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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1911.01321 | Daniel Friedman | Daniel A Friedman, Brian R Johnson, Timothy Linksvayer | Decentralized physiology and the molecular basis of social life in
eusocial insects | 32 pages, 1 Figure | null | null | null | q-bio.PE q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The traditional focus of physiological and functional genomic research is on
molecular processes that play out within a single body. In contrast, when
social interactions occur, molecular and behavioral responses in interacting
individuals can lead to physiological processes that are distributed across
multiple indiv... | [
{
"created": "Mon, 4 Nov 2019 16:32:09 GMT",
"version": "v1"
}
] | 2019-11-05 | [
[
"Friedman",
"Daniel A",
""
],
[
"Johnson",
"Brian R",
""
],
[
"Linksvayer",
"Timothy",
""
]
] | The traditional focus of physiological and functional genomic research is on molecular processes that play out within a single body. In contrast, when social interactions occur, molecular and behavioral responses in interacting individuals can lead to physiological processes that are distributed across multiple individ... |
2205.05789 | Daniel Hesslow | Daniel Hesslow, Niccol\'o Zanichelli, Pascal Notin, Iacopo Poli and
Debora Marks | RITA: a Study on Scaling Up Generative Protein Sequence Models | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work we introduce RITA: a suite of autoregressive generative models
for protein sequences, with up to 1.2 billion parameters, trained on over 280
million protein sequences belonging to the UniRef-100 database. Such generative
models hold the promise of greatly accelerating protein design. We conduct the
first... | [
{
"created": "Wed, 11 May 2022 22:06:03 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Jul 2022 21:46:47 GMT",
"version": "v2"
}
] | 2022-07-18 | [
[
"Hesslow",
"Daniel",
""
],
[
"Zanichelli",
"Niccoló",
""
],
[
"Notin",
"Pascal",
""
],
[
"Poli",
"Iacopo",
""
],
[
"Marks",
"Debora",
""
]
] | In this work we introduce RITA: a suite of autoregressive generative models for protein sequences, with up to 1.2 billion parameters, trained on over 280 million protein sequences belonging to the UniRef-100 database. Such generative models hold the promise of greatly accelerating protein design. We conduct the first s... |
2401.00476 | Chinwe Anyanwu Dr. | Anyanwu, C. F, Georgewill, O. A. and Obinna, Victoria C | Reproductive outcome in female wistar rats treated with nhexane,
dichloromethane and aqueous ethanol extracts of Cucurbita pepo seed | 5 tables, 2 figures | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | In developing countries, healthcare challenges and expensive infertility
treatments has resulted in resurgent interest in medicinal plants. This study
was designed to determine if Curcubita pepo seed can enhance female fertility,
by assessing the reproductive outcome in female wistar rats treated with
n-hexane (nHE),... | [
{
"created": "Sun, 31 Dec 2023 12:32:05 GMT",
"version": "v1"
}
] | 2024-01-02 | [
[
"Anyanwu",
"",
""
],
[
"F",
"C.",
""
],
[
"Georgewill",
"",
""
],
[
"A.",
"O.",
""
],
[
"Obinna",
"",
""
],
[
"C",
"Victoria",
""
]
] | In developing countries, healthcare challenges and expensive infertility treatments has resulted in resurgent interest in medicinal plants. This study was designed to determine if Curcubita pepo seed can enhance female fertility, by assessing the reproductive outcome in female wistar rats treated with n-hexane (nHE), d... |
q-bio/0608040 | Ting Chen | Ting Chen and Sharon C. Glotzer | Simulation Studies of A Phenomenological Model for the Assembly of
Elongated Virus Capsids | 17 pages and 5 figures | null | null | null | q-bio.BM | null | We extend our previously developed general approach (1) to study a
phenomenological model in which the simulated packing of hard, attractive
spheres on a prolate spheroid surface with convexity constraints produces
structures identical to those of prolate virus capsid structures. Our
simulation approach combines the ... | [
{
"created": "Mon, 28 Aug 2006 21:12:32 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Chen",
"Ting",
""
],
[
"Glotzer",
"Sharon C.",
""
]
] | We extend our previously developed general approach (1) to study a phenomenological model in which the simulated packing of hard, attractive spheres on a prolate spheroid surface with convexity constraints produces structures identical to those of prolate virus capsid structures. Our simulation approach combines the tr... |
2001.02371 | Debaldev Jana | N. S. N. V. K. Vyshnavi Devi, Debaldev Jana and M. Lakshmanan | Dynamics of a non-autonomous system with age-structured growth and
harvesting of prey and mutually interfering predator with reliance on
alternative food | null | null | null | null | q-bio.PE nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We perform a detailed analysis of the behaviour of a non-autonomous
prey-predator model where age based growth with age discriminatory harvesting
in prey and predator's reliance upon alternative food in the absence of that
particular prey are considered. We begin by deriving certain sufficient
conditions for permanen... | [
{
"created": "Wed, 8 Jan 2020 04:51:53 GMT",
"version": "v1"
}
] | 2020-01-09 | [
[
"Devi",
"N. S. N. V. K. Vyshnavi",
""
],
[
"Jana",
"Debaldev",
""
],
[
"Lakshmanan",
"M.",
""
]
] | We perform a detailed analysis of the behaviour of a non-autonomous prey-predator model where age based growth with age discriminatory harvesting in prey and predator's reliance upon alternative food in the absence of that particular prey are considered. We begin by deriving certain sufficient conditions for permanence... |
q-bio/0701051 | Brigitte Gaillard | C. Gilbert (DEPE-Iphc), G. Robertson, Y. Le Maho (DEPE-Iphc), Y.
Naito, A. Ancel (DEPE-Iphc) | Huddling behavior in emperor penguins : dynamics of huddling | null | Physiol. Behav. 88 (2006) 479-488 | 10.1016/j.physbeth.2006.04.024 | null | q-bio.PE | null | Although huddling was shown to be the key by which emperor penguins
(Aptenodytes forsteri) save energy and sustain their breeding fast during the
Antarctic winter, the intricacies of this social behavior have been poorly
studied. We recorded abiotic variables with data loggers glued to the feathers
of eight individua... | [
{
"created": "Tue, 30 Jan 2007 15:16:25 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Gilbert",
"C.",
"",
"DEPE-Iphc"
],
[
"Robertson",
"G.",
"",
"DEPE-Iphc"
],
[
"Maho",
"Y. Le",
"",
"DEPE-Iphc"
],
[
"Naito",
"Y.",
"",
"DEPE-Iphc"
],
[
"Ancel",
"A.",
"",
"DEPE-Iphc"
]
] | Although huddling was shown to be the key by which emperor penguins (Aptenodytes forsteri) save energy and sustain their breeding fast during the Antarctic winter, the intricacies of this social behavior have been poorly studied. We recorded abiotic variables with data loggers glued to the feathers of eight individuall... |
1108.1979 | Bohdan Kozarzewski | B. Kozarzewski | Similarity of symbolic sequences | null | null | null | null | q-bio.QM physics.bio-ph q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A new numerical characterization of symbolic sequences is proposed. The
partition of sequence based on Ke and Tong algorithm is a starting point.
Algorithm decomposes original sequence into set of distinct subsequences - a
patterns. The set of subsequences common for two symbolic sequences (their
intersection) is pro... | [
{
"created": "Tue, 9 Aug 2011 16:52:36 GMT",
"version": "v1"
},
{
"created": "Wed, 7 Sep 2011 17:26:08 GMT",
"version": "v2"
}
] | 2011-09-08 | [
[
"Kozarzewski",
"B.",
""
]
] | A new numerical characterization of symbolic sequences is proposed. The partition of sequence based on Ke and Tong algorithm is a starting point. Algorithm decomposes original sequence into set of distinct subsequences - a patterns. The set of subsequences common for two symbolic sequences (their intersection) is propo... |
2211.09642 | Angelina Brilliantova | Angelina Brilliantova, Hannah Miller, Ivona Bez\'akov\'a | GRASMOS: Graph Signage Model Selection for Gene Regulatory Networks | null | null | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Signed networks, i.e., networks with positive and negative edges, commonly
arise in various domains from social media to epidemiology. Modeling signed
networks has many practical applications, including the creation of synthetic
data sets for experiments where obtaining real data is difficult. Influential
prior works... | [
{
"created": "Thu, 17 Nov 2022 16:41:30 GMT",
"version": "v1"
}
] | 2022-11-18 | [
[
"Brilliantova",
"Angelina",
""
],
[
"Miller",
"Hannah",
""
],
[
"Bezáková",
"Ivona",
""
]
] | Signed networks, i.e., networks with positive and negative edges, commonly arise in various domains from social media to epidemiology. Modeling signed networks has many practical applications, including the creation of synthetic data sets for experiments where obtaining real data is difficult. Influential prior works p... |
1612.01571 | Konstantin Blyuss | G. Neofytou, Y.N. Kyrychko, K.B. Blyuss | Time-delayed model of RNA interference | 31 pages, 11 figures, accepted for publication to Ecological
Complexity | Ecol. Compl. 30, 11-25 (2017) | 10.1016/j.ecocom.2016.12.003 | null | q-bio.QM nlin.CD q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | RNA interference (RNAi) is a fundamental cellular process that inhibits gene
expression through cleavage and destruction of target mRNA. It is responsible
for a number of important intracellular functions, from being the first line of
immune defence against pathogens to regulating development and morphogenesis.
In th... | [
{
"created": "Mon, 5 Dec 2016 21:55:52 GMT",
"version": "v1"
}
] | 2017-07-12 | [
[
"Neofytou",
"G.",
""
],
[
"Kyrychko",
"Y. N.",
""
],
[
"Blyuss",
"K. B.",
""
]
] | RNA interference (RNAi) is a fundamental cellular process that inhibits gene expression through cleavage and destruction of target mRNA. It is responsible for a number of important intracellular functions, from being the first line of immune defence against pathogens to regulating development and morphogenesis. In this... |
2206.11416 | Sergiy Koshkin | Sergiy Koshkin, Zachary Zalles, Michael F. Tobin, Nicolas Toumbacaris,
Cameron Spiess | Optimal allocation in annual plants with density dependent fitness | 29 pages, 12 figures | Theory in Biosciences, 140 (2021) no.2, 177-196 | 10.1007/s12064-021-00343-9 | null | q-bio.PE math.OC | http://creativecommons.org/licenses/by/4.0/ | We study optimal two-sector (vegetative and reproductive) allocation models
of annual plants in temporally variable environments, that incorporate effects
of density dependent lifetime variability and juvenile mortality in a fitness
function whose expected value is maximized. Only special cases of arithmetic
and geom... | [
{
"created": "Wed, 22 Jun 2022 23:21:38 GMT",
"version": "v1"
}
] | 2022-06-24 | [
[
"Koshkin",
"Sergiy",
""
],
[
"Zalles",
"Zachary",
""
],
[
"Tobin",
"Michael F.",
""
],
[
"Toumbacaris",
"Nicolas",
""
],
[
"Spiess",
"Cameron",
""
]
] | We study optimal two-sector (vegetative and reproductive) allocation models of annual plants in temporally variable environments, that incorporate effects of density dependent lifetime variability and juvenile mortality in a fitness function whose expected value is maximized. Only special cases of arithmetic and geomet... |
0706.0760 | Jing Qin | Emma Y. Jin, Jing Qin and Christian M. Reidys | Neutral Networks of Sequence to Shape Maps | 24 pages,4 figures | null | null | null | q-bio.QM math-ph math.CO math.MP q-bio.BM | null | In this paper we present a novel framework for sequence to shape maps. These
combinatorial maps realize exponentially many shapes, and have preimages which
contain extended connected subgraphs of diameter n (neutral networks). We prove
that all basic properties of RNA folding maps also hold for combinatorial maps.
