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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1309.4712 | Liane Gabora | Liane Gabora, Diederik Aerts | Distilling the Essence of an Evolutionary Process and Implications for a
Formal Description of Culture | In (W. Kistler, Ed.) Proceedings of Center for Human Evolution
Workshop #4: Cultural Evolution, May 18-19, 2000. Bellevue, WA: Foundation
for the Future (2005) | null | null | null | q-bio.PE q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has been proposed that, since the origin of life and the ensuing evolution
of biological species, a second evolutionary process has appeared on our
planet. It is the evolution of culture-e.g., ideas, beliefs, and artifacts.
Does culture evolve in the same genuine sense as biological life? And if so,
does it evolve... | [
{
"created": "Wed, 18 Sep 2013 17:22:25 GMT",
"version": "v1"
},
{
"created": "Sun, 30 Jun 2019 02:27:33 GMT",
"version": "v2"
},
{
"created": "Fri, 5 Jul 2019 21:51:46 GMT",
"version": "v3"
}
] | 2019-07-09 | [
[
"Gabora",
"Liane",
""
],
[
"Aerts",
"Diederik",
""
]
] | It has been proposed that, since the origin of life and the ensuing evolution of biological species, a second evolutionary process has appeared on our planet. It is the evolution of culture-e.g., ideas, beliefs, and artifacts. Does culture evolve in the same genuine sense as biological life? And if so, does it evolve t... |
1105.0126 | Neri Niccolai | Andrea Bernini, Vincenzo Venditti, Ottavia Spiga, Filippo Prischi,
Mauro Botta, Angela Pui-Ling Tong, Wing-Tak Wong and Neri Niccolai | The surface accessibility of {\alpha}-bungarotoxin monitored by a novel
paramagnetic probe | 13 pages, 4 figures,preliminary report | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The surface accessibility of {\alpha}-bungarotoxin has been investigated by
using Gd2L7, a newly designed paramagnetic NMR probe. Signal attenuations
induced by Gd2L7 on {\alpha}-bungarotoxin C{\alpha}H peaks of 1H-13C HSQC
spectra have been analyzed and compared with the ones previously obtained in
the presence of G... | [
{
"created": "Sat, 30 Apr 2011 23:02:50 GMT",
"version": "v1"
}
] | 2011-05-03 | [
[
"Bernini",
"Andrea",
""
],
[
"Venditti",
"Vincenzo",
""
],
[
"Spiga",
"Ottavia",
""
],
[
"Prischi",
"Filippo",
""
],
[
"Botta",
"Mauro",
""
],
[
"Tong",
"Angela Pui-Ling",
""
],
[
"Wong",
"Wing-Tak",
""
]... | The surface accessibility of {\alpha}-bungarotoxin has been investigated by using Gd2L7, a newly designed paramagnetic NMR probe. Signal attenuations induced by Gd2L7 on {\alpha}-bungarotoxin C{\alpha}H peaks of 1H-13C HSQC spectra have been analyzed and compared with the ones previously obtained in the presence of GdD... |
q-bio/0601024 | Denis Boyer | Denis Boyer, Gabriel Ramos-Fern\'andez, Octavio Miramontes, Jos\'e L.
Mateos, Germinal Cocho, Hern\'an Larralde, Humberto Ramos, Fernando Rojas | Scale-free foraging by primates emerges from their interaction with a
complex environment | 31 pages, 4 figures. To appear in Proc. Roy. Soc. B. Minor revisions | null | null | null | q-bio.PE cond-mat.dis-nn | null | Scale-free foraging patterns are widespread among animals. These may be the
outcome of an optimal searching strategy to find scarce randomly distributed
resources, but a less explored alternative is that this behaviour may result
from the interaction of foraging animals with a particular distribution of
resources. We... | [
{
"created": "Tue, 17 Jan 2006 22:48:55 GMT",
"version": "v1"
},
{
"created": "Tue, 31 Jan 2006 17:20:16 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Boyer",
"Denis",
""
],
[
"Ramos-Fernández",
"Gabriel",
""
],
[
"Miramontes",
"Octavio",
""
],
[
"Mateos",
"José L.",
""
],
[
"Cocho",
"Germinal",
""
],
[
"Larralde",
"Hernán",
""
],
[
"Ramos",
"Humberto",
... | Scale-free foraging patterns are widespread among animals. These may be the outcome of an optimal searching strategy to find scarce randomly distributed resources, but a less explored alternative is that this behaviour may result from the interaction of foraging animals with a particular distribution of resources. We i... |
2004.12665 | Jae Woo Lee | Seo Yoon Chae, Kyoung-Eun Lee, Hyun Min Lee, Nam Jun, Quang Ahn Le,
Biseko Juma Mafwele, Tae Ho Lee, Doo Hwan Kim, and Jae Woo Lee | Estimation of Infection Rate and Prediction of Initial Infected
Individuals of COVID-19 | 12 pages, 2 figures | null | null | null | q-bio.PE nlin.AO physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the pandemic spreading of COVID-19 for some selected countries
after the outbreak of the coronavirus in Wuhan City, China. We estimated the
infection rate and the initial infected individuals of COVID-19 by using the
officially reported data at the early stage of the epidemic for the susceptible
(S), infe... | [
{
"created": "Mon, 27 Apr 2020 09:27:09 GMT",
"version": "v1"
}
] | 2020-04-28 | [
[
"Chae",
"Seo Yoon",
""
],
[
"Lee",
"Kyoung-Eun",
""
],
[
"Lee",
"Hyun Min",
""
],
[
"Jun",
"Nam",
""
],
[
"Le",
"Quang Ahn",
""
],
[
"Mafwele",
"Biseko Juma",
""
],
[
"Lee",
"Tae Ho",
""
],
[
"Kim",... | We consider the pandemic spreading of COVID-19 for some selected countries after the outbreak of the coronavirus in Wuhan City, China. We estimated the infection rate and the initial infected individuals of COVID-19 by using the officially reported data at the early stage of the epidemic for the susceptible (S), infect... |
1902.10975 | Jean-Paul Saint Martin | Jean-Paul Saint Martin (CR2P), Simona Saint Martin (CR2P) | Beltanelliformis brunsae Menner in Keller et al., 1974: an undoubted
Ediacaran fossil from Neoproterozoic of Dobrogea (Romania) | null | Geodiversitas, Museum National d'Histoire Naturelle Paris, 2018 | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ediacaran fossils are now largely known in different parts of the world.
However, some countries are poorly documented on these remains of a still
enigmatic life. Thus, rare fossils from the Neoproterozoic Histria Formation of
central Dobrogea (Romania) have been reported. Two specimens with discoid
imprints are desc... | [
{
"created": "Thu, 28 Feb 2019 09:43:53 GMT",
"version": "v1"
}
] | 2019-03-01 | [
[
"Martin",
"Jean-Paul Saint",
"",
"CR2P"
],
[
"Martin",
"Simona Saint",
"",
"CR2P"
]
] | Ediacaran fossils are now largely known in different parts of the world. However, some countries are poorly documented on these remains of a still enigmatic life. Thus, rare fossils from the Neoproterozoic Histria Formation of central Dobrogea (Romania) have been reported. Two specimens with discoid imprints are descri... |
2202.05389 | Viplove Arora | Viplove Arora, Enrico Amico, Joaqu\'in Go\~ni, Mario Ventresca | Investigating cognitive ability using action-based models of structural
brain networks | null | null | 10.1093/comnet/cnac037 | null | q-bio.NC stat.ME | http://creativecommons.org/licenses/by/4.0/ | Recent developments in network neuroscience have highlighted the importance
of developing techniques for analyzing and modeling brain networks. A
particularly powerful approach for studying complex neural systems is to
formulate generative models that use wiring rules to synthesize networks
closely resembling the top... | [
{
"created": "Wed, 19 Jan 2022 14:24:11 GMT",
"version": "v1"
}
] | 2022-09-09 | [
[
"Arora",
"Viplove",
""
],
[
"Amico",
"Enrico",
""
],
[
"Goñi",
"Joaquín",
""
],
[
"Ventresca",
"Mario",
""
]
] | Recent developments in network neuroscience have highlighted the importance of developing techniques for analyzing and modeling brain networks. A particularly powerful approach for studying complex neural systems is to formulate generative models that use wiring rules to synthesize networks closely resembling the topol... |
q-bio/0507006 | Dietrich Stauffer | Michael Masa, Stanislaw Cebrat and Dietrich Stauffer | Does telomere elongation lead to a longer lifespan if cancer is
considered? | 9 pages including 5 figures | null | 10.1016/j.physa.2005.08.043 | null | q-bio.PE | null | As cell proliferation is limited due to the loss of telomere repeats in DNA
of normal somatic cells during division, telomere attrition can possibly play
an important role in determining the maximum life span of organisms as well as
contribute to the process of biological ageing. With computer simulations of
cell cul... | [
{
"created": "Mon, 4 Jul 2005 17:54:10 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Masa",
"Michael",
""
],
[
"Cebrat",
"Stanislaw",
""
],
[
"Stauffer",
"Dietrich",
""
]
] | As cell proliferation is limited due to the loss of telomere repeats in DNA of normal somatic cells during division, telomere attrition can possibly play an important role in determining the maximum life span of organisms as well as contribute to the process of biological ageing. With computer simulations of cell cultu... |
2012.03290 | Claudia Solis-Lemus | Yizhou Liu and Claudia Solis-Lemus | WI Fast Stats: a collection of web apps for the visualization and
analysis of WI Fast Plants data | 5 pages, 4 figures | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | WI Fast Stats is the first and only dedicated tool tailored to the WI Fast
Plants educational objectives. WI Fast Stats is an integrated animated web page
with a collection of R-developed web apps that provide Data Visualization and
Data Analysis tools for WI Fast Plants data. WI Fast Stats is a user-friendly
easy-to... | [
{
"created": "Sun, 6 Dec 2020 15:39:59 GMT",
"version": "v1"
}
] | 2020-12-08 | [
[
"Liu",
"Yizhou",
""
],
[
"Solis-Lemus",
"Claudia",
""
]
] | WI Fast Stats is the first and only dedicated tool tailored to the WI Fast Plants educational objectives. WI Fast Stats is an integrated animated web page with a collection of R-developed web apps that provide Data Visualization and Data Analysis tools for WI Fast Plants data. WI Fast Stats is a user-friendly easy-to-u... |
1309.5717 | Giovanni Bussi | Francesco Di Palma, Francesco Colizzi, and Giovanni Bussi | Ligand-induced stabilization of the aptamer terminal helix in the add
adenine riboswitch | Accepted on RNA Journal | Di Palma, Colizzi, and Bussi, RNA 19, 1517 (2013) | 10.1261/rna.040493.113 | null | q-bio.BM physics.bio-ph physics.chem-ph physics.comp-ph | http://creativecommons.org/licenses/by/3.0/ | Riboswitches are structured mRNA elements that modulate gene expression. They
undergo conformational changes triggered by highly specific interactions with
sensed metabolites. Among the structural rearrangements engaged by
riboswitches, the forming and melting of the aptamer terminal helix, the
so-called P1 stem, is ... | [
{
"created": "Mon, 23 Sep 2013 07:27:52 GMT",
"version": "v1"
}
] | 2013-10-29 | [
[
"Di Palma",
"Francesco",
""
],
[
"Colizzi",
"Francesco",
""
],
[
"Bussi",
"Giovanni",
""
]
] | Riboswitches are structured mRNA elements that modulate gene expression. They undergo conformational changes triggered by highly specific interactions with sensed metabolites. Among the structural rearrangements engaged by riboswitches, the forming and melting of the aptamer terminal helix, the so-called P1 stem, is es... |
1603.08432 | Lida Kanari | Lida Kanari, Pawe{\l} D{\l}otko, Martina Scolamiero, Ran Levi, Julian
Shillcock, Kathryn Hess, Henry Markram | Quantifying topological invariants of neuronal morphologies | 10 pages, 5 figures, conference or other essential info | null | null | null | q-bio.NC cs.DS math.AT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nervous systems are characterized by neurons displaying a diversity of
morphological shapes. Traditionally, different shapes have been qualitatively
described based on visual inspection and quantitatively described based on
morphometric parameters. Neither process provides a solid foundation for
categorizing the vari... | [
{
"created": "Mon, 28 Mar 2016 16:32:44 GMT",
"version": "v1"
}
] | 2016-03-29 | [
[
"Kanari",
"Lida",
""
],
[
"Dłotko",
"Paweł",
""
],
[
"Scolamiero",
"Martina",
""
],
[
"Levi",
"Ran",
""
],
[
"Shillcock",
"Julian",
""
],
[
"Hess",
"Kathryn",
""
],
[
"Markram",
"Henry",
""
]
] | Nervous systems are characterized by neurons displaying a diversity of morphological shapes. Traditionally, different shapes have been qualitatively described based on visual inspection and quantitatively described based on morphometric parameters. Neither process provides a solid foundation for categorizing the variou... |
1304.5324 | Sergey Dobretsov | Raeid M. M. Abed, Sergey Dobretsov, Marwan Al-Fori, Sarath P.
