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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2303.09094 | Masod Sadipour | Masod Sadipour, Ali N. Azadani | The measurement of bovine pericardium density and its implications on
leaflet stress distribution in bioprosthetic heart valves | 13 pages, 7 figures | null | 10.1007/s13239-023-00692-0 | null | q-bio.TO | http://creativecommons.org/publicdomain/zero/1.0/ | Purpose: Bioprosthetic Heart Valves (BHVs) are currently in widespread use
with promising outcomes. Computational modeling provides a framework for
quantitatively describing BHVs in the preclinical phase. To obtain reliable
solutions in computational modeling, it is essential to consider accurate
leaflet properties s... | [
{
"created": "Thu, 16 Mar 2023 05:38:54 GMT",
"version": "v1"
}
] | 2024-01-23 | [
[
"Sadipour",
"Masod",
""
],
[
"Azadani",
"Ali N.",
""
]
] | Purpose: Bioprosthetic Heart Valves (BHVs) are currently in widespread use with promising outcomes. Computational modeling provides a framework for quantitatively describing BHVs in the preclinical phase. To obtain reliable solutions in computational modeling, it is essential to consider accurate leaflet properties suc... |
2009.11241 | Xuan Guo | Xuan Guo, Shichao Feng | Deep learning for peptide identification from metaproteomics datasets | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Metaproteomics are becoming widely used in microbiome research for gaining
insights into the functional state of the microbial community. Current
metaproteomics studies are generally based on high-throughput tandem mass
spectrometry (MS/MS) coupled with liquid chromatography. The identification of
peptides and protei... | [
{
"created": "Wed, 23 Sep 2020 16:25:22 GMT",
"version": "v1"
}
] | 2020-09-24 | [
[
"Guo",
"Xuan",
""
],
[
"Feng",
"Shichao",
""
]
] | Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS) coupled with liquid chromatography. The identification of peptides and proteins... |
2101.01752 | Giuseppe Tronci | Heather E. Owston, Katrina M. Moisley, Giuseppe Tronci, Stephen J.
Russell, Peter V. Giannoudis, Elena Jones | Induced Periosteum-Mimicking Membrane with Cell Barrier and
Multipotential Stromal Cell (MSC) Homing Functionalities | null | null | 10.3390/ijms21155233 | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | The current management of critical size bone defects (CSBDs) remains
challenging and requires multiple surgeries. To reduce the number of surgeries,
wrapping a biodegradable fibrous membrane around the defect to contain the
graft and carry biological stimulants for repair is highly desirable.
Poly(epsilon-caprolacton... | [
{
"created": "Tue, 5 Jan 2021 19:36:50 GMT",
"version": "v1"
}
] | 2021-01-07 | [
[
"Owston",
"Heather E.",
""
],
[
"Moisley",
"Katrina M.",
""
],
[
"Tronci",
"Giuseppe",
""
],
[
"Russell",
"Stephen J.",
""
],
[
"Giannoudis",
"Peter V.",
""
],
[
"Jones",
"Elena",
""
]
] | The current management of critical size bone defects (CSBDs) remains challenging and requires multiple surgeries. To reduce the number of surgeries, wrapping a biodegradable fibrous membrane around the defect to contain the graft and carry biological stimulants for repair is highly desirable. Poly(epsilon-caprolactone)... |
1909.00404 | Alexander Spirov | Victoria Yu. Samuta, Alexander V. Spirov | Quantitative analysis of the dynamics of maternal gradients of the early
Drosophila embryo | 19 pages, in russian | null | null | null | q-bio.QM q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The predetermination, formation and maintenance of the primary morphogenetic
gradient (bicoid gradient) of the early Drosophila embryo involves many
interrelated processes. Here we focus on a system-biological analysis of the
processes of redistribution of bicoid mRNA in an early embryo. The results of a
quantitative... | [
{
"created": "Sun, 1 Sep 2019 14:00:30 GMT",
"version": "v1"
}
] | 2019-09-04 | [
[
"Samuta",
"Victoria Yu.",
""
],
[
"Spirov",
"Alexander V.",
""
]
] | The predetermination, formation and maintenance of the primary morphogenetic gradient (bicoid gradient) of the early Drosophila embryo involves many interrelated processes. Here we focus on a system-biological analysis of the processes of redistribution of bicoid mRNA in an early embryo. The results of a quantitative a... |
2104.11852 | Tiberiu Tesileanu | Tiberiu Tesileanu, Siavash Golkar, Samaneh Nasiri, Anirvan M.
Sengupta, Dmitri B. Chklovskii | Neural circuits for dynamics-based segmentation of time series | v2.1; 34 pages, 14 figures | null | null | null | q-bio.NC physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | The brain must extract behaviorally relevant latent variables from the
signals streamed by the sensory organs. Such latent variables are often encoded
in the dynamics that generated the signal rather than in the specific
realization of the waveform. Therefore, one problem faced by the brain is to
segment time series ... | [
{
"created": "Sat, 24 Apr 2021 01:54:27 GMT",
"version": "v1"
},
{
"created": "Wed, 29 Sep 2021 18:59:27 GMT",
"version": "v2"
},
{
"created": "Tue, 5 Oct 2021 21:11:50 GMT",
"version": "v3"
}
] | 2021-10-07 | [
[
"Tesileanu",
"Tiberiu",
""
],
[
"Golkar",
"Siavash",
""
],
[
"Nasiri",
"Samaneh",
""
],
[
"Sengupta",
"Anirvan M.",
""
],
[
"Chklovskii",
"Dmitri B.",
""
]
] | The brain must extract behaviorally relevant latent variables from the signals streamed by the sensory organs. Such latent variables are often encoded in the dynamics that generated the signal rather than in the specific realization of the waveform. Therefore, one problem faced by the brain is to segment time series ba... |
1806.11557 | Francis Aweda | O.A. Falaiye and F. O Aweda | Mineralogical Characteristics of Harmattan Dust Across Jos North Central
and Potiskum North Earthern Cities of Nigeria | 18 pqges, 7 figures | null | null | null | q-bio.OT astro-ph.EP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The trace metals and mineralogical composition of harmattan dust carried out
on the samples collected at Jos ((9 55'N, 8 55'E)) and Potiskum ((11 43'N, 11
02'E) as revealed by PIXE and AAS machine using clean Petri Dishes and Plastic
bowls of 10 cm in diameter aimed on the characteristics of the mineralogical
and ele... | [
{
"created": "Tue, 19 Jun 2018 21:14:03 GMT",
"version": "v1"
}
] | 2018-07-02 | [
[
"Falaiye",
"O. A.",
""
],
[
"Aweda",
"F. O",
""
]
] | The trace metals and mineralogical composition of harmattan dust carried out on the samples collected at Jos ((9 55'N, 8 55'E)) and Potiskum ((11 43'N, 11 02'E) as revealed by PIXE and AAS machine using clean Petri Dishes and Plastic bowls of 10 cm in diameter aimed on the characteristics of the mineralogical and eleme... |
1908.01876 | Patrick Holmes | Patrick D. Holmes, Shannon M. Danforth, Xiao-Yu Fu, Talia Y. Moore,
and Ram Vasudevan | Characterizing the limits of human stability during motion: perturbative
experiment validates a model-based approach for the Sit-to-Stand task | 19 pages, 9 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Falls affect a growing number of the population each year. Clinical methods
to identify those at greatest risk for falls usually evaluate individuals while
they perform specific motions such as balancing or Sit-to-Stand (STS).
Unfortunately these techniques have been shown to have poor predictive power
and are unable... | [
{
"created": "Mon, 5 Aug 2019 21:54:52 GMT",
"version": "v1"
}
] | 2019-08-07 | [
[
"Holmes",
"Patrick D.",
""
],
[
"Danforth",
"Shannon M.",
""
],
[
"Fu",
"Xiao-Yu",
""
],
[
"Moore",
"Talia Y.",
""
],
[
"Vasudevan",
"Ram",
""
]
] | Falls affect a growing number of the population each year. Clinical methods to identify those at greatest risk for falls usually evaluate individuals while they perform specific motions such as balancing or Sit-to-Stand (STS). Unfortunately these techniques have been shown to have poor predictive power and are unable t... |
2007.02855 | Gilberto Nakamura | Gilberto Nakamura, Basil Grammaticos, Christophe Deroulers, Mathilde
Badoual | Effective epidemic model for COVID-19 using accumulated deaths | 20 pages, 7 figures | null | 10.1016/j.chaos.2021.110667 | null | q-bio.PE physics.bio-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The severe acute respiratory syndrome COVID-19 has been in the center of the
ongoing global health crisis in 2020. The high prevalence of mild cases
facilitates sub-notification outside hospital environments and the number of
those who are or have been infected remains largely unknown, leading to poor
estimates of th... | [
{
"created": "Mon, 6 Jul 2020 16:13:45 GMT",
"version": "v1"
}
] | 2021-05-26 | [
[
"Nakamura",
"Gilberto",
""
],
[
"Grammaticos",
"Basil",
""
],
[
"Deroulers",
"Christophe",
""
],
[
"Badoual",
"Mathilde",
""
]
] | The severe acute respiratory syndrome COVID-19 has been in the center of the ongoing global health crisis in 2020. The high prevalence of mild cases facilitates sub-notification outside hospital environments and the number of those who are or have been infected remains largely unknown, leading to poor estimates of the ... |
2402.17252 | Thomas-Otavio Peulen | Thomas-Otavio Peulen (1,2,3,4), Katherina Hemmen (4), Annemarie Greife
(5), Benjamin M. Webb (1,2,3), Suren Felekyan (5), Andrej Sali (1,2,3), Claus
A. M. Seidel (5), Hugo Sanabria (6), Katrin G. Heinze (4) ((1) Department of
Bioengineering and Therapeutic Sciences, University of California, San
Francisco, (2) ... | tttrlib: modular software for integrating fluorescence spectroscopy,
imaging, and molecular modeling | null | null | null | null | q-bio.QM physics.bio-ph | http://creativecommons.org/licenses/by-sa/4.0/ | We introduce software for reading, writing and processing fluorescence
single-molecule and image spectroscopy data and developing analysis pipelines
that unifies various spectroscopic analysis tools. Our software can be used for
processing multiple experiment types, e.g., for time-resolved single-molecule
(sm) spectr... | [
{
"created": "Tue, 27 Feb 2024 06:53:18 GMT",
"version": "v1"
}
] | 2024-02-28 | [
[
"Peulen",
"Thomas-Otavio",
""
],
[
"Hemmen",
"Katherina",
""
],
[
"Greife",
"Annemarie",
""
],
[
"Webb",
"Benjamin M.",
""
],
[
"Felekyan",
"Suren",
""
],
[
"Sali",
"Andrej",
""
],
[
"Seidel",
"Claus A. M.",
... | We introduce software for reading, writing and processing fluorescence single-molecule and image spectroscopy data and developing analysis pipelines that unifies various spectroscopic analysis tools. Our software can be used for processing multiple experiment types, e.g., for time-resolved single-molecule (sm) spectros... |
1912.08735 | Can Firtina | Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali,
Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu | AirLift: A Fast and Comprehensive Technique for Remapping Alignments
between Reference Genomes | null | null | null | null | q-bio.GN cs.CE | http://creativecommons.org/licenses/by/4.0/ | As genome sequencing tools and techniques improve, researchers are able to
incrementally assemble more accurate reference genomes, which enable
sensitivity in read mapping and downstream analysis such as variant calling. A
more sensitive downstream analysis is critical for a better understanding of
the genome donor (... | [
{
"created": "Wed, 18 Dec 2019 16:58:27 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Feb 2021 00:07:40 GMT",
"version": "v2"
},
{
"created": "Fri, 12 Aug 2022 04:38:54 GMT",
"version": "v3"
},
{
"created": "Mon, 21 Nov 2022 13:12:27 GMT",
"version": "v4"
}
] | 2022-11-22 | [
[
"Kim",
"Jeremie S.",
""
],
[
"Firtina",
"Can",
""
],
[
"Cavlak",
"Meryem Banu",
""
],
[
"Cali",
"Damla Senol",
""
],
[
"Alser",
"Mohammed",
""
],
[
"Hajinazar",
"Nastaran",
""
],
[
"Alkan",
"Can",
""
],
... | As genome sequencing tools and techniques improve, researchers are able to incrementally assemble more accurate reference genomes, which enable sensitivity in read mapping and downstream analysis such as variant calling. A more sensitive downstream analysis is critical for a better understanding of the genome donor (e.... |
2004.14787 | Biman Bagchi - | Saumyak Mukherjee, Sayantan Mondal and Biman Bagchi | Dynamical Theory and Cellular Automata Simulations of Pandemic Spread:
Understanding Different Temporal Patterns of Infections | 11 pages, 11 figures, 3 tables | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Here we propose and implement a generalized mathematical model to find the
time evolution of population in infectious diseases and apply the model to
study the recent COVID-19 pandemic. Our model at the core is a non-local
generalization of the widely used Kermack-McKendrick(KM) model where the
susceptible(S) populat... | [
{
"created": "Thu, 30 Apr 2020 14:02:49 GMT",
"version": "v1"
}
] | 2020-05-01 | [
[
"Mukherjee",
"Saumyak",
""
],
[
"Mondal",
"Sayantan",
""
],
[
"Bagchi",
"Biman",
""
]
] | Here we propose and implement a generalized mathematical model to find the time evolution of population in infectious diseases and apply the model to study the recent COVID-19 pandemic. Our model at the core is a non-local generalization of the widely used Kermack-McKendrick(KM) model where the susceptible(S) populatio... |
1706.05568 | Mareike Fischer | Michelle Galla and Kristina Wicke and Mareike Fischer | On the statistical inconsistency of Maximum Parsimony for $k$-tuple-site
data | null | null | null | null | q-bio.PE math.CO math.PR stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One of the main aims of phylogenetics is to reconstruct the \enquote{Tree of
Life}. In this respect, different methods and criteria are used to analyze DNA
sequences of different species and to compare them in order to derive the
evolutionary relationships of these species. Maximum Parsimony is one such
criterion for... | [
{
"created": "Sat, 17 Jun 2017 18:03:27 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Dec 2017 21:32:47 GMT",
"version": "v2"
},
{
"created": "Thu, 4 Oct 2018 07:58:45 GMT",
"version": "v3"
}
] | 2018-10-05 | [
[
"Galla",
"Michelle",
""
],
[
"Wicke",
"Kristina",
""
],
[
"Fischer",
"Mareike",
""
]
] | One of the main aims of phylogenetics is to reconstruct the \enquote{Tree of Life}. In this respect, different methods and criteria are used to analyze DNA sequences of different species and to compare them in order to derive the evolutionary relationships of these species. Maximum Parsimony is one such criterion for t... |
q-bio/0506018 | Antonio T. Costa Jr | Monica F. B. Moreira, Marcio P. Dantas, A. T. Costa Jr | Spontaneous natural selection in a model for spatially distributed
interacting populations | RevTeX4, 8 figures | null | null | null | q-bio.PE | null | We present an individual-based model for two interacting populations
diffusing on lattices in which a strong natural selection develops
spontaneously. The models combine traditional local predator-prey dynamics with
random walks. Individual's mobility is considered as an inherited trait. Small
variations upon inherit... | [
{
"created": "Wed, 15 Jun 2005 21:39:33 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Moreira",
"Monica F. B.",
""
],
[
"Dantas",
"Marcio P.",
""
],
[
"Costa",
"A. T.",
"Jr"
]
] | We present an individual-based model for two interacting populations diffusing on lattices in which a strong natural selection develops spontaneously. The models combine traditional local predator-prey dynamics with random walks. Individual's mobility is considered as an inherited trait. Small variations upon inheritan... |
1902.01257 | Vesna Vuksanovic | Vesna Vuksanovi\'c | Cortical thickness and functional networks modules by cortical lobes | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | This study aims to investigate topological organization of cortical thickness
and functional networks by cortical lobes. First, I demonstrated modular
organization of these networks by the cortical surface frontal, temporal,
parietal and occipital divisions. Secondly, I mapped the overlapping edges of
cortical thickn... | [
{
"created": "Mon, 4 Feb 2019 15:39:10 GMT",
"version": "v1"
},
{
"created": "Thu, 13 Jun 2019 09:16:27 GMT",
"version": "v2"
}
] | 2019-06-14 | [
[
"Vuksanović",
"Vesna",
""
]
] | This study aims to investigate topological organization of cortical thickness and functional networks by cortical lobes. First, I demonstrated modular organization of these networks by the cortical surface frontal, temporal, parietal and occipital divisions. Secondly, I mapped the overlapping edges of cortical thicknes... |
2006.03420 | Robert Worden | R.P. Worden | Is there a wave excitation in the Thalamus? | 11 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper proposes that the thalamus is the site of a wave excitation, whose
function is to represent the locations of things around the animal. Neurons
couple to the wave as transmitters and receivers. The wave acts as an analogue
representation of local space. This has benefits over a purely neural
representation ... | [
{
"created": "Wed, 20 May 2020 14:28:02 GMT",
"version": "v1"
}
] | 2020-06-08 | [
[
"Worden",
"R. P.",
""
]
] | This paper proposes that the thalamus is the site of a wave excitation, whose function is to represent the locations of things around the animal. Neurons couple to the wave as transmitters and receivers. The wave acts as an analogue representation of local space. This has benefits over a purely neural representation of... |
2404.09059 | Rayanne Luke | Prajakta Bedekar and Rayanne A. Luke and Anthony J. Kearsley | Prevalence estimation methods for time-dependent antibody kinetics of
infected and vaccinated individuals: a graph-theoretic approach | 27 pages, 7 figures | null | null | null | q-bio.PE math.PR physics.bio-ph q-bio.QM stat.ME | http://creativecommons.org/licenses/by/4.0/ | Immune events such as infection, vaccination, and a combination of the two
result in distinct time-dependent antibody responses in affected individuals.
