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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1605.07074 | Pedro Antonio Vald\'es-Hern\'andez | Pedro A. Valdes-Hernandez, Thomas Knoesche | Initial conditions in the neural field model | null | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In spite of the large amount of existing neural models in the literature,
there is a lack of a systematic review of the possible effect of choosing
different initial conditions on the dynamic evolution of neural systems. In
this short review we intend to give insights into this topic by discussing some
published exam... | [
{
"created": "Mon, 23 May 2016 16:15:21 GMT",
"version": "v1"
}
] | 2016-05-24 | [
[
"Valdes-Hernandez",
"Pedro A.",
""
],
[
"Knoesche",
"Thomas",
""
]
] | In spite of the large amount of existing neural models in the literature, there is a lack of a systematic review of the possible effect of choosing different initial conditions on the dynamic evolution of neural systems. In this short review we intend to give insights into this topic by discussing some published exampl... |
1310.3234 | Darren Kessner | Darren Kessner and John Novembre | forqs: Forward-in-time Simulation of Recombination, Quantitative Traits,
and Selection | preprint include Supplementary Information.
https://bitbucket.org/dkessner/forqs | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | forqs is a forward-in-time simulation of recombination, quantitative traits,
and selection. It was designed to investigate haplotype patterns resulting from
scenarios where substantial evolutionary change has taken place in a small
number of generations due to recombination and/or selection on polygenic
quantitative ... | [
{
"created": "Fri, 11 Oct 2013 18:31:09 GMT",
"version": "v1"
}
] | 2013-10-14 | [
[
"Kessner",
"Darren",
""
],
[
"Novembre",
"John",
""
]
] | forqs is a forward-in-time simulation of recombination, quantitative traits, and selection. It was designed to investigate haplotype patterns resulting from scenarios where substantial evolutionary change has taken place in a small number of generations due to recombination and/or selection on polygenic quantitative tr... |
1302.5507 | Ruibang Luo | Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi-Man Liu, Edward Wu,
Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting,
Siu-Ming Yiu, Chang Yu, Yingrui Li, Ruiqiang Li, Tak-Wah Lam | SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner | 21 pages, 6 figures, submitted to PLoS ONE, additional files
available at "https://www.dropbox.com/sh/bhclhxpoiubh371/O5CO_CkXQE".
Comments most welcome | null | 10.1371/journal.pone.0065632 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To tackle the exponentially increasing throughput of Next-Generation
Sequencing (NGS), most of the existing short-read aligners can be configured to
favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging
the computational power of both CPU and GPU with optimized algorithms, delivers
high speed... | [
{
"created": "Fri, 22 Feb 2013 07:56:11 GMT",
"version": "v1"
},
{
"created": "Sun, 24 Mar 2013 03:23:24 GMT",
"version": "v2"
}
] | 2015-06-15 | [
[
"Luo",
"Ruibang",
""
],
[
"Wong",
"Thomas",
""
],
[
"Zhu",
"Jianqiao",
""
],
[
"Liu",
"Chi-Man",
""
],
[
"Wu",
"Edward",
""
],
[
"Lee",
"Lap-Kei",
""
],
[
"Lin",
"Haoxiang",
""
],
[
"Zhu",
"Wenj... | To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed a... |
1103.4621 | Armando G. M. Neves | Armando G. M. Neves and Maurizio Serva | Extremely rare interbreeding events can explain Neanderthal DNA in
modern humans | 26 pages, 6 figures, updated version | null | null | null | q-bio.PE math-ph math.MP math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Considering the recent experimental discovery of Green et al that present day
non-Africans have 1 to 4% of their nuclear DNA of Neanderthal origin, we
propose here a model which is able to quantify the interbreeding events between
Africans and Neanderthals at the time they coexisted in the Middle East. The
model cons... | [
{
"created": "Wed, 23 Mar 2011 20:23:11 GMT",
"version": "v1"
},
{
"created": "Fri, 3 Jun 2011 14:20:42 GMT",
"version": "v2"
}
] | 2011-06-06 | [
[
"Neves",
"Armando G. M.",
""
],
[
"Serva",
"Maurizio",
""
]
] | Considering the recent experimental discovery of Green et al that present day non-Africans have 1 to 4% of their nuclear DNA of Neanderthal origin, we propose here a model which is able to quantify the interbreeding events between Africans and Neanderthals at the time they coexisted in the Middle East. The model consis... |
2311.03394 | Gopinath Sadhu | Gopinath Sadhu, K S Yadav, Siddhartha Sankar Ghosh and D C Dalal | On impact of oxygen distribution on tumor necrotic region: A Multiphase
Model | null | null | null | null | q-bio.TO math.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background and Objective: In an in-vivo situation, the tissue near the blood
vessels is rich in oxygen supply compared to the one far from blood vessels.
Hence, non-uniform oxygen distribution is observed in biological tissues. Our
objective is to explore the influence of non-uniform oxygen supply in the
development ... | [
{
"created": "Sun, 5 Nov 2023 05:37:33 GMT",
"version": "v1"
}
] | 2023-11-08 | [
[
"Sadhu",
"Gopinath",
""
],
[
"Yadav",
"K S",
""
],
[
"Ghosh",
"Siddhartha Sankar",
""
],
[
"Dalal",
"D C",
""
]
] | Background and Objective: In an in-vivo situation, the tissue near the blood vessels is rich in oxygen supply compared to the one far from blood vessels. Hence, non-uniform oxygen distribution is observed in biological tissues. Our objective is to explore the influence of non-uniform oxygen supply in the development of... |
1611.08760 | Robert Cameron | R. P. Cameron, J. A. Cameron and S. M. Barnett | Stegosaurus chirality | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We explain that Stegosaurus exhibited exterior chirality and observe that the
largest plate in particular of USNM 4394, USNM 4714, DMNS 2818 and NHMUK R36730
appears to have tilted to the right rather than to the left in each case.
Several instances in which Stegosaurus specimens have been confused with their
distinc... | [
{
"created": "Sat, 26 Nov 2016 23:14:34 GMT",
"version": "v1"
}
] | 2016-11-29 | [
[
"Cameron",
"R. P.",
""
],
[
"Cameron",
"J. A.",
""
],
[
"Barnett",
"S. M.",
""
]
] | We explain that Stegosaurus exhibited exterior chirality and observe that the largest plate in particular of USNM 4394, USNM 4714, DMNS 2818 and NHMUK R36730 appears to have tilted to the right rather than to the left in each case. Several instances in which Stegosaurus specimens have been confused with their distinct,... |
1506.04443 | Barry Slaff | Barry M. Slaff, Shane T. Jensen, and Aalim M. Weljie | Probabilistic Approach for Evaluating Metabolite Sample Integrity | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The success of metabolomics studies depends upon the "fitness" of each
biological sample used for analysis: it is critical that metabolite levels
reported for a biological sample represent an accurate snapshot of the studied
organism's metabolite profile at time of sample collection. Numerous factors
may compromise m... | [
{
"created": "Sun, 14 Jun 2015 21:50:09 GMT",
"version": "v1"
}
] | 2015-06-16 | [
[
"Slaff",
"Barry M.",
""
],
[
"Jensen",
"Shane T.",
""
],
[
"Weljie",
"Aalim M.",
""
]
] | The success of metabolomics studies depends upon the "fitness" of each biological sample used for analysis: it is critical that metabolite levels reported for a biological sample represent an accurate snapshot of the studied organism's metabolite profile at time of sample collection. Numerous factors may compromise met... |
1910.08157 | Thomas Booth | Thomas Booth | An Update on Machine Learning in Neuro-oncology Diagnostics | arXiv admin note: substantial text overlap with arXiv:1910.07440 | null | 10.1007/978-3-030-11723-8_4 | null | q-bio.QM cs.CV cs.LG eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Imaging biomarkers in neuro-oncology are used for diagnosis, prognosis and
treatment response monitoring. Magnetic resonance imaging is typically used
throughout the patient pathway because routine structural imaging provides
detailed anatomical and pathological information and advanced techniques
provide additional ... | [
{
"created": "Fri, 9 Aug 2019 08:57:51 GMT",
"version": "v1"
}
] | 2019-10-21 | [
[
"Booth",
"Thomas",
""
]
] | Imaging biomarkers in neuro-oncology are used for diagnosis, prognosis and treatment response monitoring. Magnetic resonance imaging is typically used throughout the patient pathway because routine structural imaging provides detailed anatomical and pathological information and advanced techniques provide additional ph... |
1803.07352 | Heiko Sch\"utt | Heiko H. Sch\"utt, Lars O. M. Rothkegel, Hans A. Trukenbrod, Ralf
Engbert, Felix A. Wichmann | Disentangling top-down vs. bottom-up and low-level vs. high-level
influences on eye movements over time | Submitted to Journal of Vision | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bottom-up and top-down, as well as low-level and high-level factors influence
where we fixate when viewing natural scenes. However, the importance of each of
these factors and how they interact remains a matter of debate. Here, we
disentangle these factors by analysing their influence over time. For this
purpose we d... | [
{
"created": "Tue, 20 Mar 2018 10:33:44 GMT",
"version": "v1"
},
{
"created": "Thu, 17 May 2018 03:45:47 GMT",
"version": "v2"
}
] | 2018-05-18 | [
[
"Schütt",
"Heiko H.",
""
],
[
"Rothkegel",
"Lars O. M.",
""
],
[
"Trukenbrod",
"Hans A.",
""
],
[
"Engbert",
"Ralf",
""
],
[
"Wichmann",
"Felix A.",
""
]
] | Bottom-up and top-down, as well as low-level and high-level factors influence where we fixate when viewing natural scenes. However, the importance of each of these factors and how they interact remains a matter of debate. Here, we disentangle these factors by analysing their influence over time. For this purpose we dev... |
1602.05227 | Konstantin Blyuss | N. Sherborne, K.B. Blyuss, I.Z. Kiss | Compact pairwise models for epidemics with multiple infectious stages on
degree heterogeneous and clustered networks | 22 pages, 9 figures | J. Theor. Biol. 407, 387-400 (2016) | 10.1016/j.jtbi.2016.07.015 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper presents a compact pairwise model that describes the spread of
multi-stage epidemics on networks. The multi-stage model corresponds to a
gamma-distributed infectious period which interpolates between the classical
Markovian models with exponentially distributed infectious period and epidemics
with a consta... | [
{
"created": "Sun, 14 Feb 2016 16:45:26 GMT",
"version": "v1"
}
] | 2016-12-08 | [
[
"Sherborne",
"N.",
""
],
[
"Blyuss",
"K. B.",
""
],
[
"Kiss",
"I. Z.",
""
]
] | This paper presents a compact pairwise model that describes the spread of multi-stage epidemics on networks. The multi-stage model corresponds to a gamma-distributed infectious period which interpolates between the classical Markovian models with exponentially distributed infectious period and epidemics with a constant... |
2211.12856 | Rafael Navajas-P\'erez | Gregor Mendel (translated by Juan Rojas-Garc\'ia and Rafael
Navajas-P\'erez) | Experimentos sobre la Hibridaci\'on en Plantas | in Spanish language | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Mendel performed his experiments from 1856 and 1863, presented his results in
two meetings of the Natural Science Society in Brunn in February and March of
1865, and finally published them in the iconical paper of 1866, Versuche uber
Plflanzenhybriden. Two main translations to Spanish are available: the one done
by P... | [
{
"created": "Wed, 23 Nov 2022 11:02:14 GMT",
"version": "v1"
}
] | 2022-11-24 | [
[
"Mendel",
"Gregor",
"",
"translated by Juan Rojas-García and Rafael\n Navajas-Pérez"
]
] | Mendel performed his experiments from 1856 and 1863, presented his results in two meetings of the Natural Science Society in Brunn in February and March of 1865, and finally published them in the iconical paper of 1866, Versuche uber Plflanzenhybriden. Two main translations to Spanish are available: the one done by Pre... |
2306.06156 | Timothy Truong Jr | Timothy F. Truong Jr, Tristan Bepler | PoET: A generative model of protein families as sequences-of-sequences | null | Advances in Neural Information Processing Systems (Vol. 36), 2023 | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Generative protein language models are a natural way to design new proteins
with desired functions. However, current models are either difficult to direct
to produce a protein from a specific family of interest, or must be trained on
a large multiple sequence alignment (MSA) from the specific family of interest,
maki... | [
{
"created": "Fri, 9 Jun 2023 16:06:36 GMT",
"version": "v1"
},
{
"created": "Mon, 30 Oct 2023 13:48:49 GMT",
"version": "v2"
},
{
"created": "Wed, 1 Nov 2023 12:34:47 GMT",
"version": "v3"
}
] | 2024-01-08 | [
[
"Truong",
"Timothy F.",
"Jr"
],
[
"Bepler",
"Tristan",
""
]
] | Generative protein language models are a natural way to design new proteins with desired functions. However, current models are either difficult to direct to produce a protein from a specific family of interest, or must be trained on a large multiple sequence alignment (MSA) from the specific family of interest, making... |
1202.1266 | Chia Ying Lee | Chia Ying Lee | Stochastic simulation of biochemical systems with randomly fluctuating
rate constants | null | null | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In an experimental study of single enzyme reactions, it has been proposed
that the rate constants of the enzymatic reactions fluctuate randomly,
according to a given distribution. To quantify the uncertainty arising from
random rate constants, it is necessary to investigate how one can simulate such
a biochemical sys... | [
{
"created": "Mon, 6 Feb 2012 20:28:20 GMT",
"version": "v1"
}
] | 2012-02-07 | [
[
"Lee",
"Chia Ying",
""
]
] | In an experimental study of single enzyme reactions, it has been proposed that the rate constants of the enzymatic reactions fluctuate randomly, according to a given distribution. To quantify the uncertainty arising from random rate constants, it is necessary to investigate how one can simulate such a biochemical syste... |
