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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1804.10493 | Jicun Wang-Michelitsch | Jicun Wang-Michelitsch, Thomas M Michelitsch | Three pathways of cell transformation of lymphoid cell: a slow, a rapid,
and an accelerated | 24 pages, 4 figures | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Lymphoid leukemia (LL) and lymphoma are neoplasms developed from lymphoid
cells (LCs). To understand why different forms of LL/lymphoma occur at
different ages, we analyzed the effects of different types of DNA changes on a
LC and the cellular characteristics of LCs. Point DNA mutations (PDMs) and
chromosome changes ... | [
{
"created": "Fri, 27 Apr 2018 13:28:20 GMT",
"version": "v1"
}
] | 2018-04-30 | [
[
"Wang-Michelitsch",
"Jicun",
""
],
[
"Michelitsch",
"Thomas M",
""
]
] | Lymphoid leukemia (LL) and lymphoma are neoplasms developed from lymphoid cells (LCs). To understand why different forms of LL/lymphoma occur at different ages, we analyzed the effects of different types of DNA changes on a LC and the cellular characteristics of LCs. Point DNA mutations (PDMs) and chromosome changes (C... |
q-bio/0611054 | Nicolas Jacq | N. Jacq (LPC-Clermont, CS-Si), J. Salzemann (LPC-Clermont), F. Jacq
(LPC-Clermont), Y. Legr\'e (LPC-Clermont), E. Medernach (LPC-Clermont), J.
Montagnat (Informatique Signaux Et Syst\`emes), A. Maass (SCAI), M.
Reichstadt (LPC-Clermont), H. Schwichtenberg (SCAI), M. Sridhar (SCAI), V.
Kasam (SCAI), M. Zimmerman... | Grid enabled virtual screening against malaria | 34 pages, 5 figures, 3 tables, to appear in Journal of Grid Computing | Journal of Grid Computing 6 (2008) 29-43 | null | null | q-bio.QM cs.DC | null | WISDOM is an international initiative to enable a virtual screening pipeline
on a grid infrastructure. Its first attempt was to deploy large scale in silico
docking on a public grid infrastructure. Protein-ligand docking is about
computing the binding energy of a protein target to a library of potential
drugs using a... | [
{
"created": "Fri, 17 Nov 2006 10:26:07 GMT",
"version": "v1"
}
] | 2008-12-09 | [
[
"Jacq",
"N.",
"",
"LPC-Clermont, CS-Si"
],
[
"Salzemann",
"J.",
"",
"LPC-Clermont"
],
[
"Jacq",
"F.",
"",
"LPC-Clermont"
],
[
"Legré",
"Y.",
"",
"LPC-Clermont"
],
[
"Medernach",
"E.",
"",
"LPC-Clermont"
],
[
"M... | WISDOM is an international initiative to enable a virtual screening pipeline on a grid infrastructure. Its first attempt was to deploy large scale in silico docking on a public grid infrastructure. Protein-ligand docking is about computing the binding energy of a protein target to a library of potential drugs using a s... |
1709.00339 | Mirko Lukovic | Tatiana A. Amor, Mirko Lukovic, Hans J. Herrmann, and Jose S. Andrade
Jr | How images determine our visual search strategy | null | J. R. Soc. Interface 14, 20170406, 2017 | 10.1098/rsif.2017.0406 | null | q-bio.NC cond-mat.other | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When searching for a target within an image our brain can adopt different
strategies, but which one does it choose? This question can be answered by
tracking the motion of the eye while it executes the task. Following many
individuals performing various search tasks we distinguish between two
competing strategies. Mo... | [
{
"created": "Thu, 31 Aug 2017 11:14:59 GMT",
"version": "v1"
}
] | 2017-09-04 | [
[
"Amor",
"Tatiana A.",
""
],
[
"Lukovic",
"Mirko",
""
],
[
"Herrmann",
"Hans J.",
""
],
[
"Andrade",
"Jose S.",
"Jr"
]
] | When searching for a target within an image our brain can adopt different strategies, but which one does it choose? This question can be answered by tracking the motion of the eye while it executes the task. Following many individuals performing various search tasks we distinguish between two competing strategies. Moti... |
1808.04262 | Anvar Kurmukov | Anvar Kurmukov and Ayagoz Mussabayeva and Yulia Denisova and Daniel
Moyer and Boris Gutman | Connectivity-Driven Brain Parcellation via Consensus Clustering | null | null | null | null | q-bio.NC cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present two related methods for deriving connectivity-based brain atlases
from individual connectomes. The proposed methods exploit a previously proposed
dense connectivity representation, termed continuous connectivity, by first
performing graph-based hierarchical clustering of individual brains, and
subsequently... | [
{
"created": "Fri, 10 Aug 2018 08:54:31 GMT",
"version": "v1"
}
] | 2018-08-14 | [
[
"Kurmukov",
"Anvar",
""
],
[
"Mussabayeva",
"Ayagoz",
""
],
[
"Denisova",
"Yulia",
""
],
[
"Moyer",
"Daniel",
""
],
[
"Gutman",
"Boris",
""
]
] | We present two related methods for deriving connectivity-based brain atlases from individual connectomes. The proposed methods exploit a previously proposed dense connectivity representation, termed continuous connectivity, by first performing graph-based hierarchical clustering of individual brains, and subsequently a... |
0707.4321 | Razvan Radulescu M.D. | Razvan Tudor Radulescu | The insulin superfamily of growth-promoting proteins | 3 pages, 1 figure | null | null | null | q-bio.BM q-bio.SC | null | Recently, structural analysis of the human transferrin and growth hormone
(GH) amino acid sequences has unravelled that they harbor a motif identical to
a pattern found in viral oncoproteins known to bind the primarily nuclear tumor
suppressor retinoblastoma protein (RB). Since related signatures had previously
been ... | [
{
"created": "Sun, 29 Jul 2007 22:54:16 GMT",
"version": "v1"
}
] | 2007-07-31 | [
[
"Radulescu",
"Razvan Tudor",
""
]
] | Recently, structural analysis of the human transferrin and growth hormone (GH) amino acid sequences has unravelled that they harbor a motif identical to a pattern found in viral oncoproteins known to bind the primarily nuclear tumor suppressor retinoblastoma protein (RB). Since related signatures had previously been id... |
2102.03667 | Mohammed Alser | Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr, Stefan W. Tell,
Onur Mutlu | COVIDHunter: An Accurate, Flexible, and Environment-Aware Open-Source
COVID-19 Outbreak Simulation Model | null | null | null | null | q-bio.PE cs.LG cs.SI stat.OT | http://creativecommons.org/licenses/by/4.0/ | Background: Early detection and isolation of COVID-19 patients are essential
for successful implementation of mitigation strategies and eventually curbing
the disease spread. With a limited number of daily COVID-19 tests performed in
every country, simulating the COVID-19 spread along with the potential effect
of eac... | [
{
"created": "Sat, 6 Feb 2021 21:01:56 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Jun 2022 10:41:02 GMT",
"version": "v2"
}
] | 2022-06-09 | [
[
"Alser",
"Mohammed",
""
],
[
"Kim",
"Jeremie S.",
""
],
[
"Alserr",
"Nour Almadhoun",
""
],
[
"Tell",
"Stefan W.",
""
],
[
"Mutlu",
"Onur",
""
]
] | Background: Early detection and isolation of COVID-19 patients are essential for successful implementation of mitigation strategies and eventually curbing the disease spread. With a limited number of daily COVID-19 tests performed in every country, simulating the COVID-19 spread along with the potential effect of each ... |
2210.03488 | Igor Melnyk | Igor Melnyk, Aurelie Lozano, Payel Das, Vijil Chenthamarakshan | AlphaFold Distillation for Protein Design | Preprint | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Inverse protein folding, the process of designing sequences that fold into a
specific 3D structure, is crucial in bio-engineering and drug discovery.
Traditional methods rely on experimentally resolved structures, but these cover
only a small fraction of protein sequences. Forward folding models like
AlphaFold offer ... | [
{
"created": "Wed, 5 Oct 2022 19:43:06 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Nov 2023 22:52:47 GMT",
"version": "v2"
}
] | 2023-11-27 | [
[
"Melnyk",
"Igor",
""
],
[
"Lozano",
"Aurelie",
""
],
[
"Das",
"Payel",
""
],
[
"Chenthamarakshan",
"Vijil",
""
]
] | Inverse protein folding, the process of designing sequences that fold into a specific 3D structure, is crucial in bio-engineering and drug discovery. Traditional methods rely on experimentally resolved structures, but these cover only a small fraction of protein sequences. Forward folding models like AlphaFold offer a ... |
2405.19936 | Anindita Bhadra | Srijaya Nandi, Mousumi Chakraborty, Aesha Lahiri, Hindolii Gope,
Sujata Khan Bhaduri, Anindita Bhadra | Free-ranging dogs quickly learn to recognize a rewarding person | null | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Individual human recognition is important for species that live in close
proximity to humans. Numerous studies on domesticated species and urban-adapted
birds have highlighted this ability. One such species which is heavily reliant
on humans is the free-ranging dog. Very little knowledge exists on the amount
of time ... | [
{
"created": "Thu, 30 May 2024 10:56:32 GMT",
"version": "v1"
}
] | 2024-05-31 | [
[
"Nandi",
"Srijaya",
""
],
[
"Chakraborty",
"Mousumi",
""
],
[
"Lahiri",
"Aesha",
""
],
[
"Gope",
"Hindolii",
""
],
[
"Bhaduri",
"Sujata Khan",
""
],
[
"Bhadra",
"Anindita",
""
]
] | Individual human recognition is important for species that live in close proximity to humans. Numerous studies on domesticated species and urban-adapted birds have highlighted this ability. One such species which is heavily reliant on humans is the free-ranging dog. Very little knowledge exists on the amount of time ta... |
1307.3857 | Osamu Narikiyo | Hayato Tsuda, Osamu Narikiyo | Translation by adaptor-helicase cycle in oligomer world | null | null | null | null | q-bio.BM q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A mechanism of the translation in oligomer world is proposed. The translation
is carried out by a minimum cycle, which is sustained by adaptors and
helicases, and the first information processing in oligomer world. We expect
that such a cycle actually worked in a primitive cell and can be constructed in
vitro. By com... | [
{
"created": "Mon, 15 Jul 2013 09:08:42 GMT",
"version": "v1"
}
] | 2013-07-16 | [
[
"Tsuda",
"Hayato",
""
],
[
"Narikiyo",
"Osamu",
""
]
] | A mechanism of the translation in oligomer world is proposed. The translation is carried out by a minimum cycle, which is sustained by adaptors and helicases, and the first information processing in oligomer world. We expect that such a cycle actually worked in a primitive cell and can be constructed in vitro. By compu... |
1109.2239 | Joel Zylberberg | Joel Zylberberg, Jason Timothy Murphy, and Michael Robert DeWeese | A sparse coding model with synaptically local plasticity and spiking
neurons can account for the diverse shapes of V1 simple cell receptive fields | 33 pages, 6 figures. To appear in PLoS Computational Biology. Some of
these data were presented by author JZ at the 2011 CoSyNe meeting in Salt
Lake City | PLoS Computational Biology (2011) 7(10): e1002250 | 10.1371/journal.pcbi.1002250 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sparse coding algorithms trained on natural images can accurately predict the
features that excite visual cortical neurons, but it is not known whether such
codes can be learned using biologically realistic plasticity rules. We have
developed a biophysically motivated spiking network, relying solely on
synaptically l... | [
{
"created": "Sat, 10 Sep 2011 17:36:38 GMT",
"version": "v1"
}
] | 2011-11-01 | [
[
"Zylberberg",
"Joel",
""
],
[
"Murphy",
"Jason Timothy",
""
],
[
"DeWeese",
"Michael Robert",
""
]
] | Sparse coding algorithms trained on natural images can accurately predict the features that excite visual cortical neurons, but it is not known whether such codes can be learned using biologically realistic plasticity rules. We have developed a biophysically motivated spiking network, relying solely on synaptically loc... |
1607.00437 | Rafael Tuma Guariento | Rafael Tuma Guariento, Thiago Schiavo Mosqueiro, Paulo Matias,
Vinicius Burani Cesarino, Lirio Onofre Baptista de Almeida, Jan Frans Willem
Slaets, Leonardo Paulo Maia, Reynaldo Daniel Pinto | Automated pulse discrimination of two freely-swimming weakly electric
fish and analysis of their electrical behavior during a dominance contest | 15 pages, 8 figures | null | 10.1016/j.jphysparis.2017.02.001 | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Electric fishes modulate their electric organ discharges with a remarkable
variability. Some patterns can be easily identified, such as pulse rate
changes, offs and chirps, which are often associated with important behavioral
contexts, including aggression, hiding and mating. However, these behaviors are
only observe... | [
{
"created": "Sat, 2 Jul 2016 00:14:43 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Mar 2017 14:38:40 GMT",
"version": "v2"
}
] | 2017-03-23 | [
[
"Guariento",
"Rafael Tuma",
""
],
[
"Mosqueiro",
"Thiago Schiavo",
""
],
[
"Matias",
"Paulo",
""
],
[
"Cesarino",
"Vinicius Burani",
""
],
[
"de Almeida",
"Lirio Onofre Baptista",
""
],
[
"Slaets",
"Jan Frans Willem",
""
... | Electric fishes modulate their electric organ discharges with a remarkable variability. Some patterns can be easily identified, such as pulse rate changes, offs and chirps, which are often associated with important behavioral contexts, including aggression, hiding and mating. However, these behaviors are only observed ... |
2301.06454 | Jonas Ditz | Jonas Christian Ditz and Jacqueline Wistuba-Hamprecht and Timo Maier
and Rolf Fendel and Nico Pfeifer and Bernhard Reuter | PlasmoFAB: A Benchmark to Foster Machine Learning for Plasmodium
falciparum Protein Antigen Candidate Prediction | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by-sa/4.0/ | Motivation: Machine learning methods can be used to support scientific
discovery in healthcare-related research fields. However, these methods can
only be reliably used if they can be trained on high-quality and curated
datasets. Currently, no such dataset for the exploration of Plasmodium
falciparum protein antigen ... | [
{
"created": "Mon, 16 Jan 2023 14:57:42 GMT",
"version": "v1"
},
{
"created": "Wed, 3 May 2023 11:41:56 GMT",
"version": "v2"
}
] | 2023-05-04 | [
[
"Ditz",
"Jonas Christian",
""
],
[
"Wistuba-Hamprecht",
"Jacqueline",
""
],
[
"Maier",
"Timo",
""
],
[
"Fendel",
"Rolf",
""
],
[
"Pfeifer",
"Nico",
""
],
[
"Reuter",
"Bernhard",
""
]
] | Motivation: Machine learning methods can be used to support scientific discovery in healthcare-related research fields. However, these methods can only be reliably used if they can be trained on high-quality and curated datasets. Currently, no such dataset for the exploration of Plasmodium falciparum protein antigen ca... |
q-bio/0702051 | Ralf Blossey | C. Russo, C.V. Giuraniuc, R. Blossey and J.-F. Bodart | On the equilibria of the MAPK cascade: cooperativity, modularity and
bistability | null | Physica A 388 (2009), pp. 5070-5080 | 10.1016/j.physa.2009.08.018 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we present a discussion of a phenomenological model of the MAPK
cascade which was originally proposed by Angeli et al. (PNAS 101, 1822 (2004)).
