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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
q-bio/0611016 | John Bechhoefer | John Bechhoefer and Brandon Marshall | How Xenopus laevis replicates DNA reliably even though its origins of
replication are located and initiated stochastically | 10 pages, 4 figures | Phys. Rev. Lett. 98, 098105 (2007) | 10.1103/PhysRevLett.98.098105 | null | q-bio.CB q-bio.QM | null | DNA replication in Xenopus laevis is extremely reliable, failing to complete
before cell division no more than once in 10,000 times; yet replication origins
sites are located and initiated stochastically. Using a model based on 1d
theories of nucleation and growth and using concepts from extreme-value
statistics, we ... | [
{
"created": "Sat, 4 Nov 2006 23:40:07 GMT",
"version": "v1"
}
] | 2015-04-02 | [
[
"Bechhoefer",
"John",
""
],
[
"Marshall",
"Brandon",
""
]
] | DNA replication in Xenopus laevis is extremely reliable, failing to complete before cell division no more than once in 10,000 times; yet replication origins sites are located and initiated stochastically. Using a model based on 1d theories of nucleation and growth and using concepts from extreme-value statistics, we de... |
2404.14658 | Guerard Byrne | Guerard Byrne and Christopher McGregor | Anti-pig Antibodies in Swine Veterinarian Serum: Implications for
Clinical Xenotransplantation | 13 pages, 2 Tables, 3 Figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent clinical xenotransplantation and human decedent studies demonstrate
that clinical hyperacute rejection of genetically engineered porcine organs can
be reliably avoided but that antibody mediated rejection continues to limit
graft survival. We previously identified porcine glycans and proteins which are
immunog... | [
{
"created": "Tue, 23 Apr 2024 01:41:48 GMT",
"version": "v1"
}
] | 2024-04-24 | [
[
"Byrne",
"Guerard",
""
],
[
"McGregor",
"Christopher",
""
]
] | Recent clinical xenotransplantation and human decedent studies demonstrate that clinical hyperacute rejection of genetically engineered porcine organs can be reliably avoided but that antibody mediated rejection continues to limit graft survival. We previously identified porcine glycans and proteins which are immunogen... |
1206.0529 | Mustafa Barasa | M. Barasa, Z.W. Ng'ang'a, G.A. Sowayi, J.M. Okoth, M.B.O. Barasa,
F.B.M. Namulanda, E.A. Kagasi, M.M. Gicheru and S.H. Ozwara | Cytokine expression in malaria-infected non-human primate placentas | Open Veterinary Journal 1st June 2012. Seven pages, Three Figures.
arXiv admin note: text overlap with arXiv:1201.3232 | M. Barasa, Z.W. Ng'ang'a et al. Cytokine expression in
malaria-infected non-human primate placentas. Open Veterinary Journal,
(2012), Vol. 2: 58-64 | null | null | q-bio.CB q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Malaria parasites are known to mediate the induction of inflammatory immune
responses at the maternal-foetal interface during placental malaria (PM)
leading to adverse consequences like pre-term deliveries and abortions.
Immunological events that take place within the malaria-infected placental
micro-environment lead... | [
{
"created": "Mon, 4 Jun 2012 06:44:57 GMT",
"version": "v1"
}
] | 2012-06-05 | [
[
"Barasa",
"M.",
""
],
[
"Ng'ang'a",
"Z. W.",
""
],
[
"Sowayi",
"G. A.",
""
],
[
"Okoth",
"J. M.",
""
],
[
"Barasa",
"M. B. O.",
""
],
[
"Namulanda",
"F. B. M.",
""
],
[
"Kagasi",
"E. A.",
""
],
[
"G... | Malaria parasites are known to mediate the induction of inflammatory immune responses at the maternal-foetal interface during placental malaria (PM) leading to adverse consequences like pre-term deliveries and abortions. Immunological events that take place within the malaria-infected placental micro-environment leadin... |
1303.4784 | Matthew Wyczalkowski | Matthew A. Wyczalkowski and Victor D. Varner and Larry A. Taber | Computational and Experimental Study of the Mechanics of Embryonic Wound
Healing | 32 pages, 13 figures | null | 10.1016/j.bpj.2012.11.1764 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Wounds in the embryo show a remarkable ability to heal quickly without
leaving a scar. Previous studies have found that an actomyosin ring ("purse
string") forms around the wound perimeter and contracts to close the wound over
the course of several dozens of minutes. Here, we report experiments that
reveal an even fa... | [
{
"created": "Tue, 19 Mar 2013 22:55:05 GMT",
"version": "v1"
},
{
"created": "Wed, 4 Sep 2013 00:28:32 GMT",
"version": "v2"
},
{
"created": "Fri, 6 Sep 2013 03:38:16 GMT",
"version": "v3"
}
] | 2015-06-15 | [
[
"Wyczalkowski",
"Matthew A.",
""
],
[
"Varner",
"Victor D.",
""
],
[
"Taber",
"Larry A.",
""
]
] | Wounds in the embryo show a remarkable ability to heal quickly without leaving a scar. Previous studies have found that an actomyosin ring ("purse string") forms around the wound perimeter and contracts to close the wound over the course of several dozens of minutes. Here, we report experiments that reveal an even fast... |
2104.11739 | Carlo Fulvi Mari Ph.D. | Carlo Fulvi Mari | Memory retrieval dynamics and storage capacity of a modular network
model of association cortex with featural decomposition | v2: 17 pages, 7+2 figures, pdflatex. Minor Revision: Further
observations and references were included, the wording of some paragraphs was
improved, and several typos were corrected | BioSystems 211, 104570 (2022) | 10.1016/j.biosystems.2021.104570 | null | q-bio.NC cond-mat.dis-nn physics.bio-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The primate heteromodal cortex presents an evident functional modularity at a
mesoscopic level, with physiological and anatomical evidence pointing to it as
likely substrate of long-term memory. In order to investigate some of its
properties, a model of multimodular autoassociator is studied. Each of the many
modules... | [
{
"created": "Fri, 23 Apr 2021 17:50:49 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Dec 2021 21:43:19 GMT",
"version": "v2"
}
] | 2021-12-09 | [
[
"Mari",
"Carlo Fulvi",
""
]
] | The primate heteromodal cortex presents an evident functional modularity at a mesoscopic level, with physiological and anatomical evidence pointing to it as likely substrate of long-term memory. In order to investigate some of its properties, a model of multimodular autoassociator is studied. Each of the many modules r... |
1701.01433 | Ignacio Arganda-Carreras | Ignacio Arganda-Carreras, Darcy G Gordon, Sara Arganda, Maxime
Beaudoin, James FA Traniello | Group-wise 3D registration based templates to study the evolution of ant
worker neuroanatomy | 10 pages, 5 figures, preprint for conference (not reviewed) | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The evolutionary success of ants and other social insects is considered to be
intrinsically linked to division of labor and emergent collective intelligence.
The role of the brains of individual ants in generating these processes,
however, is poorly understood. One genus of ant of special interest is
Pheidole, which ... | [
{
"created": "Thu, 5 Jan 2017 14:44:41 GMT",
"version": "v1"
},
{
"created": "Fri, 13 Jan 2017 17:14:08 GMT",
"version": "v2"
},
{
"created": "Wed, 8 Feb 2017 15:22:39 GMT",
"version": "v3"
},
{
"created": "Mon, 21 Aug 2017 20:13:06 GMT",
"version": "v4"
}
] | 2017-08-23 | [
[
"Arganda-Carreras",
"Ignacio",
""
],
[
"Gordon",
"Darcy G",
""
],
[
"Arganda",
"Sara",
""
],
[
"Beaudoin",
"Maxime",
""
],
[
"Traniello",
"James FA",
""
]
] | The evolutionary success of ants and other social insects is considered to be intrinsically linked to division of labor and emergent collective intelligence. The role of the brains of individual ants in generating these processes, however, is poorly understood. One genus of ant of special interest is Pheidole, which in... |
2109.10449 | Cody Petrie | Cody Petrie, Christian Anderson, Casie Maekawa, Travis Maekawa, Mark
K. Transtrum | The supremum principle selects simple, transferable models | 6 pages, 3 figures | null | null | null | q-bio.QM cond-mat.stat-mech physics.bio-ph physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider how mathematical models enable predictions for conditions that
are qualitatively different from the training data. We propose techniques based
on information topology to find models that can apply their learning in regimes
for which there is no data. The first step is to use the Manifold Boundary
Approxim... | [
{
"created": "Tue, 21 Sep 2021 22:28:16 GMT",
"version": "v1"
},
{
"created": "Fri, 11 Feb 2022 20:14:12 GMT",
"version": "v2"
},
{
"created": "Wed, 25 May 2022 21:36:39 GMT",
"version": "v3"
}
] | 2022-05-27 | [
[
"Petrie",
"Cody",
""
],
[
"Anderson",
"Christian",
""
],
[
"Maekawa",
"Casie",
""
],
[
"Maekawa",
"Travis",
""
],
[
"Transtrum",
"Mark K.",
""
]
] | We consider how mathematical models enable predictions for conditions that are qualitatively different from the training data. We propose techniques based on information topology to find models that can apply their learning in regimes for which there is no data. The first step is to use the Manifold Boundary Approximat... |
0801.4164 | Matthias Kaschube | Matthias Kaschube, Michael Schnabel, Siegrid L\"owel and Fred Wolf | Inter-areal coordination of columnar architectures during visual
cortical development | 30 pages, 1 table, 6 figures | null | 10.1073/pnas.0901615106 | null | q-bio.NC q-bio.QM | null | The occurrence of a critical period of plasticity in the visual cortex has
long been established, yet its function in normal development is not fully
understood. Here we show that as the late phase of the critical period unfolds,
different areas of cat visual cortex develop in a coordinated manner.
Orientation column... | [
{
"created": "Sun, 27 Jan 2008 22:48:53 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Kaschube",
"Matthias",
""
],
[
"Schnabel",
"Michael",
""
],
[
"Löwel",
"Siegrid",
""
],
[
"Wolf",
"Fred",
""
]
] | The occurrence of a critical period of plasticity in the visual cortex has long been established, yet its function in normal development is not fully understood. Here we show that as the late phase of the critical period unfolds, different areas of cat visual cortex develop in a coordinated manner. Orientation columns ... |
q-bio/0401013 | Tatiana Verechtchaguina | T. Verechtchaguina, L. Schimansky-Geier, I.M. Sokolov | Spectra and waiting-time densities in firing resonant and nonresonant
neurons | 7 pages, 8 figures | Phys. Rev. E 70, 031916 (2004) | 10.1103/PhysRevE.70.031916 | null | q-bio.NC | null | The response of a neural cell to an external stimulus can follow one of the
two patterns: Nonresonant neurons monotonously relax to the resting state after
excitation while resonant ones show subthreshold oscillations. We investigate
how do these subthreshold properties of neurons affect their suprathreshold
response... | [
{
"created": "Thu, 8 Jan 2004 22:59:11 GMT",
"version": "v1"
},
{
"created": "Thu, 30 Jun 2005 15:06:00 GMT",
"version": "v2"
}
] | 2009-11-10 | [
[
"Verechtchaguina",
"T.",
""
],
[
"Schimansky-Geier",
"L.",
""
],
[
"Sokolov",
"I. M.",
""
]
] | The response of a neural cell to an external stimulus can follow one of the two patterns: Nonresonant neurons monotonously relax to the resting state after excitation while resonant ones show subthreshold oscillations. We investigate how do these subthreshold properties of neurons affect their suprathreshold response. ... |
1412.7958 | Alexander K. Vidybida | Alexander K.Vidybida | Relation between firing statistics of spiking neuron with instantaneous
feedback and without feedback | 5 pages letter. In this version, section about moments and variances
is added, text style and language improved | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a wide class of spiking neuron models, defined by rather general
set of conditions typical for basic models like leaky integrate and fire, or
binding neuron model. A neuron is fed with a point renewal process. A relation
between the three probability density functions (pdf): (i) pdf of input
interspike in... | [
{
"created": "Fri, 26 Dec 2014 16:50:28 GMT",
"version": "v1"
},
{
"created": "Thu, 8 Jan 2015 12:57:09 GMT",
"version": "v2"
},
{
"created": "Thu, 12 Feb 2015 14:59:51 GMT",
"version": "v3"
}
] | 2015-02-13 | [
[
"Vidybida",
"Alexander K.",
""
]
] | We consider a wide class of spiking neuron models, defined by rather general set of conditions typical for basic models like leaky integrate and fire, or binding neuron model. A neuron is fed with a point renewal process. A relation between the three probability density functions (pdf): (i) pdf of input interspike inte... |
1704.01761 | Hans Trukenbrod | Hans A. Trukenbrod, Simon Barthelm\'e, Felix A. Wichmann and Ralf
Engbert | Spatial statistics for gaze patterns in scene viewing: Effects of
repeated viewing | 27 pages, 10 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Scene viewing is used to study attentional selection in complex but still
controlled environments. One of the main observations on eye movements during
scene viewing is the inhomogeneous distribution of fixation locations: While
some parts of an image are fixated by almost all observers and are inspected
repeatedly b... | [
{
"created": "Thu, 6 Apr 2017 09:46:01 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Nov 2018 08:35:59 GMT",
"version": "v2"
}
] | 2018-11-14 | [
[
"Trukenbrod",
"Hans A.",
""
],
[
"Barthelmé",
"Simon",
""
],
[
"Wichmann",
"Felix A.",
""
],
[
"Engbert",
"Ralf",
""
]
] | Scene viewing is used to study attentional selection in complex but still controlled environments. One of the main observations on eye movements during scene viewing is the inhomogeneous distribution of fixation locations: While some parts of an image are fixated by almost all observers and are inspected repeatedly by ... |
2304.06273 | Masod Sadipour | Masod Sadipour, Mohammad Masoud Momeni, Majid Soltani | Effect of hydraulic conductivity and permeability on drug distribution,
an investigation based on a part of a real tissue | 15 pages | null | null | null | q-bio.TO cs.NA math.NA | http://creativecommons.org/publicdomain/zero/1.0/ | In this study, a computational simulation is employed to place two essential
parameters, the permeability of vessels and hydraulic conductivity, under
assessment. These parameters impact the movement of drug particles through
vessels, and normal and tumoral tissue to examine the concentration of
nanoparticles, inters... | [
{
"created": "Thu, 13 Apr 2023 05:16:36 GMT",
"version": "v1"
}
] | 2023-04-14 | [
[
"Sadipour",
"Masod",
""
],
[
"Momeni",
"Mohammad Masoud",
""
],
[
"Soltani",
"Majid",
""
]
] | In this study, a computational simulation is employed to place two essential parameters, the permeability of vessels and hydraulic conductivity, under assessment. These parameters impact the movement of drug particles through vessels, and normal and tumoral tissue to examine the concentration of nanoparticles, intersti... |
1206.0311 | Pamela Reinagel | Pamela Reinagel, Emily Mankin, and Adam Calhoun | Speed and accuracy in a visual motion discrimination task as performed
by rats | Content is identical to a poster presented at the 2009 Society for
Neuroscience meeting: Reinagel P, Mankin E, and Calhoun A (2009) Speed and
accuracy in a visual motion discrimination task as performed by rats. Program
No. 281.12. 2009 Neuroscience Meeting Planner. Chicago, IL: Society for
Neuroscience, 2009. ... | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We find that rats, like primates and humans, perform better on the random dot
motion task when they take more time to respond. We provide evidence that this
improvement is due to stimulus integration. Rats increase their response
latency modestly as a function of trial difficulty. Rats can modulate response
latency m... | [
{
"created": "Fri, 1 Jun 2012 21:26:53 GMT",
"version": "v1"
}
] | 2012-06-05 | [
[
"Reinagel",
"Pamela",
""
],
[
"Mankin",
"Emily",
""
],
[
"Calhoun",
"Adam",
""
]
] | We find that rats, like primates and humans, perform better on the random dot motion task when they take more time to respond. We provide evidence that this improvement is due to stimulus integration. Rats increase their response latency modestly as a function of trial difficulty. Rats can modulate response latency mor... |
2201.06687 | Evan Johnson | Evan C. Johnson, Oscar Godoy, and Alan Hastings | The storage effect is not about bet-hedging or population
stage-structure | 20 pages, 8 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The storage effect is a well-known explanation for coexistence in temporally
varying environments. Like many complex ecological theories, the storage effect
is often used as an explanation for observed coexistence on the basis of
heuristic understanding, rather than careful application of a detailed model.
