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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2011.02372 | Elod Mehes | Elod Mehes, Tana S Pottorf, Marton Gulyas, Sandor Paku, Pamela V.
Tran, Andras Czirok | A biomimetic kidney tubule model | 11 pages, 4 figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A critical barrier in the nephrology field is the lack of appropriate in
vitro renal tubule models that allow manipulation of various mechanical
factors, facilitating studies of disease pathophysiology and drug discovery.
Here we report development of a novel in vitro assay system comprised of a
renal tubule within a... | [
{
"created": "Wed, 4 Nov 2020 16:02:55 GMT",
"version": "v1"
}
] | 2020-11-05 | [
[
"Mehes",
"Elod",
""
],
[
"Pottorf",
"Tana S",
""
],
[
"Gulyas",
"Marton",
""
],
[
"Paku",
"Sandor",
""
],
[
"Tran",
"Pamela V.",
""
],
[
"Czirok",
"Andras",
""
]
] | A critical barrier in the nephrology field is the lack of appropriate in vitro renal tubule models that allow manipulation of various mechanical factors, facilitating studies of disease pathophysiology and drug discovery. Here we report development of a novel in vitro assay system comprised of a renal tubule within an ... |
2109.08718 | Kaifu Gao | Kaifu Gao, Dong Chen, Alfred J Robison, and Guo-Wei Wei | Proteome-informed machine learning studies of cocaine addiction | null | null | null | null | q-bio.MN cs.LG | http://creativecommons.org/licenses/by/4.0/ | Cocaine addiction accounts for a large portion of substance use disorders and
threatens millions of lives worldwide. There is an urgent need to come up with
efficient anti-cocaine addiction drugs. Unfortunately, no medications have been
approved by the Food and Drug Administration (FDA), despite the extensive
effort ... | [
{
"created": "Fri, 17 Sep 2021 18:58:24 GMT",
"version": "v1"
}
] | 2021-09-21 | [
[
"Gao",
"Kaifu",
""
],
[
"Chen",
"Dong",
""
],
[
"Robison",
"Alfred J",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Cocaine addiction accounts for a large portion of substance use disorders and threatens millions of lives worldwide. There is an urgent need to come up with efficient anti-cocaine addiction drugs. Unfortunately, no medications have been approved by the Food and Drug Administration (FDA), despite the extensive effort in... |
2302.04481 | Louis Kang | Louis Kang, Taro Toyoizumi | A Hopfield-like model with complementary encodings of memories | 34 pages including 21 pages of appendices, 9 figures | null | null | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a Hopfield-like autoassociative network for memories representing
examples of concepts. Each memory is encoded by two activity patterns with
complementary properties. The first is dense and correlated across examples
within concepts, and the second is sparse and exhibits no correlation among
examples. The ... | [
{
"created": "Thu, 9 Feb 2023 07:51:09 GMT",
"version": "v1"
},
{
"created": "Fri, 12 May 2023 06:41:52 GMT",
"version": "v2"
},
{
"created": "Fri, 25 Aug 2023 08:42:03 GMT",
"version": "v3"
}
] | 2023-08-28 | [
[
"Kang",
"Louis",
""
],
[
"Toyoizumi",
"Taro",
""
]
] | We present a Hopfield-like autoassociative network for memories representing examples of concepts. Each memory is encoded by two activity patterns with complementary properties. The first is dense and correlated across examples within concepts, and the second is sparse and exhibits no correlation among examples. The ne... |
2208.13326 | Yi-Lin Tsai | Yi-Lin Tsai (1), Dymasius Y. Sitepu (2), Karyn E. Chappell (3), Rishi
P. Mediratta (4), C. Jason Wang (4, 5), Peter K. Kitanidis (1, 6, 7, and 8),
Christopher B. Field (6, 9, 10, and 11) ((1) Department of Civil and
Environmental Engineering, Stanford University, Stanford, CA, USA, (2)
Department of Engineering... | Effective approaches to disaster evacuation during a COVID-like pandemic | Supplementary information:
https://drive.google.com/file/d/1Lc8QpeEYX4n7S_l9CZ2mrREa2e6MwnIC/view?usp=sharing | null | null | null | q-bio.PE cs.AI cs.CY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Since COVID-19 vaccines became available, no studies have quantified how
different disaster evacuation strategies can mitigate pandemic risks in
shelters. Therefore, we applied an age-structured epidemiological model, known
as the Susceptible-Exposed-Infectious-Recovered (SEIR) model, to investigate to
what extent di... | [
{
"created": "Mon, 29 Aug 2022 01:38:07 GMT",
"version": "v1"
}
] | 2022-08-30 | [
[
"Tsai",
"Yi-Lin",
"",
"1, 6, 7, and 8"
],
[
"Sitepu",
"Dymasius Y.",
"",
"1, 6, 7, and 8"
],
[
"Chappell",
"Karyn E.",
"",
"1, 6, 7, and 8"
],
[
"Mediratta",
"Rishi P.",
"",
"1, 6, 7, and 8"
],
[
"Wang",
"C. Jason",
"",
... | Since COVID-19 vaccines became available, no studies have quantified how different disaster evacuation strategies can mitigate pandemic risks in shelters. Therefore, we applied an age-structured epidemiological model, known as the Susceptible-Exposed-Infectious-Recovered (SEIR) model, to investigate to what extent diff... |
2407.06805 | Xell Brunet Guasch | Meritxell Brunet Guasch, Nathalie Feeley, Ignacio Soriano, Steve
Thorn, Ian Tomlinson, Michael D. Nicholson, Tibor Antal | Quantifying "just-right" APC inactivation for colorectal cancer
initiation | Main: 32 pages, 7 figures Supplements: 17 pages, 7 figures | null | null | null | q-bio.QM q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Dysregulation of the tumour suppressor gene Adenomatous Polyposis Coli (APC)
is a canonical step in colorectal cancer development. Curiously, most
colorectal tumours carry biallelic mutations that result in only partial loss
of APC function, suggesting that a "just-right" level of APC inactivation, and
hence Wnt sign... | [
{
"created": "Tue, 9 Jul 2024 12:24:01 GMT",
"version": "v1"
}
] | 2024-07-10 | [
[
"Guasch",
"Meritxell Brunet",
""
],
[
"Feeley",
"Nathalie",
""
],
[
"Soriano",
"Ignacio",
""
],
[
"Thorn",
"Steve",
""
],
[
"Tomlinson",
"Ian",
""
],
[
"Nicholson",
"Michael D.",
""
],
[
"Antal",
"Tibor",
"... | Dysregulation of the tumour suppressor gene Adenomatous Polyposis Coli (APC) is a canonical step in colorectal cancer development. Curiously, most colorectal tumours carry biallelic mutations that result in only partial loss of APC function, suggesting that a "just-right" level of APC inactivation, and hence Wnt signal... |
1909.10116 | Audrey Sederberg | Audrey J. Sederberg, Ilya Nemenman | Randomly connected networks generate emergent selectivity and predict
decoding properties of large populations of neurons | null | null | 10.1371/journal.pcbi.1007875 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Advances in neural recording methods enable sampling from populations of
thousands of neurons during the performance of behavioral tasks, raising the
question of how recorded activity relates to the theoretical models of
computations underlying performance. In the context of decision making in
rodents, patterns of fu... | [
{
"created": "Mon, 23 Sep 2019 01:26:02 GMT",
"version": "v1"
}
] | 2020-07-01 | [
[
"Sederberg",
"Audrey J.",
""
],
[
"Nemenman",
"Ilya",
""
]
] | Advances in neural recording methods enable sampling from populations of thousands of neurons during the performance of behavioral tasks, raising the question of how recorded activity relates to the theoretical models of computations underlying performance. In the context of decision making in rodents, patterns of func... |
1503.03373 | Arni S.R. Srinivasa Rao | Arni S.R. Srinivasa Rao | Population Stability and Momentum | Research Article | Notices of the American Mathematical Society (2014), 9, 61:
1062-1065 | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A new approach is developed to understand stability of a population and
further understanding of population momentum.
| [
{
"created": "Tue, 10 Feb 2015 18:36:54 GMT",
"version": "v1"
}
] | 2021-06-24 | [
[
"Rao",
"Arni S. R. Srinivasa",
""
]
] | A new approach is developed to understand stability of a population and further understanding of population momentum. |
1912.04724 | Guo-Wei Wei | Duc D Nguyen, Zixuan Cang, and Guo-Wei Wei | A review of mathematical representations of biomolecules | 33 pages, 13 pages, and 4 tables | null | 10.1039/C9CP06554G | null | q-bio.BM math.AT math.DG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, machine learning (ML) has established itself in various worldwide
benchmarking competitions in computational biology, including Critical
Assessment of Structure Prediction (CASP) and Drug Design Data Resource (D3R)
Grand Challenges. However, the intricate structural complexity and high ML
dimensionality of ... | [
{
"created": "Tue, 3 Dec 2019 21:15:45 GMT",
"version": "v1"
}
] | 2020-04-22 | [
[
"Nguyen",
"Duc D",
""
],
[
"Cang",
"Zixuan",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Recently, machine learning (ML) has established itself in various worldwide benchmarking competitions in computational biology, including Critical Assessment of Structure Prediction (CASP) and Drug Design Data Resource (D3R) Grand Challenges. However, the intricate structural complexity and high ML dimensionality of bi... |
1208.0154 | Vinod Scaria | Saakshi Jalali, Deeksha Bhartiya, Vinod Scaria | Systematic transcriptome wide analysis of lncRNA-miRNA interactions | null | null | 10.1371/journal.pone.0053823 | null | q-bio.GN q-bio.MN | http://creativecommons.org/licenses/publicdomain/ | Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein
coding RNAs which have now increasingly been shown to be involved in a wide
variety of biological processes as regulatory molecules. Little is known
regarding the regulatory interactions between noncoding RNA classes. Recent
reports have sug... | [
{
"created": "Wed, 1 Aug 2012 09:48:39 GMT",
"version": "v1"
}
] | 2015-06-11 | [
[
"Jalali",
"Saakshi",
""
],
[
"Bhartiya",
"Deeksha",
""
],
[
"Scaria",
"Vinod",
""
]
] | Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs which have now increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. Little is known regarding the regulatory interactions between noncoding RNA classes. Recent reports have sugge... |
1809.05024 | Akram Yazdani PhD | Azam Yazdani, Akram Yazdani, Philip L. Lorenzi, Ahmad Samiei | Integrated systems approach identifies pathways from the genome to
triglycerides through a metabolomic causal network | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Introduction: To leverage functionality and clinical relevance into
understanding systems biology, one needs to understand the pathway of the
genetic effects on risk factors/disease through intermediate molecular levels,
such as metabolomics. Systems approaches integrate multi-omic information to
find pathways to dis... | [
{
"created": "Thu, 13 Sep 2018 15:51:40 GMT",
"version": "v1"
}
] | 2018-09-14 | [
[
"Yazdani",
"Azam",
""
],
[
"Yazdani",
"Akram",
""
],
[
"Lorenzi",
"Philip L.",
""
],
[
"Samiei",
"Ahmad",
""
]
] | Introduction: To leverage functionality and clinical relevance into understanding systems biology, one needs to understand the pathway of the genetic effects on risk factors/disease through intermediate molecular levels, such as metabolomics. Systems approaches integrate multi-omic information to find pathways to disea... |
1708.03990 | Hiroshi Ashikaga | Hiroshi Ashikaga and Ameneh Asgari-Targhi | Locating Order-Disorder Phase Transition in a Cardiac System | 20 pages, 8 figures | Sci Rep 8: 1967, 2018 | null | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To prevent sudden cardiac death, predicting where in the cardiac system an
order-disorder phase transition into ventricular fibrillation begins is as
important as when it begins. We present a computationally efficient,
information-theoretic approach to predicting the locations of wavebreaks that
initiate fibrillation... | [
{
"created": "Mon, 14 Aug 2017 02:11:12 GMT",
"version": "v1"
},
{
"created": "Tue, 15 Aug 2017 04:38:30 GMT",
"version": "v2"
}
] | 2018-02-02 | [
[
"Ashikaga",
"Hiroshi",
""
],
[
"Asgari-Targhi",
"Ameneh",
""
]
] | To prevent sudden cardiac death, predicting where in the cardiac system an order-disorder phase transition into ventricular fibrillation begins is as important as when it begins. We present a computationally efficient, information-theoretic approach to predicting the locations of wavebreaks that initiate fibrillation i... |
1908.09067 | Okyaz Eminaga | Okyaz Eminaga, Mahmoud Abbas, Christian Kunder, Andreas M. Loening,
Jeanne Shen, James D. Brooks, Curtis P. Langlotz, and Daniel L. Rubin | Plexus Convolutional Neural Network (PlexusNet): A novel neural network
architecture for histologic image analysis | null | null | null | null | q-bio.QM cs.AI cs.CV eess.IV q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Different convolutional neural network (CNN) models have been tested for
their application in histological image analyses. However, these models are
prone to overfitting due to their large parameter capacity, requiring more data
or valuable computational resources for model training. Given these
limitations, we intro... | [
{
"created": "Sat, 24 Aug 2019 01:29:34 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Jun 2020 04:43:21 GMT",
"version": "v2"
}
] | 2020-06-04 | [
[
"Eminaga",
"Okyaz",
""
],
[
"Abbas",
"Mahmoud",
""
],
[
"Kunder",
"Christian",
""
],
[
"Loening",
"Andreas M.",
""
],
[
"Shen",
"Jeanne",
""
],
[
"Brooks",
"James D.",
""
],
[
"Langlotz",
"Curtis P.",
""
... | Different convolutional neural network (CNN) models have been tested for their application in histological image analyses. However, these models are prone to overfitting due to their large parameter capacity, requiring more data or valuable computational resources for model training. Given these limitations, we introdu... |
1712.04339 | Kedi Wu | Kedi Wu, Guo-Wei Wei | Quantitative toxicity prediction using topology based multi-task deep