These responses and event prevalences combine non-trivially to govern antibody
levels sampled from a population. Time-dependence and disease prevalence pose
consider... | [
{
"created": "Sat, 13 Apr 2024 18:43:59 GMT",
"version": "v1"
}
] | 2024-04-16 | [
[
"Bedekar",
"Prajakta",
""
],
[
"Luke",
"Rayanne A.",
""
],
[
"Kearsley",
"Anthony J.",
""
]
] | Immune events such as infection, vaccination, and a combination of the two result in distinct time-dependent antibody responses in affected individuals. These responses and event prevalences combine non-trivially to govern antibody levels sampled from a population. Time-dependence and disease prevalence pose considerab... |
1706.02327 | Christian Negre | Christian F. A. Negre, Uriel N. Morzan, Heidi Hendrickson, Rhitankar
Pal, George P. Lisi, J. Patrick Loria, Ivan Rivalta, Junming Ho, Victor S.
Batista | Eigenvector Centrality Distribution for Characterization of Protein
Allosteric Pathways | null | null | 10.1073/pnas.1810452115 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Determining the principal energy pathways for allosteric communication in
biomolecules, that occur as a result of thermal motion, remains challenging due
to the intrinsic complexity of the systems involved. Graph theory provides an
approach for making sense of such complexity, where allosteric proteins can be
represe... | [
{
"created": "Wed, 7 Jun 2017 18:32:59 GMT",
"version": "v1"
},
{
"created": "Mon, 25 Jun 2018 15:33:04 GMT",
"version": "v2"
}
] | 2022-05-04 | [
[
"Negre",
"Christian F. A.",
""
],
[
"Morzan",
"Uriel N.",
""
],
[
"Hendrickson",
"Heidi",
""
],
[
"Pal",
"Rhitankar",
""
],
[
"Lisi",
"George P.",
""
],
[
"Loria",
"J. Patrick",
""
],
[
"Rivalta",
"Ivan",
"... | Determining the principal energy pathways for allosteric communication in biomolecules, that occur as a result of thermal motion, remains challenging due to the intrinsic complexity of the systems involved. Graph theory provides an approach for making sense of such complexity, where allosteric proteins can be represent... |
2002.10372 | Mauro Mobilia | Ami Taitelbaum, Robert West, Michael Assaf, Mauro Mobilia | Population Dynamics in a Changing Environment: Random versus Periodic
Switching | 22 pages, 7 figures: main text (6 pages, 3 figures) followed by
Supplementary Material (16 pages, 4 figures). Published in Physical Review
Letters. Additional supporting resources available at
https://figshare.com/articles/Supplementary_Material/12613370 | Phys. Rev. Lett. 125, 048105 (2020) | 10.1103/PhysRevLett.125.048105 | null | q-bio.PE cond-mat.stat-mech nlin.AO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Environmental changes greatly influence the evolution of populations. Here,
we study the dynamics of a population of two strains, one growing slightly
faster than the other, competing for resources in a time-varying binary
environment modeled by a carrying capacity switching either randomly or
periodically between st... | [
{
"created": "Mon, 24 Feb 2020 16:57:17 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Jul 2020 00:22:13 GMT",
"version": "v2"
},
{
"created": "Mon, 27 Jul 2020 14:26:40 GMT",
"version": "v3"
}
] | 2020-07-28 | [
[
"Taitelbaum",
"Ami",
""
],
[
"West",
"Robert",
""
],
[
"Assaf",
"Michael",
""
],
[
"Mobilia",
"Mauro",
""
]
] | Environmental changes greatly influence the evolution of populations. Here, we study the dynamics of a population of two strains, one growing slightly faster than the other, competing for resources in a time-varying binary environment modeled by a carrying capacity switching either randomly or periodically between stat... |
1205.6867 | Frederick Matsen IV | Frederick A. Matsen, Aaron Gallagher, Connor McCoy | Minimizing the average distance to a closest leaf in a phylogenetic tree | Please contact us with any comments or questions! | null | null | null | q-bio.PE cs.DM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When performing an analysis on a collection of molecular sequences, it can be
convenient to reduce the number of sequences under consideration while
maintaining some characteristic of a larger collection of sequences. For
example, one may wish to select a subset of high-quality sequences that
represent the diversity ... | [
{
"created": "Thu, 31 May 2012 01:41:37 GMT",
"version": "v1"
},
{
"created": "Fri, 31 Aug 2012 18:05:58 GMT",
"version": "v2"
}
] | 2012-09-03 | [
[
"Matsen",
"Frederick A.",
""
],
[
"Gallagher",
"Aaron",
""
],
[
"McCoy",
"Connor",
""
]
] | When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may wish to select a subset of high-quality sequences that represent the diversity of... |
2404.10807 | Joseph Marsh | Benjamin J. Livesey, Mihaly Badonyi, Mafalda Dias, Jonathan Frazer,
Sushant Kumar, Kresten Lindorff-Larsen, David M. McCandlish, Rose Orenbuch,
Courtney A. Shearer, Lara Muffley, Julia Foreman, Andrew M. Glazer, Ben
Lehner, Debora S. Marks, Frederick P. Roth, Alan F. Rubin, Lea M. Starita and
Joseph A. Marsh | Guidelines for releasing a variant effect predictor | 14 pages, 1 figure | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Computational methods for assessing the likely impacts of mutations, known as
variant effect predictors (VEPs), are widely used in the assessment and
interpretation of human genetic variation, as well as in other applications
like protein engineering. Many different VEPs have been released to date, and
there is treme... | [
{
"created": "Tue, 16 Apr 2024 13:37:07 GMT",
"version": "v1"
}
] | 2024-04-18 | [
[
"Livesey",
"Benjamin J.",
""
],
[
"Badonyi",
"Mihaly",
""
],
[
"Dias",
"Mafalda",
""
],
[
"Frazer",
"Jonathan",
""
],
[
"Kumar",
"Sushant",
""
],
[
"Lindorff-Larsen",
"Kresten",
""
],
[
"McCandlish",
"David M."... | Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well as in other applications like protein engineering. Many different VEPs have been released to date, and there is tremend... |
1503.00529 | Sergei Maslov | Sergei Maslov and Kim Sneppen | Diversity waves in collapse-driven population dynamics | 15 pages (including SI), 6 figures + 7 supplementary figures | null | 10.1371/journal.pcbi.1004440 | null | q-bio.PE nlin.AO physics.soc-ph q-fin.EC q-fin.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Populations of species in ecosystems are often constrained by availability of
resources within their environment. In effect this means that a growth of one
population, needs to be balanced by comparable reduction in populations of
others. In neutral models of biodiversity all populations are assumed to change
increme... | [
{
"created": "Mon, 2 Mar 2015 14:03:39 GMT",
"version": "v1"
},
{
"created": "Tue, 14 Jul 2015 18:39:20 GMT",
"version": "v2"
}
] | 2016-02-17 | [
[
"Maslov",
"Sergei",
""
],
[
"Sneppen",
"Kim",
""
]
] | Populations of species in ecosystems are often constrained by availability of resources within their environment. In effect this means that a growth of one population, needs to be balanced by comparable reduction in populations of others. In neutral models of biodiversity all populations are assumed to change increment... |
2004.07440 | Masaki Watabe | Masaki Watabe, Hideaki Yoshimura, Satya N. V. Arjunan, Kazunari Kaizu,
and Koichi Takahashi | Signaling activations through G-protein-coupled-receptor aggregations | 6 pages, 4 figures | Phys. Rev. E 102, 032413 (2020) | 10.1103/PhysRevE.102.032413 | null | q-bio.MN q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Eukaryotic cells transmit extracellular signal information to cellular
interiors through the formation of a ternary complex made up of a ligand (or
agonist), G-protein, and G-protein coupled receptor (GPCR). Previously
formalized theories of ternary complex formation have mainly assumed that
observable states of rece... | [
{
"created": "Thu, 16 Apr 2020 03:51:21 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Sep 2020 23:10:22 GMT",
"version": "v2"
}
] | 2020-09-24 | [
[
"Watabe",
"Masaki",
""
],
[
"Yoshimura",
"Hideaki",
""
],
[
"Arjunan",
"Satya N. V.",
""
],
[
"Kaizu",
"Kazunari",
""
],
[
"Takahashi",
"Koichi",
""
]
] | Eukaryotic cells transmit extracellular signal information to cellular interiors through the formation of a ternary complex made up of a ligand (or agonist), G-protein, and G-protein coupled receptor (GPCR). Previously formalized theories of ternary complex formation have mainly assumed that observable states of recept... |
q-bio/0611024 | Iraziet Charret | I. C. Charret and M. V. Carneiro | Spontaneous emergence of spatial patterns ina a predator-prey model | 17 pages and 15 figures | PRE v.76. e061902, 2007 | 10.1103/PhysRevE.76.061902 | null | q-bio.PE | null | We present studies for an individual based model of three interacting
populations whose individuals are mobile in a 2D-lattice. We focus on the
pattern formation in the spatial distributions of the populations. Also
relevant is the relationship between pattern formation and features of the
populations' time series. O... | [
{
"created": "Tue, 7 Nov 2006 13:37:35 GMT",
"version": "v1"
}
] | 2007-12-18 | [
[
"Charret",
"I. C.",
""
],
[
"Carneiro",
"M. V.",
""
]
] | We present studies for an individual based model of three interacting populations whose individuals are mobile in a 2D-lattice. We focus on the pattern formation in the spatial distributions of the populations. Also relevant is the relationship between pattern formation and features of the populations' time series. Our... |
2003.00009 | Carlo Vittorio Cannistraci | Yan Ge, Philipp Rosendahl, Claudio Dur\'an, Nicole T\"opfner, Sara
Ciucci, Jochen Guck, and Carlo Vittorio Cannistraci | Cell Mechanics Based Computational Classification of Red Blood Cells Via
Machine Intelligence Applied to Morpho-Rheological Markers | 13 pages, 3 figures, 4 tables | IEEE/ACM Trans. Comput. Biol. Bioinform (2019) | 10.1109/TCBB.2019.2945762 | null | q-bio.QM cs.LG stat.ML | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Despite fluorescent cell-labelling being widely employed in biomedical
studies, some of its drawbacks are inevitable, with unsuitable fluorescent
probes or probes inducing a functional change being the main limitations.
