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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2006.07209 | Thomas Wieland | Thomas Wieland | Change points in the spread of COVID-19 question the effectiveness of
nonpharmaceutical interventions in Germany | Updated with German COVID-19 case data (RKI) from June 28, 2020 | Saf. Sci. 131 (2020) 104924 | 10.1016/j.ssci.2020.104924 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Aims: Nonpharmaceutical interventions against the spread of SARS-CoV-2 in
Germany included the cancellation of mass events (from March 8), closures of
schools and child day care facilities (from March 16) as well as a "lockdown"
(from March 23). This study attempts to assess the effectiveness of these
interventions i... | [
{
"created": "Fri, 12 Jun 2020 14:13:32 GMT",
"version": "v1"
},
{
"created": "Mon, 29 Jun 2020 21:52:35 GMT",
"version": "v2"
},
{
"created": "Mon, 6 Jul 2020 11:54:59 GMT",
"version": "v3"
}
] | 2020-08-27 | [
[
"Wieland",
"Thomas",
""
]
] | Aims: Nonpharmaceutical interventions against the spread of SARS-CoV-2 in Germany included the cancellation of mass events (from March 8), closures of schools and child day care facilities (from March 16) as well as a "lockdown" (from March 23). This study attempts to assess the effectiveness of these interventions in ... |
1902.09625 | Pedro Constantino | Pedro H. Constantino and Yiannis N. Kaznessis | Moment Closure Stability Analysis of Stochastic Reaction Networks with
Oscillatory Dynamics | 29 pages, 10 figures | null | null | null | q-bio.MN cond-mat.stat-mech | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Biochemical reactions with oscillatory behavior play an essential role in
synthetic biology at the microscopic scale. Although a robust stability theory
for deterministic chemical oscillators in the macroscopic limit exists, the
dynamical stability of stochastic oscillators is an object of ongoing research.
The Chemi... | [
{
"created": "Mon, 25 Feb 2019 21:25:37 GMT",
"version": "v1"
}
] | 2019-02-27 | [
[
"Constantino",
"Pedro H.",
""
],
[
"Kaznessis",
"Yiannis N.",
""
]
] | Biochemical reactions with oscillatory behavior play an essential role in synthetic biology at the microscopic scale. Although a robust stability theory for deterministic chemical oscillators in the macroscopic limit exists, the dynamical stability of stochastic oscillators is an object of ongoing research. The Chemica... |
2405.16524 | Polina Lakrisenko | Polina Lakrisenko, Dilan Pathirana, Daniel Weindl, Jan Hasenauer | Exploration of methods for computing sensitivities in ODE models at
dynamic and steady states | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Estimating parameters of dynamic models from experimental data is a
challenging, and often computationally-demanding task. It requires a large
number of model simulations and objective function gradient computations, if
gradient-based optimization is used. The gradient depends on derivatives of the
state variables wi... | [
{
"created": "Sun, 26 May 2024 11:21:05 GMT",
"version": "v1"
}
] | 2024-05-28 | [
[
"Lakrisenko",
"Polina",
""
],
[
"Pathirana",
"Dilan",
""
],
[
"Weindl",
"Daniel",
""
],
[
"Hasenauer",
"Jan",
""
]
] | Estimating parameters of dynamic models from experimental data is a challenging, and often computationally-demanding task. It requires a large number of model simulations and objective function gradient computations, if gradient-based optimization is used. The gradient depends on derivatives of the state variables with... |
2005.08443 | Cameron Mura | Menuka Jaiswal, Saad Saleem, Yonghyeon Kweon, Eli J Draizen, Stella
Veretnik, Cameron Mura, Philip E. Bourne | Deep Learning of Protein Structural Classes: Any Evidence for an
'Urfold'? | 6 pages, 3 figures, 1 table; IEEE SIEDS conference submission | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent computational advances in the accurate prediction of protein
three-dimensional (3D) structures from amino acid sequences now present a
unique opportunity to decipher the interrelationships between proteins. This
task entails--but is not equivalent to--a problem of 3D structure comparison
and classification. Hi... | [
{
"created": "Mon, 18 May 2020 03:55:01 GMT",
"version": "v1"
}
] | 2020-05-19 | [
[
"Jaiswal",
"Menuka",
""
],
[
"Saleem",
"Saad",
""
],
[
"Kweon",
"Yonghyeon",
""
],
[
"Draizen",
"Eli J",
""
],
[
"Veretnik",
"Stella",
""
],
[
"Mura",
"Cameron",
""
],
[
"Bourne",
"Philip E.",
""
]
] | Recent computational advances in the accurate prediction of protein three-dimensional (3D) structures from amino acid sequences now present a unique opportunity to decipher the interrelationships between proteins. This task entails--but is not equivalent to--a problem of 3D structure comparison and classification. Hist... |
1504.06732 | Paul Moore | P. J. Moore | A predictive coding account of OCD | arXiv admin note: substantial text overlap with arXiv:1503.00999 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper presents a predictive coding account of obsessive-compulsive
disorder (OCD). We extend the predictive coding model to include the concept of
a 'formal narrative', or temporal sequence of cognitive states inferred from
sense data. We propose that human cognition uses a hierarchy of narratives to
predict cha... | [
{
"created": "Sat, 25 Apr 2015 14:40:07 GMT",
"version": "v1"
},
{
"created": "Mon, 8 Jun 2015 14:15:16 GMT",
"version": "v2"
}
] | 2015-06-09 | [
[
"Moore",
"P. J.",
""
]
] | This paper presents a predictive coding account of obsessive-compulsive disorder (OCD). We extend the predictive coding model to include the concept of a 'formal narrative', or temporal sequence of cognitive states inferred from sense data. We propose that human cognition uses a hierarchy of narratives to predict chang... |
2003.09861 | Giulia Giordano | Giulia Giordano, Franco Blanchini, Raffaele Bruno, Patrizio Colaneri,
Alessandro Di Filippo, Angela Di Matteo, Marta Colaneri, and the COVID19
IRCCS San Matteo Pavia Task Force | A SIDARTHE Model of COVID-19 Epidemic in Italy | null | Nature Medicine, 26, pages 855-860 (2020) | 10.1038/s41591-020-0883-7 | null | q-bio.PE cs.SY eess.SY math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In late December 2019, a novel strand of Coronavirus (SARS-CoV-2) causing a
severe, potentially fatal respiratory syndrome (COVID-19) was identified in
Wuhan, Hubei Province, China and is causing outbreaks in multiple world
countries, soon becoming a pandemic. Italy has now become the most hit country
outside of Asia... | [
{
"created": "Sun, 22 Mar 2020 11:17:18 GMT",
"version": "v1"
}
] | 2021-08-23 | [
[
"Giordano",
"Giulia",
""
],
[
"Blanchini",
"Franco",
""
],
[
"Bruno",
"Raffaele",
""
],
[
"Colaneri",
"Patrizio",
""
],
[
"Di Filippo",
"Alessandro",
""
],
[
"Di Matteo",
"Angela",
""
],
[
"Colaneri",
"Marta",
... | In late December 2019, a novel strand of Coronavirus (SARS-CoV-2) causing a severe, potentially fatal respiratory syndrome (COVID-19) was identified in Wuhan, Hubei Province, China and is causing outbreaks in multiple world countries, soon becoming a pandemic. Italy has now become the most hit country outside of Asia: ... |
2406.03197 | Filippo Agnesi | Filippo Agnesi, Lucia Carlucci, Gia Burjanadze, Fabio Bernini, Khatia
Gabisonia, John W Osborn, Silvestro Micera and Fabio A. Recchia | Complex hemodynamic responses to trans-vascular electrical stimulation
of the renal nerve in anesthetized pigs | 5 pages, 2 tables, 5 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The objective of this study was to characterize hemodynamic changes during
trans-vascular stimulation of the renal nerve and their dependence on
stimulation parameters. We employed a stimulation catheter inserted in the
right renal artery under fluoroscopic guidance, in pigs. Systolic, diastolic
and pulse blood press... | [
{
"created": "Wed, 29 May 2024 14:36:47 GMT",
"version": "v1"
}
] | 2024-06-06 | [
[
"Agnesi",
"Filippo",
""
],
[
"Carlucci",
"Lucia",
""
],
[
"Burjanadze",
"Gia",
""
],
[
"Bernini",
"Fabio",
""
],
[
"Gabisonia",
"Khatia",
""
],
[
"Osborn",
"John W",
""
],
[
"Micera",
"Silvestro",
""
],
... | The objective of this study was to characterize hemodynamic changes during trans-vascular stimulation of the renal nerve and their dependence on stimulation parameters. We employed a stimulation catheter inserted in the right renal artery under fluoroscopic guidance, in pigs. Systolic, diastolic and pulse blood pressur... |
1406.5197 | Danielle Bassett | Shi Gu, Fabio Pasqualetti, Matthew Cieslak, Scott T. Grafton, Danielle
S. Bassett | Controllability of Brain Networks | 14 pages, 4 figures, supplementary materials | null | 10.1038/ncomms9414 | null | q-bio.NC cs.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cognitive function is driven by dynamic interactions between large-scale
neural circuits or networks, enabling behavior. Fundamental principles
constraining these dynamic network processes have remained elusive. Here we use
network control theory to offer a mechanistic explanation for how the brain
moves between cogn... | [
{
"created": "Thu, 19 Jun 2014 20:05:48 GMT",
"version": "v1"
}
] | 2015-10-28 | [
[
"Gu",
"Shi",
""
],
[
"Pasqualetti",
"Fabio",
""
],
[
"Cieslak",
"Matthew",
""
],
[
"Grafton",
"Scott T.",
""
],
[
"Bassett",
"Danielle S.",
""
]
] | Cognitive function is driven by dynamic interactions between large-scale neural circuits or networks, enabling behavior. Fundamental principles constraining these dynamic network processes have remained elusive. Here we use network control theory to offer a mechanistic explanation for how the brain moves between cognit... |
1010.4127 | Pierre Sens | Pierre Sens and Matthew S. Turner | Microphase separation in nonequilibrium biomembranes | null | null | 10.1103/PhysRevLett.106.238101 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Microphase separation of membrane components is thought to play an important
role in many physiological processes, from cell signaling to endocytosis and
cellular trafficking. Here, we study how variations in the membrane composition
can be driven by fluctuating forces. We show that the membrane steady state is
not o... | [
{
"created": "Wed, 20 Oct 2010 08:40:50 GMT",
"version": "v1"
}
] | 2015-05-20 | [
[
"Sens",
"Pierre",
""
],
[
"Turner",
"Matthew S.",
""
]
] | Microphase separation of membrane components is thought to play an important role in many physiological processes, from cell signaling to endocytosis and cellular trafficking. Here, we study how variations in the membrane composition can be driven by fluctuating forces. We show that the membrane steady state is not onl... |
0708.0186 | Eduardo Candelario-Jalil | E. Candelario-Jalil, H. Slawik, I. Ridelis, A. Waschbisch, R.S.
Akundi, M. Hull, B.L. Fiebich | Regional distribution of the prostaglandin E2 receptor EP1 in the rat
brain: accumulation in Purkinje cells of the cerebellum | null | Journal of Molecular Neuroscience 27(3): 303-310 (2005) | null | null | q-bio.TO | null | Prostaglandin E2 (PGE2), is a major prostanoid produced by the activity of
cyclooxygenases (COX) in response to various physiological and pathological
stimuli. PGE2 exerts its effects by activating four specific E-type prostanoid
receptors (EP1, EP2, EP3, and EP4). In the present study, we analyzed the
expression of ... | [
{
"created": "Wed, 1 Aug 2007 16:02:56 GMT",
"version": "v1"
}
] | 2007-08-02 | [
[
"Candelario-Jalil",
"E.",
""
],
[
"Slawik",
"H.",
""
],
[
"Ridelis",
"I.",
""
],
[
"Waschbisch",
"A.",
""
],
[
"Akundi",
"R. S.",
""
],
[
"Hull",
"M.",
""
],
[
"Fiebich",
"B. L.",
""
]
] | Prostaglandin E2 (PGE2), is a major prostanoid produced by the activity of cyclooxygenases (COX) in response to various physiological and pathological stimuli. PGE2 exerts its effects by activating four specific E-type prostanoid receptors (EP1, EP2, EP3, and EP4). In the present study, we analyzed the expression of th... |
1211.6348 | Fernando Fabian Montani | Fernando Montani, Elena Phoka, Mariela Portesi, Simon R. Schultz | Statistical modelling of higher-order correlations in pools of neural
activity | 42 pages, 12 Figures; Submitted to Physica A | Physica A 392 (2013) 3066-3086 | 10.1016/j.physa.2013.03.012 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Simultaneous recordings from multiple neural units allow us to investigate
the activity of very large neural ensembles. To understand how large ensembles
of neurons process sensory information, it is necessary to develop suitable
statistical models to describe the response variability of the recorded spike
trains. Us... | [
{
"created": "Tue, 27 Nov 2012 16:26:15 GMT",
"version": "v1"
}
] | 2013-05-30 | [
[
"Montani",
"Fernando",
""
],
[
"Phoka",
"Elena",
""
],
[
"Portesi",
"Mariela",
""
],
[
"Schultz",
"Simon R.",
""
]
] | Simultaneous recordings from multiple neural units allow us to investigate the activity of very large neural ensembles. To understand how large ensembles of neurons process sensory information, it is necessary to develop suitable statistical models to describe the response variability of the recorded spike trains. Usin... |
1503.06726 | Simon Tanaka Mr. | Simon Tanaka, David Sichau, Dagmar Iber | LBIBCell: A Cell-Based Simulation Environment for Morphogenetic Problems | 15 pages, 23 pages with supplementary, 6 figures; Bioinformatics 2015 | null | 10.1093/bioinformatics/btv147 | null | q-bio.QM q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The simulation of morphogenetic problems requires the simultaneous and
coupled simulation of signalling and tissue dynamics. A cellular resolution of
the tissue domain is important to adequately describe the impact of cell-based
events, such as cell division, cell-cell interactions, and spatially restricted
signallin... | [
{
"created": "Mon, 23 Mar 2015 16:59:14 GMT",
"version": "v1"
}
] | 2015-03-29 | [
[
"Tanaka",
"Simon",
""
],
[
"Sichau",
"David",
""
],
[
"Iber",
"Dagmar",
""
]
] | The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events, such as cell division, cell-cell interactions, and spatially restricted signalling ... |
q-bio/0401014 | Mark Alber | Mark S. Alber, Yi Jiang and Maria A. Kiskowski | Lattice gas cellular automata model for rippling and aggregation in
myxobacteria | null | null | 10.1016/j.physd.2003.11.012 | null | q-bio.QM q-bio.OT | null | A lattice-gas cellular automaton (LGCA) model is used to simulate rippling
and aggregation in myxobacteria. An efficient way of representing cells of
different cell size, shape and orientation is presented that may be easily
extended to model later stages of fruiting body formation. This LGCA model is
designed to inv... | [
{
"created": "Fri, 9 Jan 2004 22:21:11 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Alber",
"Mark S.",
""
],
[
"Jiang",
"Yi",
""
],
[
"Kiskowski",
"Maria A.",
""
]
] | A lattice-gas cellular automaton (LGCA) model is used to simulate rippling and aggregation in myxobacteria. An efficient way of representing cells of different cell size, shape and orientation is presented that may be easily extended to model later stages of fruiting body formation. This LGCA model is designed to inves... |
1610.00121 | Victor Solovyev | Victor Solovyev and Ramzan Umarov | Prediction of Prokaryotic and Eukaryotic Promoters Using Convolutional
Deep Learning Neural Networks | 12 pages, 4 figures | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Accurate computational identification of promoters remains a challenge as
these key DNA regulatory regions have variable structures composed of
functional motifs that provide gene specific initiation of transcription. In
this paper we utilize Convolutional Neural Networks (CNN) to analyze sequence
characteristics of ... | [
{
"created": "Sat, 1 Oct 2016 11:24:47 GMT",
"version": "v1"
}
] | 2016-10-04 | [
[
"Solovyev",
"Victor",
""
],
[
"Umarov",
"Ramzan",
""
]
] | Accurate computational identification of promoters remains a challenge as these key DNA regulatory regions have variable structures composed of functional motifs that provide gene specific initiation of transcription. In this paper we utilize Convolutional Neural Networks (CNN) to analyze sequence characteristics of pr... |
1306.2167 | Gergely J Sz\"oll\H{o}si | Gergely J. Sz\"oll\H{o}si and Wojciech Rosikiewicz and Bastien Boussau
and Eric Tannier and Vincent Daubin | Efficient Exploration of the Space of Reconciled Gene Trees | Manuscript accepted pending revision in Systematic Biology | null | null | null | q-bio.PE q-bio.BM q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Gene trees record the combination of gene level events, such as duplication,
transfer and loss, and species level events, such as speciation and extinction.
