | q-bio.QM cs.AI cs.CV eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Breast cancer is the most commonly diagnosed cancer and registers the highest
number of deaths for women with cancer. Recent advancements in diagnostic
activities combined with large-scale screening policies have significantly
lowered the mortality rates for breast cancer patients. However, the manual
inspection of t... | [
{
"created": "Mon, 8 Nov 2021 15:04:16 GMT",
"version": "v1"
}
] | 2021-11-10 | [
[
"Brancati",
"Nadia",
""
],
[
"Anniciello",
"Anna Maria",
""
],
[
"Pati",
"Pushpak",
""
],
[
"Riccio",
"Daniel",
""
],
[
"Scognamiglio",
"Giosuè",
""
],
[
"Jaume",
"Guillaume",
""
],
[
"De Pietro",
"Giuseppe",
... | Breast cancer is the most commonly diagnosed cancer and registers the highest number of deaths for women with cancer. Recent advancements in diagnostic activities combined with large-scale screening policies have significantly lowered the mortality rates for breast cancer patients. However, the manual inspection of tis... |
q-bio/0504034 | Jayprokas Chakrabarti | Bibekanand Mallick, Jayprokas Chakrabarti, Zhumur Ghosh, Smarajit Das
and Satyabrata Sahoo | tRNA-alike in Nanoarchaeum equitans ? | null | null | null | null | q-bio.GN q-bio.QM | null | The recent algorithm for five split tRNA-genes in N.equitans is new . It
locates missing tRNA-trp, tRNA-imet, tRNA-glu and tRNA-his . But the split
tRNA-trp(CCA) solution is anomalous ; the tRNA-imet lacks cognition elements
for aminoacylation . In view therefore we present here alternate non-split
composite solution... | [
{
"created": "Fri, 29 Apr 2005 06:45:47 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Mallick",
"Bibekanand",
""
],
[
"Chakrabarti",
"Jayprokas",
""
],
[
"Ghosh",
"Zhumur",
""
],
[
"Das",
"Smarajit",
""
],
[
"Sahoo",
"Satyabrata",
""
]
] | The recent algorithm for five split tRNA-genes in N.equitans is new . It locates missing tRNA-trp, tRNA-imet, tRNA-glu and tRNA-his . But the split tRNA-trp(CCA) solution is anomalous ; the tRNA-imet lacks cognition elements for aminoacylation . In view therefore we present here alternate non-split composite solutions ... |
1609.08880 | Alexey Miroshnikov | Alexey Miroshnikov, Matthias Steinr\"ucken | Computing the joint distribution of the total tree length across loci in
populations with variable size | 11 figures, 2 tables | Theoretical Population Biology, Volume 118, December 2017, Pages
1-19 | 10.1016/j.tpb.2017.09.002 | null | q-bio.PE math.AP math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent years, a number of methods have been developed to infer complex
demographic histories, especially historical population size changes, from
genomic sequence data. Coalescent Hidden Markov Models have proven to be
particularly useful for this type of inference. Due to the Markovian structure
of these models, ... | [
{
"created": "Wed, 28 Sep 2016 12:21:52 GMT",
"version": "v1"
},
{
"created": "Fri, 7 Oct 2016 07:44:55 GMT",
"version": "v2"
},
{
"created": "Wed, 23 Nov 2016 07:47:31 GMT",
"version": "v3"
},
{
"created": "Fri, 8 Sep 2017 05:25:39 GMT",
"version": "v4"
},
{
"cre... | 2017-10-10 | [
[
"Miroshnikov",
"Alexey",
""
],
[
"Steinrücken",
"Matthias",
""
]
] | In recent years, a number of methods have been developed to infer complex demographic histories, especially historical population size changes, from genomic sequence data. Coalescent Hidden Markov Models have proven to be particularly useful for this type of inference. Due to the Markovian structure of these models, an... |
2001.02132 | Xin Zhang | Xin Zhang, Zhao Zhang, Yanan Wei, Muhan Li, Pengxiang Zhao, Yao
Mawulikplimi Adzavon, Mengyu Liu, Xiaokang Zhang, Fei Xie, Andong Wang,
Jihong Sun, Yunlong Shao, Xiayan Wang, Xuejun Sun, Xuemei Ma (Corresponding
author) | Mitochondria in higher plants possess H2 evolving activity which is
closely related to complex I | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Hydrogenase occupy a central place in the energy metabolism of anaerobic
bacteria. Although the structure of mitochondrial complex I is similar to that
of hydrogenase, whether it has hydrogen metabolic activity remain unclear.
