id stringlengths 9 13 | submitter stringlengths 4 48 | authors stringlengths 4 9.62k | title stringlengths 4 343 | comments stringlengths 2 480 ⌀ | journal-ref stringlengths 9 309 ⌀ | doi stringlengths 12 138 ⌀ | report-no stringclasses 277
values | categories stringlengths 8 87 | license stringclasses 9
values | orig_abstract stringlengths 27 3.76k | versions listlengths 1 15 | update_date stringlengths 10 10 | authors_parsed listlengths 1 147 | abstract stringlengths 24 3.75k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0801.0691 | George Tsibidis | George D. Tsibidis | A FRAP model to investigate reaction-diffusion of proteins within a
bounded domain: a theoretical approach | 25 pages. Abstracts Proceedings, The American Society for Cell
Biology, 46th Annual Meeting, December 9-13, 2006, San Diego | Journal of Theoretical Biology 253 (2008) 755-768 | 10.1016/j.jtbi.2008.04.010 | null | q-bio.SC physics.bio-ph q-bio.BM q-bio.QM | null | Temporally and spatially resolved measurements of protein transport inside
cells provide important clues to the functional architecture and dynamics of
biological systems. Fluorescence Recovery After Photobleaching (FRAP) technique
has been used over the past three decades to measure the mobility of
macromolecules an... | [
{
"created": "Fri, 4 Jan 2008 15:33:28 GMT",
"version": "v1"
}
] | 2009-03-04 | [
[
"Tsibidis",
"George D.",
""
]
] | Temporally and spatially resolved measurements of protein transport inside cells provide important clues to the functional architecture and dynamics of biological systems. Fluorescence Recovery After Photobleaching (FRAP) technique has been used over the past three decades to measure the mobility of macromolecules and ... |
1012.1281 | Daniel Hernan Barmak | Marcelo J Otero, Daniel H Barmak, Claudio O Dorso, Hern\'an G Solari,
Mario A Natiello | Modeling Dengue Outbreaks | 18 pages, 6 figures, submited to Mathematical Biosciences | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a dengue model (SEIR) where the human individuals are treated on
an individual basis (IBM) while the mosquito population, produced by an
independent model, is treated by compartments (SEI). We study the spread of
epidemics by the sole action of the mosquito. Exponential, deterministic and
experimental di... | [
{
"created": "Mon, 6 Dec 2010 18:55:28 GMT",
"version": "v1"
}
] | 2015-03-17 | [
[
"Otero",
"Marcelo J",
""
],
[
"Barmak",
"Daniel H",
""
],
[
"Dorso",
"Claudio O",
""
],
[
"Solari",
"Hernán G",
""
],
[
"Natiello",
"Mario A",
""
]
] | We introduce a dengue model (SEIR) where the human individuals are treated on an individual basis (IBM) while the mosquito population, produced by an independent model, is treated by compartments (SEI). We study the spread of epidemics by the sole action of the mosquito. Exponential, deterministic and experimental dist... |
1801.09165 | Vadim Zotev | Vadim Zotev, Raquel Phillips, Masaya Misaki, Chung Ki Wong, Brent E.
Wurfel, Frank Krueger, Matthew Feldner, Jerzy Bodurka | Real-time fMRI neurofeedback training of the amygdala activity with
simultaneous EEG in veterans with combat-related PTSD | 26 pages, 16 figures, to appear in NeuroImage: Clinical | NeuroImage: Clinical 19 (2018) 106-121 | 10.1016/j.nicl.2018.04.010 | null | q-bio.NC physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Posttraumatic stress disorder (PTSD) is a chronic and disabling
neuropsychiatric disorder characterized by insufficient top-down modulation of
the amygdala activity by the prefrontal cortex. Real-time fMRI neurofeedback
(rtfMRI-nf) is an emerging method with potential for modifying the
amygdala-prefrontal interaction... | [
{
"created": "Sun, 28 Jan 2018 01:41:00 GMT",
"version": "v1"
},
{
"created": "Tue, 10 Apr 2018 22:11:15 GMT",
"version": "v2"
}
] | 2018-04-13 | [
[
"Zotev",
"Vadim",
""
],
[
"Phillips",
"Raquel",
""
],
[
"Misaki",
"Masaya",
""
],
[
"Wong",
"Chung Ki",
""
],
[
"Wurfel",
"Brent E.",
""
],
[
"Krueger",
"Frank",
""
],
[
"Feldner",
"Matthew",
""
],
[
... | Posttraumatic stress disorder (PTSD) is a chronic and disabling neuropsychiatric disorder characterized by insufficient top-down modulation of the amygdala activity by the prefrontal cortex. Real-time fMRI neurofeedback (rtfMRI-nf) is an emerging method with potential for modifying the amygdala-prefrontal interactions.... |
1902.07386 | Spyridon Baltsavias | Spyridon Baltsavias, Will Van Treuren, Marcus J. Weber, Jayant
Charthad, Sam Baker, Justin L. Sonnenburg, Amin Arbabian | In Vivo Wireless Sensors for Gut Microbiome Redox Monitoring | Minor revision. Supplementary information included at the end of the
main paper | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A perturbed gut microbiome has recently been linked with multiple disease
processes, yet researchers currently lack tools that can provide in vivo,
quantitative, and real-time insight into these processes and associated
host-microbe interactions. We propose an in vivo wireless implant for
monitoring gastrointestinal ... | [
{
"created": "Wed, 20 Feb 2019 03:19:56 GMT",
"version": "v1"
},
{
"created": "Sun, 28 Jul 2019 01:55:10 GMT",
"version": "v2"
}
] | 2019-07-30 | [
[
"Baltsavias",
"Spyridon",
""
],
[
"Van Treuren",
"Will",
""
],
[
"Weber",
"Marcus J.",
""
],
[
"Charthad",
"Jayant",
""
],
[
"Baker",
"Sam",
""
],
[
"Sonnenburg",
"Justin L.",
""
],
[
"Arbabian",
"Amin",
""... | A perturbed gut microbiome has recently been linked with multiple disease processes, yet researchers currently lack tools that can provide in vivo, quantitative, and real-time insight into these processes and associated host-microbe interactions. We propose an in vivo wireless implant for monitoring gastrointestinal tr... |
2211.00581 | Tetsuhiro Hatakeyama | Tetsuhiro S. Hatakeyama and Ryudo Ohbayashi | Evolutionary Innovation by Polyploidy | 10 pages, 5 figures, 1 tables | null | null | null | q-bio.PE physics.bio-ph | http://creativecommons.org/licenses/by-sa/4.0/ | The preferred conditions for evolutionary innovation is a fundamental
question, but little is known, in part because the question involves rare
events. We focused on the potential role of polyploidy in the evolution of
novel traits. There are two hypotheses regarding the effects of polyploidy on
evolution: Polyploidy... | [
{
"created": "Tue, 1 Nov 2022 16:55:45 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Apr 2024 08:06:16 GMT",
"version": "v2"
}
] | 2024-04-16 | [
[
"Hatakeyama",
"Tetsuhiro S.",
""
],
[
"Ohbayashi",
"Ryudo",
""
]
] | The preferred conditions for evolutionary innovation is a fundamental question, but little is known, in part because the question involves rare events. We focused on the potential role of polyploidy in the evolution of novel traits. There are two hypotheses regarding the effects of polyploidy on evolution: Polyploidy r... |
2407.12897 | Sai Spandana Chintapalli | Sai Spandana Chintapalli, Rongguang Wang, Zhijian Yang, Vasiliki
Tassopoulou, Fanyang Yu, Vishnu Bashyam, Guray Erus, Pratik Chaudhari,
Haochang Shou, Christos Davatzikos | NeuroSynth: MRI-Derived Neuroanatomical Generative Models and Associated
Dataset of 18,000 Samples | null | null | null | null | q-bio.QM stat.ML | http://creativecommons.org/licenses/by/4.0/ | Availability of large and diverse medical datasets is often challenged by
privacy and data sharing restrictions. For successful application of machine
learning techniques for disease diagnosis, prognosis, and precision medicine,
large amounts of data are necessary for model building and optimization. To
help overcome... | [
{
"created": "Wed, 17 Jul 2024 15:33:10 GMT",
"version": "v1"
}
] | 2024-07-19 | [
[
"Chintapalli",
"Sai Spandana",
""
],
[
"Wang",
"Rongguang",
""
],
[
"Yang",
"Zhijian",
""
],
[
"Tassopoulou",
"Vasiliki",
""
],
[
"Yu",
"Fanyang",
""
],
[
"Bashyam",
"Vishnu",
""
],
[
"Erus",
"Guray",
""
... | Availability of large and diverse medical datasets is often challenged by privacy and data sharing restrictions. For successful application of machine learning techniques for disease diagnosis, prognosis, and precision medicine, large amounts of data are necessary for model building and optimization. To help overcome s... |
1501.00197 | Liane Gabora | Liane Gabora and Apara Ranjan | Nuancing the Neuron: A Review of 'The Memory Process: Neuroscientific
and Humanistic Perspectives' by Suzanne Nalbantian, Paul M. Matthews, and
James L. McClelland (Eds.) | null | PsycCritiques: Contemporary Psychology APA Review of Books, 56(39)
(2011) | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Memory Process, edited by Suzanne Nalbantian, Paul M. Matthews, and James
L. McClelland, is an intriguing and well-written book that provides a
groundbreaking overview of diverse approaches to understanding memory that sets
the agenda for an interdisciplinary approach to the topic. Memory has long been
a focus of... | [
{
"created": "Sun, 28 Dec 2014 06:05:36 GMT",
"version": "v1"
}
] | 2015-01-05 | [
[
"Gabora",
"Liane",
""
],
[
"Ranjan",
"Apara",
""
]
] | The Memory Process, edited by Suzanne Nalbantian, Paul M. Matthews, and James L. McClelland, is an intriguing and well-written book that provides a groundbreaking overview of diverse approaches to understanding memory that sets the agenda for an interdisciplinary approach to the topic. Memory has long been a focus of i... |
1703.07996 | Sarwan Kumar | Jagdev Singh Kular and Sarwan Kumar | Quantification of avoidable yield losses in oilseed Brassica caused by
insect pests | null | Journal of Plant Protection Research, 51(1): 38-43 (2011) | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A six year field study was conducted from 2001 2002 to 2006 2007 at Punjab
Agricultural University, Ludhiana, India to study the losses in seed yield of
different Brassica species (B. juncea, B. napus, B. carinata, B. rapa and Eruca
sativa) by the infestation of insect pests. The experiment was conducted in two
diffe... | [
{
"created": "Thu, 23 Mar 2017 10:45:56 GMT",
"version": "v1"
}
] | 2017-03-24 | [
[
"Kular",
"Jagdev Singh",
""
],
[
"Kumar",
"Sarwan",
""
]
] | A six year field study was conducted from 2001 2002 to 2006 2007 at Punjab Agricultural University, Ludhiana, India to study the losses in seed yield of different Brassica species (B. juncea, B. napus, B. carinata, B. rapa and Eruca sativa) by the infestation of insect pests. The experiment was conducted in two differe... |
1309.3075 | Filip Bielejec | Filip Bielejec, Philippe Lemey, Guy Baele, Andrew Rambaut, Marc A
Suchard | Inferring Heterogeneous Evolutionary Processes Through Time: from
sequence substitution to phylogeography | 30 pages, 6 figure, 3 tables | null | null | null | q-bio.PE stat.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular phylogenetic and phylogeographic reconstructions generally assume
time-homogeneous substitution processes. Motivated by computational
convenience, this assumption sacrifices biological realism and offers little
opportunity to uncover the temporal dynamics in evolutionary histories. Here,
we extend and gener... | [
{
"created": "Thu, 12 Sep 2013 09:38:43 GMT",
"version": "v1"
}
] | 2013-09-13 | [
[
"Bielejec",
"Filip",
""
],
[
"Lemey",
"Philippe",
""
],
[
"Baele",
"Guy",
""
],
[
"Rambaut",
"Andrew",
""
],
[
"Suchard",
"Marc A",
""
]
] | Molecular phylogenetic and phylogeographic reconstructions generally assume time-homogeneous substitution processes. Motivated by computational convenience, this assumption sacrifices biological realism and offers little opportunity to uncover the temporal dynamics in evolutionary histories. Here, we extend and general... |
2308.08864 | Dipam Das | Debasish Bhattacharjee, Nabajit Ray, Dipam Das, Hemanta Kumar Sarmah | A discrete-time dynamical model of prey and stage-structured predator
with juvenile hunting incorporating negative effects of prey refuge | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | This paper examines a discrete predator-prey model that incorporates prey
refuge and its detrimental impact on the growth of the prey population. Age
structure is taken into account for predator species. Furthermore, juvenile
hunting as well as prey counter-attack are also considered. This paper provides
a comprehens... | [
{
"created": "Thu, 17 Aug 2023 08:47:03 GMT",
"version": "v1"
}
] | 2023-08-21 | [
[
"Bhattacharjee",
"Debasish",
""
],
[
"Ray",
"Nabajit",
""
],
[
"Das",
"Dipam",
""
],
[
"Sarmah",
"Hemanta Kumar",
""
]
] | This paper examines a discrete predator-prey model that incorporates prey refuge and its detrimental impact on the growth of the prey population. Age structure is taken into account for predator species. Furthermore, juvenile hunting as well as prey counter-attack are also considered. This paper provides a comprehensiv... |
1308.2107 | Peter Wills | Peter R. Wills | Genetic information, physical interpreters and thermodynamics; the
material-informatic basis of biosemiosis | 27 pages, 1 figure, oral presentation at 12th Annual Gatherings in
Biosemiotics, Tartu, Estonia, 2012 | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The sequence of nucleotide bases occurring in an organism's DNA is often
regarded as a codescript for its construction. However, information in a DNA
sequence can only be regarded as a codescript relative to an operational
biochemical machine, which the information constrains in such a way as to
direct the process of... | [
{
"created": "Fri, 9 Aug 2013 12:33:36 GMT",
"version": "v1"
}
] | 2013-08-12 | [
[
"Wills",
"Peter R.",
""
]
] | The sequence of nucleotide bases occurring in an organism's DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical machine, which the information constrains in such a way as to direct the process of c... |
2005.14496 | Biman Bagchi - | Sayantan Mondal, Saumyak Mukherjee and Biman Bagchi | Attainment of Herd Immunity: Mathematical Modelling of Survival Rate | 9 pages, 9 figures, 2 tables | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the influence of the rate of the attainment of herd immunity (HI),
in the absence of an approved vaccine, on the vulnerable population. We
essentially ask the question: how hard the evolution towards the desired herd
immunity could be on the life of the vulnerables? We employ mathematical
modelling (chemical... | [
{
"created": "Fri, 29 May 2020 10:49:06 GMT",
"version": "v1"
}
] | 2020-06-01 | [
[
"Mondal",
"Sayantan",
""
],
[
"Mukherjee",
"Saumyak",
""
],
[
"Bagchi",
"Biman",
""
]
] | We study the influence of the rate of the attainment of herd immunity (HI), in the absence of an approved vaccine, on the vulnerable population. We essentially ask the question: how hard the evolution towards the desired herd immunity could be on the life of the vulnerables? We employ mathematical modelling (chemical n... |
