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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0707.0026 | Maria A. Avi\~no-Diaz | Maria A. Avino-Diaz | Introducing a Probabilistic Structure on Sequential Dynamical Systems,
Simulation and Reduction of Probabilistic Sequential Networks | 14 pages | null | null | null | q-bio.GN math.PR q-bio.MN | null | A probabilistic structure on sequential dynamical systems is introduced here,
the new model will be called Probabilistic Sequential Network, PSN. The
morphisms of Probabilistic Sequential Networks are defined using two algebraic
conditions. It is proved here that two homomorphic Probabilistic Sequential
Networks have... | [
{
"created": "Fri, 29 Jun 2007 23:34:16 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Apr 2008 13:44:03 GMT",
"version": "v2"
}
] | 2008-04-30 | [
[
"Avino-Diaz",
"Maria A.",
""
]
] | A probabilistic structure on sequential dynamical systems is introduced here, the new model will be called Probabilistic Sequential Network, PSN. The morphisms of Probabilistic Sequential Networks are defined using two algebraic conditions. It is proved here that two homomorphic Probabilistic Sequential Networks have t... |
1810.12954 | Li Xiao | Li Xiao, Julia M. Stephen, Tony W. Wilson, Vince D. Calhoun, and
Yu-Ping Wang | Alternating Diffusion Map Based Fusion of Multimodal Brain Connectivity
Networks for IQ Prediction | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To explain individual differences in development, behavior, and cognition,
most previous studies focused on projecting resting-state functional MRI (fMRI)
based functional connectivity (FC) data into a low-dimensional space via linear
dimensionality reduction techniques, followed by executing analysis operations.
How... | [
{
"created": "Tue, 30 Oct 2018 18:29:50 GMT",
"version": "v1"
}
] | 2018-11-01 | [
[
"Xiao",
"Li",
""
],
[
"Stephen",
"Julia M.",
""
],
[
"Wilson",
"Tony W.",
""
],
[
"Calhoun",
"Vince D.",
""
],
[
"Wang",
"Yu-Ping",
""
]
] | To explain individual differences in development, behavior, and cognition, most previous studies focused on projecting resting-state functional MRI (fMRI) based functional connectivity (FC) data into a low-dimensional space via linear dimensionality reduction techniques, followed by executing analysis operations. Howev... |
2111.08507 | Akankshita Dash | Akankshita Dash | Machine Learning for Genomic Data | Number of pages: 53 | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | This report explores the application of machine learning techniques on short
timeseries gene expression data. Although standard machine learning algorithms
work well on longer time-series', they often fail to find meaningful insights
from fewer timepoints. In this report, we explore model-based clustering
techniques.... | [
{
"created": "Mon, 15 Nov 2021 14:34:20 GMT",
"version": "v1"
}
] | 2021-11-17 | [
[
"Dash",
"Akankshita",
""
]
] | This report explores the application of machine learning techniques on short timeseries gene expression data. Although standard machine learning algorithms work well on longer time-series', they often fail to find meaningful insights from fewer timepoints. In this report, we explore model-based clustering techniques. W... |
1401.8028 | Mercedes P\'erez Mill\'an | Mercedes P\'erez Mill\'an and Alicia Dickenstein | Implicit dose-response curves | The final publication is available at Springer via
http://dx.doi.org/10.1007/s00285-014-0809-4 | null | 10.1007/s00285-014-0809-4 | null | q-bio.QM math.AG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop tools from computational algebraic geometry for the study of
steady state features of autonomous polynomial dynamical systems via
elimination of variables. In particular, we obtain nontrivial bounds for the
steady state concentration of a given species in biochemical reaction networks
with mass-action kine... | [
{
"created": "Thu, 30 Jan 2014 23:25:46 GMT",
"version": "v1"
},
{
"created": "Fri, 11 Jul 2014 10:25:00 GMT",
"version": "v2"
}
] | 2014-07-14 | [
[
"Millán",
"Mercedes Pérez",
""
],
[
"Dickenstein",
"Alicia",
""
]
] | We develop tools from computational algebraic geometry for the study of steady state features of autonomous polynomial dynamical systems via elimination of variables. In particular, we obtain nontrivial bounds for the steady state concentration of a given species in biochemical reaction networks with mass-action kineti... |
2003.13932 | Samuel Willian Schwertner Costiche | Rodrigo A. Schulz, Carlos H. Coimbra-Ara\'ujo and Samuel W. S.
Costiche | COVID-19: A model for studying the evolution of contamination in Brazil | 18 pages, 4 figures; corrected references and parameters | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the present article we introduce an epidemiological model for the
investigation of the spread of epidemics caused by viruses. The model is
applied specifically to COVID-19, the disease caused by the SARS-Cov-2 virus
(aka "novel coronavirus"). The SIR (Susceptible - Infectious - Recovered) model
is used as a basis ... | [
{
"created": "Tue, 31 Mar 2020 03:12:14 GMT",
"version": "v1"
},
{
"created": "Wed, 1 Apr 2020 05:00:47 GMT",
"version": "v2"
},
{
"created": "Thu, 2 Apr 2020 12:57:16 GMT",
"version": "v3"
},
{
"created": "Wed, 8 Apr 2020 23:07:57 GMT",
"version": "v4"
}
] | 2020-04-10 | [
[
"Schulz",
"Rodrigo A.",
""
],
[
"Coimbra-Araújo",
"Carlos H.",
""
],
[
"Costiche",
"Samuel W. S.",
""
]
] | In the present article we introduce an epidemiological model for the investigation of the spread of epidemics caused by viruses. The model is applied specifically to COVID-19, the disease caused by the SARS-Cov-2 virus (aka "novel coronavirus"). The SIR (Susceptible - Infectious - Recovered) model is used as a basis fo... |
2009.10378 | Jean-Sebastien Guez | Val\'erie Lecl\'ere, Max B\'echet, Akram Adam, Jean-Sebastien Guez
(IP), Bernard Wathelet, Marc Ongena, Philippe Thonart, Fr\'ed\'erique Gancel,
Marl\'ene Chollet-Imbert, Philippe Jacques | Mycosubtilin Overproduction by Bacillus subtilis BBG100 Enhances the
Organism's Antagonistic and Biocontrol Activities | null | Applied and Environmental Microbiology, American Society for
Microbiology, 2005, 71, pp.4577 - 4584 | 10.1128/AEM.71.8.4577-4584.2005 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A Bacillus subtilis derivative was obtained from strain ATCC 6633 by
replacement of the native promoter of the mycosubtilin operon by a constitutive
promoter originating from the replication gene repU of the Staphylococcus
aureus plasmid pUB110. The recombinant strain, designated BBG100, produced up
to 15-fold more m... | [
{
"created": "Tue, 22 Sep 2020 08:10:13 GMT",
"version": "v1"
}
] | 2020-09-23 | [
[
"Leclére",
"Valérie",
"",
"IP"
],
[
"Béchet",
"Max",
"",
"IP"
],
[
"Adam",
"Akram",
"",
"IP"
],
[
"Guez",
"Jean-Sebastien",
"",
"IP"
],
[
"Wathelet",
"Bernard",
""
],
[
"Ongena",
"Marc",
""
],
[
"Th... | A Bacillus subtilis derivative was obtained from strain ATCC 6633 by replacement of the native promoter of the mycosubtilin operon by a constitutive promoter originating from the replication gene repU of the Staphylococcus aureus plasmid pUB110. The recombinant strain, designated BBG100, produced up to 15-fold more myc... |
1503.07552 | Andrey Shilnikov L | D. Alacam and A.L. Shilnikov | Making a swim central pattern generator out of latent parabolic bursters | null | null | null | null | q-bio.NC nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the rhythmogenesis of oscillatory patterns emerging in network
motifs composed of inhibitory coupled tonic spiking neurons represented by the
Plant model of R15 nerve cells. Such motifs are argued to be used as building
blocks for a larger central pattern generator network controlling swim
locomotion of sea ... | [
{
"created": "Wed, 25 Mar 2015 20:54:56 GMT",
"version": "v1"
}
] | 2015-03-27 | [
[
"Alacam",
"D.",
""
],
[
"Shilnikov",
"A. L.",
""
]
] | We study the rhythmogenesis of oscillatory patterns emerging in network motifs composed of inhibitory coupled tonic spiking neurons represented by the Plant model of R15 nerve cells. Such motifs are argued to be used as building blocks for a larger central pattern generator network controlling swim locomotion of sea sl... |
0706.3195 | George Bass Ph.D. | George E. Bass | Genetic Transferability of Anomalous Irradiation Alterations of
Antibiotic Activity | 17 pages, 3 figures | null | null | null | q-bio.BM | null | It previously has been discovered that visible light irradiation of
crystalline substrates can lead to enhancement of subsequent enzymatic reaction
rates as sharply peaked oscillatory functions of irradiation time. The
particular activating irradiation times can vary with source of a given enzyme
and thus, presumably... | [
{
"created": "Thu, 21 Jun 2007 17:24:15 GMT",
"version": "v1"
}
] | 2007-06-22 | [
[
"Bass",
"George E.",
""
]
] | It previously has been discovered that visible light irradiation of crystalline substrates can lead to enhancement of subsequent enzymatic reaction rates as sharply peaked oscillatory functions of irradiation time. The particular activating irradiation times can vary with source of a given enzyme and thus, presumably, ... |
2106.10041 | Michael Inouye | Ewan Birney, Michael Inouye, Jennifer Raff, Adam Rutherford, Aylwyn
Scally | The language of race, ethnicity, and ancestry in human genetic research | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The language commonly used in human genetics can inadvertently pose problems
for multiple reasons. Terms like "ancestry", "ethnicity", and other ways of
grouping people can have complex, often poorly understood, or multiple meanings
within the various fields of genetics, between different domains of biological
scienc... | [
{
"created": "Fri, 18 Jun 2021 10:24:15 GMT",
"version": "v1"
}
] | 2021-06-21 | [
[
"Birney",
"Ewan",
""
],
[
"Inouye",
"Michael",
""
],
[
"Raff",
"Jennifer",
""
],
[
"Rutherford",
"Adam",
""
],
[
"Scally",
"Aylwyn",
""
]
] | The language commonly used in human genetics can inadvertently pose problems for multiple reasons. Terms like "ancestry", "ethnicity", and other ways of grouping people can have complex, often poorly understood, or multiple meanings within the various fields of genetics, between different domains of biological sciences... |
1812.05780 | Silke Bergeler | Matthias Kober, Silke Bergeler, Erwin Frey | Can a flux-based mechanism explain positioning of protein clusters in a
three-dimensional cell geometry? | 9 pages, 4 figures, 10 pages of supplemental information (including 4
figures and 1 table) | null | 10.1016/j.bpj.2019.06.031 | null | q-bio.SC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The plane of bacterial cell division must be precisely positioned. In the
bacterium Myxococcus xanthus, the proteins PomX and PomY form a large cluster,
which is tethered to the nucleoid by the ATPase PomZ and moves in a stochastic,
but biased manner towards midcell, where it initiates cell division.
