id stringlengths 9 13 | submitter stringlengths 4 48 | authors stringlengths 4 9.62k | title stringlengths 4 343 | comments stringlengths 2 480 ⌀ | journal-ref stringlengths 9 309 ⌀ | doi stringlengths 12 138 ⌀ | report-no stringclasses 277
values | categories stringlengths 8 87 | license stringclasses 9
values | orig_abstract stringlengths 27 3.76k | versions listlengths 1 15 | update_date stringlengths 10 10 | authors_parsed listlengths 1 147 | abstract stringlengths 24 3.75k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2404.19235 | Weiyi Wang | Weiyi Wang, Shailendra Sawleshwarkar and Mahendra Piraveenan | Computational Approaches of Modelling Human Papillomavirus Transmission
and Prevention Strategies: A Systematic Review | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Human papillomavirus (HPV) infection is the most common sexually transmitted
infection in the world. Persistent oncogenic Human papillomavirus infection has
been a leading threat to global health and can lead to serious complications
such as cervical cancer. Prevention interventions including vaccination and
screenin... | [
{
"created": "Tue, 30 Apr 2024 03:32:06 GMT",
"version": "v1"
}
] | 2024-05-01 | [
[
"Wang",
"Weiyi",
""
],
[
"Sawleshwarkar",
"Shailendra",
""
],
[
"Piraveenan",
"Mahendra",
""
]
] | Human papillomavirus (HPV) infection is the most common sexually transmitted infection in the world. Persistent oncogenic Human papillomavirus infection has been a leading threat to global health and can lead to serious complications such as cervical cancer. Prevention interventions including vaccination and screening ... |
2307.08758 | Ivan Maksymov | Ivan S. Maksymov and Ganna Pogrebna | Linking Physics and Psychology of Bistable Perception Using an Eye Blink
Inspired Quantum Harmonic Oscillator Model | null | null | null | null | q-bio.NC cs.CV physics.bio-ph quant-ph | http://creativecommons.org/licenses/by/4.0/ | This paper introduces a novel quantum-mechanical model that describes
psychological phenomena using the analogy of a harmonic oscillator represented
by an electron trapped in a potential well. Study~1 demonstrates the
application of the proposed model to bistable perception of ambiguous figures
(i.e., optical illusio... | [
{
"created": "Fri, 23 Jun 2023 06:10:00 GMT",
"version": "v1"
}
] | 2023-07-19 | [
[
"Maksymov",
"Ivan S.",
""
],
[
"Pogrebna",
"Ganna",
""
]
] | This paper introduces a novel quantum-mechanical model that describes psychological phenomena using the analogy of a harmonic oscillator represented by an electron trapped in a potential well. Study~1 demonstrates the application of the proposed model to bistable perception of ambiguous figures (i.e., optical illusions... |
2402.04274 | Elham E Khoda | Xiaohan Liu, ChiJui Chen, YanLun Huang, LingChi Yang, Elham E Khoda,
Yihui Chen, Scott Hauck, Shih-Chieh Hsu, Bo-Cheng Lai | FPGA Deployment of LFADS for Real-time Neuroscience Experiments | 6 pages, 8 figures | Fast Machine Learning for Science, ICCAD 2023 | null | null | q-bio.NC cs.LG cs.NE | http://creativecommons.org/licenses/by/4.0/ | Large-scale recordings of neural activity are providing new opportunities to
study neural population dynamics. A powerful method for analyzing such
high-dimensional measurements is to deploy an algorithm to learn the
low-dimensional latent dynamics. LFADS (Latent Factor Analysis via Dynamical
Systems) is a deep learn... | [
{
"created": "Fri, 2 Feb 2024 07:52:20 GMT",
"version": "v1"
}
] | 2024-02-08 | [
[
"Liu",
"Xiaohan",
""
],
[
"Chen",
"ChiJui",
""
],
[
"Huang",
"YanLun",
""
],
[
"Yang",
"LingChi",
""
],
[
"Khoda",
"Elham E",
""
],
[
"Chen",
"Yihui",
""
],
[
"Hauck",
"Scott",
""
],
[
"Hsu",
"S... | Large-scale recordings of neural activity are providing new opportunities to study neural population dynamics. A powerful method for analyzing such high-dimensional measurements is to deploy an algorithm to learn the low-dimensional latent dynamics. LFADS (Latent Factor Analysis via Dynamical Systems) is a deep learnin... |
2403.07920 | Zewen Chi | Le Zhuo, Zewen Chi, Minghao Xu, Heyan Huang, Heqi Zheng, Conghui He,
Xian-Ling Mao, Wentao Zhang | ProtLLM: An Interleaved Protein-Language LLM with Protein-as-Word
Pre-Training | https://protllm.github.io/project/ | null | null | null | q-bio.BM cs.AI cs.CL cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose ProtLLM, a versatile cross-modal large language model (LLM) for
both protein-centric and protein-language tasks. ProtLLM features a unique
dynamic protein mounting mechanism, enabling it to handle complex inputs where
the natural language text is interspersed with an arbitrary number of proteins.
Besides, ... | [
{
"created": "Wed, 28 Feb 2024 01:29:55 GMT",
"version": "v1"
}
] | 2024-03-14 | [
[
"Zhuo",
"Le",
""
],
[
"Chi",
"Zewen",
""
],
[
"Xu",
"Minghao",
""
],
[
"Huang",
"Heyan",
""
],
[
"Zheng",
"Heqi",
""
],
[
"He",
"Conghui",
""
],
[
"Mao",
"Xian-Ling",
""
],
[
"Zhang",
"Wentao",
... | We propose ProtLLM, a versatile cross-modal large language model (LLM) for both protein-centric and protein-language tasks. ProtLLM features a unique dynamic protein mounting mechanism, enabling it to handle complex inputs where the natural language text is interspersed with an arbitrary number of proteins. Besides, we... |
1304.7670 | Timothy Sackton | Timothy B. Sackton, Russell B. Corbett-Detig, Javaregowda Nagaraju, R.
Lakshmi Vaishna, Kallare P. Arunkumar, and Daniel L. Hartl | Positive selection drives faster-Z evolution in silkmoths | 19 pages, 3 figures; revised results, discussion, and methods from
previous version | null | 10.1111/evo.12449 | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genes linked to X or Z chromosomes, which are hemizygous in the heterogametic
sex, are predicted to evolve at different rates than those on autosomes. This
faster-X effect can arise either as a consequence of hemizygosity, which leads
to more efficient selection for recessive beneficial mutations in the
heterogametic... | [
{
"created": "Mon, 29 Apr 2013 14:26:02 GMT",
"version": "v1"
},
{
"created": "Thu, 29 Aug 2013 05:56:43 GMT",
"version": "v2"
}
] | 2014-06-10 | [
[
"Sackton",
"Timothy B.",
""
],
[
"Corbett-Detig",
"Russell B.",
""
],
[
"Nagaraju",
"Javaregowda",
""
],
[
"Vaishna",
"R. Lakshmi",
""
],
[
"Arunkumar",
"Kallare P.",
""
],
[
"Hartl",
"Daniel L.",
""
]
] | Genes linked to X or Z chromosomes, which are hemizygous in the heterogametic sex, are predicted to evolve at different rates than those on autosomes. This faster-X effect can arise either as a consequence of hemizygosity, which leads to more efficient selection for recessive beneficial mutations in the heterogametic s... |
2303.15712 | Frederik Van Daele | Frederik Van Daele, Olivier Honnay, Steven Janssens, Hanne De Kort | Habitat fragmentation affects climate adaptation in a forest herb | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Climate change and the resulting increased drought frequencies pose
considerable threats to forest herb populations, especially when compounded by
additional environmental challenges. Specifically, habitat fragmentation may
disrupt climate adaptation and cause shifts in mating systems. To examine this,
we conducted a... | [
{
"created": "Tue, 28 Mar 2023 03:47:39 GMT",
"version": "v1"
},
{
"created": "Sat, 22 Apr 2023 11:21:02 GMT",
"version": "v2"
},
{
"created": "Wed, 17 May 2023 16:05:29 GMT",
"version": "v3"
}
] | 2023-05-18 | [
[
"Van Daele",
"Frederik",
""
],
[
"Honnay",
"Olivier",
""
],
[
"Janssens",
"Steven",
""
],
[
"De Kort",
"Hanne",
""
]
] | Climate change and the resulting increased drought frequencies pose considerable threats to forest herb populations, especially when compounded by additional environmental challenges. Specifically, habitat fragmentation may disrupt climate adaptation and cause shifts in mating systems. To examine this, we conducted a g... |
1306.2808 | Wolfgang Keil | Manuel Schottdorf, Stephen J. Eglen, Fred Wolf and Wolfgang Keil | Can retinal ganglion cell dipoles seed iso-orientation domains in the
visual cortex? | 9 figures + 1 Supplementary figure and 1 Supplementary table | PLoS ONE 9(1): e86139 (2014) | 10.1371/journal.pone.0086139 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has been argued that the emergence of roughly periodic orientation
preference maps (OPMs) in the primary visual cortex (V1) of carnivores and
primates can be explained by a so-called statistical connectivity model. This
model assumes that input to V1 neurons is dominated by feed-forward projections
originating fro... | [
{
"created": "Wed, 12 Jun 2013 12:57:13 GMT",
"version": "v1"
},
{
"created": "Tue, 19 Nov 2013 14:58:37 GMT",
"version": "v2"
}
] | 2023-10-18 | [
[
"Schottdorf",
"Manuel",
""
],
[
"Eglen",
"Stephen J.",
""
],
[
"Wolf",
"Fred",
""
],
[
"Keil",
"Wolfgang",
""
]
] | It has been argued that the emergence of roughly periodic orientation preference maps (OPMs) in the primary visual cortex (V1) of carnivores and primates can be explained by a so-called statistical connectivity model. This model assumes that input to V1 neurons is dominated by feed-forward projections originating from ... |
2407.19454 | Fran\c{c}ois Bienvenu | Fran\c{c}ois Bienvenu, Jean-Jil Duchamps, Michael Fuchs and Tsan-Cheng
Yu | The $B_2$ index of galled trees | null | null | null | null | q-bio.PE math.CO math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent years, there has been an effort to extend the classical notion of
phylogenetic balance, originally defined in the context of trees, to networks.
One of the most natural ways to do this is with the so-called $B_2$ index. In
this paper, we study the $B_2$ index for a prominent class of phylogenetic
networks: ... | [
{
"created": "Sun, 28 Jul 2024 10:11:36 GMT",
"version": "v1"
}
] | 2024-07-30 | [
[
"Bienvenu",
"François",
""
],
[
"Duchamps",
"Jean-Jil",
""
],
[
"Fuchs",
"Michael",
""
],
[
"Yu",
"Tsan-Cheng",
""
]
] | In recent years, there has been an effort to extend the classical notion of phylogenetic balance, originally defined in the context of trees, to networks. One of the most natural ways to do this is with the so-called $B_2$ index. In this paper, we study the $B_2$ index for a prominent class of phylogenetic networks: ga... |
1211.6615 | Werner Ehm | Werner Ehm and Jiri Wackermann | Modeling geometric-optical illusions: A variational approach | Minor corrections, final version | Journal of Mathematical Psychology 56 (2012), 404-416 | null | null | q-bio.NC math.CA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Visual distortions of perceived lengths, angles, or forms, are generally
known as "geometric-optical illusions" (GOI). In the present paper we focus on
a class of GOIs where the distortion of a straight line segment (the "target"
stimulus) is induced by an array of non-intersecting curvilinear elements
("context" sti... | [
{
"created": "Wed, 28 Nov 2012 14:39:16 GMT",
"version": "v1"
},
{
"created": "Mon, 22 Apr 2013 20:06:00 GMT",
"version": "v2"
}
] | 2013-04-24 | [
[
"Ehm",
"Werner",
""
],
[
"Wackermann",
"Jiri",
""
]
] | Visual distortions of perceived lengths, angles, or forms, are generally known as "geometric-optical illusions" (GOI). In the present paper we focus on a class of GOIs where the distortion of a straight line segment (the "target" stimulus) is induced by an array of non-intersecting curvilinear elements ("context" stimu... |
1406.1734 | Christian T\"onsing | Christian T\"onsing, Jens Timmer and Clemens Kreutz | Cause and Cure of Sloppiness in Ordinary Differential Equation Models | 17 pages, 15 figures, submitted to Phys. Rev. E on 12 April 2014 | Phys. Rev. E 90 (2014), 023303 | 10.1103/PhysRevE.90.023303 | null | q-bio.MN physics.data-an q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Data-based mathematical modeling of biochemical reaction networks, e.g. by
nonlinear ordinary differential equation (ODE) models, has been successfully
applied. In this context, parameter estimation and uncertainty analysis is a
major task in order to assess the quality of the description of the system by
the model. ... | [
{
"created": "Fri, 6 Jun 2014 16:49:18 GMT",
"version": "v1"
}
] | 2014-09-02 | [
[
"Tönsing",
"Christian",
""
],
[
"Timmer",
"Jens",
""
],
[
"Kreutz",
"Clemens",
""
]
] | Data-based mathematical modeling of biochemical reaction networks, e.g. by nonlinear ordinary differential equation (ODE) models, has been successfully applied. In this context, parameter estimation and uncertainty analysis is a major task in order to assess the quality of the description of the system by the model. Re... |
1904.10375 | Nadya Morozova | N. Bessonov, O.Butuzova, A.Minarsky, R. Penner, C. Soule, A.