1804.01906 | Yannik Stradmann | Syed Ahmed Aamir, Yannik Stradmann, Paul M\"uller, Christian Pehle,
Andreas Hartel, Andreas Gr\"ubl, Johannes Schemmel and Karlheinz Meier | An Accelerated LIF Neuronal Network Array for a Large Scale Mixed-Signal
Neuromorphic Architecture | 14 pages, 9 Figures, accepted for publication in IEEE Transactions on
Circuits and Systems I | null | 10.1109/TCSI.2018.2840718 | null | q-bio.NC cs.ET physics.bio-ph physics.comp-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present an array of leaky integrate-and-fire (LIF) neuron circuits
designed for the second-generation BrainScaleS mixed-signal 65-nm CMOS
neuromorphic hardware. The neuronal array is embedded in the analog network
core of a scaled-down prototype HICANN-DLS chip. Designed as continuous-time
circuits, the neurons ar... | [
{
"created": "Thu, 5 Apr 2018 15:19:00 GMT",
"version": "v1"
},
{
"created": "Tue, 15 May 2018 11:44:07 GMT",
"version": "v2"
},
{
"created": "Wed, 23 May 2018 12:40:58 GMT",
"version": "v3"
}
] | 2019-03-28 | [
[
"Aamir",
"Syed Ahmed",
""
],
[
"Stradmann",
"Yannik",
""
],
[
"Müller",
"Paul",
""
],
[
"Pehle",
"Christian",
""
],
[
"Hartel",
"Andreas",
""
],
[
"Grübl",
"Andreas",
""
],
[
"Schemmel",
"Johannes",
""
],... | We present an array of leaky integrate-and-fire (LIF) neuron circuits designed for the second-generation BrainScaleS mixed-signal 65-nm CMOS neuromorphic hardware. The neuronal array is embedded in the analog network core of a scaled-down prototype HICANN-DLS chip. Designed as continuous-time circuits, the neurons are ... |
1611.03488 | Yi-Xiang Wang | Xian Jun Zeng, Min Deng, Yi Xiang Wang, James F. Griffith, Lai Chang
He, Anthony W. L. Kwok, Jason C. S. Leung, Timothy Kwok, Ping Chung Leung | Prevalence of algorithm-based qualitative (ABQ) method osteoporotic
vertebral fracture in elderly Chinese men and women with reference to
semi-quantitative (SQ) method: Mr. Os and Ms Os. (Hong Kong) studies | 26 pages,4 figures, 6 tables | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Introduction: This study evaluated algorithm-based qualitative (ABQ) method
for vertebral fracture (VF) evaluation with reference to semi-quantitative (SQ)
method and bone mineral density (BMD) measurement. Methods: Mr. OS (Hong Kong)
and Ms. OS (Hong Kong) represent the first large-scale cohort studies on bone
healt... | [
{
"created": "Thu, 10 Nov 2016 09:59:48 GMT",
"version": "v1"
}
] | 2016-11-14 | [
[
"Zeng",
"Xian Jun",
""
],
[
"Deng",
"Min",
""
],
[
"Wang",
"Yi Xiang",
""
],
[
"Griffith",
"James F.",
""
],
[
"He",
"Lai Chang",
""
],
[
"Kwok",
"Anthony W. L.",
""
],
[
"Leung",
"Jason C. S.",
""
],
[... | Introduction: This study evaluated algorithm-based qualitative (ABQ) method for vertebral fracture (VF) evaluation with reference to semi-quantitative (SQ) method and bone mineral density (BMD) measurement. Methods: Mr. OS (Hong Kong) and Ms. OS (Hong Kong) represent the first large-scale cohort studies on bone health ... |
q-bio/0612044 | Ingileif Hallgrimsdottir | Ingileif B. Hallgrimsdottir and Debbie S. Yuster | A complete classification of epistatic two-locus models | 24 pages, 7 figures | null | null | null | q-bio.QM | null | The study of epistasis is of great importance in statistical genetics in
fields such as linkage and association analysis and QTL mapping. In an effort
to classify the types of epistasis in the case of two biallelic loci Li and
Reich listed and described all models in the simplest case of 0/1 penetrance
values. Howeve... | [
{
"created": "Sun, 24 Dec 2006 03:41:19 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Hallgrimsdottir",
"Ingileif B.",
""
],
[
"Yuster",
"Debbie S.",
""
]
] | The study of epistasis is of great importance in statistical genetics in fields such as linkage and association analysis and QTL mapping. In an effort to classify the types of epistasis in the case of two biallelic loci Li and Reich listed and described all models in the simplest case of 0/1 penetrance values. However,... |
2305.16160 | Jeff Guo | Jeff Guo, Philippe Schwaller | Augmented Memory: Capitalizing on Experience Replay to Accelerate De
Novo Molecular Design | null | null | null | null | q-bio.BM cs.LG q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Sample efficiency is a fundamental challenge in de novo molecular design.
Ideally, molecular generative models should learn to satisfy a desired
objective under minimal oracle evaluations (computational prediction or wet-lab
experiment). This problem becomes more apparent when using oracles that can
provide increased... | [
{
"created": "Wed, 10 May 2023 14:00:50 GMT",
"version": "v1"
}
] | 2023-05-26 | [
[
"Guo",
"Jeff",
""
],
[
"Schwaller",
"Philippe",
""
]
] | Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal oracle evaluations (computational prediction or wet-lab experiment). This problem becomes more apparent when using oracles that can provide increased p... |
2402.03967 | Alia Abbara | Alia Abbara, Lisa Pagani, Celia Garc\'ia-Pareja, Anne-Florence Bitbol | Mutant fate in spatially structured populations on graphs: connecting
models to experiments | Main text: 13 pages, 5 figures. 6 supplementary figures | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In nature, most microbial populations have complex spatial structures that
can affect their evolution. Evolutionary graph theory predicts that some
spatial structures modelled by placing individuals on the nodes of a graph
affect the probability that a mutant will fix. Evolution experiments are
beginning to explicitl... | [
{
"created": "Tue, 6 Feb 2024 12:57:29 GMT",
"version": "v1"
}
] | 2024-02-07 | [
[
"Abbara",
"Alia",
""
],
[
"Pagani",
"Lisa",
""
],
[
"García-Pareja",
"Celia",
""
],
[
"Bitbol",
"Anne-Florence",
""
]
] | In nature, most microbial populations have complex spatial structures that can affect their evolution. Evolutionary graph theory predicts that some spatial structures modelled by placing individuals on the nodes of a graph affect the probability that a mutant will fix. Evolution experiments are beginning to explicitly ... |
2003.06882 | Larissa Terumi Arashiro | Maria Jesus Garcia-Galan, Larissa Arashiro, Lucia H.M.L.M. Santos,
Sara Insa, Sara Rodriguez-Mozaz, Damia Barcelo, Ivet Ferrer, Marianna Garfi | Fate of priority pharmaceuticals and their main metabolites and
transformation products in microalgae-based wastewater treatment systems | null | null | 10.1016/j.jhazmat.2019.121771 | null | q-bio.QM q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The present study evaluates the removal capacity of two high rate algae ponds
(HRAPs) to eliminate 12 pharmaceuticals (PhACs) and 26 of their corresponding
main metabolites and transformation products. The efficiency of these ponds,
operating with and without primary treatment, was compared in order to study
their ca... | [
{
"created": "Sun, 15 Mar 2020 18:09:06 GMT",
"version": "v1"
}
] | 2020-03-17 | [
[
"Garcia-Galan",
"Maria Jesus",
""
],
[
"Arashiro",
"Larissa",
""
],
[
"Santos",
"Lucia H. M. L. M.",
""
],
[
"Insa",
"Sara",
""
],
[
"Rodriguez-Mozaz",
"Sara",
""
],
[
"Barcelo",
"Damia",
""
],
[
"Ferrer",
"Ive... | The present study evaluates the removal capacity of two high rate algae ponds (HRAPs) to eliminate 12 pharmaceuticals (PhACs) and 26 of their corresponding main metabolites and transformation products. The efficiency of these ponds, operating with and without primary treatment, was compared in order to study their capa... |
2009.03753 | Afroza Shirin | Afroza Shirin, Yen Ting Lin, Francesco Sorrentino | Data-driven Optimized Control of the COVID-19 Epidemics | 5 figures | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Optimizing the impact on the economy of control strategies aiming at
containing the spread of COVID-19 is a critical challenge. We use daily new
case counts of COVID-19 patients reported by local health administrations from
different Metropolitan Statistical Areas (MSAs) within the US to parametrize a
model that well... | [
{
"created": "Fri, 4 Sep 2020 19:19:13 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Feb 2021 17:38:07 GMT",
"version": "v2"
},
{
"created": "Wed, 10 Mar 2021 23:19:31 GMT",
"version": "v3"
}
] | 2021-03-12 | [
[
"Shirin",
"Afroza",
""
],
[
"Lin",
"Yen Ting",
""
],
[
"Sorrentino",
"Francesco",
""
]
] | Optimizing the impact on the economy of control strategies aiming at containing the spread of COVID-19 is a critical challenge. We use daily new case counts of COVID-19 patients reported by local health administrations from different Metropolitan Statistical Areas (MSAs) within the US to parametrize a model that well d... |
2001.07092 | Grace Lindsay | Grace W. Lindsay | Convolutional Neural Networks as a Model of the Visual System: Past,
Present, and Future | Review Article to be published in Journal of Cognitive Neuroscience,
18 pages, 5 figures plus 8 pages of references | null | 10.1162/jocn_a_01544 | null | q-bio.NC cs.CV cs.NE | http://creativecommons.org/licenses/by-sa/4.0/ | Convolutional neural networks (CNNs) were inspired by early findings in the
study of biological vision. They have since become successful tools in computer
vision and state-of-the-art models of both neural activity and behavior on
visual tasks. This review highlights what, in the context of CNNs, it means to
be a goo... | [
{
"created": "Mon, 20 Jan 2020 13:04:37 GMT",
"version": "v1"
},
{
"created": "Mon, 10 Feb 2020 11:37:16 GMT",
"version": "v2"
}
] | 2020-02-11 | [
[
"Lindsay",
"Grace W.",
""
]
] | Convolutional neural networks (CNNs) were inspired by early findings in the study of biological vision. They have since become successful tools in computer vision and state-of-the-art models of both neural activity and behavior on visual tasks. This review highlights what, in the context of CNNs, it means to be a good ... |
q-bio/0606003 | Georgy Karev | Georgy P. Karev | Inhomogeneous maps: the basic theorems and some applications | 10 pages, 3 figures; submitted to Conference on Differential &
Difference Equations and Applications, Florida Institute of Technology, 2005 | null | null | null | q-bio.PE q-bio.QM | null | Non-linear maps can possess various dynamical behaviors varying from stable
steady states and cycles to chaotic oscillations. Most models assume that
individuals within a given population are identical ignoring the fundamental
role of variation. Here we develop a theory of inhomogeneous maps and apply the
general app... | [
{
"created": "Fri, 2 Jun 2006 18:16:02 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Karev",
"Georgy P.",
""
]
] | Non-linear maps can possess various dynamical behaviors varying from stable steady states and cycles to chaotic oscillations. Most models assume that individuals within a given population are identical ignoring the fundamental role of variation. Here we develop a theory of inhomogeneous maps and apply the general appro... |
2004.11763 | Sebastian Gottwald | Sebastian Gottwald, Daniel A. Braun | The Two Kinds of Free Energy and the Bayesian Revolution | null | PLOS Computational Biology 16(12), 2020 | 10.1371/journal.pcbi.1008420 | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | The concept of free energy has its origins in 19th century thermodynamics,
but has recently found its way into the behavioral and neural sciences, where
it has been promoted for its wide applicability and has even been suggested as
a fundamental principle of understanding intelligent behavior and brain
function. We a... | [
{
"created": "Fri, 24 Apr 2020 14:09:28 GMT",
"version": "v1"
},
{
"created": "Sat, 15 Aug 2020 11:56:08 GMT",
"version": "v2"
},
{
"created": "Thu, 10 Sep 2020 07:17:59 GMT",
"version": "v3"
},
{
"created": "Mon, 7 Dec 2020 00:03:21 GMT",
"version": "v4"
}
] | 2020-12-08 | [
[
"Gottwald",
"Sebastian",
""
],
[
"Braun",
"Daniel A.",
""
]
] | The concept of free energy has its origins in 19th century thermodynamics, but has recently found its way into the behavioral and neural sciences, where it has been promoted for its wide applicability and has even been suggested as a fundamental principle of understanding intelligent behavior and brain function. We arg... |
1601.05700 | Jody Reimer | Jody R. Reimer, Michael B. Bonsall, Philip K. Maini | The Critical Domain Size of Stochastic Population Models | null | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Identifying the critical domain size necessary for a population to persist is
an important question in ecology. Both demographic and environmental
stochasticity impact a population's ability to persist. Here we explore ways of
including this variability. We study populations which have traditionally been
modelled usi... | [
{
"created": "Thu, 21 Jan 2016 16:27:54 GMT",
"version": "v1"
}
] | 2016-01-22 | [
[
"Reimer",
"Jody R.",
""
],
[
"Bonsall",
"Michael B.",
""
],
[
"Maini",
"Philip K.",
""
]
] | Identifying the critical domain size necessary for a population to persist is an important question in ecology. Both demographic and environmental stochasticity impact a population's ability to persist. Here we explore ways of including this variability. We study populations which have traditionally been modelled using... |
1506.03400 | Andreas Hanke | Stefan M. Giovan, Andreas Hanke, and Stephen D. Levene | DNA cyclization and looping in the wormlike limit: normal modes and the
validity of the harmonic approximation | 23 pages, 6 figures. Typos corrected. Manuscript improved | Biopolymers 103, 528-38 (2015) (special issue in honor of Don
Crothers) | null | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | For much of the last three decades Monte Carlo-simulation methods have been
the standard approach for accurately calculating the cyclization probability,
$J$, or J factor, for DNA models having sequence-dependent bends or
inhomogeneous bending flexibility. Within the last ten years, however,
approaches based on harmo... | [
{
"created": "Wed, 10 Jun 2015 17:17:04 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Jul 2015 23:02:22 GMT",
"version": "v2"
}
] | 2015-07-30 | [
[
"Giovan",
"Stefan M.",
""
],
[
