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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
q-bio/0505048 | Daniel G. M. Silvestre | Daniel G. M. Silvestre, Jose F. Fontanari | Template coexistence in prebiotic vesicle models | 7 pages, 8 figures | Eur. Phys. J. B 47, 423-429 (2005) | 10.1140/epjb/e2005-00346-5 | null | q-bio.PE | null | The coexistence of distinct templates is a common feature of the diverse
proposals advanced to resolve the information crisis of prebiotic evolution.
However, achieving robust template coexistence turned out to be such a
difficult demand that only a class of models, the so-called package models,
seems to have met it ... | [
{
"created": "Wed, 25 May 2005 14:17:06 GMT",
"version": "v1"
},
{
"created": "Thu, 30 Nov 2006 18:19:44 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Silvestre",
"Daniel G. M.",
""
],
[
"Fontanari",
"Jose F.",
""
]
] | The coexistence of distinct templates is a common feature of the diverse proposals advanced to resolve the information crisis of prebiotic evolution. However, achieving robust template coexistence turned out to be such a difficult demand that only a class of models, the so-called package models, seems to have met it so... |
1010.4145 | Christophe Magnani | Christophe Magnani, Daniel Eug\`ene, Erwin Idoux, L.E. Moore | Voltage clamp analysis of nonlinear dendritic propertie in prepositus
hypoglossi neurons | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The nonlinear properties of the dendrites in prepositus hypoglossi neurons
are involved in maintenance of eye position. The biophysical properties of
these neurons are essential for the operation of the vestibular neural
integrator that converts a head velocity signal to one that controls eye
position. A novel method... | [
{
"created": "Wed, 20 Oct 2010 09:48:52 GMT",
"version": "v1"
},
{
"created": "Fri, 29 Oct 2010 14:29:24 GMT",
"version": "v2"
}
] | 2010-11-01 | [
[
"Magnani",
"Christophe",
""
],
[
"Eugène",
"Daniel",
""
],
[
"Idoux",
"Erwin",
""
],
[
"Moore",
"L. E.",
""
]
] | The nonlinear properties of the dendrites in prepositus hypoglossi neurons are involved in maintenance of eye position. The biophysical properties of these neurons are essential for the operation of the vestibular neural integrator that converts a head velocity signal to one that controls eye position. A novel method n... |
2002.02803 | Junping Shi | Jimin Zhang, Junping Shi and Xiaoyuan Chang | Model of Algal Growth Depending on Nutrients and Inorganic Carbon in a
Poorly Mixed Water Column | 27 pages, 7 figures | null | null | null | q-bio.PE math.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we establish a reaction-diffusion-advection partial
differential equation model to describe the growth of algae depending on both
nutrients and inorganic carbon in a poorly mixed water column. Nutrients from
the water bottom and inorganic carbon from the water surface form an asymmetric
resource supply... | [
{
"created": "Fri, 31 Jan 2020 17:00:49 GMT",
"version": "v1"
}
] | 2020-02-10 | [
[
"Zhang",
"Jimin",
""
],
[
"Shi",
"Junping",
""
],
[
"Chang",
"Xiaoyuan",
""
]
] | In this paper, we establish a reaction-diffusion-advection partial differential equation model to describe the growth of algae depending on both nutrients and inorganic carbon in a poorly mixed water column. Nutrients from the water bottom and inorganic carbon from the water surface form an asymmetric resource supply m... |
1502.02689 | Kazuhiro Takemoto | Kazuhiro Takemoto | Heterogeneity of cells may explain allometric scaling of metabolic rate | 8 pages, 5 figures | Biosystems 130, 11-16 (2015) | 10.1016/j.biosystems.2015.02.003 | null | q-bio.OT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The origin of allometric scaling of metabolic rate is a long-standing
question in biology. Several models have been proposed for explaining the
origin; however, they have advantages and disadvantages. In particular,
previous models only demonstrate either two important observations for the
allometric scaling: the var... | [
{
"created": "Wed, 4 Feb 2015 13:59:49 GMT",
"version": "v1"
},
{
"created": "Tue, 17 Feb 2015 08:01:21 GMT",
"version": "v2"
}
] | 2015-02-23 | [
[
"Takemoto",
"Kazuhiro",
""
]
] | The origin of allometric scaling of metabolic rate is a long-standing question in biology. Several models have been proposed for explaining the origin; however, they have advantages and disadvantages. In particular, previous models only demonstrate either two important observations for the allometric scaling: the varia... |
1808.00595 | Jonathan Tyler | Jonathan Tyler, Anne Shiu, Jay Walton | Revisiting a synthetic intracellular regulatory network that exhibits
oscillations | null | null | null | null | q-bio.MN math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In 2000, Elowitz and Leibler introduced the repressilator--a synthetic gene
circuit with three genes that cyclically repress transcription of the next
gene--as well as a corresponding mathematical model. Experimental data and
model simulations exhibited oscillations in the protein concentrations across
generations. I... | [
{
"created": "Wed, 1 Aug 2018 23:10:27 GMT",
"version": "v1"
},
{
"created": "Mon, 31 Dec 2018 16:48:47 GMT",
"version": "v2"
}
] | 2019-01-01 | [
[
"Tyler",
"Jonathan",
""
],
[
"Shiu",
"Anne",
""
],
[
"Walton",
"Jay",
""
]
] | In 2000, Elowitz and Leibler introduced the repressilator--a synthetic gene circuit with three genes that cyclically repress transcription of the next gene--as well as a corresponding mathematical model. Experimental data and model simulations exhibited oscillations in the protein concentrations across generations. In ... |
2303.08496 | Jorge Vila-Tom\'as | Jorge Vila-Tom\'as, Pablo Hern\'andez-C\'amara and Jes\'us Malo | Psychophysics of Artificial Neural Networks Questions Classical Hue
Cancellation Experiments | 17 pages, 7 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | We show that classical hue cancellation experiments lead to human-like
opponent curves even if the task is done by trivial (identity) artificial
networks. Specifically, human-like opponent spectral sensitivities always
emerge in artificial networks as long as (i) the retina converts the input
radiation into any trist... | [
{
"created": "Wed, 15 Mar 2023 10:13:34 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Mar 2023 14:54:30 GMT",
"version": "v2"
}
] | 2023-03-29 | [
[
"Vila-Tomás",
"Jorge",
""
],
[
"Hernández-Cámara",
"Pablo",
""
],
[
"Malo",
"Jesús",
""
]
] | We show that classical hue cancellation experiments lead to human-like opponent curves even if the task is done by trivial (identity) artificial networks. Specifically, human-like opponent spectral sensitivities always emerge in artificial networks as long as (i) the retina converts the input radiation into any tristim... |
1404.4482 | Oliver Burren Mr | Oliver S Burren, Hui Guo and Chris Wallace | VSEAMS: A pipeline for variant set enrichment analysis using summary
GWAS data identifies IKZF3, BATF and ESRRA as key transcription factors in
type 1 diabetes | null | null | 10.1093/bioinformatics/btu571 | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Genome-wide association studies (GWAS) have identified many loci
implicated in disease susceptibility. Integration of GWAS summary statistics (p
values) and functional genomic datasets should help to elucidate mechanisms.
Results: We describe the extension of a previously described non-parametric
method t... | [
{
"created": "Thu, 17 Apr 2014 11:02:03 GMT",
"version": "v1"
}
] | 2014-10-17 | [
[
"Burren",
"Oliver S",
""
],
[
"Guo",
"Hui",
""
],
[
"Wallace",
"Chris",
""
]
] | Motivation: Genome-wide association studies (GWAS) have identified many loci implicated in disease susceptibility. Integration of GWAS summary statistics (p values) and functional genomic datasets should help to elucidate mechanisms. Results: We describe the extension of a previously described non-parametric method to ... |
1901.07429 | Nik Khadijah Nik Aznan | Nik Khadijah Nik Aznan, Amir Atapour-Abarghouei, Stephen Bonner, Jason
Connolly, Noura Al Moubayed and Toby Breckon | Simulating Brain Signals: Creating Synthetic EEG Data via Neural-Based
Generative Models for Improved SSVEP Classification | Accepted as a full paper at International Joint Conference on Neural
Network (IJCNN) 2019 | null | 10.1109/IJCNN.2019.8852227 | null | q-bio.QM eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite significant recent progress in the area of Brain-Computer Interface
(BCI), there are numerous shortcomings associated with collecting
Electroencephalography (EEG) signals in real-world environments. These include,
but are not limited to, subject and session data variance, long and arduous
calibration processe... | [
{
"created": "Tue, 15 Jan 2019 19:25:35 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Apr 2019 09:49:57 GMT",
"version": "v2"
}
] | 2019-10-14 | [
[
"Aznan",
"Nik Khadijah Nik",
""
],
[
"Atapour-Abarghouei",
"Amir",
""
],
[
"Bonner",
"Stephen",
""
],
[
"Connolly",
"Jason",
""
],
[
"Moubayed",
"Noura Al",
""
],
[
"Breckon",
"Toby",
""
]
] | Despite significant recent progress in the area of Brain-Computer Interface (BCI), there are numerous shortcomings associated with collecting Electroencephalography (EEG) signals in real-world environments. These include, but are not limited to, subject and session data variance, long and arduous calibration processes ... |
0912.4189 | Christel Kamp | Christel Kamp | Untangling the interplay between epidemic spreading and transmission
network dynamic | 16 pages, 3 figures | PLoS Comput Biol 6(11): e1000984 (2010) | 10.1371/journal.pcbi.1000984 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Epidemic spreading of infectious diseases is ubiquitous and has often
considerable impact on public health and economic wealth. The large variability
in spatio-temporal patterns of epidemics prohibits simple interventions and
demands for a detailed analysis of each epidemic with respect to its infectious
agent and th... | [
{
"created": "Mon, 21 Dec 2009 16:08:36 GMT",
"version": "v1"
}
] | 2010-11-25 | [
[
"Kamp",
"Christel",
""
]
] | Epidemic spreading of infectious diseases is ubiquitous and has often considerable impact on public health and economic wealth. The large variability in spatio-temporal patterns of epidemics prohibits simple interventions and demands for a detailed analysis of each epidemic with respect to its infectious agent and the ... |
1605.08454 | Yuanjun Gao | Yuanjun Gao, Evan Archer, Liam Paninski, John P. Cunningham | Linear dynamical neural population models through nonlinear embeddings | NIPS 2016 | null | null | null | q-bio.NC stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A body of recent work in modeling neural activity focuses on recovering
low-dimensional latent features that capture the statistical structure of
large-scale neural populations. Most such approaches have focused on linear
generative models, where inference is computationally tractable. Here, we
propose fLDS, a genera... | [
{
"created": "Thu, 26 May 2016 21:25:26 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Oct 2016 19:44:03 GMT",
"version": "v2"
}
] | 2016-10-26 | [
[
"Gao",
"Yuanjun",
""
],
[
"Archer",
"Evan",
""
],
[
"Paninski",
"Liam",
""
],
[
"Cunningham",
"John P.",
""
]
] | A body of recent work in modeling neural activity focuses on recovering low-dimensional latent features that capture the statistical structure of large-scale neural populations. Most such approaches have focused on linear generative models, where inference is computationally tractable. Here, we propose fLDS, a general ... |
1212.0031 | Carina Curto | Carina Curto and Anda Degeratu and Vladimir Itskov | Encoding binary neural codes in networks of threshold-linear neurons | 35 pages, 5 figures. Minor revisions only. Accepted to Neural
Computation | Neural Computation, Vol 25, pp. 2858-2903, 2013 | null | null | q-bio.NC math.CO math.MG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Networks of neurons in the brain encode preferred patterns of neural activity
via their synaptic connections. Despite receiving considerable attention, the
precise relationship between network connectivity and encoded patterns is still
poorly understood. Here we consider this problem for networks of
threshold-linear ... | [
{
"created": "Fri, 30 Nov 2012 22:43:11 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Apr 2013 22:45:57 GMT",
"version": "v2"
},
{
"created": "Thu, 16 May 2013 20:44:24 GMT",
"version": "v3"
}
] | 2015-02-25 | [
[
"Curto",
"Carina",
""
],
[
"Degeratu",
"Anda",
""
],
[
"Itskov",
"Vladimir",
""
]
] | Networks of neurons in the brain encode preferred patterns of neural activity via their synaptic connections. Despite receiving considerable attention, the precise relationship between network connectivity and encoded patterns is still poorly understood. Here we consider this problem for networks of threshold-linear ne... |
1009.4801 | Monica Zoppe' | Maria Francesca Zini, Yuri Porozov, Raluca Mihaela Andrei, Tiziana
Loni, Claudia Caudai and Monica Zopp\`e | BioBlender: Fast and Efficient All Atom Morphing of Proteins Using
Blender Game Engine | Paper strictly associated with other paper 'BioBlender: A Software
for Intuitive Representation of Surface Properties of Biomolecules', also
submitted at the same time. This paper 14 pages, including 7 figures. Paper
submitted | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this and the associated article 'BioBlender: A Software for Intuitive
Representation of Surface Properties of Biomolecules', (Andrei et al) we
present BioBlender as a complete instrument for the elaboration of motion
(here) and the visualization (Andrei et al) of proteins and other
macromolecules, using instrument... | [
{
"created": "Fri, 24 Sep 2010 10:40:30 GMT",
"version": "v1"
}
] | 2010-09-27 | [
[
"Zini",
"Maria Francesca",
""
],
[
"Porozov",
"Yuri",
""
],
[
"Andrei",
"Raluca Mihaela",
""
],
[
"Loni",
"Tiziana",
""
],
[
"Caudai",
"Claudia",
""
],
[
"Zoppè",
"Monica",
""
]
] | In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the visualization (Andrei et al) of proteins and other macromolecules, using instruments ... |
2301.06640 | Yixiang Wu | Shanshan Chen, Jie Liu, Yixiang Wu | On the impact of spatial heterogeneity and drift rate in a three-patch
two-species Lotka-Volterra competition model over a stream | null | null | 10.1007/s00033-023-02009-6 | null | q-bio.PE math.DS | http://creativecommons.org/licenses/by/4.0/ | In this paper, we study a three-patch two-species Lotka-Volterra competition
patch model over a stream network. The individuals are subject to both random
and directed movements, and the two species are assumed to be identical except
for the movement rates. The environment is heterogeneous, and the carrying
capacity ... | [
{
"created": "Mon, 16 Jan 2023 23:48:30 GMT",
"version": "v1"
}
] | 2023-06-07 | [
[
"Chen",
"Shanshan",
""
],
[
"Liu",
"Jie",
""
],
[
"Wu",
"Yixiang",
""
]
] | In this paper, we study a three-patch two-species Lotka-Volterra competition patch model over a stream network. The individuals are subject to both random and directed movements, and the two species are assumed to be identical except for the movement rates. The environment is heterogeneous, and the carrying capacity is... |
q-bio/0406048 | Elchanan Mossel | Elchanan Mossel and Mike Steel | How much can evolved characters tell us about the tree that generated
them? | null | null | null | null | q-bio.PE math.ST stat.TH | null | In this paper we review some recent results that shed light on a fundamental
question in molecular systematics: how much phylogenetic `signal' can we expect
from characters that have evolved under some Markov process? There are many
sides to this question and we begin by describing some explicit bounds on the
probabi... | [
{
"created": "Thu, 24 Jun 2004 18:38:07 GMT",
"version": "v1"
}
] | 2011-11-10 | [
[
"Mossel",
"Elchanan",
""
],
[
"Steel",
"Mike",
""
]
] | In this paper we review some recent results that shed light on a fundamental question in molecular systematics: how much phylogenetic `signal' can we expect from characters that have evolved under some Markov process? There are many sides to this question and we begin by describing some explicit bounds on the probabili... |
2405.12225 | Ignacio Alvarez Illan | F.J. Alcaide, I.A. Illan, J. Ramirez, J.M. Gorriz | Unraveling the Autism spectrum heterogeneity: Insights from ABIDE I
Database using data/model-driven permutation testing approaches | 54 pages, 14 figures | null | null | null | q-bio.QM cs.LG eess.IV eess.SP | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Autism Spectrum Condition (ASC) is a neurodevelopmental condition
characterized by impairments in communication, social interaction and
restricted or repetitive behaviors. Extensive research has been conducted to
identify distinctions between individuals with ASC and neurotypical
individuals. However, limited attenti... | [
{
"created": "Mon, 22 Apr 2024 13:21:57 GMT",
"version": "v1"
}
] | 2024-05-22 | [
[
"Alcaide",
"F. J.",
""
],
[
"Illan",
"I. A.",
""
],
[
"Ramirez",
"J.",
""
],
[
"Gorriz",
"J. M.",
""
]
] | Autism Spectrum Condition (ASC) is a neurodevelopmental condition characterized by impairments in communication, social interaction and restricted or repetitive behaviors. Extensive research has been conducted to identify distinctions between individuals with ASC and neurotypical individuals. However, limited attention... |
1107.0334 | Michael Bachmann | Tristan Bereau, Markus Deserno, and Michael Bachmann | Structural Basis of Folding Cooperativity in Model Proteins: Insights
from a Microcanonical Perspective | 28 pages, 7 figures | Biophys. J. 100, 2764-2772 (2011) | 10.1016/j.bpj.2011.03.056 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Two-state cooperativity is an important characteristic in protein folding. It
is defined by a depletion of states lying energetically between folded and
unfolded conformations. While there are different ways to test for two-state
cooperativity, most of them probe indirect proxies of this depletion. Yet,
generalized-e... | [
{
"created": "Fri, 1 Jul 2011 20:51:28 GMT",
"version": "v1"
}
] | 2015-05-28 | [
[
"Bereau",
"Tristan",
""
],
[
"Deserno",
"Markus",
""
],
[
"Bachmann",
"Michael",
""
]
] | Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state cooperativity, most of them probe indirect proxies of this depletion. Yet, generalized-ens... |
0812.3344 | Vahid Shahrezaei | Vahid Shahrezaei and Peter S. Swain | Analytical distributions for stochastic gene expression | Supplementary information can be found on PNAS website | Proc Natl Acad Sci U S A. 2008 Nov 11;105(45):17256-61 | 10.1073/pnas.0803850105 | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene expression is significantly stochastic making modeling of genetic
networks challenging. We present an approximation that allows the calculation
of not only the mean and variance but also the distribution of protein numbers.