0807.3089 | James Fowler | James H. Fowler, Christopher T. Dawes, Nicholas A. Christakis | Model of Genetic Variation in Human Social Networks | Additional materials related to the paper are available at
http://jhfowler.ucsd.edu | PNAS 106 (6): 1720-1724 (10 February 2009) | 10.1073/pnas.0806746106 | null | q-bio.GN physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Social networks exhibit strikingly systematic patterns across a wide range of
human contexts. While genetic variation accounts for a significant portion of
the variation in many complex social behaviors, the heritability of egocentric
social network attributes is unknown. Here we show that three of these
attributes (... | [
{
"created": "Sat, 19 Jul 2008 13:20:00 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Oct 2008 06:42:27 GMT",
"version": "v2"
},
{
"created": "Tue, 18 Nov 2008 23:07:27 GMT",
"version": "v3"
},
{
"created": "Wed, 11 Feb 2009 16:31:14 GMT",
"version": "v4"
}
] | 2009-02-11 | [
[
"Fowler",
"James H.",
""
],
[
"Dawes",
"Christopher T.",
""
],
[
"Christakis",
"Nicholas A.",
""
]
] | Social networks exhibit strikingly systematic patterns across a wide range of human contexts. While genetic variation accounts for a significant portion of the variation in many complex social behaviors, the heritability of egocentric social network attributes is unknown. Here we show that three of these attributes (in... |
2009.00388 | Michel Destrade | Ilaria Cinelli, Michel Destrade, Peter McHugh, Antonia Trotta, Michael
Gilchrist, Maeve Duffy | Head-to-nerve analysis of electromechanical impairments of diffuse
axonal injury | null | Biomechanics and Modeling in Mechanobiology volume 18, pages
361-374(2019) | 10.1007/s10237-018-1086-8 | null | q-bio.TO cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The aim was to investigate mechanical and functional failure of diffuse
axonal injury (DAI) in nerve bundles following frontal head impacts, by finite
element simulations. Anatomical changes following traumatic brain injury are
simulated at the macroscale by using a 3D head model. Frontal head impacts at
speeds of 2.... | [
{
"created": "Mon, 31 Aug 2020 15:03:18 GMT",
"version": "v1"
}
] | 2020-09-02 | [
[
"Cinelli",
"Ilaria",
""
],
[
"Destrade",
"Michel",
""
],
[
"McHugh",
"Peter",
""
],
[
"Trotta",
"Antonia",
""
],
[
"Gilchrist",
"Michael",
""
],
[
"Duffy",
"Maeve",
""
]
] | The aim was to investigate mechanical and functional failure of diffuse axonal injury (DAI) in nerve bundles following frontal head impacts, by finite element simulations. Anatomical changes following traumatic brain injury are simulated at the macroscale by using a 3D head model. Frontal head impacts at speeds of 2.5-... |
1610.07306 | Anand Bhaskar | Anand Bhaskar, Adel Javanmard, Thomas A. Courtade, David Tse | Novel probabilistic models of spatial genetic ancestry with applications
to stratification correction in genome-wide association studies | Supplementary information included to the main text | null | null | null | q-bio.PE stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genetic variation in human populations is influenced by geographic ancestry
due to spatial locality in historical mating and migration patterns. Spatial
population structure in genetic datasets has been traditionally analyzed using
either model-free algorithms, such as principal components analysis (PCA) and
multidim... | [
{
"created": "Mon, 24 Oct 2016 07:22:43 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Oct 2016 04:55:27 GMT",
"version": "v2"
}
] | 2016-10-26 | [
[
"Bhaskar",
"Anand",
""
],
[
"Javanmard",
"Adel",
""
],
[
"Courtade",
"Thomas A.",
""
],
[
"Tse",
"David",
""
]
] | Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either model-free algorithms, such as principal components analysis (PCA) and multidimen... |
1005.0899 | Thierry Rabilloud | Thierry Rabilloud (BBSI) | Variations on a theme: Changes to electrophoretic separations that can
make a difference | null | Journal of proteomics (2010) epub ahead of print | 10.1016/j.jprot.2010.04.001 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Electrophoretic separations of proteins are widely used in proteomic
analyses, and rely heavily on SDS electrophoresis. This mode of separation is
almost exclusively used when a single dimension separation is performed, and
generally represents the second dimension of two-dimensional separations.
Electrophoretic sepa... | [
{
"created": "Thu, 6 May 2010 06:53:31 GMT",
"version": "v1"
}
] | 2010-05-07 | [
[
"Rabilloud",
"Thierry",
"",
"BBSI"
]
] | Electrophoretic separations of proteins are widely used in proteomic analyses, and rely heavily on SDS electrophoresis. This mode of separation is almost exclusively used when a single dimension separation is performed, and generally represents the second dimension of two-dimensional separations. Electrophoretic separa... |
2007.04370 | Gloria Cecchini | Lorenzo Chicchi, Gloria Cecchini, Ihusan Adam, Giuseppe de Vito,
Roberto Livi, Francesco Saverio Pavone, Ludovico Silvestri, Lapo Turrini,
Francesco Vanzi, Duccio Fanelli | Reconstruction scheme for excitatory and inhibitory dynamics with
quenched disorder: application to zebrafish imaging | null | Journal of Computational Neuroscience 49, 159-174 (2021) | 10.1007/s10827-020-00774-1 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An inverse procedure is developed and tested to recover functional and
structural information from global signals of brains activity. The method
assumes a leaky-integrate and fire model with excitatory and inhibitory
neurons, coupled via a directed network. Neurons are endowed with a
heterogenous current value, which... | [
{
"created": "Wed, 8 Jul 2020 18:58:23 GMT",
"version": "v1"
}
] | 2021-05-14 | [
[
"Chicchi",
"Lorenzo",
""
],
[
"Cecchini",
"Gloria",
""
],
[
"Adam",
"Ihusan",
""
],
[
"de Vito",
"Giuseppe",
""
],
[
"Livi",
"Roberto",
""
],
[
"Pavone",
"Francesco Saverio",
""
],
[
"Silvestri",
"Ludovico",
... | An inverse procedure is developed and tested to recover functional and structural information from global signals of brains activity. The method assumes a leaky-integrate and fire model with excitatory and inhibitory neurons, coupled via a directed network. Neurons are endowed with a heterogenous current value, which s... |
2006.15128 | John Antrobus Ph.D. | John S. Antrobus, Yusuke Shono, Wolfgang M. Pauli, and Bala Sundaram | All Recognition is Accomplished By Interacting Bottom-Up Sensory and
Top-Down Context Bias in Occipital to Frontal Cortex Neural Networks | 39 pages, 1 figure | null | null | null | q-bio.NC | http://creativecommons.org/publicdomain/zero/1.0/ | Recognition of every word is accomplished by close collaboration of bottom-up
sub-word and word recognition neural networks with top-down cognitive word
context expectations. The utility of this context appropriate collaboration is
substantial savings in recognition time, accuracy and cortical neural
processing resou... | [
{
"created": "Fri, 26 Jun 2020 17:36:58 GMT",
"version": "v1"
}
] | 2020-06-29 | [
[
"Antrobus",
"John S.",
""
],
[
"Shono",
"Yusuke",
""
],
[
"Pauli",
"Wolfgang M.",
""
],
[
"Sundaram",
"Bala",
""
]
] | Recognition of every word is accomplished by close collaboration of bottom-up sub-word and word recognition neural networks with top-down cognitive word context expectations. The utility of this context appropriate collaboration is substantial savings in recognition time, accuracy and cortical neural processing resourc... |
1708.04103 | Vince Grolmusz | Balazs Szalkai and Vince Grolmusz | SECLAF: A Webserver and Deep Neural Network Design Tool for Biological
Sequence Classification | null | null | null | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Artificial intelligence (AI) tools are gaining more and more ground each year
in bioinformatics. Learning algorithms can be taught easily by using the
existing enormous biological databases, and the resulting models can be used
for the high-quality classification of novel, un-categorized data in numerous
areas, inclu... | [
{
"created": "Mon, 14 Aug 2017 13:00:03 GMT",
"version": "v1"
}
] | 2017-08-15 | [
[
"Szalkai",
"Balazs",
""
],
[
"Grolmusz",
"Vince",
""
]
] | Artificial intelligence (AI) tools are gaining more and more ground each year in bioinformatics. Learning algorithms can be taught easily by using the existing enormous biological databases, and the resulting models can be used for the high-quality classification of novel, un-categorized data in numerous areas, includi... |
2201.00663 | Quentin Thommen | Quentin Thommen, Julien Hurbain, and Benjamin Pfeuty | Stochastic simulation algorithm for isotope-based dynamic flux analysis | 9 pages, 4 figures | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Carbon isotope labeling method is a standard metabolic engineering tool for
flux quantification in living cells. To cope with the high dimensionality of
isotope labeling systems, diverse algorithms have been developed to reduce the
number of variables or operations in metabolic flux analysis (MFA), but lacks
generali... | [
{
"created": "Mon, 3 Jan 2022 13:56:54 GMT",
"version": "v1"
},
{
"created": "Thu, 10 Feb 2022 09:40:25 GMT",
"version": "v2"
}
] | 2022-02-11 | [
[
"Thommen",
"Quentin",
""
],
[
"Hurbain",
"Julien",
""
],
[
"Pfeuty",
"Benjamin",
""
]
] | Carbon isotope labeling method is a standard metabolic engineering tool for flux quantification in living cells. To cope with the high dimensionality of isotope labeling systems, diverse algorithms have been developed to reduce the number of variables or operations in metabolic flux analysis (MFA), but lacks generaliza... |
1903.00197 | Eryu Xia | Eryu Xia, Xin Du, Jing Mei, Wen Sun, Suijun Tong, Zhiqing Kang, Jian
Sheng, Jian Li, Changsheng Ma, Jianzeng Dong, Shaochun Li | Outcome-Driven Clustering of Acute Coronary Syndrome Patients using
Multi-Task Neural Network with Attention | null | null | null | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cluster analysis aims at separating patients into phenotypically heterogenous
groups and defining therapeutically homogeneous patient subclasses. It is an
important approach in data-driven disease classification and subtyping. Acute
coronary syndrome (ACS) is a syndrome due to sudden decrease of coronary artery
blood... | [
{
"created": "Fri, 1 Mar 2019 08:20:28 GMT",
"version": "v1"
},
{
"created": "Wed, 27 Mar 2019 07:08:04 GMT",
"version": "v2"
}
] | 2019-03-28 | [
[
"Xia",
"Eryu",
""
],
[
"Du",
"Xin",
""
],
[
"Mei",
"Jing",
""
],
[
"Sun",
"Wen",
""
],
[
"Tong",
"Suijun",
""
],
[
"Kang",
"Zhiqing",
""
],
[
"Sheng",
"Jian",
""
],
[
"Li",
"Jian",
""
],
... | Cluster analysis aims at separating patients into phenotypically heterogenous groups and defining therapeutically homogeneous patient subclasses. It is an important approach in data-driven disease classification and subtyping. Acute coronary syndrome (ACS) is a syndrome due to sudden decrease of coronary artery blood f... |
2003.06349 | Georgy Karev | Georgiy Karev | Dynamics of Strategy Distribution in a One-Dimensional Continuous Trait
Space with a Bi-linear and Quadratic Payoff Functions | 28 pages,13 Figures; it is an extended version of the paper published
in "Games", 2020 | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Evolution of distribution of strategies in game theory is an interesting
question that has been studied only for specific cases. Here I develop a
general method to extend analysis of the evolution of continuous strategy
distributions given bi-linear and quadratic payoff functions for any initial
distribution to answe... | [
{
"created": "Fri, 13 Mar 2020 15:46:40 GMT",
"version": "v1"
}
] | 2020-03-16 | [
[
"Karev",
"Georgiy",
""
]
] | Evolution of distribution of strategies in game theory is an interesting question that has been studied only for specific cases. Here I develop a general method to extend analysis of the evolution of continuous strategy distributions given bi-linear and quadratic payoff functions for any initial distribution to answer ... |
2209.02365 | Alan Smeaton | Victoria Rhodes and Maureen Maguire and Meghana Shetty and Conor
McAloon and Alan F. Smeaton | Periodicity Intensity of the 24 h Circadian Rhythm in Newborn Calves
Show Indicators of Herd Welfare | null | Sensors 2022, 22(15), 5843 | 10.3390/s22155843 | null | q-bio.QM stat.AP | http://creativecommons.org/licenses/by/4.0/ | Circadian rhythms are a process of the sleep-wake cycle that regulates the
physical, mental and behavioural changes in all living beings with a period of
roughly 24 h. Wearable accelerometers are typically used in livestock
applications to record animal movement from which we can estimate the activity
type. Here, we ... | [
{
"created": "Mon, 8 Aug 2022 08:52:20 GMT",
"version": "v1"
}
] | 2022-09-07 | [
[
"Rhodes",
"Victoria",
""
],
[
"Maguire",
"Maureen",
""
],
[
"Shetty",
"Meghana",
""
],
[
"McAloon",
"Conor",
""
],
[
"Smeaton",
"Alan F.",
""
]
] | Circadian rhythms are a process of the sleep-wake cycle that regulates the physical, mental and behavioural changes in all living beings with a period of roughly 24 h. Wearable accelerometers are typically used in livestock applications to record animal movement from which we can estimate the activity type. Here, we us... |
2407.00002 | Peter M{\o}rch Groth | Peter M{\o}rch Groth and Mads Herbert Kerrn and Lars Olsen and Jesper
Salomon and Wouter Boomsma | Kermut: Composite kernel regression for protein variant effects | 10 pages (36 in total with appendix), 4 figures (26 figures in total
with appendix) | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Reliable prediction of protein variant effects is crucial for both protein
optimization and for advancing biological understanding. For practical use in
protein engineering, it is important that we can also provide reliable
uncertainty estimates for our predictions, and while prediction accuracy has
seen much progres... | [
{
"created": "Tue, 9 Apr 2024 14:08:06 GMT",
"version": "v1"
},
{
"created": "Tue, 9 Jul 2024 08:28:57 GMT",
"version": "v2"
}
] | 2024-07-10 | [
[
"Groth",
"Peter Mørch",
""
],
[
"Kerrn",
"Mads Herbert",
""
],
[
"Olsen",
"Lars",
""
],
[
"Salomon",
"Jesper",
""
],
[
"Boomsma",
"Wouter",
""
]
] | Reliable prediction of protein variant effects is crucial for both protein optimization and for advancing biological understanding. For practical use in protein engineering, it is important that we can also provide reliable uncertainty estimates for our predictions, and while prediction accuracy has seen much progress ... |
1610.04579 | Andrew Leifer | Jeffrey P. Nguyen, Ashley N. Linder, George S. Plummer, Joshua W.
