id stringlengths 9 13 | submitter stringlengths 4 48 | authors stringlengths 4 9.62k | title stringlengths 4 343 | comments stringlengths 2 480 ⌀ | journal-ref stringlengths 9 309 ⌀ | doi stringlengths 12 138 ⌀ | report-no stringclasses 277
values | categories stringlengths 8 87 | license stringclasses 9
values | orig_abstract stringlengths 27 3.76k | versions listlengths 1 15 | update_date stringlengths 10 10 | authors_parsed listlengths 1 147 | abstract stringlengths 24 3.75k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1905.02552 | Yang Qin | Yang Qin, Louise Freebairn, Jo-An Atkinson, Weicheng Qian, Anahita
Safarishahrbijari, Nathaniel D Osgood | Multi-Scale Simulation Modeling for Prevention and Public Health
Management of Diabetes in Pregnancy and Sequelae | 10 pages, SBP-BRiMS 2019 | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Diabetes in pregnancy (DIP) is an increasing public health priority in the
Australian Capital Territory, particularly due to its impact on risk for
developing Type 2 diabetes. While earlier diagnostic screening results in
greater capacity for early detection and treatment, such benefits must be
balanced with the grea... | [
{
"created": "Fri, 3 May 2019 01:32:36 GMT",
"version": "v1"
}
] | 2019-05-08 | [
[
"Qin",
"Yang",
""
],
[
"Freebairn",
"Louise",
""
],
[
"Atkinson",
"Jo-An",
""
],
[
"Qian",
"Weicheng",
""
],
[
"Safarishahrbijari",
"Anahita",
""
],
[
"Osgood",
"Nathaniel D",
""
]
] | Diabetes in pregnancy (DIP) is an increasing public health priority in the Australian Capital Territory, particularly due to its impact on risk for developing Type 2 diabetes. While earlier diagnostic screening results in greater capacity for early detection and treatment, such benefits must be balanced with the greate... |
1510.06863 | Daniel Wilson | Sarah G Earle, Chieh-Hsi Wu, Jane Charlesworth, Nicole Stoesser, N
Claire Gordon, Timothy M Walker, Chris C A Spencer, Zamin Iqbal, David A
Clifton, Katie L Hopkins, Neil Woodford, E Grace Smith, Nazir Ismail, Martin
J Llewelyn, Tim E Peto, Derrick W Crook, Gil McVean, A Sarah Walker, Daniel J
Wilson | Identifying lineage effects when controlling for population structure
improves power in bacterial association studies | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Bacteria pose unique challenges for genome-wide association studies (GWAS)
because of strong structuring into distinct strains and substantial linkage
disequilibrium across the genome. While methods developed for human studies can
correct for strain structure, this risks considerable loss- of-power because
genetic di... | [
{
"created": "Fri, 23 Oct 2015 09:21:53 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Oct 2015 19:15:08 GMT",
"version": "v2"
},
{
"created": "Mon, 8 Feb 2016 17:01:23 GMT",
"version": "v3"
}
] | 2016-02-09 | [
[
"Earle",
"Sarah G",
""
],
[
"Wu",
"Chieh-Hsi",
""
],
[
"Charlesworth",
"Jane",
""
],
[
"Stoesser",
"Nicole",
""
],
[
"Gordon",
"N Claire",
""
],
[
"Walker",
"Timothy M",
""
],
[
"Spencer",
"Chris C A",
""
... | Bacteria pose unique challenges for genome-wide association studies (GWAS) because of strong structuring into distinct strains and substantial linkage disequilibrium across the genome. While methods developed for human studies can correct for strain structure, this risks considerable loss- of-power because genetic diff... |
2212.07790 | Oben \"Ozg\"ur | Oben \"Ozg\"ur, Arwa Rekik, Islem Rekik | Population Template-Based Brain Graph Augmentation for Improving
One-Shot Learning Classification | null | null | null | null | q-bio.NC cs.AI cs.LG cs.NE q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The challenges of collecting medical data on neurological disorder diagnosis
problems paved the way for learning methods with scarce number of samples. Due
to this reason, one-shot learning still remains one of the most challenging and
trending concepts of deep learning as it proposes to simulate the human-like
learn... | [
{
"created": "Wed, 14 Dec 2022 14:56:00 GMT",
"version": "v1"
}
] | 2022-12-16 | [
[
"Özgür",
"Oben",
""
],
[
"Rekik",
"Arwa",
""
],
[
"Rekik",
"Islem",
""
]
] | The challenges of collecting medical data on neurological disorder diagnosis problems paved the way for learning methods with scarce number of samples. Due to this reason, one-shot learning still remains one of the most challenging and trending concepts of deep learning as it proposes to simulate the human-like learnin... |
1611.06893 | Catalina Obando | Catalina Obando, Fabrizio De Vico Fallani | A statistical model for brain networks inferred from large-scale
electrophysiological signals | Due to the limitation "The abstract field cannot be longer than 1,920
characters", the abstract appearing here is slightly shorter than that in the
PDF file | null | 10.1098/rsif.2016.0940 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Network science has been extensively developed to characterize structural
properties of complex systems, including brain networks inferred from
neuroimaging data. As a result of the inference process, networks estimated
from experimentally obtained biological data, represent one instance of a
larger number of realiza... | [
{
"created": "Mon, 21 Nov 2016 16:38:06 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Nov 2016 17:11:38 GMT",
"version": "v2"
},
{
"created": "Wed, 23 Nov 2016 20:29:02 GMT",
"version": "v3"
},
{
"created": "Fri, 17 Feb 2017 16:49:14 GMT",
"version": "v4"
}
] | 2017-03-10 | [
[
"Obando",
"Catalina",
""
],
[
"Fallani",
"Fabrizio De Vico",
""
]
] | Network science has been extensively developed to characterize structural properties of complex systems, including brain networks inferred from neuroimaging data. As a result of the inference process, networks estimated from experimentally obtained biological data, represent one instance of a larger number of realizati... |
1009.1841 | Stuart Borrett Stuart Borrett | Andria K. Salas and Stuart R. Borrett | Evidence for the Dominance of Indirect Effects in 50 Trophically-Based
Ecosystem Networks | 26 pages, 5 figures, 1 table | Ecological Modelling 222: 1192--1204 | 10.1016/j.ecolmodel.2010.12.002 | null | q-bio.PE q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Indirect effects are powerful influences in ecosystems that may maintain
species diversity and alter apparent relationships between species in
surprising ways. Here, we applied Network Environ Analysis to 50
empirically-based trophic ecosystem models to test the hypothesis that indirect
flows dominate direct flows in... | [
{
"created": "Thu, 9 Sep 2010 18:14:33 GMT",
"version": "v1"
}
] | 2011-04-04 | [
[
"Salas",
"Andria K.",
""
],
[
"Borrett",
"Stuart R.",
""
]
] | Indirect effects are powerful influences in ecosystems that may maintain species diversity and alter apparent relationships between species in surprising ways. Here, we applied Network Environ Analysis to 50 empirically-based trophic ecosystem models to test the hypothesis that indirect flows dominate direct flows in e... |
1307.1499 | Kazuhiro Takemoto | Kazuhiro Takemoto, Kaori Kihara | Modular organization of cancer signaling networks is associated with
patient survivability | 17 pages, 5 figures | Biosystems 113, 149-154 (2013) | 10.1016/j.biosystems.2013.06.003 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular signaling networks are believed to determine cancer robustness.
Although cancer patient survivability was reported to correlate with the
heterogeneous connectivity of the signaling networks inspired by theoretical
studies on the increase of network robustness due to the heterogeneous
connectivity, other the... | [
{
"created": "Thu, 4 Jul 2013 23:24:13 GMT",
"version": "v1"
}
] | 2013-07-18 | [
[
"Takemoto",
"Kazuhiro",
""
],
[
"Kihara",
"Kaori",
""
]
] | Molecular signaling networks are believed to determine cancer robustness. Although cancer patient survivability was reported to correlate with the heterogeneous connectivity of the signaling networks inspired by theoretical studies on the increase of network robustness due to the heterogeneous connectivity, other theor... |
0906.2281 | Thierry Rabilloud | Thierry Rabilloud (BBSI) | Membrane proteins and proteomics: Love is possible, but so difficult | null | Electrophoresis 30, S1 (2009) S174-S180 | 10.1002/elps.200900050 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite decades of extensive research, the large-scale analysis of membrane
proteins remains a difficult task. This is due to the fact that membrane
proteins require a carefully balanced hydrophilic and lipophilic environment,
which optimum varies with different proteins, while most protein chemistry
methods work mai... | [
{
"created": "Fri, 12 Jun 2009 09:11:38 GMT",
"version": "v1"
}
] | 2009-06-15 | [
[
"Rabilloud",
"Thierry",
"",
"BBSI"
]
] | Despite decades of extensive research, the large-scale analysis of membrane proteins remains a difficult task. This is due to the fact that membrane proteins require a carefully balanced hydrophilic and lipophilic environment, which optimum varies with different proteins, while most protein chemistry methods work mainl... |
2103.10477 | Nicholas Boyd | Nicholas Boyd, Samuel Woodhouse, Kalim Mir | Sequencing by Emergence: Modeling and Estimation | null | null | null | null | q-bio.GN stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid
(DNA/RNA) sequencing technology that estimates sequence as an emergent property
of the binding and localization of a repertoire of short oligonucleotide
probes. SEQE promises to deliver accurate, ultra-long, haplotype-phased reads
at the whole genom... | [
{
"created": "Thu, 18 Mar 2021 18:55:13 GMT",
"version": "v1"
},
{
"created": "Tue, 3 Aug 2021 15:05:47 GMT",
"version": "v2"
}
] | 2021-08-04 | [
[
"Boyd",
"Nicholas",
""
],
[
"Woodhouse",
"Samuel",
""
],
[
"Mir",
"Kalim",
""
]
] | Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid (DNA/RNA) sequencing technology that estimates sequence as an emergent property of the binding and localization of a repertoire of short oligonucleotide probes. SEQE promises to deliver accurate, ultra-long, haplotype-phased reads at the whole genome-... |
2406.06731 | Yujiang Wang | Peter N. Taylor, Yujiang Wang, Callum Simpson, Vytene Janiukstyte,
Jonathan Horsley, Karoline Leiberg, Beth Little, Harry Clifford, Sophie
Adler, Sjoerd B. Vos, Gavin P Winston, Andrew W McEvoy, Anna Miserocchi, Jane
de Tisi, John S Duncan | The Imaging Database for Epilepsy And Surgery (IDEAS) | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Magnetic resonance imaging (MRI) is a crucial tool to identify brain
abnormalities in a wide range of neurological disorders. In focal epilepsy MRI
is used to identify structural cerebral abnormalities. For covert lesions,
machine learning and artificial intelligence algorithms may improve lesion
detection if abnorma... | [
{
"created": "Mon, 10 Jun 2024 18:53:09 GMT",
"version": "v1"
}
] | 2024-06-12 | [
[
"Taylor",
"Peter N.",
""
],
[
"Wang",
"Yujiang",
""
],
[
"Simpson",
"Callum",
""
],
[
"Janiukstyte",
"Vytene",
""
],
[
"Horsley",
"Jonathan",
""
],
[
"Leiberg",
"Karoline",
""
],
[
"Little",
"Beth",
""
],... | Magnetic resonance imaging (MRI) is a crucial tool to identify brain abnormalities in a wide range of neurological disorders. In focal epilepsy MRI is used to identify structural cerebral abnormalities. For covert lesions, machine learning and artificial intelligence algorithms may improve lesion detection if abnormali... |
1803.07883 | Ernest Greene | Ernest Greene, Yash Patel | Scan transcription of two-dimensional shapes as an alternative
neuromorphic concept | 7 pages, 4 figures, 53 references | Trends in Artificial Intelligence, 2018, 1, 27-33 | null | null | q-bio.NC | http://creativecommons.org/publicdomain/zero/1.0/ | Selfridge, along with Sutherland and Marr provided some of the earliest
proposals for how to program computers to recognize shapes. Their emphasis on
filtering for contour features, especially the orientation of boundary
segments, was reinforced by the Nobel Prize winning work of Hubel & Wiesel who
discovered that ne... | [
{
"created": "Wed, 21 Mar 2018 12:27:53 GMT",
"version": "v1"
}
] | 2018-03-22 | [
[
"Greene",
"Ernest",
""
],
[
"Patel",
"Yash",
""
]
] | Selfridge, along with Sutherland and Marr provided some of the earliest proposals for how to program computers to recognize shapes. Their emphasis on filtering for contour features, especially the orientation of boundary segments, was reinforced by the Nobel Prize winning work of Hubel & Wiesel who discovered that neur... |
2012.15697 | Rene Warren | Rene L. Warren and Inanc Birol | Interactive SARS-CoV-2 mutation timemaps | 3 pages, 1 figure | F1000Research 2021, 10:68 | 10.12688/f1000research.50857.1 | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | As the year 2020 draws to an end, several new strains have been reported for
the SARS-CoV-2 coronavirus, the agent responsible for the COVID-19 pandemic
that has afflicted us all this past year. However, it is difficult to
comprehend the scale, in sequence space, geographical location and time, at
which SARS-CoV-2 mu... | [
{
"created": "Thu, 31 Dec 2020 16:23:13 GMT",
"version": "v1"
}
] | 2023-06-09 | [
[
"Warren",
"Rene L.",
""
],
[
"Birol",
"Inanc",
""
]
] | As the year 2020 draws to an end, several new strains have been reported for the SARS-CoV-2 coronavirus, the agent responsible for the COVID-19 pandemic that has afflicted us all this past year. However, it is difficult to comprehend the scale, in sequence space, geographical location and time, at which SARS-CoV-2 muta... |
1512.08798 | Carlo Piermarocchi | Anthony Szedlak, Nicholas Smith, Li Liu, Giovanni Paternostro, Carlo
Piermarocchi | Evolutionary and topological properties of gene modules and driver
mutations in a leukemia gene regulatory network | 9 pages, 3 figures | null | 10.1371/journal.pcbi.1005009 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The diverse, specialized genes in today's lifeforms evolved from a common
core of ancient, elementary genes. However, these genes did not evolve
individually: gene expression is controlled by a complex network of
interactions, and alterations in one gene may drive reciprocal changes in its
proteins' binding partners.... | [
{
"created": "Tue, 29 Dec 2015 21:15:22 GMT",
"version": "v1"
}
] | 2016-09-28 | [
[
"Szedlak",
"Anthony",
""
],
[
"Smith",
"Nicholas",
""
],
[
"Liu",
"Li",
""
],
[
"Paternostro",
"Giovanni",
""
],
[
"Piermarocchi",
"Carlo",
""
]
] | The diverse, specialized genes in today's lifeforms evolved from a common core of ancient, elementary genes. However, these genes did not evolve individually: gene expression is controlled by a complex network of interactions, and alterations in one gene may drive reciprocal changes in its proteins' binding partners. W... |
1912.01890 | Maryam Nazarieh | Maryam Nazarieh, Volkhard Helms | Identification of Biomarkers Driving Blood Cell Development | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A blood cell lineage consists of several consecutive developmental stages
