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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
q-bio/0604015 | Radhakrishnan Nagarajan | Radhakrishnan Nagarajan, Meenakshi Upreti | Qualitative Assessment of Gene Expression in Affymetrix Genechip Arrays | 22 Pages, 7 Figures, 1 Table | null | 10.1016/j.physa.2006.06.004 | null | q-bio.GN | null | Affymetrix Genechip microarrays are used widely to determine the simultaneous
expression of genes in a given biological paradigm. Probes on the Genechip
array are atomic entities which by definition are randomly distributed across
the array and in turn govern the gene expression. In the present study, we make
several... | [
{
"created": "Wed, 12 Apr 2006 20:20:03 GMT",
"version": "v1"
},
{
"created": "Fri, 19 May 2006 15:27:25 GMT",
"version": "v2"
}
] | 2009-11-13 | [
[
"Nagarajan",
"Radhakrishnan",
""
],
[
"Upreti",
"Meenakshi",
""
]
] | Affymetrix Genechip microarrays are used widely to determine the simultaneous expression of genes in a given biological paradigm. Probes on the Genechip array are atomic entities which by definition are randomly distributed across the array and in turn govern the gene expression. In the present study, we make several i... |
2407.09509 | Heng Huang | Heng Huang, Lin Zhao, Zihao Wu, Xiaowei Yu, Jing Zhang, Xintao Hu,
Dajiang Zhu, Tianming Liu | Brain Dialogue Interface (BDI): A User-Friendly fMRI Model for
Interactive Brain Decoding | null | null | null | null | q-bio.NC cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Brain decoding techniques are essential for understanding the neurocognitive
system. Although numerous methods have been introduced in this field,
accurately aligning complex external stimuli with brain activities remains a
formidable challenge. To alleviate alignment difficulties, many studies have
simplified their ... | [
{
"created": "Mon, 17 Jun 2024 04:38:19 GMT",
"version": "v1"
}
] | 2024-07-16 | [
[
"Huang",
"Heng",
""
],
[
"Zhao",
"Lin",
""
],
[
"Wu",
"Zihao",
""
],
[
"Yu",
"Xiaowei",
""
],
[
"Zhang",
"Jing",
""
],
[
"Hu",
"Xintao",
""
],
[
"Zhu",
"Dajiang",
""
],
[
"Liu",
"Tianming",
... | Brain decoding techniques are essential for understanding the neurocognitive system. Although numerous methods have been introduced in this field, accurately aligning complex external stimuli with brain activities remains a formidable challenge. To alleviate alignment difficulties, many studies have simplified their mo... |
1608.05855 | Christophe Guyeux | Jacques M. Bahi and Nathalie C\^ot\'e and Christophe Guyeux and Michel
Salomon | Protein Folding in the 2D Hydrophobic-Hydrophilic (HP) Square Lattice
Model is Chaotic | Cognitive Computation (2012). arXiv admin note: text overlap with
arXiv:1511.00139 | null | null | null | q-bio.BM math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Among the unsolved problems in computational biology, protein folding is one
of the most interesting challenges. To study this folding, tools like neural
networks and genetic algorithms have received a lot of attention, mainly due to
the NP-completeness of the folding process. The background idea that has given
rise ... | [
{
"created": "Sat, 20 Aug 2016 17:57:02 GMT",
"version": "v1"
}
] | 2016-08-23 | [
[
"Bahi",
"Jacques M.",
""
],
[
"Côté",
"Nathalie",
""
],
[
"Guyeux",
"Christophe",
""
],
[
"Salomon",
"Michel",
""
]
] | Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the NP-completeness of the folding process. The background idea that has given rise to... |
1912.12980 | Benjamin Cramer | Sebastian Billaudelle, Yannik Stradmann, Korbinian Schreiber, Benjamin
Cramer, Andreas Baumbach, Dominik Dold, Julian G\"oltz, Akos F. Kungl, Timo
C. Wunderlich, Andreas Hartel, Eric M\"uller, Oliver Breitwieser, Christian
Mauch, Mitja Kleider, Andreas Gr\"ubl, David St\"ockel, Christian Pehle,
Arthur Heimbrech... | Versatile emulation of spiking neural networks on an accelerated
neuromorphic substrate | null | null | 10.1109/ISCAS45731.2020.9180741 | null | q-bio.NC cs.NE | http://creativecommons.org/licenses/by/4.0/ | We present first experimental results on the novel BrainScaleS-2 neuromorphic
architecture based on an analog neuro-synaptic core and augmented by embedded
microprocessors for complex plasticity and experiment control. The high
acceleration factor of 1000 compared to biological dynamics enables the
execution of compu... | [
{
"created": "Mon, 30 Dec 2019 16:12:14 GMT",
"version": "v1"
},
{
"created": "Mon, 9 May 2022 10:27:37 GMT",
"version": "v2"
}
] | 2022-05-10 | [
[
"Billaudelle",
"Sebastian",
""
],
[
"Stradmann",
"Yannik",
""
],
[
"Schreiber",
"Korbinian",
""
],
[
"Cramer",
"Benjamin",
""
],
[
"Baumbach",
"Andreas",
""
],
[
"Dold",
"Dominik",
""
],
[
"Göltz",
"Julian",
... | We present first experimental results on the novel BrainScaleS-2 neuromorphic architecture based on an analog neuro-synaptic core and augmented by embedded microprocessors for complex plasticity and experiment control. The high acceleration factor of 1000 compared to biological dynamics enables the execution of computa... |
1004.3162 | Frank Le Foll | Jennifer Pasquier, Pierre Magal, C\'eline Boulang\'e-Lecomte, Glenn
Webb and Frank Le Foll | Consequences of cell-to-cell P-glycoprotein transfer on acquired
multidrug resistance in breast cancer: a cell population dynamics model | 13 pages, 8 figures, 1 table | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cancer is a proliferation disease affecting a genetically unstable cell
population, in which molecular alterations can be somatically inherited by
genetic, epigenetic or extragenetic transmission processes, leading to a
cooperation of neoplastic cells within tumoral tissue. The efflux protein
P-glycoprotein (P gp) is... | [
{
"created": "Mon, 19 Apr 2010 11:32:31 GMT",
"version": "v1"
}
] | 2010-04-20 | [
[
"Pasquier",
"Jennifer",
""
],
[
"Magal",
"Pierre",
""
],
[
"Boulangé-Lecomte",
"Céline",
""
],
[
"Webb",
"Glenn",
""
],
[
"Foll",
"Frank Le",
""
]
] | Cancer is a proliferation disease affecting a genetically unstable cell population, in which molecular alterations can be somatically inherited by genetic, epigenetic or extragenetic transmission processes, leading to a cooperation of neoplastic cells within tumoral tissue. The efflux protein P-glycoprotein (P gp) is o... |
2004.09133 | Laura Wadkin MMath | Laura E Wadkin, Sirio Orozco-Fuentes, Irina Neganova, Majlinda Lako, R
A Barrio, A W Baggaley, Nicholas G Parker, Anvar Shukurov | OCT4 expression in human embryonic stem cells: spatio-temporal dynamics
and fate transitions | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The improved in-vitro regulation of human embryonic stem cell (hESC)
pluripotency and differentiation trajectories is required for their promising
clinical applications. The temporal and spatial quantification of the molecular
interactions controlling pluripotency is also necessary for the development of
successful m... | [
{
"created": "Mon, 20 Apr 2020 08:55:27 GMT",
"version": "v1"
},
{
"created": "Mon, 4 May 2020 13:48:42 GMT",
"version": "v2"
},
{
"created": "Thu, 21 May 2020 16:39:49 GMT",
"version": "v3"
},
{
"created": "Tue, 27 Oct 2020 13:50:45 GMT",
"version": "v4"
}
] | 2020-10-28 | [
[
"Wadkin",
"Laura E",
""
],
[
"Orozco-Fuentes",
"Sirio",
""
],
[
"Neganova",
"Irina",
""
],
[
"Lako",
"Majlinda",
""
],
[
"Barrio",
"R A",
""
],
[
"Baggaley",
"A W",
""
],
[
"Parker",
"Nicholas G",
""
],
... | The improved in-vitro regulation of human embryonic stem cell (hESC) pluripotency and differentiation trajectories is required for their promising clinical applications. The temporal and spatial quantification of the molecular interactions controlling pluripotency is also necessary for the development of successful mat... |
1207.6090 | Steven Kelk | Teresa Piovesan and Steven Kelk | A simple fixed parameter tractable algorithm for computing the
hybridization number of two (not necessarily binary) trees | null | null | null | null | q-bio.QM math.CO q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Here we present a new fixed parameter tractable algorithm to compute the
hybridization number r of two rooted, not necessarily binary phylogenetic trees
on taxon set X in time (6^r.r!).poly(n)$, where n=|X|. The novelty of this
approach is its use of terminals, which are maximal elements of a natural
partial order on... | [
{
"created": "Wed, 25 Jul 2012 19:11:42 GMT",
"version": "v1"
}
] | 2012-07-26 | [
[
"Piovesan",
"Teresa",
""
],
[
"Kelk",
"Steven",
""
]
] | Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6^r.r!).poly(n)$, where n=|X|. The novelty of this approach is its use of terminals, which are maximal elements of a natural partial order on X... |
1808.08033 | Lucas Patty | C.H. Lucas Patty, Freek Ariese, Wybren Jan Buma, Inge Loes ten Kate,
Rob J.M. van Spanning, Frans Snik | Circular spectropolarimetric sensing of higher plant and algal
chloroplast structural variations | 25 pages, 9 figures | null | 10.1007/s11120-018-0572-2 | null | q-bio.BM physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Photosynthetic eukaryotes show a remarkable variability in photosynthesis,
including large differences in light harvesting proteins and pigment
composition. In vivo circular spectropolarimetry enables us to probe the
molecular architecture of photosynthesis in a non-invasive and non-destructive
way and, as such, can ... | [
{
"created": "Fri, 24 Aug 2018 07:36:36 GMT",
"version": "v1"
}
] | 2018-08-27 | [
[
"Patty",
"C. H. Lucas",
""
],
[
"Ariese",
"Freek",
""
],
[
"Buma",
"Wybren Jan",
""
],
[
"Kate",
"Inge Loes ten",
""
],
[
"van Spanning",
"Rob J. M.",
""
],
[
"Snik",
"Frans",
""
]
] | Photosynthetic eukaryotes show a remarkable variability in photosynthesis, including large differences in light harvesting proteins and pigment composition. In vivo circular spectropolarimetry enables us to probe the molecular architecture of photosynthesis in a non-invasive and non-destructive way and, as such, can of... |
2211.07294 | Xianhang Luo | Enqiang Zhu, Xianhang Luo, Chanjuan Liu, Xiaolong Shi, Jin Xu | A universal DNA computing model for solving NP-hard subset problems | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | DNA computing, a nontraditional computing mechanism, provides a feasible and
effective method for solving NP-hard problems because of the vast parallelism
and high-density storage of DNA molecules. Although DNA computing has been
exploited to solve various intractable computational problems, such as the
Hamiltonian p... | [
{
"created": "Mon, 14 Nov 2022 11:59:18 GMT",
"version": "v1"
},
{
"created": "Wed, 16 Nov 2022 04:18:11 GMT",
"version": "v2"
}
] | 2022-11-17 | [
[
"Zhu",
"Enqiang",
""
],
[
"Luo",
"Xianhang",
""
],
[
"Liu",
"Chanjuan",
""
],
[
"Shi",
"Xiaolong",
""
],
[
"Xu",
"Jin",
""
]
] | DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited to solve various intractable computational problems, such as the Hamiltonian pat... |
0808.0220 | Ping Ao | P. Ao, L.W. Lee, Me Lidstrom, L. Yin, X. M. Zhu | Towards Kinetic Modeling of Global Metabolic Networks with Incomplete
Experimental Input on Kinetic Parameters | 15 pages, pdf format | Towards Kinetic Modeling of Global Metabolic Networks:
Methylobacterium extorquens AM1 Growth as Validation, Chinese J. Biotech 24
(2008) 980-994 | null | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This is the first report, to our knowledge, on a systematic method for
constructing a large scale kinetic metabolic model with incomplete information
on kinetic parametersr, and its initial application to the modeling of central
metabolism of Methylobacterium extorquens AM1, a methylotrophic and
environmental importa... | [
{
"created": "Sat, 2 Aug 2008 00:57:05 GMT",
"version": "v1"
}
] | 2008-08-05 | [
[
"Ao",
"P.",
""
],
[
"Lee",
"L. W.",
""
],
[
"Lidstrom",
"Me",
""
],
[
"Yin",
"L.",
""
],
[
"Zhu",
"X. M.",
""
]
] | This is the first report, to our knowledge, on a systematic method for constructing a large scale kinetic metabolic model with incomplete information on kinetic parametersr, and its initial application to the modeling of central metabolism of Methylobacterium extorquens AM1, a methylotrophic and environmental important... |
2210.01772 | Anne-Marie Rickmann | Anne-Marie Rickmann, Fabian Bongratz, Sebastian P\"olsterl, Ignacio
Sarasua, Christian Wachinger | Joint Reconstruction and Parcellation of Cortical Surfaces | accepted at MLCN workshop 2022 | null | null | null | q-bio.NC cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The reconstruction of cerebral cortex surfaces from brain MRI scans is
instrumental for the analysis of brain morphology and the detection of cortical
thinning in neurodegenerative diseases like Alzheimer's disease (AD). Moreover,
for a fine-grained analysis of atrophy patterns, the parcellation of the
cortical surfa... | [
{
"created": "Mon, 19 Sep 2022 11:45:39 GMT",
"version": "v1"
}
] | 2022-10-05 | [
[
"Rickmann",
"Anne-Marie",
""
],
[
"Bongratz",
"Fabian",
""
],
[
"Pölsterl",
"Sebastian",
""
],
[
"Sarasua",
"Ignacio",
""
],
[
"Wachinger",
"Christian",
""
]
] | The reconstruction of cerebral cortex surfaces from brain MRI scans is instrumental for the analysis of brain morphology and the detection of cortical thinning in neurodegenerative diseases like Alzheimer's disease (AD). Moreover, for a fine-grained analysis of atrophy patterns, the parcellation of the cortical surface... |
2212.12114 | Nan Xi | Angelos Vasilopoulos and Nan Miles Xi | Predicting Survival of Tongue Cancer Patients by Machine Learning Models | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Tongue cancer is a common oral cavity malignancy that originates in the mouth
and throat. Much effort has been invested in improving its diagnosis,
treatment, and management. Surgical removal, chemotherapy, and radiation
therapy remain the major treatment for tongue cancer. The survival of patients
determines the tre... | [
{
"created": "Fri, 23 Dec 2022 03:00:20 GMT",
"version": "v1"
}
] | 2022-12-26 | [
[
"Vasilopoulos",
"Angelos",
""
],
[
"Xi",
"Nan Miles",
""
]
] | Tongue cancer is a common oral cavity malignancy that originates in the mouth and throat. Much effort has been invested in improving its diagnosis, treatment, and management. Surgical removal, chemotherapy, and radiation therapy remain the major treatment for tongue cancer. The survival of patients determines the treat... |
1702.00489 | Ryan Evans | Ryan M. Evans and David A. Edwards | Transport Effects on Multiple-Component Reactions in Optical Biosensors | null | Bulletin of Mathematical Biology, 79 (2017): 2214--2241 | 10.1007/s11538-017-0327-9 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Optical biosensors are often used to measure kinetic rate constants
associated with chemical reactions. Such instruments operate in the
\textit{surface-volume} configuration, in which ligand molecules are convected
through a fluid-filled volume over a surface to which receptors are confined.