Shaevitz, and Andrew M. Leifer | Automatically tracking neurons in a moving and deforming brain | 33 pages, 7 figures, code available | PLoS Comput Biol 13(5): e1005517 (2017) | 10.1371/journal.pcbi.1005517 | null | q-bio.NC cs.CV physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Advances in optical neuroimaging techniques now allow neural activity to be
recorded with cellular resolution in awake and behaving animals. Brain motion
in these recordings pose a unique challenge. The location of individual neurons
must be tracked in 3D over time to accurately extract single neuron activity
traces.... | [
{
"created": "Fri, 14 Oct 2016 18:51:30 GMT",
"version": "v1"
}
] | 2017-05-22 | [
[
"Nguyen",
"Jeffrey P.",
""
],
[
"Linder",
"Ashley N.",
""
],
[
"Plummer",
"George S.",
""
],
[
"Shaevitz",
"Joshua W.",
""
],
[
"Leifer",
"Andrew M.",
""
]
] | Advances in optical neuroimaging techniques now allow neural activity to be recorded with cellular resolution in awake and behaving animals. Brain motion in these recordings pose a unique challenge. The location of individual neurons must be tracked in 3D over time to accurately extract single neuron activity traces. R... |
1407.2548 | Katja Reichel | Katja Reichel, Valentin Bahier, C\'edric Midoux, Jean-Pierre Masson,
Solenn Stoeckel | Interpretation and approximation tools for big, dense Markov chain
transition matrices in ecology and evolution | 8 pages, 4 figures, supplement: 2 figures, visual abstract,
highlights, source code | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Markov chains are a common framework for individual-based state and time
discrete models in ecology and evolution. Their use, however, is largely
limited to systems with a low number of states, since the transition matrices
involved pose considerable challenges as their size and their density increase.
Big, dense tra... | [
{
"created": "Wed, 9 Jul 2014 16:12:39 GMT",
"version": "v1"
}
] | 2014-07-10 | [
[
"Reichel",
"Katja",
""
],
[
"Bahier",
"Valentin",
""
],
[
"Midoux",
"Cédric",
""
],
[
"Masson",
"Jean-Pierre",
""
],
[
"Stoeckel",
"Solenn",
""
]
] | Markov chains are a common framework for individual-based state and time discrete models in ecology and evolution. Their use, however, is largely limited to systems with a low number of states, since the transition matrices involved pose considerable challenges as their size and their density increase. Big, dense trans... |
1201.3022 | Sachin Talathi | Roxana A. Stephanescu, R.G. Shivakeshavan, Sachin S. Talathi | Computational Models For Epilepsy | 4 figures | Seizure: European Journal of Epilepsy, 2012 Dec;21(10):748-59 | 10.1016/j.seizure.2012.08.012 | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Epilepsy is a neurological disease characterized by recurrent and spontaneous
seizures. It affects approximately 50 million people worldwide. In majority of
the cases accurate diagnosis of the disease can be made without using any
technologically advanced techniques and seizures are controlled using standard
treatmen... | [
{
"created": "Sat, 14 Jan 2012 14:49:09 GMT",
"version": "v1"
}
] | 2013-04-05 | [
[
"Stephanescu",
"Roxana A.",
""
],
[
"Shivakeshavan",
"R. G.",
""
],
[
"Talathi",
"Sachin S.",
""
]
] | Epilepsy is a neurological disease characterized by recurrent and spontaneous seizures. It affects approximately 50 million people worldwide. In majority of the cases accurate diagnosis of the disease can be made without using any technologically advanced techniques and seizures are controlled using standard treatment ... |
1510.00198 | Charles Fisher | Charles K. Fisher, Thierry Mora, and Aleksandra M. Walczak | Habitat Fluctuations Drive Species Covariation in the Human Microbiota | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Two species with similar resource requirements respond in a characteristic
way to variations in their habitat -- their abundances rise and fall in
concert. We use this idea to learn how bacterial populations in the microbiota
respond to habitat conditions that vary from person-to-person across the human
population. O... | [
{
"created": "Thu, 1 Oct 2015 12:12:00 GMT",
"version": "v1"
}
] | 2015-10-02 | [
[
"Fisher",
"Charles K.",
""
],
[
"Mora",
"Thierry",
""
],
[
"Walczak",
"Aleksandra M.",
""
]
] | Two species with similar resource requirements respond in a characteristic way to variations in their habitat -- their abundances rise and fall in concert. We use this idea to learn how bacterial populations in the microbiota respond to habitat conditions that vary from person-to-person across the human population. Our... |
q-bio/0505005 | Paolo Provero | Davide Cora', Carl Herrmann, Christoph Dieterich, Ferdinando Di Cunto,
Paolo Provero and Michele Caselle | Ab initio identification of putative human transcription factor binding
sites by comparative genomics | 22 pages, 2 figures. Supplementary material available from the
authors | BMC Bioinformatics 2005, 6:110 | null | null | q-bio.GN | null | We discuss a simple and powerful approach for the ab initio identification of
cis-regulatory motifs involved in transcriptional regulation. The method we
present integrates several elements: human-mouse comparison, statistical
analysis of genomic sequences and the concept of coregulation. We apply it to a
complete sc... | [
{
"created": "Tue, 3 May 2005 10:37:54 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Cora'",
"Davide",
""
],
[
"Herrmann",
"Carl",
""
],
[
"Dieterich",
"Christoph",
""
],
[
"Di Cunto",
"Ferdinando",
""
],
[
"Provero",
"Paolo",
""
],
[
"Caselle",
"Michele",
""
]
] | We discuss a simple and powerful approach for the ab initio identification of cis-regulatory motifs involved in transcriptional regulation. The method we present integrates several elements: human-mouse comparison, statistical analysis of genomic sequences and the concept of coregulation. We apply it to a complete scan... |
1511.04944 | Sunyoung Kwon | Sunyoung Kwon, Gyuwan Kim, Byunghan Lee, Jongsik Chun, Sungroh Yoon,
and Young-Han Kim | NASCUP: Nucleic Acid Sequence Classification by Universal Probability | null | null | null | null | q-bio.GN cs.IT math.IT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivated by the need for fast and accurate classification of unlabeled
nucleotide sequences on a large scale, we developed NASCUP, a new
classification method that captures statistical structures of nucleotide
sequences by compact context-tree models and universal probability from
information theory. NASCUP achieved... | [
{
"created": "Mon, 16 Nov 2015 13:04:03 GMT",
"version": "v1"
},
{
"created": "Thu, 29 Nov 2018 14:49:23 GMT",
"version": "v2"
}
] | 2018-11-30 | [
[
"Kwon",
"Sunyoung",
""
],
[
"Kim",
"Gyuwan",
""
],
[
"Lee",
"Byunghan",
""
],
[
"Chun",
"Jongsik",
""
],
[
"Yoon",
"Sungroh",
""
],
[
"Kim",
"Young-Han",
""
]
] | Motivated by the need for fast and accurate classification of unlabeled nucleotide sequences on a large scale, we developed NASCUP, a new classification method that captures statistical structures of nucleotide sequences by compact context-tree models and universal probability from information theory. NASCUP achieved B... |
1610.04224 | Indika Rajapakse | Indika Rajapakse, Steve Smale | Emergence of Function | null | null | null | null | q-bio.OT math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This work gives a mathematical study of tissue dynamics. We combine
within-cell genome dynamics and diffusion between cells, where the synthesis of
the two gives rise to the emergence of function. We introduce a concept of
monotonicity and prove that monotonicity together with hardwiring, defined as
all cells of the ... | [
{
"created": "Wed, 12 Oct 2016 23:56:21 GMT",
"version": "v1"
}
] | 2016-10-17 | [
[
"Rajapakse",
"Indika",
""
],
[
"Smale",
"Steve",
""
]
] | This work gives a mathematical study of tissue dynamics. We combine within-cell genome dynamics and diffusion between cells, where the synthesis of the two gives rise to the emergence of function. We introduce a concept of monotonicity and prove that monotonicity together with hardwiring, defined as all cells of the sa... |
0905.2932 | Thomas Butler | Thomas Butler and Nigel Goldenfeld | Optimality Properties of a Proposed Precursor to the Genetic Code | null | null | 10.1103/PhysRevE.80.032901 | null | q-bio.OT q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We calculate the optimality of a doublet precursor to the canonical genetic
code with respect to mitigating the effects of point mutations and compare our
results to corresponding ones for the canonical genetic code. We find that the
proposed precursor has much less optimality than that of the canonical code.
Our res... | [
{
"created": "Mon, 18 May 2009 16:32:10 GMT",
"version": "v1"
}
] | 2013-05-29 | [
[
"Butler",
"Thomas",
""
],
[
"Goldenfeld",
"Nigel",
""
]
] | We calculate the optimality of a doublet precursor to the canonical genetic code with respect to mitigating the effects of point mutations and compare our results to corresponding ones for the canonical genetic code. We find that the proposed precursor has much less optimality than that of the canonical code. Our resul... |
0810.1833 | Jose Emilio Jimenez | Stephen A. Wells, J. Emilio Jimenez-Roldan, Rudolf A. R\"omer | Sensitivity of protein rigidity analysis to small structural variations:
a large-scale comparative analysis | 10 Figures, 3 Tables, 16 pages, submitted to physicalbiology | physicalbiology 6, 046005-11 (2009) | 10.1088/1478-3975/6/4/046005 | null | q-bio.MN q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rigidity analysis using the "pebble game" can usefully be applied to protein
crystal structures to obtain information on protein folding, assembly and the
structure-function relationship. However, previous work using this technique
has not made clear how sensitive rigidity analysis is to small structural
variations. ... | [
{
"created": "Fri, 10 Oct 2008 10:02:54 GMT",
"version": "v1"
}
] | 2009-09-25 | [
[
"Wells",
"Stephen A.",
""
],
[
"Jimenez-Roldan",
"J. Emilio",
""
],
[
"Römer",
"Rudolf A.",
""
]
] | Rigidity analysis using the "pebble game" can usefully be applied to protein crystal structures to obtain information on protein folding, assembly and the structure-function relationship. However, previous work using this technique has not made clear how sensitive rigidity analysis is to small structural variations. We... |
2210.04111 | Michael Baker Ph.D. | Yoshinao Katsu (Hokkaido University), Xiaozhi Lin (Hokkaido
University), Ruigeng Ji (Hokkaido University), Ze Chen (Hokkaido University),
Yui Kamisaka (Hokkaido University), Koto Bamba (Hokkaido University), Michael
E. Baker (University of California, San Diego) | Corticosteroid Activation of Atlantic Sea Lamprey Corticoid Receptor:
Allosteric Regulation by the N-terminal Domain | 27 pages, 6 figures | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Lampreys are jawless fish that evolved about 550 million years ago at the
base of the vertebrate line. Modern lampreys contain a corticoid receptor (CR),
the common ancestor of the glucocorticoid receptor (GR) and mineralocorticoid
receptor (MR), which first appear in cartilaginous fish, such as sharks. Until
recentl... | [
{
"created": "Sat, 8 Oct 2022 21:54:36 GMT",
"version": "v1"
}
] | 2022-10-11 | [
[
"Katsu",
"Yoshinao",
"",
"Hokkaido University"
],
[
"Lin",
"Xiaozhi",
"",
"Hokkaido\n University"
],
[
"Ji",
"Ruigeng",
"",
"Hokkaido University"
],
[
"Chen",
"Ze",
"",
"Hokkaido University"
],
[
"Kamisaka",
"Yui",
"",
... | Lampreys are jawless fish that evolved about 550 million years ago at the base of the vertebrate line. Modern lampreys contain a corticoid receptor (CR), the common ancestor of the glucocorticoid receptor (GR) and mineralocorticoid receptor (MR), which first appear in cartilaginous fish, such as sharks. Until recently,... |
1003.0836 | Dominique Rousie DL | D. L. Rousie (1), J.P. Deroubaix (2), O. Joly (1), P. Salvetti (2), J.
Vasseur (2), A. Berthoz (1), ((1) Laboratoire de la perception et de l
action-College de France-Paris, (2) IFR 49 INSERM/CNRS-Orsay) | Semi-Circular Canals Anomalies//Idiopathic Scoliosis | 15 pages, 8 figures Name and adress for correspondence: Docteur
Rousie, 3 rue Saint Louis, 59113 Seclin France. Fax: 0033 320 32 35 44, Tel.