One interp... | [
{
"created": "Tue, 18 Jan 2022 01:16:36 GMT",
"version": "v1"
},
{
"created": "Thu, 12 Jan 2023 04:43:13 GMT",
"version": "v2"
}
] | 2023-01-13 | [
[
"Johnson",
"Evan C.",
""
],
[
"Godoy",
"Oscar",
""
],
[
"Hastings",
"Alan",
""
]
] | The storage effect is a well-known explanation for coexistence in temporally varying environments. Like many complex ecological theories, the storage effect is often used as an explanation for observed coexistence on the basis of heuristic understanding, rather than careful application of a detailed model. One interpre... |
0810.4580 | Tijana Ivancevic | Tijana T. Ivancevic, Murk J. Bottema and Lakhmi C. Jain | A Mathematical Model of Chaotic Attractor in Tumor Growth and Decay | 4 pages, 1 figure, latex | null | null | null | q-bio.CB q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a strange-attractor model of tumor growth and metastasis. It is a
4-dimensional spatio-temporal cancer model with strong nonlinear couplings.
Even the same type of tumor is different in every patient both in size and
appearance, as well as in temporal behavior. This is clearly a characteristic
of dynamical... | [
{
"created": "Mon, 27 Oct 2008 12:50:13 GMT",
"version": "v1"
}
] | 2008-10-28 | [
[
"Ivancevic",
"Tijana T.",
""
],
[
"Bottema",
"Murk J.",
""
],
[
"Jain",
"Lakhmi C.",
""
]
] | We propose a strange-attractor model of tumor growth and metastasis. It is a 4-dimensional spatio-temporal cancer model with strong nonlinear couplings. Even the same type of tumor is different in every patient both in size and appearance, as well as in temporal behavior. This is clearly a characteristic of dynamical s... |
1806.04037 | Andriy Temko Dr | Mark O'Sullivan, Sergi Gomez, Alison O'Shea, Eduard Salgado, Kevin
Huillca, Sean Mathieson, Geraldine Boylan, Emanuel Popovici, Andriy Temko | Neonatal EEG Interpretation and Decision Support Framework for Mobile
Platforms | EMBC 2018 | null | null | null | q-bio.NC cs.SE stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper proposes and implements an intuitive and pervasive solution for
neonatal EEG monitoring assisted by sonification and deep learning AI that
provides information about neonatal brain health to all neonatal healthcare
professionals, particularly those without EEG interpretation expertise. The
system aims to i... | [
{
"created": "Fri, 8 Jun 2018 09:35:02 GMT",
"version": "v1"
}
] | 2018-06-12 | [
[
"O'Sullivan",
"Mark",
""
],
[
"Gomez",
"Sergi",
""
],
[
"O'Shea",
"Alison",
""
],
[
"Salgado",
"Eduard",
""
],
[
"Huillca",
"Kevin",
""
],
[
"Mathieson",
"Sean",
""
],
[
"Boylan",
"Geraldine",
""
],
[
... | This paper proposes and implements an intuitive and pervasive solution for neonatal EEG monitoring assisted by sonification and deep learning AI that provides information about neonatal brain health to all neonatal healthcare professionals, particularly those without EEG interpretation expertise. The system aims to inc... |
2009.12422 | Daniel Martins | Daniel P. Martins, Huong Q.-O'Reilly, Lee Coffey, Paul D. Cotter,
Sasitharan Balasubramaniam | Hydrogel-based Bio-nanomachine Transmitters for Bacterial Molecular
Communications | This work has been submitted to an ACM conference for possible
publication | null | 10.1145/3416006.3431271 | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bacterial quorum sensing can be engineered with a view to the design of
biotechnological applications based on their intrinsic role as a means of
communication. We propose the creation of a positive feedback loop that will
promote the emission of a superfolded green fluorescence protein from a
bacterial population th... | [
{
"created": "Fri, 25 Sep 2020 20:13:05 GMT",
"version": "v1"
}
] | 2021-04-15 | [
[
"Martins",
"Daniel P.",
""
],
[
"-O'Reilly",
"Huong Q.",
""
],
[
"Coffey",
"Lee",
""
],
[
"Cotter",
"Paul D.",
""
],
[
"Balasubramaniam",
"Sasitharan",
""
]
] | Bacterial quorum sensing can be engineered with a view to the design of biotechnological applications based on their intrinsic role as a means of communication. We propose the creation of a positive feedback loop that will promote the emission of a superfolded green fluorescence protein from a bacterial population that... |
2110.15200 | Matthew Ragoza | Matthew Ragoza, Tomohide Masuda, David Ryan Koes | Generating 3D Molecules Conditional on Receptor Binding Sites with Deep
Generative Models | Main: 12 pages, 7 figures; Supplement: 6 pages, 14 figures | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by-sa/4.0/ | The goal of structure-based drug discovery is to find small molecules that
bind to a given target protein. Deep learning has been used to generate
drug-like molecules with certain cheminformatic properties, but has not yet
been applied to generating 3D molecules predicted to bind to proteins by
sampling the condition... | [
{
"created": "Thu, 28 Oct 2021 15:17:24 GMT",
"version": "v1"
},
{
"created": "Wed, 26 Jan 2022 16:26:17 GMT",
"version": "v2"
}
] | 2022-01-27 | [
[
"Ragoza",
"Matthew",
""
],
[
"Masuda",
"Tomohide",
""
],
[
"Koes",
"David Ryan",
""
]
] | The goal of structure-based drug discovery is to find small molecules that bind to a given target protein. Deep learning has been used to generate drug-like molecules with certain cheminformatic properties, but has not yet been applied to generating 3D molecules predicted to bind to proteins by sampling the conditional... |
0806.1063 | Suani Pinho | E. A. Reis, L. B. L. Santos, S. T. R. Pinho | A cellular automata model for avascular solid tumor growth under the
effect of therapy | 18 pages, 15 figures (jpeg) | null | 10.1016/j.physa.2008.11.038 | null | q-bio.TO nlin.CG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tumor growth has long been a target of investigation within the context of
mathematical and computer modelling. The objective of this study is to propose
and analyze a two-dimensional probabilistic cellular automata model to describe
avascular solid tumor growth, taking into account both the competition between
cance... | [
{
"created": "Thu, 5 Jun 2008 21:48:37 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Reis",
"E. A.",
""
],
[
"Santos",
"L. B. L.",
""
],
[
"Pinho",
"S. T. R.",
""
]
] | Tumor growth has long been a target of investigation within the context of mathematical and computer modelling. The objective of this study is to propose and analyze a two-dimensional probabilistic cellular automata model to describe avascular solid tumor growth, taking into account both the competition between cancer ... |
2111.01282 | Ross Kedl | Ross M. Kedl | An immunological autobiography: my year as a COVID-19 vaccine trial
participant | null | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-nd/4.0/ | I present here longitudinal evaluation of T and B cell immunity to SARS-CoV2
and variants of concern (VOC) from a single subject (me) over an entire year
post vaccination. After enrolling in the Moderna phase III clinical trial, I
collected my own biological samples pre- and post-immunization in the event of
being a ... | [
{
"created": "Mon, 1 Nov 2021 22:19:40 GMT",
"version": "v1"
},
{
"created": "Wed, 5 Jan 2022 22:41:05 GMT",
"version": "v2"
}
] | 2022-01-07 | [
[
"Kedl",
"Ross M.",
""
]
] | I present here longitudinal evaluation of T and B cell immunity to SARS-CoV2 and variants of concern (VOC) from a single subject (me) over an entire year post vaccination. After enrolling in the Moderna phase III clinical trial, I collected my own biological samples pre- and post-immunization in the event of being a re... |
1405.3331 | Marcus Kaiser | Ana M. Mihut, Graham Morgan, Marcus Kaiser | Graphic Processing Unit Simulation of Axon Growth and Guidance through
Cue Diffusion on Massively Parallel Processors | Dynamic Connectome Lab, Technical Report 2 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neural development represents not only an exciting and complex field of
study, with ongoing progress, but it also became the epicentre of neuroscience
and developmental biology, as it strives to describe the underlying cellular
and molecular mechanisms by which the central nervous system emerges during the
various le... | [
{
"created": "Tue, 13 May 2014 23:57:39 GMT",
"version": "v1"
}
] | 2014-05-15 | [
[
"Mihut",
"Ana M.",
""
],
[
"Morgan",
"Graham",
""
],
[
"Kaiser",
"Marcus",
""
]
] | Neural development represents not only an exciting and complex field of study, with ongoing progress, but it also became the epicentre of neuroscience and developmental biology, as it strives to describe the underlying cellular and molecular mechanisms by which the central nervous system emerges during the various leve... |
1506.07889 | Antonio Galves | D. Fraiman, M.F. Miranda, F. Erthal, P.F. Buur, M. Elschot, L. Souza,
S.A.R.B. Rombouts, M.J.P. van Osch, C.A. Schimmelpenninck, D.G. Norris,
M.J.A. Malessy, A. Galves and C.D. Vargas | Reduced functional connectivity within the primary motor cortex of
patients with brachial plexus injury | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This study aims at the effects of traumatic brachial plexus lesion with root
avulsions (BPA) upon the organization of the primary motor cortex (M1). Nine
right-handed patients with a right BPA in whom an intercostal to
musculocutaneous (ICN-MC) nerve transfer was performed had post-operative
resting state fRMI scanni... | [
{
"created": "Thu, 25 Jun 2015 20:07:26 GMT",
"version": "v1"
}
] | 2015-06-29 | [
[
"Fraiman",
"D.",
""
],
[
"Miranda",
"M. F.",
""
],
[
"Erthal",
"F.",
""
],
[
"Buur",
"P. F.",
""
],
[
"Elschot",
"M.",
""
],
[
"Souza",
"L.",
""
],
[
"Rombouts",
"S. A. R. B.",
""
],
[
"van Osch",
... | This study aims at the effects of traumatic brachial plexus lesion with root avulsions (BPA) upon the organization of the primary motor cortex (M1). Nine right-handed patients with a right BPA in whom an intercostal to musculocutaneous (ICN-MC) nerve transfer was performed had post-operative resting state fRMI scanning... |
1809.04461 | Vinayakumar R | Anu Vazhayil, Vinayakumar R and Soman KP | DeepProteomics: Protein family classification using Shallow and Deep
Networks | null | null | null | null | q-bio.QM cs.LG cs.NE stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The knowledge regarding the function of proteins is necessary as it gives a
clear picture of biological processes. Nevertheless, there are many protein
sequences found and added to the databases but lacks functional annotation. The
laboratory experiments take a considerable amount of time for annotation of the
sequen... | [
{
"created": "Tue, 11 Sep 2018 17:48:01 GMT",
"version": "v1"
}
] | 2018-09-13 | [
[
"Vazhayil",
"Anu",
""
],
[
"R",
"Vinayakumar",
""
],
[
"KP",
"Soman",
""
]
] | The knowledge regarding the function of proteins is necessary as it gives a clear picture of biological processes. Nevertheless, there are many protein sequences found and added to the databases but lacks functional annotation. The laboratory experiments take a considerable amount of time for annotation of the sequence... |
1512.04495 | Dimiter Prodanov | Dimiter Prodanov and Jean Delbeke | A model of fractional-order diffusion in the glial scar | Figures excluded due to technical issues | null | null | null | q-bio.TO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Implantation of neuroprosthetic electrodes induces a stereotypical state of
neuroinflammation, which is thought to be detrimental for the neurons
surrounding the electrode. Mechanisms of this type of neuroinflammation are
still not understood well. Recent experimental and theoretical results point
out possible role o... | [
{
"created": "Mon, 14 Dec 2015 20:01:01 GMT",
"version": "v1"
}
] | 2015-12-15 | [
[
"Prodanov",
"Dimiter",
""
],
[
"Delbeke",
"Jean",
""
]
] | Implantation of neuroprosthetic electrodes induces a stereotypical state of neuroinflammation, which is thought to be detrimental for the neurons surrounding the electrode. Mechanisms of this type of neuroinflammation are still not understood well. Recent experimental and theoretical results point out possible role of ... |
0801.2302 | Paolo Tieri | Paolo Tieri, Gastone C. Castellani, Claudio Franceschi | Towards an unifying perspective of the fundamental properties and
structural principles governing the immune system | 3 pages, abstract of the poster and oral presentation at SBH2007
SysBioHealth Symposium, Systems Biology for Health, Milano, 17-19 October
2007 | null | null | null | q-bio.OT | null | In the study of the basic properties observed in the immune system and, in a
broader view, in biological systems, several concepts have already been
mathematically formulated or treated in an analytical perspective, such as
degeneracy, robustness, noise, and bow tie architecture. These properties,
among others, seem ... | [
{
"created": "Tue, 15 Jan 2008 14:05:56 GMT",
"version": "v1"
}
] | 2008-01-16 | [
[
"Tieri",
"Paolo",
""
],
[
"Castellani",
"Gastone C.",
""
],
[
"Franceschi",
"Claudio",
""
]
] | In the study of the basic properties observed in the immune system and, in a broader view, in biological systems, several concepts have already been mathematically formulated or treated in an analytical perspective, such as degeneracy, robustness, noise, and bow tie architecture. These properties, among others, seem to... |
2301.04815 | Hongsong Feng | Hongsong Feng, Rana Elladki, Jian Jiang, and Guo-Wei Wei | Machine-learning Analysis of Opioid Use Disorder Informed by MOR, DOR,
KOR, NOR and ZOR-Based Interactome Networks | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Opioid use disorder (OUD) continuously poses major public health challenges
and social implications worldwide with dramatic rise of opioid dependence
leading to potential abuse. Despite that a few pharmacological agents have been
approved for OUD treatment, the efficacy of said agents for OUD requires
further improve... | [
{
"created": "Thu, 12 Jan 2023 05:05:25 GMT",
"version": "v1"
}
] | 2023-01-13 | [
[
"Feng",
"Hongsong",
""
],
[
"Elladki",
"Rana",
""
],
[
"Jiang",