Ou... | [
{
"created": "Wed, 6 Jun 2007 04:21:12 GMT",
"version": "v1"
},
{
"created": "Sat, 4 Aug 2007 07:53:26 GMT",
"version": "v2"
}
] | 2009-09-29 | [
[
"Jin",
"Emma Y.",
""
],
[
"Qin",
"Jing",
""
],
[
"Reidys",
"Christian M.",
""
]
] | In this paper we present a novel framework for sequence to shape maps. These combinatorial maps realize exponentially many shapes, and have preimages which contain extended connected subgraphs of diameter n (neutral networks). We prove that all basic properties of RNA folding maps also hold for combinatorial maps. Our ... |
1804.02952 | J.H. van Hateren | J. H. van Hateren | A theory of consciousness: computation, algorithm, and neurobiological
realization | minor revision, 21 pages, 10 figures, 1 table | Biological Cybernetics 113, 357-372 (2019) | 10.1007/s00422-019-00803-y | null | q-bio.NC cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The most enigmatic aspect of consciousness is the fact that it is felt, as a
subjective sensation. The theory proposed here aims to explain this particular
aspect. The theory encompasses both the computation that is presumably involved
and the way in which that computation may be realized in the brain's
neurobiology.... | [
{
"created": "Mon, 9 Apr 2018 13:02:35 GMT",
"version": "v1"
},
{
"created": "Wed, 1 Aug 2018 09:44:18 GMT",
"version": "v2"
},
{
"created": "Mon, 21 Jan 2019 10:39:29 GMT",
"version": "v3"
},
{
"created": "Thu, 20 Jun 2019 09:00:48 GMT",
"version": "v4"
}
] | 2019-07-29 | [
[
"van Hateren",
"J. H.",
""
]
] | The most enigmatic aspect of consciousness is the fact that it is felt, as a subjective sensation. The theory proposed here aims to explain this particular aspect. The theory encompasses both the computation that is presumably involved and the way in which that computation may be realized in the brain's neurobiology. I... |
1207.0689 | Ramon Ferrer i Cancho | Ramon Ferrer-i-Cancho, N\'uria Forns, Antoni Hern\'andez-Fern\'andez,
Gemma Bel-Enguix and Jaume Baixeries | The challenges of statistical patterns of language: the case of
Menzerath's law in genomes | Title changed, abstract and introduction improved and little
corrections on the statistical arguments | null | 10.1002/cplx.21429 | null | q-bio.GN cs.CE physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The importance of statistical patterns of language has been debated over
decades. Although Zipf's law is perhaps the most popular case, recently,
Menzerath's law has begun to be involved. Menzerath's law manifests in
language, music and genomes as a tendency of the mean size of the parts to
decrease as the number of ... | [
{
"created": "Tue, 3 Jul 2012 14:10:38 GMT",
"version": "v1"
},
{
"created": "Sat, 29 Sep 2012 07:07:19 GMT",
"version": "v2"
}
] | 2014-12-03 | [
[
"Ferrer-i-Cancho",
"Ramon",
""
],
[
"Forns",
"Núria",
""
],
[
"Hernández-Fernández",
"Antoni",
""
],
[
"Bel-Enguix",
"Gemma",
""
],
[
"Baixeries",
"Jaume",
""
]
] | The importance of statistical patterns of language has been debated over decades. Although Zipf's law is perhaps the most popular case, recently, Menzerath's law has begun to be involved. Menzerath's law manifests in language, music and genomes as a tendency of the mean size of the parts to decrease as the number of pa... |
1910.01940 | Marc Robinson-Rechavi | Marc Robinson-Rechavi | Molecular evolution and gene function | To be published in book "Phylogenomics" (Nicolas Galtier, C\'eline
Scornavacca, Fr\'ed\'eric Delsuc, Eds.) | null | null | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | One of the basic questions of phylogenomics is how gene function evolves,
whether among species or inside gene families. In this chapter, we provide a
brief overview of the problems associated with defining gene function in a
manner which allows comparisons which are both large scale and evolutionarily
relevant. The ... | [
{
"created": "Fri, 4 Oct 2019 13:12:53 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Oct 2019 07:50:21 GMT",
"version": "v2"
}
] | 2019-10-08 | [
[
"Robinson-Rechavi",
"Marc",
""
]
] | One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which allows comparisons which are both large scale and evolutionarily relevant. The ma... |
1910.02532 | Jesse Geerts | Jesse P. Geerts, Kimberly L. Stachenfeld, Neil Burgess | Probabilistic Successor Representations with Kalman Temporal Differences | Conference on Cognitive Computational Neuroscience | null | 10.32470/CCN.2019.1323-0 | null | q-bio.NC cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The effectiveness of Reinforcement Learning (RL) depends on an animal's
ability to assign credit for rewards to the appropriate preceding stimuli. One
aspect of understanding the neural underpinnings of this process involves
understanding what sorts of stimulus representations support generalisation.
The Successor Re... | [
{
"created": "Sun, 6 Oct 2019 21:32:46 GMT",
"version": "v1"
}
] | 2019-10-08 | [
[
"Geerts",
"Jesse P.",
""
],
[
"Stachenfeld",
"Kimberly L.",
""
],
[
"Burgess",
"Neil",
""
]
] | The effectiveness of Reinforcement Learning (RL) depends on an animal's ability to assign credit for rewards to the appropriate preceding stimuli. One aspect of understanding the neural underpinnings of this process involves understanding what sorts of stimulus representations support generalisation. The Successor Repr... |
1705.08670 | Giovanna Jona Lasinio professor | Giovanna Jona Lasinio, Alessio Pollice, Eric Marcon, Elisa Anna Fano | Assessing the role of the spatial scale in the analysis of lagoon
biodiversity. A case-study on the macrobenthic fauna of the Po River Delta | Keywords: Lagoon biodiversity; Macrobenthic fauna; Tsallis entropy;
Biodiversity partitioning; Mixed effects models | Ecological Indicators, Volume 80, September 2017, Pages 303-315,
ISSN 1470-160X,
(http://www.sciencedirect.com/science/article/pii/S1470160X17302923) | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The analysis of benthic assemblages is a valuable tool to describe the
ecological status of transitional water ecosystems, but species are extremely
sensitive and respond to both microhabitat and seasonal differences. The
identification of changes in the composition of the macrobenthic community in
specific microhabi... | [
{
"created": "Wed, 24 May 2017 09:36:28 GMT",
"version": "v1"
}
] | 2017-05-25 | [
[
"Lasinio",
"Giovanna Jona",
""
],
[
"Pollice",
"Alessio",
""
],
[
"Marcon",
"Eric",
""
],
[
"Fano",
"Elisa Anna",
""
]
] | The analysis of benthic assemblages is a valuable tool to describe the ecological status of transitional water ecosystems, but species are extremely sensitive and respond to both microhabitat and seasonal differences. The identification of changes in the composition of the macrobenthic community in specific microhabita... |
1308.2145 | Sergei Maslov | Tin Yau Pang and Sergei Maslov | Universal distribution of component frequencies in biological and
technological systems | null | Proc Natl Acad Sci USA (PNAS) 110 (2013) 6235-6239 | 10.1073/pnas.1217795110 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bacterial genomes and large-scale computer software projects both consist of
a large number of components (genes or software packages) connected via a
network of mutual dependencies. Components can be easily added or removed from
individual systems and their usage frequencies vary over many orders of
magnitude. We st... | [
{
"created": "Fri, 9 Aug 2013 15:01:03 GMT",
"version": "v1"
}
] | 2013-08-12 | [
[
"Pang",
"Tin Yau",
""
],
[
"Maslov",
"Sergei",
""
]
] | Bacterial genomes and large-scale computer software projects both consist of a large number of components (genes or software packages) connected via a network of mutual dependencies. Components can be easily added or removed from individual systems and their usage frequencies vary over many orders of magnitude. We stud... |
2008.01202 | Chris Groendyke | Chris Groendyke and Adam Combs | Modifying the Network-Based Stochastic SEIR Model to Account for
Quarantine | 26 pages, 7 figures | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this article, we present a modification to the network-based stochastic
SEIR epidemic model which allows for modifications to the underlying contact
network to account for the effects of quarantine. We also discuss the changes
needed to the model to incorporate situations where some proportion of the
individuals w... | [
{
"created": "Mon, 3 Aug 2020 21:19:23 GMT",
"version": "v1"
}
] | 2020-08-05 | [
[
"Groendyke",
"Chris",
""
],
[
"Combs",
"Adam",
""
]
] | In this article, we present a modification to the network-based stochastic SEIR epidemic model which allows for modifications to the underlying contact network to account for the effects of quarantine. We also discuss the changes needed to the model to incorporate situations where some proportion of the individuals who... |
2208.03726 | Diederik Aerts | Diederik Aerts and Jonito Aerts Argu\"elles | Human Perception as a Phenomenon of Quantization | 28 pages, 8 figures | Entropy 24, 1207 (2022) | 10.3390/e24091207 | null | q-bio.NC cs.CL quant-ph | http://creativecommons.org/licenses/by/4.0/ | For two decades, the formalism of quantum mechanics has been successfully
used to describe human decision processes, situations of heuristic reasoning,
and the contextuality of concepts and their combinations. The phenomenon of
'categorical perception' has put us on track to find a possible deeper cause of
the presen... | [
{
"created": "Sun, 7 Aug 2022 13:59:23 GMT",
"version": "v1"
},
{
"created": "Sat, 8 Oct 2022 21:24:47 GMT",
"version": "v2"
}
] | 2023-02-27 | [
[
"Aerts",
"Diederik",
""
],
[
"Arguëlles",
"Jonito Aerts",
""
]
] | For two decades, the formalism of quantum mechanics has been successfully used to describe human decision processes, situations of heuristic reasoning, and the contextuality of concepts and their combinations. The phenomenon of 'categorical perception' has put us on track to find a possible deeper cause of the presence... |
2307.08828 | Abdullah Alqarni | Abdullah Alqarni, Wei Wen, Ben C.P. Lam, Nicole Kochan, Henry Brodaty,
Perminder S. Sachdev, Jiyang Jiang | Sex Differences in 6-Year Progression of White Matter Hyperintensities
in Non-Demented Older Adults: Sydney Memory and Ageing Study | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Objectives: To examine sex differences in the associations between vascular
risk factors and 6-year changes in the volume of white matter hyperintensities
(WMH), and between changes in WMH volumes and changes in cognitive performance,
in a cohort of non-demented older adults.
Methods: WMH volumes at 3 time-points (... | [
{
"created": "Mon, 17 Jul 2023 20:43:55 GMT",
"version": "v1"
}
] | 2023-07-19 | [
[
"Alqarni",
"Abdullah",
""
],
[
"Wen",
"Wei",
""
],
[
"Lam",
"Ben C. P.",
""
],
[
"Kochan",
"Nicole",
""
],
[
"Brodaty",
"Henry",
""
],
[
"Sachdev",
"Perminder S.",
""
],
[
"Jiang",
"Jiyang",
""
]
] | Objectives: To examine sex differences in the associations between vascular risk factors and 6-year changes in the volume of white matter hyperintensities (WMH), and between changes in WMH volumes and changes in cognitive performance, in a cohort of non-demented older adults. Methods: WMH volumes at 3 time-points (base... |
2302.03752 | Markus Adamek | Markus Adamek (1 and 2) and Alexander P Rockhill (4) and Peter Brunner
(1 and 2) and Dora Hermes (3) ((1) Department of Neurosurgery, Washington
University in Saint Louis MO USA, (2) National Center for Adaptive
Neurotechnologies Albany NY USA, (3) Department of Physiology & Biomedical
Engineering Mayo Clinic R... | Dynamic Visualization of Gyral and Sulcal Stereoelectroencephalographic
contacts in Humans | submitted as a contributed paper to EMBC 2023 | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Stereoelectroencephalography (SEEG) is a neurosurgical method to survey
electrophysiological activity within the brain to treat disorders such as
Epilepsy. In this stereotactic approach, leads are implanted through straight
trajectories to survey both cortical and sub-cortical activity. Visualizing the
recorded locat... | [
{
"created": "Tue, 7 Feb 2023 20:57:15 GMT",
"version": "v1"
}
] | 2023-02-09 | [
[
"Adamek",
"Markus",
"",
"1 and 2"
],
[
"Rockhill",
"Alexander P",
"",
"1 and 2"
],
[
"Brunner",
"Peter",
"",
"1 and 2"
],
[
"Hermes",
"Dora",
""
]
] | Stereoelectroencephalography (SEEG) is a neurosurgical method to survey electrophysiological activity within the brain to treat disorders such as Epilepsy. In this stereotactic approach, leads are implanted through straight trajectories to survey both cortical and sub-cortical activity. Visualizing the recorded locatio... |
1406.6641 | Augusto Gonzalez | Augusto Gonzalez | Mutagenesis and Background Neutron Radiation | submitted to Revista Cubana de Fisica | Rev. Cub. Fis. 31 (2014) 71 | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We suggest a possible correlation between the ionization events caused by the
background neutron radiation and the experimental data on mutations with damage
in the DNA repair mechanism, coming from the Long Term Evolution Experiment in
E. Coli populations.
| [
{
"created": "Wed, 25 Jun 2014 17:03:42 GMT",
"version": "v1"
},
{
"created": "Fri, 27 Jun 2014 13:30:51 GMT",
"version": "v2"
}
] | 2015-04-28 | [
[
"Gonzalez",
"Augusto",
""
]
] | We suggest a possible correlation between the ionization events caused by the background neutron radiation and the experimental data on mutations with damage in the DNA repair mechanism, coming from the Long Term Evolution Experiment in E. Coli populations. |
1802.02962 | Michael Sadovsky | Michael Sadovsky, Maria Senashova, Andrew Malyshev | Eight-cluster structure of chloroplast genomes differs from similar one
observed for bacteria | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Previously, a seven-cluster pattern claiming to be a universal one in
bacterial genomes has been reported. Keeping in mind the most popular theory of
chloroplast origin, we checked whether a similar pattern is observed in
chloroplast genomes. Surprisingly, eight cluster structure has been found, for
chloroplasts. The... | [
{
"created": "Thu, 8 Feb 2018 16:49:26 GMT",
"version": "v1"
}
] | 2018-02-09 | [
[
"Sadovsky",
"Michael",
""
],
[
"Senashova",
"Maria",
""
],
[
"Malyshev",
"Andrew",
""
]
] | Previously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported. Keeping in mind the most popular theory of chloroplast origin, we checked whether a similar pattern is observed in chloroplast genomes. Surprisingly, eight cluster structure has been found, for chloroplasts. The p... |
2401.11192 | Jos\'e Manuel Peula-Garc\'ia | Paola Sanchez-Moreno, Juan Luis Ortega-Vinuesa, Jose Manuel
Peula-Garcia, Juan Antonio Marchal and Houria Boulaiz | Smart Drug-Delivery Systems for Cancer Nanotherapy | Preprint version, 25 pages, 7 figures, 3 tables. Authors thank to
Bentham Science the posibility of deposit the ACCEPTED VERSION of the
peer-reviewed article after 12 months of publication on journal web site on
arXiv repository. The published manuscript is available at EurekaSelect via
https://www.eurekaselect... | Current Drug Targets, 2018, 19(4), 339 | 10.2174/1389450117666160527142544 | null | q-bio.TO cond-mat.mes-hall physics.app-ph physics.bio-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Despite all the advances achieved in the field of tumor-biology research, in
most cases conventional therapies including chemotherapy are still the leading
choices. The main disadvantage of these treatments, in addition to the low
solubility of many antitumor drugs, is their lack of specificity, which
explains the fr... | [
{
"created": "Sat, 20 Jan 2024 10:03:56 GMT",
"version": "v1"
}
] | 2024-01-25 | [
[
"Sanchez-Moreno",
"Paola",
""
],
[
"Ortega-Vinuesa",
"Juan Luis",
""
],
[
"Peula-Garcia",
"Jose Manuel",
""
],
[
"Marchal",
"Juan Antonio",
""
],
[
"Boulaiz",
"Houria",
""
]
] | Despite all the advances achieved in the field of tumor-biology research, in most cases conventional therapies including chemotherapy are still the leading choices. The main disadvantage of these treatments, in addition to the low solubility of many antitumor drugs, is their lack of specificity, which explains the freq... |
1204.5421 | Luis Enrique Correa da Rocha Mr | Luis Enrique Correa Rocha, Adeline Decuyper, Vincent D Blondel | Epidemics on a stochastic model of temporal network | null | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Contacts between individuals serve as pathways where infections may
propagate. These contact patterns can be represented by network structures.
