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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2004.00498 | Jordi Garcia-Ojalvo | Miguel A. Casal, Santiago Galella, Oscar Vilarroya and Jordi
Garcia-Ojalvo | Soft-wired long-term memory in a natural recurrent neuronal network | 16 pages, 6 figures | null | 10.1063/5.0009709 | null | q-bio.NC cond-mat.dis-nn nlin.CD physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neuronal networks provide living organisms with the ability to process
information. They are also characterized by abundant recurrent connections,
which give rise to strong feedback that dictates their dynamics and endows them
with fading (short-term) memory. The role of recurrence in long-term memory, on
the other h... | [
{
"created": "Wed, 1 Apr 2020 15:22:36 GMT",
"version": "v1"
}
] | 2020-06-24 | [
[
"Casal",
"Miguel A.",
""
],
[
"Galella",
"Santiago",
""
],
[
"Vilarroya",
"Oscar",
""
],
[
"Garcia-Ojalvo",
"Jordi",
""
]
] | Neuronal networks provide living organisms with the ability to process information. They are also characterized by abundant recurrent connections, which give rise to strong feedback that dictates their dynamics and endows them with fading (short-term) memory. The role of recurrence in long-term memory, on the other han... |
1606.01372 | John Helliwell R | John R. Helliwell, Simon W. M. Tanley, Antoine M. M. Schreurs and Loes
M. J. Kroon-Batenburg | Cisplatin coordination chemistry determination at hen egg white lysozyme
His15 with ligand distances and angles, and their standard uncertainties, and
also reporting a split occupancy effect | 10 pages. One figure with two stereos and two further separate
(identical to the stereos) figures with atom labels. This arXiv article is
the first part of a Data Review | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Following the interest of L Messori and A Merlino 2016 Coordination Chemistry
Reviews in the platinum ions coordination geometries in our PDB entries 4dd4
and 4dd6 we have extended our original analyses.
| [
{
"created": "Sat, 4 Jun 2016 11:36:03 GMT",
"version": "v1"
}
] | 2016-06-07 | [
[
"Helliwell",
"John R.",
""
],
[
"Tanley",
"Simon W. M.",
""
],
[
"Schreurs",
"Antoine M. M.",
""
],
[
"Kroon-Batenburg",
"Loes M. J.",
""
]
] | Following the interest of L Messori and A Merlino 2016 Coordination Chemistry Reviews in the platinum ions coordination geometries in our PDB entries 4dd4 and 4dd6 we have extended our original analyses. |
1511.07313 | Antti Niemi | Jin Dai, Antti J. Niemi, Jianfeng He, Adam Sieradzan, Nevena Ilieva | Bloch spin waves and emergent structure in protein folding with HIV
envelope glycoprotein as an example | 20 pages 29 figures | Phys. Rev. E 93, 032409 (2016) | 10.1103/PhysRevE.93.032409 | null | q-bio.BM cond-mat.soft nlin.PS physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We inquire how structure emerges during the process of protein folding. For
this we scrutinise col- lective many-atom motions during all-atom molecular
dynamics simulations. We introduce, develop and employ various topological
techniques, in combination with analytic tools that we deduce from the concept
of integrabl... | [
{
"created": "Mon, 23 Nov 2015 17:03:00 GMT",
"version": "v1"
}
] | 2016-04-06 | [
[
"Dai",
"Jin",
""
],
[
"Niemi",
"Antti J.",
""
],
[
"He",
"Jianfeng",
""
],
[
"Sieradzan",
"Adam",
""
],
[
"Ilieva",
"Nevena",
""
]
] | We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques, in combination with analytic tools that we deduce from the concept of integrable ... |
q-bio/0408025 | Alexey Mazur K. | Alexey K. Mazur | Sequence-dependent B-A transitions in DNA in silico: Electrostatic
condensation mechanism | 12 pages, 6 figures, RevTeX4 | null | null | null | q-bio.BM physics.bio-ph | null | Dynamics of the polymorphic A<->B transitions in DNA is compared for two
polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to
exhibit contrasting properties in experiments. In free molecular dynamics
simulations reversible transitions are induced by changing the size of a water
drop around DNA... | [
{
"created": "Sat, 28 Aug 2004 16:42:19 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Mazur",
"Alexey K.",
""
]
] | Dynamics of the polymorphic A<->B transitions in DNA is compared for two polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to exhibit contrasting properties in experiments. In free molecular dynamics simulations reversible transitions are induced by changing the size of a water drop around DNA n... |
0803.0850 | Thierry Rabilloud | Estelle Rousselet (LCBM), Alain Martelli (LCBM), Mireille Chevallet
(BBSI), H\'el\`ene Diemer (IPHC), Alain Van Dorssealer (IPHC), Thierry
Rabilloud (BBSI), Jean-Marc Moulis (LCBM) | Zinc adaptation and resistance to cadmium toxicity in mammalian cells.
Molecular insight by proteomic analysis | in press in Proteomics | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To identify proteins involved in cellular adaptive responses to zinc, a
comparative proteome analysis between a previously developed high zinc- and
cadmium- resistant human epithelial cell line (HZR) and the parental HeLa cells
has been carried out. Differentially produced proteins included co-chaperones,
proteins as... | [
{
"created": "Thu, 6 Mar 2008 12:40:10 GMT",
"version": "v1"
}
] | 2008-12-18 | [
[
"Rousselet",
"Estelle",
"",
"LCBM"
],
[
"Martelli",
"Alain",
"",
"LCBM"
],
[
"Chevallet",
"Mireille",
"",
"BBSI"
],
[
"Diemer",
"Hélène",
"",
"IPHC"
],
[
"Van Dorssealer",
"Alain",
"",
"IPHC"
],
[
"Rabilloud",
... | To identify proteins involved in cellular adaptive responses to zinc, a comparative proteome analysis between a previously developed high zinc- and cadmium- resistant human epithelial cell line (HZR) and the parental HeLa cells has been carried out. Differentially produced proteins included co-chaperones, proteins asso... |
q-bio/0402026 | John Hertz | Alexander Lerchner, Mandana Ahmadi and John Hertz | High conductance states in a mean field cortical network model | 7 pages, 3 figures, presented at CNS 2003, to be published in
Neurocomputing | null | null | 2004-14 | q-bio.NC | null | Measured responses from visual cortical neurons show that spike times tend to
be correlated rather than exactly Poisson distributed. Fano factors vary and
are usually greater than 1 due to the tendency of spikes being clustered into
bursts. We show that this behavior emerges naturally in a balanced cortical
network m... | [
{
"created": "Wed, 11 Feb 2004 21:00:07 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Lerchner",
"Alexander",
""
],
[
"Ahmadi",
"Mandana",
""
],
[
"Hertz",
"John",
""
]
] | Measured responses from visual cortical neurons show that spike times tend to be correlated rather than exactly Poisson distributed. Fano factors vary and are usually greater than 1 due to the tendency of spikes being clustered into bursts. We show that this behavior emerges naturally in a balanced cortical network mod... |
2307.02680 | Charles Puelz | Marshall Davey, Charles Puelz, Simone Rossi, Margaret Anne Smith,
David R. Wells, Greg Sturgeon, W. Paul Segars, John P. Vavalle, Charles S.
Peskin and Boyce E. Griffith | Simulating Cardiac Fluid Dynamics in the Human Heart | null | null | null | null | q-bio.TO cs.NA math.NA physics.flu-dyn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cardiac fluid dynamics fundamentally involves interactions between complex
blood flows and the structural deformations of the muscular heart walls and the
thin, flexible valve leaflets. There has been longstanding scientific,
engineering, and medical interest in creating mathematical models of the heart
that capture,... | [
{
"created": "Wed, 5 Jul 2023 22:43:59 GMT",
"version": "v1"
},
{
"created": "Tue, 24 Oct 2023 14:50:13 GMT",
"version": "v2"
}
] | 2023-10-25 | [
[
"Davey",
"Marshall",
""
],
[
"Puelz",
"Charles",
""
],
[
"Rossi",
"Simone",
""
],
[
"Smith",
"Margaret Anne",
""
],
[
"Wells",
"David R.",
""
],
[
"Sturgeon",
"Greg",
""
],
[
"Segars",
"W. Paul",
""
],
... | Cardiac fluid dynamics fundamentally involves interactions between complex blood flows and the structural deformations of the muscular heart walls and the thin, flexible valve leaflets. There has been longstanding scientific, engineering, and medical interest in creating mathematical models of the heart that capture, e... |
2309.11458 | Samuel M. Fischer | Samuel M. Fischer, Xugao Wang, Andreas Huth | Distinguishing mature and immature trees allows to estimate forest
carbon uptake from stand structure | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Relating forest productivity to local variations in forest structure has been
a long-standing challenge. Previous studies often focused on the connection
between forest structure and stand-level photosynthesis (GPP). However, biomass
production (NPP) and net ecosystem exchange (NEE) are also subject to
respiration an... | [
{
"created": "Wed, 20 Sep 2023 16:52:54 GMT",
"version": "v1"
},
{
"created": "Fri, 17 Nov 2023 12:32:51 GMT",
"version": "v2"
}
] | 2023-11-20 | [
[
"Fischer",
"Samuel M.",
""
],
[
"Wang",
"Xugao",
""
],
[
"Huth",
"Andreas",
""
]
] | Relating forest productivity to local variations in forest structure has been a long-standing challenge. Previous studies often focused on the connection between forest structure and stand-level photosynthesis (GPP). However, biomass production (NPP) and net ecosystem exchange (NEE) are also subject to respiration and ... |
0801.1296 | Atul Narang | Jason T. Noel and Atul Narang | Gene regulation in continuous cultures: A unified theory for bacteria
and yeasts | 67 pages, 20 figures | null | null | null | q-bio.CB q-bio.MN | null | During batch growth on mixtures of two growth-limiting substrates, microbes
consume the substrates either sequentially or simultaneously. These growth
patterns are manifested in all types of bacteria and yeasts. The ubiquity of
these growth patterns suggests that they are driven by a universal mechanism
common to all... | [
{
"created": "Tue, 8 Jan 2008 19:00:40 GMT",
"version": "v1"
}
] | 2008-01-09 | [
[
"Noel",
"Jason T.",
""
],
[
"Narang",
"Atul",
""
]
] | During batch growth on mixtures of two growth-limiting substrates, microbes consume the substrates either sequentially or simultaneously. These growth patterns are manifested in all types of bacteria and yeasts. The ubiquity of these growth patterns suggests that they are driven by a universal mechanism common to all m... |
2206.02290 | Sachin Gavali | Sachin Gavali, Karen Ross, Chuming Chen, Julie Cowart, Cathy H. Wu | A knowledge graph representation learning approach to predict novel
kinase-substrate interactions | null | null | null | null | q-bio.QM cs.AI q-bio.MN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The human proteome contains a vast network of interacting kinases and
substrates. Even though some kinases have proven to be immensely useful as
therapeutic targets, a majority are still understudied. In this work, we
present a novel knowledge graph representation learning approach to predict
novel interaction partne... | [
{
"created": "Sun, 5 Jun 2022 23:55:40 GMT",
"version": "v1"
},
{
"created": "Fri, 10 Jun 2022 00:09:23 GMT",
"version": "v2"
}
] | 2022-06-13 | [
[
"Gavali",
"Sachin",
""
],
[
"Ross",
"Karen",
""
],
[
"Chen",
"Chuming",
""
],
[
"Cowart",
"Julie",
""
],
[
"Wu",
"Cathy H.",
""
]
] | The human proteome contains a vast network of interacting kinases and substrates. Even though some kinases have proven to be immensely useful as therapeutic targets, a majority are still understudied. In this work, we present a novel knowledge graph representation learning approach to predict novel interaction partners... |
1607.05175 | Philip Patton | Philip T. Patton, Krishna Pacifici and Jaime Collazo | Inferring habitat quality and habitat selection using static site
occupancy models | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When evaluating the ecological value of land use within a landscape,
investigators typically rely on measures of habitat selection and habitat
quality. Traditional measures of habitat selection and habitat quality require
data from resource intensive study designs (e.g., telemetry or mark-recapture).
Often, managers ... | [
{
"created": "Mon, 18 Jul 2016 16:46:24 GMT",
"version": "v1"
}
] | 2016-07-19 | [
[
"Patton",
"Philip T.",
""
],
[
"Pacifici",
"Krishna",
""
],
[
"Collazo",
"Jaime",
""
]
] | When evaluating the ecological value of land use within a landscape, investigators typically rely on measures of habitat selection and habitat quality. Traditional measures of habitat selection and habitat quality require data from resource intensive study designs (e.g., telemetry or mark-recapture). Often, managers mu... |
2203.06138 | Taylor Petty | Taylor Petty, Jan Hannig, Tunde I Huszar, Hari Iyer | A New String Edit Distance and Applications | 24 pages, 3 figures. Submitted to MDPI Algorithms | null | null | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | String edit distances have been used for decades in applications ranging from
spelling correction and web search suggestions to DNA analysis. Most string
edit distances are variations of the Levenshtein distance and consider only
single-character edits. In forensic applications polymorphic genetic markers
such as sho... | [
{
"created": "Fri, 11 Mar 2022 18:10:49 GMT",
"version": "v1"
},
{
"created": "Thu, 17 Mar 2022 21:33:17 GMT",
"version": "v2"
},
{
"created": "Wed, 11 May 2022 17:27:26 GMT",
"version": "v3"
}
] | 2022-05-12 | [
[
"Petty",
"Taylor",
""
],
[
"Hannig",
"Jan",
""
],
[
"Huszar",
"Tunde I",
""
],
[
"Iyer",
"Hari",
""
]
] | String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only single-character edits. In forensic applications polymorphic genetic markers such as short... |
q-bio/0501029 | Ophir Flomenbom | Ophir Flomenbom, and Joseph Klafter | Uncorrelated two-state single molecule trajectories from reducible
kinetic schemes | null | Acta Phys. Pol. B 36, 1527-1535 (2005) | null | null | q-bio.SC | null | Trajectories of on-off events are the output of many single molecule
experiments. Usually, one describes the underlying mechanism that generates the
trajectory using a kinetic scheme, and by analyzing the trajectory aims at
deducing this scheme. In a previous work [O. Flomenbom, J. Klafter, and A.
