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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0801.0844 | E. Ahmed | E. Ahmed and A.S.Hegazi | Survival May Not be for the Fittest (Lessons from some TV games) | none | null | null | null | q-bio.PE | null | In this paper we argue that biological fitness is a multi-objective concept
hence the statement "fittest" is inappropriate. The following statement is
proposed "Survival is mostly for those with non-dominated fitness". Also we use
some TV games to show that under the following conditions: i) There are no
dominant pla... | [
{
"created": "Sun, 6 Jan 2008 08:05:51 GMT",
"version": "v1"
},
{
"created": "Thu, 10 Jan 2008 08:23:31 GMT",
"version": "v2"
}
] | 2008-01-10 | [
[
"Ahmed",
"E.",
""
],
[
"Hegazi",
"A. S.",
""
]
] | In this paper we argue that biological fitness is a multi-objective concept hence the statement "fittest" is inappropriate. The following statement is proposed "Survival is mostly for those with non-dominated fitness". Also we use some TV games to show that under the following conditions: i) There are no dominant playe... |
1506.04080 | V. G. Gurzadyan | V.G. Gurzadyan, H. Yan, G. Vlahovic, A. Kashin, P. Killela, Z.
Reitman, S. Sargsyan, G. Yegorian, G. Milledge, B. Vlahovic | Detecting somatic mutations in genomic sequences by means of
Kolmogorov-Arnold analysis | To appear in Royal Society Open Science, 12 pages, 2 figures | Royal Society Open Science, 2, 150143, 2015 | 10.1098/rsos.150143 | null | q-bio.GN physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Kolmogorov-Arnold stochasticity parameter technique is applied for the
first time to the study of cancer genome sequencing, to reveal mutations. Using
data generated by next generation sequencing technologies, we have analyzed the
exome sequences of brain tumor patients with matched tumor and normal blood. We
sho... | [
{
"created": "Fri, 12 Jun 2015 17:31:40 GMT",
"version": "v1"
}
] | 2018-11-05 | [
[
"Gurzadyan",
"V. G.",
""
],
[
"Yan",
"H.",
""
],
[
"Vlahovic",
"G.",
""
],
[
"Kashin",
"A.",
""
],
[
"Killela",
"P.",
""
],
[
"Reitman",
"Z.",
""
],
[
"Sargsyan",
"S.",
""
],
[
"Yegorian",
"G.",... | The Kolmogorov-Arnold stochasticity parameter technique is applied for the first time to the study of cancer genome sequencing, to reveal mutations. Using data generated by next generation sequencing technologies, we have analyzed the exome sequences of brain tumor patients with matched tumor and normal blood. We show ... |
2101.05336 | Anastasiya Belyaeva | Anastasiya Belyaeva, Kaie Kubjas, Lawrence J. Sun, Caroline Uhler | Identifying 3D Genome Organization in Diploid Organisms via Euclidean
Distance Geometry | null | null | null | null | q-bio.GN math.MG math.OC | http://creativecommons.org/licenses/by/4.0/ | The spatial organization of the DNA in the cell nucleus plays an important
role for gene regulation, DNA replication, and genomic integrity. Through the
development of chromosome conformation capture experiments (such as 3C, 4C,
Hi-C) it is now possible to obtain the contact frequencies of the DNA at the
whole-genome... | [
{
"created": "Wed, 13 Jan 2021 20:26:49 GMT",
"version": "v1"
}
] | 2021-01-15 | [
[
"Belyaeva",
"Anastasiya",
""
],
[
"Kubjas",
"Kaie",
""
],
[
"Sun",
"Lawrence J.",
""
],
[
"Uhler",
"Caroline",
""
]
] | The spatial organization of the DNA in the cell nucleus plays an important role for gene regulation, DNA replication, and genomic integrity. Through the development of chromosome conformation capture experiments (such as 3C, 4C, Hi-C) it is now possible to obtain the contact frequencies of the DNA at the whole-genome l... |
1907.12718 | Victor Solovyev | Oleg Fokin (1), Anastasia Bakulina (1 and 2), Igor Seledtsov (1) and
Victor Solovyev (1) | ReadsClean: a new approach to error correction of sequencing reads based
on alignments clustering | 13 pages, 2 figures, 9 tables, Supplemental information | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Next generation methods of DNA sequencing produce relatively high
rate of reading errors, which interfere with de novo genome assembly of newly
sequenced organisms and particularly affect the quality of SNP detection
important for diagnostics of many hereditary diseases. There exists a number of
programs ... | [
{
"created": "Tue, 30 Jul 2019 03:08:29 GMT",
"version": "v1"
}
] | 2019-07-31 | [
[
"Fokin",
"Oleg",
"",
"1 and 2"
],
[
"Bakulina",
"Anastasia",
"",
"1 and 2"
],
[
"Seledtsov",
"Igor",
""
],
[
"Solovyev",
"Victor",
""
]
] | Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important for diagnostics of many hereditary diseases. There exists a number of programs de... |
2308.04381 | Genji Kawakita | Genji Kawakita, Ariel Zeleznikow-Johnston, Naotsugu Tsuchiya, Masafumi
Oizumi | Gromov-Wasserstein unsupervised alignment reveals structural
correspondences between the color similarity structures of humans and large
language models | null | Sci Rep 14, 15917 (2024) | 10.1038/s41598-024-65604-1 10.1038/s41598-024-65604-1
10.1038/s41598-024-65604-1 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Large Language Models (LLMs), such as the General Pre-trained Transformer
(GPT), have shown remarkable performance in various cognitive tasks. However,
it remains unclear whether these models have the ability to accurately infer
human perceptual representations. Previous research has addressed this question
by quanti... | [
{
"created": "Tue, 8 Aug 2023 16:32:41 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Jun 2024 10:41:08 GMT",
"version": "v2"
},
{
"created": "Tue, 13 Aug 2024 17:11:25 GMT",
"version": "v3"
}
] | 2024-08-16 | [
[
"Kawakita",
"Genji",
""
],
[
"Zeleznikow-Johnston",
"Ariel",
""
],
[
"Tsuchiya",
"Naotsugu",
""
],
[
"Oizumi",
"Masafumi",
""
]
] | Large Language Models (LLMs), such as the General Pre-trained Transformer (GPT), have shown remarkable performance in various cognitive tasks. However, it remains unclear whether these models have the ability to accurately infer human perceptual representations. Previous research has addressed this question by quantify... |
2012.00672 | Guojing Cong | David Bell, Giacomo Domeniconi, Chih-Chieh Yang, Ruhong Zhou, Leili
Zhang, Guojing Cong | Dynamics-based peptide-MHC binding optimization by a convolutional
variational autoencoder: a use-case model for CASTELO | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | An unsolved challenge in the development of antigen specific immunotherapies
is determining the optimal antigens to target. Comprehension of antigen-MHC
binding is paramount towards achieving this goal. Here, we present CASTELO, a
combined machine learning-molecular dynamics (ML-MD) approach to design novel
antigens ... | [
{
"created": "Sun, 29 Nov 2020 13:41:18 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Dec 2020 13:57:31 GMT",
"version": "v2"
}
] | 2020-12-09 | [
[
"Bell",
"David",
""
],
[
"Domeniconi",
"Giacomo",
""
],
[
"Yang",
"Chih-Chieh",
""
],
[
"Zhou",
"Ruhong",
""
],
[
"Zhang",
"Leili",
""
],
[
"Cong",
"Guojing",
""
]
] | An unsolved challenge in the development of antigen specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen-MHC binding is paramount towards achieving this goal. Here, we present CASTELO, a combined machine learning-molecular dynamics (ML-MD) approach to design novel antigens of... |
1509.07990 | Raymond Goldstein | Philipp Khuc Trong, H\'el\`ene Doerflinger, J\"orn Dunkel, Daniel St.
Johnston, and Raymond E. Goldstein | Cortical microtubule nucleation can organise the cytoskeleton of
$Drosophila$ oocytes to define the anteroposterior axis | 54 pages, 12 figures, open access, see additional information online
at eLife | eLife 4, e06088 (2015) | 10.7554/eLife.06088 | null | q-bio.SC cond-mat.soft physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Many cells contain non-centrosomal arrays of microtubules (MT), but the
assembly, organisation and function of these arrays are poorly understood. We
present the first theoretical model for the non-centrosomal MT cytoskeleton in
$Drosophila$ oocytes, in which $bicoid$ and $oskar$ mRNAs become localised to
establish t... | [
{
"created": "Sat, 26 Sep 2015 15:07:23 GMT",
"version": "v1"
}
] | 2015-09-29 | [
[
"Trong",
"Philipp Khuc",
""
],
[
"Doerflinger",
"Hélène",
""
],
[
"Dunkel",
"Jörn",
""
],
[
"Johnston",
"Daniel St.",
""
],
[
"Goldstein",
"Raymond E.",
""
]
] | Many cells contain non-centrosomal arrays of microtubules (MT), but the assembly, organisation and function of these arrays are poorly understood. We present the first theoretical model for the non-centrosomal MT cytoskeleton in $Drosophila$ oocytes, in which $bicoid$ and $oskar$ mRNAs become localised to establish the... |
q-bio/0510002 | Herbert Sauro Dr | Vijay Chickarmane, Ali Nadim, Animesh Ray and Herbert M. Sauro | A p53 Oscillator Model of DNA Break Repair Control | 31 pages, 8 figures | null | null | null | q-bio.MN | null | The transcription factor p53 is an important regulator of cell fate.
Mutations in p53 gene are associated with many cancers. In response to signals
such as DNA damage, p53 controls the transcription of a series of genes that
cause cell cycle arrest during which DNA damage is repaired, or triggers
programmed cell deat... | [
{
"created": "Sat, 1 Oct 2005 00:11:33 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Chickarmane",
"Vijay",
""
],
[
"Nadim",
"Ali",
""
],
[
"Ray",
"Animesh",
""
],
[
"Sauro",
"Herbert M.",
""
]
] | The transcription factor p53 is an important regulator of cell fate. Mutations in p53 gene are associated with many cancers. In response to signals such as DNA damage, p53 controls the transcription of a series of genes that cause cell cycle arrest during which DNA damage is repaired, or triggers programmed cell death ... |
2311.09236 | Peter Coppola PhD | Peter Coppola | A review of the sufficient conditions for consciousness | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | How subjective experience (i.e., consciousness) arises out of objective
material processes has been called the hard problem. The neuroscience of
consciousness has set out to find the sufficient conditions for consciousness
and theoretical and empirical endeavours have placed a particular focus on the
cortex and subco... | [
{
"created": "Fri, 20 Oct 2023 15:50:41 GMT",
"version": "v1"
}
] | 2023-11-17 | [
[
"Coppola",
"Peter",
""
]
] | How subjective experience (i.e., consciousness) arises out of objective material processes has been called the hard problem. The neuroscience of consciousness has set out to find the sufficient conditions for consciousness and theoretical and empirical endeavours have placed a particular focus on the cortex and subcort... |
q-bio/0506020 | Jayprokas Chakrabarti | Bibekanand Mallick, Jayprokas Chakrabarti, Satyabrata Sahoo, Zhumur
Ghosh and Smarajit Das | Identity Elements of Archaeal tRNA | null | DNA Research 12, 235--246 (2005) | 10.1093/dnares/dsi008 | null | q-bio.GN | null | Features unique to a transfer-RNA are recognized by the corresponding
tRNA-synthetase. Keeping this in view we isolate the discriminating features of
all archaeal tRNA. These are our identity elements. Further, we investigate
tRNA-characteristics that delineate the different orders of archaea.
| [
{
"created": "Thu, 16 Jun 2005 04:55:57 GMT",
"version": "v1"
},
{
"created": "Sat, 27 May 2006 13:57:40 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Mallick",
"Bibekanand",
""
],
[
"Chakrabarti",
"Jayprokas",
""
],
[
"Sahoo",
"Satyabrata",
""
],
[
"Ghosh",
"Zhumur",
""
],
[
"Das",
"Smarajit",
""
]
] | Features unique to a transfer-RNA are recognized by the corresponding tRNA-synthetase. Keeping this in view we isolate the discriminating features of all archaeal tRNA. These are our identity elements. Further, we investigate tRNA-characteristics that delineate the different orders of archaea. |
1108.0736 | Ilya M. Nemenman | Ilya Nemenman | Gain control in molecular information processing: Lessons from
neuroscience | 10 pages, 5 figures | Phys. Biol. 9 026003, 2012 | 10.1088/1478-3975/9/2/026003 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Statistical properties of environments experienced by biological signaling
systems in the real world change, which necessitate adaptive responses to
achieve high fidelity information transmission. One form of such adaptive
response is gain control. Here we argue that a certain simple mechanism of gain
control, unders... | [
{
"created": "Wed, 3 Aug 2011 04:35:52 GMT",
"version": "v1"
}
] | 2012-05-01 | [
[
"Nemenman",
"Ilya",
""
]
] | Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitate adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain control. Here we argue that a certain simple mechanism of gain control, understo... |
1901.04803 | Fulgensia Mbabazi | Fulgensia Kamugisha Mbabazi, Joseph Y.T. Mugisha, Mark Kimathi | Hopf-bifurcation analysis of pneumococcal pneumonia with time delays | 36 pages, 24 figures | null | null | null | q-bio.PE math.CA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, a mathematical model of pneumococcal pneumonia with time
delays is proposed. The stability theory of delay differential equations is
used to analyze the model. The results show that the disease-free equilibrium
is asymptotically stable if the control reproduction ratio R0 is less than
unity and unstabl... | [
{
"created": "Tue, 15 Jan 2019 13:07:43 GMT",
"version": "v1"
}
] | 2019-01-16 | [
[
"Mbabazi",
"Fulgensia Kamugisha",
""
],
[
"Mugisha",
"Joseph Y. T.",
""
],
[
"Kimathi",
"Mark",
""
]
] | In this paper, a mathematical model of pneumococcal pneumonia with time delays is proposed. The stability theory of delay differential equations is used to analyze the model. The results show that the disease-free equilibrium is asymptotically stable if the control reproduction ratio R0 is less than unity and unstable ... |
1906.07546 | Qiongge Li | Qiongge Li, Gino Del Ferraro, Luca Pasquini, Kyung K. Peck, Hernan A.
