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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1801.01533 | D'Artagnan Greene | D'Artagnan Greene, Theodora Po, Jennifer Pan, Tanya Tabibian, Ray Luo | Computational Analysis for the Rational Design of Anti-Amyloid Beta
(ABeta) Antibodies | null | null | 10.1021/acs.jpcb.8b01837 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Alzheimer's Disease (AD) is a neurodegenerative disorder that lacks effective
treatment options. Anti-amyloid beta (ABeta) antibodies are the leading drug
candidates to treat AD, but the results of clinical trials have been
disappointing. Introducing rational mutations into anti-ABeta antibodies to
increase their eff... | [
{
"created": "Thu, 4 Jan 2018 20:11:54 GMT",
"version": "v1"
},
{
"created": "Thu, 22 Feb 2018 19:25:51 GMT",
"version": "v2"
}
] | 2018-04-24 | [
[
"Greene",
"D'Artagnan",
""
],
[
"Po",
"Theodora",
""
],
[
"Pan",
"Jennifer",
""
],
[
"Tabibian",
"Tanya",
""
],
[
"Luo",
"Ray",
""
]
] | Alzheimer's Disease (AD) is a neurodegenerative disorder that lacks effective treatment options. Anti-amyloid beta (ABeta) antibodies are the leading drug candidates to treat AD, but the results of clinical trials have been disappointing. Introducing rational mutations into anti-ABeta antibodies to increase their effec... |
q-bio/0601034 | Hiroshi Fujisaki | Hiroshi Fujisaki, Yong Zhang, John E. Straub | Time-dependent perturbation theory for vibrational energy relaxation and
dephasing in peptides and proteins | 16 pages, 5 figures, 5 tables, submitted to J. Chem. Phys | null | 10.1063/1.2191038 | null | q-bio.BM | null | Without invoking the Markov approximation, we derive formulas for vibrational
energy relaxation (VER) and dephasing for an anharmonic system oscillator using
a time-dependent perturbation theory. The system-bath Hamiltonian contains more
than the third order coupling terms since we take a normal mode picture as a
zer... | [
{
"created": "Sat, 21 Jan 2006 23:06:18 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Fujisaki",
"Hiroshi",
""
],
[
"Zhang",
"Yong",
""
],
[
"Straub",
"John E.",
""
]
] | Without invoking the Markov approximation, we derive formulas for vibrational energy relaxation (VER) and dephasing for an anharmonic system oscillator using a time-dependent perturbation theory. The system-bath Hamiltonian contains more than the third order coupling terms since we take a normal mode picture as a zerot... |
1806.00128 | Emma Towlson | Emma K. Towlson, Petra E. V\'ertes, Ulrich M\"uller, and Sebastian E.
Ahnert | Brain networks reveal the effects of antipsychotic drugs on
schizophrenia patients and controls | 18 pages, 2 figures, 3 tables | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The study of brain networks, including derived from functional neuroimaging
data, attracts broad interest and represents a rapidly growing
interdisciplinary field. Comparing networks of healthy volunteers with those of
patients can potentially offer new, quantitative diagnostic methods, and a
framework for better und... | [
{
"created": "Thu, 31 May 2018 23:05:04 GMT",
"version": "v1"
},
{
"created": "Mon, 4 Jun 2018 00:58:10 GMT",
"version": "v2"
}
] | 2018-06-05 | [
[
"Towlson",
"Emma K.",
""
],
[
"Vértes",
"Petra E.",
""
],
[
"Müller",
"Ulrich",
""
],
[
"Ahnert",
"Sebastian E.",
""
]
] | The study of brain networks, including derived from functional neuroimaging data, attracts broad interest and represents a rapidly growing interdisciplinary field. Comparing networks of healthy volunteers with those of patients can potentially offer new, quantitative diagnostic methods, and a framework for better under... |
2011.05595 | Yu Liu | Yu Liu, Yinghong Zhao and Mo Chen | Desires and Motivation: The Computational Rule, the Underlying Neural
Circuitry, and the Relevant Clinical Disorders | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | As organism is a dissipative system. The process from multi desires to
exclusive motivation is of great importance among all sensory-action loops. In
this paper we argued that a proper Desire-Motivation model should be a
continuous dynamic mapping from the dynamic desire vector to the sparse
motivation vector. Meanwh... | [
{
"created": "Wed, 11 Nov 2020 06:46:51 GMT",
"version": "v1"
}
] | 2020-11-12 | [
[
"Liu",
"Yu",
""
],
[
"Zhao",
"Yinghong",
""
],
[
"Chen",
"Mo",
""
]
] | As organism is a dissipative system. The process from multi desires to exclusive motivation is of great importance among all sensory-action loops. In this paper we argued that a proper Desire-Motivation model should be a continuous dynamic mapping from the dynamic desire vector to the sparse motivation vector. Meanwhil... |
2110.05231 | Shentong Mo | Shentong Mo, Xi Fu, Chenyang Hong, Yizhen Chen, Yuxuan Zheng, Xiangru
Tang, Zhiqiang Shen, Eric P Xing, Yanyan Lan | Multi-modal Self-supervised Pre-training for Regulatory Genome Across
Cell Types | null | null | null | null | q-bio.GN cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the genome biology research, regulatory genome modeling is an important
topic for many regulatory downstream tasks, such as promoter classification,
transaction factor binding sites prediction. The core problem is to model how
regulatory elements interact with each other and its variability across
different cell t... | [
{
"created": "Mon, 11 Oct 2021 12:48:44 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Nov 2021 08:27:38 GMT",
"version": "v2"
}
] | 2021-11-04 | [
[
"Mo",
"Shentong",
""
],
[
"Fu",
"Xi",
""
],
[
"Hong",
"Chenyang",
""
],
[
"Chen",
"Yizhen",
""
],
[
"Zheng",
"Yuxuan",
""
],
[
"Tang",
"Xiangru",
""
],
[
"Shen",
"Zhiqiang",
""
],
[
"Xing",
"Eri... | In the genome biology research, regulatory genome modeling is an important topic for many regulatory downstream tasks, such as promoter classification, transaction factor binding sites prediction. The core problem is to model how regulatory elements interact with each other and its variability across different cell typ... |
1810.12441 | Gustav Markkula | Gustav Markkula, Richard Romano, Rachel Waldram, Oscar Giles, Callum
Mole, Richard Wilkie | Modelling visual-vestibular integration and behavioural adaptation in
the driving simulator | Changes in v2: Minor language improvements to Abstract and
Conclusion; Changes in v3: Added acknowledgments and data statement | null | null | null | q-bio.NC cs.CE cs.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is well established that not only vision but also other sensory modalities
affect drivers' control of their vehicles, and that drivers adapt over time to
persistent changes in sensory cues (for example in driving simulators), but the
mechanisms underlying these behavioural phenomena are poorly understood. Here,
we... | [
{
"created": "Mon, 29 Oct 2018 22:30:06 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Nov 2018 16:58:36 GMT",
"version": "v2"
},
{
"created": "Wed, 7 Nov 2018 09:14:46 GMT",
"version": "v3"
}
] | 2018-11-08 | [
[
"Markkula",
"Gustav",
""
],
[
"Romano",
"Richard",
""
],
[
"Waldram",
"Rachel",
""
],
[
"Giles",
"Oscar",
""
],
[
"Mole",
"Callum",
""
],
[
"Wilkie",
"Richard",
""
]
] | It is well established that not only vision but also other sensory modalities affect drivers' control of their vehicles, and that drivers adapt over time to persistent changes in sensory cues (for example in driving simulators), but the mechanisms underlying these behavioural phenomena are poorly understood. Here, we c... |
1705.05191 | Philippe Terrier PhD | Fabienne Reynard and Philippe Terrier | Determinants of gait stability while walking on a treadmill: a machine
learning approach | This is the author's version of a manuscript published in the Journal
of Biomechanics | Journnal of Biomechanics Volume 65, 8 December 2017, Pages 212-215 | 10.1016/j.jbiomech.2017.10.020 | null | q-bio.QM q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Dynamic balance in human locomotion can be assessed through the local dynamic
stability (LDS) method. Whereas gait LDS has been used successfully in many
settings and applications, little is known about its sensitivity to individual
characteristics of healthy adults. Therefore, we reanalyzed a large dataset of
accele... | [
{
"created": "Mon, 15 May 2017 12:47:46 GMT",
"version": "v1"
},
{
"created": "Thu, 26 Oct 2017 12:43:14 GMT",
"version": "v2"
}
] | 2018-12-27 | [
[
"Reynard",
"Fabienne",
""
],
[
"Terrier",
"Philippe",
""
]
] | Dynamic balance in human locomotion can be assessed through the local dynamic stability (LDS) method. Whereas gait LDS has been used successfully in many settings and applications, little is known about its sensitivity to individual characteristics of healthy adults. Therefore, we reanalyzed a large dataset of accelero... |
2305.19394 | Roman Pogodin | Roman Pogodin, Jonathan Cornford, Arna Ghosh, Gauthier Gidel,
Guillaume Lajoie, Blake Richards | Synaptic Weight Distributions Depend on the Geometry of Plasticity | ICLR 2024 | The Twelfth International Conference on Learning Representations,
2024 | null | null | q-bio.NC cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A growing literature in computational neuroscience leverages gradient descent
and learning algorithms that approximate it to study synaptic plasticity in the
brain. However, the vast majority of this work ignores a critical underlying
assumption: the choice of distance for synaptic changes - i.e. the geometry of
syna... | [
{
"created": "Tue, 30 May 2023 20:16:23 GMT",
"version": "v1"
},
{
"created": "Mon, 4 Mar 2024 20:22:16 GMT",
"version": "v2"
}
] | 2024-03-06 | [
[
"Pogodin",
"Roman",
""
],
[
"Cornford",
"Jonathan",
""
],
[
"Ghosh",
"Arna",
""
],
[
"Gidel",
"Gauthier",
""
],
[
"Lajoie",
"Guillaume",
""
],
[
"Richards",
"Blake",
""
]
] | A growing literature in computational neuroscience leverages gradient descent and learning algorithms that approximate it to study synaptic plasticity in the brain. However, the vast majority of this work ignores a critical underlying assumption: the choice of distance for synaptic changes - i.e. the geometry of synapt... |
2107.02995 | Kaiyuan Yang | Zhanghao Yu, Joshua C. Chen, Fatima T. Alrashdan, Benjamin W. Avants,
Yan He, Amanda Singer, Jacob T. Robinson, Kaiyuan Yang | MagNI: A Magnetoelectrically Powered and Controlled Wireless
Neurostimulating Implant | This work has been accepted to 2020 IEEE Transactions on Biomedical
Circuits and Systems (TBioCAS) | IEEE Transactions on Biomedical Circuits and Systems (TBioCAS),
Volume: 14, Issue: 6, Pages: 1241-1252, Dec. 2020 | 10.1109/TBCAS.2020.3037862 | null | q-bio.NC eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper presents the first wireless and programmable neural stimulator
leveraging magnetoelectric (ME) effects for power and data transfer. Thanks to
low tissue absorption, low misalignment sensitivity and high power transfer
efficiency, the ME effect enables safe delivery of high power levels (a few
milliwatts) a... | [
{
"created": "Wed, 7 Jul 2021 03:30:10 GMT",
"version": "v1"
}
] | 2021-07-08 | [
[
"Yu",
"Zhanghao",
""
],
[
"Chen",
"Joshua C.",
""
],
[
"Alrashdan",
"Fatima T.",
""
],
[
"Avants",
"Benjamin W.",
""
],
[
"He",
"Yan",
""
],
[
"Singer",
"Amanda",
""
],
[
"Robinson",
"Jacob T.",
""
],
[... | This paper presents the first wireless and programmable neural stimulator leveraging magnetoelectric (ME) effects for power and data transfer. Thanks to low tissue absorption, low misalignment sensitivity and high power transfer efficiency, the ME effect enables safe delivery of high power levels (a few milliwatts) at ... |
2006.14295 | Gemma Massonis | Gemma Massonis, Julio R. Banga, Alejandro F. Villaverde | Structural Identifiability and Observability of Compartmental Models of
the COVID-19 Pandemic | 25 pages, 7 figures | null | null | null | q-bio.PE physics.soc-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The recent coronavirus disease (COVID-19) outbreak has dramatically increased
the public awareness and appreciation of the utility of dynamic models. At the
same time, the dissemination of contradictory model predictions has highlighted
their limitations. If some parameters and/or state variables of a model cannot
be... | [
{
"created": "Thu, 25 Jun 2020 10:30:24 GMT",
"version": "v1"
}
] | 2020-06-26 | [
[
"Massonis",
"Gemma",
""
],
[
"Banga",
"Julio R.",
""
],
[
"Villaverde",
"Alejandro F.",
""
]
] | The recent coronavirus disease (COVID-19) outbreak has dramatically increased the public awareness and appreciation of the utility of dynamic models. At the same time, the dissemination of contradictory model predictions has highlighted their limitations. If some parameters and/or state variables of a model cannot be d... |
1710.03786 | Brett McClintock | Brett T. McClintock and Theo Michelot | momentuHMM: R package for generalized hidden Markov models of animal
movement | null | Methods in Ecology and Evolution 2018, Vol. 9, No. 6, 1518-1530 | 10.1111/2041-210X.12995 | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Discrete-time hidden Markov models (HMMs) have become an immensely popular
tool for inferring latent animal behaviors from telemetry data. Here we
introduce an open-source R package, momentuHMM, that addresses many of the
deficiencies in existing HMM software. Features include: 1) data pre-processing
and visualizatio... | [
{
"created": "Tue, 10 Oct 2017 19:03:53 GMT",
"version": "v1"
},
{
"created": "Fri, 9 Mar 2018 23:51:40 GMT",
"version": "v2"
}
] | 2018-06-13 | [
[
"McClintock",
"Brett T.",
""
],
[
"Michelot",
"Theo",
""
]
] | Discrete-time hidden Markov models (HMMs) have become an immensely popular tool for inferring latent animal behaviors from telemetry data. Here we introduce an open-source R package, momentuHMM, that addresses many of the deficiencies in existing HMM software. Features include: 1) data pre-processing and visualization;... |
0806.0108 | Dirson Jian Li | Dirson Jian Li, Shengli Zhang | The C-value enigma and timing of the Cambrian explosion | 46 pages, 10 figures | Biochemical and Biophysical Research Communications 392, 240-245
(2010) | 10.1016/j.bbrc.2010.01.032 | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Cambrian explosion is a grand challenge to science today and involves
multidisciplinary study. This event is generally believed as a result of
genetic innovations, environmental factors and ecological interactions, even
though there are many conflicts on nature and timing of metazoan origins. The
crux of the matt... | [
{
"created": "Sat, 31 May 2008 21:13:31 GMT",
"version": "v1"
}
] | 2010-02-10 | [
[
"Li",
"Dirson Jian",
""
],
[
"Zhang",
"Shengli",
""
]
] | The Cambrian explosion is a grand challenge to science today and involves multidisciplinary study. This event is generally believed as a result of genetic innovations, environmental factors and ecological interactions, even though there are many conflicts on nature and timing of metazoan origins. The crux of the matter... |
1311.3952 | Agnieszka Szymanska | Chang Won Lee, Agnieszka A. Szymanska, Shun Chi Wu, A. Lee
Swindlehurst, Zoran Nenadic | A Method for Neuronal Source Identification | 14 pages, 5 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multi-sensor microelectrodes for extracellular action potential recording
have significantly improved the quality of in vivo recorded neuronal signals.