Gene tree-species tree reconciliation methods model these processes by drawing
gene trees into the species tree using a series of gene and species level
events. ... | [
{
"created": "Mon, 10 Jun 2013 11:33:28 GMT",
"version": "v1"
}
] | 2013-06-11 | [
[
"Szöllősi",
"Gergely J.",
""
],
[
"Rosikiewicz",
"Wojciech",
""
],
[
"Boussau",
"Bastien",
""
],
[
"Tannier",
"Eric",
""
],
[
"Daubin",
"Vincent",
""
]
] | Gene trees record the combination of gene level events, such as duplication, transfer and loss, and species level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species level events. Th... |
1204.3123 | Mustafa Barasa | Barasa Mustafa, Mwangi Irungu Michael, Mutiso Muli Joshua, Kagasi
Ambogo Esther, Ozwara Suba Hastings, Gicheru Muita Michael | Plasmodium knowlesi H strain pregnancy malaria immune responses in olive
baboons (Papio anubis) | Five pages, six figures;This study was funded by the research
capability strengthening WHO grant (Grant Number: A 50075) for malaria
research in Africa under the Multilateral Initiative on Malaria/Special
Programme for Research and Training in Tropical Diseases (WHO-MIM/TDR).The
Institute of Primate Research (I... | Int. J. Integ. Biol: Year 2010, Volume 10, Issue No. 1: 54 - 58 | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Approximately 24 million pregnant women in Sub-Saharan Africa are at risk of
suffering from pregnancy malaria complications. Mechanisms responsible for
increased susceptibility to malaria in pregnant women are not fully understood.
Baboons are susceptible to Plasmodium knowlesi and their reproductive
physiology and h... | [
{
"created": "Sat, 14 Apr 2012 00:11:19 GMT",
"version": "v1"
},
{
"created": "Tue, 17 Apr 2012 08:01:13 GMT",
"version": "v2"
}
] | 2012-04-18 | [
[
"Mustafa",
"Barasa",
""
],
[
"Michael",
"Mwangi Irungu",
""
],
[
"Joshua",
"Mutiso Muli",
""
],
[
"Esther",
"Kagasi Ambogo",
""
],
[
"Hastings",
"Ozwara Suba",
""
],
[
"Michael",
"Gicheru Muita",
""
]
] | Approximately 24 million pregnant women in Sub-Saharan Africa are at risk of suffering from pregnancy malaria complications. Mechanisms responsible for increased susceptibility to malaria in pregnant women are not fully understood. Baboons are susceptible to Plasmodium knowlesi and their reproductive physiology and hos... |
2006.02459 | Slobodan Vucetic | Benjamin Seibold, Zivjena Vucetic, Slobodan Vucetic | Quantitative Relationship between Population Mobility and COVID-19
Growth Rate based on 14 Countries | null | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This study develops a framework for quantification of the impact of changes
in population mobility due to social distancing on the COVID-19 infection
growth rate. Using the Susceptible-Infected-Recovered (SIR) epidemiological
model we establish that under some mild assumptions the growth rate of COVID-19
deaths is a ... | [
{
"created": "Wed, 3 Jun 2020 18:10:38 GMT",
"version": "v1"
}
] | 2020-06-05 | [
[
"Seibold",
"Benjamin",
""
],
[
"Vucetic",
"Zivjena",
""
],
[
"Vucetic",
"Slobodan",
""
]
] | This study develops a framework for quantification of the impact of changes in population mobility due to social distancing on the COVID-19 infection growth rate. Using the Susceptible-Infected-Recovered (SIR) epidemiological model we establish that under some mild assumptions the growth rate of COVID-19 deaths is a ti... |
2109.12799 | Cameron Zachreson | Cameron Zachreson, Freya M. Shearer, David J. Price, Michael J.
Lydeamore, Jodie McVernon, James McCaw, and Nicholas Geard | COVID-19 in low-tolerance border quarantine systems: impact of the Delta
variant of SARS-CoV-2 | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In controlling transmission of COVID-19, the effectiveness of border
quarantine strategies is a key concern for jurisdictions in which the local
prevalence of disease and immunity is low. In settings like this such as China,
Australia, and New Zealand, rare outbreak events can lead to escalating
epidemics and trigger... | [
{
"created": "Mon, 27 Sep 2021 05:09:32 GMT",
"version": "v1"
}
] | 2021-09-28 | [
[
"Zachreson",
"Cameron",
""
],
[
"Shearer",
"Freya M.",
""
],
[
"Price",
"David J.",
""
],
[
"Lydeamore",
"Michael J.",
""
],
[
"McVernon",
"Jodie",
""
],
[
"McCaw",
"James",
""
],
[
"Geard",
"Nicholas",
""
... | In controlling transmission of COVID-19, the effectiveness of border quarantine strategies is a key concern for jurisdictions in which the local prevalence of disease and immunity is low. In settings like this such as China, Australia, and New Zealand, rare outbreak events can lead to escalating epidemics and trigger t... |
1302.1944 | Anil Korkut | Anil Korkut, Wayne A Hendrickson | Stereochemistry of Polypeptide Conformation in Coarse Grained Analysis | 12 pages, 3 figures, Postprint of book chapter submitted to the
Biomolecular Forms and Functions, M. Bansal and N. Srinivasan, Eds. copyright
(2013) [copyright World Scientific Publishing Company] | Biomolecular Forms and Functions, M. Bansal and N. Srinivasan,
Eds. IISc Press - World Scientific Publishing, Singapore, pp. 136-147 (2013) | null | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The conformations available to polypeptides are determined by the interatomic
forces acting on the peptide units, whereby backbone torsion angles are
restricted as described by the Ramachandran plot. Although typical proteins are
composed predominantly from {\alpha}-helices and {\beta}-sheets, they
nevertheless adopt... | [
{
"created": "Fri, 8 Feb 2013 04:59:36 GMT",
"version": "v1"
}
] | 2013-02-11 | [
[
"Korkut",
"Anil",
""
],
[
"Hendrickson",
"Wayne A",
""
]
] | The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed predominantly from {\alpha}-helices and {\beta}-sheets, they nevertheless adopt d... |
1810.11195 | Tianming Wang | Hailong Dou, Haitao Yang, James L.D. Smith, Limin Feng, Tianming Wang,
Jianping Ge | Prey selection of Amur tigers in relation to the spatiotemporal overlap
with prey across the Sino-Russian border | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The endangered Amur tiger is confined primarily to a narrow area along the
border with Russia in Northeast China. Little is known about the foraging
strategies of this small subpopulation in Hunchun Nature Reserve on the Chinese
side of the border; at this location, the prey base and land use patterns are
distinctly ... | [
{
"created": "Fri, 26 Oct 2018 05:56:36 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Mar 2019 09:33:09 GMT",
"version": "v2"
}
] | 2019-03-29 | [
[
"Dou",
"Hailong",
""
],
[
"Yang",
"Haitao",
""
],
[
"Smith",
"James L. D.",
""
],
[
"Feng",
"Limin",
""
],
[
"Wang",
"Tianming",
""
],
[
"Ge",
"Jianping",
""
]
] | The endangered Amur tiger is confined primarily to a narrow area along the border with Russia in Northeast China. Little is known about the foraging strategies of this small subpopulation in Hunchun Nature Reserve on the Chinese side of the border; at this location, the prey base and land use patterns are distinctly di... |
2203.09798 | Francisco Rowe Dr | Niall Newsham, Francisco Rowe | Understanding the Trajectories of Population Decline Across Rural and
Urban Europe: A Sequence Analysis | 24 pages, 5 tables, 5 figures | null | null | null | q-bio.PE stat.AP | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Population decline is projected to become widespread in Europe, with the
continental population set to reverse its longstanding trajectory of growth
within the next five years. This represents unfamiliar demographic territory.
Despite this, literature on decline remains sparse and our understanding
porous. Particular... | [
{
"created": "Fri, 18 Mar 2022 08:29:57 GMT",
"version": "v1"
},
{
"created": "Tue, 10 May 2022 13:47:38 GMT",
"version": "v2"
}
] | 2022-05-11 | [
[
"Newsham",
"Niall",
""
],
[
"Rowe",
"Francisco",
""
]
] | Population decline is projected to become widespread in Europe, with the continental population set to reverse its longstanding trajectory of growth within the next five years. This represents unfamiliar demographic territory. Despite this, literature on decline remains sparse and our understanding porous. Particular e... |
1212.2617 | Peter Richtarik | William Hulme, Peter Richt\'arik, Lynne McGuire and Alison Green | Optimal diagnostic tests for sporadic Creutzfeldt-Jakob disease based on
support vector machine classification of RT-QuIC data | 32 pages, 12 figures, 1 table | null | null | null | q-bio.QM cs.LG stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work we study numerical construction of optimal clinical diagnostic
tests for detecting sporadic Creutzfeldt-Jakob disease (sCJD). A cerebrospinal
fluid sample (CSF) from a suspected sCJD patient is subjected to a process
which initiates the aggregation of a protein present only in cases of sCJD.
This aggrega... | [
{
"created": "Tue, 11 Dec 2012 20:33:16 GMT",
"version": "v1"
}
] | 2012-12-12 | [
[
"Hulme",
"William",
""
],
[
"Richtárik",
"Peter",
""
],
[
"McGuire",
"Lynne",
""
],
[
"Green",
"Alison",
""
]
] | In this work we study numerical construction of optimal clinical diagnostic tests for detecting sporadic Creutzfeldt-Jakob disease (sCJD). A cerebrospinal fluid sample (CSF) from a suspected sCJD patient is subjected to a process which initiates the aggregation of a protein present only in cases of sCJD. This aggregati... |
q-bio/0703038 | Zhong Li | Zhong Li, Aris Floratos, David Wang, Andrea Califano | A Pattern Discovery-Based Method for Detecting Multi-Locus Genetic
Association | 49 pages, 4 tables, 4 figures | null | null | null | q-bio.GN q-bio.PE | null | Methods to effectively detect multi-locus genetic association are becoming
increasingly relevant in the genetic dissection of complex trait in humans.
Current approaches typically consider a limited number of hypotheses, most of
which are related to the effect of a single locus or of a relatively small
number of neig... | [
{
"created": "Fri, 16 Mar 2007 18:08:01 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Li",
"Zhong",
""
],
[
"Floratos",
"Aris",
""
],
[
"Wang",
"David",
""
],
[
"Califano",
"Andrea",
""
]
] | Methods to effectively detect multi-locus genetic association are becoming increasingly relevant in the genetic dissection of complex trait in humans. Current approaches typically consider a limited number of hypotheses, most of which are related to the effect of a single locus or of a relatively small number of neighb... |
1808.07154 | Ralf Schwamborn | R. Schwamborn, T. K. Mildenberger, M. H. Taylor | Assessing sources of uncertainty in length-based estimates of body
growth in populations of fishes and macroinvertebrates with bootstrapped
ELEFAN | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The determination of rates of body growth is the first step in many aquatic
population studies and fisheries stock assessments. ELEFAN (Electronic LEngth
Frequency ANalysis) is a widely used method to fit a growth curve to
length-frequency distribution (LFD) data. However, up to now, it was not
possible to assess its... | [
{
"created": "Tue, 21 Aug 2018 22:35:04 GMT",
"version": "v1"
}
] | 2018-08-23 | [
[
"Schwamborn",
"R.",
""
],
[
"Mildenberger",
"T. K.",
""
],
[
"Taylor",
"M. H.",
""
]
] | The determination of rates of body growth is the first step in many aquatic population studies and fisheries stock assessments. ELEFAN (Electronic LEngth Frequency ANalysis) is a widely used method to fit a growth curve to length-frequency distribution (LFD) data. However, up to now, it was not possible to assess its a... |
q-bio/0606005 | Yoram Burak | Yoram Burak, Ted Brookings, and Ila Fiete | Triangular lattice neurons may implement an advanced numeral system to
precisely encode rat position over large ranges | 4 pages with one figure, and 2 pages of supplementary information | null | null | null | q-bio.NC | null | We argue by observation of the neural data that neurons in area dMEC of rats,
which fire whenever the rat is on any vertex of a regular triangular lattice
that tiles 2-d space, may be using an advanced numeral system to reversibly
encode rat position. We interpret measured dMEC properties within the framework
of a re... | [
{
"created": "Sun, 4 Jun 2006 06:15:39 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Burak",
"Yoram",
""
],
[
"Brookings",
"Ted",
""
],
[
"Fiete",
"Ila",
""
]
] | We argue by observation of the neural data that neurons in area dMEC of rats, which fire whenever the rat is on any vertex of a regular triangular lattice that tiles 2-d space, may be using an advanced numeral system to reversibly encode rat position. We interpret measured dMEC properties within the framework of a resi... |
1203.5914 | Martin Burger | Michael Moeller and Martin Burger and Peter Dieterich and Albrecht
Schwab | A Framework for Automated Cell Tracking in Phase Contrast Microscopic
Videos based on Normal Velocities | null | null | null | null | q-bio.QM cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper introduces a novel framework for the automated tracking of cells,
with a particular focus on the challenging situation of phase contrast
microscopic videos. Our framework is based on a topology preserving variational
segmentation approach applied to normal velocity components obtained from
optical flow com... | [
{
"created": "Tue, 27 Mar 2012 10:05:19 GMT",
"version": "v1"
}
] | 2012-03-28 | [
[
"Moeller",
"Michael",
""
],
[
"Burger",
"Martin",
""
],
[
"Dieterich",
"Peter",
""
],
[
"Schwab",
"Albrecht",
""
]
] | This paper introduces a novel framework for the automated tracking of cells, with a particular focus on the challenging situation of phase contrast microscopic videos. Our framework is based on a topology preserving variational segmentation approach applied to normal velocity components obtained from optical flow compu... |
1408.2298 | Atsushi Kamimura | Atsushi Kamimura and Kunihiko Kaneko | Transition to diversification by competition for resources in catalytic
reaction networks | 18 pages, 13 figure, submitted for publication | null | null | null | q-bio.CB q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | All life, including cells and artificial protocells, must integrate diverse
molecules into a single unit in order to reproduce. Despite expected pressure
to evolve a simple system with the fastest replication speed, the mechanism by
which the use of the great variety of components, and the coexistence of
diverse cell... | [
{
"created": "Mon, 11 Aug 2014 03:24:41 GMT",
"version": "v1"
}
] | 2014-08-12 | [
[
"Kamimura",
"Atsushi",
""
],
[
"Kaneko",
"Kunihiko",
""
]
] | All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which the use of the great variety of components, and the coexistence of diverse cell-t... |
2003.12017 | Ganesh Kumar M | Ganesh Kumar M, Soman K.P, Gopalakrishnan E.A, Vijay Krishna Menon,
Sowmya V | Prediction of number of cases expected and estimation of the final size
of coronavirus epidemic in India using the logistic model and genetic
algorithm | null | null | null | null | q-bio.PE cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we have applied the logistic growth regression model and
genetic algorithm to predict the number of coronavirus infected cases that can
be expected in upcoming days in India and also estimated the final size and its
peak time of the coronavirus epidemic in India.
