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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1608.03464 | Alan Paris | Alan Paris, George Atia, Azadeh Vosoughi, Stephen Berman | A New Statistical Model of Electroencephalogram Noise Spectra for
Real-time Brain-Computer Interfaces | Revised submission to IEEE EMBS Trans. Biomed. Eng. 12 pages, 9
figures | null | 10.1109/TBME.2016.2606595 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | $Objective$: A characteristic of neurological signal processing is high
levels of noise from sub-cellular ion channels up to whole-brain processes. In
this paper, we propose a new model of electroencephalogram (EEG) background
periodograms, based on a family of functions which we call generalized van der
Ziel--McWhor... | [
{
"created": "Sun, 24 Jul 2016 06:36:59 GMT",
"version": "v1"
}
] | 2016-11-17 | [
[
"Paris",
"Alan",
""
],
[
"Atia",
"George",
""
],
[
"Vosoughi",
"Azadeh",
""
],
[
"Berman",
"Stephen",
""
]
] | $Objective$: A characteristic of neurological signal processing is high levels of noise from sub-cellular ion channels up to whole-brain processes. In this paper, we propose a new model of electroencephalogram (EEG) background periodograms, based on a family of functions which we call generalized van der Ziel--McWhorte... |
1510.03224 | Matteo Figliuzzi | Matteo Figliuzzi, Herv\'e Jacquier, Alexander Schug, Olivier
Tenaillon, Martin Weigt | Coevolutionary landscape inference and the context-dependence of
mutations in beta-lactamase TEM-1 | 14 pages, 5 figures. Supplementary files on the publisher's website:
http://mbe.oxfordjournals.org/content/early/2015/10/06/molbev.msv211.short?rss=1 | Mol Biol Evol (2015) doi: 10.1093/molbev/msv211 | 10.1093/molbev/msv211 | null | q-bio.QM cond-mat.stat-mech q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The quantitative characterization of mutational landscapes is a task of
outstanding importance in evolutionary and medical biology: It is, e.g., of
central importance for our understanding of the phenotypic effect of mutations
related to disease and antibiotic drug resistance. Here we develop a novel
inference scheme... | [
{
"created": "Mon, 12 Oct 2015 11:05:22 GMT",
"version": "v1"
}
] | 2015-10-13 | [
[
"Figliuzzi",
"Matteo",
""
],
[
"Jacquier",
"Hervé",
""
],
[
"Schug",
"Alexander",
""
],
[
"Tenaillon",
"Olivier",
""
],
[
"Weigt",
"Martin",
""
]
] | The quantitative characterization of mutational landscapes is a task of outstanding importance in evolutionary and medical biology: It is, e.g., of central importance for our understanding of the phenotypic effect of mutations related to disease and antibiotic drug resistance. Here we develop a novel inference scheme f... |
0902.2404 | Eugene Shakhnovich | Muyoung Heo, Louis Kang and Eugene Shakhnovich | Adaptation through stochastic switching into transient mutators in
finite asexual populations | null | null | null | null | q-bio.BM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The importance of mutator clones in the adaptive evolution of asexual
populations is not fully understood. Here we address this problem by using an
ab initio microscopic model of living cells, whose fitness is derived directly
from their genomes using a biophysically realistic model of protein folding and
interaction... | [
{
"created": "Fri, 13 Feb 2009 22:10:40 GMT",
"version": "v1"
}
] | 2009-02-17 | [
[
"Heo",
"Muyoung",
""
],
[
"Kang",
"Louis",
""
],
[
"Shakhnovich",
"Eugene",
""
]
] | The importance of mutator clones in the adaptive evolution of asexual populations is not fully understood. Here we address this problem by using an ab initio microscopic model of living cells, whose fitness is derived directly from their genomes using a biophysically realistic model of protein folding and interactions ... |
2006.12536 | Yannick Tchaptchie Kouakep | S. Y. Tchoumi, Y. T. Kouakep, D. J. Fotsa Mbogne, J. C. Kamgang, J. M.
Tchuenche | Optimal Control of a Malaria Model with Long-Lasting Insecticide-Treated
Nets | Submitted to a scientific journal | null | null | null | q-bio.PE math.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A deterministic multi-stage malaria model with a non-therapeutic control
measure, the use of mosquito bednet is formulated and analyzed. The model basic
reproduction number is derived, and analytical results show that the models
equilibria are locally and globally asymptotically stable when certain
threshold conditio... | [
{
"created": "Mon, 22 Jun 2020 18:06:57 GMT",
"version": "v1"
},
{
"created": "Sat, 18 Jul 2020 11:11:11 GMT",
"version": "v2"
}
] | 2020-07-21 | [
[
"Tchoumi",
"S. Y.",
""
],
[
"Kouakep",
"Y. T.",
""
],
[
"Mbogne",
"D. J. Fotsa",
""
],
[
"Kamgang",
"J. C.",
""
],
[
"Tchuenche",
"J. M.",
""
]
] | A deterministic multi-stage malaria model with a non-therapeutic control measure, the use of mosquito bednet is formulated and analyzed. The model basic reproduction number is derived, and analytical results show that the models equilibria are locally and globally asymptotically stable when certain threshold conditions... |
0906.5028 | Mari Watanabe | Tomofumi Kimotsuki (Saint Louis University), Noriko Niwa (Washington
Univ. St. Louis), Martin N. Hicks (Glasgow University), Michael Dunne
(Glasgow University), Stuart M. Cobbe (Glasgow University), Mari A. Watanabe
(Saint Louis University) | Isoprenaline increases Excursive Restitution Slope in the Conscious
Rabbit with Ischaemic Heart Failure | 27 pages | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: An increased QT/RR slope is hypothesized to be predictive of
sudden cardiac death after myocardial infarction. Previous studies have shown
that beta-adrenergic stimulation increases QT/RR slope, but the effects of
beta-adrenergic stimulation on QT/RR slope in heart failure are unknown.
Methods: New Zealan... | [
{
"created": "Sat, 27 Jun 2009 02:31:20 GMT",
"version": "v1"
}
] | 2009-06-30 | [
[
"Kimotsuki",
"Tomofumi",
"",
"Saint Louis University"
],
[
"Niwa",
"Noriko",
"",
"Washington\n Univ. St. Louis"
],
[
"Hicks",
"Martin N.",
"",
"Glasgow University"
],
[
"Dunne",
"Michael",
"",
"Glasgow University"
],
[
"Cobbe",
... | Background: An increased QT/RR slope is hypothesized to be predictive of sudden cardiac death after myocardial infarction. Previous studies have shown that beta-adrenergic stimulation increases QT/RR slope, but the effects of beta-adrenergic stimulation on QT/RR slope in heart failure are unknown. Methods: New Zealand ... |
1301.7254 | Michael B\"orsch | Nawid Zarrabi, Caterina Clausen, Monika G. Dueser, Michael Boersch | Manipulating freely diffusing single 20-nm particles in an Anti-Brownian
Electrokinetic Trap (ABELtrap) | 11 pages, 6 figures | null | 10.1117/12.2002952 | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Conformational changes of individual fluorescently labeled proteins can be
followed in solution using a confocal microscope. Two fluorophores attached to
selected domains of the protein report fluctuating conformations. Based on
F\"orster resonance energy transfer (FRET) between these fluorophores on a
single protein... | [
{
"created": "Wed, 30 Jan 2013 15:22:13 GMT",
"version": "v1"
}
] | 2015-06-12 | [
[
"Zarrabi",
"Nawid",
""
],
[
"Clausen",
"Caterina",
""
],
[
"Dueser",
"Monika G.",
""
],
[
"Boersch",
"Michael",
""
]
] | Conformational changes of individual fluorescently labeled proteins can be followed in solution using a confocal microscope. Two fluorophores attached to selected domains of the protein report fluctuating conformations. Based on F\"orster resonance energy transfer (FRET) between these fluorophores on a single protein, ... |
0911.0215 | Manuel Rivas | Manuel A. Rivas, Mark J. Daly, Itsik Pe'er | Age, Sex, and Genetic Architecture of Human Gene Expression in EBV
Transformed Cell Lines | 27 pages, 3 figures | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Individual expression profiles from EBV transformed cell lines are an
emerging resource for genomic investigation. In this study we characterize the
effects of age, sex, and genetic variation on gene expression by surveying
public datasets of such profiles. We establish that the expression space of
cell lines maintai... | [
{
"created": "Sun, 1 Nov 2009 23:17:06 GMT",
"version": "v1"
}
] | 2009-11-03 | [
[
"Rivas",
"Manuel A.",
""
],
[
"Daly",
"Mark J.",
""
],
[
"Pe'er",
"Itsik",
""
]
] | Individual expression profiles from EBV transformed cell lines are an emerging resource for genomic investigation. In this study we characterize the effects of age, sex, and genetic variation on gene expression by surveying public datasets of such profiles. We establish that the expression space of cell lines maintains... |
1305.7411 | Jiapu Zhang | Jiapu Zhang | The Methicillin-Resistant Staphylococcus Aureus Infection Controls | null | Journal Review of Bioinformatics and Biometrics (RBB) 2(4),
pp.83-87 (2013) | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Multi-resistant organisms (MROs), the bacteria that are resistant to a number
of different antibiotics, have been very popular around the world in recent
years. They are very difficult to treat but highly infectious in humans. MRSA
(Methicillin-Resistant Staphylococcus Aureus) is one of the MROs. It is
believed that ... | [
{
"created": "Thu, 30 May 2013 12:33:57 GMT",
"version": "v1"
}
] | 2013-12-09 | [
[
"Zhang",
"Jiapu",
""
]
] | Multi-resistant organisms (MROs), the bacteria that are resistant to a number of different antibiotics, have been very popular around the world in recent years. They are very difficult to treat but highly infectious in humans. MRSA (Methicillin-Resistant Staphylococcus Aureus) is one of the MROs. It is believed that in... |
1509.02816 | John Platig | John Platig, Peter Castaldi, Dawn DeMeo, and John Quackenbush | Bipartite Community Structure of eQTLs | null | null | 10.1371/journal.pcbi.1005033 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genome Wide Association Studies (GWAS) and eQTL analyses have produced a
large and growing number of genetic associations linked to a wide range of
human phenotypes. As of 2013, there were more than 11,000 SNPs associated with
a trait as reported in the NHGRI GWAS Catalog. However, interpreting the
functional roles p... | [
{
"created": "Wed, 9 Sep 2015 15:52:09 GMT",
"version": "v1"
}
] | 2016-09-28 | [
[
"Platig",
"John",
""
],
[
"Castaldi",
"Peter",
""
],
[
"DeMeo",
"Dawn",
""
],
[
"Quackenbush",
"John",
""
]
] | Genome Wide Association Studies (GWAS) and eQTL analyses have produced a large and growing number of genetic associations linked to a wide range of human phenotypes. As of 2013, there were more than 11,000 SNPs associated with a trait as reported in the NHGRI GWAS Catalog. However, interpreting the functional roles pla... |
1508.00613 | Maria Kochugaeva | Martin Lange, Maria Kochugaeva and Anatoly B. Kolomeisky | Protein search for multiple targets on DNA | null | null | 10.1063/1.4930113 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein-DNA interactions are crucial for all biological processes. One of the
most important fundamental aspects of these interactions is the process of
protein searching and recognizing specific binding sites on DNA. A large number
of experimental and theoretical investigations have been devoted to uncovering
the mo... | [
{
"created": "Mon, 3 Aug 2015 22:21:11 GMT",
"version": "v1"
}
] | 2015-09-30 | [
[
"Lange",
"Martin",
""
],
[
"Kochugaeva",
"Maria",
""
],
[
"Kolomeisky",
"Anatoly B.",
""
]
] | Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of experimental and theoretical investigations have been devoted to uncovering the mole... |
q-bio/0603036 | Otger Camp\`as | Otger Campas, Jaume Casademunt, Ignacio Pagonabarraga | Dynamic stability of spindles controlled by molecular motor kinetics | 4 pages, 3 figures | null | null | null | q-bio.SC physics.bio-ph | null | We analyze the role of the force-dependent kinetics of motor proteins in the
stability of antiparallel arrays of polar filaments, such as those in the
mitotic spindle. We determine the possible stable structures and show that
there exists an instability associated to the collective behavior of motors
that leads to th... | [
{
"created": "Thu, 30 Mar 2006 19:11:43 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Campas",
"Otger",
""
],
[
"Casademunt",
"Jaume",
""
],
[
"Pagonabarraga",
"Ignacio",
""
]
] | We analyze the role of the force-dependent kinetics of motor proteins in the stability of antiparallel arrays of polar filaments, such as those in the mitotic spindle. We determine the possible stable structures and show that there exists an instability associated to the collective behavior of motors that leads to the ... |
1401.6207 | Huisheng Liu | Huisheng Liu, Hua Bai, Enfu Hui, Lu Yang, Chantell Evans, Zhao Wang,
Sung Kwon, and Edwin Chapman | Synaptotagmin 7 Functions as a Ca2+-sensor for Synaptic Vesicle
Replenishment | 41 pages, 17 Figures | null | 10.7554/eLife.01524 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Synaptotagmin (syt) 7 is one of three syt isoforms found in all metazoans; it
is ubiquitously expressed, yet its function in neurons remains obscure. Here,
we resolved Ca2+-dependent and Ca2+-independent synaptic vesicle (SV)
replenishment pathways, and found that syt 7 plays a selective and critical
role in the Ca2+... | [
{
"created": "Thu, 23 Jan 2014 22:48:27 GMT",
"version": "v1"
}
] | 2014-01-27 | [
[
"Liu",
"Huisheng",
""
],
[
"Bai",
"Hua",
""
],
[
"Hui",
"Enfu",
""
],
[
"Yang",
"Lu",
""
],
[
"Evans",
"Chantell",
""
],
[
"Wang",
"Zhao",
""
],
[
"Kwon",
"Sung",
""
],
[
"Chapman",
"Edwin",
... | Synaptotagmin (syt) 7 is one of three syt isoforms found in all metazoans; it is ubiquitously expressed, yet its function in neurons remains obscure. Here, we resolved Ca2+-dependent and Ca2+-independent synaptic vesicle (SV) replenishment pathways, and found that syt 7 plays a selective and critical role in the Ca2+-d... |
2104.02881 | Seung Ki Baek | Sanghun Lee, Yohsuke Murase, and Seung Ki Baek | Local stability of cooperation in a continuous model of indirect
reciprocity | 13 pages, 3 figures | Sci. Rep. 11, 14225 (2021) | 10.1038/s41598-021-93598-7 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reputation is a powerful mechanism to enforce cooperation among unrelated