Gunasekera, Kumar Sudesh and Valerie J. Paul | Quorum sensing inhibitory compounds from extremophilic microorganisms
isolated from a hypersaline cyanobacterial mat | First evidence of production of quorum sensing inhibitors from
hypersaline bacteria. Accepted for publication by Journal Industrial
Microbiology and Biotechnology | null | null | null | q-bio.CB q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this study extremely halophilic and moderately thermophilic microorganisms
from a hypersaline microbial mat were screened for their ability to produce
antibacterial, antidiatom, antialgal and quorum sensing (QS) inhibitory
compounds. Five bacterial strains belonging to the genera Marinobacter and
Halomonas and one... | [
{
"created": "Fri, 19 Apr 2013 06:43:39 GMT",
"version": "v1"
}
] | 2013-04-22 | [
[
"Abed",
"Raeid M. M.",
""
],
[
"Dobretsov",
"Sergey",
""
],
[
"Al-Fori",
"Marwan",
""
],
[
"Gunasekera",
"Sarath P.",
""
],
[
"Sudesh",
"Kumar",
""
],
[
"Paul",
"Valerie J.",
""
]
] | In this study extremely halophilic and moderately thermophilic microorganisms from a hypersaline microbial mat were screened for their ability to produce antibacterial, antidiatom, antialgal and quorum sensing (QS) inhibitory compounds. Five bacterial strains belonging to the genera Marinobacter and Halomonas and one a... |
2104.04457 | Kevin Yang | Zachary Wu, Kadina E. Johnston, Frances H. Arnold, Kevin K. Yang | Protein sequence design with deep generative models | 11 pages, 2 figures | null | 10.1016/j.cbpa.2021.04.004 | null | q-bio.QM cs.LG q-bio.BM stat.ML | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Protein engineering seeks to identify protein sequences with optimized
properties. When guided by machine learning, protein sequence generation
methods can draw on prior knowledge and experimental efforts to improve this
process. In this review, we highlight recent applications of machine learning
to generate protein... | [
{
"created": "Fri, 9 Apr 2021 16:08:15 GMT",
"version": "v1"
}
] | 2021-05-28 | [
[
"Wu",
"Zachary",
""
],
[
"Johnston",
"Kadina E.",
""
],
[
"Arnold",
"Frances H.",
""
],
[
"Yang",
"Kevin K.",
""
]
] | Protein engineering seeks to identify protein sequences with optimized properties. When guided by machine learning, protein sequence generation methods can draw on prior knowledge and experimental efforts to improve this process. In this review, we highlight recent applications of machine learning to generate protein s... |
1801.10144 | Manlio De Domenico | Giuseppe Mangioni, Giuseppe Jurman, Manlio De Domenico | Multilayer flows in molecular networks identify biological modules in
the human proteome | 9 pages, 6 figures | null | null | null | q-bio.MN physics.bio-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A variety of complex systems exhibit different types of relationships
simultaneously that can be modeled by multiplex networks. A typical problem is
to determine the community structure of such systems that, in general, depend
on one or more parameters to be tuned. In this study we propose one measure,
grounded on in... | [
{
"created": "Tue, 30 Jan 2018 18:52:35 GMT",
"version": "v1"
}
] | 2018-01-31 | [
[
"Mangioni",
"Giuseppe",
""
],
[
"Jurman",
"Giuseppe",
""
],
[
"De Domenico",
"Manlio",
""
]
] | A variety of complex systems exhibit different types of relationships simultaneously that can be modeled by multiplex networks. A typical problem is to determine the community structure of such systems that, in general, depend on one or more parameters to be tuned. In this study we propose one measure, grounded on info... |
2005.05653 | Shahaf Armon | S. Armon, M. Moshe, E. Sharon | The Intermittent Nature of Leaf Growth Fields | 20 pages, 4 figures, 4 sections of supplementary material -with one
supplementary figure | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | What are the general principles that allow proper growth of a tissue or an
organ? A growing leaf is an example of such a system: it increases its area by
orders of magnitude, maintaining a proper (usually flat) shape. How can this be
achieved without a central control unit? One would think that a combination of
unifo... | [
{
"created": "Tue, 12 May 2020 10:03:23 GMT",
"version": "v1"
}
] | 2020-05-13 | [
[
"Armon",
"S.",
""
],
[
"Moshe",
"M.",
""
],
[
"Sharon",
"E.",
""
]
] | What are the general principles that allow proper growth of a tissue or an organ? A growing leaf is an example of such a system: it increases its area by orders of magnitude, maintaining a proper (usually flat) shape. How can this be achieved without a central control unit? One would think that a combination of uniform... |
2407.14794 | Toni Giorgino | Antonio Mirarchi, Toni Giorgino, Gianni De Fabritiis | mdCATH: A Large-Scale MD Dataset for Data-Driven Computational
Biophysics | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent advancements in protein structure determination are revolutionizing
our understanding of proteins. Still, a significant gap remains in the
availability of comprehensive datasets that focus on the dynamics of proteins,
which are crucial for understanding protein function, folding, and
interactions. To address t... | [
{
"created": "Sat, 20 Jul 2024 07:48:11 GMT",
"version": "v1"
}
] | 2024-07-23 | [
[
"Mirarchi",
"Antonio",
""
],
[
"Giorgino",
"Toni",
""
],
[
"De Fabritiis",
"Gianni",
""
]
] | Recent advancements in protein structure determination are revolutionizing our understanding of proteins. Still, a significant gap remains in the availability of comprehensive datasets that focus on the dynamics of proteins, which are crucial for understanding protein function, folding, and interactions. To address thi... |
2111.01961 | Eli Shlizerman | Rahul Biswas and Eli Shlizerman | Statistical Perspective on Functional and Causal Neural Connectomics: A
Comparative Study | null | Front. Syst. Neurosci. (2022) | 10.3389/fnsys.2022.817962 | null | q-bio.NC q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Representation of brain network interactions is fundamental to the
translation of neural structure to brain function. As such, methodologies for
mapping neural interactions into structural models, i.e., inference of
functional connectome from neural recordings, are key for the study of brain
networks. While multiple ... | [
{
"created": "Wed, 3 Nov 2021 00:59:33 GMT",
"version": "v1"
}
] | 2022-03-18 | [
[
"Biswas",
"Rahul",
""
],
[
"Shlizerman",
"Eli",
""
]
] | Representation of brain network interactions is fundamental to the translation of neural structure to brain function. As such, methodologies for mapping neural interactions into structural models, i.e., inference of functional connectome from neural recordings, are key for the study of brain networks. While multiple ap... |
1605.07371 | Jan Humplik | Jan Humplik, Ga\v{s}per Tka\v{c}ik | Semiparametric energy-based probabilistic models | 8 pages, 3 figures | null | null | null | q-bio.NC cond-mat.stat-mech stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Probabilistic models can be defined by an energy function, where the
probability of each state is proportional to the exponential of the state's
negative energy. This paper considers a generalization of energy-based models
in which the probability of a state is proportional to an arbitrary positive,
strictly decreasi... | [
{
"created": "Tue, 24 May 2016 10:51:13 GMT",
"version": "v1"
}
] | 2016-05-25 | [
[
"Humplik",
"Jan",
""
],
[
"Tkačik",
"Gašper",
""
]
] | Probabilistic models can be defined by an energy function, where the probability of each state is proportional to the exponential of the state's negative energy. This paper considers a generalization of energy-based models in which the probability of a state is proportional to an arbitrary positive, strictly decreasing... |
1506.06048 | Bhaskar Sen | Bhaskar Sen, Zheng Shi, and Gregory Burlet | Diagnosing ADHD from fMRI Scans Using Hidden Markov Models | null | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper applies a hidden Markov model to the problem of Attention Deficit
Hyperactivity Disorder (ADHD) diagnosis from resting-state functional Magnetic
Resonance Image (fMRI) scans of subjects. The proposed model considers the
temporal evolution of fMRI voxel activations in the cortex, cingulate gyrus,
and thalam... | [
{
"created": "Fri, 19 Jun 2015 15:19:35 GMT",
"version": "v1"
}
] | 2015-06-22 | [
[
"Sen",
"Bhaskar",
""
],
[
"Shi",
"Zheng",
""
],
[
"Burlet",
"Gregory",
""
]
] | This paper applies a hidden Markov model to the problem of Attention Deficit Hyperactivity Disorder (ADHD) diagnosis from resting-state functional Magnetic Resonance Image (fMRI) scans of subjects. The proposed model considers the temporal evolution of fMRI voxel activations in the cortex, cingulate gyrus, and thalamus... |
2008.00126 | Jacques Demongeot | Jacques Demongeot, Herv\'e Seligmann | SARS-CoV-2 and miRNA-like inhibition power | 14 pages, 12 figures | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | (1) Background: RNA viruses and especially coronaviruses could act inside
host cells not only by building their own proteins, but also by perturbing the
cell metabolism. We show the possibility of miRNA-like inhibitions by the
SARS-CoV-2 concerning for example the hemoglobin and type I interferons
syntheses, hence hi... | [
{
"created": "Fri, 31 Jul 2020 23:56:03 GMT",
"version": "v1"
}
] | 2020-08-04 | [
[
"Demongeot",
"Jacques",
""
],
[
"Seligmann",
"Hervé",
""
]
] | (1) Background: RNA viruses and especially coronaviruses could act inside host cells not only by building their own proteins, but also by perturbing the cell metabolism. We show the possibility of miRNA-like inhibitions by the SARS-CoV-2 concerning for example the hemoglobin and type I interferons syntheses, hence high... |
1611.09149 | Hendrik Richter | Hendrik Richter | Dynamic landscape models of coevolutionary games | arXiv admin note: substantial text overlap with arXiv:1603.06374 | BioSystems 153-154, 26-44, 2017 | null | null | q-bio.PE cs.NE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Players of coevolutionary games may update not only their strategies but also
their networks of interaction. Based on interpreting the payoff of players as
fitness, dynamic landscape models are proposed. The modeling procedure is
carried out for Prisoner's Dilemma (PD) and Snowdrift (SD) games that both use
either bi... | [
{
"created": "Mon, 28 Nov 2016 14:55:50 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Mar 2017 12:50:04 GMT",
"version": "v2"
}
] | 2017-03-16 | [
[
"Richter",
"Hendrik",
""
]
] | Players of coevolutionary games may update not only their strategies but also their networks of interaction. Based on interpreting the payoff of players as fitness, dynamic landscape models are proposed. The modeling procedure is carried out for Prisoner's Dilemma (PD) and Snowdrift (SD) games that both use either birt... |
q-bio/0502010 | Karen Luz Burgoa K. Luz-Burgoa | K. Luz-Burgoa, Tony Dell and Toshinori Okuyama | Sympatric Speciation in a Simple Food Web | Contribution to the Proceedings of the Complex Systems Summer School
2004, organized by the Santa Fe Institute (9 pages and 6 figures) | null | null | null | q-bio.PE | null | Observations of the evolution of species groups in nature, such as well
recognized Galapagos finches, have motivated much theoretical research aimed at
understanding the processes associated with such radiations. The Penna model is
one such model and has been widely used to study aging. In this paper we use
the basic... | [
{
"created": "Fri, 11 Feb 2005 20:39:47 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Luz-Burgoa",
"K.",
""
],
[
"Dell",
"Tony",
""
],
[
"Okuyama",
"Toshinori",
""
]
] | Observations of the evolution of species groups in nature, such as well recognized Galapagos finches, have motivated much theoretical research aimed at understanding the processes associated with such radiations. The Penna model is one such model and has been widely used to study aging. In this paper we use the basic P... |
2005.08701 | Taegeun Song | Woo Seok Lee, Junghyo Jo, and Taegeun Song | Machine learning for the diagnosis of early stage diabetes using
temporal glucose profiles | 4 pages, 2 figure | null | 10.1007/s40042-021-00056-8 | null | q-bio.QM cs.LG eess.SP stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Machine learning shows remarkable success for recognizing patterns in data.