Currently, scientists are... | [
{
"created": "Thu, 26 Jan 2017 20:11:40 GMT",
"version": "v1"
},
{
"created": "Thu, 12 Oct 2017 16:09:54 GMT",
"version": "v2"
}
] | 2017-10-13 | [
[
"Evans",
"Ryan M.",
""
],
[
"Edwards",
"David A.",
""
]
] | Optical biosensors are often used to measure kinetic rate constants associated with chemical reactions. Such instruments operate in the \textit{surface-volume} configuration, in which ligand molecules are convected through a fluid-filled volume over a surface to which receptors are confined. Currently, scientists are u... |
q-bio/0605035 | Mathieu Emily | Mathieu Emily and Olivier Francois | A continuous model for cell sorting | 21 pages; 6 Figures; 1 Table | null | null | null | q-bio.TO | null | The differential Adhesion Hypothesis (DAH) is a theory of the organization of
cells within a tissue. In this study we introduce a stochastic model supporting
the DAH, that can be seen as a continuous version of a discrete model of Graner
and Glazier. Our approach is based on the mathematical framework of Gibbsian
mar... | [
{
"created": "Sat, 20 May 2006 12:59:31 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Emily",
"Mathieu",
""
],
[
"Francois",
"Olivier",
""
]
] | The differential Adhesion Hypothesis (DAH) is a theory of the organization of cells within a tissue. In this study we introduce a stochastic model supporting the DAH, that can be seen as a continuous version of a discrete model of Graner and Glazier. Our approach is based on the mathematical framework of Gibbsian marke... |
2310.16439 | Gennadi Glinsky | Gennadi Glinsky | Genomic regulatory architecture of human embryo retroviral LTR elements
affecting evolution, development, and pathophysiology of Modern Humans | 66 pages, 16 figures | null | null | null | q-bio.GN q-bio.MN q-bio.NC q-bio.PE q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Two distinct families of pan-primate endogenous retroviruses, namely HERVL
and HERVH, infected primates germline, colonized host genomes, and evolved into
the global retroviral genomic regulatory dominion (GRD) operating during human
embryogenesis (HE). HE retroviral GRD constitutes 8839 highly conserved fixed
LTR el... | [
{
"created": "Wed, 25 Oct 2023 08:04:58 GMT",
"version": "v1"
}
] | 2023-10-26 | [
[
"Glinsky",
"Gennadi",
""
]
] | Two distinct families of pan-primate endogenous retroviruses, namely HERVL and HERVH, infected primates germline, colonized host genomes, and evolved into the global retroviral genomic regulatory dominion (GRD) operating during human embryogenesis (HE). HE retroviral GRD constitutes 8839 highly conserved fixed LTR elem... |
1902.10117 | Giovanni Stilo | Lorenzo Madeddu, Giovanni Stilo, Paola Velardi | Network-based methods for disease-gene prediction | null | null | null | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We predict disease-genes relations on the Human Interactome network using a
methodology that jointly learns functional and connectivity patterns
surrounding proteins. Contrary to other data structures, the Interactome is
characterized by high incompleteness and absence of explicit negative
knowledge, which makes pred... | [
{
"created": "Tue, 26 Feb 2019 18:48:27 GMT",
"version": "v1"
}
] | 2019-02-27 | [
[
"Madeddu",
"Lorenzo",
""
],
[
"Stilo",
"Giovanni",
""
],
[
"Velardi",
"Paola",
""
]
] | We predict disease-genes relations on the Human Interactome network using a methodology that jointly learns functional and connectivity patterns surrounding proteins. Contrary to other data structures, the Interactome is characterized by high incompleteness and absence of explicit negative knowledge, which makes predic... |
1303.4835 | Justin Fay | Gareth A. Cromie, Katie E. Hyma, Catherine L. Ludlow, Cecilia
Garmendia-Torres, Teresa L. Gilbert, Patrick May, Angela A. Huang, Aim\'ee M.
Dudley, Justin C. Fay | Genomic Sequence Diversity and Population Structure of Saccharomyces
cerevisiae Assessed by RAD-seq | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/3.0/ | The budding yeast Saccharomyces cerevisiae is important for human food
production and as a model organism for biological research. The genetic
diversity contained in the global population of yeast strains represents a
valuable resource for a number of fields, including genetics, bioengineering,
and studies of evoluti... | [
{
"created": "Wed, 20 Mar 2013 04:08:54 GMT",
"version": "v1"
}
] | 2015-03-13 | [
[
"Cromie",
"Gareth A.",
""
],
[
"Hyma",
"Katie E.",
""
],
[
"Ludlow",
"Catherine L.",
""
],
[
"Garmendia-Torres",
"Cecilia",
""
],
[
"Gilbert",
"Teresa L.",
""
],
[
"May",
"Patrick",
""
],
[
"Huang",
"Angela A."... | The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution... |
1212.1067 | Christian Hilbe | Christian Hilbe and Martin A. Nowak and Karl Sigmund | The Evolution of Extortion in Iterated Prisoner's Dilemma Games | contains 4 figures | null | 10.1073/pnas.1214834110 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Iterated games are a fundamental component of economic and evolutionary game
theory. They describe situations where two players interact repeatedly and have
the possibility to use conditional strategies that depend on the outcome of
previous interactions. In the context of evolution of cooperation, repeated
games rep... | [
{
"created": "Wed, 5 Dec 2012 15:56:04 GMT",
"version": "v1"
}
] | 2015-06-12 | [
[
"Hilbe",
"Christian",
""
],
[
"Nowak",
"Martin A.",
""
],
[
"Sigmund",
"Karl",
""
]
] | Iterated games are a fundamental component of economic and evolutionary game theory. They describe situations where two players interact repeatedly and have the possibility to use conditional strategies that depend on the outcome of previous interactions. In the context of evolution of cooperation, repeated games repre... |
1909.05910 | Jahan Schad | Jahan N. Schad | Brain Neurological Constructs: The Neuronal Computational Schemes for
Resolution of Life's Complexities | 5 Pages | J Neurol Neurophysiol 2016, 7:1 | 10.4172/2155-9562.1000356 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | For complex life to evolve, a sophisticated nervous system for handling its
complexities was fundamental. The demand resulted in the emergence of brain's
computational facility, the neuronal network. This facet of the brain is
attested solidly by its inspired scientific computational neural nets which
(mathematically... | [
{
"created": "Tue, 10 Sep 2019 18:58:24 GMT",
"version": "v1"
}
] | 2019-09-16 | [
[
"Schad",
"Jahan N.",
""
]
] | For complex life to evolve, a sophisticated nervous system for handling its complexities was fundamental. The demand resulted in the emergence of brain's computational facility, the neuronal network. This facet of the brain is attested solidly by its inspired scientific computational neural nets which (mathematically) ... |
2110.06352 | Nazmi Burak Budanur | Nazmi Burak Budanur and Bj\"orn Hof | An autonomous compartmental model for accelerating epidemics | null | PLoS ONE 17(7): e0269975 (2022) | 10.1371/journal.pone.0269975 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In Fall 2020, several European countries reported rapid increases in COVID-19
cases along with growing estimates of the effective reproduction rates. Such an
acceleration in epidemic spread is usually attributed to time-dependent
effects, e.g. human travel, seasonal behavioral changes, mutations of the
pathogen etc. ... | [
{
"created": "Tue, 12 Oct 2021 20:53:53 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Jul 2022 09:47:01 GMT",
"version": "v2"
}
] | 2022-11-30 | [
[
"Budanur",
"Nazmi Burak",
""
],
[
"Hof",
"Björn",
""
]
] | In Fall 2020, several European countries reported rapid increases in COVID-19 cases along with growing estimates of the effective reproduction rates. Such an acceleration in epidemic spread is usually attributed to time-dependent effects, e.g. human travel, seasonal behavioral changes, mutations of the pathogen etc. In... |
1812.03321 | Mitchell Eithun | Mitchell Eithun, Daniel H. Chitwood, James Larson, Gregory Lang,
Elizabeth Munch | Isolating phyllotactic patterns embedded in the secondary growth of
sweet cherry (Prunus avium L.) using magnetic resonance imaging | Code: https://github.com/eithun/cherry-phyllotaxy | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Epicormic branches arise from dormant buds patterned during the growth of
previous years. Dormant epicormic buds remain on the surface of trees, pushed
outward from the pith during secondary growth, but maintaining vascular
connections. Epicormic buds can be reactivated, either through natural
processes or intentiona... | [
{
"created": "Sat, 8 Dec 2018 14:00:48 GMT",
"version": "v1"
}
] | 2018-12-11 | [
[
"Eithun",
"Mitchell",
""
],
[
"Chitwood",
"Daniel H.",
""
],
[
"Larson",
"James",
""
],
[
"Lang",
"Gregory",
""
],
[
"Munch",
"Elizabeth",
""
]
] | Epicormic branches arise from dormant buds patterned during the growth of previous years. Dormant epicormic buds remain on the surface of trees, pushed outward from the pith during secondary growth, but maintaining vascular connections. Epicormic buds can be reactivated, either through natural processes or intentionall... |
1508.06936 | Alex Barnett | Alex H. Barnett, Jeremy F. Magland, and Leslie F. Greengard | Validation of neural spike sorting algorithms without ground-truth
information | 22 pages, 7 figures; submitted to J. Neurosci. Meth | null | null | null | q-bio.NC cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We describe a suite of validation metrics that assess the credibility of a
given automatic spike sorting algorithm applied to a given electrophysiological
recording, when ground-truth is unavailable. By rerunning the spike sorter two
or more times, the metrics measure stability under various perturbations
consistent ... | [
{
"created": "Thu, 27 Aug 2015 16:53:20 GMT",
"version": "v1"
}
] | 2015-08-28 | [
[
"Barnett",
"Alex H.",
""
],
[
"Magland",
"Jeremy F.",
""
],
[
"Greengard",
"Leslie F.",
""
]
] | We describe a suite of validation metrics that assess the credibility of a given automatic spike sorting algorithm applied to a given electrophysiological recording, when ground-truth is unavailable. By rerunning the spike sorter two or more times, the metrics measure stability under various perturbations consistent wi... |
1212.0159 | C. Titus Brown | Adina Chuang Howe, Jason Pell, Rosangela Canino-Koning, Rachel
Mackelprang, Susannah Tringe, Janet Jansson, James M. Tiedje, C. Titus Brown | Illumina Sequencing Artifacts Revealed by Connectivity Analysis of
Metagenomic Datasets | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/publicdomain/ | Sequencing errors and biases in metagenomic datasets affect coverage-based
assemblies and are often ignored during analysis. Here, we analyze read
connectivity in metagenomes and identify the presence of problematic and likely
a-biological connectivity within metagenome assembly graphs. Specifically, we
identify high... | [
{
"created": "Sat, 1 Dec 2012 20:57:59 GMT",
"version": "v1"
}
] | 2012-12-04 | [
[
"Howe",
"Adina Chuang",
""
],
[
"Pell",
"Jason",
""
],
[
"Canino-Koning",
"Rosangela",
""
],
[
"Mackelprang",
"Rachel",
""
],
[
"Tringe",
"Susannah",
""
],
[
"Jansson",
"Janet",
""
],
[
"Tiedje",
"James M.",
... | Sequencing errors and biases in metagenomic datasets affect coverage-based assemblies and are often ignored during analysis. Here, we analyze read connectivity in metagenomes and identify the presence of problematic and likely a-biological connectivity within metagenome assembly graphs. Specifically, we identify highly... |
1505.04828 | Jaegil Kim | Jaegil Kim, Atanas Kamburov, Michal Lawrence, Yosef Maruvka, Gad Getz | An exact method to compute a $p$-value for the beyond-pairwise
correlations among cancer gene mutations | null | null | null | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The increasing observation of mutual exclusivity correlations among cancer
gene mutations is a key component for identifying driver events or pathways in
cancer genome analysis. Here we report a rigorous statistical method to compute
an exact $p$-value for the beyond-pairwise mutual exclusivity or co-occurrence
relat... | [
{
"created": "Mon, 18 May 2015 21:56:48 GMT",
"version": "v1"
}
] | 2015-05-20 | [
[
"Kim",
"Jaegil",
""
],
[
"Kamburov",
"Atanas",
""
],
[
"Lawrence",
"Michal",
""
],
[
"Maruvka",
"Yosef",
""
],
[
"Getz",
"Gad",
""
]
] | The increasing observation of mutual exclusivity correlations among cancer gene mutations is a key component for identifying driver events or pathways in cancer genome analysis. Here we report a rigorous statistical method to compute an exact $p$-value for the beyond-pairwise mutual exclusivity or co-occurrence relatio... |
2302.14064 | Adrian Bach | Adrian Bach | Exploring locust hopper bands emergent patterns using parallel computing | Masters project supervised by Jerome Buhl (The University of
Adelaide) | null | null | null | q-bio.NC nlin.AO physics.soc-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | To date, the mechanisms underlying the diversity of the emergent patterns of
collective motion in locust hopper bands remain to be unveiled. This study
investigates the role of speed heterogeneity in the emergence of the most
common patterns (frontal and columnar), following the Self-Organization
framework. To addres... | [
{
"created": "Tue, 28 Feb 2023 16:32:07 GMT",
"version": "v1"
}
] | 2023-03-01 | [
[
"Bach",
"Adrian",
""
]
] | To date, the mechanisms underlying the diversity of the emergent patterns of collective motion in locust hopper bands remain to be unveiled. This study investigates the role of speed heterogeneity in the emergence of the most common patterns (frontal and columnar), following the Self-Organization framework. To address ... |
1503.02846 | Steven Lade | Steven J. Lade, Susa Niiranen | Generalized modeling of empirical social-ecological systems | This is the authors' accepted manuscript. The final version of the
paper including copy-editing can be accessed at
http://onlinelibrary.wiley.com/doi/10.1111/nrm.12129/full | null | 10.1111/nrm.12129 | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modeling social-ecological systems is difficult due to the complexity of
ecosystems and of individual and collective human behavior. Key components of
the social-ecological system are often over-simplified or omitted. Generalized
modeling is a dynamical systems approach that can overcome some of these
challenges. It ... | [
{
"created": "Tue, 10 Mar 2015 10:15:23 GMT",
"version": "v1"
},
{
"created": "Wed, 24 May 2017 16:17:15 GMT",
"version": "v2"
}
] | 2017-05-25 | [
[
"Lade",
"Steven J.",
""
],
[
"Niiranen",
"Susa",
""
]
] | Modeling social-ecological systems is difficult due to the complexity of ecosystems and of individual and collective human behavior. Key components of the social-ecological system are often over-simplified or omitted. Generalized modeling is a dynamical systems approach that can overcome some of these challenges. It ca... |
2012.02831 | Aurelien Tellier | Wolfgang Stephan and Aur\'elien Tellier | Stochastic processes and host-parasite coevolution: linking
coevolutionary dynamics and DNA polymorphism data | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Between-species coevolution, and in particular antagonistic host-parasite
coevolution, is a major process shaping within-species diversity. In this paper
we investigate the role of various stochastic processes affecting the outcome
of the deterministic coevolutionary models. Specifically, we assess 1) the
impact of g... | [
{
"created": "Fri, 4 Dec 2020 20:10:50 GMT",
"version": "v1"
}
] | 2020-12-08 | [
[
"Stephan",
"Wolfgang",
""
],
[
"Tellier",
"Aurélien",
""
]
] | Between-species coevolution, and in particular antagonistic host-parasite coevolution, is a major process shaping within-species diversity. In this paper we investigate the role of various stochastic processes affecting the outcome of the deterministic coevolutionary models. Specifically, we assess 1) the impact of gen... |
1905.08912 | Max Allen | Maximilian L. Allen, Nathan M. Roberts, Andrew S. Norton, Timothy R.
