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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1503.00399 | Hamidreza Badri | Hamidreza Badri and Yoichi Watanabe and Kevin Leder | Robust and probabilistic optimization of dose schedules in radiotherapy | null | null | null | null | q-bio.TO physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the effects of parameter uncertainty on the optimal radiation
schedule in the context of the linear-quadratic model. Our interest arises from
the observation that if inter-patient variations in OAR and tumor sensitivities
to radiation or sparing factor of the OAR are not accounted for during
radiation sch... | [
{
"created": "Mon, 2 Mar 2015 03:10:16 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Jun 2015 21:33:11 GMT",
"version": "v2"
}
] | 2015-06-05 | [
[
"Badri",
"Hamidreza",
""
],
[
"Watanabe",
"Yoichi",
""
],
[
"Leder",
"Kevin",
""
]
] | We consider the effects of parameter uncertainty on the optimal radiation schedule in the context of the linear-quadratic model. Our interest arises from the observation that if inter-patient variations in OAR and tumor sensitivities to radiation or sparing factor of the OAR are not accounted for during radiation sched... |
2201.04739 | Marcos Trevisan Dr. | Alejandro Pardo Pintos, Diego E Shalom, Enzo Tagliazucchi, Gabriel
Mindlin and Marcos A Trevisan | Cognitive forces shape the dynamics of word usage across multiple
languages | 8 pages, 3 figures | null | 10.1016/j.chaos.2022.112327 | null | q-bio.NC q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The analysis of thousands of time series in different languages reveals that
word usage presents oscillations with a prevalence of 16-year cycles, mounted
on slowly varying trends. These components carry different information: while
similar oscillatory patterns gather semantically related words, similar trends
group ... | [
{
"created": "Wed, 12 Jan 2022 23:32:38 GMT",
"version": "v1"
},
{
"created": "Thu, 10 Feb 2022 18:26:33 GMT",
"version": "v2"
}
] | 2022-07-20 | [
[
"Pintos",
"Alejandro Pardo",
""
],
[
"Shalom",
"Diego E",
""
],
[
"Tagliazucchi",
"Enzo",
""
],
[
"Mindlin",
"Gabriel",
""
],
[
"Trevisan",
"Marcos A",
""
]
] | The analysis of thousands of time series in different languages reveals that word usage presents oscillations with a prevalence of 16-year cycles, mounted on slowly varying trends. These components carry different information: while similar oscillatory patterns gather semantically related words, similar trends group to... |
1904.12652 | Azam Yazdani | Azam Yazdani, Akram Yazdani, Sarah H. Elsea, Daniel J. Schaid, Michael
R. Kosorok, Gita Dangol, Ahmad Samiei | Genome analysis and pleiotropy assessment using causal networks with
loss of function mutation and metabolomics | null | null | null | null | q-bio.GN stat.AP stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Many genome-wide association studies have detected genomic
regions associated with traits, yet understanding the functional causes of
association often remains elusive. Utilizing systems approaches and focusing on
intermediate molecular phenotypes might facilitate biologic understanding.
Results: The avai... | [
{
"created": "Mon, 29 Apr 2019 12:45:06 GMT",
"version": "v1"
}
] | 2019-04-30 | [
[
"Yazdani",
"Azam",
""
],
[
"Yazdani",
"Akram",
""
],
[
"Elsea",
"Sarah H.",
""
],
[
"Schaid",
"Daniel J.",
""
],
[
"Kosorok",
"Michael R.",
""
],
[
"Dangol",
"Gita",
""
],
[
"Samiei",
"Ahmad",
""
]
] | Background: Many genome-wide association studies have detected genomic regions associated with traits, yet understanding the functional causes of association often remains elusive. Utilizing systems approaches and focusing on intermediate molecular phenotypes might facilitate biologic understanding. Results: The availa... |
1811.05649 | Ramon Grima | Emma M. Keizer, Bjorn Bastian, Robert W. Smith, Ramon Grima and
Christian Fleck | Extending the linear-noise approximation to biochemical systems
influenced by intrinsic noise and slow lognormally distributed extrinsic
noise | 43 pages, 4 figures | Phys. Rev. E 99, 052417 (2019) | 10.1103/PhysRevE.99.052417 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is well known that the kinetics of an intracellular biochemical network is
stochastic. This is due to intrinsic noise arising from the random timing of
biochemical reactions in the network as well as due to extrinsic noise stemming
from the interaction of unknown molecular components with the network and from
the ... | [
{
"created": "Wed, 14 Nov 2018 05:25:10 GMT",
"version": "v1"
}
] | 2019-06-05 | [
[
"Keizer",
"Emma M.",
""
],
[
"Bastian",
"Bjorn",
""
],
[
"Smith",
"Robert W.",
""
],
[
"Grima",
"Ramon",
""
],
[
"Fleck",
"Christian",
""
]
] | It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from the interaction of unknown molecular components with the network and from the ce... |
2004.15018 | Wesley Pegden | Maria Chikina and Wesley Pegden | Failure of monotonicity in epidemic models | 7 pages, 4 figures. Code is available in arXiv'd files | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We discuss the failure of monotonicity properties for even simple
compartmental epidemic models, for the case where transmission rates are
non-constant. We also identify a special case in which monotonicity holds.
| [
{
"created": "Thu, 30 Apr 2020 17:58:17 GMT",
"version": "v1"
}
] | 2020-05-01 | [
[
"Chikina",
"Maria",
""
],
[
"Pegden",
"Wesley",
""
]
] | We discuss the failure of monotonicity properties for even simple compartmental epidemic models, for the case where transmission rates are non-constant. We also identify a special case in which monotonicity holds. |
1112.3357 | Steven Frank | Steven A. Frank | A general model of the public goods dilemma | null | Journal of Evolutionary Biology 23:1245-1250 (2010) | 10.1111/j.1420-9101.2010.01986.x | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An individually costly act that benefits all group members is a public good.
Natural selection favors individual contribution to public goods only when some
benefit to the individual offsets the cost of contribution. Problems of sex
ratio, parasite virulence, microbial metabolism, punishment of noncooperators,
and ne... | [
{
"created": "Wed, 14 Dec 2011 21:05:51 GMT",
"version": "v1"
}
] | 2011-12-16 | [
[
"Frank",
"Steven A.",
""
]
] | An individually costly act that benefits all group members is a public good. Natural selection favors individual contribution to public goods only when some benefit to the individual offsets the cost of contribution. Problems of sex ratio, parasite virulence, microbial metabolism, punishment of noncooperators, and near... |
q-bio/0403019 | Hiroshi Fujisaki | Hiroshi Fujisaki, Lintao Bu, and John E. Straub | Vibrational energy relaxation (VER) of a CD stretching mode in
cytochrome c | 20 pages, 7 figures, 3 tables, submitted to Adv. Chem. Phys. for the
proceedings of the YITP international symposium on "Geometrical structure of
phase space in multi-dimensional chaos: Applications to chemical reaction
dynamics in complex systems" | null | null | null | q-bio.BM | null | We first review how to determine the rate of vibrational energy relaxation
(VER) using perturbation theory. We then apply those theoretical results to the
problem of VER of a CD stretching mode in the protein cytochrome c. We model
cytochrome c in vacuum as a normal mode system with the lowest-order anharmonic
coupli... | [
{
"created": "Mon, 15 Mar 2004 20:42:06 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Mar 2004 17:11:29 GMT",
"version": "v2"
},
{
"created": "Thu, 26 Aug 2004 23:52:49 GMT",
"version": "v3"
}
] | 2007-05-23 | [
[
"Fujisaki",
"Hiroshi",
""
],
[
"Bu",
"Lintao",
""
],
[
"Straub",
"John E.",
""
]
] | We first review how to determine the rate of vibrational energy relaxation (VER) using perturbation theory. We then apply those theoretical results to the problem of VER of a CD stretching mode in the protein cytochrome c. We model cytochrome c in vacuum as a normal mode system with the lowest-order anharmonic coupling... |
q-bio/0409005 | Anders Irb\"ack | Giorgio Favrin, Anders Irb\"ack, Sandipan Mohanty | Oligomerization of amyloid Abeta peptides using hydrogen bonds and
hydrophobicity forces | 19 pages, 7 figures (to appear in Biophys. J.) | Biophys. J. 87 (2004) 3657-3664 | 10.1529/biophysj.104.046839 | LU TP 04-18 | q-bio.BM | null | The 16-22 amino acid fragment of the beta-amyloid peptide associated with the
Alzheimer's disease, Abeta, is capable of forming amyloid fibrils. Here we
study the aggregation mechanism of Abeta(16-22) peptides by unbiased
thermodynamic simulations at the atomic level for systems of one, three and six
Abeta(16-22) pep... | [
{
"created": "Wed, 1 Sep 2004 17:32:45 GMT",
"version": "v1"
},
{
"created": "Tue, 14 Sep 2004 20:50:48 GMT",
"version": "v2"
}
] | 2009-11-10 | [
[
"Favrin",
"Giorgio",
""
],
[
"Irbäck",
"Anders",
""
],
[
"Mohanty",
"Sandipan",
""
]
] | The 16-22 amino acid fragment of the beta-amyloid peptide associated with the Alzheimer's disease, Abeta, is capable of forming amyloid fibrils. Here we study the aggregation mechanism of Abeta(16-22) peptides by unbiased thermodynamic simulations at the atomic level for systems of one, three and six Abeta(16-22) pepti... |
1604.00268 | David Schwab | DJ Strouse, David J Schwab | The deterministic information bottleneck | 15 pages, 4 figures | null | null | null | q-bio.NC cond-mat.stat-mech cs.IT math.IT q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Lossy compression and clustering fundamentally involve a decision about what
features are relevant and which are not. The information bottleneck method (IB)
by Tishby, Pereira, and Bialek formalized this notion as an
information-theoretic optimization problem and proposed an optimal tradeoff
between throwing away as ... | [
{
"created": "Fri, 1 Apr 2016 14:48:31 GMT",
"version": "v1"
},
{
"created": "Mon, 19 Dec 2016 05:26:11 GMT",
"version": "v2"
}
] | 2017-02-23 | [
[
"Strouse",
"DJ",
""
],
[
"Schwab",
"David J",
""
]
] | Lossy compression and clustering fundamentally involve a decision about what features are relevant and which are not. The information bottleneck method (IB) by Tishby, Pereira, and Bialek formalized this notion as an information-theoretic optimization problem and proposed an optimal tradeoff between throwing away as ma... |
1812.10421 | Vyacheslav Volov | V.V. Eskov, V.T. Volov, V.M. Eskov, L.K. Ilyashenko | Chaotic dynamics of movements stochastic instability and the hypothesis
of N.A. Bernstein about "repetition without repetition" | 13 pages, 2 figures, 6 tables | null | null | null | q-bio.OT nlin.CD physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The registration of tremor was performed in two groups of subjects (15 people
in each group) with different physical fitness at rest and at a static loads of
3N. Each subject has been tested 15 series (number of series N=15) in both
states (with and without physical loads) and each series contained 15 samples
(n=15) ... | [
{
"created": "Fri, 21 Dec 2018 16:39:00 GMT",
"version": "v1"
}
] | 2018-12-27 | [
[
"Eskov",
"V. V.",
""
],
[
"Volov",
"V. T.",
""
],
[
"Eskov",
"V. M.",
""
],
[
"Ilyashenko",
"L. K.",
""
]
] | The registration of tremor was performed in two groups of subjects (15 people in each group) with different physical fitness at rest and at a static loads of 3N. Each subject has been tested 15 series (number of series N=15) in both states (with and without physical loads) and each series contained 15 samples (n=15) of... |
1312.7532 | Carsten Maedler | Carsten Maedler, Daniel Kim, Remco A. Spanjaard, Mi Hong, Shyamsunder
Erramilli, Pritiraj Mohanty | Detection of the melanoma biomarker TROY using silicon nanowire
field-effect transistors | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Antibody-functionalized silicon nanowire field-effect transistors have been
shown to exhibit excellent analyte detection sensitivity enabling sensing of
analyte concentrations at levels not readily accessible by other methods. One
example where accurate measurement of small concentrations is necessary is
detection of... | [
{
"created": "Sun, 29 Dec 2013 13:04:05 GMT",
"version": "v1"
}
] | 2013-12-31 | [
[
"Maedler",
"Carsten",
""
],
[
"Kim",
"Daniel",
""
],
[
"Spanjaard",
"Remco A.",
""
],
[
"Hong",
"Mi",
""
],
[
"Erramilli",
"Shyamsunder",
""
],
[
"Mohanty",
"Pritiraj",
""
]
] | Antibody-functionalized silicon nanowire field-effect transistors have been shown to exhibit excellent analyte detection sensitivity enabling sensing of analyte concentrations at levels not readily accessible by other methods. One example where accurate measurement of small concentrations is necessary is detection of s... |
q-bio/0402031 | Mauro Copelli | M. Copelli, M. H. R. Tragtenberg and O. Kinouchi | Stability diagrams for bursting neurons modeled by three-variable maps | 7 pages, 3 figures, accepted for publication | Physica A, 342, 263-269 (2004) | 10.1016/j.physa.2004.04.087 | null | q-bio.NC cond-mat.dis-nn nlin.CD physics.bio-ph | null | We study a simple map as a minimal model of excitable cells. The map has two
fast variables which mimic the behavior of class I neurons, undergoing a
sub-critical Hopf bifurcation. Adding a third slow variable allows the system
to present bursts and other interesting biological behaviors. Bifurcation lines
which loca... | [
{
"created": "Fri, 13 Feb 2004 22:51:17 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Copelli",
"M.",
""
],
[
"Tragtenberg",
"M. H. R.",
""
],
[
"Kinouchi",
"O.",
""
]
] | We study a simple map as a minimal model of excitable cells. The map has two fast variables which mimic the behavior of class I neurons, undergoing a sub-critical Hopf bifurcation. Adding a third slow variable allows the system to present bursts and other interesting biological behaviors. Bifurcation lines which locate... |
1903.04921 | Zi Chen | Catalina-Paula Spatarelu, Hao Zhang, Dung Trung Nguyen, Xinyue Han,
Ruchuan Liu, Qiaohang Guo, Jacob Notbohm, Jing Fan, Liyu Liu, and Zi Chen | Biomechanics of Collective Cell Migration in Cancer Progression --
Experimental and Computational Methods | null | null | null | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cell migration is essential for regulating many biological processes in
physiological or pathological conditions, including embryonic development and
cancer invasion. In vitro and in silico studies suggest that collective cell
migration is associated with some biomechanical particularities, such as
restructuring of e... | [
{
"created": "Tue, 12 Mar 2019 13:55:09 GMT",
"version": "v1"
}
] | 2019-03-13 | [
[
"Spatarelu",
"Catalina-Paula",
""
],
[
"Zhang",
"Hao",
""
],
[
"Nguyen",
"Dung Trung",
""
],
[
"Han",
"Xinyue",
""
],
[
"Liu",
"Ruchuan",
""
],
[
"Guo",
"Qiaohang",
""
],
[
"Notbohm",
"Jacob",
""
],
[
... | Cell migration is essential for regulating many biological processes in physiological or pathological conditions, including embryonic development and cancer invasion. In vitro and in silico studies suggest that collective cell migration is associated with some biomechanical particularities, such as restructuring of ext... |
0712.1970 | Julien Dervaux | Julien Dervaux, Martine Ben Amar | Morphogenesis of growing soft tissues | 4 pages, 3 figures | null | 10.1103/PhysRevLett.101.068101 | null | q-bio.TO | null | Recently, much attention has been given to a noteworthy property of some soft
