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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2010.15493 | Laura Wadkin MMath | Laura E Wadkin, Sirio Orozco-Fuentes, Irina Neganova, Majlinda Lako,
Nicholas G Parker and Anvar Shukurov | An introduction to the mathematical modelling of iPSCs | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The aim of this chapter is to convey the importance and usefulness of
mathematical modelling as a tool to achieve a deeper understanding of stem cell
biology. We introduce key mathematical concepts (random walk theory,
differential equations and agent-based modelling) which form the basis of
current descriptions of i... | [
{
"created": "Thu, 29 Oct 2020 11:25:47 GMT",
"version": "v1"
}
] | 2020-10-30 | [
[
"Wadkin",
"Laura E",
""
],
[
"Orozco-Fuentes",
"Sirio",
""
],
[
"Neganova",
"Irina",
""
],
[
"Lako",
"Majlinda",
""
],
[
"Parker",
"Nicholas G",
""
],
[
"Shukurov",
"Anvar",
""
]
] | The aim of this chapter is to convey the importance and usefulness of mathematical modelling as a tool to achieve a deeper understanding of stem cell biology. We introduce key mathematical concepts (random walk theory, differential equations and agent-based modelling) which form the basis of current descriptions of ind... |
1706.05121 | Massimo Stella | Massimo Stella, Sanja Selakovic, Alberto Antonioni and Cecilia S.
Andreazzi | Community interactions determine role of species in parasite spread
amplification: the ecomultiplex network model | 11 pages, 5 figures | null | null | null | q-bio.QM physics.bio-ph physics.data-an q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most of zoonoses are multi-host parasites with multiple transmission routes
that are usually investigated separately despite their potential interplay. As
a unifying framework for modelling parasite spread through different paths of
infection, we suggest "ecomultiplex" networks, i.e. multiplex networks
representing i... | [
{
"created": "Fri, 16 Jun 2017 00:41:53 GMT",
"version": "v1"
}
] | 2017-06-19 | [
[
"Stella",
"Massimo",
""
],
[
"Selakovic",
"Sanja",
""
],
[
"Antonioni",
"Alberto",
""
],
[
"Andreazzi",
"Cecilia S.",
""
]
] | Most of zoonoses are multi-host parasites with multiple transmission routes that are usually investigated separately despite their potential interplay. As a unifying framework for modelling parasite spread through different paths of infection, we suggest "ecomultiplex" networks, i.e. multiplex networks representing int... |
2201.00921 | Chris Fields | Chris Fields, James F. Glazebrook and Michael Levin | Neurons as hierarchies of quantum reference frames | 40 pgs, 7 figures | BioSystems 219: 104714, 2022 | 10.1016/j.biosystems.2022.104714 | null | q-bio.NC quant-ph | http://creativecommons.org/licenses/by/4.0/ | Conceptual and mathematical models of neurons have lagged behind empirical
understanding for decades. Here we extend previous work in modeling biological
systems with fully scale-independent quantum information-theoretic tools to
develop a uniform, scalable representation of synapses, dendritic and axonal
processes, ... | [
{
"created": "Tue, 4 Jan 2022 00:53:56 GMT",
"version": "v1"
}
] | 2022-07-21 | [
[
"Fields",
"Chris",
""
],
[
"Glazebrook",
"James F.",
""
],
[
"Levin",
"Michael",
""
]
] | Conceptual and mathematical models of neurons have lagged behind empirical understanding for decades. Here we extend previous work in modeling biological systems with fully scale-independent quantum information-theoretic tools to develop a uniform, scalable representation of synapses, dendritic and axonal processes, ne... |
q-bio/0612005 | Henrik Jeldtoft Jensen | Alastair Windus and Henrik Jeldtoft Jensen | Allee Effects and Extinction in a Lattice Model | 7 pages and 8 figures | null | null | null | q-bio.PE | null | In the interest of conservation, the importance of having a large habitat
available for a species is widely known. Here, we introduce a lattice-based
model for a population and look at the importance of fluctuations as well as
that of the population density, particularly with respect to Allee effects. We
examine the ... | [
{
"created": "Tue, 5 Dec 2006 13:26:55 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Windus",
"Alastair",
""
],
[
"Jensen",
"Henrik Jeldtoft",
""
]
] | In the interest of conservation, the importance of having a large habitat available for a species is widely known. Here, we introduce a lattice-based model for a population and look at the importance of fluctuations as well as that of the population density, particularly with respect to Allee effects. We examine the mo... |
2010.15334 | Hayato Chiba | Kiyoshi Kotani, Akihiko Akao, Hayato Chiba | Bifurcation of the neuronal population dynamics of the modified theta
model: transition to macroscopic gamma oscillation | null | null | 10.1016/j.physd.2020.132789 | null | q-bio.NC math.DS nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Interactions of inhibitory neurons produce gamma oscillations (30--80 Hz) in
the local field potential, which is known to be involved in functions such as
cognition and attention. In this study, the modified theta model is considered
to investigate the theoretical relationship between the microscopic structure
of inh... | [
{
"created": "Thu, 29 Oct 2020 03:18:20 GMT",
"version": "v1"
}
] | 2021-02-03 | [
[
"Kotani",
"Kiyoshi",
""
],
[
"Akao",
"Akihiko",
""
],
[
"Chiba",
"Hayato",
""
]
] | Interactions of inhibitory neurons produce gamma oscillations (30--80 Hz) in the local field potential, which is known to be involved in functions such as cognition and attention. In this study, the modified theta model is considered to investigate the theoretical relationship between the microscopic structure of inhib... |
2201.06725 | Yijun Li | Stefan Stanojevic, Yijun Li, Lana X. Garmire | Computational Methods for Single-Cell Multi-Omics Integration and
Alignment | 26 pages, 4 figures | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-sa/4.0/ | Recently developed technologies to generate single-cell genomic data have
made a revolutionary impact in the field of biology. Multi-omics assays offer
even greater opportunities to understand cellular states and biological
processes. However, the problem of integrating different -omics data with very
different dimen... | [
{
"created": "Tue, 18 Jan 2022 04:00:58 GMT",
"version": "v1"
}
] | 2022-01-19 | [
[
"Stanojevic",
"Stefan",
""
],
[
"Li",
"Yijun",
""
],
[
"Garmire",
"Lana X.",
""
]
] | Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology. Multi-omics assays offer even greater opportunities to understand cellular states and biological processes. However, the problem of integrating different -omics data with very different dimensi... |
1311.1496 | Juli\'an Candia | Juli\'an Candia, Jayanth R. Banavar, Wolfgang Losert | Understanding Health and Disease with Multidimensional Single-Cell
Methods | 25 pages, 7 figures; revised version with minor changes. To appear in
J. Phys.: Cond. Matt | J. Phys.: Condens. Matter 26 (2014) 073102 | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Current efforts in the biomedical sciences and related interdisciplinary
fields are focused on gaining a molecular understanding of health and disease,
which is a problem of daunting complexity that spans many orders of magnitude
in characteristic length scales, from small molecules that regulate cell
function to cel... | [
{
"created": "Wed, 6 Nov 2013 20:53:53 GMT",
"version": "v1"
},
{
"created": "Sun, 1 Dec 2013 16:12:22 GMT",
"version": "v2"
}
] | 2014-01-24 | [
[
"Candia",
"Julián",
""
],
[
"Banavar",
"Jayanth R.",
""
],
[
"Losert",
"Wolfgang",
""
]
] | Current efforts in the biomedical sciences and related interdisciplinary fields are focused on gaining a molecular understanding of health and disease, which is a problem of daunting complexity that spans many orders of magnitude in characteristic length scales, from small molecules that regulate cell function to cell ... |
0901.4589 | Tijana Milenkovic | Natasa Przulj | Biological network comparison using graphlet degree distribution | Proceedings of the 2006 European Conference on Computational Biology,
ECCB'06, Eilat, Israel, January 21-24, 2007 | Bioinformatics 2007 23: e177-e183 | 10.1093/bioinformatics/btl301 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Analogous to biological sequence comparison, comparing cellular networks is
an important problem that could provide insight into biological understanding
and therapeutics. For technical reasons, comparing large networks is
computationally infeasible, and thus heuristics such as the degree distribution
have been sough... | [
{
"created": "Thu, 29 Jan 2009 00:30:12 GMT",
"version": "v1"
}
] | 2009-01-30 | [
[
"Przulj",
"Natasa",
""
]
] | Analogous to biological sequence comparison, comparing cellular networks is an important problem that could provide insight into biological understanding and therapeutics. For technical reasons, comparing large networks is computationally infeasible, and thus heuristics such as the degree distribution have been sought.... |
1309.0455 | Bahram Houchmandzadeh | Bahram Houchmandzadeh (LIPhy) | An alternative to the breeder's and Lande's equations | null | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The breeder's equation is a cornerstone of quantitative genetics and is
widely used in evolutionary modeling. The equation which reads R=h^{2}S relates
response to selection R (the mean phenotype of the progeny) to the selection
differential S (mean phenotype of selected parents) through a simple
proportionality rela... | [
{
"created": "Mon, 2 Sep 2013 16:25:28 GMT",
"version": "v1"
}
] | 2013-09-03 | [
[
"Houchmandzadeh",
"Bahram",
"",
"LIPhy"
]
] | The breeder's equation is a cornerstone of quantitative genetics and is widely used in evolutionary modeling. The equation which reads R=h^{2}S relates response to selection R (the mean phenotype of the progeny) to the selection differential S (mean phenotype of selected parents) through a simple proportionality relati... |
2404.15805 | Wei Chen | Shujian Jiao, Bingxuan Li, Lei Wang, Xiaojin Zhang, Wei Chen, Jiajie
Peng, Zhongyu Wei | Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient
Clustering | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Proteins are essential to life's processes, underpinning evolution and
diversity. Advances in sequencing technology have revealed millions of
proteins, underscoring the need for sophisticated pre-trained protein models
for biological analysis and AI development. Facebook's ESM2, the most advanced
protein language mod... | [
{
"created": "Wed, 24 Apr 2024 11:09:43 GMT",
"version": "v1"
}
] | 2024-04-25 | [
[
"Jiao",
"Shujian",
""
],
[
"Li",
"Bingxuan",
""
],
[
"Wang",
"Lei",
""
],
[
"Zhang",
"Xiaojin",
""
],
[
"Chen",
"Wei",
""
],
[
"Peng",
"Jiajie",
""
],
[
"Wei",
"Zhongyu",
""
]
] | Proteins are essential to life's processes, underpinning evolution and diversity. Advances in sequencing technology have revealed millions of proteins, underscoring the need for sophisticated pre-trained protein models for biological analysis and AI development. Facebook's ESM2, the most advanced protein language model... |
2407.12382 | Hugues Berry | Nathan Quiblier (AISTROSIGHT), Jan-Michael Rye (AISTROSIGHT), Pierre
Leclerc (PhLAM), Henri Truong (PhLAM), Abdelkrim Hannou (PhLAM), Laurent
H\'eliot (PhLAM), Hugues Berry (AISTROSIGHT) | Enhancing Fluorescence Correlation Spectroscopy with Machine Learning
for Advanced Analysis of Anomalous Diffusion | null | null | null | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The random motion of molecules in living cells has consistently been reported
to deviate from standard Brownian motion, a behavior coined as ``anomalous
diffusion''. Fluorescence Correlation Spectroscopy (FCS) is a powerful method
to quantify molecular motions in living cells but its application is limited to
a subse... | [
{
"created": "Wed, 17 Jul 2024 08:02:25 GMT",
"version": "v1"
}
] | 2024-07-18 | [
[
"Quiblier",
"Nathan",
"",
"AISTROSIGHT"
],
[
"Rye",
"Jan-Michael",
"",
"AISTROSIGHT"
],
[
"Leclerc",
"Pierre",
"",
"PhLAM"
],
[
"Truong",
"Henri",
"",
"PhLAM"
],
[
"Hannou",
"Abdelkrim",
"",
"PhLAM"
],
[
"Hélio... | The random motion of molecules in living cells has consistently been reported to deviate from standard Brownian motion, a behavior coined as ``anomalous diffusion''. Fluorescence Correlation Spectroscopy (FCS) is a powerful method to quantify molecular motions in living cells but its application is limited to a subset ... |
q-bio/0610055 | Illes Farkas | Illes J. Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar, Zoltan N.
Oltvai | Topological basis of signal integration in the
transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae | Color figures, supplement and free full text article available at
http://www.biomedcentral.com/1471-2105/7/478/abstract | BMC Bioinformatics 2006, 7:478 | 10.1186/1471-2105-7-478 | null | q-bio.MN q-bio.GN | null | BACKGROUND. Signal recognition and information processing is a fundamental
cellular function, which in part involves comprehensive transcriptional
regulatory (TR) mechanisms carried out in response to complex environmental
signals in the context of the cell's own internal state. However, the network
topological basis... | [
{
"created": "Mon, 30 Oct 2006 09:19:53 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Farkas",
"Illes J.",
""
],
[
"Wu",
"Chuang",
""
],
[
"Chennubhotla",
"Chakra",
""
],
[
"Bahar",
"Ivet",
""
],
[
"Oltvai",
"Zoltan N.",
""
]
] | BACKGROUND. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the context of the cell's own internal state. However, the network topological basis o... |
1905.07279 | Sirio Orozco-Fuentes | Sirio Orozco-Fuentes, Irina Neganova, Laura E. Wadkin, Andrew W.