from the pluripotent or multipotent stem cell to a particular stage of
terminally differentiated cells. There is considerable interest in identifying
the key regulatory genes that govern blood cell development from the gene
expression data with... | [
{
"created": "Wed, 4 Dec 2019 10:57:25 GMT",
"version": "v1"
}
] | 2019-12-05 | [
[
"Nazarieh",
"Maryam",
""
],
[
"Helms",
"Volkhard",
""
]
] | A blood cell lineage consists of several consecutive developmental stages from the pluripotent or multipotent stem cell to a particular stage of terminally differentiated cells. There is considerable interest in identifying the key regulatory genes that govern blood cell development from the gene expression data withou... |
1411.6039 | Stuart Sevier | Stuart A. Sevier, Herbert Levine | Properties of Cooperatively Induced Phases in Sensing Models | 8 pages, 5 figures | Phys. Rev. E 91, 052707 (2015) | 10.1103/PhysRevE.91.052707 | null | q-bio.CB cond-mat.stat-mech nlin.AO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A large number of eukaryotic cells are able to directly detect external
chemical gradients with great accuracy and the ultimate limit to their
sensitivity has been a topic of debate for many years. Previous work has been
done to understand many aspects of this process but little attention has been
paid to the possibi... | [
{
"created": "Fri, 21 Nov 2014 22:04:51 GMT",
"version": "v1"
},
{
"created": "Mon, 1 Dec 2014 16:57:53 GMT",
"version": "v2"
}
] | 2015-05-20 | [
[
"Sevier",
"Stuart A.",
""
],
[
"Levine",
"Herbert",
""
]
] | A large number of eukaryotic cells are able to directly detect external chemical gradients with great accuracy and the ultimate limit to their sensitivity has been a topic of debate for many years. Previous work has been done to understand many aspects of this process but little attention has been paid to the possibili... |
2203.06505 | Lucas M. Stolerman | Lucas M. Stolerman, Leonardo Clemente, Canelle Poirier, Kris V. Parag,
Atreyee Majumder, Serge Masyn, Bernd Resch, and Mauricio Santillana | Using digital traces to build prospective and real-time county-level
early warning systems to anticipate COVID-19 outbreaks in the United States | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ongoing COVID-19 pandemic continues to affect communities around the
world. To date, almost 6 million people have died as a consequence of COVID-19,
and more than one-quarter of a billion people are estimated to have been
infected worldwide. The design of appropriate and timely mitigation strategies
to curb the e... | [
{
"created": "Sat, 12 Mar 2022 19:51:26 GMT",
"version": "v1"
}
] | 2022-03-15 | [
[
"Stolerman",
"Lucas M.",
""
],
[
"Clemente",
"Leonardo",
""
],
[
"Poirier",
"Canelle",
""
],
[
"Parag",
"Kris V.",
""
],
[
"Majumder",
"Atreyee",
""
],
[
"Masyn",
"Serge",
""
],
[
"Resch",
"Bernd",
""
],
... | The ongoing COVID-19 pandemic continues to affect communities around the world. To date, almost 6 million people have died as a consequence of COVID-19, and more than one-quarter of a billion people are estimated to have been infected worldwide. The design of appropriate and timely mitigation strategies to curb the eff... |
2212.03123 | Aliza Sloan | Aliza T. Sloan, J. A. Scott Kelso | On the emergence of agency | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How do human beings make sense of their relation to the world and realize
their ability to effect change? Applying modern concepts and methods of
coordination dynamics we demonstrate that patterns of movement and coordination
in 3-4 month-olds may be used to identify states and behavioral phenotypes of
emergent agenc... | [
{
"created": "Tue, 6 Dec 2022 16:38:36 GMT",
"version": "v1"
},
{
"created": "Wed, 29 Mar 2023 23:18:18 GMT",
"version": "v2"
}
] | 2023-03-31 | [
[
"Sloan",
"Aliza T.",
""
],
[
"Kelso",
"J. A. Scott",
""
]
] | How do human beings make sense of their relation to the world and realize their ability to effect change? Applying modern concepts and methods of coordination dynamics we demonstrate that patterns of movement and coordination in 3-4 month-olds may be used to identify states and behavioral phenotypes of emergent agency.... |
2302.13298 | Chlo\'e Colson | Chlo\'e Colson, Philip K. Maini, Helen M. Byrne | Investigating the influence of growth arrest mechanisms on tumour
responses to radiotherapy | 33 pages, 22 figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cancer is a heterogeneous disease and tumours of the same type can differ
greatly at the genetic and phenotypic levels. Understanding how these
differences impact sensitivity to treatment is an essential step towards
patient-specific treatment design. In this paper, we investigate how two
different mechanisms for gro... | [
{
"created": "Sun, 26 Feb 2023 11:36:52 GMT",
"version": "v1"
}
] | 2023-02-28 | [
[
"Colson",
"Chloé",
""
],
[
"Maini",
"Philip K.",
""
],
[
"Byrne",
"Helen M.",
""
]
] | Cancer is a heterogeneous disease and tumours of the same type can differ greatly at the genetic and phenotypic levels. Understanding how these differences impact sensitivity to treatment is an essential step towards patient-specific treatment design. In this paper, we investigate how two different mechanisms for growt... |
1503.05485 | Johann Mart\'inez | Carlos B. Moreno, Jos\'e-Luis. D\'iaz, J. H. Mart\'inez | Petri Net Modeling of the Brain Circuit Involved in Aggressive Behavior | 30 pages, in Spanish. 15 figures, 1 table, Submitted to SaludMental
2015, Mexico, Print version ISSN 0185-3325, SJR, SciELO, Scimago; SaludMental
Print version ISSN 0185-3325, (2015) | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The purpose of this work in to demonstrate the initial results of a research
project having as its goal to develop dynamic models of the brain network
involved in aggressive behavior. In this way, the complex neural process
correlated to basic anger emotions and resulting in aggressive behaviors is
purportedly schema... | [
{
"created": "Wed, 18 Mar 2015 16:58:26 GMT",
"version": "v1"
}
] | 2015-03-19 | [
[
"Moreno",
"Carlos B.",
""
],
[
"Díaz",
"José-Luis.",
""
],
[
"Martínez",
"J. H.",
""
]
] | The purpose of this work in to demonstrate the initial results of a research project having as its goal to develop dynamic models of the brain network involved in aggressive behavior. In this way, the complex neural process correlated to basic anger emotions and resulting in aggressive behaviors is purportedly schemati... |
1409.2299 | Claus Vogl | Claus Vogl | Biallelic Mutation-Drift Diffusion in the Limit of Small Scaled Mutation
Rates | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The evolution of the allelic proportion $x$ of a biallelic locus subject to
the forces of mutation and drift is investigated in a diffusion model, assuming
small scaled mutation rates. The overall scaled mutation rate is parametrized
with $\theta=(\mu_1+\mu_0)N$ and the ratio of mutation rates with
$\alpha=\mu_1/(\mu... | [
{
"created": "Mon, 8 Sep 2014 11:41:13 GMT",
"version": "v1"
}
] | 2014-09-09 | [
[
"Vogl",
"Claus",
""
]
] | The evolution of the allelic proportion $x$ of a biallelic locus subject to the forces of mutation and drift is investigated in a diffusion model, assuming small scaled mutation rates. The overall scaled mutation rate is parametrized with $\theta=(\mu_1+\mu_0)N$ and the ratio of mutation rates with $\alpha=\mu_1/(\mu_1... |
1203.2503 | Francesc Rossell\'o | Gabriel Cardona, Arnau Mir, Francesc Rossello | The expected value under the Yule model of the squared path-difference
distance | 10 pages, extended version of a paper submitted to Applied
Mathematics Letter | null | null | null | q-bio.PE math.PR q-bio.QM | http://creativecommons.org/licenses/publicdomain/ | The path-difference metric is one of the oldest and most popular distances
for the comparison of phylogenetic trees, but its statistical properties are
still quite unknown. In this paper we compute the expected value under the Yule
model of evolution of its square on the space of fully resolved rooted
phylogenetic tr... | [
{
"created": "Mon, 12 Mar 2012 14:33:52 GMT",
"version": "v1"
}
] | 2012-03-13 | [
[
"Cardona",
"Gabriel",
""
],
[
"Mir",
"Arnau",
""
],
[
"Rossello",
"Francesc",
""
]
] | The path-difference metric is one of the oldest and most popular distances for the comparison of phylogenetic trees, but its statistical properties are still quite unknown. In this paper we compute the expected value under the Yule model of evolution of its square on the space of fully resolved rooted phylogenetic tree... |
2307.14367 | Hadi Abdine | Hadi Abdine, Michail Chatzianastasis, Costas Bouyioukos, Michalis
Vazirgiannis | Prot2Text: Multimodal Protein's Function Generation with GNNs and
Transformers | null | Proceedings of the AAAI Conference on Artificial Intelligence,
38(10), 10757-10765 (2024) | 10.1609/aaai.v38i10.28948 | null | q-bio.QM cs.CL cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In recent years, significant progress has been made in the field of protein
function prediction with the development of various machine-learning
approaches. However, most existing methods formulate the task as a
multi-classification problem, i.e. assigning predefined labels to proteins. In
this work, we propose a nov... | [
{
"created": "Tue, 25 Jul 2023 09:35:43 GMT",
"version": "v1"
},
{
"created": "Thu, 21 Dec 2023 16:46:35 GMT",
"version": "v2"
},
{
"created": "Sat, 20 Apr 2024 09:10:47 GMT",
"version": "v3"
}
] | 2024-04-23 | [
[
"Abdine",
"Hadi",
""
],
[
"Chatzianastasis",
"Michail",
""
],
[
"Bouyioukos",
"Costas",
""
],
[
"Vazirgiannis",
"Michalis",
""
]
] | In recent years, significant progress has been made in the field of protein function prediction with the development of various machine-learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e. assigning predefined labels to proteins. In this work, we propose a novel... |
1003.2111 | Jens Christian Claussen | Hong-Viet V. Ngo, Jan K\"ohler, J\"org Mayer, Jens Christian Claussen
and Heinz Georg Schuster | Triggering up states in all-to-all coupled neurons | epl Europhysics Letters, accepted (2010) | EPL (Europhysics Letters) 89, 68002 (2010) | 10.1209/0295-5075/89/68002 | null | q-bio.NC cond-mat.stat-mech nlin.CD physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Slow-wave sleep in mammalians is characterized by a change of large-scale
cortical activity currently paraphrased as cortical Up/Down states. A recent
experiment demonstrated a bistable collective behaviour in ferret slices, with
the remarkable property that the Up states can be switched on and off with
pulses, or ex... | [
{
"created": "Wed, 10 Mar 2010 13:50:57 GMT",
"version": "v1"
}
] | 2012-06-12 | [
[
"Ngo",
"Hong-Viet V.",
""
],
[
"Köhler",
"Jan",
""
],
[
"Mayer",
"Jörg",
""
],
[
"Claussen",
"Jens Christian",
""
],
[
"Schuster",
"Heinz Georg",
""
]
] | Slow-wave sleep in mammalians is characterized by a change of large-scale cortical activity currently paraphrased as cortical Up/Down states. A recent experiment demonstrated a bistable collective behaviour in ferret slices, with the remarkable property that the Up states can be switched on and off with pulses, or exci... |
q-bio/0311028 | Rodrick Wallace | Rodrick Wallace | Systemic lupus erythematosus in African-American women: Cognitive
physiological modules, autoimmune disease, and structured psychosocial stress | 18 pages, 1 figure | null | null | null | q-bio.NC q-bio.MN | null | Examining elevated rates of systemic lupus erythematosus in African-American
women from perspectives of immune cognition suggests the disease constitutes an
internalized physiological image of external structured psychosocial stress, a
'pathogenic social hierarchy' involving the synergism of racism and gender
discrim... | [
{
"created": "Thu, 20 Nov 2003 18:26:25 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Wallace",
"Rodrick",
""
]
] | Examining elevated rates of systemic lupus erythematosus in African-American women from perspectives of immune cognition suggests the disease constitutes an internalized physiological image of external structured psychosocial stress, a 'pathogenic social hierarchy' involving the synergism of racism and gender discrimin... |
1610.04656 | J. C. Phillips | J. C. Phillips | Giant Hub Src and Syk Tyrosine Kinase Thermodynamic Profiles
Recapitulate Evolution | 18 pages, 8 figures | null | 10.1016/j.physa.2017.04.180 | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Thermodynamic scaling theory, previously applied mainly to small proteins,
here analyzes quantitative evolution of the titled functional network giant hub
enzymes. The broad domain structure identified homologically is confirmed
hydropathically using amino acid sequences only. The most surprising results
concern the ... | [
{
"created": "Fri, 14 Oct 2016 22:02:31 GMT",
"version": "v1"
}
] | 2017-05-24 | [
[
"Phillips",
"J. C.",
""
]
] | Thermodynamic scaling theory, previously applied mainly to small proteins, here analyzes quantitative evolution of the titled functional network giant hub enzymes. The broad domain structure identified homologically is confirmed hydropathically using amino acid sequences only. The most surprising results concern the ev... |
1810.10893 | Juergen Reingruber | Johannes Reisert, J\"urgen Reingruber | The $Ca^{2+}$-activated $Cl^-$ current ensures robust and reliable
signal amplification in vertebrate olfactory receptor neurons | 31 pages, 10 figures (including SI) | null | 10.1073/pnas.1816371116 | null | q-bio.NC q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Activation of most primary sensory neurons results in transduction currents
that are carried by cations. One notable exception is the vertebrate olfactory
receptor neuron (ORN), where the transduction current is carried largely by the
anion $Cl^-$. However, it remains unclear why ORNs use an anionic current for
signa... | [
{
"created": "Thu, 25 Oct 2018 14:26:17 GMT",
"version": "v1"
}
] | 2022-06-08 | [
[
"Reisert",
"Johannes",
""
],
[
"Reingruber",
"Jürgen",
""
]
] | Activation of most primary sensory neurons results in transduction currents that are carried by cations. One notable exception is the vertebrate olfactory receptor neuron (ORN), where the transduction current is carried largely by the anion $Cl^-$. However, it remains unclear why ORNs use an anionic current for signal ... |
2003.00241 | Pawel Krajewski | Pawel Krajewski, Piotr Kachlicki, Anna Piasecka, Maria Surma, Anetta
Kuczynska, Krzysztof Mikolajczak, Piotr Ogrodowicz, Aneta Sawikowska, Hanna
Cwiek-Kupczynska, Maciej Stobiecki, Pawel Rodziewicz, Lukasz Marczak | In search of biomarkers and the ideotype of barley tolerant to water
scarcity | 12 pages, 8 figures, 2 supplementary tables | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | In barley plants, water shortage causes many changes on the morphological,
physiological and biochemical levels resulting in the reduction of grain yield.