Consequently, the demand for and development of label-free methodologies to
classify cells is stro... | [
{
"created": "Mon, 2 Mar 2020 15:11:46 GMT",
"version": "v1"
}
] | 2020-03-03 | [
[
"Ge",
"Yan",
""
],
[
"Rosendahl",
"Philipp",
""
],
[
"Durán",
"Claudio",
""
],
[
"Töpfner",
"Nicole",
""
],
[
"Ciucci",
"Sara",
""
],
[
"Guck",
"Jochen",
""
],
[
"Cannistraci",
"Carlo Vittorio",
""
]
] | Despite fluorescent cell-labelling being widely employed in biomedical studies, some of its drawbacks are inevitable, with unsuitable fluorescent probes or probes inducing a functional change being the main limitations. Consequently, the demand for and development of label-free methodologies to classify cells is strong... |
2401.06294 | Clement Soubrier | Cl\'ement Soubrier, Eric Foxall, Luca Ciandrini, Khanh Dao Duc | Optimal control of ribosome population for gene expression under
periodic nutrient intake | 16 pages (plus 13 pages of appendices). 4 figures (plus 1 figure and
1 table in appendices). Submitted to the Journal of The Royal Society
Interface | J. R. Soc. Interface. 2120230652 | 10.1098/rsif.2023.0652 | null | q-bio.SC | http://creativecommons.org/licenses/by/4.0/ | Translation of proteins is a fundamental part of gene expression that is
mediated by ribosomes. As ribosomes significantly contribute to both cellular
mass and energy consumption, achieving efficient management of the ribosome
population is also crucial to metabolism and growth. Inspired by biological
evidence for nu... | [
{
"created": "Thu, 11 Jan 2024 23:27:13 GMT",
"version": "v1"
}
] | 2024-04-18 | [
[
"Soubrier",
"Clément",
""
],
[
"Foxall",
"Eric",
""
],
[
"Ciandrini",
"Luca",
""
],
[
"Duc",
"Khanh Dao",
""
]
] | Translation of proteins is a fundamental part of gene expression that is mediated by ribosomes. As ribosomes significantly contribute to both cellular mass and energy consumption, achieving efficient management of the ribosome population is also crucial to metabolism and growth. Inspired by biological evidence for nutr... |
2311.17066 | Ke Yuhe | Yuhe Ke, Matilda Swee Sun Tang, Celestine Jia Ling Loh, Hairil Rizal
Abdullah, Nicholas Brian Shannon | Cluster trajectory of SOFA score in predicting mortality in sepsis | 26 pages, 4 figures, 2 tables | null | null | null | q-bio.QM cs.AI | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Objective: Sepsis is a life-threatening condition. Sequential Organ Failure
Assessment (SOFA) score is commonly used to assess organ dysfunction and
predict ICU mortality, but it is taken as a static measurement and fails to
capture dynamic changes. This study aims to investigate the relationship
between dynamic chan... | [
{
"created": "Thu, 23 Nov 2023 12:29:00 GMT",
"version": "v1"
}
] | 2023-11-30 | [
[
"Ke",
"Yuhe",
""
],
[
"Tang",
"Matilda Swee Sun",
""
],
[
"Loh",
"Celestine Jia Ling",
""
],
[
"Abdullah",
"Hairil Rizal",
""
],
[
"Shannon",
"Nicholas Brian",
""
]
] | Objective: Sepsis is a life-threatening condition. Sequential Organ Failure Assessment (SOFA) score is commonly used to assess organ dysfunction and predict ICU mortality, but it is taken as a static measurement and fails to capture dynamic changes. This study aims to investigate the relationship between dynamic change... |
1401.1755 | Tobias Reichenbach | Alexander Dobrinevski, Mikko Alava, Tobias Reichenbach, Erwin Frey | Mobility-Dependent Selection of Competing Strategy Associations | 9 pages, six figures; accepted in Physical Review E | Phys. Rev. E 89, 012721 (2014) | 10.1103/PhysRevE.89.012721 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Standard models of population dynamics focus on the the interaction,
survival, and extinction of the competing species individually. Real ecological
systems, however, are characterized by an abundance of species (or strategies,
in the terminology of evolutionary-game theory) that form intricate, complex
interaction n... | [
{
"created": "Wed, 8 Jan 2014 17:11:20 GMT",
"version": "v1"
}
] | 2014-05-27 | [
[
"Dobrinevski",
"Alexander",
""
],
[
"Alava",
"Mikko",
""
],
[
"Reichenbach",
"Tobias",
""
],
[
"Frey",
"Erwin",
""
]
] | Standard models of population dynamics focus on the the interaction, survival, and extinction of the competing species individually. Real ecological systems, however, are characterized by an abundance of species (or strategies, in the terminology of evolutionary-game theory) that form intricate, complex interaction net... |
2011.10126 | Brandon Hayes | Brandon H Hayes, Mathieu Andraud, Luis G Salazar, Nicolas Rose, and
Timothee Vergne | Mechanistic modeling of African swine fever: A systematic review | 19 pages, 3 figures, 4 tables. Accepted to Preventive Veterinary
Medicine. Revised from previous preprint to include models published through
Dec 2020 | null | 10.1016/j.prevetmed.2021.105358 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The spread of African swine fever (ASF) poses a grave threat to the global
swine industry. Understanding transmission dynamics, such as through
mechanistic modeling, is critical for designing effective control strategies.
Articles were examined across multiple epidemiological and model
characteristics. Model filiatio... | [
{
"created": "Thu, 19 Nov 2020 22:11:14 GMT",
"version": "v1"
},
{
"created": "Thu, 29 Apr 2021 07:44:11 GMT",
"version": "v2"
}
] | 2021-04-30 | [
[
"Hayes",
"Brandon H",
""
],
[
"Andraud",
"Mathieu",
""
],
[
"Salazar",
"Luis G",
""
],
[
"Rose",
"Nicolas",
""
],
[
"Vergne",
"Timothee",
""
]
] | The spread of African swine fever (ASF) poses a grave threat to the global swine industry. Understanding transmission dynamics, such as through mechanistic modeling, is critical for designing effective control strategies. Articles were examined across multiple epidemiological and model characteristics. Model filiation ... |
1208.0029 | Tobias Reichenbach | Tobias Reichenbach, Aleksandra Stefanovic, Fumiaki Nin, A. J. Hudspeth | Waves on Reissner's membrane: a mechanism for the propagation of
otoacoustic emissions from the cochlea | 30 pages, 6 figures, and Supplemental information | Cell Reports 1, 374-384 (2012) | 10.1016/j.celrep.2012.02.013 | null | q-bio.TO physics.bio-ph physics.comp-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sound is detected and converted into electrical signals within the ear. The
cochlea not only acts as a passive detector of sound, however, but can also
produce tones itself. These otoacoustic emissions are a striking manifestation
of the cochlea's mechanical active process. A controversy remains of how these
mechanic... | [
{
"created": "Tue, 31 Jul 2012 20:49:32 GMT",
"version": "v1"
}
] | 2012-08-02 | [
[
"Reichenbach",
"Tobias",
""
],
[
"Stefanovic",
"Aleksandra",
""
],
[
"Nin",
"Fumiaki",
""
],
[
"Hudspeth",
"A. J.",
""
]
] | Sound is detected and converted into electrical signals within the ear. The cochlea not only acts as a passive detector of sound, however, but can also produce tones itself. These otoacoustic emissions are a striking manifestation of the cochlea's mechanical active process. A controversy remains of how these mechanical... |
2003.01409 | Niceto R. Luque | Francisco Naveros, Niceto R. Luque, Eduardo Ros, Angelo Arleo | VOR Adaptation on a Humanoid iCub Robot Using a Spiking Cerebellar Model | null | null | 10.1109/TCYB.2019.2899246 | null | q-bio.NC cs.NE cs.RO cs.SY eess.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We embed a spiking cerebellar model within an adaptive real-time (RT) control
loop that is able to operate a real robotic body (iCub) when performing
different vestibulo-ocular reflex (VOR) tasks. The spiking neural network
computation, including event- and time-driven neural dynamics, neural activity,
and spike-timi... | [
{
"created": "Tue, 3 Mar 2020 09:48:15 GMT",
"version": "v1"
},
{
"created": "Tue, 31 Mar 2020 07:26:00 GMT",
"version": "v2"
}
] | 2020-04-01 | [
[
"Naveros",
"Francisco",
""
],
[
"Luque",
"Niceto R.",
""
],
[
"Ros",
"Eduardo",
""
],
[
"Arleo",
"Angelo",
""
]
] | We embed a spiking cerebellar model within an adaptive real-time (RT) control loop that is able to operate a real robotic body (iCub) when performing different vestibulo-ocular reflex (VOR) tasks. The spiking neural network computation, including event- and time-driven neural dynamics, neural activity, and spike-timing... |
1311.2665 | Chen Jia | Chen Jia, Daquan Jiang, Minping Qian | An allosteric model of the inositol trisphosphate receptor with
nonequilibrium binding | 23 pages, 5 figures | Physical Biology, 11(5):056001, 2014 | 10.1088/1478-3975/11/5/056001 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The inositol trisphosphate receptor (IPR) is a crucial ion channel that
regulates the Ca$^{2+}$ influx from the endoplasmic reticulum (ER) to the
cytoplasm. A thorough study of the IPR channel contributes to a better
understanding of calcium oscillations and waves. It has long been observed that
the IPR channel is a ... | [
{
"created": "Tue, 12 Nov 2013 03:23:05 GMT",
"version": "v1"
},
{
"created": "Fri, 4 Jul 2014 15:21:35 GMT",
"version": "v2"
}
] | 2014-08-28 | [
[
"Jia",
"Chen",
""
],
[
"Jiang",
"Daquan",
""
],
[
"Qian",
"Minping",
""
]
] | The inositol trisphosphate receptor (IPR) is a crucial ion channel that regulates the Ca$^{2+}$ influx from the endoplasmic reticulum (ER) to the cytoplasm. A thorough study of the IPR channel contributes to a better understanding of calcium oscillations and waves. It has long been observed that the IPR channel is a ty... |
2102.12602 | Guillermo Lorenzo | Guillermo Lorenzo, David A. Hormuth II, Angela M. Jarrett, Ernesto A.
B. F. Lima, Shashank Subramanian, George Biros, J. Tinsley Oden, Thomas J. R.
Hughes, and Thomas E. Yankeelov | Quantitative in vivo imaging to enable tumor forecasting and treatment
optimization | null | null | null | null | q-bio.TO cs.CE q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Current clinical decision-making in oncology relies on averages of large
patient populations to both assess tumor status and treatment outcomes.
However, cancers exhibit an inherent evolving heterogeneity that requires an
individual approach based on rigorous and precise predictions of cancer growth
and treatment res... | [
{
"created": "Wed, 24 Feb 2021 23:32:48 GMT",
"version": "v1"
}
] | 2021-02-26 | [
[
"Lorenzo",
"Guillermo",
""
],
[
"Hormuth",
"David A.",
"II"
],
[
"Jarrett",
"Angela M.",
""
],
[
"Lima",
"Ernesto A. B. F.",
""
],
[
"Subramanian",
"Shashank",
""
],
[
"Biros",
"George",
""
],
[
"Oden",
"J. Tin... | Current clinical decision-making in oncology relies on averages of large patient populations to both assess tumor status and treatment outcomes. However, cancers exhibit an inherent evolving heterogeneity that requires an individual approach based on rigorous and precise predictions of cancer growth and treatment respo... |
1802.00102 | Laura Schaposnik | Laura P. Schaposnik, Anlin Zhang | Modeling epidemics on d-cliqued graphs | 11 pages, 16 figures | Letters in Biomathematics, Vol. 5, Iss. 1, 2018 | 10.1080/23737867.2017.1419080 | null | q-bio.PE cs.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Since social interactions have been shown to lead to symmetric clusters, we
propose here that symmetries play a key role in epidemic modeling. Mathematical
models on d-ary tree graphs were recently shown to be particularly effective
for modeling epidemics in simple networks [Seibold & Callender, 2016]. To
account for... | [
{
"created": "Wed, 31 Jan 2018 23:35:04 GMT",
"version": "v1"
}
] | 2019-05-24 | [
[
"Schaposnik",
"Laura P.",
""
],
[
"Zhang",
"Anlin",
""
]
] | Since social interactions have been shown to lead to symmetric clusters, we propose here that symmetries play a key role in epidemic modeling. Mathematical models on d-ary tree graphs were recently shown to be particularly effective for modeling epidemics in simple networks [Seibold & Callender, 2016]. To account for s... |
2109.01571 | Karl Grieshop | Karl Grieshop, Eddie K.H. Ho, Katja R. Kasimatis | Dominance reversals: The resolution of genetic conflict and maintenance
of genetic variation | Review paper with some original theory, 1 Figure, 1 table, 1 box, and
Supporting Information (including 11 Figures and 2 tables) | Proceedings of the Royal Society B, 291(2018), p.20232816 (2024) | 10.1098/rspb.2023.2816 | null | q-bio.PE q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Beneficial reversals of dominance reduce the costs of genetic trade-offs and
can enable selection to maintain genetic variation for fitness. Beneficial
dominance reversals are characterized by the beneficial allele for a given
context (e.g. habitat, developmental stage, trait, or sex) being dominant in
that context b... | [
{
"created": "Fri, 3 Sep 2021 14:52:31 GMT",
"version": "v1"
},
{
"created": "Sat, 15 Oct 2022 16:15:07 GMT",
"version": "v2"
},
{
"created": "Wed, 13 Dec 2023 13:08:56 GMT",
"version": "v3"
},
{
"created": "Fri, 26 Jan 2024 09:32:50 GMT",
"version": "v4"
}
] | 2024-03-28 | [
[
"Grieshop",
"Karl",
""
],
[
"Ho",
"Eddie K. H.",
""
],
[
"Kasimatis",
"Katja R.",
""
]
] | Beneficial reversals of dominance reduce the costs of genetic trade-offs and can enable selection to maintain genetic variation for fitness. Beneficial dominance reversals are characterized by the beneficial allele for a given context (e.g. habitat, developmental stage, trait, or sex) being dominant in that context but... |
2201.11748 | Roberto Rojas-Cessa | Jorge Medina, Roberto Rojas-Cessa, and Vatcharapan Umpaichitra | Reducing COVID-19 Cases and Deaths by Applying Blockchain in Vaccination
Rollout Management | Peer reviewed | in IEEE Open Journal of Engineering in Medicine and Biology, vol.
2, pp. 249-255, 2021 | 10.1109/OJEMB.2021.3093774 | null | q-bio.QM cs.CY | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Because a fast vaccination rollout against coronavirus disease 2019
(COVID-19) is critical to restore daily life and avoid virus mutations, it is
tempting to have a relaxed vaccination-administration management system.
However, a robust management system can support the enforcement of preventive
measures, and in turn... | [
{
"created": "Thu, 27 Jan 2022 18:31:41 GMT",
"version": "v1"
},
{
"created": "Wed, 16 Mar 2022 13:29:18 GMT",
"version": "v2"
}
] | 2022-03-17 | [
[
"Medina",
"Jorge",
""
],
[
"Rojas-Cessa",
"Roberto",
""
],
[
"Umpaichitra",
"Vatcharapan",
""
]
] | Because a fast vaccination rollout against coronavirus disease 2019 (COVID-19) is critical to restore daily life and avoid virus mutations, it is tempting to have a relaxed vaccination-administration management system. However, a robust management system can support the enforcement of preventive measures, and in turn, ... |
1907.04953 | Da-Young Lee | Da-Young Lee, Dong-Yeop Na, Yong Seok Heo, and Guo-Liang Wang | Digital image quantification of rice sheath blight: Optimized
segmentation and automatic classification | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Rapid and accurate phenotypic screening of rice germplasms is crucial in
screening for sources of rice sheath blight resistance. However, visual and/or
caliper-based estimations of coalescing, necrotic, ShB disease lesions are
time-consuming, labor-intensive and exposed to human rater subjectivity. Here,
we propose t... | [
{
"created": "Wed, 10 Jul 2019 23:11:27 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Apr 2021 06:04:03 GMT",
"version": "v2"
}
] | 2021-04-14 | [
[
"Lee",
"Da-Young",
""
],
[
"Na",
"Dong-Yeop",
""
],
[
"Heo",
"Yong Seok",
""
],
[
"Wang",
"Guo-Liang",
""
]
] | Rapid and accurate phenotypic screening of rice germplasms is crucial in screening for sources of rice sheath blight resistance. However, visual and/or caliper-based estimations of coalescing, necrotic, ShB disease lesions are time-consuming, labor-intensive and exposed to human rater subjectivity. Here, we propose the... |
2006.09818 | Nathaniel Barlow | Steven J. Weinstein, Morgan S. Holland, Kelly E. Rogers, Nathaniel S.