neural networks | arXiv admin note: substantial text overlap with arXiv:1703.10951 | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The understanding of toxicity is of paramount importance to human health and
environmental protection. Quantitative toxicity analysis has become a new
standard in the field. This work introduces element specific persistent
homology (ESPH), an algebraic topology approach, for quantitative toxicity
prediction. ESPH ret... | [
{
"created": "Sat, 9 Dec 2017 21:52:42 GMT",
"version": "v1"
}
] | 2017-12-13 | [
[
"Wu",
"Kedi",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | The understanding of toxicity is of paramount importance to human health and environmental protection. Quantitative toxicity analysis has become a new standard in the field. This work introduces element specific persistent homology (ESPH), an algebraic topology approach, for quantitative toxicity prediction. ESPH retai... |
2405.12344 | Daniel Sadasivan | Daniel Sadasivan, Cole Cantu, Cecilia Marsh, Andrew Graham | A Test of the Thermodynamics of Evolution | 10 pages, 3 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Recent research has extended methods from the fields of thermodynamics and
statistical mechanics into other disciplines. Most notably, one recent work
creates a unified theoretical framework to understand evolutionary biology,
machine learning, and thermodynamics. We present simulations of biological
evolution used t... | [
{
"created": "Mon, 20 May 2024 19:36:34 GMT",
"version": "v1"
}
] | 2024-05-22 | [
[
"Sadasivan",
"Daniel",
""
],
[
"Cantu",
"Cole",
""
],
[
"Marsh",
"Cecilia",
""
],
[
"Graham",
"Andrew",
""
]
] | Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine learning, and thermodynamics. We present simulations of biological evolution used to ... |
2111.05092 | Elcin Huseyn | Elcin Huseyn | Electrostimulation of Brain Deep Structures in Parkinson's Disease | 7 Pages | null | null | null | q-bio.NC cs.NE physics.med-ph | http://creativecommons.org/licenses/by/4.0/ | The study involved 56 patients with advanced and late stages of Parkinsons
disease, which could be considered as potentially requiring neurosurgical
treatment-electrical stimulation of deep brain structures. An algorithm has
been developed for selecting patients with advanced and late stages of
Parkinsons disease for... | [
{
"created": "Sat, 18 Sep 2021 06:01:46 GMT",
"version": "v1"
}
] | 2021-11-10 | [
[
"Huseyn",
"Elcin",
""
]
] | The study involved 56 patients with advanced and late stages of Parkinsons disease, which could be considered as potentially requiring neurosurgical treatment-electrical stimulation of deep brain structures. An algorithm has been developed for selecting patients with advanced and late stages of Parkinsons disease for n... |
2407.00201 | Yifan Wang | Yifan Wang and Vikram Ravindra and Ananth Grama | Deconvolving Complex Neuronal Networks into Interpretable Task-Specific
Connectomes | 9 pages, 5 figures | null | null | null | q-bio.NC cs.LG eess.IV | http://creativecommons.org/licenses/by/4.0/ | Task-specific functional MRI (fMRI) images provide excellent modalities for
studying the neuronal basis of cognitive processes. We use fMRI data to
formulate and solve the problem of deconvolving task-specific aggregate
neuronal networks into a set of basic building blocks called canonical
networks, to use these netw... | [
{
"created": "Fri, 28 Jun 2024 19:13:48 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Jul 2024 15:37:54 GMT",
"version": "v2"
}
] | 2024-07-04 | [
[
"Wang",
"Yifan",
""
],
[
"Ravindra",
"Vikram",
""
],
[
"Grama",
"Ananth",
""
]
] | Task-specific functional MRI (fMRI) images provide excellent modalities for studying the neuronal basis of cognitive processes. We use fMRI data to formulate and solve the problem of deconvolving task-specific aggregate neuronal networks into a set of basic building blocks called canonical networks, to use these networ... |
1507.08747 | Kavita Vemuri | Kavita Vemuri, Kulvinder Bisla, SaiKrishna Mulpuru, Srinivasa
Varadarajan | Does normal pupil diameter differences in population underlie the color
selection of the #dress? | 6 pages, 4 figures | null | 10.1364/JOSAA.33.00A137 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The fundamental question that arises from the color composition of the #dress
is: 'What are the phenomena that underlie the individual differences in colors
reported given all other conditions like light and device for display being
identical?'. The main color camps are blue/black (b/b) and white/gold (w/g) and
a sur... | [
{
"created": "Fri, 31 Jul 2015 04:17:42 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Nov 2015 08:45:46 GMT",
"version": "v2"
}
] | 2016-04-20 | [
[
"Vemuri",
"Kavita",
""
],
[
"Bisla",
"Kulvinder",
""
],
[
"Mulpuru",
"SaiKrishna",
""
],
[
"Varadarajan",
"Srinivasa",
""
]
] | The fundamental question that arises from the color composition of the #dress is: 'What are the phenomena that underlie the individual differences in colors reported given all other conditions like light and device for display being identical?'. The main color camps are blue/black (b/b) and white/gold (w/g) and a surve... |
0704.2896 | Adrian Melott | Bruce S.Lieberman and Adrian L. Melott (University of Kansas) | Considering the Case for Biodiversity Cycles: Reexamining the Evidence
for Periodicity in the Fossil Record | Minor modifications to reflect final published version | PLoS ONE 2(8): e759 (2007) | 10.1371/journal.pone.0000759 | null | q-bio.PE astro-ph physics.geo-ph | null | Medvedev and Melott (2007) have suggested that periodicity in fossil
biodiversity may be induced by cosmic rays which vary as the Solar System
oscillates normal to the galactic disk. We re-examine the evidence for a 62
million year (Myr) periodicity in biodiversity throughout the Phanerozoic
history of animal life re... | [
{
"created": "Sun, 22 Apr 2007 12:08:35 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Jul 2007 18:25:49 GMT",
"version": "v2"
},
{
"created": "Wed, 22 Aug 2007 15:03:22 GMT",
"version": "v3"
}
] | 2007-08-22 | [
[
"Lieberman",
"Bruce S.",
"",
"University of Kansas"
],
[
"Melott",
"Adrian L.",
"",
"University of Kansas"
]
] | Medvedev and Melott (2007) have suggested that periodicity in fossil biodiversity may be induced by cosmic rays which vary as the Solar System oscillates normal to the galactic disk. We re-examine the evidence for a 62 million year (Myr) periodicity in biodiversity throughout the Phanerozoic history of animal life repo... |
1007.3122 | Samuel Johnson | Samuel Johnson, J. Marro, and Joaqu\'in J. Torres | Robust short-term memory without synaptic learning | 20 pages, 9 figures. Amended to include section on spiking neurons,
with general rewrite | Johnson S, Marro J, Torres JJ (2013) Robust Short-Term Memory
without Synaptic Learning. PLoS ONE 8(1): e50276 | 10.1371/journal.pone.0050276 | null | q-bio.NC cond-mat.dis-nn nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Short-term memory in the brain cannot in general be explained the way
long-term memory can -- as a gradual modification of synaptic weights -- since
it takes place too quickly. Theories based on some form of cellular
bistability, however, do not seem able to account for the fact that noisy
neurons can collectively st... | [
{
"created": "Mon, 19 Jul 2010 11:11:48 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Jan 2013 19:34:49 GMT",
"version": "v2"
}
] | 2013-01-31 | [
[
"Johnson",
"Samuel",
""
],
[
"Marro",
"J.",
""
],
[
"Torres",
"Joaquín J.",
""
]
] | Short-term memory in the brain cannot in general be explained the way long-term memory can -- as a gradual modification of synaptic weights -- since it takes place too quickly. Theories based on some form of cellular bistability, however, do not seem able to account for the fact that noisy neurons can collectively stor... |
0806.3980 | Le Zhang | Le Zhang, L. Leon Chen and Thomas S. Deisboeck | Multi-Scale, Multi-Resolution Brain Cancer Modeling | 26 pages, 7 figures | null | null | null | q-bio.CB q-bio.MN q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In advancing discrete-based computational cancer models towards clinical
applications, one faces the dilemma of how to deal with an ever growing amount
of biomedical data that ought to be incorporated eventually in one form or
another. Model scalability becomes of paramount interest. In an effort to start
addressing ... | [
{
"created": "Tue, 24 Jun 2008 20:20:19 GMT",
"version": "v1"
}
] | 2008-06-26 | [
[
"Zhang",
"Le",
""
],
[
"Chen",
"L. Leon",
""
],
[
"Deisboeck",
"Thomas S.",
""
]
] | In advancing discrete-based computational cancer models towards clinical applications, one faces the dilemma of how to deal with an ever growing amount of biomedical data that ought to be incorporated eventually in one form or another. Model scalability becomes of paramount interest. In an effort to start addressing th... |
0706.2328 | Ophir Flomenbom | Ophir Flomenbom, Robert J. Silbey | Unique mechanisms from finite two-state trajectories | null | E. Barkai, F. L. H. Brown, M. Orrit & H. Yang Eds. THEORY AND
EVALUATION OF SINGLE-MOLECULE SIGNALS, (October, 2008) | null | null | q-bio.QM cond-mat.other q-bio.OT | null | Single molecule data made of on and off events are ubiquitous. Famous
examples include enzyme turnover, probed via fluorescence, and opening and
closing of ion-channel, probed via the flux of ions. The data reflects the
dynamics in the underlying multi-substate on-off kinetic scheme (KS) of the
process, but the deter... | [
{
"created": "Fri, 15 Jun 2007 16:17:11 GMT",
"version": "v1"
},
{
"created": "Fri, 31 Aug 2007 22:27:44 GMT",
"version": "v2"
}
] | 2010-08-16 | [
[
"Flomenbom",
"Ophir",
""
],
[
"Silbey",
"Robert J.",
""
]
] | Single molecule data made of on and off events are ubiquitous. Famous examples include enzyme turnover, probed via fluorescence, and opening and closing of ion-channel, probed via the flux of ions. The data reflects the dynamics in the underlying multi-substate on-off kinetic scheme (KS) of the process, but the determi... |
0804.2696 | Shuhei Mano | Shuhei Mano | Duality, Ancestral and Diffusion Processes in Models with Selection | 36 pages, 5 figures; minor correction, figures added | Theor. Popul. Biol. 75 (2009) 164-175 | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ancestral selection graph in population genetics was introduced by
KroneNeuhauser (1997) as an analogue of the coalescent genealogy of a sample of
genes from a neutrally evolving population. The number of particles in this
graph, followed backwards in time, is a birth and death process with quadratic
death and li... | [
{
"created": "Wed, 16 Apr 2008 23:12:27 GMT",
"version": "v1"
},
{
"created": "Mon, 2 Feb 2009 05:32:17 GMT",
"version": "v2"
}
] | 2013-04-08 | [
[
"Mano",
"Shuhei",
""
]
] | The ancestral selection graph in population genetics was introduced by KroneNeuhauser (1997) as an analogue of the coalescent genealogy of a sample of genes from a neutrally evolving population. The number of particles in this graph, followed backwards in time, is a birth and death process with quadratic death and line... |
0801.4543 | Attila Szolnoki | G. Szabo, A. Szolnoki, and I. Borsos | Self-organizing patterns maintained by competing associations in a
six-species predator-prey model | 6 pages, 8 figures | Phys. Rev. E 77 (2008) 041919 | 10.1103/PhysRevE.77.041919 | null | q-bio.PE cond-mat.stat-mech physics.bio-ph | null | Formation and competition of associations are studied in a six-species
ecological model where each species has two predators and two prey. Each site
of a square lattice is occupied by an individual belonging to one of the six
species. The evolution of the spatial distribution of species is governed by
iterated invasi... | [
{
"created": "Tue, 29 Jan 2008 19:01:07 GMT",
"version": "v1"
}
] | 2008-08-26 | [
[
"Szabo",
"G.",
""
],
[
"Szolnoki",
"A.",
""
],
[
"Borsos",
"I.",
""
]
] | Formation and competition of associations are studied in a six-species ecological model where each species has two predators and two prey. Each site of a square lattice is occupied by an individual belonging to one of the six species. The evolution of the spatial distribution of species is governed by iterated invasion... |
0809.1138 | Alex Feigel | Alexander Feigel, Avraham Englander and Assaf Engel | Derivation of evolutionary payoffs from observable behavior | 9 pages, 3 figures | null | null | null | q-bio.PE cs.GT physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Interpretation of animal behavior, especially as cooperative or selfish, is a
challenge for evolutionary theory. Strategy of a competition should follow from
corresponding Darwinian payoffs for the available behavioral options. The
payoffs and decision making processes, however, are difficult to observe and
quantify.... | [
{
"created": "Sat, 6 Sep 2008 06:43:57 GMT",
"version": "v1"
}
] | 2008-09-09 | [
[
"Feigel",
"Alexander",
""
],
[
"Englander",
"Avraham",
""
],
[
"Engel",
"Assaf",
""
]
] | Interpretation of animal behavior, especially as cooperative or selfish, is a challenge for evolutionary theory. Strategy of a competition should follow from corresponding Darwinian payoffs for the available behavioral options. The payoffs and decision making processes, however, are difficult to observe and quantify. H... |
1509.03516 | Yuri Shestopaloff | Yuri K. Shestopaloff | Method for finding metabolic properties based on the general growth law.
Liver examples. A General framework for biological modeling | 20 pages, 6 figures, 4 tables | PLoS ONE, 2014, 9(6): e99836 | 10.1371/journal.pone.0099836 | null | q-bio.TO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a method for finding metabolic parameters of cells, organs and
whole organisms, which is based on the earlier discovered general growth law.
