id stringlengths 9 13 | submitter stringlengths 4 48 | authors stringlengths 4 9.62k | title stringlengths 4 343 | comments stringlengths 2 480 ⌀ | journal-ref stringlengths 9 309 ⌀ | doi stringlengths 12 138 ⌀ | report-no stringclasses 277
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1310.4232 | Alexander Goltsev | K.-E. Lee, M. A. Lopes, J. F. F. Mendes, and A. V. Goltsev | Critical phenomena and noise-induced phase transitions in neuronal
networks | 15 pages, 9 figures. arXiv admin note: substantial text overlap with
arXiv:1304.3237 | Phys. Rev. E. 89, 012701 (2014) | 10.1103/PhysRevE.89.012701 | null | q-bio.NC nlin.AO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study numerically and analytically first- and second-order phase
transitions in neuronal networks stimulated by shot noise (a flow of random
spikes bombarding neurons). Using an exactly solvable cortical model of
neuronal networks on classical random networks, we find critical phenomena
accompanying the transition... | [
{
"created": "Wed, 16 Oct 2013 00:42:29 GMT",
"version": "v1"
}
] | 2015-08-25 | [
[
"Lee",
"K. -E.",
""
],
[
"Lopes",
"M. A.",
""
],
[
"Mendes",
"J. F. F.",
""
],
[
"Goltsev",
"A. V.",
""
]
] | We study numerically and analytically first- and second-order phase transitions in neuronal networks stimulated by shot noise (a flow of random spikes bombarding neurons). Using an exactly solvable cortical model of neuronal networks on classical random networks, we find critical phenomena accompanying the transitions ... |
2311.00616 | Steffen Werner | W. Mathijs Rozemuller, Steffen Werner, Antonio Carlos Costa, Liam
O'Shaughnessy, Greg J. Stephens, Thomas S. Shimizu | Statistics of C. elegans turning behavior reveals optimality under
biasing constraints | 32 pages, 17 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Animal locomotion is often subject to constraints arising from
anatomical/physiological asymmetries. We use the nematode C.~elegans as a
minimal model system to ask whether such constraints might shape locomotion
patterns optimized during evolution. We focus on turning behaviours in two
contrasting environmental cont... | [
{
"created": "Wed, 1 Nov 2023 16:08:26 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Jan 2024 11:58:02 GMT",
"version": "v2"
}
] | 2024-01-17 | [
[
"Rozemuller",
"W. Mathijs",
""
],
[
"Werner",
"Steffen",
""
],
[
"Costa",
"Antonio Carlos",
""
],
[
"O'Shaughnessy",
"Liam",
""
],
[
"Stephens",
"Greg J.",
""
],
[
"Shimizu",
"Thomas S.",
""
]
] | Animal locomotion is often subject to constraints arising from anatomical/physiological asymmetries. We use the nematode C.~elegans as a minimal model system to ask whether such constraints might shape locomotion patterns optimized during evolution. We focus on turning behaviours in two contrasting environmental contex... |
q-bio/0602023 | Gyorgy Korniss | Lauren O'Malley, James Basham, Joseph A. Yasi, G. Korniss, Andrew
Allstadt, and Tom Caraco | Invasive advance of an advantageous mutation: nucleation theory | null | Theoretical Population Biology, 70, 464-478 (2006). | 10.1016/j.tpb.2006.06.006 | null | q-bio.PE cond-mat.stat-mech | null | For most organisms with viscous population structure, spatially localized
growth drives the invasive advance of a favorable mutation. We model a
two-allele competition where recurrent mutation introduces a genotype with a
rate of local propagation exceeding the resident's rate. We capture
ecologically important prope... | [
{
"created": "Wed, 22 Feb 2006 22:25:45 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"O'Malley",
"Lauren",
""
],
[
"Basham",
"James",
""
],
[
"Yasi",
"Joseph A.",
""
],
[
"Korniss",
"G.",
""
],
[
"Allstadt",
"Andrew",
""
],
[
"Caraco",
"Tom",
""
]
] | For most organisms with viscous population structure, spatially localized growth drives the invasive advance of a favorable mutation. We model a two-allele competition where recurrent mutation introduces a genotype with a rate of local propagation exceeding the resident's rate. We capture ecologically important propert... |
1409.1637 | Toru Aonishi | Kazuhiko Morinaga, Ryota Miyata and Toru Aonishi | Optimal Colored Noise for Estimating Phase Response Curves | 12 pages, 4 figures | J. Phys. Soc. Jpn., 84(9): 094801 (2015) | 10.7566/JPSJ.84.094801 | null | q-bio.QM nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The phase response curve (PRC) is an important measure representing the
interaction between oscillatory elements. To understand synchrony in biological
systems, many research groups have sought to measure PRCs directly from
biological cells including neurons. Ermentrout et al. and Ota et al. showed
that PRCs can be i... | [
{
"created": "Fri, 5 Sep 2014 01:11:26 GMT",
"version": "v1"
},
{
"created": "Wed, 7 Jan 2015 07:55:33 GMT",
"version": "v2"
},
{
"created": "Mon, 6 Jul 2015 03:30:50 GMT",
"version": "v3"
}
] | 2015-08-03 | [
[
"Morinaga",
"Kazuhiko",
""
],
[
"Miyata",
"Ryota",
""
],
[
"Aonishi",
"Toru",
""
]
] | The phase response curve (PRC) is an important measure representing the interaction between oscillatory elements. To understand synchrony in biological systems, many research groups have sought to measure PRCs directly from biological cells including neurons. Ermentrout et al. and Ota et al. showed that PRCs can be ide... |
2103.15182 | Pan Wang | Pan Wang, Danlin Peng, Simiao Yu, Chao Wu, Peter Childs, Yike Guo and
Ling Li | Verifying Design through Generative Visualization of Neural Activities | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Current neuroscience focused approaches for evaluating the effectiveness of a
design do not use direct visualisation of mental activity. A recurrent neural
network is used as the encoder to learn latent representation from
electroencephalogram (EEG) signals, recorded while subjects looked at 50
categories of images. ... | [
{
"created": "Sun, 28 Mar 2021 17:42:21 GMT",
"version": "v1"
}
] | 2021-03-30 | [
[
"Wang",
"Pan",
""
],
[
"Peng",
"Danlin",
""
],
[
"Yu",
"Simiao",
""
],
[
"Wu",
"Chao",
""
],
[
"Childs",
"Peter",
""
],
[
"Guo",
"Yike",
""
],
[
"Li",
"Ling",
""
]
] | Current neuroscience focused approaches for evaluating the effectiveness of a design do not use direct visualisation of mental activity. A recurrent neural network is used as the encoder to learn latent representation from electroencephalogram (EEG) signals, recorded while subjects looked at 50 categories of images. A ... |
1709.01852 | Marcos Amaku | Eduardo Massad, Marcos Amaku, Francisco Antonio Bezerra Coutinho,
Claudio Jos\'e Struchiner, Luis Fernandez Lopez, Annelies Wilder-Smith and
Marcelo Nascimento Burattini | Estimating the Size of Aedes aegypti Populations from Dengue Incidence
Data: Implications for the Risk of Yellow Fever, Zika Virus and Chikungunya
Outbreaks | 31 pages, 9 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we present a model to estimate the density of aedes mosquitoes
in a community affected by dengue. The model is based on the fitting of a
continuous function to the incidence of dengue infections, from which the
density of infected mosquitoes is derived straightforwardly. Further
derivations allows the c... | [
{
"created": "Wed, 6 Sep 2017 15:09:31 GMT",
"version": "v1"
},
{
"created": "Thu, 26 Oct 2017 16:11:47 GMT",
"version": "v2"
},
{
"created": "Tue, 7 Nov 2017 16:04:14 GMT",
"version": "v3"
}
] | 2017-11-08 | [
[
"Massad",
"Eduardo",
""
],
[
"Amaku",
"Marcos",
""
],
[
"Coutinho",
"Francisco Antonio Bezerra",
""
],
[
"Struchiner",
"Claudio José",
""
],
[
"Lopez",
"Luis Fernandez",
""
],
[
"Wilder-Smith",
"Annelies",
""
],
[
... | In this paper we present a model to estimate the density of aedes mosquitoes in a community affected by dengue. The model is based on the fitting of a continuous function to the incidence of dengue infections, from which the density of infected mosquitoes is derived straightforwardly. Further derivations allows the cal... |
2108.06264 | Marta Bienkiewicz Dr | M. M. N. Bie\'nkiewicz (1), A. Smykovskyi (1), T. Olugbade (2), S.
Janaqi (1), A. Camurri (3), N. Bianchi-Berthouze (2), M. Bj\"orkman (4), B.
G. Bardy (1) ((1) EuroMov Digital Health in Motion Univ. Montpellier IMT
Mines Ales France, (2) UCL, University College of London UK, (3) UNIGE
InfoMus Casa Paganini Ita... | Bridging the gap between emotion and joint action | Pages 44, Figures 6, Table 1, Article in press, Neuroscience and
Biobehavioral Reviews | null | null | null | q-bio.NC cs.LG cs.MA cs.RO math.DS | http://creativecommons.org/licenses/by/4.0/ | Our daily human life is filled with a myriad of joint action moments, be it
children playing, adults working together (i.e., team sports), or strangers
navigating through a crowd. Joint action brings individuals (and embodiment of
their emotions) together, in space and in time. Yet little is known about how
individua... | [
{
"created": "Fri, 13 Aug 2021 14:21:37 GMT",
"version": "v1"
}
] | 2021-08-16 | [
[
"Bieńkiewicz",
"M. M. N.",
""
],
[
"Smykovskyi",
"A.",
""
],
[
"Olugbade",
"T.",
""
],
[
"Janaqi",
"S.",
""
],
[
"Camurri",
"A.",
""
],
[
"Bianchi-Berthouze",
"N.",
""
],
[
"Björkman",
"M.",
""
],
[
... | Our daily human life is filled with a myriad of joint action moments, be it children playing, adults working together (i.e., team sports), or strangers navigating through a crowd. Joint action brings individuals (and embodiment of their emotions) together, in space and in time. Yet little is known about how individual ... |
2102.12299 | Jennifer Loria Sorio | Vinicius V. L. Albani, Jennifer Loria, Eduardo Massad and Jorge P.
Zubelli | The Impact of COVID-19 Vaccination Delay: A Modelling Study for Chicago
and NYC Data | 21 pages, 6 figures, 3 tables | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Background: By the beginning of December 2020, some vaccines against COVID-19
already presented efficacy and security, which qualify them to be used in mass
vaccination campaigns. Thus, setting up strategies of vaccination became
crucial to control the COVID19 pandemic. Methods: We use daily COVID-19 reports
from Chi... | [
{
"created": "Wed, 24 Feb 2021 14:29:30 GMT",
"version": "v1"
}
] | 2021-02-25 | [
[
"Albani",
"Vinicius V. L.",
""
],
[
"Loria",
"Jennifer",
""
],
[
"Massad",
"Eduardo",
""
],
[
"Zubelli",
"Jorge P.",
""
]
] | Background: By the beginning of December 2020, some vaccines against COVID-19 already presented efficacy and security, which qualify them to be used in mass vaccination campaigns. Thus, setting up strategies of vaccination became crucial to control the COVID19 pandemic. Methods: We use daily COVID-19 reports from Chica... |
1910.09510 | Emmanuelle Jousselin | Emmanuelle Jousselin, Marianne Elias | Testing host-plant driven speciation in phytophagous insects : a
phylogenetic perspective | 35 pages, 3 figures, 2 tables. Peer-reviewed and recommended by PCI
Evolutionary Biology (2019) | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | During the last two decades, ecological speciation has been a major research
theme in evolutionary biology. Ecological speciation occurs when reproductive
isolation between populations evolves as a result of niche differentiation.
Phytophagous insects represent model systems for the study of this evolutionary
process... | [
{
"created": "Mon, 21 Oct 2019 16:58:23 GMT",
"version": "v1"
},
{
"created": "Wed, 23 Oct 2019 08:55:08 GMT",
"version": "v2"
}
] | 2019-10-24 | [
[
"Jousselin",
"Emmanuelle",
""
],
[
"Elias",
"Marianne",
""
]
] | During the last two decades, ecological speciation has been a major research theme in evolutionary biology. Ecological speciation occurs when reproductive isolation between populations evolves as a result of niche differentiation. Phytophagous insects represent model systems for the study of this evolutionary process. ... |
2301.05782 | Steven Rossi | Steven P. Rossi, Sean P. Cox, Samuel D.N. Johnson, Ashleen J. Benson | Evaluating the sustainability of a de facto harvest strategy for British
Columbia's Spot Prawn (Pandalus platyceros) fishery in the presence of
environmental drivers of recruitment and hyperstable catch rates | 86 pages, 12 figures, 33 appendix figures | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Spot Prawn trap fishery off the west coast of British Columbia (BC) is
managed using a fixed escapement strategy that aims to prevent recruitment
overfishing while maximizing expected long-term yield by closing the fishery
when the catch rate of spawners, projected to the following spring, drops below
1.7 spawner... | [
{
"created": "Fri, 13 Jan 2023 22:56:21 GMT",
"version": "v1"
}
] | 2023-01-18 | [
[
"Rossi",
"Steven P.",
""
],
[
"Cox",
"Sean P.",
""
],
[
"Johnson",
"Samuel D. N.",
""
],
[
"Benson",
"Ashleen J.",
""
]
] | The Spot Prawn trap fishery off the west coast of British Columbia (BC) is managed using a fixed escapement strategy that aims to prevent recruitment overfishing while maximizing expected long-term yield by closing the fishery when the catch rate of spawners, projected to the following spring, drops below 1.7 spawners ... |
1512.09370 | Emma Perracchione | Giorgio Sabetta, Emma Perracchione, Ezio Venturino | Wild herbivores in forests: four case studies | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A three population system with a top predator population, i.e. the
herbivores, and two prey populations, grass and trees, is considered to model
the interaction of herbivores with natural resources. We apply the model for
four natural mountain parks in Northern Italy, three located in the Eastern
Alps, two of which i... | [
{
"created": "Sat, 12 Dec 2015 19:02:03 GMT",
"version": "v1"
}
] | 2019-07-09 | [
[
"Sabetta",
"Giorgio",
""
],
[
"Perracchione",
"Emma",
""
],
[
"Venturino",
"Ezio",
""
]
] | A three population system with a top predator population, i.e. the herbivores, and two prey populations, grass and trees, is considered to model the interaction of herbivores with natural resources. We apply the model for four natural mountain parks in Northern Italy, three located in the Eastern Alps, two of which in ... |
1701.07243 | Francois Meyer | Fran\c{c}ois G. Meyer, Alexander M. Benison, Zachariah Smith, and
Daniel S. Barth | Decoding Epileptogenesis in a Reduced State Space | null | null | null | null | q-bio.NC cs.LG q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We describe here the recent results of a multidisciplinary effort to design a
biomarker that can actively and continuously decode the progressive changes in
neuronal organization leading to epilepsy, a process known as epileptogenesis.