Van Deelen | Estimation of black bear abundance by management zone in Wisconsin | 1 table, 2 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Estimates of population abundance are fundamental to wildlife management and
conservation, but are difficult to obtain across large geographic scales and
for cryptic species. We used a state-space model with age-at-harvest data in a
Bayesian framework to model American black bear (Ursus americanus) abundance
and demo... | [
{
"created": "Wed, 22 May 2019 01:06:20 GMT",
"version": "v1"
}
] | 2019-05-23 | [
[
"Allen",
"Maximilian L.",
""
],
[
"Roberts",
"Nathan M.",
""
],
[
"Norton",
"Andrew S.",
""
],
[
"Van Deelen",
"Timothy R.",
""
]
] | Estimates of population abundance are fundamental to wildlife management and conservation, but are difficult to obtain across large geographic scales and for cryptic species. We used a state-space model with age-at-harvest data in a Bayesian framework to model American black bear (Ursus americanus) abundance and demogr... |
2107.08575 | Claire Miller | Claire Miller, Edmund Crampin, James Osborne | Multiscale modelling of desquamation in the interfollicular epidermis | null | PLOS Computational Biology 18(8): e1010368 (2022) | 10.1371/journal.pcbi.1010368 | null | q-bio.TO q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Maintenance of epidermal thickness is critical to the barrier function of the
skin. Decreased tissue thickness, specifically in the stratum corneum (the
outermost layer of the tissue), causes discomfort and inflammation, and is
related to several severe diseases of the tissue. In order to maintain both
stratum corneu... | [
{
"created": "Mon, 19 Jul 2021 01:43:52 GMT",
"version": "v1"
},
{
"created": "Tue, 3 Aug 2021 04:17:54 GMT",
"version": "v2"
},
{
"created": "Mon, 12 Sep 2022 00:48:53 GMT",
"version": "v3"
}
] | 2022-09-13 | [
[
"Miller",
"Claire",
""
],
[
"Crampin",
"Edmund",
""
],
[
"Osborne",
"James",
""
]
] | Maintenance of epidermal thickness is critical to the barrier function of the skin. Decreased tissue thickness, specifically in the stratum corneum (the outermost layer of the tissue), causes discomfort and inflammation, and is related to several severe diseases of the tissue. In order to maintain both stratum corneum ... |
2110.15400 | Beth Martin | Beth K. Martin, Chengxiang Qiu, Eva Nichols, Melissa Phung, Rula
Green-Gladden, Sanjay Srivatsan, Ronnie Blecher-Gonen, Brian J. Beliveau,
Cole Trapnell, Junyue Cao, Jay Shendure | An optimized protocol for single cell transcriptional profiling by
combinatorial indexing | fixed a couple errors | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful
method for recovering gene expression data from an exponentially scalable
number of individual cells or nuclei. However, sci-RNA-seq is a complex
protocol that has historically exhibited variable performance on different
tissues, as well as... | [
{
"created": "Thu, 28 Oct 2021 19:01:59 GMT",
"version": "v1"
},
{
"created": "Tue, 2 Nov 2021 19:55:28 GMT",
"version": "v2"
},
{
"created": "Mon, 6 Dec 2021 17:57:58 GMT",
"version": "v3"
},
{
"created": "Thu, 6 Jan 2022 17:22:51 GMT",
"version": "v4"
}
] | 2022-01-07 | [
[
"Martin",
"Beth K.",
""
],
[
"Qiu",
"Chengxiang",
""
],
[
"Nichols",
"Eva",
""
],
[
"Phung",
"Melissa",
""
],
[
"Green-Gladden",
"Rula",
""
],
[
"Srivatsan",
"Sanjay",
""
],
[
"Blecher-Gonen",
"Ronnie",
""
... | Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that has historically exhibited variable performance on different tissues, as well as l... |
1606.00054 | Ronan M.T. Fleming Dr | Ding Ma, Laurence Yang, Ronan M. T. Fleming, Ines Thiele, Bernhard O.
Palsson and Michael A. Saunders | Reliable and efficient solution of genome-scale models of Metabolism and
macromolecular Expression | 14 pages, 1 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Constraint-Based Reconstruction and Analysis (COBRA) is currently the only
methodology that permits integrated modeling of Metabolism and macromolecular
Expression (ME) at genome-scale. Linear optimization computes steady-state flux
solutions to ME models, but flux values are spread over many orders of
magnitude. Sta... | [
{
"created": "Tue, 31 May 2016 21:38:04 GMT",
"version": "v1"
},
{
"created": "Mon, 26 Sep 2016 21:02:08 GMT",
"version": "v2"
}
] | 2016-09-28 | [
[
"Ma",
"Ding",
""
],
[
"Yang",
"Laurence",
""
],
[
"Fleming",
"Ronan M. T.",
""
],
[
"Thiele",
"Ines",
""
],
[
"Palsson",
"Bernhard O.",
""
],
[
"Saunders",
"Michael A.",
""
]
] | Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many orders of magnitude. Stand... |
1506.05647 | Luiz Henrique Bertolucci | L. H. B. Bertolucci, E. F. Costa, V. A. Oliveira, D. Karam | A unified model for wild resistance dynamics and weed control using
herbicide | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A major issue in the modelling of weed resistance to herbicide lies in
effectively handling the wild dynamics, that is, the allele frequency prior to
the herbicide application, and in particular when starting to use the
herbicide. The wild allele frequency is a key variable as the resistance
evolution is highly sensi... | [
{
"created": "Thu, 18 Jun 2015 12:21:50 GMT",
"version": "v1"
}
] | 2015-06-19 | [
[
"Bertolucci",
"L. H. B.",
""
],
[
"Costa",
"E. F.",
""
],
[
"Oliveira",
"V. A.",
""
],
[
"Karam",
"D.",
""
]
] | A major issue in the modelling of weed resistance to herbicide lies in effectively handling the wild dynamics, that is, the allele frequency prior to the herbicide application, and in particular when starting to use the herbicide. The wild allele frequency is a key variable as the resistance evolution is highly sensiti... |
1404.6453 | Gabriel Kreiman | Thomas Miconi, Laura Groomes, Gabriel Kreiman | A normalization model of visual search predicts single trial human
fixations in an object search task | 8 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When searching for an object in a scene, how does the brain decide where to
look next? Theories of visual search suggest the existence of a global
attentional map, computed by integrating bottom-up visual information with
top-down, target-specific signals. Where, when and how this integration is
performed remains unc... | [
{
"created": "Fri, 25 Apr 2014 15:16:42 GMT",
"version": "v1"
}
] | 2014-04-28 | [
[
"Miconi",
"Thomas",
""
],
[
"Groomes",
"Laura",
""
],
[
"Kreiman",
"Gabriel",
""
]
] | When searching for an object in a scene, how does the brain decide where to look next? Theories of visual search suggest the existence of a global attentional map, computed by integrating bottom-up visual information with top-down, target-specific signals. Where, when and how this integration is performed remains uncle... |
0711.2497 | Pankaj Mehta | Pankaj Mehta, Ranjan Mukhopadhyay, Ned S. Wingreen | Exponential sensitivity of noise-driven switching in genetic networks | 5 pages, 3 figures | Physical Biology 5, 026005 (2008) | 10.1088/1478-3975/5/2/026005 | null | q-bio.MN cond-mat.stat-mech q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cells are known to utilize biochemical noise to probabilistically switch
between distinct gene expression states. We demonstrate that such noise-driven
switching is dominated by tails of probability distributions and is therefore
exponentially sensitive to changes in physiological parameters such as
transcription and... | [
{
"created": "Thu, 15 Nov 2007 20:04:50 GMT",
"version": "v1"
},
{
"created": "Tue, 2 Sep 2008 21:27:06 GMT",
"version": "v2"
}
] | 2009-11-13 | [
[
"Mehta",
"Pankaj",
""
],
[
"Mukhopadhyay",
"Ranjan",
""
],
[
"Wingreen",
"Ned S.",
""
]
] | Cells are known to utilize biochemical noise to probabilistically switch between distinct gene expression states. We demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore exponentially sensitive to changes in physiological parameters such as transcription and t... |
1809.03393 | Nikolai Zolotykh | Alena I. Kalyakulina, Igor I. Yusipov, Victor A. Moskalenko, Alexander
V. Nikolskiy, Konstantin A. Kosonogov, Grigory V. Osipov, Nikolai Yu.
Zolotykh, Mikhail V. Ivanchenko | LUDB: a new open-access validation tool for electrocardiogram
delineation algorithms | 11 pages, 10 figures, 6 tables | null | null | null | q-bio.QM eess.SP physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We report Lobachevsky University Database (LUDB) of ECG signals, an open tool
for validating ECG delineation algorithms, that is superior to the existing
publicly available data bases in several aspects. LUDB contains 200 recordings
of 10-second 12-lead electrocardiograms (ECG) from different subjects,
representative... | [
{
"created": "Thu, 30 Aug 2018 16:05:16 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Sep 2018 20:27:57 GMT",
"version": "v2"
},
{
"created": "Fri, 28 Aug 2020 16:39:07 GMT",
"version": "v3"
},
{
"created": "Wed, 16 Sep 2020 09:08:54 GMT",
"version": "v4"
}
] | 2020-09-17 | [
[
"Kalyakulina",
"Alena I.",
""
],
[
"Yusipov",
"Igor I.",
""
],
[
"Moskalenko",
"Victor A.",
""
],
[
"Nikolskiy",
"Alexander V.",
""
],
[
"Kosonogov",
"Konstantin A.",
""
],
[
"Osipov",
"Grigory V.",
""
],
[
"Zoloty... | We report Lobachevsky University Database (LUDB) of ECG signals, an open tool for validating ECG delineation algorithms, that is superior to the existing publicly available data bases in several aspects. LUDB contains 200 recordings of 10-second 12-lead electrocardiograms (ECG) from different subjects, representative o... |
1604.08314 | Jonathan Harrison | Jonathan U. Harrison, Christian A. Yates | A hybrid algorithm for coupling PDE and compartment-based dynamics | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stochastic simulation methods can be applied successfully to model exact
spatio-temporally resolved reaction-diffusion systems. However, in many cases,
these methods can quickly become extremely computationally intensive with
increasing particle numbers. An alternative description of many of these
systems can be deri... | [
{
"created": "Thu, 28 Apr 2016 05:55:22 GMT",
"version": "v1"
}
] | 2016-04-29 | [
[
"Harrison",
"Jonathan U.",
""
],
[
"Yates",
"Christian A.",
""
]
] | Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction-diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing particle numbers. An alternative description of many of these systems can be derive... |
1206.3108 | Alfonso P\'erez-Escudero | Sara Arganda, Alfonso P\'erez-Escudero, Gonzalo G. de Polavieja | A common rule for decision-making in animal collectives across species | null | Proc Natl Acad Sci USA vol. 109 no. 50 20508-20513 (2012) | 10.1073/pnas.1210664109 | null | q-bio.PE q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A diversity of decision-making systems has been observed in animal
collectives. In some species, choices depend on the differences of the numbers
of animals that have chosen each of the available options, while in other
species on the relative differences (a behavior known as Weber's law) or follow
more complex rules... | [
{
"created": "Thu, 14 Jun 2012 13:57:28 GMT",
"version": "v1"
},
{
"created": "Mon, 8 Oct 2012 17:56:38 GMT",
"version": "v2"
},
{
"created": "Wed, 12 Dec 2012 07:00:59 GMT",
"version": "v3"
}
] | 2012-12-13 | [
[
"Arganda",
"Sara",
""
],
[
"Pérez-Escudero",
"Alfonso",
""
],
[
"de Polavieja",
"Gonzalo G.",
""
]
] | A diversity of decision-making systems has been observed in animal collectives. In some species, choices depend on the differences of the numbers of animals that have chosen each of the available options, while in other species on the relative differences (a behavior known as Weber's law) or follow more complex rules. ... |
2209.01060 | Chao Wang | Chao Wang | The path integral formula for the stochastic evolutionary game dynamics
in the Moran process | 14 pages, 2 figures | null | null | null | q-bio.PE math-ph math.MP physics.app-ph | http://creativecommons.org/licenses/by/4.0/ | The Moran process is one of an basic mathematical structure in the
evolutionary game theory. In this work, we introduce the formulation of the
path integral approach for evolutionary game theory based on the Moran process.