Here, we show that a H2 evolving activity exists in higher plants mitochondria
and is close... | [
{
"created": "Tue, 7 Jan 2020 15:47:08 GMT",
"version": "v1"
}
] | 2020-01-08 | [
[
"Zhang",
"Xin",
"",
"Corresponding\n author"
],
[
"Zhang",
"Zhao",
"",
"Corresponding\n author"
],
[
"Wei",
"Yanan",
"",
"Corresponding\n author"
],
[
"Li",
"Muhan",
"",
"Corresponding\n author"
],
[
"Zhao",
"Pengxiang",
... | Hydrogenase occupy a central place in the energy metabolism of anaerobic bacteria. Although the structure of mitochondrial complex I is similar to that of hydrogenase, whether it has hydrogen metabolic activity remain unclear. Here, we show that a H2 evolving activity exists in higher plants mitochondria and is closely... |
1902.05915 | Jamila Andoh | Mario Rosero Pahi, Juliana Cavalli, Frauke Nees, Herta Flor and Jamila
Andoh | Disruption of the prefrontal cortex improves implicit contextual
memory-guided attention: combined behavioural and electrophysiological
evidence | 24 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many studies have shown that the dorsolateral prefrontal cortex (DLPFC) plays
an important role in top-down cognitive control over intentional and deliberate
behavior. However, recent studies have reported that DLPFC-mediated top-down
control interferes with implicit forms of learning. Here we used continuous
theta b... | [
{
"created": "Fri, 15 Feb 2019 17:56:25 GMT",
"version": "v1"
}
] | 2019-02-18 | [
[
"Pahi",
"Mario Rosero",
""
],
[
"Cavalli",
"Juliana",
""
],
[
"Nees",
"Frauke",
""
],
[
"Flor",
"Herta",
""
],
[
"Andoh",
"Jamila",
""
]
] | Many studies have shown that the dorsolateral prefrontal cortex (DLPFC) plays an important role in top-down cognitive control over intentional and deliberate behavior. However, recent studies have reported that DLPFC-mediated top-down control interferes with implicit forms of learning. Here we used continuous theta bur... |
1405.2596 | Mohammad Soltani | Mohammad Soltani, Pavol Bokes, Zachary Fox, Abhyudai Singh | Nonspecific transcription factor binding reduces variability in
transcription factor and target protein expression | 10 pages, 5 figures, Physical Biology | null | null | null | q-bio.SC q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transcription factors (TFs) interact with a multitude of binding sites on DNA
and partner proteins inside cells. We investigate how nonspecific
binding/unbinding to such decoy binding sites affects the magnitude and
time-scale of random fluctuations in TF copy numbers arising from stochastic
gene expression. A stocha... | [
{
"created": "Sun, 11 May 2014 22:48:34 GMT",
"version": "v1"
},
{
"created": "Tue, 14 Apr 2015 19:07:27 GMT",
"version": "v2"
}
] | 2015-04-15 | [
[
"Soltani",
"Mohammad",
""
],
[
"Bokes",
"Pavol",
""
],
[
"Fox",
"Zachary",
""
],
[
"Singh",
"Abhyudai",
""
]
] | Transcription factors (TFs) interact with a multitude of binding sites on DNA and partner proteins inside cells. We investigate how nonspecific binding/unbinding to such decoy binding sites affects the magnitude and time-scale of random fluctuations in TF copy numbers arising from stochastic gene expression. A stochast... |
2007.04897 | Sungsoo Ahn | Sungsoo Ahn, Junsu Kim, Hankook Lee, Jinwoo Shin | Guiding Deep Molecular Optimization with Genetic Exploration | null | null | null | null | q-bio.QM cs.NE stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | De novo molecular design attempts to search over the chemical space for
molecules with the desired property. Recently, deep learning has gained
considerable attention as a promising approach to solve the problem. In this
paper, we propose genetic expert-guided learning (GEGL), a simple yet novel
framework for trainin... | [
{
"created": "Sat, 4 Jul 2020 05:01:26 GMT",
"version": "v1"
},
{
"created": "Fri, 17 Jul 2020 11:23:07 GMT",
"version": "v2"
},
{
"created": "Tue, 27 Oct 2020 10:49:47 GMT",
"version": "v3"
}
] | 2020-10-28 | [
[
"Ahn",
"Sungsoo",
""
],
[
"Kim",
"Junsu",
""
],
[
"Lee",
"Hankook",
""
],
[
"Shin",
"Jinwoo",
""
]
] | De novo molecular design attempts to search over the chemical space for molecules with the desired property. Recently, deep learning has gained considerable attention as a promising approach to solve the problem. In this paper, we propose genetic expert-guided learning (GEGL), a simple yet novel framework for training ... |
q-bio/0506014 | Patricia Faisca | P. F. N. Faisca and M. M. Telo da Gama | Folding of small proteins: A matter of geometry? | To appear in Molecular Physics | Molec. Phys. 103, 2903-2910 (2005) | 10.1080/00268970500221891 | null | q-bio.BM | null | We review some of our recent results obtained within the scope of simple
lattice models and Monte Carlo simulations that illustrate the role of native
geometry in the folding kinetics of two state folders.
| [
{
"created": "Fri, 10 Jun 2005 14:53:02 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Faisca",
"P. F. N.",
""
],
[
"da Gama",
"M. M. Telo",
""
]
] | We review some of our recent results obtained within the scope of simple lattice models and Monte Carlo simulations that illustrate the role of native geometry in the folding kinetics of two state folders. |
0804.0838 | Dmitry Tsigankov | Dmitry Tsigankov and Alexei Koulakov | Optimal axonal and dendritic branching strategies during the development
of neural circuitry | 13 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In developing brain, axons and dendrites are capable of connecting to each
other with high precision. Recent advances in imaging have allowed for the
monitoring of axonal, dendritic, and synapse dynamics in vivo. It is observed
that the majority of axonal and dendritic branches are formed 'in error', only
to be retra... | [
{
"created": "Sat, 5 Apr 2008 05:02:29 GMT",
"version": "v1"
}
] | 2008-04-08 | [
[
"Tsigankov",
"Dmitry",
""
],
[
"Koulakov",
"Alexei",
""
]
] | In developing brain, axons and dendrites are capable of connecting to each other with high precision. Recent advances in imaging have allowed for the monitoring of axonal, dendritic, and synapse dynamics in vivo. It is observed that the majority of axonal and dendritic branches are formed 'in error', only to be retract... |
