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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2006.01265 | Misha Perepelitsa | Misha Perepelitsa | A model of cultural evolution in the context of strategic conflict | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a model of cultural evolution for a strategy selection in a
population of individuals who interact in a game theoretic framework. The
evolution combines individual learning of the environment (population strategy
profile), reproduction, proportional to the success of the acquired knowledge,
and social tra... | [
{
"created": "Mon, 1 Jun 2020 21:06:53 GMT",
"version": "v1"
}
] | 2020-06-03 | [
[
"Perepelitsa",
"Misha",
""
]
] | We consider a model of cultural evolution for a strategy selection in a population of individuals who interact in a game theoretic framework. The evolution combines individual learning of the environment (population strategy profile), reproduction, proportional to the success of the acquired knowledge, and social trans... |
1808.07539 | Michael Baker Ph.D. | Yoshinao Katsu, Satomi Kohno, Kaori Oka, Xiaozhi Lin, Sumika Otake,
Nisha E. Pillai, Wataru Takagi, Susumu Hyodo, Byrappa Venkatesh, Michael E.
Baker | Transcriptional Activation of Elephant Shark Mineralocorticoid Receptor
by Corticosteroids, Progesterone and Spironolactone | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We report the analysis of activation by corticosteroids and progesterone of
full-length mineralocorticoid receptor (MR) from elephant shark, a
cartilaginous fish belonging to the oldest group of jawed vertebrates. Based on
their measured activities, aldosterone, cortisol, 11-deoxycorticosterone,
corticosterone, 11-de... | [
{
"created": "Wed, 22 Aug 2018 19:43:02 GMT",
"version": "v1"
}
] | 2018-08-24 | [
[
"Katsu",
"Yoshinao",
""
],
[
"Kohno",
"Satomi",
""
],
[
"Oka",
"Kaori",
""
],
[
"Lin",
"Xiaozhi",
""
],
[
"Otake",
"Sumika",
""
],
[
"Pillai",
"Nisha E.",
""
],
[
"Takagi",
"Wataru",
""
],
[
"Hyodo"... | We report the analysis of activation by corticosteroids and progesterone of full-length mineralocorticoid receptor (MR) from elephant shark, a cartilaginous fish belonging to the oldest group of jawed vertebrates. Based on their measured activities, aldosterone, cortisol, 11-deoxycorticosterone, corticosterone, 11-deox... |
1909.07737 | Christoph Simon Hundschell | Christoph Simon Hundschell, Frank Jakob, Anja Maria Wagemans | Molecular Weight Dependent Structure and Polymer Density of the
Exopolysaccharide Levan | null | null | null | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Levan is a bacterial homopolysaccharide, which consists of beta-2,6 linked
beta-D-fructose monomers. Because of its structural properties and its health
promoting effects, levan is a promising functional ingredient for the food,
cosmetic and pharma industry. The properties of levan have been reported to be
linked to ... | [
{
"created": "Tue, 17 Sep 2019 12:02:58 GMT",
"version": "v1"
},
{
"created": "Wed, 18 Sep 2019 08:26:32 GMT",
"version": "v2"
}
] | 2019-09-19 | [
[
"Hundschell",
"Christoph Simon",
""
],
[
"Jakob",
"Frank",
""
],
[
"Wagemans",
"Anja Maria",
""
]
] | Levan is a bacterial homopolysaccharide, which consists of beta-2,6 linked beta-D-fructose monomers. Because of its structural properties and its health promoting effects, levan is a promising functional ingredient for the food, cosmetic and pharma industry. The properties of levan have been reported to be linked to it... |
1209.5006 | Deep Ganguli | Deep Ganguli and Eero Simoncelli | Implicit embedding of prior probabilities in optimally efficient neural
populations | 15 pages, 2 figures, generalizes and extends Ganguli & Simoncelli,
NIPS 2010 | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We examine how the prior probability distribution of a sensory variable in
the environment influences the optimal allocation of neurons and spikes in a
population that represents that variable. We start with a conventional response
model, in which the spikes of each neuron are drawn from a Poisson distribution
with a... | [
{
"created": "Sat, 22 Sep 2012 17:30:53 GMT",
"version": "v1"
}
] | 2012-09-25 | [
[
"Ganguli",
"Deep",
""
],
[
"Simoncelli",
"Eero",
""
]
] | We examine how the prior probability distribution of a sensory variable in the environment influences the optimal allocation of neurons and spikes in a population that represents that variable. We start with a conventional response model, in which the spikes of each neuron are drawn from a Poisson distribution with a m... |
0903.3825 | Artur Garcia-Saez | Artur Garcia-Saez and J. Miguel Rubi | Strong cooperativity and inhibitory effects in DNA multi-looping
processes | 4 pages, 4 figures | null | null | null | q-bio.BM q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We show the existence of a high interrelation between the different loops
that may appear in a DNA segment. Conformational changes in a chain segment
caused by the formation of a particular loop may either promote or prevent the
appearance of another. The underlying loop selection mechanism is analyzed by
means of a ... | [
{
"created": "Mon, 23 Mar 2009 10:16:32 GMT",
"version": "v1"
}
] | 2009-03-24 | [
[
"Garcia-Saez",
"Artur",
""
],
[
"Rubi",
"J. Miguel",
""
]
] | We show the existence of a high interrelation between the different loops that may appear in a DNA segment. Conformational changes in a chain segment caused by the formation of a particular loop may either promote or prevent the appearance of another. The underlying loop selection mechanism is analyzed by means of a Ha... |
0810.3877 | Emilio Hernandez-Garcia | Emilio Hernandez-Garcia, Murat Tugrul, E. Alejandro Herrada, Victor M.
Eguiluz (IFISC, Palma de Mallorca, Spain), Konstantin Klemm (IFISC and
Bioinformatics, Leipzig, Germany) | Simple models for scaling in phylogenetic trees | 7 pages, 4 figures. A new figure, with example trees, has been added.
To appear in Int. J. Bifurcation and Chaos | International Journal of Bifurcation and Chaos 20, 805-811 (2010) | 10.1142/S0218127410026095 | null | q-bio.QM cond-mat.stat-mech q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many processes and models --in biological, physical, social, and other
contexts-- produce trees whose depth scales logarithmically with the number of
leaves. Phylogenetic trees, describing the evolutionary relationships between
biological species, are examples of trees for which such scaling is not
observed. With thi... | [
{
"created": "Tue, 21 Oct 2008 17:21:40 GMT",
"version": "v1"
},
{
"created": "Mon, 2 Feb 2009 17:08:49 GMT",
"version": "v2"
}
] | 2010-05-11 | [
[
"Hernandez-Garcia",
"Emilio",
"",
"IFISC, Palma de Mallorca, Spain"
],
[
"Tugrul",
"Murat",
"",
"IFISC, Palma de Mallorca, Spain"
],
[
"Herrada",
"E. Alejandro",
"",
"IFISC, Palma de Mallorca, Spain"
],
[
"Eguiluz",
"Victor M.",
"",
"IFIS... | Many processes and models --in biological, physical, social, and other contexts-- produce trees whose depth scales logarithmically with the number of leaves. Phylogenetic trees, describing the evolutionary relationships between biological species, are examples of trees for which such scaling is not observed. With this ... |
1307.1934 | Michiaki Hamada | Michiaki Hamada | RNA secondary structure prediction from multi-aligned sequences | A preprint of an invited review manuscript that will be published in
a chapter of the book `Methods in Molecular Biology'. Note that this version
of the manuscript may differ from the published version | null | null | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has been well accepted that the RNA secondary structures of most
functional non-coding RNAs (ncRNAs) are closely related to their functions and
are conserved during evolution. Hence, prediction of conserved secondary
structures from evolutionarily related sequences is one important task in RNA
bioinformatics; the ... | [
{
"created": "Mon, 8 Jul 2013 01:38:29 GMT",
"version": "v1"
}
] | 2013-07-09 | [
[
"Hamada",
"Michiaki",
""
]
] | It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the me... |
2102.08335 | Juul Goossens | Juul Goossens, Gilles Oudebrouckx, Seppe Bormans, Thijs Vandenryt,
Ronald Thoelen | Detecting cell and protein concentrations by the use of a thermal based
sensor | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biosensors are frequently used nowadays for the sake of their attractive
capabilities. Because of their high accuracy and precision, they are more and
more used in the medical sector. Natural receptors are mostly used, but their
use have some specific drawbacks. Therefore, new read-out methods are being
developed whe... | [
{
"created": "Tue, 16 Feb 2021 18:20:31 GMT",
"version": "v1"
}
] | 2021-02-17 | [
[
"Goossens",
"Juul",
""
],
[
"Oudebrouckx",
"Gilles",
""
],
[
"Bormans",
"Seppe",
""
],
[
"Vandenryt",
"Thijs",
""
],
[
"Thoelen",
"Ronald",
""
]
] | Biosensors are frequently used nowadays for the sake of their attractive capabilities. Because of their high accuracy and precision, they are more and more used in the medical sector. Natural receptors are mostly used, but their use have some specific drawbacks. Therefore, new read-out methods are being developed where... |
2003.07602 | Malik Magdon-Ismail | Malik Magdon-Ismail | Machine Learning the Phenomenology of COVID-19 From Early Infection
Dynamics | Test data up to April 02. Reorganized a little | null | null | null | q-bio.PE cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a robust data-driven machine learning analysis of the COVID-19
pandemic from its early infection dynamics, specifically infection counts over
time. The goal is to extract actionable public health insights. These insights
include the infectious force, the rate of a mild infection becoming serious,
estimates... | [
{
"created": "Tue, 17 Mar 2020 09:42:14 GMT",
"version": "v1"
},
{
"created": "Mon, 23 Mar 2020 02:05:04 GMT",
"version": "v2"
},
{
"created": "Fri, 3 Apr 2020 13:21:58 GMT",
"version": "v3"
}
] | 2020-04-06 | [
[
"Magdon-Ismail",
"Malik",
""
]
] | We present a robust data-driven machine learning analysis of the COVID-19 pandemic from its early infection dynamics, specifically infection counts over time. The goal is to extract actionable public health insights. These insights include the infectious force, the rate of a mild infection becoming serious, estimates f... |
1903.05615 | Pablo Rodr\'iguez-S\'anchez | Pablo Rodr\'iguez-S\'anchez, Egbert H. van Nes, Marten Scheffer | Climbing Escher's stairs: a way to approximate stability landscapes in
multidimensional systems | null | Rodriguez-Sanchez P. at al. (2020) PLOS Computational Biology
16(4): e1007788 | 10.1371/journal.pcbi.1007788 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stability landscapes are useful for understanding the properties of dynamical
systems. These landscapes can be calculated from the system's dynamical
equations using the physical concept of scalar potential. Unfortunately, for
most biological systems with two or more state variables such potentials do not
exist. Here... | [
{
"created": "Wed, 13 Mar 2019 17:28:12 GMT",
"version": "v1"
},
{
"created": "Thu, 18 Apr 2019 07:45:11 GMT",
"version": "v2"
}
] | 2020-04-24 | [
[
"Rodríguez-Sánchez",
"Pablo",
""
],
[
"van Nes",
"Egbert H.",
""
],
[
"Scheffer",
"Marten",
""
]
] | Stability landscapes are useful for understanding the properties of dynamical systems. These landscapes can be calculated from the system's dynamical equations using the physical concept of scalar potential. Unfortunately, for most biological systems with two or more state variables such potentials do not exist. Here w... |
1911.08398 | Alexandru Hening | Alexandru Hening | Coexistence, extinction, and optimal harvesting in discrete-time
stochastic population models | 37 pages, 9 figures | Journal of Nonlinear Science, vol. 31, 2021 | null | null | q-bio.PE math.OC math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze the long term behavior of interacting populations which can be
controlled through harvesting. The dynamics is assumed to be discrete in time
and stochastic due to the effect of environmental fluctuations. We present
extinction and coexistence criteria when there are one or two interacting
species. We then ... | [
{
"created": "Tue, 19 Nov 2019 17:02:20 GMT",
"version": "v1"
}
] | 2021-02-18 | [
[
"Hening",
"Alexandru",
""
]
] | We analyze the long term behavior of interacting populations which can be controlled through harvesting. The dynamics is assumed to be discrete in time and stochastic due to the effect of environmental fluctuations. We present extinction and coexistence criteria when there are one or two interacting species. We then us... |
1002.2644 | Jan-Timm Kuhr | Gerlinde Schwake, Simon Youssef, Jan-Timm Kuhr, Sebastian Gude, Maria
Pamela David, Eduardo Mendoza, Erwin Frey, Joachim O. R\"adler | Predictive Modeling of Non-Viral Gene Transfer | 20 pages, 6 figures, 12 pages supporting information | Biotechnology and Bioengineering, Volume 105, Issue 4, 805-813,
(2010) | 10.1002/bit.22604 | LMU-ASC 44/09 | q-bio.QM q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In non-viral gene delivery, the variance of transgenic expression stems from
the low number of plasmids successfully transferred. Here, we experimentally
determine Lipofectamine- and PEI-mediated exogenous gene expression
distributions from single cell time-lapse analysis. Broad Poisson-like
distributions of steady s... | [
{
"created": "Fri, 12 Feb 2010 21:13:37 GMT",
"version": "v1"
}
] | 2010-02-16 | [
[
"Schwake",
"Gerlinde",
""
],
[
"Youssef",
"Simon",
""
],
[
"Kuhr",
"Jan-Timm",
""
],
[
"Gude",
"Sebastian",
""
],
[
"David",
"Maria Pamela",
""
],
[
"Mendoza",
"Eduardo",
""
],
[
"Frey",
"Erwin",
""
],
... | In non-viral gene delivery, the variance of transgenic expression stems from the low number of plasmids successfully transferred. Here, we experimentally determine Lipofectamine- and PEI-mediated exogenous gene expression distributions from single cell time-lapse analysis. Broad Poisson-like distributions of steady sta... |
q-bio/0701036 | Robert Maier | Robert S. Maier | Parametrized Stochastic Grammars for RNA Secondary Structure Prediction | 5 pages, submitted to the 2007 Information Theory and Applications
Workshop (ITA 2007) | null | 10.1109/ITA.2007.4357589 | null | q-bio.BM math.PR | null | We propose a two-level stochastic context-free grammar (SCFG) architecture
for parametrized stochastic modeling of a family of RNA sequences, including
their secondary structure. A stochastic model of this type can be used for
maximum a posteriori estimation of the secondary structure of any new sequence
in the famil... | [
{
"created": "Wed, 24 Jan 2007 16:58:56 GMT",
"version": "v1"
}
] | 2014-03-06 | [
[
"Maier",
"Robert S.",
""
]
] | We propose a two-level stochastic context-free grammar (SCFG) architecture for parametrized stochastic modeling of a family of RNA sequences, including their secondary structure. A stochastic model of this type can be used for maximum a posteriori estimation of the secondary structure of any new sequence in the family.... |
1908.06872 | Jeyashree Krishnan | Jeyashree Krishnan, Reza Torabi, Edoardo Di Napoli, Andreas Schuppert | A Modified Ising Model of Barab\'asi-Albert Network with Gene-type Spins | 30 pages, 8 figures, presented in poster form in SBHD'18, LA, USA; as
a talk in SIAM CSE'19 | null | null | null | q-bio.QM cond-mat.stat-mech physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The central question of systems biology is to understand how individual
components of a biological system such as genes or proteins cooperate in
emerging phenotypes resulting in the evolution of diseases. As living cells are
open systems in quasi-steady state type equilibrium in continuous exchange with
their environ... | [
{
"created": "Mon, 19 Aug 2019 15:13:24 GMT",
"version": "v1"
}
] | 2019-08-20 | [
[
"Krishnan",
"Jeyashree",
""
],
[
"Torabi",
"Reza",
""
],
[
"Di Napoli",
"Edoardo",
""
],
[
"Schuppert",
"Andreas",
""
]
] | The central question of systems biology is to understand how individual components of a biological system such as genes or proteins cooperate in emerging phenotypes resulting in the evolution of diseases. As living cells are open systems in quasi-steady state type equilibrium in continuous exchange with their environme... |
2211.12935 | Sihao Liu | Sihao Liu (Daniel), Augustine N Mavor-Parker, Caswell Barry | Functional Connectome: Approximating Brain Networks with Artificial
Neural Networks | 13 pages, 10 figures | null | null | null | q-bio.NC cs.LG cs.NE | http://creativecommons.org/licenses/by/4.0/ | We aimed to explore the capability of deep learning to approximate the
function instantiated by biological neural circuits-the functional connectome.
