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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2312.00191 | Patricia Suriana | Patricia Suriana, Ron O. Dror | Enhancing Ligand Pose Sampling for Molecular Docking | Published at the Machine Learning for Structural Biology Workshop,
NeurIPS 2023 | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Deep learning promises to dramatically improve scoring functions for
molecular docking, leading to substantial advances in binding pose prediction
and virtual screening. To train scoring functions-and to perform molecular
docking-one must generate a set of candidate ligand binding poses.
Unfortunately, the sampling p... | [
{
"created": "Thu, 30 Nov 2023 21:02:37 GMT",
"version": "v1"
}
] | 2023-12-04 | [
[
"Suriana",
"Patricia",
""
],
[
"Dror",
"Ron O.",
""
]
] | Deep learning promises to dramatically improve scoring functions for molecular docking, leading to substantial advances in binding pose prediction and virtual screening. To train scoring functions-and to perform molecular docking-one must generate a set of candidate ligand binding poses. Unfortunately, the sampling pro... |
0903.4844 | Anirban Banerji | Aniket Magarkar, Anirban Banerji, Shweta Kolhi | Quantification of Biological Robustness at the Systemic Level | Biological robustness, negative entropy, game theory. Computational
methodology to quantify negative entropy | null | null | null | q-bio.SC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biological systems possess negative entropy. In them, one form of order
produces another, more organized form of order. We propose a formal scheme to
calculate robustness of an entire biological system by quantifying the negative
entropy present in it. Our Methodology is based upon a computational
implementation of t... | [
{
"created": "Fri, 27 Mar 2009 16:43:00 GMT",
"version": "v1"
},
{
"created": "Fri, 3 Apr 2009 14:44:13 GMT",
"version": "v2"
},
{
"created": "Tue, 20 Dec 2011 09:07:25 GMT",
"version": "v3"
}
] | 2011-12-21 | [
[
"Magarkar",
"Aniket",
""
],
[
"Banerji",
"Anirban",
""
],
[
"Kolhi",
"Shweta",
""
]
] | Biological systems possess negative entropy. In them, one form of order produces another, more organized form of order. We propose a formal scheme to calculate robustness of an entire biological system by quantifying the negative entropy present in it. Our Methodology is based upon a computational implementation of two... |
2304.11474 | Eric Jones | Eric W. Jones, Joshua Derrick, Roger M. Nisbet, Will Ludington, David
A. Sivak | Signal in the noise: temporal variation in exponentially growing
populations | 6 page main text with 5 figures, 8 page supplement with 4 figures.
Updated with substantially revised manuscript | Sci. Rep. 13, 21340 (2023) | 10.1038/s41598-023-48726-w | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In exponential population growth, variability in the timing of individual
division events and environmental factors (including stochastic inoculation)
compound to produce variable growth trajectories. In several stochastic models
of exponential growth we show power-law relationships that relate variability
in the tim... | [
{
"created": "Sat, 22 Apr 2023 20:10:53 GMT",
"version": "v1"
},
{
"created": "Wed, 26 Apr 2023 21:01:36 GMT",
"version": "v2"
},
{
"created": "Mon, 7 Aug 2023 19:49:50 GMT",
"version": "v3"
}
] | 2023-12-25 | [
[
"Jones",
"Eric W.",
""
],
[
"Derrick",
"Joshua",
""
],
[
"Nisbet",
"Roger M.",
""
],
[
"Ludington",
"Will",
""
],
[
"Sivak",
"David A.",
""
]
] | In exponential population growth, variability in the timing of individual division events and environmental factors (including stochastic inoculation) compound to produce variable growth trajectories. In several stochastic models of exponential growth we show power-law relationships that relate variability in the time ... |
q-bio/0509004 | Junghyo Jo | J. Jo, H. Kang, M. Y. Choi and D. S. Koh | How Noise and Coupling Induce Bursting Action Potentials in Pancreatic
beta-cells | 40 pages, 10 figures | published in Biophysical Journal 89:1534-1542 (2005) | 10.1529/biophysj.104.053181 | null | q-bio.CB physics.bio-ph | null | Unlike isolated beta-cells, which usually produce continuous spikes or fast
and irregular bursts, electrically coupled beta-cells are apt to exhibit robust
bursting action potentials. We consider the noise induced by thermal
fluctuations as well as that by channel gating stochasticity and examine its
effects on the a... | [
{
"created": "Mon, 5 Sep 2005 10:25:13 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Jo",
"J.",
""
],
[
"Kang",
"H.",
""
],
[
"Choi",
"M. Y.",
""
],
[
"Koh",
"D. S.",
""
]
] | Unlike isolated beta-cells, which usually produce continuous spikes or fast and irregular bursts, electrically coupled beta-cells are apt to exhibit robust bursting action potentials. We consider the noise induced by thermal fluctuations as well as that by channel gating stochasticity and examine its effects on the act... |
1405.4024 | Thomas House | Thomas House | Algebraic moment closure for population dynamics on discrete structures | 12 pages, 4 figures | null | null | null | q-bio.PE math.OA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Moment closure on general discrete structures often requires one of the
following: (i) an absence of short closed loops (zero clustering); (ii)
existence of a spatial scale; (iii) ad hoc assumptions. Algebraic methods are
presented to avoid the use of such assumptions for populations based on clumps,
and are applied ... | [
{
"created": "Thu, 15 May 2014 21:59:04 GMT",
"version": "v1"
}
] | 2014-05-19 | [
[
"House",
"Thomas",
""
]
] | Moment closure on general discrete structures often requires one of the following: (i) an absence of short closed loops (zero clustering); (ii) existence of a spatial scale; (iii) ad hoc assumptions. Algebraic methods are presented to avoid the use of such assumptions for populations based on clumps, and are applied to... |
1405.2965 | Andrew Francis | Andrew R. Francis and Mike Steel | Tree-like Reticulation Networks - When Do Tree-like Distances Also
Support Reticulate Evolution? | 19 pages, 9 figures. Revised version includes clarification in proof
of Theorem 2, and a new figure (Fig 9) | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Hybrid evolution and horizontal gene transfer (HGT) are processes where
evolutionary relationships may more accurately be described by a reticulated
network than by a tree. In such a network, there will often be several paths
between any two extant species, reflecting the possible pathways that genetic
material may h... | [
{
"created": "Mon, 12 May 2014 21:11:39 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Sep 2014 01:32:49 GMT",
"version": "v2"
}
] | 2014-09-24 | [
[
"Francis",
"Andrew R.",
""
],
[
"Steel",
"Mike",
""
]
] | Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any two extant species, reflecting the possible pathways that genetic material may hav... |
2202.07171 | Hyunjin Shim | Hyunjin Shim | Investigating the genomic background of CRISPR-Cas genomes for
CRISPR-based antimicrobials | 27 pages, 5 figures | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | CRISPR-Cas systems are an adaptive immunity that protects prokaryotes against
foreign genetic elements. Genetic templates acquired during past infection
events enable DNA-interacting enzymes to recognize foreign DNA for destruction.
Due to the programmability and specificity of these genetic templates,
CRISPR-Cas sys... | [
{
"created": "Tue, 15 Feb 2022 03:47:26 GMT",
"version": "v1"
}
] | 2022-02-16 | [
[
"Shim",
"Hyunjin",
""
]
] | CRISPR-Cas systems are an adaptive immunity that protects prokaryotes against foreign genetic elements. Genetic templates acquired during past infection events enable DNA-interacting enzymes to recognize foreign DNA for destruction. Due to the programmability and specificity of these genetic templates, CRISPR-Cas syste... |
1309.2576 | Reinhard Buerger | Reinhard B\"urger | A Survey on Migration-Selection Models in Population Genetics | null | Discrete Cont. Dyn. Syst. B 19, 883 - 959 (2014) | 10.3934/dcdsb.2014.19.883 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This survey focuses on the most important aspects of the mathematical theory
of population genetic models of selection and migration between discrete
niches. Such models are most appropriate if the dispersal distance is short
compared to the scale at which the environment changes, or if the habitat is
fragmented. The... | [
{
"created": "Tue, 10 Sep 2013 17:09:39 GMT",
"version": "v1"
}
] | 2019-12-13 | [
[
"Bürger",
"Reinhard",
""
]
] | This survey focuses on the most important aspects of the mathematical theory of population genetic models of selection and migration between discrete niches. Such models are most appropriate if the dispersal distance is short compared to the scale at which the environment changes, or if the habitat is fragmented. The g... |
0808.2922 | Craig Powell | Craig R. Powell, Alan J. McKane | Effects of food web construction by evolution or immigration | 12 pages, 7 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present results contrasting food webs constructed using the same model
where the source of species was either evolution or immigration from a
previously evolved species pool. The overall structure of the webs are
remarkably similar, although we find some important differences which mainly
relate to the percentage ... | [
{
"created": "Thu, 21 Aug 2008 13:06:24 GMT",
"version": "v1"
}
] | 2008-08-22 | [
[
"Powell",
"Craig R.",
""
],
[
"McKane",
"Alan J.",
""
]
] | We present results contrasting food webs constructed using the same model where the source of species was either evolution or immigration from a previously evolved species pool. The overall structure of the webs are remarkably similar, although we find some important differences which mainly relate to the percentage of... |
1704.05748 | Nicolai Pedersen | Rasmus S. Andersen, Anders U. Eliasen, Nicolai Pedersen, Michael Riis
Andersen, Sofie Therese Hansen, Lars Kai Hansen | EEG source imaging assists decoding in a face recognition task | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | EEG based brain state decoding has numerous applications. State of the art
decoding is based on processing of the multivariate sensor space signal,
however evidence is mounting that EEG source reconstruction can assist
decoding. EEG source imaging leads to high-dimensional representations and
rather strong a priori i... | [
{
"created": "Mon, 17 Apr 2017 10:19:16 GMT",
"version": "v1"
}
] | 2017-04-20 | [
[
"Andersen",
"Rasmus S.",
""
],
[
"Eliasen",
"Anders U.",
""
],
[
"Pedersen",
"Nicolai",
""
],
[
"Andersen",
"Michael Riis",
""
],
[
"Hansen",
"Sofie Therese",
""
],
[
"Hansen",
"Lars Kai",
""
]
] | EEG based brain state decoding has numerous applications. State of the art decoding is based on processing of the multivariate sensor space signal, however evidence is mounting that EEG source reconstruction can assist decoding. EEG source imaging leads to high-dimensional representations and rather strong a priori inf... |
2312.13465 | Thierry Mora | Maria Francesca Abbate, Thomas Dupic, Emmanuelle Vigne, Melody A.