In the present study the results of various experiments on the response of the
same barley recombinant inbred lines to water shortage, including phenotypic,
proteo... | [
{
"created": "Sat, 29 Feb 2020 11:36:50 GMT",
"version": "v1"
}
] | 2020-03-03 | [
[
"Krajewski",
"Pawel",
""
],
[
"Kachlicki",
"Piotr",
""
],
[
"Piasecka",
"Anna",
""
],
[
"Surma",
"Maria",
""
],
[
"Kuczynska",
"Anetta",
""
],
[
"Mikolajczak",
"Krzysztof",
""
],
[
"Ogrodowicz",
"Piotr",
""... | In barley plants, water shortage causes many changes on the morphological, physiological and biochemical levels resulting in the reduction of grain yield. In the present study the results of various experiments on the response of the same barley recombinant inbred lines to water shortage, including phenotypic, proteomi... |
1704.03855 | Richard Granger | Richard Granger | How brains are built: Principles of computational neuroscience | http://dana.org/news/cerebrum/detail.aspx?id=30356 | Cerebrum; Dana Foundation 2011 | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | 'If I cannot build it, I do not understand it.' So said Nobel laureate
Richard Feynman, and by his metric, we understand a bit about physics, less
about chemistry, and almost nothing about biology.
When we fully understand a phenomenon, we can specify its entire sequence of
events, causes, and effects so completely... | [
{
"created": "Wed, 29 Mar 2017 01:18:13 GMT",
"version": "v1"
}
] | 2017-04-13 | [
[
"Granger",
"Richard",
""
]
] | 'If I cannot build it, I do not understand it.' So said Nobel laureate Richard Feynman, and by his metric, we understand a bit about physics, less about chemistry, and almost nothing about biology. When we fully understand a phenomenon, we can specify its entire sequence of events, causes, and effects so completely tha... |
1502.01326 | Lucas Valdez D. | L. D. Valdez, H. H. A. R\^ego, H. E. Stanley, L. A. Braunstein | Predicting the extinction of Ebola spreading in Liberia due to
mitigation strategies | null | Scientific Reports 5, Article number: 12172 (2015) | 10.1038/srep12172 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Ebola virus is spreading throughout West Africa and is causing thousands
of deaths. In order to quantify the effectiveness of different strategies for
controlling the spread, we develop a mathematical model in which the
propagation of the Ebola virus through Liberia is caused by travel between
counties. For the i... | [
{
"created": "Wed, 4 Feb 2015 20:43:29 GMT",
"version": "v1"
},
{
"created": "Thu, 5 Feb 2015 20:45:47 GMT",
"version": "v2"
},
{
"created": "Sun, 24 May 2015 03:05:59 GMT",
"version": "v3"
},
{
"created": "Sun, 31 May 2015 15:34:41 GMT",
"version": "v4"
},
{
"cre... | 2015-07-22 | [
[
"Valdez",
"L. D.",
""
],
[
"Rêgo",
"H. H. A.",
""
],
[
"Stanley",
"H. E.",
""
],
[
"Braunstein",
"L. A.",
""
]
] | The Ebola virus is spreading throughout West Africa and is causing thousands of deaths. In order to quantify the effectiveness of different strategies for controlling the spread, we develop a mathematical model in which the propagation of the Ebola virus through Liberia is caused by travel between counties. For the ini... |
2109.12434 | Satpreet Harcharan Singh | Satpreet Harcharan Singh, Floris van Breugel, Rajesh P. N. Rao, Bingni
Wen Brunton | Emergent behavior and neural dynamics in artificial agents tracking
turbulent plumes | null | null | null | null | q-bio.NC cs.AI cs.LG cs.NE cs.SY eess.SY | http://creativecommons.org/licenses/by-sa/4.0/ | Tracking a turbulent plume to locate its source is a complex control problem
because it requires multi-sensory integration and must be robust to
intermittent odors, changing wind direction, and variable plume statistics.
This task is routinely performed by flying insects, often over long distances,
in pursuit of food... | [
{
"created": "Sat, 25 Sep 2021 20:57:02 GMT",
"version": "v1"
},
{
"created": "Sat, 18 Dec 2021 00:58:21 GMT",
"version": "v2"
}
] | 2021-12-21 | [
[
"Singh",
"Satpreet Harcharan",
""
],
[
"van Breugel",
"Floris",
""
],
[
"Rao",
"Rajesh P. N.",
""
],
[
"Brunton",
"Bingni Wen",
""
]
] | Tracking a turbulent plume to locate its source is a complex control problem because it requires multi-sensory integration and must be robust to intermittent odors, changing wind direction, and variable plume statistics. This task is routinely performed by flying insects, often over long distances, in pursuit of food o... |
1808.03471 | Larry Bull | Larry Bull | The Evolution of Sex Chromosomes through the Baldwin Effect | 14 pages | null | null | null | q-bio.PE cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has recently been suggested that the fundamental haploid-diploid cycle of
eukaryotic sex exploits a rudimentary form of the Baldwin effect. Thereafter
the other associated phenomena can be explained as evolution tuning the amount
and frequency of learning experienced by an organism. Using the well-known NK
model o... | [
{
"created": "Fri, 10 Aug 2018 09:54:30 GMT",
"version": "v1"
},
{
"created": "Fri, 15 Feb 2019 14:21:57 GMT",
"version": "v2"
},
{
"created": "Thu, 12 Mar 2020 13:40:45 GMT",
"version": "v3"
},
{
"created": "Mon, 16 Mar 2020 12:15:33 GMT",
"version": "v4"
}
] | 2020-03-17 | [
[
"Bull",
"Larry",
""
]
] | It has recently been suggested that the fundamental haploid-diploid cycle of eukaryotic sex exploits a rudimentary form of the Baldwin effect. Thereafter the other associated phenomena can be explained as evolution tuning the amount and frequency of learning experienced by an organism. Using the well-known NK model of ... |
q-bio/0504026 | Sanjay Jain | Areejit Samal, Shalini Singh, Varun Giri, Sandeep Krishna, N. Raghuram
and Sanjay Jain | Low Degree Metabolites Explain Essential Reactions and Enhance
Modularity in Biological Networks | 12 pages main text with 2 figures and 2 tables. 16 pages of
Supplementary material. Revised version has title changed and contains study
of 3 organisms instead of 1 earlier | BMC Bioinformatics 7:118 (2006) | null | null | q-bio.MN | null | Recently there has been a lot of interest in identifying modules at the level
of genetic and metabolic networks of organisms, as well as in identifying
single genes and reactions that are essential for the organism. A goal of
computational and systems biology is to go beyond identification towards an
explanation of s... | [
{
"created": "Wed, 20 Apr 2005 18:43:03 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Oct 2005 18:52:16 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Samal",
"Areejit",
""
],
[
"Singh",
"Shalini",
""
],
[
"Giri",
"Varun",
""
],
[
"Krishna",
"Sandeep",
""
],
[
"Raghuram",
"N.",
""
],
[
"Jain",
"Sanjay",
""
]
] | Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational and systems biology is to go beyond identification towards an explanation of spe... |
1304.7992 | Nikos Vlassis | Nikos Vlassis, Maria Pires Pacheco, Thomas Sauter | Fast Reconstruction of Compact Context-Specific Metabolic Network Models | fixed an error in the functional analysis of the liver model | null | 10.1371/journal.pcbi.1003424 | null | q-bio.MN cs.CE math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Systemic approaches to the study of a biological cell or tissue rely
increasingly on the use of context-specific metabolic network models. The
reconstruction of such a model from high-throughput data can routinely involve
large numbers of tests under different conditions and extensive parameter
tuning, which calls fo... | [
{
"created": "Tue, 30 Apr 2013 13:31:40 GMT",
"version": "v1"
},
{
"created": "Thu, 10 Oct 2013 14:12:56 GMT",
"version": "v2"
},
{
"created": "Sat, 23 Nov 2013 22:17:18 GMT",
"version": "v3"
}
] | 2015-06-15 | [
[
"Vlassis",
"Nikos",
""
],
[
"Pacheco",
"Maria Pires",
""
],
[
"Sauter",
"Thomas",
""
]
] | Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of context-specific metabolic network models. The reconstruction of such a model from high-throughput data can routinely involve large numbers of tests under different conditions and extensive parameter tuning, which calls for ... |
2106.03563 | Roel Ceballos | Roel F. Ceballos | Mortality Analysis of Early COVID-19 Cases in the Philippines Based on
Observed Demographic and Clinical Characteristics | null | Recoletos Multidisciplinary Research Journal, 9(1), 91-106 (2021) | 10.32871/rmrj2109.01.09 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | This study aims to determine the demographic, epidemiologic, and clinical
characteristics of COVID-19 cases that are highly susceptible to COVID-19
infection, with longer hospitalization and at higher risk of mortality and to
provide insights that may be useful to assess the vaccination priority program
and allocate ... | [
{
"created": "Thu, 3 Jun 2021 23:56:01 GMT",
"version": "v1"
}
] | 2021-06-08 | [
[
"Ceballos",
"Roel F.",
""
]
] | This study aims to determine the demographic, epidemiologic, and clinical characteristics of COVID-19 cases that are highly susceptible to COVID-19 infection, with longer hospitalization and at higher risk of mortality and to provide insights that may be useful to assess the vaccination priority program and allocate ho... |
0812.1279 | Emilio Hernandez-Garcia | Emilio Hernandez-Garcia, Cristobal Lopez (IFISC), Simone Pigolotti
(NBI), Ken H. Andersen (AQUA) | Species competition: coexistence, exclusion and clustering | 9 pages, 4 figures. Replaced with published version. Freely available
from the publisher site under the Creative Commons Attribution license | Philosophical Transactions of the Royal Society A 367, 3183-3195
(2009) | 10.1098/rsta.2009.0086 | null | q-bio.PE nlin.PS q-bio.QM | http://creativecommons.org/licenses/by/3.0/ | We present properties of Lotka-Volterra equations describing ecological
competition among a large number of competing species. First we extend to the
case of a non-homogeneous niche space stability conditions for solutions
representing species coexistence. Second, we discuss mechanisms leading to
species clustering a... | [
{
"created": "Sat, 6 Dec 2008 12:09:02 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Jul 2009 07:16:28 GMT",
"version": "v2"
}
] | 2009-07-22 | [
[
"Hernandez-Garcia",
"Emilio",
"",
"IFISC"
],
[
"Lopez",
"Cristobal",
"",
"IFISC"
],
[
"Pigolotti",
"Simone",
"",
"NBI"
],
[
"Andersen",
"Ken H.",
"",
"AQUA"
]
] | We present properties of Lotka-Volterra equations describing ecological competition among a large number of competing species. First we extend to the case of a non-homogeneous niche space stability conditions for solutions representing species coexistence. Second, we discuss mechanisms leading to species clustering and... |
2111.02692 | Salman Mohamadi | Salman Mohamadi, Gianfranco.Doretto, Nasser M. Nasrabadi, Donald A.
Adjeroh | Human Age Estimation from Gene Expression Data using Artificial Neural
Networks | 8 pages, 5 figures, This paper is accepted to 2021 IEEE International
Conference on Bioinformatics and Biomedicine (BIBM) | null | null | null | q-bio.GN cs.AI | http://creativecommons.org/licenses/by/4.0/ | The study of signatures of aging in terms of genomic biomarkers can be
uniquely helpful in understanding the mechanisms of aging and developing models
to accurately predict the age. Prior studies have employed gene expression and
DNA methylation data aiming at accurate prediction of age. In this line, we
propose a ne... | [
{
"created": "Thu, 4 Nov 2021 08:57:35 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Nov 2021 03:51:18 GMT",
"version": "v2"
}
] | 2021-11-08 | [
[
"Mohamadi",
"Salman",
""
],
[
"Doretto",
"Gianfranco.",
""
],
[
"Nasrabadi",
"Nasser M.",
""
],
[
"Adjeroh",
"Donald A.",
""
]
] | The study of signatures of aging in terms of genomic biomarkers can be uniquely helpful in understanding the mechanisms of aging and developing models to accurately predict the age. Prior studies have employed gene expression and DNA methylation data aiming at accurate prediction of age. In this line, we propose a new ... |
1305.6259 | Binay Panda | Prachi Jain (1), Neeraja M. Krishnan (1) and Binay Panda (1 and 2)
((1) Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied
Biotechnology, Bangalore, India, (2) Strand Life Sciences, Bangalore, India) | Augmenting transcriptome assembly combinatorially | "for associated supplementary file, see
ftp://115.119.160.213/transcriptome_assembly_supp_text | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | RNA-seq allows detection and precise quantification of transcripts, provides
comprehensive understanding of exon/intron boundaries, aids discovery of
alternatively spliced isoforms and fusion transcripts along with measurement of
allele-specific expression. Researchers interested in studying and constructing
transcri... | [
{
"created": "Mon, 27 May 2013 15:50:46 GMT",
"version": "v1"
},
{
"created": "Fri, 31 May 2013 07:09:43 GMT",
"version": "v2"
}
] | 2013-06-03 | [
[
"Jain",
"Prachi",
"",
"1 and 2"
],
[
"Krishnan",
"Neeraja M.",
"",
"1 and 2"
],
[
"Panda",
"Binay",
"",
"1 and 2"
]
] | RNA-seq allows detection and precise quantification of transcripts, provides comprehensive understanding of exon/intron boundaries, aids discovery of alternatively spliced isoforms and fusion transcripts along with measurement of allele-specific expression. Researchers interested in studying and constructing transcript... |
q-bio/0505013 | Kate Davison | K. Davison (1), P. M. Dolukhanov (2), G. R. Sarson (1) and A. Shukurov
(1), ((1) School of Mathematics and Statistics, University of Newcastle upon
Tyne, (2) School of Historical Studies, University of Newcastle upon Tyne) | Environmental effects on the spread of the Neolithic | 36 Pages, 4 Figures, submitted for publication to the Journal of
Archaeological Science | null | null | null | q-bio.PE | null | The causes and implications of the regional variations in the spread of the
incipient agriculture in Europe remain poorly understood. We apply population
dynamics models to study the dispersal of the Neolithic in Europe from a
localized area in the Near East, solving the two-dimensional reaction-diffusion
equation on... | [
{
"created": "Fri, 6 May 2005 09:36:06 GMT",
"version": "v1"
},
{
"created": "Mon, 9 May 2005 15:11:33 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Davison",
"K.",
""
],
[
"Dolukhanov",
"P. M.",
""
],
[
"Sarson",
"G. R.",
""
],
[
"Shukurov",
"A.",
""
]
] | The causes and implications of the regional variations in the spread of the incipient agriculture in Europe remain poorly understood. We apply population dynamics models to study the dispersal of the Neolithic in Europe from a localized area in the Near East, solving the two-dimensional reaction-diffusion equation on a... |
1303.2935 | Sergiy Popov | Zoja Medjanik, Lyudmila Popova, Sergiy Popov | On Systemic Destruction of Human Locomotor System | 15 pages, 1 figure | null | null | null | q-bio.TO physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Locomotor system disorders affect a vast majority of people at some time in
their life bringing pain, functional limitations, social and economic
implications. Modern medicine cannot offer prevention and effective treatment
for most chronic musculoskeletal conditions, because their etiology and
pathogenesis are unkno... | [
{
"created": "Sun, 10 Mar 2013 15:05:51 GMT",
"version": "v1"
}
] | 2013-03-13 | [
[
"Medjanik",
"Zoja",
""
],
[
"Popova",
"Lyudmila",
""
],
[
"Popov",
"Sergiy",
""
]
] | Locomotor system disorders affect a vast majority of people at some time in their life bringing pain, functional limitations, social and economic implications. Modern medicine cannot offer prevention and effective treatment for most chronic musculoskeletal conditions, because their etiology and pathogenesis are unknown... |
1401.3668 | Simon Gravel | Simon Gravel, Mike Steel | The existence and abundance of ghost ancestors in biparental populations | 15 pages + appendix, 6 figures; updated version contains additional
simulations and clarifications | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In a randomly-mating biparental population of size $N$ there are, with high
probability, individuals who are genealogical ancestors of every extant
individual within approximately $\log_2(N)$ generations into the past. We use
this result of J. Chang to prove a curious corollary under standard models of
recombination:... | [
{
"created": "Wed, 15 Jan 2014 17:00:33 GMT",
"version": "v1"
},
{
"created": "Mon, 2 Mar 2015 20:58:40 GMT",
"version": "v2"
}
] | 2015-03-03 | [
[
"Gravel",
"Simon",
""
],
[
"Steel",
"Mike",
""
]
] | In a randomly-mating biparental population of size $N$ there are, with high probability, individuals who are genealogical ancestors of every extant individual within approximately $\log_2(N)$ generations into the past. We use this result of J. Chang to prove a curious corollary under standard models of recombination: t... |
2012.12961 | Brian Cleary | Brian Cleary and Aviv Regev | The necessity and power of random, under-sampled experiments in biology | null | null | null | null | q-bio.QM stat.AP | http://creativecommons.org/licenses/by-nc-sa/4.0/ | A vast array of transformative technologies developed over the past decade
has enabled measurement and perturbation at ever increasing scale, yet our
understanding of many systems remains limited by experimental capacity.