We assume that proteins decay substantially slower than their mRNA and confirm
that many ... | [
{
"created": "Wed, 17 Dec 2008 17:09:23 GMT",
"version": "v1"
}
] | 2008-12-18 | [
[
"Shahrezaei",
"Vahid",
""
],
[
"Swain",
"Peter S.",
""
]
] | Gene expression is significantly stochastic making modeling of genetic networks challenging. We present an approximation that allows the calculation of not only the mean and variance but also the distribution of protein numbers. We assume that proteins decay substantially slower than their mRNA and confirm that many ge... |
1304.3577 | Richard Savage | Richard S. Savage, Zoubin Ghahramani, Jim E. Griffin, Paul Kirk, David
L. Wild | Identifying cancer subtypes in glioblastoma by combining genomic,
transcriptomic and epigenomic data | null | International Conference on Machine Learning (ICML) 2012: Workshop
on Machine Learning in Genetics and Genomics | null | null | q-bio.GN stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a nonparametric Bayesian method for disease subtype discovery in
multi-dimensional cancer data. Our method can simultaneously analyse a wide
range of data types, allowing for both agreement and disagreement between their
underlying clustering structure. It includes feature selection and infers the
most lik... | [
{
"created": "Fri, 12 Apr 2013 09:06:45 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Apr 2013 09:40:34 GMT",
"version": "v2"
}
] | 2013-04-16 | [
[
"Savage",
"Richard S.",
""
],
[
"Ghahramani",
"Zoubin",
""
],
[
"Griffin",
"Jim E.",
""
],
[
"Kirk",
"Paul",
""
],
[
"Wild",
"David L.",
""
]
] | We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering structure. It includes feature selection and infers the most likel... |
0906.4471 | Alexey Mazur K | Alexey K. Mazur | Analysis of Accordion DNA Stretching Revealed by The Gold Cluster Ruler | 9 pages, 4 figures, to appear in Phys. Rev. E | Phys. Rev. E, 80, 010901, 2009 | 10.1103/PhysRevE.80.010901 | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A promising new method for measuring intramolecular distances in solution
uses small-angle X-ray scattering interference between gold nanocrystal labels
(Mathew-Fenn et al, Science, 322, 446 (2008)). When applied to double stranded
DNA, it revealed that the DNA length fluctuations are strikingly strong and
correlated... | [
{
"created": "Wed, 24 Jun 2009 13:31:17 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Mazur",
"Alexey K.",
""
]
] | A promising new method for measuring intramolecular distances in solution uses small-angle X-ray scattering interference between gold nanocrystal labels (Mathew-Fenn et al, Science, 322, 446 (2008)). When applied to double stranded DNA, it revealed that the DNA length fluctuations are strikingly strong and correlated o... |
2306.10038 | John Buckleton | Tim Kalafut, James Curran, Mike Coble, John Buckleton | Comments arising from WJ Thompson "Uncertainty in probabilistic
genotyping of low template DNA A case study comparing STRmix and TrueAllele" | 9 pages 1 figure | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Thompson reports a comparison of data from STRmix and TrueAllele. The data he
has arises from different inputs to the two software. If the input data are
made more similar the outputs become more similar. Thompson argues that the
Analytical Threshold, AT, should be varied in casework. This produced different
LRs but ... | [
{
"created": "Sat, 10 Jun 2023 01:51:23 GMT",
"version": "v1"
}
] | 2023-06-21 | [
[
"Kalafut",
"Tim",
""
],
[
"Curran",
"James",
""
],
[
"Coble",
"Mike",
""
],
[
"Buckleton",
"John",
""
]
] | Thompson reports a comparison of data from STRmix and TrueAllele. The data he has arises from different inputs to the two software. If the input data are made more similar the outputs become more similar. Thompson argues that the Analytical Threshold, AT, should be varied in casework. This produced different LRs but th... |
1109.2683 | Hui Zeng | Wei-Mou Zheng, Hui Zeng, Dong-Bo Bu, Ming-Fu Shao, Ke-Song Liu and
Chao Wang | Looking for packing units of the protein structure | 10 pages, 5 tables | null | null | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Lattice-model simulations and experiments of some small proteins suggest that
folding is essentially controlled by a few conserved contacts. Residues of
these conserved contacts form the minimum set of native contacts needed to
ensure foldability. Keeping such conserved specific contacts in mind, we
examine contacts ... | [
{
"created": "Tue, 13 Sep 2011 07:03:06 GMT",
"version": "v1"
}
] | 2011-09-14 | [
[
"Zheng",
"Wei-Mou",
""
],
[
"Zeng",
"Hui",
""
],
[
"Bu",
"Dong-Bo",
""
],
[
"Shao",
"Ming-Fu",
""
],
[
"Liu",
"Ke-Song",
""
],
[
"Wang",
"Chao",
""
]
] | Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure foldability. Keeping such conserved specific contacts in mind, we examine contacts ma... |
2308.12325 | Colin Zhang | John Ho, Zhao-Heng Yin, Colin Zhang, Nicole Guo, Yang Ha | Predicting Drug Solubility Using Different Machine Learning Methods --
Linear Regression Model with Extracted Chemical Features vs Graph
Convolutional Neural Network | 7 pages, 4 figures, 2 tables | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Predicting the solubility of given molecules remains crucial in the
pharmaceutical industry. In this study, we revisited this extensively studied
topic, leveraging the capabilities of contemporary computing resources. We
employed two machine learning models: a linear regression model and a graph
convolutional neural ... | [
{
"created": "Wed, 23 Aug 2023 15:35:20 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Jan 2024 01:28:36 GMT",
"version": "v2"
}
] | 2024-01-08 | [
[
"Ho",
"John",
""
],
[
"Yin",
"Zhao-Heng",
""
],
[
"Zhang",
"Colin",
""
],
[
"Guo",
"Nicole",
""
],
[
"Ha",
"Yang",
""
]
] | Predicting the solubility of given molecules remains crucial in the pharmaceutical industry. In this study, we revisited this extensively studied topic, leveraging the capabilities of contemporary computing resources. We employed two machine learning models: a linear regression model and a graph convolutional neural ne... |
2109.09649 | Gregory Kiar | Gregory Kiar, Yohan Chatelain, Ali Salari, Alan C. Evans, Tristan
Glatard | Data Augmentation Through Monte Carlo Arithmetic Leads to More
Generalizable Classification in Connectomics | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Machine learning models are commonly applied to human brain imaging datasets
in an effort to associate function or structure with behaviour, health, or
other individual phenotypes. Such models often rely on low-dimensional maps
generated by complex processing pipelines. However, the numerical instabilities
inherent t... | [
{
"created": "Mon, 20 Sep 2021 16:06:05 GMT",
"version": "v1"
}
] | 2021-09-21 | [
[
"Kiar",
"Gregory",
""
],
[
"Chatelain",
"Yohan",
""
],
[
"Salari",
"Ali",
""
],
[
"Evans",
"Alan C.",
""
],
[
"Glatard",
"Tristan",
""
]
] | Machine learning models are commonly applied to human brain imaging datasets in an effort to associate function or structure with behaviour, health, or other individual phenotypes. Such models often rely on low-dimensional maps generated by complex processing pipelines. However, the numerical instabilities inherent to ... |
0902.0602 | Ramana Dodla | Ramana Dodla, Charles J. Wilson | Asynchronous response of coupled pacemaker neurons | 11 pages, 4 figures. To appear in Phys. Rev. Lett | null | 10.1103/PhysRevLett.102.068102 | null | q-bio.NC nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study a network model of two conductance-based pacemaker neurons of
differing natural frequency, coupled with either mutual excitation or
inhibition, and receiving shared random inhibitory synaptic input. The networks
may phase-lock spike-to-spike for strong mutual coupling. But the shared input
can desynchronize ... | [
{
"created": "Tue, 3 Feb 2009 20:49:32 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Dodla",
"Ramana",
""
],
[
"Wilson",
"Charles J.",
""
]
] | We study a network model of two conductance-based pacemaker neurons of differing natural frequency, coupled with either mutual excitation or inhibition, and receiving shared random inhibitory synaptic input. The networks may phase-lock spike-to-spike for strong mutual coupling. But the shared input can desynchronize th... |
1003.0902 | Nikita Sakhanenko | Nikita A. Sakhanenko, David J. Galas | Markov Logic Networks in the Analysis of Genetic Data | 29 pages, 9 figures, 1 table | null | null | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Complex, non-additive genetic interactions are common and can be critical in
determining phenotypes. Genome-wide association studies (GWAS) and similar
statistical studies of linkage data, however, assume additive models of gene
interactions in looking for genotype-phenotype associations. These statistical
methods vi... | [
{
"created": "Wed, 3 Mar 2010 21:01:10 GMT",
"version": "v1"
}
] | 2010-03-05 | [
[
"Sakhanenko",
"Nikita A.",
""
],
[
"Galas",
"David J.",
""
]
] | Complex, non-additive genetic interactions are common and can be critical in determining phenotypes. Genome-wide association studies (GWAS) and similar statistical studies of linkage data, however, assume additive models of gene interactions in looking for genotype-phenotype associations. These statistical methods view... |
1408.6616 | Federico Maggi | Maggi Federico, Domenico Bosco, Cristina Marzachi' | Conceptual and mathematical modeling of insect-borne plant diseases:
theory and application to flavescence doree in grapevine | null | null | null | School of Civil Engineering, Research Report R947, ISSN 1833-2781 | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Insect-borne plant diseases recur commonly in wild plants and in agricultural
crops, and are responsible for severe losses in terms of produce yield and
monetary return. Mathematical models of insect-borne plant diseases are
therefore an essential tool to help predicting the progression of an epidemic
disease and aid... | [
{
"created": "Thu, 28 Aug 2014 03:22:55 GMT",
"version": "v1"
}
] | 2014-08-29 | [
[
"Federico",
"Maggi",
""
],
[
"Bosco",
"Domenico",
""
],
[
"Marzachi'",
"Cristina",
""
]
] | Insect-borne plant diseases recur commonly in wild plants and in agricultural crops, and are responsible for severe losses in terms of produce yield and monetary return. Mathematical models of insect-borne plant diseases are therefore an essential tool to help predicting the progression of an epidemic disease and aid i... |
1602.04099 | Ryan Morris | Ryan J. Morris, Giovanni B. Brandani, Vibhuti Desai, Brian O. Smith,
Marieke Schor, Cait E. MacPhee | The Conformation of Interfacially Adsorbed Ranaspumin-2 is an Arrested
State on the Unfolding Pathway | 8 figures | Biophys. J. 111(4), 732-742, (2016) | 10.1016/j.bpj.2016.06.006 | null | q-bio.BM cond-mat.soft q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ranaspumin-2 (Rsn-2) is a surfactant protein found in the foam nests of the
t\'{u}ngara frog. Previous experimental work has led to a proposed model of
adsorption which involves an unusual clam shell-like `unhinging' of the protein
at an interface. Interestingly, there is no concomitant denaturation of the
secondary ... | [
{
"created": "Fri, 12 Feb 2016 16:12:35 GMT",
"version": "v1"
}
] | 2016-08-30 | [
[
"Morris",
"Ryan J.",
""
],
[
"Brandani",
"Giovanni B.",
""
],
[
"Desai",
"Vibhuti",
""
],
[
"Smith",
"Brian O.",
""
],
[
"Schor",
"Marieke",
""
],
[
"MacPhee",
"Cait E.",
""
]
] | Ranaspumin-2 (Rsn-2) is a surfactant protein found in the foam nests of the t\'{u}ngara frog. Previous experimental work has led to a proposed model of adsorption which involves an unusual clam shell-like `unhinging' of the protein at an interface. Interestingly, there is no concomitant denaturation of the secondary st... |
1112.1510 | Ganesh Bagler Dr | Shikha Vashisht and Ganesh Bagler | An approach for the identification of targets specific to bone
metastasis using cancer genes interactome and gene ontology analysis | 54 pages (19 pages main text; 11 Figures; 26 pages of supplementary
information). Revised after critical reviews. Accepted for Publication in
PLoS ONE | null | 10.1371/journal.pone.0049401 | CSIR-IHBT communication number 2245 | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Metastasis is one of the most enigmatic aspects of cancer pathogenesis and is
a major cause of cancer-associated mortality. Secondary bone cancer (SBC) is a
complex disease caused by metastasis of tumor cells from their primary site and
is characterized by intricate interplay of molecular interactions.