"Hanke",
"Andreas",
""
],
[
"Levene",
"Stephen D.",
""
]
] | For much of the last three decades Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, $J$, or J factor, for DNA models having sequence-dependent bends or inhomogeneous bending flexibility. Within the last ten years, however, approaches based on harmoni... |
2207.12897 | Lam Ho | Nhat L. Vu, Thanh P. Nguyen, Binh T. Nguyen, Vu Dinh, Lam Si Tung Ho | When can we reconstruct the ancestral state? Beyond Brownian motion | null | null | null | null | q-bio.PE math.ST stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reconstructing the ancestral state of a group of species helps answer many
important questions in evolutionary biology. Therefore, it is crucial to
understand when we can estimate the ancestral state accurately. Previous works
provide a necessary and sufficient condition, called the big bang condition,
for the existe... | [
{
"created": "Tue, 26 Jul 2022 13:45:20 GMT",
"version": "v1"
},
{
"created": "Thu, 20 Apr 2023 03:07:47 GMT",
"version": "v2"
}
] | 2023-04-21 | [
[
"Vu",
"Nhat L.",
""
],
[
"Nguyen",
"Thanh P.",
""
],
[
"Nguyen",
"Binh T.",
""
],
[
"Dinh",
"Vu",
""
],
[
"Ho",
"Lam Si Tung",
""
]
] | Reconstructing the ancestral state of a group of species helps answer many important questions in evolutionary biology. Therefore, it is crucial to understand when we can estimate the ancestral state accurately. Previous works provide a necessary and sufficient condition, called the big bang condition, for the existenc... |
2207.07930 | Yan-Liang Shi | Yan-Liang Shi, Roxana Zeraati, Anna Levina, Tatiana A. Engel | Spatial and temporal correlations in neural networks with structured
connectivity | 25 pages, 20 figures | null | null | null | q-bio.NC cond-mat.dis-nn cond-mat.stat-mech | http://creativecommons.org/licenses/by/4.0/ | Correlated fluctuations in the activity of neural populations reflect the
network's dynamics and connectivity. The temporal and spatial dimensions of
neural correlations are interdependent. However, prior theoretical work mainly
analyzed correlations in either spatial or temporal domains, oblivious to their
interplay... | [
{
"created": "Sat, 16 Jul 2022 12:47:32 GMT",
"version": "v1"
}
] | 2022-07-19 | [
[
"Shi",
"Yan-Liang",
""
],
[
"Zeraati",
"Roxana",
""
],
[
"Levina",
"Anna",
""
],
[
"Engel",
"Tatiana A.",
""
]
] | Correlated fluctuations in the activity of neural populations reflect the network's dynamics and connectivity. The temporal and spatial dimensions of neural correlations are interdependent. However, prior theoretical work mainly analyzed correlations in either spatial or temporal domains, oblivious to their interplay. ... |
2309.09816 | Niklas Tillmanns | Niklas Tillmanns, Jan Lost, Joanna Tabor, Sagar Vasandani, Shaurey
Vetsa, Neelan Marianayagam, Kanat Yalcin, E. Zeynep Erson-Omay, Marc von
Reppert, Leon Jekel, Sara Merkaj, Divya Ramakrishnan, Arman Avesta, Irene
Dixe de Oliveira Santo, Lan Jin, Anita Huttner, Khaled Bousabarah, Ichiro
Ikuta, MingDe Lin, Sanja... | Application of Novel PACS-based Informatics Platform to Identify Imaging
Based Predictors of CDKN2A Allelic Status in Glioblastomas | 23 pages, 5 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Gliomas with CDKN2A mutations are known to have worse prognosis but imaging
features of these gliomas are unknown. Our goal is to identify CDKN2A specific
qualitative imaging biomarkers in glioblastomas using a new informatics
workflow that enables rapid analysis of qualitative imaging features with
Visually AcceSAbl... | [
{
"created": "Mon, 18 Sep 2023 14:37:31 GMT",
"version": "v1"
}
] | 2023-09-19 | [
[
"Tillmanns",
"Niklas",
""
],
[
"Lost",
"Jan",
""
],
[
"Tabor",
"Joanna",
""
],
[
"Vasandani",
"Sagar",
""
],
[
"Vetsa",
"Shaurey",
""
],
[
"Marianayagam",
"Neelan",
""
],
[
"Yalcin",
"Kanat",
""
],
[
... | Gliomas with CDKN2A mutations are known to have worse prognosis but imaging features of these gliomas are unknown. Our goal is to identify CDKN2A specific qualitative imaging biomarkers in glioblastomas using a new informatics workflow that enables rapid analysis of qualitative imaging features with Visually AcceSAble ... |
0903.0031 | Alexander Spirov | Alexander V. Spirov | Design of a dynamic model of genes with multiple autonomous regulatory
modules by evolution in silico | 24 pages | null | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | New approach to design a dynamic model of genes with multiple autonomous
regulatory modules by evolution in silico is proposed. The approach is based on
Genetic Algorithms, enforced by new crossover operators, especially worked out
for these purposes. The approach exploits the subbasin-portal architecture of
the fitn... | [
{
"created": "Sat, 28 Feb 2009 01:35:32 GMT",
"version": "v1"
}
] | 2009-03-03 | [
[
"Spirov",
"Alexander V.",
""
]
] | New approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, enforced by new crossover operators, especially worked out for these purposes. The approach exploits the subbasin-portal architecture of the fitnes... |
1912.12047 | Sebastian Billaudelle | Sebastian Billaudelle, Benjamin Cramer, Mihai A. Petrovici, Korbinian
Schreiber, David Kappel, Johannes Schemmel, Karlheinz Meier | Structural plasticity on an accelerated analog neuromorphic hardware
system | null | null | null | null | q-bio.NC cs.NE | http://creativecommons.org/licenses/by/4.0/ | In computational neuroscience, as well as in machine learning, neuromorphic
devices promise an accelerated and scalable alternative to neural network
simulations. Their neural connectivity and synaptic capacity depends on their
specific design choices, but is always intrinsically limited. Here, we present
a strategy ... | [
{
"created": "Fri, 27 Dec 2019 10:15:58 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Sep 2020 08:20:35 GMT",
"version": "v2"
}
] | 2020-10-01 | [
[
"Billaudelle",
"Sebastian",
""
],
[
"Cramer",
"Benjamin",
""
],
[
"Petrovici",
"Mihai A.",
""
],
[
"Schreiber",
"Korbinian",
""
],
[
"Kappel",
"David",
""
],
[
"Schemmel",
"Johannes",
""
],
[
"Meier",
"Karlhein... | In computational neuroscience, as well as in machine learning, neuromorphic devices promise an accelerated and scalable alternative to neural network simulations. Their neural connectivity and synaptic capacity depends on their specific design choices, but is always intrinsically limited. Here, we present a strategy to... |
1811.00004 | Carlos Domingo-Felez | Carlos Domingo-F\'elez and Barth F. Smets | Modelling N2O dynamics of activated sludge biomass under nitrifying and
denitrifying conditions: pathway contributions and uncertainty analysis | Text and Supporting Information | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Nitrous oxide (N2O) is a potent greenhouse gas emitted during biological
wastewater treatment. A pseudo-mechanistic model describing three biological
pathways for nitric oxide (NO) and N2O production was calibrated for mixed
culture biomass from an activated sludge process using laboratory-scale
experiments. The mode... | [
{
"created": "Wed, 31 Oct 2018 09:52:44 GMT",
"version": "v1"
}
] | 2018-11-02 | [
[
"Domingo-Félez",
"Carlos",
""
],
[
"Smets",
"Barth F.",
""
]
] | Nitrous oxide (N2O) is a potent greenhouse gas emitted during biological wastewater treatment. A pseudo-mechanistic model describing three biological pathways for nitric oxide (NO) and N2O production was calibrated for mixed culture biomass from an activated sludge process using laboratory-scale experiments. The model ... |
1809.08179 | Patrick Dondl | Patrina S.P. Poh, Dvina Valainis, Kaushik Bhattacharya, Martijn van
Griensven, Patrick Dondl | Optimizing Bone Scaffold Porosity Distributions | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a simple one-dimensional time-dependent model for bone
regeneration in the presence of a bio-resorbable polymer scaffold. Within the
framework of the model, we optimize the effective mechanical stiffness of the
polymer scaffold together with the regenerated bone matrix. The result of the
optimization proc... | [
{
"created": "Fri, 21 Sep 2018 15:52:47 GMT",
"version": "v1"
}
] | 2018-09-24 | [
[
"Poh",
"Patrina S. P.",
""
],
[
"Valainis",
"Dvina",
""
],
[
"Bhattacharya",
"Kaushik",
""
],
[
"van Griensven",
"Martijn",
""
],
[
"Dondl",
"Patrick",
""
]
] | We consider a simple one-dimensional time-dependent model for bone regeneration in the presence of a bio-resorbable polymer scaffold. Within the framework of the model, we optimize the effective mechanical stiffness of the polymer scaffold together with the regenerated bone matrix. The result of the optimization proced... |
1708.00662 | Meurig Thomas Gallagher | Meurig Thomas Gallagher, Cara Victoria Neal, Kenton P. Arkill and
David John Smith | Model-based image analysis of a tethered Brownian fibre for shear stress
sensing | Submitted for publication | null | null | null | q-bio.QM cond-mat.soft physics.flu-dyn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The measurement of shear stress acting on a biologically relevant surface is
a challenging problem, particularly in the complex environment of, for example,
the vasculature. While an experimental method for the direct detection of wall
shear stress via the imaging of a synthetic biology nanorod has recently been
deve... | [
{
"created": "Wed, 2 Aug 2017 09:29:18 GMT",
"version": "v1"
}
] | 2017-08-03 | [
[
"Gallagher",
"Meurig Thomas",
""
],
[
"Neal",
"Cara Victoria",
""
],
[
"Arkill",
"Kenton P.",
""
],
[
"Smith",
"David John",
""
]
] | The measurement of shear stress acting on a biologically relevant surface is a challenging problem, particularly in the complex environment of, for example, the vasculature. While an experimental method for the direct detection of wall shear stress via the imaging of a synthetic biology nanorod has recently been develo... |
1409.6378 | Dante Chialvo | Enzo Tagliazucchi, Helmut Laufs, Dante R. Chialvo | A few points suffice: Efficient large-scale computation of brain
voxel-wise functional connectomes from a sparse spatio-temporal point-process | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Large efforts are currently under way to systematically map functional
connectivity between all pairs of millimeter-scale brain regions using big
volumes of neuroimaging data. Functional magnetic resonance imaging (fMRI) can
produce these functional connectomes, however, large amounts of data and
lengthy computation ... | [
{
"created": "Tue, 23 Sep 2014 00:43:48 GMT",
"version": "v1"
}
] | 2014-09-24 | [
[
"Tagliazucchi",
"Enzo",
""
],
[
"Laufs",
"Helmut",
""
],
[
"Chialvo",
"Dante R.",
""
]
] | Large efforts are currently under way to systematically map functional connectivity between all pairs of millimeter-scale brain regions using big volumes of neuroimaging data. Functional magnetic resonance imaging (fMRI) can produce these functional connectomes, however, large amounts of data and lengthy computation ti... |
1706.01312 | Marc Dinh | M. Dinh and V. Fromion | RBA like problem with thermo-kinetics is non convex | null | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The aim of this short note is to show that the class of problem involving
kinetic or thermo-kinetic constraints in addition to the usual stoechiometric
one is non convex.
| [
{
"created": "Tue, 23 May 2017 12:52:56 GMT",
"version": "v1"
}
] | 2017-06-06 | [
[
"Dinh",
"M.",
""
],
[
"Fromion",
"V.",
""
]
] | The aim of this short note is to show that the class of problem involving kinetic or thermo-kinetic constraints in addition to the usual stoechiometric one is non convex. |
2404.10031 | Ammar Ahmed Pallikonda Latheef | Ammar Ahmed Pallikonda Latheef, Alberto Santamaria-Pang, Craig K
Jones, Haris I Sair | Emergent Language Symbolic Autoencoder (ELSA) with Weak Supervision to
Model Hierarchical Brain Networks | 10 pages, 4 figures | null | null | null | q-bio.NC cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Brain networks display a hierarchical organization, a complexity that poses a
challenge for existing deep learning models, often structured as flat
classifiers, leading to difficulties in interpretability and the 'black box'
issue. To bridge this gap, we propose a novel architecture: a symbolic
autoencoder informed b... | [
{
"created": "Mon, 15 Apr 2024 13:51:05 GMT",
"version": "v1"
}
] | 2024-04-17 | [
[
"Latheef",
"Ammar Ahmed Pallikonda",
""
],
[
"Santamaria-Pang",
"Alberto",
""
],
[
"Jones",
"Craig K",
""
],
[
"Sair",
"Haris I",
""
]
] | Brain networks display a hierarchical organization, a complexity that poses a challenge for existing deep learning models, often structured as flat classifiers, leading to difficulties in interpretability and the 'black box' issue. To bridge this gap, we propose a novel architecture: a symbolic autoencoder informed by ... |
1806.05172 | Rubem Mondaini | R.P. Mondaini, S.C. de Albuquerque Neto | The Protein Family Classification in Protein Databases via Entropy
Measures | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the present work, we review the fundamental methods which have been
developed in the last few years for classifying into families and clans the
distribution of amino acids in protein databases. This is done through
functions of random variables, the Entropy Measures of probabilities of
occurrence of the amino acid... | [
{
"created": "Tue, 12 Jun 2018 22:47:04 GMT",
"version": "v1"
}
] | 2018-06-15 | [
[
"Mondaini",
"R. P.",
""
],
[
"Neto",
"S. C. de Albuquerque",
""
]
] | In the present work, we review the fundamental methods which have been developed in the last few years for classifying into families and clans the distribution of amino acids in protein databases. This is done through functions of random variables, the Entropy Measures of probabilities of occurrence of the amino acids.... |
2305.19801 | Oliver Bent | Sebastien Boyer, Sam Money-Kyrle, Oliver Bent | Predicting protein stability changes under multiple amino acid
substitutions using equivariant graph neural networks | null | null | null | null | q-bio.BM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | The accurate prediction of changes in protein stability under multiple amino
acid substitutions is essential for realising true in-silico protein re-design.