Shahsavarian, Aleksandra M. Walczak, Thierry Mora | Computational detection of antigen specific B cell receptors following
immunization | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | B cell receptors (BCRs) play a crucial role in recognizing and fighting
foreign antigens. High-throughput sequencing enables in-depth sampling of the
BCRs repertoire after immunization. However, only a minor fraction of BCRs
actively participate in any given infection. To what extent can we accurately
identify antige... | [
{
"created": "Wed, 20 Dec 2023 22:32:02 GMT",
"version": "v1"
}
] | 2023-12-22 | [
[
"Abbate",
"Maria Francesca",
""
],
[
"Dupic",
"Thomas",
""
],
[
"Vigne",
"Emmanuelle",
""
],
[
"Shahsavarian",
"Melody A.",
""
],
[
"Walczak",
"Aleksandra M.",
""
],
[
"Mora",
"Thierry",
""
]
] | B cell receptors (BCRs) play a crucial role in recognizing and fighting foreign antigens. High-throughput sequencing enables in-depth sampling of the BCRs repertoire after immunization. However, only a minor fraction of BCRs actively participate in any given infection. To what extent can we accurately identify antigen-... |
2201.08110 | Gianni De Fabritiis | Raimondas Galvelis, Alejandro Varela-Rial, Stefan Doerr, Roberto Fino,
Peter Eastman, Thomas E. Markland, John D. Chodera and Gianni De Fabritiis | NNP/MM: Accelerating molecular dynamics simulations with machine
learning potentials and molecular mechanic | null | null | null | null | q-bio.BM cs.LG physics.bio-ph physics.comp-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Machine learning potentials have emerged as a means to enhance the accuracy
of biomolecular simulations. However, their application is constrained by the
significant computational cost arising from the vast number of parameters
compared to traditional molecular mechanics. To tackle this issue, we introduce
an optimiz... | [
{
"created": "Thu, 20 Jan 2022 10:57:20 GMT",
"version": "v1"
},
{
"created": "Mon, 28 Aug 2023 12:04:46 GMT",
"version": "v2"
}
] | 2023-08-29 | [
[
"Galvelis",
"Raimondas",
""
],
[
"Varela-Rial",
"Alejandro",
""
],
[
"Doerr",
"Stefan",
""
],
[
"Fino",
"Roberto",
""
],
[
"Eastman",
"Peter",
""
],
[
"Markland",
"Thomas E.",
""
],
[
"Chodera",
"John D.",
... | Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to traditional molecular mechanics. To tackle this issue, we introduce an optimized... |
1804.01694 | Anvita Gupta | Anvita Gupta and James Zou | Feedback GAN (FBGAN) for DNA: a Novel Feedback-Loop Architecture for
Optimizing Protein Functions | null | null | null | null | q-bio.GN cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Generative Adversarial Networks (GANs) represent an attractive and novel
approach to generate realistic data, such as genes, proteins, or drugs, in
synthetic biology. Here, we apply GANs to generate synthetic DNA sequences
encoding for proteins of variable length. We propose a novel feedback-loop
architecture, called... | [
{
"created": "Thu, 5 Apr 2018 07:17:42 GMT",
"version": "v1"
}
] | 2018-04-06 | [
[
"Gupta",
"Anvita",
""
],
[
"Zou",
"James",
""
]
] | Generative Adversarial Networks (GANs) represent an attractive and novel approach to generate realistic data, such as genes, proteins, or drugs, in synthetic biology. Here, we apply GANs to generate synthetic DNA sequences encoding for proteins of variable length. We propose a novel feedback-loop architecture, called F... |
2001.08264 | Martin Frasch | Martin G. Frasch | Heart rate variability code: Does it exist and can we hack it? | null | Bioengineering 2023 | 10.3390/bioengineering10070822 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Heart rate variability (HRV) has been studied for over 50 years, yet an
integrative concept is missing on what HRV's mathematical properties represent
physiologically. Here I introduce the notion of HRV code as an attempt to
address this challenge systematically. I review the existing evidence from
physiological stud... | [
{
"created": "Wed, 22 Jan 2020 20:23:50 GMT",
"version": "v1"
},
{
"created": "Wed, 12 Feb 2020 02:05:22 GMT",
"version": "v2"
},
{
"created": "Wed, 6 May 2020 22:25:50 GMT",
"version": "v3"
},
{
"created": "Mon, 10 May 2021 18:17:22 GMT",
"version": "v4"
}
] | 2023-07-18 | [
[
"Frasch",
"Martin G.",
""
]
] | Heart rate variability (HRV) has been studied for over 50 years, yet an integrative concept is missing on what HRV's mathematical properties represent physiologically. Here I introduce the notion of HRV code as an attempt to address this challenge systematically. I review the existing evidence from physiological studie... |
1102.5528 | Henry L\"utcke | Henry L\"utcke and Fritjof Helmchen | Two-photon imaging and analysis of neural network dynamics | 36 pages, 4 figures, accepted for publication in Reports on Progress
in Physics | null | 10.1088/0034-4885/74/8/086602 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The glow of a starry night sky, the smell of a freshly brewed cup of coffee
or the sound of ocean waves breaking on the beach are representations of the
physical world that have been created by the dynamic interactions of thousands
of neurons in our brains. How the brain mediates perceptions, creates thoughts,
stores... | [
{
"created": "Sun, 27 Feb 2011 17:48:50 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Jul 2011 21:42:27 GMT",
"version": "v2"
}
] | 2011-07-28 | [
[
"Lütcke",
"Henry",
""
],
[
"Helmchen",
"Fritjof",
""
]
] | The glow of a starry night sky, the smell of a freshly brewed cup of coffee or the sound of ocean waves breaking on the beach are representations of the physical world that have been created by the dynamic interactions of thousands of neurons in our brains. How the brain mediates perceptions, creates thoughts, stores m... |
2107.07574 | Sayantan Nag Chowdhury | Sayantan Nag Chowdhury, Srilena Kundu, Jeet Banerjee, Matja\v{z} Perc,
Dibakar Ghosh | Eco-evolutionary dynamics of cooperation in the presence of policing | null | J. Theor. Biol. 518, 110606 (2021) | 10.1016/j.jtbi.2021.110606 | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Ecology and evolution are inherently linked, and studying a mathematical
model that considers both holds promise of insightful discoveries related to
the dynamics of cooperation. In the present article, we use the prisoner's
dilemma (PD) game as a basis for long-term apprehension of the essential social
dilemma relat... | [
{
"created": "Thu, 15 Jul 2021 19:16:10 GMT",
"version": "v1"
}
] | 2021-08-10 | [
[
"Chowdhury",
"Sayantan Nag",
""
],
[
"Kundu",
"Srilena",
""
],
[
"Banerjee",
"Jeet",
""
],
[
"Perc",
"Matjaž",
""
],
[
"Ghosh",
"Dibakar",
""
]
] | Ecology and evolution are inherently linked, and studying a mathematical model that considers both holds promise of insightful discoveries related to the dynamics of cooperation. In the present article, we use the prisoner's dilemma (PD) game as a basis for long-term apprehension of the essential social dilemma related... |
2403.07475 | Zhiheng Lyu | Zhiheng Lyu, Jiannan Yang, Zhongzhi Xu, Weilan Wang, Weibin Cheng,
Kwok-Leung Tsui, Gary Tse and Qingpeng Zhang | Predicting the Risk of Ischemic Stroke in Patients with Atrial
Fibrillation using Heterogeneous Drug-protein-disease Network-based Deep
Learning | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop a deep learning model, ABioSPATH, to predict the one-year risk of
ischemic stroke (IS) in atrial fibrillation (AF) patients. The model integrates
drug-protein-disease pathways and real-world clinical data of AF patients to
generate the IS risk and potential pathways for each patient. The model uses a
multi... | [
{
"created": "Tue, 12 Mar 2024 10:10:55 GMT",
"version": "v1"
}
] | 2024-03-13 | [
[
"Lyu",
"Zhiheng",
""
],
[
"Yang",
"Jiannan",
""
],
[
"Xu",
"Zhongzhi",
""
],
[
"Wang",
"Weilan",
""
],
[
"Cheng",
"Weibin",
""
],
[
"Tsui",
"Kwok-Leung",
""
],
[
"Tse",
"Gary",
""
],
[
"Zhang",
... | We develop a deep learning model, ABioSPATH, to predict the one-year risk of ischemic stroke (IS) in atrial fibrillation (AF) patients. The model integrates drug-protein-disease pathways and real-world clinical data of AF patients to generate the IS risk and potential pathways for each patient. The model uses a multila... |
2305.14185 | Fabio Chalub | Fabio A.C.C. Chalub, Antonio G\'omez-Corral, Mart\'in
L\'opez-Garc\'ia, and F\'atima Palacios-Rodr\'iguez | A Markov chain model to investigate the spread of antibiotic-resistant
bacteria in hospitals | 30 pages, 9 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Ordinary differential equation (ODE) models used in mathematical epidemiology
assume explicitly or implicitly large populations. For the study of infections
in a hospital this is an extremely restrictive assumption as typically a
hospital ward has a few dozen, or even fewer, patients. This work reframes a
well-known ... | [
{
"created": "Tue, 23 May 2023 16:06:56 GMT",
"version": "v1"
},
{
"created": "Fri, 18 Aug 2023 10:59:21 GMT",
"version": "v2"
}
] | 2023-08-21 | [
[
"Chalub",
"Fabio A. C. C.",
""
],
[
"Gómez-Corral",
"Antonio",
""
],
[
"López-García",
"Martín",
""
],
[
"Palacios-Rodríguez",
"Fátima",
""
]
] | Ordinary differential equation (ODE) models used in mathematical epidemiology assume explicitly or implicitly large populations. For the study of infections in a hospital this is an extremely restrictive assumption as typically a hospital ward has a few dozen, or even fewer, patients. This work reframes a well-known mo... |
0911.5315 | Timothy Saunders | Timothy E Saunders and Martin Howard | When it Pays to Rush: Interpreting Morphogen Gradients Prior to
Steady-State | 18 pages, 3 figures | Physical Biology, 6, 046020 (2009) | 10.1088/1478-3975/6/4/046020 | null | q-bio.MN q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During development, morphogen gradients precisely determine the position of
gene expression boundaries despite the inevitable presence of fluctuations.
Recent experiments suggest that some morphogen gradients may be interpreted
prior to reaching steady-state. Theoretical work has predicted that such
systems will be m... | [
{
"created": "Fri, 27 Nov 2009 17:22:13 GMT",
"version": "v1"
}
] | 2009-11-30 | [
[
"Saunders",
"Timothy E",
""
],
[
"Howard",
"Martin",
""
]
] | During development, morphogen gradients precisely determine the position of gene expression boundaries despite the inevitable presence of fluctuations. Recent experiments suggest that some morphogen gradients may be interpreted prior to reaching steady-state. Theoretical work has predicted that such systems will be mor... |
2206.02438 | Matej Hoffmann Ph.D. | Matej Hoffmann | Body schema or the body as its own best model | 7 pages, 2 figures. arXiv admin note: text overlap with
arXiv:2010.09325 | in G. \v{S}ejnov\'a and M. Vavre\v{c}ka and J. Hvoreck\'y, ed.,
'Kognice a um\v{e}l\'y \v{z}ivot XX (Cognition and Artificial Life XX)', CTU
in Prague, , pp. 45-51 (2022) | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Rodney Brooks (1991) put forth the idea that during an agent's interaction
with its environment, representations of the world often stand in the way.
Instead, using the world as its own best model, i.e. interacting with it
directly without making models, often leads to better and more natural
behavior. The same persp... | [
{
"created": "Mon, 6 Jun 2022 08:57:33 GMT",
"version": "v1"
}
] | 2022-06-07 | [
[
"Hoffmann",
"Matej",
""
]
] | Rodney Brooks (1991) put forth the idea that during an agent's interaction with its environment, representations of the world often stand in the way. Instead, using the world as its own best model, i.e. interacting with it directly without making models, often leads to better and more natural behavior. The same perspec... |
2205.01790 | Soumyajit Seth | Zeric Tabekoueng Njitacke, Sishu Shankar Muni, Soumyajit Seth, Jan
Awrejcewicz, Jacques Kengne | Complex dynamics of a heterogeneous network of Hindmarsh-Rose neurons | null | null | 10.1088/1402-4896/acbdd1 | null | q-bio.NC nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this contribution, we have considered the collective behavior of the two
as well as the network of heterogeneous coupled Hindmarsh Rose (HR) neurons.
The heterogeneous models were made of a memristive 2D (HR) and the traditional
3D HR neurons. Investigating a model of two coupled neurons through an
electrical syna... | [
{
"created": "Tue, 3 May 2022 21:33:32 GMT",
"version": "v1"
}
] | 2023-02-24 | [
[
"Njitacke",
"Zeric Tabekoueng",
""
],
[
"Muni",
"Sishu Shankar",
""
],
[
"Seth",
"Soumyajit",
""
],
[
"Awrejcewicz",
"Jan",
""
],
[
"Kengne",
"Jacques",
""
]
] | In this contribution, we have considered the collective behavior of the two as well as the network of heterogeneous coupled Hindmarsh Rose (HR) neurons. The heterogeneous models were made of a memristive 2D (HR) and the traditional 3D HR neurons. Investigating a model of two coupled neurons through an electrical synaps... |
0704.3263 | Dominique Jean-Marie Mornet | Karim Hnia, G\'erald Hugon, Ahmed Masmoudi, Jacques Mercier,
Fran\c{c}ois Rivier, Dominique Jean-Marie Mornet | Effect of beta-Dystroglycan Processing on Utrophin / DP116 Anchorage in
Normal and MDX Mouse Schwann Cell Membrane | null | Neuroscience 141 (18/04/2006) 607-620 | 10.1016/J.neuroscience.2006.04.043 | null | q-bio.NC | null | In the peripheral nervous system, utrophin and the short dystrophin isoform
(Dp116) are co-localized at the outermost layer of the myelin sheath of nerve
fibers; together with the dystroglycan complex. In peripheral nerve, matrix
metalloproteinase (MMP) creates a 30 kDa fragment of beta-dystroglycan, leading
to a dis... | [
{
"created": "Tue, 24 Apr 2007 19:17:45 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Hnia",
"Karim",
""
],
[
"Hugon",
"Gérald",
""
],
[
"Masmoudi",
"Ahmed",
""
],
[
"Mercier",
"Jacques",
""
],
[
"Rivier",
"François",
""
],
[
"Mornet",
"Dominique Jean-Marie",
""
]
] | In the peripheral nervous system, utrophin and the short dystrophin isoform (Dp116) are co-localized at the outermost layer of the myelin sheath of nerve fibers; together with the dystroglycan complex. In peripheral nerve, matrix metalloproteinase (MMP) creates a 30 kDa fragment of beta-dystroglycan, leading to a disru... |
1711.03332 | Alberto Sorrentino | Sara Sommariva and Alberto Sorrentino and Michele Piana and Vittorio
Pizzella and Laura Marzetti | A comparative study of the robustness of frequency--domain connectivity
measures to finite data length | 32 pages, 13 figures | null | null | null | q-bio.QM math.NA q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work we use numerical simulation to investigate how the temporal
length of the data affects the reliability of the estimates of brain
connectivity from EEG time--series. We assume that the neural sources follow a
stable MultiVariate AutoRegressive model, and consider three connectivity
metrics: Imaginary part... | [
{
"created": "Thu, 9 Nov 2017 11:25:29 GMT",
"version": "v1"
}
] | 2017-11-10 | [
[
"Sommariva",
"Sara",
""
],
[
"Sorrentino",
"Alberto",
""
],
[
"Piana",
"Michele",
""
],
[
"Pizzella",
"Vittorio",
""
],
[
"Marzetti",
"Laura",
""
]
] | In this work we use numerical simulation to investigate how the temporal length of the data affects the reliability of the estimates of brain connectivity from EEG time--series. We assume that the neural sources follow a stable MultiVariate AutoRegressive model, and consider three connectivity metrics: Imaginary part o... |
q-bio/0407040 | Jie Liang | Changyu Hu, Xiang Li and Jie Liang | Developing optimal nonlinear scoring function for protein design | 25 pages, 6 figures, 7 tables. Accepted by Bioinformatics | null | null | null | q-bio.BM | null | Motivation. Protein design aims to identify sequences compatible with a given
protein fold but incompatible to any alternative folds. To select the correct
sequences and to guide the search process, a design scoring function is
critically important. Such a scoring function should be able to characterize
the global fi... | [
{
"created": "Thu, 29 Jul 2004 18:14:02 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Hu",
"Changyu",
""
],
[
"Li",
"Xiang",
""
],
[
"Liang",
"Jie",
""
]
] | Motivation. Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process, a design scoring function is critically important. Such a scoring function should be able to characterize the global fitn... |
2007.04853 | Victor Popescu | Victor-Bogdan Popescu and Krishna Kanhaiya and Iulian N\u{a}stac and
Eugen Czeizler and Ion Petre | Identifying efficient controls of complex interaction networks using
genetic algorithms | The submission contains 34 pages, 9 figures and 6 tables | null | null | null | q-bio.MN cs.NE cs.SY eess.SY q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Control theory has seen recently impactful applications in network science,
especially in connections with applications in network medicine. A key topic of
research is that of finding minimal external interventions that offer control
over the dynamics of a given network, a problem known as network
controllability. We... | [
{
"created": "Thu, 9 Jul 2020 14:56:54 GMT",
"version": "v1"
}
] | 2020-07-10 | [
[
"Popescu",
"Victor-Bogdan",
""
],
[
"Kanhaiya",
"Krishna",
""
],
[
"Năstac",
"Iulian",
""
],
[
"Czeizler",
"Eugen",
""
],
[
"Petre",
"Ion",
""
]
] | Control theory has seen recently impactful applications in network science, especially in connections with applications in network medicine. A key topic of research is that of finding minimal external interventions that offer control over the dynamics of a given network, a problem known as network controllability. We p... |
2012.08973 | Tara Van Viegen | Tara van Viegen (1), Athena Akrami (2), Kate Bonnen (3), Eric DeWitt
(4), Alexandre Hyafil (5), Helena Ledmyr (6), Grace W. Lindsay (7), Patrick
Mineault, John D. Murray (8), Xaq Pitkow (9 and 10 and 11), Aina Puce (12),
Madineh Sedigh-Sarvestani (13), Carsen Stringer (14), Titipat Achakulvisut
(15), Elnaz Alik... | Neuromatch Academy: Teaching Computational Neuroscience with global
accessibility | 10 pages, 3 figures. Equal contribution by the executive committee
members of Neuromatch Academy: Tara van Viegen, Athena Akrami, Kate Bonnen,
Eric DeWitt, Alexandre Hyafil, Helena Ledmyr, Grace W. Lindsay, Patrick
Mineault, John D. Murray, Xaq Pitkow, Aina Puce, Madineh Sedigh-Sarvestani,
Carsen Stringer. and ... | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Neuromatch Academy designed and ran a fully online 3-week Computational
Neuroscience summer school for 1757 students with 191 teaching assistants
working in virtual inverted (or flipped) classrooms and on small group
projects. Fourteen languages, active community management, and low cost allowed
for an unprecedented ... | [
{
"created": "Tue, 15 Dec 2020 17:20:17 GMT",
"version": "v1"
}
] | 2020-12-17 | [
[
"van Viegen",
"Tara",
"",
"9 and 10 and 11"
],
[
"Akrami",
"Athena",
"",
"9 and 10 and 11"
],
[
"Bonnen",
"Kate",
"",
"9 and 10 and 11"
],
[
"DeWitt",
"Eric",
"",
"9 and 10 and 11"
],
[
"Hyafil",
"Alexandre",
"",
"9 an... | Neuromatch Academy designed and ran a fully online 3-week Computational Neuroscience summer school for 1757 students with 191 teaching assistants working in virtual inverted (or flipped) classrooms and on small group projects. Fourteen languages, active community management, and low cost allowed for an unprecedented le... |
1202.3384 | Scott McKinley | Andrew M. Hein, Scott A. McKinley | Sensing and decision-making in random search | null | null | 10.1073/pnas.1202686109 | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While microscopic organisms can use gradient-based search to locate
resources, this strategy can be poorly suited to the sensory signals available
to macroscopic organisms. We propose a framework that models search-decision
making in cases where sensory signals are infrequent, subject to large
fluctuations, and conta... | [
{
"created": "Wed, 15 Feb 2012 17:42:44 GMT",
"version": "v1"
}
] | 2015-06-04 | [
[
"Hein",
"Andrew M.",
""
],
[
"McKinley",
"Scott A.",
""
]
] | While microscopic organisms can use gradient-based search to locate resources, this strategy can be poorly suited to the sensory signals available to macroscopic organisms. We propose a framework that models search-decision making in cases where sensory signals are infrequent, subject to large fluctuations, and contain... |
1710.03655 | Erick Martins Ratamero | Erick Martins Ratamero, Dom Bellini, Christopher G. Dowson, Rudolf A.