0033 320 90 12 29, mrousie@nordnet.fr | null | null | null | q-bio.NC physics.med-ph q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Thanks to a novel modelling programme to detect anomalies in the membranous
semi circular canals (SSC) of idiopathic scoliosis (IS) we found severe
anomalies mainly located in lateral SCC devoted to trunk rotation and lateral
deviations. We also found a specific communication between the lateral and
posterior canal i... | [
{
"created": "Wed, 3 Mar 2010 15:31:05 GMT",
"version": "v1"
}
] | 2016-09-08 | [
[
"Rousie",
"D. L.",
""
],
[
"Deroubaix",
"J. P.",
""
],
[
"Joly",
"O.",
""
],
[
"Salvetti",
"P.",
""
],
[
"Vasseur",
"J.",
""
],
[
"Berthoz",
"A.",
""
]
] | Thanks to a novel modelling programme to detect anomalies in the membranous semi circular canals (SSC) of idiopathic scoliosis (IS) we found severe anomalies mainly located in lateral SCC devoted to trunk rotation and lateral deviations. We also found a specific communication between the lateral and posterior canal inv... |
2311.17756 | Serge Bouaziz | Steven R. Laplante (INRS-IAF), Pascale Coric (UPCG), Serge Bouaziz
(CiTCoM), Tanos Celmar Costa Fran\c{c}a (INRS-IAF) | NMR Spectroscopy Can Help Accelerate Antiviral Drug Discovery Programs | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Small molecule drugs have an important role to play in combating viral
infections, and biophysics support has been central for contributing to the
discovery and design of direct acting antivirals. Perhaps one of the most
successful biophysical tools for this purpose is NMR spectroscopy when utilized
strategically and... | [
{
"created": "Wed, 29 Nov 2023 15:58:25 GMT",
"version": "v1"
}
] | 2023-11-30 | [
[
"Laplante",
"Steven R.",
"",
"INRS-IAF"
],
[
"Coric",
"Pascale",
"",
"UPCG"
],
[
"Bouaziz",
"Serge",
"",
"CiTCoM"
],
[
"França",
"Tanos Celmar Costa",
"",
"INRS-IAF"
]
] | Small molecule drugs have an important role to play in combating viral infections, and biophysics support has been central for contributing to the discovery and design of direct acting antivirals. Perhaps one of the most successful biophysical tools for this purpose is NMR spectroscopy when utilized strategically and p... |
2011.10955 | Tyler Maltba | Tyler E. Maltba (1), Hongli Zhao (1), Daniel M. Tartakovsky (2) ((1)
UC Berkeley, (2) Stanford University) | Autonomous learning of nonlocal stochastic neuron dynamics | 28 pages, 12 figures, First author: Tyler E. Maltba, Corresponding
author: Daniel M. Tartakovsky | Cogn Neurodyn 16, 683-705 (2022) | 10.1007/s11571-021-09731-9 | null | q-bio.NC cs.NA math.NA q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neuronal dynamics is driven by externally imposed or internally generated
random excitations/noise, and is often described by systems of random or
stochastic ordinary differential equations. Such systems admit a distribution
of solutions, which is (partially) characterized by the single-time joint
probability density... | [
{
"created": "Sun, 22 Nov 2020 06:47:18 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Sep 2021 19:13:34 GMT",
"version": "v2"
}
] | 2023-12-19 | [
[
"Maltba",
"Tyler E.",
""
],
[
"Zhao",
"Hongli",
""
],
[
"Tartakovsky",
"Daniel M.",
""
]
] | Neuronal dynamics is driven by externally imposed or internally generated random excitations/noise, and is often described by systems of random or stochastic ordinary differential equations. Such systems admit a distribution of solutions, which is (partially) characterized by the single-time joint probability density f... |
1010.5019 | James P. Crutchfield | Steve T. Piantadosi and James P. Crutchfield | How the Dimension of Space Affects the Products of Pre-Biotic Evolution:
The Spatial Population Dynamics of Structural Complexity and The Emergence of
Membranes | 9 pages, 7 figures, 2 tables;
http://cse.ucdavis.edu/~cmg/compmech/pubs/ss.htm | null | null | null | q-bio.PE nlin.AO q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We show that autocatalytic networks of epsilon-machines and their population
dynamics differ substantially between spatial (geographically distributed) and
nonspatial (panmixia) populations. Generally, regions of spacetime-invariant
autocatalytic networks---or domains---emerge in geographically distributed
population... | [
{
"created": "Sun, 24 Oct 2010 22:43:32 GMT",
"version": "v1"
}
] | 2010-10-26 | [
[
"Piantadosi",
"Steve T.",
""
],
[
"Crutchfield",
"James P.",
""
]
] | We show that autocatalytic networks of epsilon-machines and their population dynamics differ substantially between spatial (geographically distributed) and nonspatial (panmixia) populations. Generally, regions of spacetime-invariant autocatalytic networks---or domains---emerge in geographically distributed populations.... |
2403.13005 | Antonia Calvi | Antonia Calvi, Th\'eophile Gaudin, Dominik Miketa, Dominique Sydow,
Liam Wilbraham | Leap: molecular synthesisability scoring with intermediates | New Frontiers of AI for Drug Discovery and Development workshop paper | null | null | null | q-bio.BM cs.LG physics.chem-ph | http://creativecommons.org/licenses/by/4.0/ | Assessing whether a molecule can be synthesised is a primary task in drug
discovery. It enables computational chemists to filter for viable compounds or
bias molecular generative models. The notion of synthesisability is dynamic as
it evolves depending on the availability of key compounds. A common approach in
drug d... | [
{
"created": "Thu, 14 Mar 2024 11:53:35 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Apr 2024 16:26:04 GMT",
"version": "v2"
}
] | 2024-04-15 | [
[
"Calvi",
"Antonia",
""
],
[
"Gaudin",
"Théophile",
""
],
[
"Miketa",
"Dominik",
""
],
[
"Sydow",
"Dominique",
""
],
[
"Wilbraham",
"Liam",
""
]
] | Assessing whether a molecule can be synthesised is a primary task in drug discovery. It enables computational chemists to filter for viable compounds or bias molecular generative models. The notion of synthesisability is dynamic as it evolves depending on the availability of key compounds. A common approach in drug dis... |
2204.02130 | Yikang Zhang | Yikang Zhang, Xiaomin Chu, Yelu Jiang, Hongjie Wu and Lijun Quan | SemanticCAP: Chromatin Accessibility Prediction Enhanced by Features
Learning from a Language Model | null | null | null | null | q-bio.GN cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A large number of inorganic and organic compounds are able to bind DNA and
form complexes, among which drug-related molecules are important. Chromatin
accessibility changes not only directly affects drug-DNA interactions, but also
promote or inhibit the expression of critical genes associated with drug
resistance by ... | [
{
"created": "Tue, 5 Apr 2022 11:47:58 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Apr 2022 10:25:29 GMT",
"version": "v2"
}
] | 2022-04-07 | [
[
"Zhang",
"Yikang",
""
],
[
"Chu",
"Xiaomin",
""
],
[
"Jiang",
"Yelu",
""
],
[
"Wu",
"Hongjie",
""
],
[
"Quan",
"Lijun",
""
]
] | A large number of inorganic and organic compounds are able to bind DNA and form complexes, among which drug-related molecules are important. Chromatin accessibility changes not only directly affects drug-DNA interactions, but also promote or inhibit the expression of critical genes associated with drug resistance by af... |
q-bio/0502004 | James P. Brody | Hermann B. Frieboes and James P. Brody | Telomere loss limits the rate of human epithelial tumor formation | 15 pages, includes 7 figures | null | null | null | q-bio.TO | null | Most human carcinomas exhibit telomere abnormalities early in the
carcinogenesis process suggesting that crisis caused by telomere shortening may
be a necessary event leading to human carcinomas. Epidemiological records of
the age at which each patient in a population develops carcinoma are known as
age-incidence dat... | [
{
"created": "Sun, 6 Feb 2005 20:48:54 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Frieboes",
"Hermann B.",
""
],
[
"Brody",
"James P.",
""
]
] | Most human carcinomas exhibit telomere abnormalities early in the carcinogenesis process suggesting that crisis caused by telomere shortening may be a necessary event leading to human carcinomas. Epidemiological records of the age at which each patient in a population develops carcinoma are known as age-incidence data;... |
q-bio/0507012 | Johannes K\"astner | Johannes Kaestner (1 and 2), Sascha Hemmen (1), and Peter E. Bloechl
(1) ((1) Clausthal University of Technology, Germany, (2) Max-Planck-Institue
for Coal Research, Germany) | Activation and Protonation of Dinitrogen at the FeMo-Cofactor of
Nitrogenase | 9 Pages, 6 figures, accepted in J. Chem. Phys. Typos corrected
according to the galley proofs of JCP | J. Chem. Phys. 123, 074306 (2005) | 10.1063/1.2008227 | null | q-bio.BM | null | The protonation of N2 bound to the active center of nitrogenase has been
investigated using state-of-the-art DFT calculations. Dinitrogen in the
bridging mode is activated by forming two bonds to Fe sites, which results in a
reduction of the energy for the first hydrogen transfer by 123 kJ/mol. The
axial binding mode... | [
{
"created": "Fri, 8 Jul 2005 10:07:44 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Aug 2005 07:27:00 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Kaestner",
"Johannes",
"",
"1 and 2"
],
[
"Hemmen",
"Sascha",
""
],
[
"Bloechl",
"Peter E.",
""
]
] | The protonation of N2 bound to the active center of nitrogenase has been investigated using state-of-the-art DFT calculations. Dinitrogen in the bridging mode is activated by forming two bonds to Fe sites, which results in a reduction of the energy for the first hydrogen transfer by 123 kJ/mol. The axial binding mode w... |
2111.13992 | Samson Petrosyan | Samson Petrosyan, Grigory Tikhomirov | NanoFrame: A web-based DNA wireframe design tool for 3D structures | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The rapid development of the DNA nanotechnology field has been facilitated by
advances in CAD software. However, as more complex concepts arose, the lag
between the needs and software capabilities appeared. Further derailed by
manual installation and software incompatibility across different platforms and
often tedio... | [
{
"created": "Sat, 27 Nov 2021 22:05:33 GMT",
"version": "v1"
}
] | 2021-11-30 | [
[
"Petrosyan",
"Samson",
""
],
[
"Tikhomirov",
"Grigory",
""
]
] | The rapid development of the DNA nanotechnology field has been facilitated by advances in CAD software. However, as more complex concepts arose, the lag between the needs and software capabilities appeared. Further derailed by manual installation and software incompatibility across different platforms and often tedious... |
0806.3772 | Eugene Shakhnovich | Konstantin B. Zeldovich and Eugene I. Shakhnovich | Emergence of mutationally robust proteins in a microscopic model of
evolution | null | null | null | null | q-bio.BM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ability to absorb mutations while retaining structure and function, or
mutational robustness, is a remarkable property of natural proteins. In this
Letter, we use a computational model of organismic evolution [Zeldovich et al,
PLOS Comp Biol 3(7):e139 (2007)], which explicitly couples protein physics and
populati... | [
{
"created": "Mon, 23 Jun 2008 20:59:00 GMT",
"version": "v1"
}
] | 2008-06-25 | [
[
"Zeldovich",
"Konstantin B.",
""
],
[
"Shakhnovich",
"Eugene I.",
""
]
] | The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp Biol 3(7):e139 (2007)], which explicitly couples protein physics and population... |
1912.09154 | Eugene Terentjev M. | Jiri Kucera and Eugene M. Terentjev | FliI6-FliJ molecular motor assists with unfolding in the type III
secretion export apparatus | null | Scientific Reports (2020) 10:7127 | 10.1038/s41598-020-63330-y | null | q-bio.SC cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The role of rotational molecular motors of the ATP synthase class is integral
to the metabolism of cells. Yet the function of FliI6-FliJ complex - homologous
to the F1 ATPase motor - within the flagellar export apparatus remains unclear.