Baggaley, Rafael A. Barrio, Majlinda Lako, Anvar Shukurov, Nicholas G. Parker | Quantification of the morphological characteristics of hESC colonies | null | null | null | null | q-bio.QM q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The maintenance of the pluripotent state in human embryonic stem cells
(hESCs) is critical for further application in regenerative medicine, drug
testing and studies of fundamental biology. Currently, the selection of the
best quality cells and colonies for propagation is typically performed by eye,
in terms of the d... | [
{
"created": "Fri, 17 May 2019 14:11:44 GMT",
"version": "v1"
}
] | 2019-05-20 | [
[
"Orozco-Fuentes",
"Sirio",
""
],
[
"Neganova",
"Irina",
""
],
[
"Wadkin",
"Laura E.",
""
],
[
"Baggaley",
"Andrew W.",
""
],
[
"Barrio",
"Rafael A.",
""
],
[
"Lako",
"Majlinda",
""
],
[
"Shukurov",
"Anvar",
... | The maintenance of the pluripotent state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells and colonies for propagation is typically performed by eye, in terms of the dis... |
2402.17153 | Yun S. Song | Michael Celentano, William S. DeWitt, Sebastian Prillo, Yun S. Song | Exact and efficient phylodynamic simulation from arbitrarily large
populations | 37 pages, 7 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Many biological studies involve inferring the evolutionary history of a
sample of individuals from a large population and interpreting the
reconstructed tree. Such an ascertained tree typically represents only a small
part of a comprehensive population tree and is distorted by survivorship and
sampling biases. Inferr... | [
{
"created": "Tue, 27 Feb 2024 02:37:53 GMT",
"version": "v1"
},
{
"created": "Sat, 10 Aug 2024 07:59:31 GMT",
"version": "v2"
}
] | 2024-08-13 | [
[
"Celentano",
"Michael",
""
],
[
"DeWitt",
"William S.",
""
],
[
"Prillo",
"Sebastian",
""
],
[
"Song",
"Yun S.",
""
]
] | Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a comprehensive population tree and is distorted by survivorship and sampling biases. Inferrin... |
1208.4973 | Simone Pigolotti | Simone Pigolotti, Roberto Benzi, Prasad Perlekar Mogens H. Jensen,
Federico Toschi, David R. Nelson | Growth, competition and cooperation in spatial population genetics | 29 pages, 14 figures; revised version including a section with
results in the presence of fluid flows | Theoretical Population Biology 84, 72-86 (2013) | 10.1016/j.tpb.2012.12.002 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study an individual based model describing competition in space between
two different alleles. Although the model is similar in spirit to classic
models of spatial population genetics such as the stepping stone model, here
however space is continuous and the total density of competing individuals
fluctuates due to... | [
{
"created": "Fri, 24 Aug 2012 13:33:37 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Dec 2012 12:53:15 GMT",
"version": "v2"
}
] | 2015-03-20 | [
[
"Pigolotti",
"Simone",
""
],
[
"Benzi",
"Roberto",
""
],
[
"Jensen",
"Prasad Perlekar Mogens H.",
""
],
[
"Toschi",
"Federico",
""
],
[
"Nelson",
"David R.",
""
]
] | We study an individual based model describing competition in space between two different alleles. Although the model is similar in spirit to classic models of spatial population genetics such as the stepping stone model, here however space is continuous and the total density of competing individuals fluctuates due to d... |
2110.10483 | Thorsten Hugel | Benedikt Sohmen, Christian Beck, Tilo Seydel, Ingo Hoffmann, Bianca
Hermann, Mark N\"uesch, Marco Grimaldo, Frank Schreiber, Steffen Wolf, Felix
Roosen-Runge and Thorsten Hugel | The onset of molecule-spanning dynamics in a multi-domain protein | 29 main text pages, 7 main text figures; 27 SI pages, 15 SI figures | null | null | null | q-bio.BM physics.bio-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Protein dynamics has been investigated on a wide range of time scales. Nano-
and picosecond dynamics have been assigned to local fluctuations, while slower
dynamics have been attributed to larger conformational changes. However, it is
largely unknown how local fluctuations can lead to global allosteric changes.
Here ... | [
{
"created": "Wed, 20 Oct 2021 10:59:02 GMT",
"version": "v1"
},
{
"created": "Thu, 17 Mar 2022 15:45:40 GMT",
"version": "v2"
}
] | 2022-03-18 | [
[
"Sohmen",
"Benedikt",
""
],
[
"Beck",
"Christian",
""
],
[
"Seydel",
"Tilo",
""
],
[
"Hoffmann",
"Ingo",
""
],
[
"Hermann",
"Bianca",
""
],
[
"Nüesch",
"Mark",
""
],
[
"Grimaldo",
"Marco",
""
],
[
"... | Protein dynamics has been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is largely unknown how local fluctuations can lead to global allosteric changes. Here we... |
2208.02818 | Fran\c{c}ois Hug | Fran\c{c}ois Hug, Simon Avrillon, Jaime Ib\'a\~nez, Dario Farina | Common Synaptic Input, Synergies, and Size Principle: Control of Spinal
Motor Neurons for Movement Generation | 12 pages; 1 figure; review paper or opinion piece | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Understanding how movement is controlled by the central nervous system
remains a major challenge, with ongoing debate about basic features underlying
this control. In this review, we introduce a new conceptual framework for the
distribution of common input to spinal motor neurons. Specifically, this
framework is base... | [
{
"created": "Wed, 27 Jul 2022 05:10:13 GMT",
"version": "v1"
}
] | 2022-08-08 | [
[
"Hug",
"François",
""
],
[
"Avrillon",
"Simon",
""
],
[
"Ibáñez",
"Jaime",
""
],
[
"Farina",
"Dario",
""
]
] | Understanding how movement is controlled by the central nervous system remains a major challenge, with ongoing debate about basic features underlying this control. In this review, we introduce a new conceptual framework for the distribution of common input to spinal motor neurons. Specifically, this framework is based ... |
1604.01943 | Michele Giugliano | Rocco Pulizzi, Gabriele Musumeci, Chris Van Den Haute, Sebastian Van
De Vijver, Veerle Baekelandt, Michele Giugliano | Brief wide-field photostimuli evoke and modulate oscillatory
reverberating activity in cortical networks | 23 pages, 7 figures, 2 supplemental figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cell assemblies manipulation by optogenetics is pivotal to advance
neuroscience and neuroengineering. In in vivo applications, photostimulation
often broadly addresses a population of cells simultaneously, leading to
feed-forward and to reverberating responses in recurrent microcircuits. The
former arise from direct ... | [
{
"created": "Thu, 7 Apr 2016 10:02:02 GMT",
"version": "v1"
}
] | 2016-04-08 | [
[
"Pulizzi",
"Rocco",
""
],
[
"Musumeci",
"Gabriele",
""
],
[
"Haute",
"Chris Van Den",
""
],
[
"Van De Vijver",
"Sebastian",
""
],
[
"Baekelandt",
"Veerle",
""
],
[
"Giugliano",
"Michele",
""
]
] | Cell assemblies manipulation by optogenetics is pivotal to advance neuroscience and neuroengineering. In in vivo applications, photostimulation often broadly addresses a population of cells simultaneously, leading to feed-forward and to reverberating responses in recurrent microcircuits. The former arise from direct ac... |
2311.06034 | Guido Tiana | A. Zambon, R. Zecchina, G. Tiana | Structure of the space of folding protein sequences defined by large
language models | null | null | null | null | q-bio.BM q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Proteins populate a manifold in the high-dimensional sequence space whose
geometrical structure guides their natural evolution. Leveraging
recently-developed structure prediction tools based on transformer models, we
first examine the protein sequence landscape as defined by the folding score
function. This landscape... | [
{
"created": "Fri, 10 Nov 2023 12:43:06 GMT",
"version": "v1"
}
] | 2023-11-13 | [
[
"Zambon",
"A.",
""
],
[
"Zecchina",
"R.",
""
],
[
"Tiana",
"G.",
""
]
] | Proteins populate a manifold in the high-dimensional sequence space whose geometrical structure guides their natural evolution. Leveraging recently-developed structure prediction tools based on transformer models, we first examine the protein sequence landscape as defined by the folding score function. This landscape s... |
1001.0113 | Nikesh Dattani | Nikesh S. Dattani | A new method for identifying vertebrates using only their mitochondrial
DNA | 7 Pages, 6 Figures | null | null | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A new method for determining whether or not a mitrochondrial DNA (mtDNA)
sequence belongs to a vertebrate is described and tested. This method only
needs the mtDNA sequence of the organism in question, and unlike alignment
based methods, it does not require it to be compared with anything else. The
method is tested o... | [
{
"created": "Thu, 31 Dec 2009 10:41:18 GMT",
"version": "v1"
}
] | 2010-01-05 | [
[
"Dattani",
"Nikesh S.",
""
]
] | A new method for determining whether or not a mitrochondrial DNA (mtDNA) sequence belongs to a vertebrate is described and tested. This method only needs the mtDNA sequence of the organism in question, and unlike alignment based methods, it does not require it to be compared with anything else. The method is tested on ... |
1001.0170 | Michael Khasin | M. Khasin, M.I. Dykman and B. Meerson | Speeding up disease extinction with a limited amount of vaccine | null | null | 10.1103/PhysRevE.81.051925 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider optimal vaccination protocol where the vaccine is in short
supply. In this case, disease extinction results from a large and rare
fluctuation. We show that the probability of such fluctuation can be
exponentially increased by vaccination. For periodic vaccination with fixed
average rate, the optimal vacci... | [
{
"created": "Thu, 31 Dec 2009 19:01:58 GMT",
"version": "v1"
},
{
"created": "Sun, 31 Jan 2010 23:29:07 GMT",
"version": "v2"
}
] | 2013-05-29 | [
[
"Khasin",
"M.",
""
],
[
"Dykman",
"M. I.",
""
],
[
"Meerson",
"B.",
""
]
] | We consider optimal vaccination protocol where the vaccine is in short supply. In this case, disease extinction results from a large and rare fluctuation. We show that the probability of such fluctuation can be exponentially increased by vaccination. For periodic vaccination with fixed average rate, the optimal vaccina... |
1801.04824 | Radha Srinivasan | Kiran Vishwasrao, Arjumanara Surti, S. Radha | Susceptibility of Methicillin Resistant Staphylococcus aureus to
Vancomycin using Liposomal Drug Delivery System | null | null | null | null | q-bio.TO cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Staphylococcus aureus responsible for nosocomial infections is a significant
threat to the public health. The increasing resistance of S.aureus to various
antibiotics has drawn it to a prime focus for research on designing an
appropriate drug delivery system. Emergence of Methicillin Resistant
Staphylococcus aureus (... | [
{
"created": "Mon, 15 Jan 2018 14:39:10 GMT",
"version": "v1"
}
] | 2018-01-16 | [
[
"Vishwasrao",
"Kiran",
""
],
[
"Surti",
"Arjumanara",
""
],
[
"Radha",
"S.",
""
]
] | Staphylococcus aureus responsible for nosocomial infections is a significant threat to the public health. The increasing resistance of S.aureus to various antibiotics has drawn it to a prime focus for research on designing an appropriate drug delivery system. Emergence of Methicillin Resistant Staphylococcus aureus (MR... |
q-bio/0403006 | Matthew Berryman | Sabrina L. Spencer, Matthew J. Berryman, Jose A. Garcia and Derek
Abbott | An ordinary differential equation model for the multistep transformation
to cancer | 12 pages, submitted to Journal of Theoretical Biology | null | null | null | q-bio.CB q-bio.TO | null | Cancer is viewed as a multistep process whereby a normal cell is transformed
into a cancer cell through the acquisition of mutations. We reduce the
complexities of cancer progression to a simple set of underlying rules that
govern the transformation of normal cells to malignant cells. In doing so, we
derive an ordina... | [
{
"created": "Thu, 4 Mar 2004 03:37:58 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Spencer",
"Sabrina L.",
""
],
[
"Berryman",
"Matthew J.",
""
],
[
"Garcia",
"Jose A.",
""
],
[
"Abbott",
"Derek",
""
]
] | Cancer is viewed as a multistep process whereby a normal cell is transformed into a cancer cell through the acquisition of mutations. We reduce the complexities of cancer progression to a simple set of underlying rules that govern the transformation of normal cells to malignant cells. In doing so, we derive an ordinary... |
2009.04518 | Kristine Heiney | Kristine Heiney, Gunnar Tufte, Stefano Nichele | On Artificial Life and Emergent Computation in Physical Substrates | Accepted conference paper. HPCS2020, Session 3: BICAS | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | In living systems, we often see the emergence of the ingredients necessary
for computation -- the capacity for information transmission, storage, and
modification -- begging the question of how we may exploit or imitate such
biological systems in unconventional computing applications. What can we gain
from artificial... | [
{
"created": "Wed, 9 Sep 2020 18:59:53 GMT",
"version": "v1"
}
] | 2020-09-11 | [
[
"Heiney",
"Kristine",
""
],
[
"Tufte",
"Gunnar",
""
],
[
"Nichele",
"Stefano",
""
]
] | In living systems, we often see the emergence of the ingredients necessary for computation -- the capacity for information transmission, storage, and modification -- begging the question of how we may exploit or imitate such biological systems in unconventional computing applications. What can we gain from artificial l... |
1407.3812 | Brenno Cabella | Brenno Caetano Troca Cabella, Fernando Meloni and Alexandre Souto
Martinez | Could sampling make hares eat lynxes? | null | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cycles in population dynamics are widely found in nature. These cycles are
understood as emerging from the interaction between two or more coupled
species. Here, we argue that data regarding population dynamics are prone to
misinterpretation when sampling is conducted at a slow rate compared to the
population cycle p... | [
{
"created": "Mon, 14 Jul 2014 20:46:17 GMT",
"version": "v1"
}
] | 2014-07-16 | [
[
"Cabella",
"Brenno Caetano Troca",
""
],
[
"Meloni",
"Fernando",
""
],
[
"Martinez",
"Alexandre Souto",
""
]
] | Cycles in population dynamics are widely found in nature. These cycles are understood as emerging from the interaction between two or more coupled species. Here, we argue that data regarding population dynamics are prone to misinterpretation when sampling is conducted at a slow rate compared to the population cycle per... |
2311.09260 | Anh Bui Huynh Quoc | Huynh Quoc Anh Bui, Trong Hop Do, Thanh Binh Nguyen | A Proposed Artificial Neural Network based Approach for Molecules Bitter
Prediction | null | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In recent years, the development of Artificial Intelligence (AI) has offered
the possibility to tackle many interdisciplinary problems, and the field of
chemistry is not an exception. Drug analysis is crucial in drug discovery,
playing an important role in human life. However, this task encounters many
difficulties d... | [
{
"created": "Wed, 15 Nov 2023 04:22:29 GMT",
"version": "v1"
}
] | 2023-11-17 | [
[
"Bui",
"Huynh Quoc Anh",
""
],
[
"Do",
"Trong Hop",
""
],
[
"Nguyen",
"Thanh Binh",
""
]
] | In recent years, the development of Artificial Intelligence (AI) has offered the possibility to tackle many interdisciplinary problems, and the field of chemistry is not an exception. Drug analysis is crucial in drug discovery, playing an important role in human life. However, this task encounters many difficulties due... |
1309.0248 | Hayriye Gulbudak | Hayriye Gulbudak and Maia Martcheva | Forward Hysteresis and Backward Bifurcation Caused by Culling in an
Avian Influenza Model | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The emerging threat of a human pandemic caused by the H5N1 avian influenza
virus strain magnifies the need for controlling the incidence of H5N1 infection
