id stringlengths 9 13 | submitter stringlengths 4 48 | authors stringlengths 4 9.62k | title stringlengths 4 343 | comments stringlengths 2 480 ⌀ | journal-ref stringlengths 9 309 ⌀ | doi stringlengths 12 138 ⌀ | report-no stringclasses 277
values | categories stringlengths 8 87 | license stringclasses 9
values | orig_abstract stringlengths 27 3.76k | versions listlengths 1 15 | update_date stringlengths 10 10 | authors_parsed listlengths 1 147 | abstract stringlengths 24 3.75k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2405.06729 | Aleix Lafita | Aleix Lafita, Ferran Gonzalez, Mahmoud Hossam, Paul Smyth, Jacob
Deasy, Ari Allyn-Feuer, Daniel Seaton, Stephen Young | Fine-tuning Protein Language Models with Deep Mutational Scanning
improves Variant Effect Prediction | Machine Learning for Genomics Explorations workshop at ICLR 2024 | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by/4.0/ | Protein Language Models (PLMs) have emerged as performant and scalable tools
for predicting the functional impact and clinical significance of
protein-coding variants, but they still lag experimental accuracy. Here, we
present a novel fine-tuning approach to improve the performance of PLMs with
experimental maps of v... | [
{
"created": "Fri, 10 May 2024 14:50:40 GMT",
"version": "v1"
}
] | 2024-05-14 | [
[
"Lafita",
"Aleix",
""
],
[
"Gonzalez",
"Ferran",
""
],
[
"Hossam",
"Mahmoud",
""
],
[
"Smyth",
"Paul",
""
],
[
"Deasy",
"Jacob",
""
],
[
"Allyn-Feuer",
"Ari",
""
],
[
"Seaton",
"Daniel",
""
],
[
"Yo... | Protein Language Models (PLMs) have emerged as performant and scalable tools for predicting the functional impact and clinical significance of protein-coding variants, but they still lag experimental accuracy. Here, we present a novel fine-tuning approach to improve the performance of PLMs with experimental maps of var... |
2111.06920 | Johannes Friedrich | Johannes Friedrich, Siavash Golkar, Shiva Farashahi, Alexander Genkin,
Anirvan M. Sengupta, Dmitri B. Chklovskii | Neural optimal feedback control with local learning rules | Manuscript and supplementary material of NeurIPS 2021 paper | null | null | null | q-bio.NC cs.NE cs.SY eess.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A major problem in motor control is understanding how the brain plans and
executes proper movements in the face of delayed and noisy stimuli. A prominent
framework for addressing such control problems is Optimal Feedback Control
(OFC). OFC generates control actions that optimize behaviorally relevant
criteria by inte... | [
{
"created": "Fri, 12 Nov 2021 20:02:00 GMT",
"version": "v1"
}
] | 2021-11-16 | [
[
"Friedrich",
"Johannes",
""
],
[
"Golkar",
"Siavash",
""
],
[
"Farashahi",
"Shiva",
""
],
[
"Genkin",
"Alexander",
""
],
[
"Sengupta",
"Anirvan M.",
""
],
[
"Chklovskii",
"Dmitri B.",
""
]
] | A major problem in motor control is understanding how the brain plans and executes proper movements in the face of delayed and noisy stimuli. A prominent framework for addressing such control problems is Optimal Feedback Control (OFC). OFC generates control actions that optimize behaviorally relevant criteria by integr... |
0908.3170 | Ferm\'in Moscoso del Prado PhD | Ferm\'in Moscoso del Prado Mart\'in | The thermodynamics of human reaction times | Submitted manuscript | null | null | null | q-bio.NC cond-mat.dis-nn cond-mat.stat-mech cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | I present a new approach for the interpretation of reaction time (RT) data
from behavioral experiments. From a physical perspective, the entropy of the RT
distribution provides a model-free estimate of the amount of processing
performed by the cognitive system. In this way, the focus is shifted from the
conventional ... | [
{
"created": "Fri, 21 Aug 2009 17:00:12 GMT",
"version": "v1"
}
] | 2009-08-24 | [
[
"Martín",
"Fermín Moscoso del Prado",
""
]
] | I present a new approach for the interpretation of reaction time (RT) data from behavioral experiments. From a physical perspective, the entropy of the RT distribution provides a model-free estimate of the amount of processing performed by the cognitive system. In this way, the focus is shifted from the conventional in... |
2311.09312 | Gian Marco Visani | Gian Marco Visani, William Galvin, Michael Neal Pun, Armita
Nourmohammad | H-Packer: Holographic Rotationally Equivariant Convolutional Neural
Network for Protein Side-Chain Packing | Accepted as a conference paper at MLCB 2023. 8 pages main body, 20
pages with appendix. 10 figures | null | null | null | q-bio.BM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Accurately modeling protein 3D structure is essential for the design of
functional proteins. An important sub-task of structure modeling is protein
side-chain packing: predicting the conformation of side-chains (rotamers) given
the protein's backbone structure and amino-acid sequence. Conventional
approaches for this... | [
{
"created": "Wed, 15 Nov 2023 19:12:47 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Nov 2023 18:31:07 GMT",
"version": "v2"
}
] | 2023-11-29 | [
[
"Visani",
"Gian Marco",
""
],
[
"Galvin",
"William",
""
],
[
"Pun",
"Michael Neal",
""
],
[
"Nourmohammad",
"Armita",
""
]
] | Accurately modeling protein 3D structure is essential for the design of functional proteins. An important sub-task of structure modeling is protein side-chain packing: predicting the conformation of side-chains (rotamers) given the protein's backbone structure and amino-acid sequence. Conventional approaches for this t... |
0808.3853 | Alain Destexhe | Claude Bedard and Alain Destexhe | Macroscopic models of local field potentials and the apparent 1/f noise
in brain activity | null | Biophysical Journal 96: 2589-2603, 2009. | 10.1016/j.bpj.2008.12.3951 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The power spectrum of local field potentials (LFPs) has been reported to
scale as the inverse of the frequency, but the origin of this "1/f noise" is at
present unclear. Macroscopic measurements in cortical tissue demonstrated that
electric conductivity (as well as permittivity) is frequency dependent, while
other me... | [
{
"created": "Thu, 28 Aug 2008 09:12:40 GMT",
"version": "v1"
},
{
"created": "Mon, 22 Dec 2008 09:53:56 GMT",
"version": "v2"
}
] | 2009-11-13 | [
[
"Bedard",
"Claude",
""
],
[
"Destexhe",
"Alain",
""
]
] | The power spectrum of local field potentials (LFPs) has been reported to scale as the inverse of the frequency, but the origin of this "1/f noise" is at present unclear. Macroscopic measurements in cortical tissue demonstrated that electric conductivity (as well as permittivity) is frequency dependent, while other meas... |
2111.04293 | Shubhadeep Sadhukhan | Shubhadeep Sadhukhan, Ashutosh Shukla, Sagar Chakraborty | Subduing always defecting mutants by multiplayer reactive strategies:
Non-reciprocity versus generosity | 10 pages, 5 figures | null | null | null | q-bio.PE nlin.AO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A completely non-generous and reciprocal population of players can create a
robust cooperating state that cannot be invaded by always defecting free riders
if the interactions among players are repeated for long enough. However, strict
non-generosity and strict reciprocity are ideal concepts, and may not even be
desi... | [
{
"created": "Mon, 8 Nov 2021 06:34:36 GMT",
"version": "v1"
}
] | 2021-11-09 | [
[
"Sadhukhan",
"Shubhadeep",
""
],
[
"Shukla",
"Ashutosh",
""
],
[
"Chakraborty",
"Sagar",
""
]
] | A completely non-generous and reciprocal population of players can create a robust cooperating state that cannot be invaded by always defecting free riders if the interactions among players are repeated for long enough. However, strict non-generosity and strict reciprocity are ideal concepts, and may not even be desira... |
1505.05816 | Peter Ralph | Peter L. Ralph | An empirical approach to demographic inference with genomic data | null | null | null | null | q-bio.PE math.PR stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inference with population genetic data usually treats the population pedigree
as a nuisance parameter, the unobserved product of a past history of random
mating. However, the history of genetic relationships in a given population is
a fixed, unobserved object, and so an alternative approach is to treat this
network o... | [
{
"created": "Thu, 21 May 2015 18:13:54 GMT",
"version": "v1"
},
{
"created": "Wed, 11 Jul 2018 23:12:10 GMT",
"version": "v2"
},
{
"created": "Mon, 1 Apr 2019 17:05:36 GMT",
"version": "v3"
}
] | 2019-04-02 | [
[
"Ralph",
"Peter L.",
""
]
] | Inference with population genetic data usually treats the population pedigree as a nuisance parameter, the unobserved product of a past history of random mating. However, the history of genetic relationships in a given population is a fixed, unobserved object, and so an alternative approach is to treat this network of ... |
2401.09857 | Agnieszka Pregowska | Zofia Rudnicka, Janusz Szczepanski, Agnieszka Pregowska | Artificial Intelligence-based algorithms in medical image scan
seg-mentation and intelligent visual-content generation -- a concise overview | null | https://www.mdpi.com/2079-9292/13/4/746 | 10.3390/electronics13040746 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, Artificial Intelligence (AI)-based algorithms have revolutionized
the medical image segmentation processes. Thus, the precise segmentation of
organs and their lesions may contribute to an efficient diagnostics process and
a more effective selection of targeted therapies as well as increasing the
effectivene... | [
{
"created": "Thu, 18 Jan 2024 10:12:50 GMT",
"version": "v1"
}
] | 2024-03-21 | [
[
"Rudnicka",
"Zofia",
""
],
[
"Szczepanski",
"Janusz",
""
],
[
"Pregowska",
"Agnieszka",
""
]
] | Recently, Artificial Intelligence (AI)-based algorithms have revolutionized the medical image segmentation processes. Thus, the precise segmentation of organs and their lesions may contribute to an efficient diagnostics process and a more effective selection of targeted therapies as well as increasing the effectiveness... |
1601.04253 | Yuri A. Dabaghian | Kentaro Hoffman, Andrey Babichev and Yuri Dabaghian | Topological mapping of space in bat hippocampus | 14 pages, 4 figures, 3 supplementary figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mammalian hippocampus plays a key role in spatial learning and memory, but
the exact nature of the hippocampal representation of space is still being
explored. Recently, there has been a fair amount of success in modeling
hippocampal spatial maps in rats, assuming a topological perspective on spatial
information proc... | [
{
"created": "Sun, 17 Jan 2016 05:56:02 GMT",
"version": "v1"
}
] | 2016-01-19 | [
[
"Hoffman",
"Kentaro",
""
],
[
"Babichev",
"Andrey",
""
],
[
"Dabaghian",
"Yuri",
""
]
] | Mammalian hippocampus plays a key role in spatial learning and memory, but the exact nature of the hippocampal representation of space is still being explored. Recently, there has been a fair amount of success in modeling hippocampal spatial maps in rats, assuming a topological perspective on spatial information proces... |
1507.02812 | Jianxi Luo | Jianxi Luo | Loops and autonomy promote evolvability of ecosystem networks | null | Scientific Reports 4, 6440 (2014) | 10.1038/srep06440 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The structure of ecological networks, in particular food webs, determines
their ability to evolve further, i.e. evolvability. The knowledge about how
food web evolvability is determined by the structures of diverse ecological
networks can guide human interventions purposefully to either promote or limit
evolvability ... | [
{
"created": "Fri, 10 Jul 2015 09:09:48 GMT",
"version": "v1"
}
] | 2015-07-13 | [
[
"Luo",
"Jianxi",
""
]
] | The structure of ecological networks, in particular food webs, determines their ability to evolve further, i.e. evolvability. The knowledge about how food web evolvability is determined by the structures of diverse ecological networks can guide human interventions purposefully to either promote or limit evolvability of... |
2007.11911 | Manoj Kumar | Manoj Kumar, Syed Abbas | Age structured SIR model for the spread of infectious diseases through
indirect contacts | 14 pages, 3 figures | null | null | null | q-bio.PE math.DS physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this article, we discuss an age-structured SIR model in which disease not
only spread through direct person to person contacts for e.g. infection due to
surface contamination but it can also spread through indirect contacts. It is
evident that age also plays a crucial role in SARS virus infection including
COVID-1... | [
{
"created": "Thu, 23 Jul 2020 10:35:08 GMT",
"version": "v1"
}
] | 2020-07-24 | [
[
"Kumar",
"Manoj",
""
],
[
"Abbas",
"Syed",
""
]
] | In this article, we discuss an age-structured SIR model in which disease not only spread through direct person to person contacts for e.g. infection due to surface contamination but it can also spread through indirect contacts. It is evident that age also plays a crucial role in SARS virus infection including COVID-19 ... |
2005.12441 | Eve Armstrong | Eve Armstrong, Manuela Runge, Jaline Gerardin | Identifying the measurements required to estimate rates of COVID-19
transmission, infection, and detection, using variational data assimilation | 9 pages, 7 figures | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We demonstrate the ability of statistical data assimilation to identify the
measurements required for accurate state and parameter estimation in an
epidemiological model for the novel coronavirus disease COVID-19. Our context
is an effort to inform policy regarding social behavior, to mitigate strain on
hospital capa... | [
{
"created": "Mon, 25 May 2020 23:29:26 GMT",
"version": "v1"
},
{
"created": "Fri, 31 Jul 2020 18:17:40 GMT",
"version": "v2"
}
] | 2020-08-04 | [
[
"Armstrong",
"Eve",
""
],
[
"Runge",
"Manuela",
""
],
[
"Gerardin",
"Jaline",
""
]
] | We demonstrate the ability of statistical data assimilation to identify the measurements required for accurate state and parameter estimation in an epidemiological model for the novel coronavirus disease COVID-19. Our context is an effort to inform policy regarding social behavior, to mitigate strain on hospital capaci... |
2211.14169 | Tim Dockhorn | Karsten Kreis, Tim Dockhorn, Zihao Li, Ellen Zhong | Latent Space Diffusion Models of Cryo-EM Structures | Machine Learning for Structural Biology Workshop, NeurIPS 2022 (Oral) | null | null | null | q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cryo-electron microscopy (cryo-EM) is unique among tools in structural
biology in its ability to image large, dynamic protein complexes. Key to this
ability is image processing algorithms for heterogeneous cryo-EM
reconstruction, including recent deep learning-based approaches. The
state-of-the-art method cryoDRGN us... | [
{
"created": "Fri, 25 Nov 2022 15:17:10 GMT",
"version": "v1"
}
] | 2022-11-28 | [
[
"Kreis",
"Karsten",
""
],
[
"Dockhorn",
"Tim",
""
],
[
"Li",
"Zihao",
""
],
[
"Zhong",
"Ellen",
""
]
] | Cryo-electron microscopy (cryo-EM) is unique among tools in structural biology in its ability to image large, dynamic protein complexes. Key to this ability is image processing algorithms for heterogeneous cryo-EM reconstruction, including recent deep learning-based approaches. The state-of-the-art method cryoDRGN uses... |
1602.06404 | Da Zhou Dr. | Bin Wu, Shanjun Mao, Jiazeng Wang, Da Zhou | Control of epidemics via social partnership adjustment | 29 pages, 8 figures | Phys. Rev. E 94, 062314 (2016) | 10.1103/PhysRevE.94.062314 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Epidemic control is of great importance for human society. Adjusting
interacting partners is an effective individualized control strategy.