We use a simple two-state model adapted from studies of linear molecular motors
... | [
{
"created": "Thu, 19 Dec 2019 12:16:26 GMT",
"version": "v1"
}
] | 2020-05-12 | [
[
"Kucera",
"Jiri",
""
],
[
"Terentjev",
"Eugene M.",
""
]
] | The role of rotational molecular motors of the ATP synthase class is integral to the metabolism of cells. Yet the function of FliI6-FliJ complex - homologous to the F1 ATPase motor - within the flagellar export apparatus remains unclear. We use a simple two-state model adapted from studies of linear molecular motors to... |
1903.07541 | Yuri Eisaki | Yuri Eisaki, Ikkyu Aihara, Isamu Hikosaka and Tohru Kawabe | Landing Dynamics of a Seagull Examined by Field Observation and
Mathematical Modeling | 11 pages, 11 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A seagull ({\it Larus crassirostris}) has a high ability to realize its safe,
accurate and smooth landing. We examined how a seagull controls its angle of
attack when landing on a specific target. First, we recorded the landing
behavior of an actual seagull by multiple video cameras and quantified the
flight trajecto... | [
{
"created": "Fri, 15 Mar 2019 15:41:49 GMT",
"version": "v1"
}
] | 2019-03-19 | [
[
"Eisaki",
"Yuri",
""
],
[
"Aihara",
"Ikkyu",
""
],
[
"Hikosaka",
"Isamu",
""
],
[
"Kawabe",
"Tohru",
""
]
] | A seagull ({\it Larus crassirostris}) has a high ability to realize its safe, accurate and smooth landing. We examined how a seagull controls its angle of attack when landing on a specific target. First, we recorded the landing behavior of an actual seagull by multiple video cameras and quantified the flight trajectory... |
1310.7277 | Emmanuelle Tognoli | Emmanuelle Tognoli and J. A. Scott Kelso | Enlarging the scope: grasping brain complexity | 8 pages, 2 figures | Frontiers in Systems Neuroscience, 2014 8:122 | 10.3389/fnsys.2014.00122 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To further advance our understanding of the brain, new concepts and theories
are needed. In particular, the ability of the brain to create information flows
must be reconciled with its propensity for synchronization and mass action. The
framework of Coordination Dynamics and the theory of metastability are
presented ... | [
{
"created": "Sun, 27 Oct 2013 23:49:37 GMT",
"version": "v1"
}
] | 2014-07-04 | [
[
"Tognoli",
"Emmanuelle",
""
],
[
"Kelso",
"J. A. Scott",
""
]
] | To further advance our understanding of the brain, new concepts and theories are needed. In particular, the ability of the brain to create information flows must be reconciled with its propensity for synchronization and mass action. The framework of Coordination Dynamics and the theory of metastability are presented as... |
2007.14926 | Mai He | Yu-Whuei Hu (1), Li-Shan Huang (2), Eric J. Yeh (3), Mai He (4) ((1)
National Dong Hwa University, Hualian, Taiwan (2) National Tsing Hua
University, Hsinchu, Taiwan (3) Amgen Inc. Thousand Oaks, CA, USA (4)
Department of Pathology & Immunology, Washington University School of
Medicine, St. Louis, MO, USA) | Healthcare Utilization and Perceived Health Status from Falun Gong
Practitioners in Taiwan: A Pilot SF-36 Survey | Five tables | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objective: Falun Gong (FLG) is a practice of mind and body focusing on moral
character improvement along with meditative exercises. This 2002 pilot study
explored perceived health status, medical resource utilization and related
factors among Taiwanese FLG practitioners, compared to the general Taiwanese
norm estimat... | [
{
"created": "Wed, 29 Jul 2020 16:00:28 GMT",
"version": "v1"
}
] | 2020-07-30 | [
[
"Hu",
"Yu-Whuei",
""
],
[
"Huang",
"Li-Shan",
""
],
[
"Yeh",
"Eric J.",
""
],
[
"He",
"Mai",
""
]
] | Objective: Falun Gong (FLG) is a practice of mind and body focusing on moral character improvement along with meditative exercises. This 2002 pilot study explored perceived health status, medical resource utilization and related factors among Taiwanese FLG practitioners, compared to the general Taiwanese norm estimated... |
1005.1465 | Steffen Waldherr | Steffen Waldherr, Jingbo Wu, Frank Allg\"ower | Bridging Time Scales in Cellular Decision Making with a Stochastic
Bistable Switch | 14 pages, 4 figures | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cellular transformations which involve a significant phenotypical change of
the cell's state use bistable biochemical switches as underlying decision
systems. In this work, we aim at linking cellular decisions taking place on a
time scale of years to decades with the biochemical dynamics in signal
transduction and ge... | [
{
"created": "Mon, 10 May 2010 07:42:22 GMT",
"version": "v1"
}
] | 2010-05-11 | [
[
"Waldherr",
"Steffen",
""
],
[
"Wu",
"Jingbo",
""
],
[
"Allgöwer",
"Frank",
""
]
] | Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale of years to decades with the biochemical dynamics in signal transduction and gene... |
0811.1081 | Mircea Andrecut Dr | M. Andrecut | Parallel GPU Implementation of Iterative PCA Algorithms | 45 pages, 1 figure, source code included | null | null | null | q-bio.QM cs.MS physics.comp-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Principal component analysis (PCA) is a key statistical technique for
multivariate data analysis. For large data sets the common approach to PCA
computation is based on the standard NIPALS-PCA algorithm, which unfortunately
suffers from loss of orthogonality, and therefore its applicability is usually
limited to the ... | [
{
"created": "Fri, 7 Nov 2008 04:34:01 GMT",
"version": "v1"
}
] | 2008-11-10 | [
[
"Andrecut",
"M.",
""
]
] | Principal component analysis (PCA) is a key statistical technique for multivariate data analysis. For large data sets the common approach to PCA computation is based on the standard NIPALS-PCA algorithm, which unfortunately suffers from loss of orthogonality, and therefore its applicability is usually limited to the es... |
2306.15074 | Ilya Shirokov | D. V. Alekseevsky, I.M. Shirokov | Geometry of saccades and saccadic cycles | 9 pages, 3 figures | null | null | null | q-bio.NC math.DG | http://creativecommons.org/licenses/by/4.0/ | The paper is devoted to the development of the differential geometry of
saccades and saccadic cycles. We recall an interpretation of Donder's and
Listing's law in terms of the Hopf fibration of the $3$-sphere over the
$2$-sphere. In particular, the configuration space of the eye ball (when the
head is fixed) is the 2... | [
{
"created": "Mon, 26 Jun 2023 21:22:07 GMT",
"version": "v1"
}
] | 2023-06-28 | [
[
"Alekseevsky",
"D. V.",
""
],
[
"Shirokov",
"I. M.",
""
]
] | The paper is devoted to the development of the differential geometry of saccades and saccadic cycles. We recall an interpretation of Donder's and Listing's law in terms of the Hopf fibration of the $3$-sphere over the $2$-sphere. In particular, the configuration space of the eye ball (when the head is fixed) is the 2-d... |
1208.3847 | Miroslaw Rewekant PhD MD | S. Piekarski, M. Rewekant | On applications of conservation laws in pharmacokinetics | 6 pages | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There has been certain criticism raised by A. Rescigno [2,8,9,12-15] against
the standard formulation of pharmacokinetics. In 2011 it has been suggested
that inconsistencies in pharmacokinetics should be eliminated after deriving
"pharmacokinetic parameters" from conservation laws [3]. In the following text
a simple ... | [
{
"created": "Sun, 19 Aug 2012 15:46:23 GMT",
"version": "v1"
}
] | 2012-08-21 | [
[
"Piekarski",
"S.",
""
],
[
"Rewekant",
"M.",
""
]
] | There has been certain criticism raised by A. Rescigno [2,8,9,12-15] against the standard formulation of pharmacokinetics. In 2011 it has been suggested that inconsistencies in pharmacokinetics should be eliminated after deriving "pharmacokinetic parameters" from conservation laws [3]. In the following text a simple sy... |
1605.09697 | Augusto Gonzalez | Dario Leon and Augusto Gonzalez | Mutations as Levy flights | null | Scientific Reports volume 11, Article number: 9889 (2021) | 10.1038/s41598-021-88012-1 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Data from a long time evolution experiment with Escherichia Coli and from a
large study on copy number variations in subjects with european ancestry are
analyzed in order to argue that mutations can be described as Levy flights in
the mutation space. These Levy flights have at least two components: random
single-base... | [
{
"created": "Tue, 31 May 2016 16:13:10 GMT",
"version": "v1"
},
{
"created": "Fri, 1 Jul 2016 19:50:08 GMT",
"version": "v2"
},
{
"created": "Tue, 6 Jun 2017 20:27:52 GMT",
"version": "v3"
},
{
"created": "Mon, 16 Apr 2018 13:54:46 GMT",
"version": "v4"
},
{
"cre... | 2022-05-20 | [
[
"Leon",
"Dario",
""
],
[
"Gonzalez",
"Augusto",
""
]
] | Data from a long time evolution experiment with Escherichia Coli and from a large study on copy number variations in subjects with european ancestry are analyzed in order to argue that mutations can be described as Levy flights in the mutation space. These Levy flights have at least two components: random single-base s... |
1610.03443 | Axel Wedemeyer | Axel Wedemeyer, Lasse Kliemann, Anand Srivastav, Christian Schielke,
Thorsten B. Reusch, Philip Rosenstiel | An Improved Filtering Algorithm for Big Read Datasets | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | For single-cell or metagenomic sequencing projects, it is necessary to
sequence with a very high mean coverage in order to make sure that all parts of
the sample DNA get covered by the reads produced. This leads to huge datasets
with lots of redundant data. A filtering of this data prior to assembly is
advisable. Tit... | [
{
"created": "Tue, 11 Oct 2016 17:49:26 GMT",
"version": "v1"
}
] | 2016-10-12 | [
[
"Wedemeyer",
"Axel",
""
],
[
"Kliemann",
"Lasse",
""
],
[
"Srivastav",
"Anand",
""
],
[
"Schielke",
"Christian",
""
],
[
"Reusch",
"Thorsten B.",
""
],
[
"Rosenstiel",
"Philip",
""
]
] | For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots of redundant data. A filtering of this data prior to assembly is advisable. Titus... |
1305.5411 | Javier Galeano | Javier Garcia-Algarra, Javier Galeano, Juan Manuel Pastor, Jose Maria
Iriondo, and Jose J. Ramasco | Rethinking the logistic approach for population dynamics of mutualistic
interactions | 13 pages, 7 figures | Journal of Theoretical Biology 363, 332 (2014) | 10.1016/j.jtbi.2014.08.039 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mutualistic communities have an internal structure that makes them resilient
to external per- turbations. Late research has focused on their stability and
the topology of the relations between the different organisms to explain the
reasons of the system robustness. Much less attention has been invested in
analyzing t... | [
{
"created": "Thu, 23 May 2013 13:22:17 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Feb 2014 16:50:00 GMT",
"version": "v2"
}
] | 2014-09-19 | [
[
"Garcia-Algarra",
"Javier",
""
],
[
"Galeano",
"Javier",
""
],
[
"Pastor",
"Juan Manuel",
""
],
[
"Iriondo",
"Jose Maria",
""
],
[
"Ramasco",
"Jose J.",
""
]
] | Mutualistic communities have an internal structure that makes them resilient to external per- turbations. Late research has focused on their stability and the topology of the relations between the different organisms to explain the reasons of the system robustness. Much less attention has been invested in analyzing the... |
q-bio/0607042 | Miodrag Krmar | Vladan Pankovic, Banjac Dejan, Rade Glavatovic, Milan Predojevic | A Simple Solution of the Lotka-Volterra Equations | 6 pages, no figures | null | null | NS-PH-19/06 | q-bio.QM | null | In this work we consider a simple, approximate, tending toward exact,
solution of the system of two usual Lotka-Volterra differential equations.
Given solution is obtained by an iterative method. In any finite approximation
order of this solution, exponents of the corresponding Lotka-Volterra variables
have simple, t... | [
{
"created": "Mon, 24 Jul 2006 08:47:17 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Pankovic",
"Vladan",
""
],
[
"Dejan",
"Banjac",
""
],
[
"Glavatovic",
"Rade",
""
],
[
"Predojevic",
"Milan",
""
]
] | In this work we consider a simple, approximate, tending toward exact, solution of the system of two usual Lotka-Volterra differential equations. Given solution is obtained by an iterative method. In any finite approximation order of this solution, exponents of the corresponding Lotka-Volterra variables have simple, tim... |
2101.11712 | Adrian Buganza Tepole | Yue Leng, Vahidullah Tac, Sarah Calve, Adrian Buganza Tepole | Predicting the Mechanical Properties of Biopolymer Gels Using Neural
Networks Trained on Discrete Fiber Network Data | 20 pages, 9 figures, for associated files please see
https://bitbucket.org/buganzalab/nn_rve/src/master/ | null | 10.1016/j.cma.2021.114160 | null | q-bio.QM cs.CE cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biopolymer gels, such as those made out of fibrin or collagen, are widely
used in tissue engineering applications and biomedical research. Moreover,
fibrin naturally assembles into gels in vivo during wound healing and thrombus
formation. Macroscale biopolymer gel mechanics are dictated by the microscale
fiber networ... | [
{
"created": "Sat, 23 Jan 2021 23:52:33 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Aug 2021 15:04:29 GMT",
"version": "v2"
}
] | 2021-11-03 | [
[
"Leng",
"Yue",
""
],
[
"Tac",
"Vahidullah",
""
],
[
"Calve",
"Sarah",
""
],
[
"Tepole",
"Adrian Buganza",
""
]
] | Biopolymer gels, such as those made out of fibrin or collagen, are widely used in tissue engineering applications and biomedical research. Moreover, fibrin naturally assembles into gels in vivo during wound healing and thrombus formation. Macroscale biopolymer gel mechanics are dictated by the microscale fiber network.... |
2005.04424 | Avijit Maji | Avijit Maji, Tushar Choudhari, M.B. Sushma | Implication of Repatriating Migrant Workers on COVID-19 Spread and
Transportation Requirements | 22 pages, 8 figures, 8 tables | null | null | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by-sa/4.0/ | Nationwide lockdown for COVID-19 created an urgent demand for public
transportation among migrant workers stranded at different parts of India to
return to their native places. Arranging transportation could spike the number
of COVID-19 infected cases. Hence, this paper investigates the potential surge
in confirmed a... | [
{
"created": "Sat, 9 May 2020 12:24:01 GMT",
"version": "v1"
},
{
"created": "Thu, 30 Jul 2020 18:01:12 GMT",
"version": "v2"
}
] | 2020-08-03 | [
[
"Maji",
"Avijit",
""
],
[
"Choudhari",
"Tushar",
""
],
[
"Sushma",
"M. B.",
""
]
] | Nationwide lockdown for COVID-19 created an urgent demand for public transportation among migrant workers stranded at different parts of India to return to their native places. Arranging transportation could spike the number of COVID-19 infected cases. Hence, this paper investigates the potential surge in confirmed and... |
q-bio/0411032 | Michael LaMar | M. Drew LaMar, J. Xin, Y. Qi | Signal processing of acoustic signals in the time domain with an active
nonlinear nonlocal cochlear model | 19 pages, 9 figures | null | null | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A two space dimensional active nonlinear nonlocal cochlear model is
formulated in the time domain to capture nonlinear hearing effects such as
compression, multi-tone suppression and difference tones. The micromechanics of
the basilar membrane (BM) are incorporated to model active cochlear properties.
An active gain ... | [
{
"created": "Mon, 15 Nov 2004 19:06:19 GMT",
"version": "v1"
},
{
"created": "Tue, 6 Jul 2010 15:41:51 GMT",
"version": "v2"
}
] | 2010-07-07 | [
[
"LaMar",
"M. Drew",
""
],
[
"Xin",
"J.",
""
],
[
"Qi",
"Y.",
""
]
] | A two space dimensional active nonlinear nonlocal cochlear model is formulated in the time domain to capture nonlinear hearing effects such as compression, multi-tone suppression and difference tones. The micromechanics of the basilar membrane (BM) are incorporated to model active cochlear properties. An active gain pa... |
1807.04665 | Dirson Jian Li | Dirson Jian Li | Observations and perspectives on the prebiotic sequence evolution | 53 pages, 9 figures | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The post-genomic era has brought opportunities to bridge traditionally
separate fields of early history of life and brought new insight into origin
and evolution of biodiversity. According to distributions of codons in genome
sequences, I found a relationship between the genetic code and the tree of
life. This remote... | [
{
"created": "Thu, 12 Jul 2018 15:13:12 GMT",
"version": "v1"
}
] | 2018-07-13 | [
[
"Li",
"Dirson Jian",
""
]
] | The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I found a relationship between the genetic code and the tree of life. This remote a... |
1302.7301 | Krzysztof Argasinski | Krzysztof Argasinski and Mark Broom | Background fitness, eco-evolutionary feedbacks and the Hawk-Dove game | This paper is the research report from the grant and soon will be
replaced by two papers containing generalized extensins of the results
introduced in this paper | null | null | null | q-bio.PE math.CA nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper further develops work from a previous article which introduced a
new way of modelling evolutionary game models with an emphasis on ecological
realism, concerned with how ecological factors determine payoffs in
evolutionary games. The current paper is focused on the impact of selectively
neutral factors (i.... | [
{
"created": "Thu, 28 Feb 2013 19:56:16 GMT",
"version": "v1"
},
{
"created": "Sun, 2 Mar 2014 23:03:23 GMT",
"version": "v2"
}
] | 2014-03-05 | [
[
"Argasinski",
"Krzysztof",
""
],
[
"Broom",
"Mark",
""
]
] | This paper further develops work from a previous article which introduced a new way of modelling evolutionary game models with an emphasis on ecological realism, concerned with how ecological factors determine payoffs in evolutionary games. The current paper is focused on the impact of selectively neutral factors (i.e.... |
2202.05761 | Zachary Kilpatrick PhD | Subekshya Bidari, Ahmed El Hady, Jacob Davidson, and Zachary P
Kilpatrick | Stochastic dynamics of social patch foraging decisions | 24 pages, 7 figures | null | null | null | q-bio.PE q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Animals typically forage in groups. Social foraging can help animals avoid
predation and decrease their uncertainty about the richness of food resources.