The model and its solution are extended in several respects: a) an analytical
solution is given for the cascade equilibria, exploiting a parameter-based
symmetr... | [
{
"created": "Sat, 24 Feb 2007 12:13:57 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Oct 2008 15:23:54 GMT",
"version": "v2"
},
{
"created": "Mon, 2 Feb 2009 10:52:44 GMT",
"version": "v3"
},
{
"created": "Wed, 26 Aug 2009 13:03:52 GMT",
"version": "v4"
}
] | 2009-09-21 | [
[
"Russo",
"C.",
""
],
[
"Giuraniuc",
"C. V.",
""
],
[
"Blossey",
"R.",
""
],
[
"Bodart",
"J. -F.",
""
]
] | In this paper we present a discussion of a phenomenological model of the MAPK cascade which was originally proposed by Angeli et al. (PNAS 101, 1822 (2004)). The model and its solution are extended in several respects: a) an analytical solution is given for the cascade equilibria, exploiting a parameter-based symmetry ... |
1301.3981 | Armita Nourmohammad | Armita Nourmohammad, Stephan Schiffels, Michael Laessig | Evolution of molecular phenotypes under stabilizing selection | null | J. Stat. Mech. (2013) P01012 | 10.1088/1742-5468/2013/01/P01012 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular phenotypes are important links between genomic information and
organismic functions, fitness, and evolution. Complex phenotypes, which are
also called quantitative traits, often depend on multiple genomic loci. Their
evolution builds on genome evolution in a complicated way, which involves
selection, geneti... | [
{
"created": "Thu, 17 Jan 2013 04:51:07 GMT",
"version": "v1"
}
] | 2015-06-12 | [
[
"Nourmohammad",
"Armita",
""
],
[
"Schiffels",
"Stephan",
""
],
[
"Laessig",
"Michael",
""
]
] | Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic ... |
1410.2990 | R.K. Brojen Singh | Md. Jahoor Alam, Sanjay Kumar, Vikram Singh and R.K. Brojen Singh | Bifurcation in cell cycle dynamics regulated by p53 | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the regulating mechanism of p53 on the properties of cell cycle
dynamics in the light of the proposed model of interacting p53 and cell cycle
networks via p53. Irradiation (IR) introduce to p53 compel p53 dynamics to
suffer different phases, namely oscillating and oscillation death (stabilized)
phases. The I... | [
{
"created": "Sat, 11 Oct 2014 12:04:46 GMT",
"version": "v1"
}
] | 2014-10-14 | [
[
"Alam",
"Md. Jahoor",
""
],
[
"Kumar",
"Sanjay",
""
],
[
"Singh",
"Vikram",
""
],
[
"Singh",
"R. K. Brojen",
""
]
] | We study the regulating mechanism of p53 on the properties of cell cycle dynamics in the light of the proposed model of interacting p53 and cell cycle networks via p53. Irradiation (IR) introduce to p53 compel p53 dynamics to suffer different phases, namely oscillating and oscillation death (stabilized) phases. The IR ... |
2006.13530 | Thierry Mora | Thomas Dupic, Meriem Bensouda Koraichi, Anastasia Minervina, Mikhail
Pogorelyy, Thierry Mora, Aleksandra M. Walczak | Immune Fingerprinting through Repertoire Similarity | null | PLoS Genetics 17 (1) e1009301 (2021) | 10.1371/journal.pgen.1009301 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Immune repertoires provide a unique fingerprint reflecting the immune history
of individuals, with potential applications in precision medicine. However, the
question of how personal that information is and how it can be used to identify
individuals has not been explored. Here, we show that individuals can be
uniquel... | [
{
"created": "Wed, 24 Jun 2020 07:33:10 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Oct 2020 19:55:05 GMT",
"version": "v2"
}
] | 2021-02-05 | [
[
"Dupic",
"Thomas",
""
],
[
"Koraichi",
"Meriem Bensouda",
""
],
[
"Minervina",
"Anastasia",
""
],
[
"Pogorelyy",
"Mikhail",
""
],
[
"Mora",
"Thierry",
""
],
[
"Walczak",
"Aleksandra M.",
""
]
] | Immune repertoires provide a unique fingerprint reflecting the immune history of individuals, with potential applications in precision medicine. However, the question of how personal that information is and how it can be used to identify individuals has not been explored. Here, we show that individuals can be uniquely ... |
2308.04478 | Ziyu Zhu | Ziyu Zhu and Ximing Xu | EasyMergeR: an interactive Shiny application to manipulate multiple XLSX
files of multiple sheets | 6 pages, 1 figure | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | The integration of sequencing data with clinical information is a widely
accepted strategy in bioinformatics and health informatics. Despite advanced
databases and sophisticated tools for processing omics data, challenges remain
in handling the raw clinical data (typically in XLSX format with multiple
sheets inside),... | [
{
"created": "Tue, 8 Aug 2023 15:08:55 GMT",
"version": "v1"
}
] | 2023-08-10 | [
[
"Zhu",
"Ziyu",
""
],
[
"Xu",
"Ximing",
""
]
] | The integration of sequencing data with clinical information is a widely accepted strategy in bioinformatics and health informatics. Despite advanced databases and sophisticated tools for processing omics data, challenges remain in handling the raw clinical data (typically in XLSX format with multiple sheets inside), e... |
1602.05981 | Amit Chattopadhyay | Arghya Panigrahi, Amit K Chattopadhyay, Goutam Paul and Soumya
Panigrahi | HIV, Cardiovascular Diseases, and Chronic Arsenic Exposure co-exist in a
Positive Synergy | 15 pages, 4 figures; accepted in Bengal Heart Journal | null | null | null | q-bio.TO physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent epidemiological evidences indicate that arsenic exposure increases
risk of atherosclerosis, cardiovascular diseases and microangiopathies in
addition to the serious global health concern related to its carcinogenic
effects. In experiments on animals, acute and chronic exposure to arsenic
directly correlates ca... | [
{
"created": "Tue, 9 Feb 2016 21:36:51 GMT",
"version": "v1"
}
] | 2016-02-22 | [
[
"Panigrahi",
"Arghya",
""
],
[
"Chattopadhyay",
"Amit K",
""
],
[
"Paul",
"Goutam",
""
],
[
"Panigrahi",
"Soumya",
""
]
] | Recent epidemiological evidences indicate that arsenic exposure increases risk of atherosclerosis, cardiovascular diseases and microangiopathies in addition to the serious global health concern related to its carcinogenic effects. In experiments on animals, acute and chronic exposure to arsenic directly correlates card... |
2401.08605 | Michael Shapiro | Anna Laddach, Michael Shapiro | Long cycles in linear thresholding systems | 3 pages | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Linear thresholding systems have been used as a model of neural activation
and more recently proposed as a model of gene regulation. Here we exhibit
linear thresholding systems whose dynamics produce surprisingly long cycles.
| [
{
"created": "Wed, 22 Nov 2023 13:05:47 GMT",
"version": "v1"
},
{
"created": "Thu, 18 Jan 2024 10:38:47 GMT",
"version": "v2"
}
] | 2024-01-19 | [
[
"Laddach",
"Anna",
""
],
[
"Shapiro",
"Michael",
""
]
] | Linear thresholding systems have been used as a model of neural activation and more recently proposed as a model of gene regulation. Here we exhibit linear thresholding systems whose dynamics produce surprisingly long cycles. |
2204.12607 | Charlie Burlingham | Charlie S. Burlingham, Mengjian Hua, Oliver Xu, Kathryn Bonnen, David
J. Heeger | Heading perception and the structure of the optic acceleration field | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Visual estimation of heading in the human brain is widely believed to be
based on instantaneous optic flow, the velocity of retinal image motion.
However, we previously found that humans are unable to use instantaneous optic
flow to accurately estimate heading and require time-varying optic flow
(Burlingham and Heege... | [
{
"created": "Tue, 26 Apr 2022 21:44:22 GMT",
"version": "v1"
}
] | 2022-04-28 | [
[
"Burlingham",
"Charlie S.",
""
],
[
"Hua",
"Mengjian",
""
],
[
"Xu",
"Oliver",
""
],
[
"Bonnen",
"Kathryn",
""
],
[
"Heeger",
"David J.",
""
]
] | Visual estimation of heading in the human brain is widely believed to be based on instantaneous optic flow, the velocity of retinal image motion. However, we previously found that humans are unable to use instantaneous optic flow to accurately estimate heading and require time-varying optic flow (Burlingham and Heeger,... |
1808.03666 | Rocio Joo | Rocio Joo, Marie-Pierre Etienne, Nicolas Bez, St\'ephanie Mah\'evas | Metrics for describing dyadic movement: a review | 4 tables, 10 figures and 8 supplementary sections | null | 10.1186/s40462-018-0144-2 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In movement ecology, the few works that have taken collective behaviour into
account are data-driven and rely on simplistic theoretical assumptions, relying
in metrics that may or may not be measuring what is intended. In the present
paper, we focus on pairwise joint-movement behaviour, where individuals move
togethe... | [
{
"created": "Fri, 10 Aug 2018 18:32:28 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Aug 2018 17:37:29 GMT",
"version": "v2"
}
] | 2019-03-18 | [
[
"Joo",
"Rocio",
""
],
[
"Etienne",
"Marie-Pierre",
""
],
[
"Bez",
"Nicolas",
""
],
[
"Mahévas",
"Stéphanie",
""
]
] | In movement ecology, the few works that have taken collective behaviour into account are data-driven and rely on simplistic theoretical assumptions, relying in metrics that may or may not be measuring what is intended. In the present paper, we focus on pairwise joint-movement behaviour, where individuals move together ... |
2008.06051 | Tatsushi Oka | Tatsushi Oka and Wei Wei and Dan Zhu | A Spatial Stochastic SIR Model for Transmission Networks with
Application to COVID-19 Epidemic in China | Typos were fixed | null | null | null | q-bio.PE econ.GN physics.soc-ph q-fin.EC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Governments around the world have implemented preventive measures against the
spread of the coronavirus disease (COVID-19). In this study, we consider a
multivariate discrete-time Markov model to analyze the propagation of COVID-19
across 33 provincial regions in China. This approach enables us to evaluate the
effect... | [
{
"created": "Thu, 13 Aug 2020 14:25:40 GMT",
"version": "v1"
},
{
"created": "Mon, 17 Aug 2020 01:54:26 GMT",
"version": "v2"
}
] | 2020-08-18 | [
[
"Oka",
"Tatsushi",
""
],
[
"Wei",
"Wei",
""
],
[
"Zhu",
"Dan",
""
]
] | Governments around the world have implemented preventive measures against the spread of the coronavirus disease (COVID-19). In this study, we consider a multivariate discrete-time Markov model to analyze the propagation of COVID-19 across 33 provincial regions in China. This approach enables us to evaluate the effect o... |
1103.5279 | Chun-Chung Chen | Chun-Chung Chen and David Jasnow | Event-driven simulations of a plastic, spiking neural network | 9 pages, 6 figures | Phys. Rev. E 84, 031908 (2011) | 10.1103/PhysRevE.84.031908 | null | q-bio.NC cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a fully-connected network of leaky integrate-and-fire neurons
with spike-timing-dependent plasticity. The plasticity is controlled by a
parameter representing the expected weight of a synapse between neurons that
are firing randomly with the same mean frequency. For low values of the
plasticity parameter,... | [
{
"created": "Mon, 28 Mar 2011 04:22:50 GMT",
"version": "v1"
}
] | 2011-09-23 | [
[
"Chen",
"Chun-Chung",
""
],
[
"Jasnow",
"David",
""
]
] | We consider a fully-connected network of leaky integrate-and-fire neurons with spike-timing-dependent plasticity. The plasticity is controlled by a parameter representing the expected weight of a synapse between neurons that are firing randomly with the same mean frequency. For low values of the plasticity parameter, t... |
1705.07182 | Jayavel Arumugam | Jayavel Arumugam, Arun Srinivasa | A Novel Simplified Model for Blood Coagulation: A piecewise dynamical
model for thrombin with robust predictive capabilities | 20 pages, 15 figues | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Realistic description of patient-specific mechanical properties of clotting
dynamics presents a major challenge. Available patient-specific data falls
short of robustly characterizing myriads of complex dynamic interactions that
happen during clotting. We propose a simplified switching model for a key part
of the coa... | [
{
"created": "Fri, 19 May 2017 20:55:28 GMT",
"version": "v1"
}
] | 2017-05-23 | [
[
"Arumugam",
"Jayavel",
""
],
[
"Srinivasa",
"Arun",
""
]
] | Realistic description of patient-specific mechanical properties of clotting dynamics presents a major challenge. Available patient-specific data falls short of robustly characterizing myriads of complex dynamic interactions that happen during clotting. We propose a simplified switching model for a key part of the coagu... |
2104.09424 | Yu-Juan Sun | Yu-Juan Sun and Wei-Min Zhang | Modeling the Nervous System as An Open Quantum System | 9 pages, 9 figures | null | null | null | q-bio.NC quant-ph | http://creativecommons.org/licenses/by/4.0/ | We propose a neural network model of multi-neuron interacting system that
simulates neurons to interact each other through the surroundings of neuronal
cell bodies. We physically model the neuronal cell surroundings, include the
dendrites, the axons and the synapses as well as the surrounding glial cells,
as a collec... | [
{
"created": "Thu, 18 Mar 2021 10:17:09 GMT",
"version": "v1"
},
{
"created": "Fri, 2 Jul 2021 08:56:21 GMT",
"version": "v2"
}
] | 2021-07-05 | [
[
"Sun",
"Yu-Juan",
""
],
[
"Zhang",
"Wei-Min",
""
]
] | We propose a neural network model of multi-neuron interacting system that simulates neurons to interact each other through the surroundings of neuronal cell bodies. We physically model the neuronal cell surroundings, include the dendrites, the axons and the synapses as well as the surrounding glial cells, as a collecti... |
1312.3206 | Joel Adamson | Joel James Adamson | Evolution of female choice and age-dependent male traits with paternal
germ-line mutation | 10 pages, 5 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Several studies question the adaptive value of female preferences for older
males. Theory and evidence show that older males carry more deleterious
mutations in their sperm than younger males carry. These mutations are not
visible to females choosing mates. Germ-line mutations could oppose preferences
for "good genes... | [
{
"created": "Wed, 11 Dec 2013 15:20:04 GMT",
"version": "v1"
}
] | 2013-12-12 | [
[
"Adamson",
"Joel James",
""
]
] | Several studies question the adaptive value of female preferences for older males. Theory and evidence show that older males carry more deleterious mutations in their sperm than younger males carry. These mutations are not visible to females choosing mates. Germ-line mutations could oppose preferences for "good genes."... |
2112.13271 | Seyedeh Sajedeh Mousavi Dr | S. Sajedeh Mousavi, Sara Razi | Cell-in-cell structures are involved in the competition between cells in
breast cancer | Presented as a poster in 4th International biotechnology congress of
Islamic Republic of Iran (2021) | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Breast cancer is the most common cancer in women worldwide, and discovering
the biomarkers of this disease became so vital nowadays and Cell in Cell
structure could be one of them, and it may be used as an available proxy for
tumor malignancy. (CICs) are unusual in that keep morphologically healthy cells
within anoth... | [
{
"created": "Sat, 25 Dec 2021 19:17:59 GMT",
"version": "v1"
}
] | 2021-12-28 | [
[
"Mousavi",
"S. Sajedeh",
""
],
[
"Razi",
"Sara",
""
]
] | Breast cancer is the most common cancer in women worldwide, and discovering the biomarkers of this disease became so vital nowadays and Cell in Cell structure could be one of them, and it may be used as an available proxy for tumor malignancy. (CICs) are unusual in that keep morphologically healthy cells within another... |
q-bio/0509009 | Georgy Karev | Georgy P. Karev, Artem S. Novozhilov, and Faina S. Berezovskaya | Modeling the dynamics of inhomogeneous natural rotifer populations under
toxicant exposure | 12 pages, 4 figures; submitted to Ecological Modelling | null | null | null | q-bio.PE q-bio.QM | null | Most population models assume that individuals within a given population are
identical, that is, the fundamental role of variation is ignored. Here we
develop a general approach to modeling heterogeneous populations with discrete
evolutionary time step. The theory is applied to population dynamics of natural
rotifer ... | [
{
"created": "Fri, 9 Sep 2005 14:50:44 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Karev",
"Georgy P.",
""
],
[
"Novozhilov",
"Artem S.",
""
],
[
"Berezovskaya",
"Faina S.",
""
]
] | Most population models assume that individuals within a given population are identical, that is, the fundamental role of variation is ignored. Here we develop a general approach to modeling heterogeneous populations with discrete evolutionary time step. The theory is applied to population dynamics of natural rotifer po... |
1702.08560 | Deborah Shutt | Deborah P. Shutt, Carrie A. Manore, Stephen Pankavich, Aaron T.