Intuitively, it is done either by shortening the interaction time between
susceptible and infected individuals or by increasing the opportunities for
contact between susceptible i... | [
{
"created": "Sat, 20 Feb 2016 13:03:20 GMT",
"version": "v1"
},
{
"created": "Tue, 29 Nov 2016 11:30:39 GMT",
"version": "v2"
},
{
"created": "Sat, 24 Dec 2016 07:05:37 GMT",
"version": "v3"
}
] | 2016-12-28 | [
[
"Wu",
"Bin",
""
],
[
"Mao",
"Shanjun",
""
],
[
"Wang",
"Jiazeng",
""
],
[
"Zhou",
"Da",
""
]
] | Epidemic control is of great importance for human society. Adjusting interacting partners is an effective individualized control strategy. Intuitively, it is done either by shortening the interaction time between susceptible and infected individuals or by increasing the opportunities for contact between susceptible ind... |
1808.01963 | Romain M. Yvinec | Mohammed Akli Ayoub, Romain Yvinec, Pascale Cr\'epieux and Anne Poupon | Computational modeling approaches in gonadotropin signaling | null | Theriogenology, 86(1):22-31 (2016) | 10.1016/j.theriogenology.2016.04.015 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Follicle-stimulating hormone (FSH) and luteinizing hormone (LH) play
essential roles in animal reproduction. They exert their function through
binding to their cognate receptors, which belong to the large family of G
protein-coupled receptors (GPCRs). This recognition at the plasma membrane
triggers a plethora of cel... | [
{
"created": "Tue, 31 Jul 2018 13:29:50 GMT",
"version": "v1"
}
] | 2018-08-07 | [
[
"Ayoub",
"Mohammed Akli",
""
],
[
"Yvinec",
"Romain",
""
],
[
"Crépieux",
"Pascale",
""
],
[
"Poupon",
"Anne",
""
]
] | Follicle-stimulating hormone (FSH) and luteinizing hormone (LH) play essential roles in animal reproduction. They exert their function through binding to their cognate receptors, which belong to the large family of G protein-coupled receptors (GPCRs). This recognition at the plasma membrane triggers a plethora of cellu... |
1104.2515 | Alain Barrat | L. Isella, M. Romano, A. Barrat, C. Cattuto, V. Colizza, W. Van den
Broeck, F. Gesualdo, E. Pandolfi, L. Rav\`a, C. Rizzo, A.E. Tozzi | Close encounters in a pediatric ward: measuring face-to-face proximity
and mixing patterns with wearable sensors | null | PLoS ONE 6(2): e17144 (2011) | 10.1371/journal.pone.0017144 | null | q-bio.QM cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nosocomial infections place a substantial burden on health care systems and
represent a major issue in current public health, requiring notable efforts for
its prevention. Understanding the dynamics of infection transmission in a
hospital setting is essential for tailoring interventions and predicting the
spread amon... | [
{
"created": "Wed, 13 Apr 2011 14:42:48 GMT",
"version": "v1"
}
] | 2011-04-14 | [
[
"Isella",
"L.",
""
],
[
"Romano",
"M.",
""
],
[
"Barrat",
"A.",
""
],
[
"Cattuto",
"C.",
""
],
[
"Colizza",
"V.",
""
],
[
"Broeck",
"W. Van den",
""
],
[
"Gesualdo",
"F.",
""
],
[
"Pandolfi",
"E... | Nosocomial infections place a substantial burden on health care systems and represent a major issue in current public health, requiring notable efforts for its prevention. Understanding the dynamics of infection transmission in a hospital setting is essential for tailoring interventions and predicting the spread among ... |
1912.02138 | Jes\'us Fern\'andez-S\'anchez | Marta Casanellas, Jes\'us Fern\'andez-S\'anchez, Marina
Garrote-L\'opez | Distance to the stochastic part of phylogenetic varieties | 33 pages; 11 figures; to appear in Journal of Symbolic Computation | null | 10.1016/j.jsc.2020.09.003 | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modelling the substitution of nucleotides along a phylogenetic tree is
usually done by a hidden Markov process. This allows to define a distribution
of characters at the leaves of the trees and one might be able to obtain
polynomial relationships among the probabilities of different characters. The
study of these pol... | [
{
"created": "Wed, 4 Dec 2019 17:41:11 GMT",
"version": "v1"
},
{
"created": "Fri, 9 Oct 2020 06:57:25 GMT",
"version": "v2"
}
] | 2020-10-12 | [
[
"Casanellas",
"Marta",
""
],
[
"Fernández-Sánchez",
"Jesús",
""
],
[
"Garrote-López",
"Marina",
""
]
] | Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial relationships among the probabilities of different characters. The study of these polyn... |
q-bio/0609051 | Dietrich Stauffer | Krzysztof Malarz and Dietrich Stauffer | Search for bottleneck effects in Penna ageing and Schulze language model | RevTeX4, 2 pages, 2 figures with 3 eps files | Adv. Complex Syst. 11 (2008) 165 | 10.1142/S0219525908001489 | null | q-bio.PE physics.soc-ph | null | No influence was seen when in two models with memory effects the populations
were drastically decreased after equilibrium was established, and then allowed
to increase again.
| [
{
"created": "Thu, 28 Sep 2006 13:37:03 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Sep 2006 20:42:16 GMT",
"version": "v2"
}
] | 2008-03-16 | [
[
"Malarz",
"Krzysztof",
""
],
[
"Stauffer",
"Dietrich",
""
]
] | No influence was seen when in two models with memory effects the populations were drastically decreased after equilibrium was established, and then allowed to increase again. |
1802.08683 | Henry Van Den Bedem | Dominik Budday, Sigrid Leyendecker and Henry van den Bedem | Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a
Spatial Hierarchy of Protein Motion | null | null | null | null | q-bio.BM cs.CG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Elastic network models (ENM) and constraint-based, topological rigidity
analysis are two distinct, coarse-grained approaches to study conformational
flexibility of macromolecules. In the two decades since their introduction,
both have contributed significantly to insights into protein molecular
mechanisms and functio... | [
{
"created": "Fri, 23 Feb 2018 06:08:13 GMT",
"version": "v1"
}
] | 2018-02-27 | [
[
"Budday",
"Dominik",
""
],
[
"Leyendecker",
"Sigrid",
""
],
[
"Bedem",
"Henry van den",
""
]
] | Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have contributed significantly to insights into protein molecular mechanisms and function.... |
1802.10451 | Julien Modolo | Julien Modolo, Mahmoud Hassan, Alexandre Legros | Reconstruction of brain networks involved in magnetophosphene perception
using dense electroencephalography | 6 pages, 1 figure | BioEM2018 conference proceedings | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Characterizing functional brain networks in humans during magnetophosphene
perception. Dense electroencephalography (EEG, 128 channels) was performed in
N=3 volunteers during high-level (50 mT) magnetic field (MF) exposure.
Functional brain networks were reconstructed, at the cortical level from scalp
recordings, usi... | [
{
"created": "Wed, 28 Feb 2018 14:52:07 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Mar 2018 08:39:41 GMT",
"version": "v2"
}
] | 2018-03-02 | [
[
"Modolo",
"Julien",
""
],
[
"Hassan",
"Mahmoud",
""
],
[
"Legros",
"Alexandre",
""
]
] | Characterizing functional brain networks in humans during magnetophosphene perception. Dense electroencephalography (EEG, 128 channels) was performed in N=3 volunteers during high-level (50 mT) magnetic field (MF) exposure. Functional brain networks were reconstructed, at the cortical level from scalp recordings, using... |
2204.12861 | Hendrik Richter | Hendrik Richter | Spectral dynamics of guided edge removals and identifying transient
amplifiers for death-Birth updating | null | null | null | null | q-bio.PE cs.SI math.CO | http://creativecommons.org/licenses/by/4.0/ | The paper deals with two interrelated topics, identifying transient
amplifiers in an iterative process and analyzing the process by its spectral
dynamics, which is the change in the graph spectra by edge manipulations.
Transient amplifiers are networks representing population structures which
shift the balance betwee... | [
{
"created": "Wed, 27 Apr 2022 11:50:12 GMT",
"version": "v1"
}
] | 2022-04-28 | [
[
"Richter",
"Hendrik",
""
]
] | The paper deals with two interrelated topics, identifying transient amplifiers in an iterative process and analyzing the process by its spectral dynamics, which is the change in the graph spectra by edge manipulations. Transient amplifiers are networks representing population structures which shift the balance between ... |
1709.07319 | Michael Hayashi | Michael A.L. Hayashi and Marisa C. Eisenberg | Changing Burial Practices Explain Temporal Trends in the 2014 Ebola
Outbreak | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: The 2014 Ebola outbreak in West Africa was the largest on record,
resulting in over 25,000 total infections and 15,000 total deaths. Mathematical
modeling can be used to investigate the mechanisms driving transmission during
this outbreak -- in particular, burial practices appear to have been major
source... | [
{
"created": "Wed, 20 Sep 2017 17:24:05 GMT",
"version": "v1"
}
] | 2017-09-22 | [
[
"Hayashi",
"Michael A. L.",
""
],
[
"Eisenberg",
"Marisa C.",
""
]
] | Background: The 2014 Ebola outbreak in West Africa was the largest on record, resulting in over 25,000 total infections and 15,000 total deaths. Mathematical modeling can be used to investigate the mechanisms driving transmission during this outbreak -- in particular, burial practices appear to have been major source o... |
2301.07171 | Kaichao Wu | Kaichao Wu, Beth Jelfs, Katrina Neville, John Q. Fang | fMRI-based Static and Dynamic Functional Connectivity Analysis for
Post-stroke Motor Dysfunction Patient: A Review | Review paper | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Functional magnetic resonance imaging (fMRI) has been widely utilized to
study the motor deficits and rehabilitation following stroke. In particular,
functional connectivity(FC) analyses with fMRI at rest can be employed to
reveal the neural connectivity rationale behind this post-stroke motor function
impairment and... | [
{
"created": "Thu, 15 Dec 2022 04:16:07 GMT",
"version": "v1"
}
] | 2023-01-19 | [
[
"Wu",
"Kaichao",
""
],
[
"Jelfs",
"Beth",
""
],
[
"Neville",
"Katrina",
""
],
[
"Fang",
"John Q.",
""
]
] | Functional magnetic resonance imaging (fMRI) has been widely utilized to study the motor deficits and rehabilitation following stroke. In particular, functional connectivity(FC) analyses with fMRI at rest can be employed to reveal the neural connectivity rationale behind this post-stroke motor function impairment and r... |
1901.07461 | Farshid Alambeigi | Mahsan Bakhtiarinejad, Farshid Alambeigi, Alireza Chamani, Mathias
Unberath, Harpal Khanuja, Mehran Armand | A Biomechanical Study on the Use of Curved Drilling Technique for
Treatment of Osteonecrosis of Femoral Head | Accepted for 2018 MICCAI Workshop on Computational Biomechanics for
Medicine XIII | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Osteonecrosis occurs due to the loss of blood supply to the bone, leading to
spontaneous death of the trabecular bone. Delayed treatment of the involved
patients results in collapse of the femoral head, which leads to a need for
total hip arthroplasty surgery. Core decompression, as the most popular
technique for tre... | [
{
"created": "Mon, 14 Jan 2019 05:15:35 GMT",
"version": "v1"
}
] | 2019-01-23 | [
[
"Bakhtiarinejad",
"Mahsan",
""
],
[
"Alambeigi",
"Farshid",
""
],
[
"Chamani",
"Alireza",
""
],
[
"Unberath",
"Mathias",
""
],
[
"Khanuja",
"Harpal",
""
],
[
"Armand",
"Mehran",
""
]
] | Osteonecrosis occurs due to the loss of blood supply to the bone, leading to spontaneous death of the trabecular bone. Delayed treatment of the involved patients results in collapse of the femoral head, which leads to a need for total hip arthroplasty surgery. Core decompression, as the most popular technique for treat... |
2311.00975 | William Poole | William Poole, Thomas E. Ouldridge, and Manoj Gopalkrishnan | Autonomous Learning of Generative Models with Chemical Reaction Network
Ensembles | null | null | null | null | q-bio.MN cs.ET cs.LG cs.NE cs.SY eess.SY physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Can a micron sized sack of interacting molecules autonomously learn an
internal model of a complex and fluctuating environment? We draw insights from
control theory, machine learning theory, chemical reaction network theory, and
statistical physics to develop a general architecture whereby a broad class of
chemical s... | [
{
"created": "Thu, 2 Nov 2023 03:46:23 GMT",
"version": "v1"
},
{
"created": "Mon, 6 Nov 2023 19:07:59 GMT",
"version": "v2"
}
] | 2023-11-08 | [
[
"Poole",
"William",
""
],
[
"Ouldridge",
"Thomas E.",
""
],
[
"Gopalkrishnan",
"Manoj",
""
]
] | Can a micron sized sack of interacting molecules autonomously learn an internal model of a complex and fluctuating environment? We draw insights from control theory, machine learning theory, chemical reaction network theory, and statistical physics to develop a general architecture whereby a broad class of chemical sys... |
2312.03773 | Li Pan | Haoyue Wang, Li Pan, Bo Yang, Junqiang Jiang and Wenbin Li | A multi-layer refined network model for the identification of essential
proteins | null | null | null | null | q-bio.MN cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The identification of essential proteins in protein-protein interaction
networks (PINs) can help to discover drug targets and prevent disease. In order
to improve the accuracy of the identification of essential proteins,
researchers attempted to obtain a refined PIN by combining multiple biological
information to fil... | [
{
"created": "Wed, 6 Dec 2023 00:11:08 GMT",
"version": "v1"
}
] | 2023-12-08 | [
[
"Wang",
"Haoyue",
""
],
[
"Pan",
"Li",
""
],
[
"Yang",
"Bo",
""
],
[
"Jiang",
"Junqiang",
""
],
[
"Li",
"Wenbin",
""
]
] | The identification of essential proteins in protein-protein interaction networks (PINs) can help to discover drug targets and prevent disease. In order to improve the accuracy of the identification of essential proteins, researchers attempted to obtain a refined PIN by combining multiple biological information to filte... |
2210.03745 | Dawid Rymarczyk | Dawid Rymarczyk, Daniel Dobrowolski, Tomasz Danel | ProGReST: Prototypical Graph Regression Soft Trees for Molecular
Property Prediction | Accepted to SDM2023 | null | null | null | q-bio.QM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | In this work, we propose the novel Prototypical Graph Regression
Self-explainable Trees (ProGReST) model, which combines prototype learning,
soft decision trees, and Graph Neural Networks. In contrast to other works, our
model can be used to address various challenging tasks, including compound
property prediction. I... | [
{
"created": "Fri, 7 Oct 2022 10:21:24 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Dec 2022 11:21:02 GMT",
"version": "v2"
}
] | 2022-12-29 | [
[
"Rymarczyk",
"Dawid",
""
],
[
"Dobrowolski",
"Daniel",
""
],
[
"Danel",
"Tomasz",
""
]
] | In this work, we propose the novel Prototypical Graph Regression Self-explainable Trees (ProGReST) model, which combines prototype learning, soft decision trees, and Graph Neural Networks. In contrast to other works, our model can be used to address various challenging tasks, including compound property prediction. In ... |
1311.1345 | Marc-Oliver Gewaltig | Marc-Oliver Gewaltig | Self-sustained activity, bursts, and variability in recurrent networks | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There is consensus in the current literature that stable states of
asynchronous irregular spiking activity require (i) large networks of 10 000 or
more neurons and (ii) external background activity or pacemaker neurons. Yet
already in 1963, Griffith showed that networks of simple threshold elements can
be persistentl... | [
{
"created": "Wed, 6 Nov 2013 10:58:04 GMT",
"version": "v1"
}
] | 2013-11-07 | [
[
"Gewaltig",
"Marc-Oliver",
""
]
] | There is consensus in the current literature that stable states of asynchronous irregular spiking activity require (i) large networks of 10 000 or more neurons and (ii) external background activity or pacemaker neurons. Yet already in 1963, Griffith showed that networks of simple threshold elements can be persistently ... |
q-bio/0702030 | Tristan Ursell | Tristan Ursell, Rob Phillips, Jane' Kondev, Dan Reeves, Paul A.