Despite this, theoretical mechanistic models of patch foraging have
overwhelmingly focused on the behavior of single foragers. In this study, we
develop a mechanist... | [
{
"created": "Fri, 11 Feb 2022 16:52:13 GMT",
"version": "v1"
}
] | 2022-02-14 | [
[
"Bidari",
"Subekshya",
""
],
[
"Hady",
"Ahmed El",
""
],
[
"Davidson",
"Jacob",
""
],
[
"Kilpatrick",
"Zachary P",
""
]
] | Animals typically forage in groups. Social foraging can help animals avoid predation and decrease their uncertainty about the richness of food resources. Despite this, theoretical mechanistic models of patch foraging have overwhelmingly focused on the behavior of single foragers. In this study, we develop a mechanistic... |
1301.1017 | Andre Brown | Andr\'e E.X. Brown and William R. Schafer | Automated behavioural fingerprinting of C. elegans mutants | Accepted for publication in "Linking Phenotypes and Genotypes - How
to Infer Genetic Architecture from Perturbation Studies", edited by Florian
Markowetz (Cambridge) and Michael Boutros (Heidelberg), Cambridge University
Press. 28 pages, 6 figures | null | null | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rapid advances in genetics, genomics, and imaging have given insight into the
molecular and cellular basis of behaviour in a variety of model organisms with
unprecedented detail and scope. It is increasingly routine to isolate
behavioural mutants, clone and characterise mutant genes, and discern the
molecular and neu... | [
{
"created": "Sun, 6 Jan 2013 16:01:24 GMT",
"version": "v1"
}
] | 2013-01-08 | [
[
"Brown",
"André E. X.",
""
],
[
"Schafer",
"William R.",
""
]
] | Rapid advances in genetics, genomics, and imaging have given insight into the molecular and cellular basis of behaviour in a variety of model organisms with unprecedented detail and scope. It is increasingly routine to isolate behavioural mutants, clone and characterise mutant genes, and discern the molecular and neura... |
1212.0119 | Justin Fay | Elizabeth K. Engle and Justin C. Fay | ZRT1 harbors an excess of nonsynonymous polymorphism and shows evidence
of balancing selection in Saccharomyces cerevisiae | null | null | null | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by/3.0/ | Estimates of the fraction of nucleotide substitutions driven by positive
selection vary widely across different species. Accounting for different
estimates of positive selection has been difficult, in part because selection
on polymorphism within a species is known to obscure a signal of positive
selection between sp... | [
{
"created": "Sat, 1 Dec 2012 14:49:35 GMT",
"version": "v1"
}
] | 2012-12-04 | [
[
"Engle",
"Elizabeth K.",
""
],
[
"Fay",
"Justin C.",
""
]
] | Estimates of the fraction of nucleotide substitutions driven by positive selection vary widely across different species. Accounting for different estimates of positive selection has been difficult, in part because selection on polymorphism within a species is known to obscure a signal of positive selection between spec... |
1506.04437 | Tim Peterson | Timothy R. Peterson, Mathieu Laplante, Ed Van Veen, Marcel Van Vugt,
Carson C. Thoreen, David M. Sabatini | mTORC1 regulates cytokinesis through activation of Rho-ROCK signaling | https://onarbor.com/work/3/mtorc1-regulates-cytokinesis-through-activation-of-rho-rock-signaling | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the mechanisms by which cells coordinate their size with their
ability to divide has long attracted the interest of biologists. The Target of
Rapamycin (TOR) pathway is becoming increasingly recognized as a master
regulator of cell size, however less is known how TOR activity might be coupled
with the c... | [
{
"created": "Sun, 14 Jun 2015 20:47:56 GMT",
"version": "v1"
}
] | 2015-06-16 | [
[
"Peterson",
"Timothy R.",
""
],
[
"Laplante",
"Mathieu",
""
],
[
"Van Veen",
"Ed",
""
],
[
"Van Vugt",
"Marcel",
""
],
[
"Thoreen",
"Carson C.",
""
],
[
"Sabatini",
"David M.",
""
]
] | Understanding the mechanisms by which cells coordinate their size with their ability to divide has long attracted the interest of biologists. The Target of Rapamycin (TOR) pathway is becoming increasingly recognized as a master regulator of cell size, however less is known how TOR activity might be coupled with the cel... |
2201.11849 | Francesca Ballarini | J. Schuemann, A. McNamara, J. W. Warmenhoven, N. T. Henthorn, K.
Kirkby, M. J. Merchant, S. Ingram, H. Paganetti, KD. Held, J. Ramos-Mendez,
B. Faddegon, J. Perl, D. Goodhead, I. Plante, H. Rabus, H. Nettelbeck, W.
Friedland, P. Kundrat, A. Ottolenghi, G. Baiocco, S. Barbieri, M. Dingfelder,
S. Incerti, C. Vill... | A new Standard DNA damage (SDD) data format | null | Radiation Research, 191(1): 76-92 | 10.1667/RR15209.1 | null | q-bio.OT physics.med-ph | http://creativecommons.org/licenses/by/4.0/ | Our understanding of radiation induced cellular damage has greatly improved
over the past decades. Despite this progress, there are still many obstacles to
fully understanding how radiation interacts with biologically relevant cellular
components to form observable endpoints. One hurdle is the difficulty faced by
mem... | [
{
"created": "Tue, 11 Jan 2022 11:43:13 GMT",
"version": "v1"
}
] | 2022-01-31 | [
[
"Schuemann",
"J.",
""
],
[
"McNamara",
"A.",
""
],
[
"Warmenhoven",
"J. W.",
""
],
[
"Henthorn",
"N. T.",
""
],
[
"Kirkby",
"K.",
""
],
[
"Merchant",
"M. J.",
""
],
[
"Ingram",
"S.",
""
],
[
"Pagane... | Our understanding of radiation induced cellular damage has greatly improved over the past decades. Despite this progress, there are still many obstacles to fully understanding how radiation interacts with biologically relevant cellular components to form observable endpoints. One hurdle is the difficulty faced by membe... |
1211.6662 | Abdelmalik Moujahid | Abdelmalik Moujahid and Alicia D'Anjou | Metabolic efficiency with fast spiking in the squid axon | null | Front. Comput. Neurosci. (2012) 6:95 | 10.3389/fncom.2012.00095 | null | q-bio.NC math.DS physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fundamentally, action potentials in the squid axon are consequence of the
entrance of sodium ions during the depolarization of the rising phase of the
spike mediated by the outflow of potassium ions during the hyperpolarization of
the falling phase. Perfect metabolic efficiency with a minimum charge needed
for the ch... | [
{
"created": "Wed, 28 Nov 2012 17:09:14 GMT",
"version": "v1"
}
] | 2012-11-29 | [
[
"Moujahid",
"Abdelmalik",
""
],
[
"D'Anjou",
"Alicia",
""
]
] | Fundamentally, action potentials in the squid axon are consequence of the entrance of sodium ions during the depolarization of the rising phase of the spike mediated by the outflow of potassium ions during the hyperpolarization of the falling phase. Perfect metabolic efficiency with a minimum charge needed for the chan... |
1805.00548 | Mike Steel Prof. | Lina Herbst, Thomas Li, Mike Steel | Quantifying the accuracy of ancestral state prediction in a phylogenetic
tree under maximum parsimony | 26 pages, 4 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In phylogenetic studies, biologists often wish to estimate the ancestral
discrete character state at an interior vertex $v$ of an evolutionary tree $T$
from the states that are observed at the leaves of the tree. A simple and fast
estimation method --- maximum parsimony --- takes the ancestral state at $v$ to
be any ... | [
{
"created": "Tue, 1 May 2018 20:50:52 GMT",
"version": "v1"
}
] | 2018-05-03 | [
[
"Herbst",
"Lina",
""
],
[
"Li",
"Thomas",
""
],
[
"Steel",
"Mike",
""
]
] | In phylogenetic studies, biologists often wish to estimate the ancestral discrete character state at an interior vertex $v$ of an evolutionary tree $T$ from the states that are observed at the leaves of the tree. A simple and fast estimation method --- maximum parsimony --- takes the ancestral state at $v$ to be any st... |
q-bio/0410001 | Ken Kiyono | Zbigniew R. Struzik, Junichiro Hayano, Seiichiro Sakata, Shin Kwak,
Yoshiharu Yamamoto | 1/f Scaling in Heart Rate Requires Antagonistic Autonomic Control | 4 pages, 3 figures, to appear in Phys. Rev. E (2004) | null | 10.1103/PhysRevE.70.050901 | null | q-bio.OT | null | We present the first systematic evidence for the origins of 1/f-type temporal
scaling in human heart rate. The heart rate is regulated by the activity of two
branches of the autonomic nervous system: the parasympathetic (PNS) and the
sympathetic (SNS) nervous systems. We examine alterations in the scaling
property wh... | [
{
"created": "Fri, 1 Oct 2004 09:57:24 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Struzik",
"Zbigniew R.",
""
],
[
"Hayano",
"Junichiro",
""
],
[
"Sakata",
"Seiichiro",
""
],
[
"Kwak",
"Shin",
""
],
[
"Yamamoto",
"Yoshiharu",
""
]
] | We present the first systematic evidence for the origins of 1/f-type temporal scaling in human heart rate. The heart rate is regulated by the activity of two branches of the autonomic nervous system: the parasympathetic (PNS) and the sympathetic (SNS) nervous systems. We examine alterations in the scaling property when... |
2406.12064 | Yun William Yu | Xiaolei Brian Zhang, Grace Oualline, Jim Shaw, Yun William Yu | skandiver: a divergence-based analysis tool for identifying
intercellular mobile genetic elements | 9 pages, 6 figures | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mobile genetic elements (MGEs) are as ubiquitous in nature as they are varied
in type, ranging from viral insertions to transposons to incorporated plasmids.
Horizontal transfer of MGEs across bacterial species may also pose a
significant threat to global health due to their capability to harbour
antibiotic resistanc... | [
{
"created": "Mon, 17 Jun 2024 20:06:22 GMT",
"version": "v1"
}
] | 2024-06-19 | [
[
"Zhang",
"Xiaolei Brian",
""
],
[
"Oualline",
"Grace",
""
],
[
"Shaw",
"Jim",
""
],
[
"Yu",
"Yun William",
""
]
] | Mobile genetic elements (MGEs) are as ubiquitous in nature as they are varied in type, ranging from viral insertions to transposons to incorporated plasmids. Horizontal transfer of MGEs across bacterial species may also pose a significant threat to global health due to their capability to harbour antibiotic resistance ... |
2006.03017 | Matthew Mizuhara | Nicolas Bolle, Matthew S. Mizuhara | Dynamics of a cell motility model near the sharp interface limit | 18 pages, 5 figures | null | 10.1016/j.jtbi.2020.110420 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phase-field models have recently had great success in describing the dynamic
morphologies and motility of eukaryotic cells. In this work we investigate the
minimal phase-field model introduced in [Berlyand, Potomkin, Rybalko (2017)].
Rigorous analysis of its sharp interface limit dynamics was completed in
[Mizuhara, ... | [
{
"created": "Thu, 4 Jun 2020 17:09:58 GMT",
"version": "v1"
},
{
"created": "Fri, 31 Jul 2020 15:11:11 GMT",
"version": "v2"
}
] | 2020-08-03 | [
[
"Bolle",
"Nicolas",
""
],
[
"Mizuhara",
"Matthew S.",
""
]
] | Phase-field models have recently had great success in describing the dynamic morphologies and motility of eukaryotic cells. In this work we investigate the minimal phase-field model introduced in [Berlyand, Potomkin, Rybalko (2017)]. Rigorous analysis of its sharp interface limit dynamics was completed in [Mizuhara, Be... |
1901.04143 | Sheryl Chang | Sheryl L. Chang and Mahendra Piraveenan and Philippa Pattison and
Mikhail Prokopenko | Game theoretic modelling of infectious disease dynamics and intervention
methods: a mini-review | 24 pages, 10 figures | Journal of biological dynamics 14(1),2020,p p.57-89 | 10.1080/17513758.2020.1720322 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We review research papers which use game theory to model the decision making
of individuals during an epidemic, attempting to classify the literature and
identify the emerging trends in this field. We show that the literature can be
classified based on (i) type of population modelling (compartmental or
network-based)... | [
{
"created": "Mon, 14 Jan 2019 06:15:55 GMT",
"version": "v1"
}
] | 2020-02-13 | [
[
"Chang",
"Sheryl L.",
""
],
[
"Piraveenan",
"Mahendra",
""
],
[
"Pattison",
"Philippa",
""
],
[
"Prokopenko",
"Mikhail",
""
]
] | We review research papers which use game theory to model the decision making of individuals during an epidemic, attempting to classify the literature and identify the emerging trends in this field. We show that the literature can be classified based on (i) type of population modelling (compartmental or network-based), ... |
0808.4016 | Nikolai Sinitsyn | N. A. Sinitsyn, Nicolas Hengartner, Ilya Nemenman | Coarse-graining stochastic biochemical networks: quasi-stationary
approximation and fast simulations using a stochastic path integral technique | 29 pages, 8 figures | Proceed. Natl. Acad. Sci. U. S. A., 2009 106:10546-10551 | null | Technical Report: LA-UR 08-0025 | q-bio.MN cond-mat.stat-mech physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a universal approach for analysis and fast simulations of stiff
stochastic biochemical kinetics networks, which rests on elimination of fast
chemical species without a loss of information about mesoscopic, non-Poissonian
fluctuations of the slow ones. Our approach, which is similar to the
Born-Oppenheimer ... | [
{
"created": "Fri, 29 Aug 2008 02:18:21 GMT",
"version": "v1"
}
] | 2009-07-07 | [
[
"Sinitsyn",
"N. A.",
""
],
[
"Hengartner",
"Nicolas",
""
],
[
"Nemenman",
"Ilya",
""
]
] | We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian fluctuations of the slow ones. Our approach, which is similar to the Born-Oppenheimer ap... |
q-bio/0605019 | Javier Buldu | Pablo Balenzuela, Javier M. Buldu, Marcos Casanova and Jordi
Garcia-Ojalvo | Episodic synchronization in dynamically driven neurons | 7 pages, 8 figures | null | 10.1103/PhysRevE.74.061910 | null | q-bio.NC | null | We examine the response of type II excitable neurons to trains of synaptic
pulses, as a function of the pulse frequency and amplitude. We show that the
resonant behavior characteristic of type II excitability, already described for
harmonic inputs, is also present for pulsed inputs. With this in mind, we study
the re... | [
{
"created": "Fri, 12 May 2006 08:07:42 GMT",
"version": "v1"
}
] | 2015-06-26 | [
[
"Balenzuela",
"Pablo",
""
],
[
"Buldu",
"Javier M.",
""
],
[
"Casanova",
"Marcos",
""
],
[
"Garcia-Ojalvo",
"Jordi",
""
]
] | We examine the response of type II excitable neurons to trains of synaptic pulses, as a function of the pulse frequency and amplitude. We show that the resonant behavior characteristic of type II excitability, already described for harmonic inputs, is also present for pulsed inputs. With this in mind, we study the resp... |
2406.05170 | Danyi Huang | Danyi Huang, Ziang Liu and Yizhou Li | Research on Tumors Segmentation based on Image Enhancement Method | null | null | null | null | q-bio.OT cs.CV eess.IV | http://creativecommons.org/licenses/by-nc-nd/4.0/ | One of the most effective ways to treat liver cancer is to perform precise
liver resection surgery, the key step of which includes precise digital image
segmentation of the liver and its tumor. However, traditional liver parenchymal
segmentation techniques often face several challenges in performing liver
segmentatio... | [
{
"created": "Fri, 7 Jun 2024 12:25:04 GMT",
"version": "v1"
}
] | 2024-06-11 | [
[
"Huang",
"Danyi",
""
],
[
"Liu",
"Ziang",
""
],
[
"Li",
"Yizhou",
""
]
] | One of the most effective ways to treat liver cancer is to perform precise liver resection surgery, the key step of which includes precise digital image segmentation of the liver and its tumor. However, traditional liver parenchymal segmentation techniques often face several challenges in performing liver segmentation:... |
2402.04241 | Alexey Ovchinnikov | Helen Byrne, Heather Harrington, Alexey Ovchinnikov, Gleb Pogudin,
Hamid Rahkooy, and Pedro Soto | Algebraic identifiability of partial differential equation models | null | null | null | null | q-bio.QM cs.SC cs.SY eess.SY math.AP | http://creativecommons.org/licenses/by/4.0/ | Differential equation models are crucial to scientific processes. The values
of model parameters are important for analyzing the behaviour of solutions. A
parameter is called globally identifiable if its value can be uniquely
determined from the input and output functions. To determine if a parameter
estimation probl... | [
{
"created": "Tue, 6 Feb 2024 18:49:51 GMT",
"version": "v1"
}
] | 2024-02-07 | [
[
"Byrne",
"Helen",
""
],
[
"Harrington",
"Heather",
""
],
[
"Ovchinnikov",
"Alexey",
""
],
[
"Pogudin",
"Gleb",
""
],
[
"Rahkooy",
"Hamid",
""
],
[
"Soto",
"Pedro",
""
]
] | Differential equation models are crucial to scientific processes. The values of model parameters are important for analyzing the behaviour of solutions. A parameter is called globally identifiable if its value can be uniquely determined from the input and output functions. To determine if a parameter estimation problem... |
2202.01104 | Charles Puelz | Zan Ahmad, Lynn H. Jin, Daniel J. Penny, Craig G. Rusin, Charles S.