Porter, Sara Y. Del Valle | Estimating the reproductive number, total outbreak size, and reporting
rates for Zika epidemics in South and Central America | 35 pages, 16 figures | null | null | null | q-bio.PE q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As South and Central American countries prepare for increased birth defects
from Zika virus outbreaks and plan for mitigation strategies to minimize
ongoing and future outbreaks, understanding important characteristics of Zika
outbreaks and how they vary across regions is a challenging and important
problem. We devel... | [
{
"created": "Mon, 27 Feb 2017 22:22:03 GMT",
"version": "v1"
}
] | 2017-03-01 | [
[
"Shutt",
"Deborah P.",
""
],
[
"Manore",
"Carrie A.",
""
],
[
"Pankavich",
"Stephen",
""
],
[
"Porter",
"Aaron T.",
""
],
[
"Del Valle",
"Sara Y.",
""
]
] | As South and Central American countries prepare for increased birth defects from Zika virus outbreaks and plan for mitigation strategies to minimize ongoing and future outbreaks, understanding important characteristics of Zika outbreaks and how they vary across regions is a challenging and important problem. We develop... |
1806.06724 | Enrico Gavagnin | Enrico Gavagnin and Christian A. Yates | Stochastic and deterministic modelling of cell migration | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mathematical models are vital interpretive and predictive tools used to
assist in the understanding of cell migration. There are typically two
approaches to modelling cell migration: either micro-scale, discrete or
macro-scale, continuum. The discrete approach, using agent-based models (ABMs),
is typically stochastic... | [
{
"created": "Mon, 18 Jun 2018 14:18:14 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Aug 2018 10:05:44 GMT",
"version": "v2"
}
] | 2018-08-16 | [
[
"Gavagnin",
"Enrico",
""
],
[
"Yates",
"Christian A.",
""
]
] | Mathematical models are vital interpretive and predictive tools used to assist in the understanding of cell migration. There are typically two approaches to modelling cell migration: either micro-scale, discrete or macro-scale, continuum. The discrete approach, using agent-based models (ABMs), is typically stochastic a... |
1505.04656 | Fernando Vericat | C. Manuel Carlevaro, Ramiro M. Irastorza and Fernando Vericat | Quaternionic representation of the genetic code | 19 pages, 11 figures | null | null | null | q-bio.OT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A heuristic diagram of the evolution of the standard genetic code is
presented. It incorporates, in a way that resembles the energy levels of an
atom, the physical notion of broken symmetry and it is consistent with original
ideas by Crick on the origin and evolution of the code as well as with the
chronological orde... | [
{
"created": "Mon, 18 May 2015 14:23:18 GMT",
"version": "v1"
},
{
"created": "Tue, 29 Dec 2015 19:15:25 GMT",
"version": "v2"
}
] | 2015-12-31 | [
[
"Carlevaro",
"C. Manuel",
""
],
[
"Irastorza",
"Ramiro M.",
""
],
[
"Vericat",
"Fernando",
""
]
] | A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order ... |
1811.09673 | Veronica Tozzo | Veronica Tozzo, Federico Tomasi, Margherita Squillario, Annalisa Barla | Group induced graphical lasso allows for discovery of molecular
pathways-pathways interactions | Machine Learning for Health (ML4H) Workshop at NeurIPS 2018
arXiv:1811.07216 | null | null | null | q-bio.QM cs.LG q-bio.GN stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Complex systems may contain heterogeneous types of variables that interact in
a multi-level and multi-scale manner. In this context, high-level layers may
considered as groups of variables interacting in lower-level layers. This is
particularly true in biology, where, for example, genes are grouped in pathways
and tw... | [
{
"created": "Wed, 21 Nov 2018 10:39:59 GMT",
"version": "v1"
}
] | 2018-11-28 | [
[
"Tozzo",
"Veronica",
""
],
[
"Tomasi",
"Federico",
""
],
[
"Squillario",
"Margherita",
""
],
[
"Barla",
"Annalisa",
""
]
] | Complex systems may contain heterogeneous types of variables that interact in a multi-level and multi-scale manner. In this context, high-level layers may considered as groups of variables interacting in lower-level layers. This is particularly true in biology, where, for example, genes are grouped in pathways and two ... |
2408.00040 | Maximilian Schuh | Maximilian G. Schuh, Davide Boldini, Stephan A. Sieber | Barlow Twins Deep Neural Network for Advanced 1D Drug-Target Interaction
Prediction | 9 pages, 2 figures | null | null | null | q-bio.BM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Accurate prediction of drug-target interactions is critical for advancing
drug discovery. By reducing time and cost, machine learning and deep learning
can accelerate this discovery process. Our approach utilises the powerful
Barlow Twins architecture for feature-extraction while considering the
structure of the targ... | [
{
"created": "Wed, 31 Jul 2024 14:06:18 GMT",
"version": "v1"
}
] | 2024-08-02 | [
[
"Schuh",
"Maximilian G.",
""
],
[
"Boldini",
"Davide",
""
],
[
"Sieber",
"Stephan A.",
""
]
] | Accurate prediction of drug-target interactions is critical for advancing drug discovery. By reducing time and cost, machine learning and deep learning can accelerate this discovery process. Our approach utilises the powerful Barlow Twins architecture for feature-extraction while considering the structure of the target... |
1809.08045 | Dominik Dold | Dominik Dold, Ilja Bytschok, Akos F. Kungl, Andreas Baumbach, Oliver
Breitwieser, Walter Senn, Johannes Schemmel, Karlheinz Meier, Mihai A.
Petrovici | Stochasticity from function -- why the Bayesian brain may need no noise | null | Neural Networks 119C (2019) pp. 200-213 | 10.1016/j.neunet.2019.08.002 | null | q-bio.NC cond-mat.dis-nn cs.NE physics.bio-ph stat.ML | http://creativecommons.org/licenses/by/4.0/ | An increasing body of evidence suggests that the trial-to-trial variability
of spiking activity in the brain is not mere noise, but rather the reflection
of a sampling-based encoding scheme for probabilistic computing. Since the
precise statistical properties of neural activity are important in this
context, many mod... | [
{
"created": "Fri, 21 Sep 2018 11:37:14 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Aug 2019 15:53:49 GMT",
"version": "v2"
},
{
"created": "Sat, 24 Aug 2019 12:58:19 GMT",
"version": "v3"
}
] | 2019-08-27 | [
[
"Dold",
"Dominik",
""
],
[
"Bytschok",
"Ilja",
""
],
[
"Kungl",
"Akos F.",
""
],
[
"Baumbach",
"Andreas",
""
],
[
"Breitwieser",
"Oliver",
""
],
[
"Senn",
"Walter",
""
],
[
"Schemmel",
"Johannes",
""
],
... | An increasing body of evidence suggests that the trial-to-trial variability of spiking activity in the brain is not mere noise, but rather the reflection of a sampling-based encoding scheme for probabilistic computing. Since the precise statistical properties of neural activity are important in this context, many model... |
2310.16057 | Jonathon Mellor | Jonathon Mellor, Rachel Christie, James Guilder, Robert S Paton,
Suzanne Elgohari, Conall Watson, Sarah Deeny, Thomas Ward | Influenza Hospitalisations in England during the 2022/23 Season: do
different data sources drive divergence in modelled waves? A comparison of
surveillance and administrative data | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Accurate and representative data is vital for precisely reporting the impact
of influenza in healthcare systems. Northern hemisphere winter 2022/23
experienced the most substantial influenza wave since the COVID-19 pandemic
began in 2020. Simultaneously, new data streams become available within health
services becaus... | [
{
"created": "Mon, 16 Oct 2023 15:22:19 GMT",
"version": "v1"
}
] | 2023-10-26 | [
[
"Mellor",
"Jonathon",
""
],
[
"Christie",
"Rachel",
""
],
[
"Guilder",
"James",
""
],
[
"Paton",
"Robert S",
""
],
[
"Elgohari",
"Suzanne",
""
],
[
"Watson",
"Conall",
""
],
[
"Deeny",
"Sarah",
""
],
[
... | Accurate and representative data is vital for precisely reporting the impact of influenza in healthcare systems. Northern hemisphere winter 2022/23 experienced the most substantial influenza wave since the COVID-19 pandemic began in 2020. Simultaneously, new data streams become available within health services because ... |
1912.00672 | Zina Ibrahim | Zina Ibrahim and Honghan Wu and Ahmed Hamoud and Lukas Stappen and
Richard Dobson and Andrea Agarossi | On Classifying Sepsis Heterogeneity in the ICU: Insight Using Machine
Learning | 3 Figures and 2 tables. Accepted for publication at the Journal of
American Medical Informatics Association | Journal of the American Medical Informatics Association 27 (2020)
437-443 | 10.1093/jamia/ocz211 | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Current machine learning models aiming to predict sepsis from Electronic
Health Records (EHR) do not account for the heterogeneity of the condition,
despite its emerging importance in prognosis and treatment. This work
demonstrates the added value of stratifying the types of organ dysfunction
observed in patients who... | [
{
"created": "Mon, 2 Dec 2019 10:32:40 GMT",
"version": "v1"
},
{
"created": "Tue, 3 Dec 2019 12:42:51 GMT",
"version": "v2"
}
] | 2020-11-24 | [
[
"Ibrahim",
"Zina",
""
],
[
"Wu",
"Honghan",
""
],
[
"Hamoud",
"Ahmed",
""
],
[
"Stappen",
"Lukas",
""
],
[
"Dobson",
"Richard",
""
],
[
"Agarossi",
"Andrea",
""
]
] | Current machine learning models aiming to predict sepsis from Electronic Health Records (EHR) do not account for the heterogeneity of the condition, despite its emerging importance in prognosis and treatment. This work demonstrates the added value of stratifying the types of organ dysfunction observed in patients who d... |
1405.5128 | Michael Sadovsky | Michael G.Sadovsky | Evidence for strong co-evolution of mitochondrial and somatic genomes | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We studied a relations between the triplet frequency composition of
mitochondria genomes, and the phylogeny of their bearers. First, the clusters
in 63dimensional space were developed due to $K$-means. Second, the clade
composition of those clusters has been studied. It was found that genomes are
distributed among th... | [
{
"created": "Tue, 20 May 2014 15:35:01 GMT",
"version": "v1"
}
] | 2014-05-21 | [
[
"Sadovsky",
"Michael G.",
""
]
] | We studied a relations between the triplet frequency composition of mitochondria genomes, and the phylogeny of their bearers. First, the clusters in 63dimensional space were developed due to $K$-means. Second, the clade composition of those clusters has been studied. It was found that genomes are distributed among the ... |
1904.08094 | Atsushi Kamimura | Atsushi Kamimura and Kunihiko Kaneko | Molecular Diversity and Network Complexity in Growing Protocells | 16 pages, 7 figures, submitted for publication | null | null | null | q-bio.CB q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A great variety of molecular components is encapsulated in cells. Each of
these components is replicated for cell reproduction. To address an essential
role of the huge diversity of cellular components, we study a model of
protocells that convert resources into catalysts with the aid of a catalytic
reaction network. ... | [
{
"created": "Wed, 17 Apr 2019 06:02:19 GMT",
"version": "v1"
}
] | 2019-04-18 | [
[
"Kamimura",
"Atsushi",
""
],
[
"Kaneko",
"Kunihiko",
""
]
] | A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. As... |
2310.11854 | Dibakar Ghosh Dr. | Palash Kumar Pal, Md Sayeed Anwar and Dibakar Ghosh | Desynchrony induced by higher-order interactions in triplex
metapopulations | 12 Pages, 10 figures. Accepted for publication in Physical Review E,
2023 | null | null | null | q-bio.PE nlin.AO nlin.CD physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | In a predator-prey metapopulation, the two traits are adversely related:
synchronization and persistence. A decrease in synchrony apparently leads to an
increase in persistence and, therefore, necessitates the study of desynchrony
in a metapopulation. In this article, we study predator-prey patches that
communicate w... | [
{
"created": "Wed, 18 Oct 2023 10:09:03 GMT",
"version": "v1"
}
] | 2023-10-19 | [
[
"Pal",
"Palash Kumar",
""
],
[
"Anwar",
"Md Sayeed",
""
],
[
"Ghosh",
"Dibakar",
""
]
] | In a predator-prey metapopulation, the two traits are adversely related: synchronization and persistence. A decrease in synchrony apparently leads to an increase in persistence and, therefore, necessitates the study of desynchrony in a metapopulation. In this article, we study predator-prey patches that communicate wit... |
1704.02693 | Jiancheng Zhuang | Jiancheng Zhuang | Detecting neural activity and connectivity by perfusion-based fMRI | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This study proposes an approach to estimate the functional localization and
connectivity from CBF and BOLD signals simultaneously measured by ASL (arterial
spin labeling) MRI, especially using exploratory Structural Equation Modeling
analysis. In a visual task experiment, the primary visual cortices were located
by a... | [
{
"created": "Mon, 10 Apr 2017 03:23:16 GMT",
"version": "v1"
}
] | 2017-04-11 | [
[
"Zhuang",
"Jiancheng",
""
]
] | This study proposes an approach to estimate the functional localization and connectivity from CBF and BOLD signals simultaneously measured by ASL (arterial spin labeling) MRI, especially using exploratory Structural Equation Modeling analysis. In a visual task experiment, the primary visual cortices were located by ana... |
2301.06692 | Yue Wang | Yue Wang and Siqi He | Using Fano factors to determine certain types of gene autoregulation | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | The expression of one gene might be regulated by its corresponding protein,
which is called autoregulation. Although gene regulation is a central topic in
biology, autoregulation is much less studied. In general, it is extremely
difficult to determine the existence of autoregulation with direct biochemical
approaches... | [
{
"created": "Tue, 17 Jan 2023 04:13:09 GMT",
"version": "v1"
},
{
"created": "Thu, 30 Mar 2023 02:15:49 GMT",
"version": "v2"
}
] | 2023-03-31 | [
[
"Wang",
"Yue",
""
],
[
"He",
"Siqi",
""
]
] | The expression of one gene might be regulated by its corresponding protein, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult to determine the existence of autoregulation with direct biochemical approaches. ... |
1811.11443 | Irina Mizeva | Irina A. Mizeva, Elena V. Potapova, Viktor V. Dremin, Evgeny A.