Using an animal model of acquired epilepsy, wechronically record hippocampal
evoke... | [
{
"created": "Wed, 25 Jan 2017 10:25:59 GMT",
"version": "v1"
}
] | 2017-01-26 | [
[
"Meyer",
"François G.",
""
],
[
"Benison",
"Alexander M.",
""
],
[
"Smith",
"Zachariah",
""
],
[
"Barth",
"Daniel S.",
""
]
] | We describe here the recent results of a multidisciplinary effort to design a biomarker that can actively and continuously decode the progressive changes in neuronal organization leading to epilepsy, a process known as epileptogenesis. Using an animal model of acquired epilepsy, wechronically record hippocampal evoked ... |
1912.13417 | Changcheng Sheng | Changcheng Sheng, Qun Zhao, Wanjie Niu, Xiaoyan Qiu, Ming Zhang, Zheng
Jiao | Effect of protein binding on exposure of unbound and total mycophenolic
acid: a population pharmacokinetic analysis in Chinese adult kidney
transplant recipients | 39 pages, 3 tables, 5 figures, 1 supplementary table and 1
supplementary figure | Front. Pharmacol. (2020) 11:340 | 10.3389/fphar.2020.00340 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | AIMS A population pharmacokinetic (PK) analysis was performed to: (1)
characterise the PK of unbound and total mycophenolic acid (MPA) and its
7-O-mycophenolic acid glucuronide (MPAG) metabolite, and (2) identify the
clinically significant covariates that cause variability in the dose-exposure
relationship to facilit... | [
{
"created": "Sat, 21 Dec 2019 03:11:22 GMT",
"version": "v1"
}
] | 2020-03-24 | [
[
"Sheng",
"Changcheng",
""
],
[
"Zhao",
"Qun",
""
],
[
"Niu",
"Wanjie",
""
],
[
"Qiu",
"Xiaoyan",
""
],
[
"Zhang",
"Ming",
""
],
[
"Jiao",
"Zheng",
""
]
] | AIMS A population pharmacokinetic (PK) analysis was performed to: (1) characterise the PK of unbound and total mycophenolic acid (MPA) and its 7-O-mycophenolic acid glucuronide (MPAG) metabolite, and (2) identify the clinically significant covariates that cause variability in the dose-exposure relationship to facilitat... |
1003.1896 | Dietrich Stauffer | D. Stauffer and S. Cebrat | Love kills Penna ageing model | Two pages including figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | No abstract needed since short
| [
{
"created": "Tue, 9 Mar 2010 15:18:26 GMT",
"version": "v1"
}
] | 2010-03-10 | [
[
"Stauffer",
"D.",
""
],
[
"Cebrat",
"S.",
""
]
] | No abstract needed since short |
1310.0424 | Susan Holmes | Paul J. McMurdie and Susan Holmes | Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissible | 22 pages, 5 figures, 2 supplementary sections | null | 10.1371/journal.pcbi.1003531 | null | q-bio.QM q-bio.GN stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The interpretation of count data originating from the current generation of
DNA sequencing platforms requires special attention. In particular, the
per-sample library sizes often vary by orders of magnitude from the same
sequencing run, and the counts are overdispersed relative to a simple Poisson
model These challen... | [
{
"created": "Tue, 1 Oct 2013 18:54:24 GMT",
"version": "v1"
},
{
"created": "Thu, 12 Dec 2013 08:57:05 GMT",
"version": "v2"
}
] | 2015-06-17 | [
[
"McMurdie",
"Paul J.",
""
],
[
"Holmes",
"Susan",
""
]
] | The interpretation of count data originating from the current generation of DNA sequencing platforms requires special attention. In particular, the per-sample library sizes often vary by orders of magnitude from the same sequencing run, and the counts are overdispersed relative to a simple Poisson model These challenge... |
0811.0055 | Christopher L. Henley | Christopher L. Henley (Cornell Univ.) | Possible mechanisms for initiating macroscopic left-right asymmetry in
developing organisms | 9 pp latex, 6 figures. Proc. Landau 100 Memorial Conf.
(Chernogolovka, June 2008); to appear AIP Conf. series. (v2: added 4 ref's +
revised Sec 2.2.) | null | 10.1063/1.3149499 | null | q-bio.TO q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How might systematic left-right (L/R) asymmetry of the body plan originate in
multicellular animals (and plants)? Somehow, the microscopic handedness of
biological molecules must be brought up to macroscopic scales. Basic symmetry
principles suggest that the usual "biological" mechanisms -- diffusion and gene
regulat... | [
{
"created": "Sat, 1 Nov 2008 02:52:58 GMT",
"version": "v1"
},
{
"created": "Sat, 29 Nov 2008 19:40:29 GMT",
"version": "v2"
}
] | 2015-05-13 | [
[
"Henley",
"Christopher L.",
"",
"Cornell Univ."
]
] | How might systematic left-right (L/R) asymmetry of the body plan originate in multicellular animals (and plants)? Somehow, the microscopic handedness of biological molecules must be brought up to macroscopic scales. Basic symmetry principles suggest that the usual "biological" mechanisms -- diffusion and gene regulatio... |
1302.3022 | Michel Destrade | Aisling Ni Annaidh, Karine Bruyere, Michel Destrade, Michael D.
Gilchrist, Melanie Ottenio | Characterising the Anisotropic Mechanical Properties of Excised Human
Skin | 23 pages | Journal of the Mechanical Behavior of Biomedical Materials, 5
(2012) 139-148 | 10.1016/j.jmbbm.2011.08.016 | null | q-bio.TO cond-mat.soft physics.bio-ph physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The mechanical properties of skin are important for a number of applications
including surgery, dermatology, impact biomechanics and forensic science. In
this study we have investigated the influence of location and orientation on
the deformation characteristics of 56 samples of excised human skin. Uniaxial
tensile t... | [
{
"created": "Wed, 13 Feb 2013 09:06:42 GMT",
"version": "v1"
}
] | 2013-02-14 | [
[
"Annaidh",
"Aisling Ni",
""
],
[
"Bruyere",
"Karine",
""
],
[
"Destrade",
"Michel",
""
],
[
"Gilchrist",
"Michael D.",
""
],
[
"Ottenio",
"Melanie",
""
]
] | The mechanical properties of skin are important for a number of applications including surgery, dermatology, impact biomechanics and forensic science. In this study we have investigated the influence of location and orientation on the deformation characteristics of 56 samples of excised human skin. Uniaxial tensile tes... |
1411.4704 | Neil Page | N.W. Page, C. Hall and S.D. Page | Deep Brain Stimulation for Parkinson's Disease: a survey of experiences
perceived by recipients and carers | 45 pages, 32 figures and 23 tables | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Perceived outcomes from DBS for PD were sampled for 52 cases by surveying 46
DBS recipients and 45 carers. Post-DBS experience ranged from 10-129 months.
There were significant variations in perceived outcomes over time. In some
cases extreme variations were experienced as a consequence of hardware and
other problems... | [
{
"created": "Tue, 18 Nov 2014 00:45:44 GMT",
"version": "v1"
},
{
"created": "Mon, 10 Aug 2015 00:00:51 GMT",
"version": "v2"
}
] | 2015-08-11 | [
[
"Page",
"N. W.",
""
],
[
"Hall",
"C.",
""
],
[
"Page",
"S. D.",
""
]
] | Perceived outcomes from DBS for PD were sampled for 52 cases by surveying 46 DBS recipients and 45 carers. Post-DBS experience ranged from 10-129 months. There were significant variations in perceived outcomes over time. In some cases extreme variations were experienced as a consequence of hardware and other problems r... |
1304.4201 | Karin Vadovi\v{c}ov\'a | Karin Vadovi\v{c}ov\'a, Roberto Gasparotti | Reward and adversity processing circuits, their competition and
interactions with dopamine and serotonin signaling | Reference [27] was updated to: Vadovi\v{c}ov\'a K: Affective and
cognitive prefrontal cortex projections to the lateral habenula in humans.
arXiv:1402.2196, re-published in Front Hum Neurosci 2014, 8:819. doi:
10.3389/fnhum.2014.00819 Few English errors were corrected and the
Abbreviations chapter was deleted | null | 10.14293/S2199-1006.1.SOR-LIFE.AEKZPZ.v1 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose that dACC, AI and caudolateral OFC(clOFC) project to lateral
habenula (LHb) and D2 loop of ventral striatum (VS), forming a functional
adversity processing circuit, directed towards inhibitory avoidance and
self-control. This circuit learns what is bad or harmful to us and predicts
risks, to stop us from g... | [
{
"created": "Mon, 15 Apr 2013 19:05:50 GMT",
"version": "v1"
},
{
"created": "Wed, 14 May 2014 14:54:51 GMT",
"version": "v10"
},
{
"created": "Tue, 9 Sep 2014 10:10:38 GMT",
"version": "v11"
},
{
"created": "Thu, 16 Oct 2014 08:18:23 GMT",
"version": "v12"
},
{
... | 2014-11-18 | [
[
"Vadovičová",
"Karin",
""
],
[
"Gasparotti",
"Roberto",
""
]
] | We propose that dACC, AI and caudolateral OFC(clOFC) project to lateral habenula (LHb) and D2 loop of ventral striatum (VS), forming a functional adversity processing circuit, directed towards inhibitory avoidance and self-control. This circuit learns what is bad or harmful to us and predicts risks, to stop us from goi... |
2311.07168 | No First Name Abdul Samad | Muhammad Hamza, Hafeez Ur Rehman Ali Khera, Muhammad Umair Waqas,
Ayesha Muazzam, Sania Tariq, Zain Kaleem, Waseem Akram, M Talha Mumtaz,
Shehroz Ahmad, and Abdul Samad | Misuse of Antibiotics in Poultry Threatens Pakistan Communitys Health | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | A survey was conducted from February 2022 to May 2022 on the usage of
antibiotics at a poultry farm in different areas of Multan, Punjab Pakistan. A
well-organized questionnaire was used for the collection of data. Sixty poultry
farms were surveyed randomly in the Multan district. All of these Farms were
using antibi... | [
{
"created": "Mon, 13 Nov 2023 09:02:57 GMT",
"version": "v1"
}
] | 2023-11-14 | [
[
"Hamza",
"Muhammad",
""
],
[
"Khera",
"Hafeez Ur Rehman Ali",
""
],
[
"Waqas",
"Muhammad Umair",
""
],
[
"Muazzam",
"Ayesha",
""
],
[
"Tariq",
"Sania",
""
],
[
"Kaleem",
"Zain",
""
],
[
"Akram",
"Waseem",
"... | A survey was conducted from February 2022 to May 2022 on the usage of antibiotics at a poultry farm in different areas of Multan, Punjab Pakistan. A well-organized questionnaire was used for the collection of data. Sixty poultry farms were surveyed randomly in the Multan district. All of these Farms were using antibiot... |
1604.02733 | Thibaud Taillefumier | Thibaud Taillefumier, Anna Posfai, Yigal Meir and Ned S. Wingreen | Bacterial cartels at steady supply | null | null | null | null | q-bio.PE q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Metagenomics has revealed hundreds of bacterial species in almost all
microbiota. In a few well-studied cases, bacterial communities have been
observed to coordinate their metabolic fluxes. In principle, bacteria can
divide tasks to reap the benefits of specialization, as in human economies.
However, the benefits and... | [
{
"created": "Sun, 10 Apr 2016 21:01:53 GMT",
"version": "v1"
}
] | 2016-04-12 | [
[
"Taillefumier",
"Thibaud",
""
],
[
"Posfai",
"Anna",
""
],
[
"Meir",
"Yigal",
""
],
[
"Wingreen",
"Ned S.",
""
]
] | Metagenomics has revealed hundreds of bacterial species in almost all microbiota. In a few well-studied cases, bacterial communities have been observed to coordinate their metabolic fluxes. In principle, bacteria can divide tasks to reap the benefits of specialization, as in human economies. However, the benefits and s... |
1201.0384 | Victor Novikov PhD | Victor P. Novikov | Three-stage Origin of Life as a Result of Directional Darwinian
Evolution | 10 pages, 3 figures | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The original hypothesis about Three-stage origin of life (TOL) on the Earth
is developed and discussed. The role of the temperature factor in life origin
is considered. It is supposed, that three stages of abiogenesis (DNA world, RNA
world and the Protein world) consistently followed each other during Darwinian
evolu... | [
{
"created": "Sun, 1 Jan 2012 20:55:58 GMT",
"version": "v1"
}
] | 2012-01-04 | [
[
"Novikov",
"Victor P.",
""
]
] | The original hypothesis about Three-stage origin of life (TOL) on the Earth is developed and discussed. The role of the temperature factor in life origin is considered. It is supposed, that three stages of abiogenesis (DNA world, RNA world and the Protein world) consistently followed each other during Darwinian evoluti... |
1501.04078 | Maxim Koroteev | M.V. Koroteev | On a chain of fragmentation equations for duplication-mutation dynamics
in DNA sequences | 8 pages, 7 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent studies have revealed that for the majority of species the length
distributions of duplicated sequences in natural DNA follow a power-law tail.
