id stringlengths 9 13 | submitter stringlengths 4 48 | authors stringlengths 4 9.62k | title stringlengths 4 343 | comments stringlengths 2 480 ⌀ | journal-ref stringlengths 9 309 ⌀ | doi stringlengths 12 138 ⌀ | report-no stringclasses 277
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1609.04636 | Erik van Oort | Erik S.B. van Oort, Maarten Mennes, Tobias Navarro Schr\"oder, Vinod
J. Kumar, Nestor I. Zaragoza Jimenez, Wolfgang Grodd, Christian F. Doeller,
Christian F. Beckmann | Human brain parcellation using time courses of instantaneous
connectivity | null | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Functional neuroimaging studies have lead to understanding the brain as a
collection of spatially segregated functional networks. It is thought that each
of these networks is in turn composed of a set of distinct sub-regions that
together support each network's function. Considering the sub-regions to be an
essential... | [
{
"created": "Thu, 15 Sep 2016 13:32:56 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Nov 2016 12:34:17 GMT",
"version": "v2"
}
] | 2016-11-22 | [
[
"van Oort",
"Erik S. B.",
""
],
[
"Mennes",
"Maarten",
""
],
[
"Schröder",
"Tobias Navarro",
""
],
[
"Kumar",
"Vinod J.",
""
],
[
"Jimenez",
"Nestor I. Zaragoza",
""
],
[
"Grodd",
"Wolfgang",
""
],
[
"Doeller",
... | Functional neuroimaging studies have lead to understanding the brain as a collection of spatially segregated functional networks. It is thought that each of these networks is in turn composed of a set of distinct sub-regions that together support each network's function. Considering the sub-regions to be an essential p... |
2402.00024 | Shaghayegh Sadeghi | Shaghayegh Sadeghi, Alan Bui, Ali Forooghi, Jianguo Lu, Alioune Ngom | Can Large Language Models Understand Molecules? | null | null | null | null | q-bio.BM cs.AI cs.CL cs.LG | http://creativecommons.org/licenses/by/4.0/ | Purpose: Large Language Models (LLMs) like GPT (Generative Pre-trained
Transformer) from OpenAI and LLaMA (Large Language Model Meta AI) from Meta AI
are increasingly recognized for their potential in the field of
cheminformatics, particularly in understanding Simplified Molecular Input Line
Entry System (SMILES), a ... | [
{
"created": "Fri, 5 Jan 2024 18:31:34 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Feb 2024 18:24:51 GMT",
"version": "v2"
},
{
"created": "Tue, 21 May 2024 03:40:19 GMT",
"version": "v3"
}
] | 2024-05-22 | [
[
"Sadeghi",
"Shaghayegh",
""
],
[
"Bui",
"Alan",
""
],
[
"Forooghi",
"Ali",
""
],
[
"Lu",
"Jianguo",
""
],
[
"Ngom",
"Alioune",
""
]
] | Purpose: Large Language Models (LLMs) like GPT (Generative Pre-trained Transformer) from OpenAI and LLaMA (Large Language Model Meta AI) from Meta AI are increasingly recognized for their potential in the field of cheminformatics, particularly in understanding Simplified Molecular Input Line Entry System (SMILES), a st... |
1612.00168 | Adam Martin-Schwarze | Adam Martin-Schwarze, Jarad Niemi, and Philip Dixon | Assessing the impacts of time to detection distribution assumptions on
detection probability estimation | Expands previous simulation study and adds simulations across a range
of `true' detection values | JABES (2017) 22: 465-480 | 10.1007/s13253-017-0300-y | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Abundance estimates from animal point-count surveys require accurate
estimates of detection probabilities. The standard model for estimating
detection from removal-sampled point-count surveys assumes that organisms at a
survey site are detected at a constant rate; however, this assumption is often
not justified. We c... | [
{
"created": "Thu, 1 Dec 2016 08:04:07 GMT",
"version": "v1"
},
{
"created": "Fri, 19 May 2017 19:05:13 GMT",
"version": "v2"
}
] | 2019-04-09 | [
[
"Martin-Schwarze",
"Adam",
""
],
[
"Niemi",
"Jarad",
""
],
[
"Dixon",
"Philip",
""
]
] | Abundance estimates from animal point-count surveys require accurate estimates of detection probabilities. The standard model for estimating detection from removal-sampled point-count surveys assumes that organisms at a survey site are detected at a constant rate; however, this assumption is often not justified. We con... |
2312.07286 | Pedro Carelli | Rafael M. Jungmann, Tha\'is Feliciano, Leandro A. A. Aguiar, Carina
Soares-Cunha, B\'arbara Coimbra, Ana Jo\~ao Rodrigues, Mauro Copelli,
Fernanda S. Matias, Nivaldo A. P. de Vasconcelos, Pedro V. Carelli | State-dependent complexity of the local field potential in the primary
visual cortex | null | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The local field potential (LFP) is as a measure of the combined activity of
neurons within a region of brain tissue. While biophysical modeling schemes for
LFP in cortical circuits are well established, there is a paramount lack of
understanding regarding the LFP properties along the states assumed in cortical
circui... | [
{
"created": "Tue, 12 Dec 2023 14:00:52 GMT",
"version": "v1"
},
{
"created": "Wed, 13 Dec 2023 14:21:01 GMT",
"version": "v2"
}
] | 2023-12-14 | [
[
"Jungmann",
"Rafael M.",
""
],
[
"Feliciano",
"Thaís",
""
],
[
"Aguiar",
"Leandro A. A.",
""
],
[
"Soares-Cunha",
"Carina",
""
],
[
"Coimbra",
"Bárbara",
""
],
[
"Rodrigues",
"Ana João",
""
],
[
"Copelli",
"Mau... | The local field potential (LFP) is as a measure of the combined activity of neurons within a region of brain tissue. While biophysical modeling schemes for LFP in cortical circuits are well established, there is a paramount lack of understanding regarding the LFP properties along the states assumed in cortical circuits... |
2309.06540 | Natalie M. Isenberg | Natalie M. Isenberg, Susan D. Mertins, Byung-Jun Yoon, Kristofer
Reyes, Nathan M. Urban | Identifying Bayesian Optimal Experiments for Uncertain Biochemical
Pathway Models | null | null | null | null | q-bio.MN stat.AP stat.CO | http://creativecommons.org/licenses/by/4.0/ | Pharmacodynamic (PD) models are mathematical models of cellular reaction
networks that include drug mechanisms of action. These models are useful for
studying predictive therapeutic outcomes of novel drug therapies in silico.
However, PD models are known to possess significant uncertainty with respect to
constituent ... | [
{
"created": "Tue, 12 Sep 2023 19:28:26 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Sep 2023 17:55:33 GMT",
"version": "v2"
}
] | 2023-09-27 | [
[
"Isenberg",
"Natalie M.",
""
],
[
"Mertins",
"Susan D.",
""
],
[
"Yoon",
"Byung-Jun",
""
],
[
"Reyes",
"Kristofer",
""
],
[
"Urban",
"Nathan M.",
""
]
] | Pharmacodynamic (PD) models are mathematical models of cellular reaction networks that include drug mechanisms of action. These models are useful for studying predictive therapeutic outcomes of novel drug therapies in silico. However, PD models are known to possess significant uncertainty with respect to constituent pa... |
1307.1337 | Bernard Ycart | Bernard Ycart and Fr\'ed\'eric Pont and Jean-Jacques Fourni\'e | Statistical data mining for symbol associations in genomic databases | null | null | null | null | q-bio.GN q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A methodology is proposed to automatically detect significant symbol
associations in genomic databases. A new statistical test is proposed to assess
the significance of a group of symbols when found in several genesets of a
given database. Applied to symbol pairs, the thresholded p-values of the test
define a graph s... | [
{
"created": "Thu, 4 Jul 2013 14:10:11 GMT",
"version": "v1"
},
{
"created": "Tue, 10 Sep 2013 15:24:46 GMT",
"version": "v2"
}
] | 2013-09-11 | [
[
"Ycart",
"Bernard",
""
],
[
"Pont",
"Frédéric",
""
],
[
"Fournié",
"Jean-Jacques",
""
]
] | A methodology is proposed to automatically detect significant symbol associations in genomic databases. A new statistical test is proposed to assess the significance of a group of symbols when found in several genesets of a given database. Applied to symbol pairs, the thresholded p-values of the test define a graph str... |
1809.10504 | Alexander Ecker | Alexander S. Ecker, Fabian H. Sinz, Emmanouil Froudarakis, Paul G.
Fahey, Santiago A. Cadena, Edgar Y. Walker, Erick Cobos, Jacob Reimer,
Andreas S. Tolias, Matthias Bethge | A rotation-equivariant convolutional neural network model of primary
visual cortex | null | null | null | null | q-bio.NC cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Classical models describe primary visual cortex (V1) as a filter bank of
orientation-selective linear-nonlinear (LN) or energy models, but these models
fail to predict neural responses to natural stimuli accurately. Recent work
shows that models based on convolutional neural networks (CNNs) lead to much
more accurate... | [
{
"created": "Thu, 27 Sep 2018 13:16:37 GMT",
"version": "v1"
}
] | 2018-09-28 | [
[
"Ecker",
"Alexander S.",
""
],
[
"Sinz",
"Fabian H.",
""
],
[
"Froudarakis",
"Emmanouil",
""
],
[
"Fahey",
"Paul G.",
""
],
[
"Cadena",
"Santiago A.",
""
],
[
"Walker",
"Edgar Y.",
""
],
[
"Cobos",
"Erick",
... | Classical models describe primary visual cortex (V1) as a filter bank of orientation-selective linear-nonlinear (LN) or energy models, but these models fail to predict neural responses to natural stimuli accurately. Recent work shows that models based on convolutional neural networks (CNNs) lead to much more accurate p... |
2308.05118 | Daniel Um | Daniel H. Um, David A. Knowles, Gail E. Kaiser | Vector Embeddings by Sequence Similarity and Context for Improved
Compression, Similarity Search, Clustering, Organization, and Manipulation of
cDNA Libraries | 15 pages, 8 figures | null | null | null | q-bio.GN cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper demonstrates the utility of organized numerical representations of
genes in research involving flat string gene formats (i.e., FASTA/FASTQ5).
FASTA/FASTQ files have several current limitations, such as their large file
sizes, slow processing speeds for mapping and alignment, and contextual
dependencies. Th... | [
{
"created": "Tue, 8 Aug 2023 17:31:17 GMT",
"version": "v1"
}
] | 2023-08-11 | [
[
"Um",
"Daniel H.",
""
],
[
"Knowles",
"David A.",
""
],
[
"Kaiser",
"Gail E.",
""
]
] | This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). FASTA/FASTQ files have several current limitations, such as their large file sizes, slow processing speeds for mapping and alignment, and contextual dependencies. Thes... |
1809.01051 | Matthias Hennig | Matthias H. Hennig, Cole Hurwitz and Martino Sorbaro | Scaling Spike Detection and Sorting for Next Generation
Electrophysiology | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reliable spike detection and sorting, the process of assigning each detected
spike to its originating neuron, is an essential step in the analysis of
extracellular electrical recordings from neurons. The volume and complexity of
the data from recently developed large scale, high density microelectrode
arrays and prob... | [
{
"created": "Tue, 4 Sep 2018 15:42:00 GMT",
"version": "v1"
}
] | 2018-09-05 | [
[
"Hennig",
"Matthias H.",
""
],
[
"Hurwitz",
"Cole",
""
],
[
"Sorbaro",
"Martino",
""
]
] | Reliable spike detection and sorting, the process of assigning each detected spike to its originating neuron, is an essential step in the analysis of extracellular electrical recordings from neurons. The volume and complexity of the data from recently developed large scale, high density microelectrode arrays and probes... |
2012.09948 | Lucas Flores | Lucas S. Flores and Heitor C. M. Fernandes and Marco A. Amaral and
Mendeli H. Vainstein | Symbiotic behaviour in the Public Goods game with altruistic punishment | null | null | 10.1016/j.jtbi.2021.110737 | null | q-bio.PE cond-mat.stat-mech physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | Finding ways to overcome the temptation to exploit one another is still a
challenge in behavioural sciences. In the framework of evolutionary game
theory, punishing strategies are frequently used to promote cooperation in
competitive environments. Here, we introduce altruistic punishers in the
spatial public goods ga... | [
{
"created": "Thu, 17 Dec 2020 21:55:56 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Apr 2021 16:57:13 GMT",
"version": "v2"
}
] | 2022-07-06 | [
[
"Flores",
"Lucas S.",
""
],
[
"Fernandes",
"Heitor C. M.",
""
],
[
"Amaral",
"Marco A.",
""
],
[
"Vainstein",
"Mendeli H.",
""
]
] | Finding ways to overcome the temptation to exploit one another is still a challenge in behavioural sciences. In the framework of evolutionary game theory, punishing strategies are frequently used to promote cooperation in competitive environments. Here, we introduce altruistic punishers in the spatial public goods game... |
1302.3753 | Bart Haegeman | Bart Haegeman, J\'er\^ome Hamelin, John Moriarty, Peter Neal, Jonathan
Dushoff, Joshua S. Weitz | Robust estimation of microbial diversity in theory and in practice | To be published in The ISME Journal. Main text: 16 pages, 5 figures.