Based on the obtained results and analysis of available biological models, we
propose a general framework for modeling biological phenomena and discuss how
it can be ... | [
{
"created": "Thu, 10 Sep 2015 01:02:25 GMT",
"version": "v1"
}
] | 2015-09-14 | [
[
"Shestopaloff",
"Yuri K.",
""
]
] | We propose a method for finding metabolic parameters of cells, organs and whole organisms, which is based on the earlier discovered general growth law. Based on the obtained results and analysis of available biological models, we propose a general framework for modeling biological phenomena and discuss how it can be us... |
1609.02893 | Leandro Alonso | Leandro M. Alonso | Emergent computation in simple model of neural activity | Reason for withdrawal is that in the draft the study is not
sufficiently well-motivated and incomplete. The draft as it is may be
misleading. The network introduced in this draft was studied thoroughly and
the results were published elsewhere. Please see
https://doi.org/10.1063/1.4984800 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the dynamics of a network consisting of an array of identical
cortical units with nearest neighbor interactions under periodic arousal. Each
unit consists of two interconnected populations of neurons tuned to a state in
which many nonlinear resonances are available. The network is critically
balanced d... | [
{
"created": "Fri, 9 Sep 2016 19:16:34 GMT",
"version": "v1"
},
{
"created": "Sat, 9 Feb 2019 20:45:33 GMT",
"version": "v2"
}
] | 2019-02-12 | [
[
"Alonso",
"Leandro M.",
""
]
] | We investigate the dynamics of a network consisting of an array of identical cortical units with nearest neighbor interactions under periodic arousal. Each unit consists of two interconnected populations of neurons tuned to a state in which many nonlinear resonances are available. The network is critically balanced due... |
2207.05197 | Rodrigo Cofre | Matthieu Gilson, Enzo Tagliazucchi and Rodrigo Cofre | Entropy production of Multivariate Ornstein-Uhlenbeck processes
correlates with consciousness levels in the human brain | null | null | 10.1103/PhysRevE.107.024121 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Consciousness is supported by complex patterns of brain activity which are
indicative of irreversible non-equilibrium dynamics. While the framework of
stochastic thermodynamics has facilitated the understanding of physical systems
of this kind, its application to infer the level of consciousness from
empirical data r... | [
{
"created": "Mon, 11 Jul 2022 21:27:27 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Jan 2023 16:05:54 GMT",
"version": "v2"
}
] | 2023-03-01 | [
[
"Gilson",
"Matthieu",
""
],
[
"Tagliazucchi",
"Enzo",
""
],
[
"Cofre",
"Rodrigo",
""
]
] | Consciousness is supported by complex patterns of brain activity which are indicative of irreversible non-equilibrium dynamics. While the framework of stochastic thermodynamics has facilitated the understanding of physical systems of this kind, its application to infer the level of consciousness from empirical data rem... |
2208.11631 | Andrew Murphy | Andrew C. Murphy, Romain Duprat, Theodore D. Satterthwaite, Desmond J.
Oathes, Dani S. Bassett | A structurally informed model for modulating functional connectivity | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Functional connectivity (FC) between brain regions tracks symptom severity in
many neuropsychiatric disorders. Transcranial magnetic stimulation (TMS)
directly alters regional activity and indirectly alters FC. Predicting how FC
will change following TMS is difficult, but would allow novel therapies that
target FC to... | [
{
"created": "Wed, 24 Aug 2022 16:06:01 GMT",
"version": "v1"
}
] | 2022-08-25 | [
[
"Murphy",
"Andrew C.",
""
],
[
"Duprat",
"Romain",
""
],
[
"Satterthwaite",
"Theodore D.",
""
],
[
"Oathes",
"Desmond J.",
""
],
[
"Bassett",
"Dani S.",
""
]
] | Functional connectivity (FC) between brain regions tracks symptom severity in many neuropsychiatric disorders. Transcranial magnetic stimulation (TMS) directly alters regional activity and indirectly alters FC. Predicting how FC will change following TMS is difficult, but would allow novel therapies that target FC to i... |
2205.08015 | Alexander Strang | Christopher Cebra, and Alexander Strang | Similarity Suppresses Cyclicity: Why Similar Competitors Form
Hierarchies | 37 pages, 9 figures | null | null | null | q-bio.PE math.PR | http://creativecommons.org/licenses/by/4.0/ | Competitive systems can exhibit both hierarchical (transitive) and cyclic
(intransitive) structures. Despite theoretical interest in cyclic competition,
which offers richer dynamics, and occupies a larger subset of the space of
possible competitive systems, most real-world systems are predominantly
transitive. Why? H... | [
{
"created": "Mon, 16 May 2022 23:09:59 GMT",
"version": "v1"
}
] | 2022-05-18 | [
[
"Cebra",
"Christopher",
""
],
[
"Strang",
"Alexander",
""
]
] | Competitive systems can exhibit both hierarchical (transitive) and cyclic (intransitive) structures. Despite theoretical interest in cyclic competition, which offers richer dynamics, and occupies a larger subset of the space of possible competitive systems, most real-world systems are predominantly transitive. Why? Her... |
1604.01674 | Sean Robinson | C. Brandon Ogbunugafor and Sean P. Robinson | OFFl models: novel schema for dynamical modeling of biological systems | 23 pages, 6 figures. Revised to match published version in PLoS ONE | PLoS ONE 11(6): e0156844 (2016) | 10.1371/journal.pone.0156844 | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Flow diagrams are a common tool used to help build and interpret models of
dynamical systems, often in biological contexts such as consumer-resource
models and similar compartmental models. Typically, their usage is intuitive
and informal. Here, we present a formalized version of flow diagrams as a kind
of weighted d... | [
{
"created": "Wed, 6 Apr 2016 16:04:03 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Jun 2016 20:09:27 GMT",
"version": "v2"
}
] | 2016-06-10 | [
[
"Ogbunugafor",
"C. Brandon",
""
],
[
"Robinson",
"Sean P.",
""
]
] | Flow diagrams are a common tool used to help build and interpret models of dynamical systems, often in biological contexts such as consumer-resource models and similar compartmental models. Typically, their usage is intuitive and informal. Here, we present a formalized version of flow diagrams as a kind of weighted dir... |
1211.4263 | Diana David-Rus | Diana David-Rus | Mathematical framework of epigenetic DNA methylation in gene body
Arabidopsis | 23 pp, 5 figures, Appendix file | null | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In aiming to explain the establishment, maintenance and stability of
methylation pattern in gene body of Arabidopsis we propose here a theoretical
framework for understanding how the methylated and unmethylated states of
cytosine residues are maintained and transmitted during DNA replication. Routed
in statistical me... | [
{
"created": "Sun, 18 Nov 2012 22:20:23 GMT",
"version": "v1"
}
] | 2012-11-20 | [
[
"David-Rus",
"Diana",
""
]
] | In aiming to explain the establishment, maintenance and stability of methylation pattern in gene body of Arabidopsis we propose here a theoretical framework for understanding how the methylated and unmethylated states of cytosine residues are maintained and transmitted during DNA replication. Routed in statistical mech... |
2004.04604 | Antonio Bianconi Prof. | Antonio Bianconi, Augusto Marcelli, Gaetano Campi, Andrea Perali | Efficiency of Covid-19 Mobile Contact Tracing Containment by Measuring
Time Dependent Doubling Time | 20 pages, 4 figures, 2 table | Phys. Biol. 17 065006 (2020) | 10.1088/1478-3975/abac51 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Covid-19 epidemic of the novel coronavirus (severe acute respiratory
syndrome SARS - CoV-2) has been spreading around the world. While different
containment policies using non-pharmaceutical interventions have been applied,
their efficiency are not known quantitatively. We show that the doubling time
Td(t) with t... | [
{
"created": "Thu, 9 Apr 2020 15:40:45 GMT",
"version": "v1"
},
{
"created": "Sun, 12 Apr 2020 15:41:22 GMT",
"version": "v2"
},
{
"created": "Wed, 29 Jul 2020 04:41:36 GMT",
"version": "v3"
}
] | 2020-10-28 | [
[
"Bianconi",
"Antonio",
""
],
[
"Marcelli",
"Augusto",
""
],
[
"Campi",
"Gaetano",
""
],
[
"Perali",
"Andrea",
""
]
] | The Covid-19 epidemic of the novel coronavirus (severe acute respiratory syndrome SARS - CoV-2) has been spreading around the world. While different containment policies using non-pharmaceutical interventions have been applied, their efficiency are not known quantitatively. We show that the doubling time Td(t) with the... |
2302.00855 | Zheng Yuan | Zheng Yuan, Yaoyun Zhang, Chuanqi Tan, Wei Wang, Fei Huang, Songfang
Huang | Molecular Geometry-aware Transformer for accurate 3D Atomic System
modeling | null | null | null | null | q-bio.MN cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Molecular dynamic simulations are important in computational physics,
chemistry, material, and biology. Machine learning-based methods have shown
strong abilities in predicting molecular energy and properties and are much
faster than DFT calculations. Molecular energy is at least related to atoms,
bonds, bond angles,... | [
{
"created": "Thu, 2 Feb 2023 03:49:57 GMT",
"version": "v1"
}
] | 2023-02-03 | [
[
"Yuan",
"Zheng",
""
],
[
"Zhang",
"Yaoyun",
""
],
[
"Tan",
"Chuanqi",
""
],
[
"Wang",
"Wei",
""
],
[
"Huang",
"Fei",
""
],
[
"Huang",
"Songfang",
""
]
] | Molecular dynamic simulations are important in computational physics, chemistry, material, and biology. Machine learning-based methods have shown strong abilities in predicting molecular energy and properties and are much faster than DFT calculations. Molecular energy is at least related to atoms, bonds, bond angles, t... |
2210.06512 | Zhenyu Yang | Zhenyu Yang, Kyle Lafata, Eugene Vaios, Zongsheng Hu, Trey Mullikin,
Fang-Fang Yin, Chunhao Wang | Quantifying U-Net Uncertainty in Multi-Parametric MRI-based Glioma
Segmentation by Spherical Image Projection | 31 pages, 9 figures, 1 table | null | null | null | q-bio.QM cs.CV eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The projection of planar MRI data onto a spherical surface is equivalent to a
nonlinear image transformation that retains global anatomical information. By
incorporating this image transformation process in our proposed spherical
projection-based U-Net (SPU-Net) segmentation model design, multiple
independent segment... | [
{
"created": "Wed, 12 Oct 2022 18:11:49 GMT",
"version": "v1"
},
{
"created": "Tue, 14 Mar 2023 20:16:51 GMT",
"version": "v2"
},
{
"created": "Sun, 13 Aug 2023 03:48:51 GMT",
"version": "v3"
}
] | 2023-08-15 | [
[
"Yang",
"Zhenyu",
""
],
[
"Lafata",
"Kyle",
""
],
[
"Vaios",
"Eugene",
""
],
[
"Hu",
"Zongsheng",
""
],
[
"Mullikin",
"Trey",
""
],
[
"Yin",
"Fang-Fang",
""
],
[
"Wang",
"Chunhao",
""
]
] | The projection of planar MRI data onto a spherical surface is equivalent to a nonlinear image transformation that retains global anatomical information. By incorporating this image transformation process in our proposed spherical projection-based U-Net (SPU-Net) segmentation model design, multiple independent segmentat... |
1710.11582 | Debashish Chowdhury | Soumendu Ghosh, Bhavya Mishra, Shubhadeep Patra, Andreas
Schadschneider and Debashish Chowdhury | A biologically inspired two-species exclusion model: effects of RNA
polymerase motor traffic on simultaneous DNA replication | 10 pages, including 7 figures | null | 10.1088/1742-5468/aab021 | null | q-bio.SC cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a two-species exclusion model to describe the key features of
the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the
transcription of a segment of DNA, concomitant with the progress of two DNA
replication forks on the same DNA segment. One of the species of particles
($P$) represent... | [
{
"created": "Tue, 31 Oct 2017 16:57:20 GMT",
"version": "v1"
},
{
"created": "Mon, 22 Jan 2018 11:40:53 GMT",
"version": "v2"
}
] | 2018-04-18 | [
[
"Ghosh",
"Soumendu",
""
],
[
"Mishra",
"Bhavya",
""
],
[
"Patra",
"Shubhadeep",
""
],
[
"Schadschneider",
"Andreas",
""
],
[
"Chowdhury",
"Debashish",
""
]
] | We introduce a two-species exclusion model to describe the key features of the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication forks on the same DNA segment. One of the species of particles ($P$) represents ... |
0902.3132 | Claude Pasquier | Vasilis Promponas, Giorgos Palaios, Claude Pasquier, Ioannis
Hamodrakas, Stavros Hamodrakas | CoPreTHi: a Web tool which combines transmembrane protein segment
prediction methods | null | In Silico Biology 1, 3 (1999) 159-62 | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | CoPreTHi is a Java based web application, which combines the results of
methods that predict the location of transmembrane segments in protein
sequences into a joint prediction histogram. Clearly, the joint prediction
algorithm, produces superior quality results than individual prediction
schemes. The program is avai... | [
{
"created": "Wed, 18 Feb 2009 13:23:00 GMT",
"version": "v1"
}
] | 2009-02-19 | [
[
"Promponas",
"Vasilis",
""
],
[
"Palaios",
"Giorgos",
""
],
[
"Pasquier",
"Claude",
""
],
[
"Hamodrakas",
"Ioannis",
""
],
[
"Hamodrakas",
"Stavros",
""
]
] | CoPreTHi is a Java based web application, which combines the results of methods that predict the location of transmembrane segments in protein sequences into a joint prediction histogram. Clearly, the joint prediction algorithm, produces superior quality results than individual prediction schemes. The program is availa... |
1711.09489 | Christos Skiadas H | Christos H Skiadas and Charilaos Skiadas | The Health Status of a Population estimated: The History of Health State
Curves | 11 pages, 13 figures | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Following the recent publication of our book on Exploring the Health State of
a Population by Dynamic Modeling Methods in The Springer Series on Demographic
Methods and Population Analysis (DOI 10.1007/978-3-319-65142-2) we provide this
brief presentation of the main findings and improvements regarding the Health
Sta... | [
{
"created": "Sun, 26 Nov 2017 23:22:34 GMT",
"version": "v1"
}
] | 2017-11-28 | [
[
"Skiadas",
"Christos H",
""
],
[
"Skiadas",
"Charilaos",
""
]