We study duplication-mutation models for processes in natural DNA sequences and
the length distributions of exact matches computed from both synthetic and
natural sequ... | [
{
"created": "Thu, 15 Jan 2015 11:02:08 GMT",
"version": "v1"
},
{
"created": "Mon, 9 Feb 2015 18:28:24 GMT",
"version": "v2"
},
{
"created": "Tue, 17 Feb 2015 22:04:17 GMT",
"version": "v3"
},
{
"created": "Wed, 3 Jun 2015 13:15:01 GMT",
"version": "v4"
}
] | 2015-06-04 | [
[
"Koroteev",
"M. V.",
""
]
] | Recent studies have revealed that for the majority of species the length distributions of duplicated sequences in natural DNA follow a power-law tail. We study duplication-mutation models for processes in natural DNA sequences and the length distributions of exact matches computed from both synthetic and natural sequen... |
1401.7803 | Ben Shirt-Ediss | Ben Shirt-Ediss, Kepa Ruiz-Mirazo, Fabio Mavelli and Ricard V. Sol\'e | Modelling Lipid Competition Dynamics in Heterogeneous Protocell
Populations | 15 pages, 6 figures, 1 table | null | 10.1038/srep05675 | null | q-bio.QM q-bio.SC | http://creativecommons.org/licenses/by/3.0/ | In addressing the origins of Darwinian evolution, recent experimental work
has been focussed on the discovery of simple physical effects which would
provide a relevant selective advantage to protocells competing with each other
for a limited supply of lipid. In particular, data coming from Szostak's lab
suggest that ... | [
{
"created": "Thu, 30 Jan 2014 11:31:11 GMT",
"version": "v1"
}
] | 2014-07-15 | [
[
"Shirt-Ediss",
"Ben",
""
],
[
"Ruiz-Mirazo",
"Kepa",
""
],
[
"Mavelli",
"Fabio",
""
],
[
"Solé",
"Ricard V.",
""
]
] | In addressing the origins of Darwinian evolution, recent experimental work has been focussed on the discovery of simple physical effects which would provide a relevant selective advantage to protocells competing with each other for a limited supply of lipid. In particular, data coming from Szostak's lab suggest that th... |
1201.6320 | Michael B\"orsch | Stefan Ernst, Monika G. Dueser, Nawid Zarrabi, Michael Boersch | Monitoring transient elastic energy storage within the rotary motors of
single FoF1-ATP synthase by DCO-ALEX FRET | 14 pages, 7 figures | null | 10.1117/12.907086 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The enzyme FoF1-ATP synthase provides the 'chemical energy currency'
adenosine triphosphate (ATP) for living cells. Catalysis is driven by
mechanochemical coupling of subunit rotation within the enzyme with
conformational changes in the three ATP binding sites. Proton translocation
through the membrane-bound Fo part ... | [
{
"created": "Mon, 30 Jan 2012 18:54:14 GMT",
"version": "v1"
}
] | 2015-06-04 | [
[
"Ernst",
"Stefan",
""
],
[
"Dueser",
"Monika G.",
""
],
[
"Zarrabi",
"Nawid",
""
],
[
"Boersch",
"Michael",
""
]
] | The enzyme FoF1-ATP synthase provides the 'chemical energy currency' adenosine triphosphate (ATP) for living cells. Catalysis is driven by mechanochemical coupling of subunit rotation within the enzyme with conformational changes in the three ATP binding sites. Proton translocation through the membrane-bound Fo part of... |
1707.05636 | Valerey Grytsay Dr | V.I. Grytsay | Self-Organization and Fractality in the Metabolic Process of Glycolysis | 13 pages, 5 figures | Ukr. J. Phys., Vol. 59, N 12, p.1251-1262 (2015) | 10.15407/ujpe60.12.1251 | null | q-bio.OT nlin.AO nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Within a mathematical model, the metabolic process of glycolysis is studied.
The general scheme of glycolysis is considered as a natural result of the
biochemical evolution. By using the theory of dissipative structures, the
conditions of self-organization of the given process are sought. The
autocatalytic processes ... | [
{
"created": "Fri, 14 Jul 2017 10:08:18 GMT",
"version": "v1"
}
] | 2017-07-19 | [
[
"Grytsay",
"V. I.",
""
]
] | Within a mathematical model, the metabolic process of glycolysis is studied. The general scheme of glycolysis is considered as a natural result of the biochemical evolution. By using the theory of dissipative structures, the conditions of self-organization of the given process are sought. The autocatalytic processes re... |
q-bio/0410023 | Sheng Li | Fangping Wei, Sheng Li and Hongru Ma | Network of tRNA Gene Sequences | Latex, 18 pages, 17 figures | null | null | null | q-bio.MN cond-mat.stat-mech q-bio.PE | null | We showed in this paper that similarity network can be used as an powerful
tools to study the relationship of tRNA genes. We constructed a network of 3719
tRNA gene sequences using simplest alignment and studied its topology, degree
distribution and clustering coefficient. It is found that the behavior of the
network... | [
{
"created": "Wed, 20 Oct 2004 06:36:29 GMT",
"version": "v1"
},
{
"created": "Sat, 23 Oct 2004 12:22:21 GMT",
"version": "v2"
},
{
"created": "Tue, 14 Dec 2004 12:52:57 GMT",
"version": "v3"
}
] | 2009-09-29 | [
[
"Wei",
"Fangping",
""
],
[
"Li",
"Sheng",
""
],
[
"Ma",
"Hongru",
""
]
] | We showed in this paper that similarity network can be used as an powerful tools to study the relationship of tRNA genes. We constructed a network of 3719 tRNA gene sequences using simplest alignment and studied its topology, degree distribution and clustering coefficient. It is found that the behavior of the network s... |
1911.01988 | Laura Schaposnik | Yuyuan Luo and Laura P. Schaposnik | Minimal percolating sets for mutating infectious diseases | 11 pages, 10 figures | Phys. Rev. Research 2, 023001 (2020) | 10.1103/PhysRevResearch.2.023001 | null | q-bio.PE cs.SI math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper is dedicated to the study of the interaction between dynamical
systems and percolation models, with views towards the study of viral
infections whose virus mutate with time. Recall that r-bootstrap percolation
describes a deterministic process where vertices of a graph are infected once r
neighbors of it a... | [
{
"created": "Tue, 5 Nov 2019 18:27:03 GMT",
"version": "v1"
}
] | 2020-04-08 | [
[
"Luo",
"Yuyuan",
""
],
[
"Schaposnik",
"Laura P.",
""
]
] | This paper is dedicated to the study of the interaction between dynamical systems and percolation models, with views towards the study of viral infections whose virus mutate with time. Recall that r-bootstrap percolation describes a deterministic process where vertices of a graph are infected once r neighbors of it are... |
2210.05269 | Liam Maher | Katharina T. Huber and Liam J. Maher | Autopolyploidy, allopolyploidy, and phylogenetic networks with
horizontal arcs | 26 pages, 9 figures, 38 citations | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Polyploidization is an evolutionary process by which a species acquires
multiple copies of its complete set of chromosomes. The reticulate nature of
the signal left behind by it means that phylogenetic networks offer themselves
as a framework to reconstruct the evolutionary past of species affected by it.
The main st... | [
{
"created": "Tue, 11 Oct 2022 09:11:23 GMT",
"version": "v1"
},
{
"created": "Sun, 19 Feb 2023 13:19:42 GMT",
"version": "v2"
}
] | 2023-02-21 | [
[
"Huber",
"Katharina T.",
""
],
[
"Maher",
"Liam J.",
""
]
] | Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a framework to reconstruct the evolutionary past of species affected by it. The main stra... |
2003.10073 | Hideyoshi Yanagisawa | Hideyoshi Yanagisawa | Information-Theoretic Free Energy as Emotion Potential: Emotional
Valence as a Function of Complexity and Novelty | null | Frontiers in Computational Neuroscience, 15, 107 (2021) | 10.3389/fncom.2021.698252 | null | q-bio.NC cs.AI cs.IT math.IT | http://creativecommons.org/licenses/by/4.0/ | This study extends the mathematical model of emotion dimensions that we
previously proposed (Yanagisawa, et al. 2019, Front Comput Neurosci) to
consider perceived complexity as well as novelty, as a source of arousal
potential. Berlyne's hedonic function of arousal potential (or the inverse
U-shaped curve, the so-cal... | [
{
"created": "Mon, 23 Mar 2020 04:10:23 GMT",
"version": "v1"
}
] | 2021-11-23 | [
[
"Yanagisawa",
"Hideyoshi",
""
]
] | This study extends the mathematical model of emotion dimensions that we previously proposed (Yanagisawa, et al. 2019, Front Comput Neurosci) to consider perceived complexity as well as novelty, as a source of arousal potential. Berlyne's hedonic function of arousal potential (or the inverse U-shaped curve, the so-calle... |
2303.08158 | Sayantan Nag Chowdhury | Sayantan Nag Chowdhury, Jeet Banerjee, Matja\v{z} Perc, Dibakar Ghosh | Eco-evolutionary cyclic dominance among predators, prey, and parasites | 14 pages, 6 figures, Supplementary material related to this article
can be found online at https://doi.org/10.1016/j.jtbi.2023.111446 | J. Theor. Biol. 564, 111446 (2023) | 10.1016/j.jtbi.2023.111446 | null | q-bio.PE nlin.AO | http://creativecommons.org/licenses/by/4.0/ | Predator prey interactions are one of ecology's central research themes, but
with many interdisciplinary implications across the social and natural
sciences. Here we consider an often-overlooked species in these interactions,
namely parasites. We first show that a simple predator prey parasite model,
inspired by the ... | [
{
"created": "Tue, 14 Mar 2023 18:14:53 GMT",
"version": "v1"
}
] | 2024-07-16 | [
[
"Chowdhury",
"Sayantan Nag",
""
],
[
"Banerjee",
"Jeet",
""
],
[
"Perc",
"Matjaž",
""
],
[
"Ghosh",
"Dibakar",
""
]
] | Predator prey interactions are one of ecology's central research themes, but with many interdisciplinary implications across the social and natural sciences. Here we consider an often-overlooked species in these interactions, namely parasites. We first show that a simple predator prey parasite model, inspired by the cl... |
2307.15083 | Mircea Andrecut Dr | M. Andrecut | Reaction Diffusion TAP | 11 pages, 4 figures, revised version accepted for publication in Int.
J. Mod. Phys. C | null | null | null | q-bio.PE physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The recently introduced Theory of the Adjacent Possible (TAP) is a model of
combinatorial innovation aiming to explain the "hockey-stick" upward trend of
human technological evolution, where an explosion in the number of produced
items with increasing complexity suddenly occurs. In addition, the TAP model
was also us... | [
{
"created": "Tue, 25 Jul 2023 20:52:07 GMT",
"version": "v1"
},
{
"created": "Mon, 31 Jul 2023 03:40:57 GMT",
"version": "v2"
},
{
"created": "Wed, 6 Sep 2023 16:08:11 GMT",
"version": "v3"
}
] | 2023-09-07 | [
[
"Andrecut",
"M.",
""
]
] | The recently introduced Theory of the Adjacent Possible (TAP) is a model of combinatorial innovation aiming to explain the "hockey-stick" upward trend of human technological evolution, where an explosion in the number of produced items with increasing complexity suddenly occurs. In addition, the TAP model was also used... |
2007.14762 | Peter Gawthrop | Peter J Gawthrop | Energy-based Modelling of the Feedback Control of Biomolecular Systems
with Cyclic Flow Modulation | null | IEEE Transactions on NanoBioscience, 2021 | 10.1109/TNB.2021.3058440 | null | q-bio.MN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Energy-based modelling brings engineering insight to the understanding of
biomolecular systems. It is shown how well-established control engineering
concepts, such as loop-gain, arise from energy feedback loops and are therefore
amenable to control engineering insight. In particular, a novel method is
introduced to a... | [
{
"created": "Wed, 29 Jul 2020 12:00:21 GMT",
"version": "v1"
},
{
"created": "Fri, 11 Dec 2020 11:57:15 GMT",
"version": "v2"
},
{
"created": "Thu, 28 Jan 2021 11:04:30 GMT",
"version": "v3"
}
] | 2021-03-30 | [
[
"Gawthrop",
"Peter J",
""
]
] | Energy-based modelling brings engineering insight to the understanding of biomolecular systems. It is shown how well-established control engineering concepts, such as loop-gain, arise from energy feedback loops and are therefore amenable to control engineering insight. In particular, a novel method is introduced to all... |
0902.0313 | Benzi Roberto | Roberto Benzi and David R. Nelson | Fisher equation with turbulence in one dimension | 15 pages | null | 10.1016/j.physd.2009.07.015 | null | q-bio.PE cond-mat.stat-mech nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the dynamics of the Fisher equation for the spreading of
micro-organisms in one dimension subject to both turbulent convection and
diffusion. We show that for strong enough turbulence, bacteria, for example,
track in a quasilocalized fashion (with remakably long persistance times) sinks
in the turbulen... | [
{
"created": "Mon, 2 Feb 2009 16:49:54 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Benzi",
"Roberto",
""
],
[
"Nelson",
"David R.",
""
]
] | We investigate the dynamics of the Fisher equation for the spreading of micro-organisms in one dimension subject to both turbulent convection and diffusion. We show that for strong enough turbulence, bacteria, for example, track in a quasilocalized fashion (with remakably long persistance times) sinks in the turbulent ... |
2311.16686 | Rim Adenane | Florin Avram, Rim Adenane, Lasko Basnarkov, Matthew Johnston | Algorithmic approach for an unique definition of the next generation
matrix | null | null | null | null | q-bio.PE math.DS | http://creativecommons.org/licenses/by/4.0/ | The basic reproduction number R0 is a concept which originated in population
dynamics, mathematical epidemiology, and ecology and is closely related to the
mean number of children in branching processes.We offer below three new
contributions to the literature: 1) We order a universal algorithmic definition
of a (F, V... | [
{
"created": "Tue, 28 Nov 2023 10:56:21 GMT",
"version": "v1"
},
{
"created": "Wed, 29 Nov 2023 13:48:51 GMT",
"version": "v2"
}
] | 2023-11-30 | [
[
"Avram",
"Florin",
""
],
[
"Adenane",
"Rim",
""
],
[
"Basnarkov",
"Lasko",
""
],
[
"Johnston",
"Matthew",
""
]
] | The basic reproduction number R0 is a concept which originated in population dynamics, mathematical epidemiology, and ecology and is closely related to the mean number of children in branching processes.We offer below three new contributions to the literature: 1) We order a universal algorithmic definition of a (F, V) ... |
1911.02893 | Tatiana Yakushkina S. | Sergei Drozhzhin, Tatiana Yakushkina, Alexander Bratus | Fitness Optimization and Evolution of Permanent Replicator Systems | 31 page, 32 figures | null | null | null | q-bio.PE nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we discuss the fitness landscape evolution of permanent
replicator systems using a hypothesis that the specific time of evolutionary
adaptation of the system parameters is much slower than the time of internal
evolutionary dynamics. In other words, we suppose that the extreme principle of
Darwinian evo... | [
{
"created": "Thu, 7 Nov 2019 13:28:21 GMT",
"version": "v1"
}
] | 2019-11-11 | [
[
"Drozhzhin",
"Sergei",
""
],
[
"Yakushkina",
"Tatiana",
""
],
[
"Bratus",
"Alexander",
""
]
] | In this paper, we discuss the fitness landscape evolution of permanent replicator systems using a hypothesis that the specific time of evolutionary adaptation of the system parameters is much slower than the time of internal evolutionary dynamics. In other words, we suppose that the extreme principle of Darwinian evolu... |
1411.1658 | Peter Thomas PhD | Peter J. Thomas and Benjamin Lindner | Asymptotic Phase for Stochastic Oscillators | 5 pages, 3 figures | Phys. Rev. Lett. 113(25):254101, Dec. 2014 | 10.1103/PhysRevLett.113.254101 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Oscillations and noise are ubiquitous in physical and biological systems.