To this purpose, we propose improvements to state-of-the-art Deep learning (DL)
protein stability prediction models, enabling first-of-a-kind predictions for
var... | [
{
"created": "Tue, 30 May 2023 14:48:06 GMT",
"version": "v1"
}
] | 2023-06-01 | [
[
"Boyer",
"Sebastien",
""
],
[
"Money-Kyrle",
"Sam",
""
],
[
"Bent",
"Oliver",
""
]
] | The accurate prediction of changes in protein stability under multiple amino acid substitutions is essential for realising true in-silico protein re-design. To this purpose, we propose improvements to state-of-the-art Deep learning (DL) protein stability prediction models, enabling first-of-a-kind predictions for varia... |
2311.18527 | Chun-Hsiang Chuang | Chun-Hsiang Chuang, Shao-Xun Fang, Chih-Sheng Huang, Weiping Ding | InfoFlowNet: A Multi-head Attention-based Self-supervised Learning Model
with Surrogate Approach for Uncovering Brain Effective Connectivity | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Deciphering brain network topology can enhance the depth of neuroscientific
knowledge and facilitate the development of neural engineering methods.
Effective connectivity, a measure of brain network dynamics, is particularly
useful for investigating the directional influences among different brain
regions. In this st... | [
{
"created": "Thu, 30 Nov 2023 13:06:04 GMT",
"version": "v1"
}
] | 2023-12-01 | [
[
"Chuang",
"Chun-Hsiang",
""
],
[
"Fang",
"Shao-Xun",
""
],
[
"Huang",
"Chih-Sheng",
""
],
[
"Ding",
"Weiping",
""
]
] | Deciphering brain network topology can enhance the depth of neuroscientific knowledge and facilitate the development of neural engineering methods. Effective connectivity, a measure of brain network dynamics, is particularly useful for investigating the directional influences among different brain regions. In this stud... |
2108.12938 | Patricio Foncea | Patricio Foncea, Susana Mondschein, Marcelo Olivares | Replacing quarantine of COVID-19 contacts with periodic testing is also
effective in mitigating the risk of transmission | To appear in Scientific Reports. 23 pages, 15 pages of appendix, 14
figures, 4 tables | null | 10.1038/s41598-022-07447-2 | null | q-bio.PE physics.soc-ph stat.AP | http://creativecommons.org/licenses/by/4.0/ | The quarantine of identified close contacts has been vital to reducing
transmission rates and averting secondary infection risk before symptom onset
and by asymptomatic cases. The effectiveness of this contact tracing strategy
to mitigate transmission is sensitive to the adherence to quarantines, which
may be lower f... | [
{
"created": "Mon, 30 Aug 2021 00:17:09 GMT",
"version": "v1"
},
{
"created": "Sun, 13 Feb 2022 20:02:24 GMT",
"version": "v2"
}
] | 2022-03-11 | [
[
"Foncea",
"Patricio",
""
],
[
"Mondschein",
"Susana",
""
],
[
"Olivares",
"Marcelo",
""
]
] | The quarantine of identified close contacts has been vital to reducing transmission rates and averting secondary infection risk before symptom onset and by asymptomatic cases. The effectiveness of this contact tracing strategy to mitigate transmission is sensitive to the adherence to quarantines, which may be lower for... |
2406.07269 | Leo D'Amato | Leo D'Amato, Gian Luca Lancia and Giovanni Pezzulo | The geometry of efficient codes: how rate-distortion trade-offs distort
the latent representations of generative models | null | null | null | null | q-bio.NC cs.IT math.IT | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Living organisms rely on internal models of the world to act adaptively.
These models cannot encode every detail and hence need to compress information.
From a cognitive standpoint, information compression can manifest as a
distortion of latent representations, resulting in the emergence of
representations that may n... | [
{
"created": "Tue, 11 Jun 2024 13:53:27 GMT",
"version": "v1"
}
] | 2024-06-12 | [
[
"D'Amato",
"Leo",
""
],
[
"Lancia",
"Gian Luca",
""
],
[
"Pezzulo",
"Giovanni",
""
]
] | Living organisms rely on internal models of the world to act adaptively. These models cannot encode every detail and hence need to compress information. From a cognitive standpoint, information compression can manifest as a distortion of latent representations, resulting in the emergence of representations that may not... |
0909.1411 | Byungjoon Min | Byungjoon Min, K.-I. Goh, and I.-M. Kim | Noise Characteristics of Molecular Oscillations in Simple Genetic
Oscillatory Systems | 7 pages, 6 figures, minor changes, final published version | J. Korean Phys. Soc. 56, 911 (2010) | 10.3938/jkps.56.911 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the noise characteristics of stochastic oscillations in protein
number dynamics of simple genetic oscillatory systems. Using the
three-component negative feedback transcription regulatory system called the
repressilator as a prototypical example, we quantify the degree of fluctuations
in oscillation periods ... | [
{
"created": "Tue, 8 Sep 2009 07:29:29 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Apr 2010 08:08:21 GMT",
"version": "v2"
}
] | 2015-03-13 | [
[
"Min",
"Byungjoon",
""
],
[
"Goh",
"K. -I.",
""
],
[
"Kim",
"I. -M.",
""
]
] | We study the noise characteristics of stochastic oscillations in protein number dynamics of simple genetic oscillatory systems. Using the three-component negative feedback transcription regulatory system called the repressilator as a prototypical example, we quantify the degree of fluctuations in oscillation periods an... |
2011.05846 | Petr Hedenec | Petr Hed\v{e}nec, Lars Ola Nilsson, Haifeng Zheng, Per Gundersen,
Inger Kappel Schmidt, Johannes Rousk, Lars Vesterdal | Mycorrhizal association of common European tree species shapes biomass
and metabolic activity of bacterial and fungal communities in soil | Authors Accepted Manuscript | In: Soil Biology & Biochemistry. 2020 ; Vol. 149 | 10.1016/j.soilbio.2020.107933 | null | q-bio.PE | http://creativecommons.org/licenses/by-sa/4.0/ | Recent studies have revealed effects of various tree species on soil physical
and chemical properties. However, effects of various tree species on
composition and activity of soil microbiota and the relevant controls remain
poorly understood. We evaluated the influence of tree species associated with
two different my... | [
{
"created": "Tue, 10 Nov 2020 18:10:33 GMT",
"version": "v1"
},
{
"created": "Sun, 15 Nov 2020 10:45:05 GMT",
"version": "v2"
},
{
"created": "Wed, 25 Nov 2020 13:57:07 GMT",
"version": "v3"
}
] | 2020-11-26 | [
[
"Heděnec",
"Petr",
""
],
[
"Nilsson",
"Lars Ola",
""
],
[
"Zheng",
"Haifeng",
""
],
[
"Gundersen",
"Per",
""
],
[
"Schmidt",
"Inger Kappel",
""
],
[
"Rousk",
"Johannes",
""
],
[
"Vesterdal",
"Lars",
""
]
... | Recent studies have revealed effects of various tree species on soil physical and chemical properties. However, effects of various tree species on composition and activity of soil microbiota and the relevant controls remain poorly understood. We evaluated the influence of tree species associated with two different myco... |
2111.06979 | Jenelle Feather | Joel Dapello, Jenelle Feather, Hang Le, Tiago Marques, David D. Cox,
Josh H. McDermott, James J. DiCarlo, SueYeon Chung | Neural Population Geometry Reveals the Role of Stochasticity in Robust
Perception | 35th Conference on Neural Information Processing Systems (NeurIPS
2021) | null | null | null | q-bio.NC cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Adversarial examples are often cited by neuroscientists and machine learning
researchers as an example of how computational models diverge from biological
sensory systems. Recent work has proposed adding biologically-inspired
components to visual neural networks as a way to improve their adversarial
robustness. One s... | [
{
"created": "Fri, 12 Nov 2021 22:59:45 GMT",
"version": "v1"
}
] | 2021-11-16 | [
[
"Dapello",
"Joel",
""
],
[
"Feather",
"Jenelle",
""
],
[
"Le",
"Hang",
""
],
[
"Marques",
"Tiago",
""
],
[
"Cox",
"David D.",
""
],
[
"McDermott",
"Josh H.",
""
],
[
"DiCarlo",
"James J.",
""
],
[
"... | Adversarial examples are often cited by neuroscientists and machine learning researchers as an example of how computational models diverge from biological sensory systems. Recent work has proposed adding biologically-inspired components to visual neural networks as a way to improve their adversarial robustness. One sur... |
0905.1916 | Vitaly Ganusov | Vitaly V. Ganusov, Aron E. Lukacher, and Anthony M. Byers | Similar in vivo killing efficacy of polyoma virus-specific CD8 T cells
during acute and chronic phases of the infection | null | null | null | null | q-bio.PE q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Viral infections can be broadly divided into infections that are cleared from
the host (acute) and those that persist (chronic). Why some viruses establish
chronic infections while other do not is poorly understood. One possibility is
that the host's immune response is impaired during chronic infections and is
unable... | [
{
"created": "Tue, 12 May 2009 17:34:52 GMT",
"version": "v1"
}
] | 2009-05-13 | [
[
"Ganusov",
"Vitaly V.",
""
],
[
"Lukacher",
"Aron E.",
""
],
[
"Byers",
"Anthony M.",
""
]
] | Viral infections can be broadly divided into infections that are cleared from the host (acute) and those that persist (chronic). Why some viruses establish chronic infections while other do not is poorly understood. One possibility is that the host's immune response is impaired during chronic infections and is unable t... |
2005.08968 | Fengqi You | Abdulelah S. Alshehri, Rafiqul Gani, Fengqi You | Deep Learning and Knowledge-Based Methods for Computer Aided Molecular
Design -- Toward a Unified Approach: State-of-the-Art and Future Directions | null | Computers and Chemical Engineering 141 (2020) 107005 | 10.1016/j.compchemeng.2020.107005 | null | q-bio.BM cs.LG physics.chem-ph stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The optimal design of compounds through manipulating properties at the
molecular level is often the key to considerable scientific advances and
improved process systems performance. This paper highlights key trends,
challenges, and opportunities underpinning the Computer-Aided Molecular Design
(CAMD) problems. A brie... | [
{
"created": "Mon, 18 May 2020 14:17:51 GMT",
"version": "v1"
},
{
"created": "Sun, 5 Jul 2020 15:00:54 GMT",
"version": "v2"
}
] | 2020-07-13 | [
[
"Alshehri",
"Abdulelah S.",
""
],
[
"Gani",
"Rafiqul",
""
],
[
"You",
"Fengqi",
""
]
] | The optimal design of compounds through manipulating properties at the molecular level is often the key to considerable scientific advances and improved process systems performance. This paper highlights key trends, challenges, and opportunities underpinning the Computer-Aided Molecular Design (CAMD) problems. A brief ... |
1607.00276 | Pushpam Aji John | Kristiina Ausmees, Pushpam Aji John | Analysis of Chromosome 20 - A Study | 6 pages, 7 figures | The 6th International Conference on Computational Systems-Biology
and Bioinformatics 2015 | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Since the arrival of next-generation sequencing technologies the amount of
genetic sequencing data has increased dramatically. This has has fueled an
increase in human genetics research. At the same time, with the recent advent
of technologies in processing large data sets, lot of these technologies are
proving valua... | [
{
"created": "Thu, 30 Jun 2016 07:34:43 GMT",
"version": "v1"
}
] | 2016-07-04 | [
[
"Ausmees",
"Kristiina",
""
],
[
"John",
"Pushpam Aji",
""
]
] | Since the arrival of next-generation sequencing technologies the amount of genetic sequencing data has increased dramatically. This has has fueled an increase in human genetics research. At the same time, with the recent advent of technologies in processing large data sets, lot of these technologies are proving valuabl... |
0808.3609 | Mareike Fischer | Mareike Fischer, Bhalchandra D. Thatte | Revisiting an equivalence between maximum parsimony and maximum
likelihood methods in phylogenetics | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tuffley and Steel (1997) proved that Maximum Likelihood and Maximum Parsimony
methods in phylogenetics are equivalent for sequences of characters under a
simple symmetric model of substitution with no common mechanism. This result
has been widely cited ever since. We show that small changes to the model
assumptions s... | [
{
"created": "Wed, 27 Aug 2008 00:08:56 GMT",
"version": "v1"
},
{
"created": "Mon, 6 Jul 2009 16:20:44 GMT",
"version": "v2"
}
] | 2009-07-06 | [
[
"Fischer",
"Mareike",
""
],
[
"Thatte",
"Bhalchandra D.",
""
]
] | Tuffley and Steel (1997) proved that Maximum Likelihood and Maximum Parsimony methods in phylogenetics are equivalent for sequences of characters under a simple symmetric model of substitution with no common mechanism. This result has been widely cited ever since. We show that small changes to the model assumptions suf... |
2211.04730 | Marko Jusup | Hirotaka Ijima, Carolina Minte-Vera, Yi-Jay Chang, Daisuke Ochi,
Yuichi Tsuda, Marko Jusup | Inferring the ecology of north-Pacific albacore tuna from
catch-and-effort data | 9 pages, 4 figures | null | null | null | q-bio.PE q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Catch-and-effort data are among the primary sources of information for
assessing the status of terrestrial wildlife and fish. In fishery science,
elaborate stock-assessment models are fitted to such data in order to estimate
fish-population sizes and guide management decisions. Given the importance of
catch-and-effor... | [
{
"created": "Wed, 9 Nov 2022 08:01:42 GMT",
"version": "v1"
}
] | 2022-11-10 | [
[
"Ijima",
"Hirotaka",
""
],
[
"Minte-Vera",
"Carolina",
""
],
[
"Chang",
"Yi-Jay",
""
],
[
"Ochi",
"Daisuke",
""
],
[
"Tsuda",
"Yuichi",
""
],
[
"Jusup",
"Marko",
""
]
] | Catch-and-effort data are among the primary sources of information for assessing the status of terrestrial wildlife and fish. In fishery science, elaborate stock-assessment models are fitted to such data in order to estimate fish-population sizes and guide management decisions. Given the importance of catch-and-effort ... |
2303.06076 | Zedong Bi | Zedong Bi | Cognition of time and thinkings beyond | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | A pervasive research protocol of cognitive neuroscience is to train subjects
to perform deliberately designed experiments and record brain activity
simultaneously, aiming to understand the brain mechanism underlying cognition.