Using deep neural networks, we performed supervised learning with firing rate
observations drawn from synthetically constructed neural circuits, as well as
from an empi... | [
{
"created": "Wed, 23 Nov 2022 13:12:13 GMT",
"version": "v1"
}
] | 2022-11-24 | [
[
"Liu",
"Sihao",
"",
"Daniel"
],
[
"Mavor-Parker",
"Augustine N",
""
],
[
"Barry",
"Caswell",
""
]
] | We aimed to explore the capability of deep learning to approximate the function instantiated by biological neural circuits-the functional connectome. Using deep neural networks, we performed supervised learning with firing rate observations drawn from synthetically constructed neural circuits, as well as from an empiri... |
q-bio/0311018 | Lior Pachter | Nicolas Bray, Lior Pachter | MAVID: Constrained ancestral alignment of multiple sequences | null | null | null | null | q-bio.GN | null | We describe a new global multiple alignment program capable of aligning a
large number of genomic regions. Our progressive alignment approach
incorporates the following ideas: maximum-likelihood inference of ancestral
sequences, automatic guide-tree construction, protein based anchoring of
ab-initio gene predictions,... | [
{
"created": "Thu, 13 Nov 2003 10:12:39 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bray",
"Nicolas",
""
],
[
"Pachter",
"Lior",
""
]
] | We describe a new global multiple alignment program capable of aligning a large number of genomic regions. Our progressive alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic guide-tree construction, protein based anchoring of ab-initio gene predictions, a... |
1602.05135 | Mark Transtrum | Andrew White, Malachi Tolman, Howard D. Thames, Hubert Rodney Withers,
Kathy A. Mason, Mark K. Transtrum | The limitations of model-based experimental design and parameter
estimation in sloppy systems | 27 pages, 8 figures | null | 10.1371/journal.pcbi.1005227 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We explore the relationship among model fidelity, experimental design, and
parameter estimation in sloppy models. We show that the approximate nature of
mathematical models poses challenges for experimental design in sloppy models.
In many models of complex biological processes it is unknown what are the
relevant phy... | [
{
"created": "Tue, 16 Feb 2016 18:43:47 GMT",
"version": "v1"
},
{
"created": "Fri, 6 May 2016 23:04:07 GMT",
"version": "v2"
},
{
"created": "Tue, 14 Jun 2016 15:02:13 GMT",
"version": "v3"
}
] | 2017-02-08 | [
[
"White",
"Andrew",
""
],
[
"Tolman",
"Malachi",
""
],
[
"Thames",
"Howard D.",
""
],
[
"Withers",
"Hubert Rodney",
""
],
[
"Mason",
"Kathy A.",
""
],
[
"Transtrum",
"Mark K.",
""
]
] | We explore the relationship among model fidelity, experimental design, and parameter estimation in sloppy models. We show that the approximate nature of mathematical models poses challenges for experimental design in sloppy models. In many models of complex biological processes it is unknown what are the relevant physi... |
2301.07599 | Viktoria Blavatska | Viktoria Blavatska, Bartlomiej Waclaw | Evolutionary adaptation is facilitated by the presence of lethal
genotypes | null | Phys. Rev. Research, 6 (2024) 013286 | 10.1103/PhysRevResearch.6.013286 | null | q-bio.PE physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | The adaptation rate in theoretical models of biological evolution increases
with the mutation rate but only to a point when mutations into lethal states
cause extinction. One would expect that removing such states should be
beneficial for evolution. We show here that, counter-intuitively, lethal
mutations speed up ad... | [
{
"created": "Wed, 18 Jan 2023 15:26:50 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Feb 2023 14:03:09 GMT",
"version": "v2"
}
] | 2024-06-27 | [
[
"Blavatska",
"Viktoria",
""
],
[
"Waclaw",
"Bartlomiej",
""
]
] | The adaptation rate in theoretical models of biological evolution increases with the mutation rate but only to a point when mutations into lethal states cause extinction. One would expect that removing such states should be beneficial for evolution. We show here that, counter-intuitively, lethal mutations speed up adap... |
2405.12022 | Giampiero Bardella | Giampiero Bardella, Simone Franchini, Pierpaolo Pani and Stefano
Ferraina | Lattice physics approaches for neural networks | 10 pages | null | null | null | q-bio.NC physics.app-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Modern neuroscience has evolved into a frontier field that draws on numerous
disciplines, resulting in the flourishing of novel conceptual frames primarily
inspired by physics and complex systems science. Contributing in this
direction, we recently introduced a mathematical framework to describe the
spatiotemporal in... | [
{
"created": "Mon, 20 May 2024 13:42:54 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Jun 2024 09:47:56 GMT",
"version": "v2"
}
] | 2024-06-24 | [
[
"Bardella",
"Giampiero",
""
],
[
"Franchini",
"Simone",
""
],
[
"Pani",
"Pierpaolo",
""
],
[
"Ferraina",
"Stefano",
""
]
] | Modern neuroscience has evolved into a frontier field that draws on numerous disciplines, resulting in the flourishing of novel conceptual frames primarily inspired by physics and complex systems science. Contributing in this direction, we recently introduced a mathematical framework to describe the spatiotemporal inte... |
1906.05390 | Mattia Miotto | Mattia Miotto, Lorenzo Di Rienzo, Pietro Corsi, Giancarlo Ruocco,
Domenico Raimondo, Edoardo Milanetti | Simulated Epidemics in 3D Protein Structures to Detect Functional
Properties | 9 pages, 5 figures | Journal of chemical information and modeling 60 (3), 1884-1891
(2020) | 10.1021/acs.jcim.9b01027 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The outcome of an epidemic is closely related to the network of interactions
between the individuals. Likewise, protein functions depend on the 3D
arrangement of their residues and on the underlying energetic interaction
network. Borrowing ideas from the theoretical framework that has been developed
to address the sp... | [
{
"created": "Wed, 12 Jun 2019 21:33:56 GMT",
"version": "v1"
},
{
"created": "Thu, 12 Dec 2019 11:41:41 GMT",
"version": "v2"
}
] | 2021-07-19 | [
[
"Miotto",
"Mattia",
""
],
[
"Di Rienzo",
"Lorenzo",
""
],
[
"Corsi",
"Pietro",
""
],
[
"Ruocco",
"Giancarlo",
""
],
[
"Raimondo",
"Domenico",
""
],
[
"Milanetti",
"Edoardo",
""
]
] | The outcome of an epidemic is closely related to the network of interactions between the individuals. Likewise, protein functions depend on the 3D arrangement of their residues and on the underlying energetic interaction network. Borrowing ideas from the theoretical framework that has been developed to address the spre... |
2011.13533 | Arnd Pralle | Weixiang Jin, Michael Zucker and Arnd Pralle | Membrane Nanodomains Homeostasis During Propofol Anesthesia as Function
of Dosage and Temperature | null | null | 10.1016/j.bbamem.2020.183511 | null | q-bio.CB q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Some anesthetics bind and potentiate gamma-aminobutyric-acid-type receptors,
but no universal mechanism for general anesthesia is known. Furthermore, often
encountered complications such as anesthesia induced amnesia are not
understood. General anesthetics are hydrophobic molecules easily dissolving
into lipid bilaye... | [
{
"created": "Fri, 27 Nov 2020 03:05:54 GMT",
"version": "v1"
}
] | 2020-11-30 | [
[
"Jin",
"Weixiang",
""
],
[
"Zucker",
"Michael",
""
],
[
"Pralle",
"Arnd",
""
]
] | Some anesthetics bind and potentiate gamma-aminobutyric-acid-type receptors, but no universal mechanism for general anesthesia is known. Furthermore, often encountered complications such as anesthesia induced amnesia are not understood. General anesthetics are hydrophobic molecules easily dissolving into lipid bilayers... |
2002.07655 | Johannes Kleiner | Johannes Kleiner and Sean Tull | The Mathematical Structure of Integrated Information Theory | null | null | null | null | q-bio.NC cs.AI cs.IT math.IT quant-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Integrated Information Theory is one of the leading models of consciousness.
It aims to describe both the quality and quantity of the conscious experience
of a physical system, such as the brain, in a particular state. In this
contribution, we propound the mathematical structure of the theory, separating
the essentia... | [
{
"created": "Tue, 18 Feb 2020 15:44:02 GMT",
"version": "v1"
}
] | 2020-02-19 | [
[
"Kleiner",
"Johannes",
""
],
[
"Tull",
"Sean",
""
]
] | Integrated Information Theory is one of the leading models of consciousness. It aims to describe both the quality and quantity of the conscious experience of a physical system, such as the brain, in a particular state. In this contribution, we propound the mathematical structure of the theory, separating the essentials... |
1711.06325 | Anthony Greenberg | Anthony J. Greenberg | Fast ordered sampling of DNA sequence variants | six figures | null | null | null | q-bio.GN stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Explosive growth in the amount of genomic data is matched by increasing power
of consumer-grade computers. Even applications that require powerful servers
can be quickly tested on desktop or laptop machines if we can generate
representative samples from large data sets. I describe a fast and
memory-efficient implemen... | [
{
"created": "Thu, 16 Nov 2017 21:35:12 GMT",
"version": "v1"
}
] | 2017-11-20 | [
[
"Greenberg",
"Anthony J.",
""
]
] | Explosive growth in the amount of genomic data is matched by increasing power of consumer-grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative samples from large data sets. I describe a fast and memory-efficient implementa... |
1801.03316 | Ekaterina Myasnikova | Ekaterina Myasnikova and Alexander Spirov | Modeling of gap gene regulatory networks in Drosophila with the account
of the gene modular structure (in Russian) | in Russian | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genes are frequently regulated in complex manners, necessitating modelling
approaches which go beyond simple (linear) gene-to-gene interactions and
address the modularity of cis-regulatory regions and alternate transcription
initiation sites. In particular, sharp expression patterns (peaks or stripes)
indicate that g... | [
{
"created": "Wed, 10 Jan 2018 11:38:43 GMT",
"version": "v1"
}
] | 2018-01-11 | [
[
"Myasnikova",
"Ekaterina",
""
],
[
"Spirov",
"Alexander",
""
]
] | Genes are frequently regulated in complex manners, necessitating modelling approaches which go beyond simple (linear) gene-to-gene interactions and address the modularity of cis-regulatory regions and alternate transcription initiation sites. In particular, sharp expression patterns (peaks or stripes) indicate that gen... |
1110.1091 | Carsten Lemmen | Carsten Lemmen and Aurangzeb Khan | A simulation of the Neolithic transition in the Indus valley | Chapter manuscript revision submitted to AGU monograph "Climates,
landscapes and civilizations", 6 pages, 2 figures | null | 10.1029/2012GM001217 | null | q-bio.PE cs.MA | http://creativecommons.org/licenses/by/3.0/ | The Indus Valley Civilization (IVC) was one of the first great civilizations
in prehistory. This bronze age civilization flourished from the end of the
fourth millennium BC. It disintegrated during the second millennium BC; despite
much research effort, this decline is not well understood. Less research has
been devo... | [
{
"created": "Wed, 5 Oct 2011 20:04:10 GMT",
"version": "v1"
},
{
"created": "Wed, 18 Apr 2012 08:56:26 GMT",
"version": "v2"
},
{
"created": "Mon, 7 May 2012 08:47:42 GMT",
"version": "v3"
}
] | 2017-02-24 | [
[
"Lemmen",
"Carsten",
""
],
[
"Khan",
"Aurangzeb",
""
]
] | The Indus Valley Civilization (IVC) was one of the first great civilizations in prehistory. This bronze age civilization flourished from the end of the fourth millennium BC. It disintegrated during the second millennium BC; despite much research effort, this decline is not well understood. Less research has been devote... |
2405.16865 | Dehong Xu | Dehong Xu, Ruiqi Gao, Wen-Hao Zhang, Xue-Xin Wei, Ying Nian Wu | An Investigation of Conformal Isometry Hypothesis for Grid Cells | arXiv admin note: text overlap with arXiv:2310.19192 | null | null | null | q-bio.NC cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper investigates the conformal isometry hypothesis as a potential
explanation for the emergence of hexagonal periodic patterns in the response
maps of grid cells. The hypothesis posits that the activities of the population
of grid cells form a high-dimensional vector in the neural space, representing
the agent... | [
{
"created": "Mon, 27 May 2024 06:31:39 GMT",
"version": "v1"
}
] | 2024-05-28 | [
[
"Xu",
"Dehong",
""
],
[
"Gao",
"Ruiqi",
""
],
[
"Zhang",
"Wen-Hao",
""
],
[
"Wei",
"Xue-Xin",
""
],
[
"Wu",
"Ying Nian",
""
]
] | This paper investigates the conformal isometry hypothesis as a potential explanation for the emergence of hexagonal periodic patterns in the response maps of grid cells. The hypothesis posits that the activities of the population of grid cells form a high-dimensional vector in the neural space, representing the agent's... |
1901.09861 | Vishwa Parekh | Vishwa S. Parekh, Michael A. Jacobs | Tumor Connectomics: Mapping the intra-tumoral complex interaction
network | 7 pages, 5 figures, SPIE Medical Imaging | null | null | null | q-bio.QM cs.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tumors are extremely heterogeneous and comprise of a number of intratumor
microenvironments or sub-regions. These tumor microenvironments may interact
with eac based on complex high-level relationships, which could provide
important insight into the organizational structure of the tumor network. To
that end, we devel... | [
{
"created": "Mon, 28 Jan 2019 18:07:46 GMT",
"version": "v1"
}
] | 2019-01-29 | [
[
"Parekh",
"Vishwa S.",
""
],
[
"Jacobs",
"Michael A.",
""
]
] | Tumors are extremely heterogeneous and comprise of a number of intratumor microenvironments or sub-regions. These tumor microenvironments may interact with eac based on complex high-level relationships, which could provide important insight into the organizational structure of the tumor network. To that end, we develop... |
1303.4383 | J. C. Phillips | J. C. Phillips | Hierarchical hydropathic evolution of influenza glycoproteins (N2, H3,
A/H3N2) under relentless vaccination pressure | null | null | null | null | q-bio.BM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Hemagglutinin (HA) and neuraminidase (NA) are highly variable envelope
glycoproteins. Here hydropathic analysis, previously applied to quantify common
flu (H1N1) evolution (1934-), is applied to the evolution of less common but
more virulent (avian derived) H3N2 (1968-), beginning with N2. Whereas N1
exhibited opposi... | [
{
"created": "Sat, 16 Mar 2013 16:54:18 GMT",
"version": "v1"
}
] | 2013-03-20 | [
[
"Phillips",
"J. C.",
""
]
] | Hemagglutinin (HA) and neuraminidase (NA) are highly variable envelope glycoproteins. Here hydropathic analysis, previously applied to quantify common flu (H1N1) evolution (1934-), is applied to the evolution of less common but more virulent (avian derived) H3N2 (1968-), beginning with N2. Whereas N1 exhibited opposing... |
1806.01078 | Pedro Mendes | Pedro Mendes | Reproducible research using biomodels | null | Bulletin of Mathematical Biology 80:3081-3087 (2018) | 10.1007/s11538-018-0498-z | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Like other types of computational research, modeling and simulation of
biological processes (biomodels) is still largely communicated without
sufficient detail to allow independent reproduction of results. But
reproducibility in this area of research could easily be achieved by making use
of existing resources, such ... | [
{
"created": "Mon, 4 Jun 2018 12:45:54 GMT",
"version": "v1"
}
] | 2023-04-19 | [
[
"Mendes",
"Pedro",
""
]
] | Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area of research could easily be achieved by making use of existing resources, such as... |
1902.06630 | Eugene Shakhnovich | Jo\~ao V. Rodrigues and Eugene Shakhnovich | Evolutionary dynamics determines adaptation to inactivation of an
essential gene | null | null | null | null | q-bio.PE q-bio.BM | http://creativecommons.org/publicdomain/zero/1.0/ | Genetic inactivation of essential genes creates an evolutionary scenario
distinct from escape from drug inhibition, but the mechanisms of microbe
adaptations in such cases remain unknown. Here we inactivate E. coli
dihydrofolate reductase (DHFR) by introducing D27G,N,F chromosomal mutations in
a key catalytic residue... | [
{
"created": "Mon, 18 Feb 2019 16:06:58 GMT",
"version": "v1"
}
] | 2019-02-19 | [
[
"Rodrigues",
"João V.",
""
],
[
"Shakhnovich",
"Eugene",
""
]
] | Genetic inactivation of essential genes creates an evolutionary scenario distinct from escape from drug inhibition, but the mechanisms of microbe adaptations in such cases remain unknown. Here we inactivate E. coli dihydrofolate reductase (DHFR) by introducing D27G,N,F chromosomal mutations in a key catalytic residue w... |
1609.07293 | Antoine Recanati | Antoine Recanati, Thomas Br\"uls, Alexandre d'Aspremont | A spectral algorithm for fast de novo layout of uncorrected long
nanopore reads | Now includes additional experiments, with a comparison of the method
to Canu, Miniasm and Racon with other datasets, and evaluation of the
computational performance | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: New long read sequencers promise to transform sequencing and
genome assembly by producing reads tens of kilobases long. However their high
error rate significantly complicates assembly and requires expensive correction
steps to layout the reads using standard assembly engines.