When oscillations arise from a deterministic limit cycle, entrainment and
synchronization may be analyzed in terms of the asymptotic phase function. In
the presence of noise, the asymptotic phase is no longer well defined. We
introduce a new de... | [
{
"created": "Thu, 6 Nov 2014 16:41:46 GMT",
"version": "v1"
},
{
"created": "Sun, 18 Jan 2015 21:17:02 GMT",
"version": "v2"
}
] | 2015-01-20 | [
[
"Thomas",
"Peter J.",
""
],
[
"Lindner",
"Benjamin",
""
]
] | Oscillations and noise are ubiquitous in physical and biological systems. When oscillations arise from a deterministic limit cycle, entrainment and synchronization may be analyzed in terms of the asymptotic phase function. In the presence of noise, the asymptotic phase is no longer well defined. We introduce a new defi... |
2005.13607 | Hehuan Ma | Hehuan Ma, Yatao Bian, Yu Rong, Wenbing Huang, Tingyang Xu, Weiyang
Xie, Geyan Ye, Junzhou Huang | Multi-View Graph Neural Networks for Molecular Property Prediction | null | null | null | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The crux of molecular property prediction is to generate meaningful
representations of the molecules. One promising route is to exploit the
molecular graph structure through Graph Neural Networks (GNNs). It is well
known that both atoms and bonds significantly affect the chemical properties of
a molecule, so an expre... | [
{
"created": "Sun, 17 May 2020 04:46:07 GMT",
"version": "v1"
},
{
"created": "Fri, 29 May 2020 08:57:04 GMT",
"version": "v2"
},
{
"created": "Fri, 12 Jun 2020 06:09:52 GMT",
"version": "v3"
}
] | 2020-06-15 | [
[
"Ma",
"Hehuan",
""
],
[
"Bian",
"Yatao",
""
],
[
"Rong",
"Yu",
""
],
[
"Huang",
"Wenbing",
""
],
[
"Xu",
"Tingyang",
""
],
[
"Xie",
"Weiyang",
""
],
[
"Ye",
"Geyan",
""
],
[
"Huang",
"Junzhou",
... | The crux of molecular property prediction is to generate meaningful representations of the molecules. One promising route is to exploit the molecular graph structure through Graph Neural Networks (GNNs). It is well known that both atoms and bonds significantly affect the chemical properties of a molecule, so an express... |
1201.5557 | Shuhei Mano | Shuhei Mano | Duality between the two-locus Wright-Fisher Diffusion Model and the
Ancestral Process with Recombination | 25 pages, no figures | J. Appl. Probab. 50 (2013) 256-271 | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Known results on the moments of the distribution generated by the two-locus
Wright-Fisher diffusion model and a duality between the diffusion process and
the ancestral process with recombination are briefly summarized. A numerical
methods for computing moments by a Markov chain Monte Carlo and a method to
compute clo... | [
{
"created": "Thu, 26 Jan 2012 15:38:01 GMT",
"version": "v1"
},
{
"created": "Sat, 18 Feb 2012 03:17:14 GMT",
"version": "v2"
}
] | 2013-04-08 | [
[
"Mano",
"Shuhei",
""
]
] | Known results on the moments of the distribution generated by the two-locus Wright-Fisher diffusion model and a duality between the diffusion process and the ancestral process with recombination are briefly summarized. A numerical methods for computing moments by a Markov chain Monte Carlo and a method to compute close... |
1311.4206 | Moritz Deger | Moritz Deger, Tilo Schwalger, Richard Naud, Wulfram Gerstner | Fluctuations and information filtering in coupled populations of spiking
neurons with adaptation | null | Phys. Rev. E 90, 062704 (2014) | 10.1103/PhysRevE.90.062704 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Finite-sized populations of spiking elements are fundamental to brain
function, but also used in many areas of physics. Here we present a theory of
the dynamics of finite-sized populations of spiking units, based on a
quasi-renewal description of neurons with adaptation. We derive an integral
equation with colored no... | [
{
"created": "Sun, 17 Nov 2013 19:27:41 GMT",
"version": "v1"
},
{
"created": "Tue, 3 Mar 2015 13:52:23 GMT",
"version": "v2"
}
] | 2015-03-04 | [
[
"Deger",
"Moritz",
""
],
[
"Schwalger",
"Tilo",
""
],
[
"Naud",
"Richard",
""
],
[
"Gerstner",
"Wulfram",
""
]
] | Finite-sized populations of spiking elements are fundamental to brain function, but also used in many areas of physics. Here we present a theory of the dynamics of finite-sized populations of spiking units, based on a quasi-renewal description of neurons with adaptation. We derive an integral equation with colored nois... |
1606.08629 | Alexey Mazur K | Alexey K. Mazur | Weak Nanoscale Chaos And Anomalous Relaxation in DNA | 8 pages, 4 figures | Phys. Rev. E 95, 062417 (2017) | 10.1103/PhysRevE.95.062417 | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Anomalous non-exponential relaxation in hydrated biomolecules is commonly
attributed to the complexity of the free-energy landscapes, similarly to
polymers and glasses. It was found recently that the hydrogen-bond breathing of
terminal DNA base pairs exhibits a slow power-law relaxation attributable to
weak Hamiltoni... | [
{
"created": "Tue, 28 Jun 2016 09:49:55 GMT",
"version": "v1"
},
{
"created": "Fri, 23 Jun 2017 09:07:23 GMT",
"version": "v2"
}
] | 2017-07-05 | [
[
"Mazur",
"Alexey K.",
""
]
] | Anomalous non-exponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA base pairs exhibits a slow power-law relaxation attributable to weak Hamiltonian... |
1802.02546 | Valeriy Grytsay Dr | V.I. Grytsay, I.V. Musatenko | A mathematical model of the metabolism of a cell. Self-organization and
chaos | 11 pages, 9 figures | null | null | null | q-bio.OT nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Using the classical tools of nonlinear dynamics, we study the process of
self-organization and the appearance of the chaos in the metabolic process in a
cell with the help of a mathematical model of the transformation of steroids by
a cell Arthrobacter globiformis. We constructed the phase-parametric diagrams
obtaine... | [
{
"created": "Wed, 31 Jan 2018 09:29:50 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Mar 2018 18:40:21 GMT",
"version": "v2"
}
] | 2018-03-15 | [
[
"Grytsay",
"V. I.",
""
],
[
"Musatenko",
"I. V.",
""
]
] | Using the classical tools of nonlinear dynamics, we study the process of self-organization and the appearance of the chaos in the metabolic process in a cell with the help of a mathematical model of the transformation of steroids by a cell Arthrobacter globiformis. We constructed the phase-parametric diagrams obtained ... |
1610.06240 | Semid\'an Robaina-Est\'evez | Semid\'an Robaina-Est\'evez, Zoran Nikoloski | On the effects of alternative optima in context-specific metabolic model
predictions | null | PLoS Comput Biol 13(5): e1005568 (2017) | 10.1371/journal.pcbi.1005568 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent methodological developments have facilitated the integration of
high-throughput data into genome-scale models to obtain context-specific
metabolic reconstructions. A unique solution to this data integration problem
often may not be guaranteed, leading to a multitude of context-specific
predictions equally conc... | [
{
"created": "Wed, 19 Oct 2016 22:08:44 GMT",
"version": "v1"
},
{
"created": "Thu, 15 Jun 2017 14:39:30 GMT",
"version": "v2"
}
] | 2017-06-16 | [
[
"Robaina-Estévez",
"Semidán",
""
],
[
"Nikoloski",
"Zoran",
""
]
] | Recent methodological developments have facilitated the integration of high-throughput data into genome-scale models to obtain context-specific metabolic reconstructions. A unique solution to this data integration problem often may not be guaranteed, leading to a multitude of context-specific predictions equally concor... |
q-bio/0309022 | V. Krishnan Ramanujan | R.V.Krishnan, A.Masuda, V.E.Centoze and B.Herman | Quantitative Imaging of Protein-Protein Interactions by Multiphoton
Fluorescence Lifetime Imaging Microscopy using a Streak camera | Overview of FLIM techniques, StreakFLIM instrument, FRET applications | Journal of Biomedical Optics Vo.8, 362 (July 2003) | 10.1117/1.1577574 | null | q-bio.QM q-bio.CB | null | Fluorescence Lifetime Imaging Microscopy (FLIM) using multiphoton excitation
techniques is now finding an important place in quantitative imaging of
protein-protein interactions and intracellular physiology. We review here the
recent developments in multiphoton FLIM methods and also present a description
of a novel m... | [
{
"created": "Tue, 30 Sep 2003 14:19:35 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Krishnan",
"R. V.",
""
],
[
"Masuda",
"A.",
""
],
[
"Centoze",
"V. E.",
""
],
[
"Herman",
"B.",
""
]
] | Fluorescence Lifetime Imaging Microscopy (FLIM) using multiphoton excitation techniques is now finding an important place in quantitative imaging of protein-protein interactions and intracellular physiology. We review here the recent developments in multiphoton FLIM methods and also present a description of a novel mul... |
1307.4954 | Robert Kofler | Robert Kofler and Christian Schl\"otterer | Guidelines for the design of evolve and resequencing studies | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Standing genetic variation provides a rich reservoir of potentially useful
mutations facilitating the adaptation to novel environments. Experimental
evolution studies have demonstrated that rapid and strong phenotypic responses
to selection can also be obtained in the laboratory. When combined with the
Next Generatio... | [
{
"created": "Thu, 18 Jul 2013 14:16:16 GMT",
"version": "v1"
}
] | 2013-07-19 | [
[
"Kofler",
"Robert",
""
],
[
"Schlötterer",
"Christian",
""
]
] | Standing genetic variation provides a rich reservoir of potentially useful mutations facilitating the adaptation to novel environments. Experimental evolution studies have demonstrated that rapid and strong phenotypic responses to selection can also be obtained in the laboratory. When combined with the Next Generation ... |
2309.13319 | Catherine Beauchemin | Jamie Porthiyas, Daniel Nussey, Catherine A. A. Beauchemin, Donald C.
Warren, Christian Quirouette, Kathleen P. Wilkie | A closer look at parameter identifiability, model selection and handling
of censored data with Bayesian Inference in mathematical models of tumour
growth | 15 pages, 7 figures | NPJ Syst. Biol. Appl., 10:89 (2024) | 10.1038/s41540-024-00409-6 | RIKEN-iTHEMS-Report-23 | q-bio.QM | http://creativecommons.org/licenses/by-sa/4.0/ | Mathematical models (MMs) are a powerful tool to help us understand and
predict the dynamics of tumour growth under various conditions. In this work,
we use 5 MMs with an increasing number of parameters to explore how certain
(often overlooked) decisions in estimating parameters from data of experimental
tumour growt... | [
{
"created": "Sat, 23 Sep 2023 09:27:38 GMT",
"version": "v1"
}
] | 2024-08-16 | [
[
"Porthiyas",
"Jamie",
""
],
[
"Nussey",
"Daniel",
""
],
[
"Beauchemin",
"Catherine A. A.",
""
],
[
"Warren",
"Donald C.",
""
],
[
"Quirouette",
"Christian",
""
],
[
"Wilkie",
"Kathleen P.",
""
]
] | Mathematical models (MMs) are a powerful tool to help us understand and predict the dynamics of tumour growth under various conditions. In this work, we use 5 MMs with an increasing number of parameters to explore how certain (often overlooked) decisions in estimating parameters from data of experimental tumour growth ... |
1610.07161 | Mihai Alexandru Petrovici | Mihai A. Petrovici, Johannes Bill, Ilja Bytschok, Johannes Schemmel,
Karlheinz Meier | Stochastic inference with spiking neurons in the high-conductance state | null | Phys. Rev. E 94, 042312 (2016) | 10.1103/PhysRevE.94.042312 | null | q-bio.NC cond-mat.dis-nn cs.NE physics.bio-ph stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The highly variable dynamics of neocortical circuits observed in vivo have
been hypothesized to represent a signature of ongoing stochastic inference but
stand in apparent contrast to the deterministic response of neurons measured in
vitro. Based on a propagation of the membrane autocorrelation across spike
bursts, w... | [
{
"created": "Sun, 23 Oct 2016 12:27:05 GMT",
"version": "v1"
}
] | 2017-03-14 | [
[
"Petrovici",
"Mihai A.",
""
],
[
"Bill",
"Johannes",
""
],
[
"Bytschok",
"Ilja",
""
],
[
"Schemmel",
"Johannes",
""
],
[
"Meier",
"Karlheinz",
""
]
] | The highly variable dynamics of neocortical circuits observed in vivo have been hypothesized to represent a signature of ongoing stochastic inference but stand in apparent contrast to the deterministic response of neurons measured in vitro. Based on a propagation of the membrane autocorrelation across spike bursts, we ... |
2312.03954 | Rylan Schaeffer | Rylan Schaeffer, Mikail Khona, Sanmi Koyejo, and Ila Rani Fiete | Disentangling Fact from Grid Cell Fiction in Trained Deep Path
Integrators | arXiv admin note: text overlap with arXiv:2311.16295 | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Work on deep learning-based models of grid cells suggests that grid cells
generically and robustly arise from optimizing networks to path integrate,
i.e., track one's spatial position by integrating self-velocity signals. In
previous work, we challenged this path integration hypothesis by showing that
deep neural net... | [
{
"created": "Wed, 6 Dec 2023 23:44:43 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Dec 2023 04:14:42 GMT",
"version": "v2"
},
{
"created": "Sat, 16 Dec 2023 15:01:17 GMT",
"version": "v3"
}
] | 2023-12-19 | [
[
"Schaeffer",
"Rylan",
""
],
[
"Khona",
"Mikail",
""
],
[
"Koyejo",
"Sanmi",
""
],
[
"Fiete",
"Ila Rani",
""
]
] | Work on deep learning-based models of grid cells suggests that grid cells generically and robustly arise from optimizing networks to path integrate, i.e., track one's spatial position by integrating self-velocity signals. In previous work, we challenged this path integration hypothesis by showing that deep neural netwo... |
1007.5235 | Pietro Faccioli | S. a Beccara, P. Faccioli, G. Garberoglio, M. Sega, F. Pederiva and H.
