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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2106.07865 | Brandon Munn | Brandon R. Munn, Eli J. M\"uller, and James M. Shine | Noradrenergic neuromodulation of nonlinear bursting neurons controls
critical dynamics | 17 pages, 5 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In order to remain adaptable to a dynamic environment, neural activity must
be simultaneously both sensitive and stable. To solve this problem, the brain
has been hypothesised to sit near a critical boundary. Yet, precisely how
criticality and these opposing information processing modes are implemented in
the brain r... | [
{
"created": "Tue, 15 Jun 2021 03:59:16 GMT",
"version": "v1"
},
{
"created": "Thu, 10 Feb 2022 22:32:10 GMT",
"version": "v2"
},
{
"created": "Thu, 6 Apr 2023 10:35:42 GMT",
"version": "v3"
}
] | 2023-04-07 | [
[
"Munn",
"Brandon R.",
""
],
[
"Müller",
"Eli J.",
""
],
[
"Shine",
"James M.",
""
]
] | In order to remain adaptable to a dynamic environment, neural activity must be simultaneously both sensitive and stable. To solve this problem, the brain has been hypothesised to sit near a critical boundary. Yet, precisely how criticality and these opposing information processing modes are implemented in the brain rem... |
2104.12571 | Sebastian Lotter | Sebastian Lotter and Lukas Brand and Maximilian Sch\"afer and Robert
Schober | Statistical Modeling of Airborne Virus Transmission Through Imperfectly
Fitted Face Masks | 7 pages, 5 figures, 1 table. Presented at the 8th ACM International
Conference on Nanoscale Computing and Communication (NANOCOM) | null | 10.1145/3477206.3477478 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The rapid emergence and the disastrous impact of the severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) pandemic on public health, societies, and
economies around the world has created an urgent need for understanding the
pathways critical for virus transmission. Airborne virus transmission by
asymptomatic ... | [
{
"created": "Mon, 26 Apr 2021 13:40:42 GMT",
"version": "v1"
},
{
"created": "Sat, 1 May 2021 14:03:11 GMT",
"version": "v2"
},
{
"created": "Mon, 16 Jan 2023 13:50:00 GMT",
"version": "v3"
}
] | 2023-01-18 | [
[
"Lotter",
"Sebastian",
""
],
[
"Brand",
"Lukas",
""
],
[
"Schäfer",
"Maximilian",
""
],
[
"Schober",
"Robert",
""
]
] | The rapid emergence and the disastrous impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic on public health, societies, and economies around the world has created an urgent need for understanding the pathways critical for virus transmission. Airborne virus transmission by asymptomatic SA... |
2401.06959 | Shirui Bian | Shirui Bian, Ruisong Zhou, Wei Lin, Chunhe Li | Quantifying energy landscape of oscillatory systems: Explosion,
pre-solution, and diffusion decomposition | 13 pages, 4 figures | null | null | null | q-bio.QM q-bio.MN | http://creativecommons.org/publicdomain/zero/1.0/ | The energy landscape theory finds its both extensive and intensive
application in studying stochastic dynamics of physical and biological systems.
Although the weighted summation of the Gaussian approximation (WSGA) approach
has been proposed for quantifying the energy landscape in multistable systems
by solving the ... | [
{
"created": "Sat, 13 Jan 2024 03:15:13 GMT",
"version": "v1"
}
] | 2024-01-17 | [
[
"Bian",
"Shirui",
""
],
[
"Zhou",
"Ruisong",
""
],
[
"Lin",
"Wei",
""
],
[
"Li",
"Chunhe",
""
]
] | The energy landscape theory finds its both extensive and intensive application in studying stochastic dynamics of physical and biological systems. Although the weighted summation of the Gaussian approximation (WSGA) approach has been proposed for quantifying the energy landscape in multistable systems by solving the di... |
1809.01699 | Robert Grossman | Robert L. Grossman | Data Lakes, Clouds and Commons: A Review of Platforms for Analyzing and
Sharing Genomic Data | 28 pages, 4 figures | null | null | null | q-bio.GN cs.CY | http://creativecommons.org/licenses/by/4.0/ | Data commons collate data with cloud computing infrastructure and commonly
used software services, tools and applications to create biomedical resources
for the large-scale management, analysis, harmonization, and sharing of
biomedical data. Over the past few years, data commons have been used to
analyze, harmonize a... | [
{
"created": "Wed, 5 Sep 2018 19:24:13 GMT",
"version": "v1"
},
{
"created": "Mon, 24 Dec 2018 19:57:33 GMT",
"version": "v2"
}
] | 2018-12-27 | [
[
"Grossman",
"Robert L.",
""
]
] | Data commons collate data with cloud computing infrastructure and commonly used software services, tools and applications to create biomedical resources for the large-scale management, analysis, harmonization, and sharing of biomedical data. Over the past few years, data commons have been used to analyze, harmonize and... |
1402.0385 | Guido Tiana | R. Capelli, C. Paissoni, P. Sormanni and G. Tiana | Iterative derivation of effective potentials to sample the
conformational space of proteins at atomistic scale | null | null | 10.1063/1.4876219 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The current capacity of computers makes it possible to perform simulations of
small systems with portable, explicit-solvent potentials achieving high degree
of accuracy. However, simplified models must be employed to exploit the
behaviour of large systems or to perform systematic scans of smaller systems.
While power... | [
{
"created": "Mon, 3 Feb 2014 14:11:01 GMT",
"version": "v1"
}
] | 2015-06-18 | [
[
"Capelli",
"R.",
""
],
[
"Paissoni",
"C.",
""
],
[
"Sormanni",
"P.",
""
],
[
"Tiana",
"G.",
""
]
] | The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour of large systems or to perform systematic scans of smaller systems. While powerfu... |
1004.2072 | Vadas Gintautas | Michael I. Ham, Vadas Gintautas, Guenter W. Gross | Spontaneous coordinated activity in cultured networks: Analysis of
multiple ignition sites, primary circuits, burst phase delay distributions
and functional structures | 4 pages, 3 figures. Presented at 6th International Meeting on
Substrate-Integrated Micro Electrode Arrays in Reutlingen in July 2008. | Published in 6th International Meeting on Substrate-Integrated
Micro Electrode Arrays, 2008. | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | All higher order central nervous systems exhibit spontaneous neural activity,
though the purpose and mechanistic origin of such activity remains poorly
understood. We explore the ignition and spread of collective spontaneous
electrophysiological burst activity in networks of cultured cortical neurons
growing on micro... | [
{
"created": "Mon, 12 Apr 2010 22:23:15 GMT",
"version": "v1"
}
] | 2010-04-14 | [
[
"Ham",
"Michael I.",
""
],
[
"Gintautas",
"Vadas",
""
],
[
"Gross",
"Guenter W.",
""
]
] | All higher order central nervous systems exhibit spontaneous neural activity, though the purpose and mechanistic origin of such activity remains poorly understood. We explore the ignition and spread of collective spontaneous electrophysiological burst activity in networks of cultured cortical neurons growing on microel... |
1606.08233 | Raul Isea | Raul Isea and Karl E Lonngren | A Preliminary Mathematical Model for the Dynamic Transmission of Dengue,
Chikungunya and Zika | 5 pages, 2 figures, open access | American Journal of Modern Physics and Application. 2016. Vol 3(2)
11-15 | null | null | q-bio.PE | http://creativecommons.org/publicdomain/zero/1.0/ | Aedes aegypti is a known vector of Dengue, Chikungunya and Zika and the goal
of this study is to propose the first mathematical model to describe the
dynamic transmission of these three diseases. We present two preliminary models
that consist of the SEIR model for the human populations and an SEI model for
the vector... | [
{
"created": "Mon, 27 Jun 2016 12:17:24 GMT",
"version": "v1"
}
] | 2016-06-28 | [
[
"Isea",
"Raul",
""
],
[
"Lonngren",
"Karl E",
""
]
] | Aedes aegypti is a known vector of Dengue, Chikungunya and Zika and the goal of this study is to propose the first mathematical model to describe the dynamic transmission of these three diseases. We present two preliminary models that consist of the SEIR model for the human populations and an SEI model for the vector t... |
1710.03563 | Laszlo Pecze | Michael Dougoud, Christian Mazza, Beat Schwaller, Laszlo Pecze | Extending the mathematical palette for developmental pattern formation:
Piebaldism | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Piebaldism usually manifests as white areas of fur, hair or skin due to the
absence of pigment-producing cells in those regions. The distribution of the
white and colored zones does not follow the classical Turing patterns. Here we
present a modeling framework for pattern formation that enables to easily
modify the r... | [
{
"created": "Tue, 10 Oct 2017 13:24:12 GMT",
"version": "v1"
}
] | 2017-10-11 | [
[
"Dougoud",
"Michael",
""
],
[
"Mazza",
"Christian",
""
],
[
"Schwaller",
"Beat",
""
],
[
"Pecze",
"Laszlo",
""
]
] | Piebaldism usually manifests as white areas of fur, hair or skin due to the absence of pigment-producing cells in those regions. The distribution of the white and colored zones does not follow the classical Turing patterns. Here we present a modeling framework for pattern formation that enables to easily modify the rel... |
2106.01602 | Ignazio Lazzizzera | Ignazio Lazzizzera | The SIR model towards he data. One year of Covid-19 pandemic in Italy
case study and plausible "real" numbers | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | In this work, the SIR epidemiological model is reformulated so to highlight
the important {\em effective reproduction number}, as well as to account for
the {\em generation time}, inverse of the {\em incidence rate}, and the {\em
infectious period} (or {\em removal period}), inverse of the {\em removal
rate}. The aim... | [
{
"created": "Thu, 3 Jun 2021 05:32:14 GMT",
"version": "v1"
},
{
"created": "Sun, 25 Jul 2021 09:45:35 GMT",
"version": "v2"
}
] | 2021-07-27 | [
[
"Lazzizzera",
"Ignazio",
""
]
] | In this work, the SIR epidemiological model is reformulated so to highlight the important {\em effective reproduction number}, as well as to account for the {\em generation time}, inverse of the {\em incidence rate}, and the {\em infectious period} (or {\em removal period}), inverse of the {\em removal rate}. The aim i... |
2208.05228 | Ijaz Gul | Ijaz Gul, Changyue Liu, Yuan Xi, Zhicheng Du, Shiyao Zhai, Zhengyang
Lei, Chen Qun, Muhammad Akmal Raheem, Qian He, Zhang Haihui, Canyang Zhang,
Runming Wang, Sanyang Han, Du Ke, Peiwu Qin | Current and perspective sensing methods for monkeypox virus: a
reemerging zoonosis in its infancy | 36 pages, 5 figures, 1 table | null | null | null | q-bio.QM q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Objectives The review is dedicated to evaluate the current monkeypox virus
(MPXV) detection methods, discuss their pros and cons, and provide recommended
solutions to the problems.