2104.12479 | Muhammad Ardiyansyah | Muhammad Ardiyansyah | Distinguishing Level-2 Phylogenetic Networks Using Phylogenetic
Invariants | 35 pages, 3 tables, and 20 figures | null | null | null | q-bio.PE math.AG math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In phylogenetics, it is important for the phylogenetic network model
parameters to be identifiable so that the evolutionary histories of a group of
species can be consistently inferred. However, as the complexity of the
phylogenetic network models grows, the identifiability of network models
becomes increasingly diff... | [
{
"created": "Mon, 26 Apr 2021 11:25:36 GMT",
"version": "v1"
}
] | 2021-04-27 | [
[
"Ardiyansyah",
"Muhammad",
""
]
] | In phylogenetics, it is important for the phylogenetic network model parameters to be identifiable so that the evolutionary histories of a group of species can be consistently inferred. However, as the complexity of the phylogenetic network models grows, the identifiability of network models becomes increasingly diffic... |
2105.07337 | Xiaoliang Wang | Xiaoliang Wang and Dongyun Bai | Self-organization principles of cell cycles and gene expressions in the
development of cell populations | 28 pages, 18 figures | null | null | null | q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | A big challenge in current biology is to understand the exact
self-organization mechanism underlying complex multi-physics coupling
developmental processes. With multiscale computations of from subcellular gene
expressions to cell population dynamics that is based on first principles, we
show that cell cycles can sel... | [
{
"created": "Sun, 16 May 2021 03:20:13 GMT",
"version": "v1"
}
] | 2021-05-18 | [
[
"Wang",
"Xiaoliang",
""
],
[
"Bai",
"Dongyun",
""
]
] | A big challenge in current biology is to understand the exact self-organization mechanism underlying complex multi-physics coupling developmental processes. With multiscale computations of from subcellular gene expressions to cell population dynamics that is based on first principles, we show that cell cycles can self-... |
2306.15280 | Etienne Moullet | Etienne Moullet (CAMIN, WILLOW), Fran\c{c}ois Bailly (CAMIN), Justin
Carpentier (WILLOW, DI-ENS), Christine Azevedo Coste (CAMIN) | Vision-based interface for grasping intention detection and grip
selection : towards intuitive upper-limb assistive devices | null | Congr{\`e}s annuel de la Soci{\'e}t{\'e} de Biom{\'e}canique, Oct
2023, Grenoble, France | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Assistive devices for indivuals with upper-limb movement often lack
controllability and intuitiveness, in particular for grasping function. In this
work, we introduce a novel user interface for grasping movement control in
which the user delegates the grasping task decisions to the device, only moving
their (potentia... | [
{
"created": "Tue, 27 Jun 2023 08:12:05 GMT",
"version": "v1"
}
] | 2023-06-28 | [
[
"Moullet",
"Etienne",
"",
"CAMIN, WILLOW"
],
[
"Bailly",
"François",
"",
"CAMIN"
],
[
"Carpentier",
"Justin",
"",
"WILLOW, DI-ENS"
],
[
"Coste",
"Christine Azevedo",
"",
"CAMIN"
]
] | Assistive devices for indivuals with upper-limb movement often lack controllability and intuitiveness, in particular for grasping function. In this work, we introduce a novel user interface for grasping movement control in which the user delegates the grasping task decisions to the device, only moving their (potentiall... |
1803.05855 | Andrew Belmonte | Russ deForest and Andrew Belmonte | A game-theoretic mechanism for aggregation and dispersal of interacting
populations | 47 pages, 12 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We adapt a fitness function from evolutionary game theory as a mechanism for
aggregation and dispersal in a partial differential equation (PDE) model of two
interacting populations, described by density functions $u$ and $v$. We
consider a spatial model where individuals migrate up local fitness gradients,
seeking ou... | [
{
"created": "Thu, 15 Mar 2018 16:48:47 GMT",
"version": "v1"
}
] | 2018-03-16 | [
[
"deForest",
"Russ",
""
],
[
"Belmonte",
"Andrew",
""
]
] | We adapt a fitness function from evolutionary game theory as a mechanism for aggregation and dispersal in a partial differential equation (PDE) model of two interacting populations, described by density functions $u$ and $v$. We consider a spatial model where individuals migrate up local fitness gradients, seeking out ... |
1605.09489 | Rajamanickam Murugan | G. Niranjani and R. Murugan | Theory on the mechanism of site-specific DNA-protein interactions in the
presence of traps | 23 pages, 5 figures, 1 table | null | 10.1088/1478-3975/13/4/046003 | null | q-bio.SC q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The speed of site-specific binding of transcription factor (TFs) proteins
with genomic DNA seems to be strongly retarded by the randomly occurring
sequence traps. Traps are those DNA sequences sharing significant similarity
with the original specific binding sites. It is an intriguing question how the
naturally occur... | [
{
"created": "Tue, 31 May 2016 04:11:53 GMT",
"version": "v1"
}
] | 2016-07-22 | [
[
"Niranjani",
"G.",
""
],
[
"Murugan",
"R.",
""
]
] | The speed of site-specific binding of transcription factor (TFs) proteins with genomic DNA seems to be strongly retarded by the randomly occurring sequence traps. Traps are those DNA sequences sharing significant similarity with the original specific binding sites. It is an intriguing question how the naturally occurri... |
1808.10045 | Juan Daniel Sebastia-Saez | Daniel Sebastia-Saez, Adam Burbidge, Jan Engmann, Marco Ramaioli | New trends in mechanistic transdermal drug delivery modelling: Towards
an accurate description of skin microstructure | null | null | 10.1016/j.compchemeng.2020.106976 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Interest for in silico modelling of the absorption of xenobiotics into the
skin has been growing in the last years, owing to their lower cost compared to
experimental alternatives, and the desire to avoid animal experimentation. This
review presents an overview of Physiologically-Based Pharmacokinetic (PBPK)
models a... | [
{
"created": "Wed, 29 Aug 2018 21:22:05 GMT",
"version": "v1"
},
{
"created": "Mon, 3 Sep 2018 15:31:51 GMT",
