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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2106.08820 | Aram Ansary Ogholbake | Aram Ansary Ogholbake, Hana Khamfroush | A Modified SEIR Model for the Spread of COVID-19 Considering Different
Vaccine Types | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The COVID-19 pandemic has influenced the lives of people globally. In the
past year many researchers have proposed different models and approaches to
explore in what ways the spread of the disease could be mitigated. One of the
models that have been used a great deal is the
Susceptible-Exposed-Infectious-Recovered (S... | [
{
"created": "Sun, 6 Jun 2021 16:35:20 GMT",
"version": "v1"
}
] | 2021-06-17 | [
[
"Ogholbake",
"Aram Ansary",
""
],
[
"Khamfroush",
"Hana",
""
]
] | The COVID-19 pandemic has influenced the lives of people globally. In the past year many researchers have proposed different models and approaches to explore in what ways the spread of the disease could be mitigated. One of the models that have been used a great deal is the Susceptible-Exposed-Infectious-Recovered (SEI... |
1902.00067 | Yue Cao | Yue Cao and Yang Shen | Bayesian active learning for optimization and uncertainty quantification
in protein docking | null | null | null | null | q-bio.BM cs.LG math.OC stat.ML | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Motivation: Ab initio protein docking represents a major challenge for
optimizing a noisy and costly "black box"-like function in a high-dimensional
space. Despite progress in this field, there is no docking method available for
rigorous uncertainty quantification (UQ) of its solution quality (e.g.
interface RMSD or ... | [
{
"created": "Thu, 31 Jan 2019 20:52:06 GMT",
"version": "v1"
}
] | 2019-02-04 | [
[
"Cao",
"Yue",
""
],
[
"Shen",
"Yang",
""
]
] | Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space. Despite progress in this field, there is no docking method available for rigorous uncertainty quantification (UQ) of its solution quality (e.g. interface RMSD or iR... |
1201.0689 | L.T. Handoko | A. Sulaiman, F. P. Zen, H. Alatas, L. T. Handoko | Dynamics of DNA Bubble in Viscous Medium | 4 pages. arXiv admin note: substantial text overlap with
arXiv:1112.4715 | AIP Conference Proceeding 1454 (2012) pp. 298-301 | 10.1063/1.4730745 | FISIKALIPI-11047 | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The damping effect to the DNA bubble is investigated within the
Peyrard-Bishop model. In the continuum limit, the dynamics of the bubble of DNA
is described by the damped nonlinear Schrodinger equation and studied by means
of variational method. It is shown that the propagation of solitary wave
pattern is not vanishi... | [
{
"created": "Tue, 3 Jan 2012 16:38:53 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Jun 2012 14:38:09 GMT",
"version": "v2"
}
] | 2012-06-25 | [
[
"Sulaiman",
"A.",
""
],
[
"Zen",
"F. P.",
""
],
[
"Alatas",
"H.",
""
],
[
"Handoko",
"L. T.",
""
]
] | The damping effect to the DNA bubble is investigated within the Peyrard-Bishop model. In the continuum limit, the dynamics of the bubble of DNA is described by the damped nonlinear Schrodinger equation and studied by means of variational method. It is shown that the propagation of solitary wave pattern is not vanishing... |
1211.6493 | Changbong Hyeon | Jong-Chin Lin, Changbong Hyeon, D. Thirumalai | RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism,
and Molecular Tensegrity | 24 pages, 6 figures | J. Phys. Chem. Lett., 2012, vol 3, 3616 | 10.1021/jz301537t | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Non-coding RNA sequences play a great role in controlling a number of
cellular functions, thus raising the need to understand their complex
conformational dynamics in quantitative detail. In this perspective, we first
show that single molecule pulling experiments when combined with with theory
and simulations can be ... | [
{
"created": "Wed, 28 Nov 2012 01:20:04 GMT",
"version": "v1"
}
] | 2012-11-29 | [
[
"Lin",
"Jong-Chin",
""
],
[
"Hyeon",
"Changbong",
""
],
[
"Thirumalai",
"D.",
""
]
] | Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single molecule pulling experiments when combined with with theory and simulations can be us... |
2011.05755 | Szu-Chi Chung | Szu-Chi Chung, Cheng-Yu Hung, Huei-Lun Siao, Hung-Yi Wu, Wei-Hau Chang
and I-Ping Tu | Cryo-RALib -- a modular library for accelerating alignment in cryo-EM | null | null | null | null | q-bio.QM cs.DC eess.IV | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Thanks to automated cryo-EM and GPU-accelerated processing, single-particle
cryo-EM has become a rapid structure determination method that permits capture
of dynamical structures of molecules in solution, which has been recently
demonstrated by the determination of COVID-19 spike protein in March, shortly
after its b... | [
{
"created": "Wed, 11 Nov 2020 13:15:22 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Nov 2020 05:32:16 GMT",
"version": "v2"
},
{
"created": "Tue, 12 Jan 2021 02:28:45 GMT",
"version": "v3"
},
{
"created": "Thu, 25 Feb 2021 08:48:26 GMT",
"version": "v4"
}
] | 2021-02-26 | [
[
"Chung",
"Szu-Chi",
""
],
[
"Hung",
"Cheng-Yu",
""
],
[
"Siao",
"Huei-Lun",
""
],
[
"Wu",
"Hung-Yi",
""
],
[
"Chang",
"Wei-Hau",
""
],
[
"Tu",
"I-Ping",
""
]
] | Thanks to automated cryo-EM and GPU-accelerated processing, single-particle cryo-EM has become a rapid structure determination method that permits capture of dynamical structures of molecules in solution, which has been recently demonstrated by the determination of COVID-19 spike protein in March, shortly after its bre... |
2107.10332 | Abicumaran Uthamacumaran | Abicumaran Uthamacumaran, Samir Elouatik, Mohamed Abdouh, Michael
Berteau-Rainville, Zu-hua Gao, and Goffredo Arena | Machine Learning Characterization of Cancer Patients-Derived
Extracellular Vesicles using Vibrational Spectroscopies | 41 pages | Applied Intelligence (2022) | 10.1007/s10489-022-03203-1 | null | q-bio.OT cs.AI cs.LG physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The early detection of cancer is a challenging problem in medicine. The blood
sera of cancer patients are enriched with heterogeneous secretory lipid bound
extracellular vesicles (EVs), which present a complex repertoire of information
and biomarkers, representing their cell of origin, that are being currently
studie... | [
{
"created": "Wed, 21 Jul 2021 19:56:33 GMT",
"version": "v1"
},
{
"created": "Wed, 4 Aug 2021 15:41:05 GMT",
"version": "v2"
},
{
"created": "Wed, 25 Aug 2021 15:01:41 GMT",
"version": "v3"
},
{
"created": "Tue, 16 Nov 2021 16:14:36 GMT",
"version": "v4"
},
{
"cr... | 2022-02-15 | [
[
"Uthamacumaran",
"Abicumaran",
""
],
[
"Elouatik",
"Samir",
""
],
[
"Abdouh",
"Mohamed",
""
],
[
"Berteau-Rainville",
"Michael",
""
],
[
"Gao",
"Zu-hua",
""
],
[
"Arena",
"Goffredo",
""
]
] | The early detection of cancer is a challenging problem in medicine. The blood sera of cancer patients are enriched with heterogeneous secretory lipid bound extracellular vesicles (EVs), which present a complex repertoire of information and biomarkers, representing their cell of origin, that are being currently studied ... |
2209.13561 | Jacob Granley | Jacob Granley, Alexander Riedel, Michael Beyeler | Adapting Brain-Like Neural Networks for Modeling Cortical Visual
Prostheses | null | null | null | null | q-bio.NC cs.LG cs.NE | http://creativecommons.org/licenses/by/4.0/ | Cortical prostheses are devices implanted in the visual cortex that attempt
to restore lost vision by electrically stimulating neurons. Currently, the
vision provided by these devices is limited, and accurately predicting the
visual percepts resulting from stimulation is an open challenge. We propose to
address this ... | [
{
"created": "Tue, 27 Sep 2022 17:33:19 GMT",
"version": "v1"
}
] | 2022-09-28 | [
[
"Granley",
"Jacob",
""
],
[
"Riedel",
"Alexander",
""
],
[
"Beyeler",
"Michael",
""
]
] | Cortical prostheses are devices implanted in the visual cortex that attempt to restore lost vision by electrically stimulating neurons. Currently, the vision provided by these devices is limited, and accurately predicting the visual percepts resulting from stimulation is an open challenge. We propose to address this ch... |
2010.10443 | Mattia Sensi | Tommaso Lorenzi, Andrea Pugliese, Mattia Sensi, Agnese Zardini | Evolutionary dynamics in an SI epidemic model with phenotype-structured
susceptible compartment | 29 pages, 8 figures | Journal of Mathematical Biology volume 83, Article number: 72
(2021) | 10.1007/s00285-021-01703-1 | null | q-bio.PE math.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present an SI epidemic model whereby a continuous variable captures
variability in proliferative potential and resistance to infection among
susceptibles. The occurrence of heritable, spontaneous changes in these
phenotype and the presence of a fitness trade-off between resistance to
infection and proliferative po... | [
{
"created": "Tue, 20 Oct 2020 16:56:34 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Nov 2021 09:55:36 GMT",
"version": "v2"
}
] | 2021-12-30 | [
[
"Lorenzi",
"Tommaso",
""
],
[
"Pugliese",
"Andrea",
""
],
[
"Sensi",
"Mattia",
""
],
[
"Zardini",
"Agnese",
""
]
] | We present an SI epidemic model whereby a continuous variable captures variability in proliferative potential and resistance to infection among susceptibles. The occurrence of heritable, spontaneous changes in these phenotype and the presence of a fitness trade-off between resistance to infection and proliferative pote... |
1805.05682 | Begona Diaz | Begona Diaz, Helen Blank, and Katharina von Kriegstein | Task-dependent modulation of the visual sensory thalamus assists
visual-speech recognition | null | null | 10.1016/j.neuroimage.2018.05.032 | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The cerebral cortex modulates early sensory processing via feed-back
connections to sensory pathway nuclei. The functions of this top-down
modulation for human behavior are poorly understood. Here, we show that
top-down modulation of the visual sensory thalamus (the lateral geniculate
body, LGN) is involved in visual... | [
{
"created": "Tue, 15 May 2018 10:10:59 GMT",
"version": "v1"
},
{
"created": "Thu, 24 May 2018 15:32:48 GMT",
"version": "v2"
}
] | 2018-05-25 | [
[
"Diaz",
"Begona",
""
],
[
"Blank",
"Helen",
""
],
[
"von Kriegstein",
"Katharina",
""
]
] | The cerebral cortex modulates early sensory processing via feed-back connections to sensory pathway nuclei. The functions of this top-down modulation for human behavior are poorly understood. Here, we show that top-down modulation of the visual sensory thalamus (the lateral geniculate body, LGN) is involved in visual-s... |
1801.10262 | Yasser A. Ahmed | Yasser A. Ahmed, Mohammed Abdelsabour-Khalaf, Elsaysed Mohammed | Histological insight into the hepatic tissue of the Nile monitor
(Varanus niloticus) | 10 pages, 2 figures, original article | null | null | null | q-bio.TO | http://creativecommons.org/publicdomain/zero/1.0/ | The liver of reptiles is considered an important study model for the
interaction between environment and hepatic tissue. Little is known about the
histology of the liver of reptiles. The aim of the current study was to
elucidate the histological architecture of the liver of the Nile monitor
(Varanus niloticus). Liver... | [
{
"created": "Wed, 31 Jan 2018 01:02:57 GMT",
"version": "v1"
}
] | 2018-02-01 | [
[
"Ahmed",
"Yasser A.",
""
],
[
"Abdelsabour-Khalaf",
"Mohammed",
""
],
[
"Mohammed",
"Elsaysed",
""
]
] | The liver of reptiles is considered an important study model for the interaction between environment and hepatic tissue. Little is known about the histology of the liver of reptiles. The aim of the current study was to elucidate the histological architecture of the liver of the Nile monitor (Varanus niloticus). Liver f... |
2201.08224 | Samuel Okyere | Samuel Okyere, Joseph Ackora-Prah and Ebenezer Bonyah | A Mathematical Model of Transmission Dynamics of SARS-Cov-2 (Covid-19)
with an Underlying Condition of Diabetes | 41 pages, 22 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | It is well established that people with diabetes are more likely to have
serious complications from COVID-19. Nearly 1 in 5 COVID-19 deaths in the
African region are linked to diabetes. World Health Organization (WHO) finds
that 18.3% of COVID-19 deaths in Africa are among people with diabetes. In this
paper, we have... | [
{
"created": "Wed, 12 Jan 2022 22:48:57 GMT",
"version": "v1"
},
{
"created": "Wed, 20 Apr 2022 17:37:12 GMT",
"version": "v2"
}
] | 2022-04-21 | [
[
"Okyere",
"Samuel",
""
],
[
"Ackora-Prah",
"Joseph",
""
],
[
"Bonyah",
"Ebenezer",
""
]
] | It is well established that people with diabetes are more likely to have serious complications from COVID-19. Nearly 1 in 5 COVID-19 deaths in the African region are linked to diabetes. World Health Organization (WHO) finds that 18.3% of COVID-19 deaths in Africa are among people with diabetes. In this paper, we have f... |
1605.03952 | Mattia Rigotti | Mattia Rigotti and Stefano Fusi | Estimating the dimensionality of neural responses with fMRI Repetition
Suppression | Appears in Proceedings of the 5th NIPS Workshop on Machine Learning
and Interpretation in Neuroimaging, Montreal, 2015 | null | null | MLINI/2015/10 | q-bio.QM q-bio.NC stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a novel method that exploits fMRI Repetition Suppression (RS-fMRI)
to measure the dimensionality of the set response vectors, i.e. the dimension
of the space of linear combinations of neural population activity patterns in
response to specific task conditions. RS-fMRI measures the overlap between
response ... | [
{
"created": "Thu, 12 May 2016 19:44:05 GMT",
"version": "v1"
}
] | 2016-06-07 | [
[
"Rigotti",
"Mattia",
""
],
[
"Fusi",
"Stefano",
""
]
] | We propose a novel method that exploits fMRI Repetition Suppression (RS-fMRI) to measure the dimensionality of the set response vectors, i.e. the dimension of the space of linear combinations of neural population activity patterns in response to specific task conditions. RS-fMRI measures the overlap between response ve... |
2212.12795 | Diederik Aerts | Diederik Aerts, Jonito Aerts Argu\"elles, Lester Beltran and Sandro
Sozzo | Development of a Thermodynamics of Human Cognition and Human Culture | 20 pages, 3 figures | null | null | null | q-bio.NC cs.CL quant-ph | http://creativecommons.org/licenses/by/4.0/ | Inspired by foundational studies in classical and quantum physics, and by
information retrieval studies in quantum information theory, we prove that the
notions of 'energy' and 'entropy' can be consistently introduced in human
language and, more generally, in human culture. More explicitly, if energy is
attributed to... | [
{
"created": "Sat, 24 Dec 2022 18:19:05 GMT",
"version": "v1"
},
{
"created": "Fri, 24 Feb 2023 09:04:08 GMT",
"version": "v2"
}
] | 2023-02-27 | [
[
"Aerts",
"Diederik",
""
],
[
"Arguëlles",
"Jonito Aerts",
""
],
[
"Beltran",
"Lester",
""
],
[
"Sozzo",
"Sandro",
""
]
] | Inspired by foundational studies in classical and quantum physics, and by information retrieval studies in quantum information theory, we prove that the notions of 'energy' and 'entropy' can be consistently introduced in human language and, more generally, in human culture. More explicitly, if energy is attributed to w... |
1509.03777 | Alex McAvoy | Alex McAvoy, Christoph Hauert | Structural symmetry in evolutionary games | to appear in J. Roy. Soc. Interface | Journal of the Royal Society Interface vol. 12 no. 111, 20150420
(2015) | 10.1098/rsif.2015.0420 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In evolutionary game theory, an important measure of a mutant trait
(strategy) is its ability to invade and take over an otherwise-monomorphic
population. Typically, one quantifies the success of a mutant strategy via the
probability that a randomly occurring mutant will fixate in the population.