Previously, a po... | [
{
"created": "Fri, 14 Dec 2018 05:01:04 GMT",
"version": "v1"
}
] | 2019-09-04 | [
[
"Kober",
"Matthias",
""
],
[
"Bergeler",
"Silke",
""
],
[
"Frey",
"Erwin",
""
]
] | The plane of bacterial cell division must be precisely positioned. In the bacterium Myxococcus xanthus, the proteins PomX and PomY form a large cluster, which is tethered to the nucleoid by the ATPase PomZ and moves in a stochastic, but biased manner towards midcell, where it initiates cell division. Previously, a posi... |
2206.07542 | Abdulah Fawaz | Abdulah Fawaz, Logan Z. Williams, A. David Edwards, Emma Robinson | A Deep Generative Model of Neonatal Cortical Surface Development | null | null | null | null | q-bio.NC cs.CV cs.LG eess.IV | http://creativecommons.org/licenses/by/4.0/ | The neonatal cortical surface is known to be affected by preterm birth, and
the subsequent changes to cortical organisation have been associated with
poorer neurodevelopmental outcomes. Deep Generative models have the potential
to lead to clinically interpretable models of disease, but developing these on
the cortica... | [
{
"created": "Wed, 15 Jun 2022 13:59:43 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Jun 2022 12:16:33 GMT",
"version": "v2"
}
] | 2022-06-23 | [
[
"Fawaz",
"Abdulah",
""
],
[
"Williams",
"Logan Z.",
""
],
[
"Edwards",
"A. David",
""
],
[
"Robinson",
"Emma",
""
]
] | The neonatal cortical surface is known to be affected by preterm birth, and the subsequent changes to cortical organisation have been associated with poorer neurodevelopmental outcomes. Deep Generative models have the potential to lead to clinically interpretable models of disease, but developing these on the cortical ... |
1912.09929 | Benjamin M. Friedrich | Jens Karschau, Andre Scholich, Jonathan Wise, Hernan
Morales-Navarette, Yannis Kalaidzidis, Marino Zerial, Benjamin M Friedrich | Resilience of three-dimensional sinusoidal networks in liver tissue | 20 pages, 7 figures | null | 10.1371/journal.pcbi.1007965 | null | q-bio.TO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Can three-dimensional, microvasculature networks still ensure blood supply if
individual links fail? We address this question in the sinusoidal network, a
plexus-like microvasculature network, which transports nutrient-rich blood to
every hepatocyte in liver tissue, by building on recent advances in
high-resolution i... | [
{
"created": "Fri, 20 Dec 2019 16:41:54 GMT",
"version": "v1"
}
] | 2020-09-09 | [
[
"Karschau",
"Jens",
""
],
[
"Scholich",
"Andre",
""
],
[
"Wise",
"Jonathan",
""
],
[
"Morales-Navarette",
"Hernan",
""
],
[
"Kalaidzidis",
"Yannis",
""
],
[
"Zerial",
"Marino",
""
],
[
"Friedrich",
"Benjamin M"... | Can three-dimensional, microvasculature networks still ensure blood supply if individual links fail? We address this question in the sinusoidal network, a plexus-like microvasculature network, which transports nutrient-rich blood to every hepatocyte in liver tissue, by building on recent advances in high-resolution ima... |
0809.1127 | Naoki Masuda Dr. | Yuko K. Takahashi, Hiroshi Kori, Naoki Masuda | Self-organization of feedforward structure and entrainment in excitatory
neural networks with spike-timing-dependent plasticity | 11 figures, 1 table | Physical Review E, 79, 051904 (2009) | 10.1103/PhysRevE.79.051904 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spike-timing dependent plasticity (STDP) is an organizing principle of
biological neural networks. While synchronous firing of neurons is considered
to be an important functional block in the brain, how STDP shapes neural
networks possibly toward synchrony is not entirely clear. We examine relations
between STDP and ... | [
{
"created": "Sat, 6 Sep 2008 03:44:09 GMT",
"version": "v1"
},
{
"created": "Thu, 11 Sep 2008 11:41:50 GMT",
"version": "v2"
},
{
"created": "Wed, 20 May 2009 11:23:05 GMT",
"version": "v3"
}
] | 2009-05-20 | [
[
"Takahashi",
"Yuko K.",
""
],
[
"Kori",
"Hiroshi",
""
],
[
"Masuda",
"Naoki",
""
]
] | Spike-timing dependent plasticity (STDP) is an organizing principle of biological neural networks. While synchronous firing of neurons is considered to be an important functional block in the brain, how STDP shapes neural networks possibly toward synchrony is not entirely clear. We examine relations between STDP and sy... |
2305.14369 | Eloy Philip Theo Geenjaar | Eloy Geenjaar, Donghyun Kim, Riyasat Ohib, Marlena Duda, Amrit
Kashyap, Sergey Plis, Vince Calhoun | Learning low-dimensional dynamics from whole-brain data improves task
capture | 9 pages, 4 figures | null | null | null | q-bio.NC cs.CE cs.LG | http://creativecommons.org/licenses/by/4.0/ | The neural dynamics underlying brain activity are critical to understanding
cognitive processes and mental disorders. However, current voxel-based
whole-brain dimensionality reduction techniques fall short of capturing these
dynamics, producing latent timeseries that inadequately relate to behavioral
tasks. To addres... | [
{
"created": "Thu, 18 May 2023 18:43:13 GMT",
"version": "v1"
}
] | 2023-05-25 | [
[
"Geenjaar",
"Eloy",
""
],
[
"Kim",
"Donghyun",
""
],
[
"Ohib",
"Riyasat",
""
],
[
"Duda",
"Marlena",
""
],
[
"Kashyap",
"Amrit",
""
],
[
"Plis",
"Sergey",
""
],
[
"Calhoun",
"Vince",
""
]
] | The neural dynamics underlying brain activity are critical to understanding cognitive processes and mental disorders. However, current voxel-based whole-brain dimensionality reduction techniques fall short of capturing these dynamics, producing latent timeseries that inadequately relate to behavioral tasks. To address ... |
q-bio/0607028 | Garegin Papoian | Yueheng Lan, Garegin A. Papoian | The interplay between discrete noise and nonlinear chemical kinetics in
a signal amplification cascade | 16 pages, 9 figures | null | 10.1063/1.2358342 | null | q-bio.MN q-bio.QM | null | We used various analytical and numerical techniques to elucidate signal
propagation in a small enzymatic cascade which is subjected to external and
internal noise. The nonlinear character of catalytic reactions, which underlie
protein signal transduction cascades, renders stochastic signaling dynamics in
cytosol bioc... | [
{
"created": "Wed, 19 Jul 2006 06:41:28 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Lan",
"Yueheng",
""
],
[
"Papoian",
"Garegin A.",
""
]
] | We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein signal transduction cascades, renders stochastic signaling dynamics in cytosol bioche... |
1611.00285 | Till Frank | J.M. Gordon, S. Kim, T.D. Frank | Linear non-equilibrium thermodynamics of human voluntary behavior: a
canonical-dissipative Fokker-Planck equation approach involving potentials
beyond the harmonic oscillator case | 6 pages, 0 figure | Condens. Matter Phys., vol. 19, No. 3, 34001 (2016) | 10.5488/CMP.19.34001 | null | q-bio.NC cond-mat.soft cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A novel experimental paradigm and a novel modelling approach are presented to
investigate oscillatory human motor performance by means of a key concept from
condensed matter physics, namely, thermodynamic state variables. To this end,
in the novel experimental paradigm participants performed pendulum swinging
movemen... | [
{
"created": "Thu, 15 Sep 2016 16:10:43 GMT",
"version": "v1"
}
] | 2017-02-13 | [
[
"Gordon",
"J. M.",
""
],
[
"Kim",
"S.",
""
],
[
"Frank",
"T. D.",
""
]
] | A novel experimental paradigm and a novel modelling approach are presented to investigate oscillatory human motor performance by means of a key concept from condensed matter physics, namely, thermodynamic state variables. To this end, in the novel experimental paradigm participants performed pendulum swinging movements... |
1909.06442 | Devin Taylor | Devin Taylor, Simeon Spasov and Pietro Li\`o | Co-Attentive Cross-Modal Deep Learning for Medical Evidence Synthesis
and Decision Making | 7 pages, 2 figures, Machine Learning for Health (ML4H) at NeurIPS
2019 - Extended Abstract, clarified graph and math notation, typos corrected | null | null | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modern medicine requires generalised approaches to the synthesis and
integration of multimodal data, often at different biological scales, that can
be applied to a variety of evidence structures, such as complex disease
analyses and epidemiological models. However, current methods are either slow
and expensive, or in... | [
{
"created": "Fri, 13 Sep 2019 20:49:55 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Nov 2019 06:58:53 GMT",
"version": "v2"
}
] | 2019-11-11 | [
[
"Taylor",
"Devin",
""
],
[
"Spasov",
"Simeon",
""
],
[
"Liò",
"Pietro",
""
]
] | Modern medicine requires generalised approaches to the synthesis and integration of multimodal data, often at different biological scales, that can be applied to a variety of evidence structures, such as complex disease analyses and epidemiological models. However, current methods are either slow and expensive, or inef... |
1101.3570 | Lev Soyfer | Lev Isaakovich Soyfer | Processes of the correlation of space (lengths) and time (duration)in
human perception | The text of this work, which totals of 183 pages, consists of seven
chapters, references, and four appendices. Major part of the work includes 30
tables and 3 figures. Appendices consist of 37 tables and 4 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/3.0/ | To study the processes and mechanisms of the correlation between space and
time, particularly between lengths and durations in human perception, a special
method (device and procedure) to conduct this experiment was designed and
called LDR (Length Duration Relation) In the present study a pilot and three
series of th... | [
{
"created": "Mon, 17 Jan 2011 20:38:38 GMT",
"version": "v1"
}
] | 2011-01-20 | [
[
"Soyfer",
"Lev Isaakovich",
""
]
] | To study the processes and mechanisms of the correlation between space and time, particularly between lengths and durations in human perception, a special method (device and procedure) to conduct this experiment was designed and called LDR (Length Duration Relation) In the present study a pilot and three series of the ... |
1304.4274 | Natalia Denesyuk | Natalia A. Denesyuk and D. Thirumalai | Entropic stabilization of the folded states of RNA due to macromolecular
crowding | null | null | 10.1007/s12551-013-0119-x | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We review the effects of macromolecular crowding on the folding of RNA by
considering the simplest scenario when excluded volume interactions between
crowding particles and RNA dominate. Using human telomerase enzyme as an
example, we discuss how crowding can alter the equilibrium between pseudoknot
and hairpin state... | [
{
"created": "Mon, 15 Apr 2013 21:37:49 GMT",
"version": "v1"
}
] | 2013-04-17 | [
[
"Denesyuk",
"Natalia A.",
""
],
[
"Thirumalai",
"D.",
""
]
] | We review the effects of macromolecular crowding on the folding of RNA by considering the simplest scenario when excluded volume interactions between crowding particles and RNA dominate. Using human telomerase enzyme as an example, we discuss how crowding can alter the equilibrium between pseudoknot and hairpin states ... |
2402.03675 | Chenqing Hua | Chenqing Hua, Connor Coley, Guy Wolf, Doina Precup, Shuangjia Zheng | Effective Protein-Protein Interaction Exploration with PPIretrieval | null | null | null | null | q-bio.BM cs.AI cs.CE cs.LG | http://creativecommons.org/publicdomain/zero/1.0/ | Protein-protein interactions (PPIs) are crucial in regulating numerous
cellular functions, including signal transduction, transportation, and immune
defense. As the accuracy of multi-chain protein complex structure prediction
improves, the challenge has shifted towards effectively navigating the vast
complex universe... | [
{
"created": "Tue, 6 Feb 2024 03:57:06 GMT",
"version": "v1"
}
] | 2024-02-07 | [
[
"Hua",
"Chenqing",
""
],
[
"Coley",
"Connor",
""
],
[
"Wolf",
"Guy",
""
],
[
"Precup",
"Doina",
""
],
[
"Zheng",
"Shuangjia",
""
]
] | Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the challenge has shifted towards effectively navigating the vast complex universe t... |
1407.4854 | Kazuhiro Takemoto | Kazuhiro Takemoto | Metabolic networks are almost nonfractal: A comprehensive evaluation | 7 pages, 5 figures | Phys. Rev. E 90, 022802 (2014) | 10.1103/PhysRevE.90.022802 | null | q-bio.MN physics.data-an physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Network self-similarity or fractality are widely accepted as an important
topological property of metabolic networks; however, recent studies cast doubt
on the reality of self-similarity in the networks. Therefore, we perform a
comprehensive evaluation of metabolic network fractality using a box-covering
method with ... | [
{
"created": "Thu, 17 Jul 2014 22:39:23 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Jul 2014 03:18:32 GMT",
"version": "v2"
}
] | 2014-08-05 | [
[
"Takemoto",
"Kazuhiro",
""
]
] | Network self-similarity or fractality are widely accepted as an important topological property of metabolic networks; however, recent studies cast doubt on the reality of self-similarity in the networks. Therefore, we perform a comprehensive evaluation of metabolic network fractality using a box-covering method with an... |
2112.10230 | Johannes M\"uller | Johannes M\"uller and Aurelien Tellier and Michael Kurschilgen | A model of opinion dynamics with echo chambers explains the spatial
distribution of vaccine hesitancy | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Vaccination hesitancy is a major obstacle to achieving and maintaining herd
immunity. It is therefore of prime importance for public health authorities to
understand the dynamics of an anti-vaccine opinion in the population. We
introduce a novel mathematical model of opinion dynamics with spatial
reinforcement, which... | [
{
"created": "Sun, 19 Dec 2021 19:02:22 GMT",
"version": "v1"
}
] | 2021-12-21 | [
[
"Müller",
"Johannes",
""
],
[
"Tellier",
"Aurelien",
""
],
[
"Kurschilgen",
"Michael",
""
]
] | Vaccination hesitancy is a major obstacle to achieving and maintaining herd immunity. It is therefore of prime importance for public health authorities to understand the dynamics of an anti-vaccine opinion in the population. We introduce a novel mathematical model of opinion dynamics with spatial reinforcement, which c... |
2008.01781 | Wentian Li | Wentian Li, Yannis Almirantis, Astero Provata | Revisiting the Neutral Dynamics Derived Limiting Guanine-Cytosine
Content Using the Human De Novo Point Mutation Data | 4 figures | Meta Gene 31: 100994 (2022) | 10.1016/j.mgene.2021.100994 | null | q-bio.GN q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | We revisit the topic of human genome guanine-cytosine content under neutral
evolution. For this study, the de novo mutation data within human is used to
estimate mutational rate instead of using base substitution data between
related species. We then define a new measure of mutation bias which separate
the de novo mu... | [
{
"created": "Tue, 4 Aug 2020 19:31:21 GMT",
"version": "v1"
}
] | 2022-03-15 | [
[
"Li",
"Wentian",
""
],
[
"Almirantis",
"Yannis",
""
],
[
"Provata",
"Astero",
""
]
] | We revisit the topic of human genome guanine-cytosine content under neutral evolution. For this study, the de novo mutation data within human is used to estimate mutational rate instead of using base substitution data between related species. We then define a new measure of mutation bias which separate the de novo muta... |
0810.4547 | Bradly Alicea | Bradly Alicea | Hierarchies of Biocomplexity: modeling lifes energetic complexity | 11 pages, 9 figures, 1 table | null | null | null | q-bio.PE q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, a model for understanding the effects of selection using
systems- level computational approaches is introduced. A number of concepts and
principles essential for understanding the motivation for constructing the
model will be introduced first. This will be followed by a description of
parameters, measu... | [
{
"created": "Fri, 24 Oct 2008 20:32:11 GMT",
"version": "v1"
},
{
"created": "Fri, 7 Nov 2008 19:19:15 GMT",
"version": "v2"
},
{
"created": "Wed, 4 Mar 2009 15:53:36 GMT",
"version": "v3"
}
] | 2009-03-04 | [
[
"Alicea",
"Bradly",
""
]
] | In this paper, a model for understanding the effects of selection using systems- level computational approaches is introduced. A number of concepts and principles essential for understanding the motivation for constructing the model will be introduced first. This will be followed by a description of parameters, measure... |
1410.6763 | Denis Semenov A. | Denis A. Semenov | Epigenetic effects of cytosine derivatives are caused by their tautomers
in Hoogsteen base pairs | 6 pages, 5 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Deoxycitidine in solution exists as two tautomers one of which is an
uncanonical imino one. The latter can dominate with such derivatives as
5-methyl, 5-hydroxymethyl- and 5-formylcytosine. The imino tautomer potentially
is able to form a hoosteen GC base pair. To detect such pair, it is suggested
to use 1H15N NMR. F... | [
{
"created": "Sat, 30 Aug 2014 18:15:05 GMT",
"version": "v1"
}
] | 2014-10-27 | [
[
"Semenov",
"Denis A.",
""
]
] | Deoxycitidine in solution exists as two tautomers one of which is an uncanonical imino one. The latter can dominate with such derivatives as 5-methyl, 5-hydroxymethyl- and 5-formylcytosine. The imino tautomer potentially is able to form a hoosteen GC base pair. To detect such pair, it is suggested to use 1H15N NMR. For... |
1606.03630 | Cameron Mura | Cameron Mura | The Structures, Functions, and Evolution of Sm-like Archaeal Proteins
(SmAPs) | 215 pages, distributed across an Abstract, Synopsis, five Chapters
(the main body) and an Appendix; the work in this dissertation was performed
in the Eisenberg lab at UCLA from ca. 1999 to 2002 | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sm proteins were discovered nearly 20 years ago as a group of small antigenic
proteins ($\approx$ 90-120 residues). Since then, an extensive amount of
biochemical and genetic data have illuminated the crucial roles of these
proteins in forming ribonucleoprotein (RNP) complexes that are used in RNA
processing, e.g., s... | [
{
"created": "Sat, 11 Jun 2016 21:20:30 GMT",
"version": "v1"
}
] | 2016-06-14 | [
[
"Mura",
"Cameron",
""
]
] | Sm proteins were discovered nearly 20 years ago as a group of small antigenic proteins ($\approx$ 90-120 residues). Since then, an extensive amount of biochemical and genetic data have illuminated the crucial roles of these proteins in forming ribonucleoprotein (RNP) complexes that are used in RNA processing, e.g., spl... |
1905.00555 | Abhishek Deshpande | Abhishek Deshpande, Thomas E. Ouldridge | Optimizing enzymatic catalysts for rapid turnover of substrates with low
enzyme sequestration | 16 pages, 9 figures | Biological Cybernetics 2020 | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyse the mechanism of enzyme-substrate catalysis from the perspective
of minimizing the load on the enzymes through sequestration, whilst maintaining
at least a minimum reaction flux. In particular, we ask: which binding free
energies of the enzyme-substrate and enzyme-product reaction intermediates
minimize th... | [
{
"created": "Thu, 2 May 2019 02:41:46 GMT",
"version": "v1"
},
{
"created": "Thu, 17 Sep 2020 19:31:15 GMT",
"version": "v2"
}
] | 2020-09-21 | [
[
"Deshpande",
"Abhishek",
""
],
[
"Ouldridge",
"Thomas E.",
""
]
] | We analyse the mechanism of enzyme-substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, whilst maintaining at least a minimum reaction flux. In particular, we ask: which binding free energies of the enzyme-substrate and enzyme-product reaction intermediates minimize the ... |
1502.07793 | James Herbert-Read | James E. Herbert-Read, Ashley J.W. Ward, David J.T. Sumpter, Richard
P. Mann | Escape path complexity and its context dependency in Pacific blue-eyes
(Pseudomugil signifer) | 9 pages | null | 10.1242/jeb.154534 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The escape trajectories animals take following a predatory attack appear to
show high degrees of apparent 'randomness' - a property that has been described
as 'protean behaviour'. Here we present a method of quantifying the escape
trajectories of individual animals using a path complexity approach. When fish
(Pseudom... | [
{
"created": "Thu, 26 Feb 2015 23:47:14 GMT",
"version": "v1"
}
] | 2022-09-13 | [
[
"Herbert-Read",
"James E.",
""
],
[
"Ward",
"Ashley J. W.",
""
],
[
"Sumpter",
"David J. T.",
""
],
[
"Mann",
"Richard P.",
""
]
] | The escape trajectories animals take following a predatory attack appear to show high degrees of apparent 'randomness' - a property that has been described as 'protean behaviour'. Here we present a method of quantifying the escape trajectories of individual animals using a path complexity approach. When fish (Pseudomug... |
1607.02642 | Wayne Hayes | Nil Mamano and Wayne Hayes | SANA: Simulated Annealing Network Alignment Applied to Biological
Networks | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The alignment of biological networks has the potential to teach us as much
about biology and disease as has sequence alignment. Sequence alignment can be
optimally solved in polynomial time. In contrast, network alignment is
$NP$-hard, meaning optimal solutions are impossible to find, and the quality of
found alignme... | [
{
"created": "Sat, 9 Jul 2016 18:13:30 GMT",
"version": "v1"
}
] | 2016-07-12 | [
[
"Mamano",
"Nil",
""
],
[
"Hayes",
"Wayne",
""
]
] | The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard, meaning optimal solutions are impossible to find, and the quality of found alignment... |
2310.10598 | Jenna Fromer | Jenna C. Fromer, David E. Graff, Connor W. Coley | Pareto Optimization to Accelerate Multi-Objective Virtual Screening | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The discovery of therapeutic molecules is fundamentally a multi-objective
optimization problem. One formulation of the problem is to identify molecules
that simultaneously exhibit strong binding affinity for a target protein,
minimal off-target interactions, and suitable pharmacokinetic properties.