Tosenberger and N. Morozova | Morphogenesis Software based on Epigenetic Code Concept | null | Computational and Structural Biotechnology Journal 17 (2019)
p.1203 | 10.1016/j.csbj.2019.08.007 10.1016/j.csbj.2019.08.007
10.1016/j.csbj.2019.08.007 10.1016/j.csbj.2019.08.007
10.1016/j.csbj.2019.08.007 | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The process of morphogenesis is an evolution of the shape of an organism
together with the differentiation of its parts. This process encompasses
numerous biological processes ranging from embryogenesis to regeneration
following crisis such as amputation or transplantation. A fundamental
theoretical question is where... | [
{
"created": "Tue, 23 Apr 2019 15:18:30 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Sep 2019 17:58:04 GMT",
"version": "v2"
}
] | 2019-09-23 | [
[
"Bessonov",
"N.",
""
],
[
"Butuzova",
"O.",
""
],
[
"Minarsky",
"A.",
""
],
[
"Penner",
"R.",
""
],
[
"Soule",
"C.",
""
],
[
"Tosenberger",
"A.",
""
],
[
"Morozova",
"N.",
""
]
] | The process of morphogenesis is an evolution of the shape of an organism together with the differentiation of its parts. This process encompasses numerous biological processes ranging from embryogenesis to regeneration following crisis such as amputation or transplantation. A fundamental theoretical question is where e... |
1812.06315 | Erik Fagerholm | Erik D. Fagerholm, Rosalyn J. Moran, In\^es R. Violante, Robert Leech,
Karl J. Friston | Breaking the bonds of weak coupling: the dynamic causal modelling of
oscillator amplitudes | 17 pages, 5 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Models of coupled oscillators are useful in describing a wide variety of
phenomena in physics, biology and economics. These models typically rest on the
premise that the oscillators are weakly coupled, meaning that amplitudes can be
assumed to be constant and dynamics can therefore be described purely in terms
of pha... | [
{
"created": "Sat, 15 Dec 2018 16:26:07 GMT",
"version": "v1"
}
] | 2018-12-18 | [
[
"Fagerholm",
"Erik D.",
""
],
[
"Moran",
"Rosalyn J.",
""
],
[
"Violante",
"Inês R.",
""
],
[
"Leech",
"Robert",
""
],
[
"Friston",
"Karl J.",
""
]
] | Models of coupled oscillators are useful in describing a wide variety of phenomena in physics, biology and economics. These models typically rest on the premise that the oscillators are weakly coupled, meaning that amplitudes can be assumed to be constant and dynamics can therefore be described purely in terms of phase... |
2405.05712 | Masato Suzuki | Makiko Aok, Mai Nishimura, Masato Suzuki, Eiriko Terasawa, Hisayo
Okayama | Characterization of the Autonomic Nervous System Activity in Females
Classified According to Mood Scores During the Follicular Phase | 5 pages, 2 figures, 1 table, 2024 IEEE International Conference on
Robotics and Automation (ICRA 2024) | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many sexually mature females suffer from premenstrual syndrome (PMS), but
effective coping methods for PMS are limited due to the complexity of symptoms
and unclear pathogenesis. Awareness has shown promise in alleviating PMS
symptoms but faces challenges in long-term recording and consistency. Our
research goal is t... | [
{
"created": "Wed, 8 May 2024 16:31:06 GMT",
"version": "v1"
}
] | 2024-05-10 | [
[
"Aok",
"Makiko",
""
],
[
"Nishimura",
"Mai",
""
],
[
"Suzuki",
"Masato",
""
],
[
"Terasawa",
"Eiriko",
""
],
[
"Okayama",
"Hisayo",
""
]
] | Many sexually mature females suffer from premenstrual syndrome (PMS), but effective coping methods for PMS are limited due to the complexity of symptoms and unclear pathogenesis. Awareness has shown promise in alleviating PMS symptoms but faces challenges in long-term recording and consistency. Our research goal is to ... |
1505.04195 | Zachary Kilpatrick PhD | Alan Veliz-Cuba, Zachary P. Kilpatrick, and Kresimir Josic | Stochastic models of evidence accumulation in changing environments | 26 pages, 7 figures | null | null | null | q-bio.NC math.ST stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Organisms and ecological groups accumulate evidence to make decisions.
Classic experiments and theoretical studies have explored this process when the
correct choice is fixed during each trial. However, we live in a constantly
changing world. What effect does such impermanence have on classical results
about decision... | [
{
"created": "Fri, 15 May 2015 20:07:28 GMT",
"version": "v1"
},
{
"created": "Sat, 13 Jun 2015 17:38:03 GMT",
"version": "v2"
},
{
"created": "Tue, 8 Sep 2015 18:41:42 GMT",
"version": "v3"
},
{
"created": "Wed, 30 Sep 2015 14:40:45 GMT",
"version": "v4"
}
] | 2015-10-01 | [
[
"Veliz-Cuba",
"Alan",
""
],
[
"Kilpatrick",
"Zachary P.",
""
],
[
"Josic",
"Kresimir",
""
]
] | Organisms and ecological groups accumulate evidence to make decisions. Classic experiments and theoretical studies have explored this process when the correct choice is fixed during each trial. However, we live in a constantly changing world. What effect does such impermanence have on classical results about decision m... |
0712.0170 | Johannes Berg | Johannes Berg | Non-equilibrium dynamics of gene expression and the Jarzynski equality | null | null | 10.1103/PhysRevLett.100.188101 | null | q-bio.MN cond-mat.stat-mech | null | In order to express specific genes at the right time, the transcription of
genes is regulated by the presence and absence of transcription factor
molecules. With transcription factor concentrations undergoing constant
changes, gene transcription takes place out of equilibrium. In this paper we
discuss a simple mappin... | [
{
"created": "Mon, 3 Dec 2007 18:18:08 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Berg",
"Johannes",
""
]
] | In order to express specific genes at the right time, the transcription of genes is regulated by the presence and absence of transcription factor molecules. With transcription factor concentrations undergoing constant changes, gene transcription takes place out of equilibrium. In this paper we discuss a simple mapping ... |
2009.04581 | Andr\'es David B\'aez-S\'anchez | Andr\'es David B\'aez-S\'anchez and Nara Bobko | Effects of anti-infection behavior on the equilibrium states of an
infectious disease | 23 pages, 2 Figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a mathematical model to analyze the effects of anti-infection
behavior on the equilibrium states of an infectious disease. The anti-infection
behavior is incorporated into a classical epidemiological SIR model, by
considering the behavior adoption rate across the population as an additional
variable. We co... | [
{
"created": "Wed, 9 Sep 2020 21:33:30 GMT",
"version": "v1"
}
] | 2020-09-11 | [
[
"Báez-Sánchez",
"Andrés David",
""
],
[
"Bobko",
"Nara",
""
]
] | We propose a mathematical model to analyze the effects of anti-infection behavior on the equilibrium states of an infectious disease. The anti-infection behavior is incorporated into a classical epidemiological SIR model, by considering the behavior adoption rate across the population as an additional variable. We cons... |
2406.15537 | Matteo Ciferri | Matteo Ferrante, Matteo Ciferri, Nicola Toschi | R&B -- Rhythm and Brain: Cross-subject Decoding of Music from Human
Brain Activity | The first two authors contributed equally to this work | null | null | null | q-bio.NC cs.AI cs.SD eess.AS | http://creativecommons.org/licenses/by/4.0/ | Music is a universal phenomenon that profoundly influences human experiences
across cultures. This study investigates whether music can be decoded from
human brain activity measured with functional MRI (fMRI) during its perception.
Leveraging recent advancements in extensive datasets and pre-trained
computational mod... | [
{
"created": "Fri, 21 Jun 2024 17:11:45 GMT",
"version": "v1"
}
] | 2024-06-25 | [
[
"Ferrante",
"Matteo",
""
],
[
"Ciferri",
"Matteo",
""
],
[
"Toschi",
"Nicola",
""
]
] | Music is a universal phenomenon that profoundly influences human experiences across cultures. This study investigates whether music can be decoded from human brain activity measured with functional MRI (fMRI) during its perception. Leveraging recent advancements in extensive datasets and pre-trained computational model... |
q-bio/0312046 | Anders Irb\"ack | Giorgio Favrin, Anders Irb\"ack, Bj\"orn Samuelsson, Stefan Wallin | Two-state folding over a weak free-energy barrier | 22 pages, 5 figures | Biophys. J. 85 (2003) 1457-1465 | 10.1016/S0006-3495(03)74578-0 | LU TP 03-07 | q-bio.BM cond-mat.soft | null | We present a Monte Carlo study of a model protein with 54 amino acids that
folds directly to its native three-helix-bundle state without forming any
well-defined intermediate state. The free-energy barrier separating the native
and unfolded states of this protein is found to be weak, even at the folding
temperature. ... | [
{
"created": "Tue, 30 Dec 2003 20:23:07 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Favrin",
"Giorgio",
""
],
[
"Irbäck",
"Anders",
""
],
[
"Samuelsson",
"Björn",
""
],
[
"Wallin",
"Stefan",
""
]
] | We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded states of this protein is found to be weak, even at the folding temperature. Ne... |
1809.02623 | Greg Gloor Dr | Andrew D. Fernandes, Michael T.H.Q. Vu, Lisa-Monique Edward, Jean M.
Macklaim, and Gregory B. Gloor | A reproducible effect size is more useful than an irreproducible
hypothesis test to analyze high throughput sequencing datasets | Draft paper explaining the properties and utility of the ALDEx2
effect size metric | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-sa/4.0/ | Motivation: P values derived from the null hypothesis significance testing
framework are strongly affected by sample size, and are known to be
irreproducible in underpowered studies, yet no suitable replacement has been
proposed. Results: Here we present implementations of non-parametric
standardized median effect si... | [
{
"created": "Fri, 7 Sep 2018 18:07:28 GMT",
"version": "v1"
},
{
"created": "Mon, 13 May 2019 16:03:17 GMT",
"version": "v2"
}
] | 2019-05-14 | [
[
"Fernandes",
"Andrew D.",
""
],
[
"Vu",
"Michael T. H. Q.",
""
],
[
"Edward",
"Lisa-Monique",
""
],
[
"Macklaim",
"Jean M.",
""
],
[
"Gloor",
"Gregory B.",
""
]
] | Motivation: P values derived from the null hypothesis significance testing framework are strongly affected by sample size, and are known to be irreproducible in underpowered studies, yet no suitable replacement has been proposed. Results: Here we present implementations of non-parametric standardized median effect size... |
1405.6673 | Simona Cocco | Simona Cocco (LPS), John F. Marko, Remi Monasson (LPTENS) | Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA | \`a paraitre en PHys. Rev. Lett. june 2014 | null | 10.1103/PhysRevLett.112.238101 | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Experiments indicate that unbinding rates of proteins from DNA can depend on
the concentration of proteins in nearby solution. Here we present a theory of
multi-step replacement of DNA-bound proteins by solution-phase proteins. For
four different kinetic scenarios we calculate the depen- dence of protein
unbinding an... | [
{
"created": "Mon, 26 May 2014 18:40:57 GMT",
"version": "v1"
}
] | 2015-06-19 | [
[
"Cocco",
"Simona",
"",
"LPS"
],
[
"Marko",
"John F.",
"",
"LPTENS"
],
[
"Monasson",
"Remi",
"",
"LPTENS"
]
] | Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four different kinetic scenarios we calculate the depen- dence of protein unbinding and ... |
2109.05796 | Rosa Hernansaiz-Ballesteros | Rosa Hernansaiz-Ballesteros, Christian H. Holland, Aurelien Dugourd,
Julio Saez-Rodriguez | FUNKI: Interactive functional footprint-based analysis of omics data | 4 main pages, 2 supplementary pages, 1 figure | null | null | null | q-bio.GN cs.CE | http://creativecommons.org/licenses/by/4.0/ | Motivation: Omics data, such as transcriptomics or phosphoproteomics, are
broadly used to get a snap-shot of the molecular status of cells. In
particular, changes in omics can be used to estimate the activity of pathways,
transcription factors and kinases based on known regulated targets, that we
call footprints. The... | [
{
"created": "Mon, 13 Sep 2021 09:19:21 GMT",
"version": "v1"
}
] | 2021-09-14 | [
[
"Hernansaiz-Ballesteros",
"Rosa",
""
],
[
"Holland",
"Christian H.",
""
],
[
"Dugourd",
"Aurelien",
""
],
[
"Saez-Rodriguez",
"Julio",
""
]
] | Motivation: Omics data, such as transcriptomics or phosphoproteomics, are broadly used to get a snap-shot of the molecular status of cells. In particular, changes in omics can be used to estimate the activity of pathways, transcription factors and kinases based on known regulated targets, that we call footprints. Then ... |
1410.1417 | J. C. Phillips | J. C. Phillips | Filovirus Glycoprotein Sequence, Structure and Virulence | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Leading Ebola subtypes exhibit a wide mortality range, here explained at the
molecular level by using fractal hydropathic scaling of amino acid sequences
based on protein self-organized criticality. Specific hydrophobic features in
the hydrophilic mucin-like domain suffice to account for the wide mortality
range. Sig... | [
{
"created": "Fri, 26 Sep 2014 21:21:06 GMT",
"version": "v1"
}
] | 2014-10-07 | [
[
"Phillips",
"J. C.",
""
]
] | Leading Ebola subtypes exhibit a wide mortality range, here explained at the molecular level by using fractal hydropathic scaling of amino acid sequences based on protein self-organized criticality. Specific hydrophobic features in the hydrophilic mucin-like domain suffice to account for the wide mortality range. Signi... |
2205.02645 | Arshed Nabeel | Arshed Nabeel, Ashwin Karichannavar, Shuaib Palathingal, Jitesh
Jhawar, David B. Br\"uckner, Danny Raj M., Vishwesha Guttal | Discovering stochastic dynamical equations from biological time series
data | Updates: v3: Significantly reorganized the paper and added a section
analysis of a cell migration dataset. v4: Update arXiv title to match the
updated title of the manuscript. v5: Added sections detailing the limitations
of the approach | null | null | null | q-bio.QM cs.LG math.DS | http://creativecommons.org/licenses/by-sa/4.0/ | Stochastic differential equations (SDEs) are an important framework to model
dynamics with randomness, as is common in most biological systems. The inverse
problem of integrating these models with empirical data remains a major
challenge. Here, we present an equation discovery methodology that takes time
series data ... | [
{
"created": "Thu, 5 May 2022 13:44:24 GMT",
"version": "v1"
},
{
"created": "Wed, 2 Nov 2022 18:43:41 GMT",
"version": "v2"
},
{
"created": "Tue, 21 Nov 2023 09:48:28 GMT",
"version": "v3"
},
{
"created": "Wed, 22 Nov 2023 03:43:55 GMT",
"version": "v4"
},
{
"cre... | 2024-02-20 | [
[
"Nabeel",
"Arshed",
""
],
[
"Karichannavar",
"Ashwin",
""
],
[
"Palathingal",
"Shuaib",
""
],
[
"Jhawar",
"Jitesh",
""
],
[
"Brückner",
"David B.",
""
],
[
"M.",
"Danny Raj",
""
],
[
"Guttal",
"Vishwesha",
... | Stochastic differential equations (SDEs) are an important framework to model dynamics with randomness, as is common in most biological systems. The inverse problem of integrating these models with empirical data remains a major challenge. Here, we present an equation discovery methodology that takes time series data as... |
1104.0021 | Stuart Borrett Stuart Borrett | Stuart R. Borrett, Andria K. Salas | Evidence for Resource Homogenization in 50 Trophic Ecosystem Networks | 10 pages, 3 figures, 1 table | Borrett, S.R., A.K. Salas. 2010. Evidence for resource
homogenization in 50 trophic ecosystem networks. Ecological Modelling 221:
1710-1716 | 10.1016/j.ecolmodel.2010.04.004 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Connectivity patterns of ecological elements are often the core concern of
ecologists working at multiple levels of organization (e.g., populations,
ecosystems, and landscapes) because these patterns often reflect the forces
shaping the system's development as well as constraining their operation. One
reason these pa... | [
{
"created": "Thu, 31 Mar 2011 20:16:04 GMT",
"version": "v1"
}
] | 2011-04-04 | [
[
"Borrett",
"Stuart R.",
""
],
[
"Salas",
"Andria K.",
""
]
] | Connectivity patterns of ecological elements are often the core concern of ecologists working at multiple levels of organization (e.g., populations, ecosystems, and landscapes) because these patterns often reflect the forces shaping the system's development as well as constraining their operation. One reason these patt... |
0902.1292 | Michael B\"orsch | N. Zarrabi, S. Ernst, M. G. Dueser, A. Golovina-Leiker, W. Becker, R.