"Jian",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Opioid use disorder (OUD) continuously poses major public health challenges and social implications worldwide with dramatic rise of opioid dependence leading to potential abuse. Despite that a few pharmacological agents have been approved for OUD treatment, the efficacy of said agents for OUD requires further improveme... |
2111.04784 | Zahra Nasiriavanaki | Roger B. H. Tootell and Zahra Nasiriavanaki, Baktash Babadi, Douglas
N. Greve, Shahin Nasr, Daphne J. Holt | Interdigitated Columnar Representation of Personal Space and Visual
Space in Human Parietal Cortex | 19 pages, 10 figures and 1 table. Tootell and Nasiriavanaki share
joint first authorship | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Personal space (PS) is the distance that people prefer to maintain between
themselves and unfamiliar others. Interpersonal intrusion into a given persons
PS evokes discomfort, and an urge to move further apart. We hypothesized that
in parietal cortex: 1. PS processing involves a previously-described
threat-sensitive ... | [
{
"created": "Mon, 8 Nov 2021 19:43:15 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Jan 2022 15:55:27 GMT",
"version": "v2"
},
{
"created": "Tue, 15 Mar 2022 03:53:56 GMT",
"version": "v3"
}
] | 2022-03-16 | [
[
"Tootell",
"Roger B. H.",
""
],
[
"Nasiriavanaki",
"Zahra",
""
],
[
"Babadi",
"Baktash",
""
],
[
"Greve",
"Douglas N.",
""
],
[
"Nasr",
"Shahin",
""
],
[
"Holt",
"Daphne J.",
""
]
] | Personal space (PS) is the distance that people prefer to maintain between themselves and unfamiliar others. Interpersonal intrusion into a given persons PS evokes discomfort, and an urge to move further apart. We hypothesized that in parietal cortex: 1. PS processing involves a previously-described threat-sensitive br... |
2308.03406 | Neta Maimon | Lior Molcho, Neta B. Maimon, Neomi Hezi, Talya Zeimer, Nathan
Intrator, Tanya Gurevich | Evaluation of Parkinsons disease with early diagnosis using
single-channel EEG features and auditory cognitive assessment | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Parkinsons disease (PD) diagnosis is challenging due to subtle early clinical
signs. F-DOPA PET is commonly used for early PD diagnosis. We explore the
potential of machine-learning (ML) based EEG features extracted from
single-channel EEG during auditory cognitive assessment as a noninvasive,
low-cost support for PD... | [
{
"created": "Mon, 7 Aug 2023 08:48:20 GMT",
"version": "v1"
}
] | 2023-08-08 | [
[
"Molcho",
"Lior",
""
],
[
"Maimon",
"Neta B.",
""
],
[
"Hezi",
"Neomi",
""
],
[
"Zeimer",
"Talya",
""
],
[
"Intrator",
"Nathan",
""
],
[
"Gurevich",
"Tanya",
""
]
] | Parkinsons disease (PD) diagnosis is challenging due to subtle early clinical signs. F-DOPA PET is commonly used for early PD diagnosis. We explore the potential of machine-learning (ML) based EEG features extracted from single-channel EEG during auditory cognitive assessment as a noninvasive, low-cost support for PD d... |
1212.1323 | David Saakian | David B. Saakian, Michael W. Deem, Chin Kun Hu | Finite population size effects in quasispecies models with single-peak
fitness landscape | 7 pages, 1 figure | EPL, 98 (2012) 18001 | 10.1209/0295-5075/98/18001 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider finite population size effects for Crow-Kimura and Eigen
quasispecies models with single peak fitness landscape. We formulate accurately
the iteration procedure for the finite population models, then derive
Hamilton-Jacobi equation (HJE) to describe the dynamic of the probability
distribution. The steady ... | [
{
"created": "Thu, 6 Dec 2012 13:26:28 GMT",
"version": "v1"
}
] | 2015-06-12 | [
[
"Saakian",
"David B.",
""
],
[
"Deem",
"Michael W.",
""
],
[
"Hu",
"Chin Kun",
""
]
] | We consider finite population size effects for Crow-Kimura and Eigen quasispecies models with single peak fitness landscape. We formulate accurately the iteration procedure for the finite population models, then derive Hamilton-Jacobi equation (HJE) to describe the dynamic of the probability distribution. The steady st... |
2108.02706 | K. Anton Feenstra | Halima Mouhib, Bas Stringer, Hugo van Ingen, Jose Gavald\'a-Garc\'ia,
Katharina Waury, Sanne Abeln, K. Anton Feenstra | Structure determination | This chapter is part of the book "Introduction to Protein Structural
Bioinformatics". The Preface arxiv:1801.09442 contains links to all the
(published) chapters | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | While many good textbooks are available on Protein Structure, Molecular
Simulations, Thermodynamics and Bioinformatics methods in general, there is no
good introductory level book for the field of Structural Bioinformatics. This
book aims to give an introduction into Structural Bioinformatics, which is
where the prev... | [
{
"created": "Thu, 5 Aug 2021 16:16:10 GMT",
"version": "v1"
}
] | 2021-08-06 | [
[
"Mouhib",
"Halima",
""
],
[
"Stringer",
"Bas",
""
],
[
"van Ingen",
"Hugo",
""
],
[
"Gavaldá-García",
"Jose",
""
],
[
"Waury",
"Katharina",
""
],
[
"Abeln",
"Sanne",
""
],
[
"Feenstra",
"K. Anton",
""
]
] | While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previo... |
q-bio/0608014 | Anders Eriksson | Anders Eriksson and Kristian Lindgren | The effect of finite population size on the evolutionary dynamics in
multi-person Prisoner's Dilemma | Accepted for publication in conference proceedings of ECCS'06 | null | null | null | q-bio.PE | null | We study the influence of stochastic effects due to finite population size in
the evolutionary dynamics of populations interacting in the multi-person
Prisoner's Dilemma game. This paper is an extension of the investigation
presented in a recent paper [Eriksson and Lindgren (2005), J. Theor. Biol.
232(3), 399]. One o... | [
{
"created": "Mon, 7 Aug 2006 14:56:00 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Eriksson",
"Anders",
""
],
[
"Lindgren",
"Kristian",
""
]
] | We study the influence of stochastic effects due to finite population size in the evolutionary dynamics of populations interacting in the multi-person Prisoner's Dilemma game. This paper is an extension of the investigation presented in a recent paper [Eriksson and Lindgren (2005), J. Theor. Biol. 232(3), 399]. One of ... |
1903.09535 | Laura Murphy | Laura Murphy, Anotida Madzvamuse | A moving grid finite element method applied to a mechanobiochemical
model for 3D cell migration | null | null | null | null | q-bio.CB math.NA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This work presents the development, analysis and numerical simulations of a
biophysical model for 3D cell deformation and movement, which couples
biochemical reactions and biomechanical forces. We propose a mechanobiochemical
model which considers the actin filament network as a viscoelastic and
contractile gel. The ... | [
{
"created": "Fri, 22 Mar 2019 14:48:14 GMT",
"version": "v1"
}
] | 2019-03-25 | [
[
"Murphy",
"Laura",
""
],
[
"Madzvamuse",
"Anotida",
""
]
] | This work presents the development, analysis and numerical simulations of a biophysical model for 3D cell deformation and movement, which couples biochemical reactions and biomechanical forces. We propose a mechanobiochemical model which considers the actin filament network as a viscoelastic and contractile gel. The me... |
1712.04987 | Kevin O'Regan | Aurora Rizza, Alexander V. Terekhov, Guglielmo Montone, Marta Olivetti
Belardinelli, J. Kevin O'Regan | Why early tactile speech aids may have failed: no perceptual integration
of tactile and auditory signals | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tactile speech aids, though extensively studied in the 1980s and 90s, never
became a commercial success. A hypothesis to explain this failure might be that
it is difficult to obtain true perceptual integration of a tactile signal with
information from auditory speech: exploitation of tactile cues from a tactile
aid m... | [
{
"created": "Tue, 28 Nov 2017 09:30:34 GMT",
"version": "v1"
}
] | 2017-12-15 | [
[
"Rizza",
"Aurora",
""
],
[
"Terekhov",
"Alexander V.",
""
],
[
"Montone",
"Guglielmo",
""
],
[
"Belardinelli",
"Marta Olivetti",
""
],
[
"O'Regan",
"J. Kevin",
""
]
] | Tactile speech aids, though extensively studied in the 1980s and 90s, never became a commercial success. A hypothesis to explain this failure might be that it is difficult to obtain true perceptual integration of a tactile signal with information from auditory speech: exploitation of tactile cues from a tactile aid mig... |
2005.01491 | Elmira Jalilian | Elmira Jalilian, William Raimes | Transcriptional profiling reveals fundamental differences in iPS-derived
progenitors of endothelial cells (PECs) versus adult circulating EPCs | null | null | null | null | q-bio.CB q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There are a number of different stem cell sources that have the potential to
be used as therapeutics in vascular degenerative diseases. On the one hand,
there are so called endothelial progenitor cells (EPCs), which are typically
derived from adult blood. They carry the marker CD34, but the true nature and
definition... | [
{
"created": "Mon, 4 May 2020 13:47:25 GMT",
"version": "v1"
}
] | 2020-05-05 | [
[
"Jalilian",
"Elmira",
""
],
[
"Raimes",
"William",
""
]
] | There are a number of different stem cell sources that have the potential to be used as therapeutics in vascular degenerative diseases. On the one hand, there are so called endothelial progenitor cells (EPCs), which are typically derived from adult blood. They carry the marker CD34, but the true nature and definition o... |
1104.2261 | Antti Niemi | Martin Lundgren, Antti J. Niemi and Fan Sha | On universal aspects of the left-handed helix region | 13 figures | null | null | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We inspect the geometry of proteins by identifying their backbones as framed
polygons. We find that the left-handed helix region of the Ramachandran map for
non-glycyl residues corresponds to an isolated and highly localized sector in
the orientation of the $C_\beta$ carbons, when viewed in a Frenet frame that is
cen... | [
{
"created": "Tue, 12 Apr 2011 16:25:49 GMT",
"version": "v1"
}
] | 2011-04-13 | [
[
"Lundgren",
"Martin",
""
],
[
"Niemi",
"Antti J.",
""
],
[
"Sha",
"Fan",
""
]
] | We inspect the geometry of proteins by identifying their backbones as framed polygons. We find that the left-handed helix region of the Ramachandran map for non-glycyl residues corresponds to an isolated and highly localized sector in the orientation of the $C_\beta$ carbons, when viewed in a Frenet frame that is cente... |
2203.13043 | Yannik Sch\"alte | Yannik Sch\"alte, Emmanuel Klinger, Emad Alamoudi, Jan Hasenauer | pyABC: Efficient and robust easy-to-use approximate Bayesian computation | 8 pages, 1 figure | null | null | null | q-bio.QM stat.CO | http://creativecommons.org/licenses/by/4.0/ | The Python package pyABC provides a framework for approximate Bayesian
computation (ABC), a likelihood-free parameter inference method popular in many
research areas. At its core, it implements a sequential Monte-Carlo (SMC)
scheme, with various algorithms to adapt to the problem structure and
automatically tune hype... | [
{
"created": "Thu, 24 Mar 2022 12:44:21 GMT",
"version": "v1"
}
] | 2022-03-25 | [
[
"Schälte",
"Yannik",
""
],
[
"Klinger",
"Emmanuel",
""
],
[
"Alamoudi",
"Emad",
""
],
[
"Hasenauer",
"Jan",
""
]
] | The Python package pyABC provides a framework for approximate Bayesian computation (ABC), a likelihood-free parameter inference method popular in many research areas. At its core, it implements a sequential Monte-Carlo (SMC) scheme, with various algorithms to adapt to the problem structure and automatically tune hyperp... |
1803.11559 | Eve Armstrong | Eve Armstrong | Colonel Mustard in the Aviary with the Candlestick: a limit cycle
attractor transitions to a stable focus via supercritical Andronov-Hopf
bifurcation | 5 figures, 8 pages | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We establish the means by which Mr. Boddy came to transition from a stable
trajectory within the global phase space of Philadelphia, Pennsylvania to a
stable point on the cement floor of an aviary near the west bank of the
Schuylkill River. There exist no documented murder motives, and so the
dynamical interaction le... | [
{
"created": "Sun, 1 Apr 2018 18:22:01 GMT",
"version": "v1"
},
{
"created": "Wed, 11 Jul 2018 19:34:24 GMT",
"version": "v2"
},
{
"created": "Wed, 25 Jul 2018 23:50:15 GMT",
"version": "v3"
}
] | 2018-07-27 | [
[
"Armstrong",
"Eve",
""
]
] | We establish the means by which Mr. Boddy came to transition from a stable trajectory within the global phase space of Philadelphia, Pennsylvania to a stable point on the cement floor of an aviary near the west bank of the Schuylkill River. There exist no documented murder motives, and so the dynamical interaction lead... |
1702.04088 | Andreas Gunawan | Andreas Gunawan | Solving Tree Containment Problem for Reticulation-visible Networks with
Optimal Running Time | null | null | null | null | q-bio.PE cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tree containment problem is a fundamental problem in phylogenetic study, as
it is used to verify a network model. It asks whether a given network contain a
subtree that resembles a binary tree. The problem is NP-complete in general,
even in the class of binary network. Recently, it was proven to be solvable in
cubic ... | [
{
"created": "Tue, 14 Feb 2017 06:15:28 GMT",
"version": "v1"
}
] | 2017-02-15 | [
[
"Gunawan",
"Andreas",
""
]
] | Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in the class of binary network. Recently, it was proven to be solvable in cubic ti... |
1802.01980 | Jingjing Xu | Shengyong Xu, Jingjing Xu and Rujun Dai | Layered structure and leveled function of a human brain | null | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The anatomically layered structure of a human brain results in leveled
functions. In all these levels of different functions, comparison, feedback and
imitation are the universal and crucial mechanisms. Languages, symbols and
tools play key roles in the development of human brain and entire civilization.