Static structures have been the common modeling paradigm but recent results
suggest that temporal structures play different roles to regulate the spread of
infections or infe... | [
{
"created": "Tue, 24 Apr 2012 16:11:55 GMT",
"version": "v1"
}
] | 2012-04-25 | [
[
"Rocha",
"Luis Enrique Correa",
""
],
[
"Decuyper",
"Adeline",
""
],
[
"Blondel",
"Vincent D",
""
]
] | Contacts between individuals serve as pathways where infections may propagate. These contact patterns can be represented by network structures. Static structures have been the common modeling paradigm but recent results suggest that temporal structures play different roles to regulate the spread of infections or infect... |
1012.1974 | Thomas House | Thomas House and Matt J Keeling | Epidemic prediction and control in clustered populations | 13 pages, 3 figures, to appear in the Journal of Theoretical Biology | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There has been much recent interest in modelling epidemics on networks,
particularly in the presence of substantial clustering. Here, we develop
pairwise methods to answer questions that are often addressed using epidemic
models, in particular: on the basis of potential observations early in an
outbreak, what can be ... | [
{
"created": "Thu, 9 Dec 2010 10:59:24 GMT",
"version": "v1"
}
] | 2010-12-10 | [
[
"House",
"Thomas",
""
],
[
"Keeling",
"Matt J",
""
]
] | There has been much recent interest in modelling epidemics on networks, particularly in the presence of substantial clustering. Here, we develop pairwise methods to answer questions that are often addressed using epidemic models, in particular: on the basis of potential observations early in an outbreak, what can be pr... |
1709.09125 | Lee Worden | Lee Worden | Regulation of community functional composition across taxonomic
variation by resource-consumer dynamics | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | High-throughput sequencing techniques such as metagenomic and
metatranscriptomic technologies allow cataloging of functional characteristics
of microbial community members as well as their taxonomic identity. Such
studies have found that a community's composition in terms of ecologically
relevant functional traits or... | [
{
"created": "Tue, 26 Sep 2017 16:50:40 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Jun 2019 09:15:47 GMT",
"version": "v2"
}
] | 2019-06-24 | [
[
"Worden",
"Lee",
""
]
] | High-throughput sequencing techniques such as metagenomic and metatranscriptomic technologies allow cataloging of functional characteristics of microbial community members as well as their taxonomic identity. Such studies have found that a community's composition in terms of ecologically relevant functional traits or g... |
2406.08521 | Aakash Tripathi | Asim Waqas, Aakash Tripathi, Paul Stewart, Mia Naeini, Ghulam Rasool | Embedding-based Multimodal Learning on Pan-Squamous Cell Carcinomas for
Improved Survival Outcomes | null | null | null | null | q-bio.CB cs.LG | http://creativecommons.org/licenses/by/4.0/ | Cancer clinics capture disease data at various scales, from genetic to organ
level. Current bioinformatic methods struggle to handle the heterogeneous
nature of this data, especially with missing modalities. We propose PARADIGM, a
Graph Neural Network (GNN) framework that learns from multimodal, heterogeneous
dataset... | [
{
"created": "Tue, 11 Jun 2024 22:19:14 GMT",
"version": "v1"
}
] | 2024-06-14 | [
[
"Waqas",
"Asim",
""
],
[
"Tripathi",
"Aakash",
""
],
[
"Stewart",
"Paul",
""
],
[
"Naeini",
"Mia",
""
],
[
"Rasool",
"Ghulam",
""
]
] | Cancer clinics capture disease data at various scales, from genetic to organ level. Current bioinformatic methods struggle to handle the heterogeneous nature of this data, especially with missing modalities. We propose PARADIGM, a Graph Neural Network (GNN) framework that learns from multimodal, heterogeneous datasets ... |
1601.00979 | Mehrashk Meidani | Mehrashk Meidani | Fracture toughness of leaves: Overview and observations | null | null | null | null | q-bio.TO cond-mat.mtrl-sci physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One might ask why is it important to know the mechanism of fracture in leaves
when Mother Nature is doing her job perfectly. I could list the following
reasons to address that question: (a) Leaves are natural composite structures,
during millions of years of evolution, they have adapted themselves to their
surroundin... | [
{
"created": "Mon, 21 Dec 2015 20:40:19 GMT",
"version": "v1"
},
{
"created": "Thu, 7 Jan 2016 04:40:47 GMT",
"version": "v2"
}
] | 2016-01-08 | [
[
"Meidani",
"Mehrashk",
""
]
] | One might ask why is it important to know the mechanism of fracture in leaves when Mother Nature is doing her job perfectly. I could list the following reasons to address that question: (a) Leaves are natural composite structures, during millions of years of evolution, they have adapted themselves to their surrounding ... |
2212.06529 | Karoline Leiberg | Karoline Leiberg, Jane de Tisi, John S Duncan, Bethany Little, Peter N
Taylor, Sjoerd B Vos, Gavin P Winston, Bruno Mota and Yujiang Wang | Effects of anterior temporal lobe resection on cortical morphology | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Anterior temporal lobe resection (ATLR) is a surgical procedure to treat
drug-resistant temporal lobe epilepsy (TLE). Resection may involve large
amounts of cortical tissue. Here, we examine the effects of this surgery on
cortical morphology measured in independent variables both near the resection
and remotely.
We... | [
{
"created": "Tue, 13 Dec 2022 12:26:12 GMT",
"version": "v1"
}
] | 2022-12-14 | [
[
"Leiberg",
"Karoline",
""
],
[
"de Tisi",
"Jane",
""
],
[
"Duncan",
"John S",
""
],
[
"Little",
"Bethany",
""
],
[
"Taylor",
"Peter N",
""
],
[
"Vos",
"Sjoerd B",
""
],
[
"Winston",
"Gavin P",
""
],
[
... | Anterior temporal lobe resection (ATLR) is a surgical procedure to treat drug-resistant temporal lobe epilepsy (TLE). Resection may involve large amounts of cortical tissue. Here, we examine the effects of this surgery on cortical morphology measured in independent variables both near the resection and remotely. We stu... |
2212.14041 | Cheng Tan | Cheng Tan, Zhangyang Gao, Hanqun Cao, Xingran Chen, Ge Wang, Lirong
Wu, Jun Xia, Jiangbin Zheng, Stan Z. Li | Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook
Matching Perspective | Accepted by ICML 2024 | null | null | null | q-bio.BM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The secondary structure of ribonucleic acid (RNA) is more stable and
accessible in the cell than its tertiary structure, making it essential for
functional prediction. Although deep learning has shown promising results in
this field, current methods suffer from poor generalization and high
complexity. In this work, w... | [
{
"created": "Fri, 2 Dec 2022 16:34:56 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Apr 2023 12:26:17 GMT",
"version": "v2"
},
{
"created": "Fri, 24 May 2024 12:05:40 GMT",
"version": "v3"
},
{
"created": "Fri, 31 May 2024 14:18:31 GMT",
"version": "v4"
},
{
"cr... | 2024-06-21 | [
[
"Tan",
"Cheng",
""
],
[
"Gao",
"Zhangyang",
""
],
[
"Cao",
"Hanqun",
""
],
[
"Chen",
"Xingran",
""
],
[
"Wang",
"Ge",
""
],
[
"Wu",
"Lirong",
""
],
[
"Xia",
"Jun",
""
],
[
"Zheng",
"Jiangbin",
... | The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field, current methods suffer from poor generalization and high complexity. In this work, we ... |
2111.07776 | Alex McAvoy | Alex McAvoy, Yoichiro Mori, Joshua B. Plotkin | Selfish optimization and collective learning in populations | 33 pages; final version | null | 10.1016/j.physd.2022.133426 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A selfish learner seeks to maximize their own success, disregarding others.
When success is measured as payoff in a game played against another learner,
mutual selfishness typically fails to produce the optimal outcome for a pair of
individuals. However, learners often operate in populations, and each learner
may hav... | [
{
"created": "Mon, 15 Nov 2021 14:17:07 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Jul 2022 15:53:03 GMT",
"version": "v2"
}
] | 2022-07-07 | [
[
"McAvoy",
"Alex",
""
],
[
"Mori",
"Yoichiro",
""
],
[
"Plotkin",
"Joshua B.",
""
]
] | A selfish learner seeks to maximize their own success, disregarding others. When success is measured as payoff in a game played against another learner, mutual selfishness typically fails to produce the optimal outcome for a pair of individuals. However, learners often operate in populations, and each learner may have ... |
1607.00697 | Nora Youngs | Elizabeth Gross, Nida Kazi Obatake, Nora Youngs | Neural ideals and stimulus space visualization | null | null | null | null | q-bio.NC cs.GR math.AC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A neural code $\mathcal{C}$ is a collection of binary vectors of a given
length n that record the co-firing patterns of a set of neurons. Our focus is
on neural codes arising from place cells, neurons that respond to geographic
stimulus. In this setting, the stimulus space can be visualized as subset of
$\mathbb{R}^2... | [
{
"created": "Sun, 3 Jul 2016 22:54:11 GMT",
"version": "v1"
}
] | 2016-07-05 | [
[
"Gross",
"Elizabeth",
""
],
[
"Obatake",
"Nida Kazi",
""
],
[
"Youngs",
"Nora",
""
]
] | A neural code $\mathcal{C}$ is a collection of binary vectors of a given length n that record the co-firing patterns of a set of neurons. Our focus is on neural codes arising from place cells, neurons that respond to geographic stimulus. In this setting, the stimulus space can be visualized as subset of $\mathbb{R}^2$ ... |
1104.5278 | Parin Sripakdeevong | Parin Sripakdeevong, Wipapat Kladwang, Rhiju Das | Can biopolymer structures be sampled enumeratively? Atomic-accuracy RNA
loop modeling by a stepwise ansatz | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Atomic-accuracy structure prediction of macromolecules is a long-sought goal
of computational biophysics. Accurate modeling should be achievable by
optimizing a physically realistic energy function but is presently precluded by
incomplete sampling of a biopolymer's many degrees of freedom. We present
herein a working... | [
{
"created": "Thu, 28 Apr 2011 02:15:07 GMT",
"version": "v1"
}
] | 2011-04-29 | [
[
"Sripakdeevong",
"Parin",
""
],
[
"Kladwang",
"Wipapat",
""
],
[
"Das",
"Rhiju",
""
]
] | Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete sampling of a biopolymer's many degrees of freedom. We present herein a working h... |
1604.04553 | Pieter Trapman | Pieter Trapman, Frank Ball, Jean-St\'ephane Dhersin, Viet Chi Tran,
Jacco Wallinga and Tom Britton | Inferring $R_0$ in emerging epidemics - the effect of common population
structure is small | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When controlling an emerging outbreak of an infectious disease it is
essential to know the key epidemiological parameters, such as the basic
reproduction number $R_0$ and the control effort required to prevent a large
outbreak. These parameters are estimated from the observed incidence of new
cases and information ab... | [
{
"created": "Fri, 15 Apr 2016 16:06:53 GMT",
"version": "v1"
}
] | 2016-04-18 | [
[
"Trapman",
"Pieter",
""
],
[
"Ball",
"Frank",
""
],
[
"Dhersin",
"Jean-Stéphane",
""
],
[
"Tran",
"Viet Chi",
""
],
[
"Wallinga",
"Jacco",
""
],
[
"Britton",
"Tom",
""
]
] | When controlling an emerging outbreak of an infectious disease it is essential to know the key epidemiological parameters, such as the basic reproduction number $R_0$ and the control effort required to prevent a large outbreak. These parameters are estimated from the observed incidence of new cases and information abou... |
2301.09494 | Thomas Klotz | Thomas Klotz, Lena Lehmann, Francesco Negro and Oliver R\"ohrle | High-density magnetomyography is superior to high-density surface
electromyography for motor unit decomposition: a simulation study | null | null | null | null | q-bio.TO q-bio.CB q-bio.NC q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Objective: Studying motor units (MUs) is essential for understanding motor
control, the detection of neuromuscular disorders and the control of
human-machine interfaces. Individual motor unit firings are currently
identified in vivo by decomposing electromyographic (EMG) signals. Due to our
body's properties and anat... | [
{
"created": "Mon, 23 Jan 2023 15:45:00 GMT",
"version": "v1"
},
{
"created": "Fri, 30 Jun 2023 09:49:40 GMT",
"version": "v2"
}
] | 2023-07-03 | [
[
"Klotz",
"Thomas",
""
],
[
"Lehmann",
"Lena",
""
],
[
"Negro",
"Francesco",
""
],
[
"Röhrle",
"Oliver",
""
]
] | Objective: Studying motor units (MUs) is essential for understanding motor control, the detection of neuromuscular disorders and the control of human-machine interfaces. Individual motor unit firings are currently identified in vivo by decomposing electromyographic (EMG) signals. Due to our body's properties and anatom... |
1809.07734 | Tal Einav | Tal Einav, Shahrzad Yazdi, Aaron Coey, Pamela J. Bjorkman, Rob
Phillips | Harnessing Avidity: Quantifying Entropic and Energetic Effects of Linker
Length and Rigidity Required for Multivalent Binding of Antibodies to HIV-1
Spikes | null | null | 10.1016/j.cels.2019.09.007 | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Due to the low density of envelope (Env) spikes on the surface of HIV-1,
neutralizing IgG antibodies rarely bind bivalently using both antigen-binding
arms (Fabs) to crosslink between spikes (inter-spike crosslinking), instead
resorting to weaker monovalent binding that is more sensitive to Env mutations.