However, how the results of this protocol can be applied in technology is
seldom discussed.... | [
{
"created": "Wed, 8 Mar 2023 01:20:08 GMT",
"version": "v1"
}
] | 2023-03-13 | [
[
"Bi",
"Zedong",
""
]
] | A pervasive research protocol of cognitive neuroscience is to train subjects to perform deliberately designed experiments and record brain activity simultaneously, aiming to understand the brain mechanism underlying cognition. However, how the results of this protocol can be applied in technology is seldom discussed. H... |
1910.02293 | Peter Shaffery | Peter Shaffery, Bret D. Elderd, and Vanja Dukic | A Note on Species Richness and the Variance of Epidemic Severity | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The commonly observed negative correlation between the number of species in
an ecological community and disease risk, typically referred to as "the
dilution effect", has received a substantial amount of attention over the past
decade. Attempts to test this relationship experimentally have revealed that,
in addition t... | [
{
"created": "Sat, 5 Oct 2019 16:34:18 GMT",
"version": "v1"
},
{
"created": "Mon, 20 Jan 2020 20:39:50 GMT",
"version": "v2"
}
] | 2020-01-22 | [
[
"Shaffery",
"Peter",
""
],
[
"Elderd",
"Bret D.",
""
],
[
"Dukic",
"Vanja",
""
]
] | The commonly observed negative correlation between the number of species in an ecological community and disease risk, typically referred to as "the dilution effect", has received a substantial amount of attention over the past decade. Attempts to test this relationship experimentally have revealed that, in addition to ... |
0904.3844 | Guillermo Raul Zemba | Matias G. dell'Erba, Guillermo R. Zemba | Topological phase transition in a RNA model in the de Gennes regime | 15 pages, 4 figures | null | 10.1103/PhysRevE.80.041926 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study a simplified model of the RNA molecule proposed by G. Vernizzi, H.
Orland and A. Zee in the regime of strong concentration of positive ions in
solution. The model considers a flexible chain of equal bases that can pairwise
interact with any other one along the chain, while preserving the property of
saturati... | [
{
"created": "Fri, 24 Apr 2009 13:08:47 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"dell'Erba",
"Matias G.",
""
],
[
"Zemba",
"Guillermo R.",
""
]
] | We study a simplified model of the RNA molecule proposed by G. Vernizzi, H. Orland and A. Zee in the regime of strong concentration of positive ions in solution. The model considers a flexible chain of equal bases that can pairwise interact with any other one along the chain, while preserving the property of saturation... |
0904.4705 | Michael Deem | Rao Zhou, Ramdas S. Pophale, and Michael W. Deem | Computer-assisted vaccine design | 25 pages; 5 figures; 1 table; to appear in Influenza: Molecular
Virology, Horizon Scientific Press, edited by Qinghua Wang and Yizhi Jane
Tao, 2009 | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We define a new parameter to quantify the antigenic distance between two H3N2
influenza strains: we use this parameter to measure antigenic distance between
circulating H3N2 strains and the closest vaccine component of the influenza
vaccine. For the data between 1971 and 2004, the measure of antigenic distance
correl... | [
{
"created": "Wed, 29 Apr 2009 21:18:11 GMT",
"version": "v1"
},
{
"created": "Wed, 27 May 2009 21:24:17 GMT",
"version": "v2"
}
] | 2009-05-28 | [
[
"Zhou",
"Rao",
""
],
[
"Pophale",
"Ramdas S.",
""
],
[
"Deem",
"Michael W.",
""
]
] | We define a new parameter to quantify the antigenic distance between two H3N2 influenza strains: we use this parameter to measure antigenic distance between circulating H3N2 strains and the closest vaccine component of the influenza vaccine. For the data between 1971 and 2004, the measure of antigenic distance correlat... |
q-bio/0403033 | C. Soule | Christophe Soule | Graphic requirements for multistationarity | null | ComplexUs 1 (2003) 123-133 | null | null | q-bio.MN | null | We discuss properties which must be satisfied by a genetic network in order
for it to allow differentiation.
These conditions are expressed as follows in mathematical terms. Let $F$ be a
differentiable mapping from a finite dimensional real vector space to itself.
The signs of the entries of the Jacobian matrix of ... | [
{
"created": "Tue, 23 Mar 2004 16:31:35 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Soule",
"Christophe",
""
]
] | We discuss properties which must be satisfied by a genetic network in order for it to allow differentiation. These conditions are expressed as follows in mathematical terms. Let $F$ be a differentiable mapping from a finite dimensional real vector space to itself. The signs of the entries of the Jacobian matrix of $F$ ... |
0708.2121 | Ashok Palaniappan | Ashok Palaniappan | Detection of an ancient principle and an elegant solution to the protein
classification problem | 13p | null | null | null | q-bio.GN q-bio.BM q-bio.QM | null | This work is concerned with the development of a well-founded, theoretically
justified, and least complicated metric for the classification of proteins with
reference to enzymes. As the signature of an enzyme family, a catalytic domain
is easily fingerprinted. Given that the classification problem has so far
seemed i... | [
{
"created": "Thu, 16 Aug 2007 16:58:25 GMT",
"version": "v1"
}
] | 2007-08-17 | [
[
"Palaniappan",
"Ashok",
""
]
] | This work is concerned with the development of a well-founded, theoretically justified, and least complicated metric for the classification of proteins with reference to enzymes. As the signature of an enzyme family, a catalytic domain is easily fingerprinted. Given that the classification problem has so far seemed int... |
2311.16925 | Devin Greene | Devin Greene | Multiallelic Walsh transforms | null | null | null | null | q-bio.QM q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | A closed formula multiallelic Walsh (or Hadamard) transform is introduced.
Basic results are derived, and a statistical interpretation of some of the
resulting linear forms is discussed.
| [
{
"created": "Tue, 28 Nov 2023 16:30:58 GMT",
"version": "v1"
}
] | 2023-11-29 | [
[
"Greene",
"Devin",
""
]
] | A closed formula multiallelic Walsh (or Hadamard) transform is introduced. Basic results are derived, and a statistical interpretation of some of the resulting linear forms is discussed. |
2304.12378 | Gui Araujo | Gui Araujo | A framework of population dynamics from first principles | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The aim of this manuscript is to contain the arguments and define the
theoretical objects for building a general framework to model population
dynamics from the ground up, relying mainly on the probabilistic landscapes
defining the dynamics instead of the context-dependent physical specification
of systems. I intend ... | [
{
"created": "Mon, 24 Apr 2023 18:14:21 GMT",
"version": "v1"
}
] | 2023-04-26 | [
[
"Araujo",
"Gui",
""
]
] | The aim of this manuscript is to contain the arguments and define the theoretical objects for building a general framework to model population dynamics from the ground up, relying mainly on the probabilistic landscapes defining the dynamics instead of the context-dependent physical specification of systems. I intend to... |
1902.04341 | Can Firtina | Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A.
Ercument Cicek, Can Alkan, Onur Mutlu | Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate
Assembly Polishing Algorithm | 9 pages, 1 figure. Accepted in Bioinformatics | Bioinformatics . 2020 Jun 1;36(12):3669-3679 | 10.1093/bioinformatics/btaa179 | null | q-bio.GN cs.CE cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Long reads produced by third-generation sequencing technologies are used to
construct an assembly (i.e., the subject's genome), which is further used in
downstream genome analysis. Unfortunately, long reads have high sequencing
error rates and a large proportion of bps in these long reads are incorrectly
identified. ... | [
{
"created": "Tue, 12 Feb 2019 11:45:55 GMT",
"version": "v1"
},
{
"created": "Sat, 7 Mar 2020 23:31:34 GMT",
"version": "v2"
}
] | 2020-10-29 | [
[
"Firtina",
"Can",
""
],
[
"Kim",
"Jeremie S.",
""
],
[
"Alser",
"Mohammed",
""
],
[
"Cali",
"Damla Senol",
""
],
[
"Cicek",
"A. Ercument",
""
],
[
"Alkan",
"Can",
""
],
[
"Mutlu",
"Onur",
""
]
] | Long reads produced by third-generation sequencing technologies are used to construct an assembly (i.e., the subject's genome), which is further used in downstream genome analysis. Unfortunately, long reads have high sequencing error rates and a large proportion of bps in these long reads are incorrectly identified. Th... |
1506.06359 | Sandrine Pavoine | Sandrine Pavoine | A guide through a family of phylogenetic dissimilarity measures among
sites | 88 pages, including main text, 5 figures and appendixes | null | 10.1111/oik.03262 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ecological studies have now gone beyond measures of species turnover towards
measures of phylogenetic and functional dissimilarity with a main objective:
disentangling the processes that drive species distributions from local to
broad scales. A fundamental difference between phylogenetic and functional
analyses is th... | [
{
"created": "Sun, 21 Jun 2015 12:45:35 GMT",
"version": "v1"
}
] | 2018-06-26 | [
[
"Pavoine",
"Sandrine",
""
]
] | Ecological studies have now gone beyond measures of species turnover towards measures of phylogenetic and functional dissimilarity with a main objective: disentangling the processes that drive species distributions from local to broad scales. A fundamental difference between phylogenetic and functional analyses is that... |
q-bio/0703029 | M. Cristina Marchetti | Tanniemola B. Liverpool and M. Cristina Marchetti | Hydrodynamic and rheology of active polar filaments | 30 pages, 5 figures. To appear in "Cell Motility", Peter Lenz, ed.
(Springer, New York, 2007) | in "Cell Motility", P. Lenz, editor (Springer, New York, 2007) | null | null | q-bio.CB cond-mat.soft | null | The cytoskeleton provides eukaryotic cells with mechanical support and helps
them perform their biological functions. It is a network of semiflexible polar
protein filaments and many accessory proteins that bind to these filaments,
regulate their assembly, link them to organelles and continuously remodel the
network.... | [
{
"created": "Mon, 12 Mar 2007 14:47:20 GMT",
"version": "v1"
}
] | 2008-01-01 | [
[
"Liverpool",
"Tanniemola B.",
""
],
[
"Marchetti",
"M. Cristina",
""
]
] | The cytoskeleton provides eukaryotic cells with mechanical support and helps them perform their biological functions. It is a network of semiflexible polar protein filaments and many accessory proteins that bind to these filaments, regulate their assembly, link them to organelles and continuously remodel the network. H... |
2311.00085 | Brian Camley | Wei Wang and Brian A. Camley | Limits on the accuracy of contact inhibition of locomotion | null | Phys. Rev. E 109, 054408 (2024) | 10.1103/PhysRevE.109.054408 | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cells that collide with each other repolarize away from contact, in a process
called contact inhibition of locomotion (CIL), which is necessary for correct
development of the embryo. CIL can occur even when cells make a micron-scale
contact with a neighbor - much smaller than their size. How precisely can a
cell sens... | [
{
"created": "Tue, 31 Oct 2023 18:52:48 GMT",
"version": "v1"
}
] | 2024-06-17 | [
[
"Wang",
"Wei",
""
],
[
"Camley",
"Brian A.",
""
]
] | Cells that collide with each other repolarize away from contact, in a process called contact inhibition of locomotion (CIL), which is necessary for correct development of the embryo. CIL can occur even when cells make a micron-scale contact with a neighbor - much smaller than their size. How precisely can a cell sense ... |
2310.19950 | Reza Bozorgpour | Reza Bozorgpour, Sana Sheybanikashani, Matin Mohebi | Exploring the Role of Molecular Dynamics Simulations in Most Recent
Cancer Research: Insights into Treatment Strategies | 49 pages, 2 figures | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Cancer is a complex disease that is characterized by uncontrolled growth and
division of cells. It involves a complex interplay between genetic and
environmental factors that lead to the initiation and progression of tumors.
Recent advances in molecular dynamics simulations have revolutionized our
understanding of th... | [
{
"created": "Mon, 30 Oct 2023 19:01:55 GMT",
"version": "v1"
}
] | 2023-11-01 | [
[
"Bozorgpour",
"Reza",
""
],
[
"Sheybanikashani",
"Sana",
""
],
[
"Mohebi",
"Matin",
""
]
] | Cancer is a complex disease that is characterized by uncontrolled growth and division of cells. It involves a complex interplay between genetic and environmental factors that lead to the initiation and progression of tumors. Recent advances in molecular dynamics simulations have revolutionized our understanding of the ... |
2308.07586 | Zachary Sexton | Zachary A. Sexton, Andrew R. Hudson, Jessica E. Herrmann, Dan J.
Shiwarski, Jonathan Pham, Jason M. Szafron, Sean M. Wu, Mark Skylar-Scott,
Adam W. Feinberg, Alison Marsden | Rapid model-guided design of organ-scale synthetic vasculature for
biomanufacturing | 58 pages (19 main and 39 supplement pages), 4 main figures, 9
supplement figures | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Our ability to produce human-scale bio-manufactured organs is critically
limited by the need for vascularization and perfusion. For tissues of variable
size and shape, including arbitrarily complex geometries, designing and
printing vasculature capable of adequate perfusion has posed a major hurdle.
Here, we introduc... | [
{
"created": "Tue, 15 Aug 2023 06:16:52 GMT",
"version": "v1"
}
] | 2023-08-16 | [
[
"Sexton",
"Zachary A.",
""
],
[
"Hudson",
"Andrew R.",
""
],
[
"Herrmann",
"Jessica E.",
""
],
[
"Shiwarski",
"Dan J.",
""
],
[
"Pham",
"Jonathan",
""
],
[
"Szafron",
"Jason M.",
""
],
[
"Wu",
"Sean M.",
""... | Our ability to produce human-scale bio-manufactured organs is critically limited by the need for vascularization and perfusion. For tissues of variable size and shape, including arbitrarily complex geometries, designing and printing vasculature capable of adequate perfusion has posed a major hurdle. Here, we introduce ... |
1710.11413 | Johann H. Mart\'inez | J. H. Mart\'inez, J. M. Buld\'u, D. Papo, F. De Vico Fallani and M.