Zherebtsov, Mikhail A. Mezentsev, Valerii V. Shupletsov, Andrey V. Dunaev | Optical probe pressure effects on cutaneous blood flow | 8 pages, 6 figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The variation of blood flow characteristics caused by the probe pressure
during noninvasive studies is of particular interest within the context of
fundamental and applied research. It has been shown previously that the weak
local pressure induces vasodilation, whereas the increased pressure is able to
stop the blood... | [
{
"created": "Wed, 28 Nov 2018 08:38:59 GMT",
"version": "v1"
}
] | 2018-11-29 | [
[
"Mizeva",
"Irina A.",
""
],
[
"Potapova",
"Elena V.",
""
],
[
"Dremin",
"Viktor V.",
""
],
[
"Zherebtsov",
"Evgeny A.",
""
],
[
"Mezentsev",
"Mikhail A.",
""
],
[
"Shupletsov",
"Valerii V.",
""
],
[
"Dunaev",
"... | The variation of blood flow characteristics caused by the probe pressure during noninvasive studies is of particular interest within the context of fundamental and applied research. It has been shown previously that the weak local pressure induces vasodilation, whereas the increased pressure is able to stop the blood f... |
q-bio/0509036 | Felix Naef | Jacques Rougemont and Felix Naef | Collective synchronization in populations of globally coupled phase
oscillators with drifting frequencies | 5 pages, 5 figures, accepted in Phys. Rev. E | null | 10.1103/PhysRevE.73.011104 | null | q-bio.QM cond-mat.stat-mech | null | We generalize the Kuramoto model for coupled phase oscillators by allowing
the frequencies to drift in time according to Ornstein-Uhlenbeck dynamics. Such
drifting frequencies were recently measured in cellular populations of
circadian oscillator and inspired our work. Linear stability analysis of the
Fokker-Planck e... | [
{
"created": "Tue, 27 Sep 2005 13:14:12 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Nov 2005 14:13:27 GMT",
"version": "v2"
}
] | 2009-11-11 | [
[
"Rougemont",
"Jacques",
""
],
[
"Naef",
"Felix",
""
]
] | We generalize the Kuramoto model for coupled phase oscillators by allowing the frequencies to drift in time according to Ornstein-Uhlenbeck dynamics. Such drifting frequencies were recently measured in cellular populations of circadian oscillator and inspired our work. Linear stability analysis of the Fokker-Planck equ... |
2011.02081 | Matthew Aguirre | Matthew Aguirre, Jan Sokol, Guhan Venkataraman, Alexander Ioannidis | A deep learning classifier for local ancestry inference | Accepted to Learning Meaningful Representations of Life (LMRL),
Workshop at the 34th Conference on Neural Information Processing Systems
(NeurIPS 2020), Vancouver, Canada | null | null | null | q-bio.GN cs.LG cs.NE | http://creativecommons.org/licenses/by/4.0/ | Local ancestry inference (LAI) identifies the ancestry of each segment of an
individual's genome and is an important step in medical and population genetic
studies of diverse cohorts. Several techniques have been used for LAI,
including Hidden Markov Models and Random Forests. Here, we formulate the LAI
task as an im... | [
{
"created": "Wed, 4 Nov 2020 00:42:01 GMT",
"version": "v1"
}
] | 2020-11-05 | [
[
"Aguirre",
"Matthew",
""
],
[
"Sokol",
"Jan",
""
],
[
"Venkataraman",
"Guhan",
""
],
[
"Ioannidis",
"Alexander",
""
]
] | Local ancestry inference (LAI) identifies the ancestry of each segment of an individual's genome and is an important step in medical and population genetic studies of diverse cohorts. Several techniques have been used for LAI, including Hidden Markov Models and Random Forests. Here, we formulate the LAI task as an imag... |
1408.6849 | Liane Gabora | Nicole Carbert, Liane Gabora, Jasmine Schwartz, and Apara Ranjan | Cognitive States of Potentiality in Art-making | 6 pages | Carbert, N., Gabora, L., Schwartz, J., & Ranjan, A. (2014). States
of cognitive potentiality in art-making. Proceedings of the AIEA Congress on
Empirical Aesthetics (pp. 121-126). Held August 22-24, New York | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Creativity is thought to involve searching and selecting amongst multiple
discrete idea candidates. Honing theory predicts that it involves actualizing
the potentiality of as few as a single ill-defined idea by viewing it from
different contexts. This paper reports on a study that tests between these
theories. Partic... | [
{
"created": "Thu, 28 Aug 2014 20:05:17 GMT",
"version": "v1"
}
] | 2014-09-01 | [
[
"Carbert",
"Nicole",
""
],
[
"Gabora",
"Liane",
""
],
[
"Schwartz",
"Jasmine",
""
],
[
"Ranjan",
"Apara",
""
]
] | Creativity is thought to involve searching and selecting amongst multiple discrete idea candidates. Honing theory predicts that it involves actualizing the potentiality of as few as a single ill-defined idea by viewing it from different contexts. This paper reports on a study that tests between these theories. Particip... |
1907.03512 | S Chatterjee | S. Chatterjee, B. S. Sanjeev | Role of Toll-Like Receptors in the interplay between pathogen and damage
associated molecular patterns | 10 pages, 11 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Various theoretical studies have been carried out to infer relevant
protein-protein interactions among pathogens and their hosts. Such studies are
generally based on preferential attachment of bacteria / virus to their human
receptor homologs. We have analyzed 17 pathogenic species mainly belonging to
bacterial and v... | [
{
"created": "Mon, 8 Jul 2019 11:13:31 GMT",
"version": "v1"
}
] | 2019-07-09 | [
[
"Chatterjee",
"S.",
""
],
[
"Sanjeev",
"B. S.",
""
]
] | Various theoretical studies have been carried out to infer relevant protein-protein interactions among pathogens and their hosts. Such studies are generally based on preferential attachment of bacteria / virus to their human receptor homologs. We have analyzed 17 pathogenic species mainly belonging to bacterial and vir... |
2405.12422 | Wera M Schmerer | Wera M Schmerer | Extraction of Human DNA from Soil: Protocol Adaptations | 11 pages, 3 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | PCR-based analysis of DNA is utilized in a wide variety of fields, including
Forensic Science. Aside from the more common ample sources, material analyzed
here can refer to specimen excavated from a soil environment, or a sampling of
the soil itself to recover DNA leached into the soil from decomposing human
remains ... | [
{
"created": "Tue, 21 May 2024 00:01:06 GMT",
"version": "v1"
}
] | 2024-05-22 | [
[
"Schmerer",
"Wera M",
""
]
] | PCR-based analysis of DNA is utilized in a wide variety of fields, including Forensic Science. Aside from the more common ample sources, material analyzed here can refer to specimen excavated from a soil environment, or a sampling of the soil itself to recover DNA leached into the soil from decomposing human remains or... |
2402.18396 | Gabriele Corso | Gabriele Corso, Arthur Deng, Benjamin Fry, Nicholas Polizzi, Regina
Barzilay, Tommi Jaakkola | Deep Confident Steps to New Pockets: Strategies for Docking
Generalization | null | International Conference on Learning Representations 2024 | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Accurate blind docking has the potential to lead to new biological
breakthroughs, but for this promise to be realized, docking methods must
generalize well across the proteome. Existing benchmarks, however, fail to
rigorously assess generalizability. Therefore, we develop DockGen, a new
benchmark based on the ligand-... | [
{
"created": "Wed, 28 Feb 2024 15:15:23 GMT",
"version": "v1"
}
] | 2024-02-29 | [
[
"Corso",
"Gabriele",
""
],
[
"Deng",
"Arthur",
""
],
[
"Fry",
"Benjamin",
""
],
[
"Polizzi",
"Nicholas",
""
],
[
"Barzilay",
"Regina",
""
],
[
"Jaakkola",
"Tommi",
""
]
] | Accurate blind docking has the potential to lead to new biological breakthroughs, but for this promise to be realized, docking methods must generalize well across the proteome. Existing benchmarks, however, fail to rigorously assess generalizability. Therefore, we develop DockGen, a new benchmark based on the ligand-bi... |
2408.01949 | Jonathan Kadmon | Jonathan Kadmon | Efficient coding with chaotic neural networks: A journey from
neuroscience to physics and back | null | null | null | null | q-bio.NC nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This essay, derived from a lecture at "The Physics Modeling of Thought"
workshop in Berlin in winter 2023, explores the mutually beneficial
relationship between theoretical neuroscience and statistical physics through
the lens of efficient coding and computation in cortical circuits. It
highlights how the study of ne... | [
{
"created": "Sun, 4 Aug 2024 07:34:35 GMT",
"version": "v1"
}
] | 2024-08-06 | [
[
"Kadmon",
"Jonathan",
""
]
] | This essay, derived from a lecture at "The Physics Modeling of Thought" workshop in Berlin in winter 2023, explores the mutually beneficial relationship between theoretical neuroscience and statistical physics through the lens of efficient coding and computation in cortical circuits. It highlights how the study of neur... |
2405.14545 | Hongzhi Zhang | Hongzhi Zhang, Xiuwen Gong, Shirui Pan, Jia Wu, Bo Du, Wenbin Hu | A Cross-Field Fusion Strategy for Drug-Target Interaction Prediction | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Drug-target interaction (DTI) prediction is a critical component of the drug
discovery process. In the drug development engineering field, predicting novel
drug-target interactions is extremely crucial.However, although existing
methods have achieved high accuracy levels in predicting known drugs and drug
targets, th... | [
{
"created": "Thu, 23 May 2024 13:25:20 GMT",
"version": "v1"
}
] | 2024-05-24 | [
[
"Zhang",
"Hongzhi",
""
],
[
"Gong",
"Xiuwen",
""
],
[
"Pan",
"Shirui",
""
],
[
"Wu",
"Jia",
""
],
[
"Du",
"Bo",
""
],
[
"Hu",
"Wenbin",
""
]
] | Drug-target interaction (DTI) prediction is a critical component of the drug discovery process. In the drug development engineering field, predicting novel drug-target interactions is extremely crucial.However, although existing methods have achieved high accuracy levels in predicting known drugs and drug targets, they... |
2402.09703 | Claus Kadelka | Claus Kadelka and David Murrugarra | Canalization reduces the nonlinearity of regulation in biological
networks | 21 pages, 8 figures | null | null | null | q-bio.MN math.DS | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Biological networks such as gene regulatory networks possess desirable
properties. They are more robust and controllable than random networks. This
motivates the search for structural and dynamical features that evolution has
incorporated in biological networks. A recent meta-analysis of published,
expert-curated Boo... | [
{
"created": "Thu, 15 Feb 2024 04:38:26 GMT",
"version": "v1"
}
] | 2024-02-16 | [
[
"Kadelka",
"Claus",
""
],
[
"Murrugarra",
"David",
""
]
] | Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated in biological networks. A recent meta-analysis of published, expert-curated Boole... |
1608.02574 | Robert J. Gooding | Neil L Wesch, Laura J Burlock and Robert J Gooding | Critical Telomerase Activity for Uncontrolled Cell Growth | null | Physical Biology 13 (2016) 046005 | 10.1088/1478-3975/13/4/046005 | null | q-bio.MN q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The lengths of the telomere regions of chromosomes in a population of cells
are modelled using a chemical master equation formalism, from which the
evolution of the average number of cells of each telomere length is extracted.