Overcoming this limitation is not simply a matter of reducing costs with
existing approaches; fo... | [
{
"created": "Wed, 23 Dec 2020 20:38:33 GMT",
"version": "v1"
}
] | 2020-12-25 | [
[
"Cleary",
"Brian",
""
],
[
"Regev",
"Aviv",
""
]
] | A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this limitation is not simply a matter of reducing costs with existing approaches; for ... |
1712.00306 | Rodrigo Felipe de Oliveira Pena | Rodrigo F.O. Pena, Cesar C. Ceballos, Vinicius Lima, and Antonio C.
Roque | Interplay of activation kinetics and the derivative conductance
determines resonance properties of neurons | 11 pages, 9 figures | Phys. Rev. E 97, 042408 (2018) | 10.1103/PhysRevE.97.042408 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In a neuron with hyperpolarization activated current ($I_h$), the correct
input frequency leads to an enhancement of the output response. This behavior
is known as resonance and is well described by the neuronal impedance. In a
simple neuron model we derive equations for the neuron's resonance and we link
its frequen... | [
{
"created": "Fri, 1 Dec 2017 13:21:16 GMT",
"version": "v1"
},
{
"created": "Sat, 9 Dec 2017 13:19:56 GMT",
"version": "v2"
},
{
"created": "Thu, 12 Apr 2018 18:38:47 GMT",
"version": "v3"
}
] | 2018-04-18 | [
[
"Pena",
"Rodrigo F. O.",
""
],
[
"Ceballos",
"Cesar C.",
""
],
[
"Lima",
"Vinicius",
""
],
[
"Roque",
"Antonio C.",
""
]
] | In a neuron with hyperpolarization activated current ($I_h$), the correct input frequency leads to an enhancement of the output response. This behavior is known as resonance and is well described by the neuronal impedance. In a simple neuron model we derive equations for the neuron's resonance and we link its frequency... |
2005.14149 | Jakob Jordan | Jakob Jordan, Maximilian Schmidt, Walter Senn, and Mihai A. Petrovici | Evolving to learn: discovering interpretable plasticity rules for
spiking networks | 33 pages, 10 figures; J. Jordan and M. Schmidt contributed equally to
this work | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Continuous adaptation allows survival in an ever-changing world. Adjustments
in the synaptic coupling strength between neurons are essential for this
capability, setting us apart from simpler, hard-wired organisms. How these
changes can be mathematically described at the phenomenological level, as so
called "plastici... | [
{
"created": "Thu, 28 May 2020 17:06:03 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Jun 2020 13:32:27 GMT",
"version": "v2"
},
{
"created": "Tue, 5 Jan 2021 16:44:40 GMT",
"version": "v3"
}
] | 2021-01-06 | [
[
"Jordan",
"Jakob",
""
],
[
"Schmidt",
"Maximilian",
""
],
[
"Senn",
"Walter",
""
],
[
"Petrovici",
"Mihai A.",
""
]
] | Continuous adaptation allows survival in an ever-changing world. Adjustments in the synaptic coupling strength between neurons are essential for this capability, setting us apart from simpler, hard-wired organisms. How these changes can be mathematically described at the phenomenological level, as so called "plasticity... |
1609.00157 | Guido Tiana | R. Meloni, C. Camilloni and G. Tiana | Properties of low-dimensional collective variables in the molecular
dynamics of biopolymers | null | Phys. Rev. E 94, 052406 (2016) | 10.1103/PhysRevE.94.052406 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The description of the dynamics of a complex, high-dimensional system in
terms of a low-dimensional set of collective variables Y can be fruitful if the
low dimensional representation satisfies a Langevin equation with drift and
diffusion coefficients which depend only on Y. We present a computational
scheme to evalu... | [
{
"created": "Thu, 1 Sep 2016 09:33:52 GMT",
"version": "v1"
},
{
"created": "Mon, 28 Nov 2016 10:01:02 GMT",
"version": "v2"
}
] | 2016-11-29 | [
[
"Meloni",
"R.",
""
],
[
"Camilloni",
"C.",
""
],
[
"Tiana",
"G.",
""
]
] | The description of the dynamics of a complex, high-dimensional system in terms of a low-dimensional set of collective variables Y can be fruitful if the low dimensional representation satisfies a Langevin equation with drift and diffusion coefficients which depend only on Y. We present a computational scheme to evaluat... |
0807.0721 | Bob Eisenberg | Bob Eisenberg | Permeation as a Diffusion Process | This is a posting of a paper written in 2000, for the Biophysics
Textbook On Line Channels, Receptors, and Transporters Louis J. DeFelice,
Volume Editor which is hard to find. Bob Eisenberg is also known as RS
Eisenberg | Chapter 4 in Biophysics Textbook On Line Channels, Receptors, and
Transporters Louis J. DeFelice, Volume Editor, 2000 | null | null | q-bio.BM physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The paper shows how the diffusive movement of ions through a channel protein
can be described as a chemical reaction over an arbitrary shaped potential
barrier. The result is simple and intuitive but without approximation beyond
the electrodiffusion description of ion movement.
| [
{
"created": "Fri, 4 Jul 2008 11:21:20 GMT",
"version": "v1"
}
] | 2008-07-10 | [
[
"Eisenberg",
"Bob",
""
]
] | The paper shows how the diffusive movement of ions through a channel protein can be described as a chemical reaction over an arbitrary shaped potential barrier. The result is simple and intuitive but without approximation beyond the electrodiffusion description of ion movement. |
1503.04620 | Myoungwon Cho | Myoung Won Cho | Two symmetry breaking mechanisms for the development of orientation
selectivity in a neural system | null | null | 10.3938/jkps.67.1661 | null | q-bio.NC stat.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Orientation selectivity is a remarkable feature of the neurons located in the
primary visual cortex. Provided that the visual neurons acquire orientation
selectivity through activity-dependent Hebbian learning, the development
process could be understood as a kind of symmetry breaking phenomenon in the
view of physic... | [
{
"created": "Mon, 16 Mar 2015 12:26:04 GMT",
"version": "v1"
}
] | 2016-01-20 | [
[
"Cho",
"Myoung Won",
""
]
] | Orientation selectivity is a remarkable feature of the neurons located in the primary visual cortex. Provided that the visual neurons acquire orientation selectivity through activity-dependent Hebbian learning, the development process could be understood as a kind of symmetry breaking phenomenon in the view of physics.... |
1207.4145 | Nebojsa Jojic | Nebojsa Jojic, Vladimir Jojic, David Heckerman | Joint discovery of haplotype blocks and complex trait associations from
SNP sequences | Appears in Proceedings of the Twentieth Conference on Uncertainty in
Artificial Intelligence (UAI2004) | null | null | UAI-P-2004-PG-286-292 | q-bio.GN cs.CE stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Haplotypes, the global patterns of DNA sequence variation, have important
implications for identifying complex traits. Recently, blocks of limited
haplotype diversity have been discovered in human chromosomes, intensifying the
research on modelling the block structure as well as the transitions or
co-occurrence of th... | [
{
"created": "Wed, 11 Jul 2012 14:55:26 GMT",
"version": "v1"
}
] | 2012-07-19 | [
[
"Jojic",
"Nebojsa",
""
],
[
"Jojic",
"Vladimir",
""
],
[
"Heckerman",
"David",
""
]
] | Haplotypes, the global patterns of DNA sequence variation, have important implications for identifying complex traits. Recently, blocks of limited haplotype diversity have been discovered in human chromosomes, intensifying the research on modelling the block structure as well as the transitions or co-occurrence of the ... |
1606.01802 | Philip Pearce | Philip Pearce, Paul Brownbill, Jiri Janacek, Marie Jirkovska, Lucie
Kubinova, Igor L. Chernyavsky and Oliver E. Jensen | Image-Based Modeling of Blood Flow and Oxygen Transfer in Feto-Placental
Capillaries | Final version of manuscript | PLoS ONE 11(10):e0165369 (2016) | 10.1371/journal.pone.0165369 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During pregnancy, oxygen diffuses from maternal to fetal blood through
villous trees in the placenta. In this paper, we simulate blood flow and oxygen
transfer in feto-placental capillaries by converting three-dimensional
representations of villous and capillary surfaces, reconstructed from confocal
laser scanning mi... | [
{
"created": "Mon, 6 Jun 2016 16:00:54 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Jun 2016 08:47:23 GMT",
"version": "v2"
},
{
"created": "Tue, 9 Aug 2016 16:49:33 GMT",
"version": "v3"
},
{
"created": "Thu, 27 Oct 2016 18:15:33 GMT",
"version": "v4"
}
] | 2016-10-28 | [
[
"Pearce",
"Philip",
""
],
[
"Brownbill",
"Paul",
""
],
[
"Janacek",
"Jiri",
""
],
[
"Jirkovska",
"Marie",
""
],
[
"Kubinova",
"Lucie",
""
],
[
"Chernyavsky",
"Igor L.",
""
],
[
"Jensen",
"Oliver E.",
""
]... | During pregnancy, oxygen diffuses from maternal to fetal blood through villous trees in the placenta. In this paper, we simulate blood flow and oxygen transfer in feto-placental capillaries by converting three-dimensional representations of villous and capillary surfaces, reconstructed from confocal laser scanning micr... |
2404.16866 | Chaohao Yuan | Chaohao Yuan, Songyou Li, Geyan Ye, Yikun Zhang, Long-Kai Huang,
Wenbing Huang, Wei Liu, Jianhua Yao, Yu Rong | Functional Protein Design with Local Domain Alignment | null | null | null | null | q-bio.QM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The core challenge of de novo protein design lies in creating proteins with
specific functions or properties, guided by certain conditions. Current models
explore to generate protein using structural and evolutionary guidance, which
only provide indirect conditions concerning functions and properties. However,
textua... | [
{
"created": "Thu, 18 Apr 2024 09:37:54 GMT",
"version": "v1"
},
{
"created": "Mon, 27 May 2024 07:23:26 GMT",
"version": "v2"
}
] | 2024-05-28 | [
[
"Yuan",
"Chaohao",
""
],
[
"Li",
"Songyou",
""
],
[
"Ye",
"Geyan",
""
],
[
"Zhang",
"Yikun",
""
],
[
"Huang",
"Long-Kai",
""
],
[
"Huang",
"Wenbing",
""
],
[
"Liu",
"Wei",
""
],
[
"Yao",
"Jianhu... | The core challenge of de novo protein design lies in creating proteins with specific functions or properties, guided by certain conditions. Current models explore to generate protein using structural and evolutionary guidance, which only provide indirect conditions concerning functions and properties. However, textual ... |
q-bio/0610018 | Michael Deem | Guanyu Wang and Michael W. Deem | A Physical Theory of the Competition that Allows HIV to Escape from the
Immune System | 5 pages, 2 figures, to appear in Phys. Rev. Lett | null | 10.1103/PhysRevLett.97.188106 | null | q-bio.PE | null | Competition within the immune system may degrade immune control of viral
infections. We formalize the evolution that occurs in both HIV-1 and the immune
system quasispecies. Inclusion of competition in the immune system leads to a
novel balance between the immune response and HIV-1, in which the eventual
outcome is H... | [
{
"created": "Sun, 8 Oct 2006 06:14:41 GMT",
"version": "v1"
},
{
"created": "Mon, 16 Oct 2006 15:59:04 GMT",
"version": "v2"
}
] | 2009-11-13 | [
[
"Wang",
"Guanyu",
""
],
[
"Deem",
"Michael W.",
""
]
] | Competition within the immune system may degrade immune control of viral infections. We formalize the evolution that occurs in both HIV-1 and the immune system quasispecies. Inclusion of competition in the immune system leads to a novel balance between the immune response and HIV-1, in which the eventual outcome is HIV... |
1310.5017 | Lu\'is F. Seoane MSc | Lu\'is F. Seoane and Ricard V. Sol\'e | Synthetic biocomputation design using supervised gene regulatory
networks | 13 pages, 5 figures | null | null | null | q-bio.NC q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The potential of synthetic biology techniques for designing complex cellular
circuits able to solve complicated computations opens a whole domain of
exploration, beyond experiments and theory. Such cellular circuits could be
used to carry out hard tasks involving decision-making, storage of information,
or signal pro... | [
{
"created": "Fri, 18 Oct 2013 13:42:34 GMT",
"version": "v1"
}
] | 2013-10-21 | [
[
"Seoane",
"Luís F.",
""
],
[
"Solé",
"Ricard V.",
""
]
] | The potential of synthetic biology techniques for designing complex cellular circuits able to solve complicated computations opens a whole domain of exploration, beyond experiments and theory. Such cellular circuits could be used to carry out hard tasks involving decision-making, storage of information, or signal proce... |
2408.01425 | Tajudeen Yahaya Dr. | CD Obadiah, TO Yahaya, AA Aliero, M Abdulkareem | Comparative Evaluation of the Proximate and Cytogenotoxicity of Ash and
Rice Chips Used as Mango Fruit Artificial Ripening Agents in Birnin Kebbi,
Nigeria | Accept | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | The high demand for mango (Mangifera indica L.) fruits has led sellers to
employ ripening agents. However, concerns are growing regarding the potential
toxicities of induced ripening, emphasizing the need for scientific
investigation. Samples of artificially and naturally ripened mangoes were
analyzed for proximate c... | [
{
"created": "Sat, 29 Jun 2024 12:06:44 GMT",
"version": "v1"
}
] | 2024-08-06 | [
[
"Obadiah",
"CD",
""
],
[
"Yahaya",
"TO",
""
],
[
"Aliero",