Supplement: 16 pages, 4 figures | ISME J. 7, 1092--1101 (2013) | 10.1038/ismej.2013.10 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quantifying diversity is of central importance for the study of structure,
function and evolution of microbial communities. The estimation of microbial
diversity has received renewed attention with the advent of large-scale
metagenomic studies. Here, we consider what the diversity observed in a sample
tells us about ... | [
{
"created": "Fri, 15 Feb 2013 13:53:59 GMT",
"version": "v1"
},
{
"created": "Sat, 23 Feb 2013 07:51:23 GMT",
"version": "v2"
}
] | 2013-08-06 | [
[
"Haegeman",
"Bart",
""
],
[
"Hamelin",
"Jérôme",
""
],
[
"Moriarty",
"John",
""
],
[
"Neal",
"Peter",
""
],
[
"Dushoff",
"Jonathan",
""
],
[
"Weitz",
"Joshua S.",
""
]
] | Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about th... |
2304.00256 | Suman Chakraborty | Suman Chakraborty and Sagar Chakraborty | Selection-recombination-mutation dynamics: Gradient, limit cycle, and
closed invariant curve | 10 pages, 1 figure | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, the replicator dynamics of the two-locus two-allele system
under weak mutation and weak selection is investigated in a generation-wise
non-overlapping unstructured population of individuals mating at random. Our
main finding is that the dynamics is gradient-like when the point mutations at
the two loci... | [
{
"created": "Sat, 1 Apr 2023 08:13:15 GMT",
"version": "v1"
}
] | 2023-04-04 | [
[
"Chakraborty",
"Suman",
""
],
[
"Chakraborty",
"Sagar",
""
]
] | In this paper, the replicator dynamics of the two-locus two-allele system under weak mutation and weak selection is investigated in a generation-wise non-overlapping unstructured population of individuals mating at random. Our main finding is that the dynamics is gradient-like when the point mutations at the two loci a... |
0903.1012 | Nail Khusnutdinov Mr | F. Gafarov, N. Khusnutdinov, and F. Galimyanov | The simulation of the activity dependent neural network growth | 10 pages, 2 figures | null | 10.1142/S0219635209002058 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is currently accepted that cortical maps are dynamic constructions that
are altered in response to external input. Experience-dependent structural
changes in cortical microcurcuts lead to changes of activity, i.e. to changes
in information encoded. Specific patterns of external stimulation can lead to
creation of ... | [
{
"created": "Thu, 5 Mar 2009 14:48:10 GMT",
"version": "v1"
}
] | 2013-02-26 | [
[
"Gafarov",
"F.",
""
],
[
"Khusnutdinov",
"N.",
""
],
[
"Galimyanov",
"F.",
""
]
] | It is currently accepted that cortical maps are dynamic constructions that are altered in response to external input. Experience-dependent structural changes in cortical microcurcuts lead to changes of activity, i.e. to changes in information encoded. Specific patterns of external stimulation can lead to creation of ne... |
1901.06105 | A. K. M. Azad | A. K. M. Azad, Fatemeh Vafaee | Single cell data explosion: Deep learning to the rescue | null | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The plethora of single-cell multi-omics data is getting treatment with deep
learning, a revolutionary method in artificial intelligence, which has been
increasingly expanding its reign over the bioscience frontiers.
| [
{
"created": "Fri, 18 Jan 2019 07:05:56 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Mar 2019 02:22:51 GMT",
"version": "v2"
}
] | 2019-03-12 | [
[
"Azad",
"A. K. M.",
""
],
[
"Vafaee",
"Fatemeh",
""
]
] | The plethora of single-cell multi-omics data is getting treatment with deep learning, a revolutionary method in artificial intelligence, which has been increasingly expanding its reign over the bioscience frontiers. |
q-bio/0412017 | Jesus Gomez-Gardenes | Luis A. Campos, Santiago Cuesta-Lopez, Jon Lopez-Llano, Fernando Falo,
Javier Sancho (BIFI-Universidad de Zaragoza) | A double-deletion method to quantifying incremental binding energies in
proteins from experiment. Example of a destabilizing hydrogen bonding pair | 41 pages, To appear in Biophysical Journal (in press) | null | 10.1529/biophysj.104.050203 | null | q-bio.BM q-bio.QM | null | The contribution of a specific hydrogen bond in apoflavodoxin to protein
stability is investigated by combining theory, experiment and simulation.
Although hydrogen bonds are major determinants of protein structure and
function, their contribution to protein stability is still unclear and widely
debated. The best met... | [
{
"created": "Thu, 9 Dec 2004 18:48:49 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Campos",
"Luis A.",
"",
"BIFI-Universidad de Zaragoza"
],
[
"Cuesta-Lopez",
"Santiago",
"",
"BIFI-Universidad de Zaragoza"
],
[
"Lopez-Llano",
"Jon",
"",
"BIFI-Universidad de Zaragoza"
],
[
"Falo",
"Fernando",
"",
"BIFI-Universidad de Za... | The contribution of a specific hydrogen bond in apoflavodoxin to protein stability is investigated by combining theory, experiment and simulation. Although hydrogen bonds are major determinants of protein structure and function, their contribution to protein stability is still unclear and widely debated. The best metho... |
2002.11532 | Arnaud Gissot | S\'ebastien Benizri (ARNA), Arnaud Gissot (ARNA), Andrew Martin, Brune
Vialet (ARNA), Mark Grinstaff (BU), Philippe Barth\'el\'emy (ARNA) | Bioconjugated oligonucleotides: recent developments and thera-eutic
applications | null | Bioconjugate Chemistry, American Chemical Society, 2019, 30,
pp.366-383 | 10.1021/acs.bioconjchem.8b00761 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Oligonucleotide-based agents have the potential to treat or cure almost any
disease, and are one of the key therapeutic drug classes of the future.
Bioconjugated oligonucleotides, a subset of this class, are emerging from basic
research and being successfully translated to the clinic. In this review, we
first briefly... | [
{
"created": "Wed, 26 Feb 2020 14:35:06 GMT",
"version": "v1"
}
] | 2020-02-27 | [
[
"Benizri",
"Sébastien",
"",
"ARNA"
],
[
"Gissot",
"Arnaud",
"",
"ARNA"
],
[
"Martin",
"Andrew",
"",
"ARNA"
],
[
"Vialet",
"Brune",
"",
"ARNA"
],
[
"Grinstaff",
"Mark",
"",
"BU"
],
[
"Barthélémy",
"Philippe"... | Oligonucleotide-based agents have the potential to treat or cure almost any disease, and are one of the key therapeutic drug classes of the future. Bioconjugated oligonucleotides, a subset of this class, are emerging from basic research and being successfully translated to the clinic. In this review, we first briefly d... |
2011.10372 | Umar Ahmad Dr. | Umar Ahmad, Buhari Ibrahim, Mustapha Mohammed, Ahmed Faris Aldoghachi,
Mahmood Usman, Abdulbasit Haliru Yakubu, Abubakar Sadiq Tanko, Khadijat
Abubakar Bobbo, Usman Adamu Garkuwa, Abdullahi Adamu Faggo, Sagir Mustapha,
Mahmoud Al-Masaeed, Syahril Abdullah, Yong Yoke Keong, Abhi Veerakumarasivam | Transcriptome profiling research in urothelial cell carcinoma | 47 pages, 2 figures, 2 Tables | null | null | null | q-bio.GN q-bio.QM q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Urothelial cell carcinoma (UCC) is the ninth most common cancer that accounts
for 4.7% of all the new cancer cases globally. UCC development and progression
are due to complex and stochastic genetic programmes. To study the cascades of
molecular events underlying the poor prognosis that may lead to limited
treatment ... | [
{
"created": "Fri, 20 Nov 2020 12:22:50 GMT",
"version": "v1"
},
{
"created": "Mon, 23 Nov 2020 08:50:58 GMT",
"version": "v2"
},
{
"created": "Sun, 29 Nov 2020 00:16:38 GMT",
"version": "v3"
},
{
"created": "Sun, 31 Jan 2021 21:27:43 GMT",
"version": "v4"
}
] | 2021-02-02 | [
[
"Ahmad",
"Umar",
""
],
[
"Ibrahim",
"Buhari",
""
],
[
"Mohammed",
"Mustapha",
""
],
[
"Aldoghachi",
"Ahmed Faris",
""
],
[
"Usman",
"Mahmood",
""
],
[
"Yakubu",
"Abdulbasit Haliru",
""
],
[
"Tanko",
"Abubakar S... | Urothelial cell carcinoma (UCC) is the ninth most common cancer that accounts for 4.7% of all the new cancer cases globally. UCC development and progression are due to complex and stochastic genetic programmes. To study the cascades of molecular events underlying the poor prognosis that may lead to limited treatment op... |
q-bio/0309018 | Robert C. Hilborn | Robert C. Hilborn and Rebecca J. Erwin | Coherence resonance in models of an excitable neuron with both fast and
slow dynamics | null | null | 10.1016/j.physleta.2003.12.040 | null | q-bio.NC cond-mat.stat-mech q-bio.QM | null | We demonstrate the existence of noise-induced periodicity (coherence
resonance) in both a discrete-time model and a continuous-time model of an
excitable neuron. In particular, we show that the effects of noise added to the
fast and slow dynamics of the models are dramatically different. A
Fokker-Planck analysis give... | [
{
"created": "Sat, 27 Sep 2003 18:44:25 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Hilborn",
"Robert C.",
""
],
[
"Erwin",
"Rebecca J.",
""
]
] | We demonstrate the existence of noise-induced periodicity (coherence resonance) in both a discrete-time model and a continuous-time model of an excitable neuron. In particular, we show that the effects of noise added to the fast and slow dynamics of the models are dramatically different. A Fokker-Planck analysis gives ... |
1903.12199 | Petr Sulc | Fan Hong, Petr \v{S}ulc | Strand displacement: a fundamental mechanism in RNA biology? | null | null | null | null | q-bio.BM physics.bio-ph q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | DNA and RNA are generally regarded as central molecules in molecular biology.
Recent advancements in the field of DNA/RNA nanotechnology successfully used
DNA/RNA as programmable molecules to construct molecular machines and
nanostructures with predefined shapes and functions. The key mechanism for
dynamic control of... | [
{
"created": "Thu, 28 Mar 2019 18:05:29 GMT",
"version": "v1"
}
] | 2019-04-01 | [
[
"Hong",
"Fan",
""
],
[
"Šulc",
"Petr",
""
]
] | DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures with predefined shapes and functions. The key mechanism for dynamic control of t... |
1804.01722 | Feng Huang | Feng Huang, Xiaojie Chen, and Long Wang | Role of the effective payoff function in evolutionary game dynamics | This paper has been accepted to publish on EPL | EPL 124 40002 (2018) | 10.1209/0295-5075/124/40002 | null | q-bio.PE physics.bio-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In most studies regarding evolutionary game dynamics, the effective payoff, a
quantity that translates the payoff derived from game interactions into
reproductive success, is usually assumed to be a specific function of the
payoff. Meanwhile, the effect of different function forms of effective payoff
on evolutionary ... | [
{
"created": "Thu, 5 Apr 2018 08:15:41 GMT",
"version": "v1"
},
{
"created": "Sun, 8 Jul 2018 02:28:44 GMT",
"version": "v2"
},
{
"created": "Tue, 7 Aug 2018 08:21:20 GMT",
"version": "v3"
},
{
"created": "Sat, 8 Dec 2018 05:21:21 GMT",
"version": "v4"
}
] | 2021-05-18 | [
[
"Huang",
"Feng",
""
],
[
"Chen",
"Xiaojie",
""
],
[
"Wang",
"Long",
""
]
] | In most studies regarding evolutionary game dynamics, the effective payoff, a quantity that translates the payoff derived from game interactions into reproductive success, is usually assumed to be a specific function of the payoff. Meanwhile, the effect of different function forms of effective payoff on evolutionary dy... |
1207.3211 | Andrey Dovzhenok | A. Dovzhenok, A. S. Kuznetsov | Exploring Neuronal Bistability at the Depolarization Block | 26 pages, 8 figures, accepted to PLoS ONE | (2012) PLoS ONE 7(8): e42811 | 10.1371/journal.pone.0042811 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many neurons display bistability - coexistence of two firing modes such as
bursting and tonic spiking or tonic spiking and silence. Bistability has been
proposed to endow neurons with richer forms of information processing in
general and to be involved in short-term memory in particular by allowing a
brief signal to ... | [
{
"created": "Fri, 13 Jul 2012 11:59:57 GMT",
"version": "v1"
}
] | 2012-08-14 | [
[
"Dovzhenok",
"A.",
""
],
[
"Kuznetsov",
"A. S.",
""
]
] | Many neurons display bistability - coexistence of two firing modes such as bursting and tonic spiking or tonic spiking and silence. Bistability has been proposed to endow neurons with richer forms of information processing in general and to be involved in short-term memory in particular by allowing a brief signal to el... |
2209.11730 | Claudia Solis-Lemus | Samuel Ozminkowski, Yuke Wu, Liule Yang, Zhiwen Xu, Luke Selberg,
Chunrong Huang, Claudia Solis-Lemus | BioKlustering: a web app for semi-supervised learning of maximally
imbalanced genomic data | null | null | null | null | q-bio.GN stat.AP | http://creativecommons.org/licenses/by/4.0/ | Summary: Accurate phenotype prediction from genomic sequences is a highly
coveted task in biological and medical research. While machine-learning holds
the key to accurate prediction in a variety of fields, the complexity of
biological data can render many methodologies inapplicable. We introduce
BioKlustering, a use... | [
{
"created": "Fri, 23 Sep 2022 17:23:59 GMT",
"version": "v1"
},
{
"created": "Mon, 26 Sep 2022 21:18:42 GMT",
"version": "v2"
}
] | 2022-09-28 | [
[
"Ozminkowski",
"Samuel",
""
],
[
"Wu",
"Yuke",
""
],
[
"Yang",
"Liule",
""
],
[
"Xu",
"Zhiwen",
""
],
[
"Selberg",
"Luke",
""
],
[
"Huang",
"Chunrong",
""
],
[
"Solis-Lemus",
"Claudia",
""
]
] | Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data can render many methodologies inapplicable. We introduce BioKlustering, a user-... |
1509.00171 | Yuri A. Dabaghian | A. Babichev, S. Cheng and Yu. Dabaghian | Topological schemas of cognitive maps and spatial learning in the
hippocampus | 17 pages, 11 figures, Frontiers in Computational Neuroscience, 2016 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spatial navigation in mammals is based on building a mental representation of
their environment---a cognitive map. However, both the nature of this cognitive
map and its underpinning in neural structures and activity remains vague. A key
difficulty is that these maps are collective, emergent phenomena that cannot be
... | [
{
"created": "Tue, 1 Sep 2015 08:13:59 GMT",
"version": "v1"
},
{
"created": "Sun, 20 Mar 2016 19:33:00 GMT",
"version": "v2"
}
] | 2016-03-22 | [
[
"Babichev",
"A.",
""
],
[
"Cheng",
"S.",
""
],
[
"Dabaghian",
"Yu.",
""
]
] | Spatial navigation in mammals is based on building a mental representation of their environment---a cognitive map. However, both the nature of this cognitive map and its underpinning in neural structures and activity remains vague. A key difficulty is that these maps are collective, emergent phenomena that cannot be re... |
2311.08269 | Nodar Gogoberidze | Nodar Gogoberidze, Beth A. Cimini | Defining the boundaries: challenges and advances in identifying cells in
microscopy images | 12 pages, 1 figure, submitted to "Current Opinion in Biotechnology" | null | 10.1016/j.copbio.2023.103055 | null | q-bio.QM cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Segmentation, or the outlining of objects within images, is a critical step
in the measurement and analysis of cells within microscopy images. While
improvements continue to be made in tools that rely on classical methods for
segmentation, deep learning-based tools increasingly dominate advances in the
technology. Sp... | [
{
"created": "Tue, 14 Nov 2023 16:02:18 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Nov 2023 17:18:44 GMT",
"version": "v2"
}
] | 2024-03-15 | [
[
"Gogoberidze",
"Nodar",
""
],
[
"Cimini",
"Beth A.",
""
]
] | Segmentation, or the outlining of objects within images, is a critical step in the measurement and analysis of cells within microscopy images. While improvements continue to be made in tools that rely on classical methods for segmentation, deep learning-based tools increasingly dominate advances in the technology. Spec... |
1309.0926 | Mike Steel Prof. | Olivier Gascuel and Mike Steel | Predicting the ancestral character changes in a tree is typically easier
than predicting the root state | 58 pages, 4 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Predicting the ancestral sequences of a group of homologous sequences related
by a phylogenetic tree has been the subject of many studies, and numerous
methods have been proposed to this purpose. Theoretical results are available
that show that when the mutation rate become too large, reconstructing the
ancestral sta... | [
{
"created": "Wed, 4 Sep 2013 06:36:01 GMT",
"version": "v1"
}
] | 2013-09-05 | [
[
"Gascuel",
"Olivier",
""
],
[
"Steel",
"Mike",
""
]
] | Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show that when the mutation rate become too large, reconstructing the ancestral state... |
1612.03541 | Michael Lydeamore | M. Lydeamore, P. T. Campbell, D. G. Regan, S. Y. C. Tong, R. Andrews,