| [
{
"created": "Thu, 26 Mar 2020 16:32:54 GMT",
"version": "v1"
}
] | 2020-03-27 | [
[
"M",
"Ganesh Kumar",
""
],
[
"P",
"Soman K.",
""
],
[
"A",
"Gopalakrishnan E.",
""
],
[
"Menon",
"Vijay Krishna",
""
],
[
"V",
"Sowmya",
""
]
] | In this paper, we have applied the logistic growth regression model and genetic algorithm to predict the number of coronavirus infected cases that can be expected in upcoming days in India and also estimated the final size and its peak time of the coronavirus epidemic in India. |
1805.09603 | Chen Beer | Chen Beer, Omri Barak | One step back, two steps forward: interference and learning in recurrent
neural networks | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Artificial neural networks, trained to perform cognitive tasks, have recently
been used as models for neural recordings from animals performing these tasks.
While some progress has been made in performing such comparisons, the evolution
of network dynamics throughout learning remains unexplored. This is paralleled
by... | [
{
"created": "Thu, 24 May 2018 11:05:12 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Jan 2019 07:06:09 GMT",
"version": "v2"
},
{
"created": "Thu, 2 May 2019 14:32:44 GMT",
"version": "v3"
}
] | 2019-05-03 | [
[
"Beer",
"Chen",
""
],
[
"Barak",
"Omri",
""
]
] | Artificial neural networks, trained to perform cognitive tasks, have recently been used as models for neural recordings from animals performing these tasks. While some progress has been made in performing such comparisons, the evolution of network dynamics throughout learning remains unexplored. This is paralleled by a... |
1303.0256 | Marcelo Tragtenberg Dr. | M. Girardi-Schappo, M. H. R. Tragtenberg, O. Kinouchi | A Brief History of Excitable Map-Based Neurons and Neural Networks | 53 pages, 13 figures, submitted to Journal of Neuroscience Methods | Journal of Neuroscience Methods, Volume 220, Issue 2, 15 November
2013, Pages 116-130 | 10.1016/j.jneumeth.2013.07.014 | null | q-bio.NC cond-mat.dis-nn nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This review gives a short historical account of the excitable maps approach
for modeling neurons and neuronal networks. Some early models, due to Pasemann
(1993), Chialvo (1995) and Kinouchi and Tragtenberg (1996), are compared with
more recent proposals by Rulkov (2002) and Izhikevich (2003). We also review
map-base... | [
{
"created": "Fri, 1 Mar 2013 19:25:54 GMT",
"version": "v1"
}
] | 2016-02-03 | [
[
"Girardi-Schappo",
"M.",
""
],
[
"Tragtenberg",
"M. H. R.",
""
],
[
"Kinouchi",
"O.",
""
]
] | This review gives a short historical account of the excitable maps approach for modeling neurons and neuronal networks. Some early models, due to Pasemann (1993), Chialvo (1995) and Kinouchi and Tragtenberg (1996), are compared with more recent proposals by Rulkov (2002) and Izhikevich (2003). We also review map-based ... |
1605.06790 | Marisa Eisenberg | Elizabeth C. Lee, Michael R. Kelly, Brad M. Ochocki, Segun M.
Akinwumi, Karen E. S. Hamre, Joseph H. Tien, Marisa C. Eisenberg | Model distinguishability and inference robustness in mechanisms of
cholera transmission and loss of immunity | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mathematical models of cholera and waterborne disease vary widely in their
structures, in terms of transmission pathways, loss of immunity, and other
features. These differences may yield different predictions and parameter
estimates from the same data. Given the increasing use of models to inform
public health decis... | [
{
"created": "Sun, 22 May 2016 13:35:40 GMT",
"version": "v1"
}
] | 2016-05-24 | [
[
"Lee",
"Elizabeth C.",
""
],
[
"Kelly",
"Michael R.",
""
],
[
"Ochocki",
"Brad M.",
""
],
[
"Akinwumi",
"Segun M.",
""
],
[
"Hamre",
"Karen E. S.",
""
],
[
"Tien",
"Joseph H.",
""
],
[
"Eisenberg",
"Marisa C.",... | Mathematical models of cholera and waterborne disease vary widely in their structures, in terms of transmission pathways, loss of immunity, and other features. These differences may yield different predictions and parameter estimates from the same data. Given the increasing use of models to inform public health decisio... |
1905.09888 | Farzad Khalvati | Yucheng Zhang, Edrise M. Lobo-Mueller, Paul Karanicolas, Steven
Gallinger, Masoom A. Haider, Farzad Khalvati | Prognostic Value of Transfer Learning Based Features in Resectable
Pancreatic Ductal Adenocarcinoma | null | null | null | null | q-bio.QM cs.CV cs.LG eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Pancreatic Ductal Adenocarcinoma (PDAC) is one of the most aggressive cancers
with an extremely poor prognosis. Radiomics has shown prognostic ability in
multiple types of cancer including PDAC. However, the prognostic value of
traditional radiomics pipelines, which are based on hand-crafted radiomic
features alone i... | [
{
"created": "Thu, 23 May 2019 19:35:41 GMT",
"version": "v1"
},
{
"created": "Wed, 21 Aug 2019 15:16:00 GMT",
"version": "v2"
}
] | 2019-08-22 | [
[
"Zhang",
"Yucheng",
""
],
[
"Lobo-Mueller",
"Edrise M.",
""
],
[
"Karanicolas",
"Paul",
""
],
[
"Gallinger",
"Steven",
""
],
[
"Haider",
"Masoom A.",
""
],
[
"Khalvati",
"Farzad",
""
]
] | Pancreatic Ductal Adenocarcinoma (PDAC) is one of the most aggressive cancers with an extremely poor prognosis. Radiomics has shown prognostic ability in multiple types of cancer including PDAC. However, the prognostic value of traditional radiomics pipelines, which are based on hand-crafted radiomic features alone is ... |
1501.06149 | Iain Johnston | Iain G. Johnston and Nick S. Jones | Closed-form stochastic solutions for non-equilibrium dynamics and
inheritance of cellular components over many cell divisions | null | null | 10.1098/rspa.2015.0050 | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stochastic dynamics govern many important processes in cellular biology, and
an underlying theoretical approach describing these dynamics is desirable to
address a wealth of questions in biology and medicine. Mathematical tools exist
for treating several important examples of these stochastic processes, most
notably ... | [
{
"created": "Sun, 25 Jan 2015 12:56:04 GMT",
"version": "v1"
}
] | 2016-02-17 | [
[
"Johnston",
"Iain G.",
""
],
[
"Jones",
"Nick S.",
""
]
] | Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for treating several important examples of these stochastic processes, most notably ge... |
1704.08585 | G Ambika | K. P. Harikrishnan, Rinku Jacob, R. Misra, G. Ambika | Determining the minimum embedding dimension for state space
reconstruction through recurrence networks | 13 pages, 8 figures, submitted to Pramana( J Phys) | Indian Academy of Sciences Conference Series (2017) 1:1 | 10.29195/iascs.01.01.0004 | null | q-bio.NC nlin.CD physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The analysis of observed time series from nonlinear systems is usually done
by making a time-delay reconstruction to unfold the dynamics on a
multi-dimensional state space. An important aspect of the analysis is the
choice of the correct embedding dimension. The conventional procedure used for
this is either the meth... | [
{
"created": "Wed, 26 Apr 2017 02:20:18 GMT",
"version": "v1"
}
] | 2018-09-05 | [
[
"Harikrishnan",
"K. P.",
""
],
[
"Jacob",
"Rinku",
""
],
[
"Misra",
"R.",
""
],
[
"Ambika",
"G.",
""
]
] | The analysis of observed time series from nonlinear systems is usually done by making a time-delay reconstruction to unfold the dynamics on a multi-dimensional state space. An important aspect of the analysis is the choice of the correct embedding dimension. The conventional procedure used for this is either the method... |
2303.07250 | Amit Samadder | Amit Samadder, Arnab Chattopadhyay, Sabyasachi Bhattacharya | The balance between contamination and predation determine species
existence in prey-predator dynamics with contaminated and uncontaminated prey | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In freshwater ecosystems, aquatic insects that ontogenetically shift their
habitat from aquatic to terrestrial play vital roles as prey subsidies that
move nutrients and energy from aquatic to terrestrial food webs. As a result,
these subsidies negatively affect alternative terrestrial prey by enhancing
predator dens... | [
{
"created": "Mon, 13 Mar 2023 16:24:08 GMT",
"version": "v1"
},
{
"created": "Tue, 14 Mar 2023 12:50:47 GMT",
"version": "v2"
}
] | 2023-03-15 | [
[
"Samadder",
"Amit",
""
],
[
"Chattopadhyay",
"Arnab",
""
],
[
"Bhattacharya",
"Sabyasachi",
""
]
] | In freshwater ecosystems, aquatic insects that ontogenetically shift their habitat from aquatic to terrestrial play vital roles as prey subsidies that move nutrients and energy from aquatic to terrestrial food webs. As a result, these subsidies negatively affect alternative terrestrial prey by enhancing predator densit... |
2003.11008 | Emanuele Olivetti | Gabriele Amorosino, Denis Peruzzo, Pietro Astolfi, Daniela Redaelli,
Paolo Avesani, Filippo Arrigoni, Emanuele Olivetti | Automatic Tissue Segmentation with Deep Learning in Patients with
Congenital or Acquired Distortion of Brain Anatomy | null | null | null | null | q-bio.TO eess.IV | http://creativecommons.org/licenses/by/4.0/ | Brains with complex distortion of cerebral anatomy present several challenges
to automatic tissue segmentation methods of T1-weighted MR images. First, the
very high variability in the morphology of the tissues can be incompatible with
the prior knowledge embedded within the algorithms. Second, the availability of
MR... | [
{
"created": "Tue, 24 Mar 2020 17:50:39 GMT",
"version": "v1"
}
] | 2020-03-25 | [
[
"Amorosino",
"Gabriele",
""
],
[
"Peruzzo",
"Denis",
""
],
[
"Astolfi",
"Pietro",
""
],
[
"Redaelli",
"Daniela",
""
],
[
"Avesani",
"Paolo",
""
],
[
"Arrigoni",
"Filippo",
""
],
[
"Olivetti",
"Emanuele",
""... | Brains with complex distortion of cerebral anatomy present several challenges to automatic tissue segmentation methods of T1-weighted MR images. First, the very high variability in the morphology of the tissues can be incompatible with the prior knowledge embedded within the algorithms. Second, the availability of MR i... |
1706.03920 | Bernhard Mehlig | M. Rafajlovic, D. Kleinhans, C. Gulliksson, J. Fries, D. Johansson, A.
Ardehed, L. Sundqvist, R. T. Pereyra, B. Mehlig, P. R. Jonsson and K.
