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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1709.03031 | Alex McAvoy | Kamran Kaveh, Alex McAvoy, Martin A. Nowak | Environmental fitness heterogeneity in the Moran process | 23 pages, 9 figures; final version | null | 10.1098/rsos.181661 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many mathematical models of evolution assume that all individuals experience
the same environment. Here, we study the Moran process in heterogeneous
environments. The population is of finite size with two competing types, which
are exposed to a fixed number of environmental conditions. Reproductive rate is
determined... | [
{
"created": "Sun, 10 Sep 2017 03:20:17 GMT",
"version": "v1"
},
{
"created": "Mon, 14 May 2018 17:00:23 GMT",
"version": "v2"
},
{
"created": "Tue, 18 Dec 2018 15:04:32 GMT",
"version": "v3"
}
] | 2018-12-19 | [
[
"Kaveh",
"Kamran",
""
],
[
"McAvoy",
"Alex",
""
],
[
"Nowak",
"Martin A.",
""
]
] | Many mathematical models of evolution assume that all individuals experience the same environment. Here, we study the Moran process in heterogeneous environments. The population is of finite size with two competing types, which are exposed to a fixed number of environmental conditions. Reproductive rate is determined b... |
0807.1041 | Thierry Rabilloud | Thierry Rabilloud (BBSI), Mireille Chevallet (BBSI), Sylvie Luche
(BBSI), Emmanuelle Leize-Wagner | Oxidative stress response: a proteomic view | null | Expert Rev Proteomics 2, 6 (2005) 949-56 | 10.1586/14789450.2.6.949 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The oxidative stress response is characterized by various effects on a range
of biologic molecules. When examined at the protein level, both expression
levels and protein modifications are altered by oxidative stress. While these
effects have been studied in the past by classic biochemical methods, the
recent onset o... | [
{
"created": "Mon, 7 Jul 2008 15:30:32 GMT",
"version": "v1"
}
] | 2008-07-08 | [
[
"Rabilloud",
"Thierry",
"",
"BBSI"
],
[
"Chevallet",
"Mireille",
"",
"BBSI"
],
[
"Luche",
"Sylvie",
"",
"BBSI"
],
[
"Leize-Wagner",
"Emmanuelle",
""
]
] | The oxidative stress response is characterized by various effects on a range of biologic molecules. When examined at the protein level, both expression levels and protein modifications are altered by oxidative stress. While these effects have been studied in the past by classic biochemical methods, the recent onset of ... |
0805.1085 | Liaofu Luo | Liaofu Luo | On the Law of Directionality of Genome Evolution | 18 pages | null | null | Version 2-2011 | q-bio.GN q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The problem of the directionality of genome evolution is studied from the
information-theoretic view. We propose that the function-coding information
quantity of a genome always grows in the course of evolution through sequence
duplication, expansion of code, and gene transfer between genomes. The
function-coding inf... | [
{
"created": "Thu, 8 May 2008 01:13:20 GMT",
"version": "v1"
},
{
"created": "Thu, 4 Aug 2011 01:01:54 GMT",
"version": "v2"
}
] | 2011-08-05 | [
[
"Luo",
"Liaofu",
""
]
] | The problem of the directionality of genome evolution is studied from the information-theoretic view. We propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication, expansion of code, and gene transfer between genomes. The function-coding infor... |
2006.16189 | Dmytro Fishman | Ian Walsh, Dmytro Fishman, Dario Garcia-Gasulla, Tiina Titma, Gianluca
Pollastri, The ELIXIR Machine Learning focus group, Jen Harrow, Fotis E.
Psomopoulos and Silvio C.E. Tosatto | DOME: Recommendations for supervised machine learning validation in
biology | null | null | null | null | q-bio.OT cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modern biology frequently relies on machine learning to provide predictions
and improve decision processes. There have been recent calls for more scrutiny
on machine learning performance and possible limitations. Here we present a set
of community-wide recommendations aiming to help establish standards of
supervised ... | [
{
"created": "Thu, 25 Jun 2020 12:01:39 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Oct 2020 12:54:48 GMT",
"version": "v2"
},
{
"created": "Tue, 6 Oct 2020 07:57:00 GMT",
"version": "v3"
},
{
"created": "Thu, 7 Jan 2021 07:29:24 GMT",
"version": "v4"
}
] | 2021-01-08 | [
[
"Walsh",
"Ian",
""
],
[
"Fishman",
"Dmytro",
""
],
[
"Garcia-Gasulla",
"Dario",
""
],
[
"Titma",
"Tiina",
""
],
[
"Pollastri",
"Gianluca",
""
],
[
"group",
"The ELIXIR Machine Learning focus",
""
],
[
"Harrow",
... | Modern biology frequently relies on machine learning to provide predictions and improve decision processes. There have been recent calls for more scrutiny on machine learning performance and possible limitations. Here we present a set of community-wide recommendations aiming to help establish standards of supervised ma... |
1907.03005 | Japan Patel | Japan K. Patel, John J. Kuczek, and Richard Vasques | One-Way Coupled Tumor Response Model for
Combined-Hyperthermia-Radiotherapy Treatment with Anisotropic Scattering | 4 pages, 2 figures, submitted to ANS Winter Meeting and Expo. arXiv
admin note: substantial text overlap with arXiv:1905.10441 | Transactions of the American Nuclear Society 121 (2019), 65-68 | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Therapies such as combined-hyperthermia-radiotherapy (CHR) take advantage of
excellent radiosensitization properties of hyperthermia and treat of tumors
with both radiation and heat. To appropriately model a CHR treatment, features
like tumor heating (heat transfer), dosimetry (radiation transport), and tumor
dynamic... | [
{
"created": "Wed, 3 Jul 2019 18:47:33 GMT",
"version": "v1"
}
] | 2020-05-14 | [
[
"Patel",
"Japan K.",
""
],
[
"Kuczek",
"John J.",
""
],
[
"Vasques",
"Richard",
""
]
] | Therapies such as combined-hyperthermia-radiotherapy (CHR) take advantage of excellent radiosensitization properties of hyperthermia and treat of tumors with both radiation and heat. To appropriately model a CHR treatment, features like tumor heating (heat transfer), dosimetry (radiation transport), and tumor dynamics ... |
2012.00252 | Pankaj Mehta | Robert Marsland III, Owen Howell, Andreas Mayer, Pankaj Mehta | Tregs self-organize into a "computing ecosystem" and implement a
sophisticated optimization algorithm for mediating immune response | 8 pages, 4 figures + Appendix; Accepted at PNAS | null | null | null | q-bio.PE cond-mat.soft cond-mat.stat-mech nlin.AO q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Regulatory T cells (Tregs) play a crucial role in mediating immune response.
Yet an algorithmic understanding of the role of Tregs in adaptive immunity
remains lacking. Here, we present a biophysically realistic model of Treg
mediated self-tolerance in which Tregs bind to self-antigens and locally
inhibit the prolife... | [
{
"created": "Tue, 1 Dec 2020 04:12:40 GMT",
"version": "v1"
}
] | 2020-12-02 | [
[
"Marsland",
"Robert",
"III"
],
[
"Howell",
"Owen",
""
],
[
"Mayer",
"Andreas",
""
],
[
"Mehta",
"Pankaj",
""
]
] | Regulatory T cells (Tregs) play a crucial role in mediating immune response. Yet an algorithmic understanding of the role of Tregs in adaptive immunity remains lacking. Here, we present a biophysically realistic model of Treg mediated self-tolerance in which Tregs bind to self-antigens and locally inhibit the prolifera... |
1605.03060 | Matthew Ricci | Matthew Ricci, Junkyung Kim, Fredrik Johansson | A Passage-of-time Model of the Cerebellar Purkinje Cell | 14 pages, 10 figures; fixed typos on page 6, 7 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The cerebellar Purkinje cell controlling eyeblinks can learn, remember and
reproduce the interstimulus interval in a classical conditioning paradigm.
Given temporally separated inputs, the cerebellar Purkinje cell learns to pause
its tonic inhibition of a motor pathway with high temporal precision so that an
overt bl... | [
{
"created": "Tue, 10 May 2016 15:32:03 GMT",
"version": "v1"
},
{
"created": "Thu, 12 May 2016 17:48:13 GMT",
"version": "v2"
}
] | 2016-05-13 | [
[
"Ricci",
"Matthew",
""
],
[
"Kim",
"Junkyung",
""
],
[
"Johansson",
"Fredrik",
""
]
] | The cerebellar Purkinje cell controlling eyeblinks can learn, remember and reproduce the interstimulus interval in a classical conditioning paradigm. Given temporally separated inputs, the cerebellar Purkinje cell learns to pause its tonic inhibition of a motor pathway with high temporal precision so that an overt blin... |
q-bio/0601019 | Jie Liang | Yan Y. Tseng and Jie Liang | Estimation of Amino Acid Residue Substitution Rates at Local Spatial
Regions and Application in Protein Function Inference: A Bayesian Monte Carlo
Approach | 27 pages, 7 figures | Mol Biol Evol. 2006 Feb;23(2):421-36. Epub 2005 Oct 26 | 10.1093/molbev/msj048 | null | q-bio.BM | null | The amino acid sequences of proteins provide rich information for inferring
distant phylogenetic relationships and for predicting protein functions.
Estimating the rate matrix of residue substitutions from amino acid sequences
is also important because the rate matrix can be used to develop scoring
matrices for seque... | [
{
"created": "Fri, 13 Jan 2006 07:39:12 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Tseng",
"Yan Y.",
""
],
[
"Liang",
"Jie",
""
]
] | The amino acid sequences of proteins provide rich information for inferring distant phylogenetic relationships and for predicting protein functions. Estimating the rate matrix of residue substitutions from amino acid sequences is also important because the rate matrix can be used to develop scoring matrices for sequenc... |
2208.00153 | Kwadwo Antwi-Fordjour | Rana D. Parshad, Sureni Wickramsooriya, Kwadwo Antwi-Fordjour, Aniket
Banerjee | Additional food causes predator "explosion" -- unless the predators
compete | 30 pages | null | 10.1142/S0218127423500347 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The literature posits that an introduced predator population, is able to
drive it's target pest population extinct, if supplemented with high quality
additional food of quantity $\xi > \xi_{critical}$, \cite{SP11, SPV18, SPD17,
SPM13}. We show this approach leads to infinite time blow-up of the predator
population. W... | [
{
"created": "Sat, 30 Jul 2022 07:10:35 GMT",
"version": "v1"
}
] | 2023-04-05 | [
[
"Parshad",
"Rana D.",
""
],
[
"Wickramsooriya",
"Sureni",
""
],
[
"Antwi-Fordjour",
"Kwadwo",
""
],
[
"Banerjee",
"Aniket",
""
]
] | The literature posits that an introduced predator population, is able to drive it's target pest population extinct, if supplemented with high quality additional food of quantity $\xi > \xi_{critical}$, \cite{SP11, SPV18, SPD17, SPM13}. We show this approach leads to infinite time blow-up of the predator population. We ... |
2006.07882 | Bastian Rieck | Bastian Rieck, Tristan Yates, Christian Bock, Karsten Borgwardt, Guy
Wolf, Nicholas Turk-Browne, Smita Krishnaswamy | Uncovering the Topology of Time-Varying fMRI Data using Cubical
Persistence | Accepted at the Conference on Neural Information Processing Systems
(NeurIPS) 2020; camera-ready version | null | null | null | q-bio.NC cs.LG eess.IV math.AT stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Functional magnetic resonance imaging (fMRI) is a crucial technology for
gaining insights into cognitive processes in humans. Data amassed from fMRI
measurements result in volumetric data sets that vary over time. However,
analysing such data presents a challenge due to the large degree of noise and
person-to-person ... | [
{
"created": "Sun, 14 Jun 2020 12:29:37 GMT",
"version": "v1"
},
{
"created": "Thu, 22 Oct 2020 17:35:21 GMT",
"version": "v2"
}
] | 2020-10-23 | [
[
"Rieck",
"Bastian",
""
],
[
"Yates",
"Tristan",
""
],
[
"Bock",
"Christian",
""
],
[
"Borgwardt",
"Karsten",
""
],
[
"Wolf",
"Guy",
""
],
[
"Turk-Browne",
"Nicholas",
""
],
[
"Krishnaswamy",
"Smita",
""
]... | Functional magnetic resonance imaging (fMRI) is a crucial technology for gaining insights into cognitive processes in humans. Data amassed from fMRI measurements result in volumetric data sets that vary over time. However, analysing such data presents a challenge due to the large degree of noise and person-to-person va... |
0809.1231 | Franco Bagnoli | Franco Bagnoli | Evolutionary models for simple biosystems | new version | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The concept of evolutionary development of structures constituted a
\emph{real} revolution in biology: it was possible to understand how the very
complex structures of life can arise in an out-of-equilibrium system. The
investigation of such systems has shown that indeed, systems under a flux of
energy or matter can ... | [
{
"created": "Sun, 7 Sep 2008 16:31:18 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Aug 2009 13:00:02 GMT",
"version": "v2"
}
] | 2009-08-27 | [
[
"Bagnoli",
"Franco",
""
]
] | The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of such systems has shown that indeed, systems under a flux of energy or matter can se... |
1005.1088 | Ryan Gutenkunst | Ryan N. Gutenkunst, Daniel Coombs, Toby Star, Michael L. Dustin and
Byron Goldstein | A biophysical model of cell adhesion mediated by immunoadhesin drugs and
antibodies | 13 pages, 5 figures | null | 10.1371/journal.pone.0019701 | LA-UR 10-02105 | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A promising direction in drug development is to exploit the ability of
natural killer cells to kill antibody-labeled target cells. Monoclonal
antibodies and drugs designed to elicit this effect typically bind cell-surface
epitopes that are overexpressed on target cells but also present on other
cells. Thus it is impo... | [
{
"created": "Thu, 6 May 2010 21:21:31 GMT",
"version": "v1"
}
] | 2015-05-18 | [
[
"Gutenkunst",
"Ryan N.",
""
],
[
"Coombs",
"Daniel",
""
],
[
"Star",
"Toby",
""
],
[
"Dustin",
"Michael L.",
""
],
[
"Goldstein",
"Byron",
""
]
] | A promising direction in drug development is to exploit the ability of natural killer cells to kill antibody-labeled target cells. Monoclonal antibodies and drugs designed to elicit this effect typically bind cell-surface epitopes that are overexpressed on target cells but also present on other cells. Thus it is import... |