tissues: their ability to grow. Many attempts have been made to model this
behaviour in biology, chemistry and physics. Using the theory of finite
elasticity, Rodriguez has postulated a multiplicative decomposition of the
geometric deformat... | [
{
"created": "Wed, 12 Dec 2007 16:21:02 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Dervaux",
"Julien",
""
],
[
"Amar",
"Martine Ben",
""
]
] | Recently, much attention has been given to a noteworthy property of some soft tissues: their ability to grow. Many attempts have been made to model this behaviour in biology, chemistry and physics. Using the theory of finite elasticity, Rodriguez has postulated a multiplicative decomposition of the geometric deformatio... |
1606.03071 | Umut G\"u\c{c}l\"u | Umut G\"u\c{c}l\"u, Marcel A. J. van Gerven | Modeling the dynamics of human brain activity with recurrent neural
networks | null | null | 10.3389/fncom.2017.00007 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Encoding models are used for predicting brain activity in response to sensory
stimuli with the objective of elucidating how sensory information is
represented in the brain. Encoding models typically comprise a nonlinear
transformation of stimuli to features (feature model) and a linear
transformation of features to r... | [
{
"created": "Thu, 9 Jun 2016 19:22:13 GMT",
"version": "v1"
}
] | 2017-03-13 | [
[
"Güçlü",
"Umut",
""
],
[
"van Gerven",
"Marcel A. J.",
""
]
] | Encoding models are used for predicting brain activity in response to sensory stimuli with the objective of elucidating how sensory information is represented in the brain. Encoding models typically comprise a nonlinear transformation of stimuli to features (feature model) and a linear transformation of features to res... |
q-bio/0309006 | Sven Bilke | S. Bilke, T. Breslin, M. Sigvardsson | Probabilistic estimation of microarray data reliability and underlying
gene expression | 11 pages, 4 figures | BMC Bioinformatics 4:40 (2003) | null | LU TP 02-14 | q-bio.QM | null | Background: The availability of high throughput methods for measurement of
mRNA concentrations makes the reliability of conclusions drawn from the data
and global quality control of samples and hybridization important issues. We
address these issues by an information theoretic approach, applied to
discretized express... | [
{
"created": "Thu, 18 Sep 2003 15:22:50 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bilke",
"S.",
""
],
[
"Breslin",
"T.",
""
],
[
"Sigvardsson",
"M.",
""
]
] | Background: The availability of high throughput methods for measurement of mRNA concentrations makes the reliability of conclusions drawn from the data and global quality control of samples and hybridization important issues. We address these issues by an information theoretic approach, applied to discretized expressio... |
2111.14159 | Uria Mor | Uria Mor, Yotam Cohen, Rafael Valdes-Mas, Denise Kviatcovsky, Eran
Elinav, Haim Avron | Dimensionality Reduction of Longitudinal 'Omics Data using Modern Tensor
Factorization | null | null | 10.1371/journal.pcbi.1010212 | null | q-bio.QM cs.CE cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Precision medicine is a clinical approach for disease prevention, detection
and treatment, which considers each individual's genetic background,
environment and lifestyle. The development of this tailored avenue has been
driven by the increased availability of omics methods, large cohorts of
temporal samples, and the... | [
{
"created": "Sun, 28 Nov 2021 14:50:14 GMT",
"version": "v1"
}
] | 2022-07-26 | [
[
"Mor",
"Uria",
""
],
[
"Cohen",
"Yotam",
""
],
[
"Valdes-Mas",
"Rafael",
""
],
[
"Kviatcovsky",
"Denise",
""
],
[
"Elinav",
"Eran",
""
],
[
"Avron",
"Haim",
""
]
] | Precision medicine is a clinical approach for disease prevention, detection and treatment, which considers each individual's genetic background, environment and lifestyle. The development of this tailored avenue has been driven by the increased availability of omics methods, large cohorts of temporal samples, and their... |
1307.4141 | Naoki Masuda Dr. | Naoki Masuda | Evolution via imitation among like-minded individuals | 3 figures | Journal of Theoretical Biology, 349, 100-108 (2014) | 10.1016/j.jtbi.2014.02.003 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In social situations with which evolutionary game is concerned, individuals
are considered to be heterogeneous in various aspects. In particular, they may
differently perceive the same outcome of the game owing to heterogeneity in
idiosyncratic preferences, fighting abilities, and positions in a social
network. In su... | [
{
"created": "Tue, 16 Jul 2013 01:20:47 GMT",
"version": "v1"
},
{
"created": "Thu, 6 Mar 2014 17:20:32 GMT",
"version": "v2"
}
] | 2014-03-07 | [
[
"Masuda",
"Naoki",
""
]
] | In social situations with which evolutionary game is concerned, individuals are considered to be heterogeneous in various aspects. In particular, they may differently perceive the same outcome of the game owing to heterogeneity in idiosyncratic preferences, fighting abilities, and positions in a social network. In such... |
1203.4771 | Jens Christian Claussen | Markus Sch\"utt and Jens Christian Claussen | Desynchronizing effect of high-frequency stimulation in a generic
cortical network model | 9 pages, figs included. Accepted for publication in Cognitive
Neurodynamics | Cognitive Neurodynamics 6 (4), 343-351 (2012) | 10.1007/s11571-012-9199-8 | null | q-bio.NC cond-mat.dis-nn nlin.CD physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transcranial Electrical Stimulation (TCES) and Deep Brain Stimulation (DBS)
are two different applications of electrical current to the brain used in
different areas of medicine. Both have a similar frequency dependence of their
efficiency, with the most pronounced effects around 100Hz. We apply
superthreshold electr... | [
{
"created": "Wed, 21 Mar 2012 16:16:30 GMT",
"version": "v1"
}
] | 2019-07-15 | [
[
"Schütt",
"Markus",
""
],
[
"Claussen",
"Jens Christian",
""
]
] | Transcranial Electrical Stimulation (TCES) and Deep Brain Stimulation (DBS) are two different applications of electrical current to the brain used in different areas of medicine. Both have a similar frequency dependence of their efficiency, with the most pronounced effects around 100Hz. We apply superthreshold electric... |
2003.11094 | Borko D. Stosic | Borko Stosic | Phenomenological analysis of the 2020 COVID-19 outbreak dynamics | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the wake of the COVID-19 virus outbreak, a brief phenomenological
(descriptive, comparative) analysis of the dynamics of the disease spread among
different countries is presented. Results indicate that the infection spread
dynamics is currently the most pronounced in the USA (confirmed cases are
currently doubling... | [
{
"created": "Tue, 24 Mar 2020 19:59:17 GMT",
"version": "v1"
}
] | 2020-03-26 | [
[
"Stosic",
"Borko",
""
]
] | In the wake of the COVID-19 virus outbreak, a brief phenomenological (descriptive, comparative) analysis of the dynamics of the disease spread among different countries is presented. Results indicate that the infection spread dynamics is currently the most pronounced in the USA (confirmed cases are currently doubling e... |
2010.02368 | Delfim F. M. Torres | Cristiana J. Silva, Guillaume Cantin, Carla Cruz, Rui Fonseca-Pinto,
Rui Passadouro da Fonseca, Estevao Soares dos Santos, Delfim F. M. Torres | Complex network model for COVID-19: human behavior, pseudo-periodic
solutions and multiple epidemic waves | 23 pages, 10 figures, submitted 5-Oct-2020 | J. Math. Anal. Appl. 514 (2022), no. 2, Art. 125171, 25pp | 10.1016/j.jmaa.2021.125171 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a mathematical model for the transmission dynamics of SARS-CoV-2
in a homogeneously mixing non constant population, and generalize it to a model
where the parameters are given by piecewise constant functions. This allows us
to model the human behavior and the impact of public health policies on the
dynamic... | [
{
"created": "Mon, 5 Oct 2020 22:22:40 GMT",
"version": "v1"
}
] | 2022-06-20 | [
[
"Silva",
"Cristiana J.",
""
],
[
"Cantin",
"Guillaume",
""
],
[
"Cruz",
"Carla",
""
],
[
"Fonseca-Pinto",
"Rui",
""
],
[
"da Fonseca",
"Rui Passadouro",
""
],
[
"Santos",
"Estevao Soares dos",
""
],
[
"Torres",
... | We propose a mathematical model for the transmission dynamics of SARS-CoV-2 in a homogeneously mixing non constant population, and generalize it to a model where the parameters are given by piecewise constant functions. This allows us to model the human behavior and the impact of public health policies on the dynamics ... |
2405.03370 | Magnus Haraldson H{\o}ie | Magnus Haraldson H{\o}ie and Alissa Hummer and Tobias H. Olsen and
Broncio Aguilar-Sanjuan and Morten Nielsen and Charlotte M. Deane | AntiFold: Improved antibody structure-based design using inverse folding | null | null | null | null | q-bio.BM q-bio.QM | http://creativecommons.org/licenses/by-sa/4.0/ | The design and optimization of antibodies requires an intricate balance
across multiple properties. Protein inverse folding models, capable of
generating diverse sequences folding into the same structure, are promising
tools for maintaining structural integrity during antibody design. Here, we
present AntiFold, an an... | [
{
"created": "Mon, 6 May 2024 11:23:47 GMT",
"version": "v1"
}
] | 2024-05-07 | [
[
"Høie",
"Magnus Haraldson",
""
],
[
"Hummer",
"Alissa",
""
],
[
"Olsen",
"Tobias H.",
""
],
[
"Aguilar-Sanjuan",
"Broncio",
""
],
[
"Nielsen",
"Morten",
""
],
[
"Deane",
"Charlotte M.",
""
]
] | The design and optimization of antibodies requires an intricate balance across multiple properties. Protein inverse folding models, capable of generating diverse sequences folding into the same structure, are promising tools for maintaining structural integrity during antibody design. Here, we present AntiFold, an anti... |
1405.4357 | John Canning prof | Md. Arafat Hossain, John Canning, Sandra Ast, Peter J. Rutledge, Teh
Li Yen, Abbas Jamalipour | Lab-in-a-phone: Smartphone-based Portable Fluorometer for pH Field
Measurements of Environmental Water | Submitted to IEEE Sensors Journal 21_2_2014 | null | 10.1109/JSEN.2014.2361651 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A novel portable fluorometer combining the attributes of a smartphone with an
easy fit, simple and compact sample chamber fabricated using 3D printing has
been developed for pH measurements of environmental water in the field. The
results were then compared directly with those obtained using conventional
electrode ba... | [
{
"created": "Sat, 17 May 2014 06:40:13 GMT",
"version": "v1"
}
] | 2015-06-11 | [
[
"Hossain",
"Md. Arafat",
""
],
[
"Canning",
"John",
""
],
[
"Ast",
"Sandra",
""
],
[
"Rutledge",
"Peter J.",
""
],
[
"Yen",
"Teh Li",
""
],
[
"Jamalipour",
"Abbas",
""
]
] | A novel portable fluorometer combining the attributes of a smartphone with an easy fit, simple and compact sample chamber fabricated using 3D printing has been developed for pH measurements of environmental water in the field. The results were then compared directly with those obtained using conventional electrode base... |
2404.19309 | Noam Ben-Eliezer | Liad Doniza (1), Mitchel Lee (2), Tamar Blumenfeld Katzir (3), Moran
Artzi (4,5,6), Dafna Ben Bashat (4,5,6), Dvir Radunsky (3), Karin Shmueli
(2), Noam Ben-Eliezer (3,5,7) ((1) Department of Electrical Engineering, Tel
Aviv University, Tel Aviv, Israel, (2) Department of Medical Physics and
Biomedical Engineer... | Noise propagation and MP-PCA image denoising for high-resolution
quantitative T2* and magnetic susceptibility mapping (QSM) | 9 pages, 8 figures, 3 tables. It was accepted to be presented in a
peer-reviewed annual ISMRM meeting, which will be held in Singapore in May
2024 | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quantitative Susceptibility Mapping (QSM) is a technique for measuring
magnetic susceptibility of tissues, aiding in the detection of pathologies like
traumatic brain injury and multiple sclerosis by analyzing variations in
substances such as iron and calcium. Despite its clinical value, achieving
high-resolution QSM... | [
{
"created": "Tue, 30 Apr 2024 07:28:14 GMT",
"version": "v1"
}
] | 2024-05-01 | [
[
"Doniza",
"Liad",
""
],
[
"Lee",
"Mitchel",
""
],
[
"Katzir",
"Tamar Blumenfeld",
""
],
[
"Artzi",
"Moran",
""
],
[
"Bashat",
"Dafna Ben",
""
],
[
"Radunsky",
"Dvir",
""
],
[
"Shmueli",
"Karin",
""
],
[... | Quantitative Susceptibility Mapping (QSM) is a technique for measuring magnetic susceptibility of tissues, aiding in the detection of pathologies like traumatic brain injury and multiple sclerosis by analyzing variations in substances such as iron and calcium. Despite its clinical value, achieving high-resolution QSM (... |
1504.07833 | Ovidiu Radulescu | Ovidiu Radulescu, Satya Swarup Samal, Aur\'elien Naldi, Dima
Grigoriev, Andreas Weber | Symbolic dynamics of biochemical pathways as finite states machines | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We discuss the symbolic dynamics of biochemical networks with separate
timescales. We show that symbolic dynamics of monomolecular reaction networks
with separated rate constants can be described by deterministic, acyclic
automata with a number of states that is inferior to the number of biochemical
species. For nonl... | [
{
"created": "Wed, 29 Apr 2015 12:38:17 GMT",
"version": "v1"
},
{
"created": "Sun, 5 Jul 2015 20:25:22 GMT",
"version": "v2"
}
] | 2015-07-07 | [
[
"Radulescu",
"Ovidiu",
""
],
[
"Samal",
"Satya Swarup",
""
],
[
"Naldi",
"Aurélien",
""
],
[
"Grigoriev",
"Dima",
""
],
[
"Weber",
"Andreas",
""
]
] | We discuss the symbolic dynamics of biochemical networks with separate timescales. We show that symbolic dynamics of monomolecular reaction networks with separated rate constants can be described by deterministic, acyclic automata with a number of states that is inferior to the number of biochemical species. For nonlin... |
2310.09175 | Kingsley Cox | Kingsley J.A. Cox and Paul R. Adams | Shedding light on social learning | 11 pages 8 figures | null | null | null | q-bio.NC q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Culture involves the origination and transmission of ideas, but the
conditions in which culture can emerge and evolve are unclear. We constructed
and studied a highly simplified neural-network model of these processes. In
this model ideas originate by individual learning from the environment and are
transmitted by co... | [
{
"created": "Fri, 13 Oct 2023 15:09:44 GMT",
"version": "v1"
}
] | 2023-10-16 | [
[
"Cox",
"Kingsley J. A.",
""
],
[
"Adams",
"Paul R.",
""
]
] | Culture involves the origination and transmission of ideas, but the conditions in which culture can emerge and evolve are unclear. We constructed and studied a highly simplified neural-network model of these processes. In this model ideas originate by individual learning from the environment and are transmitted by comm... |
2011.05853 | Robert Worden | Robert Worden | The Aggregator Model of Spatial Cognition | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tracking the positions of objects in local space is a core function of animal
brains. We do not yet understand how it is done with limited neural resources.