Johannesson | Stochastic mechanisms forming large clones during colonisation of new
areas | 33 pages, 5 figures, supplementary figures | J. Evol. Biol. 30 (2017) 1544 | 10.1111/jeb.13124 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In species reproducing both sexually and asexually clones are often more
common in recently established populations. Earlier studies have suggested that
this pattern arises from natural selection favouring asexual recruitment in
young populations. Alternatively, as we show here, this pattern may result from
stochasti... | [
{
"created": "Tue, 13 Jun 2017 06:45:57 GMT",
"version": "v1"
}
] | 2017-12-06 | [
[
"Rafajlovic",
"M.",
""
],
[
"Kleinhans",
"D.",
""
],
[
"Gulliksson",
"C.",
""
],
[
"Fries",
"J.",
""
],
[
"Johansson",
"D.",
""
],
[
"Ardehed",
"A.",
""
],
[
"Sundqvist",
"L.",
""
],
[
"Pereyra",
... | In species reproducing both sexually and asexually clones are often more common in recently established populations. Earlier studies have suggested that this pattern arises from natural selection favouring asexual recruitment in young populations. Alternatively, as we show here, this pattern may result from stochastic ... |
1903.07276 | Nancy Forde | Michael W.H. Kirkness, Kathrin Lehmann and Nancy R. Forde | Mechanics and Structural Stability of the Collagen Triple Helix | Review article | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The primary building block of the body is collagen, which is found in the
extracellular matrix and in many stress-bearing tissues such as tendon and
cartilage. It provides elasticity and support to cells and tissues while
influencing biological pathways including cell signaling, motility and
differentiation. Collagen... | [
{
"created": "Mon, 18 Mar 2019 07:00:50 GMT",
"version": "v1"
},
{
"created": "Thu, 25 Jul 2019 18:59:36 GMT",
"version": "v2"
}
] | 2019-07-29 | [
[
"Kirkness",
"Michael W. H.",
""
],
[
"Lehmann",
"Kathrin",
""
],
[
"Forde",
"Nancy R.",
""
]
] | The primary building block of the body is collagen, which is found in the extracellular matrix and in many stress-bearing tissues such as tendon and cartilage. It provides elasticity and support to cells and tissues while influencing biological pathways including cell signaling, motility and differentiation. Collagen's... |
2406.14246 | Maren Philipps | Maren Philipps, Antonia K\"orner, Jakob Vanhoefer, Dilan Pathirana,
Jan Hasenauer | Non-Negative Universal Differential Equations With Applications in
Systems Biology | 6 pages, This work has been submitted to IFAC for possible
publication. Initial submission was March 18, 2024 | null | null | null | q-bio.QM cs.LG math.DS stat.ML | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Universal differential equations (UDEs) leverage the respective advantages of
mechanistic models and artificial neural networks and combine them into one
dynamic model. However, these hybrid models can suffer from unrealistic
solutions, such as negative values for biochemical quantities. We present
non-negative UDE (... | [
{
"created": "Thu, 20 Jun 2024 12:14:09 GMT",
"version": "v1"
}
] | 2024-06-21 | [
[
"Philipps",
"Maren",
""
],
[
"Körner",
"Antonia",
""
],
[
"Vanhoefer",
"Jakob",
""
],
[
"Pathirana",
"Dilan",
""
],
[
"Hasenauer",
"Jan",
""
]
] | Universal differential equations (UDEs) leverage the respective advantages of mechanistic models and artificial neural networks and combine them into one dynamic model. However, these hybrid models can suffer from unrealistic solutions, such as negative values for biochemical quantities. We present non-negative UDE (nU... |
1805.00757 | Ricardo Ruiz Baier I | Ricardo Ruiz Baier, Alessio Gizzi, Alessandro Loppini, Christian
Cherubini, Simonetta Filippi | Modelling thermo-electro-mechanical effects in orthotropic cardiac
tissue | null | Communications in Computational Physics (2019) | 10.4208/cicp.OA-2018-0253 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we introduce a new mathematical model for the active
contraction of cardiac muscle, featuring different thermo-electric and
nonlinear conductivity properties. The passive hyperelastic response of the
tissue is described by an orthotropic exponential model, whereas the ionic
activity dictates active cont... | [
{
"created": "Wed, 2 May 2018 12:06:57 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Jul 2018 10:18:16 GMT",
"version": "v2"
},
{
"created": "Tue, 6 Nov 2018 15:49:40 GMT",
"version": "v3"
}
] | 2019-05-02 | [
[
"Baier",
"Ricardo Ruiz",
""
],
[
"Gizzi",
"Alessio",
""
],
[
"Loppini",
"Alessandro",
""
],
[
"Cherubini",
"Christian",
""
],
[
"Filippi",
"Simonetta",
""
]
] | In this paper we introduce a new mathematical model for the active contraction of cardiac muscle, featuring different thermo-electric and nonlinear conductivity properties. The passive hyperelastic response of the tissue is described by an orthotropic exponential model, whereas the ionic activity dictates active contra... |
1903.04925 | Angana Chakraborty | Angana Chakraborty and Sanghamitra Bandyopadhyay | conLSH: Context based Locality Sensitive Hashing for Mapping of noisy
SMRT Reads | arXiv admin note: text overlap with arXiv:1705.03933 | null | null | null | q-bio.GN cs.DS cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Single Molecule Real-Time (SMRT) sequencing is a recent advancement of Next
Gen technology developed by Pacific Bio (PacBio). It comes with an explosion of
long and noisy reads demanding cutting edge research to get most out of it. To
deal with the high error probability of SMRT data, a novel contextual Locality
Sens... | [
{
"created": "Mon, 11 Mar 2019 17:49:01 GMT",
"version": "v1"
}
] | 2019-03-13 | [
[
"Chakraborty",
"Angana",
""
],
[
"Bandyopadhyay",
"Sanghamitra",
""
]
] | Single Molecule Real-Time (SMRT) sequencing is a recent advancement of Next Gen technology developed by Pacific Bio (PacBio). It comes with an explosion of long and noisy reads demanding cutting edge research to get most out of it. To deal with the high error probability of SMRT data, a novel contextual Locality Sensit... |
2011.08632 | Thomas G\"otz | Thomas G\"otz, Silja Mohrmann, Robert Rockenfeller, Moritz Sch\"afer
and Karunia Putra Wijaya | Calculation of a local COVID-19 reproduction number for the northern
Rhineland-Palatinate | 16 pages, 23 figures, in German | null | null | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | Since the beginning of the corona pandemic in March 2020, various parameters
for describing the spread of the disease have been specified for Germany in
addition to the daily infection figures (new infections and total infections),
which are also used for political decisions. In addition to excess mortality
and the w... | [
{
"created": "Tue, 17 Nov 2020 13:52:15 GMT",
"version": "v1"
}
] | 2020-11-18 | [
[
"Götz",
"Thomas",
""
],
[
"Mohrmann",
"Silja",
""
],
[
"Rockenfeller",
"Robert",
""
],
[
"Schäfer",
"Moritz",
""
],
[
"Wijaya",
"Karunia Putra",
""
]
] | Since the beginning of the corona pandemic in March 2020, various parameters for describing the spread of the disease have been specified for Germany in addition to the daily infection figures (new infections and total infections), which are also used for political decisions. In addition to excess mortality and the wee... |
1808.04443 | Chuanqi Tan | Chuanqi Tan, Fuchun Sun, Wenchang Zhang, Shaobo Liu and Chunfang Liu | Spatial and Spectral Features Fusion for EEG Classification during Motor
Imagery in BCI | International Conference on Biomedical and Health Informatics (BHI
2017) | null | null | null | q-bio.QM eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Brain computer interface (BCI) is the only way for some special patients to
communicate with the outside world and provide a direct control channel between
brain and the external devices. As a non-invasive interface, the scalp
electroencephalography (EEG) has a significant potential to be a major input
signal for fut... | [
{
"created": "Mon, 6 Aug 2018 07:52:06 GMT",
"version": "v1"
}
] | 2018-08-15 | [
[
"Tan",
"Chuanqi",
""
],
[
"Sun",
"Fuchun",
""
],
[
"Zhang",
"Wenchang",
""
],
[
"Liu",
"Shaobo",
""
],
[
"Liu",
"Chunfang",
""
]
] | Brain computer interface (BCI) is the only way for some special patients to communicate with the outside world and provide a direct control channel between brain and the external devices. As a non-invasive interface, the scalp electroencephalography (EEG) has a significant potential to be a major input signal for futur... |
1601.03412 | Jana Gevertz | Ami B. Shah, Katarzyna A. Rejniak, Jana L. Gevertz | Limiting the Development of Anti-Cancer Drug Resistance in a Spatial
Model of Micrometastases | 25 pages, 8 figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While chemoresistance in primary tumors is well-studied, much less is known
about the influence of systemic chemotherapy on the development of drug
resistance at metastatic sites. In this work, we use a hybrid spatial model of
tumor response to a DNA damaging drug to study how the development of
chemoresistance in mi... | [
{
"created": "Wed, 13 Jan 2016 21:19:32 GMT",
"version": "v1"
},
{
"created": "Wed, 2 Mar 2016 21:41:24 GMT",
"version": "v2"
}
] | 2016-03-04 | [
[
"Shah",
"Ami B.",
""
],
[
"Rejniak",
"Katarzyna A.",
""
],
[
"Gevertz",
"Jana L.",
""
]
] | While chemoresistance in primary tumors is well-studied, much less is known about the influence of systemic chemotherapy on the development of drug resistance at metastatic sites. In this work, we use a hybrid spatial model of tumor response to a DNA damaging drug to study how the development of chemoresistance in micr... |
1710.00869 | Nick Wasylyshyn | Nick Wasylyshyn (1, 2), Brett Hemenway (2), Javier O. Garcia (1, 2),
Christopher N. Cascio (2), Matthew Brook O'Donnell (2), C. Raymond Bingham
(3), Bruce Simons-Morton (4), Jean M. Vettel (1, 2, 5), Emily B. Falk (2)
((1) US Army Research Laboratory, (2) University of Pennsylvania, (3)
University of Michigan T... | Global Brain Dynamics During Social Exclusion Predict Subsequent
Behavioral Conformity | 32 pages, 5 figures, 1 table | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Individuals react differently to social experiences; for example, people who
are more sensitive to negative social experiences, such as being excluded, may
be more likely to adapt their behavior to fit in with others. We examined
whether functional brain connectivity during social exclusion in the fMRI
scanner can be... | [
{
"created": "Mon, 2 Oct 2017 19:08:41 GMT",
"version": "v1"
}
] | 2017-10-04 | [
[
"Wasylyshyn",
"Nick",
""
],
[
"Hemenway",
"Brett",
""
],
[
"Garcia",
"Javier O.",
""
],
[
"Cascio",
"Christopher N.",
""
],
[
"O'Donnell",
"Matthew Brook",
""
],
[
"Bingham",
"C. Raymond",
""
],
[
"Simons-Morton",
... | Individuals react differently to social experiences; for example, people who are more sensitive to negative social experiences, such as being excluded, may be more likely to adapt their behavior to fit in with others. We examined whether functional brain connectivity during social exclusion in the fMRI scanner can be u... |
2309.07271 | Yujiang Wang | Christopher Thornton, Mariella Panagiotopoulou, Fahmida A Chowdhury,
Beate Diehl, John S Duncan, Sarah J Gascoigne, Guillermo Besne, Andrew W
McEvoy, Anna Miserocchi, Billy C Smith, Jane de Tisi, Peter N Taylor, Yujiang
Wang | Diminished circadian and ultradian rhythms of human brain activity in
pathological tissue in vivo | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chronobiological rhythms, such as the circadian rhythm, have long been linked
to neurological disorders, but it is currently unknown how pathological
processes affect the expression of biological rhythms in the brain.
Here, we use the unique opportunity of long-term, continuous intracranially
recorded EEG from 38 p... | [
{
"created": "Wed, 13 Sep 2023 19:21:16 GMT",
"version": "v1"
},
{
"created": "Wed, 7 Aug 2024 17:55:13 GMT",
"version": "v2"
}
] | 2024-08-08 | [
[
"Thornton",
"Christopher",
""
],
[
"Panagiotopoulou",
"Mariella",
""
],
[
"Chowdhury",
"Fahmida A",
""
],
[
"Diehl",
"Beate",
""
],
[
"Duncan",
"John S",
""
],
[
"Gascoigne",
"Sarah J",
""
],
[
"Besne",
"Guille... | Chronobiological rhythms, such as the circadian rhythm, have long been linked to neurological disorders, but it is currently unknown how pathological processes affect the expression of biological rhythms in the brain. Here, we use the unique opportunity of long-term, continuous intracranially recorded EEG from 38 patie... |
2303.14986 | Niharika S. D'Souza | Niharika S. D'Souza and Archana Venkataraman | mSPD-NN: A Geometrically Aware Neural Framework for Biomarker Discovery
from Functional Connectomics Manifolds | Accepted into IPMI 2023 | null | null | null | q-bio.QM cs.LG cs.NE eess.SP q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Connectomics has emerged as a powerful tool in neuroimaging and has spurred
recent advancements in statistical and machine learning methods for
connectivity data. Despite connectomes inhabiting a matrix manifold, most
analytical frameworks ignore the underlying data geometry. This is largely
because simple operations... | [
{
"created": "Mon, 27 Mar 2023 08:30:11 GMT",
"version": "v1"
}
] | 2023-03-28 | [
[
"D'Souza",
"Niharika S.",
""
],
[
"Venkataraman",
"Archana",
""
]
] | Connectomics has emerged as a powerful tool in neuroimaging and has spurred recent advancements in statistical and machine learning methods for connectivity data. Despite connectomes inhabiting a matrix manifold, most analytical frameworks ignore the underlying data geometry. This is largely because simple operations, ... |
1605.07793 | Mark Leake | Adam J. M. Wollman, Aisha H. Syeda, Peter McGlynn, Mark C. Leake | Single-molecule observation of DNA replication repair pathways in E.
coli | null | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The method of action of many antibiotics is to interfere with DNA replication
- quinolones trap DNA gyrase and topoisomerase proteins onto DNA while
metronidazole causes single and double stranded breaks in DNA. To understand
how bacteria respond to these drugs, it is important to understand the repair
processes util... | [
{
"created": "Wed, 25 May 2016 09:21:23 GMT",
"version": "v1"
}
] | 2016-05-26 | [
[
"Wollman",
"Adam J. M.",
""
],
[
"Syeda",
"Aisha H.",
""
],
[
"McGlynn",
"Peter",
""
],
[
"Leake",
"Mark C.",
""
]
] | The method of action of many antibiotics is to interfere with DNA replication - quinolones trap DNA gyrase and topoisomerase proteins onto DNA while metronidazole causes single and double stranded breaks in DNA. To understand how bacteria respond to these drugs, it is important to understand the repair processes utilis... |
2311.17194 | Qian Gao | Qian Gao (1), G. Gurdeniz (1), Giulia Pratico (1), Camilla T.
Damsgaard (1), Eduvigis Roldan-Marin (2), M. Pilar Cano (3), Concepcion
Sanchez-Moreno (2), Lars O. Dragsted (1) ((1) Department of Nutrition,
Exercise and Sports, University of Copenhagen, Copenhagen, Denmark (2)
Institute of Food Science, Technolog... | Identification of urinary biomarkers of food intake for onion by
untargeted LC-MS metabolomics | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Scope: Biomarkers of food intake (BFIs) are useful tools for objective
assessment of food intake and compliance. The aim of this study was to discover
and identify urinary BFIs for onion. Methods and results: In a randomized
controlled cross-over trial, 6 overweight participants (age 24-62 years)
consumed meals with ... | [
{
"created": "Tue, 28 Nov 2023 19:55:01 GMT",
"version": "v1"
}
] | 2023-11-30 | [
[
"Gao",
"Qian",
""
],
[
"Gurdeniz",
"G.",
""
],
[
"Pratico",
"Giulia",
""
],
[
"Damsgaard",
"Camilla T.",
""
],
[
"Roldan-Marin",
"Eduvigis",
""
],
[
"Cano",
"M. Pilar",
""
],
[
"Sanchez-Moreno",
"Concepcion",
... | Scope: Biomarkers of food intake (BFIs) are useful tools for objective assessment of food intake and compliance. The aim of this study was to discover and identify urinary BFIs for onion. Methods and results: In a randomized controlled cross-over trial, 6 overweight participants (age 24-62 years) consumed meals with 20... |
1808.04322 | Dong Xu | Chao Fang, Yi Shang and Dong Xu | MUFold-BetaTurn: A Deep Dense Inception Network for Protein Beta-Turn
Prediction | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Beta-turn prediction is useful in protein function studies and experimental
design. Although recent approaches using machine-learning techniques such as
SVM, neural networks, and K-NN have achieved good results for beta-turn
pre-diction, there is still significant room for improvement. As previous
predictors utilized... | [
{
"created": "Mon, 13 Aug 2018 16:28:50 GMT",
"version": "v1"
}
] | 2018-08-14 | [
[
"Fang",
"Chao",
""
],
[
"Shang",
"Yi",
""
],
[
"Xu",
"Dong",
""
]
] | Beta-turn prediction is useful in protein function studies and experimental design. Although recent approaches using machine-learning techniques such as SVM, neural networks, and K-NN have achieved good results for beta-turn pre-diction, there is still significant room for improvement. As previous predictors utilized f... |
1701.08443 | Sebastian Schreiber | Sebastian J. Schreiber | A dynamical trichotomy for structured populations experiencing positive
density-dependence in stochastic environments | null | (2017) In: Elaydi S., Hamaya Y., Matsunaga H., P\"otzsche C. (eds)
Advances in Difference Equations and Discrete Dynamical Systems. ICDEA 2016.