However, in a struct... | [
{
"created": "Sat, 12 Sep 2015 20:25:06 GMT",
"version": "v1"
}
] | 2016-04-12 | [
[
"McAvoy",
"Alex",
""
],
[
"Hauert",
"Christoph",
""
]
] | In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structur... |
1407.5104 | Pulkit Agrawal | Pulkit Agrawal, Dustin Stansbury, Jitendra Malik, Jack L. Gallant | Pixels to Voxels: Modeling Visual Representation in the Human Brain | null | null | null | null | q-bio.NC cs.CV cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human brain is adept at solving difficult high-level visual processing
problems such as image interpretation and object recognition in natural scenes.
Over the past few years neuroscientists have made remarkable progress in
understanding how the human brain represents categories of objects and actions
in natural ... | [
{
"created": "Fri, 18 Jul 2014 20:10:06 GMT",
"version": "v1"
}
] | 2014-07-22 | [
[
"Agrawal",
"Pulkit",
""
],
[
"Stansbury",
"Dustin",
""
],
[
"Malik",
"Jitendra",
""
],
[
"Gallant",
"Jack L.",
""
]
] | The human brain is adept at solving difficult high-level visual processing problems such as image interpretation and object recognition in natural scenes. Over the past few years neuroscientists have made remarkable progress in understanding how the human brain represents categories of objects and actions in natural sc... |
2201.03630 | Sweta Agrawal | Sweta Agrawal and John C Tuthill | The two body problem: proprioception and motor control across the
metamorphic divide | 17 pages, 3 figures, review paper | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Like a rocket being propelled into space, evolution has engineered flies to
launch into adulthood via multiple stages. Flies develop and deploy two
distinct bodies, linked by the transformative process of metamorphosis. The fly
larva is a soft hydraulic tube that can crawl to find food and avoid predators.
The adult ... | [
{
"created": "Mon, 10 Jan 2022 20:26:03 GMT",
"version": "v1"
}
] | 2022-01-12 | [
[
"Agrawal",
"Sweta",
""
],
[
"Tuthill",
"John C",
""
]
] | Like a rocket being propelled into space, evolution has engineered flies to launch into adulthood via multiple stages. Flies develop and deploy two distinct bodies, linked by the transformative process of metamorphosis. The fly larva is a soft hydraulic tube that can crawl to find food and avoid predators. The adult fl... |
1911.02301 | Kesheng Xu Dr | Kesheng Xu and Jean Paul Maidana and Patricio Orio | Diversity of neuronal activity is provided by hybrid synapses | null | Nonlinear Dynamics ,2021 | 10.1007/s11071-021-06704-9 | null | q-bio.NC nlin.AO physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Many experiments have evidenced that electrical and chemical synapses --
hybrid synapses -- coexist in most organisms and brain structures. The role of
electrical and chemical synapse connection in diversity of neural activity
generation has been investigated separately in networks of varying
complexities. Neverthele... | [
{
"created": "Wed, 6 Nov 2019 10:49:00 GMT",
"version": "v1"
}
] | 2021-08-11 | [
[
"Xu",
"Kesheng",
""
],
[
"Maidana",
"Jean Paul",
""
],
[
"Orio",
"Patricio",
""
]
] | Many experiments have evidenced that electrical and chemical synapses -- hybrid synapses -- coexist in most organisms and brain structures. The role of electrical and chemical synapse connection in diversity of neural activity generation has been investigated separately in networks of varying complexities. Nevertheless... |
2309.16704 | Alan Smeaton | Lorin Sweeney and Graham Healy and Alan F. Smeaton | Memories in the Making: Predicting Video Memorability with Encoding
Phase EEG | Content-Based Multimedia Indexing, CBMI, September 20-22, Orleans,
France, 2023 | null | null | null | q-bio.NC cs.CV eess.SP | http://creativecommons.org/licenses/by/4.0/ | In a world of ephemeral moments, our brain diligently sieves through a
cascade of experiences, like a skilled gold prospector searching for precious
nuggets amidst the river's relentless flow. This study delves into the elusive
"moment of memorability" -- a fleeting, yet vital instant where experiences are
prioritise... | [
{
"created": "Wed, 16 Aug 2023 22:39:27 GMT",
"version": "v1"
}
] | 2023-10-02 | [
[
"Sweeney",
"Lorin",
""
],
[
"Healy",
"Graham",
""
],
[
"Smeaton",
"Alan F.",
""
]
] | In a world of ephemeral moments, our brain diligently sieves through a cascade of experiences, like a skilled gold prospector searching for precious nuggets amidst the river's relentless flow. This study delves into the elusive "moment of memorability" -- a fleeting, yet vital instant where experiences are prioritised ... |
2407.16063 | Salil Patel | Salil B Patel, Oliver B Bredemeyer, James J FitzGerald, Chrystalina A
Antoniades | Hierarchical Machine Learning Classification of Parkinsonian Disorders
using Saccadic Eye Movements: A Development and Validation Study | 2 table, 7 Figure, 27 pages | null | null | null | q-bio.QM q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Discriminating between Parkinson's Disease (PD) and Progressive Supranuclear
Palsy (PSP) is difficult due to overlapping symptoms, especially early on.
Saccades (rapid conjugate eye movements between fixation points) are affected
by both diseases but conventional saccade analyses exhibit group level
differences only.... | [
{
"created": "Mon, 22 Jul 2024 21:41:04 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Jul 2024 11:24:54 GMT",
"version": "v2"
}
] | 2024-07-25 | [
[
"Patel",
"Salil B",
""
],
[
"Bredemeyer",
"Oliver B",
""
],
[
"FitzGerald",
"James J",
""
],
[
"Antoniades",
"Chrystalina A",
""
]
] | Discriminating between Parkinson's Disease (PD) and Progressive Supranuclear Palsy (PSP) is difficult due to overlapping symptoms, especially early on. Saccades (rapid conjugate eye movements between fixation points) are affected by both diseases but conventional saccade analyses exhibit group level differences only. W... |
2310.15753 | Sam Subbey | S. Arabeei and S. Subbey | Efficient CPU-Optimized Parameter Estimation for Modeling Fish Schooling
Behavior in Large Particle Systems | 10pages | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The schooling behavior of fish can be studied through simulations involving a
large number of interacting particles. In such systems, each individual
particle is guided by behavior rules, which include aggregation towards a
centroid, collision avoidance, and direction alignment. The movement vector of
each particle m... | [
{
"created": "Tue, 24 Oct 2023 11:56:13 GMT",
"version": "v1"
}
] | 2023-10-25 | [
[
"Arabeei",
"S.",
""
],
[
"Subbey",
"S.",
""
]
] | The schooling behavior of fish can be studied through simulations involving a large number of interacting particles. In such systems, each individual particle is guided by behavior rules, which include aggregation towards a centroid, collision avoidance, and direction alignment. The movement vector of each particle may... |
1505.01744 | David Krakauer | David Krakauer | Cryptographic Nature | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | I consider the many ways in which evolved information-flows are restricted
and metabolic resources protected and hidden -- the thesis of living phenomena
as evolutionary cryptosystems. I present the information theory of secrecy
systems and discuss mechanisms acquired by evolved lineages that encrypt
sensitive herita... | [
{
"created": "Thu, 7 May 2015 15:27:25 GMT",
"version": "v1"
}
] | 2015-05-08 | [
[
"Krakauer",
"David",
""
]
] | I consider the many ways in which evolved information-flows are restricted and metabolic resources protected and hidden -- the thesis of living phenomena as evolutionary cryptosystems. I present the information theory of secrecy systems and discuss mechanisms acquired by evolved lineages that encrypt sensitive heritabl... |
1707.01962 | Kamesh Krishnamurthy | Kamesh Krishnamurthy, Ann M Hermundstad, Thierry Mora, Aleksandra M
Walczak, Vijay Balasubramanian | Disorder and the neural representation of complex odors: smelling in the
real world | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Animals smelling in the real world use a small number of receptors to sense a
vast number of natural molecular mixtures, and proceed to learn arbitrary
associations between odors and valences. Here, we propose a new interpretation
of how the architecture of olfactory circuits is adapted to meet these immense
compleme... | [
{
"created": "Thu, 6 Jul 2017 20:52:50 GMT",
"version": "v1"
}
] | 2017-07-10 | [
[
"Krishnamurthy",
"Kamesh",
""
],
[
"Hermundstad",
"Ann M",
""
],
[
"Mora",
"Thierry",
""
],
[
"Walczak",
"Aleksandra M",
""
],
[
"Balasubramanian",
"Vijay",
""
]
] | Animals smelling in the real world use a small number of receptors to sense a vast number of natural molecular mixtures, and proceed to learn arbitrary associations between odors and valences. Here, we propose a new interpretation of how the architecture of olfactory circuits is adapted to meet these immense complement... |
1211.6664 | Fabien Campagne | Fabien Campagne, Kevin C. Dorff, Nyasha Chambwe, James T. Robinson,
Jill P. Mesirov and Thomas D. Wu | Compression of structured high-throughput sequencing data | main article: 2 figures, 2 tables. Supplementary material: 2 figures,
4 tables. Comment on this manuscript on Twitter or Google Plus using handle
#Goby2Paper | null | 10.1371/journal.pone.0079871 | null | q-bio.QM cs.DB q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Large biological datasets are being produced at a rapid pace and create
substantial storage challenges, particularly in the domain of high-throughput
sequencing (HTS). Most approaches currently used to store HTS data are either
unable to quickly adapt to the requirements of new sequencing or analysis
methods (because... | [
{
"created": "Wed, 28 Nov 2012 17:11:54 GMT",
"version": "v1"
}
] | 2014-03-05 | [
[
"Campagne",
"Fabien",
""
],
[
"Dorff",
"Kevin C.",
""
],
[
"Chambwe",
"Nyasha",
""
],
[
"Robinson",
"James T.",
""
],
[
"Mesirov",
"Jill P.",
""
],
[
"Wu",
"Thomas D.",
""
]
] | Large biological datasets are being produced at a rapid pace and create substantial storage challenges, particularly in the domain of high-throughput sequencing (HTS). Most approaches currently used to store HTS data are either unable to quickly adapt to the requirements of new sequencing or analysis methods (because t... |
2408.08069 | Murat Ersalman | Murat Ersalman, Mervi Kunnasranta, Markus Ahola, Anja M. Carlsson,
Sara Persson, Britt-Marie B\"acklin, Inari Helle, Linnea Cervin, Jarno
Vanhatalo | Integrated population model reveals human and environment driven changes
in Baltic ringed seal (Pusa hispida botnica) demography and behavior | null | null | null | null | q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Integrated population models (IPMs) are a promising approach to test
ecological theories and assess wildlife populations in dynamic and uncertain
conditions. By combining multiple data sources into a single, unified model,
they enable the parametrization of versatile, mechanistic models that can
predict population dy... | [
{
"created": "Thu, 15 Aug 2024 10:34:23 GMT",
"version": "v1"
}
] | 2024-08-16 | [
[
"Ersalman",
"Murat",
""
],
[
"Kunnasranta",
"Mervi",
""
],
[
"Ahola",
"Markus",
""
],
[
"Carlsson",
"Anja M.",
""
],
[
"Persson",
"Sara",
""
],
[
"Bäcklin",
"Britt-Marie",
""
],
[
"Helle",
"Inari",
""
],
... | Integrated population models (IPMs) are a promising approach to test ecological theories and assess wildlife populations in dynamic and uncertain conditions. By combining multiple data sources into a single, unified model, they enable the parametrization of versatile, mechanistic models that can predict population dyna... |
2312.10707 | Li Kun | Kun Li, Wenbin Hu | CLDR: Contrastive Learning Drug Response Models from Natural Language
Supervision | 9 pages, 4 figures, 3 tables | null | null | null | q-bio.BM cs.AI cs.LG q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Deep learning-based drug response prediction (DRP) methods can accelerate the
drug discovery process and reduce R\&D costs. Although the mainstream methods
achieve high accuracy in predicting response regression values, the
regression-aware representations of these methods are fragmented and fail to
capture the conti... | [
{
"created": "Sun, 17 Dec 2023 12:51:49 GMT",
"version": "v1"
}
] | 2023-12-19 | [
[
"Li",
"Kun",
""
],
[
"Hu",
"Wenbin",
""
]
] | Deep learning-based drug response prediction (DRP) methods can accelerate the drug discovery process and reduce R\&D costs. Although the mainstream methods achieve high accuracy in predicting response regression values, the regression-aware representations of these methods are fragmented and fail to capture the continu... |
2106.00628 | Martin Frasch | Martin G. Frasch, Shadrian B. Strong, David Nilosek, Joshua Leaverton,
Barry S. Schifrin | Detection of preventable fetal distress during labor from scanned