Erdmann, S. D. Dunn, M. Borsch | Simultaneous monitoring of the two coupled motors of a single FoF1-ATP
synthase by three-color FRET using duty cycle-optimized triple-ALEX | 14 pages, 8 figures | null | 10.1117/12.809610 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | FoF1-ATP synthase is the enzyme that provides the 'chemical energy currency'
adenosine triphosphate, ATP, for living cells. The formation of ATP is
accomplished by a stepwise internal rotation of subunits within the enzyme.
Briefly, proton translocation through the membrane-bound Fo part of ATP
synthase drives a 10-s... | [
{
"created": "Sun, 8 Feb 2009 23:17:18 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Zarrabi",
"N.",
""
],
[
"Ernst",
"S.",
""
],
[
"Dueser",
"M. G.",
""
],
[
"Golovina-Leiker",
"A.",
""
],
[
"Becker",
"W.",
""
],
[
"Erdmann",
"R.",
""
],
[
"Dunn",
"S. D.",
""
],
[
"Borsch",
"M... | FoF1-ATP synthase is the enzyme that provides the 'chemical energy currency' adenosine triphosphate, ATP, for living cells. The formation of ATP is accomplished by a stepwise internal rotation of subunits within the enzyme. Briefly, proton translocation through the membrane-bound Fo part of ATP synthase drives a 10-ste... |
2404.12029 | Chaitanya A. Athale | Dhruv Khatri, Shivani A. Yadav and Chaitanya A. Athale | KnotResolver: Tracking self-intersecting filaments in microscopy using
directed graphs | Manuscript in submission | null | null | null | q-bio.QM physics.bio-ph q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Quantification of microscopy time-series of in vitro reconstituted motor
driven microtubule (MT) transport in 'gliding assays' is typically performed
using computational object tracking tools. However, these are limited to
non-intersecting and rod-like filaments. Here, we describe a novel
computational image-analysis... | [
{
"created": "Thu, 18 Apr 2024 09:28:43 GMT",
"version": "v1"
}
] | 2024-04-19 | [
[
"Khatri",
"Dhruv",
""
],
[
"Yadav",
"Shivani A.",
""
],
[
"Athale",
"Chaitanya A.",
""
]
] | Quantification of microscopy time-series of in vitro reconstituted motor driven microtubule (MT) transport in 'gliding assays' is typically performed using computational object tracking tools. However, these are limited to non-intersecting and rod-like filaments. Here, we describe a novel computational image-analysis p... |
1102.5658 | Antti Niemi | Shuangwei Hu, Martin Lundgren and Antti J. Niemi | The Discrete Frenet Frame, Inflection Point Solitons And Curve
Visualization with Applications to Folded Proteins | 14 pages 12 figures | null | 10.1103/PhysRevE.83.061908 | null | q-bio.BM cond-mat.soft hep-th physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop a transfer matrix formalism to visualize the framing of discrete
piecewise linear curves in three dimensional space. Our approach is based on
the concept of an intrinsically discrete curve, which enables us to more
effectively describe curves that in the limit where the length of line segments
vanishes app... | [
{
"created": "Mon, 28 Feb 2011 13:40:12 GMT",
"version": "v1"
}
] | 2015-05-27 | [
[
"Hu",
"Shuangwei",
""
],
[
"Lundgren",
"Martin",
""
],
[
"Niemi",
"Antti J.",
""
]
] | We develop a transfer matrix formalism to visualize the framing of discrete piecewise linear curves in three dimensional space. Our approach is based on the concept of an intrinsically discrete curve, which enables us to more effectively describe curves that in the limit where the length of line segments vanishes appro... |
2107.07131 | Tsvi Tlusty | Somya Mani and Tsvi Tlusty | A topological look into the evolution of developmental programs | null | null | null | null | q-bio.MN physics.bio-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rapid advance of experimental techniques provides an unprecedented in-depth
view into complex developmental processes. Still, little is known on how the
complexity of multicellular organisms evolved by elaborating developmental
programs and inventing new cell types. A hurdle to understanding developmental
evolution i... | [
{
"created": "Thu, 15 Jul 2021 05:33:19 GMT",
"version": "v1"
}
] | 2021-07-16 | [
[
"Mani",
"Somya",
""
],
[
"Tlusty",
"Tsvi",
""
]
] | Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and inventing new cell types. A hurdle to understanding developmental evolution is ... |
2011.01750 | Susanna Gordleeva | Susanna Yu. Gordleeva, Yulia A. Tsybina, Mikhail I. Krivonosov,
Mikhail V. Ivanchenko, Alexey A. Zaikin, Victor B. Kazantsev, Alexander N.
Gorban | Formation of working memory in a spiking neuron network accompanied by
astrocytes | null | Frontiers in Cellular Neuroscience, 15, 2021, Article 631485 | 10.3389/fncel.2021.631485 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | We propose a biologically plausible computational model of working memory
(WM) implemented by the spiking neuron network (SNN) interacting with a network
of astrocytes. SNN is modelled by the synaptically coupled Izhikevich neurons
with a non-specific architecture connection topology. Astrocytes generating
calcium si... | [
{
"created": "Tue, 3 Nov 2020 14:56:35 GMT",
"version": "v1"
}
] | 2022-05-17 | [
[
"Gordleeva",
"Susanna Yu.",
""
],
[
"Tsybina",
"Yulia A.",
""
],
[
"Krivonosov",
"Mikhail I.",
""
],
[
"Ivanchenko",
"Mikhail V.",
""
],
[
"Zaikin",
"Alexey A.",
""
],
[
"Kazantsev",
"Victor B.",
""
],
[
"Gorban",
... | We propose a biologically plausible computational model of working memory (WM) implemented by the spiking neuron network (SNN) interacting with a network of astrocytes. SNN is modelled by the synaptically coupled Izhikevich neurons with a non-specific architecture connection topology. Astrocytes generating calcium sign... |
2008.02547 | Matthijs Meijers | Matthijs Meijers, Kanika Vanshylla, Henning Gruell, Florian Klein, and
Michael Laessig | Predicting in vivo escape dynamics of HIV-1 from a broadly neutralizing
antibody | 16 pages, 6 figures | null | 10.1073/pnas.2104651118 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Broadly neutralizing antibodies are promising candidates for treatment and
prevention of HIV-1 infections. Such antibodies can temporarily suppress viral
load in infected individuals; however, the virus often rebounds by escape
mutants that have evolved resistance. In this paper, we map an in vivo fitness
landscape o... | [
{
"created": "Thu, 6 Aug 2020 09:56:32 GMT",
"version": "v1"
}
] | 2022-10-12 | [
[
"Meijers",
"Matthijs",
""
],
[
"Vanshylla",
"Kanika",
""
],
[
"Gruell",
"Henning",
""
],
[
"Klein",
"Florian",
""
],
[
"Laessig",
"Michael",
""
]
] | Broadly neutralizing antibodies are promising candidates for treatment and prevention of HIV-1 infections. Such antibodies can temporarily suppress viral load in infected individuals; however, the virus often rebounds by escape mutants that have evolved resistance. In this paper, we map an in vivo fitness landscape of ... |
2307.10585 | Yonatan Ashenafi | Yonatan Ashenafi, Peter R. Kramer | Statistical Mobility of Multicellular Colonies of Flagellated Swimming
Cells | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | We study the stochastic hydrodynamics of colonies of flagellated swimming
cells, typified by multicellular choanoflagellates, which can form both rosette
and chainlike shapes. The objective is to link cell-scale dynamics to
colony-scale dynamics for various colonial morphologies. Via autoregressive
stochastic models ... | [
{
"created": "Thu, 20 Jul 2023 04:58:10 GMT",
"version": "v1"
}
] | 2023-07-21 | [
[
"Ashenafi",
"Yonatan",
""
],
[
"Kramer",
"Peter R.",
""
]
] | We study the stochastic hydrodynamics of colonies of flagellated swimming cells, typified by multicellular choanoflagellates, which can form both rosette and chainlike shapes. The objective is to link cell-scale dynamics to colony-scale dynamics for various colonial morphologies. Via autoregressive stochastic models fo... |
1707.07771 | Andrea Giometto Dr | Silvia Zaoli, Andrea Giometto, Amos Maritan, Andrea Rinaldo | Covariations in ecological scaling laws fostered by community dynamics | S.Z. and A.G. contributed equally to this work | Proceedings of the National Academy of Sciences, 114(40),
10672-10677 | 10.1073/pnas.1708376114 | null | q-bio.PE nlin.AO physics.bio-ph physics.data-an q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Scaling laws in ecology, intended both as functional relationships among
ecologically-relevant quantities and the probability distributions that
characterize their occurrence, have long attracted the interest of empiricists
and theoreticians. Empirical evidence exists of power laws associated with the
number of speci... | [
{
"created": "Mon, 24 Jul 2017 23:26:58 GMT",
"version": "v1"
},
{
"created": "Tue, 17 Oct 2017 21:02:33 GMT",
"version": "v2"
}
] | 2017-10-19 | [
[
"Zaoli",
"Silvia",
""
],
[
"Giometto",
"Andrea",
""
],
[
"Maritan",
"Amos",
""
],
[
"Rinaldo",
"Andrea",
""
]
] | Scaling laws in ecology, intended both as functional relationships among ecologically-relevant quantities and the probability distributions that characterize their occurrence, have long attracted the interest of empiricists and theoreticians. Empirical evidence exists of power laws associated with the number of species... |
2107.03971 | Julien Lagarde | Julien Lagarde | The classical mean negative asynchrony in sensorimotor synchronization
is not universal in humans. A cross-cultural study | null | null | null | null | q-bio.NC nlin.AO | http://creativecommons.org/licenses/by/4.0/ | The present study examines to what extent cultural background determines
sensorimotor synchronization in humans
| [
{
"created": "Thu, 8 Jul 2021 16:56:05 GMT",
"version": "v1"
}
] | 2021-07-12 | [
[
"Lagarde",
"Julien",
""
]
] | The present study examines to what extent cultural background determines sensorimotor synchronization in humans |
1212.3214 | Yupeng Cun | Yupeng Cun, Holger Fr\"ohlich | Integrating Prior Knowledge Into Prognostic Biomarker Discovery based on
Network Structure | null | null | null | null | q-bio.GN stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Predictive, stable and interpretable gene signatures are
generally seen as an important step towards a better personalized medicine.
During the last decade various methods have been proposed for that purpose.