| [
{
"created": "Sun, 4 Feb 2018 05:58:42 GMT",
"version": "v1"
}
] | 2018-02-07 | [
[
"Xu",
"Shengyong",
""
],
[
"Xu",
"Jingjing",
""
],
[
"Dai",
"Rujun",
""
]
] | The anatomically layered structure of a human brain results in leveled functions. In all these levels of different functions, comparison, feedback and imitation are the universal and crucial mechanisms. Languages, symbols and tools play key roles in the development of human brain and entire civilization. |
1303.5785 | Dan DeBlasio | Dan DeBlasio and Jennifer Wiscaver | SICLE: A high-throughput tool for extracting evolutionary relationships
from phylogenetic trees | 8 pages, 4 figures in journal submission format | null | 10.7717/peerj.2359 | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | We present the phylogeny analysis software SICLE (Sister Clade Extractor), an
easy-to-use, high- throughput tool to describe the nearest neighbors to a node
of interest in a phylogenetic tree as well as the support value for the
relationship. The application is a command line utility that can be embedded
into a phylo... | [
{
"created": "Fri, 22 Mar 2013 22:07:04 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Jun 2016 20:06:29 GMT",
"version": "v2"
},
{
"created": "Fri, 17 Jun 2016 00:42:43 GMT",
"version": "v3"
}
] | 2016-08-24 | [
[
"DeBlasio",
"Dan",
""
],
[
"Wiscaver",
"Jennifer",
""
]
] | We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high- throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phyloge... |
1301.2397 | Sepehr Ehsani | Sepehr Ehsani | Macro-trends in research on the central dogma of molecular biology | 9 pages, 2 figures, 1 supplementary table, 3 supplementary figures | null | null | null | q-bio.QM cs.DL | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The central dogma of molecular biology, formulated more than five decades
ago, compartmentalized information exchange in the cell into the DNA, RNA and
protein domains. This formalization has served as an implicit thematic
distinguisher for cell biological research ever since. However, a clear account
of the distribu... | [
{
"created": "Fri, 11 Jan 2013 07:00:57 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Oct 2013 22:18:25 GMT",
"version": "v2"
}
] | 2013-10-09 | [
[
"Ehsani",
"Sepehr",
""
]
] | The central dogma of molecular biology, formulated more than five decades ago, compartmentalized information exchange in the cell into the DNA, RNA and protein domains. This formalization has served as an implicit thematic distinguisher for cell biological research ever since. However, a clear account of the distributi... |
2112.01081 | Santiago Rivera | Pauline Zipfel (CERMN), Christophe Rochais (CERMN), K\'evin Baranger
(INP), Santiago Rivera (INP), Patrick Dallemagne (CERMN) | Matrix metalloproteinases as new targets in Alzheimer's disease:
Opportunities and Challenges | null | Journal of Medicinal Chemistry, American Chemical Society, 2020 | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although matrix metalloproteinases (MMPs) are implicated in the regulation of
numerous physiological processes, evidences of their pathological roles have
also been obtained in the last decades, making MMPs attractive therapeutic
targets for several diseases. Recent discoveries of their involvement in
central nervous... | [
{
"created": "Thu, 2 Dec 2021 09:49:20 GMT",
"version": "v1"
}
] | 2021-12-03 | [
[
"Zipfel",
"Pauline",
"",
"CERMN"
],
[
"Rochais",
"Christophe",
"",
"CERMN"
],
[
"Baranger",
"Kévin",
"",
"INP"
],
[
"Rivera",
"Santiago",
"",
"INP"
],
[
"Dallemagne",
"Patrick",
"",
"CERMN"
]
] | Although matrix metalloproteinases (MMPs) are implicated in the regulation of numerous physiological processes, evidences of their pathological roles have also been obtained in the last decades, making MMPs attractive therapeutic targets for several diseases. Recent discoveries of their involvement in central nervous s... |
2308.00298 | Hyunjoong Kim | Hyunjoong Kim, Yoichiro Mori, Joshua B Plotkin | Finite population effects on optimal communication for social foragers | null | null | null | null | q-bio.PE math.PR physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Foraging is crucial for animals to survive. Many species forage in groups, as
individuals communicate to share information about the location of available
resources. For example, eusocial foragers, such as honey bees and many ants,
recruit members from their central hive or nest to a known foraging site.
However, the... | [
{
"created": "Tue, 1 Aug 2023 05:39:49 GMT",
"version": "v1"
}
] | 2023-08-02 | [
[
"Kim",
"Hyunjoong",
""
],
[
"Mori",
"Yoichiro",
""
],
[
"Plotkin",
"Joshua B",
""
]
] | Foraging is crucial for animals to survive. Many species forage in groups, as individuals communicate to share information about the location of available resources. For example, eusocial foragers, such as honey bees and many ants, recruit members from their central hive or nest to a known foraging site. However, the o... |
1810.00501 | Rohan Maddamsetti | Rohan Maddamsetti and Jacob Bower-Bir | Parallels and promising directions in the study of genetic, cultural,
and moral evolution | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Experimental evolution has yielded surprising insights into human history and
evolution by shedding light on the roles of chance and contingency in history
and evolution, and on the deep evolutionary roots of cooperation, conflict and
kin discrimination. We argue that an interesting research direction would be to
dev... | [
{
"created": "Mon, 1 Oct 2018 01:55:38 GMT",
"version": "v1"
}
] | 2018-10-02 | [
[
"Maddamsetti",
"Rohan",
""
],
[
"Bower-Bir",
"Jacob",
""
]
] | Experimental evolution has yielded surprising insights into human history and evolution by shedding light on the roles of chance and contingency in history and evolution, and on the deep evolutionary roots of cooperation, conflict and kin discrimination. We argue that an interesting research direction would be to devel... |
1406.1391 | Donald Forsdyke Dr. | Donald R. Forsdyke | 'A Vehicle of Symbols and Nothing More.' George Romanes, Theory of Mind,
Information, and Samuel Butler | Accepted for publication in History of Psychiatry. 31 pages including
3 footnotes. Based on a lecture given at Santa Clara University, February
28th 2014, at a Bannan Institute Symposium on 'Science and Seeking:
Rethinking the God Question in the Lab, Cosmos, and Classroom.' - See more at
either http://www.yout... | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Today's 'theory of mind' (ToM) concept is rooted in the distinction of
nineteenth century philosopher William Clifford between 'objects' that can be
directly perceived, and 'ejects,' such as the mind of another person, which are
inferred from one's subjective knowledge of one's own mind. A founder, with
Charles Darwi... | [
{
"created": "Wed, 4 Jun 2014 03:04:49 GMT",
"version": "v1"
},
{
"created": "Thu, 13 Nov 2014 22:19:37 GMT",
"version": "v2"
}
] | 2014-11-17 | [
[
"Forsdyke",
"Donald R.",
""
]
] | Today's 'theory of mind' (ToM) concept is rooted in the distinction of nineteenth century philosopher William Clifford between 'objects' that can be directly perceived, and 'ejects,' such as the mind of another person, which are inferred from one's subjective knowledge of one's own mind. A founder, with Charles Darwin,... |
1605.07094 | Sebastian Weichwald | Sebastian Weichwald, Tatiana Fomina, Bernhard Sch\"olkopf, Moritz
Grosse-Wentrup | A note on the expected minimum error probability in equientropic
channels | null | null | null | null | q-bio.NC cs.IT cs.LG math.IT stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While the channel capacity reflects a theoretical upper bound on the
achievable information transmission rate in the limit of infinitely many bits,
it does not characterise the information transfer of a given encoding routine
with finitely many bits. In this note, we characterise the quality of a code
(i. e. a given ... | [
{
"created": "Mon, 23 May 2016 17:04:57 GMT",
"version": "v1"
},
{
"created": "Tue, 4 Apr 2017 16:55:42 GMT",
"version": "v2"
}
] | 2017-04-05 | [
[
"Weichwald",
"Sebastian",
""
],
[
"Fomina",
"Tatiana",
""
],
[
"Schölkopf",
"Bernhard",
""
],
[
"Grosse-Wentrup",
"Moritz",
""
]
] | While the channel capacity reflects a theoretical upper bound on the achievable information transmission rate in the limit of infinitely many bits, it does not characterise the information transfer of a given encoding routine with finitely many bits. In this note, we characterise the quality of a code (i. e. a given en... |
1510.03241 | Tom Lorimer | Florian Gomez, Tom Lorimer, Ruedi Stoop | Hopf-type neurons increase input-sensitivity by forming forcing-coupled
ensembles | null | null | null | null | q-bio.NC nlin.AO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Astounding properties of biological sensors can often be mapped onto a
dynamical system in the vicinity a bifurcation. For mammalian hearing, a Hopf
bifurcation description has been shown to work across a whole range of scales,
from individual hair bundles to whole regions of the cochlea. We reveal here
the origin of... | [
{
"created": "Mon, 12 Oct 2015 11:56:39 GMT",
"version": "v1"
}
] | 2015-10-13 | [
[
"Gomez",
"Florian",
""
],
[
"Lorimer",
"Tom",
""
],
[
"Stoop",
"Ruedi",
""
]
] | Astounding properties of biological sensors can often be mapped onto a dynamical system in the vicinity a bifurcation. For mammalian hearing, a Hopf bifurcation description has been shown to work across a whole range of scales, from individual hair bundles to whole regions of the cochlea. We reveal here the origin of t... |
q-bio/0508035 | Jonathan Z. Simon | Jonathan Z. Simon and Yadong Wang | Fully Complex Magnetoencephalography | 23 pages, 1 table, 5 figures; to appear in Journal of Neuroscience
Methods | null | 10.1016/j.jneumeth.2005.05.005 | null | q-bio.NC q-bio.QM | null | Complex numbers appear naturally in biology whenever a system can be analyzed
in the frequency domain, such as physiological data from magnetoencephalography
(MEG). For example, the MEG steady state response to a modulated auditory
stimulus generates a complex magnetic field for each MEG channel, equal to the
Fourier... | [
{
"created": "Thu, 25 Aug 2005 17:19:29 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Simon",
"Jonathan Z.",
""
],
[
"Wang",
"Yadong",
""
]
] | Complex numbers appear naturally in biology whenever a system can be analyzed in the frequency domain, such as physiological data from magnetoencephalography (MEG). For example, the MEG steady state response to a modulated auditory stimulus generates a complex magnetic field for each MEG channel, equal to the Fourier t... |
1410.2973 | Peter Jagers | Kais Hamza, Peter Jagers, and Fima C. Klebaner | On the Establishment, Persistence, and Inevitable Extinction of
Populations | null | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Comprehensive models of stochastic, clonally reproducing populations are
defined in terms of general branching processes, allowing birth during maternal
life, as for higher organisms, or by splitting, as in cell division. The
populations are assumed to start small, by mutation or immigration, reproduce
supercriticall... | [
{
"created": "Sat, 11 Oct 2014 08:32:45 GMT",
"version": "v1"
}
] | 2014-10-14 | [
[
"Hamza",
"Kais",
""
],
[
"Jagers",
"Peter",
""
],
[
"Klebaner",
"Fima C.",
""
]
] | Comprehensive models of stochastic, clonally reproducing populations are defined in terms of general branching processes, allowing birth during maternal life, as for higher organisms, or by splitting, as in cell division. The populations are assumed to start small, by mutation or immigration, reproduce supercritically ... |
2007.06468 | Lucas B\"ottcher | Lucas B\"ottcher and Hans Gersbach | Incentivizing Narrow-Spectrum Antibiotic Development with Refunding | 21 pages and 10 figures | Bull Math Biol 84, 59 (2022) | 10.1007/s11538-022-01013-7 | null | q-bio.PE econ.GN q-fin.EC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The rapid rise of antibiotic resistance is a serious threat to global public
health. Without further incentives, pharmaceutical companies have little
interest in developing antibiotics, since the success probability is low and
development costs are huge. The situation is exacerbated by the "antibiotics
dilemma": Deve... | [
{
"created": "Mon, 13 Jul 2020 16:00:13 GMT",
"version": "v1"
}
] | 2022-06-22 | [
[
"Böttcher",
"Lucas",
""
],
[
"Gersbach",
"Hans",
""
]
] | The rapid rise of antibiotic resistance is a serious threat to global public health. Without further incentives, pharmaceutical companies have little interest in developing antibiotics, since the success probability is low and development costs are huge. The situation is exacerbated by the "antibiotics dilemma": Develo... |
1312.4440 | Vasily Ogryzko V | Vasily Ogryzko | Comment on Masanari Asano et al. A model of epigenetic evolution based
on theory of open quantum systems. Syst Synth Biol, 2013 | 4 pages | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The comment mostly concerns mis-representation of my position on Quantum
Biology, by stating that I am 'reducing cell's behavior to quantum particles
inside the cell'. I contrast my position with that of McFadden-Al-Khalili, as
well as with the position of Asano et al. I also advertise an idea, described
in our lates... | [
{
"created": "Mon, 16 Dec 2013 18:08:07 GMT",
"version": "v1"
}
] | 2013-12-17 | [
[
"Ogryzko",
"Vasily",
""
]
] | The comment mostly concerns mis-representation of my position on Quantum Biology, by stating that I am 'reducing cell's behavior to quantum particles inside the cell'. I contrast my position with that of McFadden-Al-Khalili, as well as with the position of Asano et al. I also advertise an idea, described in our latest ... |
1901.06790 | Yu-Hui Lin | Yu-Hui Lin, Joshua S. Weitz | Spatial interactions and oscillatory tragedies of the commons | 5 pages and 3 figures in main text, 9 pages and 4 figures in
supplementary material | Phys. Rev. Lett. 122, 148102 (2019) | 10.1103/PhysRevLett.122.148102 | null | q-bio.PE physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | A tragedy of the commons (TOC) occurs when individuals acting in their own
self-interest deplete commonly-held resources, leading to a worse outcome than
had they cooperated. Over time, the depletion of resources can change
incentives for subsequent actions. Here, we investigate long-term feedback
between game and en... | [
{
"created": "Mon, 21 Jan 2019 04:49:02 GMT",
"version": "v1"
}
] | 2019-04-17 | [
[
"Lin",
"Yu-Hui",
""
],
[
"Weitz",
"Joshua S.",
""
]
] | A tragedy of the commons (TOC) occurs when individuals acting in their own self-interest deplete commonly-held resources, leading to a worse outcome than had they cooperated. Over time, the depletion of resources can change incentives for subsequent actions. Here, we investigate long-term feedback between game and envi... |
2302.09445 | Siddhartha Srivastava | Patrick C. Kinnunen, Siddhartha Srivastava, Zhenlin Wang, Kenneth K.Y.