These microelectrodes have also been instrumental in the localization of
neuronal signal sources. However, existing neuron localization methods have
been mostly utili... | [
{
"created": "Fri, 15 Nov 2013 19:07:41 GMT",
"version": "v1"
}
] | 2013-11-18 | [
[
"Lee",
"Chang Won",
""
],
[
"Szymanska",
"Agnieszka A.",
""
],
[
"Wu",
"Shun Chi",
""
],
[
"Swindlehurst",
"A. Lee",
""
],
[
"Nenadic",
"Zoran",
""
]
] | Multi-sensor microelectrodes for extracellular action potential recording have significantly improved the quality of in vivo recorded neuronal signals. These microelectrodes have also been instrumental in the localization of neuronal signal sources. However, existing neuron localization methods have been mostly utilize... |
1501.00202 | Alexander Iomin | V. M\'endez and A. Iomin | Comb models for transport along spiny dendrites | null | null | null | null | q-bio.NC cond-mat.dis-nn physics.bio-ph physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This chapter is a contribution in the "Handbook of Applications of Chaos
Theory" ed. by Prof. Christos H Skiadas. The chapter is organized as follows.
First we study the statistical properties of combs and explain how to reduce
the effect of teeth on the movement along the backbone as a waiting time
distribution betw... | [
{
"created": "Wed, 31 Dec 2014 20:34:56 GMT",
"version": "v1"
}
] | 2015-01-05 | [
[
"Méndez",
"V.",
""
],
[
"Iomin",
"A.",
""
]
] | This chapter is a contribution in the "Handbook of Applications of Chaos Theory" ed. by Prof. Christos H Skiadas. The chapter is organized as follows. First we study the statistical properties of combs and explain how to reduce the effect of teeth on the movement along the backbone as a waiting time distribution betwee... |
2207.07504 | Anton Arkhipov | Anton Arkhipov | Non-separability of Physical Systems as a Foundation of Consciousness | null | null | 10.3390/e24111539 | null | q-bio.NC cond-mat.dis-nn | http://creativecommons.org/licenses/by/4.0/ | A hypothesis is presented that non-separability of degrees of freedom is the
fundamental property underlying consciousness in physical systems. The amount
of consciousness in a system is determined by the extent of non-separability
and the number of degrees of freedom involved. Non-interacting and feedforward
systems... | [
{
"created": "Tue, 28 Jun 2022 19:37:45 GMT",
"version": "v1"
}
] | 2022-11-09 | [
[
"Arkhipov",
"Anton",
""
]
] | A hypothesis is presented that non-separability of degrees of freedom is the fundamental property underlying consciousness in physical systems. The amount of consciousness in a system is determined by the extent of non-separability and the number of degrees of freedom involved. Non-interacting and feedforward systems h... |
2001.11125 | Alex Stivala | Alex Stivala and Alessandro Lomi | Testing biological network motif significance with exponential random
graph models | Major revision after reviewer comments. Includes supplementary tables
and figures | Applied Network Science (2021) 6:91 | 10.1007/s41109-021-00434-y | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Analysis of the structure of biological networks often uses statistical tests
to establish the over-representation of motifs, which are thought to be
important building blocks of such networks, related to their biological
functions. However, there is disagreement as to the statistical significance of
these motifs, an... | [
{
"created": "Wed, 29 Jan 2020 23:05:26 GMT",
"version": "v1"
},
{
"created": "Thu, 6 Aug 2020 05:27:08 GMT",
"version": "v2"
},
{
"created": "Sun, 28 Feb 2021 23:36:56 GMT",
"version": "v3"
},
{
"created": "Wed, 9 Jun 2021 06:11:06 GMT",
"version": "v4"
},
{
"cre... | 2021-11-24 | [
[
"Stivala",
"Alex",
""
],
[
"Lomi",
"Alessandro",
""
]
] | Analysis of the structure of biological networks often uses statistical tests to establish the over-representation of motifs, which are thought to be important building blocks of such networks, related to their biological functions. However, there is disagreement as to the statistical significance of these motifs, and ... |
q-bio/0401036 | Axel Brandenburg | A. Brandenburg, A. C. Andersen, S. H\"ofner, and M. Nilsson (all at
NORDITA) | Homochiral growth through enantiomeric cross-inhibition | 20 pages, 6 figures, Orig. Life Evol. Biosph. (accepted) | Orig. Life Evol. Biosph. 35, 225-241 (2005) | 10.1007/s11084-005-0656-9 | NORDITA-2004-5 | q-bio.BM astro-ph physics.bio-ph | null | The stability and conservation properties of a recently proposed
polymerization model are studied. The achiral (racemic) solution is linearly
unstable once the relevant control parameter (here the fidelity of the
catalyst) exceeds a critical value. The growth rate is calculated for different
fidelity parameters and c... | [
{
"created": "Tue, 27 Jan 2004 15:12:24 GMT",
"version": "v1"
},
{
"created": "Mon, 26 Apr 2004 19:08:20 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Brandenburg",
"A.",
"",
"all at\n NORDITA"
],
[
"Andersen",
"A. C.",
"",
"all at\n NORDITA"
],
[
"Höfner",
"S.",
"",
"all at\n NORDITA"
],
[
"Nilsson",
"M.",
"",
"all at\n NORDITA"
]
] | The stability and conservation properties of a recently proposed polymerization model are studied. The achiral (racemic) solution is linearly unstable once the relevant control parameter (here the fidelity of the catalyst) exceeds a critical value. The growth rate is calculated for different fidelity parameters and cro... |
2211.03208 | Christoph Gorgulla | Christoph Gorgulla | Recent Developments in Structure-Based Virtual Screening Approaches | 22 pages, 2 figures | null | null | null | q-bio.BM cs.LG physics.bio-ph physics.chem-ph q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Drug development is a wide scientific field that faces many challenges these
days. Among them are extremely high development costs, long development times,
as well as a low number of new drugs that are approved each year. To solve
these problems, new and innovate technologies are needed that make the drug
discovery p... | [
{
"created": "Sun, 6 Nov 2022 19:28:25 GMT",
"version": "v1"
}
] | 2022-11-08 | [
[
"Gorgulla",
"Christoph",
""
]
] | Drug development is a wide scientific field that faces many challenges these days. Among them are extremely high development costs, long development times, as well as a low number of new drugs that are approved each year. To solve these problems, new and innovate technologies are needed that make the drug discovery pro... |
1402.6752 | Alexander Goltsev | M. A. Lopes, K.-E. Lee, A. V. Goltsev, and J. F. F. Mendes | Noise-enhanced nonlinear response and the role of modular structure for
signal detection in neuronal networks | 10 pages, 8 figures | Phys Rev E 90, 052709 (2014) | 10.1103/PhysRevE.90.052709 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We find that sensory noise delivered together with a weak periodic signal not
only enhances nonlinear response of neuronal networks, but also improves the
synchronization of the response to the signal. We reveal this phenomenon in
neuronal networks that are in a dynamical state near a saddle-node bifurcation
correspo... | [
{
"created": "Thu, 27 Feb 2014 00:42:07 GMT",
"version": "v1"
}
] | 2015-08-25 | [
[
"Lopes",
"M. A.",
""
],
[
"Lee",
"K. -E.",
""
],
[
"Goltsev",
"A. V.",
""
],
[
"Mendes",
"J. F. F.",
""
]
] | We find that sensory noise delivered together with a weak periodic signal not only enhances nonlinear response of neuronal networks, but also improves the synchronization of the response to the signal. We reveal this phenomenon in neuronal networks that are in a dynamical state near a saddle-node bifurcation correspond... |
2302.00960 | Abhishek Senapati | Biplab Maity, Swarnendu Banerjee, Abhishek Senapati, Joydev
Chattopadhyay | Quantifying optimal resource allocation strategies for controlling
epidemics | 44 Pages, 10 Figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Frequent emergence of communicable diseases has been a major concern
worldwide. Lack of sufficient resources to mitigate the disease-burden makes
the situation even more challenging for lower-income countries. Hence, strategy
development towards disease eradication and optimal management of the social
and economic bu... | [
{
"created": "Thu, 2 Feb 2023 09:01:58 GMT",
"version": "v1"
}
] | 2023-02-03 | [
[
"Maity",
"Biplab",
""
],
[
"Banerjee",
"Swarnendu",
""
],
[
"Senapati",
"Abhishek",
""
],
[
"Chattopadhyay",
"Joydev",
""
]
] | Frequent emergence of communicable diseases has been a major concern worldwide. Lack of sufficient resources to mitigate the disease-burden makes the situation even more challenging for lower-income countries. Hence, strategy development towards disease eradication and optimal management of the social and economic burd... |
2006.09928 | Biao Cai | Biao Cai, Gemeng Zhang, Aiying Zhang, Li Xiao, Wenxing Hu, Julia M.
Stephen, Tony W. Wilson, Vince D. Calhoun, Yu-Ping Wang | Functional connectome fingerprinting: Identifying individuals and
predicting cognitive function via deep learning | null | null | null | null | q-bio.NC eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The dynamic characteristics of functional network connectivity have been
widely acknowledged and studied. Both shared and unique information has been
shown to be present in the connectomes. However, very little has been known
about whether and how this common pattern can predict the individual
variability of the brai... | [
{
"created": "Wed, 17 Jun 2020 15:15:35 GMT",
"version": "v1"
}
] | 2020-06-18 | [
[
"Cai",
"Biao",
""
],
[
"Zhang",
"Gemeng",
""
],
[
"Zhang",
"Aiying",
""
],
[
"Xiao",
"Li",
""
],
[
"Hu",
"Wenxing",
""
],
[
"Stephen",
"Julia M.",
""
],
[
"Wilson",
"Tony W.",
""
],
[
"Calhoun",
... | The dynamic characteristics of functional network connectivity have been widely acknowledged and studied. Both shared and unique information has been shown to be present in the connectomes. However, very little has been known about whether and how this common pattern can predict the individual variability of the brain,... |
1308.5257 | James Fowler | Nicholas A. Christakis and James H. Fowler | Friendship and Natural Selection | null | PNAS July 22, 2014 vol. 111 no. Supplement 3 10796-10801 | 10.1073/pnas.1400825111 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | More than any other species, humans form social ties to individuals who are
neither kin nor mates, and these ties tend to be with similar people. Here, we
show that this similarity extends to genotypes. Across the whole genome,
friends' genotypes at the SNP level tend to be positively correlated
(homophilic); however... | [
{
"created": "Fri, 23 Aug 2013 22:28:34 GMT",
"version": "v1"
},
{
"created": "Thu, 4 Dec 2014 16:33:13 GMT",
"version": "v2"
}
] | 2014-12-05 | [
[
"Christakis",
"Nicholas A.",
""
],
[
"Fowler",
"James H.",
""
]
] | More than any other species, humans form social ties to individuals who are neither kin nor mates, and these ties tend to be with similar people. Here, we show that this similarity extends to genotypes. Across the whole genome, friends' genotypes at the SNP level tend to be positively correlated (homophilic); however, ... |
2310.18278 | Cecilia Clementi | Nicholas E. Charron, Felix Musil, Andrea Guljas, Yaoyi Chen, Klara
Bonneau, Aldo S. Pasos-Trejo, Jacopo Venturin, Daria Gusew, Iryna
Zaporozhets, Andreas Kr\"amer, Clark Templeton, Atharva Kelkar, Aleksander E.
P. Durumeric, Simon Olsson, Adri\`a P\'erez, Maciej Majewski, Brooke E.
Husic, Ankit Patel, Gianni De... | Navigating protein landscapes with a machine-learned transferable
coarse-grained model | null | null | null | null | q-bio.BM physics.bio-ph physics.chem-ph stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The most popular and universally predictive protein simulation models employ
all-atom molecular dynamics (MD), but they come at extreme computational cost.
The development of a universal, computationally efficient coarse-grained (CG)
model with similar prediction performance has been a long-standing challenge.
By com... | [
{
"created": "Fri, 27 Oct 2023 17:10:23 GMT",
"version": "v1"
}
] | 2023-10-30 | [
[
"Charron",
"Nicholas E.",
""
],
[
"Musil",
"Felix",
""
],
[
"Guljas",
"Andrea",
""
],
[
"Chen",
"Yaoyi",
""
],
[
"Bonneau",
"Klara",
""
],
[
"Pasos-Trejo",
"Aldo S.",
""
],
[
"Venturin",
"Jacopo",
""
],
... | The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model with similar prediction performance has been a long-standing challenge. By combi... |
1810.12758 | Cheng Qian | Cheng Qian, Nicholas D. Sidiropoulos, Magda Amiridi, Amin Emad | From Gene Expression to Drug Response: A Collaborative Filtering
Approach | null | null | null | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Predicting the response of cancer cells to drugs is an important problem in
pharmacogenomics. Recent efforts in generation of large scale datasets
profiling gene expression and drug sensitivity in cell lines have provided a
unique opportunity to study this problem. However, one major challenge is the
small number of ... | [
{
"created": "Mon, 29 Oct 2018 13:25:35 GMT",
"version": "v1"
},
{
"created": "Wed, 31 Oct 2018 03:05:47 GMT",
"version": "v2"
}
] | 2018-11-01 | [
[
"Qian",
"Cheng",
""
],
[
"Sidiropoulos",
"Nicholas D.",
""
],
[
"Amiridi",
"Magda",
""
],
[
"Emad",
"Amin",
""
]
] | Predicting the response of cancer cells to drugs is an important problem in pharmacogenomics. Recent efforts in generation of large scale datasets profiling gene expression and drug sensitivity in cell lines have provided a unique opportunity to study this problem. However, one major challenge is the small number of sa... |
1208.0520 | Simon Powers | Simon T. Powers and Christopher Heys and Richard A. Watson | How to measure group selection in real-world populations | pp. 672-679 in Proceedings of the Eleventh European Conference on the
Synthesis and Simulation of Living Systems (Advances in Artificial Life, ECAL
2011). Edited by Tom Lenaerts, Mario Giacobini, Hugues Bersini, Paul
Bourgine, Marco Dorigo and Ren\'e Doursat. MIT Press (2011).
http://mitpress.mit.edu/catalog/it... | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multilevel selection and the evolution of cooperation are fundamental to the
formation of higher-level organisation and the evolution of biocomplexity, but
such notions are controversial and poorly understood in natural populations.