Makse and Andrei I. Holodny | Core language brain network for fMRI-language task used in clinical
applications | 14 pages, 7 figures | null | null | null | q-bio.NC physics.bio-ph physics.med-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Functional magnetic resonance imaging (fMRI) is widely used in clinical
applications to highlight brain areas involved in specific cognitive processes.
Brain impairments, such as tumors, suppress the fMRI activation of the
anatomical areas they invade and, thus, brain-damaged functional networks
present missing links... | [
{
"created": "Wed, 12 Jun 2019 19:15:15 GMT",
"version": "v1"
}
] | 2019-06-20 | [
[
"Li",
"Qiongge",
""
],
[
"Del Ferraro",
"Gino",
""
],
[
"Pasquini",
"Luca",
""
],
[
"Peck",
"Kyung K.",
""
],
[
"Makse",
"Hernan A.",
""
],
[
"Holodny",
"Andrei I.",
""
]
] | Functional magnetic resonance imaging (fMRI) is widely used in clinical applications to highlight brain areas involved in specific cognitive processes. Brain impairments, such as tumors, suppress the fMRI activation of the anatomical areas they invade and, thus, brain-damaged functional networks present missing links/a... |
1802.02378 | Francoise Schoentgen | Francoise Schoentgen and Slavica Jonic | PEBP1/RKIP: from multiple functions to a common role in cellular
processes | This is a review article | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | PEBPs (PhosphatidylEthanolamine Binding Proteins) form a protein family
widely present in the living world since they are encountered in
microorganisms, plants and animals. In all organisms PEBPs appear to regulate
important mechanisms that govern cell cycle, proliferation, differentiation and
motility. In humans, th... | [
{
"created": "Wed, 7 Feb 2018 10:39:48 GMT",
"version": "v1"
}
] | 2018-02-08 | [
[
"Schoentgen",
"Francoise",
""
],
[
"Jonic",
"Slavica",
""
]
] | PEBPs (PhosphatidylEthanolamine Binding Proteins) form a protein family widely present in the living world since they are encountered in microorganisms, plants and animals. In all organisms PEBPs appear to regulate important mechanisms that govern cell cycle, proliferation, differentiation and motility. In humans, thre... |
2007.06291 | Yoav Kolumbus | Yoav Kolumbus and Noam Nisan | On the Effectiveness of Tracking and Testing in SEIR Models | null | null | null | null | q-bio.PE cs.MA cs.SI physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the effectiveness of tracking and testing in mitigating or
suppressing epidemic outbreaks, in combination with or as an alternative to
quarantines and global lockdowns. We study these intervention methods on a
network-based SEIR model, augmented with an additional probability to model
symptomatic, asymptomat... | [
{
"created": "Mon, 13 Jul 2020 10:19:00 GMT",
"version": "v1"
}
] | 2020-07-15 | [
[
"Kolumbus",
"Yoav",
""
],
[
"Nisan",
"Noam",
""
]
] | We study the effectiveness of tracking and testing in mitigating or suppressing epidemic outbreaks, in combination with or as an alternative to quarantines and global lockdowns. We study these intervention methods on a network-based SEIR model, augmented with an additional probability to model symptomatic, asymptomatic... |
1604.07110 | Christopher Marriott | Chris Marriott and Jobran Chebib | Divergent Cumulative Cultural Evolution | 8 pages, ALIFE 2016 | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Divergent cumulative cultural evolution occurs when the cultural evolutionary
trajectory diverges from the biological evolutionary trajectory. We consider
the conditions under which divergent cumulative cultural evolution can occur.
We hypothesize that two conditions are necessary. First that genetic and
cultural inf... | [
{
"created": "Mon, 25 Apr 2016 02:24:57 GMT",
"version": "v1"
}
] | 2016-04-26 | [
[
"Marriott",
"Chris",
""
],
[
"Chebib",
"Jobran",
""
]
] | Divergent cumulative cultural evolution occurs when the cultural evolutionary trajectory diverges from the biological evolutionary trajectory. We consider the conditions under which divergent cumulative cultural evolution can occur. We hypothesize that two conditions are necessary. First that genetic and cultural infor... |
2406.05738 | Thomas Le Menestrel | Thomas Le Menestrel, Manuel Rivas | Smiles2Dock: an open large-scale multi-task dataset for ML-based
molecular docking | null | null | null | null | q-bio.BM cs.LG stat.AP stat.CO | http://creativecommons.org/licenses/by/4.0/ | Docking is a crucial component in drug discovery aimed at predicting the
binding conformation and affinity between small molecules and target proteins.
ML-based docking has recently emerged as a prominent approach, outpacing
traditional methods like DOCK and AutoDock Vina in handling the growing scale
and complexity ... | [
{
"created": "Sun, 9 Jun 2024 11:13:03 GMT",
"version": "v1"
}
] | 2024-06-11 | [
[
"Menestrel",
"Thomas Le",
""
],
[
"Rivas",
"Manuel",
""
]
] | Docking is a crucial component in drug discovery aimed at predicting the binding conformation and affinity between small molecules and target proteins. ML-based docking has recently emerged as a prominent approach, outpacing traditional methods like DOCK and AutoDock Vina in handling the growing scale and complexity of... |
1408.6187 | Jack Dekker | J. Dekker and J. Gilbert | Weedy adaptation in Setaria spp.: IX. Effects of salinity, temperature,
light and seed dormancy on Setaria faberi seed germination | 11 pages, 1 table | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Life in salty habitats is a function of tolerance to those chemicals at all
critical phases of a plant's life history. The ability to withstand salt as an
established plant may require different mechanisms and plant traits than those
needed to germinate in salty soils. Seeds establishing themselves in high salt
conte... | [
{
"created": "Tue, 26 Aug 2014 17:30:07 GMT",
"version": "v1"
}
] | 2014-08-27 | [
[
"Dekker",
"J.",
""
],
[
"Gilbert",
"J.",
""
]
] | Life in salty habitats is a function of tolerance to those chemicals at all critical phases of a plant's life history. The ability to withstand salt as an established plant may require different mechanisms and plant traits than those needed to germinate in salty soils. Seeds establishing themselves in high salt content... |
1807.07687 | Ursula Tooley | Ursula A. Tooley, Allyson P. Mackey, Rastko Ciric, Kosha Ruparel,
Tyler M. Moore, Ruben C. Gur, Raquel E. Gur, Theodore D. Satterthwaite,
Danielle S. Bassett | Influence of Neighborhood SES on Functional Brain Network Development | 9 pages, 6 figures. Cerebral Cortex (2019) | null | 10.1093/cercor/bhz066 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Higher socioeconomic status (SES) in childhood is associated with increased
cognitive abilities, higher academic achievement, and decreased incidence of
mental illness later in development. Accumulating evidence suggests that these
effects may be due to changes in brain development induced by environmental
factors. W... | [
{
"created": "Fri, 20 Jul 2018 01:32:22 GMT",
"version": "v1"
},
{
"created": "Mon, 23 Jul 2018 01:25:11 GMT",
"version": "v2"
}
] | 2019-04-17 | [
[
"Tooley",
"Ursula A.",
""
],
[
"Mackey",
"Allyson P.",
""
],
[
"Ciric",
"Rastko",
""
],
[
"Ruparel",
"Kosha",
""
],
[
"Moore",
"Tyler M.",
""
],
[
"Gur",
"Ruben C.",
""
],
[
"Gur",
"Raquel E.",
""
],
[
... | Higher socioeconomic status (SES) in childhood is associated with increased cognitive abilities, higher academic achievement, and decreased incidence of mental illness later in development. Accumulating evidence suggests that these effects may be due to changes in brain development induced by environmental factors. Whi... |
2009.00539 | M. Ali Al-Radhawi | Jared Miller, M. Ali Al-Radhawi, and Eduardo D. Sontag | Mediating Ribosomal Competition by Splitting Pools | null | LCSS Vol 5 Issue 5 (Nov 2020) | 10.1109/LCSYS.2020.3041213 | null | q-bio.MN math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Synthetic biology constructs often rely upon the introduction of "circuit"
genes into host cells, in order to express novel proteins and thus endow the
host with a desired behavior. The expression of these new genes "consumes"
existing resources in the cell, such as ATP, RNA polymerase, amino acids, and
ribosomes. Ri... | [
{
"created": "Tue, 1 Sep 2020 16:17:46 GMT",
"version": "v1"
},
{
"created": "Wed, 2 Sep 2020 01:08:05 GMT",
"version": "v2"
},
{
"created": "Fri, 4 Sep 2020 17:34:44 GMT",
"version": "v3"
}
] | 2022-01-10 | [
[
"Miller",
"Jared",
""
],
[
"Al-Radhawi",
"M. Ali",
""
],
[
"Sontag",
"Eduardo D.",
""
]
] | Synthetic biology constructs often rely upon the introduction of "circuit" genes into host cells, in order to express novel proteins and thus endow the host with a desired behavior. The expression of these new genes "consumes" existing resources in the cell, such as ATP, RNA polymerase, amino acids, and ribosomes. Ribo... |
2401.10295 | Piyumi Chathurangika | Piumi Chathurangika, Sanjeewa Perera, Kushani De Silva | Forecasting dengue outbreaks with uncertainty using seasonal weather
patterns | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dengue is a vector-borne disease transmitted to humans by vectors of genus
Aedes and is a global threat with health, social, and economic impact in many
of the tropical countries including Sri Lanka. The virus transmission is
significantly impacted by environmental conditions, with a notable contribution
from elevate... | [
{
"created": "Thu, 18 Jan 2024 04:00:20 GMT",
"version": "v1"
}
] | 2024-01-22 | [
[
"Chathurangika",
"Piumi",
""
],
[
"Perera",
"Sanjeewa",
""
],
[
"De Silva",
"Kushani",
""
]
] | Dengue is a vector-borne disease transmitted to humans by vectors of genus Aedes and is a global threat with health, social, and economic impact in many of the tropical countries including Sri Lanka. The virus transmission is significantly impacted by environmental conditions, with a notable contribution from elevated ... |
1611.05443 | Francesco Alderisio | Chao Zhai, Michael Z. Q. Chen, Francesco Alderisio, Alexei Yu.