] | Following the recent publication of our book on Exploring the Health State of a Population by Dynamic Modeling Methods in The Springer Series on Demographic Methods and Population Analysis (DOI 10.1007/978-3-319-65142-2) we provide this brief presentation of the main findings and improvements regarding the Health State... |
1709.06950 | Damian Berger | Damian L. Berger, Lucilla de Arcangelis, and Hans J. Herrmann | Spatial features of synaptic adaptation affecting learning performance | null | Scientific Reports 7, 11016 (2017) | 10.1038/s41598-017-11424-5 | null | q-bio.NC cond-mat.dis-nn cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent studies have proposed that the diffusion of messenger molecules, such
as monoamines, can mediate the plastic adaptation of synapses in supervised
learning of neural networks. Based on these findings we developed a model for
neural learning, where the signal for plastic adaptation is assumed to
propagate throug... | [
{
"created": "Wed, 20 Sep 2017 16:18:17 GMT",
"version": "v1"
}
] | 2017-09-21 | [
[
"Berger",
"Damian L.",
""
],
[
"de Arcangelis",
"Lucilla",
""
],
[
"Herrmann",
"Hans J.",
""
]
] | Recent studies have proposed that the diffusion of messenger molecules, such as monoamines, can mediate the plastic adaptation of synapses in supervised learning of neural networks. Based on these findings we developed a model for neural learning, where the signal for plastic adaptation is assumed to propagate through ... |
2201.11418 | Sakuntala Chatterjee | Shobhan Dev Mandal and Sakuntala Chatterjee | Effect of receptor cooperativity on methylation dynamics in bacterial
chemotaxis with weak and strong gradient | null | Physical Review E 105, 014411 (2022) | 10.1103/PhysRevE.105.014411 | null | q-bio.CB cond-mat.stat-mech physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | We study methylation dynamics of the chemoreceptors as an {\sl E.coli} cell
moves around in a spatially varying chemo-attractant environment. We consider
attractant concentration with strong and weak spatial gradient. During the
uphill and downhill motion of the cell along the gradient, we measure the
temporal variat... | [
{
"created": "Thu, 27 Jan 2022 10:12:14 GMT",
"version": "v1"
}
] | 2022-01-28 | [
[
"Mandal",
"Shobhan Dev",
""
],
[
"Chatterjee",
"Sakuntala",
""
]
] | We study methylation dynamics of the chemoreceptors as an {\sl E.coli} cell moves around in a spatially varying chemo-attractant environment. We consider attractant concentration with strong and weak spatial gradient. During the uphill and downhill motion of the cell along the gradient, we measure the temporal variatio... |
1705.03460 | Leroy Cronin Prof | Stuart M. Marshall, Alastair R. G. Murray, and Leroy Cronin | A Probabilistic Framework for Quantifying Biological Complexity | 21 pages, 7 figures | null | 10.1098/rsta.2016.0342 | null | q-bio.OT cs.IT math.IT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One thing that discriminates living things from inanimate matter is their
ability to generate similarly complex or non-random architectures in a large
abundance. From DNA sequences to folded protein structures, living cells,
microbial communities and multicellular structures, the material configurations
in biology ca... | [
{
"created": "Tue, 9 May 2017 21:13:25 GMT",
"version": "v1"
}
] | 2018-02-07 | [
[
"Marshall",
"Stuart M.",
""
],
[
"Murray",
"Alastair R. G.",
""
],
[
"Cronin",
"Leroy",
""
]
] | One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random architectures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can ... |
1406.5855 | Sang Hoon Lee | Sang Hoon Lee, Mark D. Fricker, Mason A. Porter | Mesoscale analyses of fungal networks as an approach for quantifying
phenotypic traits | 16 pages, 3 figures, 1 table | Journal of Complex Networks 5, 145 (2017) | 10.1093/comnet/cnv034 | null | q-bio.QM cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the application of mesoscopic response functions (MRFs) to
characterize a large set of networks of fungi and slime moulds grown under a
wide variety of different experimental treatments, including inter-species
competition and attack by fungivores. We construct 'structural networks' by
estimating cord ... | [
{
"created": "Mon, 23 Jun 2014 10:24:33 GMT",
"version": "v1"
},
{
"created": "Tue, 24 Mar 2015 15:02:33 GMT",
"version": "v2"
},
{
"created": "Tue, 22 Dec 2015 16:46:42 GMT",
"version": "v3"
},
{
"created": "Sun, 1 May 2016 11:35:50 GMT",
"version": "v4"
},
{
"cr... | 2017-03-03 | [
[
"Lee",
"Sang Hoon",
""
],
[
"Fricker",
"Mark D.",
""
],
[
"Porter",
"Mason A.",
""
]
] | We investigate the application of mesoscopic response functions (MRFs) to characterize a large set of networks of fungi and slime moulds grown under a wide variety of different experimental treatments, including inter-species competition and attack by fungivores. We construct 'structural networks' by estimating cord co... |
q-bio/0703040 | Oskar Hallatschek | Oskar Hallatschek, David R. Nelson | Gene surfing | null | Theoretical Population Biology, 73 (1), p. 158, 2008. | 10.1016/j.tpb.2007.08.008 | null | q-bio.PE | null | Spatially resolved genetic data is increasingly used to reconstruct the
migrational history of species. To assist such inference, we study, by means of
simulations and analytical methods, the dynamics of neutral gene frequencies in
a population undergoing a continual range expansion in one dimension. During
such a co... | [
{
"created": "Sun, 18 Mar 2007 01:27:09 GMT",
"version": "v1"
}
] | 2008-01-15 | [
[
"Hallatschek",
"Oskar",
""
],
[
"Nelson",
"David R.",
""
]
] | Spatially resolved genetic data is increasingly used to reconstruct the migrational history of species. To assist such inference, we study, by means of simulations and analytical methods, the dynamics of neutral gene frequencies in a population undergoing a continual range expansion in one dimension. During such a colo... |
1806.00215 | So Nakashima | So Nakashima, Yuki Sughiyama, Tetsuya J. Kobayashi | Lineage EM Algorithm for Inferring Latent States from Cellular Lineage
Trees | 12 pages; Supplementary Information and full-resolution figures are
available at bioarxiv (https://doi.org/10.1101/488981 ) | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phenotypic variability in a population of cells can work as the bet-hedging
of the cells under an unpredictably changing environment, the typical example
of which is the bacterial persistence. To understand the strategy to control
such phenomena, it is indispensable to identify the phenotype of each cell and
its inhe... | [
{
"created": "Fri, 1 Jun 2018 06:49:17 GMT",
"version": "v1"
},
{
"created": "Wed, 13 Jun 2018 09:08:02 GMT",
"version": "v2"
},
{
"created": "Mon, 10 Dec 2018 03:44:29 GMT",
"version": "v3"
},
{
"created": "Fri, 29 Nov 2019 09:15:20 GMT",
"version": "v4"
}
] | 2019-12-02 | [
[
"Nakashima",
"So",
""
],
[
"Sughiyama",
"Yuki",
""
],
[
"Kobayashi",
"Tetsuya J.",
""
]
] | Phenotypic variability in a population of cells can work as the bet-hedging of the cells under an unpredictably changing environment, the typical example of which is the bacterial persistence. To understand the strategy to control such phenomena, it is indispensable to identify the phenotype of each cell and its inheri... |
1007.4471 | Tsvi Tlusty | Tsvi Tlusty | The physical language of molecular codes: A rate-distortion approach to
the evolution and emergence of biological codes | Index Terms--Molecular codes, rate-distortion theory, biological
information networks, molecular recognition.
http://www.weizmann.ac.il/complex/tlusty/papers/IEEE2009.pdf | Workshop on Biological and Bio-Inspired Information Theory, 43rd
Annual Conference on Information Sciences and Systems, March 18-20, 2009 2009
, Page(s): 841 - 846 | 10.1109/CISS.2009.5054834 | null | q-bio.BM cs.IT math.IT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The function of the organism hinges on the performance of its
information-processing networks, which convey information via molecular
recognition. Many paths within these networks utilize molecular codebooks, such
as the genetic code, to translate information written in one class of molecules
into another molecular "... | [
{
"created": "Mon, 26 Jul 2010 14:24:05 GMT",
"version": "v1"
}
] | 2010-07-27 | [
[
"Tlusty",
"Tsvi",
""
]
] | The function of the organism hinges on the performance of its information-processing networks, which convey information via molecular recognition. Many paths within these networks utilize molecular codebooks, such as the genetic code, to translate information written in one class of molecules into another molecular "la... |
1605.05685 | Eugen Tarnow | Eugen Tarnow | First direct evidence of two stages in free recall and three
corresponding estimates of working memory capacity | null | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | I find that exactly two stages can be seen directly in sequential free recall
distributions. These distributions show that the first three recalls come from
the emptying of working memory, recalls 6 and above come from a second stage
and the 4th and 5th recalls are mixtures of the two. A discontinuity, a rounded
step... | [
{
"created": "Wed, 6 Apr 2016 11:17:03 GMT",
"version": "v1"
}
] | 2016-05-19 | [
[
"Tarnow",
"Eugen",
""
]
] | I find that exactly two stages can be seen directly in sequential free recall distributions. These distributions show that the first three recalls come from the emptying of working memory, recalls 6 and above come from a second stage and the 4th and 5th recalls are mixtures of the two. A discontinuity, a rounded step f... |
0908.1685 | Tihamer Geyer | Uwe Winter and Tihamer Geyer | Coarse Grained Simulations of a Small Peptide: Effects of Finite Damping
and Hydrodynamic Interactions | 7 pages, 6 figures, submitted to J Chem Phys | null | 10.1063/1.3216573 | null | q-bio.BM cond-mat.soft physics.chem-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the coarse grained Brownian Dynamics simulation method the many solvent
molecules are replaced by random thermal kicks and an effective friction acting
on the particles of interest. For Brownian Dynamics the friction has to be so
strong that the particles' velocities are damped much faster than the duration
of an ... | [
{
"created": "Wed, 12 Aug 2009 12:09:45 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Winter",
"Uwe",
""
],
[
"Geyer",
"Tihamer",
""
]
] | In the coarse grained Brownian Dynamics simulation method the many solvent molecules are replaced by random thermal kicks and an effective friction acting on the particles of interest. For Brownian Dynamics the friction has to be so strong that the particles' velocities are damped much faster than the duration of an in... |
q-bio/0611050 | Changbong Hyeon | Changbong Hyeon, Ruxandra I Dima and D. Thirumalai | Pathways and kinetic barriers in mechanical unfolding and refolding of
RNA and proteins | 33 pages 7 figures | Structure (2006) vol 14. 1633-1645 | null | null | q-bio.BM cond-mat.soft | null | Using self-organized polymer models, we predict mechanical unfolding and
refolding pathways of ribo-zymes, and the green fluorescent protein. In
agreement with experiments, there are between six and eight unfolding
transitions in the Tetrahymena ribozyme. Depending on the loading rate, the
number of rips in the force... | [
{
"created": "Thu, 16 Nov 2006 22:03:38 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Hyeon",
"Changbong",
""
],
[
"Dima",
"Ruxandra I",
""
],
[
"Thirumalai",
"D.",
""
]
] | Using self-organized polymer models, we predict mechanical unfolding and refolding pathways of ribo-zymes, and the green fluorescent protein. In agreement with experiments, there are between six and eight unfolding transitions in the Tetrahymena ribozyme. Depending on the loading rate, the number of rips in the force-r... |
1709.02386 | Carsten Lemmen | Kaela Slavik, Carsten Lemmen, Wenyan Zhang, Onur Kerimoglu, Knut
Klingbeil, Kai W. Wirtz | The large scale impact of offshore wind farm structures on pelagic
primary productivity in the southern North Sea | 17 pages, 6 figures, re-revised manuscript submitted to Hydrobiologia | null | 10.1007/s10750-018-3653-5 | null | q-bio.PE | http://creativecommons.org/licenses/by-sa/4.0/ | The increasing demand for renewable energy is projected to result in a
40-fold increase in offshore wind electricity in the European Union by 2030.
Despite a great number of local impact studies for selected marine populations,
the regional ecosystem impacts of offshore wind farm structures are not yet
well assessed ... | [
{
"created": "Thu, 7 Sep 2017 16:43:34 GMT",
"version": "v1"
},
{
"created": "Fri, 30 Mar 2018 11:59:17 GMT",
"version": "v2"
},
{
"created": "Wed, 9 May 2018 10:58:17 GMT",
"version": "v3"
}
] | 2023-12-14 | [
[
"Slavik",
"Kaela",
""
],
[
"Lemmen",
"Carsten",
""
],
[
"Zhang",
"Wenyan",
""
],
[
"Kerimoglu",
"Onur",
""
],
[
"Klingbeil",
"Knut",
""
],
[
"Wirtz",
"Kai W.",
""
]
] | The increasing demand for renewable energy is projected to result in a 40-fold increase in offshore wind electricity in the European Union by 2030. Despite a great number of local impact studies for selected marine populations, the regional ecosystem impacts of offshore wind farm structures are not yet well assessed no... |
1304.2955 | Arindam RoyChoudhury | Arindam RoyChoudhury | Change in Recessive Lethal Alleles Frequency in Inbred Populations | 9 pages, 3 figures | null | null | null | q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In a population practicing consanguineous marriage, rare recessive lethal
alleles (RRLA) have higher chances of affecting phenotypes. As inbreeding
causes more homozygosity and subsequently more deaths, the loss of individuals
with RRLA decreases the frequency of these alleles. Although this phenomenon is
well studie... | [
{
"created": "Wed, 10 Apr 2013 13:39:06 GMT",
"version": "v1"
}
] | 2013-04-11 | [
[
"RoyChoudhury",
"Arindam",
""
]
] | In a population practicing consanguineous marriage, rare recessive lethal alleles (RRLA) have higher chances of affecting phenotypes. As inbreeding causes more homozygosity and subsequently more deaths, the loss of individuals with RRLA decreases the frequency of these alleles. Although this phenomenon is well studied ... |
2101.04532 | Wlodzislaw Duch | W{\l}odzis{\l}aw Duch | Experiential Learning Styles and Neurocognitive Phenomics | 20 pages, extended version of article published in "Brains and
Education: Towards Neurocognitive Phenomics", proceedings of: Learning while
we are connected, Vol. 3, Eds. N. Reynolds, M. Webb, M.M. Sys{\l}o, V.