However, one important obstacle for making gene signatures a standard tool in
clinics is the typi... | [
{
"created": "Thu, 13 Dec 2012 16:44:55 GMT",
"version": "v1"
},
{
"created": "Mon, 27 May 2013 13:47:19 GMT",
"version": "v2"
}
] | 2013-05-28 | [
[
"Cun",
"Yupeng",
""
],
[
"Fröhlich",
"Holger",
""
]
] | Background: Predictive, stable and interpretable gene signatures are generally seen as an important step towards a better personalized medicine. During the last decade various methods have been proposed for that purpose. However, one important obstacle for making gene signatures a standard tool in clinics is the typica... |
1111.4597 | Iaroslav Ispolatov | Iaroslav Ispolatov, Martin Ackermann, and Michael Doebeli | Division of labour and the evolution of multicellularity | 28 pages, 2 figures | Proc.R.Soc.B(2012)279,1768 | 10.1098/rspb.2011.1999 | null | q-bio.PE cond-mat.other | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the emergence and evolution of multicellularity and cellular
differentiation is a core problem in biology. We develop a quantitative model
that shows that a multicellular form emerges from genetically identical
unicellular ancestors when the compartmentalization of poorly compatible
physiological proces... | [
{
"created": "Sun, 20 Nov 2011 00:16:06 GMT",
"version": "v1"
}
] | 2017-02-07 | [
[
"Ispolatov",
"Iaroslav",
""
],
[
"Ackermann",
"Martin",
""
],
[
"Doebeli",
"Michael",
""
]
] | Understanding the emergence and evolution of multicellularity and cellular differentiation is a core problem in biology. We develop a quantitative model that shows that a multicellular form emerges from genetically identical unicellular ancestors when the compartmentalization of poorly compatible physiological processe... |
2205.08610 | Ali H Husseen Al-Nuaimi Mr | Ali H. Al-Nuaimi, Emmanuel Jammeh, Lingfen Sun, and Emmanuel Ifeachor | Complexity Measures for Quantifying Changes in Electroencephalogram in
Alzheimers Disease | null | null | 10.1155/2018/8915079 | null | q-bio.NC eess.SP | http://creativecommons.org/licenses/by/4.0/ | Alzheimers disease (AD) is a progressive disorder that affects cognitive
brain functions and starts many years before its clinical manifestations. A
biomarker that provides a quantitative measure of changes in the brain due to
AD in the early stages would be useful for early diagnosis of AD, but this
would involve de... | [
{
"created": "Tue, 17 May 2022 19:57:57 GMT",
"version": "v1"
}
] | 2022-05-19 | [
[
"Al-Nuaimi",
"Ali H.",
""
],
[
"Jammeh",
"Emmanuel",
""
],
[
"Sun",
"Lingfen",
""
],
[
"Ifeachor",
"Emmanuel",
""
]
] | Alzheimers disease (AD) is a progressive disorder that affects cognitive brain functions and starts many years before its clinical manifestations. A biomarker that provides a quantitative measure of changes in the brain due to AD in the early stages would be useful for early diagnosis of AD, but this would involve deal... |
1705.03329 | Anne Robertson | Fangzhou Cheng, Anne M. Robertson, Lori Birder, F. Aura Kullmann, Jack
Hornsby, Paul Watton, Simon C. Watkins | Layer dependent role of collagen recruitment during loading of the rat
bladder wall | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work, we reevaluated long standing conjectures as to the source of
the exceptionally large compliance of the bladder wall. Whereas, these
conjectures were based on indirect measures of loading mechanisms, in this work
we take advantage of advances in bioimaging to directly assess collagen fibers
and wall arch... | [
{
"created": "Tue, 9 May 2017 13:44:06 GMT",
"version": "v1"
}
] | 2017-05-10 | [
[
"Cheng",
"Fangzhou",
""
],
[
"Robertson",
"Anne M.",
""
],
[
"Birder",
"Lori",
""
],
[
"Kullmann",
"F. Aura",
""
],
[
"Hornsby",
"Jack",
""
],
[
"Watton",
"Paul",
""
],
[
"Watkins",
"Simon C.",
""
]
] | In this work, we reevaluated long standing conjectures as to the source of the exceptionally large compliance of the bladder wall. Whereas, these conjectures were based on indirect measures of loading mechanisms, in this work we take advantage of advances in bioimaging to directly assess collagen fibers and wall archit... |
2110.01731 | David Nguyen | David H Nguyen | Heritable Nongenetic Information in the Form of the DNA-Autonomous
Tissue Spatial Code that Governs Organismal Development, Tissue Regeneration,
and Tumor Architecture | null | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Numerous studies of the tumor microenvironment, interspecies xenografting,
and limb regeneration suggest the existence of a tissue spatial code [TSC] that
controls tissue structure in a quasi "epigenetic" fashion. Epigenetic is an
inadequate label, because this information does not act directly upon DNA
molecules lik... | [
{
"created": "Mon, 4 Oct 2021 22:23:51 GMT",
"version": "v1"
}
] | 2021-10-06 | [
[
"Nguyen",
"David H",
""
]
] | Numerous studies of the tumor microenvironment, interspecies xenografting, and limb regeneration suggest the existence of a tissue spatial code [TSC] that controls tissue structure in a quasi "epigenetic" fashion. Epigenetic is an inadequate label, because this information does not act directly upon DNA molecules like ... |
2110.10040 | Olivier Faugeras | Olivier D. Faugeras, Anna Song and Romain Veltz | Spatial and color hallucinations in a mathematical model of primary
visual cortex | 30 pages, 12 figures | Comptes Rendus. Math\'ematique, Tome 360 (2022), pp. 59-87 | 10.5802/crmath.289 | null | q-bio.NC cs.NA math.DS math.NA nlin.PS | http://creativecommons.org/licenses/by/4.0/ | We study a simplified model of the representation of colors in the primate
primary cortical visual area V1. The model is described by an initial value
problem related to a Hammerstein equation. The solutions to this problem
represent the variation of the activity of populations of neurons in V1 as a
function of space... | [
{
"created": "Tue, 19 Oct 2021 15:08:51 GMT",
"version": "v1"
}
] | 2022-09-16 | [
[
"Faugeras",
"Olivier D.",
""
],
[
"Song",
"Anna",
""
],
[
"Veltz",
"Romain",
""
]
] | We study a simplified model of the representation of colors in the primate primary cortical visual area V1. The model is described by an initial value problem related to a Hammerstein equation. The solutions to this problem represent the variation of the activity of populations of neurons in V1 as a function of space a... |
1804.02867 | Mona Arabzadeh | Mona Arabzadeh, Mehdi Sedighi, Morteza Saheb Zamani, Sayed-Amir
Marashi | A system architecture for parallel analysis of flux-balanced metabolic
pathways | 33 pages, 13 figures, 3 tables | Computational Biology and Chemistry, Available online 24 June 2020 | 10.1016/j.compbiolchem.2020.107309 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, a system architecture is proposed that approximately models
the functionality of metabolic networks. The AND/OR graph model is used to
represent the metabolic network and each processing element in the system
emulates the functionality of a metabolite. The system is implemented on a
graphics processing... | [
{
"created": "Mon, 9 Apr 2018 08:42:46 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Nov 2018 07:59:04 GMT",
"version": "v2"
},
{
"created": "Thu, 2 Jul 2020 07:33:15 GMT",
"version": "v3"
}
] | 2020-07-03 | [
[
"Arabzadeh",
"Mona",
""
],
[
"Sedighi",
"Mehdi",
""
],
[
"Zamani",
"Morteza Saheb",
""
],
[
"Marashi",
"Sayed-Amir",
""
]
] | In this paper, a system architecture is proposed that approximately models the functionality of metabolic networks. The AND/OR graph model is used to represent the metabolic network and each processing element in the system emulates the functionality of a metabolite. The system is implemented on a graphics processing u... |
2306.04658 | Yuchi Qiu | Yuchi Qiu, Guo-Wei Wei | Mathematics-assisted directed evolution and protein engineering | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Directed evolution is a molecular biology technique that is transforming
protein engineering by creating proteins with desirable properties and
functions. However, it is experimentally impossible to perform the deep
mutational scanning of the entire protein library due to the enormous
mutational space, which scales a... | [
{
"created": "Tue, 6 Jun 2023 19:27:11 GMT",
"version": "v1"
}
] | 2023-06-09 | [
[
"Qiu",
"Yuchi",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Directed evolution is a molecular biology technique that is transforming protein engineering by creating proteins with desirable properties and functions. However, it is experimentally impossible to perform the deep mutational scanning of the entire protein library due to the enormous mutational space, which scales as ... |
1503.01880 | Chuan-Chao Wang | Hong-Bing Yao, Chuan-Chao Wang, Jiang Wang, Xiaolan Tao, Shao-Qing
Wen, Qiajun Du, Qiongying Deng, Bingying Xu, Ying Huang, Hong-Dan Wang,
Shujin Li, Bin Cong, Liying Ma, Li Jin, Johannes Krause, Hui Li | Genetic structure of Sino-Tibetan populations revealed by forensic STR
loci | 11 pages, 2 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/3.0/ | The origin and diversification of Sino-Tibetan populations have been a
long-standing hot debate. However, the limited genetic information of Tibetan
populations keeps this topic far from clear. In the present study, we genotyped
15 forensic autosomal STRs from 803 unrelated Tibetan individuals from Gansu
Province (63... | [
{
"created": "Fri, 6 Mar 2015 09:01:41 GMT",
"version": "v1"
}
] | 2015-03-09 | [
[
"Yao",
"Hong-Bing",
""
],
[
"Wang",
"Chuan-Chao",
""
],
[
"Wang",
"Jiang",
""
],
[
"Tao",
"Xiaolan",
""
],
[
"Wen",
"Shao-Qing",
""
],
[
"Du",
"Qiajun",
""
],
[
"Deng",
"Qiongying",
""
],
[
"Xu",
... | The origin and diversification of Sino-Tibetan populations have been a long-standing hot debate. However, the limited genetic information of Tibetan populations keeps this topic far from clear. In the present study, we genotyped 15 forensic autosomal STRs from 803 unrelated Tibetan individuals from Gansu Province (635 ... |
2306.14926 | Christopher Thron | Francis G. T. Kamba, Leonard C. Eze, Jean Claude Kamgang, Christopher
P. Thron | Analysis of Control Measures for Vector-borne Diseases Using a
Multistage Vector Model with Multi-Host Sub-populations | 42 pages, 3 figures. arXiv admin note: substantial text overlap with
arXiv:1808.07574 | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | We propose and analyze an epidemiological model for vector borne diseases
that integrates a multi-stage vector population and several host
sub-populations which may be characterized by a variety of compartmental model
types: subpopulations all include Susceptible and Infected compartments, but
may or may not include ... | [
{
"created": "Sat, 24 Jun 2023 11:26:03 GMT",
"version": "v1"
}
] | 2023-06-28 | [
[
"Kamba",
"Francis G. T.",
""
],
[
"Eze",
"Leonard C.",
""
],
[
"Kamgang",
"Jean Claude",
""
],
[
"Thron",
"Christopher P.",
""
]
] | We propose and analyze an epidemiological model for vector borne diseases that integrates a multi-stage vector population and several host sub-populations which may be characterized by a variety of compartmental model types: subpopulations all include Susceptible and Infected compartments, but may or may not include Ex... |
2401.15047 | Akil Narayan | Caleb C. Berggren, David Jiang, Y.F. Jack Wang, Jake A. Bergquist,
Lindsay C. Rupp, Zexin Liu, Rob S. MacLeod, Akil Narayan, Lucas H. Timmins | Influence of Material Parameter Variability on the Predicted Coronary
Artery Biomechanical Environment via Uncertainty Quantification | To appear: Biomechanics and Modeling in Mechanobiology | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Central to the clinical adoption of patient-specific modeling strategies is
demonstrating that simulation results are reliable and safe. Simulation
frameworks must be robust to uncertainty in model input(s), and levels of
confidence should accompany results. In this study we applied a coupled
uncertainty quantificati... | [
{
"created": "Fri, 26 Jan 2024 18:19:15 GMT",
"version": "v1"
}
] | 2024-01-29 | [
[
"Berggren",
"Caleb C.",
""
],
[
"Jiang",
"David",
""
],
[
"Wang",
"Y. F. Jack",
""
],
[
"Bergquist",
"Jake A.",
""
],
[
"Rupp",
"Lindsay C.",
""
],
[
"Liu",
"Zexin",
""
],
[
"MacLeod",
"Rob S.",
""
],
[... | Central to the clinical adoption of patient-specific modeling strategies is demonstrating that simulation results are reliable and safe. Simulation frameworks must be robust to uncertainty in model input(s), and levels of confidence should accompany results. In this study we applied a coupled uncertainty quantification... |
1406.2405 | Andrew Vlasic | Andrew Vlasic | Stochastic Replicator Dynamics Subject to Markovian Switching | 14 pages | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Population dynamics are often subject to random independent changes in the
environment. For the two strategy stochastic replicator dynamic, we assume that
stochastic changes in the environment replace the payoffs and variance. This is
modeled by a continuous time Markov chain in a finite atom space. We establish
cond... | [
{
"created": "Tue, 10 Jun 2014 02:33:33 GMT",
"version": "v1"
}
] | 2014-06-11 | [
[
"Vlasic",
"Andrew",
""
]
] | Population dynamics are often subject to random independent changes in the environment. For the two strategy stochastic replicator dynamic, we assume that stochastic changes in the environment replace the payoffs and variance. This is modeled by a continuous time Markov chain in a finite atom space. We establish condit... |
2405.09809 | Joshua Pickard | Joshua Pickard, Cooper Stansbury, Amit Surana, Lindsey Muir, Anthony
Bloch, and Indika Rajapakse | Biomarker Selection for Adaptive Systems | null | null | null | null | q-bio.MN math.OC | http://creativecommons.org/licenses/by/4.0/ | Biomarkers enable objective monitoring of a given cell or state in a
biological system and are widely used in research, biomanufacturing, and
clinical practice. However, identifying appropriate biomarkers that are both
robustly measurable and capture a state accurately remains challenging. We
present a framework for ... | [
{
"created": "Thu, 16 May 2024 04:42:21 GMT",
"version": "v1"
},
{
"created": "Mon, 20 May 2024 15:19:21 GMT",
"version": "v2"
},
{
"created": "Mon, 12 Aug 2024 18:49:38 GMT",
"version": "v3"
}
] | 2024-08-14 | [
[
"Pickard",
"Joshua",
""
],
[
"Stansbury",
"Cooper",
""
],
[
"Surana",
"Amit",
""
],
[
"Muir",
"Lindsey",
""
],
[
"Bloch",
"Anthony",
""
],
[
"Rajapakse",
"Indika",
""
]
] | Biomarkers enable objective monitoring of a given cell or state in a biological system and are widely used in research, biomanufacturing, and clinical practice. However, identifying appropriate biomarkers that are both robustly measurable and capture a state accurately remains challenging. We present a framework for bi... |
2208.00684 | Thomas Williams | Thomas Williams, James McCaw, James Osborne | Choice of spatial discretisation influences the progression of viral
infection within multicellular tissues | 28 pages, 11 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | There has been an increasing recognition of the utility of models of the
spatial dynamics of viral spread within tissues. Multicellular models, where
cells are represented as discrete regions of space coupled to a virus density
surface, are a popular approach to capture these dynamics. Conventionally, such
models are... | [
{
"created": "Mon, 1 Aug 2022 08:36:27 GMT",
"version": "v1"
}
] | 2022-08-02 | [
[
"Williams",
"Thomas",
""
],
[
"McCaw",
"James",
""
],
[
"Osborne",
"James",
""
]
] | There has been an increasing recognition of the utility of models of the spatial dynamics of viral spread within tissues. Multicellular models, where cells are represented as discrete regions of space coupled to a virus density surface, are a popular approach to capture these dynamics. Conventionally, such models are s... |
1607.01656 | Jean-Francois Berret | G. Ramniceanu, B.-T. Doan, C. Vezignol, A. Graillot, C. Loubat, N.
Mignet and J.-F. Berret | Delayed hepatic uptake of multi-phosphonic acid poly(ethylene glycol)
coated iron oxide measured by real-time Magnetic Resonance Imaging | 19 pages 8 figures, RSC Advances, 2016 | RSC Advances 6, 63788 - 63800 (2016) | 10.1039/C6RA09896G | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We report on the synthesis, characterization, stability and pharmacokinetics
of novel iron based contrast agents for magnetic resonance imaging (MRI).
Statistical copolymers combining multiple phosphonic acid groups and
poly(ethylene glycol) (PEG) were synthesized and used as coating agents for 10
nm iron oxide nanoc... | [
{
"created": "Tue, 5 Jul 2016 15:40:32 GMT",
"version": "v1"
}
] | 2021-09-21 | [
[
"Ramniceanu",
"G.",
""
],
[
"Doan",
"B. -T.",
""
],
[
"Vezignol",
"C.",
""
],
[
"Graillot",
"A.",
""
],
[
"Loubat",
"C.",
""
],
[
"Mignet",
"N.",
""
],
[
"Berret",
"J. -F.",
""
]
] | We report on the synthesis, characterization, stability and pharmacokinetics of novel iron based contrast agents for magnetic resonance imaging (MRI). Statistical copolymers combining multiple phosphonic acid groups and poly(ethylene glycol) (PEG) were synthesized and used as coating agents for 10 nm iron oxide nanocry... |
2104.06686 | Marco Baity-Jesi | E. Merz, T. Kozakiewicz, M. Reyes, C. Ebi, P. Isles, M. Baity-Jesi, P.
Roberts, J. S. Jaffe, S. Dennis, T. Hardeman, N. Stevens, T. Lorimer, F.