"AA",
""
],
[
"Abdulkareem",
"M",
""
]
] | The high demand for mango (Mangifera indica L.) fruits has led sellers to employ ripening agents. However, concerns are growing regarding the potential toxicities of induced ripening, emphasizing the need for scientific investigation. Samples of artificially and naturally ripened mangoes were analyzed for proximate com... |
q-bio/0609049 | Haret Rosu | P. Escalante-Minakata, V. Ibarra-Junquera, H.C. Rosu, A. De
Leon-Rodriguez, R. Gonzalez-Garcia | An algorithm for real-time estimation of Mezcal fermentation parameters
based on redox potential measurements | 13 pp, 5 figs, misprints corrected | null | null | null | q-bio.QM | null | We present an algorithm for the continuous monitoring of the biomass and
ethanol concentrations and moreover the kinetic rate in the Mezcal fermentation
process. This algorithm performs its task having only available the on-line
measurements of the redox potential. The procedure includes an artificial
neural network ... | [
{
"created": "Thu, 28 Sep 2006 07:24:28 GMT",
"version": "v1"
},
{
"created": "Wed, 16 Jan 2008 23:10:04 GMT",
"version": "v2"
}
] | 2008-01-17 | [
[
"Escalante-Minakata",
"P.",
""
],
[
"Ibarra-Junquera",
"V.",
""
],
[
"Rosu",
"H. C.",
""
],
[
"De Leon-Rodriguez",
"A.",
""
],
[
"Gonzalez-Garcia",
"R.",
""
]
] | We present an algorithm for the continuous monitoring of the biomass and ethanol concentrations and moreover the kinetic rate in the Mezcal fermentation process. This algorithm performs its task having only available the on-line measurements of the redox potential. The procedure includes an artificial neural network (A... |
1803.02905 | Ahmad Maqboul | Ahmad Maqboul and Bakheet Elsadek | A Novel Model of Cancer-Induced Peripheral Neuropathy and the Role of
TRPA1 in Pain Transduction | 12 pages | Pain Research and Management, Volume 2017, Article ID 3517207 | 10.1155/2017/3517207 | null | q-bio.TO q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Background. Models of cancer-induced neuropathy are designed by injecting
cancer cells near the peripheral nerves. The interference of tissue-resident
immune cells does not allow a direct contact with nerve fibres which affects
the tumor microenvironment and the invasion process. Methods. Anaplastic
tumor-1 (AT-1) ce... | [
{
"created": "Wed, 7 Mar 2018 22:43:41 GMT",
"version": "v1"
}
] | 2018-03-09 | [
[
"Maqboul",
"Ahmad",
""
],
[
"Elsadek",
"Bakheet",
""
]
] | Background. Models of cancer-induced neuropathy are designed by injecting cancer cells near the peripheral nerves. The interference of tissue-resident immune cells does not allow a direct contact with nerve fibres which affects the tumor microenvironment and the invasion process. Methods. Anaplastic tumor-1 (AT-1) cell... |
0905.0994 | Roberto Amato | Roberto Amato, Michele Pinelli, Daniel D'Andrea, Gennaro Miele, Mario
Nicodemi, Giancarlo Raiconi, Sergio Cocozza | A novel approach to simulate gene-environment interactions in complex
diseases | null | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Complex diseases are multifactorial traits caused by both genetic and
environmental factors. They represent the most part of human diseases and
include those with largest prevalence and mortality (cancer, heart disease,
obesity, etc.). Despite of a large amount of information that have been
collected about both genet... | [
{
"created": "Thu, 7 May 2009 10:51:42 GMT",
"version": "v1"
}
] | 2009-05-08 | [
[
"Amato",
"Roberto",
""
],
[
"Pinelli",
"Michele",
""
],
[
"D'Andrea",
"Daniel",
""
],
[
"Miele",
"Gennaro",
""
],
[
"Nicodemi",
"Mario",
""
],
[
"Raiconi",
"Giancarlo",
""
],
[
"Cocozza",
"Sergio",
""
]
] | Complex diseases are multifactorial traits caused by both genetic and environmental factors. They represent the most part of human diseases and include those with largest prevalence and mortality (cancer, heart disease, obesity, etc.). Despite of a large amount of information that have been collected about both genetic... |
1001.5420 | Dhagash Mehta | William Hanan, Dhagash Mehta, Guillaume Moroz, Sepanda Pouryahya | Stability and Bifurcation Analysis of Coupled Fitzhugh-Nagumo
Oscillators | "Extended abstract" published in the Joint Conference of ASCM2009 and
MACIS2009, Japan, 2009 | null | null | null | q-bio.NC cs.SC nlin.CD q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neurons are the central biological objects in understanding how the brain
works. The famous Hodgkin-Huxley model, which describes how action potentials
of a neuron are initiated and propagated, consists of four coupled nonlinear
differential equations. Because these equations are difficult to deal with,
there also ex... | [
{
"created": "Fri, 29 Jan 2010 15:25:26 GMT",
"version": "v1"
}
] | 2010-02-01 | [
[
"Hanan",
"William",
""
],
[
"Mehta",
"Dhagash",
""
],
[
"Moroz",
"Guillaume",
""
],
[
"Pouryahya",
"Sepanda",
""
]
] | Neurons are the central biological objects in understanding how the brain works. The famous Hodgkin-Huxley model, which describes how action potentials of a neuron are initiated and propagated, consists of four coupled nonlinear differential equations. Because these equations are difficult to deal with, there also exis... |
1806.10656 | Monique Tirion | Hyuntae Na, Daniel ben-Avraham, Monique M. Tirion | Slow Normal Modes of Proteins are Accurately Reproduced across Different
Platforms | 20 pages plus 7 figures/tables (version to conform with referees
remarks) | null | 10.1088/1478-3975/aae333 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Protein Data Bank (PDB) contains the atomic structures of over 105
biomolecules with better than 2.8A resolution. The listing of the identities
and coordinates of the atoms comprising each macromolecule permits an analysis
of the slow-time vibrational response of these large systems to minor
perturbations. 3D vid... | [
{
"created": "Wed, 27 Jun 2018 19:41:54 GMT",
"version": "v1"
},
{
"created": "Tue, 4 Sep 2018 19:35:09 GMT",
"version": "v2"
}
] | 2018-12-05 | [
[
"Na",
"Hyuntae",
""
],
[
"ben-Avraham",
"Daniel",
""
],
[
"Tirion",
"Monique M.",
""
]
] | The Protein Data Bank (PDB) contains the atomic structures of over 105 biomolecules with better than 2.8A resolution. The listing of the identities and coordinates of the atoms comprising each macromolecule permits an analysis of the slow-time vibrational response of these large systems to minor perturbations. 3D video... |
1605.09019 | Yi-Hsuan Lin | Yi-Hsuan Lin, Julie D. Forman-Kay, and Hue Sun Chan | Sequence-specific polyampholyte phase separation in membraneless
organelles | 5 pages, 3 figures; additional results; accepted for publication in
PRL | Phys. Rev. Lett. 117, 178101 (2016) | 10.1103/PhysRevLett.117.178101 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Liquid-liquid phase separation of charge/aromatic-enriched intrinsically
disordered proteins (IDPs) is critical in the biological function of
membraneless organelles. Much of the physics of this recent discovery remains
to be elucidated. Here we present a theory in the random phase approximation to
account for electr... | [
{
"created": "Sun, 29 May 2016 16:02:03 GMT",
"version": "v1"
},
{
"created": "Wed, 21 Sep 2016 19:30:41 GMT",
"version": "v2"
}
] | 2016-10-18 | [
[
"Lin",
"Yi-Hsuan",
""
],
[
"Forman-Kay",
"Julie D.",
""
],
[
"Chan",
"Hue Sun",
""
]
] | Liquid-liquid phase separation of charge/aromatic-enriched intrinsically disordered proteins (IDPs) is critical in the biological function of membraneless organelles. Much of the physics of this recent discovery remains to be elucidated. Here we present a theory in the random phase approximation to account for electros... |
1603.06142 | Ralph Brinks | Ralph Brinks | How to assess case-finding in chronic diseases: Comparison of different
indices | 18 pages, 9 figures | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, we have proposed a new illness-death model that comprises a state
of undiagnosed chronic disease preceding the diagnosed disease. Based on this
model, the question arises how case-finding can be assessed in the presence of
mortality from all these states. We simulate two scenarios of different
performance o... | [
{
"created": "Sat, 19 Mar 2016 20:47:11 GMT",
"version": "v1"
}
] | 2016-03-22 | [
[
"Brinks",
"Ralph",
""
]
] | Recently, we have proposed a new illness-death model that comprises a state of undiagnosed chronic disease preceding the diagnosed disease. Based on this model, the question arises how case-finding can be assessed in the presence of mortality from all these states. We simulate two scenarios of different performance of ... |
2407.20711 | Francesco Sannino | Bruno Buonomo, Alessandra D'Alise, Rossella Della Marca, Francesco
Sannino | Information index augmented eRG to model vaccination behaviour: A case
study of COVID-19 in the US | 19 pages, 4 figures | null | null | null | q-bio.PE math.DS physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | Recent pandemics triggered the development of a number of mathematical models
and computational tools apt at curbing the socio-economic impact of these and
future pandemics. The need to acquire solid estimates from the data led to the
introduction of effective approaches such as the \emph{epidemiological
Renormalizat... | [
{
"created": "Tue, 30 Jul 2024 10:11:45 GMT",
"version": "v1"
}
] | 2024-07-31 | [
[
"Buonomo",
"Bruno",
""
],
[
"D'Alise",
"Alessandra",
""
],
[
"Della Marca",
"Rossella",
""
],
[
"Sannino",
"Francesco",
""
]
] | Recent pandemics triggered the development of a number of mathematical models and computational tools apt at curbing the socio-economic impact of these and future pandemics. The need to acquire solid estimates from the data led to the introduction of effective approaches such as the \emph{epidemiological Renormalizatio... |
1510.05631 | Yun S. Song | Jeffrey P. Spence, John A. Kamm, Yun S. Song | The site frequency spectrum for general coalescents | 20 pages, 4 figure | Genetics, Vol. 202 No. 4 (2016) 1549-1561 | 10.1534/genetics.115.184101 | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | General genealogical processes such as $\Lambda$- and $\Xi$-coalescents,
which respectively model multiple and simultaneous mergers, have important
applications in studying marine species, strong positive selection, recurrent
selective sweeps, strong bottlenecks, large sample sizes, and so on. Recently,
there has bee... | [
{
"created": "Mon, 19 Oct 2015 19:35:38 GMT",
"version": "v1"
},
{
"created": "Thu, 11 Feb 2016 23:43:46 GMT",
"version": "v2"
}
] | 2016-05-10 | [
[
"Spence",
"Jeffrey P.",
""
],
[
"Kamm",
"John A.",
""
],
[
"Song",
"Yun S.",
""
]
] | General genealogical processes such as $\Lambda$- and $\Xi$-coalescents, which respectively model multiple and simultaneous mergers, have important applications in studying marine species, strong positive selection, recurrent selective sweeps, strong bottlenecks, large sample sizes, and so on. Recently, there has been ... |
2212.05880 | Claudia Solis-Lemus | Reed Nelson, Rosa Aghdam, Claudia Solis-Lemus | MiNAA: Microbiome Network Alignment Algorithm | null | null | null | null | q-bio.MN q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Our Microbiome Network Alignment Algorithm (MiNAA) aligns two microbial
networks using a combination of the GRAph ALigner (GRAAL) algorithm and the
Hungarian algorithm. Network alignment algorithms find pairs of nodes (one node
from the first network and the other node from the second network) that have
the highest s... | [
{
"created": "Mon, 12 Dec 2022 13:37:21 GMT",
"version": "v1"
}
] | 2022-12-13 | [
[
"Nelson",
"Reed",
""
],
[
"Aghdam",
"Rosa",
""
],
[
"Solis-Lemus",
"Claudia",
""
]
] | Our Microbiome Network Alignment Algorithm (MiNAA) aligns two microbial networks using a combination of the GRAph ALigner (GRAAL) algorithm and the Hungarian algorithm. Network alignment algorithms find pairs of nodes (one node from the first network and the other node from the second network) that have the highest sim... |
q-bio/0412029 | Claus O. Wilke | Robert Forster (Caltech) and Claus O. Wilke (UT Austin, Caltech) | Tradeoff between short-term and long-term adaptation in a changing
environment | 9 pages, 3 figures, PRE in press | null | 10.1103/PhysRevE.72.041922 | null | q-bio.PE | null | We investigate the competition dynamics of two microbial or viral strains
that live in an environment that switches periodically between two states. One
of the strains is adapted to the long-term environment, but pays a short-term
cost, while the other is adapted to the short-term environment and pays a cost
in the l... | [
{
"created": "Thu, 16 Dec 2004 01:07:23 GMT",
"version": "v1"
},
{
"created": "Sat, 3 Sep 2005 19:32:19 GMT",
"version": "v2"
}
] | 2013-05-29 | [
[
"Forster",
"Robert",
"",
"Caltech"
],
[
"Wilke",
"Claus O.",
"",
"UT Austin, Caltech"
]
] | We investigate the competition dynamics of two microbial or viral strains that live in an environment that switches periodically between two states. One of the strains is adapted to the long-term environment, but pays a short-term cost, while the other is adapted to the short-term environment and pays a cost in the lon... |
2007.15476 | Roman Reshetnikov | Sergey P. Morozov, Roman V. Reshetnikov, Victor A. Gombolevskiy,
Natalia V. Ledikhova, Ivan A. Blokhin, Vladislav G. Kljashtorny, Olesya A.