Szabo, submitted (2... | [
{
"created": "Thu, 20 Jan 2005 19:05:47 GMT",
"version": "v1"
}
] | 2010-08-16 | [
[
"Flomenbom",
"Ophir",
""
],
[
"Klafter",
"Joseph",
""
]
] | Trajectories of on-off events are the output of many single molecule experiments. Usually, one describes the underlying mechanism that generates the trajectory using a kinetic scheme, and by analyzing the trajectory aims at deducing this scheme. In a previous work [O. Flomenbom, J. Klafter, and A. Szabo, submitted (200... |
1711.02624 | Glenn Young | Glenn Young and Andrew Belmonte | Fast cheater migration stabilizes coexistence in a public goods dilemma
on networks | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Through the lens of game theory, cooperation is frequently considered an
unsustainable strategy: if an entire population is cooperating, each indi-
vidual can increase its overall fitness by choosing not to cooperate, thereby
still receiving all the benefit of its cooperating neighbors while no longer
expending its o... | [
{
"created": "Tue, 7 Nov 2017 17:39:37 GMT",
"version": "v1"
}
] | 2017-11-08 | [
[
"Young",
"Glenn",
""
],
[
"Belmonte",
"Andrew",
""
]
] | Through the lens of game theory, cooperation is frequently considered an unsustainable strategy: if an entire population is cooperating, each indi- vidual can increase its overall fitness by choosing not to cooperate, thereby still receiving all the benefit of its cooperating neighbors while no longer expending its own... |
1703.10927 | Duc Nguyen | Bao Wang, Zhixiong Zhao, Duc D. Nguyen, Guo-Wei Wei | Feature functional theory - binding predictor (FFT-BP) for the blind
prediction of binding free energies | 25 pages, 11 figures | null | null | null | q-bio.QM cs.LG physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a feature functional theory - binding predictor (FFT-BP) for the
protein-ligand binding affinity prediction. The underpinning assumptions of
FFT-BP are as follows: i) representability: there exists a microscopic feature
vector that can uniquely characterize and distinguish one protein-ligand
complex from a... | [
{
"created": "Fri, 31 Mar 2017 15:00:07 GMT",
"version": "v1"
}
] | 2017-04-03 | [
[
"Wang",
"Bao",
""
],
[
"Zhao",
"Zhixiong",
""
],
[
"Nguyen",
"Duc D.",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | We present a feature functional theory - binding predictor (FFT-BP) for the protein-ligand binding affinity prediction. The underpinning assumptions of FFT-BP are as follows: i) representability: there exists a microscopic feature vector that can uniquely characterize and distinguish one protein-ligand complex from ano... |
2303.14440 | Fatemeh Malekinejad | Atefeh Akbarnia Dafrazi, Tahmineh Mehrabi, Fatemeh Malekinejad | A Bioinformatics Study for Recognition of Hub Genes and Pathways in
Pancreatic Ductal Adenocarcinoma | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | Background: The aim of this study is to use bioinformatics to discover the
biomarkers associated with patients with Pancreatic Ductal
Adenocarcinoma(PDAC).
Material and Methods: GSE28735, GSE15471, and GSE62452 are gene microarray
datasets drived from the GEO database, included 153 PDAC samples and 145 normal
sampl... | [
{
"created": "Sat, 25 Mar 2023 11:26:55 GMT",
"version": "v1"
}
] | 2023-03-28 | [
[
"Dafrazi",
"Atefeh Akbarnia",
""
],
[
"Mehrabi",
"Tahmineh",
""
],
[
"Malekinejad",
"Fatemeh",
""
]
] | Background: The aim of this study is to use bioinformatics to discover the biomarkers associated with patients with Pancreatic Ductal Adenocarcinoma(PDAC). Material and Methods: GSE28735, GSE15471, and GSE62452 are gene microarray datasets drived from the GEO database, included 153 PDAC samples and 145 normal samples. ... |
1609.04699 | Owen Richfield | Owen Richfield, Md. Ashad Alam, Vince Calhoun, Yu-Ping Wang | Learning Schizophrenia Imaging Genetics Data Via Multiple Kernel
Canonical Correlation Analysis | arXiv admin note: text overlap with arXiv:1606.00113 | null | null | null | q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Kernel and Multiple Kernel Canonical Correlation Analysis (CCA) are employed
to classify schizophrenic and healthy patients based on their SNPs, DNA
Methylation and fMRI data. Kernel and Multiple Kernel CCA are popular methods
for finding nonlinear correlations between high-dimensional datasets. Data was
gathered fro... | [
{
"created": "Thu, 15 Sep 2016 15:26:37 GMT",
"version": "v1"
}
] | 2016-09-16 | [
[
"Richfield",
"Owen",
""
],
[
"Alam",
"Md. Ashad",
""
],
[
"Calhoun",
"Vince",
""
],
[
"Wang",
"Yu-Ping",
""
]
] | Kernel and Multiple Kernel Canonical Correlation Analysis (CCA) are employed to classify schizophrenic and healthy patients based on their SNPs, DNA Methylation and fMRI data. Kernel and Multiple Kernel CCA are popular methods for finding nonlinear correlations between high-dimensional datasets. Data was gathered from ... |
1307.4415 | Carl Boettiger | Carl Boettiger and Alan Hastings | No early warning signals for stochastic transitions: insights from large
deviation theory | null | 2013. Proceedings of the Royal Society B: Biological Sciences 280,
20131372-20131372 | 10.1098/rspb.2013.1372 | null | q-bio.PE | http://creativecommons.org/licenses/by/3.0/ | A reply to Drake (2013) "Early warning signals of stochastic switching"
http://dx.doi.org/10.1098/rspb.2013.0686
| [
{
"created": "Tue, 16 Jul 2013 20:11:28 GMT",
"version": "v1"
}
] | 2013-07-18 | [
[
"Boettiger",
"Carl",
""
],
[
"Hastings",
"Alan",
""
]
] | A reply to Drake (2013) "Early warning signals of stochastic switching" http://dx.doi.org/10.1098/rspb.2013.0686 |
1605.02869 | Xiaoli Wu | Qi She, Xiaoli Wu, Beth Jelfs, Adam S. Charles, Rosa H.M.Chan | An Efficient and Flexible Spike Train Model via Empirical Bayes | 16 pages, 20 figures, 3 tables | IEEE Trans. Signal Processing 69 (2021) 3236-3251 | 10.1109/TSP.2021.3076885 | null | q-bio.QM eess.SP q-bio.NC stat.ML | http://creativecommons.org/licenses/by-sa/4.0/ | Accurate statistical models of neural spike responses can characterize the
information carried by neural populations. But the limited samples of spike
counts during recording usually result in model overfitting. Besides, current
models assume spike counts to be Poisson-distributed, which ignores the fact
that many ne... | [
{
"created": "Tue, 10 May 2016 06:57:16 GMT",
"version": "v1"
},
{
"created": "Sat, 24 Sep 2016 07:39:29 GMT",
"version": "v2"
},
{
"created": "Mon, 28 May 2018 01:34:32 GMT",
"version": "v3"
},
{
"created": "Wed, 20 Jan 2021 13:20:57 GMT",
"version": "v4"
},
{
"c... | 2021-06-17 | [
[
"She",
"Qi",
""
],
[
"Wu",
"Xiaoli",
""
],
[
"Jelfs",
"Beth",
""
],
[
"Charles",
"Adam S.",
""
],
[
"Chan",
"Rosa H. M.",
""
]
] | Accurate statistical models of neural spike responses can characterize the information carried by neural populations. But the limited samples of spike counts during recording usually result in model overfitting. Besides, current models assume spike counts to be Poisson-distributed, which ignores the fact that many neur... |
0910.2526 | Lee Worden | Lee Worden | Notes from the Greenhouse World: A Study in Coevolution, Planetary
Sustainability, and Community Structure | To appear in a special issue of Ecological Economics in honor of
Richard B. Norgaard | null | 10.1016/j.ecolecon.2009.06.017 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper explores coevolution and governance of common goods using models
of coevolving biospheres, in which adapting populations must collectively
regulate their planet's climate or face extinction. The results support the
Gaia hypothesis against challenges based on the tragedy of the commons: model
creatures are ... | [
{
"created": "Wed, 14 Oct 2009 04:42:04 GMT",
"version": "v1"
}
] | 2009-10-15 | [
[
"Worden",
"Lee",
""
]
] | This paper explores coevolution and governance of common goods using models of coevolving biospheres, in which adapting populations must collectively regulate their planet's climate or face extinction. The results support the Gaia hypothesis against challenges based on the tragedy of the commons: model creatures are of... |
2103.15561 | Arash Mehrjou | Arash Mehrjou, Ashkan Soleymani, Amin Abyaneh, Samir Bhatt, Bernhard
Sch\"olkopf, Stefan Bauer | Pyfectious: An individual-level simulator to discover optimal
containment polices for epidemic diseases | null | null | null | null | q-bio.PE cs.AI cs.LG cs.MA cs.SY eess.SY | http://creativecommons.org/licenses/by/4.0/ | Simulating the spread of infectious diseases in human communities is critical
for predicting the trajectory of an epidemic and verifying various policies to
control the devastating impacts of the outbreak. Many existing simulators are
based on compartment models that divide people into a few subsets and simulate
the ... | [
{
"created": "Wed, 24 Mar 2021 10:54:46 GMT",
"version": "v1"
},
{
"created": "Wed, 21 Apr 2021 00:13:57 GMT",
"version": "v2"
}
] | 2021-04-22 | [
[
"Mehrjou",
"Arash",
""
],
[
"Soleymani",
"Ashkan",
""
],
[
"Abyaneh",
"Amin",
""
],
[
"Bhatt",
"Samir",
""
],
[
"Schölkopf",
"Bernhard",
""
],
[
"Bauer",
"Stefan",
""
]
] | Simulating the spread of infectious diseases in human communities is critical for predicting the trajectory of an epidemic and verifying various policies to control the devastating impacts of the outbreak. Many existing simulators are based on compartment models that divide people into a few subsets and simulate the dy... |
2110.00293 | Mattia Zanella | Giacomo Albi, Giulia Bertaglia, Walter Boscheri, Giacomo Dimarco,
Lorenzo Pareschi, Giuseppe Toscani, Mattia Zanella | Kinetic modelling of epidemic dynamics: social contacts, control with
uncertain data, and multiscale spatial dynamics | null | In: Bellomo N., Chaplain M.A.J. (eds) Predicting Pandemics in a
Globally Connected World, Vol. 1 (2022) Modeling and Simulation in Science,
Engineering and Technology | 10.1007/978-3-030-96562-4_3 | null | q-bio.PE math.OC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this survey we report some recent results in the mathematical modeling of
epidemic phenomena through the use of kinetic equations. We initially consider
models of interaction between agents in which social characteristics play a key
role in the spread of an epidemic, such as the age of individuals, the number
of s... | [
{
"created": "Fri, 1 Oct 2021 09:59:55 GMT",
"version": "v1"
}
] | 2023-09-11 | [
[
"Albi",
"Giacomo",
""
],
[
"Bertaglia",
"Giulia",
""
],
[
"Boscheri",
"Walter",
""
],
[
"Dimarco",
"Giacomo",
""
],
[
"Pareschi",
"Lorenzo",
""
],
[
"Toscani",
"Giuseppe",
""
],
[
"Zanella",
"Mattia",
""
... | In this survey we report some recent results in the mathematical modeling of epidemic phenomena through the use of kinetic equations. We initially consider models of interaction between agents in which social characteristics play a key role in the spread of an epidemic, such as the age of individuals, the number of soc... |
1408.2945 | Jean-Charles Walter | Luca Ciandrini, I. Neri, Jean-Charles Walter, O. Dauloudet, A.
Parmeggiani | Motor proteins traffic regulation by supply-demand balance of resources | 31 pages, 10 figures | Phys. Biol. 11 (2014) 056006 | 10.1088/1478-3975/11/5/056006 | null | q-bio.SC cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In cells and in vitro assays the number of motor proteins involved in
biological transport processes is far from being unlimited. The cytoskeletal
binding sites are in contact with the same finite reservoir of motors (either
the cytosol or the flow chamber) and hence compete for recruiting the available
motors, poten... | [
{
"created": "Wed, 13 Aug 2014 08:50:16 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Sep 2014 13:15:59 GMT",
"version": "v2"
}
] | 2014-09-26 | [
[
"Ciandrini",
"Luca",
""
],
[
"Neri",
"I.",
""
],
[
"Walter",
"Jean-Charles",
""
],
[
"Dauloudet",
"O.",
""
],
[
"Parmeggiani",
"A.",
""
]
] | In cells and in vitro assays the number of motor proteins involved in biological transport processes is far from being unlimited. The cytoskeletal binding sites are in contact with the same finite reservoir of motors (either the cytosol or the flow chamber) and hence compete for recruiting the available motors, potenti... |
0901.0530 | Aaron Clauset | Aaron Clauset | Comment on Yu et al., "High Quality Binary Protein Interaction Map of
the Yeast Interactome Network." Science 322, 104 (2008) | 4 pages, 2 figures, 1 table | null | null | null | q-bio.MN physics.data-an q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We test the claim by Yu et al. -- presented in Science 322, 104 (2008) --
that the degree distribution of the yeast (Saccharomyces cerevisiae)
protein-interaction network is best approximated by a power law. Yu et al.
consider three versions of this network. In all three cases, however, we find
the most likely power-... | [
{
"created": "Mon, 5 Jan 2009 18:11:42 GMT",
"version": "v1"
}
] | 2009-01-06 | [
[
"Clauset",
"Aaron",
""
]
] | We test the claim by Yu et al. -- presented in Science 322, 104 (2008) -- that the degree distribution of the yeast (Saccharomyces cerevisiae) protein-interaction network is best approximated by a power law. Yu et al. consider three versions of this network. In all three cases, however, we find the most likely power-la... |
1805.06950 | Kymberleigh Pagel | Wazim Mohammed Ismail, Kymberleigh A. Pagel, Vikas Pejaver, Simo V.