Roemer | Touching proteins with virtual bare hands: how to visualize protein-drug
complexes and their dynamics in virtual reality | null | Journal of Computer-Aided Molecular Design 32(6), 703-709 (2018) | 10.1007/s10822-018-0123-0 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ability to precisely visualize the atomic geometry of the interactions
between a drug and its protein target in structural models is critical in
predicting the correct modifications in previously identified inhibitors to
create more effective next generation drugs. It is currently common practice
among medicinal ... | [
{
"created": "Tue, 10 Oct 2017 15:28:23 GMT",
"version": "v1"
}
] | 2018-08-14 | [
[
"Ratamero",
"Erick Martins",
""
],
[
"Bellini",
"Dom",
""
],
[
"Dowson",
"Christopher G.",
""
],
[
"Roemer",
"Rudolf A.",
""
]
] | The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal ch... |
2109.06031 | Steffen Lange | Steffen Lange, Richard Mogwitz, Denis H\"unniger, Anja Voss-B\"ohme | Modeling age-specific incidence of colon cancer via niche competition | 28 pages, 13 figures | PLoS Comput Biol 18(8): e1010403 (2022) | 10.1371/journal.pcbi.1010403 | null | q-bio.TO nlin.CG physics.bio-ph physics.data-an physics.med-ph | http://creativecommons.org/licenses/by/4.0/ | Cancer development is a multistep process often starting with a single cell
in which a number of epigenetic and genetic alterations have accumulated thus
transforming it into a tumor cell. The progeny of such a single benign tumor
cell expands in the tissue and can at some point progress to malignant tumor
cells unti... | [
{
"created": "Sat, 4 Sep 2021 10:03:46 GMT",
"version": "v1"
},
{
"created": "Fri, 15 Jul 2022 08:11:54 GMT",
"version": "v2"
}
] | 2022-09-21 | [
[
"Lange",
"Steffen",
""
],
[
"Mogwitz",
"Richard",
""
],
[
"Hünniger",
"Denis",
""
],
[
"Voss-Böhme",
"Anja",
""
]
] | Cancer development is a multistep process often starting with a single cell in which a number of epigenetic and genetic alterations have accumulated thus transforming it into a tumor cell. The progeny of such a single benign tumor cell expands in the tissue and can at some point progress to malignant tumor cells until ... |
2109.05833 | Johannes Wirtz | Johannes Wirtz and St\'ephane Guindon | Rate of coalescence of pairs of lineages in the spatial
{\lambda}-Fleming-Viot process | 31 pages, 8 figures | null | null | null | q-bio.PE math.PR | http://creativecommons.org/licenses/by/4.0/ | We revisit the spatial ${\lambda}$-Fleming-Viot process introduced in [1].
Particularly, we are interested in the time $T_0$ to the most recent common
ancestor for two lineages. We distinguish between the case where the process
acts on the entire two-dimensional plane, and on a finite rectangle. Utilizing
a different... | [
{
"created": "Mon, 13 Sep 2021 10:01:53 GMT",
"version": "v1"
}
] | 2021-09-14 | [
[
"Wirtz",
"Johannes",
""
],
[
"Guindon",
"Stéphane",
""
]
] | We revisit the spatial ${\lambda}$-Fleming-Viot process introduced in [1]. Particularly, we are interested in the time $T_0$ to the most recent common ancestor for two lineages. We distinguish between the case where the process acts on the entire two-dimensional plane, and on a finite rectangle. Utilizing a differentia... |
2008.05591 | Daniel L. Cox | Yuduo Zhi and Daniel L. Cox | Neurodegenerative damage reduces firing coherence in a continuous
attractor model of grid cells | 24 pages, 9 figures | null | 10.1103/PhysRevE.104.044414 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Grid cells in the dorsolateral band of the medial entorhinal cortex(dMEC)
display strikingly regular periodic firing patterns on a lattice of positions
in 2-D space. This helps animals to encode relative spatial location without
reference to external cues. The dMEC is damaged in the early stages of
Alzheimer's Diseas... | [
{
"created": "Wed, 12 Aug 2020 22:38:33 GMT",
"version": "v1"
},
{
"created": "Wed, 14 Apr 2021 00:45:00 GMT",
"version": "v2"
}
] | 2021-11-10 | [
[
"Zhi",
"Yuduo",
""
],
[
"Cox",
"Daniel L.",
""
]
] | Grid cells in the dorsolateral band of the medial entorhinal cortex(dMEC) display strikingly regular periodic firing patterns on a lattice of positions in 2-D space. This helps animals to encode relative spatial location without reference to external cues. The dMEC is damaged in the early stages of Alzheimer's Disease,... |
2105.15123 | Onkar Sadekar | Onkar Sadekar, Mansi Budamagunta, G. J. Sreejith, Sachin Jain, and M.
S. Santhanam | An infectious diseases hazard map for India based on mobility and
transportation networks | 25 pages, 8 figures, including supplementary material | Current Science 121, 1208 (2021) | 10.18520/cs/v121/i9/1208-1215 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a risk measure and construct an infectious diseases hazard map for
India. Given an outbreak location, a hazard index is assigned to each city
using an effective distance that depends on inter-city mobilities instead of
geographical distance. We demonstrate its utility using an SIR model augmented
with air,... | [
{
"created": "Mon, 24 May 2021 06:38:10 GMT",
"version": "v1"
},
{
"created": "Wed, 2 Jun 2021 00:21:40 GMT",
"version": "v2"
},
{
"created": "Wed, 4 Aug 2021 07:50:55 GMT",
"version": "v3"
}
] | 2021-11-18 | [
[
"Sadekar",
"Onkar",
""
],
[
"Budamagunta",
"Mansi",
""
],
[
"Sreejith",
"G. J.",
""
],
[
"Jain",
"Sachin",
""
],
[
"Santhanam",
"M. S.",
""
]
] | We propose a risk measure and construct an infectious diseases hazard map for India. Given an outbreak location, a hazard index is assigned to each city using an effective distance that depends on inter-city mobilities instead of geographical distance. We demonstrate its utility using an SIR model augmented with air, r... |
1710.06274 | Christopher Spalding Mr | Christopher Spalding, Charles R. Doering, Glenn R. Flierl | Resonant Activation of Population Extinctions | 12 pages, 7 Figures, Accepted for publication in Physical Review E | null | 10.1103/PhysRevE.96.042411 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the mechanisms governing population extinctions is of key
importance to many problems in ecology and evolution. Stochastic factors are
known to play a central role in extinction, but the interactions between a
population's demographic stochasticity and environmental noise remain poorly
understood. Here,... | [
{
"created": "Tue, 17 Oct 2017 13:41:25 GMT",
"version": "v1"
}
] | 2017-11-22 | [
[
"Spalding",
"Christopher",
""
],
[
"Doering",
"Charles R.",
""
],
[
"Flierl",
"Glenn R.",
""
]
] | Understanding the mechanisms governing population extinctions is of key importance to many problems in ecology and evolution. Stochastic factors are known to play a central role in extinction, but the interactions between a population's demographic stochasticity and environmental noise remain poorly understood. Here, w... |
2307.15540 | Shuhei Kitamura PhD | Shuhei Kitamura | Quantifying the Influence of Climate on Human Mind and Culture: Evidence
from Visual Art | null | null | null | null | q-bio.PE econ.GN q-fin.EC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | While connections between climate and the human mind and culture are widely
acknowledged, they are not thoroughly quantified. Analyzing 100,000 paintings
and data on 2,000 artists from the 13th to 21st centuries, the study reveals
that the lightness of the paintings exhibited an interesting U-shaped pattern
mirroring... | [
{
"created": "Fri, 28 Jul 2023 13:11:52 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Apr 2024 03:11:45 GMT",
"version": "v2"
}
] | 2024-04-15 | [
[
"Kitamura",
"Shuhei",
""
]
] | While connections between climate and the human mind and culture are widely acknowledged, they are not thoroughly quantified. Analyzing 100,000 paintings and data on 2,000 artists from the 13th to 21st centuries, the study reveals that the lightness of the paintings exhibited an interesting U-shaped pattern mirroring g... |
0806.0690 | Vladimir Ivancevic | Vladimir Ivancevic, Eugene Aidman, Leong Yen and Darryn Reid | Phase Transitions, Chaos and Joint Action in the Life Space Foam | 20 pages, no figures, elsart | null | null | null | q-bio.NC q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper extends our recently developed Life Space Foam (LSF) model of
motivated cognitive dynamics \cite{IA}. LSF uses adaptive path integrals to
generate Lewinian force--fields on smooth manifolds, in order to characterize
the dynamics of individual goal--directed action. According to explanatory
theories growing... | [
{
"created": "Wed, 4 Jun 2008 05:06:16 GMT",
"version": "v1"
}
] | 2008-06-05 | [
[
"Ivancevic",
"Vladimir",
""
],
[
"Aidman",
"Eugene",
""
],
[
"Yen",
"Leong",
""
],
[
"Reid",
"Darryn",
""
]
] | This paper extends our recently developed Life Space Foam (LSF) model of motivated cognitive dynamics \cite{IA}. LSF uses adaptive path integrals to generate Lewinian force--fields on smooth manifolds, in order to characterize the dynamics of individual goal--directed action. According to explanatory theories growing i... |
2112.08961 | Holger Maier | Dominik Thalmeier, Gregor Miller, Elida Schneltzer, Anja Hurt, Martin
Hrab\v{e} de Angelis, Lore Becker, Christian L. M\"uller, Holger Maier | Objective hearing threshold identification from auditory brainstem
response measurements using supervised and self-supervised approaches | 41 pages, 17 figures | BMC Neurosci 23, 81 (2022) | 10.1186/s12868-022-00758-0 | null | q-bio.NC cs.LG q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Hearing loss is a major health problem and psychological burden in humans.
Mouse models offer a possibility to elucidate genes involved in the underlying
developmental and pathophysiological mechanisms of hearing impairment. To this
end, large-scale mouse phenotyping programs include auditory phenotyping of
single-ge... | [
{
"created": "Thu, 16 Dec 2021 15:24:31 GMT",
"version": "v1"
}
] | 2023-01-12 | [
[
"Thalmeier",
"Dominik",
""
],
[
"Miller",
"Gregor",
""
],
[
"Schneltzer",
"Elida",
""
],
[
"Hurt",
"Anja",
""
],
[
"de Angelis",
"Martin Hrabě",
""
],
[
"Becker",
"Lore",
""
],
[
"Müller",
"Christian L.",
"... | Hearing loss is a major health problem and psychological burden in humans. Mouse models offer a possibility to elucidate genes involved in the underlying developmental and pathophysiological mechanisms of hearing impairment. To this end, large-scale mouse phenotyping programs include auditory phenotyping of single-gene... |
1703.05406 | Andrew Sornborger | Yuxiu Shao, Andrew T. Sornborger, Louis Tao | A Pulse-Gated, Predictive Neural Circuit | This invited paper was presented at the 50th Asilomar Conference on
Signals, Systems and Computers | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent evidence suggests that neural information is encoded in packets and
may be flexibly routed from region to region. We have hypothesized that neural
circuits are split into sub-circuits where one sub-circuit controls information
propagation via pulse gating and a second sub-circuit processes graded
information u... | [
{
"created": "Wed, 15 Mar 2017 22:25:29 GMT",
"version": "v1"
}
] | 2017-03-17 | [
[
"Shao",
"Yuxiu",
""
],
[
"Sornborger",
"Andrew T.",
""
],
[
"Tao",
"Louis",
""
]
] | Recent evidence suggests that neural information is encoded in packets and may be flexibly routed from region to region. We have hypothesized that neural circuits are split into sub-circuits where one sub-circuit controls information propagation via pulse gating and a second sub-circuit processes graded information und... |
1907.09841 | Chun Tung Chou | Chun Tung Chou | Using biochemical circuits to approximately compute log-likelihood ratio
for detecting persistent signals | null | IEEE Access, 2021 | 10.1109/ACCESS.2021.3113377 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Given that biochemical circuits can process information by using analog
computation, a question is: What can biochemical circuits compute? This paper
considers the problem of using biochemical circuits to distinguish persistent
signals from transient ones. We define a statistical detection problem over a
reaction pat... | [
{
"created": "Tue, 23 Jul 2019 12:34:49 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Sep 2021 07:29:41 GMT",
"version": "v10"
},
{
"created": "Fri, 26 Jul 2019 04:06:52 GMT",
"version": "v2"
},
{
"created": "Thu, 19 Dec 2019 01:13:53 GMT",
"version": "v3"
},
{
"... | 2021-09-20 | [
[
"Chou",
"Chun Tung",
""
]
] | Given that biochemical circuits can process information by using analog computation, a question is: What can biochemical circuits compute? This paper considers the problem of using biochemical circuits to distinguish persistent signals from transient ones. We define a statistical detection problem over a reaction pathw... |
2104.05645 | Jaime Ashander | Jaime Ashander, Kailin Kroetz, Rebecca S Epanchin-Niell, Nicholas B.