Identification... | [
{
"created": "Wed, 7 Dec 2011 10:11:20 GMT",
"version": "v1"
},
{
"created": "Thu, 11 Oct 2012 06:46:23 GMT",
"version": "v2"
}
] | 2015-06-03 | [
[
"Vashisht",
"Shikha",
""
],
[
"Bagler",
"Ganesh",
""
]
] | Metastasis is one of the most enigmatic aspects of cancer pathogenesis and is a major cause of cancer-associated mortality. Secondary bone cancer (SBC) is a complex disease caused by metastasis of tumor cells from their primary site and is characterized by intricate interplay of molecular interactions. Identification o... |
1309.6692 | Varunyu Khamviwath | Varunyu Khamviwath and Hans G. Othmer | Signal transduction and directional sensing in eukaryotes | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Control of the cytoskeleton and mechanical contacts with the extracellular
environment are essential component of motility in eukaryotic cells. In the
absence of signals, cells continuously rebuild the cytoskeleton and
periodically extend pseudopods or other protrusions at random membrane
locations. Extracellular sig... | [
{
"created": "Wed, 25 Sep 2013 23:30:50 GMT",
"version": "v1"
}
] | 2013-09-27 | [
[
"Khamviwath",
"Varunyu",
""
],
[
"Othmer",
"Hans G.",
""
]
] | Control of the cytoskeleton and mechanical contacts with the extracellular environment are essential component of motility in eukaryotic cells. In the absence of signals, cells continuously rebuild the cytoskeleton and periodically extend pseudopods or other protrusions at random membrane locations. Extracellular signa... |
0712.2932 | Leo van Iersel | Leo van Iersel, Steven Kelk and Matthias Mnich | Uniqueness, intractability and exact algorithms: reflections on level-k
phylogenetic networks | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic networks provide a way to describe and visualize evolutionary
histories that have undergone so-called reticulate evolutionary events such as
recombination, hybridization or horizontal gene transfer. The level k of a
network determines how non-treelike the evolution can be, with level-0 networks
being tre... | [
{
"created": "Tue, 18 Dec 2007 11:59:51 GMT",
"version": "v1"
},
{
"created": "Mon, 14 Jan 2008 09:24:17 GMT",
"version": "v2"
},
{
"created": "Mon, 21 Jul 2008 10:53:23 GMT",
"version": "v3"
}
] | 2008-07-21 | [
[
"van Iersel",
"Leo",
""
],
[
"Kelk",
"Steven",
""
],
[
"Mnich",
"Matthias",
""
]
] | Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network determines how non-treelike the evolution can be, with level-0 networks being trees... |
2401.07016 | Samira Bolandghamat | Samira Bolandghamat, Morteza Behnam-Rassouli | Iron role paradox in nerve degeneration and regeneration | null | Bolandghamat, S., & Behnam-Rassouli, M. (2024). Iron role paradox
in nerve degeneration and regeneration. Physiological Reports, 12, e15908 | 10.14814/phy2.15908 | null | q-bio.NC q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Iron accumulates in the neural tissue during peripheral nerve degeneration.
Some studies have already been suggested that iron facilitates Wallerian
degeneration (WD) events such as Schwann cell de-differentiation. On the other
hand, intracellular iron levels remain elevated during nerve regeneration and
gradually de... | [
{
"created": "Sat, 13 Jan 2024 08:56:53 GMT",
"version": "v1"
}
] | 2024-01-23 | [
[
"Bolandghamat",
"Samira",
""
],
[
"Behnam-Rassouli",
"Morteza",
""
]
] | Iron accumulates in the neural tissue during peripheral nerve degeneration. Some studies have already been suggested that iron facilitates Wallerian degeneration (WD) events such as Schwann cell de-differentiation. On the other hand, intracellular iron levels remain elevated during nerve regeneration and gradually decr... |
2007.08464 | Luca Parma | S. Busti (1), A. Bonaldo (1), F. Dondi (1), D. Cavallini (1), M.
Yufera (2), N. Gilannejad (2), F. J. Moyano (3), P.P Gatta (1), L. Parma (1)
((1) Department of Veterinary Medical Sciences University of Bologna, (2)
Instituto de Ciencias Marinas de Andaluc\'ia, (3) Department of Biology and
Geology Universidad ... | Effects of different feeding frequencies on growth, feed utilisation,
digestive enzyme activities and plasma biochemistry of gilthead sea bream
(Sparus aurata) fed with different fishmeal and fish oil dietary levels | null | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In the context of Mediterranean aquaculture little attention has been paid to
the manipulation of feeding frequency at the on-growing phase. The effects of
different feeding frequencies: one meal per day, two meals per day, three meals
per day on growth, digestive enzyme activity, feed digestibility and plasma
bioche... | [
{
"created": "Tue, 14 Jul 2020 13:26:28 GMT",
"version": "v1"
},
{
"created": "Wed, 10 Feb 2021 11:14:24 GMT",
"version": "v2"
}
] | 2021-02-11 | [
[
"Busti",
"S.",
""
],
[
"Bonaldo",
"A.",
""
],
[
"Dondi",
"F.",
""
],
[
"Cavallini",
"D.",
""
],
[
"Yufera",
"M.",
""
],
[
"Gilannejad",
"N.",
""
],
[
"Moyano",
"F. J.",
""
],
[
"Gatta",
"P. P",
... | In the context of Mediterranean aquaculture little attention has been paid to the manipulation of feeding frequency at the on-growing phase. The effects of different feeding frequencies: one meal per day, two meals per day, three meals per day on growth, digestive enzyme activity, feed digestibility and plasma biochemi... |
1508.07616 | Stephen Pankavich | Stephen Pankavich and Deborah Shutt | An in-host model of HIV incorporating latent infection and viral
mutation | 10 pages, 7 figures, Proceedings of AIMS Conference on Differential
Equations and Dynamical Systems (2015) | Dynamical Systems, Differential Equations and Applications, AIMS
Proceedings, 2015 pp. 913-922 | 10.3934/proc.2015.0913 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We construct a seven-component model of the in-host dynamics of the Human
Immunodeficiency Virus Type-1 (i.e, HIV) that accounts for latent infection and
the propensity of viral mutation. A dynamical analysis is conducted and a
theorem is presented which characterizes the long time behavior of the model.
Finally, we ... | [
{
"created": "Sun, 30 Aug 2015 19:01:00 GMT",
"version": "v1"
}
] | 2016-04-18 | [
[
"Pankavich",
"Stephen",
""
],
[
"Shutt",
"Deborah",
""
]
] | We construct a seven-component model of the in-host dynamics of the Human Immunodeficiency Virus Type-1 (i.e, HIV) that accounts for latent infection and the propensity of viral mutation. A dynamical analysis is conducted and a theorem is presented which characterizes the long time behavior of the model. Finally, we st... |
1611.01842 | Daniel B. Weissman | Daniel B. Weissman, Oskar Hallatschek | Minimal-assumption inference from population-genomic data | 21 pages, 9 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Samples of multiple complete genome sequences contain vast amounts of
information about the evolutionary history of populations, much of it in the
associations among polymorphisms at different loci. Current methods that take
advantage of this linkage information rely on models of recombination and
coalescence, limiti... | [
{
"created": "Sun, 6 Nov 2016 20:50:24 GMT",
"version": "v1"
}
] | 2016-11-08 | [
[
"Weissman",
"Daniel B.",
""
],
[
"Hallatschek",
"Oskar",
""
]
] | Samples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. Current methods that take advantage of this linkage information rely on models of recombination and coalescence, limiting... |
1905.02007 | Ahmed El Hady | Pepe Alcami, Ahmed El Hady | Axonal Computations | 25 pages, 6 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Axons functionally link the somato-dendritic compartment to synaptic
terminals. Structurally and functionally diverse, they accomplish a central
role in determining the delays and reliability with which neuronal ensembles
communicate. By combining their active and passive biophysical properties, they
ensure a plethor... | [
{
"created": "Mon, 6 May 2019 12:57:12 GMT",
"version": "v1"
}
] | 2019-05-07 | [
[
"Alcami",
"Pepe",
""
],
[
"Hady",
"Ahmed El",
""
]
] | Axons functionally link the somato-dendritic compartment to synaptic terminals. Structurally and functionally diverse, they accomplish a central role in determining the delays and reliability with which neuronal ensembles communicate. By combining their active and passive biophysical properties, they ensure a plethora ... |
2103.14419 | Pierre Morisse | Pierre Morisse, Claire Lemaitre, Fabrice Legeai | LRez: C++ API and toolkit for analyzing and managing Linked-Reads data | 4 pages, 1 table | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Linked-Reads technologies, such as 10x Genomics, combine both the
high-quality and low cost of short-reads sequencing and a long-range
information, through the use of barcodes able to tag reads which originate from
a common long DNA fragment. This technology has been employed in a broad range
of applications includin... | [
{
"created": "Fri, 26 Mar 2021 11:59:52 GMT",
"version": "v1"
},
{
"created": "Mon, 29 Mar 2021 07:23:09 GMT",
"version": "v2"
}
] | 2021-03-30 | [
[
"Morisse",
"Pierre",
""
],
[
"Lemaitre",
"Claire",
""
],
[
"Legeai",
"Fabrice",
""
]
] | Linked-Reads technologies, such as 10x Genomics, combine both the high-quality and low cost of short-reads sequencing and a long-range information, through the use of barcodes able to tag reads which originate from a common long DNA fragment. This technology has been employed in a broad range of applications including ... |
1810.05470 | \'Alvaro Garc\'ia L\'opez | \'Alvaro G. L\'opez, Kelly C. Iarosz, Antonio M. Batista, Jes\'us M.
Seoane, Ricardo L. Viana, Miguel A. F. Sanju\'an | Nonlinear cancer chemotherapy: modelling the Norton-Simon hypothesis | null | null | 10.1016/j.cnsns.2018.11.006 | null | q-bio.PE q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A fundamental model of tumor growth in the presence of cytotoxic
chemotherapeutic agents is formulated. The model allows to study the role of
the Norton-Simon hypothesis in the context of dose-dense chemotherapy.