Methods The literature for this review is identified through searches in
PubMed, Web of Science, Google Scholar, ResearchGate, and Scie... | [
{
"created": "Wed, 10 Aug 2022 09:03:02 GMT",
"version": "v1"
}
] | 2022-08-11 | [
[
"Gul",
"Ijaz",
""
],
[
"Liu",
"Changyue",
""
],
[
"Xi",
"Yuan",
""
],
[
"Du",
"Zhicheng",
""
],
[
"Zhai",
"Shiyao",
""
],
[
"Lei",
"Zhengyang",
""
],
[
"Qun",
"Chen",
""
],
[
"Raheem",
"Muhammad... | Objectives The review is dedicated to evaluate the current monkeypox virus (MPXV) detection methods, discuss their pros and cons, and provide recommended solutions to the problems. Methods The literature for this review is identified through searches in PubMed, Web of Science, Google Scholar, ResearchGate, and Science ... |
1807.09400 | Nicholas Chia | Stephanie Danni Song, Patricio Jeraldo, Jun Chen, Nicholas Chia | Extreme value analysis of gut microbial alterations in colorectal cancer | null | Phys. Rev. E 99, 032413 (2019) | 10.1103/PhysRevE.99.032413 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gut microbes play a key role in colorectal carcinogenesis, yet reaching a
consensus on microbial signatures remains a challenge. This is in part due to a
reliance on mean value estimates. We present an extreme value analysis for
overcoming these limitations. By characterizing a power law fit to the relative
abundance... | [
{
"created": "Wed, 25 Jul 2018 00:15:21 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Jan 2019 21:03:48 GMT",
"version": "v2"
},
{
"created": "Wed, 13 Feb 2019 14:05:54 GMT",
"version": "v3"
}
] | 2019-03-27 | [
[
"Song",
"Stephanie Danni",
""
],
[
"Jeraldo",
"Patricio",
""
],
[
"Chen",
"Jun",
""
],
[
"Chia",
"Nicholas",
""
]
] | Gut microbes play a key role in colorectal carcinogenesis, yet reaching a consensus on microbial signatures remains a challenge. This is in part due to a reliance on mean value estimates. We present an extreme value analysis for overcoming these limitations. By characterizing a power law fit to the relative abundances ... |
1411.6843 | Jose Fontanari | Mauro Santos, E\"ors Szathm\'ary and Jos\'e F. Fontanari | Phenotypic Plasticity, the Baldwin Effect, and the Speeding up of
Evolution: the Computational Roots of an Illusion | null | Journal of Theoretical Biology 371, 127-136 (2015) | 10.1016/j.jtbi.2015.02.012 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An increasing number of dissident voices claim that the standard
neo-Darwinian view of genes as 'leaders' and phenotypes as 'followers' during
the process of adaptive evolution should be turned on its head. This idea is
older than the rediscovery of Mendel's laws of inheritance and has been given
several names before... | [
{
"created": "Tue, 25 Nov 2014 12:55:08 GMT",
"version": "v1"
}
] | 2015-03-10 | [
[
"Santos",
"Mauro",
""
],
[
"Szathmáry",
"Eörs",
""
],
[
"Fontanari",
"José F.",
""
]
] | An increasing number of dissident voices claim that the standard neo-Darwinian view of genes as 'leaders' and phenotypes as 'followers' during the process of adaptive evolution should be turned on its head. This idea is older than the rediscovery of Mendel's laws of inheritance and has been given several names before i... |
1805.01425 | Delfim F. M. Torres | Jasmina Djordjevic, Cristiana J. Silva, Delfim F. M. Torres | A stochastic SICA epidemic model for HIV transmission | This is a preprint of a paper whose final and definite form is with
'Applied Mathematics Letters', ISSN 0893-9659. Submitted 22/Jan/2018; Revised
03/May/2018; Accepted for publication 03/May/2018 | Appl. Math. Lett. 84 (2018), 168--175 | 10.1016/j.aml.2018.05.005 | null | q-bio.PE math.CA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a stochastic SICA epidemic model for HIV transmission, described
by stochastic ordinary differential equations, and discuss its perturbation by
environmental white noise. Existence and uniqueness of the global positive
solution to the stochastic HIV system is proven, and conditions under which
extinction a... | [
{
"created": "Thu, 3 May 2018 16:58:07 GMT",
"version": "v1"
}
] | 2018-05-30 | [
[
"Djordjevic",
"Jasmina",
""
],
[
"Silva",
"Cristiana J.",
""
],
[
"Torres",
"Delfim F. M.",
""
]
] | We propose a stochastic SICA epidemic model for HIV transmission, described by stochastic ordinary differential equations, and discuss its perturbation by environmental white noise. Existence and uniqueness of the global positive solution to the stochastic HIV system is proven, and conditions under which extinction and... |
2106.09979 | Taisuke Kobayashi | Taisuke Kobayashi, Eiji Watanabe | Artificial Perception Meets Psychophysics, Revealing a Fundamental Law
of Illusory Motion | 15 pages, 11 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rotating Snakes is a visual illusion in which a stationary design is
perceived to move dramatically. In the current study, the mechanism that
generates perception of motion was analyzed using a combination of
psychophysics experiments and deep neural network models that mimic human
vision. We prepared three- and four... | [
{
"created": "Fri, 18 Jun 2021 07:59:18 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Jun 2021 06:06:02 GMT",
"version": "v2"
},
{
"created": "Thu, 24 Jun 2021 05:26:51 GMT",
"version": "v3"
},
{
"created": "Fri, 11 Feb 2022 06:17:19 GMT",
"version": "v4"
},
{
"c... | 2022-03-31 | [
[
"Kobayashi",
"Taisuke",
""
],
[
"Watanabe",
"Eiji",
""
]
] | Rotating Snakes is a visual illusion in which a stationary design is perceived to move dramatically. In the current study, the mechanism that generates perception of motion was analyzed using a combination of psychophysics experiments and deep neural network models that mimic human vision. We prepared three- and four-c... |
2006.12479 | Nana Geraldine Cabo Bizet Dr | Nana Geraldine Cabo Bizet, Dami\'an Kaloni Mayorga Pe\~na | Time-dependent and time-independent SIR models applied to the COVID-19
outbreak in Argentina, Brazil, Colombia, Mexico and South Africa | 26 pages, 5 figures, 9 tables | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the SIR epidemiological model applied to the evolution of
COVID-19 with two approaches. In the first place we fit a global SIR model,
with time delay, and constant parameters throughout the outbreak, including the
contagion rate. The contention measures are reflected on an effective reduced
susceptible po... | [
{
"created": "Mon, 22 Jun 2020 17:55:52 GMT",
"version": "v1"
}
] | 2020-06-23 | [
[
"Bizet",
"Nana Geraldine Cabo",
""
],
[
"Peña",
"Damián Kaloni Mayorga",
""
]
] | We consider the SIR epidemiological model applied to the evolution of COVID-19 with two approaches. In the first place we fit a global SIR model, with time delay, and constant parameters throughout the outbreak, including the contagion rate. The contention measures are reflected on an effective reduced susceptible popu... |
2403.01332 | Tyler Ross | Tyler D. Ross, Ashwin Gopinath | Chaining thoughts and LLMs to learn DNA structural biophysics | null | null | null | null | q-bio.QM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | The future development of an AI scientist, a tool that is capable of
integrating a variety of experimental data and generating testable hypotheses,
holds immense potential. So far, bespoke machine learning models have been
created to specialize in singular scientific tasks, but otherwise lack the
flexibility of a gen... | [
{
"created": "Sat, 2 Mar 2024 22:38:01 GMT",
"version": "v1"
}
] | 2024-03-05 | [
[
"Ross",
"Tyler D.",
""
],
[
"Gopinath",
"Ashwin",
""
]
] | The future development of an AI scientist, a tool that is capable of integrating a variety of experimental data and generating testable hypotheses, holds immense potential. So far, bespoke machine learning models have been created to specialize in singular scientific tasks, but otherwise lack the flexibility of a gener... |
0801.3940 | Eleonora Alfinito Dr. | Eleonora Alfinito, Cecilia Pennetta, Lino Reggiani | Topological change and impedance spectrum of rat olfactory receptor I7:
A comparative analysis with bovine rhodopsin and bacterior | 6 pages, 8 figures | J. Appl. Phys. 105 084703 (2009) | 10.1063/1.3100210 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a theoretical investigation on possible selection of olfactory
receptors (ORs) as sensing components of nanobiosensors. Accordingly, we
generate the impedance spectra of the rat OR I7 in the native and activated
state and analyze their differences. In this way, we connect the protein
morphological transfor... | [
{
"created": "Fri, 25 Jan 2008 13:27:51 GMT",
"version": "v1"
},
{
"created": "Tue, 19 May 2009 08:20:58 GMT",
"version": "v2"
}
] | 2011-02-17 | [
[
"Alfinito",
"Eleonora",
""
],
[
"Pennetta",
"Cecilia",
""
],
[
"Reggiani",
"Lino",
""
]
] | We present a theoretical investigation on possible selection of olfactory receptors (ORs) as sensing components of nanobiosensors. Accordingly, we generate the impedance spectra of the rat OR I7 in the native and activated state and analyze their differences. In this way, we connect the protein morphological transforma... |
1908.06671 | Francesco Cagnetta | F. Cagnetta, D. Michieletto and D. Marenduzzo | A nonequilibrium strategy for fast target search on the genome | 5 pages, 5 figures | Phys. Rev. Lett. 124, 198101 (2020) | 10.1103/PhysRevLett.124.198101 | null | q-bio.SC cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Vital biological processes such as genome repair require fast and efficient
binding of selected proteins to specific target sites on DNA. Here we propose
an active target search mechanism based on "chromophoresis", the dynamics of
DNA-binding proteins up or down gradients in the density of epigenetic marks,
or colour... | [
{
"created": "Mon, 19 Aug 2019 09:57:07 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Apr 2020 06:37:00 GMT",
"version": "v2"
},
{
"created": "Thu, 23 Apr 2020 10:04:33 GMT",
"version": "v3"
}
] | 2020-05-20 | [
[
"Cagnetta",
"F.",
""
],
[
"Michieletto",
"D.",
""
],
[
"Marenduzzo",
"D.",
""
]
] | Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on "chromophoresis", the dynamics of DNA-binding proteins up or down gradients in the density of epigenetic marks, or colours ... |
1106.3771 | Yann Ponty | Yann Ponty (INRIA Saclay - Ile de France, LIX), C\'edric Saule (INRIA
Saclay - Ile de France, LRI, IRIC) | A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms | null | 11th Workshop on Algorithms in Bioinformatics (WABI'11) (2011) | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We extend an hypergraph representation, introduced by Finkelstein and
Roytberg, to unify dynamic programming algorithms in the context of RNA folding
with pseudoknots. Classic applications of RNA dynamic programming energy
minimization, partition function, base-pair probabilities...) are reformulated
within this fram... | [
{
"created": "Sun, 19 Jun 2011 18:50:54 GMT",
"version": "v1"
}
] | 2011-06-21 | [
[
"Ponty",
"Yann",
"",
"INRIA Saclay - Ile de France, LIX"
],
[
"Saule",
"Cédric",
"",
"INRIA\n Saclay - Ile de France, LRI, IRIC"
]
] | We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization, partition function, base-pair probabilities...) are reformulated within this framew... |
1903.10120 | Andrey Kuznetsov | Ivan A. Kuznetsov and Andrey V. Kuznetsov | Modeling transport and mean age of dense core vesicles in large axonal
arbors | Added an acknowledgement to Holger Metzler | Proceedings of the Royal Society A, vol. 475, 20190284, 2019 | 10.1098/rspa.2019.0284 | null | q-bio.NC q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A model simulating transport of dense core vesicles (DCVs) in type II axonal
terminals of Drosophila motoneurons has been developed. The morphology of type
II terminals is characterized by the large number of en passant boutons. The
lack of both scaled up DCV transport and scaled down DCV capture in boutons
results i... | [
{
"created": "Mon, 25 Mar 2019 03:44:22 GMT",
"version": "v1"
},
{
"created": "Thu, 2 May 2019 17:57:58 GMT",
"version": "v2"
},
{
"created": "Sat, 7 Sep 2019 14:33:09 GMT",
"version": "v3"
},
{
"created": "Sat, 1 Feb 2020 18:36:09 GMT",
"version": "v4"
}
] | 2020-02-04 | [
[
"Kuznetsov",
"Ivan A.",
""
],
[
"Kuznetsov",
"Andrey V.",
""
]
] | A model simulating transport of dense core vesicles (DCVs) in type II axonal terminals of Drosophila motoneurons has been developed. The morphology of type II terminals is characterized by the large number of en passant boutons. The lack of both scaled up DCV transport and scaled down DCV capture in boutons results in ... |
1612.05882 | Giovanni Bussi | Ji\v{r}\'i \v{S}poner, Giovanni Bussi, Petr Stadlbauer, Petra
K\"uhrov\'a, Pavel Ban\'a\v{s}, Barira Islam, Shozeb Haider, Stephen Neidle,
Michal Otyepka | Folding of guanine quadruplex molecules -- funnel-like mechanism or
kinetic partitioning? An overview from MD simulation studies | \c{opyright} 2016. This manuscript version is made available under
the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ | BBA-Gen. Subjects 1861, 1246 (2017) | 10.1016/j.bbagen.2016.12.008 | null | q-bio.BM physics.bio-ph physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Guanine quadruplexes (GQs) play vital roles in many cellular
processes and are of much interest as drug targets. In contrast to the
availability of many structural studies, there is still limited knowledge on GQ
folding.
Scope of review: We review recent molecular dynamics (MD) simulation studies
of the... | [
{
"created": "Sun, 18 Dec 2016 09:58:16 GMT",
"version": "v1"
}
] | 2020-05-05 | [
[
"Šponer",
"Jiří",
""
],
[
"Bussi",
"Giovanni",
""
],
[
"Stadlbauer",
"Petr",
""
],
[
"Kührová",
"Petra",
""
],
[
"Banáš",
"Pavel",
""
],
[
"Islam",
"Barira",
""
],
[
"Haider",
"Shozeb",
""
],
[
"Nei... | Background: Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural studies, there is still limited knowledge on GQ folding. Scope of review: We review recent molecular dynamics (MD) simulation studies of the fol... |
2112.06256 | Pierre Haas | Pierre A. Haas and Maria A. Gutierrez and Nuno M. Oliveira and Raymond
E. Goldstein | Stabilization of Microbial Communities by Responsive Phenotypic
Switching | 27 pages, 13 figures, (structure of paper reorganized, typos
corrected) | null | null | null | q-bio.PE cond-mat.soft | http://creativecommons.org/licenses/by/4.0/ | Clonal microbes can switch between different phenotypes and recent
theoretical work has shown that stochastic switching between these
subpopulations can stabilize microbial communities. This phenotypic switching
need not be stochastic, however, but could also be in response to environmental
factors, both biotic and a... | [
{
"created": "Sun, 12 Dec 2021 15:08:52 GMT",
"version": "v1"
},
{
"created": "Tue, 14 Jun 2022 07:52:22 GMT",
"version": "v2"
}
] | 2022-06-15 | [
[
"Haas",
"Pierre A.",
""
],
[
"Gutierrez",
"Maria A.",
""
],
[
"Oliveira",
"Nuno M.",
""
],
[
"Goldstein",
"Raymond E.",
""
]
] | Clonal microbes can switch between different phenotypes and recent theoretical work has shown that stochastic switching between these subpopulations can stabilize microbial communities. This phenotypic switching need not be stochastic, however, but could also be in response to environmental factors, both biotic and abi... |
1812.10227 | Yangsong Zhang | Yangsong Zhang, Erwei Yin, Fali Li, Yu Zhang, Daqing Guo, Dezhong Yao,
Peng Xu | Hierarchical feature fusion framework for frequency recognition in
SSVEP-based BCIs | 25 pages, 9 figures | null | null | null | q-bio.NC eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Effective frequency recognition algorithms are critical in steady-state
visual evoked potential (SSVEP) based brain-computer interfaces (BCIs). In this
study, we present a hierarchical feature fusion framework which can be used to
design high-performance frequency recognition methods. The proposed framework
includes ... | [
{
"created": "Wed, 26 Dec 2018 05:06:16 GMT",
"version": "v1"
},
{
"created": "Thu, 21 Mar 2019 14:41:35 GMT",
"version": "v2"
}
] | 2019-03-22 | [
[
"Zhang",
"Yangsong",
""
],
[
"Yin",
"Erwei",
""
],
[
"Li",
"Fali",
""
],
[
"Zhang",
"Yu",
""
],
[
"Guo",
"Daqing",
""
],
[
"Yao",
"Dezhong",
""
],
[
"Xu",
"Peng",
""
]
] | Effective frequency recognition algorithms are critical in steady-state visual evoked potential (SSVEP) based brain-computer interfaces (BCIs). In this study, we present a hierarchical feature fusion framework which can be used to design high-performance frequency recognition methods. The proposed framework includes tw... |
2402.10251 | Zhizhang Yuan | Zhizhang Yuan, Daoze Zhang, Junru Chen, Gefei Gu, Yang Yang | Brant-2: Foundation Model for Brain Signals | 14 pages, 7 figures | null | null | null | q-bio.NC cs.AI cs.LG eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Foundational models benefit from pre-training on large amounts of unlabeled
data and enable strong performance in a wide variety of applications with a