Chavez | Role of inter-hemispheric connections in functional brain networks | 12 pages 5 figures (main), 9 pages and 8 figures (Supp Info) | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Today the human brain can be modeled as a graph where nodes represent
different regions and links stand for statistical interactions between their
activities as recorded by different neuroimaging techniques. Empirical studies
have lead to the hypothesis that brain functions rely on the coordination of a
scattered mos... | [
{
"created": "Tue, 31 Oct 2017 11:37:55 GMT",
"version": "v1"
}
] | 2017-11-01 | [
[
"Martínez",
"J. H.",
""
],
[
"Buldú",
"J. M.",
""
],
[
"Papo",
"D.",
""
],
[
"Fallani",
"F. De Vico",
""
],
[
"Chavez",
"M.",
""
]
] | Today the human brain can be modeled as a graph where nodes represent different regions and links stand for statistical interactions between their activities as recorded by different neuroimaging techniques. Empirical studies have lead to the hypothesis that brain functions rely on the coordination of a scattered mosai... |
1909.11451 | Geoffrey Iwata | Geoffrey Z. Iwata, Yinan Hu, Tilmann Sander, Muthuraman Muthuraman,
Venkata Chaitanya Chirumamilla, Sergiu Groppa, Dmitry Budker, and Arne
Wickenbrock | Biomagnetic signals recorded during transcranial magnetic stimulation
(TMS)-evoked peripheral muscular activity | 16 pages, 4 figures | null | null | null | q-bio.NC eess.SP physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objective: We present magnetomyograms (MMG) of TMS-evoked movement in a human
hand, together with a simultaneous surface electromyograph (EMG) and
electroencephalograph (EEG) data. Approach: We combined TMS with non-contact
magnetic detection of TMS-evoked muscle activity in peripheral limbs to explore
a new diagnost... | [
{
"created": "Wed, 25 Sep 2019 12:46:27 GMT",
"version": "v1"
},
{
"created": "Tue, 19 May 2020 15:03:40 GMT",
"version": "v2"
}
] | 2020-05-20 | [
[
"Iwata",
"Geoffrey Z.",
""
],
[
"Hu",
"Yinan",
""
],
[
"Sander",
"Tilmann",
""
],
[
"Muthuraman",
"Muthuraman",
""
],
[
"Chirumamilla",
"Venkata Chaitanya",
""
],
[
"Groppa",
"Sergiu",
""
],
[
"Budker",
"Dmitry... | Objective: We present magnetomyograms (MMG) of TMS-evoked movement in a human hand, together with a simultaneous surface electromyograph (EMG) and electroencephalograph (EEG) data. Approach: We combined TMS with non-contact magnetic detection of TMS-evoked muscle activity in peripheral limbs to explore a new diagnostic... |
2201.05198 | Konstantinos Xylogiannopoulos | Konstantinos Xylogiannopoulos | Multiple Genome Analytics Framework: The Case of All SARS-CoV-2 Complete
Variants | null | null | null | null | q-bio.GN cs.DS | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Pattern detection and string matching are fundamental problems in computer
science and the accelerated expansion of bioinformatics and computational
biology have made them a core topic for both disciplines. The SARS-CoV-2
pandemic has made such problems more demanding with hundreds or thousands of
new genome variants... | [
{
"created": "Thu, 13 Jan 2022 20:19:35 GMT",
"version": "v1"
}
] | 2022-01-17 | [
[
"Xylogiannopoulos",
"Konstantinos",
""
]
] | Pattern detection and string matching are fundamental problems in computer science and the accelerated expansion of bioinformatics and computational biology have made them a core topic for both disciplines. The SARS-CoV-2 pandemic has made such problems more demanding with hundreds or thousands of new genome variants d... |
2203.00722 | Lukas Brand | Lukas Brand, Moritz Garkisch, Sebastian Lotter, Maximilian Sch\"afer,
Andreas Burkovski, Heinrich Sticht, Kathrin Castiglione, and Robert Schober | Media Modulation based Molecular Communication | 16 pages double-column, 9 figures, 1 table. This work has been
published in IEEE Transactions on Communications | in IEEE Trans. Commun., vol. 70, no. 11, pp. 7207-7223, Nov. 2022 | 10.1109/TCOMM.2022.3205949 | null | q-bio.BM cs.ET | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In conventional molecular communication (MC) systems, the signaling molecules
used for information transmission are stored, released, and then replenished by
a transmitter (TX). However, the replenishment of signaling molecules at the TX
is challenging in practice. Furthermore, in most envisioned MC applications,
e.g... | [
{
"created": "Tue, 1 Mar 2022 19:54:16 GMT",
"version": "v1"
},
{
"created": "Tue, 15 Aug 2023 14:41:01 GMT",
"version": "v2"
}
] | 2023-08-16 | [
[
"Brand",
"Lukas",
""
],
[
"Garkisch",
"Moritz",
""
],
[
"Lotter",
"Sebastian",
""
],
[
"Schäfer",
"Maximilian",
""
],
[
"Burkovski",
"Andreas",
""
],
[
"Sticht",
"Heinrich",
""
],
[
"Castiglione",
"Kathrin",
... | In conventional molecular communication (MC) systems, the signaling molecules used for information transmission are stored, released, and then replenished by a transmitter (TX). However, the replenishment of signaling molecules at the TX is challenging in practice. Furthermore, in most envisioned MC applications, e.g.,... |
0907.4115 | Davide Cora | Angela Re, Davide Cora', Daniela Taverna and Michele Caselle | Genome-Wide Survey of MicroRNA - Transcription Factor Feed-Forward
Regulatory Circuits in Human | 51 pages, 5 figures, 4 tables. Supporting information included.
Accepted for publication in Molecular BioSystems | Mol Biosyst. 2009 Aug;5(8):854-67 | 10.1039/b900177h | null | q-bio.GN q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work, we describe a computational framework for the genome-wide
identification and characterization of mixed
transcriptional/post-transcriptional regulatory circuits in humans. We
concentrated in particular on feed-forward loops (FFL), in which a master
transcription factor regulates a microRNA, and together ... | [
{
"created": "Thu, 23 Jul 2009 16:36:16 GMT",
"version": "v1"
}
] | 2009-07-24 | [
[
"Re",
"Angela",
""
],
[
"Cora'",
"Davide",
""
],
[
"Taverna",
"Daniela",
""
],
[
"Caselle",
"Michele",
""
]
] | In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops (FFL), in which a master transcription factor regulates a microRNA, and together wi... |
1611.02597 | Gerardo F. Goya | Beatriz Sanz, M. Pilar Calatayud, Teobaldo E. Torres, M\'onica L.
Fanarraga, M. Ricardo Ibarra and Gerardo F. Goya | Magnetic hyperthermia enhances cell toxicity with respect to exogenous
heating | 32 pages, Biomaterials 2017 | null | 10.1016/j.biomaterials.2016.11.008 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Magnetic hyperthermia is a new type of cancer treatment designed for
overcoming resistance to chemotherapy during the treatment of solid,
inaccessible human tumors. The main challenge of this technology is increasing
the local tumoral temperature with minimal side effects on the surrounding
healthy tissue. This work ... | [
{
"created": "Mon, 7 Nov 2016 14:04:03 GMT",
"version": "v1"
}
] | 2016-11-09 | [
[
"Sanz",
"Beatriz",
""
],
[
"Calatayud",
"M. Pilar",
""
],
[
"Torres",
"Teobaldo E.",
""
],
[
"Fanarraga",
"Mónica L.",
""
],
[
"Ibarra",
"M. Ricardo",
""
],
[
"Goya",
"Gerardo F.",
""
]
] | Magnetic hyperthermia is a new type of cancer treatment designed for overcoming resistance to chemotherapy during the treatment of solid, inaccessible human tumors. The main challenge of this technology is increasing the local tumoral temperature with minimal side effects on the surrounding healthy tissue. This work co... |
2309.04924 | Jai Pal | Bryan Hong, Jai Pal | MATLAB Plasmonic Nanoparticle Virion Counting and Interpretation System
in Urban Populations | 11 Pages, 16 Figures, Presented at 5 conferences | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | One of the biggest issues currently plaguing the field of medicine is the
lack of an accurate and efficient form of disease diagnosis especially in urban
settings such as major cities. For example, the two most commonly utilized test
diagnosis systems, the PCR and rapid test, sacrifice either accuracy or speed
to ach... | [
{
"created": "Sun, 10 Sep 2023 03:05:57 GMT",
"version": "v1"
},
{
"created": "Thu, 7 Dec 2023 15:46:43 GMT",
"version": "v2"
},
{
"created": "Tue, 9 Jan 2024 02:26:41 GMT",
"version": "v3"
}
] | 2024-01-10 | [
[
"Hong",
"Bryan",
""
],
[
"Pal",
"Jai",
""
]
] | One of the biggest issues currently plaguing the field of medicine is the lack of an accurate and efficient form of disease diagnosis especially in urban settings such as major cities. For example, the two most commonly utilized test diagnosis systems, the PCR and rapid test, sacrifice either accuracy or speed to achie... |
1302.5801 | Michael B\"orsch | Hendrik Sielaff, Thomas Heitkamp, Andrea Zappe, Nawid Zarrabi, Michael
Boersch | Subunit rotation in single FRET-labeled F1-ATPase hold in solution by an
anti-Brownian electrokinetic trap | 12 pages, 3 figures | null | 10.1117/12.2002955 | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | FoF1-ATP synthase catalyzes the synthesis of adenosine triphosphate (ATP).
The F1 portion can be stripped from the membrane-embedded Fo portion of the
enzyme. F1 acts as an ATP hydrolyzing enzyme, and ATP hydrolysis is associated
with stepwise rotation of the gamma and epsilon subunits of F1. This rotary
motion was s... | [
{
"created": "Sat, 23 Feb 2013 14:06:37 GMT",
"version": "v1"
}
] | 2018-02-14 | [
[
"Sielaff",
"Hendrik",
""
],
[
"Heitkamp",
"Thomas",
""
],
[
"Zappe",
"Andrea",
""
],
[
"Zarrabi",
"Nawid",
""
],
[
"Boersch",
"Michael",
""
]
] | FoF1-ATP synthase catalyzes the synthesis of adenosine triphosphate (ATP). The F1 portion can be stripped from the membrane-embedded Fo portion of the enzyme. F1 acts as an ATP hydrolyzing enzyme, and ATP hydrolysis is associated with stepwise rotation of the gamma and epsilon subunits of F1. This rotary motion was stu... |
2012.00068 | Iaroslav Ispolatov | Michael Doebeli, Eduardo Cancino Jaque, Iaroslav Ispolatov | Boom-bust population dynamics can increase diversity in evolving
competitive communities | 37 pages, 9 figures | null | null | null | q-bio.PE cond-mat.dis-nn nlin.CD | http://creativecommons.org/licenses/by/4.0/ | The processes and mechanisms underlying the origin and maintenance of
biological diversity have long been of central importance in ecology and
evolution. The competitive exclusion principle states that the number of
coexisting species is limited by the number of resources, or by the species'
similarity in resource us... | [
{
"created": "Mon, 30 Nov 2020 19:41:11 GMT",
"version": "v1"
}
] | 2020-12-02 | [
[
"Doebeli",
"Michael",
""
],
[
"Jaque",
"Eduardo Cancino",
""
],
[
"Ispolatov",
"Iaroslav",
""
]
] | The processes and mechanisms underlying the origin and maintenance of biological diversity have long been of central importance in ecology and evolution. The competitive exclusion principle states that the number of coexisting species is limited by the number of resources, or by the species' similarity in resource use.... |
1503.05575 | Vince Grolmusz | Csaba Kerepesi and Vince Grolmusz | The "Giant Virus Finder" Discovers an Abundance of Giant Viruses in the
Antarctic Dry Valleys | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The first giant virus was identified in 2003 from a biofilm of an industrial
water-cooling tower in England. Later, numerous new giant viruses were found in
oceans and freshwater habitats, some of them having even 2,500 genes. We have
demonstrated their very likely presence in four soil samples taken from the
Kutch D... | [
{
"created": "Wed, 18 Mar 2015 20:33:18 GMT",
"version": "v1"
},
{
"created": "Wed, 5 Aug 2015 11:34:07 GMT",
"version": "v2"
},
{
"created": "Tue, 24 Nov 2015 21:17:08 GMT",
"version": "v3"
}
] | 2015-11-26 | [
[
"Kerepesi",
"Csaba",
""
],
[
"Grolmusz",
"Vince",
""
]
] | The first giant virus was identified in 2003 from a biofilm of an industrial water-cooling tower in England. Later, numerous new giant viruses were found in oceans and freshwater habitats, some of them having even 2,500 genes. We have demonstrated their very likely presence in four soil samples taken from the Kutch Des... |
1009.5667 | Kyung Hyuk Kim | Kyung Hyuk Kim and Herbert M. Sauro | Fan-out in Gene Regulatory Networks | 28 pages, 5 figures | Journal of Biological Engineering 2010, 4:16 | 10.1186/1754-1611-4-16 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In synthetic biology, gene regulatory circuits are often constructed by
combining smaller circuit components. Connections between components are
achieved by transcription factors acting on promoters. If the individual
components behave as true modules and certain module interface conditions are
satisfied, the functio... | [
{
"created": "Tue, 28 Sep 2010 19:51:13 GMT",
"version": "v1"
}
] | 2011-02-15 | [
[
"Kim",
"Kyung Hyuk",
""
],
[
"Sauro",
"Herbert M.",
""
]
] | In synthetic biology, gene regulatory circuits are often constructed by combining smaller circuit components. Connections between components are achieved by transcription factors acting on promoters. If the individual components behave as true modules and certain module interface conditions are satisfied, the function ... |
2305.09480 | Cheng Tan | Cheng Tan, Zhangyang Gao, Lirong Wu, Jun Xia, Jiangbin Zheng, Xihong
Yang, Yue Liu, Bozhen Hu, Stan Z. Li | Cross-Gate MLP with Protein Complex Invariant Embedding is A One-Shot
Antibody Designer | Accepted by AAAI 2024 | null | null | null | q-bio.BM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Antibodies are crucial proteins produced by the immune system in response to
foreign substances or antigens. The specificity of an antibody is determined by
its complementarity-determining regions (CDRs), which are located in the
variable domains of the antibody chains and form the antigen-binding site.