1705.05090 | Caterina La Porta AM | Costanza Giampietro, Maria Chiara Lionetti, Giulio Costantini,
Federico Mutti, Stefano Zapperi, Caterina A.M. La Porta | Cholesterol impairment contributes to neuroserpin aggregation | 7 figures | Scientific Reports 7, Article number: 43669 (2017) | 10.1038/srep43669 | null | q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | Intraneural accumulation of misfolded proteins is a common feature of several
neurodegenerative pathologies including Alzheimer's and Parkinson's diseases,
and Familial Encephalopathy with Neuroserpin Inclusion Bodies (FENIB). FENIB is
a rare disease due to a point mutation in neuroserpin which accelerates protein
ag... | [
{
"created": "Mon, 15 May 2017 07:18:47 GMT",
"version": "v1"
}
] | 2017-05-16 | [
[
"Giampietro",
"Costanza",
""
],
[
"Lionetti",
"Maria Chiara",
""
],
[
"Costantini",
"Giulio",
""
],
[
"Mutti",
"Federico",
""
],
[
"Zapperi",
"Stefano",
""
],
[
"La Porta",
"Caterina A. M.",
""
]
] | Intraneural accumulation of misfolded proteins is a common feature of several neurodegenerative pathologies including Alzheimer's and Parkinson's diseases, and Familial Encephalopathy with Neuroserpin Inclusion Bodies (FENIB). FENIB is a rare disease due to a point mutation in neuroserpin which accelerates protein aggr... |
1903.02795 | Miquel Palmer | Miquel Palmer, Borja Tolosa, Antoni Maria Grau, Maria del Mar Gil,
Clara Obregona, Beatriz Morales-Nin | Combining sale records of landings and fishers knowledge for predicting
metiers in a small-scale, multi-gear, multispecies fishery | 7 figures, 5 tables, http://hdl.handle.net/10261/174686 | Journal of Fisheries Research, Volume 195, November 2017, Pages
59-70 | 10.1016/j.fishres.2017.07.001 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Stock management should be guided by assessment models that, among others,
need to be fed by reliable data of catch and effort. However, precise data are
difficult to obtain in heterogeneous fisheries. Specifically, small scale,
multi gear, multispecies fisheries are dynamic systems where fishers may lively
change fi... | [
{
"created": "Thu, 7 Mar 2019 09:51:29 GMT",
"version": "v1"
}
] | 2019-03-08 | [
[
"Palmer",
"Miquel",
""
],
[
"Tolosa",
"Borja",
""
],
[
"Grau",
"Antoni Maria",
""
],
[
"Gil",
"Maria del Mar",
""
],
[
"Obregona",
"Clara",
""
],
[
"Morales-Nin",
"Beatriz",
""
]
] | Stock management should be guided by assessment models that, among others, need to be fed by reliable data of catch and effort. However, precise data are difficult to obtain in heterogeneous fisheries. Specifically, small scale, multi gear, multispecies fisheries are dynamic systems where fishers may lively change fish... |
1606.00463 | Nihal Temamogullari | N Ezgi Temamogullari, H Frederik Nijhout, Michael C Reed | Mathematical Modeling of Perifusion Cell Culture Experiments on GnRH
Signaling | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The effects of pulsatile GnRH stimulation on anterior pituitary cells are
studied using perifusion cell cultures, where constantly moving medium over the
immo- bilized cells allows intermittent GnRH delivery. The LH content of the
outgoing medium serves as a readout of the GnRH signaling pathway activation in
the cel... | [
{
"created": "Wed, 9 Dec 2015 21:09:16 GMT",
"version": "v1"
}
] | 2016-06-03 | [
[
"Temamogullari",
"N Ezgi",
""
],
[
"Nijhout",
"H Frederik",
""
],
[
"Reed",
"Michael C",
""
]
] | The effects of pulsatile GnRH stimulation on anterior pituitary cells are studied using perifusion cell cultures, where constantly moving medium over the immo- bilized cells allows intermittent GnRH delivery. The LH content of the outgoing medium serves as a readout of the GnRH signaling pathway activation in the cells... |
1708.07612 | Akira Kinjo | Akira R. Kinjo | Cooperative "folding transition" in the sequence space facilitates
function-driven evolution of protein families | 13 pages, 7 figures, 2 tables (a new subsection added) | Journal of Theoretical Biology 443:18-27 (2018) | 10.1016/j.jtbi.2018.01.019 | null | q-bio.BM physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | In the protein sequence space, natural proteins form clusters of families
which are characterized by their unique native folds whereas the great majority
of random polypeptides are neither clustered nor foldable to unique structures.
Since a given polypeptide can be either foldable or unfoldable, a kind of
"folding t... | [
{
"created": "Fri, 25 Aug 2017 04:38:47 GMT",
"version": "v1"
},
{
"created": "Wed, 27 Dec 2017 00:16:09 GMT",
"version": "v2"
},
{
"created": "Tue, 16 Jan 2018 05:22:05 GMT",
"version": "v3"
}
] | 2018-02-06 | [
[
"Kinjo",
"Akira R.",
""
]
] | In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since a given polypeptide can be either foldable or unfoldable, a kind of "folding tra... |
1411.4624 | John Abel | John H. Abel, Lukas A. Widmer, Peter C. St. John, J\"org Stelling,
Francis J. Doyle III | A Coupled Stochastic Model Explains Differences in Circadian Behavior of
Cry1 and Cry2 Knockouts | 15 pages, 5 figures update 22-Feb 2015: text revisions, typographical
error fixes | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the mammalian suprachiasmatic nucleus (SCN), a population of noisy
cell-autonomous oscillators synchronizes to generate robust circadian rhythms
at the organism-level. Within these cells two isoforms of Cryptochrome, Cry1
and Cry2, participate in a negative feedback loop driving circadian
rhythmicity. Previous wor... | [
{
"created": "Mon, 17 Nov 2014 20:24:37 GMT",
"version": "v1"
},
{
"created": "Sun, 22 Feb 2015 19:59:49 GMT",
"version": "v2"
}
] | 2015-02-24 | [
[
"Abel",
"John H.",
""
],
[
"Widmer",
"Lukas A.",
""
],
[
"John",
"Peter C. St.",
""
],
[
"Stelling",
"Jörg",
""
],
[
"Doyle",
"Francis J.",
"III"
]
] | In the mammalian suprachiasmatic nucleus (SCN), a population of noisy cell-autonomous oscillators synchronizes to generate robust circadian rhythms at the organism-level. Within these cells two isoforms of Cryptochrome, Cry1 and Cry2, participate in a negative feedback loop driving circadian rhythmicity. Previous work ... |
1411.1672 | Rafael Frigori | Rafael B. Frigori | Breakout character of islet amyloid polypeptide hydrophobic mutations at
the onset of type-2 diabetes | 8 pages, 6 figures, 1 table; final version to appear in Physical
Review E | Physical Review E 90, 052716 (2014) | 10.1103/PhysRevE.90.052716 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Toxic fibrillar aggregates of Islet Amyloid PolyPeptide (IAPP) appear as the
physical outcome of a peptidic phase-transition signaling the onset of type-2
diabetes mellitus in different mammalian species. In particular, experimentally
verified mutations on the amyloidogenic segment 20-29 in humans, cats and rats
are ... | [
{
"created": "Wed, 5 Nov 2014 11:10:49 GMT",
"version": "v1"
}
] | 2014-11-27 | [
[
"Frigori",
"Rafael B.",
""
]
] | Toxic fibrillar aggregates of Islet Amyloid PolyPeptide (IAPP) appear as the physical outcome of a peptidic phase-transition signaling the onset of type-2 diabetes mellitus in different mammalian species. In particular, experimentally verified mutations on the amyloidogenic segment 20-29 in humans, cats and rats are hi... |
2204.00583 | Vincent Painchaud | Vincent Painchaud, Nicolas Doyon and Patrick Desrosiers | Beyond Wilson-Cowan dynamics: oscillations and chaos without inhibition | 21 pages, 15 figures | Biological Cybernetics (2022) | 10.1007/s00422-022-00941-w | null | q-bio.NC physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Fifty years ago, Wilson and Cowan developed a mathematical model to describe
the activity of neural populations. In this seminal work, they divided the
cells in three groups: active, sensitive and refractory, and obtained a
dynamical system to describe the evolution of the average firing rates of the
populations. In ... | [
{
"created": "Fri, 1 Apr 2022 17:13:55 GMT",
"version": "v1"
},
{
"created": "Mon, 30 May 2022 19:08:13 GMT",
"version": "v2"
}
] | 2022-09-07 | [
[
"Painchaud",
"Vincent",
""
],
[
"Doyon",
"Nicolas",
""
],
[
"Desrosiers",
"Patrick",
""
]
] | Fifty years ago, Wilson and Cowan developed a mathematical model to describe the activity of neural populations. In this seminal work, they divided the cells in three groups: active, sensitive and refractory, and obtained a dynamical system to describe the evolution of the average firing rates of the populations. In th... |
1311.2260 | Chen Jia | Chen Jia, Minping Qian, Daquan Jiang | Overshoot in biological systems modeled by Markov chains: a
nonequilibrium dynamic phenomenon | 15 pages, 3 figures | IET Systems Biology, 8(4):138-145, 2014 | 10.1049/iet-syb.2013.0050 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A number of biological systems can be modeled by Markov chains. Recently,
there has been an increasing concern about when biological systems modeled by
Markov chains will perform a dynamic phenomenon called overshoot. In this
article, we found that the steady-state behavior of the system will have a
great effect on t... | [
{
"created": "Sun, 10 Nov 2013 11:47:15 GMT",
"version": "v1"
},
{
"created": "Sat, 24 May 2014 17:14:37 GMT",
"version": "v2"
}
] | 2014-08-27 | [
[
"Jia",
"Chen",
""
],
[
"Qian",
"Minping",
""
],
[
"Jiang",
"Daquan",
""
]
] | A number of biological systems can be modeled by Markov chains. Recently, there has been an increasing concern about when biological systems modeled by Markov chains will perform a dynamic phenomenon called overshoot. In this article, we found that the steady-state behavior of the system will have a great effect on the... |
2002.06616 | Bernard Offmann | Surbhi Dhingra, Ramanathan Sowdhamini, Fr\'ed\'eric Cadet, and Bernard
Offmann | A glance into the evolution of template-free protein structure
prediction methodologies | 17 pages, 1 figure, 1 table | null | 10.1016/j.biochi.2020.04.026 | null | q-bio.QM q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Prediction of protein structures using computational approaches has been
explored for over two decades, paving a way for more focused research and
development of algorithms in comparative modelling, ab intio modelling and
structure refinement protocols. A tremendous success has been witnessed in
template-based modell... | [
{
"created": "Sun, 16 Feb 2020 16:36:58 GMT",
"version": "v1"
},
{
"created": "Fri, 24 Apr 2020 12:50:27 GMT",
"version": "v2"
}
] | 2020-05-19 | [
[
"Dhingra",
"Surbhi",
""
],
[
"Sowdhamini",
"Ramanathan",
""
],
[
"Cadet",
"Frédéric",
""
],
[
"Offmann",
"Bernard",
""
]
] | Prediction of protein structures using computational approaches has been explored for over two decades, paving a way for more focused research and development of algorithms in comparative modelling, ab intio modelling and structure refinement protocols. A tremendous success has been witnessed in template-based modellin... |
2202.05031 | Jiahui Chen | Jiahui Chen and Guo-Wei Wei | Omicron BA.2 (B.1.1.529.2): high potential to becoming the next
dominating variant | null | null | null | null | q-bio.PE q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | The Omicron variant of severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2) has rapidly replaced the Delta variant as a dominating SARS-CoV-2
variant because of natural selection, which favors the variant with higher
infectivity and stronger vaccine breakthrough ability. Omicron has three
lineages or subvaria... | [
{
"created": "Thu, 10 Feb 2022 13:38:44 GMT",
"version": "v1"
}
] | 2022-02-11 | [
[
"Chen",
"Jiahui",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly replaced the Delta variant as a dominating SARS-CoV-2 variant because of natural selection, which favors the variant with higher infectivity and stronger vaccine breakthrough ability. Omicron has three lineages or subvariant... |
2101.03323 | Jingwei Liu | Jingwei Liu | SARS-Cov-2 RNA Sequence Classification Based on Territory Information | 7 figures | null | null | null | q-bio.QM cs.LG stat.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | CovID-19 genetics analysis is critical to determine virus type,virus variant
and evaluate vaccines. In this paper, SARS-Cov-2 RNA sequence analysis relative
to region or territory is investigated. A uniform framework of sequence SVM
model with various genetics length from short to long and mixed-bases is
developed by... | [
{
"created": "Sat, 9 Jan 2021 09:12:27 GMT",
"version": "v1"
}
] | 2021-01-12 | [
[
"Liu",
"Jingwei",
""
]
] | CovID-19 genetics analysis is critical to determine virus type,virus variant and evaluate vaccines. In this paper, SARS-Cov-2 RNA sequence analysis relative to region or territory is investigated. A uniform framework of sequence SVM model with various genetics length from short to long and mixed-bases is developed by p... |
1412.2818 | Fabian Chersi | Fabian Chersi | The hippocampal-striatal circuit for goal-directed and habitual choice | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/3.0/ | It is now widely accepted that one of the roles of the hippocampus is to
maintain episodic spatial representations, while parallel striatal pathways
contribute to both declarative and procedural value computations by encoding
different input-specific outcome predictions. In this paper we investigate the
use of these ... | [
{
"created": "Tue, 9 Dec 2014 00:19:25 GMT",
"version": "v1"
}
] | 2014-12-10 | [
[
"Chersi",
"Fabian",
""
]
] | It is now widely accepted that one of the roles of the hippocampus is to maintain episodic spatial representations, while parallel striatal pathways contribute to both declarative and procedural value computations by encoding different input-specific outcome predictions. In this paper we investigate the use of these br... |
1306.6656 | Gergely J Sz\"oll\H{o}si | Murray Patterson and Gergely J Sz\"oll\H{o}si and Vincent Daubin and
Eric Tannier | Lateral Gene Transfer, Rearrangement and Reconciliation | submitted for RECOMB CG 2013 | null | null | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Background.
Models of ancestral gene order reconstruction have progressively integrated
different evolutionary patterns and processes such as unequal gene content,
gene duplications, and implicitly sequence evolution via reconciled gene trees.