A. C. Steer, L. Romani, J. M. Kaldor, J. McVernon, J. M. McCaw | A biological model of scabies infection dynamics and treatment explains
why mass drug administration does not lead to elimination | 22 pages, 10 figures | null | 10.1016/j.mbs.2018.08.007 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite a low global prevalence, infections with Sarcoptes scabiei, or
scabies, are still common in remote communities such as in northern Australia
and the Solomon Islands. Mass drug administration (MDA) has been utilised in
these communities, and although prevalence drops substantially initially, these
reductions h... | [
{
"created": "Mon, 12 Dec 2016 04:32:53 GMT",
"version": "v1"
}
] | 2018-11-26 | [
[
"Lydeamore",
"M.",
""
],
[
"Campbell",
"P. T.",
""
],
[
"Regan",
"D. G.",
""
],
[
"Tong",
"S. Y. C.",
""
],
[
"Andrews",
"R.",
""
],
[
"Steer",
"A. C.",
""
],
[
"Romani",
"L.",
""
],
[
"Kaldor",
... | Despite a low global prevalence, infections with Sarcoptes scabiei, or scabies, are still common in remote communities such as in northern Australia and the Solomon Islands. Mass drug administration (MDA) has been utilised in these communities, and although prevalence drops substantially initially, these reductions hav... |
1407.3622 | Kunihiko Kaneko | Kunihiko Kaneko, Chikara Furusawa, and Tetsuya Yomo | Universal relationship in gene-expression changes for cells in
steady-growth state | 7 pages (5 figures) + 2 Supplementary pages (figures) | null | null | null | q-bio.CB q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cells adapt to different conditions by altering a vast number of components,
which is measurable using transcriptome analysis. Given that a cell undergoing
steady growth is constrained to sustain each of its internal components, the
abundance of all the components in the cell has to be roughly doubled during
each cel... | [
{
"created": "Mon, 14 Jul 2014 12:31:58 GMT",
"version": "v1"
}
] | 2014-07-15 | [
[
"Kaneko",
"Kunihiko",
""
],
[
"Furusawa",
"Chikara",
""
],
[
"Yomo",
"Tetsuya",
""
]
] | Cells adapt to different conditions by altering a vast number of components, which is measurable using transcriptome analysis. Given that a cell undergoing steady growth is constrained to sustain each of its internal components, the abundance of all the components in the cell has to be roughly doubled during each cell ... |
2303.04607 | Jer\'onimo Fotin\'os | Jer\'onimo Fotin\'os, Lucas Barberis, Carlos A. Condat | Effects of a Differentiating Therapy on Cancer-Stem-Cell-Driven Tumors | 21 pages, 10 figures (17 images) | null | null | null | q-bio.TO physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | The growth of many solid tumors has been found to be driven by chemo- and
radiotherapy-resistant cancer stem cells (CSCs). A suitable therapeutic avenue
in these cases may involve the use of a differentiating agent (DA) to force the
differentiation of the CSCs and of conventional therapies to eliminate the
remaining ... | [
{
"created": "Wed, 8 Mar 2023 14:19:55 GMT",
"version": "v1"
}
] | 2023-03-09 | [
[
"Fotinós",
"Jerónimo",
""
],
[
"Barberis",
"Lucas",
""
],
[
"Condat",
"Carlos A.",
""
]
] | The growth of many solid tumors has been found to be driven by chemo- and radiotherapy-resistant cancer stem cells (CSCs). A suitable therapeutic avenue in these cases may involve the use of a differentiating agent (DA) to force the differentiation of the CSCs and of conventional therapies to eliminate the remaining di... |
2207.04869 | Zhichun Guo | Zhichun Guo, Kehan Guo, Bozhao Nan, Yijun Tian, Roshni G. Iyer, Yihong
Ma, Olaf Wiest, Xiangliang Zhang, Wei Wang, Chuxu Zhang, Nitesh V. Chawla | Graph-based Molecular Representation Learning | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular representation learning (MRL) is a key step to build the connection
between machine learning and chemical science. In particular, it encodes
molecules as numerical vectors preserving the molecular structures and
features, on top of which the downstream tasks (e.g., property prediction) can
be performed. Rec... | [
{
"created": "Fri, 8 Jul 2022 17:43:20 GMT",
"version": "v1"
},
{
"created": "Thu, 20 Apr 2023 13:28:06 GMT",
"version": "v2"
},
{
"created": "Wed, 29 Nov 2023 03:16:59 GMT",
"version": "v3"
}
] | 2023-11-30 | [
[
"Guo",
"Zhichun",
""
],
[
"Guo",
"Kehan",
""
],
[
"Nan",
"Bozhao",
""
],
[
"Tian",
"Yijun",
""
],
[
"Iyer",
"Roshni G.",
""
],
[
"Ma",
"Yihong",
""
],
[
"Wiest",
"Olaf",
""
],
[
"Zhang",
"Xiangl... | Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top of which the downstream tasks (e.g., property prediction) can be performed. Recen... |
0901.0089 | Ewa Nurowska | Ewa Nurowska, Mykola Bratiichuk, Beata Dworakowska, Roman J. Nowak | A physical model of nicotinic ACh receptor kinetics | null | null | null | null | q-bio.NC q-bio.CB q-bio.QM q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a new approach to nicotinic receptor kinetics and a new model
explaining random variabilities in the duration of open events. The model gives
new interpretation on brief and long receptor openings and predicts (for two
identical binding sites) the presence of three components in the open time
distribution:... | [
{
"created": "Wed, 31 Dec 2008 12:14:05 GMT",
"version": "v1"
}
] | 2009-01-07 | [
[
"Nurowska",
"Ewa",
""
],
[
"Bratiichuk",
"Mykola",
""
],
[
"Dworakowska",
"Beata",
""
],
[
"Nowak",
"Roman J.",
""
]
] | We present a new approach to nicotinic receptor kinetics and a new model explaining random variabilities in the duration of open events. The model gives new interpretation on brief and long receptor openings and predicts (for two identical binding sites) the presence of three components in the open time distribution: t... |
2305.01663 | Prayag Tiwari Dr. | Manish Bhatia, Balram Meena, Vipin Kumar Rathi, Prayag Tiwari, Amit
Kumar Jaiswal, Shagaf M Ansari, Ajay Kumar, Pekka Marttinen | A Novel Deep Learning based Model for Erythrocytes Classification and
Quantification in Sickle Cell Disease | null | null | null | null | q-bio.QM cs.LG eess.IV | http://creativecommons.org/licenses/by/4.0/ | The shape of erythrocytes or red blood cells is altered in several
pathological conditions. Therefore, identifying and quantifying different
erythrocyte shapes can help diagnose various diseases and assist in designing a
treatment strategy. Machine Learning (ML) can be efficiently used to identify
and quantify distor... | [
{
"created": "Tue, 2 May 2023 10:28:07 GMT",
"version": "v1"
}
] | 2023-05-04 | [
[
"Bhatia",
"Manish",
""
],
[
"Meena",
"Balram",
""
],
[
"Rathi",
"Vipin Kumar",
""
],
[
"Tiwari",
"Prayag",
""
],
[
"Jaiswal",
"Amit Kumar",
""
],
[
"Ansari",
"Shagaf M",
""
],
[
"Kumar",
"Ajay",
""
],
[... | The shape of erythrocytes or red blood cells is altered in several pathological conditions. Therefore, identifying and quantifying different erythrocyte shapes can help diagnose various diseases and assist in designing a treatment strategy. Machine Learning (ML) can be efficiently used to identify and quantify distorte... |
q-bio/0406049 | Muhittin Mungan | Muhittin Mungan, Alkan Kabakcioglu, Duygu Balcan, and Ayse Erzan | Analytical Solution of a Stochastic Content Based Network Model | 13 pages, 5 figures. Rewrote conclusions regarding the relevance to
gene regulation networks, fixed minor errors and replaced fig. 4. Main body
of paper (model and calculations) remains unchanged. Submitted for
publication | J. Phys. A: Math. Gen. 38 (2005) 9599--9620 | 10.1088/0305-4470/38/44/001 | null | q-bio.MN cond-mat.stat-mech q-bio.GN | null | We define and completely solve a content-based directed network whose nodes
consist of random words and an adjacency rule involving perfect or approximate
matches, for an alphabet with an arbitrary number of letters. The analytic
expression for the out-degree distribution shows a crossover from a leading
power law be... | [
{
"created": "Fri, 25 Jun 2004 12:20:28 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Jul 2005 08:03:34 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Mungan",
"Muhittin",
""
],
[
"Kabakcioglu",
"Alkan",
""
],
[
"Balcan",
"Duygu",
""
],
[
"Erzan",
"Ayse",
""
]
] | We define and completely solve a content-based directed network whose nodes consist of random words and an adjacency rule involving perfect or approximate matches, for an alphabet with an arbitrary number of letters. The analytic expression for the out-degree distribution shows a crossover from a leading power law beha... |
2304.07178 | Jorge Carrasco Muriel | Jorge Carrasco Muriel, Nicholas Cowie, Marjan Mansouvar, Teddy Groves
and Lars Keld Nielsen | Shu: Visualization of high dimensional biological pathways | 3 pages, 1 figure, supplementary material at
https://github.com/biosustain/shu_case_studies | null | 10.1093/bioinformatics/btae140 | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | Summary: Shu is a visualization tool that integrates diverse data types into
a metabolic map, with a focus on supporting multiple conditions and visualizing
distributions. The goal is to provide a unified platform for handling the
growing volume of multi-omics data, leveraging the metabolic maps developed by
the meta... | [
{
"created": "Fri, 14 Apr 2023 14:53:45 GMT",
"version": "v1"
}
] | 2024-03-08 | [
[
"Muriel",
"Jorge Carrasco",
""
],
[
"Cowie",
"Nicholas",
""
],
[
"Mansouvar",
"Marjan",
""
],
[
"Groves",
"Teddy",
""
],
[
"Nielsen",
"Lars Keld",
""
]
] | Summary: Shu is a visualization tool that integrates diverse data types into a metabolic map, with a focus on supporting multiple conditions and visualizing distributions. The goal is to provide a unified platform for handling the growing volume of multi-omics data, leveraging the metabolic maps developed by the metabo... |
2111.05902 | Nicholas Barendregt | Nicholas W. Barendregt and Peter J. Thomas | Heteroclinic cycling and extinction in May-Leonard models with
demographic stochasticity | 21 pages, 6 figures | null | null | null | q-bio.PE math.PR q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | May and Leonard (SIAM J. Appl. Math 1975) introduced a three-species
Lotka-Volterra type population model that exhibits heteroclinic cycling. Rather
than producing a periodic limit cycle, the trajectory takes longer and longer
to complete each "cycle", passing closer and closer to unstable fixed points in
which one p... | [
{
"created": "Wed, 10 Nov 2021 19:44:45 GMT",
"version": "v1"
}
] | 2021-11-12 | [
[
"Barendregt",
"Nicholas W.",
""
],
[
"Thomas",
"Peter J.",
""
]
] | May and Leonard (SIAM J. Appl. Math 1975) introduced a three-species Lotka-Volterra type population model that exhibits heteroclinic cycling. Rather than producing a periodic limit cycle, the trajectory takes longer and longer to complete each "cycle", passing closer and closer to unstable fixed points in which one pop... |
1407.8210 | Javad Noorbakhsh | Javad Noorbakhsh, David Schwab, Allyson Sgro, Thomas Gregor, Pankaj
Mehta | Multiscale modeling of oscillations and spiral waves in Dictyostelium
populations | null | Phys. Rev. E 91, 062711 (2015) | 10.1103/PhysRevE.91.062711 | null | q-bio.CB math-ph math.MP nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Unicellular organisms exhibit elaborate collective behaviors in response to
environmental cues. These behaviors are controlled by complex biochemical
networks within individual cells and coordinated through cell-to-cell
communication. Describing these behaviors requires new mathematical models that
can bridge scales ... | [
{
"created": "Wed, 30 Jul 2014 20:42:56 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Sep 2014 20:32:56 GMT",
"version": "v2"
}
] | 2015-06-24 | [
[
"Noorbakhsh",
"Javad",
""
],
[
"Schwab",
"David",
""
],
[
"Sgro",
"Allyson",
""
],
[
"Gregor",
"Thomas",
""
],
[
"Mehta",
"Pankaj",
""
]
] | Unicellular organisms exhibit elaborate collective behaviors in response to environmental cues. These behaviors are controlled by complex biochemical networks within individual cells and coordinated through cell-to-cell communication. Describing these behaviors requires new mathematical models that can bridge scales --... |
2407.07265 | Pranav Kantroo | Pranav Kantroo, G\"unter P. Wagner, Benjamin B. Machta | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation | null | null | null | null | q-bio.BM q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Protein language models trained on the masked language modeling objective
learn to predict the identity of hidden amino acid residues within a sequence
using the remaining observable sequence as context. They do so by embedding the
residues into a high dimensional space that encapsulates the relevant
contextual cues.... | [
{
"created": "Tue, 9 Jul 2024 22:46:08 GMT",
"version": "v1"
}
] | 2024-07-11 | [
[
"Kantroo",
"Pranav",
""
],
[
"Wagner",
"Günter P.",
""
],
[
"Machta",
"Benjamin B.",
""
]
] | Protein language models trained on the masked language modeling objective learn to predict the identity of hidden amino acid residues within a sequence using the remaining observable sequence as context. They do so by embedding the residues into a high dimensional space that encapsulates the relevant contextual cues. T... |
1710.03399 | Sael Lee | Vasundhara Dehiya, Jaya Thomas, Lee Sael | Prior Knowledge based mutation prioritization towards causal variant
finding in rare disease | 21 pages, 5 figures, submitted for journal publication in 2017 | null | null | null | q-bio.GN cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How do we determine the mutational effects in exome sequencing data with
little or no statistical evidence? Can protein structural information fill in
the gap of not having enough statistical evidence? In this work, we answer the
two questions with the goal towards determining pathogenic effects of rare
variants in r... | [
{
"created": "Tue, 10 Oct 2017 04:51:17 GMT",
"version": "v1"
}
] | 2017-10-11 | [
[
"Dehiya",
"Vasundhara",
""
],
[
"Thomas",
"Jaya",
""
],
[
"Sael",
"Lee",
""
]
] | How do we determine the mutational effects in exome sequencing data with little or no statistical evidence? Can protein structural information fill in the gap of not having enough statistical evidence? In this work, we answer the two questions with the goal towards determining pathogenic effects of rare variants in rar... |
1609.01570 | Mette Olufsen | Renee Brady, Dennis O. Frank-Ito, Hien T. Tran, Susanne Janum, Kirsten
M{\o}ller, Susanne Brix, Johnny T. Ottesen, Jesper Mehlsen, Mette S. Olufsen | Personalized Mathematical Model Predicting Endotoxin-Induced
Inflammatory Responses in Young Men | Keywords: Cytokines, LPS, TNF-, IL-6, IL-10, CXCL8 | null | null | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The initial reaction of the body to pathogenic microbial infection or severe
tissue trauma is an acute inflammatory response. The magnitude of such a
response is of critical importance, since an uncontrolled response can cause
further tissue damage, sepsis, and ultimately death, while an insufficient
response can res... | [
{
"created": "Tue, 6 Sep 2016 14:24:35 GMT",
"version": "v1"
}
] | 2016-09-07 | [
[
"Brady",
"Renee",
""
],
[
"Frank-Ito",
"Dennis O.",
""
],
[
"Tran",
"Hien T.",
""
],
[
"Janum",
"Susanne",
""
],
[
"Møller",
"Kirsten",
""
],
[
"Brix",
"Susanne",
""
],
[
"Ottesen",
"Johnny T.",
""
],
[... | The initial reaction of the body to pathogenic microbial infection or severe tissue trauma is an acute inflammatory response. The magnitude of such a response is of critical importance, since an uncontrolled response can cause further tissue damage, sepsis, and ultimately death, while an insufficient response can resul... |
1405.2419 | Mohsen Bakouri | Mohsen A. Bakouri | Sensorless Physiological Control of Implantable Rotary Blood Pumps for
Heart Failure Patients Using Modern Control Techniques | null | null | null | null | q-bio.QM cs.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sufferers of heart failure disease have a life expectancy of one year and
heart transplantation is usually the only guarantee of survival beyond this
period. The number of donor hearts available currently is less than 3,000 per
annum worldwide. Apart from the relatively fortunate people who receive donor
hearts for t... | [
{
"created": "Sat, 10 May 2014 11:07:53 GMT",
"version": "v1"
}
] | 2014-05-13 | [
[
"Bakouri",
"Mohsen A.",
""
]
] | Sufferers of heart failure disease have a life expectancy of one year and heart transplantation is usually the only guarantee of survival beyond this period. The number of donor hearts available currently is less than 3,000 per annum worldwide. Apart from the relatively fortunate people who receive donor hearts for tra... |
1605.06309 | Fabiano L. Ribeiro | Fabiano L. Ribeiro | First Principles Attempt to Unify some Population Growth Models | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work, some phenomenological models, those that are based only on the
population information (macroscopic level), are deduced in an intuitive way.