Peskin, Charles Puelz | Optimal fenestration of the Fontan circulation | null | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | In this paper, we develop a pulsatile compartmental model of the Fontan
circulation and use it to explore the effects of a fenestration added to this
physiology. A fenestration is a shunt between the systemic and pulmonary veins
that is added either at the time of Fontan conversion or at a later time for
the treatmen... | [
{
"created": "Wed, 2 Feb 2022 16:04:12 GMT",
"version": "v1"
},
{
"created": "Tue, 21 Jun 2022 19:43:01 GMT",
"version": "v2"
}
] | 2022-06-23 | [
[
"Ahmad",
"Zan",
""
],
[
"Jin",
"Lynn H.",
""
],
[
"Penny",
"Daniel J.",
""
],
[
"Rusin",
"Craig G.",
""
],
[
"Peskin",
"Charles S.",
""
],
[
"Puelz",
"Charles",
""
]
] | In this paper, we develop a pulsatile compartmental model of the Fontan circulation and use it to explore the effects of a fenestration added to this physiology. A fenestration is a shunt between the systemic and pulmonary veins that is added either at the time of Fontan conversion or at a later time for the treatment ... |
1608.06723 | Bo Sun | Amani A. Alobaidi and Bo Sun | Probing Three-dimensional Collective Cancer Invasion with DIGME | null | null | null | null | q-bio.TO q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multicellular migration and pattern formation play important roles in
developmental biology, cancer metastasis and wound healing. To understand the
collective cell dynamics in three dimensional extracellular matrix (ECM), we
have developed a simple and mechanical-based strategy, Diskoid In Geometrically
Micropatterne... | [
{
"created": "Wed, 24 Aug 2016 06:02:12 GMT",
"version": "v1"
}
] | 2016-08-25 | [
[
"Alobaidi",
"Amani A.",
""
],
[
"Sun",
"Bo",
""
]
] | Multicellular migration and pattern formation play important roles in developmental biology, cancer metastasis and wound healing. To understand the collective cell dynamics in three dimensional extracellular matrix (ECM), we have developed a simple and mechanical-based strategy, Diskoid In Geometrically Micropatterned ... |
q-bio/0606032 | Maria A. Avi\~no-Diaz | Maria A. Avino-Diaz and Oscar Moreno | Probabilistic Regulatory Networks: Modeling Genetic Networks | 8 pages, 2 figures, International Congress of Matematicians, to be
published in Proceedings of the Fifth International Conference on Engineering
Computational Technology, 2006, Las Palmas, Gran Canaria | null | null | null | q-bio.GN math.DS | null | We describe here the new concept of $\epsilon$-Homomorphisms of Probabilistic
Regulatory Gene Networks(PRN). The $\epsilon$-homomorphisms are special
mappings between two probabilistic networks, that consider the algebraic action
of the iteration of functions and the probabilistic dynamic of the two
networks. It is p... | [
{
"created": "Thu, 22 Jun 2006 18:39:47 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Avino-Diaz",
"Maria A.",
""
],
[
"Moreno",
"Oscar",
""
]
] | We describe here the new concept of $\epsilon$-Homomorphisms of Probabilistic Regulatory Gene Networks(PRN). The $\epsilon$-homomorphisms are special mappings between two probabilistic networks, that consider the algebraic action of the iteration of functions and the probabilistic dynamic of the two networks. It is pro... |
0811.3514 | Noa Sela | Galit Lev-Maor, Amir Goren, Noa Sela, Eddo Kim, Hadas Keren, Adi
Doron-Faigenboim, Shelly Leibman-Barak, Tal Pupko, Gil Ast | The Alternative Choice of Constitutive Exons throughout Evolution | null | PLoS Genet 2007 3(11): e203 | null | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Alternative cassette exons are known to originate from two processes
exonization of intronic sequences and exon shuffling. Herein, we suggest an
additional mechanism by which constitutively spliced exons become alternative
cassette exons during evolution. We compiled a dataset of orthologous exons
from human and mous... | [
{
"created": "Fri, 21 Nov 2008 11:05:21 GMT",
"version": "v1"
}
] | 2008-11-24 | [
[
"Lev-Maor",
"Galit",
""
],
[
"Goren",
"Amir",
""
],
[
"Sela",
"Noa",
""
],
[
"Kim",
"Eddo",
""
],
[
"Keren",
"Hadas",
""
],
[
"Doron-Faigenboim",
"Adi",
""
],
[
"Leibman-Barak",
"Shelly",
""
],
[
"P... | Alternative cassette exons are known to originate from two processes exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced exons become alternative cassette exons during evolution. We compiled a dataset of orthologous exons from human and mouse ... |
2305.01475 | Teddy Lazebnik Dr. | Teddy Lazebnik, Liron Simon-Keren | Cancer-inspired Genomics Mapper Model for the Generation of Synthetic
DNA Sequences with Desired Genomics Signatures | null | null | 10.1016/j.compbiomed.2023.107221 | null | q-bio.GN cs.LG cs.NE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Genome data are crucial in modern medicine, offering significant potential
for diagnosis and treatment. Thanks to technological advancements, many
millions of healthy and diseased genomes have already been sequenced; however,
obtaining the most suitable data for a specific study, and specifically for
validation studi... | [
{
"created": "Mon, 1 May 2023 07:16:40 GMT",
"version": "v1"
}
] | 2024-06-18 | [
[
"Lazebnik",
"Teddy",
""
],
[
"Simon-Keren",
"Liron",
""
]
] | Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the most suitable data for a specific study, and specifically for validation studies... |
1410.7346 | Paolo Zuliani | Bing Liu, Soonho Kong, Sicun Gao, Paolo Zuliani, Edmund M. Clarke | Towards Personalized Prostate Cancer Therapy Using Delta-Reachability
Analysis | HSCC 2015 | null | 10.1145/2728606.2728634 | null | q-bio.QM cs.LO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent clinical studies suggest that the efficacy of hormone therapy for
prostate cancer depends on the characteristics of individual patients. In this
paper, we develop a computational framework for identifying patient-specific
androgen ablation therapy schedules for postponing the potential cancer
relapse. We model... | [
{
"created": "Mon, 27 Oct 2014 18:36:40 GMT",
"version": "v1"
},
{
"created": "Thu, 19 Mar 2015 09:33:47 GMT",
"version": "v2"
},
{
"created": "Tue, 19 May 2015 13:17:29 GMT",
"version": "v3"
}
] | 2015-05-20 | [
[
"Liu",
"Bing",
""
],
[
"Kong",
"Soonho",
""
],
[
"Gao",
"Sicun",
""
],
[
"Zuliani",
"Paolo",
""
],
[
"Clarke",
"Edmund M.",
""
]
] | Recent clinical studies suggest that the efficacy of hormone therapy for prostate cancer depends on the characteristics of individual patients. In this paper, we develop a computational framework for identifying patient-specific androgen ablation therapy schedules for postponing the potential cancer relapse. We model t... |
2112.07295 | Alexey Zharinov | A. I. Zharinov, Y. A. Tsybina, S. Y. Gordleeva | Review: CPG as a controller for biomimetic floating robots | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | All vertebrates are capable of performing various types of physical activity.
Locomotor patterns are created by the cyclical coordinated work of the skeletal
muscles. The organization of such a system in living organisms is responsible
for networks of interconnected populations of neurons capable of forming
rhythmic ... | [
{
"created": "Tue, 14 Dec 2021 11:03:40 GMT",
"version": "v1"
}
] | 2021-12-15 | [
[
"Zharinov",
"A. I.",
""
],
[
"Tsybina",
"Y. A.",
""
],
[
"Gordleeva",
"S. Y.",
""
]
] | All vertebrates are capable of performing various types of physical activity. Locomotor patterns are created by the cyclical coordinated work of the skeletal muscles. The organization of such a system in living organisms is responsible for networks of interconnected populations of neurons capable of forming rhythmic ac... |
1307.7820 | Aaron Darling | Balaji Venkatachalam, Dan Gusfield, and Yelena Frid | Faster Algorithms for RNA-folding using the Four-Russians method | Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013). Editor's note: abstract was
shortened to comply with arxiv requirements. Full abstract in PDF | null | null | null | q-bio.QM cs.CE cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The secondary structure that maximizes the number of non-crossing matchings
between complimentary bases of an RNA sequence of length n can be computed in
O(n^3) time using Nussinov's dynamic programming algorithm. The Four-Russians
method is a technique that will reduce the running time for certain dynamic
programmin... | [
{
"created": "Tue, 30 Jul 2013 05:13:11 GMT",
"version": "v1"
}
] | 2013-08-02 | [
[
"Venkatachalam",
"Balaji",
""
],
[
"Gusfield",
"Dan",
""
],
[
"Frid",
"Yelena",
""
]
] | The secondary structure that maximizes the number of non-crossing matchings between complimentary bases of an RNA sequence of length n can be computed in O(n^3) time using Nussinov's dynamic programming algorithm. The Four-Russians method is a technique that will reduce the running time for certain dynamic programming ... |
1210.6998 | Jong-Chin Lin | Jong-Chin Lin and D. Thirumalai | Gene Regulation by Riboswitches with and without Negative Feedback Loop | 12 pages, 8 figures | null | 10.1016/j.bpj.2012.10.026 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Riboswitches, structured elements in the untranslated regions of messenger
RNAs, regulate gene expression by binding specific metabolites. We introduce a
kinetic network model that describes the functions of riboswitches at the
systems level. Using experimental data for flavin mono nucleotide riboswitch as
a guide we... | [
{
"created": "Thu, 25 Oct 2012 20:55:48 GMT",
"version": "v1"
}
] | 2015-06-11 | [
[
"Lin",
"Jong-Chin",
""
],
[
"Thirumalai",
"D.",
""
]
] | Riboswitches, structured elements in the untranslated regions of messenger RNAs, regulate gene expression by binding specific metabolites. We introduce a kinetic network model that describes the functions of riboswitches at the systems level. Using experimental data for flavin mono nucleotide riboswitch as a guide we s... |
2211.13231 | Kishan K C | Kishan KC, Rui Li, Paribesh Regmi, Anne R. Haake | Predicting Biomedical Interactions with Probabilistic Model Selection
for Graph Neural Networks | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | A biological system is a complex network of heterogeneous molecular entities
and their interactions contributing to various biological characteristics of
the system. However, current biological networks are noisy, sparse, and
incomplete, limiting our ability to create a holistic view of the biological
system and unde... | [
{
"created": "Tue, 22 Nov 2022 20:44:28 GMT",
"version": "v1"
},
{
"created": "Sat, 3 Dec 2022 20:02:35 GMT",
"version": "v2"
}
] | 2022-12-06 | [
[
"KC",
"Kishan",
""
],
[
"Li",
"Rui",
""
],
[
"Regmi",
"Paribesh",
""
],
[
"Haake",
"Anne R.",
""
]
] | A biological system is a complex network of heterogeneous molecular entities and their interactions contributing to various biological characteristics of the system. However, current biological networks are noisy, sparse, and incomplete, limiting our ability to create a holistic view of the biological system and unders... |
2406.05347 | Bo Chen | Bo Chen, Zhilei Bei, Xingyi Cheng, Pan Li, Jie Tang, Le Song | MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative
Pre-Training | null | null | null | null | q-bio.BM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the
evolutionary trajectories of protein families. The accuracy of protein
structure predictions is often compromised for protein sequences that lack
sufficient homologous information to construct high quality MSA. Although
various methods have been ... | [
{
"created": "Sat, 8 Jun 2024 04:23:57 GMT",
"version": "v1"
},
{
"created": "Tue, 11 Jun 2024 02:42:17 GMT",
"version": "v2"
}
] | 2024-06-12 | [
[
"Chen",
"Bo",
""
],
[
"Bei",
"Zhilei",
""
],
[
"Cheng",
"Xingyi",
""
],
[
"Li",
"Pan",
""
],
[
"Tang",
"Jie",
""
],
[
"Song",
"Le",
""
]
] | Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been pr... |
2206.14566 | Rong Ma | Tal Einav and Rong Ma | Using Interpretable Machine Learning to Massively Increase the Number of
Antibody-Virus Interactions Across Studies | null | Cell Reports Methods, 2023 | 10.1016/j.crmeth.2023.100540 | null | q-bio.QM cs.LG q-bio.BM q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | A central challenge in every field of biology is to use existing measurements
to predict the outcomes of future experiments. In this work, we consider the
wealth of antibody inhibition data against variants of the influenza virus. Due
to this viru's genetic diversity and evolvability, the variants examined in one
stu... | [
{
"created": "Fri, 10 Jun 2022 20:14:01 GMT",
"version": "v1"
},
{
"created": "Sun, 30 Oct 2022 12:35:32 GMT",
"version": "v2"
}
] | 2023-07-27 | [
[
"Einav",
"Tal",
""
],
[
"Ma",
"Rong",
""
]
] | A central challenge in every field of biology is to use existing measurements to predict the outcomes of future experiments. In this work, we consider the wealth of antibody inhibition data against variants of the influenza virus. Due to this viru's genetic diversity and evolvability, the variants examined in one study... |
1512.04982 | Pascal Fieth | Pascal Fieth and Alexander K. Hartmann | Score distributions of gapped multiple sequence alignments down to the
low-probability tail | null | Phys. Rev. E 94, 022127 (2016) | 10.1103/PhysRevE.94.022127 | null | q-bio.QM cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Assessing the significance of alignment scores of optimally aligned DNA or
amino acid sequences can be achieved via the knowledge of the score