"version": "v2"
},
{
"created": "Sun, 9 Sep 2018 21:28:13 GMT",
"version": "v3"
},
{
"created": "Fri, 22 Nov 2019 14:11:45 GMT",
"version": "v4"
}
] | 2020-12-08 | [
[
"Sebastia-Saez",
"Daniel",
""
],
[
"Burbidge",
"Adam",
""
],
[
"Engmann",
"Jan",
""
],
[
"Ramaioli",
"Marco",
""
]
] | Interest for in silico modelling of the absorption of xenobiotics into the skin has been growing in the last years, owing to their lower cost compared to experimental alternatives, and the desire to avoid animal experimentation. This review presents an overview of Physiologically-Based Pharmacokinetic (PBPK) models and... |
2005.05572 | Michael Kummer | Michael Kummer, Arunava Banerjee | Spike-Triggered Descent | null | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The characterization of neural responses to sensory stimuli is a central
problem in neuroscience. Spike-triggered average (STA), an influential
technique, has been used to extract optimal linear kernels in a variety of
animal subjects. However, when the model assumptions are not met, it can lead
to misleading and imp... | [
{
"created": "Tue, 12 May 2020 06:48:04 GMT",
"version": "v1"
}
] | 2020-05-13 | [
[
"Kummer",
"Michael",
""
],
[
"Banerjee",
"Arunava",
""
]
] | The characterization of neural responses to sensory stimuli is a central problem in neuroscience. Spike-triggered average (STA), an influential technique, has been used to extract optimal linear kernels in a variety of animal subjects. However, when the model assumptions are not met, it can lead to misleading and impre... |
1904.12960 | Andrew Durden | Andrew Durden | Modelling Diffuse Subcellular Protein Structures as Dynamic Social
Networks | Master's Thesis Submitted to the Graduate Faculty of The University
of Georgia in Partial Fulfillment of the Requirements for the Degree. Under
Direction of: Shannon Quinn | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fluorescence microscopy has led to impressive quantitative models and new
insights gained from richer sets of biomedical imagery. However, there is a
dearth of rigorous and established bioimaging strategies for modeling
spatiotemporal behavior of diffuse, subcellular components such as mitochondria
or actin. In many ... | [
{
"created": "Wed, 17 Apr 2019 01:32:31 GMT",
"version": "v1"
}
] | 2019-05-01 | [
[
"Durden",
"Andrew",
""
]
] | Fluorescence microscopy has led to impressive quantitative models and new insights gained from richer sets of biomedical imagery. However, there is a dearth of rigorous and established bioimaging strategies for modeling spatiotemporal behavior of diffuse, subcellular components such as mitochondria or actin. In many ca... |
0708.3171 | Bhaswar Ghosh | Indrani Bose and Bhaswar Ghosh | The p53-MDM2 network: from oscillations to apoptosis | null | null | null | null | q-bio.MN | null | The p53 protein is well-known for its tumour suppressor function. The
p53-MDM2 negative feedback loop constitutes the core module of a network of
regulatory interactions activated under cellular stress. In normal cells, the
level of p53 proteins is kept low by MDM2, i.e. MDM2 negatively regulates the
activity of p53.... | [
{
"created": "Thu, 23 Aug 2007 14:36:43 GMT",
"version": "v1"
}
] | 2007-08-24 | [
[
"Bose",
"Indrani",
""
],
[
"Ghosh",
"Bhaswar",
""
]
] | The p53 protein is well-known for its tumour suppressor function. The p53-MDM2 negative feedback loop constitutes the core module of a network of regulatory interactions activated under cellular stress. In normal cells, the level of p53 proteins is kept low by MDM2, i.e. MDM2 negatively regulates the activity of p53. I... |
2207.10794 | C\'edric Beaulac | C\'edric Beaulac, Sidi Wu, Erin Gibson, Michelle F. Miranda, Jiguo
Cao, Leno Rocha, Mirza Faisal Beg, Farouk S. Nathoo | Neuroimaging Feature Extraction using a Neural Network Classifier for
Imaging Genetics | Under review | BMC Bioinformatics 24, 271 (2023) | 10.1186/s12859-023-05394-x | null | q-bio.QM cs.CV cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | A major issue in the association of genes to neuroimaging phenotypes is the
high dimension of both genetic data and neuroimaging data. In this article, we
tackle the latter problem with an eye toward developing solutions that are
relevant for disease prediction. Supported by a vast literature on the
predictive power ... | [
{
"created": "Fri, 8 Jul 2022 19:03:00 GMT",
"version": "v1"
}
] | 2023-07-03 | [
[
"Beaulac",
"Cédric",
""
],
[
"Wu",
"Sidi",
""
],
[
"Gibson",
"Erin",
""
],
[
"Miranda",
"Michelle F.",
""
],
[
"Cao",
"Jiguo",
""
],
[
"Rocha",
"Leno",
""
],
[
"Beg",
"Mirza Faisal",
""
],
[
"Nathoo... | A major issue in the association of genes to neuroimaging phenotypes is the high dimension of both genetic data and neuroimaging data. In this article, we tackle the latter problem with an eye toward developing solutions that are relevant for disease prediction. Supported by a vast literature on the predictive power of... |
2202.10921 | Hua Jiang | Zhijun Zeng, Zhen Hou, Ting Li, Lei Deng, Jianguo Hou, Xinran Huang,
Jun Li, Meirou Sun, Yunhan Wang, Qiyu Wu, Wenhao Zheng, Hua Jiang, and Qi
Wang | A Deep Learning Approach to Predicting Ventilator Parameters for
Mechanically Ventilated Septic Patients | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We develop a deep learning approach to predicting a set of ventilator
parameters for a mechanically ventilated septic patient using a long and short
term memory (LSTM) recurrent neural network (RNN) model. We focus on short-term
predictions of a set of ventilator parameters for the septic patient in
emergency intensi... | [
{
"created": "Mon, 21 Feb 2022 04:17:22 GMT",
"version": "v1"
}
] | 2022-02-23 | [
[
"Zeng",
"Zhijun",
""
],
[
"Hou",
"Zhen",
""
],
[
"Li",
"Ting",
""
],
[
"Deng",
"Lei",
""
],
[
"Hou",
"Jianguo",
""
],
[
"Huang",
"Xinran",
""
],
[
"Li",
"Jun",
""
],
[
"Sun",
"Meirou",
""
... | We develop a deep learning approach to predicting a set of ventilator parameters for a mechanically ventilated septic patient using a long and short term memory (LSTM) recurrent neural network (RNN) model. We focus on short-term predictions of a set of ventilator parameters for the septic patient in emergency intensive... |