Zhang, Sofia Casasa, Matthew Mort, David N. Cooper, Matthew W. Hahn, and
Predrag Radivojac | The sequencing and interpretation of the genome obtained from a Serbian
individual | 18 pages, 2 figures | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Recent genetic studies and whole-genome sequencing projects have greatly
improved our understanding of human variation and clinically actionable genetic
information. Smaller ethnic populations, however, remain underrepresented in
both individual and large-scale sequencing efforts and hence present an
opportunity to d... | [
{
"created": "Thu, 17 May 2018 20:08:02 GMT",
"version": "v1"
}
] | 2018-05-21 | [
[
"Ismail",
"Wazim Mohammed",
""
],
[
"Pagel",
"Kymberleigh A.",
""
],
[
"Pejaver",
"Vikas",
""
],
[
"Zhang",
"Simo V.",
""
],
[
"Casasa",
"Sofia",
""
],
[
"Mort",
"Matthew",
""
],
[
"Cooper",
"David N.",
""
... | Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both individual and large-scale sequencing efforts and hence present an opportunity to dis... |
2111.05727 | Carlos Oscar S. Sorzano | C.O.S. Sorzano | The mathematics of contagious diseases and their limitations in
forecasting | null | null | null | null | q-bio.PE stat.AP | http://creativecommons.org/licenses/by-nc-nd/4.0/ | This article explores mathematical models for understanding the evolution of
contagious diseases. The most widely known set of models are the compartmental
ones, which are based on a set of differential equations. But these are not the
only models. This review visits many different families of models.
Additionally, w... | [
{
"created": "Wed, 10 Nov 2021 15:11:11 GMT",
"version": "v1"
},
{
"created": "Sat, 4 Dec 2021 06:56:02 GMT",
"version": "v2"
}
] | 2021-12-07 | [
[
"Sorzano",
"C. O. S.",
""
]
] | This article explores mathematical models for understanding the evolution of contagious diseases. The most widely known set of models are the compartmental ones, which are based on a set of differential equations. But these are not the only models. This review visits many different families of models. Additionally, we ... |
1904.05375 | Daniel Moyer | Daniel Moyer, Greg Ver Steeg, Chantal M. W. Tax, Paul M. Thompson | Scanner Invariant Representations for Diffusion MRI Harmonization | null | null | null | null | q-bio.QM cs.LG eess.IV stat.AP stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Purpose: In the present work we describe the correction of diffusion-weighted
MRI for site and scanner biases using a novel method based on invariant
representation.
Theory and Methods: Pooled imaging data from multiple sources are subject to
variation between the sources. Correcting for these biases has become ver... | [
{
"created": "Wed, 10 Apr 2019 18:10:19 GMT",
"version": "v1"
},
{
"created": "Fri, 31 Jan 2020 19:11:39 GMT",
"version": "v2"
}
] | 2020-02-04 | [
[
"Moyer",
"Daniel",
""
],
[
"Steeg",
"Greg Ver",
""
],
[
"Tax",
"Chantal M. W.",
""
],
[
"Thompson",
"Paul M.",
""
]
] | Purpose: In the present work we describe the correction of diffusion-weighted MRI for site and scanner biases using a novel method based on invariant representation. Theory and Methods: Pooled imaging data from multiple sources are subject to variation between the sources. Correcting for these biases has become very im... |
0811.1289 | Eytan Domany | Yuval Tabach, Ran Brosh, Yossi Buganim, Anat Reiner, Or Zuk, Assif
Yitzhaky, Mark Koudritsky, Varda Rotter and Eytan Domany | Wide-Scale Analysis of Human Functional Transcription Factor Binding
Reveals a Strong Bias towards the Transcription Start Site | 31 pages, including Supplementary Information and figures | PLoS ONE Issue 8, e807 Aug 2007 | 10.1371/journal.pone.0000807 | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a novel method to screen the promoters of a set of genes with
shared biological function, against a precompiled library of motifs, and find
those motifs which are statistically over-represented in the gene set. The gene
sets were obtained from the functional Gene Ontology (GO) classification; for
each se... | [
{
"created": "Sat, 8 Nov 2008 18:45:02 GMT",
"version": "v1"
}
] | 2008-11-11 | [
[
"Tabach",
"Yuval",
""
],
[
"Brosh",
"Ran",
""
],
[
"Buganim",
"Yossi",
""
],
[
"Reiner",
"Anat",
""
],
[
"Zuk",
"Or",
""
],
[
"Yitzhaky",
"Assif",
""
],
[
"Koudritsky",
"Mark",
""
],
[
"Rotter",
... | We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. The gene sets were obtained from the functional Gene Ontology (GO) classification; for each set ... |
2310.01562 | Matus Medo | Mat\'u\v{s} Medo, Michaela Medov\'a | A comprehensive comparison of tools for fitting mutational signatures | 15 pages, 6 figures, Supporting Information included | null | null | null | q-bio.GN q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Mutational signatures connect characteristic mutational patterns in the
genome with biological processes that take place in the tumor tissues. Analysis
of mutational signatures can help elucidate tumor evolution, prognosis, and
therapeutic strategies. Although tools for extracting mutational signatures de
novo have b... | [
{
"created": "Mon, 2 Oct 2023 18:53:44 GMT",
"version": "v1"
}
] | 2023-10-04 | [
[
"Medo",
"Matúš",
""
],
[
"Medová",
"Michaela",
""
]
] | Mutational signatures connect characteristic mutational patterns in the genome with biological processes that take place in the tumor tissues. Analysis of mutational signatures can help elucidate tumor evolution, prognosis, and therapeutic strategies. Although tools for extracting mutational signatures de novo have bee... |
1306.0199 | Osamu Narikiyo | Daisuke Sato, Osamu Narikiyo | Replication of proto-RNAs sustained by ligase-helicase cycle in oligomer
world | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A mechanism of the replication of proto-RNAs in oligomer world is proposed.
The replication is carried out by a minimum cycle which is sustained by a
ligase and a helicase. We expect that such a cycle actually worked in the
primordial soup and can be constructed in vitro. By computer simulation the
products of the re... | [
{
"created": "Sun, 2 Jun 2013 11:54:22 GMT",
"version": "v1"
}
] | 2013-06-04 | [
[
"Sato",
"Daisuke",
""
],
[
"Narikiyo",
"Osamu",
""
]
] | A mechanism of the replication of proto-RNAs in oligomer world is proposed. The replication is carried out by a minimum cycle which is sustained by a ligase and a helicase. We expect that such a cycle actually worked in the primordial soup and can be constructed in vitro. By computer simulation the products of the repl... |
1910.05546 | Zedong Bi | Zedong Bi and Changsong Zhou | Understanding the computation of time using neural network models | null | PNAS 117 (19) 10530-10540, 2020 | 10.1073/pnas.1921609117 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | To maximize future rewards in this ever-changing world, animals must be able
to discover the temporal structure of stimuli and then anticipate or act
correctly at the right time. How the animals perceive, maintain, and use time
intervals ranging from hundreds of milliseconds to multi-seconds in working
memory? How te... | [
{
"created": "Sat, 12 Oct 2019 10:07:42 GMT",
"version": "v1"
},
{
"created": "Mon, 9 Dec 2019 12:48:46 GMT",
"version": "v2"
},
{
"created": "Mon, 2 Mar 2020 14:41:37 GMT",
"version": "v3"
},
{
"created": "Tue, 7 Jul 2020 11:58:25 GMT",
"version": "v4"
}
] | 2020-07-08 | [
[
"Bi",
"Zedong",
""
],
[
"Zhou",
"Changsong",
""
]
] | To maximize future rewards in this ever-changing world, animals must be able to discover the temporal structure of stimuli and then anticipate or act correctly at the right time. How the animals perceive, maintain, and use time intervals ranging from hundreds of milliseconds to multi-seconds in working memory? How temp... |
1305.6635 | Peter Pfaffelhuber | Martin Jansen and Peter Pfaffelhuber | Stochastic gene expression with delay | 14 pages | null | null | null | q-bio.MN math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The expression of genes usually follows a two-step procedure. First, a gene
(encoded in the genome) is transcribed resulting in a strand of (messenger)
RNA. Afterwards, the RNA is translated into protein. Classically, this gene
expression is modeled using a Markov jump process including activation and
deactivation of... | [
{
"created": "Tue, 28 May 2013 21:14:02 GMT",
"version": "v1"
},
{
"created": "Thu, 7 Aug 2014 15:24:36 GMT",
"version": "v2"
}
] | 2014-08-08 | [
[
"Jansen",
"Martin",
""
],
[
"Pfaffelhuber",
"Peter",
""
]
] | The expression of genes usually follows a two-step procedure. First, a gene (encoded in the genome) is transcribed resulting in a strand of (messenger) RNA. Afterwards, the RNA is translated into protein. Classically, this gene expression is modeled using a Markov jump process including activation and deactivation of t... |
1509.05121 | Irineo Cabreros | Irineo Cabreros, Emmanuel Abbe and Aristotelis Tsirigos | Detecting Community Structures in Hi-C Genomic Data | null | null | null | null | q-bio.GN cs.SI stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Community detection (CD) algorithms are applied to Hi-C data to discover new
communities of loci in the 3D conformation of human and mouse DNA. We find that
CD has some distinct advantages over pre-existing methods: (1) it is capable of
finding a variable number of communities, (2) it can detect communities of DNA
lo... | [
{
"created": "Thu, 17 Sep 2015 04:23:55 GMT",
"version": "v1"
}
] | 2015-09-18 | [
[
"Cabreros",
"Irineo",
""
],
[
"Abbe",
"Emmanuel",
""
],
[
"Tsirigos",
"Aristotelis",
""
]
] | Community detection (CD) algorithms are applied to Hi-C data to discover new communities of loci in the 3D conformation of human and mouse DNA. We find that CD has some distinct advantages over pre-existing methods: (1) it is capable of finding a variable number of communities, (2) it can detect communities of DNA loci... |
0812.2451 | Michel Aoun | Michel Aoun, Annick Hourmant, Jean-Yves Cabon | Efficacy of Put and Spd sprayed on leaves from Brassica juncea plants
against Cd2+-induced oxidative stress | Submitted to Chemosphere, 30 pages, 10 Figures and 3 tables | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The protective effect exerted by polyamines (Put and Spd) against cadmium
(Cd) stress was investigated in Brassica juncea plants. Treatment with CdCl2
(75 micro-Mole) resulted in a rise of Cd accumulation, a decrease of fresh and
dry weights in every plant organ, an increase of free polyamine content at limb
and stem... | [
{
"created": "Fri, 12 Dec 2008 18:28:05 GMT",
"version": "v1"
}
] | 2008-12-15 | [
[
"Aoun",
"Michel",
""
],
[
"Hourmant",
"Annick",
""
],
[
"Cabon",
"Jean-Yves",
""
]
] | The protective effect exerted by polyamines (Put and Spd) against cadmium (Cd) stress was investigated in Brassica juncea plants. Treatment with CdCl2 (75 micro-Mole) resulted in a rise of Cd accumulation, a decrease of fresh and dry weights in every plant organ, an increase of free polyamine content at limb and stem l... |
2303.11944 | Kevin Schmidt | Kevin Schmidt, Othalia Larue, Ray Kulhanek, Dylan Flaute, Razvan
Veliche, Christian Manasseh, Nelson Dellis, Scott Clouse, Jared Culbertson,
Steve Rogers | Representational Tenets for Memory Athletics | null | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/publicdomain/zero/1.0/ | We describe the current state of world-class memory competitions, including
the methods used to prepare for and compete in memory competitions, based on
the subjective report of World Memory Championship Grandmaster and co-author
Nelson Dellis. We then explore the reported experiences through the lens of the
Simulate... | [
{
"created": "Wed, 22 Feb 2023 19:40:59 GMT",
"version": "v1"
}
] | 2023-03-22 | [
[
"Schmidt",
"Kevin",
""
],
[
"Larue",
"Othalia",
""
],
[
"Kulhanek",
"Ray",
""
],
[
"Flaute",
"Dylan",
""
],
[
"Veliche",
"Razvan",
""
],
[
"Manasseh",
"Christian",
""
],
[
"Dellis",
"Nelson",
""
],
[
... | We describe the current state of world-class memory competitions, including the methods used to prepare for and compete in memory competitions, based on the subjective report of World Memory Championship Grandmaster and co-author Nelson Dellis. We then explore the reported experiences through the lens of the Simulated,... |
2304.04662 | Tunca Do\u{g}an | Atakan Y\"uksel, Erva Ulusoy, Atabey \"Unl\"u, Tunca Do\u{g}an | SELFormer: Molecular Representation Learning via SELFIES Language Models | 22 pages, 4 figures, 8 tables | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Automated computational analysis of the vast chemical space is critical for
numerous fields of research such as drug discovery and material science.
Representation learning techniques have recently been employed with the primary
objective of generating compact and informative numerical expressions of
complex data. On... | [
{
"created": "Mon, 10 Apr 2023 15:38:25 GMT",
"version": "v1"
},
{
"created": "Thu, 25 May 2023 09:14:14 GMT",
"version": "v2"
}
] | 2023-05-26 | [
[
"Yüksel",
"Atakan",
""
],
[
"Ulusoy",
"Erva",
""
],
[
"Ünlü",
"Atabey",
""
],
[
"Doğan",
"Tunca",
""
]
] | Automated computational analysis of the vast chemical space is critical for numerous fields of research such as drug discovery and material science. Representation learning techniques have recently been employed with the primary objective of generating compact and informative numerical expressions of complex data. One ... |
2304.04977 | Hesham Abdullah | Ahmed M. Mousbah, Hesham M. Abdullah, Waleed S. Mohammed, Ali M.