Previous stud... | [
{
"created": "Fri, 21 Apr 2023 13:24:26 GMT",
"version": "v1"
},
{
"created": "Wed, 17 May 2023 13:13:00 GMT",
"version": "v2"
},
{
"created": "Sat, 20 May 2023 10:30:02 GMT",
"version": "v3"
},
{
"created": "Thu, 28 Dec 2023 06:33:30 GMT",
"version": "v4"
},
{
"c... | 2024-01-11 | [
[
"Tan",
"Cheng",
""
],
[
"Gao",
"Zhangyang",
""
],
[
"Wu",
"Lirong",
""
],
[
"Xia",
"Jun",
""
],
[
"Zheng",
"Jiangbin",
""
],
[
"Yang",
"Xihong",
""
],
[
"Liu",
"Yue",
""
],
[
"Hu",
"Bozhen",
... | Antibodies are crucial proteins produced by the immune system in response to foreign substances or antigens. The specificity of an antibody is determined by its complementarity-determining regions (CDRs), which are located in the variable domains of the antibody chains and form the antigen-binding site. Previous studie... |
q-bio/0503026 | Neda Zoltan | Z. Neda and M. Ravasz | Species Abundances Distribution in Neutral Community Models | Revtex, 13 pages, 3 figures | null | null | null | q-bio.PE q-bio.QM | null | An analytical approximation is derived for the Zero Sum Multinomial
distribution which gives the Species Abundance Distribution in Neutral
Community Models. The obtained distribution function describes well computer
simulation results on the model, and leads to an interesting relation between
the total number of indi... | [
{
"created": "Thu, 17 Mar 2005 09:51:16 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Neda",
"Z.",
""
],
[
"Ravasz",
"M.",
""
]
] | An analytical approximation is derived for the Zero Sum Multinomial distribution which gives the Species Abundance Distribution in Neutral Community Models. The obtained distribution function describes well computer simulation results on the model, and leads to an interesting relation between the total number of indivi... |
2005.06938 | Rolf Bader | Lenz Hartmann, Rolf Bader | Neural Synchronization of Music Large-Scale Form | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Music large-scale form, the structure of musical units ranging over several
bars, are studied using EEG measurements of 25 participants listened to the
first four minutes of a piece of electronic dance music (EDM). Grand-averages
of event-related potentials (ERPs) calculated for all electrodes show dynamics
in phase ... | [
{
"created": "Thu, 14 May 2020 13:18:29 GMT",
"version": "v1"
}
] | 2020-05-15 | [
[
"Hartmann",
"Lenz",
""
],
[
"Bader",
"Rolf",
""
]
] | Music large-scale form, the structure of musical units ranging over several bars, are studied using EEG measurements of 25 participants listened to the first four minutes of a piece of electronic dance music (EDM). Grand-averages of event-related potentials (ERPs) calculated for all electrodes show dynamics in phase sy... |
2211.15667 | Thomas Jacob | Harsh Shah, Thomas Jacob, Amruta Parulekar, Anjali Amarapurkar, Amit
Sethi | Artificial Intelligence-based Eosinophil Counting in Gastrointestinal
Biopsies | 4 pages, 2 figures | null | null | null | q-bio.QM cs.CV eess.IV | http://creativecommons.org/licenses/by/4.0/ | Normally eosinophils are present in the gastrointestinal (GI) tract of
healthy individuals. When the eosinophils increase beyond their usual amount in
the GI tract, a patient gets varied symptoms. Clinicians find it difficult to
diagnose this condition called eosinophilia. Early diagnosis can help in
treating patient... | [
{
"created": "Fri, 25 Nov 2022 07:18:28 GMT",
"version": "v1"
}
] | 2022-11-30 | [
[
"Shah",
"Harsh",
""
],
[
"Jacob",
"Thomas",
""
],
[
"Parulekar",
"Amruta",
""
],
[
"Amarapurkar",
"Anjali",
""
],
[
"Sethi",
"Amit",
""
]
] | Normally eosinophils are present in the gastrointestinal (GI) tract of healthy individuals. When the eosinophils increase beyond their usual amount in the GI tract, a patient gets varied symptoms. Clinicians find it difficult to diagnose this condition called eosinophilia. Early diagnosis can help in treating patients.... |
1304.5031 | Yu-Fei He | Min Hu, Yu-Fei He | Tumor can originate from not only rare cancer stem cells | This work was finished 4 years ago and is still valuable nowadays | null | null | null | q-bio.CB q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tumors are believed to consist of a heterogeneous population of tumor cells
originating from rare cancer stem cells (CSCs). However, emerging evidences
show that tumor may also originate from non-CSCs. Here, we give evidences
supporting that the number of tumorigenic tumor cells is higher than the number
of CSCs and ... | [
{
"created": "Thu, 18 Apr 2013 06:26:56 GMT",
"version": "v1"
}
] | 2013-04-19 | [
[
"Hu",
"Min",
""
],
[
"He",
"Yu-Fei",
""
]
] | Tumors are believed to consist of a heterogeneous population of tumor cells originating from rare cancer stem cells (CSCs). However, emerging evidences show that tumor may also originate from non-CSCs. Here, we give evidences supporting that the number of tumorigenic tumor cells is higher than the number of CSCs and tu... |
1908.10523 | Dan Chen | Dan Chen, Yusuke Kikuchi, Kenichiro Fujiyama, Shunsuke Akimoto, Shinji
Oominato, Toshihiro Hasegawa | Improving the soil water module of the Decision Support System for
Agrotechnology Transfer cropping system model for subsurface irrigation | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ensuring that crops use water and nutrients efficiently is an important
strategy for increasing the profitability of farming and reducing the
environmental load from agriculture. Subsurface irrigation can be an
alternative to surface irrigation as a means of losing less irrigation water,
but the application timing an... | [
{
"created": "Wed, 28 Aug 2019 02:25:19 GMT",
"version": "v1"
}
] | 2019-08-29 | [
[
"Chen",
"Dan",
""
],
[
"Kikuchi",
"Yusuke",
""
],
[
"Fujiyama",
"Kenichiro",
""
],
[
"Akimoto",
"Shunsuke",
""
],
[
"Oominato",
"Shinji",
""
],
[
"Hasegawa",
"Toshihiro",
""
]
] | Ensuring that crops use water and nutrients efficiently is an important strategy for increasing the profitability of farming and reducing the environmental load from agriculture. Subsurface irrigation can be an alternative to surface irrigation as a means of losing less irrigation water, but the application timing and ... |
2405.18587 | Gorka Zamora-L\'opez | Rapha\"el Bergoin and Alessandro Torcini and Gustavo Deco and Mathias
Quoy and Gorka Zamora-L\'opez | Emergence and long-term maintenance of modularity in plastic networks of
spiking neurons | 28 pages, 11 figures | null | null | null | q-bio.NC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the last three decades it has become clear that cortical regions,
interconnected via white-matter fibers, form a modular and hierarchical
network. This organization, which has also been seen at the microscopic level
in the form of interconnected neural assemblies, is believed to support the
coexistence of segregat... | [
{
"created": "Tue, 28 May 2024 21:07:53 GMT",
"version": "v1"
},
{
"created": "Sat, 13 Jul 2024 10:36:25 GMT",
"version": "v2"
}
] | 2024-07-16 | [
[
"Bergoin",
"Raphaël",
""
],
[
"Torcini",
"Alessandro",
""
],
[
"Deco",
"Gustavo",
""
],
[
"Quoy",
"Mathias",
""
],
[
"Zamora-López",
"Gorka",
""
]
] | In the last three decades it has become clear that cortical regions, interconnected via white-matter fibers, form a modular and hierarchical network. This organization, which has also been seen at the microscopic level in the form of interconnected neural assemblies, is believed to support the coexistence of segregatio... |
2305.08830 | Josinaldo Menezes | J. Menezes and M. Tenorio | Spatial patterns and biodiversity in rock-paper-scissors models with
regional unevenness | 17 pages, 7 figures | Journal of Physics: Complexity 4, 025015 (2023) | 10.1088/2632-072X/acd610 | null | q-bio.PE nlin.AO nlin.PS physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Climate changes may affect ecosystems destabilising relationships among
species. We investigate the spatial rock-paper-scissors models with a regional
unevenness that reduces the selection capacity of organisms of one species. Our
results show that the regionally weak species predominates in the local
ecosystem, whil... | [
{
"created": "Mon, 15 May 2023 17:45:50 GMT",
"version": "v1"
}
] | 2023-06-06 | [
[
"Menezes",
"J.",
""
],
[
"Tenorio",
"M.",
""
]
] | Climate changes may affect ecosystems destabilising relationships among species. We investigate the spatial rock-paper-scissors models with a regional unevenness that reduces the selection capacity of organisms of one species. Our results show that the regionally weak species predominates in the local ecosystem, while ... |
1712.09462 | Tetsuya Kobayashi | Tetsuya J. Kobayashi and Yuki Sughiyama | Individual Sensing can Gain more Fitness than its Information | 5figures | null | null | null | q-bio.PE physics.bio-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mutual information and its causal variant, directed information, have been
widely used to quantitatively characterize the performance of biological
sensing and information transduction. However, once coupled with selection in
response to decision-making, the sensing signal could have more or less
evolutionary value t... | [
{
"created": "Wed, 27 Dec 2017 00:15:39 GMT",
"version": "v1"
}
] | 2017-12-29 | [
[
"Kobayashi",
"Tetsuya J.",
""
],
[
"Sughiyama",
"Yuki",
""
]
] | Mutual information and its causal variant, directed information, have been widely used to quantitatively characterize the performance of biological sensing and information transduction. However, once coupled with selection in response to decision-making, the sensing signal could have more or less evolutionary value tha... |
2406.11178 | Nathaniel Linden | Nathaniel Linden-Santangeli, Jin Zhang, Boris Kramer, Padmini
Rangamani | Increasing certainty in systems biology models using Bayesian multimodel
inference | 25 pages; 5 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Mathematical models are indispensable to the system biology toolkit for
studying the structure and behavior of intracellular signaling networks. A
common approach to modeling is to develop a system of equations that encode the
known biology using approximations and simplifying assumptions. As a result,
the same signa... | [
{
"created": "Mon, 17 Jun 2024 03:30:20 GMT",
"version": "v1"
}
] | 2024-06-18 | [
[
"Linden-Santangeli",
"Nathaniel",
""
],
[
"Zhang",
"Jin",
""
],
[
"Kramer",
"Boris",
""
],
[
"Rangamani",
"Padmini",
""
]
] | Mathematical models are indispensable to the system biology toolkit for studying the structure and behavior of intracellular signaling networks. A common approach to modeling is to develop a system of equations that encode the known biology using approximations and simplifying assumptions. As a result, the same signali... |
q-bio/0608006 | Ulrich S. Schwarz | Ulrich S. Schwarz, Thorsten Erdmann and Ilka B. Bischofs (Heidelberg
University) | Focal adhesions as mechanosensors: the two-spring model | Latex, 17 pages, 5 postscript figures included | BioSystems 83: 225-232 (2006) | null | null | q-bio.SC q-bio.BM | null | Adhesion-dependent cells actively sense the mechanical properties of their
environment through mechanotransductory processes at focal adhesions, which are
integrin-based contacts connecting the extracellular matrix to the
cytoskeleton. Here we present first steps towards a quantitative understanding
of focal adhesion... | [
{
"created": "Thu, 3 Aug 2006 15:38:57 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Schwarz",
"Ulrich S.",
"",
"Heidelberg\n University"
],
[
"Erdmann",
"Thorsten",
"",
"Heidelberg\n University"
],
[
"Bischofs",
"Ilka B.",
"",
"Heidelberg\n University"
]
] | Adhesion-dependent cells actively sense the mechanical properties of their environment through mechanotransductory processes at focal adhesions, which are integrin-based contacts connecting the extracellular matrix to the cytoskeleton. Here we present first steps towards a quantitative understanding of focal adhesions ... |
1211.2160 | Christophe Dessimoz | Stefano Iantorno, Kevin Gori, Nick Goldman, Manuel Gil, and Christophe
Dessimoz | Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple
Sequence Alignment | Review | Methods Mol Biol. 2014;1079:59-73 | 10.1007/978-1-62703-646-7_4 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique
in bioinformatics used to infer related residues among biological sequences.