1912.06306 | Wenze Ding | Wenze Ding and Haipeng Gong | Predicting the real-valued distances between residue pairs for proteins | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Predicting protein structure from the amino acid sequence has been a
challenge with theoretical and practical significance in biophysics. Despite
the recent progresses elicited by improved residue-residue contact prediction,
contact-based structure prediction has gradually reached the performance
ceiling. New methods... | [
{
"created": "Fri, 13 Dec 2019 03:15:28 GMT",
"version": "v1"
},
{
"created": "Wed, 18 Dec 2019 15:25:17 GMT",
"version": "v2"
}
] | 2019-12-19 | [
[
"Ding",
"Wenze",
""
],
[
"Gong",
"Haipeng",
""
]
] | Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved residue-residue contact prediction, contact-based structure prediction has gradually reached the performance ceiling. New methods h... |
1501.04032 | Ken Kreutz-Delgado | Ken Kreutz-Delgado | Mean Time-to-Fire for the Noisy LIF Neuron - A Detailed Derivation of
the Siegert Formula | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When stimulated by a very large number of Poisson-like presynaptic current
input spikes, the temporal dynamics of the soma membrane potential $V(t)$ of a
leaky integrate-and-fire (LIF) neuron is typically modeled in the diffusion
limit and treated as a Ornstein-Uhlenbeck process (OUP). When the potential
reaches a th... | [
{
"created": "Fri, 16 Jan 2015 16:21:45 GMT",
"version": "v1"
}
] | 2015-01-19 | [
[
"Kreutz-Delgado",
"Ken",
""
]
] | When stimulated by a very large number of Poisson-like presynaptic current input spikes, the temporal dynamics of the soma membrane potential $V(t)$ of a leaky integrate-and-fire (LIF) neuron is typically modeled in the diffusion limit and treated as a Ornstein-Uhlenbeck process (OUP). When the potential reaches a thre... |
2010.06066 | Ben Frederick Intoy | Qianyi Sheng and Ben Intoy and J.W. Halley | Quenching to fix metastable states in models of prebiotic chemistry | 13 pages, 13 figures | Phys. Rev. E 102, 062412 (2020) | 10.1103/PhysRevE.102.062412 | null | q-bio.PE q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | For prebiotic chemistry to succeed in producing a starting metastable,
autocatalytic and reproducing system subject to evolutionary selection it must
satisfy at least two apparently contradictory requirements: Because such
systems are rare, a search among vast numbers of molecular combinations must
take place natural... | [
{
"created": "Mon, 12 Oct 2020 23:00:34 GMT",
"version": "v1"
}
] | 2021-01-04 | [
[
"Sheng",
"Qianyi",
""
],
[
"Intoy",
"Ben",
""
],
[
"Halley",
"J. W.",
""
]
] | For prebiotic chemistry to succeed in producing a starting metastable, autocatalytic and reproducing system subject to evolutionary selection it must satisfy at least two apparently contradictory requirements: Because such systems are rare, a search among vast numbers of molecular combinations must take place naturally... |
1310.1668 | Liane Gabora | Liane Gabora | Why the Creative Process is Not Darwinian | 8 pages | Creativity Research Journal, 19(4), 361-365 (2007) | null | null | q-bio.PE q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Simonton (2006) makes the unwarranted assumption that nonmonotonicity
supports a Darwinian view of creativity. Darwin's theory of natural selection
was motivated by a paradox that has no equivalent in creative thought: the
paradox of how change accumulates when acquired traits are not inherited. To
describe a process... | [
{
"created": "Mon, 7 Oct 2013 04:13:53 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Jul 2019 20:33:55 GMT",
"version": "v2"
}
] | 2019-07-09 | [
[
"Gabora",
"Liane",
""
]
] | Simonton (2006) makes the unwarranted assumption that nonmonotonicity supports a Darwinian view of creativity. Darwin's theory of natural selection was motivated by a paradox that has no equivalent in creative thought: the paradox of how change accumulates when acquired traits are not inherited. To describe a process o... |
1912.06275 | Oliver Beckstein | Oliver Beckstein and Fiona Naughton | General Principles of Secondary Active Transporter Function | accepted for publication in Biophysics Reviews | null | 10.1063/5.0047967 | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Transport of ions and small molecules across the cell membrane against
electrochemical gradients is catalyzed by integral membrane proteins that use a
source of free energy to drive the energetically uphill flux of the transported
substrate. Secondary active transporters couple the spontaneous influx of a
"driving" i... | [
{
"created": "Fri, 13 Dec 2019 00:52:41 GMT",
"version": "v1"
},
{
"created": "Thu, 18 Feb 2021 04:46:05 GMT",
"version": "v2"
},
{
"created": "Fri, 17 Dec 2021 19:14:37 GMT",
"version": "v3"
},
{
"created": "Wed, 23 Feb 2022 22:28:57 GMT",
"version": "v4"
},
{
"c... | 2022-03-25 | [
[
"Beckstein",
"Oliver",
""
],
[
"Naughton",
"Fiona",
""
]
] | Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported substrate. Secondary active transporters couple the spontaneous influx of a "driving" ion... |
0811.0541 | Gerhard Werner MD | Gerhard Werner | On critical State Transitions between different levels in Neural Systems | 11 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The framework of Modern Theory of Critical State Transitions considers the
relation between different levels of organization in complex systems in terms
of Critical State Transitions. A State Transition between levels entails
changes of scale of observables and, concurrently, new formats of description
at reduced dim... | [
{
"created": "Tue, 4 Nov 2008 15:44:46 GMT",
"version": "v1"
}
] | 2008-11-05 | [
[
"Werner",
"Gerhard",
""
]
] | The framework of Modern Theory of Critical State Transitions considers the relation between different levels of organization in complex systems in terms of Critical State Transitions. A State Transition between levels entails changes of scale of observables and, concurrently, new formats of description at reduced dimen... |
1809.02886 | Anne Shiu | Carsten Conradi, Maya Mincheva, Anne Shiu | Emergence of oscillations in a mixed-mechanism phosphorylation system | 24 pages | null | null | null | q-bio.MN math.AG math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This work investigates the emergence of oscillations in one of the simplest