small amount of labeled data. Such models can be particularly effective in
analyzing brain signals, as this field encompasses numerous application
scenarios, and it i... | [
{
"created": "Thu, 15 Feb 2024 16:04:11 GMT",
"version": "v1"
},
{
"created": "Thu, 22 Feb 2024 12:32:53 GMT",
"version": "v2"
},
{
"created": "Wed, 6 Mar 2024 09:04:32 GMT",
"version": "v3"
},
{
"created": "Thu, 28 Mar 2024 13:55:31 GMT",
"version": "v4"
}
] | 2024-03-29 | [
[
"Yuan",
"Zhizhang",
""
],
[
"Zhang",
"Daoze",
""
],
[
"Chen",
"Junru",
""
],
[
"Gu",
"Gefei",
""
],
[
"Yang",
"Yang",
""
]
] | Foundational models benefit from pre-training on large amounts of unlabeled data and enable strong performance in a wide variety of applications with a small amount of labeled data. Such models can be particularly effective in analyzing brain signals, as this field encompasses numerous application scenarios, and it is ... |
1912.07925 | Joachim Krug | Benjamin Schmiegelt and Joachim Krug | Accessibility Percolation on Cartesian Power Graphs | 43 pages, 9 figures, 2 tables | Journal of Mathematical Biology 86, article number 46 (2023) | 10.1007/s00285-023-01882-z | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A fitness landscape is a mapping from a space of discrete genotypes to the
real numbers. A path in a fitness landscape is a sequence of genotypes
connected by single mutational steps. Such a path is said to be accessible if
the fitness values of the genotypes encountered along the path increase
monotonically. We stud... | [
{
"created": "Tue, 17 Dec 2019 11:11:36 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Apr 2021 13:58:49 GMT",
"version": "v2"
},
{
"created": "Thu, 12 Jan 2023 13:28:46 GMT",
"version": "v3"
},
{
"created": "Mon, 20 Feb 2023 17:46:49 GMT",
"version": "v4"
}
] | 2023-02-21 | [
[
"Schmiegelt",
"Benjamin",
""
],
[
"Krug",
"Joachim",
""
]
] | A fitness landscape is a mapping from a space of discrete genotypes to the real numbers. A path in a fitness landscape is a sequence of genotypes connected by single mutational steps. Such a path is said to be accessible if the fitness values of the genotypes encountered along the path increase monotonically. We study ... |
1005.0103 | Giuseppe Jurman | Giuseppe Jurman, Roberto Visintainer, Cesare Furlanello | An introduction to spectral distances in networks (extended version) | null | G. Jurman, R. Visintainer, C. Furlanello. An introduction to
spectral distances in networks. Frontiers in Artificial Intelligence and
Applications, 226:227-234, 2011 | null | null | q-bio.MN math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many functions have been recently defined to assess the similarity among
networks as tools for quantitative comparison. They stem from very different
frameworks - and they are tuned for dealing with different situations. Here we
show an overview of the spectral distances, highlighting their behavior in some
basic cas... | [
{
"created": "Sat, 1 May 2010 20:44:04 GMT",
"version": "v1"
},
{
"created": "Tue, 25 May 2010 16:06:54 GMT",
"version": "v2"
},
{
"created": "Tue, 26 Oct 2010 16:21:14 GMT",
"version": "v3"
}
] | 2012-08-21 | [
[
"Jurman",
"Giuseppe",
""
],
[
"Visintainer",
"Roberto",
""
],
[
"Furlanello",
"Cesare",
""
]
] | Many functions have been recently defined to assess the similarity among networks as tools for quantitative comparison. They stem from very different frameworks - and they are tuned for dealing with different situations. Here we show an overview of the spectral distances, highlighting their behavior in some basic cases... |
1808.07259 | Yu Sun | Yu Sun and Siv G.E. Andersson | SSCU: an R/Bioconductor package for analyzing selective profile in
synonymous codon usage | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background Synonymous codon choice is mainly affected by mutation and
selection. For the majority of genes within a genome, mutational pressure is
the major driving force, but selective strength can be strong and dominant for
specific set of genes or codons. More specifically, the selective strength on
translational ... | [
{
"created": "Wed, 22 Aug 2018 07:52:25 GMT",
"version": "v1"
}
] | 2018-08-23 | [
[
"Sun",
"Yu",
""
],
[
"Andersson",
"Siv G. E.",
""
]
] | Background Synonymous codon choice is mainly affected by mutation and selection. For the majority of genes within a genome, mutational pressure is the major driving force, but selective strength can be strong and dominant for specific set of genes or codons. More specifically, the selective strength on translational ef... |
1903.01233 | Simon Girel | Simon Girel (ICJ, DRACULA), Christophe Arpin (CIRI), Jacqueline Marvel
(CIRI), Olivier Gandrillon (DRACULA, LBMC UMR 5239), Fabien Crauste (DRACULA,
ICJ) | Model-based assessment of the Role of Uneven Partitioning of Molecular
Content on Heterogeneity and Regulation of Differentiation in CD8 T-cell
Immune Responses | Frontiers in Immunology, Frontiers, In press | null | 10.3389/fimmu.2019.00230 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Activation of naive CD8 T-cells can lead to the generation of multiple
effector and memory subsets. Multiple parameters associated with activation
conditions are involved in generating this diversity that is associated with
heterogeneous molecular contents of activated cells. Although naive cell
polarisation upon ant... | [
{
"created": "Thu, 7 Feb 2019 15:01:31 GMT",
"version": "v1"
}
] | 2019-03-05 | [
[
"Girel",
"Simon",
"",
"ICJ, DRACULA"
],
[
"Arpin",
"Christophe",
"",
"CIRI"
],
[
"Marvel",
"Jacqueline",
"",
"CIRI"
],
[
"Gandrillon",
"Olivier",
"",
"DRACULA, LBMC UMR 5239"
],
[
"Crauste",
"Fabien",
"",
"DRACULA,\n ... | Activation of naive CD8 T-cells can lead to the generation of multiple effector and memory subsets. Multiple parameters associated with activation conditions are involved in generating this diversity that is associated with heterogeneous molecular contents of activated cells. Although naive cell polarisation upon antig... |
0909.1935 | Natalja Strelkowa | Natalja Strelkowa, Mauricio Barahona | Switchable Genetic Oscillator Operating in Quasi-Stable Mode | 24 pages, 5 main figures | null | 10.1098/rsif.2009.0487 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ring topologies of repressing genes have qualitatively different long-term
dynamics if the number of genes is odd (they oscillate) or even (they exhibit
bistability). However, these attractors may not fully explain the observed
behavior in transient and stochastic environments such as the cell. We show
here that even... | [
{
"created": "Thu, 10 Sep 2009 12:31:34 GMT",
"version": "v1"
},
{
"created": "Thu, 19 Nov 2009 21:06:04 GMT",
"version": "v2"
}
] | 2010-01-22 | [
[
"Strelkowa",
"Natalja",
""
],
[
"Barahona",
"Mauricio",
""
]
] | Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behavior in transient and stochastic environments such as the cell. We show here that even r... |
1909.07540 | Yuri A. Dabaghian | Yuri Dabaghian | Topological stability of the hippocampal spatial map and synaptic
transience | 14 pages, 4 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spatial awareness in mammals is based on internalized representations of the
environment---cognitive maps---encoded by networks of spiking neurons. Although
behavioral studies suggest that these maps can remain stable for long periods,
it is also well-known that the underlying networks of synaptic connections
constan... | [
{
"created": "Tue, 17 Sep 2019 01:17:22 GMT",
"version": "v1"
}
] | 2019-09-18 | [
[
"Dabaghian",
"Yuri",
""
]
] | Spatial awareness in mammals is based on internalized representations of the environment---cognitive maps---encoded by networks of spiking neurons. Although behavioral studies suggest that these maps can remain stable for long periods, it is also well-known that the underlying networks of synaptic connections constantl... |
1812.08328 | Duc Nguyen | Duc Duy Nguyen, Guo-Wei Wei | Algebraic graph learning of protein-ligand binding affinity | 13 pages, 6 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although algebraic graph theory based models have been widely applied in
physical modeling and molecular studies, they are typically incompetent in the
analysis and prediction of biomolecular properties when compared with other
quantitative approaches. There is a need to explore the capability and
limitation of algeb... | [
{
"created": "Thu, 20 Dec 2018 02:33:47 GMT",
"version": "v1"
}
] | 2018-12-21 | [
[
"Nguyen",
"Duc Duy",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Although algebraic graph theory based models have been widely applied in physical modeling and molecular studies, they are typically incompetent in the analysis and prediction of biomolecular properties when compared with other quantitative approaches. There is a need to explore the capability and limitation of algebra... |
2104.01279 | John Zobolas | John Zobolas, Pedro T. Monteiro, Martin Kuiper and {\AA}smund Flobak | Boolean function metrics can assist modelers to check and choose logical
rules | 30 pages, 4 Figures, 3 Tables | Journal of Theoretical Biology 109 (2022) | 10.1016/j.jtbi.2022.111025 | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | Computational models of biological processes provide one of the most powerful
methods for a detailed analysis of the mechanisms that drive the behavior of
complex systems. Logic-based modeling has enhanced our understanding and
interpretation of those systems. Defining rules that determine how the output
activity of ... | [
{
"created": "Fri, 2 Apr 2021 23:58:42 GMT",
"version": "v1"
}
] | 2022-02-08 | [
[
"Zobolas",
"John",
""
],
[
"Monteiro",
"Pedro T.",
""
],
[
"Kuiper",
"Martin",
""
],
[
"Flobak",
"Åsmund",
""
]
] | Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and interpretation of those systems. Defining rules that determine how the output activity of bi... |
0906.2232 | Thomas Gurry | Thomas Gurry, Ozan Kahramanogullari, Robert G. Endres | Biophysical mechanism for Ras-nanocluster formation and signaling in
plasma membrane | 8 figures. PLoS ONE, in press | null | 10.1371/journal.pone.0006148 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ras GTPases are lipid-anchored G proteins which play a fundamental role in
cell signaling processes. Electron micrographs of immunogold-labeled Ras have
shown that membrane-bound Ras molecules segregate into nanocluster domains.
Several models have been developed in attempts to obtain quantitative
descriptions of nan... | [
{
"created": "Fri, 12 Jun 2009 00:45:03 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Gurry",
"Thomas",
""
],
[
"Kahramanogullari",
"Ozan",
""
],
[
"Endres",
"Robert G.",
""
]
] | Ras GTPases are lipid-anchored G proteins which play a fundamental role in cell signaling processes. Electron micrographs of immunogold-labeled Ras have shown that membrane-bound Ras molecules segregate into nanocluster domains. Several models have been developed in attempts to obtain quantitative descriptions of nanoc... |
q-bio/0406009 | Nicholas Chia | Ralf Bundschuh and Nicholas Chia | Finite Width Model Sequence Comparison | null | null | null | null | q-bio.QM | null | Sequence comparison is a widely used computational technique in modern
molecular biology. In spite of the frequent use of sequence comparisons the
important problem of assigning statistical significance to a given degree of
similarity is still outstanding. Analytical approaches to filling this gap
usually make use of... | [
{
"created": "Thu, 3 Jun 2004 17:09:35 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bundschuh",
"Ralf",
""
],
[
"Chia",
"Nicholas",
""
]
] | Sequence comparison is a widely used computational technique in modern molecular biology. In spite of the frequent use of sequence comparisons the important problem of assigning statistical significance to a given degree of similarity is still outstanding. Analytical approaches to filling this gap usually make use of a... |
2211.13673 | Celine Teplitsky | David L\'opez-Idi\'aquez (CEFE), C\'eline Teplitsky (CEFE), Arnaud
Gr\'egoire (CEFE), Am\'elie Fargevieille (CEFE), Mar\'ia del Rey (CEFE),
Christophe de Franceschi (CEFE), Anne Charmantier (CEFE), Claire Doutrelant
(CEFE) | Long-Term Decrease in Coloration: A Consequence of Climate Change? | null | The American Naturalist, 2022, 200 (1), pp.32-47 | 10.1086/719655 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Climate change has been shown to affect fitness-related traits in a wide
range of taxa; for instance, warming leads to phenological advancements in many
plant and animal species. The influence of climate change on social and
secondary sexual traits, that are associated with fitness due to their role as
quality signal... | [
{
"created": "Thu, 24 Nov 2022 15:39:46 GMT",
"version": "v1"
}
] | 2022-11-28 | [
[
"López-Idiáquez",
"David",
"",
"CEFE"
],
[
"Teplitsky",
"Céline",
"",
"CEFE"
],
[
"Grégoire",
"Arnaud",
"",
"CEFE"
],
[
"Fargevieille",
"Amélie",
"",
"CEFE"
],
[
"del Rey",
"María",
"",
"CEFE"
],
[
"de Francesc... | Climate change has been shown to affect fitness-related traits in a wide range of taxa; for instance, warming leads to phenological advancements in many plant and animal species. The influence of climate change on social and secondary sexual traits, that are associated with fitness due to their role as quality signals,... |
1910.01726 | Jianhong Chen | Jianhong Chen, Huang Huang, Wenrui Hao, Jinchao Xu | A machine learning method correlating pulse pressure wave data with
pregnancy | null | null | null | null | q-bio.QM cs.LG eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Pulse feeling, representing the tactile arterial palpation of the heartbeat,
has been widely used in traditional Chinese medicine (TCM) to diagnose various
diseases. The quantitative relationship between the pulse wave and health
conditions however has not been investigated in modern medicine. In this paper,
we explo... | [
{
"created": "Thu, 3 Oct 2019 21:35:05 GMT",
"version": "v1"
}
] | 2019-10-07 | [
[
"Chen",
"Jianhong",
""
],
[
"Huang",
"Huang",
""
],
[
"Hao",
"Wenrui",
""
],
[
"Xu",
"Jinchao",
""
]
] | Pulse feeling, representing the tactile arterial palpation of the heartbeat, has been widely used in traditional Chinese medicine (TCM) to diagnose various diseases. The quantitative relationship between the pulse wave and health conditions however has not been investigated in modern medicine. In this paper, we explore... |
0802.1902 | Nicolas Vuillerme | Nicolas Vuillerme (TIMC), Nicolas Pinsault (TIMC), Jacques Vaillant
(TIMC) | Postural control during quiet standing following cervical muscular
fatigue: effects of changes in sensory inputs | null | Neuroscience Letters 378, 3 (2005) 135-9 | 10.1016/j.neulet.2004.12.024 | null | q-bio.NC | null | The purpose of the present experiment was to investigate the effects of
cervical muscular fatigue on postural control during quiet standing under
different conditions of reliability and/or availability of somatosensory inputs
from the plantar soles and the ankles and visual information. To this aim, 14
young healthy ... | [
{
"created": "Wed, 13 Feb 2008 20:08:49 GMT",
"version": "v1"
}
] | 2008-02-14 | [
[
"Vuillerme",
"Nicolas",
"",
"TIMC"
],
[
"Pinsault",
"Nicolas",
"",
"TIMC"
],
[
"Vaillant",
"Jacques",
"",
"TIMC"
]
] | The purpose of the present experiment was to investigate the effects of cervical muscular fatigue on postural control during quiet standing under different conditions of reliability and/or availability of somatosensory inputs from the plantar soles and the ankles and visual information. To this aim, 14 young healthy ad... |
1704.03150 | Sang-Yoon Kim | Sang-Yoon Kim and Woochang Lim | Stochastic Spike Synchronization in A Small-World Neural Network with
Spike-Timing-Dependent Plasticity | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the Watts-Strogatz small-world network consisting of subthreshold
neurons which exhibit noise-induced spikings. This neuronal network has
adaptive dynamic synaptic strengths governed by the spike-timing-dependent
plasticity (STDP). In previous works without STDP, stochastic spike
synchronization (SSS) bet... | [
{
"created": "Tue, 11 Apr 2017 05:42:39 GMT",
"version": "v1"
},
{
"created": "Wed, 12 Apr 2017 01:56:32 GMT",
"version": "v2"
},
{
"created": "Thu, 13 Apr 2017 02:27:33 GMT",
"version": "v3"
},
{
"created": "Mon, 14 Aug 2017 19:16:44 GMT",
"version": "v4"
}
] | 2017-08-16 | [
[
"Kim",
"Sang-Yoon",
""
],
[
"Lim",
"Woochang",
""
]
] | We consider the Watts-Strogatz small-world network consisting of subthreshold neurons which exhibit noise-induced spikings. This neuronal network has adaptive dynamic synaptic strengths governed by the spike-timing-dependent plasticity (STDP). In previous works without STDP, stochastic spike synchronization (SSS) betwe... |
2405.03601 | Tatiana Levanova | Sergey V. Stasenko, Sergey M. Olenin, Eugene A. Grines, Tatiana A.