We derive the transition probability by the path integral from the initial
state to the final s... | [
{
"created": "Fri, 2 Sep 2022 13:52:20 GMT",
"version": "v1"
}
] | 2022-09-05 | [
[
"Wang",
"Chao",
""
]
] | The Moran process is one of an basic mathematical structure in the evolutionary game theory. In this work, we introduce the formulation of the path integral approach for evolutionary game theory based on the Moran process. We derive the transition probability by the path integral from the initial state to the final sta... |
q-bio/0506030 | Pierre Sens | Pierre Sens and Matthew S. Turner | Budded membrane microdomains as regulators for cellular tension | http://hogarth.pct.espci.fr/~pierre/ | null | null | null | q-bio.SC cond-mat.soft | null | We propose a mechanism for mechanical regulation at the membrane of living
cells, based on the exchange of membrane area between the cell membrane and a
membrane reservoir. The reservoir is composed of invaginated membrane
microdomains which are liable to flatten upon increase of membrane strain,
effectively controll... | [
{
"created": "Tue, 21 Jun 2005 06:58:41 GMT",
"version": "v1"
},
{
"created": "Mon, 19 Sep 2005 23:56:37 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Sens",
"Pierre",
""
],
[
"Turner",
"Matthew S.",
""
]
] | We propose a mechanism for mechanical regulation at the membrane of living cells, based on the exchange of membrane area between the cell membrane and a membrane reservoir. The reservoir is composed of invaginated membrane microdomains which are liable to flatten upon increase of membrane strain, effectively controllin... |
2402.07012 | Gabriel Calvo | Gabriel F. Calvo, Bel\'en Cort\'es-Llanos, Juan Belmonte-Beitia, Gorka
Salas and \'Angel Ayuso-Sacido | Modelling the role of flux density and coating on nanoparticle
internalization by tumor cells under centrifugation | 39 pages, 9 figures. Manuscript published in Applied Mathematical
Modelling 78, 98-116 (2020) | Applied Mathematical Modelling 78, 98-116 (2020) | 10.1016/j.apm.2019.10.005 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nanoparticle (NP)-based applications are becoming increasingly important in
the biomedical field. However, understanding the interactions of NPs with
biofluids and cells is a major issue in order to develop novel approaches aimed
at boosting their internalization and, therefore, their translation into the
clinic. To ... | [
{
"created": "Sat, 10 Feb 2024 18:19:51 GMT",
"version": "v1"
}
] | 2024-02-13 | [
[
"Calvo",
"Gabriel F.",
""
],
[
"Cortés-Llanos",
"Belén",
""
],
[
"Belmonte-Beitia",
"Juan",
""
],
[
"Salas",
"Gorka",
""
],
[
"Ayuso-Sacido",
"Ángel",
""
]
] | Nanoparticle (NP)-based applications are becoming increasingly important in the biomedical field. However, understanding the interactions of NPs with biofluids and cells is a major issue in order to develop novel approaches aimed at boosting their internalization and, therefore, their translation into the clinic. To th... |
1810.07367 | Ryan Renslow | Jamie R. Nu\~nez, Sean M. Colby, Dennis G. Thomas, Malak M. Tfaily,
Nikola Tolic, Elin M. Ulrich, Jon R. Sobus, Thomas O. Metz, Justin G.
Teeguarden, and Ryan S. Renslow | Advancing Standards-Free Methods for the Identification of Small
Molecules in Complex Samples | null | null | null | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The current gold standard for unambiguous identification in metabolomics
analysis is based on comparing two or more orthogonal properties from the
analysis of authentic, pure reference materials (standards) to experimental
data acquired in the same laboratory with the same analytical methods. This
represents a signif... | [
{
"created": "Wed, 17 Oct 2018 03:08:41 GMT",
"version": "v1"
}
] | 2018-10-18 | [
[
"Nuñez",
"Jamie R.",
""
],
[
"Colby",
"Sean M.",
""
],
[
"Thomas",
"Dennis G.",
""
],
[
"Tfaily",
"Malak M.",
""
],
[
"Tolic",
"Nikola",
""
],
[
"Ulrich",
"Elin M.",
""
],
[
"Sobus",
"Jon R.",
""
],
[
... | The current gold standard for unambiguous identification in metabolomics analysis is based on comparing two or more orthogonal properties from the analysis of authentic, pure reference materials (standards) to experimental data acquired in the same laboratory with the same analytical methods. This represents a signific... |
2304.01356 | Robert Corless | Chris Brimacombe and Robert M. Corless and Mair Zamir | Elliptic cross sections in blood flow regulation | 31 pages, 17 figures | null | null | null | q-bio.TO cs.NA math.NA | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Arterial deformations arise in blood flow when surrounding tissue invades the
space available for a blood vessel to maintain its circular cross section, the
most immediate effects being a reduction in blood flow and redistribution of
shear stress. Here we consider deformations from circular to elliptic cross
sections... | [
{
"created": "Thu, 19 Jan 2023 21:57:51 GMT",
"version": "v1"
}
] | 2023-04-05 | [
[
"Brimacombe",
"Chris",
""
],
[
"Corless",
"Robert M.",
""
],
[
"Zamir",
"Mair",
""
]
] | Arterial deformations arise in blood flow when surrounding tissue invades the space available for a blood vessel to maintain its circular cross section, the most immediate effects being a reduction in blood flow and redistribution of shear stress. Here we consider deformations from circular to elliptic cross sections. ... |
q-bio/0512036 | Jose Vilar | Leonor Saiz, J. Miguel Rubi, and Jose M. G. Vilar | Inferring the in vivo looping properties of DNA | 20 pages, 4 figures | Proc. Natl. Acad. Sci. USA 102, 17642-17645 (2005) | 10.1073/pnas.0505693102 | null | q-bio.BM cond-mat.soft physics.bio-ph q-bio.QM q-bio.SC | null | The free energy of looping DNA by proteins and protein complexes determines
to what extent distal DNA sites can affect each other. We inferred its in vivo
value through a combined computational-experimental approach for different
lengths of the loop and found that, in addition to the intrinsic periodicity of
the DNA ... | [
{
"created": "Tue, 20 Dec 2005 00:52:51 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Saiz",
"Leonor",
""
],
[
"Rubi",
"J. Miguel",
""
],
[
"Vilar",
"Jose M. G.",
""
]
] | The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of the loop and found that, in addition to the intrinsic periodicity of the DNA do... |
1809.00759 | Angus McLure | Angus McLure, Archie C. A. Clements, Martyn Kirk, Kathryn Glass | Modelling diverse sources of Clostridium difficile in the community:
importance of animals, infants and asymptomatic carriers | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Clostridium difficile infections (CDIs) affect patients in hospitals and in
the community, but the relative importance of transmission in each setting is
unknown. We developed a mathematical model of C. difficile transmission in a
hospital and surrounding community that included infants, adults, and
transmission from... | [
{
"created": "Tue, 4 Sep 2018 00:54:37 GMT",
"version": "v1"
}
] | 2018-09-05 | [
[
"McLure",
"Angus",
""
],
[
"Clements",
"Archie C. A.",
""
],
[
"Kirk",
"Martyn",
""
],
[
"Glass",
"Kathryn",
""
]
] | Clostridium difficile infections (CDIs) affect patients in hospitals and in the community, but the relative importance of transmission in each setting is unknown. We developed a mathematical model of C. difficile transmission in a hospital and surrounding community that included infants, adults, and transmission from a... |
2003.12457 | Daniele Lanteri | D.Lanteri, D.Carco' and P.Castorina | How macroscopic laws describe complex dynamics: asymptomatic population
and CoviD-19 spreading | null | International Journal of Modern Physics CVol. 31, No. 08, 2050112
(2020) | 10.1142/S0129183120501120 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Macroscopic growth laws, solutions of mean field equations, describe in an
effective way an underlying complex dynamics. They are applied to study the
spreading of infections, as in the case of CoviD-19, where the counting of the
cumulated number $N(t)$ of detected infected individuals is a generally
accepted, coarse... | [
{
"created": "Fri, 27 Mar 2020 15:03:38 GMT",
"version": "v1"
},
{
"created": "Sun, 19 Apr 2020 09:53:05 GMT",
"version": "v2"
}
] | 2020-12-01 | [
[
"Lanteri",
"D.",
""
],
[
"Carco'",
"D.",
""
],
[
"Castorina",
"P.",
""
]
] | Macroscopic growth laws, solutions of mean field equations, describe in an effective way an underlying complex dynamics. They are applied to study the spreading of infections, as in the case of CoviD-19, where the counting of the cumulated number $N(t)$ of detected infected individuals is a generally accepted, coarse-g... |
2103.16496 | Timothee Brochier | Timoth\'ee Brochier (IRD, SU, ESP Dakar, UMMISCO), Alassane Bah (ESP
Dakar, UMMISCO) | FisherMob : a bioeconomic model of fishers' migrations | in French | null | null | null | q-bio.PE cs.MA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sea fishing is a highly mobile activity, favoured by the vastness of the
oceans, the absence of physical boundaries and the abstraction of legislative
boundaries. Understanding and anticipating this mobility is a major challenge
for fisheries management issues, both at the national and international levels.
''FisherM... | [
{
"created": "Mon, 29 Mar 2021 14:34:16 GMT",
"version": "v1"
}
] | 2021-03-31 | [
[
"Brochier",
"Timothée",
"",
"IRD, SU, ESP Dakar, UMMISCO"
],
[
"Bah",
"Alassane",
"",
"ESP\n Dakar, UMMISCO"
]
] | Sea fishing is a highly mobile activity, favoured by the vastness of the oceans, the absence of physical boundaries and the abstraction of legislative boundaries. Understanding and anticipating this mobility is a major challenge for fisheries management issues, both at the national and international levels. ''FisherMob... |
q-bio/0611070 | Herv\'e Isambert | Kirill Evlampiev and Herve Isambert | Asymptotic Evolution of Protein-Protein Interaction Networks for General
Duplication-Divergence Models | 6 pages, 5 figures (+ supporting information: 17 pages 3 figures) | null | null | null | q-bio.MN q-bio.PE | null | Genomic duplication-divergence events, which are the primary source of new
protein functions, occur stochastically at a wide range of genomic scales, from
single gene to whole genome duplications. Clearly, this fundamental
evolutionary process must have largely conditioned the emerging structure of
protein-protein in... | [
{
"created": "Wed, 22 Nov 2006 13:40:15 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Evlampiev",
"Kirill",
""
],
[
"Isambert",
"Herve",
""
]
] | Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary process must have largely conditioned the emerging structure of protein-protein inte... |
2312.16097 | Si Wen | Si Wen and Brandon D. Gallas | Expanding to Arbitrary Study Designs: ANOVA to Estimate Limits of
Agreement for MRMC Studies | null | null | null | null | q-bio.QM | http://creativecommons.org/publicdomain/zero/1.0/ | A multi-reader multi-case (MRMC) analysis is applied to account for both
reader and case variability when evaluating the clinical performance of a
medical imaging device or reader performance under different reading
modalities. For a clinical task that measures a quantitative biomarker an
agreement analysis, such as ... | [
{
"created": "Tue, 26 Dec 2023 15:49:42 GMT",
"version": "v1"
}
] | 2023-12-27 | [
[
"Wen",
"Si",
""
],
[
"Gallas",
"Brandon D.",
""
]
] | A multi-reader multi-case (MRMC) analysis is applied to account for both reader and case variability when evaluating the clinical performance of a medical imaging device or reader performance under different reading modalities. For a clinical task that measures a quantitative biomarker an agreement analysis, such as li... |
2102.05459 | Olivier Rivoire | Anton S Zadorin, Olivier Rivoire | Sex as information processing: optimality and evolution | null | Phys. Rev. E 103, 062413 (2021) | 10.1103/PhysRevE.103.062413 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The long-term growth rate of populations in varying environments quantifies
the evolutionary value of processing the information that biological
individuals inherit from their ancestors and acquire from their environment.