The challenges of spatial cognition are discussed under the criteria: (a)
scaling of computational costs; (b) feature binding; (c) precise calculation of
spatial... | [
{
"created": "Wed, 4 Nov 2020 12:22:59 GMT",
"version": "v1"
},
{
"created": "Thu, 19 Nov 2020 18:01:40 GMT",
"version": "v2"
}
] | 2020-11-20 | [
[
"Worden",
"Robert",
""
]
] | Tracking the positions of objects in local space is a core function of animal brains. We do not yet understand how it is done with limited neural resources. The challenges of spatial cognition are discussed under the criteria: (a) scaling of computational costs; (b) feature binding; (c) precise calculation of spatial d... |
2306.09408 | Zachary G. Nicolaou | Zachary G. Nicolaou, Schuyler B. Nicholson, Adilson E. Motter, and
Jason R. Green | Prevalence of multistability and nonstationarity in driven chemical
networks | 12 pages, 4 figures | J. Chem. Phys. 158, 225101 (2023) | 10.1063/5.0142589 | null | q-bio.MN nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | External flows of energy, entropy, and matter can cause sudden transitions in
the stability of biological and industrial systems, fundamentally altering
their dynamical function. How might we control and design these transitions in
chemical reaction networks? Here, we analyze transitions giving rise to complex
behavi... | [
{
"created": "Thu, 15 Jun 2023 18:00:02 GMT",
"version": "v1"
}
] | 2023-06-19 | [
[
"Nicolaou",
"Zachary G.",
""
],
[
"Nicholson",
"Schuyler B.",
""
],
[
"Motter",
"Adilson E.",
""
],
[
"Green",
"Jason R.",
""
]
] | External flows of energy, entropy, and matter can cause sudden transitions in the stability of biological and industrial systems, fundamentally altering their dynamical function. How might we control and design these transitions in chemical reaction networks? Here, we analyze transitions giving rise to complex behavior... |
2207.04568 | Tom Chou | Xiangting Li and Tom Chou | Stochastic dynamics and ribosome-RNAP interactions in
Transcription-Translation Coupling | Submitted to Biophysical Journal. 23 pages, 11 figures | null | 10.1016/j.bpj.2022.09.041 | null | q-bio.SC cond-mat.stat-mech q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Under certain cellular conditions, transcription and mRNA translation in
prokaryotes appear to be "coupled," in which the formation of mRNA transcript
and production of its associated protein are temporally correlated. Such
transcription-translation coupling (TTC) has been evoked as a mechanism that
speeds up the ove... | [
{
"created": "Sun, 10 Jul 2022 23:55:46 GMT",
"version": "v1"
}
] | 2023-01-18 | [
[
"Li",
"Xiangting",
""
],
[
"Chou",
"Tom",
""
]
] | Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such transcription-translation coupling (TTC) has been evoked as a mechanism that speeds up the overa... |
2405.07771 | Samuel Gornard-Laidet | Samuel Gornard (EGCE), Florence Mougel, Isabelle Germon, V\'eronique
Borday-Birraux, Pascaline Venon, Salimata Drabo, Laure Marie-Paule
Kaiser-Arnauld | Cellular dynamics of host-parasitoid interactions: Insights from the
encapsulation process in a partially resistant host | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cotesia typhae is an eastern African endoparasitoid braconid wasp that
targets the larval stage of the lepidopteran stem borer, Sesamia nonagrioides,
a maize crop pest in Europe. The French host population is partially resistant
to the Makindu strain of the wasp, allowing its development in only 40% of the
cases. Res... | [
{
"created": "Mon, 13 May 2024 14:16:19 GMT",
"version": "v1"
}
] | 2024-05-14 | [
[
"Gornard",
"Samuel",
"",
"EGCE"
],
[
"Mougel",
"Florence",
""
],
[
"Germon",
"Isabelle",
""
],
[
"Borday-Birraux",
"Véronique",
""
],
[
"Venon",
"Pascaline",
""
],
[
"Drabo",
"Salimata",
""
],
[
"Kaiser-Arnauld... | Cotesia typhae is an eastern African endoparasitoid braconid wasp that targets the larval stage of the lepidopteran stem borer, Sesamia nonagrioides, a maize crop pest in Europe. The French host population is partially resistant to the Makindu strain of the wasp, allowing its development in only 40% of the cases. Resis... |
2006.15706 | Rudy Kusdiantara | H. Susanto, V.R. Tjahjono, A. Hasan, M.F. Kasim, N. Nuraini, E.R.M.
Putri, R. Kusdiantara, H. Kurniawan | How many can you infect? Simple (and naive) methods of estimating the
reproduction number | http://journals.itb.ac.id/index.php/cbms/article/view/13808 | COMMUN. BIOMATH. SCI., VOL. 3, NO. 1, 2020, PP. 28-36, 2020 | null | null | q-bio.PE physics.soc-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This is a pedagogical paper on estimating the number of people that can be
infected by one infectious person during an epidemic outbreak, known as the
reproduction number. Knowing the number is crucial for developing policy
responses. There are generally two types of such a number, i.e., basic and
effective (or insta... | [
{
"created": "Sun, 28 Jun 2020 20:45:29 GMT",
"version": "v1"
}
] | 2020-06-30 | [
[
"Susanto",
"H.",
""
],
[
"Tjahjono",
"V. R.",
""
],
[
"Hasan",
"A.",
""
],
[
"Kasim",
"M. F.",
""
],
[
"Nuraini",
"N.",
""
],
[
"Putri",
"E. R. M.",
""
],
[
"Kusdiantara",
"R.",
""
],
[
"Kurniawan",... | This is a pedagogical paper on estimating the number of people that can be infected by one infectious person during an epidemic outbreak, known as the reproduction number. Knowing the number is crucial for developing policy responses. There are generally two types of such a number, i.e., basic and effective (or instant... |
q-bio/0512048 | Marek Czachor | Diederik Aerts, Marek Czachor | Two-state dynamics for replicating two-strand systems | revtex, 3 eps figures | Open Systems & Inf. Dynamics 14, 397-410 (2007) | null | null | q-bio.PE nlin.PS quant-ph | null | We propose a formalism for describing two-strand systems of a DNA type by
means of soliton von Neumann equations, and illustrate how it works on a simple
example exactly solvably by a Darboux transformation. The main idea behind the
construction is the link between solutions of von Neumann equations and
entangled sta... | [
{
"created": "Fri, 30 Dec 2005 16:15:13 GMT",
"version": "v1"
}
] | 2008-01-30 | [
[
"Aerts",
"Diederik",
""
],
[
"Czachor",
"Marek",
""
]
] | We propose a formalism for describing two-strand systems of a DNA type by means of soliton von Neumann equations, and illustrate how it works on a simple example exactly solvably by a Darboux transformation. The main idea behind the construction is the link between solutions of von Neumann equations and entangled state... |
2106.02948 | Yu Takagi | Yu Takagi, Laurence T. Hunt, Ryu Ohata, Hiroshi Imamizu, Jun-ichiro
Hirayama | Neural dSCA: demixing multimodal interaction among brain areas during
naturalistic experiments | null | null | null | null | q-bio.NC cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Multi-regional interaction among neuronal populations underlies the brain's
processing of rich sensory information in our daily lives. Recent neuroscience
and neuroimaging studies have increasingly used naturalistic stimuli and
experimental design to identify such realistic sensory computation in the
brain. However, ... | [
{
"created": "Sat, 5 Jun 2021 19:16:21 GMT",
"version": "v1"
}
] | 2021-06-08 | [
[
"Takagi",
"Yu",
""
],
[
"Hunt",
"Laurence T.",
""
],
[
"Ohata",
"Ryu",
""
],
[
"Imamizu",
"Hiroshi",
""
],
[
"Hirayama",
"Jun-ichiro",
""
]
] | Multi-regional interaction among neuronal populations underlies the brain's processing of rich sensory information in our daily lives. Recent neuroscience and neuroimaging studies have increasingly used naturalistic stimuli and experimental design to identify such realistic sensory computation in the brain. However, ex... |
1710.10860 | Christopher Lester | Christopher Lester | Efficient simulation techniques for biochemical reaction networks | Doctor of Philosophy thesis submitted at the University of Oxford.
This research was supervised by Prof Ruth E. Baker and Dr Christian A. Yates | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Discrete-state, continuous-time Markov models are becoming commonplace in the
modelling of biochemical processes. The mathematical formulations that such
models lead to are opaque, and, due to their complexity, are often considered
analytically intractable. As such, a variety of Monte Carlo simulation
algorithms have... | [
{
"created": "Mon, 30 Oct 2017 10:48:02 GMT",
"version": "v1"
}
] | 2017-10-31 | [
[
"Lester",
"Christopher",
""
]
] | Discrete-state, continuous-time Markov models are becoming commonplace in the modelling of biochemical processes. The mathematical formulations that such models lead to are opaque, and, due to their complexity, are often considered analytically intractable. As such, a variety of Monte Carlo simulation algorithms have b... |
2004.03934 | Ginestra Bianconi | Ginestra Bianconi, Pavel L. Krapivsky | Epidemics with containment measures | (15 pages, 6 figures) | Phys. Rev. E 102, 032305 (2020) | 10.1103/PhysRevE.102.032305 | null | q-bio.PE cond-mat.dis-nn cond-mat.stat-mech physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a tractable epidemic model that includes containment measures. In
the absence of containment measures, the epidemics spread exponentially fast
whenever the infectivity rate is positive, $\lambda>0$. The containment
measures are modeled by considering a time-dependent modulation of the bare
infectivity $\la... | [
{
"created": "Wed, 8 Apr 2020 11:06:20 GMT",
"version": "v1"
},
{
"created": "Wed, 28 Oct 2020 09:22:46 GMT",
"version": "v2"
}
] | 2020-10-29 | [
[
"Bianconi",
"Ginestra",
""
],
[
"Krapivsky",
"Pavel L.",
""
]
] | We propose a tractable epidemic model that includes containment measures. In the absence of containment measures, the epidemics spread exponentially fast whenever the infectivity rate is positive, $\lambda>0$. The containment measures are modeled by considering a time-dependent modulation of the bare infectivity $\lamb... |
2407.06596 | Benjamin Morillon | J\'er\'emy Giroud, Benjamin Morillon (INS) | Beyond acoustics -- capacity limitations of linguistic levels | Rhythms of Speech and Language-Table of Contents, In press | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Speech is a multiplexed signal displaying levels of complexity,
organizational principles and perceptual units of analysis at distinct
timescales. This critical acoustic signal for human communication is thus
characterized at distinct representational and temporal scales, related to
distinct linguistic features, from... | [
{
"created": "Tue, 9 Jul 2024 06:57:07 GMT",
"version": "v1"
}
] | 2024-07-10 | [
[
"Giroud",
"Jérémy",
"",
"INS"
],
[
"Morillon",
"Benjamin",
"",
"INS"
]
] | Speech is a multiplexed signal displaying levels of complexity, organizational principles and perceptual units of analysis at distinct timescales. This critical acoustic signal for human communication is thus characterized at distinct representational and temporal scales, related to distinct linguistic features, from a... |
1506.02539 | Christian Matek | Christian Matek, Petr \v{S}ulc, Ferdinando Randisi, Jonathan P. K.