individuals through indirect reciprocity, but it suffers from disagreement
originating from private assessment, noise, and incomplete information. In this
work, we investigate stability of cooperation in the donation game by regarding
each play... | [
{
"created": "Wed, 7 Apr 2021 03:14:22 GMT",
"version": "v1"
},
{
"created": "Fri, 9 Jul 2021 13:18:57 GMT",
"version": "v2"
}
] | 2021-07-12 | [
[
"Lee",
"Sanghun",
""
],
[
"Murase",
"Yohsuke",
""
],
[
"Baek",
"Seung Ki",
""
]
] | Reputation is a powerful mechanism to enforce cooperation among unrelated individuals through indirect reciprocity, but it suffers from disagreement originating from private assessment, noise, and incomplete information. In this work, we investigate stability of cooperation in the donation game by regarding each player... |
2307.00253 | Rahul Biswas | Rahul Biswas and SuryaNarayana Sripada | Application of Time-Aware PC algorithm to compute Causal Functional
Connectivity in Alzheimer's Disease from fMRI data | null | null | null | null | q-bio.NC q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Functional Connectivity between brain regions is known to be altered in
Alzheimer's disease, and promises to be a biomarker for early diagnosis of the
disease. While several approaches for functional connectivity obtain an
un-directed network representing stochastic associations (correlations) between
brain regions, ... | [
{
"created": "Sat, 1 Jul 2023 07:20:04 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Feb 2024 00:18:19 GMT",
"version": "v2"
}
] | 2024-02-21 | [
[
"Biswas",
"Rahul",
""
],
[
"Sripada",
"SuryaNarayana",
""
]
] | Functional Connectivity between brain regions is known to be altered in Alzheimer's disease, and promises to be a biomarker for early diagnosis of the disease. While several approaches for functional connectivity obtain an un-directed network representing stochastic associations (correlations) between brain regions, as... |
q-bio/0603021 | Ovidiu Radulescu | O.Radulescu, A.Siegel, E. Pecou, and S.Lagarrigue | A model for regulated fatty acid metabolism in liver; equilibria and
their changes | null | null | null | null | q-bio.CB | null | We build a model for the hepatic fatty acid metabolism and its metabolic and
genetic regulations. The model has two functioning modes: synthesis and
oxidation of fatty acids. We provide a sufficient condition (the strong
lipolytic condition) for the uniqueness of its equilibrium. Under this
condition, modifications o... | [
{
"created": "Sat, 18 Mar 2006 22:30:57 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Radulescu",
"O.",
""
],
[
"Siegel",
"A.",
""
],
[
"Pecou",
"E.",
""
],
[
"Lagarrigue",
"S.",
""
]
] | We build a model for the hepatic fatty acid metabolism and its metabolic and genetic regulations. The model has two functioning modes: synthesis and oxidation of fatty acids. We provide a sufficient condition (the strong lipolytic condition) for the uniqueness of its equilibrium. Under this condition, modifications of ... |
2011.08024 | Shailaja Akella | Shailaja Akella, Ali Mohebi, Kiersten Riels, Andreas Keil, Karim
Oweiss, Jose C. Principe | Local power estimation of neuromodulations using point process modeling | 6 pages | null | null | null | q-bio.NC eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Extracellular electrical potentials (EEP) recorded from the brain are an
active manifestation of all cellular processes that propagate within a volume
of brain tissue. A standard approach for their quantification are power
spectral analyses methods that reflect the global distribution of signal power
over frequency. ... | [
{
"created": "Mon, 16 Nov 2020 15:20:33 GMT",
"version": "v1"
}
] | 2020-11-17 | [
[
"Akella",
"Shailaja",
""
],
[
"Mohebi",
"Ali",
""
],
[
"Riels",
"Kiersten",
""
],
[
"Keil",
"Andreas",
""
],
[
"Oweiss",
"Karim",
""
],
[
"Principe",
"Jose C.",
""
]
] | Extracellular electrical potentials (EEP) recorded from the brain are an active manifestation of all cellular processes that propagate within a volume of brain tissue. A standard approach for their quantification are power spectral analyses methods that reflect the global distribution of signal power over frequency. Ho... |
0903.4491 | Aleksandra Walczak | Gasper Tkacik, Aleksandra M. Walczak, and William Bialek | Optimizing information flow in small genetic networks. I | null | Phys. Rev. E 80, 031920 (2009) | 10.1103/PhysRevE.80.031920 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In order to survive, reproduce and (in multicellular organisms)
differentiate, cells must control the concentrations of the myriad different
proteins that are encoded in the genome. The precision of this control is
limited by the inevitable randomness of individual molecular events. Here we
explore how cells can maxi... | [
{
"created": "Thu, 26 Mar 2009 00:12:20 GMT",
"version": "v1"
},
{
"created": "Sun, 1 Nov 2009 22:39:25 GMT",
"version": "v2"
}
] | 2013-08-01 | [
[
"Tkacik",
"Gasper",
""
],
[
"Walczak",
"Aleksandra M.",
""
],
[
"Bialek",
"William",
""
]
] | In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable randomness of individual molecular events. Here we explore how cells can maximi... |
1509.08158 | Sara Clifton | Sara M. Clifton, Rosemary I. Braun, Daniel M. Abrams | Handicap principle implies emergence of dimorphic mating displays | 7 pages, 4 figures, supplementary information included | Proceedings of the Royal Society B 283, 1970: November 30 2016 | 10.1098/rspb.2016.1970 | null | q-bio.PE math.DS nlin.AO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Species spanning the animal kingdom have evolved extravagant and costly
ornaments to attract mating partners. Zahavi's handicap principle offers an
elegant explanation for this: ornaments signal individual quality, and must be
costly to ensure honest signalling, making mate selection more efficient. Here
we incorpora... | [
{
"created": "Sun, 27 Sep 2015 22:35:32 GMT",
"version": "v1"
},
{
"created": "Mon, 9 May 2016 18:20:21 GMT",
"version": "v2"
},
{
"created": "Tue, 1 Nov 2016 00:44:29 GMT",
"version": "v3"
}
] | 2016-12-02 | [
[
"Clifton",
"Sara M.",
""
],
[
"Braun",
"Rosemary I.",
""
],
[
"Abrams",
"Daniel M.",
""
]
] | Species spanning the animal kingdom have evolved extravagant and costly ornaments to attract mating partners. Zahavi's handicap principle offers an elegant explanation for this: ornaments signal individual quality, and must be costly to ensure honest signalling, making mate selection more efficient. Here we incorporate... |
1809.02849 | Eli Cornblath | Eli J. Cornblath, Arian Ashourvan, Jason Z. Kim, Richard F. Betzel,
Rastko Ciric, Azeez Adebimpe, Graham L. Baum, Xiaosong He, Kosha Ruparel,
Tyler M. Moore, Ruben C. Gur, Raquel E. Gur, Russell T. Shinohara, David R.
Roalf, Theodore D. Satterthwaite, and Danielle S. Bassett | Temporal sequences of brain activity at rest are constrained by white
matter structure and modulated by cognitive demands | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A diverse white matter network and finely tuned neuronal membrane properties
allow the brain to transition seamlessly between cognitive states. However, it
remains unclear how static structural connections guide the temporal
progression of large-scale brain activity patterns in different cognitive
states. Here, we an... | [
{
"created": "Sat, 8 Sep 2018 18:14:29 GMT",
"version": "v1"
},
{
"created": "Mon, 30 Sep 2019 23:14:02 GMT",
"version": "v2"
}
] | 2019-10-02 | [
[
"Cornblath",
"Eli J.",
""
],
[
"Ashourvan",
"Arian",
""
],
[
"Kim",
"Jason Z.",
""
],
[
"Betzel",
"Richard F.",
""
],
[
"Ciric",
"Rastko",
""
],
[
"Adebimpe",
"Azeez",
""
],
[
"Baum",
"Graham L.",
""
],
... | A diverse white matter network and finely tuned neuronal membrane properties allow the brain to transition seamlessly between cognitive states. However, it remains unclear how static structural connections guide the temporal progression of large-scale brain activity patterns in different cognitive states. Here, we anal... |
2104.01458 | Mar\'ia Vallet-Regi | M. Natividad Gomez-Cerezo, Juan Pena, Saso Ivanovski, Daniel Arcos,
Maria Vallet-Regi, Cedryck Vaquette | Multiscale porosity in mesoporous bioglass 3D-printed scaffolds for bone
regeneration | 34 pages, 10 figures | Materials Science and Engineering: C, Volume 120, January 2021,
111706 | 10.1016/j.msec.2020.111706 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In order to increase the bone forming ability of MBG-PCL composite scaffold,
microporosity was created in the struts of 3D-printed MBG-PCL scaffolds for the
manufacturing of a construct with a multiscale porosity consisting of meso-,
micro- and macro-pores. 3D-printing imparted macroporosity while the
microporosity w... | [
{
"created": "Sat, 3 Apr 2021 18:34:03 GMT",
"version": "v1"
}
] | 2021-04-06 | [
[
"Gomez-Cerezo",
"M. Natividad",
""
],
[
"Pena",
"Juan",
""
],
[
"Ivanovski",
"Saso",
""
],
[
"Arcos",
"Daniel",
""
],
[
"Vallet-Regi",
"Maria",
""
],
[
"Vaquette",
"Cedryck",
""
]
] | In order to increase the bone forming ability of MBG-PCL composite scaffold, microporosity was created in the struts of 3D-printed MBG-PCL scaffolds for the manufacturing of a construct with a multiscale porosity consisting of meso-, micro- and macro-pores. 3D-printing imparted macroporosity while the microporosity was... |
2408.03942 | Davood Karimi | Camilo Calixto, Matheus D. Soldatelli, Bo Li, Lana Pierotich, Ali
Gholipour, Simon K. Warfield, Davood Karimi | White matter tract crossing and bottleneck regions in the fetal brain | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | There is a growing interest in using diffusion MRI to study the white matter
tracts and structural connectivity of the fetal brain. Recent progress in data
acquisition and processing suggests that this imaging modality has a unique
role in elucidating the normal and abnormal patterns of neurodevelopment in
utero. How... | [
{
"created": "Sat, 20 Jul 2024 21:20:50 GMT",
"version": "v1"
}
] | 2024-08-09 | [
[
"Calixto",
"Camilo",
""
],
[
"Soldatelli",
"Matheus D.",
""
],
[
"Li",
"Bo",
""
],
[
"Pierotich",
"Lana",
""
],
[
"Gholipour",
"Ali",
""
],
[
"Warfield",
"Simon K.",
""
],
[
"Karimi",
"Davood",
""
]
] | There is a growing interest in using diffusion MRI to study the white matter tracts and structural connectivity of the fetal brain. Recent progress in data acquisition and processing suggests that this imaging modality has a unique role in elucidating the normal and abnormal patterns of neurodevelopment in utero. Howev... |
2309.06636 | Chaoqian Wang | Chaoqian Wang | Evolution of trust in structured populations | 14 pages, 2 figures, accepted for publication in Applied Mathematics
and Computation | Applied Mathematics and Computation, Volume 471, 15 June 2024,
128595 | 10.1016/j.amc.2024.128595 | null | q-bio.PE nlin.AO physics.soc-ph | http://creativecommons.org/publicdomain/zero/1.0/ | The trust game, derived from an economics experiment, has recently attracted
interest in the field of evolutionary dynamics. In a recent version of the
evolutionary trust game, players adopt one of three strategies: investor,
trustworthy trustee, or untrustworthy trustee. Trustworthy trustees enhance and
share the in... | [
{
"created": "Tue, 12 Sep 2023 22:54:45 GMT",
"version": "v1"
},
{
"created": "Sun, 17 Dec 2023 02:44:09 GMT",
"version": "v2"
},
{
"created": "Sat, 10 Feb 2024 03:08:42 GMT",
"version": "v3"
}
] | 2024-02-13 | [
[
"Wang",
"Chaoqian",
""
]
] | The trust game, derived from an economics experiment, has recently attracted interest in the field of evolutionary dynamics. In a recent version of the evolutionary trust game, players adopt one of three strategies: investor, trustworthy trustee, or untrustworthy trustee. Trustworthy trustees enhance and share the inve... |
2201.09647 | Alex Zhavoronkov | Feng Ren, Xiao Ding, Min Zheng, Mikhail Korzinkin, Xin Cai, Wei Zhu,
Alexey Mantsyzov, Alex Aliper, Vladimir Aladinskiy, Zhongying Cao, Shanshan
Kong, Xi Long, Bonnie Hei Man Liu, Yingtao Liu, Vladimir Naumov, Anastasia
Shneyderman, Ivan V. Ozerov, Ju Wang, Frank W. Pun, Alan Aspuru-Guzik,
Michael Levitt, and A... | AlphaFold Accelerates Artificial Intelligence Powered Drug Discovery:
Efficient Discovery of a Novel Cyclin-dependent Kinase 20 (CDK20) Small
Molecule Inhibitor | 9 pages, 6 figures | null | null | null | q-bio.BM cs.AI cs.LG q-bio.MN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The AlphaFold computer program predicted protein structures for the whole
human genome, which has been considered as a remarkable breakthrough both in
artificial intelligence (AI) application and structural biology. Despite the
varying confidence level, these predicted structures still could significantly
contribute ... | [
{
"created": "Fri, 21 Jan 2022 07:35:24 GMT",
"version": "v1"
},
{
"created": "Sun, 13 Feb 2022 04:26:30 GMT",
"version": "v2"
}
] | 2022-02-15 | [
[
"Ren",
"Feng",
""
],
[
"Ding",
"Xiao",
""
],
[
"Zheng",
"Min",
""
],
[
"Korzinkin",
"Mikhail",
""
],
[
"Cai",
"Xin",
""
],
[
"Zhu",
"Wei",
""
],
[
"Mantsyzov",
"Alexey",
""
],
[
"Aliper",
"Alex"... | The AlphaFold computer program predicted protein structures for the whole human genome, which has been considered as a remarkable breakthrough both in artificial intelligence (AI) application and structural biology. Despite the varying confidence level, these predicted structures still could significantly contribute to... |
1809.08959 | Joaquin Goni | Sumra Bari, Enrico Amico, Nicole Vike, Thomas M. Talavage, Joaqu\'in
Go\~ni | Uncovering Multi-Site Identifiability Based on Resting-State Functional
Connectomes | 28 pages, 11 figures in main text, 5 figures in supplementary | NeuroImage, 2019, Vol 202, 115967 | 10.1016/j.neuroimage.2019.06.045 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multi-site studies are becoming important to increase statistical power,
enhance generalizability, and to improve the likelihood of pooling relevant
subgroups together activities. Even with harmonized imaging sequences,
site-dependent variability can mask the advantages of these multi-site studies.