Synthetic a... | [
{
"created": "Sun, 2 Sep 2018 01:19:03 GMT",
"version": "v1"
},
{
"created": "Wed, 22 May 2019 06:27:44 GMT",
"version": "v2"
}
] | 2022-07-27 | [
[
"Einav",
"Tal",
""
],
[
"Yazdi",
"Shahrzad",
""
],
[
"Coey",
"Aaron",
""
],
[
"Bjorkman",
"Pamela J.",
""
],
[
"Phillips",
"Rob",
""
]
] | Due to the low density of envelope (Env) spikes on the surface of HIV-1, neutralizing IgG antibodies rarely bind bivalently using both antigen-binding arms (Fabs) to crosslink between spikes (inter-spike crosslinking), instead resorting to weaker monovalent binding that is more sensitive to Env mutations. Synthetic ant... |
2309.04498 | Marton Aron Goda Dr. | Joachim A. Behar, Jeremy Levy, Eran Zvuloni, Sheina Gendelman, Aviv
Rosenberg, Shany Biton, Raphael Derman, Jonathan A. Sobel, Alexandra
Alexandrovich, Peter Charlton and M\'arton \'A Goda | PhysioZoo: The Open Digital Physiological Biomarkers Resource | 4 pages, 2 figure, 50th Computing in Cardiology conference in
Atlanta, Georgia, USA on 1st - 4th October 2023 | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | PhysioZoo is a collaborative platform designed for the analysis of continuous
physiological time series. The platform currently comprises four modules, each
consisting of a library, a user interface, and a set of tutorials: (1)
PhysioZoo HRV, dedicated to studying heart rate variability (HRV) in humans and
other mamm... | [
{
"created": "Thu, 7 Sep 2023 21:38:28 GMT",
"version": "v1"
}
] | 2023-09-12 | [
[
"Behar",
"Joachim A.",
""
],
[
"Levy",
"Jeremy",
""
],
[
"Zvuloni",
"Eran",
""
],
[
"Gendelman",
"Sheina",
""
],
[
"Rosenberg",
"Aviv",
""
],
[
"Biton",
"Shany",
""
],
[
"Derman",
"Raphael",
""
],
[
... | PhysioZoo is a collaborative platform designed for the analysis of continuous physiological time series. The platform currently comprises four modules, each consisting of a library, a user interface, and a set of tutorials: (1) PhysioZoo HRV, dedicated to studying heart rate variability (HRV) in humans and other mammal... |
2101.06788 | Tajudeen Yahaya Dr. | Tajudeen O. Yahaya and Shemishere B. Ufuoma | Genetics and Pathophysiology of Maturity-onset Diabetes of the Young
(MODY): A Review of Current Trends | 10 pages | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Single gene mutations have been implicated in the pathogenesis of a form of
diabetes mellitus (DM) known as the maturity-onset diabetes of the young
(MODY). However, there are diverse opinions on the suspect genes and
pathophysiology, necessitating the need to review and communicate the genes to
raise public awarenes... | [
{
"created": "Sun, 17 Jan 2021 21:21:59 GMT",
"version": "v1"
}
] | 2021-01-19 | [
[
"Yahaya",
"Tajudeen O.",
""
],
[
"Ufuoma",
"Shemishere B.",
""
]
] | Single gene mutations have been implicated in the pathogenesis of a form of diabetes mellitus (DM) known as the maturity-onset diabetes of the young (MODY). However, there are diverse opinions on the suspect genes and pathophysiology, necessitating the need to review and communicate the genes to raise public awareness.... |
2007.14965 | Changjiang Liu | Changjiang Liu, Paolo Elvati, Angela Violi | Antiviral Drug-Membrane Permeability: the Viral Envelope and Cellular
Organelles | null | null | null | null | q-bio.BM q-bio.QM q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To shorten the time required to find effective new drugs, like antivirals, a
key parameter to consider is membrane permeability, as a compound intended for
an intracellular target with poor permeability will have low efficacy. Here, we
present a computational model that considers both drug characteristics and
membran... | [
{
"created": "Wed, 29 Jul 2020 17:16:45 GMT",
"version": "v1"
}
] | 2020-07-30 | [
[
"Liu",
"Changjiang",
""
],
[
"Elvati",
"Paolo",
""
],
[
"Violi",
"Angela",
""
]
] | To shorten the time required to find effective new drugs, like antivirals, a key parameter to consider is membrane permeability, as a compound intended for an intracellular target with poor permeability will have low efficacy. Here, we present a computational model that considers both drug characteristics and membrane ... |
2106.13082 | Robert Rosenbaum | Robert Rosenbaum | On the relationship between predictive coding and backpropagation | null | null | 10.1371/journal.pone.0266102 | null | q-bio.NC cs.LG cs.NE | http://creativecommons.org/licenses/by/4.0/ | Artificial neural networks are often interpreted as abstract models of
biological neuronal networks, but they are typically trained using the
biologically unrealistic backpropagation algorithm and its variants. Predictive
coding has been proposed as a potentially more biologically realistic
alternative to backpropaga... | [
{
"created": "Sun, 20 Jun 2021 18:22:50 GMT",
"version": "v1"
},
{
"created": "Fri, 25 Jun 2021 11:13:15 GMT",
"version": "v2"
},
{
"created": "Thu, 21 Oct 2021 20:19:55 GMT",
"version": "v3"
},
{
"created": "Fri, 18 Feb 2022 12:28:20 GMT",
"version": "v4"
},
{
"c... | 2024-04-25 | [
[
"Rosenbaum",
"Robert",
""
]
] | Artificial neural networks are often interpreted as abstract models of biological neuronal networks, but they are typically trained using the biologically unrealistic backpropagation algorithm and its variants. Predictive coding has been proposed as a potentially more biologically realistic alternative to backpropagati... |
1212.4125 | Katarzyna Bryc Katarzyna Bryc | Katarzyna Bryc, Nick Patterson, and David Reich | Estimating heterozygosity from a low-coverage genome sequence,
leveraging data from other individuals sequenced at the same sites | 18 pages, 4 figures, 1 table | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | High-throughput shotgun sequence data makes it possible in principle to
accurately estimate population genetic parameters without confounding by SNP
ascertainment bias. One such statistic of interest is the proportion of
heterozygous sites within an individual's genome, which is informative about
inbreeding and effec... | [
{
"created": "Mon, 17 Dec 2012 20:22:05 GMT",
"version": "v1"
}
] | 2012-12-18 | [
[
"Bryc",
"Katarzyna",
""
],
[
"Patterson",
"Nick",
""
],
[
"Reich",
"David",
""
]
] | High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites within an individual's genome, which is informative about inbreeding and effecti... |
0704.3715 | Pablo Echenique | Pablo Echenique, J. L. Alonso | Efficient model chemistries for peptides. I. Split-valence Gaussian
basis sets and the heterolevel approximation in RHF and MP2 | 54 pages, 16 figures, LaTeX, AMSTeX, Submitted to J. Comp. Chem | J. Comp. Chem. (2008) 1408-1422 | 10.1002/jcc.20900 | null | q-bio.QM cond-mat.soft q-bio.BM | null | We present an exhaustive study of more than 250 ab initio potential energy
surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries
(MCs) used are constructed as homo- and heterolevels involving possibly
different RHF and MP2 calculations for the geometry and the energy. The basis
sets used belong ... | [
{
"created": "Fri, 27 Apr 2007 17:26:29 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Jun 2007 08:36:49 GMT",
"version": "v2"
}
] | 2013-06-21 | [
[
"Echenique",
"Pablo",
""
],
[
"Alonso",
"J. L.",
""
]
] | We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries (MCs) used are constructed as homo- and heterolevels involving possibly different RHF and MP2 calculations for the geometry and the energy. The basis sets used belong to... |
1811.00941 | Yuri A. Dabaghian | Andrey Babichev, Dmitriy Morozov and Yuri Dabaghian | Replays of spatial memories suppress topological fluctuations in
cognitive map | 21 pages, 5 figures, 3 supplementary figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The spiking activity of the hippocampal place cells plays a key role in
producing and sustaining an internalized representation of the ambient
space---a cognitive map. These cells do not only exhibit location-specific
spiking during navigation, but also may rapidly replay the navigated routs
through endogenous dynami... | [
{
"created": "Fri, 2 Nov 2018 15:43:40 GMT",
"version": "v1"
}
] | 2018-11-05 | [
[
"Babichev",
"Andrey",
""
],
[
"Morozov",
"Dmitriy",
""
],
[
"Dabaghian",
"Yuri",
""
]
] | The spiking activity of the hippocampal place cells plays a key role in producing and sustaining an internalized representation of the ambient space---a cognitive map. These cells do not only exhibit location-specific spiking during navigation, but also may rapidly replay the navigated routs through endogenous dynamics... |
1212.3205 | Olivier Rivoire | Olivier Rivoire | Elements of Coevolution in Biological Sequences | null | Phys. Rev. Lett. 110, 178102 (2013) | 10.1103/PhysRevLett.110.178102 | null | q-bio.BM cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Studies of coevolution of amino acids within and between proteins have
revealed two types of coevolving units: coevolving contacts, which are pairs of
amino acids distant along the sequence but in contact in the three-dimensional
structure, and sectors, which are larger groups of structurally connected amino
acids th... | [
{
"created": "Thu, 13 Dec 2012 16:05:33 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Apr 2013 07:16:05 GMT",
"version": "v2"
}
] | 2015-06-12 | [
[
"Rivoire",
"Olivier",
""
]
] | Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure, and sectors, which are larger groups of structurally connected amino acids that... |
1205.6194 | Patrick Coquillard | Patrick Coquillard (IBSV), Alexandre Muzy (LISA), Francine Diener | Optimal phenotypic plasticity in a stochastic environment minimizes the
cost/benefit ratio | null | Ecological Modelling 242 (2012) 28-36 | 10.1016/j.ecolmodel.2012.05.019 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper addresses the question of optimal phenotypic plasticity as a
response to environmental fluctuations while optimizing the cost/benefit ratio,
where the cost is energetic expense of plasticity, and benefit is fitness. The
dispersion matrix \Sigma of the genes' response (H = ln|\Sigma|) is used: (i)
in a nume... | [
{
"created": "Mon, 28 May 2012 19:36:11 GMT",
"version": "v1"
}
] | 2012-11-12 | [
[
"Coquillard",
"Patrick",
"",
"IBSV"
],
[
"Muzy",
"Alexandre",
"",
"LISA"
],
[
"Diener",
"Francine",
""
]
] | This paper addresses the question of optimal phenotypic plasticity as a response to environmental fluctuations while optimizing the cost/benefit ratio, where the cost is energetic expense of plasticity, and benefit is fitness. The dispersion matrix \Sigma of the genes' response (H = ln|\Sigma|) is used: (i) in a numeri... |
q-bio/0501023 | Alan McKane | A. J. McKane and T. J. Newman | Predator-prey cycles from resonant amplification of demographic
stochasticity | 4 pages, 2 figures | null | 10.1103/PhysRevLett.94.218102 | null | q-bio.PE | null | In this paper we present the simplest individual level model of predator-prey
dynamics and show, via direct calculation, that it exhibits cycling behavior.
The deterministic analogue of our model, recovered when the number of
individuals is infinitely large, is the Volterra system (with density-dependent
prey reprodu... | [
{
"created": "Sun, 16 Jan 2005 14:53:23 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"McKane",
"A. J.",
""
],
[
"Newman",
"T. J.",
""
]
] | In this paper we present the simplest individual level model of predator-prey dynamics and show, via direct calculation, that it exhibits cycling behavior. The deterministic analogue of our model, recovered when the number of individuals is infinitely large, is the Volterra system (with density-dependent prey reproduct... |
1809.04872 | Tanja Slotte | Tiina M. Mattila, Benjamin Laenen, Tanja Slotte | Population genomics of transitions to selfing in Brassicaceae model
systems | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Many plants harbor complex mechanisms that promote outcrossing and efficient
pollen transfer. These include floral adaptations as well as genetic
mechanisms, such as molecular self-incompatibility (SI) systems. The
maintenance of such systems over long evolutionary timescales suggests that
outcrossing is favorable ov... | [
{
"created": "Thu, 13 Sep 2018 10:19:05 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Jan 2019 14:18:07 GMT",
"version": "v2"
}
] | 2019-01-08 | [
[
"Mattila",
"Tiina M.",
""
],
[
"Laenen",
"Benjamin",
""
],
[
"Slotte",
"Tanja",
""
]
] | Many plants harbor complex mechanisms that promote outcrossing and efficient pollen transfer. These include floral adaptations as well as genetic mechanisms, such as molecular self-incompatibility (SI) systems. The maintenance of such systems over long evolutionary timescales suggests that outcrossing is favorable over... |
2009.08101 | Robert Prentner | Robert Prentner | Attracting Sets in Perceptual Networks | null | null | null | null | q-bio.NC cs.NE | http://creativecommons.org/licenses/by/4.0/ | This document gives a specification for the model used in [1]. It presents a
simple way of optimizing mutual information between some input and the
attractors of a (noisy) network, using a genetic algorithm. The nodes of this
network are modeled as simplified versions of the structures described in the
"interface the... | [
{
"created": "Thu, 17 Sep 2020 06:46:44 GMT",
"version": "v1"
}
] | 2020-09-18 | [
[
"Prentner",
"Robert",
""
]
] | This document gives a specification for the model used in [1]. It presents a simple way of optimizing mutual information between some input and the attractors of a (noisy) network, using a genetic algorithm. The nodes of this network are modeled as simplified versions of the structures described in the "interface theor... |
2202.13004 | Michael Kochen | Michael A. Kochen, H. Steven Wiley, Song Feng, Herbert M. Sauro | SBbadger: Biochemical Reaction Networks with Definable Degree
Distributions | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Motivation: An essential step in developing computational tools for the
inference, optimization, and simulation of biochemical reaction networks is
gauging tool performance against earlier efforts using an appropriate set of
benchmarks. General strategies for the assembly of benchmark models include
collection from t... | [
{
"created": "Fri, 25 Feb 2022 22:32:17 GMT",
"version": "v1"
},
{
"created": "Sun, 24 Jul 2022 20:23:21 GMT",
"version": "v2"
},
{
"created": "Sun, 28 Aug 2022 23:57:05 GMT",
"version": "v3"
},
{
"created": "Mon, 12 Sep 2022 19:03:14 GMT",
"version": "v4"
}
] | 2022-09-14 | [
[
"Kochen",
"Michael A.",
""
],
[
"Wiley",
"H. Steven",
""
],
[
"Feng",
"Song",
""
],
[
"Sauro",
"Herbert M.",
""
]
] | Motivation: An essential step in developing computational tools for the inference, optimization, and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the... |
1602.05832 | Karolis Uziela | Karolis Uziela, Bj\"orn Wallner, Arne Elofsson | ProQ3: Improved model quality assessments using Rosetta energy terms | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: To assess the quality of a protein model, i.e. to estimate how
close it is to its native structure, using no other information than the
structure of the model has been shown to be useful for structure prediction.