Wiggins | The Role of Lipid Bilayer Mechanics in Mechanosensation | 38 pages, 14 figures, 81 references, accepted for publication in
"Mechanosensitivity in Cells and Tissues", Springer (2007) | null | null | null | q-bio.SC q-bio.QM | null | Mechanosensation is a key part of the sensory repertoire of a vast array of
different cells and organisms. The molecular dissection of the origins of
mechanosensation is rapidly advancing as a result of both structural and
functional studies. One intriguing mode of mechanosensation results from
tension in the membran... | [
{
"created": "Tue, 13 Feb 2007 23:22:11 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Ursell",
"Tristan",
""
],
[
"Phillips",
"Rob",
""
],
[
"Kondev",
"Jane'",
""
],
[
"Reeves",
"Dan",
""
],
[
"Wiggins",
"Paul A.",
""
]
] | Mechanosensation is a key part of the sensory repertoire of a vast array of different cells and organisms. The molecular dissection of the origins of mechanosensation is rapidly advancing as a result of both structural and functional studies. One intriguing mode of mechanosensation results from tension in the membrane ... |
0805.1640 | Luciano da Fontoura Costa | Sebastian Ahnert and Luciano da Fontoura Costa | Connectivity and Dynamics of Neuronal Networks as Defined by the Shape
of Individual Neurons | 11 pages, 9 figures. A working manuscript | null | 10.1088/1367-2630/11/10/103053 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neuronal networks constitute a special class of dynamical systems, as they
are formed by individual geometrical components, namely the neurons. In the
existing literature, relatively little attention has been given to the
influence of neuron shape on the overall connectivity and dynamics of the
emerging networks. The... | [
{
"created": "Mon, 12 May 2008 14:02:45 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Ahnert",
"Sebastian",
""
],
[
"Costa",
"Luciano da Fontoura",
""
]
] | Neuronal networks constitute a special class of dynamical systems, as they are formed by individual geometrical components, namely the neurons. In the existing literature, relatively little attention has been given to the influence of neuron shape on the overall connectivity and dynamics of the emerging networks. The c... |
2102.08992 | Aubain Nzokem PhD | A. H. Nzokem | SIS Epidemic Model: Birth-and-Death Markov Chain Approach | 14 pages, 5 figures | International Journal of Statistics and Probability; Vol. 10, No.
4; July 2021 | 10.5539/ijsp.v10n4p10 | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We are interested in describing the infected size of the SIS Epidemic model
using Birth-Death Markov process. The Susceptible-Infected-Susceptible (SIS)
model is defined within a population of constant size $M$; the size is kept
constant by replacing each death with a newborn healthy individual. The life
span of each... | [
{
"created": "Wed, 17 Feb 2021 19:37:30 GMT",
"version": "v1"
}
] | 2021-06-01 | [
[
"Nzokem",
"A. H.",
""
]
] | We are interested in describing the infected size of the SIS Epidemic model using Birth-Death Markov process. The Susceptible-Infected-Susceptible (SIS) model is defined within a population of constant size $M$; the size is kept constant by replacing each death with a newborn healthy individual. The life span of each i... |
2407.11720 | Steven Kelk | M. Frohn, N. Holtgrefe, L. van Iersel, M. Jones, and S. Kelk | Invariants for level-1 phylogenetic networks under the random walk
4-state Markov model | Submitted to journal. 24 pages | null | null | null | q-bio.PE math.AG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic networks can represent evolutionary events that cannot be
described by phylogenetic trees, such as hybridization, introgression, and
lateral gene transfer. Studying phylogenetic networks under a statistical model
of DNA sequence evolution can aid the inference of phylogenetic networks. Most
notably Marko... | [
{
"created": "Tue, 16 Jul 2024 13:39:22 GMT",
"version": "v1"
}
] | 2024-07-17 | [
[
"Frohn",
"M.",
""
],
[
"Holtgrefe",
"N.",
""
],
[
"van Iersel",
"L.",
""
],
[
"Jones",
"M.",
""
],
[
"Kelk",
"S.",
""
]
] | Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees, such as hybridization, introgression, and lateral gene transfer. Studying phylogenetic networks under a statistical model of DNA sequence evolution can aid the inference of phylogenetic networks. Most notably Markov ... |
2111.08742 | Francisco J. Cao Garcia | Rodrigo Crespo-Miguel, Javier Jarillo, Francisco J. Cao-Garc\'ia | Scaling of population resilience with dispersal length and habitat size | 24 pages | null | 10.1088/1742-5468/ac4982 | null | q-bio.PE cond-mat.stat-mech | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Environmental fluctuations can create population-depleted areas and even
extinct areas for the population. This effect is more severe in the presence of
the Allee effect (decreasing growth rate at low population densities).
Dispersal inside the habitat provides a rescue effect on population-depleted
areas, enhancing ... | [
{
"created": "Tue, 16 Nov 2021 19:29:14 GMT",
"version": "v1"
}
] | 2022-02-23 | [
[
"Crespo-Miguel",
"Rodrigo",
""
],
[
"Jarillo",
"Javier",
""
],
[
"Cao-García",
"Francisco J.",
""
]
] | Environmental fluctuations can create population-depleted areas and even extinct areas for the population. This effect is more severe in the presence of the Allee effect (decreasing growth rate at low population densities). Dispersal inside the habitat provides a rescue effect on population-depleted areas, enhancing th... |
1306.5048 | Ben Nolting | Ben C. Nolting, Travis M. Hinkelman, Chad E. Brassil, Brigitte
Tenhumberg | Composite random search strategies based on non-directional sensory cues | null | null | 10.1016/j.ecocom.2015.03.002 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many foraging animals find food using composite random search strategies,
which consist of intensive and extensive search modes. Models of composite
search can generate predictions about how optimal foragers should behave in
each search mode, and how they should determine when to switch between search
modes. Most of ... | [
{
"created": "Fri, 21 Jun 2013 05:21:41 GMT",
"version": "v1"
},
{
"created": "Fri, 27 Feb 2015 21:16:16 GMT",
"version": "v2"
}
] | 2017-09-26 | [
[
"Nolting",
"Ben C.",
""
],
[
"Hinkelman",
"Travis M.",
""
],
[
"Brassil",
"Chad E.",
""
],
[
"Tenhumberg",
"Brigitte",
""
]
] | Many foraging animals find food using composite random search strategies, which consist of intensive and extensive search modes. Models of composite search can generate predictions about how optimal foragers should behave in each search mode, and how they should determine when to switch between search modes. Most of th... |
1806.10161 | Yarden Katz | Yarden Katz, Michael Springer, Walter Fontana | Embodying probabilistic inference in biochemical circuits | 11 figures | null | null | null | q-bio.MN q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Probabilistic inference provides a language for describing how organisms may
learn from and adapt to their environment. The computations needed to implement
probabilistic inference often require specific representations, akin to having
the suitable data structures for implementing certain algorithms in computer
progr... | [
{
"created": "Tue, 26 Jun 2018 18:28:30 GMT",
"version": "v1"
}
] | 2018-06-28 | [
[
"Katz",
"Yarden",
""
],
[
"Springer",
"Michael",
""
],
[
"Fontana",
"Walter",
""
]
] | Probabilistic inference provides a language for describing how organisms may learn from and adapt to their environment. The computations needed to implement probabilistic inference often require specific representations, akin to having the suitable data structures for implementing certain algorithms in computer program... |
1305.2249 | David Basanta | David Basanta and Alexander R. A. Anderson | Exploiting ecological principles to better understand cancer progression
and treatment | 6 figures, 1 example | null | null | null | q-bio.TO q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A small but growing number of people are finding interesting parallels
between ecosystems as studied by ecologists (think of a Savanna or the Amazon
rain forest or a Coral reef) and tumours1-3. The idea of viewing cancer from an
ecological perspective has many implications but fundamentally, it means that
we should n... | [
{
"created": "Fri, 10 May 2013 02:36:26 GMT",
"version": "v1"
}
] | 2013-05-13 | [
[
"Basanta",
"David",
""
],
[
"Anderson",
"Alexander R. A.",
""
]
] | A small but growing number of people are finding interesting parallels between ecosystems as studied by ecologists (think of a Savanna or the Amazon rain forest or a Coral reef) and tumours1-3. The idea of viewing cancer from an ecological perspective has many implications but fundamentally, it means that we should not... |
2406.00873 | Pedro Ballester | Qianrong Guo, Saiveth Hernandez-Hernandez, and Pedro J Ballester | Scaffold Splits Overestimate Virtual Screening Performance | null | null | null | null | q-bio.QM cs.AI cs.CE cs.LG q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Virtual Screening (VS) of vast compound libraries guided by Artificial
Intelligence (AI) models is a highly productive approach to early drug
discovery. Data splitting is crucial for better benchmarking of such AI models.
Traditional random data splits produce similar molecules between training and
test sets, conflic... | [
{
"created": "Sun, 2 Jun 2024 21:40:13 GMT",
"version": "v1"
},
{
"created": "Sun, 30 Jun 2024 12:12:23 GMT",
"version": "v2"
}
] | 2024-07-02 | [
[
"Guo",
"Qianrong",
""
],
[
"Hernandez-Hernandez",
"Saiveth",
""
],
[
"Ballester",
"Pedro J",
""
]
] | Virtual Screening (VS) of vast compound libraries guided by Artificial Intelligence (AI) models is a highly productive approach to early drug discovery. Data splitting is crucial for better benchmarking of such AI models. Traditional random data splits produce similar molecules between training and test sets, conflicti... |
2402.13260 | Gerardo F. Goya | Gerardo F. Goya, Vittoria Raffa | Magnetic Nanoparticles for Neural Engineering | 35 pages; 6 figures; Chapter 22 of Magnetic Nanoparticles: From
Fabrication to Clinical Applications | Thanh, Nguyen TK (ed.). Clinical applications of magnetic
nanoparticles: From Fabrication to Clinical Applications. CRC press, 2018 | 10.1201/b11760 | null | q-bio.NC physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Magnetic nanoparticles (MNPs) are the foundation of several new strategies
for neural repair and neurological therapies. The fact that a remote force can
act on MNPs at the cytoplasmic space constitutes the essence of many new
neurotherapeutic concepts. MNPs with a predesigned physicochemical
characteristic can inter... | [
{
"created": "Mon, 5 Feb 2024 08:38:41 GMT",
"version": "v1"
}
] | 2024-02-22 | [
[
"Goya",
"Gerardo F.",
""
],
[
"Raffa",
"Vittoria",
""
]
] | Magnetic nanoparticles (MNPs) are the foundation of several new strategies for neural repair and neurological therapies. The fact that a remote force can act on MNPs at the cytoplasmic space constitutes the essence of many new neurotherapeutic concepts. MNPs with a predesigned physicochemical characteristic can interac... |
1011.2079 | Jose A. Cuesta | Jose A. Cuesta | Huge progeny production during the transient of a quasi-species model of
viral infection, reproduction and mutation | 9 pages, no figures, uses Elsevier elsarticle class | Mathematical and Computer Modelling 54, 1676-1681 (2011) | 10.1016/j.mcm.2010.11.055 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Eigen's quasi-species model describes viruses as ensembles of different
mutants of a high fitness "master" genotype. Mutants are assumed to have lower
fitness than the master type, yet they coexist with it forming the
quasi-species. When the mutation rate is sufficiently high, the master type no
longer survives and g... | [
{
"created": "Tue, 9 Nov 2010 13:37:24 GMT",
"version": "v1"
}
] | 2012-02-02 | [
[
"Cuesta",
"Jose A.",
""
]
] | Eigen's quasi-species model describes viruses as ensembles of different mutants of a high fitness "master" genotype. Mutants are assumed to have lower fitness than the master type, yet they coexist with it forming the quasi-species. When the mutation rate is sufficiently high, the master type no longer survives and get... |
q-bio/0506034 | Francis Edward Su | Claus-Jochen Haake, Akemi Kashiwada, Francis Edward Su | The Shapley Value of Phylogenetic Trees | References added, and a section (calculating the Shapley value of a
tree game from its subtrees) was removed for length reasons (request of
referee) and may appear in another paper. 16 pages; related work at
http://www.math.hmc.edu/~su/papers.html. Journal of Mathematical Biology, to
appear. The original articl... | J. Mathematical Biology 56 (2008), 479--497 | 10.1007/s00285-007-0126-2 | null | q-bio.QM cs.GT math.CO q-bio.PE | null | Every weighted tree corresponds naturally to a cooperative game that we call
a "tree game"; it assigns to each subset of leaves the sum of the weights of
the minimal subtree spanned by those leaves. In the context of phylogenetic
trees, the leaves are species and this assignment captures the diversity
present in the ... | [
{
"created": "Wed, 22 Jun 2005 15:47:33 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Aug 2007 00:34:31 GMT",
"version": "v2"
}
] | 2009-09-02 | [
[
"Haake",
"Claus-Jochen",
""
],
[
"Kashiwada",
"Akemi",
""
],
[
"Su",
"Francis Edward",
""
]
] | Every weighted tree corresponds naturally to a cooperative game that we call a "tree game"; it assigns to each subset of leaves the sum of the weights of the minimal subtree spanned by those leaves. In the context of phylogenetic trees, the leaves are species and this assignment captures the diversity present in the co... |
1510.01195 | Richard A Neher | Richard A. Neher, Trevor Bedford, Rodney S. Daniels, Colin A. Russell,
and Boris I. Shraiman | Prediction, dynamics, and visualization of antigenic phenotypes of
seasonal influenza viruses | visualization available at http://HI.nextflu.org | null | 10.1073/pnas.1525578113 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Human seasonal influenza viruses evolve rapidly, enabling the virus
population to evade immunity and re-infect previously infected individuals.