Inspired by prior ... | [
{
"created": "Mon, 16 Oct 2023 17:19:46 GMT",
"version": "v1"
}
] | 2023-10-17 | [
[
"Fromer",
"Jenna C.",
""
],
[
"Graff",
"David E.",
""
],
[
"Coley",
"Connor W.",
""
]
] | The discovery of therapeutic molecules is fundamentally a multi-objective optimization problem. One formulation of the problem is to identify molecules that simultaneously exhibit strong binding affinity for a target protein, minimal off-target interactions, and suitable pharmacokinetic properties. Inspired by prior wo... |
1611.05918 | Sujoy Ganguly | Sujoy Ganguly and Olivier Trottier and Xin Liang and Hugo
Bowne-Anderson and Jonathon Howard | Morphology of Fly Larval Class IV Dendrites Accords with a Random
Branching and Contact Based Branch Deletion Model | 12 pages, 4 figures. Supplementary Information: 3 Figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dendrites are branched neuronal processes that receive input signals from
other neurons or the outside world [1]. To maintain connectivity as the
organism grows, dendrites must also continue to grow. For example, the
dendrites in the peripheral nervous system continue to grow and branch to
maintain proper coverage of... | [
{
"created": "Thu, 17 Nov 2016 22:08:20 GMT",
"version": "v1"
}
] | 2016-11-21 | [
[
"Ganguly",
"Sujoy",
""
],
[
"Trottier",
"Olivier",
""
],
[
"Liang",
"Xin",
""
],
[
"Bowne-Anderson",
"Hugo",
""
],
[
"Howard",
"Jonathon",
""
]
] | Dendrites are branched neuronal processes that receive input signals from other neurons or the outside world [1]. To maintain connectivity as the organism grows, dendrites must also continue to grow. For example, the dendrites in the peripheral nervous system continue to grow and branch to maintain proper coverage of t... |
1708.02603 | Tae Seung Kang | Tae Seung Kang and Arunava Banerjee | Learning Feedforward and Recurrent Deterministic Spiking Neuron Network
Feedback Controllers | null | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We address the problem of learning feedback control where the controller is a
network constructed solely of deterministic spiking neurons. In contrast to
previous investigations that were based on a spike rate model of the neuron,
the control signal here is determined by the precise temporal positions of
spikes gener... | [
{
"created": "Tue, 8 Aug 2017 18:42:17 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Sep 2018 22:54:29 GMT",
"version": "v2"
}
] | 2018-09-27 | [
[
"Kang",
"Tae Seung",
""
],
[
"Banerjee",
"Arunava",
""
]
] | We address the problem of learning feedback control where the controller is a network constructed solely of deterministic spiking neurons. In contrast to previous investigations that were based on a spike rate model of the neuron, the control signal here is determined by the precise temporal positions of spikes generat... |
1307.5468 | Changbong Hyeon | Jeseong Yoon, D. Thirumalai, Changbong Hyeon | Urea-induced denaturation of PreQ1-riboswitch | 41 pages, 18 figures | J. Am. Chem. Soc. 2013 | 10.1016/j.bpj.2012.11.1853 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Urea, a polar molecule with a large dipole moment, not only destabilizes the
folded RNA structures, but can also enhance the folding rates of large
ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is
well understood, the action of urea on RNA has barely been explored. We
performed extensiv... | [
{
"created": "Sat, 20 Jul 2013 22:02:38 GMT",
"version": "v1"
}
] | 2017-08-23 | [
[
"Yoon",
"Jeseong",
""
],
[
"Thirumalai",
"D.",
""
],
[
"Hyeon",
"Changbong",
""
]
] | Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well understood, the action of urea on RNA has barely been explored. We performed extensive ... |
2010.12127 | Dongqi Han | Dongqi Han, Erik De Schutter, Sungho Hong | Lamina-specific neuronal properties promote robust, stable signal
propagation in feedforward networks | NeurIPS 2020 | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Feedforward networks (FFN) are ubiquitous structures in neural systems and
have been studied to understand mechanisms of reliable signal and information
transmission. In many FFNs, neurons in one layer have intrinsic properties that
are distinct from those in their pre-/postsynaptic layers, but how this affects
netwo... | [
{
"created": "Fri, 23 Oct 2020 01:57:46 GMT",
"version": "v1"
}
] | 2020-10-26 | [
[
"Han",
"Dongqi",
""
],
[
"De Schutter",
"Erik",
""
],
[
"Hong",
"Sungho",
""
]
] | Feedforward networks (FFN) are ubiquitous structures in neural systems and have been studied to understand mechanisms of reliable signal and information transmission. In many FFNs, neurons in one layer have intrinsic properties that are distinct from those in their pre-/postsynaptic layers, but how this affects network... |
2201.07338 | Noelia Ferruz | Noelia Ferruz and Birte H\"ocker | Controllable Protein Design with Language Models | This is a version before peer-review. A view-only, peer-reviewed,
published version can be found here: https://rdcu.be/cQbmH. The peer-reviewed
version is under embargo at Nat Mach Intell until 12/2022 | Controllable protein design with language models. Nat Mach Intell
4, 521-532, 2022 | 10.1038/s42256-022-00499-z | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The 21st century is presenting humankind with unprecedented environmental and
medical challenges. The ability to design novel proteins tailored for specific
purposes could transform our ability to respond timely to these issues. Recent
advances in the field of artificial intelligence are now setting the stage to
make... | [
{
"created": "Tue, 18 Jan 2022 22:23:03 GMT",
"version": "v1"
},
{
"created": "Mon, 22 Aug 2022 18:44:27 GMT",
"version": "v2"
}
] | 2022-08-24 | [
[
"Ferruz",
"Noelia",
""
],
[
"Höcker",
"Birte",
""
]
] | The 21st century is presenting humankind with unprecedented environmental and medical challenges. The ability to design novel proteins tailored for specific purposes could transform our ability to respond timely to these issues. Recent advances in the field of artificial intelligence are now setting the stage to make t... |
1602.08314 | Pramod Shinde | Pramod Shinde and Sarika Jalan | A multilayer PPI network analysis of different life stages in C. elegans | null | EPL (Europhysics Letters). 2015 Dec 17;112(5):58001 | 10.1209/0295-5075/112/58001 | null | q-bio.MN q-bio.PE q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular networks act as the backbone of cellular activities, providing an
{excellent} opportunity to understand the developmental changes in an organism.
While network data usually constitute only stationary network graphs,
constructing multilayer PPI network may provide clues to the particular
developmental role a... | [
{
"created": "Fri, 26 Feb 2016 13:26:52 GMT",
"version": "v1"
}
] | 2016-02-29 | [
[
"Shinde",
"Pramod",
""
],
[
"Jalan",
"Sarika",
""
]
] | Molecular networks act as the backbone of cellular activities, providing an {excellent} opportunity to understand the developmental changes in an organism. While network data usually constitute only stationary network graphs, constructing multilayer PPI network may provide clues to the particular developmental role at ... |
q-bio/0501013 | Anthonie Muller | Anthonie W. J. Muller | Thermosynthesis as energy source for the RNA World: a new model for the
origin of life | 12 pages, 6 figures; changes in text (minor) and 2 figures | null | null | null | q-bio.PE | null | The thermosynthesis concept, biological free energy gain from thermal
cycling, is combined with the concept of the RNA World. The resulting overall
origin of life model gives new explanations for the emergence of the genetic
code and the ribosome. The first protein named pF1 obtains the energy to
support the RNA worl... | [
{
"created": "Tue, 11 Jan 2005 19:06:12 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Mar 2005 21:48:04 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Muller",
"Anthonie W. J.",
""
]
] | The thermosynthesis concept, biological free energy gain from thermal cycling, is combined with the concept of the RNA World. The resulting overall origin of life model gives new explanations for the emergence of the genetic code and the ribosome. The first protein named pF1 obtains the energy to support the RNA world ... |
1702.02510 | Juan Abdon Miranda Correa | Juan Abdon Miranda-Correa and Mojtaba Khomami Abadi and Nicu Sebe and
Ioannis Patras | AMIGOS: A Dataset for Affect, Personality and Mood Research on
Individuals and Groups | 14 pages, Transaction on Affective Computing | null | null | null | q-bio.NC cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present AMIGOS-- A dataset for Multimodal research of affect, personality
traits and mood on Individuals and GrOupS. Different to other databases, we
elicited affect using both short and long videos in two social contexts, one
with individual viewers and one with groups of viewers. The database allows the
multimod... | [
{
"created": "Thu, 2 Feb 2017 08:04:47 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Mar 2017 14:27:10 GMT",
"version": "v2"
},
{
"created": "Thu, 13 Apr 2017 16:10:00 GMT",
"version": "v3"
}
] | 2017-04-14 | [
[
"Miranda-Correa",
"Juan Abdon",
""
],
[
"Abadi",
"Mojtaba Khomami",
""
],
[
"Sebe",
"Nicu",
""
],
[
"Patras",
"Ioannis",
""
]
] | We present AMIGOS-- A dataset for Multimodal research of affect, personality traits and mood on Individuals and GrOupS. Different to other databases, we elicited affect using both short and long videos in two social contexts, one with individual viewers and one with groups of viewers. The database allows the multimodal... |
2008.08758 | Affan Affan | Affan Affan and Tamer Inanc | Semi-Blind and l1 Robust System Identification for Anemia Management | Under-review at The Fifth IEEE/ACM conference on Connected Health:
Applications, Systems and Engineering Technologies (CHASE) 2020 | null | null | null | q-bio.QM cs.SY eess.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chronic diseases such as cancer, diabetes, heart diseases, chronic kidney
disease (CKD) require a drug management system that ensures a stable and robust
output of the patient's condition in response to drug dosage. In the case of
CKD, the patients suffer from the deficiency of red blood cell count and
external human... | [
{
"created": "Thu, 20 Aug 2020 03:50:10 GMT",
"version": "v1"
}
] | 2020-08-21 | [
[
"Affan",
"Affan",
""
],
[
"Inanc",
"Tamer",
""
]
] | Chronic diseases such as cancer, diabetes, heart diseases, chronic kidney disease (CKD) require a drug management system that ensures a stable and robust output of the patient's condition in response to drug dosage. In the case of CKD, the patients suffer from the deficiency of red blood cell count and external human r... |
1111.6916 | Nilima Nigam | Marc Ryser, Svetlana V. Komarova, Nilima Nigam | The cellular dynamics of bone remodeling: a mathematical model | null | SIAM J. Appl. Math. 70, pp. 1899-1921 | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The mechanical properties of vertebrate bone are largely determined by a
process which involves the complex interplay of three different cell types.
This process is called {\it bone remodeling}, and occurs asynchronously at
multiple sites in the mature skeleton. The cells involved are bone resorbing
osteoclasts, bone... | [
{
"created": "Sun, 27 Nov 2011 21:43:03 GMT",
"version": "v1"
}
] | 2011-11-30 | [
[
"Ryser",
"Marc",
""
],
[
"Komarova",
"Svetlana V.",
""
],
[
"Nigam",
"Nilima",
""
]
] | The mechanical properties of vertebrate bone are largely determined by a process which involves the complex interplay of three different cell types. This process is called {\it bone remodeling}, and occurs asynchronously at multiple sites in the mature skeleton. The cells involved are bone resorbing osteoclasts, bone m... |
1111.6631 | Arash Sangari Mr. | Arash Sangari, Adel Ardalan, Larry Lambe, Hamid Eghbalnia and Amir H.