In particular, the role of the telomere-elongating enzyme telomerase on these
dynamics is i... | [
{
"created": "Mon, 8 Aug 2016 19:56:42 GMT",
"version": "v1"
}
] | 2016-08-09 | [
[
"Wesch",
"Neil L",
""
],
[
"Burlock",
"Laura J",
""
],
[
"Gooding",
"Robert J",
""
]
] | The lengths of the telomere regions of chromosomes in a population of cells are modelled using a chemical master equation formalism, from which the evolution of the average number of cells of each telomere length is extracted. In particular, the role of the telomere-elongating enzyme telomerase on these dynamics is inv... |
1608.06305 | Benjamin Pope | Michael W. Dee and Benjamin J. S. Pope | Anchoring historical sequences using a new source of astro-chronological
tie-points | 11 pages, accepted to Royal Society Proc A | Proc. R. Soc. A 2016 472 20160263; Published 17 August 2016 | 10.1098/rspa.2016.0263 | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The discovery of past spikes in atmospheric radiocarbon activity, caused by
major solar energetic particle events, has opened up new possibilities for
high-precision chronometry. The two spikes, or Miyake Events, have now been
widely identified in tree-rings that grew in the years 775 and 994 CE.
Furthermore, all oth... | [
{
"created": "Wed, 17 Aug 2016 12:47:02 GMT",
"version": "v1"
}
] | 2016-08-24 | [
[
"Dee",
"Michael W.",
""
],
[
"Pope",
"Benjamin J. S.",
""
]
] | The discovery of past spikes in atmospheric radiocarbon activity, caused by major solar energetic particle events, has opened up new possibilities for high-precision chronometry. The two spikes, or Miyake Events, have now been widely identified in tree-rings that grew in the years 775 and 994 CE. Furthermore, all other... |
1512.04293 | Torbj{\o}rn V Ness | Torbj{\o}rn V Ness, Michiel W H Remme, Gaute T Einevoll | Active subthreshold dendritic conductances shape the local field
potential | null | J Physiol 2016, 594 (13) | 10.1113/JP272022 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The main contribution to the local field potential (LFP) is thought to stem
from synaptic input to neurons and the ensuing subthreshold dendritic
processing. The role of active dendritic conductances in shaping the LFP has
received little attention, even though such ion channels are known to affect
the subthreshold n... | [
{
"created": "Mon, 14 Dec 2015 13:02:56 GMT",
"version": "v1"
}
] | 2016-11-22 | [
[
"Ness",
"Torbjørn V",
""
],
[
"Remme",
"Michiel W H",
""
],
[
"Einevoll",
"Gaute T",
""
]
] | The main contribution to the local field potential (LFP) is thought to stem from synaptic input to neurons and the ensuing subthreshold dendritic processing. The role of active dendritic conductances in shaping the LFP has received little attention, even though such ion channels are known to affect the subthreshold neu... |
2310.01454 | Adrien Berquer | Adrien Berquer, Antoine Gazaix, Laura Czerniak, Valentin Dromard,
Guillaume Meire, Ga\"etan Rivi\`ere | Improving alkaline fen functioning and Liparis loeselii (L.) Rich., 1817
preservation: towards a better water level management | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Alkaline fens are known to be wetlands that host large quantities of carbon,
but also a huge biodiversity. However, anthropic pressures are degrading the
peatlands with drainage, and conversion to agriculture or urbanization. These
pressures induce externalities like a large release of greenhouse gas (GHG) by
peat mi... | [
{
"created": "Mon, 2 Oct 2023 09:25:13 GMT",
"version": "v1"
}
] | 2023-10-04 | [
[
"Berquer",
"Adrien",
""
],
[
"Gazaix",
"Antoine",
""
],
[
"Czerniak",
"Laura",
""
],
[
"Dromard",
"Valentin",
""
],
[
"Meire",
"Guillaume",
""
],
[
"Rivière",
"Gaëtan",
""
]
] | Alkaline fens are known to be wetlands that host large quantities of carbon, but also a huge biodiversity. However, anthropic pressures are degrading the peatlands with drainage, and conversion to agriculture or urbanization. These pressures induce externalities like a large release of greenhouse gas (GHG) by peat mine... |
0806.3340 | Vladimir Ivancevic | Vladimir G. Ivancevic | New Mechanics of Spinal Injury | 14 pages, 1 figure, Latex | null | 10.1142/S1758825109000174 | null | q-bio.TO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The prediction and prevention of spinal injury is an important aspect of
preventive health science. The spine, or vertebral column, represents a chain
of 26 movable vertebral bodies, joint together by transversal viscoelastic
intervertebral discs and longitudinal elastic tendons. This paper proposes a
new locally-cou... | [
{
"created": "Fri, 20 Jun 2008 08:08:10 GMT",
"version": "v1"
},
{
"created": "Fri, 4 Jul 2008 03:31:30 GMT",
"version": "v2"
},
{
"created": "Thu, 10 Jul 2008 02:38:32 GMT",
"version": "v3"
},
{
"created": "Mon, 4 Aug 2008 04:59:08 GMT",
"version": "v4"
},
{
"cre... | 2015-05-13 | [
[
"Ivancevic",
"Vladimir G.",
""
]
] | The prediction and prevention of spinal injury is an important aspect of preventive health science. The spine, or vertebral column, represents a chain of 26 movable vertebral bodies, joint together by transversal viscoelastic intervertebral discs and longitudinal elastic tendons. This paper proposes a new locally-coupl... |
0803.1923 | Adam Barrett | Adam B. Barrett and M.C.W. van Rossum | Shannon Information Capacity of Discrete Synapses | 5 pages, 2 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There is evidence that biological synapses have only a fixed number of
discrete weight states. Memory storage with such synapses behaves quite
differently from synapses with unbounded, continuous weights as old memories
are automatically overwritten by new memories. We calculate the storage
capacity of discrete, boun... | [
{
"created": "Thu, 13 Mar 2008 09:15:27 GMT",
"version": "v1"
}
] | 2008-03-14 | [
[
"Barrett",
"Adam B.",
""
],
[
"van Rossum",
"M. C. W.",
""
]
] | There is evidence that biological synapses have only a fixed number of discrete weight states. Memory storage with such synapses behaves quite differently from synapses with unbounded, continuous weights as old memories are automatically overwritten by new memories. We calculate the storage capacity of discrete, bounde... |
1409.0024 | Maria Fabiana Laguna | M. F. Laguna, G. Abramson, M. N. Kuperman, J. L. Lanata and J. A.
Monjeau | Mathematical model of livestock and wildlife: Predation and competition
under environmental disturbances | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inspired by real scenarios in Northern Patagonia, we analyze a mathematical
model of a simple trophic web with two herbivores and one predator. The studied
situations represent a common practice in the steppes of Argentine Patagonia,
where livestock are raised in a semi-wild state, either on the open range or
enclose... | [
{
"created": "Fri, 29 Aug 2014 20:12:05 GMT",
"version": "v1"
},
{
"created": "Wed, 4 Feb 2015 16:57:18 GMT",
"version": "v2"
}
] | 2015-02-05 | [
[
"Laguna",
"M. F.",
""
],
[
"Abramson",
"G.",
""
],
[
"Kuperman",
"M. N.",
""
],
[
"Lanata",
"J. L.",
""
],
[
"Monjeau",
"J. A.",
""
]
] | Inspired by real scenarios in Northern Patagonia, we analyze a mathematical model of a simple trophic web with two herbivores and one predator. The studied situations represent a common practice in the steppes of Argentine Patagonia, where livestock are raised in a semi-wild state, either on the open range or enclosed,... |
1702.02876 | Esteban Vargas Bernal | Esteban Vargas and Camilo Sanabria | The role of disease cycles in the endemicity of infectious diseases | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Vector-borne diseases with reservoir cycles are complex to understand because
new infections come from contacts of the vector with humans and different
reservoirs. In this scenario, the basic reproductive number $\mathcal{R}^h_0$
of the system where the reservoirs are not included could turn out to be less
than one, ... | [
{
"created": "Wed, 8 Feb 2017 03:50:33 GMT",
"version": "v1"
}
] | 2017-02-10 | [
[
"Vargas",
"Esteban",
""
],
[
"Sanabria",
"Camilo",
""
]
] | Vector-borne diseases with reservoir cycles are complex to understand because new infections come from contacts of the vector with humans and different reservoirs. In this scenario, the basic reproductive number $\mathcal{R}^h_0$ of the system where the reservoirs are not included could turn out to be less than one, ye... |
1204.3670 | Svetlana Poznanovik | Svetlana Poznanovik and Christine E. Heitsch | Asymptotic distribution of motifs in a stochastic context-free grammar
model of RNA folding | 22 pages, 3 figures | null | null | null | q-bio.BM math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze the distribution of RNA secondary structures given by the
Knudsen-Hein stochastic context-free grammar used in the prediction program
Pfold. We prove that the distribution of base pairs, helices and various types
of loops in RNA secondary structures in this probabilistic model is
asymptotically Gaussian, f... | [
{
"created": "Mon, 16 Apr 2012 23:34:39 GMT",
"version": "v1"
}
] | 2012-04-18 | [
[
"Poznanovik",
"Svetlana",
""
],
[
"Heitsch",
"Christine E.",
""
]
] | We analyze the distribution of RNA secondary structures given by the Knudsen-Hein stochastic context-free grammar used in the prediction program Pfold. We prove that the distribution of base pairs, helices and various types of loops in RNA secondary structures in this probabilistic model is asymptotically Gaussian, for... |
2004.08588 | Sumit Kumar | Sumit Kumar, Sandeep Sharma and Nitu Kumari | Future of COVID-19 in Italy: A mathematical perspective | null | Mathematical Engineering. Springer, Singapore. (2021) 101--124 | 10.1007/978-981-33-6264-2_6 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have proposed an SEIR compartmental mathematical model. The prime
objective of this study is to analyze and forecast the pandemic in Italy for
the upcoming months. The basic reproduction number has been calculated. Based
on the current situation in Italy, in this paper, we will estimate the possible
time for the e... | [
{
"created": "Sat, 18 Apr 2020 10:44:03 GMT",
"version": "v1"
}
] | 2021-04-06 | [
[
"Kumar",
"Sumit",
""
],
[
"Sharma",
"Sandeep",
""
],
[
"Kumari",
"Nitu",
""
]
] | We have proposed an SEIR compartmental mathematical model. The prime objective of this study is to analyze and forecast the pandemic in Italy for the upcoming months. The basic reproduction number has been calculated. Based on the current situation in Italy, in this paper, we will estimate the possible time for the end... |
2405.18639 | Brian Yuan | Brian A. Yuan, Joseph G. Makin | Improving Speech Decoding from ECoG with Self-Supervised Pretraining | null | null | null | null | q-bio.NC cs.CL cs.LG cs.SD eess.AS | http://creativecommons.org/licenses/by/4.0/ | Recent work on intracranial brain-machine interfaces has demonstrated that
spoken speech can be decoded with high accuracy, essentially by treating the
problem as an instance of supervised learning and training deep neural networks
to map from neural activity to text. However, such networks pay for their
expressivene... | [
{
"created": "Tue, 28 May 2024 22:48:53 GMT",
"version": "v1"
}
] | 2024-05-30 | [
[
"Yuan",
"Brian A.",
""
],
[
"Makin",
"Joseph G.",
""
]
] | Recent work on intracranial brain-machine interfaces has demonstrated that spoken speech can be decoded with high accuracy, essentially by treating the problem as an instance of supervised learning and training deep neural networks to map from neural activity to text. However, such networks pay for their expressiveness... |
1201.1740 | Bao-quan Ai | Bao-quan Ai and Shi-liang Zhu | Quantum scattering model of energy transfer in photosynthetic complexes | 5 pages, 3 figures | Laser Physics Letters 12 (2015) 125201 | 10.1088/1612-2011/12/12/125201 | null | q-bio.BM physics.chem-ph quant-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop a quantum scattering model to describe the exciton transport
through the Fenna-Matthews-Olson(FMO) complex. It is found that the exciton
transport involved the optimal quantum coherence is more efficient than that
involved classical behavior alone. Furthermore, we also find that the quantum
resonance condi... | [
{
"created": "Mon, 9 Jan 2012 11:38:42 GMT",
"version": "v1"
}
] | 2016-12-28 | [
[
"Ai",
"Bao-quan",
""
],
[
"Zhu",
"Shi-liang",
""
]
] | We develop a quantum scattering model to describe the exciton transport through the Fenna-Matthews-Olson(FMO) complex. It is found that the exciton transport involved the optimal quantum coherence is more efficient than that involved classical behavior alone. Furthermore, we also find that the quantum resonance conditi... |
2010.15308 | Kohei Ichikawa | Kohei Ichikawa and Kunihiko Kaneko | Short term memory by transient oscillatory dynamics in recurrent neural
networks | null | Phys. Rev. Research 3, 033193 (2021) | 10.1103/PhysRevResearch.3.033193 | null | q-bio.NC nlin.AO | http://creativecommons.org/licenses/by/4.0/ | Despite the significance of short-term memory in cognitive function, the
process of encoding and sustaining the input information in neural activity
dynamics remains elusive. Herein, we unveiled the significance of transient
neural dynamics to short-term memory. By training recurrent neural networks to
short-term mem... | [
{
"created": "Thu, 29 Oct 2020 01:50:34 GMT",
"version": "v1"
},
{
"created": "Sat, 14 Aug 2021 01:30:09 GMT",
"version": "v2"
}
] | 2021-09-01 | [
[
"Ichikawa",
"Kohei",
""
],
[
"Kaneko",
"Kunihiko",
""
]
] | Despite the significance of short-term memory in cognitive function, the process of encoding and sustaining the input information in neural activity dynamics remains elusive. Herein, we unveiled the significance of transient neural dynamics to short-term memory. By training recurrent neural networks to short-term memor... |
q-bio/0611073 | Eugene Shakhnovich | Stefan Wallin, Konstantin B Zeldovich, Eugene I Shakhnovich | The folding mechanics of a knotted protein | null | null | null | null | q-bio.BM | null | An increasing number of proteins are being discovered with a remarkable and
somewhat surprising feature, a knot in their native structures. How the
polypeptide chain is able to knot itself during the folding process to form
these highly intricate protein topologies is not known. Here, we perform a
computational study... | [
{
"created": "Wed, 22 Nov 2006 23:59:54 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Wallin",
"Stefan",
""
],
[
"Zeldovich",
"Konstantin B",
""
],
[
"Shakhnovich",
"Eugene I",
""
]
] | An increasing number of proteins are being discovered with a remarkable and somewhat surprising feature, a knot in their native structures. How the polypeptide chain is able to knot itself during the folding process to form these highly intricate protein topologies is not known. Here, we perform a computational study o... |
1611.05474 | Rubem Mondaini | R.P. Mondaini, S.C. de Albuquerque Neto (Federal University of Rio de
Janeiro, Rio de Janeiro, RJ, Brazil) | The Pattern Recognition of Probability Distributions of Amino acids in
protein families | 20 pages, 13 figures, 02 tables | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A pattern Recognition of a probability distribution of amino acids is
obtained for selected families of proteins. The mathematical model is derived
from a theory of protein families formation which is derived from application
of a Pauli's master equation method.