Antigenic properties are largely determined by the surface glycoprotein
hemagglutinin (HA) and amino acid substitutions at exposed epitope sites in HA
mediate loss of recogni... | [
{
"created": "Mon, 5 Oct 2015 15:50:28 GMT",
"version": "v1"
}
] | 2016-04-27 | [
[
"Neher",
"Richard A.",
""
],
[
"Bedford",
"Trevor",
""
],
[
"Daniels",
"Rodney S.",
""
],
[
"Russell",
"Colin A.",
""
],
[
"Shraiman",
"Boris I.",
""
]
] | Human seasonal influenza viruses evolve rapidly, enabling the virus population to evade immunity and re-infect previously infected individuals. Antigenic properties are largely determined by the surface glycoprotein hemagglutinin (HA) and amino acid substitutions at exposed epitope sites in HA mediate loss of recogniti... |
q-bio/0309015 | Michael Desai | Michael M. Desai, David R. Nelson | A Quasispecies on a Moving Oasis | 12 pages, 5 figures | null | null | null | q-bio.PE cond-mat.soft | null | A population evolving in an inhomogeneous environment will adapt differently
to different regions. We study the conditions under which such a population can
maintain adaptations to a particular region when that region is not stationary,
but can move. In particular, we study a quasispecies living near a favorable
patc... | [
{
"created": "Fri, 26 Sep 2003 17:23:31 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Desai",
"Michael M.",
""
],
[
"Nelson",
"David R.",
""
]
] | A population evolving in an inhomogeneous environment will adapt differently to different regions. We study the conditions under which such a population can maintain adaptations to a particular region when that region is not stationary, but can move. In particular, we study a quasispecies living near a favorable patch ... |
2205.07258 | Shaoli Wang | Shaoli Wang, Tengfei Wang, Ya-nen Qi, Fei Xu | Backward bifurcation, basic reinfection number and robustness of a SEIRE
epidemic model with reinfection | 19 pages, 7 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-sa/4.0/ | Recent evidences show that individuals who recovered from COVID-19 can be
reinfected. However, this phenomenon has rarely been studied using mathematical
models. In this paper, we propose a SEIRE epidemic model to describe the spread
of the epidemic with reinfection. We obtain the important thresholds $R_0$ (the
basi... | [
{
"created": "Sun, 15 May 2022 10:56:00 GMT",
"version": "v1"
}
] | 2022-05-17 | [
[
"Wang",
"Shaoli",
""
],
[
"Wang",
"Tengfei",
""
],
[
"Qi",
"Ya-nen",
""
],
[
"Xu",
"Fei",
""
]
] | Recent evidences show that individuals who recovered from COVID-19 can be reinfected. However, this phenomenon has rarely been studied using mathematical models. In this paper, we propose a SEIRE epidemic model to describe the spread of the epidemic with reinfection. We obtain the important thresholds $R_0$ (the basic ... |
2208.11963 | Mantegazza Massimo | Massimo Mantegazza (IPMC), Vania Broccoli | SCN 1A /Na V 1.1 channelopathies: Mechanisms in expression systems,
animal models, and human iPSC models | null | Epilepsia, Wiley, 2019, 60 (S3) | 10.1111/epi.14700 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Pathogenic SCN1A/NaV1.1 mutations cause well defined epilepsies, including
Genetic Epilepsy with Febrile Seizures Plus (GEFS+) and the severe epileptic
encephalopathy Dravet syndrome. In addition, they cause a severe form of
migraine with aura, Familial Hemiplegic Migraine. Moreover, SCN1A/NaV1.1
variants have been i... | [
{
"created": "Thu, 25 Aug 2022 09:40:54 GMT",
"version": "v1"
}
] | 2022-08-26 | [
[
"Mantegazza",
"Massimo",
"",
"IPMC"
],
[
"Broccoli",
"Vania",
""
]
] | Pathogenic SCN1A/NaV1.1 mutations cause well defined epilepsies, including Genetic Epilepsy with Febrile Seizures Plus (GEFS+) and the severe epileptic encephalopathy Dravet syndrome. In addition, they cause a severe form of migraine with aura, Familial Hemiplegic Migraine. Moreover, SCN1A/NaV1.1 variants have been inf... |
0712.3773 | William Hlavacek | Jin Yang, Michael I. Monine, James R. Faeder and William S. Hlavacek | Kinetic Monte Carlo Method for Rule-based Modeling of Biochemical
Networks | 18 pages, 5 figures | Phys. Rev. E, 78:31910, 2008 | 10.1103/PhysRevE.78.031910 | LA-UR-07-8103 | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a kinetic Monte Carlo method for simulating chemical
transformations specified by reaction rules, which can be viewed as generators
of chemical reactions, or equivalently, definitions of reaction classes. A rule
identifies the molecular components involved in a transformation, how these
components change, ... | [
{
"created": "Fri, 21 Dec 2007 18:46:39 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Apr 2008 18:10:31 GMT",
"version": "v2"
},
{
"created": "Sun, 29 Jun 2008 03:49:51 GMT",
"version": "v3"
},
{
"created": "Fri, 22 Aug 2008 05:51:33 GMT",
"version": "v4"
}
] | 2010-07-09 | [
[
"Yang",
"Jin",
""
],
[
"Monine",
"Michael I.",
""
],
[
"Faeder",
"James R.",
""
],
[
"Hlavacek",
"William S.",
""
]
] | We present a kinetic Monte Carlo method for simulating chemical transformations specified by reaction rules, which can be viewed as generators of chemical reactions, or equivalently, definitions of reaction classes. A rule identifies the molecular components involved in a transformation, how these components change, co... |
1511.02545 | Anna McGann | Christopher N Angstmann, Bruce I Henry, Anna V McGann | A Fractional-Order Infectivity SIR Model | 16 pages, no figures | Physica A: Statistical Mechanics and its Applications, Volume 452,
15 June 2016, Pages 86-93 | 10.1016/j.physa.2016.02.029 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fractional-order SIR models have become increasingly popular in the
literature in recent years, however unlike the standard SIR model, they often
lack a derivation from an underlying stochastic process. Here we derive a
fractional-order infectivity SIR model from a stochastic process that
incorporates a time-since-in... | [
{
"created": "Mon, 9 Nov 2015 01:05:22 GMT",
"version": "v1"
}
] | 2016-03-31 | [
[
"Angstmann",
"Christopher N",
""
],
[
"Henry",
"Bruce I",
""
],
[
"McGann",
"Anna V",
""
]
] | Fractional-order SIR models have become increasingly popular in the literature in recent years, however unlike the standard SIR model, they often lack a derivation from an underlying stochastic process. Here we derive a fractional-order infectivity SIR model from a stochastic process that incorporates a time-since-infe... |
2310.03411 | Rolf Bader | Rolf Bader | Modeling Temporal Lobe Epilepsy during Music Large-Scale Form Perception
using the Impulse Pattern Formulation (IPF) Brain Mode | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Musical large-scale form is investigated using an Electronic Dance Music
(EDM) piece fed into a Finite-Difference Time Domain (FDTD) physical model of
the cochlear which again inputs into an Impulse-Pattern Formulation (IPF) brain
model. In previous studies, experimental EEG data showed an enhanced
correlation betwee... | [
{
"created": "Thu, 5 Oct 2023 09:29:49 GMT",
"version": "v1"
}
] | 2023-10-06 | [
[
"Bader",
"Rolf",
""
]
] | Musical large-scale form is investigated using an Electronic Dance Music (EDM) piece fed into a Finite-Difference Time Domain (FDTD) physical model of the cochlear which again inputs into an Impulse-Pattern Formulation (IPF) brain model. In previous studies, experimental EEG data showed an enhanced correlation between ... |
2001.07810 | Marco Ramaioli | Marco Marconati, Marco Ramaioli | The role of extensional rheology in the oral phase of swallowing: an in
vitro study | null | null | null | null | q-bio.TO cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Swallowing disorders deteriorate significantly the quality of life and can be
lifethreatening. Texture modification using shear thinning food thickeners have
proven effective in the management of dysphagia. Some studies have recently
considered the positive role of cohesiveness, but there is still an
insufficient und... | [
{
"created": "Tue, 21 Jan 2020 23:29:13 GMT",
"version": "v1"
}
] | 2020-01-23 | [
[
"Marconati",
"Marco",
""
],
[
"Ramaioli",
"Marco",
""
]
] | Swallowing disorders deteriorate significantly the quality of life and can be lifethreatening. Texture modification using shear thinning food thickeners have proven effective in the management of dysphagia. Some studies have recently considered the positive role of cohesiveness, but there is still an insufficient under... |
2311.13874 | Giovanni Pezzulo | Francesco Mannella and Giovanni Pezzulo | Transitive inference as probabilistic preference learning | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Transitive Inference (TI) is a cognitive task that assesses an organism's
ability to infer novel relations between items based on previously acquired
knowledge. TI is known for exhibiting various behavioral and neural signatures,
such as the Serial Position Effect (SPE), Symbolic Distance Effect (SDE), and
the brain'... | [
{
"created": "Thu, 23 Nov 2023 09:40:56 GMT",
"version": "v1"
},
{
"created": "Sat, 6 Jul 2024 08:45:21 GMT",
"version": "v2"
}
] | 2024-07-09 | [
[
"Mannella",
"Francesco",
""
],
[
"Pezzulo",
"Giovanni",
""
]
] | Transitive Inference (TI) is a cognitive task that assesses an organism's ability to infer novel relations between items based on previously acquired knowledge. TI is known for exhibiting various behavioral and neural signatures, such as the Serial Position Effect (SPE), Symbolic Distance Effect (SDE), and the brain's ... |
1304.6796 | Adnan Sljoka | Adnan Sljoka and Derek Wilson | Probing Protein Ensemble Rigidity and Hydrogen-Deuterium exchange | 26 pages, 12 figures, Supplementary Information available at
http://www.math.yorku.ca/~adnanslj/SljokaWilsonSupplementary.pdf | null | 10.1088/1478-3975/10/5/056013 | null | q-bio.BM physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein rigidity and flexibility can be analyzed accurately and efficiently
using the program FIRST. Previous studies using FIRST were designed to analyze
the rigidity and flexibility of proteins using a single static (snapshot)
structure. It is however well known that proteins can undergo spontaneous
sub-molecular u... | [
{
"created": "Thu, 25 Apr 2013 04:05:39 GMT",
"version": "v1"
},
{
"created": "Fri, 26 Apr 2013 17:20:20 GMT",
"version": "v2"
},
{
"created": "Wed, 8 May 2013 03:28:28 GMT",
"version": "v3"
}
] | 2015-06-15 | [
[
"Sljoka",
"Adnan",
""
],
[
"Wilson",
"Derek",
""
]
] | Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure. It is however well known that proteins can undergo spontaneous sub-molecular unf... |
2111.01969 | Yingying Wu | Yingying Wu, Shusheng Xu, Shing-Tung Yau, Yi Wu | PhyloTransformer: A Discriminative Model for Mutation Prediction Based
on a Multi-head Self-attention Mechanism | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an
ongoing pandemic infecting 219 million people as of 10/19/21, with a 3.6%
mortality rate. Natural selection can generate favorable mutations with
improved fitness advantages; however, the identified coronaviruses may be the
tip of the iceberg,... | [
{
"created": "Wed, 3 Nov 2021 01:30:57 GMT",
"version": "v1"
}
] | 2021-11-04 | [
[
"Wu",
"Yingying",
""
],
[
"Xu",
"Shusheng",
""
],
[
"Yau",
"Shing-Tung",
""
],
[
"Wu",
"Yi",
""
]
] | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an ongoing pandemic infecting 219 million people as of 10/19/21, with a 3.6% mortality rate. Natural selection can generate favorable mutations with improved fitness advantages; however, the identified coronaviruses may be the tip of the iceberg, a... |
2302.05316 | Forrest Sheldon | Forrest Sheldon | Characterizing contaminant noise in barcoded perturbation experiments | 12 pages including supplemental material, 4 main text figures, 2
figures in supplemental material | null | null | null | q-bio.QM stat.AP | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Bursting cells lead to ambient RNA that contaminates sequencing data. This
process is especially problematic in perturbation experiments where
transcription factors are implanted into cells to determine their effects. The
presence of contaminants makes it difficult to determine whether a factor is
truly expressed in ... | [
{
"created": "Fri, 10 Feb 2023 15:24:45 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Mar 2023 09:08:52 GMT",
"version": "v2"
},
{
"created": "Wed, 20 Sep 2023 08:53:20 GMT",
"version": "v3"
}
] | 2023-09-21 | [
[
"Sheldon",
"Forrest",
""
]
] | Bursting cells lead to ambient RNA that contaminates sequencing data. This process is especially problematic in perturbation experiments where transcription factors are implanted into cells to determine their effects. The presence of contaminants makes it difficult to determine whether a factor is truly expressed in th... |
2004.07119 | Xiaojie Guo | Xiaojie Guo, Yuanqi Du, Sivani Tadepalli, Liang Zhao, and Amarda Shehu | Generating Tertiary Protein Structures via an Interpretative Variational
Autoencoder | null | null | null | null | q-bio.BM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Much scientific enquiry across disciplines is founded upon a mechanistic