In unicellular organisms, these models have so far ignored lateral gene
... | [
{
"created": "Thu, 27 Jun 2013 20:38:34 GMT",
"version": "v1"
}
] | 2013-07-01 | [
[
"Patterson",
"Murray",
""
],
[
"Szöllősi",
"Gergely J",
""
],
[
"Daubin",
"Vincent",
""
],
[
"Tannier",
"Eric",
""
]
] | Background. Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene trees. In unicellular organisms, these models have so far ignored lateral gene tran... |
q-bio/0403008 | Mark Ya. Azbel' | Mark Ya. Azbel' | Immortality as a physical problem | refined version | null | null | null | q-bio.QM q-bio.PE | null | Well protected human and laboratory animal populations with abundant
resources are evolutionary unprecedented. Physical approach, which takes
advantage of their extensively quantified mortality, establishes that its
dominant fraction yields the exact law, whose universality from yeast to humans
is unprecedented, and ... | [
{
"created": "Thu, 4 Mar 2004 14:04:31 GMT",
"version": "v1"
},
{
"created": "Mon, 3 May 2004 15:48:36 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Azbel'",
"Mark Ya.",
""
]
] | Well protected human and laboratory animal populations with abundant resources are evolutionary unprecedented. Physical approach, which takes advantage of their extensively quantified mortality, establishes that its dominant fraction yields the exact law, whose universality from yeast to humans is unprecedented, and su... |
2007.10048 | Nadav M. Shnerb | Jayant Pande and Nadav M. Shnerb | Population dynamics in stochastic environments | null | null | null | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Populations are made up of an integer number of individuals and are subject
to stochastic birth-death processes whose rates may vary in time. Useful
quantities, like the chance of ultimate fixation, satisfy an appropriate
difference (master) equation, but closed-form solutions of these equations are
rare. Analytical ... | [
{
"created": "Mon, 20 Jul 2020 12:41:05 GMT",
"version": "v1"
},
{
"created": "Tue, 21 Jul 2020 06:52:07 GMT",
"version": "v2"
}
] | 2020-07-22 | [
[
"Pande",
"Jayant",
""
],
[
"Shnerb",
"Nadav M.",
""
]
] | Populations are made up of an integer number of individuals and are subject to stochastic birth-death processes whose rates may vary in time. Useful quantities, like the chance of ultimate fixation, satisfy an appropriate difference (master) equation, but closed-form solutions of these equations are rare. Analytical in... |
1908.02434 | Fabio Sanchez PhD | Fabio Sanchez and Juan G. Calvo | Dengue model with early-life stage of vectors and age-structure within
host | 16 pages, 11 figures | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We construct an epidemic model for the transmission of dengue fever with an
early-life stage in the vector dynamics and age-structure within hosts. The
early-life stage of the vector is modeled via a general function that supports
multiple vector densities. The {\it basic reproductive number} and {\it vector
demograp... | [
{
"created": "Wed, 7 Aug 2019 04:09:07 GMT",
"version": "v1"
},
{
"created": "Mon, 30 Sep 2019 15:49:24 GMT",
"version": "v2"
}
] | 2019-10-01 | [
[
"Sanchez",
"Fabio",
""
],
[
"Calvo",
"Juan G.",
""
]
] | We construct an epidemic model for the transmission of dengue fever with an early-life stage in the vector dynamics and age-structure within hosts. The early-life stage of the vector is modeled via a general function that supports multiple vector densities. The {\it basic reproductive number} and {\it vector demographi... |
1806.03872 | Zachary Kilpatrick PhD | Khanh P Nguyen, Kresimir Josic, and Zachary P Kilpatrick | Optimizing sequential decisions in the drift-diffusion model | 20 pages, 6 figures | null | null | null | q-bio.NC math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To make decisions organisms often accumulate information across multiple
timescales. However, most experimental and modeling studies of decision-making
focus on sequences of independent trials. On the other hand, natural
environments are characterized by long temporal correlations, and evidence used
to make a present... | [
{
"created": "Mon, 11 Jun 2018 09:24:54 GMT",
"version": "v1"
}
] | 2018-06-12 | [
[
"Nguyen",
"Khanh P",
""
],
[
"Josic",
"Kresimir",
""
],
[
"Kilpatrick",
"Zachary P",
""
]
] | To make decisions organisms often accumulate information across multiple timescales. However, most experimental and modeling studies of decision-making focus on sequences of independent trials. On the other hand, natural environments are characterized by long temporal correlations, and evidence used to make a present c... |
1710.07365 | Themistoklis Melissourgos | Themistoklis Melissourgos, Sotiris Nikoletseas, Christoforos
Raptopoulos and Paul Spirakis | An extension of the Moran process using type-specific connection graphs | null | null | null | null | q-bio.PE cs.DM cs.GT cs.SI math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Moran process, as studied by [Lieberman, E., Hauert, C. and Nowak, M.
Evolutionary dynamics on graphs. Nature 433, pp. 312-316 (2005)], is a
stochastic process modeling the spread of genetic mutations in populations. In
this process, agents of a two-type population (i.e. mutants and residents) are
associated with... | [
{
"created": "Thu, 19 Oct 2017 22:48:51 GMT",
"version": "v1"
},
{
"created": "Wed, 23 May 2018 11:38:08 GMT",
"version": "v2"
},
{
"created": "Mon, 26 Jul 2021 15:12:29 GMT",
"version": "v3"
}
] | 2021-07-27 | [
[
"Melissourgos",
"Themistoklis",
""
],
[
"Nikoletseas",
"Sotiris",
""
],
[
"Raptopoulos",
"Christoforos",
""
],
[
"Spirakis",
"Paul",
""
]
] | The Moran process, as studied by [Lieberman, E., Hauert, C. and Nowak, M. Evolutionary dynamics on graphs. Nature 433, pp. 312-316 (2005)], is a stochastic process modeling the spread of genetic mutations in populations. In this process, agents of a two-type population (i.e. mutants and residents) are associated with t... |
1512.03825 | Maani Beigy | Maani Beigy | Generalized Resemblance Theory of Evidence: a Proposal for
Precision/Personalized Evidence-Based Medicine | null | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Precision medicine emerges as the most important contemporary paradigm shift
of medical practice but has several challenges in evidence formation and
implementation for clinical practice. Precision/Personalized evidence-based
medicine (pEBM) requires theoretical support for decision making and
information management.... | [
{
"created": "Sun, 13 Dec 2015 11:15:30 GMT",
"version": "v1"
}
] | 2015-12-15 | [
[
"Beigy",
"Maani",
""
]
] | Precision medicine emerges as the most important contemporary paradigm shift of medical practice but has several challenges in evidence formation and implementation for clinical practice. Precision/Personalized evidence-based medicine (pEBM) requires theoretical support for decision making and information management. T... |
1906.05369 | Eduardo Mart\'inez-Montes | Julio A. Peraza-Goicolea, Eduardo Mart\'inez-Montes, Eduardo Aubert,
Pedro A. Vald\'es-Hern\'andez, Roberto Mulet | Modeling functional resting-state brain networks through neural message
passing on the human connectome | null | null | null | null | q-bio.NC cond-mat.dis-nn cond-mat.stat-mech nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the relationship between the structure and function of the
human brain is one of the most important open questions in Neurosciences. In
particular, Resting State Networks (RSN) and more specifically the Default Mode
Network (DMN) of the brain, which are defined from the analysis of functional
data lack ... | [
{
"created": "Wed, 12 Jun 2019 20:32:57 GMT",
"version": "v1"
}
] | 2019-06-14 | [
[
"Peraza-Goicolea",
"Julio A.",
""
],
[
"Martínez-Montes",
"Eduardo",
""
],
[
"Aubert",
"Eduardo",
""
],
[
"Valdés-Hernández",
"Pedro A.",
""
],
[
"Mulet",
"Roberto",
""
]
] | Understanding the relationship between the structure and function of the human brain is one of the most important open questions in Neurosciences. In particular, Resting State Networks (RSN) and more specifically the Default Mode Network (DMN) of the brain, which are defined from the analysis of functional data lack a ... |
1010.0919 | Jaewook Joo | Luong Nguyen, Dubravka Bodiroga, Reka Kelemen, Jaewook Joo, and
Kimberly D. Gwinn | Modeling the effects of cymene on the distribution of germination and
growth of Beauveria bassiana | Student draft submitted to NIMBioS REU program, 19 pages, 12 figures | null | null | null | q-bio.QM q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Essential oils have antifungal and antipathogenic effects and therefore are
targets in plant pathology research for their potential uses as natural
substitutes for inorganic plant pesticides. Beauveria bassiana, an
entomopathogenic fungus, can endophytically colonize a vast number of plant
species and trigger induced... | [
{
"created": "Tue, 5 Oct 2010 15:31:11 GMT",
"version": "v1"
}
] | 2010-10-06 | [
[
"Nguyen",
"Luong",
""
],
[
"Bodiroga",
"Dubravka",
""
],
[
"Kelemen",
"Reka",
""
],
[
"Joo",
"Jaewook",
""
],
[
"Gwinn",
"Kimberly D.",
""
]
] | Essential oils have antifungal and antipathogenic effects and therefore are targets in plant pathology research for their potential uses as natural substitutes for inorganic plant pesticides. Beauveria bassiana, an entomopathogenic fungus, can endophytically colonize a vast number of plant species and trigger induced s... |
1810.06066 | Thomas House | A. Bishop, I. Z. Kiss and T. House | Consistent Approximation of Epidemic Dynamics on Degree-heterogeneous
Clustered Networks | 14 pages, 7 figures | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Realistic human contact networks capable of spreading infectious disease, for
example studied in social contact surveys, exhibit both significant degree
heterogeneity and clustering, both of which greatly affect epidemic dynamics.
To understand the joint effects of these two network properties on epidemic
dynamics, t... | [
{
"created": "Sun, 14 Oct 2018 17:13:51 GMT",
"version": "v1"
}
] | 2018-10-16 | [
[
"Bishop",
"A.",
""
],
[
"Kiss",
"I. Z.",
""
],
[
"House",
"T.",
""
]
] | Realistic human contact networks capable of spreading infectious disease, for example studied in social contact surveys, exhibit both significant degree heterogeneity and clustering, both of which greatly affect epidemic dynamics. To understand the joint effects of these two network properties on epidemic dynamics, the... |
1902.05845 | Michel Kana PhD | Michel Kana | Assessing the Level of Autonomic Nervous Activity for Effective
Biofeedback Training | null | null | null | null | q-bio.NC physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper proposes a prototype of a new biofeedback training based on
mathematical models of cardiovascular control. For this purpose we develop a
low-cost device that is able to record and process arterial pulse wave via
photoplethysmograph and skin temperature on the peripheral part of the arm. A
benchmark analysi... | [
{
"created": "Fri, 15 Feb 2019 15:30:38 GMT",
"version": "v1"
}
] | 2019-02-18 | [
[
"Kana",
"Michel",
""
]
] | This paper proposes a prototype of a new biofeedback training based on mathematical models of cardiovascular control. For this purpose we develop a low-cost device that is able to record and process arterial pulse wave via photoplethysmograph and skin temperature on the peripheral part of the arm. A benchmark analysis ... |
2303.12813 | Sarah Pungitore | Sarah Pungitore, Toluwanimi Olorunnisola, Jarrod Mosier, Vignesh
Subbian | Computable Phenotypes for Post-acute sequelae of SARS-CoV-2: A National
COVID Cohort Collaborative Analysis | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Post-acute sequelae of SARS-CoV-2 (PASC) is an increasingly recognized yet
incompletely understood public health concern. Several studies have examined
various ways to phenotype PASC to better characterize this heterogeneous
condition. However, many gaps in PASC phenotyping research exist, including a
lack of the fol... | [
{
"created": "Wed, 22 Mar 2023 02:14:31 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Aug 2023 00:04:42 GMT",
"version": "v2"
}
] | 2023-08-09 | [
[
"Pungitore",
"Sarah",
""
],
[
"Olorunnisola",
"Toluwanimi",
""
],
[
"Mosier",
"Jarrod",
""
],
[
"Subbian",
"Vignesh",
""
]
] | Post-acute sequelae of SARS-CoV-2 (PASC) is an increasingly recognized yet incompletely understood public health concern. Several studies have examined various ways to phenotype PASC to better characterize this heterogeneous condition. However, many gaps in PASC phenotyping research exist, including a lack of the follo... |
2006.14790 | Emilio Angelina Angelina | Emilio Angelina, Sebastian Andujar, Oscar Parravicini, Daniel Enriz
and Nelida Peruchena | Drug Repurposing to find Inhibitors of SARS-CoV-2 Main Protease | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the strain of
coronavirus that causes coronavirus disease 2019 (COVID-19), the respiratory
illness responsible for the COVID-19 pandemic. Currently there is no known
vaccine or specific antiviral treatment for COVID-19 and so, there is an urgent
need for... | [
{
"created": "Fri, 26 Jun 2020 04:19:28 GMT",
"version": "v1"
}
] | 2020-06-29 | [
[
"Angelina",
"Emilio",
""
],
[
"Andujar",
"Sebastian",
""
],
[
"Parravicini",
"Oscar",
""
],
[
"Enriz",
"Daniel",
""
],
[
"Peruchena",
"Nelida",
""
]
] | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the strain of coronavirus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the COVID-19 pandemic. Currently there is no known vaccine or specific antiviral treatment for COVID-19 and so, there is an urgent need for e... |
2102.06125 | Dong Si | Dong Si, Andrew Nakamura, Runbang Tang, Haowen Guan, Jie Hou, Ammaar
Firozi, Renzhi Cao, Kyle Hippe, Minglei Zhao | Artificial Intelligence Advances for De Novo Molecular Structure
Modeling in Cryo-EM | null | Wiley Interdisciplinary Reviews: Computational Molecular Science,
e1542 (2021) | 10.1002/wcms.1542 | null | q-bio.BM cs.AI physics.bio-ph physics.comp-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Cryo-electron microscopy (cryo-EM) has become a major experimental technique
to determine the structures of large protein complexes and molecular
assemblies, as evidenced by the 2017 Nobel Prize. Although cryo-EM has been
drastically improved to generate high-resolution three-dimensional (3D) maps
that contain detail... | [
{
"created": "Thu, 11 Feb 2021 17:06:20 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Feb 2021 02:03:01 GMT",
"version": "v2"
}
] | 2021-06-01 | [
[
"Si",
"Dong",
""
],
[
"Nakamura",
"Andrew",
""
],
[
"Tang",
"Runbang",
""
],
[
"Guan",
"Haowen",
""
],
[
"Hou",
"Jie",
""
],
[
"Firozi",
"Ammaar",
""
],
[
"Cao",
"Renzhi",
""
],
[
"Hippe",
"Kyle... | Cryo-electron microscopy (cryo-EM) has become a major experimental technique to determine the structures of large protein complexes and molecular assemblies, as evidenced by the 2017 Nobel Prize. Although cryo-EM has been drastically improved to generate high-resolution three-dimensional (3D) maps that contain detailed... |
2201.00287 | Jatin Kashyap | Jatin Kashyap, Dibakar Datta | Drug repurposing for SARS-COV-2: A high-throughput molecular docking,
molecular dynamics, machine learning, & ab-initio study | null | null | 10.1007/s10853-022-07195-8 | null | q-bio.BM physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | A molecule of dimension 125nm has caused around 479 Million human infections
(80M for the USA) & 6.1 Million human deaths (977,000 for the USA) worldwide
and slashed the global economy by US$ 8.5 Trillion over two years. The only
other events in recent history that caused comparative human life loss through
direct us... | [
{
"created": "Sun, 2 Jan 2022 04:22:50 GMT",
"version": "v1"
},
{
"created": "Sat, 2 Apr 2022 03:17:50 GMT",
"version": "v2"
},
{
"created": "Thu, 7 Apr 2022 03:52:06 GMT",
"version": "v3"
}
] | 2022-06-29 | [
[
"Kashyap",
"Jatin",
""
],
[
"Datta",
"Dibakar",
""
]
] | A molecule of dimension 125nm has caused around 479 Million human infections (80M for the USA) & 6.1 Million human deaths (977,000 for the USA) worldwide and slashed the global economy by US$ 8.5 Trillion over two years. The only other events in recent history that caused comparative human life loss through direct usag... |
0808.3870 | Utz-Uwe Haus | Utz-Uwe Haus (1), Kathrin Niermann (1), Klaus Truemper (2), Robert
Weismantel (1) ((1) Magdeburg, Germany, (2) Dallas, Texas) | Logic Integer Programming Models for Signaling Networks | null | Journal of Computational Biology. May 2009, 16(5): 725-743 | 10.1089/cmb.2008.0163 | null | q-bio.QM q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a static and a dynamic approach to model biological signaling
networks, and show how each can be used to answer relevant biological
questions. For this we use the two different mathematical tools of
Propositional Logic and Integer Programming. The power of discrete mathematics
for handling qualitative as w... | [
{
"created": "Thu, 28 Aug 2008 10:11:18 GMT",
"version": "v1"
}
] | 2009-05-13 | [
[
"Haus",
"Utz-Uwe",
"",
"Magdeburg, Germany"
],
[
"Niermann",
"Kathrin",
"",
"Magdeburg, Germany"
],
[
"Truemper",
"Klaus",
"",
"Dallas, Texas"
],
[
"Weismantel",
"Robert",
"",
"Magdeburg, Germany"
]
] | We propose a static and a dynamic approach to model biological signaling networks, and show how each can be used to answer relevant biological questions. For this we use the two different mathematical tools of Propositional Logic and Integer Programming. The power of discrete mathematics for handling qualitative as wel... |
2212.00692 | Denise Grappein | Stefano Berrone, Chiara Giverso, Denise Grappein, Luigi Preziosi,
Stefano Scial\`o | An optimization based 3D-1D coupling strategy for tissue perfusion and
chemical transport during tumor-induced angiogenesis | null | null | null | null | q-bio.TO cs.NA math.NA | http://creativecommons.org/licenses/by-nc-nd/4.0/ | A new mathematical model and numerical approach are proposed for the
simulation of fluid and chemical exchanges between a growing capillary network
and the surrounding tissue, in the context of tumor-induced angiogenesis.