cardiotocogram tracings using deep learning | null | null | 10.3389/fped.2021.736834 | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Despite broad application during labor and delivery, there remains
considerable debate about the value of electronic fetal monitoring (EFM). EFM
includes the surveillance of the fetal heart rate (FHR) patterns in conjunction
with the maternal uterine contractions providing a wealth of data about fetal
behavior and th... | [
{
"created": "Tue, 1 Jun 2021 16:40:50 GMT",
"version": "v1"
},
{
"created": "Thu, 15 Jul 2021 20:09:13 GMT",
"version": "v2"
}
] | 2021-12-06 | [
[
"Frasch",
"Martin G.",
""
],
[
"Strong",
"Shadrian B.",
""
],
[
"Nilosek",
"David",
""
],
[
"Leaverton",
"Joshua",
""
],
[
"Schifrin",
"Barry S.",
""
]
] | Despite broad application during labor and delivery, there remains considerable debate about the value of electronic fetal monitoring (EFM). EFM includes the surveillance of the fetal heart rate (FHR) patterns in conjunction with the maternal uterine contractions providing a wealth of data about fetal behavior and the ... |
0911.4032 | Peter Klimek | Peter Klimek, Stefan Thurner, Rudolf Hanel | Evolutionary dynamics from a variational principle | 13 pages, 3 figures, 2 tables | null | 10.1103/PhysRevE.82.011901 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We demonstrate with a thought experiment that fitness-based population
dynamical approaches to evolution are not able to make quantitative,
falsifiable predictions about the long-term behavior of evolutionary systems. A
key characteristic of evolutionary systems is the ongoing endogenous production
of new species. Th... | [
{
"created": "Fri, 20 Nov 2009 12:52:42 GMT",
"version": "v1"
}
] | 2015-05-14 | [
[
"Klimek",
"Peter",
""
],
[
"Thurner",
"Stefan",
""
],
[
"Hanel",
"Rudolf",
""
]
] | We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of evolutionary systems. A key characteristic of evolutionary systems is the ongoing endogenous production of new species. Thes... |
2204.01675 | Tilo Schwalger | Bastian Pietras, Valentin Schmutz, Tilo Schwalger | Mesoscopic description of hippocampal replay and metastability in
spiking neural networks with short-term plasticity | 43 pages, 8 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Bottom-up models of functionally relevant patterns of neural activity provide
an explicit link between neuronal dynamics and computation. A prime example of
functional activity pattern is hippocampal replay, which is critical for memory
consolidation. The switchings between replay events and a low-activity state in
n... | [
{
"created": "Mon, 4 Apr 2022 17:45:10 GMT",
"version": "v1"
},
{
"created": "Fri, 29 Apr 2022 21:47:09 GMT",
"version": "v2"
}
] | 2022-05-03 | [
[
"Pietras",
"Bastian",
""
],
[
"Schmutz",
"Valentin",
""
],
[
"Schwalger",
"Tilo",
""
]
] | Bottom-up models of functionally relevant patterns of neural activity provide an explicit link between neuronal dynamics and computation. A prime example of functional activity pattern is hippocampal replay, which is critical for memory consolidation. The switchings between replay events and a low-activity state in neu... |
2006.11495 | Manuel Baltieri Dr | Manuel Baltieri, Christopher L. Buckley, Jelle Bruineberg | Predictions in the eye of the beholder: an active inference account of
Watt governors | Accepted at ALife 2020 | null | 10.1162/isal_a_00288 | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Active inference introduces a theory describing action-perception loops via
the minimisation of variational (and expected) free energy or, under
simplifying assumptions, (weighted) prediction error. Recently, active
inference has been proposed as part of a new and unifying framework in the
cognitive sciences: predict... | [
{
"created": "Sat, 20 Jun 2020 04:55:39 GMT",
"version": "v1"
},
{
"created": "Fri, 26 Jun 2020 03:02:44 GMT",
"version": "v2"
}
] | 2022-03-10 | [
[
"Baltieri",
"Manuel",
""
],
[
"Buckley",
"Christopher L.",
""
],
[
"Bruineberg",
"Jelle",
""
]
] | Active inference introduces a theory describing action-perception loops via the minimisation of variational (and expected) free energy or, under simplifying assumptions, (weighted) prediction error. Recently, active inference has been proposed as part of a new and unifying framework in the cognitive sciences: predictiv... |
1907.01092 | Dumitru Trucu | Robyn Shuttleworth and Dumitru Trucu | Multiscale dynamics of a heterotypic cancer cell population within a
fibrous extracellular matrix | null | null | null | null | q-bio.TO math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Local cancer cell invasion is a complex process involving many cellular and
tissue interactions and is an important prerequisite for metastatic spread, the
main cause of cancer related deaths. Occurring over many different temporal and
spatial scales, the first stage of local invasion is the secretion of
matrix-degra... | [
{
"created": "Mon, 1 Jul 2019 23:02:19 GMT",
"version": "v1"
}
] | 2019-07-03 | [
[
"Shuttleworth",
"Robyn",
""
],
[
"Trucu",
"Dumitru",
""
]
] | Local cancer cell invasion is a complex process involving many cellular and tissue interactions and is an important prerequisite for metastatic spread, the main cause of cancer related deaths. Occurring over many different temporal and spatial scales, the first stage of local invasion is the secretion of matrix-degradi... |
1801.04901 | Grace Brannigan | Reza Salari and Thomas Joseph and Ruchi Lohia and Jerome Henin and
Grace Brannigan | A streamlined, general approach for computing ligand binding free
energies and its application to GPCR-bound cholesterol | 4 figures | null | null | null | q-bio.QM cond-mat.soft cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The theory of receptor-ligand binding equilibria has long been
well-established in biochemistry, and was primarily constructed to describe
dilute aqueous solutions. Accordingly, few computational approaches have been
developed for making quantitative predictions of binding probabilities in
environments other than dil... | [
{
"created": "Mon, 15 Jan 2018 18:18:35 GMT",
"version": "v1"
},
{
"created": "Tue, 8 May 2018 21:45:49 GMT",
"version": "v2"
},
{
"created": "Fri, 28 Sep 2018 18:27:08 GMT",
"version": "v3"
}
] | 2018-10-02 | [
[
"Salari",
"Reza",
""
],
[
"Joseph",
"Thomas",
""
],
[
"Lohia",
"Ruchi",
""
],
[
"Henin",
"Jerome",
""
],
[
"Brannigan",
"Grace",
""
]
] | The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making quantitative predictions of binding probabilities in environments other than dilut... |
1811.01175 | Lee Worden | Lee Worden, Rae Wannier, Nicole A. Hoff, Kamy Musene, Bernice Selo,
Mathias Mossoko, Emile Okitolonda-Wemakoy, Jean Jacques Muyembe-Tamfum,
George W. Rutherford, Thomas M. Lietman, Anne W. Rimoin, Travis C. Porco, J.
Daniel Kelly | Real-time projections of epidemic transmission and estimation of
vaccination impact during an Ebola virus disease outbreak in the Eastern
region of the Democratic Republic of Congo | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As of October 12, 2018, 211 cases of Ebola virus disease (EVD) were reported
in North Kivu Province, Democratic Republic of Congo. Since the beginning of
October the outbreak has largely shifted into regions in which active armed
conflict is occurring, and in which EVD cases and their contacts are difficult
for healt... | [
{
"created": "Sat, 3 Nov 2018 08:31:41 GMT",
"version": "v1"
}
] | 2018-11-06 | [
[
"Worden",
"Lee",
""
],
[
"Wannier",
"Rae",
""
],
[
"Hoff",
"Nicole A.",
""
],
[
"Musene",
"Kamy",
""
],
[
"Selo",
"Bernice",
""
],
[
"Mossoko",
"Mathias",
""
],
[
"Okitolonda-Wemakoy",
"Emile",
""
],
[
... | As of October 12, 2018, 211 cases of Ebola virus disease (EVD) were reported in North Kivu Province, Democratic Republic of Congo. Since the beginning of October the outbreak has largely shifted into regions in which active armed conflict is occurring, and in which EVD cases and their contacts are difficult for health ... |
1208.0133 | Max Alekseyev | Sergey Aganezov, Jr. and Max A. Alekseyev | On pairwise distances and median score of three genomes under DCJ | Proceedings of the 10-th Annual RECOMB Satellite Workshop on
Comparative Genomics (RECOMB-CG), 2012. (to appear) | BMC Bioinformatics 2012, 13(Suppl 19):S1 | 10.1186/1471-2105-13-S19-S1 | null | q-bio.GN cs.DM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In comparative genomics, the rearrangement distance between two genomes
(equal the minimal number of genome rearrangements required to transform them
into a single genome) is often used for measuring their evolutionary
remoteness. Generalization of this measure to three genomes is known as the
median score (while a r... | [
{
"created": "Wed, 1 Aug 2012 08:20:16 GMT",
"version": "v1"
},
{
"created": "Mon, 22 Oct 2012 21:54:36 GMT",
"version": "v2"
}
] | 2014-01-03 | [
[
"Aganezov,",
"Sergey",
"Jr."
],
[
"Alekseyev",
"Max A.",
""
]
] | In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a res... |
1011.2797 | Andrea Barreiro | Andrea K. Barreiro, Julijana Gjorgjieva, Fred Rieke, Eric Shea-Brown | When are microcircuits well-modeled by maximum entropy methods? | Submitted Nov 1, 2010; Updated version submitted Feb 24, 2011;
Revised version submitted Feb 1, 2012 | null | null | null | q-bio.NC cond-mat.dis-nn cs.IT math.IT physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Describing the collective activity of neural populations is a daunting task:
the number of possible patterns grows exponentially with the number of cells,
resulting in practically unlimited complexity. Recent empirical studies,
however, suggest a vast simplification in how multi-neuron spiking occurs: the
activity pa... | [
{
"created": "Thu, 11 Nov 2010 23:38:55 GMT",
"version": "v1"
},
{
"created": "Sat, 26 Feb 2011 18:31:28 GMT",
"version": "v2"
},
{
"created": "Wed, 1 Feb 2012 16:14:01 GMT",
"version": "v3"
}
] | 2012-02-02 | [
[
"Barreiro",
"Andrea K.",
""
],
[
"Gjorgjieva",
"Julijana",
""
],
[
"Rieke",
"Fred",
""
],
[
"Shea-Brown",
"Eric",
""
]
] | Describing the collective activity of neural populations is a daunting task: the number of possible patterns grows exponentially with the number of cells, resulting in practically unlimited complexity. Recent empirical studies, however, suggest a vast simplification in how multi-neuron spiking occurs: the activity patt... |
2312.01833 | Leonardo Novelli | Leonardo Novelli, Lionel Barnett, Anil Seth, Adeel Razi | Minimum-phase property of the hemodynamic response function, and
implications for Granger Causality in fMRI | null | null | null | null | q-bio.NC q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Granger Causality (GC) is widely used in neuroimaging to estimate directed
statistical dependence among brain regions using time series of brain activity.
An important issue is that functional MRI (fMRI) measures brain activity
indirectly via the blood-oxygen-level-dependent (BOLD) signal, which affects
the temporal ... | [
{
"created": "Mon, 4 Dec 2023 12:12:26 GMT",
"version": "v1"
}
] | 2023-12-05 | [
[
"Novelli",
"Leonardo",
""
],
[
"Barnett",
"Lionel",
""
],
[
"Seth",
"Anil",
""
],
[
"Razi",
"Adeel",
""
]
] | Granger Causality (GC) is widely used in neuroimaging to estimate directed statistical dependence among brain regions using time series of brain activity. An important issue is that functional MRI (fMRI) measures brain activity indirectly via the blood-oxygen-level-dependent (BOLD) signal, which affects the temporal st... |
1808.00065 | Nassim Nicholas Taleb | Nassim Nicholas Taleb | (Anti)Fragility and Convex Responses in Medicine | Proceedings of the Ninth International Conference on Complex Systems
(2018) | Unifying Themes in Complex Systems IX, Proceedings of the Ninth
International Conference on Complex Systems (2018), in Alfredo J. Morales ,
Carlos Gershenson, Dan Braha, Ali A. Minai, & Yaneer Bar-Yam, Eds., Springer,
pp. 299-325 | null | null | q-bio.QM physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper applies risk analysis to medical problems, through the properties
of nonlinear responses (convex or concave). It shows 1) necessary relations
between the nonlinearity of dose-response and the statistical properties of the
outcomes, particularly the effect of the variance (i.e., the expected frequency
of th... | [
{
"created": "Tue, 31 Jul 2018 20:35:26 GMT",
"version": "v1"
}
] | 2018-08-02 | [
[
"Taleb",
"Nassim Nicholas",
""
]
] | This paper applies risk analysis to medical problems, through the properties of nonlinear responses (convex or concave). It shows 1) necessary relations between the nonlinearity of dose-response and the statistical properties of the outcomes, particularly the effect of the variance (i.e., the expected frequency of the ... |
1210.0168 | Sepehr Ehsani | Sepehr Ehsani | Time in the cell: a plausible role for the plasma membrane | 6 pages, 2 figures | null | null | null | q-bio.SC q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | All cells must keep time to consistently perform vital biological functions.