distribution of random sequences. But this requires obtaining the distribution
in the biologically relevant high-scoring region, where the probabilities are
exponentially smal... | [
{
"created": "Mon, 7 Dec 2015 16:22:15 GMT",
"version": "v1"
}
] | 2016-08-24 | [
[
"Fieth",
"Pascal",
""
],
[
"Hartmann",
"Alexander K.",
""
]
] | Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are exponentially small.... |
2004.09644 | Carlos Pajares | J. E. Ram\'irez and C. Pajares and M. I. Mart\'inez and R. Rodr\'iguez
Fern\'andez and E. Molina-Gayosso and J. Lozada-Lechuga and A. Fern\'andez
T\'ellez | Site-bond percolation solution to preventing the propagation of
\textit{Phytophthora} zoospores on plantations | 13 pages, 7 figures | Phys. Rev. E, 101, 032301, 2020 | 10.1103/PhysRevE.101.032301 | null | q-bio.PE cond-mat.stat-mech physics.soc-ph | http://creativecommons.org/publicdomain/zero/1.0/ | We propose a strategy based on the site-bond percolation to minimize the
propagation of \textit{Phytophthora} zoospores on plantations, consisting in
introducing physical barriers between neighboring plants. Two clustering
processes are distinguished: i) one of cells with the presence of the pathogen,
detected on soi... | [
{
"created": "Mon, 20 Apr 2020 21:27:15 GMT",
"version": "v1"
}
] | 2020-04-22 | [
[
"Ramírez",
"J. E.",
""
],
[
"Pajares",
"C.",
""
],
[
"Martínez",
"M. I.",
""
],
[
"Fernández",
"R. Rodríguez",
""
],
[
"Molina-Gayosso",
"E.",
""
],
[
"Lozada-Lechuga",
"J.",
""
],
[
"Téllez",
"A. Fernández",
... | We propose a strategy based on the site-bond percolation to minimize the propagation of \textit{Phytophthora} zoospores on plantations, consisting in introducing physical barriers between neighboring plants. Two clustering processes are distinguished: i) one of cells with the presence of the pathogen, detected on soil ... |
1311.4384 | Wan-Chung Hu Dr. | Wan-Chung Hu | Acute Respiratory Distress Syndrome is a TH17-like and Treg immune
disease | null | null | null | null | q-bio.TO q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Acute Respiratory Distress Syndrome (ARDS) is a very severe syndrome leading
to respiratory failure and subsequent mortality. Sepsis is one of the leading
causes of ARDS. Thus, extracellular bacteria play an important role in the
pathophysiology of ARDS. Overactivated neutrophils are the major effector cells
in ARDS.... | [
{
"created": "Mon, 18 Nov 2013 14:11:05 GMT",
"version": "v1"
}
] | 2013-11-19 | [
[
"Hu",
"Wan-Chung",
""
]
] | Acute Respiratory Distress Syndrome (ARDS) is a very severe syndrome leading to respiratory failure and subsequent mortality. Sepsis is one of the leading causes of ARDS. Thus, extracellular bacteria play an important role in the pathophysiology of ARDS. Overactivated neutrophils are the major effector cells in ARDS. T... |
2012.04968 | Luis Aniello La Rocca | Luis A. La Rocca, Julia Frank, Heidi Beate Bentzen, Jean-Tori Pantel,
Konrad Gerischer, Anton Bovier and Peter M. Krawitz | A lower prevalence for recessive disorders in a random mating population
is a transient phenomenon during and after a growth phase | A video clip of our simulations can be found at
https://youtu.be/5hOgLyRqWPg | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Despite increasing data from population-wide sequencing studies, the risk for
recessive disorders in consanguineous partnerships is still heavily debated. An
important aspect that has not sufficiently been investigated theoretically, is
the influence of inbreeding on mutation load and incidence rates when the
populat... | [
{
"created": "Wed, 9 Dec 2020 10:45:25 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Dec 2020 12:49:48 GMT",
"version": "v2"
}
] | 2020-12-23 | [
[
"La Rocca",
"Luis A.",
""
],
[
"Frank",
"Julia",
""
],
[
"Bentzen",
"Heidi Beate",
""
],
[
"Pantel",
"Jean-Tori",
""
],
[
"Gerischer",
"Konrad",
""
],
[
"Bovier",
"Anton",
""
],
[
"Krawitz",
"Peter M.",
""
... | Despite increasing data from population-wide sequencing studies, the risk for recessive disorders in consanguineous partnerships is still heavily debated. An important aspect that has not sufficiently been investigated theoretically, is the influence of inbreeding on mutation load and incidence rates when the populatio... |
1304.7905 | Sergej Mironov | S. L. Mironov | Theory and experiment reveal unexpected calcium profiles in
one-dimensional systems | null | null | null | null | q-bio.SC q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Calcium is an ubiquitous second messenger that triggers a plethora of key
physiological responses. The events are initiated in micro- or nano-sized
compartments and determined by the complex interactions with calcium-binding
proteins and mechanisms of calcium clearance. Local calcium increases in the
vicinity of sing... | [
{
"created": "Tue, 30 Apr 2013 07:51:19 GMT",
"version": "v1"
}
] | 2013-05-01 | [
[
"Mironov",
"S. L.",
""
]
] | Calcium is an ubiquitous second messenger that triggers a plethora of key physiological responses. The events are initiated in micro- or nano-sized compartments and determined by the complex interactions with calcium-binding proteins and mechanisms of calcium clearance. Local calcium increases in the vicinity of single... |
1401.4832 | Magnus Ekeberg | Magnus Ekeberg, Tuomo Hartonen, Erik Aurell | Fast pseudolikelihood maximization for direct-coupling analysis of
protein structure from many homologous amino-acid sequences | 33 pages, 4 figures; M. Ekeberg and T. Hartonen are joint first
authors; code and supplementary information on http://plmdca.csc.kth.se/ | Journal of Computational Physics 276 (2014) 341-356 | 10.1016/j.jcp.2014.07.024 | null | q-bio.QM physics.comp-ph physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Direct-Coupling Analysis is a group of methods to harvest information about
coevolving residues in a protein family by learning a generative model in an
exponential family from data. In protein families of realistic size, this
learning can only be done approximately, and there is a trade-off between
inference precisi... | [
{
"created": "Mon, 20 Jan 2014 09:15:01 GMT",
"version": "v1"
}
] | 2014-09-16 | [
[
"Ekeberg",
"Magnus",
""
],
[
"Hartonen",
"Tuomo",
""
],
[
"Aurell",
"Erik",
""
]
] | Direct-Coupling Analysis is a group of methods to harvest information about coevolving residues in a protein family by learning a generative model in an exponential family from data. In protein families of realistic size, this learning can only be done approximately, and there is a trade-off between inference precision... |
2004.11244 | Aurelie Nakamura | Aurelie Nakamura (iPLESP), Fabienne El-Khoury (iPLESP), Anne-Laure
Sutter-Dallay (BPH), Jeanna-Eve Franck (iPLESP), Xavier Thierry (ELFE), Maria
Melchior (iPLESP), Judith van der Waerden (iPLESP) | Partner support during pregnancy mediates social inequalities in
maternal postpartum depression for non-migrant and first generation migrant
women | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background An advantaged socioeconomic position (SEP) and satisfying social
support during pregnancy (SSP) have been found to be protective factors of
maternal postpartum depression (PDD). An advantaged SEP is also associated with
satisfying SSP, making SSP a potential mediator of social inequalities in PPD.
SEP, SSP... | [
{
"created": "Wed, 22 Apr 2020 08:20:17 GMT",
"version": "v1"
}
] | 2020-04-24 | [
[
"Nakamura",
"Aurelie",
"",
"iPLESP"
],
[
"El-Khoury",
"Fabienne",
"",
"iPLESP"
],
[
"Sutter-Dallay",
"Anne-Laure",
"",
"BPH"
],
[
"Franck",
"Jeanna-Eve",
"",
"iPLESP"
],
[
"Thierry",
"Xavier",
"",
"ELFE"
],
[
"... | Background An advantaged socioeconomic position (SEP) and satisfying social support during pregnancy (SSP) have been found to be protective factors of maternal postpartum depression (PDD). An advantaged SEP is also associated with satisfying SSP, making SSP a potential mediator of social inequalities in PPD. SEP, SSP a... |
0802.4010 | Marcus Kaiser | Marcus Kaiser | Brain architecture: A design for natural computation | null | Philosophical Transactions of The Royal Society A, 365: 3033-3045,
2007 | 10.1098/rsta.2007.0007 | null | q-bio.NC cs.AI cs.NE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fifty years ago, John von Neumann compared the architecture of the brain with
that of computers that he invented and which is still in use today. In those
days, the organisation of computers was based on concepts of brain
organisation. Here, we give an update on current results on the global
organisation of neural sy... | [
{
"created": "Wed, 27 Feb 2008 13:00:38 GMT",
"version": "v1"
}
] | 2008-02-28 | [
[
"Kaiser",
"Marcus",
""
]
] | Fifty years ago, John von Neumann compared the architecture of the brain with that of computers that he invented and which is still in use today. In those days, the organisation of computers was based on concepts of brain organisation. Here, we give an update on current results on the global organisation of neural syst... |
1804.04839 | Emanuel Weitschek | Fabrizio Celli, Fabio Cumbo, and Emanuel Weitschek | Classification of large DNA methylation datasets for identifying cancer
drivers | null | F. Celli, F. Cumbo, E. Weitschek: Classification of Large DNA
Methylation Datasets for Identifying Cancer Drivers. Big Data Research,
10.1016/j.bdr.2018.02.005, 2018 | 10.1016/j.bdr.2018.02.005 | null | q-bio.GN cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | DNA methylation is a well-studied genetic modification crucial to regulate
the functioning of the genome. Its alterations play an important role in
tumorigenesis and tumor-suppression. Thus, studying DNA methylation data may
help biomarker discovery in cancer. Since public data on DNA methylation become
abundant, and... | [
{
"created": "Fri, 13 Apr 2018 08:53:39 GMT",
"version": "v1"
}
] | 2018-04-16 | [
[
"Celli",
"Fabrizio",
""
],
[
"Cumbo",
"Fabio",
""
],
[
"Weitschek",
"Emanuel",
""
]
] | DNA methylation is a well-studied genetic modification crucial to regulate the functioning of the genome. Its alterations play an important role in tumorigenesis and tumor-suppression. Thus, studying DNA methylation data may help biomarker discovery in cancer. Since public data on DNA methylation become abundant, and c... |
2206.06096 | Vadim Weinstein | Vadim Weinstein, Basak Sakcak, Steven M. LaValle | An Enactivist-Inspired Mathematical Model of Cognition | null | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by-nc-sa/4.0/ | We formulate five basic tenets of enactivist cognitive science that we have
carefully identified in the relevant literature as the main underlying
principles of that philosophy. We then develop a mathematical framework to talk
about cognitive systems (both artificial and natural) which complies with these
enactivist ... | [
{
"created": "Fri, 10 Jun 2022 13:03:47 GMT",
"version": "v1"
}
] | 2022-06-14 | [
[
"Weinstein",
"Vadim",
""
],
[
"Sakcak",
"Basak",
""
],
[
"LaValle",
"Steven M.",
""
]
] | We formulate five basic tenets of enactivist cognitive science that we have carefully identified in the relevant literature as the main underlying principles of that philosophy. We then develop a mathematical framework to talk about cognitive systems (both artificial and natural) which complies with these enactivist te... |
1412.2622 | Alexander K. Vidybida | Alexander Vidybida | Output stream of binding neuron with delayed feedback | 10 pages, 5 figures, 14-th International Congress of Cybernetics and
Systems of WOSC, Wroclaw, September 9-12, 2008, Proceedings, pages 292-302,
Oficyna Wydawnicza Politechniki Wroclawskiej, ISBN 978-83-7493-400-8 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A binding neuron (BN) whith delayed feedback is considered. The neuron is fed
externally with a Poisson stream of intensity $\lambda$. The neuron's output
spikes are fed into its input with time delay $\Delta$. The resulting output
stream of the BN is not Poissonian, and we look for its interspike intervals
(ISI) dis... | [
{
"created": "Mon, 8 Dec 2014 15:49:58 GMT",
"version": "v1"
}
] | 2014-12-09 | [
[
"Vidybida",
"Alexander",
""
]
] | A binding neuron (BN) whith delayed feedback is considered. The neuron is fed externally with a Poisson stream of intensity $\lambda$. The neuron's output spikes are fed into its input with time delay $\Delta$. The resulting output stream of the BN is not Poissonian, and we look for its interspike intervals (ISI) distr... |
2207.07714 | Ver\'onica Moreno Vero | Gabriel Pena, Ver\'onica Moreno, Nestor Barraza | Measuring COVID-19 spreading speed through the mean time between
infections indicator | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose to use the mean time between infections (MTBI) metric as obtained
from a recently introduced non-homogeneous Markov stochastic model. Different
types of parameter calibration are performed. We estimate the MTBI using data
from different time windows and from the whole stage history and compare the
results.... | [
{
"created": "Fri, 15 Jul 2022 19:12:53 GMT",
"version": "v1"
}
] | 2022-07-19 | [
[
"Pena",
"Gabriel",
""
],
[
"Moreno",
"Verónica",
""
],
[
"Barraza",
"Nestor",
""
]
] | We propose to use the mean time between infections (MTBI) metric as obtained from a recently introduced non-homogeneous Markov stochastic model. Different types of parameter calibration are performed. We estimate the MTBI using data from different time windows and from the whole stage history and compare the results. I... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.