Thanks to proper modeling assumptions the capillaries are reduced to their
centerline: a well po... | [
{
"created": "Thu, 17 Nov 2022 11:07:51 GMT",
"version": "v1"
}
] | 2022-12-02 | [
[
"Berrone",
"Stefano",
""
],
[
"Giverso",
"Chiara",
""
],
[
"Grappein",
"Denise",
""
],
[
"Preziosi",
"Luigi",
""
],
[
"Scialò",
"Stefano",
""
]
] | A new mathematical model and numerical approach are proposed for the simulation of fluid and chemical exchanges between a growing capillary network and the surrounding tissue, in the context of tumor-induced angiogenesis. Thanks to proper modeling assumptions the capillaries are reduced to their centerline: a well pose... |
2209.13038 | Ankush Aggarwal | Ankush Aggarwal, Luke T. Hudson, Devin W. Laurence, Chung-Hao Lee,
Sanjay Pant | A Bayesian constitutive model selection framework for biaxial mechanical
testing of planar soft tissues: application to porcine aortic valves | null | null | 10.1016/j.jmbbm.2023.105657 | null | q-bio.TO physics.bio-ph physics.med-ph | http://creativecommons.org/licenses/by/4.0/ | A variety of constitutive models have been developed for soft tissue
mechanics. However, there is no established criterion to select a suitable
model for a specific application. Although the model that best fits the
experimental data can be deemed the most suitable model, this practice often
can be insufficient given... | [
{
"created": "Mon, 26 Sep 2022 21:39:44 GMT",
"version": "v1"
},
{
"created": "Tue, 3 Jan 2023 10:19:09 GMT",
"version": "v2"
}
] | 2023-01-06 | [
[
"Aggarwal",
"Ankush",
""
],
[
"Hudson",
"Luke T.",
""
],
[
"Laurence",
"Devin W.",
""
],
[
"Lee",
"Chung-Hao",
""
],
[
"Pant",
"Sanjay",
""
]
] | A variety of constitutive models have been developed for soft tissue mechanics. However, there is no established criterion to select a suitable model for a specific application. Although the model that best fits the experimental data can be deemed the most suitable model, this practice often can be insufficient given t... |
2203.14194 | Chang Sub Kim | Chang Sub Kim | Free energy and inference in living systems | 31 pages, 5 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Organisms are nonequilibrium, stationary systems self-organized via
spontaneous symmetry breaking and undergoing metabolic cycles with broken
detailed balance in the environment. The thermodynamic free-energy principle
describes an organism's homeostasis as the regulation of biochemical work
constrained by the physic... | [
{
"created": "Sun, 27 Mar 2022 03:16:06 GMT",
"version": "v1"
},
{
"created": "Wed, 23 Nov 2022 10:28:39 GMT",
"version": "v2"
}
] | 2022-11-24 | [
[
"Kim",
"Chang Sub",
""
]
] | Organisms are nonequilibrium, stationary systems self-organized via spontaneous symmetry breaking and undergoing metabolic cycles with broken detailed balance in the environment. The thermodynamic free-energy principle describes an organism's homeostasis as the regulation of biochemical work constrained by the physical... |
2101.05012 | Hasindu Gamaarachchi | Hasindu Gamaarachchi | Computer Architecture-Aware Optimisation of DNA Analysis Systems | Supervisors: Parameswaran, Sri , Computer Science & Engineering,
Faculty of Engineering, UNSW; Ignjatovic, Aleksandar , Computer Science &
Engineering, Faculty of Engineering, UNSW; Smith, Martin A., Garvan Institute
of Medical Research, Faculty of Medicine, UNSW unsworks:
http://handle.unsw.edu.au/1959.4/70488 | null | null | null | q-bio.GN cs.CE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | DNA sequencing is revolutionising the field of medicine. DNA sequencers, the
machines which perform DNA sequencing, have evolved from the size of a fridge
to that of a mobile phone over the last two decades. The cost of sequencing a
human genome also has reduced from billions of dollars to hundreds of dollars.
Despit... | [
{
"created": "Wed, 13 Jan 2021 11:29:12 GMT",
"version": "v1"
}
] | 2021-01-14 | [
[
"Gamaarachchi",
"Hasindu",
""
]
] | DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human genome also has reduced from billions of dollars to hundreds of dollars. Despite ... |
1310.7568 | Atsushi Tero | Atsushi Tero, Masakazu Akiyama, Dai Owaki, Takeshi Kano, Akio
Ishiguro, and Ryo Kobayashi | Interlimb neural connection is not required for gait transition in
quadruped locomotion | 6 pages, 2figures | null | null | null | q-bio.QM cs.RO cs.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quadrupeds transition spontaneously to various gait patterns (e.g., walk,
trot, pace, gallop) in response to the locomotion speed. The generation of
these gait patterns has been the subject of debate for a long time. We propose
a coupled oscillator model that is coupled with the physical interactions of
the body. The... | [
{
"created": "Mon, 28 Oct 2013 08:59:30 GMT",
"version": "v1"
}
] | 2013-10-30 | [
[
"Tero",
"Atsushi",
""
],
[
"Akiyama",
"Masakazu",
""
],
[
"Owaki",
"Dai",
""
],
[
"Kano",
"Takeshi",
""
],
[
"Ishiguro",
"Akio",
""
],
[
"Kobayashi",
"Ryo",
""
]
] | Quadrupeds transition spontaneously to various gait patterns (e.g., walk, trot, pace, gallop) in response to the locomotion speed. The generation of these gait patterns has been the subject of debate for a long time. We propose a coupled oscillator model that is coupled with the physical interactions of the body. The r... |
1202.5092 | Masamichi Sato | Masamichi Sato and Kenji Fukumizu | Deformed Toric Ideal Constraints for Stoichiometric Networks | null | null | null | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We discuss chemical reaction networks and metabolic pathways based on
stoichiometric network analysis, and introduce deformed toric ideal constraints
by the algebraic geometrical approach. This paper concerns steady state flux of
chemical reaction networks and metabolic pathways. With the deformed toric
ideal constra... | [
{
"created": "Thu, 23 Feb 2012 05:42:41 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Apr 2013 09:20:36 GMT",
"version": "v2"
}
] | 2013-04-24 | [
[
"Sato",
"Masamichi",
""
],
[
"Fukumizu",
"Kenji",
""
]
] | We discuss chemical reaction networks and metabolic pathways based on stoichiometric network analysis, and introduce deformed toric ideal constraints by the algebraic geometrical approach. This paper concerns steady state flux of chemical reaction networks and metabolic pathways. With the deformed toric ideal constrain... |
2010.12054 | Christopher Eddy | Christopher Z. Eddy, Helena Raposo, Ryan Wong, Bo Sun | Extracellular Matrix regulates the morphodynamics of 3D migrating cancer
cells | null | null | 10.1038/s41598-021-99902-9 | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cell shape is linked to cell function. The significance of cell
morphodynamics, namely the temporal fluctuation of cell shape, is much less
understood. Here we study the morphodynamics of MDA-MB-231 cells in type I
collagen extracellular matrix (ECM). We systematically vary ECM physical
properties by tuning collagen ... | [
{
"created": "Thu, 22 Oct 2020 20:48:15 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Oct 2021 18:05:22 GMT",
"version": "v2"
}
] | 2021-10-12 | [
[
"Eddy",
"Christopher Z.",
""
],
[
"Raposo",
"Helena",
""
],
[
"Wong",
"Ryan",
""
],
[
"Sun",
"Bo",
""
]
] | Cell shape is linked to cell function. The significance of cell morphodynamics, namely the temporal fluctuation of cell shape, is much less understood. Here we study the morphodynamics of MDA-MB-231 cells in type I collagen extracellular matrix (ECM). We systematically vary ECM physical properties by tuning collagen co... |
0708.0181 | Eduardo Candelario-Jalil | E Candelario-Jalil, A Gonzalez-Falcon, M Garcia-Cabrera, OS Leon, BL
Fiebich | Post-ischaemic treatment with the cyclooxygenase-2 inhibitor nimesulide
reduces blood-brain barrier disruption and leukocyte infiltration following
transient focal cerebral ischaemia in rats | null | Journal of Neurochemistry 100(4): 1108-1120 (2007) | null | null | q-bio.NC q-bio.TO | null | Several studies suggest that cyclooxygenase (COX)-2 plays a pivotal role in
the progression of ischaemic brain damage. In the present study, we
investigated the effects of selective inhibition of COX-2 with nimesulide (12
mg/kg) and selective inhibition of COX-1 with valeryl salicylate (VAS, 12-120
mg/kg) on prostagl... | [
{
"created": "Wed, 1 Aug 2007 15:47:39 GMT",
"version": "v1"
}
] | 2007-08-02 | [
[
"Candelario-Jalil",
"E",
""
],
[
"Gonzalez-Falcon",
"A",
""
],
[
"Garcia-Cabrera",
"M",
""
],
[
"Leon",
"OS",
""
],
[
"Fiebich",
"BL",
""
]
] | Several studies suggest that cyclooxygenase (COX)-2 plays a pivotal role in the progression of ischaemic brain damage. In the present study, we investigated the effects of selective inhibition of COX-2 with nimesulide (12 mg/kg) and selective inhibition of COX-1 with valeryl salicylate (VAS, 12-120 mg/kg) on prostaglan... |
q-bio/0412018 | Wannapong Triampo | Waipot Ngamsaad, Wannapong Triampo, Paisan Kanthang, I-Ming Tang,
Narin Nuttawut and Charin Modjung | A one-dimensional Lattice Boltzmann method for modeling the dynamic
pole-to-pole oscillations of Min proteins for determining the position of the
midcell division plane | 13 pages, 2 figures | null | null | null | q-bio.QM q-bio.SC | null | Determining the middle of the bacteria cell and the proper placement of the
septum is essential to the division of the bacterial cell. In E. coli, this
process depends on the proteins MinC, MinD, and MinE. Here, the Lattice
Boltzmann method (LBM) is used to study the dynamics of the oscillations of the
min proteins f... | [
{
"created": "Thu, 9 Dec 2004 21:38:41 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Ngamsaad",
"Waipot",
""
],
[
"Triampo",
"Wannapong",
""
],
[
"Kanthang",
"Paisan",
""
],
[
"Tang",
"I-Ming",
""
],
[
"Nuttawut",
"Narin",
""
],
[
"Modjung",
"Charin",
""
]
] | Determining the middle of the bacteria cell and the proper placement of the septum is essential to the division of the bacterial cell. In E. coli, this process depends on the proteins MinC, MinD, and MinE. Here, the Lattice Boltzmann method (LBM) is used to study the dynamics of the oscillations of the min proteins fro... |
2402.16652 | John Helliwell R | John R. Helliwell, James R. Hester, Loes Kroon-Batenburg, Brian
McMahon and Selina L. S. Storm | The Evolution of Raw Data Archiving and the Growth of Its Importance in
Crystallography | 34 pages, 2 figures, 2 tables | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | The hardware for data archiving has expanded capacities for digital storage
enormously in the past decade or more. This article charts the efforts of IUCr
to facilitate discussions and plans relating to raw data archiving and reuse
within the various communities of crystallography, diffraction, and scattering.