Springer Proceedings in Mathematics & Statistics, vol 212. Springer,
Singapore | 10.1007/978-981-10-6409-8_3 | null | q-bio.PE math.DS math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Positive density-dependence occurs when individuals experience increased
survivorship, growth, or reproduction with increased population densities.
Mechanisms leading to these positive relationships include mate limitation,
saturating predation risk, and cooperative breeding and foraging. Individuals
within these pop... | [
{
"created": "Sun, 29 Jan 2017 22:21:11 GMT",
"version": "v1"
}
] | 2019-02-12 | [
[
"Schreiber",
"Sebastian J.",
""
]
] | Positive density-dependence occurs when individuals experience increased survivorship, growth, or reproduction with increased population densities. Mechanisms leading to these positive relationships include mate limitation, saturating predation risk, and cooperative breeding and foraging. Individuals within these popul... |
2212.03859 | Keith Li Chambers | Keith L Chambers, Mary R Myerscough and Helen M Byrne | A new lipid-structured model to investigate the opposing effects of LDL
and HDL on atherosclerotic plaque macrophages | 44 pages, 13 figures | null | null | null | q-bio.CB q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Atherosclerotic plaques form in artery walls due to a chronic inflammatory
response driven by lipid accumulation. A key component of the inflammatory
response is the interaction between monocyte-derived macrophages and
extracellular lipid. Although concentrations of low-density lipoprotein (LDL)
and high-density lipo... | [
{
"created": "Wed, 7 Dec 2022 18:57:59 GMT",
"version": "v1"
}
] | 2022-12-08 | [
[
"Chambers",
"Keith L",
""
],
[
"Myerscough",
"Mary R",
""
],
[
"Byrne",
"Helen M",
""
]
] | Atherosclerotic plaques form in artery walls due to a chronic inflammatory response driven by lipid accumulation. A key component of the inflammatory response is the interaction between monocyte-derived macrophages and extracellular lipid. Although concentrations of low-density lipoprotein (LDL) and high-density lipopr... |
2111.07760 | Rinaldo Schinazi | Rinaldo B. Schinazi | Evolutionary paths under catastrophes | null | null | null | null | q-bio.PE math.PR | http://creativecommons.org/licenses/by/4.0/ | We introduce a model to study the impact of catastrophes on evolutionary
paths. If we do not allow catastrophes the number of changes in the maximum
fitness of a population grows logarithmically with respect to time. Allowing
catastrophes (no matter how rare) yields a drastically different behavior. When
catastrophes... | [
{
"created": "Mon, 15 Nov 2021 13:58:35 GMT",
"version": "v1"
}
] | 2021-11-16 | [
[
"Schinazi",
"Rinaldo B.",
""
]
] | We introduce a model to study the impact of catastrophes on evolutionary paths. If we do not allow catastrophes the number of changes in the maximum fitness of a population grows logarithmically with respect to time. Allowing catastrophes (no matter how rare) yields a drastically different behavior. When catastrophes a... |
1803.05357 | Yasuaki Kobayashi | Yasuaki Kobayashi, Yusuke Yasugahira, Hiroyuki Kitahata, Mika
Watanabe, Ken Natsuga, Masaharu Nagayama | Interplay between epidermal stem cell dynamics and dermal deformations | 10 pages, 8 figures | npj Computational Materials 4, 45 (2018) | 10.1038/s41524-018-0101-z | null | q-bio.TO nlin.AO q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a particle-based model of self-replicating cells on a deformable
substrate composed of the dermis and the basement membrane and investigate the
relationship between dermal deformations and stem cell pattering on it. We show
that our model reproduces the formation of dermal papillae, protuberances
directi... | [
{
"created": "Thu, 8 Mar 2018 07:50:29 GMT",
"version": "v1"
},
{
"created": "Mon, 18 Jun 2018 08:41:56 GMT",
"version": "v2"
}
] | 2018-08-22 | [
[
"Kobayashi",
"Yasuaki",
""
],
[
"Yasugahira",
"Yusuke",
""
],
[
"Kitahata",
"Hiroyuki",
""
],
[
"Watanabe",
"Mika",
""
],
[
"Natsuga",
"Ken",
""
],
[
"Nagayama",
"Masaharu",
""
]
] | We introduce a particle-based model of self-replicating cells on a deformable substrate composed of the dermis and the basement membrane and investigate the relationship between dermal deformations and stem cell pattering on it. We show that our model reproduces the formation of dermal papillae, protuberances directing... |
q-bio/0505030 | Guido Tiana | A. Amatori, G. Tiana, L. Sutto, J.Ferkinghoff-Borg, A. Trovato and R.
A. Broglia | Design of amino acid sequences to fold into C_alpha-model proteins | null | null | 10.1063/1.1992447 | null | q-bio.BM | null | In order to extend the results obtained with minimal lattice models to more
realistic systems, we study a model where proteins are described as a chain of
20 kinds of structureless amino acids moving in a continuum space and
interacting through a contact potential controlled by a 20x20 quenched random
matrix. The goa... | [
{
"created": "Mon, 16 May 2005 15:11:00 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Amatori",
"A.",
""
],
[
"Tiana",
"G.",
""
],
[
"Sutto",
"L.",
""
],
[
"Ferkinghoff-Borg",
"J.",
""
],
[
"Trovato",
"A.",
""
],
[
"Broglia",
"R. A.",
""
]
] | In order to extend the results obtained with minimal lattice models to more realistic systems, we study a model where proteins are described as a chain of 20 kinds of structureless amino acids moving in a continuum space and interacting through a contact potential controlled by a 20x20 quenched random matrix. The goal ... |
1310.3693 | Andrea De Martino | Daniele De Martino, Fabrizio Capuani, Matteo Mori, Andrea De Martino,
Enzo Marinari | Counting and correcting thermodynamically infeasible flux cycles in
genome-scale metabolic networks | 10 pages; see http://chimera.roma1.infn.it/SYSBIO/ for supporting
files | Metabolites 3:946 (2013) | 10.3390/metabo3040946 | null | q-bio.MN cond-mat.dis-nn cond-mat.stat-mech physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Thermodynamics constrains the flow of matter in a reaction network to occur
through routes along which the Gibbs energy decreases, implying that viable
steady-state flux patterns should be void of closed reaction cycles.
Identifying and removing cycles in large reaction networks can unfortunately be
a highly challeng... | [
{
"created": "Mon, 14 Oct 2013 14:26:35 GMT",
"version": "v1"
}
] | 2013-10-15 | [
[
"De Martino",
"Daniele",
""
],
[
"Capuani",
"Fabrizio",
""
],
[
"Mori",
"Matteo",
""
],
[
"De Martino",
"Andrea",
""
],
[
"Marinari",
"Enzo",
""
]
] | Thermodynamics constrains the flow of matter in a reaction network to occur through routes along which the Gibbs energy decreases, implying that viable steady-state flux patterns should be void of closed reaction cycles. Identifying and removing cycles in large reaction networks can unfortunately be a highly challengin... |
2310.09178 | Simone Franchini Dr. | Giampiero Bardella, Simone Franchini, Liming Pan, Riccardo Balzan,
Surabhi Ramawat, Emiliano Brunamonti, Pierpaolo Pani, and Stefano Ferraina | Neural activity in quarks language: Lattice Field Theory for a network
of real neurons | 79 pages, 20 figures | Entropy 2024, 26(6), 495 | 10.3390/e26060495 | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Brain-computer interfaces surged extraordinary developments in recent years,
and a significant discrepancy now exists between the abundance of available
data and the limited headway made in achieving a unified theoretical framework.
This discrepancy becomes particularly pronounced when examining the collective
neural... | [
{
"created": "Fri, 13 Oct 2023 15:14:23 GMT",
"version": "v1"
},
{
"created": "Mon, 18 Dec 2023 09:27:45 GMT",
"version": "v2"
},
{
"created": "Sun, 24 Mar 2024 03:29:11 GMT",
"version": "v3"
}
] | 2024-06-07 | [
[
"Bardella",
"Giampiero",
""
],
[
"Franchini",
"Simone",
""
],
[
"Pan",
"Liming",
""
],
[
"Balzan",
"Riccardo",
""
],
[
"Ramawat",
"Surabhi",
""
],
[
"Brunamonti",
"Emiliano",
""
],
[
"Pani",
"Pierpaolo",
""... | Brain-computer interfaces surged extraordinary developments in recent years, and a significant discrepancy now exists between the abundance of available data and the limited headway made in achieving a unified theoretical framework. This discrepancy becomes particularly pronounced when examining the collective neural a... |
2004.12979 | Patricio Arru\'e Pa | Patricio Arrue, Nima Toosizadeh, Hessam Babaee, Kaveh Laksari | Low-rank representation of head impact kinematics: A data-driven
emulator | 20 pages, 13 figures, 4 tables | Front. Bioeng. Biotechnol. (2020) 8:555493 | 10.3389/fbioe.2020.555493 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Head motion induced by impacts has been deemed as one of the most important
measures in brain injury prediction, given that the majority of brain injury
metrics use head kinematics as input. Recently, researchers have focused on
using fast approaches, such as machine learning, to approximate brain
deformation in real... | [
{
"created": "Mon, 27 Apr 2020 17:47:59 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Dec 2020 21:59:11 GMT",
"version": "v2"
}
] | 2020-12-11 | [
[
"Arrue",
"Patricio",
""
],
[
"Toosizadeh",
"Nima",
""
],
[
"Babaee",
"Hessam",
""
],
[
"Laksari",
"Kaveh",
""
]
] | Head motion induced by impacts has been deemed as one of the most important measures in brain injury prediction, given that the majority of brain injury metrics use head kinematics as input. Recently, researchers have focused on using fast approaches, such as machine learning, to approximate brain deformation in real-t... |
q-bio/0701040 | Brigitte Gaillard | J.Y. Georges (DEPE-Iphc), A. Billes, S. Ferraroli (DEPE-Iphc), S.