Doye, Ard A. Louis | Coarse-grained modelling of supercoiled RNA | 8 pages + 5 pages Supplementary Material | J. Chem. Phys. 143, 243122 (2015) | 10.1063/1.4933066 | null | q-bio.BM cond-mat.soft physics.bio-ph physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the behaviour of double-stranded RNA under twist and tension using
oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit
salt-dependence into the model allows us to directly compare our results to
data from recent single-molecule experiments. The model reproduces extension
curves as a... | [
{
"created": "Mon, 8 Jun 2015 15:14:42 GMT",
"version": "v1"
}
] | 2016-01-19 | [
[
"Matek",
"Christian",
""
],
[
"Šulc",
"Petr",
""
],
[
"Randisi",
"Ferdinando",
""
],
[
"Doye",
"Jonathan P. K.",
""
],
[
"Louis",
"Ard A.",
""
]
] | We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a f... |
1612.01150 | Richard Granger | A Rodriguez, R Granger | The grammar of mammalian brain capacity | 18 pages, 2 figures, 2 tables | Theoretical Computer Science 633 (2016) 100-111 | 10.1016/j.tcs.2016.03.021 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Uniquely human abilities may arise from special-purpose brain circuitry, or
from concerted general capacity increases due to our outsized brains. We
forward a novel hypothesis of the relation between computational capacity and
brain size, linking mathematical formalisms of grammars with the allometric
increases in co... | [
{
"created": "Sun, 4 Dec 2016 17:40:44 GMT",
"version": "v1"
}
] | 2016-12-06 | [
[
"Rodriguez",
"A",
""
],
[
"Granger",
"R",
""
]
] | Uniquely human abilities may arise from special-purpose brain circuitry, or from concerted general capacity increases due to our outsized brains. We forward a novel hypothesis of the relation between computational capacity and brain size, linking mathematical formalisms of grammars with the allometric increases in cort... |
2406.06985 | Huiming Xia | Huiming Xia, My Hoang, Evelyn Schmidt, Susanna Kiwala, Joshua
McMichael, Zachary L. Skidmore, Bryan Fisk, Jonathan J. Song, Jasreet Hundal,
Thomas Mooney, Jason R. Walker, S. Peter Goedegebuure, Christopher A. Miller,
William E. Gillanders, Obi L. Griffith, Malachi Griffith | pVACview: an interactive visualization tool for efficient neoantigen
prioritization and selection | Supplemental tables available at 10.5281/zenodo.11534338 | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Neoantigen targeting therapies including personalized vaccines have shown
promise in the treatment of cancers. Accurate identification/prioritization of
neoantigens is highly relevant to designing clinical trials, predicting
treatment response, and understanding mechanisms of resistance. With the advent
of massively ... | [
{
"created": "Tue, 11 Jun 2024 06:28:56 GMT",
"version": "v1"
}
] | 2024-06-12 | [
[
"Xia",
"Huiming",
""
],
[
"Hoang",
"My",
""
],
[
"Schmidt",
"Evelyn",
""
],
[
"Kiwala",
"Susanna",
""
],
[
"McMichael",
"Joshua",
""
],
[
"Skidmore",
"Zachary L.",
""
],
[
"Fisk",
"Bryan",
""
],
[
"... | Neoantigen targeting therapies including personalized vaccines have shown promise in the treatment of cancers. Accurate identification/prioritization of neoantigens is highly relevant to designing clinical trials, predicting treatment response, and understanding mechanisms of resistance. With the advent of massively pa... |
q-bio/0612037 | Le Zhang | Le Zhang, Costas G. Strouthos, Zhihui Wang, and Thomas S. Deisboeck | Simulating Brain Tumor Heterogeneity with a Multiscale Agent-Based
Model: Linking Molecular Signatures, Phenotypes and Expansion Rate | 37 pages, 10 figures | Mathematical and Computer Modelling 49 (1-2), pp. 307-319, 2009 | 10.1016/j.mcm.2008.05.011 | null | q-bio.TO q-bio.MN | null | We have extended our previously developed 3D multi-scale agent-based brain
tumor model to simulate cancer heterogeneity and to analyze its impact across
the scales of interest. While our algorithm continues to employ an epidermal
growth factor receptor (EGFR) gene-protein interaction network to determine the
cells' p... | [
{
"created": "Mon, 18 Dec 2006 20:20:37 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Jan 2007 18:50:02 GMT",
"version": "v2"
},
{
"created": "Mon, 16 Jul 2007 16:47:50 GMT",
"version": "v3"
}
] | 2010-03-23 | [
[
"Zhang",
"Le",
""
],
[
"Strouthos",
"Costas G.",
""
],
[
"Wang",
"Zhihui",
""
],
[
"Deisboeck",
"Thomas S.",
""
]
] | We have extended our previously developed 3D multi-scale agent-based brain tumor model to simulate cancer heterogeneity and to analyze its impact across the scales of interest. While our algorithm continues to employ an epidermal growth factor receptor (EGFR) gene-protein interaction network to determine the cells' phe... |
0811.4581 | Michal Wojciechowski dr | M. Wojciechowski and Marek Cieplak | Effects of confinement and crowding on folding of model proteins | null | Biosystems. 2008 Dec;94(3):248-52 | 10.1016/j.biosystems.2008.06.016 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We perform molecular dynamics simulations for a simple coarse-grained model
of crambin placed inside of a softly repulsive sphere of radius R. The
confinement makes folding at the optimal temperature slower and affects the
folding scenarios, but both effects are not dramatic. The influence of crowding
on folding are ... | [
{
"created": "Thu, 27 Nov 2008 16:21:42 GMT",
"version": "v1"
}
] | 2008-12-01 | [
[
"Wojciechowski",
"M.",
""
],
[
"Cieplak",
"Marek",
""
]
] | We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding scenarios, but both effects are not dramatic. The influence of crowding on folding are st... |
q-bio/0401040 | Thorsten Poeschel | Thorsten Poeschel, Werner Ebeling, Cornelius Froemmel, Rosa Ramirez | Correction algorithm for finite sample statistics | 11 pages, 9 figures | Eur. Phys. J. E, Vol. 12, 531-541 (2003). | null | null | q-bio.OT cond-mat.stat-mech | null | Assume in a sample of size M one finds M_i representatives of species i with
i=1...N^*. The normalized frequency p^*_i=M_i/M, based on the finite sample,
may deviate considerably from the true probabilities p_i. We propose a method
to infer rank-ordered true probabilities r_i from measured frequencies M_i. We
show th... | [
{
"created": "Wed, 28 Jan 2004 10:11:19 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Poeschel",
"Thorsten",
""
],
[
"Ebeling",
"Werner",
""
],
[
"Froemmel",
"Cornelius",
""
],
[
"Ramirez",
"Rosa",
""
]
] | Assume in a sample of size M one finds M_i representatives of species i with i=1...N^*. The normalized frequency p^*_i=M_i/M, based on the finite sample, may deviate considerably from the true probabilities p_i. We propose a method to infer rank-ordered true probabilities r_i from measured frequencies M_i. We show that... |
1501.02402 | Ariana Anderson | Ariana E. Anderson, Wesley T. Kerr, April Thames, Tong Li, Jiayang
Xiao, Mark S. Cohen | Electronic health record phenotyping improves detection and screening of
type 2 diabetes in the general United States population: A cross-sectional,
unselected, retrospective study | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objectives: In the United States, 25% of people with type 2 diabetes are
undiagnosed. Conventional screening models use limited demographic information
to assess risk. We evaluated whether electronic health record (EHR) phenotyping
could improve diabetes screening, even when records are incomplete and data are
not re... | [
{
"created": "Sat, 10 Jan 2015 23:21:23 GMT",
"version": "v1"
}
] | 2015-01-13 | [
[
"Anderson",
"Ariana E.",
""
],
[
"Kerr",
"Wesley T.",
""
],
[
"Thames",
"April",
""
],
[
"Li",
"Tong",
""
],
[
"Xiao",
"Jiayang",
""
],
[
"Cohen",
"Mark S.",
""
]
] | Objectives: In the United States, 25% of people with type 2 diabetes are undiagnosed. Conventional screening models use limited demographic information to assess risk. We evaluated whether electronic health record (EHR) phenotyping could improve diabetes screening, even when records are incomplete and data are not reco... |
2208.09813 | Sheng Xu | Sheng Xu, Junkang Wei, Yu Li | Genome-wide nucleotide-resolution model of single-strand break site
reveals species evolutionary hierarchy | null | null | null | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Single-strand breaks (SSBs) are the major DNA damage in the genome arising
spontaneously as the outcome of genotoxins and intermediates of DNA
transactions. SSBs play a crucial role in various biological processes and show
a non-random distribution in the genome. Several SSB detection approaches such
as S1 END-seq an... | [
{
"created": "Sun, 21 Aug 2022 06:07:19 GMT",
"version": "v1"
}
] | 2022-08-23 | [
[
"Xu",
"Sheng",
""
],
[
"Wei",
"Junkang",
""
],
[
"Li",
"Yu",
""
]
] | Single-strand breaks (SSBs) are the major DNA damage in the genome arising spontaneously as the outcome of genotoxins and intermediates of DNA transactions. SSBs play a crucial role in various biological processes and show a non-random distribution in the genome. Several SSB detection approaches such as S1 END-seq and ... |
q-bio/0702013 | Jiafu Wang | Ting Zeng, Jiafu Wang, Shenbing Kuang | Influence of Temperature on Neuronal Excitability in Cochlear Nucleus | 5 pages, 4 figures | null | null | null | q-bio.NC | null | The influence of temperature on neuronal excitability is studied by numerical
simulations on the spiking threshold characteristics of bushy cells in cochlear
nucleus periodically stimulated by synaptic currents. The results reveal that
there is a cut-off frequency for the spiking of bushy cell in a specific
temperatu... | [
{
"created": "Wed, 7 Feb 2007 23:38:42 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Zeng",
"Ting",
""
],
[
"Wang",
"Jiafu",
""
],
[
"Kuang",
"Shenbing",
""
]
] | The influence of temperature on neuronal excitability is studied by numerical simulations on the spiking threshold characteristics of bushy cells in cochlear nucleus periodically stimulated by synaptic currents. The results reveal that there is a cut-off frequency for the spiking of bushy cell in a specific temperature... |
2210.15044 | Bartek Rajwa | Abida Sanjana Shemonti, Joshua D. Eisenberg, Robert O. Heuckeroth,
Marthe J. Howard, Alex Pothen and Bartek Rajwa | Generative modeling of the enteric nervous system employing point
pattern analysis and graph construction | 17 pages, 5 figures | null | null | null | q-bio.NC cs.CV q-bio.QM stat.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We describe a generative network model of the architecture of the enteric
nervous system (ENS) in the colon employing data from images of human and mouse
tissue samples obtained through confocal microscopy. Our models combine spatial
point pattern analysis with graph generation to characterize the spatial and
topolog... | [
{
"created": "Wed, 26 Oct 2022 21:22:41 GMT",
"version": "v1"
}
] | 2022-10-28 | [
[
"Shemonti",
"Abida Sanjana",
""
],
[
"Eisenberg",
"Joshua D.",
""
],
[
"Heuckeroth",
"Robert O.",
""
],
[
"Howard",
"Marthe J.",
""
],
[
"Pothen",
"Alex",
""
],
[
"Rajwa",
"Bartek",
""
]
] | We describe a generative network model of the architecture of the enteric nervous system (ENS) in the colon employing data from images of human and mouse tissue samples obtained through confocal microscopy. Our models combine spatial point pattern analysis with graph generation to characterize the spatial and topologic... |
2403.07902 | Xiangxin Zhou | Jiaqi Guan, Xiangxin Zhou, Yuwei Yang, Yu Bao, Jian Peng, Jianzhu Ma,
Qiang Liu, Liang Wang, Quanquan Gu | DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based
Drug Design | Accepted to ICML 2023 | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Designing 3D ligands within a target binding site is a fundamental task in
drug discovery. Existing structured-based drug design methods treat all ligand
atoms equally, which ignores different roles of atoms in the ligand for drug
design and can be less efficient for exploring the large drug-like molecule
space. In t... | [
{
"created": "Mon, 26 Feb 2024 05:21:21 GMT",
"version": "v1"
}
] | 2024-03-14 | [
[
"Guan",
"Jiaqi",
""
],
[
"Zhou",
"Xiangxin",
""
],
[
"Yang",
"Yuwei",
""
],
[
"Bao",
"Yu",
""
],
[
"Peng",
"Jian",
""
],
[
"Ma",
"Jianzhu",
""
],
[
"Liu",
"Qiang",
""
],
[
"Wang",
"Liang",
"... | Designing 3D ligands within a target binding site is a fundamental task in drug discovery. Existing structured-based drug design methods treat all ligand atoms equally, which ignores different roles of atoms in the ligand for drug design and can be less efficient for exploring the large drug-like molecule space. In thi... |
1701.05970 | Matti Gralka | Matti Gralka, Diana Fusco, Stephen Martis, Oskar Hallatschek | Convection shapes the trade-off between antibiotic efficacy and the
selection for resistance in spatial gradients | null | null | 10.1088/1478-3975/aa7bb3 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Since penicillin was discovered about 90 years ago, we have become used to
using drugs to eradicate unwanted pathogenic cells. However, using drugs to
kill bacteria, viruses or cancer cells has the serious side effect of selecting
for mutant types that survive the drug attack. A key question therefore is how
one coul... | [
{
"created": "Sat, 21 Jan 2017 02:38:18 GMT",
"version": "v1"
},
{
"created": "Tue, 2 May 2017 20:34:47 GMT",
"version": "v2"
}
] | 2017-08-02 | [
[
"Gralka",
"Matti",
""
],
[
"Fusco",
"Diana",
""
],
[
"Martis",
"Stephen",
""
],
[
"Hallatschek",
"Oskar",
""
]
] | Since penicillin was discovered about 90 years ago, we have become used to using drugs to eradicate unwanted pathogenic cells. However, using drugs to kill bacteria, viruses or cancer cells has the serious side effect of selecting for mutant types that survive the drug attack. A key question therefore is how one could ... |
1711.01632 | Khalid Raza | Muniba Faiza, Khushnuma Tanveer, Saman Fatihi, Yonghua Wang, Khalid
Raza | Comprehensive overview and assessment of miRNA target prediction tools
in human and drosophila melanogaster | 26 pages, 9 figures | Current Bioinformatics (2019), 14(5): 432-445 | 10.2174/1574893614666190103101033 | null | q-bio.GN q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression at
the post-transcriptional level through complementary base pairing with the
target mRNA, leading to mRNA degradation and blocking translation process. Any
dysfunctions of these small regulatory molecules have been linked with the
development ... | [
{
"created": "Sun, 5 Nov 2017 18:19:01 GMT",
"version": "v1"
}
] | 2020-05-01 | [
[
"Faiza",
"Muniba",
""
],
[
"Tanveer",
"Khushnuma",
""
],
[
"Fatihi",
"Saman",
""
],
[
"Wang",
"Yonghua",
""
],
[
"Raza",
"Khalid",
""
]
] | MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression at the post-transcriptional level through complementary base pairing with the target mRNA, leading to mRNA degradation and blocking translation process. Any dysfunctions of these small regulatory molecules have been linked with the development an... |
q-bio/0407011 | Tonau Nakai | Tonau Nakai, Kohji Hizume, Shige. H. Yoshimura, Kunio Takeyasu, and
Kenichi Yoshikawa | Phase Transition in Reconstituted Chromatin | 16 pages, 3 figures | Europhysics Letters, Vol. 69, Iss. 6, pp. 1024-1030 (2005) | 10.1209/epl/i2004-10444-6 | null | q-bio.SC | null | By observing reconstituted chromatin by fluorescence microscopy (FM) and
atomic force microscopy (AFM), we found that the density of nucleosomes
exhibits a bimodal profile, i.e., there is a large transition between the dense
and dispersed states in reconstituted chromatin. Based on an analysis of the
spatial distribu... | [
{
"created": "Wed, 7 Jul 2004 16:39:37 GMT",
"version": "v1"
},
{
"created": "Sun, 11 Jul 2004 01:24:32 GMT",
"version": "v2"
},
{
"created": "Fri, 10 Sep 2004 06:32:36 GMT",
"version": "v3"
}
] | 2015-06-26 | [
[
"Nakai",
"Tonau",
""
],
[
"Hizume",
"Kohji",
""
],
[
"Yoshimura",
"Shige. H.",
""
],
[
"Takeyasu",
"Kunio",
""
],
[
"Yoshikawa",
"Kenichi",
""
]
] | By observing reconstituted chromatin by fluorescence microscopy (FM) and atomic force microscopy (AFM), we found that the density of nucleosomes exhibits a bimodal profile, i.e., there is a large transition between the dense and dispersed states in reconstituted chromatin. Based on an analysis of the spatial distributi... |
1309.0853 | David Schneider Dr | David M. Schneider, Ayana B. Martins, Eduardo do Carmo and Marcus A.M.
de Aguiar | Evolutionary consequences of assortativeness in haploid genotypes | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the evolution of allele frequencies in a large population where
random mating is violated in a particular way that is related to recent works
on speciation. Specifically, we consider non-random encounters in haploid
organisms described by biallelic genes at two loci and assume that individuals
whose alleles ... | [
{
"created": "Tue, 3 Sep 2013 22:07:54 GMT",
"version": "v1"
}
] | 2013-09-05 | [
[
"Schneider",
"David M.",
""
],
[
"Martins",
"Ayana B.",
""
],
[
"Carmo",
"Eduardo do",
""
],
[
"de Aguiar",
"Marcus A. M.",
""
]
] | We study the evolution of allele frequencies in a large population where random mating is violated in a particular way that is related to recent works on speciation. Specifically, we consider non-random encounters in haploid organisms described by biallelic genes at two loci and assume that individuals whose alleles di... |
2205.04464 | Feng Liang | Ngan Nguyen, Feng Liang, Dominik Engel, Ciril Bohak, Peter Wonka, Timo
Ropinski, Ivan Viola | Differentiable Electron Microscopy Simulation: Methods and Applications
for Visualization | Version 2: Page 10: Fix the rendering problem in in Line 12 of
Algorithm 2 Page 12: Table 2: Fix wrong data entries in the table | null | null | null | q-bio.QM cs.CV cs.GR cs.LG eess.IV | http://creativecommons.org/licenses/by-sa/4.0/ | We propose a new microscopy simulation system that can depict atomistic
models in a micrograph visual style, similar to results of physical electron
microscopy imaging. This system is scalable, able to represent simulation of
electron microscopy of tens of viral particles and synthesizes the image faster
than previou... | [
{
"created": "Sun, 8 May 2022 12:39:04 GMT",
"version": "v1"
},
{
"created": "Thu, 26 May 2022 13:25:20 GMT",
"version": "v2"
}
] | 2022-05-27 | [
[
"Nguyen",
"Ngan",
""
],
[
"Liang",
"Feng",
""
],
[
"Engel",
"Dominik",
""
],
[
"Bohak",
"Ciril",
""
],
[
"Wonka",
"Peter",
""
],
[
"Ropinski",
"Timo",
""
],
[
"Viola",
"Ivan",
""
]
] | We propose a new microscopy simulation system that can depict atomistic models in a micrograph visual style, similar to results of physical electron microscopy imaging. This system is scalable, able to represent simulation of electron microscopy of tens of viral particles and synthesizes the image faster than previous ... |
2303.04215 | Debayan Chakraborty | D. Thirumalai, Abhinaw Kumar, Debayan Chakraborty, John E. Straub,
Mauro L. Mugnai | Conformational Fluctuations and Phases in Fused in Sarcoma (FUS)
Low-Complexity Domain | null | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The well known phenomenon of phase separation in synthetic polymers and
proteins has become a major topic in biophysics because it has been invoked as
a mechanism of compartment formation in cells, without the need for membranes.