| [
{
"created": "Fri, 23 Feb 2024 15:03:53 GMT",
"version": "v1"
}
] | 2024-02-27 | [
[
"Helliwell",
"John R.",
""
],
[
"Hester",
"James R.",
""
],
[
"Kroon-Batenburg",
"Loes",
""
],
[
"McMahon",
"Brian",
""
],
[
"Storm",
"Selina L. S.",
""
]
] | The hardware for data archiving has expanded capacities for digital storage enormously in the past decade or more. This article charts the efforts of IUCr to facilitate discussions and plans relating to raw data archiving and reuse within the various communities of crystallography, diffraction, and scattering. |
2405.06110 | Anastasiya Salova | Anastasiya Salova, Istv\'an A. Kov\'acs | Combined topological and spatial constraints are required to capture the
structure of neural connectomes | 24 pages, 20 figures | null | null | null | q-bio.NC physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Volumetric brain reconstructions provide an unprecedented opportunity to gain
insights into the complex connectivity patterns of neurons in an increasing
number of organisms. Here, we model and quantify the complexity of the
resulting neural connectomes in the fruit fly, mouse, and human and unveil a
simple set of sh... | [
{
"created": "Thu, 9 May 2024 21:31:50 GMT",
"version": "v1"
}
] | 2024-05-13 | [
[
"Salova",
"Anastasiya",
""
],
[
"Kovács",
"István A.",
""
]
] | Volumetric brain reconstructions provide an unprecedented opportunity to gain insights into the complex connectivity patterns of neurons in an increasing number of organisms. Here, we model and quantify the complexity of the resulting neural connectomes in the fruit fly, mouse, and human and unveil a simple set of shar... |
1401.3262 | Jianmin Sun | Jianmin Sun and Michael Grabe | Cooperativity Can Enhance Cellular Signal Detection | null | null | null | null | q-bio.MN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most sensory cells use surface receptors to detect environmental stimuli and
initiate downstream signaling. Cooperative interactions among sensory receptors
is known to play a crucial role in enhancing the sensitivity of biochemical
processes such as oxygen sensing by hemoglobin, but whether cooperativity
enhances th... | [
{
"created": "Tue, 14 Jan 2014 17:15:19 GMT",
"version": "v1"
}
] | 2014-01-15 | [
[
"Sun",
"Jianmin",
""
],
[
"Grabe",
"Michael",
""
]
] | Most sensory cells use surface receptors to detect environmental stimuli and initiate downstream signaling. Cooperative interactions among sensory receptors is known to play a crucial role in enhancing the sensitivity of biochemical processes such as oxygen sensing by hemoglobin, but whether cooperativity enhances the ... |
2108.02678 | Kevin Esvelt | The Nucleic Acid Observatory Consortium | A Global Nucleic Acid Observatory for Biodefense and Planetary Health | null | null | null | null | q-bio.GN q-bio.PE q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | The spread of pandemic viruses and invasive species can be catastrophic for
human societies and natural ecosystems. SARS-CoV-2 demonstrated that the speed
of our response is critical, as each day of delay permitted exponential growth
and dispersion of the virus. Here we propose a global Nucleic Acid Observatory
(NAO)... | [
{
"created": "Thu, 5 Aug 2021 15:19:05 GMT",
"version": "v1"
}
] | 2021-08-06 | [
[
"Consortium",
"The Nucleic Acid Observatory",
""
]
] | The spread of pandemic viruses and invasive species can be catastrophic for human societies and natural ecosystems. SARS-CoV-2 demonstrated that the speed of our response is critical, as each day of delay permitted exponential growth and dispersion of the virus. Here we propose a global Nucleic Acid Observatory (NAO) t... |
q-bio/0607018 | Branko Dragovich | Branko Dragovich and Alexandra Dragovich | A p-Adic Model of DNA Sequence and Genetic Code | 13 pages, 2 tables | p-Adic Numbers, Ultrametric Analysis and Applications 1 (2009)
34-41 | 10.1134/S2070046609010038 | null | q-bio.GN cs.IT math-ph math.IT math.MP physics.bio-ph | null | Using basic properties of p-adic numbers, we consider a simple new approach
to describe main aspects of DNA sequence and genetic code. Central role in our
investigation plays an ultrametric p-adic information space which basic
elements are nucleotides, codons and genes. We show that a 5-adic model is
appropriate for ... | [
{
"created": "Thu, 13 Jul 2006 16:41:35 GMT",
"version": "v1"
}
] | 2010-12-01 | [
[
"Dragovich",
"Branko",
""
],
[
"Dragovich",
"Alexandra",
""
]
] | Using basic properties of p-adic numbers, we consider a simple new approach to describe main aspects of DNA sequence and genetic code. Central role in our investigation plays an ultrametric p-adic information space which basic elements are nucleotides, codons and genes. We show that a 5-adic model is appropriate for DN... |
q-bio/0702046 | Erel Levine | Erel Levine, Peter McHale and Herbert Levine | microRNAs may sharpen spatial expression patterns | null | null | 10.1371/journal.pcbi.0030233 | null | q-bio.MN | null | The precise layout of gene expression patterns is a crucial step in
development. Formation of a sharp boundary between high and low expression
domains requires a genetic mechanism which is both sensitive and robust to
fluctuations, a demand that may not be easily achieved by morphogens alone.
Recently it has been dem... | [
{
"created": "Thu, 22 Feb 2007 19:31:09 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Jun 2007 00:07:29 GMT",
"version": "v2"
}
] | 2015-06-26 | [
[
"Levine",
"Erel",
""
],
[
"McHale",
"Peter",
""
],
[
"Levine",
"Herbert",
""
]
] | The precise layout of gene expression patterns is a crucial step in development. Formation of a sharp boundary between high and low expression domains requires a genetic mechanism which is both sensitive and robust to fluctuations, a demand that may not be easily achieved by morphogens alone. Recently it has been demon... |
1707.00320 | Daniele De Martino | Daniele De Martino | A Van-Der-Waals picture for metabolic networks from MaxEnt modeling:
inherent bistability and elusive coexistence | 9 pages, 4 figures | Phys. Rev. E 96, 060401 (2017) | 10.1103/PhysRevE.96.060401 | null | q-bio.MN cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work maximum entropy distributions in the space of steady states of
metabolic networks are defined upon constraining the first and second moment of
the growth rate. Inherent bistability of fast and slow phenotypes, akin to a
Van-Der Waals picture, emerges upon considering control on the average growth
(optimi... | [
{
"created": "Sun, 2 Jul 2017 16:51:36 GMT",
"version": "v1"
}
] | 2017-12-27 | [
[
"De Martino",
"Daniele",
""
]
] | In this work maximum entropy distributions in the space of steady states of metabolic networks are defined upon constraining the first and second moment of the growth rate. Inherent bistability of fast and slow phenotypes, akin to a Van-Der Waals picture, emerges upon considering control on the average growth (optimiza... |
1510.08045 | Richard Betzel | Richard F. Betzel, Bratislav Mi\v{s}i\'c, Ye He, Jeffrey Rumschlag,
Xi-Nian Zuo, Olaf Sporns | Functional brain modules reconfigure at multiple scales across the human
lifespan | 56 pages, 7 figures, 6 supplemental figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human brain is a complex network of interconnected brain regions
organized into functional modules with distinct roles in cognition and
behavior. An important question concerns the persistence and stability of these
modules over the human lifespan. Here we use graph-theoretic analysis to
algorithmically uncover t... | [
{
"created": "Tue, 27 Oct 2015 19:53:24 GMT",
"version": "v1"
}
] | 2015-10-28 | [
[
"Betzel",
"Richard F.",
""
],
[
"Mišić",
"Bratislav",
""
],
[
"He",
"Ye",
""
],
[
"Rumschlag",
"Jeffrey",
""
],
[
"Zuo",
"Xi-Nian",
""
],
[
"Sporns",
"Olaf",
""
]
] | The human brain is a complex network of interconnected brain regions organized into functional modules with distinct roles in cognition and behavior. An important question concerns the persistence and stability of these modules over the human lifespan. Here we use graph-theoretic analysis to algorithmically uncover the... |
1403.7660 | Ion Udroiu | Ion Udroiu | Estimation of erythrocyte surface area in mammals | null | Methods Protoc. 2024, 7(1), 11 | 10.3390/mps7010011 | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Measures of erythrocytes volume and surface are helpful in several
physiological studies, both for zoologists and veterinarians. Whilst diameter
and volume are assessed with ease from observations of blood smears and
complete blood count, respectively, thickness and surface area, instead, are
much more difficult to b... | [
{
"created": "Sat, 29 Mar 2014 18:40:43 GMT",
"version": "v1"
}
] | 2024-06-10 | [
[
"Udroiu",
"Ion",
""
]
] | Measures of erythrocytes volume and surface are helpful in several physiological studies, both for zoologists and veterinarians. Whilst diameter and volume are assessed with ease from observations of blood smears and complete blood count, respectively, thickness and surface area, instead, are much more difficult to be ... |
2104.12249 | Hong-Gyu Yoon | Hong-Gyu Yoon and Pilwon Kim | A STDP-based Encoding Algorithm for Associative and Composite Data | 12 pages of main text. Source for simplified MATLAB programs
performing two numerical tests presented in this article can be found in the
following link: https://github.com/hkyoon94/NRSTDP.git | null | null | null | q-bio.NC cs.NE math.DS nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spike-timing-dependent plasticity(STDP) is a biological process of synaptic
modification caused by the difference of firing order and timing between
neurons. One of the neurodynamical roles of STDP is to form a macroscopic
geometrical structure in the neuronal state space in response to a periodic
input. This work pr... | [
{
"created": "Sun, 25 Apr 2021 20:26:52 GMT",
"version": "v1"
},
{
"created": "Fri, 16 Jul 2021 00:56:36 GMT",
"version": "v2"
},
{
"created": "Mon, 9 Aug 2021 01:52:05 GMT",
"version": "v3"
}
] | 2021-08-10 | [
[
"Yoon",
"Hong-Gyu",
""
],
[
"Kim",
"Pilwon",
""
]
] | Spike-timing-dependent plasticity(STDP) is a biological process of synaptic modification caused by the difference of firing order and timing between neurons. One of the neurodynamical roles of STDP is to form a macroscopic geometrical structure in the neuronal state space in response to a periodic input. This work prop... |
2302.00146 | Xiaowei Yu | Xiaowei Yu, Lu Zhang, Haixing Dai, Lin Zhao, Yanjun Lyu, Zihao Wu,
Tianming Liu, Dajiang Zhu | Gyri vs. Sulci: Disentangling Brain Core-Periphery Functional Networks
via Twin-Transformer | 13 pages, 4 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human cerebral cortex is highly convoluted into convex gyri and concave
sulci. It has been demonstrated that gyri and sulci are significantly different
in their anatomy, connectivity, and function, besides exhibiting opposite shape
patterns, long-distance axonal fibers connected to gyri are much denser than
those... | [
{
"created": "Tue, 31 Jan 2023 23:45:40 GMT",
"version": "v1"
}
] | 2023-02-02 | [
[
"Yu",
"Xiaowei",
""
],
[
"Zhang",
"Lu",
""
],
[
"Dai",
"Haixing",
""
],
[
"Zhao",
"Lin",
""
],
[
"Lyu",
"Yanjun",
""
],
[
"Wu",
"Zihao",
""
],
[
"Liu",
"Tianming",
""
],
[
"Zhu",
"Dajiang",
... | The human cerebral cortex is highly convoluted into convex gyri and concave sulci. It has been demonstrated that gyri and sulci are significantly different in their anatomy, connectivity, and function, besides exhibiting opposite shape patterns, long-distance axonal fibers connected to gyri are much denser than those c... |
0705.1974 | Franco Bagnoli | Franco Bagnoli, Pietro Lio, Luca Sguanci | Risk perception in epidemic modeling | 6 pages, 6 figures, completely new version | Phys. Rev. E 76, 061904 (2007) | 10.1103/PhysRevE.76.061904 | null | q-bio.PE q-bio.OT | null | We investigate the effects of risk perception in a simple model of epidemic
spreading. We assume that the perception of the risk of being infected depends
on the fraction of neighbors that are ill. The effect of this factor is to
decrease the infectivity, that therefore becomes a dynamical component of the
model. We ... | [
{
"created": "Mon, 14 May 2007 16:16:34 GMT",
"version": "v1"
},
{
"created": "Fri, 18 May 2007 12:54:36 GMT",
"version": "v2"
},
{
"created": "Thu, 23 Aug 2007 15:56:01 GMT",
"version": "v3"
}
] | 2007-12-06 | [
[
"Bagnoli",
"Franco",
""
],
[
"Lio",
"Pietro",
""
],
[
"Sguanci",
"Luca",
""
]
] | We investigate the effects of risk perception in a simple model of epidemic spreading. We assume that the perception of the risk of being infected depends on the fraction of neighbors that are ill. The effect of this factor is to decrease the infectivity, that therefore becomes a dynamical component of the model. We st... |
2203.01175 | Herbert Sauro Dr | Ciaran Welsh, Jin Xu, Lucian Smith, Matthias K\"onig, Kiri Choi,
Herbert M. Sauro | libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis
Library | null | null | null | null | q-bio.QM cs.CE q-bio.MN q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: This paper presents libRoadRunner 2.0, an extensible,
high-performance, cross-platform, open-source software library for the
simulation and analysis of models expressed using Systems Biology Markup
Language SBML).