The state of the art method, ProQ2, is based on a machine learning approach
that uses a numbe... | [
{
"created": "Mon, 25 Jan 2016 14:32:48 GMT",
"version": "v1"
}
] | 2016-02-19 | [
[
"Uziela",
"Karolis",
""
],
[
"Wallner",
"Björn",
""
],
[
"Elofsson",
"Arne",
""
]
] | Motivation: To assess the quality of a protein model, i.e. to estimate how close it is to its native structure, using no other information than the structure of the model has been shown to be useful for structure prediction. The state of the art method, ProQ2, is based on a machine learning approach that uses a number ... |
1908.03264 | Ruben Sanchez-Romero | Ruben Sanchez-Romero, Joseph D. Ramsey, Kun Zhang, Clark Glymour | Identification of Effective Connectivity Subregions | null | null | null | null | q-bio.NC cs.LG eess.IV q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Standard fMRI connectivity analyses depend on aggregating the time series of
individual voxels within regions of interest (ROIs). In certain cases, this
spatial aggregation implies a loss of valuable functional and anatomical
information about smaller subsets of voxels that drive the ROI level
connectivity. We use tw... | [
{
"created": "Thu, 8 Aug 2019 20:43:22 GMT",
"version": "v1"
}
] | 2019-08-12 | [
[
"Sanchez-Romero",
"Ruben",
""
],
[
"Ramsey",
"Joseph D.",
""
],
[
"Zhang",
"Kun",
""
],
[
"Glymour",
"Clark",
""
]
] | Standard fMRI connectivity analyses depend on aggregating the time series of individual voxels within regions of interest (ROIs). In certain cases, this spatial aggregation implies a loss of valuable functional and anatomical information about smaller subsets of voxels that drive the ROI level connectivity. We use two ... |
2301.09570 | Ahmed Ayman | Ahmed Ayman - Mohamed Sabry | A Novel Power-optimized CMOS sEMG Device with Ultra Low-noise integrated
with ConvNet (VGG16) for Biomedical Applications | null | null | 10.13140/RG.2.2.28054.63044 | null | q-bio.NC | http://creativecommons.org/licenses/by-sa/4.0/ | The needle bio-potential sensors for measuring muscle and brain activity need
invasive surgical targeted muscle reinnervation (TMR) and a demanding process
to maintain, but surface bio-potential sensors lack clear bio-signal reading
(Signal-Interference). In this research, a novel power-optimized complementary
metal-... | [
{
"created": "Wed, 4 Jan 2023 01:46:55 GMT",
"version": "v1"
},
{
"created": "Wed, 10 May 2023 14:45:52 GMT",
"version": "v2"
}
] | 2023-05-11 | [
[
"Sabry",
"Ahmed Ayman - Mohamed",
""
]
] | The needle bio-potential sensors for measuring muscle and brain activity need invasive surgical targeted muscle reinnervation (TMR) and a demanding process to maintain, but surface bio-potential sensors lack clear bio-signal reading (Signal-Interference). In this research, a novel power-optimized complementary metal-ox... |
1308.0668 | David Lusseau | David Lusseau | Quantum-like perception entanglement leads to advantageous collective
decisions | 8 pages, 3 figures, paper presented at the XXXIII International
Ethological Congress, 8 August 2013, Newcastle-upon-Tyne, UK | null | null | null | q-bio.PE q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Social animals have to make collective decisions on a daily basis. In most
instances, these decisions are taken by consensus, when the group does what the
majority of individuals want. Individuals have to base these decisions on the
information they perceive from their socioecological landscape. The perception
mechan... | [
{
"created": "Sat, 3 Aug 2013 07:54:08 GMT",
"version": "v1"
}
] | 2013-08-06 | [
[
"Lusseau",
"David",
""
]
] | Social animals have to make collective decisions on a daily basis. In most instances, these decisions are taken by consensus, when the group does what the majority of individuals want. Individuals have to base these decisions on the information they perceive from their socioecological landscape. The perception mechanis... |
1902.05621 | Saeed Ranjbar | Ali Esmaeili and Saeed Ranjbar | A Revision of the Bernoulli Equation as a Controller of the Fick's
Diffusion Equation in Drug Delivery Modeling | 5 pages, 1 figure | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mathematical equations can be used as effectual tools in drug delivery
systems modeling and are also highly helpful to have a theoretical
understanding of controlled drug release and diffusion mechanisms. In this
study we aim to present a mathematical combination between the Bernoulli
equation and the Fick's equation... | [
{
"created": "Wed, 30 Jan 2019 13:49:21 GMT",
"version": "v1"
}
] | 2019-02-18 | [
[
"Esmaeili",
"Ali",
""
],
[
"Ranjbar",
"Saeed",
""
]
] | Mathematical equations can be used as effectual tools in drug delivery systems modeling and are also highly helpful to have a theoretical understanding of controlled drug release and diffusion mechanisms. In this study we aim to present a mathematical combination between the Bernoulli equation and the Fick's equation a... |
q-bio/0311012 | Pau Fern\'andez | Pau Fernandez and Ricard V. Sole | The Role of Computation in Complex Regulatory Networks | to appear in "Scale-free Networks and Genome Biology", E. Koonin et
al. (eds.), Landes Bioscience (2003) | null | null | null | q-bio.MN q-bio.GN q-bio.PE | null | Biological phenomena differ significantly from physical phenomena. At the
heart of this distinction is the fact that biological entities have
computational abilities and thus they are inherently difficult to predict. This
is the reason why simplified models that provide the minimal requirements for
computation turn o... | [
{
"created": "Mon, 10 Nov 2003 13:22:35 GMT",
"version": "v1"
}
] | 2009-09-29 | [
[
"Fernandez",
"Pau",
""
],
[
"Sole",
"Ricard V.",
""
]
] | Biological phenomena differ significantly from physical phenomena. At the heart of this distinction is the fact that biological entities have computational abilities and thus they are inherently difficult to predict. This is the reason why simplified models that provide the minimal requirements for computation turn out... |
1011.2071 | Steven Duplij | Diana Duplij (Institute of Molecular Biology and Genetics, Kiev,
Ukraine) | Comparative analysis of the nucleotide composition biases in exons and
introns of human genes | 8 pages, 2 figures, 1 table | null | null | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The nucleotide composition of human genes with a special emphasis on
transcription-related strand asymmetries is analyzed. Such asymmetries may be
associated with different mutational rates in two principal factors. The first
one is transcription-coupled repair and the second one is the selective
pressure related to ... | [
{
"created": "Tue, 9 Nov 2010 13:11:31 GMT",
"version": "v1"
}
] | 2010-11-10 | [
[
"Duplij",
"Diana",
"",
"Institute of Molecular Biology and Genetics, Kiev,\n Ukraine"
]
] | The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is transcription-coupled repair and the second one is the selective pressure related to op... |
1609.08611 | Jimmy Garnier | Jimmy Garnier (CNRS, USMB, Universit\'e de Savoie, Universit\'e de
Chamb\'ery), Mark Lewis | Expansion under climate change: the genetic consequences | null | Bulletin of Mathematical Biology, Springer Verlag, 2016 | null | null | q-bio.PE math.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Range expansion and range shifts are crucial population responses to climate
change. Genetic consequences are not well understood but are clearly coupled to
ecological dynamics that, in turn, are driven by shifting climate conditions.
We model a population with a deterministic reaction-- diffusion model coupled
to a ... | [
{
"created": "Tue, 27 Sep 2016 14:39:42 GMT",
"version": "v1"
}
] | 2016-09-29 | [
[
"Garnier",
"Jimmy",
"",
"CNRS, USMB, Université de Savoie, Université de\n Chambéry"
],
[
"Lewis",
"Mark",
""
]
] | Range expansion and range shifts are crucial population responses to climate change. Genetic consequences are not well understood but are clearly coupled to ecological dynamics that, in turn, are driven by shifting climate conditions. We model a population with a deterministic reaction-- diffusion model coupled to a he... |
1712.00351 | Wilfred Ndifon | A. M. Degoot, Faraimunashe Chirove, and Wilfred Ndifon | Trans-allelic model for prediction of peptide:MHC-II interactions | null | null | null | null | q-bio.QM q-bio.BM q-bio.GN stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Major histocompatibility complex class two (MHC-II) molecules are
trans-membrane proteins and key components of the cellular immune system. Upon
recognition of foreign peptides expressed on the MHC-II binding groove, helper
T cells mount an immune response against invading pathogens. Therefore,
mechanistic identifica... | [
{
"created": "Fri, 1 Dec 2017 15:03:40 GMT",
"version": "v1"
}
] | 2017-12-05 | [
[
"Degoot",
"A. M.",
""
],
[
"Chirove",
"Faraimunashe",
""
],
[
"Ndifon",
"Wilfred",
""
]
] | Major histocompatibility complex class two (MHC-II) molecules are trans-membrane proteins and key components of the cellular immune system. Upon recognition of foreign peptides expressed on the MHC-II binding groove, helper T cells mount an immune response against invading pathogens. Therefore, mechanistic identificati... |
2306.10168 | Mitchell Ostrow | Mitchell Ostrow, Adam Eisen, Leo Kozachkov, Ila Fiete | Beyond Geometry: Comparing the Temporal Structure of Computation in
Neural Circuits with Dynamical Similarity Analysis | 22 pages, 9 figures | null | null | null | q-bio.NC cs.LG cs.NE q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | How can we tell whether two neural networks utilize the same internal
processes for a particular computation? This question is pertinent for multiple
subfields of neuroscience and machine learning, including neuroAI, mechanistic
interpretability, and brain-machine interfaces. Standard approaches for
comparing neural ... | [
{
"created": "Fri, 16 Jun 2023 20:11:38 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Aug 2023 15:57:35 GMT",
"version": "v2"
},
{
"created": "Sun, 29 Oct 2023 18:13:46 GMT",
"version": "v3"
}
] | 2023-10-31 | [
[
"Ostrow",
"Mitchell",
""
],
[
"Eisen",
"Adam",
""
],
[
"Kozachkov",
"Leo",
""
],
[
"Fiete",
"Ila",
""
]
] | How can we tell whether two neural networks utilize the same internal processes for a particular computation? This question is pertinent for multiple subfields of neuroscience and machine learning, including neuroAI, mechanistic interpretability, and brain-machine interfaces. Standard approaches for comparing neural ne... |
1606.07497 | Keith Burghardt | Keith Burghardt, Christopher Verzijl, Junming Huang, Matthew Ingram,
Binyang Song, Marie-Pierre Hasne | Testing Modeling Assumptions in the West Africa Ebola Outbreak | 16 pages, 14 figures | Sci. Rep., 6: 34598 (2016) | 10.1038/srep34598 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Ebola virus in West Africa has infected almost 30,000 and killed over
11,000 people. Recent models of Ebola Virus Disease (EVD) have often made
assumptions about how the disease spreads, such as uniform transmissibility and
homogeneous mixing within a population. In this paper, we test whether these
assumptions a... | [
{
"created": "Thu, 23 Jun 2016 22:09:37 GMT",
"version": "v1"
},
{
"created": "Wed, 12 Oct 2016 18:12:43 GMT",
"version": "v2"
}
] | 2016-10-13 | [
[
"Burghardt",
"Keith",
""
],
[
"Verzijl",
"Christopher",
""
],
[
"Huang",
"Junming",
""
],
[
"Ingram",
"Matthew",
""
],
[
"Song",
"Binyang",
""
],
[
"Hasne",
"Marie-Pierre",
""
]
] | The Ebola virus in West Africa has infected almost 30,000 and killed over 11,000 people. Recent models of Ebola Virus Disease (EVD) have often made assumptions about how the disease spreads, such as uniform transmissibility and homogeneous mixing within a population. In this paper, we test whether these assumptions are... |
1712.10280 | Hongbo Jia | Hongbo Jia | First Draft on the xInf Model for Universal Physical Computation and
Reverse Engineering of Natural Intelligence | 32 pages, 4 figures | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Turing Machines are universal computing machines in theory. It has been a
long debate whether Turing Machines can simulate the consciousness mind
behaviors in the materialistic universe. Three different hypotheses come out of
such debate, in short:(A) Can; (B) Cannot; (C) Super-Turing machines can.