These models, as for instance Verhulst, Gompertz and Bertalanffy models, are
posted in such a manner that all the parameters involved have physical
interpretation. ... | [
{
"created": "Fri, 20 May 2016 12:05:00 GMT",
"version": "v1"
}
] | 2016-05-23 | [
[
"Ribeiro",
"Fabiano L.",
""
]
] | In this work, some phenomenological models, those that are based only on the population information (macroscopic level), are deduced in an intuitive way. These models, as for instance Verhulst, Gompertz and Bertalanffy models, are posted in such a manner that all the parameters involved have physical interpretation. A ... |
2304.03131 | Stephane Jamain | Ana Lokmer (UPEC), Charanraj Goud Alladi (OPTeN), R\'ejane Troudet
(UPEC), Delphine Bacq-Daian (CNRGH), Anne Boland-Auge (CNRGH), Violaine
Latapie (UPEC), Jean-Fran\c{c}ois Deleuze (CNRGH), Ravi Philip Rajkumar,
Deepak Gopal Shewade, Frank B\'elivier (OPTeN), Cynthia Marie-Claire (OPTeN),
St\'ephane Jamain (UPE... | Risperidone response in patients with schizophrenia drives DNA
methylation changes in immune and neuronal systems | Epigenomics, 2023 | null | 10.2217/epi-2023-0017 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: The choice of efficient antipsychotic therapy for schizophrenia
relies on a time-consuming trial-and-error approach, whereas the social and
economic burdens of the disease call for faster alternatives. Material \&
methods: In a search for predictive biomarkers of antipsychotic response, blood
methylomes o... | [
{
"created": "Thu, 6 Apr 2023 15:05:45 GMT",
"version": "v1"
}
] | 2023-04-07 | [
[
"Lokmer",
"Ana",
"",
"UPEC"
],
[
"Alladi",
"Charanraj Goud",
"",
"OPTeN"
],
[
"Troudet",
"Réjane",
"",
"UPEC"
],
[
"Bacq-Daian",
"Delphine",
"",
"CNRGH"
],
[
"Boland-Auge",
"Anne",
"",
"CNRGH"
],
[
"Latapie",
... | Background: The choice of efficient antipsychotic therapy for schizophrenia relies on a time-consuming trial-and-error approach, whereas the social and economic burdens of the disease call for faster alternatives. Material \& methods: In a search for predictive biomarkers of antipsychotic response, blood methylomes of ... |
1308.3277 | Aaron Golden | Aaron Golden, S. George Djorgovski, John M. Greally | Astrogenomics: big data, old problems, old solutions? | 11 pages, 1 figure, accepted for publication in Genome Biology | null | null | null | q-bio.GN astro-ph.IM | http://creativecommons.org/licenses/by-nc-sa/3.0/ | The ominous warnings of a `data deluge' in the life sciences from
high-throughput DNA sequencing data are being supplanted by a second deluge, of
cliches bemoaning our collective scientific fate unless we address the genomic
data `tsunami'. It is imperative that we explore the many facets of the genome,
not just sequ... | [
{
"created": "Thu, 15 Aug 2013 00:01:05 GMT",
"version": "v1"
}
] | 2013-08-16 | [
[
"Golden",
"Aaron",
""
],
[
"Djorgovski",
"S. George",
""
],
[
"Greally",
"John M.",
""
]
] | The ominous warnings of a `data deluge' in the life sciences from high-throughput DNA sequencing data are being supplanted by a second deluge, of cliches bemoaning our collective scientific fate unless we address the genomic data `tsunami'. It is imperative that we explore the many facets of the genome, not just sequen... |
1912.01769 | Ling-Fei Huang | Lingfei Huang, Yixi Liu, Zheng Jiao, Junyan Wang, Luo Fang, Jianhua
Mao | Population Pharmacokinetic Study of Tacrolimus in Pediatric Patients
with Primary Nephrotic Syndrome: A Comparison of Linear and Nonlinear
Michaelis Menten Pharmacokinetic Model | 22 pages, 4 tables and 4 figures | Eur J Pharm Sci. 2020 Feb 15;143:105199 | 10.1016/j.ejps.2019.105199 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background Little is known about the population pharmacokinetics (PPK) of
tacrolimus (TAC) in pediatric primary nephrotic syndrome (PNS). This study
aimed to compare the predictive performance between nonlinear and linear PK
models and investigate the significant factors of TAC PK characteristics in
pediatric PNS. Me... | [
{
"created": "Wed, 4 Dec 2019 02:12:07 GMT",
"version": "v1"
},
{
"created": "Wed, 26 Feb 2020 10:04:13 GMT",
"version": "v2"
}
] | 2020-02-27 | [
[
"Huang",
"Lingfei",
""
],
[
"Liu",
"Yixi",
""
],
[
"Jiao",
"Zheng",
""
],
[
"Wang",
"Junyan",
""
],
[
"Fang",
"Luo",
""
],
[
"Mao",
"Jianhua",
""
]
] | Background Little is known about the population pharmacokinetics (PPK) of tacrolimus (TAC) in pediatric primary nephrotic syndrome (PNS). This study aimed to compare the predictive performance between nonlinear and linear PK models and investigate the significant factors of TAC PK characteristics in pediatric PNS. Meth... |
1311.3997 | Ron Nielsen | Ron W Nielsen aka Jan Nurzynski | No stagnation in the growth of population | 9 pages, 1 figure, 2 tables | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Growth of human population shows no signs of stagnation. The only small
disturbance is identified as being probably associated with the coinciding
impacts of five demographic catastrophes. The concept of the Epoch of
Malthusian Stagnation is convincingly contradicted by empirical evidence.
| [
{
"created": "Fri, 15 Nov 2013 23:11:54 GMT",
"version": "v1"
}
] | 2013-11-19 | [
[
"Nurzynski",
"Ron W Nielsen aka Jan",
""
]
] | Growth of human population shows no signs of stagnation. The only small disturbance is identified as being probably associated with the coinciding impacts of five demographic catastrophes. The concept of the Epoch of Malthusian Stagnation is convincingly contradicted by empirical evidence. |
q-bio/0512033 | Pablo Echenique | Pablo Echenique and Ivan Calvo | Explicit factorization of external coordinates in constrained
Statistical Mechanics models | 22 pages, 2 figures, LaTeX, AMSTeX. v2: Introduccion slightly
extended. Version in arXiv is slightly larger than the published one | J. Comp. Chem. 27 (2006) 1748-1755 | 10.1002/jcc.20499 | null | q-bio.QM cond-mat.soft | null | If a macromolecule is described by curvilinear coordinates or rigid
constraints are imposed, the equilibrium probability density that must be
sampled in Monte Carlo simulations includes the determinants of different
mass-metric tensors. In this work, we explicitly write the determinant of the
mass-metric tensor G and... | [
{
"created": "Thu, 15 Dec 2005 18:49:43 GMT",
"version": "v1"
},
{
"created": "Tue, 14 Feb 2006 16:28:28 GMT",
"version": "v2"
},
{
"created": "Wed, 26 Apr 2006 11:09:30 GMT",
"version": "v3"
},
{
"created": "Mon, 4 Dec 2006 17:46:41 GMT",
"version": "v4"
}
] | 2007-12-19 | [
[
"Echenique",
"Pablo",
""
],
[
"Calvo",
"Ivan",
""
]
] | If a macromolecule is described by curvilinear coordinates or rigid constraints are imposed, the equilibrium probability density that must be sampled in Monte Carlo simulations includes the determinants of different mass-metric tensors. In this work, we explicitly write the determinant of the mass-metric tensor G and o... |
2010.02897 | Emerson Sadurn\'i | E. Sadurn\'i and G. Luna-Acosta | Exactly solvable SIR models, their extensions and their application to
sensitive pandemic forecasting | 27 pages, single column, 10 figures | null | null | null | q-bio.PE nlin.CD physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The classic SIR model of epidemic dynamics is solved completely by
quadratures, including a time integral transform expanded in a series of
incomplete gamma functions. The model is also generalized to arbitrary
time-dependent infection rates and solved explicitly when the control parameter
depends on the accumulated ... | [
{
"created": "Tue, 6 Oct 2020 17:28:23 GMT",
"version": "v1"
}
] | 2020-10-07 | [
[
"Sadurní",
"E.",
""
],
[
"Luna-Acosta",
"G.",
""
]
] | The classic SIR model of epidemic dynamics is solved completely by quadratures, including a time integral transform expanded in a series of incomplete gamma functions. The model is also generalized to arbitrary time-dependent infection rates and solved explicitly when the control parameter depends on the accumulated in... |
0912.2955 | Pan-Jun Kim | Caroline B. Milne, Pan-Jun Kim, James A. Eddy, Nathan D. Price | Accomplishments in Genome-Scale In Silico Modeling for Industrial and
Medical Biotechnology | Highlighted in "In this issue" section of Biotechnology Journal
12/2009 | Biotechnol. J. 4, 1653 (2009) | 10.1002/biot.200900234 | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Driven by advancements in high-throughput biological technologies and the
growing number of sequenced genomes, the construction of in silico models at
the genome scale has provided powerful tools to investigate a vast array of
biological systems and applications. Here, we review comprehensively the uses
of such model... | [
{
"created": "Tue, 15 Dec 2009 17:13:55 GMT",
"version": "v1"
}
] | 2009-12-16 | [
[
"Milne",
"Caroline B.",
""
],
[
"Kim",
"Pan-Jun",
""
],
[
"Eddy",
"James A.",
""
],
[
"Price",
"Nathan D.",
""
]
] | Driven by advancements in high-throughput biological technologies and the growing number of sequenced genomes, the construction of in silico models at the genome scale has provided powerful tools to investigate a vast array of biological systems and applications. Here, we review comprehensively the uses of such models ... |
0711.0874 | Damian H. Zanette | Damian H. Zanette, Sebastian Risau Gusman | Infection spreading in a population with evolving contacts | null | null | null | null | q-bio.PE cond-mat.stat-mech physics.soc-ph | null | We study the spreading of an infection within an SIS epidemiological model on
a network. Susceptible agents are given the opportunity of breaking their links
with infected agents. Broken links are either permanently removed or
reconnected with the rest of the population. Thus, the network coevolves with
the populatio... | [
{
"created": "Tue, 6 Nov 2007 13:47:51 GMT",
"version": "v1"
}
] | 2007-11-07 | [
[
"Zanette",
"Damian H.",
""
],
[
"Gusman",
"Sebastian Risau",
""
]
] | We study the spreading of an infection within an SIS epidemiological model on a network. Susceptible agents are given the opportunity of breaking their links with infected agents. Broken links are either permanently removed or reconnected with the rest of the population. Thus, the network coevolves with the population ... |
2005.10644 | Alun Stokes | Alun Stokes, William Hum, Jonathan Zaslavsky | A Minimal-Input Multilayer Perceptron for Predicting Drug-Drug
Interactions Without Knowledge of Drug Structure | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The necessity of predictive models in the drug discovery industry cannot be
understated. With the sheer volume of potentially useful compounds that are
considered for use, it is becoming increasingly computationally difficult to
investigate the overlapping interactions between drugs. Understanding this is
also import... | [
{
"created": "Wed, 20 May 2020 17:15:19 GMT",
"version": "v1"
}
] | 2020-05-22 | [
[
"Stokes",
"Alun",
""
],
[
"Hum",
"William",
""
],
[
"Zaslavsky",
"Jonathan",
""
]
] | The necessity of predictive models in the drug discovery industry cannot be understated. With the sheer volume of potentially useful compounds that are considered for use, it is becoming increasingly computationally difficult to investigate the overlapping interactions between drugs. Understanding this is also importan... |
q-bio/0401020 | Ryan Taft | R.J. Taft and J.S. Mattick | Increasing biological complexity is positively correlated with the
relative genome-wide expansion of non-protein-coding DNA sequences | 25 pages, 2 figures, 1 table | Genome Biology Preprint Depository -
http://genomebiology.com/2003/5/1/P1 | null | null | q-bio.GN q-bio.PE | null | Background: Prior to the current genomic era it was suggested that the number
of protein-coding genes that an organism made use of was a valid measure of its
complexity. It is now clear, however, that major incongruities exist and that
there is only a weak relationship between biological complexity and the number
of ... | [
{
"created": "Thu, 15 Jan 2004 00:39:29 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Taft",
"R. J.",
""
],
[
"Mattick",
"J. S.",
""
]
] | Background: Prior to the current genomic era it was suggested that the number of protein-coding genes that an organism made use of was a valid measure of its complexity. It is now clear, however, that major incongruities exist and that there is only a weak relationship between biological complexity and the number of pr... |
1108.1788 | Marco Zoli | Marco Zoli | Thermodynamics of Twisted DNA with Solvent Interaction | The Journal of Chemical Physics (2011) in press | J. Chem. Phys. vol. 135, 115101 (2011).