Barlow | Analytic solution of the SEIR epidemic model via asymptotic approximant | original version had substantial text overlap with arXiv:2004.07833;
this is now less so | null | 10.1016/j.physd.2020.132633 | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by-sa/4.0/ | An analytic solution is obtained to the SEIR Epidemic Model. The solution is
created by constructing a single second-order nonlinear differential equation
in $\ln S$ and analytically continuing its divergent power series solution such
that it matches the correct long-time exponential damping of the epidemic
model. Th... | [
{
"created": "Fri, 12 Jun 2020 20:18:44 GMT",
"version": "v1"
},
{
"created": "Tue, 30 Jun 2020 01:52:51 GMT",
"version": "v2"
}
] | 2020-07-01 | [
[
"Weinstein",
"Steven J.",
""
],
[
"Holland",
"Morgan S.",
""
],
[
"Rogers",
"Kelly E.",
""
],
[
"Barlow",
"Nathaniel S.",
""
]
] | An analytic solution is obtained to the SEIR Epidemic Model. The solution is created by constructing a single second-order nonlinear differential equation in $\ln S$ and analytically continuing its divergent power series solution such that it matches the correct long-time exponential damping of the epidemic model. This... |
1108.4642 | Steven Kelk | Steven Kelk | A note on efficient computation of hybridization number via softwired
clusters | null | null | null | null | q-bio.PE cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Here we present a new fixed parameter tractable algorithm to compute the
hybridization number r of two rooted binary phylogenetic trees on taxon set X
in time (6r)^r.poly(n), where n=|X|. The novelty of this approach is that it
avoids the use of Maximum Acyclic Agreement Forests (MAAFs) and instead
exploits the equiv... | [
{
"created": "Tue, 23 Aug 2011 15:54:02 GMT",
"version": "v1"
}
] | 2011-08-24 | [
[
"Kelk",
"Steven",
""
]
] | Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted binary phylogenetic trees on taxon set X in time (6r)^r.poly(n), where n=|X|. The novelty of this approach is that it avoids the use of Maximum Acyclic Agreement Forests (MAAFs) and instead exploits the equival... |
2102.06490 | Michael Grinfeld | Michael Grinfeld, Nigel Mottram and Jozsef Farkas | A General Model of Structured Cell Kinetics | 8 pages, 1 figure | null | null | null | q-bio.CB nlin.PS | http://creativecommons.org/licenses/by/4.0/ | We present a modelling framework for the dynamics of cells structured by the
concentration of a micromolecule they contain. We derive general equations for
the evolution of the cell population and of the extra-cellular concentration of
the molecule and apply this approach to models of silicosis and quorum sensing
in ... | [
{
"created": "Fri, 12 Feb 2021 12:44:56 GMT",
"version": "v1"
}
] | 2021-02-15 | [
[
"Grinfeld",
"Michael",
""
],
[
"Mottram",
"Nigel",
""
],
[
"Farkas",
"Jozsef",
""
]
] | We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the molecule and apply this approach to models of silicosis and quorum sensing in Gr... |
1703.10677 | Yang Chen | Yang Chen, Dong-Jie Zhao, Chao Song, Wei-He Liu, Zi-Yang Wang,
Zhong-Yi Wang, Guiliang Tang, and Lan Huang | Detecting causality in Plant electrical signal by a hybrid causal
analysis approach | 12 figures | null | null | null | q-bio.NC q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | At present, multi-electrode array (MEA) approach and optical recording allow
us to acquire plant electrical activity with higher spatio-temporal resolution.
To understand the dynamic information flow of the electrical signaling system
and estimate the effective connectivity, we proposed a solution to combine the
two ... | [
{
"created": "Wed, 22 Mar 2017 02:11:45 GMT",
"version": "v1"
}
] | 2017-04-03 | [
[
"Chen",
"Yang",
""
],
[
"Zhao",
"Dong-Jie",
""
],
[
"Song",
"Chao",
""
],
[
"Liu",
"Wei-He",
""
],
[
"Wang",
"Zi-Yang",
""
],
[
"Wang",
"Zhong-Yi",
""
],
[
"Tang",
"Guiliang",
""
],
[
"Huang",
"... | At present, multi-electrode array (MEA) approach and optical recording allow us to acquire plant electrical activity with higher spatio-temporal resolution. To understand the dynamic information flow of the electrical signaling system and estimate the effective connectivity, we proposed a solution to combine the two ca... |
0811.3464 | Elfi Kraka | Sushilee Ranganathan, Dmitry Izotov, Elfi Kraka, and Dieter Cremer | Classification of Supersecondary Structures in Proteins Using the
Automated Protein Structure Analysis Method | 40 pages, 5 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Automated Protein Structure Analysis (APSA) method is used for the
classification of supersecondary structures. Basis for the classification is
the encoding of three-dimensional (3D) residue conformations into a 16-letter
code (3D-1D projection). It is shown that the letter code of the protein makes
it possible t... | [
{
"created": "Fri, 21 Nov 2008 04:24:40 GMT",
"version": "v1"
},
{
"created": "Mon, 24 Nov 2008 20:52:14 GMT",
"version": "v2"
}
] | 2008-11-24 | [
[
"Ranganathan",
"Sushilee",
""
],
[
"Izotov",
"Dmitry",
""
],
[
"Kraka",
"Elfi",
""
],
[
"Cremer",
"Dieter",
""
]
] | The Automated Protein Structure Analysis (APSA) method is used for the classification of supersecondary structures. Basis for the classification is the encoding of three-dimensional (3D) residue conformations into a 16-letter code (3D-1D projection). It is shown that the letter code of the protein makes it possible to ... |
1205.2358 | Thomas R. Weikl | Thomas R. Weikl and David D. Boehr | Conformational selection and induced changes along the catalytic cycle
of E. coli DHFR | 14 pages, 8 figures, 2 tables | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein function often involves changes between different conformations.
Central questions are how these conformational changes are coupled to the
binding or catalytic processes during which they occur, and how they affect the
catalytic rates of enzymes. An important model system is the enzyme
dihydrofolate reductase... | [
{
"created": "Thu, 10 May 2012 19:25:53 GMT",
"version": "v1"
}
] | 2012-05-11 | [
[
"Weikl",
"Thomas R.",
""
],
[
"Boehr",
"David D.",
""
]
] | Protein function often involves changes between different conformations. Central questions are how these conformational changes are coupled to the binding or catalytic processes during which they occur, and how they affect the catalytic rates of enzymes. An important model system is the enzyme dihydrofolate reductase (... |
2311.12080 | Alaa Sadiq | Alaa M. Sadeq | Exploring the Relationship Between COVID-19 Induced Economic Downturn
and Women's Nutritional Health Disparities | null | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | This study explores how the COVID-19 pandemic's economic impact has
exacerbated nutritional health disparities among women. It sought to understand
the effects of economic challenges on women's dietary choices and access to
nutritious food across different socioeconomic groups. Using a mixed-methods
approach, the res... | [
{
"created": "Mon, 20 Nov 2023 09:10:25 GMT",
"version": "v1"
}
] | 2023-11-22 | [
[
"Sadeq",
"Alaa M.",
""
]
] | This study explores how the COVID-19 pandemic's economic impact has exacerbated nutritional health disparities among women. It sought to understand the effects of economic challenges on women's dietary choices and access to nutritious food across different socioeconomic groups. Using a mixed-methods approach, the resea... |
1307.7872 | Claudius Gros | Claudius Gros | Generating functionals for guided self-organization | To be published in "Guided Self-Organization: Inception", Springer
Series on Emergence, Complexity and Computation, M. Prokopenko (ed),
Proceedings of Fifth International Workshop on Guided Self-Organization,
Sydney 2012 | M. Prokopenko (ed.), Guided Self-Organization: Inception, 53-66,
Springer (2014) | null | null | q-bio.NC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Time evolution equations for dynamical systems can often be derived from
generating functionals. Examples are Newton's equations of motion in classical
dynamics which can be generated within the Lagrange or the Hamiltonian
formalism. We propose that generating functionals for self-organizing complex
systems offer sev... | [
{
"created": "Tue, 30 Jul 2013 08:53:04 GMT",
"version": "v1"
}
] | 2014-04-23 | [
[
"Gros",
"Claudius",
""
]
] | Time evolution equations for dynamical systems can often be derived from generating functionals. Examples are Newton's equations of motion in classical dynamics which can be generated within the Lagrange or the Hamiltonian formalism. We propose that generating functionals for self-organizing complex systems offer sever... |
1211.2458 | Paul H\'eroux | Su Dong, Paul Heroux | Survey of Extra-Low Frequency and Very-Low Frequency Magnetic Fields in
Cell Culture Incubators | 59 pages, 20 figures, 7 appendices | null | null | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A typical cell culture CO2 incubator was probed in detail to document the
pattern of 60-Hz magnetic fields (MFs) inside the unit, as well as the ability
of the incubator to attenuate environmental MFs. Subsequently, a survey of 46
cell culture incubators was performed. The survey measured MFs outside and
inside the i... | [
{
"created": "Sun, 11 Nov 2012 20:40:00 GMT",
"version": "v1"
}
] | 2012-11-13 | [
[
"Dong",
"Su",
""
],
[
"Heroux",
"Paul",
""
]
] | A typical cell culture CO2 incubator was probed in detail to document the pattern of 60-Hz magnetic fields (MFs) inside the unit, as well as the ability of the incubator to attenuate environmental MFs. Subsequently, a survey of 46 cell culture incubators was performed. The survey measured MFs outside and inside the inc... |
2406.15987 | Francis Motta | Francis C. Motta, Kevin McGoff, Breschine Cummins, Steven B. Haase | Generalized Measures of Population Synchrony | null | null | null | null | q-bio.PE math.PR q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Synchronized behavior among individuals is a ubiquitous feature of
populations. Understanding mechanisms of (de)synchronization demands
meaningful, interpretable, computable quantifications of synchrony, relevant to
measurements that can be made of dynamic populations. Despite the importance to
analyzing and modeling... | [
{
"created": "Sun, 23 Jun 2024 02:46:43 GMT",
"version": "v1"
}
] | 2024-06-25 | [
[
"Motta",
"Francis C.",
""
],
[
"McGoff",
"Kevin",
""
],
[
"Cummins",
"Breschine",
""
],
[
"Haase",
"Steven B.",
""
]
] | Synchronized behavior among individuals is a ubiquitous feature of populations. Understanding mechanisms of (de)synchronization demands meaningful, interpretable, computable quantifications of synchrony, relevant to measurements that can be made of dynamic populations. Despite the importance to analyzing and modeling p... |
2106.10234 | Yingce Xia | Jinhua Zhu, Yingce Xia, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan
Liu | Dual-view Molecule Pre-training | Add new results of retrosynthesis | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inspired by its success in natural language processing and computer vision,
pre-training has attracted substantial attention in cheminformatics and
bioinformatics, especially for molecule based tasks. A molecule can be
represented by either a graph (where atoms are connected by bonds) or a SMILES
sequence (where dept... | [
{
"created": "Thu, 17 Jun 2021 03:58:38 GMT",
"version": "v1"
},
{
"created": "Wed, 13 Oct 2021 03:09:28 GMT",
"version": "v2"
}
] | 2021-10-14 | [
[
"Zhu",
"Jinhua",
""
],
[
"Xia",
"Yingce",
""
],
[
"Qin",
"Tao",
""
],
[
"Zhou",
"Wengang",
""
],
[
"Li",
"Houqiang",
""
],
[
"Liu",
"Tie-Yan",
""
]
] | Inspired by its success in natural language processing and computer vision, pre-training has attracted substantial attention in cheminformatics and bioinformatics, especially for molecule based tasks. A molecule can be represented by either a graph (where atoms are connected by bonds) or a SMILES sequence (where depth-... |
2002.09062 | Weiqi Ji | Weiqi Ji and Sili Deng | Autonomous Discovery of Unknown Reaction Pathways from Data by Chemical
Reaction Neural Network | null | The Journal of Physical Chemistry A, 2021 | 10.1021/acs.jpca.0c09316 | null | q-bio.MN cs.LG physics.chem-ph stat.ML | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Chemical reactions occur in energy, environmental, biological, and many other
natural systems, and the inference of the reaction networks is essential to
understand and design the chemical processes in engineering and life sciences.
Yet, revealing the reaction pathways for complex systems and processes is still
chall... | [
{
"created": "Thu, 20 Feb 2020 23:36:46 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Jan 2021 22:18:36 GMT",
"version": "v2"
}
] | 2021-01-22 | [
[
"Ji",
"Weiqi",
""
],
[
"Deng",
"Sili",
""
]
] | Chemical reactions occur in energy, environmental, biological, and many other natural systems, and the inference of the reaction networks is essential to understand and design the chemical processes in engineering and life sciences. Yet, revealing the reaction pathways for complex systems and processes is still challen... |
1607.08552 | Tobias K\"uhn | Tobias K\"uhn, Moritz Helias | Locking of correlated neural activity to ongoing oscillations | 57 pages, 12 figures, published version | PLoS Comput Biol 13(6): e1005534 (2017) | 10.1371/journal.pcbi.1005534 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Population-wide oscillations are ubiquitously observed in mesoscopic signals
of cortical activity. In these network states a global oscillatory cycle
modulates the propensity of neurons to fire. Synchronous activation of neurons
has been hypothesized to be a separate channel of signal processing information
in the br... | [
{
"created": "Thu, 28 Jul 2016 18:09:49 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Oct 2016 09:58:28 GMT",
"version": "v2"
},
{
"created": "Mon, 3 Jul 2017 15:25:12 GMT",
"version": "v3"
}
] | 2017-07-04 | [
[
"Kühn",
"Tobias",
""
],
[
"Helias",
"Moritz",
""
]
] | Population-wide oscillations are ubiquitously observed in mesoscopic signals of cortical activity. In these network states a global oscillatory cycle modulates the propensity of neurons to fire. Synchronous activation of neurons has been hypothesized to be a separate channel of signal processing information in the brai... |
1811.08068 | Xiaochen Liu | X. Liu, P. Sanz-Leon, P. A. Robinson | Gamma-Band Correlations in Primary Visual Cortex | 23 pages; 12 figures | Phys. Rev. E 101, 042406 (2020) | 10.1103/PhysRevE.101.042406 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neural field theory is used to quantitatively analyze the two-dimensional
spatiotemporal correlation properties of gamma-band (30 -- 70 Hz) oscillations
evoked by stimuli arriving at the primary visual cortex (V1), and modulated by
patchy connectivities that depend on orientation preference (OP). Correlation
function... | [
{
"created": "Tue, 20 Nov 2018 04:28:28 GMT",
"version": "v1"
}
] | 2021-03-19 | [
[
"Liu",
"X.",
""
],
[
"Sanz-Leon",
"P.",
""
],
[
"Robinson",
"P. A.",
""
]
] | Neural field theory is used to quantitatively analyze the two-dimensional spatiotemporal correlation properties of gamma-band (30 -- 70 Hz) oscillations evoked by stimuli arriving at the primary visual cortex (V1), and modulated by patchy connectivities that depend on orientation preference (OP). Correlation functions ... |
2007.16018 | Daniele Marinazzo | Sebastiano Stramaglia, Tomas Scagliarini, Bryan C. Daniels, and
Daniele Marinazzo | Quantifying dynamical high-order interdependencies from the
O-information: an application to neural spiking dynamics | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | We address the problem of efficiently and informatively quantifying how
multiplets of variables carry information about the future of the dynamical
system they belong to. In particular we want to identify groups of variables
carrying redundant or synergistic information, and track how the size and the
composition of ... | [
{
"created": "Fri, 31 Jul 2020 12:34:19 GMT",
"version": "v1"
}
] | 2020-08-03 | [
[
"Stramaglia",
"Sebastiano",
""
],
[
"Scagliarini",
"Tomas",
""
],
[
"Daniels",
"Bryan C.",
""
],
[
"Marinazzo",
"Daniele",
""
]
] | We address the problem of efficiently and informatively quantifying how multiplets of variables carry information about the future of the dynamical system they belong to. In particular we want to identify groups of variables carrying redundant or synergistic information, and track how the size and the composition of th... |
1706.03835 | Christian Meisel | Christian Meisel, Kimberlyn Bailey, Peter Achermann and Dietmar Plenz | Decline of long-range temporal correlations in the human brain during
sustained wakefulness | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sleep is crucial for daytime functioning, cognitive performance and general
well-being. These aspects of daily life are known to be impaired after extended
wake, yet, the underlying neuronal correlates have been difficult to identify.