Uteshev, Mario di Bernardo | Bridging the Gap between Individuality and Joint Improvisation in the
Mirror Game | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Extensive experiments in Human Movement Science suggest that solo motions are
characterized by unique features that define the individuality or motor
signature of people. While interacting with others, humans tend to
spontaneously coordinate their movement and unconsciously give rise to joint
improvisation. However, ... | [
{
"created": "Wed, 16 Nov 2016 14:27:12 GMT",
"version": "v1"
}
] | 2016-11-18 | [
[
"Zhai",
"Chao",
""
],
[
"Chen",
"Michael Z. Q.",
""
],
[
"Alderisio",
"Francesco",
""
],
[
"Uteshev",
"Alexei Yu.",
""
],
[
"di Bernardo",
"Mario",
""
]
] | Extensive experiments in Human Movement Science suggest that solo motions are characterized by unique features that define the individuality or motor signature of people. While interacting with others, humans tend to spontaneously coordinate their movement and unconsciously give rise to joint improvisation. However, it... |
1806.00975 | Louis Kang | Louis Kang, Vijay Balasubramanian | A geometric attractor mechanism for self-organization of entorhinal grid
modules | Main text, Supplementary Information and Figures, Supplementary Video | null | null | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Grid cells in the medial entorhinal cortex (MEC) respond when an animal
occupies a periodic lattice of "grid fields" in the environment. The grids are
organized in modules with spatial periods, or scales, clustered around discrete
values separated by ratios in the range 1.2--2.0. We propose a mechanism that
produces ... | [
{
"created": "Mon, 4 Jun 2018 06:38:58 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Mar 2019 18:08:42 GMT",
"version": "v2"
}
] | 2019-03-13 | [
[
"Kang",
"Louis",
""
],
[
"Balasubramanian",
"Vijay",
""
]
] | Grid cells in the medial entorhinal cortex (MEC) respond when an animal occupies a periodic lattice of "grid fields" in the environment. The grids are organized in modules with spatial periods, or scales, clustered around discrete values separated by ratios in the range 1.2--2.0. We propose a mechanism that produces th... |
2305.13127 | Junwei Kuang | Junwei Kuang, Jiaheng Xie and Zhijun Yan | What Symptoms and How Long? An Interpretable AI Approach for Depression
Detection in Social Media | 56 pages, 10 figures, 21 tables | null | null | null | q-bio.QM cs.AI cs.CY cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Depression is the most prevalent and serious mental illness, which induces
grave financial and societal ramifications. Depression detection is key for
early intervention to mitigate those consequences. Such a high-stake decision
inherently necessitates interpretability. Although a few depression detection
studies att... | [
{
"created": "Thu, 18 May 2023 20:15:04 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Jul 2023 01:54:26 GMT",
"version": "v2"
}
] | 2023-07-26 | [
[
"Kuang",
"Junwei",
""
],
[
"Xie",
"Jiaheng",
""
],
[
"Yan",
"Zhijun",
""
]
] | Depression is the most prevalent and serious mental illness, which induces grave financial and societal ramifications. Depression detection is key for early intervention to mitigate those consequences. Such a high-stake decision inherently necessitates interpretability. Although a few depression detection studies attem... |
1807.09617 | Soham Chatterjee Mr. | Soham Chatterjee, Archana Iyer, Satya Avva, Abhai Kollara, Malaikannan
Sankarasubbu | Convolutional Neural Networks In Classifying Cancer Through DNA
Methylation | null | null | null | null | q-bio.GN cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | DNA Methylation has been the most extensively studied epigenetic mark.
Usually a change in the genotype, DNA sequence, leads to a change in the
phenotype, observable characteristics of the individual. But DNA methylation,
which happens in the context of CpG (cytosine and guanine bases linked by
phosphate backbone) di... | [
{
"created": "Tue, 24 Jul 2018 17:11:58 GMT",
"version": "v1"
}
] | 2018-07-26 | [
[
"Chatterjee",
"Soham",
""
],
[
"Iyer",
"Archana",
""
],
[
"Avva",
"Satya",
""
],
[
"Kollara",
"Abhai",
""
],
[
"Sankarasubbu",
"Malaikannan",
""
]
] | DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in the context of CpG (cytosine and guanine bases linked by phosphate backbone) dinu... |
1301.7277 | Samuel Ocko | Samuel A. Ocko, L. Mahadevan | Collective thermoregulation in bee clusters | 19 pages, 8 figures | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Swarming is an essential part of honeybee behaviour, wherein thousands of
bees cling onto each other to form a dense cluster that may be exposed to the
environment for several days. This cluster has the ability to maintain its core
temperature actively without a central controller, and raises the question of
how this... | [
{
"created": "Wed, 30 Jan 2013 16:32:05 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Nov 2013 20:05:59 GMT",
"version": "v2"
}
] | 2013-11-07 | [
[
"Ocko",
"Samuel A.",
""
],
[
"Mahadevan",
"L.",
""
]
] | Swarming is an essential part of honeybee behaviour, wherein thousands of bees cling onto each other to form a dense cluster that may be exposed to the environment for several days. This cluster has the ability to maintain its core temperature actively without a central controller, and raises the question of how this i... |
1211.7330 | Alexander Stewart | Alexander J. Stewart and Joshua B. Plotkin | The evolution of complex gene regulation by low specificity binding
sites | null | Proc. R. Soc. B 7 October 2013 vol. 280 no. 1768 20131313 | 10.1098/rspb.2013.1313 | null | q-bio.PE q-bio.GN q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transcription factor binding sites vary in their specificity, both within and
between species. Binding specificity has a strong impact on the evolution of
gene expression, because it determines how easily regulatory interactions are
gained and lost. Nevertheless, we have a relatively poor understanding of what
evolut... | [
{
"created": "Fri, 30 Nov 2012 18:21:59 GMT",
"version": "v1"
}
] | 2013-12-30 | [
[
"Stewart",
"Alexander J.",
""
],
[
"Plotkin",
"Joshua B.",
""
]
] | Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained and lost. Nevertheless, we have a relatively poor understanding of what evolutio... |
2001.07247 | Christopher Lester | Christopher Lester, Ruth E. Baker, Christian A. Yates | Efficiently simulating discrete-state models with binary decision trees | 26 pages | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stochastic simulation algorithms (SSAs) are widely used to numerically
investigate the properties of stochastic, discrete-state models. The Gillespie
Direct Method is the pre-eminent SSA, and is widely used to generate sample
paths of so-called agent-based or individual-based models. However, the
simplicity of the Gi... | [
{
"created": "Mon, 20 Jan 2020 20:40:59 GMT",
"version": "v1"
}
] | 2020-01-22 | [
[
"Lester",
"Christopher",
""
],
[
"Baker",
"Ruth E.",
""
],
[
"Yates",
"Christian A.",
""
]
] | Stochastic simulation algorithms (SSAs) are widely used to numerically investigate the properties of stochastic, discrete-state models. The Gillespie Direct Method is the pre-eminent SSA, and is widely used to generate sample paths of so-called agent-based or individual-based models. However, the simplicity of the Gill... |
1810.11769 | Yuri A. Dabaghian | Y. Dabaghian | Through synapses to spatial memory maps: a topological model | 18 pages, 9 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Various neurophysiological and cognitive functions are based on transferring
information between spiking neurons via a complex system of synaptic
connections. In particular, the capacity of presynaptic inputs to influence the
postsynaptic outputs---the efficacy of the synapses---plays a principal role in
all aspects ... | [
{
"created": "Sun, 28 Oct 2018 07:05:16 GMT",
"version": "v1"
}
] | 2018-10-30 | [
[
"Dabaghian",
"Y.",
""
]
] | Various neurophysiological and cognitive functions are based on transferring information between spiking neurons via a complex system of synaptic connections. In particular, the capacity of presynaptic inputs to influence the postsynaptic outputs---the efficacy of the synapses---plays a principal role in all aspects of... |
1107.1998 | Miloje Rakocevic M. | Miloje M. Rakocevic | Genetic Code: Four Diversity Types of Protein Amino Acids | 63 pages, 3 figures, 11 tables, 7 appendices | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper presents, for the first time, four diversity types of protein
amino acids. The first type includes two amino acids (G, P), both without
standard hydrocarbon side chains; the second one four amino acids, as two pairs
[(A, L), (V, I)], all with standard hydrocarbon side chains; the third type
comprises the s... | [
{
"created": "Mon, 11 Jul 2011 11:16:59 GMT",
"version": "v1"
},
{
"created": "Tue, 19 Jul 2011 08:18:30 GMT",
"version": "v2"
}
] | 2011-07-20 | [
[
"Rakocevic",
"Miloje M.",
""
]
] | This paper presents, for the first time, four diversity types of protein amino acids. The first type includes two amino acids (G, P), both without standard hydrocarbon side chains; the second one four amino acids, as two pairs [(A, L), (V, I)], all with standard hydrocarbon side chains; the third type comprises the six... |
2211.12949 | Xiaoyuan Liu | Xiaoyuan Liu, George W.A. Constable, Jonathan W. Pitchford | Feasibility and stability in large Lotka Volterra systems with
interaction structure | Manuscript is 8 pages long, containing 4 figures. Pages 9 to 25 is
the Supplemental Material | null | 10.1103/PhysRevE.107.054301 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Complex system stability can be studied via linear stability analysis using
Random Matrix Theory (RMT) or via feasibility (requiring positive equilibrium
abundances). Both approaches highlight the importance of interaction structure.
Here we show, analytically and numerically, how RMT and feasibility approaches
can b... | [
{
"created": "Wed, 23 Nov 2022 13:51:52 GMT",
"version": "v1"
},
{
"created": "Thu, 20 Apr 2023 08:35:42 GMT",
"version": "v2"
}
] | 2023-05-17 | [
[
"Liu",
"Xiaoyuan",
""
],
[
"Constable",
"George W. A.",
""
],
[
"Pitchford",
"Jonathan W.",
""
]
] | Complex system stability can be studied via linear stability analysis using Random Matrix Theory (RMT) or via feasibility (requiring positive equilibrium abundances). Both approaches highlight the importance of interaction structure. Here we show, analytically and numerically, how RMT and feasibility approaches can be ... |
1403.5185 | Jan Karbowski | Franciszek Rakowski, Jagan Srinivasan, Paul W. Sternberg, Jan
Karbowski | Synaptic polarity of the interneuron circuit controlling C. elegans
locomotion | Connectivity patterns of neural network controlling C. elegans motion | Front. Comput. Neurosci. 7: 128 (2013) | 10.3389/fncom.2013.00128 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | C. elegans is the only animal for which a detailed neural connectivity
diagram has been constructed. However, synaptic polarities in this diagram, and
thus, circuit functions are largely unknown. Here, we deciphered the likely
polarities of 7 pre-motor neurons implicated in the control of worm's
locomotion, using a c... | [
{
"created": "Thu, 20 Mar 2014 16:00:56 GMT",
"version": "v1"
}
] | 2014-03-21 | [
[
"Rakowski",
"Franciszek",
""
],
[
"Srinivasan",
"Jagan",
""
],
[
"Sternberg",
"Paul W.",
""
],
[
"Karbowski",
"Jan",
""
]
] | C. elegans is the only animal for which a detailed neural connectivity diagram has been constructed. However, synaptic polarities in this diagram, and thus, circuit functions are largely unknown. Here, we deciphered the likely polarities of 7 pre-motor neurons implicated in the control of worm's locomotion, using a com... |
0706.2007 | Ilya M. Nemenman | Ilya Nemenman, G. Sean Escola, William S. Hlavacek, Pat J. Unkefer,
Clifford J. Unkefer, Michael E. Wall | Reconstruction of metabolic networks from high-throughput metabolite
profiling data: in silico analysis of red blood cell metabolism | 14 pages, 3 figures. Presented at the DIMACS Workshop on Dialogue on
Reverse Engineering Assessment and Methods (DREAM), Sep 2006 | Ann. N.Y. Acad. Sci. 1115: 102\^a?"115 (2007) | 10.1196/annals.1407.013 | LANL LA-UR-07-3646 | q-bio.MN | null | We investigate the ability of algorithms developed for reverse engineering of
transcriptional regulatory networks to reconstruct metabolic networks from
high-throughput metabolite profiling data. For this, we generate synthetic
metabolic profiles for benchmarking purposes based on a well-established model
for red blo... | [
{
"created": "Wed, 13 Jun 2007 22:41:36 GMT",
"version": "v1"
}
] | 2007-11-19 | [
[
"Nemenman",
"Ilya",
""
],
[
"Escola",
"G. Sean",
""
],
[
"Hlavacek",
"William S.",
""
],
[
"Unkefer",
"Pat J.",
""
],
[
"Unkefer",
"Clifford J.",
""
],
[
"Wall",
"Michael E.",
""
]
] | We investigate the ability of algorithms developed for reverse engineering of transcriptional regulatory networks to reconstruct metabolic networks from high-throughput metabolite profiling data. For this, we generate synthetic metabolic profiles for benchmarking purposes based on a well-established model for red blood... |
1312.4576 | Vipul Periwal | Zeina Shreif, Deborah A. Striegel, and Vipul Periwal | The jigsaw puzzle of sequence phenotype inference: Piecing together
Shannon entropy, importance sampling, and Empirical Bayes | 61 pages | null | 10.1016/j.jtbi.2015.06.010 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A nucleotide sequence 35 base pairs long can take
1,180,591,620,717,411,303,424 possible values. An example of systems biology
datasets, protein binding microarrays, contain activity data from about 40000
such sequences. The discrepancy between the number of possible configurations
and the available activities is eno... | [
{
"created": "Mon, 16 Dec 2013 21:55:10 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Jun 2015 12:40:48 GMT",
"version": "v2"
}
] | 2015-06-15 | [
[
"Shreif",
"Zeina",
""
],
[
"Striegel",
"Deborah A.",
""
],
[
"Periwal",
"Vipul",
""
]
] | A nucleotide sequence 35 base pairs long can take 1,180,591,620,717,411,303,424 possible values. An example of systems biology datasets, protein binding microarrays, contain activity data from about 40000 such sequences. The discrepancy between the number of possible configurations and the available activities is enorm... |
1812.11758 | Timothy O'Leary | Dhruva V Raman, Timothy O'Leary | Fundamental bounds on learning performance in neural circuits | null | Proceedings of the National Academy of Sciences May 2019,
201813416 | 10.1073/pnas.1813416116 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How does the size of a neural circuit influence its learning performance?