http://link.aip.org/link/?JCP/135/115101 | 10.1063/1.3631564 | null | q-bio.BM cond-mat.soft cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The imaginary time path integral formalism is applied to a nonlinear
Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing
solvent interaction term. Torsional effects are modeled by a twist angle
between neighboring base pairs stacked along the molecule backbone. The base
pair displacements are des... | [
{
"created": "Mon, 8 Aug 2011 19:43:40 GMT",
"version": "v1"
}
] | 2011-09-19 | [
[
"Zoli",
"Marco",
""
]
] | The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base pairs stacked along the molecule backbone. The base pair displacements are descr... |
1503.02901 | Eugenio Urdapilleta | Eugenio Urdapilleta and In\'es Samengo | Effects of spike-triggered negative feedback on receptive-field
properties | 46 pages, 10 figures. Preprint accepted for publication in J. Comput.
Neurosci | J. Comput. Neurosci. 38(2), 405-425, 2015 | 10.1007/s10827-014-0546-0 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sensory neurons are often described in terms of a receptive field, that is, a
linear kernel through which stimuli are filtered before they are further
processed. If information transmission is assumed to proceed in a feedforward
cascade, the receptive field may be interpreted as the external stimulus'
profile maximiz... | [
{
"created": "Tue, 10 Mar 2015 13:45:59 GMT",
"version": "v1"
}
] | 2015-03-11 | [
[
"Urdapilleta",
"Eugenio",
""
],
[
"Samengo",
"Inés",
""
]
] | Sensory neurons are often described in terms of a receptive field, that is, a linear kernel through which stimuli are filtered before they are further processed. If information transmission is assumed to proceed in a feedforward cascade, the receptive field may be interpreted as the external stimulus' profile maximizin... |
q-bio/0411045 | Eli Eisenberg | Erez Y. Levanon, Eli Eisenberg, Rodrigo Yelin, Sergey Nemzer, Martina
Hallegger, Ronen Shemesh, Zipora Y. Fligelman, Avi Shoshan, Sarah R. Pollock,
Dan Sztybel, Moshe Olshansky, Gideon Rechavi and Michael F. Jantsch | Systematic identification of abundant A-to-I editing sites in the human
transcriptome | Pre-print version. See http://dx.doi.org/10.1038/nbt996 for a reprint | Nature Biotechnology 22, 1001-1005 (2004) | 10.1038/nbt996 | null | q-bio.GN | null | RNA editing by members of the double-stranded RNA-specific ADAR family leads
to site-specific conversion of adenosine to inosine (A-to-I) in precursor
messenger RNAs. Editing by ADARs is believed to occur in all metazoa, and is
essential for mammalian development. Currently, only a limited number of human
ADAR substr... | [
{
"created": "Thu, 25 Nov 2004 20:47:34 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Levanon",
"Erez Y.",
""
],
[
"Eisenberg",
"Eli",
""
],
[
"Yelin",
"Rodrigo",
""
],
[
"Nemzer",
"Sergey",
""
],
[
"Hallegger",
"Martina",
""
],
[
"Shemesh",
"Ronen",
""
],
[
"Fligelman",
"Zipora Y.",
""
]... | RNA editing by members of the double-stranded RNA-specific ADAR family leads to site-specific conversion of adenosine to inosine (A-to-I) in precursor messenger RNAs. Editing by ADARs is believed to occur in all metazoa, and is essential for mammalian development. Currently, only a limited number of human ADAR substrat... |
1002.4903 | Alexei Koulakov | Alexei A. Koulakov and Dmitry Rinberg | Sparse incomplete representations: A novel role for olfactory granule
cells | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mitral cells of the olfactory bulb form sparse representations of the
odorants and transmit this information to the cortex. The olfactory code
carried by the mitral cells is sparser than the inputs that they receive. In
this study we analyze the mechanisms and functional significance of sparse
olfactory codes. We con... | [
{
"created": "Fri, 26 Feb 2010 00:33:16 GMT",
"version": "v1"
}
] | 2010-03-01 | [
[
"Koulakov",
"Alexei A.",
""
],
[
"Rinberg",
"Dmitry",
""
]
] | Mitral cells of the olfactory bulb form sparse representations of the odorants and transmit this information to the cortex. The olfactory code carried by the mitral cells is sparser than the inputs that they receive. In this study we analyze the mechanisms and functional significance of sparse olfactory codes. We consi... |
0810.2872 | Matthias Bethge | Jan Eichhorn, Fabian Sinz and Matthias Bethge | Natural Image Coding in V1: How Much Use is Orientation Selectivity? | null | null | 10.1371/journal.pcbi.1000336 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Orientation selectivity is the most striking feature of simple cell coding in
V1 which has been shown to emerge from the reduction of higher-order
correlations in natural images in a large variety of statistical image models.
The most parsimonious one among these models is linear Independent Component
Analysis (ICA),... | [
{
"created": "Thu, 16 Oct 2008 19:11:39 GMT",
"version": "v1"
},
{
"created": "Thu, 16 Oct 2008 20:26:01 GMT",
"version": "v2"
}
] | 2015-05-13 | [
[
"Eichhorn",
"Jan",
""
],
[
"Sinz",
"Fabian",
""
],
[
"Bethge",
"Matthias",
""
]
] | Orientation selectivity is the most striking feature of simple cell coding in V1 which has been shown to emerge from the reduction of higher-order correlations in natural images in a large variety of statistical image models. The most parsimonious one among these models is linear Independent Component Analysis (ICA), w... |
2005.14533 | Ling Xue Dr | Ling Xue, Shuanglin Jing, Joel C. Miller, Wei Sun, Huafeng Li, Jose
Guillermo Estrada-Franco, James M Hyman, Huaiping Zhu | A Data-Driven Network Model for the Emerging COVID-19 Epidemics in
Wuhan, Toronto and Italy | null | Mathematical Biosciences 2020 | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ongoing Coronavirus Disease 2019 (COVID-19) pandemic threatens the health
of humans and causes great economic losses. Predictive modelling and
forecasting the epidemic trends are essential for developing countermeasures to
mitigate this pandemic. We develop a network model, where each node represents
an individua... | [
{
"created": "Thu, 28 May 2020 14:35:32 GMT",
"version": "v1"
}
] | 2020-06-01 | [
[
"Xue",
"Ling",
""
],
[
"Jing",
"Shuanglin",
""
],
[
"Miller",
"Joel C.",
""
],
[
"Sun",
"Wei",
""
],
[
"Li",
"Huafeng",
""
],
[
"Estrada-Franco",
"Jose Guillermo",
""
],
[
"Hyman",
"James M",
""
],
[
... | The ongoing Coronavirus Disease 2019 (COVID-19) pandemic threatens the health of humans and causes great economic losses. Predictive modelling and forecasting the epidemic trends are essential for developing countermeasures to mitigate this pandemic. We develop a network model, where each node represents an individual ... |
1806.07341 | Dong Xu | Chao Fang, Yi Shang, and Dong Xu | Improving Protein Gamma-Turn Prediction Using Inception Capsule Networks | null | null | null | null | q-bio.QM q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein gamma-turn prediction is useful in protein function studies and
experimental design. Several methods for gamma-turn prediction have been
developed, but the results were unsatisfactory with Matthew correlation
coefficients (MCC) around 0.2-0.4. One reason for the low prediction accuracy
is the limited capacity... | [
{
"created": "Mon, 11 Jun 2018 09:07:35 GMT",
"version": "v1"
}
] | 2018-06-20 | [
[
"Fang",
"Chao",
""
],
[
"Shang",
"Yi",
""
],
[
"Xu",
"Dong",
""
]
] | Protein gamma-turn prediction is useful in protein function studies and experimental design. Several methods for gamma-turn prediction have been developed, but the results were unsatisfactory with Matthew correlation coefficients (MCC) around 0.2-0.4. One reason for the low prediction accuracy is the limited capacity o... |
1308.3673 | Michael Thomas | Wendy K. Caldwell, Benjamin Freedman, Luke Settles, Michael M. Thomas,
Anarina Murillo, Erika Camacho, Stephen Wirkus | Substance Abuse via Legally Prescribed Drugs: The Case of Vicodin in the
United States | null | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Vicodin is the most commonly prescribed pain reliever in the United States.
Research indicates that there are two million people who are currently abusing
Vicodin, and the majority of those who abuse Vicodin were initially exposed to
it via prescription. Our goal is to determine the most effective strategies for
redu... | [
{
"created": "Fri, 26 Jul 2013 19:26:55 GMT",
"version": "v1"
}
] | 2013-08-19 | [
[
"Caldwell",
"Wendy K.",
""
],
[
"Freedman",
"Benjamin",
""
],
[
"Settles",
"Luke",
""
],
[
"Thomas",
"Michael M.",
""
],
[
"Murillo",
"Anarina",
""
],
[
"Camacho",
"Erika",
""
],
[
"Wirkus",
"Stephen",
""
... | Vicodin is the most commonly prescribed pain reliever in the United States. Research indicates that there are two million people who are currently abusing Vicodin, and the majority of those who abuse Vicodin were initially exposed to it via prescription. Our goal is to determine the most effective strategies for reduci... |
2309.11732 | Matthew Macaulay | Matthew Macaulay, Mathieu Fourment | Differentiable Phylogenetics via Hyperbolic Embeddings with Dodonaphy | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Motivation: Navigating the high dimensional space of discrete trees for
phylogenetics presents a challenging problem for tree optimisation. To address
this, hyperbolic embeddings of trees offer a promising approach to encoding
trees efficiently in continuous spaces. However, they require a differentiable
tree decoder... | [
{
"created": "Thu, 21 Sep 2023 02:06:53 GMT",
"version": "v1"
}
] | 2023-09-22 | [
[
"Macaulay",
"Matthew",
""
],
[
"Fourment",
"Mathieu",
""
]
] | Motivation: Navigating the high dimensional space of discrete trees for phylogenetics presents a challenging problem for tree optimisation. To address this, hyperbolic embeddings of trees offer a promising approach to encoding trees efficiently in continuous spaces. However, they require a differentiable tree decoder t... |
1401.5049 | Michael Deem | Pu Han, Liang Ren Niestemski, Jeffrey E. Barrick, and Michael W. Deem | Physical Model of the Immune Response of Bacteria Against Bacteriophage
Through the Adaptive CRISPR-Cas Immune System | 37 pages, 13 figures | Phys. Biol. 10 (2013) 025004 | 10.1088/1478-3975/10/2/025004 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bacteria and archaea have evolved an adaptive, heritable immune system that
recognizes and protects against viruses or plasmids. This system, known as the
CRISPR-Cas system, allows the host to recognize and incorporate short foreign
DNA or RNA sequences, called `spacers' into its CRISPR system. Spacers in the
CRISPR ... | [
{
"created": "Mon, 20 Jan 2014 20:41:57 GMT",
"version": "v1"
}
] | 2014-01-21 | [
[
"Han",
"Pu",
""
],
[
"Niestemski",
"Liang Ren",
""
],
[
"Barrick",
"Jeffrey E.",
""
],
[
"Deem",
"Michael W.",
""
]
] | Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called `spacers' into its CRISPR system. Spacers in the CRISPR sy... |
1505.03176 | Cheng Ly | Cheng Ly | Firing Rate Dynamics in Recurrent Spiking Neural Networks with Intrinsic
and Network Heterogeneity | 21 pages, 5 figures | null | 10.1007/s10827-015-0578-0 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Heterogeneity of neural attributes has recently gained a lot of attention and
is increasing recognized as a crucial feature in neural processing. Despite its
importance, this physiological feature has traditionally been neglected in
theoretical studies of cortical neural networks. Thus, there is still a lot
unknown a... | [
{
"created": "Tue, 12 May 2015 21:49:36 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Nov 2016 16:22:35 GMT",
"version": "v2"
}
] | 2016-11-22 | [
[
"Ly",
"Cheng",
""
]
] | Heterogeneity of neural attributes has recently gained a lot of attention and is increasing recognized as a crucial feature in neural processing. Despite its importance, this physiological feature has traditionally been neglected in theoretical studies of cortical neural networks. Thus, there is still a lot unknown abo... |
1509.05767 | Mallenahalli Naresh Kumar Prof. Dr. | M.Naresh Kumar, M.V.R Seshasai, K.S Vara Prasad, V. Kamala, K.V
Ramana, R.S. Dwivedi, P.S. Roy | A new hybrid spectral similarity measure for discrimination of Vigna
species | null | International Journal of Remote Sensing, 32(14),4041-4053, 2011 | 10.1080/01431161.2010.484431 | null | q-bio.QM physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The reflectance spectrum of the species in a hyperspectral data can be
modelled as an n-dimensional vector. The spectral angle mapper computes the
angle between the vectors which is used to discriminate the species. The
spectral information divergence models the data as a probability distribution
so that the spectral... | [
{
"created": "Fri, 18 Sep 2015 04:17:11 GMT",
"version": "v1"
}
] | 2015-09-30 | [
[
"Kumar",
"M. Naresh",
""
],
[
"Seshasai",
"M. V. R",
""
],
[
"Prasad",
"K. S Vara",
""
],
[
"Kamala",
"V.",
""
],
[
"Ramana",
"K. V",
""
],
[
"Dwivedi",
"R. S.",
""
],
[
"Roy",
"P. S.",
""
]
] | The reflectance spectrum of the species in a hyperspectral data can be modelled as an n-dimensional vector. The spectral angle mapper computes the angle between the vectors which is used to discriminate the species. The spectral information divergence models the data as a probability distribution so that the spectral v... |
q-bio/0508033 | Igor Volkov | Tommaso Zillio, Igor Volkov, Jayanth R. Banavar, Stephen P. Hubbell,
Amos Maritan | Spatial Scaling in Model Plant Communities | 10 pages, 3 figures | Phys. Rev. Lett. 95, 098101 (2005) | 10.1103/PhysRevLett.95.098101 | null | q-bio.PE q-bio.QM | null | We present an analytically tractable variant of the voter model that provides