Most of the coacervates (or condensates) are composed of Intrinsically
Disordered Protei... | [
{
"created": "Tue, 7 Mar 2023 20:12:06 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Jun 2023 03:24:08 GMT",
"version": "v2"
}
] | 2023-06-06 | [
[
"Thirumalai",
"D.",
""
],
[
"Kumar",
"Abhinaw",
""
],
[
"Chakraborty",
"Debayan",
""
],
[
"Straub",
"John E.",
""
],
[
"Mugnai",
"Mauro L.",
""
]
] | The well known phenomenon of phase separation in synthetic polymers and proteins has become a major topic in biophysics because it has been invoked as a mechanism of compartment formation in cells, without the need for membranes. Most of the coacervates (or condensates) are composed of Intrinsically Disordered Proteins... |
2105.04042 | Xiaobin Guan | Xiaobin Guan, Jing M. Chen, Huanfeng Shen, Xinyao Xie | A modified two-leaf light use efficiency model for improving the
simulation of GPP using a radiation scalar | 40 pages, 9 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | A TL-LUE model modified with a radiation scalar (RTL-LUE) is developed in
this paper. The same maximum LUE is used for both sunlit and shaded leaves, and
the difference in LUE between sunlit and shaded leaf groups is determined by
the same radiation scalar. The RTL-LUE model was calibrated and validated at
global 169... | [
{
"created": "Sun, 9 May 2021 22:59:25 GMT",
"version": "v1"
}
] | 2021-05-11 | [
[
"Guan",
"Xiaobin",
""
],
[
"Chen",
"Jing M.",
""
],
[
"Shen",
"Huanfeng",
""
],
[
"Xie",
"Xinyao",
""
]
] | A TL-LUE model modified with a radiation scalar (RTL-LUE) is developed in this paper. The same maximum LUE is used for both sunlit and shaded leaves, and the difference in LUE between sunlit and shaded leaf groups is determined by the same radiation scalar. The RTL-LUE model was calibrated and validated at global 169 F... |
0904.3654 | Yves Jouanneau | Luc Schuler (UCL), Sinead M. Ni Chadhain (BCAE), Yves Jouanneau
(LCBM), Christine Meyer (LCBM), Gerben J. Zylstra (BCAE), Pascal Hols (UCL),
Spiros N. Agathos (UCL) | Characterization of a novel angular dioxygenase from fluorene-degrading
Sphingomonas sp. strain LB126 | null | Applied and Environmental Microbiology 74 (2008) 1050-1057 | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this study, the genes involved in the initial attack on fluorene by
Sphingomonas sp. LB126 were investigated. The ? and ? subunits of a dioxygenase
complex (FlnA1A2), showing 63% and 51% sequence identity respectively, with the
subunits of an angular dioxygenase from Gram-positive Terrabacter sp. DBF63,
were ident... | [
{
"created": "Thu, 23 Apr 2009 10:54:24 GMT",
"version": "v1"
}
] | 2009-04-24 | [
[
"Schuler",
"Luc",
"",
"UCL"
],
[
"Chadhain",
"Sinead M. Ni",
"",
"BCAE"
],
[
"Jouanneau",
"Yves",
"",
"LCBM"
],
[
"Meyer",
"Christine",
"",
"LCBM"
],
[
"Zylstra",
"Gerben J.",
"",
"BCAE"
],
[
"Hols",
"Pasca... | In this study, the genes involved in the initial attack on fluorene by Sphingomonas sp. LB126 were investigated. The ? and ? subunits of a dioxygenase complex (FlnA1A2), showing 63% and 51% sequence identity respectively, with the subunits of an angular dioxygenase from Gram-positive Terrabacter sp. DBF63, were identif... |
1410.2098 | Philippe Terrier PhD | Philippe Terrier and Fabienne Reynard | Effect of age on the variability and stability of gait: a
cross-sectional treadmill study in healthy individuals between 20 and 69
years of age | Author's version of an article published in Gait & Posture (2014) | null | 10.1016/j.gaitpost.2014.09.024 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Falls during walking are a major health issue in the elderly population.
Older individuals are usually more cautious, work more slowly, take shorter
steps, and exhibit increased step-to-step variability. They often have impaired
dynamic balance, which explains their increased falling risk. Those locomotor
characteris... | [
{
"created": "Tue, 7 Oct 2014 07:27:17 GMT",
"version": "v1"
},
{
"created": "Fri, 10 Oct 2014 13:06:50 GMT",
"version": "v2"
}
] | 2014-10-13 | [
[
"Terrier",
"Philippe",
""
],
[
"Reynard",
"Fabienne",
""
]
] | Falls during walking are a major health issue in the elderly population. Older individuals are usually more cautious, work more slowly, take shorter steps, and exhibit increased step-to-step variability. They often have impaired dynamic balance, which explains their increased falling risk. Those locomotor characteristi... |
2304.11863 | Maksim Kitsak | Long MA and Piet Van Mieghem and Maksim Kitsak | Reporting delays: a widely neglected impact factor in COVID-19 forecasts | 10 pages, 4 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Epidemic forecasts are only as good as the accuracy of epidemic measurements.
Is epidemic data, particularly COVID-19 epidemic data, clean and devoid of
noise? Common sense implies the negative answer. While we cannot evaluate the
cleanliness of the COVID-19 epidemic data in a holistic fashion, we can assess
the data... | [
{
"created": "Mon, 24 Apr 2023 07:18:38 GMT",
"version": "v1"
}
] | 2023-04-25 | [
[
"MA",
"Long",
""
],
[
"Van Mieghem",
"Piet",
""
],
[
"Kitsak",
"Maksim",
""
]
] | Epidemic forecasts are only as good as the accuracy of epidemic measurements. Is epidemic data, particularly COVID-19 epidemic data, clean and devoid of noise? Common sense implies the negative answer. While we cannot evaluate the cleanliness of the COVID-19 epidemic data in a holistic fashion, we can assess the data f... |
2301.13387 | Owen Queen | Cai W. John, Owen Queen, Wellington Muchero, and Scott J. Emrich | Deep Learning for Reference-Free Geolocation for Poplar Trees | Accepted at NeurIPS 2022 AI for Science Workshop | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by/4.0/ | A core task in precision agriculture is the identification of climatic and
ecological conditions that are advantageous for a given crop. The most succinct
approach is geolocation, which is concerned with locating the native region of
a given sample based on its genetic makeup. Here, we investigate genomic
geolocation... | [
{
"created": "Tue, 31 Jan 2023 03:37:47 GMT",
"version": "v1"
}
] | 2023-02-01 | [
[
"John",
"Cai W.",
""
],
[
"Queen",
"Owen",
""
],
[
"Muchero",
"Wellington",
""
],
[
"Emrich",
"Scott J.",
""
]
] | A core task in precision agriculture is the identification of climatic and ecological conditions that are advantageous for a given crop. The most succinct approach is geolocation, which is concerned with locating the native region of a given sample based on its genetic makeup. Here, we investigate genomic geolocation o... |
q-bio/0401029 | Laszlo Papp | S. Bumble | Toy Models and Statistical Mechanics of Subgraphs and Motifs of Genetic
and Protein Networks | 7 pages, 2 figures | null | null | null | q-bio.MN | null | Theoretical physics is used for a toy model of molecular biology to assess
conditions that lead to the edge of chaos (EOC) in a network of biomolecules.
Results can enhance our ability to understand complex diseases and their
treatment or cure.
| [
{
"created": "Thu, 22 Jan 2004 07:47:03 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bumble",
"S.",
""
]
] | Theoretical physics is used for a toy model of molecular biology to assess conditions that lead to the edge of chaos (EOC) in a network of biomolecules. Results can enhance our ability to understand complex diseases and their treatment or cure. |
2112.15252 | Eleodor Nichita | Eleodor Nichita, Mary-Anne Pietrusiak, Fangli Xie, Peter Schwanke and
Anjali Pandya | Modeling COVID-19 Transmission using IDSIM, an Epidemiological-Modelling
Desktop App with Multi-Level Immunization Capabilities | 28 pages, 8 figures | null | 10.14745/ccdr.v48i10a05 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The COVID-19 pandemic has placed unprecedented demands on local public health
units in Ontario, Canada, one of which was the need for in-house
epidemiological-modelling capabilities. To address this need, Ontario Tech
University and the Durham Region Health Department developed a native Windows
desktop app that perfo... | [
{
"created": "Fri, 31 Dec 2021 00:32:23 GMT",
"version": "v1"
},
{
"created": "Sat, 5 Mar 2022 02:37:17 GMT",
"version": "v2"
}
] | 2022-11-10 | [
[
"Nichita",
"Eleodor",
""
],
[
"Pietrusiak",
"Mary-Anne",
""
],
[
"Xie",
"Fangli",
""
],
[
"Schwanke",
"Peter",
""
],
[
"Pandya",
"Anjali",
""
]
] | The COVID-19 pandemic has placed unprecedented demands on local public health units in Ontario, Canada, one of which was the need for in-house epidemiological-modelling capabilities. To address this need, Ontario Tech University and the Durham Region Health Department developed a native Windows desktop app that perform... |
1604.02909 | Benjamin Schott M.Sc. | Benjamin Schott, Johannes Stegmaier, Alexandre Arbaud, Markus Reischl,
Ralf Mikut, Francis L\'evi | Robust Individual Circadian Parameter Estimation for Biosignal-based
Personalisation of Cancer Chronotherapy | Conference Biosig 2016, Berlin | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In cancer treatment, chemotherapy is administered according a constant
schedule. The chronotherapy approach, considering chronobiological drug
delivery, adapts the chemotherapy profile to the circadian rhythms of the human
organism. This reduces toxicity effects and at the same time enhances
efficiency of chemotherap... | [
{
"created": "Mon, 11 Apr 2016 12:14:07 GMT",
"version": "v1"
}
] | 2016-04-12 | [
[
"Schott",
"Benjamin",
""
],
[
"Stegmaier",
"Johannes",
""
],
[
"Arbaud",
"Alexandre",
""
],
[
"Reischl",
"Markus",
""
],
[
"Mikut",
"Ralf",
""
],
[
"Lévi",
"Francis",
""
]
] | In cancer treatment, chemotherapy is administered according a constant schedule. The chronotherapy approach, considering chronobiological drug delivery, adapts the chemotherapy profile to the circadian rhythms of the human organism. This reduces toxicity effects and at the same time enhances efficiency of chemotherapy.... |
1910.04824 | Nassim Versbraegen | Pieter Libin, Nassim Versbraegen, Ana B. Abecasis, Perpetua Gomes, Tom
Lenaerts, Ann Now\'e | Towards a phylogenetic measure to quantify HIV incidence | Accepted at BNAIC 2019 (Benelux AI conference) | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | One of the cornerstones in combating the HIV pandemic is being able to assess
the current state and evolution of local HIV epidemics. This remains a complex
problem, as many HIV infected individuals remain unaware of their infection
status, leading to parts of HIV epidemics being undiagnosed and under-reported.