Mokienko, Anton V. Vladzymyrskyy | Diagnostic Accuracy of Computed Tomography for Identifying
Hospitalization in Patients with Suspected COVID-19 | 10 pages, 2 figures, 3 tables | null | null | null | q-bio.QM physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The controversy of computed tomography (CT) use in COVID-19 screening is
associated with ambiguous characteristics of chest CT as a diagnostic test. The
reported values of CT sensitivity and specificity calculated using RT-PCR as a
reference standard vary widely. The objective of this study was to reevaluate
the diag... | [
{
"created": "Wed, 29 Jul 2020 13:02:55 GMT",
"version": "v1"
},
{
"created": "Fri, 31 Jul 2020 10:43:48 GMT",
"version": "v2"
}
] | 2020-08-03 | [
[
"Morozov",
"Sergey P.",
""
],
[
"Reshetnikov",
"Roman V.",
""
],
[
"Gombolevskiy",
"Victor A.",
""
],
[
"Ledikhova",
"Natalia V.",
""
],
[
"Blokhin",
"Ivan A.",
""
],
[
"Kljashtorny",
"Vladislav G.",
""
],
[
"Mokie... | The controversy of computed tomography (CT) use in COVID-19 screening is associated with ambiguous characteristics of chest CT as a diagnostic test. The reported values of CT sensitivity and specificity calculated using RT-PCR as a reference standard vary widely. The objective of this study was to reevaluate the diagno... |
2104.01489 | Daniel Yamins | Rosa Cao and Daniel Yamins | Explanatory models in neuroscience: Part 2 -- constraint-based
intelligibility | null | null | null | null | q-bio.NC cs.NE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Computational modeling plays an increasingly important role in neuroscience,
highlighting the philosophical question of how computational models explain. In
the context of neural network models for neuroscience, concerns have been
raised about model intelligibility, and how they relate (if at all) to what is
found in... | [
{
"created": "Sat, 3 Apr 2021 22:14:01 GMT",
"version": "v1"
},
{
"created": "Wed, 14 Apr 2021 16:59:48 GMT",
"version": "v2"
}
] | 2021-04-15 | [
[
"Cao",
"Rosa",
""
],
[
"Yamins",
"Daniel",
""
]
] | Computational modeling plays an increasingly important role in neuroscience, highlighting the philosophical question of how computational models explain. In the context of neural network models for neuroscience, concerns have been raised about model intelligibility, and how they relate (if at all) to what is found in t... |
1705.07998 | Koray Ciftci | Koray \c{C}ift\c{c}i | Synaptic Noise Facilitates the Emergence of Self-Organized Criticality
in the Caenorhabditis elegans Neuronal Network | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Avalanches with power-law distributed size parameters have been observed in
neuronal networks. This observation might be a manifestation of the
self-organized criticality (SOC). Yet, the physiological mechanicsm of this
behavior is currently unknown. Describing synaptic noise as transmission
failures mainly originati... | [
{
"created": "Mon, 22 May 2017 20:55:43 GMT",
"version": "v1"
}
] | 2017-05-24 | [
[
"Çiftçi",
"Koray",
""
]
] | Avalanches with power-law distributed size parameters have been observed in neuronal networks. This observation might be a manifestation of the self-organized criticality (SOC). Yet, the physiological mechanicsm of this behavior is currently unknown. Describing synaptic noise as transmission failures mainly originating... |
2305.19544 | Liu Hong | Dongyan Zhang, Wuyue Yang, Wanqi Wen, Liangrong Peng, Changjingn
Zhuge, Liu Hong | A data-driven analysis on the mediation effect of compartment models
between control measures and COVID-19 epidemics | 21 pages, 6 figures, 1 tables | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We make a retrospective review on various control measures taken by 127
countries/territories during the first wave of COVID-19 pandemic until July 7,
2020, and evaluate their impacts on the epidemic dynamics quantitatively. The
SEIR-QD model, as a representative for general compartment models, is used to
fit the epi... | [
{
"created": "Wed, 31 May 2023 04:18:57 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Sep 2023 08:44:50 GMT",
"version": "v2"
}
] | 2023-09-25 | [
[
"Zhang",
"Dongyan",
""
],
[
"Yang",
"Wuyue",
""
],
[
"Wen",
"Wanqi",
""
],
[
"Peng",
"Liangrong",
""
],
[
"Zhuge",
"Changjingn",
""
],
[
"Hong",
"Liu",
""
]
] | We make a retrospective review on various control measures taken by 127 countries/territories during the first wave of COVID-19 pandemic until July 7, 2020, and evaluate their impacts on the epidemic dynamics quantitatively. The SEIR-QD model, as a representative for general compartment models, is used to fit the epide... |
2109.04903 | Marcelo Nocelle De Almeida Doutor | Marcelo N. Almeida, Rodolfo Alves de Oliveira, Luiz Olmes, Gustavo S.
Semaan, Daniel de Oliveira, Lucio Santos, Marcos Bedo | HELIX: Data-driven characterization of Brazilian land snails | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Decision-support systems benefit from hidden patterns extracted from digital
information. In the specific domain of gastropod characterization,
morphometrical measurements support biologists in the identification of land
snail specimens. Although snails can be easily identified by their excretory
and reproductive sys... | [
{
"created": "Fri, 10 Sep 2021 14:23:52 GMT",
"version": "v1"
},
{
"created": "Tue, 14 Sep 2021 13:38:17 GMT",
"version": "v2"
}
] | 2021-09-15 | [
[
"Almeida",
"Marcelo N.",
""
],
[
"de Oliveira",
"Rodolfo Alves",
""
],
[
"Olmes",
"Luiz",
""
],
[
"Semaan",
"Gustavo S.",
""
],
[
"de Oliveira",
"Daniel",
""
],
[
"Santos",
"Lucio",
""
],
[
"Bedo",
"Marcos",
... | Decision-support systems benefit from hidden patterns extracted from digital information. In the specific domain of gastropod characterization, morphometrical measurements support biologists in the identification of land snail specimens. Although snails can be easily identified by their excretory and reproductive syste... |
q-bio/0312008 | Bindu Govindan | Bindu S. Govindan and William B. Spillman, Jr. (Applied Biosciences
Center, Virginia Tech) | Stabilization of microtubules due to microtubule-associated proteins: A
simple model | 23 pages, RevTeX, 7 figures included, submitted to Phys. Rev. E | null | null | null | q-bio.SC q-bio.CB | null | A theoretical model of stabilization of a microtubule assembly due to
microtubule-associated-proteins(MAP) is presented. MAPs are assumed to bind to
the microtubule filaments, thus preventing their disintegration following
hydrolysis and enhancing further polymerization. Using mean-field rate
equations and explicit n... | [
{
"created": "Fri, 5 Dec 2003 21:52:26 GMT",
"version": "v1"
}
] | 2012-08-27 | [
[
"Govindan",
"Bindu S.",
"",
"Applied Biosciences\n Center, Virginia Tech"
],
[
"Spillman,",
"William B.",
"Jr.",
"Applied Biosciences\n Center, Virginia Tech"
]
] | A theoretical model of stabilization of a microtubule assembly due to microtubule-associated-proteins(MAP) is presented. MAPs are assumed to bind to the microtubule filaments, thus preventing their disintegration following hydrolysis and enhancing further polymerization. Using mean-field rate equations and explicit num... |
1203.5932 | Jost Neigenfind | Jost Neigenfind and Sergio Grimbs and Zoran Nikoloski | On the relation between reactions and complexes of (bio)chemical
reaction networks | null | null | null | null | q-bio.MN math.CA math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Robustness of biochemical systems has become one of the central questions in
systems biology although it is notoriously difficult to formally capture its
multifaceted nature. Maintenance of normal system function depends not only on
the stoichiometry of the underlying interrelated components, but also on a
multitude ... | [
{
"created": "Tue, 27 Mar 2012 11:06:05 GMT",
"version": "v1"
}
] | 2012-03-28 | [
[
"Neigenfind",
"Jost",
""
],
[
"Grimbs",
"Sergio",
""
],
[
"Nikoloski",
"Zoran",
""
]
] | Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the stoichiometry of the underlying interrelated components, but also on a multitude of... |
2003.08150 | Indrajit Ghosh | Sk Shahid Nadim, Indrajit Ghosh, Joydev Chattopadhyay | Short-term predictions and prevention strategies for COVID-19: A model
based study | NA | null | 10.1016/j.amc.2021.126251 | null | q-bio.PE math.DS | http://creativecommons.org/licenses/by/4.0/ | An outbreak of respiratory disease caused by a novel coronavirus is ongoing
from December 2019. As of July 22, 2020, it has caused an epidemic outbreak
with more than 15 million confirmed infections and above 6 hundred thousand
reported deaths worldwide. During this period of an epidemic when
human-to-human transmiss... | [
{
"created": "Wed, 18 Mar 2020 10:59:32 GMT",
"version": "v1"
},
{
"created": "Thu, 2 Jul 2020 17:04:16 GMT",
"version": "v2"
},
{
"created": "Wed, 22 Jul 2020 10:29:58 GMT",
"version": "v3"
}
] | 2021-05-21 | [
[
"Nadim",
"Sk Shahid",
""
],
[
"Ghosh",
"Indrajit",
""
],
[
"Chattopadhyay",
"Joydev",
""
]
] | An outbreak of respiratory disease caused by a novel coronavirus is ongoing from December 2019. As of July 22, 2020, it has caused an epidemic outbreak with more than 15 million confirmed infections and above 6 hundred thousand reported deaths worldwide. During this period of an epidemic when human-to-human transmissio... |
1803.09018 | Abraham Nunes | Abraham Nunes and Alexander Rudiuk | The Importance of Constraint Smoothness for Parameter Estimation in
Computational Cognitive Modeling | null | null | null | null | q-bio.QM cs.LG q-bio.NC stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Psychiatric neuroscience is increasingly aware of the need to define
psychopathology in terms of abnormal neural computation. The central tool in
this endeavour is the fitting of computational models to behavioural data. The
most prominent example of this procedure is fitting reinforcement learning (RL)
models to dec... | [
{
"created": "Sat, 24 Mar 2018 00:25:20 GMT",
"version": "v1"
}
] | 2018-03-28 | [
[
"Nunes",
"Abraham",
""
],
[
"Rudiuk",
"Alexander",
""
]
] | Psychiatric neuroscience is increasingly aware of the need to define psychopathology in terms of abnormal neural computation. The central tool in this endeavour is the fitting of computational models to behavioural data. The most prominent example of this procedure is fitting reinforcement learning (RL) models to decis... |
0811.4149 | Aleksandra Walczak | Aleksandra M. Walczak, Andrew Mugler and Chris H. Wiggins | A stochastic spectral analysis of transcriptional regulatory cascades | null | PNAS 106, 6529-6534 (2009) | 10.1073/pnas.0811999106 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The past decade has seen great advances in our understanding of the role of
noise in gene regulation and the physical limits to signaling in biological
networks. Here we introduce the spectral method for computation of the joint
probability distribution over all species in a biological network. The spectral
method ex... | [
{
"created": "Tue, 25 Nov 2008 18:28:23 GMT",
"version": "v1"
}
] | 2009-09-19 | [
[
"Walczak",
"Aleksandra M.",
""
],
[
"Mugler",
"Andrew",
""
],
[
"Wiggins",
"Chris H.",
""
]
] | The past decade has seen great advances in our understanding of the role of noise in gene regulation and the physical limits to signaling in biological networks. Here we introduce the spectral method for computation of the joint probability distribution over all species in a biological network. The spectral method expl... |
2010.14898 | Francesco Gargano | F. Bagarello, F. Gargano, F. Roccati | Modeling epidemics through ladder operators | null | Chaos, Solitons & Fractals, Volume 140, November 2020, 110193 | 10.1016/j.chaos.2020.110193 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a simple model of spreading of some infection in an originally
healthy population which is different from other models existing in the
literature. In particular, we use an operator technique which allows us to
describe in a natural way the possible interactions between healthy and
un-healthy populations, a... | [
{
"created": "Wed, 28 Oct 2020 11:35:20 GMT",
"version": "v1"
}
] | 2020-10-29 | [
[
"Bagarello",
"F.",
""
],
[
"Gargano",
"F.",
""
],
[
"Roccati",
"F.",
""
]
] | We propose a simple model of spreading of some infection in an originally healthy population which is different from other models existing in the literature. In particular, we use an operator technique which allows us to describe in a natural way the possible interactions between healthy and un-healthy populations, and... |
1907.03532 | Sarwar Khan | Sarwar Khan and Faisal Ghaffar, Imad Ali, Qazi Mazhar | Classification of Macromolecule Type Based on Sequences of Amino Acids
Using Deep Learning | under review | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The classification of amino acids and their sequence analysis plays a vital
role in life sciences and is a challenging task. This article uses and compares
state-of-the-art deep learning models like convolution neural networks (CNN),
long short-term memory (LSTM), and gated recurrent units (GRU) to solve
macromolecul... | [
{
"created": "Mon, 1 Jul 2019 03:49:01 GMT",
"version": "v1"
},
{
"created": "Thu, 21 Jul 2022 09:57:31 GMT",
"version": "v2"
},
{
"created": "Sat, 23 Jul 2022 05:34:24 GMT",
"version": "v3"
}
] | 2022-07-26 | [
[
"Khan",
"Sarwar",
""
],
[
"Ghaffar",
"Faisal",
""
],
[
"Ali",
"Imad",
""
],
[
"Mazhar",
"Qazi",
""
]
] | The classification of amino acids and their sequence analysis plays a vital role in life sciences and is a challenging task. This article uses and compares state-of-the-art deep learning models like convolution neural networks (CNN), long short-term memory (LSTM), and gated recurrent units (GRU) to solve macromolecule ... |
1511.04786 | Mark Flegg | Mark B. Flegg | Smoluchowski reaction kinetics for reactions of any order | null | null | null | null | q-bio.QM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In 1917, Marian von Smoluchowski presented a simple mathematical description
of diffusion-controlled reactions on the scale of individual molecules. His
model postulated that a reaction would occur when two reactants were
sufficiently close and, more specifically, presented a succinct relationship
between the relativ... | [
{
"created": "Mon, 16 Nov 2015 00:11:21 GMT",
"version": "v1"
}
] | 2015-11-17 | [
[
"Flegg",
"Mark B.",
""
]
] | In 1917, Marian von Smoluchowski presented a simple mathematical description of diffusion-controlled reactions on the scale of individual molecules. His model postulated that a reaction would occur when two reactants were sufficiently close and, more specifically, presented a succinct relationship between the relative ... |
1609.00620 | Marc D Ryser | Marc D. Ryser and Kevin A. Murgas | Bone Remodeling as a Spatial Evolutionary Game | 29 pages, 6 figures, 1 table | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bone remodeling is a complex process involving cell-cell interactions,
biochemical signaling and mechanical stimuli. Early models of the biological
aspects of remodeling were non-spatial and focused on the local dynamics at a
fixed location in the bone. Several spatial extensions of these models have
been proposed, b... | [
{
"created": "Fri, 2 Sep 2016 14:35:51 GMT",
"version": "v1"
}
] | 2016-09-05 | [
[
"Ryser",
"Marc D.",
""
],
[
"Murgas",
"Kevin A.",
""
]
] | Bone remodeling is a complex process involving cell-cell interactions, biochemical signaling and mechanical stimuli. Early models of the biological aspects of remodeling were non-spatial and focused on the local dynamics at a fixed location in the bone. Several spatial extensions of these models have been proposed, but... |