in domestic bird populations. Culling is one of the most widely used control
measures and has proved effective for isolated outbreaks. However, the
socio-economic ... | [
{
"created": "Sun, 1 Sep 2013 17:51:16 GMT",
"version": "v1"
}
] | 2013-09-03 | [
[
"Gulbudak",
"Hayriye",
""
],
[
"Martcheva",
"Maia",
""
]
] | The emerging threat of a human pandemic caused by the H5N1 avian influenza virus strain magnifies the need for controlling the incidence of H5N1 infection in domestic bird populations. Culling is one of the most widely used control measures and has proved effective for isolated outbreaks. However, the socio-economic im... |
2103.13844 | Ali Kishk | Ali Kishk, Maria Pires Pacheco, Thomas Sauter | DCcov: Repositioning of Drugs and Drug Combinations for SARS-CoV-2
Infected Lung through Constraint-Based Modelling | null | null | 10.1016/j.isci.2021.103331 | null | q-bio.MN q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The 2019 coronavirus disease (COVID-19) became a worldwide pandemic with
currently no effective antiviral drug except treatments for symptomatic
therapy. Flux balance analysis is an efficient method to analyze metabolic
networks. It allows optimizing for a metabolic function and thus e.g.,
predicting the growth rate ... | [
{
"created": "Thu, 25 Mar 2021 13:51:37 GMT",
"version": "v1"
}
] | 2021-11-12 | [
[
"Kishk",
"Ali",
""
],
[
"Pacheco",
"Maria Pires",
""
],
[
"Sauter",
"Thomas",
""
]
] | The 2019 coronavirus disease (COVID-19) became a worldwide pandemic with currently no effective antiviral drug except treatments for symptomatic therapy. Flux balance analysis is an efficient method to analyze metabolic networks. It allows optimizing for a metabolic function and thus e.g., predicting the growth rate of... |
q-bio/0510020 | Miodrag Krmar | Vladan Pankovic, Rade Glavatovic, Milan Predojevic | $C_{E}PT$ Symmetry of the Simple Ecological Dynamical Equations | 11 pages, no figures | null | null | NS-05/B-12 | q-bio.PE | null | It is shown that all simple ecological, i.e. population dynamical equations
(unlimited exponential population growth (or decrease) dynamics, logistic or
Verhulst equation, usual and generalized Lotka-Volterra equations) hold a
symmetry, called $C_{E}PT$ symmetry. Namely, all simple ecological dynamical
equations are ... | [
{
"created": "Mon, 10 Oct 2005 09:26:22 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Pankovic",
"Vladan",
""
],
[
"Glavatovic",
"Rade",
""
],
[
"Predojevic",
"Milan",
""
]
] | It is shown that all simple ecological, i.e. population dynamical equations (unlimited exponential population growth (or decrease) dynamics, logistic or Verhulst equation, usual and generalized Lotka-Volterra equations) hold a symmetry, called $C_{E}PT$ symmetry. Namely, all simple ecological dynamical equations are in... |
2210.17270 | Egor I. Kiselev | Egor I. Kiselev and Florian G. Pflug and Arndt von Haeseler | Critical growth of cerebral tissue in organoids: theory and experiments | null | null | 10.1103/PhysRevLett.131.178402 | null | q-bio.NC cond-mat.soft q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop a Fokker-Planck theory of tissue growth with three types of cells
(symmetrically dividing, asymmetrically dividing and non-dividing) as main
agents to study the growth dynamics of human cerebral organoids. Fitting the
theory to lineage tracing data obtained in next generation sequencing
experiments, we sho... | [
{
"created": "Mon, 31 Oct 2022 12:58:27 GMT",
"version": "v1"
},
{
"created": "Sun, 13 Aug 2023 15:45:55 GMT",
"version": "v2"
},
{
"created": "Fri, 25 Aug 2023 15:51:29 GMT",
"version": "v3"
}
] | 2024-06-28 | [
[
"Kiselev",
"Egor I.",
""
],
[
"Pflug",
"Florian G.",
""
],
[
"von Haeseler",
"Arndt",
""
]
] | We develop a Fokker-Planck theory of tissue growth with three types of cells (symmetrically dividing, asymmetrically dividing and non-dividing) as main agents to study the growth dynamics of human cerebral organoids. Fitting the theory to lineage tracing data obtained in next generation sequencing experiments, we show ... |
2308.15225 | Mrugsen Gopnarayan | Mrugsen Nagsen Gopnarayan, Jaan Aru, Sebastian Gluth | From DDMs to DNNs: Using process data and models of decision-making to
improve human-AI interactions | Review paper, 13 pages, 1 figure | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | Over the past decades, cognitive neuroscientists and behavioral economists
have recognized the value of describing the process of decision making in
detail and modeling the emergence of decisions over time. For example, the time
it takes to decide can reveal more about an agent's true hidden preferences
than only the... | [
{
"created": "Tue, 29 Aug 2023 11:27:22 GMT",
"version": "v1"
},
{
"created": "Thu, 7 Sep 2023 15:54:26 GMT",
"version": "v2"
}
] | 2023-09-08 | [
[
"Gopnarayan",
"Mrugsen Nagsen",
""
],
[
"Aru",
"Jaan",
""
],
[
"Gluth",
"Sebastian",
""
]
] | Over the past decades, cognitive neuroscientists and behavioral economists have recognized the value of describing the process of decision making in detail and modeling the emergence of decisions over time. For example, the time it takes to decide can reveal more about an agent's true hidden preferences than only the d... |
2111.02961 | Essam Rashed | Sachiko Kodera, Essam A. Rashed, Akimasa Hirata | Mobility-Dependent and Mobility-Compensated Effective Reproduction
Number of COVID-19 Viral Variants: New Metric for Infectivity Evaluation | 14 pages, 4 figures, 2 tables | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During epidemics, estimation of the effective reproduction number (ERN)
associated with infectious disease is a challenging topic for policy
development and medical resource management. There is still an open question
about the dominant factors to characterize in corona virus disease 2019
(COVID-19), although recent ... | [
{
"created": "Mon, 1 Nov 2021 07:53:51 GMT",
"version": "v1"
}
] | 2021-11-05 | [
[
"Kodera",
"Sachiko",
""
],
[
"Rashed",
"Essam A.",
""
],
[
"Hirata",
"Akimasa",
""
]
] | During epidemics, estimation of the effective reproduction number (ERN) associated with infectious disease is a challenging topic for policy development and medical resource management. There is still an open question about the dominant factors to characterize in corona virus disease 2019 (COVID-19), although recent st... |
1701.05619 | Yani Zhao | Yani Zhao, Mateusz Chwastyk and Marek Cieplak | Topological transformations in proteins: effects of heating and
proximity of an interface | 7 figures | Scientific Reports 7, 39851 (2017) | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Using a structure-based coarse-grained model of proteins, we study the
mechanism of unfolding of knotted proteins through heating. We find that the
dominant mechanisms of unfolding depend on the temperature applied and are
generally distinct from those identified for folding at its optimal
temperature. In particular,... | [
{
"created": "Thu, 19 Jan 2017 22:05:03 GMT",
"version": "v1"
}
] | 2017-01-23 | [
[
"Zhao",
"Yani",
""
],
[
"Chwastyk",
"Mateusz",
""
],
[
"Cieplak",
"Marek",
""
]
] | Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally distinct from those identified for folding at its optimal temperature. In particular, f... |
q-bio/0604025 | Alexei Koulakov | A. Koulakov, A. Gelperin, and D. Rinberg | Combinatorial on/off Model for Olfactory Coding | null | null | null | null | q-bio.NC | null | We present a model for olfactory coding based on spatial representation of
glomerular responses. In this model distinct odorants activate specific subsets
of glomeruli, dependent upon the odorant's chemical identity and concentration.
The glomerular response specificities are understood statistically, based on
experi... | [
{
"created": "Wed, 19 Apr 2006 16:22:45 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Koulakov",
"A.",
""
],
[
"Gelperin",
"A.",
""
],
[
"Rinberg",
"D.",
""
]
] | We present a model for olfactory coding based on spatial representation of glomerular responses. In this model distinct odorants activate specific subsets of glomeruli, dependent upon the odorant's chemical identity and concentration. The glomerular response specificities are understood statistically, based on experime... |
2006.06109 | Jona Carmon | Jona Carmon, Moritz Bammel, Peter Brugger, Bigna Lenggenhager | Uncertainty promotes neuroreductionism: A behavioral online study on
folk psychological causal inference from neuroimaging data | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Introduction. Increased efforts in neuroscience try to understand mental
disorders as brain disorders. In the present study we investigate how common a
neuroreductionist inclination is among highly educated people. In particular,
we shed light on implicit presuppositions of mental disorders little is known
about in t... | [
{
"created": "Wed, 10 Jun 2020 23:28:00 GMT",
"version": "v1"
},
{
"created": "Wed, 26 May 2021 13:55:57 GMT",
"version": "v2"
}
] | 2021-05-27 | [
[
"Carmon",
"Jona",
""
],
[
"Bammel",
"Moritz",
""
],
[
"Brugger",
"Peter",
""
],
[
"Lenggenhager",
"Bigna",
""
]
] | Introduction. Increased efforts in neuroscience try to understand mental disorders as brain disorders. In the present study we investigate how common a neuroreductionist inclination is among highly educated people. In particular, we shed light on implicit presuppositions of mental disorders little is known about in the... |
1805.11081 | Emma Towlson | Emma K. Towlson, Petra E. Vertes, Gang Yan, Yee Lian Chew, Denise S.
Walker, William R. Schafer, and Albert-Laszlo Barabasi | Caenorhabditis elegans and the network control framework - FAQs | 19 pages, 5 figures, 1 table | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Control is essential to the functioning of any neural system. Indeed, under
healthy conditions the brain must be able to continuously maintain a tight
functional control between the system's inputs and outputs. One may therefore
hypothesise that the brain's wiring is predetermined by the need to maintain
control acro... | [
{
"created": "Mon, 28 May 2018 17:49:12 GMT",
"version": "v1"
}
] | 2018-05-29 | [
[
"Towlson",
"Emma K.",
""
],
[
"Vertes",
"Petra E.",
""
],
[
"Yan",
"Gang",
""
],
[
"Chew",
"Yee Lian",
""
],
[
"Walker",
"Denise S.",
""
],
[
"Schafer",
"William R.",
""
],
[
"Barabasi",
"Albert-Laszlo",
""... | Control is essential to the functioning of any neural system. Indeed, under healthy conditions the brain must be able to continuously maintain a tight functional control between the system's inputs and outputs. One may therefore hypothesise that the brain's wiring is predetermined by the need to maintain control across... |
1309.7405 | Liane Gabora | Liane Gabora and Patrick Colgan | A Model of the Mechanisms Underlying Exploratory Behaviour | 17 pages | In S. Wilson & J. A. Meyer (Eds.), Proceedings of the First
International Conference on the Simulation of Adaptive Behavior (pp.
475-484). Cambridge, MA: MIT Press. (1990) | null | null | q-bio.PE cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A model of the mechanisms underlying exploratory behaviour, based on
empirical research and refined using a computer simulation, is presented. The
behaviour of killifish from two lakes, one with killifish predators and one
without, was compared in the laboratory. Plotting average activity in a novel
environment versu... | [
{
"created": "Sat, 28 Sep 2013 01:57:54 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Jul 2019 20:09:19 GMT",
"version": "v2"
},
{
"created": "Tue, 9 Jul 2019 20:01:08 GMT",
"version": "v3"
}
] | 2019-07-11 | [
[
"Gabora",
"Liane",
""
],
[
"Colgan",
"Patrick",
""
]
] | A model of the mechanisms underlying exploratory behaviour, based on empirical research and refined using a computer simulation, is presented. The behaviour of killifish from two lakes, one with killifish predators and one without, was compared in the laboratory. Plotting average activity in a novel environment versus ... |
2011.03419 | Isabelle Landrieu | Francesco Bosica (TU/e), Sebastian Andrei (TU/e), Jo\~ao Filipe Neves
(ERL 9002 - BSI, RID-AGE), Peter Brandt, Anders Gunnarsson, Isabelle Landrieu
(ERL 9002 - BSI, RID-AGE), Christian Ottmann (TU/e), Gavin O'Mahony | Design Of Drug-Like Protein-Protein Interaction Stabilizers Guided By
Chelation-Controlled Bioactive Conformation Stabilization | null | Chemistry - A European Journal, Wiley-VCH Verlag, 2020, 26 (31),
pp.7131-7139 | 10.1002/chem.202001608 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The protein-protein interactions (PPIs) of 14-3-3 proteins are a model system
for studying PPI stabilization. The complex natural product Fusicoccin A
stabilizes many 14-3-3 PPIs but is not amenable for use in SAR studies,
motivating the search for more drug-like chemical matter. However, drug-like
14-3-3 PPI stabili... | [
{
"created": "Fri, 6 Nov 2020 15:12:02 GMT",
"version": "v1"
}
] | 2020-11-09 | [
[
"Bosica",
"Francesco",
"",
"TU/e"
],
[
"Andrei",
"Sebastian",
"",
"TU/e"
],
[
"Neves",
"João Filipe",
"",
"ERL 9002 - BSI, RID-AGE"
],
[
"Brandt",
"Peter",
"",
"ERL 9002 - BSI, RID-AGE"
],
[
"Gunnarsson",
"Anders",
"",
... | The protein-protein interactions (PPIs) of 14-3-3 proteins are a model system for studying PPI stabilization. The complex natural product Fusicoccin A stabilizes many 14-3-3 PPIs but is not amenable for use in SAR studies, motivating the search for more drug-like chemical matter. However, drug-like 14-3-3 PPI stabilize... |
1802.10131 | Christoph Bauermeister | Christoph Bauermeister, Hanna Keren, Jochen Braun | Broadly heterogeneous network topology begets order-based representation
by privileged neurons | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How spiking activity reverberates through neuronal networks, how evoked and
spontaneous activity interact and blend, and how the combined activities
represent external stimulation are pivotal questions in neuroscience. We
simulated minimal models of unstructured spiking networks in silico, asking
whether and how gent... | [
{
"created": "Tue, 27 Feb 2018 19:36:05 GMT",
"version": "v1"
}
] | 2018-03-01 | [
[
"Bauermeister",
"Christoph",
""
],
[
"Keren",
"Hanna",
""
],
[
"Braun",
"Jochen",
""
]
] | How spiking activity reverberates through neuronal networks, how evoked and spontaneous activity interact and blend, and how the combined activities represent external stimulation are pivotal questions in neuroscience. We simulated minimal models of unstructured spiking networks in silico, asking whether and how gentle... |
1510.06629 | Gard Spreemann | Gard Spreemann, Benjamin Dunn, Magnus Bakke Botnan, Nils A. Baas | Using persistent homology to reveal hidden information in neural data | null | null | null | null | q-bio.NC math.AT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a method, based on persistent homology, to uncover topological
properties of a priori unknown covariates of neuron activity. Our input data
consist of spike train measurements of a set of neurons of interest, a
candidate list of the known stimuli that govern neuron activity, and the
corresponding state of ... | [
{
"created": "Thu, 22 Oct 2015 13:57:03 GMT",
"version": "v1"
}
] | 2015-10-23 | [
[
"Spreemann",
"Gard",
""
],
[
"Dunn",
"Benjamin",
""
],
[
"Botnan",
"Magnus Bakke",
""
],
[
"Baas",
"Nils A.",
""
]
] | We propose a method, based on persistent homology, to uncover topological properties of a priori unknown covariates of neuron activity. Our input data consist of spike train measurements of a set of neurons of interest, a candidate list of the known stimuli that govern neuron activity, and the corresponding state of th... |
2406.02610 | Li Wang | Li Wang, Xiangzheng Fu, Jiahao Yang, Xinyi Zhang, Xiucai Ye, Yiping
Liu, Tetsuya Sakurai, and Xiangxiang Zeng | MoFormer: Multi-objective Antimicrobial Peptide Generation Based on
Conditional Transformer Joint Multi-modal Fusion Descriptor | null | null | null | null | q-bio.QM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Deep learning holds a big promise for optimizing existing peptides with more
desirable properties, a critical step towards accelerating new drug discovery.