cellular signaling networks exhibiting oscillations, namely, the dual-site
phosphorylation and dephosphorylation network (futile cycle), in which the
mechanism for phosphorylation is processive while the one for dephosphorylation
is distribut... | [
{
"created": "Sat, 8 Sep 2018 22:10:58 GMT",
"version": "v1"
},
{
"created": "Fri, 1 Feb 2019 20:44:38 GMT",
"version": "v2"
}
] | 2019-02-05 | [
[
"Conradi",
"Carsten",
""
],
[
"Mincheva",
"Maya",
""
],
[
"Shiu",
"Anne",
""
]
] | This work investigates the emergence of oscillations in one of the simplest cellular signaling networks exhibiting oscillations, namely, the dual-site phosphorylation and dephosphorylation network (futile cycle), in which the mechanism for phosphorylation is processive while the one for dephosphorylation is distributiv... |
1909.02148 | Claus Seidel | Mykola Dimura, Thomas O. Peulen, Hugo Sanabria, Dmitro Rodnin,
Katherina Hemmen, Claus A.M. Seidel and Holger Gohlke | Automated and optimally FRET-assisted structural modeling | 18 pages, 2 figures, 1 table | null | 10.1016/j.bpj.2018.11.1815 | null | q-bio.QM physics.bio-ph q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | FRET experiments can yield state-specific structural information on complex
dynamic biomolecular assemblies. However, FRET experiments need to be combined
with computer simulations to overcome their sparsity. We introduce (i) an
automated FRET experiment design tool determining optimal FRET pairs for
structural model... | [
{
"created": "Wed, 4 Sep 2019 23:12:26 GMT",
"version": "v1"
}
] | 2019-09-11 | [
[
"Dimura",
"Mykola",
""
],
[
"Peulen",
"Thomas O.",
""
],
[
"Sanabria",
"Hugo",
""
],
[
"Rodnin",
"Dmitro",
""
],
[
"Hemmen",
"Katherina",
""
],
[
"Seidel",
"Claus A. M.",
""
],
[
"Gohlke",
"Holger",
""
]
... | FRET experiments can yield state-specific structural information on complex dynamic biomolecular assemblies. However, FRET experiments need to be combined with computer simulations to overcome their sparsity. We introduce (i) an automated FRET experiment design tool determining optimal FRET pairs for structural modelin... |
q-bio/0503020 | Adam Lipowski | Adam Lipowski and Dorota Lipowska | Long-term evolution of an ecosystem with spontaneous periodicity of mass
extinctions | 10 pages, Theory in Biosciences (in press). For associated Java
applet see http://spin.amu.edu.pl/~lipowski/prey_pred.html | Theory in Biosciences vol.125, pp. 67-77 (2006) | 10.1016/j.thbio.2006.01.001 | null | q-bio.PE cond-mat.other q-bio.OT | null | Twenty years ago, after analysing palaeontological data, Raup and Sepkoski
suggested that mass extinctions on Earth appear cyclically in time with a
period of approximately 26 million years (My). To explain the 26My period, a
number of proposals were made involving, e.g., astronomical effects, increased
volcanic acti... | [
{
"created": "Sun, 13 Mar 2005 17:52:39 GMT",
"version": "v1"
},
{
"created": "Fri, 10 Jun 2005 20:17:36 GMT",
"version": "v2"
},
{
"created": "Sun, 26 Jun 2005 13:03:55 GMT",
"version": "v3"
},
{
"created": "Fri, 6 Jan 2006 20:14:37 GMT",
"version": "v4"
}
] | 2007-05-23 | [
[
"Lipowski",
"Adam",
""
],
[
"Lipowska",
"Dorota",
""
]
] | Twenty years ago, after analysing palaeontological data, Raup and Sepkoski suggested that mass extinctions on Earth appear cyclically in time with a period of approximately 26 million years (My). To explain the 26My period, a number of proposals were made involving, e.g., astronomical effects, increased volcanic activi... |
1412.2110 | Amit Chattopadhyay | Amit K. Chattopadhyay and Subhasish Bandyopadhyay | Seasonal variations of EPG Levels in gastro-intestinal parasitic
infection in a southeast asian controlled locale: a statistical analysis | 9 pages, 12 figures | SpringerPlus 2013, 2:205 | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a data based statistical study on the effects of seasonal
variations in the growth rates of the gastro-intestinal (GI) parasitic
infection in livestock. The alluded growth rate is estimated through the
variation in the number of eggs per gram (EPG) of faeces in animals. In
accordance with earlier studies, ... | [
{
"created": "Wed, 3 Dec 2014 23:15:52 GMT",
"version": "v1"
}
] | 2014-12-08 | [
[
"Chattopadhyay",
"Amit K.",
""
],
[
"Bandyopadhyay",
"Subhasish",
""
]
] | We present a data based statistical study on the effects of seasonal variations in the growth rates of the gastro-intestinal (GI) parasitic infection in livestock. The alluded growth rate is estimated through the variation in the number of eggs per gram (EPG) of faeces in animals. In accordance with earlier studies, ou... |
1907.09270 | Afshin Montakhab | Mahsa Khoshkhou and Afshin Montakhab | Spike-timing-dependent plasticity with axonal delay tunes networks of
Izhikevich neurons to the edge of synchronization transition with scale-free
avalanches | 9 pages, 7 figures, 42 references | Front. Syst. Neurosci., 04 December 2019 | 10.3389/fnsys.2019.00073 | null | q-bio.NC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Critical brain hypothesis has been intensively studied both in experimental
and theoretical neuroscience over the past two decades. However, some important
questions still remain: (i) What is the critical point the brain operates at?
(ii) What is the regulatory mechanism that brings about and maintains such a
critica... | [
{
"created": "Mon, 22 Jul 2019 12:28:45 GMT",
"version": "v1"
}
] | 2019-12-19 | [
[
"Khoshkhou",
"Mahsa",
""
],
[
"Montakhab",
"Afshin",
""
]
] | Critical brain hypothesis has been intensively studied both in experimental and theoretical neuroscience over the past two decades. However, some important questions still remain: (i) What is the critical point the brain operates at? (ii) What is the regulatory mechanism that brings about and maintains such a critical ... |
2103.15544 | Claudius Gros | Claudius Gros, Thomas Czypionka, Daniel Gros | When to end a lock down? How fast must vaccination campaigns proceed in
order to keep health costs in check? | null | Royal Society Open Science 9, 211055 (2022) | 10.1098/rsos.211055 | null | q-bio.PE econ.TH physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a simple rule of thumb for countries which have embarked on a