To that end, the coupling and interrelatedness of diverse subsecond events in
the complex cellular environment, such as protein folding or translation rates,
cannot simply result from the chance convergence of the inherent chemical
propertie... | [
{
"created": "Sun, 30 Sep 2012 04:38:45 GMT",
"version": "v1"
}
] | 2012-10-02 | [
[
"Ehsani",
"Sepehr",
""
]
] | All cells must keep time to consistently perform vital biological functions. To that end, the coupling and interrelatedness of diverse subsecond events in the complex cellular environment, such as protein folding or translation rates, cannot simply result from the chance convergence of the inherent chemical properties ... |
2009.03857 | William Podlaski | Michele Nardin, James W Phillips, William F Podlaski, Sander W Keemink | Nonlinear computations in spiking neural networks through multiplicative
synapses | This article has been peer-reviewed and recommended by Peer Community
In Neuroscience | Peer Community In Neuroscience, 2021 | 10.24072/pci.cneuro.100003 | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The brain efficiently performs nonlinear computations through its intricate
networks of spiking neurons, but how this is done remains elusive. While
nonlinear computations can be implemented successfully in spiking neural
networks, this requires supervised training and the resulting connectivity can
be hard to interp... | [
{
"created": "Tue, 8 Sep 2020 16:47:27 GMT",
"version": "v1"
},
{
"created": "Wed, 31 Mar 2021 16:36:28 GMT",
"version": "v2"
},
{
"created": "Mon, 2 Aug 2021 10:45:47 GMT",
"version": "v3"
},
{
"created": "Mon, 22 Nov 2021 10:41:58 GMT",
"version": "v4"
}
] | 2021-11-23 | [
[
"Nardin",
"Michele",
""
],
[
"Phillips",
"James W",
""
],
[
"Podlaski",
"William F",
""
],
[
"Keemink",
"Sander W",
""
]
] | The brain efficiently performs nonlinear computations through its intricate networks of spiking neurons, but how this is done remains elusive. While nonlinear computations can be implemented successfully in spiking neural networks, this requires supervised training and the resulting connectivity can be hard to interpre... |
2110.03526 | Mohammadreza Ahmadi | Mohammadreza Ahmadi | Tissue Engineering of Skin Regeneration and Hair Growth | null | null | null | null | q-bio.TO | http://creativecommons.org/publicdomain/zero/1.0/ | Many people suffering from skin disorders such as chronic wounds, non-healing
ulcers, and diabetic ulcers need skin repair and regeneration. Aside from the
diseases listed above, the industry needed a skin rejuvenation system and
regeneration for cosmetic purposes. The procedure used to deliver pluripotent
stem cells... | [
{
"created": "Sat, 2 Oct 2021 23:53:58 GMT",
"version": "v1"
}
] | 2021-10-08 | [
[
"Ahmadi",
"Mohammadreza",
""
]
] | Many people suffering from skin disorders such as chronic wounds, non-healing ulcers, and diabetic ulcers need skin repair and regeneration. Aside from the diseases listed above, the industry needed a skin rejuvenation system and regeneration for cosmetic purposes. The procedure used to deliver pluripotent stem cells t... |
2107.01376 | Sergii Kovalchuk | Sergii Kovalchuk (Geolab, Odessa, Ukraine) | Study of conduction, block and reflection at the excitable tissues
boundary in terms of the interval model of action potential | null | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Some mechanisms of cardiac arrhythmias can be presented as a composition of
elementary acts of block and reflection on the contacts of homogeneous areas of
the conducting tissue. For study this phenomena we use an axiomatic
one-dimensional model of interaction of cells of excitable tissue. The model
has four function... | [
{
"created": "Sat, 3 Jul 2021 08:17:32 GMT",
"version": "v1"
}
] | 2021-07-06 | [
[
"Kovalchuk",
"Sergii",
"",
"Geolab, Odessa, Ukraine"
]
] | Some mechanisms of cardiac arrhythmias can be presented as a composition of elementary acts of block and reflection on the contacts of homogeneous areas of the conducting tissue. For study this phenomena we use an axiomatic one-dimensional model of interaction of cells of excitable tissue. The model has four functional... |
2109.00038 | Magdalena Djordjevic | Sofija Markovic, Andjela Rodic, Igor Salom, Ognjen Milicevic,
Magdalena Djordjevic, Marko Djordjevic | COVID-19 severity determinants inferred through ecological and
epidemiological modeling | 14 pages, 7 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Determinants of COVID-19 clinical severity are commonly assessed by
transverse or longitudinal studies of the fatality counts. However, the
fatality counts depend both on disease clinical severity and transmissibility,
as more infected also lead to more deaths. Moreover, fatality counts (and
related measures such as ... | [
{
"created": "Tue, 31 Aug 2021 18:49:16 GMT",
"version": "v1"
}
] | 2021-09-02 | [
[
"Markovic",
"Sofija",
""
],
[
"Rodic",
"Andjela",
""
],
[
"Salom",
"Igor",
""
],
[
"Milicevic",
"Ognjen",
""
],
[
"Djordjevic",
"Magdalena",
""
],
[
"Djordjevic",
"Marko",
""
]
] | Determinants of COVID-19 clinical severity are commonly assessed by transverse or longitudinal studies of the fatality counts. However, the fatality counts depend both on disease clinical severity and transmissibility, as more infected also lead to more deaths. Moreover, fatality counts (and related measures such as Ca... |
1711.10814 | Hiroshi Tsukimoto | Hiroshi Tsukimoto and Takefumi Matsubara | A new fMRI data analysis method using cross validation: Negative BOLD
responses may be the deactivations of interneurons | 23 pages, 2 figures, 8 tables | null | null | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although functional magnetic resonance imaging (fMRI) is widely used for the
study of brain functions, the blood oxygenation level dependent (BOLD) effect
is incompletely understood. Particularly, negative BOLD responses(NBRs) is
controversial. This paper presents a new fMRI data analysis method, which is
more accura... | [
{
"created": "Wed, 29 Nov 2017 12:32:51 GMT",
"version": "v1"
},
{
"created": "Sun, 10 Dec 2017 08:43:26 GMT",
"version": "v2"
}
] | 2017-12-12 | [
[
"Tsukimoto",
"Hiroshi",
""
],
[
"Matsubara",
"Takefumi",
""
]
] | Although functional magnetic resonance imaging (fMRI) is widely used for the study of brain functions, the blood oxygenation level dependent (BOLD) effect is incompletely understood. Particularly, negative BOLD responses(NBRs) is controversial. This paper presents a new fMRI data analysis method, which is more accurate... |
1005.4830 | Anca Radulescu | Anca Radulescu | Mechanisms explaining transitions between tonic and phasic firing in
neuronal populations as predicted by a low dimensional firing rate model | 25 pages (including references and appendices); 12 figures uploaded
as separate files | null | 10.1371/journal.pone.0012695 | null | q-bio.CB math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Several firing patterns experimentally observed in neural populations have
been successfully correlated to animal behavior. Population bursting, hereby
regarded as a period of high firing rate followed by a period of quiescence, is
typically observed in groups of neurons during behavior. Biophysical
membrane-potentia... | [
{
"created": "Wed, 26 May 2010 14:34:30 GMT",
"version": "v1"
}
] | 2015-05-19 | [
[
"Radulescu",
"Anca",
""
]
] | Several firing patterns experimentally observed in neural populations have been successfully correlated to animal behavior. Population bursting, hereby regarded as a period of high firing rate followed by a period of quiescence, is typically observed in groups of neurons during behavior. Biophysical membrane-potential ... |
2106.15733 | Aritro Sinha Roy | Aritro Sinha Roy | Optimal Background Correction in Double Quantum Coherence Electron Spin
Resonance Spectroscopy for Accurate Data Analysis | null | null | null | null | q-bio.QM physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Electron spin resonance (ESR) pulsed dipolar spectroscopy (PDS) is used in
protein 3D structure determination. However, the accuracy of the signal
analysis depends heavily on the background correction process. In this work, we
derive the functional forms of double quantum coherence (DQC) ESR signal in
typical frozen ... | [
{
"created": "Tue, 29 Jun 2021 21:39:27 GMT",
"version": "v1"
}
] | 2021-07-01 | [
[
"Roy",
"Aritro Sinha",
""
]
] | Electron spin resonance (ESR) pulsed dipolar spectroscopy (PDS) is used in protein 3D structure determination. However, the accuracy of the signal analysis depends heavily on the background correction process. In this work, we derive the functional forms of double quantum coherence (DQC) ESR signal in typical frozen sa... |
1506.01142 | Gerardo F. Goya | G.F. Goya, L. Asin, M. P. Calatayud, A. Tres and M.R. Ibarra | Cell bystander effect induced by radiofrequency electromagnetic fields
and magnetic nanoparticles | 16 pages, 4 figures, submitted to International Journal of Radiation
Biology | null | null | null | q-bio.SC physics.bio-ph q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Induced effects by direct exposure to ionizing radiation (IR) are a central
issue in many fields like radiation protection, clinic diagnosis and
oncological therapies. Direct irradiation at certain doses induce cell death,
but similar effects can also occur in cells no directly exposed to IR, a
mechanism known as bys... | [
{
"created": "Wed, 3 Jun 2015 06:58:47 GMT",
"version": "v1"
}
] | 2015-06-04 | [
[
"Goya",
"G. F.",
""
],
[
"Asin",
"L.",
""
],
[
"Calatayud",
"M. P.",
""
],
[
"Tres",
"A.",
""
],
[
"Ibarra",
"M. R.",
""
]
] | Induced effects by direct exposure to ionizing radiation (IR) are a central issue in many fields like radiation protection, clinic diagnosis and oncological therapies. Direct irradiation at certain doses induce cell death, but similar effects can also occur in cells no directly exposed to IR, a mechanism known as bysta... |
0907.2192 | Charles Ross FBCS FIAP FIMIS | Charles Ross and Shirley Redpath | Physical Foundations of Consciousness: Brain Organisation: The Role of
Synapses | 9 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have analysed the many facets of Consciousness into two distinct
categories. First: the organisational state of the neural networks at any one
time, which determines whether a person is conscious - awake, or unconscious -
asleep. Second: the processes that underlie the traffic of electrical signals
across these ne... | [
{
"created": "Mon, 13 Jul 2009 15:39:43 GMT",
"version": "v1"
}
] | 2009-07-14 | [
[
"Ross",
"Charles",
""
],
[
"Redpath",
"Shirley",
""
]
] | We have analysed the many facets of Consciousness into two distinct categories. First: the organisational state of the neural networks at any one time, which determines whether a person is conscious - awake, or unconscious - asleep. Second: the processes that underlie the traffic of electrical signals across these netw... |
2305.15590 | Marc Boubnovski Martell | Marc Boubnovski Martell, Kristofer Linton-Reid, Sumeet Hindocha,
Mitchell Chen, OCTAPUS-AI, Paula Moreno, Marina \'Alvarez-Benito, \'Angel
Salvatierra, Richard Lee, Joram M. Posma, Marco A Calzado and Eric O Aboagye | Deep Representation Learning of Tissue Metabolome and Computed
Tomography Images Annotates Non-invasive Classification and Prognosis
Prediction of NSCLC | null | null | null | null | q-bio.QM eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The rich chemical information from tissue metabolomics provides a powerful
means to elaborate tissue physiology or tumor characteristics at cellular and
tumor microenvironment levels. However, the process of obtaining such
information requires invasive biopsies, is costly, and can delay clinical
patient management. C... | [
{
"created": "Wed, 24 May 2023 21:57:29 GMT",
"version": "v1"
},
{
"created": "Fri, 26 May 2023 09:47:03 GMT",
"version": "v2"
}
] | 2023-05-29 | [
[
"Martell",
"Marc Boubnovski",
""
],
[
"Linton-Reid",
"Kristofer",
""
],
[
"Hindocha",
"Sumeet",
""
],
[
"Chen",
"Mitchell",
""
],
[
"OCTAPUS-AI",
"",
""
],
[
"Moreno",
"Paula",
""
],
[
"Álvarez-Benito",
"Marina... | The rich chemical information from tissue metabolomics provides a powerful means to elaborate tissue physiology or tumor characteristics at cellular and tumor microenvironment levels. However, the process of obtaining such information requires invasive biopsies, is costly, and can delay clinical patient management. Con... |
2404.12565 | Andreas Tiffeau-Mayer | James Henderson, Yuta Nagano, Martina Milighetti, Andreas
Tiffeau-Mayer | Limits on Inferring T-cell Specificity from Partial Information | 24 pages, 15 figures | null | null | null | q-bio.BM cond-mat.stat-mech cs.IT math.IT | http://creativecommons.org/licenses/by/4.0/ | A key challenge in molecular biology is to decipher the mapping of protein
sequence to function. To perform this mapping requires the identification of
sequence features most informative about function. Here, we quantify the amount
of information (in bits) that T-cell receptor (TCR) sequence features provide
about an... | [
{
"created": "Fri, 19 Apr 2024 01:02:08 GMT",
"version": "v1"
}
] | 2024-04-22 | [
[
"Henderson",
"James",
""
],
[
"Nagano",
"Yuta",
""
],
[
"Milighetti",
"Martina",
""
],
[
"Tiffeau-Mayer",
"Andreas",
""
]
] | A key challenge in molecular biology is to decipher the mapping of protein sequence to function. To perform this mapping requires the identification of sequence features most informative about function. Here, we quantify the amount of information (in bits) that T-cell receptor (TCR) sequence features provide about anti... |
1112.2630 | Leonid Shapiro | Leonid A. Shapiro | Generalized Functions & Experimental Methods of Obtaining Statistical
Variable-Quantities Which Fully Determine Preferences in Choice-Rich
Environments | 26 pages, 1 figures, Version 3 (January 19), Version 2 (December 31),
Version 1 (December 12), in review process | null | null | null | q-bio.NC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Preferences of individuals are distributions of elements generated by
generalized functions. Models of economic decision-making derived from such
distributions are consistent with results of physiological experiments, and
explain any behavioral situations without simplifying assumptions. Quantities
in such models pre... | [
{
"created": "Mon, 12 Dec 2011 17:19:26 GMT",
"version": "v1"
},
{
"created": "Tue, 3 Jan 2012 20:55:17 GMT",
"version": "v2"
},
{
"created": "Thu, 19 Jan 2012 20:46:53 GMT",
"version": "v3"
}
] | 2012-01-20 | [
[
"Shapiro",
"Leonid A.",
""
]
] | Preferences of individuals are distributions of elements generated by generalized functions. Models of economic decision-making derived from such distributions are consistent with results of physiological experiments, and explain any behavioral situations without simplifying assumptions. Quantities in such models preci... |
2407.04799 | Noel Cadigan Dr | Noel G. Cadigan, Andrea M. Perreault, Hoang Nguyen, Jiaying Chen,
Andres Beita-Jimenez, Natalie Fuller, Krista Ransier | A state-space catch-at-length assessment model for redfish on the
Eastern Grand Bank of Newfoundland reveals large uncertainties in data and
stock dynamics | 27 pages including references, tables, and figures. In addition 12
pages figures in an Appendix | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We developed a state-space age-structured catch-at-length (ACL) assessment
model for redfish in NAFO Divisions 3LN. The model was developed to address
limitations in the surplus production model that was previously used to assess
this stock. The ACL model included temporal variations in recruitment, growth,
and morta... | [
{
"created": "Fri, 5 Jul 2024 18:15:35 GMT",
"version": "v1"
}
] | 2024-07-09 | [
[
"Cadigan",
"Noel G.",
""
],
[
"Perreault",
"Andrea M.",
""
],
[
"Nguyen",
"Hoang",
""
],
[
"Chen",
"Jiaying",
""
],
[
"Beita-Jimenez",
"Andres",
""
],
[
"Fuller",
"Natalie",
""
],
[
"Ransier",
"Krista",
""
... | We developed a state-space age-structured catch-at-length (ACL) assessment model for redfish in NAFO Divisions 3LN. The model was developed to address limitations in the surplus production model that was previously used to assess this stock. The ACL model included temporal variations in recruitment, growth, and mortali... |
2005.02251 | Vladislav Goncharenko | V. Goncharenko, R. Grigoryan, A. Samokhina | Raccoons vs Demons: multiclass labeled P300 dataset | null | null | null | null | q-bio.NC cs.HC cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We publish dataset of visual P300 BCI performed in Virtual Reality (VR) game
Raccoons versus Demons (RvD). Data contains reach labels incorporating
information about stimulus chosen enabling us to estimate model's confidence at
each stimulus prediction stage. Data and experiments code are available at
https://gitlab.... | [
{
"created": "Wed, 22 Apr 2020 20:10:31 GMT",
"version": "v1"
},
{
"created": "Mon, 11 May 2020 15:47:38 GMT",
"version": "v2"
}
] | 2020-05-12 | [
[
"Goncharenko",
"V.",
""
],
[
"Grigoryan",
"R.",
""
],
[
"Samokhina",
"A.",
""
]
] | We publish dataset of visual P300 BCI performed in Virtual Reality (VR) game Raccoons versus Demons (RvD). Data contains reach labels incorporating information about stimulus chosen enabling us to estimate model's confidence at each stimulus prediction stage. Data and experiments code are available at https://gitlab.co... |
2211.09240 | Rados{\l}aw Kycia | Agata Dziwulska-Hunek, Agnieszka Niemczynowicz, Rados{\l}aw A. Kycia,
Arkadiusz Matwijczuk, Krzysztof Kornarzy\'nski, Joanna Stadnik, Mariusz
Szymanek | Stimulation of soy seeds using environmentally friendly magnetic and
electric fields | null | null | null | null | q-bio.QM cs.LG stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The study analyzes the impact of constant and alternating magnetic fields and
alternating electric fields on various growth parameters of soy plants: the
germination energy and capacity, plants emergence and number, the Yield(II) of
the fresh mass of seedlings, protein content, and photosynthetic parameters.