Assadi | Mathematical Analysis and Computational Integration of Massive
Heterogeneous Data from the Human Retina | 9 pages, 3 figures, submitted and accepted in Damor2012 conference:
http://www.uninova.pt/damor2012/index.php?page=authors | null | null | null | q-bio.QM cs.IR math.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modern epidemiology integrates knowledge from heterogeneous collections of
data consisting of numerical, descriptive and imaging. Large-scale
epidemiological studies use sophisticated statistical analysis, mathematical
models using differential equations and versatile analytic tools that handle
numerical data. In con... | [
{
"created": "Mon, 28 Nov 2011 22:01:19 GMT",
"version": "v1"
},
{
"created": "Wed, 10 Oct 2012 19:52:29 GMT",
"version": "v2"
}
] | 2012-10-11 | [
[
"Sangari",
"Arash",
""
],
[
"Ardalan",
"Adel",
""
],
[
"Lambe",
"Larry",
""
],
[
"Eghbalnia",
"Hamid",
""
],
[
"Assadi",
"Amir H.",
""
]
] | Modern epidemiology integrates knowledge from heterogeneous collections of data consisting of numerical, descriptive and imaging. Large-scale epidemiological studies use sophisticated statistical analysis, mathematical models using differential equations and versatile analytic tools that handle numerical data. In contr... |
1411.2103 | Michael Schaub | Yazan N. Billeh, Michael T. Schaub, Costas A. Anastassiou, Mauricio
Barahona, Christof Koch | Revealing cell assemblies at multiple levels of granularity | 18 pages; 13 Figures; published as open access in J Neuro Methods | Journal of Neuroscience Methods, Volume 236, 30 October 2014,
Pages 92-106, ISSN 0165-0270 | 10.1016/j.jneumeth.2014.08.011 | null | q-bio.NC physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Current neuronal monitoring techniques, such as calcium imaging
and multi-electrode arrays, enable recordings of spiking activity from hundreds
of neurons simultaneously. Of primary importance in systems neuroscience is the
identification of cell assemblies: groups of neurons that cooperate in some
form w... | [
{
"created": "Sat, 8 Nov 2014 10:02:33 GMT",
"version": "v1"
}
] | 2014-11-11 | [
[
"Billeh",
"Yazan N.",
""
],
[
"Schaub",
"Michael T.",
""
],
[
"Anastassiou",
"Costas A.",
""
],
[
"Barahona",
"Mauricio",
""
],
[
"Koch",
"Christof",
""
]
] | Background: Current neuronal monitoring techniques, such as calcium imaging and multi-electrode arrays, enable recordings of spiking activity from hundreds of neurons simultaneously. Of primary importance in systems neuroscience is the identification of cell assemblies: groups of neurons that cooperate in some form wit... |
1510.05917 | Gestionnaire Hal-Upmc | Genevi\'eve Rodier (IGMM, IRCM), Olivier Kirsh (IGMM), Mart\'in
Baraibar (B2A), Thibault Houl\'es (IGMM, IPBS, IRCM), Matthieu Lacroix (UTA,
IRCM), H\'el\'ene Delpech (IGMM, IRCM), Elodie Hatchi (IGMM), St\'ephanie
Arnould (IGMM, IRCM), Dany Severac, Emeric Dubois, Julie Caramel (IGMM), Eric
Julien (IGMM, IRCM)... | The Transcription Factor E4F1 Coordinates CHK1-Dependent Checkpoint and
Mitochondrial Functions | null | Cell Reports, Elsevier, 2015, 11 (2), pp.220-233.
\<10.1016/j.celrep.2015.03.024\> | 10.1016/j.celrep.2015.03.024 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent data support the notion that a group of key transcriptional regulators
involved in tumorigenesis, including MYC, p53, E2F1, and BMI1, share an
intriguing capacity to simultaneously regulate metabolism and cell cycle. Here,
we show that another factor, the multifunctional protein E4F1, directly
controls genes i... | [
{
"created": "Wed, 14 Oct 2015 13:28:27 GMT",
"version": "v1"
}
] | 2015-10-21 | [
[
"Rodier",
"Geneviéve",
"",
"IGMM, IRCM"
],
[
"Kirsh",
"Olivier",
"",
"IGMM"
],
[
"Baraibar",
"Martín",
"",
"B2A"
],
[
"Houlés",
"Thibault",
"",
"IGMM, IPBS, IRCM"
],
[
"Lacroix",
"Matthieu",
"",
"UTA,\n IRCM"
],
[... | Recent data support the notion that a group of key transcriptional regulators involved in tumorigenesis, including MYC, p53, E2F1, and BMI1, share an intriguing capacity to simultaneously regulate metabolism and cell cycle. Here, we show that another factor, the multifunctional protein E4F1, directly controls genes inv... |
2310.09529 | Katherine Ge | Katherine Ge, Dayna Olson, and Michel F. Sanner | Docking Peptides into HIV/FIV Protease with Deep Learning and Focused
Peptide Docking Methods | 9 Pages, 5 Figures, 2 Tables | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular docking is a structure-based computational drug design technique
for predicting the interaction between a small molecule (ligand) and a
macromolecule (receptor). Over the past three decades various docking software
programs have been developed, mostly for drug-like molecules. With the recent
interest in pep... | [
{
"created": "Sat, 14 Oct 2023 08:14:54 GMT",
"version": "v1"
}
] | 2023-10-18 | [
[
"Ge",
"Katherine",
""
],
[
"Olson",
"Dayna",
""
],
[
"Sanner",
"Michel F.",
""
]
] | Molecular docking is a structure-based computational drug design technique for predicting the interaction between a small molecule (ligand) and a macromolecule (receptor). Over the past three decades various docking software programs have been developed, mostly for drug-like molecules. With the recent interest in pepti... |
2311.09261 | Yongqi Zhang | Yongqi Zhang, Quanming Yao, Ling Yue, Xian Wu, Ziheng Zhang, Zhenxi
Lin, Yefeng Zheng | Emerging Drug Interaction Prediction Enabled by Flow-based Graph Neural
Network with Biomedical Network | Accepted by Nature Computational Science | null | null | null | q-bio.QM cs.AI cs.CE cs.LG | http://creativecommons.org/licenses/by/4.0/ | Accurately predicting drug-drug interactions (DDI) for emerging drugs, which
offer possibilities for treating and alleviating diseases, with computational
methods can improve patient care and contribute to efficient drug development.
However, many existing computational methods require large amounts of known DDI
info... | [
{
"created": "Wed, 15 Nov 2023 06:34:00 GMT",
"version": "v1"
}
] | 2023-11-17 | [
[
"Zhang",
"Yongqi",
""
],
[
"Yao",
"Quanming",
""
],
[
"Yue",
"Ling",
""
],
[
"Wu",
"Xian",
""
],
[
"Zhang",
"Ziheng",
""
],
[
"Lin",
"Zhenxi",
""
],
[
"Zheng",
"Yefeng",
""
]
] | Accurately predicting drug-drug interactions (DDI) for emerging drugs, which offer possibilities for treating and alleviating diseases, with computational methods can improve patient care and contribute to efficient drug development. However, many existing computational methods require large amounts of known DDI inform... |
1403.2160 | Tiberiu Harko | Tiberiu Harko, Francisco S. N. Lobo, M. K. Mak | Exact analytical solutions of the Susceptible-Infected-Recovered (SIR)
epidemic model and of the SIR model with equal death and birth rates | 13 pages, 4 figures, accepted for publication in Applied Mathematics
and Computation | Applied Mathematics and Computation, 236, 2014, 184-194 | 10.1016/j.amc.2014.03.030 | null | q-bio.PE nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, the exact analytical solution of the
Susceptible-Infected-Recovered (SIR) epidemic model is obtained in a parametric
form. By using the exact solution we investigate some explicit models
corresponding to fixed values of the parameters, and show that the numerical
solution reproduces exactly the analyti... | [
{
"created": "Mon, 10 Mar 2014 08:21:07 GMT",
"version": "v1"
}
] | 2014-04-24 | [
[
"Harko",
"Tiberiu",
""
],
[
"Lobo",
"Francisco S. N.",
""
],
[
"Mak",
"M. K.",
""
]
] | In this paper, the exact analytical solution of the Susceptible-Infected-Recovered (SIR) epidemic model is obtained in a parametric form. By using the exact solution we investigate some explicit models corresponding to fixed values of the parameters, and show that the numerical solution reproduces exactly the analytica... |
1703.00226 | Thierry Mora | Jonathan Desponds, Andreas Mayer, Thierry Mora, Aleksandra M. Walczak | Population dynamics of immune repertoires | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The evolution of the adaptive immune system is characterized by changes in
the relative abundances of the B- and T-cell clones that make up its
repertoires. To fully capture this evolution, we need to describe the complex
dynamics of the response to pathogenic and self-antigenic stimulations, as well
as the statistic... | [
{
"created": "Wed, 1 Mar 2017 10:54:59 GMT",
"version": "v1"
}
] | 2017-03-02 | [
[
"Desponds",
"Jonathan",
""
],
[
"Mayer",
"Andreas",
""
],
[
"Mora",
"Thierry",
""
],
[
"Walczak",
"Aleksandra M.",
""
]
] | The evolution of the adaptive immune system is characterized by changes in the relative abundances of the B- and T-cell clones that make up its repertoires. To fully capture this evolution, we need to describe the complex dynamics of the response to pathogenic and self-antigenic stimulations, as well as the statistics ... |
2006.13752 | Paulo Zingano | Paulo R. Zingano, Janaina P. Zingano, Alessandra M. Silva and Carolina
P. Zingano | A matlab code to compute reproduction numbers with applications to the
Covid-19 outbreak | A complete matlab program (with about 500 lines) implementing the
algorithm described in this work can be downloaded for free at the following
URL address:
https://drive.google.com/drive/folders/16kLxlZyqH-QATOLQI6QWTx7qZnL3IoCP | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We discuss the generation of various reproduction ratios or numbers that are
very useful to monitor an ongoing epidemic like Covid-19 and examine the
effects of intervention measures. A detailed SEIR algorithm is described for
their computation, with applications given to the current Covid-19 outbreaks in
a number of... | [
{
"created": "Tue, 23 Jun 2020 17:57:28 GMT",
"version": "v1"
}
] | 2020-06-25 | [
[
"Zingano",
"Paulo R.",
""
],
[
"Zingano",
"Janaina P.",
""
],
[
"Silva",
"Alessandra M.",
""
],
[
"Zingano",
"Carolina P.",
""
]
] | We discuss the generation of various reproduction ratios or numbers that are very useful to monitor an ongoing epidemic like Covid-19 and examine the effects of intervention measures. A detailed SEIR algorithm is described for their computation, with applications given to the current Covid-19 outbreaks in a number of c... |
1902.01574 | Tzvetomir Tzvetanov | Tzvetomir Tzvetanov | Suppression and facilitation of motion perception in humans: a reply to
Schallmo & Murray (2018) | 9 pages | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In a recent publication (Tzvetanov (2018), bioRxiv 465807), I made an
extensive analysis with computational modelling and psychophysics of the simple
experimental design of Dr. D.Tadin (Tadin, Lappin, Gilroy and Blake (2003),
Nature, 424:312-315) about motion perception changes in humans due to size and
contrast of t... | [
{
"created": "Tue, 5 Feb 2019 07:34:35 GMT",
"version": "v1"
}
] | 2019-02-06 | [
[
"Tzvetanov",
"Tzvetomir",
""
]
] | In a recent publication (Tzvetanov (2018), bioRxiv 465807), I made an extensive analysis with computational modelling and psychophysics of the simple experimental design of Dr. D.Tadin (Tadin, Lappin, Gilroy and Blake (2003), Nature, 424:312-315) about motion perception changes in humans due to size and contrast of the... |
2103.06256 | Perrine Paul-Gilloteaux | Guillaume Potier, Fr\'ed\'eric Lavancier, Stephan Kunne and Perrine
Paul-Gilloteaux | A registration error estimation framework for correlative imaging | 10 pages 2 figures (made of 10 panels in total) | null | 10.1109/ICIP42928.2021.9506474 | null | q-bio.QM cs.CV | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Correlative imaging workflows are now widely used in bioimaging and aims to
image the same sample using at least two different and complementary imaging
modalities. Part of the workflow relies on finding the transformation linking a
source image to a target image. We are specifically interested in the
estimation of r... | [
{
"created": "Wed, 10 Mar 2021 18:43:18 GMT",
"version": "v1"
}
] | 2021-08-30 | [
[
"Potier",
"Guillaume",
""
],
[
"Lavancier",
"Frédéric",
""
],
[
"Kunne",
"Stephan",
""
],
[
"Paul-Gilloteaux",
"Perrine",
""
]
] | Correlative imaging workflows are now widely used in bioimaging and aims to image the same sample using at least two different and complementary imaging modalities. Part of the workflow relies on finding the transformation linking a source image to a target image. We are specifically interested in the estimation of reg... |
2012.05045 | Anindita Bhadra | Debottam Bhattacharjee and Anindita Bhadra | Response to sudden surge in human movement by an urban-adapted animal | 1 figure | Behav Ecol Sociobiol 75, 111 (2021) | 10.1007/s00265-021-03052-x | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Interaction with its immediate environment determines the ecology of an
organism. Species present in any habitat, wild or urban, may face extreme
pressure due to sudden perturbations. When such disturbances are unpredictable,
it becomes more challenging to tackle. Implementation of specific strategies is
therefore es... | [
{
"created": "Mon, 7 Dec 2020 12:27:34 GMT",
"version": "v1"
}
] | 2022-08-12 | [
[
"Bhattacharjee",
"Debottam",
""
],
[
"Bhadra",
"Anindita",
""
]
] | Interaction with its immediate environment determines the ecology of an organism. Species present in any habitat, wild or urban, may face extreme pressure due to sudden perturbations. When such disturbances are unpredictable, it becomes more challenging to tackle. Implementation of specific strategies is therefore esse... |
2407.07114 | Josh Morgan | Josh L. Morgan | Alternatives to the statistical mass confusion of testing for no-effect | 13 pages, 1 figure | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Statisticians and researchers have argued about the merits of effect size
estimation relative to hypothesis testing for decades. Cell biology has largely
avoided this debate and is now in a quantitation crisis. In experimental cell
biology, statistical analysis has grown to mean testing the null hypothesis
that there... | [
{
"created": "Fri, 28 Jun 2024 00:08:38 GMT",
"version": "v1"
}
] | 2024-07-11 | [
[
"Morgan",
"Josh L.",
""
]
] | Statisticians and researchers have argued about the merits of effect size estimation relative to hypothesis testing for decades. Cell biology has largely avoided this debate and is now in a quantitation crisis. In experimental cell biology, statistical analysis has grown to mean testing the null hypothesis that there w... |
2009.12023 | Alessandro Sanzeni | Alessandro Sanzeni and Mark H Histed and Nicolas Brunel | Emergence of irregular activity in networks of strongly coupled
conductance-based neurons | null | null | null | null | q-bio.NC physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Cortical neurons are characterized by irregular firing and a broad
distribution of rates. The balanced state model explains these observations
with a cancellation of mean excitatory and inhibitory currents, which makes
fluctuations drive firing. In networks of neurons with current-based synapses,
the balanced state e... | [
{