vaccination campaign while still facing the need to keep non-pharmaceutical
interventions (NPI) in place because of the ongoing spread of SARS-CoV-2. If
the aim is to keep the death rate from increasing, NPIs can be loosened when it
is possible ... | [
{
"created": "Mon, 29 Mar 2021 12:20:34 GMT",
"version": "v1"
},
{
"created": "Tue, 30 Mar 2021 13:47:37 GMT",
"version": "v2"
},
{
"created": "Wed, 31 Mar 2021 14:27:51 GMT",
"version": "v3"
},
{
"created": "Wed, 26 Jan 2022 08:45:53 GMT",
"version": "v4"
}
] | 2022-01-27 | [
[
"Gros",
"Claudius",
""
],
[
"Czypionka",
"Thomas",
""
],
[
"Gros",
"Daniel",
""
]
] | We propose a simple rule of thumb for countries which have embarked on a vaccination campaign while still facing the need to keep non-pharmaceutical interventions (NPI) in place because of the ongoing spread of SARS-CoV-2. If the aim is to keep the death rate from increasing, NPIs can be loosened when it is possible to... |
q-bio/0504031 | Romulus Breban | Romulus Breban and Sally Blower | Parametric Resonance May Explain Virologic Failure to HIV Treatment
Interruptions | 15 pages, 2 figures, 1 table | null | null | null | q-bio.PE | null | Pilot studies of structured treatment interruptions (STI) in HIV therapy have
shown that patients can maintain low viral loads whilst benefiting from reduced
treatment toxicity. However, a recent STI clinical trial reported a high degree
of virologic failure. Here we present a novel hypothesis that could explain
viro... | [
{
"created": "Wed, 27 Apr 2005 21:57:53 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Breban",
"Romulus",
""
],
[
"Blower",
"Sally",
""
]
] | Pilot studies of structured treatment interruptions (STI) in HIV therapy have shown that patients can maintain low viral loads whilst benefiting from reduced treatment toxicity. However, a recent STI clinical trial reported a high degree of virologic failure. Here we present a novel hypothesis that could explain virolo... |
2010.02952 | Chinchin Wang | Chinchin Wang, Tyrel Stokes, jorge Trejo Vargas, Russell Steele, Niels
Wedderkopp, Ian Shrier | Injury risk increases minimally over a large range of changes in
activity level in children | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Background: Limited research exists on the association between changes in
physical activity levels and injury in children. Objective: To assess how well
different variations of the acute:chronic workload ratio (ACWR), a measure of
change in activity, predict injury in children. Methods: We conducted a
prospective coh... | [
{
"created": "Tue, 6 Oct 2020 18:03:50 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Jan 2021 01:25:50 GMT",
"version": "v2"
}
] | 2021-01-25 | [
[
"Wang",
"Chinchin",
""
],
[
"Stokes",
"Tyrel",
""
],
[
"Vargas",
"jorge Trejo",
""
],
[
"Steele",
"Russell",
""
],
[
"Wedderkopp",
"Niels",
""
],
[
"Shrier",
"Ian",
""
]
] | Background: Limited research exists on the association between changes in physical activity levels and injury in children. Objective: To assess how well different variations of the acute:chronic workload ratio (ACWR), a measure of change in activity, predict injury in children. Methods: We conducted a prospective cohor... |
2006.14930 | Sumra Bari | Sumra Bari, Nicole L. Vike, Khrystyna Stetsiv, Linda Papa, Eric A.
Nauman, Thomas M. Talavage, Semyon Slobounov, Hans C. Breiter | A metabolomic measure of energy metabolism moderates how an inflammatory
miRNA relates to rs-fMRI network and motor control in football athletes | 64 pages, 4 figures, 1 table. arXiv admin note: text overlap with
arXiv:2006.13264 | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Collision sports athletes experience many head acceleration events (HAEs) per
season. The effects of these subconcussive events are largely understudied
since HAEs may produce no overt symptoms, and are likely to diffusely manifest
across multiple scales of study (e.g., molecular, cellular network, and
behavior). Thi... | [
{
"created": "Tue, 23 Jun 2020 18:44:02 GMT",
"version": "v1"
}
] | 2020-06-29 | [
[
"Bari",
"Sumra",
""
],
[
"Vike",
"Nicole L.",
""
],
[
"Stetsiv",
"Khrystyna",
""
],
[
"Papa",
"Linda",
""
],
[
"Nauman",
"Eric A.",
""
],
[
"Talavage",
"Thomas M.",
""
],
[
"Slobounov",
"Semyon",
""
],
... | Collision sports athletes experience many head acceleration events (HAEs) per season. The effects of these subconcussive events are largely understudied since HAEs may produce no overt symptoms, and are likely to diffusely manifest across multiple scales of study (e.g., molecular, cellular network, and behavior). This ... |
2003.00329 | Gerhard Mayer | Gerhard Mayer | XLMOD: Cross-linking and chromatography derivatization reagents ontology | 30 pages | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mass spectrometry has experienced a rapid development since its first
application for protein analysis in the 1980s. While the most common use of
mass spectrometry for protein analysis is identification and quantification
workflows on peptides (digested from their parent protein), there is also a
rapidly growing use ... | [
{
"created": "Sat, 29 Feb 2020 18:45:43 GMT",
"version": "v1"
}
] | 2020-03-03 | [
[
"Mayer",
"Gerhard",
""
]
] | Mass spectrometry has experienced a rapid development since its first application for protein analysis in the 1980s. While the most common use of mass spectrometry for protein analysis is identification and quantification workflows on peptides (digested from their parent protein), there is also a rapidly growing use of... |
1304.6570 | Thierry Platini | Hodjat Pendar, Thierry Platini, Rahul V. Kulkarni | Exact protein distributions for stochastic models of gene expression
using partitioning of Poisson processes | 10 pages, 5 figures | null | 10.1103/PhysRevE.87.042720 | null | q-bio.MN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stochasticity in gene expression gives rise to fluctuations in protein levels
across a population of genetically identical cells. Such fluctuations can lead
to phenotypic variation in clonal populations, hence there is considerable
interest in quantifying noise in gene expression using stochastic models.