Dose-dense protocols aim at reducing the period between courses of chemotherapy
from three weeks to two w... | [
{
"created": "Fri, 12 Oct 2018 12:16:35 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Oct 2018 18:29:32 GMT",
"version": "v2"
}
] | 2018-12-05 | [
[
"López",
"Álvaro G.",
""
],
[
"Iarosz",
"Kelly C.",
""
],
[
"Batista",
"Antonio M.",
""
],
[
"Seoane",
"Jesús M.",
""
],
[
"Viana",
"Ricardo L.",
""
],
[
"Sanjuán",
"Miguel A. F.",
""
]
] | A fundamental model of tumor growth in the presence of cytotoxic chemotherapeutic agents is formulated. The model allows to study the role of the Norton-Simon hypothesis in the context of dose-dense chemotherapy. Dose-dense protocols aim at reducing the period between courses of chemotherapy from three weeks to two wee... |
q-bio/0608031 | Carlos Escudero | Carlos Escudero | Geometrical approach to tumor growth | null | Phys. Rev. E 74, 021901 (2006) | 10.1103/PhysRevE.74.021901 | null | q-bio.QM cond-mat.stat-mech nlin.AO q-bio.TO | null | Tumor growth has a number of features in common with a physical process known
as molecular beam epitaxy. Both growth processes are characterized by the
constraint of growth development to the body border, and surface diffusion of
cells/particles at the growing edge. However, tumor growth implies an
approximate spheri... | [
{
"created": "Fri, 18 Aug 2006 17:49:54 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Escudero",
"Carlos",
""
]
] | Tumor growth has a number of features in common with a physical process known as molecular beam epitaxy. Both growth processes are characterized by the constraint of growth development to the body border, and surface diffusion of cells/particles at the growing edge. However, tumor growth implies an approximate spherica... |
2312.00932 | Elbert Branscomb | Elbert Branscomb | Boltzmann's casino and the unbridgeable chasm in emergence of life
research | 68 Pages | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Notwithstanding its long history and compelling motivation, research seeking
to explicate the emergence life (EoL) has throughout been a cacophony of
unresolved speculation and dispute; absent still any clear convergence or other
inarguable evidence of progress. This notwithstanding that it has also produced
a rich a... | [
{
"created": "Fri, 1 Dec 2023 21:20:20 GMT",
"version": "v1"
}
] | 2023-12-05 | [
[
"Branscomb",
"Elbert",
""
]
] | Notwithstanding its long history and compelling motivation, research seeking to explicate the emergence life (EoL) has throughout been a cacophony of unresolved speculation and dispute; absent still any clear convergence or other inarguable evidence of progress. This notwithstanding that it has also produced a rich and... |
2211.04195 | Lucas Hedstr\"om | Lucas Hedstr\"om and Ludvig Lizana | Modelling chromosome-wide target search | 15 pages, 11 figures | New J. Phys. 25 033024 (2023= | 10.1088/1367-2630/acc127 | null | q-bio.QM cond-mat.stat-mech physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | The most common gene regulation mechanism is when a transcription factor
protein binds to a regulatory sequence to increase or decrease RNA
transcription. However, transcription factors face two main challenges when
searching for these sequences. First, they are vanishingly short relative to
the genome length. Second... | [
{
"created": "Tue, 8 Nov 2022 12:22:19 GMT",
"version": "v1"
}
] | 2023-11-21 | [
[
"Hedström",
"Lucas",
""
],
[
"Lizana",
"Ludvig",
""
]
] | The most common gene regulation mechanism is when a transcription factor protein binds to a regulatory sequence to increase or decrease RNA transcription. However, transcription factors face two main challenges when searching for these sequences. First, they are vanishingly short relative to the genome length. Second, ... |
2401.10334 | Longyue Wang | Geyan Ye, Xibao Cai, Houtim Lai, Xing Wang, Junhong Huang, Longyue
Wang, Wei Liu, Xiangxiang Zeng | DrugAssist: A Large Language Model for Molecule Optimization | Geyan Ye and Xibao Cai are equal contributors; Longyue Wang is
corresponding author | null | null | null | q-bio.QM cs.AI cs.CL cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Recently, the impressive performance of large language models (LLMs) on a
wide range of tasks has attracted an increasing number of attempts to apply
LLMs in drug discovery. However, molecule optimization, a critical task in the
drug discovery pipeline, is currently an area that has seen little involvement
from LLMs.... | [
{
"created": "Thu, 28 Dec 2023 10:46:56 GMT",
"version": "v1"
}
] | 2024-01-22 | [
[
"Ye",
"Geyan",
""
],
[
"Cai",
"Xibao",
""
],
[
"Lai",
"Houtim",
""
],
[
"Wang",
"Xing",
""
],
[
"Huang",
"Junhong",
""
],
[
"Wang",
"Longyue",
""
],
[
"Liu",
"Wei",
""
],
[
"Zeng",
"Xiangxiang",... | Recently, the impressive performance of large language models (LLMs) on a wide range of tasks has attracted an increasing number of attempts to apply LLMs in drug discovery. However, molecule optimization, a critical task in the drug discovery pipeline, is currently an area that has seen little involvement from LLMs. M... |
2312.15320 | Da Wu | Da Wu, Jingye Yang, Cong Liu, Tzung-Chien Hsieh, Elaine Marchi, Justin
Blair, Peter Krawitz, Chunhua Weng, Wendy Chung, Gholson J. Lyon, Ian D.
Krantz, Jennifer M. Kalish, Kai Wang | GestaltMML: Enhancing Rare Genetic Disease Diagnosis through Multimodal
Machine Learning Combining Facial Images and Clinical Texts | Significant revisions | null | null | null | q-bio.QM cs.CV cs.LG cs.MM q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Individuals with suspected rare genetic disorders often undergo multiple
clinical evaluations, imaging studies, laboratory tests and genetic tests, to
find a possible answer over a prolonged period of time. Addressing this
"diagnostic odyssey" thus has substantial clinical, psychosocial, and economic
benefits. Many r... | [
{
"created": "Sat, 23 Dec 2023 18:40:25 GMT",
"version": "v1"
},
{
"created": "Mon, 22 Apr 2024 00:41:34 GMT",
"version": "v2"
}
] | 2024-04-23 | [
[
"Wu",
"Da",
""
],
[
"Yang",
"Jingye",
""
],
[
"Liu",
"Cong",
""
],
[
"Hsieh",
"Tzung-Chien",
""
],
[
"Marchi",
"Elaine",
""
],
[
"Blair",
"Justin",
""
],
[
"Krawitz",
"Peter",
""
],
[
"Weng",
"C... | Individuals with suspected rare genetic disorders often undergo multiple clinical evaluations, imaging studies, laboratory tests and genetic tests, to find a possible answer over a prolonged period of time. Addressing this "diagnostic odyssey" thus has substantial clinical, psychosocial, and economic benefits. Many rar... |
1212.0672 | David Saakian | David B. Saakian, Laurent Schwartz | The three different phases in the dynamics of chemical reaction networks
and their relationship to cancer | 5 pages, 2 figures, EPL, in press | null | 10.1209/0295-5075/100/68003 | null | q-bio.OT cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the catalytic reactions model used in cell modeling. The
reaction kinetic is defined through the energies of different species of
molecules following random independent distribution. The related statistical
physics model has three phases and these three phases emerged in the dynamics:
fast dynamics pha... | [
{
"created": "Tue, 4 Dec 2012 10:50:16 GMT",
"version": "v1"
}
] | 2015-06-12 | [
[
"Saakian",
"David B.",
""
],
[
"Schwartz",
"Laurent",
""
]
] | We investigate the catalytic reactions model used in cell modeling. The reaction kinetic is defined through the energies of different species of molecules following random independent distribution. The related statistical physics model has three phases and these three phases emerged in the dynamics: fast dynamics phase... |
2001.03781 | Arfeen Khalid | Arfeen Khalid | BioMETA: A multiple specification parameter estimation system for
stochastic biochemical models | null | null | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The inherent behavioral variability exhibited by stochastic biochemical
systems makes it a challenging task for human experts to manually analyze them.
Computational modeling of such systems helps in investigating and predicting
the behaviors of the underlying biochemical processes but at the same time
introduces the... | [
{
"created": "Sun, 5 Jan 2020 03:04:53 GMT",
"version": "v1"
}
] | 2020-01-14 | [
[
"Khalid",
"Arfeen",
""
]
] | The inherent behavioral variability exhibited by stochastic biochemical systems makes it a challenging task for human experts to manually analyze them. Computational modeling of such systems helps in investigating and predicting the behaviors of the underlying biochemical processes but at the same time introduces the p... |
2407.00560 | Wenda Wang | Wenda Wang, Jiaqi Zhai, He Huang, Xinqi Gong | DCI: An Accurate Quality Assessment Criteria for Protein Complex
Structure Models | null | null | null | null | q-bio.BM math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The structure of proteins is the basis for studying protein function and drug
design. The emergence of AlphaFold 2 has greatly promoted the prediction of
protein 3D structures, and it is of great significance to give an overall and
accurate evaluation of the predicted models, especially the complex models.
Among the ... | [
{
"created": "Sun, 30 Jun 2024 02:02:04 GMT",
"version": "v1"
}
] | 2024-07-02 | [
[
"Wang",
"Wenda",
""
],
[
"Zhai",
"Jiaqi",
""
],
[
"Huang",
"He",
""
],
[
"Gong",
"Xinqi",
""
]
] | The structure of proteins is the basis for studying protein function and drug design. The emergence of AlphaFold 2 has greatly promoted the prediction of protein 3D structures, and it is of great significance to give an overall and accurate evaluation of the predicted models, especially the complex models. Among the ex... |
1302.5917 | N Khusnutdinov | Y. Suleymanov, F. Gafarov, N. Khusnutdinov | Modeling of interstitial branching of axonal networks | 12 pages, 7 figures | 1. J. Integr. Neurosci. 12, 1-14, (2013) | 10.1142/S0219635213500064 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A single axon can generate branches connecting with plenty synaptic targets.
Process of branching is very important for making connections in central
nervous system. The interstitial branching along primary axon shaft occurs
during nervous system development. Growing axon makes pause in its movement and
leaves active... | [
{
"created": "Sun, 24 Feb 2013 15:53:19 GMT",
"version": "v1"
}
] | 2013-04-25 | [
[
"Suleymanov",
"Y.",
""
],
[
"Gafarov",
"F.",
""
],
[
"Khusnutdinov",
"N.",
""
]
] | A single axon can generate branches connecting with plenty synaptic targets. Process of branching is very important for making connections in central nervous system. The interstitial branching along primary axon shaft occurs during nervous system development. Growing axon makes pause in its movement and leaves active p... |
2002.04402 | Lasse Frey | Lasse Jannis Frey, David Vorl\"ander, Detlev Rasch, Sven Meinen,
Bernhard M\"uller, Torsten Mayr, Andreas Dietzel, Jan-Hendrik Grosch, Rainer
Krull | Defining mass transfer in a capillary wave micro-bioreactor | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | For high-throughput cell culture and associated analytics, droplet-based
cultivation systems open up the opportunities for parallelization and rapid
data generation. In contrast to microfluidics with continuous flow, sessile
droplet approaches enhance the flexibility for fluid manipulation with usually
less operation... | [
{
"created": "Tue, 4 Feb 2020 09:23:23 GMT",
"version": "v1"
}
] | 2020-02-12 | [
[
"Frey",
"Lasse Jannis",
""
],
[
"Vorländer",
"David",
""
],
[
"Rasch",
"Detlev",
""
],
[
"Meinen",
"Sven",
""
],
[
"Müller",
"Bernhard",
""
],
[
"Mayr",
"Torsten",
""
],
[
"Dietzel",
"Andreas",
""
],
[
... | For high-throughput cell culture and associated analytics, droplet-based cultivation systems open up the opportunities for parallelization and rapid data generation. In contrast to microfluidics with continuous flow, sessile droplet approaches enhance the flexibility for fluid manipulation with usually less operational... |
1201.1107 | Brajesh Kumar JHA | Brajesh Kumar Jha, Neeru Adlakha and M. N. Mehta | Finite Volume Model to Study the Effect of ER flux on Cytosolic Calcium
Distribution in Astrocytes | 7 pages, 9 figures, journal; ISSN 2151-9617
https://sites.google.com/site/journalofcomputing;
http://www.journalofcomputing.org | Journal of Computing, Volume 3, Issue 11, 2011, 74-80 | null | null | q-bio.CB math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most of the intra-cellular events involved in the initiation and propagation
phases of this process has now been identified astrocytes. The control of the
spread of intracellular calcium signaling has been demonstrated to occur at
several levels including IP3 receptors, intracellular Ca2+ stores like
endoplasmic reti... | [
{
"created": "Thu, 5 Jan 2012 10:35:40 GMT",
"version": "v1"
}
] | 2013-01-08 | [
[
"Jha",
"Brajesh Kumar",
""
],
[
"Adlakha",
"Neeru",
""
],
[
"Mehta",
"M. N.",
""
]
] | Most of the intra-cellular events involved in the initiation and propagation phases of this process has now been identified astrocytes. The control of the spread of intracellular calcium signaling has been demonstrated to occur at several levels including IP3 receptors, intracellular Ca2+ stores like endoplasmic reticu... |
2306.17566 | Ruriko Yoshida | Ruriko Yoshida | Imputing phylogenetic trees using tropical polytopes over the space of
phylogenetic trees | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | When we apply comparative phylogenetic analyses to genome data, it is a
well-known problem and challenge that some of given species (or taxa) often
have missing genes. In such a case, we have to impute a missing part of a gene
tree from a sample of gene trees. In this short paper we propose a novel method
to infer a ... | [
{
"created": "Fri, 30 Jun 2023 11:39:48 GMT",
"version": "v1"
},
{
"created": "Mon, 3 Jul 2023 18:55:04 GMT",
"version": "v2"
}
] | 2023-07-06 | [
[
"Yoshida",
"Ruriko",
""
]
] | When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a sample of gene trees. In this short paper we propose a novel method to infer a mi... |
2305.04120 | Cong Fu | Cong Fu, Keqiang Yan, Limei Wang, Wing Yee Au, Michael McThrow, Tao
Komikado, Koji Maruhashi, Kanji Uchino, Xiaoning Qian, Shuiwang Ji | A Latent Diffusion Model for Protein Structure Generation | Accepted by the Second Learning on Graphs Conference (LoG 2023) | null | null | null | q-bio.BM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Proteins are complex biomolecules that perform a variety of crucial functions
within living organisms. Designing and generating novel proteins can pave the
way for many future synthetic biology applications, including drug discovery.