"created": "Fri, 25 Sep 2020 04:05:22 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Oct 2020 22:02:23 GMT",
"version": "v2"
}
] | 2020-10-15 | [
[
"Sanzeni",
"Alessandro",
""
],
[
"Histed",
"Mark H",
""
],
[
"Brunel",
"Nicolas",
""
]
] | Cortical neurons are characterized by irregular firing and a broad distribution of rates. The balanced state model explains these observations with a cancellation of mean excitatory and inhibitory currents, which makes fluctuations drive firing. In networks of neurons with current-based synapses, the balanced state eme... |
2003.09796 | Jun Chen | Jun Chen, Komi Messan, Marisabel Rodriguez Messan, Gloria
DeGrandi-Hoffman, Dingyong Bai, Yun Kang | How to model honeybee population dynamics: stage structure and
seasonality | null | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Western honeybees (Apis Mellifera) serve extremely important roles in our
ecosystem and economics as they are responsible for pollinating $ 215 billion
dollars annually over the world. Unfortunately, honeybee population and their
colonies have been declined dramatically. The purpose of this article is to
explore how ... | [
{
"created": "Sun, 22 Mar 2020 03:34:49 GMT",
"version": "v1"
}
] | 2020-03-24 | [
[
"Chen",
"Jun",
""
],
[
"Messan",
"Komi",
""
],
[
"Messan",
"Marisabel Rodriguez",
""
],
[
"DeGrandi-Hoffman",
"Gloria",
""
],
[
"Bai",
"Dingyong",
""
],
[
"Kang",
"Yun",
""
]
] | Western honeybees (Apis Mellifera) serve extremely important roles in our ecosystem and economics as they are responsible for pollinating $ 215 billion dollars annually over the world. Unfortunately, honeybee population and their colonies have been declined dramatically. The purpose of this article is to explore how we... |
1301.6561 | Alexey Mikaberidze | Alexey Mikaberidze, Bruce A. McDonald, Sebastian Bonhoeffer | Can high risk fungicides be used in mixtures without selecting for
fungicide resistance? | 51 pages, 6 figures, accepted for publication in Phytopathology | null | 10.1094/PHYTO-07-13-0204-R | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fungicide mixtures produced by the agrochemical industry often contain
low-risk fungicides, to which fungal pathogens are fully sensitive, together
with high-risk fungicides known to be prone to fungicide resistance. Can these
mixtures provide adequate disease control while minimizing the risk for the
development of ... | [
{
"created": "Mon, 28 Jan 2013 14:42:46 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Sep 2013 08:59:21 GMT",
"version": "v2"
}
] | 2013-09-23 | [
[
"Mikaberidze",
"Alexey",
""
],
[
"McDonald",
"Bruce A.",
""
],
[
"Bonhoeffer",
"Sebastian",
""
]
] | Fungicide mixtures produced by the agrochemical industry often contain low-risk fungicides, to which fungal pathogens are fully sensitive, together with high-risk fungicides known to be prone to fungicide resistance. Can these mixtures provide adequate disease control while minimizing the risk for the development of re... |
2009.03629 | Jozef Skakala | Jozef Skakala and Paolo Lazzari | Low complexity model to study scale dependence of phytoplankton dynamics
in the tropical Pacific | 21 pages, 12 figures | Phys. Rev. E 103, 012401 (2021) | 10.1103/PhysRevE.103.012401 | null | q-bio.PE physics.ao-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We demonstrate that a simple model based on reaction-diffusion-advection
(RDA) equation forced by realistic surface velocities and nutrients is skilled
in reproducing the distributions of the surface phytoplankton chlorophyll in
the tropical Pacific. We use the low-complexity RDA model to investigate the
scale-relati... | [
{
"created": "Tue, 8 Sep 2020 10:21:50 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Jan 2021 22:02:03 GMT",
"version": "v2"
}
] | 2021-01-13 | [
[
"Skakala",
"Jozef",
""
],
[
"Lazzari",
"Paolo",
""
]
] | We demonstrate that a simple model based on reaction-diffusion-advection (RDA) equation forced by realistic surface velocities and nutrients is skilled in reproducing the distributions of the surface phytoplankton chlorophyll in the tropical Pacific. We use the low-complexity RDA model to investigate the scale-relation... |
2010.00504 | Sarah Marzen | Alexander Hsu and Sarah Marzen | Time cells might be optimized for predictive capacity, not redundancy
reduction or memory capacity | null | null | 10.1103/PhysRevE.102.062404 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, researchers have found time cells in the hippocampus that appear to
contain information about the timing of past events. Some researchers have
argued that time cells are taking a Laplace transform of their input in order
to reconstruct the past stimulus. We argue that stimulus prediction, not
stimulus recon... | [
{
"created": "Thu, 1 Oct 2020 15:53:43 GMT",
"version": "v1"
}
] | 2020-12-30 | [
[
"Hsu",
"Alexander",
""
],
[
"Marzen",
"Sarah",
""
]
] | Recently, researchers have found time cells in the hippocampus that appear to contain information about the timing of past events. Some researchers have argued that time cells are taking a Laplace transform of their input in order to reconstruct the past stimulus. We argue that stimulus prediction, not stimulus reconst... |
2311.09354 | Kylie Trettner | Kylie J. Trettner, Jeremy Hsieh, Weikun Xiao, Jerry S.H. Lee, Andrea
M. Armani | Nondestructive, quantitative viability analysis of 3D tissue cultures
using machine learning image segmentation | 52 total pages, Main text and SI included, 35 figures (5 main text,
30 supplemental), 9 tables, 6 datasets (provided on linked GitHub), linked
image files on Zenodo | null | 10.1063/5.0189222 | null | q-bio.QM cs.LG eess.IV | http://creativecommons.org/licenses/by/4.0/ | Ascertaining the collective viability of cells in different cell culture
conditions has typically relied on averaging colorimetric indicators and is
often reported out in simple binary readouts. Recent research has combined
viability assessment techniques with image-based deep-learning models to
automate the characte... | [
{
"created": "Wed, 15 Nov 2023 20:28:31 GMT",
"version": "v1"
},
{
"created": "Mon, 4 Mar 2024 21:43:02 GMT",
"version": "v2"
},
{
"created": "Mon, 11 Mar 2024 22:12:25 GMT",
"version": "v3"
}
] | 2024-04-03 | [
[
"Trettner",
"Kylie J.",
""
],
[
"Hsieh",
"Jeremy",
""
],
[
"Xiao",
"Weikun",
""
],
[
"Lee",
"Jerry S. H.",
""
],
[
"Armani",
"Andrea M.",
""
]
] | Ascertaining the collective viability of cells in different cell culture conditions has typically relied on averaging colorimetric indicators and is often reported out in simple binary readouts. Recent research has combined viability assessment techniques with image-based deep-learning models to automate the characteri... |
1310.1593 | Tomasz Rutkowski | Shota Kono, Daiki Aminaka, Shoji Makino, and Tomasz M. Rutkowski | EEG Signal Processing and Classification for the Novel Tactile-Force
Brain-Computer Interface Paradigm | 6 pages (in conference proceedings original version); 6 figures,
submitted to The 9th International Conference on Signal Image Technology &
Internet Based Systems, December 2-5, 2013, Kyoto, Japan; to be available at
IEEE Xplore; IEEE Copyright 2013 | Proceedings of the 9th International Conference on Signal Image
Technology and Internet Based Systems, (Kyoto, Japan), pp. 812-817, IEEE
Computer Society, December 3-5, 2013 | 10.1109/SITIS.2013.132 | null | q-bio.NC cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The presented study explores the extent to which tactile-force stimulus
delivered to a hand holding a joystick can serve as a platform for a brain
computer interface (BCI). The four pressure directions are used to evoke
tactile brain potential responses, thus defining a tactile-force brain computer
interface (tfBCI).... | [
{
"created": "Sun, 6 Oct 2013 15:18:34 GMT",
"version": "v1"
},
{
"created": "Thu, 17 Oct 2013 07:52:01 GMT",
"version": "v2"
}
] | 2013-12-17 | [
[
"Kono",
"Shota",
""
],
[
"Aminaka",
"Daiki",
""
],
[
"Makino",
"Shoji",
""
],
[
"Rutkowski",
"Tomasz M.",
""
]
] | The presented study explores the extent to which tactile-force stimulus delivered to a hand holding a joystick can serve as a platform for a brain computer interface (BCI). The four pressure directions are used to evoke tactile brain potential responses, thus defining a tactile-force brain computer interface (tfBCI). W... |
1608.06146 | Sophie Kay | Sophie K. Kay, Heather A. Harrington, Sarah Shepherd, Keith Brennan,
Trevor Dale, James M. Osborne, David J. Gavaghan and Helen M. Byrne | The Role of the Hes1 Crosstalk Hub in Notch-Wnt Interactions of the
Intestinal Crypt | null | null | 10.1371/journal.pcbi.1005400 | null | q-bio.SC q-bio.CB q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Notch pathway plays a vital role in determining whether cells in the
intestinal epithelium adopt a secretory or an absorptive phenotype. Cell fate
specification is coordinated via Notch's interaction with the canonical Wnt
pathway. Here, we propose a new mathematical model of the Notch and Wnt
pathways, in which ... | [
{
"created": "Mon, 22 Aug 2016 12:32:08 GMT",
"version": "v1"
}
] | 2017-04-12 | [
[
"Kay",
"Sophie K.",
""
],
[
"Harrington",
"Heather A.",
""
],
[
"Shepherd",
"Sarah",
""
],
[
"Brennan",
"Keith",
""
],
[
"Dale",
"Trevor",
""
],
[
"Osborne",
"James M.",
""
],
[
"Gavaghan",
"David J.",
""
... | The Notch pathway plays a vital role in determining whether cells in the intestinal epithelium adopt a secretory or an absorptive phenotype. Cell fate specification is coordinated via Notch's interaction with the canonical Wnt pathway. Here, we propose a new mathematical model of the Notch and Wnt pathways, in which th... |
1310.2968 | Tracy Heath | Tracy A. Heath, John P. Huelsenbeck, Tanja Stadler | The Fossilized Birth-Death Process: A Coherent Model of Fossil
Calibration for Divergence Time Estimation | 42 total pages including: 29 text pages, 5 tables, and 12 figures.
Work presented at Evolution 2013
(http://www.slideshare.net/trayc7/heath-evolution-2013) | null | 10.1073/pnas.1319091111 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Time-calibrated species phylogenies are critical for addressing a wide range
of questions in evolutionary biology, such as those that elucidate historical
biogeography or uncover patterns of coevolution and diversification. Because
molecular sequence data are not informative on absolute time, external data,
most comm... | [
{
"created": "Thu, 10 Oct 2013 22:04:03 GMT",
"version": "v1"
},
{
"created": "Fri, 18 Oct 2013 20:48:23 GMT",
"version": "v2"
}
] | 2014-07-11 | [
[
"Heath",
"Tracy A.",
""
],
[
"Huelsenbeck",
"John P.",
""
],
[
"Stadler",
"Tanja",
""
]
] | Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because molecular sequence data are not informative on absolute time, external data, most common... |
2312.14267 | Catalina Vich | Cristina Giossi and Jonathan E. Rubin and Aryn Gittis and Timothy
Verstynen and Catalina Vich | Rethinking the external globus pallidus and information flow in
cortico-basal ganglia-thalamic circuits | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | For decades the external globus pallidus (GPe) has been viewed as a passive
way-station in the indirect pathway of the cortico-basal ganglia-thalamic
(CBGT) circuit, sandwiched between striatal inputs and basal ganglia outputs.
According to this model, one-way descending striatal signals in the indirect
pathway ampli... | [
{
"created": "Thu, 21 Dec 2023 19:30:11 GMT",
"version": "v1"
},
{
"created": "Wed, 27 Dec 2023 12:48:28 GMT",
"version": "v2"
}
] | 2023-12-29 | [
[
"Giossi",
"Cristina",
""
],
[
"Rubin",
"Jonathan E.",
""
],
[
"Gittis",
"Aryn",
""
],
[
"Verstynen",
"Timothy",
""
],
[
"Vich",
"Catalina",
""
]
] | For decades the external globus pallidus (GPe) has been viewed as a passive way-station in the indirect pathway of the cortico-basal ganglia-thalamic (CBGT) circuit, sandwiched between striatal inputs and basal ganglia outputs. According to this model, one-way descending striatal signals in the indirect pathway amplify... |
1303.5111 | Marcelo A. Montemurro | In\'es Samengo, Germ\'an Mato, Daniel H. Elijah, Susanne Schreiber,
and Marcelo A. Montemurro | Linking dynamical and functional properties of intrinsically bursting
neurons | 22 pages, 11 figure, to appear in the Journal of Computational
Neuroscience | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Several studies have shown that bursting neurons can encode information in
the number of spikes per burst: As the stimulus varies, so does the length of
individual bursts. The represented stimuli, however, vary substantially among
different sensory modalities and different neurons. The goal of this paper is
to determ... | [
{
"created": "Wed, 20 Mar 2013 22:30:46 GMT",
"version": "v1"
}
] | 2013-03-22 | [
[
"Samengo",
"Inés",
""
],
[
"Mato",
"Germán",
""
],
[
"Elijah",
"Daniel H.",
""
],
[
"Schreiber",
"Susanne",
""
],
[
"Montemurro",
"Marcelo A.",
""
]
] | Several studies have shown that bursting neurons can encode information in the number of spikes per burst: As the stimulus varies, so does the length of individual bursts. The represented stimuli, however, vary substantially among different sensory modalities and different neurons. The goal of this paper is to determin... |
1905.12382 | Amir Hossein Ansari | Amir Hossein Ansari, Perumpillichira Joseph Cherian, Alexander
Caicedo, Anneleen Dereymaeker, Katrien Jansen, Leen De Wispelaere, Charlotte
Dielman, Jan Vervisch, Paul Govaert, Maarten De Vos, Gunnar Naulaers, Sabine
Van Huffel | NeoGuard: a public, online learning platform for neonatal seizures | null | null | null | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Seizures occur in the neonatal period more frequently than other periods of
life and usually denote the presence of serious brain dysfunction. The gold
standard for detecting seizures is based on visual inspection of continuous
electroencephalogram (cEEG) complemented by video analysis, performed by an
expert clinica... | [
{
"created": "Wed, 29 May 2019 12:45:38 GMT",
"version": "v1"
}
] | 2019-05-30 | [
[
"Ansari",
"Amir Hossein",
""
],
[
"Cherian",
"Perumpillichira Joseph",
""
],
[
"Caicedo",
"Alexander",
""
],
[
"Dereymaeker",
"Anneleen",
""
],
[
"Jansen",
"Katrien",
""
],
[
"De Wispelaere",
"Leen",
""
],
[
"Dielm... | Seizures occur in the neonatal period more frequently than other periods of life and usually denote the presence of serious brain dysfunction. The gold standard for detecting seizures is based on visual inspection of continuous electroencephalogram (cEEG) complemented by video analysis, performed by an expert clinical ... |
2404.16907 | Thomas Gaudelet | Thomas Gaudelet, Alice Del Vecchio, Eli M Carrami, Juliana Cudini,
Chantriolnt-Andreas Kapourani, Caroline Uhler, Lindsay Edwards | Season combinatorial intervention predictions with Salt & Peper | null | null | null | null | q-bio.GN cs.LG q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | Interventions play a pivotal role in the study of complex biological systems.