Levanova | Firing rate model for brain rhythms controlled by astrocytes | 12 pages, 4 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | We propose a new mean-field model of brain rhythms governed by astrocytes.
This theoretical framework describes how astrocytes can regulate neuronal
activity and contribute to the generation of brain rhythms. The model describes
at the population level the interactions between two large groups of excitatory
and inhib... | [
{
"created": "Mon, 6 May 2024 16:14:19 GMT",
"version": "v1"
}
] | 2024-05-07 | [
[
"Stasenko",
"Sergey V.",
""
],
[
"Olenin",
"Sergey M.",
""
],
[
"Grines",
"Eugene A.",
""
],
[
"Levanova",
"Tatiana A.",
""
]
] | We propose a new mean-field model of brain rhythms governed by astrocytes. This theoretical framework describes how astrocytes can regulate neuronal activity and contribute to the generation of brain rhythms. The model describes at the population level the interactions between two large groups of excitatory and inhibit... |
1401.6004 | Clinton Goss Ph.D. | Eric B. Miller and Clinton F. Goss | An Exploration of Physiological Responses to the Native American Flute | 17 pages, 7 figures, 4 tables, presented at ISQRMM 2013, Athens, GA,
July 26, 2013 | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/3.0/ | This pilot study explored physiological responses to playing and listening to
the Native American flute. Autonomic, electroencephalographic (EEG), and heart
rate variability (HRV) metrics were recorded while participants (N = 15) played
flutes and listened to several styles of music. Flute playing was accompanied
by ... | [
{
"created": "Wed, 22 Jan 2014 02:44:01 GMT",
"version": "v1"
},
{
"created": "Fri, 24 Jan 2014 03:57:28 GMT",
"version": "v2"
}
] | 2014-01-27 | [
[
"Miller",
"Eric B.",
""
],
[
"Goss",
"Clinton F.",
""
]
] | This pilot study explored physiological responses to playing and listening to the Native American flute. Autonomic, electroencephalographic (EEG), and heart rate variability (HRV) metrics were recorded while participants (N = 15) played flutes and listened to several styles of music. Flute playing was accompanied by an... |
1511.06546 | Antti Honkela | Aravind Sankar, Brandon Malone, Sion Bayliss, Ben Pascoe, Guillaume
M\'eric, Matthew D. Hitchings, Samuel K. Sheppard, Edward J. Feil, Jukka
Corander and Antti Honkela | Bayesian identification of bacterial strains from sequencing data | 16 pages, 7 figures | null | null | null | q-bio.GN q-bio.QM stat.AP | http://creativecommons.org/licenses/by/4.0/ | Rapidly assaying the diversity of a bacterial species present in a sample
obtained from a hospital patient or an evironmental source has become possible
after recent technological advances in DNA sequencing. For several applications
it is important to accurately identify the presence and estimate relative
abundances ... | [
{
"created": "Fri, 20 Nov 2015 10:12:06 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Feb 2016 17:16:45 GMT",
"version": "v2"
}
] | 2016-02-18 | [
[
"Sankar",
"Aravind",
""
],
[
"Malone",
"Brandon",
""
],
[
"Bayliss",
"Sion",
""
],
[
"Pascoe",
"Ben",
""
],
[
"Méric",
"Guillaume",
""
],
[
"Hitchings",
"Matthew D.",
""
],
[
"Sheppard",
"Samuel K.",
""
]... | Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is important to accurately identify the presence and estimate relative abundances of... |
1301.0960 | Amy Maxmen | Amy Maxmen | Sea Spider development: How the encysting Anoplodactylus eroticus
matures from a buoyant nymph to a grounded adult | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In order to understand how animals evolved over time, biologists must learn
how their body parts form during their development. The following is a detailed
description of how one species of sea spider transforms from a hatchling to an
8-legged adult. Pycnogonids, or sea spiders, comprise a primitive lineage of
arthro... | [
{
"created": "Sun, 6 Jan 2013 02:29:53 GMT",
"version": "v1"
}
] | 2013-01-08 | [
[
"Maxmen",
"Amy",
""
]
] | In order to understand how animals evolved over time, biologists must learn how their body parts form during their development. The following is a detailed description of how one species of sea spider transforms from a hatchling to an 8-legged adult. Pycnogonids, or sea spiders, comprise a primitive lineage of arthropo... |
2006.16379 | Ian Craig | Laurentz E. Olivier, Stefan Botha and Ian K. Craig | Optimized lockdown strategies for curbing the spread of COVID-19: A
South African case study | 11 pages, 7 figures, 4 tables | null | 10.1109/ACCESS.2020.3037415 | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | To curb the spread of COVID-19, many governments around the world have
implemented tiered lockdowns with varying degrees of stringency. Lockdown
levels are typically increased when the disease spreads and reduced when the
disease abates. A predictive control approach is used to develop optimized
lockdown strategies f... | [
{
"created": "Mon, 29 Jun 2020 20:59:08 GMT",
"version": "v1"
},
{
"created": "Fri, 13 Nov 2020 06:58:52 GMT",
"version": "v2"
}
] | 2020-11-16 | [
[
"Olivier",
"Laurentz E.",
""
],
[
"Botha",
"Stefan",
""
],
[
"Craig",
"Ian K.",
""
]
] | To curb the spread of COVID-19, many governments around the world have implemented tiered lockdowns with varying degrees of stringency. Lockdown levels are typically increased when the disease spreads and reduced when the disease abates. A predictive control approach is used to develop optimized lockdown strategies for... |
1304.1865 | Alessandro Torcini Dr | Kaare Mikkelsen, Alberto Imparato, Alessandro Torcini | Emergence of slow collective oscillations in neural networks with spike
timing dependent plasticity | 8 pages, 6 figures to appear in Physical Review Letters plus
additional material | Phys. Rev. Lett. 110, 208101 (2013) | 10.1103/PhysRevLett.110.208101 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The collective dynamics of excitatory pulse coupled neurons with spike timing
dependent plasticity (STDP) is studied. The introduction of STDP induces
persistent irregular oscillations between strongly and weakly synchronized
states, reminiscent of brain activity during slow-wave sleep. We explain the
oscillations by... | [
{
"created": "Sat, 6 Apr 2013 08:18:24 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Apr 2013 17:32:48 GMT",
"version": "v2"
}
] | 2013-05-21 | [
[
"Mikkelsen",
"Kaare",
""
],
[
"Imparato",
"Alberto",
""
],
[
"Torcini",
"Alessandro",
""
]
] | The collective dynamics of excitatory pulse coupled neurons with spike timing dependent plasticity (STDP) is studied. The introduction of STDP induces persistent irregular oscillations between strongly and weakly synchronized states, reminiscent of brain activity during slow-wave sleep. We explain the oscillations by a... |
1310.7501 | Daniel Beard | Jason N. Bazil, Karl D. Stamm, Xing Li, Timothy J. Nelson, Aoy
Tomita-Mitchell, and Daniel A. Beard | The Inferred Cardiogenic Gene Regulatory Network in the Mammalian Heart | 18 pages; 4 figures | null | 10.1371/journal.pone.0100842 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cardiac development is complex, multiscale process encompassing cell fate
adoption, differentiation and morphogenesis. To elucidate pathways underlying
this process, a recently developed algorithm to reverse engineer gene
regulatory networks was applied to time-course microarray data obtained from
the developing mous... | [
{
"created": "Mon, 28 Oct 2013 17:21:53 GMT",
"version": "v1"
}
] | 2017-02-08 | [
[
"Bazil",
"Jason N.",
""
],
[
"Stamm",
"Karl D.",
""
],
[
"Li",
"Xing",
""
],
[
"Nelson",
"Timothy J.",
""
],
[
"Tomita-Mitchell",
"Aoy",
""
],
[
"Beard",
"Daniel A.",
""
]
] | Cardiac development is complex, multiscale process encompassing cell fate adoption, differentiation and morphogenesis. To elucidate pathways underlying this process, a recently developed algorithm to reverse engineer gene regulatory networks was applied to time-course microarray data obtained from the developing mouse ... |
2306.10905 | Mattia Miotto | Mattia Miotto, Simone Scalise, Marco Leonetti, Giancarlo Ruocco,
Giovanna Peruzzi, Giorgio Gosti | Determining cancer cells division strategy | 16 pages, 5 figures | null | null | null | q-bio.CB physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Heterogeneity in the size distribution of cancer cell populations has been
recently linked to drug resistance and invasiveness. However, despite many
progresses have been made in understanding how such heterogeneous size
distributions arise in fast-proliferating cell types -like bacteria and yeast-,
comprehensive inv... | [
{
"created": "Mon, 19 Jun 2023 13:05:30 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Oct 2023 10:29:25 GMT",
"version": "v2"
}
] | 2023-10-23 | [
[
"Miotto",
"Mattia",
""
],
[
"Scalise",
"Simone",
""
],
[
"Leonetti",
"Marco",
""
],
[
"Ruocco",
"Giancarlo",
""
],
[
"Peruzzi",
"Giovanna",
""
],
[
"Gosti",
"Giorgio",
""
]
] | Heterogeneity in the size distribution of cancer cell populations has been recently linked to drug resistance and invasiveness. However, despite many progresses have been made in understanding how such heterogeneous size distributions arise in fast-proliferating cell types -like bacteria and yeast-, comprehensive inves... |
2006.14304 | Irina Higgins | Irina Higgins, Le Chang, Victoria Langston, Demis Hassabis,
Christopher Summerfield, Doris Tsao, Matthew Botvinick | Unsupervised deep learning identifies semantic disentanglement in single
inferotemporal neurons | null | null | 10.1038/s41467-021-26751-5 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Deep supervised neural networks trained to classify objects have emerged as
popular models of computation in the primate ventral stream. These models
represent information with a high-dimensional distributed population code,
implying that inferotemporal (IT) responses are also too complex to interpret
at the single-n... | [
{
"created": "Thu, 25 Jun 2020 10:50:51 GMT",
"version": "v1"
}
] | 2022-01-19 | [
[
"Higgins",
"Irina",
""
],
[
"Chang",
"Le",
""
],
[
"Langston",
"Victoria",
""
],
[
"Hassabis",
"Demis",
""
],
[
"Summerfield",
"Christopher",
""
],
[
"Tsao",
"Doris",
""
],
[
"Botvinick",
"Matthew",
""
]
... | Deep supervised neural networks trained to classify objects have emerged as popular models of computation in the primate ventral stream. These models represent information with a high-dimensional distributed population code, implying that inferotemporal (IT) responses are also too complex to interpret at the single-neu... |
1309.5076 | Wilten Nicola | Wilten Nicola and Sue Ann Campbell | Mean-Field Models for Heterogeneous Networks of Two-Dimensional
Integrate and Fire Models | 39 pages, 12 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analytically derive mean-field models for all-to-all coupled networks of
heterogeneous, adapting, two-dimensional integrate and fire neurons. The class
of models we consider includes the Izhikevich, adaptive exponential, and
quartic integrate and fire models. The heterogeneity in the parameters leads to
different ... | [
{
"created": "Thu, 19 Sep 2013 19:23:37 GMT",
"version": "v1"
}
] | 2013-09-20 | [
[
"Nicola",
"Wilten",
""
],
[
"Campbell",
"Sue Ann",
""
]
] | We analytically derive mean-field models for all-to-all coupled networks of heterogeneous, adapting, two-dimensional integrate and fire neurons. The class of models we consider includes the Izhikevich, adaptive exponential, and quartic integrate and fire models. The heterogeneity in the parameters leads to different mo... |
1503.07998 | Benjamin Schmid | Benjamin Schmid and Jan Huisken | Real-time multi-view deconvolution | 8 pages, 5 figures, submitted to Bioinformatics | null | null | null | q-bio.QM cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In light-sheet microscopy, overall image content and resolution are improved
by acquiring and fusing multiple views of the sample from different directions.
State-of-the-art multi-view (MV) deconvolution employs the point spread
functions (PSF) of the different views to simultaneously fuse and deconvolve
the images i... | [
{
"created": "Fri, 27 Mar 2015 09:17:27 GMT",
"version": "v1"
}
] | 2015-03-30 | [
[
"Schmid",
"Benjamin",
""
],
[
"Huisken",
"Jan",
""
]
] | In light-sheet microscopy, overall image content and resolution are improved by acquiring and fusing multiple views of the sample from different directions. State-of-the-art multi-view (MV) deconvolution employs the point spread functions (PSF) of the different views to simultaneously fuse and deconvolve the images in ... |
2306.14080 | Qianqian Wang | Qianqian Wang, Wei Wang, Yuqi Fang, P.-T. Yap, Hongtu Zhu, Hong-Jun
Li, Lishan Qiao and Mingxia Liu | Leveraging Brain Modularity Prior for Interpretable Representation
Learning of fMRI | null | null | null | null | q-bio.QM cs.LG q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Resting-state functional magnetic resonance imaging (rs-fMRI) can reflect
spontaneous neural activities in brain and is widely used for brain disorder
analysis.Previous studies propose to extract fMRI representations through
diverse machine/deep learning methods for subsequent analysis. But the learned
features typic... | [
{
"created": "Sat, 24 Jun 2023 23:45:47 GMT",
"version": "v1"
}
] | 2023-06-27 | [
[
"Wang",
"Qianqian",
""
],
[
"Wang",
"Wei",
""
],
[
"Fang",
"Yuqi",
""
],
[
"Yap",
"P. -T.",
""
],
[
"Zhu",
"Hongtu",
""
],
[
"Li",
"Hong-Jun",
""
],
[
"Qiao",
"Lishan",
""
],
[
"Liu",
"Mingxia",... | Resting-state functional magnetic resonance imaging (rs-fMRI) can reflect spontaneous neural activities in brain and is widely used for brain disorder analysis.Previous studies propose to extract fMRI representations through diverse machine/deep learning methods for subsequent analysis. But the learned features typical... |
2008.00131 | Rebekah Rogers | Rebekah L. Rogers, Stephanie L. Grizzard, James E. Titus-McQuillan,
Katherine Bockrath, Sagar Patel, John P. Wares, Jeffrey T. Garner, Cathy C.