However, it remains a challenging computational task due to the large modeling
space... | [
{
"created": "Sat, 6 May 2023 19:10:19 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Dec 2023 23:53:20 GMT",
"version": "v2"
}
] | 2023-12-08 | [
[
"Fu",
"Cong",
""
],
[
"Yan",
"Keqiang",
""
],
[
"Wang",
"Limei",
""
],
[
"Au",
"Wing Yee",
""
],
[
"McThrow",
"Michael",
""
],
[
"Komikado",
"Tao",
""
],
[
"Maruhashi",
"Koji",
""
],
[
"Uchino",
... | Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery. However, it remains a challenging computational task due to the large modeling space o... |
2111.05882 | Mohamed Amgad | Lantian Zhang (1 and 2), Mohamed Amgad (2), Lee A.D. Cooper (2) ((1)
North Shore Country Day, Winnetka, IL, USA, (2) Department of Pathology,
Northwestern University, Chicago, IL, USA) | A Histopathology Study Comparing Contrastive Semi-Supervised and Fully
Supervised Learning | 7 pages, 4 figures, 4 tables | null | null | null | q-bio.QM cs.CV eess.IV | http://creativecommons.org/licenses/by/4.0/ | Data labeling is often the most challenging task when developing
computational pathology models. Pathologist participation is necessary to
generate accurate labels, and the limitations on pathologist time and demand
for large, labeled datasets has led to research in areas including weakly
supervised learning using pa... | [
{
"created": "Wed, 10 Nov 2021 19:04:08 GMT",
"version": "v1"
}
] | 2021-11-12 | [
[
"Zhang",
"Lantian",
"",
"1 and 2"
],
[
"Amgad",
"Mohamed",
""
],
[
"Cooper",
"Lee A. D.",
""
]
] | Data labeling is often the most challenging task when developing computational pathology models. Pathologist participation is necessary to generate accurate labels, and the limitations on pathologist time and demand for large, labeled datasets has led to research in areas including weakly supervised learning using pati... |
0910.5057 | Christian Mulder PhD | A. Jan Hendriks, Christian Mulder | Delayed Logistic and Rosenzweig - MacArthur Models with Allometric
Parameter Setting Estimate Population Cycles Well | 15 pages, 3 figures, 4 tables, 50 references | Ecological Complexity 9 (2012) | 10.1016/j.ecocom.2011.12.001 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Context. So far, theoretical explanations for body-size patterns in periodic
population dynamics have received little attention. In particular, tuning and
testing of allometric models on empirical data and regressions has not been
carried out yet. Here, oscillations expected from a one-species (delayed
logistic) and ... | [
{
"created": "Tue, 27 Oct 2009 08:25:57 GMT",
"version": "v1"
}
] | 2013-05-24 | [
[
"Hendriks",
"A. Jan",
""
],
[
"Mulder",
"Christian",
""
]
] | Context. So far, theoretical explanations for body-size patterns in periodic population dynamics have received little attention. In particular, tuning and testing of allometric models on empirical data and regressions has not been carried out yet. Here, oscillations expected from a one-species (delayed logistic) and a ... |
q-bio/0502038 | Rui Dilao | Rui Dilao and Joaquim Sainhas | Modelling butterfly wing eyespot patterns | 12 pages, 3 figures | null | 10.1098/rspb.2004.2761 | M03-49 | q-bio.TO | null | Eyespots are concentric motifs with contrasting colours on butterfly wings.
Eyespots have intra- and inter-specific visual signalling functions with
adaptive and selective roles. We propose a reaction-diffusion model that
accounts for eyespot development. The model considers two diffusive morphogens
and three non-dif... | [
{
"created": "Thu, 24 Feb 2005 23:18:53 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Dilao",
"Rui",
""
],
[
"Sainhas",
"Joaquim",
""
]
] | Eyespots are concentric motifs with contrasting colours on butterfly wings. Eyespots have intra- and inter-specific visual signalling functions with adaptive and selective roles. We propose a reaction-diffusion model that accounts for eyespot development. The model considers two diffusive morphogens and three non-diffu... |
2311.11004 | Uriah Israel | Uriah Israel, Markus Marks, Rohit Dilip, Qilin Li, Morgan Schwartz,
Elora Pradhan, Edward Pao, Shenyi Li, Alexander Pearson-Goulart, Pietro
Perona, Georgia Gkioxari, Ross Barnowski, Yisong Yue, David Van Valen | A Foundation Model for Cell Segmentation | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Cells are the fundamental unit of biological organization, and identifying
them in imaging data - cell segmentation - is a critical task for various
cellular imaging experiments. While deep learning methods have led to
substantial progress on this problem, models that have seen wide use are
specialist models that wor... | [
{
"created": "Sat, 18 Nov 2023 07:55:09 GMT",
"version": "v1"
}
] | 2023-11-21 | [
[
"Israel",
"Uriah",
""
],
[
"Marks",
"Markus",
""
],
[
"Dilip",
"Rohit",
""
],
[
"Li",
"Qilin",
""
],
[
"Schwartz",
"Morgan",
""
],
[
"Pradhan",
"Elora",
""
],
[
"Pao",
"Edward",
""
],
[
"Li",
"S... | Cells are the fundamental unit of biological organization, and identifying them in imaging data - cell segmentation - is a critical task for various cellular imaging experiments. While deep learning methods have led to substantial progress on this problem, models that have seen wide use are specialist models that work ... |
1907.11885 | Kai Qiao | Kai Qiao, Chi Zhang, Jian Chen, Linyuan Wang, Li Tong, Bin Yan | Effective and efficient ROI-wise visual encoding using an end-to-end CNN
regression model and selective optimization | under review in Computational Intelligence and Neuroscience | null | null | null | q-bio.NC cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, visual encoding based on functional magnetic resonance imaging
(fMRI) have realized many achievements with the rapid development of deep
network computation. Visual encoding model is aimed at predicting brain
activity in response to presented image stimuli. Currently, visual encoding is
accomplished mainly ... | [
{
"created": "Sat, 27 Jul 2019 10:09:05 GMT",
"version": "v1"
}
] | 2019-07-30 | [
[
"Qiao",
"Kai",
""
],
[
"Zhang",
"Chi",
""
],
[
"Chen",
"Jian",
""
],
[
"Wang",
"Linyuan",
""
],
[
"Tong",
"Li",
""
],
[
"Yan",
"Bin",
""
]
] | Recently, visual encoding based on functional magnetic resonance imaging (fMRI) have realized many achievements with the rapid development of deep network computation. Visual encoding model is aimed at predicting brain activity in response to presented image stimuli. Currently, visual encoding is accomplished mainly by... |
0809.1605 | P. Grassberger | Alexander Kraskov and Peter Grassberger | MIC: Mutual Information based hierarchical Clustering | 22 pages, including 7 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Clustering is a concept used in a huge variety of applications. We review a
conceptually very simple algorithm for hierarchical clustering called in the
following the {\it mutual information clustering} (MIC) algorithm. It uses
mutual information (MI) as a similarity measure and exploits its grouping
property: The MI... | [
{
"created": "Tue, 9 Sep 2008 16:50:09 GMT",
"version": "v1"
}
] | 2008-09-10 | [
[
"Kraskov",
"Alexander",
""
],
[
"Grassberger",
"Peter",
""
]
] | Clustering is a concept used in a huge variety of applications. We review a conceptually very simple algorithm for hierarchical clustering called in the following the {\it mutual information clustering} (MIC) algorithm. It uses mutual information (MI) as a similarity measure and exploits its grouping property: The MI b... |
1211.2878 | Erick Chastain | Erick Chastain, Rustom Antia, Carl T. Bergstrom | Defensive complexity and the phylogenetic conservation of immune control | arXiv admin note: substantial text overlap with arXiv:1203.4601 | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One strategy for winning a coevolutionary struggle is to evolve rapidly. Most
of the literature on host-pathogen coevolution focuses on this phenomenon, and
looks for consequent evidence of coevolutionary arms races. An alternative
strategy, less often considered in the literature, is to deter rapid
evolutionary chan... | [
{
"created": "Tue, 13 Nov 2012 03:26:45 GMT",
"version": "v1"
}
] | 2012-11-14 | [
[
"Chastain",
"Erick",
""
],
[
"Antia",
"Rustom",
""
],
[
"Bergstrom",
"Carl T.",
""
]
] | One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative strategy, less often considered in the literature, is to deter rapid evolutionary change... |
1007.0858 | Christophe Magnani | Christophe Magnani and L.E.Moore | Quadratic Sinusoidal Analysis of Neurons in Voltage Clamp | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nonlinear biophysical properties of individual neurons are known to play a
major role in the nervous system. Earlier electrophysiological studies have
made use of piecewise linear characterization of voltage clamped neurons, which
consists of a sequence of linear admittances computed at different voltage
levels. In t... | [
{
"created": "Tue, 6 Jul 2010 10:45:10 GMT",
"version": "v1"
}
] | 2010-07-07 | [
[
"Magnani",
"Christophe",
""
],
[
"Moore",
"L. E.",
""
]
] | Nonlinear biophysical properties of individual neurons are known to play a major role in the nervous system. Earlier electrophysiological studies have made use of piecewise linear characterization of voltage clamped neurons, which consists of a sequence of linear admittances computed at different voltage levels. In thi... |
2111.04866 | Marcus Aguiar de | D\'ebora Princepe, Marcus A. M. de Aguiar and Joshua B. Plotkin | Mito-nuclear selection induces a trade-off between species ecological
dominance and evolutionary lifespan | 26 pages, 6 figures, supplemental material | Nature Ecology & Evolution, 2022 | 10.1038/s41559-022-01901-0 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Mitochondrial and nuclear genomes must be co-adapted to ensure proper
cellular respiration and energy production. Mito-nuclear incompatibility
reduces individual fitness and induces hybrid infertility, suggesting a
possible role in reproductive barriers and speciation. Here we develop a
birth-death model for evolutio... | [
{
"created": "Mon, 8 Nov 2021 23:13:24 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Jun 2022 16:51:07 GMT",
"version": "v2"
}
] | 2022-10-12 | [
[
"Princepe",
"Débora",
""
],
[
"de Aguiar",
"Marcus A. M.",
""
],
[
"Plotkin",
"Joshua B.",
""
]
] | Mitochondrial and nuclear genomes must be co-adapted to ensure proper cellular respiration and energy production. Mito-nuclear incompatibility reduces individual fitness and induces hybrid infertility, suggesting a possible role in reproductive barriers and speciation. Here we develop a birth-death model for evolution ... |
0904.2466 | Siew-Ann Cheong | Siew-Ann Cheong, Paul Stodghill, David J. Schneider, Samuel W.
Cartinhour, and Christopher R. Myers | Extending the Recursive Jensen-Shannon Segmentation of Biological
Sequences | IEEEtran class, 30 pages, 7 figures | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we extend a previously developed recursive entropic
segmentation scheme for applications to biological sequences. Instead of
Bernoulli chains, we model the statistically stationary segments in a
biological sequence as Markov chains, and define a generalized Jensen-Shannon
divergence for distinguishing ... | [
{
"created": "Thu, 16 Apr 2009 11:15:33 GMT",
"version": "v1"
}
] | 2009-04-17 | [
[
"Cheong",
"Siew-Ann",
""
],
[
"Stodghill",
"Paul",
""
],
[
"Schneider",
"David J.",
""
],
[
"Cartinhour",
"Samuel W.",
""
],
[
"Myers",
"Christopher R.",
""
]
] | In this paper, we extend a previously developed recursive entropic segmentation scheme for applications to biological sequences. Instead of Bernoulli chains, we model the statistically stationary segments in a biological sequence as Markov chains, and define a generalized Jensen-Shannon divergence for distinguishing be... |
2403.06331 | Pablo Zambrano Ph.D. | Pablo Zambrano | Membrane Interactions in Alzheimer`s Treatment Strategies with
Multitarget Molecules | 6 pages, 1 figure | null | 10.1016/j.bioorg.2024.107407 | null | q-bio.BM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Addressing Alzheimer's disease (AD) requires innovative strategies beyond
current single-target drugs. This Letter to the Editor suggests that
multitarget molecules, especially those targeting neuronal membrane protection,
could offer a comprehensive approach to AD therapy, advocating for further
research into their ... | [
{
"created": "Sun, 10 Mar 2024 22:34:25 GMT",
"version": "v1"
}
] | 2024-06-04 | [
[
"Zambrano",
"Pablo",
""
]
] | Addressing Alzheimer's disease (AD) requires innovative strategies beyond current single-target drugs. This Letter to the Editor suggests that multitarget molecules, especially those targeting neuronal membrane protection, could offer a comprehensive approach to AD therapy, advocating for further research into their me... |
2405.03726 | Andac Demir | Andac Demir, Elizaveta Solovyeva, James Boylan, Mei Xiao, Fabrizio
Serluca, Sebastian Hoersch, Jeremy Jenkins, Murthy Devarakonda, Bulent
Kiziltan | sc-OTGM: Single-Cell Perturbation Modeling by Solving Optimal Mass
Transport on the Manifold of Gaussian Mixtures | ICLR 2024, Machine Learning for Genomics Explorations Workshop | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Influenced by breakthroughs in LLMs, single-cell foundation models are
emerging. While these models show successful performance in cell type
clustering, phenotype classification, and gene perturbation response
prediction, it remains to be seen if a simpler model could achieve comparable
or better results, especially ... | [
{
"created": "Mon, 6 May 2024 06:46:11 GMT",
"version": "v1"
}
] | 2024-05-08 | [
[
"Demir",
"Andac",
""
],
[
"Solovyeva",
"Elizaveta",
""