The theoretic principles of group selection are well developed in idealised
models wh... | [
{
"created": "Thu, 2 Aug 2012 15:48:18 GMT",
"version": "v1"
}
] | 2012-08-03 | [
[
"Powers",
"Simon T.",
""
],
[
"Heys",
"Christopher",
""
],
[
"Watson",
"Richard A.",
""
]
] | Multilevel selection and the evolution of cooperation are fundamental to the formation of higher-level organisation and the evolution of biocomplexity, but such notions are controversial and poorly understood in natural populations. The theoretic principles of group selection are well developed in idealised models wher... |
1010.5602 | Pedro Marijuan | Pedro C. Marijuan and Jorge Navarro | The Bonds of Laughter: A Multidisciplinary Inquiry into the Information
Processes of Human Laughter | 14 pages, 5 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A new core hypothesis on laughter is presented. It has been built by putting
together ideas from several disciplines: neurodynamics, evolutionary
neurobiology, paleoanthropology, social networks, and communication studies.
The hypothesis contributes to ascertain the evolutionary origins of human
laughter in connectio... | [
{
"created": "Wed, 27 Oct 2010 08:29:30 GMT",
"version": "v1"
}
] | 2010-10-28 | [
[
"Marijuan",
"Pedro C.",
""
],
[
"Navarro",
"Jorge",
""
]
] | A new core hypothesis on laughter is presented. It has been built by putting together ideas from several disciplines: neurodynamics, evolutionary neurobiology, paleoanthropology, social networks, and communication studies. The hypothesis contributes to ascertain the evolutionary origins of human laughter in connection ... |
1008.0431 | Carsten Wiuf | Elisenda Feliu, Michael Knudsen, Lars N. Andersen and Carsten Wiuf | An Algebraic Approach to Signaling Cascades with n Layers | null | null | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Posttranslational modification of proteins is key in transmission of signals
in cells. Many signaling pathways contain several layers of modification cycles
that mediate and change the signal through the pathway. Here, we study a simple
signaling cascade consisting of n layers of modification cycles, such that the
mo... | [
{
"created": "Tue, 3 Aug 2010 00:37:02 GMT",
"version": "v1"
},
{
"created": "Sat, 18 Dec 2010 18:31:23 GMT",
"version": "v2"
}
] | 2010-12-21 | [
[
"Feliu",
"Elisenda",
""
],
[
"Knudsen",
"Michael",
""
],
[
"Andersen",
"Lars N.",
""
],
[
"Wiuf",
"Carsten",
""
]
] | Posttranslational modification of proteins is key in transmission of signals in cells. Many signaling pathways contain several layers of modification cycles that mediate and change the signal through the pathway. Here, we study a simple signaling cascade consisting of n layers of modification cycles, such that the modi... |
1302.4051 | Alexander E. Hramov | Evgenia Sitnikova, Alexander E. Hramov, Alexey A. Ovchinnikov, Alexey
A. Koronovskii | On-off intermittency of thalamo-cortical oscillations in the
electroencephalogram of rats with genetic predisposition to absence epilepsy | 15 pages, 5 figures | Brain research. 1436 (2012) 147-156 | 10.1016/j.brainres.2011.12.006 | null | q-bio.NC nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spike-wave discharges (SWD) are electroencephalographic hallmarks of absence
epilepsy. SWD are known to originate from thalamo-cortical neuronal network
that normally produce sleep spindle oscillations. Although both sleep spindles
and SWD are considered as thalamo-cortical oscillations, functional
relationship betwe... | [
{
"created": "Sun, 17 Feb 2013 10:17:58 GMT",
"version": "v1"
}
] | 2013-02-19 | [
[
"Sitnikova",
"Evgenia",
""
],
[
"Hramov",
"Alexander E.",
""
],
[
"Ovchinnikov",
"Alexey A.",
""
],
[
"Koronovskii",
"Alexey A.",
""
]
] | Spike-wave discharges (SWD) are electroencephalographic hallmarks of absence epilepsy. SWD are known to originate from thalamo-cortical neuronal network that normally produce sleep spindle oscillations. Although both sleep spindles and SWD are considered as thalamo-cortical oscillations, functional relationship between... |
1708.03593 | Hugo Fort | Hugo Fort | Quantitative predictions from competition theory with incomplete
information on model parameters tested against experiments across diverse
taxa | 15 pages, 2 figures, one table, two boxes | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We derive an analytical approximation for making quantitative predictions for
ecological communities as a function of the mean intensity of the
inter-specific competition and the species richness. This method, with only a
fraction of the model parameters (carrying capacities and competition
coefficients), is able to ... | [
{
"created": "Fri, 11 Aug 2017 16:07:59 GMT",
"version": "v1"
}
] | 2017-08-14 | [
[
"Fort",
"Hugo",
""
]
] | We derive an analytical approximation for making quantitative predictions for ecological communities as a function of the mean intensity of the inter-specific competition and the species richness. This method, with only a fraction of the model parameters (carrying capacities and competition coefficients), is able to pr... |
q-bio/0611026 | Sergei Maslov | Sergei Maslov, Kim Sneppen, Iaroslav Ispolatov | Propagation of fluctuations in interaction networks governed by the law
of mass action | 4 pages; 2 figures | New J. Phys. v.9, 273 (2007). | 10.1088/1367-2630/9/8/273 | null | q-bio.MN cond-mat.stat-mech physics.bio-ph q-bio.GN | null | Using an example of physical interactions between proteins, we study how
perturbations propagate in interconnected networks whose equilibrium state is
governed by the law of mass action. We introduce a comprehensive matrix
formalism which predicts the response of this equilibrium to small changes in
total concentrati... | [
{
"created": "Tue, 7 Nov 2006 23:09:26 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Maslov",
"Sergei",
""
],
[
"Sneppen",
"Kim",
""
],
[
"Ispolatov",
"Iaroslav",
""
]
] | Using an example of physical interactions between proteins, we study how perturbations propagate in interconnected networks whose equilibrium state is governed by the law of mass action. We introduce a comprehensive matrix formalism which predicts the response of this equilibrium to small changes in total concentration... |
1901.07274 | Andras Jakab | Eliane Meuwly, Maria Feldmann, Walter Knirsch, Michael von Rhein,
Kelly Payette, Hitendu Dave, Ruth Tuura, Raimund Kottke, Cornelia Hagmann,
Beatrice Latal, Andras Jakab | Postoperative brain volumes are associated with one-year
neurodevelopmental outcome in children with severe congenital heart disease | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Children with congenital heart disease (CHD) remain at risk for
neurodevelopmental impairment despite improved peri- and intraoperative care.
Our prospective cohort study aimed to determine the relationship between
perioperative brain volumes and neurodevelopmental outcome in neonates with
severe CHD. Pre- and postop... | [
{
"created": "Tue, 22 Jan 2019 11:55:59 GMT",
"version": "v1"
}
] | 2019-01-23 | [
[
"Meuwly",
"Eliane",
""
],
[
"Feldmann",
"Maria",
""
],
[
"Knirsch",
"Walter",
""
],
[
"von Rhein",
"Michael",
""
],
[
"Payette",
"Kelly",
""
],
[
"Dave",
"Hitendu",
""
],
[
"Tuura",
"Ruth",
""
],
[
... | Children with congenital heart disease (CHD) remain at risk for neurodevelopmental impairment despite improved peri- and intraoperative care. Our prospective cohort study aimed to determine the relationship between perioperative brain volumes and neurodevelopmental outcome in neonates with severe CHD. Pre- and postoper... |
1805.01552 | Don Krieger | Don Krieger, Paul Shepard, David O. Okonkwo | Normative atlases of neuroelectric brain activity and connectivity from
a large human cohort | 37 pages, 13 figures, 13 tables | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Magnetoencephalographic (MEG) recordings from a large normative cohort (n =
619) were processed to extract measures of regional neuroelectric activity. The
overall objective of the effort was to use these measures to identify normative
human neuroelectric brain function. The aims were (a) to identify and measure
the ... | [
{
"created": "Thu, 3 May 2018 21:47:09 GMT",
"version": "v1"
},
{
"created": "Thu, 16 Aug 2018 14:15:41 GMT",
"version": "v2"
},
{
"created": "Sat, 17 Nov 2018 04:03:38 GMT",
"version": "v3"
}
] | 2018-11-20 | [
[
"Krieger",
"Don",
""
],
[
"Shepard",
"Paul",
""
],
[
"Okonkwo",
"David O.",
""
]
] | Magnetoencephalographic (MEG) recordings from a large normative cohort (n = 619) were processed to extract measures of regional neuroelectric activity. The overall objective of the effort was to use these measures to identify normative human neuroelectric brain function. The aims were (a) to identify and measure the va... |
q-bio/0503041 | Luciano da Fontoura Costa | Luciano da Fontoura Costa | Morphological complex networks: Can individual morphology determine the
general connectivity and dynamics of networks? | 17 pages, 2 figures. Presented at the COSIN final meeting, Salou,
Spain, March 2005 | null | null | null | q-bio.MN cond-mat.dis-nn | null | This article discusses how the individual morphological properties of basic
objects (e.g. neurons, molecules and aggregates), jointly with their particular
spatial distribution, can determine the connectivity and dynamics of systems
composed by those objects. This problem is characterized as a particular case
of the ... | [
{
"created": "Thu, 31 Mar 2005 18:17:56 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Costa",
"Luciano da Fontoura",
""
]
] | This article discusses how the individual morphological properties of basic objects (e.g. neurons, molecules and aggregates), jointly with their particular spatial distribution, can determine the connectivity and dynamics of systems composed by those objects. This problem is characterized as a particular case of the mo... |
q-bio/0505012 | Ines Samengo | Marcos A. Trevisan, Sebastian Bouzat, Ines Samengo, Gabriel B. Mindlin | Dynamics of learning in coupled oscillators tutored with delayed
reinforcements | 10 pages, 6 figures, to be published in Phys. Rev. E | null | 10.1103/PhysRevE.72.011907 | null | q-bio.NC | null | In this work we analyze the solutions of a simple system of coupled phase
oscillators in which the connectivity is learned dynamically. The model is
inspired in the process of learning of birdsong by oscine birds. An oscillator
acts as the generator of a basic rhythm, and drives slave oscillators which are
responsibl... | [
{
"created": "Thu, 5 May 2005 14:25:26 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Trevisan",
"Marcos A.",
""
],
[
"Bouzat",
"Sebastian",
""
],
[
"Samengo",
"Ines",
""
],
[
"Mindlin",
"Gabriel B.",
""
]
] | In this work we analyze the solutions of a simple system of coupled phase oscillators in which the connectivity is learned dynamically. The model is inspired in the process of learning of birdsong by oscine birds. An oscillator acts as the generator of a basic rhythm, and drives slave oscillators which are responsible ... |
1510.01420 | Debora Marks | Caleb Weinreb, Adam J. Riesselman, John B. Ingraham, Torsten Gross,
Chris Sander, Debora S. Marks | 3D RNA and functional interactions from evolutionary couplings | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences
far outpaces research on their structure and functional interactions. We mine
the evolutionary sequence record to derive precise information about function
and structure of RNAs and RNA-protein complexes. As in protein structure
prediction, w... | [
{
"created": "Tue, 6 Oct 2015 03:43:41 GMT",
"version": "v1"
},
{
"created": "Wed, 14 Oct 2015 21:30:24 GMT",
"version": "v2"
},
{
"created": "Thu, 21 Apr 2016 18:27:30 GMT",
"version": "v3"
}
] | 2016-04-22 | [
[
"Weinreb",
"Caleb",
""
],
[
"Riesselman",
"Adam J.",
""
],
[
"Ingraham",
"John B.",
""
],
[
"Gross",
"Torsten",
""
],
[
"Sander",
"Chris",
""
],
[
"Marks",
"Debora S.",
""
]
] | Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and structure of RNAs and RNA-protein complexes. As in protein structure prediction, we ... |
1708.06579 | Mihalis Kavousanakis | Panagiotis Chrysinas, Michail E. Kavousanakis, Andreas G. Boudouvis | Effect of cell heterogeneity on isogenic populations with the synthetic
genetic toggle switch network: bifurcation analysis of two-dimensional Cell
Population Balance Models | null | null | null | null | q-bio.PE q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The dynamics of gene regulatory networks are often modeled with the
assumption of cellular homogeneity. However, this assumption contradicts the
plethora of experimental results in a variety of systems, which designates that
cell populations are heterogeneous systems in the sense that properties such as
size, shape, ... | [
{
"created": "Tue, 22 Aug 2017 12:22:58 GMT",
"version": "v1"
}
] | 2017-08-23 | [
[
"Chrysinas",
"Panagiotis",
""
],
[
"Kavousanakis",
"Michail E.",
""
],
[
"Boudouvis",
"Andreas G.",
""
]
] | The dynamics of gene regulatory networks are often modeled with the assumption of cellular homogeneity. However, this assumption contradicts the plethora of experimental results in a variety of systems, which designates that cell populations are heterogeneous systems in the sense that properties such as size, shape, an... |
2009.11531 | Ana Carpio | A. Carpio, A. Sim\'on, L.F. Villa | Clustering methods and Bayesian inference for the analysis of the
evolution of immune disorders | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Choosing appropriate hyperparameters for unsupervised clustering algorithms
in an optimal way depending on the problem under study is a long standing
challenge, which we tackle while adapting clustering algorithms for immune
disorder diagnoses. We compare the potential ability of unsupervised clustering
algorithms to... | [
{
"created": "Thu, 24 Sep 2020 07:43:14 GMT",
"version": "v1"
}
] | 2020-09-25 | [
[
"Carpio",
"A.",
""
],
[
"Simón",
"A.",
""
],
[
"Villa",
"L. F.",
""
]
] | Choosing appropriate hyperparameters for unsupervised clustering algorithms in an optimal way depending on the problem under study is a long standing challenge, which we tackle while adapting clustering algorithms for immune disorder diagnoses. We compare the potential ability of unsupervised clustering algorithms to d... |
2202.11635 | Tom Burkart | Tom Burkart, Jan Willeke, and Erwin Frey | Periodic temporal environmental variations induce coexistence in
resource competition models | 21 pages, 10 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Natural ecosystems, in particular on the microbial scale, are inhabited by a
large number of species. The population size of each species is affected by
interactions of individuals with each other and by spatial and temporal changes