Moore | Gene family amplification facilitates adaptation in freshwater Unionid
bivalve Megalonaias nervosa | Main text 42 pages, 1 table 8 figures; SI 12 pages, 8 tables, 2
figures; Gene tree phylogenies added to directly address incomplete lineage
sorting | null | 10.1111/mec.15786 | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As organisms are faced with intense rapidly changing selective pressures, new
genetic material is required to facilitate adaptation. Among sources of genetic
novelty, gene duplications and transposable elements (TEs) offer new genes or
new regulatory patterns that can facilitate evolutionary change. With advances
in ... | [
{
"created": "Sat, 1 Aug 2020 00:22:50 GMT",
"version": "v1"
},
{
"created": "Mon, 16 Nov 2020 15:33:19 GMT",
"version": "v2"
}
] | 2021-01-06 | [
[
"Rogers",
"Rebekah L.",
""
],
[
"Grizzard",
"Stephanie L.",
""
],
[
"Titus-McQuillan",
"James E.",
""
],
[
"Bockrath",
"Katherine",
""
],
[
"Patel",
"Sagar",
""
],
[
"Wares",
"John P.",
""
],
[
"Garner",
"Jeffr... | As organisms are faced with intense rapidly changing selective pressures, new genetic material is required to facilitate adaptation. Among sources of genetic novelty, gene duplications and transposable elements (TEs) offer new genes or new regulatory patterns that can facilitate evolutionary change. With advances in ge... |
2406.00382 | Michele Piana | Davide Parodi, Edoardo Dighero, Giorgia Biddau, Francesca D'Amico,
Matteo Bauckneht, Cecilia Marini, Sara Garbarino, Cristina Campi, Michele
Piana, Gianmario Sambuceti | Localized FDG loss in lung cancer lesions | null | null | null | null | q-bio.TO stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Purpose: Analysis of [18F]-Fluorodeoxyglucose (FDG) kinetics in cancer has
been most often limited to the evaluation of the average uptake over relatively
large volumes. Nevertheless, tumor lesion almost contains inflammatory
infiltrates whose cells are characterized by a significant radioactivity
washout due to the ... | [
{
"created": "Sat, 1 Jun 2024 09:41:48 GMT",
"version": "v1"
}
] | 2024-06-04 | [
[
"Parodi",
"Davide",
""
],
[
"Dighero",
"Edoardo",
""
],
[
"Biddau",
"Giorgia",
""
],
[
"D'Amico",
"Francesca",
""
],
[
"Bauckneht",
"Matteo",
""
],
[
"Marini",
"Cecilia",
""
],
[
"Garbarino",
"Sara",
""
]... | Purpose: Analysis of [18F]-Fluorodeoxyglucose (FDG) kinetics in cancer has been most often limited to the evaluation of the average uptake over relatively large volumes. Nevertheless, tumor lesion almost contains inflammatory infiltrates whose cells are characterized by a significant radioactivity washout due to the hy... |
2005.09108 | Sebastian Lotter | Sebastian Lotter, Arman Ahmadzadeh, Robert Schober | Synaptic Channel Modeling for DMC: Neurotransmitter Uptake and Spillover
in the Tripartite Synapse | 42 pages, 8 figures, 1 table. Accepted for publication in IEEE
Transactions on Communications. This article is the extended version of the
conference paper arXiv:1912.04025 | null | 10.1109/TCOMM.2020.3040318 | null | q-bio.SC cs.IT math.IT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In Diffusive Molecular Communication (DMC), information is transmitted by
diffusing molecules. Synaptic signaling, as a natural implementation of this
paradigm, encompasses functional components that, once understood, can
facilitate the development of synthetic DMC systems. To unleash this potential,
however, a thoro... | [
{
"created": "Mon, 18 May 2020 21:52:56 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Nov 2020 12:26:08 GMT",
"version": "v2"
}
] | 2020-11-26 | [
[
"Lotter",
"Sebastian",
""
],
[
"Ahmadzadeh",
"Arman",
""
],
[
"Schober",
"Robert",
""
]
] | In Diffusive Molecular Communication (DMC), information is transmitted by diffusing molecules. Synaptic signaling, as a natural implementation of this paradigm, encompasses functional components that, once understood, can facilitate the development of synthetic DMC systems. To unleash this potential, however, a thoroug... |
1212.4996 | Alberto d'Onofrio | Sebastiano de Franciscis and Alberto d'Onofrio | Cellular polarization: interaction between extrinsic bounded noises and
wave-pinning mechanism | 21 pages, 9 figures | null | 10.1103/PhysRevE.88.032709 | null | q-bio.MN cond-mat.stat-mech nlin.PS q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cued and un-cued cell polarization is a fundamental mechanism in cell
biology. As an alternative to the classical Turing bifurcation, it has been
proposed that the cell polarity might onset by means of the well-known
phenomenon of wave-pinning (Gamba et al, PNAS, 2005). A particularly simple and
elegant model of wave... | [
{
"created": "Thu, 20 Dec 2012 11:57:57 GMT",
"version": "v1"
}
] | 2015-06-12 | [
[
"de Franciscis",
"Sebastiano",
""
],
[
"d'Onofrio",
"Alberto",
""
]
] | Cued and un-cued cell polarization is a fundamental mechanism in cell biology. As an alternative to the classical Turing bifurcation, it has been proposed that the cell polarity might onset by means of the well-known phenomenon of wave-pinning (Gamba et al, PNAS, 2005). A particularly simple and elegant model of wave-p... |
2209.01792 | Tobias Paul | Jochen Blath, Tobias Paul, Andr\'as Tobi\'as, Maite Wilke Berenguer | The impact of dormancy on evolutionary branching | 17 pages, 6 figures | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we investigate the consequences of dormancy in the `rare
mutation' and `large population' regime of stochastic adaptive dynamics.
Starting from an individual-based micro-model, we first derive the polymorphic
evolution sequence of the population, based on previous work by Baar and Bovier
(2018). After ... | [
{
"created": "Mon, 5 Sep 2022 07:03:02 GMT",
"version": "v1"
}
] | 2022-09-07 | [
[
"Blath",
"Jochen",
""
],
[
"Paul",
"Tobias",
""
],
[
"Tobiás",
"András",
""
],
[
"Berenguer",
"Maite Wilke",
""
]
] | In this paper, we investigate the consequences of dormancy in the `rare mutation' and `large population' regime of stochastic adaptive dynamics. Starting from an individual-based micro-model, we first derive the polymorphic evolution sequence of the population, based on previous work by Baar and Bovier (2018). After pa... |
1605.07792 | Mark Leake | Zhaokun Zhou, Mark C. Leake | Force spectroscopy in studying infection | null | null | null | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biophysical force spectroscopy tools - for example optical tweezers, magnetic
tweezers, atomic force microscopy, - have been used to study elastic,
mechanical, conformational and dynamic properties of single biological
specimens from single proteins to whole cells to reveal information not
accessible by ensemble aver... | [
{
"created": "Wed, 25 May 2016 09:19:50 GMT",
"version": "v1"
}
] | 2016-06-09 | [
[
"Zhou",
"Zhaokun",
""
],
[
"Leake",
"Mark C.",
""
]
] | Biophysical force spectroscopy tools - for example optical tweezers, magnetic tweezers, atomic force microscopy, - have been used to study elastic, mechanical, conformational and dynamic properties of single biological specimens from single proteins to whole cells to reveal information not accessible by ensemble averag... |
1308.2547 | Bal\'azs Madas | Bal\'azs G. Madas, Katalin Varga | Biophysical modelling of the effects of inhaled radon progeny on the
bronchial epithelium for the estimation of the relationships applied in the
two stage clonal expansion model of carcinogenesis | paper presented in the conference EPRBioDose2013 (Leiden, the
Netherlands, March 24-28, 2013) and submitted to Radiation Protection
Dosimetry published by Oxford University Press, 9 pages, 4 figures | null | 10.1093/rpd/ncu125 | null | q-bio.TO physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There is a considerable debate between research groups applying the two stage
clonal expansion model for lung cancer risk estimation, whether radon exposure
affects initiation and transformation or promotion. The objective of the
present study is to quantify the effects of radon progeny on these stages with
biophysic... | [
{
"created": "Mon, 12 Aug 2013 13:03:27 GMT",
"version": "v1"
}
] | 2014-04-23 | [
[
"Madas",
"Balázs G.",
""
],
[
"Varga",
"Katalin",
""
]
] | There is a considerable debate between research groups applying the two stage clonal expansion model for lung cancer risk estimation, whether radon exposure affects initiation and transformation or promotion. The objective of the present study is to quantify the effects of radon progeny on these stages with biophysical... |
1907.03223 | Johannes Kleiner | Johannes Kleiner | Mathematical Models of Consciousness | null | null | 10.3390/e22060609 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent years, promising mathematical models have been suggested which aim
to describe conscious experience and its relation to the physical domain.
Whereas the axioms and metaphysical ideas of these theories have been carefully
motivated, their mathematical formalism has not. In this article we aim to
remedy this ... | [
{
"created": "Sun, 7 Jul 2019 05:35:24 GMT",
"version": "v1"
},
{
"created": "Mon, 20 Apr 2020 10:44:33 GMT",
"version": "v2"
}
] | 2020-07-15 | [
[
"Kleiner",
"Johannes",
""
]
] | In recent years, promising mathematical models have been suggested which aim to describe conscious experience and its relation to the physical domain. Whereas the axioms and metaphysical ideas of these theories have been carefully motivated, their mathematical formalism has not. In this article we aim to remedy this si... |
0906.0756 | Jorge F. Mejias | Jorge F. Mejias, Joaquin J. Torres | Emergence of resonances in neural systems: the interplay between
threshold adaptation and short-term synaptic plasticity | 24 pages, 8 figures, submitted to Neural Computation | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work we study the detection of weak stimuli by spiking neurons in the
presence of certain level of noisy background neural activity. Our study has
focused in the realistic assumption that the synapses in the network present
activity-dependent processes, such as short-term synaptic depression and
facilitation.... | [
{
"created": "Wed, 3 Jun 2009 17:58:27 GMT",
"version": "v1"
}
] | 2009-06-04 | [
[
"Mejias",
"Jorge F.",
""
],
[
"Torres",
"Joaquin J.",
""
]
] | In this work we study the detection of weak stimuli by spiking neurons in the presence of certain level of noisy background neural activity. Our study has focused in the realistic assumption that the synapses in the network present activity-dependent processes, such as short-term synaptic depression and facilitation. E... |
2008.08667 | Bernadette Stolz | Bernadette J. Stolz, Jakob Kaeppler, Bostjan Markelc, Franziska Mech,
Florian Lipsmeier, Ruth J. Muschel, Helen M. Byrne, Heather A. Harrington | Multiscale Topology Characterises Dynamic Tumour Vascular Networks | null | null | null | null | q-bio.QM math.AT q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Advances in imaging techniques enable high resolution 3D visualisation of
vascular networks over time and reveal abnormal structural features such as
twists and loops, and their quantification is an active area of research. Here
we showcase how topological data analysis (TDA), the mathematical field that
studies `sha... | [
{
"created": "Wed, 19 Aug 2020 21:06:27 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Mar 2022 16:23:33 GMT",
"version": "v2"
},
{
"created": "Tue, 26 Apr 2022 20:06:24 GMT",
"version": "v3"
}
] | 2022-04-28 | [
[
"Stolz",
"Bernadette J.",
""
],
[
"Kaeppler",
"Jakob",
""
],
[
"Markelc",
"Bostjan",
""
],
[
"Mech",
"Franziska",
""
],
[
"Lipsmeier",
"Florian",
""
],
[
"Muschel",
"Ruth J.",
""
],
[
"Byrne",
"Helen M.",
"... | Advances in imaging techniques enable high resolution 3D visualisation of vascular networks over time and reveal abnormal structural features such as twists and loops, and their quantification is an active area of research. Here we showcase how topological data analysis (TDA), the mathematical field that studies `shape... |
1301.2694 | Ian Dworkin | Chris H. Chandler, Sudarshan Chari and Ian Dworkin | Does your gene need a background check? How genetic background impacts
the analysis of mutations, genes, and evolution | In review at Trends in Genetics | Trends in Genetics 2013 29(6):358-366 | 10.1016/j.tig.2013.01.009 | null | q-bio.GN q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The premise of genetic analysis is that a causal link exists between
phenotypic and allelic variation. Yet it has long been documented that mutant
phenotypes are not a simple result of a single DNA lesion, but rather are due
to interactions of the focal allele with other genes and the environment.