El-Refy, Mohamed Helmy | Buffalo Genome Projects: Current Situation and Future Perspective in
Improving Breeding Programs | two figures | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Buffaloes are farm animals that contribute to food security by providing high
quality meat and milk. They can better tolerate the adverse effects of global
climate change on their meat and milk production. Despite their advantages,
buffaloes are heavily neglected animals with fewer studies compared to other
farm anim... | [
{
"created": "Tue, 11 Apr 2023 04:50:05 GMT",
"version": "v1"
}
] | 2023-04-12 | [
[
"Mousbah",
"Ahmed M.",
""
],
[
"Abdullah",
"Hesham M.",
""
],
[
"Mohammed",
"Waleed S.",
""
],
[
"El-Refy",
"Ali M.",
""
],
[
"Helmy",
"Mohamed",
""
]
] | Buffaloes are farm animals that contribute to food security by providing high quality meat and milk. They can better tolerate the adverse effects of global climate change on their meat and milk production. Despite their advantages, buffaloes are heavily neglected animals with fewer studies compared to other farm animal... |
1401.8205 | Florian Hartig | Florian Hartig, Claudia Dislich, Thorsten Wiegand and Andreas Huth | Technical Note: Approximate Bayesian parameterization of a process-based
tropical forest model | Corresponds, apart from layout, to the final version published in
Biogeosciences | Biogeosciences (2014) 11, 1261-1272 | 10.5194/bg-11-1261-2014 | null | q-bio.PE stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inverse parameter estimation of process-based models is a long-standing
problem in many scientific disciplines. A key question for inverse parameter
estimation is how to define the metric that quantifies how well model
predictions fit to the data. This metric can be expressed by general cost or
objective functions, b... | [
{
"created": "Fri, 31 Jan 2014 16:02:33 GMT",
"version": "v1"
},
{
"created": "Thu, 8 May 2014 15:35:45 GMT",
"version": "v2"
}
] | 2014-05-09 | [
[
"Hartig",
"Florian",
""
],
[
"Dislich",
"Claudia",
""
],
[
"Wiegand",
"Thorsten",
""
],
[
"Huth",
"Andreas",
""
]
] | Inverse parameter estimation of process-based models is a long-standing problem in many scientific disciplines. A key question for inverse parameter estimation is how to define the metric that quantifies how well model predictions fit to the data. This metric can be expressed by general cost or objective functions, but... |
1711.04266 | David Holcman | Zeev Schuss, Kimsy Tor, David Holcman | Do cells sense time by number of divisions? | No comments | null | null | null | q-bio.SC math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Do biological cells sense time by the number of their divisions, a process
that ends at senescence? We consider the question "can the cell's perception of
time be expressed through the length of the shortest telomere?" The answer is
that the absolute time before senescence cannot be expressed by the telomere's
length... | [
{
"created": "Sun, 12 Nov 2017 10:38:53 GMT",
"version": "v1"
}
] | 2017-11-15 | [
[
"Schuss",
"Zeev",
""
],
[
"Tor",
"Kimsy",
""
],
[
"Holcman",
"David",
""
]
] | Do biological cells sense time by the number of their divisions, a process that ends at senescence? We consider the question "can the cell's perception of time be expressed through the length of the shortest telomere?" The answer is that the absolute time before senescence cannot be expressed by the telomere's length a... |
2201.11717 | Cristiano Capone | Cristiano Capone, Cosimo Lupo, Paolo Muratore, Pier Stanislao Paolucci | Burst-dependent plasticity and dendritic amplification support
target-based learning and hierarchical imitation learning | 9 pages, 3 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The brain can learn to solve a wide range of tasks with high temporal and
energetic efficiency. However, most biological models are composed of simple
single compartment neurons and cannot achieve the state-of-art performances of
artificial intelligence. We propose a multi-compartment model of pyramidal
neuron, in wh... | [
{
"created": "Thu, 27 Jan 2022 18:17:45 GMT",
"version": "v1"
}
] | 2022-01-28 | [
[
"Capone",
"Cristiano",
""
],
[
"Lupo",
"Cosimo",
""
],
[
"Muratore",
"Paolo",
""
],
[
"Paolucci",
"Pier Stanislao",
""
]
] | The brain can learn to solve a wide range of tasks with high temporal and energetic efficiency. However, most biological models are composed of simple single compartment neurons and cannot achieve the state-of-art performances of artificial intelligence. We propose a multi-compartment model of pyramidal neuron, in whic... |
2106.13527 | Kang Hao Cheong Prof | Tao Wen, Eugene V. Koonin, Kang Hao Cheong | Alternating active-dormitive strategy enables overtaking by
disadvantaged prey through Parrondo's paradox | null | null | null | null | q-bio.PE nlin.CD | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Dormancy is a costly adaptive strategy that is widespread among living
organisms inhabiting diverse environments. We explore mathematical models of
predator-prey systems, in order to assess the impact of prey dormancy on the
competition between two types of prey, a perennially active (PA) and capable of
entering dorm... | [
{
"created": "Fri, 25 Jun 2021 09:37:06 GMT",
"version": "v1"
}
] | 2021-06-28 | [
[
"Wen",
"Tao",
""
],
[
"Koonin",
"Eugene V.",
""
],
[
"Cheong",
"Kang Hao",
""
]
] | Dormancy is a costly adaptive strategy that is widespread among living organisms inhabiting diverse environments. We explore mathematical models of predator-prey systems, in order to assess the impact of prey dormancy on the competition between two types of prey, a perennially active (PA) and capable of entering dorman... |
1907.08946 | Misha Tsodyks | Antonios Georgiou, Mikhail Katkov, Misha Tsodyks | Retroactive Interference Model of Power-Law Forgetting | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Memory and forgetting constitute two sides of the same coin, and although the
first has been rigorously investigated, the latter is often overlooked. A
number of experiments under the realm of psychology and experimental
neuroscience have described the properties of forgetting in humans and animals,
showing that forg... | [
{
"created": "Sun, 21 Jul 2019 09:49:23 GMT",
"version": "v1"
}
] | 2019-07-23 | [
[
"Georgiou",
"Antonios",
""
],
[
"Katkov",
"Mikhail",
""
],
[
"Tsodyks",
"Misha",
""
]
] | Memory and forgetting constitute two sides of the same coin, and although the first has been rigorously investigated, the latter is often overlooked. A number of experiments under the realm of psychology and experimental neuroscience have described the properties of forgetting in humans and animals, showing that forget... |
1210.0495 | Andr\'as Szil\'agyi | D\'aniel Gy\"orffy, P\'eter Z\'avodszky and Andr\'as Szil\'agyi | "Pull moves" for rectangular lattice polymer models are not fully
reversible | 4 pages, 2 figures. To be published in IEEE/ACM Transactions on
Computational Biology and Bioinformatics | IEEE/ACM Trans Comput Biol Bioinform., vol. 9(6), pp. 1847-49,
2012 | 10.1109/TCBB.2012.129 | null | q-bio.BM cond-mat.soft physics.comp-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | "Pull moves" is a popular move set for lattice polymer model simulations. We
show that the proof given for its reversibility earlier is flawed, and some
moves are irreversible, which leads to biases in the parameters estimated from
the simulations. We show how to make the move set fully reversible.
| [
{
"created": "Mon, 1 Oct 2012 18:23:48 GMT",
"version": "v1"
}
] | 2013-01-04 | [
[
"Györffy",
"Dániel",
""
],
[
"Závodszky",
"Péter",
""
],
[
"Szilágyi",
"András",
""
]
] | "Pull moves" is a popular move set for lattice polymer model simulations. We show that the proof given for its reversibility earlier is flawed, and some moves are irreversible, which leads to biases in the parameters estimated from the simulations. We show how to make the move set fully reversible. |
1907.01504 | Nikolay Koshev | Nikolay Koshev, Nikolay Yavich, Mikhail Malovichko, Ekaterina
Skidchenko, Maxim Fedorov | FEM-based Scalp-to-Cortex data mapping via the solution of the Cauchy
problem | 16 pages, 6 figures | null | null | null | q-bio.NC physics.comp-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose an approach and the numerical algorithm for pre-processing of the
electroencephalography (EEG) data, enabling to generate an accurate mapping of
the potential from the measurement area - scalp - to the brain surface. The
algorithm based on the solution of ill-posed Cauchy problem for the Laplace's
equation... | [
{
"created": "Fri, 21 Jun 2019 12:47:12 GMT",
"version": "v1"
}
] | 2019-07-03 | [
[
"Koshev",
"Nikolay",
""
],
[
"Yavich",
"Nikolay",
""
],
[
"Malovichko",
"Mikhail",
""
],
[
"Skidchenko",
"Ekaterina",
""
],
[
"Fedorov",
"Maxim",
""
]
] | We propose an approach and the numerical algorithm for pre-processing of the electroencephalography (EEG) data, enabling to generate an accurate mapping of the potential from the measurement area - scalp - to the brain surface. The algorithm based on the solution of ill-posed Cauchy problem for the Laplace's equation u... |
1605.01096 | Daniel Toker | Daniel Toker and Friedrich Sommer | Moving Past the Minimum Information Partition: How To Quickly and
Accurately Calculate Integrated Information | 21 pages, 9 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An outstanding challenge with the Integrated Information Theory of
Consciousness (IIT) is to find a way of rapidly and accurately calculating
integrated information from neural data. A number of measures of integrated
information based on time series data have been proposed, but most measures
require finding the Mini... | [
{
"created": "Tue, 3 May 2016 21:26:17 GMT",
"version": "v1"
}
] | 2016-05-05 | [
[
"Toker",
"Daniel",
""
],
[
"Sommer",
"Friedrich",
""
]
] | An outstanding challenge with the Integrated Information Theory of Consciousness (IIT) is to find a way of rapidly and accurately calculating integrated information from neural data. A number of measures of integrated information based on time series data have been proposed, but most measures require finding the Minimu... |
2010.03277 | Niklas Kolbe | Anne Dietrich, Niklas Kolbe, Nikolaos Sfakianakis and Christina
Surulescu | Multiscale modeling of glioma invasion: from receptor binding to
flux-limited macroscopic PDEs | 28 pages, 7 figures | null | null | null | q-bio.TO math.AP q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a novel approach to modeling cell migration in an anisotropic
environment with biochemical heterogeneity and interspecies interactions, using
as a paradigm glioma invasion in brain tissue under the influence of
hypoxia-triggered angiogenesis. The multiscale procedure links single-cell and
mesoscopic dynami... | [
{
"created": "Wed, 7 Oct 2020 08:58:44 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Apr 2021 11:04:32 GMT",
"version": "v2"
}
] | 2021-04-14 | [
[
"Dietrich",
"Anne",
""
],
[
"Kolbe",
"Niklas",
""
],
[
"Sfakianakis",
"Nikolaos",
""
],
[
"Surulescu",
"Christina",
""
]
] | We propose a novel approach to modeling cell migration in an anisotropic environment with biochemical heterogeneity and interspecies interactions, using as a paradigm glioma invasion in brain tissue under the influence of hypoxia-triggered angiogenesis. The multiscale procedure links single-cell and mesoscopic dynamics... |
2005.05784 | Mengjia Xu | Mengjia Xu, David Lopez Sanz, Pilar Garces, Fernando Maestu, Quanzheng
Li, Dimitrios Pantazis | A Graph Gaussian Embedding Method for Predicting Alzheimer's Disease
Progression with MEG Brain Networks | null | null | null | null | q-bio.NC cs.LG eess.SP stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Characterizing the subtle changes of functional brain networks associated
with the pathological cascade of Alzheimer's disease (AD) is important for
early diagnosis and prediction of disease progression prior to clinical
symptoms. We developed a new deep learning method, termed multiple graph
Gaussian embedding model... | [
{
"created": "Fri, 8 May 2020 02:29:24 GMT",
"version": "v1"
},
{
"created": "Tue, 10 Nov 2020 21:00:39 GMT",
"version": "v2"
}
] | 2020-11-12 | [
[
"Xu",
"Mengjia",
""
],
[
"Sanz",
"David Lopez",
""
],
[
"Garces",
"Pilar",
""
],
[
"Maestu",
"Fernando",
""
],
[
"Li",
"Quanzheng",
""
],
[
"Pantazis",
"Dimitrios",
""
]
] | Characterizing the subtle changes of functional brain networks associated with the pathological cascade of Alzheimer's disease (AD) is important for early diagnosis and prediction of disease progression prior to clinical symptoms. We developed a new deep learning method, termed multiple graph Gaussian embedding model (... |
1405.2044 | Fernando Antoneli Jr | Jean P. Zukurov, Sieberth do Nascimento-Brito, Angela C. Volpini,
Guilherme Oliveira, Luiz Mario R. Janini and Fernando Antoneli | Estimation of genetic diversity in viral populations from next
generation sequencing data with extremely deep coverage | 30 pages, 5 figures, 2 tables, Tanden is written in C# (Microsoft),
runs on the Windows operating system, and can be downloaded from:
http://tanden.url.ph | Algorithms for Molecular Biology, 2016, 11:2 | 10.1186/s13015-016-0064-x | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we propose a method and discuss its computational
implementation as an integrated tool for the analysis of viral genetic
diversity on data generated by high-throughput sequencing. Most methods for
viral diversity estimation proposed so far are intended to take benefit of the
longer reads produced by som... | [
{
"created": "Thu, 8 May 2014 18:58:12 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Sep 2014 17:11:20 GMT",
"version": "v2"
},
{
"created": "Tue, 9 Dec 2014 12:24:46 GMT",
"version": "v3"
},
{
"created": "Fri, 24 Apr 2015 13:27:13 GMT",
"version": "v4"
}
] | 2016-03-22 | [
[
"Zukurov",
"Jean P.",
""
],
[
"Nascimento-Brito",
"Sieberth do",
""
],
[
"Volpini",
"Angela C.",
""
],
[
"Oliveira",
"Guilherme",
""
],
[
"Janini",
"Luiz Mario R.",
""
],
[
"Antoneli",
"Fernando",
""
]
] | In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. Most methods for viral diversity estimation proposed so far are intended to take benefit of the longer reads produced by some ... |
1512.05039 | Trinh Xuan Hoang | Trinh X. Hoang, Hoa Lan Trinh, Achille Giacometti, Rudolf Podgornik,
Jayanth R. Banavar and Amos Maritan | Phase diagram of the ground states of DNA condensates | 5 pages, 5 figures, to appear in PRE Rapid Communication | Phys. Rev. E (Rapid Communications) 92, 060701(R) (2015) | 10.1103/PhysRevE.92.060701 | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phase diagram of the ground states of DNA in a bad solvent is studied for a
semi-flexible polymer model with a generalized local elastic bending potential
characterized by a nonlinearity parameter $x$ and effective self-attraction
promoting compaction. $x=1$ corresponds to the worm-like chain model.