Results: libRoadRunner is a self-contained library, able to run both as a
component inside... | [
{
"created": "Sat, 26 Feb 2022 00:59:08 GMT",
"version": "v1"
}
] | 2022-03-03 | [
[
"Welsh",
"Ciaran",
""
],
[
"Xu",
"Jin",
""
],
[
"Smith",
"Lucian",
""
],
[
"König",
"Matthias",
""
],
[
"Choi",
"Kiri",
""
],
[
"Sauro",
"Herbert M.",
""
]
] | Motivation: This paper presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language SBML). Results: libRoadRunner is a self-contained library, able to run both as a component inside oth... |
1103.5685 | Jakub Otwinowski | Jakub Otwinowski, Stefan Boettcher | Accumulation of beneficial mutations in one dimension | null | Physical Review E, 84(1), 011925, 2011 | 10.1103/PhysRevE.84.011925 | null | q-bio.PE cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When beneficial mutations are relatively common, competition between multiple
unfixed mutations can reduce the rate of fixation in well-mixed asexual
populations. We introduce a one dimensional model with a steady accumulation of
beneficial mutations. We find a transition between periodic selection and
multiple-mutat... | [
{
"created": "Tue, 29 Mar 2011 15:38:36 GMT",
"version": "v1"
},
{
"created": "Fri, 15 Feb 2013 21:06:20 GMT",
"version": "v2"
}
] | 2013-02-19 | [
[
"Otwinowski",
"Jakub",
""
],
[
"Boettcher",
"Stefan",
""
]
] | When beneficial mutations are relatively common, competition between multiple unfixed mutations can reduce the rate of fixation in well-mixed asexual populations. We introduce a one dimensional model with a steady accumulation of beneficial mutations. We find a transition between periodic selection and multiple-mutatio... |
1202.0012 | Miguel Navascues | Miguel Navascu\'es, Solenn Stoeckel, Stephanie Mariette | Genetic diversity and fitness in small populations of partially asexual,
self-incompatible plants | null | Heredity 104, 5 (2010) 482-92 | 10.1038/hdy.2009.159 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How self-incompatibility systems are maintained in plant populations is still
a debated issue. Theoretical models predict that self-incompatibility systems
break down according to the intensity of inbreeding depression and number of
S-alleles. Other studies have explored the function of asexual reproduction in
the ma... | [
{
"created": "Tue, 31 Jan 2012 21:00:56 GMT",
"version": "v1"
}
] | 2012-02-02 | [
[
"Navascués",
"Miguel",
""
],
[
"Stoeckel",
"Solenn",
""
],
[
"Mariette",
"Stephanie",
""
]
] | How self-incompatibility systems are maintained in plant populations is still a debated issue. Theoretical models predict that self-incompatibility systems break down according to the intensity of inbreeding depression and number of S-alleles. Other studies have explored the function of asexual reproduction in the main... |
1912.02474 | Sergei Shedko | S.V. Shedko | Assembly ASM291031v2 (Genbank: GCA_002910315.2) identified as assembly
of the Northern Dolly Varden (Salvelinus malma malma) genome, and not the
Arctic char (S. alpinus) genome | 15 pages, in Russian; typos corrected | null | null | null | q-bio.GN q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | To date, twelve complete genomes representing eleven species belonging to six
genera have been sequenced in salmonids. For the genus Salvelinus, it was
supposed to sequence the genome of Arctic char, one of the most variable
species of vertebrate animals. Sequencing was carried out (Christensen et al.,
2018) using th... | [
{
"created": "Thu, 5 Dec 2019 10:13:07 GMT",
"version": "v1"
},
{
"created": "Mon, 23 Dec 2019 11:23:02 GMT",
"version": "v2"
}
] | 2019-12-24 | [
[
"Shedko",
"S. V.",
""
]
] | To date, twelve complete genomes representing eleven species belonging to six genera have been sequenced in salmonids. For the genus Salvelinus, it was supposed to sequence the genome of Arctic char, one of the most variable species of vertebrate animals. Sequencing was carried out (Christensen et al., 2018) using the ... |
1703.09780 | Thierry Mora | Andreas Mayer, Thierry Mora, Olivier Rivoire, Aleksandra M. Walczak | Transitions in optimal adaptive strategies for populations in
fluctuating environments | null | Phys. Rev. E 96, 032412 (2017) | 10.1103/PhysRevE.96.032412 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biological populations are subject to fluctuating environmental conditions.
Different adaptive strategies can allow them to cope with these fluctuations:
specialization to one particular environmental condition, adoption of a
generalist phenotype that compromise between conditions, or population-wise
diversification ... | [
{
"created": "Tue, 28 Mar 2017 20:14:54 GMT",
"version": "v1"
}
] | 2017-09-27 | [
[
"Mayer",
"Andreas",
""
],
[
"Mora",
"Thierry",
""
],
[
"Rivoire",
"Olivier",
""
],
[
"Walczak",
"Aleksandra M.",
""
]
] | Biological populations are subject to fluctuating environmental conditions. Different adaptive strategies can allow them to cope with these fluctuations: specialization to one particular environmental condition, adoption of a generalist phenotype that compromise between conditions, or population-wise diversification (b... |
1802.07875 | Robert Griffiths Professor | Conrad J. Burden and Robert C. Griffiths | The stationary distribution of a sample from the Wright-Fisher diffusion
model with general small mutation rates | 14 pages, 0 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The stationary distribution of a sample taken from a Wright-Fisher diffusion
with general small mutation rates is found using a coalescent approach. The
approximation is equivalent to having at most one mutation in the coalescent
tree to the first order in the rates. The sample probabilities characterize an
approxima... | [
{
"created": "Thu, 22 Feb 2018 02:26:57 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Mar 2018 10:25:08 GMT",
"version": "v2"
},
{
"created": "Fri, 1 Jun 2018 07:09:20 GMT",
"version": "v3"
},
{
"created": "Tue, 25 Sep 2018 23:27:55 GMT",
"version": "v4"
},
{
"cre... | 2018-10-31 | [
[
"Burden",
"Conrad J.",
""
],
[
"Griffiths",
"Robert C.",
""
]
] | The stationary distribution of a sample taken from a Wright-Fisher diffusion with general small mutation rates is found using a coalescent approach. The approximation is equivalent to having at most one mutation in the coalescent tree to the first order in the rates. The sample probabilities characterize an approximati... |
2208.13283 | Samuel Neuenschwander | Samuel Neuenschwander (1 and 2), Diana I. Cruz D\'avalos (1 and 3),
Lucas Anchieri (1 and 3), B\'arbara Sousa da Mota (1 and 3), Davide Bozzi (1
and 3), Simone Rubinacci (1 and 3), Olivier Delaneau (1 and 3), Simon
Rasmussen (4), and Anna-Sapfo Malaspinas (1 and 3) ((1) Department of
Computational Biology, Univ... | Mapache: a flexible pipeline to map ancient DNA | Availability: Mapache is freely available on GitHub
(https://github.com/sneuensc/mapache). Supplementary information: An
extensive manual is provided at https://github.com/sneuensc/mapache/wiki | null | 10.1093/bioinformatics/btad028 | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Summary: Mapping ancient DNA to a reference genome is challenging as it
involves numerous steps, is time-consuming and has to be repeated within a
study to assess the quality of extracts and libraries; as a result, the mapping
needs to be automatized to handle large amounts of data in a reproducible way.
We present m... | [
{
"created": "Sun, 28 Aug 2022 20:24:44 GMT",
"version": "v1"
}
] | 2023-03-09 | [
[
"Neuenschwander",
"Samuel",
"",
"1 and 2"
],
[
"Dávalos",
"Diana I. Cruz",
"",
"1 and 3"
],
[
"Anchieri",
"Lucas",
"",
"1 and 3"
],
[
"da Mota",
"Bárbara Sousa",
"",
"1 and 3"
],
[
"Bozzi",
"Davide",
"",
"1\n and 3"
... | Summary: Mapping ancient DNA to a reference genome is challenging as it involves numerous steps, is time-consuming and has to be repeated within a study to assess the quality of extracts and libraries; as a result, the mapping needs to be automatized to handle large amounts of data in a reproducible way. We present map... |
1410.8499 | Brian Williams Dr | Brian G. Williams and Christopher Dye | Dynamics and Control of Infections on Social Networks | 9 pages | null | null | null | q-bio.QM q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Random mixing in host populations has been a convenient simplifying
assumption in the study of epidemics, but neglects important differences in
contact rates within and between population groups. For HIV/AIDS, the
assumption of random mixing is inappropriate for epidemics that are
concentrated in groups of people at ... | [
{
"created": "Tue, 21 Oct 2014 12:14:29 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Feb 2016 13:47:34 GMT",
"version": "v2"
}
] | 2016-02-24 | [
[
"Williams",
"Brian G.",
""
],
[
"Dye",
"Christopher",
""
]
] | Random mixing in host populations has been a convenient simplifying assumption in the study of epidemics, but neglects important differences in contact rates within and between population groups. For HIV/AIDS, the assumption of random mixing is inappropriate for epidemics that are concentrated in groups of people at hi... |
1211.7022 | Preetish K L | Milind M. Rao and K.L. Preetish | Stability and Hopf Bifurcation Analysis of the Delay Logistic Equation | 12 pages | null | null | null | q-bio.PE math.CA nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Logistic functions are good models of biological population growth. They are
also popular in marketing in modelling demand-supply curves and in a different
context, to chart the sales of new products over time. Delays being inherent in
any biological system, we seek to analyse the effect of delays on the growth of
po... | [
{
"created": "Thu, 29 Nov 2012 19:03:18 GMT",
"version": "v1"
}
] | 2012-11-30 | [
[
"Rao",
"Milind M.",
""
],
[
"Preetish",
"K. L.",
""
]
] | Logistic functions are good models of biological population growth. They are also popular in marketing in modelling demand-supply curves and in a different context, to chart the sales of new products over time. Delays being inherent in any biological system, we seek to analyse the effect of delays on the growth of popu... |
2011.10494 | Neil Sheeley Jr. | Neil R. Sheeley Jr | A Mathematical Model For the Spread of a Virus | 86 pages, 44 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | This paper describes a mathematical model for the spread of a virus through
an isolated population of a given size. The model uses three, color-coded
components, called molecules (red for infected and still contagious; green for
infected, but no longer contagious; and blue for uninfected). In retrospect,
the model tu... | [
{
"created": "Fri, 20 Nov 2020 16:39:49 GMT",
"version": "v1"
},
{
"created": "Fri, 28 May 2021 21:10:31 GMT",
"version": "v2"
}
] | 2021-06-01 | [
[
"Sheeley",
"Neil R.",
"Jr"
]
] | This paper describes a mathematical model for the spread of a virus through an isolated population of a given size. The model uses three, color-coded components, called molecules (red for infected and still contagious; green for infected, but no longer contagious; and blue for uninfected). In retrospect, the model turn... |
2101.10215 | Yakup Kutlu | Enver Kaan Alpturk, Yakup Kutlu | Analysis of Relation between Motor Activity and Imaginary EEG Records | 6 pages, 4 figures, Journal of Artificial Intellicence with
Application | Journal of Artificial Intellicence with Application, 2020 | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | Electroencephalography (EEG) signals signals are often used to learn about
brain structure and to learn what thinking. EEG signals can be easily affected
by external factors. For this reason, they should be applied various
pre-process during their analysis. In this study, it is used the EEG signals
received from 109 ... | [
{
"created": "Thu, 21 Jan 2021 05:02:05 GMT",
"version": "v1"
}
] | 2021-01-26 | [
[
"Alpturk",
"Enver Kaan",
""
],
[
"Kutlu",
"Yakup",
""
]
] | Electroencephalography (EEG) signals signals are often used to learn about brain structure and to learn what thinking. EEG signals can be easily affected by external factors. For this reason, they should be applied various pre-process during their analysis. In this study, it is used the EEG signals received from 109 su... |
2402.06992 | Raja Marjieh | Raja Marjieh, Pol van Rijn, Ilia Sucholutsky, Harin Lee, Thomas L.