Intuitively, we expect the learning capacity of a neural circuit to grow with
the number of neurons and synapses. Larger brains tend to be found in species
with higher cognitive function and learning ability. Similarly, adding
connections and u... | [
{
"created": "Mon, 31 Dec 2018 10:59:17 GMT",
"version": "v1"
}
] | 2019-05-09 | [
[
"Raman",
"Dhruva V",
""
],
[
"O'Leary",
"Timothy",
""
]
] | How does the size of a neural circuit influence its learning performance? Intuitively, we expect the learning capacity of a neural circuit to grow with the number of neurons and synapses. Larger brains tend to be found in species with higher cognitive function and learning ability. Similarly, adding connections and uni... |
2303.04285 | Sergey Shuvaev | Sergey Shuvaev, Evgeny Amelchenko, Dmitry Smagin, Natalia
Kudryavtseva, Grigori Enikolopov, Alexei Koulakov | A normative theory of social conflict | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Social hierarchy in animal groups carries a crucial adaptive function by
reducing conflict and injury while protecting valuable group resources. Social
hierarchy is dynamic and can be altered by social conflict, agonistic
interactions, and aggression. Understanding social conflict and aggressive
behavior is of profou... | [
{
"created": "Tue, 7 Mar 2023 23:16:44 GMT",
"version": "v1"
},
{
"created": "Wed, 26 Apr 2023 17:23:21 GMT",
"version": "v2"
}
] | 2023-04-27 | [
[
"Shuvaev",
"Sergey",
""
],
[
"Amelchenko",
"Evgeny",
""
],
[
"Smagin",
"Dmitry",
""
],
[
"Kudryavtseva",
"Natalia",
""
],
[
"Enikolopov",
"Grigori",
""
],
[
"Koulakov",
"Alexei",
""
]
] | Social hierarchy in animal groups carries a crucial adaptive function by reducing conflict and injury while protecting valuable group resources. Social hierarchy is dynamic and can be altered by social conflict, agonistic interactions, and aggression. Understanding social conflict and aggressive behavior is of profound... |
2106.04123 | Giorgio Papitto | Giorgio Papitto, Luisa Lugli, Anna M. Borghi, Antonello Pellicano and
Ferdinand Binkofski | Embodied negation and levels of concreteness: A TMS Study on German and
Italian language processing | 30 pages, 3 figures, 1 table, research paper | null | 10.1016/j.brainres.2021.147523 | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | According to the embodied cognition perspective, linguistic negation may
block the motor simulations induced by language processing. Transcranial
magnetic stimulation (TMS) was applied to the left primary motor cortex (hand
area) of monolingual Italian and German healthy participants during a rapid
serial visual pres... | [
{
"created": "Tue, 8 Jun 2021 06:19:47 GMT",
"version": "v1"
}
] | 2021-06-09 | [
[
"Papitto",
"Giorgio",
""
],
[
"Lugli",
"Luisa",
""
],
[
"Borghi",
"Anna M.",
""
],
[
"Pellicano",
"Antonello",
""
],
[
"Binkofski",
"Ferdinand",
""
]
] | According to the embodied cognition perspective, linguistic negation may block the motor simulations induced by language processing. Transcranial magnetic stimulation (TMS) was applied to the left primary motor cortex (hand area) of monolingual Italian and German healthy participants during a rapid serial visual presen... |
1503.04978 | Daniel Rabosky | Daniel L. Rabosky | No substitute for real data: phylogenies from birth-death polytomy
resolvers should not be used for many downstream comparative analyses | null | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The statistical estimation of phylogenies is always associated with
uncertainty, and accommodating this uncertainty is an important component of
modern phylogenetic comparative analysis. The birth-death polytomy resolver is
a method of accounting for phylogenetic uncertainty that places missing
(unsampled) taxa onto ... | [
{
"created": "Tue, 17 Mar 2015 10:23:01 GMT",
"version": "v1"
}
] | 2015-03-18 | [
[
"Rabosky",
"Daniel L.",
""
]
] | The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of accounting for phylogenetic uncertainty that places missing (unsampled) taxa onto ph... |
1508.05717 | Ovidiu Radulescu | Satya Swarup Samal, Dima Grigoriev, Holger Fr\"ohlich and Ovidiu
Radulescu | Analysis of Reaction Network Systems Using Tropical Geometry | Proceedings Computer Algebra in Scientific Computing CASC 2015 | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We discuss a novel analysis method for reaction network systems with
polynomial or rational rate functions. This method is based on computing
tropical equilibrations defined by the equality of at least two dominant
monomials of opposite signs in the differential equations of each dynamic
variable. In algebraic geomet... | [
{
"created": "Mon, 24 Aug 2015 08:24:56 GMT",
"version": "v1"
}
] | 2015-08-25 | [
[
"Samal",
"Satya Swarup",
""
],
[
"Grigoriev",
"Dima",
""
],
[
"Fröhlich",
"Holger",
""
],
[
"Radulescu",
"Ovidiu",
""
]
] | We discuss a novel analysis method for reaction network systems with polynomial or rational rate functions. This method is based on computing tropical equilibrations defined by the equality of at least two dominant monomials of opposite signs in the differential equations of each dynamic variable. In algebraic geometry... |
1903.07885 | Jannes Jegminat | Jannes Jegminat, Maya Jastrzebowska, Matt Pachai, Michael Herzog,
Jean-Pascal Pfister | Bayesian regression explains how human participants handle parameter
uncertainty | null | null | 10.1371/journal.pcbi.1007886 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human brain copes with sensory uncertainty in accordance with Bayes'
rule. However, it is unknown how the brain makes predictions in the presence of
parameter uncertainty. Here, we tested whether and how humans take parameter
uncertainty into account in a regression task. Participants extrapolated a
parabola from... | [
{
"created": "Tue, 19 Mar 2019 09:01:46 GMT",
"version": "v1"
}
] | 2020-07-01 | [
[
"Jegminat",
"Jannes",
""
],
[
"Jastrzebowska",
"Maya",
""
],
[
"Pachai",
"Matt",
""
],
[
"Herzog",
"Michael",
""
],
[
"Pfister",
"Jean-Pascal",
""
]
] | The human brain copes with sensory uncertainty in accordance with Bayes' rule. However, it is unknown how the brain makes predictions in the presence of parameter uncertainty. Here, we tested whether and how humans take parameter uncertainty into account in a regression task. Participants extrapolated a parabola from a... |
1701.04315 | Shlomi Reuveni | Tal Robin, Shlomi Reuveni and Michael Urbakh | Single-molecule theory of enzymatic inhibition predicts the emergence of
inhibitor-activator duality | null | Nature communications, 9(1), pp.1-9, 2018 | 10.1038/s41467-018-02995-6 | null | q-bio.QM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The classical theory of enzymatic inhibition aims to quantitatively describe
the effect of certain molecules -- called inhibitors -- on the progression of
enzymatic reactions, but growing signs indicate that it must be revised to keep
pace with the single-molecule revolution that is sweeping through the sciences.
Her... | [
{
"created": "Wed, 14 Dec 2016 14:51:42 GMT",
"version": "v1"
},
{
"created": "Sat, 21 Oct 2017 13:52:56 GMT",
"version": "v2"
}
] | 2020-10-27 | [
[
"Robin",
"Tal",
""
],
[
"Reuveni",
"Shlomi",
""
],
[
"Urbakh",
"Michael",
""
]
] | The classical theory of enzymatic inhibition aims to quantitatively describe the effect of certain molecules -- called inhibitors -- on the progression of enzymatic reactions, but growing signs indicate that it must be revised to keep pace with the single-molecule revolution that is sweeping through the sciences. Here,... |
1703.10307 | Takashi Okada | Takashi Okada and Atsushi Mochizuki | Sensitivity and Network Topology in Chemical Reaction Systems | 14 pages, 13 figures | Phys. Rev. E 96, 022322 (2017) | 10.1103/PhysRevE.96.022322 | null | q-bio.MN physics.bio-ph q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In living cells, biochemical reactions are catalyzed by specific enzymes and
connect to one another by sharing substrates and products, forming complex
networks. In our previous studies, we established a framework determining the
responses to enzyme perturbations only from network topology, and then proved a
theorem,... | [
{
"created": "Thu, 30 Mar 2017 04:13:20 GMT",
"version": "v1"
},
{
"created": "Tue, 5 Sep 2017 01:37:00 GMT",
"version": "v2"
}
] | 2017-09-06 | [
[
"Okada",
"Takashi",
""
],
[
"Mochizuki",
"Atsushi",
""
]
] | In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses to enzyme perturbations only from network topology, and then proved a theorem, c... |
2102.09409 | Alberto P\'erez-Cervera | Gregory Dumont, Alberto P\'erez-Cervera, Boris Gutkin | Adjoint Method for Macroscopic Phase-Resetting Curves of Generic Spiking
Neural Networks | null | null | 10.1371/journal.pcbi.1010363 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Brain rhythms emerge as a result of synchronization among interconnected
spiking neurons. Key properties of such rhythms can be gleaned from the
phase-resetting curve (PRC). Inferring the macroscopic PRC and developing a
systematic phase reduction theory for emerging rhythms remains an outstanding
theoretical challen... | [
{
"created": "Thu, 18 Feb 2021 14:53:42 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Feb 2021 15:18:46 GMT",
"version": "v2"
}
] | 2022-10-12 | [
[
"Dumont",
"Gregory",
""
],
[
"Pérez-Cervera",
"Alberto",
""
],
[
"Gutkin",
"Boris",
""
]
] | Brain rhythms emerge as a result of synchronization among interconnected spiking neurons. Key properties of such rhythms can be gleaned from the phase-resetting curve (PRC). Inferring the macroscopic PRC and developing a systematic phase reduction theory for emerging rhythms remains an outstanding theoretical challenge... |
1808.09052 | Marco Ramaioli | Marco Marconati, Felipe Lopez, Catherine Tuleu, Mine Orlu, Marco
Ramaioli | In vitro and sensory tests to design easy-to-swallow multi-particulate
formulations | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Flexible dosing and ease of swallowing are key factors when designing oral
drug delivery systems for paediatric and geriatric populations.