2107.05569 | Emma Leschiera | Emma Leschiera, Tommaso Lorenzi, Shensi Shen, Luis Almeida and Chloe
Audebert | A mathematical model to study the impact of intra-tumour heterogeneity
on anti-tumour CD8+ T cell immune response | null | null | null | null | q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | Intra-tumour heterogeneity (ITH) has a strong impact on the efficacy of the
immune response against solid tumours. The number of sub-populations of cancer
cells expressing different antigens and the percentage of immunogenic cells
(i.e. tumour cells that are effectively targeted by immune cells) in a tumour
are both ... | [
{
"created": "Mon, 12 Jul 2021 16:51:43 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Dec 2021 09:13:23 GMT",
"version": "v2"
}
] | 2021-12-08 | [
[
"Leschiera",
"Emma",
""
],
[
"Lorenzi",
"Tommaso",
""
],
[
"Shen",
"Shensi",
""
],
[
"Almeida",
"Luis",
""
],
[
"Audebert",
"Chloe",
""
]
] | Intra-tumour heterogeneity (ITH) has a strong impact on the efficacy of the immune response against solid tumours. The number of sub-populations of cancer cells expressing different antigens and the percentage of immunogenic cells (i.e. tumour cells that are effectively targeted by immune cells) in a tumour are both ex... |
2203.17255 | Jared Reser | Jared Edward Reser | A Cognitive Architecture for Machine Consciousness and Artificial
Superintelligence: Thought Is Structured by the Iterative Updating of Working
Memory | null | null | null | null | q-bio.NC cs.CL cs.CV | http://creativecommons.org/licenses/by-nc-sa/4.0/ | This article provides an analytical framework for how to simulate human-like
thought processes within a computer. It describes how attention and memory
should be structured, updated, and utilized to search for associative additions
to the stream of thought. The focus is on replicating the dynamics of the
mammalian wo... | [
{
"created": "Tue, 29 Mar 2022 22:28:30 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Jul 2022 01:10:56 GMT",
"version": "v2"
},
{
"created": "Tue, 21 Feb 2023 20:46:38 GMT",
"version": "v3"
},
{
"created": "Fri, 10 Nov 2023 05:44:26 GMT",
"version": "v4"
},
{
"cr... | 2023-12-15 | [
[
"Reser",
"Jared Edward",
""
]
] | This article provides an analytical framework for how to simulate human-like thought processes within a computer. It describes how attention and memory should be structured, updated, and utilized to search for associative additions to the stream of thought. The focus is on replicating the dynamics of the mammalian work... |
1106.1612 | Stephen Ellner | Stephen P. Ellner and Sebastian J. Schreiber | Temporally variable dispersal and demography can accelerate the spread
of invading species | Final version accepted for publication in Theoretical Population
Biology, special issue "Developments in structured models: construction,
analysis and inference" | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze how temporal variability in local demography and dispersal combine
to affect the rate of spread of an invading species. Our model combines
state-structured local demography (specified by an integral or matrix
projection model) with general dispersal distributions that may depend on the
state of the individ... | [
{
"created": "Wed, 8 Jun 2011 18:08:34 GMT",
"version": "v1"
},
{
"created": "Fri, 6 Apr 2012 16:27:02 GMT",
"version": "v2"
}
] | 2012-04-09 | [
[
"Ellner",
"Stephen P.",
""
],
[
"Schreiber",
"Sebastian J.",
""
]
] | We analyze how temporal variability in local demography and dispersal combine to affect the rate of spread of an invading species. Our model combines state-structured local demography (specified by an integral or matrix projection model) with general dispersal distributions that may depend on the state of the individua... |
1203.0872 | Jing Kang Dr. | Jing Kang, Hugh P. C. Robinson, Jianfeng Feng | Diversity of Intrinsic Frequency Encoding Patterns in Rat Cortical
Neurons -Mechanisms and Possible Functions | 11 pages, 7 figures; PloS One 2010 | null | 10.1371/journal.pone.0009608 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Extracellular recordings of single neurons in primary and secondary
somatosensory cortices of monkeys in vivo have shown that their firing rate can
increase, decrease, or remain constant in different cells, as the external
stimulus frequency increases. We observed similar intrinsic firing patterns
(increasing, decrea... | [
{
"created": "Mon, 5 Mar 2012 11:45:39 GMT",
"version": "v1"
}
] | 2012-03-06 | [
[
"Kang",
"Jing",
""
],
[
"Robinson",
"Hugh P. C.",
""
],
[
"Feng",
"Jianfeng",
""
]
] | Extracellular recordings of single neurons in primary and secondary somatosensory cortices of monkeys in vivo have shown that their firing rate can increase, decrease, or remain constant in different cells, as the external stimulus frequency increases. We observed similar intrinsic firing patterns (increasing, decreasi... |
2004.09230 | Alexander Nesterov-Mueller Dr. | A. Nesterov-Mueller and R. Popov | On the origin of the standard genetic code as a fusion of prebiotic
single-base-pair codes | 6 pages | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The genesis of the stand genetic code is considered as a result of a fusion
of two AU- and GC-codes distributed in two dominant and two recessive domains.
The fusion of these codes is described with simple empirical rules. This formal
approach explains the number of the proteinogenic amino acids and the codon
assignm... | [
{
"created": "Mon, 20 Apr 2020 12:15:39 GMT",
"version": "v1"
}
] | 2020-04-21 | [
[
"Nesterov-Mueller",
"A.",
""
],
[
"Popov",
"R.",
""
]
] | The genesis of the stand genetic code is considered as a result of a fusion of two AU- and GC-codes distributed in two dominant and two recessive domains. The fusion of these codes is described with simple empirical rules. This formal approach explains the number of the proteinogenic amino acids and the codon assignmen... |
1106.5061 | Sharon Aviran | Sharon Aviran, Julius B. Lucks, and Lior Pachter | RNA structure characterization from chemical mapping experiments | 8 pages, 3 figures | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite great interest in solving RNA secondary structures due to their
impact on function, it remains an open problem to determine structure from
sequence. Among experimental approaches, a promising candidate is the "chemical
modification strategy", which involves application of chemicals to RNA that are
sensitive t... | [
{
"created": "Fri, 24 Jun 2011 20:29:06 GMT",
"version": "v1"
},
{
"created": "Wed, 29 Jun 2011 16:49:19 GMT",
"version": "v2"
}
] | 2011-06-30 | [
[
"Aviran",
"Sharon",
""
],
[
"Lucks",
"Julius B.",
""
],
[
"Pachter",
"Lior",
""
]
] | Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental approaches, a promising candidate is the "chemical modification strategy", which involves application of chemicals to RNA that are sensitive to ... |
1301.2610 | Marcus Kinsella | Shay Zakov, Marcus Kinsella, Vineet Bafna | Detecting Breakage Fusion Bridge cycles in tumor genomes -- an
algorithmic approach | null | null | 10.1073/pnas.1220977110 | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Breakage-Fusion-Bridge (BFB) is a mechanism of genomic instability
characterized by the joining and subsequent tearing apart of sister chromatids.
When this process is repeated during multiple rounds of cell division, it leads
to patterns of copy number increases of chromosomal segments as well as
fold-back inversion... | [
{
"created": "Fri, 11 Jan 2013 21:28:33 GMT",
"version": "v1"
}
] | 2013-03-20 | [
[
"Zakov",
"Shay",
""
],
[
"Kinsella",
"Marcus",
""
],
[
"Bafna",
"Vineet",
""
]
] | Breakage-Fusion-Bridge (BFB) is a mechanism of genomic instability characterized by the joining and subsequent tearing apart of sister chromatids. When this process is repeated during multiple rounds of cell division, it leads to patterns of copy number increases of chromosomal segments as well as fold-back inversions ... |
1212.0413 | Rafael Najmanovich | Jean-Pierre Sehi Glouzon, Fran\c{c}ois Bolduc, Rafael Najmanovich,
Shengrui Wang, Jean-Pierre Perreault | Deep-sequencing of the Peach Latent Mosaic Viroid Reveals New Aspects of
Population Heterogeneity | Manuscript submitted to PLoS ONE October 3rd, 2012. Supplementary
data can be found at: http://dx.doi.org/10.6084/m9.figshare.100858 | PLoS ONE 9(1): e87297 | 10.1371/journal.pone.0087297 | null | q-bio.PE q-bio.BM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Viroids are small circular single-stranded infectious RNAs that are
characterized by a relatively high mutation level. Knowledge of their sequence
heterogeneity remains largely elusive, and, as yet, no strategy attempting to
address this question from a population dynamics point of view is in place. In
order to addre... | [
{
"created": "Mon, 3 Dec 2012 15:17:25 GMT",
"version": "v1"
}
] | 2014-02-04 | [
[
"Glouzon",
"Jean-Pierre Sehi",
""
],
[
"Bolduc",
"François",
""
],
[
"Najmanovich",
"Rafael",
""
],
[
"Wang",
"Shengrui",
""
],
[
"Perreault",
"Jean-Pierre",
""
]
] | Viroids are small circular single-stranded infectious RNAs that are characterized by a relatively high mutation level. Knowledge of their sequence heterogeneity remains largely elusive, and, as yet, no strategy attempting to address this question from a population dynamics point of view is in place. In order to address... |
2403.03230 | Xiaoliang Luo | Xiaoliang Luo, Akilles Rechardt, Guangzhi Sun, Kevin K. Nejad, Felipe
Y\'a\~nez, Bati Yilmaz, Kangjoo Lee, Alexandra O. Cohen, Valentina
Borghesani, Anton Pashkov, Daniele Marinazzo, Jonathan Nicholas, Alessandro
Salatiello, Ilia Sucholutsky, Pasquale Minervini, Sepehr Razavi, Roberta
Rocca, Elkhan Yusifov, Ter... | Large language models surpass human experts in predicting neuroscience
results | null | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | Scientific discoveries often hinge on synthesizing decades of research, a
task that potentially outstrips human information processing capacities. Large
language models (LLMs) offer a solution. LLMs trained on the vast scientific
literature could potentially integrate noisy yet interrelated findings to
forecast novel... | [
{
"created": "Mon, 4 Mar 2024 15:27:59 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Mar 2024 23:32:15 GMT",
"version": "v2"
},
{
"created": "Fri, 21 Jun 2024 17:35:46 GMT",
"version": "v3"
}
] | 2024-06-24 | [
[
"Luo",
"Xiaoliang",
""
],
[
"Rechardt",
"Akilles",
""
],
[
"Sun",
"Guangzhi",
""
],
[
"Nejad",
"Kevin K.",
""
],
[
"Yáñez",
"Felipe",
""
],
[
"Yilmaz",
"Bati",
""
],
[
"Lee",
"Kangjoo",
""
],
[
"Coh... | Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel r... |
1305.5319 | Bin He | Bin Z. He, Michael Z. Ludwig, Desiree A. Dickerson, Levi Barse,
Bharath Arun, Soo Young Park, Natalia A. Tamarina, Scott B. Selleck, Patricia
Wittkopp, Graeme I. Bell and Martin Kreitman | Effect of Genetic Variation in a Drosophila Model of Diabetes-Associated
Misfolded Human Proinsulin | null | Genetics 196 (2014) 557-567 | 10.1534/genetics.113.157800 | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The identification and validation of gene-gene interactions is a major
challenge in human studies. Here, we explore an approach for studying epistasis
in humans using a Drosophila melanogaster model of neonatal diabetes mellitus.
Expression of mutant preproinsulin, hINSC96Y, in the eye imaginal disc mimics
the human ... | [
{
"created": "Thu, 23 May 2013 05:54:09 GMT",
"version": "v1"
},
{
"created": "Mon, 27 May 2013 15:18:33 GMT",
"version": "v2"
}
] | 2014-04-01 | [
[
"He",
"Bin Z.",
""
],
[
"Ludwig",
"Michael Z.",
""
],
[
"Dickerson",
"Desiree A.",
""
],
[
"Barse",
"Levi",
""
],
[
"Arun",
"Bharath",
""
],
[
"Park",
"Soo Young",
""
],
[
"Tamarina",
"Natalia A.",
""
],
... | The identification and validation of gene-gene interactions is a major challenge in human studies. Here, we explore an approach for studying epistasis in humans using a Drosophila melanogaster model of neonatal diabetes mellitus. Expression of mutant preproinsulin, hINSC96Y, in the eye imaginal disc mimics the human di... |
2303.13984 | Alfred Achieng | Alfred O. Achieng, George B. Arhonditsis, Nicholas E. Mandrack,
Catherine M. Febria, Bernard Opaa, Tracey J. Coffey, Ken Irvine, Frank O.
Masese, Zeph M. Ajode, James E. Barasa, Kevin Obiero and Boaz Kaunda-Arara | Monitoring biodiversity loss in rapidly changing Afrotropical
ecosystems: An emerging imperative for governance and research | 12 pages, 2 figures and 1 Table and a supplementary table. Accepted
for publication in a special issue with Philosophical Transactions of the
Royal Society B 2023 | null | 10.1098/rstb.2022.0271 | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Africa is experiencing extensive biodiversity loss due to rapid changes in
the environment, where natural resources constitute the main instrument for
socioeconomic development and a mainstay source of livelihoods for an
increasing population. Lack of data and information deficiency on biodiversity,
but also budget c... | [
{
"created": "Fri, 24 Mar 2023 13:11:00 GMT",
"version": "v1"
}
] | 2023-06-01 | [
[
"Achieng",
"Alfred O.",
""
],
[
"Arhonditsis",
"George B.",
""
],
[
"Mandrack",
"Nicholas E.",
""
],
[
"Febria",
"Catherine M.",
""
],
[
"Opaa",
"Bernard",
""
],
[
"Coffey",
"Tracey J.",
""
],
[
"Irvine",
"Ken"... | Africa is experiencing extensive biodiversity loss due to rapid changes in the environment, where natural resources constitute the main instrument for socioeconomic development and a mainstay source of livelihoods for an increasing population. Lack of data and information deficiency on biodiversity, but also budget con... |
1303.7186 | Thouis Jones | Verena Kaynig, Amelio Vazquez-Reina, Seymour Knowles-Barley, Mike
Roberts, Thouis R. Jones, Narayanan Kasthuri, Eric Miller, Jeff Lichtman,
Hanspeter Pfister | Large-Scale Automatic Reconstruction of Neuronal Processes from Electron
Microscopy Images | null | null | null | null | q-bio.NC cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Automated sample preparation and electron microscopy enables acquisition of
very large image data sets. These technical advances are of special importance
to the field of neuroanatomy, as 3D reconstructions of neuronal processes at
the nm scale can provide new insight into the fine grained structure of the
brain. Seg... | [
{
"created": "Thu, 28 Mar 2013 17:20:20 GMT",
"version": "v1"
}
] | 2013-03-29 | [
[
"Kaynig",
"Verena",
""
],
[
"Vazquez-Reina",
"Amelio",
""
],
[
"Knowles-Barley",
"Seymour",
""
],
[
"Roberts",
"Mike",
""
],
[
"Jones",
"Thouis R.",
""
],
[
"Kasthuri",
"Narayanan",
""
],
[
"Miller",
"Eric",
... | Automated sample preparation and electron microscopy enables acquisition of very large image data sets. These technical advances are of special importance to the field of neuroanatomy, as 3D reconstructions of neuronal processes at the nm scale can provide new insight into the fine grained structure of the brain. Segme... |
1407.7392 | Paolo Moretti | Paula Villa Mart\'in, Paolo Moretti, Miguel A. Mu\~noz | Rounding of abrupt phase transitions in brain networks | 10 pages | null | 10.1088/1742-5468/2015/01/P01003 | null | q-bio.NC cond-mat.dis-nn nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The observation of critical-like behavior in cortical networks represents a
major step forward in elucidating how the brain manages information.