In drug discovery, genetic interventions (such as CRISPR base editing) have
become central to both identifying potential therapeutic targets and
understanding a drug's mechanism of action. With the advancement of CRISPR and
the proliferatio... | [
{
"created": "Thu, 25 Apr 2024 12:48:11 GMT",
"version": "v1"
}
] | 2024-04-29 | [
[
"Gaudelet",
"Thomas",
""
],
[
"Del Vecchio",
"Alice",
""
],
[
"Carrami",
"Eli M",
""
],
[
"Cudini",
"Juliana",
""
],
[
"Kapourani",
"Chantriolnt-Andreas",
""
],
[
"Uhler",
"Caroline",
""
],
[
"Edwards",
"Lindsa... | Interventions play a pivotal role in the study of complex biological systems. In drug discovery, genetic interventions (such as CRISPR base editing) have become central to both identifying potential therapeutic targets and understanding a drug's mechanism of action. With the advancement of CRISPR and the proliferation ... |
2204.07110 | Anne-Florence Bitbol | Damiano Sgarbossa, Umberto Lupo and Anne-Florence Bitbol | Generative power of a protein language model trained on multiple
sequence alignments | 46 pages, 20 figures, 6 tables | null | null | null | q-bio.BM cs.LG q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Computational models starting from large ensembles of evolutionarily related
protein sequences capture a representation of protein families and learn
constraints associated to protein structure and function. They thus open the
possibility for generating novel sequences belonging to protein families.
Protein language ... | [
{
"created": "Thu, 14 Apr 2022 16:59:05 GMT",
"version": "v1"
},
{
"created": "Sun, 20 Nov 2022 20:04:16 GMT",
"version": "v2"
}
] | 2022-11-22 | [
[
"Sgarbossa",
"Damiano",
""
],
[
"Lupo",
"Umberto",
""
],
[
"Bitbol",
"Anne-Florence",
""
]
] | Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating novel sequences belonging to protein families. Protein language mo... |
2401.12232 | Damilola Oshunyinka | Damilola Oshunyinka | Machine Learning Modeling Of SiRNA Structure-Potency Relationship With
Applications Against Sars-Cov-2 Spike Gene | Master's thesis | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | The pharmaceutical Research and development (R&D) process is lengthy and
costly, taking nearly a decade to bring a new drug to the market. However,
advancements in biotechnology, computational methods, and machine learning
algorithms have the potential to revolutionize drug discovery, speeding up the
process and impr... | [
{
"created": "Thu, 18 Jan 2024 23:00:34 GMT",
"version": "v1"
}
] | 2024-01-24 | [
[
"Oshunyinka",
"Damilola",
""
]
] | The pharmaceutical Research and development (R&D) process is lengthy and costly, taking nearly a decade to bring a new drug to the market. However, advancements in biotechnology, computational methods, and machine learning algorithms have the potential to revolutionize drug discovery, speeding up the process and improv... |
1807.04862 | Jose Fontanari | Paulo R. A. Campos and Jos\'e F. Fontanari | Predictability of the imitative learning trajectories | null | J. Stat. Mech. (2019) 013501 | 10.1088/1742-5468/aaf634 | null | q-bio.PE cs.MA physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The fitness landscape metaphor plays a central role on the modeling of
optimizing principles in many research fields, ranging from evolutionary
biology, where it was first introduced, to management research. Here we
consider the ensemble of trajectories of the imitative learning search, in
which agents exchange infor... | [
{
"created": "Thu, 12 Jul 2018 23:32:47 GMT",
"version": "v1"
},
{
"created": "Mon, 16 Jul 2018 23:46:40 GMT",
"version": "v2"
},
{
"created": "Thu, 15 Nov 2018 17:42:47 GMT",
"version": "v3"
}
] | 2019-01-30 | [
[
"Campos",
"Paulo R. A.",
""
],
[
"Fontanari",
"José F.",
""
]
] | The fitness landscape metaphor plays a central role on the modeling of optimizing principles in many research fields, ranging from evolutionary biology, where it was first introduced, to management research. Here we consider the ensemble of trajectories of the imitative learning search, in which agents exchange informa... |
2404.13093 | Tyler Clark | Tyler Clark | The N-Gene Model for Evolutionary Games | 11 pages | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | In this study, we develop a novel evolutionary model that incorporates
Mendelian genetics, continuous strategies, and the potential for multiple genes
to contribute to a single phenotypic trait. The evolution of altruistic
behavior, which confers benefits to others at a cost to the individual, remains
a fundamental q... | [
{
"created": "Fri, 19 Apr 2024 01:31:00 GMT",
"version": "v1"
}
] | 2024-04-23 | [
[
"Clark",
"Tyler",
""
]
] | In this study, we develop a novel evolutionary model that incorporates Mendelian genetics, continuous strategies, and the potential for multiple genes to contribute to a single phenotypic trait. The evolution of altruistic behavior, which confers benefits to others at a cost to the individual, remains a fundamental que... |
2010.00659 | Linden Parkes | Linden Parkes, Tyler M. Moore, Monica E. Calkins, Matthew Cieslak,
David R. Roalf, Daniel H. Wolf, Ruben C. Gur, Raquel E. Gur, Theodore D.
Satterthwaite, Danielle S. Bassett | Network controllability in transmodal cortex predicts psychosis spectrum
symptoms | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The psychosis spectrum is associated with structural dysconnectivity
concentrated in transmodal association cortex. However, understanding of this
pathophysiology has been limited by an exclusive focus on the direct
connections to a region. Using Network Control Theory, we measured variation in
both direct and indire... | [
{
"created": "Thu, 1 Oct 2020 19:40:42 GMT",
"version": "v1"
}
] | 2020-10-05 | [
[
"Parkes",
"Linden",
""
],
[
"Moore",
"Tyler M.",
""
],
[
"Calkins",
"Monica E.",
""
],
[
"Cieslak",
"Matthew",
""
],
[
"Roalf",
"David R.",
""
],
[
"Wolf",
"Daniel H.",
""
],
[
"Gur",
"Ruben C.",
""
],
... | The psychosis spectrum is associated with structural dysconnectivity concentrated in transmodal association cortex. However, understanding of this pathophysiology has been limited by an exclusive focus on the direct connections to a region. Using Network Control Theory, we measured variation in both direct and indirect... |
1307.3515 | Guillaume Mar\c{c}ais | Guillaume Mar\c{c}ais and James A. Yorke and Aleksey Zimin | QuorUM: an error corrector for Illumina reads | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Illumina Sequencing data can provide high coverage of a genome by
relatively short (100 bp150 bp) reads at a low cost. Our goal is to produce
trimmed and error-corrected reads to improve genome assemblies. Our error
correction procedure aims at producing a set of error-corrected reads (1)
minimizing the n... | [
{
"created": "Fri, 12 Jul 2013 17:10:28 GMT",
"version": "v1"
}
] | 2013-07-15 | [
[
"Marçais",
"Guillaume",
""
],
[
"Yorke",
"James A.",
""
],
[
"Zimin",
"Aleksey",
""
]
] | Motivation: Illumina Sequencing data can provide high coverage of a genome by relatively short (100 bp150 bp) reads at a low cost. Our goal is to produce trimmed and error-corrected reads to improve genome assemblies. Our error correction procedure aims at producing a set of error-corrected reads (1) minimizing the num... |
1808.05143 | Vernon Lawhern | Amelia J. Solon, Stephen M. Gordon, Jonathan R. McDaniel, Vernon J.
Lawhern | Collaborative Brain-Computer Interface for Human Interest Detection in
Complex and Dynamic Settings | 6 pages, 6 figures | 2018 IEEE International Conference on Systems, Man and
Cybernetics, pp. 970-975 | 10.1109/SMC.2018.00172 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Humans can fluidly adapt their interest in complex environments in ways that
machines cannot. Here, we lay the groundwork for a real-world system that
passively monitors and merges neural correlates of visual interest across team
members via Collaborative Brain Computer Interface (cBCI). When group interest
is detect... | [
{
"created": "Wed, 15 Aug 2018 15:31:14 GMT",
"version": "v1"
}
] | 2019-01-21 | [
[
"Solon",
"Amelia J.",
""
],
[
"Gordon",
"Stephen M.",
""
],
[
"McDaniel",
"Jonathan R.",
""
],
[
"Lawhern",
"Vernon J.",
""
]
] | Humans can fluidly adapt their interest in complex environments in ways that machines cannot. Here, we lay the groundwork for a real-world system that passively monitors and merges neural correlates of visual interest across team members via Collaborative Brain Computer Interface (cBCI). When group interest is detected... |
1609.07799 | Scott Elliott | S. Elliott, N. Jeffery, E. Hunke, C. Deal, M. Jin, S. Wang, E. Elliott
Smith and S. Oestreicher | Strategies for the Simulation of Sea Ice Organic Chemistry: Arctic Tests
and Development | In preparation for submission to Biogeosciences (Copernicus, EGU) | null | null | null | q-bio.QM physics.ao-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A mechanism connecting ice algal ecodynamics with the buildup of organic
macromolecules in brine channels is tested offline in a reduced model of pack
geochemistry. Driver physical quantities are extracted from the global sea ice
dynamics code CICE, including snow height, column thickness and internal
temperature. Th... | [
{
"created": "Sun, 25 Sep 2016 21:00:59 GMT",
"version": "v1"
}
] | 2016-09-27 | [
[
"Elliott",
"S.",
""
],
[
"Jeffery",
"N.",
""
],
[
"Hunke",
"E.",
""
],
[
"Deal",
"C.",
""
],
[
"Jin",
"M.",
""
],
[
"Wang",
"S.",
""
],
[
"Smith",
"E. Elliott",
""
],
[
"Oestreicher",
"S.",
... | A mechanism connecting ice algal ecodynamics with the buildup of organic macromolecules in brine channels is tested offline in a reduced model of pack geochemistry. Driver physical quantities are extracted from the global sea ice dynamics code CICE, including snow height, column thickness and internal temperature. The ... |
1611.07999 | Moritz Augustin | Moritz Augustin, Josef Ladenbauer, Fabian Baumann, Klaus Obermayer | Low-dimensional spike rate models derived from networks of adaptive
integrate-and-fire neurons: Comparison and implementation | concatenation of main text (including 8 figures), supplementary
methods text and supporting figure | PLOS Comput Biol 13, e1005545 (2017) | 10.1371/journal.pcbi.1005545 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The spiking activity of single neurons can be well described by a nonlinear
integrate-and-fire model that includes somatic adaptation. When exposed to
fluctuating inputs sparsely coupled populations of these model neurons exhibit
stochastic collective dynamics that can be effectively characterized using the
Fokker-Pl... | [
{
"created": "Wed, 23 Nov 2016 21:17:07 GMT",
"version": "v1"
},
{
"created": "Wed, 19 Jul 2017 14:21:20 GMT",
"version": "v2"
}
] | 2017-07-20 | [
[
"Augustin",
"Moritz",
""
],
[
"Ladenbauer",
"Josef",
""
],
[
"Baumann",
"Fabian",
""
],
[
"Obermayer",
"Klaus",
""
]
] | The spiking activity of single neurons can be well described by a nonlinear integrate-and-fire model that includes somatic adaptation. When exposed to fluctuating inputs sparsely coupled populations of these model neurons exhibit stochastic collective dynamics that can be effectively characterized using the Fokker-Plan... |
1702.07246 | Tatiana Tatarinova | Chan Kuang Lim, Tatiana V. Tatarinova, Rozana Rosli, Nadzirah
Amiruddin, Norazah Azizi, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi,
Jayanthi Nagappan, Petr Ponomarenko, Martin Triska, Victor Solovyev, Mohd
Firdaus-Raih, Ravigadevi Sambanthamurthi, Denis Murphy, Leslie Low Eng Ti | Evidence-based gene models for structural and functional annotations of
the oil palm genome | null | Biology Direct (2017)12:21 | 10.1186/s13062-017-0191-4 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The advent of rapid and inexpensive DNA sequencing has led to an explosion of
data waiting to be transformed into knowledge about genome organization and
function. Gene prediction is customarily the starting point for genome
analysis. This paper presents a bioinformatics study of the oil palm genome,
including compar... | [
{
"created": "Thu, 23 Feb 2017 14:57:48 GMT",
"version": "v1"
},
{
"created": "Wed, 5 Apr 2017 05:22:35 GMT",
"version": "v2"
}
] | 2017-09-12 | [
[
"Lim",
"Chan Kuang",
""
],
[
"Tatarinova",
"Tatiana V.",
""
],
[
"Rosli",
"Rozana",
""
],
[
"Amiruddin",
"Nadzirah",
""
],
[
"Azizi",
"Norazah",
""
],
[
"Halim",
"Mohd Amin Ab",
""
],
[
"Sanusi",
"Nik Shazana N... | The advent of rapid and inexpensive DNA sequencing has led to an explosion of data waiting to be transformed into knowledge about genome organization and function. Gene prediction is customarily the starting point for genome analysis. This paper presents a bioinformatics study of the oil palm genome, including comparat... |
2305.13420 | Alexander Schmidt | Alexander Schmidt, Peter Hiemeyer, Fred Wolf | An Analytically Solvable Model of Firing Rate Heterogeneity in Balanced
State Networks | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Distributions of neuronal activity within cortical circuits are often found
to display highly skewed shapes with many neurons emitting action potentials at
low or vanishing rates, while some are active at high rates. Theoretical
studies were able to reproduce such distributions, but come with a lack of
mathematical t... | [
{
"created": "Mon, 22 May 2023 19:10:32 GMT",
"version": "v1"
}
] | 2023-05-24 | [
[
"Schmidt",
"Alexander",
""
],
[
"Hiemeyer",
"Peter",
""
],
[
"Wolf",
"Fred",
""
]
] | Distributions of neuronal activity within cortical circuits are often found to display highly skewed shapes with many neurons emitting action potentials at low or vanishing rates, while some are active at high rates. Theoretical studies were able to reproduce such distributions, but come with a lack of mathematical tra... |
0707.4533 | Nicholas Guttenberg | Nicholas Guttenberg and Nigel Goldenfeld | Cascade of Complexity in Evolving Predator-Prey Dynamics | 5 pages, 3 figures; added comments on system size scaling and
turbulence analogy, added error estimates of data collapse parameters.