Fossette (DEPE-Iphc), J. Fretey, D. Gr\'emillet (DEPE-Iphc), Y. Le Maho
(DEPE-Iphc), A. E. Myers, H. Tanaka, G. C. Hays | Meta-analysis of movements in Atlantic leatherback turtles during
nesting season : conservation implications | null | null | null | null | q-bio.PE | null | Despite decades of conservation efforts on the nesting beaches, the critical
status of leatherback turtles shows that their survival predominantly depends
on our ability to reduce at-sea mortality. Although areas where leatherbacks
meet fisheries have been identified during the long distance movements between
two con... | [
{
"created": "Thu, 25 Jan 2007 14:34:19 GMT",
"version": "v1"
}
] | 2016-08-14 | [
[
"Georges",
"J. Y.",
"",
"DEPE-Iphc"
],
[
"Billes",
"A.",
"",
"DEPE-Iphc"
],
[
"Ferraroli",
"S.",
"",
"DEPE-Iphc"
],
[
"Fossette",
"S.",
"",
"DEPE-Iphc"
],
[
"Fretey",
"J.",
"",
"DEPE-Iphc"
],
[
"Grémillet",
... | Despite decades of conservation efforts on the nesting beaches, the critical status of leatherback turtles shows that their survival predominantly depends on our ability to reduce at-sea mortality. Although areas where leatherbacks meet fisheries have been identified during the long distance movements between two conse... |
2304.05908 | Moo K. Chung | Moo K. Chung, Tahmineh Azizi, Jamie L. Hanson, Andrew L. Alexander,
Richard J. Davidson, Seth D. Pollak | Altered Topological Structure of the Brain White Matter in Maltreated
Children through Topological Data Analysis | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Childhood maltreatment may adversely affect brain development and
consequently influence behavioral, emotional, and psychological patterns during
adulthood. In this study, we propose an analytical pipeline for modeling the
altered topological structure of brain white matter in maltreated and typically
developing chil... | [
{
"created": "Wed, 12 Apr 2023 15:25:01 GMT",
"version": "v1"
},
{
"created": "Wed, 27 Sep 2023 18:07:05 GMT",
"version": "v2"
},
{
"created": "Wed, 15 Nov 2023 02:12:50 GMT",
"version": "v3"
}
] | 2023-11-16 | [
[
"Chung",
"Moo K.",
""
],
[
"Azizi",
"Tahmineh",
""
],
[
"Hanson",
"Jamie L.",
""
],
[
"Alexander",
"Andrew L.",
""
],
[
"Davidson",
"Richard J.",
""
],
[
"Pollak",
"Seth D.",
""
]
] | Childhood maltreatment may adversely affect brain development and consequently influence behavioral, emotional, and psychological patterns during adulthood. In this study, we propose an analytical pipeline for modeling the altered topological structure of brain white matter in maltreated and typically developing childr... |
1108.1775 | Natalia Denesyuk | Natalia A. Denesyuk and D. Thirumalai | Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in
Human Telomerase RNA | File "JACS_MAIN_archive_PDF_from_DOC.pdf" (PDF created from DOC)
contains the main text of the paper File JACS_SI_archive.tex + 7 figures are
the supplementary info | J. Am. Chem. Soc., 2011, 133 (31), pp 11858--11861 | 10.1021/ja2035128 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Formation of a pseudoknot in the conserved RNA core domain in the
ribonucleoprotein human telomerase is required for function. In vitro
experiments show that the pseudoknot (PK) is in equilibrium with an extended
hairpin (HP) structure. We use molecular simulations of a coarse-grained model,
which reproduces most of ... | [
{
"created": "Mon, 8 Aug 2011 18:25:40 GMT",
"version": "v1"
}
] | 2011-08-09 | [
[
"Denesyuk",
"Natalia A.",
""
],
[
"Thirumalai",
"D.",
""
]
] | Formation of a pseudoknot in the conserved RNA core domain in the ribonucleoprotein human telomerase is required for function. In vitro experiments show that the pseudoknot (PK) is in equilibrium with an extended hairpin (HP) structure. We use molecular simulations of a coarse-grained model, which reproduces most of th... |
1703.10627 | Mans Henningson | M{\aa}ns Henningson and Sebastian Illes | Analysis and Modelling of Subthreshold Neural Multi-electrode Array Data
by Statistical Field Theory | 27 pages, 13 figures | null | null | null | q-bio.NC cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multi-electrode arrays (MEA) are increasingly used to investigate spontaneous
neuronal network activity. The recorded signals comprise several distinct
components: Apart from artefacts without biological significance, one can
distinguish between spikes (action potentials) and subthreshold fluctuations
(local fields p... | [
{
"created": "Thu, 30 Mar 2017 18:21:30 GMT",
"version": "v1"
}
] | 2017-04-03 | [
[
"Henningson",
"Måns",
""
],
[
"Illes",
"Sebastian",
""
]
] | Multi-electrode arrays (MEA) are increasingly used to investigate spontaneous neuronal network activity. The recorded signals comprise several distinct components: Apart from artefacts without biological significance, one can distinguish between spikes (action potentials) and subthreshold fluctuations (local fields pot... |
1307.7302 | Thomas Dean | Thomas Dean, Biafra Ahanonu, Mainak Chowdhury, Anjali Datta, Andre
Esteva, Daniel Eth, Nobie Redmon, Oleg Rumyantsev, Ysis Tarter | On the Technology Prospects and Investment Opportunities for Scalable
Neuroscience | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Two major initiatives to accelerate research in the brain sciences have
focused attention on developing a new generation of scientific instruments for
neuroscience. These instruments will be used to record static (structural) and
dynamic (behavioral) information at unprecedented spatial and temporal
resolution and re... | [
{
"created": "Sat, 27 Jul 2013 20:25:00 GMT",
"version": "v1"
}
] | 2013-07-30 | [
[
"Dean",
"Thomas",
""
],
[
"Ahanonu",
"Biafra",
""
],
[
"Chowdhury",
"Mainak",
""
],
[
"Datta",
"Anjali",
""
],
[
"Esteva",
"Andre",
""
],
[
"Eth",
"Daniel",
""
],
[
"Redmon",
"Nobie",
""
],
[
"Rumya... | Two major initiatives to accelerate research in the brain sciences have focused attention on developing a new generation of scientific instruments for neuroscience. These instruments will be used to record static (structural) and dynamic (behavioral) information at unprecedented spatial and temporal resolution and repo... |
1604.06300 | Serge Sheremet'ev | Serge Sheremet'ev, Xenia Chebotareva | Current and Cretaceous-Cenozoic diversification of Angiosperms | 51 pp with 18 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cretaceous-Cenozoic history of angiosperms led to the a certain character of
the distribution of taxa of different levels (the number of species and genera
in families, species/genera ratio in families, the number of species in the
genera). In most cases, these distributions are satisfactorily described by a
power la... | [
{
"created": "Thu, 21 Apr 2016 13:37:11 GMT",
"version": "v1"
}
] | 2016-04-22 | [
[
"Sheremet'ev",
"Serge",
""
],
[
"Chebotareva",
"Xenia",
""
]
] | Cretaceous-Cenozoic history of angiosperms led to the a certain character of the distribution of taxa of different levels (the number of species and genera in families, species/genera ratio in families, the number of species in the genera). In most cases, these distributions are satisfactorily described by a power law ... |
2211.16638 | Justin Yeakel | Taran Rallings, Christopher P. Kempes, Justin D. Yeakel | On the dynamics of mortality and the ephemeral nature of mammalian
megafauna | 10 pages, 5 figures, 1 table, 4 appendices, 8 supplementary figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Energy flow through consumer-resource interactions is largely determined by
body size. Allometric relationships govern the dynamics of populations by
impacting rates of reproduction, as well as alternative sources of mortality,
which have differential impacts on smaller to larger organisms. Here we derive
and investi... | [
{
"created": "Wed, 30 Nov 2022 00:08:45 GMT",
"version": "v1"
},
{
"created": "Thu, 24 Aug 2023 21:46:54 GMT",
"version": "v2"
}
] | 2023-08-28 | [
[
"Rallings",
"Taran",
""
],
[
"Kempes",
"Christopher P.",
""
],
[
"Yeakel",
"Justin D.",
""
]
] | Energy flow through consumer-resource interactions is largely determined by body size. Allometric relationships govern the dynamics of populations by impacting rates of reproduction, as well as alternative sources of mortality, which have differential impacts on smaller to larger organisms. Here we derive and investiga... |
1804.06050 | Jingyi Jessica Li | Wei Vivian Li, Jingyi Jessica Li | Modeling and analysis of RNA-seq data: a review from a statistical
perspective | null | Quantitative Biology 6 (2018) 195-209 | 10.1007/s40484-018-0144-7 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Since the invention of next-generation RNA sequencing (RNA-seq)
technologies, they have become a powerful tool to study the presence and
quantity of RNA molecules in biological samples and have revolutionized
transcriptomic studies. The analysis of RNA-seq data at four different levels
(samples, genes, tr... | [
{
"created": "Tue, 17 Apr 2018 05:26:53 GMT",
"version": "v1"
},
{
"created": "Sun, 29 Apr 2018 09:10:58 GMT",
"version": "v2"
},
{
"created": "Tue, 1 May 2018 15:01:45 GMT",
"version": "v3"
}
] | 2021-12-01 | [
[
"Li",
"Wei Vivian",
""
],
[
"Li",
"Jingyi Jessica",
""
]
] | Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic studies. The analysis of RNA-seq data at four different levels (samples, genes, tran... |
2101.00500 | Akke Mats Houben | Akke Mats Houben | Signal anticipation and delay in excitable media: group delay of the
FitzHugh-Nagumo model | 9 pages, 6 figures | null | null | null | q-bio.NC nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An expression for the group delay of the FitzHugh-Nagumo model in response to
low amplitude input is obtained by linearisation of the cubic term of the
voltage equation around its stable fixed-point. It is found that a negative
group delay exists for low frequencies, indicating that the evolution of slowly
fluctuatin... | [
{
"created": "Sat, 2 Jan 2021 19:14:24 GMT",
"version": "v1"
}
] | 2021-01-05 | [
[
"Houben",
"Akke Mats",
""
]
] | An expression for the group delay of the FitzHugh-Nagumo model in response to low amplitude input is obtained by linearisation of the cubic term of the voltage equation around its stable fixed-point. It is found that a negative group delay exists for low frequencies, indicating that the evolution of slowly fluctuating ... |
1612.07468 | Sang Kwan Choi | Sang Kwan Choi, Chaiho Rim and Hwajin Um | RNA substructure as a random matrix ensemble | 8 pages, 12 figures; v2: data set and figure added, comments added,
references updated; v3: appendix and references added, few sentences
including abstract paraphrased for clarification, remarks added in the
conclusion; v4: published version | Phys. Rev. E 100, 062404 (2019) | 10.1103/PhysRevE.100.062404 | null | q-bio.QM cond-mat.stat-mech hep-th q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Combinatorial analysis of a certain abstract of RNA structures has been
studied to investigate their statistics. Our approach regards the backbone of
secondary structures as an alternate sequence of paired and unpaired sets of
nucleotides, which can be described by random matrix model. We obtain the
generating functi... | [
{
"created": "Thu, 22 Dec 2016 07:25:43 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Feb 2017 04:55:00 GMT",
"version": "v2"
},
{
"created": "Wed, 17 Jul 2019 02:17:11 GMT",
"version": "v3"
},
{
"created": "Mon, 9 Mar 2020 08:44:44 GMT",
"version": "v4"
}
] | 2020-03-10 | [
[
"Choi",
"Sang Kwan",
""
],
[
"Rim",
"Chaiho",
""
],
[
"Um",
"Hwajin",
""
]
] | Combinatorial analysis of a certain abstract of RNA structures has been studied to investigate their statistics. Our approach regards the backbone of secondary structures as an alternate sequence of paired and unpaired sets of nucleotides, which can be described by random matrix model. We obtain the generating function... |
1308.6014 | Robert Rosenbaum | Robert Rosenbaum and Brent Doiron | Balanced networks of spiking neurons with spatially dependent recurrent
connections | null | null | 10.1103/PhysRevX.4.021039 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Networks of model neurons with balanced recurrent excitation and inhibition
produce irregular and asynchronous spiking activity. We extend the analysis of
balanced networks to include the known dependence of connection probability on
the spatial separation between neurons. In the continuum limit we derive that
stable... | [
{
"created": "Tue, 27 Aug 2013 23:39:34 GMT",
"version": "v1"
},
{
"created": "Fri, 15 Nov 2013 18:14:06 GMT",
"version": "v2"
}
] | 2014-06-02 | [
[
"Rosenbaum",
"Robert",
""
],
[
"Doiron",
"Brent",
""
]
] | Networks of model neurons with balanced recurrent excitation and inhibition produce irregular and asynchronous spiking activity. We extend the analysis of balanced networks to include the known dependence of connection probability on the spatial separation between neurons. In the continuum limit we derive that stable, ... |
2103.08198 | Li Xu | Li Xu, Denis Patterson, Ann Carla Staver, Simon Asher Levin, Jin Wang | Unifying deterministic and stochastic ecological dynamics via a
landscape-flux approach | null | null | 10.1073/pnas.2103779118 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop a landscape-flux framework to investigate observed frequency
distributions of vegetation and the stability of these ecological systems under
fluctuations. The frequency distributions can characterize the
population-potential landscape related to the stability of ecological states.
We illustrate the practic... | [
{
"created": "Mon, 15 Mar 2021 08:09:31 GMT",
"version": "v1"
},
{
"created": "Sat, 27 Mar 2021 06:18:34 GMT",
"version": "v2"
}
] | 2022-10-12 | [
[
"Xu",
"Li",
""
],
[
"Patterson",
"Denis",
""
],
[
"Staver",
"Ann Carla",
""
],
[
"Levin",
"Simon Asher",
""
],
[
"Wang",
"Jin",
""
]
] | We develop a landscape-flux framework to investigate observed frequency distributions of vegetation and the stability of these ecological systems under fluctuations. The frequency distributions can characterize the population-potential landscape related to the stability of ecological states. We illustrate the practical... |
2103.04162 | Junqiu Wu | Ke Liu, Zekun Ni, Zhenyu Zhou, Suocheng Tan, Xun Zou, Haoming Xing,
Xiangyan Sun, Qi Han, Junqiu Wu and Jie Fan | Molecular modeling with machine-learned universal potential functions | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular modeling is an important topic in drug discovery. Decades of
research have led to the development of high quality scalable molecular force
fields. In this paper, we show that neural networks can be used to train a
universal approximator for energy potential functions. By incorporating a fully
automated trai... | [
{
"created": "Sat, 6 Mar 2021 17:36:39 GMT",
"version": "v1"
},
{
"created": "Mon, 19 Apr 2021 06:30:52 GMT",
"version": "v2"
}
] | 2021-04-20 | [
[
"Liu",
"Ke",
""
],
[
"Ni",
"Zekun",
""
],
[
"Zhou",
"Zhenyu",
""
],
[
"Tan",
"Suocheng",
""
],
[
"Zou",
"Xun",
""
],
[
"Xing",
"Haoming",
""
],
[
"Sun",
"Xiangyan",
""
],
[
"Han",
"Qi",
""
... | Molecular modeling is an important topic in drug discovery. Decades of research have led to the development of high quality scalable molecular force fields. In this paper, we show that neural networks can be used to train a universal approximator for energy potential functions. By incorporating a fully automated traini... |
2311.09140 | Ying-Cheng Lai | Shirin Panahi, Younghae Do, Alan Hastings, and Ying-Cheng Lai | Rate-induced tipping in complex high-dimensional ecological networks | 8 pages, 5 figures | null | null | null | q-bio.PE math.DS nlin.AO | http://creativecommons.org/licenses/by/4.0/ | In an ecosystem, environmental changes as a result of natural and human
processes can cause some key parameters of the system to change with time.
Depending on how fast such a parameter changes, a tipping point can occur.
Existing works on rate-induced tipping, or R-tipping, offered a theoretical way
to study this ph... | [
{
"created": "Wed, 15 Nov 2023 17:32:08 GMT",
"version": "v1"
}
] | 2023-11-16 | [
[
"Panahi",
"Shirin",
""
],
[
"Do",
"Younghae",
""
],
[
"Hastings",
"Alan",
""
],
[
"Lai",
"Ying-Cheng",
""
]
] | In an ecosystem, environmental changes as a result of natural and human processes can cause some key parameters of the system to change with time. Depending on how fast such a parameter changes, a tipping point can occur. Existing works on rate-induced tipping, or R-tipping, offered a theoretical way to study this phen... |
2306.11536 | Yu Takagi | Yu Takagi, Shinji Nishimoto | Improving visual image reconstruction from human brain activity using
latent diffusion models via multiple decoded inputs | null | null | null | null | q-bio.NC cs.AI cs.CV | http://creativecommons.org/licenses/by/4.0/ | The integration of deep learning and neuroscience has been advancing rapidly,
which has led to improvements in the analysis of brain activity and the
understanding of deep learning models from a neuroscientific perspective. The
reconstruction of visual experience from human brain activity is an area that
has particul... | [
{
"created": "Tue, 20 Jun 2023 13:48:02 GMT",
"version": "v1"
}
] | 2023-06-21 | [
[
"Takagi",
"Yu",
""
],
[
"Nishimoto",
"Shinji",
""
]
] | The integration of deep learning and neuroscience has been advancing rapidly, which has led to improvements in the analysis of brain activity and the understanding of deep learning models from a neuroscientific perspective. The reconstruction of visual experience from human brain activity is an area that has particular... |
2204.10073 | Gabriel Palma | Gabriel R. Palma, Silvio S. Zocchi, Wesley A.C. Godoy and Jorge A.