To th... | [
{
"created": "Thu, 10 Oct 2019 19:20:48 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Oct 2019 12:46:29 GMT",
"version": "v2"
},
{
"created": "Wed, 23 Oct 2019 16:52:42 GMT",
"version": "v3"
}
] | 2019-10-24 | [
[
"Libin",
"Pieter",
""
],
[
"Versbraegen",
"Nassim",
""
],
[
"Abecasis",
"Ana B.",
""
],
[
"Gomes",
"Perpetua",
""
],
[
"Lenaerts",
"Tom",
""
],
[
"Nowé",
"Ann",
""
]
] | One of the cornerstones in combating the HIV pandemic is being able to assess the current state and evolution of local HIV epidemics. This remains a complex problem, as many HIV infected individuals remain unaware of their infection status, leading to parts of HIV epidemics being undiagnosed and under-reported. To that... |
2103.09954 | Xiaochen Liu | Xiaochen Liu, Peter A. Robinson | Analytic model for feature maps in the primary visual cortex | 28 pages, 15 figures | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A compact analytic model is proposed to describe the combined orientation
preference (OP) and ocular dominance (OD) features of simple cells and their
layout in the primary visual cortex (V1). This model consists of three parts:
(i) an anisotropic Laplacian (AL) operator that represents the local neural
sensitivity t... | [
{
"created": "Wed, 17 Mar 2021 23:56:15 GMT",
"version": "v1"
}
] | 2021-03-19 | [
[
"Liu",
"Xiaochen",
""
],
[
"Robinson",
"Peter A.",
""
]
] | A compact analytic model is proposed to describe the combined orientation preference (OP) and ocular dominance (OD) features of simple cells and their layout in the primary visual cortex (V1). This model consists of three parts: (i) an anisotropic Laplacian (AL) operator that represents the local neural sensitivity to ... |
2204.05109 | Peng Liu | Peng Liu and Yanyan Zheng | Temporal and spatial evolution of the distribution related to the number
of COVID-19 pandemic | null | Physica A 603, 127837 (2022) | 10.1016/j.physa.2022.127837 | null | q-bio.PE physics.data-an physics.soc-ph stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This work systematically conducts a data analysis based on the numbers of
both cumulative and daily confirmed COVID-19 cases and deaths in a time span
through April 2020 to June 2022 for over 200 countries around the world. Such
research feature aims to reveal the temporal and spatial evolution of the
country-level d... | [
{
"created": "Fri, 8 Apr 2022 04:51:03 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Aug 2022 12:44:56 GMT",
"version": "v2"
}
] | 2023-03-20 | [
[
"Liu",
"Peng",
""
],
[
"Zheng",
"Yanyan",
""
]
] | This work systematically conducts a data analysis based on the numbers of both cumulative and daily confirmed COVID-19 cases and deaths in a time span through April 2020 to June 2022 for over 200 countries around the world. Such research feature aims to reveal the temporal and spatial evolution of the country-level dis... |
2005.06180 | Marco Piangerelli | Andrea De Simone and Marco Piangerelli | The impact of undetected cases on tracking epidemics: the case of
COVID-19 | 23 Pages, 10 Figures | Chaos, Solitons & Fractals, Volume 140, 2020, 110167 | 10.1016/j.chaos.2020.110167 | null | q-bio.PE q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One of the key indicators used in tracking the evolution of an infectious
disease isthe reproduction number. This quantity is usually computed using the
reportednumber of cases, but ignoring that many more individuals may be
infected (e.g.asymptomatics). We propose a statistical procedure to quantify
the impact of un... | [
{
"created": "Wed, 13 May 2020 06:49:46 GMT",
"version": "v1"
}
] | 2020-09-11 | [
[
"De Simone",
"Andrea",
""
],
[
"Piangerelli",
"Marco",
""
]
] | One of the key indicators used in tracking the evolution of an infectious disease isthe reproduction number. This quantity is usually computed using the reportednumber of cases, but ignoring that many more individuals may be infected (e.g.asymptomatics). We propose a statistical procedure to quantify the impact of un-d... |
2003.05462 | Armando G. M. Neves | Evandro P. de Souza and Armando G. M. Neves | Exact fixation probabilities for the Birth-Death and Death-Birth
frequency-dependent Moran processes on the star graph | 20 pages, 4 figures | null | null | null | q-bio.PE math.PR physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Broom and Rycht\'{a}\v{r} [Proc. R. Soc. A (2008) 464, 2609--2627] found an
exact solution for the fixation probabilities of the Moran process for a
structured population, in which the interaction structure among individuals is
given by the so-called star graph, i.e. one central vertex and $n$ leaves, the
leaves conn... | [
{
"created": "Wed, 11 Mar 2020 18:01:40 GMT",
"version": "v1"
},
{
"created": "Wed, 18 Mar 2020 13:41:17 GMT",
"version": "v2"
}
] | 2020-03-19 | [
[
"de Souza",
"Evandro P.",
""
],
[
"Neves",
"Armando G. M.",
""
]
] | Broom and Rycht\'{a}\v{r} [Proc. R. Soc. A (2008) 464, 2609--2627] found an exact solution for the fixation probabilities of the Moran process for a structured population, in which the interaction structure among individuals is given by the so-called star graph, i.e. one central vertex and $n$ leaves, the leaves connec... |
2008.07417 | Kuang Liu | Kuang Liu, Alison E. Patteson, Edward J. Banigan, J. M. Schwarz | Dynamic nuclear structure emerges from chromatin crosslinks and motors | 18 pages, 21 figures | Phys. Rev. Lett. 126, 158101 (2021) | 10.1103/PhysRevLett.126.158101 | null | q-bio.SC | http://creativecommons.org/licenses/by/4.0/ | The cell nucleus houses the chromosomes, which are linked to a soft shell of
lamin filaments. Experiments indicate that correlated chromosome dynamics and
nuclear shape fluctuations arise from motor activity. To identify the physical
mechanisms, we develop a model of an active, crosslinked Rouse chain bound to a
poly... | [
{
"created": "Mon, 17 Aug 2020 15:42:01 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Mar 2021 21:10:13 GMT",
"version": "v2"
}
] | 2021-04-21 | [
[
"Liu",
"Kuang",
""
],
[
"Patteson",
"Alison E.",
""
],
[
"Banigan",
"Edward J.",
""
],
[
"Schwarz",
"J. M.",
""
]
] | The cell nucleus houses the chromosomes, which are linked to a soft shell of lamin filaments. Experiments indicate that correlated chromosome dynamics and nuclear shape fluctuations arise from motor activity. To identify the physical mechanisms, we develop a model of an active, crosslinked Rouse chain bound to a polyme... |
1403.4033 | Markus Pagitz Dr | Markus Pagitz and Remco I. Leine | Continuum Model for Pressure Actuated Cellular Structures | 11 pages, 9 figures | null | null | null | q-bio.QM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Previous work introduced a lower-dimensional numerical model for the
geometric nonlinear simulation and optimization of compliant pressure actuated
cellular structures. This model takes into account hinge eccentricities as well
as rotational and axial cell side springs. The aim of this article is twofold.
First, prev... | [
{
"created": "Mon, 17 Mar 2014 09:16:37 GMT",
"version": "v1"
},
{
"created": "Mon, 27 Jul 2015 16:15:57 GMT",
"version": "v2"
},
{
"created": "Wed, 5 Aug 2015 12:58:31 GMT",
"version": "v3"
},
{
"created": "Fri, 28 Jul 2017 14:07:13 GMT",
"version": "v4"
}
] | 2017-07-31 | [
[
"Pagitz",
"Markus",
""
],
[
"Leine",
"Remco I.",
""
]
] | Previous work introduced a lower-dimensional numerical model for the geometric nonlinear simulation and optimization of compliant pressure actuated cellular structures. This model takes into account hinge eccentricities as well as rotational and axial cell side springs. The aim of this article is twofold. First, previo... |
1803.11270 | Melanie Hopkins | Melanie J. Hopkins, David W. Bapst, Carl Simpson, Rachel C. M. Warnock | The inseparability of sampling and time and its influence on attempts to
unify the molecular and fossil records | 29 pages, 1 figure. All others contributed equally to this work | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The two major approaches to studying macroevolution in deep time are the
fossil record and reconstructed relationships among extant taxa from molecular
data. Results based on one approach sometimes conflict with those based on the
other, with inconsistencies often attributed to inherent flaws of one (or the
other) da... | [
{
"created": "Thu, 29 Mar 2018 22:08:09 GMT",
"version": "v1"
}
] | 2018-04-02 | [
[
"Hopkins",
"Melanie J.",
""
],
[
"Bapst",
"David W.",
""
],
[
"Simpson",
"Carl",
""
],
[
"Warnock",
"Rachel C. M.",
""
]
] | The two major approaches to studying macroevolution in deep time are the fossil record and reconstructed relationships among extant taxa from molecular data. Results based on one approach sometimes conflict with those based on the other, with inconsistencies often attributed to inherent flaws of one (or the other) data... |
1602.00650 | Romeil Sandhu | Romeil Sandhu, Sarah Tannenbaum, Daniel Diolaiti, Alberto
Ambesi-Impiombato, Andrew Kung, and Allen Tannenbaum | A Quantitative Analysis of Localized Robustness of MYCN in Neuroblastoma | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The amplification of the gene MYCN (V-myc myelocytomatosis viral-valeted
oncogene, neuroblastoma derived) has been a well-documented indicator for poor
prognosis in neuroblastoma, a childhood cancer. Unfortunately, there has been
limited success in understanding MYCN functionality in the landscape of
neuroblastoma an... | [
{
"created": "Sun, 13 Dec 2015 20:43:21 GMT",
"version": "v1"
}
] | 2016-02-02 | [
[
"Sandhu",
"Romeil",
""
],
[
"Tannenbaum",
"Sarah",
""
],
[
"Diolaiti",
"Daniel",
""
],
[
"Ambesi-Impiombato",
"Alberto",
""
],
[
"Kung",
"Andrew",
""
],
[
"Tannenbaum",
"Allen",
""
]
] | The amplification of the gene MYCN (V-myc myelocytomatosis viral-valeted oncogene, neuroblastoma derived) has been a well-documented indicator for poor prognosis in neuroblastoma, a childhood cancer. Unfortunately, there has been limited success in understanding MYCN functionality in the landscape of neuroblastoma and ... |
2010.00541 | Ines Samengo Dr. | Nicol\'as Vattuone (1,2), Thomas Wachtler (1), In\'es Samengo (1) ((1)
Department of Biology II, Ludwig-Maximilians-Universit\"at M\"unchen and
Bernstein Center for Computational Neuroscience, Munich, Germany. (2)
Department of Medical Physics and Instituto Balseiro, Centro At\'omico
Bariloche, Argentina) | Perceptual spaces and their symmetries: The geometry of color space | (v1) 42 pages, 9 figures, 1 appendix. (v2) 47 pages, 10 figures, 1
appendix. (v3) Text modified after peer-review process. (v4) 34 pages, 1
appendix, 10 figures. Article accepted to be published at Mathematical
Neuroscience and Applications (v5) ISSN added | Mathematical Neuroscience and Applications, Volume 1 (July 15,
2021) mna:7108 | 10.46298/mna.7108 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Our sensory systems transform external signals into neural activity, thereby
producing percepts. We are endowed with an intuitive notion of similarity
between percepts, that need not reflect the proximity of the physical
properties of the corresponding external stimuli. The quantitative
characterization of the geomet... | [
{
"created": "Thu, 1 Oct 2020 16:52:29 GMT",
"version": "v1"
},
{
"created": "Sat, 16 Jan 2021 22:11:26 GMT",
"version": "v2"
},
{
"created": "Wed, 19 May 2021 14:26:16 GMT",
"version": "v3"
},
{
"created": "Wed, 14 Jul 2021 14:38:57 GMT",
"version": "v4"
},
{
"cr... | 2023-06-22 | [
[
"Vattuone",
"Nicolás",
""
],
[
"Wachtler",
"Thomas",
""
],
[
"Samengo",
"Inés",
""
]
] | Our sensory systems transform external signals into neural activity, thereby producing percepts. We are endowed with an intuitive notion of similarity between percepts, that need not reflect the proximity of the physical properties of the corresponding external stimuli. The quantitative characterization of the geometry... |
1909.09111 | Leo Polansky | Leo Polansky, Ken B. Newman, Lara Mitchell | Improving inference for nonlinear state-space models of animal
population dynamics given biased sequential life stage data | null | null | null | null | q-bio.PE q-bio.QM stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | State-space models (SSMs) are a popular tool for modeling animal abundances.
Inference difficulties for simple linear SSMs are well known, particularly in
relation to simultaneous estimation of process and observation variances.
Several remedies to overcome estimation problems have been studied for
relatively simple ... | [
{
"created": "Thu, 19 Sep 2019 17:38:24 GMT",
"version": "v1"
}
] | 2019-09-20 | [
[
"Polansky",
"Leo",
""
],
[
"Newman",
"Ken B.",
""
],
[
"Mitchell",
"Lara",
""
]
] | State-space models (SSMs) are a popular tool for modeling animal abundances. Inference difficulties for simple linear SSMs are well known, particularly in relation to simultaneous estimation of process and observation variances. Several remedies to overcome estimation problems have been studied for relatively simple SS... |
2102.03910 | Rossana Segreto | Rossana Segreto (1), Yuri Deigin (2), Kevin McCairn (3), Alejandro
Sousa (4 and 5), Dan Sirotkin (6), Karl Sirotkin (6), Jonathan J. Couey (7),
Adrian Jones (8), Daoyu Zhang (9) ((1) Department of Microbiology, University
of Innsbruck, Austria, (2) Youthereum Genetics Inc., Toronto, Ontario,
Canada, (3) Synapte... | An open debate on SARS-CoV-2's proximal origin is long overdue | null | null | null | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | There is a near consensus view that SARS-CoV-2 has a natural zoonotic origin;
however, several characteristics of SARS-CoV-2 taken together are not easily
explained by a natural zoonotic origin hypothesis. These include: a low rate of
evolution in the early phase of transmission; the lack of evidence of
recombination... | [
{
"created": "Sun, 7 Feb 2021 20:54:08 GMT",
"version": "v1"
},
{
"created": "Tue, 9 Feb 2021 14:22:19 GMT",
"version": "v2"
}
] | 2021-02-10 | [
[
"Segreto",
"Rossana",
"",
"4 and 5"
],
[
"Deigin",
"Yuri",
"",
"4 and 5"
],
[
"McCairn",
"Kevin",
"",
"4 and 5"
],
[
"Sousa",
"Alejandro",
"",
"4 and 5"
],
[
"Sirotkin",
"Dan",
""
],
[
"Sirotkin",
"Karl",
"... | There is a near consensus view that SARS-CoV-2 has a natural zoonotic origin; however, several characteristics of SARS-CoV-2 taken together are not easily explained by a natural zoonotic origin hypothesis. These include: a low rate of evolution in the early phase of transmission; the lack of evidence of recombination e... |
2102.02077 | Pilar Cossio Dr. | Julian Giraldo-Barreto, Sebastian Ortiz, Erik H. Thiede, Karen
Palacio-Rodriguez, Bob Carpenter, Alex H. Barnett, Pilar Cossio | A Bayesian approach for extracting free energy profiles from
cryo-electron microscopy experiments using a path collective variable | null | null | null | null | q-bio.BM physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Cryo-electron microscopy (cryo-EM) extracts single-particle density
projections of individual biomolecules. Although cryo-EM is widely used for 3D
reconstruction, due to its single-particle nature, it has the potential to
provide information about the biomolecule's conformational variability and
underlying free energ... | [
{
"created": "Wed, 3 Feb 2021 14:22:28 GMT",
"version": "v1"
}
] | 2021-02-04 | [
[
"Giraldo-Barreto",
"Julian",
""
],
[
"Ortiz",
"Sebastian",
""
],
[
"Thiede",
"Erik H.",
""
],
[
"Palacio-Rodriguez",
"Karen",
""
],
[
"Carpenter",
"Bob",
""
],
[
"Barnett",
"Alex H.",
""
],
[
"Cossio",
"Pilar",... | Cryo-electron microscopy (cryo-EM) extracts single-particle density projections of individual biomolecules. Although cryo-EM is widely used for 3D reconstruction, due to its single-particle nature, it has the potential to provide information about the biomolecule's conformational variability and underlying free energy ... |
2311.13337 | Michiel Van Der Vlag | Michiel van der Vlag, Lionel Kusch, Alain Destexhe, Viktor Jirsa,
Sandra Diaz-Pier and Jennifer S. Goldman | Vast TVB parameter space exploration: A Modular Framework for
Accelerating the Multi-Scale Simulation of Human Brain Dynamics | 21 pages, 9 figures | null | null | null | q-bio.NC cs.DC | http://creativecommons.org/licenses/by/4.0/ | Global neural dynamics emerge from multi-scale brain structures, with neurons
communicating through synapses to form transiently communicating networks.