Results: We present an ori... | [
{
"created": "Fri, 23 Sep 2016 09:54:42 GMT",
"version": "v1"
},
{
"created": "Mon, 6 Mar 2017 13:25:44 GMT",
"version": "v2"
},
{
"created": "Mon, 17 Jul 2017 15:50:11 GMT",
"version": "v3"
}
] | 2017-07-18 | [
[
"Recanati",
"Antoine",
""
],
[
"Brüls",
"Thomas",
""
],
[
"d'Aspremont",
"Alexandre",
""
]
] | Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to layout the reads using standard assembly engines. Results: We present an origina... |
2011.11343 | Yu Zhang | Yueran Yang, Yu Zhang, Shuai Li, Xubin Zheng, Man-Hon Wong, Kwong-Sak
Leung, Lixin Cheng | A robust and generalizable immune-relatedsignature for sepsis
diagnostics | null | null | 10.1109/TCBB.2021.3107874 | null | q-bio.GN q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | High-throughput sequencing can detect tens of thousands of genes in parallel,
providing opportunities for improving the diagnostic accuracy of multiple
diseases including sepsis, which is an aggressive inflammatory response to
infection that can cause organ failure and death. Early screening of sepsis is
essential in... | [
{
"created": "Mon, 23 Nov 2020 11:49:26 GMT",
"version": "v1"
},
{
"created": "Mon, 16 Aug 2021 14:42:43 GMT",
"version": "v2"
},
{
"created": "Wed, 8 Dec 2021 17:52:50 GMT",
"version": "v3"
}
] | 2021-12-09 | [
[
"Yang",
"Yueran",
""
],
[
"Zhang",
"Yu",
""
],
[
"Li",
"Shuai",
""
],
[
"Zheng",
"Xubin",
""
],
[
"Wong",
"Man-Hon",
""
],
[
"Leung",
"Kwong-Sak",
""
],
[
"Cheng",
"Lixin",
""
]
] | High-throughput sequencing can detect tens of thousands of genes in parallel, providing opportunities for improving the diagnostic accuracy of multiple diseases including sepsis, which is an aggressive inflammatory response to infection that can cause organ failure and death. Early screening of sepsis is essential in c... |
1612.06319 | Anton Sinitskiy | Anton V. Sinitskiy, Nathaniel H. Stanley, David H. Hackos, Jesse E.
Hanson, Benjamin D. Sellers, Vijay S. Pande | Computationally Discovered Potentiating Role of Glycans on NMDA
Receptors | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | N-methyl-D-aspartate receptors (NMDARs) are glycoproteins in the brain
central to learning and memory. The effects of glycosylation on the structure
and dynamics of NMDARs are largely unknown. In this work, we use extensive
molecular dynamics simulations of GluN1 and GluN2B ligand binding domains
(LBDs) of NMDARs to ... | [
{
"created": "Mon, 19 Dec 2016 19:29:06 GMT",
"version": "v1"
}
] | 2016-12-20 | [
[
"Sinitskiy",
"Anton V.",
""
],
[
"Stanley",
"Nathaniel H.",
""
],
[
"Hackos",
"David H.",
""
],
[
"Hanson",
"Jesse E.",
""
],
[
"Sellers",
"Benjamin D.",
""
],
[
"Pande",
"Vijay S.",
""
]
] | N-methyl-D-aspartate receptors (NMDARs) are glycoproteins in the brain central to learning and memory. The effects of glycosylation on the structure and dynamics of NMDARs are largely unknown. In this work, we use extensive molecular dynamics simulations of GluN1 and GluN2B ligand binding domains (LBDs) of NMDARs to in... |
1511.07977 | Rani Parvathy Venkitakrishnan | Rani P Venkitakrishnan and Manojendu Choudhury | Importance of method validation: Implications of non-correlated
observables in sweet taste receptor studies | 2 tables, 2 figures, information on common sweeteners and
methodology. Submitted to: current science | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Validation of research methodology is critical in research design.
Correlation between experimental observables must be established before
undertaking extensive experiments or propose mechanisms. This article shows
that, observables in the popular calcium flux strength assay used in the
characterization of sweetener-... | [
{
"created": "Wed, 25 Nov 2015 07:30:07 GMT",
"version": "v1"
}
] | 2015-11-26 | [
[
"Venkitakrishnan",
"Rani P",
""
],
[
"Choudhury",
"Manojendu",
""
]
] | Validation of research methodology is critical in research design. Correlation between experimental observables must be established before undertaking extensive experiments or propose mechanisms. This article shows that, observables in the popular calcium flux strength assay used in the characterization of sweetener-sw... |
1810.07215 | Elizabeth Hobson | Elizabeth A. Hobson, Dan M{\o}nster, Simon DeDeo | Aggression heuristics underlie animal dominance hierarchies and provide
evidence of group-level social information | Comments welcome | Proceedings of the National Academy of Sciences, 118(10),
e2022912118. 2021 | 10.1073/pnas.2022912118 | null | q-bio.PE nlin.AO physics.soc-ph q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Members of a social species need to make appropriate decisions about who,
how, and when to interact with others in their group. However, it has been
difficult for researchers to detect the inputs to these decisions and, in
particular, how much information individuals actually have about their social
context. We prese... | [
{
"created": "Tue, 16 Oct 2018 18:18:44 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Mar 2019 19:15:31 GMT",
"version": "v2"
},
{
"created": "Thu, 12 Nov 2020 15:09:12 GMT",
"version": "v3"
}
] | 2024-07-15 | [
[
"Hobson",
"Elizabeth A.",
""
],
[
"Mønster",
"Dan",
""
],
[
"DeDeo",
"Simon",
""
]
] | Members of a social species need to make appropriate decisions about who, how, and when to interact with others in their group. However, it has been difficult for researchers to detect the inputs to these decisions and, in particular, how much information individuals actually have about their social context. We present... |
0807.0673 | Satoru Morita | Satoru Morita, Kei-ichi Tainaka, Hiroyasu Nagata, and Jin Yoshimura | Population Uncertainty in Model Ecosystem: Analysis by Stochastic
Differential Equation | 16 pages, 4 figure, submitted to J. Phys. Soc. Jpn | Journal of the Physical Society of Japan, 77, 093801 1-4 (2008) | 10.1143/JPSJ.77.093801 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Perturbation experiments are carried out by contact process and its
mean-field version. Here, the mortality rate is increased or decreased
suddenly. It is known that the fluctuation enhancement (FE) occurs after the
perturbation, where FE means a population uncertainty. In the present paper, we
develop a new theory o... | [
{
"created": "Fri, 4 Jul 2008 03:00:19 GMT",
"version": "v1"
}
] | 2012-07-20 | [
[
"Morita",
"Satoru",
""
],
[
"Tainaka",
"Kei-ichi",
""
],
[
"Nagata",
"Hiroyasu",
""
],
[
"Yoshimura",
"Jin",
""
]
] | Perturbation experiments are carried out by contact process and its mean-field version. Here, the mortality rate is increased or decreased suddenly. It is known that the fluctuation enhancement (FE) occurs after the perturbation, where FE means a population uncertainty. In the present paper, we develop a new theory of ... |
2107.02906 | Alessandro Casa | Maria Frizzarin, Antonio Bevilacqua, Bhaskar Dhariyal, Katarina
Domijan, Federico Ferraccioli, Elena Hayes, Georgiana Ifrim, Agnieszka
Konkolewska, Thach Le Nguyen, Uche Mbaka, Giovanna Ranzato, Ashish Singh,
Marco Stefanucci, Alessandro Casa | Mid infrared spectroscopy and milk quality traits: a data analysis
competition at the "International Workshop on Spectroscopy and Chemometrics
2021" | 17 pages, 6 figures, 6 tables | Chemometrics and Intelligent Laboratory Systems, 2021, Volume 219,
104442 | 10.1016/j.chemolab.2021.104442 | null | q-bio.QM stat.AP | http://creativecommons.org/licenses/by/4.0/ | A chemometric data analysis challenge has been arranged during the first
edition of the "International Workshop on Spectroscopy and Chemometrics",
organized by the Vistamilk SFI Research Centre and held online in April 2021.
The aim of the competition was to build a calibration model in order to predict
milk quality ... | [
{
"created": "Mon, 5 Jul 2021 14:40:17 GMT",
"version": "v1"
},
{
"created": "Mon, 19 Sep 2022 07:40:37 GMT",
"version": "v2"
}
] | 2022-09-20 | [
[
"Frizzarin",
"Maria",
""
],
[
"Bevilacqua",
"Antonio",
""
],
[
"Dhariyal",
"Bhaskar",
""
],
[
"Domijan",
"Katarina",
""
],
[
"Ferraccioli",
"Federico",
""
],
[
"Hayes",
"Elena",
""
],
[
"Ifrim",
"Georgiana",
... | A chemometric data analysis challenge has been arranged during the first edition of the "International Workshop on Spectroscopy and Chemometrics", organized by the Vistamilk SFI Research Centre and held online in April 2021. The aim of the competition was to build a calibration model in order to predict milk quality tr... |
1905.01337 | Ulrich S. Schwarz | Felix Frey, Falko Ziebert, Ulrich S. Schwarz (Heidelberg University) | Dynamics of particle uptake at cell membranes | 20 pages, 19 figures | Phys. Rev. E 100, 052403 (2019) | 10.1103/PhysRevE.100.052403 | null | q-bio.SC cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Receptor-mediated endocytosis requires that the energy of adhesion overcomes
the deformation energy of the plasma membrane. The resulting driving force is
balanced by dissipative forces, leading to deterministic dynamical equations.