Surprisingly, the... | [
{
"created": "Wed, 16 Dec 2015 03:43:12 GMT",
"version": "v1"
}
] | 2016-01-28 | [
[
"Hoang",
"Trinh X.",
""
],
[
"Trinh",
"Hoa Lan",
""
],
[
"Giacometti",
"Achille",
""
],
[
"Podgornik",
"Rudolf",
""
],
[
"Banavar",
"Jayanth R.",
""
],
[
"Maritan",
"Amos",
""
]
] | Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter $x$ and effective self-attraction promoting compaction. $x=1$ corresponds to the worm-like chain model. Surprisingly, the p... |
2208.09559 | Chengyu Liu | Chengyu Liu, Wei Wang | Neural network facilitated ab initio derivation of linear formula: A
case study on formulating the relationship between DNA motifs and gene
expression | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Developing models with high interpretability and even deriving formulas to
quantify relationships between biological data is an emerging need. We propose
here a framework for ab initio derivation of sequence motifs and linear formula
using a new approach based on the interpretable neural network model called
contextu... | [
{
"created": "Fri, 19 Aug 2022 22:29:30 GMT",
"version": "v1"
}
] | 2022-08-23 | [
[
"Liu",
"Chengyu",
""
],
[
"Wang",
"Wei",
""
]
] | Developing models with high interpretability and even deriving formulas to quantify relationships between biological data is an emerging need. We propose here a framework for ab initio derivation of sequence motifs and linear formula using a new approach based on the interpretable neural network model called contextual... |
2405.09748 | Okezue Bell | Okezue Bell, Anthony Bell | A Mathematical Reconstruction of Endothelial Cell Networks | 14 pages, 9 figures | null | null | null | q-bio.CB math.CO math.GR q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Endothelial cells form the linchpin of vascular and lymphatic systems,
creating intricate networks that are pivotal for angiogenesis, controlling
vessel permeability, and maintaining tissue homeostasis. Despite their critical
roles, there is no rigorous mathematical framework to represent the
connectivity structure o... | [
{
"created": "Thu, 16 May 2024 01:14:13 GMT",
"version": "v1"
}
] | 2024-05-17 | [
[
"Bell",
"Okezue",
""
],
[
"Bell",
"Anthony",
""
]
] | Endothelial cells form the linchpin of vascular and lymphatic systems, creating intricate networks that are pivotal for angiogenesis, controlling vessel permeability, and maintaining tissue homeostasis. Despite their critical roles, there is no rigorous mathematical framework to represent the connectivity structure of ... |
q-bio/0401025 | Alan McKane | Barbara Drossel, Alan McKane and Christopher Quince | The impact of non-linear functional responses on the long-term evolution
of food web structure | 16 pages, 7 figures | null | null | null | q-bio.PE cond-mat.stat-mech | null | We investigate the long-term web structure emerging in evolutionary food web
models when different types of functional responses are used. We find that
large and complex webs with several trophic layers arise only if the population
dynamics is such that it allows predators to focus on their best prey species.
This ca... | [
{
"created": "Mon, 19 Jan 2004 15:07:55 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Drossel",
"Barbara",
""
],
[
"McKane",
"Alan",
""
],
[
"Quince",
"Christopher",
""
]
] | We investigate the long-term web structure emerging in evolutionary food web models when different types of functional responses are used. We find that large and complex webs with several trophic layers arise only if the population dynamics is such that it allows predators to focus on their best prey species. This can ... |
1107.1507 | Carla Goldman | Lucas W. Rossi and Carla Goldman | Jamming of molecular motors as a tool for transport cargos along
microtubules | null | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The hopping model for cargo transport by molecular motors introduced in Refs.
goldman1, goldman2, is extended here in order to incorporate the movement of
cargo-motor complexes. In this context, hopping process expresses the
possibility for cargo to be exchanged between neighbor motors at a microtubule
where the tran... | [
{
"created": "Thu, 7 Jul 2011 20:09:58 GMT",
"version": "v1"
},
{
"created": "Tue, 1 Nov 2011 20:07:03 GMT",
"version": "v2"
},
{
"created": "Thu, 26 Jan 2012 15:47:49 GMT",
"version": "v3"
}
] | 2012-01-27 | [
[
"Rossi",
"Lucas W.",
""
],
[
"Goldman",
"Carla",
""
]
] | The hopping model for cargo transport by molecular motors introduced in Refs. goldman1, goldman2, is extended here in order to incorporate the movement of cargo-motor complexes. In this context, hopping process expresses the possibility for cargo to be exchanged between neighbor motors at a microtubule where the transp... |
q-bio/0506002 | D. Allan Drummond | D. Allan Drummond, Jesse D. Bloom, Christoph Adami, Claus O. Wilke,
Frances H. Arnold | Why highly expressed proteins evolve slowly | 40 pages, 3 figures, with supporting information | Proc. Nat'l. Acad. Sci. USA 102(40):14338-14343 (2005) | 10.1073/pnas.0504070102 | null | q-bio.PE q-bio.GN | null | Much recent work has explored molecular and population-genetic constraints on
the rate of protein sequence evolution. The best predictor of evolutionary rate
is expression level, for reasons which have remained unexplained. Here, we
hypothesize that selection to reduce the burden of protein misfolding will
favor prot... | [
{
"created": "Thu, 2 Jun 2005 17:20:47 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Aug 2005 04:32:03 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Drummond",
"D. Allan",
""
],
[
"Bloom",
"Jesse D.",
""
],
[
"Adami",
"Christoph",
""
],
[
"Wilke",
"Claus O.",
""
],
[
"Arnold",
"Frances H.",
""
]
] | Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons which have remained unexplained. Here, we hypothesize that selection to reduce the burden of protein misfolding will favor protei... |
1507.08734 | Ruriko Yoshida | Jing Xi and Jin Xie and Ruriko Yoshida and Stefan Forcey | Stochastic safety radius on Neighbor-Joining method and Balanced Minimal
Evolution on small trees | 6 figures. 12 pages | null | null | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A distance-based method to reconstruct a phylogenetic tree with $n$ leaves
takes a distance matrix, $n \times n$ symmetric matrix with $0$s in the
diagonal, as its input and reconstructs a tree with $n$ leaves using tools in
combinatorics. A safety radius is a radius from a tree metric (a distance
matrix realizing a ... | [
{
"created": "Fri, 31 Jul 2015 02:47:11 GMT",
"version": "v1"
}
] | 2015-08-03 | [
[
"Xi",
"Jing",
""
],
[
"Xie",
"Jin",
""
],
[
"Yoshida",
"Ruriko",
""
],
[
"Forcey",
"Stefan",
""
]
] | A distance-based method to reconstruct a phylogenetic tree with $n$ leaves takes a distance matrix, $n \times n$ symmetric matrix with $0$s in the diagonal, as its input and reconstructs a tree with $n$ leaves using tools in combinatorics. A safety radius is a radius from a tree metric (a distance matrix realizing a tr... |
0907.5539 | Leah B. Shaw | Leah B. Shaw, Ira B. Schwartz | Enhanced vaccine control of epidemics in adaptive networks | null | null | 10.1103/PhysRevE.81.046120 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study vaccine control for disease spread on an adaptive network modeling
disease avoidance behavior. Control is implemented by adding Poisson
distributed vaccination of susceptibles. We show that vaccine control is much
more effective in adaptive networks than in static networks due to an
interaction between the a... | [
{
"created": "Fri, 31 Jul 2009 14:12:44 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Shaw",
"Leah B.",
""
],
[
"Schwartz",
"Ira B.",
""
]
] | We study vaccine control for disease spread on an adaptive network modeling disease avoidance behavior. Control is implemented by adding Poisson distributed vaccination of susceptibles. We show that vaccine control is much more effective in adaptive networks than in static networks due to an interaction between the ada... |
1808.04860 | Mohsen Nabian | Mohsen Nabian, Uichiro Narusawa | Quantification of Alveolar Recruitment for the Optimization of
Mechanical Ventilation using Quasi-static Pressure Volume Curve | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quasi-static, pulmonary pressure-volume (P-V) curves over an
inflation-deflation cycle are analyzed using a respiratory system model (RSM),
which had been developed for quantitative characterization of the mechanical
behavior of the total respiratory system. Optimum mechanical ventilation
setting of Positive End Expi... | [
{
"created": "Sat, 11 Aug 2018 02:05:27 GMT",
"version": "v1"
}
] | 2018-08-16 | [
[
"Nabian",
"Mohsen",
""
],
[
"Narusawa",
"Uichiro",
""
]
] | Quasi-static, pulmonary pressure-volume (P-V) curves over an inflation-deflation cycle are analyzed using a respiratory system model (RSM), which had been developed for quantitative characterization of the mechanical behavior of the total respiratory system. Optimum mechanical ventilation setting of Positive End Expira... |
1210.2140 | Sheng-Yong Xu | Jiongwei Xue and Shengyong Xu | Natural electromagnetic waveguide structures based on myelin sheath in
the neural system | 24 pages, 7 figures | null | null | null | q-bio.NC cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The saltatory propagation of action potentials on myelinated axons is
conventionally explained by the mechanism employing local circuit ionic current
flows between nodes of Ranvier. Under this framework, the myelin sheath with up
to 100 layers of membrane only serves as the insulating shell. The speed of
action poten... | [
{
"created": "Mon, 8 Oct 2012 03:41:45 GMT",
"version": "v1"
}
] | 2012-10-09 | [
[
"Xue",
"Jiongwei",
""
],
[
"Xu",
"Shengyong",
""
]
] | The saltatory propagation of action potentials on myelinated axons is conventionally explained by the mechanism employing local circuit ionic current flows between nodes of Ranvier. Under this framework, the myelin sheath with up to 100 layers of membrane only serves as the insulating shell. The speed of action potenti... |
1701.01355 | Catherine Matias | Vincent Miele, Catherine Matias (LPMA) | Revealing the hidden structure of dynamic ecological networks | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent technological advances and long-term data studies provide interaction
data that can be modelled through dynamic networks, i.e a sequence of different
snapshots of an evolving ecological network. Most often time is the parameter
along which these networks evolve but any other one-dimensional gradient
(temperatu... | [
{
"created": "Thu, 5 Jan 2017 15:34:48 GMT",
"version": "v1"
}
] | 2017-01-06 | [
[
"Miele",
"Vincent",
"",
"LPMA"
],
[
"Matias",
"Catherine",
"",
"LPMA"
]
] | Recent technological advances and long-term data studies provide interaction data that can be modelled through dynamic networks, i.e a sequence of different snapshots of an evolving ecological network. Most often time is the parameter along which these networks evolve but any other one-dimensional gradient (temperature... |
1611.00259 | Fevzi Buyukkilic | F.Buyukk{\i}l{\i}\c{c}, Z.Ok Bayrakdar, D.Demirhan | A study on the evolution of a community population by cumulative and
fractional calculus approaches | 21 pages,4figures,research manuscript, biodynamics, cumulative
approaches, fractional calculus | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nowadays, in our globalized world,the local and intercountry movements of
population have been increased. This situation makes it important for host
countries to do right predictions for the future population of their native
people as well as immigrant people. The knowledge of the attained number of
accumulated popul... | [
{
"created": "Mon, 31 Oct 2016 14:41:03 GMT",
"version": "v1"
}
] | 2016-11-02 | [
[
"Buyukkılıç",
"F.",
""
],
[
"Bayrakdar",
"Z. Ok",
""
],
[
"Demirhan",
"D.",
""
]
] | Nowadays, in our globalized world,the local and intercountry movements of population have been increased. This situation makes it important for host countries to do right predictions for the future population of their native people as well as immigrant people. The knowledge of the attained number of accumulated populat... |
1810.01747 | Gard Spreemann | Jean-Baptiste Bardin, Gard Spreemann, Kathryn Hess | Topological exploration of artificial neuronal network dynamics | null | null | 10.1162/netn_a_00080 | null | q-bio.NC math.AT | http://creativecommons.org/licenses/by/4.0/ | One of the paramount challenges in neuroscience is to understand the dynamics
of individual neurons and how they give rise to network dynamics when
interconnected. Historically, researchers have resorted to graph theory,
statistics, and statistical mechanics to describe the spatiotemporal structure
of such network dy... | [
{
"created": "Wed, 3 Oct 2018 14:11:24 GMT",
"version": "v1"
},
{
"created": "Mon, 28 Jan 2019 10:28:30 GMT",
"version": "v2"
}
] | 2019-02-08 | [
[
"Bardin",
"Jean-Baptiste",
""
],
[
"Spreemann",
"Gard",
""
],
[
"Hess",
"Kathryn",
""
]
] | One of the paramount challenges in neuroscience is to understand the dynamics of individual neurons and how they give rise to network dynamics when interconnected. Historically, researchers have resorted to graph theory, statistics, and statistical mechanics to describe the spatiotemporal structure of such network dyna... |
q-bio/0610047 | Michele Caselle | A. Re, D. Cora, A. M. Puliti, M. Caselle and I. Sbrana | Correlated fragile site expression allows the identification of
candidate fragile genes involved in immunity and associated with
carcinogenesis | 18 pages, accepted for publication in BMC Bioinformatics | BMC Bioinformatics 2006, 7:413 | null | DFTT 23/2006 | q-bio.GN | null | Common fragile sites (cfs) are specific regions in the human genome that are
particularly prone to genomic instability under conditions of replicative
stress. Several investigations support the view that common fragile sites play
a role in carcinogenesis. We discuss a genome-wide approach based on graph
theory and Ge... | [
{
"created": "Wed, 25 Oct 2006 10:08:50 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Re",
"A.",
""
],
[
"Cora",
"D.",
""
],
[
"Puliti",
"A. M.",
""
],
[
"Caselle",
"M.",
""
],
[
"Sbrana",
"I.",
""
]
] | Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in carcinogenesis. We discuss a genome-wide approach based on graph theory and Gene... |
1909.10007 | Tilo Schwalger | Tilo Schwalger and Anton V. Chizhov | Mind the Last Spike -- Firing Rate Models for Mesoscopic Populations of
Spiking Neurons | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The dominant modeling framework for understanding cortical computations are
heuristic firing rate models. Despite their success, these models fall short to
capture spike synchronization effects, to link to biophysical parameters and to
describe finite-size fluctuations. In this opinion article, we propose that the
re... | [
{
"created": "Sun, 22 Sep 2019 13:57:44 GMT",
"version": "v1"
}
] | 2019-09-24 | [
[
"Schwalger",
"Tilo",
""
],
[
"Chizhov",
"Anton V.",
""
]
] | The dominant modeling framework for understanding cortical computations are heuristic firing rate models. Despite their success, these models fall short to capture spike synchronization effects, to link to biophysical parameters and to describe finite-size fluctuations. In this opinion article, we propose that the refr... |
1303.3520 | Tobias Marschall | Tobias Marschall and Alexander Sch\"onhuth | Sensitive Long-Indel-Aware Alignment of Sequencing Reads | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The tremdendous advances in high-throughput sequencing technologies have made
population-scale sequencing as performed in the 1000 Genomes project and the
Genome of the Netherlands project possible. Next-generation sequencing has