Here we apply the machine learning (ML) for the diagnosis of early stage
diabetes, which is known as a challenging task in medicine. Blood glucose
levels are tightly regulated by two counter-regulatory hormones, insulin and
glucagon, and the ... | [
{
"created": "Mon, 18 May 2020 13:31:12 GMT",
"version": "v1"
}
] | 2021-02-24 | [
[
"Lee",
"Woo Seok",
""
],
[
"Jo",
"Junghyo",
""
],
[
"Song",
"Taegeun",
""
]
] | Machine learning shows remarkable success for recognizing patterns in data. Here we apply the machine learning (ML) for the diagnosis of early stage diabetes, which is known as a challenging task in medicine. Blood glucose levels are tightly regulated by two counter-regulatory hormones, insulin and glucagon, and the fa... |
1206.4862 | Matjaz Perc | Daqing Guo, Qingyun Wang, Matjaz Perc | Complex synchronous behavior in interneuronal networks with delayed
inhibitory and fast electrical synapses | 8 two-column pages, 7 figures; accepted for publication in Physical
Review E | Phys. Rev. E 85 (2012) 061905 | 10.1103/PhysRevE.85.061905 | null | q-bio.NC nlin.PS physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Networks of fast-spiking interneurons are crucial for the generation of
neural oscillations in the brain. Here we study the synchronous behavior of
interneuronal networks that are coupled by delayed inhibitory and fast
electrical synapses. We find that both coupling modes play a crucial role by
the synchronization of... | [
{
"created": "Thu, 21 Jun 2012 13:08:32 GMT",
"version": "v1"
}
] | 2012-06-22 | [
[
"Guo",
"Daqing",
""
],
[
"Wang",
"Qingyun",
""
],
[
"Perc",
"Matjaz",
""
]
] | Networks of fast-spiking interneurons are crucial for the generation of neural oscillations in the brain. Here we study the synchronous behavior of interneuronal networks that are coupled by delayed inhibitory and fast electrical synapses. We find that both coupling modes play a crucial role by the synchronization of t... |
1507.01731 | Kumar Sankar Ray | Kumar Sankar Ray and Mandrita Mondal | Prediction of Radiation Fog by DNA Computing | 36 pages | null | null | null | q-bio.BM cs.AI cs.ET | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we propose a wet lab algorithm for prediction of radiation fog
by DNA computing. The concept of DNA computing is essentially exploited for
generating the classifier algorithm in the wet lab. The classifier is based on
a new concept of similarity based fuzzy reasoning suitable for wet lab
implementation.... | [
{
"created": "Tue, 7 Jul 2015 09:57:44 GMT",
"version": "v1"
}
] | 2015-07-08 | [
[
"Ray",
"Kumar Sankar",
""
],
[
"Mondal",
"Mandrita",
""
]
] | In this paper we propose a wet lab algorithm for prediction of radiation fog by DNA computing. The concept of DNA computing is essentially exploited for generating the classifier algorithm in the wet lab. The classifier is based on a new concept of similarity based fuzzy reasoning suitable for wet lab implementation. T... |
1304.1072 | Matthew Seetin | Matthew G. Seetin, Wipapat Kladwang, J. P. Bida, and Rhiju Das | Massively Parallel RNA Chemical Mapping with a Reduced Bias MAP-seq
Protocol | 22 pages, 5 figures | null | null | null | q-bio.BM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chemical mapping methods probe RNA structure by revealing and leveraging
correlations of a nucleotide's structural accessibility or flexibility with its
reactivity to various chemical probes. Pioneering work by Lucks and colleagues
has expanded this method to probe hundreds of molecules at once on an Illumina
sequenc... | [
{
"created": "Wed, 3 Apr 2013 19:53:19 GMT",
"version": "v1"
}
] | 2013-04-04 | [
[
"Seetin",
"Matthew G.",
""
],
[
"Kladwang",
"Wipapat",
""
],
[
"Bida",
"J. P.",
""
],
[
"Das",
"Rhiju",
""
]
] | Chemical mapping methods probe RNA structure by revealing and leveraging correlations of a nucleotide's structural accessibility or flexibility with its reactivity to various chemical probes. Pioneering work by Lucks and colleagues has expanded this method to probe hundreds of molecules at once on an Illumina sequencin... |
1509.03775 | Ronald Vale | Ronald D. Vale | Accelerating Scientific Publication in Biology | 39 pages, 6 figures, 1 table, and a Q&A related to pre-prints | null | 10.1073/pnas.1511912112 | null | q-bio.OT cs.DL | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Scientific publications enable results and ideas to be transmitted throughout
the scientific community. The number and type of journal publications also have
become the primary criteria used in evaluating career advancement. Our analysis
suggests that publication practices have changed considerably in the life
scienc... | [
{
"created": "Sat, 12 Sep 2015 20:11:21 GMT",
"version": "v1"
}
] | 2016-04-27 | [
[
"Vale",
"Ronald D.",
""
]
] | Scientific publications enable results and ideas to be transmitted throughout the scientific community. The number and type of journal publications also have become the primary criteria used in evaluating career advancement. Our analysis suggests that publication practices have changed considerably in the life sciences... |
1612.04049 | Coralie Fritsch | Coralie Fritsch (IECL, CMAP, TOSCA), Fabien Campillo (MATHNEURO), Otso
Ovaskainen | A numerical approach to determine mutant invasion fitness and
evolutionary singular strategies | null | Theoretical Population Biology, Elsevier, 2017, 115 | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a numerical approach to study the invasion fitness of a mutant and
to determine evolutionary singular strategies in evolutionary structured models
in which the competitive exclusion principle holds. Our approach is based on a
dual representation, which consists of the modelling of the small size mutant
pop... | [
{
"created": "Tue, 13 Dec 2016 07:41:25 GMT",
"version": "v1"
},
{
"created": "Tue, 23 May 2017 13:49:18 GMT",
"version": "v2"
}
] | 2017-05-24 | [
[
"Fritsch",
"Coralie",
"",
"IECL, CMAP, TOSCA"
],
[
"Campillo",
"Fabien",
"",
"MATHNEURO"
],
[
"Ovaskainen",
"Otso",
""
]
] | We propose a numerical approach to study the invasion fitness of a mutant and to determine evolutionary singular strategies in evolutionary structured models in which the competitive exclusion principle holds. Our approach is based on a dual representation, which consists of the modelling of the small size mutant popul... |
0706.2383 | Jason Locasale W | Jason W. Locasale | Allovalency revisited: an analysis of multisite phosphorylation and
substrate rebinding | 44 pages, 5 figures; accepted Journal of Chemical Physics | null | 10.1063/1.2841124 | null | q-bio.SC q-bio.MN | null | The utilization of multiple phosphorylation sites in regulating a biological
response is ubiquitous in cell signaling. If each site contributes an
additional, equivalent binding site, then one consequence of an increase in the
number of phosphorylations may be to increase the probability that, upon
disassociation, a ... | [
{
"created": "Fri, 15 Jun 2007 22:49:09 GMT",
"version": "v1"
},
{
"created": "Tue, 19 Jun 2007 13:14:07 GMT",
"version": "v2"
},
{
"created": "Mon, 25 Jun 2007 17:35:08 GMT",
"version": "v3"
},
{
"created": "Wed, 9 Jan 2008 22:17:27 GMT",
"version": "v4"
}
] | 2009-11-13 | [
[
"Locasale",
"Jason W.",
""
]
] | The utilization of multiple phosphorylation sites in regulating a biological response is ubiquitous in cell signaling. If each site contributes an additional, equivalent binding site, then one consequence of an increase in the number of phosphorylations may be to increase the probability that, upon disassociation, a li... |
1302.6771 | Su-Chan Park | Su-Chan Park and Joachim Krug | Rate of adaptation in sexuals and asexuals: A solvable model of the
Fisher-Muller effect | Title has been changed. Supporting Information (animation) can be
found in the source file. 53 pages. 10 figures. To appear in Genetics | null | null | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The adaptation of large asexual populations is hampered by the competition
between independently arising beneficial mutations in different individuals,
which is known as clonal interference. Fisher and Muller proposed that
recombination provides an evolutionary advantage in large populations by
alleviating this compe... | [
{
"created": "Wed, 27 Feb 2013 13:54:21 GMT",
"version": "v1"
},
{
"created": "Thu, 15 Aug 2013 15:31:51 GMT",
"version": "v2"
}
] | 2013-08-16 | [
[
"Park",
"Su-Chan",
""
],
[
"Krug",
"Joachim",
""
]
] | The adaptation of large asexual populations is hampered by the competition between independently arising beneficial mutations in different individuals, which is known as clonal interference. Fisher and Muller proposed that recombination provides an evolutionary advantage in large populations by alleviating this competi... |
1307.0451 | Valentina Agoni | Valentina Agoni | Insights Into Quantitative Biology: analysis of cellular adaptation | 8 pages, 3 figures | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the last years many powerful techniques have emerged to measure protein
interactions as well as gene expression. Many progresses have been done since
the introduction of these techniques but not toward quantitative analysis of
data. In this paper we show how to study cellular adaptation and how to detect
cellular ... | [
{
"created": "Mon, 1 Jul 2013 17:52:37 GMT",
"version": "v1"
}
] | 2013-07-02 | [
[
"Agoni",
"Valentina",
""
]
] | In the last years many powerful techniques have emerged to measure protein interactions as well as gene expression. Many progresses have been done since the introduction of these techniques but not toward quantitative analysis of data. In this paper we show how to study cellular adaptation and how to detect cellular su... |
1608.05665 | Danielle Bassett | Danielle S. Bassett and Edward T. Bullmore | Small-World Brain Networks Revisited | 13 pages, 8 figures in The Neuroscientist, 2016 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is nearly 20 years since the concept of a small-world network was first
quantitatively defined, by a combination of high clustering and short path
length; and about 10 years since this metric of complex network topology began
to be widely applied to analysis of neuroimaging and other neuroscience data as
part of t... | [
{
"created": "Fri, 19 Aug 2016 16:34:24 GMT",
"version": "v1"
}
] | 2016-08-22 | [
[
"Bassett",
"Danielle S.",
""
],
[
"Bullmore",
"Edward T.",
""
]
] | It is nearly 20 years since the concept of a small-world network was first quantitatively defined, by a combination of high clustering and short path length; and about 10 years since this metric of complex network topology began to be widely applied to analysis of neuroimaging and other neuroscience data as part of the... |
q-bio/0406013 | G\'abor Cs\'anyi | Bal\'azs Szendr\"oi, G\'abor Cs\'anyi | Polynomial epidemics and clustering in contact networks | null | null | null | null | q-bio.PE | null | It is widely known that the spread of the HIV virus was slower than
exponential in several populations, even at the very beginning of the epidemic.
We show that this implies a significant reduction in the effective reproductive
rate of the epidemic, and describe a general mechanism, related to the
clustering properti... | [
{
"created": "Fri, 4 Jun 2004 21:12:53 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Szendröi",
"Balázs",
""
],
[
"Csányi",
"Gábor",
""
]
] | It is widely known that the spread of the HIV virus was slower than exponential in several populations, even at the very beginning of the epidemic. We show that this implies a significant reduction in the effective reproductive rate of the epidemic, and describe a general mechanism, related to the clustering properties... |
2207.04487 | Steven Frank | Steven A. Frank | Automatic differentiation and the optimization of differential equation
models in biology | null | null | 10.3389/fevo.2022.1010278 | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | A computational revolution unleashed the power of artificial neural networks.
At the heart of that revolution is automatic differentiation, which calculates
the derivative of a performance measure relative to a large number of
parameters. Differentiation enhances the discovery of improved performance in
large models,... | [
{
"created": "Sun, 10 Jul 2022 15:27:26 GMT",
"version": "v1"
},
{
"created": "Tue, 11 Oct 2022 14:54:56 GMT",
"version": "v2"
}
] | 2023-12-27 | [
[
"Frank",
"Steven A.",
""
]
] | A computational revolution unleashed the power of artificial neural networks. At the heart of that revolution is automatic differentiation, which calculates the derivative of a performance measure relative to a large number of parameters. Differentiation enhances the discovery of improved performance in large models, a... |
1210.7164 | Roeland M.H. Merks | Margriet M. Palm and Roeland M. H. Merks | Vascular networks due to dynamically arrested crystalline ordering of
elongated cells | 11 pages, 4 figures. Published as: Palm and Merks (2013) Physical
Review E 87, 012725. The present version includes a correction in the
calculation of the nematic order parameter. Erratum submitted to PRE on Jun
5th 2013. The correction does not affect the conclusions | Physical Review E 87, 012725 (2013) | 10.1103/PhysRevE.87.012725 | null | q-bio.CB cond-mat.soft physics.bio-ph q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent experimental and theoretical studies suggest that crystallization and
glass-like solidification are useful analogies for understanding cell ordering
in confluent biological tissues. It remains unexplored how cellular ordering
contributes to pattern formation during morphogenesis. With a computational
model we ... | [
{
"created": "Fri, 26 Oct 2012 15:08:36 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Jan 2013 21:19:01 GMT",
"version": "v2"
},
{
"created": "Wed, 5 Jun 2013 13:21:12 GMT",
"version": "v3"
}
] | 2015-03-13 | [
[
"Palm",
"Margriet M.",
""
],
[
"Merks",
"Roeland M. H.",
""
]
] | Recent experimental and theoretical studies suggest that crystallization and glass-like solidification are useful analogies for understanding cell ordering in confluent biological tissues. It remains unexplored how cellular ordering contributes to pattern formation during morphogenesis. With a computational model we sh... |
2010.07897 | James Zou | James Zou, Aubrey Johnson, Jeanelle France, Srinidhi Bharadwaj, Zeljko
Tomljanovic, Yaakov Stern, Adam M. Brickman, Devangere P. Devanand, Jose A.
Luchsinger, William C. Kreisl, and Frank A. Provenzano | Spatial Registration Evaluation of [18F]-MK6240 PET | 19 pages, 8 Figures, 4 Tables | null | null | null | q-bio.QM eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Image registration is an important preprocessing step in neuroimaging which
allows for the matching of anatomical and functional information between
modalities and subjects. This can be challenging if there are gross differences
in image geometry or in signal intensity, such as in the case of some molecular
PET radio... | [
{
"created": "Thu, 15 Oct 2020 17:21:59 GMT",
"version": "v1"
}
] | 2020-10-16 | [
[
"Zou",
"James",
""
],
[
"Johnson",
"Aubrey",
""
],
[
"France",
"Jeanelle",
""
],
[
"Bharadwaj",
"Srinidhi",
""
],
[
"Tomljanovic",
"Zeljko",
""
],
[
"Stern",
"Yaakov",
""
],
[
"Brickman",
"Adam M.",
""
],... | Image registration is an important preprocessing step in neuroimaging which allows for the matching of anatomical and functional information between modalities and subjects. This can be challenging if there are gross differences in image geometry or in signal intensity, such as in the case of some molecular PET radioli... |
1808.07850 | Jorge F. Mejias | R. R. Deza, J. I. Deza, N. Martinez, J. F. Mejias, H. S. Wio | A nonequilibrium-potential approach to competition in neural populations | 16 pages, 3 figures | null | null | null | q-bio.NC cond-mat.stat-mech | http://creativecommons.org/licenses/by/4.0/ | Energy landscapes are a useful aid for the understanding of dynamical
systems, and a valuable tool for their analysis. For a broad class of rate
models of neural networks, we derive a global Lyapunov function which provides
an energy landscape without any symmetry constraint. This newly obtained
`nonequilibrium poten... | [
{
"created": "Thu, 23 Aug 2018 17:18:53 GMT",
"version": "v1"
}
] | 2018-08-24 | [
[
"Deza",
"R. R.",
""
],
[
"Deza",
"J. I.",
""
],
[
"Martinez",
"N.",
""
],
[
"Mejias",
"J. F.",
""
],
[
"Wio",
"H. S.",
""
]
] | Energy landscapes are a useful aid for the understanding of dynamical systems, and a valuable tool for their analysis. For a broad class of rate models of neural networks, we derive a global Lyapunov function which provides an energy landscape without any symmetry constraint. This newly obtained `nonequilibrium potenti... |
2402.17650 | Mohammad Ghalavand | Mohammad Ghalavand, Javad Hatami, Seyed Kamaledin Setarehdan, Fatimah
Nosrati, Hananeh Ghalavand, Ali Nikhalat-Jahromi | Comparison of the Effects of Interaction with Intentional Agent and
Artificial Intelligence using fNIRS | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | As societal interactions increasingly involve both intentional and
unintentional agents, understanding their effects on human cognition becomes
paramount. This study investigates the neural correlates of interacting with
intentional versus artificial agents in a simulated tennis game scenario.