Despite the recent emergence of several optimized Antimicrobial peptides(AMP)
generation methods, multi-objective optimizations remain still quite
challenging for... | [
{
"created": "Mon, 3 Jun 2024 07:17:18 GMT",
"version": "v1"
}
] | 2024-06-06 | [
[
"Wang",
"Li",
""
],
[
"Fu",
"Xiangzheng",
""
],
[
"Yang",
"Jiahao",
""
],
[
"Zhang",
"Xinyi",
""
],
[
"Ye",
"Xiucai",
""
],
[
"Liu",
"Yiping",
""
],
[
"Sakurai",
"Tetsuya",
""
],
[
"Zeng",
"Xian... | Deep learning holds a big promise for optimizing existing peptides with more desirable properties, a critical step towards accelerating new drug discovery. Despite the recent emergence of several optimized Antimicrobial peptides(AMP) generation methods, multi-objective optimizations remain still quite challenging for t... |
2301.09565 | Mark van Rossum | Maxime Girard, Jiamu Jiang, Mark CW van Rossum | Estimating the energy requirements for long term memory formation | 7 pages, 1 figure | null | null | null | q-bio.NC cs.LG cs.NE | http://creativecommons.org/licenses/by/4.0/ | Brains consume metabolic energy to process information, but also to store
memories. The energy required for memory formation can be substantial, for
instance in fruit flies memory formation leads to a shorter lifespan upon
subsequent starvation (Mery and Kawecki, 2005). Here we estimate that the
energy required corre... | [
{
"created": "Mon, 16 Jan 2023 13:02:22 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Feb 2023 11:29:32 GMT",
"version": "v2"
}
] | 2023-02-09 | [
[
"Girard",
"Maxime",
""
],
[
"Jiang",
"Jiamu",
""
],
[
"van Rossum",
"Mark CW",
""
]
] | Brains consume metabolic energy to process information, but also to store memories. The energy required for memory formation can be substantial, for instance in fruit flies memory formation leads to a shorter lifespan upon subsequent starvation (Mery and Kawecki, 2005). Here we estimate that the energy required corresp... |
2005.11279 | Eric Ngondiep | Eric Ngondiep | An efficient explicit approach for predicting the Covid-19 spreading
with undetected infectious: The case of Cameroon | 26 pages, 11 figures, 11 tables | null | null | null | q-bio.PE cs.NA math.NA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper considers an explicit numerical scheme for solving the
mathematical model of the propagation of Covid-19 epidemic with undetected
infectious cases. We analyze the stability and convergence rate of the new
approach in $L^{\infty}$-norm. The proposed method is less time consuming.
Furthermore, the method is ... | [
{
"created": "Thu, 21 May 2020 05:37:57 GMT",
"version": "v1"
},
{
"created": "Tue, 26 May 2020 05:09:52 GMT",
"version": "v2"
}
] | 2020-05-27 | [
[
"Ngondiep",
"Eric",
""
]
] | This paper considers an explicit numerical scheme for solving the mathematical model of the propagation of Covid-19 epidemic with undetected infectious cases. We analyze the stability and convergence rate of the new approach in $L^{\infty}$-norm. The proposed method is less time consuming. Furthermore, the method is st... |
2310.00139 | Youssef Kora | Youssef Kora and Christoph Simon | Coarse-graining and criticality in the human connectome | 11 pages, 11 figures | null | null | null | q-bio.NC nlin.AO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the face of the stupefying complexity of the human brain, network analysis
is a most useful tool that allows one to greatly simplify the problem,
typically by approximating the billions of neurons comprising the brain by
means of a coarse-grained picture with a practicable number of nodes. But even
such relatively... | [
{
"created": "Fri, 29 Sep 2023 20:57:14 GMT",
"version": "v1"
}
] | 2023-10-03 | [
[
"Kora",
"Youssef",
""
],
[
"Simon",
"Christoph",
""
]
] | In the face of the stupefying complexity of the human brain, network analysis is a most useful tool that allows one to greatly simplify the problem, typically by approximating the billions of neurons comprising the brain by means of a coarse-grained picture with a practicable number of nodes. But even such relatively s... |
2110.05574 | Andreas K\"uhnapfel | Andreas K\"uhnapfel, Katrin Horn, Ulrike Klotz, Michael Kiehntopf,
Maciej Rosolowski, Markus Loeffler, Peter Ahnert, Norbert Suttorp, Martin
Witzenrath, Markus Scholz | Genetic Regulation of Cytokine Response in Patients with Acute
Community-acquired Pneumonia | null | null | null | null | q-bio.QM stat.AP | http://creativecommons.org/licenses/by/4.0/ | Background: Community-acquired pneumonia (CAP) is an acute disease condition
with a high risk of rapid deteriorations. We analysed the influence of genetics
on cytokine regulation to obtain a better understanding of patient's
heterogeneity. Methods: For up to N=389 genotyped participants of the PROGRESS
study of hosp... | [
{
"created": "Mon, 11 Oct 2021 19:32:43 GMT",
"version": "v1"
}
] | 2021-10-13 | [
[
"Kühnapfel",
"Andreas",
""
],
[
"Horn",
"Katrin",
""
],
[
"Klotz",
"Ulrike",
""
],
[
"Kiehntopf",
"Michael",
""
],
[
"Rosolowski",
"Maciej",
""
],
[
"Loeffler",
"Markus",
""
],
[
"Ahnert",
"Peter",
""
],
... | Background: Community-acquired pneumonia (CAP) is an acute disease condition with a high risk of rapid deteriorations. We analysed the influence of genetics on cytokine regulation to obtain a better understanding of patient's heterogeneity. Methods: For up to N=389 genotyped participants of the PROGRESS study of hospit... |
1909.04557 | Iain Moyles | Iain R Moyles, John G. Donohue, Andrew C. Fowler | Quasi-steady uptake and bacterial community assembly in a mathematical
model of soil-phosphorus mobility | null | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We mathematically model the uptake of phosphorus by a soil community
consisting of a plant and two bacterial groups: copiotrophs and oligotrophs.
Four equilibrium states emerge, one for each of the species monopolising the
resource and dominating the community and one with coexistence of all species.
We show that the... | [
{
"created": "Tue, 10 Sep 2019 15:08:06 GMT",
"version": "v1"
},
{
"created": "Mon, 26 Oct 2020 19:18:52 GMT",
"version": "v2"
}
] | 2020-10-28 | [
[
"Moyles",
"Iain R",
""
],
[
"Donohue",
"John G.",
""
],
[
"Fowler",
"Andrew C.",
""
]
] | We mathematically model the uptake of phosphorus by a soil community consisting of a plant and two bacterial groups: copiotrophs and oligotrophs. Four equilibrium states emerge, one for each of the species monopolising the resource and dominating the community and one with coexistence of all species. We show that the d... |
2008.07183 | Adam Griffin | Adam Griffin and Simon E.F. Spencer and Gareth O. Roberts | An epidemic model for an evolving pathogen with strain-dependent
immunity | 34 pages, 7 figures, in review | null | null | null | q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Between pandemics, the influenza virus exhibits periods of incremental
evolution via a process known as antigenic drift. This process gives rise to a
sequence of strains of the pathogen that are continuously replaced by newer
strains, preventing a build up of immunity in the host population. In this
paper, a parsimon... | [
{
"created": "Mon, 17 Aug 2020 09:53:54 GMT",
"version": "v1"
}
] | 2020-08-18 | [
[
"Griffin",
"Adam",
""
],
[
"Spencer",
"Simon E. F.",
""
],
[
"Roberts",
"Gareth O.",
""
]
] | Between pandemics, the influenza virus exhibits periods of incremental evolution via a process known as antigenic drift. This process gives rise to a sequence of strains of the pathogen that are continuously replaced by newer strains, preventing a build up of immunity in the host population. In this paper, a parsimonio... |
2106.05440 | Estari Mamidala Dr | Estari Mamidalaa, Rakesh Davella, Swapna Gurrapu, Munipally Praveen
Kumar, Abhiav | In silico Prediction of Mozenavir as potential drug for SARS-CoV-2
infection via Binding Multiple Drug Targets | 32 pages, 11 figures, 2 tables | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Since the epidemic began in November 2019, no viable medicine against
SARS-CoV-2 has been discovered. The typical medication discovery strategy
requires several years of rigorous research and development as well as a
significant financial commitment, which is not feasible in the face of the
current epidemic. Through ... | [
{
"created": "Thu, 10 Jun 2021 00:43:23 GMT",
"version": "v1"
}
] | 2021-06-11 | [
[
"Mamidalaa",
"Estari",
""
],
[
"Davella",
"Rakesh",
""
],
[
"Gurrapu",
"Swapna",
""
],
[
"Kumar",
"Munipally Praveen",
""
],
[
"Abhiav",
"",
""
]
] | Since the epidemic began in November 2019, no viable medicine against SARS-CoV-2 has been discovered. The typical medication discovery strategy requires several years of rigorous research and development as well as a significant financial commitment, which is not feasible in the face of the current epidemic. Through mo... |
q-bio/0606008 | Indranil Mitra Mr | Indranil Mitra, Sisir Roy | Relevance of Quantum Mechanics in Circuit Implementation of Ion channels
in Brain Dynamics | 12 pages, Submitted to Physical Rev. E | null | null | PACS No.:87.10.+e | q-bio.NC quant-ph | null | With an increasing amount of experimental evidence pouring in from
neurobiological investigations, it is quite appropriate to study viable
reductionist models which may explain some of the features of brain activities.