The aim of this st... | [
{
"created": "Mon, 24 Sep 2018 14:14:32 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Apr 2019 19:06:42 GMT",
"version": "v2"
}
] | 2019-09-11 | [
[
"Bari",
"Sumra",
""
],
[
"Amico",
"Enrico",
""
],
[
"Vike",
"Nicole",
""
],
[
"Talavage",
"Thomas M.",
""
],
[
"Goñi",
"Joaquín",
""
]
] | Multi-site studies are becoming important to increase statistical power, enhance generalizability, and to improve the likelihood of pooling relevant subgroups together activities. Even with harmonized imaging sequences, site-dependent variability can mask the advantages of these multi-site studies. The aim of this stud... |
2307.02561 | Samuel Church | Samuel H. Church, Jasmine L. Mah, Casey W. Dunn | Unification of species, gene, and cell trees for single-cell expression
analyses | 16 pages, 4 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can
reveal links between cellular gene expression and the evolution of cell
functions, features, and phenotypes. These comparisons invoke evolutionary
histories, as depicted with phylogenetic trees, that define relationships
between species, ge... | [
{
"created": "Wed, 5 Jul 2023 18:02:17 GMT",
"version": "v1"
}
] | 2023-07-07 | [
[
"Church",
"Samuel H.",
""
],
[
"Mah",
"Jasmine L.",
""
],
[
"Dunn",
"Casey W.",
""
]
] | Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as depicted with phylogenetic trees, that define relationships between species, gene... |
2004.08973 | Gabor Vattay | Gabor Vattay | Forecasting the outcome and estimating the epidemic model parameters
from the fatality time series in COVID-19 outbreaks | null | Physical Biology 2020 | 10.1088/1478-3975/abac69 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the absence of other tools, monitoring the effects of protective measures,
including social distancing and forecasting the outcome of outbreaks is of
immense interest. Real-time data is noisy and very often hampered by systematic
errors in reporting. Detailed epidemic models may contain a large number of
empirical... | [
{
"created": "Sun, 19 Apr 2020 22:14:17 GMT",
"version": "v1"
},
{
"created": "Sat, 1 Aug 2020 09:53:57 GMT",
"version": "v2"
}
] | 2020-08-11 | [
[
"Vattay",
"Gabor",
""
]
] | In the absence of other tools, monitoring the effects of protective measures, including social distancing and forecasting the outcome of outbreaks is of immense interest. Real-time data is noisy and very often hampered by systematic errors in reporting. Detailed epidemic models may contain a large number of empirical p... |
q-bio/0605005 | Willy Valdivia-Granda | Willy Valdivia-Granda and Christopher Dwan | Microarray Data Management. An Enterprise Information Approach:
Implementations and Challenges | 10 pages, 12 figures, To apperar in: Database Modeling in Biology:
Practices and Challenges. Ma, Zongmin; Chen, Jake (Eds.) Springer Sciences &
Business Media, Inc., New York, USA (2006). ISBN: 0-387-30238-7 | null | null | null | q-bio.GN | null | The extraction of information form high-throughput experiments is a key
aspect of modern biology. Early in the development of microarray technology,
researchers recognized that the size of the datasets and the limitations of
both computational and visualization techniques restricted their ability to
find the biologic... | [
{
"created": "Wed, 3 May 2006 13:51:38 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Valdivia-Granda",
"Willy",
""
],
[
"Dwan",
"Christopher",
""
]
] | The extraction of information form high-throughput experiments is a key aspect of modern biology. Early in the development of microarray technology, researchers recognized that the size of the datasets and the limitations of both computational and visualization techniques restricted their ability to find the biological... |
1903.01316 | Romain M. Yvinec | Fr\'ed\'erique Cl\'ement and Fr\'ed\'erique Robin and Romain Yvinec | Stochastic nonlinear model for somatic cell population dynamics during
ovarian follicle activation | Accepted in Journal of Mathematical Biology | null | null | null | q-bio.CB math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In mammals, female germ cells are sheltered within somatic structures called
ovarian follicles, which remain in a quiescent state until they get activated,
all along reproductive life. We investigate the sequence of somatic cell events
occurring just after follicle activation, starting by the awakening of
precursor s... | [
{
"created": "Mon, 4 Mar 2019 15:48:38 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Dec 2020 08:07:29 GMT",
"version": "v2"
}
] | 2020-12-10 | [
[
"Clément",
"Frédérique",
""
],
[
"Robin",
"Frédérique",
""
],
[
"Yvinec",
"Romain",
""
]
] | In mammals, female germ cells are sheltered within somatic structures called ovarian follicles, which remain in a quiescent state until they get activated, all along reproductive life. We investigate the sequence of somatic cell events occurring just after follicle activation, starting by the awakening of precursor som... |
1508.00623 | Nicholas Noll | Nicholas Noll, Madhav Mani, Idse Heemskerk, Sebastian Streichan, Boris
I. Shraiman | Active Tension Network model reveals an exotic mechanical state realized
in epithelial tissues | The central argument as well as the initial reported results remain
unchanged. This revision represents a restructuring of the initial arguments
to make it more readable and easier to understand to a wider audience.
Furthermore, additional movies were analyzed to bolster our claim made that
VF formation is prim... | null | null | null | q-bio.TO q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is now widely recognized that mechanical interactions between cells play a
crucial role in epithelial morphogenesis, yet understanding the mechanisms
through which stress and deformation affect cell behavior remains an open
problem due to the complexity inherent in the mechanical behavior of cells and
the difficul... | [
{
"created": "Mon, 3 Aug 2015 23:53:26 GMT",
"version": "v1"
},
{
"created": "Wed, 18 Jan 2017 23:31:46 GMT",
"version": "v2"
}
] | 2017-01-20 | [
[
"Noll",
"Nicholas",
""
],
[
"Mani",
"Madhav",
""
],
[
"Heemskerk",
"Idse",
""
],
[
"Streichan",
"Sebastian",
""
],
[
"Shraiman",
"Boris I.",
""
]
] | It is now widely recognized that mechanical interactions between cells play a crucial role in epithelial morphogenesis, yet understanding the mechanisms through which stress and deformation affect cell behavior remains an open problem due to the complexity inherent in the mechanical behavior of cells and the difficulty... |
1812.08031 | Gestionnaire Hal-Su | St\'ephane Epelbaum (ICM, IM2A, UPMC), Vincent Bouteloup (ISPED, BPH),
Jean Mangin (CATI, NEUROSPIN), Valentina La Corte (UPD5 Psychologie, CPN -
U894), Raffaela Migliaccio (ICM, IM2A, UPMC), Hugo Bertin (LIB, CATI, UPMC),
Marie O. Habert (LIB, CATI, UPMC), Clara Fischer (CATI, NEUROSPIN), Chabha
Azouani (CATI)... | Neural correlates of episodic memory in the Memento cohort | null | Alzheimer's & Dementia: Translational Research & Clinical
Interventions, 2018, 4, pp.224-233 | 10.1016/j.trci.2018.03.010 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | IntroductionThe free and cued selective reminding test is used to identify
memory deficits in mild cognitive impairment and demented patients. It allows
assessing three processes: encoding, storage, and recollection of verbal
episodic memory.MethodsWe investigated the neural correlates of these three
memory processes... | [
{
"created": "Wed, 19 Dec 2018 15:44:51 GMT",
"version": "v1"
}
] | 2018-12-20 | [
[
"Epelbaum",
"Stéphane",
"",
"ICM, IM2A, UPMC"
],
[
"Bouteloup",
"Vincent",
"",
"ISPED, BPH"
],
[
"Mangin",
"Jean",
"",
"CATI, NEUROSPIN"
],
[
"La Corte",
"Valentina",
"",
"UPD5 Psychologie, CPN -\n U894"
],
[
"Migliaccio",
"R... | IntroductionThe free and cued selective reminding test is used to identify memory deficits in mild cognitive impairment and demented patients. It allows assessing three processes: encoding, storage, and recollection of verbal episodic memory.MethodsWe investigated the neural correlates of these three memory processes i... |
1511.01810 | Sebastien Benzekry | S\'ebastien Benzekry (IMB, MONC), J. M. L. Ebos | On the growth and dissemination laws in a mathematical model of
metastatic growth | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Metastasis represents one of the main clinical challenge in cancer treatment
since it is associated with the majority of deaths. Recent technological
advances allow quantification of the dynamics of the process by means of
noninvasive techniques such as longitudinal tracking of bioluminescent cells.
The metastatic pr... | [
{
"created": "Wed, 4 Nov 2015 12:59:36 GMT",
"version": "v1"
}
] | 2015-11-06 | [
[
"Benzekry",
"Sébastien",
"",
"IMB, MONC"
],
[
"Ebos",
"J. M. L.",
""
]
] | Metastasis represents one of the main clinical challenge in cancer treatment since it is associated with the majority of deaths. Recent technological advances allow quantification of the dynamics of the process by means of noninvasive techniques such as longitudinal tracking of bioluminescent cells. The metastatic proc... |
2308.14715 | Ethan Levien | Ethan Levien | Coalescent processes emerging from large deviations | 15 pages, 3 figures. Major revision incorporating comments from
anonymous referees | null | null | null | q-bio.PE cond-mat.stat-mech | http://creativecommons.org/licenses/by/4.0/ | The classical model for the genealogies of a neutrally evolving population in
a fixed environment is due to Kingman. Kingman's coalescent process, which
produces a binary tree, universally emerges from many microscopic models in
which the variance in the number of offspring is finite. It is understood that
power-law ... | [
{
"created": "Mon, 28 Aug 2023 17:15:54 GMT",
"version": "v1"
},
{
"created": "Tue, 5 Sep 2023 01:22:17 GMT",
"version": "v2"
},
{
"created": "Mon, 4 Dec 2023 16:13:45 GMT",
"version": "v3"
}
] | 2023-12-05 | [
[
"Levien",
"Ethan",
""
]
] | The classical model for the genealogies of a neutrally evolving population in a fixed environment is due to Kingman. Kingman's coalescent process, which produces a binary tree, universally emerges from many microscopic models in which the variance in the number of offspring is finite. It is understood that power-law of... |
2307.16231 | R\'edoane Daoudi | R\'edoane Daoudi | Strategies for targeting chondrosarcomas in vivo and molecular
dissection of oncogenic events in chondrosarcomas: is epigenetics the
culprit? | 21 pages, 1 figure, 1 table | null | null | null | q-bio.MN q-bio.SC | http://creativecommons.org/licenses/by/4.0/ | It is obvious that both epigenetic and non-epigenetic actors contribute to
tumorigenesis in chondrosarcomas and more generally in other cancers. Thus, the
main altered pathways in chondrosarcomas are now well established and include
both epigenetic and non-epigenetic pathways such as the PI3K-AKT signaling,
EGFR over... | [
{
"created": "Sun, 30 Jul 2023 13:43:33 GMT",
"version": "v1"
}
] | 2023-08-01 | [
[
"Daoudi",
"Rédoane",
""
]
] | It is obvious that both epigenetic and non-epigenetic actors contribute to tumorigenesis in chondrosarcomas and more generally in other cancers. Thus, the main altered pathways in chondrosarcomas are now well established and include both epigenetic and non-epigenetic pathways such as the PI3K-AKT signaling, EGFR overex... |
1511.04001 | Burkhard Morgenstern | Lars Hahn, Chris-Andr\'e Leimeister, Rachid Ounit, Stefano Lonardi,
Burkhard Morgenstern | RasBhari: optimizing spaced seeds for database searching, read mapping
and alignment-free sequence comparison | null | null | 10.1371/journal.pcbi.1005107 | null | q-bio.GN cs.DS q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many algorithms for sequence analysis rely on word matching or word
statistics. Often, these approaches can be improved if binary patterns
representing match and don't-care positions are used as a filter, such that
only those positions of words are considered that correspond to the match
positions of the patterns. Th... | [
{
"created": "Thu, 12 Nov 2015 18:48:08 GMT",
"version": "v1"
},
{
"created": "Wed, 20 Jul 2016 13:06:46 GMT",
"version": "v2"
}
] | 2017-02-08 | [
[
"Hahn",
"Lars",
""
],
[
"Leimeister",
"Chris-André",
""
],
[
"Ounit",
"Rachid",
""
],
[
"Lonardi",
"Stefano",
""
],
[
"Morgenstern",
"Burkhard",
""
]
] | Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The ... |
1801.04825 | Radha Srinivasan | Kiran Vishwasrao, Yasmin Khan and S. Radha | The cellular uptake mechanism of SPIONs: an in-vitro study | 8 pages, 3 figures, Part of work presented at International
Conference of Magnetism 2012 (Busan, S.Korea) | null | null | null | q-bio.CB cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Superparamagnetic Iron Oxide Nanoparticles (SPIONs) of sizes ranging from
10-50 nm are being used in a large number of biological studies because of
their peculiar characteristics of inducing local hyperthermia, MR imaging,
specific targeting and drug delivery. An in-vitro study of the cytotoxicity and
an underst... | [
{
"created": "Mon, 15 Jan 2018 14:40:35 GMT",
"version": "v1"
}
] | 2018-01-16 | [
[
"Vishwasrao",
"Kiran",
""
],
[
"Khan",
"Yasmin",
""
],
[
"Radha",
"S.",
""
]
] | The Superparamagnetic Iron Oxide Nanoparticles (SPIONs) of sizes ranging from 10-50 nm are being used in a large number of biological studies because of their peculiar characteristics of inducing local hyperthermia, MR imaging, specific targeting and drug delivery. An in-vitro study of the cytotoxicity and an understan... |
2204.01847 | Qi Zhang | Qi Zhang, Chang Liu, Stephen Wu and Ryo Yoshida | Bayesian Sequential Stacking Algorithm for Concurrently Designing
Molecules and Synthetic Reaction Networks | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the last few years, de novo molecular design using machine learning has
made great technical progress but its practical deployment has not been as
successful. This is mostly owing to the cost and technical difficulty of
synthesizing such computationally designed molecules. To overcome such
barriers, various method... | [
{
"created": "Tue, 1 Mar 2022 14:55:32 GMT",
"version": "v1"
}
] | 2022-04-06 | [
[
"Zhang",
"Qi",
""
],
[
"Liu",
"Chang",
""
],
[
"Wu",
"Stephen",
""
],
[
"Yoshida",
"Ryo",
""
]
] | In the last few years, de novo molecular design using machine learning has made great technical progress but its practical deployment has not been as successful. This is mostly owing to the cost and technical difficulty of synthesizing such computationally designed molecules. To overcome such barriers, various methods ... |
2306.08015 | Reindorf Borkor | Reindorf Nartey Borkor and Adu Sakyi and Peter Amoako-Yirenkyi | Investigation of Fractional Compartmental Models with Application to
Amiodarone Drug Diffusion in Pharmacokinetics | null | null | null | null | q-bio.QM cs.NA math.NA | http://creativecommons.org/licenses/by/4.0/ | This paper presents three fractional models formulated from a classical
Pharmacokinetics compartmental system: commensurable, non-commensurable, and
implicit non-commensurable models. Their distinguishing characteristics are
further examined comprehensively. Because analytic solutions for such models
are typically ch... | [
{
"created": "Tue, 13 Jun 2023 12:23:26 GMT",
"version": "v1"
}
] | 2023-06-16 | [
[
"Borkor",
"Reindorf Nartey",
""
],
[
"Sakyi",
"Adu",
""
],
[
"Amoako-Yirenkyi",
"Peter",
""
]
] | This paper presents three fractional models formulated from a classical Pharmacokinetics compartmental system: commensurable, non-commensurable, and implicit non-commensurable models. Their distinguishing characteristics are further examined comprehensively. Because analytic solutions for such models are typically chal... |
1611.02272 | Alexander Tait | Alexander N. Tait, Thomas Ferreira de Lima, Ellen Zhou, Allie X. Wu,
Mitchell A. Nahmias, Bhavin J. Shastri, and Paul R. Prucnal | Neuromorphic Silicon Photonic Networks | 12 pages, 4 figures, accepted in Scientific Reports | Sci.Rep. 7 (2017) 7430 | 10.1038/s41598-017-07754-z | null | q-bio.NC cs.NE physics.optics | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Photonic systems for high-performance information processing have attracted
renewed interest. Neuromorphic silicon photonics has the potential to integrate
processing functions that vastly exceed the capabilities of electronics. We
report first observations of a recurrent silicon photonic neural network, in
which con... | [
{
"created": "Sat, 5 Nov 2016 00:15:59 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Mar 2017 17:35:37 GMT",
"version": "v2"
},
{
"created": "Mon, 12 Jun 2017 15:56:45 GMT",
"version": "v3"
}
] | 2017-11-17 | [
[
"Tait",
"Alexander N.",
""
],
[
"de Lima",
"Thomas Ferreira",
""
],
[
"Zhou",
"Ellen",
""
],
[
"Wu",
"Allie X.",
""
],
[
"Nahmias",
"Mitchell A.",
""
],
[
"Shastri",
"Bhavin J.",
""
],
[
"Prucnal",
"Paul R.",
... | Photonic systems for high-performance information processing have attracted renewed interest. Neuromorphic silicon photonics has the potential to integrate processing functions that vastly exceed the capabilities of electronics. We report first observations of a recurrent silicon photonic neural network, in which conne... |
1603.09415 | Benjamin Drinkwater | Benjamin Drinkwater, Angela Qiao, and Michael A. Charleston | WiSPA: A new approach for dealing with widespread parasitism | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Traditionally, studies of coevolving systems have considered cases where a
parasite may inhabit only a single host. The case where a parasite may infect
many hosts, widespread parasitism, has until recently gained little traction.