Multi-particulate oral dosage forms can offer significant benefits over
conventional capsules and tablets. This study proposes the use of an in vitro
model to quantitatively inves... | [
{
"created": "Mon, 27 Aug 2018 22:34:55 GMT",
"version": "v1"
}
] | 2018-08-29 | [
[
"Marconati",
"Marco",
""
],
[
"Lopez",
"Felipe",
""
],
[
"Tuleu",
"Catherine",
""
],
[
"Orlu",
"Mine",
""
],
[
"Ramaioli",
"Marco",
""
]
] | Flexible dosing and ease of swallowing are key factors when designing oral drug delivery systems for paediatric and geriatric populations. Multi-particulate oral dosage forms can offer significant benefits over conventional capsules and tablets. This study proposes the use of an in vitro model to quantitatively investi... |
2111.04943 | Mi Jin Lee | Mi Jin Lee and Deok-Sun Lee | Heterogeneous popularity of metabolic reactions from evolution | Main: 5 pages, 4 figures, Supplemental Material: 4 pages, 6 figures | Physical Review Letters 132, 018401 (2024) | 10.1103/PhysRevLett.132.018401 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The composition of cellular metabolism is different across species. Empirical
data reveal that bacterial species contain similar numbers of metabolic
reactions but that the cross-species popularity of reactions is so heterogenous
that some reactions are found in all the species while others are in just few
species, c... | [
{
"created": "Tue, 9 Nov 2021 03:52:29 GMT",
"version": "v1"
},
{
"created": "Tue, 24 Oct 2023 14:36:26 GMT",
"version": "v2"
},
{
"created": "Fri, 5 Jan 2024 05:10:56 GMT",
"version": "v3"
}
] | 2024-01-08 | [
[
"Lee",
"Mi Jin",
""
],
[
"Lee",
"Deok-Sun",
""
]
] | The composition of cellular metabolism is different across species. Empirical data reveal that bacterial species contain similar numbers of metabolic reactions but that the cross-species popularity of reactions is so heterogenous that some reactions are found in all the species while others are in just few species, cha... |
1805.07098 | Yutaka Hori | Yuta Sakurai, Yutaka Hori | Bounding Transient Moments of Stochastic Chemical Reactions | null | IEEE Control Systems Letters, vol. 3, No. 2, pp. 290-295, 2019 | 10.1109/LCSYS.2018.2869639 | null | q-bio.QM cs.SY q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The predictive ability of stochastic chemical reactions is currently limited
by the lack of closed form solutions to the governing chemical master equation.
To overcome this limitation, this paper proposes a computational method capable
of predicting mathematically rigorous upper and lower bounds of transient
moments... | [
{
"created": "Fri, 18 May 2018 08:47:42 GMT",
"version": "v1"
},
{
"created": "Tue, 22 May 2018 15:46:25 GMT",
"version": "v2"
},
{
"created": "Mon, 6 Aug 2018 05:13:29 GMT",
"version": "v3"
},
{
"created": "Sun, 6 Jan 2019 01:47:13 GMT",
"version": "v4"
}
] | 2019-01-08 | [
[
"Sakurai",
"Yuta",
""
],
[
"Hori",
"Yutaka",
""
]
] | The predictive ability of stochastic chemical reactions is currently limited by the lack of closed form solutions to the governing chemical master equation. To overcome this limitation, this paper proposes a computational method capable of predicting mathematically rigorous upper and lower bounds of transient moments f... |
2006.07879 | Moeez Subhani | Moeez M. Subhani, Ashiq Anjum | Multiclass Disease Predictions Based on Integrated Clinical and Genomics
Datasets | null | In Poceedings of The Eleventh International Conference on
Bioinformatics, Biocomputational Systems and Biotechnologies. Athens. 2019.
IARA: Wilmington, pp. 20-27 | null | null | q-bio.GN cs.AI cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Clinical predictions using clinical data by computational methods are common
in bioinformatics. However, clinical predictions using information from
genomics datasets as well is not a frequently observed phenomenon in research.
Precision medicine research requires information from all available datasets to
provide in... | [
{
"created": "Sun, 14 Jun 2020 12:23:49 GMT",
"version": "v1"
}
] | 2021-06-25 | [
[
"Subhani",
"Moeez M.",
""
],
[
"Anjum",
"Ashiq",
""
]
] | Clinical predictions using clinical data by computational methods are common in bioinformatics. However, clinical predictions using information from genomics datasets as well is not a frequently observed phenomenon in research. Precision medicine research requires information from all available datasets to provide inte... |
2010.03048 | Arbel Harpak | Arbel Harpak and Molly Przeworski | The evolution of group differences in changing environments | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The selection pressures that have shaped the evolution of complex traits in
humans remain largely unknown, and in some contexts highly contentious, perhaps
above all where they concern mean trait differences among groups. To date, the
discussion has focused on whether such group differences have any genetic
basis, an... | [
{
"created": "Tue, 6 Oct 2020 21:40:21 GMT",
"version": "v1"
}
] | 2020-10-08 | [
[
"Harpak",
"Arbel",
""
],
[
"Przeworski",
"Molly",
""
]
] | The selection pressures that have shaped the evolution of complex traits in humans remain largely unknown, and in some contexts highly contentious, perhaps above all where they concern mean trait differences among groups. To date, the discussion has focused on whether such group differences have any genetic basis, and ... |
1102.4904 | Bhaskar DasGupta | Bhaskar DasGupta and Paola Vera-Licona and Eduardo Sontag | Reverse Engineering of Molecular Networks from a Common Combinatorial
Approach | 15 pages; in Algorithms in Computational Molecular Biology:
Techniques, Approaches and Applications, M. Elloumi and A. Zomaya (editors),
John Wiley & Sons, Inc., January 2011 | null | null | null | q-bio.MN cs.CE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The understanding of molecular cell biology requires insight into the
structure and dynamics of networks that are made up of thousands of interacting
molecules of DNA, RNA, proteins, metabolites, and other components. One of the
central goals of systems biology is the unraveling of the as yet poorly
characterized com... | [
{
"created": "Thu, 24 Feb 2011 04:56:37 GMT",
"version": "v1"
}
] | 2011-02-25 | [
[
"DasGupta",
"Bhaskar",
""
],
[
"Vera-Licona",
"Paola",
""
],
[
"Sontag",
"Eduardo",
""
]
] | The understanding of molecular cell biology requires insight into the structure and dynamics of networks that are made up of thousands of interacting molecules of DNA, RNA, proteins, metabolites, and other components. One of the central goals of systems biology is the unraveling of the as yet poorly characterized compl... |
2107.06281 | Islem Rekik | Islem Mhiri and Ahmed Nebli and Mohamed Ali Mahjoub and Islem Rekik | Non-isomorphic Inter-modality Graph Alignment and Synthesis for Holistic
Brain Mapping | null | null | null | null | q-bio.NC cs.CV cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Brain graph synthesis marked a new era for predicting a target brain graph
from a source one without incurring the high acquisition cost and processing
time of neuroimaging data. However, existing multi-modal graph synthesis
frameworks have several limitations. First, they mainly focus on generating
graphs from the s... | [
{
"created": "Wed, 30 Jun 2021 08:59:55 GMT",
"version": "v1"
}
] | 2021-07-15 | [
[
"Mhiri",
"Islem",
""
],
[
"Nebli",
"Ahmed",
""
],
[
"Mahjoub",
"Mohamed Ali",
""
],
[
"Rekik",
"Islem",
""
]
] | Brain graph synthesis marked a new era for predicting a target brain graph from a source one without incurring the high acquisition cost and processing time of neuroimaging data. However, existing multi-modal graph synthesis frameworks have several limitations. First, they mainly focus on generating graphs from the sam... |
1902.06250 | Anna M. Hagenston Hertle | Anna M. Hagenston, Sara Ben Ayed, Hilmar Bading | Afferent Fiber Activity-Induced Cytoplasmic Calcium Signaling in
Parvalbumin-Positive Inhibitory Interneurons of the Spinal Cord Dorsal Horn | 15 pages including 1 figure | null | null | null | q-bio.NC q-bio.TO | http://creativecommons.org/publicdomain/zero/1.0/ | Neuronal calcium (Ca2+) signaling represents a molecular trigger for diverse
central nervous system adaptations and maladaptions. The altered function of
dorsal spinal inhibitory interneurons is strongly implicated in the mechanisms
underlying central sensitization in chronic pain. Surprisingly little is known,
howev... | [
{
"created": "Sun, 17 Feb 2019 12:32:50 GMT",
"version": "v1"
}
] | 2019-02-19 | [
[
"Hagenston",
"Anna M.",
""
],
[
"Ayed",
"Sara Ben",
""
],
[
"Bading",
"Hilmar",
""
]
] | Neuronal calcium (Ca2+) signaling represents a molecular trigger for diverse central nervous system adaptations and maladaptions. The altered function of dorsal spinal inhibitory interneurons is strongly implicated in the mechanisms underlying central sensitization in chronic pain. Surprisingly little is known, however... |
2004.06029 | Harsh Vashistha | Harsh Vashistha, Maryam Kohram and Hanna Salman | Non-genetic inheritance restraint of cell-to-cell variation | null | null | 10.7554/eLife.64779 | null | q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | Heterogeneity in physical and functional characteristics of cells (e.g. size,
cycle time, growth rate, protein concentration) proliferates within an isogenic
population due to stochasticity in intracellular biochemical processes and in
the distribution of resources during divisions. Conversely, it is limited in
part ... | [
{
"created": "Mon, 13 Apr 2020 16:01:08 GMT",
"version": "v1"
},
{
"created": "Thu, 6 Aug 2020 19:18:42 GMT",
"version": "v2"
},
{
"created": "Wed, 20 Jan 2021 15:21:04 GMT",
"version": "v3"
}
] | 2021-02-02 | [
[
"Vashistha",
"Harsh",
""
],
[
"Kohram",
"Maryam",
""
],
[
"Salman",
"Hanna",
""
]
] | Heterogeneity in physical and functional characteristics of cells (e.g. size, cycle time, growth rate, protein concentration) proliferates within an isogenic population due to stochasticity in intracellular biochemical processes and in the distribution of resources during divisions. Conversely, it is limited in part by... |
1007.0942 | Pascal Ferraro | Julien Allali (LaBRI), C\'edric Chauve, Pascal Ferraro (LaBRI, PIMS),
Anne-Laure Gaillard (LaBRI) | Efficient chaining of seeds in ordered trees | null | 21st International Workshop on Combinatorial Algorithms, London :
United Kingdom (2010) | 10.1007/978-3-642-19222-7_27 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider here the problem of chaining seeds in ordered trees. Seeds are
mappings between two trees Q and T and a chain is a subset of non overlapping
seeds that is consistent with respect to postfix order and ancestrality. This
problem is a natural extension of a similar problem for sequences, and has
applications... | [
{
"created": "Tue, 6 Jul 2010 16:31:11 GMT",
"version": "v1"
}
] | 2015-05-19 | [
[
"Allali",
"Julien",
"",
"LaBRI"
],
[
"Chauve",
"Cédric",
"",
"LaBRI, PIMS"
],
[
"Ferraro",
"Pascal",
"",
"LaBRI, PIMS"
],
[
"Gaillard",
"Anne-Laure",
"",
"LaBRI"
]
] | We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications i... |
q-bio/0511008 | Dieter W. Heermann | S. Ritter, J. Odenheimer, D. W. Heermann, F. Bantignies, C. Grimaud,
G. Cavalli | Modelling and simulation of polycomb-dependent chromosomal interactions
in drosophila | null | null | null | null | q-bio.SC | null | The conditions of the chromosomes inside the nucleus in the Rabl
configuration have been modelled as self-avoiding polymer chains under
restraining conditions. To ensure that the chromosomes remain stretched out and
lined up, we fixed their end points to two opposing walls. The numbers of
segments $N$, the distances ... | [
{
"created": "Tue, 8 Nov 2005 22:22:06 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Ritter",
"S.",
""
],
[
"Odenheimer",
"J.",
""
],
[
"Heermann",
"D. W.",
""
],
[
"Bantignies",
"F.",
""
],
[
"Grimaud",
"C.",
""
],
[
"Cavalli",
"G.",
""
]
] | The conditions of the chromosomes inside the nucleus in the Rabl configuration have been modelled as self-avoiding polymer chains under restraining conditions. To ensure that the chromosomes remain stretched out and lined up, we fixed their end points to two opposing walls. The numbers of segments $N$, the distances $d... |
0707.4431 | Mathilde Himgi | Emilie Carr\'e (IMNSSA), Emmanuel Cantais, Olivier Darbin, Jean-Pierre
Terrier, Michel Lonjon, Bruno Palmier, Jean-Jacques Risso | Technical aspects of an impact acceleration traumatic brain injury rat
model with potential suitability for both microdialysis and PtiO2 monitoring | null | Journal of Neuroscience Methods 140, 1-2 (2004) 23-8 | 10.1016/j.jneumeth.2004.04.037 | null | q-bio.NC | null | This report describes technical adaptations of a traumatic brain injury (TBI)
model-largely inspired by Marmarou-in order to monitor microdialysis data and
PtiO2 (brain tissue oxygen) before, during and after injury. We particularly
focalize on our model requirements which allows us to re-create some drastic
patholog... | [
{
"created": "Mon, 30 Jul 2007 15:23:50 GMT",
"version": "v1"
}
] | 2007-07-31 | [
[
"Carré",
"Emilie",
"",
"IMNSSA"
],
[
"Cantais",
"Emmanuel",
""
],
[
"Darbin",
"Olivier",
""
],
[
"Terrier",
"Jean-Pierre",
""
],
[
"Lonjon",
"Michel",
""
],
[
"Palmier",
"Bruno",
""
],
[
"Risso",
"Jean-Jacq... | This report describes technical adaptations of a traumatic brain injury (TBI) model-largely inspired by Marmarou-in order to monitor microdialysis data and PtiO2 (brain tissue oxygen) before, during and after injury. We particularly focalize on our model requirements which allows us to re-create some drastic pathologic... |
1807.02155 | Konstantinos Michmizos | Guangzhi Tang, Konstantinos P. Michmizos | Gridbot: An autonomous robot controlled by a Spiking Neural Network
mimicking the brain's navigational system | 8 pages, 3 Figures, International Conference on Neuromorphic Systems
(ICONS 2018) | null | 10.1145/3229884.3229888 | null | q-bio.NC cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is true that the "best" neural network is not necessarily the one with the
most "brain-like" behavior. Understanding biological intelligence, however, is
a fundamental goal for several distinct disciplines. Translating our
understanding of intelligence to machines is a fundamental problem in robotics.