Griffiths, Nori Jacoby | A Rational Analysis of the Speech-to-Song Illusion | 7 pages, 5 figures | null | null | null | q-bio.NC cs.AI cs.CL stat.AP | http://creativecommons.org/licenses/by/4.0/ | The speech-to-song illusion is a robust psychological phenomenon whereby a
spoken sentence sounds increasingly more musical as it is repeated. Despite
decades of research, a complete formal account of this transformation is still
lacking, and some of its nuanced characteristics, namely, that certain phrases
appear to... | [
{
"created": "Sat, 10 Feb 2024 16:54:28 GMT",
"version": "v1"
}
] | 2024-02-13 | [
[
"Marjieh",
"Raja",
""
],
[
"van Rijn",
"Pol",
""
],
[
"Sucholutsky",
"Ilia",
""
],
[
"Lee",
"Harin",
""
],
[
"Griffiths",
"Thomas L.",
""
],
[
"Jacoby",
"Nori",
""
]
] | The speech-to-song illusion is a robust psychological phenomenon whereby a spoken sentence sounds increasingly more musical as it is repeated. Despite decades of research, a complete formal account of this transformation is still lacking, and some of its nuanced characteristics, namely, that certain phrases appear to t... |
2009.01894 | Nitin Kamra | Nitin Kamra, Yizhou Zhang, Sirisha Rambhatla, Chuizheng Meng, Yan Liu | PolSIRD: Modeling Epidemic Spread under Intervention Policies | Modeling the spread of the first wave of Covid-19 in the United
States | Journal of Healthcare Informatics Research (2021) | 10.1007/s41666-021-00099-3 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Epidemic spread in a population is traditionally modeled via
compartmentalized models which represent the free evolution of disease in
absence of any intervention policies. In addition, these models assume full
observability of disease cases and do not account for under-reporting. We
present a mathematical model, nam... | [
{
"created": "Thu, 3 Sep 2020 19:26:02 GMT",
"version": "v1"
},
{
"created": "Wed, 12 May 2021 08:13:43 GMT",
"version": "v2"
}
] | 2021-06-16 | [
[
"Kamra",
"Nitin",
""
],
[
"Zhang",
"Yizhou",
""
],
[
"Rambhatla",
"Sirisha",
""
],
[
"Meng",
"Chuizheng",
""
],
[
"Liu",
"Yan",
""
]
] | Epidemic spread in a population is traditionally modeled via compartmentalized models which represent the free evolution of disease in absence of any intervention policies. In addition, these models assume full observability of disease cases and do not account for under-reporting. We present a mathematical model, namel... |
2402.12188 | David Clark | David G. Clark, Manuel Beiran | Structure of activity in multiregion recurrent neural networks | 18 pages, 10 figures; updated author info | null | null | null | q-bio.NC cond-mat.dis-nn cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neural circuits are composed of multiple regions, each with rich dynamics and
engaging in communication with other regions. The combination of local,
within-region dynamics and global, network-level dynamics is thought to provide
computational flexibility. However, the nature of such multiregion dynamics and
the unde... | [
{
"created": "Mon, 19 Feb 2024 14:51:55 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Feb 2024 17:32:32 GMT",
"version": "v2"
}
] | 2024-02-21 | [
[
"Clark",
"David G.",
""
],
[
"Beiran",
"Manuel",
""
]
] | Neural circuits are composed of multiple regions, each with rich dynamics and engaging in communication with other regions. The combination of local, within-region dynamics and global, network-level dynamics is thought to provide computational flexibility. However, the nature of such multiregion dynamics and the underl... |
1601.04110 | I-Lin Ho | I Lin Ho, Arash Moshkforoush, Kwangseok Hong, Gerald A. Meininger,
Michael A. Hill, Nikolaos M. Tsoukias, Watson Kuo | Inherent rhythm of smooth muscle cells in rat mesenteric arterioles: an
eigensystem formulation | 56 pages, 18 figures | Phys. Rev. E 93, 042415 (2016) | 10.1103/PhysRevE.93.042415 | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | On the basis of experimental data and mathematical equations in the
literature, we remodel the ionic dynamics of smooth muscle cells (SMCs) as an
eigensystem formulation, which is valid for investigating finite variations of
variables from the equilibrium like in common experimental operations. This
algorithm provide... | [
{
"created": "Sat, 16 Jan 2016 01:36:53 GMT",
"version": "v1"
},
{
"created": "Sat, 19 Mar 2016 20:24:08 GMT",
"version": "v2"
}
] | 2021-06-08 | [
[
"Ho",
"I Lin",
""
],
[
"Moshkforoush",
"Arash",
""
],
[
"Hong",
"Kwangseok",
""
],
[
"Meininger",
"Gerald A.",
""
],
[
"Hill",
"Michael A.",
""
],
[
"Tsoukias",
"Nikolaos M.",
""
],
[
"Kuo",
"Watson",
""
... | On the basis of experimental data and mathematical equations in the literature, we remodel the ionic dynamics of smooth muscle cells (SMCs) as an eigensystem formulation, which is valid for investigating finite variations of variables from the equilibrium like in common experimental operations. This algorithm provides ... |
1801.03953 | Mike Steel Prof. | Mike Steel and Wim Hordijk | Tractable models of self-sustaining autocatalytic networks | 19 pages, 7 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Self-sustaining autocatalytic networks play a central role in living systems,
from metabolism at the origin of life, simple RNA networks, and the modern
cell, to ecology and cognition. A collectively autocatalytic network that can
be sustained from an ambient food set is also referred to more formally as a
`Reflexive... | [
{
"created": "Thu, 11 Jan 2018 19:02:09 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Mar 2018 22:55:52 GMT",
"version": "v2"
}
] | 2018-03-29 | [
[
"Steel",
"Mike",
""
],
[
"Hordijk",
"Wim",
""
]
] | Self-sustaining autocatalytic networks play a central role in living systems, from metabolism at the origin of life, simple RNA networks, and the modern cell, to ecology and cognition. A collectively autocatalytic network that can be sustained from an ambient food set is also referred to more formally as a `Reflexively... |
0902.4640 | Gabriel Cardona | Gabriel Cardona, Merce Llabres, Francesc Rossello, Gabriel Valiente | The comparison of tree-sibling time consistent phylogenetic networks is
graph isomorphism-complete | 10 pages, 3 figures | null | null | null | q-bio.PE cs.DM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In a previous work, we gave a metric on the class of semibinary tree-sibling
time consistent phylogenetic networks that is computable in polynomial time; in
particular, the problem of deciding if two networks of this kind are isomorphic
is in P. In this paper, we show that if we remove the semibinarity condition
abov... | [
{
"created": "Thu, 26 Feb 2009 17:30:07 GMT",
"version": "v1"
}
] | 2009-02-27 | [
[
"Cardona",
"Gabriel",
""
],
[
"Llabres",
"Merce",
""
],
[
"Rossello",
"Francesc",
""
],
[
"Valiente",
"Gabriel",
""
]
] | In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is in P. In this paper, we show that if we remove the semibinarity condition above,... |
1908.05214 | Michael Holst | L.M. Stolerman, M. Getz, S.G. Llewellyn Smith, M. Holst, P. Rangamani | Stability Analysis of a Bulk-Surface Reaction Model for Membrane-Protein
Clustering | 30 pages, 13 figures | null | null | null | q-bio.SC math.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein aggregation on the plasma membrane (PM) is of critical importance to
many cellular processes such as cell adhesion, endocytosis, fibrillar
conformation, and vesicle transport. Lateral diffusion of protein aggregates or
clusters on the surface of the PM plays an important role in governing their
heterogeneous ... | [
{
"created": "Wed, 14 Aug 2019 16:41:41 GMT",
"version": "v1"
}
] | 2019-08-15 | [
[
"Stolerman",
"L. M.",
""
],
[
"Getz",
"M.",
""
],
[
"Smith",
"S. G. Llewellyn",
""
],
[
"Holst",
"M.",
""
],
[
"Rangamani",
"P.",
""
]
] | Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on the surface of the PM plays an important role in governing their heterogeneous su... |
q-bio/0401037 | Alan McKane | Christopher Quince, Paul Higgs and Alan McKane | Deleting species from model food webs | 30 pages, 9 figures | null | null | null | q-bio.PE cond-mat.stat-mech | null | We use food webs generated by a model to investigate the effects of deleting
species on other species in the web and on the web as a whole. The model
incorporates a realistic population dynamics, adaptive foragers and other
features which allow for the construction of model webs which resemble
empirical food webs. A ... | [
{
"created": "Tue, 27 Jan 2004 12:22:21 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Quince",
"Christopher",
""
],
[
"Higgs",
"Paul",
""
],
[
"McKane",
"Alan",
""
]
] | We use food webs generated by a model to investigate the effects of deleting species on other species in the web and on the web as a whole. The model incorporates a realistic population dynamics, adaptive foragers and other features which allow for the construction of model webs which resemble empirical food webs. A la... |
1405.0044 | Benjamin Dunn | Benjamin Dunn, Maria M{\o}rreaunet, Yasser Roudi | Correlations and functional connections in a population of grid cells | Accepted for publication in PLoS Computational Biology | null | 10.1371/journal.pcbi.1004052 | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the statistics of spike trains of simultaneously recorded grid cells
in freely behaving rats. We evaluate pairwise correlations between these cells
and, using a generalized linear model (kinetic Ising model), study their
functional connectivity. Even when we account for the covariations in firing
rates due t... | [
{
"created": "Wed, 30 Apr 2014 22:05:47 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Oct 2014 11:27:25 GMT",
"version": "v2"
}
] | 2015-06-19 | [
[
"Dunn",
"Benjamin",
""
],
[
"Mørreaunet",
"Maria",
""
],
[
"Roudi",
"Yasser",
""
]
] | We study the statistics of spike trains of simultaneously recorded grid cells in freely behaving rats. We evaluate pairwise correlations between these cells and, using a generalized linear model (kinetic Ising model), study their functional connectivity. Even when we account for the covariations in firing rates due to ... |
1611.03191 | Hon-Cheong So | Hon-Cheong So, Carlos Kwan-Long Chau, Fu-Kiu Ao, Cheuk-Hei Mo,
Pak-Chung Sham | Exploring shared genetic bases and causal relationships of schizophrenia
and bipolar disorder with 28 cardiovascular and metabolic traits | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cardiovascular diseases (CVD) represent a major health issue in patients with
schizophrneia (SCZ) and bipolar disorder (BD), but the exact nature of
cardiometabolic (CM) abnormalities involved and the underlying mechanisms
remain unclear. Using polygenic risk scores (PRS) and LD score regression, we
investigated the ... | [
{
"created": "Thu, 10 Nov 2016 05:47:23 GMT",
"version": "v1"
},
{
"created": "Sat, 7 Jan 2017 22:56:21 GMT",
"version": "v2"
},
{
"created": "Wed, 14 Jun 2017 04:01:15 GMT",
"version": "v3"
},
{
"created": "Fri, 24 Nov 2017 13:38:37 GMT",
"version": "v4"
},
{
"cr... | 2017-12-06 | [
[
"So",
"Hon-Cheong",
""
],
[
"Chau",
"Carlos Kwan-Long",
""
],
[
"Ao",
"Fu-Kiu",
""
],
[
"Mo",
"Cheuk-Hei",
""
],
[
"Sham",
"Pak-Chung",
""
]
] | Cardiovascular diseases (CVD) represent a major health issue in patients with schizophrneia (SCZ) and bipolar disorder (BD), but the exact nature of cardiometabolic (CM) abnormalities involved and the underlying mechanisms remain unclear. Using polygenic risk scores (PRS) and LD score regression, we investigated the sh... |
1111.2992 | Adnan Ali | Adnan Ali, Ell\'ak Somfai, Stefan Grosskinsky | Reproduction time statistics and segregation patterns in growing
populations | null | Phys. Rev. E 85(2), 021923 (2012) | 10.1103/PhysRevE.85.021923 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Pattern formation in microbial colonies of competing strains under purely
space-limited population growth has recently attracted considerable research
interest. We show that the reproduction time statistics of individuals has a
significant impact on the sectoring patterns. Generalizing the standard Eden
growth model,... | [
{
"created": "Sun, 13 Nov 2011 07:07:44 GMT",
"version": "v1"
},
{
"created": "Sun, 15 Apr 2012 21:14:49 GMT",
"version": "v2"
}
] | 2015-06-30 | [
[
"Ali",
"Adnan",
""
],
[
"Somfai",
"Ellák",
""
],
[
"Grosskinsky",
"Stefan",
""
]
] | Pattern formation in microbial colonies of competing strains under purely space-limited population growth has recently attracted considerable research interest. We show that the reproduction time statistics of individuals has a significant impact on the sectoring patterns. Generalizing the standard Eden growth model, w... |
1212.2832 | C. Titus Brown | Adina Chuang Howe, Janet Jansson, Stephanie A. Malfatti, Susannah G.
Tringe, James M. Tiedje, C. Titus Brown | Assembling large, complex environmental metagenomes | Includes supporting information | null | null | null | q-bio.GN | http://creativecommons.org/licenses/publicdomain/ | The large volumes of sequencing data required to sample complex environments
deeply pose new challenges to sequence analysis approaches. De novo metagenomic
assembly effectively reduces the total amount of data to be analyzed but
requires significant computational resources. We apply two pre-assembly
filtering approa... | [
{
"created": "Wed, 12 Dec 2012 14:56:18 GMT",
"version": "v1"
},
{
"created": "Fri, 28 Dec 2012 20:34:13 GMT",
"version": "v2"
}
] | 2013-01-01 | [
[
"Howe",
"Adina Chuang",
""
],
[
"Jansson",
"Janet",
""
],
[
"Malfatti",
"Stephanie A.",
""
],
[
"Tringe",
"Susannah G.",
""
],
[
"Tiedje",
"James M.",
""
],
[
"Brown",
"C. Titus",
""
]
] | The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approach... |
2307.02502 | Renato P. Dos Santos | Melanie Swan, Takashi Kido, Eric Roland, Renato P. dos Santos | Math Agents: Computational Infrastructure, Mathematical Embedding, and
Genomics | null | null | null | null | q-bio.OT cs.AI cs.CL | http://creativecommons.org/licenses/by-sa/4.0/ | The advancement in generative AI could be boosted with more accessible
mathematics. Beyond human-AI chat, large language models (LLMs) are emerging in
programming, algorithm discovery, and theorem proving, yet their genomics
application is limited. This project introduces Math Agents and mathematical
embedding as fre... | [
{
"created": "Tue, 4 Jul 2023 20:16:32 GMT",
"version": "v1"
}
] | 2023-07-07 | [
[
"Swan",
"Melanie",
""
],
[
"Kido",
"Takashi",
""
],
[
"Roland",
"Eric",
""
],
[
"Santos",
"Renato P. dos",
""
]
] | The advancement in generative AI could be boosted with more accessible mathematics. Beyond human-AI chat, large language models (LLMs) are emerging in programming, algorithm discovery, and theorem proving, yet their genomics application is limited. This project introduces Math Agents and mathematical embedding as fresh... |
2105.08856 | Rohan Williams | Elizabeth A. McDaniel, Sebastian Aljoscha Wahl, Shun'ichi Ishii, Ameet
Pinto, Ryan Ziels, Per H. Nielsen, Katherine D. McMahon, Rohan B.H. Williams | Prospects for Multi-omics in the Microbial Ecology of Water Engineering | Review article | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Advances in high-throughput sequencing technologies and bioinformatics
approaches over almost the last three decades have substantially increased our
ability to explore microorganisms and their functions-including those that have
yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches
have enab... | [
{
"created": "Tue, 18 May 2021 23:49:31 GMT",
"version": "v1"
}
] | 2021-05-20 | [
[
"McDaniel",
"Elizabeth A.",
""
],
[
"Wahl",
"Sebastian Aljoscha",
""
],
[
"Ishii",
"Shun'ichi",
""
],
[
"Pinto",
"Ameet",
""
],
[
"Ziels",
"Ryan",
""
],
[
"Nielsen",
"Per H.",
""
],
[
"McMahon",
"Katherine D.",... | Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions-including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enable... |
1202.6670 | Yashar Ahmadian | Yashar Ahmadian, Daniel B. Rubin and Kenneth D. Miller | Analysis of the stabilized supralinear network | 45 pages, 4 figures | Neural Computation 25, 1994-2037 (2013) | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study a rate-model neural network composed of excitatory and inhibitory
neurons in which neuronal input-output functions are power laws with a power
greater than 1, as observed in primary visual cortex. This supralinear
input-output function leads to supralinear summation of network responses to
multiple inputs fo... | [
{
"created": "Wed, 29 Feb 2012 20:14:17 GMT",
"version": "v1"
},
{
"created": "Tue, 5 Jun 2012 23:13:47 GMT",
"version": "v2"
},
{
"created": "Thu, 6 Dec 2012 22:23:31 GMT",
"version": "v3"
},
{
"created": "Sun, 5 May 2013 19:02:44 GMT",
"version": "v4"
},
{
"crea... | 2015-03-20 | [
[
"Ahmadian",
"Yashar",
""
],
[
"Rubin",
"Daniel B.",
""
],
[
"Miller",
"Kenneth D.",
""
]
] | We study a rate-model neural network composed of excitatory and inhibitory neurons in which neuronal input-output functions are power laws with a power greater than 1, as observed in primary visual cortex. This supralinear input-output function leads to supralinear summation of network responses to multiple inputs for ... |
2402.16271 | Ming-Jia Fu | Ming-Jia Fu | Rebuildable biochronometer: inferences and hypothesis on eukaryotic
timing system | 29 pages, 9 figures | null | null | null | q-bio.BM q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | The biochronometers used to keep time in eukaryotes include short-period
biochronometer (SPB) and long-period biochronometer (LPB). Because the
circadian clock reflects the biological time rhythm of a day, it is considered
as SPB. Telomere shortening, which reflects the decreasing of telomere DNA
length of chromosome... | [
{
"created": "Mon, 26 Feb 2024 03:15:13 GMT",
"version": "v1"
}
] | 2024-02-27 | [
[
"Fu",
"Ming-Jia",
""
]
] | The biochronometers used to keep time in eukaryotes include short-period biochronometer (SPB) and long-period biochronometer (LPB). Because the circadian clock reflects the biological time rhythm of a day, it is considered as SPB. Telomere shortening, which reflects the decreasing of telomere DNA length of chromosomes ... |
2004.09478 | Luca Magri | Luca Magri, Nguyen Anh Khoa Doan | First-principles machine learning modelling of COVID-19 | 39 pages, 53 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The coronavirus disease 2019 (COVID-19) has changed the world since the World
Health Organization declared its outbreak on 30th January 2020, recognizing the
outbreak as a pandemic on 11th March 2020. As often said by politicians and
scientific advisors, the objective is "to flatten the curve", or "push the peak
down... | [
{
"created": "Mon, 20 Apr 2020 17:54:02 GMT",
"version": "v1"
}
] | 2020-04-21 | [
[
"Magri",
"Luca",
""
],
[
"Doan",
"Nguyen Anh Khoa",
""
]
] | The coronavirus disease 2019 (COVID-19) has changed the world since the World Health Organization declared its outbreak on 30th January 2020, recognizing the outbreak as a pandemic on 11th March 2020. As often said by politicians and scientific advisors, the objective is "to flatten the curve", or "push the peak down",... |
2006.02100 | Ju Lynn Ong | J.L. Ong, T.Y. Lau, S.A.A. Massar, Z.T. Chong, B.K.L. Ng, D. Koek, W.