Employing functional ne... | [
{
"created": "Tue, 27 Feb 2024 16:20:46 GMT",
"version": "v1"
},
{
"created": "Tue, 4 Jun 2024 07:31:10 GMT",
"version": "v2"
}
] | 2024-06-05 | [
[
"Ghalavand",
"Mohammad",
""
],
[
"Hatami",
"Javad",
""
],
[
"Setarehdan",
"Seyed Kamaledin",
""
],
[
"Nosrati",
"Fatimah",
""
],
[
"Ghalavand",
"Hananeh",
""
],
[
"Nikhalat-Jahromi",
"Ali",
""
]
] | As societal interactions increasingly involve both intentional and unintentional agents, understanding their effects on human cognition becomes paramount. This study investigates the neural correlates of interacting with intentional versus artificial agents in a simulated tennis game scenario. Employing functional near... |
1506.02321 | Ildefonso De la Fuente M | Ildefonso M. De la Fuente, Iker Malaina, Alberto Perez-Samartin, Jesus
M. Cortes, Asier Erramuzpe, Maria Dolores Boyano, Carlos Bringas, Maria
Fedetz and Luis Martinez | Information and long term memory in calcium signals | 35 pages and 7 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Unicellular organisms are open metabolic systems that need to process
information about their external environment in order to survive. In most types
of tissues and organisms, cells use calcium signaling to carry information from
the extracellular side of the plasma membrane to the different metabolic
targets of thei... | [
{
"created": "Sun, 7 Jun 2015 22:56:24 GMT",
"version": "v1"
}
] | 2015-06-09 | [
[
"De la Fuente",
"Ildefonso M.",
""
],
[
"Malaina",
"Iker",
""
],
[
"Perez-Samartin",
"Alberto",
""
],
[
"Cortes",
"Jesus M.",
""
],
[
"Erramuzpe",
"Asier",
""
],
[
"Boyano",
"Maria Dolores",
""
],
[
"Bringas",
... | Unicellular organisms are open metabolic systems that need to process information about their external environment in order to survive. In most types of tissues and organisms, cells use calcium signaling to carry information from the extracellular side of the plasma membrane to the different metabolic targets of their ... |
1604.08134 | M. D. Betterton | Zachary Gergely, Ammon Crapo, Loren E. Hough, J. Richard McIntosh,
Meredith D. Betterton | Kinesin-8 effects on mitotic microtubule dynamics contribute to spindle
function in fission yeast | Accepted by Molecular Biology of the Cell | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Kinesin-8 motor proteins destabilize microtubules. Their absence during cell
division is associated with disorganized mitotic chromosome movements and
chromosome loss. Despite recent work studying effects of kinesin 8s on
microtubule dynamics, it remains unclear whether the kinesin-8 mitotic
phenotypes are consequenc... | [
{
"created": "Wed, 27 Apr 2016 16:33:14 GMT",
"version": "v1"
}
] | 2016-04-28 | [
[
"Gergely",
"Zachary",
""
],
[
"Crapo",
"Ammon",
""
],
[
"Hough",
"Loren E.",
""
],
[
"McIntosh",
"J. Richard",
""
],
[
"Betterton",
"Meredith D.",
""
]
] | Kinesin-8 motor proteins destabilize microtubules. Their absence during cell division is associated with disorganized mitotic chromosome movements and chromosome loss. Despite recent work studying effects of kinesin 8s on microtubule dynamics, it remains unclear whether the kinesin-8 mitotic phenotypes are consequences... |
1202.4868 | Pascal Szacherski | Pierre Grangeat (LE2S), Pascal Szacherski (LE2S, IMS), Laurent
Gerfault (LE2S), Jean-Fran\c{c}ois Giovannelli (IMS) | Bayesian hierarchical reconstruction of protein profiles including a
digestion model | pr\'esentation orale; 59th American Society for Mass Spectrometry
Conference, Dallas : France (2011) | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Introduction : Mass spectrometry approaches are very attractive to detect
protein panels in a sensitive and high speed way. MS can be coupled to many
proteomic separation techniques. However, controlling technological variability
on these analytical chains is a critical point. Adequate information processing
is manda... | [
{
"created": "Wed, 22 Feb 2012 09:49:22 GMT",
"version": "v1"
}
] | 2012-02-23 | [
[
"Grangeat",
"Pierre",
"",
"LE2S"
],
[
"Szacherski",
"Pascal",
"",
"LE2S, IMS"
],
[
"Gerfault",
"Laurent",
"",
"LE2S"
],
[
"Giovannelli",
"Jean-François",
"",
"IMS"
]
] | Introduction : Mass spectrometry approaches are very attractive to detect protein panels in a sensitive and high speed way. MS can be coupled to many proteomic separation techniques. However, controlling technological variability on these analytical chains is a critical point. Adequate information processing is mandato... |
1310.0479 | Ranjeetha Bharath | Ranjeetha Bharath and Jean-Jacques Slotine | Nonlinear Observer Design and Synchronization Analysis for Classical
Models of Neural Oscillators | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This work explores four nonlinear classical models of neural oscillators, the
Hodgkin-Huxley model, the Fitzhugh-Nagumo model, the Morris-Lecar model, and
the Hindmarsh-Rose model. Nonlinear contraction theory is used to develop
observers and perform synchronization analysis on these systems. Neural
oscillation and s... | [
{
"created": "Tue, 1 Oct 2013 20:20:13 GMT",
"version": "v1"
}
] | 2013-10-03 | [
[
"Bharath",
"Ranjeetha",
""
],
[
"Slotine",
"Jean-Jacques",
""
]
] | This work explores four nonlinear classical models of neural oscillators, the Hodgkin-Huxley model, the Fitzhugh-Nagumo model, the Morris-Lecar model, and the Hindmarsh-Rose model. Nonlinear contraction theory is used to develop observers and perform synchronization analysis on these systems. Neural oscillation and sig... |
0808.4014 | Aaron Clauset | Aaron Clauset and Sidney Redner | Evolutionary Model of Species Body Mass Diversification | 4 pages, 4 figures | Phys. Rev. Lett. 102, 038103 (2009) | 10.1103/PhysRevLett.102.038103 | null | q-bio.PE physics.bio-ph physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a quantitative model for the biological evolution of species body
masses within large groups of related species, e.g., terrestrial mammals, in
which body mass M evolves according to branching (speciation), multiplicative
diffusion, and an extinction probability that increases logarithmically with
mass. We ... | [
{
"created": "Fri, 29 Aug 2008 01:37:04 GMT",
"version": "v1"
},
{
"created": "Thu, 22 Jan 2009 16:42:14 GMT",
"version": "v2"
}
] | 2009-01-22 | [
[
"Clauset",
"Aaron",
""
],
[
"Redner",
"Sidney",
""
]
] | We present a quantitative model for the biological evolution of species body masses within large groups of related species, e.g., terrestrial mammals, in which body mass M evolves according to branching (speciation), multiplicative diffusion, and an extinction probability that increases logarithmically with mass. We de... |
2303.01444 | Hector Zenil | Hector Zenil, Francisco Hern\'andez-Quiroz, Santiago
Hern\'andez-Orozco, Abicumaran Uthamacumaran and Kourosh Saeb-Parsy | An Adaptive Computational Intelligence Approach to Personalised Health
and Immune Age Characterisation from Common Haematological Markers | 30 pages + appendix | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a simulated digital model that learns a person's optimal blood
health over time. Using a learning adaptive algorithm, our model provides a
risk assessment score that compares an individual's chronological age from
birth to an estimation of a biological immune age derived from the score. We
demonstrate it... | [
{
"created": "Thu, 2 Mar 2023 18:03:03 GMT",
"version": "v1"
},
{
"created": "Fri, 15 Sep 2023 21:34:24 GMT",
"version": "v2"
},
{
"created": "Thu, 16 Nov 2023 16:14:39 GMT",
"version": "v3"
},
{
"created": "Thu, 14 Mar 2024 00:36:53 GMT",
"version": "v4"
},
{
"cr... | 2024-03-21 | [
[
"Zenil",
"Hector",
""
],
[
"Hernández-Quiroz",
"Francisco",
""
],
[
"Hernández-Orozco",
"Santiago",
""
],
[
"Uthamacumaran",
"Abicumaran",
""
],
[
"Saeb-Parsy",
"Kourosh",
""
]
] | We introduce a simulated digital model that learns a person's optimal blood health over time. Using a learning adaptive algorithm, our model provides a risk assessment score that compares an individual's chronological age from birth to an estimation of a biological immune age derived from the score. We demonstrate its ... |
1001.4845 | Sitabhra Sinha | Sitabhra Sinha, T Jesan and Nivedita Chatterjee | Systems biology: From the cell to the brain | 6 pages, 5 figures | Current Trends in Science: Platinum Jubilee Special (Ed. N
Mukunda), Bangalore: Indian Academy of Sciences, 2009, pp 199-205 | null | null | q-bio.MN physics.bio-ph q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | With the completion of human genome mapping, the focus of scientists seeking
to explain the biological complexity of living systems is shifting from
analyzing the individual components (such as a particular gene or biochemical
reaction) to understanding the set of interactions amongst the large number of
components t... | [
{
"created": "Wed, 27 Jan 2010 03:35:20 GMT",
"version": "v1"
}
] | 2010-01-28 | [
[
"Sinha",
"Sitabhra",
""
],
[
"Jesan",
"T",
""
],
[
"Chatterjee",
"Nivedita",
""
]
] | With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to understanding the set of interactions amongst the large number of components tha... |
1611.04030 | Konstantin Blyuss | N. Sherborne, J.C. Miller, K.B. Blyuss, I.Z. Kiss | Mean-field models for non-Markovian epidemics on networks: from
edge-based compartmental to pairwise models | 24 pages, 4 figures, submitted | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper presents a novel extension of the edge-based compartmental model
for epidemics with arbitrary distributions of transmission and recovery times.
Using the message passing approach we also derive a new pairwise-like model for
epidemics with Markovian transmission and an arbitrary recovery period. The new
pai... | [
{
"created": "Sat, 12 Nov 2016 18:13:32 GMT",
"version": "v1"
}
] | 2016-11-15 | [
[
"Sherborne",
"N.",
""
],
[
"Miller",
"J. C.",
""
],
[
"Blyuss",
"K. B.",
""
],
[
"Kiss",
"I. Z.",
""
]
] | This paper presents a novel extension of the edge-based compartmental model for epidemics with arbitrary distributions of transmission and recovery times. Using the message passing approach we also derive a new pairwise-like model for epidemics with Markovian transmission and an arbitrary recovery period. The new pairw... |
2001.06881 | Maurizio De Pitt\`a | Maurizio De Pitt\`a | Neuron-Glial Interactions | 43 pages, 2 figures, 1 table. Accepted for publication in the
"Encyclopedia of Computational Neuroscience," D. Jaeger and R. Jung eds.,
Springer-Verlag New York, 2020 (2nd edition) | null | 10.1007/978-1-4614-7320-6_100691-1 | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Although lagging behind classical computational neuroscience, theoretical and
computational approaches are beginning to emerge to characterize different
aspects of neuron-glial interactions. This chapter aims to provide essential
knowledge on neuron-glial interactions in the mammalian brain, leveraging on
computation... | [
{
"created": "Sun, 19 Jan 2020 18:30:07 GMT",
"version": "v1"
}
] | 2021-03-10 | [
[
"De Pittà",
"Maurizio",
""
]
] | Although lagging behind classical computational neuroscience, theoretical and computational approaches are beginning to emerge to characterize different aspects of neuron-glial interactions. This chapter aims to provide essential knowledge on neuron-glial interactions in the mammalian brain, leveraging on computational... |
2008.07054 | Kevin Maurin | K\'evin J. L. Maurin | An empirical guide for producing a dated phylogeny with treePL in a
maximum likelihood framework | 11 pages, 3 figures, supplementary material available at
https://doi.org/10.5281/zenodo.3989030 | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | treePL uses a penalised likelihood approach to produce a dated phylogeny in a
maximum likelihood framework. Since its publication in 2012, few resources have
been developed to explain how to use it properly. In this guide, I provide a
step-by-step protocol for producing a dated phylogeny using treePL, based on my
exp... | [
{
"created": "Mon, 17 Aug 2020 01:42:19 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Aug 2020 08:25:52 GMT",
"version": "v2"
}
] | 2020-08-19 | [
[
"Maurin",
"Kévin J. L.",
""
]
] | treePL uses a penalised likelihood approach to produce a dated phylogeny in a maximum likelihood framework. Since its publication in 2012, few resources have been developed to explain how to use it properly. In this guide, I provide a step-by-step protocol for producing a dated phylogeny using treePL, based on my exper... |
q-bio/0702050 | John Rhodes | Elizabeth S. Allman, John A. Rhodes | Identifying evolutionary trees and substitution parameters for the
general Markov model with invariable sites | null | null | null | null | q-bio.PE math.AG math.ST stat.TH | null | The general Markov plus invariable sites (GM+I) model of biological sequence
evolution is a two-class model in which an unknown proportion of sites are not
allowed to change, while the remainder undergo substitutions according to a
Markov process on a tree. For statistical use it is important to know if the
model is ... | [
{
"created": "Fri, 23 Feb 2007 23:08:32 GMT",
"version": "v1"
}
] | 2011-11-10 | [
[
"Allman",
"Elizabeth S.",
""
],
[
"Rhodes",
"John A.",
""
]
] | The general Markov plus invariable sites (GM+I) model of biological sequence evolution is a two-class model in which an unknown proportion of sites are not allowed to change, while the remainder undergo substitutions according to a Markov process on a tree. For statistical use it is important to know if the model is id... |
2212.13543 | Sebastian Lobentanzer | Sebastian Lobentanzer, Patrick Aloy, Jan Baumbach, Balazs Bohar,
Pornpimol Charoentong, Katharina Danhauser, Tunca Do\u{g}an, Johann Dreo, Ian
Dunham, Adri\`a Fernandez-Torras, Benjamin M. Gyori, Michael Hartung, Charles
Tapley Hoyt, Christoph Klein, Tamas Korcsmaros, Andreas Maier, Matthias Mann,
David Ochoa, ... | Democratising Knowledge Representation with BioCypher | 34 pages, 6 figures; submitted to Nature Biotechnology | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Standardising the representation of biomedical knowledge among all
researchers is an insurmountable task, hindering the effectiveness of many
computational methods. To facilitate harmonisation and interoperability despite
this fundamental challenge, we propose to standardise the framework of
knowledge graph creation ... | [
{
"created": "Tue, 27 Dec 2022 16:29:52 GMT",
"version": "v1"
},
{
"created": "Wed, 11 Jan 2023 12:10:09 GMT",
"version": "v2"
},
{
"created": "Tue, 17 Jan 2023 17:08:25 GMT",
"version": "v3"
}
] | 2023-01-18 | [
[
"Lobentanzer",
"Sebastian",
""
],
[
"Aloy",
"Patrick",
""
],
[
"Baumbach",
"Jan",
""
],
[
"Bohar",
"Balazs",
""
],
[
"Charoentong",
"Pornpimol",
""
],
[
"Danhauser",
"Katharina",
""
],
[
"Doğan",
"Tunca",
"... | Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation in... |
1501.02847 | Peter Wilton R | Peter R. Wilton, Shai Carmi, Asger Hobolth | The SMC' is a highly accurate approximation to the ancestral
recombination graph | Revised manuscript | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Two sequentially Markov coalescent models (SMC and SMC') are available as
tractable approximations to the ancestral recombination graph (ARG). We present
a Markov process describing coalescence at two fixed points along a pair of
sequences evolving under the SMC'. Using our Markov process, we derive a number
of new q... | [
{
"created": "Mon, 12 Jan 2015 23:09:09 GMT",
"version": "v1"
},
{
"created": "Wed, 4 Mar 2015 22:05:40 GMT",
"version": "v2"
}
] | 2015-03-06 | [
[
"Wilton",
"Peter R.",
""
],
[
"Carmi",
"Shai",
""
],
[
"Hobolth",
"Asger",
""
]
] | Two sequentially Markov coalescent models (SMC and SMC') are available as tractable approximations to the ancestral recombination graph (ARG). We present a Markov process describing coalescence at two fixed points along a pair of sequences evolving under the SMC'. Using our Markov process, we derive a number of new qua... |
0812.0256 | Steffen Waldherr | Steffen Waldherr and Frank Allg\"ower | Searching bifurcations in high-dimensional parameter space via a
feedback loop breaking approach | 25 pages, 2 tables, 4 figures | International Journal of Systems Science 40:769-782, 2009 | 10.1080/00207720902957269 | null | q-bio.MN math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bifurcations leading to complex dynamical behaviour of non-linear systems are
often encountered when the characteristics of feedback circuits in the system
are varied. In systems with many unknown or varying parameters, it is an
interesting, but difficult problem to find parameter values for which specific
bifurcatio... | [
{
"created": "Mon, 1 Dec 2008 10:46:58 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Sep 2010 13:40:54 GMT",
"version": "v2"
}
] | 2010-09-23 | [
[
"Waldherr",
"Steffen",
""
],
[
"Allgöwer",
"Frank",
""
]
] | Bifurcations leading to complex dynamical behaviour of non-linear systems are often encountered when the characteristics of feedback circuits in the system are varied. In systems with many unknown or varying parameters, it is an interesting, but difficult problem to find parameter values for which specific bifurcations... |
1711.02791 | Grzegorz A Rempala | Hye-Won Kang, Wasiur R. KhudaBukhsh, Heinz Koeppl and Grzegorz A.