allowed genom-wide discovery of variations beyond single-nucleotide
polymorphisms (SNPs)... | [
{
"created": "Thu, 14 Mar 2013 17:31:13 GMT",
"version": "v1"
}
] | 2013-03-15 | [
[
"Marschall",
"Tobias",
""
],
[
"Schönhuth",
"Alexander",
""
]
] | The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed genom-wide discovery of variations beyond single-nucleotide polymorphisms (SNPs), ... |
2112.11681 | Swadesh Pal | Swadesh Pal and Roderick Melnik | Nonlocal Models in the Analysis of Brain Neurodegenerative Protein
Dynamics with Application to Alzheimer's Disease | 15 pages, 9 figures, 4 tables | null | null | null | q-bio.NC math.DS | http://creativecommons.org/licenses/by-nc-nd/4.0/ | It is well known that today nearly one in six of the world's population has
to deal with neurodegenerative disorders. While a number of medical devices
have been developed for the detection, prevention, and treatments of such
disorders, some fundamentals of the progression of associated diseases are in
urgent need of... | [
{
"created": "Wed, 22 Dec 2021 06:11:11 GMT",
"version": "v1"
}
] | 2021-12-23 | [
[
"Pal",
"Swadesh",
""
],
[
"Melnik",
"Roderick",
""
]
] | It is well known that today nearly one in six of the world's population has to deal with neurodegenerative disorders. While a number of medical devices have been developed for the detection, prevention, and treatments of such disorders, some fundamentals of the progression of associated diseases are in urgent need of f... |
2306.00236 | Yuzhu Chen | Yuzhu Chen, David Saintillan, and Padmini Rangamani | Cell motility modes are selected by the interplay of mechanosensitive
adhesion and membrane tension | 21 pages, 8 figures | null | null | null | q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | The initiation of directional cell motion requires symmetry breaking that can
happen both with or without external stimuli. During cell crawling, forces
generated by the cytoskeleton and their transmission through mechanosensitive
adhesions to the extracellular substrate play a crucial role. In a recently
proposed 1D... | [
{
"created": "Wed, 31 May 2023 23:16:26 GMT",
"version": "v1"
}
] | 2023-06-02 | [
[
"Chen",
"Yuzhu",
""
],
[
"Saintillan",
"David",
""
],
[
"Rangamani",
"Padmini",
""
]
] | The initiation of directional cell motion requires symmetry breaking that can happen both with or without external stimuli. During cell crawling, forces generated by the cytoskeleton and their transmission through mechanosensitive adhesions to the extracellular substrate play a crucial role. In a recently proposed 1D m... |
0807.2893 | Joshua Milstein | J.N. Milstein, F. Mormann, I. Fried, C. Koch | Neuronal Shot Noise and Brownian $1/f^2$ Behavior in the Local Field
Potential | null | null | 10.1371/journal.pone.0004338 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We demonstrate that human electrophysiological recordings of the local field
potential (LFP) from intracranial electrodes, acquired from a variety of
cerebral regions, show a ubiquitous $1/f^2$ scaling within the power spectrum.
We develop a quantitative model that treats the generation of these fields in
an analogou... | [
{
"created": "Fri, 18 Jul 2008 01:45:45 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Milstein",
"J. N.",
""
],
[
"Mormann",
"F.",
""
],
[
"Fried",
"I.",
""
],
[
"Koch",
"C.",
""
]
] | We demonstrate that human electrophysiological recordings of the local field potential (LFP) from intracranial electrodes, acquired from a variety of cerebral regions, show a ubiquitous $1/f^2$ scaling within the power spectrum. We develop a quantitative model that treats the generation of these fields in an analogous ... |
1410.5377 | Sebastian Maerkl | Francesca Volpetti, Jose Garcia-Cordero, Sebastian Maerkl | A microfluidic platform for high-throughput multiplexed protein
quantitation | null | null | 10.1371/journal.pone.0117744 | null | q-bio.QM physics.bio-ph q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a high-throughput microfluidic platform capable of quantitating up
to 384 biomarkers in 4 distinct samples by immunoassay. The microfluidic device
contains 384 unit cells, which can be individually programmed with pairs of
capture and detection antibody. Samples are quantitated in each unit cell by
four in... | [
{
"created": "Mon, 20 Oct 2014 18:06:05 GMT",
"version": "v1"
}
] | 2015-06-23 | [
[
"Volpetti",
"Francesca",
""
],
[
"Garcia-Cordero",
"Jose",
""
],
[
"Maerkl",
"Sebastian",
""
]
] | We present a high-throughput microfluidic platform capable of quantitating up to 384 biomarkers in 4 distinct samples by immunoassay. The microfluidic device contains 384 unit cells, which can be individually programmed with pairs of capture and detection antibody. Samples are quantitated in each unit cell by four inde... |
1812.06594 | Sebastian Mathias Keller | Sebastian Mathias Keller, Maxim Samarin, Antonia Meyer, Vitalii Kosak
(Cozak), Ute Gschwandtner, Peter Fuhr, Volker Roth | Computational EEG in Personalized Medicine: A study in Parkinson's
Disease | Machine Learning for Health (ML4H) Workshop at NeurIPS 2018
arXiv:811.07216 | null | null | null | q-bio.NC cs.LG eess.SP q-bio.QM stat.ML | http://creativecommons.org/licenses/by/4.0/ | Recordings of electrical brain activity carry information about a person's
cognitive health. For recording EEG signals, a very common setting is for a
subject to be at rest with its eyes closed. Analysis of these recordings often
involve a dimensionality reduction step in which electrodes are grouped into 10
or more ... | [
{
"created": "Sun, 2 Dec 2018 15:15:44 GMT",
"version": "v1"
}
] | 2018-12-18 | [
[
"Keller",
"Sebastian Mathias",
"",
"Cozak"
],
[
"Samarin",
"Maxim",
"",
"Cozak"
],
[
"Meyer",
"Antonia",
"",
"Cozak"
],
[
"Kosak",
"Vitalii",
"",
"Cozak"
],
[
"Gschwandtner",
"Ute",
""
],
[
"Fuhr",
"Peter",
... | Recordings of electrical brain activity carry information about a person's cognitive health. For recording EEG signals, a very common setting is for a subject to be at rest with its eyes closed. Analysis of these recordings often involve a dimensionality reduction step in which electrodes are grouped into 10 or more re... |
1612.02108 | Stuart Sevier | Stuart A. Sevier, Herbert Levine | Mechanical Properties of Transcription | null | Phys. Rev. Lett. 118, 268101 (2017) | 10.1103/PhysRevLett.118.268101 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently the physical characterization of a number of biological processes
has proven indispensable for a full understanding of natural phenomena. One
such example is the mechanical properties of transcription, which have been
shown to have significant effects in gene expression. In this letter we
introduce a simple ... | [
{
"created": "Wed, 7 Dec 2016 04:06:59 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Feb 2017 16:40:45 GMT",
"version": "v2"
}
] | 2017-07-05 | [
[
"Sevier",
"Stuart A.",
""
],
[
"Levine",
"Herbert",
""
]
] | Recently the physical characterization of a number of biological processes has proven indispensable for a full understanding of natural phenomena. One such example is the mechanical properties of transcription, which have been shown to have significant effects in gene expression. In this letter we introduce a simple de... |
2111.03456 | Younes Bouhadjar | Younes Bouhadjar, Dirk J. Wouters, Markus Diesmann, Tom Tetzlaff | Sequence learning, prediction, and replay in networks of spiking neurons | 35 pages, 18 figures, 3 tables, 1 video | null | 10.1371/journal.pcbi.1010233 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sequence learning, prediction and replay have been proposed to constitute the
universal computations performed by the neocortex. The Hierarchical Temporal
Memory (HTM) algorithm realizes these forms of computation. It learns sequences
in an unsupervised and continuous manner using local learning rules, permits a
cont... | [
{
"created": "Fri, 5 Nov 2021 12:32:17 GMT",
"version": "v1"
},
{
"created": "Tue, 19 Jul 2022 18:38:35 GMT",
"version": "v2"
}
] | 2022-07-21 | [
[
"Bouhadjar",
"Younes",
""
],
[
"Wouters",
"Dirk J.",
""
],
[
"Diesmann",
"Markus",
""
],
[
"Tetzlaff",
"Tom",
""
]
] | Sequence learning, prediction and replay have been proposed to constitute the universal computations performed by the neocortex. The Hierarchical Temporal Memory (HTM) algorithm realizes these forms of computation. It learns sequences in an unsupervised and continuous manner using local learning rules, permits a contex... |
2212.00023 | Tianyu Wu | Tianyu Wu, Yang Tang | Random Copolymer inverse design system orienting on Accurate discovering
of Antimicrobial peptide-mimetic copolymers | We decide to make deep modifacation on this paper, and we would like
to add further provement on the final results generated to prove the
rationality. In this way, we hope this work can be withdrew temporarily and
we would open the final version in near furture. Thank you | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Antimicrobial resistance is one of the biggest health problem, especially in
the current period of COVID-19 pandemic. Due to the unique membrane-destruction
bactericidal mechanism, antimicrobial peptide-mimetic copolymers are paid more
attention and it is urgent to find more potential candidates with
broad-spectrum a... | [
{
"created": "Wed, 30 Nov 2022 14:29:50 GMT",
"version": "v1"
},
{
"created": "Thu, 8 Dec 2022 01:52:20 GMT",
"version": "v2"
}
] | 2022-12-09 | [
[
"Wu",
"Tianyu",
""
],
[
"Tang",
"Yang",
""
]
] | Antimicrobial resistance is one of the biggest health problem, especially in the current period of COVID-19 pandemic. Due to the unique membrane-destruction bactericidal mechanism, antimicrobial peptide-mimetic copolymers are paid more attention and it is urgent to find more potential candidates with broad-spectrum ant... |
1808.01058 | Jyothi Swaroop Guntupalli | Dileep George, Alexander Lavin, J. Swaroop Guntupalli, David Mely,
Nick Hay, Miguel Lazaro-Gredilla | Cortical Microcircuits from a Generative Vision Model | null | null | null | null | q-bio.NC cs.CV | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Understanding the information processing roles of cortical circuits is an
outstanding problem in neuroscience and artificial intelligence. The
theoretical setting of Bayesian inference has been suggested as a framework for
understanding cortical computation. Based on a recently published generative
model for visual i... | [
{
"created": "Fri, 3 Aug 2018 01:20:08 GMT",
"version": "v1"
}
] | 2018-08-06 | [
[
"George",
"Dileep",
""
],
[
"Lavin",
"Alexander",
""
],
[
"Guntupalli",
"J. Swaroop",
""
],
[
"Mely",
"David",
""
],
[
"Hay",
"Nick",
""
],
[
"Lazaro-Gredilla",
"Miguel",
""
]
] | Understanding the information processing roles of cortical circuits is an outstanding problem in neuroscience and artificial intelligence. The theoretical setting of Bayesian inference has been suggested as a framework for understanding cortical computation. Based on a recently published generative model for visual inf... |
q-bio/0404039 | Walton Gutierrez | Walton R. Gutierrez | Site Model of Allometric Scaling and Fractal Distribution Networks of
Organs | 9 pages, 1 fig., 3 tables | null | null | null | q-bio.TO q-bio.QM | null | At the basic geometric level, the distribution networks carrying vital
materials in living organisms, and the units such as the nephrons and alveoli,
form a scaling structure named here the site model. This unified view of the
allometry of the kidney and lung of mammals is in agreement with the existing
data, and in ... | [
{
"created": "Tue, 27 Apr 2004 17:17:26 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Gutierrez",
"Walton R.",
""
]
] | At the basic geometric level, the distribution networks carrying vital materials in living organisms, and the units such as the nephrons and alveoli, form a scaling structure named here the site model. This unified view of the allometry of the kidney and lung of mammals is in agreement with the existing data, and in so... |
q-bio/0405004 | Chris Adami | Christoph Adami (KGI, Caltech) | Information theory in molecular biology | 29 pages, 7 figs | Physics of Life Reviews 1 (2004) 3-22 | 10.1016/j.plrev.2004.01.002 | null | q-bio.BM q-bio.PE | null | This article introduces the physics of information in the context of
molecular biology and genomics. Entropy and information, the two central
concepts of Shannon's theory of information and communication, are often
confused with each other but play transparent roles when applied to statistical
ensembles (i.e., identi... | [
{
"created": "Wed, 5 May 2004 20:52:48 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Adami",
"Christoph",
"",
"KGI, Caltech"
]
] | This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other but play transparent roles when applied to statistical ensembles (i.e., identica... |
1805.09497 | Kazuhiro Takemoto | Midori Iida, Kazuhiro Takemoto | A network biology-based approach to evaluating the effect of
environmental contaminants on human interactome and diseases | 35 pages, 12 figures | Ecotoxicology and Environmental Safety 160, 316-327 (2018) | 10.1016/j.ecoenv.2018.05.065 | null | q-bio.MN physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Environmental contaminant exposure can pose significant risks to human
health. Therefore, evaluating the impact of this exposure is of great
importance; however, it is often difficult because both the molecular mechanism
of disease and the mode of action of the contaminants are complex. We used
network biology techni... | [
{
"created": "Thu, 24 May 2018 03:43:37 GMT",
"version": "v1"
}
] | 2018-06-01 | [
[
"Iida",
"Midori",
""
],
[
"Takemoto",
"Kazuhiro",
""
]
] | Environmental contaminant exposure can pose significant risks to human health. Therefore, evaluating the impact of this exposure is of great importance; however, it is often difficult because both the molecular mechanism of disease and the mode of action of the contaminants are complex. We used network biology techniqu... |
1802.04794 | Joshua Goldwyn | Joshua H Goldwyn, Bradley R Slabe, Joseph B Travers, David Terman | Gain control with A-type potassium current: IA as a switch between
divisive and subtractive inhibition | 20 pages, 11 figures | null | 10.1371/journal.pcbi.1006292 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neurons process information by transforming barrages of synaptic inputs into
spiking activity. Synaptic inhibition suppresses the output firing activity of
a neuron, and is commonly classified as having a subtractive or divisive effect
on a neuron's output firing activity. Subtractive inhibition can narrow the
range ... | [
{
"created": "Tue, 13 Feb 2018 18:56:57 GMT",
"version": "v1"
}
] | 2018-09-05 | [
[
"Goldwyn",
"Joshua H",
""
],
[
"Slabe",
"Bradley R",
""
],
[
"Travers",
"Joseph B",
""
],
[
"Terman",
"David",
""
]
] | Neurons process information by transforming barrages of synaptic inputs into spiking activity. Synaptic inhibition suppresses the output firing activity of a neuron, and is commonly classified as having a subtractive or divisive effect on a neuron's output firing activity. Subtractive inhibition can narrow the range of... |
1306.3063 | Robert Ekblom | Robert Ekblom, Dennis Hasselquist, Stein Are S{\Ae}Ther, Peder Fiske,
John Atle K{\Aa}L{\Aa}S, Mats Grahn, Jacob H\"Oglund | Humoral immunocompetence in relation to condition, size, asymmetry and
MHC class II variation in great snipe (Gallinago media) males | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | 1. In recent years many studies have investigated the relationships between
different aspects of the immune system and ecology in various organisms. Yet,
it remains unclear why individuals differ in their ability to mount an immune
response against various antigens (often referred to as 'immunocompetence').