It is now quite well known that the Hodgkin-Huxley (HH) Model has been quite
successful in explaini... | [
{
"created": "Thu, 8 Jun 2006 20:59:34 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Mitra",
"Indranil",
""
],
[
"Roy",
"Sisir",
""
]
] | With an increasing amount of experimental evidence pouring in from neurobiological investigations, it is quite appropriate to study viable reductionist models which may explain some of the features of brain activities. It is now quite well known that the Hodgkin-Huxley (HH) Model has been quite successful in explaining... |
0803.3717 | Claudiu Giuraniuc | R. Blossey and C. V. Giuraniuc | Mean-field vs. stochastic models for transcriptional regulation | null | Physical Review E 78, 031909 (2008) | 10.1103/PhysRevE.78.031909 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a minimal model description for the dynamics of transcriptional
regulatory networks. It is studied within a mean-field approximation, i.e., by
deterministic ode's representing the reaction kinetics, and by stochastic
simulations employing the Gillespie algorithm. We elucidate the different
results both a... | [
{
"created": "Wed, 26 Mar 2008 12:39:19 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Apr 2008 13:52:54 GMT",
"version": "v2"
},
{
"created": "Wed, 20 Aug 2008 11:08:34 GMT",
"version": "v3"
}
] | 2009-11-13 | [
[
"Blossey",
"R.",
""
],
[
"Giuraniuc",
"C. V.",
""
]
] | We introduce a minimal model description for the dynamics of transcriptional regulatory networks. It is studied within a mean-field approximation, i.e., by deterministic ode's representing the reaction kinetics, and by stochastic simulations employing the Gillespie algorithm. We elucidate the different results both app... |
1010.1866 | Jakub Truszkowski | Daniel G. Brown and Jakub Truszkowski | Fast error-tolerant quartet phylogeny algorithms | null | null | null | null | q-bio.PE cs.CE cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present an algorithm for phylogenetic reconstruction using quartets that
returns the correct topology for $n$ taxa in $O(n \log n)$ time with high
probability, in a probabilistic model where a quartet is not consistent with
the true topology of the tree with constant probability, independent of other
quartets. Our... | [
{
"created": "Sat, 9 Oct 2010 19:16:55 GMT",
"version": "v1"
}
] | 2010-10-12 | [
[
"Brown",
"Daniel G.",
""
],
[
"Truszkowski",
"Jakub",
""
]
] | We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true topology of the tree with constant probability, independent of other quartets. Our i... |
1307.5684 | Lucas Paletta | Jason Satel, Ross Story, Matthew D. Hilchey, Zhiguo Wang and Raymond
M. Klein | Using a Dynamic Neural Field Model to Explore a Direct Collicular
Inhibition Account of Inhibition of Return | null | null | null | ISACS/2013/01 | q-bio.NC cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When the interval between a transient ash of light (a "cue") and a second
visual response signal (a "target") exceeds at least 200ms, responding is
slowest in the direction indicated by the first signal. This phenomenon is
commonly referred to as inhibition of return (IOR). The dynamic neural field
model (DNF) has pr... | [
{
"created": "Mon, 22 Jul 2013 12:47:18 GMT",
"version": "v1"
}
] | 2013-07-23 | [
[
"Satel",
"Jason",
""
],
[
"Story",
"Ross",
""
],
[
"Hilchey",
"Matthew D.",
""
],
[
"Wang",
"Zhiguo",
""
],
[
"Klein",
"Raymond M.",
""
]
] | When the interval between a transient ash of light (a "cue") and a second visual response signal (a "target") exceeds at least 200ms, responding is slowest in the direction indicated by the first signal. This phenomenon is commonly referred to as inhibition of return (IOR). The dynamic neural field model (DNF) has prov... |
1912.06207 | Hidenori Tanaka | Hidenori Tanaka, Aran Nayebi, Niru Maheswaranathan, Lane McIntosh,
Stephen A. Baccus, Surya Ganguli | From deep learning to mechanistic understanding in neuroscience: the
structure of retinal prediction | null | Neural Information Processing Systems (NeurIPS), 2019 | null | null | q-bio.NC cs.LG physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, deep feedforward neural networks have achieved considerable success
in modeling biological sensory processing, in terms of reproducing the
input-output map of sensory neurons. However, such models raise profound
questions about the very nature of explanation in neuroscience. Are we simply
replacing one comp... | [
{
"created": "Thu, 12 Dec 2019 20:54:08 GMT",
"version": "v1"
}
] | 2019-12-16 | [
[
"Tanaka",
"Hidenori",
""
],
[
"Nayebi",
"Aran",
""
],
[
"Maheswaranathan",
"Niru",
""
],
[
"McIntosh",
"Lane",
""
],
[
"Baccus",
"Stephen A.",
""
],
[
"Ganguli",
"Surya",
""
]
] | Recently, deep feedforward neural networks have achieved considerable success in modeling biological sensory processing, in terms of reproducing the input-output map of sensory neurons. However, such models raise profound questions about the very nature of explanation in neuroscience. Are we simply replacing one comple... |
2205.10912 | Diksha Gupta | Diksha Gupta and Carlos D. Brody | Limitations of a proposed correction for slow drifts in decision
criterion | 18 pages, 4 figures | null | null | null | q-bio.NC cs.LG cs.NE q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Trial history biases in decision-making tasks are thought to reflect
systematic updates of decision variables, therefore their precise nature
informs conclusions about underlying heuristic strategies and learning
processes. However, random drifts in decision variables can corrupt this
inference by mimicking the signa... | [
{
"created": "Sun, 22 May 2022 19:33:19 GMT",
"version": "v1"
}
] | 2022-05-24 | [
[
"Gupta",
"Diksha",
""
],
[
"Brody",
"Carlos D.",
""
]
] | Trial history biases in decision-making tasks are thought to reflect systematic updates of decision variables, therefore their precise nature informs conclusions about underlying heuristic strategies and learning processes. However, random drifts in decision variables can corrupt this inference by mimicking the signatu... |
1304.7496 | Nabanita Dasgupta-Schubert | Omar S. Castillo Baltasar, Nabanita Dasgupta-Schubert, Christian
Schubert | A Systems Model of the Eco-physiological Response of Plants to
Environmental Heavy Metal Concentrations | 33 pages, 12 figures. 1 table | Published in JOURNAL OF ENVIRONMENTAL STATISTICS, volume 4, issue
10, page 1, April 2013 | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ecophysiological response of plants to environmental heavy metal stress
is indicated by the profile of its tissue HM concentrations (Cp) versus the
concentration of the HM in the substrate (Cs). We report a systems biology
approach to the modelling of the Cp- Cs profile using as loose analogy, the
Verhulst model ... | [
{
"created": "Sun, 28 Apr 2013 18:45:45 GMT",
"version": "v1"
}
] | 2013-04-30 | [
[
"Baltasar",
"Omar S. Castillo",
""
],
[
"Dasgupta-Schubert",
"Nabanita",
""
],
[
"Schubert",
"Christian",
""
]
] | The ecophysiological response of plants to environmental heavy metal stress is indicated by the profile of its tissue HM concentrations (Cp) versus the concentration of the HM in the substrate (Cs). We report a systems biology approach to the modelling of the Cp- Cs profile using as loose analogy, the Verhulst model of... |
2305.01520 | Namkyeong Lee | Namkyeong Lee, Dongmin Hyun, Gyoung S. Na, Sungwon Kim, Junseok Lee,
Chanyoung Park | Conditional Graph Information Bottleneck for Molecular Relational
Learning | ICML 2023 | null | null | null | q-bio.MN cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular relational learning, whose goal is to learn the interaction
behavior between molecular pairs, got a surge of interest in molecular sciences
due to its wide range of applications. Recently, graph neural networks have
recently shown great success in molecular relational learning by modeling a
molecule as a gr... | [
{
"created": "Sat, 29 Apr 2023 01:17:43 GMT",
"version": "v1"
},
{
"created": "Sun, 9 Jul 2023 23:30:46 GMT",
"version": "v2"
}
] | 2023-07-11 | [
[
"Lee",
"Namkyeong",
""
],
[
"Hyun",
"Dongmin",
""
],
[
"Na",
"Gyoung S.",
""
],
[
"Kim",
"Sungwon",
""
],
[
"Lee",
"Junseok",
""
],
[
"Park",
"Chanyoung",
""
]
] | Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a grap... |
1604.02467 | Fabio Vandin | Tommy Hansen, Fabio Vandin | Finding Mutated Subnetworks Associated with Survival in Cancer | This paper was selected for oral presentation at RECOMB 2016 and an
abstract is published in the conference proceedings | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Next-generation sequencing technologies allow the measurement of somatic
mutations in a large number of patients from the same cancer type. One of the
main goals in analyzing these mutations is the identification of mutations
associated with clinical parameters, such as survival time. This goal is
hindered by the gen... | [
{
"created": "Fri, 8 Apr 2016 20:09:07 GMT",
"version": "v1"
},
{
"created": "Sat, 10 Sep 2016 11:25:43 GMT",
"version": "v2"
}
] | 2016-09-13 | [
[
"Hansen",
"Tommy",
""
],
[
"Vandin",
"Fabio",
""
]
] | Next-generation sequencing technologies allow the measurement of somatic mutations in a large number of patients from the same cancer type. One of the main goals in analyzing these mutations is the identification of mutations associated with clinical parameters, such as survival time. This goal is hindered by the genet... |
2404.10869 | Yujiang Wang | Vytene Janiukstyte, Csaba Kozma, Thomas W. Owen, Umair J Chaudhury,
Beate Diehl, Louis Lemieux, John S Duncan, Fergus Rugg-Gunn, Jane de Tisi,
Yujiang Wang, Peter N. Taylor | Alpha rhythm slowing in temporal epilepsy across Scalp EEG and MEG | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | EEG slowing is reported in various neurological disorders including
Alzheimer's, Parkinson's and Epilepsy. Here, we investigate alpha rhythm
slowing in individuals with refractory temporal lobe epilepsy (TLE), compared
to healthy controls, using scalp electroencephalography (EEG) and
magnetoencephalography (MEG).
W... | [
{
"created": "Tue, 16 Apr 2024 19:37:28 GMT",
"version": "v1"
}
] | 2024-04-18 | [
[
"Janiukstyte",
"Vytene",
""
],
[
"Kozma",
"Csaba",
""
],
[
"Owen",
"Thomas W.",
""
],
[
"Chaudhury",
"Umair J",
""
],
[
"Diehl",
"Beate",
""
],
[
"Lemieux",
"Louis",
""
],
[
"Duncan",
"John S",
""
],
[
... | EEG slowing is reported in various neurological disorders including Alzheimer's, Parkinson's and Epilepsy. Here, we investigate alpha rhythm slowing in individuals with refractory temporal lobe epilepsy (TLE), compared to healthy controls, using scalp electroencephalography (EEG) and magnetoencephalography (MEG). We re... |
1704.02342 | Elizaveta Solomonova | Elizaveta Solomonova | Sleep Paralysis: phenomenology, neurophysiology and treatment | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Sleep paralysis is an experience of being temporarily unable to move or talk
during the transitional periods between sleep and wakefulness: at sleep onset
or upon awakening. Feeling of paralysis may be accompanied by a variety of
vivid and intense sensory experiences, including mentation in visual, auditory,
and tact... | [
{
"created": "Fri, 7 Apr 2017 18:33:59 GMT",
"version": "v1"
}
] | 2017-04-11 | [
[
"Solomonova",
"Elizaveta",
""
]
] | Sleep paralysis is an experience of being temporarily unable to move or talk during the transitional periods between sleep and wakefulness: at sleep onset or upon awakening. Feeling of paralysis may be accompanied by a variety of vivid and intense sensory experiences, including mentation in visual, auditory, and tactil... |
1801.09247 | Nikolaos Sfakianakis PhD | Nikolaos Sfakianakis and Aaron Brunk | Stability, convergence, and sensitivity analysis of the Filament Based
Lamellipodium Model and the corresponding FEM | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper focuses on the study of the Filament Based Lamellipodium Model
(FBLM) and the corresponding Finite Element Method (FEM) from a numerical point
of view. We study fundamental numerical properties of the FEM and justify the
further use of the FBLM. We exhibit that the FEM satisfies a timestep stability
condit... | [
{
"created": "Sun, 28 Jan 2018 16:44:07 GMT",
"version": "v1"
}
] | 2018-01-30 | [
[
"Sfakianakis",
"Nikolaos",
""
],
[
"Brunk",
"Aaron",
""
]
] | This paper focuses on the study of the Filament Based Lamellipodium Model (FBLM) and the corresponding Finite Element Method (FEM) from a numerical point of view. We study fundamental numerical properties of the FEM and justify the further use of the FBLM. We exhibit that the FEM satisfies a timestep stability conditio... |
q-bio/0702031 | Tristan Ursell | Tristan Ursell, Kerwyn Huang, Eric Peterson, Rob Phillips | Cooperative Gating and Spatial Organization of Membrane Proteins through
Elastic Interactions | 12 pages, 6 figures, 63 references, submitted to PLoS Computational
Biology | null | 10.1371/journal.pcbi.0030081 | null | q-bio.SC q-bio.QM | null | Biological membranes are elastic media in which the presence of a
transmembrane protein leads to local bilayer deformation. The energetics of
deformation allow two membrane proteins in close proximity to influence each
other's equilibrium conformation via their local deformations, and spatially
organize the proteins ... | [
{
"created": "Wed, 14 Feb 2007 00:19:43 GMT",
"version": "v1"
}
] | 2015-06-26 | [
[
"Ursell",
"Tristan",
""
],
[
"Huang",
"Kerwyn",
""
],
[
"Peterson",
"Eric",
""
],
[
"Phillips",
"Rob",
""
]
] | Biological membranes are elastic media in which the presence of a transmembrane protein leads to local bilayer deformation. The energetics of deformation allow two membrane proteins in close proximity to influence each other's equilibrium conformation via their local deformations, and spatially organize the proteins ba... |
2207.02339 | Hisashi Inaba | Odo Diekmann and Hisashi Inaba | A systematic procedure for incorporating separable static heterogeneity
into compartmental epidemic models | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we show how to modify a compartmental epidemic model, without
changing the dimension, such that separable static heterogeneity is taken into
account. The derivation is based on the Kermack-McKendrick renewal equation.
| [
{
"created": "Tue, 5 Jul 2022 22:11:34 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Nov 2022 23:42:10 GMT",
"version": "v2"
}
] | 2022-11-24 | [
[
"Diekmann",
"Odo",
""
],
[
"Inaba",
"Hisashi",
""
]
] | In this paper, we show how to modify a compartmental epidemic model, without changing the dimension, such that separable static heterogeneity is taken into account. The derivation is based on the Kermack-McKendrick renewal equation. |
2008.02484 | O\u{g}ul Esen | O\u{g}ul Esen, Eduardo Fern\'andez-Saiz, Cristina Sard\'on, Marcin
Zaj\k{a}c | Geometry and solutions of an epidemic SIS model permitting fluctuations
and quantization | null | null | null | null | q-bio.PE math-ph math.MP physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Some recent works reveal that there are models of differential equations for
the mean and variance of infected individuals that reproduce the SIS epidemic
model at some point. This stochastic SIS epidemic model can be interpreted as a
Hamiltonian system, therefore we wondered if it could be geometrically handled
thro... | [
{
"created": "Thu, 6 Aug 2020 07:15:30 GMT",
"version": "v1"
}
] | 2020-08-07 | [
[
"Esen",
"Oğul",
""
],
[
"Fernández-Saiz",
"Eduardo",
""
],
[
"Sardón",
"Cristina",
""
],
[
"Zając",
"Marcin",
""
]
] | Some recent works reveal that there are models of differential equations for the mean and variance of infected individuals that reproduce the SIS epidemic model at some point. This stochastic SIS epidemic model can be interpreted as a Hamiltonian system, therefore we wondered if it could be geometrically handled throug... |
2004.07397 | Gustavo Libotte | Gustavo Barbosa Libotte, Fran S\'ergio Lobato, Gustavo Mendes Platt,
Ant\^onio Jos\'e da Silva Neto | Determination of an Optimal Control Strategy for Vaccine Administration
in COVID-19 Pandemic Treatment | null | null | null | null | q-bio.PE math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During decades, mathematical models have been used to predict the behavior of
physical and biologic systems, and to define strategies aiming the minimization
of the effects regarding different types of diseases. In the present days, the
development of mathematical models to simulate the dynamic behavior of novel
coro... | [
{
"created": "Wed, 15 Apr 2020 23:50:01 GMT",
"version": "v1"
},
{
"created": "Mon, 20 Apr 2020 23:18:32 GMT",
"version": "v2"
}
] | 2020-04-22 | [
[
"Libotte",
"Gustavo Barbosa",
""
],
[
"Lobato",
"Fran Sérgio",
""
],
[
"Platt",
"Gustavo Mendes",
""
],
[
"Neto",
"Antônio José da Silva",
""
]
] | During decades, mathematical models have been used to predict the behavior of physical and biologic systems, and to define strategies aiming the minimization of the effects regarding different types of diseases. In the present days, the development of mathematical models to simulate the dynamic behavior of novel corona... |
q-bio/0607047 | Vadim N. Biktashev | Vadim N. Biktashev, Rebecca Suckley, Yury E. Elkin and Radostin D.