],
[
"Boylan",
"James",
""
],
[
"Xiao",
"Mei",
""
],
[
"Serluca",
"Fabrizio",
""
],
[
"Hoersch",
"Sebastian",
""
],
[
"Jenkins",
"Jeremy",
""
],
[
... | Influenced by breakthroughs in LLMs, single-cell foundation models are emerging. While these models show successful performance in cell type clustering, phenotype classification, and gene perturbation response prediction, it remains to be seen if a simpler model could achieve comparable or better results, especially wi... |
1110.1516 | Daniel Kaschek | Daniel Kaschek and Jens Timmer | A Variational Approach to Parameter Estimation in Ordinary Differential
Equations | null | null | null | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ordinary differential equations are widely-used in the field of systems
biology and chemical engineering to model chemical reaction networks. Numerous
techniques have been developed to estimate parameters like rate constants,
initial conditions or steady state concentrations from time-resolved data. In
contrast to th... | [
{
"created": "Fri, 7 Oct 2011 13:05:35 GMT",
"version": "v1"
},
{
"created": "Thu, 5 Jul 2012 08:47:28 GMT",
"version": "v2"
}
] | 2012-07-06 | [
[
"Kaschek",
"Daniel",
""
],
[
"Timmer",
"Jens",
""
]
] | Ordinary differential equations are widely-used in the field of systems biology and chemical engineering to model chemical reaction networks. Numerous techniques have been developed to estimate parameters like rate constants, initial conditions or steady state concentrations from time-resolved data. In contrast to this... |
1906.08612 | Kevin Parker PhD | Kevin J. Parker, Thomas Szabo, Sverre Holm | Towards a consensus on rheological models for shear waves in soft
tissues | 39 pages, 11 figures | Phys Med Biol 64(21) p.215012, 2019 | 10.1088/1361-6560/ab453d | null | q-bio.TO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A rising wave of technologies and instruments are enabling more labs and
clinics to make a variety of measurements related to tissue viscoelastic
properties. These instruments include elastography imaging scanners,
rheological shear viscometers, and a variety of calibrated stress-strain
analyzers. From these many sou... | [
{
"created": "Thu, 20 Jun 2019 13:43:21 GMT",
"version": "v1"
},
{
"created": "Thu, 19 Sep 2019 18:04:20 GMT",
"version": "v2"
}
] | 2020-02-14 | [
[
"Parker",
"Kevin J.",
""
],
[
"Szabo",
"Thomas",
""
],
[
"Holm",
"Sverre",
""
]
] | A rising wave of technologies and instruments are enabling more labs and clinics to make a variety of measurements related to tissue viscoelastic properties. These instruments include elastography imaging scanners, rheological shear viscometers, and a variety of calibrated stress-strain analyzers. From these many sourc... |
2105.06049 | Fan Wang | Fan Wang, Saarthak Kapse, Steven Liu, Prateek Prasanna, Chao Chen | TopoTxR: A Topological Biomarker for Predicting Treatment Response in
Breast Cancer | 12 pages, 5 figures, 2 tables, accepted to International Conference
on Information Processing in Medical Imaging (IPMI) 2021 | null | null | null | q-bio.QM cs.CV eess.IV | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Characterization of breast parenchyma on dynamic contrast-enhanced magnetic
resonance imaging (DCE-MRI) is a challenging task owing to the complexity of
underlying tissue structures. Current quantitative approaches, including
radiomics and deep learning models, do not explicitly capture the complex and
subtle parench... | [
{
"created": "Thu, 13 May 2021 02:38:48 GMT",
"version": "v1"
}
] | 2021-05-14 | [
[
"Wang",
"Fan",
""
],
[
"Kapse",
"Saarthak",
""
],
[
"Liu",
"Steven",
""
],
[
"Prasanna",
"Prateek",
""
],
[
"Chen",
"Chao",
""
]
] | Characterization of breast parenchyma on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a challenging task owing to the complexity of underlying tissue structures. Current quantitative approaches, including radiomics and deep learning models, do not explicitly capture the complex and subtle parenchym... |
0809.2950 | Kamenev Alex | Alex Kamenev, Baruch Meerson, Boris Shklovskii | Population extinction in a fluctuating environment | 4 pages, 3 figure | Phys. Rev. Lett. 101, 268103 (2008) | 10.1103/PhysRevLett.101.268103 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Environmental noise can cause an exponential reduction in the mean time to
extinction (MTE) of an isolated population. We study this effect on an example
of a stochastic birth-death process with rates modulated by a colored Gaussian
noise. A path integral formulation yields a transparent way of evaluating the
MTE and... | [
{
"created": "Wed, 17 Sep 2008 17:35:01 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Kamenev",
"Alex",
""
],
[
"Meerson",
"Baruch",
""
],
[
"Shklovskii",
"Boris",
""
]
] | Environmental noise can cause an exponential reduction in the mean time to extinction (MTE) of an isolated population. We study this effect on an example of a stochastic birth-death process with rates modulated by a colored Gaussian noise. A path integral formulation yields a transparent way of evaluating the MTE and f... |
2004.04271 | Michael Nikolaou | Michael Nikolaou | Simple Formulas for a Two-Tier Strategy to Flatten the Curve | 6 pages 7 figures arXiv:2003.12055v1 [q-bio.PE] 26 Mar 2020 | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Some basic facts that enable or constrain efforts to "flatten the curve" by
non-pharmaceutical interventions (NPI) are summarized and placed in the current
context of the COVID-19 epidemic. Analytical formulas are presented for a
simple two-tier NPI strategy that places different social distancing targets
for high- a... | [
{
"created": "Wed, 8 Apr 2020 21:27:44 GMT",
"version": "v1"
},
{
"created": "Sun, 12 Apr 2020 21:38:45 GMT",
"version": "v2"
}
] | 2020-04-14 | [
[
"Nikolaou",
"Michael",
""
]
] | Some basic facts that enable or constrain efforts to "flatten the curve" by non-pharmaceutical interventions (NPI) are summarized and placed in the current context of the COVID-19 epidemic. Analytical formulas are presented for a simple two-tier NPI strategy that places different social distancing targets for high- and... |
1010.1099 | Junbai Wang | Junbai Wang, Leo Wang-Kit Cheung and Jan Delabie | Application of new probabilistic graphical models in the genetic
regulatory networks studies | 38 pages, 3 figures | J Biomed Inform. 2005 Dec;38(6):443-55. Epub 2005 Jun 9 | 10.1016/j.jbi.2005.04.003 | null | q-bio.QM q-bio.MN | http://creativecommons.org/licenses/publicdomain/ | This paper introduces two new probabilistic graphical models for
reconstruction of genetic regulatory networks using DNA microarray data. One is
an Independence Graph (IG) model with either a forward or a backward search
algorithm and the other one is a Gaussian Network (GN) model with a novel
greedy search method. T... | [
{
"created": "Wed, 6 Oct 2010 09:25:42 GMT",
"version": "v1"
}
] | 2010-10-07 | [
[
"Wang",
"Junbai",
""
],
[
"Cheung",
"Leo Wang-Kit",
""
],
[
"Delabie",
"Jan",
""
]
] | This paper introduces two new probabilistic graphical models for reconstruction of genetic regulatory networks using DNA microarray data. One is an Independence Graph (IG) model with either a forward or a backward search algorithm and the other one is a Gaussian Network (GN) model with a novel greedy search method. The... |
q-bio/0412008 | Suan Li Mai | Mai Suan Li, D. K. Klimov and D. Thirumalai | Finite size effects on calorimetric cooperativity of two-state proteins | 3 eps figures. To appear in the special issue of Physica A | null | 10.1016/j.physa.2004.11.029 | null | q-bio.BM q-bio.QM | null | Finite size effects on the calorimetric cooperatity of the folding-unfolding
transition in two-state proteins are considered using the Go lattice models
with and without side chains. We show that for models without side chains a
dimensionless measure of calorimetric cooperativity kappa2 defined as the ratio
of the va... | [
{
"created": "Sun, 5 Dec 2004 13:59:14 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Li",
"Mai Suan",
""
],
[
"Klimov",
"D. K.",
""
],
[
"Thirumalai",
"D.",
""
]
] | Finite size effects on the calorimetric cooperatity of the folding-unfolding transition in two-state proteins are considered using the Go lattice models with and without side chains. We show that for models without side chains a dimensionless measure of calorimetric cooperativity kappa2 defined as the ratio of the van'... |
2310.10544 | Laurence Maloney | Laurence T Maloney, Maria F Dal Martello, Vivian Fei and Valerie Ma | Use of probabilistic phrases in a coordination game: human versus GPT-4 | Corrected typos, extended discussion, added references | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | English speakers use probabilistic phrases such as likely to communicate
information about the probability or likelihood of events. Communication is
successful to the extent that the listener grasps what the speaker means to
convey and, if communication is successful, individuals can potentially
coordinate their acti... | [
{
"created": "Mon, 16 Oct 2023 16:14:27 GMT",
"version": "v1"
},
{
"created": "Fri, 3 Nov 2023 18:13:43 GMT",
"version": "v2"
},
{
"created": "Sat, 25 Nov 2023 19:12:02 GMT",
"version": "v3"
}
] | 2023-11-28 | [
[
"Maloney",
"Laurence T",
""
],
[
"Martello",
"Maria F Dal",
""
],
[
"Fei",
"Vivian",
""
],
[
"Ma",
"Valerie",
""
]
] | English speakers use probabilistic phrases such as likely to communicate information about the probability or likelihood of events. Communication is successful to the extent that the listener grasps what the speaker means to convey and, if communication is successful, individuals can potentially coordinate their action... |
2110.10866 | Ashkaan Fahimipour | Ashkaan K. Fahimipour, Fanqi Zeng, Martin Homer, Arne Traulsen, Simon
A. Levin, Thilo Gross | Sharp thresholds limit the benefit of defector avoidance in cooperation
on networks | 14 pages, 4 figures | null | 10.1073/pnas.2120120119 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Consider a cooperation game on a spatial network of habitat patches, where
players can relocate between patches if they judge the local conditions to be
unfavorable. In time, the relocation events may lead to a homogeneous state
where all patches harbor the same relative densities of cooperators and
defectors or they... | [
{
"created": "Thu, 21 Oct 2021 02:57:55 GMT",
"version": "v1"
},
{
"created": "Tue, 12 Jul 2022 19:46:30 GMT",
"version": "v2"
}
] | 2022-10-12 | [
[
"Fahimipour",
"Ashkaan K.",
""
],
[
"Zeng",
"Fanqi",
""
],
[
"Homer",
"Martin",
""
],
[
"Traulsen",
"Arne",
""
],
[
"Levin",
"Simon A.",
""
],
[
"Gross",
"Thilo",
""
]
] | Consider a cooperation game on a spatial network of habitat patches, where players can relocate between patches if they judge the local conditions to be unfavorable. In time, the relocation events may lead to a homogeneous state where all patches harbor the same relative densities of cooperators and defectors or they m... |
1911.00325 | Marzio Pennisi | Giulia Russo, Francesco Pappalardo, Miguel A. Juarez, Marzio Pennisi,
Pere Joan Cardona, Rhea Coler, Epifanio Fichera, Marco Viceconti | Evaluation of the efficacy of RUTI and ID93/GLA-SE vaccines in
tuberculosis treatment: in silico trial through UISS-TB simulator | 5 pages | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Tuberculosis (TB) is one of the deadliest diseases worldwide, with 1,5
million fatalities every year along with potential devastating effects on
society, families and individuals. To address this alarming burden, vaccines
can play a fundamental role, even though to date no fully effective TB vaccine
really exists. Cu... | [
{
"created": "Sat, 26 Oct 2019 12:42:52 GMT",
"version": "v1"
}
] | 2019-11-04 | [
[
"Russo",
"Giulia",
""
],
[
"Pappalardo",
"Francesco",
""
],
[
"Juarez",
"Miguel A.",
""
],
[
"Pennisi",
"Marzio",
""
],
[
"Cardona",
"Pere Joan",
""
],
[
"Coler",
"Rhea",
""
],
[
"Fichera",
"Epifanio",
""
... | Tuberculosis (TB) is one of the deadliest diseases worldwide, with 1,5 million fatalities every year along with potential devastating effects on society, families and individuals. To address this alarming burden, vaccines can play a fundamental role, even though to date no fully effective TB vaccine really exists. Curr... |
1503.05791 | Filippo Disanto | Filippo Disanto and Noah A. Rosenberg | Asymptotic properties of the number of matching coalescent histories for
caterpillar-like families of species trees | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Coalescent histories provide lists of species tree branches on which gene
tree coalescences can take place, and their enumerative properties assist in
understanding the computational complexity of calculations central in the study
of gene trees and species trees. Here, we solve an enumerative problem left
open by Ros... | [
{
"created": "Thu, 19 Mar 2015 15:05:07 GMT",
"version": "v1"
}
] | 2015-03-20 | [
[
"Disanto",
"Filippo",
""
],
[
"Rosenberg",
"Noah A.",
""
]
] | Coalescent histories provide lists of species tree branches on which gene tree coalescences can take place, and their enumerative properties assist in understanding the computational complexity of calculations central in the study of gene trees and species trees. Here, we solve an enumerative problem left open by Rosen... |
2110.05232 | Romain Weppe | R. Weppe (UMR ISEM), Ma\"eva Orliac (UMR ISEM), G. Guinot (UMR ISEM),
Fabien L. Condamine (UMR ISEM) | Evolutionary drivers, morphological evolution and diversity dynamics of
a surviving mammal clade: cainotherioids at the Eocene--Oligocene transition | null | Proceedings of the Royal Society B: Biological Sciences, Royal
Society, The, 2021, 288 (1952), pp.20210173.