Slightly enhanced from the version which will appear in PRL | null | 10.1103/PhysRevLett.100.058102 | null | q-bio.PE | null | We simulate an individual-based model that represents both the phenotype and
genome of digital organisms with predator-prey interactions. We show how
open-ended growth of complexity arises from the invariance of genetic evolution
operators with respect to changes in the complexity, and that the dynamics
which emerges... | [
{
"created": "Tue, 31 Jul 2007 05:00:30 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Oct 2007 13:38:51 GMT",
"version": "v2"
},
{
"created": "Thu, 20 Dec 2007 22:26:46 GMT",
"version": "v3"
}
] | 2009-11-13 | [
[
"Guttenberg",
"Nicholas",
""
],
[
"Goldenfeld",
"Nigel",
""
]
] | We simulate an individual-based model that represents both the phenotype and genome of digital organisms with predator-prey interactions. We show how open-ended growth of complexity arises from the invariance of genetic evolution operators with respect to changes in the complexity, and that the dynamics which emerges i... |
1308.4951 | David Enard | David Enard, Philipp W. Messer, Dmitri Petrov | Genome wide signals of pervasive positive selection in human evolution | null | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The role of positive selection in human evolution remains controversial. On
the one hand, scans for positive selection have identified hundreds of
candidate loci and the genome-wide patterns of polymorphism show signatures
consistent with frequent positive selection. On the other hand, recent studies
have argued that... | [
{
"created": "Thu, 22 Aug 2013 18:38:52 GMT",
"version": "v1"
}
] | 2013-08-23 | [
[
"Enard",
"David",
""
],
[
"Messer",
"Philipp W.",
""
],
[
"Petrov",
"Dmitri",
""
]
] | The role of positive selection in human evolution remains controversial. On the one hand, scans for positive selection have identified hundreds of candidate loci and the genome-wide patterns of polymorphism show signatures consistent with frequent positive selection. On the other hand, recent studies have argued that m... |
0806.0744 | Janos Locsei | Janos Tobias Locsei and Timothy J Pedley | Bacterial tracking of motile algae assisted by algal cell's vorticity
field | 21 pages, 15 figures | null | null | null | q-bio.CB q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Previously published experimental work by other authors has shown that
certain motile marine bacteria are able to track free swimming algae by
executing a zigzag path and steering toward the algae at each turn. Here, we
propose that the apparent steering behaviour could be a hydrodynamic effect,
whereby an algal cell... | [
{
"created": "Wed, 4 Jun 2008 10:45:49 GMT",
"version": "v1"
}
] | 2008-06-05 | [
[
"Locsei",
"Janos Tobias",
""
],
[
"Pedley",
"Timothy J",
""
]
] | Previously published experimental work by other authors has shown that certain motile marine bacteria are able to track free swimming algae by executing a zigzag path and steering toward the algae at each turn. Here, we propose that the apparent steering behaviour could be a hydrodynamic effect, whereby an algal cell's... |
1906.05024 | Arman Karshenas Mr. | Arman Karshenas, Joseph Windo, Bhuvana, Jonathan Stocks, Adrian
Kozhevnikov, Jhanna Kryukova, Eleanor Beard, Laurel Constanti Crosby, Max
Taylor | Frequency and Time Domain Analysis ofsRNA-based Treatment for
Inflammatory BowelDisease | 8 pages , 18 figures | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The validity of a complex reaction pathway proposed to treat Inflammatory
Bowel Disease (IBD) was verified by a comprehensive time and frequency domain
analysis. The model was taken to the frequency domain to study the effect and
the significance of the negative feedback loop introduced by the reaction
pathways. It c... | [
{
"created": "Wed, 12 Jun 2019 09:24:35 GMT",
"version": "v1"
}
] | 2019-06-13 | [
[
"Karshenas",
"Arman",
""
],
[
"Windo",
"Joseph",
""
],
[
"Bhuvana",
"",
""
],
[
"Stocks",
"Jonathan",
""
],
[
"Kozhevnikov",
"Adrian",
""
],
[
"Kryukova",
"Jhanna",
""
],
[
"Beard",
"Eleanor",
""
],
[
... | The validity of a complex reaction pathway proposed to treat Inflammatory Bowel Disease (IBD) was verified by a comprehensive time and frequency domain analysis. The model was taken to the frequency domain to study the effect and the significance of the negative feedback loop introduced by the reaction pathways. It cou... |
2406.13292 | Giorgio Dolci | Giorgio Dolci (1,2), Federica Cruciani (1), Md Abdur Rahaman (2),
Anees Abrol (2), Jiayu Chen (2), Zening Fu (2), Ilaria Boscolo Galazzo (1),
Gloria Menegaz (1) and Vince D. Calhoun (2) ((1) Department of Engineering
for Innovation Medicine, University of Verona, Verona, Italy, (2)
Tri-Institutional Center for ... | An interpretable generative multimodal neuroimaging-genomics framework
for decoding Alzheimer's disease | 27 pages, 7 figures, submitted to a journal | null | null | null | q-bio.QM cs.AI eess.IV | http://creativecommons.org/licenses/by/4.0/ | Alzheimer's disease (AD) is the most prevalent form of dementia with a
progressive decline in cognitive abilities. The AD continuum encompasses a
prodormal stage known as Mild Cognitive Impairment (MCI), where patients may
either progress to AD or remain stable. In this study, we leveraged structural
and functional M... | [
{
"created": "Wed, 19 Jun 2024 07:31:47 GMT",
"version": "v1"
}
] | 2024-06-21 | [
[
"Dolci",
"Giorgio",
""
],
[
"Cruciani",
"Federica",
""
],
[
"Rahaman",
"Md Abdur",
""
],
[
"Abrol",
"Anees",
""
],
[
"Chen",
"Jiayu",
""
],
[
"Fu",
"Zening",
""
],
[
"Galazzo",
"Ilaria Boscolo",
""
],
[... | Alzheimer's disease (AD) is the most prevalent form of dementia with a progressive decline in cognitive abilities. The AD continuum encompasses a prodormal stage known as Mild Cognitive Impairment (MCI), where patients may either progress to AD or remain stable. In this study, we leveraged structural and functional MRI... |
q-bio/0502023 | Gabriele Scheler | Gabriele Scheler | Learning intrinsic excitability in medium spiny neurons | 20 pages, 8 figures | F1000Research 2014, 2:88 | 10.12688/f1000research.2-88.v2 | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present an unsupervised, local activation-dependent learning rule for
intrinsic plasticity (IP) which affects the composition of ion channel
conductances for single neurons in a use-dependent way. We use a
single-compartment conductance-based model for medium spiny striatal neurons in
order to show the effects of ... | [
{
"created": "Mon, 21 Feb 2005 02:42:32 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Jul 2005 18:32:22 GMT",
"version": "v2"
},
{
"created": "Sun, 6 Aug 2006 01:18:31 GMT",
"version": "v3"
},
{
"created": "Thu, 13 Dec 2012 00:17:05 GMT",
"version": "v4"
}
] | 2017-08-29 | [
[
"Scheler",
"Gabriele",
""
]
] | We present an unsupervised, local activation-dependent learning rule for intrinsic plasticity (IP) which affects the composition of ion channel conductances for single neurons in a use-dependent way. We use a single-compartment conductance-based model for medium spiny striatal neurons in order to show the effects of pa... |
1607.06285 | Celine Scornavacca | Philippe Gambette, Leo van Iersel, Steven Kelk, Fabio Pardi and Celine
Scornavacca | Do branch lengths help to locate a tree in a phylogenetic network? | null | null | 10.1007/s11538-016-0199-4 | null | q-bio.PE cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic networks are increasingly used in evolutionary biology to
represent the history of species that have undergone reticulate events such as
horizontal gene transfer, hybrid speciation and recombination. One of the most
fundamental questions that arise in this context is whether the evolution of a
gene with ... | [
{
"created": "Thu, 21 Jul 2016 11:57:28 GMT",
"version": "v1"
}
] | 2016-10-07 | [
[
"Gambette",
"Philippe",
""
],
[
"van Iersel",
"Leo",
""
],
[
"Kelk",
"Steven",
""
],
[
"Pardi",
"Fabio",
""
],
[
"Scornavacca",
"Celine",
""
]
] | Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental questions that arise in this context is whether the evolution of a gene with on... |
1710.08645 | Gao-De Li Dr | Gao-De Li | Nucleus may be the key site of chloroquine antimalarial action and
resistance development | 4 pages. arXiv admin note: This version has been removed because it
is in violation of arXiv's copyright policy | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The first proposed hypothesis about the mechanism of chloroquine (CQ) action
on malaria parasites is DNA intercalation hypothesis which indicates that the
site of CQ action is within the nucleus. Later on the interest of research was
shifted from nucleus to lysosome due to the report of CQ accumulation within
lysosom... | [
{
"created": "Tue, 24 Oct 2017 08:29:43 GMT",
"version": "v1"
}
] | 2017-10-26 | [
[
"Li",
"Gao-De",
""
]
] | The first proposed hypothesis about the mechanism of chloroquine (CQ) action on malaria parasites is DNA intercalation hypothesis which indicates that the site of CQ action is within the nucleus. Later on the interest of research was shifted from nucleus to lysosome due to the report of CQ accumulation within lysosome.... |
1012.4501 | Mike Klymkowsky | Michael W. Klymkowsky, Sonia M. Underwood, R. Kathleen Garvin-Doxas | Biological Concepts Instrument (BCI): A diagnostic tool for revealing
student thinking | null | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/3.0/ | A key to effective teaching is an awareness and accurate understanding of the
thinking and implicit assumptions that students bring to the subject to be
learned. In the absence of extensive Socratic interactions with students, one
strategy to assess student thinking involves the use of concept inventories
(CIs). CIs ... | [
{
"created": "Mon, 20 Dec 2010 23:18:58 GMT",
"version": "v1"
}
] | 2010-12-22 | [
[
"Klymkowsky",
"Michael W.",
""
],
[
"Underwood",
"Sonia M.",
""
],
[
"Garvin-Doxas",
"R. Kathleen",
""
]
] | A key to effective teaching is an awareness and accurate understanding of the thinking and implicit assumptions that students bring to the subject to be learned. In the absence of extensive Socratic interactions with students, one strategy to assess student thinking involves the use of concept inventories (CIs). CIs ar... |
1812.11183 | Junhao Wen | Junhao Wen, Jorge Samper-Gonzalez, Simona Bottani, Alexandre Routier,
Ninon Burgos, Thomas Jacquemont, Sabrina Fontanella, Stanley Durrleman,
Stephane Epelbaum, Anne Bertrand, Olivier Colliot (for the Alzheimers Disease
Neuroimaging Initiative) | Reproducible evaluation of diffusion MRI features for automatic
classification of patients with Alzheimers disease | 51 pages, 5 figure and 6 tables | null | null | null | q-bio.QM cs.LG eess.IV stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Diffusion MRI is the modality of choice to study alterations of white matter.
In past years, various works have used diffusion MRI for automatic
classification of AD. However, classification performance obtained with
different approaches is difficult to compare and these studies are also
difficult to reproduce. In th... | [
{
"created": "Fri, 28 Dec 2018 17:11:28 GMT",
"version": "v1"
},
{
"created": "Tue, 24 Mar 2020 14:20:37 GMT",
"version": "v2"
},
{
"created": "Wed, 25 Mar 2020 00:36:19 GMT",
"version": "v3"
},
{
"created": "Thu, 11 Jun 2020 15:07:45 GMT",
"version": "v4"
}
] | 2020-06-12 | [
[
"Wen",
"Junhao",
"",
"for the Alzheimers Disease\n Neuroimaging Initiative"
],
[
"Samper-Gonzalez",
"Jorge",
"",
"for the Alzheimers Disease\n Neuroimaging Initiative"
],
[
"Bottani",
"Simona",
"",
"for the Alzheimers Disease\n Neuroimaging Initiative"
... | Diffusion MRI is the modality of choice to study alterations of white matter. In past years, various works have used diffusion MRI for automatic classification of AD. However, classification performance obtained with different approaches is difficult to compare and these studies are also difficult to reproduce. In the ... |
2201.10895 | Hirokuni Miyamoto | Hirokuni Miyamoto, Wataru Suda, Hiroaki Kodama, Hideyuki Takahashi,
Yumiko Nakanishi, Shigeharu Moriya, Kana Adachi, Nao Kiriyama, Masaya Wada,
Daisuke Sudo, Shunsuke Ito, Shunsuke Ito, Minami Shibata, Shinji Wada, Takako
Murano, Hitoshi Taguchi, Chie Shindo, Arisa Tsuboi, Naoko Tsuji, Makiko
Matsuura, Chitose ... | A novel sustainable role of compost as a universal protective substitute
for fish, chicken, pig, and cattle, and its estimation by structural equation
modeling | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Natural decomposition of organic matter is essential in food systems, and
compost is used worldwide as an organic fermented fertilizer. However, as a
feature of the ecosystem, its effects on the animals are poorly understood.