in environmental conditions, such as resource abundance. Here, we use a generic
popul... | [
{
"created": "Wed, 23 Feb 2022 17:10:03 GMT",
"version": "v1"
},
{
"created": "Fri, 25 Feb 2022 10:03:53 GMT",
"version": "v2"
},
{
"created": "Thu, 22 Jun 2023 10:28:46 GMT",
"version": "v3"
}
] | 2023-06-23 | [
[
"Burkart",
"Tom",
""
],
[
"Willeke",
"Jan",
""
],
[
"Frey",
"Erwin",
""
]
] | Natural ecosystems, in particular on the microbial scale, are inhabited by a large number of species. The population size of each species is affected by interactions of individuals with each other and by spatial and temporal changes in environmental conditions, such as resource abundance. Here, we use a generic populat... |
1710.02387 | Chrystopher L. Nehaniv | Chrystopher L. Nehaniv and Elena Antonova | Simulating and Reconstructing Neurodynamics with Epsilon-Automata
Applied to Electroencephalography (EEG) Microstate Sequences | null | null | null | null | q-bio.NC cs.FL nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce new techniques to the analysis of neural spatiotemporal dynamics
via applying $\epsilon$-machine reconstruction to electroencephalography (EEG)
microstate sequences. Microstates are short duration quasi-stable states of the
dynamically changing electrical field topographies recorded via an array of
elect... | [
{
"created": "Fri, 29 Sep 2017 09:19:14 GMT",
"version": "v1"
}
] | 2017-10-09 | [
[
"Nehaniv",
"Chrystopher L.",
""
],
[
"Antonova",
"Elena",
""
]
] | We introduce new techniques to the analysis of neural spatiotemporal dynamics via applying $\epsilon$-machine reconstruction to electroencephalography (EEG) microstate sequences. Microstates are short duration quasi-stable states of the dynamically changing electrical field topographies recorded via an array of electro... |
1906.09622 | Anne Churchland | Simon Musall, Anne Urai, David Sussillo, Anne Churchland | Harnessing behavioral diversity to understand circuits for cognition | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | With the increasing acquisition of large-scale neural recordings comes the
challenge of inferring the computations they perform and understanding how
these give rise to behavior. Here, we review emerging conceptual and
technological advances that begin to address this challenge, garnering insights
from both biologica... | [
{
"created": "Sun, 23 Jun 2019 18:14:37 GMT",
"version": "v1"
}
] | 2019-06-25 | [
[
"Musall",
"Simon",
""
],
[
"Urai",
"Anne",
""
],
[
"Sussillo",
"David",
""
],
[
"Churchland",
"Anne",
""
]
] | With the increasing acquisition of large-scale neural recordings comes the challenge of inferring the computations they perform and understanding how these give rise to behavior. Here, we review emerging conceptual and technological advances that begin to address this challenge, garnering insights from both biological ... |
2208.14996 | Thomas Fink | Thomas M. A. Fink | Regulatory motifs: structural and functional building blocks of genetic
computation | null | null | null | null | q-bio.MN cond-mat.stat-mech | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Developing and maintaining life requires a lot of computation. This is done
by gene regulatory networks. But we have little understanding of how this
computation is organized. I show that there is a direct correspondence between
the structural and functional building blocks of regulatory networks, which I
call regula... | [
{
"created": "Wed, 31 Aug 2022 17:51:18 GMT",
"version": "v1"
}
] | 2022-09-01 | [
[
"Fink",
"Thomas M. A.",
""
]
] | Developing and maintaining life requires a lot of computation. This is done by gene regulatory networks. But we have little understanding of how this computation is organized. I show that there is a direct correspondence between the structural and functional building blocks of regulatory networks, which I call regulato... |
2107.06025 | Manh Hong Duong | Manh Hong Duong and The Anh Han | Statistics of the number of equilibria in random social dilemma
evolutionary games with mutation | 17 pages | null | 10.1140/epjb/s10051-021-00181-0 | null | q-bio.PE math.DS math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we study analytically the statistics of the number of
equilibria in pairwise social dilemma evolutionary games with mutation where a
game's payoff entries are random variables. Using the replicator-mutator
equations, we provide explicit formulas for the probability distributions of
the number of equili... | [
{
"created": "Tue, 13 Jul 2021 12:23:30 GMT",
"version": "v1"
}
] | 2021-09-15 | [
[
"Duong",
"Manh Hong",
""
],
[
"Han",
"The Anh",
""
]
] | In this paper, we study analytically the statistics of the number of equilibria in pairwise social dilemma evolutionary games with mutation where a game's payoff entries are random variables. Using the replicator-mutator equations, we provide explicit formulas for the probability distributions of the number of equilibr... |
1807.03174 | Tito Arecchi | F. T. Arecchi | A quantum uncertainty entails entangled linguistic sequences | 14 pages. arXiv admin note: substantial text overlap with
arXiv:1506.00610 | null | null | null | q-bio.NC quant-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Synchronization of finite spike sequences is the way two brain regions
compare their content and extract the most suitable sequence. This is the core
of the linguistic comparison between a word and a previous one retrieved by
memory. Classifying the information content of neural spike trains, an
uncertainty relation ... | [
{
"created": "Fri, 6 Jul 2018 09:04:59 GMT",
"version": "v1"
}
] | 2018-07-10 | [
[
"Arecchi",
"F. T.",
""
]
] | Synchronization of finite spike sequences is the way two brain regions compare their content and extract the most suitable sequence. This is the core of the linguistic comparison between a word and a previous one retrieved by memory. Classifying the information content of neural spike trains, an uncertainty relation em... |
1504.00165 | Andy Chung | Stephanie Portet and Anotida Madzvamuse and Andy Chung and Rudolf E.
Leube and Reinhard Windoffer | Keratin Dynamics: Modeling the Interplay between Turnover and Transport | 27 pages, 11 Figures | null | 10.1371/journal.pone.0121090 | null | q-bio.SC q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Keratin are among the most abundant proteins in epithelial cells. Functions
of the keratin network in cells are shaped by their dynamical organization.
Using a collection of experimentally-driven mathematical models, different
hypotheses for the turnover and transport of the keratin material in epithelial
cells are t... | [
{
"created": "Wed, 1 Apr 2015 09:54:36 GMT",
"version": "v1"
}
] | 2015-08-19 | [
[
"Portet",
"Stephanie",
""
],
[
"Madzvamuse",
"Anotida",
""
],
[
"Chung",
"Andy",
""
],
[
"Leube",
"Rudolf E.",
""
],
[
"Windoffer",
"Reinhard",
""
]
] | Keratin are among the most abundant proteins in epithelial cells. Functions of the keratin network in cells are shaped by their dynamical organization. Using a collection of experimentally-driven mathematical models, different hypotheses for the turnover and transport of the keratin material in epithelial cells are tes... |
0906.4875 | Mike Steel Prof. | Mike Steel and Michael J. Sanderson | Characterizing phylogenetically decisive taxon coverage | 6 pages, 1 figure | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Increasingly, biologists are constructing evolutionary trees on large numbers
of overlapping sets of taxa, and then combining them into a `supertree' that
classifies all the taxa. In this paper, we ask how much coverage of the total
set of taxa is required by these subsets in order to ensure we have enough
informatio... | [
{
"created": "Fri, 26 Jun 2009 08:39:35 GMT",
"version": "v1"
}
] | 2009-06-29 | [
[
"Steel",
"Mike",
""
],
[
"Sanderson",
"Michael J.",
""
]
] | Increasingly, biologists are constructing evolutionary trees on large numbers of overlapping sets of taxa, and then combining them into a `supertree' that classifies all the taxa. In this paper, we ask how much coverage of the total set of taxa is required by these subsets in order to ensure we have enough information ... |
2110.12927 | Sitabhra Sinha | Chandrashekar Kuyyamudi, Shakti N. Menon and Sitabhra Sinha | Precision of morphogen-driven tissue patterning during development is
enhanced through contact-mediated cellular interactions | 7 pages, 3 figures + 4 pages Supplementary Information | Phys. Rev. E 107, 024407 (2023) | 10.1103/PhysRevE.107.024407 | null | q-bio.TO nlin.PS physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Embryonic development involves pattern formation characterized by the
emergence of spatially localized domains characterized by distinct cell fates
resulting from differential gene expression. The boundaries demarcating these
domains are precise and consistent within a species despite stochastic
fluctuations in the m... | [
{
"created": "Mon, 25 Oct 2021 13:04:03 GMT",
"version": "v1"
}
] | 2024-06-11 | [
[
"Kuyyamudi",
"Chandrashekar",
""
],
[
"Menon",
"Shakti N.",
""
],
[
"Sinha",
"Sitabhra",
""
]
] | Embryonic development involves pattern formation characterized by the emergence of spatially localized domains characterized by distinct cell fates resulting from differential gene expression. The boundaries demarcating these domains are precise and consistent within a species despite stochastic fluctuations in the mor... |
2306.00046 | Helen Moore | Raja Al-Bahou, Julia Bruner, Helen Moore, Ali Zarrinpar | Quantitative Methods for Optimizing Patient Outcomes in Liver
Transplantation | 2 figures, including a graphical abstract | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Liver transplantation continues to be the gold standard for treating patients
with end-stage liver diseases. However, despite the huge success of liver
transplantation in improving patient outcomes, long term graft survival
continues to be a major problem. The current clinical practice in the
management of liver tran... | [
{
"created": "Wed, 31 May 2023 16:45:44 GMT",
"version": "v1"
}
] | 2023-06-02 | [
[
"Al-Bahou",
"Raja",
""
],
[
"Bruner",
"Julia",
""
],
[
"Moore",
"Helen",
""
],
[
"Zarrinpar",
"Ali",
""
]
] | Liver transplantation continues to be the gold standard for treating patients with end-stage liver diseases. However, despite the huge success of liver transplantation in improving patient outcomes, long term graft survival continues to be a major problem. The current clinical practice in the management of liver transp... |
1802.04532 | Luca Telesca | Luca Telesca, Kati Michalek, Trystan Sanders, Lloyd S. Peck, Jakob
Thyrring, Elizabeth M. Harper | Blue mussel shell shape plasticity and natural environments: a
quantitative approach | null | Scientific Reports 8 (2018) 2865 | 10.1038/s41598-018-20122-9 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Shape variability represents an important direct response of organisms to
selective environments. Here, we use a combination of geometric morphometrics
and generalised additive mixed models (GAMMs) to identify spatial patterns of
natural shell shape variation in the North Atlantic and Arctic blue mussels,
Mytilus edu... | [
{
"created": "Tue, 13 Feb 2018 10:06:11 GMT",
"version": "v1"
}
] | 2018-02-14 | [
[
"Telesca",
"Luca",
""
],
[
"Michalek",
"Kati",
""
],
[
"Sanders",
"Trystan",
""
],
[
"Peck",
"Lloyd S.",
""
],
[
"Thyrring",
"Jakob",
""
],
[
"Harper",
"Elizabeth M.",
""
]
] | Shape variability represents an important direct response of organisms to selective environments. Here, we use a combination of geometric morphometrics and generalised additive mixed models (GAMMs) to identify spatial patterns of natural shell shape variation in the North Atlantic and Arctic blue mussels, Mytilus eduli... |
2212.13617 | Li Shen | Li Shen, Hongsong Feng, Yuchi Qiu, Guo-Wei Wei | SVSBI: Sequence-based virtual screening of biomolecular interactions | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Virtual screening (VS) is an essential technique for understanding
biomolecular interactions, particularly, drug design and discovery. The
best-performing VS models depend vitally on three-dimensional (3D) structures,
which are not available in general but can be obtained from molecular docking.
However, current dock... | [
{
"created": "Tue, 27 Dec 2022 21:18:47 GMT",
"version": "v1"
}
] | 2022-12-29 | [
[
"Shen",
"Li",
""
],
[
"Feng",
"Hongsong",
""
],
[
"Qiu",
"Yuchi",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Virtual screening (VS) is an essential technique for understanding biomolecular interactions, particularly, drug design and discovery. The best-performing VS models depend vitally on three-dimensional (3D) structures, which are not available in general but can be obtained from molecular docking. However, current dockin... |
q-bio/0406031 | Guido Tiana | R. A. Broglia and G. Tiana | Simple models of protein folding and of non--conventional drug design | null | null | 10.1088/0953-8984/16/6/R02 | null | q-bio.BM | null | While all the information required for the folding of a protein is contained
in its amino acid sequence, one has not yet learned how to extract this
information to predict the three--dimensional, biologically active, native
conformation of a protein whose sequence is known. Using insight obtained from
simple model si... | [
{
"created": "Tue, 15 Jun 2004 12:26:48 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Broglia",
"R. A.",
""
],
[
"Tiana",
"G.",
""
]
] | While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of a protein whose sequence is known. Using insight obtained from simple model simu... |
1109.5633 | Steven Frank | Steven A. Frank | Natural selection. II. Developmental variability and evolutionary rate | null | Journal of Evolutionary Biology 24:2310-2320 (2011) | 10.1111/j.1420-9101.2011.02373.x | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In classical evolutionary theory, genetic variation provides the source of
heritable phenotypic variation on which natural selection acts. Against this
classical view, several theories have emphasized that developmental variability
and learning enhance nonheritable phenotypic variation, which in turn can
accelerate e... | [
{
"created": "Mon, 26 Sep 2011 16:47:29 GMT",
"version": "v1"
}
] | 2011-11-08 | [
[
"Frank",
"Steven A.",
""
]
] | In classical evolutionary theory, genetic variation provides the source of heritable phenotypic variation on which natural selection acts. Against this classical view, several theories have emphasized that developmental variability and learning enhance nonheritable phenotypic variation, which in turn can accelerate evo... |
1803.00871 | Paolo Olivero | L. Guarina, C. Calorio, D. Gavello, E. Moreva, P. Traina, A. Battiato,