Four cul... | [
{
"created": "Wed, 16 Nov 2022 22:05:58 GMT",
"version": "v1"
}
] | 2022-11-18 | [
[
"Dziwulska-Hunek",
"Agata",
""
],
[
"Niemczynowicz",
"Agnieszka",
""
],
[
"Kycia",
"Radosław A.",
""
],
[
"Matwijczuk",
"Arkadiusz",
""
],
[
"Kornarzyński",
"Krzysztof",
""
],
[
"Stadnik",
"Joanna",
""
],
[
"Szyman... | The study analyzes the impact of constant and alternating magnetic fields and alternating electric fields on various growth parameters of soy plants: the germination energy and capacity, plants emergence and number, the Yield(II) of the fresh mass of seedlings, protein content, and photosynthetic parameters. Four culti... |
2306.09855 | Gianmarco Tiddia | Bruno Golosio, Jose Villamar, Gianmarco Tiddia, Elena Pastorelli,
Jonas Stapmanns, Viviana Fanti, Pier Stanislao Paolucci, Abigail Morrison and
Johanna Senk | Runtime Construction of Large-Scale Spiking Neuronal Network Models on
GPU Devices | 29 pages, 9 figures | Appl. Sci. 2023, 13(17), 9598 | 10.3390/app13179598 | null | q-bio.NC cs.NE | http://creativecommons.org/licenses/by/4.0/ | Simulation speed matters for neuroscientific research: this includes not only
how quickly the simulated model time of a large-scale spiking neuronal network
progresses, but also how long it takes to instantiate the network model in
computer memory. On the hardware side, acceleration via highly parallel GPUs is
being ... | [
{
"created": "Fri, 16 Jun 2023 14:08:27 GMT",
"version": "v1"
}
] | 2023-09-01 | [
[
"Golosio",
"Bruno",
""
],
[
"Villamar",
"Jose",
""
],
[
"Tiddia",
"Gianmarco",
""
],
[
"Pastorelli",
"Elena",
""
],
[
"Stapmanns",
"Jonas",
""
],
[
"Fanti",
"Viviana",
""
],
[
"Paolucci",
"Pier Stanislao",
... | Simulation speed matters for neuroscientific research: this includes not only how quickly the simulated model time of a large-scale spiking neuronal network progresses, but also how long it takes to instantiate the network model in computer memory. On the hardware side, acceleration via highly parallel GPUs is being in... |
2303.10819 | Ivan Junier | Ivan Junier and Elham Ghobadpour and Olivier Espeli and Ralf Everaers | DNA supercoiling in bacteria: state of play and challenges from a
viewpoint of physics based modeling | 11 figures | Front. Microbiol. 14:1192831 (2023) | 10.3389/fmicb.2023.1192831 | null | q-bio.BM physics.bio-ph q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | DNA supercoiling is central to many fundamental processes of living
organisms. Its average level along the chromosome and over time reflects the
dynamic equilibrium of opposite activities of topoisomerases, which are
required to relax mechanical stresses that are inevitably produced during DNA
replication and gene tr... | [
{
"created": "Mon, 20 Mar 2023 01:25:33 GMT",
"version": "v1"
},
{
"created": "Sun, 3 Sep 2023 15:47:14 GMT",
"version": "v2"
},
{
"created": "Wed, 4 Oct 2023 10:06:35 GMT",
"version": "v3"
},
{
"created": "Fri, 6 Oct 2023 12:53:13 GMT",
"version": "v4"
}
] | 2023-10-09 | [
[
"Junier",
"Ivan",
""
],
[
"Ghobadpour",
"Elham",
""
],
[
"Espeli",
"Olivier",
""
],
[
"Everaers",
"Ralf",
""
]
] | DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax mechanical stresses that are inevitably produced during DNA replication and gene tran... |
2105.04305 | Jan Krumsiek | Kelsey Chetnik, Elisa Benedetti, Daniel P. Gomari, Annalise
Schweickart, Richa Batra, Mustafa Buyukozkan, Zeyu Wang, Matthias Arnold,
Jonas Zierer, Karsten Suhre, Jan Krumsiek | maplet: An extensible R toolbox for modular and reproducible omics
pipelines | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | This paper presents maplet, an open-source R package for the creation of
highly customizable, fully reproducible statistical pipelines for omics data
analysis, with a special focus on metabolomics-based methods. It builds on the
SummarizedExperiment data structure to create a centralized pipeline framework
for storin... | [
{
"created": "Thu, 6 May 2021 18:54:13 GMT",
"version": "v1"
}
] | 2021-05-11 | [
[
"Chetnik",
"Kelsey",
""
],
[
"Benedetti",
"Elisa",
""
],
[
"Gomari",
"Daniel P.",
""
],
[
"Schweickart",
"Annalise",
""
],
[
"Batra",
"Richa",
""
],
[
"Buyukozkan",
"Mustafa",
""
],
[
"Wang",
"Zeyu",
""
]... | This paper presents maplet, an open-source R package for the creation of highly customizable, fully reproducible statistical pipelines for omics data analysis, with a special focus on metabolomics-based methods. It builds on the SummarizedExperiment data structure to create a centralized pipeline framework for storing ... |
1307.0737 | Daniel B. Weissman | D. B. Weissman and O. Hallatschek | The rate of adaptation in large sexual populations with linear
chromosomes | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In large populations, multiple beneficial mutations may be simultaneously
spreading. In asexual populations, these mutations must either arise on the
same background or compete against each other. In sexual populations,
recombination can bring together beneficial alleles from different backgrounds,
but tightly linked... | [
{
"created": "Tue, 2 Jul 2013 15:57:59 GMT",
"version": "v1"
},
{
"created": "Sat, 14 Dec 2013 04:52:05 GMT",
"version": "v2"
},
{
"created": "Wed, 18 Dec 2013 05:57:09 GMT",
"version": "v3"
}
] | 2013-12-19 | [
[
"Weissman",
"D. B.",
""
],
[
"Hallatschek",
"O.",
""
]
] | In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked a... |
1302.2724 | Michael Assaf | Michael Assaf, Elijah Roberts, Zaida Luthey-Schulten and Nigel
Goldenfeld | Extrinsic noise driven phenotype switching in a self-regulating gene | 5 pages, 4 figures | null | 10.1103/PhysRevLett.111.058102 | null | q-bio.MN cond-mat.stat-mech q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Due to inherent noise in intracellular networks cellular decisions can be
random, so genetically identical cells can display different phenotypic
behavior even in identical environments. Most previous work in understanding
the decision-making process has focused on the role of intrinsic noise in these
systems. Yet, e... | [
{
"created": "Tue, 12 Feb 2013 07:41:10 GMT",
"version": "v1"
}
] | 2015-06-15 | [
[
"Assaf",
"Michael",
""
],
[
"Roberts",
"Elijah",
""
],
[
"Luthey-Schulten",
"Zaida",
""
],
[
"Goldenfeld",
"Nigel",
""
]
] | Due to inherent noise in intracellular networks cellular decisions can be random, so genetically identical cells can display different phenotypic behavior even in identical environments. Most previous work in understanding the decision-making process has focused on the role of intrinsic noise in these systems. Yet, esp... |
1107.0313 | Michael Bachmann | Tristan Bereau, Michael Bachmann, and Markus Deserno | Interplay between Secondary and Tertiary Structure Formation in Protein
Folding Cooperativity | 3 pages, 3 figures | J. Am. Chem. Soc. 132, 13129-13131 (2010) | 10.1016/j.bpj.2010.12.1361 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein folding cooperativity is defined by the nature of the finite-size
thermodynamic transition exhibited upon folding: two-state transitions show a
free energy barrier between the folded and unfolded ensembles, while downhill
folding is barrierless. A microcanonical analysis, where the energy is the
natural varia... | [
{
"created": "Fri, 1 Jul 2011 19:59:45 GMT",
"version": "v1"
}
] | 2017-08-23 | [
[
"Bereau",
"Tristan",
""
],
[
"Bachmann",
"Michael",
""
],
[
"Deserno",
"Markus",
""
]
] | Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is barrierless. A microcanonical analysis, where the energy is the natural variabl... |
2201.09837 | Gustavo Mockaitis | Mahmood Mahmoodi-Eshkaftaki, Gustavo Mockaitis, Mohammad Rafie Rafiee | Dynamic optimization of volatile fatty acids to enrich biohydrogen
production using a deep learning neural network | null | null | null | null | q-bio.QM q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | A new strategy was developed to investigate the effect of volatile fatty
acids (VFAs) on the efficiency of biogas production with a focus on improving
bio-H$_2$. The inoculum used, anaerobic granular sludge obtained from a UASB
reactor treating poultry slaughterhouse wastewater, was pretreated with five
different pre... | [
{
"created": "Mon, 24 Jan 2022 17:59:06 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Feb 2022 18:01:46 GMT",
"version": "v2"
}
] | 2022-02-09 | [
[
"Mahmoodi-Eshkaftaki",
"Mahmood",
""
],
[
"Mockaitis",
"Gustavo",
""
],
[
"Rafiee",
"Mohammad Rafie",
""
]
] | A new strategy was developed to investigate the effect of volatile fatty acids (VFAs) on the efficiency of biogas production with a focus on improving bio-H$_2$. The inoculum used, anaerobic granular sludge obtained from a UASB reactor treating poultry slaughterhouse wastewater, was pretreated with five different pretr... |
1603.03694 | Philippe Marcq | V. Nier, S. Jain, C. T. Lim, S. Ishihara, B. Ladoux and P. Marcq | Inference of internal stress in a cell monolayer | 38 pages, 14 figures | null | 10.1016/j.bpj.2016.03.002 | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We combine traction force data with Bayesian inversion to obtain an absolute
estimate of the internal stress field of a cell monolayer. The method, Bayesian
inversion stress microscopy (BISM), is validated using numerical simulations
performed in a wide range of conditions. It is robust to changes in each
ingredient ... | [
{
"created": "Fri, 11 Mar 2016 17:09:44 GMT",
"version": "v1"
}
] | 2016-05-04 | [
[
"Nier",
"V.",
""
],
[
"Jain",
"S.",
""
],
[
"Lim",
"C. T.",
""
],
[
"Ishihara",
"S.",
""
],
[
"Ladoux",
"B.",
""
],
[
"Marcq",
"P.",
""
]
] | We combine traction force data with Bayesian inversion to obtain an absolute estimate of the internal stress field of a cell monolayer. The method, Bayesian inversion stress microscopy (BISM), is validated using numerical simulations performed in a wide range of conditions. It is robust to changes in each ingredient of... |
2207.12827 | Thierry Mora | Andrea Mazzolini, Thierry Mora, Aleksandra M Walczak | Inspecting the interaction between HIV and the immune system through
genetic turnover | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chronic infections of the human immunodeficiency virus (HIV) create a very
complex co-evolutionary process, where the virus tries to escape the
continuously adapting host immune system. Quantitative details of this process
are largely unknown and could help in disease treatment and vaccine
development. Here we study ... | [
{
"created": "Tue, 26 Jul 2022 11:47:26 GMT",
"version": "v1"
}
] | 2022-07-27 | [
[
"Mazzolini",
"Andrea",
""
],
[
"Mora",
"Thierry",
""
],
[
"Walczak",
"Aleksandra M",
""
]
] | Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely unknown and could help in disease treatment and vaccine development. Here we study a ... |
1712.00009 | Paulo Laerte Natti | T.M. Saita, P.L. Natti, E.R. Cirilo, N.M.L. Romeiro, M.A.C. Candezano,
R.B Acu\~na and L.C.G. Moreno | Numerical Simulation of Fecal Coliform Dynamics in Luruaco Lake,
Colombia | 13 pages, in Portuguese, 4 figures | TEMA, v.18, n.3, p.435-447, 2017 | 10.5540/tema.2017.018.03.0435 | null | q-bio.QM cs.CE math.NA q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Luruaco Lake located in the Department of Atl\'antico, Colombia, is
damaged by the discharge of untreated sewage, bringing risks to the health of
all who use its waters. The present study aims to perform the numerical
simulation of the concentration dynamics of fecal coliforms in the lake. The
simulation of the h... | [
{
"created": "Thu, 30 Nov 2017 13:19:47 GMT",
"version": "v1"
}
] | 2017-12-05 | [
[
"Saita",
"T. M.",
""
],
[
"Natti",
"P. L.",
""
],
[
"Cirilo",
"E. R.",
""
],
[
"Romeiro",
"N. M. L.",
""
],
[
"Candezano",
"M. A. C.",
""
],
[
"Acuña",
"R. B",
""
],
[
"Moreno",
"L. C. G.",
""
]
] | The Luruaco Lake located in the Department of Atl\'antico, Colombia, is damaged by the discharge of untreated sewage, bringing risks to the health of all who use its waters. The present study aims to perform the numerical simulation of the concentration dynamics of fecal coliforms in the lake. The simulation of the hyd... |
1108.1484 | Song Xu | Song Xu, Shuyun Jiao, Pengyao Jiang, Bo Yuan, Ping Ao | Non-fixation in infinite potential | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Under the effects of strong genetic drift, it is highly probable to observe
gene fixation or loss in a population, shown by divergent probability density
functions, or infinite adaptive peaks on a landscape. It is then interesting to
ask what such infinite peaks imply, with or without combining other biological
facto... | [
{
"created": "Sat, 6 Aug 2011 14:10:41 GMT",
"version": "v1"
},
{
"created": "Tue, 1 Nov 2011 15:26:21 GMT",
"version": "v2"
},
{
"created": "Sat, 5 Nov 2011 01:48:54 GMT",
"version": "v3"
},
{
"created": "Mon, 9 Apr 2012 14:59:57 GMT",
"version": "v4"
},
{
"creat... | 2012-10-29 | [
[
"Xu",
"Song",
""
],
[
"Jiao",
"Shuyun",
""
],
[
"Jiang",
"Pengyao",
""
],
[
"Yuan",
"Bo",
""
],
[
"Ao",
"Ping",
""
]
] | Under the effects of strong genetic drift, it is highly probable to observe gene fixation or loss in a population, shown by divergent probability density functions, or infinite adaptive peaks on a landscape. It is then interesting to ask what such infinite peaks imply, with or without combining other biological factors... |
1210.3970 | Gianluca Martelloni | Gianluca Martelloni, Franco Bagnoli and Stefano Marsili Libelli | A dynamical population modeling of invasive species with reference to
the crayfish Procambarus Clarkii | null | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we present a discrete dynamical population modeling of invasive
species, with reference to the swamp crayfish Procambarus clarkii. Since this
species can cause environmental damage of various kinds, it is necessary to
evaluate its expected in not yet infested areas. A structured discrete model is
built,... | [
{
"created": "Mon, 15 Oct 2012 10:33:24 GMT",
"version": "v1"
}
] | 2012-10-16 | [
[
"Martelloni",
"Gianluca",
""
],
[
"Bagnoli",
"Franco",
""
],
[
"Libelli",
"Stefano Marsili",
""
]
] | In this paper we present a discrete dynamical population modeling of invasive species, with reference to the swamp crayfish Procambarus clarkii. Since this species can cause environmental damage of various kinds, it is necessary to evaluate its expected in not yet infested areas. A structured discrete model is built, t... |
2303.11056 | Michael Gilson | Chapin E. Cavender, David A. Case, Julian C.-H. Chen, Lillian T.