Pomati | Underwater dual-magnification imaging for automated lake plankton
monitoring | 49 pages | Water Research, 203, 117524 (2021) | 10.1016/j.watres.2021.117524 | null | q-bio.PE physics.ins-det | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We present an approach for automated in-situ monitoring of phytoplankton and
zooplankton communities based on a dual magnification dark-field imaging
microscope/camera. We describe the Dual Scripps Plankton Camera (DSPC) system
and associated image processing, and assess its capabilities in detecting and
characterizi... | [
{
"created": "Wed, 14 Apr 2021 08:16:08 GMT",
"version": "v1"
}
] | 2021-09-17 | [
[
"Merz",
"E.",
""
],
[
"Kozakiewicz",
"T.",
""
],
[
"Reyes",
"M.",
""
],
[
"Ebi",
"C.",
""
],
[
"Isles",
"P.",
""
],
[
"Baity-Jesi",
"M.",
""
],
[
"Roberts",
"P.",
""
],
[
"Jaffe",
"J. S.",
"... | We present an approach for automated in-situ monitoring of phytoplankton and zooplankton communities based on a dual magnification dark-field imaging microscope/camera. We describe the Dual Scripps Plankton Camera (DSPC) system and associated image processing, and assess its capabilities in detecting and characterizing... |
1111.4106 | Jose Vilar | Jose M. G. Vilar and Leonor Saiz | Trafficking Coordinate Description of Intracellular Transport Control of
Signaling Networks | 17 pages, 5 figures | Biophys. J. 101, 2315-2323 (2011) | 10.1016/j.bpj.2011.09.035 | null | q-bio.SC physics.bio-ph q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many cellular networks rely on the regulated transport of their components to
transduce extracellular information into precise intracellular signals. The
dynamics of these networks is typically described in terms of compartmentalized
chemical reactions. There are many important situations, however, in which the
prope... | [
{
"created": "Thu, 17 Nov 2011 14:17:18 GMT",
"version": "v1"
}
] | 2011-11-18 | [
[
"Vilar",
"Jose M. G.",
""
],
[
"Saiz",
"Leonor",
""
]
] | Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized chemical reactions. There are many important situations, however, in which the propert... |
2007.07789 | Zeina Khan PhD | Fazle Hussain, Zeina S. Khan, Frank Van Bussel | US faces endemic Covid-19 infections and deaths; ways to stop the
pandemic | 8 pages, 3 figures | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A new epidemic model for Covid-19 has been constructed and simulated for
eight US states. The coefficients for this model, based on seven coupled
differential equations, are carefully evaluated against recorded data on cases
and deaths. These projections reveal that Covid-19 will become endemic,
spreading for more th... | [
{
"created": "Wed, 15 Jul 2020 16:14:25 GMT",
"version": "v1"
},
{
"created": "Tue, 21 Jul 2020 19:09:14 GMT",
"version": "v2"
}
] | 2020-07-23 | [
[
"Hussain",
"Fazle",
""
],
[
"Khan",
"Zeina S.",
""
],
[
"Van Bussel",
"Frank",
""
]
] | A new epidemic model for Covid-19 has been constructed and simulated for eight US states. The coefficients for this model, based on seven coupled differential equations, are carefully evaluated against recorded data on cases and deaths. These projections reveal that Covid-19 will become endemic, spreading for more than... |
1102.4749 | Jean-Pierre Nadal | Laurent Bonnasse-Gahot and Jean-Pierre Nadal | Perception of categories: from coding efficiency to reaction times | null | Brain Research, Volume 1434 (2012) pp. 47-61 | 10.1016/j.brainres.2011.08.014 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reaction-times in perceptual tasks are the subject of many experimental and
theoretical studies. With the neural decision making process as main focus,
most of these works concern discrete (typically binary) choice tasks, implying
the identification of the stimulus as an exemplar of a category. Here we
address issues... | [
{
"created": "Wed, 23 Feb 2011 14:32:28 GMT",
"version": "v1"
}
] | 2012-03-01 | [
[
"Bonnasse-Gahot",
"Laurent",
""
],
[
"Nadal",
"Jean-Pierre",
""
]
] | Reaction-times in perceptual tasks are the subject of many experimental and theoretical studies. With the neural decision making process as main focus, most of these works concern discrete (typically binary) choice tasks, implying the identification of the stimulus as an exemplar of a category. Here we address issues s... |
0809.0029 | Emmanuel Tannenbaum | Pavel Gorodetsky and Emmanuel Tannenbaum | A Dual Role for Sex? | 7 pages, 4 figures | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The two classic theories for the existence of sexual replication are that sex
purges deleterious mutations from a population, and that sex allows a
population to adapt more rapidly to changing environments. These two theories
have often been presented as opposing explanations for the existence of sex.
Here, we develo... | [
{
"created": "Fri, 29 Aug 2008 23:58:49 GMT",
"version": "v1"
}
] | 2008-09-02 | [
[
"Gorodetsky",
"Pavel",
""
],
[
"Tannenbaum",
"Emmanuel",
""
]
] | The two classic theories for the existence of sexual replication are that sex purges deleterious mutations from a population, and that sex allows a population to adapt more rapidly to changing environments. These two theories have often been presented as opposing explanations for the existence of sex. Here, we develop ... |
q-bio/0509022 | Can Ozan Tan Mr. | Can O. Tan and Uygar Ozesmi | A Cognitive Model of an Epistemic Community: Mapping the Dynamics of
Shallow Lake Ecosystems | 24 pages, 5 Figures | Hydrobiologia, 563:125-142 | 10.1007/s10750-005-1397-5 | null | q-bio.NC q-bio.OT | null | We used fuzzy cognitive mapping (FCM) to develop a generic shallow lake
ecosystem model by augmenting the individual cognitive maps drawn by 8
scientists working in the area of shallow lake ecology. We calculated graph
theoretical indices of the individual cognitive maps and the collective
cognitive map produced by a... | [
{
"created": "Sun, 18 Sep 2005 16:50:32 GMT",
"version": "v1"
}
] | 2011-07-29 | [
[
"Tan",
"Can O.",
""
],
[
"Ozesmi",
"Uygar",
""
]
] | We used fuzzy cognitive mapping (FCM) to develop a generic shallow lake ecosystem model by augmenting the individual cognitive maps drawn by 8 scientists working in the area of shallow lake ecology. We calculated graph theoretical indices of the individual cognitive maps and the collective cognitive map produced by aug... |
0803.3061 | Thierry Mora | Marc Mezard and Thierry Mora | Constraint satisfaction problems and neural networks: a statistical
physics perspective | Prepared for the proceedings of the 2007 Tauc Conference on
Complexity in Neural Network Dynamics | null | null | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A new field of research is rapidly expanding at the crossroad between
statistical physics, information theory and combinatorial optimization. In
particular, the use of cutting edge statistical physics concepts and methods
allow one to solve very large constraint satisfaction problems like random
satisfiability, color... | [
{
"created": "Thu, 20 Mar 2008 19:22:18 GMT",
"version": "v1"
}
] | 2008-03-28 | [
[
"Mezard",
"Marc",
""
],
[
"Mora",
"Thierry",
""
]
] | A new field of research is rapidly expanding at the crossroad between statistical physics, information theory and combinatorial optimization. In particular, the use of cutting edge statistical physics concepts and methods allow one to solve very large constraint satisfaction problems like random satisfiability, colorin... |
2202.08825 | Parsifal Islas-Morales Mr | Parsifal Fidelio Islas-Morales and Luis Felipe Jimenez-Garcia | On the ideas of the origin of eukaryotes: a critical review | 31 pages, review | null | null | null | q-bio.PE q-bio.SC | http://creativecommons.org/licenses/by/4.0/ | The origin and early evolution of eukaryotes are one of the major transitions
in the evolution of life on earth. One of its most interesting aspects is the
emergence of cellular organelles, their dynamics, their functions, and their
divergence. Cell compartmentalization and architecture in prokaryotes is a less
under... | [
{
"created": "Thu, 17 Feb 2022 18:46:53 GMT",
"version": "v1"
}
] | 2022-02-18 | [
[
"Islas-Morales",
"Parsifal Fidelio",
""
],
[
"Jimenez-Garcia",
"Luis Felipe",
""
]
] | The origin and early evolution of eukaryotes are one of the major transitions in the evolution of life on earth. One of its most interesting aspects is the emergence of cellular organelles, their dynamics, their functions, and their divergence. Cell compartmentalization and architecture in prokaryotes is a less underst... |
1208.3766 | Daniele Marinazzo | G. Wu, W.Liao, S. Stramaglia, J. Ding, H. Chen, D. Marinazzo | A blind deconvolution approach to recover effective connectivity brain
networks from resting state fMRI data | null | null | null | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A great improvement to the insight on brain function that we can get from
fMRI data can come from effective connectivity analysis, in which the flow of
information between even remote brain regions is inferred by the parameters of
a predictive dynamical model. As opposed to biologically inspired models, some
techniqu... | [
{
"created": "Sat, 18 Aug 2012 17:02:26 GMT",
"version": "v1"
}
] | 2012-08-21 | [
[
"Wu",
"G.",
""
],
[
"Liao",
"W.",
""
],
[
"Stramaglia",
"S.",
""
],
[
"Ding",
"J.",
""
],
[
"Chen",
"H.",
""
],
[
"Marinazzo",
"D.",
""
]
] | A great improvement to the insight on brain function that we can get from fMRI data can come from effective connectivity analysis, in which the flow of information between even remote brain regions is inferred by the parameters of a predictive dynamical model. As opposed to biologically inspired models, some techniques... |
2103.10433 | Catherine Matias | Marc Ohlmann (LECA ), Catherine Matias (LPSM (UMR\_8001)), Giovanni
Poggiato (LECA, STATIFY), St\'ephane Dray, Wilfried Thuiller (LECA, LECA),
Vincent Miele (LBBE) | Quantifying the overall effect of biotic interactions on species
distributions along environmental gradients | null | null | 10.1016/j.ecolmodel.2023.110424 | null | q-bio.PE stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Separating environmental effects from those of interspecific interactions on
species distributions has always been a central objective of community ecology.
Despite years of effort in analysing patterns of species co-occurrences and the
developments of sophisticated tools, we are still unable to address this major
ob... | [
{
"created": "Thu, 18 Mar 2021 14:41:26 GMT",
"version": "v1"
},
{
"created": "Wed, 12 Oct 2022 07:30:45 GMT",
"version": "v2"
},
{
"created": "Fri, 13 Jan 2023 13:25:23 GMT",
"version": "v3"
},
{
"created": "Tue, 2 May 2023 12:43:35 GMT",
"version": "v4"
}
] | 2023-08-30 | [
[
"Ohlmann",
"Marc",
"",
"LECA"
],
[
"Matias",
"Catherine",
"",
"LPSM"
],
[
"Poggiato",
"Giovanni",
"",
"LECA, STATIFY"
],
[
"Dray",
"Stéphane",
"",
"LECA, LECA"
],
[
"Thuiller",
"Wilfried",
"",
"LECA, LECA"
],
[
... | Separating environmental effects from those of interspecific interactions on species distributions has always been a central objective of community ecology. Despite years of effort in analysing patterns of species co-occurrences and the developments of sophisticated tools, we are still unable to address this major obje... |
q-bio/0611045 | Gergely J Sz\"oll\H{o}si | Balint Szabo, Gergely J. Szollosi, Balazs Gonci, Zsofi Juranyi, David
Selmeczi and Tamas Vicsek | Phase transition in the collective migration of tissue cells: experiment
and model | Submitted to Physical Review E. Supplementary material available at
http://angel.elte.hu/~bszabo/collectivecells/ | Phys. Rev. E 74, 061908 (2006). | 10.1103/PhysRevE.74.061908 | null | q-bio.CB cond-mat.stat-mech physics.bio-ph q-bio.QM q-bio.TO | null | We have recorded the swarming-like collective migration of a large number of
keratocytes (tissue cells obtained from the scales of goldfish) using long-term
videomicroscopy. By increasing the overall density of the migrating cells, we
have been able to demonstrate experimentally a kinetic phase transition from a
diso... | [
{
"created": "Wed, 15 Nov 2006 11:51:22 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Szabo",
"Balint",
""
],
[
"Szollosi",
"Gergely J.",
""
],
[
"Gonci",
"Balazs",
""
],
[
"Juranyi",
"Zsofi",
""
],
[
"Selmeczi",
"David",
""
],
[
"Vicsek",
"Tamas",
""
]
] | We have recorded the swarming-like collective migration of a large number of keratocytes (tissue cells obtained from the scales of goldfish) using long-term videomicroscopy. By increasing the overall density of the migrating cells, we have been able to demonstrate experimentally a kinetic phase transition from a disord... |
2005.06336 | Isabel San Martin | M. Isabel San-Martin, Adrian Escapaa, Raul M. Alonso, Moises Canle,
Antonio Moran | Degradation of 2-mercaptobenzothizaole in microbial electrolysis cells:
intermediates, toxicity, and microbial communities | null | published on Science of The Total Environment, 2020 | 10.1016/j.scitotenv.2020.139155 | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The compound 2-mercaptobenzothizaole (MBT) has been frequently detected in
wastewater and surface water and is a potential threat to both aquatic
organisms and human health (its mutagenic potential has been demonstrated).
This study investigated the degradation routes of MBT in the anode of a
microbial electrolysis c... | [
{
"created": "Wed, 13 May 2020 14:25:18 GMT",
"version": "v1"
}
] | 2020-05-14 | [
[
"San-Martin",
"M. Isabel",
""
],
[
"Escapaa",
"Adrian",
""
],
[
"Alonso",
"Raul M.",
""
],
[
"Canle",
"Moises",
""
],
[
"Moran",
"Antonio",
""
]
] | The compound 2-mercaptobenzothizaole (MBT) has been frequently detected in wastewater and surface water and is a potential threat to both aquatic organisms and human health (its mutagenic potential has been demonstrated). This study investigated the degradation routes of MBT in the anode of a microbial electrolysis cel... |
1501.05605 | Vahid Salari | Vahid Salari, Maryam Sajadi, Hassan Bassereh, Vahid Rezania, Mojtaba
Alaei, Jack Tuszynski | On the Classical Vibrational Coherence of Carbonyl Groups in the
Selectivity Filter Backbone of KcsA Ion Channel | 8 pages, 8 figures | J Integrative Neuroscience, 14 (2), 1-12, 2015 | null | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has been suggested that quantum coherence in the selectivity filter of ion
channel may play a key role in fast conduction and selectivity of ions.