Rempa{\l}a | Quasi-steady-state approximations derived from the stochastic model of
enzyme kinetics | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we derive several quasi steady-state approximations (QSSAs) to
the stochastic reaction network describing the Michaelis-Menten enzyme
kinetics. We show how the different assumptions about chemical species
abundance and reaction rates lead to the standard QSSA (sQSSA), the total QSSA
(tQSSA), and the rev... | [
{
"created": "Wed, 8 Nov 2017 01:24:13 GMT",
"version": "v1"
}
] | 2017-11-09 | [
[
"Kang",
"Hye-Won",
""
],
[
"KhudaBukhsh",
"Wasiur R.",
""
],
[
"Koeppl",
"Heinz",
""
],
[
"Rempała",
"Grzegorz A.",
""
]
] | In this paper we derive several quasi steady-state approximations (QSSAs) to the stochastic reaction network describing the Michaelis-Menten enzyme kinetics. We show how the different assumptions about chemical species abundance and reaction rates lead to the standard QSSA (sQSSA), the total QSSA (tQSSA), and the rever... |
1603.06634 | Fabio Zanini | Fabio Zanini, Vadim Puller, Johanna Brodin, Jan Albert, Richard Neher | In-vivo mutation rates and fitness landscape of HIV-1 | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-sa/4.0/ | Mutation rates and fitness costs of deleterious mutations are difficult to
measure in vivo but essential for a quantitative understanding of evolution.
Using whole genome deep sequencing data from longitudinal samples during
untreated HIV-1 infection, we estimated mutation rates and fitness costs in
HIV-1 from the te... | [
{
"created": "Mon, 21 Mar 2016 22:08:43 GMT",
"version": "v1"
},
{
"created": "Fri, 1 Jul 2016 19:25:32 GMT",
"version": "v2"
}
] | 2016-07-04 | [
[
"Zanini",
"Fabio",
""
],
[
"Puller",
"Vadim",
""
],
[
"Brodin",
"Johanna",
""
],
[
"Albert",
"Jan",
""
],
[
"Neher",
"Richard",
""
]
] | Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but essential for a quantitative understanding of evolution. Using whole genome deep sequencing data from longitudinal samples during untreated HIV-1 infection, we estimated mutation rates and fitness costs in HIV-1 from the temp... |
1311.6857 | Chuan-Chao Wang | Chuan-Chao Wang, Yunzhi Huang, Shao-Qing Wen, Chun Chen, Li Jin, Hui
Li | Agriculture driving male expansion in Neolithic Time | 9 pages, 2 figures | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The emergence of agriculture is suggested to have driven extensive human
population growths. However, genetic evidence from maternal mitochondrial
genomes suggests major population expansions began before the emergence of
agriculture. Therefore, role of agriculture that played in initial population
expansions still r... | [
{
"created": "Wed, 27 Nov 2013 02:04:29 GMT",
"version": "v1"
}
] | 2013-11-28 | [
[
"Wang",
"Chuan-Chao",
""
],
[
"Huang",
"Yunzhi",
""
],
[
"Wen",
"Shao-Qing",
""
],
[
"Chen",
"Chun",
""
],
[
"Jin",
"Li",
""
],
[
"Li",
"Hui",
""
]
] | The emergence of agriculture is suggested to have driven extensive human population growths. However, genetic evidence from maternal mitochondrial genomes suggests major population expansions began before the emergence of agriculture. Therefore, role of agriculture that played in initial population expansions still rem... |
1412.7187 | Rajita Menon | Rajita Menon and Kirill S. Korolev | Public good diffusion limits microbial mutualism | 12 pages, 4 figures | Phys. Rev. Lett. 114, (2015) 168102 | 10.1103/PhysRevLett.114.168102 | null | q-bio.PE cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Standard game theory cannot describe microbial interactions mediated by
diffusible molecules. Nevertheless, we show that one can still model microbial
dynamics using game theory with parameters renormalized by diffusion. Contrary
to expectations, greater sharing of metabolites reduces the strength of
cooperation and ... | [
{
"created": "Mon, 22 Dec 2014 22:22:33 GMT",
"version": "v1"
},
{
"created": "Thu, 5 Mar 2015 00:35:56 GMT",
"version": "v2"
},
{
"created": "Mon, 4 May 2015 22:07:28 GMT",
"version": "v3"
},
{
"created": "Sat, 23 May 2015 23:57:47 GMT",
"version": "v4"
}
] | 2015-05-26 | [
[
"Menon",
"Rajita",
""
],
[
"Korolev",
"Kirill S.",
""
]
] | Standard game theory cannot describe microbial interactions mediated by diffusible molecules. Nevertheless, we show that one can still model microbial dynamics using game theory with parameters renormalized by diffusion. Contrary to expectations, greater sharing of metabolites reduces the strength of cooperation and le... |
2311.00417 | David A. Kessler | David A. Kessler and Herbert Levine | Multiple possible patterns can emerge from virus-immune coevolution | Revised version | null | null | null | q-bio.PE cond-mat.stat-mech nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The adaptive immune system engages in an arms race with evolving viruses,
trying to generate new responses to viral strains that continually move away
from the set of variants that have already elicited a functional immune
response. In previous work, it has been argued that this dynamical process can
lead to a propag... | [
{
"created": "Wed, 1 Nov 2023 10:19:41 GMT",
"version": "v1"
},
{
"created": "Sat, 1 Jun 2024 20:03:27 GMT",
"version": "v2"
}
] | 2024-06-04 | [
[
"Kessler",
"David A.",
""
],
[
"Levine",
"Herbert",
""
]
] | The adaptive immune system engages in an arms race with evolving viruses, trying to generate new responses to viral strains that continually move away from the set of variants that have already elicited a functional immune response. In previous work, it has been argued that this dynamical process can lead to a propagat... |
2304.09050 | Vernon Lawhern | Stephen M. Gordon, Jonathan R. McDaniel, Kevin W. King, Vernon J.
Lawhern, Jonathan Touryan | Decoding Neural Activity to Assess Individual Latent State in
Ecologically Valid Contexts | null | Journal of Neural Engineering, vol. 20(4), 2023 | 10.1088/1741-2552/acee20 | null | q-bio.NC cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There exist very few ways to isolate cognitive processes, historically
defined via highly controlled laboratory studies, in more ecologically valid
contexts. Specifically, it remains unclear as to what extent patterns of neural
activity observed under such constraints actually manifest outside the
laboratory in a man... | [
{
"created": "Tue, 18 Apr 2023 15:15:00 GMT",
"version": "v1"
}
] | 2023-10-13 | [
[
"Gordon",
"Stephen M.",
""
],
[
"McDaniel",
"Jonathan R.",
""
],
[
"King",
"Kevin W.",
""
],
[
"Lawhern",
"Vernon J.",
""
],
[
"Touryan",
"Jonathan",
""
]
] | There exist very few ways to isolate cognitive processes, historically defined via highly controlled laboratory studies, in more ecologically valid contexts. Specifically, it remains unclear as to what extent patterns of neural activity observed under such constraints actually manifest outside the laboratory in a manne... |
1408.5128 | Stefano Bo | Stefano Bo, Marco Del Giudice and Antonio Celani | Thermodynamic limits to information harvesting by sensory systems | Revised version: 18 pages, 5 figures | null | 10.1088/1742-5468/2015/01/P01014 | null | q-bio.QM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In view of the relation between information and thermodynamics we investigate
how much information about an external protocol can be stored in the memory of
a stochastic measurement device given an energy budget. We consider a layered
device with a memory component storing information about the external
environment b... | [
{
"created": "Thu, 21 Aug 2014 16:35:22 GMT",
"version": "v1"
},
{
"created": "Mon, 27 Jul 2015 12:21:59 GMT",
"version": "v2"
}
] | 2015-07-28 | [
[
"Bo",
"Stefano",
""
],
[
"Del Giudice",
"Marco",
""
],
[
"Celani",
"Antonio",
""
]
] | In view of the relation between information and thermodynamics we investigate how much information about an external protocol can be stored in the memory of a stochastic measurement device given an energy budget. We consider a layered device with a memory component storing information about the external environment by ... |
q-bio/0510044 | Danuta Makowiec | Danuta Makowiec, Rafal Galaska, Aleksandra Dudkowska, Andrzej
Rynkiewicz, Marcin Zwierz | Long-range dependencies in heart rate signals- revisited | 24 pages | null | 10.1016/j.physa.2006.02.038 | null | q-bio.TO | null | The RR series extracted from human electrocardiogram signal (ECG) is
considered as a fractal stochastic process. The manifestation of long-range
dependencies is the presence of power laws in scale dependent process
characteristics. Exponents of these laws: $\beta$ - describing power spectrum
decay, $\alpha$ - respons... | [
{
"created": "Mon, 24 Oct 2005 07:00:16 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Makowiec",
"Danuta",
""
],
[
"Galaska",
"Rafal",
""
],
[
"Dudkowska",
"Aleksandra",
""
],
[
"Rynkiewicz",
"Andrzej",
""
],
[
"Zwierz",
"Marcin",
""
]
] | The RR series extracted from human electrocardiogram signal (ECG) is considered as a fractal stochastic process. The manifestation of long-range dependencies is the presence of power laws in scale dependent process characteristics. Exponents of these laws: $\beta$ - describing power spectrum decay, $\alpha$ - responsib... |
2104.09135 | Mar\'ia Vallet-Regi | Cicuendez M, Doadrio JC, Hernandez A, Portoles MT, Izquierdo-Barba I,
Vallet-Regi M | Multifunctional pH sensitive 3D scaffolds for treatment and prevention
of bone infection | 31 pages, 8 figures | Acta Biomaterialia. 65, 450-461 (2018) | 10.1016/j.actbio.2017.11.009 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Multifunctional-therapeutic 3D scaffolds have been prepared. These
biomaterials are able to destroy the S. aureus bacteria biofilm and to allow
bone regeneration at the same time. The present study is focused on the design
of pH sensitive 3D hierarchical meso-macroporous scaffolds based on MGHA
nanocomposite formed b... | [
{
"created": "Mon, 19 Apr 2021 08:33:06 GMT",
"version": "v1"
}
] | 2021-04-20 | [
[
"M",
"Cicuendez",
""
],
[
"JC",
"Doadrio",
""
],
[
"A",
"Hernandez",
""
],
[
"MT",
"Portoles",
""
],
[
"I",
"Izquierdo-Barba",
""
],
[
"M",
"Vallet-Regi",
""
]
] | Multifunctional-therapeutic 3D scaffolds have been prepared. These biomaterials are able to destroy the S. aureus bacteria biofilm and to allow bone regeneration at the same time. The present study is focused on the design of pH sensitive 3D hierarchical meso-macroporous scaffolds based on MGHA nanocomposite formed by ... |
1711.04377 | James Hope Mr | J. Hope, F. Vanholsbeeck, A. McDaid | A model of electrical impedance tomography on peripheral nerves for a
neural-prosthetic control interface | 13 pages, 9 figures | Hope, J., Vanholsbeeck, F., McDaid, A., A model of electrical
impedance tomography implemented in nerve-cuff for neural-prosthetics
control. Physiological Measurement, 2018 | 10.1088/1361-6579/aab73a | null | q-bio.NC physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objective: A model is presented to evaluate the viability of using electrical
impedance tomography (EIT) with a nerve cuff to record neural activity in
peripheral nerves. Approach: Established modelling approaches in neural-EIT are
expanded on to be used, for the first time, on myelinated fibres which are
abundant in... | [
{
"created": "Sun, 12 Nov 2017 22:52:48 GMT",
"version": "v1"
}
] | 2018-05-09 | [
[
"Hope",
"J.",
""
],
[
"Vanholsbeeck",
"F.",
""
],
[
"McDaid",
"A.",
""
]
] | Objective: A model is presented to evaluate the viability of using electrical impedance tomography (EIT) with a nerve cuff to record neural activity in peripheral nerves. Approach: Established modelling approaches in neural-EIT are expanded on to be used, for the first time, on myelinated fibres which are abundant in m... |
2304.04673 | Mengjin Dong | Mengjin Dong, Long Xie, Sandhitsu R. Das, Jiancong Wang, Laura E.M.