Ho, Brock A. Humphries, Siyi Chen, Jennifer J. Linderman, Gary D. Luker,
Kathryn E. Luker, Krishna Garikipati | Partial differential equation-based inference of migration and
proliferation mechanisms in cancer cell populations | null | null | null | null | q-bio.CB | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Targeting signaling pathways that drive cancer cell migration or
proliferation is a common therapeutic approach. A popular experimental
technique, the scratch assay, measures the migration and proliferation-driven
cell monolayer formation. Scratch assay analyses do not differentiate between
migration and proliferatio... | [
{
"created": "Sun, 19 Feb 2023 00:23:46 GMT",
"version": "v1"
}
] | 2023-02-21 | [
[
"Kinnunen",
"Patrick C.",
""
],
[
"Srivastava",
"Siddhartha",
""
],
[
"Wang",
"Zhenlin",
""
],
[
"Ho",
"Kenneth K. Y.",
""
],
[
"Humphries",
"Brock A.",
""
],
[
"Chen",
"Siyi",
""
],
[
"Linderman",
"Jennifer J.... | Targeting signaling pathways that drive cancer cell migration or proliferation is a common therapeutic approach. A popular experimental technique, the scratch assay, measures the migration and proliferation-driven cell monolayer formation. Scratch assay analyses do not differentiate between migration and proliferation ... |
1711.02994 | Harish Chandra | Rama Bhargava and Harish Chandra | Study of bioheat transfer phase change during cryosurgery for an
irregular tumor tissue using EFGM | 16 pages and 9 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cryosurgery has been consistently used as an effective treatment to eradicate
irregular tumor tissues. During this process, many difficulties occur such as
intense cooling may also damage the neighboring normal tissues due to the
release of large amount of cold from the cooling probe. In order to protect the
normal t... | [
{
"created": "Mon, 6 Nov 2017 19:38:22 GMT",
"version": "v1"
}
] | 2017-11-09 | [
[
"Bhargava",
"Rama",
""
],
[
"Chandra",
"Harish",
""
]
] | Cryosurgery has been consistently used as an effective treatment to eradicate irregular tumor tissues. During this process, many difficulties occur such as intense cooling may also damage the neighboring normal tissues due to the release of large amount of cold from the cooling probe. In order to protect the normal tis... |
1905.12100 | Owen Marschall | Owen Marschall, Kyunghyun Cho, Cristina Savin | Using local plasticity rules to train recurrent neural networks | Abstract submission to Computational and Systems Neuroscience
(Cosyne) 2019, accepted | null | null | null | q-bio.NC cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To learn useful dynamics on long time scales, neurons must use plasticity
rules that account for long-term, circuit-wide effects of synaptic changes. In
other words, neural circuits must solve a credit assignment problem to
appropriately assign responsibility for global network behavior to individual
circuit componen... | [
{
"created": "Tue, 28 May 2019 21:32:26 GMT",
"version": "v1"
}
] | 2019-05-30 | [
[
"Marschall",
"Owen",
""
],
[
"Cho",
"Kyunghyun",
""
],
[
"Savin",
"Cristina",
""
]
] | To learn useful dynamics on long time scales, neurons must use plasticity rules that account for long-term, circuit-wide effects of synaptic changes. In other words, neural circuits must solve a credit assignment problem to appropriately assign responsibility for global network behavior to individual circuit components... |
1706.02187 | Victor Manuel Trejos Montoya | Ang\'elica M. Alzate Iba\~nez, Carlos Ocampo-Martinez, Carlos A.
Cardona Alzate, V\'ictor M. Trejos M | Monitoring management criterion of an anaerobic digester using an
explicit model based on temperature and pH | 20 pages, 9 figures, full paper | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, the stability analysis of an anaerobic digestion process is
presented. The analysis is performed using a simplified mathematical model,
which includes explicit temperature and pH dependence on kinetic growth rates.
A detailed nonlinear and bifurcation analyses are performed in order to study
the effect... | [
{
"created": "Tue, 6 Jun 2017 15:44:06 GMT",
"version": "v1"
}
] | 2017-06-08 | [
[
"Ibañez",
"Angélica M. Alzate",
""
],
[
"Ocampo-Martinez",
"Carlos",
""
],
[
"Alzate",
"Carlos A. Cardona",
""
],
[
"M",
"Víctor M. Trejos",
""
]
] | In this paper, the stability analysis of an anaerobic digestion process is presented. The analysis is performed using a simplified mathematical model, which includes explicit temperature and pH dependence on kinetic growth rates. A detailed nonlinear and bifurcation analyses are performed in order to study the effects ... |
2401.06823 | Pengyi Yang | Manoj M Wagle, Siqu Long, Carissa Chen, Chunlei Liu, Pengyi Yang | Interpretable deep learning in single-cell omics | null | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by/4.0/ | Recent developments in single-cell omics technologies have enabled the
quantification of molecular profiles in individual cells at an unparalleled
resolution. Deep learning, a rapidly evolving sub-field of machine learning,
has instilled a significant interest in single-cell omics research due to its
remarkable succe... | [
{
"created": "Thu, 11 Jan 2024 23:59:37 GMT",
"version": "v1"
}
] | 2024-01-17 | [
[
"Wagle",
"Manoj M",
""
],
[
"Long",
"Siqu",
""
],
[
"Chen",
"Carissa",
""
],
[
"Liu",
"Chunlei",
""
],
[
"Yang",
"Pengyi",
""
]
] | Recent developments in single-cell omics technologies have enabled the quantification of molecular profiles in individual cells at an unparalleled resolution. Deep learning, a rapidly evolving sub-field of machine learning, has instilled a significant interest in single-cell omics research due to its remarkable success... |
1704.01379 | Valentine Svensson | Valentine Svensson, Roser Vento-Tormo, Sarah A Teichmann | Exponential scaling of single-cell RNA-seq in the last decade | 13 pages, 1 figure. Manuscript restructured for readability, with
improved language | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | The ability to measure the transcriptomes of single cells has only been
feasible for a few years, and is becoming an extremely popular assay. While
many types of analysis and questions can be answered using single cell
RNA-sequencing, a central focus is the ability to survey the diversity of cell
types within a sampl... | [
{
"created": "Wed, 5 Apr 2017 12:18:29 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Aug 2017 16:54:08 GMT",
"version": "v2"
}
] | 2017-08-09 | [
[
"Svensson",
"Valentine",
""
],
[
"Vento-Tormo",
"Roser",
""
],
[
"Teichmann",
"Sarah A",
""
]
] | The ability to measure the transcriptomes of single cells has only been feasible for a few years, and is becoming an extremely popular assay. While many types of analysis and questions can be answered using single cell RNA-sequencing, a central focus is the ability to survey the diversity of cell types within a sample.... |
1008.5390 | Hesam Dashti | Hesam T. Dashti, Jernej Tonejc, Adel Ardalan, Alireza F. Siahpirani,
Sabrina Guettes, Zohreh Sharif, Liya Wang, Amir H. Assadi | Applications of Machine Learning Methods to Quantifying Phenotypic
Traits that Distinguish the Wild Type from the Mutant Arabidopsis Thaliana
Seedlings during Root Gravitropism | International Conference on Bioinformatics and Computational Biology,
WorldComp 2010 | null | null | null | q-bio.QM cs.CE cs.LG q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Post-genomic research deals with challenging problems in screening genomes of
organisms for particular functions or potential for being the targets of
genetic engineering for desirable biological features. 'Phenotyping' of wild
type and mutants is a time-consuming and costly effort by many individuals.
This article i... | [
{
"created": "Tue, 31 Aug 2010 18:54:33 GMT",
"version": "v1"
}
] | 2010-09-06 | [
[
"Dashti",
"Hesam T.",
""
],
[
"Tonejc",
"Jernej",
""
],
[
"Ardalan",
"Adel",
""
],
[
"Siahpirani",
"Alireza F.",
""
],
[
"Guettes",
"Sabrina",
""
],
[
"Sharif",
"Zohreh",
""
],
[
"Wang",
"Liya",
""
],
[... | Post-genomic research deals with challenging problems in screening genomes of organisms for particular functions or potential for being the targets of genetic engineering for desirable biological features. 'Phenotyping' of wild type and mutants is a time-consuming and costly effort by many individuals. This article is ... |
1009.0857 | Chris Wiggins PhD | Jonathan E. Bronson, Jake M. Hofman, Jingyi Fei, Ruben L. Gonzalez
Jr., Chris H. Wiggins | Graphical models for inferring single molecule dynamics | 22 pages, 5 figures; Journal special issue for workshop papers from
"New Problems and Methods in Computational Biology" A workshop at the
Twenty-Third Annual Conference on Neural Information Processing Systems (NIPS
2009) Whistler, BC, Canada, December 11 or 12, 2009. (cf.
http://videolectures.net/nipsworkshops... | null | null | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: The recent explosion of experimental techniques in single
molecule biophysics has generated a variety of novel time series data requiring
equally novel computational tools for analysis and inference. This article
describes in general terms how graphical modeling may be used to learn from
biophysical time ... | [
{
"created": "Sat, 4 Sep 2010 18:15:19 GMT",
"version": "v1"
}
] | 2010-09-07 | [
[
"Bronson",
"Jonathan E.",
""
],
[
"Hofman",
"Jake M.",
""
],
[
"Fei",
"Jingyi",
""
],
[
"Gonzalez",
"Ruben L.",
"Jr."
],
[
"Wiggins",
"Chris H.",
""
]
] | Background: The recent explosion of experimental techniques in single molecule biophysics has generated a variety of novel time series data requiring equally novel computational tools for analysis and inference. This article describes in general terms how graphical modeling may be used to learn from biophysical time se... |
q-bio/0505052 | Antonio Trovato | Jayanth R. Banavar, Marek Cieplak, Alessandro Flammini, Trinh X.