Because Turing Mac... | [
{
"created": "Tue, 26 Dec 2017 23:36:43 GMT",
"version": "v1"
}
] | 2018-01-01 | [
[
"Jia",
"Hongbo",
""
]
] | Turing Machines are universal computing machines in theory. It has been a long debate whether Turing Machines can simulate the consciousness mind behaviors in the materialistic universe. Three different hypotheses come out of such debate, in short:(A) Can; (B) Cannot; (C) Super-Turing machines can. Because Turing Machi... |
2011.12832 | Ailar Mahdizadeh | Emad Arasteh Emamzadeh-Hashemi, Ailar Mahdizadeh | External Electromagnetic Wave Excitation of a PreSynaptic Neuron Based
on LIF model | 5pages,4figures,etech2020 | null | null | null | q-bio.NC cs.SY eess.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Interaction of electromagnetic (EM) waves with human tissue has been a
longstanding research topic for electrical and biomedical engineers. However,
few numbers of publications discuss the impacts of external EM-waves on neural
stimulation and communication through the nervous system. In fact, complex
biological neur... | [
{
"created": "Wed, 25 Nov 2020 15:40:38 GMT",
"version": "v1"
}
] | 2020-11-26 | [
[
"Emamzadeh-Hashemi",
"Emad Arasteh",
""
],
[
"Mahdizadeh",
"Ailar",
""
]
] | Interaction of electromagnetic (EM) waves with human tissue has been a longstanding research topic for electrical and biomedical engineers. However, few numbers of publications discuss the impacts of external EM-waves on neural stimulation and communication through the nervous system. In fact, complex biological neural... |
2004.14467 | Nida Obatake | Nida Obatake, Anne Shiu, Dilruba Sofia | Mixed volume of small reaction networks | null | Involve 13 (2020) 845-860 | 10.2140/involve.2020.13.845 | null | q-bio.MN math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An important invariant of a chemical reaction network is its maximum number
of positive steady states. This number, however, is in general difficult to
compute. Nonetheless, there is an upper bound on this number -- namely, a
network's mixed volume -- that is easy to compute. Moreover, recent work has
shown that, for... | [
{
"created": "Wed, 29 Apr 2020 20:45:48 GMT",
"version": "v1"
}
] | 2020-12-09 | [
[
"Obatake",
"Nida",
""
],
[
"Shiu",
"Anne",
""
],
[
"Sofia",
"Dilruba",
""
]
] | An important invariant of a chemical reaction network is its maximum number of positive steady states. This number, however, is in general difficult to compute. Nonetheless, there is an upper bound on this number -- namely, a network's mixed volume -- that is easy to compute. Moreover, recent work has shown that, for c... |
2005.02859 | Carles Rovira | Xavier Bardina, Marco Ferrante, Carles Rovira | A stochastic epidemic model of COVID-19 disease | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To model the evolution of diseases with extended latency periods and the
presence of asymptomatic patients like COVID-19, we define a simple discrete
time stochastic SIR-type epidemic model. We include both latent periods as well
as the presence of quarantine areas, to capture the evolutionary dynamics of
such diseas... | [
{
"created": "Mon, 4 May 2020 14:43:49 GMT",
"version": "v1"
},
{
"created": "Wed, 13 May 2020 09:34:38 GMT",
"version": "v2"
}
] | 2020-05-14 | [
[
"Bardina",
"Xavier",
""
],
[
"Ferrante",
"Marco",
""
],
[
"Rovira",
"Carles",
""
]
] | To model the evolution of diseases with extended latency periods and the presence of asymptomatic patients like COVID-19, we define a simple discrete time stochastic SIR-type epidemic model. We include both latent periods as well as the presence of quarantine areas, to capture the evolutionary dynamics of such diseases... |
1703.10713 | Jiancheng Zhuang | Jiancheng Zhuang | Detecting Resting-state Neural Connectivity Using Dynamic Network
Analysis on Multiband fMRI Data | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper describes an approach of using dynamic Structural Equation
Modeling (SEM) analysis to estimate the connectivity networks from
resting-state fMRI data measured by a multiband EPI sequence. Two structural
equation models were estimated at each voxel with respect to the sensory-motor
network and default-mode ... | [
{
"created": "Thu, 30 Mar 2017 23:38:20 GMT",
"version": "v1"
}
] | 2017-04-03 | [
[
"Zhuang",
"Jiancheng",
""
]
] | This paper describes an approach of using dynamic Structural Equation Modeling (SEM) analysis to estimate the connectivity networks from resting-state fMRI data measured by a multiband EPI sequence. Two structural equation models were estimated at each voxel with respect to the sensory-motor network and default-mode ne... |
2309.16513 | Yannis Drossinos | Yannis Drossinos and Nikolaos I. Stilianakis | On modeling airborne infection risk | 15 pages, 3 figures | R. Soc. Open Sci. 11:231976 (2024) | 10.1098/rsos.231976 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Airborne infection risk analysis is usually performed for enclosed spaces
where susceptible individuals are exposed to infectious airborne respiratory
droplets by inhalation. It is usually based on exponential, dose-response
models of which a widely used variant is the Wells-Riley (WR) model. We revisit
this infectio... | [
{
"created": "Thu, 28 Sep 2023 15:19:39 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Dec 2023 17:03:48 GMT",
"version": "v2"
}
] | 2024-08-01 | [
[
"Drossinos",
"Yannis",
""
],
[
"Stilianakis",
"Nikolaos I.",
""
]
] | Airborne infection risk analysis is usually performed for enclosed spaces where susceptible individuals are exposed to infectious airborne respiratory droplets by inhalation. It is usually based on exponential, dose-response models of which a widely used variant is the Wells-Riley (WR) model. We revisit this infection-... |
1301.3318 | Tomas Tokar | Csilla Ulicna and Jozef Ulicny | Integration of TNF induced apoptosis model and quantitative proteomics
data of HeLa cells - our first experience | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The TNF initiated processes are simulated using our integrative computational
model with new quantitative proteomics data obtained on HeLa cell line. In
spite of fact, that the model development is based on limited experimental
information, with missing data estimated by simulations and parametrization
using indirect... | [
{
"created": "Tue, 15 Jan 2013 12:21:32 GMT",
"version": "v1"
}
] | 2013-01-16 | [
[
"Ulicna",
"Csilla",
""
],
[
"Ulicny",
"Jozef",
""
]
] | The TNF initiated processes are simulated using our integrative computational model with new quantitative proteomics data obtained on HeLa cell line. In spite of fact, that the model development is based on limited experimental information, with missing data estimated by simulations and parametrization using indirect e... |
2203.13132 | Yan Yang | Yan Yang and Zakir Hossain and Khandaker Asif and Liyuan Pan and
Shafin Rahman and Eric Stone | DPST: De Novo Peptide Sequencing with Amino-Acid-Aware Transformers | null | null | null | null | q-bio.QM cs.LG q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | De novo peptide sequencing aims to recover amino acid sequences of a peptide
from tandem mass spectrometry (MS) data. Existing approaches for de novo
analysis enumerate MS evidence for all amino acid classes during inference. It
leads to over-trimming on receptive fields of MS data and restricts MS evidence
associate... | [
{
"created": "Wed, 23 Mar 2022 08:01:06 GMT",
"version": "v1"
}
] | 2022-03-25 | [
[
"Yang",
"Yan",
""
],
[
"Hossain",
"Zakir",
""
],
[
"Asif",
"Khandaker",
""
],
[
"Pan",
"Liyuan",
""
],
[
"Rahman",
"Shafin",
""
],
[
"Stone",
"Eric",
""
]
] | De novo peptide sequencing aims to recover amino acid sequences of a peptide from tandem mass spectrometry (MS) data. Existing approaches for de novo analysis enumerate MS evidence for all amino acid classes during inference. It leads to over-trimming on receptive fields of MS data and restricts MS evidence associated ... |
0912.0750 | Aran Nayebi | Aran Nayebi | Fast matrix multiplication techniques based on the Adleman-Lipton model | To appear in the International Journal of Computer Engineering
Research. Minor changes made to make the preprint as similar as possible to
the published version | International Journal of Computer Engineering Research,
3(1):10-19, January 2012 | 10.5897/IJCER10.016 | null | q-bio.QM cs.DS cs.ET | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | On distributed memory electronic computers, the implementation and
association of fast parallel matrix multiplication algorithms has yielded
astounding results and insights. In this discourse, we use the tools of
molecular biology to demonstrate the theoretical encoding of Strassen's fast
matrix multiplication algori... | [
{
"created": "Thu, 3 Dec 2009 23:04:18 GMT",
"version": "v1"
},
{
"created": "Sun, 5 Sep 2010 16:43:23 GMT",
"version": "v2"
},
{
"created": "Wed, 16 Feb 2011 15:44:55 GMT",
"version": "v3"
},
{
"created": "Sat, 28 May 2011 16:25:32 GMT",
"version": "v4"
},
{
"cre... | 2012-02-10 | [
[
"Nayebi",
"Aran",
""
]
] | On distributed memory electronic computers, the implementation and association of fast parallel matrix multiplication algorithms has yielded astounding results and insights. In this discourse, we use the tools of molecular biology to demonstrate the theoretical encoding of Strassen's fast matrix multiplication algorith... |
q-bio/0401011 | Eivind T{\o}stesen | E. Tostesen, F. Liu, T.-K. Jenssen, E. Hovig | Speed-Up of DNA Melting Algorithm with Complete Nearest Neighbor
Properties | 20 pages, 4 figures | Biopolymers, 70, 364-376 (2003) | 10.1002/bip.10495 | null | q-bio.BM | null | We describe a faster and more accurate algorithm for computing the
statistical mechanics of DNA denaturation according to the Poland-Scheraga
type. Nearest neighbor thermodynamics is included in a complete and general
way. The algorithm represents an optimization with respect to algorithmic
complexity of the partitio... | [
{
"created": "Thu, 8 Jan 2004 12:05:22 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Tostesen",
"E.",
""
],
[
"Liu",
"F.",
""
],
[
"Jenssen",
"T. -K.",
""
],
[
"Hovig",
"E.",
""
]
] | We describe a faster and more accurate algorithm for computing the statistical mechanics of DNA denaturation according to the Poland-Scheraga type. Nearest neighbor thermodynamics is included in a complete and general way. The algorithm represents an optimization with respect to algorithmic complexity of the partition ... |
q-bio/0609027 | Antonio Leon | Antonio Leon | Coevolution. Extending Prigogine Theorem | 16 pages, 9 figures | null | null | null | q-bio.PE math.DS | null | The formal consideration of the concept of interaction in thermodynamic
analysis makes it possible to deduce, in the broadest terms, new results
related to the coevolution of interacting systems, irrespective of their
distance from thermodynamic equilibrium. In this paper I prove the existence of
privileged coevoluti... | [
{
"created": "Tue, 19 Sep 2006 10:31:13 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Apr 2008 18:33:32 GMT",
"version": "v2"
}
] | 2008-05-04 | [
[
"Leon",
"Antonio",
""
]
] | The formal consideration of the concept of interaction in thermodynamic analysis makes it possible to deduce, in the broadest terms, new results related to the coevolution of interacting systems, irrespective of their distance from thermodynamic equilibrium. In this paper I prove the existence of privileged coevolution... |
2004.01602 | David F. Nettleton | David F. Nettleton, Dimitrios Katsantonis, Argyris Kalaitzidis, Natasa
Sarafijanovic-Djukic, Pau Puigdollers and Roberto Confalonieri | Predicting rice blast disease: machine learning versus process based
models | null | BMC Bioinformatics volume 20, Article number: 514 (2019) | 10.1186/s12859-019-3065-1 | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rice is the second most important cereal crop worldwide, and the first in
terms of number of people who depend on it as a major staple food. Rice blast
disease is the most important biotic constraint of rice cultivation causing
each year millions of dollars of losses. Despite the efforts for breeding new
resistant va... | [
{
"created": "Fri, 3 Apr 2020 14:48:14 GMT",
"version": "v1"
}
] | 2021-01-07 | [
[
"Nettleton",
"David F.",
""
],
[
"Katsantonis",
"Dimitrios",
""
],
[
"Kalaitzidis",
"Argyris",
""
],
[
"Sarafijanovic-Djukic",
"Natasa",
""
],
[
"Puigdollers",
"Pau",
""
],
[
"Confalonieri",
"Roberto",
""
]
] | Rice is the second most important cereal crop worldwide, and the first in terms of number of people who depend on it as a major staple food. Rice blast disease is the most important biotic constraint of rice cultivation causing each year millions of dollars of losses. Despite the efforts for breeding new resistant vari... |
1606.08363 | Matthew Spencer | Katherine A. Allen, John F. Bruno, Fiona Chong, Damian Clancy, Tim R.