Previous models were limited to asexual reproduction with inherited information
coming from a si... | [
{
"created": "Wed, 10 Feb 2021 14:26:35 GMT",
"version": "v1"
},
{
"created": "Tue, 15 Jun 2021 09:33:12 GMT",
"version": "v2"
}
] | 2021-06-30 | [
[
"Zadorin",
"Anton S",
""
],
[
"Rivoire",
"Olivier",
""
]
] | The long-term growth rate of populations in varying environments quantifies the evolutionary value of processing the information that biological individuals inherit from their ancestors and acquire from their environment. Previous models were limited to asexual reproduction with inherited information coming from a sing... |
2109.04261 | Nicolas Deperrois | Nicolas Deperrois, Mihai A. Petrovici, Walter Senn, and Jakob Jordan | Learning cortical representations through perturbed and adversarial
dreaming | 35 pages, 15 figures; ; Jakob Jordan and Walter Senn share senior
authorship | null | null | null | q-bio.NC cs.LG | http://creativecommons.org/licenses/by/4.0/ | Humans and other animals learn to extract general concepts from sensory
experience without extensive teaching. This ability is thought to be
facilitated by offline states like sleep where previous experiences are
systemically replayed. However, the characteristic creative nature of dreams
suggests that learning seman... | [
{
"created": "Thu, 9 Sep 2021 13:31:13 GMT",
"version": "v1"
},
{
"created": "Mon, 3 Jan 2022 15:49:18 GMT",
"version": "v2"
},
{
"created": "Fri, 18 Feb 2022 18:01:48 GMT",
"version": "v3"
}
] | 2022-02-21 | [
[
"Deperrois",
"Nicolas",
""
],
[
"Petrovici",
"Mihai A.",
""
],
[
"Senn",
"Walter",
""
],
[
"Jordan",
"Jakob",
""
]
] | Humans and other animals learn to extract general concepts from sensory experience without extensive teaching. This ability is thought to be facilitated by offline states like sleep where previous experiences are systemically replayed. However, the characteristic creative nature of dreams suggests that learning semanti... |
1203.3884 | Philippe Desjardins-Proulx | Philippe Desjardins-Proulx and Dominique Gravel | A complex speciation-richness relationship in a simple neutral model | 9 pages, 5 figures, 1 table, 50 references | Ecology and Evolution 2(8): 1781-1790, 2012 | 10.1002/ece3.292 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Speciation is the "elephant in the room" of community ecology. As the
ultimate source of biodiversity, its integration in ecology's theoretical
corpus is necessary to understand community assembly. Yet, speciation is often
completely ignored or stripped of its spatial dimension. Recent approaches
based on network the... | [
{
"created": "Sat, 17 Mar 2012 18:25:57 GMT",
"version": "v1"
},
{
"created": "Fri, 11 May 2012 00:30:32 GMT",
"version": "v2"
}
] | 2012-08-07 | [
[
"Desjardins-Proulx",
"Philippe",
""
],
[
"Gravel",
"Dominique",
""
]
] | Speciation is the "elephant in the room" of community ecology. As the ultimate source of biodiversity, its integration in ecology's theoretical corpus is necessary to understand community assembly. Yet, speciation is often completely ignored or stripped of its spatial dimension. Recent approaches based on network theor... |
1903.10310 | Danilo Bzdok | Danilo Bzdok (PARIETAL), John Ioannidis | Exploration, inference and prediction in neuroscience and biomedicine | null | Trends in Neurosciences, Elsevier, 2019 | null | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The last decades saw dramatic progress in brain research. These advances were
often buttressed by probing single variables to make circumscribed discoveries,
typically through null hypothesis significance testing. New ways for generating
massive data fueled tension between the traditional methodology, used to infer
s... | [
{
"created": "Thu, 21 Feb 2019 13:08:29 GMT",
"version": "v1"
}
] | 2019-03-26 | [
[
"Bzdok",
"Danilo",
"",
"PARIETAL"
],
[
"Ioannidis",
"John",
""
]
] | The last decades saw dramatic progress in brain research. These advances were often buttressed by probing single variables to make circumscribed discoveries, typically through null hypothesis significance testing. New ways for generating massive data fueled tension between the traditional methodology, used to infer sta... |
q-bio/0309007 | Voislav Golo | Voislav Golo | The Inter-Strand Modes of the DNA as a Probe into MW-Radiation | 13 pages | null | null | null | q-bio.BM | null | We consider the regime in which the bands of the torsional acoustic (TA) and
the hydrogen-bond-stretch (HBS) modes of the DNA interpenetrate each other.
Within the framework of a model that accommodates the structure of the double
helix, we find the three-wave interaction between the TA- and the HBS-modes,
and show t... | [
{
"created": "Fri, 19 Sep 2003 05:55:55 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Golo",
"Voislav",
""
]
] | We consider the regime in which the bands of the torsional acoustic (TA) and the hydrogen-bond-stretch (HBS) modes of the DNA interpenetrate each other. Within the framework of a model that accommodates the structure of the double helix, we find the three-wave interaction between the TA- and the HBS-modes, and show tha... |
1707.08337 | Daniel Mart\'i | Daniel Mart\'i, Nicolas Brunel, Srdjan Ostojic | Correlations between synapses in pairs of neurons slow down dynamics in
randomly connected neural networks | 17 pages, 7 figures | Phys. Rev. E 97, 062314 (2018) | 10.1103/PhysRevE.97.062314 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Networks of randomly connected neurons are among the most popular models in
theoretical neuroscience. The connectivity between neurons in the cortex is
however not fully random, the simplest and most prominent deviation from
randomness found in experimental data being the overrepresentation of
bidirectional connectio... | [
{
"created": "Wed, 26 Jul 2017 09:41:25 GMT",
"version": "v1"
},
{
"created": "Tue, 22 May 2018 20:36:52 GMT",
"version": "v2"
},
{
"created": "Fri, 6 Jul 2018 08:17:33 GMT",
"version": "v3"
}
] | 2018-07-09 | [
[
"Martí",
"Daniel",
""
],
[
"Brunel",
"Nicolas",
""
],
[
"Ostojic",
"Srdjan",
""
]
] | Networks of randomly connected neurons are among the most popular models in theoretical neuroscience. The connectivity between neurons in the cortex is however not fully random, the simplest and most prominent deviation from randomness found in experimental data being the overrepresentation of bidirectional connections... |
0906.0886 | Mikko Tuomi | M. Tuomi, T. Thum, H. J\"arvinen, S. Fronzek, B. Berg, M. Harmon, J.
A. Trofymow, S. Sevanto, J. Liski | Leaf litter decomposition -- Estimates of global variability based on
Yasso07 model | 19 Pages, to appear in Ecological Modelling | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Litter decomposition is an important process in the global carbon cycle. It
accounts for most of the heterotrophic soil respiration and results in
formation of more stable soil organic carbon (SOC) which is the largest
terrestrial carbon stock. Litter decomposition may induce remarkable feedbacks
to climate change be... | [
{
"created": "Thu, 4 Jun 2009 11:35:07 GMT",
"version": "v1"
}
] | 2009-06-05 | [
[
"Tuomi",
"M.",
""
],
[
"Thum",
"T.",
""
],
[
"Järvinen",
"H.",
""
],
[
"Fronzek",
"S.",
""
],
[
"Berg",
"B.",
""
],
[
"Harmon",
"M.",
""
],
[
"Trofymow",
"J. A.",
""
],
[
"Sevanto",
"S.",
""... | Litter decomposition is an important process in the global carbon cycle. It accounts for most of the heterotrophic soil respiration and results in formation of more stable soil organic carbon (SOC) which is the largest terrestrial carbon stock. Litter decomposition may induce remarkable feedbacks to climate change beca... |
1305.0758 | Jean-Beno\^it Lalanne | Jean-Beno\^it Lalanne and Paul Fran\c{c}ois | Principles of Adaptive Sorting Revealed by In Silico Evolution | 50 pages, 28 figures, including supplementary information | null | 10.1103/PhysRevLett.110.218102 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many biological networks have to filter out useful information from a vast
excess of spurious interactions. We use computational evolution to predict
design features of networks processing ligand categorization. The important
problem of early immune response is considered as a case-study. Rounds of
evolution with dif... | [
{
"created": "Fri, 3 May 2013 15:52:08 GMT",
"version": "v1"
}
] | 2013-05-27 | [
[
"Lalanne",
"Jean-Benoît",
""
],
[
"François",
"Paul",
""
]
] | Many biological networks have to filter out useful information from a vast excess of spurious interactions. We use computational evolution to predict design features of networks processing ligand categorization. The important problem of early immune response is considered as a case-study. Rounds of evolution with diffe... |
1109.5681 | Valerie Hower | Valerie Hower, Richard Starfield, Adam Roberts, Lior Pachter | Quantifying uniformity of mapped reads | withdrawing based on the journal's policy | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Summary: We describe a tool for quantifying the uniformity of mapped reads in
high-throughput sequencing experiments. Our statistic directly measures the
uniformity of both read position and fragment length, and we explain how to
compute a p-value that can be used to quantify biases arising from experimental
protocol... | [
{
"created": "Mon, 26 Sep 2011 19:33:37 GMT",
"version": "v1"
},
{
"created": "Tue, 3 Jul 2012 20:41:08 GMT",
"version": "v2"
},
{
"created": "Tue, 17 Jul 2012 18:51:26 GMT",
"version": "v3"
}
] | 2013-10-22 | [
[
"Hower",
"Valerie",
""
],
[
"Starfield",
"Richard",
""
],
[
"Roberts",
"Adam",
""
],
[
"Pachter",
"Lior",
""
]
] | Summary: We describe a tool for quantifying the uniformity of mapped reads in high-throughput sequencing experiments. Our statistic directly measures the uniformity of both read position and fragment length, and we explain how to compute a p-value that can be used to quantify biases arising from experimental protocols ... |
1312.7735 | Jens Christian Claussen | Arne Weigenand, Thomas Martinetz and Jens Christian Claussen | The phase response of the cortical slow oscillation | null | Cognitive Neurodynamics 6(4), 367-375 (2012) | 10.1007/s11571-012-9207-z | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cortical slow oscillations occur in the mammalian brain during deep sleep and
have been shown to contribute to memory consolidation, an effect that can be
enhanced by electrical stimulation. As the precise underlying working
mechanisms are not known it is desired to develop and analyze computational
models of slow os... | [
{
"created": "Mon, 30 Dec 2013 15:15:28 GMT",
"version": "v1"
}
] | 2013-12-31 | [
[
"Weigenand",
"Arne",
""
],
[
"Martinetz",
"Thomas",
""
],
[
"Claussen",
"Jens Christian",
""
]
] | Cortical slow oscillations occur in the mammalian brain during deep sleep and have been shown to contribute to memory consolidation, an effect that can be enhanced by electrical stimulation. As the precise underlying working mechanisms are not known it is desired to develop and analyze computational models of slow osci... |
q-bio/0411046 | Patricia Faisca | P.F.N. Faisca, M.M. Telo da Gama, A. Nunes | The Go model revisited: Native structure and the geometric coupling
between local and long-range contacts | 12 pages, 26 figures, RevTex. Accepted in Proteins: Structure,
Function and Bioinformatics | Proteins: Structure, Function and Bioinformatics 60, 712-722
(2005) | 10.1002/prot.20521 | null | q-bio.BM | null | Monte Carlo simulations show that long-range interactions play a major role
in determining the folding rates of 48-mer three-dimensional lattice polymers
modelled by the Go potential. For three target structures with different native
geometries we found a sharp increase in the folding time when the relative
contribut... | [
{
"created": "Fri, 26 Nov 2004 17:23:52 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Mar 2005 16:07:31 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Faisca",
"P. F. N.",
""
],
[
"da Gama",
"M. M. Telo",
""
],
[
"Nunes",
"A.",
""
]
] | Monte Carlo simulations show that long-range interactions play a major role in determining the folding rates of 48-mer three-dimensional lattice polymers modelled by the Go potential. For three target structures with different native geometries we found a sharp increase in the folding time when the relative contributio... |
0812.3276 | Luis G. Morelli | Luis G. Morelli, Saul Ares, Leah Herrgen, Christian Schroeter, Frank
Julicher, and Andrew C. Oates | Delayed coupling theory of vertebrate segmentation | published online 10 December 2008, Adv. Online Pub. HFSP Journal
(free access) | null | 10.2976/1.3027088 | null | q-bio.MN nlin.AO physics.bio-ph q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rhythmic and sequential subdivision of the elongating vertebrate embryonic
body axis into morphological somites is controlled by an oscillating
multicellular genetic network termed the segmentation clock. This clock
operates in the presomitic mesoderm (PSM), generating dynamic stripe patterns
of oscillatory gene-expr... | [
{
"created": "Wed, 17 Dec 2008 14:02:19 GMT",
"version": "v1"
}
] | 2009-01-08 | [
[
"Morelli",
"Luis G.",
""
],
[
"Ares",
"Saul",
""
],
[
"Herrgen",
"Leah",
""
],
[
"Schroeter",
"Christian",
""
],
[
"Julicher",
"Frank",
""
],
[
"Oates",
"Andrew C.",
""
]
] | Rhythmic and sequential subdivision of the elongating vertebrate embryonic body axis into morphological somites is controlled by an oscillating multicellular genetic network termed the segmentation clock. This clock operates in the presomitic mesoderm (PSM), generating dynamic stripe patterns of oscillatory gene-expres... |
2210.03910 | Sat Byul Seo | Sat byul Seo, Jianzhong Su | Quantifying constraints determining independent activation on NMDA
receptors mediated currents from evoked and spontaneous synaptic transmission
at an individual synapse | null | null | null | null | q-bio.NC math.DS | http://creativecommons.org/licenses/by/4.0/ | A synapse acts on neural transmission through a chemical process called
synapses fusion between pre-synaptic and post-synaptic terminals. Presynaptic
terminals release neurotransmitters either in response to action potential or
spontaneously independent of presynaptic activity. However, it is still unclear
the mechan... | [
{
"created": "Sat, 8 Oct 2022 04:20:10 GMT",
"version": "v1"
}
] | 2022-10-11 | [
[
"Seo",
"Sat byul",
""
],
[
"Su",
"Jianzhong",
""
]
] | A synapse acts on neural transmission through a chemical process called synapses fusion between pre-synaptic and post-synaptic terminals. Presynaptic terminals release neurotransmitters either in response to action potential or spontaneously independent of presynaptic activity. However, it is still unclear the mechanis... |
1505.05983 | Yann Ponty | Cedric Chauve, Julien Courtiel, Yann Ponty (LIX, AMIB) | Counting, generating and sampling tree alignments | ALCOB - 3rd International Conference on Algorithms for Computational
Biology - 2016, Jun 2016, Trujillo, Spain. 2016 | null | null | null | q-bio.QM cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Pairwise ordered tree alignment are combinatorial objects that appear in RNA
secondary structure comparison. However, the usual representation of tree
alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce
identical sets of matches between identical pairs of trees. This ambiguity is
uninformat... | [
{
"created": "Fri, 22 May 2015 08:25:05 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Dec 2015 13:03:28 GMT",
"version": "v2"
},
{
"created": "Mon, 7 Mar 2016 19:44:22 GMT",
"version": "v3"
}
] | 2016-03-08 | [
[
"Chauve",
"Cedric",
"",
"LIX, AMIB"
],
[
"Courtiel",
"Julien",
"",
"LIX, AMIB"
],
[
"Ponty",
"Yann",
"",
"LIX, AMIB"
]
] | Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical sets of matches between identical pairs of trees. This ambiguity is uninformativ... |
2201.07879 | Jacominus van Baalen | Robert Penner (IHES), Minus van Baalen (CNRS, IBENS) | On the origins of the Omicron variant of the SARS-CoV-2 virus | null | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A possible explanation based on first principles for the appearance of the
Omicron variant of the SARS-CoV-2 virus is proposed involving coinfection with