Wiendl | New confidence interval methods for Shannon index | 17 pages | null | null | null | q-bio.QM stat.AP | http://creativecommons.org/licenses/by/4.0/ | Several factors affect the structure of communities, including biological,
physical and chemical phenomena, impacting the quantification of biodiversity,
measured by diversity indexes such as Shannon's entropy. Then, once a point
estimate is obtained, confidence intervals methods such as the bootstrap ones
are often ... | [
{
"created": "Thu, 21 Apr 2022 13:08:35 GMT",
"version": "v1"
}
] | 2022-04-22 | [
[
"Palma",
"Gabriel R.",
""
],
[
"Zocchi",
"Silvio S.",
""
],
[
"Godoy",
"Wesley A. C.",
""
],
[
"Wiendl",
"Jorge A.",
""
]
] | Several factors affect the structure of communities, including biological, physical and chemical phenomena, impacting the quantification of biodiversity, measured by diversity indexes such as Shannon's entropy. Then, once a point estimate is obtained, confidence intervals methods such as the bootstrap ones are often us... |
1305.0159 | Anthony J Cox | Lilian Janin and Giovanna Rosone and Anthony J. Cox | Adaptive reference-free compression of sequence quality scores | Accepted paper for HiTSeq 2013, to appear in Bioinformatics.
Bioinformatics should be considered the original place of publication of this
work, please cite accordingly | null | null | null | q-bio.GN cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation:
Rapid technological progress in DNA sequencing has stimulated interest in
compressing the vast datasets that are now routinely produced. Relatively
little attention has been paid to compressing the quality scores that are
assigned to each sequence, even though these scores may be harder to compress
than... | [
{
"created": "Wed, 1 May 2013 12:51:10 GMT",
"version": "v1"
}
] | 2013-05-02 | [
[
"Janin",
"Lilian",
""
],
[
"Rosone",
"Giovanna",
""
],
[
"Cox",
"Anthony J.",
""
]
] | Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are assigned to each sequence, even though these scores may be harder to compress than the... |
1908.03686 | Yiqiang Wang | Yiqiang Wang | Shuyi, A Name After Dendritic Cell-mediated Immunological Memory | 6 pages; 2 figures, 13 references | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Immunological memory is a fundamental theory of modern immunology, which is
traditionally believed to be mediated only by B and T lymphocytes that
recognize antigen epitopes in a receptor-restricted manner. During the last
decade data accumulated to show that monocytes and macrophages, the two main
initiators of inna... | [
{
"created": "Sat, 10 Aug 2019 04:14:24 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Nov 2021 01:59:28 GMT",
"version": "v2"
}
] | 2023-09-27 | [
[
"Wang",
"Yiqiang",
""
]
] | Immunological memory is a fundamental theory of modern immunology, which is traditionally believed to be mediated only by B and T lymphocytes that recognize antigen epitopes in a receptor-restricted manner. During the last decade data accumulated to show that monocytes and macrophages, the two main initiators of innate... |
q-bio/0607024 | Claire Christensen | C. Christensen, A. Gupta, C.D. Maranas and R. Albert | Large-scale inference and graph theoretical analysis of gene-regulatory
networks in B. stubtilis | 22 pages, 4 figures, accepted for publication in Physica A (2006) | null | 10.1016/j.physa.2006.04.118 | null | q-bio.MN cond-mat.stat-mech q-bio.SC | null | We present the methods and results of a two-stage modeling process that
generates candidate gene-regulatory networks of the bacterium B. subtilis from
experimentally obtained, yet mathematically underdetermined microchip array
data. By employing a computational, linear correlative procedure to generate
these networks... | [
{
"created": "Tue, 18 Jul 2006 20:50:53 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Christensen",
"C.",
""
],
[
"Gupta",
"A.",
""
],
[
"Maranas",
"C. D.",
""
],
[
"Albert",
"R.",
""
]
] | We present the methods and results of a two-stage modeling process that generates candidate gene-regulatory networks of the bacterium B. subtilis from experimentally obtained, yet mathematically underdetermined microchip array data. By employing a computational, linear correlative procedure to generate these networks, ... |
2204.12526 | Sakira Hassan | Syeda Sakira Hassan, Rahul Mangayil, Tommi Aho, Olli Yli-Harja, Matti
Karp | Identification of feasible pathway information for c-di-GMP binding
proteins in cellulose production | null | EMBEC & NBC 2017. EMBEC NBC 2017 2017. IFMBE Proceedings, vol 65.
Springer, Singapore | null | null | q-bio.QM cs.LG stat.ML | http://creativecommons.org/licenses/by/4.0/ | In this paper, we utilize a machine learning approach to identify the
significant pathways for c-di-GMP signaling proteins. The dataset involves gene
counts from 12 pathways and 5 essential c-di-GMP binding domains for 1024
bacterial genomes. Two novel approaches, Least absolute shrinkage and selection
operator (Lass... | [
{
"created": "Tue, 26 Apr 2022 18:22:13 GMT",
"version": "v1"
}
] | 2022-04-28 | [
[
"Hassan",
"Syeda Sakira",
""
],
[
"Mangayil",
"Rahul",
""
],
[
"Aho",
"Tommi",
""
],
[
"Yli-Harja",
"Olli",
""
],
[
"Karp",
"Matti",
""
]
] | In this paper, we utilize a machine learning approach to identify the significant pathways for c-di-GMP signaling proteins. The dataset involves gene counts from 12 pathways and 5 essential c-di-GMP binding domains for 1024 bacterial genomes. Two novel approaches, Least absolute shrinkage and selection operator (Lasso)... |
1904.03290 | Mike Steel Prof. | Mike Steel, Wim Hordijk, Stuart A. Kauffman | Dynamics of a birth-death process based on combinatorial innovation | 21 pages, 4 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A feature of human creativity is the ability to take a subset of existing
items (e.g. objects, ideas, or techniques) and combine them in various ways to
give rise to new items, which, in turn, fuel further growth. Occasionally, some
of these items may also disappear (extinction). We model this process by a
simple sto... | [
{
"created": "Fri, 5 Apr 2019 21:38:14 GMT",
"version": "v1"
},
{
"created": "Mon, 19 Aug 2019 20:16:43 GMT",
"version": "v2"
}
] | 2019-08-21 | [
[
"Steel",
"Mike",
""
],
[
"Hordijk",
"Wim",
""
],
[
"Kauffman",
"Stuart A.",
""
]
] | A feature of human creativity is the ability to take a subset of existing items (e.g. objects, ideas, or techniques) and combine them in various ways to give rise to new items, which, in turn, fuel further growth. Occasionally, some of these items may also disappear (extinction). We model this process by a simple stoch... |
0911.2387 | Sylvain Hanneton | Sylvain Hanneton (NPSM), Ana\"is Varenne (NPSM) | Coaching the Wii : evaluation of a physical training experiment assisted
by a video game | 4 pages | "Haptic, Audio, Visual Environments and Games" (HAVE'09), Lecco :
Italy (2009) | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Aging or sedentary behavior can decrease motor capabilities causing a loss of
autonomy. Prevention or readaptation programs that involve practice of physical
activities can be precious tools to fight against this phenomenon. ?Serious?
video game have the potential to help people to train their body mainly due to
the ... | [
{
"created": "Thu, 12 Nov 2009 13:31:33 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Hanneton",
"Sylvain",
"",
"NPSM"
],
[
"Varenne",
"Anaïs",
"",
"NPSM"
]
] | Aging or sedentary behavior can decrease motor capabilities causing a loss of autonomy. Prevention or readaptation programs that involve practice of physical activities can be precious tools to fight against this phenomenon. ?Serious? video game have the potential to help people to train their body mainly due to the im... |
2311.17785 | Claire Guerrier | Claire Guerrier (LJAD, IRL CRM-CNRS), Tristan Dellazizzo Toth, Nicolas
Galtier, Kurt Haas | An Algorithm Based on a Cable-Nernst Planck Model Predicting Synaptic
Activity throughout the Dendritic Arbor with Micron Specificity | null | Neuroinformatics, 2023, 21 (1), pp.207-220 | 10.1007/s12021-022-09609-z | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent technological advances have enabled the recording of neurons in intact
circuits with a high spatial and temporal resolution, creating the need for
modeling with the same precision. In particular, the development of ultra-fast
two-photon microscopy combined with fluorescence-based genetically-encoded
Ca2+-indic... | [
{
"created": "Wed, 29 Nov 2023 16:32:06 GMT",
"version": "v1"
}
] | 2023-11-30 | [
[
"Guerrier",
"Claire",
"",
"LJAD, IRL CRM-CNRS"
],
[
"Toth",
"Tristan Dellazizzo",
""
],
[
"Galtier",
"Nicolas",
""
],
[
"Haas",
"Kurt",
""
]
] | Recent technological advances have enabled the recording of neurons in intact circuits with a high spatial and temporal resolution, creating the need for modeling with the same precision. In particular, the development of ultra-fast two-photon microscopy combined with fluorescence-based genetically-encoded Ca2+-indicat... |
1902.05723 | Iaroslav Ispolatov | Iaroslav Ispolatov, Evgeniia Alekseeva, and Michael Doebeli | Competition-driven evolution of organismal complexity | Open PDF with Acrobat to see movies, 22 pages, 9 figures | PLoS Comput Biol 15(10): e1007388.
https://doi.org/10.1371/journal.pcbi.1007388 (2019) | 10.1371/journal.pcbi.1007388 | null | q-bio.PE cond-mat.stat-mech nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Non-uniform rates of morphological evolution and evolutionary increases in
organismal complexity, captured in metaphors like "adaptive zones", "punctuated
equilibrium" and "blunderbuss patterns", require more elaborate explanations
than a simple gradual accumulation of mutations. Here we argue that non-uniform
evolut... | [
{
"created": "Fri, 15 Feb 2019 08:41:40 GMT",
"version": "v1"
}
] | 2020-07-01 | [
[
"Ispolatov",
"Iaroslav",
""
],
[
"Alekseeva",
"Evgeniia",
""
],
[
"Doebeli",
"Michael",
""
]
] | Non-uniform rates of morphological evolution and evolutionary increases in organismal complexity, captured in metaphors like "adaptive zones", "punctuated equilibrium" and "blunderbuss patterns", require more elaborate explanations than a simple gradual accumulation of mutations. Here we argue that non-uniform evolutio... |
1604.04903 | Thorsten Pr\"ustel | Thorsten Pr\"ustel and Martin Meier-Schellersheim | Path integral approach to theories of diffusion-influenced reactions | 13 pages | null | 10.1103/PhysRevE.96.022151 | null | q-bio.QM cond-mat.stat-mech | http://creativecommons.org/publicdomain/zero/1.0/ | The path decomposition expansion represents the propagator of the
irreversible reaction as a convolution of the first-passage, last-passage and
rebinding time probability densities. Using path integral technique, we give an
elementary, yet rigorous, proof of the path decomposition expansion of the
Green's functions d... | [
{
"created": "Sun, 17 Apr 2016 18:05:02 GMT",
"version": "v1"
}
] | 2017-09-13 | [
[
"Prüstel",
"Thorsten",
""
],
[
"Meier-Schellersheim",
"Martin",
""
]
] | The path decomposition expansion represents the propagator of the irreversible reaction as a convolution of the first-passage, last-passage and rebinding time probability densities. Using path integral technique, we give an elementary, yet rigorous, proof of the path decomposition expansion of the Green's functions des... |
2009.01923 | Yaron Oz | Yaron Oz, Ittai Rubinstein, Muli Safra | Heterogeneity and Superspreading Effect on Herd Immunity | 16 pages, 5 figures, includes population based simulations | null | null | null | q-bio.PE cond-mat.stat-mech physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We model and calculate the fraction of infected population necessary to reach
herd immunity, taking into account the heterogeneity in infectiousness and
susceptibility, as well as the correlation between those two parameters. We
show that these cause the effective reproduction number to decrease more
rapidly, and con... | [
{
"created": "Tue, 1 Sep 2020 09:43:38 GMT",
"version": "v1"
},
{
"created": "Mon, 12 Oct 2020 18:03:04 GMT",
"version": "v2"
},
{
"created": "Fri, 15 Jan 2021 15:06:06 GMT",
"version": "v3"
}
] | 2021-01-19 | [
[
"Oz",
"Yaron",
""
],
[
"Rubinstein",
"Ittai",
""
],
[
"Safra",
"Muli",
""
]
] | We model and calculate the fraction of infected population necessary to reach herd immunity, taking into account the heterogeneity in infectiousness and susceptibility, as well as the correlation between those two parameters. We show that these cause the effective reproduction number to decrease more rapidly, and conse... |
2401.12498 | Chuanbo Liu | Chuanbo Liu, Yu Fu, Lu Lin, Elliot L. Elson and Jin Wang | Understanding Cellular Noise with Optical Perturbation and Deep Learning | 33 pages, 4 figures | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | Noise plays a crucial role in the regulation of cellular and organismal
function and behavior.
Exploring noise's impact is key to understanding fundamental biological
processes, such as gene expression, signal transduction, and the mechanisms of
development and evolution.
Currently, a comprehensive method to quan... | [
{
"created": "Tue, 23 Jan 2024 05:48:20 GMT",
"version": "v1"
}
] | 2024-01-24 | [
[
"Liu",
"Chuanbo",
""
],
[
"Fu",
"Yu",
""
],
[
"Lin",
"Lu",
""
],
[
"Elson",
"Elliot L.",
""
],
[
"Wang",
"Jin",
""
]
] | Noise plays a crucial role in the regulation of cellular and organismal function and behavior. Exploring noise's impact is key to understanding fundamental biological processes, such as gene expression, signal transduction, and the mechanisms of development and evolution. Currently, a comprehensive method to quantify d... |
1510.02989 | Emmanuel Quansah Mr | Aladeen Basheer, Emmanuel Quansah, Schuman Bhowmick and Rana D.