S. Ditalia Tchernij, J. Forneris, M. Gai, F. Picollo, P. Olivero, M.
Genovese, E. Carbone, A. Marcantoni, V. Carabelli | Nanodiamonds-induced effects on neuronal firing of mouse hippocampal
microcircuits | 34 pages, 9 figures | Scientific Reports 8, 2221 (2018) | 10.1038/s41598-018-20528-5 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fluorescent nanodiamonds (FND) are carbon-based nanomaterials that can
efficiently incorporate optically active photoluminescent centers such as the
nitrogen-vacancy complex, thus making them promising candidates as optical
biolabels and drug-delivery agents. FNDs exhibit bright fluorescence without
photobleaching co... | [
{
"created": "Fri, 2 Mar 2018 14:50:56 GMT",
"version": "v1"
}
] | 2018-03-05 | [
[
"Guarina",
"L.",
""
],
[
"Calorio",
"C.",
""
],
[
"Gavello",
"D.",
""
],
[
"Moreva",
"E.",
""
],
[
"Traina",
"P.",
""
],
[
"Battiato",
"A.",
""
],
[
"Tchernij",
"S. Ditalia",
""
],
[
"Forneris",
... | Fluorescent nanodiamonds (FND) are carbon-based nanomaterials that can efficiently incorporate optically active photoluminescent centers such as the nitrogen-vacancy complex, thus making them promising candidates as optical biolabels and drug-delivery agents. FNDs exhibit bright fluorescence without photobleaching comb... |
1910.11180 | Eric Batsche | Eric Batsch\'e, Oriane Mauger, Etienne Kornobis, Benjamin Hopkins,
Charlotte Hanmer-Lloyd, Christian Muchardt | CD44 alternative splicing is a sensor of intragenic DNA methylation in
tumors | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | DNA methylation (meDNA) is a suspected modulator of alternative splicing,
while splicing in turn is involved in tumour formations nearly as frequently as
DNA mutations. Yet, the impact of meDNA on tumorigenesis via its effect on
splicing has not been thoroughly explored. Here, we find that HCT116 colon
carcinoma cell... | [
{
"created": "Thu, 24 Oct 2019 14:35:26 GMT",
"version": "v1"
}
] | 2019-10-25 | [
[
"Batsché",
"Eric",
""
],
[
"Mauger",
"Oriane",
""
],
[
"Kornobis",
"Etienne",
""
],
[
"Hopkins",
"Benjamin",
""
],
[
"Hanmer-Lloyd",
"Charlotte",
""
],
[
"Muchardt",
"Christian",
""
]
] | DNA methylation (meDNA) is a suspected modulator of alternative splicing, while splicing in turn is involved in tumour formations nearly as frequently as DNA mutations. Yet, the impact of meDNA on tumorigenesis via its effect on splicing has not been thoroughly explored. Here, we find that HCT116 colon carcinoma cells ... |
1105.2830 | Oren Elrad | Michael F. Hagan, Oren M. Elrad and Robert L. Jack | Mechanisms of kinetic trapping in self-assembly and phase transformation | null | null | 10.1063/1.3635775 | null | q-bio.BM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In self-assembly processes, kinetic trapping effects often hinder the
formation of thermodynamically stable ordered states. In a model of viral
capsid assembly and in the phase transformation of a lattice gas, we show how
simulations in a self-assembling steady state can be used to identify two
distinct mechanisms of... | [
{
"created": "Fri, 13 May 2011 20:14:50 GMT",
"version": "v1"
}
] | 2015-05-28 | [
[
"Hagan",
"Michael F.",
""
],
[
"Elrad",
"Oren M.",
""
],
[
"Jack",
"Robert L.",
""
]
] | In self-assembly processes, kinetic trapping effects often hinder the formation of thermodynamically stable ordered states. In a model of viral capsid assembly and in the phase transformation of a lattice gas, we show how simulations in a self-assembling steady state can be used to identify two distinct mechanisms of k... |
2010.13458 | Cintya Dutta | Cintya Nirvana Dutta, Pamela K. Douglas, Hernando Ombao | Structural Brain Asymmetries in Youths with Combined and Inattentive
Presentations of Attention Deficit Hyperactivity Disorder | 5 pages, 3 figures, 1 table, submitted to ISBI conference | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Alterations in structural brain laterality are reported in
attention-deficit/hyperactivity disorder (ADHD). However, few studies examined
differences within presentations of ADHD. We investigate asymmetry index (AI)
across 13 subcortical and 33 cortical regions from anatomical metrics of
volume, surface area, and thi... | [
{
"created": "Mon, 26 Oct 2020 09:54:18 GMT",
"version": "v1"
}
] | 2020-10-27 | [
[
"Dutta",
"Cintya Nirvana",
""
],
[
"Douglas",
"Pamela K.",
""
],
[
"Ombao",
"Hernando",
""
]
] | Alterations in structural brain laterality are reported in attention-deficit/hyperactivity disorder (ADHD). However, few studies examined differences within presentations of ADHD. We investigate asymmetry index (AI) across 13 subcortical and 33 cortical regions from anatomical metrics of volume, surface area, and thick... |
1904.08190 | Bosco Emmanuel | Bosco Emmanuel | Regulation of Heart Beats by the Autonomous Nervous System in Health and
Disease: Point-Process-Theory based Models and Simulation [V-I] | 42 pages 20 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have advanced a point-process based framework for the regulation of heart
beats by the autonomous nervous system and analyzed the model with and without
feedback. The model without feedback was found amenable to several analytical
results that help develop an intuition about the way the heart interacts with
the ne... | [
{
"created": "Wed, 17 Apr 2019 11:20:41 GMT",
"version": "v1"
}
] | 2019-04-18 | [
[
"Emmanuel",
"Bosco",
""
]
] | We have advanced a point-process based framework for the regulation of heart beats by the autonomous nervous system and analyzed the model with and without feedback. The model without feedback was found amenable to several analytical results that help develop an intuition about the way the heart interacts with the nerv... |
2306.15485 | Diego Vidaurre | Diego Vidaurre | Dynamic functional connectivity: why the controversy? | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In principle, dynamic functional connectivity in fMRI is just a statistical
measure. A passer-by might think it to be a specialist topic, but it continues
to attract widespread attention and spark controversy. Why?
| [
{
"created": "Tue, 27 Jun 2023 14:06:05 GMT",
"version": "v1"
}
] | 2023-06-28 | [
[
"Vidaurre",
"Diego",
""
]
] | In principle, dynamic functional connectivity in fMRI is just a statistical measure. A passer-by might think it to be a specialist topic, but it continues to attract widespread attention and spark controversy. Why? |
1705.03115 | Eli Shlizerman | David Blaszka, Elischa Sanders, Jeffrey Riffell, Eli Shlizerman | Classification of Fixed Point Network Dynamics From Multiple Node
Timeseries Data | submitted for publication | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fixed point networks are dynamic networks that encode stimuli via distinct
output patterns. Although such networks are omnipresent in neural systems,
their structures are typically unknown or poorly characterized. It is therefore
valuable to use a supervised approach for resolving how a network encodes
distinct input... | [
{
"created": "Mon, 8 May 2017 22:47:40 GMT",
"version": "v1"
}
] | 2017-05-10 | [
[
"Blaszka",
"David",
""
],
[
"Sanders",
"Elischa",
""
],
[
"Riffell",
"Jeffrey",
""
],
[
"Shlizerman",
"Eli",
""
]
] | Fixed point networks are dynamic networks that encode stimuli via distinct output patterns. Although such networks are omnipresent in neural systems, their structures are typically unknown or poorly characterized. It is therefore valuable to use a supervised approach for resolving how a network encodes distinct inputs ... |
q-bio/0404031 | Paul Higgs | Cendrine Hudelot, Vivek Gowri-Shankar, Howsun Jow, Magnus Rattray and
Paul G. Higgs | RNA-based Phylogenetic Methods: Application to Mammalian Mitochondrial
RNA Sequences | null | Mol. Phyl. Evol. 28, 241-252. (2003) | null | null | q-bio.PE | null | The PHASE software package allows phylogenetic tree construction with a
number of evolutionary models designed specifically for use with RNA sequences
that have conserved secondary structure. Evolution in the paired regions of
RNAs occurs via compensatory substitutions, hence changes on either side of a
pair are corr... | [
{
"created": "Fri, 23 Apr 2004 14:39:02 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Hudelot",
"Cendrine",
""
],
[
"Gowri-Shankar",
"Vivek",
""
],
[
"Jow",
"Howsun",
""
],
[
"Rattray",
"Magnus",
""
],
[
"Higgs",
"Paul G.",
""
]
] | The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs via compensatory substitutions, hence changes on either side of a pair are correl... |
1706.05656 | Stefan Frank | Stefan Frank, Jinbiao Yang | Lexical representation explains cortical entrainment during speech
comprehension | Submitted for publication | null | 10.1371/journal.pone.0197304 | null | q-bio.NC cs.CL | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Results from a recent neuroimaging study on spoken sentence comprehension
have been interpreted as evidence for cortical entrainment to hierarchical
syntactic structure. We present a simple computational model that predicts the
power spectra from this study, even though the model's linguistic knowledge is
restricted ... | [
{
"created": "Sun, 18 Jun 2017 14:04:09 GMT",
"version": "v1"
},
{
"created": "Wed, 12 Jul 2017 07:33:02 GMT",
"version": "v2"
},
{
"created": "Thu, 20 Jul 2017 11:26:48 GMT",
"version": "v3"
},
{
"created": "Mon, 9 Oct 2017 14:24:45 GMT",
"version": "v4"
},
{
"cr... | 2018-06-15 | [
[
"Frank",
"Stefan",
""
],
[
"Yang",
"Jinbiao",
""
]
] | Results from a recent neuroimaging study on spoken sentence comprehension have been interpreted as evidence for cortical entrainment to hierarchical syntactic structure. We present a simple computational model that predicts the power spectra from this study, even though the model's linguistic knowledge is restricted to... |
2301.02623 | Rudy Arthur | Rudy Arthur and Arwen Nicholson | Does Gaia Play Dice? : Simple Models of non-Darwinian Selection | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | In this paper we introduce some simple models, based on rolling dice, to
explore mechanisms proposed to explain planetary habitability. The idea is to
study these selection mechanisms in an analytically tractable setting,
isolating their consequences from other details which can confound or obscure
their effect in mo... | [
{
"created": "Fri, 6 Jan 2023 17:58:36 GMT",
"version": "v1"
},
{
"created": "Sat, 27 Jul 2024 14:18:40 GMT",
"version": "v2"
}
] | 2024-07-30 | [
[
"Arthur",
"Rudy",
""
],
[
"Nicholson",
"Arwen",
""
]
] | In this paper we introduce some simple models, based on rolling dice, to explore mechanisms proposed to explain planetary habitability. The idea is to study these selection mechanisms in an analytically tractable setting, isolating their consequences from other details which can confound or obscure their effect in more... |
1809.09321 | Bryan Daniels | Bryan C. Daniels, William S. Ryu, and Ilya Nemenman | Automated, predictive, and interpretable inference of C. elegans escape
dynamics | 19 pages, 5 figures | null | 10.1073/pnas.1816531116 | null | q-bio.NC q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The roundworm C. elegans exhibits robust escape behavior in response to
rapidly rising temperature. The behavior lasts for a few seconds, shows history
dependence, involves both sensory and motor systems, and is too complicated to
model mechanistically using currently available knowledge. Instead we model the
process... | [
{
"created": "Tue, 25 Sep 2018 05:15:40 GMT",
"version": "v1"
}
] | 2019-06-19 | [
[
"Daniels",
"Bryan C.",
""
],
[
"Ryu",
"William S.",
""
],
[
"Nemenman",
"Ilya",
""
]
] | The roundworm C. elegans exhibits robust escape behavior in response to rapidly rising temperature. The behavior lasts for a few seconds, shows history dependence, involves both sensory and motor systems, and is too complicated to model mechanistically using currently available knowledge. Instead we model the process p... |
2407.12148 | Daniel Villela | Daniel A.M. Villela | On the Evolution of Virulence in Vector-borne Diseases | 14 pages; 5 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The emergence or adaptation of pathogens may lead to epidemics or even
pandemics, highlighting the need for a thorough understanding of pathogen
evolution. The tradeoff hypothesis suggests that virulence evolves to reach an
optimal transmission intensity relative to the mortality caused by the disease.