Hoang, Randall D. Kamien, Timothy Lezon, Davide Marenduzzo, Amos Maritan,
Flavio Seno, Yehuda Snir, Antonio Trovato | Geometry of proteins: hydrogen bonding, sterics and marginally compact
tubes | 12 pages, no figures, revised version accepted for publication in
Phisycal Review E | null | 10.1103/PhysRevE.73.031921 | null | q-bio.BM | null | The functionality of proteins is related to their structure in the native
state. Protein structures are made up of emergent building blocks of helices
and almost planar sheets. A simple coarse-grained geometrical model of a
flexible tube barely subject to compaction provides a unified framework for
understanding the ... | [
{
"created": "Fri, 27 May 2005 10:30:38 GMT",
"version": "v1"
},
{
"created": "Mon, 20 Mar 2006 11:39:44 GMT",
"version": "v2"
}
] | 2009-11-11 | [
[
"Banavar",
"Jayanth R.",
""
],
[
"Cieplak",
"Marek",
""
],
[
"Flammini",
"Alessandro",
""
],
[
"Hoang",
"Trinh X.",
""
],
[
"Kamien",
"Randall D.",
""
],
[
"Lezon",
"Timothy",
""
],
[
"Marenduzzo",
"Davide",
... | The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube barely subject to compaction provides a unified framework for understanding the co... |
1803.08541 | Andrea Avena-Koenigsberger | Andrea Avena-Koenigsberger, Xiaoran Yan, Artemy Kolchinsky, Martijn
van den Heuvel, Patric Hagmann and Olaf Sporns | A spectrum of routing strategies for brain networks | null | null | 10.1371/journal.pcbi.1006833 | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Communication of signals among nodes in a complex network poses fundamental
problems of efficiency and cost. Routing of messages along shortest paths
requires global information about the topology, while spreading by diffusion,
which operates according to local topological features, is informationally
"cheap" but ine... | [
{
"created": "Thu, 22 Mar 2018 18:46:21 GMT",
"version": "v1"
}
] | 2019-06-19 | [
[
"Avena-Koenigsberger",
"Andrea",
""
],
[
"Yan",
"Xiaoran",
""
],
[
"Kolchinsky",
"Artemy",
""
],
[
"Heuvel",
"Martijn van den",
""
],
[
"Hagmann",
"Patric",
""
],
[
"Sporns",
"Olaf",
""
]
] | Communication of signals among nodes in a complex network poses fundamental problems of efficiency and cost. Routing of messages along shortest paths requires global information about the topology, while spreading by diffusion, which operates according to local topological features, is informationally "cheap" but ineff... |
0710.4030 | Benjamin Audit | Edward-Benedict Brodie (of Brodie) (Phys-ENS), Samuel Nicolay
(Phys-ENS), Marie Touchon (CGM), Benjamin Audit (Phys-ENS), Yves
D'Aubenton-Carafa (CGM), Claude Thermes (CGM), Alain Arneodo (Phys-ENS) | From DNA sequence analysis to modeling replication in the human genome | null | Physical Review Letters 94, 24 (2005) 248103 | null | null | q-bio.GN | null | We explore the large-scale behavior of nucleotide compositional strand
asymmetries along human chromosomes. As we observe for 7 of 9 origins of
replication experimentally identified so far, the (TA+GC) skew displays rather
sharp upward jumps, with a linear decreasing profile in between two successive
jumps. We presen... | [
{
"created": "Mon, 22 Oct 2007 12:01:37 GMT",
"version": "v1"
}
] | 2007-10-23 | [
[
"Brodie",
"Edward-Benedict",
"",
"of Brodie"
],
[
"Nicolay",
"Samuel",
"",
"Phys-ENS"
],
[
"Touchon",
"Marie",
"",
"CGM"
],
[
"Audit",
"Benjamin",
"",
"Phys-ENS"
],
[
"D'Aubenton-Carafa",
"Yves",
"",
"CGM"
],
[
... | We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward jumps, with a linear decreasing profile in between two successive jumps. We present ... |
1501.05006 | Sarthok Sircar | S. Sircar and J.N. Majumdar | Chapter 9 TISSUE ENGINEERING | Book chapter: 17 pages, 18 figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tissue Engineering (TE) is an interdisciplinary field dealing with the
principles of engineering and life sciences toward the development of
biological substitutes that restore, maintain, or improve tissue function or a
whole organ. Currently, TE is emerging as an invaluable field of study and is
one of the most prom... | [
{
"created": "Tue, 20 Jan 2015 22:33:41 GMT",
"version": "v1"
}
] | 2015-01-22 | [
[
"Sircar",
"S.",
""
],
[
"Majumdar",
"J. N.",
""
]
] | Tissue Engineering (TE) is an interdisciplinary field dealing with the principles of engineering and life sciences toward the development of biological substitutes that restore, maintain, or improve tissue function or a whole organ. Currently, TE is emerging as an invaluable field of study and is one of the most promis... |
q-bio/0403002 | Steven N. Evans | David Steinsaltz, Steven N. Evans, Kenneth W. Wachter | A generalized model of mutation-selection balance with applications to
aging | 20 pages Updated to include more historical comment and references to
the literature, as well as to make clear how our non-linear, non-Markovian
model differs from previous linear, Markovian particle system and
measure-valued diffusion models. Further updated to take into account
referee's comments | null | null | null | q-bio.PE math.PR | null | A probability model is presented for the dynamics of mutation-selection
balance in a haploid infinite-population infinite-sites setting sufficiently
general to cover mutation-driven changes in full age-specific demographic
schedules. The model accommodates epistatic as well as additive selective
costs. Closed form ch... | [
{
"created": "Mon, 1 Mar 2004 17:24:39 GMT",
"version": "v1"
},
{
"created": "Wed, 2 Jun 2004 18:35:44 GMT",
"version": "v2"
},
{
"created": "Thu, 7 Oct 2004 03:53:48 GMT",
"version": "v3"
}
] | 2007-05-23 | [
[
"Steinsaltz",
"David",
""
],
[
"Evans",
"Steven N.",
""
],
[
"Wachter",
"Kenneth W.",
""
]
] | A probability model is presented for the dynamics of mutation-selection balance in a haploid infinite-population infinite-sites setting sufficiently general to cover mutation-driven changes in full age-specific demographic schedules. The model accommodates epistatic as well as additive selective costs. Closed form char... |
q-bio/0701008 | Arne Traulsen | Jorge M. Pacheco, Arne Traulsen, Martin A. Nowak | Co-evolution of strategy and structure in complex networks with
dynamical linking | null | Physical Review Letters 97, 025103 (2006) | 10.1103/PhysRevLett.97.258103 | null | q-bio.PE | null | Here we introduce a model in which individuals differ in the rate at which
they seek new interactions with others, making rational decisions modeled as
general symmetric two-player games. Once a link between two individuals has
formed, the productivity of this link is evaluated. Links can be broken off at
different r... | [
{
"created": "Wed, 3 Jan 2007 23:07:49 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Pacheco",
"Jorge M.",
""
],
[
"Traulsen",
"Arne",
""
],
[
"Nowak",
"Martin A.",
""
]
] | Here we introduce a model in which individuals differ in the rate at which they seek new interactions with others, making rational decisions modeled as general symmetric two-player games. Once a link between two individuals has formed, the productivity of this link is evaluated. Links can be broken off at different rat... |
1208.0537 | Tom Michoel | Jianlong Qi, Tom Michoel | Context-specific transcriptional regulatory network inference from
global gene expression maps using double two-way t-tests | 8 pages, 9 figures, 2 tables; software available at
http://twixtrix.googlecode.com | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transcriptional regulatory network inference methods have been studied for
years. Most of them relie on complex mathematical and algorithmic concepts,
making them hard to adapt, re-implement or integrate with other methods. To
address this problem, we introduce a novel method based on a minimal
statistical model for ... | [
{
"created": "Thu, 2 Aug 2012 16:41:29 GMT",
"version": "v1"
}
] | 2012-08-03 | [
[
"Qi",
"Jianlong",
""
],
[
"Michoel",
"Tom",
""
]
] | Transcriptional regulatory network inference methods have been studied for years. Most of them relie on complex mathematical and algorithmic concepts, making them hard to adapt, re-implement or integrate with other methods. To address this problem, we introduce a novel method based on a minimal statistical model for ob... |
2207.06630 | Fikret Aydin | Fikret Aydin (1), Konstantia Georgouli (1), Gautham Dharuman (1),
James N. Glosli (1), Felice C. Lightstone (1), Helgi I. Ing\'olfsson (1),
Peer-Timo Bremer (2), Harsh Bhatia (2) ((1) Physical & Life Sciences,
Lawrence Livermore National Laboratory, (2) Center for Applied Scientific
Computing, Lawrence Livermor... | Identifying Orientation-specific Lipid-protein Fingerprints using Deep
Learning | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Improved understanding of the relation between the behavior of RAS and RAF
proteins and the local lipid environment in the cell membrane is critical for
getting insights into the mechanisms underlying cancer formation. In this work,
we employ deep learning (DL) to learn this relationship by predicting protein
orienta... | [
{
"created": "Thu, 14 Jul 2022 03:01:49 GMT",
"version": "v1"
}
] | 2022-07-15 | [
[
"Aydin",
"Fikret",
""
],
[
"Georgouli",
"Konstantia",
""
],
[
"Dharuman",
"Gautham",
""
],
[
"Glosli",
"James N.",
""
],
[
"Lightstone",
"Felice C.",
""
],
[
"Ingólfsson",
"Helgi I.",
""
],
[
"Bremer",
"Peer-Ti... | Improved understanding of the relation between the behavior of RAS and RAF proteins and the local lipid environment in the cell membrane is critical for getting insights into the mechanisms underlying cancer formation. In this work, we employ deep learning (DL) to learn this relationship by predicting protein orientati... |
1010.0339 | Jin Yang | Qiang Chang and Jin Yang | Monte Carlo Algorithm for Simulating Reversible Aggregation of Multisite
Particles | 8 pages, 3 figures | Physical Review E, 83, 056701, 2011 | 10.1103/PhysRevE.83.056701 | null | q-bio.QM physics.comp-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present an efficient and exact Monte Carlo algorithm to simulate
reversible aggregation of particles with dedicated binding sites. This method
introduces a novel data structure of dynamic bond tree to record clusters and
sequences of bond formations. The algorithm achieves a constant time cost for
processing clust... | [
{
"created": "Sat, 2 Oct 2010 14:29:06 GMT",
"version": "v1"
},
{
"created": "Mon, 26 Sep 2011 06:03:54 GMT",
"version": "v2"
}
] | 2011-09-27 | [
[
"Chang",
"Qiang",
""
],
[
"Yang",
"Jin",
""
]
] | We present an efficient and exact Monte Carlo algorithm to simulate reversible aggregation of particles with dedicated binding sites. This method introduces a novel data structure of dynamic bond tree to record clusters and sequences of bond formations. The algorithm achieves a constant time cost for processing cluster... |
2005.11767 | Suban Sahoo | Seshu Vardhan, Bharat Z. Dholakiya and Suban K Sahoo | Protein-ligand interaction study to identify potential dietary compounds
binding at the active site of therapeutic target proteins of SARS-CoV-2 | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objective: Total 186 biologically important phenylpropanoids and polyketides
compounds from different Indian medicinal plants and dietary sources were
screened to filter potential compounds that bind at the active site of the
therapeutic target proteins of SARS-CoV-2. Method: The molecular docking
studies were carrie... | [
{
"created": "Sun, 24 May 2020 15:04:52 GMT",
"version": "v1"
}
] | 2020-05-26 | [
[
"Vardhan",
"Seshu",
""
],
[
"Dholakiya",
"Bharat Z.",
""
],
[
"Sahoo",
"Suban K",
""
]
] | Objective: Total 186 biologically important phenylpropanoids and polyketides compounds from different Indian medicinal plants and dietary sources were screened to filter potential compounds that bind at the active site of the therapeutic target proteins of SARS-CoV-2. Method: The molecular docking studies were carried ... |
q-bio/0612022 | Andrei Khrennikov | Andrei Khrennikov and Marcus Nilsson | A number theoretical observation about the degeneracy of the genetic
code | References | null | null | Reports MSI, N 06166, Vaxjo University Press (ISSN 1650-2647) | q-bio.OT | null | We discuss the similarity of the degeneration structure of the genetic code
with a pure number theoretic -- ``divisors code.'' The most interesting thing
about our observation is not that there is a connection between number theory
and the genetic code, but the simplicity of the rule. We hope that the
observation and... | [
{
"created": "Wed, 13 Dec 2006 15:59:36 GMT",
"version": "v1"
},
{
"created": "Mon, 25 Dec 2006 10:34:48 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Khrennikov",
"Andrei",
""
],
[
"Nilsson",
"Marcus",
""
]
] | We discuss the similarity of the degeneration structure of the genetic code with a pure number theoretic -- ``divisors code.'' The most interesting thing about our observation is not that there is a connection between number theory and the genetic code, but the simplicity of the rule. We hope that the observation and t... |
1810.00224 | Luiz Gadelha Jr. | Luiz M. R. Gadelha Jr., Pedro C. de Siracusa, Artur Ziviani, Eduardo
Couto Dalcin, Helen Michelle Affe, Marinez Ferreira de Siqueira, Lu\'is
Alexandre Estev\~ao da Silva, Douglas A. Augusto, Eduardo Krempser, Marcia
Chame, Raquel Lopes Costa, Pedro Milet Meirelles, Fabiano Thompson | A survey of biodiversity informatics: Concepts, practices, and
challenges | null | WIREs Data Mining and Knowledge Discovery (2020) | 10.1002/widm.1394 | null | q-bio.PE cs.DB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The unprecedented size of the human population, along with its associated
economic activities, have an ever increasing impact on global environments.
Across the world, countries are concerned about the growing resource
consumption and the capacity of ecosystems to provide them. To effectively
conserve biodiversity, i... | [
{
"created": "Sat, 29 Sep 2018 15:41:17 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Dec 2020 11:22:48 GMT",
"version": "v2"
}
] | 2020-12-15 | [
[
"Gadelha",
"Luiz M. R.",
"Jr."
],
[
"de Siracusa",
"Pedro C.",
""
],
[
"Ziviani",
"Artur",
""
],
[
"Dalcin",
"Eduardo Couto",
""
],
[
"Affe",
"Helen Michelle",
""
],
[
"de Siqueira",
"Marinez Ferreira",
""
],
[
"da... | The unprecedented size of the human population, along with its associated economic activities, have an ever increasing impact on global environments. Across the world, countries are concerned about the growing resource consumption and the capacity of ecosystems to provide them. To effectively conserve biodiversity, it ... |
0901.2227 | Ellen Baake | Florian Lipsmeier, Ellen Baake | Rare event simulation for T-cell activation | 29 pages, 14 figures; J. Stat. Phys., in press | J. Stat. Phys. 134 (2009), 537-566 | 10.1007/s10955-008-9672-2 | null | q-bio.SC math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The problem of \emph{statistical recognition} is considered, as it arises in
immunobiology, namely, the discrimination of foreign antigens against a
background of the body's own molecules. The precise mechanism of this
foreign-self-distinction, though one of the major tasks of the immune system,
continues to be a fun... | [
{
"created": "Thu, 15 Jan 2009 10:52:25 GMT",
"version": "v1"
}
] | 2009-09-30 | [
[
"Lipsmeier",
"Florian",
""
],
[
"Baake",
"Ellen",
""
]
] | The problem of \emph{statistical recognition} is considered, as it arises in immunobiology, namely, the discrimination of foreign antigens against a background of the body's own molecules. The precise mechanism of this foreign-self-distinction, though one of the major tasks of the immune system, continues to be a funda... |
q-bio/0504017 | Giovanni Meacci | G. Meacci, K. Kruse | Min-oscillations in Escherichia coli induced by interactions of
membrane-bound proteins | 17 pages, 5 figures. Submitted to Physical Biology | Phys. Biol. 2 (2005) 89-97 | 10.1088/1478-3975/2/2/002 | null | q-bio.SC cond-mat.stat-mech physics.bio-ph | null | During division it is of primary importance for a cell to correctly determine
the site of cleavage. The bacterium Escherichia coli divides in the center,
producing two daughter cells of equal size. Selection of the center as the
correct division site is in part achieved by the Min-proteins. They oscillate
between the... | [
{
"created": "Wed, 13 Apr 2005 15:27:31 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Meacci",
"G.",
""
],
[
"Kruse",
"K.",
""
]
] | During division it is of primary importance for a cell to correctly determine the site of cleavage. The bacterium Escherichia coli divides in the center, producing two daughter cells of equal size. Selection of the center as the correct division site is in part achieved by the Min-proteins. They oscillate between the t... |
2103.09709 | Neta Maimon | Neta B. Maimon, Dominique Lamy, and Zohar Eitan | Do Picardy thirds smile? Tonal hierarchy and tonal valence: explicit and
implicit measures | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Western tonality provides a hierarchy of stability among melodic
scale-degrees, from the maximally stable tonic to unstable chromatic notes.
Tonal stability has been linked to emotion, yet systematic investigations of
the associations between the hierarchy of melodic scale-degrees and perceived
emotional valence are ... | [
{
"created": "Wed, 17 Mar 2021 15:08:18 GMT",
"version": "v1"
}
] | 2021-03-18 | [
[
"Maimon",
"Neta B.",
""
],
[
"Lamy",
"Dominique",
""
],
[
"Eitan",
"Zohar",
""
]
] | Western tonality provides a hierarchy of stability among melodic scale-degrees, from the maximally stable tonic to unstable chromatic notes. Tonal stability has been linked to emotion, yet systematic investigations of the associations between the hierarchy of melodic scale-degrees and perceived emotional valence are la... |
1303.6227 | Eric Gamazon | Eric R. Gamazon, Hae Kyung Im, Chunyu Liu, Members of the Bipolar
Disorder Genome Study (BiGS) Consortium, Dan L. Nicolae, Nancy J. Cox | The Convergence of eQTL Mapping, Heritability Estimation and Polygenic
Modeling: Emerging Spectrum of Risk Variation in Bipolar Disorder | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is widely held that a substantial genetic component underlies Bipolar
Disorder (BD) and other neuropsychiatric disease traits. Recent efforts have
been aimed at understanding the genetic basis of disease susceptibility, with
genome-wide association studies (GWAS) unveiling some promising associations.