Simitev | Asymptotic analysis and analytical solutions of a model of cardiac
excitation | 43 pages, 10 figures, submitted to Bull Math Biol 2007/04/04 | null | null | null | q-bio.TO | null | We describe an asymptotic approach to gated ionic models of single-cell
cardiac excitability. It has a form essentially different from the Tikhonov
fast-slow form assumed in standard asymptotic reductions of excitable systems.
This is of interest since the standard approaches have been previously found
inadequate to ... | [
{
"created": "Tue, 25 Jul 2006 18:36:21 GMT",
"version": "v1"
},
{
"created": "Mon, 9 Apr 2007 18:53:24 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Biktashev",
"Vadim N.",
""
],
[
"Suckley",
"Rebecca",
""
],
[
"Elkin",
"Yury E.",
""
],
[
"Simitev",
"Radostin D.",
""
]
] | We describe an asymptotic approach to gated ionic models of single-cell cardiac excitability. It has a form essentially different from the Tikhonov fast-slow form assumed in standard asymptotic reductions of excitable systems. This is of interest since the standard approaches have been previously found inadequate to de... |
1511.00083 | Subutai Ahmad | Jeff Hawkins and Subutai Ahmad | Why Neurons Have Thousands of Synapses, A Theory of Sequence Memory in
Neocortex | Submitted for publication | Frontiers in Neural Circuits 10:23 (2016) 1-13 | 10.3389/fncir.2016.00023 | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | Neocortical neurons have thousands of excitatory synapses. It is a mystery
how neurons integrate the input from so many synapses and what kind of
large-scale network behavior this enables. It has been previously proposed that
non-linear properties of dendrites enable neurons to recognize multiple
patterns. In this pa... | [
{
"created": "Sat, 31 Oct 2015 06:03:05 GMT",
"version": "v1"
},
{
"created": "Tue, 1 Dec 2015 21:20:26 GMT",
"version": "v2"
}
] | 2016-04-25 | [
[
"Hawkins",
"Jeff",
""
],
[
"Ahmad",
"Subutai",
""
]
] | Neocortical neurons have thousands of excitatory synapses. It is a mystery how neurons integrate the input from so many synapses and what kind of large-scale network behavior this enables. It has been previously proposed that non-linear properties of dendrites enable neurons to recognize multiple patterns. In this pape... |
2403.14149 | Jaroslav Albert | Jaroslav Albert | Exact analytic expressions for discrete first-passage time probability
distributions in Markov networks | 11 pages, 4 figures | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | The first-passage time (FPT) is the time it takes a system variable to cross
a given boundary for the first time. In the context of Markov networks, the FPT
is the time a random walker takes to reach a particular node (target) by
hopping from one node to another. If the walker pauses at each node for a
period of time... | [
{
"created": "Thu, 21 Mar 2024 05:50:52 GMT",
"version": "v1"
}
] | 2024-03-22 | [
[
"Albert",
"Jaroslav",
""
]
] | The first-passage time (FPT) is the time it takes a system variable to cross a given boundary for the first time. In the context of Markov networks, the FPT is the time a random walker takes to reach a particular node (target) by hopping from one node to another. If the walker pauses at each node for a period of time d... |
1706.06031 | Dmitry Petrov | Dmitry Petrov, Alexander Ivanov, Joshua Faskowitz, Boris Gutman,
Daniel Moyer, Julio Villalon, Neda Jahanshad and Paul Thompson | Evaluating 35 Methods to Generate Structural Connectomes Using Pairwise
Classification | Accepted for MICCAI 2017, 8 pages, 3 figures | null | null | null | q-bio.NC cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There is no consensus on how to construct structural brain networks from
diffusion MRI. How variations in pre-processing steps affect network
reliability and its ability to distinguish subjects remains opaque. In this
work, we address this issue by comparing 35 structural connectome-building
pipelines. We vary diffus... | [
{
"created": "Mon, 19 Jun 2017 16:05:11 GMT",
"version": "v1"
}
] | 2017-06-20 | [
[
"Petrov",
"Dmitry",
""
],
[
"Ivanov",
"Alexander",
""
],
[
"Faskowitz",
"Joshua",
""
],
[
"Gutman",
"Boris",
""
],
[
"Moyer",
"Daniel",
""
],
[
"Villalon",
"Julio",
""
],
[
"Jahanshad",
"Neda",
""
],
[
... | There is no consensus on how to construct structural brain networks from diffusion MRI. How variations in pre-processing steps affect network reliability and its ability to distinguish subjects remains opaque. In this work, we address this issue by comparing 35 structural connectome-building pipelines. We vary diffusio... |
1211.6397 | Jason Graham | Jason M. Graham, Bruce P. Ayati, Sarah A. Holstein, James A. Martin | The Role of Osteocytes in Targeted Bone Remodeling: A Mathematical Model | null | PLoS ONE 2013 May 22; 8(5): e63884 | 10.1371/journal.pone.0063884 | null | q-bio.TO q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Until recently many studies of bone remodeling at the cellular level have
focused on the behavior of mature osteoblasts and osteoclasts, and their
respective precursor cells, with the role of osteocytes and bone lining cells
left largely unexplored. This is particularly true with respect to the
mathematical modeling ... | [
{
"created": "Tue, 27 Nov 2012 19:30:33 GMT",
"version": "v1"
},
{
"created": "Wed, 28 Nov 2012 22:10:16 GMT",
"version": "v2"
},
{
"created": "Tue, 28 May 2013 18:42:20 GMT",
"version": "v3"
}
] | 2013-05-29 | [
[
"Graham",
"Jason M.",
""
],
[
"Ayati",
"Bruce P.",
""
],
[
"Holstein",
"Sarah A.",
""
],
[
"Martin",
"James A.",
""
]
] | Until recently many studies of bone remodeling at the cellular level have focused on the behavior of mature osteoblasts and osteoclasts, and their respective precursor cells, with the role of osteocytes and bone lining cells left largely unexplored. This is particularly true with respect to the mathematical modeling of... |
2310.15206 | Petra Proch\'azkov\'a Schrumpfov\'a | Luk\'a\v{s} Nevos\'ad, Bo\v{z}ena Klodov\'a, David Honys, Radka
Svobodov\'a, Tom\'a\v{s} Ra\v{c}ek and Petra Proch\'azkov\'a Schrumpfov\'a | GOLEM: distribution of Gene regulatOry eLEMents within the plant
promoters | 4 pages, 1 figure | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Motivation: The regulation of gene expression during tissue development is
extremely complex. One of the key regulatory mechanisms of gene expression
involves the recognition of regulatory motifs by various proteins in the
promoter regions of many genes. Localisation of these motifs in proximity to
the transcription ... | [
{
"created": "Mon, 23 Oct 2023 11:49:12 GMT",
"version": "v1"
}
] | 2023-10-25 | [
[
"Nevosád",
"Lukáš",
""
],
[
"Klodová",
"Božena",
""
],
[
"Honys",
"David",
""
],
[
"Svobodová",
"Radka",
""
],
[
"Raček",
"Tomáš",
""
],
[
"Schrumpfová",
"Petra Procházková",
""
]
] | Motivation: The regulation of gene expression during tissue development is extremely complex. One of the key regulatory mechanisms of gene expression involves the recognition of regulatory motifs by various proteins in the promoter regions of many genes. Localisation of these motifs in proximity to the transcription st... |
2008.11718 | Ville-Pekka Sepp\"a | Ville-Pekka Sepp\"a, Javier Gracia-Tabuenca, Anne
Kotaniemi-Syrj\"anen, Kristiina Malmstr\"om, Anton Hult, Anna Pelkonen, Mika
J. M\"akel\"a, Jari Viik, L. Pekka Malmberg | Expiratory variability index (EVI) is associated with asthma risk,
wheeze and lung function in infants with recurrent respiratory symptoms | null | null | null | null | q-bio.QM physics.med-ph | http://creativecommons.org/licenses/by/4.0/ | Recurrent respiratory symptoms are common in infants but the paucity of lung
function tests suitable for routine use in infants is a widely acknowledged
clinical problem. In this study we evaluated tidal breathing variability
(expiratory variability index, EVI) measured at home during sleep using
impedance pneumograp... | [
{
"created": "Wed, 26 Aug 2020 10:05:16 GMT",
"version": "v1"
}
] | 2020-08-28 | [
[
"Seppä",
"Ville-Pekka",
""
],
[
"Gracia-Tabuenca",
"Javier",
""
],
[
"Kotaniemi-Syrjänen",
"Anne",
""
],
[
"Malmström",
"Kristiina",
""
],
[
"Hult",
"Anton",
""
],
[
"Pelkonen",
"Anna",
""
],
[
"Mäkelä",
"Mika ... | Recurrent respiratory symptoms are common in infants but the paucity of lung function tests suitable for routine use in infants is a widely acknowledged clinical problem. In this study we evaluated tidal breathing variability (expiratory variability index, EVI) measured at home during sleep using impedance pneumography... |
2011.03344 | Cathal Ryan Mr. | Cathal Ryan, Christophe Gu\'eret, Donagh Berry, Brian Mac Namee | Can We Detect Mastitis earlier than Farmers? | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The aim of this study was to build a modelling framework that would allow us
to be able to detect mastitis infections before they would normally be found by
farmers through the introduction of machine learning techniques. In the making
of this we created two different modelling framework's, one that works on the
prem... | [
{
"created": "Thu, 5 Nov 2020 14:36:01 GMT",
"version": "v1"
}
] | 2020-11-09 | [
[
"Ryan",
"Cathal",
""
],
[
"Guéret",
"Christophe",
""
],
[
"Berry",
"Donagh",
""
],
[
"Mac Namee",
"Brian",
""
]
] | The aim of this study was to build a modelling framework that would allow us to be able to detect mastitis infections before they would normally be found by farmers through the introduction of machine learning techniques. In the making of this we created two different modelling framework's, one that works on the premis... |
2009.00403 | Ferdinando Insalata | Ferdinando Insalata, Hanne Hoitzing, Juvid Aryaman and Nick S. Jones | Survival of the densest accounts for the expansion of mitochondrial
mutations in ageing | 48 pages, 8 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The expansion of deleted mitochondrial DNA (mtDNA) molecules has been linked
to ageing, particularly in skeletal muscle fibres; its mechanism has remained
unclear for three decades. Previous accounts assigned a replicative advantage
to the deletions, but there is evidence that cells can, instead, selectively
remove d... | [
{
"created": "Tue, 1 Sep 2020 13:13:33 GMT",
"version": "v1"
}
] | 2020-09-02 | [
[
"Insalata",
"Ferdinando",
""
],
[
"Hoitzing",
"Hanne",
""
],
[
"Aryaman",
"Juvid",
""
],
[
"Jones",
"Nick S.",
""
]
] | The expansion of deleted mitochondrial DNA (mtDNA) molecules has been linked to ageing, particularly in skeletal muscle fibres; its mechanism has remained unclear for three decades. Previous accounts assigned a replicative advantage to the deletions, but there is evidence that cells can, instead, selectively remove def... |
1503.00999 | Paul Moore | P.J. Moore | A hierarchical narrative framework for OCD | null | null | null | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper gives an explanatory framework for obsessive-compulsive disorder
(OCD) based on a generative model of cognition. The framework is constructed
using the new concept of a 'formal narrative' which is a sequence of cognitive
states inferred from sense data. First we propose that human cognition uses a
hierarch... | [
{
"created": "Tue, 3 Mar 2015 16:33:04 GMT",
"version": "v1"
}
] | 2015-03-04 | [
[
"Moore",
"P. J.",
""
]
] | This paper gives an explanatory framework for obsessive-compulsive disorder (OCD) based on a generative model of cognition. The framework is constructed using the new concept of a 'formal narrative' which is a sequence of cognitive states inferred from sense data. First we propose that human cognition uses a hierarchy ... |
1509.02507 | Gennadi Glinsky | Gennadi Glinsky | Phenotypic divergence of Homo sapiens is driven by the evolution of
human-specific genomic regulatory networks via two mechanistically distinct
pathways of creation of divergent regulatory DNA sequences | 13 pages; 15 references; 12 tables; 1 figure | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Thousands of candidate human-specific regulatory sequences (HSRS) have been
identified, supporting the hypothesis that unique to human phenotypes result
from human-specific alterations of genomic regulatory networks. Here,
conservation patterns analysis of 18,364 candidate HSRS was carried out based
on definition of ... | [
{
"created": "Tue, 8 Sep 2015 19:27:52 GMT",
"version": "v1"
},
{
"created": "Fri, 30 Oct 2015 18:35:56 GMT",
"version": "v2"
}
] | 2015-11-02 | [
[
"Glinsky",
"Gennadi",
""
]
] | Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Here, conservation patterns analysis of 18,364 candidate HSRS was carried out based on definition of th... |
1904.10399 | Lili Su | Lili Su and Chia-Jung Chang and Nancy Lynch | Spike-Based Winner-Take-All Computation: Fundamental Limits and
Order-Optimal Circuits | null | null | null | null | q-bio.NC cs.DC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Winner-Take-All (WTA) refers to the neural operation that selects a
(typically small) group of neurons from a large neuron pool. It is conjectured
to underlie many of the brain's fundamental computational abilities. However,
not much is known about the robustness of a spike-based WTA network to the
inherent randomnes... | [
{
"created": "Sun, 21 Apr 2019 02:45:09 GMT",
"version": "v1"
}
] | 2019-04-24 | [
[
"Su",
"Lili",
""
],
[
"Chang",
"Chia-Jung",
""
],
[
"Lynch",
"Nancy",
""
]
] | Winner-Take-All (WTA) refers to the neural operation that selects a (typically small) group of neurons from a large neuron pool. It is conjectured to underlie many of the brain's fundamental computational abilities. However, not much is known about the robustness of a spike-based WTA network to the inherent randomness ... |
2005.13618 | Martin Frasch | Aude Castel, Yael Frank, John Feltner, Floyd Karp, Catherine Albright,
Martin G. Frasch | Monitoring fetal electroencephalogram intrapartum: a systematic
literature review | Prospero number: CRD42020147474. 55 pages, 8 figures | Front. Pediatr. 2020 | 10.3389/fped.2020.00584 | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Background: Studies about the feasibility of monitoring fetal
electroencephalogram (fEEG) during labor began in the early 1940s. By the
1970s, clear diagnostic and prognostic benefits from intrapartum fEEG
monitoring were reported, but until today, this monitoring technology has
remained a curiosity.