Here we show that oral administration of compost and/or its derived
thermophilic Bacillaceae... | [
{
"created": "Wed, 26 Jan 2022 12:19:50 GMT",
"version": "v1"
},
{
"created": "Fri, 28 Jan 2022 21:29:16 GMT",
"version": "v2"
},
{
"created": "Tue, 1 Mar 2022 22:53:17 GMT",
"version": "v3"
},
{
"created": "Sun, 27 Nov 2022 05:45:18 GMT",
"version": "v4"
}
] | 2022-11-29 | [
[
"Miyamoto",
"Hirokuni",
""
],
[
"Suda",
"Wataru",
""
],
[
"Kodama",
"Hiroaki",
""
],
[
"Takahashi",
"Hideyuki",
""
],
[
"Nakanishi",
"Yumiko",
""
],
[
"Moriya",
"Shigeharu",
""
],
[
"Adachi",
"Kana",
""
]... | Natural decomposition of organic matter is essential in food systems, and compost is used worldwide as an organic fermented fertilizer. However, as a feature of the ecosystem, its effects on the animals are poorly understood. Here we show that oral administration of compost and/or its derived thermophilic Bacillaceae, ... |
1508.07866 | Lee Altenberg Ph.D. | Lee Altenberg | Fundamental Properties of the Evolution of Mutational Robustness | 17 pages, 1 figure | null | null | null | q-bio.PE math.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Evolution on neutral networks of genotypes has been found in models to
concentrate on genotypes with high mutational robustness, to a degree
determined by the topology of the network. Here analysis is generalized beyond
neutral networks to arbitrary selection and parent-offspring transmission. In
this larger realm, g... | [
{
"created": "Mon, 31 Aug 2015 15:22:31 GMT",
"version": "v1"
}
] | 2015-09-01 | [
[
"Altenberg",
"Lee",
""
]
] | Evolution on neutral networks of genotypes has been found in models to concentrate on genotypes with high mutational robustness, to a degree determined by the topology of the network. Here analysis is generalized beyond neutral networks to arbitrary selection and parent-offspring transmission. In this larger realm, geo... |
1612.06921 | Kim Whoriskey | Kim Whoriskey, Marie Auger-M\'eth\'e, Christoffer Moesgaard Albertsen,
Frederick G. Whoriskey, Thomas R. Binder, Charles C. Krueger, and Joanna
Mills Flemming | A Hidden Markov Movement Model for rapidly identifying behavioral states
from animal tracks | 30 pages, 4 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | 1. Electronic telemetry is frequently used to document animal movement
through time. Methods that can identify underlying behaviors driving specific
movement patterns can help us understand how and why animals use available
space, thereby aiding conservation and management efforts. For aquatic animal
tracking data wi... | [
{
"created": "Tue, 20 Dec 2016 23:33:04 GMT",
"version": "v1"
}
] | 2016-12-22 | [
[
"Whoriskey",
"Kim",
""
],
[
"Auger-Méthé",
"Marie",
""
],
[
"Albertsen",
"Christoffer Moesgaard",
""
],
[
"Whoriskey",
"Frederick G.",
""
],
[
"Binder",
"Thomas R.",
""
],
[
"Krueger",
"Charles C.",
""
],
[
"Flemmi... | 1. Electronic telemetry is frequently used to document animal movement through time. Methods that can identify underlying behaviors driving specific movement patterns can help us understand how and why animals use available space, thereby aiding conservation and management efforts. For aquatic animal tracking data with... |
2002.10849 | Su-Chan Park | Su-Chan Park, Sungmin Hwang, Joachim Krug | Distribution of the number of fitness maxima in Fisher's Geometric Model | 36 pages, 5 figures. Minor corrections | J. Phys. A: Math. Theor. 53, 385601 (2020) | 10.1088/1751-8121/ab9780 | null | q-bio.PE cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fisher's geometric model describes biological fitness landscapes by combining
a linear map from the discrete space of genotypes to an $n$-dimensional
Euclidean phenotype space with a nonlinear, single-peaked phenotype-fitness
map. Genotypes are represented by binary sequences of length $L$, and the
phenotypic effects... | [
{
"created": "Tue, 25 Feb 2020 13:25:38 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Aug 2020 00:48:48 GMT",
"version": "v2"
}
] | 2020-08-28 | [
[
"Park",
"Su-Chan",
""
],
[
"Hwang",
"Sungmin",
""
],
[
"Krug",
"Joachim",
""
]
] | Fisher's geometric model describes biological fitness landscapes by combining a linear map from the discrete space of genotypes to an $n$-dimensional Euclidean phenotype space with a nonlinear, single-peaked phenotype-fitness map. Genotypes are represented by binary sequences of length $L$, and the phenotypic effects o... |
1305.3043 | Benjamin Werner | B. Werner, D. Dingli, A. Traulsen | A deterministic model for the occurrence and dynamics of multiple
mutations in hierarchically organized tissues | 4 figures, to appear in Royal Society Interface | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/3.0/ | We model a general, hierarchically organized tissue by a multi compartment
approach, allowing any number of mutations within a cell. We derive closed
solutions for the deterministic clonal dynamics and the reproductive capacity
of single clones. Our results hold for the average dynamics in a hierarchical
tissue chara... | [
{
"created": "Tue, 14 May 2013 07:20:35 GMT",
"version": "v1"
}
] | 2013-05-15 | [
[
"Werner",
"B.",
""
],
[
"Dingli",
"D.",
""
],
[
"Traulsen",
"A.",
""
]
] | We model a general, hierarchically organized tissue by a multi compartment approach, allowing any number of mutations within a cell. We derive closed solutions for the deterministic clonal dynamics and the reproductive capacity of single clones. Our results hold for the average dynamics in a hierarchical tissue charact... |
0809.1549 | Mark McDonnell | Alexander P. Nikitin, Nigel G. Stocks, Robert P. Morse and Mark D.
McDonnell | Neural Population Coding is Optimized by Discrete Tuning Curves | 7 pages total, including 2 figures, published by Physical Review
Letters | Physical Review Letters 103, 138101, 2009 | 10.1103/PhysRevLett.103.138101 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The sigmoidal tuning curve that maximizes the mutual information for a
Poisson neuron, or population of Poisson neurons, is obtained. The optimal
tuning curve is found to have a discrete structure that results in a
quantization of the input signal. The number of quantization levels undergoes a
hierarchy of phase tran... | [
{
"created": "Tue, 9 Sep 2008 13:02:48 GMT",
"version": "v1"
},
{
"created": "Thu, 24 Sep 2009 07:20:33 GMT",
"version": "v2"
}
] | 2009-09-24 | [
[
"Nikitin",
"Alexander P.",
""
],
[
"Stocks",
"Nigel G.",
""
],
[
"Morse",
"Robert P.",
""
],
[
"McDonnell",
"Mark D.",
""
]
] | The sigmoidal tuning curve that maximizes the mutual information for a Poisson neuron, or population of Poisson neurons, is obtained. The optimal tuning curve is found to have a discrete structure that results in a quantization of the input signal. The number of quantization levels undergoes a hierarchy of phase transi... |
1404.1061 | Jakub Otwinowski | Jakub Otwinowski, Joshua B. Plotkin | Inferring fitness landscapes by regression produces biased estimates of
epistasis | null | Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2301-9 | 10.1073/pnas.1400849111 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The genotype-fitness map plays a fundamental role in shaping the dynamics of
evolution. However, it is difficult to directly measure a fitness landscape in
practice, because the number of possible genotypes is astronomical. One
approach is to sample as many genotypes as possible, measure their fitnesses,
and fit a st... | [
{
"created": "Thu, 3 Apr 2014 19:42:55 GMT",
"version": "v1"
}
] | 2014-11-11 | [
[
"Otwinowski",
"Jakub",
""
],
[
"Plotkin",
"Joshua B.",
""
]
] | The genotype-fitness map plays a fundamental role in shaping the dynamics of evolution. However, it is difficult to directly measure a fitness landscape in practice, because the number of possible genotypes is astronomical. One approach is to sample as many genotypes as possible, measure their fitnesses, and fit a stat... |
1712.04386 | Amrita Gupta | Amrita Gupta, Mehrdad Farajtabar, Bistra Dilkina and Hongyuan Zha | Hawkes Processes for Invasive Species Modeling and Management | null | null | null | null | q-bio.PE cs.AI cs.CE cs.SI physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The spread of invasive species to new areas threatens the stability of
ecosystems and causes major economic losses in agriculture and forestry. We
propose a novel approach to minimizing the spread of an invasive species given
a limited intervention budget. We first model invasive species propagation
using Hawkes proc... | [
{
"created": "Tue, 12 Dec 2017 16:54:27 GMT",
"version": "v1"
}
] | 2017-12-13 | [
[
"Gupta",
"Amrita",
""
],
[
"Farajtabar",
"Mehrdad",
""
],
[
"Dilkina",
"Bistra",
""
],
[
"Zha",
"Hongyuan",
""
]
] | The spread of invasive species to new areas threatens the stability of ecosystems and causes major economic losses in agriculture and forestry. We propose a novel approach to minimizing the spread of an invasive species given a limited intervention budget. We first model invasive species propagation using Hawkes proces... |
q-bio/0507037 | Gabriele Scheler | Gabriele Scheler | Neuromodulation Influences Synchronization and Intrinsic Read-out | 14 pages, 12 figures | F1000Research 2018, 7:1277 | 10.12688/f1000research.15804.2 | null | q-bio.NC cs.NE nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: The roles of neuromodulation in a neural network, such as in a
cortical microcolumn, are still incompletely understood. Neuromodulation
influences neural processing by presynaptic and postsynaptic regulation of
synaptic efficacy. Neuromodulation also affects ion channels and intrinsic
excitability. Method... | [
{
"created": "Mon, 25 Jul 2005 21:01:32 GMT",
"version": "v1"
},
{
"created": "Thu, 25 Aug 2016 19:18:16 GMT",
"version": "v2"
},
{
"created": "Tue, 23 Jan 2018 20:29:57 GMT",
"version": "v3"
},
{
"created": "Sat, 22 Jun 2019 21:14:07 GMT",
"version": "v4"
}
] | 2019-06-25 | [
[
"Scheler",
"Gabriele",
""
]
] | Background: The roles of neuromodulation in a neural network, such as in a cortical microcolumn, are still incompletely understood. Neuromodulation influences neural processing by presynaptic and postsynaptic regulation of synaptic efficacy. Neuromodulation also affects ion channels and intrinsic excitability. Methods:... |
0908.3268 | Alain Destexhe | Claude Bedard, Serafim Rodrigues, Noah Roy, Diego Contreras and Alain
Destexhe | Evidence for frequency-dependent extracellular impedance from the
transfer function between extracellular and intracellular potentials | Journal of Computational Neuroscience (revised, May 2010) | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We examine the properties of the transfer function F_T = V_m / V_{LFP}
between the intracellular membrane potential (V_m) and the local field
potential (V_{LFP}) in cerebral cortex. We first show theoretically that, in
the subthreshold regime, the frequency dependence of the extracellular medium
and that of the membr... | [
{
"created": "Sat, 22 Aug 2009 17:28:44 GMT",
"version": "v1"
},
{
"created": "Fri, 13 Nov 2009 17:41:27 GMT",
"version": "v2"
},
{
"created": "Sun, 7 Mar 2010 17:48:41 GMT",
"version": "v3"
},
{
"created": "Mon, 26 Apr 2010 16:26:06 GMT",
"version": "v4"
},
{
"cr... | 2015-03-13 | [
[
"Bedard",
"Claude",
""
],
[
"Rodrigues",
"Serafim",
""
],
[
"Roy",
"Noah",
""
],
[
"Contreras",
"Diego",
""
],
[
"Destexhe",
"Alain",
""
]
] | We examine the properties of the transfer function F_T = V_m / V_{LFP} between the intracellular membrane potential (V_m) and the local field potential (V_{LFP}) in cerebral cortex. We first show theoretically that, in the subthreshold regime, the frequency dependence of the extracellular medium and that of the membran... |
1705.02529 | David Holcman | Uli Dobramysl and David Holcman | Reconstructing the gradient source position from steady-state fluxes to
small receptors | 5 pages, revision in PRL 2017 | null | null | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recovering the position of a source from the fluxes of diffusing particles
through small receptors allows a biological cell to determine its relative
position, spatial localization and guide it to a final target. However, how a
source can be recovered from point fluxes remains unclear. Using the Narrow
Escape Time ap... | [
{
"created": "Sat, 6 May 2017 20:53:51 GMT",
"version": "v1"
}
] | 2017-05-09 | [
[
"Dobramysl",
"Uli",
""
],
[
"Holcman",
"David",
""
]
] | Recovering the position of a source from the fluxes of diffusing particles through small receptors allows a biological cell to determine its relative position, spatial localization and guide it to a final target. However, how a source can be recovered from point fluxes remains unclear. Using the Narrow Escape Time appr... |
2204.00405 | Alexandre Souto Martinez PhD | Newton La Scala Jr. and Alexandre Souto Martinez and Kurt Arnold
Spokas and Daniel Ruiz Potma Gon\c{c}alves and Rafael Mazer Etto | Should alterations in water viscosity be addressed in soil carbon
models? | 15 pages and 3 figures | null | null | null | q-bio.QM physics.geo-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Despite all the efforts, there is no agreement on how temperature affects
soil carbon decay and consequently soil CO2 emission, due to overlapping of
environmental constraints. To gain further insight into the driving forces of
soil microbial processes, we herein examine the abiotic physical environment
and its poten... | [
{
"created": "Fri, 1 Apr 2022 13:07:10 GMT",
"version": "v1"
}
] | 2022-04-04 | [
[
"Scala",
"Newton La",
"Jr."
],
[
"Martinez",
"Alexandre Souto",
""
],
[
"Spokas",
"Kurt Arnold",
""
],
[
"Gonçalves",
"Daniel Ruiz Potma",
""
],
[
"Etto",
"Rafael Mazer",
""
]
] | Despite all the efforts, there is no agreement on how temperature affects soil carbon decay and consequently soil CO2 emission, due to overlapping of environmental constraints. To gain further insight into the driving forces of soil microbial processes, we herein examine the abiotic physical environment and its potenti... |
2111.03739 | Haohan Wang | Haohan Wang, Bryon Aragam, Eric Xing | Tradeoffs of Linear Mixed Models in Genome-wide Association Studies | in final revision of Journal of Computational Biology | null | null | null | q-bio.QM cs.LG q-bio.PE stat.ME | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Motivated by empirical arguments that are well-known from the genome-wide
association studies (GWAS) literature, we study the statistical properties of
linear mixed models (LMMs) applied to GWAS. First, we study the sensitivity of
LMMs to the inclusion of a candidate SNP in the kinship matrix, which is often
done in ... | [
{
"created": "Fri, 5 Nov 2021 22:05:59 GMT",
"version": "v1"
}
] | 2021-11-09 | [
[
"Wang",
"Haohan",
""
],
[
"Aragam",
"Bryon",
""
],
[
"Xing",
"Eric",
""
]
] | Motivated by empirical arguments that are well-known from the genome-wide association studies (GWAS) literature, we study the statistical properties of linear mixed models (LMMs) applied to GWAS. First, we study the sensitivity of LMMs to the inclusion of a candidate SNP in the kinship matrix, which is often done in pr... |
2011.10449 | Vincent Huin | Vincent Huin (JPArc), Isabelle Strubi-Vuillaume, Kathy Dujardin
(TCDV), Marine Brion, Marie Delliaux, Delphine Dellacherie, Jean-Christophe
Cuvellier, Jean-Marie Cuisset, Audrey Riquet, Caroline Moreau (TCDV), Luc
Defebvre (TCDV), Bernard Sablonniere (JPArc), David Devos (TCDV) | Expanding the phenotype of SCA19/22: Parkinsonism, cognitive impairment
and epilepsy | null | Parkinsonism and Related Disorders, Elsevier, 45, pp.85-89 (2017) | 10.1016/j.parkreldis.2017.09.014 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | BACKGROUND: Spinocerebellar ataxia types 19 and 22 (SCA19/22) are rare
conditions in which relatively isolated cerebellar involvement is frequently
associated with cognitive impairment. Here, we report on new clinical features
and provide details of the cognitive profile in two SCA19/22 families.METHODS:
Two families... | [
{
"created": "Fri, 20 Nov 2020 15:23:50 GMT",
"version": "v1"
}
] | 2020-11-23 | [
[
"Huin",
"Vincent",
"",
"JPArc"
],
[
"Strubi-Vuillaume",
"Isabelle",
"",
"TCDV"
],
[
"Dujardin",
"Kathy",
"",
"TCDV"
],
[
"Brion",
"Marine",
"",
"TCDV"
],
[
"Delliaux",
"Marie",
"",
"TCDV"
],
[
"Dellacherie",
... | BACKGROUND: Spinocerebellar ataxia types 19 and 22 (SCA19/22) are rare conditions in which relatively isolated cerebellar involvement is frequently associated with cognitive impairment. Here, we report on new clinical features and provide details of the cognitive profile in two SCA19/22 families.METHODS: Two families d... |
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