Wisse, Robin deFlores, David A. Wolk, Paul A. Yushkevich (for the Alzheimer's
Disease Neuroimaging Initiative) | Regional Deep Atrophy: a Self-Supervised Learning Method to
Automatically Identify Regions Associated With Alzheimer's Disease
Progression From Longitudinal MRI | Submitted to NeuroImage for review | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Longitudinal assessment of brain atrophy, particularly in the hippocampus, is
a well-studied biomarker for neurodegenerative diseases, such as Alzheimer's
disease (AD). In clinical trials, estimation of brain progressive rates can be
applied to track therapeutic efficacy of disease modifying treatments. However,
most... | [
{
"created": "Mon, 10 Apr 2023 15:50:19 GMT",
"version": "v1"
}
] | 2023-04-11 | [
[
"Dong",
"Mengjin",
"",
"for the Alzheimer's\n Disease Neuroimaging Initiative"
],
[
"Xie",
"Long",
"",
"for the Alzheimer's\n Disease Neuroimaging Initiative"
],
[
"Das",
"Sandhitsu R.",
"",
"for the Alzheimer's\n Disease Neuroimaging Initiative"
],
[... | Longitudinal assessment of brain atrophy, particularly in the hippocampus, is a well-studied biomarker for neurodegenerative diseases, such as Alzheimer's disease (AD). In clinical trials, estimation of brain progressive rates can be applied to track therapeutic efficacy of disease modifying treatments. However, most s... |
2307.10343 | Tony Tu | Tony Tu, Gautham Krishna, Amirali Aghazadeh | ProtiGeno: a prokaryotic short gene finder using protein language models | Accepted at the 2023 ICML Workshop on Computational Biology | null | null | null | q-bio.GN cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Prokaryotic gene prediction plays an important role in understanding the
biology of organisms and their function with applications in medicine and
biotechnology. Although the current gene finders are highly sensitive in
finding long genes, their sensitivity decreases noticeably in finding shorter
genes (<180 nts). Th... | [
{
"created": "Wed, 19 Jul 2023 16:46:42 GMT",
"version": "v1"
}
] | 2023-07-21 | [
[
"Tu",
"Tony",
""
],
[
"Krishna",
"Gautham",
""
],
[
"Aghazadeh",
"Amirali",
""
]
] | Prokaryotic gene prediction plays an important role in understanding the biology of organisms and their function with applications in medicine and biotechnology. Although the current gene finders are highly sensitive in finding long genes, their sensitivity decreases noticeably in finding shorter genes (<180 nts). The ... |
0904.1900 | Merek Siu | Merek Siu, Hari Shroff, Jake Siegel, Ann McEvoy, David Sivak, Ann
Maris, Andrew Spakowitz, Jan Liphardt | Mechanical conversion of low-affinity Integration Host Factor binding
sites into high-affinity sites | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although DNA is often bent in vivo, it is unclear how DNA-bending forces
modulate DNA-protein binding affinity. Here, we report how a range of
DNA-bending forces modulates the binding of the Integration Host Factor (IHF)
protein to various DNAs. Using solution fluorimetry and electrophoretic
mobility shift assays, we... | [
{
"created": "Mon, 13 Apr 2009 02:38:33 GMT",
"version": "v1"
}
] | 2009-04-14 | [
[
"Siu",
"Merek",
""
],
[
"Shroff",
"Hari",
""
],
[
"Siegel",
"Jake",
""
],
[
"McEvoy",
"Ann",
""
],
[
"Sivak",
"David",
""
],
[
"Maris",
"Ann",
""
],
[
"Spakowitz",
"Andrew",
""
],
[
"Liphardt",
... | Although DNA is often bent in vivo, it is unclear how DNA-bending forces modulate DNA-protein binding affinity. Here, we report how a range of DNA-bending forces modulates the binding of the Integration Host Factor (IHF) protein to various DNAs. Using solution fluorimetry and electrophoretic mobility shift assays, we m... |
q-bio/0509001 | Eric J. Deeds | Eric J. Deeds, Orr Ashenberg and Eugene I. Shakhnovich | A simple physical model for scaling in protein-protein interaction
networks | 50 pages, 17 figures | null | 10.1073/pnas.0509715102 | null | q-bio.MN q-bio.BM | null | It has recently been demonstrated that many biological networks exhibit a
scale-free topology where the probability of observing a node with a certain
number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has
been reproduced by evolutionary models. Here we consider the network of
protein-protein... | [
{
"created": "Wed, 31 Aug 2005 22:05:48 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Deeds",
"Eric J.",
""
],
[
"Ashenberg",
"Orr",
""
],
[
"Shakhnovich",
"Eugene I.",
""
]
] | It has recently been demonstrated that many biological networks exhibit a scale-free topology where the probability of observing a node with a certain number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has been reproduced by evolutionary models. Here we consider the network of protein-protein i... |
1309.4761 | Benjamin Greenbaum | Benjamin Greenbaum, Pradeep Kumar, and Albert Libchaber | Amino Acid Distributions and the Effect of Optimal Growth Temperature | 31 pages, 7 Figures, 2 Tables | null | null | null | q-bio.GN q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We perform an exhaustive analysis of genome statistics for organisms,
particularly extremophiles, growing in a wide range of physicochemical
conditions. Specifically, we demonstrate how the correlation between the
frequency of amino acids and their molecular weight, preserved on average,
typically decreases as optima... | [
{
"created": "Wed, 18 Sep 2013 19:28:35 GMT",
"version": "v1"
}
] | 2013-09-19 | [
[
"Greenbaum",
"Benjamin",
""
],
[
"Kumar",
"Pradeep",
""
],
[
"Libchaber",
"Albert",
""
]
] | We perform an exhaustive analysis of genome statistics for organisms, particularly extremophiles, growing in a wide range of physicochemical conditions. Specifically, we demonstrate how the correlation between the frequency of amino acids and their molecular weight, preserved on average, typically decreases as optimal ... |
1907.06954 | Cecilia Clementi | Eugen Hruska, Vivekanandan Balasubramanian, Hyungro Lee, Shantenu Jha,
Cecilia Clementi | Extensible and Scalable Adaptive Sampling on Supercomputers | 17 pages, 9 figures | null | null | null | q-bio.QM physics.comp-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The accurate sampling of protein dynamics is an ongoing challenge despite the
utilization of High-Performance Computers (HPC) systems. Utilizing only "brute
force" MD simulations requires an unacceptably long time to solution. Adaptive
sampling methods allow a more effective sampling of protein dynamics than
standard... | [
{
"created": "Tue, 16 Jul 2019 12:08:51 GMT",
"version": "v1"
},
{
"created": "Thu, 24 Sep 2020 13:55:22 GMT",
"version": "v2"
}
] | 2020-09-25 | [
[
"Hruska",
"Eugen",
""
],
[
"Balasubramanian",
"Vivekanandan",
""
],
[
"Lee",
"Hyungro",
""
],
[
"Jha",
"Shantenu",
""
],
[
"Clementi",
"Cecilia",
""
]
] | The accurate sampling of protein dynamics is an ongoing challenge despite the utilization of High-Performance Computers (HPC) systems. Utilizing only "brute force" MD simulations requires an unacceptably long time to solution. Adaptive sampling methods allow a more effective sampling of protein dynamics than standard M... |
1803.09364 | Katherine Meyer | Katherine Meyer | Extinction debt repayment via timely habitat restoration | 14 pages, 3 figures | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Habitat destruction threatens the viability of many populations, but its full
consequences can take considerable time to unfold. Much of the discourse
surrounding extinction debts--the number of species that persist transiently
following habitat loss, despite being headed for extinction--frames ultimate
population cr... | [
{
"created": "Sun, 25 Mar 2018 23:14:38 GMT",
"version": "v1"
}
] | 2018-03-28 | [
[
"Meyer",
"Katherine",
""
]
] | Habitat destruction threatens the viability of many populations, but its full consequences can take considerable time to unfold. Much of the discourse surrounding extinction debts--the number of species that persist transiently following habitat loss, despite being headed for extinction--frames ultimate population cras... |
2404.06481 | Alexis Molina | Ra\'ul Mi\~n\'an, Javier Gallardo, \'Alvaro Ciudad, Alexis Molina | GeoDirDock: Guiding Docking Along Geodesic Paths | Generative and Experimental Perspectives for Biomolecular Design
Workshop at ICLR 2024 | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | This work introduces GeoDirDock (GDD), a novel approach to molecular docking
that enhances the accuracy and physical plausibility of ligand docking
predictions. GDD guides the denoising process of a diffusion model along
geodesic paths within multiple spaces representing translational, rotational,
and torsional degre... | [
{
"created": "Tue, 9 Apr 2024 17:31:18 GMT",
"version": "v1"
}
] | 2024-04-10 | [
[
"Miñán",
"Raúl",
""
],
[
"Gallardo",
"Javier",
""
],
[
"Ciudad",
"Álvaro",
""
],
[
"Molina",
"Alexis",
""
]
] | This work introduces GeoDirDock (GDD), a novel approach to molecular docking that enhances the accuracy and physical plausibility of ligand docking predictions. GDD guides the denoising process of a diffusion model along geodesic paths within multiple spaces representing translational, rotational, and torsional degrees... |
1801.09848 | Ardavan Salehi Nobandegani | Ardavan S. Nobandegani, Kevin da Silva Castanheira, A. Ross Otto,
Thomas R. Shultz | Over-representation of Extreme Events in Decision-Making: A Rational
Metacognitive Account | null | null | null | null | q-bio.NC cs.AI stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Availability bias, manifested in the over-representation of extreme
eventualities in decision-making, is a well-known cognitive bias, and is
generally taken as evidence of human irrationality. In this work, we present
the first rational, metacognitive account of the Availability bias, formally
articulated at Marr... | [
{
"created": "Tue, 30 Jan 2018 04:33:25 GMT",
"version": "v1"
}
] | 2018-01-31 | [
[
"Nobandegani",
"Ardavan S.",
""
],
[
"Castanheira",
"Kevin da Silva",
""
],
[
"Otto",
"A. Ross",
""
],
[
"Shultz",
"Thomas R.",
""
]
] | The Availability bias, manifested in the over-representation of extreme eventualities in decision-making, is a well-known cognitive bias, and is generally taken as evidence of human irrationality. In this work, we present the first rational, metacognitive account of the Availability bias, formally articulated at Marr's... |
1701.03993 | Christoph Adami | Nitash C G, Thomas LaBar, Arend Hintze, and Christoph Adami (Michigan
State University) | Origin of life in a digital microcosm | 20 pages, 7 figures. To appear in special issue of Philosophical
Transactions of the Royal Society A: Re-Conceptualizing the Origins of Life
from a Physical Sciences Perspective | null | null | null | q-bio.PE cs.IT math.IT nlin.AO q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While all organisms on Earth descend from a common ancestor, there is no
consensus on whether the origin of this ancestral self-replicator was a one-off
event or whether it was only the final survivor of multiple origins. Here we
use the digital evolution system Avida to study the origin of self-replicating
computer ... | [
{
"created": "Sun, 15 Jan 2017 05:26:11 GMT",
"version": "v1"
}
] | 2017-01-17 | [
[
"G",
"Nitash C",
"",
"Michigan\n State University"
],
[
"LaBar",
"Thomas",
"",
"Michigan\n State University"
],
[
"Hintze",
"Arend",
"",
"Michigan\n State University"
],
[
"Adami",
"Christoph",
"",
"Michigan\n State University"
]
] | While all organisms on Earth descend from a common ancestor, there is no consensus on whether the origin of this ancestral self-replicator was a one-off event or whether it was only the final survivor of multiple origins. Here we use the digital evolution system Avida to study the origin of self-replicating computer pr... |
2306.06450 | Pablo de Castro | Vivian Dornelas, Pablo de Castro, Justin M. Calabrese, William F.
Fagan, Ricardo Martinez-Garcia | Movement bias in asymmetric landscapes and its impact on population
distribution and critical habitat size | 21 pages, 8 figures | null | null | null | q-bio.PE physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Ecologists have long investigated how demographic and movement parameters
determine the spatial distribution and critical habitat size of a population.
However, most models oversimplify movement behavior, neglecting how landscape
heterogeneity influences individual movement. We relax this assumption and
introduce a r... | [
{
"created": "Sat, 10 Jun 2023 14:14:10 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Mar 2024 18:39:15 GMT",
"version": "v2"
}
] | 2024-03-11 | [
[
"Dornelas",
"Vivian",
""
],
[
"de Castro",
"Pablo",
""
],
[
"Calabrese",
"Justin M.",
""
],
[
"Fagan",
"William F.",
""
],
[
"Martinez-Garcia",
"Ricardo",
""
]
] | Ecologists have long investigated how demographic and movement parameters determine the spatial distribution and critical habitat size of a population. However, most models oversimplify movement behavior, neglecting how landscape heterogeneity influences individual movement. We relax this assumption and introduce a rea... |
1508.02930 | Francois Baccelli | Eliza O'Reilly, Francois Baccelli, Gustavo de Veciana and Haris Vikalo | End-to-End Optimization of High Throughput DNA Sequencing | null | null | null | null | q-bio.GN math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | At the core of high throughput DNA sequencing platforms lies a bio-physical
surface process that results in a random geometry of clusters of homogenous
short DNA fragments typically hundreds of base pairs long - bridge
amplification. The statistical properties of this random process and length of
the fragments are cr... | [
{
"created": "Tue, 4 Aug 2015 13:50:52 GMT",
"version": "v1"
}
] | 2015-08-13 | [
[
"O'Reilly",
"Eliza",
""
],
[
"Baccelli",
"Francois",
""
],
[
"de Veciana",
"Gustavo",
""
],
[
"Vikalo",
"Haris",
""
]
] | At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The statistical properties of this random process and length of the fragments are crit... |
1604.02554 | P. Gaspard | Pierre Gaspard | Kinetics and thermodynamics of DNA polymerases with exonuclease
proofreading | Physical Review E (2016) | Phys. Rev. E 93, 042420 (2016) | 10.1103/PhysRevE.93.042420 | null | q-bio.SC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Kinetic theory and thermodynamics are applied to DNA polymerases with
exonuclease activity, taking into account the dependence of the rates on the
previously incorportated nucleotide. The replication fidelity is shown to
increase significantly thanks to this dependence at the basis of the mechanism
of exonuclease pro... | [
{
"created": "Sat, 9 Apr 2016 12:22:16 GMT",
"version": "v1"
}
] | 2018-01-04 | [
[
"Gaspard",
"Pierre",
""
]
] | Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase significantly thanks to this dependence at the basis of the mechanism of exonuclease proof... |
2001.05430 | Jason Kamran Jr Eshraghian | Jason K. Eshraghian and Seungbum Baek and Wesley Thio and Yulia
Sandamirskaya and Herbert H.C. Iu and Wei D. Lu | A Real-Time Retinomorphic Simulator Using a Conductance-Based Discrete
Neuronal Network | 5 pages, 4 figures, accepted for 2020 IEEE AICAS | null | null | null | q-bio.NC eess.IV q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present an optimized conductance-based retina microcircuit simulator which
transforms light stimuli into a series of graded and spiking action potentials
through photo transduction. We use discrete retinal neuron blocks based on a
collation of single-compartment models and morphologically realistic
formulations, a... | [
{
"created": "Thu, 26 Dec 2019 20:23:13 GMT",
"version": "v1"
}
] | 2020-01-16 | [
[
"Eshraghian",
"Jason K.",
""
],
[
"Baek",
"Seungbum",
""
],
[
"Thio",
"Wesley",
""
],
[
"Sandamirskaya",
"Yulia",
""
],
[
"Iu",
"Herbert H. C.",
""
],
[
"Lu",
"Wei D.",
""
]
] | We present an optimized conductance-based retina microcircuit simulator which transforms light stimuli into a series of graded and spiking action potentials through photo transduction. We use discrete retinal neuron blocks based on a collation of single-compartment models and morphologically realistic formulations, and... |
q-bio/0609003 | Yunfeng Shan Dr. | Yunfeng Shan and Xiu-Qing Li | Maximum-frequency gene tree: a simplified genome-scale approach to
overcoming incongruence in molecular phylogenies | 10 pages, 5 figures, Evolution 2006, July 23-27 Stony Brook
University, NY, USA | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genomes and genes diversify during evolution; however, it is unclear to what
extent genes still retain the relationship among species. Model species for
molecular phylogenetic studies include yeasts and viruses whose genomes were
sequenced as well as plants that have the fossil-supported true phylogenetic
trees avail... | [
{
"created": "Sat, 2 Sep 2006 14:20:49 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Sep 2006 03:05:54 GMT",
"version": "v2"
},
{
"created": "Sat, 7 Jun 2008 21:21:19 GMT",
"version": "v3"
}
] | 2008-06-09 | [
[
"Shan",
"Yunfeng",
""
],
[
"Li",
"Xiu-Qing",
""
]
] | Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees availab... |
2102.03847 | Suzette Geriente | Diederik Aerts, Jonito Aerts Argu\"elles, Lester Beltran, Suzette
Geriente (Center Leo Apostel for Interdisciplinary Studies, Free University
of Brussels (VUB), Brussels, Belgium), and Sandro Sozzo (School of Business
and Centre IQSCS, University of Leicester, Leicester, United Kingdom) | Entanglement in Cognition violating Bell Inequalities Beyond Cirel'son's
Bound | 22 pages | null | null | null | q-bio.NC quant-ph | http://creativecommons.org/licenses/by/4.0/ | We present the results of two tests where a sample of human participants were
asked to make judgements about the conceptual combinations {\it The Animal
Acts} and {\it The Animal eats the Food}. Both tests significantly violate the
Clauser-Horne-Shimony-Holt version of Bell inequalities (`CHSH inequality'),
thus exhi... | [
{
"created": "Sun, 7 Feb 2021 16:57:59 GMT",
"version": "v1"
}
] | 2021-02-09 | [
[
"Aerts",
"Diederik",
"",
"Center Leo Apostel for Interdisciplinary Studies, Free University\n of Brussels"
],
[
"Arguëlles",
"Jonito Aerts",
"",
"Center Leo Apostel for Interdisciplinary Studies, Free University\n of Brussels"
],
[
"Beltran",
"Lester",
"",
... | We present the results of two tests where a sample of human participants were asked to make judgements about the conceptual combinations {\it The Animal Acts} and {\it The Animal eats the Food}. Both tests significantly violate the Clauser-Horne-Shimony-Holt version of Bell inequalities (`CHSH inequality'), thus exhibi... |
1304.5232 | Anca Radulescu | Anca Radulescu | Neural network spectral robustness under perturbations of the underlying
graph | manuscript: 27 pages; references: 5 pages; 2 appendices; 16 figures | null | null | null | q-bio.NC cs.DM math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent studies have been using graph theoretical approaches to model complex
networks (such as social, infrastructural or biological networks), and how
their hardwired circuitry relates to their dynamic evolution in time.