However, it has not been clearly elucidated yet why classical coherence is not
sufficient for this purpose. In this paper, we investigate the classical
vibrational cohe... | [
{
"created": "Sat, 3 Jan 2015 18:28:55 GMT",
"version": "v1"
},
{
"created": "Mon, 27 Apr 2015 12:15:22 GMT",
"version": "v2"
}
] | 2015-04-28 | [
[
"Salari",
"Vahid",
""
],
[
"Sajadi",
"Maryam",
""
],
[
"Bassereh",
"Hassan",
""
],
[
"Rezania",
"Vahid",
""
],
[
"Alaei",
"Mojtaba",
""
],
[
"Tuszynski",
"Jack",
""
]
] | It has been suggested that quantum coherence in the selectivity filter of ion channel may play a key role in fast conduction and selectivity of ions. However, it has not been clearly elucidated yet why classical coherence is not sufficient for this purpose. In this paper, we investigate the classical vibrational cohere... |
0907.2824 | Andrea De Martino | A. De Martino, D. Granata, E. Marinari, C. Martelli, V. Van
Kerrebroeck | Optimal flux states, reaction replaceability and response to knockouts
in the human red blood cell | 7 pages | null | null | null | q-bio.MN cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Characterizing the capabilities, criticalities and response to perturbations
of genome-scale metabolic networks is a basic problem with important
applications. A key question concerns the identification of the potentially
most harmful knockouts. The integration of combinatorial methods with sampling
techniques to exp... | [
{
"created": "Thu, 16 Jul 2009 12:56:05 GMT",
"version": "v1"
}
] | 2009-07-17 | [
[
"De Martino",
"A.",
""
],
[
"Granata",
"D.",
""
],
[
"Marinari",
"E.",
""
],
[
"Martelli",
"C.",
""
],
[
"Van Kerrebroeck",
"V.",
""
]
] | Characterizing the capabilities, criticalities and response to perturbations of genome-scale metabolic networks is a basic problem with important applications. A key question concerns the identification of the potentially most harmful knockouts. The integration of combinatorial methods with sampling techniques to explo... |
q-bio/0507003 | Christian Emig | Christian Emig (DIMAR), Patrick Geistdoerfer (LOV) | The Mediterranean deep-sea fauna: historical evolution, bathymetric
variations and geographical changes | null | Carnets de G\'{e}ologie / Notebooks on Geology Article 2004/01
(CG2004_A01_CCE-PG) (2004) 10 p., 4 fig., 3 tabl | null | null | q-bio.PE | null | The deep-water fauna of the Mediterranean is characterized by an absence of
distinctive characteristics and by a relative impoverishment. Both are a result
of events after the Messinian salinity crisis (Late Miocene). The three main
classes of phenomena involved in producing or recording these effects are
analysed an... | [
{
"created": "Sat, 2 Jul 2005 09:32:32 GMT",
"version": "v1"
}
] | 2019-05-01 | [
[
"Emig",
"Christian",
"",
"DIMAR"
],
[
"Geistdoerfer",
"Patrick",
"",
"LOV"
]
] | The deep-water fauna of the Mediterranean is characterized by an absence of distinctive characteristics and by a relative impoverishment. Both are a result of events after the Messinian salinity crisis (Late Miocene). The three main classes of phenomena involved in producing or recording these effects are analysed and ... |
0704.0634 | Mark Bathe | Mark Bathe | A Finite Element framework for computation of protein normal modes and
mechanical response | null | null | null | null | q-bio.BM q-bio.QM | null | A coarse-grained computational procedure based on the Finite Element Method
is proposed to calculate the normal modes and mechanical response of proteins
and their supramolecular assemblies. Motivated by the elastic network model,
proteins are modeled as homogeneous isotropic elastic solids with volume
defined by the... | [
{
"created": "Wed, 4 Apr 2007 19:02:54 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bathe",
"Mark",
""
]
] | A coarse-grained computational procedure based on the Finite Element Method is proposed to calculate the normal modes and mechanical response of proteins and their supramolecular assemblies. Motivated by the elastic network model, proteins are modeled as homogeneous isotropic elastic solids with volume defined by their... |
2407.05076 | Yihang Zhou | Yihang Zhou | Metagenomic analysis reveals shared and distinguishing features in horse
and donkey gut microbiome and maternal resemblance of the microbiota in
hybrid equids | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Mammalian gut microbiomes are essential for host functions like digestion,
immunity, and nutrient utilization. This study examines the gut microbiome of
horses, donkeys, and their hybrids, mules and hinnies, to explore the role of
microbiomes in hybrid vigor. We performed whole-genome sequencing on rectal
microbiota ... | [
{
"created": "Sat, 6 Jul 2024 13:37:11 GMT",
"version": "v1"
}
] | 2024-07-09 | [
[
"Zhou",
"Yihang",
""
]
] | Mammalian gut microbiomes are essential for host functions like digestion, immunity, and nutrient utilization. This study examines the gut microbiome of horses, donkeys, and their hybrids, mules and hinnies, to explore the role of microbiomes in hybrid vigor. We performed whole-genome sequencing on rectal microbiota fr... |
2310.05639 | Miroslav Semotiuk Vasilevich | M. V. Semotiuk, A. V. Palagin | Technocratic model of the human auditory system | 30 pages, 19 figures | null | null | null | q-bio.NC cs.SD eess.AS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work, we investigate the phenomenon of transverse resonance and
transverse standing waves that occur within the cochlea of living organisms. It
is demonstrated that the predisposing factor for their occurrence is the
cochlear shape, which resembles a conical acoustic tube coiled into a spiral
and exhibits non... | [
{
"created": "Mon, 9 Oct 2023 11:51:22 GMT",
"version": "v1"
}
] | 2023-10-10 | [
[
"Semotiuk",
"M. V.",
""
],
[
"Palagin",
"A. V.",
""
]
] | In this work, we investigate the phenomenon of transverse resonance and transverse standing waves that occur within the cochlea of living organisms. It is demonstrated that the predisposing factor for their occurrence is the cochlear shape, which resembles a conical acoustic tube coiled into a spiral and exhibits non-u... |
2306.03117 | Jiarui Lu | Jiarui Lu, Bozitao Zhong, Zuobai Zhang, Jian Tang | Str2Str: A Score-based Framework for Zero-shot Protein Conformation
Sampling | Published as a conference paper at ICLR 2024, see
https://openreview.net/forum?id=C4BikKsgmK | null | null | null | q-bio.QM cs.LG q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The dynamic nature of proteins is crucial for determining their biological
functions and properties, for which Monte Carlo (MC) and molecular dynamics
(MD) simulations stand as predominant tools to study such phenomena. By
utilizing empirically derived force fields, MC or MD simulations explore the
conformational spa... | [
{
"created": "Mon, 5 Jun 2023 15:19:06 GMT",
"version": "v1"
},
{
"created": "Thu, 15 Feb 2024 16:59:42 GMT",
"version": "v2"
},
{
"created": "Mon, 11 Mar 2024 19:54:30 GMT",
"version": "v3"
}
] | 2024-03-13 | [
[
"Lu",
"Jiarui",
""
],
[
"Zhong",
"Bozitao",
""
],
[
"Zhang",
"Zuobai",
""
],
[
"Tang",
"Jian",
""
]
] | The dynamic nature of proteins is crucial for determining their biological functions and properties, for which Monte Carlo (MC) and molecular dynamics (MD) simulations stand as predominant tools to study such phenomena. By utilizing empirically derived force fields, MC or MD simulations explore the conformational space... |
1002.4485 | Ulrich S. Schwarz | Jakob Schluttig, Christian B. Korn, and Ulrich S. Schwarz (University
of Heidelberg, Institute for Theoretical Physics and Bioquant) | Role of anisotropy for protein-protein encounter | 4 pages, Revtex with 3 figures, to appear as a Rapid Communication in
Physical Review E | null | 10.1103/PhysRevE.81.030902 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein-protein interactions comprise both transport and reaction steps.
During the transport step, anisotropy of proteins and their complexes is
important both for hydrodynamic diffusion and accessibility of the binding
site. Using a Brownian dynamics approach and extensive computer simulations, we
quantify the effe... | [
{
"created": "Wed, 24 Feb 2010 08:14:19 GMT",
"version": "v1"
}
] | 2015-05-18 | [
[
"Schluttig",
"Jakob",
"",
"University\n of Heidelberg, Institute for Theoretical Physics and Bioquant"
],
[
"Korn",
"Christian B.",
"",
"University\n of Heidelberg, Institute for Theoretical Physics and Bioquant"
],
[
"Schwarz",
"Ulrich S.",
"",
"Universit... | Protein-protein interactions comprise both transport and reaction steps. During the transport step, anisotropy of proteins and their complexes is important both for hydrodynamic diffusion and accessibility of the binding site. Using a Brownian dynamics approach and extensive computer simulations, we quantify the effect... |
0803.2092 | Yoann Pigne | Fr\'ed\'eric Guinand (LITIS), Yoann Pign\'e (LITIS) | An Ant-Based Model for Multiple Sequence Alignment | null | Dans Large-Scale Scientific Computing - Large-Scale Scientific
Computing, 6th International Conference, LSSC 2007, Sozopol : Bulgarie (2007) | null | null | q-bio.QM cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multiple sequence alignment is a key process in today's biology, and finding
a relevant alignment of several sequences is much more challenging than just
optimizing some improbable evaluation functions. Our approach for addressing
multiple sequence alignment focuses on the building of structures in a new
graph model:... | [
{
"created": "Fri, 14 Mar 2008 06:58:56 GMT",
"version": "v1"
}
] | 2008-12-18 | [
[
"Guinand",
"Frédéric",
"",
"LITIS"
],
[
"Pigné",
"Yoann",
"",
"LITIS"
]
] | Multiple sequence alignment is a key process in today's biology, and finding a relevant alignment of several sequences is much more challenging than just optimizing some improbable evaluation functions. Our approach for addressing multiple sequence alignment focuses on the building of structures in a new graph model: t... |
1408.2114 | Peter Clote Peter Clote | Ivan Dotu, Juan Antonio Garcia-Martin, Betty L. Slinger, Vinodh
Mechery, Michelle M. Meyer, Peter Clote | Complete RNA inverse folding: computational design of functional
hammerhead ribozymes | 17 pages, 2 tables, 7 figures, final version to appear in Nucleic
Acids Research | Nucl. Acids Res. (2014) 42 (18): 11752-11762 | 10.1093/nar/gku740 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nanotechnology and synthetic biology currently constitute one of the most
innovative, interdisciplinary fields of research, poised to radically transform
society in the 21st century. This paper concerns the synthetic design of
ribonucleic acid molecules, using our recent algorithm, RNAiFold, which can
determine all R... | [
{
"created": "Sat, 9 Aug 2014 14:42:00 GMT",
"version": "v1"
}
] | 2015-05-29 | [
[
"Dotu",
"Ivan",
""
],
[
"Garcia-Martin",
"Juan Antonio",
""
],
[
"Slinger",
"Betty L.",
""
],
[
"Mechery",
"Vinodh",
""
],
[
"Meyer",
"Michelle M.",
""
],
[
"Clote",
"Peter",
""
]
] | Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold, which can determine all RNA... |
1605.07488 | Wei Zhang | Ke Tang and Wei Zhang | Transcriptional Similarity in Couples Reveals the Impact of Shared
Environment and Lifestyle on Gene Regulation through Modified Cytosines | null | null | 10.7717/peerj.2123. | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene expression is a complex and quantitative trait that is influenced by
both genetic and non-genetic regulators including environmental factors.
Evaluating the contribution of environment to gene expression regulation and
identifying which genes are more likely to be influenced by environmental
factors are importan... | [
{
"created": "Tue, 24 May 2016 14:53:03 GMT",
"version": "v1"
}
] | 2019-06-27 | [
[
"Tang",
"Ke",
""
],
[
"Zhang",
"Wei",
""
]
] | Gene expression is a complex and quantitative trait that is influenced by both genetic and non-genetic regulators including environmental factors. Evaluating the contribution of environment to gene expression regulation and identifying which genes are more likely to be influenced by environmental factors are important ... |
2103.13120 | Mar\'ia Vallet-Regi | L. Casarrubios, N. Gomez-Cerezo, S. Sanchez-Salcedo, M.J. Feito, M.C.
Serrano, M. Saiz-Pardo, L. Ortega, D. de Pablo, I. Diaz-Guemes, B.
Fernandez-Tome, S. Enciso, F.M. Sanchez-Margallo, M.T. Portoles, D. Arcos, M.
Vallet-Regi | Silicon substituted hydroxyapatite/VEGF scaffolds stimulate bone
regeneration in osteoporotic sheep | 23 pages | Acta Biomaterialia 101, 544-553 (2019) | 10.1016/j.actbio.2019.10.033 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Silicon-substituted hydroxyapatite (SiHA) macroporous scaffolds have been
prepared by robocasting. In order to optimize their bone regeneration
properties, we have manufactured these scaffolds presenting different
microstructures: nanocrystalline and crystalline. Moreover, their surfaces have
been decorated with vasc... | [
{
"created": "Wed, 24 Mar 2021 11:51:09 GMT",
"version": "v1"
}
] | 2021-03-25 | [
[
"Casarrubios",
"L.",
""
],
[
"Gomez-Cerezo",
"N.",
""
],
[
"Sanchez-Salcedo",
"S.",
""
],
[
"Feito",
"M. J.",
""
],
[
"Serrano",
"M. C.",
""
],
[
"Saiz-Pardo",
"M.",
""
],
[
"Ortega",
"L.",
""
],
[
... | Silicon-substituted hydroxyapatite (SiHA) macroporous scaffolds have been prepared by robocasting. In order to optimize their bone regeneration properties, we have manufactured these scaffolds presenting different microstructures: nanocrystalline and crystalline. Moreover, their surfaces have been decorated with vascul... |
2007.13469 | Niharika Pandala | Niharika Pandala (1), Casey A. Cole (1), Devaun McFarland (1), Anita
Nag (2), Homayoun Valafar (1) ((1) University of South Carolina Columbia, (2)
University of South Carolina Upstate) | A Preliminary Investigation in the Molecular Basis of Host Shutoff
Mechanism in SARS-CoV | Consists of 9 pages, 8 figures and 7 tables. 11th ACM Conference on
Bioinformatics, Computational Biology, and Health Informatics 2020 | null | null | null | q-bio.BM cs.CE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent events leading to the worldwide pandemic of COVID-19 have demonstrated
the effective use of genomic sequencing technologies to establish the genetic
sequence of this virus. In contrast, the COVID-19 pandemic has demonstrated the
absence of computational approaches to understand the molecular basis of this
infe... | [
{
"created": "Thu, 23 Jul 2020 21:56:07 GMT",
"version": "v1"
}
] | 2020-07-28 | [
[
"Pandala",
"Niharika",
""
],
[
"Cole",
"Casey A.",
""
],
[
"McFarland",
"Devaun",
""
],
[
"Nag",
"Anita",
""
],
[
"Valafar",
"Homayoun",
""
]
] | Recent events leading to the worldwide pandemic of COVID-19 have demonstrated the effective use of genomic sequencing technologies to establish the genetic sequence of this virus. In contrast, the COVID-19 pandemic has demonstrated the absence of computational approaches to understand the molecular basis of this infect... |
1906.11679 | Anna Melnykova | Vincent Calvez (ICJ), Susely Figueroa Iglesias (IMT), H\'el\`ene
Hivert (ICJ), Sylvie M\'el\'eard (CMAP), Anna Melnykova (LJK, AGM), Samuel
Nordmann (CAMS) | Horizontal gene transfer: numerical comparison between stochastic and
deterministic approaches | null | null | 10.1051/proc/202067009 | null | q-bio.PE math.AP math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Horizontal gene Transfer (HT) denotes the transmission of genetic material
between two living organisms, while the vertical transmission refers to a DNA
transfer from parents to their offspring. Consistent experimental evidence
report that this phenomenon plays an essential role in the evolution of certain
bacterias.... | [
{
"created": "Thu, 27 Jun 2019 14:23:28 GMT",
"version": "v1"
}
] | 2021-02-12 | [
[
"Calvez",
"Vincent",
"",
"ICJ"
],
[
"Iglesias",
"Susely Figueroa",
"",
"IMT"
],
[
"Hivert",
"Hélène",
"",
"ICJ"
],
[
"Méléard",
"Sylvie",
"",
"CMAP"
],
[
"Melnykova",
"Anna",
"",
"LJK, AGM"
],
[
"Nordmann",
... | Horizontal gene Transfer (HT) denotes the transmission of genetic material between two living organisms, while the vertical transmission refers to a DNA transfer from parents to their offspring. Consistent experimental evidence report that this phenomenon plays an essential role in the evolution of certain bacterias. I... |
1612.01396 | Antti Niemi | Jiaojiao Liu, Jin Dai, Jianfeng He, Antti J. Niemi, Nevena Ilieva | Towards multistage modelling of protein dynamics with monomeric Myc
oncoprotein as an example | 17 figures | Phys. Rev. E 95, 032406 (2017) | 10.1103/PhysRevE.95.032406 | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose to combine a mean field approach with all atom molecular dynamics
into a multistage algorithm that can model protein folding and dynamics over
very long time periods yet with atomic level precision. As an example we
investigate an isolated monomeric Myc oncoprotein that has been implicated in
carcinomas in... | [
{
"created": "Mon, 5 Dec 2016 15:30:55 GMT",
"version": "v1"
}
] | 2017-03-15 | [
[
"Liu",
"Jiaojiao",
""
],
[
"Dai",
"Jin",
""
],
[
"He",
"Jianfeng",
""
],
[
"Niemi",
"Antti J.",
""
],
[
"Ilieva",
"Nevena",
""
]
] | We propose to combine a mean field approach with all atom molecular dynamics into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic level precision. As an example we investigate an isolated monomeric Myc oncoprotein that has been implicated in carcinomas incl... |
1006.1730 | Atheer Matroud | A. A. Matroud, M. D. Hendy and C. P. Tuffley | NTRFINDER: A Software Tool to Find Nested Tandem Repeats | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce the software tool NTRFinder to find the complex repetitive
structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence
of two or more distinct tandem motifs interspersed with each other. We propose
that nested tandem repeats can be used as phylogenetic and population markers.