Objectives: Ou... | [
{
"created": "Wed, 27 May 2020 19:58:31 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Jun 2020 07:22:11 GMT",
"version": "v2"
}
] | 2020-08-11 | [
[
"Castel",
"Aude",
""
],
[
"Frank",
"Yael",
""
],
[
"Feltner",
"John",
""
],
[
"Karp",
"Floyd",
""
],
[
"Albright",
"Catherine",
""
],
[
"Frasch",
"Martin G.",
""
]
] | Background: Studies about the feasibility of monitoring fetal electroencephalogram (fEEG) during labor began in the early 1940s. By the 1970s, clear diagnostic and prognostic benefits from intrapartum fEEG monitoring were reported, but until today, this monitoring technology has remained a curiosity. Objectives: Our go... |
0707.0329 | Mareike Fischer | Mareike Fischer, Mike Steel | Expected Anomalies in the Fossil Record | null | Fischer, M. and Steel, M. (2008). Expected anomalies in the fossil
record. Evolutionary bioinformatics online 4: 61--67 | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The problem of intermediates in the fossil record has been frequently
discussed ever since Darwin. The extent of `gaps' (missing transitional stages)
has been used to argue against gradual evolution from a common ancestor.
Traditionally, gaps have often been explained by the improbability of
fossilization and the dis... | [
{
"created": "Tue, 3 Jul 2007 01:24:43 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Aug 2008 23:50:22 GMT",
"version": "v2"
}
] | 2008-08-27 | [
[
"Fischer",
"Mareike",
""
],
[
"Steel",
"Mike",
""
]
] | The problem of intermediates in the fossil record has been frequently discussed ever since Darwin. The extent of `gaps' (missing transitional stages) has been used to argue against gradual evolution from a common ancestor. Traditionally, gaps have often been explained by the improbability of fossilization and the disco... |
1512.07459 | Steven Kelk | Steven Kelk, Mareike Fischer, Vincent Moulton, Taoyang Wu | Reduction rules for the maximum parsimony distance on phylogenetic trees | Added material on graph minors, MSOL and treewidth | null | null | null | q-bio.PE cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In phylogenetics, distances are often used to measure the incongruence
between a pair of phylogenetic trees that are reconstructed by different
methods or using different regions of genome. Motivated by the maximum
parsimony principle in tree inference, we recently introduced the maximum
parsimony (MP) distance, whic... | [
{
"created": "Wed, 23 Dec 2015 13:07:16 GMT",
"version": "v1"
},
{
"created": "Sat, 30 Apr 2016 09:22:27 GMT",
"version": "v2"
},
{
"created": "Thu, 7 Jul 2016 09:28:18 GMT",
"version": "v3"
}
] | 2016-07-08 | [
[
"Kelk",
"Steven",
""
],
[
"Fischer",
"Mareike",
""
],
[
"Moulton",
"Vincent",
""
],
[
"Wu",
"Taoyang",
""
]
] | In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in tree inference, we recently introduced the maximum parsimony (MP) distance, which ... |
1709.01076 | Daniele Ramazzotti | Daniele Ramazzotti and Alex Graudenzi and Luca De Sano and Marco
Antoniotti and Giulio Caravagna | Learning mutational graphs of individual tumour evolution from
single-cell and multi-region sequencing data | null | null | null | null | q-bio.GN cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background. A large number of algorithms is being developed to reconstruct
evolutionary models of individual tumours from genome sequencing data. Most
methods can analyze multiple samples collected either through bulk multi-region
sequencing experiments or the sequencing of individual cancer cells. However,
rarely th... | [
{
"created": "Mon, 4 Sep 2017 15:35:11 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Mar 2019 23:42:19 GMT",
"version": "v2"
}
] | 2019-03-26 | [
[
"Ramazzotti",
"Daniele",
""
],
[
"Graudenzi",
"Alex",
""
],
[
"De Sano",
"Luca",
""
],
[
"Antoniotti",
"Marco",
""
],
[
"Caravagna",
"Giulio",
""
]
] | Background. A large number of algorithms is being developed to reconstruct evolutionary models of individual tumours from genome sequencing data. Most methods can analyze multiple samples collected either through bulk multi-region sequencing experiments or the sequencing of individual cancer cells. However, rarely the ... |
1812.02870 | Liane Gabora | Liane Gabora and Mike Unrau | The Role of Engagement, Honing, and Mindfulness in Creativity | 22 pages; | in Mullen, C. (Ed.) Creativity under duress in education?
Resistive theories, practices, and actions, Creativity Theory and Action in
Education Vol. 3.(2019) | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As both our external world and inner worlds become more complex, we are faced
with more novel challenges, hardships, and duress. Creative thinking is needed
to provide fresh perspectives and solve new problems.Because creativity can be
conducive to accessing and reliving traumatic memories, emotional scars may be
exa... | [
{
"created": "Fri, 7 Dec 2018 01:55:30 GMT",
"version": "v1"
},
{
"created": "Wed, 13 Mar 2019 21:31:36 GMT",
"version": "v2"
},
{
"created": "Fri, 5 Jul 2019 21:18:11 GMT",
"version": "v3"
}
] | 2019-07-09 | [
[
"Gabora",
"Liane",
""
],
[
"Unrau",
"Mike",
""
]
] | As both our external world and inner worlds become more complex, we are faced with more novel challenges, hardships, and duress. Creative thinking is needed to provide fresh perspectives and solve new problems.Because creativity can be conducive to accessing and reliving traumatic memories, emotional scars may be exace... |
1110.2966 | Irina Manina | I.V. Manina, N.M. Peretolchina, N.S. Saprikina, A.M. Kozlov, I.N.
Mikhaylova, A.Yu.Barishnikov | Experimental Researches of Cutaneous Melanoma Immunotherapy by Antitumor
Cell-Whole GM-CSF-Producing Vaccines | 8 pages, 4 figures; ISSN 1726-9784. Russian Journal of Biotherapy.
/2010.-#3- P.47-50 | Russian Journal of Biotherapy. 3/2010.-#3- P.47-50 | null | null | q-bio.OT | http://creativecommons.org/licenses/publicdomain/ | Various approaches to increase efficiency of antitumor therapy by a
combination of vaccinotherapy, chemotherapy and surgical excision of primary
tumor nodes, and also the comparative analyses of therapeutic and preventive
application of antitumoral vaccines were carried out in melanoma experimental
model. It was post... | [
{
"created": "Wed, 12 Oct 2011 18:32:11 GMT",
"version": "v1"
}
] | 2011-10-14 | [
[
"Manina",
"I. V.",
""
],
[
"Peretolchina",
"N. M.",
""
],
[
"Saprikina",
"N. S.",
""
],
[
"Kozlov",
"A. M.",
""
],
[
"Mikhaylova",
"I. N.",
""
],
[
"Barishnikov",
"A. Yu.",
""
]
] | Various approaches to increase efficiency of antitumor therapy by a combination of vaccinotherapy, chemotherapy and surgical excision of primary tumor nodes, and also the comparative analyses of therapeutic and preventive application of antitumoral vaccines were carried out in melanoma experimental model. It was postul... |
2405.10911 | Riccardo Ravasio | Riccardo Ravasio, Kabir Husain, Constantine G. Evans, Rob Phillips,
Marco Ribezzi, Jack W. Szostak, Arvind Murugan | A minimal scenario for the origin of non-equilibrium order | null | null | null | null | q-bio.PE cond-mat.stat-mech q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Extant life contains numerous non-equilibrium mechanisms to create order not
achievable at equilibrium; it is generally assumed that these mechanisms
evolved because the resulting order was sufficiently beneficial to overcome
associated costs of time and energy. Here, we identify a broad range of
conditions under whi... | [
{
"created": "Fri, 17 May 2024 16:59:19 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Jul 2024 03:50:04 GMT",
"version": "v2"
}
] | 2024-07-25 | [
[
"Ravasio",
"Riccardo",
""
],
[
"Husain",
"Kabir",
""
],
[
"Evans",
"Constantine G.",
""
],
[
"Phillips",
"Rob",
""
],
[
"Ribezzi",
"Marco",
""
],
[
"Szostak",
"Jack W.",
""
],
[
"Murugan",
"Arvind",
""
]
... | Extant life contains numerous non-equilibrium mechanisms to create order not achievable at equilibrium; it is generally assumed that these mechanisms evolved because the resulting order was sufficiently beneficial to overcome associated costs of time and energy. Here, we identify a broad range of conditions under which... |
1909.05660 | Juan Miguel Valverde | Juan Miguel Valverde, Vandad Imani, John D. Lewis, Jussi Tohka | Predicting intelligence based on cortical WM/GM contrast, cortical
thickness and volumetry | Submission to the ABCD Neurocognitive Prediction Challenge at MICCAI
2019 | null | null | null | q-bio.NC cs.LG eess.IV stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a four-layer fully-connected neural network (FNN) for predicting
fluid intelligence scores from T1-weighted MR images for the ABCD-challenge. In
addition to the volumes of brain structures, the FNN uses cortical WM/GM
contrast and cortical thickness at 78 cortical regions. These last two
measurements were ... | [
{
"created": "Mon, 9 Sep 2019 11:53:19 GMT",
"version": "v1"
}
] | 2019-09-13 | [
[
"Valverde",
"Juan Miguel",
""
],
[
"Imani",
"Vandad",
""
],
[
"Lewis",
"John D.",
""
],
[
"Tohka",
"Jussi",
""
]
] | We propose a four-layer fully-connected neural network (FNN) for predicting fluid intelligence scores from T1-weighted MR images for the ABCD-challenge. In addition to the volumes of brain structures, the FNN uses cortical WM/GM contrast and cortical thickness at 78 cortical regions. These last two measurements were de... |
1712.04519 | David Cowburn | Samuel Sparks, Deniz B. Temel, Michael P. Rout, and David Cowburn | Deciphering the 'fuzzy' interaction of FG nucleoporins and transport
factors using SANS | Minor revisions and reformatting | Structure 2018 26 477-84 | 10.1016/j.str.2018.01.010 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The largely intrinsically disordered phenylalanine-glycine-rich nucleoporins
(FG Nups) underline a selectivity mechanism, which enables the rapid
translocation of transport factors (TFs) through the nuclear pore complexes
(NPCs). Conflicting models of NPC transport have assumed that FG Nups undergo
different conforma... | [
{
"created": "Tue, 12 Dec 2017 21:04:30 GMT",
"version": "v1"
},
{
"created": "Wed, 10 Jan 2018 21:31:29 GMT",
"version": "v2"
}
] | 2019-03-14 | [
[
"Sparks",
"Samuel",
""
],
[
"Temel",
"Deniz B.",
""
],
[
"Rout",
"Michael P.",
""
],
[
"Cowburn",
"David",
""
]
] | The largely intrinsically disordered phenylalanine-glycine-rich nucleoporins (FG Nups) underline a selectivity mechanism, which enables the rapid translocation of transport factors (TFs) through the nuclear pore complexes (NPCs). Conflicting models of NPC transport have assumed that FG Nups undergo different conformati... |
q-bio/0401034 | Maximilian Schlosshauer | Maximilian Schlosshauer and David Baker | Realistic protein-protein association rates from a simple diffusional
model neglecting long-range interactions, free energy barriers, and landscape
ruggedness | 9 pages, 5 figures, 1 table. One figure and a few comments added for
clarification | Protein Science (13), 1660-1669 (2004) | null | null | q-bio.BM | null | We develop a simple but rigorous model of protein-protein association
kinetics based on diffusional association on free energy landscapes obtained by
sampling configurations within and surrounding the native complex binding
funnels. Guided by results obtained on exactly solvable model problems, we
transform the probl... | [
{
"created": "Mon, 26 Jan 2004 21:11:21 GMT",
"version": "v1"
},
{
"created": "Mon, 19 Jul 2004 22:16:54 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Schlosshauer",
"Maximilian",
""
],
[
"Baker",
"David",
""
]
] | We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided by results obtained on exactly solvable model problems, we transform the problem... |
1912.09205 | Viktor Stojkoski MSc | Viktor Stojkoski, Marko Karbevski, Zoran Utkovski, Lasko Basnarkov,
Ljupco Kocarev | Evolution of cooperation in networked heterogeneous fluctuating
environments | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fluctuating environments are situations where the spatio-temporal
stochasticity plays a significant role in the evolutionary dynamics. The study
of the evolution of cooperation in these environments typically assumes a
homogeneous, well mixed population, whose constituents are endowed with
identical capabilities. In ... | [
{
"created": "Thu, 19 Dec 2019 14:07:09 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Apr 2020 20:09:07 GMT",
"version": "v2"
},
{
"created": "Tue, 16 Jun 2020 13:19:37 GMT",
"version": "v3"
},
{
"created": "Tue, 9 Mar 2021 16:19:44 GMT",
"version": "v4"
}
] | 2021-03-10 | [
[
"Stojkoski",
"Viktor",
""
],
[
"Karbevski",
"Marko",
""
],
[
"Utkovski",
"Zoran",
""
],
[
"Basnarkov",
"Lasko",
""
],
[
"Kocarev",
"Ljupco",
""
]
] | Fluctuating environments are situations where the spatio-temporal stochasticity plays a significant role in the evolutionary dynamics. The study of the evolution of cooperation in these environments typically assumes a homogeneous, well mixed population, whose constituents are endowed with identical capabilities. In th... |
2002.10804 | Yangsong Zhang | Cunbo Li, Peiyang Li, Yangsong Zhang, Ning Li, Yajing Si, Fali Li,
Dezhong Yao and Peng Xu | Hierarchical emotion-recognition framework based on discriminative brain
neural network topology and ensemble co-decision strategy | null | null | null | null | q-bio.NC eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Brain neural networks characterize various information propagation patterns
for different emotional states. However, the statistical features based on
traditional graph theory may ignore the spacial network difference. To reveal
these inherent spatial features and increase the stability of emotional
recognition, we p... | [
{
"created": "Tue, 25 Feb 2020 11:47:53 GMT",
"version": "v1"
}
] | 2020-02-26 | [
[
"Li",
"Cunbo",
""
],
[
"Li",
"Peiyang",
""
],
[
"Zhang",
"Yangsong",
""
],
[
"Li",
"Ning",
""
],
[
"Si",
"Yajing",
""
],
[
"Li",
"Fali",
""
],
[
"Yao",
"Dezhong",
""
],
[
"Xu",
"Peng",
""