Parshad | Prey cannibalism alters the dynamics of Holling-Tanner type
predator-prey models | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cannibalism, which is the act of killing and at least partial consumption of
conspecifics, is ubiquitous in nature. Mathematical models have considered
cannibalism in the predator primarily, and show that predator cannibalism in
two species ODE models provides a strong stabilizing effect. There is strong
ecological e... | [
{
"created": "Sat, 10 Oct 2015 23:11:48 GMT",
"version": "v1"
}
] | 2015-10-13 | [
[
"Basheer",
"Aladeen",
""
],
[
"Quansah",
"Emmanuel",
""
],
[
"Bhowmick",
"Schuman",
""
],
[
"Parshad",
"Rana D.",
""
]
] | Cannibalism, which is the act of killing and at least partial consumption of conspecifics, is ubiquitous in nature. Mathematical models have considered cannibalism in the predator primarily, and show that predator cannibalism in two species ODE models provides a strong stabilizing effect. There is strong ecological evi... |
2406.09989 | Zhichao Liang | Zhichao Liang, Guanyi Zhao, Yinuo Zhang, Weiting Sun, Jingzhe Lin,
Jialin Wang, Quanying Liu | Suppressing seizure via optimal electrical stimulation to the hub of
epileptic brain network | null | null | null | null | q-bio.NC cs.SY eess.SY | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The electrical stimulation to the seizure onset zone (SOZ) serves as an
efficient approach to seizure suppression. Recently, seizure dynamics have
gained widespread attendance in its network propagation mechanisms. Compared
with the direct stimulation to SOZ, other brain network-level approaches that
can effectively ... | [
{
"created": "Fri, 14 Jun 2024 12:54:12 GMT",
"version": "v1"
}
] | 2024-06-17 | [
[
"Liang",
"Zhichao",
""
],
[
"Zhao",
"Guanyi",
""
],
[
"Zhang",
"Yinuo",
""
],
[
"Sun",
"Weiting",
""
],
[
"Lin",
"Jingzhe",
""
],
[
"Wang",
"Jialin",
""
],
[
"Liu",
"Quanying",
""
]
] | The electrical stimulation to the seizure onset zone (SOZ) serves as an efficient approach to seizure suppression. Recently, seizure dynamics have gained widespread attendance in its network propagation mechanisms. Compared with the direct stimulation to SOZ, other brain network-level approaches that can effectively su... |
q-bio/0404030 | Paul Higgs | Bin Tang, Philippe Boisvert and Paul G. Higgs | Comparison of tRNA and rRNA Phylogenies in Proteobacteria: Implications
for the Frequency of Horizontal Gene Transfer | null | null | null | null | q-bio.PE | null | The current picture of bacterial evolution is based largely on studies of 16S
rRNA. However, this is just one gene. It is known that horizontal gene transfer
can occur between bacterial species, although the frequency and implications of
this are not fully understood. If horizontal transfer were frequent, there
would... | [
{
"created": "Fri, 23 Apr 2004 14:08:34 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Tang",
"Bin",
""
],
[
"Boisvert",
"Philippe",
""
],
[
"Higgs",
"Paul G.",
""
]
] | The current picture of bacterial evolution is based largely on studies of 16S rRNA. However, this is just one gene. It is known that horizontal gene transfer can occur between bacterial species, although the frequency and implications of this are not fully understood. If horizontal transfer were frequent, there would b... |
1912.10302 | Polly Y. Yu | Bal\'azs Boros, Gheorghe Craciun, Polly Y. Yu | Weakly reversible mass-action systems with infinitely many positive
steady states | null | SIAM Journal on Applied Mathematics, 80(4):1936-1946, 2020 | 10.1137/19M1303034 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We show that weakly reversible mass-action systems can have a continuum of
positive steady states, coming from the zeroes of a multivariate polynomial.
Moreover, the same is true of systems whose underlying reaction network is
reversible and has a single connected component. In our construction, we relate
operations ... | [
{
"created": "Sat, 21 Dec 2019 17:31:27 GMT",
"version": "v1"
},
{
"created": "Thu, 10 Sep 2020 16:27:09 GMT",
"version": "v2"
}
] | 2022-09-14 | [
[
"Boros",
"Balázs",
""
],
[
"Craciun",
"Gheorghe",
""
],
[
"Yu",
"Polly Y.",
""
]
] | We show that weakly reversible mass-action systems can have a continuum of positive steady states, coming from the zeroes of a multivariate polynomial. Moreover, the same is true of systems whose underlying reaction network is reversible and has a single connected component. In our construction, we relate operations on... |
1908.00572 | Guo-Wei Wei | Rundong Zhao, Menglun Wang, Yiying Tong and Guo-Wei Wei | The de Rham-Hodge analysis and modeling of biomolecules | 13 figures, one table | null | null | null | q-bio.BM math.AT math.DG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent years have witnessed a trend that advanced mathematical tools, such as
algebraic topology, differential geometry, graph theory, and partial
differential equations, have been developed for describing biological
macromolecules. These tools have considerably strengthened our ability to
understand the molecular me... | [
{
"created": "Thu, 1 Aug 2019 18:37:13 GMT",
"version": "v1"
}
] | 2019-08-05 | [
[
"Zhao",
"Rundong",
""
],
[
"Wang",
"Menglun",
""
],
[
"Tong",
"Yiying",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Recent years have witnessed a trend that advanced mathematical tools, such as algebraic topology, differential geometry, graph theory, and partial differential equations, have been developed for describing biological macromolecules. These tools have considerably strengthened our ability to understand the molecular mech... |
1504.03832 | Laura Hindersin | Laura Hindersin and Arne Traulsen | Most undirected random graphs are amplifiers of selection for
Birth-death dynamics, but suppressors of selection for death-Birth dynamics | null | Hindersin, L. & Traulsen A. PLoS Comput. Biol. 2015;
11(11):e1004437 | 10.1371/journal.pcbi.1004437 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze evolutionary dynamics on graphs, where the nodes represent
individuals of a population. The links of a node describe which other
individuals can be displaced by the offspring of the individual on that node.
Amplifiers of selection are graphs for which the fixation probability is
increased for advantageous ... | [
{
"created": "Wed, 15 Apr 2015 09:14:44 GMT",
"version": "v1"
},
{
"created": "Wed, 26 Oct 2016 14:52:53 GMT",
"version": "v2"
}
] | 2016-10-27 | [
[
"Hindersin",
"Laura",
""
],
[
"Traulsen",
"Arne",
""
]
] | We analyze evolutionary dynamics on graphs, where the nodes represent individuals of a population. The links of a node describe which other individuals can be displaced by the offspring of the individual on that node. Amplifiers of selection are graphs for which the fixation probability is increased for advantageous mu... |
2009.04027 | Sophia David | Sophia U. David (1), Sophie E. Loman (1), Christopher W. Lynn (1 and
2), Ann S. Blevins (1), Danielle S. Bassett (1-6) ((1) Department of
Bioengineering, School of Engineering & Applied Science, University of
Pennsylvania, Philadelphia, USA, (2) Department of Physics & Astronomy,
College of Arts & Sciences Univ... | How We Learn About our Networked World | 11 pages, 3 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When presented with information of any type, from music to language to
mathematics, the human mind subconsciously arranges it into a network. A
network puts pieces of information like musical notes, syllables or
mathematical concepts into context by linking them together. These networks
help our minds organize inform... | [
{
"created": "Tue, 8 Sep 2020 23:17:54 GMT",
"version": "v1"
}
] | 2020-09-10 | [
[
"David",
"Sophia U.",
"",
"1 and\n 2"
],
[
"Loman",
"Sophie E.",
"",
"1 and\n 2"
],
[
"Lynn",
"Christopher W.",
"",
"1 and\n 2"
],
[
"Blevins",
"Ann S.",
"",
"1-6"
],
[
"Bassett",
"Danielle S.",
"",
"1-6"
]
] | When presented with information of any type, from music to language to mathematics, the human mind subconsciously arranges it into a network. A network puts pieces of information like musical notes, syllables or mathematical concepts into context by linking them together. These networks help our minds organize informat... |
1701.01975 | Bar{\i}\c{s} Ekim | Bar{\i}\c{s} Ekim | A novel entropy-based hierarchical clustering framework for ultrafast
protein structure search and alignment | 16 pages, 13 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Identification and alignment of three-dimensional folding of proteins may
yield useful information about relationships too remote to be detected by
conventional methods, such as sequence comparison, and may potentially lead to
prediction of patterns and motifs in mutual structural fragments. With the
exponential incr... | [
{
"created": "Sun, 8 Jan 2017 15:51:07 GMT",
"version": "v1"
}
] | 2017-01-10 | [
[
"Ekim",
"Barış",
""
]
] | Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of patterns and motifs in mutual structural fragments. With the exponential increa... |
1909.07508 | Changbong Hyeon | D. Thirumalai and George H. Lorimer and Changbong Hyeon | Iterative Annealing Mechanism Explains the Functions of the GroEL and
RNA Chaperones | 39 pages, 11 figures | null | null | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular chaperones are ATP-consuming biological machines, which facilitate
the folding of proteins and RNA molecules that are kinetically trapped in
misfolded states for long times. Unassisted folding occurs by the kinetic
partitioning mechanism according to which folding to the native state, with low
probability a... | [
{
"created": "Mon, 16 Sep 2019 22:42:11 GMT",
"version": "v1"
}
] | 2019-09-18 | [
[
"Thirumalai",
"D.",
""
],
[
"Lorimer",
"George H.",
""
],
[
"Hyeon",
"Changbong",
""
]
] | Molecular chaperones are ATP-consuming biological machines, which facilitate the folding of proteins and RNA molecules that are kinetically trapped in misfolded states for long times. Unassisted folding occurs by the kinetic partitioning mechanism according to which folding to the native state, with low probability as ... |
1102.3793 | Arni S.R. Srinivasa Rao | Arni S.R. Srinivasa Rao and Thomas Kurien | Theoretical Framework and Empirical Modeling for Time Required to
Vaccinate a Population in an Epidemic | 14 pages, 1 Table, 5 Figures (A preliminary draft) | Handbook of Statistics (2017), Volume 37 | 10.1016/bs.host.2017.07.005 | null | q-bio.QM physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The paper describes a method to understand time required to vaccinate against
viruses in total as well as subpopulations. As a demonstration, a model based
estimate for time required to vaccinate H1N1 in India, given its administrative
difficulties is provided. We have proved novel theorems for the time functions
def... | [
{
"created": "Fri, 18 Feb 2011 09:41:30 GMT",
"version": "v1"
}
] | 2021-06-15 | [
[
"Rao",
"Arni S. R. Srinivasa",
""
],
[
"Kurien",
"Thomas",
""
]
] | The paper describes a method to understand time required to vaccinate against viruses in total as well as subpopulations. As a demonstration, a model based estimate for time required to vaccinate H1N1 in India, given its administrative difficulties is provided. We have proved novel theorems for the time functions defin... |
1801.09831 | Sanjana Gupta | Sanjana Gupta, Liam Hainsworth, Justin S. Hogg, Robin E. C. Lee, and
James R. Faeder | Evaluation of Parallel Tempering to Accelerate Bayesian Parameter
Estimation in Systems Biology | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Models of biological systems often have many unknown parameters that must be
determined in order for model behavior to match experimental observations.
Commonly-used methods for parameter estimation that return point estimates of
the best-fit parameters are insufficient when models are high dimensional and
under-cons... | [
{
"created": "Tue, 30 Jan 2018 02:45:59 GMT",
"version": "v1"
}
] | 2018-01-31 | [
[
"Gupta",
"Sanjana",
""
],
[
"Hainsworth",
"Liam",
""
],
[
"Hogg",
"Justin S.",
""
],
[
"Lee",
"Robin E. C.",
""
],
[
"Faeder",
"James R.",
""
]
] | Models of biological systems often have many unknown parameters that must be determined in order for model behavior to match experimental observations. Commonly-used methods for parameter estimation that return point estimates of the best-fit parameters are insufficient when models are high dimensional and under-constr... |
2012.05454 | Adrian Joseph Alva | Adrian Joseph Alva and Harjinder Singh | A minimal model for synaptic integration in simple neurons | 25 pages, 8 figures | Physica D 426 (2021) 132988 | 10.1016/j.physd.2021.132988 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Synaptic integration is a prominent aspect of neuronal information
processing. The detailed mechanisms that modulate synaptic inputs determine the
computational properties of any given neuron. We study a simple model for the
summation of excitatory inputs from synapses and illustrate its use by
characterizing some fu... | [
{
"created": "Thu, 10 Dec 2020 05:03:07 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Feb 2021 13:54:48 GMT",
"version": "v2"
},
{
"created": "Wed, 14 Jul 2021 06:14:20 GMT",
"version": "v3"
}
] | 2021-07-15 | [
[
"Alva",
"Adrian Joseph",
""
],
[
"Singh",
"Harjinder",
""
]
] | Synaptic integration is a prominent aspect of neuronal information processing. The detailed mechanisms that modulate synaptic inputs determine the computational properties of any given neuron. We study a simple model for the summation of excitatory inputs from synapses and illustrate its use by characterizing some func... |
1706.08422 | Edmund Barter | Edmund Barter and Thilo Gross | Spatial effects in meta-food-webs | 15 pages, 8 figures | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In ecology it is widely recognised that many landscapes comprise a network of
discrete patches of habitat. The species that inhabit the patches interact with
each other through a foodweb, the network of feeding interactions. The
meta-foodweb model proposed by Pillai et al. combines the feeding relationships
at each p... | [
{
"created": "Mon, 26 Jun 2017 14:56:01 GMT",
"version": "v1"
},
{
"created": "Thu, 10 Aug 2017 09:47:35 GMT",
"version": "v2"
}
] | 2017-08-11 | [
[
"Barter",
"Edmund",
""
],
[
"Gross",
"Thilo",
""
]
] | In ecology it is widely recognised that many landscapes comprise a network of discrete patches of habitat. The species that inhabit the patches interact with each other through a foodweb, the network of feeding interactions. The meta-foodweb model proposed by Pillai et al. combines the feeding relationships at each pat... |
1009.4480 | Adriaan (Ard) A. Louis | Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye | Structural, mechanical and thermodynamic properties of a coarse-grained
DNA model | 25 pages, 16 figures | J. Chem. Phys, 134, 085101 (2011) | 10.1063/1.3552946 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We explore in detail the structural, mechanical and thermodynamic properties
of a coarse-grained model of DNA similar to that introduced in Thomas E.
Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101
(2010). Effective interactions are used to represent chain connectivity,
excluded volume, base ... | [
{
"created": "Wed, 22 Sep 2010 21:14:06 GMT",
"version": "v1"
}
] | 2013-06-25 | [
[
"Ouldridge",
"Thomas E.",
""
],
[
"Louis",
"Ard A.",
""
],
[
"Doye",
"Jonathan P. K.",
""
]
] | We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective interactions are used to represent chain connectivity, excluded volume, base st... |
2110.09204 | Andrea De Martino | A.R. Batista-Tomas, Andrea De Martino, Roberto Mulet | Path-integral solution of MacArthur's resource-competition model for
large ecosystems with random species-resources couplings | This article may be downloaded for personal use only. Any other use
requires prior permission of the author and AIP Publishing. This article
appeared in Chaos 31, 103113 (2021) and may be found at
https://aip.scitation.org/doi/full/10.1063/5.0046972 | Chaos 31, 103113 (2021) | 10.1063/5.0046972 | null | q-bio.PE cond-mat.dis-nn cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We solve MacArthur's resource-competition model with random species-resource
couplings in the `thermodynamic' limit of infinitely many species and resources
using dynamical path-integrals a la De Domincis. We analyze how the steady
state picture changes upon modifying several parameters, including the degree
of heter... | [
{
"created": "Mon, 18 Oct 2021 11:43:05 GMT",
"version": "v1"
}
] | 2021-10-19 | [
[
"Batista-Tomas",
"A. R.",
""
],
[
"De Martino",
"Andrea",
""
],
[
"Mulet",
"Roberto",
""
]
] | We solve MacArthur's resource-competition model with random species-resource couplings in the `thermodynamic' limit of infinitely many species and resources using dynamical path-integrals a la De Domincis. We analyze how the steady state picture changes upon modifying several parameters, including the degree of heterog... |
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