Dagiene, pp. 12-23. X World Conference on Computers in Education, 2013;
Toru\'n, Poland | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Phenomics is concerned with detailed description of all aspects of organisms,
from their physical foundations at genetic, molecular and cellular level, to
behavioural and psychological traits. Neuropsychiatric phenomics, endorsed by
NIMH, provides such broad perspective to understand mental disorders. It is
clear tha... | [
{
"created": "Tue, 12 Jan 2021 15:10:06 GMT",
"version": "v1"
}
] | 2021-01-13 | [
[
"Duch",
"Włodzisław",
""
]
] | Phenomics is concerned with detailed description of all aspects of organisms, from their physical foundations at genetic, molecular and cellular level, to behavioural and psychological traits. Neuropsychiatric phenomics, endorsed by NIMH, provides such broad perspective to understand mental disorders. It is clear that ... |
1611.00730 | William Holmes | William R. Holmes, JinSeok Park, Andre Levchenko, Leah
Edelstein-Keshet | A mathematical model coupling polarity signaling to cell adhesion
explains diverse cell migration patterns | null | null | 10.1371/journal.pcbi.1005524 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cells crawling through tissues migrate inside a complex fibrous environment
called the extracellular matrix (ECM), which provides signals regulating
motility. Here we investigate one such well-known pathway, involving mutually
antagonistic signalling molecules (small GTPases Rac and Rho) that control the
protrusion a... | [
{
"created": "Wed, 2 Nov 2016 19:10:01 GMT",
"version": "v1"
}
] | 2017-07-05 | [
[
"Holmes",
"William R.",
""
],
[
"Park",
"JinSeok",
""
],
[
"Levchenko",
"Andre",
""
],
[
"Edelstein-Keshet",
"Leah",
""
]
] | Cells crawling through tissues migrate inside a complex fibrous environment called the extracellular matrix (ECM), which provides signals regulating motility. Here we investigate one such well-known pathway, involving mutually antagonistic signalling molecules (small GTPases Rac and Rho) that control the protrusion and... |
1904.09504 | Steven Tompson | Steven H. Tompson, Ari E. Kahn, Emily B. Falk, Jean M. Vettel,
Danielle S. Bassett | Functional brain network architecture supporting the learning of social
networks in humans | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most humans have the good fortune to live their lives embedded in richly
structured social groups. Yet, it remains unclear how humans acquire knowledge
about these social structures to successfully navigate social relationships.
Here we address this knowledge gap with an interdisciplinary neuroimaging study
drawing o... | [
{
"created": "Sat, 20 Apr 2019 22:04:44 GMT",
"version": "v1"
}
] | 2019-04-23 | [
[
"Tompson",
"Steven H.",
""
],
[
"Kahn",
"Ari E.",
""
],
[
"Falk",
"Emily B.",
""
],
[
"Vettel",
"Jean M.",
""
],
[
"Bassett",
"Danielle S.",
""
]
] | Most humans have the good fortune to live their lives embedded in richly structured social groups. Yet, it remains unclear how humans acquire knowledge about these social structures to successfully navigate social relationships. Here we address this knowledge gap with an interdisciplinary neuroimaging study drawing on ... |
2001.05416 | Martin Oheim | Martin Oheim, Adi Salomon, Maia Brunstein | Supercritical angle microscopy and spectroscopy | 3 figures | null | 10.1016/j.bpj.2020.03.029 | null | q-bio.QM physics.optics | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fluorescence detection, either involving propagating or near-field emission,
is widely being used in spectroscopy, sensing and microscopy. Total internal
reflection fluorescence (TIRF) confines fluorescence excitation by an
evanescent (near-) field and it is a popular contrast generator for
surface-selective fluoresc... | [
{
"created": "Wed, 15 Jan 2020 16:34:58 GMT",
"version": "v1"
}
] | 2020-06-24 | [
[
"Oheim",
"Martin",
""
],
[
"Salomon",
"Adi",
""
],
[
"Brunstein",
"Maia",
""
]
] | Fluorescence detection, either involving propagating or near-field emission, is widely being used in spectroscopy, sensing and microscopy. Total internal reflection fluorescence (TIRF) confines fluorescence excitation by an evanescent (near-) field and it is a popular contrast generator for surface-selective fluorescen... |
1712.03891 | Cameron Smith | Cameron A. Smith and Christian A. Yates | Spatially-extended hybrid methods: a review | 43 Pages, 13 Figures, 4 Tables | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many biological and physical systems exhibit behaviour at multiple spatial,
temporal or population scales. Multiscale processes provide challenges when
they are to be simulated using numerical techniques. While coarser methods such
as partial differential equations are typically fast to simulate, they lack the
indivi... | [
{
"created": "Mon, 11 Dec 2017 17:08:06 GMT",
"version": "v1"
},
{
"created": "Fri, 9 Feb 2018 16:02:05 GMT",
"version": "v2"
}
] | 2018-02-12 | [
[
"Smith",
"Cameron A.",
""
],
[
"Yates",
"Christian A.",
""
]
] | Many biological and physical systems exhibit behaviour at multiple spatial, temporal or population scales. Multiscale processes provide challenges when they are to be simulated using numerical techniques. While coarser methods such as partial differential equations are typically fast to simulate, they lack the individu... |
2004.00443 | Stephen Edward Moore | Stephen E. Moore and Eric Okyere | Controlling the Transmission Dynamics of COVID-19 | 13pages, 37 figures | null | null | null | q-bio.PE math.DS math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The outbreak of COVID-19 caused by SARS-CoV-2 in Wuhan and other cities in
China in 2019 has become a global pandemic as declared by World Health
Organization (WHO) in the first quarter of 2020 . The delay in diagnosis,
limited hospital resources and other treatment resources leads to rapid spread
of COVID-19. In thi... | [
{
"created": "Tue, 31 Mar 2020 11:37:40 GMT",
"version": "v1"
},
{
"created": "Thu, 2 Apr 2020 15:35:58 GMT",
"version": "v2"
}
] | 2020-04-03 | [
[
"Moore",
"Stephen E.",
""
],
[
"Okyere",
"Eric",
""
]
] | The outbreak of COVID-19 caused by SARS-CoV-2 in Wuhan and other cities in China in 2019 has become a global pandemic as declared by World Health Organization (WHO) in the first quarter of 2020 . The delay in diagnosis, limited hospital resources and other treatment resources leads to rapid spread of COVID-19. In this ... |
q-bio/0309010 | Prashant Purohit | Prashant K. Purohit (1), Jane' Kondev (2) and Rob Phillips (1) ((1)
California Institute of Technology, (2) Brandeis University) | Force steps during viral DNA packaging ? | 18 pages, 7 figures, To appear in the Journal of Mechanics and
Physics of Solids | null | 10.1016/j.jmps.2003.09.016 | null | q-bio.BM q-bio.SC | null | Biophysicists and structural biologists increasingly acknowledge the role
played by the mechanical properties of macromolecules as a critical element in
many biological processes. This change has been brought about, in part, by the
advent of single molecule biophysics techniques that have made it possible to
exert pi... | [
{
"created": "Mon, 22 Sep 2003 21:49:15 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Purohit",
"Prashant K.",
""
],
[
"Kondev",
"Jane'",
""
],
[
"Phillips",
"Rob",
""
]
] | Biophysicists and structural biologists increasingly acknowledge the role played by the mechanical properties of macromolecules as a critical element in many biological processes. This change has been brought about, in part, by the advent of single molecule biophysics techniques that have made it possible to exert pico... |
2301.04355 | Thomas G\"otz | Philipp Doenges, Thomas G\"otz, Tyll Krueger, Karol Niedzielewski,
Viola Priesemann, Moritz Schaefer | SIR-Model for Households | 17 pages,10 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-sa/4.0/ | Households play an important role in disease dynamics. Many infections
happening there due to the close contact, while mitigation measures mainly
target the transmission between households. Therefore, one can see households
as boosting the transmission depending on household size. To study the effect
of household siz... | [
{
"created": "Wed, 11 Jan 2023 08:46:21 GMT",
"version": "v1"
}
] | 2023-01-12 | [
[
"Doenges",
"Philipp",
""
],
[
"Götz",
"Thomas",
""
],
[
"Krueger",
"Tyll",
""
],
[
"Niedzielewski",
"Karol",
""
],
[
"Priesemann",
"Viola",
""
],
[
"Schaefer",
"Moritz",
""
]
] | Households play an important role in disease dynamics. Many infections happening there due to the close contact, while mitigation measures mainly target the transmission between households. Therefore, one can see households as boosting the transmission depending on household size. To study the effect of household size ... |
2208.04771 | Ignacio Enrique S\'anchez | Lucio Aliperti Car, Gonzalo Farfa\~nuk, Luciana L. Couso, Alfonso
Soler-Bistu\'e, Ariel A. Aptekmann, Ignacio E. S\'anchez | r/K selection of GC content in prokaryotes | 15 pages, 6 figures | null | null | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | The GC content of prokaryotic genomes is species-specific and takes values
from 16 to 77 percent. There are currently no accepted explanations for this
diversity of selection for GC content. We analyzed the known correlations
between GC content, genome size and amino acid cost in thousands of
prokaryotes, together wi... | [
{
"created": "Tue, 9 Aug 2022 13:29:28 GMT",
"version": "v1"
},
{
"created": "Fri, 16 Dec 2022 12:35:09 GMT",
"version": "v2"
}
] | 2022-12-19 | [
[
"Car",
"Lucio Aliperti",
""
],
[
"Farfañuk",
"Gonzalo",
""
],
[
"Couso",
"Luciana L.",
""
],
[
"Soler-Bistué",
"Alfonso",
""
],
[
"Aptekmann",
"Ariel A.",
""
],
[
"Sánchez",
"Ignacio E.",
""
]
] | The GC content of prokaryotic genomes is species-specific and takes values from 16 to 77 percent. There are currently no accepted explanations for this diversity of selection for GC content. We analyzed the known correlations between GC content, genome size and amino acid cost in thousands of prokaryotes, together with... |
1504.03746 | Willem Wybo | Willem A.M. Wybo, Daniele Boccalini, Benjamin Torben-Nielsen,
Marc-Oliver Gewaltig | A sparse reformulation of the Green's function formalism allows
efficient simulations of partial differential equations on tree graphs | 41 pages, 4 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We prove that when a class of partial differential equations, generalized
from the cable equation, is defined on tree graphs, and when the inputs are
restricted to a spatially discrete, well chosen set of points, the Green's
function (GF) formalism can be rewritten to scale as $O(n)$ with the number $n$
of input loca... | [
{
"created": "Tue, 14 Apr 2015 23:59:40 GMT",
"version": "v1"
},
{
"created": "Wed, 16 Sep 2015 09:47:52 GMT",
"version": "v2"
}
] | 2015-09-17 | [
[
"Wybo",
"Willem A. M.",
""
],
[
"Boccalini",
"Daniele",
""
],
[
"Torben-Nielsen",
"Benjamin",
""
],
[
"Gewaltig",
"Marc-Oliver",
""
]
] | We prove that when a class of partial differential equations, generalized from the cable equation, is defined on tree graphs, and when the inputs are restricted to a spatially discrete, well chosen set of points, the Green's function (GF) formalism can be rewritten to scale as $O(n)$ with the number $n$ of input locati... |
2305.07482 | Braden Brinkman | Jacob T. Crosser and Braden A. W. Brinkman | Applications of information geometry to spiking neural network behavior | 36 pages, 14 figures | null | null | null | q-bio.NC cond-mat.dis-nn | http://creativecommons.org/licenses/by/4.0/ | The space of possible behaviors complex biological systems may exhibit is
unimaginably vast, and these systems often appear to be stochastic, whether due
to variable noisy environmental inputs or intrinsically generated chaos. The
brain is a prominent example of a biological system with complex behaviors. The
number ... | [
{
"created": "Fri, 12 May 2023 13:50:41 GMT",
"version": "v1"
}
] | 2023-05-15 | [
[
"Crosser",
"Jacob T.",
""
],
[
"Brinkman",
"Braden A. W.",
""
]
] | The space of possible behaviors complex biological systems may exhibit is unimaginably vast, and these systems often appear to be stochastic, whether due to variable noisy environmental inputs or intrinsically generated chaos. The brain is a prominent example of a biological system with complex behaviors. The number of... |
2110.03529 | Feng Cheng | Feng Cheng | Using Single-Trial Representational Similarity Analysis with EEG to
track semantic similarity in emotional word processing | null | null | null | null | q-bio.NC cs.CL | http://creativecommons.org/licenses/by/4.0/ | Electroencephalography (EEG) is a powerful non-invasive brain imaging
technique with a high temporal resolution that has seen extensive use across
multiple areas of cognitive science research. This thesis adapts
representational similarity analysis (RSA) to single-trial EEG datasets and
introduces its principles to E... | [
{
"created": "Mon, 4 Oct 2021 17:17:38 GMT",
"version": "v1"
}
] | 2021-10-08 | [
[
"Cheng",
"Feng",
""
]
] | Electroencephalography (EEG) is a powerful non-invasive brain imaging technique with a high temporal resolution that has seen extensive use across multiple areas of cognitive science research. This thesis adapts representational similarity analysis (RSA) to single-trial EEG datasets and introduces its principles to EEG... |
1004.4116 | Simon Tavar\'e | A. D. Barbour and Simon Tavar\'e | Assessing molecular variability in cancer genomes | 22 pages, 1 figure. Chapter 4 of "Probability and Mathematical
Genetics: Papers in Honour of Sir John Kingman" (Editors N.H. Bingham and
C.M. Goldie), Cambridge University Press, 2010 | null | null | null | q-bio.PE stat.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The dynamics of tumour evolution are not well understood. In this paper we
provide a statistical framework for evaluating the molecular variation observed
in different parts of a colorectal tumour. A multi-sample version of the Ewens
Sampling Formula forms the basis for our modelling of the data, and we provide
a sim... | [
{
"created": "Tue, 13 Apr 2010 22:07:53 GMT",
"version": "v1"
}
] | 2010-04-26 | [
[
"Barbour",
"A. D.",
""
],
[
"Tavaré",
"Simon",
""
]
] | The dynamics of tumour evolution are not well understood. In this paper we provide a statistical framework for evaluating the molecular variation observed in different parts of a colorectal tumour. A multi-sample version of the Ewens Sampling Formula forms the basis for our modelling of the data, and we provide a simul... |
1410.6049 | Dmitry Kobak | Luke Bashford, Dmitry Kobak, Carsten Mehring | Motor skill learning by increasing the movement planning horizon | 45 pages, 7 figures | Journal of Neurophysiology 127 (4) 2022, 995-1006 | 10.1152/jn.00631.2020 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigated motor skill learning using a path tracking task, where human
subjects had to track various curved paths as fast as possible, in the absence
of any external perturbations. Subjects became better with practice, producing
faster and smoother movements even when tracking novel untrained paths. Using a
"se... | [
{
"created": "Wed, 22 Oct 2014 14:21:05 GMT",
"version": "v1"
},
{
"created": "Sat, 17 Oct 2015 21:14:22 GMT",
"version": "v2"
}
] | 2024-06-06 | [
[
"Bashford",
"Luke",
""
],
[
"Kobak",
"Dmitry",
""
],
[
"Mehring",
"Carsten",
""
]
] | We investigated motor skill learning using a path tracking task, where human subjects had to track various curved paths as fast as possible, in the absence of any external perturbations. Subjects became better with practice, producing faster and smoother movements even when tracking novel untrained paths. Using a "sear... |
2106.10344 | Hamidreza Ramezanpour | Hamidreza Ramezanpour and Mazyar Fallah | The role of temporal cortex in the control of attention | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Attention is an indispensable component of active vision. Contrary to the
widely accepted notion that temporal cortex processing primarily focusses on
passive object recognition, a series of very recent studies emphasize the role
of temporal cortex structures, specifically the superior temporal sulcus (STS)
and infer... | [
{
"created": "Fri, 18 Jun 2021 20:17:15 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Nov 2021 03:08:09 GMT",
"version": "v2"
}
] | 2021-11-25 | [
[
"Ramezanpour",
"Hamidreza",
""
],
[
"Fallah",
"Mazyar",
""
]
] | Attention is an indispensable component of active vision. Contrary to the widely accepted notion that temporal cortex processing primarily focusses on passive object recognition, a series of very recent studies emphasize the role of temporal cortex structures, specifically the superior temporal sulcus (STS) and inferot... |
2108.04090 | Abby Stylianou | Abby Stylianou, Robert Pless, Nadia Shakoor and Todd Mockler | Classification and Visualization of Genotype x Phenotype Interactions in
Biomass Sorghum | ICCV 2021 Workshop on Computer Vision Problems in Plant Phenotyping
and Agriculture (CVPPA) | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a simple approach to understanding the relationship between
single nucleotide polymorphisms (SNPs), or groups of related SNPs, and the
phenotypes they control. The pipeline involves training deep convolutional
neural networks (CNNs) to differentiate between images of plants with reference
and alternate v... | [
{
"created": "Mon, 9 Aug 2021 14:39:23 GMT",
"version": "v1"
}
] | 2021-08-10 | [
[
"Stylianou",
"Abby",
""
],
[
"Pless",
"Robert",
""
],
[
"Shakoor",
"Nadia",
""
],
[
"Mockler",
"Todd",
""
]
] | We introduce a simple approach to understanding the relationship between single nucleotide polymorphisms (SNPs), or groups of related SNPs, and the phenotypes they control. The pipeline involves training deep convolutional neural networks (CNNs) to differentiate between images of plants with reference and alternate ver... |
1409.7589 | Gon\c{c}alo Prista | Francisco Cabral, Mario Cachao, Rui Jorge Agostinho, Goncalo Prista | Short note on the Sirenia disappearance from the Euro-North African
realm during the Cenozoic: a link between climate and Supernovae? | 9 pages, 2 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sirenia are marine mammals that colonized the European shores up to 2.7 Ma.