Accumulating evidence suggests that normal functioning of the brain is
characterize... | [
{
"created": "Mon, 12 Jun 2017 20:15:43 GMT",
"version": "v1"
}
] | 2017-06-14 | [
[
"Meisel",
"Christian",
""
],
[
"Bailey",
"Kimberlyn",
""
],
[
"Achermann",
"Peter",
""
],
[
"Plenz",
"Dietmar",
""
]
] | Sleep is crucial for daytime functioning, cognitive performance and general well-being. These aspects of daily life are known to be impaired after extended wake, yet, the underlying neuronal correlates have been difficult to identify. Accumulating evidence suggests that normal functioning of the brain is characterized ... |
q-bio/0504025 | Edwin Wang Dr. | Edwin Wang and Enrico Purisima | Self-organization of gene regulatory network motifs enriched with short
transcript's half-life transcription factors | Trends Genet (in press), main text 1, supplementary notes 1, 40
pages, 7 tables, 4 figs, minor modifications | Trends Genet, 21:492-495, 2005 | 10.1016/j.tig.2005.06.013 | null | q-bio.MN | null | Network motifs, the recurring regulatory structural patterns in networks, are
able to self-organize to produce networks. Three major motifs, feedforward
loop, single input modules and bi-fan are found in gene regulatory networks.
The large ratio of genes to transcription factors (TFs) in genomes leads to a
sharing of... | [
{
"created": "Mon, 18 Apr 2005 23:20:19 GMT",
"version": "v1"
},
{
"created": "Mon, 25 Apr 2005 22:36:25 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Wang",
"Edwin",
""
],
[
"Purisima",
"Enrico",
""
]
] | Network motifs, the recurring regulatory structural patterns in networks, are able to self-organize to produce networks. Three major motifs, feedforward loop, single input modules and bi-fan are found in gene regulatory networks. The large ratio of genes to transcription factors (TFs) in genomes leads to a sharing of T... |
q-bio/0701031 | Miroslaw Dudek | Miroslaw R. Dudek | Lotka-Volterra population model of genetic evolution | 10 pages, 6 figures | null | null | null | q-bio.PE q-bio.OT | null | A deterministic model of an age-structured population with genetics analogous
to the discrete time Penna model of genetic evolution is constructed on the
basis of the Lotka-Volterra scheme. It is shown that if, as in the Penna model,
genetic information is represented by the fraction of defective genes in the
populat... | [
{
"created": "Sat, 20 Jan 2007 15:54:21 GMT",
"version": "v1"
},
{
"created": "Sun, 28 Jan 2007 08:18:45 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Dudek",
"Miroslaw R.",
""
]
] | A deterministic model of an age-structured population with genetics analogous to the discrete time Penna model of genetic evolution is constructed on the basis of the Lotka-Volterra scheme. It is shown that if, as in the Penna model, genetic information is represented by the fraction of defective genes in the populatio... |
1911.04585 | Ralf Engbert | Johan Chandra, Andre Kruegel, Ralf Engbert | Modulation of oculomotor control during reading of mirrored and inverted
texts | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The interplay between cognitive and oculomotor processes during reading can
be explored when the spatial layout of text deviates from the typical display.
In this study, we investigate various eye-movement measures during reading of
text with experimentally manipulated layout (word-wise and letter-wise
mirrored-rever... | [
{
"created": "Mon, 11 Nov 2019 22:21:22 GMT",
"version": "v1"
}
] | 2019-11-13 | [
[
"Chandra",
"Johan",
""
],
[
"Kruegel",
"Andre",
""
],
[
"Engbert",
"Ralf",
""
]
] | The interplay between cognitive and oculomotor processes during reading can be explored when the spatial layout of text deviates from the typical display. In this study, we investigate various eye-movement measures during reading of text with experimentally manipulated layout (word-wise and letter-wise mirrored-reverse... |
2102.00316 | Michael Wilkinson | Michael Wilkinson, David Yllanes and Greg Huber | Polysomally Protected Viruses | 14 pages, 4 figures, Physical Biology, in press | Phys. Biol. 18 046009 (2021) | 10.1088/1478-3975/abf5b5 | null | q-bio.SC q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is conceivable that an RNA virus could use a polysome, that is, a string
of ribosomes covering the RNA strand, to protect the genetic material from
degradation inside a host cell. This paper discusses how such a virus might
operate, and how its presence might be detected by ribosome profiling. There
are two possib... | [
{
"created": "Sat, 30 Jan 2021 21:34:11 GMT",
"version": "v1"
},
{
"created": "Thu, 8 Apr 2021 21:50:34 GMT",
"version": "v2"
}
] | 2021-06-24 | [
[
"Wilkinson",
"Michael",
""
],
[
"Yllanes",
"David",
""
],
[
"Huber",
"Greg",
""
]
] | It is conceivable that an RNA virus could use a polysome, that is, a string of ribosomes covering the RNA strand, to protect the genetic material from degradation inside a host cell. This paper discusses how such a virus might operate, and how its presence might be detected by ribosome profiling. There are two possible... |
2104.04161 | Simone Pigolotti | Anzhelika Koldaeva, Hsieh-Fu Tsai, Amy Q. Shen, and Simone Pigolotti | Population genetics in microchannels | 20 pages, 9 figures, combined main text + SI | Proc. Natl. Acad. Sci. 119(12), e2120821119 (2022) | 10.1073/pnas.2120821119 | null | q-bio.PE cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spatial constraints such as rigid barriers affect the dynamics of cell
populations, potentially altering the course of natural evolution. In this
paper, we investigate the population genetics of Escherichia coli proliferating
in microchannels with open ends. Our analysis is based on a population model in
which reprod... | [
{
"created": "Fri, 9 Apr 2021 02:33:01 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Sep 2021 06:11:01 GMT",
"version": "v2"
},
{
"created": "Fri, 25 Mar 2022 08:02:11 GMT",
"version": "v3"
}
] | 2022-03-28 | [
[
"Koldaeva",
"Anzhelika",
""
],
[
"Tsai",
"Hsieh-Fu",
""
],
[
"Shen",
"Amy Q.",
""
],
[
"Pigolotti",
"Simone",
""
]
] | Spatial constraints such as rigid barriers affect the dynamics of cell populations, potentially altering the course of natural evolution. In this paper, we investigate the population genetics of Escherichia coli proliferating in microchannels with open ends. Our analysis is based on a population model in which reproduc... |
2002.02642 | Narendra Dixit | Rajat Desikan, Rustom Antia, Narendra M. Dixit | The weakest link bridging germinal center B cells and follicular
dendritic cells limits antibody affinity maturation | null | BioEssays, 2021 | 10.1002/bies.202000159 | null | q-bio.PE q-bio.BM q-bio.CB | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The affinity of antibodies (Abs) produced in vivo for their target antigens
(Ags) is typically well below the maximum affinity possible. Nearly 25 years
ago, Foote and Eisen explained how an 'affinity ceiling' could arise from
constraints associated with the acquisition of soluble antigen by B cells.
However, recent ... | [
{
"created": "Fri, 7 Feb 2020 06:47:25 GMT",
"version": "v1"
}
] | 2021-02-16 | [
[
"Desikan",
"Rajat",
""
],
[
"Antia",
"Rustom",
""
],
[
"Dixit",
"Narendra M.",
""
]
] | The affinity of antibodies (Abs) produced in vivo for their target antigens (Ags) is typically well below the maximum affinity possible. Nearly 25 years ago, Foote and Eisen explained how an 'affinity ceiling' could arise from constraints associated with the acquisition of soluble antigen by B cells. However, recent st... |
1605.01219 | Michele Caselle | Antonio Rosanova, Alberto Colliva, Matteo Osella, Michele Caselle | Modelling the evolution of transcription factor binding preferences in
complex eukaryotes | 14 pages, 5 figures. Minor changes. Final version, accepted for
publication | Sci Rep. 2017 Aug 8;7(1):7596 | 10.1038/s41598-017-07761-0. | null | q-bio.GN q-bio.MN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transcription factors (TFs) exert their regulatory action by binding to DNA
with specific sequence preferences. However, different TFs can partially share
their binding sequences due to their common evolutionary origin. This
`redundancy' of binding defines a way of organizing TFs in `motif families' by
grouping TFs w... | [
{
"created": "Wed, 4 May 2016 10:52:25 GMT",
"version": "v1"
},
{
"created": "Tue, 4 Dec 2018 16:05:21 GMT",
"version": "v2"
}
] | 2018-12-05 | [
[
"Rosanova",
"Antonio",
""
],
[
"Colliva",
"Alberto",
""
],
[
"Osella",
"Matteo",
""
],
[
"Caselle",
"Michele",
""
]
] | Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This `redundancy' of binding defines a way of organizing TFs in `motif families' by grouping TFs wit... |
0901.1598 | Frederick Matsen IV | Frederick A. Matsen | constNJ: an algorithm to reconstruct sets of phylogenetic trees
satisfying pairwise topological constraints | Please contact me with any questions or comments! | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper introduces constNJ, the first algorithm for phylogenetic
reconstruction of sets of trees with constrained pairwise rooted subtree-prune
regraft (rSPR) distance. We are motivated by the problem of constructing sets
of trees which must fit into a recombination, hybridization, or similar
network. Rather than ... | [
{
"created": "Mon, 12 Jan 2009 15:46:13 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Jan 2009 19:41:29 GMT",
"version": "v2"
}
] | 2009-09-30 | [
[
"Matsen",
"Frederick A.",
""
]
] | This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which must fit into a recombination, hybridization, or similar network. Rather than fi... |
1812.02467 | Jessie Renton | Jessie Renton and Karen M. Page | Evolution of cooperation on an epithelium | 19 pages, 8 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cooperation is prevalent in nature, not only in the context of social
interactions within the animal kingdom, but also on the cellular level. In
cancer for example, tumour cells can cooperate by producing growth factors. The
evolution of cooperation has traditionally been studied for well-mixed
populations under the ... | [
{
"created": "Thu, 6 Dec 2018 11:22:28 GMT",
"version": "v1"
}
] | 2018-12-07 | [
[
"Renton",
"Jessie",
""
],
[
"Page",
"Karen M.",
""
]
] | Cooperation is prevalent in nature, not only in the context of social interactions within the animal kingdom, but also on the cellular level. In cancer for example, tumour cells can cooperate by producing growth factors. The evolution of cooperation has traditionally been studied for well-mixed populations under the fr... |
2005.11454 | Aydogan Ozcan | Calvin Brown, Derek Tseng, Paige M. K. Larkin, Susan Realegeno, Leanne
Mortimer, Arjun Subramonian, Dino Di Carlo, Omai B. Garner, Aydogan Ozcan | An Automated, Cost-Effective Optical System for Accelerated
Anti-microbial Susceptibility Testing (AST) using Deep Learning | 13 Pages, 6 Figures, 1 Table | ACS Photonics (2020) | 10.1021/acsphotonics.0c00841 | null | q-bio.QM physics.app-ph physics.ins-det physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Antimicrobial susceptibility testing (AST) is a standard clinical procedure
used to quantify antimicrobial resistance (AMR). Currently, the gold standard
method requires incubation for 18-24 h and subsequent inspection for growth by
a trained medical technologist. We demonstrate an automated, cost-effective
optical s... | [
{
"created": "Sat, 23 May 2020 02:38:26 GMT",
"version": "v1"
}
] | 2020-07-17 | [
[
"Brown",
"Calvin",
""
],
[
"Tseng",
"Derek",
""
],
[
"Larkin",
"Paige M. K.",
""
],
[
"Realegeno",
"Susan",
""
],
[
"Mortimer",
"Leanne",
""
],
[
"Subramonian",
"Arjun",
""
],
[
"Di Carlo",
"Dino",
""
],
... | Antimicrobial susceptibility testing (AST) is a standard clinical procedure used to quantify antimicrobial resistance (AMR). Currently, the gold standard method requires incubation for 18-24 h and subsequent inspection for growth by a trained medical technologist. We demonstrate an automated, cost-effective optical sys... |
1007.5022 | Tsvi Tlusty | Ilan Breskin, Jordi Soriano, Elisha Moses, and Tsvi Tlusty | Percolation in living neural networks | PACS numbers: 87.18.Sn, 87.19.La, 64.60.Ak
http://www.weizmann.ac.il/complex/tlusty/papers/PhysRevLett2006.pdf | Breskin I Soriano J Moses E & Tlusty T Percolation in Living
Neural Networks Phys Rev Lett 97 188102-4 (2006) | 10.1103/PhysRevLett.97.188102 | null | q-bio.NC cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study living neural networks by measuring the neurons' response to a
global electrical stimulation. Neural connectivity is lowered by reducing the
synaptic strength, chemically blocking neurotransmitter receptors. We use a
graph-theoretic approach to show that the connectivity undergoes a percolation
transition. T... | [
{
"created": "Wed, 28 Jul 2010 16:12:39 GMT",
"version": "v1"
}
] | 2010-07-30 | [
[
"Breskin",
"Ilan",
""
],
[
"Soriano",
"Jordi",
""
],
[
"Moses",
"Elisha",
""
],
[
"Tlusty",
"Tsvi",
""
]
] | We study living neural networks by measuring the neurons' response to a global electrical stimulation. Neural connectivity is lowered by reducing the synaptic strength, chemically blocking neurotransmitter receptors. We use a graph-theoretic approach to show that the connectivity undergoes a percolation transition. Thi... |
1910.05881 | Taiping Zeng | Taiping Zeng, XiaoLi Li, and Bailu Si | Bayesian Integration of Multi-resolutional Grid Codes for Spatial
Cognition | arXiv admin note: text overlap with arXiv:1910.04590 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fourier-like summation of several grid cell modules with different spatial
frequencies in the medial entorhinal cortex (MEC) has long been proposed to
form the contours of place firing fields. Recent experiments largely, but not
completely, support this theory. Place fields are obviously expanded by
inactivation of d... | [
{
"created": "Mon, 14 Oct 2019 01:43:11 GMT",
"version": "v1"
}
] | 2019-10-15 | [
[
"Zeng",
"Taiping",
""
],
[
"Li",
"XiaoLi",
""
],
[
"Si",
"Bailu",
""
]
] | Fourier-like summation of several grid cell modules with different spatial frequencies in the medial entorhinal cortex (MEC) has long been proposed to form the contours of place firing fields. Recent experiments largely, but not completely, support this theory. Place fields are obviously expanded by inactivation of dor... |
1405.1610 | Nico Riedel | Nico Riedel, Bhavin S. Khatri, Michael L\"assig, Johannes Berg | Multiple-line inference of selection on quantitative traits | 21 pages, 11 figures; to appear in Genetics | Genetics 201 (1), 305-322 (2015) | 10.1534/genetics.115.178988 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Trait differences between species may be attributable to natural selection.