This study int... | [
{
"created": "Tue, 16 Jul 2024 20:06:48 GMT",
"version": "v1"
},
{
"created": "Wed, 14 Aug 2024 20:21:59 GMT",
"version": "v2"
}
] | 2024-08-16 | [
[
"Villela",
"Daniel A. M.",
""
]
] | The emergence or adaptation of pathogens may lead to epidemics or even pandemics, highlighting the need for a thorough understanding of pathogen evolution. The tradeoff hypothesis suggests that virulence evolves to reach an optimal transmission intensity relative to the mortality caused by the disease. This study intro... |
q-bio/0412010 | Hernan Garcia | Lacramioara Bintu, Nicolas E. Buchler, Hernan G. Garcia, Ulrich
Gerland, Terence Hwa, Jane' Kondev, and Rob Phillips | Transcriptional Regulation by the Numbers 1: Models | 11 pages and 4 figures in PDF format | null | null | null | q-bio.MN q-bio.QM | null | The study of gene regulation and expression is often discussed in
quantitative terms. In particular, the expression of genes is regularly
characterized with respect to how much, how fast, when and where. Whether
discussing the level of gene expression in a bacterium or its precise location
within a developing embryo,... | [
{
"created": "Sun, 5 Dec 2004 23:20:53 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bintu",
"Lacramioara",
""
],
[
"Buchler",
"Nicolas E.",
""
],
[
"Garcia",
"Hernan G.",
""
],
[
"Gerland",
"Ulrich",
""
],
[
"Hwa",
"Terence",
""
],
[
"Kondev",
"Jane'",
""
],
[
"Phillips",
"Rob",
""
]
] | The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene expression in a bacterium or its precise location within a developing embryo, t... |
2006.02357 | Seungho Choe | Seungho Choe | Molecular dynamics studies of interactions between Arg9(nona-arginine)
and a DOPC/DOPG(4:1) membrane | 10 pages, 12 figures | AIP Advances 10, 105103 (2020) | null | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has been known that the uptake mechanisms of cell-penetrating
peptides(CPPs) depend on the experimental conditions such as concentration of
peptides, lipid composition, temperature, etc. In this study we investigate the
temperature dependence of the penetration of Arg9s into a DOPC/DOPG(4:1)
membrane using molecul... | [
{
"created": "Wed, 3 Jun 2020 16:04:56 GMT",
"version": "v1"
},
{
"created": "Wed, 7 Oct 2020 07:24:53 GMT",
"version": "v2"
}
] | 2020-10-08 | [
[
"Choe",
"Seungho",
""
]
] | It has been known that the uptake mechanisms of cell-penetrating peptides(CPPs) depend on the experimental conditions such as concentration of peptides, lipid composition, temperature, etc. In this study we investigate the temperature dependence of the penetration of Arg9s into a DOPC/DOPG(4:1) membrane using molecular... |
2005.02271 | Augusto Gonzalez | Augusto Gonzalez, Frank Quintela, Dario A. Leon, Maria Luisa Bringas
Vega, Pedro Valdes Sosa | Estimating the number of available states for normal and tumor tissues
in gene expression space | null | Biophysical Reports Volume 2, Issue 2, 8 June 2022, 100053 | 10.1016/j.bpr.2022.100053 | null | q-bio.TO q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The topology of gene expression space for a set of 12 cancer types is studied
by means of an entropy-like magnitude, which allows the characterization of the
regions occupied by tumor and normal samples. The comparison indicates that the
number of available states in gene expression space is much greater for tumors
t... | [
{
"created": "Tue, 5 May 2020 15:07:05 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Nov 2021 22:00:16 GMT",
"version": "v2"
},
{
"created": "Sat, 13 Nov 2021 22:40:36 GMT",
"version": "v3"
}
] | 2022-05-19 | [
[
"Gonzalez",
"Augusto",
""
],
[
"Quintela",
"Frank",
""
],
[
"Leon",
"Dario A.",
""
],
[
"Vega",
"Maria Luisa Bringas",
""
],
[
"Sosa",
"Pedro Valdes",
""
]
] | The topology of gene expression space for a set of 12 cancer types is studied by means of an entropy-like magnitude, which allows the characterization of the regions occupied by tumor and normal samples. The comparison indicates that the number of available states in gene expression space is much greater for tumors tha... |
1703.03444 | Fernanda Matias | Fernanda S. Matias, Pedro V. Carelli, Claudio R. Mirasso, Mauro
Copelli | Anticipated synchronization in neuronal circuits unveiled by a
phase-resetting curve analysis | null | Phys. Rev. E 95, 052410 (2017) | 10.1103/PhysRevE.95.052410 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Anticipated synchronization (AS) is a counter intuitive behavior that has
been observed in several systems. When AS establishes in a sender-receiver
configuration, the latter can predict the future dynamics of the former for
certain parameter values. In particular, in neuroscience AS was proposed to
explain the appar... | [
{
"created": "Thu, 9 Mar 2017 19:58:42 GMT",
"version": "v1"
}
] | 2017-05-31 | [
[
"Matias",
"Fernanda S.",
""
],
[
"Carelli",
"Pedro V.",
""
],
[
"Mirasso",
"Claudio R.",
""
],
[
"Copelli",
"Mauro",
""
]
] | Anticipated synchronization (AS) is a counter intuitive behavior that has been observed in several systems. When AS establishes in a sender-receiver configuration, the latter can predict the future dynamics of the former for certain parameter values. In particular, in neuroscience AS was proposed to explain the apparen... |
0801.0654 | Michael Welter | Michael Welter, Katalin Bartha and Heiko Rieger | Hot spot formation in tumor vasculature during tumor growth in an
arterio-venous-network environment | 37 pages, 16 figures (full paper with higher resolution figures at
http://www.uni-saarland.de/fak7/rieger/Paper/JTB-welter2-subm.pdf) | null | null | null | q-bio.TO | null | Hot spots in tumors are regions of high vascular density in the center of the
tumor and their analysis is an important diagnostic tool in cancer treatment.
We present a model for vascular remodeling in tumors predicting that the
formation of hot spots correlates with local inhomogeneities of the original
arterio-veno... | [
{
"created": "Fri, 4 Jan 2008 11:22:49 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Jan 2008 11:13:47 GMT",
"version": "v2"
}
] | 2008-01-07 | [
[
"Welter",
"Michael",
""
],
[
"Bartha",
"Katalin",
""
],
[
"Rieger",
"Heiko",
""
]
] | Hot spots in tumors are regions of high vascular density in the center of the tumor and their analysis is an important diagnostic tool in cancer treatment. We present a model for vascular remodeling in tumors predicting that the formation of hot spots correlates with local inhomogeneities of the original arterio-venous... |
2107.03334 | Andrea Allen | Andrea J. Allen, Mariah C. Boudreau, Nicholas J. Roberts, Antoine
Allard, Laurent H\'ebert-Dufresne | Predicting the diversity of early epidemic spread on networks | null | Phys. Rev. Research 4, 013123 (2022) | 10.1103/PhysRevResearch.4.013123 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The interplay of biological, social, structural and random factors makes
disease forecasting extraordinarily complex. The course of an epidemic exhibits
average growth dynamics determined by features of the pathogen and the
population, yet also features significant variability reflecting the stochastic
nature of dise... | [
{
"created": "Wed, 7 Jul 2021 16:23:27 GMT",
"version": "v1"
},
{
"created": "Wed, 23 Feb 2022 18:45:07 GMT",
"version": "v2"
}
] | 2022-02-24 | [
[
"Allen",
"Andrea J.",
""
],
[
"Boudreau",
"Mariah C.",
""
],
[
"Roberts",
"Nicholas J.",
""
],
[
"Allard",
"Antoine",
""
],
[
"Hébert-Dufresne",
"Laurent",
""
]
] | The interplay of biological, social, structural and random factors makes disease forecasting extraordinarily complex. The course of an epidemic exhibits average growth dynamics determined by features of the pathogen and the population, yet also features significant variability reflecting the stochastic nature of diseas... |
1704.05912 | Konstantin Blyuss | G.O. Agaba, Y.N. Kyrychko, K.B. Blyuss | Time-delayed SIS epidemic model with population awareness | 15 pages, 5 figures | Ecol. Compl. 31, 50-56 (2017) | 10.1016/j.ecocom.2017.03.002 | null | q-bio.PE nlin.CD q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper analyses the dynamics of infectious disease with a concurrent
spread of disease awareness. The model includes local awareness due to contacts
with aware individuals, as well as global awareness due to reported cases of
infection and awareness campaigns. We investigate the effects of time delay in
response ... | [
{
"created": "Wed, 19 Apr 2017 19:45:52 GMT",
"version": "v1"
}
] | 2017-04-21 | [
[
"Agaba",
"G. O.",
""
],
[
"Kyrychko",
"Y. N.",
""
],
[
"Blyuss",
"K. B.",
""
]
] | This paper analyses the dynamics of infectious disease with a concurrent spread of disease awareness. The model includes local awareness due to contacts with aware individuals, as well as global awareness due to reported cases of infection and awareness campaigns. We investigate the effects of time delay in response of... |
2101.11526 | Catherine Beauchemin | Daniel Cresta, Donald C. Warren, Christian Quirouette, Amanda P.
Smith, Lindey C. Lane, Amber M. Smith, and Catherine A. A. Beauchemin | Time to revisit the endpoint dilution assay and to replace TCID$_{50}$
and PFU as measures of a virus sample's infection concentration | 22 pages, 8 figures | PLOS Comput. Biol., 17(10):e1009480, October, 2021 | 10.1371/journal.pcbi.1009480 | RIKEN-iTHEMS-Report-21 | q-bio.QM | http://creativecommons.org/licenses/by-sa/4.0/ | The infectivity of a virus sample is measured by the infections it causes,
via a plaque or focus forming assay (PFU or FFU) or an endpoint dilution (ED)
assay (TCID$_{50}$, CCID$_{50}$, EID$_{50}$, etc., hereafter collectively
ID$_{50}$). The counting of plaques or foci at a given dilution intuitively and
directly pr... | [
{
"created": "Wed, 27 Jan 2021 16:31:51 GMT",
"version": "v1"
}
] | 2024-04-02 | [
[
"Cresta",
"Daniel",
""
],
[
"Warren",
"Donald C.",
""
],
[
"Quirouette",
"Christian",
""
],
[
"Smith",
"Amanda P.",
""
],
[
"Lane",
"Lindey C.",
""
],
[
"Smith",
"Amber M.",
""
],
[
"Beauchemin",
"Catherine A. ... | The infectivity of a virus sample is measured by the infections it causes, via a plaque or focus forming assay (PFU or FFU) or an endpoint dilution (ED) assay (TCID$_{50}$, CCID$_{50}$, EID$_{50}$, etc., hereafter collectively ID$_{50}$). The counting of plaques or foci at a given dilution intuitively and directly prov... |
2101.08815 | Vasudevan Lakshminarayanan | Sam Yu and Vasudevan Lakshminarayanan | Fractal Dimension and Retinal Pathology: A Meta-analysis | submitted for publication to MDPI Applied Sciences | null | null | null | q-bio.QM physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Due to the fractal nature of retinal blood vessels, the retinal fractal
dimension is a natural parameter for researchers to explore and has garnered
interest as a potential diagnostic tool. This review aims to summarize the
current scientific evidence regarding the relationship between fractal
dimension and retinal p... | [
{
"created": "Thu, 21 Jan 2021 19:11:16 GMT",
"version": "v1"
}
] | 2021-01-25 | [
[
"Yu",
"Sam",
""
],
[
"Lakshminarayanan",
"Vasudevan",
""
]
] | Due to the fractal nature of retinal blood vessels, the retinal fractal dimension is a natural parameter for researchers to explore and has garnered interest as a potential diagnostic tool. This review aims to summarize the current scientific evidence regarding the relationship between fractal dimension and retinal pat... |
2010.07143 | Simon Wein | Simon Wein, Wilhelm Malloni, Ana Maria Tom\'e, Sebastian M. Frank,
Gina-Isabelle Henze, Stefan W\"ust, Mark W. Greenlee, Elmar W. Lang | A Graph Neural Network Framework for Causal Inference in Brain Networks | null | null | null | null | q-bio.NC cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A central question in neuroscience is how self-organizing dynamic
interactions in the brain emerge on their relatively static structural
backbone. Due to the complexity of spatial and temporal dependencies between
different brain areas, fully comprehending the interplay between structure and
function is still challen... | [
{
"created": "Wed, 14 Oct 2020 15:01:21 GMT",
"version": "v1"
}
] | 2020-10-15 | [
[
"Wein",
"Simon",
""
],
[
"Malloni",
"Wilhelm",
""
],
[
"Tomé",
"Ana Maria",
""
],
[
"Frank",
"Sebastian M.",
""
],
[
"Henze",
"Gina-Isabelle",
""
],
[
"Wüst",
"Stefan",
""
],
[
"Greenlee",
"Mark W.",
""
]... | A central question in neuroscience is how self-organizing dynamic interactions in the brain emerge on their relatively static structural backbone. Due to the complexity of spatial and temporal dependencies between different brain areas, fully comprehending the interplay between structure and function is still challengi... |
q-bio/0606040 | Francoise Tchang | Mohamed Doulazmi (NPA), Francesca Capone (NPA), Florence Frederic
(NPA), Jo\"Elle Bakouche (NPA), Yolande Lemaigre-Dubreuil (NPA), Jean Mariani
(NPA) | Cerebellar Purkinje Cell Loss in Heterozygous Rora+/-Mice: A