treatment of dynamic systems that ties form to function. A highly visible
instance of this is in molecular biology, where an important goal is to
determine functionally-relevant forms/structures that a protein molecule
employs to interact with m... | [
{
"created": "Wed, 8 Apr 2020 17:40:21 GMT",
"version": "v1"
},
{
"created": "Wed, 16 Jun 2021 06:02:16 GMT",
"version": "v2"
}
] | 2021-06-17 | [
[
"Guo",
"Xiaojie",
""
],
[
"Du",
"Yuanqi",
""
],
[
"Tadepalli",
"Sivani",
""
],
[
"Zhao",
"Liang",
""
],
[
"Shehu",
"Amarda",
""
]
] | Much scientific enquiry across disciplines is founded upon a mechanistic treatment of dynamic systems that ties form to function. A highly visible instance of this is in molecular biology, where an important goal is to determine functionally-relevant forms/structures that a protein molecule employs to interact with mol... |
2006.06215 | Zhanhui Wang | Kai Wen, Yuchen Bai, Yujie Wei, Chenglong Li, Suxia Zhang, Jianzhong
Shen, Zhanhui Wang | Influence of Small Molecule Property on Antibody Response | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Antibodies with high titer and affinity to small molecule are critical in the
field for the development of vaccines against drugs of abuse, antidotes to
toxins and immunoassays for compounds. However, little is known regarding how
properties of small molecule influence and which chemical descriptor could
indicate the... | [
{
"created": "Thu, 11 Jun 2020 06:05:12 GMT",
"version": "v1"
}
] | 2020-06-12 | [
[
"Wen",
"Kai",
""
],
[
"Bai",
"Yuchen",
""
],
[
"Wei",
"Yujie",
""
],
[
"Li",
"Chenglong",
""
],
[
"Zhang",
"Suxia",
""
],
[
"Shen",
"Jianzhong",
""
],
[
"Wang",
"Zhanhui",
""
]
] | Antibodies with high titer and affinity to small molecule are critical in the field for the development of vaccines against drugs of abuse, antidotes to toxins and immunoassays for compounds. However, little is known regarding how properties of small molecule influence and which chemical descriptor could indicate the d... |
2201.02461 | Christoph Daube | Christoph Daube, Joachim Gross and Robin A. A. Ince | A whitening approach for Transfer Entropy permits the application to
narrow-band signals | null | null | null | null | q-bio.NC q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Transfer Entropy, a generalisation of Granger Causality, promises to measure
"information transfer" from a source to a target signal by ignoring
self-predictability of a target signal when quantifying the source-target
relationship. A simple example for signals with such self-predictability are
narrowband signals. Th... | [
{
"created": "Fri, 7 Jan 2022 14:19:00 GMT",
"version": "v1"
},
{
"created": "Fri, 20 May 2022 09:24:51 GMT",
"version": "v2"
}
] | 2022-05-23 | [
[
"Daube",
"Christoph",
""
],
[
"Gross",
"Joachim",
""
],
[
"Ince",
"Robin A. A.",
""
]
] | Transfer Entropy, a generalisation of Granger Causality, promises to measure "information transfer" from a source to a target signal by ignoring self-predictability of a target signal when quantifying the source-target relationship. A simple example for signals with such self-predictability are narrowband signals. Thes... |
2307.06344 | QieHe Sun | Qiehe Sun, Jiawen Li, Jin Xu, Junru Cheng, Tian Guan, Yonghong He | The Whole Pathological Slide Classification via Weakly Supervised
Learning | null | null | null | null | q-bio.QM cs.CV eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Due to its superior efficiency in utilizing annotations and addressing
gigapixel-sized images, multiple instance learning (MIL) has shown great
promise as a framework for whole slide image (WSI) classification in digital
pathology diagnosis. However, existing methods tend to focus on advanced
aggregators with differe... | [
{
"created": "Wed, 12 Jul 2023 16:14:23 GMT",
"version": "v1"
}
] | 2023-07-14 | [
[
"Sun",
"Qiehe",
""
],
[
"Li",
"Jiawen",
""
],
[
"Xu",
"Jin",
""
],
[
"Cheng",
"Junru",
""
],
[
"Guan",
"Tian",
""
],
[
"He",
"Yonghong",
""
]
] | Due to its superior efficiency in utilizing annotations and addressing gigapixel-sized images, multiple instance learning (MIL) has shown great promise as a framework for whole slide image (WSI) classification in digital pathology diagnosis. However, existing methods tend to focus on advanced aggregators with different... |
q-bio/0509016 | Jose Vilar | Jose M. G. Vilar, Ronald Jansen, and Chris Sander | Signal processing in the TGF-beta superfamily ligand-receptor network | 33 pages, 7 figures | PLoS Comput Biol. 2006 Jan;2(1):e3. Epub 2006 Jan 27. | 10.1371/journal.pcbi.0020003 | null | q-bio.MN nlin.AO physics.bio-ph q-bio.SC | null | The TGF-beta pathway plays a central role in tissue homeostasis and
morphogenesis. It transduces a variety of extracellular signals into
intracellular transcriptional responses that control a plethora of cellular
processes, including cell growth, apoptosis, and differentiation. We use
computational modeling to show t... | [
{
"created": "Wed, 14 Sep 2005 18:54:33 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Vilar",
"Jose M. G.",
""
],
[
"Jansen",
"Ronald",
""
],
[
"Sander",
"Chris",
""
]
] | The TGF-beta pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora of cellular processes, including cell growth, apoptosis, and differentiation. We use computational modeling to show tha... |
1209.3083 | Christoph Haselwandter | Christoph A. Haselwandter and Rob Phillips | Directional interactions and cooperativity between mechanosensitive
membrane proteins | null | EPL 101, 68002 (2013) | 10.1209/0295-5075/101/68002 | null | q-bio.BM cond-mat.soft physics.bio-ph q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While modern structural biology has provided us with a rich and diverse
picture of membrane proteins, the biological function of membrane proteins is
often influenced by the mechanical properties of the surrounding lipid bilayer.
Here we explore the relation between the shape of membrane proteins and the
cooperative ... | [
{
"created": "Fri, 14 Sep 2012 03:38:22 GMT",
"version": "v1"
},
{
"created": "Fri, 24 May 2013 02:42:58 GMT",
"version": "v2"
}
] | 2013-05-27 | [
[
"Haselwandter",
"Christoph A.",
""
],
[
"Phillips",
"Rob",
""
]
] | While modern structural biology has provided us with a rich and diverse picture of membrane proteins, the biological function of membrane proteins is often influenced by the mechanical properties of the surrounding lipid bilayer. Here we explore the relation between the shape of membrane proteins and the cooperative fu... |
2111.04547 | Randall Beer | Randall D. Beer | The Global Structure of Codimension-2 Local Bifurcations in
Continuous-Time Recurrent Neural Networks | null | Biological Cybernetics (2022) 116:501-515 | 10.1007/s00422-022-00938-5 | null | q-bio.NC cs.NE math.DS nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | If we are ever to move beyond the study of isolated special cases in
theoretical neuroscience, we need to develop more general theories of neural
circuits over a given neural model. The present paper considers this challenge
in the context of continuous-time recurrent neural networks (CTRNNs), a simple
but dynamicall... | [
{
"created": "Mon, 8 Nov 2021 14:56:18 GMT",
"version": "v1"
}
] | 2022-10-17 | [
[
"Beer",
"Randall D.",
""
]
] | If we are ever to move beyond the study of isolated special cases in theoretical neuroscience, we need to develop more general theories of neural circuits over a given neural model. The present paper considers this challenge in the context of continuous-time recurrent neural networks (CTRNNs), a simple but dynamically-... |
1910.10210 | Stephen Eglen | Patrick W. Keeley, Stephen J. Eglen, Benjamin E. Reese | From Random to Regular: Variation in the Patterning of Retinal Mosaics | 11 Figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The various types of retinal neurons are each positioned at their respective
depths within the retina where they are believed to be assembled as orderly
mosaics, in which like-type neurons minimize proximity to one another. Two
common statistical analyses for assessing the spatial properties of retinal
mosaics includ... | [
{
"created": "Tue, 22 Oct 2019 19:50:40 GMT",
"version": "v1"
}
] | 2019-10-24 | [
[
"Keeley",
"Patrick W.",
""
],
[
"Eglen",
"Stephen J.",
""
],
[
"Reese",
"Benjamin E.",
""
]
] | The various types of retinal neurons are each positioned at their respective depths within the retina where they are believed to be assembled as orderly mosaics, in which like-type neurons minimize proximity to one another. Two common statistical analyses for assessing the spatial properties of retinal mosaics include ... |
1705.06147 | Roberto Cavoretto | Roberto Cavoretto, Alessandra De Rossi, Roberta Freda, Hanli Qiao,
Ezio Venturino | Numerical Methods for Pulmonary Image Registration | null | null | null | null | q-bio.QM math.NA physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Due to complexity and invisibility of human organs, diagnosticians need to
analyze medical images to determine where the lesion region is, and which kind
of disease is, in order to make precise diagnoses. For satisfying clinical
purposes through analyzing medical images, registration plays an essential
role. For inst... | [
{
"created": "Tue, 16 May 2017 06:42:08 GMT",
"version": "v1"
}
] | 2017-05-18 | [
[
"Cavoretto",
"Roberto",
""
],
[
"De Rossi",
"Alessandra",
""
],
[
"Freda",
"Roberta",
""
],
[
"Qiao",
"Hanli",
""
],
[
"Venturino",
"Ezio",
""
]
] | Due to complexity and invisibility of human organs, diagnosticians need to analyze medical images to determine where the lesion region is, and which kind of disease is, in order to make precise diagnoses. For satisfying clinical purposes through analyzing medical images, registration plays an essential role. For instan... |
1105.1217 | Pascal Grange | Pascal Grange and Partha P. Mitra | Marker Genes for Anatomical Regions in the Brain: Insights from the
Allen Gene Expression Atlas | 26 pages, LaTeX | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quantitative criteria are proposed to identify genes (and sets of genes)
whose expression marks a specific brain region (or a set of brain regions).
Gene-expression energies, obtained for thousands of mouse genes by numerization
of in-situ hybridization images in the Allen Gene Expression Atlas, are used to
test thes... | [
{
"created": "Fri, 6 May 2011 02:56:45 GMT",
"version": "v1"
}
] | 2011-05-09 | [
[
"Grange",
"Pascal",
""
],
[
"Mitra",
"Partha P.",
""
]
] | Quantitative criteria are proposed to identify genes (and sets of genes) whose expression marks a specific brain region (or a set of brain regions). Gene-expression energies, obtained for thousands of mouse genes by numerization of in-situ hybridization images in the Allen Gene Expression Atlas, are used to test these ... |
0902.3133 | Claude Pasquier | Claude Pasquier, Vasilis Promponas, Giorgos Palaios, Ioannis
Hamodrakas, Stavros Hamodrakas | A novel method for predicting transmembrane segments in proteins based
on a statistical analysis of the SwissProt database: the PRED-TMR algorithm | null | Protein Engineering Design & Selection, 1999, 12 (5), pp.381-5 | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a novel method that predicts transmembrane domains in proteins
using solely information contained in the sequence itself. The PRED-TMR
algorithm described, refines a standard hydrophobicity analysis with a
detection of potential termini ('edges', starts and ends) of transmembrane
regions. This allows one b... | [
{
"created": "Wed, 18 Feb 2009 13:23:03 GMT",
"version": "v1"
},
{
"created": "Mon, 9 May 2016 07:39:16 GMT",
"version": "v2"
}
] | 2016-05-10 | [
[
"Pasquier",
"Claude",
""
],
[
"Promponas",
"Vasilis",
""
],
[
"Palaios",
"Giorgos",
""
],
[
"Hamodrakas",
"Ioannis",
""
],
[
"Hamodrakas",
"Stavros",
""
]
] | We present a novel method that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The PRED-TMR algorithm described, refines a standard hydrophobicity analysis with a detection of potential termini ('edges', starts and ends) of transmembrane regions. This allows one bot... |
2005.04069 | Ziyuan Zhao | Jiapan Gu, Ziyuan Zhao, Zeng Zeng, Yuzhe Wang, Zhengyiren Qiu,
Bharadwaj Veeravalli, Brian Kim Poh Goh, Glenn Kunnath Bonney, Krishnakumar
Madhavan, Chan Wan Ying, Lim Kheng Choon, Thng Choon Hua, Pierce KH Chow | Multi-Phase Cross-modal Learning for Noninvasive Gene Mutation
Prediction in Hepatocellular Carcinoma | Accepted version to be published in the 42nd IEEE Annual
International Conference of the IEEE Engineering in Medicine and Biology
Society, EMBC 2020, Montreal, Canada | 2020 42nd Annual International Conference of the IEEE Engineering
in Medicine & Biology Society (EMBC) | 10.1109/EMBC44109.2020.9176677 | null | q-bio.QM cs.CV eess.IV q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Hepatocellular carcinoma (HCC) is the most common type of primary liver
cancer and the fourth most common cause of cancer-related death worldwide.