Orland | Dominant folding pathways of a peptide chain, from ab-initio
quantum-mechanical simulations | 9 pages, 5 figures | null | null | null | q-bio.BM cond-mat.soft cond-mat.str-el | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Using the Dominant Reaction Pathways method, we perform an ab-initio
quantum-mechanical simulation of a conformational transition of a peptide
chain. The method we propose makes it possible to investigate the
out-of-equilibrium dynamics of these systems, without resorting to an empirical
representation of the molecul... | [
{
"created": "Thu, 29 Jul 2010 14:45:58 GMT",
"version": "v1"
}
] | 2010-07-30 | [
[
"Beccara",
"S. a",
""
],
[
"Faccioli",
"P.",
""
],
[
"Garberoglio",
"G.",
""
],
[
"Sega",
"M.",
""
],
[
"Pederiva",
"F.",
""
],
[
"Orland",
"H.",
""
]
] | Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of these systems, without resorting to an empirical representation of the molecular... |
0707.4487 | Shimshon Jacobi | Jean-Pierre Eckmann, Shimshon Jacobi, Shimon Marom, Elisha Moses,
Cyrille Zbinden | Leadership in 2D living neural networks | null | null | null | New J. Phys. 10 (2008) 015011 | q-bio.NC | null | Eytan and Marom recently showed that the spontaneous burst activity of rat
neuron cultures includes `first to fire' cells that consistently fire earlier
than others. Here we analyze the behavior of these neurons in long term
recordings of spontaneous activity of rat hippocampal and rat cortical neuron
cultures from t... | [
{
"created": "Mon, 30 Jul 2007 21:14:47 GMT",
"version": "v1"
}
] | 2010-04-19 | [
[
"Eckmann",
"Jean-Pierre",
""
],
[
"Jacobi",
"Shimshon",
""
],
[
"Marom",
"Shimon",
""
],
[
"Moses",
"Elisha",
""
],
[
"Zbinden",
"Cyrille",
""
]
] | Eytan and Marom recently showed that the spontaneous burst activity of rat neuron cultures includes `first to fire' cells that consistently fire earlier than others. Here we analyze the behavior of these neurons in long term recordings of spontaneous activity of rat hippocampal and rat cortical neuron cultures from thr... |
0908.1615 | David Saakian | David B. Saakian, Olga Rozanova, Andrei Akmetzhanov | Exactly solvable dynamics of the Eigen and the Crow-Kimura models | 7 pages | Physical Review E 78, 041908 (2008) | 10.1103/PhysRevE.78.041908 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a new way to study molecular evolution within well-established
Hamilton-Jacobi formalism, showing that for a broad class of fitness landscapes
it is possible to derive dynamics analytically within the $1/N$-accuracy, where
$N$ is genome length. For smooth and monotonic fitness function this approach
give... | [
{
"created": "Wed, 12 Aug 2009 05:11:25 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Saakian",
"David B.",
""
],
[
"Rozanova",
"Olga",
""
],
[
"Akmetzhanov",
"Andrei",
""
]
] | We introduce a new way to study molecular evolution within well-established Hamilton-Jacobi formalism, showing that for a broad class of fitness landscapes it is possible to derive dynamics analytically within the $1/N$-accuracy, where $N$ is genome length. For smooth and monotonic fitness function this approach gives ... |
2303.06503 | Iheanyi Okonko Okonko | Iheanyi Omezuruike Okonko, Chisom Chimbundum Adim, Blessing Jachinma
Okonko and Edith Ijeego Mba | Semi-Quantitative Analysis and Serological Evidence of Hepatitis A Virus
IgG Antibody among children in Rumuewhor, Emuoha, Rivers State, Nigeria | 7 pages | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Hepatitis A virus (HAV) infection has been greatly reduced in most developed
countries through the use of vaccine and improved hygienic conditions. However,
the magnitude of the problem is underestimated and there are no
well-established Hepatitis A virus prevention and control strategies in
Nigeria. The aim of this ... | [
{
"created": "Sat, 11 Mar 2023 22:06:44 GMT",
"version": "v1"
}
] | 2023-03-14 | [
[
"Okonko",
"Iheanyi Omezuruike",
""
],
[
"Adim",
"Chisom Chimbundum",
""
],
[
"Okonko",
"Blessing Jachinma",
""
],
[
"Mba",
"Edith Ijeego",
""
]
] | Hepatitis A virus (HAV) infection has been greatly reduced in most developed countries through the use of vaccine and improved hygienic conditions. However, the magnitude of the problem is underestimated and there are no well-established Hepatitis A virus prevention and control strategies in Nigeria. The aim of this st... |
2406.10739 | Ananda Shikhara Bhat | Ananda Shikhara Bhat | A stochastic field theory for the evolution of quantitative traits in
finite populations | Main text is 36 pages long (with references) and contains two
figures; Supplementary material is 35 pages long (with references) and
contains one figure | null | null | null | q-bio.PE cond-mat.stat-mech math.PR physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Infinitely many distinct trait values may arise in populations bearing
quantitative traits, and modelling their population dynamics is thus a
formidable task. While classical models assume fixed or infinite population
size, models in which the total population size fluctuates due to demographic
noise in births and de... | [
{
"created": "Sat, 15 Jun 2024 20:58:02 GMT",
"version": "v1"
}
] | 2024-06-18 | [
[
"Bhat",
"Ananda Shikhara",
""
]
] | Infinitely many distinct trait values may arise in populations bearing quantitative traits, and modelling their population dynamics is thus a formidable task. While classical models assume fixed or infinite population size, models in which the total population size fluctuates due to demographic noise in births and deat... |
1911.00383 | Homayoun Valafar | Rishi Mukhopadhyay, Paul Shealy, Homayoun Valafar | Protein Fold Family Recognition From Unassigned Residual Dipolar
Coupling Data | BioComp 2008, 7 pages | null | null | null | q-bio.BM cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite many advances in computational modeling of protein structures, these
methods have not been widely utilized by experimental structural biologists.
Two major obstacles are preventing the transition from a purely-experimental to
a purely-computational mode of protein structure determination. The first
problem is... | [
{
"created": "Fri, 1 Nov 2019 14:01:25 GMT",
"version": "v1"
}
] | 2019-11-04 | [
[
"Mukhopadhyay",
"Rishi",
""
],
[
"Shealy",
"Paul",
""
],
[
"Valafar",
"Homayoun",
""
]
] | Despite many advances in computational modeling of protein structures, these methods have not been widely utilized by experimental structural biologists. Two major obstacles are preventing the transition from a purely-experimental to a purely-computational mode of protein structure determination. The first problem is t... |
2004.11961 | Alexey Ovchinnikov | Alexey Ovchinnikov, Isabel Cristina P\'erez Verona, Gleb Pogudin,
Mirco Tribastone | CLUE: Exact maximal reduction of kinetic models by constrained lumping
of differential equations | null | null | null | null | q-bio.MN cs.SC cs.SY eess.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Detailed mechanistic models of biological processes can pose
significant challenges for analysis and parameter estimations due to the large
number of equations used to track the dynamics of all distinct configurations
in which each involved biochemical species can be found. Model reduction can
help tame s... | [
{
"created": "Fri, 24 Apr 2020 19:42:51 GMT",
"version": "v1"
},
{
"created": "Tue, 15 Dec 2020 02:09:43 GMT",
"version": "v2"
}
] | 2020-12-16 | [
[
"Ovchinnikov",
"Alexey",
""
],
[
"Verona",
"Isabel Cristina Pérez",
""
],
[
"Pogudin",
"Gleb",
""
],
[
"Tribastone",
"Mirco",
""
]
] | Motivation: Detailed mechanistic models of biological processes can pose significant challenges for analysis and parameter estimations due to the large number of equations used to track the dynamics of all distinct configurations in which each involved biochemical species can be found. Model reduction can help tame suc... |
q-bio/0312026 | Brandilyn Stigler | Reinhard Laubenbacher, Brandilyn Stigler | A Computational Algebra Approach to the Reverse Engineering of Gene
Regulatory Networks | 28 pages, 5 EPS figures, uses elsart.cls | Journal of Theoretical Biology 229 (2004) 523-537 | 10.1016/j.jtbi.2004.04.037 | null | q-bio.QM q-bio.MN | null | This paper proposes a new method to reverse engineer gene regulatory networks
from experimental data. The modeling framework used is time-discrete
deterministic dynamical systems, with a finite set of states for each of the
variables. The simplest examples of such models are Boolean networks, in which
variables have ... | [
{
"created": "Wed, 17 Dec 2003 22:12:11 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Laubenbacher",
"Reinhard",
""
],
[
"Stigler",
"Brandilyn",
""
]
] | This paper proposes a new method to reverse engineer gene regulatory networks from experimental data. The modeling framework used is time-discrete deterministic dynamical systems, with a finite set of states for each of the variables. The simplest examples of such models are Boolean networks, in which variables have on... |
2011.07982 | Ricardo Martinez-Garcia | Ricardo Martinez-Garcia, Crist\'obal L\'opez, Federico Vazquez | Species exclusion and coexistence in a noisy voter model with a
competition-colonization tradeoff | 13 pages, 9 figures, 3 appendices | Phys. Rev. E 103, 032406 (2021) | 10.1103/PhysRevE.103.032406 | null | q-bio.PE cond-mat.stat-mech | http://creativecommons.org/licenses/by/4.0/ | We introduce an asymmetric noisy voter model to study the joint effect of
immigration and a competition-dispersal tradeoff in the dynamics of two species
competing for space in regular lattices. Individuals of one species can invade
a nearest-neighbor site in the lattice, while individuals of the other species
are ab... | [
{
"created": "Mon, 16 Nov 2020 14:28:05 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Feb 2021 13:12:05 GMT",
"version": "v2"
},
{
"created": "Tue, 16 Feb 2021 16:13:29 GMT",
"version": "v3"
}
] | 2021-03-17 | [
[
"Martinez-Garcia",
"Ricardo",
""
],
[
"López",
"Cristóbal",
""
],
[
"Vazquez",
"Federico",
""
]
] | We introduce an asymmetric noisy voter model to study the joint effect of immigration and a competition-dispersal tradeoff in the dynamics of two species competing for space in regular lattices. Individuals of one species can invade a nearest-neighbor site in the lattice, while individuals of the other species are able... |
1905.01158 | Gabriel Obed Fosu | Gabriel O. Fosu and Emmanuel K. Mintah | A Two-Dose Vaccine Epidemic Model with Power Incidence Rate | null | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The dynamics of a SIVR model with power relationship incidence rates $(\beta
I^p S^q)$ is investigated. It is assumed an individual can be susceptible after
receiving the first dose of the vaccine, hence a second dose is required to
attain permanent immunity. The steady states conditions of the disease-free
equilibri... | [
{
"created": "Thu, 2 May 2019 16:41:22 GMT",
"version": "v1"
}
] | 2019-05-06 | [
[
"Fosu",
"Gabriel O.",
""
],
[
"Mintah",
"Emmanuel K.",
""
]
] | The dynamics of a SIVR model with power relationship incidence rates $(\beta I^p S^q)$ is investigated. It is assumed an individual can be susceptible after receiving the first dose of the vaccine, hence a second dose is required to attain permanent immunity. The steady states conditions of the disease-free equilibrium... |
q-bio/0412033 | Robersy Sanchez | Robersy Sanchez, Eberto Morgado and Ricardo Grau | Gene Algebra from a Genetic Code Algebraic Structure | 27 pages, without figures | Journal of Mathematical Biology. 2005 Oct;51(4):431-57. | 10.1007/s00285-005-0332-8 | null | q-bio.QM q-bio.GN | null | The biological distinction between the base positions in the codon, the
chemical types of bases (purine and pyrimidine) and their hydrogen bond number
have been the most relevant codon properties used in the genetic code analysis.
Now, these properties have allowed us to build a Genetic Code ring isomorphic
to the ri... | [
{
"created": "Thu, 16 Dec 2004 16:49:14 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Sanchez",
"Robersy",
""
],
[
"Morgado",
"Eberto",
""
],
[
"Grau",
"Ricardo",
""
]
] | The biological distinction between the base positions in the codon, the chemical types of bases (purine and pyrimidine) and their hydrogen bond number have been the most relevant codon properties used in the genetic code analysis. Now, these properties have allowed us to build a Genetic Code ring isomorphic to the ring... |
1304.3720 | Brian Williams Dr | Brian G. Williams and Eleanor Gouws | R0 and the elimination of HIV in Africa: Will 90-90-90 be sufficient? | We have updated the previous version for two reasons. First, we have
given a better approximation for the estimation of R0 from epidemic doubling
times. Second, we have added comments on the new UNAIDS '90-90-90' strategy
which puts the results into a broader context | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Joint United Nations Programme on HIV and AIDS (UNAIDS) has set a new
90-90-90 global target for the coverage of anti-retroviral therapy (ART) to be
reached by 2020. This would mean that 90% of all people infected with HIV know
their status, 90% of them are on ART and 90% of them will have full viral load
suppres... | [
{
"created": "Fri, 12 Apr 2013 15:48:41 GMT",
"version": "v1"
},
{
"created": "Mon, 14 Jul 2014 15:00:51 GMT",
"version": "v2"
}
] | 2014-07-15 | [
[
"Williams",
"Brian G.",
""
],
[
"Gouws",
"Eleanor",
""
]
] | The Joint United Nations Programme on HIV and AIDS (UNAIDS) has set a new 90-90-90 global target for the coverage of anti-retroviral therapy (ART) to be reached by 2020. This would mean that 90% of all people infected with HIV know their status, 90% of them are on ART and 90% of them will have full viral load suppressi... |
q-bio/0604002 | Martin Huber | Martin Tobias Huber and Hans Albert Braun | Conductance versus current noise in a neuronal model for noisy
subthreshold oscillations and related spike generation | accepted for publication in Biosystems; 10 pages, 2 figures | null | null | null | q-bio.NC q-bio.CB | null | Biological systems are notoriously noisy. Noise, therefore, also plays an
important role in many models of neural impulse generation. Noise is not only
introduced for more realistic simulations but also to account for cooperative
effects between noisy and nonlinear dynamics. Often, this is achieved by a
simple noise ... | [
{
"created": "Mon, 3 Apr 2006 13:22:07 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Huber",
"Martin Tobias",
""
],
[
"Braun",
"Hans Albert",
""
]
] | Biological systems are notoriously noisy. Noise, therefore, also plays an important role in many models of neural impulse generation. Noise is not only introduced for more realistic simulations but also to account for cooperative effects between noisy and nonlinear dynamics. Often, this is achieved by a simple noise te... |
2405.06663 | Eunji Ko | Eunji Ko, Seul Lee, Minseon Kim, Dongki Kim | Protein Representation Learning by Capturing Protein
Sequence-Structure-Function Relationship | ICLR 2024 MLGenX Workshop (Spotlight) | null | null | null | q-bio.BM cs.AI cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The goal of protein representation learning is to extract knowledge from
protein databases that can be applied to various protein-related downstream
tasks. Although protein sequence, structure, and function are the three key
modalities for a comprehensive understanding of proteins, existing methods for
protein repres... | [
{
"created": "Mon, 29 Apr 2024 05:42:29 GMT",
"version": "v1"
}
] | 2024-05-14 | [
[
"Ko",
"Eunji",
""
],
[
"Lee",
"Seul",
""
],
[
"Kim",
"Minseon",
""
],
[
"Kim",
"Dongki",
""
]
] | The goal of protein representation learning is to extract knowledge from protein databases that can be applied to various protein-related downstream tasks. Although protein sequence, structure, and function are the three key modalities for a comprehensive understanding of proteins, existing methods for protein represen... |
1307.5565 | Giovanni Bussi | Trang N. Do, Paolo Carloni, Gabriele Varani, and Giovanni Bussi | RNA/peptide binding driven by electrostatics -- Insight from
bi-directional pulling simulations | Reprinted (adapted) with permission from J. Chem. Theory Comput.,
2013, 9 (3) 1720 (2013). Copyright (2013) American Chemical Society | J. Chem. Theory Comput. 9, 1720 (2013) | 10.1021/ct3009914 | null | q-bio.BM cond-mat.soft physics.bio-ph physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | RNA/protein interactions play crucial roles in controlling gene expression.