HIV. The gist is that the resultant HIV-induced immunocompromise allows
SARS-CoV-2 greater latitude to explore its own mutational space. This latitude
is not withou... | [
{
"created": "Wed, 8 Dec 2021 13:51:47 GMT",
"version": "v1"
}
] | 2022-01-21 | [
[
"Penner",
"Robert",
"",
"IHES"
],
[
"van Baalen",
"Minus",
"",
"CNRS, IBENS"
]
] | A possible explanation based on first principles for the appearance of the Omicron variant of the SARS-CoV-2 virus is proposed involving coinfection with HIV. The gist is that the resultant HIV-induced immunocompromise allows SARS-CoV-2 greater latitude to explore its own mutational space. This latitude is not withoutr... |
1704.03525 | Hidenori Tanaka | Hidenori Tanaka, Howard A. Stone, David R. Nelson | Spatial gene drives and pushed genetic waves | null | PNAS, vol. 114 no. 32, 8452-8457 (2017) | 10.1073/pnas.1705868114 | null | q-bio.PE cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene drives have the potential to rapidly replace a harmful wild-type allele
with a gene drive allele engineered to have desired functionalities. However,
an accidental or premature release of a gene drive construct to the natural
environment could damage an ecosystem irreversibly. Thus, it is important to
understand... | [
{
"created": "Tue, 11 Apr 2017 20:26:03 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Aug 2017 03:24:37 GMT",
"version": "v2"
}
] | 2017-08-23 | [
[
"Tanaka",
"Hidenori",
""
],
[
"Stone",
"Howard A.",
""
],
[
"Nelson",
"David R.",
""
]
] | Gene drives have the potential to rapidly replace a harmful wild-type allele with a gene drive allele engineered to have desired functionalities. However, an accidental or premature release of a gene drive construct to the natural environment could damage an ecosystem irreversibly. Thus, it is important to understand t... |
1902.07601 | Hugh Trenchard Mr. | Hugh Trenchard | Cell pelotons: a model of early evolutionary cell sorting, with
application to slime mold D. discoideum | 41 pages, 8 figures, 1 appendix, accepted manuscript in press | null | 10.1016/j.jtbi.2019.02.011 | null | q-bio.PE q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A theoretical model is presented for early evolutionary cell sorting within
cellular aggregates. The model involves an energy-saving mechanism and
principles of collective self-organization analogous to those observed in
bicycle pelotons (groups of cyclists). The theoretical framework is applied to
slime-mold slugs (... | [
{
"created": "Wed, 20 Feb 2019 15:39:30 GMT",
"version": "v1"
}
] | 2019-02-21 | [
[
"Trenchard",
"Hugh",
""
]
] | A theoretical model is presented for early evolutionary cell sorting within cellular aggregates. The model involves an energy-saving mechanism and principles of collective self-organization analogous to those observed in bicycle pelotons (groups of cyclists). The theoretical framework is applied to slime-mold slugs (Di... |
1710.08405 | Peter Foster | Bryan Kaye, Olivia Stiehl, Peter J. Foster, Michael J. Shelley, Daniel
J. Needleman, Sebastian F\"urthauer | Measuring and modeling polymer gradients argues that spindle
microtubules regulate their own nucleation | null | null | 10.1088/1367-2630/aac2a5 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spindles are self-organized microtubule-based structures that segregate
chromosomes during cell division. The mass of the spindle is controlled by the
balance between microtubule turnover and nucleation. The mechanisms that
control the spatial regulation of microtubule nucleation remain poorly
understood. Previous wo... | [
{
"created": "Mon, 23 Oct 2017 17:54:21 GMT",
"version": "v1"
}
] | 2018-06-13 | [
[
"Kaye",
"Bryan",
""
],
[
"Stiehl",
"Olivia",
""
],
[
"Foster",
"Peter J.",
""
],
[
"Shelley",
"Michael J.",
""
],
[
"Needleman",
"Daniel J.",
""
],
[
"Fürthauer",
"Sebastian",
""
]
] | Spindles are self-organized microtubule-based structures that segregate chromosomes during cell division. The mass of the spindle is controlled by the balance between microtubule turnover and nucleation. The mechanisms that control the spatial regulation of microtubule nucleation remain poorly understood. Previous work... |
1205.0381 | Sayantari Ghosh | Indrani Bose and Sayantari Ghosh | Origins of Binary Gene Expression in Post-transcriptional Regulation by
MicroRNAs | 10 Pages, 5 Figures | Eur. Phys. J. E (2012) 35:102 | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | MicroRNA-mediated regulation of gene expression is characterised by some
distinctive features that set it apart from unregulated and transcription
factor-regulated gene expression. Recently, a mathematical model has been
proposed to describe the dynamics of post-transcriptional regulation by
microRNAs. The model expl... | [
{
"created": "Wed, 2 May 2012 11:08:36 GMT",
"version": "v1"
},
{
"created": "Wed, 13 Jun 2012 09:32:02 GMT",
"version": "v2"
},
{
"created": "Thu, 18 Oct 2012 10:09:55 GMT",
"version": "v3"
}
] | 2012-10-19 | [
[
"Bose",
"Indrani",
""
],
[
"Ghosh",
"Sayantari",
""
]
] | MicroRNA-mediated regulation of gene expression is characterised by some distinctive features that set it apart from unregulated and transcription factor-regulated gene expression. Recently, a mathematical model has been proposed to describe the dynamics of post-transcriptional regulation by microRNAs. The model explai... |
2210.02366 | Rayanne Luke | Rayanne A. Luke and Anthony J. Kearsley and Paul N. Patrone | Optimal classification and generalized prevalence estimates for
diagnostic settings with more than two classes | 28 pages, 8 figures, 4 tables, 4 supplemental figures | null | 10.1016/j.mbs.2023.108982 | null | q-bio.QM math.OC math.PR physics.bio-ph stat.ME | http://creativecommons.org/licenses/by/4.0/ | An accurate multiclass classification strategy is crucial to interpreting
antibody tests. However, traditional methods based on confidence intervals or
receiver operating characteristics lack clear extensions to settings with more
than two classes. We address this problem by developing a multiclass
classification bas... | [
{
"created": "Wed, 5 Oct 2022 16:13:42 GMT",
"version": "v1"
}
] | 2024-05-07 | [
[
"Luke",
"Rayanne A.",
""
],
[
"Kearsley",
"Anthony J.",
""
],
[
"Patrone",
"Paul N.",
""
]
] | An accurate multiclass classification strategy is crucial to interpreting antibody tests. However, traditional methods based on confidence intervals or receiver operating characteristics lack clear extensions to settings with more than two classes. We address this problem by developing a multiclass classification based... |
1602.01876 | Christophe Dessimoz | Pascale Gaudet, Nives \v{S}kunca, James C. Hu, Christophe Dessimoz | Primer on the Gene Ontology | to appear in forthcoming book "The Gene Ontology Handbook" (Springer
Humana) | The Gene Ontology Handbook (Springer, New York), 25-37 (2016) | 10.1007/978-1-4939-3743-1_3 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Gene Ontology (GO) project is the largest resource for cataloguing gene
function. The combination of solid conceptual underpinnings and a practical set
of features have made the GO a widely adopted resource in the research
community and an essential resource for data analysis. In this chapter, we
provide a concis... | [
{
"created": "Thu, 4 Feb 2016 22:55:46 GMT",
"version": "v1"
}
] | 2016-12-07 | [
[
"Gaudet",
"Pascale",
""
],
[
"Škunca",
"Nives",
""
],
[
"Hu",
"James C.",
""
],
[
"Dessimoz",
"Christophe",
""
]
] | The Gene Ontology (GO) project is the largest resource for cataloguing gene function. The combination of solid conceptual underpinnings and a practical set of features have made the GO a widely adopted resource in the research community and an essential resource for data analysis. In this chapter, we provide a concise ... |
1712.02851 | Mario V Balzan | M V Balzan, J Caruana, A Zammit | Assessing the capacity and flow of ecosystem services in multifunctional
landscapes: evidence of a rural-urban gradient in a Mediterranean small
island state | null | null | 10.1016/j.landusepol.2017.08.025 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Distinguishing between the capacity of ecosystems to generate ecosystem
services (ES) and the actual use of these service (ES flow) in ES assessment
and mapping is important to develop an understanding of the sustainability of
ES use. This study assesses the spatial variation in ES capacity and flow in
the Mediterran... | [
{
"created": "Thu, 7 Dec 2017 20:10:50 GMT",
"version": "v1"
}
] | 2018-03-21 | [
[
"Balzan",
"M V",
""
],
[
"Caruana",
"J",
""
],
[
"Zammit",
"A",
""
]
] | Distinguishing between the capacity of ecosystems to generate ecosystem services (ES) and the actual use of these service (ES flow) in ES assessment and mapping is important to develop an understanding of the sustainability of ES use. This study assesses the spatial variation in ES capacity and flow in the Mediterranea... |
1411.1553 | Vadim Volkov S | Vadim Volkov | Salinity tolerance in plants: attempts to manipulate ion transport | 67 pages, 9 figures | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ion transport is the major determining factor of salinity tolerance in
plants. A simple scheme of a plant cell with ion fluxes provides basic
understanding of ion transport and the corresponding changes of ion
concentrations under salinity. The review describes in detail basic principles
of ion transport for a plant ... | [
{
"created": "Thu, 6 Nov 2014 10:24:21 GMT",
"version": "v1"
}
] | 2014-11-07 | [
[
"Volkov",
"Vadim",
""
]
] | Ion transport is the major determining factor of salinity tolerance in plants. A simple scheme of a plant cell with ion fluxes provides basic understanding of ion transport and the corresponding changes of ion concentrations under salinity. The review describes in detail basic principles of ion transport for a plant ce... |
1704.05687 | Sayan Nag | Archi Banerjee, Shankha Sanyal, Souparno Roy, Sourya Sengupta, Sayan
Biswas, Sayan Nag, Ranjan Sengupta and Dipak Ghosh | Neural (EEG) Response during Creation and Appreciation: A Novel Study
with Hindustani Raga Music | 14 pages, 5 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | What happens inside the performers brain when he is performing and composing
a particular raga. Are there some specific regions in brain which are activated
when an artist is creating or imaging a raga in his brain. Do the regions
remain the same when the artist is listening to the same raga sung by him.
These are th... | [
{
"created": "Wed, 19 Apr 2017 11:01:20 GMT",
"version": "v1"
}
] | 2017-04-20 | [
[
"Banerjee",
"Archi",
""
],
[
"Sanyal",
"Shankha",
""
],
[
"Roy",
"Souparno",
""
],
[
"Sengupta",
"Sourya",
""
],
[
"Biswas",
"Sayan",
""
],
[
"Nag",
"Sayan",
""
],
[
"Sengupta",
"Ranjan",
""
],
[
"G... | What happens inside the performers brain when he is performing and composing a particular raga. Are there some specific regions in brain which are activated when an artist is creating or imaging a raga in his brain. Do the regions remain the same when the artist is listening to the same raga sung by him. These are the ... |
1708.01280 | Sa\'ul Buitrago Boret | Sa\'ul E. Buitrago Boret and Ren\'e Escalante and Minaya Villasana | Mathematical modelling of zika virus in Brazil | null | null | null | null | q-bio.PE q-bio.QM | http://creativecommons.org/licenses/by-sa/4.0/ | In this paper we study some deterministic mathematical models that seek to
explain the expansion of zika virus, as a viral epidemic, using published data
for Brazil. SIR type models are proposed and validated using the epidemic data
found, considering several aspects in the spread of the disease. Finally, we
confirme... | [
{
"created": "Thu, 3 Aug 2017 18:58:39 GMT",
"version": "v1"
},
{
"created": "Mon, 23 Jan 2023 02:32:27 GMT",
"version": "v2"
}
] | 2023-01-24 | [
[
"Boret",
"Saúl E. Buitrago",
""
],
[
"Escalante",
"René",
""
],
[
"Villasana",
"Minaya",
""
]
] | In this paper we study some deterministic mathematical models that seek to explain the expansion of zika virus, as a viral epidemic, using published data for Brazil. SIR type models are proposed and validated using the epidemic data found, considering several aspects in the spread of the disease. Finally, we confirmed ... |
2108.08143 | Imdadullah Khan | Sarwan Ali, Tamkanat-E-Ali, Muhammad Asad Khan, Imdadullah Khan,
Murray Patterson | Effective and scalable clustering of SARS-CoV-2 sequences | To Appear in: International Conference on Big Data Research (ICBDR) | null | null | null | q-bio.PE cs.LG | http://creativecommons.org/publicdomain/zero/1.0/ | SARS-CoV-2, like any other virus, continues to mutate as it spreads,
according to an evolutionary process. Unlike any other virus, the number of
currently available sequences of SARS-CoV-2 in public databases such as GISAID
is already several million. This amount of data has the potential to uncover
the evolutionary ... | [
{
"created": "Wed, 18 Aug 2021 13:32:43 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Aug 2021 07:32:11 GMT",
"version": "v2"
},
{
"created": "Mon, 6 Sep 2021 13:13:57 GMT",
"version": "v3"
},
{
"created": "Fri, 10 Sep 2021 01:22:08 GMT",
"version": "v4"
},
{
"cr... | 2021-10-13 | [
[
"Ali",
"Sarwan",
""
],
[
"Tamkanat-E-Ali",
"",
""
],
[
"Khan",
"Muhammad Asad",
""
],
[
"Khan",
"Imdadullah",
""
],
[
"Patterson",
"Murray",
""
]
] | SARS-CoV-2, like any other virus, continues to mutate as it spreads, according to an evolutionary process. Unlike any other virus, the number of currently available sequences of SARS-CoV-2 in public databases such as GISAID is already several million. This amount of data has the potential to uncover the evolutionary dy... |
1303.6737 | Elisenda Feliu | Elisenda Feliu and Carsten Wiuf | Simplifying Biochemical Models With Intermediate Species | Published in the Journal of the Royal Society Interace. The proof of
Proposition 2 in the originally published file was erroneus. The result is
though correct and the proof has now been fixed. We thank Magali Giaroli from
the University of Buenos Aires for pointing out the error in the proof | null | 10.1098/rsif.2013.0484 | null | q-bio.MN math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mathematical models are increasingly being used to understand complex
biochemical systems, to analyze experimental data and make predictions about
unobserved quantities. However, we rarely know how robust our conclusions are
with respect to the choice and uncertainties of the model. Using algebraic
techniques we stud... | [
{
"created": "Wed, 27 Mar 2013 04:07:34 GMT",
"version": "v1"
},
{
"created": "Mon, 1 Jul 2013 14:35:07 GMT",
"version": "v2"
},
{
"created": "Wed, 4 Nov 2015 21:49:09 GMT",
"version": "v3"
}
] | 2015-11-06 | [
[
"Feliu",
"Elisenda",
""
],
[
"Wiuf",
"Carsten",
""
]
] | Mathematical models are increasingly being used to understand complex biochemical systems, to analyze experimental data and make predictions about unobserved quantities. However, we rarely know how robust our conclusions are with respect to the choice and uncertainties of the model. Using algebraic techniques we study ... |
q-bio/0609013 | Per Arne Rikvold | Per Arne Rikvold | Complex Behavior in Simple Models of Biological Coevolution | 8 pages, 5 figures | Int. J. Mod. Phys. C 20, 1387-1397 (2009) | 10.1142/S012918310901445X | null | q-bio.PE cond-mat.stat-mech nlin.AO | null | We explore the complex dynamical behavior of simple predator-prey models of
biological coevolution that account for interspecific and intraspecific
competition for resources, as well as adaptive foraging behavior. In long
kinetic Monte Carlo simulations of these models we find quite robust 1/f-like
noise in species d... | [
{
"created": "Fri, 8 Sep 2006 19:59:45 GMT",
"version": "v1"
}
] | 2009-10-26 | [
[
"Rikvold",
"Per Arne",
""
]
] | We explore the complex dynamical behavior of simple predator-prey models of biological coevolution that account for interspecific and intraspecific competition for resources, as well as adaptive foraging behavior. In long kinetic Monte Carlo simulations of these models we find quite robust 1/f-like noise in species div... |
q-bio/0703067 | Emilio Hernandez-Garcia | E. Hernandez-Garcia, E. A. Herrada, A. F. Rozenfeld, C. J. Tessone, V.