This is due in part to the computational complexity involved in reconstructing
the coev... | [
{
"created": "Wed, 30 Mar 2016 23:32:50 GMT",
"version": "v1"
}
] | 2016-04-01 | [
[
"Drinkwater",
"Benjamin",
""
],
[
"Qiao",
"Angela",
""
],
[
"Charleston",
"Michael A.",
""
]
] | Traditionally, studies of coevolving systems have considered cases where a parasite may inhabit only a single host. The case where a parasite may infect many hosts, widespread parasitism, has until recently gained little traction. This is due in part to the computational complexity involved in reconstructing the coevol... |
1402.5327 | Jian-Jun Shu | Jian-Jun Shu, Kian Yan Yong and Weng Kong Chan | An improved scoring matrix for multiple sequence alignment | null | Mathematical Problems in Engineering, Vol. 2012, No. 490649, pp.
1-9, 2012 | 10.1155/2012/490649 | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The way for performing multiple sequence alignment is based on the criterion
of the maximum scored information content computed from a weight matrix, but it
is possible to have two or more alignments to have the same highest score
leading to ambiguities in selecting the best alignment. This paper addresses
this issue... | [
{
"created": "Fri, 21 Feb 2014 15:44:25 GMT",
"version": "v1"
},
{
"created": "Fri, 28 Feb 2014 14:20:00 GMT",
"version": "v2"
}
] | 2014-03-03 | [
[
"Shu",
"Jian-Jun",
""
],
[
"Yong",
"Kian Yan",
""
],
[
"Chan",
"Weng Kong",
""
]
] | The way for performing multiple sequence alignment is based on the criterion of the maximum scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading to ambiguities in selecting the best alignment. This paper addresses this issue b... |
1309.3312 | Armita Nourmohammad | Armita Nourmohammad, Torsten Held, Michael L\"assig | Universality and predictability in molecular quantitative genetics | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular traits, such as gene expression levels or protein binding
affinities, are increasingly accessible to quantitative measurement by modern
high-throughput techniques. Such traits measure molecular functions and, from
an evolutionary point of view, are important as targets of natural selection.
We review recent... | [
{
"created": "Thu, 12 Sep 2013 21:30:16 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Nov 2013 15:23:28 GMT",
"version": "v2"
}
] | 2013-11-15 | [
[
"Nourmohammad",
"Armita",
""
],
[
"Held",
"Torsten",
""
],
[
"Lässig",
"Michael",
""
]
] | Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary point of view, are important as targets of natural selection. We review recent d... |
2406.12625 | Polina Turishcheva | Polina Turishcheva, Max Burg, Fabian H. Sinz, Alexander Ecker | Reproducibility of predictive networks for mouse visual cortex | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Deep predictive models of neuronal activity have recently enabled several new
discoveries about the selectivity and invariance of neurons in the visual
cortex. These models learn a shared set of nonlinear basis functions, which are
linearly combined via a learned weight vector to represent a neuron's function.
Such w... | [
{
"created": "Tue, 18 Jun 2024 13:50:08 GMT",
"version": "v1"
}
] | 2024-06-19 | [
[
"Turishcheva",
"Polina",
""
],
[
"Burg",
"Max",
""
],
[
"Sinz",
"Fabian H.",
""
],
[
"Ecker",
"Alexander",
""
]
] | Deep predictive models of neuronal activity have recently enabled several new discoveries about the selectivity and invariance of neurons in the visual cortex. These models learn a shared set of nonlinear basis functions, which are linearly combined via a learned weight vector to represent a neuron's function. Such wei... |
2005.13692 | Sergei Chekmarev F. | Sergei F. Chekmarev | First-Passage Time Distributions in Two-State Protein Folding Kinetics:
Exploring the Native-Like States vs Overcoming the Free Energy Barrier | 27 pages, 21 figures | null | 10.1039/D0CP06560A | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Using a beta-hairpin protein as a representative example of two-state
folders, we studied how the exploration of native-like states affects the
folding kinetics. It has been found that the first-passage time (FPT)
distributions are essentially single-exponential not only for the times to
overcome the free energy barr... | [
{
"created": "Wed, 27 May 2020 22:41:53 GMT",
"version": "v1"
},
{
"created": "Thu, 6 Aug 2020 19:13:16 GMT",
"version": "v2"
}
] | 2021-11-16 | [
[
"Chekmarev",
"Sergei F.",
""
]
] | Using a beta-hairpin protein as a representative example of two-state folders, we studied how the exploration of native-like states affects the folding kinetics. It has been found that the first-passage time (FPT) distributions are essentially single-exponential not only for the times to overcome the free energy barrie... |
2201.03306 | Diederik Aerts | Diederik Aerts and Lester Beltran | A Planck Radiation and Quantization Scheme for Human Cognition and
Language | 7 figures | Frontiers in Psychology 13, 850725 (2022) | 10.3389/fpsyg.2022.850725 | null | q-bio.NC cs.CL quant-ph | http://creativecommons.org/licenses/by/4.0/ | As a result of the identification of 'identity' and 'indistinguishability'
and strong experimental evidence for the presence of the associated
Bose-Einstein statistics in human cognition and language, we argued in previous
work for an extension of the research domain of quantum cognition. In addition
to quantum compl... | [
{
"created": "Mon, 10 Jan 2022 12:13:23 GMT",
"version": "v1"
},
{
"created": "Fri, 4 Mar 2022 10:31:22 GMT",
"version": "v2"
}
] | 2023-02-27 | [
[
"Aerts",
"Diederik",
""
],
[
"Beltran",
"Lester",
""
]
] | As a result of the identification of 'identity' and 'indistinguishability' and strong experimental evidence for the presence of the associated Bose-Einstein statistics in human cognition and language, we argued in previous work for an extension of the research domain of quantum cognition. In addition to quantum complex... |
1804.01217 | Md Nafiz Hamid | Md-Nafiz Hamid | Gene Co-expression Network analysis of Lung Squamous Cell Carcinoma data | null | null | null | null | q-bio.GN q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | We performed a gene co-expression analysis on Lung Squamous Cell Carcinoma
data to find modules (groups) of genes that may highly impact the growth of
these type of tumors. Additionally, we used cancer survival data to relate
modules to prognostic significance in terms of survival time. Analysis on
RNA-seq data revea... | [
{
"created": "Wed, 4 Apr 2018 02:38:26 GMT",
"version": "v1"
}
] | 2018-04-05 | [
[
"Hamid",
"Md-Nafiz",
""
]
] | We performed a gene co-expression analysis on Lung Squamous Cell Carcinoma data to find modules (groups) of genes that may highly impact the growth of these type of tumors. Additionally, we used cancer survival data to relate modules to prognostic significance in terms of survival time. Analysis on RNA-seq data reveale... |
1410.4711 | Sarah Hallerberg | Heike Vester, Kurt Hammerschmidt, Marc Timme, Sarah Hallerberg | Bag-of-calls analysis reveals group-specific vocal repertoire in
long-finned pilot whales | under review | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Besides humans, several marine mammal species exhibit prerequisites to evolve
language: high cognitive abilities, flexibility in vocal production and
advanced social interactions. Here, we describe and analyse the vocal
repertoire of long-finned pilot whales (Globicephalus melas) recorded in
northern Norway. Observer... | [
{
"created": "Fri, 17 Oct 2014 13:06:09 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Jun 2015 12:05:44 GMT",
"version": "v2"
}
] | 2015-06-15 | [
[
"Vester",
"Heike",
""
],
[
"Hammerschmidt",
"Kurt",
""
],
[
"Timme",
"Marc",
""
],
[
"Hallerberg",
"Sarah",
""
]
] | Besides humans, several marine mammal species exhibit prerequisites to evolve language: high cognitive abilities, flexibility in vocal production and advanced social interactions. Here, we describe and analyse the vocal repertoire of long-finned pilot whales (Globicephalus melas) recorded in northern Norway. Observer b... |
1207.3811 | Arda Halu | Arda Halu and Ginestra Bianconi | Monochromaticity in Neutral Evolutionary Network Models | 8 pages, 14 figures | Phys. Rev. E 86, 066101 (2012) | 10.1103/PhysRevE.86.066101 | null | q-bio.MN cond-mat.dis-nn cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent studies on epistatic networks of model organisms have unveiled a
certain type of modular property called monochromaticity in which the networks
are clusterable into functional modules that interact with each other through
the same type of epistasis. Here we propose and study three epistatic network
models that... | [
{
"created": "Mon, 16 Jul 2012 20:05:55 GMT",
"version": "v1"
},
{
"created": "Sat, 17 Nov 2012 05:12:47 GMT",
"version": "v2"
}
] | 2013-05-30 | [
[
"Halu",
"Arda",
""
],
[
"Bianconi",
"Ginestra",
""
]
] | Recent studies on epistatic networks of model organisms have unveiled a certain type of modular property called monochromaticity in which the networks are clusterable into functional modules that interact with each other through the same type of epistasis. Here we propose and study three epistatic network models that a... |
2007.13368 | Henning Stumpf | Henning Stumpf (1), Andreja Ambriovi\'c-Ristov (2), Aleksandra
Radenovic (3), Ana-Sun\v{c}ana Smith (1 and 4) ((1) PULS Group, Institute for
Theoretical Physics, Interdisciplinary Center for Nanostructured Films,
Friedrich-Alexander-Universit\"at Erlangen-N\"urnberg, Erlangen, Germany, (2)
Laboratory for Cell B... | Recent Advances and Prospects in the Research of Nascent Adhesions | 38 pages, 2 figures, review article | null | 10.3389/fphys.2020.574371 | null | q-bio.SC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nascent adhesions are submicron transient structures promoting the early
adhesion of cells to the extracellular matrix. Nascent adhesions typically
consist of several tens of integrins, and serve as platforms for the
recruitment and activation of proteins to build mature focal adhesions. They
are also associated with... | [
{
"created": "Mon, 27 Jul 2020 08:35:15 GMT",
"version": "v1"
}
] | 2021-01-19 | [
[
"Stumpf",
"Henning",
"",
"1 and 4"
],
[
"Ambriović-Ristov",
"Andreja",
"",
"1 and 4"
],
[
"Radenovic",
"Aleksandra",
"",
"1 and 4"
],
[
"Smith",
"Ana-Sunčana",
"",
"1 and 4"
]
] | Nascent adhesions are submicron transient structures promoting the early adhesion of cells to the extracellular matrix. Nascent adhesions typically consist of several tens of integrins, and serve as platforms for the recruitment and activation of proteins to build mature focal adhesions. They are also associated with e... |
1906.07463 | Tom Chou | Renaud Dessalles, Yunbei Pan, Mingtao Xia, Davide Maestrini, Maria R.