Understanding how configuration reflects on the coupled behavior in a system of
dynamic nodes ca... | [
{
"created": "Thu, 18 Apr 2013 19:40:49 GMT",
"version": "v1"
},
{
"created": "Thu, 16 Jul 2015 15:19:00 GMT",
"version": "v2"
}
] | 2015-07-17 | [
[
"Radulescu",
"Anca",
""
]
] | Recent studies have been using graph theoretical approaches to model complex networks (such as social, infrastructural or biological networks), and how their hardwired circuitry relates to their dynamic evolution in time. Understanding how configuration reflects on the coupled behavior in a system of dynamic nodes can ... |
2003.14288 | Daniel Cajueiro | Saulo B. Bastos and Daniel O. Cajueiro | Modeling and forecasting the early evolution of the Covid-19 pandemic in
Brazil | We received several interesting comments from a large number of
people and we decide to update the second version of the paper | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We model and forecast the early evolution of the COVID-19 pandemic in Brazil
using Brazilian recent data from February 25, 2020 to March 30, 2020. This
early period accounts for unawareness of the epidemiological characteristics of
the disease in a new territory, sub-notification of the real numbers of
infected peopl... | [
{
"created": "Tue, 31 Mar 2020 15:21:39 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Apr 2020 03:23:52 GMT",
"version": "v2"
},
{
"created": "Sat, 13 Jun 2020 03:49:48 GMT",
"version": "v3"
}
] | 2020-06-16 | [
[
"Bastos",
"Saulo B.",
""
],
[
"Cajueiro",
"Daniel O.",
""
]
] | We model and forecast the early evolution of the COVID-19 pandemic in Brazil using Brazilian recent data from February 25, 2020 to March 30, 2020. This early period accounts for unawareness of the epidemiological characteristics of the disease in a new territory, sub-notification of the real numbers of infected people ... |
2302.09558 | Maurice HT Ling | Maurice HT Ling | Of (Biological) Models and Simulations | null | MOJ Proteomics & Bioinformatics 3(4): 00093 (2016) | null | null | q-bio.QM | http://creativecommons.org/licenses/by-sa/4.0/ | Modeling and simulation are recognized as important aspects of the scientific
method for more than 70 years but its adoption in biology has been slow.
Debates on its representativeness, usefulness, and whether the effort spent on
such endeavors is worthwhile, exist to this day. Here, I argue that most of
learning is ... | [
{
"created": "Sun, 19 Feb 2023 12:35:12 GMT",
"version": "v1"
}
] | 2023-02-21 | [
[
"Ling",
"Maurice HT",
""
]
] | Modeling and simulation are recognized as important aspects of the scientific method for more than 70 years but its adoption in biology has been slow. Debates on its representativeness, usefulness, and whether the effort spent on such endeavors is worthwhile, exist to this day. Here, I argue that most of learning is mo... |
1802.01437 | Artem Efremov K | Artem K. Efremov and Jie Yan | Transfer-matrix calculations of the effects of tension and torque
constraints on DNA-protein interactions | 61 pages, including 14 figures and 2 tables | The article is published in Nucleic Acids Research journal. 2018 | 10.1093/nar/gky478 | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Organization and maintenance of the chromosomal DNA in living cells strongly
depends on the DNA interactions with a plethora of DNA-binding proteins.
Single-molecule studies show that formation of nucleoprotein complexes on DNA
by such proteins is frequently subject to force and torque constraints applied
to the DNA.... | [
{
"created": "Mon, 5 Feb 2018 14:50:29 GMT",
"version": "v1"
},
{
"created": "Wed, 9 May 2018 14:42:44 GMT",
"version": "v2"
},
{
"created": "Tue, 4 Sep 2018 04:53:54 GMT",
"version": "v3"
}
] | 2018-09-05 | [
[
"Efremov",
"Artem K.",
""
],
[
"Yan",
"Jie",
""
]
] | Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such proteins is frequently subject to force and torque constraints applied to the DNA. A... |
1207.0033 | Jose Acacio de Barros | Jos\'e Acacio de Barros | Quantum-like model of behavioral response computation using neural
oscillators | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we propose the use of neural interference as the origin of
quantum-like effects in the brain. We do so by using a neural oscillator model
consistent with neurophysiological data. The model used was shown to reproduce
well the predictions of behavioral stimulus-response theory. The quantum-like
effects a... | [
{
"created": "Fri, 29 Jun 2012 23:28:21 GMT",
"version": "v1"
},
{
"created": "Mon, 8 Oct 2012 16:32:07 GMT",
"version": "v2"
}
] | 2012-10-09 | [
[
"de Barros",
"José Acacio",
""
]
] | In this paper we propose the use of neural interference as the origin of quantum-like effects in the brain. We do so by using a neural oscillator model consistent with neurophysiological data. The model used was shown to reproduce well the predictions of behavioral stimulus-response theory. The quantum-like effects are... |
1306.5275 | Eric Shea-Brown | David Leen and Eric Shea-Brown | A simple mechanism for higher-order correlations in integrate-and-fire
neurons | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The collective dynamics of neural populations are often characterized in
terms of correlations in the spike activity of different neurons. Open
questions surround the basic nature of these correlations. In particular, what
leads to higher-order correlations -- correlations in the population activity
that extend beyon... | [
{
"created": "Fri, 21 Jun 2013 23:34:15 GMT",
"version": "v1"
}
] | 2013-06-25 | [
[
"Leen",
"David",
""
],
[
"Shea-Brown",
"Eric",
""
]
] | The collective dynamics of neural populations are often characterized in terms of correlations in the spike activity of different neurons. Open questions surround the basic nature of these correlations. In particular, what leads to higher-order correlations -- correlations in the population activity that extend beyond ... |
1604.01359 | Markus Meister | Markus Meister | Physical limits to magnetogenetics | 14 pages, 2 figures. Revision includes analysis of magnetic heating
of ferritin constructs. Spoiler alert: also implausible | null | 10.7554/eLife.17210 | null | q-bio.NC q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This is an analysis of how magnetic fields affect biological molecules and
cells. It was prompted by a series of prominent reports regarding magnetism in
biological systems. The first claims to have identified a protein complex that
acts like a compass needle to guide magnetic orientation in animals (Qin et
al., 2016... | [
{
"created": "Tue, 5 Apr 2016 18:39:49 GMT",
"version": "v1"
},
{
"created": "Sun, 24 Apr 2016 08:45:49 GMT",
"version": "v2"
},
{
"created": "Mon, 4 Jul 2016 00:17:05 GMT",
"version": "v3"
}
] | 2016-09-09 | [
[
"Meister",
"Markus",
""
]
] | This is an analysis of how magnetic fields affect biological molecules and cells. It was prompted by a series of prominent reports regarding magnetism in biological systems. The first claims to have identified a protein complex that acts like a compass needle to guide magnetic orientation in animals (Qin et al., 2016).... |
1304.4860 | Aaron Quinlan Ph.D. | Uma Paila, Brad Chapman, Rory Kirchner, and Aaron Quinlan | GEMINI: integrative exploration of genetic variation and genome
annotations | null | null | 10.1371/journal.pcbi.1003153 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modern DNA sequencing technologies enable geneticists to rapidly identify
genetic variation among many human genomes. However, isolating the minority of
variants underlying disease remains an important, yet formidable challenge for
medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software
packag... | [
{
"created": "Wed, 17 Apr 2013 15:31:05 GMT",
"version": "v1"
},
{
"created": "Thu, 18 Apr 2013 14:28:16 GMT",
"version": "v2"
}
] | 2015-06-15 | [
[
"Paila",
"Uma",
""
],
[
"Chapman",
"Brad",
""
],
[
"Kirchner",
"Rory",
""
],
[
"Quinlan",
"Aaron",
""
]
] | Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package ... |
2406.06397 | Yuta Nagano | Yuta Nagano, Andrew Pyo, Martina Milighetti, James Henderson, John
Shawe-Taylor, Benny Chain, Andreas Tiffeau-Mayer | Contrastive learning of T cell receptor representations | 19 pages, 17 figures | null | null | null | q-bio.BM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Computational prediction of the interaction of T cell receptors (TCRs) and
their ligands is a grand challenge in immunology. Despite advances in
high-throughput assays, specificity-labelled TCR data remains sparse. In other
domains, the pre-training of language models on unlabelled data has been
successfully used to ... | [
{
"created": "Mon, 10 Jun 2024 15:50:45 GMT",
"version": "v1"
}
] | 2024-06-11 | [
[
"Nagano",
"Yuta",
""
],
[
"Pyo",
"Andrew",
""
],
[
"Milighetti",
"Martina",
""
],
[
"Henderson",
"James",
""
],
[
"Shawe-Taylor",
"John",
""
],
[
"Chain",
"Benny",
""
],
[
"Tiffeau-Mayer",
"Andreas",
""
]... | Computational prediction of the interaction of T cell receptors (TCRs) and their ligands is a grand challenge in immunology. Despite advances in high-throughput assays, specificity-labelled TCR data remains sparse. In other domains, the pre-training of language models on unlabelled data has been successfully used to ad... |
1210.0330 | Peter Csermely | Peter Csermely, Tamas Korcsmaros, Huba J. M. Kiss, Gabor London and
Ruth Nussinov | Structure and dynamics of molecular networks: A novel paradigm of drug
discovery. A comprehensive review | 76 pages, 23 Figures, 12 Tables and 1270 references | Pharmacology and Therapeutics 138:333-408 (2013) | 10.1016/j.pharmthera.2013.01.016 | null | q-bio.MN cond-mat.dis-nn cs.SI nlin.AO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite considerable progress in genome- and proteome-based high-throughput
screening methods and in rational drug design, the increase in approved drugs
in the past decade did not match the increase of drug development costs.
Network description and analysis not only give a systems-level understanding of
drug action... | [
{
"created": "Mon, 1 Oct 2012 10:01:56 GMT",
"version": "v1"
},
{
"created": "Thu, 24 Jan 2013 12:18:51 GMT",
"version": "v2"
},
{
"created": "Sat, 11 May 2013 09:38:57 GMT",
"version": "v3"
}
] | 2013-05-14 | [
[
"Csermely",
"Peter",
""
],
[
"Korcsmaros",
"Tamas",
""
],
[
"Kiss",
"Huba J. M.",
""
],
[
"London",
"Gabor",
""
],
[
"Nussinov",
"Ruth",
""
]
] | Despite considerable progress in genome- and proteome-based high-throughput screening methods and in rational drug design, the increase in approved drugs in the past decade did not match the increase of drug development costs. Network description and analysis not only give a systems-level understanding of drug action a... |
2206.01047 | Imra Aqeel | Imra Aqeel, Abdul Majid, Muhammad Ismail, Hina Bashir | Drug Repurposing For SARS-COV-2 Using Molecular Docking | 7 Pages | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Drug repurposing is an unconventional approach that is used to investigate
new therapeutic aids of existing and shelved drugs. Recent advancement in
technologies and the availability of the data of genomics, proteomics,
transcriptomics, etc., and with the accessibility of large and reliable
database resources, there ... | [
{
"created": "Thu, 2 Jun 2022 13:58:13 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Jul 2022 07:34:59 GMT",
"version": "v2"
}
] | 2022-07-27 | [
[
"Aqeel",
"Imra",
""
],
[
"Majid",
"Abdul",
""
],
[
"Ismail",
"Muhammad",
""
],
[
"Bashir",
"Hina",
""
]
] | Drug repurposing is an unconventional approach that is used to investigate new therapeutic aids of existing and shelved drugs. Recent advancement in technologies and the availability of the data of genomics, proteomics, transcriptomics, etc., and with the accessibility of large and reliable database resources, there ar... |
2102.00971 | Rui Wang | Kaifu Gao, Rui Wang, Jiahui Chen, Limei Cheng, Jaclyn Frishcosy, Yuta
Huzumi, Yuchi Qiu, Tom Schluckbier, and Guo-Wei Wei | Methodology-centered review of molecular modeling, simulation, and
prediction of SARS-CoV-2 | 99 pages, 17 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The deadly coronavirus disease 2019 (COVID-19) pandemic caused by severe
acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gone out of control
globally. Despite much effort by scientists, medical experts, and society in
general, the slow progress on drug discovery and antibody therapeutic
development, the unk... | [
{
"created": "Mon, 1 Feb 2021 16:54:54 GMT",
"version": "v1"
}
] | 2021-02-02 | [
[
"Gao",
"Kaifu",
""
],
[
"Wang",
"Rui",
""
],
[
"Chen",
"Jiahui",
""
],
[
"Cheng",
"Limei",
""
],
[
"Frishcosy",
"Jaclyn",
""
],
[
"Huzumi",
"Yuta",
""
],
[
"Qiu",
"Yuchi",
""
],
[
"Schluckbier",
... | The deadly coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gone out of control globally. Despite much effort by scientists, medical experts, and society in general, the slow progress on drug discovery and antibody therapeutic development, the unkno... |
1508.04416 | Amir Toor | B. Abdul Razzaq, A. Scalora, V. Koparde, J. Meier, M. Mahmood, S.