| [
{
"created": "Thu, 13 Oct 2016 23:52:41 GMT",
"version": "v1"
}
] | 2016-11-18 | [
[
"Mondaini",
"R. P.",
"",
"Federal University of Rio de\n Janeiro, Rio de Janeiro, RJ, Brazil"
],
[
"Neto",
"S. C. de Albuquerque",
"",
"Federal University of Rio de\n Janeiro, Rio de Janeiro, RJ, Brazil"
]
] | A pattern Recognition of a probability distribution of amino acids is obtained for selected families of proteins. The mathematical model is derived from a theory of protein families formation which is derived from application of a Pauli's master equation method. |
2107.11381 | Seonwoo Min | Seonwoo Min, Byunghan Lee, and Sungroh Yoon | TargetNet: Functional microRNA Target Prediction with Deep Neural
Networks | This article has been accepted for publication in Bioinformatics
published by Oxford University Press | null | null | null | q-bio.GN cs.AI cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Motivation: MicroRNAs (miRNAs) play pivotal roles in gene expression
regulation by binding to target sites of messenger RNAs (mRNAs). While
identifying functional targets of miRNAs is of utmost importance, their
prediction remains a great challenge. Previous computational algorithms have
major limitations. They use c... | [
{
"created": "Fri, 23 Jul 2021 07:31:23 GMT",
"version": "v1"
},
{
"created": "Wed, 13 Oct 2021 06:31:29 GMT",
"version": "v2"
}
] | 2021-10-14 | [
[
"Min",
"Seonwoo",
""
],
[
"Lee",
"Byunghan",
""
],
[
"Yoon",
"Sungroh",
""
]
] | Motivation: MicroRNAs (miRNAs) play pivotal roles in gene expression regulation by binding to target sites of messenger RNAs (mRNAs). While identifying functional targets of miRNAs is of utmost importance, their prediction remains a great challenge. Previous computational algorithms have major limitations. They use con... |
1902.02016 | Thomas Schneider | Thomas D. Schneider (1) and Vishnu Jejjala (2) ((1) National
Institutes of Health, (2) University of the Witwatersrand) | Restriction enzymes use a 24 dimensional coding space to recognize 6
base long DNA sequences | Version 1: 31 pages, 3 figures, 1 table; Version 2: 33 pages, 3
figures, 1 table, responses to reviewers, new refs | null | 10.1371/journal.pone.0222419 | null | q-bio.QM cs.IT math.IT | http://creativecommons.org/publicdomain/zero/1.0/ | Restriction enzymes recognize and bind to specific sequences on invading
bacteriophage DNA. Like a key in a lock, these proteins require many contacts
to specify the correct DNA sequence. Using information theory we develop an
equation that defines the number of independent contacts, which is the
dimensionality of th... | [
{
"created": "Wed, 6 Feb 2019 03:53:22 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Oct 2019 03:10:09 GMT",
"version": "v2"
}
] | 2019-10-31 | [
[
"Schneider",
"Thomas D.",
""
],
[
"Jejjala",
"Vishnu",
""
]
] | Restriction enzymes recognize and bind to specific sequences on invading bacteriophage DNA. Like a key in a lock, these proteins require many contacts to specify the correct DNA sequence. Using information theory we develop an equation that defines the number of independent contacts, which is the dimensionality of the ... |
1511.00953 | Sergio Gabriel Quesada Acuna | Juli\'an Monge-N\'ajera and Gabriela P\'erez-G\'omez | Urban vegetation change after a hundred years in a tropical city (San
Jos\'e de Costa Rica) | 20 pages, 19 figures | Rev. Biol. Trop. (Int. J. Trop. Biol. ISSN-0034-7744) Vol. 58 (4):
1367-1386, December 2010 | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Urban vegetation is of key importance because a large proportion of the human
population lives in cities. Nevertheless, urban vegetation is understudied
outside central Europe and particularly, little is known about the flora of
tropical Asian, African and Latin American cities. We present an estimate of
how the vege... | [
{
"created": "Tue, 3 Nov 2015 15:53:07 GMT",
"version": "v1"
}
] | 2015-11-04 | [
[
"Monge-Nájera",
"Julián",
""
],
[
"Pérez-Gómez",
"Gabriela",
""
]
] | Urban vegetation is of key importance because a large proportion of the human population lives in cities. Nevertheless, urban vegetation is understudied outside central Europe and particularly, little is known about the flora of tropical Asian, African and Latin American cities. We present an estimate of how the vegeta... |
1011.4794 | Michel Pleimling | Sara O. Case, Clinton H. Durney, Michel Pleimling, and R.K.P. Zia | Cyclic competition of four species: mean field theory and stochastic
evolution | 6 pages, 4 figures, to appear in EPL | EPL 92 (2010) 58003 | 10.1209/0295-5075/92/58003 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Generalizing the cyclically competing three-species model (often referred to
as the rock-paper-scissors game), we consider a simple system of population
dynamics without spatial structures that involves four species. Unlike the
previous model, the four form alliance pairs which resemble partnership in the
game of Bri... | [
{
"created": "Mon, 22 Nov 2010 13:06:07 GMT",
"version": "v1"
}
] | 2011-01-06 | [
[
"Case",
"Sara O.",
""
],
[
"Durney",
"Clinton H.",
""
],
[
"Pleimling",
"Michel",
""
],
[
"Zia",
"R. K. P.",
""
]
] | Generalizing the cyclically competing three-species model (often referred to as the rock-paper-scissors game), we consider a simple system of population dynamics without spatial structures that involves four species. Unlike the previous model, the four form alliance pairs which resemble partnership in the game of Bridg... |
0905.2071 | Fernando Falo | Diego Prada-Gracia, Jesus Gomez-Gardenes, Pablo Echenique and Fernando
Falo | Exploring the Free Energy Landscape: From Dynamics to Networks and Back | PLoS Computational Biology (in press) | PLoS Comput Biol 5(6): e1000415 (2009) | 10.1371/journal.pcbi.1000415 | null | q-bio.BM cond-mat.soft physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The knowledge of the Free Energy Landscape topology is the essential key to
understand many biochemical processes. The determination of the conformers of a
protein and their basins of attraction takes a central role for studying
molecular isomerization reactions. In this work, we present a novel framework
to unveil t... | [
{
"created": "Wed, 13 May 2009 11:36:28 GMT",
"version": "v1"
}
] | 2009-06-26 | [
[
"Prada-Gracia",
"Diego",
""
],
[
"Gomez-Gardenes",
"Jesus",
""
],
[
"Echenique",
"Pablo",
""
],
[
"Falo",
"Fernando",
""
]
] | The knowledge of the Free Energy Landscape topology is the essential key to understand many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the... |
0906.4683 | Sa\'ul Ares | G. Kalosakas and S. Ares | Dependence on temperature and GC content of bubble length distributions
in DNA | 8 pages, 6 figures. Published on The Journal of Chemical Physics | J. Chem. Phys. 130, 235104 (2009) | 10.1063/1.3149859 | null | q-bio.BM cond-mat.stat-mech nlin.PS physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present numerical results on the temperature dependence of the
distribution of bubble lengths in DNA segments of various guanine-cytosine (GC)
concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois
model and the corresponding thermal equilibrium distributions of bubbles are
obtained through... | [
{
"created": "Thu, 25 Jun 2009 12:42:55 GMT",
"version": "v1"
}
] | 2009-06-26 | [
[
"Kalosakas",
"G.",
""
],
[
"Ares",
"S.",
""
]
] | We present numerical results on the temperature dependence of the distribution of bubble lengths in DNA segments of various guanine-cytosine (GC) concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois model and the corresponding thermal equilibrium distributions of bubbles are obtained through M... |
2204.02474 | Hsu Kiang Ooi | Mohammad Sajjad Ghaemi, Karl Grantham, Isaac Tamblyn, Yifeng Li, Hsu
Kiang Ooi | Generative Enriched Sequential Learning (ESL) Approach for Molecular
Design via Augmented Domain Knowledge | 6 pages | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Deploying generative machine learning techniques to generate novel chemical
structures based on molecular fingerprint representation has been well
established in molecular design. Typically, sequential learning (SL) schemes
such as hidden Markov models (HMM) and, more recently, in the sequential deep
learning context... | [
{
"created": "Tue, 5 Apr 2022 20:16:11 GMT",
"version": "v1"
}
] | 2022-04-07 | [
[
"Ghaemi",
"Mohammad Sajjad",
""
],
[
"Grantham",
"Karl",
""
],
[
"Tamblyn",
"Isaac",
""
],
[
"Li",
"Yifeng",
""
],
[
"Ooi",
"Hsu Kiang",
""
]
] | Deploying generative machine learning techniques to generate novel chemical structures based on molecular fingerprint representation has been well established in molecular design. Typically, sequential learning (SL) schemes such as hidden Markov models (HMM) and, more recently, in the sequential deep learning context, ... |
1904.12914 | Robert Marsland III | Robert Marsland III and Wenping Cui and Pankaj Mehta | A minimal model for microbial biodiversity can reproduce experimentally
observed ecological patterns | 35 pages, 10 figures | Scientific Reports 10:3308 (2020) | 10.1038/s41598-020-60130-2 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP)
and the Human Microbiome Project (HMP) have revealed robust ecological patterns
across different environments. A major goal in ecology is to leverage these
patterns to identify the ecological processes shaping microbial ecosystems. One
promi... | [
{
"created": "Mon, 29 Apr 2019 19:18:43 GMT",
"version": "v1"
},
{
"created": "Fri, 3 May 2019 16:12:32 GMT",
"version": "v2"
},
{
"created": "Thu, 23 Jan 2020 22:42:13 GMT",
"version": "v3"
}
] | 2020-03-05 | [
[
"Marsland",
"Robert",
"III"
],
[
"Cui",
"Wenping",
""
],
[
"Mehta",
"Pankaj",
""
]
] | Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify the ecological processes shaping microbial ecosystems. One promisi... |
1611.02482 | Roland Kr\"amer | Ulrich Warttinger, Roland Kr\"amer | Quantification of heparin in complex matrices (including urine) using a
mix-and-read fluorescence assay | Article, 16 pages, 7 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Heparin is an important anticoagulant drug, about one billion doses are
produced annually. It is a polydisperse sulfated polysaccharide, and the
inherent heterogeneity makes the analysis of heparin difficult. The global
crisis resulting from adulterated heparin in 2008 has drawn renewed attention
to the challenges th... | [
{
"created": "Tue, 8 Nov 2016 11:29:04 GMT",
"version": "v1"
}
] | 2016-11-09 | [
[
"Warttinger",
"Ulrich",
""
],
[
"Krämer",
"Roland",
""
]
] | Heparin is an important anticoagulant drug, about one billion doses are produced annually. It is a polydisperse sulfated polysaccharide, and the inherent heterogeneity makes the analysis of heparin difficult. The global crisis resulting from adulterated heparin in 2008 has drawn renewed attention to the challenges that... |
2107.00719 | Po-Yu Kao | Po-Yu Kao, Shu-Min Kao, Nan-Lan Huang, Yen-Chu Lin | Toward Drug-Target Interaction Prediction via Ensemble Modeling and
Transfer Learning | 8 pages, 1 figure, 10 tables | null | 10.1109/BIBM52615.2021.9669729 | null | q-bio.BM cs.LG q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Drug-target interaction (DTI) prediction plays a crucial role in drug
discovery, and deep learning approaches have achieved state-of-the-art
performance in this field. We introduce an ensemble of deep learning models
(EnsembleDLM) for DTI prediction. EnsembleDLM only uses the sequence
information of chemical compound... | [
{
"created": "Fri, 2 Jul 2021 04:00:03 GMT",
"version": "v1"
},
{
"created": "Wed, 28 Jul 2021 02:14:55 GMT",
"version": "v2"
},
{
"created": "Fri, 19 Nov 2021 03:21:49 GMT",
"version": "v3"
}
] | 2022-01-19 | [
[
"Kao",
"Po-Yu",
""
],
[
"Kao",
"Shu-Min",
""
],
[
"Huang",
"Nan-Lan",
""
],
[
"Lin",
"Yen-Chu",
""
]
] | Drug-target interaction (DTI) prediction plays a crucial role in drug discovery, and deep learning approaches have achieved state-of-the-art performance in this field. We introduce an ensemble of deep learning models (EnsembleDLM) for DTI prediction. EnsembleDLM only uses the sequence information of chemical compounds ... |
1911.12279 | Thierry Mora | Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad,
Aleksandra M. Walczak, Thierry Mora | On generative models of T-cell receptor sequences | null | Phys. Rev. E 101, 062414 (2020) | 10.1103/PhysRevE.101.062414 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | T-cell receptors (TCR) are key proteins of the adaptive immune system,
generated randomly in each individual, whose diversity underlies our ability to
recognize infections and malignancies. Modeling the distribution of TCR
sequences is of key importance for immunology and medical applications. Here,
we compare two in... | [
{
"created": "Wed, 27 Nov 2019 16:49:52 GMT",
"version": "v1"
},
{
"created": "Fri, 13 Mar 2020 16:49:43 GMT",
"version": "v2"
}
] | 2020-07-01 | [
[
"Isacchini",
"Giulio",
""
],
[
"Sethna",
"Zachary",
""
],
[
"Elhanati",
"Yuval",
""
],
[
"Nourmohammad",
"Armita",
""
],
[
"Walczak",
"Aleksandra M.",
""
],
[
"Mora",
"Thierry",
""
]
] | T-cell receptors (TCR) are key proteins of the adaptive immune system, generated randomly in each individual, whose diversity underlies our ability to recognize infections and malignancies. Modeling the distribution of TCR sequences is of key importance for immunology and medical applications. Here, we compare two infe... |
2004.13024 | Giuseppe Gaeta | Mariano Cadoni, Giuseppe Gaeta | Size and timescale of epidemics in the SIR framework | 16 pages in PhysRev format, 12 figures; some superposition with