D. Phelps, Robert G Haight, Laura E. Dee | Guiding large-scale management of invasive species using network metrics | 40 pages, 8 figures, 7 tables | null | 10.1038/s41893-022-00913-9 | null | q-bio.QM physics.soc-ph q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Complex socio-environmental interdependencies drive biological invasions,
causing damages across large spatial scales. For widespread invasions,
targeting of management activities based on optimization approaches may fail
due to computational or data constraints. Here we evaluate an alternative
approach that embraces... | [
{
"created": "Mon, 12 Apr 2021 17:10:57 GMT",
"version": "v1"
},
{
"created": "Tue, 31 May 2022 17:02:59 GMT",
"version": "v2"
}
] | 2022-06-07 | [
[
"Ashander",
"Jaime",
""
],
[
"Kroetz",
"Kailin",
""
],
[
"Epanchin-Niell",
"Rebecca S",
""
],
[
"Phelps",
"Nicholas B. D.",
""
],
[
"Haight",
"Robert G",
""
],
[
"Dee",
"Laura E.",
""
]
] | Complex socio-environmental interdependencies drive biological invasions, causing damages across large spatial scales. For widespread invasions, targeting of management activities based on optimization approaches may fail due to computational or data constraints. Here we evaluate an alternative approach that embraces c... |
1905.00734 | Sheryl Chang | Sheryl L. Chang, Mahendra Piraveenan, Mikhail Prokopenko | The effects of imitation dynamics on vaccination behaviours in
SIR-network model | 23 pages, 11 figures | International Journal of Environmental Research and Public Health,
16(14), 2477, 2019 | 10.3390/ijerph16142477 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a series of SIR-network models, extended with a game-theoretic
treatment of imitation dynamics which result from regular population mobility
across residential and work areas and the ensuing interactions. Each considered
SIR-network model captures a class of vaccination behaviours influenced by
epidemic ch... | [
{
"created": "Wed, 1 May 2019 06:00:16 GMT",
"version": "v1"
},
{
"created": "Wed, 8 May 2019 04:02:13 GMT",
"version": "v2"
},
{
"created": "Mon, 13 May 2019 02:18:24 GMT",
"version": "v3"
}
] | 2019-11-14 | [
[
"Chang",
"Sheryl L.",
""
],
[
"Piraveenan",
"Mahendra",
""
],
[
"Prokopenko",
"Mikhail",
""
]
] | We present a series of SIR-network models, extended with a game-theoretic treatment of imitation dynamics which result from regular population mobility across residential and work areas and the ensuing interactions. Each considered SIR-network model captures a class of vaccination behaviours influenced by epidemic char... |
2303.04624 | Yutaka Nishiyama | Yutaka Nishiyama | A Dynamic Interference Model for Benham's Top | 10 pages, 12 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | It remains a mystery why colors emerge from the black-and-white pattern of a
Benham's top. This article is an extension of one I published in 1979. Here I
discuss in greater depth the reasons for manifestations of subjective color,
with a focus on my own hypothesis, namely, that two successive stimuli are
shifted in ... | [
{
"created": "Wed, 25 Jan 2023 13:24:19 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Mar 2023 02:16:22 GMT",
"version": "v2"
},
{
"created": "Sat, 18 Mar 2023 08:54:59 GMT",
"version": "v3"
}
] | 2023-03-21 | [
[
"Nishiyama",
"Yutaka",
""
]
] | It remains a mystery why colors emerge from the black-and-white pattern of a Benham's top. This article is an extension of one I published in 1979. Here I discuss in greater depth the reasons for manifestations of subjective color, with a focus on my own hypothesis, namely, that two successive stimuli are shifted in ph... |
1807.11036 | Sandro Sozzo | Diederik Aerts, Massimiliano Sassoli de Bianchi, Sandro Sozzo, Tomas
Veloz | Modeling Human Decision-making: An Overview of the Brussels Quantum
Approach | 25 pages, Latex, 2 figures, published in Foundations of Science | Foundations of Science 26, pp. 27-54 (2021) | 10.1007/s10699-018-9559-x | null | q-bio.NC quant-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present the fundamentals of the quantum theoretical approach we have
developed in the last decade to model cognitive phenomena that resisted
modeling by means of classical logical and probabilistic structures, like
Boolean, Kolmogorovian and, more generally, set theoretical structures. We
firstly sketch the operat... | [
{
"created": "Sun, 29 Jul 2018 10:21:59 GMT",
"version": "v1"
}
] | 2023-02-27 | [
[
"Aerts",
"Diederik",
""
],
[
"de Bianchi",
"Massimiliano Sassoli",
""
],
[
"Sozzo",
"Sandro",
""
],
[
"Veloz",
"Tomas",
""
]
] | We present the fundamentals of the quantum theoretical approach we have developed in the last decade to model cognitive phenomena that resisted modeling by means of classical logical and probabilistic structures, like Boolean, Kolmogorovian and, more generally, set theoretical structures. We firstly sketch the operatio... |
2201.05431 | Sebastian Lotter | Sebastian Lotter, Maximilian Sch\"afer, Robert Schober | Molecular Noise In Synaptic Communication | 16 pages, 13 figures, 2 tables. Published in IEEE Transactions on
NanoBioscience. This article is the extended journal version of the
conference paper arXiv:2109.14986 | null | 10.1109/TNB.2022.3183692 | null | q-bio.SC cs.ET | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In synaptic molecular communication (MC), the activation of postsynaptic
receptors by neurotransmitters (NTs) is governed by a stochastic
reaction-diffusion process. This randomness of synaptic MC contributes to the
randomness of the electrochemical downstream signal in the postsynaptic cell,
called postsynaptic memb... | [
{
"created": "Fri, 14 Jan 2022 13:04:11 GMT",
"version": "v1"
},
{
"created": "Tue, 14 Jun 2022 10:02:13 GMT",
"version": "v2"
},
{
"created": "Mon, 16 Jan 2023 13:41:13 GMT",
"version": "v3"
}
] | 2023-01-18 | [
[
"Lotter",
"Sebastian",
""
],
[
"Schäfer",
"Maximilian",
""
],
[
"Schober",
"Robert",
""
]
] | In synaptic molecular communication (MC), the activation of postsynaptic receptors by neurotransmitters (NTs) is governed by a stochastic reaction-diffusion process. This randomness of synaptic MC contributes to the randomness of the electrochemical downstream signal in the postsynaptic cell, called postsynaptic membra... |
0708.4065 | Manoj Gopalakrishnan | Shivam Ghosh (St.Stephens College, Delhi), Manoj Gopalakrishnan (HRI,
Allahabad), Kimberly Forsten-Williams (Virginia Tech) | Self-consistent theory of reversible ligand binding to a spherical cell | 23 pages with 4 figures | Phys. Biol. 4 344-354 (2007) | 10.1088/1478-3975/4/4/010 | null | q-bio.SC cond-mat.stat-mech q-bio.QM | null | In this article, we study the kinetics of reversible ligand binding to
receptors on a spherical cell surface using a self-consistent stochastic
theory. Binding, dissociation, diffusion and rebinding of ligands are
incorporated into the theory in a systematic manner. We derive explicitly the
time evolution of the liga... | [
{
"created": "Thu, 30 Aug 2007 03:15:42 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Ghosh",
"Shivam",
"",
"St.Stephens College, Delhi"
],
[
"Gopalakrishnan",
"Manoj",
"",
"HRI,\n Allahabad"
],
[
"Forsten-Williams",
"Kimberly",
"",
"Virginia Tech"
]
] | In this article, we study the kinetics of reversible ligand binding to receptors on a spherical cell surface using a self-consistent stochastic theory. Binding, dissociation, diffusion and rebinding of ligands are incorporated into the theory in a systematic manner. We derive explicitly the time evolution of the ligand... |
1408.5629 | Nathan Baker | Huan Lei, Xiu Yang, Bin Zheng, Guang Lin, Nathan A. Baker | Quantifying the influence of conformational uncertainty in biomolecular
solvation | Accepted by Multiscale Modeling & Simulation | Multiscale.Model.Simul 13 (2015) 1327-1353 | 10.1137/140981587 | null | q-bio.BM stat.AP | http://creativecommons.org/licenses/by/4.0/ | Biomolecules exhibit conformational fluctuations near equilibrium states,
inducing uncertainty in various biological properties in a dynamic way. We have
developed a general method to quantify the uncertainty of target properties
induced by conformational fluctuations. Using a generalized polynomial chaos
(gPC) expan... | [
{
"created": "Sun, 24 Aug 2014 19:40:55 GMT",
"version": "v1"
},
{
"created": "Mon, 31 Aug 2015 13:39:09 GMT",
"version": "v2"
}
] | 2018-10-02 | [
[
"Lei",
"Huan",
""
],
[
"Yang",
"Xiu",
""
],
[
"Zheng",
"Bin",
""
],
[
"Lin",
"Guang",
""
],
[
"Baker",
"Nathan A.",
""
]
] | Biomolecules exhibit conformational fluctuations near equilibrium states, inducing uncertainty in various biological properties in a dynamic way. We have developed a general method to quantify the uncertainty of target properties induced by conformational fluctuations. Using a generalized polynomial chaos (gPC) expansi... |
q-bio/0602014 | Lucilla de Arcangelis | Lucilla de Arcangelis, Carla Perrone-Capano, Hans J. Herrmann | Self-Organized Criticality model for Brain Plasticity | 4 pages, 3 figures | null | 10.1103/PhysRevLett.96.028107 | null | q-bio.NC | null | Networks of living neurons exhibit an avalanche mode of activity,
experimentally found in organotypic cultures. Here we present a model based on
self-organized criticality and taking into account brain plasticity, which is
able to reproduce the spectrum of electroencephalograms (EEG). The model
consists in an electri... | [
{
"created": "Sun, 12 Feb 2006 18:40:20 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"de Arcangelis",
"Lucilla",
""
],
[
"Perrone-Capano",
"Carla",
""
],
[
"Herrmann",
"Hans J.",
""
]
] | Networks of living neurons exhibit an avalanche mode of activity, experimentally found in organotypic cultures. Here we present a model based on self-organized criticality and taking into account brain plasticity, which is able to reproduce the spectrum of electroencephalograms (EEG). The model consists in an electrica... |
1702.03492 | Xaq Pitkow | Xaq Pitkow and Dora Angelaki | How the brain might work: statistics flowing in redundant population
codes | 11 pages, 3 figures, contribution related to workshop called "How the
brain works" at the University of Copenhagen, 14-16 Sept 2016 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is widely believed that the brain performs approximate probabilistic
inference to estimate causal variables in the world from ambiguous sensory
data. To understand these computations, we need to analyze how information is
represented and transformed by the actions of nonlinear recurrent neural
networks. We propose... | [
{
"created": "Sun, 12 Feb 2017 05:32:29 GMT",
"version": "v1"
},
{
"created": "Mon, 15 May 2017 04:12:09 GMT",
"version": "v2"
}
] | 2017-05-16 | [
[
"Pitkow",
"Xaq",
""
],
[
"Angelaki",
"Dora",
""
]
] | It is widely believed that the brain performs approximate probabilistic inference to estimate causal variables in the world from ambiguous sensory data. To understand these computations, we need to analyze how information is represented and transformed by the actions of nonlinear recurrent neural networks. We propose t... |
1703.10058 | Srividya Iyer-Biswas | Farshid Jafarpour, Michael Vennettilli, and Srividya Iyer-Biswas | Biological timekeeping in the presence of stochasticity | null | null | null | null | q-bio.MN cond-mat.soft cond-mat.stat-mech q-bio.CB q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Causal ordering of key events in the cell cycle is essential for proper
functioning of an organism. Yet, it remains a mystery how a specific temporal
program of events is maintained despite ineluctable stochasticity in the
biochemical dynamics which dictate timing of cellular events. We propose that
if a change of ce... | [
{
"created": "Tue, 28 Mar 2017 15:55:56 GMT",
"version": "v1"
}
] | 2017-03-30 | [
[
"Jafarpour",
"Farshid",
""
],
[
"Vennettilli",
"Michael",
""
],
[
"Iyer-Biswas",
"Srividya",
""
]
] | Causal ordering of key events in the cell cycle is essential for proper functioning of an organism. Yet, it remains a mystery how a specific temporal program of events is maintained despite ineluctable stochasticity in the biochemical dynamics which dictate timing of cellular events. We propose that if a change of cell... |
1511.00182 | Andrew Elliott | Andrew Elliott and Elizabeth Leicht and Alan Whitmore and Gesine
Reinert and Felix Reed-Tsochas | A Nonparametric Significance Test for Sampled Networks | Bioinformatics 2017 | Bioinformatics 2017 | 10.1093/bioinformatics/btx419 | null | q-bio.QM physics.data-an q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Our work is motivated by an interest in constructing a protein-protein
interaction network that captures key features associated with Parkinson's
disease. While there is an abundance of subnetwork construction methods
available, it is often far from obvious which subnetwork is the most suitable
starting point for fur... | [
{
"created": "Sat, 31 Oct 2015 21:48:47 GMT",
"version": "v1"
},
{
"created": "Fri, 2 Sep 2016 02:40:57 GMT",
"version": "v2"
},
{
"created": "Mon, 9 Oct 2017 13:05:55 GMT",
"version": "v3"
}
] | 2017-10-11 | [
[
"Elliott",
"Andrew",
""
],
[
"Leicht",
"Elizabeth",
""
],
[
"Whitmore",
"Alan",
""
],
[
"Reinert",
"Gesine",
""
],
[
"Reed-Tsochas",
"Felix",
""
]
] | Our work is motivated by an interest in constructing a protein-protein interaction network that captures key features associated with Parkinson's disease. While there is an abundance of subnetwork construction methods available, it is often far from obvious which subnetwork is the most suitable starting point for furth... |
2202.09388 | Marc Aur\`ele Gilles | Marc Aur\`ele Gilles and Amit Singer | A Molecular Prior Distribution for Bayesian Inference Based on Wilson
Statistics | null | null | null | null | q-bio.QM cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background and Objective: Wilson statistics describe well the power spectrum
of proteins at high frequencies. Therefore, it has found several applications
in structural biology, e.g., it is the basis for sharpening steps used in
cryogenic electron microscopy (cryo-EM). A recent paper gave the first rigorous
proof of ... | [
{
"created": "Fri, 18 Feb 2022 19:14:03 GMT",
"version": "v1"
},
{
"created": "Mon, 2 May 2022 14:48:23 GMT",
"version": "v2"
}
] | 2022-05-03 | [
[
"Gilles",
"Marc Aurèle",
""
],
[
"Singer",
"Amit",
""
]
] | Background and Objective: Wilson statistics describe well the power spectrum of proteins at high frequencies. Therefore, it has found several applications in structural biology, e.g., it is the basis for sharpening steps used in cryogenic electron microscopy (cryo-EM). A recent paper gave the first rigorous proof of Wi... |
2008.10382 | Sarah Tebeka | Sarah Tebeka, Yann Le Strat, Alix De Premorel Higgons, Alexandra
Benachi, Marc Dommergues, Gilles Kayem, Jacques Lepercq, Dominique Luton,
Laurent Mandelbrot, Yves Ville, Nicolas Ramoz, Sophie Tezenas du Montcel,
IGEDEPP Groups, Jimmy Mullaert, Caroline Dubertret | Prevalence and incidence of postpartum depression and environmental
factors: the IGEDEPP cohort | 34 pages, 6 tables | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: IGEDEPP (Interaction of Gene and Environment of Depression during
PostPartum) is a prospective multicenter cohort study of 3,310 Caucasian women
who gave birth between 2011 and 2016, with follow-up until one year postpartum.