Different... | [
{
"created": "Thu, 13 Jun 2013 09:38:20 GMT",
"version": "v1"
}
] | 2013-06-14 | [
[
"Ekblom",
"Robert",
""
],
[
"Hasselquist",
"Dennis",
""
],
[
"S{\\Ae}Ther",
"Stein Are",
""
],
[
"Fiske",
"Peder",
""
],
[
"K{\\Aa}L{\\Aa}S",
"John Atle",
""
],
[
"Grahn",
"Mats",
""
],
[
"HÖglund",
"Jacob",
... | 1. In recent years many studies have investigated the relationships between different aspects of the immune system and ecology in various organisms. Yet, it remains unclear why individuals differ in their ability to mount an immune response against various antigens (often referred to as 'immunocompetence'). Different k... |
1305.0119 | Steffen Rulands | Steffen Rulands, Alejandro Zielinski, Erwin Frey | Global attractors and extinction dynamics of cyclically competing
species | 18 pages, 12 figures | Phys. Rev. E 87, 052710 (2013) | 10.1103/PhysRevE.87.052710 | null | q-bio.PE nlin.PS physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transitions to absorbing states are of fundamental importance in
non-equilibrium physics as well as ecology. In ecology, absorbing states
correspond to the extinction of species. We here study the spatial population
dynamics of three cyclically interacting species. The interaction scheme
comprises both direct competi... | [
{
"created": "Wed, 1 May 2013 08:06:30 GMT",
"version": "v1"
}
] | 2014-05-27 | [
[
"Rulands",
"Steffen",
""
],
[
"Zielinski",
"Alejandro",
""
],
[
"Frey",
"Erwin",
""
]
] | Transitions to absorbing states are of fundamental importance in non-equilibrium physics as well as ecology. In ecology, absorbing states correspond to the extinction of species. We here study the spatial population dynamics of three cyclically interacting species. The interaction scheme comprises both direct competiti... |
1610.08664 | Luigi Leonardo Palese | Luigi Leonardo Palese | A random version of principal component analysis in data clustering | 18 pages, 6 figures, 2 tables | Comput. Biol. Chem. 73 (2018) 57-64 | 10.1016/j.compbiolchem.2018.01.009 | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Principal component analysis (PCA) is a widespread technique for data
analysis that relies on the covariance-correlation matrix of the analyzed data.
However to properly work with high-dimensional data, PCA poses severe
mathematical constraints on the minimum number of different replicates or
samples that must be inc... | [
{
"created": "Thu, 27 Oct 2016 08:52:19 GMT",
"version": "v1"
}
] | 2018-10-18 | [
[
"Palese",
"Luigi Leonardo",
""
]
] | Principal component analysis (PCA) is a widespread technique for data analysis that relies on the covariance-correlation matrix of the analyzed data. However to properly work with high-dimensional data, PCA poses severe mathematical constraints on the minimum number of different replicates or samples that must be inclu... |
1505.01206 | Changshuai Wei | Changshuai Wei, Daniel J. Schaid, Qing Lu | Trees Assembling Mann Whitney Approach for Detecting Genome-wide Joint
Association among Low Marginal Effect loci | null | Genet Epidemiol. 2013 Jan;37(1):84-91 | 10.1002/gepi.21693 | null | q-bio.QM stat.CO stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Common complex diseases are likely influenced by the interplay of hundreds,
or even thousands, of genetic variants. Converging evidence shows that genetic
variants with low marginal effects (LME) play an important role in disease
development. Despite their potential significance, discovering LME genetic
variants and ... | [
{
"created": "Tue, 5 May 2015 22:14:28 GMT",
"version": "v1"
}
] | 2015-05-07 | [
[
"Wei",
"Changshuai",
""
],
[
"Schaid",
"Daniel J.",
""
],
[
"Lu",
"Qing",
""
]
] | Common complex diseases are likely influenced by the interplay of hundreds, or even thousands, of genetic variants. Converging evidence shows that genetic variants with low marginal effects (LME) play an important role in disease development. Despite their potential significance, discovering LME genetic variants and as... |
q-bio/0511030 | Radhakrishnan Nagarajan | Radhakrishnan Nagarajan, Meenakshi Upreti | Correlation Statistics for cDNA Microarray Image Analysis | 25 Pages, 8 Figures | null | null | null | q-bio.GN q-bio.QM | null | In this report, correlation of the pixels comprising a microarray spot is
investigated. Subsequently, correlation statistics namely: Pearson correlation
and Spearman rank correlation are used to segment the foreground and background
intensity of microarray spots. The performance of correlation-based
segmentation is c... | [
{
"created": "Wed, 16 Nov 2005 15:25:33 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Nagarajan",
"Radhakrishnan",
""
],
[
"Upreti",
"Meenakshi",
""
]
] | In this report, correlation of the pixels comprising a microarray spot is investigated. Subsequently, correlation statistics namely: Pearson correlation and Spearman rank correlation are used to segment the foreground and background intensity of microarray spots. The performance of correlation-based segmentation is com... |
2007.14464 | Manqing Ma | Xueming Liu, Daqing Li, Manqing Ma, Boleslaw K. Szymanski, H Eugene
Stanley, Jianxi Gao | Network resilience | Review chapter | Physics Reports 471:1-108, Aug. 12, 2022 | 10.1016/j.physrep.2022.04.002 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many systems on our planet are known to shift abruptly and irreversibly from
one state to another when they are forced across a "tipping point," such as
mass extinctions in ecological networks, cascading failures in infrastructure
systems, and social convention changes in human and animal networks. Such a
regime shif... | [
{
"created": "Sun, 26 Jul 2020 18:12:45 GMT",
"version": "v1"
},
{
"created": "Sun, 10 Apr 2022 00:02:00 GMT",
"version": "v2"
}
] | 2022-05-23 | [
[
"Liu",
"Xueming",
""
],
[
"Li",
"Daqing",
""
],
[
"Ma",
"Manqing",
""
],
[
"Szymanski",
"Boleslaw K.",
""
],
[
"Stanley",
"H Eugene",
""
],
[
"Gao",
"Jianxi",
""
]
] | Many systems on our planet are known to shift abruptly and irreversibly from one state to another when they are forced across a "tipping point," such as mass extinctions in ecological networks, cascading failures in infrastructure systems, and social convention changes in human and animal networks. Such a regime shift ... |
1910.06860 | Augustine Okolie | Augustine Okolie and Johannes M\"uller | Exact and approximate formulas for contact tracing on random trees | 24 pages, 9 figures | Mathematical Biosciences, 108320 (2020) | 10.1016/j.mbs.2020.108320 | null | q-bio.PE math.DS physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a stochastic susceptible-infected-recovered (SIR) model with
contact tracing on random trees and on the configuration model. On a rooted
tree, where initially all individuals are susceptible apart from the root which
is infected, we are able to find exact formulas for the distribution of the
infectious pe... | [
{
"created": "Tue, 15 Oct 2019 15:23:34 GMT",
"version": "v1"
},
{
"created": "Wed, 16 Oct 2019 05:46:48 GMT",
"version": "v2"
},
{
"created": "Sat, 22 Feb 2020 10:14:45 GMT",
"version": "v3"
}
] | 2020-02-25 | [
[
"Okolie",
"Augustine",
""
],
[
"Müller",
"Johannes",
""
]
] | We consider a stochastic susceptible-infected-recovered (SIR) model with contact tracing on random trees and on the configuration model. On a rooted tree, where initially all individuals are susceptible apart from the root which is infected, we are able to find exact formulas for the distribution of the infectious peri... |
0801.4556 | German Andres Enciso | Winfried Just and German Enciso | Large attractors in cooperative bi-quadratic Boolean networks. Part II | 14 pages | null | null | null | q-bio.MN q-bio.QM | null | Boolean networks have been the object of much attention, especially since S.
Kauffman proposed them in the 1960's as models for gene regulatory networks.