Although an experim... | [
{
"created": "Sat, 12 Jan 2013 15:59:35 GMT",
"version": "v1"
}
] | 2014-06-04 | [
[
"Chandler",
"Chris H.",
""
],
[
"Chari",
"Sudarshan",
""
],
[
"Dworkin",
"Ian",
""
]
] | The premise of genetic analysis is that a causal link exists between phenotypic and allelic variation. Yet it has long been documented that mutant phenotypes are not a simple result of a single DNA lesion, but rather are due to interactions of the focal allele with other genes and the environment. Although an experimen... |
2301.08698 | Laurent Evain | Laurent Evain, Jean-Jacques Loeb | Geometric approach for non pharmaceutical interventions in epidemiology | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Various non pharmaceutical interventions have been settled to minimise the
burden of the COVID-19 outbreak. We build a framework to analyse the dynamics
of non pharmaceutical interventions, to distinguish between mitigations
measures leading to objective scientific improvements and mitigations based on
both political... | [
{
"created": "Fri, 20 Jan 2023 17:35:47 GMT",
"version": "v1"
}
] | 2023-01-23 | [
[
"Evain",
"Laurent",
""
],
[
"Loeb",
"Jean-Jacques",
""
]
] | Various non pharmaceutical interventions have been settled to minimise the burden of the COVID-19 outbreak. We build a framework to analyse the dynamics of non pharmaceutical interventions, to distinguish between mitigations measures leading to objective scientific improvements and mitigations based on both political a... |
2106.11799 | Mos\`e Manni | Mos\`e Manni, Matthew R Berkeley, Mathieu Seppey, Felipe A Simao,
Evgeny M Zdobnov | BUSCO update: novel and streamlined workflows along with broader and
deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and
viral genomes | for supplementary files, see
https://gitlab.com/ezlab/busco_preprint_2021 | null | null | null | q-bio.GN q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Methods for evaluating the quality of genomic and metagenomic data are
essential to aid genome assembly and to correctly interpret the results of
subsequent analyses. BUSCO estimates the completeness and redundancy of
processed genomic data based on universal single-copy orthologs. Here we
present new functionalities... | [
{
"created": "Tue, 22 Jun 2021 14:12:18 GMT",
"version": "v1"
}
] | 2021-06-23 | [
[
"Manni",
"Mosè",
""
],
[
"Berkeley",
"Matthew R",
""
],
[
"Seppey",
"Mathieu",
""
],
[
"Simao",
"Felipe A",
""
],
[
"Zdobnov",
"Evgeny M",
""
]
] | Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here we present new functionalities a... |
1608.02621 | Bohdan Khomtchouk | Bohdan B. Khomtchouk, Edmund Weitz, Claes Wahlestedt | The Machine that Builds Itself: How the Strengths of Lisp Family
Languages Facilitate Building Complex and Flexible Bioinformatic Models | 9 pages | Briefings in Bioinformatics, Volume 19, Issue 3, 2018, pp. 537-543 | 10.1093/bib/bbw130 | null | q-bio.OT cs.SE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We address the need for expanding the presence of the Lisp family of
programming languages in bioinformatics and computational biology research.
Languages of this family, like Common Lisp, Scheme, or Clojure, facilitate the
creation of powerful and flexible software models that are required for complex
and rapidly ev... | [
{
"created": "Mon, 8 Aug 2016 20:58:32 GMT",
"version": "v1"
},
{
"created": "Mon, 19 Sep 2016 03:29:49 GMT",
"version": "v2"
}
] | 2021-02-03 | [
[
"Khomtchouk",
"Bohdan B.",
""
],
[
"Weitz",
"Edmund",
""
],
[
"Wahlestedt",
"Claes",
""
]
] | We address the need for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research. Languages of this family, like Common Lisp, Scheme, or Clojure, facilitate the creation of powerful and flexible software models that are required for complex and rapidly evol... |
1206.3340 | Sree Vamsee Chintapalli dr | Sree V. Chintapalli, Gaurav Bhardwaj, Jagadish Babu, Loukia
Hadjiyianni, Yoojin Hong, Zhenhai Zhang, Xiaofan Zhou, Hong Ma, Andriy
Anishkin, Damian B. van Rossum, Randen L. Patterson | Extraction of Deep Phylogenetic Signal and Improved Resolution of
Evolutionary Events within the recA/RAD51 Phylogeny | 21 pages, 11 figures, 1 table | null | null | null | q-bio.GN q-bio.MN q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The recA/RAD51 gene family encodes a diverse set of recombinase proteins that
effect homologous recombination, DNA-repair, and genome stability. The recA
gene family is expressed in almost all species of Eubacteria, Archaea, and
Eukaryotes, and even in some viruses. To date, efforts to resolve the deep
evolutionary o... | [
{
"created": "Thu, 14 Jun 2012 22:02:09 GMT",
"version": "v1"
}
] | 2012-06-18 | [
[
"Chintapalli",
"Sree V.",
""
],
[
"Bhardwaj",
"Gaurav",
""
],
[
"Babu",
"Jagadish",
""
],
[
"Hadjiyianni",
"Loukia",
""
],
[
"Hong",
"Yoojin",
""
],
[
"Zhang",
"Zhenhai",
""
],
[
"Zhou",
"Xiaofan",
""
],
... | The recA/RAD51 gene family encodes a diverse set of recombinase proteins that effect homologous recombination, DNA-repair, and genome stability. The recA gene family is expressed in almost all species of Eubacteria, Archaea, and Eukaryotes, and even in some viruses. To date, efforts to resolve the deep evolutionary ori... |
0709.0025 | Ping Ao | P Ao | Borges Dilemma, Fundamental Laws, and Systems Biology | 4 pages | null | null | null | q-bio.QM q-bio.OT | null | I reason here that the known folk law in biology that there is no general law
in biology because of exceptions is false. The (quantitative) systems biology
offers the potential to solve the Borges Dilemma, by transcending it. There
have already a plenty of indications on this trend.
| [
{
"created": "Sat, 1 Sep 2007 00:16:45 GMT",
"version": "v1"
}
] | 2007-09-04 | [
[
"Ao",
"P",
""
]
] | I reason here that the known folk law in biology that there is no general law in biology because of exceptions is false. The (quantitative) systems biology offers the potential to solve the Borges Dilemma, by transcending it. There have already a plenty of indications on this trend. |
2307.13608 | Marco Pegoraro | Marco Pegoraro, Cl\'ementine Domin\'e, Emanuele Rodol\`a, Petar
Veli\v{c}kovi\'c, Andreea Deac | Geometric Epitope and Paratope Prediction | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Antibody-antigen interactions play a crucial role in identifying and
neutralizing harmful foreign molecules. In this paper, we investigate the
optimal representation for predicting the binding sites in the two molecules
and emphasize the importance of geometric information. Specifically, we compare
different geometri... | [
{
"created": "Sun, 28 May 2023 12:51:42 GMT",
"version": "v1"
}
] | 2023-07-26 | [
[
"Pegoraro",
"Marco",
""
],
[
"Dominé",
"Clémentine",
""
],
[
"Rodolà",
"Emanuele",
""
],
[
"Veličković",
"Petar",
""
],
[
"Deac",
"Andreea",
""
]
] | Antibody-antigen interactions play a crucial role in identifying and neutralizing harmful foreign molecules. In this paper, we investigate the optimal representation for predicting the binding sites in the two molecules and emphasize the importance of geometric information. Specifically, we compare different geometric ... |
2210.11478 | Matthew Bryan | Matthew J. Bryan (1), Linxing Preston Jiang (1), Rajesh P N Rao (1)
((1) Neural Systems Laboratory, Paul G. Allen School of Computer Science &
Engineering, University of Washington) | Neural Co-Processors for Restoring Brain Function: Results from a
Cortical Model of Grasping | 45 pages, 19 figures. Submitted the IOP Journal of Neural Engineering | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | Objective: A major challenge in designing closed-loop brain-computer
interfaces is finding optimal stimulation patterns as a function of ongoing
neural activity for different subjects and objectives. Approach: To achieve
goal-directed closed-loop neurostimulation, we propose "neural co-processors"
which use artificia... | [
{
"created": "Wed, 19 Oct 2022 04:13:33 GMT",
"version": "v1"
},
{
"created": "Mon, 20 Mar 2023 22:25:33 GMT",
"version": "v2"
}
] | 2023-03-22 | [
[
"Bryan",
"Matthew J.",
""
],
[
"Jiang",
"Linxing Preston",
""
],
[
"Rao",
"Rajesh P N",
""
]
] | Objective: A major challenge in designing closed-loop brain-computer interfaces is finding optimal stimulation patterns as a function of ongoing neural activity for different subjects and objectives. Approach: To achieve goal-directed closed-loop neurostimulation, we propose "neural co-processors" which use artificial ... |
2207.02014 | Alexander Stewart | Saul Acevedo and Alexander J. Stewart | Eco-evolutionary tradeoffs in the dynamics of prion strain competition | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Prion and prion-like molecules are a type of self replicating aggregate
protein that have been implicated in a variety of neurodegenerative diseases.
Over recent decades the molecular dynamics of prions have been characterized
both empirically and through mathematical models, providing insights into the
epidemiology ... | [
{
"created": "Tue, 5 Jul 2022 12:51:26 GMT",
"version": "v1"
}
] | 2022-07-06 | [
[
"Acevedo",
"Saul",
""
],
[
"Stewart",
"Alexander J.",
""
]
] | Prion and prion-like molecules are a type of self replicating aggregate protein that have been implicated in a variety of neurodegenerative diseases. Over recent decades the molecular dynamics of prions have been characterized both empirically and through mathematical models, providing insights into the epidemiology of... |
1611.00313 | Joaquin Rapela | Joaquin Rapela and Marissa Westerfield and Jeanne Townsend and Scott
Makeig | A new foreperiod effect on single-trial phase coherence. Part I:
existence and relevance | null | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Expecting events in time leads to more efficient behavior. A remarkable early
finding in the study of temporal expectancy is the foreperiod effect on
reaction times; i.e., the influence or reaction time of the time period between
a warning signal and an imperative stimulus to which subjects are instructed to
respond ... | [
{
"created": "Fri, 26 Aug 2016 18:50:12 GMT",
"version": "v1"
}
] | 2016-11-02 | [
[
"Rapela",
"Joaquin",
""
],
[
"Westerfield",
"Marissa",
""
],
[
"Townsend",
"Jeanne",
""
],
[
"Makeig",
"Scott",
""
]
] | Expecting events in time leads to more efficient behavior. A remarkable early finding in the study of temporal expectancy is the foreperiod effect on reaction times; i.e., the influence or reaction time of the time period between a warning signal and an imperative stimulus to which subjects are instructed to respond as... |
2003.00327 | Gerhard Mayer | Gerhard Mayer | Modelling techniques for biomolecular networks | 44 pages | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | First we shortly review the different kinds of network modelling methods for
systems biology with an emphasis on the different subtypes of logical models,
which we review in more detail. Then we show the advantages of Boolean networks
models over more mechanistic modelling types like differential equation
techniques.... | [
{
"created": "Sat, 29 Feb 2020 18:42:56 GMT",
"version": "v1"
}
] | 2020-03-03 | [
[
"Mayer",
"Gerhard",
""
]
] | First we shortly review the different kinds of network modelling methods for systems biology with an emphasis on the different subtypes of logical models, which we review in more detail. Then we show the advantages of Boolean networks models over more mechanistic modelling types like differential equation techniques. T... |
1402.4063 | Michael Goldberg | Byron C. Williams, Joshua J. Filter, Kristina A. Blake-Hodek, Brian E.
Wadzinski, Nicholas J. Fuda, David Shalloway, and Michael L. Goldberg | Greatwall-phosphorylated Endosulfine is Both an Inhibitor and a
Substrate of PP2A-B55 Heterotrimers | 65 pages of text, 11 figures, 10 supplementary figures. This paper
will be published in the journal eLife | null | null | null | q-bio.SC q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During M phase, Endosulfine (Endos) family proteins are phosphorylated by
Greatwall kinase (Gwl), and the resultant pEndos inhibits the phosphatase
PP2A-B55, which would otherwise prematurely reverse many CDK-driven
phosphorylations. We show here that PP2A-B55 is the enzyme responsible for
dephosphorylating pEndos du... | [
{
"created": "Mon, 17 Feb 2014 17:10:42 GMT",
"version": "v1"
}
] | 2014-02-18 | [
[
"Williams",
"Byron C.",
""
],
[
"Filter",
"Joshua J.",
""
],
[
"Blake-Hodek",
"Kristina A.",
""
],
[
"Wadzinski",
"Brian E.",
""
],
[
"Fuda",
"Nicholas J.",
""
],
[
"Shalloway",
"David",
""
],
[
"Goldberg",
"Mi... | During M phase, Endosulfine (Endos) family proteins are phosphorylated by Greatwall kinase (Gwl), and the resultant pEndos inhibits the phosphatase PP2A-B55, which would otherwise prematurely reverse many CDK-driven phosphorylations. We show here that PP2A-B55 is the enzyme responsible for dephosphorylating pEndos duri... |
1709.04090 | Yanjun Qi Dr. | Chandan Singh, Beilun Wang, Yanjun Qi | A Constrained, Weighted-L1 Minimization Approach for Joint Discovery of
Heterogeneous Neural Connectivity Graphs | 8 pages | null | null | null | q-bio.NC cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Determining functional brain connectivity is crucial to understanding the
brain and neural differences underlying disorders such as autism. Recent
studies have used Gaussian graphical models to learn brain connectivity via
statistical dependencies across brain regions from neuroimaging. However,
previous studies ofte... | [
{
"created": "Wed, 13 Sep 2017 00:05:20 GMT",
"version": "v1"
},
{
"created": "Thu, 21 Sep 2017 15:18:23 GMT",
"version": "v2"
}
] | 2017-09-22 | [
[
"Singh",
"Chandan",
""
],
[
"Wang",
"Beilun",
""
],
[
"Qi",
"Yanjun",
""
]
] | Determining functional brain connectivity is crucial to understanding the brain and neural differences underlying disorders such as autism. Recent studies have used Gaussian graphical models to learn brain connectivity via statistical dependencies across brain regions from neuroimaging. However, previous studies often ... |
1407.2269 | Krystyna Lukierska-Walasek | Krystyna Lukierska-Walasek, Krzysztof Topolski, Krzysztof Trojanowski | Statistical distributions and entropy considerations in gene codes | 11 pages, 18 figures. arXiv admin note: text overlap with
arXiv:1401.4561 | null | null | null | q-bio.GN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In our paper selected linguistic features of genomes to study the statistics
of the gene codes are considered. We present the information theory from which
it follows that if the system is described by distributions of hyperbolic type
it leads to the possibility of entropy loss and stability. We show that the
histogr... | [
{
"created": "Fri, 4 Jul 2014 19:19:18 GMT",
"version": "v1"
}
] | 2014-07-10 | [
[
"Lukierska-Walasek",
"Krystyna",
""
],
[
"Topolski",
"Krzysztof",
""
],
[
"Trojanowski",
"Krzysztof",
""
]
] | In our paper selected linguistic features of genomes to study the statistics of the gene codes are considered. We present the information theory from which it follows that if the system is described by distributions of hyperbolic type it leads to the possibility of entropy loss and stability. We show that the histogram... |
q-bio/0309028 | Bijan Pesaran | P. P. Mitra and B. Pesaran | Analysis of Dynamic Brain Imaging Data | 40 pages; 26 figures with subparts including 3 figures as .gif files.