Chong, Daniel A. Keedy, Kresten Lindorff-Larsen, David L. Mobley, O. H.
Samuli Ollila, Chris Oostenbrink, Paul Robustelli, Vincent A. Voelz, Michael
E. Wall, David C. Wych, Michael K. Gilson | Structure-Based Experimental Datasets for Benchmarking of Protein
Simulation Force Fields | null | null | null | null | q-bio.BM physics.bio-ph physics.comp-ph | http://creativecommons.org/licenses/by/4.0/ | This review article provides an overview of structurally oriented,
experimental datasets that can be used to benchmark protein force fields,
focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and
room temperature (RT) protein crystallography. We discuss why these observables
are useful for as... | [
{
"created": "Thu, 2 Mar 2023 14:34:56 GMT",
"version": "v1"
}
] | 2023-03-21 | [
[
"Cavender",
"Chapin E.",
""
],
[
"Case",
"David A.",
""
],
[
"Chen",
"Julian C. -H.",
""
],
[
"Chong",
"Lillian T.",
""
],
[
"Keedy",
"Daniel A.",
""
],
[
"Lindorff-Larsen",
"Kresten",
""
],
[
"Mobley",
"David ... | This review article provides an overview of structurally oriented, experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature (RT) protein crystallography. We discuss why these observables are useful for asse... |
2003.06194 | Larissa Terumi Arashiro | Larissa Terumi Arashiro, Neus Montero, Ivet Ferrer, Francisco Gabriel
Acien, Cintia Gomez, Marianna Garfi | Life Cycle Assessment of high rate algal ponds for wastewater treatment
and resource recovery | null | Science of the total environment 622-623, 1118-1130 (2018) | 10.1016/j.scitotenv.2017.12.051 | null | q-bio.QM q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The aim of this study was to assess the potential environmental impacts
associated with high rate algal ponds (HRAP) systems for wastewater treatment
and resource recovery in small communities. To this aim, a Life Cycle
Assessment (LCA) and an economic assessment were carried out evaluating two
alternatives: i) a HRA... | [
{
"created": "Fri, 13 Mar 2020 10:46:43 GMT",
"version": "v1"
}
] | 2020-03-16 | [
[
"Arashiro",
"Larissa Terumi",
""
],
[
"Montero",
"Neus",
""
],
[
"Ferrer",
"Ivet",
""
],
[
"Acien",
"Francisco Gabriel",
""
],
[
"Gomez",
"Cintia",
""
],
[
"Garfi",
"Marianna",
""
]
] | The aim of this study was to assess the potential environmental impacts associated with high rate algal ponds (HRAP) systems for wastewater treatment and resource recovery in small communities. To this aim, a Life Cycle Assessment (LCA) and an economic assessment were carried out evaluating two alternatives: i) a HRAPs... |
2310.12901 | Reka Albert | Jordan C. Rozum, Colin Campbell, Eli Newby, Fatemeh Sadat Fatemi
Nasrollahi, Reka Albert | Boolean Networks as Predictive Models of Emergent Biological Behaviors | Review, to appear in the Cambridge Elements series | null | null | null | q-bio.MN nlin.CG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Interacting biological systems at all organizational levels display emergent
behavior. Modeling these systems is made challenging by the number and variety
of biological components and interactions (from molecules in gene regulatory
networks to species in ecological networks) and the often-incomplete state of
system ... | [
{
"created": "Thu, 19 Oct 2023 16:53:08 GMT",
"version": "v1"
}
] | 2023-10-20 | [
[
"Rozum",
"Jordan C.",
""
],
[
"Campbell",
"Colin",
""
],
[
"Newby",
"Eli",
""
],
[
"Nasrollahi",
"Fatemeh Sadat Fatemi",
""
],
[
"Albert",
"Reka",
""
]
] | Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory networks to species in ecological networks) and the often-incomplete state of system kn... |
0812.1310 | Vladimir Privman | Vladimir Privman, Mary A. Arugula, Jan Halamek, Marcos Pita, Evgeny
Katz | Network Analysis of Biochemical Logic for Noise Reduction and Stability:
A System of Three Coupled Enzymatic AND Gates | 31 pages, PDF | J. Phys. Chem. B 113, 5301--5310 (2009) | 10.1021/jp810743w | null | q-bio.MN cond-mat.soft q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop an approach aimed at optimizing the parameters of a network of
biochemical logic gates for reduction of the "analog" noise buildup.
Experiments for three coupled enzymatic AND gates are reported, illustrating
our procedure. Specifically, starch - one of the controlled network inputs - is
converted to malto... | [
{
"created": "Sat, 6 Dec 2008 20:05:08 GMT",
"version": "v1"
}
] | 2010-10-12 | [
[
"Privman",
"Vladimir",
""
],
[
"Arugula",
"Mary A.",
""
],
[
"Halamek",
"Jan",
""
],
[
"Pita",
"Marcos",
""
],
[
"Katz",
"Evgeny",
""
]
] | We develop an approach aimed at optimizing the parameters of a network of biochemical logic gates for reduction of the "analog" noise buildup. Experiments for three coupled enzymatic AND gates are reported, illustrating our procedure. Specifically, starch - one of the controlled network inputs - is converted to maltose... |
2111.11880 | Patrick Sobetzko | Marc Teufel, Carlo A. Klein, Maurice Mager, Patrick Sobetzko | CRISPR SWAPnDROP -- A multifunctional system for genome editing and
large-scale interspecies gene transfer | null | null | 10.1038/s41467-022-30843-1 | null | q-bio.GN | http://creativecommons.org/publicdomain/zero/1.0/ | The need for diverse chromosomal modifications in biotechnology, synthetic
biology and basic research requires the development of new technologies. With
CRISPR SWAPnDROP, we extend the limits of genome editing to large-scale in-vivo
DNA transfer between bacterial species. Its modular platform approach
facilitates spe... | [
{
"created": "Tue, 23 Nov 2021 13:47:07 GMT",
"version": "v1"
}
] | 2022-10-12 | [
[
"Teufel",
"Marc",
""
],
[
"Klein",
"Carlo A.",
""
],
[
"Mager",
"Maurice",
""
],
[
"Sobetzko",
"Patrick",
""
]
] | The need for diverse chromosomal modifications in biotechnology, synthetic biology and basic research requires the development of new technologies. With CRISPR SWAPnDROP, we extend the limits of genome editing to large-scale in-vivo DNA transfer between bacterial species. Its modular platform approach facilitates speci... |
q-bio/0406025 | Chi Zhang | Song Liu, Chi Zhang, Yaoqi Zhou | Unbound Protein-Protein Docking Selections by the DFIRE-based
Statistical Pair Potential | null | null | null | null | q-bio.BM q-bio.QM | null | A newly developed statistical pair potential based on Distance-scaled Finite
Ideal-gas REference (DFIRE) state is applied to unbound protein-protein docking
structure selections. The performance of the DFIRE energy function is compared
to those of the well-established ZDOCK energy scores and RosettaDock energy
functi... | [
{
"created": "Sat, 12 Jun 2004 21:00:35 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Oct 2004 17:38:18 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Liu",
"Song",
""
],
[
"Zhang",
"Chi",
""
],
[
"Zhou",
"Yaoqi",
""
]
] | A newly developed statistical pair potential based on Distance-scaled Finite Ideal-gas REference (DFIRE) state is applied to unbound protein-protein docking structure selections. The performance of the DFIRE energy function is compared to those of the well-established ZDOCK energy scores and RosettaDock energy function... |
2201.05440 | Hsin-Po Wang | Hsin-Po Wang and Ryan Gabrys and Alexander Vardy | Tropical Group Testing | 25 pages, 20 figures. v2 fixes typos | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Polymerase chain reaction (PCR) testing is the gold standard for diagnosing
COVID-19. PCR amplifies the virus DNA 40 times to produce measurements of viral
loads that span seven orders of magnitude. Unfortunately, the outputs of these
tests are imprecise and therefore quantitative group testing methods, which
rely on... | [
{
"created": "Wed, 12 Jan 2022 21:45:45 GMT",
"version": "v1"
},
{
"created": "Mon, 17 Jan 2022 20:33:34 GMT",
"version": "v2"
}
] | 2022-01-19 | [
[
"Wang",
"Hsin-Po",
""
],
[
"Gabrys",
"Ryan",
""
],
[
"Vardy",
"Alexander",
""
]
] | Polymerase chain reaction (PCR) testing is the gold standard for diagnosing COVID-19. PCR amplifies the virus DNA 40 times to produce measurements of viral loads that span seven orders of magnitude. Unfortunately, the outputs of these tests are imprecise and therefore quantitative group testing methods, which rely on p... |
2003.04096 | Francesca Romana Bertani | F. R. Bertani, L. Businaro, L. Gambacorta, A.Mencattin, D. Brenda, D.
Di Giuseppe, A. De Ninno, M. Solfrizzo, E. Martinelli, A. Gerardino | Optical detection of Aflatoxins B in grained almonds using fluorescence
spectroscopy and machine learning algorithms | null | null | null | null | q-bio.QM physics.data-an | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Aflatoxins are fungal metabolites extensively produced by many different
fungal species that may contaminate a wide range of agricultural food products.
They have been studied extensively because of being associated with various
chronic and acute diseases especially immunosuppression and cancer and their
presence in ... | [
{
"created": "Thu, 20 Feb 2020 14:53:46 GMT",
"version": "v1"
}
] | 2020-03-10 | [
[
"Bertani",
"F. R.",
""
],
[
"Businaro",
"L.",
""
],
[
"Gambacorta",
"L.",
""
],
[
"Mencattin",
"A.",
""
],
[
"Brenda",
"D.",
""
],
[
"Di Giuseppe",
"D.",
""
],
[
"De Ninno",
"A.",
""
],
[
"Solfrizzo... | Aflatoxins are fungal metabolites extensively produced by many different fungal species that may contaminate a wide range of agricultural food products. They have been studied extensively because of being associated with various chronic and acute diseases especially immunosuppression and cancer and their presence in fo... |
q-bio/0610030 | Marta Casanellas | Marta Casanellas, Jesus Fernandez-Sanchez | Performance of a new invariants method on homogeneous and
non-homogeneous quartet trees | 12 pages and 4 pages of Supplementary Material included, 8 figures.
to appear in Molecular Biology and Evolution | null | null | null | q-bio.PE | null | An attempt to use phylogenetic invariants for tree reconstruction was made at
the end of the 80s and the beginning of the 90s by several authors (the initial
idea due to Lake and Cavender and Felsenstein in 1987. However, the efficiency
of methods based on invariants is still in doubt, probably because these
methods ... | [
{
"created": "Tue, 17 Oct 2006 14:34:01 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Casanellas",
"Marta",
""
],
[
"Fernandez-Sanchez",
"Jesus",
""
]
] | An attempt to use phylogenetic invariants for tree reconstruction was made at the end of the 80s and the beginning of the 90s by several authors (the initial idea due to Lake and Cavender and Felsenstein in 1987. However, the efficiency of methods based on invariants is still in doubt, probably because these methods on... |
1103.1402 | Aleksandar Stojmirovi\'c | Aleksandar Stojmirovi\'c and Yi-Kuo Yu | ppiTrim: Constructing non-redundant and up-to-date interactomes | 21 pages, 2 figures, 6 tables, 8 supplementary tables. Minor
corrections of typos and similar | Database (Oxford). 2011:bar036 | 10.1093/database/bar036 | null | q-bio.MN | http://creativecommons.org/licenses/publicdomain/ | Robust advances in interactome analysis demand comprehensive, non-redundant
and consistently annotated datasets. By non-redundant, we mean that the
accounting of evidence for every interaction should be faithful: each
independent experimental support is counted exactly once, no more, no less.
While many interactions ... | [
{
"created": "Mon, 7 Mar 2011 22:47:55 GMT",
"version": "v1"
},
{
"created": "Thu, 16 Jun 2011 02:12:41 GMT",
"version": "v2"
},
{
"created": "Fri, 8 Jul 2011 01:53:36 GMT",
"version": "v3"
}
] | 2011-10-25 | [
[
"Stojmirović",
"Aleksandar",
""
],
[
"Yu",
"Yi-Kuo",
""
]
] | Robust advances in interactome analysis demand comprehensive, non-redundant and consistently annotated datasets. By non-redundant, we mean that the accounting of evidence for every interaction should be faithful: each independent experimental support is counted exactly once, no more, no less. While many interactions ar... |
2202.05145 | Xuan Lin | Xiaoqin Pan, Xuan Lin, Dongsheng Cao, Xiangxiang Zeng, Philip S. Yu,
Lifang He, Ruth Nussinov, Feixiong Cheng | Deep learning for drug repurposing: methods, databases, and applications | Accepted by WIREs Computational Molecular Science | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Drug development is time-consuming and expensive. Repurposing existing drugs
for new therapies is an attractive solution that accelerates drug development
at reduced experimental costs, specifically for Coronavirus Disease 2019
(COVID-19), an infectious disease caused by severe acute respiratory syndrome
coronavirus ... | [
{
"created": "Tue, 8 Feb 2022 09:42:08 GMT",
"version": "v1"
}
] | 2022-02-11 | [
[
"Pan",
"Xiaoqin",
""
],
[
"Lin",
"Xuan",
""
],
[
"Cao",
"Dongsheng",
""
],
[
"Zeng",
"Xiangxiang",
""
],
[
"Yu",
"Philip S.",
""
],
[
"He",
"Lifang",
""
],
[
"Nussinov",
"Ruth",
""
],
[
"Cheng",
... | Drug development is time-consuming and expensive. Repurposing existing drugs for new therapies is an attractive solution that accelerates drug development at reduced experimental costs, specifically for Coronavirus Disease 2019 (COVID-19), an infectious disease caused by severe acute respiratory syndrome coronavirus 2 ... |
2106.05186 | Madhavun Candadai | Madhavun Candadai | Information theoretic analysis of computational models as a tool to
understand the neural basis of behaviors | null | null | null | null | q-bio.NC cs.IT cs.NE math.IT | http://creativecommons.org/licenses/by/4.0/ | One of the greatest research challenges of this century is to understand the
neural basis for how behavior emerges in brain-body-environment systems. To
this end, research has flourished along several directions but have
predominantly focused on the brain. While there is in an increasing acceptance
and focus on inclu... | [
{
"created": "Wed, 2 Jun 2021 02:08:18 GMT",
"version": "v1"
}
] | 2021-06-10 | [
[
"Candadai",
"Madhavun",
""
]
] | One of the greatest research challenges of this century is to understand the neural basis for how behavior emerges in brain-body-environment systems. To this end, research has flourished along several directions but have predominantly focused on the brain. While there is in an increasing acceptance and focus on includi... |
2101.08841 | Robert Miller | Florian Rupprecht, S\"oren Enge, Kornelius Schmidt, Wei Gao, Clemens
Kirschbaum, Robert Miller | Automating LC-MS/MS mass chromatogram quantification. Wavelet transform
based peak detection and automated estimation of peak boundaries and
signal-to-noise ratio using signal processing methods | 20 pages, 8 figures | null | null | null | q-bio.QM stat.AP | http://creativecommons.org/licenses/by-sa/4.0/ | While there are many different methods for peak detection, no automatic
methods for marking peak boundaries to calculate area under the curve (AUC) and
signal-to-noise ratio (SNR) estimation exist. An algorithm for the automation
of liquid chromatography tandem mass spectrometry (LC-MS/MS) mass chromatogram
quantific... | [
{
"created": "Thu, 21 Jan 2021 20:25:34 GMT",
"version": "v1"
}
] | 2021-01-25 | [
[
"Rupprecht",
"Florian",
""
],
[
"Enge",
"Sören",
""
],
[
"Schmidt",
"Kornelius",
""
],
[
"Gao",
"Wei",
""
],
[
"Kirschbaum",
"Clemens",
""
],
[
"Miller",
"Robert",
""
]
] | While there are many different methods for peak detection, no automatic methods for marking peak boundaries to calculate area under the curve (AUC) and signal-to-noise ratio (SNR) estimation exist. An algorithm for the automation of liquid chromatography tandem mass spectrometry (LC-MS/MS) mass chromatogram quantificat... |
1604.00832 | Henry Tuckwell | Henry C. Tuckwell | Density independent population growth with random survival | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A simplified model for the growth of a population is studied in which random
effects arise because reproducing individuals have a certain probability of
surviving until the next breeding season and hence contributing to the next
generation. The resulting Markov chain is that of a branching process with a
known genera... | [
{
"created": "Mon, 4 Apr 2016 12:22:30 GMT",
"version": "v1"
}
] | 2016-04-05 | [
[
"Tuckwell",
"Henry C.",
""
]
] | A simplified model for the growth of a population is studied in which random effects arise because reproducing individuals have a certain probability of surviving until the next breeding season and hence contributing to the next generation. The resulting Markov chain is that of a branching process with a known generati... |
2208.06073 | Xiangzhe Kong | Xiangzhe Kong, Wenbing Huang, Yang Liu | Conditional Antibody Design as 3D Equivariant Graph Translation | Accepted to ICLR 2023 as oral presentation. Outstanding paper
honorable mentions | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Antibody design is valuable for therapeutic usage and biological research.