Understanding the origin and functionality of critical-like dynamics, as well
as their robustness, is a major challenge in contemporary neuroscience. Here,
we present an ext... | [
{
"created": "Mon, 28 Jul 2014 12:22:31 GMT",
"version": "v1"
}
] | 2015-06-22 | [
[
"Martín",
"Paula Villa",
""
],
[
"Moretti",
"Paolo",
""
],
[
"Muñoz",
"Miguel A.",
""
]
] | The observation of critical-like behavior in cortical networks represents a major step forward in elucidating how the brain manages information. Understanding the origin and functionality of critical-like dynamics, as well as their robustness, is a major challenge in contemporary neuroscience. Here, we present an exten... |
2201.03551 | Hyun Mo Yang | Hyun Mo Yang, Ariana Campos Yang and Silvia Martorano Raimundo | A model-based assessment of the cost-benefit balance and the plea
bargain in criminality -- A qualitative case study of the Covid-19 epidemic
shedding light on the "car wash operation" in Brazil | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | We developed a simple mathematical model to describe criminality and the
justice system composed of the police investigation and court trial. The model
assessed two features of organized crime -- the cost-benefit analysis done by
the crime-susceptible to commit a crime and the whistleblowing of the law
offenders. The... | [
{
"created": "Sun, 9 Jan 2022 18:50:16 GMT",
"version": "v1"
},
{
"created": "Sat, 22 Jan 2022 22:48:07 GMT",
"version": "v2"
}
] | 2022-01-25 | [
[
"Yang",
"Hyun Mo",
""
],
[
"Yang",
"Ariana Campos",
""
],
[
"Raimundo",
"Silvia Martorano",
""
]
] | We developed a simple mathematical model to describe criminality and the justice system composed of the police investigation and court trial. The model assessed two features of organized crime -- the cost-benefit analysis done by the crime-susceptible to commit a crime and the whistleblowing of the law offenders. The m... |
2108.05186 | Quynh Anh Le | Quynh-Anh Le, Rahena Akhter, Kimberly M. Coulton, Ngoc T.N Vo, Le T.Y
Duong, Hoang V. Nong, Albert Yaacoub, George Condous, Joerg Eberhard and
Ralph Nanan | Periodontitis and preeclampsia in pregnancy: A systematic review and
meta-analysis | 58 pages, 13 figures | null | null | null | q-bio.OT q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objectives: A conflicting body of evidence suggests localized periodontal
inflammation to spread systemically during pregnancy inducing adverse pregnancy
outcomes. This systematic review and meta-analysis aimed to specifically
evaluate the relationship between periodontitis and preeclampsia. Methods:
Electronic searc... | [
{
"created": "Mon, 9 Aug 2021 23:48:41 GMT",
"version": "v1"
}
] | 2021-08-12 | [
[
"Le",
"Quynh-Anh",
""
],
[
"Akhter",
"Rahena",
""
],
[
"Coulton",
"Kimberly M.",
""
],
[
"Vo",
"Ngoc T. N",
""
],
[
"Duong",
"Le T. Y",
""
],
[
"Nong",
"Hoang V.",
""
],
[
"Yaacoub",
"Albert",
""
],
[
... | Objectives: A conflicting body of evidence suggests localized periodontal inflammation to spread systemically during pregnancy inducing adverse pregnancy outcomes. This systematic review and meta-analysis aimed to specifically evaluate the relationship between periodontitis and preeclampsia. Methods: Electronic searche... |
1007.0210 | Sergei Gepshtein | Sergei Gepshtein and Ivan Tyukin | Uncertainty of visual measurement and efficient allocation of sensory
resources | 8 pages | null | null | null | q-bio.NC cs.CV cs.IT math.IT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We review the reasoning underlying two approaches to combination of sensory
uncertainties. First approach is noncommittal, making no assumptions about
properties of uncertainty or parameters of stimulation. Then we explain the
relationship between this approach and the one commonly used in modeling
"higher level" asp... | [
{
"created": "Thu, 1 Jul 2010 16:37:34 GMT",
"version": "v1"
},
{
"created": "Sat, 3 May 2014 00:57:19 GMT",
"version": "v2"
}
] | 2014-05-06 | [
[
"Gepshtein",
"Sergei",
""
],
[
"Tyukin",
"Ivan",
""
]
] | We review the reasoning underlying two approaches to combination of sensory uncertainties. First approach is noncommittal, making no assumptions about properties of uncertainty or parameters of stimulation. Then we explain the relationship between this approach and the one commonly used in modeling "higher level" aspec... |
1407.8234 | Jean Carlson | Elizabeth N. Davison, Kimberly J. Schlesinger, Danielle S. Bassett,
Mary-Ellen Lynall, Michael B. Miller, Scott T. Grafton, Jean M. Carlson | Brain Network Adaptability Across Task States | 22 pages, 9 figures, 1 table | null | 10.1371/journal.pcbi.1004029 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Activity in the human brain moves between diverse functional states to meet
the demands of our dynamic environment, but fundamental principles guiding
these transitions remain poorly understood. Here, we capitalize on recent
advances in network science to analyze patterns of functional interactions
between brain regi... | [
{
"created": "Wed, 30 Jul 2014 22:51:41 GMT",
"version": "v1"
}
] | 2015-06-22 | [
[
"Davison",
"Elizabeth N.",
""
],
[
"Schlesinger",
"Kimberly J.",
""
],
[
"Bassett",
"Danielle S.",
""
],
[
"Lynall",
"Mary-Ellen",
""
],
[
"Miller",
"Michael B.",
""
],
[
"Grafton",
"Scott T.",
""
],
[
"Carlson",
... | Activity in the human brain moves between diverse functional states to meet the demands of our dynamic environment, but fundamental principles guiding these transitions remain poorly understood. Here, we capitalize on recent advances in network science to analyze patterns of functional interactions between brain region... |
1609.05131 | Claire Yilin Lin | Mariel Bedell, Claire Yilin Lin, Emmie Roman-Melendez, Ioannis
Sgouralis | Global Sensitivity Analysis in a Mathematical Model of the Renal
Interstitium | null | null | null | null | q-bio.TO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The pressure in the renal interstitium is an important factor for normal
kidney function. Here we develop a computational model of the rat kidney and
use it to investigate the relationship between arterial blood pressure and
interstitial fluid pressure. In addition, we investigate how tissue flexibility
influences th... | [
{
"created": "Sat, 13 Aug 2016 16:52:58 GMT",
"version": "v1"
}
] | 2016-09-19 | [
[
"Bedell",
"Mariel",
""
],
[
"Lin",
"Claire Yilin",
""
],
[
"Roman-Melendez",
"Emmie",
""
],
[
"Sgouralis",
"Ioannis",
""
]
] | The pressure in the renal interstitium is an important factor for normal kidney function. Here we develop a computational model of the rat kidney and use it to investigate the relationship between arterial blood pressure and interstitial fluid pressure. In addition, we investigate how tissue flexibility influences this... |
2111.10890 | Josef Tkadlec | Josef Tkadlec, Kamran Kaveh, Krishnendu Chatterjee, Martin A. Nowak | Natural selection of mutants that modify population structure | 20 pages, 11 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Evolution occurs in populations of reproducing individuals. It is well known
that population structure can affect evolutionary dynamics. Traditionally,
natural selection is studied between mutants that differ in reproductive rate,
but are subject to the same population structure. Here we study how natural
selection a... | [
{
"created": "Sun, 21 Nov 2021 20:11:22 GMT",
"version": "v1"
}
] | 2021-11-23 | [
[
"Tkadlec",
"Josef",
""
],
[
"Kaveh",
"Kamran",
""
],
[
"Chatterjee",
"Krishnendu",
""
],
[
"Nowak",
"Martin A.",
""
]
] | Evolution occurs in populations of reproducing individuals. It is well known that population structure can affect evolutionary dynamics. Traditionally, natural selection is studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we study how natural selection act... |
q-bio/0510055 | Ovidiu Lipan | Sever Achimescu and Ovidiu Lipan | Signal Propagation in Nonlinear Stochastic Gene Regulatory Networks | 45 pages, 14 figures, Excerpts from this manuscript were presented at
the 3rd International Conference on Pathways, Networks, and Systems: Theory
and Experiments, October 2-7, Rhodes Greece 2005. A reduced version was
submitted on May 24th 2005 to IEE Systems Biology. High quality figures at
http://www.cbgm.mcg... | null | null | null | q-bio.MN q-bio.QM | null | The structure of a stochastic nonlinear gene regulatory network is uncovered
by studying its response to input signal generators. Four applications are
studied in detail: a nonlinear connection of two linear systems, the design of
a logic pulse, a molecular amplifier and the interference of three signal
generators in... | [
{
"created": "Sat, 29 Oct 2005 19:12:41 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Achimescu",
"Sever",
""
],
[
"Lipan",
"Ovidiu",
""
]
] | The structure of a stochastic nonlinear gene regulatory network is uncovered by studying its response to input signal generators. Four applications are studied in detail: a nonlinear connection of two linear systems, the design of a logic pulse, a molecular amplifier and the interference of three signal generators in E... |
q-bio/0602005 | Ulrich H.E. Hansmann | Simon Trebst, Matthias Troyer and Ulrich H.E. Hansmann | Optimized parallel tempering simulations of proteins | 22 pages, 7 figures | J. Chem. Phys. 124, 174903 (2006). | 10.1063/1.2186639 | MTU-PHY-06-HA/03 | q-bio.QM cond-mat.stat-mech physics.comp-ph | null | We apply a recently developed adaptive algorithm that systematically improves
the efficiency of parallel tempering or replica exchange methods in the
numerical simulation of small proteins. Feedback iterations allow us to
identify an optimal set of temperatures/replicas which are found to concentrate
at the bottlenec... | [
{
"created": "Mon, 6 Feb 2006 10:54:13 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Trebst",
"Simon",
""
],
[
"Troyer",
"Matthias",
""
],
[
"Hansmann",
"Ulrich H. E.",
""
]
] | We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an optimal set of temperatures/replicas which are found to concentrate at the bottlenecks... |
1607.02110 | Eugene Serebryany | Eugene Serebryany, Jaie C. Woodard, Bharat V. Adkar, Mohammed Shabab,
Jonathan A. King, and Eugene I. Shakhnovich | An internal disulfide locks a misfolded aggregation-prone intermediate
in cataract-linked mutants of human {\gamma}D-crystallin | *equal contribution; {\dag}corresponding authors | null | 10.1016/j.bpj.2016.11.923 | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Considerable mechanistic insight has been gained into amyloid aggregation;
however, a large class of non-amyloid protein aggregates are considered
'amorphous,' and in most cases little is known about their mechanisms.
Amorphous aggregation of {\gamma}-crystallins in the eye lens causes a
widespread disease of aging, ... | [
{
"created": "Thu, 7 Jul 2016 18:19:52 GMT",
"version": "v1"
}
] | 2017-04-05 | [
[
"Serebryany",
"Eugene",
""
],
[
"Woodard",
"Jaie C.",
""
],
[
"Adkar",
"Bharat V.",
""
],
[
"Shabab",
"Mohammed",
""
],
[
"King",
"Jonathan A.",
""
],
[
"Shakhnovich",
"Eugene I.",
""
]
] | Considerable mechanistic insight has been gained into amyloid aggregation; however, a large class of non-amyloid protein aggregates are considered 'amorphous,' and in most cases little is known about their mechanisms. Amorphous aggregation of {\gamma}-crystallins in the eye lens causes a widespread disease of aging, ca... |
2008.08226 | Robert Strauss | Robert Strauss | Augmenting Neural Differential Equations to Model Unknown Dynamical
Systems with Incomplete State Information | null | null | null | null | q-bio.NC cs.LG physics.comp-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neural Ordinary Differential Equations replace the right-hand side of a
conventional ODE with a neural net, which by virtue of the universal
approximation theorem, can be trained to the representation of any function.
When we do not know the function itself, but have state trajectories (time
evolution) of the ODE sys... | [
{
"created": "Wed, 19 Aug 2020 02:21:13 GMT",
"version": "v1"
},
{
"created": "Thu, 20 Aug 2020 00:11:16 GMT",
"version": "v2"
},
{
"created": "Sat, 22 Aug 2020 02:59:26 GMT",
"version": "v3"
}
] | 2020-08-25 | [
[
"Strauss",
"Robert",
""
]
] | Neural Ordinary Differential Equations replace the right-hand side of a conventional ODE with a neural net, which by virtue of the universal approximation theorem, can be trained to the representation of any function. When we do not know the function itself, but have state trajectories (time evolution) of the ODE syste... |
1901.03677 | Reid Priedhorsky | Reid Priedhorsky (1), Ashlynn R. Daughton (1 and 2), Martha Barnard
(3), Fiona O'Connell (3), Dave Osthus (1) ((1) Los Alamos National
Laboratory, (2) University of Colorado Boulder, (3) Minnetonka Public
Schools) | Estimating influenza incidence using search query deceptiveness and
generalized ridge regression | 27 pages, 8 figures | null | 10.1371/journal.pcbi.1007165 | LA-UR 18-24467 | q-bio.PE cs.SI stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Seasonal influenza is a sometimes surprisingly impactful disease, causing
thousands of deaths per year along with much additional morbidity. Timely
knowledge of the outbreak state is valuable for managing an effective response.
The current state of the art is to gather this knowledge using in-person
patient contact. ... | [
{
"created": "Fri, 11 Jan 2019 18:04:42 GMT",
"version": "v1"
}
] | 2020-07-01 | [
[
"Priedhorsky",
"Reid",
"",
"1 and 2"
],
[
"Daughton",
"Ashlynn R.",
"",
"1 and 2"
],
[
"Barnard",
"Martha",
""
],
[
"O'Connell",
"Fiona",
""
],
[
"Osthus",
"Dave",
""
]
] | Seasonal influenza is a sometimes surprisingly impactful disease, causing thousands of deaths per year along with much additional morbidity. Timely knowledge of the outbreak state is valuable for managing an effective response. The current state of the art is to gather this knowledge using in-person patient contact. Wh... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.