D'Orsogna, Tom Chou | How heterogeneous thymic output and homeostatic proliferation shape
naive T cell receptor clone abundance distributions | significant revision, including improved data fitting, 23 pages, 11
figures | null | null | null | q-bio.PE q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The set of T cells that express the same T cell receptor (TCR) sequence
represents a T cell clone. The number of different naive T cell clones in an
organism reflects the number of different T cell receptors (TCRs) arising from
recombination of the V(D)J gene segments during T cell development in the
thymus. TCR dive... | [
{
"created": "Tue, 18 Jun 2019 09:33:31 GMT",
"version": "v1"
},
{
"created": "Thu, 5 Mar 2020 04:15:31 GMT",
"version": "v2"
}
] | 2020-03-06 | [
[
"Dessalles",
"Renaud",
""
],
[
"Pan",
"Yunbei",
""
],
[
"Xia",
"Mingtao",
""
],
[
"Maestrini",
"Davide",
""
],
[
"D'Orsogna",
"Maria R.",
""
],
[
"Chou",
"Tom",
""
]
] | The set of T cells that express the same T cell receptor (TCR) sequence represents a T cell clone. The number of different naive T cell clones in an organism reflects the number of different T cell receptors (TCRs) arising from recombination of the V(D)J gene segments during T cell development in the thymus. TCR divers... |
2106.14192 | Jianye Pang | Kai Yi, Jianye Pang, Yungeng Zhang, Xiangrui Zeng, Min Xu | Disentangling semantic features of macromolecules in Cryo-Electron
Tomography | null | null | null | null | q-bio.BM cs.CV | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Cryo-electron tomography (Cryo-ET) is a 3D imaging technique that enables the
systemic study of shape, abundance, and distribution of macromolecular
structures in single cells in near-atomic resolution. However, the systematic
and efficient $\textit{de novo}$ recognition and recovery of macromolecular
structures capt... | [
{
"created": "Sun, 27 Jun 2021 10:41:26 GMT",
"version": "v1"
}
] | 2021-06-29 | [
[
"Yi",
"Kai",
""
],
[
"Pang",
"Jianye",
""
],
[
"Zhang",
"Yungeng",
""
],
[
"Zeng",
"Xiangrui",
""
],
[
"Xu",
"Min",
""
]
] | Cryo-electron tomography (Cryo-ET) is a 3D imaging technique that enables the systemic study of shape, abundance, and distribution of macromolecular structures in single cells in near-atomic resolution. However, the systematic and efficient $\textit{de novo}$ recognition and recovery of macromolecular structures captur... |
1905.01933 | Maria Masoliver | Maria Masoliver and Cristina Masoller | Neuronal coupling benefits the encoding of weak periodic signals in
symbolic spike patterns | null | null | 10.1016/j.cnsns.2019.105023 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A good understanding of how neurons use electrical pulses (i.e, spikes) to
encode the signal information remains elusive. Analyzing spike sequences
generated by individual neurons and by two coupled neurons (using the
stochastic FitzHugh-Nagumo model), recent theoretical studies have found that
the relative timing of... | [
{
"created": "Mon, 6 May 2019 11:25:24 GMT",
"version": "v1"
}
] | 2019-10-23 | [
[
"Masoliver",
"Maria",
""
],
[
"Masoller",
"Cristina",
""
]
] | A good understanding of how neurons use electrical pulses (i.e, spikes) to encode the signal information remains elusive. Analyzing spike sequences generated by individual neurons and by two coupled neurons (using the stochastic FitzHugh-Nagumo model), recent theoretical studies have found that the relative timing of t... |
1806.05753 | Thierry Mora | Andreas Mayer, Vijay Balasubramanian, Aleksandra M. Walczak, Thierry
Mora | How a well-adapting immune system remembers | null | Proc Natl Acad Sci 116(18) 8815-8823 (2019) | 10.1073/pnas.1812810116 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An adaptive agent predicting the future state of an environment must weigh
trust in new observations against prior experiences. In this light, we propose
a view of the adaptive immune system as a dynamic Bayesian machinery that
updates its memory repertoire by balancing evidence from new pathogen
encounters against p... | [
{
"created": "Thu, 14 Jun 2018 22:03:55 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Nov 2018 10:58:08 GMT",
"version": "v2"
}
] | 2019-05-14 | [
[
"Mayer",
"Andreas",
""
],
[
"Balasubramanian",
"Vijay",
""
],
[
"Walczak",
"Aleksandra M.",
""
],
[
"Mora",
"Thierry",
""
]
] | An adaptive agent predicting the future state of an environment must weigh trust in new observations against prior experiences. In this light, we propose a view of the adaptive immune system as a dynamic Bayesian machinery that updates its memory repertoire by balancing evidence from new pathogen encounters against pas... |
2009.05285 | Amit Tewari | Amit Tewari | Temporal Analysis of COVID-19 Peak Outbreak | 5 pages, 10 figures, 2 tables | null | null | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by-sa/4.0/ | Intent of this research is to explore how mathematical models, specifically
Susceptible-Infected-Removed (SIR) model, can be utilized to forecast peak
outbreak timeline of COVID-19 epidemic amongst a population of interest
starting from the date of first reported case. Till the time of this research,
there was no eff... | [
{
"created": "Fri, 11 Sep 2020 08:34:28 GMT",
"version": "v1"
}
] | 2020-09-14 | [
[
"Tewari",
"Amit",
""
]
] | Intent of this research is to explore how mathematical models, specifically Susceptible-Infected-Removed (SIR) model, can be utilized to forecast peak outbreak timeline of COVID-19 epidemic amongst a population of interest starting from the date of first reported case. Till the time of this research, there was no effec... |
1104.5458 | George Kesidis | Yaman Aksu, David J. Miller, George Kesidis, Don C. Bigler, Qing X.
Yang | An MRI-Derived Definition of MCI-to-AD Conversion for Long-Term,
Automati c Prognosis of MCI Patients | null | null | 10.1371/journal.pone.0025074 | null | q-bio.NC physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Alzheimer's disease (AD) and mild cognitive impairment (MCI), continue to be
widely studied. While there is no consensus on whether MCIs actually "convert"
to AD, the more important question is not whether MCIs convert, but what is the
best such definition. We focus on automatic prognostication, nominally using
only ... | [
{
"created": "Thu, 28 Apr 2011 17:56:32 GMT",
"version": "v1"
}
] | 2015-05-28 | [
[
"Aksu",
"Yaman",
""
],
[
"Miller",
"David J.",
""
],
[
"Kesidis",
"George",
""
],
[
"Bigler",
"Don C.",
""
],
[
"Yang",
"Qing X.",
""
]
] | Alzheimer's disease (AD) and mild cognitive impairment (MCI), continue to be widely studied. While there is no consensus on whether MCIs actually "convert" to AD, the more important question is not whether MCIs convert, but what is the best such definition. We focus on automatic prognostication, nominally using only a ... |
1303.3332 | Brent Pedersen | Brent S Pedersen, Ivana V Yang, Subhajyoti De | CruzDB: software for annotation of genomic intervals with UCSC
genome-browser data | 4 pages, 1 figure | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The biological significance of genomic features is often context-dependent.
We present CruzDB, a fast and intuitive programmatic interface to the UCSC
genome browser that facilitates integrative analyses of diverse local and
remotely hosted datasets. We showcase the syntax of CruzDB using miRNA-binding
sites as examp... | [
{
"created": "Thu, 14 Mar 2013 01:41:09 GMT",
"version": "v1"
},
{
"created": "Tue, 9 Jul 2013 22:02:30 GMT",
"version": "v2"
}
] | 2013-07-11 | [
[
"Pedersen",
"Brent S",
""
],
[
"Yang",
"Ivana V",
""
],
[
"De",
"Subhajyoti",
""
]
] | The biological significance of genomic features is often context-dependent. We present CruzDB, a fast and intuitive programmatic interface to the UCSC genome browser that facilitates integrative analyses of diverse local and remotely hosted datasets. We showcase the syntax of CruzDB using miRNA-binding sites as example... |
1912.05433 | Tiberiu Tesileanu | Tiberiu Tesileanu, Mary M. Conte, John J. Briguglio, Ann M.
Hermundstad, Jonathan D. Victor, Vijay Balasubramanian | Efficient coding of natural scene statistics predicts discrimination
thresholds for grayscale textures | 33 pages, 12 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Previously, in (Hermundstad et al., 2014), we showed that when sampling is
limiting, the efficient coding principle leads to a "variance is salience"
hypothesis, and that this hypothesis accounts for visual sensitivity to binary
image statistics. Here, using extensive new psychophysical data and image
analysis, we sh... | [
{
"created": "Wed, 11 Dec 2019 16:41:27 GMT",
"version": "v1"
},
{
"created": "Fri, 10 Jul 2020 19:39:24 GMT",
"version": "v2"
}
] | 2020-07-14 | [
[
"Tesileanu",
"Tiberiu",
""
],
[
"Conte",
"Mary M.",
""
],
[
"Briguglio",
"John J.",
""
],
[
"Hermundstad",
"Ann M.",
""
],
[
"Victor",
"Jonathan D.",
""
],
[
"Balasubramanian",
"Vijay",
""
]
] | Previously, in (Hermundstad et al., 2014), we showed that when sampling is limiting, the efficient coding principle leads to a "variance is salience" hypothesis, and that this hypothesis accounts for visual sensitivity to binary image statistics. Here, using extensive new psychophysical data and image analysis, we show... |
2306.11768 | Zaixi Zhang | Zaixi Zhang, Jiaxian Yan, Qi Liu, Enhong Chen, and Marinka Zitnik | A Systematic Survey in Geometric Deep Learning for Structure-based Drug
Design | 20 pages, under review | null | null | null | q-bio.QM cs.CE cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Structure-based drug design (SBDD) utilizes the three-dimensional geometry of
proteins to identify potential drug candidates. Traditional methods, grounded
in physicochemical modeling and informed by domain expertise, are
resource-intensive. Recent developments in geometric deep learning, focusing on
the integration ... | [
{
"created": "Tue, 20 Jun 2023 14:21:58 GMT",
"version": "v1"
},
{
"created": "Thu, 22 Jun 2023 03:05:21 GMT",
"version": "v2"
},
{
"created": "Mon, 3 Jul 2023 14:38:17 GMT",
"version": "v3"
},
{
"created": "Sat, 14 Oct 2023 20:54:09 GMT",
"version": "v4"
},
{
"cr... | 2023-10-25 | [
[
"Zhang",
"Zaixi",
""
],
[
"Yan",
"Jiaxian",
""
],
[
"Liu",
"Qi",
""
],
[
"Chen",
"Enhong",
""
],
[
"Zitnik",
"Marinka",
""
]
] | Structure-based drug design (SBDD) utilizes the three-dimensional geometry of proteins to identify potential drug candidates. Traditional methods, grounded in physicochemical modeling and informed by domain expertise, are resource-intensive. Recent developments in geometric deep learning, focusing on the integration an... |
2407.18329 | Shuqiang Wang | Yongcheng Zong, Shuqiang Wang | A New Brain Network Construction Paradigm for Brain Disorder via
Diffusion-based Graph Contrastive Learning | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Brain network analysis plays an increasingly important role in studying brain
function and the exploring of disease mechanisms. However, existing brain
network construction tools have some limitations, including dependency on
empirical users, weak consistency in repeated experiments and time-consuming
processes. In t... | [
{
"created": "Sat, 6 Jul 2024 02:47:48 GMT",
"version": "v1"
}
] | 2024-07-29 | [
[
"Zong",
"Yongcheng",
""
],
[
"Wang",
"Shuqiang",
""
]
] | Brain network analysis plays an increasingly important role in studying brain function and the exploring of disease mechanisms. However, existing brain network construction tools have some limitations, including dependency on empirical users, weak consistency in repeated experiments and time-consuming processes. In thi... |
q-bio/0310031 | Paul Higgs | P.G.Higgs, D.Jameson, H.Jow, M.Rattray | The Evolution of tRNA-Leu Genes in Animal Mitochondrial Genomes | 20 pages, 6 figures. J. Mol. Evol. (in press) | null | null | null | q-bio.PE | null | Animal mitochondrial genomes usually have two transfer RNAs for Leucine: one,
with anticodon UAG, translates the four-codon family CUN, whilst the other,
with anticodon UAA, translates the two-codon family UUR. These two genes must
differ at the third anticodon position, but in some species the genes differ at
many a... | [
{
"created": "Thu, 23 Oct 2003 22:11:13 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Higgs",
"P. G.",
""
],
[
"Jameson",
"D.",
""
],
[
"Jow",
"H.",
""
],
[
"Rattray",
"M.",
""
]
] | Animal mitochondrial genomes usually have two transfer RNAs for Leucine: one, with anticodon UAG, translates the four-codon family CUN, whilst the other, with anticodon UAA, translates the two-codon family UUR. These two genes must differ at the third anticodon position, but in some species the genes differ at many add... |
1702.01568 | Volker Pernice | Volker Pernice, Rava Azeredo da Silveira | Interpretation of Correlated Neural Variability from Models of
Feed-Forward and Recurrent Circuits | 41 pages, 10 figures | null | 10.1371/journal.pcbi.1005979 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The correlated variability in the responses of a neural population to the
repeated presentation of a sensory stimulus is a universally observed
phenomenon. Such correlations have been studied in much detail, both with
respect to their mechanistic origin and to their influence on stimulus
discrimination and on the per... | [
{
"created": "Mon, 6 Feb 2017 11:13:15 GMT",
"version": "v1"
}
] | 2018-07-04 | [
[
"Pernice",
"Volker",
""
],
[
"da Silveira",
"Rava Azeredo",
""
]
] | The correlated variability in the responses of a neural population to the repeated presentation of a sensory stimulus is a universally observed phenomenon. Such correlations have been studied in much detail, both with respect to their mechanistic origin and to their influence on stimulus discrimination and on the perfo... |
2308.08898 | Sitabhra Sinha | Anand Pathak, Shakti N. Menon and Sitabhra Sinha | A hierarchy index for networks in the brain reveals a complex entangled
organizational structure | 16 pages, 5 figures + 10 pages Supplementary Information | PNAS 121, e2314291121 (2024) | 10.1073/pnas.2314291121 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Networks involved in information processing often have their nodes arranged
hierarchically, with the majority of connections occurring in adjacent levels.
However, despite being an intuitively appealing concept, the hierarchical
organization of large networks, such as those in the brain, are difficult to
identify, es... | [
{
"created": "Thu, 17 Aug 2023 10:15:36 GMT",
"version": "v1"
}
] | 2024-07-02 | [
[
"Pathak",
"Anand",
""
],
[
"Menon",
"Shakti N.",
""
],
[
"Sinha",
"Sitabhra",
""
]
] | Networks involved in information processing often have their nodes arranged hierarchically, with the majority of connections occurring in adjacent levels. However, despite being an intuitively appealing concept, the hierarchical organization of large networks, such as those in the brain, are difficult to identify, espe... |
1102.4039 | Andrew Gray Mr | Andrew R. Gray | Notes on Hybridization in Leaf frogs of the Genus Agalychnis (Anura,
Hylidae, Phyllomedusinae) | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Two species of Endangered Leaf frogs, Agalychnis moreletii and Agalychnis
annae, belonging to the tree frog Subfamily Phyllomedusinae, Genus Agalychnis,
were hybridized for the first time whilst being maintained in captivity.
Previous to this, these allopatric Central American species were considered as
being distinc... | [
{
"created": "Sun, 20 Feb 2011 02:37:59 GMT",
"version": "v1"
}
] | 2011-02-22 | [
[
"Gray",
"Andrew R.",
""
]
] | Two species of Endangered Leaf frogs, Agalychnis moreletii and Agalychnis annae, belonging to the tree frog Subfamily Phyllomedusinae, Genus Agalychnis, were hybridized for the first time whilst being maintained in captivity. Previous to this, these allopatric Central American species were considered as being distinctl... |
q-bio/0609005 | Horacio Ceva | E. Burgos, H. Ceva, R. Perazzo, M. Devoto, D. Medan, M. Zimmermann, A.