However, obt... | [
{
"created": "Wed, 24 Apr 2013 13:11:17 GMT",
"version": "v1"
}
] | 2015-06-15 | [
[
"Pendar",
"Hodjat",
""
],
[
"Platini",
"Thierry",
""
],
[
"Kulkarni",
"Rahul V.",
""
]
] | Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations, hence there is considerable interest in quantifying noise in gene expression using stochastic models. However, obtai... |
1002.3837 | Michael Deem | Jeong-Man Park, Enrique Munoz, Michael W. Deem | Quasispecies theory for finite populations | 13 pages, 8 figures | Phys. Rev. E 81 (2010) 011902 | 10.1103/PhysRevE.81.011902 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present stochastic, finite-population formulations of the Crow-Kimura and
Eigen models of quasispecies theory, for fitness functions that depend in an
arbitrary way on the number of mutations from the wild type. We include back
mutations in our description. We show that the fluctuation of the population
numbers ab... | [
{
"created": "Fri, 19 Feb 2010 22:52:21 GMT",
"version": "v1"
}
] | 2010-02-23 | [
[
"Park",
"Jeong-Man",
""
],
[
"Munoz",
"Enrique",
""
],
[
"Deem",
"Michael W.",
""
]
] | We present stochastic, finite-population formulations of the Crow-Kimura and Eigen models of quasispecies theory, for fitness functions that depend in an arbitrary way on the number of mutations from the wild type. We include back mutations in our description. We show that the fluctuation of the population numbers abou... |
0902.1579 | Yue Chan | Yue Chan, Grant M. Cox, Richard G. Haverkamp and James M. Hill | Mechanical model for a collagen fibril pair in extracellular matrix | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we model the mechanics of a collagen pair in the connective
tissue extracellular matrix that exists in abundance throughout animals,
including the human body. This connective tissue comprises repeated units of
two main structures, namely collagens as well as axial, parallel and regular
anionic glycosam... | [
{
"created": "Tue, 10 Feb 2009 04:21:33 GMT",
"version": "v1"
}
] | 2009-02-11 | [
[
"Chan",
"Yue",
""
],
[
"Cox",
"Grant M.",
""
],
[
"Haverkamp",
"Richard G.",
""
],
[
"Hill",
"James M.",
""
]
] | In this paper, we model the mechanics of a collagen pair in the connective tissue extracellular matrix that exists in abundance throughout animals, including the human body. This connective tissue comprises repeated units of two main structures, namely collagens as well as axial, parallel and regular anionic glycosamin... |
1003.1066 | Grzegorz A Rempala | Grzegorz A. Rempala, Michal Seweryn, Leszek Ignatowicz | Model for Diversity Analysis of Antigen Receptor Repertoires | 5 figures | null | null | null | q-bio.BM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In most of the recent immunological literature the differences across antigen
receptor populations are examined via non-parametric statistical measures of
species overlap and diversity borrowed from ecological studies. While this
approach is robust in a wide range of situations, it seems to provide little
insight int... | [
{
"created": "Thu, 4 Mar 2010 15:36:11 GMT",
"version": "v1"
}
] | 2010-03-05 | [
[
"Rempala",
"Grzegorz A.",
""
],
[
"Seweryn",
"Michal",
""
],
[
"Ignatowicz",
"Leszek",
""
]
] | In most of the recent immunological literature the differences across antigen receptor populations are examined via non-parametric statistical measures of species overlap and diversity borrowed from ecological studies. While this approach is robust in a wide range of situations, it seems to provide little insight into ... |
2304.03293 | Kyoungmin Min | Seungpyo Kang, Minseon Kim, Jiwon Sun, Myeonghun Lee, and Kyoungmin
Min | Prediction of Protein Aggregation Propensity via Data-driven Approaches | null | null | null | null | q-bio.QM physics.bio-ph physics.data-an | http://creativecommons.org/licenses/by/4.0/ | Protein aggregation occurs when misfolded or unfolded proteins physically
bind together, and can promote the development of various amyloid diseases.
This study aimed to construct surrogate models for predicting protein
aggregation via data-driven methods using two types of databases. First, an
aggregation propensity... | [
{
"created": "Thu, 6 Apr 2023 06:19:37 GMT",
"version": "v1"
}
] | 2023-04-10 | [
[
"Kang",
"Seungpyo",
""
],
[
"Kim",
"Minseon",
""
],
[
"Sun",
"Jiwon",
""
],
[
"Lee",
"Myeonghun",
""
],
[
"Min",
"Kyoungmin",
""
]
] | Protein aggregation occurs when misfolded or unfolded proteins physically bind together, and can promote the development of various amyloid diseases. This study aimed to construct surrogate models for predicting protein aggregation via data-driven methods using two types of databases. First, an aggregation propensity s... |
1810.01414 | Ramzan Umarov | Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Xin Gao, Victor Solovyev | PromID: human promoter prediction by deep learning | 18 pages, 8 figures, 2 tables | null | null | null | q-bio.GN cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Computational identification of promoters is notoriously difficult as human
genes often have unique promoter sequences that provide regulation of
transcription and interaction with transcription initiation complex. While
there are many attempts to develop computational promoter identification
methods, we have no reli... | [
{
"created": "Tue, 2 Oct 2018 17:35:46 GMT",
"version": "v1"
}
] | 2018-10-04 | [
[
"Umarov",
"Ramzan",
""
],
[
"Kuwahara",
"Hiroyuki",
""
],
[
"Li",
"Yu",
""
],
[
"Gao",
"Xin",
""
],
[
"Solovyev",
"Victor",
""
]
] | Computational identification of promoters is notoriously difficult as human genes often have unique promoter sequences that provide regulation of transcription and interaction with transcription initiation complex. While there are many attempts to develop computational promoter identification methods, we have no reliab... |
0708.0548 | Eduardo Candelario-Jalil | E. Candelario-Jalil, R. S. Akundi, H. S. Bhatia, K. Lieb, K. Appel, E.
Munoz, M. Hull, B. L. Fiebich | Ascorbic acid enhances the inhibitory effect of aspirin on neuronal
cyclooxygenase-2-mediated prostaglandin E2 production | null | Journal of Neuroimmunology 174(1-2): 39-51 (2006) | null | null | q-bio.SC q-bio.MN | null | In the present study, we show that ascorbic acid dose-dependently inhibited
interleukin-1beta (IL-1beta)-mediated PGE2 synthesis in the human neuronal cell
line, SK-N-SH. Furthermore, in combination with aspirin, ascorbic acid
augmented the inhibitory effect of aspirin on PGE2 synthesis. However, ascorbic
acid had no... | [
{
"created": "Fri, 3 Aug 2007 16:46:53 GMT",
"version": "v1"
}
] | 2007-08-06 | [
[
"Candelario-Jalil",
"E.",
""
],
[
"Akundi",
"R. S.",
""
],
[
"Bhatia",
"H. S.",
""
],
[
"Lieb",
"K.",
""
],
[
"Appel",
"K.",
""
],
[
"Munoz",
"E.",
""
],
[
"Hull",
"M.",
""
],
[
"Fiebich",
"B. L... | In the present study, we show that ascorbic acid dose-dependently inhibited interleukin-1beta (IL-1beta)-mediated PGE2 synthesis in the human neuronal cell line, SK-N-SH. Furthermore, in combination with aspirin, ascorbic acid augmented the inhibitory effect of aspirin on PGE2 synthesis. However, ascorbic acid had no s... |
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