McClanahan, Matthew Spencer, Kamila Zychaluk | Among-site variability in the stochastic dynamics of East African coral
reefs | 97 pages, 49 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Coral reefs are dynamic systems whose composition is highly influenced by
unpredictable biotic and abiotic factors. Understanding the spatial scale at
which long-term predictions of reef composition can be made will be crucial for
guiding conservation efforts. Using a 22-year time series of benthic
composition data f... | [
{
"created": "Mon, 27 Jun 2016 16:44:52 GMT",
"version": "v1"
}
] | 2016-06-28 | [
[
"Allen",
"Katherine A.",
""
],
[
"Bruno",
"John F.",
""
],
[
"Chong",
"Fiona",
""
],
[
"Clancy",
"Damian",
""
],
[
"McClanahan",
"Tim R.",
""
],
[
"Spencer",
"Matthew",
""
],
[
"Zychaluk",
"Kamila",
""
]
... | Coral reefs are dynamic systems whose composition is highly influenced by unpredictable biotic and abiotic factors. Understanding the spatial scale at which long-term predictions of reef composition can be made will be crucial for guiding conservation efforts. Using a 22-year time series of benthic composition data fro... |
1403.4086 | Hande Topa | Hande Topa, \'Agnes J\'on\'as, Robert Kofler, Carolin Kosiol, Antti
Honkela | Gaussian process test for high-throughput sequencing time series:
application to experimental evolution | 41 pages, 29 figures | null | null | null | q-bio.PE q-bio.GN q-bio.QM stat.AP | http://creativecommons.org/licenses/by/3.0/ | Motivation: Recent advances in high-throughput sequencing (HTS) have made it
possible to monitor genomes in great detail. New experiments not only use HTS
to measure genomic features at one time point but to monitor them changing over
time with the aim of identifying significant changes in their abundance. In
populat... | [
{
"created": "Mon, 17 Mar 2014 13:08:06 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Mar 2014 14:14:25 GMT",
"version": "v2"
},
{
"created": "Thu, 18 Sep 2014 07:59:09 GMT",
"version": "v3"
}
] | 2014-09-19 | [
[
"Topa",
"Hande",
""
],
[
"Jónás",
"Ágnes",
""
],
[
"Kofler",
"Robert",
""
],
[
"Kosiol",
"Carolin",
""
],
[
"Honkela",
"Antti",
""
]
] | Motivation: Recent advances in high-throughput sequencing (HTS) have made it possible to monitor genomes in great detail. New experiments not only use HTS to measure genomic features at one time point but to monitor them changing over time with the aim of identifying significant changes in their abundance. In populatio... |
2303.01514 | Chris Fields | Chris Fields, Filippo Fabrocini, Karl Friston, James F. Glazebrook,
Hananel Hazan, Michael Levin, and Antonino Marciano | Control flow in active inference systems | 44 pgs | null | null | null | q-bio.NC physics.bio-ph quant-ph | http://creativecommons.org/licenses/by/4.0/ | Living systems face both environmental complexity and limited access to
free-energy resources. Survival under these conditions requires a control
system that can activate, or deploy, available perception and action resources
in a context specific way. We show here that when systems are described as
executing active i... | [
{
"created": "Sat, 25 Feb 2023 02:31:47 GMT",
"version": "v1"
}
] | 2023-03-06 | [
[
"Fields",
"Chris",
""
],
[
"Fabrocini",
"Filippo",
""
],
[
"Friston",
"Karl",
""
],
[
"Glazebrook",
"James F.",
""
],
[
"Hazan",
"Hananel",
""
],
[
"Levin",
"Michael",
""
],
[
"Marciano",
"Antonino",
""
]... | Living systems face both environmental complexity and limited access to free-energy resources. Survival under these conditions requires a control system that can activate, or deploy, available perception and action resources in a context specific way. We show here that when systems are described as executing active inf... |
1709.02268 | Giuseppe Jurman | Diego Fioravanti, Ylenia Giarratano, Valerio Maggio, Claudio
Agostinelli, Marco Chierici, Giuseppe Jurman and Cesare Furlanello | Phylogenetic Convolutional Neural Networks in Metagenomics | Presented at BMTL 2017, Naples | null | null | null | q-bio.QM cs.LG cs.NE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Convolutional Neural Networks can be effectively used only when
data are endowed with an intrinsic concept of neighbourhood in the input space,
as is the case of pixels in images. We introduce here Ph-CNN, a novel deep
learning architecture for the classification of metagenomics data based on the
Convolut... | [
{
"created": "Wed, 6 Sep 2017 12:59:14 GMT",
"version": "v1"
}
] | 2017-09-08 | [
[
"Fioravanti",
"Diego",
""
],
[
"Giarratano",
"Ylenia",
""
],
[
"Maggio",
"Valerio",
""
],
[
"Agostinelli",
"Claudio",
""
],
[
"Chierici",
"Marco",
""
],
[
"Jurman",
"Giuseppe",
""
],
[
"Furlanello",
"Cesare",
... | Background: Convolutional Neural Networks can be effectively used only when data are endowed with an intrinsic concept of neighbourhood in the input space, as is the case of pixels in images. We introduce here Ph-CNN, a novel deep learning architecture for the classification of metagenomics data based on the Convolutio... |
2303.08200 | Jacek Mi\c{e}kisz | Jacek Mi\c{e}kisz, Javad Mohamadichamgavi, Raffi Vardanyan | Small time delay approximation in replicator dynamics | 8 pages, 2 figures | null | null | null | q-bio.PE math.DS physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | We present a microscopic model of replicator dynamics with strategy-dependent
time delays. In such a model, new players are born from parents who interacted
and received payoffs in the past. In the case of small delays, we use Taylor
expansion to get ordinary differential equations for frequencies of strategies
with ... | [
{
"created": "Tue, 14 Mar 2023 19:39:37 GMT",
"version": "v1"
}
] | 2023-04-07 | [
[
"Miȩkisz",
"Jacek",
""
],
[
"Mohamadichamgavi",
"Javad",
""
],
[
"Vardanyan",
"Raffi",
""
]
] | We present a microscopic model of replicator dynamics with strategy-dependent time delays. In such a model, new players are born from parents who interacted and received payoffs in the past. In the case of small delays, we use Taylor expansion to get ordinary differential equations for frequencies of strategies with ti... |
1101.1311 | Mike Steel Prof. | Sha Zhu, James H. Degnan, Mike Steel | Clades, clans and reciprocal monophyly under neutral evolutionary models | 18 pages, 4 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Yule model and the coalescent model are two neutral stochastic models for
generating trees in phylogenetics and population genetics, respectively.
Although these models are quite different, they lead to identical distributions
concerning the probability that pre-specified groups of taxa form monophyletic
groups (... | [
{
"created": "Thu, 6 Jan 2011 21:17:38 GMT",
"version": "v1"
}
] | 2015-03-17 | [
[
"Zhu",
"Sha",
""
],
[
"Degnan",
"James H.",
""
],
[
"Steel",
"Mike",
""
]
] | The Yule model and the coalescent model are two neutral stochastic models for generating trees in phylogenetics and population genetics, respectively. Although these models are quite different, they lead to identical distributions concerning the probability that pre-specified groups of taxa form monophyletic groups (cl... |
1210.0024 | Kimberly Glass | Kimberly Glass and Michelle Girvan | Finding New Order in Biological Functions from the Network Structure of
Gene Annotations | null | null | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Gene Ontology (GO) provides biologists with a controlled terminology that
describes how genes are associated with functions and how functional terms are
related to each other. These term-term relationships encode how scientists
conceive the organization of biological functions, and they take the form of a
directe... | [
{
"created": "Fri, 28 Sep 2012 20:18:59 GMT",
"version": "v1"
},
{
"created": "Fri, 3 May 2013 21:47:39 GMT",
"version": "v2"
}
] | 2013-05-07 | [
[
"Glass",
"Kimberly",
""
],
[
"Girvan",
"Michelle",
""
]
] | The Gene Ontology (GO) provides biologists with a controlled terminology that describes how genes are associated with functions and how functional terms are related to each other. These term-term relationships encode how scientists conceive the organization of biological functions, and they take the form of a directed ... |
0812.1274 | Suan Li Mai | Mai Suan Li, D. K. Klimov, J. E. Straub, and D. Thirumalai | Probing the Mechanisms of Fibril Formation Using Lattice Models | 27 pages, 6 figures | J. Chem. Phys. 129, 175101 (2008) | 10.1063/1.2989981 | null | q-bio.BM q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Using exhaustive Monte Carlo simulations we study the kinetics and mechanism
of fibril formation using lattice models as a function of temperature and the
number of chains. While these models are, at best, caricatures of peptides, we
show that a number of generic features thought to govern fibril assembly are
present... | [
{
"created": "Sat, 6 Dec 2008 10:36:28 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Li",
"Mai Suan",
""
],
[
"Klimov",
"D. K.",
""
],
[
"Straub",
"J. E.",
""
],
[
"Thirumalai",
"D.",
""
]
] | Using exhaustive Monte Carlo simulations we study the kinetics and mechanism of fibril formation using lattice models as a function of temperature and the number of chains. While these models are, at best, caricatures of peptides, we show that a number of generic features thought to govern fibril assembly are present i... |
2207.12124 | Mohammad Alali | Mohammad Alali and Mahdi Imani | Inference of Regulatory Networks Through Temporally Sparse Data | 9 Pages, 6 Figures | Front Control Eng. 2022;3 | 10.3389/fcteg.2022.1017256 | null | q-bio.MN cs.LG stat.ME stat.ML | http://creativecommons.org/licenses/by/4.0/ | A major goal in genomics is to properly capture the complex dynamical
behaviors of gene regulatory networks (GRNs). This includes inferring the
complex interactions between genes, which can be used for a wide range of
genomics analyses, including diagnosis or prognosis of diseases and finding
effective treatments for... | [
{
"created": "Thu, 21 Jul 2022 22:48:12 GMT",
"version": "v1"
}
] | 2023-01-18 | [
[
"Alali",
"Mohammad",
""
],
[
"Imani",
"Mahdi",
""
]
] | A major goal in genomics is to properly capture the complex dynamical behaviors of gene regulatory networks (GRNs). This includes inferring the complex interactions between genes, which can be used for a wide range of genomics analyses, including diagnosis or prognosis of diseases and finding effective treatments for c... |
2307.14376 | Armita Nourmohammad | Giulio Isacchini, Valentin Quiniou, H\'el\`ene Vantomme, Paul Stys,
Encarnita Mariotti-Ferandiz, David Klatzmann, Aleksandra M. Walczak, Thierry
Mora, and Armita Nourmohammad | Variability in the local and global composition of human T-cell receptor
repertoires during thymic development across cell types and individuals | null | null | null | null | q-bio.QM q-bio.MN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The adaptive immune response relies on T cells that combine phenotypic
specialization with diversity of T cell receptors (TCRs) to recognize a wide
range of pathogens. TCRs are acquired and selected during T cell maturation in
the thymus. Characterizing TCR repertoires across individuals and T cell
maturation stages ... | [
{
"created": "Tue, 25 Jul 2023 17:17:47 GMT",
"version": "v1"
}
] | 2023-07-28 | [
[
"Isacchini",
"Giulio",
""
],
[
"Quiniou",
"Valentin",
""
],
[
"Vantomme",
"Hélène",
""
],
[
"Stys",
"Paul",
""
],
[
"Mariotti-Ferandiz",
"Encarnita",
""
],
[
"Klatzmann",
"David",
""
],
[
"Walczak",
"Aleksandra... | The adaptive immune response relies on T cells that combine phenotypic specialization with diversity of T cell receptors (TCRs) to recognize a wide range of pathogens. TCRs are acquired and selected during T cell maturation in the thymus. Characterizing TCR repertoires across individuals and T cell maturation stages is... |
q-bio/0404006 | Dorjsuren Battogtokh | Dorjsuren Battogtokh and John J. Tyson | Bifurcation analysis of a model of the budding yeast cell cycle | 31 pages,13 figures | null | 10.1063/1.1780011 | null | q-bio.MN | null | We study the bifurcations of a set of nine nonlinear ordinary differential
equations that describe the regulation of the cyclin-dependent kinase that
triggers DNA synthesis and mitosis in the budding yeast, Saccharomyces
cerevisiae. We show that Clb2-dependent kinase exhibits bistability (stable
steady states of high... | [
{
"created": "Mon, 5 Apr 2004 17:59:03 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Battogtokh",
"Dorjsuren",
""
],
[
"Tyson",
"John J.",
""
]
] | We study the bifurcations of a set of nine nonlinear ordinary differential equations that describe the regulation of the cyclin-dependent kinase that triggers DNA synthesis and mitosis in the budding yeast, Saccharomyces cerevisiae. We show that Clb2-dependent kinase exhibits bistability (stable steady states of high o... |
1108.2011 | Joachim Mathiesen | Joachim Mathiesen, Namiko Mitarai, Kim Sneppen and Ala Trusina | Ecosystems with mutually exclusive interactions self-organize to a state
of high diversity | 4 pages, 4 figures | Phys.Rev.Lett. 107, 188101 (2011) | 10.1103/PhysRevLett.107.188101 | null | q-bio.PE cond-mat.stat-mech nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ecological systems comprise an astonishing diversity of species that
cooperate or compete with each other forming complex mutual dependencies. The
minimum requirements to maintain a large species diversity on long time scales
are in general unknown. Using lichen communities as an example, we propose a
model for the e... | [
{
"created": "Mon, 8 Aug 2011 14:56:06 GMT",
"version": "v1"
}
] | 2012-09-10 | [
[
"Mathiesen",
"Joachim",
""
],
[
"Mitarai",
"Namiko",
""
],
[
"Sneppen",
"Kim",
""
],
[
"Trusina",
"Ala",
""
]
] | Ecological systems comprise an astonishing diversity of species that cooperate or compete with each other forming complex mutual dependencies. The minimum requirements to maintain a large species diversity on long time scales are in general unknown. Using lichen communities as an example, we propose a model for the evo... |
2003.01385 | Marc de Kamps | Hugh Osborne and Yi Ming Lai and Marc de Kamps | Models Currently Implemented in MIIND | null | null | null | null | q-bio.NC physics.comp-ph | http://creativecommons.org/licenses/by/4.0/ | This is a living document that will be updated when appropriate. MIIND [1, 2]
is a population-level neural simulator. It is based on population density
techniques, just like DIPDE [3]. Contrary to DIPDE, MIIND is agnostic to the
underlying neuron model used in its populations so any 1, 2 or 3 dimensional
model can be... | [
{
"created": "Tue, 3 Mar 2020 08:21:58 GMT",
"version": "v1"
},
{
"created": "Tue, 24 Mar 2020 11:26:24 GMT",
"version": "v2"
}
] | 2020-03-25 | [
[
"Osborne",
"Hugh",
""
],
[
"Lai",
"Yi Ming",
""
],
[
"de Kamps",
"Marc",
""
]
] | This is a living document that will be updated when appropriate. MIIND [1, 2] is a population-level neural simulator. It is based on population density techniques, just like DIPDE [3]. Contrary to DIPDE, MIIND is agnostic to the underlying neuron model used in its populations so any 1, 2 or 3 dimensional model can be s... |
2005.04365 | Erkki Somersalo Dr. | Daniela Calvetti, Alexander Hoover, Johnie Rose, Erkki Somersalo | Bayesian dynamical estimation of the parameters of an SE(A)IR COVID-19
spread model | 21 pages, 8 figures | null | null | null | q-bio.PE cs.NA math.NA q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this article, we consider a dynamic epidemiology model for the spread of
the COVID-19 infection. Starting from the classical SEIR model, the model is
modified so as to better describe characteristic features of the underlying
pathogen and its infectious modes. In line with the large number of secondary
infections ... | [
{
"created": "Sat, 9 May 2020 05:07:56 GMT",
"version": "v1"
},
{
"created": "Thu, 21 May 2020 17:21:06 GMT",
"version": "v2"
}
] | 2020-05-22 | [
[
"Calvetti",
"Daniela",
""
],
[
"Hoover",
"Alexander",
""
],
[
"Rose",
"Johnie",
""
],
[
"Somersalo",
"Erkki",
""
]
] | In this article, we consider a dynamic epidemiology model for the spread of the COVID-19 infection. Starting from the classical SEIR model, the model is modified so as to better describe characteristic features of the underlying pathogen and its infectious modes. In line with the large number of secondary infections no... |
1303.6793 | Nicolae Radu Zabet | Nicolae Radu Zabet and Boris Adryan | The effects of transcription factor competition on gene regulation | This is an updated version of the manuscript taking into account
comments from reviewers | Frontiers in Genetics 4:197 (2013) | 10.3389/fgene.2013.00197 | null | q-bio.SC q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transcription factor (TF) molecules translocate by facilitated diffusion (a
combination of 3D diffusion around and 1D random walk on the DNA). Despite the
attention this mechanism received in the last 40 years, only a few studies
investigated the influence of the cellular environment on the facilitated
diffusion mech... | [
{
"created": "Wed, 27 Mar 2013 11:25:28 GMT",
"version": "v1"
},
{
"created": "Tue, 6 Aug 2013 12:48:23 GMT",
"version": "v2"
}
] | 2013-09-20 | [
[
"Zabet",
"Nicolae Radu",
""
],
[
"Adryan",
"Boris",
""
]
] | Transcription factor (TF) molecules translocate by facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA). Despite the attention this mechanism received in the last 40 years, only a few studies investigated the influence of the cellular environment on the facilitated diffusion mechan... |
2204.05857 | Amanda Lea | Irene Gallego Romero and Amanda J. Lea | Leveraging massively parallel reporter assays for evolutionary questions | null | null | null | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | A long-standing goal of evolutionary biology is to decode how gene regulatory
processes contribute to organismal diversity, both within and between species.