Originally submitted to the neuro-sys archive which was never publicly
announced (was 9804003) | null | 10.1016/S0006-3495(99)77236-X | CMP-002 | q-bio.NC q-bio.QM | null | Modern imaging techniques for probing brain function, including functional
Magnetic Resonance Imaging, intrinsic and extrinsic contrast optical imaging,
and magnetoencephalography, generate large data sets with complex content. In
this paper we develop appropriate techniques of analysis and visualization of
such imag... | [
{
"created": "Mon, 20 Apr 1998 21:02:27 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Mitra",
"P. P.",
""
],
[
"Pesaran",
"B.",
""
]
] | Modern imaging techniques for probing brain function, including functional Magnetic Resonance Imaging, intrinsic and extrinsic contrast optical imaging, and magnetoencephalography, generate large data sets with complex content. In this paper we develop appropriate techniques of analysis and visualization of such imagin... |
1904.00099 | Dean Koro\v{s}ak | Dean Koro\v{s}ak, Marjan Slak Rupnik | Random matrix analysis of Ca$^{2+}$ signals in $\beta$-cell collectives | null | null | null | null | q-bio.CB cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Even within small organs like pancreatic islets, different endocrine cell
types and subtypes form a heterogeneous collective to sense the chemical
composition of the extracellular solution and compute an adequate hormonal
output. Erroneous cellular processing and hormonal output due to challenged
heterogeneity result... | [
{
"created": "Fri, 29 Mar 2019 21:53:14 GMT",
"version": "v1"
}
] | 2019-04-02 | [
[
"Korošak",
"Dean",
""
],
[
"Rupnik",
"Marjan Slak",
""
]
] | Even within small organs like pancreatic islets, different endocrine cell types and subtypes form a heterogeneous collective to sense the chemical composition of the extracellular solution and compute an adequate hormonal output. Erroneous cellular processing and hormonal output due to challenged heterogeneity result i... |
2201.09683 | Javier Jarillo | Javier Jarillo, Francisco J. Cao-Garc\'ia, and Frederik De Laender | Spatial and Ecological Scaling of Stability in Spatial Community
Networks | null | Front. Ecol. Evol. 10 (2022) 861537 | 10.3389/fevo.2022.861537 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There are many scales at which to quantify stability in spatial and
ecological networks. Local-scale analyses focus on specific nodes of the
spatial network, while regional-scale analyses consider the whole network.
Similarly, species- and community-level analyses either account for single
species or for the whole co... | [
{
"created": "Mon, 24 Jan 2022 13:28:47 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Oct 2022 08:30:39 GMT",
"version": "v2"
}
] | 2022-10-19 | [
[
"Jarillo",
"Javier",
""
],
[
"Cao-García",
"Francisco J.",
""
],
[
"De Laender",
"Frederik",
""
]
] | There are many scales at which to quantify stability in spatial and ecological networks. Local-scale analyses focus on specific nodes of the spatial network, while regional-scale analyses consider the whole network. Similarly, species- and community-level analyses either account for single species or for the whole comm... |
1407.0867 | Gibin Powathil | Gibin G Powathil, Alastair J Munro, Mark AJ Chaplain and Maciej Swat | Bystander effects and their implications for clinical radiation therapy:
Insights from multiscale in silico experiments | null | null | 10.1016/j.jtbi.2016.04.010 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Radiotherapy is a commonly used treatment for cancer and is usually given in
varying doses. At low radiation doses relatively few cells die as a direct
response to radiation but secondary radiation effects such as DNA mutation or
bystander effects affect many cells. Consequently it is at low radiation levels
where an... | [
{
"created": "Thu, 3 Jul 2014 11:22:29 GMT",
"version": "v1"
}
] | 2016-06-16 | [
[
"Powathil",
"Gibin G",
""
],
[
"Munro",
"Alastair J",
""
],
[
"Chaplain",
"Mark AJ",
""
],
[
"Swat",
"Maciej",
""
]
] | Radiotherapy is a commonly used treatment for cancer and is usually given in varying doses. At low radiation doses relatively few cells die as a direct response to radiation but secondary radiation effects such as DNA mutation or bystander effects affect many cells. Consequently it is at low radiation levels where an u... |
2004.08491 | Saroj Jayasinghe | Anuruddha Abeygunasekera and Saroj Jayasinghe | Is the anti-filarial drug diethylcarbamazine useful to treat COVID-19? | 9 pages | null | null | null | q-bio.SC q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The SARS-CoV-2 virus has resulted in a devastating pandemic of COVID-19.
Exploring compounds that could offer a breakthrough in treatment is the need of
the hour. Re-positioning cheap, freely available and safe drugs is a priority.
The paper proposes evidence for the potential use of diethylcarbamazine (DEC)
in the t... | [
{
"created": "Sat, 18 Apr 2020 00:18:08 GMT",
"version": "v1"
}
] | 2020-04-21 | [
[
"Abeygunasekera",
"Anuruddha",
""
],
[
"Jayasinghe",
"Saroj",
""
]
] | The SARS-CoV-2 virus has resulted in a devastating pandemic of COVID-19. Exploring compounds that could offer a breakthrough in treatment is the need of the hour. Re-positioning cheap, freely available and safe drugs is a priority. The paper proposes evidence for the potential use of diethylcarbamazine (DEC) in the tre... |
2006.01550 | Paul Reiser | Paul A. Reiser | Modified SIR Model Yielding a Logistic Solution | null | null | null | null | q-bio.PE | http://creativecommons.org/publicdomain/zero/1.0/ | The SIR pandemic model suffers from an unrealistic assumption: The rate of
removal from the infectious class of individuals is assumed to be proportional
to the number of infectious individuals. This means that a change in the rate
of infection is simultaneous with an equal change in the rate of removal. A
more reali... | [
{
"created": "Tue, 2 Jun 2020 12:16:19 GMT",
"version": "v1"
},
{
"created": "Sun, 7 Feb 2021 02:15:47 GMT",
"version": "v2"
},
{
"created": "Mon, 22 Feb 2021 00:26:24 GMT",
"version": "v3"
}
] | 2021-02-23 | [
[
"Reiser",
"Paul A.",
""
]
] | The SIR pandemic model suffers from an unrealistic assumption: The rate of removal from the infectious class of individuals is assumed to be proportional to the number of infectious individuals. This means that a change in the rate of infection is simultaneous with an equal change in the rate of removal. A more realist... |
2004.01207 | Mario Villalobos-Arias Dr. | Mario Villalobos-Arias | Estimation of population infected by Covid-19 using regression
Generalized logistics and optimization heuristics | 16 pages, 12 figures, prediction for covid-19, the document is in
Spanish | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In this work, a proposal for the estimation of the populations using logistic
curve fitting is presented. This type of curve is used to study population
growth, in this case population of people infected with the Covid-19 virus; and
it can also be used to approximate the survival curve used in actuarial and
similar s... | [
{
"created": "Thu, 2 Apr 2020 18:06:17 GMT",
"version": "v1"
}
] | 2020-04-06 | [
[
"Villalobos-Arias",
"Mario",
""
]
] | In this work, a proposal for the estimation of the populations using logistic curve fitting is presented. This type of curve is used to study population growth, in this case population of people infected with the Covid-19 virus; and it can also be used to approximate the survival curve used in actuarial and similar stu... |
1209.5549 | David Balduzzi | David Balduzzi and Michel Besserve | Towards a learning-theoretic analysis of spike-timing dependent
plasticity | To appear in Adv. Neural Inf. Proc. Systems | null | null | null | q-bio.NC cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper suggests a learning-theoretic perspective on how synaptic
plasticity benefits global brain functioning. We introduce a model, the
selectron, that (i) arises as the fast time constant limit of leaky
integrate-and-fire neurons equipped with spiking timing dependent plasticity
(STDP) and (ii) is amenable to t... | [
{
"created": "Tue, 25 Sep 2012 09:23:41 GMT",
"version": "v1"
}
] | 2012-09-26 | [
[
"Balduzzi",
"David",
""
],
[
"Besserve",
"Michel",
""
]
] | This paper suggests a learning-theoretic perspective on how synaptic plasticity benefits global brain functioning. We introduce a model, the selectron, that (i) arises as the fast time constant limit of leaky integrate-and-fire neurons equipped with spiking timing dependent plasticity (STDP) and (ii) is amenable to the... |
1809.05970 | Brian Cohn | Brian A. Cohn, Dilan D. Shah, Ali Marjaninejad, Martin Shapiro, Serhan
Ulkumen, Christopher M. Laine, Francisco J. Valero-Cuevas, Kenneth H.
Hayashida, Sarah Ingersoll | Quantifying and attenuating pathologic tremor in virtual reality | 3 pages; 3 figures | null | null | null | q-bio.QM cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a virtual reality (VR) experience that creates a research-grade
benchmark in assessing patients with active upper-limb tremor, while
simultaneously offering the opportunity for patients to engage with VR
experiences without their pathologic tremor. Accurate and precise use of
handheld motion controllers in... | [
{
"created": "Sun, 16 Sep 2018 22:23:04 GMT",
"version": "v1"
}
] | 2018-09-18 | [
[
"Cohn",
"Brian A.",
""
],
[
"Shah",
"Dilan D.",
""
],
[
"Marjaninejad",
"Ali",
""
],
[
"Shapiro",
"Martin",
""
],
[
"Ulkumen",
"Serhan",
""
],
[
"Laine",
"Christopher M.",
""
],
[
"Valero-Cuevas",
"Francisco J.... | We present a virtual reality (VR) experience that creates a research-grade benchmark in assessing patients with active upper-limb tremor, while simultaneously offering the opportunity for patients to engage with VR experiences without their pathologic tremor. Accurate and precise use of handheld motion controllers in V... |
1711.05574 | Laszlo Pecze | Mich\"ael Dougoud, Christian Mazza, Beat Schwaller, Laszlo Pecze | The phenomenon of growing surface interference explains the rosette
pattern of jaguar | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One possible mechanism to explain how animals got their coat patterns was
proposed by Alan Turing. He assumed that two kinds of morphogens diffuse on a
surface and interact with each other, generating a reaction-diffusion
mechanism. We developed a new framework for pattern generation incorporating a
non-diffusing tra... | [
{
"created": "Wed, 15 Nov 2017 14:03:56 GMT",
"version": "v1"
}
] | 2017-11-16 | [
[
"Dougoud",
"Michäel",
""
],
[
"Mazza",
"Christian",
""
],
[
"Schwaller",
"Beat",
""
],
[
"Pecze",
"Laszlo",
""
]
] | One possible mechanism to explain how animals got their coat patterns was proposed by Alan Turing. He assumed that two kinds of morphogens diffuse on a surface and interact with each other, generating a reaction-diffusion mechanism. We developed a new framework for pattern generation incorporating a non-diffusing trans... |
2108.09926 | Akash Gupta | Rishal Aggarwal, Akash Gupta, U Deva Priyakumar | APObind: A Dataset of Ligand Unbound Protein Conformations for Machine
Learning Applications in De Novo Drug Design | Accepted in The 2021 ICML Workshop on Computational Biology | null | null | null | q-bio.BM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein-ligand complex structures have been utilised to design benchmark
machine learning methods that perform important tasks related to drug design
such as receptor binding site detection, small molecule docking and binding
affinity prediction. However, these methods are usually trained on only ligand
bound (or hol... | [
{
"created": "Mon, 23 Aug 2021 04:29:38 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Aug 2021 04:37:33 GMT",
"version": "v2"
}
] | 2021-08-26 | [
[
"Aggarwal",
"Rishal",
""
],
[
"Gupta",
"Akash",
""
],
[
"Priyakumar",
"U Deva",
""
]
] | Protein-ligand complex structures have been utilised to design benchmark machine learning methods that perform important tasks related to drug design such as receptor binding site detection, small molecule docking and binding affinity prediction. However, these methods are usually trained on only ligand bound (or holo)... |
2102.07036 | Joaquin Torres | Jorge Pretel and Joaquin J. Torres and J. Marro | EEGs disclose significant brain activity correlated with synaptic
fickleness | 6 pages, 6 figures | null | null | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We here study a network of synaptic relations mingling excitatory and
inhibitory neuron nodes that displays oscillations quite similar to
electroencephalogram (EEG) brain waves, and identify abrupt variations brought
about by swift synaptic mediations. We thus conclude that corresponding changes
in EEG series surely ... | [
{
"created": "Sun, 14 Feb 2021 00:10:06 GMT",
"version": "v1"
},
{
"created": "Tue, 16 Feb 2021 10:22:54 GMT",
"version": "v2"
}
] | 2021-02-17 | [
[
"Pretel",
"Jorge",
""
],
[
"Torres",
"Joaquin J.",
""
],
[
"Marro",
"J.",
""
]
] | We here study a network of synaptic relations mingling excitatory and inhibitory neuron nodes that displays oscillations quite similar to electroencephalogram (EEG) brain waves, and identify abrupt variations brought about by swift synaptic mediations. We thus conclude that corresponding changes in EEG series surely co... |
2006.13693 | Richard Q Bao | Richard Bao, August Chen, Jethin Gowda, Shiva Mudide | PECAIQR: A Model for Infectious Disease Applied to the Covid-19 Epidemic | null | null | null | null | q-bio.PE cs.LG physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Covid-19 pandemic has made clear the need to improve modern multivariate
time-series forecasting models. Current state of the art predictions of future
daily deaths and, especially, hospital resource usage have confidence intervals
that are unacceptably wide. Policy makers and hospitals require accurate
forecasts... | [
{
"created": "Wed, 17 Jun 2020 17:59:55 GMT",
"version": "v1"
}
] | 2020-06-25 | [
[
"Bao",
"Richard",
""
],
[
"Chen",
"August",
""
],
[
"Gowda",
"Jethin",
""
],
[
"Mudide",
"Shiva",
""
]
] | The Covid-19 pandemic has made clear the need to improve modern multivariate time-series forecasting models. Current state of the art predictions of future daily deaths and, especially, hospital resource usage have confidence intervals that are unacceptably wide. Policy makers and hospitals require accurate forecasts t... |
1707.03302 | Matthew Spencer | Matthew Spencer | Equivalence relations on ecosystems | 17 pages, 3 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In abstract terms, ecosystem ecology is about determining when two
ecosystems, superficially different, are alike in some deeper way. An external
observer can choose any ecosystem property as being important. In contrast, two
ecosystems are equivalent from the point of view of the organisms they contain
if and only i... | [
{
"created": "Tue, 11 Jul 2017 14:30:54 GMT",
"version": "v1"
}
] | 2017-07-12 | [
[
"Spencer",
"Matthew",
""
]
] | In abstract terms, ecosystem ecology is about determining when two ecosystems, superficially different, are alike in some deeper way. An external observer can choose any ecosystem property as being important. In contrast, two ecosystems are equivalent from the point of view of the organisms they contain if and only if ... |
q-bio/0402030 | Ajit Kumar Mohanty | Ajit Kumar Mohanty (NPD, BARC, India) | A Barrier Penetration Model for DNA Double Strand Separation | 32 pages, 8 figures | null | null | null | q-bio.QM | null | A barrier penetration model has been proposed to explain the spontaneous
melting of the DNA oligomers into two separate single strands whereas the
partially melted intermediate states are shown to be the bound state solution
of the same effective potential that generates the barrier.