Network activity arises from intercellular communication that depends on the
structure of connectome tracts and local connection, intracellular signalling
cascades, ... | [
{
"created": "Wed, 22 Nov 2023 12:01:33 GMT",
"version": "v1"
}
] | 2023-11-23 | [
[
"van der Vlag",
"Michiel",
""
],
[
"Kusch",
"Lionel",
""
],
[
"Destexhe",
"Alain",
""
],
[
"Jirsa",
"Viktor",
""
],
[
"Diaz-Pier",
"Sandra",
""
],
[
"Goldman",
"Jennifer S.",
""
]
] | Global neural dynamics emerge from multi-scale brain structures, with neurons communicating through synapses to form transiently communicating networks. Network activity arises from intercellular communication that depends on the structure of connectome tracts and local connection, intracellular signalling cascades, an... |
2004.03251 | Steffen Eikenberry | Steffen E. Eikenberry, Marina Mancuso, Enahoro Iboi, Tin Phan, Keenan
Eikenberry, Yang Kuang, Eric Kostelich, Abba B. Gumel | To mask or not to mask: Modeling the potential for face mask use by the
general public to curtail the COVID-19 pandemic | 20 pages, 9 figures | Infectious Disease Modelling. 5 (2020) 248-255 | 10.1016/j.idm.2020.04.001 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Face mask use by the general public for limiting the spread of the COVID-19
pandemic is controversial, though increasingly recommended, and the potential
of this intervention is not well understood. We develop a compartmental model
for assessing the community-wide impact of mask use by the general,
asymptomatic publi... | [
{
"created": "Tue, 7 Apr 2020 10:41:30 GMT",
"version": "v1"
}
] | 2020-05-05 | [
[
"Eikenberry",
"Steffen E.",
""
],
[
"Mancuso",
"Marina",
""
],
[
"Iboi",
"Enahoro",
""
],
[
"Phan",
"Tin",
""
],
[
"Eikenberry",
"Keenan",
""
],
[
"Kuang",
"Yang",
""
],
[
"Kostelich",
"Eric",
""
],
[
... | Face mask use by the general public for limiting the spread of the COVID-19 pandemic is controversial, though increasingly recommended, and the potential of this intervention is not well understood. We develop a compartmental model for assessing the community-wide impact of mask use by the general, asymptomatic public,... |
1702.05065 | Gonzalo Hernandez Hernandez | Gonzalo Hernandez-Hernandez, Jesse Myers, Enric Alvarez-Lacalle,
Yohannes Shiferaw | Nonlinear signaling on biological networks: the role of stochasticity
and spectral clustering | 30 pages, 12 figures | null | 10.1103/PhysRevE.95.032313 | null | q-bio.MN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Signal transduction within biological cells is governed by networks of
interacting proteins. Communication between these proteins is mediated by
signaling molecules which bind to receptors and induce stochastic transitions
between different conformational states. Signaling is typically a cooperative
process which req... | [
{
"created": "Thu, 16 Feb 2017 17:48:18 GMT",
"version": "v1"
}
] | 2017-04-05 | [
[
"Hernandez-Hernandez",
"Gonzalo",
""
],
[
"Myers",
"Jesse",
""
],
[
"Alvarez-Lacalle",
"Enric",
""
],
[
"Shiferaw",
"Yohannes",
""
]
] | Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different conformational states. Signaling is typically a cooperative process which requi... |
1111.0097 | Michael Famulare | Michael Famulare and Adrienne Fairhall | Adaptive probabilistic neural coding from deterministic spiking neurons:
analysis from first principles | v2: revised/expanded results/discussion regarding contrast gain
control. 51 pages, 12 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A neuron transforms its input into output spikes, and this transformation is
the basic unit of computation in the nervous system. The spiking response of
the neuron to a complex, time-varying input can be predicted from the detailed
biophysical properties of the neuron, modeled as a deterministic nonlinear
dynamical ... | [
{
"created": "Tue, 1 Nov 2011 00:57:39 GMT",
"version": "v1"
},
{
"created": "Thu, 15 Dec 2011 22:13:03 GMT",
"version": "v2"
}
] | 2011-12-19 | [
[
"Famulare",
"Michael",
""
],
[
"Fairhall",
"Adrienne",
""
]
] | A neuron transforms its input into output spikes, and this transformation is the basic unit of computation in the nervous system. The spiking response of the neuron to a complex, time-varying input can be predicted from the detailed biophysical properties of the neuron, modeled as a deterministic nonlinear dynamical sy... |
2306.10553 | Seemi Tasnim Alam | Bushra Rahman Eipa, Md Riadul Islam, Raquiba Sultana, Seemi Tasnim
Alam, Tanaj Mehjabin, Nohor Noon Haque Bushra, S M Moniruzzaman, Md Ifrat
Hossain, Shamia Naz Rashna, Md Aftab Uddin | Determination of the antibiotic susceptibility pattern of Gram positive
bacteria causing UTI in Dhaka Bangladesh | 16 pages, 4 figures | null | null | SUB_MBO_2301 | q-bio.QM q-bio.BM | http://creativecommons.org/licenses/by-sa/4.0/ | Urinary Tract Infection (UTIs) is referred as one of the most common
infection in medical sectors worldwide and antimicrobial resistance (AMR) is
also a global threat to human that is related with many diseases. As
antibiotics used for the treatment of infectious diseases, the rate of
resistance is increasing day by ... | [
{
"created": "Sun, 18 Jun 2023 13:26:52 GMT",
"version": "v1"
}
] | 2023-06-21 | [
[
"Eipa",
"Bushra Rahman",
""
],
[
"Islam",
"Md Riadul",
""
],
[
"Sultana",
"Raquiba",
""
],
[
"Alam",
"Seemi Tasnim",
""
],
[
"Mehjabin",
"Tanaj",
""
],
[
"Bushra",
"Nohor Noon Haque",
""
],
[
"Moniruzzaman",
"S... | Urinary Tract Infection (UTIs) is referred as one of the most common infection in medical sectors worldwide and antimicrobial resistance (AMR) is also a global threat to human that is related with many diseases. As antibiotics used for the treatment of infectious diseases, the rate of resistance is increasing day by da... |
0811.3515 | Noa Sela | Galit Lev-Maor, Oren Ram, Eddo Kim, Noa Sela, Amir Goren, Erez Y
Levanon, Gil Ast | Intronic Alus Influence Alternative Splicing | null | PLoS Genet 2008 4(9): e1000204 | null | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Examination of the human transcriptome reveals higher levels of RNA editing
than in any other organism tested to date. This is indicative of extensive
double-stranded RNA (dsRNA) formation within the human transcriptome. Most of
the editing sites are located in the primate-specific retrotransposed element
called Alu.... | [
{
"created": "Fri, 21 Nov 2008 11:07:47 GMT",
"version": "v1"
}
] | 2008-11-24 | [
[
"Lev-Maor",
"Galit",
""
],
[
"Ram",
"Oren",
""
],
[
"Kim",
"Eddo",
""
],
[
"Sela",
"Noa",
""
],
[
"Goren",
"Amir",
""
],
[
"Levanon",
"Erez Y",
""
],
[
"Ast",
"Gil",
""
]
] | Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA) formation within the human transcriptome. Most of the editing sites are located in the primate-specific retrotransposed element called Alu. A... |
q-bio/0311003 | Alexey Mazur K. | Dimitri E. Kamashev and Alexey K. Mazur | Relaxation of DNA curvature by single stranded breaks: Simulations and
experiments | 13 two-column pages, 9 integrated eps plates, RevTeX4 | null | null | null | q-bio.BM cond-mat.soft physics.bio-ph | null | The recently proposed compressed backbone theory suggested that the intrinsic
curvature in DNA can result from a geometric mismatch between the specific
backbone length and optimal base stacking orientations. It predicted that the
curvature in A-tract repeats can be relaxed by introducing single stranded
breaks (nick... | [
{
"created": "Thu, 6 Nov 2003 15:08:55 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Kamashev",
"Dimitri E.",
""
],
[
"Mazur",
"Alexey K.",
""
]
] | The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature in A-tract repeats can be relaxed by introducing single stranded breaks (nicks)... |
1606.06668 | Adam Porter | Adam H. Porter, Norman A. Johnson and Alexander Y. Tulchinsky | Competitive binding of transcription factors drives Mendelian dominance
in regulatory genetic pathways | 3.3 Mb file. This revision includes a more thorough analysis of
dominance propagation and the effects of genetic background in the 3-locus
model | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We report a new mechanism for allelic dominance in regulatory genetic
interactions that we call binding dominance. We investigated a biophysical
model of gene regulation, where the fractional occupancy of a transcription
factor (TF) on the cis-regulated promoter site it binds to is determined by
binding energy (-{\De... | [
{
"created": "Tue, 21 Jun 2016 17:18:38 GMT",
"version": "v1"
},
{
"created": "Sat, 27 Aug 2016 00:49:53 GMT",
"version": "v2"
}
] | 2016-08-30 | [
[
"Porter",
"Adam H.",
""
],
[
"Johnson",
"Norman A.",
""
],
[
"Tulchinsky",
"Alexander Y.",
""
]
] | We report a new mechanism for allelic dominance in regulatory genetic interactions that we call binding dominance. We investigated a biophysical model of gene regulation, where the fractional occupancy of a transcription factor (TF) on the cis-regulated promoter site it binds to is determined by binding energy (-{\Delt... |
1308.6534 | David Wick | W. David Wick | Stopping the SuperSpreader Epidemic: the lessons from SARS (with,
perhaps, applications to MERS) | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | I discuss the so-called SuperSpreader epidemic, for which SARS is the
canonical examples (and, perhaps, MERS will be another). I use simulation by an
agent-based model as well as the mathematics of multi-type branching-processes
to illustrate how the SS epidemic differs from the more familiar uniform
epidemic (e.g., ... | [
{
"created": "Thu, 29 Aug 2013 17:44:47 GMT",
"version": "v1"
}
] | 2013-08-30 | [
[
"Wick",
"W. David",
""
]
] | I discuss the so-called SuperSpreader epidemic, for which SARS is the canonical examples (and, perhaps, MERS will be another). I use simulation by an agent-based model as well as the mathematics of multi-type branching-processes to illustrate how the SS epidemic differs from the more familiar uniform epidemic (e.g., ca... |
1807.08039 | Chieh Lo | Chieh Lo and Radu Marculescu | PGLasso: Microbial Community Detection through Phylogenetic Graphical
Lasso | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Due to the recent advances in high-throughput sequencing technologies, it
becomes possible to directly analyze microbial communities in the human body
and in the environment. Knowledge of how microbes interact with each other and
form functional communities can provide a solid foundation to understand
microbiome rela... | [
{
"created": "Fri, 20 Jul 2018 21:36:02 GMT",
"version": "v1"
}
] | 2018-07-24 | [
[
"Lo",
"Chieh",
""
],
[
"Marculescu",
"Radu",
""
]
] | Due to the recent advances in high-throughput sequencing technologies, it becomes possible to directly analyze microbial communities in the human body and in the environment. Knowledge of how microbes interact with each other and form functional communities can provide a solid foundation to understand microbiome relate... |
2107.02962 | Bin-Guo Wang | Bin-Guo Wang, Shunxiang Huang, Yongping Xiong, Ming-Zhen Xin, Jing LI,
Jiangqian Zhang, Zhihui Ma | Transmission Dynamics of COVID-19 Pandemic Non-pharmaceutical
Interventions and Vaccination | null | null | null | null | q-bio.PE math.DS | http://creativecommons.org/licenses/by/4.0/ | Non-pharmaceutical interventions(NPIs) play an important role in the early
stage control of COVID-19 pandemic. Vaccination is considered to be the
inevitable course to stop the spread of SARS-CoV-2. Based on the mechanism, a
SVEIR COVID-19 model with vaccination and NPIs is proposed. By means of the
basic reproductio... | [
{
"created": "Wed, 7 Jul 2021 00:51:09 GMT",
"version": "v1"
}
] | 2021-07-08 | [
[
"Wang",
"Bin-Guo",
""
],
[
"Huang",
"Shunxiang",
""
],
[
"Xiong",
"Yongping",
""
],
[
"Xin",
"Ming-Zhen",
""
],
[
"LI",
"Jing",
""
],
[
"Zhang",
"Jiangqian",
""
],
[
"Ma",
"Zhihui",
""
]
] | Non-pharmaceutical interventions(NPIs) play an important role in the early stage control of COVID-19 pandemic. Vaccination is considered to be the inevitable course to stop the spread of SARS-CoV-2. Based on the mechanism, a SVEIR COVID-19 model with vaccination and NPIs is proposed. By means of the basic reproduction ... |
1405.1413 | Giuseppe Pontrelli | Giuseppe Pontrelli, Filippo de Monte | A two-phase two-layer model for transdermal drug delivery and
percutaneous absorption | Mathematical Biosciences, accepted, 2014 | Mathematical Biosciences, 257, pp. 96-103, 2014 | 10.1016/j.mbs.2014.05.001 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One of the promising frontiers of bioengineering is the controlled release of
a therapeuticdrug from a vehicle across the skin (transdermal drug delivery).