Propelled by... | [
{
"created": "Thu, 5 Jul 2018 19:09:45 GMT",
"version": "v1"
}
] | 2018-07-09 | [
[
"Tang",
"Guangzhi",
""
],
[
"Michmizos",
"Konstantinos P.",
""
]
] | It is true that the "best" neural network is not necessarily the one with the most "brain-like" behavior. Understanding biological intelligence, however, is a fundamental goal for several distinct disciplines. Translating our understanding of intelligence to machines is a fundamental problem in robotics. Propelled by n... |
2403.19011 | Alan Kaplan | Alan D. Kaplan, Priyadip Ray, John D. Greene, Vincent X. Liu | Sequential Inference of Hospitalization Electronic Health Records Using
Probabilistic Models | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | In the dynamic hospital setting, decision support can be a valuable tool for
improving patient outcomes. Data-driven inference of future outcomes is
challenging in this dynamic setting, where long sequences such as laboratory
tests and medications are updated frequently. This is due in part to
heterogeneity of data t... | [
{
"created": "Wed, 27 Mar 2024 21:06:26 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Apr 2024 15:06:26 GMT",
"version": "v2"
}
] | 2024-04-25 | [
[
"Kaplan",
"Alan D.",
""
],
[
"Ray",
"Priyadip",
""
],
[
"Greene",
"John D.",
""
],
[
"Liu",
"Vincent X.",
""
]
] | In the dynamic hospital setting, decision support can be a valuable tool for improving patient outcomes. Data-driven inference of future outcomes is challenging in this dynamic setting, where long sequences such as laboratory tests and medications are updated frequently. This is due in part to heterogeneity of data typ... |
1805.06067 | Arlin Stoltzfus | Arlin Stoltzfus | Understanding bias in the introduction of variation as an evolutionary
cause | Contribution to the 2017 EES workshop on Cause and Process in
Evolution, 11 to 14 May 2017 at the Konrad Lorenz Institute, Klosterneuberg,
Austria
(http://extendedevolutionarysynthesis.com/cause-and-process-in-evolution/).
28 pages, 7 figures | null | null | null | q-bio.PE | http://creativecommons.org/publicdomain/zero/1.0/ | Our understanding of evolution is shaped strongly by how we conceive of its
fundamental causes. In the original Modern Synthesis, evolution was defined as
a process of shifting the frequencies of available alleles at many loci
affecting a trait under selection. Events of mutation that introduce novelty
were not consi... | [
{
"created": "Tue, 15 May 2018 23:27:23 GMT",
"version": "v1"
}
] | 2018-05-17 | [
[
"Stoltzfus",
"Arlin",
""
]
] | Our understanding of evolution is shaped strongly by how we conceive of its fundamental causes. In the original Modern Synthesis, evolution was defined as a process of shifting the frequencies of available alleles at many loci affecting a trait under selection. Events of mutation that introduce novelty were not conside... |
2302.13897 | Maurice HT Ling | Clarence FG Castillo, Zhu En Chay, Maurice HT Ling | Resistance Maintained in Digital Organisms despite
Guanine/Cytosine-Based Fitness Cost and Extended De-Selection: Implications
to Microbial Antibiotics Resistance | null | MOJ Proteomics & Bioinformatics 2(2): 00039 (2015) | null | null | q-bio.PE cs.NE | http://creativecommons.org/licenses/by-sa/4.0/ | Antibiotics resistance has caused much complication in the treatment of
diseases, where the pathogen is no longer susceptible to specific antibiotics
and the use of such antibiotics are no longer effective for treatment. A recent
study that utilizes digital organisms suggests that complete elimination of
specific ant... | [
{
"created": "Sun, 19 Feb 2023 11:40:36 GMT",
"version": "v1"
}
] | 2023-02-28 | [
[
"Castillo",
"Clarence FG",
""
],
[
"Chay",
"Zhu En",
""
],
[
"Ling",
"Maurice HT",
""
]
] | Antibiotics resistance has caused much complication in the treatment of diseases, where the pathogen is no longer susceptible to specific antibiotics and the use of such antibiotics are no longer effective for treatment. A recent study that utilizes digital organisms suggests that complete elimination of specific antib... |
0906.2470 | Francesc Rossell\'o | Arnau Mir, Francesc Rossello | The mean value of the squared path-difference distance for rooted
phylogenetic trees | 16 pages | null | null | null | q-bio.PE cs.DM math.CA q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/3.0/ | The path-difference metric is one of the oldest distances for the comparison
of fully resolved phylogenetic trees, but its statistical properties are still
quite unknown. In this paper we compute the mean value of the square of the
path-difference metric between two fully resolved rooted phylogenetic trees
with $n$ l... | [
{
"created": "Sat, 13 Jun 2009 11:33:28 GMT",
"version": "v1"
}
] | 2009-06-16 | [
[
"Mir",
"Arnau",
""
],
[
"Rossello",
"Francesc",
""
]
] | The path-difference metric is one of the oldest distances for the comparison of fully resolved phylogenetic trees, but its statistical properties are still quite unknown. In this paper we compute the mean value of the square of the path-difference metric between two fully resolved rooted phylogenetic trees with $n$ lea... |
2407.11453 | Coralie Fritsch | Athanase Benetos (DCAC), Coralie Fritsch (SIMBA, IECL), Emma Horton,
Lionel Lenotre (IRIMAS, ARCHIMEDE, PASTA), Simon Toupance (DCAC), Denis
Villemonais (SIMBA, IECL, IUF) | Stochastic branching models for the telomeres dynamics in a model
including telomerase activity | null | null | null | null | q-bio.CB math.PR q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Telomeres are repetitive sequences of nucleotides at the end of chromosomes,
whose evolution over time is intrinsically related to biological ageing. In
most cells, with each cell division, telomeres shorten due to the so-called end
replication problem, which can lead to replicative senescence and a variety of
age-re... | [
{
"created": "Tue, 16 Jul 2024 07:40:07 GMT",
"version": "v1"
}
] | 2024-07-17 | [
[
"Benetos",
"Athanase",
"",
"DCAC"
],
[
"Fritsch",
"Coralie",
"",
"SIMBA, IECL"
],
[
"Horton",
"Emma",
"",
"IRIMAS, ARCHIMEDE, PASTA"
],
[
"Lenotre",
"Lionel",
"",
"IRIMAS, ARCHIMEDE, PASTA"
],
[
"Toupance",
"Simon",
"",
... | Telomeres are repetitive sequences of nucleotides at the end of chromosomes, whose evolution over time is intrinsically related to biological ageing. In most cells, with each cell division, telomeres shorten due to the so-called end replication problem, which can lead to replicative senescence and a variety of age-rela... |
2207.13918 | Thomas Slawig | Markus Pfeil, Thomas Slawig | Adaptive Time Step Algorithms for the Simulation of marine Ecosystem
Models using the Transport Matrix Method Implementation Metos3D | null | null | null | null | q-bio.PE physics.ao-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The reduction of the computational effort is desirable for the simulation of
marine ecosystem models. Using a marine ecosystem model, the assessment and the
validation of annual periodic solutions (i.e., steady annual cycles) against
observational data are crucial to identify biogeochemical processes, which, for
exam... | [
{
"created": "Thu, 28 Jul 2022 07:18:43 GMT",
"version": "v1"
}
] | 2022-07-29 | [
[
"Pfeil",
"Markus",
""
],
[
"Slawig",
"Thomas",
""
]
] | The reduction of the computational effort is desirable for the simulation of marine ecosystem models. Using a marine ecosystem model, the assessment and the validation of annual periodic solutions (i.e., steady annual cycles) against observational data are crucial to identify biogeochemical processes, which, for exampl... |
q-bio/0408012 | Eduardo D. Sontag | Eduardo D. Sontag and Madalena Chaves | Computation of amplification for systems arising from cellular signaling
pathways | See http://www.math.rutgers.edu/~sontag/ for related papers | null | null | null | q-bio.QM | null | A commonly employed measure of the signal amplification properties of an
input/output system is its induced L2 norm, sometimes also known as "H
infinity" gain. In general, however, it is extremely difficult to compute the
numerical value for this norm, or even to check that it is finite, unless the
system being studi... | [
{
"created": "Mon, 16 Aug 2004 13:39:45 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Sontag",
"Eduardo D.",
""
],
[
"Chaves",
"Madalena",
""
]
] | A commonly employed measure of the signal amplification properties of an input/output system is its induced L2 norm, sometimes also known as "H infinity" gain. In general, however, it is extremely difficult to compute the numerical value for this norm, or even to check that it is finite, unless the system being studied... |
0705.4084 | Petter Holme | Petter Holme, Mikael Huss | Comment on "Regularizing capacity of metabolic networks" | null | Phys. Rev. E 77, 023901 (2008) | 10.1103/PhysRevE.77.023901 | null | q-bio.MN | null | In a recent paper, Marr, Muller-Linow and Hutt [Phys. Rev. E 75, 041917
(2007)] investigate an artificial dynamic system on metabolic networks. They
find a less complex time evolution of this dynamic system in real networks,
compared to networks of reference models. The authors argue that this suggests
that metabolic... | [
{
"created": "Mon, 28 May 2007 18:50:56 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Feb 2008 13:49:46 GMT",
"version": "v2"
}
] | 2008-02-06 | [
[
"Holme",
"Petter",
""
],
[
"Huss",
"Mikael",
""
]
] | In a recent paper, Marr, Muller-Linow and Hutt [Phys. Rev. E 75, 041917 (2007)] investigate an artificial dynamic system on metabolic networks. They find a less complex time evolution of this dynamic system in real networks, compared to networks of reference models. The authors argue that this suggests that metabolic n... |
1509.06075 | Claudia Solis-Lemus | Claudia Sol\'is-Lemus and C\'ecile An\'e | Inferring phylogenetic networks with maximum pseudolikelihood under
incomplete lineage sorting | null | null | null | null | q-bio.PE math.ST stat.AP stat.CO stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic networks are necessary to represent the tree of life expanded by
edges to represent events such as horizontal gene transfers, hybridizations or
gene flow. Not all species follow the paradigm of vertical inheritance of their
genetic material. While a great deal of research has flourished into the
inferenc... | [
{
"created": "Sun, 20 Sep 2015 23:41:03 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Jan 2016 20:48:47 GMT",
"version": "v2"
},
{
"created": "Fri, 12 Feb 2016 19:23:35 GMT",
"version": "v3"
}
] | 2016-02-15 | [
[
"Solís-Lemus",
"Claudia",
""
],
[
"Ané",
"Cécile",
""
]
] | Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their genetic material. While a great deal of research has flourished into the inference ... |
1410.0844 | Peter Butler | Hari S. Muddana, Samudra Sengupta, Ayusman Sen, Peter J. Butler | Enhanced brightness and photostability of cyanine dyes by supramolecular
containment | 20 pages, 5 figures | null | null | null | q-bio.BM physics.chem-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ultrasensitive detection and real-time monitoring of biological processes can
benefit significantly from the improved brightness and photostability of the
popular organic dyes such as cyanines. Here, using a model cyanine dye, Cy3, we
demonstrate that brightness and photostability of the dye is significantly
altered ... | [
{
"created": "Thu, 2 Oct 2014 18:56:29 GMT",
"version": "v1"
}
] | 2014-10-06 | [
[
"Muddana",
"Hari S.",
""
],
[
"Sengupta",
"Samudra",
""
],
[
"Sen",
"Ayusman",
""
],
[
"Butler",
"Peter J.",
""
]
] | Ultrasensitive detection and real-time monitoring of biological processes can benefit significantly from the improved brightness and photostability of the popular organic dyes such as cyanines. Here, using a model cyanine dye, Cy3, we demonstrate that brightness and photostability of the dye is significantly altered wh... |
1609.01569 | Liu Hong | Liu Hong, Chiu Fan Lee, Ya Jing Huang | Statistical Mechanics and Kinetics of Amyloid Fibrillation | 68 pages, 18 figures, 201 references | In Biophysics and Biochemistry of Protein Aggregation, edited by
J.-M. Yuan and H.-X. Zhou (World Scienti?c, 2017), Chapter 4, pp. 113-186 | 10.1142/9789813202382_0004 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Amyloid fibrillation is a protein self-assembly phenomenon that is intimately
related to well-known human neurodegenerative diseases. During the past few
decades, striking advances have been achieved in our understanding of the
physical origin of this phenomenon and they constitute the contents of this
review. Starti... | [
{
"created": "Tue, 6 Sep 2016 14:22:37 GMT",
"version": "v1"
}
] | 2017-09-06 | [
[
"Hong",
"Liu",
""
],
[
"Lee",
"Chiu Fan",
""
],
[
"Huang",
"Ya Jing",
""
]
] | Amyloid fibrillation is a protein self-assembly phenomenon that is intimately related to well-known human neurodegenerative diseases. During the past few decades, striking advances have been achieved in our understanding of the physical origin of this phenomenon and they constitute the contents of this review. Starting... |
2405.08391 | Laurent Goffart | Laurent Goffart (CGGG) | Cerebralization of mathematical quantities and physical features in
neural science: a critical evaluation | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | At the turn of the 20th century, Henri Poincar{\'e} explained that geometry
is a convention and that the properties of space and time are the properties of
our measuring instruments. Intriguingly, numerous contemporary authors argue
that space, time and even number are ''encoded'' within the brain, as a
consequence o... | [
{
"created": "Tue, 14 May 2024 07:40:57 GMT",
"version": "v1"
},
{
"created": "Thu, 16 May 2024 09:08:23 GMT",
"version": "v2"
}
] | 2024-05-17 | [
[
"Goffart",
"Laurent",
"",
"CGGG"
]
] | At the turn of the 20th century, Henri Poincar{\'e} explained that geometry is a convention and that the properties of space and time are the properties of our measuring instruments. Intriguingly, numerous contemporary authors argue that space, time and even number are ''encoded'' within the brain, as a consequence of ... |
0704.2554 | Yannick Brohard | Brigitte Meyer-Berthaud (AMAP), Anne-Laure Decombeix (AMAP) | A tree without leaves | null | Nature 446, 7138 (2006) 861-862 | 10.1038/446861a | A-07-09 | q-bio.PE | null | The puzzle presented by the famous stumps of Gilboa, New York, finds a
solution in the discovery of two fossil specimens that allow the entire
structure of these early trees to be reconstructed.