These systems are characterized by being defined on a Boolean state space and
by simultaneous updating at discrete time steps. Of particular importance for
biologic... | [
{
"created": "Tue, 29 Jan 2008 20:50:32 GMT",
"version": "v1"
}
] | 2008-01-30 | [
[
"Just",
"Winfried",
""
],
[
"Enciso",
"German",
""
]
] | Boolean networks have been the object of much attention, especially since S. Kauffman proposed them in the 1960's as models for gene regulatory networks. These systems are characterized by being defined on a Boolean state space and by simultaneous updating at discrete time steps. Of particular importance for biological... |
2402.15091 | Chen Shen | Zehua Si, Zhixue He, Chen Shen and Jun Tanimoto | Mixed strategy approach destabilizes cooperation in finite populations
with clustering coefficient | null | null | null | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Evolutionary game theory, encompassing discrete, continuous, and mixed
strategies, is pivotal for understanding cooperation dynamics. Discrete
strategies involve deterministic actions with a fixed probability of one,
whereas continuous strategies employ intermediate probabilities to convey the
extent of cooperation a... | [
{
"created": "Fri, 23 Feb 2024 04:34:05 GMT",
"version": "v1"
}
] | 2024-02-26 | [
[
"Si",
"Zehua",
""
],
[
"He",
"Zhixue",
""
],
[
"Shen",
"Chen",
""
],
[
"Tanimoto",
"Jun",
""
]
] | Evolutionary game theory, encompassing discrete, continuous, and mixed strategies, is pivotal for understanding cooperation dynamics. Discrete strategies involve deterministic actions with a fixed probability of one, whereas continuous strategies employ intermediate probabilities to convey the extent of cooperation and... |
2011.10318 | Vincent Huin | Sabiha Eddarkaoui (JPArc), M\'egane Homa (JPArc), Anne Loyens (JPArc),
Emilie Faivre (JPArc), Vincent Deramecourt (JPArc), Claude-Alain Maurage, Luc
Bu\'ee (JPArc), Vincent Huin (JPArc), Bernard Sablonni\`ere (JPArc) | The TMEM240 Protein, Mutated in SCA21, Is Expressed in Purkinje Cells
and Synaptic Terminals | The Cerebellum, Springer, In press, Ahead of print | null | 10.1007/s12311-020-01112-y | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A variety of missense mutations and a stop mutation in the gene coding for
transmembrane protein 240 (TMEM240) have been reported to be the causative
mutations of spinocerebellar ataxia 21 (SCA21). We aimed to investigate the
expression of TMEM240 protein in mouse brain at the tissue, cellular, and
subcellular levels... | [
{
"created": "Fri, 20 Nov 2020 10:15:41 GMT",
"version": "v1"
}
] | 2020-11-23 | [
[
"Eddarkaoui",
"Sabiha",
"",
"JPArc"
],
[
"Homa",
"Mégane",
"",
"JPArc"
],
[
"Loyens",
"Anne",
"",
"JPArc"
],
[
"Faivre",
"Emilie",
"",
"JPArc"
],
[
"Deramecourt",
"Vincent",
"",
"JPArc"
],
[
"Maurage",
"Cla... | A variety of missense mutations and a stop mutation in the gene coding for transmembrane protein 240 (TMEM240) have been reported to be the causative mutations of spinocerebellar ataxia 21 (SCA21). We aimed to investigate the expression of TMEM240 protein in mouse brain at the tissue, cellular, and subcellular levels. ... |
0809.1180 | Patricia Faisca | P.F.N. Faisca and C. M. Gomes | On the relation between native geometry and conformational plasticity | Accepted in Biophysical Chemistry | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In protein folding the term plasticity refers to the number of alternative
folding pathways encountered in response to free energy perturbations such as
those induced by mutation. Here we explore the relation between folding
plasticity and a gross, generic feature of the native geometry, namely, the
relative number o... | [
{
"created": "Sat, 6 Sep 2008 15:45:16 GMT",
"version": "v1"
}
] | 2008-09-09 | [
[
"Faisca",
"P. F. N.",
""
],
[
"Gomes",
"C. M.",
""
]
] | In protein folding the term plasticity refers to the number of alternative folding pathways encountered in response to free energy perturbations such as those induced by mutation. Here we explore the relation between folding plasticity and a gross, generic feature of the native geometry, namely, the relative number of ... |
1905.12179 | Tom Chou | Stephanie M. Lewkiewicz, Yao-Li Chuang, Tom Chou | Dynamics of T Cell Receptor Distributions Following Acute Thymic Atrophy
and Resumption | 22 pages, 7 figures | null | null | null | q-bio.PE q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Naive human T cells are produced in the thymus, which atrophies abruptly and
severely in response to physical or psychological stress. To understand how an
instance of stress affects the size and "diversity" of the peripheral naive T
cell pool, we derive a mean-field autonomous ODE model of T cell replenishment
that ... | [
{
"created": "Wed, 29 May 2019 02:21:04 GMT",
"version": "v1"
}
] | 2019-05-30 | [
[
"Lewkiewicz",
"Stephanie M.",
""
],
[
"Chuang",
"Yao-Li",
""
],
[
"Chou",
"Tom",
""
]
] | Naive human T cells are produced in the thymus, which atrophies abruptly and severely in response to physical or psychological stress. To understand how an instance of stress affects the size and "diversity" of the peripheral naive T cell pool, we derive a mean-field autonomous ODE model of T cell replenishment that al... |
0911.0656 | Randen Patterson | Gaurav Bhardwaj, Christine P. Wells, Reka Albert, Damian B. van
Rossum, and Randen L. Patterson | Mapping Complex Networks: Exploring Boolean Modeling of Signal
Transduction Pathways | 19 pages, 5 Figures, 2 Tables | null | null | null | q-bio.MN q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this study, we explored the utility of a descriptive and predictive
bionetwork model for phospholipase C-coupled calcium signaling pathways, built
with non-kinetic experimental information. Boolean models generated from these
data yield oscillatory activity patterns for both the endoplasmic reticulum
resident inos... | [
{
"created": "Tue, 3 Nov 2009 19:16:12 GMT",
"version": "v1"
},
{
"created": "Mon, 14 Dec 2009 16:47:36 GMT",
"version": "v2"
}
] | 2009-12-14 | [
[
"Bhardwaj",
"Gaurav",
""
],
[
"Wells",
"Christine P.",
""
],
[
"Albert",
"Reka",
""
],
[
"van Rossum",
"Damian B.",
""
],
[
"Patterson",
"Randen L.",
""
]
] | In this study, we explored the utility of a descriptive and predictive bionetwork model for phospholipase C-coupled calcium signaling pathways, built with non-kinetic experimental information. Boolean models generated from these data yield oscillatory activity patterns for both the endoplasmic reticulum resident inosit... |
1910.00048 | Joseph Rusinko | Sophia Huebler, Rachel Morris, Joseph Rusinko and Yifei Tao | Constructing Semi-Directed Level-1 Phylogenetic Networks from Quarnets | 17 pages | null | null | null | q-bio.GN math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce two algorithms for reconstructing semi-directed level-1
phylogenetic networks from their complete set of 4-leaf subnetworks, known as
quarnets. The first algorithm, the sequential method, begins with a single
quarnet and adds on one leaf at a time until all leaves have been placed. The
second algorithm, ... | [
{
"created": "Mon, 30 Sep 2019 18:33:27 GMT",
"version": "v1"
}
] | 2019-10-02 | [
[
"Huebler",
"Sophia",
""
],
[
"Morris",
"Rachel",
""
],
[
"Rusinko",
"Joseph",
""
],
[
"Tao",
"Yifei",
""
]
] | We introduce two algorithms for reconstructing semi-directed level-1 phylogenetic networks from their complete set of 4-leaf subnetworks, known as quarnets. The first algorithm, the sequential method, begins with a single quarnet and adds on one leaf at a time until all leaves have been placed. The second algorithm, th... |
2007.00886 | Qinbing Fu | Qinbing Fu and Shigang Yue | Modelling Drosophila Motion Vision Pathways for Decoding the Direction
of Translating Objects Against Cluttered Moving Backgrounds | 27 pages, 13 figures, been included in a future issue of the journal
of Biological Cybernetics | null | 10.1007/s00422-020-00841-x | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Decoding the direction of translating objects in front of cluttered moving
backgrounds, accurately and efficiently, is still a challenging problem. In
nature, lightweight and low-powered flying insects apply motion vision to
detect a moving target in highly variable environments during flight, which are
excellent par... | [
{
"created": "Thu, 2 Jul 2020 05:15:31 GMT",
"version": "v1"
}
] | 2020-07-03 | [
[
"Fu",
"Qinbing",
""
],
[
"Yue",
"Shigang",
""
]
] | Decoding the direction of translating objects in front of cluttered moving backgrounds, accurately and efficiently, is still a challenging problem. In nature, lightweight and low-powered flying insects apply motion vision to detect a moving target in highly variable environments during flight, which are excellent parad... |
1504.07392 | Giovanni Bussi | Francesco Di Palma, Sandro Bottaro, and Giovanni Bussi | Kissing loop interaction in adenine riboswitch: insights from umbrella
sampling simulations | Accepted for publication on BMC Bioinformatics | BMC Bioinformatics 2015, 16(Suppl 9):S6 | 10.1186/1471-2105-16-S9-S6 | null | q-bio.BM physics.bio-ph physics.chem-ph | http://creativecommons.org/licenses/by/3.0/ | Riboswitches are cis-acting regulatory RNA elements prevalently located in
the leader sequences of bacterial mRNA. An adenine sensing riboswitch
cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The
structural mechanism regulating its conformational changes upon ligand binding
mostly remains to be ... | [
{
"created": "Tue, 28 Apr 2015 09:34:02 GMT",
"version": "v1"
}
] | 2015-06-08 | [
[
"Di Palma",
"Francesco",
""
],
[
"Bottaro",
"Sandro",
""
],
[
"Bussi",
"Giovanni",
""
]
] | Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The structural mechanism regulating its conformational changes upon ligand binding mostly remains to be el... |
1802.05820 | Meng-Han Zhang | Meng-Han Zhang, Wu-Yun Pan, Shi Yan, Li Jin | Phonemic evidence reveals interwoven evolution of Chinese dialects | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Han Chinese experienced substantial population migrations and admixture in
history, yet little is known about the evolutionary process of Chinese
dialects. Here, we used phylogenetic approaches and admixture inference to
explicitly decompose the underlying structure of the diversity of Chinese
dialects, based on the ... | [
{
"created": "Fri, 16 Feb 2018 02:07:23 GMT",
"version": "v1"
}
] | 2018-02-19 | [
[
"Zhang",
"Meng-Han",
""
],
[
"Pan",
"Wu-Yun",
""
],
[
"Yan",
"Shi",
""
],
[
"Jin",
"Li",
""
]
] | Han Chinese experienced substantial population migrations and admixture in history, yet little is known about the evolutionary process of Chinese dialects. Here, we used phylogenetic approaches and admixture inference to explicitly decompose the underlying structure of the diversity of Chinese dialects, based on the to... |
1405.6258 | Mike Steel Prof. | Mike Steel and Joel D. Velasco | Axiomatic opportunities and obstacles for inferring a species tree from
gene trees | 19 pages, 2 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The reconstruction of a central tendency `species tree' from a large number
of conflicting gene trees is a central problem in systematic biology. Moreover,
it becomes particularly problematic when taxon coverage is patchy, so that not
all taxa are present in every gene tree. Here, we list four apparently
desirable pr... | [
{
"created": "Sat, 24 May 2014 02:17:43 GMT",
"version": "v1"
}
] | 2014-05-27 | [
[
"Steel",
"Mike",
""
],
[
"Velasco",
"Joel D.",
""
]
] | The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all taxa are present in every gene tree. Here, we list four apparently desirable prop... |
2109.14724 | Andrejs Tucs | Andrejs Tucs, Koji Tsuda, Adnan Sljoka | Probing conformational dynamics of antibodies with geometric simulations | Book chapter | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | This chapter describes the application of constrained geometric simulations
for prediction of antibody structural dynamics. We utilize constrained
geometric simulations method FRODAN, which is a low computational complexity
alternative to Molecular Dynamics (MD) simulations that can rapidly explore
flexible motions i... | [
{
"created": "Wed, 29 Sep 2021 21:05:49 GMT",
"version": "v1"
}
] | 2021-10-01 | [
[
"Tucs",
"Andrejs",
""
],
[
"Tsuda",
"Koji",
""
],
[
"Sljoka",
"Adnan",
""
]
] | This chapter describes the application of constrained geometric simulations for prediction of antibody structural dynamics. We utilize constrained geometric simulations method FRODAN, which is a low computational complexity alternative to Molecular Dynamics (MD) simulations that can rapidly explore flexible motions in ... |
2108.11331 | Fatma Al-Musalhi | Kifah Al-Maqrashi, Fatma Al-Musalhi, Ibrahim M. Elmojtaba, Nasser
Al-Salti | The Impact of Mobility between Rural Areas and Forests on the Spread of
Zika | 30pages,13figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | A mathematical model of Zika virus transmission incorporating human movement
between rural areas and nearby forests is presented to investigate the role of
human movement in the spread of Zika virus infections in human and mosquito
populations. Proportions of both susceptible and infected humans living in
rural areas... | [
{
"created": "Tue, 24 Aug 2021 08:50:23 GMT",
"version": "v1"
}
] | 2021-08-26 | [
[
"Al-Maqrashi",
"Kifah",
""
],
[
"Al-Musalhi",
"Fatma",
""
],
[
"Elmojtaba",
"Ibrahim M.",
""
],
[
"Al-Salti",
"Nasser",
""
]
] | A mathematical model of Zika virus transmission incorporating human movement between rural areas and nearby forests is presented to investigate the role of human movement in the spread of Zika virus infections in human and mosquito populations. Proportions of both susceptible and infected humans living in rural areas a... |
2407.12060 | Wen-Juan Ma Prof. Dr. | Barbora Augstenov\'a, Wen-Juan Ma | Decoding Dmrt1: Insights into vertebrate sex determination and gonadal
sex differentiation | 40 pages, 4 figures, 2 tables, 1 supplementary table | null | null | null | q-bio.QM q-bio.CB q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Dmrt1 is pivotal in testis formation and function by interacting with genes
crucial for Sertoli cell differentiation, such as Sox9. It represses
female-determining pathways and ovarian formation by silencing Foxl2. Across
127 vertebrate species, Dmrt1 exhibits sexually dimorphic expression, prior to
and during gonada... | [
{
"created": "Mon, 15 Jul 2024 12:55:32 GMT",
"version": "v1"
},
{
"created": "Thu, 8 Aug 2024 09:43:30 GMT",
"version": "v2"
}
] | 2024-08-09 | [
[
"Augstenová",
"Barbora",
""
],
[
"Ma",
"Wen-Juan",
""
]
] | Dmrt1 is pivotal in testis formation and function by interacting with genes crucial for Sertoli cell differentiation, such as Sox9. It represses female-determining pathways and ovarian formation by silencing Foxl2. Across 127 vertebrate species, Dmrt1 exhibits sexually dimorphic expression, prior to and during gonadal ... |
1512.05234 | Inna Kuperstein | Inna Kuperstein | Deciphering cell signaling rewiring in human disorders | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The knowledge of cell molecular mechanisms implicated in human diseases is
expanding and should be converted into guidelines for deciphering pathological
cell signaling and suggesting appropriate treatment. The basic assumption is
that during a pathological transformation, the cell does not create new
signaling mecha... | [
{
"created": "Wed, 16 Dec 2015 16:26:35 GMT",
"version": "v1"
}
] | 2015-12-17 | [
[
"Kuperstein",
"Inna",
""
]
] | The knowledge of cell molecular mechanisms implicated in human diseases is expanding and should be converted into guidelines for deciphering pathological cell signaling and suggesting appropriate treatment. The basic assumption is that during a pathological transformation, the cell does not create new signaling mechani... |
1610.03828 | Gabriel Ocker | Gabriel Koch Ocker, Kre\v{s}imir Josi\'c, Eric Shea-Brown, Michael A.
Buice | Linking structure and activity in nonlinear spiking networks | We were recently made aware of an error in this article: in Figure
13, we neglected several one-loop contributions to the two-point correlation.
For the networks we studied here, these contributions are small (third order
in the coupling strength). For further discussion, please see the correction
note appended... | PLoS Computational Biology 2017;13(6):e1005583 | 10.1371/journal.pcbi.1005583 | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent experimental advances are producing an avalanche of data on both
neural connectivity and neural activity. To take full advantage of these two
emerging datasets we need a framework that links them, revealing how collective
neural activity arises from the structure of neural connectivity and intrinsic
neural dyn... | [
{
"created": "Wed, 12 Oct 2016 19:07:45 GMT",
"version": "v1"
},
{
"created": "Fri, 10 Mar 2017 20:09:45 GMT",
"version": "v2"
},
{
"created": "Tue, 25 Feb 2020 23:31:10 GMT",
"version": "v3"
}
] | 2020-02-27 | [
[
"Ocker",
"Gabriel Koch",
""
],
[
"Josić",
"Krešimir",
""
],
[
"Shea-Brown",
"Eric",
""
],
[
"Buice",
"Michael A.",
""
]
] | Recent experimental advances are producing an avalanche of data on both neural connectivity and neural activity. To take full advantage of these two emerging datasets we need a framework that links them, revealing how collective neural activity arises from the structure of neural connectivity and intrinsic neural dynam... |
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