\&\#x27E8;10.1098/rspb.2021.0173\&\#x27E9 | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Eocene--Oligocene transition (EOT) represents a period of global
environmental changes particularly marked in Europe and coincides with a
dramatic biotic turnover. Here, using an exceptional fossil preservation, we
document and analyse the diversity dynamics of a mammal clade, Cainotherioidea
(Artiodactyla), that... | [
{
"created": "Mon, 11 Oct 2021 12:49:30 GMT",
"version": "v1"
}
] | 2021-10-12 | [
[
"Weppe",
"R.",
"",
"UMR ISEM"
],
[
"Orliac",
"Maëva",
"",
"UMR ISEM"
],
[
"Guinot",
"G.",
"",
"UMR ISEM"
],
[
"Condamine",
"Fabien L.",
"",
"UMR ISEM"
]
] | The Eocene--Oligocene transition (EOT) represents a period of global environmental changes particularly marked in Europe and coincides with a dramatic biotic turnover. Here, using an exceptional fossil preservation, we document and analyse the diversity dynamics of a mammal clade, Cainotherioidea (Artiodactyla), that s... |
2302.02692 | Jeyashree Krishnan | Jeyashree Krishnan, Zeyu Lian, Pieter E. Oomen, Xiulan He, Soodabeh
Majdi, Andreas Schuppert, Andrew Ewing | Spike-by-Spike Frequency Analysis of Amperometry Traces Provides
Statistical Validation of Observations in the Time Domain | 34 pages, 16 figures | null | null | null | q-bio.SC physics.data-an q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Amperometry is a commonly used electrochemical method for studying the
process of exocytosis in real-time. Given the high precision of recording that
amperometry procedures offer, the volume of data generated can span over
several hundreds of megabytes to a few gigabytes and therefore necessitates
systematic and repr... | [
{
"created": "Mon, 6 Feb 2023 10:49:02 GMT",
"version": "v1"
}
] | 2023-02-07 | [
[
"Krishnan",
"Jeyashree",
""
],
[
"Lian",
"Zeyu",
""
],
[
"Oomen",
"Pieter E.",
""
],
[
"He",
"Xiulan",
""
],
[
"Majdi",
"Soodabeh",
""
],
[
"Schuppert",
"Andreas",
""
],
[
"Ewing",
"Andrew",
""
]
] | Amperometry is a commonly used electrochemical method for studying the process of exocytosis in real-time. Given the high precision of recording that amperometry procedures offer, the volume of data generated can span over several hundreds of megabytes to a few gigabytes and therefore necessitates systematic and reprod... |
2008.12683 | Mohammad Ali Moni | Sakifa Aktar, Ashis Talukder, Md. Martuza Ahamad, A. H. M. Kamal,
Jahidur Rahman Khan, Md. Protikuzzaman, Nasif Hossain, Julian M.W. Quinn,
Mathew A. Summers, Teng Liaw, Valsamma Eapen, Mohammad Ali Moni | Machine Learning and Meta-Analysis Approach to Identify Patient
Comorbidities and Symptoms that Increased Risk of Mortality in COVID-19 | null | Diagnostics 2021 | 10.3390/diagnostics11081383 | 2008.12683 | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Background: Providing appropriate care for people suffering from COVID-19,
the disease caused by the pandemic SARS-CoV-2 virus is a significant global
challenge. Many individuals who become infected have pre-existing conditions
that may interact with COVID-19 to increase symptom severity and mortality
risk. COVID-19 ... | [
{
"created": "Fri, 21 Aug 2020 12:31:54 GMT",
"version": "v1"
}
] | 2023-02-24 | [
[
"Aktar",
"Sakifa",
""
],
[
"Talukder",
"Ashis",
""
],
[
"Ahamad",
"Md. Martuza",
""
],
[
"Kamal",
"A. H. M.",
""
],
[
"Khan",
"Jahidur Rahman",
""
],
[
"Protikuzzaman",
"Md.",
""
],
[
"Hossain",
"Nasif",
""... | Background: Providing appropriate care for people suffering from COVID-19, the disease caused by the pandemic SARS-CoV-2 virus is a significant global challenge. Many individuals who become infected have pre-existing conditions that may interact with COVID-19 to increase symptom severity and mortality risk. COVID-19 pa... |
1812.05872 | Fiona Macfarlane | Mark AJ Chaplain, Tommaso Lorenzi, Fiona R Macfarlane | Bridging the gap between individual-based and continuum models of
growing cell populations | null | null | 10.1007/s00285-019-01391-y | null | q-bio.TO math.AP q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Continuum models for the spatial dynamics of growing cell populations have
been widely used to investigate the mechanisms underpinning tissue development
and tumour invasion. These models consist of nonlinear partial differential
equations that describe the evolution of cellular densities in response to
pressure grad... | [
{
"created": "Fri, 14 Dec 2018 12:03:46 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Dec 2018 08:48:26 GMT",
"version": "v2"
},
{
"created": "Sat, 11 May 2019 09:59:55 GMT",
"version": "v3"
}
] | 2019-07-15 | [
[
"Chaplain",
"Mark AJ",
""
],
[
"Lorenzi",
"Tommaso",
""
],
[
"Macfarlane",
"Fiona R",
""
]
] | Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations that describe the evolution of cellular densities in response to pressure gradie... |
1703.10643 | Ann Sizemore | Ann E. Sizemore and Danielle S. Bassett | Dynamic Graph Metrics: Tutorial, Toolbox, and Tale | 21 pages, 5 figures. Toolbox not yet publicly available | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The central nervous system is composed of many individual units -- from cells
to areas -- that are connected with one another in a complex pattern of
functional interactions that supports perception, action, and cognition. One
natural and parsimonious representation of such a system is a graph in which
nodes (units) ... | [
{
"created": "Thu, 30 Mar 2017 19:16:33 GMT",
"version": "v1"
}
] | 2017-04-03 | [
[
"Sizemore",
"Ann E.",
""
],
[
"Bassett",
"Danielle S.",
""
]
] | The central nervous system is composed of many individual units -- from cells to areas -- that are connected with one another in a complex pattern of functional interactions that supports perception, action, and cognition. One natural and parsimonious representation of such a system is a graph in which nodes (units) ar... |
1302.2906 | Christoph Adami | Bj{\o}rn {\O}stman and Christoph Adami | Predicting evolution and visualizing high-dimensional fitness landscapes | 12 pages, 7 figures. To appear in "Recent Advances in the Theory and
Application of Fitness Landscapes" (A. Engelbrecht and H. Richter, eds.).
Springer Series in Emergence, Complexity, and Computation, 2013 | null | null | null | q-bio.PE nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The tempo and mode of an adaptive process is strongly determined by the
structure of the fitness landscape that underlies it. In order to be able to
predict evolutionary outcomes (even on the short term), we must know more about
the nature of realistic fitness landscapes than we do today. For example, in
order to kno... | [
{
"created": "Tue, 12 Feb 2013 20:49:54 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Feb 2013 21:24:34 GMT",
"version": "v2"
}
] | 2013-02-28 | [
[
"Østman",
"Bjørn",
""
],
[
"Adami",
"Christoph",
""
]
] | The tempo and mode of an adaptive process is strongly determined by the structure of the fitness landscape that underlies it. In order to be able to predict evolutionary outcomes (even on the short term), we must know more about the nature of realistic fitness landscapes than we do today. For example, in order to know ... |
1210.3555 | Danielle Bassett | Danielle S. Bassett, Nicholas F. Wymbs, M. Puck Rombach, Mason A.
Porter, Peter J. Mucha, Scott T. Grafton | Task-Based Core-Periphery Organisation of Human Brain Dynamics | 21 pages, 9 figures, and Supplementary Information | null | null | null | q-bio.NC cond-mat.dis-nn nlin.AO stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As a person learns a new skill, distinct synapses, brain regions, and
circuits are engaged and change over time. In this paper, we develop methods to
examine patterns of correlated activity across a large set of brain regions.
Our goal is to identify properties that enable robust learning of a motor
skill. We measure... | [
{
"created": "Fri, 12 Oct 2012 15:50:47 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Oct 2013 15:30:56 GMT",
"version": "v2"
}
] | 2013-10-31 | [
[
"Bassett",
"Danielle S.",
""
],
[
"Wymbs",
"Nicholas F.",
""
],
[
"Rombach",
"M. Puck",
""
],
[
"Porter",
"Mason A.",
""
],
[
"Mucha",
"Peter J.",
""
],
[
"Grafton",
"Scott T.",
""
]
] | As a person learns a new skill, distinct synapses, brain regions, and circuits are engaged and change over time. In this paper, we develop methods to examine patterns of correlated activity across a large set of brain regions. Our goal is to identify properties that enable robust learning of a motor skill. We measure b... |
q-bio/0503029 | Changbong Hyeon | Changbong Hyeon and D. Thirumalai | Mechanical unfolding of RNA hairpins | 23 pages, 6 Figures. in press (Proc. Natl. Acad. Sci.) | Proc. Natl. Acad. Sci. 102, 6789-6794 (2005) | 10.1073/pnas.0408314102 | null | q-bio.BM q-bio.QM | null | Mechanical unfolding trajectories, generated by applying constant force in
optical tweezer experiments, show that RNA hairpins and the P5abc subdomain of
the group I intron unfold reversibly. We use coarse-grained Go-like models for
RNA hairpins to explore forced-unfolding over a broad range of temperatures. A
number... | [
{
"created": "Fri, 18 Mar 2005 19:52:45 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Hyeon",
"Changbong",
""
],
[
"Thirumalai",
"D.",
""
]
] | Mechanical unfolding trajectories, generated by applying constant force in optical tweezer experiments, show that RNA hairpins and the P5abc subdomain of the group I intron unfold reversibly. We use coarse-grained Go-like models for RNA hairpins to explore forced-unfolding over a broad range of temperatures. A number o... |
1101.1556 | Simon DeDeo | Simon DeDeo, David C. Krakauer, Jessica C. Flack | Evidence of strategic periodicities in collective conflict dynamics | 22 pages, 7 figures, 1 table. Accepted for publication in Journal of
the Royal Society Interface | J. R. Soc. Interface (2011) vol. 8, no. 62, 1260-1273 | 10.1098/rsif.2010.0687 | SFI Working Paper #11-01-002 | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze the timescales of conflict decision-making in a primate society.
We present evidence for multiple, periodic timescales associated with social
decision-making and behavioral patterns. We demonstrate the existence of
periodicities that are not directly coupled to environmental cycles or known
ultraridian mec... | [
{
"created": "Fri, 7 Jan 2011 23:39:54 GMT",
"version": "v1"
}
] | 2011-09-21 | [
[
"DeDeo",
"Simon",
""
],
[
"Krakauer",
"David C.",
""
],
[
"Flack",
"Jessica C.",
""
]
] | We analyze the timescales of conflict decision-making in a primate society. We present evidence for multiple, periodic timescales associated with social decision-making and behavioral patterns. We demonstrate the existence of periodicities that are not directly coupled to environmental cycles or known ultraridian mecha... |
2206.11878 | Zepeng Huo | Zepeng Huo, Bobak J. Mortazavi, Theodora Chaspari, Nicolaas Deutz,
Laura Ruebush, Ricardo Gutierrez-Osuna | Predicting the meal macronutrient composition from continuous glucose
monitors | null | In 2019 IEEE EMBS International Conference on Biomedical & Health
Informatics (BHI), pp. 1-4. IEEE, 2019 | 10.1109/BHI.2019.8834488 | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Sustained high levels of blood glucose in type 2 diabetes (T2DM) can have
disastrous long-term health consequences. An essential component of clinical
interventions for T2DM is monitoring dietary intake to keep plasma glucose
levels within an acceptable range. Yet, current techniques to monitor food
intake are time i... | [
{
"created": "Thu, 23 Jun 2022 17:41:25 GMT",
"version": "v1"
}
] | 2022-06-24 | [
[
"Huo",
"Zepeng",
""
],
[
"Mortazavi",
"Bobak J.",
""
],
[
"Chaspari",
"Theodora",
""
],
[
"Deutz",
"Nicolaas",
""
],
[
"Ruebush",
"Laura",
""
],
[
"Gutierrez-Osuna",
"Ricardo",
""
]
] | Sustained high levels of blood glucose in type 2 diabetes (T2DM) can have disastrous long-term health consequences. An essential component of clinical interventions for T2DM is monitoring dietary intake to keep plasma glucose levels within an acceptable range. Yet, current techniques to monitor food intake are time int... |
2108.06666 | R.K. Brojen Singh | Keilash Chirom, Md. Zubbair Malik, Pallavi Somvanshi and R.K. Brojen
Singh | Network medicine in ovarian cancer: Topological properties to drug
discovery | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | The investigation of topological properties of ovarian cancer network (OCN)
and the roles of hubs involved in it by digging the network at various levels
of organization are important to understand how OCN is organized to understand
disease states. The OCN constructed from the experimentally verified genes
exhibits f... | [
{
"created": "Sun, 15 Aug 2021 06:44:37 GMT",
"version": "v1"
}
] | 2021-08-17 | [
[
"Chirom",
"Keilash",
""
],
[
"Malik",
"Md. Zubbair",
""
],
[
"Somvanshi",
"Pallavi",
""
],
[
"Singh",
"R. K. Brojen",
""
]
] | The investigation of topological properties of ovarian cancer network (OCN) and the roles of hubs involved in it by digging the network at various levels of organization are important to understand how OCN is organized to understand disease states. The OCN constructed from the experimentally verified genes exhibits fra... |
2008.00028 | Meijian Yang | Meijian Yang | Investigating the association between meteorological factors and the
transmission and fatality of COVID-19 in the US | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A novel coronavirus disease (COVID-19) is sweeping the world and has taken
away thousands of lives. As the current epicenter, the United States has the
largest number of confirmed and death cases of COVID-19. Meteorological factors
have been found associated with many respiratory diseases in the past studies.
In orde... | [
{
"created": "Thu, 30 Jul 2020 03:51:32 GMT",
"version": "v1"
}
] | 2020-08-04 | [
[
"Yang",
"Meijian",
""
]
] | A novel coronavirus disease (COVID-19) is sweeping the world and has taken away thousands of lives. As the current epicenter, the United States has the largest number of confirmed and death cases of COVID-19. Meteorological factors have been found associated with many respiratory diseases in the past studies. In order ... |
1807.09932 | Patryk Orzechowski | Patryk Orzechowski and Jason H. Moore | EBIC: an open source software for high-dimensional and big data
biclustering analyses | 2 pages, 1 figure | null | null | null | q-bio.GN cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: In this paper we present the latest release of EBIC, a
next-generation biclustering algorithm for mining genetic data. The major
contribution of this paper is adding support for big data, making it possible
to efficiently run large genomic data mining analyses. Additional enhancements
include integration ... | [
{
"created": "Thu, 26 Jul 2018 02:57:19 GMT",
"version": "v1"
}
] | 2018-07-27 | [
[
"Orzechowski",
"Patryk",
""
],
[
"Moore",
"Jason H.",
""
]
] | Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run large genomic data mining analyses. Additional enhancements include integration wi... |
1710.03264 | William Redman T | William T Redman | A General Approach to Coding in Early Olfactory and Visual Neural
Populations | 11 pages | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Recent experimental and theoretical work on neural populations belonging to
two separate early sensory systems, olfaction and vision, has challenged the
notion that the two operate under different computational paradigms by
providing evidence for the respective neural population codes having three
central, common fea... | [
{
"created": "Mon, 9 Oct 2017 18:56:11 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Nov 2017 23:39:01 GMT",
"version": "v2"
},
{
"created": "Sun, 12 Aug 2018 18:09:56 GMT",
"version": "v3"
}
] | 2018-08-14 | [
[
"Redman",
"William T",
""
]
] | Recent experimental and theoretical work on neural populations belonging to two separate early sensory systems, olfaction and vision, has challenged the notion that the two operate under different computational paradigms by providing evidence for the respective neural population codes having three central, common featu... |
q-bio/0311013 | Pau Fern\'andez | Ricard V. Sole, Pau Fernandez, Stuart A. Kauffman | Adaptive walks in a gene network model of morphogenesis: insights into
the Cambrian explosion | to appear in International Journal of Developmental Biology, special
issue on Evo-Devo (2003) | null | null | null | q-bio.GN q-bio.MN q-bio.PE | null | The emergence of complex patterns of organization close to the Cambrian
boundary is known to have happened over a (geologically) short period of time.
It involved the rapid diversification of body plans and stands as one of the
major transitions in evolution. How it took place is a controversial issue.