arXiv:2004.11633, in particular for the application part | Physica D 411 (2020) 132626 | 10.1016/j.physd.2020.132626 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The most important features to assess the severity of an epidemic are its
size and its timescale. We discuss these features in a systematic way in the
context of SIR and SIR-type models. We investigate in detail how the size and
timescale of the epidemic can be changed by acting on the parameters
characterizing the m... | [
{
"created": "Mon, 27 Apr 2020 09:23:29 GMT",
"version": "v1"
},
{
"created": "Sun, 7 Jun 2020 09:16:20 GMT",
"version": "v2"
}
] | 2020-06-29 | [
[
"Cadoni",
"Mariano",
""
],
[
"Gaeta",
"Giuseppe",
""
]
] | The most important features to assess the severity of an epidemic are its size and its timescale. We discuss these features in a systematic way in the context of SIR and SIR-type models. We investigate in detail how the size and timescale of the epidemic can be changed by acting on the parameters characterizing the mod... |
2404.09812 | Arkadiy Dushatskiy | Arkadiy Dushatskiy, Esther Julien, Leen Stougie, Leo van Iersel | Solving the Tree Containment Problem Using Graph Neural Networks | null | null | null | null | q-bio.PE cs.LG | http://creativecommons.org/licenses/by/4.0/ | Tree Containment is a fundamental problem in phylogenetics useful for
verifying a proposed phylogenetic network, representing the evolutionary
history of certain species. Tree Containment asks whether the given
phylogenetic tree (for instance, constructed from a DNA fragment showing
tree-like evolution) is contained ... | [
{
"created": "Mon, 15 Apr 2024 14:10:06 GMT",
"version": "v1"
},
{
"created": "Thu, 13 Jun 2024 09:20:40 GMT",
"version": "v2"
}
] | 2024-06-14 | [
[
"Dushatskiy",
"Arkadiy",
""
],
[
"Julien",
"Esther",
""
],
[
"Stougie",
"Leen",
""
],
[
"van Iersel",
"Leo",
""
]
] | Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for instance, constructed from a DNA fragment showing tree-like evolution) is contained in... |
2112.01987 | Jesse Marshall | Jesse D. Marshall, Tianqing Li, Joshua H. Wu, Timothy W. Dunn | Leaving Flatland: Advances in 3D behavioral measurement | 11 pages, 3 figures, 1 table, 1 box | null | null | null | q-bio.NC q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Animals move in three dimensions (3D). Thus, 3D measurement is necessary to
report the true kinematics of animal movement. Existing 3D measurement
techniques draw on specialized hardware, such as motion capture or depth
cameras, as well as deep multi-view and monocular computer vision. Continued
advances at the inter... | [
{
"created": "Fri, 3 Dec 2021 15:59:11 GMT",
"version": "v1"
}
] | 2021-12-06 | [
[
"Marshall",
"Jesse D.",
""
],
[
"Li",
"Tianqing",
""
],
[
"Wu",
"Joshua H.",
""
],
[
"Dunn",
"Timothy W.",
""
]
] | Animals move in three dimensions (3D). Thus, 3D measurement is necessary to report the true kinematics of animal movement. Existing 3D measurement techniques draw on specialized hardware, such as motion capture or depth cameras, as well as deep multi-view and monocular computer vision. Continued advances at the interse... |
0806.0449 | Nicanor Moldovan | Nicanor I. Moldovan | Anapedesis: Implications and Applications of Bio-Structural Robustness | null | null | null | null | q-bio.OT q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Here we develop an approach to bio-structural robustness integrated with
structure-function relationship in a unified conceptual and methodological
framework, and envision its study using adequate computational and experimental
methods. To distinguish this structural robustness from the abstract
organizational robust... | [
{
"created": "Tue, 3 Jun 2008 07:05:02 GMT",
"version": "v1"
},
{
"created": "Tue, 3 Jun 2008 23:09:43 GMT",
"version": "v2"
}
] | 2008-06-04 | [
[
"Moldovan",
"Nicanor I.",
""
]
] | Here we develop an approach to bio-structural robustness integrated with structure-function relationship in a unified conceptual and methodological framework, and envision its study using adequate computational and experimental methods. To distinguish this structural robustness from the abstract organizational robustne... |
q-bio/0509017 | Sandeep Krishna | Sandeep Krishna, Mogens H. Jensen, Kim Sneppen (Niels Bohr Institute,
Copenhagen, Denmark) | Spiky oscillations in NF-kB signalling | 11 pages, 13 figures | PNAS 2006 103: 10840-10845 | 10.1073/pnas.0604085103 | null | q-bio.MN cond-mat.other q-bio.OT | null | The NF-kB signalling system is involved in a variety of cellular processes
including immune response, inflammation, and apoptosis. Recent experiments have
found oscillations in the nuclear-cytoplasmic translocation of the NF-kB
transcription factor. How the cell uses the oscillations to differentiate input
conditions... | [
{
"created": "Wed, 14 Sep 2005 19:50:07 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Krishna",
"Sandeep",
"",
"Niels Bohr Institute,\n Copenhagen, Denmark"
],
[
"Jensen",
"Mogens H.",
"",
"Niels Bohr Institute,\n Copenhagen, Denmark"
],
[
"Sneppen",
"Kim",
"",
"Niels Bohr Institute,\n Copenhagen, Denmark"
]
] | The NF-kB signalling system is involved in a variety of cellular processes including immune response, inflammation, and apoptosis. Recent experiments have found oscillations in the nuclear-cytoplasmic translocation of the NF-kB transcription factor. How the cell uses the oscillations to differentiate input conditions a... |
q-bio/0702056 | Mark White MD | Mark White | The G-Ball, a New Icon for Codon Symmetry and the Genetic Code | PDF format, 82 pages and 33 figures. This is a low resolution
document. For a higher resolution document please contact the author | null | null | null | q-bio.OT | null | A codon table is a useful tool for mapping codons to amino acids as they have
been assigned by nature. It has become a scientific icon because of the way it
embodies our understanding of this natural process and the way it immediately
communicates this understanding. However, advancements in molecular biology
over th... | [
{
"created": "Mon, 26 Feb 2007 18:25:39 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"White",
"Mark",
""
]
] | A codon table is a useful tool for mapping codons to amino acids as they have been assigned by nature. It has become a scientific icon because of the way it embodies our understanding of this natural process and the way it immediately communicates this understanding. However, advancements in molecular biology over the ... |
0812.0841 | C.-M. Ghim | C.-M. Ghim, E. Almaas | Genetic noise control via protein oligomerization | null | BMC Systems Biology 2008, 2:94 | 10.1186/1752-0509-2-94 | null | q-bio.MN q-bio.CB | http://creativecommons.org/licenses/publicdomain/ | Gene expression in a cell entails random reaction events occurring over
disparate time scales. Thus, molecular noise that often results in phenotypic
and population-dynamic consequences sets a fundamental limit to biochemical
signaling. While there have been numerous studies correlating the architecture
of cellular r... | [
{
"created": "Thu, 4 Dec 2008 01:02:15 GMT",
"version": "v1"
}
] | 2009-02-19 | [
[
"Ghim",
"C. -M.",
""
],
[
"Almaas",
"E.",
""
]
] | Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling. While there have been numerous studies correlating the architecture of cellular rea... |
2110.11814 | Jingcheng Xu | Jingcheng Xu and C\'ecile An\'e | Identifiability of local and global features of phylogenetic networks
from average distances | null | null | null | null | q-bio.PE math.ST stat.TH | http://creativecommons.org/licenses/by/4.0/ | Phylogenetic networks extend phylogenetic trees to model non-vertical
inheritance, by which a lineage inherits material from multiple parents. The
computational complexity of estimating phylogenetic networks from genome-wide
data with likelihood-based methods limits the size of networks that can be
handled. Methods b... | [
{
"created": "Fri, 22 Oct 2021 14:36:59 GMT",
"version": "v1"
},
{
"created": "Sat, 25 Jun 2022 20:46:40 GMT",
"version": "v2"
}
] | 2022-06-28 | [
[
"Xu",
"Jingcheng",
""
],
[
"Ané",
"Cécile",
""
]
] | Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with likelihood-based methods limits the size of networks that can be handled. Methods bas... |
1905.07256 | Luciano Stucchi | Luciano Stucchi, Javier Galeano, Desiderio A. Vasquez | Pattern formation induced by intraspecific interactions in a
predator-prey system | 13 pages, 11 figures | Phys. Rev. E 100, 062414 (2019) | 10.1103/PhysRevE.100.062414 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Differential diffusion is a source of instability in population dynamics
systems when species diffuse with different rates. Predator-prey systems show
this instability only under certain specific conditions, usually requiring
Holling-type functionals involved. Here we study the effects of intraspecific
cooperation an... | [
{
"created": "Fri, 17 May 2019 13:35:20 GMT",
"version": "v1"
}
] | 2020-01-01 | [
[
"Stucchi",
"Luciano",
""
],
[
"Galeano",
"Javier",
""
],
[
"Vasquez",
"Desiderio A.",
""
]
] | Differential diffusion is a source of instability in population dynamics systems when species diffuse with different rates. Predator-prey systems show this instability only under certain specific conditions, usually requiring Holling-type functionals involved. Here we study the effects of intraspecific cooperation and ... |
0805.1859 | Leo van Iersel | Leo van Iersel and Steven Kelk | Constructing the Simplest Possible Phylogenetic Network from Triplets | The proof of Lemma 4 has been extended | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A phylogenetic network is a directed acyclic graph that visualises an
evolutionary history containing so-called reticulations such as recombinations,
hybridisations or lateral gene transfers. Here we consider the construction of
a simplest possible phylogenetic network consistent with an input set T, where
T contains... | [
{
"created": "Tue, 13 May 2008 14:02:30 GMT",
"version": "v1"
},
{
"created": "Fri, 16 May 2008 15:23:54 GMT",
"version": "v2"
}
] | 2008-05-16 | [
[
"van Iersel",
"Leo",
""
],
[
"Kelk",
"Steven",
""
]
] | A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest possible phylogenetic network consistent with an input set T, where T contains a... |
q-bio/0403041 | Anna Ochab-Marcinek | Anna Ochab-Marcinek, Ewa Gudowska-Nowak | Population growth and control in stochastic models of cancer development | Submitted to Physica A Corrected spelling errors. Title changed to
more appropriate for the content. Extended Conclusions section. Added a short
explanation about the meaning of parameters t_t and t_r. References collected
in proper order | Physica A 343 (2004) 557-572 | 10.1016/j.physa.2004.06.071 | null | q-bio.PE cond-mat.stat-mech | null | We study the joint effect of thermal bath fluctuations and an external noise
tuning activity of cytotoxic cells on the triggered immune response in a
growing cancerous tissue. The immune response is assumed to be primarily
mediated by effector cells that develop a cytotoxic activity against the
abnormal tissue. The k... | [
{
"created": "Mon, 29 Mar 2004 09:32:49 GMT",
"version": "v1"
},
{
"created": "Thu, 13 May 2004 13:46:24 GMT",
"version": "v2"
}
] | 2015-06-26 | [
[
"Ochab-Marcinek",
"Anna",
""
],
[
"Gudowska-Nowak",
"Ewa",
""
]
] | We study the joint effect of thermal bath fluctuations and an external noise tuning activity of cytotoxic cells on the triggered immune response in a growing cancerous tissue. The immune response is assumed to be primarily mediated by effector cells that develop a cytotoxic activity against the abnormal tissue. The kin... |
1109.3173 | Horacio Ceva | R.P.J. Perazzo, Laura Hern\'andez, Horacio Ceva, Enrique Burgos,
Jos\'e Ignacio Alvarez-Hamelin | Does Phylogenetic Proximity Explain Nestedness in Mutualistic
Ecosystems? | 9 pages, 4 figures. Keywords: Nested networks; Mutualistic
communities; Phylogenetic proximity; Ultrametricity. arXiv admin note: text
overlap with arXiv:1007.5519 | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate how the pattern of contacts between species in mutualistic
ecosystems is affected by the phylogenetic proximity between the species of
each guild. We develop a dynamical model geared to establish the role of such
proximity in the emergence of a nested pattern of contacts. We also define a
parameter tha... | [
{
"created": "Wed, 14 Sep 2011 19:27:28 GMT",
"version": "v1"
},
{
"created": "Thu, 6 Oct 2011 11:35:22 GMT",
"version": "v2"
},
{
"created": "Mon, 17 Oct 2011 18:03:24 GMT",
"version": "v3"
}
] | 2011-10-18 | [
[
"Perazzo",
"R. P. J.",
""
],
[
"Hernández",
"Laura",
""
],
[
"Ceva",
"Horacio",
""
],
[
"Burgos",
"Enrique",
""
],
[
"Alvarez-Hamelin",
"José Ignacio",
""
]
] | We investigate how the pattern of contacts between species in mutualistic ecosystems is affected by the phylogenetic proximity between the species of each guild. We develop a dynamical model geared to establish the role of such proximity in the emergence of a nested pattern of contacts. We also define a parameter that ... |
2003.02062 | Giuseppe Gaeta | Giuseppe Gaeta | Data analysis for the COVID-19 early dynamics in Northern Italy | 15 pages, 8 Figures. Analyzed data go until March 2 version 2: typos
corrected, discussion of SIR corrected and enlarged; data analyzed remain the
same | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The COVID-19 epidemics, started in China in January 2020, was recognized to
have reached Italy around February 20; recent estimates show that most probably
the virus circulated in the country already in January, but was not recognized.