a quantitatively accurate description of beta-diversity (two-point correlation
function) in two tropical forests. The model exhibits novel scaling behavior
that leads to links between ecological measures such as relative species
abundance a... | [
{
"created": "Wed, 24 Aug 2005 02:16:48 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Zillio",
"Tommaso",
""
],
[
"Volkov",
"Igor",
""
],
[
"Banavar",
"Jayanth R.",
""
],
[
"Hubbell",
"Stephen P.",
""
],
[
"Maritan",
"Amos",
""
]
] | We present an analytically tractable variant of the voter model that provides a quantitatively accurate description of beta-diversity (two-point correlation function) in two tropical forests. The model exhibits novel scaling behavior that leads to links between ecological measures such as relative species abundance and... |
q-bio/0501010 | Philipp Messer W. | Philipp W. Messer, Peter F. Arndt, Michael L\"assig | A Solvable Sequence Evolution Model and Genomic Correlations | 4 pages, 4 figures | Physical Review Letters 94, 138103 (2005) | 10.1103/PhysRevLett.94.138103 | null | q-bio.GN cond-mat.stat-mech | null | We study a minimal model for genome evolution whose elementary processes are
single site mutation, duplication and deletion of sequence regions and
insertion of random segments. These processes are found to generate long-range
correlations in the composition of letters as long as the sequence length is
growing, i.e.,... | [
{
"created": "Sun, 9 Jan 2005 20:37:57 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Messer",
"Philipp W.",
""
],
[
"Arndt",
"Peter F.",
""
],
[
"Lässig",
"Michael",
""
]
] | We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations in the composition of letters as long as the sequence length is growing, i.e., t... |
1003.1601 | Cencini Massimo Dr. | Simone Pigolotti and Massimo Cencini | Coexistence and invasibility in a two-species competition model with
habitat-preference | 20 Pages, 6 Figures revised version accepted on J. Theor. Bio | J. Theor. Bio. 265 (2010) 609-617 | 10.1016/j.jtbi.2010.05.041 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The outcome of competition among species is influenced by the spatial
distribution of species and effects such as demographic stochasticity,
immigration fluxes, and the existence of preferred habitats. We introduce an
individual-based model describing the competition of two species and
incorporating all the above ing... | [
{
"created": "Mon, 8 Mar 2010 11:28:49 GMT",
"version": "v1"
},
{
"created": "Wed, 2 Jun 2010 14:50:51 GMT",
"version": "v2"
}
] | 2010-07-19 | [
[
"Pigolotti",
"Simone",
""
],
[
"Cencini",
"Massimo",
""
]
] | The outcome of competition among species is influenced by the spatial distribution of species and effects such as demographic stochasticity, immigration fluxes, and the existence of preferred habitats. We introduce an individual-based model describing the competition of two species and incorporating all the above ingre... |
2312.08809 | Koujin Takeda | Yusuke Endo, Koujin Takeda | Performance evaluation of matrix factorization for fMRI data | 22 pages, 8 figures | Neural Computation (2024) 36 (1) 128-150 | 10.1162/neco_a_01628 | null | q-bio.NC cond-mat.dis-nn cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the study of the brain, there is a hypothesis that sparse coding is
realized in information representation of external stimuli, which is
experimentally confirmed for visual stimulus recently. However, unlike the
specific functional region in the brain, sparse coding in information
processing in the whole brain has... | [
{
"created": "Thu, 14 Dec 2023 10:48:50 GMT",
"version": "v1"
}
] | 2023-12-15 | [
[
"Endo",
"Yusuke",
""
],
[
"Takeda",
"Koujin",
""
]
] | In the study of the brain, there is a hypothesis that sparse coding is realized in information representation of external stimuli, which is experimentally confirmed for visual stimulus recently. However, unlike the specific functional region in the brain, sparse coding in information processing in the whole brain has n... |
1111.5297 | David Spivak | Tristan Giesa, David Spivak, Markus Buehler | Reoccurring patterns in hierarchical protein materials and music: The
power of analogies | 13 pages, 3 figures | T. Giesa, D.I. Spivak, M.J. Buehler. BioNanoScience: Volume 1,
Issue 4 (2011), Page 153-161 | 10.1007/s12668-011-0022-5 | null | q-bio.BM math.CT physics.soc-ph | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Complex hierarchical structures composed of simple nanoscale building blocks
form the basis of most biological materials. Here we demonstrate how analogies
between seemingly different fields enable the understanding of general
principles by which functional properties in hierarchical systems emerge,
similar to an ana... | [
{
"created": "Tue, 22 Nov 2011 19:30:00 GMT",
"version": "v1"
}
] | 2011-11-23 | [
[
"Giesa",
"Tristan",
""
],
[
"Spivak",
"David",
""
],
[
"Buehler",
"Markus",
""
]
] | Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by which functional properties in hierarchical systems emerge, similar to an analo... |
1203.6061 | Alexander Peyser | Alexander Peyser and Wolfgang Nonner | Voltage sensing in ion channels: Mesoscale simulations of biological
devices | arXiv admin note: substantial text overlap with arXiv:1112.2994 | Phys. Rev. E 86, 011910 (2012) | 10.1103/PhysRevE.86.011910 | null | q-bio.BM physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Electrical signaling via voltage-gated ion channels depends upon the function
of a voltage sensor (VS), identified with the S1-S4 domain in voltage-gated K+
channels. Here we investigate some energetic aspects of the sliding-helix model
of the VS using simulations based on VS charges, linear dielectrics and
whole-bod... | [
{
"created": "Tue, 27 Mar 2012 13:40:34 GMT",
"version": "v1"
},
{
"created": "Tue, 1 May 2012 23:08:48 GMT",
"version": "v2"
},
{
"created": "Mon, 4 Jun 2012 21:13:55 GMT",
"version": "v3"
},
{
"created": "Fri, 13 Jul 2012 08:46:21 GMT",
"version": "v4"
}
] | 2019-01-18 | [
[
"Peyser",
"Alexander",
""
],
[
"Nonner",
"Wolfgang",
""
]
] | Electrical signaling via voltage-gated ion channels depends upon the function of a voltage sensor (VS), identified with the S1-S4 domain in voltage-gated K+ channels. Here we investigate some energetic aspects of the sliding-helix model of the VS using simulations based on VS charges, linear dielectrics and whole-body ... |
2112.07422 | Jordan Douglas | Jordan Douglas and David Welch | PEACH Tree: A Multiple Sequence Alignment and Tree Display Tool for
Epidemiologists | 4 pages, 1 figure, under review as an Applications Node | null | null | null | q-bio.QM q-bio.GN q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | PEACH Tree is an easy-to-use, online tool for displaying multiple sequence
alignments and phylogenetic trees side-by-side. PEACH Tree is powerful for
rapidly tracing evolutionary and transmission histories by filtering invariant
sites out of the display, and allowing samples to readily be filtered out of
the display.... | [
{
"created": "Sun, 12 Dec 2021 22:51:22 GMT",
"version": "v1"
}
] | 2021-12-15 | [
[
"Douglas",
"Jordan",
""
],
[
"Welch",
"David",
""
]
] | PEACH Tree is an easy-to-use, online tool for displaying multiple sequence alignments and phylogenetic trees side-by-side. PEACH Tree is powerful for rapidly tracing evolutionary and transmission histories by filtering invariant sites out of the display, and allowing samples to readily be filtered out of the display. T... |
0905.3353 | Vitaly Ganusov | Vitaly V. Ganusov, Jose Borghans, Rob De Boer | Explicit kinetic heterogeneity: mechanistic models for interpretation of
labeling data of heterogeneous cell populations | null | null | 10.1371/journal.pcbi.1000666 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Estimation of division and death rates of lymphocytes in different conditions
is vital for quantitative understanding of the immune system. Deuterium, in the
form of deuterated glucose or heavy water, can be used to measure rates of
proliferation and death of lymphocytes in vivo. Inferring these rates from
labeling a... | [
{
"created": "Wed, 20 May 2009 16:55:01 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Ganusov",
"Vitaly V.",
""
],
[
"Borghans",
"Jose",
""
],
[
"De Boer",
"Rob",
""
]
] | Estimation of division and death rates of lymphocytes in different conditions is vital for quantitative understanding of the immune system. Deuterium, in the form of deuterated glucose or heavy water, can be used to measure rates of proliferation and death of lymphocytes in vivo. Inferring these rates from labeling and... |
2010.10862 | Mark Leake | Jack W Shepherd, Sarah Lecinski, Jasmine Wragg, Sviatlana Shashkova,
Chris MacDonald, Mark C Leake | Molecular crowding in single eukaryotic cells: using cell environment
biosensing and single-molecule optical microscopy to probe dependence on
extracellular ionic strength, local glucose conditions, and sensor copy
number | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The physical and chemical environment inside cells is of fundamental
importance to all life but has traditionally been difficult to determine on a
subcellular basis. Here we combine cutting-edge genomically integrated FRET
biosensing to readout localized molecular crowding in single live yeast cells.
Confocal microsc... | [
{
"created": "Wed, 21 Oct 2020 09:45:31 GMT",
"version": "v1"
}
] | 2020-10-22 | [
[
"Shepherd",
"Jack W",
""
],
[
"Lecinski",
"Sarah",
""
],
[
"Wragg",
"Jasmine",
""
],
[
"Shashkova",
"Sviatlana",
""
],
[
"MacDonald",
"Chris",
""
],
[
"Leake",
"Mark C",
""
]
] | The physical and chemical environment inside cells is of fundamental importance to all life but has traditionally been difficult to determine on a subcellular basis. Here we combine cutting-edge genomically integrated FRET biosensing to readout localized molecular crowding in single live yeast cells. Confocal microscop... |
1912.06786 | Swathi Tej | Swathi Tej and Sutapa Mukherji | Small RNA driven feed-forward loop: Fine-tuning of protein synthesis
through sRNA mediated cross-talk | 14 pages,9 figures | null | null | null | q-bio.MN cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Often in bacterial regulatory networks, small noncoding RNAs (sRNA) interact
with several mRNA species. The competition among mRNAs for binding to the same
pool of sRNA might lead to crosstalk between the mRNAs. This is similar to the
competing endogenous RNA (ceRNA) effect wherein the competition to bind to the
same... | [
{
"created": "Sat, 14 Dec 2019 05:23:45 GMT",
"version": "v1"
}
] | 2019-12-17 | [
[
"Tej",
"Swathi",
""
],
[
"Mukherji",
"Sutapa",
""
]
] | Often in bacterial regulatory networks, small noncoding RNAs (sRNA) interact with several mRNA species. The competition among mRNAs for binding to the same pool of sRNA might lead to crosstalk between the mRNAs. This is similar to the competing endogenous RNA (ceRNA) effect wherein the competition to bind to the same p... |
1211.1143 | Mariusz Pietruszka PhD | Mariusz Pietruszka | Frustration-induced inherent instability and growth oscillations in
pollen tubes | 35 pages, 7 figures | null | 10.1371/journal.pone.0075803 | null | q-bio.CB cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In a seed plant a pollen tube is a vessel that transports male gamete cells
to an ovule to achieve fertilization. It consists of one elongated cell, which
exhibits growth oscillations, until it bursts completing its function. Up till
now, the mechanism behind the periodic character of the growth has not been
fully un... | [
{
"created": "Tue, 6 Nov 2012 08:44:02 GMT",
"version": "v1"
},
{
"created": "Mon, 31 Dec 2012 10:42:30 GMT",
"version": "v2"
}
] | 2014-03-05 | [
[
"Pietruszka",
"Mariusz",
""
]
] | In a seed plant a pollen tube is a vessel that transports male gamete cells to an ovule to achieve fertilization. It consists of one elongated cell, which exhibits growth oscillations, until it bursts completing its function. Up till now, the mechanism behind the periodic character of the growth has not been fully unde... |
2404.05762 | Fatma Zahra Abdeldjouad | Fatma Zahra Abdeldjouad, Menaouer Brahami, Mohammed Sabri | Evaluating the Effectiveness of Artificial Intelligence in Predicting
Adverse Drug Reactions among Cancer Patients: A Systematic Review and
Meta-Analysis | Paper has been accepted at the IEEE Challenges and Innovations on TIC
(IEEE I2CIT) International Conference | null | null | null | q-bio.QM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Adverse drug reactions considerably impact patient outcomes and healthcare
costs in cancer therapy. Using artificial intelligence to predict adverse drug
reactions in real time could revolutionize oncology treatment. This study aims
to assess the performance of artificial intelligence models in predicting
adverse dru... | [
{
"created": "Sat, 6 Apr 2024 11:20:28 GMT",
"version": "v1"
}
] | 2024-04-10 | [
[
"Abdeldjouad",
"Fatma Zahra",
""
],
[
"Brahami",
"Menaouer",
""
],
[
"Sabri",
"Mohammed",
""
]
] | Adverse drug reactions considerably impact patient outcomes and healthcare costs in cancer therapy. Using artificial intelligence to predict adverse drug reactions in real time could revolutionize oncology treatment. This study aims to assess the performance of artificial intelligence models in predicting adverse drug ... |
2408.05789 | Yujiang Wang | Jonathan Horsley, Yujiang Wang, Callum Simpson, Vyte Janiukstyte,
Karoline Leiberg, Beth Little, Jane de Tisi, John Duncan, Peter N. Taylor | Status epilepticus and thinning of the entorhinal cortex | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Status epilepticus (SE) carries risks of morbidity and mortality.