The aim of the current study is to describe the cohort and estimate the
prevalenc... | [
{
"created": "Fri, 21 Aug 2020 08:28:02 GMT",
"version": "v1"
}
] | 2020-08-25 | [
[
"Tebeka",
"Sarah",
""
],
[
"Strat",
"Yann Le",
""
],
[
"Higgons",
"Alix De Premorel",
""
],
[
"Benachi",
"Alexandra",
""
],
[
"Dommergues",
"Marc",
""
],
[
"Kayem",
"Gilles",
""
],
[
"Lepercq",
"Jacques",
"... | Background: IGEDEPP (Interaction of Gene and Environment of Depression during PostPartum) is a prospective multicenter cohort study of 3,310 Caucasian women who gave birth between 2011 and 2016, with follow-up until one year postpartum. The aim of the current study is to describe the cohort and estimate the prevalence ... |
1510.05918 | Shi Huang | Shi Huang | New thoughts on an old riddle: what determines genetic diversity within
and between species? | 23 pages, 1 figure | Genomics, 108: 3-10 (2016) | 10.1016/j.ygeno.2016.01.008 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The question of what determines genetic diversity both between and within
species has long remained unsolved by the modern evolutionary theory (MET).
However, it has not deterred researchers from producing interpretations of
genetic diversity by using MET. We here examine the two key experimental
observations of gene... | [
{
"created": "Tue, 20 Oct 2015 16:36:25 GMT",
"version": "v1"
},
{
"created": "Wed, 21 Oct 2015 04:35:48 GMT",
"version": "v2"
}
] | 2019-04-04 | [
[
"Huang",
"Shi",
""
]
] | The question of what determines genetic diversity both between and within species has long remained unsolved by the modern evolutionary theory (MET). However, it has not deterred researchers from producing interpretations of genetic diversity by using MET. We here examine the two key experimental observations of geneti... |
1704.08889 | Yoo Ah Kim | Phuong Dao, Yoo-Ah Kim, Damian Wojtowicz, Sanna Madan, Roded Sharan,
and Teresa M. Przytycka | BeWith: A Between-Within Method to Discover Relationships between Cancer
Modules via Integrated Analysis of Mutual Exclusivity, Co-occurrence and
Functional Interactions | null | null | 10.1371/journal.pcbi.1005695 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The analysis of the mutational landscape of cancer, including mutual
exclusivity and co-occurrence of mutations, has been instrumental in studying
the disease. We hypothesized that exploring the interplay between
co-occurrence, mutual exclusivity, and functional interactions between genes
will further improve our und... | [
{
"created": "Fri, 28 Apr 2017 12:08:12 GMT",
"version": "v1"
}
] | 2018-02-07 | [
[
"Dao",
"Phuong",
""
],
[
"Kim",
"Yoo-Ah",
""
],
[
"Wojtowicz",
"Damian",
""
],
[
"Madan",
"Sanna",
""
],
[
"Sharan",
"Roded",
""
],
[
"Przytycka",
"Teresa M.",
""
]
] | The analysis of the mutational landscape of cancer, including mutual exclusivity and co-occurrence of mutations, has been instrumental in studying the disease. We hypothesized that exploring the interplay between co-occurrence, mutual exclusivity, and functional interactions between genes will further improve our under... |
2009.02081 | Selma Souihel | Selma Souihel (BIOVISION), Bruno Cessac (BIOVISION) | On the potential role of lateral connectivity in retinal anticipation | null | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyse the potential effects of lateral connectivity (amacrine cells and
gap junctions) on motion anticipation in the retina. Our main result is that
lateral connectivity can-under conditions analysed in the paper-trigger a wave
of activity enhancing the anticipation mechanism provided by local gain control
[8, 1... | [
{
"created": "Fri, 4 Sep 2020 09:18:41 GMT",
"version": "v1"
}
] | 2020-09-07 | [
[
"Souihel",
"Selma",
"",
"BIOVISION"
],
[
"Cessac",
"Bruno",
"",
"BIOVISION"
]
] | We analyse the potential effects of lateral connectivity (amacrine cells and gap junctions) on motion anticipation in the retina. Our main result is that lateral connectivity can-under conditions analysed in the paper-trigger a wave of activity enhancing the anticipation mechanism provided by local gain control [8, 17]... |
1404.6134 | Georgios Tsaousis N | Katerina C. Nastou, Georgios N. Tsaousis, Kimon E. Kremizas, Zoi I.
Litou and Stavros J. Hamodrakas | The Human Plasma Membrane Peripherome: Visualization and Analysis of
Interactions | 39 pages, 5 figures, 3 supplement figures, under review in BMRI | BioMed Research International, vol. 2014, Article ID 397145, 12
pages, 2014 | 10.1155/2014/397145 | null | q-bio.BM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A major part of membrane function is conducted by proteins, both integral and
peripheral. Peripheral membrane proteins temporarily adhere to biological
membranes, either to the lipid bilayer or to integral membrane proteins with
non-covalent interactions. The aim of this study was to construct and analyze
the interac... | [
{
"created": "Thu, 24 Apr 2014 14:44:45 GMT",
"version": "v1"
}
] | 2014-06-27 | [
[
"Nastou",
"Katerina C.",
""
],
[
"Tsaousis",
"Georgios N.",
""
],
[
"Kremizas",
"Kimon E.",
""
],
[
"Litou",
"Zoi I.",
""
],
[
"Hamodrakas",
"Stavros J.",
""
]
] | A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with non-covalent interactions. The aim of this study was to construct and analyze the interacti... |
q-bio/0702055 | Indrani Bose | Rajesh Karmakar and Indrani Bose | Positive Feedback, Stochasticity and Genetic Competence | Accepted for publication in Physical Biology | Phys. Biol. 4 (2007) 29--37 | 10.1088/1478-3975/4/1/004 | null | q-bio.QM cond-mat.stat-mech q-bio.OT | null | A single gene, regulating its own expression via a positive feedback loop,
constitutes a common motif in gene regulatory networks and signalling cascades.
Recent experiments on the development of competence in the bacterial population
\emph{B. subtilis} show that the autoregulatory genetic module by itself can
give r... | [
{
"created": "Mon, 26 Feb 2007 09:59:54 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Karmakar",
"Rajesh",
""
],
[
"Bose",
"Indrani",
""
]
] | A single gene, regulating its own expression via a positive feedback loop, constitutes a common motif in gene regulatory networks and signalling cascades. Recent experiments on the development of competence in the bacterial population \emph{B. subtilis} show that the autoregulatory genetic module by itself can give ris... |
2004.04741 | George Mohler | Andrea L. Bertozzi, Elisa Franco, George Mohler, Martin B. Short,
Daniel Sledge | The challenges of modeling and forecasting the spread of COVID-19 | null | null | 10.1073/pnas.2006520117 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present three data driven model-types for COVID-19 with a minimal number
of parameters to provide insights into the spread of the disease that may be
used for developing policy responses. The first is exponential growth, widely
studied in analysis of early-time data. The second is a self-exciting branching
process... | [
{
"created": "Thu, 9 Apr 2020 16:22:23 GMT",
"version": "v1"
}
] | 2022-05-25 | [
[
"Bertozzi",
"Andrea L.",
""
],
[
"Franco",
"Elisa",
""
],
[
"Mohler",
"George",
""
],
[
"Short",
"Martin B.",
""
],
[
"Sledge",
"Daniel",
""
]
] | We present three data driven model-types for COVID-19 with a minimal number of parameters to provide insights into the spread of the disease that may be used for developing policy responses. The first is exponential growth, widely studied in analysis of early-time data. The second is a self-exciting branching process m... |
1409.6744 | Antonio Galves | C. D. Vargas, M. L. Rangel and A. Galves | Predicting upcoming actions by observation: some facts, models and
challenges | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Predicting another person's upcoming action to build an appropriate response
is a regular occurrence in the domain of motor control. In this review we
discuss conceptual and experimental approaches aiming at the neural basis of
predicting and learning to predict upcoming movements by their observation.
| [
{
"created": "Tue, 23 Sep 2014 20:22:50 GMT",
"version": "v1"
}
] | 2014-09-25 | [
[
"Vargas",
"C. D.",
""
],
[
"Rangel",
"M. L.",
""
],
[
"Galves",
"A.",
""
]
] | Predicting another person's upcoming action to build an appropriate response is a regular occurrence in the domain of motor control. In this review we discuss conceptual and experimental approaches aiming at the neural basis of predicting and learning to predict upcoming movements by their observation. |
1611.00716 | Alfred Bennun BA | Alfred Bennun | The assay of the hydration shell dynamics on the turnover of the active
site of CF1-ATPase | 13 pages, 3 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Previous kinetic models had assumed that the reaction medium was reacting at
random and without a turnover associated to thermodynamics exchanges, with a
rigid active site on the enzyme. The experimental studies show that coupling
factor 1 (CF1) from spinach chloroplasts has latent ATPase activity, which
become expre... | [
{
"created": "Thu, 7 Jul 2016 21:45:49 GMT",
"version": "v1"
}
] | 2016-11-03 | [
[
"Bennun",
"Alfred",
""
]
] | Previous kinetic models had assumed that the reaction medium was reacting at random and without a turnover associated to thermodynamics exchanges, with a rigid active site on the enzyme. The experimental studies show that coupling factor 1 (CF1) from spinach chloroplasts has latent ATPase activity, which become express... |
1205.2919 | Christos Skiadas H | Christos H. Skiadas and Charilaos Skiadas | Estimating the Healthy Life Expectancy from the Health State Function of
a Population in Connection to the Life Expectancy at Birth | 17 pages, 8 figures, 4 tables | null | null | null | q-bio.PE nlin.AO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Following our previous works on the health state of a population and the
related health state function we proceed in developing a method to estimate the
Healthy Life Expectancy in connection to the relative impact of the Mortality
Area in the health state function graph. The resulting tools are applied to the
data se... | [
{
"created": "Mon, 14 May 2012 00:33:54 GMT",
"version": "v1"
}
] | 2012-05-15 | [
[
"Skiadas",
"Christos H.",
""
],
[
"Skiadas",
"Charilaos",
""
]
] | Following our previous works on the health state of a population and the related health state function we proceed in developing a method to estimate the Healthy Life Expectancy in connection to the relative impact of the Mortality Area in the health state function graph. The resulting tools are applied to the data sets... |
1603.04721 | Claus Metzner | Patrick Krauss, Konstantin Tziridis, Achim Schilling, Claus Metzner
and Holger Schulze | Stochastic resonance controlled upregulation of internal noise after
hearing loss as a putative correlate of tinnitus-related neuronal
hyperactivity | null | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Subjective tinnitus (ST) is generally assumed to be a consequence of hearing
loss (HL). In animal studies acoustic trauma can lead to behavioral signs of
ST, in human studies ST patients without increased hearing thresholds were
found to suffer from so called hidden HL. Additionally, ST is correlated with
pathologica... | [
{
"created": "Tue, 15 Mar 2016 15:27:19 GMT",
"version": "v1"
}
] | 2016-03-16 | [
[
"Krauss",
"Patrick",
""
],
[
"Tziridis",
"Konstantin",
""
],
[
"Schilling",
"Achim",
""
],
[
"Metzner",
"Claus",
""
],
[
"Schulze",
"Holger",
""
]
] | Subjective tinnitus (ST) is generally assumed to be a consequence of hearing loss (HL). In animal studies acoustic trauma can lead to behavioral signs of ST, in human studies ST patients without increased hearing thresholds were found to suffer from so called hidden HL. Additionally, ST is correlated with pathologicall... |
1205.0802 | Matjaz Perc | Yongkui Liu, Xiaojie Chen, Lin Zhang, Long Wang, Matjaz Perc | Win-stay-lose-learn promotes cooperation in the spatial prisoner's
dilemma game | 14 pages, 6 figures; accepted for publication in PLoS ONE | PLoS ONE 7 (2012) e30689 | 10.1371/journal.pone.0030689 | null | q-bio.PE cond-mat.stat-mech physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Holding on to one's strategy is natural and common if the later warrants
success and satisfaction. This goes against widespread simulation practices of
evolutionary games, where players frequently consider changing their strategy
even though their payoffs may be marginally different than those of the other
players. I... | [
{
"created": "Thu, 3 May 2012 19:56:36 GMT",
"version": "v1"
}
] | 2012-05-04 | [
[
"Liu",
"Yongkui",
""
],
[
"Chen",
"Xiaojie",
""
],
[
"Zhang",
"Lin",
""
],
[
"Wang",
"Long",
""
],
[
"Perc",
"Matjaz",
""
]
] | Holding on to one's strategy is natural and common if the later warrants success and satisfaction. This goes against widespread simulation practices of evolutionary games, where players frequently consider changing their strategy even though their payoffs may be marginally different than those of the other players. Ins... |
1610.09297 | Antonio Di Crescenzo | Antonio Di Crescenzo, Serena Spina | Analysis of a growth model inspired by Gompertz and Korf laws, and an
analogous birth-death process | 25 pages, 11 figures | Mathematical Biosciences (2016), Vol. 282, p. 121-134 | 10.1016/j.mbs.2016.10.005 | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a new deterministic growth model which captures certain features
of both the Gompertz and Korf laws. We investigate its main properties, with
special attention to the correction factor, the relative growth rate, the
inflection point, the maximum specific growth rate, the lag time and the
threshold crossing... | [
{
"created": "Fri, 28 Oct 2016 16:20:59 GMT",
"version": "v1"
}
] | 2016-10-31 | [
[
"Di Crescenzo",
"Antonio",
""
],
[
"Spina",
"Serena",
""
]
] | We propose a new deterministic growth model which captures certain features of both the Gompertz and Korf laws. We investigate its main properties, with special attention to the correction factor, the relative growth rate, the inflection point, the maximum specific growth rate, the lag time and the threshold crossing p... |
q-bio/0401032 | Svyatoslav Gabuda Petrovich | R.G.Khlebopros, V.A.Slepkov, V.G.Sukhovolsky, Y.V.Mironov,
V.E.Fedorov, S.P.Gabuda | Mathematical model of solid tumor formation | 7 pages, 5 figures, key words:tumour growth, mathematical model,
local interaction | null | null | null | q-bio.CB | null | The problem of the onset and growth of solid tumour in homogeneous tissue is
regarded using an approach based on local interaction between the tumoral and
the sane tissue cells. The characteristic sizes and growth rates of spherical
tumours, the points of the beginning and the end of spherical growth, and the
further... | [
{
"created": "Fri, 23 Jan 2004 14:59:51 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Khlebopros",
"R. G.",