Longitudinal Study | null | null | null | null | q-bio.NC | null | The staggerer (sg/sg) mutation is a spontaneous deletion in the Rora gene
that prevents the translation of the ligand-binding domain (LBD), leading to
the loss of ROR\alpha activity. The homozygous Rorasg/sg mutant mouse, whose
most obvious phenotype is ataxia associated with cerebellar degeneration, also
displays a ... | [
{
"created": "Thu, 29 Jun 2006 09:36:48 GMT",
"version": "v1"
}
] | 2016-08-16 | [
[
"Doulazmi",
"Mohamed",
"",
"NPA"
],
[
"Capone",
"Francesca",
"",
"NPA"
],
[
"Frederic",
"Florence",
"",
"NPA"
],
[
"Bakouche",
"JoËlle",
"",
"NPA"
],
[
"Lemaigre-Dubreuil",
"Yolande",
"",
"NPA"
],
[
"Mariani",
... | The staggerer (sg/sg) mutation is a spontaneous deletion in the Rora gene that prevents the translation of the ligand-binding domain (LBD), leading to the loss of ROR\alpha activity. The homozygous Rorasg/sg mutant mouse, whose most obvious phenotype is ataxia associated with cerebellar degeneration, also displays a va... |
q-bio/0605031 | Fumiko Takagi | Fumiko Takagi, Macoto Kikuchi | Structural Change of Myosin Motor Domain and Nucleotide Dissociation | null | null | null | null | q-bio.BM | null | We investigated the structural relaxation of myosin motor domain from the
pre-power stroke state to the near-rigor state using molecular dynamics
simulation of a coarse-grained protein model. To describe the structural
change, we propose a "dual Go-model," a variant of the Go-like model that has
two reference structu... | [
{
"created": "Fri, 19 May 2006 06:11:31 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Aug 2006 08:11:04 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Takagi",
"Fumiko",
""
],
[
"Kikuchi",
"Macoto",
""
]
] | We investigated the structural relaxation of myosin motor domain from the pre-power stroke state to the near-rigor state using molecular dynamics simulation of a coarse-grained protein model. To describe the structural change, we propose a "dual Go-model," a variant of the Go-like model that has two reference structure... |
1002.1100 | Vittorio Loreto | F. Tria, E. Caglioti, V. Loreto and A. Pagnani | A Stochastic Local Search algorithm for distance-based phylogeny
reconstruction | 13 pages, 8 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In many interesting cases the reconstruction of a correct phylogeny is
blurred by high mutation rates and/or horizontal transfer events. As a
consequence a divergence arises between the true evolutionary distances and the
differences between pairs of taxa as inferred from available data, making the
phylogenetic recon... | [
{
"created": "Thu, 4 Feb 2010 23:17:03 GMT",
"version": "v1"
}
] | 2010-02-08 | [
[
"Tria",
"F.",
""
],
[
"Caglioti",
"E.",
""
],
[
"Loreto",
"V.",
""
],
[
"Pagnani",
"A.",
""
]
] | In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences between pairs of taxa as inferred from available data, making the phylogenetic reconst... |
1706.02912 | Julia Gallinaro | J\'ulia V Gallinaro and Stefan Rotter | Associative properties of structural plasticity based on firing rate
homeostasis in recurrent neuronal networks | 19 pages, 4 figures | null | 10.1038/s41598-018-22077-3 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Correlation-based Hebbian plasticity is thought to shape neuronal
connectivity during development and learning, whereas homeostatic plasticity
would stabilize network activity. Here we investigate another, new aspect of
this dichotomy: Can Hebbian associative properties also emerge as a network
effect from a plastici... | [
{
"created": "Fri, 9 Jun 2017 12:03:23 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Sep 2017 10:59:32 GMT",
"version": "v2"
},
{
"created": "Mon, 22 Jan 2018 14:29:28 GMT",
"version": "v3"
},
{
"created": "Sat, 24 Feb 2018 09:42:39 GMT",
"version": "v4"
}
] | 2018-03-02 | [
[
"Gallinaro",
"Júlia V",
""
],
[
"Rotter",
"Stefan",
""
]
] | Correlation-based Hebbian plasticity is thought to shape neuronal connectivity during development and learning, whereas homeostatic plasticity would stabilize network activity. Here we investigate another, new aspect of this dichotomy: Can Hebbian associative properties also emerge as a network effect from a plasticity... |
1409.4251 | Stephan Porz | Stephan Porz, Matth\"aus Kiel, Klaus Lehnertz | Can spurious indications for phase synchronization due to superimposed
signals be avoided? | null | Porz S, Kiel M, Lehnertz K, Chaos 24, 033112 (2014) | 10.1063/1.4890568 | null | q-bio.NC nlin.CD physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the relative merit of phase-based methods---mean phase
coherence, unweighted and weighted phase lag index---for estimating the
strength of interactions between dynamical systems from empirical time series
which are affected by common sources and noise. By numerically analyzing the
interaction dynamics ... | [
{
"created": "Mon, 15 Sep 2014 13:36:00 GMT",
"version": "v1"
}
] | 2014-09-16 | [
[
"Porz",
"Stephan",
""
],
[
"Kiel",
"Matthäus",
""
],
[
"Lehnertz",
"Klaus",
""
]
] | We investigate the relative merit of phase-based methods---mean phase coherence, unweighted and weighted phase lag index---for estimating the strength of interactions between dynamical systems from empirical time series which are affected by common sources and noise. By numerically analyzing the interaction dynamics of... |
1702.03409 | Kate Inasaridze | Vera Bzhalava, Ketevan Inasaridze | Disruptive Behavior Disorder (DBD) Rating Scale for Georgian Population | 9 pages, 2 tables, 2 figures | null | null | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the presented study Parent/Teacher Disruptive Behavior Disorder (DBD)
rating scale based on the Diagnostic and Statistical Manual of Mental Disorders
(DSM-IV-TR [APA, 2000]) which was developed by Pelham and his colleagues
(Pelham et al., 1992) was translated and adopted for assessment of childhood
behavioral abno... | [
{
"created": "Sat, 11 Feb 2017 10:52:36 GMT",
"version": "v1"
}
] | 2017-02-20 | [
[
"Bzhalava",
"Vera",
""
],
[
"Inasaridze",
"Ketevan",
""
]
] | In the presented study Parent/Teacher Disruptive Behavior Disorder (DBD) rating scale based on the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV-TR [APA, 2000]) which was developed by Pelham and his colleagues (Pelham et al., 1992) was translated and adopted for assessment of childhood behavioral abnorm... |
1610.04160 | Zarrin Basharat | Zarrin Basharat, Azra Yasmin | Pan-genome Analysis of the Genus Serratia | 17 pages, 5 figures, 3 Tables | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Pan-genome analysis is a standard procedure to decipher genome heterogeneity
and diversification of bacterial species. Specie evolution is traced by
defining and comparing the core (conserved), accessory (dispensable) and unique
(strain-specific) gene pool with other strains of interest. Here, we present
pan-genome a... | [
{
"created": "Thu, 13 Oct 2016 16:32:47 GMT",
"version": "v1"
}
] | 2016-10-14 | [
[
"Basharat",
"Zarrin",
""
],
[
"Yasmin",
"Azra",
""
]
] | Pan-genome analysis is a standard procedure to decipher genome heterogeneity and diversification of bacterial species. Specie evolution is traced by defining and comparing the core (conserved), accessory (dispensable) and unique (strain-specific) gene pool with other strains of interest. Here, we present pan-genome ana... |
1611.02735 | Giacomo Falcucci | Nicole Jannelli and Rosa Anna Nastro and Viviana Cigolotti and
Mariagiovanna Minutillo and Giacomo Falcucci | Low pH, high salinity: too much for Microbial Fuel Cells? | 13 pages, 10 Figures | null | 10.1016/j.apenergy.2016.07.079 | null | q-bio.OT physics.bio-ph physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Twelve single chambered, air-cathode Tubular Microbial Fuel Cells (TMFCs)
have been filled up with fruit and vegetable residues. The anodes were realized
by means of a carbon fiber brush, while the cathodes were realized through a
graphite-based porous ceramic disk with Nafion membranes (117 Dupont). The
performances... | [
{
"created": "Fri, 4 Nov 2016 15:00:00 GMT",
"version": "v1"
}
] | 2016-11-10 | [
[
"Jannelli",
"Nicole",
""
],
[
"Nastro",
"Rosa Anna",
""
],
[
"Cigolotti",
"Viviana",
""
],
[
"Minutillo",
"Mariagiovanna",
""
],
[
"Falcucci",
"Giacomo",
""
]
] | Twelve single chambered, air-cathode Tubular Microbial Fuel Cells (TMFCs) have been filled up with fruit and vegetable residues. The anodes were realized by means of a carbon fiber brush, while the cathodes were realized through a graphite-based porous ceramic disk with Nafion membranes (117 Dupont). The performances i... |
0807.1759 | Vladimir Ivancevic | Vladimir G. Ivancevic | New Mechanics of Generic Musculo-Skeletal Injury | 13 pages, 1 figure, latex - major corrections | null | null | null | q-bio.TO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Prediction and prevention of musculo-skeletal injuries is an important aspect
of preventive health science. Using as an example a human knee joint, this
paper proposes a new coupled-loading-rate hypothesis, which states that a
generic cause of any musculo-skeletal injury is a Euclidean jolt, or
SE(3)-jolt, an impulsi... | [
{
"created": "Fri, 11 Jul 2008 01:24:45 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Aug 2008 04:16:31 GMT",
"version": "v2"
},
{
"created": "Tue, 18 Nov 2008 02:32:22 GMT",
"version": "v3"
},
{
"created": "Thu, 18 Dec 2008 02:01:20 GMT",
"version": "v4"
},
{
"c... | 2009-04-09 | [
[
"Ivancevic",
"Vladimir G.",
""
]
] | Prediction and prevention of musculo-skeletal injuries is an important aspect of preventive health science. Using as an example a human knee joint, this paper proposes a new coupled-loading-rate hypothesis, which states that a generic cause of any musculo-skeletal injury is a Euclidean jolt, or SE(3)-jolt, an impulsive... |
0809.1718 | Philippe Rondard | Haijun Tu, Philippe Rondard (IGF), Chanjuan Xu, Federica Bertaso
(IGF), Fangli Cao, Xueying Zhang, Jean-Philippe Pin (IGF), Jianfeng Liu | Dominant role of GABAB2 and Gbetagamma for GABAB
receptor-mediated-ERK1/2/CREB pathway in cerebellar neurons | null | Cellular Signalling 19, 9 (2007) 1996-2002 | 10.1016/j.cellsig.2007.05.004 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | gamma-aminobutyric acid type B (GABA(B)) receptor is an allosteric complex
made of two subunits, GABA(B1) and GABA(B2). GABA(B2) plays a major role in the
coupling to G protein whereas GABA(B1) binds GABA. It has been shown that
GABA(B) receptor activates ERK(1/2) in neurons of the central nervous system,
but the mol... | [
{
"created": "Wed, 10 Sep 2008 07:05:12 GMT",
"version": "v1"
}
] | 2008-09-11 | [
[
"Tu",
"Haijun",
"",
"IGF"
],
[
"Rondard",
"Philippe",
"",
"IGF"
],
[
"Xu",
"Chanjuan",
"",
"IGF"
],
[
"Bertaso",
"Federica",
"",
"IGF"
],
[
"Cao",
"Fangli",
"",
"IGF"
],
[
"Zhang",
"Xueying",
"",
"I... | gamma-aminobutyric acid type B (GABA(B)) receptor is an allosteric complex made of two subunits, GABA(B1) and GABA(B2). GABA(B2) plays a major role in the coupling to G protein whereas GABA(B1) binds GABA. It has been shown that GABA(B) receptor activates ERK(1/2) in neurons of the central nervous system, but the molec... |
1105.4680 | Jeremy Sumner | Jeremy Sumner, Jesus Fernandez-Sanchez, and Peter Jarvis | Lie Markov Models | 33 Pages, V2: Completed proofs of GTR non-closure | J. Theor. Biol., 298, 16--31, 2012 | null | null | q-bio.PE math.GR math.ST stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent work has discussed the importance of multiplicative closure for the
Markov models used in phylogenetics. For continuous-time Markov chains, a
sufficient condition for multiplicative closure of a model class is ensured by
demanding that the set of rate-matrices belonging to the model class form a Lie
algebra. I... | [
{
"created": "Tue, 24 May 2011 05:09:31 GMT",
"version": "v1"
},
{
"created": "Fri, 29 Jul 2011 05:47:30 GMT",
"version": "v2"
}
] | 2012-04-24 | [
[
"Sumner",
"Jeremy",
""
],
[
"Fernandez-Sanchez",
"Jesus",
""
],
[
"Jarvis",
"Peter",
""
]
] | Recent work has discussed the importance of multiplicative closure for the Markov models used in phylogenetics. For continuous-time Markov chains, a sufficient condition for multiplicative closure of a model class is ensured by demanding that the set of rate-matrices belonging to the model class form a Lie algebra. It ... |
2310.00939 | Quratul Ain Dr. | Qurat-ul-Ain, Munira Taj Muhammad Khalid Mohammed Khan and M. Iqbal
Choudhary | Estimation of In-Vitro Free Radical Scavenging and Cytotoxic Activities
of Thiocarbohydrazones Derivatives | I figure, 3 Schemes, 3 tables | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-sa/4.0/ | Objective: To investigate free radical scavenging potential of
thiocarbohydrazones derivatives for the discovery of antioxidant compounds of
synthetic origin. Method: Eighteen thiocarbohydrazones derivatives were
screened for antioxidant activities by using in vitro radical inhibition assay.