We have te... | [
{
"created": "Wed, 9 Jun 2010 07:49:37 GMT",
"version": "v1"
},
{
"created": "Tue, 3 May 2011 02:40:13 GMT",
"version": "v2"
}
] | 2011-05-04 | [
[
"Matroud",
"A. A.",
""
],
[
"Hendy",
"M. D.",
""
],
[
"Tuffley",
"C. P.",
""
]
] | We introduce the software tool NTRFinder to find the complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that nested tandem repeats can be used as phylogenetic and population markers. We have test... |
1103.4090 | Luis Rocha | An\'alia Louren\c{c}o, Michael Conover, Andrew Wong, Azadeh
Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis M. Rocha | A Linear Classifier Based on Entity Recognition Tools and a Statistical
Approach to Method Extraction in the Protein-Protein Interaction Literature | BMC Bioinformatics. In Press | null | null | null | q-bio.QM cs.CL cs.IR cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We participated, in the Article Classification and the Interaction Method
subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction task of
the BioCreative III Challenge. For the ACT, we pursued an extensive testing of
available Named Entity Recognition and dictionary tools, and used the most
promising ... | [
{
"created": "Mon, 21 Mar 2011 17:33:32 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Apr 2011 17:46:37 GMT",
"version": "v2"
}
] | 2011-04-25 | [
[
"Lourenço",
"Anália",
""
],
[
"Conover",
"Michael",
""
],
[
"Wong",
"Andrew",
""
],
[
"Nematzadeh",
"Azadeh",
""
],
[
"Pan",
"Fengxia",
""
],
[
"Shatkay",
"Hagit",
""
],
[
"Rocha",
"Luis M.",
""
]
] | We participated, in the Article Classification and the Interaction Method subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction task of the BioCreative III Challenge. For the ACT, we pursued an extensive testing of available Named Entity Recognition and dictionary tools, and used the most promising on... |
1606.03482 | Mathieu Delangle | Mathieu Delangle, \'Emilie Poirson, Jean Fran\c{c}ois Petiot | Study of human accessibility: physical tests versus numerical simulation | null | Design conference , May 2014, Cavtat, Croatia | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Consideration of physical dimensions of the user population is essential to
design adapted environment. This variability in body dimensions (called
"anthropometry") is involved in design tools commonly used today to assess
user's accommodation (physical mock-ups, population models, database, boundary
manikins, hybrid... | [
{
"created": "Tue, 22 Dec 2015 13:34:34 GMT",
"version": "v1"
}
] | 2016-06-14 | [
[
"Delangle",
"Mathieu",
""
],
[
"Poirson",
"Émilie",
""
],
[
"Petiot",
"Jean François",
""
]
] | Consideration of physical dimensions of the user population is essential to design adapted environment. This variability in body dimensions (called "anthropometry") is involved in design tools commonly used today to assess user's accommodation (physical mock-ups, population models, database, boundary manikins, hybrid m... |
1505.01289 | Jicun Wang-Michelitsch | Jicun Wang-Michelitsch and Thomas M. Michelitsch | Misrepair mechanism in the development of atherosclerotic plaques | 8 pages, 3 figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Atherosclerosis is a disease characterized by the development of
atherosclerotic plaques (APs) in arterial endothelium. The APs in part of an
arterial wall are inhomogeneous on size and on distribution. In order to
understand this in-homogeneity, the pathology of APs is analyzed by Misrepair
mechanism, a mechanism pr... | [
{
"created": "Wed, 6 May 2015 08:59:49 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Sep 2017 09:08:23 GMT",
"version": "v2"
}
] | 2017-09-07 | [
[
"Wang-Michelitsch",
"Jicun",
""
],
[
"Michelitsch",
"Thomas M.",
""
]
] | Atherosclerosis is a disease characterized by the development of atherosclerotic plaques (APs) in arterial endothelium. The APs in part of an arterial wall are inhomogeneous on size and on distribution. In order to understand this in-homogeneity, the pathology of APs is analyzed by Misrepair mechanism, a mechanism prop... |
1103.0097 | Kavita Jain | Kavita Jain and Sarada Seetharaman | Nonlinear deterministic equations in biological evolution | Invited review for J. Nonlin. Math. Phys | J. Nonlin. Math. Phys. 18, 321 (2011) | 10.1142/S1402925111001556 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We review models of biological evolution in which the population frequency
changes deterministically with time. If the population is self-replicating,
although the equations for simple prototypes can be linearised, nonlinear
equations arise in many complex situations. For sexual populations, even in the
simplest sett... | [
{
"created": "Tue, 1 Mar 2011 07:58:44 GMT",
"version": "v1"
},
{
"created": "Tue, 12 Apr 2011 11:16:25 GMT",
"version": "v2"
}
] | 2015-05-27 | [
[
"Jain",
"Kavita",
""
],
[
"Seetharaman",
"Sarada",
""
]
] | We review models of biological evolution in which the population frequency changes deterministically with time. If the population is self-replicating, although the equations for simple prototypes can be linearised, nonlinear equations arise in many complex situations. For sexual populations, even in the simplest settin... |
1609.09051 | Michelle Kendall | Michelle Kendall and Diepreye Ayabina and Caroline Colijn | Estimating transmission from genetic and epidemiological data: a metric
to compare transmission trees | 17 pages, 8 figures | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reconstructing who infected whom is a central challenge in analysing
epidemiological data. Recently, advances in sequencing technology have led to
increasing interest in Bayesian approaches to inferring who infected whom using
genetic data from pathogens. The logic behind such approaches is that isolates
that are nea... | [
{
"created": "Wed, 28 Sep 2016 19:45:05 GMT",
"version": "v1"
}
] | 2016-09-30 | [
[
"Kendall",
"Michelle",
""
],
[
"Ayabina",
"Diepreye",
""
],
[
"Colijn",
"Caroline",
""
]
] | Reconstructing who infected whom is a central challenge in analysing epidemiological data. Recently, advances in sequencing technology have led to increasing interest in Bayesian approaches to inferring who infected whom using genetic data from pathogens. The logic behind such approaches is that isolates that are nearl... |
1604.06299 | Christoph Adami | Thomas LaBar and Christoph Adami | Different evolutionary paths to complexity for small and large
populations of digital organisms | 22 pages, 5 figures, 7 Supporting Figures and 1 Supporting Table | PLoS Computational Biology 12 (2016) e1005066 | 10.1371/journal.pcbi.1005066 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A major aim of evolutionary biology is to explain the respective roles of
adaptive versus non-adaptive changes in the evolution of complexity. While
selection is certainly responsible for the spread and maintenance of complex
phenotypes, this does not automatically imply that strong selection enhances
the chance for ... | [
{
"created": "Thu, 21 Apr 2016 13:36:33 GMT",
"version": "v1"
}
] | 2017-01-17 | [
[
"LaBar",
"Thomas",
""
],
[
"Adami",
"Christoph",
""
]
] | A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes, this does not automatically imply that strong selection enhances the chance for th... |
1602.04776 | Vince Grolmusz | Bal\'azs Szalkai and Csaba Kerepesi and B\'alint Varga and Vince
Grolmusz | Parameterizable Consensus Connectomes from the Human Connectome Project:
The Budapest Reference Connectome Server v3.0 | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Connections of the living human brain, on a macroscopic scale, can be mapped
by a diffusion MR imaging based workflow. Since the same anatomic regions can
be corresponded between distinct brains, one can compare the presence or the
absence of the edges, connecting the very same two anatomic regions, among
multiple co... | [
{
"created": "Mon, 15 Feb 2016 19:38:43 GMT",
"version": "v1"
}
] | 2016-02-16 | [
[
"Szalkai",
"Balázs",
""
],
[
"Kerepesi",
"Csaba",
""
],
[
"Varga",
"Bálint",
""
],
[
"Grolmusz",
"Vince",
""
]
] | Connections of the living human brain, on a macroscopic scale, can be mapped by a diffusion MR imaging based workflow. Since the same anatomic regions can be corresponded between distinct brains, one can compare the presence or the absence of the edges, connecting the very same two anatomic regions, among multiple cort... |
2008.10758 | Manoj P. Samanta | Anne Gvozdjak and Manoj P. Samanta | Genes Preferring Non-AUG Start Codons in Bacteria | null | null | null | null | q-bio.GN q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Here we investigate translational regulation in bacteria by analyzing the
distribution of start codons in fully assembled genomes. We report 36 genes
(infC, rpoC, rnpA, etc.) showing a preference for non-AUG start codons in
evolutionarily diverse phyla ("non-AUG genes"). Most of the non-AUG genes are
functionally ass... | [
{
"created": "Tue, 25 Aug 2020 00:28:12 GMT",
"version": "v1"
}
] | 2020-08-26 | [
[
"Gvozdjak",
"Anne",
""
],
[
"Samanta",
"Manoj P.",
""
]
] | Here we investigate translational regulation in bacteria by analyzing the distribution of start codons in fully assembled genomes. We report 36 genes (infC, rpoC, rnpA, etc.) showing a preference for non-AUG start codons in evolutionarily diverse phyla ("non-AUG genes"). Most of the non-AUG genes are functionally assoc... |
1608.05494 | Joshua M. Deutsch | J. M. Deutsch | Associative memory by collective regulation of non-coding RNA | 7 pages, 2 figures | null | null | null | q-bio.MN q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The majority of mammalian genomic transcripts do not directly code for
proteins and it is currently believed that most of these are not under
evolutionary constraint. However given the abundance non-coding RNA (ncRNA) and
its strong affinity for inter-RNA binding, these molecules have the potential
to regulate protei... | [
{
"created": "Fri, 19 Aug 2016 05:07:27 GMT",
"version": "v1"
}
] | 2016-08-22 | [
[
"Deutsch",
"J. M.",
""
]
] | The majority of mammalian genomic transcripts do not directly code for proteins and it is currently believed that most of these are not under evolutionary constraint. However given the abundance non-coding RNA (ncRNA) and its strong affinity for inter-RNA binding, these molecules have the potential to regulate proteins... |
1401.2238 | Gennadi Glinsky | Gennadi V. Glinsky | Integrative genomics analysis identifies pericentromeric regions of
human chromosomes affecting patterns of inter-chromosomal interactions | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genome-wide analysis of distributions of densities of long-range interactions
of human chromosomes with each other, nucleoli, nuclear lamina, and binding
sites of chromatin state regulatory proteins, CTCF and STAT1, identifies
non-random highly correlated patterns of density distributions along the
chromosome length ... | [
{
"created": "Fri, 10 Jan 2014 06:39:08 GMT",
"version": "v1"
}
] | 2014-01-13 | [
[
"Glinsky",
"Gennadi V.",
""
]
] | Genome-wide analysis of distributions of densities of long-range interactions of human chromosomes with each other, nucleoli, nuclear lamina, and binding sites of chromatin state regulatory proteins, CTCF and STAT1, identifies non-random highly correlated patterns of density distributions along the chromosome length fo... |
2009.09150 | Christopher Rose | Christopher Rose and Andrew J. Medford and C. Franklin Goldsmith and
Tejs Vegge and Joshua Weitz and Andrew A. Peterson | Population Susceptibility Variation and Its Effect on Contagion Dynamics | 12 pages, 2 figures | null | null | null | q-bio.PE cs.SI cs.SY eess.SY | http://creativecommons.org/licenses/by/4.0/ | Susceptibility governs the dynamics of contagion. The classical SIR model is
one of the simplest compartmental models of contagion spread, assuming a single
shared susceptibility level. However, variation in susceptibility over a
population can fundamentally affect the dynamics of contagion and thus the
ultimate outc... | [
{
"created": "Sat, 19 Sep 2020 03:15:34 GMT",
"version": "v1"
}
] | 2020-09-22 | [
[
"Rose",
"Christopher",
""
],
[
"Medford",
"Andrew J.",
""
],
[
"Goldsmith",
"C. Franklin",
""
],
[
"Vegge",
"Tejs",
""
],
[
"Weitz",
"Joshua",
""
],
[
"Peterson",
"Andrew A.",
""
]
] | Susceptibility governs the dynamics of contagion. The classical SIR model is one of the simplest compartmental models of contagion spread, assuming a single shared susceptibility level. However, variation in susceptibility over a population can fundamentally affect the dynamics of contagion and thus the ultimate outcom... |
1601.02160 | Thierry Mora | Rhys M. Adams, Thierry Mora, Aleksandra M. Walczak, Justin B. Kinney | Measuring the sequence-affinity landscape of antibodies with massively
parallel titration curves | null | eLife 2016;5:e23156 (2016) | 10.7554/eLife.23156 | null | q-bio.QM q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite the central role that antibodies play in the adaptive immune system
and in biotechnology, much remains unknown about the quantitative relationship
between an antibody's amino acid sequence and its antigen binding affinity.