Here we explor... | [
{
"created": "Mon, 10 Nov 2003 15:12:32 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Sole",
"Ricard V.",
""
],
[
"Fernandez",
"Pau",
""
],
[
"Kauffman",
"Stuart A.",
""
]
] | The emergence of complex patterns of organization close to the Cambrian boundary is known to have happened over a (geologically) short period of time. It involved the rapid diversification of body plans and stands as one of the major transitions in evolution. How it took place is a controversial issue. Here we explore ... |
1505.02888 | Nadav M. Shnerb | David Kessler, Samir Suweis, Marco Formentin and Nadav M. Shnerb | Neutral dynamics with environmental noise: age-size statistics and
species lifetimes | null | Phys. Rev. E 92, 022722 (2015) | 10.1103/PhysRevE.92.022722 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neutral dynamics, where taxa are assumed to be demographically equivalent and
their abundance is governed solely by the stochasticity of the underlying
birth-death process, has proved itself as an important minimal model that
accounts for many empirical datasets in genetics and ecology. However, the
restriction of th... | [
{
"created": "Tue, 12 May 2015 07:15:50 GMT",
"version": "v1"
}
] | 2015-09-09 | [
[
"Kessler",
"David",
""
],
[
"Suweis",
"Samir",
""
],
[
"Formentin",
"Marco",
""
],
[
"Shnerb",
"Nadav M.",
""
]
] | Neutral dynamics, where taxa are assumed to be demographically equivalent and their abundance is governed solely by the stochasticity of the underlying birth-death process, has proved itself as an important minimal model that accounts for many empirical datasets in genetics and ecology. However, the restriction of the ... |
1505.06920 | Catherine Bauge | Catherine Baug\'e, Olivier Cauvard, Sylvain Leclercq, Philippe
Gal\'era (MILPAT), Karim Boum\'ediene | Modulation of transforming growth factor beta signalling pathway genes
by transforming growth factor beta in human osteoarthritic chondrocytes:
involvement of Sp1 in both early and late response cells to transforming
growth factor beta | null | Arthritis Research \& Therapy, 2010, 13 (1), pp.R23.
\<http://arthritis-research.com/content/13/1/R23\>.
\<10.1038/sj.onc.1204808\> | 10.1038/sj.onc.1204808 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transforming growth factor beta (TGF$\beta$) plays a central role in
morphogenesis, growth, and cell differentiation. This cytokine is particularly
important in cartilage where it regulates cell proliferation and extracellular
matrix synthesis. While the action of TGF$\beta$ on chondrocyte metabolism has
been extensi... | [
{
"created": "Tue, 26 May 2015 12:19:19 GMT",
"version": "v1"
}
] | 2015-05-27 | [
[
"Baugé",
"Catherine",
"",
"MILPAT"
],
[
"Cauvard",
"Olivier",
"",
"MILPAT"
],
[
"Leclercq",
"Sylvain",
"",
"MILPAT"
],
[
"Galéra",
"Philippe",
"",
"MILPAT"
],
[
"Boumédiene",
"Karim",
""
]
] | Transforming growth factor beta (TGF$\beta$) plays a central role in morphogenesis, growth, and cell differentiation. This cytokine is particularly important in cartilage where it regulates cell proliferation and extracellular matrix synthesis. While the action of TGF$\beta$ on chondrocyte metabolism has been extensive... |
1707.09361 | James Moore | James Moore, Hasan Ahmed | High Dimensional Random Walks Can Appear Low Dimensional: Application to
Influenza H3N2 Evolution | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One important feature of the mammalian immune system is the highly specific
binding of antigens to antibodies. Antibodies generated in response to one
infection may also provide some level of cross immunity to other infections.
One model to describe this cross immunity is the notion of antigenic space,
which assigns ... | [
{
"created": "Thu, 27 Jul 2017 21:20:58 GMT",
"version": "v1"
}
] | 2017-08-01 | [
[
"Moore",
"James",
""
],
[
"Ahmed",
"Hasan",
""
]
] | One important feature of the mammalian immune system is the highly specific binding of antigens to antibodies. Antibodies generated in response to one infection may also provide some level of cross immunity to other infections. One model to describe this cross immunity is the notion of antigenic space, which assigns ea... |
2307.09029 | Priya Chakraborty | Priya Chakraborty, Sayantari Ghosh | Quantitative Modelling of Diffusion-driven Pattern Formation in
microRNA-regulated Gene Expression | 31 pages | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | MicroRNAs are extensively known for post-transcriptional gene regulation and
pattern formation in the embryonic developmental stage. We explore the origin
of these spatio-temporal patterns mathematically, considering three different
motifs here. For three scenarios, (1) simple microRNA-based mRNA regulation
with a gr... | [
{
"created": "Tue, 18 Jul 2023 07:42:09 GMT",
"version": "v1"
}
] | 2023-07-19 | [
[
"Chakraborty",
"Priya",
""
],
[
"Ghosh",
"Sayantari",
""
]
] | MicroRNAs are extensively known for post-transcriptional gene regulation and pattern formation in the embryonic developmental stage. We explore the origin of these spatio-temporal patterns mathematically, considering three different motifs here. For three scenarios, (1) simple microRNA-based mRNA regulation with a grad... |
1711.02739 | Xiangming Zhang | Xiangming Zhang and Zhihua Liu | Bifurcation analysis of an age structured HIV infection model with both
virus-to-cell and cell-to-cell transmissions | arXiv admin note: text overlap with arXiv:1711.01595,
arXiv:1711.01599 | null | 10.1142/S0218127418501092 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We make a mathematical analysis of an age structured HIV infection model with
both virus-to-cell and cell-to-cell transmissions to understand the dynamical
behavior of HIV infection in vivo. In the model, we consider the proliferation
of uninfected CD4+ T cells by a logistic function and the infected CD4+ T cells
are... | [
{
"created": "Sun, 5 Nov 2017 14:26:44 GMT",
"version": "v1"
}
] | 2018-09-26 | [
[
"Zhang",
"Xiangming",
""
],
[
"Liu",
"Zhihua",
""
]
] | We make a mathematical analysis of an age structured HIV infection model with both virus-to-cell and cell-to-cell transmissions to understand the dynamical behavior of HIV infection in vivo. In the model, we consider the proliferation of uninfected CD4+ T cells by a logistic function and the infected CD4+ T cells are a... |
2101.01607 | Mark Sinzger | Mark Sinzger, Maximilian Gehri, Heinz Koeppl | Poisson channel with binary Markov input and average sojourn time
constraint | This article was accepted for publication by IEEE, ISIT 2020 | null | 10.1109/ISIT44484.2020.9174360 | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | A minimal model for gene expression, consisting of a switchable promoter
together with the resulting messenger RNA, is equivalent to a Poisson channel
with a binary Markovian input process. Determining its capacity is an
optimization problem with respect to two parameters: the average sojourn times
of the promoter's ... | [
{
"created": "Tue, 5 Jan 2021 15:47:55 GMT",
"version": "v1"
}
] | 2021-01-06 | [
[
"Sinzger",
"Mark",
""
],
[
"Gehri",
"Maximilian",
""
],
[
"Koeppl",
"Heinz",
""
]
] | A minimal model for gene expression, consisting of a switchable promoter together with the resulting messenger RNA, is equivalent to a Poisson channel with a binary Markovian input process. Determining its capacity is an optimization problem with respect to two parameters: the average sojourn times of the promoter's ac... |
0903.3451 | Jun Kitazono | Jun Kitazono, Toshiaki Omori, Masato Okada | Neural network model with discrete and continuous information
representation | 15 pages, 5 figures | null | 10.1143/JPSJ.78.114801 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An associative memory model and a neural network model with a Mexican-hat
type interaction are the two most typical attractor networks used in the
artificial neural network models. The associative memory model has discretely
distributed fixed-point attractors, and achieves a discrete information
representation. On th... | [
{
"created": "Fri, 20 Mar 2009 05:17:39 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Kitazono",
"Jun",
""
],
[
"Omori",
"Toshiaki",
""
],
[
"Okada",
"Masato",
""
]
] | An associative memory model and a neural network model with a Mexican-hat type interaction are the two most typical attractor networks used in the artificial neural network models. The associative memory model has discretely distributed fixed-point attractors, and achieves a discrete information representation. On the ... |
q-bio/0512043 | Cyrill Muratov | R. E. Lee DeVille, Cyrill B. Muratov, Eric Vanden-Eijnden | Non-meanfield deterministic limits in chemical reaction kinetics far
from equilibrium | 4 pages, 4 figures (submitted to Phys. Rev. Lett.) | J. Chem. Phys. 124, 231102 (2006). | 10.1063/1.2217013 | null | q-bio.QM q-bio.SC | null | A general mechanism is proposed by which small intrinsic fluctuations in a
system far from equilibrium can result in nearly deterministic dynamical
behaviors which are markedly distinct from those realized in the meanfield
limit. The mechanism is demonstrated for the kinetic Monte-Carlo version of the
Schnakenberg re... | [
{
"created": "Sun, 25 Dec 2005 15:42:03 GMT",
"version": "v1"
}
] | 2015-06-26 | [
[
"DeVille",
"R. E. Lee",
""
],
[
"Muratov",
"Cyrill B.",
""
],
[
"Vanden-Eijnden",
"Eric",
""
]
] | A general mechanism is proposed by which small intrinsic fluctuations in a system far from equilibrium can result in nearly deterministic dynamical behaviors which are markedly distinct from those realized in the meanfield limit. The mechanism is demonstrated for the kinetic Monte-Carlo version of the Schnakenberg reac... |
1701.02272 | Tom Portegys | Thomas E. Portegys | Morphognosis: the shape of knowledge in space and time | null | null | null | null | q-bio.NC cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Artificial intelligence research to a great degree focuses on the brain and
behaviors that the brain generates. But the brain, an extremely complex
structure resulting from millions of years of evolution, can be viewed as a
solution to problems posed by an environment existing in space and time. The
environment gener... | [
{
"created": "Thu, 5 Jan 2017 23:10:54 GMT",
"version": "v1"
},
{
"created": "Sat, 4 Mar 2017 18:20:10 GMT",
"version": "v2"
}
] | 2017-03-07 | [
[
"Portegys",
"Thomas E.",
""
]
] | Artificial intelligence research to a great degree focuses on the brain and behaviors that the brain generates. But the brain, an extremely complex structure resulting from millions of years of evolution, can be viewed as a solution to problems posed by an environment existing in space and time. The environment generat... |
2106.06506 | Abagael Sykes | Abagael L. Sykes, Gustavo S. Silva, Derald J. Holtkamp, Broc W. Mauch,
Onyekachukwu Osemeke, Daniel C.L. Linhares, Gustavo Machado | Interpretable machine learning applied to on-farm biosecurity and
porcine reproductive and respiratory syndrome virus | null | null | 10.1111/tbed.14369 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Effective biosecurity practices in swine production are key in preventing the
introduction and dissemination of infectious pathogens. Ideally, biosecurity
practices should be chosen by their impact on bio-containment and
bio-exclusion, however quantitative supporting evidence is often unavailable.
Therefore, the deve... | [
{
"created": "Fri, 11 Jun 2021 17:01:40 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Nov 2021 19:56:30 GMT",
"version": "v2"
}
] | 2021-11-23 | [
[
"Sykes",
"Abagael L.",
""
],
[
"Silva",
"Gustavo S.",
""
],
[
"Holtkamp",
"Derald J.",
""
],
[
"Mauch",
"Broc W.",
""
],
[
"Osemeke",
"Onyekachukwu",
""
],
[
"Linhares",
"Daniel C. L.",
""
],
[
"Machado",
"Gust... | Effective biosecurity practices in swine production are key in preventing the introduction and dissemination of infectious pathogens. Ideally, biosecurity practices should be chosen by their impact on bio-containment and bio-exclusion, however quantitative supporting evidence is often unavailable. Therefore, the develo... |
1205.6598 | Gasper Tkacik | Ga\v{s}per Tka\v{c}ik and Einat Granot-Atedgi and Ronen Segev and Elad
Schneidman | Retinal metric: a stimulus distance measure derived from population
neural responses | 5 pages, 4 figures, to appear in Phys Rev Lett | Phys Rev Lett 110 (2013): 058104 | 10.1103/PhysRevLett.110.058104 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ability of the organism to distinguish between various stimuli is limited
by the structure and noise in the population code of its sensory neurons. Here
we infer a distance measure on the stimulus space directly from the recorded
activity of 100 neurons in the salamander retina. In contrast to previously
used mea... | [
{
"created": "Wed, 30 May 2012 09:29:44 GMT",
"version": "v1"
},
{
"created": "Sat, 8 Dec 2012 08:07:53 GMT",
"version": "v2"
}
] | 2013-06-14 | [
[
"Tkačik",
"Gašper",
""
],
[
"Granot-Atedgi",
"Einat",
""
],
[
"Segev",
"Ronen",
""
],
[
"Schneidman",
"Elad",
""
]
] | The ability of the organism to distinguish between various stimuli is limited by the structure and noise in the population code of its sensory neurons. Here we infer a distance measure on the stimulus space directly from the recorded activity of 100 neurons in the salamander retina. In contrast to previously used measu... |
1610.06033 | Khalil Cherifi | Khalil Cherifi, El Houssein Boufous, Hassan Boubaker, Fouad Msanda | Comparative Salt Tolerance Study of Some Acacia Species at Seed
Germination Stage | 9 pages, 3 figures | Asian Journal of Plant Sciences 15(3-4) (2016) 66-74 | 10.3923/ajps.2016.66.74 | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Objective: The purpose of this study was to assess and compare the seed
germination response of six Acacia species under different NaCl concentrations
in order to explore opportunities for selection and breeding salt tolerant
genotypes. Methodology: Germination of seeds was evaluated under salt stresses
using 5 treat... | [
{
"created": "Wed, 19 Oct 2016 14:32:20 GMT",
"version": "v1"
}
] | 2016-10-20 | [
[
"Cherifi",
"Khalil",
""
],
[
"Boufous",
"El Houssein",
""
],
[
"Boubaker",
"Hassan",
""
],
[
"Msanda",
"Fouad",
""
]
] | Objective: The purpose of this study was to assess and compare the seed germination response of six Acacia species under different NaCl concentrations in order to explore opportunities for selection and breeding salt tolerant genotypes. Methodology: Germination of seeds was evaluated under salt stresses using 5 treatme... |
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