In order to study the complete process, a two-phase mathematical model
describing the dynamics of a substance between two coupled media of different
properties an... | [
{
"created": "Tue, 6 May 2014 09:07:48 GMT",
"version": "v1"
}
] | 2016-01-15 | [
[
"Pontrelli",
"Giuseppe",
""
],
[
"de Monte",
"Filippo",
""
]
] | One of the promising frontiers of bioengineering is the controlled release of a therapeuticdrug from a vehicle across the skin (transdermal drug delivery). In order to study the complete process, a two-phase mathematical model describing the dynamics of a substance between two coupled media of different properties and ... |
1912.03412 | Eric Jones | Zipeng Wang, Eric W. Jones, Joshua M. Mueller, Jean M. Carlson | Control of ecological outcomes through deliberate parameter changes in a
model of the gut microbiome | main text 9 pages, 5 figures; supplement 10 pages, 2 figures | Phys. Rev. E 101, 052402 (2020) | 10.1103/PhysRevE.101.052402 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The generalized Lotka-Volterra (gLV) equations are a mathematical proxy for
ecological dynamics. We focus on a gLV model of the gut microbiome, in which
the evolution of the gut microbial state is determined in part by pairwise
inter-species interaction parameters that encode environmentally-mediated
resource competi... | [
{
"created": "Sat, 7 Dec 2019 02:04:40 GMT",
"version": "v1"
},
{
"created": "Sun, 29 Mar 2020 06:02:17 GMT",
"version": "v2"
}
] | 2020-05-13 | [
[
"Wang",
"Zipeng",
""
],
[
"Jones",
"Eric W.",
""
],
[
"Mueller",
"Joshua M.",
""
],
[
"Carlson",
"Jean M.",
""
]
] | The generalized Lotka-Volterra (gLV) equations are a mathematical proxy for ecological dynamics. We focus on a gLV model of the gut microbiome, in which the evolution of the gut microbial state is determined in part by pairwise inter-species interaction parameters that encode environmentally-mediated resource competiti... |
0704.3748 | Gerald A. Miller | Gerald A. Miller, Yi Y. Shi, Hong Qian, and Karol Bomsztyk | Clustering Coefficients of Protein-Protein Interaction Networks | 16 pages, 3 figures, in Press PRE uses pdflatex | Phys. Rev. E 75, 051910 (2007) | 10.1103/PhysRevE.75.051910 | null | q-bio.QM cond-mat.stat-mech physics.bio-ph q-bio.MN | null | The properties of certain networks are determined by hidden variables that
are not explicitly measured. The conditional probability (propagator) that a
vertex with a given value of the hidden variable is connected to k of other
vertices determines all measurable properties. We study hidden variable models
and find an... | [
{
"created": "Fri, 27 Apr 2007 21:00:20 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Miller",
"Gerald A.",
""
],
[
"Shi",
"Yi Y.",
""
],
[
"Qian",
"Hong",
""
],
[
"Bomsztyk",
"Karol",
""
]
] | The properties of certain networks are determined by hidden variables that are not explicitly measured. The conditional probability (propagator) that a vertex with a given value of the hidden variable is connected to k of other vertices determines all measurable properties. We study hidden variable models and find an a... |
2004.12124 | Jean-Francois Berret | Milad Radiom, Jean-Franccois Berret | Common trends in the epidemic of Covid-19 disease | 15 pages, 5 figures, 2 tables | The European Physical Journal Plus 135, 517 (2020) | 10.1140/epjp/s13360-020-00526-1 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The discovery of SARS-CoV-2, the responsible virus for the Covid-19 epidemic,
has sparked a global health concern with many countries affected. Developing
models that can interpret the epidemic and give common trend parameters are
useful for prediction purposes by other countries that are at an earlier phase
of the e... | [
{
"created": "Sat, 25 Apr 2020 12:24:27 GMT",
"version": "v1"
},
{
"created": "Wed, 10 Jun 2020 16:06:44 GMT",
"version": "v2"
}
] | 2021-09-21 | [
[
"Radiom",
"Milad",
""
],
[
"Berret",
"Jean-Franccois",
""
]
] | The discovery of SARS-CoV-2, the responsible virus for the Covid-19 epidemic, has sparked a global health concern with many countries affected. Developing models that can interpret the epidemic and give common trend parameters are useful for prediction purposes by other countries that are at an earlier phase of the epi... |
2311.07793 | Marcela Svarc | Fernando A. Najman, Antonio Galves, Marcela Svarc and Claudia D.
Vargas | The brain uses renewal points to model random sequences of stimuli | 11 pages, 5 figures | null | null | null | q-bio.NC stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has been classically conjectured that the brain assigns probabilistic
models to sequences of stimuli. An important issue associated with this
conjecture is the identification of the classes of models used by the brain to
perform this task. We address this issue by using a new clustering procedure
for sets of elect... | [
{
"created": "Mon, 13 Nov 2023 23:02:32 GMT",
"version": "v1"
},
{
"created": "Wed, 27 Dec 2023 18:20:58 GMT",
"version": "v2"
}
] | 2023-12-29 | [
[
"Najman",
"Fernando A.",
""
],
[
"Galves",
"Antonio",
""
],
[
"Svarc",
"Marcela",
""
],
[
"Vargas",
"Claudia D.",
""
]
] | It has been classically conjectured that the brain assigns probabilistic models to sequences of stimuli. An important issue associated with this conjecture is the identification of the classes of models used by the brain to perform this task. We address this issue by using a new clustering procedure for sets of electro... |
1612.01409 | Santosh Tirunagari | Norman Poh, Simon Bull, Santosh Tirunagari, Nicholas Cole, Simon de
Lusignan | Probabilistic Broken-Stick Model: A Regression Algorithm for Irregularly
Sampled Data with Application to eGFR | Preprint submitted to Journal of Biomedical Informatics | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In order for clinicians to manage disease progression and make effective
decisions about drug dosage, treatment regimens or scheduling follow up
appointments, it is necessary to be able to identify both short and long-term
trends in repeated biomedical measurements. However, this is complicated by the
fact that these... | [
{
"created": "Wed, 30 Nov 2016 17:50:44 GMT",
"version": "v1"
}
] | 2016-12-06 | [
[
"Poh",
"Norman",
""
],
[
"Bull",
"Simon",
""
],
[
"Tirunagari",
"Santosh",
""
],
[
"Cole",
"Nicholas",
""
],
[
"de Lusignan",
"Simon",
""
]
] | In order for clinicians to manage disease progression and make effective decisions about drug dosage, treatment regimens or scheduling follow up appointments, it is necessary to be able to identify both short and long-term trends in repeated biomedical measurements. However, this is complicated by the fact that these m... |
q-bio/0506016 | Bob Eisenberg | Bob Eisenberg | Ions in Fluctuating Channels: Transistors Alive | Revised version of earlier submission, as invited, refereed, and
published by journal | Fluctuations and Noise Letters (2012) 11:76-96 | 10.1142/S0219477512400019 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ion channels are proteins with a hole down the middle embedded in cell
membranes. Membranes form insulating structures and the channels through them
allow and control the movement of charged particles, spherical ions, mostly
Na+, K+, Ca++, and Cl-. Membranes contain hundreds or thousands of types of
channels, fluctua... | [
{
"created": "Tue, 14 Jun 2005 14:28:58 GMT",
"version": "v1"
},
{
"created": "Sun, 3 Feb 2008 22:32:30 GMT",
"version": "v2"
},
{
"created": "Fri, 10 May 2013 18:40:14 GMT",
"version": "v3"
}
] | 2015-05-11 | [
[
"Eisenberg",
"Bob",
""
]
] | Ion channels are proteins with a hole down the middle embedded in cell membranes. Membranes form insulating structures and the channels through them allow and control the movement of charged particles, spherical ions, mostly Na+, K+, Ca++, and Cl-. Membranes contain hundreds or thousands of types of channels, fluctuati... |
1407.0865 | Gibin Powathil | Gibin G Powathil, Mark AJ Chaplain and Maciej Swat | Investigating the development of chemotherapeutic drug resistance in
cancer: A multiscale computational study | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chemotherapy is one of the most important therapeutic options used to treat
human cancers, either alone or in combination with radiation therapy and
surgery. Recent studies have indicated that intra-tumoural heterogeneity has a
significant role in driving resistance to chemotherapy in many human
malignancies. Multipl... | [
{
"created": "Thu, 3 Jul 2014 11:03:02 GMT",
"version": "v1"
}
] | 2014-07-04 | [
[
"Powathil",
"Gibin G",
""
],
[
"Chaplain",
"Mark AJ",
""
],
[
"Swat",
"Maciej",
""
]
] | Chemotherapy is one of the most important therapeutic options used to treat human cancers, either alone or in combination with radiation therapy and surgery. Recent studies have indicated that intra-tumoural heterogeneity has a significant role in driving resistance to chemotherapy in many human malignancies. Multiple ... |
2210.09308 | Nicolas F. Chaves De Plaza | Nicolas F. Chaves-de-Plaza, Klaus Hildebrandt, Anna Vilanova | ProtoFold Neighborhood Inspector | Accepted submission for the Bio+MedVis challenge @ IEEE VIS 2022 | null | null | null | q-bio.QM cs.GR | http://creativecommons.org/licenses/by/4.0/ | Post-translational modifications (PTMs) affecting a protein's residues (amino
acids) can disturb its function, leading to illness. Whether or not a PTM is
pathogenic depends on its type and the status of neighboring residues. In this
paper, we present the ProtoFold Neighborhood Inspector (PFNI), a visualization
syste... | [
{
"created": "Mon, 17 Oct 2022 09:23:24 GMT",
"version": "v1"
}
] | 2022-10-19 | [
[
"Chaves-de-Plaza",
"Nicolas F.",
""
],
[
"Hildebrandt",
"Klaus",
""
],
[
"Vilanova",
"Anna",
""
]
] | Post-translational modifications (PTMs) affecting a protein's residues (amino acids) can disturb its function, leading to illness. Whether or not a PTM is pathogenic depends on its type and the status of neighboring residues. In this paper, we present the ProtoFold Neighborhood Inspector (PFNI), a visualization system ... |
2004.11242 | Aurelie Nakamura | Aurelie Nakamura (iPLESP), Laura Pryor (iPLESP), Morgane Ballon
(CRESS), Sandrine Lioret (CRESS), Barbara Heude (CRESS), Marie-Aline Charles
(ELFE), Maria Melchior (iPLESP), El-Khoury Lesueur (iPLESP) | Maternal education and offspring birthweight for gestational age: the
mediating effect of smoking during pregnancy | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background Small for gestational age (SGA) birthweight, a risk factor of
infant mortality and delayed child development, is associated with maternal
educational attainment. Maternal tobacco smoking during pregnancy could
contribute to this association. We aimed to quantify the contribution of
maternal smoking during ... | [
{
"created": "Wed, 22 Apr 2020 09:00:35 GMT",
"version": "v1"
}
] | 2020-04-24 | [
[
"Nakamura",
"Aurelie",
"",
"iPLESP"
],
[
"Pryor",
"Laura",
"",
"iPLESP"
],
[
"Ballon",
"Morgane",
"",
"CRESS"
],
[
"Lioret",
"Sandrine",
"",
"CRESS"
],
[
"Heude",
"Barbara",
"",
"CRESS"
],
[
"Charles",
"Mar... | Background Small for gestational age (SGA) birthweight, a risk factor of infant mortality and delayed child development, is associated with maternal educational attainment. Maternal tobacco smoking during pregnancy could contribute to this association. We aimed to quantify the contribution of maternal smoking during pr... |
1006.2752 | Eva Gehrmann | Eva Gehrmann and Barbara Drossel | Boolean versus continuous dynamics on simple two-gene modules | 8 pages, 10 figures | null | 10.1103/PhysRevE.82.046120 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the dynamical behavior of simple modules composed of two genes
with two or three regulating connections. Continuous dynamics for mRNA and
protein concentrations is compared to a Boolean model for gene activity. Using
a generalized method, we study within a single framework different continuous
models a... | [
{
"created": "Mon, 14 Jun 2010 16:09:22 GMT",
"version": "v1"
}
] | 2013-05-29 | [
[
"Gehrmann",
"Eva",
""
],
[
"Drossel",
"Barbara",
""
]
] | We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a generalized method, we study within a single framework different continuous models and... |
1311.6345 | Pierre-Olivier Amblard | Pierre-Olivier Amblard | A non-parametric efficient evaluation of Partial Directed Coherence | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Studying the flow of information between different areas of the brain can be
performed by using the so-called Partial Directed Coherence. This measure is
usually evaluated by first identifying a multivariate autoregressive model, and
then by using Fourier transforms of the impulse responses identified and
applying ap... | [
{
"created": "Mon, 25 Nov 2013 16:04:18 GMT",
"version": "v1"
}
] | 2013-11-26 | [
[
"Amblard",
"Pierre-Olivier",
""
]
] | Studying the flow of information between different areas of the brain can be performed by using the so-called Partial Directed Coherence. This measure is usually evaluated by first identifying a multivariate autoregressive model, and then by using Fourier transforms of the impulse responses identified and applying appr... |
2310.14722 | bastien chassagnol | Bastien Chassagnol (LPSM), Gr\'egory Nuel (LPSM), Etienne Becht | An updated State-of-the-Art Overview of transcriptomic Deconvolution
Methods | null | null | null | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although bulk transcriptomic analyses have significantly contributed to an
enhanced comprehension of multifaceted diseases, their exploration capacity is
impeded by the heterogeneous compositions of biological samples. Indeed, by
averaging expression of multiple cell types, RNA-Seq analysis is oblivious to
variations... | [
{
"created": "Mon, 23 Oct 2023 09:00:03 GMT",
"version": "v1"
}
] | 2023-10-24 | [
[
"Chassagnol",
"Bastien",
"",
"LPSM"
],
[
"Nuel",
"Grégory",
"",
"LPSM"
],
[
"Becht",
"Etienne",
""
]
] | Although bulk transcriptomic analyses have significantly contributed to an enhanced comprehension of multifaceted diseases, their exploration capacity is impeded by the heterogeneous compositions of biological samples. Indeed, by averaging expression of multiple cell types, RNA-Seq analysis is oblivious to variations i... |
1906.07511 | Anne-Sophie Herard | Florent Letronne, Geoffroy Laumet, Anne-Marie Ayral, Julien Chapuis,
Florie Demiautte, Mathias Laga, Michel Vandenberghe (LMN), Nicolas Malmanche,
Florence Leroux, Fanny Eysert, Yoann Sottejeau, Linda Chami, Amandine Flaig,
Charlotte Bauer (IPMC), Pierre Dourlen (JPArc - U837 Inserm), Marie Lesaffre,
Charlotte ... | ADAM30 Downregulates APP-Linked Defects Through Cathepsin D Activation
in Alzheimer's Disease | null | EBioMedicine, Elsevier, 2016, 9, pp.278-292 | 10.1016/j.ebiom.2016.06.002 | null | q-bio.NC q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although several ADAMs (A disintegrin-like and metalloproteases) have been
shown to contribute to the amy-loid precursor protein (APP) metabolism, the
full spectrum of metalloproteases involved in this metabolism remains to be
established. Transcriptomic analyses centred on metalloprotease genes unraveled
a 50% decre... | [
{
"created": "Tue, 18 Jun 2019 11:56:49 GMT",
"version": "v1"
}
] | 2019-06-19 | [
[
"Letronne",
"Florent",
"",
"LMN"
],
[
"Laumet",
"Geoffroy",
"",
"LMN"
],
[
"Ayral",
"Anne-Marie",
"",
"LMN"
],
[
"Chapuis",
"Julien",
"",
"LMN"
],
[
"Demiautte",
"Florie",
"",
"LMN"
],
[
"Laga",
"Mathias",
... | Although several ADAMs (A disintegrin-like and metalloproteases) have been shown to contribute to the amy-loid precursor protein (APP) metabolism, the full spectrum of metalloproteases involved in this metabolism remains to be established. Transcriptomic analyses centred on metalloprotease genes unraveled a 50% decreas... |
0804.3939 | Raphael Plasson | Raphael Plasson | Microreversible recycled chemical systems. Comment on "A Re-Examination
of Reversibility in Reaction Models for the Spontaneous Emergence of
Homochirality" | 2 pages, 2 figures | J. Phys. Chem. B, 2008, 112, 9550-9552 | 10.1021/jp803588z | NORDITA-2008-18 | q-bio.MN physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The question of the onset of the homochirality on prebiotic Earth still
remains a fundamental question in the quest for the origin of life. Recent
works in this field introduce the concept of recycling, rather than the
traditional open-flow system described by Frank. This approach has been
criticized by Blackmond et ... | [
{
"created": "Thu, 24 Apr 2008 14:40:23 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Nov 2008 10:21:28 GMT",
"version": "v2"
}
] | 2011-05-23 | [
[
"Plasson",
"Raphael",
""
]
] | The question of the onset of the homochirality on prebiotic Earth still remains a fundamental question in the quest for the origin of life. Recent works in this field introduce the concept of recycling, rather than the traditional open-flow system described by Frank. This approach has been criticized by Blackmond et al... |
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