... | Brain neural networks characterize various information propagation patterns for different emotional states. However, the statistical features based on traditional graph theory may ignore the spacial network difference. To reveal these inherent spatial features and increase the stability of emotional recognition, we pro... |
1006.5846 | Vadim N. Biktashev | Vadim N. Biktashev, Irina V. Biktasheva, Narine A. Sarvazyan | Evolution of spiral and scroll waves of excitation in a mathematical
model of ischaemic border zone | 26 pages, 13 figures, appendix and 2 movies, as accepted to PLoS ONE
2011/08/08 | PLoS ONE, 6(9):e24388, 2011 | 10.1371/journal.pone.0024388 | null | q-bio.TO nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Abnormal electrical activity from the boundaries of ischemic cardiac tissue
is recognized as one of the major causes in generation of ischemia-reperfusion
arrhythmias. Here we present theoretical analysis of the waves of electrical
activity that can rise on the boundary of cardiac cell network upon its
recovery from ... | [
{
"created": "Wed, 30 Jun 2010 13:05:00 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Jun 2011 15:31:45 GMT",
"version": "v2"
},
{
"created": "Tue, 23 Aug 2011 06:59:57 GMT",
"version": "v3"
}
] | 2015-05-19 | [
[
"Biktashev",
"Vadim N.",
""
],
[
"Biktasheva",
"Irina V.",
""
],
[
"Sarvazyan",
"Narine A.",
""
]
] | Abnormal electrical activity from the boundaries of ischemic cardiac tissue is recognized as one of the major causes in generation of ischemia-reperfusion arrhythmias. Here we present theoretical analysis of the waves of electrical activity that can rise on the boundary of cardiac cell network upon its recovery from is... |
2003.10086 | Alexander Siegenfeld | Alexander F. Siegenfeld and Yaneer Bar-Yam | Eliminating COVID-19: The Impact of Travel and Timing | null | Communications Physics 3, 204 (2020) | 10.1038/s42005-020-00470-7 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze the spread of COVID-19 by considering the transmission of the
disease among individuals both within and between regions. A set of regions can
be defined as any partition of a population such that travel/social contact
within each region far exceeds that between them. COVID-19 can be eliminated if
the regio... | [
{
"created": "Mon, 23 Mar 2020 05:17:27 GMT",
"version": "v1"
},
{
"created": "Thu, 23 Apr 2020 19:45:40 GMT",
"version": "v2"
}
] | 2020-11-11 | [
[
"Siegenfeld",
"Alexander F.",
""
],
[
"Bar-Yam",
"Yaneer",
""
]
] | We analyze the spread of COVID-19 by considering the transmission of the disease among individuals both within and between regions. A set of regions can be defined as any partition of a population such that travel/social contact within each region far exceeds that between them. COVID-19 can be eliminated if the region-... |
1906.02086 | Harry Dudley | Harry J. Dudley, Zhiyong Jason Ren, and David M. Bortz | Competitive Exclusion in a DAE Model for Microbial Electrolysis Cells | null | null | null | null | q-bio.PE math.CA math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Microbial electrolysis cells (MECs) employ electroactive bacteria to perform
extracellular electron transfer, enabling hydrogen generation from
biodegradable substrates. In previous work, we developed and analyzed a
differential-algebraic equation (DAE) model for MECs. The model resembles a
chemostat with ordinary di... | [
{
"created": "Wed, 5 Jun 2019 15:45:36 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Feb 2020 03:50:15 GMT",
"version": "v2"
},
{
"created": "Mon, 6 Jul 2020 21:32:31 GMT",
"version": "v3"
}
] | 2022-06-03 | [
[
"Dudley",
"Harry J.",
""
],
[
"Ren",
"Zhiyong Jason",
""
],
[
"Bortz",
"David M.",
""
]
] | Microbial electrolysis cells (MECs) employ electroactive bacteria to perform extracellular electron transfer, enabling hydrogen generation from biodegradable substrates. In previous work, we developed and analyzed a differential-algebraic equation (DAE) model for MECs. The model resembles a chemostat with ordinary diff... |
2004.12541 | YangQuan Chen Prof. | Conghui Xu, Yongguang Yu, QuanChen Yang, and Zhenzhen Lu | Forecast analysis of the epidemics trend of COVID-19 in the United
States by a generalized fractional-order SEIR model | null | null | null | null | q-bio.PE math.DS | http://creativecommons.org/licenses/by/4.0/ | In this paper, a generalized fractional-order SEIR model is proposed, denoted
by SEIQRP model, which has a basic guiding significance for the prediction of
the possible outbreak of infectious diseases like COVID-19 and other insect
diseases in the future. Firstly, some qualitative properties of the model are
analyzed... | [
{
"created": "Mon, 27 Apr 2020 01:56:57 GMT",
"version": "v1"
},
{
"created": "Wed, 29 Apr 2020 06:37:47 GMT",
"version": "v2"
}
] | 2020-04-30 | [
[
"Xu",
"Conghui",
""
],
[
"Yu",
"Yongguang",
""
],
[
"Yang",
"QuanChen",
""
],
[
"Lu",
"Zhenzhen",
""
]
] | In this paper, a generalized fractional-order SEIR model is proposed, denoted by SEIQRP model, which has a basic guiding significance for the prediction of the possible outbreak of infectious diseases like COVID-19 and other insect diseases in the future. Firstly, some qualitative properties of the model are analyzed. ... |
2103.05075 | Alex Williams | Alex H. Williams and Scott W. Linderman | Statistical Neuroscience in the Single Trial Limit | 25 pages, 3 figures | null | null | null | q-bio.NC stat.AP | http://creativecommons.org/licenses/by-sa/4.0/ | Individual neurons often produce highly variable responses over nominally
identical trials, reflecting a mixture of intrinsic "noise" and systematic
changes in the animal's cognitive and behavioral state. Disentangling these
sources of variability is of great scientific interest in its own right, but it
is also incre... | [
{
"created": "Mon, 8 Mar 2021 21:08:14 GMT",
"version": "v1"
},
{
"created": "Thu, 4 Nov 2021 19:37:38 GMT",
"version": "v2"
}
] | 2021-11-08 | [
[
"Williams",
"Alex H.",
""
],
[
"Linderman",
"Scott W.",
""
]
] | Individual neurons often produce highly variable responses over nominally identical trials, reflecting a mixture of intrinsic "noise" and systematic changes in the animal's cognitive and behavioral state. Disentangling these sources of variability is of great scientific interest in its own right, but it is also increas... |
1701.00166 | J. Nathan Kutz | Lucas Stolerman, and Pedro Maia, and J. Nathan Kutz | Data-Driven Forecast of Dengue Outbreaks in Brazil: A Critical
Assessment of Climate Conditions for Different Capitals | 29 pages, 12 figures, 8 tables | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Local climate conditions play a major role in the development of the mosquito
population responsible for transmitting Dengue Fever. Since the {\em Aedes
Aegypti} mosquito is also a primary vector for the recent Zika and Chikungunya
epidemics across the Americas, a detailed monitoring of periods with favorable
climate... | [
{
"created": "Sat, 31 Dec 2016 20:55:47 GMT",
"version": "v1"
}
] | 2017-01-03 | [
[
"Stolerman",
"Lucas",
""
],
[
"Maia",
"Pedro",
""
],
[
"Kutz",
"J. Nathan",
""
]
] | Local climate conditions play a major role in the development of the mosquito population responsible for transmitting Dengue Fever. Since the {\em Aedes Aegypti} mosquito is also a primary vector for the recent Zika and Chikungunya epidemics across the Americas, a detailed monitoring of periods with favorable climate c... |
1812.06400 | Sebastian Raschka | Sebastian Raschka | Automated discovery of GPCR bioactive ligands | null | Current Opinion in Structural Biology 2019, 55:17-24 | 10.1016/j.sbi.2019.02.011 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While G-protein coupled receptors (GPCRs) constitute the largest class of
membrane proteins, structures and endogenous ligands of a large portion of
GPCRs remain unknown. Due to the involvement of GPCRs in various signaling
pathways and physiological roles, the identification of endogenous ligands as
well as designin... | [
{
"created": "Sun, 16 Dec 2018 06:00:57 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Mar 2019 03:05:04 GMT",
"version": "v2"
}
] | 2019-03-29 | [
[
"Raschka",
"Sebastian",
""
]
] | While G-protein coupled receptors (GPCRs) constitute the largest class of membrane proteins, structures and endogenous ligands of a large portion of GPCRs remain unknown. Due to the involvement of GPCRs in various signaling pathways and physiological roles, the identification of endogenous ligands as well as designing ... |
1903.04987 | Alexandra Jurczak | E. Krock, A. Jurczak, C.I. Svensson | Pain pathogenesis in rheumatoid arthritis -- what have we learned from
animal models | 33 pages, 3 figures | PAIN 2018 Sep; 159 Suppl:S98-S109 | 10.1097/j.pain.0000000000001333 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by
joint inflammation and joint pain. Much of RA treatment is focused on
suppressing inflammation, with the idea being that if inflammation is
controlled other symptoms, such as pain, will disappear. However, pain is the
most common complaint of... | [
{
"created": "Tue, 12 Mar 2019 15:20:01 GMT",
"version": "v1"
}
] | 2019-03-13 | [
[
"Krock",
"E.",
""
],
[
"Jurczak",
"A.",
""
],
[
"Svensson",
"C. I.",
""
]
] | Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by joint inflammation and joint pain. Much of RA treatment is focused on suppressing inflammation, with the idea being that if inflammation is controlled other symptoms, such as pain, will disappear. However, pain is the most common complaint of R... |
2110.11310 | Ashish B. George | Ashish B. George and Kirill S. Korolev | Ecological landscapes guide the assembly of optimal microbial
communities | null | null | null | null | q-bio.PE q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Assembling optimal microbial communities is key for various applications in
biofuel production, agriculture, and human health. Finding the optimal
community is challenging because the number of possible communities grows
exponentially with the number of species, and so an exhaustive search cannot be
performed even fo... | [
{
"created": "Thu, 21 Oct 2021 17:42:36 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Dec 2021 23:28:52 GMT",
"version": "v2"
}
] | 2021-12-17 | [
[
"George",
"Ashish B.",
""
],
[
"Korolev",
"Kirill S.",
""
]
] | Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for ... |
0905.2935 | Yuriy Pershin | Yuriy V. Pershin and Massimiliano Di Ventra | Experimental demonstration of associative memory with memristive neural
networks | null | Neural Networks 23, 881 (2010) | null | null | q-bio.NC cond-mat.mes-hall q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When someone mentions the name of a known person we immediately recall her
face and possibly many other traits. This is because we possess the so-called
associative memory, that is the ability to correlate different memories to the
same fact or event. Associative memory is such a fundamental and encompassing
human ab... | [
{
"created": "Mon, 18 May 2009 17:16:03 GMT",
"version": "v1"
},
{
"created": "Fri, 18 Sep 2009 16:00:11 GMT",
"version": "v2"
},
{
"created": "Mon, 18 Jan 2010 02:39:52 GMT",
"version": "v3"
}
] | 2010-08-26 | [
[
"Pershin",
"Yuriy V.",
""
],
[
"Di Ventra",
"Massimiliano",
""
]
] | When someone mentions the name of a known person we immediately recall her face and possibly many other traits. This is because we possess the so-called associative memory, that is the ability to correlate different memories to the same fact or event. Associative memory is such a fundamental and encompassing human abil... |
2310.13018 | Ilia Sucholutsky | Ilia Sucholutsky, Lukas Muttenthaler, Adrian Weller, Andi Peng,
Andreea Bobu, Been Kim, Bradley C. Love, Erin Grant, Iris Groen, Jascha
Achterberg, Joshua B. Tenenbaum, Katherine M. Collins, Katherine L. Hermann,
Kerem Oktar, Klaus Greff, Martin N. Hebart, Nori Jacoby, Qiuyi Zhang, Raja
Marjieh, Robert Geirhos,... | Getting aligned on representational alignment | Working paper, changes to be made in upcoming revisions | null | null | null | q-bio.NC cs.AI cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biological and artificial information processing systems form representations
that they can use to categorize, reason, plan, navigate, and make decisions.
How can we measure the extent to which the representations formed by these
diverse systems agree? Do similarities in representations then translate into
similar be... | [
{
"created": "Wed, 18 Oct 2023 17:47:58 GMT",
"version": "v1"
},
{
"created": "Thu, 2 Nov 2023 17:49:18 GMT",
"version": "v2"
}
] | 2023-11-03 | [
[
"Sucholutsky",
"Ilia",
""
],
[
"Muttenthaler",
"Lukas",
""
],
[
"Weller",
"Adrian",
""
],
[
"Peng",
"Andi",
""
],
[
"Bobu",
"Andreea",
""
],
[
"Kim",
"Been",
""
],
[
"Love",
"Bradley C.",
""
],
[
"G... | Biological and artificial information processing systems form representations that they can use to categorize, reason, plan, navigate, and make decisions. How can we measure the extent to which the representations formed by these diverse systems agree? Do similarities in representations then translate into similar beha... |
q-bio/0409034 | Enrico Carlon | Enrico Carlon, Mehdi Lejard Malki, Ralf Blossey | Exons, introns and DNA thermodynamics | 4 pages, 8 figures - Final version as published. See also Phys. Rev.
Focus 15, story 17 | Phys. Rev. Lett. 94, 178101 (2005) | 10.1103/PhysRevLett.94.178101 | null | q-bio.BM cond-mat.stat-mech physics.bio-ph | null | The genes of eukaryotes are characterized by protein coding fragments, the
exons, interrupted by introns, i.e. stretches of DNA which do not carry any
useful information for the protein synthesis. We have analyzed the melting
behavior of randomly selected human cDNA sequences obtained from the genomic
DNA by removing... | [
{
"created": "Wed, 29 Sep 2004 15:48:35 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Sep 2005 08:28:24 GMT",
"version": "v2"
}
] | 2009-11-10 | [
[
"Carlon",
"Enrico",
""
],
[
"Malki",
"Mehdi Lejard",
""
],
[
"Blossey",
"Ralf",
""
]
] | The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of randomly selected human cDNA sequences obtained from the genomic DNA by removing a... |
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