M. Eguiluz, C. M. Duarte, S. Arnaud-Haond, and E. Serrao | Evolutionary and Ecological Trees and Networks | 6 pages, 5 figures. To appear in Proceedings of the Medyfinol06
Conference | in Nonequilibrium Statistical Mechanics and Nonlinear Physics, Ed.
by O. Descalzi, O.A. Rosso and H.A. Larrondo. AIP Conference Proceedings
Volume 913, American Institute of Physics (New York, 2007), pp. 78-83 | 10.1063/1.2746728 | null | q-bio.PE cond-mat.stat-mech q-bio.QM | null | Evolutionary relationships between species are usually represented in
phylogenies, i.e. evolutionary trees, which are a type of networks. The
terminal nodes of these trees represent species, which are made of individuals
and populations among which gene flow occurs. This flow can also be represented
as a network. In ... | [
{
"created": "Fri, 30 Mar 2007 13:54:45 GMT",
"version": "v1"
}
] | 2007-07-11 | [
[
"Hernandez-Garcia",
"E.",
""
],
[
"Herrada",
"E. A.",
""
],
[
"Rozenfeld",
"A. F.",
""
],
[
"Tessone",
"C. J.",
""
],
[
"Eguiluz",
"V. M.",
""
],
[
"Duarte",
"C. M.",
""
],
[
"Arnaud-Haond",
"S.",
""
],
... | Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations among which gene flow occurs. This flow can also be represented as a network. In th... |
q-bio/0401026 | Yisroel Brumer | Yisroel Brumer and Eugene I. Shakhnovich | Host-Parasite Co-evolution and Optimal Mutation Rates for
Semi-conservative Quasispecies | null | null | 10.1103/PhysRevE.69.061909 | null | q-bio.PE cond-mat.soft | null | In this paper, we extend a model of host-parasite co-evolution to incorporate
the semi-conservative nature of DNA replication for both the host and the
parasite. We find that the optimal mutation rate for the semi-conservative and
conservative hosts converge for realistic genome lengths, thus maintaining the
admirabl... | [
{
"created": "Tue, 20 Jan 2004 22:27:39 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Brumer",
"Yisroel",
""
],
[
"Shakhnovich",
"Eugene I.",
""
]
] | In this paper, we extend a model of host-parasite co-evolution to incorporate the semi-conservative nature of DNA replication for both the host and the parasite. We find that the optimal mutation rate for the semi-conservative and conservative hosts converge for realistic genome lengths, thus maintaining the admirable ... |
q-bio/0401019 | Henry Stapp | J.M. Schwartz, H.P. Stapp, M. Beauregard | Quantum Physics in Neuroscience and Psychology: A New Theory With
Respect to Mind/Brain Interaction | 72 pages. Submitted to Behavior and Brain Sciences | null | null | LBNL 54290 | q-bio.NC | null | The cognitive frame in which most neuropsychological research on the neural
basis of behavior is conducted contains the assumption that brain mechanisms
per se fully suffice to explain all psychologically described phenomena. This
assumption stems from the idea that the brain is made up entirely of material
particles... | [
{
"created": "Wed, 14 Jan 2004 22:23:39 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Schwartz",
"J. M.",
""
],
[
"Stapp",
"H. P.",
""
],
[
"Beauregard",
"M.",
""
]
] | The cognitive frame in which most neuropsychological research on the neural basis of behavior is conducted contains the assumption that brain mechanisms per se fully suffice to explain all psychologically described phenomena. This assumption stems from the idea that the brain is made up entirely of material particles a... |
1611.04781 | Bashar Ibrahim | Bashar Ibrahim | Modeling potent pathways for APC/C inhibition: pivotal roles for MCC and
BubR1 | Journal article as preprint | OMICS: A Journal of Integrative Biology. May 2015, 19(5): 294-305 | 10.1089/omi.2015.0027 | null | q-bio.MN math.AP math.DS q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The highly conserved spindle assembly checkpoint (SAC) ensures that the
sister chromatids of the duplicated genome are not separated and distributed to
the spindle poles before all chromosomes have been properly linked to the
microtubules of the mitotic spindle. Biochemically, the SAC delays cell cycle
progression by... | [
{
"created": "Tue, 15 Nov 2016 10:41:05 GMT",
"version": "v1"
}
] | 2016-11-18 | [
[
"Ibrahim",
"Bashar",
""
]
] | The highly conserved spindle assembly checkpoint (SAC) ensures that the sister chromatids of the duplicated genome are not separated and distributed to the spindle poles before all chromosomes have been properly linked to the microtubules of the mitotic spindle. Biochemically, the SAC delays cell cycle progression by p... |
2011.10301 | Maarten Wensink | M. J. Wensink | Perturbations of lifespan inequality in natural populations | 14 pages, 0 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Correlations between high life expectancy and low lifespan inequality are
frequently observed. A recent article seeks to explain this phenomenon by
proposing that a mortality improvement maps to life expectancy and relative
lifespan equality through the same weights w(x), with an extra weight W(x)
applied for relativ... | [
{
"created": "Fri, 20 Nov 2020 09:52:30 GMT",
"version": "v1"
}
] | 2020-11-23 | [
[
"Wensink",
"M. J.",
""
]
] | Correlations between high life expectancy and low lifespan inequality are frequently observed. A recent article seeks to explain this phenomenon by proposing that a mortality improvement maps to life expectancy and relative lifespan equality through the same weights w(x), with an extra weight W(x) applied for relative ... |
1902.07650 | Maria Florencia Noriega Romero Vargas | Florencia Noriega, Adolfo Christian Montes-Medina, and Marc Timme | Quantitative analysis of timing in animal vocal sequences | 10 pages, 10 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Timing features such as the silence gaps between vocal units -- inter-call
intervals (ICIs) -- often correlate with biological information such as context
or genetic information. Such correlates between the ICIs and biological
information have been reported for a diversity of animals. Yet, few
quantitative approaches... | [
{
"created": "Wed, 20 Feb 2019 17:05:36 GMT",
"version": "v1"
}
] | 2019-02-21 | [
[
"Noriega",
"Florencia",
""
],
[
"Montes-Medina",
"Adolfo Christian",
""
],
[
"Timme",
"Marc",
""
]
] | Timing features such as the silence gaps between vocal units -- inter-call intervals (ICIs) -- often correlate with biological information such as context or genetic information. Such correlates between the ICIs and biological information have been reported for a diversity of animals. Yet, few quantitative approaches f... |
2006.15385 | Stavros Maltezos | S. Maltezos | Methodology for Modelling the new COVID-19 Pandemic Spread and
Implementation to European Countries | 8 pages, 6 figures and 2 tables | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | After the breakout of the disease caused by the new virus COVID-19, the
mitigation stage has been reached in most of the countries in the world. During
this stage, a more accurate data analysis of the daily reported cases and other
parameters became possible for the European countries and has been performed in
this w... | [
{
"created": "Sat, 27 Jun 2020 15:25:32 GMT",
"version": "v1"
},
{
"created": "Tue, 30 Jun 2020 08:47:30 GMT",
"version": "v2"
}
] | 2020-07-01 | [
[
"Maltezos",
"S.",
""
]
] | After the breakout of the disease caused by the new virus COVID-19, the mitigation stage has been reached in most of the countries in the world. During this stage, a more accurate data analysis of the daily reported cases and other parameters became possible for the European countries and has been performed in this wor... |
q-bio/0410006 | Salvatore Miccich\`e | M. Spano, F. Lillo, S. Micciche, R. N. Mantegna | Inverted Repeats in Viral Genomes | 8 pages, 3 figures | Fluctuation and Noise Letters 5(2), L193-L200, (2005) | 10.1142/S0219477505002550 | null | q-bio.QM cond-mat.stat-mech q-bio.GN | null | We investigate 738 complete genomes of viruses to detect the presence of
short inverted repeats. The number of inverted repeats found is compared with
the prediction obtained for a Bernoullian and for a Markovian control model. We
find as a statistical regularity that the number of observed inverted repeats
is often ... | [
{
"created": "Tue, 5 Oct 2004 13:32:54 GMT",
"version": "v1"
}
] | 2021-08-25 | [
[
"Spano",
"M.",
""
],
[
"Lillo",
"F.",
""
],
[
"Micciche",
"S.",
""
],
[
"Mantegna",
"R. N.",
""
]
] | We investigate 738 complete genomes of viruses to detect the presence of short inverted repeats. The number of inverted repeats found is compared with the prediction obtained for a Bernoullian and for a Markovian control model. We find as a statistical regularity that the number of observed inverted repeats is often gr... |
1707.05182 | Robert Legenstein | Robert Legenstein, Zeno Jonke, Stefan Habenschuss and Wolfgang Maass | A probabilistic model for learning in cortical microcircuit motifs with
data-based divisive inhibition | 24 pages, 5 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Previous theoretical studies on the interaction of excitatory and inhibitory
neurons proposed to model this cortical microcircuit motif as a so-called
Winner-Take-All (WTA) circuit. A recent modeling study however found that the
WTA model is not adequate for data-based softer forms of divisive inhibition as
found in ... | [
{
"created": "Mon, 17 Jul 2017 14:33:14 GMT",
"version": "v1"
}
] | 2018-03-27 | [
[
"Legenstein",
"Robert",
""
],
[
"Jonke",
"Zeno",
""
],
[
"Habenschuss",
"Stefan",
""
],
[
"Maass",
"Wolfgang",
""
]
] | Previous theoretical studies on the interaction of excitatory and inhibitory neurons proposed to model this cortical microcircuit motif as a so-called Winner-Take-All (WTA) circuit. A recent modeling study however found that the WTA model is not adequate for data-based softer forms of divisive inhibition as found in a ... |
1409.1683 | Ugo Bastolla | Alberto Pascual-Garc\'ia, Antonio Ferrera and Ugo Bastolla | Does mutualism hinder biodiversity? | Submitted on October 2012 as a Brief Communication Arising from James
et al. Nature 487, 227-230 (2012) | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A recent paper by James et al. finds that mutualistic interactions decrease
the biodiversity of model ecosystems. However, this result can be reverted if
we consider ecological trade-offs and choose parameters suitable for sparse
mutualistic networks instead of fully connected networks.