Their biodiversity evolution follows the climate evolution of the Cenozoic.
However, several climate events, as well as the global climate trend of this
Era are still struggling to be understood. When considering only Earth
processes, the cli... | [
{
"created": "Fri, 26 Sep 2014 14:25:27 GMT",
"version": "v1"
}
] | 2014-09-29 | [
[
"Cabral",
"Francisco",
""
],
[
"Cachao",
"Mario",
""
],
[
"Agostinho",
"Rui Jorge",
""
],
[
"Prista",
"Goncalo",
""
]
] | Sirenia are marine mammals that colonized the European shores up to 2.7 Ma. Their biodiversity evolution follows the climate evolution of the Cenozoic. However, several climate events, as well as the global climate trend of this Era are still struggling to be understood. When considering only Earth processes, the clima... |
1701.05157 | Satohiro Tajima | Satohiro Tajima and Ryota Kanai | Integrated information and dimensionality in continuous attractor
dynamics | null | Neurosci Conscious 2017, 3 (1): nix011 | 10.1093/nc/nix011 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There has been increasing interest in the integrated information theory (IIT)
ofconsciousness, which hypothesizes that consciousness is integrated
information withinneuronal dynamics. However, the current formulation of IIT
poses both practical andtheoretical problems when we aim to empirically test
the theory by com... | [
{
"created": "Wed, 18 Jan 2017 17:34:36 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Jan 2017 18:03:30 GMT",
"version": "v2"
}
] | 2017-07-04 | [
[
"Tajima",
"Satohiro",
""
],
[
"Kanai",
"Ryota",
""
]
] | There has been increasing interest in the integrated information theory (IIT) ofconsciousness, which hypothesizes that consciousness is integrated information withinneuronal dynamics. However, the current formulation of IIT poses both practical andtheoretical problems when we aim to empirically test the theory by compu... |
0805.3523 | Kevin Lin | Kevin K. Lin, Eric Shea-Brown, Lai-Sang Young | Reliability of Layered Neural Oscillator Networks | null | null | null | null | q-bio.NC cond-mat.dis-nn nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the reliability of large networks of coupled neural oscillators in
response to fluctuating stimuli. Reliability means that a stimulus elicits
essentially identical responses upon repeated presentations. We view the
problem on two scales: neuronal reliability, which concerns the repeatability
of spike times o... | [
{
"created": "Thu, 22 May 2008 19:12:59 GMT",
"version": "v1"
}
] | 2008-05-23 | [
[
"Lin",
"Kevin K.",
""
],
[
"Shea-Brown",
"Eric",
""
],
[
"Young",
"Lai-Sang",
""
]
] | We study the reliability of large networks of coupled neural oscillators in response to fluctuating stimuli. Reliability means that a stimulus elicits essentially identical responses upon repeated presentations. We view the problem on two scales: neuronal reliability, which concerns the repeatability of spike times of ... |
2005.03085 | Tom Britton | Tom Britton, Frank Ball and Pieter Trapman | The disease-induced herd immunity level for Covid-19 is substantially
lower than the classical herd immunity level | null | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most countries are suffering severely from the ongoing covid-19 pandemic
despite various levels of preventive measures. A common question is if and when
a country or region will reach herd immunity $h$. The classical herd immunity
level $h_C$ is defined as $h_C=1-1/R_0$, where $R_0$ is the basic reproduction
number, ... | [
{
"created": "Wed, 6 May 2020 19:22:57 GMT",
"version": "v1"
}
] | 2020-05-08 | [
[
"Britton",
"Tom",
""
],
[
"Ball",
"Frank",
""
],
[
"Trapman",
"Pieter",
""
]
] | Most countries are suffering severely from the ongoing covid-19 pandemic despite various levels of preventive measures. A common question is if and when a country or region will reach herd immunity $h$. The classical herd immunity level $h_C$ is defined as $h_C=1-1/R_0$, where $R_0$ is the basic reproduction number, fo... |
1908.11436 | Lee Friedman | Lee Friedman | Three errors and two problems in a recent paper: gazenet: End-to-end
eye-movement event detection with deep neural networks (Zemblys, Niehorster,
and Holmqvist, 2019) | 11 pages, 6 figures, Commentary on previously published article | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Zemblys et al. \cite{gazeNet} reported on a method for the classification of
eye-movements ("gazeNet"). I have found 3 errors and two problems with that
paper that are explained herein. \underline{\textit{\textbf{Error 1}}} The
gazeNet classification method was built assuming that a hand-scored dataset
from Lund Univ... | [
{
"created": "Thu, 29 Aug 2019 19:51:09 GMT",
"version": "v1"
},
{
"created": "Tue, 10 Sep 2019 19:15:44 GMT",
"version": "v2"
},
{
"created": "Wed, 6 Nov 2019 13:32:01 GMT",
"version": "v3"
},
{
"created": "Fri, 20 Dec 2019 12:01:02 GMT",
"version": "v4"
}
] | 2019-12-23 | [
[
"Friedman",
"Lee",
""
]
] | Zemblys et al. \cite{gazeNet} reported on a method for the classification of eye-movements ("gazeNet"). I have found 3 errors and two problems with that paper that are explained herein. \underline{\textit{\textbf{Error 1}}} The gazeNet classification method was built assuming that a hand-scored dataset from Lund Univer... |
1610.01189 | Jing Xu | Qiaochu Li, Stephen J. King, Ajay Gopinathan, and Jing Xu | Quantitative Determination of the Probability of Multiple-Motor
Transport in Bead-Based Assays | null | Biophysical Journal , Volume 110 , Issue 12 , 2720 - 2728 (2016) | 10.1016/j.bpj.2016.05.015 | null | q-bio.BM q-bio.QM q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | With their longest dimension typically being less than 100 nm, molecular
motors are significantly below the optical-resolution limit. Despite
substantial advances in fluorescence-based imaging methodologies, labeling with
beads remains critical for optical-trapping-based investigations of molecular
motors. A key expe... | [
{
"created": "Tue, 4 Oct 2016 20:31:02 GMT",
"version": "v1"
}
] | 2016-10-06 | [
[
"Li",
"Qiaochu",
""
],
[
"King",
"Stephen J.",
""
],
[
"Gopinathan",
"Ajay",
""
],
[
"Xu",
"Jing",
""
]
] | With their longest dimension typically being less than 100 nm, molecular motors are significantly below the optical-resolution limit. Despite substantial advances in fluorescence-based imaging methodologies, labeling with beads remains critical for optical-trapping-based investigations of molecular motors. A key experi... |
1307.7882 | Sergey Petoukhov | Sergey Petoukhov | The genetic code, algebra of projection operators and problems of
inherited biological ensembles | 110 pages,82 figures | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This article is devoted to applications of projection operators to simulate
phenomenological properties of the molecular-genetic code system. Oblique
projection operators are under consideration, which are connected with matrix
representations of the genetic coding system in forms of the Rademacher and
Hadamard matri... | [
{
"created": "Tue, 30 Jul 2013 09:15:13 GMT",
"version": "v1"
},
{
"created": "Mon, 30 Dec 2013 17:09:46 GMT",
"version": "v2"
},
{
"created": "Thu, 23 Jan 2014 18:42:26 GMT",
"version": "v3"
},
{
"created": "Sun, 4 May 2014 14:39:01 GMT",
"version": "v4"
},
{
"cr... | 2017-08-10 | [
[
"Petoukhov",
"Sergey",
""
]
] | This article is devoted to applications of projection operators to simulate phenomenological properties of the molecular-genetic code system. Oblique projection operators are under consideration, which are connected with matrix representations of the genetic coding system in forms of the Rademacher and Hadamard matrice... |
2305.08929 | Zhongju Yuan | Zhongju Yuan, Tao Shen, Sheng Xu, Leiye Yu, Ruobing Ren, Siqi Sun | AF2-Mutation: Adversarial Sequence Mutations against AlphaFold2 on
Protein Tertiary Structure Prediction | null | null | null | null | q-bio.BM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Deep learning-based approaches, such as AlphaFold2 (AF2), have significantly
advanced protein tertiary structure prediction, achieving results comparable to
real biological experimental methods. While AF2 has shown limitations in
predicting the effects of mutations, its robustness against sequence mutations
remains t... | [
{
"created": "Mon, 15 May 2023 18:06:08 GMT",
"version": "v1"
}
] | 2023-05-17 | [
[
"Yuan",
"Zhongju",
""
],
[
"Shen",
"Tao",
""
],
[
"Xu",
"Sheng",
""
],
[
"Yu",
"Leiye",
""
],
[
"Ren",
"Ruobing",
""
],
[
"Sun",
"Siqi",
""
]
] | Deep learning-based approaches, such as AlphaFold2 (AF2), have significantly advanced protein tertiary structure prediction, achieving results comparable to real biological experimental methods. While AF2 has shown limitations in predicting the effects of mutations, its robustness against sequence mutations remains to ... |
2211.10472 | Jeremy Owen | Jeremy A. Owen, Pranay Talla, John W. Biddle, Jeremy Gunawardena | Thermodynamic bounds on ultrasensitivity in covalent switching | 29 pages, 6 figures | null | 10.1016/j.bpj.2023.04.015 | null | q-bio.MN cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Switch-like motifs are among the basic building blocks of biochemical
networks. A common motif that can serve as an ultrasensitive switch consists of
two enzymes acting antagonistically on a substrate, one making and the other
removing a covalent modification. To work as a switch, such covalent
modification cycles mu... | [
{
"created": "Fri, 18 Nov 2022 19:21:56 GMT",
"version": "v1"
}
] | 2023-05-31 | [
[
"Owen",
"Jeremy A.",
""
],
[
"Talla",
"Pranay",
""
],
[
"Biddle",
"John W.",
""
],
[
"Gunawardena",
"Jeremy",
""
]
] | Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a covalent modification. To work as a switch, such covalent modification cycles must... |
1804.11249 | Julia Shore | Julia A. Shore, Jeremy G. Sumner and Barbara R. Holland | The impracticalities of multiplicatively-closed codon models: a retreat
to linear alternatives | null | Journal of Mathematical Biology, 1-25 (2020) | null | null | q-bio.PE math.RA math.ST stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A matrix Lie algebra is a linear space of matrices closed under the operation
$ [A, B] = AB-BA $. The "Lie closure" of a set of matrices is the smallest
matrix Lie algebra which contains the set. In the context of Markov chain
theory, if a set of rate matrices form a Lie algebra, their corresponding
Markov matrices a... | [
{
"created": "Thu, 26 Apr 2018 00:43:18 GMT",
"version": "v1"
},
{
"created": "Tue, 8 May 2018 05:52:32 GMT",
"version": "v2"
},
{
"created": "Thu, 6 Aug 2020 00:54:05 GMT",
"version": "v3"
}
] | 2020-08-07 | [
[
"Shore",
"Julia A.",
""
],
[
"Sumner",
"Jeremy G.",
""
],
[
"Holland",
"Barbara R.",
""
]
] | A matrix Lie algebra is a linear space of matrices closed under the operation $ [A, B] = AB-BA $. The "Lie closure" of a set of matrices is the smallest matrix Lie algebra which contains the set. In the context of Markov chain theory, if a set of rate matrices form a Lie algebra, their corresponding Markov matrices are... |
0901.0955 | Yong Chen | Guo-Yong Zhang, Yong Chen, Wei-Kai Qi, and Shao-Meng Qin | Four-state rock-paper-scissors games on constrained Newman-Watts
networks | 6 pages, 7 figures | Phys. Rev. E 79, 062901 (2009) | 10.1103/PhysRevE.79.062901 | null | q-bio.PE | http://creativecommons.org/licenses/by/3.0/ | We study the cyclic dominance of three species in two-dimensional constrained
Newman-Watts networks with a four-state variant of the rock-paper-scissors
game. By limiting the maximal connection distance $R_{max}$ in Newman-Watts
networks with the long-rang connection probability $p$, we depict more
realistically the ... | [
{
"created": "Thu, 8 Jan 2009 00:58:07 GMT",
"version": "v1"
},
{
"created": "Fri, 3 Jul 2009 03:03:12 GMT",
"version": "v2"
}
] | 2009-07-03 | [
[
"Zhang",
"Guo-Yong",
""
],
[
"Chen",
"Yong",
""
],
[
"Qi",
"Wei-Kai",
""
],
[
"Qin",
"Shao-Meng",
""
]
] | We study the cyclic dominance of three species in two-dimensional constrained Newman-Watts networks with a four-state variant of the rock-paper-scissors game. By limiting the maximal connection distance $R_{max}$ in Newman-Watts networks with the long-rang connection probability $p$, we depict more realistically the st... |
1904.12023 | Mengyu Dai | Mengyu Dai, Zhengwu Zhang and Anuj Srivastava | Discovering Common Change-Point Patterns in Functional Connectivity
Across Subjects | null | Published in Medical Image Analysis, 2019 | 10.1016/j.media.2019.101532 | null | q-bio.NC cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper studies change-points in human brain functional connectivity (FC)
and seeks patterns that are common across multiple subjects under identical
external stimulus. FC relates to the similarity of fMRI responses across
different brain regions when the brain is simply resting or performing a task.