| [
{
"created": "Thu, 19 Apr 2007 15:11:51 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Meyer-Berthaud",
"Brigitte",
"",
"AMAP"
],
[
"Decombeix",
"Anne-Laure",
"",
"AMAP"
]
] | The puzzle presented by the famous stumps of Gilboa, New York, finds a solution in the discovery of two fossil specimens that allow the entire structure of these early trees to be reconstructed. |
2007.14807 | John Kolinski | John M. Kolinski, Tobias M. Schneider | Superspreading events suggest aerosol transmission of SARS-CoV-2 by
accumulation in enclosed spaces | 6 pages, 4 figures | Phys. Rev. E 103, 033109 (2021) | 10.1103/PhysRevE.103.033109 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Viral transmission pathways have profound implications for public safety; it
is thus imperative to establish a complete understanding of viable infectious
avenues. Mounting evidence suggests SARS-CoV-2 can be transmitted via the air;
however, this has not yet been demonstrated. Here we quantitatively analyze
virion a... | [
{
"created": "Wed, 29 Jul 2020 12:47:05 GMT",
"version": "v1"
},
{
"created": "Mon, 3 Aug 2020 13:11:14 GMT",
"version": "v2"
},
{
"created": "Fri, 4 Dec 2020 11:16:02 GMT",
"version": "v3"
}
] | 2021-03-31 | [
[
"Kolinski",
"John M.",
""
],
[
"Schneider",
"Tobias M.",
""
]
] | Viral transmission pathways have profound implications for public safety; it is thus imperative to establish a complete understanding of viable infectious avenues. Mounting evidence suggests SARS-CoV-2 can be transmitted via the air; however, this has not yet been demonstrated. Here we quantitatively analyze virion acc... |
2308.16397 | Yufei Li | Yufei Li, Lingling Hou, Pengfei Liu | The Impact of Downgrading Protected Areas (PAD) on Biodiversity | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | We quantitatively assess the impacts of Downgrading Protected Areas (PAD) on
biodiversity in the U.S.. Results show that PAD events significantly reduce
biodiversity. The proximity to PAD events decreases the biodiversity by 26.0%
within 50 km compared with records of species further away from the PAD events.
We obse... | [
{
"created": "Thu, 31 Aug 2023 02:05:29 GMT",
"version": "v1"
}
] | 2023-09-01 | [
[
"Li",
"Yufei",
""
],
[
"Hou",
"Lingling",
""
],
[
"Liu",
"Pengfei",
""
]
] | We quantitatively assess the impacts of Downgrading Protected Areas (PAD) on biodiversity in the U.S.. Results show that PAD events significantly reduce biodiversity. The proximity to PAD events decreases the biodiversity by 26.0% within 50 km compared with records of species further away from the PAD events. We observ... |
1911.05259 | Mariko I. Ito | Mariko I. Ito and Takaaki Ohnishi | Weighted Network Analysis of Biologically Relevant Chemical Spaces | 12 pages, 4 figures | null | null | null | q-bio.MN physics.soc-ph q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In cheminformatics, network representations of the space of compounds have
been suggested extensively. Among these, the threshold-network consists of
nodes representing molecules. In this network representation, two molecules are
connected by a link if the Tanimoto coefficient, a similarity measure, between
them exce... | [
{
"created": "Wed, 13 Nov 2019 02:41:31 GMT",
"version": "v1"
}
] | 2019-11-14 | [
[
"Ito",
"Mariko I.",
""
],
[
"Ohnishi",
"Takaaki",
""
]
] | In cheminformatics, network representations of the space of compounds have been suggested extensively. Among these, the threshold-network consists of nodes representing molecules. In this network representation, two molecules are connected by a link if the Tanimoto coefficient, a similarity measure, between them exceed... |
2105.10461 | Jeffrey Krichmar | Jeffrey L. Krichmar | Edelman's Steps Toward a Conscious Artifact | 7 pages, 1 figure, 1 table | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | In 2006, during a meeting of a working group of scientists in La Jolla,
California at The Neurosciences Institute (NSI), Gerald Edelman described a
roadmap towards the creation of a Conscious Artifact. As far as I know, this
roadmap was not published. However, it did shape my thinking and that of many
others in the y... | [
{
"created": "Sat, 22 May 2021 00:13:06 GMT",
"version": "v1"
},
{
"created": "Tue, 25 May 2021 03:18:50 GMT",
"version": "v2"
}
] | 2021-05-26 | [
[
"Krichmar",
"Jeffrey L.",
""
]
] | In 2006, during a meeting of a working group of scientists in La Jolla, California at The Neurosciences Institute (NSI), Gerald Edelman described a roadmap towards the creation of a Conscious Artifact. As far as I know, this roadmap was not published. However, it did shape my thinking and that of many others in the yea... |
2009.09317 | Janani Ravi | Kewalin Samart, Phoebe Tuyishime, Arjun Krishnan, Janani Ravi | Reconciling Multiple Connectivity Scores for Drug Repurposing | KS and PT contributed equally to this work. Corresponding authors:
arjun@msu.edu (AK), janani@msu.edu (JR). Preprint contains 24 pages, 3
figures, 8 tables | null | null | null | q-bio.QM q-bio.GN | http://creativecommons.org/licenses/by-sa/4.0/ | The basis of several recent methods for drug repurposing is the key principle
that an efficacious drug will reverse the disease molecular 'signature' with
minimal side-effects. This principle was defined and popularized by the
influential 'connectivity map' study in 2006 regarding reversal relationships
between disea... | [
{
"created": "Sat, 19 Sep 2020 23:01:37 GMT",
"version": "v1"
},
{
"created": "Tue, 6 Oct 2020 20:57:41 GMT",
"version": "v2"
},
{
"created": "Sun, 28 Feb 2021 20:08:10 GMT",
"version": "v3"
}
] | 2021-03-02 | [
[
"Samart",
"Kewalin",
""
],
[
"Tuyishime",
"Phoebe",
""
],
[
"Krishnan",
"Arjun",
""
],
[
"Ravi",
"Janani",
""
]
] | The basis of several recent methods for drug repurposing is the key principle that an efficacious drug will reverse the disease molecular 'signature' with minimal side-effects. This principle was defined and popularized by the influential 'connectivity map' study in 2006 regarding reversal relationships between disease... |
1703.02850 | Shixiang Wan | Quan Zou, Shixiang Wan, Ying Ju, Jijun Tang and Xiangxiang Zeng | Pretata: predicting TATA binding proteins with novel features and
dimensionality reduction strategy | null | null | null | null | q-bio.QM cs.LG q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: It is necessary and essential to discovery protein function from
the novel primary sequences. Wet lab experimental procedures are not only
time-consuming, but also costly, so predicting protein structure and function
reliably based only on amino acid sequence has significant value. TATA-binding
protein (T... | [
{
"created": "Tue, 7 Mar 2017 13:48:46 GMT",
"version": "v1"
}
] | 2017-03-09 | [
[
"Zou",
"Quan",
""
],
[
"Wan",
"Shixiang",
""
],
[
"Ju",
"Ying",
""
],
[
"Tang",
"Jijun",
""
],
[
"Zeng",
"Xiangxiang",
""
]
] | Background: It is necessary and essential to discovery protein function from the novel primary sequences. Wet lab experimental procedures are not only time-consuming, but also costly, so predicting protein structure and function reliably based only on amino acid sequence has significant value. TATA-binding protein (TBP... |
1302.4693 | Peter Combs | Peter A. Combs, Michael B. Eisen | Virtual in situs: Sequencing mRNA from cryo-sliced Drosophila embryos to
determine genome-wide spatial patterns of gene expression | 6 pages, 3 figures, 7 supplemental figures (available on request from
peter.combs@berkeley.edu) | PLoS ONE 8(8): e71820 2013 | 10.1371/journal.pone.0071820 | null | q-bio.GN | http://creativecommons.org/licenses/by/3.0/ | Complex spatial and temporal patterns of gene expression underlie embryo
differentiation, yet methods do not yet exist for the efficient genome-wide
determination of spatial expression patterns during development. In situ
imaging of transcripts and proteins is the gold-standard, but it is difficult
and time consuming... | [
{
"created": "Tue, 19 Feb 2013 17:44:59 GMT",
"version": "v1"
},
{
"created": "Wed, 20 Feb 2013 18:28:21 GMT",
"version": "v2"
},
{
"created": "Mon, 15 Apr 2013 23:37:01 GMT",
"version": "v3"
},
{
"created": "Thu, 23 May 2013 22:49:57 GMT",
"version": "v4"
}
] | 2013-08-15 | [
[
"Combs",
"Peter A.",
""
],
[
"Eisen",
"Michael B.",
""
]
] | Complex spatial and temporal patterns of gene expression underlie embryo differentiation, yet methods do not yet exist for the efficient genome-wide determination of spatial expression patterns during development. In situ imaging of transcripts and proteins is the gold-standard, but it is difficult and time consuming t... |
2302.07140 | Ernest Greene | Ernest Greene and Jack Morrison | Evaluating the Talbot-Plateau Law | 34 pages, five figures | null | null | null | q-bio.NC | http://creativecommons.org/publicdomain/zero/1.0/ | The Talbot-Plateau law asserts that when the flux (light energy) of a
flicker-fused stimulus equals the flux of a steady stimulus, they will appear
equal in brightness. To be perceived as flicker-fused, the frequency of the
flash sequence must be high enough that no flicker is perceived, i.e., it
appears to be a stea... | [
{
"created": "Mon, 6 Feb 2023 15:38:27 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Apr 2023 16:32:35 GMT",
"version": "v2"
}
] | 2023-04-28 | [
[
"Greene",
"Ernest",
""
],
[
"Morrison",
"Jack",
""
]
] | The Talbot-Plateau law asserts that when the flux (light energy) of a flicker-fused stimulus equals the flux of a steady stimulus, they will appear equal in brightness. To be perceived as flicker-fused, the frequency of the flash sequence must be high enough that no flicker is perceived, i.e., it appears to be a steady... |
q-bio/0410018 | Kevin E. Cahill | Kevin Cahill and V. Adrian Parsegian | Rydberg-London Potential for Diatomic Molecules and Unbonded Atom Pairs | Five pages, 10 figures | Journal of Chemical Physics 121 (#22), 10839-10842, 2004 | 10.1063/1.1830011 | null | q-bio.BM q-bio.QM | null | We propose and test a pair potential that is accurate at all relevant
distances and simple enough for use in large-scale computer simulations. A
combination of the Rydberg potential from spectroscopy and the London
inverse-sixth-power energy, the proposed form fits spectroscopically determined
potentials better than ... | [
{
"created": "Sun, 17 Oct 2004 23:03:30 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Cahill",
"Kevin",
""
],
[
"Parsegian",
"V. Adrian",
""
]
] | We propose and test a pair potential that is accurate at all relevant distances and simple enough for use in large-scale computer simulations. A combination of the Rydberg potential from spectroscopy and the London inverse-sixth-power energy, the proposed form fits spectroscopically determined potentials better than th... |