| [
{
"created": "Fri, 5 Sep 2014 08:20:30 GMT",
"version": "v1"
}
] | 2014-09-08 | [
[
"Pascual-García",
"Alberto",
""
],
[
"Ferrera",
"Antonio",
""
],
[
"Bastolla",
"Ugo",
""
]
] | A recent paper by James et al. finds that mutualistic interactions decrease the biodiversity of model ecosystems. However, this result can be reverted if we consider ecological trade-offs and choose parameters suitable for sparse mutualistic networks instead of fully connected networks. |
1308.0699 | Ruth Nussinov | Ruth Nussinov | The spatial structure of cell signaling systems | 28 pages | Physical Biology 2013; 10(4) | 10.1088/1478-3975/10/4/045004 | null | q-bio.BM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The spatial structure of the cell is highly organized at all levels: from
small complexes and assemblies, to local nano- and micro-clusters, to global,
micrometer scales across and between cells. We suggest that this multiscale
spatial cell organization also organizes signaling and coordinates cellular
behavior. We p... | [
{
"created": "Sat, 3 Aug 2013 14:09:42 GMT",
"version": "v1"
}
] | 2013-08-06 | [
[
"Nussinov",
"Ruth",
""
]
] | The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell organization also organizes signaling and coordinates cellular behavior. We pro... |
2006.04954 | D. Delepine | Jose de Jesus Bernal-Alvarado and David Delepine (Guanajuato
University) | Morphology and numerical characteristics of epidemic curves for
SARS-Cov-II using Moyal distribution | 8 pages, 5 figures | null | null | null | q-bio.PE physics.med-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, it is shown that the Moyal distribution is an excelent tool to
study the SARS-Cov-II (Covid-19) epidemiological associated curves and its
propagation. The Moyal parameters give all the information to describe the form
and the impact of the illness outbreak in the different affected countries and
its gl... | [
{
"created": "Mon, 8 Jun 2020 21:20:17 GMT",
"version": "v1"
}
] | 2020-06-11 | [
[
"Bernal-Alvarado",
"Jose de Jesus",
"",
"Guanajuato\n University"
],
[
"Delepine",
"David",
"",
"Guanajuato\n University"
]
] | In this paper, it is shown that the Moyal distribution is an excelent tool to study the SARS-Cov-II (Covid-19) epidemiological associated curves and its propagation. The Moyal parameters give all the information to describe the form and the impact of the illness outbreak in the different affected countries and its glob... |
2005.12165 | Diego Ferreiro | Federico Coscio, Alejandro D. Nadra and Diego U. Ferreiro | A structural model for the Coronavirus Nucleocapsid | 13 pages, 5 figures | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | We propose a mesoscale model structure for the coronavirus nucleocapsid,
assembled from the high resolution structures of the basic building blocks of
the N-protein, CryoEM imaging and mathematical constraints for an overall
quasi-spherical particle. The structure is a truncated octahedron that
accommodates two layer... | [
{
"created": "Mon, 25 May 2020 15:22:04 GMT",
"version": "v1"
}
] | 2020-05-26 | [
[
"Coscio",
"Federico",
""
],
[
"Nadra",
"Alejandro D.",
""
],
[
"Ferreiro",
"Diego U.",
""
]
] | We propose a mesoscale model structure for the coronavirus nucleocapsid, assembled from the high resolution structures of the basic building blocks of the N-protein, CryoEM imaging and mathematical constraints for an overall quasi-spherical particle. The structure is a truncated octahedron that accommodates two layers:... |
2002.00070 | Cristhian Montoya | Cristhian Montoya and Jhoana P. Romero-Leiton | Analysis and optimal control of a malaria mathematical model under
resistance and population movement | null | null | null | null | q-bio.PE math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work, two mathematical models for malaria under resistance are
presented. More precisely, the first model shows the interaction between humans
and mosquitoes inside a patch under infection of malaria when the human
population is resistant to antimalarial drug and mosquitoes population is
resistant to insectic... | [
{
"created": "Fri, 31 Jan 2020 21:46:18 GMT",
"version": "v1"
}
] | 2020-02-04 | [
[
"Montoya",
"Cristhian",
""
],
[
"Romero-Leiton",
"Jhoana P.",
""
]
] | In this work, two mathematical models for malaria under resistance are presented. More precisely, the first model shows the interaction between humans and mosquitoes inside a patch under infection of malaria when the human population is resistant to antimalarial drug and mosquitoes population is resistant to insecticid... |
1607.06225 | Rodrigo Rocha Pereira | Rodrigo P. Rocha, Wagner Figueiredo, Samir Suweis, and Amos Maritan | Species survival and scaling laws in hostile and disordered environments | 20 pages, 5 Figures | Phys. Rev. E 94, 042404 (2016) | 10.1103/PhysRevE.94.042404 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work we study the likelihood of survival of single-species in the
context of hostile and disordered environments. Population dynamics in this
environment, as modeled by the Fisher equation, is characterized by negative
average growth rate, except in some random spatially distributed patches that
may support l... | [
{
"created": "Thu, 21 Jul 2016 08:03:34 GMT",
"version": "v1"
},
{
"created": "Tue, 11 Oct 2016 12:50:31 GMT",
"version": "v2"
}
] | 2018-10-25 | [
[
"Rocha",
"Rodrigo P.",
""
],
[
"Figueiredo",
"Wagner",
""
],
[
"Suweis",
"Samir",
""
],
[
"Maritan",
"Amos",
""
]
] | In this work we study the likelihood of survival of single-species in the context of hostile and disordered environments. Population dynamics in this environment, as modeled by the Fisher equation, is characterized by negative average growth rate, except in some random spatially distributed patches that may support lif... |
1807.08900 | Hideaki Shimazaki | Jimmy Gaudreault and Hideaki Shimazaki | State-space analysis of an Ising model reveals contributions of pairwise
interactions to sparseness, fluctuation, and stimulus coding of monkey V1
neurons | 10 pages, 4 figures, ICANN2018 | null | null | null | q-bio.NC cond-mat.dis-nn stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this study, we analyzed the activity of monkey V1 neurons responding to
grating stimuli of different orientations using inference methods for a
time-dependent Ising model. The method provides optimal estimation of
time-dependent neural interactions with credible intervals according to the
sequential Bayes estimati... | [
{
"created": "Tue, 24 Jul 2018 04:12:58 GMT",
"version": "v1"
}
] | 2018-07-25 | [
[
"Gaudreault",
"Jimmy",
""
],
[
"Shimazaki",
"Hideaki",
""
]
] | In this study, we analyzed the activity of monkey V1 neurons responding to grating stimuli of different orientations using inference methods for a time-dependent Ising model. The method provides optimal estimation of time-dependent neural interactions with credible intervals according to the sequential Bayes estimation... |
1712.07491 | Junzhe Zhao | Junzhe Zhao | Kinetic Modelling and Inference of Hyperpolarized 13C Molecules in
Cancer Metabolism | Use of data not accredited in full; did not obtain full approval from
the laboratory | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Hyperpolarized 13C-MRI allows real time observation of metabolism in vivo.
Imaging sequences have been developed to follow the metabolism of [1-13C]
pyruvate and extract reaction kinetics, which can show tumour treatment
response. We applied the fitting model and algorithm for the imaging data of
mice tumour models a... | [
{
"created": "Wed, 20 Dec 2017 14:15:49 GMT",
"version": "v1"
},
{
"created": "Thu, 21 Dec 2017 02:46:01 GMT",
"version": "v2"
},
{
"created": "Fri, 5 Jan 2018 01:18:58 GMT",
"version": "v3"
}
] | 2018-01-08 | [
[
"Zhao",
"Junzhe",
""
]
] | Hyperpolarized 13C-MRI allows real time observation of metabolism in vivo. Imaging sequences have been developed to follow the metabolism of [1-13C] pyruvate and extract reaction kinetics, which can show tumour treatment response. We applied the fitting model and algorithm for the imaging data of mice tumour models and... |
2006.09222 | Sebastian Bayerl | Sebastian P. Bayerl, Florian H\"onig, Joelle Reister and Korbinian
Riedhammer | Towards Automated Assessment of Stuttering and Stuttering Therapy | 10 pages, 3 figures, 1 table Accepted at TSD 2020, 23rd International
Conference on Text, Speech and Dialogue | null | null | null | q-bio.QM cs.CL cs.LG cs.SD eess.AS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stuttering is a complex speech disorder that can be identified by
repetitions, prolongations of sounds, syllables or words, and blocks while
speaking. Severity assessment is usually done by a speech therapist. While
attempts at automated assessment were made, it is rarely used in therapy.
Common methods for the asses... | [
{
"created": "Tue, 16 Jun 2020 14:50:56 GMT",
"version": "v1"
}
] | 2020-06-17 | [
[
"Bayerl",
"Sebastian P.",
""
],
[
"Hönig",
"Florian",
""
],
[
"Reister",
"Joelle",
""
],
[
"Riedhammer",
"Korbinian",
""
]
] | Stuttering is a complex speech disorder that can be identified by repetitions, prolongations of sounds, syllables or words, and blocks while speaking. Severity assessment is usually done by a speech therapist. While attempts at automated assessment were made, it is rarely used in therapy. Common methods for the assessm... |
2009.12219 | Laura Schaposnik | Vishaal Ram and Laura P. Schaposnik | A modified age-structured SIR model for COVID-19 type viruses | 12 pages, 19 figures | Nature Sci Rep 11, 15194 (2021) | 10.1038/s41598-021-94609-3 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a modified age-structured SIR model based on known patterns of
social contact and distancing measures within Washington, USA. We find that
population age-distribution has a significant effect on disease spread and
mortality rate, and contribute to the efficacy of age-specific contact and
treatment measures... | [
{
"created": "Wed, 23 Sep 2020 19:50:49 GMT",
"version": "v1"
}
] | 2022-10-18 | [
[
"Ram",
"Vishaal",
""
],
[
"Schaposnik",
"Laura P.",
""
]
] | We present a modified age-structured SIR model based on known patterns of social contact and distancing measures within Washington, USA. We find that population age-distribution has a significant effect on disease spread and mortality rate, and contribute to the efficacy of age-specific contact and treatment measures. ... |
1308.6031 | Caterina La Porta AM | C.A.M. La Porta, S Zapperi | Do cancer cells undergo phenotypic switching? The case for imperfect
cancer stem cell markers | null | Scientific Reports | 2 : 441, 2012 | 10.1038/srep00441 | null | q-bio.PE q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The identification of cancer stem cells in vivo and in vitro relies on
specific surface markers that should allow to sort cancer cells in
phenotypically distinct subpopulations. Experiments report that sorted cancer
cell populations after some time tend to express again all the original
markers, leading to the hypoth... | [
{
"created": "Wed, 28 Aug 2013 02:18:02 GMT",
"version": "v1"
}
] | 2013-08-29 | [
[
"La Porta",
"C. A. M.",
""
],
[
"Zapperi",
"S",
""
]
] | The identification of cancer stem cells in vivo and in vitro relies on specific surface markers that should allow to sort cancer cells in phenotypically distinct subpopulations. Experiments report that sorted cancer cell populations after some time tend to express again all the original markers, leading to the hypothes... |
1703.00940 | Nadav M. Shnerb | Yael Fried, Nadav M. Shnerb, David A. Kessler | Alternative steady states in random ecological networks | null | Phys. Rev. E 96, 012412 (2017) | 10.1103/PhysRevE.96.012412 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In many natural situations one observes a local system with many competing
species which is coupled by weak immigration to a regional species pool. The
dynamics of such a system is dominated by its stable and uninvadable (SU)
states. When the competition matrix is random, the number of SUs depends on the
average valu... | [
{
"created": "Thu, 2 Mar 2017 20:24:48 GMT",
"version": "v1"
}
] | 2017-07-26 | [
[
"Fried",
"Yael",
""
],
[
"Shnerb",
"Nadav M.",
""
],
[
"Kessler",
"David A.",
""
]
] | In many natural situations one observes a local system with many competing species which is coupled by weak immigration to a regional species pool. The dynamics of such a system is dominated by its stable and uninvadable (SU) states. When the competition matrix is random, the number of SUs depends on the average value ... |
2310.04596 | Liang Chen | Liang Chen and Sue Ann Campbell | Synaptic delay induced macroscopic dynamics of the large-scale network
of Izhikevich neurons | 8 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | We consider a large network of Izhikevich neurons. Each neuron has a
quadratic integrate-and-fire type model with a recovery variable modelling
spike frequency adaptation (SFA). We introduce a biologically motivated
synaptic current expression and a delay in the synaptic transmission. Following
the Ott-Antonsen theor... | [
{
"created": "Fri, 6 Oct 2023 21:21:35 GMT",
"version": "v1"
}
] | 2023-10-10 | [
[
"Chen",
"Liang",
""
],
[
"Campbell",
"Sue Ann",
""
]
] | We consider a large network of Izhikevich neurons. Each neuron has a quadratic integrate-and-fire type model with a recovery variable modelling spike frequency adaptation (SFA). We introduce a biologically motivated synaptic current expression and a delay in the synaptic transmission. Following the Ott-Antonsen theory,... |
2109.13418 | Mara Freilich | Mara Freilich and Glenn Flierl and Amala Mahadevan | Diversity of growth rates maximizes phytoplankton productivity in an
eddying ocean | null | null | 10.1029/2021GL096180 | null | q-bio.PE physics.flu-dyn | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In the subtropical gyres, phytoplankton rely on eddies for transporting
nutrients from depth to the euphotic zone. But, what controls the rate of
nutrient supply for new production? We show that vertical nutrient flux depends
both on the vertical motion within the eddying flow and varies nonlinearly with
the growth r... | [
{
"created": "Tue, 28 Sep 2021 01:12:23 GMT",
"version": "v1"
}
] | 2022-03-02 | [
[
"Freilich",
"Mara",
""
],
[
"Flierl",
"Glenn",
""
],
[
"Mahadevan",
"Amala",
""
]
] | In the subtropical gyres, phytoplankton rely on eddies for transporting nutrients from depth to the euphotic zone. But, what controls the rate of nutrient supply for new production? We show that vertical nutrient flux depends both on the vertical motion within the eddying flow and varies nonlinearly with the growth rat... |
2103.13920 | Mar\'ia Vallet-Regi | C. Heras, S. Sanchez-Salcedo, D. Lozano, J. Pe\~na, P. Esbrit, M.
Vallet-Regi, A.J. Salinas | Osteostatin potentiates the bioactivity of mesoporous glass scaffolds
containing Zn2+ ions in human mesenchymal stem cell cultures | 34 pages, 11 figures | Acta Biomaterialia. 89 (2019) 359-371 | 10.1016/j.actbio.2019.03.033 | null | q-bio.BM physics.bio-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | There is an urgent need of biosynthetic bone grafts with enhanced osteogenic
capacity. In this study, we describe the design of hierarchical
meso-macroporous 3D-scaffolds based on mesoporous bioactive glasses (MBGs),
enriched with the peptide osteostatin and Zn2+ ions, and their osteogenic
effect on human mesenchymal... | [
{
"created": "Tue, 23 Mar 2021 12:32:06 GMT",
"version": "v1"
}
] | 2021-03-26 | [
[
"Heras",
"C.",
""
],
[
"Sanchez-Salcedo",
"S.",
""
],
[
"Lozano",
"D.",
""
],
[
"Peña",
"J.",
""
],
[
"Esbrit",
"P.",
""
],
[
"Vallet-Regi",
"M.",
""
],
[
"Salinas",
"A. J.",
""
]
] | There is an urgent need of biosynthetic bone grafts with enhanced osteogenic capacity. In this study, we describe the design of hierarchical meso-macroporous 3D-scaffolds based on mesoporous bioactive glasses (MBGs), enriched with the peptide osteostatin and Zn2+ ions, and their osteogenic effect on human mesenchymal s... |
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