While the dyn... | [
{
"created": "Fri, 26 Apr 2019 19:34:52 GMT",
"version": "v1"
}
] | 2020-03-05 | [
[
"Dai",
"Mengyu",
""
],
[
"Zhang",
"Zhengwu",
""
],
[
"Srivastava",
"Anuj",
""
]
] | This paper studies change-points in human brain functional connectivity (FC) and seeks patterns that are common across multiple subjects under identical external stimulus. FC relates to the similarity of fMRI responses across different brain regions when the brain is simply resting or performing a task. While the dynam... |
1505.02492 | Christopher Angstmann | C. N. Angstmann, B. I. Henry and A. V. McGann | A fractional order recovery SIR model from a stochastic process | 32 pages, 3 figures | null | 10.1007/s11538-016-0151-7 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Over the past several decades there has been a proliferation of
epidemiological models with ordinary derivatives replaced by fractional
derivatives in an an-hoc manner. These models may be mathematically interesting
but their relevance is uncertain. Here we develop an SIR model for an epidemic,
including vital dynami... | [
{
"created": "Mon, 11 May 2015 05:57:15 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Sep 2015 05:37:16 GMT",
"version": "v2"
}
] | 2016-03-31 | [
[
"Angstmann",
"C. N.",
""
],
[
"Henry",
"B. I.",
""
],
[
"McGann",
"A. V.",
""
]
] | Over the past several decades there has been a proliferation of epidemiological models with ordinary derivatives replaced by fractional derivatives in an an-hoc manner. These models may be mathematically interesting but their relevance is uncertain. Here we develop an SIR model for an epidemic, including vital dynamics... |
1712.07879 | \"Omer Deniz Akyildiz | \"Omer Deniz Aky{\i}ld{\i}z | A probabilistic interpretation of replicator-mutator dynamics | null | null | null | null | q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this note, we investigate the relationship between probabilistic updating
mechanisms and discrete-time replicator-mutator dynamics. We consider the
recently shown connection between Bayesian updating and replicator dynamics and
extend it to the replicator-mutator dynamics by considering prediction and
filtering re... | [
{
"created": "Thu, 21 Dec 2017 11:15:25 GMT",
"version": "v1"
}
] | 2017-12-22 | [
[
"Akyıldız",
"Ömer Deniz",
""
]
] | In this note, we investigate the relationship between probabilistic updating mechanisms and discrete-time replicator-mutator dynamics. We consider the recently shown connection between Bayesian updating and replicator dynamics and extend it to the replicator-mutator dynamics by considering prediction and filtering recu... |
1904.02995 | Bj{\o}rn Juel | Bj{\o}rn Erik Juel, Renzo Comolatti, Giulio Tononi, and Larissa
Albantakis | When is an action caused from within? Quantifying the causal chain
leading to actions in simulated agents | Submitted and accepted to Alife 2019 conference. Revised version:
edits include adding more references to relevant work and clarifying minor
points in response to reviewers | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An agent's actions can be influenced by external factors through the inputs
it receives from the environment, as well as internal factors, such as memories
or intrinsic preferences. The extent to which an agent's actions are "caused
from within", as opposed to being externally driven, should depend on its
sensor capa... | [
{
"created": "Fri, 5 Apr 2019 11:23:27 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Jun 2019 13:49:26 GMT",
"version": "v2"
}
] | 2019-06-17 | [
[
"Juel",
"Bjørn Erik",
""
],
[
"Comolatti",
"Renzo",
""
],
[
"Tononi",
"Giulio",
""
],
[
"Albantakis",
"Larissa",
""
]
] | An agent's actions can be influenced by external factors through the inputs it receives from the environment, as well as internal factors, such as memories or intrinsic preferences. The extent to which an agent's actions are "caused from within", as opposed to being externally driven, should depend on its sensor capaci... |
2201.07718 | Hossam Donya Dr | Hossam Donya, Sheikh Othman, Alexis Dimitriadis | Evaluating and predicting the Efficiency Index for Stereotactic
Radiosurgery Plans using RapidMiner GO(JAVA) Based Artificial Intelligence
Algorithms | 10 pages | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Evaluation the prediction of Efficiency index by DVH parameter for SRS
treatment plans using Supervised Machine learning and the performance of
predictive model algorithms of RapidMiner GO in the parameter prediction are
investigated. Dose volume histogram (DVH) based Efficiency index was calculated
for 100 clinical ... | [
{
"created": "Wed, 19 Jan 2022 16:56:19 GMT",
"version": "v1"
}
] | 2022-01-20 | [
[
"Donya",
"Hossam",
""
],
[
"Othman",
"Sheikh",
""
],
[
"Dimitriadis",
"Alexis",
""
]
] | Evaluation the prediction of Efficiency index by DVH parameter for SRS treatment plans using Supervised Machine learning and the performance of predictive model algorithms of RapidMiner GO in the parameter prediction are investigated. Dose volume histogram (DVH) based Efficiency index was calculated for 100 clinical SR... |
2009.00251 | Tommaso Lorenzi | Giada Fiandaca, Marcello Delitala, Tommaso Lorenzi | A mathematical study of the influence of hypoxia and acidity on the
evolutionary dynamics of cancer | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Hypoxia and acidity act as environmental stressors promoting selection for
cancer cells with a more aggressive phenotype. As a result, a deeper
theoretical understanding of the spatio-temporal processes that drive the
adaptation of tumour cells to hypoxic and acidic microenvironments may open up
new avenues of resear... | [
{
"created": "Tue, 1 Sep 2020 06:10:08 GMT",
"version": "v1"
},
{
"created": "Mon, 26 Apr 2021 09:14:08 GMT",
"version": "v2"
}
] | 2021-04-27 | [
[
"Fiandaca",
"Giada",
""
],
[
"Delitala",
"Marcello",
""
],
[
"Lorenzi",
"Tommaso",
""
]
] | Hypoxia and acidity act as environmental stressors promoting selection for cancer cells with a more aggressive phenotype. As a result, a deeper theoretical understanding of the spatio-temporal processes that drive the adaptation of tumour cells to hypoxic and acidic microenvironments may open up new avenues of research... |
1806.08785 | Les Hatton | Les Hatton and Gregory Warr | CoHSI I; Detailed properties of the Canonical Distribution for Discrete
Systems such as the Proteome | 13 pages, 11 figures | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The CoHSI (Conservation of Hartley-Shannon Information) distribution is at
the heart of a wide-class of discrete systems, defining the length distribution
of their components amongst other global properties. Discrete systems such as
the known proteome where components are proteins, computer software, where
components... | [
{
"created": "Thu, 21 Jun 2018 20:14:03 GMT",
"version": "v1"
}
] | 2018-06-26 | [
[
"Hatton",
"Les",
""
],
[
"Warr",
"Gregory",
""
]
] | The CoHSI (Conservation of Hartley-Shannon Information) distribution is at the heart of a wide-class of discrete systems, defining the length distribution of their components amongst other global properties. Discrete systems such as the known proteome where components are proteins, computer software, where components a... |
2303.04034 | Rohak Jain | Rohak Jain | Deciphering a Sleeping Pathogen: Uncovering Novel Transcriptional
Regulators of Hypoxia-Induced Dormancy in Mycobacterium Tuberculosis | 21 pages, 11 figures | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Along the pathogenesis of Mycobacterium Tuberculosis (MTB), hypoxia-induced
dormancy is a process involving the oxygen-depleted environment encountered
inside the lung granuloma, where bacilli enter a viable, non-replicating state
termed as latency. Affecting nearly two billion people, latent TB can linger in
the hos... | [
{
"created": "Sat, 4 Mar 2023 18:26:03 GMT",
"version": "v1"
},
{
"created": "Sun, 5 Nov 2023 15:36:32 GMT",
"version": "v2"
}
] | 2023-11-07 | [
[
"Jain",
"Rohak",
""
]
] | Along the pathogenesis of Mycobacterium Tuberculosis (MTB), hypoxia-induced dormancy is a process involving the oxygen-depleted environment encountered inside the lung granuloma, where bacilli enter a viable, non-replicating state termed as latency. Affecting nearly two billion people, latent TB can linger in the host ... |
1207.4586 | Philippe Terrier PhD | Philippe Terrier and Olivier D\'eriaz | Persistent and anti-persistent pattern in stride-to-stride variability
of treadmill walking: influence of rhythmic auditory cueing | preprint version of an article accepted in Human Movement Science | Human Movement Science, 2012, 31(6):1585-97 | 10.1016/j.humov.2012.05.004 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has been observed that long time series of Stride Time (ST), Stride Length
(SL) and Stride Speed (SS=SL/ST) exhibited statistical persistence (long-range
auto-correlation) in overground walking. Rhythmic auditory cueing induced
anti-persistent (or anti-correlated) pattern in ST series, while SL and SS
remained per... | [
{
"created": "Thu, 19 Jul 2012 09:18:05 GMT",
"version": "v1"
}
] | 2012-12-24 | [
[
"Terrier",
"Philippe",
""
],
[
"Dériaz",
"Olivier",
""
]
] | It has been observed that long time series of Stride Time (ST), Stride Length (SL) and Stride Speed (SS=SL/ST) exhibited statistical persistence (long-range auto-correlation) in overground walking. Rhythmic auditory cueing induced anti-persistent (or anti-correlated) pattern in ST series, while SL and SS remained persi... |
1011.4496 | Adrian Melott | Adrian L. Melott (U Kansas) and Richard K. Bambach (Smithsonian Inst.,
Museum of Natural History) | A ubiquitous ~62 Myr periodic fluctuation superimposed on general trends
in fossil biodiversity: II, Evolutionary dynamics associated with periodic
fluctuation in marine diversity | Paleobiology, in press. 74 pages, 13 figures | Paleobiology 37:383-408,2011 | 10.1666/09055.1 | null | q-bio.PE astro-ph.EP astro-ph.GA physics.bio-ph physics.geo-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate evolutionary dynamics related to periodicity fossil
biodiversity. Coherent periodic fluctuation in origination/extinction of marine
genera that survive <45 million years is the source of an observed ~62 million
year periodicity analyzed in Paper I. We also show that the evolutionary
dynamics of "long-l... | [
{
"created": "Fri, 19 Nov 2010 18:51:31 GMT",
"version": "v1"
}
] | 2011-07-26 | [
[
"Melott",
"Adrian L.",
"",
"U Kansas"
],
[
"Bambach",
"Richard K.",
"",
"Smithsonian Inst.,\n Museum of Natural History"
]
] | We investigate evolutionary dynamics related to periodicity fossil biodiversity. Coherent periodic fluctuation in origination/extinction of marine genera that survive <45 million years is the source of an observed ~62 million year periodicity analyzed in Paper I. We also show that the evolutionary dynamics of "long-liv... |
1602.03379 | Anupam Mitra | Anupam Mitra, Anagh Pathak, Kaushik Majumdar | Comparison of feature extraction and dimensionality reduction methods
for single channel extracellular spike sorting | 12 pages, 2 figures | null | null | null | q-bio.QM cs.CV q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spikes in the membrane electrical potentials of neurons play a major role in
the functioning of nervous systems of animals. Obtaining the spikes from
different neurons has been a challenging problem for decades. Several schemes
have been proposed for spike sorting to isolate the spikes of individual
neurons from elec... | [
{
"created": "Wed, 10 Feb 2016 14:21:34 GMT",
"version": "v1"
}
] | 2016-02-11 | [
[
"Mitra",
"Anupam",
""
],
[
"Pathak",
"Anagh",
""
],
[
"Majumdar",
"Kaushik",
""
]
] | Spikes in the membrane electrical potentials of neurons play a major role in the functioning of nervous systems of animals. Obtaining the spikes from different neurons has been a challenging problem for decades. Several schemes have been proposed for spike sorting to isolate the spikes of individual neurons from electr... |
1312.6776 | Hao Ge | Hao Ge, Hong Qian and Sunney Xiaoliang Xie | Stochastic phenotype transition of a single cell in an intermediate
region of gene-state switching | 6 pages,4 figures | Physical Review Letters, 114, 078101 (2015) | 10.1103/PhysRevLett.114.078101 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multiple phenotypic states often arise in a single cell with different
gene-expression states that undergo transcription regulation with positive
feedback. Recent experiments have shown that at least in E. coli, the gene
state switching can be neither extremely slow nor exceedingly rapid as many
previous theoretical ... | [
{
"created": "Tue, 24 Dec 2013 08:19:29 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Oct 2015 06:40:14 GMT",
"version": "v2"
}
] | 2015-10-28 | [
[
"Ge",
"Hao",
""
],
[
"Qian",
"Hong",
""
],
[
"Xie",
"Sunney Xiaoliang",
""
]
] | Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can be neither extremely slow nor exceedingly rapid as many previous theoretical tr... |
2004.00959 | Arif Ahmed Sekh Dr | Ratnabali Pal, Arif Ahmed Sekh, Samarjit Kar, Dilip K. Prasad | Neural network based country wise risk prediction of COVID-19 | null | Applied Sciences, 2020 | 10.3390/app10186448 | null | q-bio.PE cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The recent worldwide outbreak of the novel coronavirus (COVID-19) has opened
up new challenges to the research community. Artificial intelligence (AI)
driven methods can be useful to predict the parameters, risks, and effects of
such an epidemic. Such predictions can be helpful to control and prevent the
spread of su... | [
{
"created": "Tue, 31 Mar 2020 20:03:10 GMT",
"version": "v1"
},
{
"created": "Wed, 16 Sep 2020 15:16:15 GMT",
"version": "v2"
}
] | 2020-09-17 | [
[
"Pal",
"Ratnabali",
""
],
[
"Sekh",
"Arif Ahmed",
""
],
[
"Kar",
"Samarjit",
""
],
[
"Prasad",
"Dilip K.",
""
]
] | The recent worldwide outbreak of the novel coronavirus (COVID-19) has opened up new challenges to the research community. Artificial intelligence (AI) driven methods can be useful to predict the parameters, risks, and effects of such an epidemic. Such predictions can be helpful to control and prevent the spread of such... |
1910.02951 | Nicolo' Savioli | Shihao Jin, Nicol\`o Savioli, Antonio de Marvao, Timothy JW Dawes,
Axel Gandy, Daniel Rueckert, Declan P O'Regan | Joint analysis of clinical risk factors and 4D cardiac motion for
survival prediction using a hybrid deep learning network | 4 pages, 2 figures | NeurIPS 2019, Medical Imaging meets NIPS | null | null | q-bio.QM cs.LG eess.IV stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work, a novel approach is proposed for joint analysis of high
dimensional time-resolved cardiac motion features obtained from segmented
cardiac MRI and low dimensional clinical risk factors to improve survival
prediction in heart failure. Different methods are evaluated to find the
optimal way to insert conve... | [
{
"created": "Mon, 7 Oct 2019 14:04:17 GMT",
"version": "v1"
}
] | 2019-10-09 | [
[
"Jin",
"Shihao",
""
],
[
"Savioli",
"Nicolò",
""
],
[
"de Marvao",
"Antonio",
""
],
[
"Dawes",
"Timothy JW",
""
],
[
"Gandy",
"Axel",
""
],
[
"Rueckert",
"Daniel",
""
],
[
"O'Regan",
"Declan P",
""
]
] | In this work, a novel approach is proposed for joint analysis of high dimensional time-resolved cardiac motion features obtained from segmented cardiac MRI and low dimensional clinical risk factors to improve survival prediction in heart failure. Different methods are evaluated to find the optimal way to insert convent... |
2103.01026 | Wei Li | Chenxi Zhou, Bin Yang, Wenliang Fan, Wei Li | Modelling brain based on canonical ensemble with functional MRI: A
thermodynamic exploration on neural system | 27 pages, 3 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objective. Modelling is an important way to study the working mechanism of
brain. While the characterization and understanding of brain are still
inadequate. This study tried to build a model of brain from the perspective of
thermodynamics at system level, which brought a new thinking to brain
modelling.