Experimental studies have implicated the entorhinal cortex in prolonged
seizures; however, studies in large human cohorts are limited. We hypothesised
that individuals with temporal lobe epilepsy (TLE) and a history of SE would
have more severe entorhi... | [
{
"created": "Sun, 11 Aug 2024 14:41:56 GMT",
"version": "v1"
}
] | 2024-08-13 | [
[
"Horsley",
"Jonathan",
""
],
[
"Wang",
"Yujiang",
""
],
[
"Simpson",
"Callum",
""
],
[
"Janiukstyte",
"Vyte",
""
],
[
"Leiberg",
"Karoline",
""
],
[
"Little",
"Beth",
""
],
[
"de Tisi",
"Jane",
""
],
[
... | Status epilepticus (SE) carries risks of morbidity and mortality. Experimental studies have implicated the entorhinal cortex in prolonged seizures; however, studies in large human cohorts are limited. We hypothesised that individuals with temporal lobe epilepsy (TLE) and a history of SE would have more severe entorhina... |
2006.02127 | Ajitesh Srivastava | Ajitesh Srivastava and Viktor K. Prasanna | Data-driven Identification of Number of Unreported Cases for COVID-19:
Bounds and Limitations | Fixed a typo | null | null | null | q-bio.PE cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Accurate forecasts for COVID-19 are necessary for better preparedness and
resource management. Specifically, deciding the response over months or several
months requires accurate long-term forecasts which is particularly challenging
as the model errors accumulate with time. A critical factor that can hinder
accurate ... | [
{
"created": "Wed, 3 Jun 2020 09:39:50 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Jun 2020 04:23:57 GMT",
"version": "v2"
},
{
"created": "Wed, 10 Jun 2020 21:38:38 GMT",
"version": "v3"
},
{
"created": "Mon, 15 Jun 2020 00:04:07 GMT",
"version": "v4"
},
{
"cre... | 2020-07-10 | [
[
"Srivastava",
"Ajitesh",
""
],
[
"Prasanna",
"Viktor K.",
""
]
] | Accurate forecasts for COVID-19 are necessary for better preparedness and resource management. Specifically, deciding the response over months or several months requires accurate long-term forecasts which is particularly challenging as the model errors accumulate with time. A critical factor that can hinder accurate lo... |
1606.07553 | Sakuntala Chatterjee | Raj Kumar Sadhu and Sakuntala Chatterjee | Actin filaments growing against a barrier with fluctuating shape | null | Physical Review E, vol. 93, 062414 (2016) | 10.1103/PhysRevE.93.062414 | null | q-bio.SC cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study force generation by a set of parallel actin filaments growing
against a non-rigid obstacle, in presence of an external load. The filaments
polymerize by either moving the whole obstacle, with a large energy cost, or by
causing local distortion in its shape which costs much less energy. The
non-rigid obstacle... | [
{
"created": "Fri, 24 Jun 2016 03:33:09 GMT",
"version": "v1"
}
] | 2016-06-27 | [
[
"Sadhu",
"Raj Kumar",
""
],
[
"Chatterjee",
"Sakuntala",
""
]
] | We study force generation by a set of parallel actin filaments growing against a non-rigid obstacle, in presence of an external load. The filaments polymerize by either moving the whole obstacle, with a large energy cost, or by causing local distortion in its shape which costs much less energy. The non-rigid obstacle a... |
1412.7384 | Peng Yang | Peng Yang, Xiaoquan Su, Le Ou-Yang, Hon-Nian Chua, Xiao-Li Li, Kang
Ning | Microbial community pattern detection in human body habitats via
ensemble clustering framework | BMC Systems Biology 2014 | BMC Systems Biology 2014, 8(Suppl 4):S7 | 10.1186/1752-0509-8-S4-S7 | null | q-bio.QM cs.CE cs.LG q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human habitat is a host where microbial species evolve, function, and
continue to evolve. Elucidating how microbial communities respond to human
habitats is a fundamental and critical task, as establishing baselines of human
microbiome is essential in understanding its role in human disease and health.
However, c... | [
{
"created": "Sun, 21 Dec 2014 12:52:45 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Dec 2014 02:03:08 GMT",
"version": "v2"
},
{
"created": "Sun, 4 Jan 2015 05:37:42 GMT",
"version": "v3"
}
] | 2015-01-06 | [
[
"Yang",
"Peng",
""
],
[
"Su",
"Xiaoquan",
""
],
[
"Ou-Yang",
"Le",
""
],
[
"Chua",
"Hon-Nian",
""
],
[
"Li",
"Xiao-Li",
""
],
[
"Ning",
"Kang",
""
]
] | The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. However, cur... |
2005.08740 | Alkesh Yadav | Alkesh Yadav, Quentin Vagne, Pierre Sens, Garud Iyengar and Madan Rao | Glycan processing in the Golgi -- optimal information coding and
constraints on cisternal number and enzyme specificity | 30 pages | eLife 2022 | 10.7554/eLife.76757 | 11:e76757 | q-bio.SC cond-mat.stat-mech physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Many proteins that undergo sequential enzymatic modification in the Golgi
cisternae are displayed at the plasma membrane as cell identity markers. The
modified proteins, called glycans, represent a molecular code. The fidelity of
this glycan code is measured by how accurately the glycan synthesis machinery
realises t... | [
{
"created": "Mon, 18 May 2020 14:07:41 GMT",
"version": "v1"
}
] | 2022-03-30 | [
[
"Yadav",
"Alkesh",
""
],
[
"Vagne",
"Quentin",
""
],
[
"Sens",
"Pierre",
""
],
[
"Iyengar",
"Garud",
""
],
[
"Rao",
"Madan",
""
]
] | Many proteins that undergo sequential enzymatic modification in the Golgi cisternae are displayed at the plasma membrane as cell identity markers. The modified proteins, called glycans, represent a molecular code. The fidelity of this glycan code is measured by how accurately the glycan synthesis machinery realises the... |
2103.11637 | Coralie Picoche | Coralie Picoche, Fr\'ed\'eric Barraquand | Seed banks can help to maintain the diversity of interacting
phytoplankton species | 46 pages ; 13 figures | Journal of Theoretical Biology (2022) | 10.1016/j.jtbi.2022.111020 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Seed formation is part of the reproductive cycle, leading to the accumulation
of resistance stages that can withstand harsh environmental conditions for long
periods of time. At the community level, multiple species with such
long-lasting life stages can be more likely to coexist. While the implications
of this proce... | [
{
"created": "Mon, 22 Mar 2021 07:56:18 GMT",
"version": "v1"
},
{
"created": "Wed, 2 Feb 2022 14:50:47 GMT",
"version": "v2"
}
] | 2022-02-03 | [
[
"Picoche",
"Coralie",
""
],
[
"Barraquand",
"Frédéric",
""
]
] | Seed formation is part of the reproductive cycle, leading to the accumulation of resistance stages that can withstand harsh environmental conditions for long periods of time. At the community level, multiple species with such long-lasting life stages can be more likely to coexist. While the implications of this process... |
2007.10518 | Mike Steel Prof. | Stuart Kauffman and Mike Steel | The expected number of viable autocatalytic sets in chemical reaction
systems | 16 pages, 1 figure. This version provides more detailed mathematical
proofs, a revised figure, and the correction of some minor typos | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The emergence of self-sustaining autocatalytic networks in chemical reaction
systems has been studied as a possible mechanism for modelling how living
systems first arose. It has been known for several decades that such networks
will form within systems of polymers (under cleavage and ligation reactions)
under a simp... | [
{
"created": "Mon, 20 Jul 2020 22:35:32 GMT",
"version": "v1"
},
{
"created": "Sun, 22 Nov 2020 03:49:11 GMT",
"version": "v2"
}
] | 2020-11-24 | [
[
"Kauffman",
"Stuart",
""
],
[
"Steel",
"Mike",
""
]
] | The emergence of self-sustaining autocatalytic networks in chemical reaction systems has been studied as a possible mechanism for modelling how living systems first arose. It has been known for several decades that such networks will form within systems of polymers (under cleavage and ligation reactions) under a simple... |
2004.00058 | Larissa Albantakis | Larissa Albantakis, Francesco Massari, Maggie Beheler-Amass and Giulio
Tononi | A macro agent and its actions | 18 pages, 5 figures; to appear as a chapter in "Top-Down Causation
and Emergence" published by Springer as part of the Synthese Library Book
Series; F.M. and M.B. contributed equally to this work | null | null | null | q-bio.NC cs.AI cs.NE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In science, macro level descriptions of the causal interactions within
complex, dynamical systems are typically deemed convenient, but ultimately
reducible to a complete causal account of the underlying micro constituents.
Yet, such a reductionist perspective is hard to square with several issues
related to autonomy ... | [
{
"created": "Tue, 31 Mar 2020 18:51:18 GMT",
"version": "v1"
}
] | 2020-04-02 | [
[
"Albantakis",
"Larissa",
""
],
[
"Massari",
"Francesco",
""
],
[
"Beheler-Amass",
"Maggie",
""
],
[
"Tononi",
"Giulio",
""
]
] | In science, macro level descriptions of the causal interactions within complex, dynamical systems are typically deemed convenient, but ultimately reducible to a complete causal account of the underlying micro constituents. Yet, such a reductionist perspective is hard to square with several issues related to autonomy an... |
1402.5996 | Po T. Wang | Po T. Wang, Christine E. King, Andrew Schombs, Jack J. Lin, Mona
Sazgar, Frank P. K. Hsu, Susan J. Shaw, David E. Millett, Charles Y. Liu,
Luis A. Chui, Zoran Nenadic, An H. Do | Electrocorticogram encoding of upper extremity movement trajectories | Preliminary report. We have not completed full analyses | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Electrocorticogram (ECoG)-based brain computer interfaces (BCI) can
potentially control upper extremity prostheses to restore independent function
to paralyzed individuals. However, current research is mostly restricted to the
offline decoding of finger or 2D arm movement trajectories, and these results
are modest. T... | [
{
"created": "Wed, 19 Feb 2014 20:43:35 GMT",
"version": "v1"
}
] | 2014-02-26 | [
[
"Wang",
"Po T.",
""
],
[
"King",
"Christine E.",
""
],
[
"Schombs",
"Andrew",
""
],
[
"Lin",
"Jack J.",
""
],
[
"Sazgar",
"Mona",
""
],
[
"Hsu",
"Frank P. K.",
""
],
[
"Shaw",
"Susan J.",
""
],
[
"M... | Electrocorticogram (ECoG)-based brain computer interfaces (BCI) can potentially control upper extremity prostheses to restore independent function to paralyzed individuals. However, current research is mostly restricted to the offline decoding of finger or 2D arm movement trajectories, and these results are modest. Thi... |
2106.15241 | Pawan Kumar | Pawan Kumar, Christina Surulescu, Anna Zhigun | Multiphase modelling of glioma pseudopalisading under acidosis | null | null | null | null | q-bio.TO math.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a multiphase modeling approach to describe glioma pseudopalisade
patterning under the influence of acidosis. The phases considered at the model
onset are glioma, normal tissue, necrotic matter, and interstitial fluid in a
void-free volume with acidity represented by proton concentration. We start
from mass... | [
{
"created": "Tue, 29 Jun 2021 10:52:28 GMT",
"version": "v1"
}
] | 2021-06-30 | [
[
"Kumar",
"Pawan",
""
],
[
"Surulescu",
"Christina",
""
],
[
"Zhigun",
"Anna",
""
]
] | We propose a multiphase modeling approach to describe glioma pseudopalisade patterning under the influence of acidosis. The phases considered at the model onset are glioma, normal tissue, necrotic matter, and interstitial fluid in a void-free volume with acidity represented by proton concentration. We start from mass a... |
1903.08511 | Fares Al-Shargie | Fares Al-Shargie | Early Detection of Mental Stress Using Advanced Neuroimaging and
Artificial Intelligence | 190 Pages, 67 Figure, 9 Tables | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While different neuroimaging modalities have been proposed to detect mental
stress, each modality experiences certain limitations. This study proposed
novel approaches to detect stress based on fusion of EEG and fNIRS signals in
the feature-level using joint independent component analysis (jICA) and
canonical correla... | [
{
"created": "Wed, 20 Mar 2019 14:13:41 GMT",
"version": "v1"
}
] | 2019-03-21 | [
[
"Al-Shargie",
"Fares",
""
]
] | While different neuroimaging modalities have been proposed to detect mental stress, each modality experiences certain limitations. This study proposed novel approaches to detect stress based on fusion of EEG and fNIRS signals in the feature-level using joint independent component analysis (jICA) and canonical correlati... |
1708.09097 | Kazunori Yamada | Kazunori D Yamada | Optimizing scoring function of dynamic programming of pairwise profile
alignment using derivative free neural network | null | null | 10.1186/s13015-018-0123-6 | null | q-bio.QM cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A profile comparison method with position-specific scoring matrix (PSSM) is
one of the most accurate alignment methods. Currently, cosine similarity and
correlation coefficient are used as scoring functions of dynamic programming to
calculate similarity between PSSMs. However, it is unclear that these functions
are o... | [
{
"created": "Wed, 30 Aug 2017 03:28:13 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Sep 2017 05:10:32 GMT",
"version": "v2"
}
] | 2018-02-20 | [
[
"Yamada",
"Kazunori D",
""
]
] | A profile comparison method with position-specific scoring matrix (PSSM) is one of the most accurate alignment methods. Currently, cosine similarity and correlation coefficient are used as scoring functions of dynamic programming to calculate similarity between PSSMs. However, it is unclear that these functions are opt... |
1805.00765 | Thierry Huillet | Thierry Huillet (LPTM) | Karlin-McGregor mutational occupancy problem revisited | to appear: Journal of Statistical Physics | null | 10.1007/s10955-018-2056-3 | null | q-bio.PE cond-mat.stat-mech math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Some population is made of n individuals that can be of p possible species
(or types). The update of the species abundance occupancies is from a Moran
mutational model designed by Karlin and McGregor in 1967. We first study the
equilibrium species counts as a function of n, p and the total mutation
probability $\nu$ ... | [
{
"created": "Wed, 2 May 2018 12:31:38 GMT",
"version": "v1"
}
] | 2018-05-23 | [
[
"Huillet",
"Thierry",
"",
"LPTM"
]
] | Some population is made of n individuals that can be of p possible species (or types). The update of the species abundance occupancies is from a Moran mutational model designed by Karlin and McGregor in 1967. We first study the equilibrium species counts as a function of n, p and the total mutation probability $\nu$ be... |
1308.3675 | Victor Suriel | Valerie Cheathon, Agustin Flores, Victor Suriel, Octavious Talbot,
Dustin Padilla, Marta Sarzynska, Adrian Smith, Luis Melara | Dynamics and Control of an Invasive Species: The Case of the Rasberry
Crazy Ant Colonies | null | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This project is motivated by the costs related with the documented risks of
the introduction of non-native invasive species of plants, animals, or
pathogens associated with travel and international trade. Such invasive species
often have no natural enemies in their new regions. The spatiotemporal dynamics
related to ... | [
{
"created": "Fri, 26 Jul 2013 19:25:40 GMT",
"version": "v1"
}
] | 2013-08-19 | [
[
"Cheathon",
"Valerie",
""
],
[
"Flores",
"Agustin",
""
],
[
"Suriel",
"Victor",
""
],
[
"Talbot",
"Octavious",
""
],
[
"Padilla",
"Dustin",
""
],
[
"Sarzynska",
"Marta",
""
],
[
"Smith",
"Adrian",
""
],
... | This project is motivated by the costs related with the documented risks of the introduction of non-native invasive species of plants, animals, or pathogens associated with travel and international trade. Such invasive species often have no natural enemies in their new regions. The spatiotemporal dynamics related to th... |
2303.12775 | Carsten Baldauf | Xiaojuan Hu, Kazi S. Amin, Markus Schneider, Carmay Lim, Dennis
Salahub, Carsten Baldauf | System-specific parameter optimization for non-polarizable and
polarizable force fields | 62 pages and 25 figures (including SI), manuscript to be submitted
soon | null | null | null | q-bio.BM cond-mat.soft physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The accuracy of classical force fields (FFs) has been shown to be limited for
the simulation of cation-protein systems despite their importance in
understanding the processes of life. Improvements can result from optimizing
the parameters of classical FFs or by extending the FF formulation by terms
describing charge ... | [
{
"created": "Wed, 22 Mar 2023 17:42:01 GMT",
"version": "v1"
},
{
"created": "Mon, 9 Oct 2023 12:12:04 GMT",
"version": "v2"
}
] | 2023-10-10 | [
[
"Hu",
"Xiaojuan",
""
],
[
"Amin",
"Kazi S.",
""
],
[
"Schneider",
"Markus",
""
],
[
"Lim",
"Carmay",
""
],
[
"Salahub",
"Dennis",
""
],
[
"Baldauf",
"Carsten",
""
]
] | The accuracy of classical force fields (FFs) has been shown to be limited for the simulation of cation-protein systems despite their importance in understanding the processes of life. Improvements can result from optimizing the parameters of classical FFs or by extending the FF formulation by terms describing charge tr... |
q-bio/0507026 | Georgy Karev | Artem S. Novozhilov, Georgy P. Karev, and Eugene V. Koonin | Biological applications of the theory of birth-and-death processes | 29 pages, 4 figures; submitted to "Briefings in Bioinformatics" | null | null | null | q-bio.QM q-bio.GN | null | In this review, we discuss the applications of the theory of birth-and-death
processes to problems in biology, primarily, those of evolutionary genomics.