""
],
[
"Slepkov",
"V. A.",
""
],
[
"Sukhovolsky",
"V. G.",
""
],
[
"Mironov",
"Y. V.",
""
],
[
"Fedorov",
"V. E.",
""
],
[
"Gabuda",
"S. P.",
""
]
] | The problem of the onset and growth of solid tumour in homogeneous tissue is regarded using an approach based on local interaction between the tumoral and the sane tissue cells. The characteristic sizes and growth rates of spherical tumours, the points of the beginning and the end of spherical growth, and the further d... |
2402.05903 | Giuseppe Vinci | Lauren Miako Beede and Giuseppe Vinci | Neuronal functional connectivity graph estimation with the R package
neurofuncon | 7 pages, 5 figures | null | null | null | q-bio.NC stat.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Researchers continue exploring neurons' intricate patterns of activity in the
cerebral visual cortex in response to visual stimuli. The way neurons
communicate and optimize their interactions with each other under different
experimental conditions remains a topic of active investigation. Probabilistic
Graphical Model... | [
{
"created": "Thu, 8 Feb 2024 18:42:04 GMT",
"version": "v1"
}
] | 2024-02-09 | [
[
"Beede",
"Lauren Miako",
""
],
[
"Vinci",
"Giuseppe",
""
]
] | Researchers continue exploring neurons' intricate patterns of activity in the cerebral visual cortex in response to visual stimuli. The way neurons communicate and optimize their interactions with each other under different experimental conditions remains a topic of active investigation. Probabilistic Graphical Models ... |
1001.5235 | Alexander Dobrinevski | A. Dobrinevski and E. Frey | Extinction in neutrally stable stochastic Lotka-Volterra models | 14 pages, 7 figures | Phys. Rev. E 85, 051903 (2012) | 10.1103/PhysRevE.85.051903 | LMU-ASC 03/10 | q-bio.PE cond-mat.stat-mech q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Populations of competing biological species exhibit a fascinating interplay
between the nonlinear dynamics of evolutionary selection forces and random
fluctuations arising from the stochastic nature of the interactions. The
processes leading to extinction of species, whose understanding is a key
component in the stud... | [
{
"created": "Thu, 28 Jan 2010 18:11:01 GMT",
"version": "v1"
},
{
"created": "Thu, 19 Apr 2012 08:18:15 GMT",
"version": "v2"
}
] | 2012-05-08 | [
[
"Dobrinevski",
"A.",
""
],
[
"Frey",
"E.",
""
]
] | Populations of competing biological species exhibit a fascinating interplay between the nonlinear dynamics of evolutionary selection forces and random fluctuations arising from the stochastic nature of the interactions. The processes leading to extinction of species, whose understanding is a key component in the study ... |
2403.09723 | Michele Mastella | Michele Mastella and Tesse Tiemens and Elisabetta Chicca | Texture Recognition Using a Biologically Plausible Spiking Phase-Locked
Loop Model for Spike Train Frequency Decomposition | 16 pages, 4 figures, journal | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we present a novel spiking neural network model designed to
perform frequency decomposition of spike trains. Our model emulates neural
microcircuits theorized in the somatosensory cortex, rendering it a
biologically plausible candidate for decoding the spike trains observed in
tactile peripheral nerves... | [
{
"created": "Tue, 12 Mar 2024 13:28:39 GMT",
"version": "v1"
}
] | 2024-03-18 | [
[
"Mastella",
"Michele",
""
],
[
"Tiemens",
"Tesse",
""
],
[
"Chicca",
"Elisabetta",
""
]
] | In this paper, we present a novel spiking neural network model designed to perform frequency decomposition of spike trains. Our model emulates neural microcircuits theorized in the somatosensory cortex, rendering it a biologically plausible candidate for decoding the spike trains observed in tactile peripheral nerves. ... |
q-bio/0403030 | Max Shpak | Max Shpak, Peter Stadler, Gunter Wagner, and Lee Altenberg | Simon-Ando Decomposability and Fitness Landscapes | null | null | null | null | q-bio.PE | null | In this paper, we investigate fitness landscapes (under point mutation and
recombination) from the standpoint of whether the induced evolutionary dynamics
have a "fast-slow" time scale associated with the differences in relaxation
time between local quasi-equilibria and the global equilibrium. This dynamical
behavior... | [
{
"created": "Mon, 22 Mar 2004 18:52:58 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Shpak",
"Max",
""
],
[
"Stadler",
"Peter",
""
],
[
"Wagner",
"Gunter",
""
],
[
"Altenberg",
"Lee",
""
]
] | In this paper, we investigate fitness landscapes (under point mutation and recombination) from the standpoint of whether the induced evolutionary dynamics have a "fast-slow" time scale associated with the differences in relaxation time between local quasi-equilibria and the global equilibrium. This dynamical behavior h... |
q-bio/0601045 | Edoardo Milotti | Roberto Chignola, Chiara Dalla Pellegrina, Alessio Del Fabbro, Edoardo
Milotti | Thresholds, long delays and stability from generalized allosteric effect
in protein networks | 5 figures, submitted to Physica A | null | 10.1016/j.physa.2006.03.044 | null | q-bio.CB q-bio.SC | null | Post-transductional modifications tune the functions of proteins and regulate
the collective dynamics of biochemical networks that determine how cells
respond to environmental signals. For example, protein phosphorylation and
nitrosylation are well-known to play a pivotal role in the intracellular
transduction of act... | [
{
"created": "Thu, 26 Jan 2006 18:34:57 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Chignola",
"Roberto",
""
],
[
"Pellegrina",
"Chiara Dalla",
""
],
[
"Del Fabbro",
"Alessio",
""
],
[
"Milotti",
"Edoardo",
""
]
] | Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation are well-known to play a pivotal role in the intracellular transduction of activ... |
1009.5810 | Yvinec Romain M. | Michael C. Mackey and Marta Tyran-Kami\'nska and Romain Yvinec | Molecular Distributions in Gene Regulatory Dynamics | 14 pages, 12 figures. Conferences: "2010 Annual Meeting of The
Society of Mathematical Biology", Rio de Janeiro (Brazil), 24-29/07/2010.
"First International workshop on Differential and Integral Equations with
Applications in Biology and Medicine", Aegean University, Karlovassi, Samos
island (Greece), 6-10/09/... | Journal of Theoretical Biology 274 (2011), 84-96 | 10.1016/j.jtbi.2011.01.020 | null | q-bio.MN math.CA math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We show how one may analytically compute the stationary density of the
distribution of molecular constituents in populations of cells in the presence
of noise arising from either bursting transcription or translation, or noise in
degradation rates arising from low numbers of molecules. We have compared our
results wi... | [
{
"created": "Wed, 29 Sep 2010 09:07:44 GMT",
"version": "v1"
}
] | 2015-10-15 | [
[
"Mackey",
"Michael C.",
""
],
[
"Tyran-Kamińska",
"Marta",
""
],
[
"Yvinec",
"Romain",
""
]
] | We show how one may analytically compute the stationary density of the distribution of molecular constituents in populations of cells in the presence of noise arising from either bursting transcription or translation, or noise in degradation rates arising from low numbers of molecules. We have compared our results with... |
1407.3590 | Roman Zubarev A | Xueshu Xie, Roman A. Zubarev | Effects of low-level deuterium enrichment on bacterial growth | Accepted to PLoS One. Press embargo applies | Xie X, Zubarev RA (2014) Effects of Low-Level Deuterium Enrichment
on Bacterial Growth. PLoS ONE 9(7): e102071 | 10.1371/journal.pone.0102071 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Using very precise (up to 0.05%) measurements of the growth parameters for
bacteria E. coli grown on minimal media, we aimed to determine the lowest
deuterium concentration at which the adverse effects that are prominent at
higher enrichments start to become noticeable. Such a threshold was found at
0.5% D, a surpris... | [
{
"created": "Mon, 14 Jul 2014 10:16:36 GMT",
"version": "v1"
}
] | 2015-01-06 | [
[
"Xie",
"Xueshu",
""
],
[
"Zubarev",
"Roman A.",
""
]
] | Using very precise (up to 0.05%) measurements of the growth parameters for bacteria E. coli grown on minimal media, we aimed to determine the lowest deuterium concentration at which the adverse effects that are prominent at higher enrichments start to become noticeable. Such a threshold was found at 0.5% D, a surprisin... |
1110.5865 | Eric Werner | Eric Werner | Cancer Networks: A general theoretical and computational framework for
understanding cancer | Key words: Cancer networks, cene, cenome, developmental control
networks, stem cells, stem cell networks, cancer stem cells, stochastic stem
cell networks, metastases hierarchy, linear networks, exponential networks,
geometric cancer networks, cell signaling, cancer cell communication
networks, systems biology,... | null | null | null | q-bio.MN cs.CE cs.MA q-bio.CB q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a general computational theory of cancer and its developmental
dynamics. The theory is based on a theory of the architecture and function of
developmental control networks which guide the formation of multicellular
organisms. Cancer networks are special cases of developmental control networks.
Cancer resul... | [
{
"created": "Wed, 26 Oct 2011 18:07:37 GMT",
"version": "v1"
}
] | 2011-11-16 | [
[
"Werner",
"Eric",
""
]
] | We present a general computational theory of cancer and its developmental dynamics. The theory is based on a theory of the architecture and function of developmental control networks which guide the formation of multicellular organisms. Cancer networks are special cases of developmental control networks. Cancer results... |
1405.7856 | Jose Vilar | Jose M. G. Vilar | Entropy of leukemia on multidimensional morphological and molecular
landscapes | 15 pages, 4 figures, and supplementary information | Phys. Rev. X 4, 021038 (2014) | 10.1103/PhysRevX.4.021038 | null | q-bio.QM cond-mat.stat-mech physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Leukemia epitomizes the class of highly complex diseases that new
technologies aim to tackle by using large sets of single-cell level
information. Achieving such goal depends critically not only on experimental
techniques but also on approaches to interpret the data. A most pressing issue
is to identify the salient q... | [
{
"created": "Fri, 30 May 2014 13:26:11 GMT",
"version": "v1"
}
] | 2014-06-02 | [
[
"Vilar",
"Jose M. G.",
""
]
] | Leukemia epitomizes the class of highly complex diseases that new technologies aim to tackle by using large sets of single-cell level information. Achieving such goal depends critically not only on experimental techniques but also on approaches to interpret the data. A most pressing issue is to identify the salient qua... |
1507.08245 | Fran\c{c}ois Blanquart | Fran\c{c}ois Blanquart, Thomas Bataillon | Epistasis and the structure of fitness landscapes: are experimental
fitness landscapes compatible with Fisher's Geometric model? | Added an alternative ABC algorithm based on a set of summary
statistics | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The fitness landscape defines the relationship between genotypes and fitness
in a given environment, and underlies fundamental quantities such as the
distribution of selection coefficient, or the magnitude and type of epistasis.
A better understanding of variation of landscape structure across species and
environment... | [
{
"created": "Wed, 29 Jul 2015 18:08:11 GMT",
"version": "v1"
},
{
"created": "Tue, 15 Sep 2015 17:08:01 GMT",
"version": "v2"
},
{
"created": "Tue, 17 May 2016 14:44:56 GMT",
"version": "v3"
}
] | 2016-05-18 | [
[
"Blanquart",
"François",
""
],
[
"Bataillon",
"Thomas",
""
]
] | The fitness landscape defines the relationship between genotypes and fitness in a given environment, and underlies fundamental quantities such as the distribution of selection coefficient, or the magnitude and type of epistasis. A better understanding of variation of landscape structure across species and environments ... |
1506.06936 | Pascal Grange | Pascal Grange | Computational neuroanatomy: mapping cell-type densities in the mouse
brain, simulations from the Allen Brain Atlas | Prepared for the International Conference on Mathematical Modeling in
Physical Sciences, 5th-8th June 2015, Mykonos Island, Greece | null | 10.1088/1742-6596/633/1/012070 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Allen Brain Atlas (ABA) of the adult mouse consists of digitized
expression profiles of thousands of genes in the mouse brain, co-registered to
a common three-dimensional template (the Allen Reference Atlas). This
brain-wide, genome-wide data set has triggered a renaissance in neuroanatomy.
Its voxelized version ... | [
{
"created": "Tue, 23 Jun 2015 10:35:45 GMT",
"version": "v1"
}
] | 2015-10-28 | [
[
"Grange",
"Pascal",
""
]
] | The Allen Brain Atlas (ABA) of the adult mouse consists of digitized expression profiles of thousands of genes in the mouse brain, co-registered to a common three-dimensional template (the Allen Reference Atlas). This brain-wide, genome-wide data set has triggered a renaissance in neuroanatomy. Its voxelized version (w... |
1810.04637 | Fakrul Islam Tushar | Md. Kamrul Hasan, Fakrul Islam Tushar | Quantification of Trabeculae Inside the Heart from MRI Using Fractal
Analysis | null | null | null | null | q-bio.QM cs.CV physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Left ventricular non-compaction (LVNC) is a rare cardiomyopathy (CMP) that
should be considered as a possible diagnosis because of its potential
complications which are heart failure, ventricular arrhythmias, and embolic
events. For analysis cardiac functionality, extracting information from the
Left ventricular (LV)... | [
{
"created": "Sun, 30 Sep 2018 15:05:48 GMT",
"version": "v1"
},
{
"created": "Sun, 14 Oct 2018 17:00:09 GMT",
"version": "v2"
}
] | 2018-10-16 | [
[
"Hasan",
"Md. Kamrul",
""
],
[
"Tushar",
"Fakrul Islam",
""
]
] | Left ventricular non-compaction (LVNC) is a rare cardiomyopathy (CMP) that should be considered as a possible diagnosis because of its potential complications which are heart failure, ventricular arrhythmias, and embolic events. For analysis cardiac functionality, extracting information from the Left ventricular (LV) i... |
2308.13870 | Tahereh Toosi | Tahereh Toosi and Elias B. Issa | Brain-like representational straightening of natural movies in robust
feedforward neural networks | 21 pages, 15 figures, published in ICLR 2023 | International Conference on Learning Representations (ICLR), 2023 | null | null | q-bio.NC cs.CV cs.LG | http://creativecommons.org/licenses/by/4.0/ | Representational straightening refers to a decrease in curvature of visual
feature representations of a sequence of frames taken from natural movies.