Approach. ... | [
{
"created": "Fri, 26 Feb 2021 13:23:20 GMT",
"version": "v1"
},
{
"created": "Sat, 27 Mar 2021 08:59:52 GMT",
"version": "v2"
}
] | 2021-03-30 | [
[
"Zhou",
"Chenxi",
""
],
[
"Yang",
"Bin",
""
],
[
"Fan",
"Wenliang",
""
],
[
"Li",
"Wei",
""
]
] | Objective. Modelling is an important way to study the working mechanism of brain. While the characterization and understanding of brain are still inadequate. This study tried to build a model of brain from the perspective of thermodynamics at system level, which brought a new thinking to brain modelling. Approach. Rega... |
2306.12348 | Andrea Raffo | Andrea Raffo, Ulderico Fugacci, Silvia Biasotti | GEO-Nav: a geometric dataset of voltage-gated sodium channels | null | Computers & Graphics 115 (2023) 285-295 | 10.1016/j.cag.2023.06.023 | null | q-bio.BM cs.GR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Voltage-gated sodium (Nav) channels constitute a prime target for drug design
and discovery, given their implication in various diseases such as epilepsy,
migraine and ataxia to name a few. In this regard, performing morphological
analysis is a crucial step in comprehensively understanding their biological
function a... | [
{
"created": "Wed, 21 Jun 2023 15:43:55 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Aug 2023 14:54:47 GMT",
"version": "v2"
}
] | 2023-08-10 | [
[
"Raffo",
"Andrea",
""
],
[
"Fugacci",
"Ulderico",
""
],
[
"Biasotti",
"Silvia",
""
]
] | Voltage-gated sodium (Nav) channels constitute a prime target for drug design and discovery, given their implication in various diseases such as epilepsy, migraine and ataxia to name a few. In this regard, performing morphological analysis is a crucial step in comprehensively understanding their biological function and... |
1909.05908 | Jahan Schad | Jahan N. Schad | Neurological Nature of Vision and Thought and Mechanisms of Perception
Experiences | 3 pages | J Neurol Stroke. 2016, 4(5) | 10.15406/jnsk.2016.04.00152 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding of the phenomena of vision and thought require clarification of
the general mechanism of perception. So far, philosophical inquiries and
scientific investigations have not been able to address clearly the mysteries
surrounding them. The present work is an attempt to unravel the essences of
these phenome... | [
{
"created": "Mon, 9 Sep 2019 18:13:41 GMT",
"version": "v1"
}
] | 2019-09-16 | [
[
"Schad",
"Jahan N.",
""
]
] | Understanding of the phenomena of vision and thought require clarification of the general mechanism of perception. So far, philosophical inquiries and scientific investigations have not been able to address clearly the mysteries surrounding them. The present work is an attempt to unravel the essences of these phenomena... |
1210.4313 | Vladimir Chechetkin R. | Galina I. Kravatskaya, Vladimir R. Chechetkin, Yury V. Kravatsky and
Vladimir G. Tumanyan | Structural attributes of nucleotide sequences in promoter regions of
supercoiling-sensitive genes: how to relate microarray expression data with
genomic sequences | 38 pages, 12 figures | null | 10.1016/j.ygeno.2012.10.003 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The level of supercoiling in the chromosome can affect gene expression. To
clarify the basis of supercoiling sensitivity, we analyzed the structural
features of nucleotide sequences in the vicinity of promoters for the genes
with expression enhanced and decreased in response to loss of chromosomal
supercoiling in E. ... | [
{
"created": "Tue, 16 Oct 2012 08:59:59 GMT",
"version": "v1"
}
] | 2012-10-17 | [
[
"Kravatskaya",
"Galina I.",
""
],
[
"Chechetkin",
"Vladimir R.",
""
],
[
"Kravatsky",
"Yury V.",
""
],
[
"Tumanyan",
"Vladimir G.",
""
]
] | The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression enhanced and decreased in response to loss of chromosomal supercoiling in E. co... |
1909.02336 | Jos\'e Mar\'ia Mart\'in Olalla Dr. | Jos\'e Mar\'ia Mart\'in-Olalla | Scandinavian bed and rise times in the Age of Enlightenment and in the
21st century show similarity, helped by Daylight Saving Time | 3pages, 1figure, 740 words, RevTeX RMP format, longbibliography | Journal of Sleep Research 2019 e12916 | 10.1111/jsr.12916 | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A Letter to the Editor published in the Journal of Sleep Research
| [
{
"created": "Thu, 5 Sep 2019 11:42:58 GMT",
"version": "v1"
}
] | 2019-09-06 | [
[
"Martín-Olalla",
"José María",
""
]
] | A Letter to the Editor published in the Journal of Sleep Research |
q-bio/0507007 | Martin Howard | Konstantin Doubrovinski and Martin Howard | Stochastic model for Soj relocation dynamics in Bacillus subtilis | 45 pages | Proc. Natl. Acad. Sci. 102 9808-9813 (2005) | 10.1073/pnas.0500529102 | null | q-bio.SC cond-mat.stat-mech | null | The Bacillus subtilis Spo0J/Soj proteins, implicated in chromosome
segregation and transcriptional regulation, show striking dynamics: Soj
undergoes irregular relocations from pole to pole or nucleoid to nucleoid. Here
we report on a mathematical model of the Soj dynamics. Our model, which is
closely based on the ava... | [
{
"created": "Tue, 5 Jul 2005 18:06:36 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Doubrovinski",
"Konstantin",
""
],
[
"Howard",
"Martin",
""
]
] | The Bacillus subtilis Spo0J/Soj proteins, implicated in chromosome segregation and transcriptional regulation, show striking dynamics: Soj undergoes irregular relocations from pole to pole or nucleoid to nucleoid. Here we report on a mathematical model of the Soj dynamics. Our model, which is closely based on the avail... |
2006.13264 | Nicole Vike | Nicole L. Vike, Sumra Bari, Khrystyna Stetsiv, Linda Papa, Eric A.
Nauman, Thomas M. Talavage, Semyon Slobounov, and Hans C. Breiter | Metabolomic measures of altered energy metabolism mediate the
relationship of inflammatory miRNAs to motor control in collegiate football
athletes | 55 pages, 9 figures, 5 tables | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent research has shown there can be detrimental neurological effects of
short- and long-term exposure to contact sports. In the present study,
metabolomic profiling was combined with inflammatory miRNA quantification,
computational behavior with virtual reality (VR) testing of motor control, and
head collision eve... | [
{
"created": "Tue, 23 Jun 2020 18:43:24 GMT",
"version": "v1"
}
] | 2020-06-25 | [
[
"Vike",
"Nicole L.",
""
],
[
"Bari",
"Sumra",
""
],
[
"Stetsiv",
"Khrystyna",
""
],
[
"Papa",
"Linda",
""
],
[
"Nauman",
"Eric A.",
""
],
[
"Talavage",
"Thomas M.",
""
],
[
"Slobounov",
"Semyon",
""
],
... | Recent research has shown there can be detrimental neurological effects of short- and long-term exposure to contact sports. In the present study, metabolomic profiling was combined with inflammatory miRNA quantification, computational behavior with virtual reality (VR) testing of motor control, and head collision event... |
1711.00418 | Ehtibar Dzhafarov | Victor H. Cervantes and Ehtibar N. Dzhafarov | Snow Queen is Evil and Beautiful: Experimental Evidence for
Probabilistic Contextuality in Human Choices | To be published in Decision. 12 pp., 6 figures, 4 tables; Version 8
is the proofread-for-pubpication version | Decision 5, 193-204, 2018 | null | null | q-bio.NC math.PR quant-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present unambiguous experimental evidence for (quantum-like) probabilistic
contextuality in psychology. All previous attempts to find contextuality in a
psychological experiment were unsuccessful because of the gross violations of
marginal selectivity in behavioral data, making the traditional mathematical
tests d... | [
{
"created": "Wed, 1 Nov 2017 16:16:39 GMT",
"version": "v1"
},
{
"created": "Thu, 2 Nov 2017 14:46:06 GMT",
"version": "v2"
},
{
"created": "Thu, 9 Nov 2017 03:23:22 GMT",
"version": "v3"
},
{
"created": "Mon, 13 Nov 2017 16:47:37 GMT",
"version": "v4"
},
{
"crea... | 2019-01-24 | [
[
"Cervantes",
"Victor H.",
""
],
[
"Dzhafarov",
"Ehtibar N.",
""
]
] | We present unambiguous experimental evidence for (quantum-like) probabilistic contextuality in psychology. All previous attempts to find contextuality in a psychological experiment were unsuccessful because of the gross violations of marginal selectivity in behavioral data, making the traditional mathematical tests dev... |
1303.3920 | Tobias Jeppsson | Tobias Jeppsson and P\"ar Forslund | Can Life History Predict the Effect of Demographic Stochasticity on
Extinction Risk? | null | The American Naturalist. 2012. 179(6): 706-720 | 10.1086/665696 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Demographic stochasticity is important in determining extinction risks of
small populations, but it is largely unknown how its effect depends on the life
histories of species. We modeled effects of demographic stochasticity on
extinction risk in a broad range of generalized life histories, using matrix
models and bra... | [
{
"created": "Fri, 15 Mar 2013 22:45:44 GMT",
"version": "v1"
}
] | 2013-03-19 | [
[
"Jeppsson",
"Tobias",
""
],
[
"Forslund",
"Pär",
""
]
] | Demographic stochasticity is important in determining extinction risks of small populations, but it is largely unknown how its effect depends on the life histories of species. We modeled effects of demographic stochasticity on extinction risk in a broad range of generalized life histories, using matrix models and branc... |
2403.19637 | Samir H.A. Mohammad | Samir H.A. Mohammad, Haneen Farah and Arkady Zgonnikov | In the driver's mind: modeling the dynamics of human overtaking
decisions in interactions with oncoming automated vehicles | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding human behavior in overtaking scenarios is crucial for enhancing
road safety in mixed traffic with automated vehicles (AVs). Computational
models of behavior play a pivotal role in advancing this understanding, as they
can provide insight into human behavior generalizing beyond empirical studies.
However... | [
{
"created": "Thu, 28 Mar 2024 17:50:41 GMT",
"version": "v1"
}
] | 2024-03-29 | [
[
"Mohammad",
"Samir H. A.",
""
],
[
"Farah",
"Haneen",
""
],
[
"Zgonnikov",
"Arkady",
""
]
] | Understanding human behavior in overtaking scenarios is crucial for enhancing road safety in mixed traffic with automated vehicles (AVs). Computational models of behavior play a pivotal role in advancing this understanding, as they can provide insight into human behavior generalizing beyond empirical studies. However, ... |
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