While the shape of the free membrane does not play an important role for tensed
and l... | [
{
"created": "Fri, 3 May 2019 18:34:02 GMT",
"version": "v1"
},
{
"created": "Fri, 25 Oct 2019 18:48:09 GMT",
"version": "v2"
}
] | 2019-11-20 | [
[
"Frey",
"Felix",
"",
"Heidelberg University"
],
[
"Ziebert",
"Falko",
"",
"Heidelberg University"
],
[
"Schwarz",
"Ulrich S.",
"",
"Heidelberg University"
]
] | Receptor-mediated endocytosis requires that the energy of adhesion overcomes the deformation energy of the plasma membrane. The resulting driving force is balanced by dissipative forces, leading to deterministic dynamical equations. While the shape of the free membrane does not play an important role for tensed and loo... |
0805.1776 | Andrew Mugler | Andrew Mugler, Etay Ziv, Ilya Nemenman, Chris H. Wiggins | Serially-regulated biological networks fully realize a constrained set
of functions | 9 pages, 3 figures | IET Sys. Bio. 2 (2008) 313-322 | 10.1049/iet-syb:20080097 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We show that biological networks with serial regulation (each node regulated
by at most one other node) are constrained to {\it direct functionality}, in
which the sign of the effect of an environmental input on a target species
depends only on the direct path from the input to the target, even when there
is a feedba... | [
{
"created": "Tue, 13 May 2008 05:00:26 GMT",
"version": "v1"
}
] | 2009-11-30 | [
[
"Mugler",
"Andrew",
""
],
[
"Ziv",
"Etay",
""
],
[
"Nemenman",
"Ilya",
""
],
[
"Wiggins",
"Chris H.",
""
]
] | We show that biological networks with serial regulation (each node regulated by at most one other node) are constrained to {\it direct functionality}, in which the sign of the effect of an environmental input on a target species depends only on the direct path from the input to the target, even when there is a feedback... |
1909.09478 | Ludvig Lizana | Markus Nyberg and Tobias Ambj\"ornsson and Per Stenberg and and Ludvig
Lizana | Modelling Protein Target-Search in Human Chromosomes | null | Phys. Rev. Research 3, 013055 (2021) | 10.1103/PhysRevResearch.3.013055 | null | q-bio.SC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Several processes in the cell, such as gene regulation, start when key
proteins recognise and bind to short DNA sequences. However, as these sequences
can be hundreds of million times shorter than the genome, they are hard to find
by simple diffusion: diffusion-limited association rates may underestimate
$in~vitro$ m... | [
{
"created": "Thu, 19 Sep 2019 07:18:12 GMT",
"version": "v1"
}
] | 2021-01-27 | [
[
"Nyberg",
"Markus",
""
],
[
"Ambjörnsson",
"Tobias",
""
],
[
"Stenberg",
"Per",
""
],
[
"Lizana",
"and Ludvig",
""
]
] | Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple diffusion: diffusion-limited association rates may underestimate $in~vitro$ mea... |
1501.04605 | Lee Altenberg | Lee Altenberg | Statistical Problems in a Paper on Variation In Cancer Risk Among
Tissues, and New Discoveries | 7 pages, 4 figures, 1 table | null | null | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tomasetti and Vogelstein (2015) collected data on 31 different tissue types
and found a correlation of 0.8 between the logarithms of the incidence of
cancer (LCI), and the estimated number of stem cell divisions in those tissues
(LSCD). Some of their conclusions however are statistically erroneous. Their
excess risk ... | [
{
"created": "Mon, 19 Jan 2015 20:00:11 GMT",
"version": "v1"
}
] | 2015-01-20 | [
[
"Altenberg",
"Lee",
""
]
] | Tomasetti and Vogelstein (2015) collected data on 31 different tissue types and found a correlation of 0.8 between the logarithms of the incidence of cancer (LCI), and the estimated number of stem cell divisions in those tissues (LSCD). Some of their conclusions however are statistically erroneous. Their excess risk sc... |
2203.00449 | Ruqayya Awan | Ruqayya Awan, Mohammed Nimir, Shan E Ahmed Raza, Mohsin Bilal,
Johannes Lotz, David Snead, Andrew Robinson, Nasir Rajpoot | Deep Learning based Prediction of MSI using MMR Markers in Colorectal
Cancer | null | null | null | null | q-bio.QM cs.CV eess.IV | http://creativecommons.org/licenses/by/4.0/ | The accurate diagnosis and molecular profiling of colorectal cancers are
critical for planning the best treatment options for patients. Microsatellite
instability (MSI) or mismatch repair (MMR) status plays a vital role in
appropriate treatment selection, has prognostic implications and is used to
investigate the pos... | [
{
"created": "Thu, 24 Feb 2022 18:56:59 GMT",
"version": "v1"
},
{
"created": "Sun, 17 Apr 2022 11:18:54 GMT",
"version": "v2"
},
{
"created": "Tue, 26 Apr 2022 04:07:14 GMT",
"version": "v3"
}
] | 2022-04-27 | [
[
"Awan",
"Ruqayya",
""
],
[
"Nimir",
"Mohammed",
""
],
[
"Raza",
"Shan E Ahmed",
""
],
[
"Bilal",
"Mohsin",
""
],
[
"Lotz",
"Johannes",
""
],
[
"Snead",
"David",
""
],
[
"Robinson",
"Andrew",
""
],
[
... | The accurate diagnosis and molecular profiling of colorectal cancers are critical for planning the best treatment options for patients. Microsatellite instability (MSI) or mismatch repair (MMR) status plays a vital role in appropriate treatment selection, has prognostic implications and is used to investigate the possi... |
q-bio/0607001 | Herculano Martinho | P. O. Andrade, R. A. Bitar, K. Yassoyama, H. Martinho, A. M. E. Santo,
P. M. Bruno, A. A. Martin | Study of Non-Altered Colorectal Tissue by FT-Raman Spectroscopy | 14 pages, 4 figures, submited to Analytical and Bioanalytical
Chemistry | null | null | null | q-bio.TO q-bio.BM | null | FT-Raman spectroscopy was employed to study (in-vitro) non-altered human
colorectal tissues aiming evaluate their spectral differences. The samples were
collected from 39 patients, adding 144 spectra. The results enable one
estabilish 3 well defined spectroscopic groups of what was consistently checked
by statistical... | [
{
"created": "Mon, 3 Jul 2006 13:32:40 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Andrade",
"P. O.",
""
],
[
"Bitar",
"R. A.",
""
],
[
"Yassoyama",
"K.",
""
],
[
"Martinho",
"H.",
""
],
[
"Santo",
"A. M. E.",
""
],
[
"Bruno",
"P. M.",
""
],
[
"Martin",
"A. A.",
""
]
] | FT-Raman spectroscopy was employed to study (in-vitro) non-altered human colorectal tissues aiming evaluate their spectral differences. The samples were collected from 39 patients, adding 144 spectra. The results enable one estabilish 3 well defined spectroscopic groups of what was consistently checked by statistical (... |
1609.03948 | Lee Friedman Lee Friedman | Lee Friedman, Ioannis Rigas, Mark S. Nixon, Oleg V. Komogortsev | Method to Assess the Temporal Persistence of Potential Biometric
Features: Application to Oculomotor, and Gait-Related Databases | 13 pages, 8 figures, 5 tables | null | 10.1371/journal.pone.0178501 | null | q-bio.QM cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although temporal persistence, or permanence, is a well understood
requirement for optimal biometric features, there is no general agreement on
how to assess temporal persistence. We suggest that the best way to assess
temporal persistence is to perform a test-retest study, and assess test-retest
reliability. For rat... | [
{
"created": "Tue, 13 Sep 2016 17:38:39 GMT",
"version": "v1"
}
] | 2017-07-05 | [
[
"Friedman",
"Lee",
""
],
[
"Rigas",
"Ioannis",
""
],
[
"Nixon",
"Mark S.",
""
],
[
"Komogortsev",
"Oleg V.",
""
]
] | Although temporal persistence, or permanence, is a well understood requirement for optimal biometric features, there is no general agreement on how to assess temporal persistence. We suggest that the best way to assess temporal persistence is to perform a test-retest study, and assess test-retest reliability. For ratio... |
1911.06602 | Toby St Clere Smithe | Toby B. St Clere Smithe | Radically Compositional Cognitive Concepts | 6 pages, 2 figures; NeurIPS 2019 Context and Compositionality
workshop. Work in progress | null | null | null | q-bio.NC cs.AI cs.CL cs.NE | http://creativecommons.org/licenses/by/4.0/ | Despite ample evidence that our concepts, our cognitive architecture, and
mathematics itself are all deeply compositional, few models take advantage of
this structure. We therefore propose a radically compositional approach to
computational neuroscience, drawing on the methods of applied category theory.
We describe ... | [
{
"created": "Thu, 14 Nov 2019 18:20:36 GMT",
"version": "v1"
}
] | 2019-11-18 | [
[
"Smithe",
"Toby B. St Clere",
""
]
] | Despite ample evidence that our concepts, our cognitive architecture, and mathematics itself are all deeply compositional, few models take advantage of this structure. We therefore propose a radically compositional approach to computational neuroscience, drawing on the methods of applied category theory. We describe ho... |
2403.02733 | Frederik F. Fl\"other | Frederik F. Fl\"other | Early quantum computing applications on the path towards precision
medicine | null | null | null | null | q-bio.QM quant-ph | http://creativecommons.org/licenses/by-sa/4.0/ | The last few years have seen rapid progress in transitioning quantum
computing from lab to industry. In healthcare and life sciences, more than 40
proof-of-concept experiments and studies have been conducted; an increasing
number of these are even run on real quantum hardware. Major investments have
been made with hu... | [
{
"created": "Tue, 5 Mar 2024 07:41:29 GMT",
"version": "v1"
}
] | 2024-03-06 | [
[
"Flöther",
"Frederik F.",
""
]
] | The last few years have seen rapid progress in transitioning quantum computing from lab to industry. In healthcare and life sciences, more than 40 proof-of-concept experiments and studies have been conducted; an increasing number of these are even run on real quantum hardware. Major investments have been made with hund... |
2306.15940 | Feng Xu | Feng Xu, Shuxiang Zhang, Linjie Ma, Yong Hou, Jie Li, Andrej
Denisenko, Zifu Li, Joachim Spatz, J\"org Wrachtrup, Qiang Wei, and Zhiqin
Chu | Quantum-Enhanced Diamond Molecular Tension Microscopy for Quantifying
Cellular Forces | 51 pages, 20 figures | null | null | null | q-bio.CB | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The constant interplay and information exchange between cells and their
micro-environment are essential to their survival and ability to execute
biological functions. To date, a few leading technologies such as traction
force microscopy, have been broadly used in measuring cellular forces. However,
the considerable l... | [
{
"created": "Wed, 28 Jun 2023 05:58:51 GMT",
"version": "v1"
}
] | 2023-06-29 | [
[
"Xu",
"Feng",
""
],
[
"Zhang",
"Shuxiang",
""
],
[
"Ma",
"Linjie",
""
],
[
"Hou",
"Yong",
""
],
[
"Li",
"Jie",
""
],
[
"Denisenko",
"Andrej",
""
],
[
"Li",
"Zifu",
""
],
[
"Spatz",
"Joachim",
... | The constant interplay and information exchange between cells and their micro-environment are essential to their survival and ability to execute biological functions. To date, a few leading technologies such as traction force microscopy, have been broadly used in measuring cellular forces. However, the considerable lim... |
1001.5241 | Frederick Matsen IV | Mar\'ia Ang\'elica Cueto and Frederick A. Matsen | Polyhedral geometry of Phylogenetic Rogue Taxa | In this version, we add quartet distances and fix Table 4. | null | null | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is well known among phylogeneticists that adding an extra taxon (e.g.
species) to a data set can alter the structure of the optimal phylogenetic tree
in surprising ways. However, little is known about this "rogue taxon" effect.
In this paper we characterize the behavior of balanced minimum evolution (BME)
phylogen... | [
{
"created": "Thu, 28 Jan 2010 18:40:38 GMT",
"version": "v1"
},
{
"created": "Mon, 29 Mar 2010 03:52:11 GMT",
"version": "v2"
},
{
"created": "Wed, 31 Mar 2010 01:47:11 GMT",
"version": "v3"
},
{
"created": "Sat, 24 Apr 2010 14:39:26 GMT",
"version": "v4"
}
] | 2010-04-27 | [
[
"Cueto",
"María Angélica",
""
],
[
"Matsen",
"Frederick A.",
""
]
] | It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenet... |
2011.12050 | Alessandro Sarracino | Dario Raimo, Alessandro Sarracino, Lucilla de Arcangelis | Role of inhibitory neurons in temporal correlations of critical and
supercritical spontaneous activity | 15 pages, 6 figures | Physica A, 125555 (2020) | 10.1016/j.physa.2020.125555 | null | q-bio.NC cond-mat.dis-nn cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Experimental and numerical results suggest that the brain can be viewed as a
system acting close to a critical point, as confirmed by scale-free
distributions of relevant quantities in a variety of different systems and
models. Less attention has received the investigation of the temporal
correlation functions in bra... | [
{
"created": "Tue, 24 Nov 2020 11:58:06 GMT",
"version": "v1"
}
] | 2020-11-25 | [
[
"Raimo",
"Dario",
""
],
[
"Sarracino",
"Alessandro",
""
],
[
"de Arcangelis",
"Lucilla",
""
]
] | Experimental and numerical results suggest that the brain can be viewed as a system acting close to a critical point, as confirmed by scale-free distributions of relevant quantities in a variety of different systems and models. Less attention has received the investigation of the temporal correlation functions in brain... |
1112.4589 | Hong Qian | Hong Qian and Sumit Roy | An Information Theoretical Analysis of Kinase Activated Phosphorylation
Dephosphorylation Cycle | 17 pages, 7 figures | IEEE Transactions on NanoBioscience, Volume 11, Issue 3, pp. 289 -
295 (2012) | 10.1109/TNB.2011.2182658 | null | q-bio.SC cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Signal transduction, the information processing mechanism in biological
cells, is carried out by a network of biochemical reactions. The dynamics of
driven biochemical reactions can be studied in terms of nonequilibrium
statistical physics. Such systems may also be studied in terms of Shannon's
information theory. We... | [
{
"created": "Tue, 20 Dec 2011 07:29:01 GMT",
"version": "v1"
}
] | 2012-09-13 | [
[
"Qian",
"Hong",
""
],
[
"Roy",
"Sumit",
""
]
] | Signal transduction, the information processing mechanism in biological cells, is carried out by a network of biochemical reactions. The dynamics of driven biochemical reactions can be studied in terms of nonequilibrium statistical physics. Such systems may also be studied in terms of Shannon's information theory. We c... |
2008.13229 | Ernest Greene | Ernest Greene | An evolutionary perspective on the design of neuromorphic shape filters | null | IEEE Access, 2020, 8, 114228-114238 | 10.1109/ACCESS.2020_3004412 | null | q-bio.NC cs.AI cs.CV cs.NE eess.IV | http://creativecommons.org/licenses/by/4.0/ | A substantial amount of time and energy has been invested to develop machine
vision using connectionist (neural network) principles. Most of that work has
been inspired by theories advanced by neuroscientists and behaviorists for how
cortical systems store stimulus information. Those theories call for
information flo... | [
{
"created": "Sun, 30 Aug 2020 17:53:44 GMT",
"version": "v1"
}
] | 2020-09-01 | [
[
"Greene",
"Ernest",
""
]
] | A substantial amount of time and energy has been invested to develop machine vision using connectionist (neural network) principles. Most of that work has been inspired by theories advanced by neuroscientists and behaviorists for how cortical systems store stimulus information. Those theories call for information flow ... |
1201.1424 | Mustafa Barasa | Joshua Muli Mutiso, John Chege Macharia, Mustafa Barasa, Evans
Taracha, Alain J. Bourdichon, Michael Muita Gicheru | In vitro and in vivo antileishmanial efficacy of a combination therapy
of diminazene and artesunate against Leishmania donovani in BALB /c mice | 4 Pages, 3 Figures | Rev. Inst. Med. Trop. Sao Paulo. 2011, 53 (3): 129 - 132 | 10.1590/S0036-46652011000300003 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The in vitro and in vivo activity of diminazene (Dim), artesunate (Art) and
combination of Dim and Art (Dim-Art) against Leishmania donovani was compared
to reference drug; amphotericin B. IC50 of Dim-Art was found to be $2.28 \pm
0.24 \mu$ g/mL while those of Dim and Art were $9.16 \pm 0.3 \mu$ g/mL and
$4.64 \pm 0.... | [
{
"created": "Thu, 22 Dec 2011 10:09:53 GMT",
"version": "v1"
}
] | 2012-01-17 | [
[
"Mutiso",
"Joshua Muli",
""
],
[
"Macharia",
"John Chege",
""
],
[
"Barasa",
"Mustafa",
""
],
[
"Taracha",
"Evans",
""
],
[
"Bourdichon",
"Alain J.",
""
],
[
"Gicheru",
"Michael Muita",
""
]
] | The in vitro and in vivo activity of diminazene (Dim), artesunate (Art) and combination of Dim and Art (Dim-Art) against Leishmania donovani was compared to reference drug; amphotericin B. IC50 of Dim-Art was found to be $2.28 \pm 0.24 \mu$ g/mL while those of Dim and Art were $9.16 \pm 0.3 \mu$ g/mL and $4.64 \pm 0.48... |
q-bio/0609023 | Ashok Palaniappan | Ashok Palaniappan, Eric Jakobsson | Evolutionary Analysis of Biological Excitability | Includes a contribution to Chomskyan linguistics | null | null | null | q-bio.BM q-bio.CB q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Excitability is an attribute of life, and is a driving force in the descent
of complexity. Cellular electrical activity as realized by membrane proteins
that act as either channels or transporters is the basis of excitability.