Data for the early dynamics of COVID-19 in Northern Italy are analyzed.
| [
{
"created": "Wed, 4 Mar 2020 13:14:23 GMT",
"version": "v1"
},
{
"created": "Thu, 5 Mar 2020 18:31:36 GMT",
"version": "v2"
}
] | 2020-03-09 | [
[
"Gaeta",
"Giuseppe",
""
]
] | The COVID-19 epidemics, started in China in January 2020, was recognized to have reached Italy around February 20; recent estimates show that most probably the virus circulated in the country already in January, but was not recognized. Data for the early dynamics of COVID-19 in Northern Italy are analyzed. |
2001.03656 | Sungwoo Ahn | Sungwoo Ahn, Leonid L Rubchinsky | Temporal patterns of dispersal-induced synchronization in population
dynamics | null | J Theor Biol 490:110159, 2020 | 10.1016/j.jtbi.2020.110159 | null | q-bio.PE nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The mechanisms and properties of synchronization of oscillating ecological
populations attract attention because it is a fairly common phenomenon and
because spatial synchrony may elevate a risk of extinction and may lead to
other environmental impacts. Conditions for stable synchronization in a system
of linearly co... | [
{
"created": "Fri, 10 Jan 2020 20:28:05 GMT",
"version": "v1"
}
] | 2021-04-26 | [
[
"Ahn",
"Sungwoo",
""
],
[
"Rubchinsky",
"Leonid L",
""
]
] | The mechanisms and properties of synchronization of oscillating ecological populations attract attention because it is a fairly common phenomenon and because spatial synchrony may elevate a risk of extinction and may lead to other environmental impacts. Conditions for stable synchronization in a system of linearly coup... |
1507.00327 | Vince Grolmusz | Csaba Kerepesi and Bal\'azs Szalkai and B\'alint Varga and Vince
Grolmusz | Comparative Connectomics: Mapping the Inter-Individual Variability of
Connections within the Regions of the Human Brain | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human braingraph, or connectome is a description of the connections of
the brain: the nodes of the graph correspond to small areas of the gray matter,
and two nodes are connected by an edge if a diffusion MRI-based workflow finds
fibers between those brain areas. We have constructed 1015-vertex graphs from
the di... | [
{
"created": "Wed, 1 Jul 2015 19:39:51 GMT",
"version": "v1"
}
] | 2015-07-02 | [
[
"Kerepesi",
"Csaba",
""
],
[
"Szalkai",
"Balázs",
""
],
[
"Varga",
"Bálint",
""
],
[
"Grolmusz",
"Vince",
""
]
] | The human braingraph, or connectome is a description of the connections of the brain: the nodes of the graph correspond to small areas of the gray matter, and two nodes are connected by an edge if a diffusion MRI-based workflow finds fibers between those brain areas. We have constructed 1015-vertex graphs from the diff... |
0912.2288 | Hugo Gabriel Eyherabide | Hugo Gabriel Eyherabide, Ines Samengo | The information transmitted by spike patterns in single neurons | To be published in Journal of Physiology Paris 2009 | null | 10.1016/j.jphysparis.2009.11.018 | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spike patterns have been reported to encode sensory information in several
brain areas. Here we assess the role of specific patterns in the neural code,
by comparing the amount of information transmitted with different choices of
the readout neural alphabet. This allows us to rank several alternative
alphabets depend... | [
{
"created": "Fri, 11 Dec 2009 17:29:02 GMT",
"version": "v1"
}
] | 2009-12-14 | [
[
"Eyherabide",
"Hugo Gabriel",
""
],
[
"Samengo",
"Ines",
""
]
] | Spike patterns have been reported to encode sensory information in several brain areas. Here we assess the role of specific patterns in the neural code, by comparing the amount of information transmitted with different choices of the readout neural alphabet. This allows us to rank several alternative alphabets dependin... |
1809.09757 | Joaquin Goni | Diana O. Svaldi, Joaqu\'in Go\~ni, Apoorva Bharthur Sanjay, Enrico
Amico, Shannon L. Risacher, John D. West, Mario Dzemidzic, Andrew Saykin,
Liana Apostolova | Towards Subject and Diagnostic Identifiability in the Alzheimer's
Disease Spectrum based on Functional Connectomes | 8 pages, 3 tables, 3 figures | In: Stoyanov D. et al. (eds) Graphs in Biomedical Image Analysis
and Integrating Medical Imaging and Non-Imaging Modalities. GRAIL 2018,
Beyond MIC 2018. Lecture Notes in Computer Science, vol 11044. Springer, Cham | 10.1007/978-3-030-00689-1_8 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Alzheimer's disease (AD) is the only major cause of mortality in the world
without an effective disease modifying treatment. Evidence supporting the so
called disconnection hypothesis suggests that functional connectivity
biomarkers may have clinical potential for early detection of AD. However,
known issues with low... | [
{
"created": "Tue, 25 Sep 2018 23:28:32 GMT",
"version": "v1"
}
] | 2018-09-27 | [
[
"Svaldi",
"Diana O.",
""
],
[
"Goñi",
"Joaquín",
""
],
[
"Sanjay",
"Apoorva Bharthur",
""
],
[
"Amico",
"Enrico",
""
],
[
"Risacher",
"Shannon L.",
""
],
[
"West",
"John D.",
""
],
[
"Dzemidzic",
"Mario",
"... | Alzheimer's disease (AD) is the only major cause of mortality in the world without an effective disease modifying treatment. Evidence supporting the so called disconnection hypothesis suggests that functional connectivity biomarkers may have clinical potential for early detection of AD. However, known issues with low t... |
q-bio/0311002 | Debashish Chowdhury | Debashish Chowdhury and Dietrich Stauffer | Computer simulations of history of life: speciation, emergence of
complex species from simpler organisms, and extinctions | 7 pages, including 4 EPS figures, REVTEX | null | 10.1016/j.physa.2004.05.023 | null | q-bio.PE | null | We propose a generic model of eco-systems, with a {\it hierarchical} food web
structure. In our computer simulations we let the eco-system evolve
continuously for so long that that we can monitor extinctions as well as
speciations over geological time scales. {\it Speciation} leads not only to
horizontal diversificat... | [
{
"created": "Tue, 4 Nov 2003 22:13:28 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Chowdhury",
"Debashish",
""
],
[
"Stauffer",
"Dietrich",
""
]
] | We propose a generic model of eco-systems, with a {\it hierarchical} food web structure. In our computer simulations we let the eco-system evolve continuously for so long that that we can monitor extinctions as well as speciations over geological time scales. {\it Speciation} leads not only to horizontal diversificatio... |
q-bio/0601004 | Paul Smolen | Paul Smolen, Douglas A. Baxter, and John H. Byrne | A Model of the Roles of Essential Kinases in the Induction and
Expression of Late Long-Term Potentiation | Accepted to Biophysical Journal. Single PDF, 7 figs included | null | 10.1529/biophysj.105.072470 | null | q-bio.NC q-bio.MN | null | The induction of late long-term potentiation (L-LTP) involves complex
interactions among second messenger cascades. To gain insights into these
interactions, a mathematical model was developed for L-LTP induction in the CA1
region of the hippocampus. The differential equation-based model represents
actions of protein... | [
{
"created": "Tue, 3 Jan 2006 23:51:32 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Smolen",
"Paul",
""
],
[
"Baxter",
"Douglas A.",
""
],
[
"Byrne",
"John H.",
""
]
] | The induction of late long-term potentiation (L-LTP) involves complex interactions among second messenger cascades. To gain insights into these interactions, a mathematical model was developed for L-LTP induction in the CA1 region of the hippocampus. The differential equation-based model represents actions of protein k... |
1309.4661 | John Helliwell R | Simon W.M Tanley, Kay Diederichs, Loes M.J Kroon-Batenburg, Antoine
M.M Schreurs and John R Helliwell | Carboplatin binding to a model protein in non-NaCl conditions to
eliminate partial conversion to cisplatin, and the use of different criteria
to choose the resolution limit | 14 pages; submitted to Acta Cryst D Biological Crystallography
reference number tz5044 | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Hen egg white lysozyme (HEWL) co-crystallisation conditions of carboplatin
without sodium chloride (NaCl) have been utilised to eliminate partial
conversion of carboplatin to cisplatin observed previously. Tetragonal HEWL
crystals were successfully obtained in 65% MPD with 0.1M citric acid buffer at
pH 4.0 including ... | [
{
"created": "Wed, 18 Sep 2013 14:40:56 GMT",
"version": "v1"
}
] | 2013-09-19 | [
[
"Tanley",
"Simon W. M",
""
],
[
"Diederichs",
"Kay",
""
],
[
"Kroon-Batenburg",
"Loes M. J",
""
],
[
"Schreurs",
"Antoine M. M",
""
],
[
"Helliwell",
"John R",
""
]
] | Hen egg white lysozyme (HEWL) co-crystallisation conditions of carboplatin without sodium chloride (NaCl) have been utilised to eliminate partial conversion of carboplatin to cisplatin observed previously. Tetragonal HEWL crystals were successfully obtained in 65% MPD with 0.1M citric acid buffer at pH 4.0 including DM... |
1906.11924 | Vedant Sachdeva | Vedant Sachdeva, Kabir Husain, Jiming Sheng, Shenshen Wang, Arvind
Murugan | Tuning environmental timescales to evolve and maintain generalists | null | null | 10.1073/pnas.1914586117 | null | q-bio.PE cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Natural environments can present diverse challenges, but some genotypes
remain fit across many environments. Such `generalists' can be hard to evolve,
out-competed by specialists fitter in any particular environment. Here,
inspired by the search for broadly-neutralising antibodies during B-cell
affinity maturation, w... | [
{
"created": "Thu, 27 Jun 2019 19:22:53 GMT",
"version": "v1"
}
] | 2020-07-15 | [
[
"Sachdeva",
"Vedant",
""
],
[
"Husain",
"Kabir",
""
],
[
"Sheng",
"Jiming",
""
],
[
"Wang",
"Shenshen",
""
],
[
"Murugan",
"Arvind",
""
]
] | Natural environments can present diverse challenges, but some genotypes remain fit across many environments. Such `generalists' can be hard to evolve, out-competed by specialists fitter in any particular environment. Here, inspired by the search for broadly-neutralising antibodies during B-cell affinity maturation, we ... |
1506.04230 | Almaz Mustafin | A. Mustafin | Coupling-induced oscillations in two intrinsically quiescent populations | 24 pages, 4 figures, 1 table, 38 references. Postprint of the
published article. arXiv admin note: substantial text overlap with
arXiv:1409.4404 | Communications in Nonlinear Science and Numerical Simulation,
2015, vol. 29, no. 1-3, pp. 391-399 | 10.1016/j.cnsns.2015.05.019 | null | q-bio.PE nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A model of two consumer-resource systems linked by interspecific interference
competition of consumers is considered. The basic assumption of the model is
that the dynamics of the resource is much slower than that of the consumer. In
the absence of interaction each consumer-resource pair has a unique stable
steady st... | [
{
"created": "Sat, 13 Jun 2015 06:23:44 GMT",
"version": "v1"
}
] | 2015-06-16 | [
[
"Mustafin",
"A.",
""
]
] | A model of two consumer-resource systems linked by interspecific interference competition of consumers is considered. The basic assumption of the model is that the dynamics of the resource is much slower than that of the consumer. In the absence of interaction each consumer-resource pair has a unique stable steady stat... |
1607.01959 | Shi Gu | Shi Gu, Matthew Cieslak, Benjamin Baird, Sarah F. Muldoon, Scott T.
Grafton, Fabio Pasqualetti, Danielle S. Bassett | The Energy Landscape of Neurophysiological Activity Implicit in Brain
Network Structure | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A critical mystery in neuroscience lies in determining how anatomical
structure impacts the complex functional dynamics of human thought. How does
large-scale brain circuitry constrain states of neuronal activity and
transitions between those states? We address these questions using a maximum
entropy model of brain d... | [
{
"created": "Thu, 7 Jul 2016 10:54:53 GMT",
"version": "v1"
}
] | 2016-07-08 | [
[
"Gu",
"Shi",
""
],
[
"Cieslak",
"Matthew",
""
],
[
"Baird",
"Benjamin",
""
],
[
"Muldoon",
"Sarah F.",
""
],
[
"Grafton",
"Scott T.",
""
],
[
"Pasqualetti",
"Fabio",
""
],
[
"Bassett",
"Danielle S.",
""
]... | A critical mystery in neuroscience lies in determining how anatomical structure impacts the complex functional dynamics of human thought. How does large-scale brain circuitry constrain states of neuronal activity and transitions between those states? We address these questions using a maximum entropy model of brain dyn... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.