M. Delbue | Why Nestedness in Mutualistic Networks? | Journal of Theoretical Biology (Accepted, 2007) | null | 10.1016/j.jtbi.2007.07.030 | null | q-bio.PE | null | We investigate the relationship between the nested organization of
mutualistic systems and their robustness against the extinction of species. We
establish that a nested pattern of contacts is the best possible one as far as
robustness is concerned, but only when the least linked species have the
greater probability ... | [
{
"created": "Tue, 5 Sep 2006 14:00:56 GMT",
"version": "v1"
},
{
"created": "Thu, 20 Sep 2007 16:53:20 GMT",
"version": "v2"
}
] | 2007-09-20 | [
[
"Burgos",
"E.",
""
],
[
"Ceva",
"H.",
""
],
[
"Perazzo",
"R.",
""
],
[
"Devoto",
"M.",
""
],
[
"Medan",
"D.",
""
],
[
"Zimmermann",
"M.",
""
],
[
"Delbue",
"A. M.",
""
]
] | We investigate the relationship between the nested organization of mutualistic systems and their robustness against the extinction of species. We establish that a nested pattern of contacts is the best possible one as far as robustness is concerned, but only when the least linked species have the greater probability of... |
1511.03965 | Paul Fran\c{c}ois | Paul Fran\c{c}ois, Mathieu Hemery, Kyle A. Johnson, Laura N. Saunders | Phenotypic spandrel: absolute discrimination and ligand antagonism | null | null | 10.1088/1478-3975/13/6/066011 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the general problem of sensitive and specific discrimination
between biochemical species. An important instance is immune discrimination
between self and not-self, where it is also observed experimentally that
ligands just below discrimination threshold negatively impact response, a
phenomenon called anta... | [
{
"created": "Thu, 12 Nov 2015 16:59:31 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Jan 2016 15:49:29 GMT",
"version": "v2"
},
{
"created": "Fri, 7 Oct 2016 15:52:09 GMT",
"version": "v3"
}
] | 2016-12-21 | [
[
"François",
"Paul",
""
],
[
"Hemery",
"Mathieu",
""
],
[
"Johnson",
"Kyle A.",
""
],
[
"Saunders",
"Laura N.",
""
]
] | We consider the general problem of sensitive and specific discrimination between biochemical species. An important instance is immune discrimination between self and not-self, where it is also observed experimentally that ligands just below discrimination threshold negatively impact response, a phenomenon called antago... |
1410.8087 | Gabriele Micali | Diana Clausznitzer, Gabriele Micali, Silke Neumann, Victor Sourjik and
Robert G. Endres | Predicting chemical environments of bacteria from receptor signaling | DG and GM contributed equally to this work | PLoS Comput Biol 10(10): e1003870 (2014) | 10.1371/journal.pcbi.1003870 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sensory systems have evolved to respond to input stimuli of certain
statistical properties, and to reliably transmit this information through
biochemical pathways. Hence, for an experimentally well-characterized sensory
system, one ought to be able to extract valuable information about the
statistics of the stimuli. ... | [
{
"created": "Mon, 27 Oct 2014 11:38:09 GMT",
"version": "v1"
}
] | 2014-10-30 | [
[
"Clausznitzer",
"Diana",
""
],
[
"Micali",
"Gabriele",
""
],
[
"Neumann",
"Silke",
""
],
[
"Sourjik",
"Victor",
""
],
[
"Endres",
"Robert G.",
""
]
] | Sensory systems have evolved to respond to input stimuli of certain statistical properties, and to reliably transmit this information through biochemical pathways. Hence, for an experimentally well-characterized sensory system, one ought to be able to extract valuable information about the statistics of the stimuli. Ba... |
1304.6661 | Carsten Conradi | Katharina Holstein and Dietrich Flockerzi and Carsten Conradi | Multistationarity in sequential distributed multisite phosphorylation
networks | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multisite phosphorylation networks are encountered in many intracellular
processes like signal transduction, cell-cycle control or nuclear signal
integration. In this contribution networks describing the phosphorylation and
dephosphorylation of a protein at $n$ sites in a sequential distributive
mechanism are conside... | [
{
"created": "Wed, 24 Apr 2013 16:39:38 GMT",
"version": "v1"
},
{
"created": "Tue, 7 May 2013 13:34:12 GMT",
"version": "v2"
},
{
"created": "Tue, 2 Jul 2013 16:02:06 GMT",
"version": "v3"
}
] | 2013-07-03 | [
[
"Holstein",
"Katharina",
""
],
[
"Flockerzi",
"Dietrich",
""
],
[
"Conradi",
"Carsten",
""
]
] | Multisite phosphorylation networks are encountered in many intracellular processes like signal transduction, cell-cycle control or nuclear signal integration. In this contribution networks describing the phosphorylation and dephosphorylation of a protein at $n$ sites in a sequential distributive mechanism are considere... |
q-bio/0612027 | Michael Deem | Jeong-Man Park and Michael W. Deem | Phase Diagrams of Quasispecies Theory with Recombination and Horizontal
Gene Transfer | 5 pages, 1 figure, to appear in Physics Review Letters | null | 10.1103/PhysRevLett.98.058101 | null | q-bio.PE | null | We consider how transfer of genetic information between individuals
influences the phase diagram and mean fitness of both the Eigen and the
parallel, or Crow-Kimura, models of evolution. In the absence of genetic
transfer, these physical models of evolution consider the replication and point
mutation of the genomes o... | [
{
"created": "Thu, 14 Dec 2006 21:33:05 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Park",
"Jeong-Man",
""
],
[
"Deem",
"Michael W.",
""
]
] | We consider how transfer of genetic information between individuals influences the phase diagram and mean fitness of both the Eigen and the parallel, or Crow-Kimura, models of evolution. In the absence of genetic transfer, these physical models of evolution consider the replication and point mutation of the genomes of ... |
1203.2883 | Serena Bradde | Vanni Bucci, Serena Bradde, Giulio Biroli and Joao B. Xavier | Social interaction, noise and antibiotic-mediated switches in the
intestinal microbiota | 20 pages, 5 figures accepted for publication in Plos Comp Bio.
Supplementary video and information available | null | 10.1371/journal.pcbi.1002497 | null | q-bio.QM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The intestinal microbiota plays important roles in digestion and resistance
against entero-pathogens. As with other ecosystems, its species composition is
resilient against small disturbances but strong perturbations such as
antibiotics can affect the consortium dramatically. Antibiotic cessation does
not necessarily... | [
{
"created": "Tue, 13 Mar 2012 18:05:39 GMT",
"version": "v1"
}
] | 2015-06-04 | [
[
"Bucci",
"Vanni",
""
],
[
"Bradde",
"Serena",
""
],
[
"Biroli",
"Giulio",
""
],
[
"Xavier",
"Joao B.",
""
]
] | The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically. Antibiotic cessation does not necessarily r... |
1606.02801 | Edmund Crampin | Patrick E. McSharry and Edmund J. Crampin | Identifying statistically significant patterns in gene expression data | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Clustering techniques are routinely applied to identify patterns
of co-expression in gene expression data. Co-regulation, and involvement of
genes in similar cellular function, is subsequently inferred from the clusters
which are obtained. Increasingly sophisticated algorithms have been applied to
microar... | [
{
"created": "Thu, 9 Jun 2016 02:20:57 GMT",
"version": "v1"
}
] | 2016-06-10 | [
[
"McSharry",
"Patrick E.",
""
],
[
"Crampin",
"Edmund J.",
""
]
] | Motivation: Clustering techniques are routinely applied to identify patterns of co-expression in gene expression data. Co-regulation, and involvement of genes in similar cellular function, is subsequently inferred from the clusters which are obtained. Increasingly sophisticated algorithms have been applied to microarra... |
1206.4434 | S\'ilvio Duarte Queir\'os M. | Andrea Cavagna, Silvio M. Duarte Queiros, Irene Giardina, Fabio
Stefanini, Massimiliano Viale | Diffusion of individual birds in starling flocks | 22 pages, 10 figures | Proc. R. Soc. B 280, 20122484 (2013) | 10.1098/rspb.2012.2484 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Flocking is a paradigmatic example of collective animal behaviour, where
decentralized interaction rules give rise to a globally ordered state. In the
emergence of order out of self-organization we find similarities between
biological systems, as bird flocks, and some physical systems, as ferromagnets.
In both cases,... | [
{
"created": "Wed, 20 Jun 2012 09:52:31 GMT",
"version": "v1"
},
{
"created": "Wed, 13 Feb 2013 20:34:18 GMT",
"version": "v2"
}
] | 2013-02-14 | [
[
"Cavagna",
"Andrea",
""
],
[
"Queiros",
"Silvio M. Duarte",
""
],
[
"Giardina",
"Irene",
""
],
[
"Stefanini",
"Fabio",
""
],
[
"Viale",
"Massimiliano",
""
]
] | Flocking is a paradigmatic example of collective animal behaviour, where decentralized interaction rules give rise to a globally ordered state. In the emergence of order out of self-organization we find similarities between biological systems, as bird flocks, and some physical systems, as ferromagnets. In both cases, t... |
1806.07469 | Xiaochang Leng | Xiaochang Leng, Yingchao Yang, Xiaomin Deng, Susan M. Lessner, Michael
A. Sutton, Tarek Shazly | Micromechanical Experimental and Numerical Studies of Collagen Fibers
Failure in Arterial Tissue | 33 pages, 11 figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Arterial tissue failures lead to a number of clinical conditions that develop
rapidly and unpredictably in vivo. Structural components and their interfacial
mechanical strength of arterial tissue play a critical role in the process of
arterail delamination. Therefore, there is a pressing need to understand the
microm... | [
{
"created": "Tue, 19 Jun 2018 21:11:39 GMT",
"version": "v1"
}
] | 2018-06-21 | [
[
"Leng",
"Xiaochang",
""
],
[
"Yang",
"Yingchao",
""
],
[
"Deng",
"Xiaomin",
""
],
[
"Lessner",
"Susan M.",
""
],
[
"Sutton",
"Michael A.",
""
],
[
"Shazly",
"Tarek",
""
]
] | Arterial tissue failures lead to a number of clinical conditions that develop rapidly and unpredictably in vivo. Structural components and their interfacial mechanical strength of arterial tissue play a critical role in the process of arterail delamination. Therefore, there is a pressing need to understand the micromec... |
2105.13288 | Soumyajyoti Biswas | Anvesh Reddy, Hanesh Koganti, Sai Krishna, Suhas Reddy, Soumyajyoti
Biswas | Machine learning predictions of COVID-19 second wave end-times in Indian
states | 8 pages, 6 figures, 1 table | Indian Journal of Physics (2021) | 10.1007/s12648-021-02195-x | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The estimate of the remaining time of an ongoing wave of epidemic spreading
is a critical issue. Due to the variations of a wide range of parameters in an
epidemic, for simple models such as Susceptible-Infected-Removed (SIR) model,
it is difficult to estimate such a time scale. On the other hand,
multidimensional da... | [
{
"created": "Wed, 26 May 2021 14:19:22 GMT",
"version": "v1"
}
] | 2021-10-12 | [
[
"Reddy",
"Anvesh",
""
],
[
"Koganti",
"Hanesh",
""
],
[
"Krishna",
"Sai",
""
],
[
"Reddy",
"Suhas",
""
],
[
"Biswas",
"Soumyajyoti",
""
]
] | The estimate of the remaining time of an ongoing wave of epidemic spreading is a critical issue. Due to the variations of a wide range of parameters in an epidemic, for simple models such as Susceptible-Infected-Removed (SIR) model, it is difficult to estimate such a time scale. On the other hand, multidimensional data... |
2308.05115 | Ziyang Xu | Ziyang Xu, Haitian Zhong, Bingrui He, Xueying Wang and Tianchi Lu | PTransIPs: Identification of phosphorylation sites enhanced by protein
PLM embeddings | null | null | 10.1109/JBHI.2024.3377362 | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phosphorylation is pivotal in numerous fundamental cellular processes and
plays a significant role in the onset and progression of various diseases. The
accurate identification of these phosphorylation sites is crucial for
unraveling the molecular mechanisms within cells and during viral infections,
potentially leadi... | [
{
"created": "Tue, 8 Aug 2023 07:50:38 GMT",
"version": "v1"
},
{
"created": "Fri, 18 Aug 2023 06:35:50 GMT",
"version": "v2"
},
{
"created": "Wed, 13 Mar 2024 05:02:32 GMT",
"version": "v3"
}
] | 2024-03-27 | [
[
"Xu",
"Ziyang",
""
],
[
"Zhong",
"Haitian",
""
],
[
"He",
"Bingrui",
""
],
[
"Wang",
"Xueying",
""
],
[
"Lu",
"Tianchi",
""
]
] | Phosphorylation is pivotal in numerous fundamental cellular processes and plays a significant role in the onset and progression of various diseases. The accurate identification of these phosphorylation sites is crucial for unraveling the molecular mechanisms within cells and during viral infections, potentially leading... |
2302.06842 | Gerry Gralton | S. Gerry Gralton, Farah Alkhatib, Ben Zwick, George Bourantas, Adam
Wittek, Karol Miller | Random boundaries: quantifying segmentation uncertainty in solutions to
boundary-value problems | null | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Engineering simulations using boundary-value partial differential equations
often implicitly assume that the uncertainty in the location of the boundary
has a negligible impact on the output of the simulation. In this work, we
develop a novel method for describing the geometric uncertainty in
image-derived models and... | [
{
"created": "Tue, 14 Feb 2023 05:33:06 GMT",
"version": "v1"
},
{
"created": "Sun, 28 Jan 2024 12:53:23 GMT",
"version": "v2"
},
{
"created": "Mon, 10 Jun 2024 02:56:39 GMT",
"version": "v3"
}
] | 2024-06-11 | [
[
"Gralton",
"S. Gerry",
""
],
[
"Alkhatib",
"Farah",
""
],
[
"Zwick",
"Ben",
""
],
[
"Bourantas",
"George",
""
],
[
"Wittek",
"Adam",
""
],
[
"Miller",
"Karol",
""
]
] | Engineering simulations using boundary-value partial differential equations often implicitly assume that the uncertainty in the location of the boundary has a negligible impact on the output of the simulation. In this work, we develop a novel method for describing the geometric uncertainty in image-derived models and u... |
1907.09151 | Luca Ciandrini | Pascal S. Rogalla, Timothy J. Rudge and Luca Ciandrini | An equilibrium model for ribosome competition | null | null | 10.1088/1478-3975/ab4fbc | null | q-bio.SC cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The number of ribosomes in a cell is considered as limiting, and gene
expression is thus largely determined by their cellular concentration. In this
work we develop a toy model to study the trade-off between the ribosomal supply
and the demand of the translation machinery, dictated by the composition of the