Here we describe a new experimental approach, called Tite-Seq, that is capable
of measu... | [
{
"created": "Sat, 9 Jan 2016 22:19:17 GMT",
"version": "v1"
},
{
"created": "Tue, 15 Nov 2016 14:52:39 GMT",
"version": "v2"
}
] | 2018-04-16 | [
[
"Adams",
"Rhys M.",
""
],
[
"Mora",
"Thierry",
""
],
[
"Walczak",
"Aleksandra M.",
""
],
[
"Kinney",
"Justin B.",
""
]
] | Despite the central role that antibodies play in the adaptive immune system and in biotechnology, much remains unknown about the quantitative relationship between an antibody's amino acid sequence and its antigen binding affinity. Here we describe a new experimental approach, called Tite-Seq, that is capable of measuri... |
1710.02623 | Yuri A. Dabaghian | Andrey Babichev, Dmitriy Morozov and Yuri Dabaghian | Robust spatial memory maps encoded in networks with transient
connections | 24 pages, 10 figures, 4 supplementary figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The spiking activity of principal cells in mammalian hippocampus encodes an
internalized neuronal representation of the ambient space---a cognitive map.
Once learned, such a map enables the animal to navigate a given environment for
a long period. However, the neuronal substrate that produces this map remains
transie... | [
{
"created": "Sat, 7 Oct 2017 02:50:37 GMT",
"version": "v1"
}
] | 2017-10-10 | [
[
"Babichev",
"Andrey",
""
],
[
"Morozov",
"Dmitriy",
""
],
[
"Dabaghian",
"Yuri",
""
]
] | The spiking activity of principal cells in mammalian hippocampus encodes an internalized neuronal representation of the ambient space---a cognitive map. Once learned, such a map enables the animal to navigate a given environment for a long period. However, the neuronal substrate that produces this map remains transient... |
1605.01381 | Sergey Agapov | S.N. Agapov, V.A. Bulanov, A.V. Zakharov, M.S. Sergeeva | Review of analytical instruments for EEG analysis | Review and rework | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Since it was first used in 1926, EEG has been one of the most useful
instruments of neuroscience. In order to start using EEG data we need not only
EEG apparatus, but also some analytical tools and skills to understand what our
data mean. This article describes several classical analytical tools and also
new one whic... | [
{
"created": "Fri, 4 Mar 2016 12:02:40 GMT",
"version": "v1"
},
{
"created": "Tue, 21 Jun 2022 05:34:19 GMT",
"version": "v2"
}
] | 2022-06-22 | [
[
"Agapov",
"S. N.",
""
],
[
"Bulanov",
"V. A.",
""
],
[
"Zakharov",
"A. V.",
""
],
[
"Sergeeva",
"M. S.",
""
]
] | Since it was first used in 1926, EEG has been one of the most useful instruments of neuroscience. In order to start using EEG data we need not only EEG apparatus, but also some analytical tools and skills to understand what our data mean. This article describes several classical analytical tools and also new one which ... |
0905.3728 | Matthew Parker | Matthew Parker and Alex Kamenev | Extinction in Lotka-Volterra model | 11 pages, 17 figures | null | 10.1103/PhysRevE.80.021129 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Competitive birth-death processes often exhibit an oscillatory behavior. We
investigate a particular case where the oscillation cycles are marginally
stable on the mean-field level. An iconic example of such a system is the
Lotka-Volterra model of predator-prey competition. Fluctuation effects due to
discreteness of ... | [
{
"created": "Fri, 22 May 2009 17:21:06 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Parker",
"Matthew",
""
],
[
"Kamenev",
"Alex",
""
]
] | Competitive birth-death processes often exhibit an oscillatory behavior. We investigate a particular case where the oscillation cycles are marginally stable on the mean-field level. An iconic example of such a system is the Lotka-Volterra model of predator-prey competition. Fluctuation effects due to discreteness of th... |
2109.01039 | Paolo Muratore | Cristiano Capone, Paolo Muratore and Pier Stanislao Paolucci | Error-based or target-based? A unifying framework for learning in
recurrent spiking networks | Main text: 14 pages, 5 figures Suppl. Mat.: 12 pages, 3 figures | null | 10.1371/journal.pcbi.1010221 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Learning in biological or artificial networks means changing the laws
governing the network dynamics in order to better behave in a specific
situation. In the field of supervised learning, two complementary approaches
stand out: error-based and target-based learning. However, there exists no
consensus on which is bet... | [
{
"created": "Thu, 2 Sep 2021 15:57:23 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Sep 2021 17:17:42 GMT",
"version": "v2"
}
] | 2022-10-12 | [
[
"Capone",
"Cristiano",
""
],
[
"Muratore",
"Paolo",
""
],
[
"Paolucci",
"Pier Stanislao",
""
]
] | Learning in biological or artificial networks means changing the laws governing the network dynamics in order to better behave in a specific situation. In the field of supervised learning, two complementary approaches stand out: error-based and target-based learning. However, there exists no consensus on which is bette... |
1601.06047 | Dan Graur Dan Graur | Dan Graur | Rubbish DNA: The functionless fraction of the human genome | 87 pages, 1 Figure, 1 Table | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Because genomes are products of natural processes rather than intelligent
design, all genomes contain functional and nonfunctional parts. The fraction of
the genome that has no biological function is called rubbish DNA. Rubbish DNA
consists of junk DNA, i.e., the fraction of the genome on which selection does
not ope... | [
{
"created": "Fri, 22 Jan 2016 15:41:37 GMT",
"version": "v1"
}
] | 2016-01-25 | [
[
"Graur",
"Dan",
""
]
] | Because genomes are products of natural processes rather than intelligent design, all genomes contain functional and nonfunctional parts. The fraction of the genome that has no biological function is called rubbish DNA. Rubbish DNA consists of junk DNA, i.e., the fraction of the genome on which selection does not opera... |
2405.05301 | Gary An | Gary An and Chase Cockrell | A design specification for Critical Illness Digital Twins to cure
sepsis: responding to the National Academies of Sciences, Engineering and
Medicine Report: Foundational Research Gaps and Future Directions for Digital
Twins | 31 pages, 13 Figures, 1 Table | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | On December 15, 2023, The National Academies of Sciences, Engineering and
Medicine (NASEM) released a report entitled: Foundational Research Gaps and
Future Directions for Digital Twins. The ostensible purpose of this report was
to bring some structure to the burgeoning field of digital twins by providing a
working d... | [
{
"created": "Wed, 8 May 2024 17:17:58 GMT",
"version": "v1"
},
{
"created": "Sun, 16 Jun 2024 22:26:50 GMT",
"version": "v2"
}
] | 2024-06-18 | [
[
"An",
"Gary",
""
],
[
"Cockrell",
"Chase",
""
]
] | On December 15, 2023, The National Academies of Sciences, Engineering and Medicine (NASEM) released a report entitled: Foundational Research Gaps and Future Directions for Digital Twins. The ostensible purpose of this report was to bring some structure to the burgeoning field of digital twins by providing a working def... |
2209.08792 | Robin Broersen | R. Broersen and G. J. Stuart | In vivo whole-cell recording from morphologically identified mouse
superior colliculus neurons | 29 pages including 4 figures | STAR Protocols 4 (2023) 101963 | 10.1016/j.xpro.2022.101963 | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In vivo whole-cell recording when combined with morphological
characterization after biocytin labeling is a powerful technique to study
subthreshold synaptic processing in cell-type-identified neuronal populations.
Here, we provide a step-by-step procedure for performing whole-cell recordings
in the superior collicul... | [
{
"created": "Mon, 19 Sep 2022 06:52:52 GMT",
"version": "v1"
}
] | 2022-12-26 | [
[
"Broersen",
"R.",
""
],
[
"Stuart",
"G. J.",
""
]
] | In vivo whole-cell recording when combined with morphological characterization after biocytin labeling is a powerful technique to study subthreshold synaptic processing in cell-type-identified neuronal populations. Here, we provide a step-by-step procedure for performing whole-cell recordings in the superior colliculus... |
2405.08827 | Richard Povinelli | Richard J Povinelli, Mathew Dupont | A Dynamical Systems Approach to Predicting Patient Outcome after Cardiac
Arrest | Computing in Cardiology, 2023 | null | 10.22489/CinC.2023.442 | null | q-bio.QM math.DS | http://creativecommons.org/licenses/by-sa/4.0/ | Aim: Approximately six million people suffer cardiac arrests worldwide per
year with very low survival rates (<1%). Thus, the aim of this study is to
estimate the probability of a poor outcome after cardiac arrest. Accurate
outcome predictions avoid removing care too soon for patients with potentially
good outcomes o... | [
{
"created": "Mon, 13 May 2024 15:03:34 GMT",
"version": "v1"
}
] | 2024-05-16 | [
[
"Povinelli",
"Richard J",
""
],
[
"Dupont",
"Mathew",
""
]
] | Aim: Approximately six million people suffer cardiac arrests worldwide per year with very low survival rates (<1%). Thus, the aim of this study is to estimate the probability of a poor outcome after cardiac arrest. Accurate outcome predictions avoid removing care too soon for patients with potentially good outcomes or ... |
2106.06638 | Ines Thiele | Almut Heinken, Stefan\'ia Magn\'usd\'ottir, Ronan M.T. Fleming, and
Ines Thiele | DEMETER: Efficient simultaneous curation of genome-scale reconstructions
guided by experimental data and refined gene annotations | 6 pages, 1 Figure | null | null | null | q-bio.GN q-bio.MN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Motivation: Manual curation of genome-scale reconstructions is laborious, yet
existing automated curation tools typically do not take species-specific
experimental data and manually refined genome annotations into account.
Results: We developed DEMETER, a COBRA Toolbox extension that enables the
efficient simultaneou... | [
{
"created": "Fri, 11 Jun 2021 23:28:21 GMT",
"version": "v1"
}
] | 2021-06-15 | [
[
"Heinken",
"Almut",
""
],
[
"Magnúsdóttir",
"Stefanía",
""
],
[
"Fleming",
"Ronan M. T.",
""
],
[
"Thiele",
"Ines",
""
]
] | Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manually refined genome annotations into account. Results: We developed DEMETER, a COBRA Toolbox extension that enables the efficient simultaneous ... |
1501.05973 | Ashish Kapoor | Ashish Kapoor, E. Paxon Frady, Stefanie Jegelka, William B. Kristan
and Eric Horvitz | Inferring and Learning from Neuronal Correspondences | null | null | null | null | q-bio.NC cs.AI cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce and study methods for inferring and learning from
correspondences among neurons. The approach enables alignment of data from
distinct multiunit studies of nervous systems. We show that the methods for
inferring correspondences combine data effectively from cross-animal studies to
make joint inferences ab... | [
{
"created": "Fri, 23 Jan 2015 22:29:13 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Jan 2015 08:23:24 GMT",
"version": "v2"
}
] | 2015-01-28 | [
[
"Kapoor",
"Ashish",
""
],
[
"Frady",
"E. Paxon",
""
],
[
"Jegelka",
"Stefanie",
""
],
[
"Kristan",
"William B.",
""
],
[
"Horvitz",
"Eric",
""
]
] | We introduce and study methods for inferring and learning from correspondences among neurons. The approach enables alignment of data from distinct multiunit studies of nervous systems. We show that the methods for inferring correspondences combine data effectively from cross-animal studies to make joint inferences abou... |
1906.06908 | Christian Bongiorno | Christian Bongiorno, Salvatore Miccich\`e, Rosario N. Mantegna | Nested partitions from hierarchical clustering statistical validation | null | null | 10.1016/j.physa.2022.126933 | null | q-bio.GN stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop a greedy algorithm that is fast and scalable in the detection of a
nested partition extracted from a dendrogram obtained from hierarchical
clustering of a multivariate series. Our algorithm provides a $p$-value for
each clade observed in the hierarchical tree. The $p$-value is obtained by
computing a numbe... | [
{
"created": "Mon, 17 Jun 2019 09:08:30 GMT",
"version": "v1"
}
] | 2022-01-21 | [
[
"Bongiorno",
"Christian",
""
],
[
"Miccichè",
"Salvatore",
""
],
[
"Mantegna",
"Rosario N.",
""
]
] | We develop a greedy algorithm that is fast and scalable in the detection of a nested partition extracted from a dendrogram obtained from hierarchical clustering of a multivariate series. Our algorithm provides a $p$-value for each clade observed in the hierarchical tree. The $p$-value is obtained by computing a number ... |
2103.08579 | Mar\'ia Vallet-Regi | Anna Aguilar-Colomer, Montserrat Colilla, Isabel Izquierdo-Barba,
Carla Jimenez-Jimenez, Ignacio Mahillo, Jaime Esteban and Maria Vallet-Regi | Impact of the antibiotic-cargo from MSNs on Gram-positive and
Gram-negative bacterial biofilms | 44 pages, 14 figures | Microporous and Mesoporous Materials 311 (2021), 110681 | 10.1016/j.micromeso.2020.110681 | null | q-bio.QM physics.bio-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Mesoporous silica nanoparticles (MSNs) are promising drug nanocarriers for
infection treatment. Many investigations have focused on evaluating the
capacity of MSNs to encapsulate antibiotics and release them in a controlled
fashion. However, little attention has been paid to determine the antibiotic
doses released fr... | [
{
"created": "Mon, 15 Mar 2021 17:47:24 GMT",
"version": "v1"
}
] | 2021-03-16 | [
[
"Aguilar-Colomer",
"Anna",
""
],
[
"Colilla",
"Montserrat",
""
],
[
"Izquierdo-Barba",
"Isabel",
""
],
[
"Jimenez-Jimenez",
"Carla",
""
],
[
"Mahillo",
"Ignacio",
""
],
[
"Esteban",
"Jaime",
""
],
[
"Vallet-Regi",
... | Mesoporous silica nanoparticles (MSNs) are promising drug nanocarriers for infection treatment. Many investigations have focused on evaluating the capacity of MSNs to encapsulate antibiotics and release them in a controlled fashion. However, little attention has been paid to determine the antibiotic doses released from... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.