Cytotoxicity all derivati... | [
{
"created": "Mon, 2 Oct 2023 07:09:54 GMT",
"version": "v1"
}
] | 2023-10-03 | [
[
"Qurat-ul-Ain",
"",
""
],
[
"Khan",
"Munira Taj Muhammad Khalid Mohammed",
""
],
[
"Choudhary",
"M. Iqbal",
""
]
] | Objective: To investigate free radical scavenging potential of thiocarbohydrazones derivatives for the discovery of antioxidant compounds of synthetic origin. Method: Eighteen thiocarbohydrazones derivatives were screened for antioxidant activities by using in vitro radical inhibition assay. Cytotoxicity all derivative... |
1304.0132 | Shampa Ghosh | Shampa M. Ghosh, Nicholas D. Testa, Alexander W. Shingleton | Temperature Size Rule is mediated by thermal plasticity of critical size
in Drosophila melanogaster | Accepted in Proceedings of Royal Society B: Biological Sciences | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most ectotherms show an inverse relationship between developmental
temperature and body size, a phenomenon known as the temperature size rule
(TSR). Several competing hypotheses have been proposed to explain its
occurrence. According to one set of views, the TSR results from inevitable
biophysical effects of temperat... | [
{
"created": "Sat, 30 Mar 2013 19:43:20 GMT",
"version": "v1"
}
] | 2013-04-02 | [
[
"Ghosh",
"Shampa M.",
""
],
[
"Testa",
"Nicholas D.",
""
],
[
"Shingleton",
"Alexander W.",
""
]
] | Most ectotherms show an inverse relationship between developmental temperature and body size, a phenomenon known as the temperature size rule (TSR). Several competing hypotheses have been proposed to explain its occurrence. According to one set of views, the TSR results from inevitable biophysical effects of temperatur... |
1607.00128 | Andrea De Martino | Matteo Mori, Terence Hwa, Olivier C. Martin, Andrea De Martino, Enzo
Marinari | Constrained Allocation Flux Balance Analysis | 21 pages, 6 figures (main) + 33 pages, various figures and tables
(supporting); for the supplementary MatLab code, see
http://tinyurl.com/h763es8 | PLoS Comput Biol 12(6): e1004913 (2016) | 10.1371/journal.pcbi.1004913 | null | q-bio.MN cond-mat.dis-nn physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | New experimental results on bacterial growth inspire a novel top-down
approach to study cell metabolism, combining mass balance and proteomic
constraints to extend and complement Flux Balance Analysis. We introduce here
Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic
costs associated to... | [
{
"created": "Fri, 1 Jul 2016 07:08:39 GMT",
"version": "v1"
}
] | 2016-07-04 | [
[
"Mori",
"Matteo",
""
],
[
"Hwa",
"Terence",
""
],
[
"Martin",
"Olivier C.",
""
],
[
"De Martino",
"Andrea",
""
],
[
"Marinari",
"Enzo",
""
]
] | New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to g... |
2003.07912 | Gabor Vattay | Gabor Vattay | Predicting the ultimate outcome of the COVID-19 outbreak in Italy | 2 pages | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During the COVID-19 outbreak, it is essential to monitor the effectiveness of
measures taken by governments on the course of the epidemic. Here we show that
there is already a sufficient amount of data collected in Italy to predict the
outcome of the process. We show that using the proper metric, the data from
Hubei ... | [
{
"created": "Tue, 17 Mar 2020 19:43:51 GMT",
"version": "v1"
},
{
"created": "Tue, 31 Mar 2020 18:57:34 GMT",
"version": "v2"
}
] | 2020-04-02 | [
[
"Vattay",
"Gabor",
""
]
] | During the COVID-19 outbreak, it is essential to monitor the effectiveness of measures taken by governments on the course of the epidemic. Here we show that there is already a sufficient amount of data collected in Italy to predict the outcome of the process. We show that using the proper metric, the data from Hubei Pr... |
1307.6786 | Alfredo Braunstein | Fabrizio Altarelli, Alfredo Braunstein, Luca Dall'Asta, Alejandro
Lage-Castellanos, Riccardo Zecchina | Bayesian inference of epidemics on networks via Belief Propagation | null | Phys. Rev. Lett. 112, 118701 (2014) | 10.1103/PhysRevLett.112.118701 | null | q-bio.QM cond-mat.stat-mech cs.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study several bayesian inference problems for irreversible stochastic
epidemic models on networks from a statistical physics viewpoint. We derive
equations which allow to accurately compute the posterior distribution of the
time evolution of the state of each node given some observations. At difference
with most e... | [
{
"created": "Thu, 25 Jul 2013 15:21:52 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Mar 2014 18:12:12 GMT",
"version": "v2"
}
] | 2014-03-28 | [
[
"Altarelli",
"Fabrizio",
""
],
[
"Braunstein",
"Alfredo",
""
],
[
"Dall'Asta",
"Luca",
""
],
[
"Lage-Castellanos",
"Alejandro",
""
],
[
"Zecchina",
"Riccardo",
""
]
] | We study several bayesian inference problems for irreversible stochastic epidemic models on networks from a statistical physics viewpoint. We derive equations which allow to accurately compute the posterior distribution of the time evolution of the state of each node given some observations. At difference with most exi... |
1310.2024 | Silvia Scarpetta | Silvia Scarpetta and Antonio de Candia | Neural Avalanches at the Critical Point between Replay and Non-Replay of
Spatiotemporal Patterns | null | PLOS ONE June 2013 | Volume 8 | Issue 6 | e64162 | 10.1371/journal.pone.0064162 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We model spontaneous cortical activity with a network of coupled spiking
units, in which multiple spatio-temporal patterns are stored as dynamical
attractors. We introduce an order parameter, which measures the overlap
(similarity) between the activity of the network and the stored patterns. We
find that, depending o... | [
{
"created": "Tue, 8 Oct 2013 07:58:14 GMT",
"version": "v1"
}
] | 2015-06-17 | [
[
"Scarpetta",
"Silvia",
""
],
[
"de Candia",
"Antonio",
""
]
] | We model spontaneous cortical activity with a network of coupled spiking units, in which multiple spatio-temporal patterns are stored as dynamical attractors. We introduce an order parameter, which measures the overlap (similarity) between the activity of the network and the stored patterns. We find that, depending on ... |
1711.10386 | Congrui Jin | Rakenth R. Menon, Jing Luo, Xiaobo Chen, Hui Zhou, Zhiyong Liu,
Guangwen Zhou, Ning Zhang, Congrui Jin | Screening of Fungi for the Application of Self-Healing Concrete | 21 pages. arXiv admin note: text overlap with arXiv:1708.01337 | null | null | null | q-bio.OT physics.app-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Concrete is susceptible to cracking owing to drying shrinkage, freeze-thaw
cycles, delayed ettringite formation, reinforcement corrosion, creep and
fatigue, etc. Since maintenance and inspection of concrete infrastructure
require onerous labor and high costs, self-healing of harmful cracks without
human interference ... | [
{
"created": "Thu, 23 Nov 2017 20:26:27 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Dec 2017 08:21:14 GMT",
"version": "v2"
},
{
"created": "Fri, 22 Dec 2017 03:45:44 GMT",
"version": "v3"
},
{
"created": "Thu, 1 Mar 2018 02:05:01 GMT",
"version": "v4"
},
{
"cre... | 2018-07-17 | [
[
"Menon",
"Rakenth R.",
""
],
[
"Luo",
"Jing",
""
],
[
"Chen",
"Xiaobo",
""
],
[
"Zhou",
"Hui",
""
],
[
"Liu",
"Zhiyong",
""
],
[
"Zhou",
"Guangwen",
""
],
[
"Zhang",
"Ning",
""
],
[
"Jin",
"Cong... | Concrete is susceptible to cracking owing to drying shrinkage, freeze-thaw cycles, delayed ettringite formation, reinforcement corrosion, creep and fatigue, etc. Since maintenance and inspection of concrete infrastructure require onerous labor and high costs, self-healing of harmful cracks without human interference or... |
1712.00336 | Junfang Chen | Junfang Chen and Emanuel Schwarz | BioMM: Biologically-informed Multi-stage Machine learning for
identification of epigenetic fingerprints | 6 pages, NIPS 2017 ML4H | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The identification of reproducible biological patterns from high-dimensional
data is a bottleneck for understanding the biology of complex illnesses such as
schizophrenia. To address this, we developed a biologically informed,
multi-stage machine learning (BioMM) framework. BioMM incorporates biological
pathway infor... | [
{
"created": "Fri, 1 Dec 2017 14:31:27 GMT",
"version": "v1"
}
] | 2017-12-04 | [
[
"Chen",
"Junfang",
""
],
[
"Schwarz",
"Emanuel",
""
]
] | The identification of reproducible biological patterns from high-dimensional data is a bottleneck for understanding the biology of complex illnesses such as schizophrenia. To address this, we developed a biologically informed, multi-stage machine learning (BioMM) framework. BioMM incorporates biological pathway informa... |
2212.04827 | Cyprien Tamekue | Cyprien Tamekue, Dario Prandi, Yacine Chitour | Cortical origins of MacKay-type visual illusions: A case for the
non-linearity | null | null | null | null | q-bio.NC cs.NA math.NA math.OC nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To study the interaction between retinal stimulation by redundant geometrical
patterns and the cortical response in the primary visual cortex (V1), we focus
on the MacKay effect (Nature, 1957) and Billock and Tsou's experiments (PNAS,
2007). We use a controllability approach to describe these phenomena starting
from ... | [
{
"created": "Fri, 9 Dec 2022 12:57:14 GMT",
"version": "v1"
},
{
"created": "Fri, 16 Jun 2023 14:26:16 GMT",
"version": "v2"
}
] | 2023-06-19 | [
[
"Tamekue",
"Cyprien",
""
],
[
"Prandi",
"Dario",
""
],
[
"Chitour",
"Yacine",
""
]
] | To study the interaction between retinal stimulation by redundant geometrical patterns and the cortical response in the primary visual cortex (V1), we focus on the MacKay effect (Nature, 1957) and Billock and Tsou's experiments (PNAS, 2007). We use a controllability approach to describe these phenomena starting from a ... |
2303.09669 | Thomas Bury | Thomas M. Bury, Daniel Dylewsky, Chris T. Bauch, Madhur Anand, Leon
Glass, Alvin Shrier, Gil Bub | Predicting discrete-time bifurcations with deep learning | null | Nat Commun 14, 6331 (2023) | 10.1038/s41467-023-42020-z | null | q-bio.QM cs.LG math.DS | http://creativecommons.org/licenses/by/4.0/ | Many natural and man-made systems are prone to critical transitions -- abrupt
and potentially devastating changes in dynamics. Deep learning classifiers can
provide an early warning signal (EWS) for critical transitions by learning
generic features of bifurcations (dynamical instabilities) from large simulated
traini... | [
{
"created": "Thu, 16 Mar 2023 22:08:41 GMT",
"version": "v1"
},
{
"created": "Thu, 8 Feb 2024 20:59:42 GMT",
"version": "v2"
}
] | 2024-02-12 | [
[
"Bury",
"Thomas M.",
""
],
[
"Dylewsky",
"Daniel",
""
],
[
"Bauch",
"Chris T.",
""
],
[
"Anand",
"Madhur",
""
],
[
"Glass",
"Leon",
""
],
[
"Shrier",
"Alvin",
""
],
[
"Bub",
"Gil",
""
]
] | Many natural and man-made systems are prone to critical transitions -- abrupt and potentially devastating changes in dynamics. Deep learning classifiers can provide an early warning signal (EWS) for critical transitions by learning generic features of bifurcations (dynamical instabilities) from large simulated training... |
1802.07562 | Sirio Orozco-Fuentes | S. Orozco-Fuentes, G. Griffiths, M. J. Holmes, R. Ettelaie, J. Smith,
A. W. Baggaley and N. G. Parker | Early warning signals in plant disease outbreaks | 11 pages | null | 10.1016/j.ecolmodel.2018.11.003 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Summary
1. Infectious disease outbreaks in plants threaten ecosystems, agricultural
crops and food trade. Currently, several fungal diseases are affecting forests
worldwide, posing a major risk to tree species, habitats and consequently
ecosystem decay. Prediction and control of disease spread are difficult, mainly... | [
{
"created": "Wed, 21 Feb 2018 13:29:49 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Dec 2018 22:06:14 GMT",
"version": "v2"
}
] | 2018-12-18 | [
[
"Orozco-Fuentes",
"S.",
""
],
[
"Griffiths",
"G.",
""
],
[
"Holmes",
"M. J.",
""
],
[
"Ettelaie",
"R.",
""
],
[
"Smith",
"J.",
""
],
[
"Baggaley",
"A. W.",
""
],
[
"Parker",
"N. G.",
""
]
] | Summary 1. Infectious disease outbreaks in plants threaten ecosystems, agricultural crops and food trade. Currently, several fungal diseases are affecting forests worldwide, posing a major risk to tree species, habitats and consequently ecosystem decay. Prediction and control of disease spread are difficult, mainly due... |
2301.04739 | Mike Klymkowsky | Michael W. Klymkowsky | Making sense of noise: introducing students to stochastic processes in
order to better understand biological behaviors | 10 pages, 7 embedded figures, 3 text boxes | null | null | null | q-bio.CB q-bio.MN | http://creativecommons.org/licenses/by-sa/4.0/ | Biological systems are characterized by the ubiquitous roles of weak, that
is, non-covalent molecular interactions, small, often very small, numbers of
specific molecules per cell, and Brownian motion. These combine to produce
stochastic behaviors at all levels from the molecular and cellular to the
behavioral. That ... | [
{
"created": "Wed, 11 Jan 2023 22:11:05 GMT",
"version": "v1"
},
{
"created": "Wed, 26 Apr 2023 15:03:22 GMT",
"version": "v2"
}
] | 2023-04-27 | [
[
"Klymkowsky",
"Michael W.",
""
]
] | Biological systems are characterized by the ubiquitous roles of weak, that is, non-covalent molecular interactions, small, often very small, numbers of specific molecules per cell, and Brownian motion. These combine to produce stochastic behaviors at all levels from the molecular and cellular to the behavioral. That sa... |
1708.01502 | Liang Yu | Liang Yu, Jin Zhao, Lin Gao | Predicting potential treatments for complex diseases based on miRNA and
tissue specificity | null | null | null | null | q-bio.GN cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Drug repositioning, that is finding new uses for existing drugs to treat more
patients. Cumulative studies demonstrate that the mature miRNAs as well as
their precursors can be targeted by small molecular drugs. At the same time,
human diseases result from the disordered interplay of tissue- and cell
lineage-specific... | [
{
"created": "Fri, 30 Jun 2017 09:57:54 GMT",
"version": "v1"
}
] | 2017-08-07 | [
[
"Yu",
"Liang",
""
],
[
"Zhao",
"Jin",
""
],
[
"Gao",
"Lin",
""
]
] | Drug repositioning, that is finding new uses for existing drugs to treat more patients. Cumulative studies demonstrate that the mature miRNAs as well as their precursors can be targeted by small molecular drugs. At the same time, human diseases result from the disordered interplay of tissue- and cell lineage-specific p... |
2002.04564 | John Rhodes | Samaneh Yourdkhani and John A. Rhodes | Inferring metric trees from weighted quartets via an intertaxon distance | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A metric phylogenetic tree relating a collection of taxa induces weighted
rooted triples and weighted quartets for all subsets of three and four taxa,
respectively. New intertaxon distances are defined that can be calculated from
these weights, and shown to exactly fit the same tree topology, but with edge
weights re... | [
{
"created": "Tue, 11 Feb 2020 17:39:24 GMT",
"version": "v1"
}
] | 2020-02-12 | [
[
"Yourdkhani",
"Samaneh",
""
],
[
"Rhodes",
"John A.",
""
]
] | A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these weights, and shown to exactly fit the same tree topology, but with edge weights resc... |
1105.0627 | Bernhard Mehlig | E. Schaper, A. Eriksson, M. Rafajlovic, S. Sagitov, and B. Mehlig | Linkage disequilibrium under recurrent bottlenecks | 34 pages, 7 figures | Genetics 190, 217 (2012) | 10.1534/genetics.111.134437 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding patterns of selectively neutral genetic variation is essential
in order to model deviations from neutrality, caused for example by different
forms of selection. Best understood is neutral genetic variation at a single
locus, but additional insights can be gained by investigating genetic variation
at mul... | [
{
"created": "Tue, 3 May 2011 16:30:25 GMT",
"version": "v1"
}
] | 2012-06-13 | [
[
"Schaper",
"E.",
""
],
[
"Eriksson",
"A.",
""
],
[
"Rafajlovic",
"M.",
""
],
[
"Sagitov",
"S.",
""
],
[
"Mehlig",
"B.",
""
]
] | Understanding patterns of selectively neutral genetic variation is essential in order to model deviations from neutrality, caused for example by different forms of selection. Best understood is neutral genetic variation at a single locus, but additional insights can be gained by investigating genetic variation at multi... |
2408.07250 | Alejandro Leon PhD | Carlos Alberto Hern\'andez-Linares, Porfirio Toledo, Brenda Zarah\'i
Medina-P\'erez, Varsovia Hern\'andez, Martha Lorena Avenda\~no Garrido,
V\'ictor Quintero, Alejandro Le\'on | Spatial Dynamics Behavioral Analysis of Motivational Operations Using
Weighted Voronoi Diagrams | 10 pages, 3 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper presents a novel approach to the analysis of spatial behavior
distribution, utilizing weighted Voronoi diagrams. The objective is to map and
understand how an experimental subject moves and spends time in various areas
of a given space, thus identifying the areas of greatest behavioral interest.
The techni... | [
{
"created": "Wed, 14 Aug 2024 01:26:22 GMT",
"version": "v1"
}
] | 2024-08-15 | [
[
"Hernández-Linares",
"Carlos Alberto",
""
],
[
"Toledo",
"Porfirio",
""
],
[
"Medina-Pérez",
"Brenda Zarahí",
""
],
[
"Hernández",
"Varsovia",
""
],
[
"Garrido",
"Martha Lorena Avendaño",
""
],
[
"Quintero",
"Víctor",
""
... | This paper presents a novel approach to the analysis of spatial behavior distribution, utilizing weighted Voronoi diagrams. The objective is to map and understand how an experimental subject moves and spends time in various areas of a given space, thus identifying the areas of greatest behavioral interest. The techniqu... |
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