Prior work established straightening in neural representations of the primate
primary visual cortex (V1) and perceptual straightening in human behavior as a
hallmark of... | [
{
"created": "Sat, 26 Aug 2023 13:04:36 GMT",
"version": "v1"
}
] | 2023-08-29 | [
[
"Toosi",
"Tahereh",
""
],
[
"Issa",
"Elias B.",
""
]
] | Representational straightening refers to a decrease in curvature of visual feature representations of a sequence of frames taken from natural movies. Prior work established straightening in neural representations of the primate primary visual cortex (V1) and perceptual straightening in human behavior as a hallmark of b... |
q-bio/0609046 | David Steinsaltz | Steven N. Evans and David Steinsaltz and Kenneth W. Wachter | A mutation-selection model for general genotypes with recombination | 133 pages; 4 figures. Substantially revised. Main convergence result
in chapters 7 and 8 largely rewritten. New discussion of recombination in
chapter 4, with pictures. Results improved: bounded fitness costs replaced by
Lipschitz; more general initial states; some results for mutation intensities
with infinite... | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate a continuous time, probability measure-valued dynamical system
that describes the process of mutation-selection balance in a context where the
population is infinite, there may be infinitely many loci, and there are weak
assumptions on selective costs. Our model arises when we incorporate very
general ... | [
{
"created": "Tue, 26 Sep 2006 20:48:58 GMT",
"version": "v1"
},
{
"created": "Fri, 23 Oct 2009 14:08:41 GMT",
"version": "v2"
},
{
"created": "Mon, 19 Sep 2011 11:17:36 GMT",
"version": "v3"
}
] | 2011-09-20 | [
[
"Evans",
"Steven N.",
""
],
[
"Steinsaltz",
"David",
""
],
[
"Wachter",
"Kenneth W.",
""
]
] | We investigate a continuous time, probability measure-valued dynamical system that describes the process of mutation-selection balance in a context where the population is infinite, there may be infinitely many loci, and there are weak assumptions on selective costs. Our model arises when we incorporate very general re... |
2111.09469 | Steven Massey | Steven E Massey | SARS-CoV-2's closest relative, RaTG13, was generated from a bat
transcriptome not a fecal swab: implications for the origin of COVID-19 | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | RaTG13 is the closest related coronavirus genome phylogenetically to
SARS-CoV-2, consequently understanding its provenance is of key importance to
understanding the origin of the COVID-19 pandemic. The RaTG13 NGS dataset is
attributed to a fecal swab from the intermediate horseshoe bat Rhinolophus
affinis. However, s... | [
{
"created": "Thu, 18 Nov 2021 01:30:19 GMT",
"version": "v1"
},
{
"created": "Mon, 22 Nov 2021 02:38:47 GMT",
"version": "v2"
}
] | 2021-11-23 | [
[
"Massey",
"Steven E",
""
]
] | RaTG13 is the closest related coronavirus genome phylogenetically to SARS-CoV-2, consequently understanding its provenance is of key importance to understanding the origin of the COVID-19 pandemic. The RaTG13 NGS dataset is attributed to a fecal swab from the intermediate horseshoe bat Rhinolophus affinis. However, seq... |
1304.1455 | Jakob Ruess | Jakob Ruess, Andreas Milias-Argeitis and John Lygeros | Designing Experiments to Understand the Variability in Biochemical
Reaction Networks | null | J R Soc Interface 10:20130588 (2013) | 10.1098/rsif.2013.0588 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Exploiting the information provided by the molecular noise of a biological
process has proven to be valuable in extracting knowledge about the underlying
kinetic parameters and sources of variability from single cell measurements.
However, quantifying this additional information a priori, to decide whether a
single c... | [
{
"created": "Thu, 4 Apr 2013 18:12:40 GMT",
"version": "v1"
}
] | 2013-08-30 | [
[
"Ruess",
"Jakob",
""
],
[
"Milias-Argeitis",
"Andreas",
""
],
[
"Lygeros",
"John",
""
]
] | Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However, quantifying this additional information a priori, to decide whether a single cel... |
2108.13908 | Mattia Angeli | Mattia Angeli, Georgios Neofotistos, Marios Mattheakis and Efthimios
Kaxiras | Modeling the effect of the vaccination campaign on the Covid-19 pandemic | null | null | 10.1016/j.chaos.2021.111621 | null | q-bio.PE cs.LG | http://creativecommons.org/licenses/by/4.0/ | Population-wide vaccination is critical for containing the SARS-CoV-2
(Covid-19) pandemic when combined with restrictive and prevention measures. In
this study, we introduce SAIVR, a mathematical model able to forecast the
Covid-19 epidemic evolution during the vaccination campaign. SAIVR extends the
widely used Susc... | [
{
"created": "Fri, 27 Aug 2021 19:12:13 GMT",
"version": "v1"
}
] | 2022-01-19 | [
[
"Angeli",
"Mattia",
""
],
[
"Neofotistos",
"Georgios",
""
],
[
"Mattheakis",
"Marios",
""
],
[
"Kaxiras",
"Efthimios",
""
]
] | Population-wide vaccination is critical for containing the SARS-CoV-2 (Covid-19) pandemic when combined with restrictive and prevention measures. In this study, we introduce SAIVR, a mathematical model able to forecast the Covid-19 epidemic evolution during the vaccination campaign. SAIVR extends the widely used Suscep... |
2408.07839 | Murat Okatan | Murat Okatan | Fast computation of the statistical significance test for
spatio-temporal receptive field estimates obtained using spike-triggered
averaging of binary pseudo-random sequences | This paper develops an approximate method that accelerates the exact
method of Okatan, M. A statistical significance test for spatio-temporal
receptive field estimates obtained using spike-triggered averaging of binary
pseudo-random sequences. SIViP 17, 3759-3766 (2023).
https://doi.org/10.1007/s11760-023-02603... | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Background: Spatio-temporal receptive fields (STRF) of visual neurons are
often estimated using spike-triggered averaging of binary pseudo-random
stimulus sequences. The stimuli are visual displays that contain black and
white pixels that flicker randomly at a fixed frame rate without any spatial or
temporal correlat... | [
{
"created": "Wed, 14 Aug 2024 22:24:35 GMT",
"version": "v1"
}
] | 2024-08-16 | [
[
"Okatan",
"Murat",
""
]
] | Background: Spatio-temporal receptive fields (STRF) of visual neurons are often estimated using spike-triggered averaging of binary pseudo-random stimulus sequences. The stimuli are visual displays that contain black and white pixels that flicker randomly at a fixed frame rate without any spatial or temporal correlatio... |
2401.17894 | Shruthi Viswanath | Shreyas Arvindekar, Kartik Majila, Shruthi Viswanath | Recent methods from statistical inference and machine learning to
improve integrative modeling of macromolecular assemblies | null | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-sa/4.0/ | Integrative modeling of macromolecular assemblies allows for structural
characterization of large assemblies that are recalcitrant to direct
experimental observation. A Bayesian inference approach facilitates combining
data from complementary experiments along with physical principles, statistics
of known structures,... | [
{
"created": "Wed, 31 Jan 2024 15:00:53 GMT",
"version": "v1"
},
{
"created": "Fri, 2 Feb 2024 05:09:04 GMT",
"version": "v2"
},
{
"created": "Tue, 6 Feb 2024 05:20:50 GMT",
"version": "v3"
},
{
"created": "Sat, 18 May 2024 15:02:26 GMT",
"version": "v4"
}
] | 2024-05-21 | [
[
"Arvindekar",
"Shreyas",
""
],
[
"Majila",
"Kartik",
""
],
[
"Viswanath",
"Shruthi",
""
]
] | Integrative modeling of macromolecular assemblies allows for structural characterization of large assemblies that are recalcitrant to direct experimental observation. A Bayesian inference approach facilitates combining data from complementary experiments along with physical principles, statistics of known structures, a... |
2006.04905 | Goncalo Oliveira | Goncalo Oliveira | Early epidemic spread, percolation and Covid-19 | null | null | null | null | q-bio.PE math.PR q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Human to human transmissible infectious diseases spread in a population using
human interactions as its transmission vector. The early stages of such an
outbreak can be modeled by a graph whose edges encode these interactions
between individuals, the vertices. This article attempts to account for the
case when each i... | [
{
"created": "Mon, 8 Jun 2020 19:41:20 GMT",
"version": "v1"
}
] | 2020-06-11 | [
[
"Oliveira",
"Goncalo",
""
]
] | Human to human transmissible infectious diseases spread in a population using human interactions as its transmission vector. The early stages of such an outbreak can be modeled by a graph whose edges encode these interactions between individuals, the vertices. This article attempts to account for the case when each ind... |
1906.09528 | Sergey Shuvaev | Sergey A. Shuvaev, Ngoc B. Tran, Marcus Stephenson-Jones, Bo Li, and
Alexei A. Koulakov | Neural networks with motivation | Added the Methods section | null | null | null | q-bio.NC cs.LG | http://creativecommons.org/licenses/by/4.0/ | How can animals behave effectively in conditions involving different
motivational contexts? Here, we propose how reinforcement learning neural
networks can learn optimal behavior for dynamically changing motivational
salience vectors. First, we show that Q-learning neural networks with
motivation can navigate in envi... | [
{
"created": "Sun, 23 Jun 2019 01:44:32 GMT",
"version": "v1"
},
{
"created": "Tue, 19 Nov 2019 03:27:52 GMT",
"version": "v2"
}
] | 2019-11-20 | [
[
"Shuvaev",
"Sergey A.",
""
],
[
"Tran",
"Ngoc B.",
""
],
[
"Stephenson-Jones",
"Marcus",
""
],
[
"Li",
"Bo",
""
],
[
"Koulakov",
"Alexei A.",
""
]
] | How can animals behave effectively in conditions involving different motivational contexts? Here, we propose how reinforcement learning neural networks can learn optimal behavior for dynamically changing motivational salience vectors. First, we show that Q-learning neural networks with motivation can navigate in enviro... |
2004.10478 | Nicola Cufaro Petroni | Nicola Cufaro Petroni, Salvatore De Martino and Silvio De Siena | Logistic and $\theta$-logistic models in population dynamics: General
analysis and exact results | 25 pages, 8 figures. The second part of the paper (from p. 10,
Section 3.1 on) is substantially improved w.r.t. the old version. As a
consequence Title, Abstract, Introduction, Conclusions and References have
been accordingly updated | null | 10.1088/1751-8121/abb277 | null | q-bio.PE math.PR physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the present paper we provide the closed form of the path-like solutions
for the logistic and $\theta$-logistic stochastic differential equations, along
with the exact expressions of both their probability density functions and
their moments. We simulate in addition a few typical sample trajectories, and
we provide... | [
{
"created": "Wed, 22 Apr 2020 10:21:50 GMT",
"version": "v1"
},
{
"created": "Tue, 26 May 2020 17:23:24 GMT",
"version": "v2"
}
] | 2020-10-28 | [
[
"Petroni",
"Nicola Cufaro",
""
],
[
"De Martino",
"Salvatore",
""
],
[
"De Siena",
"Silvio",
""
]
] | In the present paper we provide the closed form of the path-like solutions for the logistic and $\theta$-logistic stochastic differential equations, along with the exact expressions of both their probability density functions and their moments. We simulate in addition a few typical sample trajectories, and we provide a... |
2401.10462 | Xin Cao | Xin Cao, Michelle H. Hummel, Yuzhang Wang, Carlos Simmerling,
Evangelos A. Coutsias | Exact analytical algorithm for solvent accessible surface area and
derivatives in implicit solvent molecular simulations on GPUs | null | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In this paper, we present dSASA (differentiable SASA), an exact geometric
method to calculate solvent accessible surface area (SASA) analytically along
with atomic derivatives on GPUs. The atoms in a molecule are first assigned to
tetrahedra in groups of four atoms by Delaunay tetrahedrization adapted for
efficient G... | [
{
"created": "Fri, 19 Jan 2024 03:18:04 GMT",
"version": "v1"
},
{
"created": "Thu, 25 Apr 2024 15:52:01 GMT",
"version": "v2"
}
] | 2024-04-26 | [
[
"Cao",
"Xin",
""
],
[
"Hummel",
"Michelle H.",
""
],
[
"Wang",
"Yuzhang",
""
],
[
"Simmerling",
"Carlos",
""
],
[
"Coutsias",
"Evangelos A.",
""
]
] | In this paper, we present dSASA (differentiable SASA), an exact geometric method to calculate solvent accessible surface area (SASA) analytically along with atomic derivatives on GPUs. The atoms in a molecule are first assigned to tetrahedra in groups of four atoms by Delaunay tetrahedrization adapted for efficient GPU... |
1612.09379 | Sanzo Miyazawa | Sanzo Miyazawa | Selection originating from protein stability/foldability: Relationships
between protein folding free energy, sequence ensemble, and fitness | 31 pages, 3 Tables, and 15 figures with a supplement. Table 3 (Table
S.3) and Table S.5 are revised by employing thermochemical calorie (1 cal =
4.184 J) rather than steam table calorie (1 cal = 4.1868 J) in the previous
versions including DOI:10.1016/j.jtbi.2017.08.018 (J. Theoretical Biol., 433,
21-38, 2017);... | J. Theoretical Biol., 433, 21-38, 2017 | 10.1016/j.jtbi.2017.08.018 | null | q-bio.PE q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Assuming that mutation and fixation processes are reversible Markov
processes, we prove that the equilibrium ensemble of sequences obeys a
Boltzmann distribution with $\exp(4N_e m(1 - 1/(2N)))$, where $m$ is Malthusian
fitness and $N_e$ and $N$ are effective and actual population sizes. On the
other hand, the probabi... | [
{
"created": "Fri, 30 Dec 2016 04:11:46 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Mar 2017 02:13:07 GMT",
"version": "v2"
},
{
"created": "Sat, 16 Sep 2017 05:46:51 GMT",
"version": "v3"
},
{
"created": "Wed, 15 Sep 2021 09:37:03 GMT",
"version": "v4"
}
] | 2021-09-16 | [
[
"Miyazawa",
"Sanzo",
""
]
] | Assuming that mutation and fixation processes are reversible Markov processes, we prove that the equilibrium ensemble of sequences obeys a Boltzmann distribution with $\exp(4N_e m(1 - 1/(2N)))$, where $m$ is Malthusian fitness and $N_e$ and $N$ are effective and actual population sizes. On the other hand, the probabili... |
q-bio/0603027 | Michael E. Wall | Michael E. Wall | Ligand Binding, Protein Fluctuations, and Allosteric Free Energy | 18 pages; 7 figures; Second International Congress of the
Biocomputing and Physics of Complex Systems Research Institute, Zaragoza,
Spain, 8-11 Feb 2006; increase breadth of review of methods for analysis of
allosteric mechanisms; Add AIP in press; fix missing kTs in equations | null | 10.1063/1.2345620 | LA-UR-06-2066 | q-bio.BM q-bio.QM | null | Although the importance of protein dynamics in protein function is generally
recognized, the role of protein fluctuations in allosteric effects scarcely has
been considered. To address this gap, the Kullback-Leibler divergence (Dx)
between protein conformational distributions before and after ligand binding
was propo... | [
{
"created": "Wed, 22 Mar 2006 17:07:35 GMT",
"version": "v1"
},
{
"created": "Mon, 3 Apr 2006 17:42:15 GMT",
"version": "v2"
},
{
"created": "Mon, 3 Jul 2006 19:45:41 GMT",
"version": "v3"
}
] | 2009-11-13 | [
[
"Wall",
"Michael E.",
""
]
] | Although the importance of protein dynamics in protein function is generally recognized, the role of protein fluctuations in allosteric effects scarcely has been considered. To address this gap, the Kullback-Leibler divergence (Dx) between protein conformational distributions before and after ligand binding was propose... |
0901.2581 | Takashi Nishikawa | Takashi Nishikawa, Natali Gulbahce, Adilson E. Motter | Spontaneous Reaction Silencing in Metabolic Optimization | 34 pages, 6 figures | PLoS Comput Biol 4(12), e1000236 (2008) | 10.1371/journal.pcbi.1000236 | null | q-bio.MN cond-mat.dis-nn q-bio.CB | http://creativecommons.org/licenses/by/3.0/ | Metabolic reactions of single-cell organisms are routinely observed to become
dispensable or even incapable of carrying activity under certain circumstances.