Nevertheless... | [
{
"created": "Mon, 25 Mar 2013 17:43:16 GMT",
"version": "v1"
},
{
"created": "Fri, 29 Mar 2013 04:45:06 GMT",
"version": "v2"
}
] | 2013-04-01 | [
[
"Gamazon",
"Eric R.",
"",
"BiGS"
],
[
"Im",
"Hae Kyung",
"",
"BiGS"
],
[
"Liu",
"Chunyu",
"",
"BiGS"
],
[
"Study",
"Members of the Bipolar Disorder Genome",
"",
"BiGS"
],
[
"Consortium",
"",
""
],
[
"Nicolae",
... | It is widely held that a substantial genetic component underlies Bipolar Disorder (BD) and other neuropsychiatric disease traits. Recent efforts have been aimed at understanding the genetic basis of disease susceptibility, with genome-wide association studies (GWAS) unveiling some promising associations. Nevertheless, ... |
2302.03250 | Yuan Wang | Xingpei Zhao, Nicholas Riccardi, Rutvik H. Desai, Dirk-Bart den Ouden,
Julius Fridriksson, Yuan Wang | Network-based Statistics Distinguish Anomic and Broca Aphasia | null | null | null | null | q-bio.NC stat.AP | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Aphasia is a speech-language impairment commonly caused by damage to the left
hemisphere. Due to the complexity of speech-language processing, the neural
mechanisms that underpin various symptoms between different types of aphasia
are still not fully understood. We used the network-based statistic method to
identify ... | [
{
"created": "Tue, 7 Feb 2023 04:33:18 GMT",
"version": "v1"
},
{
"created": "Fri, 17 Feb 2023 20:45:15 GMT",
"version": "v2"
}
] | 2023-02-21 | [
[
"Zhao",
"Xingpei",
""
],
[
"Riccardi",
"Nicholas",
""
],
[
"Desai",
"Rutvik H.",
""
],
[
"Ouden",
"Dirk-Bart den",
""
],
[
"Fridriksson",
"Julius",
""
],
[
"Wang",
"Yuan",
""
]
] | Aphasia is a speech-language impairment commonly caused by damage to the left hemisphere. Due to the complexity of speech-language processing, the neural mechanisms that underpin various symptoms between different types of aphasia are still not fully understood. We used the network-based statistic method to identify di... |
1410.8826 | Adam Marblestone | Gary F. Marcus and Adam H. Marblestone and Thomas L. Dean | Frequently Asked Questions for: The Atoms of Neural Computation | Frequently Asked Questions (FAQ) for Marcus, Marblestone and Dean.
"The Atoms of Neural Computation". Science. 31 OCTOBER 2014. VOL 346 ISSUE
6209 | null | 10.1126/science.1261661 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Based on a survey of the literature, we attempt to answer Frequently Asked
Questions on issues of cortical uniformity vs. non-uniformity, the neural
mechanisms of symbolic variable binding, and other issues highlighted in
(Marcus, Marblestone and Dean. "The Atoms of Neural Computation". Science. 31
October 2014. Vol ... | [
{
"created": "Fri, 31 Oct 2014 17:38:34 GMT",
"version": "v1"
}
] | 2014-11-03 | [
[
"Marcus",
"Gary F.",
""
],
[
"Marblestone",
"Adam H.",
""
],
[
"Dean",
"Thomas L.",
""
]
] | Based on a survey of the literature, we attempt to answer Frequently Asked Questions on issues of cortical uniformity vs. non-uniformity, the neural mechanisms of symbolic variable binding, and other issues highlighted in (Marcus, Marblestone and Dean. "The Atoms of Neural Computation". Science. 31 October 2014. Vol 34... |
1202.0433 | Jens Karschau | Jens Karschau, J. Julian Blow, Alessandro P. S. de Moura | Optimal Placement of Origins for DNA Replication | 5 pages, 3 figures | Phys. Rev. Lett. 108, 058101 (2012) | 10.1103/PhysRevLett.108.058101 | null | q-bio.QM cond-mat.stat-mech physics.bio-ph q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | DNA replication is an essential process in biology and its timing must be
robust so that cells can divide properly. Random fluctuations in the formation
of replication starting points, called origins, and the subsequent activation
of proteins lead to variations in the replication time. We analyse these
stochastic pro... | [
{
"created": "Thu, 2 Feb 2012 13:46:26 GMT",
"version": "v1"
}
] | 2012-02-03 | [
[
"Karschau",
"Jens",
""
],
[
"Blow",
"J. Julian",
""
],
[
"de Moura",
"Alessandro P. S.",
""
]
] | DNA replication is an essential process in biology and its timing must be robust so that cells can divide properly. Random fluctuations in the formation of replication starting points, called origins, and the subsequent activation of proteins lead to variations in the replication time. We analyse these stochastic prope... |
1907.02160 | Mason A. Porter | Cameron L. Hall, Mason A. Porter, and Marian S. Dawkins | Dominance, Sharing, and Assessment in an Iterated Hawk--Dove Game | null | null | null | null | q-bio.PE math.DS nlin.AO physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Animals use a wide variety of strategies to reduce or avoid aggression in
conflicts over resources. These strategies range from sharing resources without
outward signs of conflict to the development of dominance hierarchies, in which
initial fighting is followed by the submission of subordinates. Although models
have... | [
{
"created": "Wed, 3 Jul 2019 23:11:05 GMT",
"version": "v1"
},
{
"created": "Thu, 31 Oct 2019 04:22:31 GMT",
"version": "v2"
}
] | 2019-11-01 | [
[
"Hall",
"Cameron L.",
""
],
[
"Porter",
"Mason A.",
""
],
[
"Dawkins",
"Marian S.",
""
]
] | Animals use a wide variety of strategies to reduce or avoid aggression in conflicts over resources. These strategies range from sharing resources without outward signs of conflict to the development of dominance hierarchies, in which initial fighting is followed by the submission of subordinates. Although models have b... |
2103.03816 | Stephan Meighen-Berger | Stephan Meighen-Berger, Li Ruohan, Golo Wimmer | Bioluminescence modeling for deep sea experiments | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop a modeling framework for bioluminescence light found in the deep
sea near neutrino telescopes by combining a hydrodynamic model with a
stochastic one. The bioluminescence is caused by organisms when exposed to a
non-constant water flow, such as past the neutrino telescopes. We model the
flow using the inco... | [
{
"created": "Tue, 9 Feb 2021 09:08:52 GMT",
"version": "v1"
},
{
"created": "Mon, 28 Jun 2021 21:04:51 GMT",
"version": "v2"
}
] | 2021-06-30 | [
[
"Meighen-Berger",
"Stephan",
""
],
[
"Ruohan",
"Li",
""
],
[
"Wimmer",
"Golo",
""
]
] | We develop a modeling framework for bioluminescence light found in the deep sea near neutrino telescopes by combining a hydrodynamic model with a stochastic one. The bioluminescence is caused by organisms when exposed to a non-constant water flow, such as past the neutrino telescopes. We model the flow using the incomp... |
1407.3432 | Randall O'Reilly | Randall C. O'Reilly and Dean Wyatte and John Rohrlich | Learning Through Time in the Thalamocortical Loops | 37 pages, 11 figures. arXiv admin note: text overlap with
arXiv:1112.0778 by other authors | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a comprehensive, novel framework for understanding how the
neocortex, including the thalamocortical loops through the deep layers, can
support a temporal context representation in the service of predictive
learning. Many have argued that predictive learning provides a compelling,
powerful source of learnin... | [
{
"created": "Sun, 13 Jul 2014 05:43:44 GMT",
"version": "v1"
}
] | 2014-07-15 | [
[
"O'Reilly",
"Randall C.",
""
],
[
"Wyatte",
"Dean",
""
],
[
"Rohrlich",
"John",
""
]
] | We present a comprehensive, novel framework for understanding how the neocortex, including the thalamocortical loops through the deep layers, can support a temporal context representation in the service of predictive learning. Many have argued that predictive learning provides a compelling, powerful source of learning ... |
1304.6394 | Alain Barrat | Anna Machens, Francesco Gesualdo, Caterina Rizzo, Alberto E Tozzi,
Alain Barrat, Ciro Cattuto | An infectious disease model on empirical networks of human contact:
bridging the gap between dynamic network data and contact matrices | null | BMC Infectious Diseases 13:185 (2013) | 10.1186/1471-2334-13-185 | null | q-bio.PE physics.comp-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The integration of empirical data in computational frameworks to model the
spread of infectious diseases poses challenges that are becoming pressing with
the increasing availability of high-resolution information on human mobility
and contacts. This deluge of data has the potential to revolutionize the
computational ... | [
{
"created": "Tue, 23 Apr 2013 19:55:32 GMT",
"version": "v1"
}
] | 2013-04-24 | [
[
"Machens",
"Anna",
""
],
[
"Gesualdo",
"Francesco",
""
],
[
"Rizzo",
"Caterina",
""
],
[
"Tozzi",
"Alberto E",
""
],
[
"Barrat",
"Alain",
""
],
[
"Cattuto",
"Ciro",
""
]
] | The integration of empirical data in computational frameworks to model the spread of infectious diseases poses challenges that are becoming pressing with the increasing availability of high-resolution information on human mobility and contacts. This deluge of data has the potential to revolutionize the computational ef... |
1605.06176 | Bernal Morera MSc | Bernal Morera-Brenes, Mauricio Melendez-Obando | The genealogy of Maria de Aguilar: evidence of admixture in the early
Spanish Colony in Costa Rica | 12 pages, 2 figures, in Spanish | Cuadernos de Investigacion 2 (1), 33-43. 2010 | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During long time, historians and genealogists have interpreted that the elite
that emerged during the Spanish Conquest was almost exclusively European. We
reconstructed a deep matrilineal genealogy which includes recent Costa Rican
ex-presidents and religious authorities back to their ancestors at the early
17th cent... | [
{
"created": "Thu, 19 May 2016 23:45:40 GMT",
"version": "v1"
}
] | 2016-05-23 | [
[
"Morera-Brenes",
"Bernal",
""
],
[
"Melendez-Obando",
"Mauricio",
""
]
] | During long time, historians and genealogists have interpreted that the elite that emerged during the Spanish Conquest was almost exclusively European. We reconstructed a deep matrilineal genealogy which includes recent Costa Rican ex-presidents and religious authorities back to their ancestors at the early 17th centur... |
1309.0670 | Surojit Biswas | Surojit Biswas, Yash N. Agrawal, Tatiana S. Mucyn, Jeffery L. Dangl,
Corbin D. Jones | Biological Averaging in RNA-Seq | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | RNA-seq has become a de facto standard for measuring gene expression.
Traditionally, RNA-seq experiments are mathematically averaged -- they sequence
the mRNA of individuals from different treatment groups, hoping to correlate
phenotype with differences in arithmetic read count averages at shared loci of
interest. Al... | [
{
"created": "Tue, 3 Sep 2013 13:37:47 GMT",
"version": "v1"
},
{
"created": "Wed, 4 Sep 2013 19:28:49 GMT",
"version": "v2"
}
] | 2013-09-05 | [
[
"Biswas",
"Surojit",
""
],
[
"Agrawal",
"Yash N.",
""
],
[
"Mucyn",
"Tatiana S.",
""
],
[
"Dangl",
"Jeffery L.",
""
],
[
"Jones",
"Corbin D.",
""
]
] | RNA-seq has become a de facto standard for measuring gene expression. Traditionally, RNA-seq experiments are mathematically averaged -- they sequence the mRNA of individuals from different treatment groups, hoping to correlate phenotype with differences in arithmetic read count averages at shared loci of interest. Alte... |
1506.04458 | Tomasz Rutkowski | Kensuke Shimizu, Shoji Makino, and Tomasz M. Rutkowski | Inter-stimulus Interval Study for the Tactile Point-pressure
Brain-computer Interface | 4 pages, 5 figures, accepted for EMBC 2015, IEEE copyright | null | 10.1109/EMBC.2015.7318756 | null | q-bio.NC cs.HC | http://creativecommons.org/licenses/by-nc-sa/3.0/ | The paper presents a study of an inter-stimulus interval (ISI) influence on a
tactile point-pressure stimulus-based brain-computer interface's (tpBCI)
classification accuracy. A novel tactile pressure generating tpBCI stimulator
is also discussed, which is based on a three-by-three pins' matrix prototype.
The six pin... | [
{
"created": "Mon, 15 Jun 2015 02:30:36 GMT",
"version": "v1"
}
] | 2016-11-17 | [
[
"Shimizu",
"Kensuke",
""
],
[
"Makino",
"Shoji",
""
],
[
"Rutkowski",
"Tomasz M.",
""
]
] | The paper presents a study of an inter-stimulus interval (ISI) influence on a tactile point-pressure stimulus-based brain-computer interface's (tpBCI) classification accuracy. A novel tactile pressure generating tpBCI stimulator is also discussed, which is based on a three-by-three pins' matrix prototype. The six pin-l... |
0707.3464 | Emmanuel Tannenbaum | Emmanuel Tannenbaum | A comparison of three replication strategies in complex multicellular
organisms: Asexual replication, sexual replication with identical gametes,
and sexual replication with distinct sperm and egg gametes | 18 pages, figures included with journal submission | null | 10.1103/PhysRevE.77.011915 | null | q-bio.PE | null | This paper studies the mutation-selection balance in three simplified
replication models. The first model considers a population of organisms
replicating via the production of asexual spores. The second model considers a
sexually replicating population that produces identical gametes. The third
model considers a sexu... | [
{
"created": "Mon, 23 Jul 2007 23:12:52 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Tannenbaum",
"Emmanuel",
""
]
] | This paper studies the mutation-selection balance in three simplified replication models. The first model considers a population of organisms replicating via the production of asexual spores. The second model considers a sexually replicating population that produces identical gametes. The third model considers a sexual... |
1405.3293 | Krishna Garikipati | Kristen L. Mills, Ralf Kemkemer, Shiva Rudraraju and Krishna
Garikipati | Elastic free energy drives the shape of prevascular solid tumors | Six figures in main text. Supporting Information with 6 additional
figures | null | 10.1371/journal.pone.0103245 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/3.0/ | It is well established that the mechanical environment influences cell
functions in health and disease. Here, we address how the mechanical
environment influences tumor growth, in particular, the shape of solid tumors.