Thus alignment accuracy is crucial to a vast range of analyses, often in ways
difficult to assess in those analyses. To compare the performance of different
aligners... | [
{
"created": "Fri, 9 Nov 2012 15:26:44 GMT",
"version": "v1"
}
] | 2015-01-09 | [
[
"Iantorno",
"Stefano",
""
],
[
"Gori",
"Kevin",
""
],
[
"Goldman",
"Nick",
""
],
[
"Gil",
"Manuel",
""
],
[
"Dessimoz",
"Christophe",
""
]
] | Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners a... |
1907.12071 | Xiaohan Lin | Yuanyuan Mi, Xiaohan Lin, Xiaolong Zou, Zilong Ji, Tiejun Huang, Si Wu | Spatiotemporal Information Processing with a Reservoir Decision-making
Network | 9 pages, 6 figures | null | null | null | q-bio.NC cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spatiotemporal information processing is fundamental to brain functions. The
present study investigates a canonic neural network model for spatiotemporal
pattern recognition. Specifically, the model consists of two modules, a
reservoir subnetwork and a decision-making subnetwork. The former projects
complex spatiotem... | [
{
"created": "Sun, 28 Jul 2019 11:04:34 GMT",
"version": "v1"
}
] | 2019-07-30 | [
[
"Mi",
"Yuanyuan",
""
],
[
"Lin",
"Xiaohan",
""
],
[
"Zou",
"Xiaolong",
""
],
[
"Ji",
"Zilong",
""
],
[
"Huang",
"Tiejun",
""
],
[
"Wu",
"Si",
""
]
] | Spatiotemporal information processing is fundamental to brain functions. The present study investigates a canonic neural network model for spatiotemporal pattern recognition. Specifically, the model consists of two modules, a reservoir subnetwork and a decision-making subnetwork. The former projects complex spatiotempo... |
2002.04945 | Tianyu Zeng | Tianyu Zeng, Yunong Zhang, Zhenyu Li, Xiao Liu, and Binbin Qiu | Predictions of 2019-nCoV Transmission Ending via Comprehensive Methods | null | null | null | null | q-bio.PE cs.LG physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Since the SARS outbreak in 2003, a lot of predictive epidemiological models
have been proposed. At the end of 2019, a novel coronavirus, termed as
2019-nCoV, has broken out and is propagating in China and the world. Here we
propose a multi-model ordinary differential equation set neural network
(MMODEs-NN) and model-... | [
{
"created": "Wed, 12 Feb 2020 12:26:08 GMT",
"version": "v1"
},
{
"created": "Thu, 20 Feb 2020 06:08:07 GMT",
"version": "v2"
}
] | 2020-02-21 | [
[
"Zeng",
"Tianyu",
""
],
[
"Zhang",
"Yunong",
""
],
[
"Li",
"Zhenyu",
""
],
[
"Liu",
"Xiao",
""
],
[
"Qiu",
"Binbin",
""
]
] | Since the SARS outbreak in 2003, a lot of predictive epidemiological models have been proposed. At the end of 2019, a novel coronavirus, termed as 2019-nCoV, has broken out and is propagating in China and the world. Here we propose a multi-model ordinary differential equation set neural network (MMODEs-NN) and model-fr... |
2105.07069 | Joshua Faskowitz | Joshua Faskowitz, Richard F. Betzel, Olaf Sporns | Edges in Brain Networks: Contributions to Models of Structure and
Function | 35 pages, 4 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Network models describe the brain as sets of nodes and edges that represent
its distributed organization. So far, most discoveries in network neuroscience
have prioritized insights that highlight distinct groupings and specialized
functional contributions of network nodes. Importantly, these functional
contributions ... | [
{
"created": "Fri, 14 May 2021 21:12:53 GMT",
"version": "v1"
}
] | 2021-05-18 | [
[
"Faskowitz",
"Joshua",
""
],
[
"Betzel",
"Richard F.",
""
],
[
"Sporns",
"Olaf",
""
]
] | Network models describe the brain as sets of nodes and edges that represent its distributed organization. So far, most discoveries in network neuroscience have prioritized insights that highlight distinct groupings and specialized functional contributions of network nodes. Importantly, these functional contributions ar... |
1008.3358 | P. Grassberger | Orion Penner, Peter Grassberger, Maya Paczuski | Sequence alignment, mutual information, and dissimilarity measures for
constructing phylogenies | 19 pages + 16 pages of supplementary material | PloS one, Vol. 6, No. 1. (4 January 2011) | 10.1371/journal.pone.0014373 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Existing sequence alignment algorithms use heuristic scoring schemes which
cannot be used as objective distance metrics. Therefore one relies on measures
like the p- or log-det distances, or makes explicit, and often simplistic,
assumptions about sequence evolution. Information theory provides an
alternative, in the ... | [
{
"created": "Thu, 19 Aug 2010 17:26:27 GMT",
"version": "v1"
}
] | 2015-05-19 | [
[
"Penner",
"Orion",
""
],
[
"Grassberger",
"Peter",
""
],
[
"Paczuski",
"Maya",
""
]
] | Existing sequence alignment algorithms use heuristic scoring schemes which cannot be used as objective distance metrics. Therefore one relies on measures like the p- or log-det distances, or makes explicit, and often simplistic, assumptions about sequence evolution. Information theory provides an alternative, in the fo... |
1008.1359 | Alexander Bershadskii | A. Bershadskii | Dynamic cluster-scaling in DNA | null | Physics Letters A 375 (2011) 335-338 | 10.1016/j.physleta.2010.11.039 | null | q-bio.BM nlin.CD q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is shown that the nucleotide sequences in DNA molecules have
cluster-scaling properties (discovered for the first time in turbulent
processes: Sreenivasan and Bershadskii, 2006, J. Stat. Phys., 125, 1141-1153.).
These properties are relevant to both types of nucleotide pair-bases
interactions: hydrogen bonds and s... | [
{
"created": "Sat, 7 Aug 2010 18:47:31 GMT",
"version": "v1"
}
] | 2011-03-04 | [
[
"Bershadskii",
"A.",
""
]
] | It is shown that the nucleotide sequences in DNA molecules have cluster-scaling properties (discovered for the first time in turbulent processes: Sreenivasan and Bershadskii, 2006, J. Stat. Phys., 125, 1141-1153.). These properties are relevant to both types of nucleotide pair-bases interactions: hydrogen bonds and sta... |
2008.11602 | Jorge Vila | Jorge A. Vila | About the Protein Space Vastness | A Letter of 9 pages without figures, tables, or supporting
information | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An accurate estimation of the Protein Space size, in light of the factors
that govern it, is a long-standing problem and of paramount importance in
evolutionary biology, since it determines the nature of protein evolvability. A
simple analysis will enable us to, firstly, reduce an unrealistic Protein Space
size of ~1... | [
{
"created": "Wed, 26 Aug 2020 14:57:15 GMT",
"version": "v1"
}
] | 2020-08-27 | [
[
"Vila",
"Jorge A.",
""
]
] | An accurate estimation of the Protein Space size, in light of the factors that govern it, is a long-standing problem and of paramount importance in evolutionary biology, since it determines the nature of protein evolvability. A simple analysis will enable us to, firstly, reduce an unrealistic Protein Space size of ~10^... |
1803.10653 | Karolis Misiunas | Karolis Misiunas, Niklas Ermann, Ulrich F. Keyser | QuipuNet: convolutional neural network for single-molecule nanopore
sensing | null | Nano Lett. 18, 6, 4040-4045 (2018) | 10.1021/acs.nanolett.8b01709 | null | q-bio.QM physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nanopore sensing is a versatile technique for the analysis of molecules on
the single-molecule level. However, extracting information from data with
established algorithms usually requires time-consuming checks by an experienced
researcher due to inherent variability of solid-state nanopores. Here, we
develop a convo... | [
{
"created": "Tue, 27 Mar 2018 17:22:39 GMT",
"version": "v1"
},
{
"created": "Wed, 18 Apr 2018 16:54:57 GMT",
"version": "v2"
},
{
"created": "Tue, 29 May 2018 17:08:33 GMT",
"version": "v3"
}
] | 2018-06-14 | [
[
"Misiunas",
"Karolis",
""
],
[
"Ermann",
"Niklas",
""
],
[
"Keyser",
"Ulrich F.",
""
]
] | Nanopore sensing is a versatile technique for the analysis of molecules on the single-molecule level. However, extracting information from data with established algorithms usually requires time-consuming checks by an experienced researcher due to inherent variability of solid-state nanopores. Here, we develop a convolu... |
1710.06259 | Eugenio Cinquemani | Eugenio Cinquemani | Stochastic reaction networks with input processes: Analysis and
applications to reporter gene systems | null | null | null | null | q-bio.QM math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stochastic reaction network models are widely utilized in biology and
chemistry to describe the probabilistic dynamics of biochemical systems in
general, and gene interaction networks in particular. Most often, statistical
analysis and inference of these systems is addressed by parametric approaches,
where the laws g... | [
{
"created": "Tue, 17 Oct 2017 13:29:10 GMT",
"version": "v1"
}
] | 2017-10-18 | [
[
"Cinquemani",
"Eugenio",
""
]
] | Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and inference of these systems is addressed by parametric approaches, where the laws gov... |
2110.02031 | Shirsendu Podder | Shirsendu Podder, Simone Righi, Francesca Pancotto | Reputation and Punishment sustain cooperation in the Optional Public
Goods Game | Phil. Trans. R. Soc | null | 10.1098/rstb.2020.0293 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Cooperative behaviour has been extensively studied as a choice between
cooperation and defection. However, the possibility to not participate is also
frequently available. This type of problem can be studied through the optional
public goods game. The introduction of the "Loner" strategy, allows players to
withdraw f... | [
{
"created": "Tue, 5 Oct 2021 13:24:00 GMT",
"version": "v1"
}
] | 2021-10-06 | [
[
"Podder",
"Shirsendu",
""
],
[
"Righi",
"Simone",
""
],
[
"Pancotto",
"Francesca",
""
]
] | Cooperative behaviour has been extensively studied as a choice between cooperation and defection. However, the possibility to not participate is also frequently available. This type of problem can be studied through the optional public goods game. The introduction of the "Loner" strategy, allows players to withdraw fro... |
1906.02321 | Olga Vsevolozhskaya | Olga A Vsevolozhskaya, Min Shi, Fengjiao Hu, Dmitri V Zaykin | DOT: Gene-set analysis by combining decorrelated association statistics | null | null | 10.1371/journal.pcbi.1007819 | null | q-bio.GN stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Historically, the majority of statistical association methods have been
designed assuming availability of SNP-level information. However, modern
genetic and sequencing data present new challenges to access and sharing of
genotype-phenotype datasets, including cost management, difficulties in
consolidation of records ... | [
{
"created": "Wed, 5 Jun 2019 21:49:09 GMT",
"version": "v1"
},
{
"created": "Mon, 10 Jun 2019 20:26:07 GMT",
"version": "v2"
}
] | 2020-07-01 | [
[
"Vsevolozhskaya",
"Olga A",
""
],
[
"Shi",
"Min",
""
],
[
"Hu",
"Fengjiao",
""
],
[
"Zaykin",
"Dmitri V",
""
]
] | Historically, the majority of statistical association methods have been designed assuming availability of SNP-level information. However, modern genetic and sequencing data present new challenges to access and sharing of genotype-phenotype datasets, including cost management, difficulties in consolidation of records ac... |
1802.06090 | Yamila Garc\'ia-Martinez | Y. B. Ruiz-Blanco, Y. Almeida, C. M. Sotomayor-Torres and Y. Garc\'ia | Unveiled electric profiles within hydrogen bonds suggest DNA base pairs
with similar bond strengths | Full version is available on:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185638 | PLoS ONE 12(10): e0185638 (2017) | 10.1371/journal.pone.0185638 | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Electrical forces are the background of all the interactions occurring in
biochemical systems. From here and by using a combination of ab-initio and
ad-hoc models, we introduce the first description of electric field profiles
with intrabond resolution to support a characterization of single bond forces
attending to i... | [
{
"created": "Sun, 4 Feb 2018 22:37:08 GMT",
"version": "v1"
}
] | 2018-02-20 | [
[
"Ruiz-Blanco",
"Y. B.",
""
],
[
"Almeida",
"Y.",
""
],
[
"Sotomayor-Torres",
"C. M.",
""
],
[
"García",
"Y.",
""
]
] | Electrical forces are the background of all the interactions occurring in biochemical systems. From here and by using a combination of ab-initio and ad-hoc models, we introduce the first description of electric field profiles with intrabond resolution to support a characterization of single bond forces attending to its... |
2102.11066 | Xiyun Zhang | Xiyun Zhang, Zhongyuan Ruan, Muhua Zheng, Jie Zhou, Stefano Boccaletti
and Baruch Barzel | Epidemic spreading under mutually independent intra- and inter-host
pathogen evolution | null | Nat Commun 13, 6218 (2022) | 10.1038/s41467-022-34027-9 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The dynamics of epidemic spreading is often reduced to the single control
parameter $R_0$, whose value, above or below unity, determines the state of the
contagion. If, however, the pathogen evolves as it spreads, $R_0$ may change
over time, potentially leading to a mutation-driven spread, in which an
initially sub-p... | [
{
"created": "Fri, 19 Feb 2021 05:18:29 GMT",
"version": "v1"
},
{
"created": "Mon, 29 Mar 2021 09:36:11 GMT",
"version": "v2"
},
{
"created": "Fri, 4 Nov 2022 04:55:12 GMT",
"version": "v3"
}
] | 2022-11-07 | [
[
"Zhang",
"Xiyun",
""
],
[
"Ruan",
"Zhongyuan",
""
],
[
"Zheng",
"Muhua",
""
],
[
"Zhou",
"Jie",
""
],
[
"Boccaletti",
"Stefano",
""
],
[
"Barzel",
"Baruch",
""
]
] | The dynamics of epidemic spreading is often reduced to the single control parameter $R_0$, whose value, above or below unity, determines the state of the contagion. If, however, the pathogen evolves as it spreads, $R_0$ may change over time, potentially leading to a mutation-driven spread, in which an initially sub-pan... |
1902.02014 | Md Fazlul Karim Khan | Fazlul MKK, Najnin A, Farzana Y, Rashid MA, Deepthi S, Srikumar C, SS
Rashid, Nazmul MHM | Detection of virulence factors and beta-lactamase encoding genes among
the clinical isolates of Pseudomonas aeruginosa | International Journal of Pharmaceutical Research, 2019 | International Journal of Pharmaceutical Research, 2019 | 10.31838/ijpr/2019.11.01.031 | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Pseudomonas aeruginosa has emerged as a significant opportunistic
bacterial pathogen that causes nosocomial infections in healthcare settings
resulting in treatment failure throughout the world. This study was carried out
to compare the relatedness between virulence characteristics and
\b{eta}-lactamase e... | [
{
"created": "Wed, 6 Feb 2019 03:52:59 GMT",
"version": "v1"
}
] | 2019-08-13 | [
[
"MKK",
"Fazlul",
""
],
[
"A",
"Najnin",
""
],
[
"Y",
"Farzana",
""
],
[
"MA",
"Rashid",
""
],
[
"S",
"Deepthi",
""
],
[
"C",
"Srikumar",
""
],
[
"Rashid",
"SS",
""
],
[
"MHM",
"Nazmul",
""
... | Background: Pseudomonas aeruginosa has emerged as a significant opportunistic bacterial pathogen that causes nosocomial infections in healthcare settings resulting in treatment failure throughout the world. This study was carried out to compare the relatedness between virulence characteristics and \b{eta}-lactamase enc... |
2103.10667 | Simone Pigolotti | Qiao Lu, Deepak Bhat, Darya Stepanenko, and Simone Pigolotti | Search and localization dynamics of the CRISPR/Cas9 system | 8 pages, 10 figures. Combined Main Text + SI. Accepted for
publication in Physical Review Letters | Phys. Rev. Lett. 127, 208102, 2021 | 10.1103/PhysRevLett.127.208102 | null | q-bio.SC cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The CRISPR/Cas9 system acts as the prokaryotic immune system and has
important applications in gene editing. The protein Cas9 is one of its crucial
components. The role of Cas9 is to search for specific target sequences on the
DNA and cleave them. In this Letter, we introduce a model of facilitated
diffusion for Cas9... | [
{
"created": "Fri, 19 Mar 2021 07:27:43 GMT",
"version": "v1"
},
{
"created": "Mon, 4 Oct 2021 01:11:14 GMT",
"version": "v2"
}
] | 2021-11-30 | [
[
"Lu",
"Qiao",
""
],
[
"Bhat",
"Deepak",
""
],
[
"Stepanenko",
"Darya",
""
],
[
"Pigolotti",
"Simone",
""
]
] | The CRISPR/Cas9 system acts as the prokaryotic immune system and has important applications in gene editing. The protein Cas9 is one of its crucial components. The role of Cas9 is to search for specific target sequences on the DNA and cleave them. In this Letter, we introduce a model of facilitated diffusion for Cas9 a... |
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