transcrip... | [
{
"created": "Mon, 22 Jul 2019 06:35:29 GMT",
"version": "v1"
},
{
"created": "Mon, 14 Oct 2019 20:42:24 GMT",
"version": "v2"
}
] | 2020-02-19 | [
[
"Rogalla",
"Pascal S.",
""
],
[
"Rudge",
"Timothy J.",
""
],
[
"Ciandrini",
"Luca",
""
]
] | The number of ribosomes in a cell is considered as limiting, and gene expression is thus largely determined by their cellular concentration. In this work we develop a toy model to study the trade-off between the ribosomal supply and the demand of the translation machinery, dictated by the composition of the transcript ... |
1806.01467 | Susan Cheng | Jeramie D. Watrous, Teemu Niiranen, Kim A. Lagerborg, Mir Henglin,
Yong-Jian Xu, Sonia Sharma, Ramachandran S. Vasan, Martin G. Larson, Aaron
Armando, Oswald Quehenberger, Edward A. Dennis, Susan Cheng, Mohit Jain | Directed Non-Targeted Mass Spectrometry and Chemical Networking for
Discovery of Eicosanoids | null | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Eicosanoids and related species are critical, small bioactive mediators of
human physiology and inflammation. While ~1100 distinct eicosanoids have been
predicted to exist, to date, less than 150 of these molecules have been
measured in humans, limiting our understanding of eicosanoids and their role in
human biology... | [
{
"created": "Tue, 5 Jun 2018 02:24:59 GMT",
"version": "v1"
}
] | 2018-06-06 | [
[
"Watrous",
"Jeramie D.",
""
],
[
"Niiranen",
"Teemu",
""
],
[
"Lagerborg",
"Kim A.",
""
],
[
"Henglin",
"Mir",
""
],
[
"Xu",
"Yong-Jian",
""
],
[
"Sharma",
"Sonia",
""
],
[
"Vasan",
"Ramachandran S.",
""
... | Eicosanoids and related species are critical, small bioactive mediators of human physiology and inflammation. While ~1100 distinct eicosanoids have been predicted to exist, to date, less than 150 of these molecules have been measured in humans, limiting our understanding of eicosanoids and their role in human biology. ... |
1208.1560 | Jiang Zhang | Jiang Zhang and Yuanjing Feng | Common Patterns of Energy Flow and Biomass Distribution on Weighted Food
Webs | 26 pages, 7 figures | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Weights of edges and nodes on food webs which are available from the
empirical data hide much information about energy flows and biomass
distributions in ecosystem. We define a set of variables related to weights for
each species $i$, including the throughflow $T_i$, the total biomass $X_i$, and
the dissipated flow $... | [
{
"created": "Wed, 8 Aug 2012 01:25:39 GMT",
"version": "v1"
}
] | 2012-08-09 | [
[
"Zhang",
"Jiang",
""
],
[
"Feng",
"Yuanjing",
""
]
] | Weights of edges and nodes on food webs which are available from the empirical data hide much information about energy flows and biomass distributions in ecosystem. We define a set of variables related to weights for each species $i$, including the throughflow $T_i$, the total biomass $X_i$, and the dissipated flow $D_... |
2102.04720 | Brian Mathias | Brian Mathias, Christian Andrae, Anika Schwager, Manuela Macedonia,
Katharina von Kriegstein | Twelve- and fourteen-year-old school children differentially benefit
from sensorimotor- and multisensory-enriched vocabulary training | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Both children and adults have been shown to benefit from the integration of
multisensory and sensorimotor enrichment into pedagogy. For example,
integrating pictures or gestures into foreign language (L2) vocabulary learning
can improve learning outcomes relative to unisensory learning. However, whereas
adults seem t... | [
{
"created": "Tue, 9 Feb 2021 09:32:12 GMT",
"version": "v1"
}
] | 2021-02-10 | [
[
"Mathias",
"Brian",
""
],
[
"Andrae",
"Christian",
""
],
[
"Schwager",
"Anika",
""
],
[
"Macedonia",
"Manuela",
""
],
[
"von Kriegstein",
"Katharina",
""
]
] | Both children and adults have been shown to benefit from the integration of multisensory and sensorimotor enrichment into pedagogy. For example, integrating pictures or gestures into foreign language (L2) vocabulary learning can improve learning outcomes relative to unisensory learning. However, whereas adults seem to ... |
q-bio/0407023 | Steven Samuel Plotkin | C. Clementi and S. S. Plotkin | The effects of non-native interactions on protein folding rates: Theory
and simulation | 35 pages, 12 figures, 1 table | Protein Science 2004 13: 1750-1766 | null | null | q-bio.BM | null | Proteins are minimally frustrated polymers. However, for realistic protein
models non-native interactions must be taken into account. In this paper we
analyze the effect of non-native interactions on the folding rate and on the
folding free energy barrier. We present an analytic theory to account for the
modification... | [
{
"created": "Thu, 15 Jul 2004 01:44:42 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Clementi",
"C.",
""
],
[
"Plotkin",
"S. S.",
""
]
] | Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free energy barrier. We present an analytic theory to account for the modification o... |
1907.06909 | Kevin Woods | Kevin J P Woods, Adam Hewett, Andrea Spencer, Benjamin Morillon,
Psyche Loui | Modulation in background music influences sustained attention | 20 pages, 5 figures. Behavioral portion of larger planned manuscript
to include neuroimaging. Comments welcome (kevin@brain.fm) | null | null | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background music is known to affect performance on cognitive tasks, possibly
due to temporal modulations in the acoustic signal, but little is known about
how music should be designed to aid performance. Since acoustic modulation has
been shown to shape neural activity in known networks, we chose to test the
effects ... | [
{
"created": "Tue, 16 Jul 2019 09:33:39 GMT",
"version": "v1"
}
] | 2019-07-17 | [
[
"Woods",
"Kevin J P",
""
],
[
"Hewett",
"Adam",
""
],
[
"Spencer",
"Andrea",
""
],
[
"Morillon",
"Benjamin",
""
],
[
"Loui",
"Psyche",
""
]
] | Background music is known to affect performance on cognitive tasks, possibly due to temporal modulations in the acoustic signal, but little is known about how music should be designed to aid performance. Since acoustic modulation has been shown to shape neural activity in known networks, we chose to test the effects of... |
1810.08362 | Gerardo F. Goya | V. Raffa, F. Falcone, M.P. Calatayud, G.F. Goya and A. Cuschieri | Pico-Newton mechanical forces promote neurite growth | 16 pages, 3 figures | null | 10.1016/j.bpj.2018.10.009 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Investigations over half a century have indicated that mechanical forces
induce neurite growth - with neurites elongating at a rate of
0.1-0.3{\mu}mh^{-1} per pico-Newton (pN) of applied force - when mechanical
tension exceeds a threshold, with this being identified as 400-1000 pN for
neurites of PC12 cells. Here we ... | [
{
"created": "Fri, 19 Oct 2018 06:20:53 GMT",
"version": "v1"
}
] | 2018-10-22 | [
[
"Raffa",
"V.",
""
],
[
"Falcone",
"F.",
""
],
[
"Calatayud",
"M. P.",
""
],
[
"Goya",
"G. F.",
""
],
[
"Cuschieri",
"A.",
""
]
] | Investigations over half a century have indicated that mechanical forces induce neurite growth - with neurites elongating at a rate of 0.1-0.3{\mu}mh^{-1} per pico-Newton (pN) of applied force - when mechanical tension exceeds a threshold, with this being identified as 400-1000 pN for neurites of PC12 cells. Here we de... |
0912.5450 | Piotr Su{\l}kowski | Joanna I. Su{\l}kowska, Piotr Su{\l}kowski, Jos\'e N. Onuchic | Dodging the crisis of folding proteins with knots | 29 pages, 11 figures, 1 table | PNAS 106 (2009) 3119-3124 | 10.1073/pnas.0811147106 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Proteins with nontrivial topology, containing knots and slipknots, have the
ability to fold to their native states without any additional external forces
invoked. A mechanism is suggested for folding of these proteins, such as YibK
and YbeA, which involves an intermediate configuration with a slipknot. It
elucidates ... | [
{
"created": "Wed, 30 Dec 2009 20:55:10 GMT",
"version": "v1"
}
] | 2010-01-06 | [
[
"Sułkowska",
"Joanna I.",
""
],
[
"Sułkowski",
"Piotr",
""
],
[
"Onuchic",
"José N.",
""
]
] | Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, which involves an intermediate configuration with a slipknot. It elucidates th... |
1702.06665 | Michael Beyeler | Michael Beyeler and Nikil Dutt and Jeffrey L. Krichmar | Visual response properties of MSTd emerge from a sparse population code | null | null | 10.1523/JNEUROSCI.0396-16.2016 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neurons in the dorsal subregion of the medial superior temporal (MSTd) area
respond to large, complex patterns of retinal flow, implying a role in the
analysis of self-motion. Some neurons are selective for the expanding radial
motion that occurs as an observer moves through the environment ("heading"),
and computati... | [
{
"created": "Wed, 22 Feb 2017 03:41:02 GMT",
"version": "v1"
}
] | 2017-02-24 | [
[
"Beyeler",
"Michael",
""
],
[
"Dutt",
"Nikil",
""
],
[
"Krichmar",
"Jeffrey L.",
""
]
] | Neurons in the dorsal subregion of the medial superior temporal (MSTd) area respond to large, complex patterns of retinal flow, implying a role in the analysis of self-motion. Some neurons are selective for the expanding radial motion that occurs as an observer moves through the environment ("heading"), and computation... |
1510.06748 | Luca Ferretti | Luca Ferretti, Alice Ledda, Guillaume Achaz, Thomas Wiehe and
Sebastian E. Ramos-Onsins | Decomposing the site frequency spectrum: the impact of tree topology on
neutrality tests | 23 pages, 8 figures | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the dependence of the site frequency spectrum (SFS) on the
topological structure of genealogical trees. We show that basic population
genetic statistics - for instance estimators of $\theta$ or neutrality tests
such as Tajima's $D$ - can be decomposed into components of waiting times
between coalescent... | [
{
"created": "Thu, 22 Oct 2015 20:10:48 GMT",
"version": "v1"
},
{
"created": "Thu, 12 Jan 2017 23:50:59 GMT",
"version": "v2"
}
] | 2017-01-16 | [
[
"Ferretti",
"Luca",
""
],
[
"Ledda",
"Alice",
""
],
[
"Achaz",
"Guillaume",
""
],
[
"Wiehe",
"Thomas",
""
],
[
"Ramos-Onsins",
"Sebastian E.",
""
]
] | We investigate the dependence of the site frequency spectrum (SFS) on the topological structure of genealogical trees. We show that basic population genetic statistics - for instance estimators of $\theta$ or neutrality tests such as Tajima's $D$ - can be decomposed into components of waiting times between coalescent e... |
0711.1010 | Akira Kinjo | Akira R. Kinjo and Haruki Nakamura | Nature of protein family signatures: Insights from singular value
analysis of position-specific scoring matrices | 22 pages, 7 figures, 4 tables | PLoS ONE, 3:e1963 (2008) | 10.1371/journal.pone.0001963 | null | q-bio.BM | null | Position-specific scoring matrices (PSSMs) are useful for detecting weak
homology in protein sequence analysis, and they are thought to contain some
essential signatures of the protein families. In order to elucidate what kind
of ingredients constitute such family-specific signatures, we apply singular
value decompos... | [
{
"created": "Wed, 7 Nov 2007 05:20:40 GMT",
"version": "v1"
}
] | 2008-04-14 | [
[
"Kinjo",
"Akira R.",
""
],
[
"Nakamura",
"Haruki",
""
]
] | Position-specific scoring matrices (PSSMs) are useful for detecting weak homology in protein sequence analysis, and they are thought to contain some essential signatures of the protein families. In order to elucidate what kind of ingredients constitute such family-specific signatures, we apply singular value decomposit... |
2305.02223 | Maryam Al Yahyai | Maryam Al-Yahyai (1), Fatma Al-Musalhi (1), Nasser Al-Salti (2) and
Ibrahim Elmojtaba (1) ((1) Department of Mathematics, College of Science,
Sultan Qaboos University, Muscat, Oman, (2) Department of Applied Mathematics
and Science, National University of Science and Technology, Muscat, Oman) | The Role of Quarantine and Isolation in Controlling COVID-19
Hospitalization in Oman | 34 pages | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we build a mathematical model for the dynamics of COVID-19 to
assess the impact of placing healthy individuals in quarantine and isolating
infected ones on the number of hospitalization and intensive care unit cases.
The proposed model is fully analyzed in order to prove the positivity of
solutions, to... | [
{
"created": "Wed, 3 May 2023 16:03:27 GMT",
"version": "v1"
}
] | 2023-05-04 | [
[
"Al-Yahyai",
"Maryam",
""
],
[
"Al-Musalhi",
"Fatma",
""
],
[
"Al-Salti",
"Nasser",
""
],
[
"Elmojtaba",
"Ibrahim",
""
]
] | In this paper, we build a mathematical model for the dynamics of COVID-19 to assess the impact of placing healthy individuals in quarantine and isolating infected ones on the number of hospitalization and intensive care unit cases. The proposed model is fully analyzed in order to prove the positivity of solutions, to s... |
2102.03676 | Xavier Michalet | Xavier Michalet | An overview of continuous and discrete phasor analysis of binned or
time-gated periodic decays | 12 pages, 4 figures, submitted as a Proceedings of SPIE (BiOS
Conference 11648, March 6-11, 2021) | Proc. SPIE 11648 (2021) 116480E | 10.1063/5.0027834 | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Time-resolved analysis of periodically excited luminescence decays by the
phasor method in the presence of time-gating or binning is revisited.
Analytical expressions for discrete configurations of square gates are derived
and the locus of the phasors of such modified periodic single-exponential
decays is compared to... | [
{
"created": "Sat, 6 Feb 2021 22:00:55 GMT",
"version": "v1"
},
{
"created": "Thu, 11 Feb 2021 21:49:10 GMT",
"version": "v2"
}
] | 2024-06-12 | [
[
"Michalet",
"Xavier",
""
]
] | Time-resolved analysis of periodically excited luminescence decays by the phasor method in the presence of time-gating or binning is revisited. Analytical expressions for discrete configurations of square gates are derived and the locus of the phasors of such modified periodic single-exponential decays is compared to t... |
2004.02398 | Siyu Liu | Jiwei Jia, Siyu Liu, Jing Ding, Guidong Liao, Lihua Zhang, Ran Zhang | The impact of multilateral imported cases of COVID-19 on the epidemic
control in China | null | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nowadays, the epidemic of COVID-19 in China is under control. However, the
epidemic are developing rapidly around the world. Due to the normal migration
of population, China is facing high risk from imported cases. The potential
specific medicine and vaccine is still in the process of clinical trials.