Yet, the mechanisms as well as the range of conditions and phenotypes
associated with this behavior remain very poorly understood. Here we predict
computational... | [
{
"created": "Fri, 16 Jan 2009 21:35:00 GMT",
"version": "v1"
}
] | 2009-01-21 | [
[
"Nishikawa",
"Takashi",
""
],
[
"Gulbahce",
"Natali",
""
],
[
"Motter",
"Adilson E.",
""
]
] | Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances. Yet, the mechanisms as well as the range of conditions and phenotypes associated with this behavior remain very poorly understood. Here we predict computationally... |
2205.04393 | Yaocong Duan | Y. Duan (1), J. Zhan (1), J. Gross (2), R.A.A. Ince (1), P.G. Schyns
(1) ((1) School of Psychology and Neuroscience, University of Glasgow, United
Kingdom, (2) Institute for Biomagnetism and Biosignalanalysis, University of
M\"unster, Germany) | Pre-frontal cortex guides dimension-reducing transformations in the
occipito-ventral pathway for categorization behaviors | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | To interpret our surroundings, the brain uses a visual categorization
process. Current theories and models suggest that this process comprises a
hierarchy of different computations that transforms complex, high-dimensional
inputs into lower-dimensional representations (i.e. manifolds) in support of
multiple categoriz... | [
{
"created": "Mon, 9 May 2022 15:56:22 GMT",
"version": "v1"
},
{
"created": "Fri, 13 May 2022 15:59:13 GMT",
"version": "v2"
},
{
"created": "Thu, 20 Jun 2024 16:07:14 GMT",
"version": "v3"
}
] | 2024-06-21 | [
[
"Duan",
"Y.",
""
],
[
"Zhan",
"J.",
""
],
[
"Gross",
"J.",
""
],
[
"Ince",
"R. A. A.",
""
],
[
"Schyns",
"P. G.",
""
]
] | To interpret our surroundings, the brain uses a visual categorization process. Current theories and models suggest that this process comprises a hierarchy of different computations that transforms complex, high-dimensional inputs into lower-dimensional representations (i.e. manifolds) in support of multiple categorizat... |
2006.02249 | Marc Hellmuth | David Schaller, Manuela Gei{\ss}, Peter F. Stadler and Marc Hellmuth | Complete Characterization of Incorrect Orthology Assignments in Best
Match Graphs | null | null | null | null | q-bio.PE cs.DM cs.DS math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genome-scale orthology assignments are usually based on reciprocal best
matches. In the absence of horizontal gene transfer (HGT), every pair of
orthologs forms a reciprocal best match. Incorrect orthology assignments
therefore are always false positives in the reciprocal best match graph. We
consider duplication/los... | [
{
"created": "Wed, 3 Jun 2020 13:06:57 GMT",
"version": "v1"
},
{
"created": "Thu, 26 Nov 2020 12:48:15 GMT",
"version": "v2"
}
] | 2020-11-30 | [
[
"Schaller",
"David",
""
],
[
"Geiß",
"Manuela",
""
],
[
"Stadler",
"Peter F.",
""
],
[
"Hellmuth",
"Marc",
""
]
] | Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the reciprocal best match graph. We consider duplication/loss ... |
2108.06397 | Firas Lethaus | Firas Lethaus and Robert Kaul | Cognitive factor forming an individual constituent in a driver model
inferred from multiplicatory relationships between cognitive sub-factors | 15 pages, 3 figures, to be published | null | null | null | q-bio.NC cs.HC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In order to reproduce human behaviour in dynamic traffic situations, a
computational representation of the requisite mental processes used to carry
out the complex driving tasks is required. A single cognitive factor has been
developed and forms a crucial component in our driver model. This cognitive
factor is compos... | [
{
"created": "Mon, 19 Jul 2021 17:29:36 GMT",
"version": "v1"
}
] | 2021-08-17 | [
[
"Lethaus",
"Firas",
""
],
[
"Kaul",
"Robert",
""
]
] | In order to reproduce human behaviour in dynamic traffic situations, a computational representation of the requisite mental processes used to carry out the complex driving tasks is required. A single cognitive factor has been developed and forms a crucial component in our driver model. This cognitive factor is composed... |
2401.01398 | Farshud Sorourifar | Farshud Sorourifar, Thomas Banker, Joel A. Paulson | Accelerating Black-Box Molecular Property Optimization by Adaptively
Learning Sparse Subspaces | 9 pages, 2 figures consisting of 6 and 4 plots, accepted to NeurIPS
2023 Workshop on Adaptive Experimental Design and Active Learning in the Real
World | null | null | null | q-bio.BM cs.CE cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Molecular property optimization (MPO) problems are inherently challenging
since they are formulated over discrete, unstructured spaces and the labeling
process involves expensive simulations or experiments, which fundamentally
limits the amount of available data. Bayesian optimization (BO) is a powerful
and popular f... | [
{
"created": "Tue, 2 Jan 2024 18:34:29 GMT",
"version": "v1"
}
] | 2024-01-04 | [
[
"Sorourifar",
"Farshud",
""
],
[
"Banker",
"Thomas",
""
],
[
"Paulson",
"Joel A.",
""
]
] | Molecular property optimization (MPO) problems are inherently challenging since they are formulated over discrete, unstructured spaces and the labeling process involves expensive simulations or experiments, which fundamentally limits the amount of available data. Bayesian optimization (BO) is a powerful and popular fra... |
2305.06334 | Isaac Filella-Merce | Isaac Filella-Merce, Alexis Molina, Marek Orzechowski, Luc\'ia D\'iaz,
Yang Ming Zhu, Julia Vilalta Mor, Laura Malo, Ajay S Yekkirala, Soumya Ray,
Victor Guallar | Optimizing Drug Design by Merging Generative AI With Active Learning
Frameworks | null | null | null | null | q-bio.BM cs.AI cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Traditional drug discovery programs are being transformed by the advent of
machine learning methods. Among these, Generative AI methods (GM) have gained
attention due to their ability to design new molecules and enhance specific
properties of existing ones. However, current GM methods have limitations, such
as low af... | [
{
"created": "Thu, 4 May 2023 13:25:14 GMT",
"version": "v1"
}
] | 2023-05-11 | [
[
"Filella-Merce",
"Isaac",
""
],
[
"Molina",
"Alexis",
""
],
[
"Orzechowski",
"Marek",
""
],
[
"Díaz",
"Lucía",
""
],
[
"Zhu",
"Yang Ming",
""
],
[
"Mor",
"Julia Vilalta",
""
],
[
"Malo",
"Laura",
""
],
... | Traditional drug discovery programs are being transformed by the advent of machine learning methods. Among these, Generative AI methods (GM) have gained attention due to their ability to design new molecules and enhance specific properties of existing ones. However, current GM methods have limitations, such as low affi... |
2009.12338 | David Danko | David C Danko and Chris Mason | The MetaSUB Microbiome Core Analysis Pipeline Enables Large Scale
Metagenomic Analysis | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Accurate data analysis and quality control is critical for
metagenomic studies. Though many tools exist to analyze metagenomic data there
is no consistent framework to integrate and run these tools across projects.
Currently, computational analysis of metagenomes is time consuming, often
misses potentiall... | [
{
"created": "Fri, 25 Sep 2020 16:57:24 GMT",
"version": "v1"
}
] | 2020-09-28 | [
[
"Danko",
"David C",
""
],
[
"Mason",
"Chris",
""
]
] | Motivation: Accurate data analysis and quality control is critical for metagenomic studies. Though many tools exist to analyze metagenomic data there is no consistent framework to integrate and run these tools across projects. Currently, computational analysis of metagenomes is time consuming, often misses potentially ... |
2207.02028 | Mohammad M. Amirian | Mohammad M. Amirian, Andrew J. Irwin, Zoe V. Finkel | Extending the Monod Model of Microbial Growth with Memory | null | null | null | null | q-bio.PE math.DS stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Monod's model describes the growth of microorganisms using a hyperbolic
function of extracellular resource concentration. Under fluctuating or limited
resource concentrations this model performs poorly against experimental data,
motivating the more complex Droop model with a time-varying internal storage
pool. We ext... | [
{
"created": "Tue, 5 Jul 2022 13:18:09 GMT",
"version": "v1"
},
{
"created": "Wed, 28 Dec 2022 18:57:34 GMT",
"version": "v2"
}
] | 2022-12-29 | [
[
"Amirian",
"Mohammad M.",
""
],
[
"Irwin",
"Andrew J.",
""
],
[
"Finkel",
"Zoe V.",
""
]
] | Monod's model describes the growth of microorganisms using a hyperbolic function of extracellular resource concentration. Under fluctuating or limited resource concentrations this model performs poorly against experimental data, motivating the more complex Droop model with a time-varying internal storage pool. We exten... |
2211.07375 | Jiashu Lou | Jiashu Lou, Leyi Cui, Wenxuan Qiu | Reconstruction of gene regulatory network via sparse optimization | null | null | null | null | q-bio.MN cs.LG math.OC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In this paper, we tested several sparse optimization algorithms based on the
public dataset of the DREAM5 Gene Regulatory Network Inference Challenge. And
we find that introducing 20% of the regulatory network as a priori known data
can provide a basis for parameter selection of inference algorithms, thus
improving p... | [
{
"created": "Fri, 11 Nov 2022 07:57:59 GMT",
"version": "v1"
}
] | 2022-11-15 | [
[
"Lou",
"Jiashu",
""
],
[
"Cui",
"Leyi",
""
],
[
"Qiu",
"Wenxuan",
""
]
] | In this paper, we tested several sparse optimization algorithms based on the public dataset of the DREAM5 Gene Regulatory Network Inference Challenge. And we find that introducing 20% of the regulatory network as a priori known data can provide a basis for parameter selection of inference algorithms, thus improving pre... |
1802.05646 | Jonathan Taylor | Vytautas Zickus and Jonathan M. Taylor | 4D blood flow mapping using SPIM-microPIV in the developing zebrafish
heart | V. Zickus and J. M. Taylor, "4D blood flow mapping using
SPIM-microPIV in the developing zebrafish heart", Photonics West BiOS 2018:
Biomedical Spectroscopy, Microscopy, and Imaging (10499), 10499-38 (2018).
Copyright 2018 Society of Photo Optical Instrumentation Engineers (SPIE) | Proc. SPIE 10499 (2018) 104991E | 10.1117/12.2289709 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fluid-structure interaction in the developing heart is an active area of
research in developmental biology. However, investigation of heart dynamics is
mostly limited to computational fluid dynamics simulations using heart wall
structure information only, or single plane blood flow information - so there
is a need fo... | [
{
"created": "Thu, 15 Feb 2018 16:37:47 GMT",
"version": "v1"
}
] | 2018-03-01 | [
[
"Zickus",
"Vytautas",
""
],
[
"Taylor",
"Jonathan M.",
""
]
] | Fluid-structure interaction in the developing heart is an active area of research in developmental biology. However, investigation of heart dynamics is mostly limited to computational fluid dynamics simulations using heart wall structure information only, or single plane blood flow information - so there is a need for ... |
2111.13344 | Matteo Smerlak | Camila Br\"autigam, Matteo Smerlak | Diffusion approximations in population genetics and the rate of Muller's
ratchet | 17 pages, 5 figures | Journal of Theoretical Biology 550, 111236, 2022 | 10.1016/j.jtbi.2022.111236 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Diffusion theory is a central tool of modern population genetics, yielding
simple expressions for fixation probabilities and other quantities that are not
easily derived from the underlying Wright-Fisher model. Unfortunately, the
textbook derivation of diffusion equations as scaling limits requires
evolutionary param... | [
{
"created": "Fri, 26 Nov 2021 07:50:00 GMT",
"version": "v1"
}
] | 2022-12-19 | [
[
"Bräutigam",
"Camila",
""
],
[
"Smerlak",
"Matteo",
""
]
] | Diffusion theory is a central tool of modern population genetics, yielding simple expressions for fixation probabilities and other quantities that are not easily derived from the underlying Wright-Fisher model. Unfortunately, the textbook derivation of diffusion equations as scaling limits requires evolutionary paramet... |
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