However, quantifying the strength of evidence for selection acting on a
particular trait is a difficult task. Here we develop a population-genetic test
for selection acting on a quantitative trait which is based on multiple-line
crosses. We s... | [
{
"created": "Wed, 7 May 2014 14:10:29 GMT",
"version": "v1"
},
{
"created": "Mon, 6 Jul 2015 09:28:36 GMT",
"version": "v2"
}
] | 2017-08-09 | [
[
"Riedel",
"Nico",
""
],
[
"Khatri",
"Bhavin S.",
""
],
[
"Lässig",
"Michael",
""
],
[
"Berg",
"Johannes",
""
]
] | Trait differences between species may be attributable to natural selection. However, quantifying the strength of evidence for selection acting on a particular trait is a difficult task. Here we develop a population-genetic test for selection acting on a quantitative trait which is based on multiple-line crosses. We sho... |
1810.12016 | Mattia Bramini | Mattia Bramini, Silvio Sacchetti, Andrea Armirotti, Anna Rocchi, Ester
V\'azquez, Ver\'onica Le\'on Castellanos, Tiziano Bandiera, Fabrizia Cesca
and Fabio Benfenati | Graphene oxide nanosheets disrupt lipid composition, Ca2+ homeostasis
and synaptic transmission in primary cortical neurons | This document is the unedited Author's version of a Submitted Work
that was subsequently accepted for publication in ACS Nano. To access the
final edited and published work see
https://pubs.acs.org/articlesonrequest/AOR-MGXEfuAxY43fnrHfBEuQ | ACS Nano 2016, 10, 7, 7154-7171 | 10.1021/acsnano.6b03438 | null | q-bio.NC physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Graphene has the potential to make a very significant impact on society, with
important applications in the biomedical field. The possibility to engineer
graphene-based medical devices at the neuronal interface is of particular
interest, making it imperative to determine the biocompatibility of graphene
materials wit... | [
{
"created": "Mon, 29 Oct 2018 09:23:01 GMT",
"version": "v1"
}
] | 2018-10-30 | [
[
"Bramini",
"Mattia",
""
],
[
"Sacchetti",
"Silvio",
""
],
[
"Armirotti",
"Andrea",
""
],
[
"Rocchi",
"Anna",
""
],
[
"Vázquez",
"Ester",
""
],
[
"Castellanos",
"Verónica León",
""
],
[
"Bandiera",
"Tiziano",
... | Graphene has the potential to make a very significant impact on society, with important applications in the biomedical field. The possibility to engineer graphene-based medical devices at the neuronal interface is of particular interest, making it imperative to determine the biocompatibility of graphene materials with ... |
2111.04326 | Felix Kramer | Felix Kramer, Carl D. Modes | On biological flow networks: Antagonism between hydrodynamic and
metabolic stimuli as driver of topological transitions | null | null | null | null | q-bio.TO nlin.AO physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | A plethora of computational models have been developed in recent decades to
account for the morphogenesis of complex biological fluid networks, such as
capillary beds. Contemporary adaptation models are based on optimization
schemes where networks react and adapt toward given flow patterns. Doing so, a
system reduces... | [
{
"created": "Mon, 8 Nov 2021 08:37:35 GMT",
"version": "v1"
},
{
"created": "Tue, 9 Nov 2021 10:25:33 GMT",
"version": "v2"
},
{
"created": "Mon, 15 Nov 2021 18:36:53 GMT",
"version": "v3"
}
] | 2021-11-16 | [
[
"Kramer",
"Felix",
""
],
[
"Modes",
"Carl D.",
""
]
] | A plethora of computational models have been developed in recent decades to account for the morphogenesis of complex biological fluid networks, such as capillary beds. Contemporary adaptation models are based on optimization schemes where networks react and adapt toward given flow patterns. Doing so, a system reduces d... |
2404.04300 | Michael Plank | Caleb Sullivan, Pubudu Senanayake, Michael J. Plank | Quantifying age-specific household contacts in Aotearoa New Zealand for
infectious disease modelling | null | null | null | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Accounting for population age structure and age-specific contact patterns is
crucial for accurate modelling of human infectious disease dynamics and impact.
A common approach is to use synthetic contact matrices, which estimate the
number of contacts between individuals of different ages in specific settings.
These c... | [
{
"created": "Thu, 4 Apr 2024 21:25:53 GMT",
"version": "v1"
}
] | 2024-04-09 | [
[
"Sullivan",
"Caleb",
""
],
[
"Senanayake",
"Pubudu",
""
],
[
"Plank",
"Michael J.",
""
]
] | Accounting for population age structure and age-specific contact patterns is crucial for accurate modelling of human infectious disease dynamics and impact. A common approach is to use synthetic contact matrices, which estimate the number of contacts between individuals of different ages in specific settings. These con... |
1110.2519 | Michele Bellingeri | Michele Bellingeri | Threshold Extinction in Food Webs | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding how an extinction event affects ecosystem is fundamental to
biodiversity conservation. For this reason, food web response to species loss
has been investigated in several ways in the last years. Several studies
focused on secondary extinction due to biodiversity loss in a bottom-up
perspective using in-... | [
{
"created": "Tue, 11 Oct 2011 22:14:05 GMT",
"version": "v1"
},
{
"created": "Fri, 4 Nov 2011 13:53:51 GMT",
"version": "v2"
}
] | 2011-11-07 | [
[
"Bellingeri",
"Michele",
""
]
] | Understanding how an extinction event affects ecosystem is fundamental to biodiversity conservation. For this reason, food web response to species loss has been investigated in several ways in the last years. Several studies focused on secondary extinction due to biodiversity loss in a bottom-up perspective using in-si... |
0709.4200 | Philip M. Kim | Philip M. Kim, Jan O. Korbel, Xueying Chen, Mark B. Gerstein | Copy Number Variants and Segmental Duplications Show Different Formation
Signatures | 13 pages | null | null | null | q-bio.GN q-bio.QM | null | In addition to variation in terms of single nucleotide polymorphisms (SNPs),
whole regions ranging from several kilobases up to a megabase in length differ
in copy number among individuals. These differences are referred to as Copy
Number Variants (CNVs) and extensive mapping of these is underway. Recent
studies have... | [
{
"created": "Wed, 26 Sep 2007 15:53:40 GMT",
"version": "v1"
}
] | 2007-09-27 | [
[
"Kim",
"Philip M.",
""
],
[
"Korbel",
"Jan O.",
""
],
[
"Chen",
"Xueying",
""
],
[
"Gerstein",
"Mark B.",
""
]
] | In addition to variation in terms of single nucleotide polymorphisms (SNPs), whole regions ranging from several kilobases up to a megabase in length differ in copy number among individuals. These differences are referred to as Copy Number Variants (CNVs) and extensive mapping of these is underway. Recent studies have h... |
2401.00562 | Tim Sziburis | Tim Sziburis, Susanne Blex, Tobias Glasmachers, Ioannis Iossifidis | Ruhr Hand Motion Catalog of Human Center-Out Transport Trajectories in
3D Task-Space Captured by a Redundant Measurement System | null | null | null | null | q-bio.QM eess.SP | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Neurological conditions are a major source of movement disorders. Motion
modelling and variability analysis have the potential to identify pathology but
require profound data. We introduce a systematic dataset of 3D center-out
task-space trajectories of human hand transport movements in a natural setting.
The transpo... | [
{
"created": "Sun, 31 Dec 2023 18:39:42 GMT",
"version": "v1"
}
] | 2024-01-02 | [
[
"Sziburis",
"Tim",
""
],
[
"Blex",
"Susanne",
""
],
[
"Glasmachers",
"Tobias",
""
],
[
"Iossifidis",
"Ioannis",
""
]
] | Neurological conditions are a major source of movement disorders. Motion modelling and variability analysis have the potential to identify pathology but require profound data. We introduce a systematic dataset of 3D center-out task-space trajectories of human hand transport movements in a natural setting. The transport... |
2104.02604 | Mar\'ia Virginia Sabando Miss | Mar\'ia Virginia Sabando, Ignacio Ponzoni, Evangelos E. Milios, Axel
J. Soto | Using Molecular Embeddings in QSAR Modeling: Does it Make a Difference? | null | Briefings in Bioinformatics, Volume 23, Issue 1, January 2022,
bbab365 | 10.1093/bib/bbab365 | null | q-bio.BM cs.LG q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | With the consolidation of deep learning in drug discovery, several novel
algorithms for learning molecular representations have been proposed. Despite
the interest of the community in developing new methods for learning molecular
embeddings and their theoretical benefits, comparing molecular embeddings with
each othe... | [
{
"created": "Sat, 20 Mar 2021 21:45:22 GMT",
"version": "v1"
},
{
"created": "Wed, 28 Jul 2021 15:30:22 GMT",
"version": "v2"
}
] | 2022-05-09 | [
[
"Sabando",
"María Virginia",
""
],
[
"Ponzoni",
"Ignacio",
""
],
[
"Milios",
"Evangelos E.",
""
],
[
"Soto",
"Axel J.",
""
]
] | With the consolidation of deep learning in drug discovery, several novel algorithms for learning molecular representations have been proposed. Despite the interest of the community in developing new methods for learning molecular embeddings and their theoretical benefits, comparing molecular embeddings with each other ... |
1911.01174 | Alexander L\"uck | Alexander L\"uck, Verena Wolf | Generalized Method of Moments Estimation for Stochastic Models of DNA
Methylation Patterns | 12 pages, 3 figures, 1 table | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | With recent advances in sequencing technologies, large amounts of epigenomic
data have become available and computational methods are contributing
significantly to the progress of epigenetic research. As an orthogonal approach
to methods based on machine learning, mechanistic modeling aims at a
description of the mec... | [
{
"created": "Mon, 4 Nov 2019 13:01:24 GMT",
"version": "v1"
}
] | 2019-11-05 | [
[
"Lück",
"Alexander",
""
],
[
"Wolf",
"Verena",
""
]
] | With recent advances in sequencing technologies, large amounts of epigenomic data have become available and computational methods are contributing significantly to the progress of epigenetic research. As an orthogonal approach to methods based on machine learning, mechanistic modeling aims at a description of the mecha... |
2405.07123 | Jordan Rozum | Austin M. Marcus, Jordan Rozum, Herbert Sizek, and Luis M. Rocha | CANA v1.0.0 and schematodes: efficient quantification of symmetry in
Boolean automata | 5 pages 1 figure (two images in figure) | null | null | null | q-bio.MN q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | The biomolecular networks underpinning cell function exhibit canalization, or
the buffering of fluctuations required to function in a noisy environment. One
understudied putative mechanism for canalization is the functional equivalence
of a biomolecular entity's regulators (e.g., among the transcription factors
for a... | [
{
"created": "Sun, 12 May 2024 01:14:00 GMT",
"version": "v1"
}
] | 2024-05-14 | [
[
"Marcus",
"Austin M.",
""
],
[
"Rozum",
"Jordan",
""
],
[
"Sizek",
"Herbert",
""
],
[
"Rocha",
"Luis M.",
""
]
] | The biomolecular networks underpinning cell function exhibit canalization, or the buffering of fluctuations required to function in a noisy environment. One understudied putative mechanism for canalization is the functional equivalence of a biomolecular entity's regulators (e.g., among the transcription factors for a g... |
2106.13202 | Ju An Park | Ju An Park, Vikram Voleti, Kathryn E. Thomas, Alexander Wong and Jason
L. Deglint | SALT: Sea lice Adaptive Lattice Tracking -- An Unsupervised Approach to
Generate an Improved Ocean Model | 5 pages, 3 figures, 3 tables | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Warming oceans due to climate change are leading to increased numbers of
ectoparasitic copepods, also known as sea lice, which can cause significant
ecological loss to wild salmon populations and major economic loss to
aquaculture sites. The main transport mechanism driving the spread of sea lice
populations are near... | [
{
"created": "Thu, 24 Jun 2021 17:29:42 GMT",
"version": "v1"
}
] | 2021-06-25 | [
[
"Park",
"Ju An",
""
],
[
"Voleti",
"Vikram",
""
],
[
"Thomas",
"Kathryn E.",
""
],
[
"Wong",
"Alexander",
""
],
[
"Deglint",
"Jason L.",
""
]
] | Warming oceans due to climate change are leading to increased numbers of ectoparasitic copepods, also known as sea lice, which can cause significant ecological loss to wild salmon populations and major economic loss to aquaculture sites. The main transport mechanism driving the spread of sea lice populations are near-s... |
1503.07116 | Bartlomiej Waclaw Dr | Bartlomiej Waclaw, Ivana Bozic, Meredith E. Pittman, Ralph H. Hruban,
Bert Vogelstein, Martin A. Nowak | Spatial model predicts dispersal and cell turnover cause reduced
intra-tumor heterogeneity | 37 pages, 14 figures | null | 10.1038/nature14971 | null | q-bio.PE q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most cancers in humans are large, measuring centimeters in diameter, composed
of many billions of cells. An equivalent mass of normal cells would be highly
heterogeneous as a result of the mutations that occur during each cell
division. What is remarkable about cancers is their homogeneity - virtually
every neoplasti... | [
{
"created": "Tue, 24 Mar 2015 17:22:54 GMT",
"version": "v1"
}
] | 2016-02-17 | [
[
"Waclaw",
"Bartlomiej",
""
],
[
"Bozic",
"Ivana",
""
],
[
"Pittman",
"Meredith E.",
""
],
[
"Hruban",
"Ralph H.",
""
],
[
"Vogelstein",
"Bert",
""
],
[
"Nowak",
"Martin A.",
""
]
] | Most cancers in humans are large, measuring centimeters in diameter, composed of many billions of cells. An equivalent mass of normal cells would be highly heterogeneous as a result of the mutations that occur during each cell division. What is remarkable about cancers is their homogeneity - virtually every neoplastic ... |
1301.1590 | Hamidreza Chitsaz | Hamidreza Chitsaz and Elmirasadat Forouzmand and Gholamreza Haffari | An Efficient Algorithm for Upper Bound on the Partition Function of
Nucleic Acids | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has been shown that minimum free energy structure for RNAs and RNA-RNA
interaction is often incorrect due to inaccuracies in the energy parameters and
inherent limitations of the energy model. In contrast, ensemble based
quantities such as melting temperature and equilibrium concentrations can be
more reliably pre... | [
{
"created": "Tue, 8 Jan 2013 16:58:28 GMT",
"version": "v1"
}
] | 2013-01-09 | [
[
"Chitsaz",
"Hamidreza",
""
],
[
"Forouzmand",
"Elmirasadat",
""
],
[
"Haffari",
"Gholamreza",
""
]
] | It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such as melting temperature and equilibrium concentrations can be more reliably predi... |
1807.07566 | Yu-Cheng Chen | Yu-Cheng Chen, Qiushu Chen, Xiaotain Tan, Grace Chen, Ingrid Bergin,
Muhammad Nadeem Aslam, and Xudong Fan | Chromatin Laser Imaging Reveals Abnormal Nuclear Changes for Early
Cancer Detection | null | null | null | null | q-bio.TO physics.bio-ph physics.optics q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We developed and applied rapid scanning laser-emission microscopy to detect
abnormal changes in cell nuclei for early diagnosis of cancer and cancer
precursors. Regulation of chromatins is essential for genetic development and
normal cell functions, while abnormal nuclear changes may lead to many
diseases, in particu... | [
{
"created": "Thu, 19 Jul 2018 11:08:10 GMT",
"version": "v1"
}
] | 2018-07-23 | [
[
"Chen",
"Yu-Cheng",
""
],
[
"Chen",
"Qiushu",
""
],
[
"Tan",
"Xiaotain",
""
],
[
"Chen",
"Grace",
""
],
[
"Bergin",
"Ingrid",
""
],
[
"Aslam",
"Muhammad Nadeem",
""
],
[
"Fan",
"Xudong",
""
]
] | We developed and applied rapid scanning laser-emission microscopy to detect abnormal changes in cell nuclei for early diagnosis of cancer and cancer precursors. Regulation of chromatins is essential for genetic development and normal cell functions, while abnormal nuclear changes may lead to many diseases, in particula... |
1902.08555 | Jes\'us Fern\'andez-S\'anchez | Marta Casanellas, Jes\'us Fern\'andez-S\'anchez, Jordi Roca-Lacostena | Embeddability and rate identifiability of Kimura 2-parameter matrices | 20 pages; 10 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Deciding whether a Markov matrix is embeddable (i.e. can be written as the
exponential of a rate matrix) is an open problem even for $4\times 4$ matrices.