Understanding the underlying gene mutations in HCC provides great prognostic
value for treatment planning and targeted therapy. Radiogenomics has revealed
an association b... | [
{
"created": "Fri, 8 May 2020 14:36:59 GMT",
"version": "v1"
}
] | 2022-03-24 | [
[
"Gu",
"Jiapan",
""
],
[
"Zhao",
"Ziyuan",
""
],
[
"Zeng",
"Zeng",
""
],
[
"Wang",
"Yuzhe",
""
],
[
"Qiu",
"Zhengyiren",
""
],
[
"Veeravalli",
"Bharadwaj",
""
],
[
"Goh",
"Brian Kim Poh",
""
],
[
"Bo... | Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and the fourth most common cause of cancer-related death worldwide. Understanding the underlying gene mutations in HCC provides great prognostic value for treatment planning and targeted therapy. Radiogenomics has revealed an association bet... |
2011.05294 | Mike Steel Prof. | Mike Steel | Modelling aspects of consciousness: a topological perspective | 13 pages, 1 figure, (version 5 is a slightly revised version of
version 4, which was a moderately revised version of 3 (which was identical
to versions 1 and 2, except that the figure was reduced in size to allow
easier downloads) | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Attention Schema Theory (AST) is a recent proposal to provide a scientific
explanation for the basis of subjective awareness. In AST, the brain constructs
a representation of attention taking place in its own (and others') mind (`the
attention schema'). Moreover, this representation is incomplete for efficiency
reaso... | [
{
"created": "Tue, 10 Nov 2020 18:32:00 GMT",
"version": "v1"
},
{
"created": "Wed, 11 Nov 2020 04:08:38 GMT",
"version": "v2"
},
{
"created": "Sun, 22 Nov 2020 03:42:26 GMT",
"version": "v3"
},
{
"created": "Fri, 9 Apr 2021 05:34:35 GMT",
"version": "v4"
},
{
"cr... | 2021-04-28 | [
[
"Steel",
"Mike",
""
]
] | Attention Schema Theory (AST) is a recent proposal to provide a scientific explanation for the basis of subjective awareness. In AST, the brain constructs a representation of attention taking place in its own (and others') mind (`the attention schema'). Moreover, this representation is incomplete for efficiency reasons... |
2408.03240 | Gabriel Palma | Jo\~ao C\'esar Reis Alves, Gabriel Rodrigues Palma, Idemauro Antonio
Rodrigues de Lara | Beta regression mixed model applied to sensory analysis | 13 pages | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Sensory analysis is an important area that the food industry can use to
innovate and improve its products. This study involves a sample of individuals
who can be trained or not to assess a product using a hedonic scale or notes,
where the experimental design is a balanced incomplete block design. In this
context, int... | [
{
"created": "Tue, 6 Aug 2024 15:01:56 GMT",
"version": "v1"
}
] | 2024-08-07 | [
[
"Alves",
"João César Reis",
""
],
[
"Palma",
"Gabriel Rodrigues",
""
],
[
"de Lara",
"Idemauro Antonio Rodrigues",
""
]
] | Sensory analysis is an important area that the food industry can use to innovate and improve its products. This study involves a sample of individuals who can be trained or not to assess a product using a hedonic scale or notes, where the experimental design is a balanced incomplete block design. In this context, integ... |
1406.2244 | Jae Kyoung Kim | Jae Kyoung Kim, Kre\v{s}imir Josi\'c, and Matthew R. Bennett | The validity of quasi steady-state approximations in discrete stochastic
simulations | 21 pages, 4 figures | null | 10.1016/j.bpj.2014.06.012 | null | q-bio.MN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In biochemical networks, reactions often occur on disparate timescales and
can be characterized as either "fast" or "slow." The quasi-steady state
approximation (QSSA) utilizes timescale separation to project models of
biochemical networks onto lower-dimensional slow manifolds. As a result, fast
elementary reactions ... | [
{
"created": "Mon, 9 Jun 2014 17:16:12 GMT",
"version": "v1"
}
] | 2015-06-19 | [
[
"Kim",
"Jae Kyoung",
""
],
[
"Josić",
"Krešimir",
""
],
[
"Bennett",
"Matthew R.",
""
]
] | In biochemical networks, reactions often occur on disparate timescales and can be characterized as either "fast" or "slow." The quasi-steady state approximation (QSSA) utilizes timescale separation to project models of biochemical networks onto lower-dimensional slow manifolds. As a result, fast elementary reactions ar... |
2207.11182 | Youssef Kora | Salma Salhi, Youssef Kora, Gisu Ham, Hadi Zadeh Haghighi, and
Christoph Simon | Network analysis of the human structural connectome including the
brainstem | 25 pages, 7 figures | null | 10.1371/journal.pone.0272688 | null | q-bio.NC cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The underlying anatomical structure is fundamental to the study of brain
networks, but the role of brainstem from a structural perspective is not very
well understood. We conduct a computational and graph-theoretical study of the
human structural connectome incorporating a variety of subcortical structures
including ... | [
{
"created": "Fri, 22 Jul 2022 16:43:08 GMT",
"version": "v1"
},
{
"created": "Mon, 30 Jan 2023 03:28:57 GMT",
"version": "v2"
}
] | 2023-04-26 | [
[
"Salhi",
"Salma",
""
],
[
"Kora",
"Youssef",
""
],
[
"Ham",
"Gisu",
""
],
[
"Haghighi",
"Hadi Zadeh",
""
],
[
"Simon",
"Christoph",
""
]
] | The underlying anatomical structure is fundamental to the study of brain networks, but the role of brainstem from a structural perspective is not very well understood. We conduct a computational and graph-theoretical study of the human structural connectome incorporating a variety of subcortical structures including th... |
1712.05906 | Seung Ki Baek | Taekho You, Minji Kwon, Hang-Hyun Jo, Woo-Sung Jung, and Seung Ki Baek | Chaos and unpredictability in evolution of cooperation in continuous
time | 9 pages; 3 figures | null | 10.1103/PhysRevE.96.062310 | null | q-bio.PE nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cooperators benefit others with paying costs. Evolution of cooperation
crucially depends on the cost-benefit ratio of cooperation, denoted as $c$. In
this work, we investigate the infinitely repeated prisoner's dilemma for
various values of $c$ with four of the representative memory-one strategies,
i.e., unconditiona... | [
{
"created": "Sat, 16 Dec 2017 05:30:26 GMT",
"version": "v1"
}
] | 2017-12-19 | [
[
"You",
"Taekho",
""
],
[
"Kwon",
"Minji",
""
],
[
"Jo",
"Hang-Hyun",
""
],
[
"Jung",
"Woo-Sung",
""
],
[
"Baek",
"Seung Ki",
""
]
] | Cooperators benefit others with paying costs. Evolution of cooperation crucially depends on the cost-benefit ratio of cooperation, denoted as $c$. In this work, we investigate the infinitely repeated prisoner's dilemma for various values of $c$ with four of the representative memory-one strategies, i.e., unconditional ... |
2310.13803 | Teresa Lo | Teresa W. Lo, Han James Choi, Dean Huang, Paul A. Wiggins | Noise robustness and metabolic load determine the principles of central
dogma regulation | Main: 10 pages, 6 figures; Supplemental Material: 27 pages, 12
figures | null | null | null | q-bio.MN physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | The processes of gene expression are inherently stochastic, even for
essential genes required for growth. How does the cell maximize fitness in
light of noise? To answer this question, we build a mathematical model to
explore the trade-off between metabolic load and growth robustness. The model
predicts novel princip... | [
{
"created": "Fri, 20 Oct 2023 20:30:52 GMT",
"version": "v1"
},
{
"created": "Mon, 8 Jan 2024 23:13:36 GMT",
"version": "v2"
},
{
"created": "Thu, 23 May 2024 22:36:04 GMT",
"version": "v3"
},
{
"created": "Thu, 15 Aug 2024 17:50:59 GMT",
"version": "v4"
}
] | 2024-08-16 | [
[
"Lo",
"Teresa W.",
""
],
[
"Choi",
"Han James",
""
],
[
"Huang",
"Dean",
""
],
[
"Wiggins",
"Paul A.",
""
]
] | The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light of noise? To answer this question, we build a mathematical model to explore the trade-off between metabolic load and growth robustness. The model predicts novel principle... |
2312.12678 | Eric Rawls | Eric Rawls, Bryan Andrews, Kelvin Lim, Erich Kummerfeld | Causal Discovery for fMRI data: Challenges, Solutions, and a Case Study | null | null | null | null | q-bio.QM cs.AI cs.LG stat.ME stat.ML | http://creativecommons.org/licenses/by/4.0/ | Designing studies that apply causal discovery requires navigating many
researcher degrees of freedom. This complexity is exacerbated when the study
involves fMRI data. In this paper we (i) describe nine challenges that occur
when applying causal discovery to fMRI data, (ii) discuss the space of
decisions that need to... | [
{
"created": "Wed, 20 Dec 2023 00:33:26 GMT",
"version": "v1"
}
] | 2023-12-21 | [
[
"Rawls",
"Eric",
""
],
[
"Andrews",
"Bryan",
""
],
[
"Lim",
"Kelvin",
""
],
[
"Kummerfeld",
"Erich",
""
]
] | Designing studies that apply causal discovery requires navigating many researcher degrees of freedom. This complexity is exacerbated when the study involves fMRI data. In this paper we (i) describe nine challenges that occur when applying causal discovery to fMRI data, (ii) discuss the space of decisions that need to b... |
q-bio/0405022 | Erik van Nimwegen | Erik van Nimwegen | Scaling laws in the functional content of genomes: Fundamental constants
of evolution? | to appear in "Power Laws, Scale-free Networks and Genome Biology", E.
Koonin et al. (eds.), Landes Bioscience (2004) | null | null | null | q-bio.GN q-bio.MN | null | With the number of fully-sequenced genomes now well over a hundred it has
become possible to start investigating if there are any quantitative
regularities in the genetic make-up of genomes. In (physics/0307001), I
originally showed that the numbers of genes in different functional categories
scale as power laws in t... | [
{
"created": "Wed, 26 May 2004 21:13:49 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"van Nimwegen",
"Erik",
""
]
] | With the number of fully-sequenced genomes now well over a hundred it has become possible to start investigating if there are any quantitative regularities in the genetic make-up of genomes. In (physics/0307001), I originally showed that the numbers of genes in different functional categories scale as power laws in the... |
1509.00411 | Ewelina Kubicz | E. Kubicz, B. Jasi\'nska, B. Zgardzi\'nska, T. Bednarski, P.
Bia{\l}as, E. Czerwi\'nski, A. Gajos, M. Gorgol, D. Kami\'nska, {\L}.
Kap{\l}on, A. Kochanowski, G. Korcyl, P. Kowalski, T. Kozik, W. Krzemie\'n,
S. Nied\'zwiecki, M. Pa{\l}ka, L. Raczy\'nski, Z. Rajfur, Z. Rudy, O. Rundel,
N.G. Sharma, M. Silarski, A... | Studies of unicellular micro-organisms Saccharomyces cerevisiae by means
of Positron Annihilation Lifetime Spectroscopy | Nukleonika (2015) | Nukleonika 60(4) (2015) 749-753 | 10.1515/nuka-2015-0135 | null | q-bio.OT physics.ins-det | http://creativecommons.org/publicdomain/zero/1.0/ | Results of Positron Annihilation Lifetime Spectroscopy (PALS) and microscopic
studies on simple microorganisms: brewing yeasts are presented. Lifetime of
ortho - positronium (o-Ps) were found to change from 2.4 to 2.9 ns (longer
lived component) for lyophilised and aqueous yeasts, respectively. Also
hygroscopicity of... | [
{
"created": "Sun, 30 Aug 2015 21:10:42 GMT",
"version": "v1"
}
] | 2016-02-17 | [
[
"Kubicz",
"E.",
""
],
[
"Jasińska",
"B.",
""
],
[
"Zgardzińska",
"B.",
""
],
[
"Bednarski",
"T.",
""
],
[
"Białas",
"P.",
""
],
[
"Czerwiński",
"E.",
""
],
[
"Gajos",
"A.",
""
],
[
"Gorgol",
"M.... | Results of Positron Annihilation Lifetime Spectroscopy (PALS) and microscopic studies on simple microorganisms: brewing yeasts are presented. Lifetime of ortho - positronium (o-Ps) were found to change from 2.4 to 2.9 ns (longer lived component) for lyophilised and aqueous yeasts, respectively. Also hygroscopicity of y... |
2210.03587 | Jason Steffener | Jason Steffener, Joanne Nicholls, Dylan Franklin | The Role of Lifetime Exposures across Cognitive Domains in Barbados
Using Data From the SABE Study | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | This study characterized the effects of aging on individual cognitive domains
and how sex, job type, and years of education alter the age effect on older
adults from Barbados. This was an analysis of the cross-sectional data
collected as part of the SABE Study (Health, Well-being and Ageing) in 2006.