Existing deep-learning-based methods encounter several key issues: 1)
incomplete context for Complementarity-Determining Regions (CDRs) generation;
2) incapability of capturing the entire 3D geometry of the input structure; 3)
inefficient pred... | [
{
"created": "Fri, 12 Aug 2022 01:00:59 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Sep 2022 12:53:10 GMT",
"version": "v2"
},
{
"created": "Mon, 5 Dec 2022 13:17:13 GMT",
"version": "v3"
},
{
"created": "Fri, 3 Feb 2023 03:10:59 GMT",
"version": "v4"
},
{
"cre... | 2023-03-31 | [
[
"Kong",
"Xiangzhe",
""
],
[
"Huang",
"Wenbing",
""
],
[
"Liu",
"Yang",
""
]
] | Antibody design is valuable for therapeutic usage and biological research. Existing deep-learning-based methods encounter several key issues: 1) incomplete context for Complementarity-Determining Regions (CDRs) generation; 2) incapability of capturing the entire 3D geometry of the input structure; 3) inefficient predic... |
2104.03140 | Fabrizio Pittorino | Marco Stucchi, Fabrizio Pittorino, Matteo di Volo, Alessandro Vezzani,
Raffaella Burioni | Order symmetry breaking and broad distribution of events in spiking
neural networks with continuous membrane potential | 10 pages, 9 figures; to appear in Chaos, Solitons & Fractals | null | 10.1016/j.chaos.2021.110946 | null | q-bio.NC cond-mat.dis-nn cond-mat.stat-mech nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce an exactly integrable version of the well-known leaky
integrate-and-fire (LIF) model, with continuous membrane potential at the
spiking event, the c-LIF. We investigate the dynamical regimes of a fully
connected network of excitatory c-LIF neurons in the presence of short-term
synaptic plasticity. By var... | [
{
"created": "Wed, 7 Apr 2021 14:14:12 GMT",
"version": "v1"
}
] | 2021-06-02 | [
[
"Stucchi",
"Marco",
""
],
[
"Pittorino",
"Fabrizio",
""
],
[
"di Volo",
"Matteo",
""
],
[
"Vezzani",
"Alessandro",
""
],
[
"Burioni",
"Raffaella",
""
]
] | We introduce an exactly integrable version of the well-known leaky integrate-and-fire (LIF) model, with continuous membrane potential at the spiking event, the c-LIF. We investigate the dynamical regimes of a fully connected network of excitatory c-LIF neurons in the presence of short-term synaptic plasticity. By varyi... |
2307.01491 | Ahmed BaHammam | Abeer Alasmari, Abdulrahman Al-Khalifah, Ahmed BaHammam, Hesham
Alodah, Ahmad Almnaizel, Noura Alshiban, Maha Alhussain | Ramadan Fasting Model Exerts Hepatoprotective, Anti-obesity, and
Anti-Hyperlipidemic Effects in an Experimentally-induced Nonalcoholic Fatty
Liver in Rats | 33 pages, 4 figures, 1 Table, pre-proof | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Background: The epidemic of nonalcoholic fatty liver disease (NAFLD) and its
metabolic effects present a serious public health concern. We hypothesized that
the Ramadan fasting model (RFM), which involves fasting from dawn to dusk for a
month, could provide potential therapeutic benefits and mitigate NAFLD.
According... | [
{
"created": "Tue, 4 Jul 2023 05:51:07 GMT",
"version": "v1"
}
] | 2023-07-06 | [
[
"Alasmari",
"Abeer",
""
],
[
"Al-Khalifah",
"Abdulrahman",
""
],
[
"BaHammam",
"Ahmed",
""
],
[
"Alodah",
"Hesham",
""
],
[
"Almnaizel",
"Ahmad",
""
],
[
"Alshiban",
"Noura",
""
],
[
"Alhussain",
"Maha",
""... | Background: The epidemic of nonalcoholic fatty liver disease (NAFLD) and its metabolic effects present a serious public health concern. We hypothesized that the Ramadan fasting model (RFM), which involves fasting from dawn to dusk for a month, could provide potential therapeutic benefits and mitigate NAFLD. Accordingly... |
1402.2584 | Peter Thomas PhD | David F. Anderson and Bard Ermentrout and Peter J. Thomas | Stochastic Representations of Ion Channel Kinetics and Exact Stochastic
Simulation of Neuronal Dynamics | 39 pages, 6 figures, appendix with XPP and Matlab code | Journal of Computational Neuroscience: Volume 38, Issue 1 (2015),
Page 67-82 | 10.1007/s10827-014-0528-2 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we provide two representations for stochastic ion channel
kinetics, and compare the performance of exact simulation with a commonly used
numerical approximation strategy. The first representation we present is a
random time change representation, popularized by Thomas Kurtz, with the second
being analog... | [
{
"created": "Tue, 11 Feb 2014 18:05:25 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Sep 2014 04:08:23 GMT",
"version": "v2"
},
{
"created": "Tue, 11 Nov 2014 21:37:42 GMT",
"version": "v3"
}
] | 2015-01-20 | [
[
"Anderson",
"David F.",
""
],
[
"Ermentrout",
"Bard",
""
],
[
"Thomas",
"Peter J.",
""
]
] | In this paper we provide two representations for stochastic ion channel kinetics, and compare the performance of exact simulation with a commonly used numerical approximation strategy. The first representation we present is a random time change representation, popularized by Thomas Kurtz, with the second being analogou... |
1707.03489 | Michael Meehan Dr | Michael T. Meehan, Daniel G. Cocks, Johannes M\"uller, Emma S. McBryde | Global stability properties of renewal epidemic models | 11 pages | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the global dynamics of a general Kermack-McKendrick-type
epidemic model formulated in terms of a system of renewal equations.
Specifically, we consider a renewal model for which both the force of infection
and the infected removal rates are arbitrary functions of the infection age,
$\tau$, and use the ... | [
{
"created": "Tue, 11 Jul 2017 23:13:39 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Oct 2018 01:20:21 GMT",
"version": "v2"
}
] | 2018-10-04 | [
[
"Meehan",
"Michael T.",
""
],
[
"Cocks",
"Daniel G.",
""
],
[
"Müller",
"Johannes",
""
],
[
"McBryde",
"Emma S.",
""
]
] | We investigate the global dynamics of a general Kermack-McKendrick-type epidemic model formulated in terms of a system of renewal equations. Specifically, we consider a renewal model for which both the force of infection and the infected removal rates are arbitrary functions of the infection age, $\tau$, and use the di... |
1411.1448 | Kamran Kaveh | Kamran Kaveh, Venkata S. K. Manem, Mohammad Kohandel, Siv
Sivaloganathan | Modeling Age-Dependent Radiation-Induced Second Cancer Risks and
Estimation of Mutation Rate: An Evolutionary Approach | 24 pages, 16 figures, appears in Rad. Env. BioPhys 2014 | null | null | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although the survival rate of cancer patients has significantly increased due
to advances in anti-cancer therapeutics, one of the major side effects of these
therapies, particularly radiotherapy, is the potential manifestation of
radiation-induced secondary malignancies. In this work, a novel evolutionary
stochastic ... | [
{
"created": "Wed, 5 Nov 2014 23:29:15 GMT",
"version": "v1"
}
] | 2014-11-07 | [
[
"Kaveh",
"Kamran",
""
],
[
"Manem",
"Venkata S. K.",
""
],
[
"Kohandel",
"Mohammad",
""
],
[
"Sivaloganathan",
"Siv",
""
]
] | Although the survival rate of cancer patients has significantly increased due to advances in anti-cancer therapeutics, one of the major side effects of these therapies, particularly radiotherapy, is the potential manifestation of radiation-induced secondary malignancies. In this work, a novel evolutionary stochastic mo... |
2312.02203 | Weikang Qiu | Weikang Qiu, Huangrui Chu, Selena Wang, Haolan Zuo, Xiaoxiao Li, Yize
Zhao, Rex Ying | Learning High-Order Relationships of Brain Regions | Accepted at ICML 2024, Camera Ready Version | null | null | null | q-bio.NC cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Discovering reliable and informative relationships among brain regions from
functional magnetic resonance imaging (fMRI) signals is essential in phenotypic
predictions. Most of the current methods fail to accurately characterize those
interactions because they only focus on pairwise connections and overlook the
high-... | [
{
"created": "Sat, 2 Dec 2023 21:39:05 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Feb 2024 22:18:36 GMT",
"version": "v2"
},
{
"created": "Sat, 8 Jun 2024 22:32:45 GMT",
"version": "v3"
}
] | 2024-06-11 | [
[
"Qiu",
"Weikang",
""
],
[
"Chu",
"Huangrui",
""
],
[
"Wang",
"Selena",
""
],
[
"Zuo",
"Haolan",
""
],
[
"Li",
"Xiaoxiao",
""
],
[
"Zhao",
"Yize",
""
],
[
"Ying",
"Rex",
""
]
] | Discovering reliable and informative relationships among brain regions from functional magnetic resonance imaging (fMRI) signals is essential in phenotypic predictions. Most of the current methods fail to accurately characterize those interactions because they only focus on pairwise connections and overlook the high-or... |
2309.06297 | Lorenzo Pavesi | Ilya Auslender and Lorenzo Pavesi | Reservoir Computing Model For Multi-Electrode Electrophysiological Data
Analysis | null | 2023 IEEE Conference on Computational Intelligence in
Bioinformatics and Computational Biology (CIBCB), Eindhoven, Netherlands,
2023 | 10.1109/CIBCB56990.2023.10264895 | null | q-bio.QM cs.ET physics.bio-ph q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In this paper we present a computational model which decodes the
spatio-temporal data from electro-physiological measurements of neuronal
networks and reconstructs the network structure on a macroscopic domain,
representing the connectivity between neuronal units. The model is based on
reservoir computing network (RC... | [
{
"created": "Tue, 12 Sep 2023 15:00:48 GMT",
"version": "v1"
}
] | 2024-03-06 | [
[
"Auslender",
"Ilya",
""
],
[
"Pavesi",
"Lorenzo",
""
]
] | In this paper we present a computational model which decodes the spatio-temporal data from electro-physiological measurements of neuronal networks and reconstructs the network structure on a macroscopic domain, representing the connectivity between neuronal units. The model is based on reservoir computing network (RCN)... |
2206.12231 | Frederic Bastian | Anne Niknejad, Christopher J. Mungall, David Osumi-Sutherland, Marc
Robinson-Rechavi, Frederic B. Bastian | Creation and unification of development and life stage ontologies for
animals | 2 pages, 1 table, accepted at Bio-Ontologies COSI ISMB 2022
conference. AN developed species-specific ontologies, links to Uberon. CJM
and DOS developed Uberon life-stage ontology, ontology design principles. DOS
developed fly ontology. MRR contributed work supervision. FBB supervised the
work, built the integr... | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | With the new era of genomics, an increasing number of animal species are
amenable to large-scale data generation. This had led to the emergence of new
multi-species ontologies to annotate and organize these data. While anatomy and
cell types are well covered by these efforts, information regarding development
and lif... | [
{
"created": "Fri, 24 Jun 2022 11:57:26 GMT",
"version": "v1"
}
] | 2022-06-27 | [
[
"Niknejad",
"Anne",
""
],
[
"Mungall",
"Christopher J.",
""
],
[
"Osumi-Sutherland",
"David",
""
],
[
"Robinson-Rechavi",
"Marc",
""
],
[
"Bastian",
"Frederic B.",
""
]
] | With the new era of genomics, an increasing number of animal species are amenable to large-scale data generation. This had led to the emergence of new multi-species ontologies to annotate and organize these data. While anatomy and cell types are well covered by these efforts, information regarding development and life ... |
2203.14201 | Chung-Hao Lee | Chung-Hao Lee | Cryopreservation of seeds of blue waterlily (Nymphaea caerulea) using
glutathione adding plant vitrification solution, PVS+ | This publish was a mistake | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Nymphaea caerulea is a valuable freshwater aquatic plant, not only because of
its ornamental value but also its extractions for chemical and medical uses. It
is necessary to store its seeds as backup resources. Cryopreservation is the
reliable, cost-effective method for long-term preservation of botanical genetic
ban... | [
{
"created": "Sun, 27 Mar 2022 03:49:43 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Mar 2022 15:07:29 GMT",
"version": "v2"
}
] | 2022-03-31 | [
[
"Lee",
"Chung-Hao",
""
]
] | Nymphaea caerulea is a valuable freshwater aquatic plant, not only because of its ornamental value but also its extractions for chemical and medical uses. It is necessary to store its seeds as backup resources. Cryopreservation is the reliable, cost-effective method for long-term preservation of botanical genetic banks... |
0901.0066 | Christopher Wylie | C. Scott Wylie, Cheol-Min Ghim, David A. Kessler, Herbert Levine | Supplementary information for "The fixation probability of rare mutators
in finite asexual populations" | Online supplementary information for arXiv:0801.4812. 14 pages, 3
figures, 1 table | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This supplementary information contains detailed derivations, comparison to
experiment, and discussion of other miscellaneous issues omitted from the main
text.