They are becoming important targets for pharmaceutical applications. Due to RNA
flexibility and to the strength of electrostatic interactions, standard docking
methods are insufficient. We here present a computational method which allows
stud... | [
{
"created": "Sun, 21 Jul 2013 20:12:24 GMT",
"version": "v1"
}
] | 2013-07-23 | [
[
"Do",
"Trang N.",
""
],
[
"Carloni",
"Paolo",
""
],
[
"Varani",
"Gabriele",
""
],
[
"Bussi",
"Giovanni",
""
]
] | RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking methods are insufficient. We here present a computational method which allows studyi... |
2102.09124 | Dietmar Plenz Dr | Dietmar Plenz, Tiago L. Ribeiro, Stephanie R. Miller, Patrick A.
Kells, Ali Vakili, Elliott L. Capek (Section on Critical Brain Dynamics,
National Institute of Mental Health, National Institutes of Health, USA) | Self-Organized Criticality in the Brain | 40 pages, 14 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Self-organized criticality (SOC) refers to the ability of complex systems to
evolve towards a 2nd-order phase transition at which interactions between
system components lead to scale-invariant events beneficial for system
performance. For the last two decades, considerable experimental evidence
accumulated that the m... | [
{
"created": "Thu, 18 Feb 2021 02:53:23 GMT",
"version": "v1"
},
{
"created": "Sat, 15 May 2021 13:37:14 GMT",
"version": "v2"
}
] | 2021-05-18 | [
[
"Plenz",
"Dietmar",
"",
"Section on Critical Brain Dynamics,\n National Institute of Mental Health, National Institutes of Health, USA"
],
[
"Ribeiro",
"Tiago L.",
"",
"Section on Critical Brain Dynamics,\n National Institute of Mental Health, National Institutes of Health, U... | Self-organized criticality (SOC) refers to the ability of complex systems to evolve towards a 2nd-order phase transition at which interactions between system components lead to scale-invariant events beneficial for system performance. For the last two decades, considerable experimental evidence accumulated that the mam... |
2407.16013 | Murat Okatan | Murat Okatan | A statistical significance test for spatio-temporal receptive field
estimates obtained using spike-triggered averaging of binary pseudo-random
sequences | This is a replacement of the article "Okatan, M. A statistical
significance test for spatio-temporal receptive field estimates obtained
using spike-triggered averaging of binary pseudo-random sequences. SIViP 17,
3759-3766 (2023). https://doi.org/10.1007/s11760-023-02603-1". The current
manuscript corrects an e... | SIViP 17, 3759-3766 (2023) | 10.1007/s11760-023-02603-1 | null | q-bio.QM q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Spatio-temporal receptive fields (STRF) of visual neurons are often estimated
using spike-triggered averaging of binary pseudo-random stimulus sequences. The
spike train of a visual neuron is recorded simultaneously with the stimulus
presentation. The neuron's STRF is estimated by averaging the stimulus frames
that c... | [
{
"created": "Mon, 22 Jul 2024 19:42:42 GMT",
"version": "v1"
}
] | 2024-07-24 | [
[
"Okatan",
"Murat",
""
]
] | Spatio-temporal receptive fields (STRF) of visual neurons are often estimated using spike-triggered averaging of binary pseudo-random stimulus sequences. The spike train of a visual neuron is recorded simultaneously with the stimulus presentation. The neuron's STRF is estimated by averaging the stimulus frames that coi... |
1511.03150 | Mazza | Micha\"el Dougoud, Christian Mazza and Laura Vinckenbosch | Ultrasensitivity and sharp threshold theorems for multisite systems | null | null | null | null | q-bio.SC math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the ultrasensitivity of multisite binding processes where ligand
molecules can bind to several binding sites, considering more particularly
recent models involving complex chemical reactions in phosphorylation systems
such as allosteric phosphorylation processes, or substrate-catalyst chain
reactions and nuc... | [
{
"created": "Tue, 10 Nov 2015 15:44:25 GMT",
"version": "v1"
},
{
"created": "Wed, 11 Nov 2015 14:44:29 GMT",
"version": "v2"
},
{
"created": "Fri, 29 Apr 2016 13:29:58 GMT",
"version": "v3"
}
] | 2016-05-02 | [
[
"Dougoud",
"Michaël",
""
],
[
"Mazza",
"Christian",
""
],
[
"Vinckenbosch",
"Laura",
""
]
] | We study the ultrasensitivity of multisite binding processes where ligand molecules can bind to several binding sites, considering more particularly recent models involving complex chemical reactions in phosphorylation systems such as allosteric phosphorylation processes, or substrate-catalyst chain reactions and nucle... |
1503.00669 | Cengiz Pehlevan | Cengiz Pehlevan, Tao Hu, Dmitri B. Chklovskii | A Hebbian/Anti-Hebbian Neural Network for Linear Subspace Learning: A
Derivation from Multidimensional Scaling of Streaming Data | Accepted for publication in Neural Computation | null | 10.1162/NECO_a_00745 | null | q-bio.NC cs.NE stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neural network models of early sensory processing typically reduce the
dimensionality of streaming input data. Such networks learn the principal
subspace, in the sense of principal component analysis (PCA), by adjusting
synaptic weights according to activity-dependent learning rules. When derived
from a principled co... | [
{
"created": "Mon, 2 Mar 2015 19:39:33 GMT",
"version": "v1"
}
] | 2015-05-18 | [
[
"Pehlevan",
"Cengiz",
""
],
[
"Hu",
"Tao",
""
],
[
"Chklovskii",
"Dmitri B.",
""
]
] | Neural network models of early sensory processing typically reduce the dimensionality of streaming input data. Such networks learn the principal subspace, in the sense of principal component analysis (PCA), by adjusting synaptic weights according to activity-dependent learning rules. When derived from a principled cost... |
2104.01554 | Hoang Ngan Nguyen | Ngan Nguyen, Ciril Bohak, Dominik Engel, Peter Mindek, Ond\v{r}ej
Strnad, Peter Wonka, Sai Li, Timo Ropinski, Ivan Viola | Finding Nano-\"Otzi: Semi-Supervised Volume Visualization for
Cryo-Electron Tomography | null | IEEE Transactions on Visualization and Computer Graphics, 2022 | 10.1109/TVCG.2022.3186146 | null | q-bio.QM | http://creativecommons.org/licenses/by-sa/4.0/ | Cryo-Electron Tomography (cryo-ET) is a new 3D imaging technique with
unprecedented potential for resolving submicron structural detail. Existing
volume visualization methods, however, cannot cope with its very low
signal-to-noise ratio. In order to design more powerful transfer functions, we
propose to leverage soft... | [
{
"created": "Sun, 4 Apr 2021 07:45:48 GMT",
"version": "v1"
}
] | 2022-06-28 | [
[
"Nguyen",
"Ngan",
""
],
[
"Bohak",
"Ciril",
""
],
[
"Engel",
"Dominik",
""
],
[
"Mindek",
"Peter",
""
],
[
"Strnad",
"Ondřej",
""
],
[
"Wonka",
"Peter",
""
],
[
"Li",
"Sai",
""
],
[
"Ropinski",
... | Cryo-Electron Tomography (cryo-ET) is a new 3D imaging technique with unprecedented potential for resolving submicron structural detail. Existing volume visualization methods, however, cannot cope with its very low signal-to-noise ratio. In order to design more powerful transfer functions, we propose to leverage soft s... |
1905.11800 | Kelin Xia | Kelin Xia, D Vijay Anand, Shikhar Saxena, Yuguang Mu | Persistent homology analysis of osmolyte molecular aggregation and their
hydrogen-bonding networks | 19 pages; 9 figures; 1 table | null | 10.1039/C9CP03009C | null | q-bio.QM q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Two types of osmolytes, i.e., trimethylamin N-oxide (TMAO) and urea,
demonstrate dramatically different properties in a protein folding process.
Even with the great progresses in revealing the potential underlying mechanism
of these two osmolyte systems, many problems still remain unsolved. In this
paper, we propose ... | [
{
"created": "Tue, 28 May 2019 13:26:43 GMT",
"version": "v1"
}
] | 2019-10-23 | [
[
"Xia",
"Kelin",
""
],
[
"Anand",
"D Vijay",
""
],
[
"Saxena",
"Shikhar",
""
],
[
"Mu",
"Yuguang",
""
]
] | Two types of osmolytes, i.e., trimethylamin N-oxide (TMAO) and urea, demonstrate dramatically different properties in a protein folding process. Even with the great progresses in revealing the potential underlying mechanism of these two osmolyte systems, many problems still remain unsolved. In this paper, we propose to... |
2408.07977 | Kimberly Nestor | Kimberly Nestor, Javier Rasero, Richard Betzel, Peter J. Gianaros,
Timothy Verstynen | Cortical network reconfiguration aligns with shifts of basal ganglia and
cerebellar influence | null | null | null | null | q-bio.NC cs.SI | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Mammalian functional architecture flexibly adapts, transitioning from
integration where information is distributed across the cortex, to segregation
where information is focal in densely connected communities of brain regions.