Zhao, B.T.T. Yeo, K. Cheong and M.W.L. Chee | COVID-19 Related Mobility Reduction: Heterogenous Effects on Sleep and
Physical Activity Rhythms | 30 pages, 3 main figures, 3 tables, 4 supplementary figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Mobility restrictions imposed to suppress coronavirus transmission can alter
physical activity (PA) and sleep patterns. Characterization of response
heterogeneity and their underlying reasons may assist in tailoring customized
interventions. We obtained wearable data covering baseline, incremental
movement restrictio... | [
{
"created": "Wed, 3 Jun 2020 08:31:50 GMT",
"version": "v1"
},
{
"created": "Tue, 14 Jul 2020 04:50:32 GMT",
"version": "v2"
}
] | 2020-07-15 | [
[
"Ong",
"J. L.",
""
],
[
"Lau",
"T. Y.",
""
],
[
"Massar",
"S. A. A.",
""
],
[
"Chong",
"Z. T.",
""
],
[
"Ng",
"B. K. L.",
""
],
[
"Koek",
"D.",
""
],
[
"Zhao",
"W.",
""
],
[
"Yeo",
"B. T. T.",
... | Mobility restrictions imposed to suppress coronavirus transmission can alter physical activity (PA) and sleep patterns. Characterization of response heterogeneity and their underlying reasons may assist in tailoring customized interventions. We obtained wearable data covering baseline, incremental movement restriction ... |
2211.08085 | Tatiana Levanova | Nikita Barabash, Tatiana Levanova and Sergey Stasenko | Rhythmogenesis in the mean field model of the neuron-glial network | 9 pages, 3 figures | null | 10.1140/epjs/s11734-023-00778-9 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Despite the fact that the phenomenon of bursting activity is important for
functioning of living neural networks, the mechanisms of its origin are still
not clear. In this paper, we propose a new phenomenological model that can
explain the mechanisms of the formation of bursting activity based on
short-term synaptic ... | [
{
"created": "Tue, 15 Nov 2022 12:11:43 GMT",
"version": "v1"
}
] | 2023-03-01 | [
[
"Barabash",
"Nikita",
""
],
[
"Levanova",
"Tatiana",
""
],
[
"Stasenko",
"Sergey",
""
]
] | Despite the fact that the phenomenon of bursting activity is important for functioning of living neural networks, the mechanisms of its origin are still not clear. In this paper, we propose a new phenomenological model that can explain the mechanisms of the formation of bursting activity based on short-term synaptic pl... |
1003.2922 | Jens Christian Claussen | Markus Sch\"utt and Jens Christian Claussen | Stabilization of biodiversity in the coevolutionary rock-paper-scissors
game on complex networks | null | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The dynamical mechanisms that can stabilize the coexistence of species (or
strategies) are of substantial interest for the maintenance of biodiversity and
in sociobehavioural dynamics. We investigate the mean extinction time in the
coevolutionary dynamics of three cyclically invading strategies for different
evolutio... | [
{
"created": "Mon, 15 Mar 2010 13:53:56 GMT",
"version": "v1"
}
] | 2010-03-16 | [
[
"Schütt",
"Markus",
""
],
[
"Claussen",
"Jens Christian",
""
]
] | The dynamical mechanisms that can stabilize the coexistence of species (or strategies) are of substantial interest for the maintenance of biodiversity and in sociobehavioural dynamics. We investigate the mean extinction time in the coevolutionary dynamics of three cyclically invading strategies for different evolutiona... |
1908.02055 | Ina Humpert | Ina Humpert, Danila Di Meo, Andreas W. P\"uschel, Jan-Frederik
Pietschmann | On the Role of Vesicle Transport in Neurite Growth: Modelling and
Experiments | null | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The processes that determine the establishment of the complex morphology of
neurons during development are still poorly understood. We present experiments
that use live imaging to examine the role of vesicle transport and propose a
lattice-based model that shows symmetry breaking features similar to a neuron
during i... | [
{
"created": "Tue, 6 Aug 2019 10:27:01 GMT",
"version": "v1"
}
] | 2019-08-07 | [
[
"Humpert",
"Ina",
""
],
[
"Di Meo",
"Danila",
""
],
[
"Püschel",
"Andreas W.",
""
],
[
"Pietschmann",
"Jan-Frederik",
""
]
] | The processes that determine the establishment of the complex morphology of neurons during development are still poorly understood. We present experiments that use live imaging to examine the role of vesicle transport and propose a lattice-based model that shows symmetry breaking features similar to a neuron during its... |
2009.02513 | Knut Heidemann | Prakhar Godara, Stephan Herminghaus, Knut M. Heidemann | A control theory approach to optimal pandemic mitigation | Error in Fig. 6 corrected (red curve for infinite immune response was
flawed) | null | 10.1371/journal.pone.0247445 | null | q-bio.PE math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the framework of homogeneous susceptible-infected-recovered (SIR) models,
we use a control theory approach to identify optimal pandemic mitigation
strategies. We derive rather general conditions for reaching herd immunity
while minimizing the costs incurred by the introduction of societal control
measures (such as... | [
{
"created": "Sat, 5 Sep 2020 10:45:04 GMT",
"version": "v1"
},
{
"created": "Fri, 16 Oct 2020 13:29:08 GMT",
"version": "v2"
},
{
"created": "Thu, 18 Feb 2021 10:31:31 GMT",
"version": "v3"
},
{
"created": "Fri, 2 Jul 2021 12:10:00 GMT",
"version": "v4"
}
] | 2021-07-05 | [
[
"Godara",
"Prakhar",
""
],
[
"Herminghaus",
"Stephan",
""
],
[
"Heidemann",
"Knut M.",
""
]
] | In the framework of homogeneous susceptible-infected-recovered (SIR) models, we use a control theory approach to identify optimal pandemic mitigation strategies. We derive rather general conditions for reaching herd immunity while minimizing the costs incurred by the introduction of societal control measures (such as c... |
q-bio/0601017 | Fei Liu | Fei Liu and Zhong-can Ou-Yang | Force Modulating Dynamic Disorder: Physical Theory of Catch-slip bond
Transitions in Receptor-Ligand Forced Dissociation Experiments | 8 pages, 3 figures, submitted | null | 10.1103/PhysRevE.74.051904 | null | q-bio.CB q-bio.BM | null | Recently experiments showed that some adhesive receptor-ligand complexes
increase their lifetimes when they are stretched by mechanical force, while the
force increase beyond some thresholds their lifetimes decrease. Several
specific chemical kinetic models have been developed to explain the intriguing
transitions fr... | [
{
"created": "Thu, 12 Jan 2006 03:06:34 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Liu",
"Fei",
""
],
[
"Ou-Yang",
"Zhong-can",
""
]
] | Recently experiments showed that some adhesive receptor-ligand complexes increase their lifetimes when they are stretched by mechanical force, while the force increase beyond some thresholds their lifetimes decrease. Several specific chemical kinetic models have been developed to explain the intriguing transitions from... |
2209.02590 | Joshua Plotkin | Guocheng Wang, Qi Su, Long Wang, Joshua B. Plotkin | The arrow of evolution when the offspring variance is large | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The concept of fitness is central to evolution, but it quantifies only the
expected number of offspring an individual will produce. The actual number of
offspring is also subject to noise, arising from environmental or demographic
stochasticity. In nature, individuals who are more fecund tend to have greater
variance... | [
{
"created": "Tue, 6 Sep 2022 15:46:24 GMT",
"version": "v1"
}
] | 2022-09-07 | [
[
"Wang",
"Guocheng",
""
],
[
"Su",
"Qi",
""
],
[
"Wang",
"Long",
""
],
[
"Plotkin",
"Joshua B.",
""
]
] | The concept of fitness is central to evolution, but it quantifies only the expected number of offspring an individual will produce. The actual number of offspring is also subject to noise, arising from environmental or demographic stochasticity. In nature, individuals who are more fecund tend to have greater variance i... |
1910.03447 | Eric Lock | Sarah Samorodnitsky, Katherine A. Hoadley, and Eric F. Lock | A Pan-Cancer and Polygenic Bayesian Hierarchical Model for the Effect of
Somatic Mutations on Survival | 20 pages, 4 figures | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We built a novel Bayesian hierarchical survival model based on the somatic
mutation profile of patients across 50 genes and 27 cancer types. The
pan-cancer quality allows for the model to "borrow" information across cancer
types, motivated by the assumption that similar mutation profiles may have
similar (but not nec... | [
{
"created": "Tue, 8 Oct 2019 15:11:29 GMT",
"version": "v1"
}
] | 2019-10-09 | [
[
"Samorodnitsky",
"Sarah",
""
],
[
"Hoadley",
"Katherine A.",
""
],
[
"Lock",
"Eric F.",
""
]
] | We built a novel Bayesian hierarchical survival model based on the somatic mutation profile of patients across 50 genes and 27 cancer types. The pan-cancer quality allows for the model to "borrow" information across cancer types, motivated by the assumption that similar mutation profiles may have similar (but not neces... |
2406.01622 | Trevor Norton | Trevor Norton and Debswapna Bhattacharya | Sifting through the Noise: A Survey of Diffusion Probabilistic Models
and Their Applications to Biomolecules | 31 pages, 6 figures | null | null | null | q-bio.BM cs.AI cs.LG q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Diffusion probabilistic models have made their way into a number of
high-profile applications since their inception. In particular, there has been
a wave of research into using diffusion models in the prediction and design of
biomolecular structures and sequences. Their growing ubiquity makes it
imperative for resear... | [
{
"created": "Fri, 31 May 2024 21:39:51 GMT",
"version": "v1"
}
] | 2024-06-05 | [
[
"Norton",
"Trevor",
""
],
[
"Bhattacharya",
"Debswapna",
""
]
] | Diffusion probabilistic models have made their way into a number of high-profile applications since their inception. In particular, there has been a wave of research into using diffusion models in the prediction and design of biomolecular structures and sequences. Their growing ubiquity makes it imperative for research... |
1910.09904 | Anke Cajar | Anke Cajar, Ralf Engbert, Jochen Laubrock | How spatial frequencies and color drive object search in real-world
scenes: A new eye-movement corpus | 29 pages, 6 figures | null | 10.1167/jov.20.7.8 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When studying how people search for objects in scenes, the inhomogeneity of
the visual field is often ignored. Due to physiological limitations peripheral
vision is blurred and mainly uses coarse-grained information (i.e., low spatial
frequencies) for selecting saccade targets, whereas high-acuity central vision
uses... | [
{
"created": "Tue, 22 Oct 2019 11:46:12 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Feb 2020 10:05:18 GMT",
"version": "v2"
},
{
"created": "Fri, 20 Mar 2020 13:24:56 GMT",
"version": "v3"
}
] | 2021-01-05 | [
[
"Cajar",
"Anke",
""
],
[
"Engbert",
"Ralf",
""
],
[
"Laubrock",
"Jochen",
""
]
] | When studying how people search for objects in scenes, the inhomogeneity of the visual field is often ignored. Due to physiological limitations peripheral vision is blurred and mainly uses coarse-grained information (i.e., low spatial frequencies) for selecting saccade targets, whereas high-acuity central vision uses f... |
1906.02603 | Kevin Parker PhD | Kevin J. Parker | The first order statistics of backscatter from the fractal branching
vasculature | 26 pages, 14 figures. This article has been submitted to The Journal
of the Acoustical Society of America. After it is published, it will be found
at http://asa.scitation.org/journal/jas | J Acoust Soc Am 146(5) p.3318-3326, 2019 | 10.1121/1.5132934 | null | q-bio.QM eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The issue of speckle statistics from ultrasound images of soft tissues such
as the liver has a long and rich history. A number of theoretical
distributions, some related to random scatterers or fades in optics and radar,
have been formulated for pulse-echo interference patterns. This work proposes
an alternative fram... | [
{
"created": "Thu, 6 Jun 2019 14:15:12 GMT",
"version": "v1"
},
{
"created": "Fri, 7 Jun 2019 13:33:35 GMT",
"version": "v2"
},
{
"created": "Thu, 19 Sep 2019 18:17:57 GMT",
"version": "v3"
}
] | 2020-02-14 | [
[
"Parker",
"Kevin J.",
""
]
] | The issue of speckle statistics from ultrasound images of soft tissues such as the liver has a long and rich history. A number of theoretical distributions, some related to random scatterers or fades in optics and radar, have been formulated for pulse-echo interference patterns. This work proposes an alternative framew... |
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