We study the embedding problem and rate identifiability for the K80 model of
nucleotide substitution. For these $4\times 4$ matrices, we fully characterize
the set... | [
{
"created": "Fri, 22 Feb 2019 16:43:07 GMT",
"version": "v1"
},
{
"created": "Wed, 27 Nov 2019 09:53:46 GMT",
"version": "v2"
}
] | 2019-11-28 | [
[
"Casanellas",
"Marta",
""
],
[
"Fernández-Sánchez",
"Jesús",
""
],
[
"Roca-Lacostena",
"Jordi",
""
]
] | Deciding whether a Markov matrix is embeddable (i.e. can be written as the exponential of a rate matrix) is an open problem even for $4\times 4$ matrices. We study the embedding problem and rate identifiability for the K80 model of nucleotide substitution. For these $4\times 4$ matrices, we fully characterize the set o... |
2106.05783 | Leonardo Dalla Porta | Leonardo Dalla Porta, Daniel M. Castro, Mauro Copelli, Pedro V.
Carelli, and Fernanda S. Matias | Feedforward and feedback influences through distinct frequency bands
between two spiking-neuron networks | null | null | 10.1103/PhysRevE.104.054404 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Several studies with brain signals suggested that bottom-up and top-down
influences are exerted through distinct frequency bands among visual cortical
areas. It has been recently shown that theta and gamma rhythms subserve
feedforward, whereas the feedback influence is dominated by the alpha-beta
rhythm in primates. ... | [
{
"created": "Thu, 10 Jun 2021 14:34:03 GMT",
"version": "v1"
}
] | 2021-11-24 | [
[
"Porta",
"Leonardo Dalla",
""
],
[
"Castro",
"Daniel M.",
""
],
[
"Copelli",
"Mauro",
""
],
[
"Carelli",
"Pedro V.",
""
],
[
"Matias",
"Fernanda S.",
""
]
] | Several studies with brain signals suggested that bottom-up and top-down influences are exerted through distinct frequency bands among visual cortical areas. It has been recently shown that theta and gamma rhythms subserve feedforward, whereas the feedback influence is dominated by the alpha-beta rhythm in primates. A ... |
1807.07127 | Charo del Genio | Erin Connelly, Charo I. del Genio, Freya Harrison | Datamining a medieval medical text reveals patterns in ingredient choice
that reflect biological activity against the causative agents of specified
infections | 27 pages, 4 figures | null | null | null | q-bio.QM cs.SI physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The pharmacopeia used by physicians and lay people in medieval Europe has
largely been dismissed as placebo or superstition. While we now recognise that
some of the materia medica used by medieval physicians could have had useful
biological properties, research in this area is limited by the labour-intensive
process ... | [
{
"created": "Wed, 18 Jul 2018 20:08:18 GMT",
"version": "v1"
}
] | 2018-07-20 | [
[
"Connelly",
"Erin",
""
],
[
"del Genio",
"Charo I.",
""
],
[
"Harrison",
"Freya",
""
]
] | The pharmacopeia used by physicians and lay people in medieval Europe has largely been dismissed as placebo or superstition. While we now recognise that some of the materia medica used by medieval physicians could have had useful biological properties, research in this area is limited by the labour-intensive process of... |
1109.5159 | Michael Knudsen | Michael Knudsen, Elisenda Feliu, Carsten Wiuf | Exact Analysis of Intrinsic Qualitative Features of Phosphorelays using
Mathematical Models | null | null | null | null | q-bio.MN q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phosphorelays are a class of signaling mechanisms used by cells to respond to
changes in their environment. Phosphorelays (of which two-component systems
constitute a special case) are particularly abundant in prokaryotes and have
been shown to be involved in many fundamental processes such as stress
response, osmoti... | [
{
"created": "Fri, 23 Sep 2011 19:08:28 GMT",
"version": "v1"
}
] | 2011-09-26 | [
[
"Knudsen",
"Michael",
""
],
[
"Feliu",
"Elisenda",
""
],
[
"Wiuf",
"Carsten",
""
]
] | Phosphorelays are a class of signaling mechanisms used by cells to respond to changes in their environment. Phosphorelays (of which two-component systems constitute a special case) are particularly abundant in prokaryotes and have been shown to be involved in many fundamental processes such as stress response, osmotic ... |
1807.08686 | Anita Mehta | Anita Mehta | Storing and retrieving long-term memories: cooperation and competition
in synaptic dynamics | 34 pages, 7 figures | Advances in Physics: X, 3:1, 755-789, (2018) | 10.1080/23746149.2018.1480415 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We first review traditional approaches to memory storage and formation,
drawing on the literature of quantitative neuroscience as well as statistical
physics. These have generally focused on the fast dynamics of neurons; however,
there is now an increasing emphasis on the slow dynamics of synapses, whose
weight chang... | [
{
"created": "Mon, 23 Jul 2018 15:54:33 GMT",
"version": "v1"
}
] | 2018-07-24 | [
[
"Mehta",
"Anita",
""
]
] | We first review traditional approaches to memory storage and formation, drawing on the literature of quantitative neuroscience as well as statistical physics. These have generally focused on the fast dynamics of neurons; however, there is now an increasing emphasis on the slow dynamics of synapses, whose weight changes... |
2008.01237 | Haoyu Cheng | Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang and Heng
Li | Haplotype-resolved de novo assembly with phased assembly graphs | 11 pages, 3 figures, 3 tables | Nature Methods, 2021 | 10.1038/s41592-020-01056-5 | null | q-bio.GN q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Haplotype-resolved de novo assembly is the ultimate solution to the study of
sequence variations in a genome. However, existing algorithms either collapse
heterozygous alleles into one consensus copy or fail to cleanly separate the
haplotypes to produce high-quality phased assemblies. Here we describe hifiasm,
a new ... | [
{
"created": "Mon, 3 Aug 2020 23:10:44 GMT",
"version": "v1"
}
] | 2021-02-03 | [
[
"Cheng",
"Haoyu",
""
],
[
"Concepcion",
"Gregory T",
""
],
[
"Feng",
"Xiaowen",
""
],
[
"Zhang",
"Haowen",
""
],
[
"Li",
"Heng",
""
]
] | Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a new de... |
0809.0391 | Masudul Haque | Alexey Mikaberidze, Masudul Haque | Survival benefits in mimicry: a quantitative framework | 9 pages, 7 figures | Journal of Theoretical Biology, Vol. 259, pages 462-468 (2009) | 10.1016/j.jtbi.2009.02.024 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mimicry is a resemblance between species that benefits at least one of the
species. It is a ubiquitous evolutionary phenomenon particularly common among
prey species, in which case the advantage involves better protection from
predation. We formulate a mathematical description of mimicry among prey
species, to invest... | [
{
"created": "Tue, 2 Sep 2008 10:19:34 GMT",
"version": "v1"
}
] | 2011-08-09 | [
[
"Mikaberidze",
"Alexey",
""
],
[
"Haque",
"Masudul",
""
]
] | Mimicry is a resemblance between species that benefits at least one of the species. It is a ubiquitous evolutionary phenomenon particularly common among prey species, in which case the advantage involves better protection from predation. We formulate a mathematical description of mimicry among prey species, to investig... |
1307.8407 | Ilya Zhbannikov | Ilya Y. Zhbannikov, Samuel S. Hunter, Matthew L. Settles and James A.
Foster | SlopMap: a software application tool for quick and flexible
identification of similar sequences using exact k-mer matching | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | With the advent of Next-Generation (NG) sequencing, it has become possible to
sequence an entire genome quickly and inexpensively. However, in some
experiments one only needs to extract and assembly a portion of the sequence
reads, for example when performing transcriptome studies, sequencing
mitochondrial genomes, o... | [
{
"created": "Wed, 31 Jul 2013 18:06:05 GMT",
"version": "v1"
}
] | 2013-08-01 | [
[
"Zhbannikov",
"Ilya Y.",
""
],
[
"Hunter",
"Samuel S.",
""
],
[
"Settles",
"Matthew L.",
""
],
[
"Foster",
"James A.",
""
]
] | With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for example when performing transcriptome studies, sequencing mitochondrial genomes, or ... |
2212.11367 | Adam Tonks | Adam Tonks (1), Trevor Harris (2), Bo Li (1), William Brown (3),
Rebecca Smith (3) ((1) Department of Statistics, University of Illinois at
Urbana-Champaign, (2) Department of Statistics, Texas A&M University, (3)
Department of Pathobiology, University of Illinois at Urbana-Champaign) | Forecasting West Nile Virus with Graph Neural Networks: Harnessing
Spatial Dependence in Irregularly Sampled Geospatial Data | null | GeoHealth 8 (7), e2023GH000784 | 10.1029/2023GH000784 | null | q-bio.PE cs.LG q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Machine learning methods have seen increased application to geospatial
environmental problems, such as precipitation nowcasting, haze forecasting, and
crop yield prediction. However, many of the machine learning methods applied to
mosquito population and disease forecasting do not inherently take into account
the und... | [
{
"created": "Wed, 21 Dec 2022 21:08:45 GMT",
"version": "v1"
}
] | 2024-07-09 | [
[
"Tonks",
"Adam",
""
],
[
"Harris",
"Trevor",
""
],
[
"Li",
"Bo",
""
],
[
"Brown",
"William",
""
],
[
"Smith",
"Rebecca",
""
]
] | Machine learning methods have seen increased application to geospatial environmental problems, such as precipitation nowcasting, haze forecasting, and crop yield prediction. However, many of the machine learning methods applied to mosquito population and disease forecasting do not inherently take into account the under... |
1105.0866 | Shivendra Tewari | Shivendra Tewari and Kaushik Majumdar | A Mathematical Model of Tripartite Synapse: Astrocyte Induced Synaptic
Plasticity | 42 pages, 14 figures, Journal of Biological Physics (to appear) | null | 10.1007/s10867-012-9267-7 | null | q-bio.NC math.DS q-bio.CB q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we present a biologically detailed mathematical model of
tripartite synapses, where astrocytes modulate short-term synaptic plasticity.