This flexibility in cortical brain networks is hypothesized to be driven by
control signals... | [
{
"created": "Thu, 15 Aug 2024 06:43:52 GMT",
"version": "v1"
}
] | 2024-08-16 | [
[
"Nestor",
"Kimberly",
""
],
[
"Rasero",
"Javier",
""
],
[
"Betzel",
"Richard",
""
],
[
"Gianaros",
"Peter J.",
""
],
[
"Verstynen",
"Timothy",
""
]
] | Mammalian functional architecture flexibly adapts, transitioning from integration where information is distributed across the cortex, to segregation where information is focal in densely connected communities of brain regions. This flexibility in cortical brain networks is hypothesized to be driven by control signals o... |
1604.07667 | Julien Cors | J. Autebert, J. F. Cors, David P. Taylor and G. V. Kaigala | Convection-Enhanced Biopatterning with Recirculation of Hydrodynamically
Confined Nanoliter Volumes of Reagents | null | null | 10.1021/acs.analchem.5b04649 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a new methodology for efficient and high-quality patterning of
biological reagents for surface-based biological assays. The method relies on
hydrodynamically confined nanoliter volumes of reagents to interact with the
substrate at the micrometer-length scale. We study the interplay between
diffusion, advec... | [
{
"created": "Tue, 26 Apr 2016 13:18:22 GMT",
"version": "v1"
}
] | 2016-04-27 | [
[
"Autebert",
"J.",
""
],
[
"Cors",
"J. F.",
""
],
[
"Taylor",
"David P.",
""
],
[
"Kaigala",
"G. V.",
""
]
] | We present a new methodology for efficient and high-quality patterning of biological reagents for surface-based biological assays. The method relies on hydrodynamically confined nanoliter volumes of reagents to interact with the substrate at the micrometer-length scale. We study the interplay between diffusion, advecti... |
2406.14516 | Hermano Velten | Hermano Velten, Carlos Felipe Pinheiro and Alcides Castro e Silva | Extended error threshold mechanism in {\it quasispecies} theory via
population dynamics | 5 pages, 1 figure | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | We investigate Eigen's model for the evolution of the genetic code of
microorganisms using a novel method based on population dynamics analysis. This
model, for a given number of offspring, determines long-term survival as a
function of the "genetic" information length and copy error probability. There
exists a maxim... | [
{
"created": "Thu, 20 Jun 2024 17:26:08 GMT",
"version": "v1"
}
] | 2024-06-21 | [
[
"Velten",
"Hermano",
""
],
[
"Pinheiro",
"Carlos Felipe",
""
],
[
"Silva",
"Alcides Castro e",
""
]
] | We investigate Eigen's model for the evolution of the genetic code of microorganisms using a novel method based on population dynamics analysis. This model, for a given number of offspring, determines long-term survival as a function of the "genetic" information length and copy error probability. There exists a maximum... |
1011.1212 | Jose Vilar | J. M. G. Vilar and L. Saiz | CplexA: a Mathematica package to study macromolecular-assembly control
of gene expression | 28 pages. Includes Mathematica, Matlab, and Python implementation
tutorials. Software can be downloaded at http://cplexa.sourceforge.net/ | null | 10.1093/bioinformatics/btq328 | null | q-bio.QM cond-mat.stat-mech cs.CE physics.bio-ph q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Summary: Macromolecular assembly vertebrates essential cellular processes,
such as gene regulation and signal transduction. A major challenge for
conventional computational methods to study these processes is tackling the
exponential increase of the number of configurational states with the number of
components. Cple... | [
{
"created": "Thu, 4 Nov 2010 16:59:09 GMT",
"version": "v1"
},
{
"created": "Thu, 13 Dec 2012 16:31:45 GMT",
"version": "v2"
},
{
"created": "Sun, 6 Jan 2013 14:23:03 GMT",
"version": "v3"
}
] | 2013-01-08 | [
[
"Vilar",
"J. M. G.",
""
],
[
"Saiz",
"L.",
""
]
] | Summary: Macromolecular assembly vertebrates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential increase of the number of configurational states with the number of components. CplexA... |
q-bio/0407001 | Laxmidhar Behera Dr. | Laxmidhar Behera, Indrani Kar and Avshalom Elitzur | Quantum Brain: A Recurrent Quantum Neural Network Model to Describe Eye
Tracking of Moving Targets | 7 pages, 7 figures submitted to Physical Review Letters | null | 10.1007/s10702-005-7125-6 | null | q-bio.NC q-bio.OT | null | A theoretical quantum brain model is proposed using a nonlinear Schroedinger
wave equation. The model proposes that there exists a quantum process that
mediates the collective response of a neural lattice (classical brain). The
model is used to explain eye movements when tracking moving targets. Using a
Recurrent Qua... | [
{
"created": "Fri, 2 Jul 2004 05:11:33 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Behera",
"Laxmidhar",
""
],
[
"Kar",
"Indrani",
""
],
[
"Elitzur",
"Avshalom",
""
]
] | A theoretical quantum brain model is proposed using a nonlinear Schroedinger wave equation. The model proposes that there exists a quantum process that mediates the collective response of a neural lattice (classical brain). The model is used to explain eye movements when tracking moving targets. Using a Recurrent Quant... |
1909.02947 | Carina Curto | Carina Curto, Jesse Geneson, Katherine Morrison | Stable fixed points of combinatorial threshold-linear networks | 30 pages, 6 figures. Minor revisions, added references. To appear in
Advances in Applied Mathematics | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Combinatorial threshold-linear networks (CTLNs) are a special class of
recurrent neural networks whose dynamics are tightly controlled by an
underlying directed graph. Recurrent networks have long been used as models for
associative memory and pattern completion, with stable fixed points playing the
role of stored me... | [
{
"created": "Tue, 27 Aug 2019 06:36:01 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Aug 2022 02:08:10 GMT",
"version": "v2"
},
{
"created": "Sun, 19 Nov 2023 02:00:19 GMT",
"version": "v3"
}
] | 2023-11-21 | [
[
"Curto",
"Carina",
""
],
[
"Geneson",
"Jesse",
""
],
[
"Morrison",
"Katherine",
""
]
] | Combinatorial threshold-linear networks (CTLNs) are a special class of recurrent neural networks whose dynamics are tightly controlled by an underlying directed graph. Recurrent networks have long been used as models for associative memory and pattern completion, with stable fixed points playing the role of stored memo... |
2009.03187 | Keith Dillon | Keith Dillon | The Resolution Matrix for Visualizing Functional Network Connectivity | null | null | null | null | q-bio.NC cs.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The resolution matrix is a mathematical tool for analyzing inverse problems
such as computational imaging systems. When treating network connectivity
estimation as an inverse problem, the resolution matrix describes the degree to
which network nodes and edges can be resolved. This is useful both for
quantifying robus... | [
{
"created": "Fri, 4 Sep 2020 13:10:19 GMT",
"version": "v1"
}
] | 2020-09-08 | [
[
"Dillon",
"Keith",
""
]
] | The resolution matrix is a mathematical tool for analyzing inverse problems such as computational imaging systems. When treating network connectivity estimation as an inverse problem, the resolution matrix describes the degree to which network nodes and edges can be resolved. This is useful both for quantifying robustn... |
2304.13796 | Mason A. Porter | Elisa C. Baek, Ryan Hyon, Karina L\'opez, Mason A. Porter, and Carolyn
Parkinson | Perceived community alignment increases information sharing | 44 pages, including main text + supplementary information | null | null | null | q-bio.NC cs.SI physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | Information sharing is a ubiquitous and consequential behavior that has been
proposed to play a critical role in cultivating and maintaining a sense of
shared reality. Across three studies, we tested this theory by investigating
whether or not people are especially likely to share information that they
believe will b... | [
{
"created": "Wed, 26 Apr 2023 19:28:49 GMT",
"version": "v1"
}
] | 2023-05-01 | [
[
"Baek",
"Elisa C.",
""
],
[
"Hyon",
"Ryan",
""
],
[
"López",
"Karina",
""
],
[
"Porter",
"Mason A.",
""
],
[
"Parkinson",
"Carolyn",
""
]
] | Information sharing is a ubiquitous and consequential behavior that has been proposed to play a critical role in cultivating and maintaining a sense of shared reality. Across three studies, we tested this theory by investigating whether or not people are especially likely to share information that they believe will be ... |
1803.03475 | Anna Doizy | Anna Doizy, Edmund Barter, Jane Memmott, Karen Varnham, Thilo Gross | Impact of cyber-invasive species on a large ecological network | 10 pages, 2 figures, 1 table | null | 10.1038/s41598-018-31423-4 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As impacts of introduced species cascade through trophic levels, they can
cause indirect and counter-intuitive effects. To investigate the impact of
invasive species at the network scale, we use a generalized food web model,
capable of propagating changes through networks with a series of ecologically
realistic crite... | [
{
"created": "Fri, 9 Mar 2018 11:33:05 GMT",
"version": "v1"
},
{
"created": "Mon, 6 Aug 2018 09:57:33 GMT",
"version": "v2"
}
] | 2019-07-23 | [
[
"Doizy",
"Anna",
""
],
[
"Barter",
"Edmund",
""
],
[
"Memmott",
"Jane",
""
],
[
"Varnham",
"Karen",
""
],
[
"Gross",
"Thilo",
""
]
] | As impacts of introduced species cascade through trophic levels, they can cause indirect and counter-intuitive effects. To investigate the impact of invasive species at the network scale, we use a generalized food web model, capable of propagating changes through networks with a series of ecologically realistic criteri... |
1307.4137 | Michael DeGiorgio | Michael DeGiorgio, Kirk E. Lohmueller, Rasmus Nielsen | A model-based approach for identifying signatures of balancing selection
in genetic data | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While much effort has focused on detecting positive and negative directional
selection in the human genome, relatively little work has been devoted to
balancing selection. This lack of attention is likely due to the paucity of
sophisticated methods for identifying sites under balancing selection. Here we
develop two ... | [
{
"created": "Tue, 16 Jul 2013 00:55:29 GMT",
"version": "v1"
}
] | 2013-07-17 | [
[
"DeGiorgio",
"Michael",
""
],
[
"Lohmueller",
"Kirk E.",
""
],
[
"Nielsen",
"Rasmus",
""
]
] | While much effort has focused on detecting positive and negative directional selection in the human genome, relatively little work has been devoted to balancing selection. This lack of attention is likely due to the paucity of sophisticated methods for identifying sites under balancing selection. Here we develop two co... |
1003.1895 | Dietrich Stauffer | D. Stauffer and S. Cebrat | Review of haplotype complementarity under mutational pressure | 13 pages including 8 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | No abstract; review only
| [
{
"created": "Tue, 9 Mar 2010 15:10:07 GMT",
"version": "v1"
}
] | 2010-03-10 | [
[
"Stauffer",
"D.",
""
],
[
"Cebrat",
"S.",
""
]
] | No abstract; review only |
2212.05184 | Mehrdad Zandigohar | Mehrdad Zandigohar and Yang Dai | Information retrieval in single cell chromatin analysis using TF-IDF
transformation methods | 6 pages, 4 figures, 3 tables. Accepted to the 2022 IEEE International
Conference on Bioinformatics and Biomedicine (BIBM) | null | null | null | q-bio.GN cs.IR cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Single-cell sequencing assay for transposase-accessible chromatin
(scATAC-seq) assesses genome-wide chromatin accessibility in thousands of cells
to reveal regulatory landscapes in high resolutions. However, the analysis
presents challenges due to the high dimensionality and sparsity of the data.
Several methods have... | [
{
"created": "Sat, 10 Dec 2022 02:50:01 GMT",
"version": "v1"
}
] | 2022-12-13 | [
[
"Zandigohar",
"Mehrdad",
""
],
[
"Dai",
"Yang",
""
]
] | Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) assesses genome-wide chromatin accessibility in thousands of cells to reveal regulatory landscapes in high resolutions. However, the analysis presents challenges due to the high dimensionality and sparsity of the data. Several methods have b... |
1110.1413 | Yuriy Mileyko | Yuriy Mileyko, Herbert Edelsbrunner, Charles A. Price, Joshua S. Weitz | Hierarchical ordering of reticular networks | 9 pages, 5 figures, During preparation of this manuscript the authors
became aware of a related work by Katifori and Magnasco, concurrently
submitted for publication | null | 10.1371/journal.pone.0036715 | null | q-bio.QM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The structure of hierarchical networks in biological and physical systems has
long been characterized using the Horton-Strahler ordering scheme. The scheme
assigns an integer order to each edge in the network based on the topology of
branching such that the order increases from distal parts of the network (e.g.,
moun... | [
{
"created": "Thu, 6 Oct 2011 23:27:01 GMT",
"version": "v1"
}
] | 2015-05-30 | [
[
"Mileyko",
"Yuriy",
""
],
[
"Edelsbrunner",
"Herbert",
""
],
[
"Price",
"Charles A.",
""
],
[
"Weitz",
"Joshua S.",
""
]
] | The structure of hierarchical networks in biological and physical systems has long been characterized using the Horton-Strahler ordering scheme. The scheme assigns an integer order to each edge in the network based on the topology of branching such that the order increases from distal parts of the network (e.g., mounta... |
q-bio/0309033 | Alexander Volkovskii | M. I. Rabinovich, R. Huerta, A. Volkovskii, Henry D. I. Abarbanel, and
G. Laurent | Sensory Coding with Dynamically Competitive Networks | 19 pages, 16 figures. Originally submitted to the neuro-sys archive
which was never publicly announced (was 9905002) | null | null | null | q-bio.NC | null | Studies of insect olfactory processing indicate that odors are represented by
rich spatio-temporal patterns of neural activity. These patterns are very
difficult to predict a priori, yet they are stimulus specific and reliable upon
repeated stimulation with the same input. We formulate here a theoretical
framework in... | [
{
"created": "Fri, 21 May 1999 23:21:02 GMT",
"version": "v1"
},
{
"created": "Mon, 24 May 1999 01:18:27 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Rabinovich",
"M. I.",
""
],
[
"Huerta",
"R.",
""
],
[
"Volkovskii",
"A.",
""
],
[
"Abarbanel",
"Henry D. I.",
""
],
[
"Laurent",
"G.",
""
]
] | Studies of insect olfactory processing indicate that odors are represented by rich spatio-temporal patterns of neural activity. These patterns are very difficult to predict a priori, yet they are stimulus specific and reliable upon repeated stimulation with the same input. We formulate here a theoretical framework in w... |
1204.1324 | Marc Emanuel | Marc Emanuel, Giovanni Lanzani, Helmut Schiessel | Multi-plectoneme phase of double-stranded DNA under torsion | 4 pages, 6 figures, submitted, 2 typo's corrected, one reference
added | null | null | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We use the worm-like chain model to study supercoiling of DNA under tension
and torque. The model reproduces experimental data for a much broader range of
forces, salt concentrations and contour lengths than previous approaches. Our
theory shows, for the first time, how the behavior of the system is controlled
by a m... | [
{
"created": "Thu, 5 Apr 2012 19:42:17 GMT",
"version": "v1"
},
{
"created": "Mon, 9 Apr 2012 09:57:28 GMT",
"version": "v2"
}
] | 2012-04-10 | [
[
"Emanuel",
"Marc",
""
],
[
"Lanzani",
"Giovanni",
""
],
[
"Schiessel",
"Helmut",
""
]
] | We use the worm-like chain model to study supercoiling of DNA under tension and torque. The model reproduces experimental data for a much broader range of forces, salt concentrations and contour lengths than previous approaches. Our theory shows, for the first time, how the behavior of the system is controlled by a mul... |
2402.06748 | Peter Mikhael | Peter G. Mikhael, Itamar Chinn, Regina Barzilay | CLIPZyme: Reaction-Conditioned Virtual Screening of Enzymes | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Computational screening of naturally occurring proteins has the potential to
identify efficient catalysts among the hundreds of millions of sequences that
remain uncharacterized. Current experimental methods remain time, cost and
labor intensive, limiting the number of enzymes they can reasonably screen. In
this work... | [
{
"created": "Fri, 9 Feb 2024 19:23:26 GMT",
"version": "v1"
}
] | 2024-02-13 | [
[
"Mikhael",
"Peter G.",
""
],
[
"Chinn",
"Itamar",
""
],
[
"Barzilay",
"Regina",
""
]