In an in vitro tumor model, which isolates mechanical interactions between
tumor cells and a hydrog... | [
{
"created": "Tue, 13 May 2014 20:04:14 GMT",
"version": "v1"
}
] | 2015-06-19 | [
[
"Mills",
"Kristen L.",
""
],
[
"Kemkemer",
"Ralf",
""
],
[
"Rudraraju",
"Shiva",
""
],
[
"Garikipati",
"Krishna",
""
]
] | It is well established that the mechanical environment influences cell functions in health and disease. Here, we address how the mechanical environment influences tumor growth, in particular, the shape of solid tumors. In an in vitro tumor model, which isolates mechanical interactions between tumor cells and a hydrogel... |
1803.02630 | Emese Drozsdik | Emese J. Drozsdik and Bal\'azs G. Madas | Quantitative analysis of the potential role of basal cell hyperplasia in
the relationship between clonal expansion and radon concentration | paper presented in the 17th International Symposium on Microdosimetry
(MICROS 2017 - Venice, Italy, 5-10 November, 2017), 5 pages, 1 table, 6
figures | null | null | null | q-bio.TO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Applying the two-stage clonal expansion model to epidemiology of lung cancer
among uranium miners, it has been revealed that radon acts as a promoting agent
facilitating the clonal expansion of already mutated cells. Clonal expansion
rate increases non-linearly by radon concentration showing a plateau above a
given e... | [
{
"created": "Wed, 7 Mar 2018 13:02:12 GMT",
"version": "v1"
}
] | 2018-03-08 | [
[
"Drozsdik",
"Emese J.",
""
],
[
"Madas",
"Balázs G.",
""
]
] | Applying the two-stage clonal expansion model to epidemiology of lung cancer among uranium miners, it has been revealed that radon acts as a promoting agent facilitating the clonal expansion of already mutated cells. Clonal expansion rate increases non-linearly by radon concentration showing a plateau above a given exp... |
q-bio/0506010 | Ciro Minichini | C. Minichini and A. Sciarrino | Mutation model for nucleotide sequences based on crystal basis | 27 pages, 9 figures | null | null | DSF 14/2005 | q-bio.BM q-bio.OT | null | A nucleotides sequence is identified, in the two (four) letters alphabet, by
the the labels of a vector state of an irreducible representation of U_q(sl(2))
(U_q(sl(2) + sl(2))), in the limit q -> 0. A master equation for the
distribution function is written, where the intensity of the one-spin flip is
assumed to dep... | [
{
"created": "Wed, 8 Jun 2005 15:25:40 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Minichini",
"C.",
""
],
[
"Sciarrino",
"A.",
""
]
] | A nucleotides sequence is identified, in the two (four) letters alphabet, by the the labels of a vector state of an irreducible representation of U_q(sl(2)) (U_q(sl(2) + sl(2))), in the limit q -> 0. A master equation for the distribution function is written, where the intensity of the one-spin flip is assumed to depen... |
1504.07523 | Luca Salasnich | Luca Salasnich | Power spectrum and diffusion of the Amari neural field | 8 pages, 2 figures, improved version with inclusion of
reaction-diffusion equation and dual neural field. To be published in the
open access journal Symmetry | Symmetry 11, 134 (2019) | 10.3390/sym11020134 | null | q-bio.NC nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the power spectrum of a space-time dependent neural field which
describes the average membrane potential of neurons in a single layer. This
neural field is modelled by a dissipative integro-differential equation, the
so-called Amari equation. By considering a small perturbation with respect to a
stationary a... | [
{
"created": "Tue, 28 Apr 2015 15:11:40 GMT",
"version": "v1"
},
{
"created": "Thu, 30 Jul 2015 10:21:56 GMT",
"version": "v2"
},
{
"created": "Mon, 31 Aug 2015 12:46:11 GMT",
"version": "v3"
},
{
"created": "Thu, 27 Jul 2017 15:28:41 GMT",
"version": "v4"
},
{
"c... | 2019-01-29 | [
[
"Salasnich",
"Luca",
""
]
] | We study the power spectrum of a space-time dependent neural field which describes the average membrane potential of neurons in a single layer. This neural field is modelled by a dissipative integro-differential equation, the so-called Amari equation. By considering a small perturbation with respect to a stationary and... |
2306.15379 | Matthew Simpson | Matthew J Simpson, Nizhum Rahman, Scott W McCue, Alexander KY Tam | Survival, extinction, and interface stability in a two--phase moving
boundary model of biological invasion | 36 pages. 10 figures | null | null | null | q-bio.PE math.AP nlin.PS physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | We consider a moving boundary mathematical model of biological invasion. The
model describes the spatiotemporal evolution of two adjacent populations: each
population undergoes linear diffusion and logistic growth, and the boundary
between the two populations evolves according to a two--phase Stefan condition.
This m... | [
{
"created": "Tue, 27 Jun 2023 10:58:31 GMT",
"version": "v1"
},
{
"created": "Thu, 6 Jul 2023 07:21:35 GMT",
"version": "v2"
},
{
"created": "Fri, 1 Sep 2023 23:32:27 GMT",
"version": "v3"
}
] | 2023-09-06 | [
[
"Simpson",
"Matthew J",
""
],
[
"Rahman",
"Nizhum",
""
],
[
"McCue",
"Scott W",
""
],
[
"Tam",
"Alexander KY",
""
]
] | We consider a moving boundary mathematical model of biological invasion. The model describes the spatiotemporal evolution of two adjacent populations: each population undergoes linear diffusion and logistic growth, and the boundary between the two populations evolves according to a two--phase Stefan condition. This mat... |
1511.05227 | Marisa Eisenberg | Olivia J. Walch, Marisa C. Eisenberg | Parameter identifiability and identifiable combinations in generalized
Hodgkin-Huxley models | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The use of Hodgkin-Huxley (HH) equations abounds in the literature, but the
identifiability of the HH model parameters has not been broadly considered.
Identifiability analysis addresses the question of whether it is possible to
estimate the model parameters for a given choice of measurement data and
experimental inp... | [
{
"created": "Mon, 16 Nov 2015 23:58:18 GMT",
"version": "v1"
}
] | 2015-11-18 | [
[
"Walch",
"Olivia J.",
""
],
[
"Eisenberg",
"Marisa C.",
""
]
] | The use of Hodgkin-Huxley (HH) equations abounds in the literature, but the identifiability of the HH model parameters has not been broadly considered. Identifiability analysis addresses the question of whether it is possible to estimate the model parameters for a given choice of measurement data and experimental input... |
2009.12413 | Katherine St. John | Nathan Davidov, Amanda Hernandez, Justin Jian, Patrick McKenna, K.A.
Medlin, Roadra Mojumder, Megan Owen, Andrew Quijano, Amanda Rodriguez,
Katherine St. John, Katherine Thai, Meliza Uraga | Maximum Covering Subtrees for Phylogenetic Networks | null | null | 10.1109/TCBB.2020.3040910 | null | q-bio.PE cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tree-based phylogenetic networks, which may be roughly defined as
leaf-labeled networks built by adding arcs only between the original tree
edges, have elegant properties for modeling evolutionary histories. We answer
an open question of Francis, Semple, and Steel about the complexity of
determining how far a phyloge... | [
{
"created": "Fri, 25 Sep 2020 19:47:36 GMT",
"version": "v1"
},
{
"created": "Tue, 24 Nov 2020 16:59:04 GMT",
"version": "v2"
}
] | 2022-10-26 | [
[
"Davidov",
"Nathan",
""
],
[
"Hernandez",
"Amanda",
""
],
[
"Jian",
"Justin",
""
],
[
"McKenna",
"Patrick",
""
],
[
"Medlin",
"K. A.",
""
],
[
"Mojumder",
"Roadra",
""
],
[
"Owen",
"Megan",
""
],
[
... | Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of Francis, Semple, and Steel about the complexity of determining how far a phylogene... |
2308.05122 | Nicha Dvornek | Nicha C. Dvornek, Catherine Sullivan, James S. Duncan, Abha R. Gupta | Copy Number Variation Informs fMRI-based Prediction of Autism Spectrum
Disorder | Accepted by Machine Learning in Clinical Neuroimaging 2023 (MICCAI
workshop), preprint version | null | null | null | q-bio.QM cs.CV cs.LG eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The multifactorial etiology of autism spectrum disorder (ASD) suggests that
its study would benefit greatly from multimodal approaches that combine data
from widely varying platforms, e.g., neuroimaging, genetics, and clinical
characterization. Prior neuroimaging-genetic analyses often apply naive feature
concatenati... | [
{
"created": "Tue, 8 Aug 2023 19:53:43 GMT",
"version": "v1"
}
] | 2023-08-11 | [
[
"Dvornek",
"Nicha C.",
""
],
[
"Sullivan",
"Catherine",
""
],
[
"Duncan",
"James S.",
""
],
[
"Gupta",
"Abha R.",
""
]
] | The multifactorial etiology of autism spectrum disorder (ASD) suggests that its study would benefit greatly from multimodal approaches that combine data from widely varying platforms, e.g., neuroimaging, genetics, and clinical characterization. Prior neuroimaging-genetic analyses often apply naive feature concatenation... |
0912.4714 | Emmanuel Tannenbaum | Eran Itan and Emmanuel Tannenbaum | Semiconservative quasispecies equations for polysomic genomes: The
general case | 16 pages, 3 figures | null | 10.1103/PhysRevE.81.061915 | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper develops a formulation of the quasispecies equations appropriate
for polysomic, semiconservatively replicating genomes. This paper is an
extension of previous work on the subject, which considered the case of haploid
genomes. Here, we develop a more general formulation of the quasispecies
equations that is... | [
{
"created": "Wed, 23 Dec 2009 19:13:10 GMT",
"version": "v1"
}
] | 2015-05-14 | [
[
"Itan",
"Eran",
""
],
[
"Tannenbaum",
"Emmanuel",
""
]
] | This paper develops a formulation of the quasispecies equations appropriate for polysomic, semiconservatively replicating genomes. This paper is an extension of previous work on the subject, which considered the case of haploid genomes. Here, we develop a more general formulation of the quasispecies equations that is a... |
2211.09096 | Thibault Niederhauser | Thibault Niederhauser, Adam Lester, Nina Miolane, Khanh Dao Duc, Manu
S. Madhav | Testing geometric representation hypotheses from simulated place cell
recordings | NeurIPS 2022: NeurReps workshop, extended abstract track | null | null | null | q-bio.NC cs.AI cs.LG q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Hippocampal place cells can encode spatial locations of an animal in physical
or task-relevant spaces. We simulated place cell populations that encoded
either Euclidean- or graph-based positions of a rat navigating to goal nodes in
a maze with a graph topology, and used manifold learning methods such as UMAP
and Auto... | [
{
"created": "Wed, 16 Nov 2022 18:29:17 GMT",
"version": "v1"
}
] | 2022-11-17 | [
[
"Niederhauser",
"Thibault",
""
],
[
"Lester",
"Adam",
""
],
[
"Miolane",
"Nina",
""
],
[
"Duc",
"Khanh Dao",
""
],
[
"Madhav",
"Manu S.",
""
]
] | Hippocampal place cells can encode spatial locations of an animal in physical or task-relevant spaces. We simulated place cell populations that encoded either Euclidean- or graph-based positions of a rat navigating to goal nodes in a maze with a graph topology, and used manifold learning methods such as UMAP and Autoen... |
q-bio/0610053 | Mauricio Barahona | Elias August, Kim H. Parker and Mauricio Barahona | A Dynamical Model of Lipoprotein Metabolism | To appear in Bulletin of Mathematical Biology | null | null | null | q-bio.QM q-bio.CB | null | We present a dynamical model of lipoprotein metabolism derived by combining a
cascading process in the blood stream and cellular level regulatory dynamics.
We analyse the existence and stability of equilibria and show that this
low-dimensional, nonlinear model exhibits bistability between a low and a high
cholesterol... | [
{
"created": "Sat, 28 Oct 2006 18:30:36 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"August",
"Elias",
""
],
[
"Parker",
"Kim H.",
""
],
[
"Barahona",
"Mauricio",
""
]
] | We present a dynamical model of lipoprotein metabolism derived by combining a cascading process in the blood stream and cellular level regulatory dynamics. We analyse the existence and stability of equilibria and show that this low-dimensional, nonlinear model exhibits bistability between a low and a high cholesterol s... |
1712.06846 | Tom\'as Revilla | Tom\'as A. Revilla and Vlastimil K\v{r}ivan | Competition, trait-mediated facilitation, and the structure of
plant-pollinator communities | ideal free distribution, isolegs, pollination services, plant
resources, critical transition | Journal of Theoretical Biology. Vol. 440, pp. 42-57 (2018) | 10.1016/j.jtbi.2017.12.019 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In plant-pollinator communities many pollinators are potential generalists
and their preferences for certain plants can change quickly in response to
changes in plant and pollinator densities. These changes in preferences affect
coexistence within pollinator guilds as well as within plant guilds. Using a
mathematical... | [
{
"created": "Tue, 19 Dec 2017 10:12:29 GMT",
"version": "v1"
}
] | 2018-01-03 | [
[
"Revilla",
"Tomás A.",
""
],
[
"Křivan",
"Vlastimil",
""
]
] | In plant-pollinator communities many pollinators are potential generalists and their preferences for certain plants can change quickly in response to changes in plant and pollinator densities. These changes in preferences affect coexistence within pollinator guilds as well as within plant guilds. Using a mathematical m... |
1312.3447 | Rub\'en J. Requejo | Rub\'en J. Requejo-Mart\'inez | Evolutionary game theory and the tower of Babel of cooperation:
Altruism, free-riding, parasitism and the structure of the interactions in a
world with finite resources | 38 pages | null | null | null | q-bio.PE physics.bio-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The study of the evolution of cooperative behaviours --which provide benefits
to others-- and altruism --which provides benefits to others at a cost to
oneself-- has been on the core of the evolutionary game theoretical framework
since its foundation. The fast development of the theory during the last years
has impro... | [
{
"created": "Thu, 12 Dec 2013 11:14:40 GMT",
"version": "v1"
}
] | 2013-12-13 | [
[
"Requejo-Martínez",
"Rubén J.",
""
]
] | The study of the evolution of cooperative behaviours --which provide benefits to others-- and altruism --which provides benefits to others at a cost to oneself-- has been on the core of the evolutionary game theoretical framework since its foundation. The fast development of the theory during the last years has improve... |
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