Salman, M. Jameson-Lee, M. Serrano, N. Sheth, M. Voelkner, D. Kobulnicky, C.
Roberts, A. Ferreira-Gonzalez, M. Manjili, G. Buck, M. Neale, A. Toor | Dynamical System Modeling to Simulate Donor T Cell Response to Whole
Exome Sequencing-Derived Recipient Peptides Demonstrates Different
Alloreactivity Potential In HLA-Matched and Mismatched Donor-Recipient Pairs | 50 pages (including references and supplementary materials), 12
figures, 3 supplementary figures | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stem cell transplants may be considered as dynamical systems to allow
sequence differences across the exomes of the transplant donors and recipients
to be used to simulate an alloreactive T cell response. Whole exome sequencing
was performed on HLA matched stem cell transplant donor-recipient pairs, and
the nucleotid... | [
{
"created": "Sun, 16 Aug 2015 16:10:44 GMT",
"version": "v1"
}
] | 2015-08-19 | [
[
"Razzaq",
"B. Abdul",
""
],
[
"Scalora",
"A.",
""
],
[
"Koparde",
"V.",
""
],
[
"Meier",
"J.",
""
],
[
"Mahmood",
"M.",
""
],
[
"Salman",
"S.",
""
],
[
"Jameson-Lee",
"M.",
""
],
[
"Serrano",
"M... | Stem cell transplants may be considered as dynamical systems to allow sequence differences across the exomes of the transplant donors and recipients to be used to simulate an alloreactive T cell response. Whole exome sequencing was performed on HLA matched stem cell transplant donor-recipient pairs, and the nucleotide ... |
2105.09158 | Wayne Huggins | Alexander J. Ropelewski, Megan A. Rizzo, Jason R. Swedlow, Jan
Huisken, Pavel Osten, Neda Khanjani, Kurt Weiss, Vesselina Bakalov, Michelle
Engle, Lauren Gridley, Michelle Krzyzanowski, Tom Madden, Deborah Maiese,
Justin Waterfield, David Williams, Carol Hamilton, and Wayne Huggins | Essential Metadata for 3D BRAIN Microscopy | 10 pages, 1 table | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Recent advances in fluorescence microscopy techniques and tissue clearing,
labeling, and staining provide unprecedented opportunities to investigate brain
structure and function. These experiments' images make it possible to catalog
brain cell types and define their location, morphology, and connectivity in a
native ... | [
{
"created": "Tue, 18 May 2021 10:32:13 GMT",
"version": "v1"
}
] | 2021-05-20 | [
[
"Ropelewski",
"Alexander J.",
""
],
[
"Rizzo",
"Megan A.",
""
],
[
"Swedlow",
"Jason R.",
""
],
[
"Huisken",
"Jan",
""
],
[
"Osten",
"Pavel",
""
],
[
"Khanjani",
"Neda",
""
],
[
"Weiss",
"Kurt",
""
],
[... | Recent advances in fluorescence microscopy techniques and tissue clearing, labeling, and staining provide unprecedented opportunities to investigate brain structure and function. These experiments' images make it possible to catalog brain cell types and define their location, morphology, and connectivity in a native co... |
1908.07662 | Dmytro Guzenko | Dmytro Guzenko, Aleix Lafita, Bohdan Monastyrskyy, Andriy
Kryshtafovych, Jose M. Duarte | Assessment of protein assembly prediction in CASP13 | null | null | 10.1002/prot.25795 | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | We present the assembly category assessment in the 13th edition of the CASP
community-wide experiment. For the second time, protein assemblies constitute
an independent assessment category. Compared to the last edition we see a clear
uptake in participation, more oligomeric targets released, and consistent,
albeit mo... | [
{
"created": "Wed, 21 Aug 2019 01:14:57 GMT",
"version": "v1"
}
] | 2019-08-22 | [
[
"Guzenko",
"Dmytro",
""
],
[
"Lafita",
"Aleix",
""
],
[
"Monastyrskyy",
"Bohdan",
""
],
[
"Kryshtafovych",
"Andriy",
""
],
[
"Duarte",
"Jose M.",
""
]
] | We present the assembly category assessment in the 13th edition of the CASP community-wide experiment. For the second time, protein assemblies constitute an independent assessment category. Compared to the last edition we see a clear uptake in participation, more oligomeric targets released, and consistent, albeit mode... |
q-bio/0411025 | Aniello Buonocore | A. Buonocore, L. Caputo, Y. Ishii, E. Pirozzi, T. Yanagida and L. M.
Ricciardi | A Phenomenological model of Myosin II dynamics in the presence of
external loads | 6 figures, 8 tables | null | null | null | q-bio.BM | null | We address the controversial hot question concerning the validity of the
loose coupling versus the lever-arm theories in the actomyosin dynamics by
re-interpreting and extending the phenomenological washboard potential model
proposed by some of us in a previous paper. In this new model a Brownian motion
harnessing th... | [
{
"created": "Thu, 11 Nov 2004 17:23:05 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Buonocore",
"A.",
""
],
[
"Caputo",
"L.",
""
],
[
"Ishii",
"Y.",
""
],
[
"Pirozzi",
"E.",
""
],
[
"Yanagida",
"T.",
""
],
[
"Ricciardi",
"L. M.",
""
]
] | We address the controversial hot question concerning the validity of the loose coupling versus the lever-arm theories in the actomyosin dynamics by re-interpreting and extending the phenomenological washboard potential model proposed by some of us in a previous paper. In this new model a Brownian motion harnessing ther... |
2306.01824 | Le Zhang | Le Zhang, Jiayang Chen, Tao Shen, Yu Li, Siqi Sun | Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence
Alignment Generation | null | null | null | null | q-bio.QM cs.CE cs.LG q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | The field of protein folding research has been greatly advanced by deep
learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance
and atomic-level precision. As co-evolution is integral to protein structure
prediction, AF2's accuracy is significantly influenced by the depth of multiple
sequence al... | [
{
"created": "Fri, 2 Jun 2023 14:13:50 GMT",
"version": "v1"
}
] | 2023-06-06 | [
[
"Zhang",
"Le",
""
],
[
"Chen",
"Jiayang",
""
],
[
"Shen",
"Tao",
""
],
[
"Li",
"Yu",
""
],
[
"Sun",
"Siqi",
""
]
] | The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision. As co-evolution is integral to protein structure prediction, AF2's accuracy is significantly influenced by the depth of multiple sequence alig... |
1206.4084 | Paul Gardner | Marc P. Hoeppner, Lars E. Barquist and Paul P. Gardner | An Introduction to RNA Databases | 27 pages, 10 figures, 1 tables. Submitted as a chapter for "An
introduction to RNA bioinformatics" to be published by "Methods in Molecular
Biology" | Methods in Molecular Biology 1097:107-123 (2013) | 10.1007/978-1-62703-709-9_6 | null | q-bio.BM q-bio.GN | http://creativecommons.org/licenses/by/3.0/ | We present an introduction to RNA databases. The history and technology
behind RNA databases is briefly discussed. We examine differing methods of data
collection and curation, and discuss their impact on both the scope and
accuracy of the resulting databases. Finally, we demonstrate these principals
through detailed... | [
{
"created": "Mon, 18 Jun 2012 21:48:47 GMT",
"version": "v1"
}
] | 2014-07-01 | [
[
"Hoeppner",
"Marc P.",
""
],
[
"Barquist",
"Lars E.",
""
],
[
"Gardner",
"Paul P.",
""
]
] | We present an introduction to RNA databases. The history and technology behind RNA databases is briefly discussed. We examine differing methods of data collection and curation, and discuss their impact on both the scope and accuracy of the resulting databases. Finally, we demonstrate these principals through detailed e... |
1811.06866 | Ulisse Ferrari | Ulisse Ferrari, St\'ephane Deny, Abhishek Sengupta, Romain Caplette,
Jos\'e-Alain Sahel, Deniz Dalkara, Serge Picaud, Jens Duebel, Olivier Marre | Optogenetic vision restoration with high resolution | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The majority of inherited retinal degenerations are due to photoreceptor cell
death. In many cases ganglion cells are spared making it possible to stimulate
them to restore visual function. Several studies (Bi et al., 2006; Lin et al.,
2008; Sengupta et al., 2016; Caporale et al., 2011; Berry et al., 2017) have
shown... | [
{
"created": "Fri, 16 Nov 2018 15:41:19 GMT",
"version": "v1"
}
] | 2018-11-19 | [
[
"Ferrari",
"Ulisse",
""
],
[
"Deny",
"Stéphane",
""
],
[
"Sengupta",
"Abhishek",
""
],
[
"Caplette",
"Romain",
""
],
[
"Sahel",
"José-Alain",
""
],
[
"Dalkara",
"Deniz",
""
],
[
"Picaud",
"Serge",
""
],
... | The majority of inherited retinal degenerations are due to photoreceptor cell death. In many cases ganglion cells are spared making it possible to stimulate them to restore visual function. Several studies (Bi et al., 2006; Lin et al., 2008; Sengupta et al., 2016; Caporale et al., 2011; Berry et al., 2017) have shown t... |
2406.18535 | Zhuo Chen | Jinzhe Liu, Xiangsheng Huang, Zhuo Chen, Yin Fang | DRAK: Unlocking Molecular Insights with Domain-Specific
Retrieval-Augmented Knowledge in LLMs | Ongoing work; 11 pages, 6 Figures, 2 Tables | null | null | null | q-bio.BM cs.AI cs.IR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Large Language Models (LLMs) encounter challenges with the unique syntax of
specific domains, such as biomolecules. Existing fine-tuning or modality
alignment techniques struggle to bridge the domain knowledge gap and understand
complex molecular data, limiting LLMs' progress in specialized fields. To
overcome these ... | [
{
"created": "Mon, 4 Mar 2024 15:04:05 GMT",
"version": "v1"
}
] | 2024-06-28 | [
[
"Liu",
"Jinzhe",
""
],
[
"Huang",
"Xiangsheng",
""
],
[
"Chen",
"Zhuo",
""
],
[
"Fang",
"Yin",
""
]
] | Large Language Models (LLMs) encounter challenges with the unique syntax of specific domains, such as biomolecules. Existing fine-tuning or modality alignment techniques struggle to bridge the domain knowledge gap and understand complex molecular data, limiting LLMs' progress in specialized fields. To overcome these li... |
2402.12210 | Charlotte Dugourd-Camus | Charlotte Dugourd-Camus and Claudia P. Ferreira and Mostafa Adimy | Modeling the mechanisms of antibody mixtures in viral infections: the
cases of sequential homologous and heterologous dengue infections | 21 pages, 3 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Antibodies play an essential role in the immune response to viral infections,
vaccination, or antibody therapy. Nevertheless, they can be either protective
or harmful during the immune response. In addition, competition or cooperation
between antibodies, when mixed, can enhance or reduce this protective or
harmful ef... | [
{
"created": "Mon, 19 Feb 2024 15:13:31 GMT",
"version": "v1"
}
] | 2024-02-20 | [
[
"Dugourd-Camus",
"Charlotte",
""
],
[
"Ferreira",
"Claudia P.",
""
],
[
"Adimy",
"Mostafa",
""
]
] | Antibodies play an essential role in the immune response to viral infections, vaccination, or antibody therapy. Nevertheless, they can be either protective or harmful during the immune response. In addition, competition or cooperation between antibodies, when mixed, can enhance or reduce this protective or harmful effe... |
1712.05606 | Venkat Bokka | Venkat Bokka, Abhishek Dey, Shaunak Sen | Period-Amplitude Co-variation in Biomolecular Oscillators | null | null | 10.1049/iet-syb.2018.0015 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The period and amplitude of biomolecular oscillators are functionally
important properties in multiple contexts. For a biomolecular oscillator, the
overall constraints in how tuning of amplitude affects period, and vice versa,
are generally unclear. Here we investigate this co-variation of the period and
amplitude in... | [
{
"created": "Fri, 15 Dec 2017 10:29:30 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Mar 2018 10:05:10 GMT",
"version": "v2"
},
{
"created": "Tue, 10 Apr 2018 06:01:56 GMT",
"version": "v3"
}
] | 2018-04-11 | [
[
"Bokka",
"Venkat",
""
],
[
"Dey",
"Abhishek",
""
],
[
"Sen",
"Shaunak",
""
]
] | The period and amplitude of biomolecular oscillators are functionally important properties in multiple contexts. For a biomolecular oscillator, the overall constraints in how tuning of amplitude affects period, and vice versa, are generally unclear. Here we investigate this co-variation of the period and amplitude in m... |
2310.07908 | Keith Murray | Keith T. Murray | Recurrent networks recognize patterns with low-dimensional oscillations | 7 pages, 8 figures | null | null | null | q-bio.NC cs.AI cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This study proposes a novel dynamical mechanism for pattern recognition
discovered by interpreting a recurrent neural network (RNN) trained on a simple
task inspired by the SET card game. We interpreted the trained RNN as
recognizing patterns via phase shifts in a low-dimensional limit cycle in a
manner analogous to ... | [
{
"created": "Wed, 11 Oct 2023 21:25:12 GMT",
"version": "v1"
}
] | 2023-10-13 | [
[
"Murray",
"Keith T.",
""
]
] | This study proposes a novel dynamical mechanism for pattern recognition discovered by interpreting a recurrent neural network (RNN) trained on a simple task inspired by the SET card game. We interpreted the trained RNN as recognizing patterns via phase shifts in a low-dimensional limit cycle in a manner analogous to tr... |
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