| [
{
"created": "Fri, 13 Feb 2004 05:45:38 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Mohanty",
"Ajit Kumar",
"",
"NPD, BARC, India"
]
] | A barrier penetration model has been proposed to explain the spontaneous melting of the DNA oligomers into two separate single strands whereas the partially melted intermediate states are shown to be the bound state solution of the same effective potential that generates the barrier. |
1911.12909 | Xiao-Jun Cai | Xiaojun Cai (1), Ruidong Li (2), Changcheng Sheng (1,3), Yifeng Tao
(2), Quanbao Zhang (2), Xiaofei Zhang (2), Juan Li (2), Conghuan Shen (2),
Xiaoyan Qiu (1), Zhengxin Wang (2), Zheng Jiao (1) | Systematic external evaluation of published population pharmacokinetic
models for tacrolimus in adult liver transplant recipients | null | Eur.J.Pharm.Sci.145(2020)105237 | 10.1016/j.ejps.2020.105237 | EJPS-D-19-01454 | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background:Diverse tacrolimus population pharmacokinetic models in adult
liver transplant recipients have been established to describe the PK
characteristics of tacrolimus in the last two decades. However, their
extrapolated predictive performance remains unclear.Therefore,in this study,we
aimed to evaluate their ext... | [
{
"created": "Fri, 29 Nov 2019 00:43:13 GMT",
"version": "v1"
}
] | 2020-02-20 | [
[
"Cai",
"Xiaojun",
""
],
[
"Li",
"Ruidong",
""
],
[
"Sheng",
"Changcheng",
""
],
[
"Tao",
"Yifeng",
""
],
[
"Zhang",
"Quanbao",
""
],
[
"Zhang",
"Xiaofei",
""
],
[
"Li",
"Juan",
""
],
[
"Shen",
"... | Background:Diverse tacrolimus population pharmacokinetic models in adult liver transplant recipients have been established to describe the PK characteristics of tacrolimus in the last two decades. However, their extrapolated predictive performance remains unclear.Therefore,in this study,we aimed to evaluate their exter... |
1605.09073 | Yu Hu | Yu Hu, Steven L. Brunton, Nicholas Cain, Stefan Mihalas, J. Nathan
Kutz, Eric Shea-Brown | Feedback through graph motifs relates structure and function in complex
networks | 31 pages, 20 figures | Phys. Rev. E 98, 062312 (2018) | 10.1103/PhysRevE.98.062312 | null | q-bio.NC cond-mat.dis-nn physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In physics, biology and engineering, network systems abound. How does the
connectivity of a network system combine with the behavior of its individual
components to determine its collective function? We approach this question for
networks with linear time-invariant dynamics by relating internal network
feedbacks to t... | [
{
"created": "Sun, 29 May 2016 22:58:04 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Dec 2018 16:33:43 GMT",
"version": "v2"
}
] | 2018-12-19 | [
[
"Hu",
"Yu",
""
],
[
"Brunton",
"Steven L.",
""
],
[
"Cain",
"Nicholas",
""
],
[
"Mihalas",
"Stefan",
""
],
[
"Kutz",
"J. Nathan",
""
],
[
"Shea-Brown",
"Eric",
""
]
] | In physics, biology and engineering, network systems abound. How does the connectivity of a network system combine with the behavior of its individual components to determine its collective function? We approach this question for networks with linear time-invariant dynamics by relating internal network feedbacks to the... |
2405.05293 | Sergei Voloboev | Sergei Voloboev | A Review on Fragment-based De Novo 2D Molecule Generation | null | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | In the field of computational molecule generation, an essential task in the
discovery of new chemical compounds, fragment-based deep generative models are
a leading approach, consistently achieving state-of-the-art results in
molecular design benchmarks as of 2023. We present a detailed comparative
assessment of thei... | [
{
"created": "Wed, 8 May 2024 09:38:38 GMT",
"version": "v1"
}
] | 2024-05-10 | [
[
"Voloboev",
"Sergei",
""
]
] | In the field of computational molecule generation, an essential task in the discovery of new chemical compounds, fragment-based deep generative models are a leading approach, consistently achieving state-of-the-art results in molecular design benchmarks as of 2023. We present a detailed comparative assessment of their ... |
1603.01297 | Bal\'azs Madas | Bal\'azs G. Madas | Radon induced hyperplasia: effective adaptation reducing the local doses
in the bronchial epithelium | 13 pages, 5 figures, 1 table | null | null | null | q-bio.TO physics.bio-ph physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There is experimental and histological evidence that chronic irritation and
cell death may cause hyperplasia in the exposed tissue. As the heterogeneous
deposition of inhaled radon progeny results in high local doses at the peak of
the bronchial bifurcations, it was proposed earlier that hyperplasia occurs in
these d... | [
{
"created": "Thu, 3 Mar 2016 22:06:42 GMT",
"version": "v1"
}
] | 2016-03-07 | [
[
"Madas",
"Balázs G.",
""
]
] | There is experimental and histological evidence that chronic irritation and cell death may cause hyperplasia in the exposed tissue. As the heterogeneous deposition of inhaled radon progeny results in high local doses at the peak of the bronchial bifurcations, it was proposed earlier that hyperplasia occurs in these dep... |
0705.2491 | Kazuya Ishibashi | Kazuya Ishibashi, Kosuke Hamaguchi, and Masato Okada | Sparse and Dense Encoding in Layered Associative Network of Spiking
Neurons | null | null | 10.1143/JPSJ.76.124801 | null | q-bio.NC | null | A synfire chain is a simple neural network model which can propagate stable
synchronous spikes called a pulse packet and widely researched. However how
synfire chains coexist in one network remains to be elucidated. We have studied
the activity of a layered associative network of Leaky Integrate-and-Fire
neurons in w... | [
{
"created": "Thu, 17 May 2007 07:18:34 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Ishibashi",
"Kazuya",
""
],
[
"Hamaguchi",
"Kosuke",
""
],
[
"Okada",
"Masato",
""
]
] | A synfire chain is a simple neural network model which can propagate stable synchronous spikes called a pulse packet and widely researched. However how synfire chains coexist in one network remains to be elucidated. We have studied the activity of a layered associative network of Leaky Integrate-and-Fire neurons in whi... |
1505.05644 | Aristides Moustakas | Marianna Louca, Ioannis N. Vogiatzakis, and Aristides Moustakas | Modelling the combined effects of land use and climatic changes:
coupling bioclimatic modelling with markov-chain cellular automata in a case
study in Cyprus | to appear (in press in Ecological Informatics (2015)) | null | null | null | q-bio.PE cs.CY cs.DM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Two endemic plant species in the Mediterranean island of Cyprus, Crocus
cyprius and Ophrys kotschyi, were used as a case study. We have coupled climate
change scenarios, and land use change models with species distribution models.
Future land use scenarios were modelled by initially calculating the rate of
current la... | [
{
"created": "Thu, 21 May 2015 08:25:16 GMT",
"version": "v1"
}
] | 2015-05-22 | [
[
"Louca",
"Marianna",
""
],
[
"Vogiatzakis",
"Ioannis N.",
""
],
[
"Moustakas",
"Aristides",
""
]
] | Two endemic plant species in the Mediterranean island of Cyprus, Crocus cyprius and Ophrys kotschyi, were used as a case study. We have coupled climate change scenarios, and land use change models with species distribution models. Future land use scenarios were modelled by initially calculating the rate of current land... |
1104.3457 | Sergei Rybalko | Sergei Rybalko and Sergei Larionov and Maria Poptsova and Alexander
Loskutov | Intermittency as a universal characteristic of the complete chromosome
DNA sequences of eukaryotes: From protozoa to human genomes | 4 pages, 5 figures | null | 10.1103/PhysRevE.84.042902 | null | q-bio.GN cond-mat.soft nlin.CD q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Large-scale dynamical properties of complete chromosome DNA sequences of
eukaryotes are considered. By the proposed deterministic models with
intermittency and symbolic dynamics we describe a wide spectrum of large-scale
patterns inherent in these sequences, such as segmental duplications, tandem
repeats, and other c... | [
{
"created": "Mon, 18 Apr 2011 12:35:47 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Apr 2011 12:49:31 GMT",
"version": "v2"
}
] | 2015-05-27 | [
[
"Rybalko",
"Sergei",
""
],
[
"Larionov",
"Sergei",
""
],
[
"Poptsova",
"Maria",
""
],
[
"Loskutov",
"Alexander",
""
]
] | Large-scale dynamical properties of complete chromosome DNA sequences of eukaryotes are considered. By the proposed deterministic models with intermittency and symbolic dynamics we describe a wide spectrum of large-scale patterns inherent in these sequences, such as segmental duplications, tandem repeats, and other com... |
2101.05746 | Rastine Merat | Aurore Bugi-Marteyn, Fanny Noulet, Nicolas Liaudet and Rastine Merat | A mutual information-based in vivo monitoring of adaptive response to
targeted therapies in melanoma | 9 pages, 5 figures Corrected typos | Neoplasia 23 (2021) pp. 775-782 | 10.1016/j.neo.2021.06.009 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The mechanisms of adaptive resistance to genetic-based targeted therapies of
solid malignancies have been the subject of intense research. These studies
hold great promise for finding co-targetable hub/pathways which in turn would
control the downstream non-genetic mechanisms of adaptive resistance. Many such
mechani... | [
{
"created": "Sun, 10 Jan 2021 18:35:51 GMT",
"version": "v1"
},
{
"created": "Fri, 15 Jan 2021 07:56:48 GMT",
"version": "v2"
}
] | 2021-07-09 | [
[
"Bugi-Marteyn",
"Aurore",
""
],
[
"Noulet",
"Fanny",
""
],
[
"Liaudet",
"Nicolas",
""
],
[
"Merat",
"Rastine",
""
]
] | The mechanisms of adaptive resistance to genetic-based targeted therapies of solid malignancies have been the subject of intense research. These studies hold great promise for finding co-targetable hub/pathways which in turn would control the downstream non-genetic mechanisms of adaptive resistance. Many such mechanism... |
2204.07362 | Keon-Woo Lee | Keon-Woo Lee and Dae-Hyeok Lee and Sung-Jin Kim and Seong-Whan Lee | Decoding Neural Correlation of Language-Specific Imagined Speech using
EEG Signals | Accepted in EMBC 2022 | null | null | null | q-bio.NC cs.HC eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Speech impairments due to cerebral lesions and degenerative disorders can be
devastating. For humans with severe speech deficits, imagined speech in the
brain-computer interface has been a promising hope for reconstructing the
neural signals of speech production. However, studies in the EEG-based imagined
speech doma... | [
{
"created": "Fri, 15 Apr 2022 07:41:04 GMT",
"version": "v1"
}
] | 2022-04-18 | [
[
"Lee",
"Keon-Woo",
""
],
[
"Lee",
"Dae-Hyeok",
""
],
[
"Kim",
"Sung-Jin",
""
],
[
"Lee",
"Seong-Whan",
""
]
] | Speech impairments due to cerebral lesions and degenerative disorders can be devastating. For humans with severe speech deficits, imagined speech in the brain-computer interface has been a promising hope for reconstructing the neural signals of speech production. However, studies in the EEG-based imagined speech domain... |
2306.13832 | David Benrimoh | David Benrimoh, Victoria L. Fisher, Rashina Seabury, Ely Sibarium,
Catalina Mourgues, Doris Chen, Albert Powers | Evidence for Reduced Sensory Precision and Increased Reliance on Priors
in Hallucination-Prone Individuals in a General Population Sample | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | There is increasing evidence that people with hallucinations overweight
perceptual beliefs relative to incoming sensory evidence. Much past work
demonstrating prior overweighting has used simple, non-linguistic stimuli.
However, auditory hallucinations in psychosis are often complex and linguistic.
There may be an in... | [
{
"created": "Sat, 24 Jun 2023 01:18:03 GMT",
"version": "v1"
}
] | 2023-06-27 | [
[
"Benrimoh",
"David",
""
],
[
"Fisher",
"Victoria L.",
""
],
[
"Seabury",
"Rashina",
""
],
[
"Sibarium",
"Ely",
""
],
[
"Mourgues",
"Catalina",
""
],
[
"Chen",
"Doris",
""
],
[
"Powers",
"Albert",
""
]
] | There is increasing evidence that people with hallucinations overweight perceptual beliefs relative to incoming sensory evidence. Much past work demonstrating prior overweighting has used simple, non-linguistic stimuli. However, auditory hallucinations in psychosis are often complex and linguistic. There may be an inte... |
2104.01256 | Deepak Gupta | Deepak Gupta, Stefano Garlaschi, Samir Suweis, Sandro Azaele, and Amos
Maritan | Effective Resource-Competition Model for Species Coexistence | 5 pages + 4 figures, Major revision | null | 10.1103/PhysRevLett.127.208101 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Local coexistence of species in large ecosystems is traditionally explained
within the broad framework of niche theory. However, its rationale hardly
justifies rich biodiversity observed in nearly homogeneous environments. Here
we consider a consumer-resource model in which a coarse-graining procedure
accounts for a ... | [
{
"created": "Fri, 2 Apr 2021 22:02:50 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Oct 2021 00:06:38 GMT",
"version": "v2"
}
] | 2021-11-17 | [
[
"Gupta",
"Deepak",
""
],
[
"Garlaschi",
"Stefano",
""
],
[
"Suweis",
"Samir",
""
],
[
"Azaele",
"Sandro",
""
],
[
"Maritan",
"Amos",
""
]
] | Local coexistence of species in large ecosystems is traditionally explained within the broad framework of niche theory. However, its rationale hardly justifies rich biodiversity observed in nearly homogeneous environments. Here we consider a consumer-resource model in which a coarse-graining procedure accounts for a va... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.