Electrical signaling is mediated by a wave of action potentials, which consist
of synchrono... | [
{
"created": "Fri, 15 Sep 2006 05:17:57 GMT",
"version": "v1"
},
{
"created": "Tue, 4 Sep 2007 06:25:02 GMT",
"version": "v2"
},
{
"created": "Mon, 20 Apr 2009 10:35:15 GMT",
"version": "v3"
},
{
"created": "Sun, 18 Oct 2009 11:53:27 GMT",
"version": "v4"
},
{
"cr... | 2009-11-05 | [
[
"Palaniappan",
"Ashok",
""
],
[
"Jakobsson",
"Eric",
""
]
] | Excitability is an attribute of life, and is a driving force in the descent of complexity. Cellular electrical activity as realized by membrane proteins that act as either channels or transporters is the basis of excitability. Electrical signaling is mediated by a wave of action potentials, which consist of synchronous... |
1909.06683 | Peter Taylor | Sriharsha Ramaraju, Simon Reichert, Yujiang Wang, Rob Forsyth, Peter N
Taylor | Carbogen inhalation during Non-Convulsive Status Epilepticus: A
quantitative analysis of EEG recordings | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Objective: To quantify the effect of inhaled 5% carbon-dioxide/95% oxygen on
EEG recordings from patients in non-convulsive status epilepticus (NCSE).
Methods: Five children of mixed aetiology in NCSE were given high flow of
inhaled carbogen (5% carbon dioxide/95% oxygen) using a face mask for maximum
120s. EEG was r... | [
{
"created": "Sat, 14 Sep 2019 21:49:06 GMT",
"version": "v1"
}
] | 2019-09-17 | [
[
"Ramaraju",
"Sriharsha",
""
],
[
"Reichert",
"Simon",
""
],
[
"Wang",
"Yujiang",
""
],
[
"Forsyth",
"Rob",
""
],
[
"Taylor",
"Peter N",
""
]
] | Objective: To quantify the effect of inhaled 5% carbon-dioxide/95% oxygen on EEG recordings from patients in non-convulsive status epilepticus (NCSE). Methods: Five children of mixed aetiology in NCSE were given high flow of inhaled carbogen (5% carbon dioxide/95% oxygen) using a face mask for maximum 120s. EEG was rec... |
2311.09131 | Farzan Vahedifard | Farzan Vahedifard, Atieh Sadeghniiat Haghighi, Tirth Dave, Mohammad
Tolouei, Fateme Hoshyar Zare | Practical Use of ChatGPT in Psychiatry for Treatment Plan and
Psychoeducation | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Artificial Intelligence (AI) has revolutionized various fields, including
medicine and mental health support. One promising application is ChatGPT, an
advanced conversational AI model that uses deep learning techniques to provide
human-like responses. This review paper explores the potential impact of
ChatGPT in psyc... | [
{
"created": "Wed, 15 Nov 2023 17:21:09 GMT",
"version": "v1"
}
] | 2023-11-16 | [
[
"Vahedifard",
"Farzan",
""
],
[
"Haghighi",
"Atieh Sadeghniiat",
""
],
[
"Dave",
"Tirth",
""
],
[
"Tolouei",
"Mohammad",
""
],
[
"Zare",
"Fateme Hoshyar",
""
]
] | Artificial Intelligence (AI) has revolutionized various fields, including medicine and mental health support. One promising application is ChatGPT, an advanced conversational AI model that uses deep learning techniques to provide human-like responses. This review paper explores the potential impact of ChatGPT in psychi... |
2011.14118 | Eberhard Bodenschatz | Freja Nordsiek and Eberhard Bodenschatz and Gholamhossein Bagheri | Risk assessment for airborne disease transmission by poly-pathogen
aerosols | updated file with link to software on GitHub | null | 10.1371/journal.pone.0248004 | null | q-bio.QM physics.med-ph | http://creativecommons.org/licenses/by/4.0/ | In the case of airborne diseases, pathogen copies are transmitted by droplets
of respiratory tract fluid that are exhaled by the infectious and, after
partial or full drying, inhaled as aerosols by the susceptible. The risk of
infection in indoor environments is typically modelled using the Wells-Riley
model or a Wel... | [
{
"created": "Sat, 28 Nov 2020 11:58:01 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Feb 2021 12:16:16 GMT",
"version": "v2"
}
] | 2021-06-09 | [
[
"Nordsiek",
"Freja",
""
],
[
"Bodenschatz",
"Eberhard",
""
],
[
"Bagheri",
"Gholamhossein",
""
]
] | In the case of airborne diseases, pathogen copies are transmitted by droplets of respiratory tract fluid that are exhaled by the infectious and, after partial or full drying, inhaled as aerosols by the susceptible. The risk of infection in indoor environments is typically modelled using the Wells-Riley model or a Wells... |
2007.07429 | Laurent H\'ebert-Dufresne | Blake J. M. Williams, Guillaume St-Onge and Laurent H\'ebert-Dufresne | Localization, epidemic transitions, and unpredictability of multistrain
epidemics with an underlying genotype network | null | PLoS Comput Biol 17(2): e1008606 (2021) | 10.1371/journal.pcbi.1008606 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mathematical disease modelling has long operated under the assumption that
any one infectious disease is caused by one transmissible pathogen spreading
among a population. This paradigm has been useful in simplifying the biological
reality of epidemics and has allowed the modelling community to focus on the
complexit... | [
{
"created": "Wed, 15 Jul 2020 01:49:49 GMT",
"version": "v1"
},
{
"created": "Tue, 1 Jun 2021 17:39:22 GMT",
"version": "v2"
}
] | 2021-06-02 | [
[
"Williams",
"Blake J. M.",
""
],
[
"St-Onge",
"Guillaume",
""
],
[
"Hébert-Dufresne",
"Laurent",
""
]
] | Mathematical disease modelling has long operated under the assumption that any one infectious disease is caused by one transmissible pathogen spreading among a population. This paradigm has been useful in simplifying the biological reality of epidemics and has allowed the modelling community to focus on the complexity ... |
1906.00944 | Aqib Hasnain | Aqib Hasnain, Nibodh Boddupalli, Enoch Yeung | Optimal reporter placement in sparsely measured genetic networks using
the Koopman operator | 6 pages, 3 figures, to appear in 2019 IEEE Conference on Decision and
Control (CDC) | null | null | null | q-bio.MN cs.SY eess.SY math.DS math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Optimal sensor placement is an important yet unsolved problem in control
theory. In biological organisms, genetic activity is often highly nonlinear,
making it difficult to design libraries of promoters to act as reporters of the
cell state. We make use of the Koopman observability gramian to develop an
algorithm for... | [
{
"created": "Mon, 3 Jun 2019 17:52:38 GMT",
"version": "v1"
},
{
"created": "Wed, 18 Sep 2019 07:37:05 GMT",
"version": "v2"
}
] | 2019-09-19 | [
[
"Hasnain",
"Aqib",
""
],
[
"Boddupalli",
"Nibodh",
""
],
[
"Yeung",
"Enoch",
""
]
] | Optimal sensor placement is an important yet unsolved problem in control theory. In biological organisms, genetic activity is often highly nonlinear, making it difficult to design libraries of promoters to act as reporters of the cell state. We make use of the Koopman observability gramian to develop an algorithm for o... |
0707.0245 | Bard Ermentrout | G. Bard Ermentrout, Roberto F. Gal\'an Nathaniel N. Urban | Relating Neural Dynamics to Neural Coding | 10 pages, 3 figures | null | null | null | q-bio.NC | null | We demonstrate that two key theoretical objects used widely in Computational
Neuroscience, the phase-resetting curve (PRC) from dynamics and the spike
triggered average (STA) from statistical analysis, are closely related under a
wide range of stimulus conditions. We prove that the STA is proportional to the
derivati... | [
{
"created": "Mon, 2 Jul 2007 14:56:43 GMT",
"version": "v1"
},
{
"created": "Wed, 26 Sep 2007 18:49:49 GMT",
"version": "v2"
}
] | 2007-09-26 | [
[
"Ermentrout",
"G. Bard",
""
],
[
"Urban",
"Roberto F. Galán Nathaniel N.",
""
]
] | We demonstrate that two key theoretical objects used widely in Computational Neuroscience, the phase-resetting curve (PRC) from dynamics and the spike triggered average (STA) from statistical analysis, are closely related under a wide range of stimulus conditions. We prove that the STA is proportional to the derivative... |
1801.07421 | Kang Hao Cheong | Jin Ming Koh, Kang Hao Cheong | Strategic nomadic-colonial switching: Stochastic noise and
subsidence-recovery cycles | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Previously, we developed a population model incorporating the Allee effect
and periodic environmental fluctuations, in which organisms alternate between
nomadic and colonial behaviours. This switching strategy is regulated by
biological clocks and the abundance of environmental resources, and can lead to
population p... | [
{
"created": "Tue, 23 Jan 2018 07:44:09 GMT",
"version": "v1"
}
] | 2018-01-24 | [
[
"Koh",
"Jin Ming",
""
],
[
"Cheong",
"Kang Hao",
""
]
] | Previously, we developed a population model incorporating the Allee effect and periodic environmental fluctuations, in which organisms alternate between nomadic and colonial behaviours. This switching strategy is regulated by biological clocks and the abundance of environmental resources, and can lead to population per... |
2110.11161 | Olha Shchur | Olha Shchur and Alexander Vidybida | Distribution of interspike intervals of a neuron with inhibitory autapse
stimulated with a renewal process | 12 pages, 3 figures | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we study analytically the impact of an inhibitory autapse on
neuronal activity. In order to do this, we formulate conditions on a set of
non-adaptive spiking neuron models with delayed feedback inhibition, instead of
considering a particular neuronal model. The neuron is stimulated with a
stochastic po... | [
{
"created": "Thu, 21 Oct 2021 14:13:37 GMT",
"version": "v1"
},
{
"created": "Wed, 12 Oct 2022 14:30:27 GMT",
"version": "v2"
}
] | 2022-10-13 | [
[
"Shchur",
"Olha",
""
],
[
"Vidybida",
"Alexander",
""
]
] | In this paper, we study analytically the impact of an inhibitory autapse on neuronal activity. In order to do this, we formulate conditions on a set of non-adaptive spiking neuron models with delayed feedback inhibition, instead of considering a particular neuronal model. The neuron is stimulated with a stochastic poin... |
1701.01361 | Christophe Gole | Pau Atela and Christophe Gole | Rhombic Tilings and Primordia Fronts of Phyllotaxis | 33 pages, 10 pictures | null | null | null | q-bio.TO math.DS | http://creativecommons.org/publicdomain/zero/1.0/ | We introduce and study properties of phyllotactic and rhombic tilings on the
cylin- der. These are discrete sets of points that generalize cylindrical
lattices. Rhombic tilings appear as periodic orbits of a discrete dynamical
system S that models plant pattern formation by stacking disks of equal radius
on the cylin... | [
{
"created": "Wed, 4 Jan 2017 20:19:44 GMT",
"version": "v1"
}
] | 2017-01-06 | [
[
"Atela",
"Pau",
""
],
[
"Gole",
"Christophe",
""
]
] | We introduce and study properties of phyllotactic and rhombic tilings on the cylin- der. These are discrete sets of points that generalize cylindrical lattices. Rhombic tilings appear as periodic orbits of a discrete dynamical system S that models plant pattern formation by stacking disks of equal radius on the cylinde... |
q-bio/0409036 | Haret Rosu | L.A. Torres, V. Ibarra-Junquera, P. Escalante-Minakata, H.C. Rosu | High-gain nonlinear observer for simple genetic regulation process | 9 pages, one figure | Physica A 380 (2007) 235-240 | 10.1016/j.physa.2007.02.105 | null | q-bio.QM q-bio.MN | null | High-gain nonlinear observers occur in the nonlinear automatic control theory
and are in standard usage in chemical engineering processes. We apply such a
type of analysis in the context of a very simple one-gene regulation circuit.
In general, an observer combines an analytical differential-equation-based
model with... | [
{
"created": "Wed, 29 Sep 2004 22:42:46 GMT",
"version": "v1"
},
{
"created": "Mon, 16 Jul 2007 17:47:20 GMT",
"version": "v2"
}
] | 2007-07-16 | [
[
"Torres",
"L. A.",
""
],
[
"Ibarra-Junquera",
"V.",
""
],
[
"Escalante-Minakata",
"P.",
""
],
[
"Rosu",
"H. C.",
""
]
] | High-gain nonlinear observers occur in the nonlinear automatic control theory and are in standard usage in chemical engineering processes. We apply such a type of analysis in the context of a very simple one-gene regulation circuit. In general, an observer combines an analytical differential-equation-based model with p... |
2006.03611 | Markus D Schirmer | Markus D. Schirmer, Archana Venkataraman, Islem Rekik, Minjeong Kim,
Stewart H. Mostofsky, Mary Beth Nebel, Keri Rosch, Karen Seymour, Deana
Crocetti, Hassna Irzan, Michael H\"utel, Sebastien Ourselin, Neil Marlow,
Andrew Melbourne, Egor Levchenko, Shuo Zhou, Mwiza Kunda, Haiping Lu, Nicha
C. Dvornek, Juntang Z... | Neuropsychiatric Disease Classification Using Functional Connectomics --
Results of the Connectomics in NeuroImaging Transfer Learning Challenge | CNI-TLC was held in conjunction with MICCAI 2019 | null | null | null | q-bio.NC cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Large, open-source consortium datasets have spurred the development of new
and increasingly powerful machine learning approaches in brain connectomics.