] | Computational screening of naturally occurring proteins has the potential to identify efficient catalysts among the hundreds of millions of sequences that remain uncharacterized. Current experimental methods remain time, cost and labor intensive, limiting the number of enzymes they can reasonably screen. In this work, ... |
1903.07855 | Axel Brandenburg | Axel Brandenburg | The limited roles of autocatalysis and enantiomeric cross inhibition in
achieving homochirality in dilute systems | 14 pages, 5 figures, 2 tables, Orig. Life Evol. Biosph., in press | Orig. Life Evol. Biosph. 49, 49-60 (2019) | 10.1007/s11084-019-09579-4 | Nordita-2019-023 | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To understand the effects of fluctuations on achieving homochirality, we
employ a Monte-Carlo method where autocatalysis and enantiomeric
cross-inhibition, as well as racemization and deracemization reactions are
included. The results of earlier work either without autocatalysis or without
cross-inhibition are reprod... | [
{
"created": "Tue, 19 Mar 2019 06:28:19 GMT",
"version": "v1"
},
{
"created": "Wed, 5 Jun 2019 11:57:56 GMT",
"version": "v2"
}
] | 2019-08-26 | [
[
"Brandenburg",
"Axel",
""
]
] | To understand the effects of fluctuations on achieving homochirality, we employ a Monte-Carlo method where autocatalysis and enantiomeric cross-inhibition, as well as racemization and deracemization reactions are included. The results of earlier work either without autocatalysis or without cross-inhibition are reproduc... |
2207.13212 | Alicia Shin | Alicia Shin | The History, Current Status, Benefits, and Challenges of 3D Printed
Organs | 7 pages | null | null | null | q-bio.TO | http://creativecommons.org/publicdomain/zero/1.0/ | There is an increase in demand for organs as transplantation is becoming a
common practice to elongate human life. To reach this demand, three-dimensional
bioprinting is developing from prior knowledge of scaffolds, growth factors,
etc. This review paper aims to determine the current status and future
possibilities o... | [
{
"created": "Tue, 26 Jul 2022 23:21:30 GMT",
"version": "v1"
},
{
"created": "Mon, 12 Sep 2022 02:17:31 GMT",
"version": "v2"
},
{
"created": "Tue, 27 Dec 2022 20:31:43 GMT",
"version": "v3"
}
] | 2022-12-29 | [
[
"Shin",
"Alicia",
""
]
] | There is an increase in demand for organs as transplantation is becoming a common practice to elongate human life. To reach this demand, three-dimensional bioprinting is developing from prior knowledge of scaffolds, growth factors, etc. This review paper aims to determine the current status and future possibilities of ... |
1903.02594 | Pavel Kraikivski | Pavel Kraikivski | Systems of Oscillators Designed for a Specific Conscious Percept | submitted to New Mathematics and Natural Computation journal on July
2017 | null | 10.1142/S1793005720500052 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As put forward by neuroscientists, the mechanisms of consciousness can be
elucidated by revealing correlations between neural dynamics and specific
conscious percepts. Recently, I have elaborated on the mathematical formulation
for a system of processes that are mutually connected to be isomorphic to a
conscious perc... | [
{
"created": "Tue, 5 Mar 2019 15:34:55 GMT",
"version": "v1"
}
] | 2019-09-10 | [
[
"Kraikivski",
"Pavel",
""
]
] | As put forward by neuroscientists, the mechanisms of consciousness can be elucidated by revealing correlations between neural dynamics and specific conscious percepts. Recently, I have elaborated on the mathematical formulation for a system of processes that are mutually connected to be isomorphic to a conscious percep... |
2403.10993 | Ryota Kobayashi | Ryota Kobayashi and Shigeru Shinomoto | Inference of Monosynaptic Connections from Parallel Spike Trains: A
Review | 11 pages, 3 figures | null | null | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This article presents a mini-review about the progress in inferring
monosynaptic connections from spike trains of multiple neurons over the past
twenty years. First, we explain a variety of meanings of ``neuronal
connectivity'' in different research areas of neuroscience, such as structural
connectivity, monosynaptic... | [
{
"created": "Sat, 16 Mar 2024 18:42:13 GMT",
"version": "v1"
}
] | 2024-03-19 | [
[
"Kobayashi",
"Ryota",
""
],
[
"Shinomoto",
"Shigeru",
""
]
] | This article presents a mini-review about the progress in inferring monosynaptic connections from spike trains of multiple neurons over the past twenty years. First, we explain a variety of meanings of ``neuronal connectivity'' in different research areas of neuroscience, such as structural connectivity, monosynaptic c... |
2401.01489 | Dmitri Chklovskii | Jason Moore, Alexander Genkin, Magnus Tournoy, Joshua Pughe-Sanford,
Rob R. de Ruyter van Steveninck, and Dmitri B. Chklovskii | The Neuron as a Direct Data-Driven Controller | null | null | null | null | q-bio.NC cs.AI cs.SY eess.SY | http://creativecommons.org/licenses/by/4.0/ | In the quest to model neuronal function amidst gaps in physiological data, a
promising strategy is to develop a normative theory that interprets neuronal
physiology as optimizing a computational objective. This study extends the
current normative models, which primarily optimize prediction, by
conceptualizing neurons... | [
{
"created": "Wed, 3 Jan 2024 01:24:10 GMT",
"version": "v1"
}
] | 2024-01-04 | [
[
"Moore",
"Jason",
""
],
[
"Genkin",
"Alexander",
""
],
[
"Tournoy",
"Magnus",
""
],
[
"Pughe-Sanford",
"Joshua",
""
],
[
"van Steveninck",
"Rob R. de Ruyter",
""
],
[
"Chklovskii",
"Dmitri B.",
""
]
] | In the quest to model neuronal function amidst gaps in physiological data, a promising strategy is to develop a normative theory that interprets neuronal physiology as optimizing a computational objective. This study extends the current normative models, which primarily optimize prediction, by conceptualizing neurons a... |
2309.09900 | Giulia Garcia Lorenzana | Giulia Garcia Lorenzana, Ada Altieri, Giulio Biroli | Interactions and migration rescuing ecological diversity | 13 pages, 10 figures, + 14 pages, 6 figures in Appendix | null | 10.1103/PRXLife.2.013014 | null | q-bio.PE cond-mat.dis-nn cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How diversity is maintained in natural ecosystems is a long-standing question
in Theoretical Ecology. By studying a system that combines ecological dynamics,
heterogeneous interactions and spatial structure, we uncover a new mechanism
for the survival of diversity-rich ecosystems in the presence of demographic
fluctu... | [
{
"created": "Mon, 18 Sep 2023 16:05:03 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Feb 2024 11:25:58 GMT",
"version": "v2"
}
] | 2024-03-21 | [
[
"Lorenzana",
"Giulia Garcia",
""
],
[
"Altieri",
"Ada",
""
],
[
"Biroli",
"Giulio",
""
]
] | How diversity is maintained in natural ecosystems is a long-standing question in Theoretical Ecology. By studying a system that combines ecological dynamics, heterogeneous interactions and spatial structure, we uncover a new mechanism for the survival of diversity-rich ecosystems in the presence of demographic fluctuat... |
1911.00072 | Gurpreet Singh Matharoo | Gurpreet S. Matharoo and Javeria A. Hashmi | Spontaneous back-pain alters randomness in functional connections in
large scale brain networks: A random matrix perspective | 18 Pages, 5 Figures | Physica A; 2019 | 10.1016/j.physa.2019.123321 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We use randomness as a measure to assess the impact of evoked pain on brain
networks. Randomness is defined here as the intrinsic correlations that exist
between different brain regions when the brain is in a task-free state. We use
fMRI data of three brain states in a set of back pain patients monitored over a
perio... | [
{
"created": "Thu, 31 Oct 2019 19:37:32 GMT",
"version": "v1"
}
] | 2019-11-04 | [
[
"Matharoo",
"Gurpreet S.",
""
],
[
"Hashmi",
"Javeria A.",
""
]
] | We use randomness as a measure to assess the impact of evoked pain on brain networks. Randomness is defined here as the intrinsic correlations that exist between different brain regions when the brain is in a task-free state. We use fMRI data of three brain states in a set of back pain patients monitored over a period ... |
2306.01793 | Giulia Chiari | Giulia Chiari, Giada Fiandaca, Marcello Edoardo Delitala | Hypoxia-resistance heterogeneity in tumours: the impact of geometrical
characterization of environmental niches and evolutionary trade-offs. A
mathematical approach | null | null | 10.1051/mmnp/2023023 | null | q-bio.PE cs.NA math.AP math.NA physics.med-ph | http://creativecommons.org/licenses/by-sa/4.0/ | In the study of cancer evolution and therapeutic strategies, scientific
evidence shows that a key dynamics lies in the tumor-environment interaction.
In particular, oxygen concentration plays a central role in the determination
of the phenotypic heterogeneity of cancer cell populations, whose qualitative
and geometri... | [
{
"created": "Thu, 1 Jun 2023 09:03:58 GMT",
"version": "v1"
}
] | 2023-07-20 | [
[
"Chiari",
"Giulia",
""
],
[
"Fiandaca",
"Giada",
""
],
[
"Delitala",
"Marcello Edoardo",
""
]
] | In the study of cancer evolution and therapeutic strategies, scientific evidence shows that a key dynamics lies in the tumor-environment interaction. In particular, oxygen concentration plays a central role in the determination of the phenotypic heterogeneity of cancer cell populations, whose qualitative and geometric ... |
2210.05713 | Ziyuan Ye | Ziyuan Ye, Youzhi Qu, Zhichao Liang, Mo Wang, Quanying Liu | Explainable fMRI-based Brain Decoding via Spatial Temporal-pyramid Graph
Convolutional Network | null | null | null | null | q-bio.NC cs.NE eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Brain decoding, aiming to identify the brain states using neural activity, is
important for cognitive neuroscience and neural engineering. However, existing
machine learning methods for fMRI-based brain decoding either suffer from low
classification performance or poor explainability. Here, we address this issue
by p... | [
{
"created": "Sat, 8 Oct 2022 12:14:33 GMT",
"version": "v1"
}
] | 2022-10-13 | [
[
"Ye",
"Ziyuan",
""
],
[
"Qu",
"Youzhi",
""
],
[
"Liang",
"Zhichao",
""
],
[
"Wang",
"Mo",
""
],
[
"Liu",
"Quanying",
""
]
] | Brain decoding, aiming to identify the brain states using neural activity, is important for cognitive neuroscience and neural engineering. However, existing machine learning methods for fMRI-based brain decoding either suffer from low classification performance or poor explainability. Here, we address this issue by pro... |
1611.07776 | David Lukatsky | Matan Goldshtein and David B. Lukatsky | Specificity-determining DNA triplet code for positioning of human
pre-initiation complex | null | null | 10.1016/j.bpj.2017.04.023 | null | q-bio.BM q-bio.GN q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The notion that transcription factors bind DNA only through specific,
consensus binding sites has been recently questioned. In a pioneering study by
Pugh and Venters no specific consensus motif for the positioning of the human
pre-initiation complex (PIC) has been identified. Here, we reveal that
nonconsensus, statis... | [
{
"created": "Wed, 23 Nov 2016 13:07:49 GMT",
"version": "v1"
}
] | 2017-06-28 | [
[
"Goldshtein",
"Matan",
""
],
[
"Lukatsky",
"David B.",
""
]
] | The notion that transcription factors bind DNA only through specific, consensus binding sites has been recently questioned. In a pioneering study by Pugh and Venters no specific consensus motif for the positioning of the human pre-initiation complex (PIC) has been identified. Here, we reveal that nonconsensus, statisti... |
2002.09631 | Alfonso Vivanco Lira | A. Vivanco-Lira | Novel therapeutic targets in chronic myeloid leukaemia through a
discrete time discrete Markov chain model of BCR-ABL1 interactions | 32 pages, 1 table, 6 figures | null | null | null | q-bio.CB q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chronic Myeloid Leukaemia (CML) is a blood-derived proliferative disorder,
which is highly associated to a translocation of chromosomes 9 and 22 or the
creation of Philadelphia chromosome Ph(+) cases, inducing the synthesis of a
chimeric fusion protein, namely BCR-ABL1 (Breakpoint Cluster Region-Abelson 1
chimeric pr... | [
{
"created": "Sat, 22 Feb 2020 05:29:04 GMT",
"version": "v1"
}
] | 2020-02-25 | [
[
"Vivanco-Lira",
"A.",
""
]
] | Chronic Myeloid Leukaemia (CML) is a blood-derived proliferative disorder, which is highly associated to a translocation of chromosomes 9 and 22 or the creation of Philadelphia chromosome Ph(+) cases, inducing the synthesis of a chimeric fusion protein, namely BCR-ABL1 (Breakpoint Cluster Region-Abelson 1 chimeric prot... |
2006.08647 | Andres Escala | Andres Escala | Universal Relation for Life-span Energy Consumption in Living Organisms:
Insights for the origin of ageing | Comments welcome aescala@das.uchile.cl | null | null | null | q-bio.OT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Metabolic energy consumption has long been thought to play a major role in
the aging process ({\it 1}). Across species, a gram of tissue on average
expends about the same amount of energy during life-span ({\it 2}). Energy
restriction has also been shown that increases maximum life-span ({\it 3}) and
retards age-asso... | [
{
"created": "Mon, 15 Jun 2020 18:00:32 GMT",
"version": "v1"
}
] | 2020-06-17 | [
[
"Escala",
"Andres",
""
]
] | Metabolic energy consumption has long been thought to play a major role in the aging process ({\it 1}). Across species, a gram of tissue on average expends about the same amount of energy during life-span ({\it 2}). Energy restriction has also been shown that increases maximum life-span ({\it 3}) and retards age-associ... |
1308.3032 | Fabio Pichierri | Fabio Pichierri | Dipole-dipole interactions in protein-protein complexes: a quantum
mechanical study of the ubiquitin-Dsk2 complex | 8 pages, 2 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quantum mechanical calculations are performed on the proteins that constitute
the ubiquitin-Dsk2 complex whose atomic structure has been experimentally
determined by NMR spectroscopy (PDB id 1WR1). The results indicate that the
dipole moment vectors of the two proteins are aligned in a head-to-tail
orientation while ... | [
{
"created": "Wed, 14 Aug 2013 04:53:31 GMT",
"version": "v1"
}
] | 2013-08-15 | [
[
"Pichierri",
"Fabio",
""
]
] | Quantum mechanical calculations are performed on the proteins that constitute the ubiquitin-Dsk2 complex whose atomic structure has been experimentally determined by NMR spectroscopy (PDB id 1WR1). The results indicate that the dipole moment vectors of the two proteins are aligned in a head-to-tail orientation while fo... |
0904.3584 | Hu Chen | Hu Chen, Yanhui Liu, Zhen Zhou, Lin Hu, Zhong-Can Ou-Yang, and Jie Yan | Temperature dependence of circular DNA topological states | 15 pages in preprint format, 4 figures | PHYSICAL REVIEW E 79, 041926 (2009) | 10.1103/PhysRevE.79.041926 | null | q-bio.BM q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Circular double stranded DNA has different topological states which are
defined by their linking numbers. Equilibrium distribution of linking numbers
can be obtained by closing a linear DNA into a circle by ligase. Using Monte
Carlo simulation, we predict the temperature dependence of the linking number
distribution ... | [
{
"created": "Thu, 23 Apr 2009 02:34:28 GMT",
"version": "v1"
}
] | 2009-05-04 | [
[
"Chen",
"Hu",
""
],
[
"Liu",
"Yanhui",
""
],
[
"Zhou",
"Zhen",
""
],
[
"Hu",
"Lin",
""
],
[
"Ou-Yang",
"Zhong-Can",
""
],
[
"Yan",
"Jie",
""
]
] | Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo simulation, we predict the temperature dependence of the linking number distribution of... |
2201.00850 | Michael McCreesh | Michael McCreesh and Jorge Cort\'es | Selective Inhibition and Recruitment of Linear-Threshold Thalamocortical
Networks | 13 pages, 5 figures | null | null | null | q-bio.NC cs.SY eess.SY | http://creativecommons.org/licenses/by/4.0/ | Neuroscientific evidence shows that for most brain networks all pathways
between cortical regions either pass through the thalamus or a transthalamic
parallel route exists for any direct corticocortical connection. This paper
seeks to formally study the dynamical behavior of the resulting thalamocortical
brain networ... | [
{
"created": "Mon, 3 Jan 2022 19:38:10 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Jul 2022 19:57:11 GMT",
"version": "v2"
}
] | 2022-07-12 | [
[
"McCreesh",
"Michael",
""
],
[
"Cortés",
"Jorge",
""
]
] | Neuroscientific evidence shows that for most brain networks all pathways between cortical regions either pass through the thalamus or a transthalamic parallel route exists for any direct corticocortical connection. This paper seeks to formally study the dynamical behavior of the resulting thalamocortical brain networks... |
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