| [
{
"created": "Wed, 31 Dec 2008 06:43:30 GMT",
"version": "v1"
}
] | 2009-01-05 | [
[
"Wylie",
"C. Scott",
""
],
[
"Ghim",
"Cheol-Min",
""
],
[
"Kessler",
"David A.",
""
],
[
"Levine",
"Herbert",
""
]
] | This supplementary information contains detailed derivations, comparison to experiment, and discussion of other miscellaneous issues omitted from the main text. |
2109.00931 | Alexander Krau{\ss} | Alexander Krau{\ss}, Thilo Gross and Barbara Drossel | Master Stability Functions for metacommunities with two types of
habitats | Submitted to Physical Review E | null | 10.1103/PhysRevE.105.044310 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Current questions in ecology revolve around instabilities in the dynamics on
spatial networks and particularly the effect of node heterogeneity. We extend
the Master Stability Function formalism to inhomogeneous biregular networks
having two types of spatial nodes. Notably, this class of systems also allows
the inves... | [
{
"created": "Thu, 2 Sep 2021 13:19:08 GMT",
"version": "v1"
},
{
"created": "Wed, 12 Jan 2022 17:42:45 GMT",
"version": "v2"
},
{
"created": "Thu, 27 Jan 2022 19:23:15 GMT",
"version": "v3"
}
] | 2022-04-27 | [
[
"Krauß",
"Alexander",
""
],
[
"Gross",
"Thilo",
""
],
[
"Drossel",
"Barbara",
""
]
] | Current questions in ecology revolve around instabilities in the dynamics on spatial networks and particularly the effect of node heterogeneity. We extend the Master Stability Function formalism to inhomogeneous biregular networks having two types of spatial nodes. Notably, this class of systems also allows the investi... |
1606.01936 | Marco Polin | Rapha\"el Jeanneret, Matteo Contino and Marco Polin | A brief introduction to the model microswimmer {\it Chlamydomonas
reinhardtii} | 16 pages, 7 figures. To be published as part of EPJ ST | null | 10.1140/epjst/e2016-60065-3 | null | q-bio.CB cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The unicellular biflagellate green alga {\it Chlamydomonas reinhardtii} has
been an important model system in biology for decades, and in recent years it
has started to attract growing attention also within the biophysics community.
Here we provide a concise review of some of the aspects of {\it Chlamydomonas}
biolog... | [
{
"created": "Mon, 6 Jun 2016 20:48:10 GMT",
"version": "v1"
}
] | 2016-11-23 | [
[
"Jeanneret",
"Raphaël",
""
],
[
"Contino",
"Matteo",
""
],
[
"Polin",
"Marco",
""
]
] | The unicellular biflagellate green alga {\it Chlamydomonas reinhardtii} has been an important model system in biology for decades, and in recent years it has started to attract growing attention also within the biophysics community. Here we provide a concise review of some of the aspects of {\it Chlamydomonas} biology ... |
2103.02339 | Omar Chehab | Omar Chehab, Alexandre Defossez, Jean-Christophe Loiseau, Alexandre
Gramfort, Jean-Remi King | Deep Recurrent Encoder: A scalable end-to-end network to model brain
signals | null | null | null | null | q-bio.NC cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding how the brain responds to sensory inputs is challenging: brain
recordings are partial, noisy, and high dimensional; they vary across sessions
and subjects and they capture highly nonlinear dynamics. These challenges have
led the community to develop a variety of preprocessing and analytical (almost
excl... | [
{
"created": "Wed, 3 Mar 2021 11:39:17 GMT",
"version": "v1"
},
{
"created": "Mon, 29 Mar 2021 07:59:33 GMT",
"version": "v2"
},
{
"created": "Fri, 30 Sep 2022 08:34:43 GMT",
"version": "v3"
}
] | 2022-10-03 | [
[
"Chehab",
"Omar",
""
],
[
"Defossez",
"Alexandre",
""
],
[
"Loiseau",
"Jean-Christophe",
""
],
[
"Gramfort",
"Alexandre",
""
],
[
"King",
"Jean-Remi",
""
]
] | Understanding how the brain responds to sensory inputs is challenging: brain recordings are partial, noisy, and high dimensional; they vary across sessions and subjects and they capture highly nonlinear dynamics. These challenges have led the community to develop a variety of preprocessing and analytical (almost exclus... |
1510.00115 | Louxin Zhang | Andreas D. M. Gunawan and Louxin Zhang | Bounding the Size of a Network Defined By Visibility Property | 23 pages, 9 figures | null | null | null | q-bio.PE cs.DM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic networks are mathematical structures for modeling and
visualization of reticulation processes in the study of evolution. Galled
networks, reticulation visible networks, nearly-stable networks and
stable-child networks are the four classes of phylogenetic networks that are
recently introduced to study the... | [
{
"created": "Thu, 1 Oct 2015 06:11:15 GMT",
"version": "v1"
}
] | 2015-10-02 | [
[
"Gunawan",
"Andreas D. M.",
""
],
[
"Zhang",
"Louxin",
""
]
] | Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the four classes of phylogenetic networks that are recently introduced to study the t... |
2102.04882 | Alexander Siegenfeld | Pratyush K. Kollepara, Alexander F. Siegenfeld, Nassim Nicholas Taleb,
Yaneer Bar-Yam | Unmasking the mask studies: why the effectiveness of surgical masks in
preventing respiratory infections has been underestimated | New version with minor changes and some edits for clarity | Journal of Travel Medicine 28 (7), taab144 (2021) | 10.1093/jtm/taab144 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Face masks have been widely used as a protective measure against COVID-19.
However, pre-pandemic empirical studies have produced mixed statistical results
on the effectiveness of masks against respiratory viruses. The implications of
the studies' recognized limitations have not been quantitatively and
statistically a... | [
{
"created": "Mon, 8 Feb 2021 08:19:52 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Feb 2021 18:43:08 GMT",
"version": "v2"
}
] | 2022-11-24 | [
[
"Kollepara",
"Pratyush K.",
""
],
[
"Siegenfeld",
"Alexander F.",
""
],
[
"Taleb",
"Nassim Nicholas",
""
],
[
"Bar-Yam",
"Yaneer",
""
]
] | Face masks have been widely used as a protective measure against COVID-19. However, pre-pandemic empirical studies have produced mixed statistical results on the effectiveness of masks against respiratory viruses. The implications of the studies' recognized limitations have not been quantitatively and statistically ana... |
2402.00014 | Alexey Melnikov | Matvei Anoshin, Asel Sagingalieva, Christopher Mansell, Vishal Shete,
Markus Pflitsch, and Alexey Melnikov | Hybrid quantum cycle generative adversarial network for small molecule
generation | 11 pages, 6 figures, 3 tables | null | null | null | q-bio.BM cs.ET cs.LG physics.bio-ph quant-ph | http://creativecommons.org/licenses/by/4.0/ | The contemporary drug design process demands considerable time and resources
to develop each new compound entering the market. Generating small molecules is
a pivotal aspect of drug discovery, essential for developing innovative
pharmaceuticals. Uniqueness, validity, diversity, druglikeliness,
synthesizability, and s... | [
{
"created": "Thu, 28 Dec 2023 14:10:26 GMT",
"version": "v1"
}
] | 2024-02-02 | [
[
"Anoshin",
"Matvei",
""
],
[
"Sagingalieva",
"Asel",
""
],
[
"Mansell",
"Christopher",
""
],
[
"Shete",
"Vishal",
""
],
[
"Pflitsch",
"Markus",
""
],
[
"Melnikov",
"Alexey",
""
]
] | The contemporary drug design process demands considerable time and resources to develop each new compound entering the market. Generating small molecules is a pivotal aspect of drug discovery, essential for developing innovative pharmaceuticals. Uniqueness, validity, diversity, druglikeliness, synthesizability, and sol... |
1401.4122 | Carsten Allefeld | Carsten Allefeld, John-Dylan Haynes | Searchlight-based multi-voxel pattern analysis of fMRI by
cross-validated MANOVA | null | NeuroImage, 89:345-357, 2014 | 10.1016/j.neuroimage.2013.11.043 | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multi-voxel pattern analysis (MVPA) is a fruitful and increasingly popular
complement to traditional univariate methods of analyzing neuroimaging data. We
propose to replace the standard 'decoding' approach to searchlight-based MVPA,
measuring the performance of a classifier by its accuracy, with a method based
on th... | [
{
"created": "Thu, 16 Jan 2014 18:44:28 GMT",
"version": "v1"
},
{
"created": "Fri, 7 Feb 2014 15:05:10 GMT",
"version": "v2"
}
] | 2014-02-10 | [
[
"Allefeld",
"Carsten",
""
],
[
"Haynes",
"John-Dylan",
""
]
] | Multi-voxel pattern analysis (MVPA) is a fruitful and increasingly popular complement to traditional univariate methods of analyzing neuroimaging data. We propose to replace the standard 'decoding' approach to searchlight-based MVPA, measuring the performance of a classifier by its accuracy, with a method based on the ... |
2406.16911 | Javier Garc\'ia Ciudad | Javier Garc\'ia Ciudad, Morten M{\o}rup, Birgitte Rahbek Kornum and
Alexander Neergaard Zahid | Evaluating the Influence of Temporal Context on Automatic Mouse Sleep
Staging through the Application of Human Models | Accepted for publication in the 46th Annual International Conference
of the IEEE Engineering in Medicine and Biology Society (2024) | null | null | null | q-bio.NC cs.AI cs.CV cs.LG eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In human sleep staging models, augmenting the temporal context of the input
to the range of tens of minutes has recently demonstrated performance
improvement. In contrast, the temporal context of mouse sleep staging models is
typically in the order of tens of seconds. While long-term time patterns are
less clear in m... | [
{
"created": "Thu, 6 Jun 2024 10:07:19 GMT",
"version": "v1"
}
] | 2024-06-26 | [
[
"Ciudad",
"Javier García",
""
],
[
"Mørup",
"Morten",
""
],
[
"Kornum",
"Birgitte Rahbek",
""
],
[
"Zahid",
"Alexander Neergaard",
""
]
] | In human sleep staging models, augmenting the temporal context of the input to the range of tens of minutes has recently demonstrated performance improvement. In contrast, the temporal context of mouse sleep staging models is typically in the order of tens of seconds. While long-term time patterns are less clear in mou... |
2201.00817 | Eduardo R. Miranda Prof | Eduardo Reck Miranda, Satvik Venkatesh, Jose D. Mart{\i}n-Guerrero,
Carlos Hernani-Morales, Lucas Lamata, Enrique Solano | An approach to interfacing the brain with quantum computers: practical
steps and caveats | Journal pre-submission draft. Revision pending | null | null | null | q-bio.NC cs.ET | http://creativecommons.org/licenses/by/4.0/ | We report on the first proof-of-concept system demonstrating how one can
control a qubit with mental activity. We developed a method to encode neural
correlates of mental activity as instructions for a quantum computer. Brain
signals are detected utilizing electrodes placed on the scalp of a person, who
learns how to... | [
{
"created": "Tue, 4 Jan 2022 08:00:16 GMT",
"version": "v1"
}
] | 2022-01-05 | [
[
"Miranda",
"Eduardo Reck",
""
],
[
"Venkatesh",
"Satvik",
""
],
[
"Martın-Guerrero",
"Jose D.",
""
],
[
"Hernani-Morales",
"Carlos",
""
],
[
"Lamata",
"Lucas",
""
],
[
"Solano",
"Enrique",
""
]
] | We report on the first proof-of-concept system demonstrating how one can control a qubit with mental activity. We developed a method to encode neural correlates of mental activity as instructions for a quantum computer. Brain signals are detected utilizing electrodes placed on the scalp of a person, who learns how to p... |
2201.07539 | Camille Gontier | Camille Gontier, Simone Carlo Surace, Igor Delvendahl, Martin M\"uller
and Jean-Pascal Pfister | Efficient Sampling-Based Bayesian Active Learning for synaptic
characterization | Major review after submission: - Change of title - Add biological
recordings | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Bayesian Active Learning (BAL) is an efficient framework for learning the
parameters of a model, in which input stimuli are selected to maximize the
mutual information between the observations and the unknown parameters.
However, the applicability of BAL to experiments is limited as it requires
performing high-dimens... | [
{
"created": "Wed, 19 Jan 2022 11:33:29 GMT",
"version": "v1"
},
{
"created": "Tue, 24 May 2022 17:53:14 GMT",
"version": "v2"
},
{
"created": "Wed, 30 Nov 2022 17:04:14 GMT",
"version": "v3"
}
] | 2022-12-01 | [
[
"Gontier",
"Camille",
""
],
[
"Surace",
"Simone Carlo",
""
],
[
"Delvendahl",
"Igor",
""
],
[
"Müller",
"Martin",
""
],
[
"Pfister",
"Jean-Pascal",
""
]
] | Bayesian Active Learning (BAL) is an efficient framework for learning the parameters of a model, in which input stimuli are selected to maximize the mutual information between the observations and the unknown parameters. However, the applicability of BAL to experiments is limited as it requires performing high-dimensio... |
2101.03762 | Thierry Douki | Marie Roser (CIBEST), David B\'eal (CIBEST), Camille Eldin (CIBEST),
Leslie Gudimard (CIBEST), Fanny Caffin, Fanny Gros-D\'esormeaux (IRBA),
Daniel L\'eon\c{c}o, Fran\c{c}ois Fenaille, Christophe Junot, Christophe
Pi\'erard (IRBA), Thierry Douki (CIBEST) | Glutathione conjugates of the mercapturic acid pathway and guanine
adduct as biomarkers of exposure to CEES, a sulfur mustard analog | Analytical and Bioanalytical Chemistry, Springer Verlag, 2020 | null | 10.1007/s00216-020-03096-4 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sulfur mustard (SM), a chemical warfare agent, is a strong alkylating
compound that readily reacts with numerous biomolecules. The goal of the
present work was to define and validate new biomarkers of exposure to SM that
could be easily accessible in urine or plasma. Because investigations using SM
are prohibited by ... | [
{
"created": "Mon, 11 Jan 2021 08:45:30 GMT",
"version": "v1"
}
] | 2021-01-12 | [
[
"Roser",
"Marie",
"",
"CIBEST"
],
[
"Béal",
"David",
"",
"CIBEST"
],
[
"Eldin",
"Camille",
"",
"CIBEST"
],
[
"Gudimard",
"Leslie",
"",
"CIBEST"
],
[
"Caffin",
"Fanny",
"",
"IRBA"
],
[
"Gros-Désormeaux",
"Fa... | Sulfur mustard (SM), a chemical warfare agent, is a strong alkylating compound that readily reacts with numerous biomolecules. The goal of the present work was to define and validate new biomarkers of exposure to SM that could be easily accessible in urine or plasma. Because investigations using SM are prohibited by th... |
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