However, one key question remains: are we capturing biologically relevant and
generalizable information about the brain, or are we simply overfitting to the
data? To ... | [
{
"created": "Fri, 5 Jun 2020 18:05:42 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Nov 2020 11:45:57 GMT",
"version": "v2"
}
] | 2020-11-26 | [
[
"Schirmer",
"Markus D.",
""
],
[
"Venkataraman",
"Archana",
""
],
[
"Rekik",
"Islem",
""
],
[
"Kim",
"Minjeong",
""
],
[
"Mostofsky",
"Stewart H.",
""
],
[
"Nebel",
"Mary Beth",
""
],
[
"Rosch",
"Keri",
""
... | Large, open-source consortium datasets have spurred the development of new and increasingly powerful machine learning approaches in brain connectomics. However, one key question remains: are we capturing biologically relevant and generalizable information about the brain, or are we simply overfitting to the data? To an... |
2407.07930 | Rui Qin | Jike Wang, Rui Qin, Mingyang Wang, Meijing Fang, Yangyang Zhang,
Yuchen Zhu, Qun Su, Qiaolin Gou, Chao Shen, Odin Zhang, Zhenxing Wu, Dejun
Jiang, Xujun Zhang, Huifeng Zhao, Xiaozhe Wan, Zhourui Wu, Liwei Liu, Yu
Kang, Chang-Yu Hsieh, Tingjun Hou | Token-Mol 1.0: Tokenized drug design with large language model | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Significant interests have recently risen in leveraging sequence-based large
language models (LLMs) for drug design. However, most current applications of
LLMs in drug discovery lack the ability to comprehend three-dimensional (3D)
structures, thereby limiting their effectiveness in tasks that explicitly
involve mole... | [
{
"created": "Wed, 10 Jul 2024 07:22:15 GMT",
"version": "v1"
}
] | 2024-07-12 | [
[
"Wang",
"Jike",
""
],
[
"Qin",
"Rui",
""
],
[
"Wang",
"Mingyang",
""
],
[
"Fang",
"Meijing",
""
],
[
"Zhang",
"Yangyang",
""
],
[
"Zhu",
"Yuchen",
""
],
[
"Su",
"Qun",
""
],
[
"Gou",
"Qiaolin",
... | Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D) structures, thereby limiting their effectiveness in tasks that explicitly involve molecu... |
1006.5560 | Jose A Capitan | Jose A. Capitan and Jose A. Cuesta | Species assembly in model ecosystems, I: Analysis of the population
model and the invasion dynamics | 16 pages, 8 figures. Revised version | Journal of Theoretical Biology 269, 330-343 (2011) | 10.1016/j.jtbi.2010.09.032 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently we have introduced a simplified model of ecosystem assembly (Capitan
et al., 2009) for which we are able to map out all assembly pathways generated
by external invasions in an exact manner. In this paper we provide a deeper
analysis of the model, obtaining analytical results and introducing some
approximatio... | [
{
"created": "Tue, 29 Jun 2010 10:26:13 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Sep 2010 11:19:01 GMT",
"version": "v2"
}
] | 2015-02-18 | [
[
"Capitan",
"Jose A.",
""
],
[
"Cuesta",
"Jose A.",
""
]
] | Recently we have introduced a simplified model of ecosystem assembly (Capitan et al., 2009) for which we are able to map out all assembly pathways generated by external invasions in an exact manner. In this paper we provide a deeper analysis of the model, obtaining analytical results and introducing some approximations... |
1403.2488 | Margarita Ifti | Margarita Ifti and Birger Bergersen | Phase Transitions in Systems of Interacting Species | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We discuss an autocatalytic reaction system: the cyclic competition model A1
+ A2 --> 2 A2, A2 + A3 --> 2 A3, A3 + A4 --> 2 A4, A4 + A1 --> 2 A1), as well
as its neutral counterpart. Migrations are introduced into the model. When
stochastic phenomena are taken into account, a phase transition between a
``fixation'' a... | [
{
"created": "Tue, 11 Mar 2014 07:13:17 GMT",
"version": "v1"
}
] | 2014-03-12 | [
[
"Ifti",
"Margarita",
""
],
[
"Bergersen",
"Birger",
""
]
] | We discuss an autocatalytic reaction system: the cyclic competition model A1 + A2 --> 2 A2, A2 + A3 --> 2 A3, A3 + A4 --> 2 A4, A4 + A1 --> 2 A1), as well as its neutral counterpart. Migrations are introduced into the model. When stochastic phenomena are taken into account, a phase transition between a ``fixation'' and... |
2011.09232 | Audrey B\"urki | Pamela Fuhrmeister, Sylvain Madec, Antje Lorenz, Shereen Elbuy, Audrey
B\"urki | Behavioral and EEG evidence for inter-individual variability in late
encoding stages of word production | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Individuals differ in the time it takes to produce words when naming a
picture. However, it is unknown whether this inter-individual variability
emerges in earlier stages of word production (e.g., lexical selection) or later
stages (e.g., articulation). The current study measured participants' (N = 45)
naming latenci... | [
{
"created": "Wed, 18 Nov 2020 11:58:32 GMT",
"version": "v1"
}
] | 2020-11-19 | [
[
"Fuhrmeister",
"Pamela",
""
],
[
"Madec",
"Sylvain",
""
],
[
"Lorenz",
"Antje",
""
],
[
"Elbuy",
"Shereen",
""
],
[
"Bürki",
"Audrey",
""
]
] | Individuals differ in the time it takes to produce words when naming a picture. However, it is unknown whether this inter-individual variability emerges in earlier stages of word production (e.g., lexical selection) or later stages (e.g., articulation). The current study measured participants' (N = 45) naming latencies... |
1611.09648 | Ranjit Bahadur P | Naga Bhushana Rao .K and Ranjit Prasad Bahadur | PeBLes: Prediction of B-cell epitope using molecular layers | 27 pages, 5 Figures and 3 Tables | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Characterization of B-cell protein epitope and developing critical parameters
for its identification is one of the long standing interests. Using Layers
algorithm, we introduced the concept of anchor residues to identify epitope. We
have shown that majority of the epitope is composed of anchor residues and have
signi... | [
{
"created": "Tue, 29 Nov 2016 14:30:56 GMT",
"version": "v1"
}
] | 2016-11-30 | [
[
"K",
"Naga Bhushana Rao .",
""
],
[
"Bahadur",
"Ranjit Prasad",
""
]
] | Characterization of B-cell protein epitope and developing critical parameters for its identification is one of the long standing interests. Using Layers algorithm, we introduced the concept of anchor residues to identify epitope. We have shown that majority of the epitope is composed of anchor residues and have signifi... |
1408.5729 | Peter Ashcroft | Peter Ashcroft, Franziska Michor and Tobias Galla | Stochastic tunneling and metastable states during the somatic evolution
of cancer | 33 pages, 7 figures | Genetics 199.4 (2015) 1213-1228 | 10.1534/genetics.114.171553 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tumors initiate when a population of proliferating cells accumulates a
certain number and type of genetic and/or epigenetic alterations. The
population dynamics of such sequential acquisition of (epi)genetic alterations
has been the topic of much investigation. The phenomenon of stochastic
tunneling, where an interme... | [
{
"created": "Mon, 25 Aug 2014 12:16:35 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Apr 2015 19:06:52 GMT",
"version": "v2"
}
] | 2015-04-09 | [
[
"Ashcroft",
"Peter",
""
],
[
"Michor",
"Franziska",
""
],
[
"Galla",
"Tobias",
""
]
] | Tumors initiate when a population of proliferating cells accumulates a certain number and type of genetic and/or epigenetic alterations. The population dynamics of such sequential acquisition of (epi)genetic alterations has been the topic of much investigation. The phenomenon of stochastic tunneling, where an intermedi... |
2001.03614 | Claire Meissner-Bernard | Claire Meissner-Bernard, Matthias Tsai, Laureline Logiaco, Wulfram
Gerstner | Paradoxical Results of Long-Term Potentiation explained by Voltage-based
Plasticity Rule | null | Front. Synaptic Neurosci. (2020) 12:585539 | 10.3389/fnsyn.2020.585539 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Experiments have shown that the same stimulation pattern that causes
Long-Term Potentiation in proximal synapses, will induce Long-Term Depression
in distal ones. In order to understand these, and other, surprising
observations we use a phenomenological model of Hebbian plasticity at the
location of the synapse. Our ... | [
{
"created": "Fri, 10 Jan 2020 18:57:06 GMT",
"version": "v1"
},
{
"created": "Mon, 12 Oct 2020 21:52:02 GMT",
"version": "v2"
},
{
"created": "Wed, 18 Nov 2020 20:03:33 GMT",
"version": "v3"
}
] | 2020-11-20 | [
[
"Meissner-Bernard",
"Claire",
""
],
[
"Tsai",
"Matthias",
""
],
[
"Logiaco",
"Laureline",
""
],
[
"Gerstner",
"Wulfram",
""
]
] | Experiments have shown that the same stimulation pattern that causes Long-Term Potentiation in proximal synapses, will induce Long-Term Depression in distal ones. In order to understand these, and other, surprising observations we use a phenomenological model of Hebbian plasticity at the location of the synapse. Our co... |
2011.01294 | Kerim Anlas | Kerim Anlas and Vikas Trivedi | Studying evolution of the primary body axis in vivo and in vitro | null | null | null | null | q-bio.PE q-bio.CB q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The metazoan body plan is established during early embryogenesis via
collective cell rearrangements and evolutionarily conserved gene networks, as
part of a process commonly referred to as gastrulation. While substantial
progress has been achieved in terms of characterizing the embryonic development
of several model ... | [
{
"created": "Mon, 2 Nov 2020 20:24:33 GMT",
"version": "v1"
},
{
"created": "Mon, 23 Nov 2020 11:26:07 GMT",
"version": "v2"
}
] | 2020-11-24 | [
[
"Anlas",
"Kerim",
""
],
[
"Trivedi",
"Vikas",
""
]
] | The metazoan body plan is established during early embryogenesis via collective cell rearrangements and evolutionarily conserved gene networks, as part of a process commonly referred to as gastrulation. While substantial progress has been achieved in terms of characterizing the embryonic development of several model or... |
2111.10628 | Andrew Whetten | Andrew B. Whetten | Localized Mutual Information Monitoring of Pairwise Associations in
Animal Movement | null | null | null | null | q-bio.QM q-bio.PE stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Advances in satellite imaging and GPS tracking devices have given rise to a
new era of remote sensing and geospatial analysis. In environmental science and
conservation ecology, biotelemetric data is often high-dimensional, spatially
and/or temporally, and functional in nature, meaning that there is an
underlying con... | [
{
"created": "Sat, 20 Nov 2021 16:45:50 GMT",
"version": "v1"
},
{
"created": "Thu, 2 Dec 2021 02:51:00 GMT",
"version": "v2"
},
{
"created": "Tue, 7 Dec 2021 05:10:11 GMT",
"version": "v3"
},
{
"created": "Thu, 6 Jan 2022 01:29:47 GMT",
"version": "v4"
}
] | 2022-01-07 | [
[
"Whetten",
"Andrew B.",
""
]
] | Advances in satellite imaging and GPS tracking devices have given rise to a new era of remote sensing and geospatial analysis. In environmental science and conservation ecology, biotelemetric data is often high-dimensional, spatially and/or temporally, and functional in nature, meaning that there is an underlying conti... |
1306.3465 | Alvaro Sanchez | Andrew Chen, Alvaro Sanchez, Lei Dai, Jeff Gore | Dynamics of a producer-parasite ecosystem on the brink of collapse | null | null | 10.1038/ncomms4713 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ecosystems can undergo sudden shifts to undesirable states, but recent
studies with simple single species ecosystems have demonstrated that advance
warning can be provided by the slowing down of population dynamics near a
tipping point. However, it is not clear how this effect of critical slowing
down will manifest i... | [
{
"created": "Fri, 14 Jun 2013 17:37:25 GMT",
"version": "v1"
}
] | 2015-06-16 | [
[
"Chen",
"Andrew",
""
],
[
"Sanchez",
"Alvaro",
""
],
[
"Dai",
"Lei",
""
],
[
"Gore",
"Jeff",
""
]
] | Ecosystems can undergo sudden shifts to undesirable states, but recent studies with simple single species ecosystems have demonstrated that advance warning can be provided by the slowing down of population dynamics near a tipping point. However, it is not clear how this effect of critical slowing down will manifest in ... |
q-bio/0605040 | Alexei Vazquez | Alexei Vazquez | Epidemic outbreaks on structured populations | 10 pages, 4 figures. J. Theor. Biol. (In press) | J. Theor. Biol. 245, 125 (2007) | null | null | q-bio.PE cond-mat.stat-mech physics.bio-ph q-bio.QM | null | Our chances to halt epidemic outbreaks rely on how accurately we represent
the population structure underlying the disease spread. When analyzing global
epidemics this force us to consider metapopulation models taking into account
intra- and inter-community interactions. Recently Watts et al introduced a
metapopulati... | [
{
"created": "Wed, 24 May 2006 16:30:45 GMT",
"version": "v1"
},
{
"created": "Wed, 20 Sep 2006 14:19:43 GMT",
"version": "v2"
}
] | 2007-12-10 | [
[
"Vazquez",
"Alexei",
""
]
] | Our chances to halt epidemic outbreaks rely on how accurately we represent the population structure underlying the disease spread. When analyzing global epidemics this force us to consider metapopulation models taking into account intra- and inter-community interactions. Recently Watts et al introduced a metapopulation... |
2103.08984 | Mar\'ia Vallet-Regi | Juan L. Paris, Paz de la Torre, M. Victoria Cabanas, Miguel Manzano,
Ana I. Flores, Maria Vallet-Regi | Suicide-Gene Transfection of Tumor-tropic Placental Stem Cells employing
Ultrasound-Responsive Nanoparticles | 24 pages, 6 figures | Acta Biomaterialia. 83, 372-378 (2018) | 10.1016/j.actbio.2018.11.006 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | A Trojan-horse strategy for cancer therapy employing tumor-tropic mesenchymal
stem cells transfected with a non-viral nanovector is here presented. In this
sense, ultrasound-responsive mesoporous silica nanoparticles were coated with a
polycation (using two different molecular weights), providing them with gene
trans... | [
{
"created": "Tue, 16 Mar 2021 11:22:19 GMT",
"version": "v1"
}
] | 2021-03-17 | [
[
"Paris",
"Juan L.",
""
],
[
"de la Torre",
"Paz",
""
],
[
"Cabanas",
"M. Victoria",
""
],
[
"Manzano",
"Miguel",
""
],
[
"Flores",
"Ana I.",
""
],
[
"Vallet-Regi",
"Maria",
""
]
] | A Trojan-horse strategy for cancer therapy employing tumor-tropic mesenchymal stem cells transfected with a non-viral nanovector is here presented. In this sense, ultrasound-responsive mesoporous silica nanoparticles were coated with a polycation (using two different molecular weights), providing them with gene transfe... |