The mathematical principles of the theory of these processes are briefly
described. Birth-and-death processes, with some straightforward additions such
as innovatio... | [
{
"created": "Fri, 15 Jul 2005 18:39:57 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Novozhilov",
"Artem S.",
""
],
[
"Karev",
"Georgy P.",
""
],
[
"Koonin",
"Eugene V.",
""
]
] | In this review, we discuss the applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described. Birth-and-death processes, with some straightforward additions such as innovation,... |
1509.03942 | Davide Barbieri | Davide Barbieri | Geometry and dimensionality reduction of feature spaces in primary
visual cortex | null | null | 10.1117/12.2187026 | null | q-bio.NC cs.CV math.GR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Some geometric properties of the wavelet analysis performed by visual neurons
are discussed and compared with experimental data. In particular, several
relationships between the cortical morphologies and the parametric dependencies
of extracted features are formalized and considered from a harmonic analysis
point of ... | [
{
"created": "Mon, 14 Sep 2015 03:21:54 GMT",
"version": "v1"
}
] | 2016-01-20 | [
[
"Barbieri",
"Davide",
""
]
] | Some geometric properties of the wavelet analysis performed by visual neurons are discussed and compared with experimental data. In particular, several relationships between the cortical morphologies and the parametric dependencies of extracted features are formalized and considered from a harmonic analysis point of vi... |
1312.6356 | Peter Csermely | Peter Csermely, Janos Hodsagi, Tamas Korcsmaros, Dezso Modos, Aron R.
Perez-Lopez, Kristof Szalay, Daniel V. Veres, Katalin Lenti, Ling-Yun Wu and
Xiang-Sun Zhang | Cancer stem cells display extremely large evolvability: alternating
plastic and rigid networks as a potential mechanism | Subtitle: Network models, novel therapeutic target strategies and the
contributions of hypoxia, inflammation and cellular senescence; 10 pages, 4
Tables, 1 Figure and 127 references | Seminars in Cancer Biology 30 (2015) 42-51 | 10.1016/j.semcancer.2013.12.004 | null | q-bio.MN cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cancer is increasingly perceived as a systems-level, network phenomenon. The
major trend of malignant transformation can be described as a two-phase
process, where an initial increase of network plasticity is followed by a
decrease of plasticity at late stages of tumor development. The fluctuating
intensity of stress... | [
{
"created": "Sun, 22 Dec 2013 10:14:00 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Dec 2014 18:05:44 GMT",
"version": "v2"
}
] | 2014-12-24 | [
[
"Csermely",
"Peter",
""
],
[
"Hodsagi",
"Janos",
""
],
[
"Korcsmaros",
"Tamas",
""
],
[
"Modos",
"Dezso",
""
],
[
"Perez-Lopez",
"Aron R.",
""
],
[
"Szalay",
"Kristof",
""
],
[
"Veres",
"Daniel V.",
""
],... | Cancer is increasingly perceived as a systems-level, network phenomenon. The major trend of malignant transformation can be described as a two-phase process, where an initial increase of network plasticity is followed by a decrease of plasticity at late stages of tumor development. The fluctuating intensity of stress f... |
2106.15852 | Michael Oellermann | Michael Oellermann, Jolle W. Jolles, Diego Ortiz, Rui Seabra, Tobias
Wenzel, Hannah Wilson, Richelle Tanner | Harnessing the Benefits of Open Electronics in Science | 20 pages, 3 figure, 2 tables | null | 10.1093/icb/icac043 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Freely and openly shared low-cost electronic applications, known as open
electronics, have sparked a new open-source movement, with much un-tapped
potential to advance scientific research. Initially designed to appeal to
electronic hobbyists, open electronics have formed a global community of
"makers" and inventors a... | [
{
"created": "Wed, 30 Jun 2021 07:17:10 GMT",
"version": "v1"
}
] | 2022-07-14 | [
[
"Oellermann",
"Michael",
""
],
[
"Jolles",
"Jolle W.",
""
],
[
"Ortiz",
"Diego",
""
],
[
"Seabra",
"Rui",
""
],
[
"Wenzel",
"Tobias",
""
],
[
"Wilson",
"Hannah",
""
],
[
"Tanner",
"Richelle",
""
]
] | Freely and openly shared low-cost electronic applications, known as open electronics, have sparked a new open-source movement, with much un-tapped potential to advance scientific research. Initially designed to appeal to electronic hobbyists, open electronics have formed a global community of "makers" and inventors and... |
q-bio/0611067 | Daniel G. M. Silvestre | Giovano de O. Cardozo, Daniel de A. M. M. Silvestre, Alexandre Colato | Periodical cicadas: a minimal automaton model | 13 pages, 6 figures, final version, conditionally accepted (Physica
A) | null | null | null | q-bio.PE | null | The Magicicada spp. life cycles with its prime periods and highly
synchronized emergence have defied reasonable scientific explanation since its
discovery. During the last decade several models and explanations for this
phenomenon appeared in the literature along with a great deal of discussion.
Despite this consider... | [
{
"created": "Mon, 20 Nov 2006 21:27:12 GMT",
"version": "v1"
},
{
"created": "Thu, 30 Nov 2006 19:33:45 GMT",
"version": "v2"
},
{
"created": "Mon, 4 Dec 2006 18:13:19 GMT",
"version": "v3"
},
{
"created": "Tue, 12 Dec 2006 04:02:22 GMT",
"version": "v4"
},
{
"cr... | 2007-05-23 | [
[
"Cardozo",
"Giovano de O.",
""
],
[
"Silvestre",
"Daniel de A. M. M.",
""
],
[
"Colato",
"Alexandre",
""
]
] | The Magicicada spp. life cycles with its prime periods and highly synchronized emergence have defied reasonable scientific explanation since its discovery. During the last decade several models and explanations for this phenomenon appeared in the literature along with a great deal of discussion. Despite this considerab... |
1507.04331 | Heather Harrington | Elizabeth Gross, Brent Davis, Kenneth L. Ho, Daniel J. Bates, Heather
A. Harrington | Numerical algebraic geometry for model selection and its application to
the life sciences | References added, additional clarifications | null | null | null | q-bio.QM math.AG math.NA q-bio.MN stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Researchers working with mathematical models are often confronted by the
related problems of parameter estimation, model validation, and model
selection. These are all optimization problems, well-known to be challenging
due to non-linearity, non-convexity and multiple local optima. Furthermore, the
challenges are com... | [
{
"created": "Wed, 15 Jul 2015 19:12:52 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Sep 2015 18:51:39 GMT",
"version": "v2"
},
{
"created": "Fri, 1 Apr 2016 19:29:19 GMT",
"version": "v3"
}
] | 2016-04-04 | [
[
"Gross",
"Elizabeth",
""
],
[
"Davis",
"Brent",
""
],
[
"Ho",
"Kenneth L.",
""
],
[
"Bates",
"Daniel J.",
""
],
[
"Harrington",
"Heather A.",
""
]
] | Researchers working with mathematical models are often confronted by the related problems of parameter estimation, model validation, and model selection. These are all optimization problems, well-known to be challenging due to non-linearity, non-convexity and multiple local optima. Furthermore, the challenges are compo... |
2108.00905 | Selina Baeza Loya | Selina Baeza Loya | Spike timing regularity in vestibular afferent neurons: How ionic
currents influence sensory encoding mechanisms | 6 pages, 1 figure | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-sa/4.0/ | Primary vestibular neurons are categorized as either regularly or irregularly
firing afferents that use rate and temporal sensory encoding strategies,
respectively. While many factors influence firing in these neurons, recent work
in mammalian vestibular afferents has demonstrated a rich diversity in ion
channels tha... | [
{
"created": "Mon, 2 Aug 2021 13:49:48 GMT",
"version": "v1"
}
] | 2021-08-03 | [
[
"Loya",
"Selina Baeza",
""
]
] | Primary vestibular neurons are categorized as either regularly or irregularly firing afferents that use rate and temporal sensory encoding strategies, respectively. While many factors influence firing in these neurons, recent work in mammalian vestibular afferents has demonstrated a rich diversity in ion channels that ... |
1411.2237 | Nadav M. Shnerb | Efrat Seri and Nadav M. Shnerb | Spatial patterns in the tropical forest reveal connections between
negative feedback, aggregation and abundance | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The spatial arrangement of trees in a tropical forest reflects the interplay
between aggregating processes, like dispersal limitation, and negative feedback
that induces effective repulsion among individuals. Monitoring the
variance-mean ratio for conspecific individuals along length-scales, we show
that the effect o... | [
{
"created": "Sun, 9 Nov 2014 14:03:32 GMT",
"version": "v1"
}
] | 2014-11-11 | [
[
"Seri",
"Efrat",
""
],
[
"Shnerb",
"Nadav M.",
""
]
] | The spatial arrangement of trees in a tropical forest reflects the interplay between aggregating processes, like dispersal limitation, and negative feedback that induces effective repulsion among individuals. Monitoring the variance-mean ratio for conspecific individuals along length-scales, we show that the effect of ... |
2304.10450 | Jiaxin Wang | Jiaxin Wang, Heidi J. Renninger, Qin Ma, Shichao Jin | StoManager1: An Enhanced, Automated, and High-throughput Tool to Measure
Leaf Stomata and Guard Cell Metrics Using Empirical and Theoretical
Algorithms | 15 pages, 6 figures, 3 tables | Plant Physiology, kiae049, 2024 | 10.1093/plphys/kiae049 | kiae049 | q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Automated stomata detection and measuring are vital for understanding plant
physiological performance and ecological functioning in global water and carbon
cycles. Current methods are laborious, time-consuming, prone to bias, and
limited in scale. We developed StoManager1, a high-throughput tool utilizing
empirical a... | [
{
"created": "Thu, 20 Apr 2023 16:45:09 GMT",
"version": "v1"
},
{
"created": "Tue, 16 May 2023 20:52:22 GMT",
"version": "v2"
},
{
"created": "Thu, 25 May 2023 10:34:04 GMT",
"version": "v3"
}
] | 2024-04-04 | [
[
"Wang",
"Jiaxin",
""
],
[
"Renninger",
"Heidi J.",
""
],
[
"Ma",
"Qin",
""
],
[
"Jin",
"Shichao",
""
]
] | Automated stomata detection and measuring are vital for understanding plant physiological performance and ecological functioning in global water and carbon cycles. Current methods are laborious, time-consuming, prone to bias, and limited in scale. We developed StoManager1, a high-throughput tool utilizing empirical and... |
q-bio/0703043 | Mingzhe Liu | Ruili Wang, Rui Jiang, Mingzhe Liu, Jiming Liu and Qing-song Wu | Effects of Langmuir Kinetics of Two-Lane Totally Asymmetric Exclusion
Processes in Protein Traffic | 15 pages, 8 figures. To be published in IJMPC | null | 10.1142/S0129183107011479 | null | q-bio.QM q-bio.BM | null | In this paper, we study a two-lane totally asymmetric simple exclusion
process (TASEP) coupled with random attachment and detachment of particles
(Langmuir kinetics) in both lanes under open boundary conditions. Our model can
describe the directed motion of molecular motors, attachment and detachment of
motors, and f... | [
{
"created": "Tue, 20 Mar 2007 09:10:33 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Wang",
"Ruili",
""
],
[
"Jiang",
"Rui",
""
],
[
"Liu",
"Mingzhe",
""
],
[
"Liu",
"Jiming",
""
],
[
"Wu",
"Qing-song",
""
]
] | In this paper, we study a two-lane totally asymmetric simple exclusion process (TASEP) coupled with random attachment and detachment of particles (Langmuir kinetics) in both lanes under open boundary conditions. Our model can describe the directed motion of molecular motors, attachment and detachment of motors, and fre... |
1207.6013 | Irmtraud Meyer | Jeff R. Proctor and Irmtraud M. Meyer | CoFold: thermodynamic RNA structure prediction with a kinetic twist | 30 pages (11 figures) | null | null | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Existing state-of-the-art methods that take a single RNA sequence and predict
the corresponding RNA secondary-structure are thermodynamic methods. These
predict the most stable RNA structure, but do not consider the process of
structure formation. We have by now ample experimental and theoretical
evidence, however, t... | [
{
"created": "Wed, 25 Jul 2012 14:52:57 GMT",
"version": "v1"
}
] | 2012-07-26 | [
[
"Proctor",
"Jeff R.",
""
],
[
"Meyer",
"Irmtraud M.",
""
]
] | Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary-structure are thermodynamic methods. These predict the most stable RNA structure, but do not consider the process of structure formation. We have by now ample experimental and theoretical evidence, however, tha... |
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