The loss of a si... | [
{
"created": "Fri, 7 Oct 2022 14:45:17 GMT",
"version": "v1"
}
] | 2022-10-10 | [
[
"Steffener",
"Jason",
""
],
[
"Nicholls",
"Joanne",
""
],
[
"Franklin",
"Dylan",
""
]
] | This study characterized the effects of aging on individual cognitive domains and how sex, job type, and years of education alter the age effect on older adults from Barbados. This was an analysis of the cross-sectional data collected as part of the SABE Study (Health, Well-being and Ageing) in 2006. The loss of a sing... |
1805.04107 | Claire N\'edellec | Claire N\'edellec, Robert Bossy, Estelle Chaix, Louise Del\'eger | Text-mining and ontologies: new approaches to knowledge discovery of
microbial diversity | 5 pages | Proceedings of the 4th International Microbial Diversity
Conference. pp. 221-227, ed. Marco Gobetti. Pub. Simtra. ISBN
978-88-943010-0-7, Bari, October 2017 | null | null | q-bio.QM cs.AI | http://creativecommons.org/licenses/by/4.0/ | Microbiology research has access to a very large amount of public information
on the habitats of microorganisms. Many areas of microbiology research uses
this information, primarily in biodiversity studies. However the habitat
information is expressed in unstructured natural language form, which hinders
its exploitat... | [
{
"created": "Thu, 10 May 2018 11:38:45 GMT",
"version": "v1"
},
{
"created": "Wed, 31 Oct 2018 14:52:02 GMT",
"version": "v2"
}
] | 2018-11-01 | [
[
"Nédellec",
"Claire",
""
],
[
"Bossy",
"Robert",
""
],
[
"Chaix",
"Estelle",
""
],
[
"Deléger",
"Louise",
""
]
] | Microbiology research has access to a very large amount of public information on the habitats of microorganisms. Many areas of microbiology research uses this information, primarily in biodiversity studies. However the habitat information is expressed in unstructured natural language form, which hinders its exploitatio... |
1210.4500 | Benjamin Good | Benjamin H Good and Michael M Desai | The equivalence between weak and strong purifying selection | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Weak purifying selection, acting on many linked mutations, may play a major
role in shaping patterns of molecular evolution in natural populations. Yet
efforts to infer these effects from DNA sequence data are limited by our
incomplete understanding of weak selection on local genomic scales. Here, we
demonstrate a na... | [
{
"created": "Tue, 16 Oct 2012 17:16:42 GMT",
"version": "v1"
}
] | 2012-10-17 | [
[
"Good",
"Benjamin H",
""
],
[
"Desai",
"Michael M",
""
]
] | Weak purifying selection, acting on many linked mutations, may play a major role in shaping patterns of molecular evolution in natural populations. Yet efforts to infer these effects from DNA sequence data are limited by our incomplete understanding of weak selection on local genomic scales. Here, we demonstrate a natu... |
1702.04195 | Vadim Zotev | Vadim Zotev, Masaya Misaki, Raquel Phillips, Chung Ki Wong, Jerzy
Bodurka | Real-time fMRI neurofeedback of the mediodorsal and anterior thalamus
enhances correlation between thalamic BOLD activity and alpha EEG rhythm | 26 pages, 14 figures, to appear in Human Brain Mapping | Human Brain Mapping 39 (2018) 1024-1042 | 10.1002/hbm.23902 | null | q-bio.NC physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Real-time fMRI neurofeedback (rtfMRI-nf) with simultaneous EEG allows
volitional modulation of BOLD activity of target brain regions and
investigation of related electrophysiological activity. We applied this
approach to study correlations between thalamic BOLD activity and alpha EEG
rhythm. Healthy volunteers in the... | [
{
"created": "Tue, 14 Feb 2017 13:25:23 GMT",
"version": "v1"
},
{
"created": "Sun, 19 Nov 2017 22:28:23 GMT",
"version": "v2"
}
] | 2018-01-15 | [
[
"Zotev",
"Vadim",
""
],
[
"Misaki",
"Masaya",
""
],
[
"Phillips",
"Raquel",
""
],
[
"Wong",
"Chung Ki",
""
],
[
"Bodurka",
"Jerzy",
""
]
] | Real-time fMRI neurofeedback (rtfMRI-nf) with simultaneous EEG allows volitional modulation of BOLD activity of target brain regions and investigation of related electrophysiological activity. We applied this approach to study correlations between thalamic BOLD activity and alpha EEG rhythm. Healthy volunteers in the e... |
0811.3163 | Stefan Klumpp | Stefan Klumpp and Terence Hwa | Stochasticity and traffic jams in the transcription of ribosomal RNA:
Intriguing role of termination and antitermination | includes Supporting Information | Proc. Natl. Acad. Sci. USA 105, 18159-18164 (2008) | 10.1073/pnas.0806084105 | null | q-bio.SC cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In fast growing bacteria, ribosomal RNA (rRNA) is required to be transcribed
at very high rates to sustain the high cellular demand on ribosome synthesis.
This results in dense traffic of RNA polymerases (RNAP). We developed a
stochastic model, integrating results of single-molecule and quantitative in
vivo studies o... | [
{
"created": "Wed, 19 Nov 2008 17:49:52 GMT",
"version": "v1"
}
] | 2008-11-24 | [
[
"Klumpp",
"Stefan",
""
],
[
"Hwa",
"Terence",
""
]
] | In fast growing bacteria, ribosomal RNA (rRNA) is required to be transcribed at very high rates to sustain the high cellular demand on ribosome synthesis. This results in dense traffic of RNA polymerases (RNAP). We developed a stochastic model, integrating results of single-molecule and quantitative in vivo studies of ... |
2403.15523 | Jordy Thielen | H. A. Scheppink, S. Ahmadi, P. Desain, M. Tangermann, J. Thielen | Towards auditory attention decoding with noise-tagging: A pilot study | 6 pages, 2 figures, 9th Graz Brain-Computer Interface Conference 2024 | null | null | null | q-bio.NC cs.AI cs.LG cs.SD eess.AS | http://creativecommons.org/licenses/by/4.0/ | Auditory attention decoding (AAD) aims to extract from brain activity the
attended speaker amidst candidate speakers, offering promising applications for
neuro-steered hearing devices and brain-computer interfacing. This pilot study
makes a first step towards AAD using the noise-tagging stimulus protocol, which
evoke... | [
{
"created": "Fri, 22 Mar 2024 13:35:34 GMT",
"version": "v1"
},
{
"created": "Fri, 17 May 2024 14:44:24 GMT",
"version": "v2"
}
] | 2024-05-20 | [
[
"Scheppink",
"H. A.",
""
],
[
"Ahmadi",
"S.",
""
],
[
"Desain",
"P.",
""
],
[
"Tangermann",
"M.",
""
],
[
"Thielen",
"J.",
""
]
] | Auditory attention decoding (AAD) aims to extract from brain activity the attended speaker amidst candidate speakers, offering promising applications for neuro-steered hearing devices and brain-computer interfacing. This pilot study makes a first step towards AAD using the noise-tagging stimulus protocol, which evokes ... |
1801.09858 | Xiaoxiao Wang | Xiaoxiao Wang, Xiao Liang, Zhoufan Jiang, Benedictor Alexander Nguchu,
Yawen Zhou, Yanming Wang, Huijuan Wang, Yu Li, Yuying Zhu, Feng Wu, Jia-Hong
Gao, Benching Qiu | Decoding and mapping task states of the human brain via deep learning | 27 pages, 8 figures, 4 table | null | 10.1002/hbm.24891 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Support vector machine (SVM) based multivariate pattern analysis (MVPA) has
delivered promising performance in decoding specific task states based on
functional magnetic resonance imaging (fMRI) of the human brain.
Conventionally, the SVM-MVPA requires careful feature selection/extraction
according to expert knowledg... | [
{
"created": "Tue, 30 Jan 2018 05:58:18 GMT",
"version": "v1"
},
{
"created": "Tue, 17 Sep 2019 03:27:16 GMT",
"version": "v2"
},
{
"created": "Wed, 4 Dec 2019 06:40:15 GMT",
"version": "v3"
}
] | 2019-12-17 | [
[
"Wang",
"Xiaoxiao",
""
],
[
"Liang",
"Xiao",
""
],
[
"Jiang",
"Zhoufan",
""
],
[
"Nguchu",
"Benedictor Alexander",
""
],
[
"Zhou",
"Yawen",
""
],
[
"Wang",
"Yanming",
""
],
[
"Wang",
"Huijuan",
""
],
[
... | Support vector machine (SVM) based multivariate pattern analysis (MVPA) has delivered promising performance in decoding specific task states based on functional magnetic resonance imaging (fMRI) of the human brain. Conventionally, the SVM-MVPA requires careful feature selection/extraction according to expert knowledge.... |
2104.08474 | Yibo Li | Yibo Li, Jianfeng Pei and Luhua Lai | Learning to design drug-like molecules in three-dimensional space using
deep generative models | null | Chem. Sci. (2021) | 10.1039/D1SC04444C | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, deep generative models for molecular graphs are gaining more and
more attention in the field of de novo drug design. A variety of models have
been developed to generate topological structures of drug-like molecules, but
explorations in generating three-dimensional structures are still limited.
Existing meth... | [
{
"created": "Sat, 17 Apr 2021 07:30:23 GMT",
"version": "v1"
}
] | 2021-09-16 | [
[
"Li",
"Yibo",
""
],
[
"Pei",
"Jianfeng",
""
],
[
"Lai",
"Luhua",
""
]
] | Recently, deep generative models for molecular graphs are gaining more and more attention in the field of de novo drug design. A variety of models have been developed to generate topological structures of drug-like molecules, but explorations in generating three-dimensional structures are still limited. Existing method... |
1703.10524 | Dmitry Ravcheev PhD | Dmitry A. Ravcheev, Ines Thiele | Comparative genomic analysis of the human gut microbiome reveals a broad
distribution of metabolic pathways for the degradation of host-synthetized
mucin glycans | 28 pages, 5 figures | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The colonic mucus layer is a dynamic and complex structure formed by secreted
and transmembrane mucins, which are high-molecular-weight and heavily
glycosylated proteins. Colonic mucus consists of a loose outer layer and a
dense epithelium-attached layer. The outer layer is inhabited by various
representatives of the... | [
{
"created": "Thu, 30 Mar 2017 15:25:13 GMT",
"version": "v1"
}
] | 2017-03-31 | [
[
"Ravcheev",
"Dmitry A.",
""
],
[
"Thiele",
"Ines",
""
]
] | The colonic mucus layer is a dynamic and complex structure formed by secreted and transmembrane mucins, which are high-molecular-weight and heavily glycosylated proteins. Colonic mucus consists of a loose outer layer and a dense epithelium-attached layer. The outer layer is inhabited by various representatives of the h... |
1201.0246 | Yu Wu | Yu Wu, Wenlian Lu, Wei Lin, Gareth Leng, Jianfeng Feng | Bifurcations of Emergent Bursting in a Neuronal Network | 7 figures, 1 table | null | 10.1371/journal.pone.0038402 | null | q-bio.QM math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Currently we routinely develop a complex neuronal network to explain observed
but often paradoxical phenomena based upon biological recordings. Here we
present a general approach to demonstrate how to mathematically tackle such a
complex neuronal network so that we can fully understand the underlying
mechanism. Using... | [
{
"created": "Sat, 31 Dec 2011 10:59:56 GMT",
"version": "v1"
}
] | 2015-06-03 | [
[
"Wu",
"Yu",
""
],
[
"Lu",
"Wenlian",
""
],
[
"Lin",
"Wei",
""
],
[
"Leng",
"Gareth",
""
],
[
"Feng",
"Jianfeng",
""
]
] | Currently we routinely develop a complex neuronal network to explain observed but often paradoxical phenomena based upon biological recordings. Here we present a general approach to demonstrate how to mathematically tackle such a complex neuronal network so that we can fully understand the underlying mechanism. Using a... |
1510.00658 | Khem Raj Ghusinga | Khem Raj Ghusinga, Abhyudai Singh | Optimal regulation of protein degradation to schedule cellular events
with precision | null | null | 10.1109/ACC.2016.7524951 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An important occurrence in many cellular contexts is the crossing of a
prescribed threshold by a regulatory protein. The timing of such events is
stochastic as a consequence of the innate randomness in gene expression. A
question of interest is to understand how gene expression is regulated to
achieve precision in ev... | [
{
"created": "Fri, 2 Oct 2015 17:39:49 GMT",
"version": "v1"
}
] | 2017-02-24 | [
[
"Ghusinga",
"Khem Raj",
""
],
[
"Singh",
"Abhyudai",
""
]
] | An important occurrence in many cellular contexts is the crossing of a prescribed threshold by a regulatory protein. The timing of such events is stochastic as a consequence of the innate randomness in gene expression. A question of interest is to understand how gene expression is regulated to achieve precision in even... |
1203.2178 | Valery Kirzhner | Valery Kirzhner and Zeev Volkovich | Evaluation of the Genome Mixture Contents by Means of the Compositional
Spectra Method | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this research, we consider a mixture of genome fragments of a certain
bacteria set. The problem of mixture separation is studied under the assumption
that all the genomes present in the mixture are completely sequenced or are
close to those already sequenced. Such assumption is relevant, e.g., in regular
observati... | [
{
"created": "Fri, 9 Mar 2012 20:57:14 GMT",
"version": "v1"
}
] | 2012-03-12 | [
[
"Kirzhner",
"Valery",
""
],
[
"Volkovich",
"Zeev",
""
]
] | In this research, we consider a mixture of genome fragments of a certain bacteria set. The problem of mixture separation is studied under the assumption that all the genomes present in the mixture are completely sequenced or are close to those already sequenced. Such assumption is relevant, e.g., in regular observation... |
2402.04845 | Bowen Jing | Bowen Jing, Bonnie Berger, Tommi Jaakkola | AlphaFold Meets Flow Matching for Generating Protein Ensembles | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The biological functions of proteins often depend on dynamic structural
ensembles. In this work, we develop a flow-based generative modeling approach
for learning and sampling the conformational landscapes of proteins. We
repurpose highly accurate single-state predictors such as AlphaFold and ESMFold
and fine-tune th... | [
{
"created": "Wed, 7 Feb 2024 13:44:47 GMT",
"version": "v1"
}
] | 2024-02-08 | [
[
"Jing",
"Bowen",
""
],
[
"Berger",
"Bonnie",
""
],
[
"Jaakkola",
"Tommi",
""
]
] | The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly accurate single-state predictors such as AlphaFold and ESMFold and fine-tune them... |
1303.7439 | Erwan Bigan | Erwan Bigan, Jean-Marc Steyaert and St\'ephane Douady | Properties of Random Complex Chemical Reaction Networks and Their
Relevance to Biological Toy Models | null | null | null | Proceedings of Journ\'ees Ouvertes Biologie Informatique
Math\'ematiques (JOBIM), Toulouse, France, July 1-4, 2013 | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the properties of large random conservative chemical reaction
networks composed of elementary reactions endowed with either mass-action or
saturating kinetics, assigning kinetic parameters in a
thermodynamically-consistent manner. We find that such complex networks exhibit
qualitatively similar behavio... | [
{
"created": "Fri, 29 Mar 2013 17:08:05 GMT",
"version": "v1"
}
] | 2014-11-26 | [
[
"Bigan",
"Erwan",
""
],
[
"Steyaert",
"Jean-Marc",
""
],
[
"Douady",
"Stéphane",
""
]
] | We investigate the properties of large random conservative chemical reaction networks composed of elementary reactions endowed with either mass-action or saturating kinetics, assigning kinetic parameters in a thermodynamically-consistent manner. We find that such complex networks exhibit qualitatively similar behavior ... |