The model consists of a pre-synaptic bouton, a post-synaptic dendritic
spine-head, a synaptic cleft and a peri-synaptic astrocyte controlling Ca2+
dynamics inside the s... | [
{
"created": "Wed, 4 May 2011 16:33:28 GMT",
"version": "v1"
},
{
"created": "Sat, 17 Dec 2011 16:43:50 GMT",
"version": "v2"
},
{
"created": "Mon, 12 Mar 2012 13:45:18 GMT",
"version": "v3"
}
] | 2012-06-05 | [
[
"Tewari",
"Shivendra",
""
],
[
"Majumdar",
"Kaushik",
""
]
] | In this paper we present a biologically detailed mathematical model of tripartite synapses, where astrocytes modulate short-term synaptic plasticity. The model consists of a pre-synaptic bouton, a post-synaptic dendritic spine-head, a synaptic cleft and a peri-synaptic astrocyte controlling Ca2+ dynamics inside the syn... |
1906.08317 | Jonathan Desponds | Jonathan Desponds, Massimo Vergassola and Aleksandra M. Walczak | Hunchback promoters can readout morphogenetic positional information in
less than a minute | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The first cell fate decisions in the developing fly embryo are made very
rapidly : hunchback genes decide in a few minutes whether a given nucleus
follows the anterior or the posterior developmental blueprint by reading out
the positional information encoded in the Bicoid morphogen. This developmental
system constitu... | [
{
"created": "Wed, 19 Jun 2019 19:20:11 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Jun 2019 17:49:01 GMT",
"version": "v2"
}
] | 2019-06-24 | [
[
"Desponds",
"Jonathan",
""
],
[
"Vergassola",
"Massimo",
""
],
[
"Walczak",
"Aleksandra M.",
""
]
] | The first cell fate decisions in the developing fly embryo are made very rapidly : hunchback genes decide in a few minutes whether a given nucleus follows the anterior or the posterior developmental blueprint by reading out the positional information encoded in the Bicoid morphogen. This developmental system constitute... |
1608.03047 | John Wentworth | Emma Wentworth and John Wentworth | Computational Limitations of First-Order Repressor Systems | null | null | null | null | q-bio.MN cs.SY math.DS q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Almost all current approaches for engineering modular logic components in
synthetic biology use first-order regulators, including most CRISPR/CAS, TAL,
zinc finger, and RNA interference systems. Many practitioners understand
intuitively that second and higher order binding is necessary for scalability,
and this is ea... | [
{
"created": "Wed, 10 Aug 2016 05:00:30 GMT",
"version": "v1"
}
] | 2016-08-11 | [
[
"Wentworth",
"Emma",
""
],
[
"Wentworth",
"John",
""
]
] | Almost all current approaches for engineering modular logic components in synthetic biology use first-order regulators, including most CRISPR/CAS, TAL, zinc finger, and RNA interference systems. Many practitioners understand intuitively that second and higher order binding is necessary for scalability, and this is easy... |
2010.00214 | Antoine Le Gall | B. Guilhas, J.C. Walter, J. Rech, G. David, N.-O. Walliser, J.
Palmeri, C. Mathieu-Demaziere, A. Parmeggiani, J.Y. Bouet, A. Le Gall, M.
Nollmann | ATP-driven separation of liquid phase condensates in bacteria | null | Molecular Cell, 2020, Pages 293-303.e4 | 10.1016/j.molcel.2020.06.034 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Liquid-liquid phase separated (LLPS) states are key to compartmentalise
components in the absence of membranes, however it is unclear whether LLPS
condensates are actively and specifically organized in the sub-cellular space
and by which mechanisms. Here, we address this question by focusing on the
ParABS DNA segrega... | [
{
"created": "Thu, 1 Oct 2020 06:44:38 GMT",
"version": "v1"
}
] | 2020-10-02 | [
[
"Guilhas",
"B.",
""
],
[
"Walter",
"J. C.",
""
],
[
"Rech",
"J.",
""
],
[
"David",
"G.",
""
],
[
"Walliser",
"N. -O.",
""
],
[
"Palmeri",
"J.",
""
],
[
"Mathieu-Demaziere",
"C.",
""
],
[
"Parmeggian... | Liquid-liquid phase separated (LLPS) states are key to compartmentalise components in the absence of membranes, however it is unclear whether LLPS condensates are actively and specifically organized in the sub-cellular space and by which mechanisms. Here, we address this question by focusing on the ParABS DNA segregati... |
1310.4522 | Orjan Carlborg | Xia Shen, Simon Forsberg, Mats Pettersson, Zheya Sheng and Orjan
Carlborg | Natural CMT2 variation is associated with genome-wide methylation
changes and temperature adaptation | Rewrite to improve clarity of presentation. Results unchanged. 43 p,
3 main fig, 1 main table, 15 suppl fig, 2 suppl tables. Particular updates -
New title - More detailed abstract and introduction - Updated results section
for clarity and focus - Updated discussion connecting work to unpublished
work in other ... | PLoS Genet 10(12): e1004842 | 10.1371/journal.pgen.1004842 | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A central problem when studying adaptation to a new environment is the
interplay between genetic variation and phenotypic plasticity. Arabidopsis
thaliana has colonized a wide range of habitats across the world and it is
therefore an attractive model for studying the genetic mechanisms underlying
environmental adapta... | [
{
"created": "Wed, 16 Oct 2013 21:27:07 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Jan 2014 10:18:27 GMT",
"version": "v2"
}
] | 2014-12-22 | [
[
"Shen",
"Xia",
""
],
[
"Forsberg",
"Simon",
""
],
[
"Pettersson",
"Mats",
""
],
[
"Sheng",
"Zheya",
""
],
[
"Carlborg",
"Orjan",
""
]
] | A central problem when studying adaptation to a new environment is the interplay between genetic variation and phenotypic plasticity. Arabidopsis thaliana has colonized a wide range of habitats across the world and it is therefore an attractive model for studying the genetic mechanisms underlying environmental adaptati... |
1310.6590 | Chuan-Chao Wang | Chuan-Chao Wang, Hui Li | Discovery of Phylogenetic Relevant Y-chromosome Variants in 1000 Genomes
Project Data | 11 pages, 14 figures | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Current Y chromosome research is limited in the poor resolution of Y
chromosome phylogenetic tree. Entirely sequenced Y chromosomes in numerous
human individuals have only recently become available by the advent of
next-generation sequencing technology. The 1000 Genomes Project has sequenced Y
chromosomes from more t... | [
{
"created": "Thu, 24 Oct 2013 13:02:50 GMT",
"version": "v1"
}
] | 2013-10-25 | [
[
"Wang",
"Chuan-Chao",
""
],
[
"Li",
"Hui",
""
]
] | Current Y chromosome research is limited in the poor resolution of Y chromosome phylogenetic tree. Entirely sequenced Y chromosomes in numerous human individuals have only recently become available by the advent of next-generation sequencing technology. The 1000 Genomes Project has sequenced Y chromosomes from more tha... |
2304.00148 | Samaila Jackson Yaga | S.J Yaga and F.W.O Saporu | A study of a deterministic model for meningitis epidemic | null | null | null | null | q-bio.PE stat.AP | http://creativecommons.org/licenses/by-nc-nd/4.0/ | A compartmental deterministic model that allows (1) immunity from two stages
of infection and carriage, and (2) disease induced death, is used in studying
the dynamics of meningitis epidemic process in a closed population. It allows
for difference in the transmission rate of infection to a susceptible by a
carrier an... | [
{
"created": "Fri, 31 Mar 2023 21:54:48 GMT",
"version": "v1"
}
] | 2023-04-04 | [
[
"Yaga",
"S. J",
""
],
[
"Saporu",
"F. W. O",
""
]
] | A compartmental deterministic model that allows (1) immunity from two stages of infection and carriage, and (2) disease induced death, is used in studying the dynamics of meningitis epidemic process in a closed population. It allows for difference in the transmission rate of infection to a susceptible by a carrier and ... |
2107.01670 | Emil Iftekhar | Emil Nafis Iftekhar, Viola Priesemann, Rudi Balling, Simon Bauer,
Philippe Beutels, Andr\'e Calero Valdez, Sarah Cuschieri, Thomas Czypionka,
Uga Dumpis, Enrico Glaab, Eva Grill, Claudia Hanson, Pirta Hotulainen, Peter
Klimek, Mirjam Kretzschmar, Tyll Kr\"uger, Jenny Krutzinna, Nicola Low,
Helena Machado, Carlo... | A look into the future of the COVID-19 pandemic in Europe: an expert
consultation | Manuscript is accepted by The Lancet Regional Health - Europe as a
Viewpoint article. Supplementary material can be accessed here:
https://owncloud.gwdg.de/index.php/f/1439962756 | Lancet Reg. Health Eur. 8, 100185 (2021) | 10.1016/j.lanepe.2021.100185 | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | How will the coronavirus disease 2019 (COVID-19) pandemic develop in the
coming months and years? Based on an expert survey, we examine key aspects that
are likely to influence COVID-19 in Europe. The future challenges and
developments will strongly depend on the progress of national and global
vaccination programs, ... | [
{
"created": "Sun, 4 Jul 2021 15:55:34 GMT",
"version": "v1"
},
{
"created": "Fri, 23 Jul 2021 09:57:38 GMT",
"version": "v2"
}
] | 2021-10-04 | [
[
"Iftekhar",
"Emil Nafis",
""
],
[
"Priesemann",
"Viola",
""
],
[
"Balling",
"Rudi",
""
],
[
"Bauer",
"Simon",
""
],
[
"Beutels",
"Philippe",
""
],
[
"Valdez",
"André Calero",
""
],
[
"Cuschieri",
"Sarah",
"... | How will the coronavirus disease 2019 (COVID-19) pandemic develop in the coming months and years? Based on an expert survey, we examine key aspects that are likely to influence COVID-19 in Europe. The future challenges and developments will strongly depend on the progress of national and global vaccination programs, th... |
1302.0395 | Vitaly Vodyanoy | T. Moore, I. Sorokulova, O. Pustovyy, L. Globa, D. Pascoe, M. Rudisill
and Vitaly Vodyanoy | Microscopic and thermodynamic evaluation of vesicles shed by
erythrocytes at elevated temperatures | 18 pages, 7 figures, Submitted to the Journal of Thermal Biology on
January 25, 2013 | null | null | null | q-bio.TO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Erythrocytes and vesicles shed by erythrocytes from human and rat blood were
collected and analyzed after temperature was elevated by physical exercise or
by exposure to external heat. The images of erythrocytes and vesicles were
analyzed by the light microscopy system with spatial resolution of better than
90 nm. Th... | [
{
"created": "Sat, 2 Feb 2013 15:58:44 GMT",
"version": "v1"
},
{
"created": "Tue, 5 Feb 2013 16:13:31 GMT",
"version": "v2"
}
] | 2013-02-06 | [
[
"Moore",
"T.",
""
],
[
"Sorokulova",
"I.",
""
],
[
"Pustovyy",
"O.",
""
],
[
"Globa",
"L.",
""
],
[
"Pascoe",
"D.",
""
],
[
"Rudisill",
"M.",
""
],
[
"Vodyanoy",
"Vitaly",
""
]
] | Erythrocytes and vesicles shed by erythrocytes from human and rat blood were collected and analyzed after temperature was elevated by physical exercise or by exposure to external heat. The images of erythrocytes and vesicles were analyzed by the light microscopy system with spatial resolution of better than 90 nm. The ... |
2403.05762 | Xinyu Yu | Hongguang Pan and Xinyu Yu and Yong Yang | Lateral Control of Brain-Controlled Vehicle Based on SVM Probability
Output Model | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The non-stationary characteristics of EEG signal and the individual
differences of brain-computer interfaces (BCIs) lead to poor performance in the
control process of the brain-controlled vehicles (BCVs). In this paper, by
combining steady-state visual evoked potential (SSVEP) interactive interface,
brain instruction... | [
{
"created": "Sat, 9 Mar 2024 02:15:06 GMT",
"version": "v1"
}
] | 2024-03-12 | [
[
"Pan",
"Hongguang",
""
],
[
"Yu",
"Xinyu",
""
],
[
"Yang",
"Yong",
""
]
] | The non-stationary characteristics of EEG signal and the individual differences of brain-computer interfaces (BCIs) lead to poor performance in the control process of the brain-controlled vehicles (BCVs). In this paper, by combining steady-state visual evoked potential (SSVEP) interactive interface, brain instructions ... |
q-bio/0505053 | Christophe Pouzat | Matthieu Delescluse (LPC), Christophe Pouzat (LPC) | Efficient spike-sorting of multi-state neurons using inter-spike
intervals information | 25 pages, to be published in Journal of Neurocience Methods | null | null | null | q-bio.QM math.ST physics.bio-ph physics.data-an stat.TH | null | We demonstrate the efficacy of a new spike-sorting method based on a Markov
Chain Monte Carlo (MCMC) algorithm by applying it to real data recorded from
Purkinje cells (PCs) in young rat cerebellar slices. This algorithm is unique
in its capability to estimate and make use of the firing statistics as well as
the spik... | [
{
"created": "Fri, 27 May 2005 11:53:44 GMT",
"version": "v1"
}
] | 2011-11-10 | [
[
"Delescluse",
"Matthieu",
"",
"LPC"
],
[
"Pouzat",
"Christophe",
"",
"LPC"
]
] | We demonstrate the efficacy of a new spike-sorting method based on a Markov Chain Monte Carlo (MCMC) algorithm by applying it to real data recorded from Purkinje cells (PCs) in young rat cerebellar slices. This algorithm is unique in its capability to estimate and make use of the firing statistics as well as the spike ... |
1711.09113 | Michael Deem | Melia E. Bonomo and Michael W. Deem | How the other half lives: CRISPR-Cas's influence on bacteriophages | 24 pages, 8 figures | Evolutionary Biology : Self, Non-Self Evolution, Species and
Complex Traits, Evolution, Methods and Concepts, ISBN 978-3-319-61569-1,
edited by Pierre Pontarotti, Springer Nature, September 2017, pp. 63-85 | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | CRISPR-Cas is a genetic adaptive immune system unique to prokaryotic cells
used to combat phage and plasmid threats. The host cell adapts by incorporating
DNA sequences from invading phages or plasmids into its CRISPR locus as
spacers. These spacers are expressed as mobile surveillance RNAs that direct
CRISPR-associa... | [
{
"created": "Fri, 24 Nov 2017 19:29:35 GMT",
"version": "v1"
}
] | 2017-11-28 | [
[
"Bonomo",
"Melia E.",
""
],
[
"Deem",
"Michael W.",
""
]
] | CRISPR-Cas is a genetic adaptive immune system unique to prokaryotic cells used to combat phage and plasmid threats. The host cell adapts by incorporating DNA sequences from invading phages or plasmids into its CRISPR locus as spacers. These spacers are expressed as mobile surveillance RNAs that direct CRISPR-associate... |
2211.09005 | Florian Nill | Florian Nill | Endemic Oscillations for SARS-CoV-2 Omicron -- A SIRS model analysis | 19 pages, 9 figures | Chaos, Solitons and Fractals 173 (2023) 113678 | 10.1016/j.chaos.2023.113678 | null | q-bio.PE math.DS physics.soc-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The SIRS model with constant vaccination and immunity waning rates is well
known to show a transition from a disease-free to an endemic equilibrium as the
basic reproduction number $r_0$ is raised above threshold. It is shown that
this model maps to Hethcote's classic endemic model originally published in
1973. In th... | [
{
"created": "Wed, 16 Nov 2022 16:02:04 GMT",
"version": "v1"
},
{
"created": "Tue, 30 May 2023 08:58:07 GMT",
"version": "v2"
}
] | 2023-06-26 | [
[
"Nill",
"Florian",
""
]
] | The SIRS model with constant vaccination and immunity waning rates is well known to show a transition from a disease-free to an endemic equilibrium as the basic reproduction number $r_0$ is raised above threshold. It is shown that this model maps to Hethcote's classic endemic model originally published in 1973. In this... |
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