2206.08813 | Richard Gast Dr. | Richard Gast, Sara A. Solla, Ann Kennedy | Effects of Neural Heterogeneity on Spiking Neural Network Dynamics | 11 pages, 4 figures | null | null | null | q-bio.NC nlin.AO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The brain is composed of complex networks of interacting neurons that express
considerable heterogeneity in their physiology and spiking characteristics. How
does neural heterogeneity affect macroscopic neural dynamics and how does it
contribute to neurodynamic functions? In this letter, we address these
questions by... | [
{
"created": "Fri, 17 Jun 2022 14:44:17 GMT",
"version": "v1"
}
] | 2022-06-20 | [
[
"Gast",
"Richard",
""
],
[
"Solla",
"Sara A.",
""
],
[
"Kennedy",
"Ann",
""
]
] | The brain is composed of complex networks of interacting neurons that express considerable heterogeneity in their physiology and spiking characteristics. How does neural heterogeneity affect macroscopic neural dynamics and how does it contribute to neurodynamic functions? In this letter, we address these questions by s... |
1604.08612 | Jerome Feldman | Jerome Feldman | Mysteries of Visual Experience | This 3/27/2022 revision retains all the original text but adds new
comments (in italics) There are several new references, connecting with
current research | Behavioral and Brain Sciences, 45, E48 (2022) | 10.1017/S0140525X21001886 | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | Science is a crowning glory of the human spirit and its applications remain
our best hope for social progress. But there are limitations to current science
and perhaps to any science. The general mind-body problem is known to be
intractable and currently mysterious. This is one of many deep problems that
are universa... | [
{
"created": "Thu, 28 Apr 2016 20:41:25 GMT",
"version": "v1"
},
{
"created": "Wed, 28 Sep 2016 17:33:49 GMT",
"version": "v2"
},
{
"created": "Tue, 10 Jan 2017 18:46:42 GMT",
"version": "v3"
},
{
"created": "Tue, 20 Mar 2018 16:07:22 GMT",
"version": "v4"
},
{
"c... | 2022-03-29 | [
[
"Feldman",
"Jerome",
""
]
] | Science is a crowning glory of the human spirit and its applications remain our best hope for social progress. But there are limitations to current science and perhaps to any science. The general mind-body problem is known to be intractable and currently mysterious. This is one of many deep problems that are universall... |
q-bio/0601031 | Sidney Redner | T. Antal, S. Redner, and V. Sood | Evolutionary dynamics on degree-heterogeneous graphs | 4 pages, 4 figures, 2 column revtex4 format. Revisions in response to
referee comments for publication in PRL. The version on arxiv.org has one
more figure than the published PRL | Phys. Rev. Lett. 96, 188104 (2006) | 10.1103/PhysRevLett.96.188104 | null | q-bio.PE cond-mat.stat-mech | null | The evolution of two species with different fitness is investigated on
degree-heterogeneous graphs. The population evolves either by one individual
dying and being replaced by the offspring of a random neighbor (voter model
(VM) dynamics) or by an individual giving birth to an offspring that takes over
a random neigh... | [
{
"created": "Sat, 21 Jan 2006 22:16:54 GMT",
"version": "v1"
},
{
"created": "Thu, 11 May 2006 21:17:21 GMT",
"version": "v2"
}
] | 2009-11-13 | [
[
"Antal",
"T.",
""
],
[
"Redner",
"S.",
""
],
[
"Sood",
"V.",
""
]
] | The evolution of two species with different fitness is investigated on degree-heterogeneous graphs. The population evolves either by one individual dying and being replaced by the offspring of a random neighbor (voter model (VM) dynamics) or by an individual giving birth to an offspring that takes over a random neighbo... |
0907.5531 | Erika Cerasti | Erika Cerasti, Alessandro Treves | How informative are spatial CA3 representations established by the
dentate gyrus? | 19 pages, 11 figures, 1 table, submitted | null | 10.1371/journal.pcbi.1000759 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the mammalian hippocampus, the dentate gyrus (DG) is characterized by
sparse and powerful unidirectional projections to CA3 pyramidal cells, the
so-called mossy fibers. Mossy fiber synapses appear to duplicate, in terms of
the information they convey, what CA3 cells already receive from entorhinal
cortex layer II ... | [
{
"created": "Fri, 31 Jul 2009 13:14:37 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Cerasti",
"Erika",
""
],
[
"Treves",
"Alessandro",
""
]
] | In the mammalian hippocampus, the dentate gyrus (DG) is characterized by sparse and powerful unidirectional projections to CA3 pyramidal cells, the so-called mossy fibers. Mossy fiber synapses appear to duplicate, in terms of the information they convey, what CA3 cells already receive from entorhinal cortex layer II ce... |
q-bio/0506009 | Kristina Klinkner | Kristina Lisa Klinkner, Cosma Rohilla Shalizi and Marcelo F. Camperi | Measuring Shared Information and Coordinated Activity in Neuronal
Networks | 8 pages, 6 figures | null | null | null | q-bio.NC math.ST nlin.CD q-bio.QM stat.TH | null | Most nervous systems encode information about stimuli in the responding
activity of large neuronal networks. This activity often manifests itself as
dynamically coordinated sequences of action potentials. Since multiple
electrode recordings are now a standard tool in neuroscience research, it is
important to have a m... | [
{
"created": "Tue, 7 Jun 2005 23:48:15 GMT",
"version": "v1"
},
{
"created": "Fri, 29 Jul 2005 16:57:38 GMT",
"version": "v2"
}
] | 2011-11-09 | [
[
"Klinkner",
"Kristina Lisa",
""
],
[
"Shalizi",
"Cosma Rohilla",
""
],
[
"Camperi",
"Marcelo F.",
""
]
] | Most nervous systems encode information about stimuli in the responding activity of large neuronal networks. This activity often manifests itself as dynamically coordinated sequences of action potentials. Since multiple electrode recordings are now a standard tool in neuroscience research, it is important to have a mea... |
1911.03509 | Samuel Lord | Samuel J. Lord, Katrina B. Velle, R. Dyche Mullins, Lillian K.
Fritz-Laylin | If your P value looks too good to be true, it probably is: Communicating
reproducibility and variability in cell biology | Modified Figure 1A to use the identical dataset as B-C. Included
tutorial for making plots in R, Python, and Excel. Replaced on comparing
biological vs technical replicates with expanded explanation of population
sampling. Included discussion of estimation statistics and forest plots as a
reasonable alternative... | J. Cell. Biol. 219 (2020) e202001064 | 10.1083/jcb.202001064 | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The cell biology literature is littered with erroneously tiny P values, often
the result of evaluating individual cells as independent samples. Because
readers use P values and error bars to infer whether a reported difference
would likely recur if the experiment were repeated, the sample size N used for
statistical ... | [
{
"created": "Fri, 8 Nov 2019 19:22:41 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Dec 2019 23:59:18 GMT",
"version": "v2"
}
] | 2020-04-30 | [
[
"Lord",
"Samuel J.",
""
],
[
"Velle",
"Katrina B.",
""
],
[
"Mullins",
"R. Dyche",
""
],
[
"Fritz-Laylin",
"Lillian K.",
""
]
] | The cell biology literature is littered with erroneously tiny P values, often the result of evaluating individual cells as independent samples. Because readers use P values and error bars to infer whether a reported difference would likely recur if the experiment were repeated, the sample size N used for statistical te... |
2311.07315 | Kristopher Jensen | Kristopher T. Jensen | An introduction to reinforcement learning for neuroscience | Code available at:
https://colab.research.google.com/drive/1ZC4lR8kTO48yySDZtcOEdMKd3NqY_ly1?usp=sharing | null | null | null | q-bio.NC cs.LG | http://creativecommons.org/licenses/by/4.0/ | Reinforcement learning has a rich history in neuroscience, from early work on
dopamine as a reward prediction error signal for temporal difference learning
(Schultz et al., 1997) to recent work suggesting that dopamine could implement
a form of 'distributional reinforcement learning' popularized in deep learning
(Dab... | [
{
"created": "Mon, 13 Nov 2023 13:10:52 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Aug 2024 16:07:02 GMT",
"version": "v2"
}
] | 2024-08-02 | [
[
"Jensen",
"Kristopher T.",
""
]
] | Reinforcement learning has a rich history in neuroscience, from early work on dopamine as a reward prediction error signal for temporal difference learning (Schultz et al., 1997) to recent work suggesting that dopamine could implement a form of 'distributional reinforcement learning' popularized in deep learning (Dabne... |
2007.01344 | Rui Wang | Rui Wang, Yuta Hozumi, Changchuan Yin, and Guo-Wei Wei | Decoding asymptomatic COVID-19 infection and transmission | 18 pages, 5 figures | null | null | null | q-bio.PE q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Coronavirus disease 2019 (COVID-19) is a continuously devastating public
health and the world economy. One of the major challenges in controlling the
COVID-19 outbreak is its asymptomatic infection and transmission, which are
elusive and defenseless in most situations. The pathogenicity and virulence of
asymptomatic ... | [
{
"created": "Thu, 2 Jul 2020 19:09:26 GMT",
"version": "v1"
}
] | 2020-07-06 | [
[
"Wang",
"Rui",
""
],
[
"Hozumi",
"Yuta",
""
],
[
"Yin",
"Changchuan",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Coronavirus disease 2019 (COVID-19) is a continuously devastating public health and the world economy. One of the major challenges in controlling the COVID-19 outbreak is its asymptomatic infection and transmission, which are elusive and defenseless in most situations. The pathogenicity and virulence of asymptomatic CO... |
2407.12870 | Jianan Fan | Jianan Fan, Dongnan Liu, Canran Li, Hang Chang, Heng Huang, Filip
Braet, Mei Chen, and Weidong Cai | Revisiting Adaptive Cellular Recognition Under Domain Shifts: A
Contextual Correspondence View | ECCV 2024 main conference | null | null | null | q-bio.QM cs.LG eess.IV | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Cellular nuclei recognition serves as a fundamental and essential step in the
workflow of digital pathology. However, with disparate source organs and
staining procedures among histology image clusters, the scanned tiles
inherently conform to a non-uniform data distribution, which induces
deteriorated promises for ge... | [
{
"created": "Sun, 14 Jul 2024 04:41:16 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Jul 2024 05:26:06 GMT",
"version": "v2"
}
] | 2024-07-22 | [
[
"Fan",
"Jianan",
""
],
[
"Liu",
"Dongnan",
""
],
[
"Li",
"Canran",
""
],
[
"Chang",
"Hang",
""
],
[
"Huang",
"Heng",
""
],
[
"Braet",
"Filip",
""
],
[
"Chen",
"Mei",
""
],
[
"Cai",
"Weidong",
... | Cellular nuclei recognition serves as a fundamental and essential step in the workflow of digital pathology. However, with disparate source organs and staining procedures among histology image clusters, the scanned tiles inherently conform to a non-uniform data distribution, which induces deteriorated promises for gene... |
2209.13521 | Yihao Chen | Shunming Tao, Yihao Chen, Jingxing Wu, Duancheng Zhao, Hanxuan Cai,
Ling Wang | VDDB: a comprehensive resource and machine learning platform for
antiviral drug discovery | null | null | null | null | q-bio.BM cs.AI cs.LG q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Virus infection is one of the major diseases that seriously threaten human
health. To meet the growing demand for mining and sharing data resources
related to antiviral drugs and to accelerate the design and discovery of new
antiviral drugs, we presented an open-access antiviral drug resource and
machine learning pla... | [
{
"created": "Sat, 17 Sep 2022 09:02:46 GMT",
"version": "v1"
}
] | 2022-09-28 | [
[
"Tao",
"Shunming",
""
],
[
"Chen",
"Yihao",
""
],
[
"Wu",
"Jingxing",
""
],
[
"Zhao",
"Duancheng",
""
],
[
"Cai",
"Hanxuan",
""
],
[
"Wang",
"Ling",
""
]
] | Virus infection is one of the major diseases that seriously threaten human health. To meet the growing demand for mining and sharing data resources related to antiviral drugs and to accelerate the design and discovery of new antiviral drugs, we presented an open-access antiviral drug resource and machine learning platf... |
2212.01508 | Rajkumar Vasudeva Raju | Rajkumar Vasudeva Raju, J. Swaroop Guntupalli, Guangyao Zhou, Miguel
L\'azaro-Gredilla and Dileep George | Space is a latent sequence: Structured sequence learning as a unified
theory of representation in the hippocampus | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Fascinating and puzzling phenomena, such as landmark vector cells, splitter
cells, and event-specific representations to name a few, are regularly
discovered in the hippocampus. Without a unifying principle that can explain
these divergent observations, each experiment seemingly discovers a new anomaly
or coding type... | [
{
"created": "Sat, 3 Dec 2022 02:00:56 GMT",
"version": "v1"
}
] | 2022-12-06 | [
[
"Raju",
"Rajkumar Vasudeva",
""
],
[
"Guntupalli",
"J. Swaroop",
""
],
[
"Zhou",
"Guangyao",
""
],
[
"Lázaro-Gredilla",
"Miguel",
""
],
[
"George",
"Dileep",
""
]
] | Fascinating and puzzling phenomena, such as landmark vector cells, splitter cells, and event-specific representations to name a few, are regularly discovered in the hippocampus. Without a unifying principle that can explain these divergent observations, each experiment seemingly discovers a new anomaly or coding type. ... |
q-bio/0310030 | Valmir Barbosa | L. E. Flores, E. J. Aguilar, V. C. Barbosa, L. A. V. de Carvalho | A graph model for the evolution of specificity in humoral immunity | null | Journal of Theoretical Biology 229 (2004), 311-325 | 10.1016/j.jtbi.2004.04.005 | ES-617/03 | q-bio.CB | null | The immune system protects the body against health-threatening entities,
known as antigens, through very complex interactions involving the antigens and
the system's own entities. One remarkable feature resulting from such
interactions is the immune system's ability to improve its capability to fight
antigens commonl... | [
{
"created": "Thu, 23 Oct 2003 17:39:33 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Flores",
"L. E.",
""
],
[
"Aguilar",
"E. J.",
""
],
[
"Barbosa",
"V. C.",
""
],
[
"de Carvalho",
"L. A. V.",
""
]