This question has remained challenging to answer, due both to the difficulties
of predicting function from non-coding sequence, and to the technological
constrai... | [
{
"created": "Tue, 12 Apr 2022 14:57:40 GMT",
"version": "v1"
}
] | 2022-04-13 | [
[
"Romero",
"Irene Gallego",
""
],
[
"Lea",
"Amanda J.",
""
]
] | A long-standing goal of evolutionary biology is to decode how gene regulatory processes contribute to organismal diversity, both within and between species. This question has remained challenging to answer, due both to the difficulties of predicting function from non-coding sequence, and to the technological constraint... |
2405.06648 | Georgii Koniukov | Georgii Koniukov | Protein atom traps as seeing by neutron scattering | null | null | null | null | q-bio.BM cond-mat.mes-hall cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The expression for the higher temperature dependence of the mean squared
displacement in proteins is obtained. The quantum multi-well model explains the
dynamic transitions of the proteins and minimizes the amount of parameters to a
single one leading to the few-state harmonic system at low-temperatures, and,
thus, j... | [
{
"created": "Mon, 25 Mar 2024 17:52:59 GMT",
"version": "v1"
}
] | 2024-05-14 | [
[
"Koniukov",
"Georgii",
""
]
] | The expression for the higher temperature dependence of the mean squared displacement in proteins is obtained. The quantum multi-well model explains the dynamic transitions of the proteins and minimizes the amount of parameters to a single one leading to the few-state harmonic system at low-temperatures, and, thus, jus... |
2212.01171 | Jae Kyoung Kim | Hyukpyo Hong, Bryan S. Hernandez, Jinsu Kim, and Jae Kyoung Kim | Computational translation framework identifies biochemical reaction
networks with special topologies and their long-term dynamics | 24 pages, 7 figures | null | null | null | q-bio.MN math.PR | http://creativecommons.org/licenses/by/4.0/ | Long-term behaviors of biochemical systems are described by steady states in
deterministic models and stationary distributions in stochastic models.
Obtaining their analytic solutions can be done for limited cases, such as
linear or finite-state systems, as it generally requires solving many coupled
equations. Intere... | [
{
"created": "Fri, 2 Dec 2022 13:51:35 GMT",
"version": "v1"
}
] | 2022-12-05 | [
[
"Hong",
"Hyukpyo",
""
],
[
"Hernandez",
"Bryan S.",
""
],
[
"Kim",
"Jinsu",
""
],
[
"Kim",
"Jae Kyoung",
""
]
] | Long-term behaviors of biochemical systems are described by steady states in deterministic models and stationary distributions in stochastic models. Obtaining their analytic solutions can be done for limited cases, such as linear or finite-state systems, as it generally requires solving many coupled equations. Interest... |
2402.01605 | Alireza Alemi | Alireza Alemi, Emre R. F. Aksay, Mark S. Goldman | A Lyapunov theory demonstrating a fundamental limit on the speed of
systems consolidation | 16 pages, 4 figures | null | null | null | q-bio.NC cs.SY eess.SY physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The nervous system reorganizes memories from an early site to a late site, a
commonly observed feature of learning and memory systems known as systems
consolidation. Previous work has suggested learning rules by which
consolidation may occur. Here, we provide conditions under which such rules are
guaranteed to lead t... | [
{
"created": "Fri, 2 Feb 2024 18:07:40 GMT",
"version": "v1"
}
] | 2024-02-05 | [
[
"Alemi",
"Alireza",
""
],
[
"Aksay",
"Emre R. F.",
""
],
[
"Goldman",
"Mark S.",
""
]
] | The nervous system reorganizes memories from an early site to a late site, a commonly observed feature of learning and memory systems known as systems consolidation. Previous work has suggested learning rules by which consolidation may occur. Here, we provide conditions under which such rules are guaranteed to lead to ... |
q-bio/0401007 | Claudio Parmeggiani | Claudio Parmeggiani | Two hypotheses about natural intelligence | 10 pages | null | null | null | q-bio.PE q-bio.NC | null | We assume that the natural intelligence (human, particularly) is equivalent
to a large inferring structure, which took shape in the last 400/500 million
years. Then two hypotheses, about this structure and its development, are put
forward for consideration. The first one concerns the transmission, from one
generation... | [
{
"created": "Wed, 7 Jan 2004 00:45:39 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Parmeggiani",
"Claudio",
""
]
] | We assume that the natural intelligence (human, particularly) is equivalent to a large inferring structure, which took shape in the last 400/500 million years. Then two hypotheses, about this structure and its development, are put forward for consideration. The first one concerns the transmission, from one generation t... |
2312.05876 | Michael A. Lomholt | Michael A. Lomholt and Ralf Metzler | Target search on DNA -- effect of coiling | 23 pages, 6 figures, some revision | null | null | null | q-bio.BM cond-mat.stat-mech physics.bio-ph q-bio.SC | http://creativecommons.org/licenses/by/4.0/ | Some proteins can find their targets on DNA faster than by pure diffusion in
the three-dimensional cytoplasm, through the process of facilitated diffusion:
They can loosely bind to DNA and temporarily slide along it, thus being guided
by the DNA molecule itself to the target. This chapter examines this process in
mat... | [
{
"created": "Sun, 10 Dec 2023 13:08:07 GMT",
"version": "v1"
},
{
"created": "Mon, 18 Dec 2023 12:52:15 GMT",
"version": "v2"
},
{
"created": "Sun, 25 Feb 2024 15:29:27 GMT",
"version": "v3"
}
] | 2024-02-27 | [
[
"Lomholt",
"Michael A.",
""
],
[
"Metzler",
"Ralf",
""
]
] | Some proteins can find their targets on DNA faster than by pure diffusion in the three-dimensional cytoplasm, through the process of facilitated diffusion: They can loosely bind to DNA and temporarily slide along it, thus being guided by the DNA molecule itself to the target. This chapter examines this process in mathe... |
1512.02577 | Andreas Daffertshofer | Robert Ton and Andreas Daffertshofer | Model selection for identifying power-law scaling | null | null | null | null | q-bio.QM physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Long-range temporal and spatial correlations have been reported in a
remarkable number of studies. In particular power-law scaling in neural
activity raised considerable interest. We here provide a straightforward
algorithm not only to quantify power-law scaling but to test it against
alternatives using (Bayesian) mo... | [
{
"created": "Tue, 8 Dec 2015 18:32:10 GMT",
"version": "v1"
}
] | 2015-12-09 | [
[
"Ton",
"Robert",
""
],
[
"Daffertshofer",
"Andreas",
""
]
] | Long-range temporal and spatial correlations have been reported in a remarkable number of studies. In particular power-law scaling in neural activity raised considerable interest. We here provide a straightforward algorithm not only to quantify power-law scaling but to test it against alternatives using (Bayesian) mode... |
q-bio/0310041 | Patrick Warren | Patrick B. Warren and Pieter Rein ten Wolde | Enhancement of the stability of genetic switches by overlapping upstream
regulatory domains | 4 pages, 5 figures, RevTeX4 | null | 10.1103/PhysRevLett.92.128101 | null | q-bio.MN | null | We study genetic switches formed from pairs of mutually repressing operons.
The switch stability is characterised by a well defined lifetime which grows
sub-exponentially with the number of copies of the most-expressed transcription
factor, in the regime accessible by our numerical simulations. The stability
can be m... | [
{
"created": "Sat, 1 Nov 2003 12:37:37 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Warren",
"Patrick B.",
""
],
[
"Wolde",
"Pieter Rein ten",
""
]
] | We study genetic switches formed from pairs of mutually repressing operons. The switch stability is characterised by a well defined lifetime which grows sub-exponentially with the number of copies of the most-expressed transcription factor, in the regime accessible by our numerical simulations. The stability can be mar... |
1512.04184 | Shyr-Shea Chang | Shyr-Shea Chang, Shenyinying Tu, Kyung In Baek, Andrew Pietersen,
Yu-Hsiu Liu, Van Savage, Sheng-Ping L. Hwang, Tzung K. Hsiai, Marcus Roper | Optimal occlusion uniformly partitions red blood cells fluxes within a
microvascular network | 22 pages, 6 figures, 1 supporting information | Chang, S. S., Tu, S., Baek, K. I., Pietersen, A., Liu, Y. H.,
Savage, V. M., ... & Roper, M. (2017). Optimal occlusion uniformly partitions
red blood cells fluxes within a microvascular network. PLoS computational
biology, 13(12), e1005892 | null | null | q-bio.TO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In animals, gas exchange between blood and tissues occurs in narrow vessels,
whose diameter is comparable to that of a red blood cell. Red blood cells must
deform to squeeze through these narrow vessels, transiently blocking or
occluding the vessels they pass through. Although the dynamics of vessel
occlusion have be... | [
{
"created": "Mon, 14 Dec 2015 06:06:02 GMT",
"version": "v1"
},
{
"created": "Wed, 23 Nov 2016 06:57:35 GMT",
"version": "v2"
},
{
"created": "Fri, 13 Jul 2018 02:19:53 GMT",
"version": "v3"
}
] | 2018-07-16 | [
[
"Chang",
"Shyr-Shea",
""
],
[
"Tu",
"Shenyinying",
""
],
[
"Baek",
"Kyung In",
""
],
[
"Pietersen",
"Andrew",
""
],
[
"Liu",
"Yu-Hsiu",
""
],
[
"Savage",
"Van",
""
],
[
"Hwang",
"Sheng-Ping L.",
""
],
[... | In animals, gas exchange between blood and tissues occurs in narrow vessels, whose diameter is comparable to that of a red blood cell. Red blood cells must deform to squeeze through these narrow vessels, transiently blocking or occluding the vessels they pass through. Although the dynamics of vessel occlusion have been... |
0911.4014 | Branko Dragovich | Branko Dragovich | Genetic Code and Number Theory | 15 pages. To apper in "Modern Topics in Science", a book of invited
papers (Eds. R. Constantinescu, G. Djordjevic, Lj. Nesic) | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Living organisms are the most complex, interesting and significant objects
regarding all substructures of the universe. Life science is regarded as a
science of the 21st century and one can expect great new discoveries in the
near futures. This article contains an introductory brief review of genetic
information, its... | [
{
"created": "Fri, 20 Nov 2009 11:09:03 GMT",
"version": "v1"
}
] | 2009-11-23 | [
[
"Dragovich",
"Branko",
""
]
] | Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures. This article contains an introductory brief review of genetic information, its c... |
2404.06691 | Ningfeng Liu | Ningfeng Liu (1 and 2), Jie Yu (1), Siyu Xiu (1), Xinfang Zhao (1),
Siyu Lin (1), Bo Qiang (1), Ruqiu Zheng (1), Hongwei Jin (1), Liangren Zhang
(1), Zhenming Liu (1 and 3) ((1) State Key Laboratory of Natural and
Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, (2)
Peking-Tsinghua Center... | Latent Chemical Space Searching for Plug-in Multi-objective Molecule
Generation | null | null | null | null | q-bio.BM cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular generation, an essential method for identifying new drug
structures, has been supported by advancements in machine learning and
computational technology. However, challenges remain in multi-objective
generation, model adaptability, and practical application in drug discovery. In
this study, we developed a v... | [
{
"created": "Wed, 10 Apr 2024 02:37:24 GMT",
"version": "v1"
}
] | 2024-04-11 | [
[
"Liu",
"Ningfeng",
"",
"1 and 2"
],
[
"Yu",
"Jie",
"",
"1 and 3"
],
[
"Xiu",
"Siyu",
"",
"1 and 3"
],
[
"Zhao",
"Xinfang",
"",
"1 and 3"
],
[
"Lin",
"Siyu",
"",
"1 and 3"
],
[
"Qiang",
"Bo",
"",
"1 ... | Molecular generation, an essential method for identifying new drug structures, has been supported by advancements in machine learning and computational technology. However, challenges remain in multi-objective generation, model adaptability, and practical application in drug discovery. In this study, we developed a ver... |
2311.01543 | Yujiang Wang | Bethany Little, Carly Flowers, Andrew Blamire, Peter Thelwall,
John-Paul Taylor, Peter Gallagher, David Andrew Cousins, Yujiang Wang | Multivariate brain-cognition associations in euthymic bipolar disorder | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: People with bipolar disorder (BD) tend to show widespread
cognitive impairment compared to healthy controls. Impairments in processing
speed (PS), attention, and executive function (EF) may represent 'core'
impairments that have a role in wider cognitive dysfunction. Cognitive
impairments appear to relate... | [
{
"created": "Thu, 2 Nov 2023 18:54:27 GMT",
"version": "v1"
}
] | 2023-11-06 | [
[
"Little",
"Bethany",
""
],
[
"Flowers",
"Carly",
""
],
[
"Blamire",
"Andrew",
""
],
[
"Thelwall",
"Peter",
""
],
[
"Taylor",
"John-Paul",
""
],
[
"Gallagher",
"Peter",
""
],
[
"Cousins",
"David Andrew",
""
... | Background: People with bipolar disorder (BD) tend to show widespread cognitive impairment compared to healthy controls. Impairments in processing speed (PS), attention, and executive function (EF) may represent 'core' impairments that have a role in wider cognitive dysfunction. Cognitive impairments appear to relate t... |
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