Currently, cont... | [
{
"created": "Mon, 6 Apr 2020 04:31:52 GMT",
"version": "v1"
}
] | 2020-04-07 | [
[
"Jia",
"Jiwei",
""
],
[
"Liu",
"Siyu",
""
],
[
"Ding",
"Jing",
""
],
[
"Liao",
"Guidong",
""
],
[
"Zhang",
"Lihua",
""
],
[
"Zhang",
"Ran",
""
]
] | Nowadays, the epidemic of COVID-19 in China is under control. However, the epidemic are developing rapidly around the world. Due to the normal migration of population, China is facing high risk from imported cases. The potential specific medicine and vaccine is still in the process of clinical trials. Currently, contro... |
1202.4691 | Teresa Ruiz Herrero | Teresa Ruiz-Herrero, Enrique Velasco, Michael F. Hagan | Mechanisms of budding of nanoscale particles through lipid bilayers | null | null | null | null | q-bio.SC cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We examine the budding of a nanoscale particle through a lipid bilayer using
molecular dynamics simulations, free energy calculations, and an elastic
theory, with the aim of determining the extent to which equilibrium elasticity
theory can describe the factors that control the mechanism and efficiency of
budding. The... | [
{
"created": "Tue, 21 Feb 2012 16:19:48 GMT",
"version": "v1"
}
] | 2012-02-22 | [
[
"Ruiz-Herrero",
"Teresa",
""
],
[
"Velasco",
"Enrique",
""
],
[
"Hagan",
"Michael F.",
""
]
] | We examine the budding of a nanoscale particle through a lipid bilayer using molecular dynamics simulations, free energy calculations, and an elastic theory, with the aim of determining the extent to which equilibrium elasticity theory can describe the factors that control the mechanism and efficiency of budding. The p... |
1806.05017 | Jordi Sol\'e-Casals | Jordi Sole-Casals, Cesar F. Caiafa, Qibin Zhao and Adrzej Cichocki | Brain-Computer Interface with Corrupted EEG Data: A Tensor Completion
Approach | 21 pages, 3 tables, 4 figures | Sole-Casals, J., Caiafa, C.F., Zhao, Q. et al. Cogn Comput (2018).
https://doi.org/10.1007/s12559-018-9574-9 | 10.1007/s12559-018-9574-9 | null | q-bio.QM eess.SP stat.ML | http://creativecommons.org/licenses/by/4.0/ | One of the current issues in Brain-Computer Interface is how to deal with
noisy Electroencephalography measurements organized as multidimensional
datasets. On the other hand, recently, significant advances have been made in
multidimensional signal completion algorithms that exploit tensor decomposition
models to capt... | [
{
"created": "Wed, 13 Jun 2018 13:16:28 GMT",
"version": "v1"
},
{
"created": "Thu, 26 Jul 2018 15:53:29 GMT",
"version": "v2"
}
] | 2018-07-27 | [
[
"Sole-Casals",
"Jordi",
""
],
[
"Caiafa",
"Cesar F.",
""
],
[
"Zhao",
"Qibin",
""
],
[
"Cichocki",
"Adrzej",
""
]
] | One of the current issues in Brain-Computer Interface is how to deal with noisy Electroencephalography measurements organized as multidimensional datasets. On the other hand, recently, significant advances have been made in multidimensional signal completion algorithms that exploit tensor decomposition models to captur... |
1909.10139 | Alex McAvoy | Alex McAvoy, Benjamin Allen, Martin A. Nowak | Social goods dilemmas in heterogeneous societies | 72 pages; final version | Nature Human Behaviour (2020) | 10.1038/s41562-020-0881-2 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Prosocial behaviors are encountered in the donation game, the prisoner's
dilemma, relaxed social dilemmas, and public goods games. Many studies assume
that the population structure is homogeneous, meaning all individuals have the
same number of interaction partners, or that the social good is of one
particular type. ... | [
{
"created": "Mon, 23 Sep 2019 03:30:07 GMT",
"version": "v1"
},
{
"created": "Fri, 1 May 2020 03:53:18 GMT",
"version": "v2"
}
] | 2020-05-28 | [
[
"McAvoy",
"Alex",
""
],
[
"Allen",
"Benjamin",
""
],
[
"Nowak",
"Martin A.",
""
]
] | Prosocial behaviors are encountered in the donation game, the prisoner's dilemma, relaxed social dilemmas, and public goods games. Many studies assume that the population structure is homogeneous, meaning all individuals have the same number of interaction partners, or that the social good is of one particular type. He... |
1605.01905 | Carina Curto | Carina Curto | What can topology tell us about the neural code? | 16 pages, 9 figures | Bulletin of the AMS, vol. 54, no. 1, pp. 63-78, January 2017 | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neuroscience is undergoing a period of rapid experimental progress and
expansion. New mathematical tools, previously unknown in the neuroscience
community, are now being used to tackle fundamental questions and analyze
emerging data sets. Consistent with this trend, the last decade has seen an
uptick in the use of to... | [
{
"created": "Fri, 6 May 2016 12:06:15 GMT",
"version": "v1"
}
] | 2016-12-28 | [
[
"Curto",
"Carina",
""
]
] | Neuroscience is undergoing a period of rapid experimental progress and expansion. New mathematical tools, previously unknown in the neuroscience community, are now being used to tackle fundamental questions and analyze emerging data sets. Consistent with this trend, the last decade has seen an uptick in the use of topo... |
2009.10049 | Ananth V S | Bishal Chhetri, Vijay M. Bhagat, D. K. K. Vamsi, Ananth V S, Bhanu
Prakash, Swapna Muthuswamy, Pradeep Deshmukh, Carani B Sanjeevi | Optimal Drug Regimen and Combined Drug Therapy and its Efficacy in the
Treatment of COVID-19 : An Within-Host Modeling Study | 16 pages, 13 figures | null | 10.1007/s10441-022-09440-8 | null | q-bio.PE math.DS math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The COVID-19 pandemic has resulted in more than 30.35 million infections and
9, 50, 625 deaths in 212 countries over the last few months. Different drug
intervention acting at multiple stages of pathogenesis of COVID-19 can
substantially reduce the infection induced mortality. The current within-host
mathematical mod... | [
{
"created": "Mon, 21 Sep 2020 17:43:20 GMT",
"version": "v1"
}
] | 2023-09-01 | [
[
"Chhetri",
"Bishal",
""
],
[
"Bhagat",
"Vijay M.",
""
],
[
"Vamsi",
"D. K. K.",
""
],
[
"S",
"Ananth V",
""
],
[
"Prakash",
"Bhanu",
""
],
[
"Muthuswamy",
"Swapna",
""
],
[
"Deshmukh",
"Pradeep",
""
],
... | The COVID-19 pandemic has resulted in more than 30.35 million infections and 9, 50, 625 deaths in 212 countries over the last few months. Different drug intervention acting at multiple stages of pathogenesis of COVID-19 can substantially reduce the infection induced mortality. The current within-host mathematical model... |
1401.0002 | Evgenii Levites | Svetlana Sergeevna Kirikovich and Evgenii Vladimirovich Levites | Phenotypic class ratios as marker signs of different types of
agamospermy | 8 pages, 2 tables, 23 references | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This article focuses on the development of the method for the genetic
classification of agamospermous reproduction types in plants using sugar beet
as an example. The classification feasibility is ensured by the use of isozymes
as genetic markers allowing the identification of all three phenotypic classes
in the prog... | [
{
"created": "Sat, 28 Dec 2013 11:39:53 GMT",
"version": "v1"
}
] | 2014-01-03 | [
[
"Kirikovich",
"Svetlana Sergeevna",
""
],
[
"Levites",
"Evgenii Vladimirovich",
""
]
] | This article focuses on the development of the method for the genetic classification of agamospermous reproduction types in plants using sugar beet as an example. The classification feasibility is ensured by the use of isozymes as genetic markers allowing the identification of all three phenotypic classes in the progen... |
1107.2834 | John Burke | John Burke, Mathieu Desroches, Anna M. Barry, Tasso J. Kaper, and Mark
A. Kramer | A showcase of torus canards in neuronal bursters | null | null | null | null | q-bio.NC math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rapid action potential generation --- spiking --- and alternating intervals
of spiking and quiescence --- bursting --- are two dynamic patterns observed in
neuronal activity. In computational models of neuronal systems, the transition
from spiking to bursting often exhibits complex bifurcation structure. One type
of ... | [
{
"created": "Thu, 14 Jul 2011 14:14:29 GMT",
"version": "v1"
}
] | 2011-07-15 | [
[
"Burke",
"John",
""
],
[
"Desroches",
"Mathieu",
""
],
[
"Barry",
"Anna M.",
""
],
[
"Kaper",
"Tasso J.",
""
],
[
"Kramer",
"Mark A.",
""
]
] | Rapid action potential generation --- spiking --- and alternating intervals of spiking and quiescence --- bursting --- are two dynamic patterns observed in neuronal activity. In computational models of neuronal systems, the transition from spiking to bursting often exhibits complex bifurcation structure. One type of tr... |
1909.13327 | Christoph Feinauer | Matteo Negri, Davide Bergamini, Carlo Baldassi, Riccardo Zecchina,
Christoph Feinauer | Natural representation of composite data with replicated autoencoders | 11 pages, 4 figures | null | null | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Generative processes in biology and other fields often produce data that can
be regarded as resulting from a composition of basic features. Here we present
an unsupervised method based on autoencoders for inferring these basic features
of data. The main novelty in our approach is that the training is based on the
opt... | [
{
"created": "Sun, 29 Sep 2019 17:41:44 GMT",
"version": "v1"
}
] | 2019-10-04 | [
[
"Negri",
"Matteo",
""
],
[
"Bergamini",
"Davide",
""
],
[
"Baldassi",
"Carlo",
""
],
[
"Zecchina",
"Riccardo",
""
],
[
"Feinauer",
"Christoph",
""
]
] | Generative processes in biology and other fields often produce data that can be regarded as resulting from a composition of basic features. Here we present an unsupervised method based on autoencoders for inferring these basic features of data. The main novelty in our approach is that the training is based on the optim... |
1408.2253 | Tatjana Tchumatchenko | T. Tchumatchenko, T. Reichenbach | Cochlear-bone wave can yield a hearing sensation as well as otoacoustic
emission | 37 pages, 4 figures, Nature Communications 2014 | null | 10.1038/ncomms5160 | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A hearing sensation arises when the elastic basilar membrane inside the
cochlea vibrates. The basilar membrane is typically set into motion through
airborne sound that displaces the middle ear and induces a pressure difference
across the membrane. A second, alternative pathway exists, however: stimulation
of the coch... | [
{
"created": "Sun, 10 Aug 2014 16:55:32 GMT",
"version": "v1"
}
] | 2015-06-22 | [
[
"Tchumatchenko",
"T.",
""
],
[
"Reichenbach",
"T.",
""
]
] | A hearing sensation arises when the elastic basilar membrane inside the cochlea vibrates. The basilar membrane is typically set into motion through airborne sound that displaces the middle ear and induces a pressure difference across the membrane. A second, alternative pathway exists, however: stimulation of the cochle... |
1005.4393 | Adrian Melott | Adrian L. Melott (University of Kansas) and Richard K. Bambach
(National Museum of Natural History) | A ubiquitous ~62-Myr periodic fluctuation superimposed on general trends
in fossil biodiversity. I. Documentation | 56 pages. In press at Paleobiology. Submitted to conform with
copyedited version | Paleobiology 37:92,2011 | null | null | q-bio.PE astro-ph.EP astro-ph.GA physics.bio-ph physics.geo-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We use Fourier analysis and related techniques to investigate the question of
periodicities in fossil biodiversity. These techniques are able to identify
cycles superimposed on the long-term trends of the Phanerozoic. We review prior
results and analyze data previously reduced and published. Joint time-series
analysi... | [
{
"created": "Mon, 24 May 2010 18:25:31 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Aug 2010 17:05:17 GMT",
"version": "v2"
}
] | 2010-11-26 | [
[
"Melott",
"Adrian L.",
"",
"University of Kansas"
],
[
"Bambach",
"Richard K.",
"",
"National Museum of Natural History"
]
] | We use Fourier analysis and related techniques to investigate the question of periodicities in fossil biodiversity. These techniques are able to identify cycles superimposed on the long-term trends of the Phanerozoic. We review prior results and analyze data previously reduced and published. Joint time-series analysis ... |
1212.1135 | Henry Tuckwell | Henry C. Tuckwell | Biophysical properties and computational modeling of calcium spikes in
serotonergic neurons of the dorsal raphe nucleus | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Serotonergic neurons of the dorsal raphe nuclei, with their extensive
innervation of nearly the whole brain have important modulatory effects on many
cognitive and physiological processes. They play important roles in clinical
depression and other psychiatric disorders. In order to quantify the effects of
serotonergi... | [
{
"created": "Wed, 5 Dec 2012 19:33:29 GMT",
"version": "v1"
}
] | 2012-12-06 | [
[
"Tuckwell",
"Henry C.",
""
]
] | Serotonergic neurons of the dorsal raphe nuclei, with their extensive innervation of nearly the whole brain have important modulatory effects on many cognitive and physiological processes. They play important roles in clinical depression and other psychiatric disorders. In order to quantify the effects of serotonergic ... |
q-bio/0612041 | Etay Ziv | Etay Ziv, Ilya Nemenman, and Chris H. Wiggins | Optimal signal processing in small stochastic biochemical networks | 41 pages 7 figures, 5 tables | null | 10.1371/journal.pone.0001077 | LA-UR-06-8411 | q-bio.MN q-bio.QM | null | We quantify the influence of the topology of a transcriptional regulatory
network on its ability to process environmental signals. By posing the problem
in terms of information theory, we may do this without specifying the function
performed by the network. Specifically, we study the maximum mutual information
betwee... | [
{
"created": "Thu, 21 Dec 2006 20:39:46 GMT",
"version": "v1"
}
] | 2015-06-26 | [
[
"Ziv",
"Etay",
""
],
[
"Nemenman",
"Ilya",
""
],
[
"Wiggins",
"Chris H.",
""
]
] | We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function performed by the network. Specifically, we study the maximum mutual information between ... |
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