1502.06256 | Gregory Kucherov | Karel Brinda and Maciej Sykulski and Gregory Kucherov | Spaced seeds improve k-mer-based metagenomic classification | 23 pages | Bioinformatics (2015) 31 (22): 3584-3592 | 10.1093/bioinformatics/btv419 | null | q-bio.GN cs.CE cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Metagenomics is a powerful approach to study genetic content of environmental
samples that has been strongly promoted by NGS technologies. To cope with
massive data involved in modern metagenomic projects, recent tools [4, 39] rely
on the analysis of k-mers shared between the read to be classified and sampled
referen... | [
{
"created": "Sun, 22 Feb 2015 18:30:58 GMT",
"version": "v1"
},
{
"created": "Thu, 5 Mar 2015 18:25:54 GMT",
"version": "v2"
},
{
"created": "Thu, 9 Jul 2015 09:47:00 GMT",
"version": "v3"
}
] | 2016-03-17 | [
[
"Brinda",
"Karel",
""
],
[
"Sykulski",
"Maciej",
""
],
[
"Kucherov",
"Gregory",
""
]
] | Metagenomics is a powerful approach to study genetic content of environmental samples that has been strongly promoted by NGS technologies. To cope with massive data involved in modern metagenomic projects, recent tools [4, 39] rely on the analysis of k-mers shared between the read to be classified and sampled reference... |
2210.09092 | Moo K. Chung | Moo K. Chung, Soumya Das, Hernando Ombao | Dynamic Topological Data Analysis of Functional Human Brain Networks | In press in journal Foundations of Data Science | null | null | null | q-bio.NC nlin.CD | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Developing reliable methods to discriminate different transient brain states
that change over time is a key neuroscientific challenge in brain imaging
studies. Topological data analysis (TDA), a novel framework based on algebraic
topology, can handle such a challenge. However, existing TDA has been somewhat
limited t... | [
{
"created": "Mon, 17 Oct 2022 13:36:00 GMT",
"version": "v1"
},
{
"created": "Mon, 30 Oct 2023 10:25:58 GMT",
"version": "v2"
},
{
"created": "Sun, 10 Dec 2023 20:33:53 GMT",
"version": "v3"
},
{
"created": "Mon, 18 Dec 2023 09:33:53 GMT",
"version": "v4"
}
] | 2023-12-19 | [
[
"Chung",
"Moo K.",
""
],
[
"Das",
"Soumya",
""
],
[
"Ombao",
"Hernando",
""
]
] | Developing reliable methods to discriminate different transient brain states that change over time is a key neuroscientific challenge in brain imaging studies. Topological data analysis (TDA), a novel framework based on algebraic topology, can handle such a challenge. However, existing TDA has been somewhat limited to ... |
1710.11296 | Yury Garcia | Yury E. Garc\'ia, Marcos A. Capistr\'an | Early pathogen replacement in a model of Influenza and Respiratory
Syncytial Virus with partial vaccination. A computational study | null | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we carry out a computational study using the spectral
decomposition of the fluctuations of a two-pathogen epidemic model around its
deterministic attractor, i.e., steady state or limit cycle, to examine the role
of partial vaccination and between-host pathogen interaction on early pathogen
replacement ... | [
{
"created": "Tue, 31 Oct 2017 01:57:32 GMT",
"version": "v1"
}
] | 2017-11-01 | [
[
"García",
"Yury E.",
""
],
[
"Capistrán",
"Marcos A.",
""
]
] | In this paper, we carry out a computational study using the spectral decomposition of the fluctuations of a two-pathogen epidemic model around its deterministic attractor, i.e., steady state or limit cycle, to examine the role of partial vaccination and between-host pathogen interaction on early pathogen replacement du... |
1307.4732 | Xiao-Jun Tian | Xiao-Jun Tian and Hang Zhang and Jianhua Xing | Coupled Reversible and Irreversible Bistable Switches Underlying
TGF-\beta-induced Epithelial to Mesenchymal Transition | 32 pages, 8 figures, accepted by Biophysical Journal | Biophys J 105, 1079 (2013) | 10.1016/j.bpj.2013.07.011 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Epithelial to mesenchymal transition (EMT) plays important roles in embryonic
development, tissue regeneration and cancer metastasis. While several feedback
loops have been shown to regulate EMT, it remains elusive how they coordinately
modulate EMT response to TGF-\beta treatment. We construct a mathematical model
f... | [
{
"created": "Wed, 17 Jul 2013 19:18:42 GMT",
"version": "v1"
},
{
"created": "Thu, 18 Jul 2013 02:00:01 GMT",
"version": "v2"
},
{
"created": "Fri, 19 Jul 2013 01:12:49 GMT",
"version": "v3"
},
{
"created": "Mon, 22 Jul 2013 20:23:38 GMT",
"version": "v4"
},
{
"c... | 2017-07-26 | [
[
"Tian",
"Xiao-Jun",
""
],
[
"Zhang",
"Hang",
""
],
[
"Xing",
"Jianhua",
""
]
] | Epithelial to mesenchymal transition (EMT) plays important roles in embryonic development, tissue regeneration and cancer metastasis. While several feedback loops have been shown to regulate EMT, it remains elusive how they coordinately modulate EMT response to TGF-\beta treatment. We construct a mathematical model for... |
1905.00334 | Johannes M\"uller | Burkhard A. Hense, Matthew McIntosh, Johannes M\"uller, Martin
Schuster | Homogeneous and Heterogeneous Response of Quorum-Sensing Bacteria in an
Evolutionary Context | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To explain the stability of cooperation is a central task of evolutionary
theory. We investigate this question in the case of quorum sensing (QS)
bacteria, which regulate cooperative traits in response to population density.
Cooperation is modeled by the prisoner's dilemma, where individuals produce a
costly public g... | [
{
"created": "Wed, 1 May 2019 14:47:05 GMT",
"version": "v1"
}
] | 2019-05-02 | [
[
"Hense",
"Burkhard A.",
""
],
[
"McIntosh",
"Matthew",
""
],
[
"Müller",
"Johannes",
""
],
[
"Schuster",
"Martin",
""
]
] | To explain the stability of cooperation is a central task of evolutionary theory. We investigate this question in the case of quorum sensing (QS) bacteria, which regulate cooperative traits in response to population density. Cooperation is modeled by the prisoner's dilemma, where individuals produce a costly public goo... |
q-bio/0309021 | V. Krishnan Ramanujan | R.V.Krishnan, H.Saitoh, H.Terada, V.E.Centonze and B.Herman | Development of a Multiphoton Fluorescence Lifetime Imaging Microscopy
(FLIM) system using a Streak Camera | null | Review of Scientific Instruments, Vol.74, 2714 (May 2003) | 10.1063/1.1569410 | null | q-bio.QM | null | We report the development and detailed calibration of a multiphoton
fluorescence lifetime imaging system (FLIM) using a streak camera. The present
system is versatile with high spatial (0.2 micron) and temporal (50 psec)
resolution and allows rapid data acquisition and reliable and reproducible
lifetime determination... | [
{
"created": "Tue, 30 Sep 2003 14:15:15 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Krishnan",
"R. V.",
""
],
[
"Saitoh",
"H.",
""
],
[
"Terada",
"H.",
""
],
[
"Centonze",
"V. E.",
""
],
[
"Herman",
"B.",
""
]
] | We report the development and detailed calibration of a multiphoton fluorescence lifetime imaging system (FLIM) using a streak camera. The present system is versatile with high spatial (0.2 micron) and temporal (50 psec) resolution and allows rapid data acquisition and reliable and reproducible lifetime determinations.... |
2403.07670 | Magnus Richardson | Magnus J E Richardson | Linear and non-linear integrate-and-fire neurons driven by synaptic shot
noise with reversal potentials | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The steady-state firing rate and firing-rate response of the leaky and
exponential integrate-and-fire models receiving synaptic shot noise with
excitatory and inhibitory reversal potentials is examined. For the particular
case where the underlying synaptic conductances are exponentially distributed,
it is shown that ... | [
{
"created": "Tue, 12 Mar 2024 14:02:15 GMT",
"version": "v1"
}
] | 2024-03-13 | [
[
"Richardson",
"Magnus J E",
""
]
] | The steady-state firing rate and firing-rate response of the leaky and exponential integrate-and-fire models receiving synaptic shot noise with excitatory and inhibitory reversal potentials is examined. For the particular case where the underlying synaptic conductances are exponentially distributed, it is shown that th... |
2407.15908 | Kevin Mitchell | Kevin J. Mitchell and Nick Cheney | The Genomic Code: The genome instantiates a generative model of the
organism | 31 pages, 4 figures | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | How does the genome encode the form of the organism? What is the nature of
this genomic code? Common metaphors, such as a blueprint or program, fail to
capture the complex, indirect, and evolutionarily dynamic relationship between
the genome and organismal form, or the constructive, interactive processes that
produce... | [
{
"created": "Mon, 22 Jul 2024 16:41:25 GMT",
"version": "v1"
}
] | 2024-07-24 | [
[
"Mitchell",
"Kevin J.",
""
],
[
"Cheney",
"Nick",
""
]
] | How does the genome encode the form of the organism? What is the nature of this genomic code? Common metaphors, such as a blueprint or program, fail to capture the complex, indirect, and evolutionarily dynamic relationship between the genome and organismal form, or the constructive, interactive processes that produce i... |
2401.13690 | Mark J. Hadley Dr | Mark J. Hadley | A generic model of consciousness | null | Journal of Artificial Intelligence and Consciousness 10
(2):291--308 (2023) | 10.1142/S2705078523500030 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | This is a model of consciousness. The hard problem of consciousness, what it
feels like, is answered. The work builds on medical research analyzing the
source and mechanisms associated with our feelings. It goes further by
describing a generic model with wide applicability. The model is fully
consistent with medical ... | [
{
"created": "Tue, 2 Jan 2024 11:41:28 GMT",
"version": "v1"
}
] | 2024-01-26 | [
[
"Hadley",
"Mark J.",
""
]
] | This is a model of consciousness. The hard problem of consciousness, what it feels like, is answered. The work builds on medical research analyzing the source and mechanisms associated with our feelings. It goes further by describing a generic model with wide applicability. The model is fully consistent with medical pa... |
0709.1916 | Andrea Cavagna | M. Ballerini, N. Cabibbo, R. Candelier, A. Cavagna, E. Cisbani, I.
Giardina, V. Lecomte, A. Orlandi, G. Parisi, A. Procaccini, M. Viale, V.
Zdravkovic | Interaction Ruling Animal Collective Behaviour Depends on Topological
rather than Metric Distance: Evidence from a Field Study | To be submitted to PNAS - 25 pages | PNAS, 105, 1232-1237 (2008) | 10.1073/pnas.0711437105 | null | q-bio.PE cond-mat.stat-mech | null | Numerical models indicate that collective animal behaviour may emerge from
simple local rules of interaction among the individuals. However, very little
is known about the nature of such interaction, so that models and theories
mostly rely on aprioristic assumptions. By reconstructing the three-dimensional
position o... | [
{
"created": "Wed, 12 Sep 2007 14:53:17 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Ballerini",
"M.",
""
],
[
"Cabibbo",
"N.",
""
],
[
"Candelier",
"R.",
""
],
[
"Cavagna",
"A.",
""
],
[
"Cisbani",
"E.",
""
],
[
"Giardina",
"I.",
""
],
[
"Lecomte",
"V.",
""
],
[
"Orlandi",
"A.... | Numerical models indicate that collective animal behaviour may emerge from simple local rules of interaction among the individuals. However, very little is known about the nature of such interaction, so that models and theories mostly rely on aprioristic assumptions. By reconstructing the three-dimensional position of ... |
1609.08297 | Namiko Mitarai | Cilie W. Feldager, Namiko Mitarai, and Hiroki Ohta | Deterministic extinction by mixing in cyclically competing species | 6 pages, 3 figures. More analysis added for even species case.
Accepted for publication in PRE | Phys. Rev. E 95, 032318 (2017) | 10.1103/PhysRevE.95.032318 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a cyclically competing species model on a ring with global mixing
at finite rate, which corresponds to the well-known Lotka-Volterra equation in
the limit of infinite mixing rate. Within a perturbation analysis of the model
from the infinite mixing rate, we provide analytical evidence that extinction
occu... | [
{
"created": "Tue, 27 Sep 2016 07:51:55 GMT",
"version": "v1"
},
{
"created": "Sat, 4 Mar 2017 10:00:05 GMT",
"version": "v2"
}
] | 2017-03-28 | [
[
"Feldager",
"Cilie W.",
""
],
[
"Mitarai",
"Namiko",
""
],
[
"Ohta",
"Hiroki",
""
]
] | We consider a cyclically competing species model on a ring with global mixing at finite rate, which corresponds to the well-known Lotka-Volterra equation in the limit of infinite mixing rate. Within a perturbation analysis of the model from the infinite mixing rate, we provide analytical evidence that extinction occurs... |
2203.05191 | Hamza Altakroury Dr. | Hamza Altakroury, Laurent Koessler, Radu Ranta, Janis Hofmanis, Sophie
Colnat Coulbois, Louis Maillard and Val\'erie Louis Dorr | Evaluation of Performance for Human In-Vivo Conductivity Estimation from
EEG and sEEG Recorded in Simultaneous with Intracerebral Electrical
Stimulation | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Assigning accurate conductivity values in human head models is an essential
factor for performing precise electroencephalographic (EEG) source localization
and targeting of transcranial electrical stimulation (TES). Unfortunately, the
literature reports diverging conductivity values of the different tissues in
the hu... | [
{
"created": "Thu, 10 Mar 2022 07:02:44 GMT",
"version": "v1"
}
] | 2022-03-11 | [
[
"Altakroury",
"Hamza",
""
],
[
"Koessler",
"Laurent",
""
],
[
"Ranta",
"Radu",
""
],
[
"Hofmanis",
"Janis",
""
],
[
"Coulbois",
"Sophie Colnat",
""
],
[
"Maillard",
"Louis",
""
],
[
"Dorr",
"Valérie Louis",
... | Assigning accurate conductivity values in human head models is an essential factor for performing precise electroencephalographic (EEG) source localization and targeting of transcranial electrical stimulation (TES). Unfortunately, the literature reports diverging conductivity values of the different tissues in the huma... |
1109.2057 | Dimitri Vvedensky | Joshua S. Gill, Mischa P. Woods, Carolyn M. Salafia, and Dimitri D.
Vvedensky | Probability distributions for measures of placental shape and morphology | 26 pages, 7 figures, 2 tables | null | null | null | q-bio.QM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Weight at delivery is a standard cumulative measure of placental growth. But
weight is a crude summary of other placental characteristics, such as the size
and shape of the chorionic plate and the location of the umbilical cord
insertion. Distributions of such measures across a cohort reveal information
about the dev... | [
{
"created": "Fri, 9 Sep 2011 16:16:15 GMT",
"version": "v1"
}
] | 2011-09-12 | [
[
"Gill",
"Joshua S.",
""
],
[
"Woods",
"Mischa P.",
""
],
[
"Salafia",
"Carolyn M.",
""
],
[
"Vvedensky",
"Dimitri D.",
""
]
] | Weight at delivery is a standard cumulative measure of placental growth. But weight is a crude summary of other placental characteristics, such as the size and shape of the chorionic plate and the location of the umbilical cord insertion. Distributions of such measures across a cohort reveal information about the devel... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.