] | The immune system protects the body against health-threatening entities, known as antigens, through very complex interactions involving the antigens and the system's own entities. One remarkable feature resulting from such interactions is the immune system's ability to improve its capability to fight antigens commonly ... |
1612.04256 | Robert Hoehndorf | Mona Alshahrani, Mohammed Asif Khan, Omar Maddouri, Akira R Kinjo,
N\'uria Queralt-Rosinach, Robert Hoehndorf | Neuro-symbolic representation learning on biological knowledge graphs | null | null | 10.1093/bioinformatics/btx275 | null | q-bio.QM cs.LG q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Biological data and knowledge bases increasingly rely on Semantic
Web technologies and the use of knowledge graphs for data integration,
retrieval and federated queries. In the past years, feature learning methods
that are applicable to graph-structured data are becoming available, but have
not yet widely... | [
{
"created": "Tue, 13 Dec 2016 16:06:39 GMT",
"version": "v1"
}
] | 2017-05-01 | [
[
"Alshahrani",
"Mona",
""
],
[
"Khan",
"Mohammed Asif",
""
],
[
"Maddouri",
"Omar",
""
],
[
"Kinjo",
"Akira R",
""
],
[
"Queralt-Rosinach",
"Núria",
""
],
[
"Hoehndorf",
"Robert",
""
]
] | Motivation: Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely b... |
1905.04283 | Dennis Dimond | Dennis Dimond, Rebecca Perry, Giuseppe Iaria, Signe Bray | Visuospatial short-term memory and dorsal visual gray matter volume | 22 pages, 2 figures | J.Cortex (2019), 113:184-190 | 10.1016/j.cortex.2018.12.007 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Visual short-term memory (VSTM) is an important cognitive capacity that
varies across the healthy adult population and is affected in several
neurodevelopmental disorders. It has been suggested that neuroanatomy places
limits on this capacity through a map architecture that creates competition for
cortical space. Thi... | [
{
"created": "Fri, 10 May 2019 17:50:21 GMT",
"version": "v1"
}
] | 2019-05-13 | [
[
"Dimond",
"Dennis",
""
],
[
"Perry",
"Rebecca",
""
],
[
"Iaria",
"Giuseppe",
""
],
[
"Bray",
"Signe",
""
]
] | Visual short-term memory (VSTM) is an important cognitive capacity that varies across the healthy adult population and is affected in several neurodevelopmental disorders. It has been suggested that neuroanatomy places limits on this capacity through a map architecture that creates competition for cortical space. This ... |
1605.00591 | Gianluca Calcagni | Gianluca Calcagni | The geometry of learning | 17 pages, 7 figures, 1 table. v2: new sections, figures and
references added, including discussions on random fractals and their
applications and on 1/f cognitive noise models; v3: consequences and
predictions of the theory added, typos corrected | J. Math. Psychol. 84 (2018) 74 | 10.1016/j.jmp.2018.03.007 | null | q-bio.QM cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We establish a correspondence between Pavlovian conditioning processes and
fractals. The association strength at a training trial corresponds to a point
in a disconnected set at a given iteration level. In this way, one can
represent a training process as a hopping on a fractal set, instead of the
traditional learnin... | [
{
"created": "Mon, 2 May 2016 18:11:17 GMT",
"version": "v1"
},
{
"created": "Sat, 17 Dec 2016 11:39:44 GMT",
"version": "v2"
},
{
"created": "Sun, 22 Apr 2018 18:28:16 GMT",
"version": "v3"
}
] | 2018-04-24 | [
[
"Calcagni",
"Gianluca",
""
]
] | We establish a correspondence between Pavlovian conditioning processes and fractals. The association strength at a training trial corresponds to a point in a disconnected set at a given iteration level. In this way, one can represent a training process as a hopping on a fractal set, instead of the traditional learning ... |
2402.06169 | Eleanor Dunlop Dr | Eleanor Dunlop, Judy Cunningham, Paul Adorno, Shari Fatupaito, Stuart
K Johnson, Lucinda J Black | Development of an updated, comprehensive food composition database for
Australian-grown horticultural commodities | 34 pages, 4 tables | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Australian agriculture supplies many horticultural commodities to domestic
and international markets; however, food composition data for many commodities
are outdated or unavailable. We produced an up-to-date, nationally
representative dataset of up to 148 nutrients and related components in 92
Australian-grown fruit... | [
{
"created": "Fri, 9 Feb 2024 03:54:35 GMT",
"version": "v1"
}
] | 2024-02-12 | [
[
"Dunlop",
"Eleanor",
""
],
[
"Cunningham",
"Judy",
""
],
[
"Adorno",
"Paul",
""
],
[
"Fatupaito",
"Shari",
""
],
[
"Johnson",
"Stuart K",
""
],
[
"Black",
"Lucinda J",
""
]
] | Australian agriculture supplies many horticultural commodities to domestic and international markets; however, food composition data for many commodities are outdated or unavailable. We produced an up-to-date, nationally representative dataset of up to 148 nutrients and related components in 92 Australian-grown fruit (... |
1805.01447 | Bryan Daniels | Bryan C. Daniels, Hyunju Kim, Douglas Moore, Siyu Zhou, Harrison
Smith, Bradley Karas, Stuart A. Kauffman, and Sara I. Walker | Logic and connectivity jointly determine criticality in biological gene
regulatory networks | 10 pages, 7 figures | Phys. Rev. Lett. 121, 138102 (2018) | 10.1103/PhysRevLett.121.138102 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The complex dynamics of gene expression in living cells can be
well-approximated using Boolean networks. The average sensitivity is a natural
measure of stability in these systems: values below one indicate typically
stable dynamics associated with an ordered phase, whereas values above one
indicate chaotic dynamics.... | [
{
"created": "Thu, 3 May 2018 17:47:30 GMT",
"version": "v1"
}
] | 2018-10-03 | [
[
"Daniels",
"Bryan C.",
""
],
[
"Kim",
"Hyunju",
""
],
[
"Moore",
"Douglas",
""
],
[
"Zhou",
"Siyu",
""
],
[
"Smith",
"Harrison",
""
],
[
"Karas",
"Bradley",
""
],
[
"Kauffman",
"Stuart A.",
""
],
[
... | The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics associated with an ordered phase, whereas values above one indicate chaotic dynamics. T... |
2009.10953 | Chiara Villa | Chiara Villa, Mark A. J. Chaplain, Alf Gerisch, Tommaso Lorenzi | Mechanical models of pattern and form in biological tissues: the role of
stress-strain constitutive equations | 33 pages + 6 pages of supplementary material, 15 figures, 6 movies | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mechanochemical models of pattern formation in biological tissues have been
used to study a variety of biomedical systems and describe the physical
interactions between cells and their local surroundings. These models generally
consist of a balance equation for the cell density, one for the density of the
extracellul... | [
{
"created": "Wed, 23 Sep 2020 06:53:55 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Oct 2020 08:23:44 GMT",
"version": "v2"
},
{
"created": "Wed, 24 Mar 2021 17:24:22 GMT",
"version": "v3"
},
{
"created": "Thu, 25 Mar 2021 08:13:55 GMT",
"version": "v4"
},
{
"cr... | 2021-05-12 | [
[
"Villa",
"Chiara",
""
],
[
"Chaplain",
"Mark A. J.",
""
],
[
"Gerisch",
"Alf",
""
],
[
"Lorenzi",
"Tommaso",
""
]
] | Mechanochemical models of pattern formation in biological tissues have been used to study a variety of biomedical systems and describe the physical interactions between cells and their local surroundings. These models generally consist of a balance equation for the cell density, one for the density of the extracellular... |
2406.01599 | Amirreza Kachabi | Amirreza Kachabi, Mitchel J. Colebank, Sofia Altieri Correa, Naomi C.
Chesler | Markov Chain Monte Carlo with Gaussian Process Emulation for a 1D
Hemodynamics Model of CTEPH | null | null | null | null | q-bio.QM cs.CE cs.LG physics.data-an stat.AP | http://creativecommons.org/licenses/by/4.0/ | Microvascular disease is a contributor to persistent pulmonary hypertension
in those with chronic thromboembolic pulmonary hypertension (CTEPH). The
heterogenous nature of the micro and macrovascular defects motivates the use of
personalized computational models, which can predict flow dynamics within
multiple genera... | [
{
"created": "Thu, 25 Apr 2024 18:22:22 GMT",
"version": "v1"
}
] | 2024-06-10 | [
[
"Kachabi",
"Amirreza",
""
],
[
"Colebank",
"Mitchel J.",
""
],
[
"Correa",
"Sofia Altieri",
""
],
[
"Chesler",
"Naomi C.",
""
]
] | Microvascular disease is a contributor to persistent pulmonary hypertension in those with chronic thromboembolic pulmonary hypertension (CTEPH). The heterogenous nature of the micro and macrovascular defects motivates the use of personalized computational models, which can predict flow dynamics within multiple generati... |
2408.00160 | Mridul Khurana | Mridul Khurana, Arka Daw, M. Maruf, Josef C. Uyeda, Wasila Dahdul,
Caleb Charpentier, Yasin Bak{\i}\c{s}, Henry L. Bart Jr., Paula M. Mabee,
Hilmar Lapp, James P. Balhoff, Wei-Lun Chao, Charles Stewart, Tanya
Berger-Wolf, Anuj Karpatne | Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for
Studying Species Evolution | null | null | null | null | q-bio.PE cs.CV cs.LG | http://creativecommons.org/licenses/by-sa/4.0/ | A central problem in biology is to understand how organisms evolve and adapt
to their environment by acquiring variations in the observable characteristics
or traits of species across the tree of life. With the growing availability of
large-scale image repositories in biology and recent advances in generative
modelin... | [
{
"created": "Wed, 31 Jul 2024 21:06:14 GMT",
"version": "v1"
}
] | 2024-08-02 | [
[
"Khurana",
"Mridul",
""
],
[
"Daw",
"Arka",
""
],
[
"Maruf",
"M.",
""
],
[
"Uyeda",
"Josef C.",
""
],
[
"Dahdul",
"Wasila",
""
],
[
"Charpentier",
"Caleb",
""
],
[
"Bakış",
"Yasin",
""
],
[
"Bart",
... | A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling,... |
1308.6808 | Alexandra Jilkine | Alexandra Jilkine, Ryan N. Gutenkunst | Effect of Dedifferentiation on Time to Mutation Acquisition in Stem
Cell-Driven Cancers | null | null | 10.1371/journal.pcbi.1003481 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Accumulating evidence suggests that many tumors have a hierarchical
organization, with the bulk of the tumor composed of relatively differentiated
short-lived progenitor cells that are maintained by a small population of
undifferentiated long-lived cancer stem cells. It is unclear, however, whether
cancer stem cells ... | [
{
"created": "Fri, 30 Aug 2013 17:50:45 GMT",
"version": "v1"
}
] | 2015-06-17 | [
[
"Jilkine",
"Alexandra",
""
],
[
"Gutenkunst",
"Ryan N.",
""
]
] | Accumulating evidence suggests that many tumors have a hierarchical organization, with the bulk of the tumor composed of relatively differentiated short-lived progenitor cells that are maintained by a small population of undifferentiated long-lived cancer stem cells. It is unclear, however, whether cancer stem cells or... |
2401.08873 | Zahra Sheikhbahaee | Zahra Sheikhbahaee and Adam Safron and Casper Hesp and Guillaume Dumas | From Physics to Sentience: Deciphering the Semantics of the Free-Energy
Principle and Evaluating its Claims | null | null | 10.1016/j.plrev.2023.11.004 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Free-Energy Principle (FEP) [1-3] has been adopted in a variety of
ambitious proposals that aim to characterize all adaptive, sentient, and
cognitive systems within a unifying framework. Judging by the amount of
attention it has received from the scientific community, the FEP has gained
significant traction in th... | [
{
"created": "Tue, 16 Jan 2024 23:11:51 GMT",
"version": "v1"
}
] | 2024-01-18 | [
[
"Sheikhbahaee",
"Zahra",
""
],
[
"Safron",
"Adam",
""
],
[
"Hesp",
"Casper",
""
],
[
"Dumas",
"Guillaume",
""
]
] | The Free-Energy Principle (FEP) [1-3] has been adopted in a variety of ambitious proposals that aim to characterize all adaptive, sentient, and cognitive systems within a unifying framework. Judging by the amount of attention it has received from the scientific community, the FEP has gained significant traction in thes... |
2109.02178 | Felix Tena | Felix Tena, Oscar Garnica, Juan Lanchares and J. Ignacio Hidalgo | A Critical Review of the state-of-the-art on Deep Neural Networks for
Blood Glucose Prediction in Patients with Diabetes | 17 pages, 20 figures and 16 tables | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This article compares ten recently proposed neural networks and proposes two
ensemble neural network-based models for blood glucose prediction. All of them
are tested under the same dataset, preprocessing workflow, and tools using the
OhioT1DM Dataset at three different prediction horizons: 30, 60, and 120
minutes. W... | [
{
"created": "Thu, 2 Sep 2021 09:08:26 GMT",
"version": "v1"
}
] | 2021-09-07 | [
[
"Tena",
"Felix",
""
],
[
"Garnica",
"Oscar",
""
],
[
"Lanchares",
"Juan",
""
],
[
"Hidalgo",
"J. Ignacio",
""
]
] | This article compares ten recently proposed neural networks and proposes two ensemble neural network-based models for blood glucose prediction. All of them are tested under the same dataset, preprocessing workflow, and tools using the OhioT1DM Dataset at three different prediction horizons: 30, 60, and 120 minutes. We ... |
1701.04905 | Michael Schaub | Yazan N. Billeh and Michael T. Schaub | Feedforward Architectures Driven by Inhibitory Interactions | 13 pages, 6 figures, J Comput Neurosci (2017) | null | 10.1007/s10827-017-0669-1 | null | q-bio.NC cond-mat.dis-nn nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Directed information transmission is paramount for many social, physical, and
biological systems. For neural systems, scientists have studied this problem
under the paradigm of feedforward networks for decades. In most models of
feedforward networks, activity is exclusively driven by excitatory neurons and
the wiring... | [
{
"created": "Wed, 18 Jan 2017 00:13:43 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Oct 2017 21:50:21 GMT",
"version": "v2"
},
{
"created": "Fri, 17 Nov 2017 22:34:51 GMT",
"version": "v3"
}
] | 2017-11-21 | [
[
"Billeh",
"Yazan N.",
""
],
[
"Schaub",
"Michael T.",
""
]
] | Directed information transmission is paramount for many social, physical, and biological systems. For neural systems, scientists have studied this problem under the paradigm of feedforward networks for decades. In most models of feedforward networks, activity is exclusively driven by excitatory neurons and the wiring p... |
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