1210.1237 | Sean Stromberg | Sean P Stromberg | Multisite Population Epigenetic Model of Passive Demethylation | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The methylation of DNA regulates gene expression. On cell division the
methylation state of the DNA is typically inherited from parent to daughter
cells. While the chemical bond between the methyl group and the DNA is very
strong, changes to the methylation state do occur and are observed to occur
rapidly in response... | [
{
"created": "Wed, 3 Oct 2012 20:54:35 GMT",
"version": "v1"
}
] | 2012-10-05 | [
[
"Stromberg",
"Sean P",
""
]
] | The methylation of DNA regulates gene expression. On cell division the methylation state of the DNA is typically inherited from parent to daughter cells. While the chemical bond between the methyl group and the DNA is very strong, changes to the methylation state do occur and are observed to occur rapidly in response t... |
2311.18134 | Sanjeev Namjoshi | Roy E. Clymer and Sanjeev V. Namjoshi | A computational model of behavioral adaptation to solve the credit
assignment problem | 18 pages, 9 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The adaptive fitness of an organism in its ecological niche is highly reliant
upon its ability to associate an environmental or internal stimulus with a
behavior response through reinforcement. This simple but powerful observation
has been successfully applied in a number of contexts within computational
neuroscience... | [
{
"created": "Wed, 29 Nov 2023 22:53:28 GMT",
"version": "v1"
}
] | 2023-12-01 | [
[
"Clymer",
"Roy E.",
""
],
[
"Namjoshi",
"Sanjeev V.",
""
]
] | The adaptive fitness of an organism in its ecological niche is highly reliant upon its ability to associate an environmental or internal stimulus with a behavior response through reinforcement. This simple but powerful observation has been successfully applied in a number of contexts within computational neuroscience a... |
2201.10960 | Jeremy Clark | Jeremy S. C. Clark, Anna Salacka, Agnieszka Boron, Thierry van de
Wetering, Konrad Podsiadlo, Kamila Rydzewska, Krzysztof Safranow, Kazimierz
Ciechanowski, Leszek Domanski, Andrzej Ciechanowicz | Repetition and reproduction of preclinical medical studies: taking a
leaf from the plant sciences with consideration of generalised systematic
errors | 40 pages, 1 figure, 3 tables. Supplemental files at
https://github.com/Abiologist/Significance.git | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Reproduction of pre-clinical results has a high failure rate. The fundamental
methodology including replication ("protocol") for hypothesis
testing/validation to a state allowing inference, varies within medical and
plant sciences with little justification. Here, five protocols are
distinguished which deal differentl... | [
{
"created": "Wed, 26 Jan 2022 14:24:34 GMT",
"version": "v1"
}
] | 2022-01-27 | [
[
"Clark",
"Jeremy S. C.",
""
],
[
"Salacka",
"Anna",
""
],
[
"Boron",
"Agnieszka",
""
],
[
"van de Wetering",
"Thierry",
""
],
[
"Podsiadlo",
"Konrad",
""
],
[
"Rydzewska",
"Kamila",
""
],
[
"Safranow",
"Krzyszt... | Reproduction of pre-clinical results has a high failure rate. The fundamental methodology including replication ("protocol") for hypothesis testing/validation to a state allowing inference, varies within medical and plant sciences with little justification. Here, five protocols are distinguished which deal differently ... |
2402.18602 | Shin-Ichi Ito | Tomoya Aono, Tatsuya Sakamoto, Toyoho Ishimura, Motomitsu Takahashi,
Tohya Yasuda, Satoshi Kitajima, Kozue Nishida, Takayoshi Matsuura, Akito
Ikari, Shin-ichi Ito | Estimation of migrate histories of the Japanese sardine in the Sea of
Japan by combining the microscale stable isotope analysis of otoliths and a
data assimilation model | 35 pages including 8 figures and 4 supplementary figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The Japanese sardine (Sardinops melanostictus) is a small pelagic fish found
in the Sea of Japan, the marginal sea of the western North Pacific. It is an
important species for regional fisheries, but their transportation and
migration patterns during early life stages remain unclear. In this study, we
analyzed the st... | [
{
"created": "Wed, 28 Feb 2024 02:13:43 GMT",
"version": "v1"
}
] | 2024-03-01 | [
[
"Aono",
"Tomoya",
""
],
[
"Sakamoto",
"Tatsuya",
""
],
[
"Ishimura",
"Toyoho",
""
],
[
"Takahashi",
"Motomitsu",
""
],
[
"Yasuda",
"Tohya",
""
],
[
"Kitajima",
"Satoshi",
""
],
[
"Nishida",
"Kozue",
""
],... | The Japanese sardine (Sardinops melanostictus) is a small pelagic fish found in the Sea of Japan, the marginal sea of the western North Pacific. It is an important species for regional fisheries, but their transportation and migration patterns during early life stages remain unclear. In this study, we analyzed the stab... |
1705.09156 | Christopher Buckley | Christopher L. Buckley, Chang Sub Kim, Simon McGregor and Anil K. Seth | The free energy principle for action and perception: A mathematical
review | 77 pages 2 fugures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The 'free energy principle' (FEP) has been suggested to provide a unified
theory of the brain, integrating data and theory relating to action,
perception, and learning. The theory and implementation of the FEP combines
insights from Helmholtzian 'perception as inference', machine learning theory,
and statistical ther... | [
{
"created": "Wed, 24 May 2017 11:40:27 GMT",
"version": "v1"
}
] | 2017-05-26 | [
[
"Buckley",
"Christopher L.",
""
],
[
"Kim",
"Chang Sub",
""
],
[
"McGregor",
"Simon",
""
],
[
"Seth",
"Anil K.",
""
]
] | The 'free energy principle' (FEP) has been suggested to provide a unified theory of the brain, integrating data and theory relating to action, perception, and learning. The theory and implementation of the FEP combines insights from Helmholtzian 'perception as inference', machine learning theory, and statistical thermo... |
1612.08790 | Su-Chan Park | Sungmin Hwang, Su-Chan Park, Joachim Krug | Genotypic complexity of Fisher's geometric model | 27 pages, 14 figures, 2 tables, minor changes (published version) | Genetics 206, 1049 (2017) | 10.1534/genetics.116.199497 | null | q-bio.PE cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fisher's geometric model was originally introduced to argue that complex
adaptations must occur in small steps because of pleiotropic constraints. When
supplemented with the assumption of additivity of mutational effects on
phenotypic traits, it provides a simple mechanism for the emergence of
genotypic epistasis fro... | [
{
"created": "Wed, 28 Dec 2016 02:32:14 GMT",
"version": "v1"
},
{
"created": "Wed, 29 Mar 2017 01:22:30 GMT",
"version": "v2"
},
{
"created": "Fri, 9 Jun 2017 05:14:16 GMT",
"version": "v3"
}
] | 2017-06-12 | [
[
"Hwang",
"Sungmin",
""
],
[
"Park",
"Su-Chan",
""
],
[
"Krug",
"Joachim",
""
]
] | Fisher's geometric model was originally introduced to argue that complex adaptations must occur in small steps because of pleiotropic constraints. When supplemented with the assumption of additivity of mutational effects on phenotypic traits, it provides a simple mechanism for the emergence of genotypic epistasis from ... |
1602.01612 | Michael Sheinman | Michael Sheinman and Anna Ramisch and Florian Massip and Peter F.
Arndt | Evolutionary dynamics of selfish DNA generates pseudo-linguistic
features of genomes | 9 pages, 5 figures | Scientific Reports 6, Article number: 30851 (2016) | 10.1038/srep30851 | null | q-bio.PE physics.bio-ph q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Since the sequencing of large genomes, many statistical features of their
sequences have been found. One intriguing feature is that certain subsequences
are much more abundant than others. In fact, abundances of subsequences of a
given length are distributed with a scale-free power-law tail, resembling
properties of ... | [
{
"created": "Thu, 4 Feb 2016 10:08:04 GMT",
"version": "v1"
}
] | 2016-08-05 | [
[
"Sheinman",
"Michael",
""
],
[
"Ramisch",
"Anna",
""
],
[
"Massip",
"Florian",
""
],
[
"Arndt",
"Peter F.",
""
]
] | Since the sequencing of large genomes, many statistical features of their sequences have been found. One intriguing feature is that certain subsequences are much more abundant than others. In fact, abundances of subsequences of a given length are distributed with a scale-free power-law tail, resembling properties of hu... |
2208.10403 | Somya Mehra | Somya Mehra, Peter G. Taylor, James M. McCaw, Jennifer A. Flegg | A hybrid transmission model for Plasmodium vivax accounting for
superinfection, immunity and the hypnozoite reservoir | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Malaria is a vector-borne disease that exacts a grave toll in the Global
South. The epidemiology of Plasmodium vivax, the most geographically expansive
agent of human malaria, is characterised by the accrual of a reservoir of
dormant parasites known as hypnozoites. Relapses, arising from hypnozoite
activation events,... | [
{
"created": "Mon, 22 Aug 2022 15:41:08 GMT",
"version": "v1"
}
] | 2022-08-23 | [
[
"Mehra",
"Somya",
""
],
[
"Taylor",
"Peter G.",
""
],
[
"McCaw",
"James M.",
""
],
[
"Flegg",
"Jennifer A.",
""
]
] | Malaria is a vector-borne disease that exacts a grave toll in the Global South. The epidemiology of Plasmodium vivax, the most geographically expansive agent of human malaria, is characterised by the accrual of a reservoir of dormant parasites known as hypnozoites. Relapses, arising from hypnozoite activation events, c... |
2108.11064 | Mahmoud Hassan | Aya Kabbara, Gabriel Robert, Mohamad Khalil, Marc Verin, Pascal
Benquet, Mahmoud Hassan | An Electroencephalography connectome predictive model of major
depressive disorder severity | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Emerging evidence showed that major depressive disorder (MDD) is associated
with disruptions of brain structural and functional networks, rather than
impairment of isolated brain region. Thus, connectome-based models capable of
predicting the depression severity at the individual level can be clinically
useful. Here,... | [
{
"created": "Wed, 25 Aug 2021 06:20:36 GMT",
"version": "v1"
},
{
"created": "Fri, 15 Oct 2021 07:26:46 GMT",
"version": "v2"
}
] | 2021-10-18 | [
[
"Kabbara",
"Aya",
""
],
[
"Robert",
"Gabriel",
""
],
[
"Khalil",
"Mohamad",
""
],
[
"Verin",
"Marc",
""
],
[
"Benquet",
"Pascal",
""
],
[
"Hassan",
"Mahmoud",
""
]
] | Emerging evidence showed that major depressive disorder (MDD) is associated with disruptions of brain structural and functional networks, rather than impairment of isolated brain region. Thus, connectome-based models capable of predicting the depression severity at the individual level can be clinically useful. Here, w... |
1806.10639 | Vianey Leos Barajas | Vianey Leos-Barajas and Th\'eo Michelot | An Introduction to Animal Movement Modeling with Hidden Markov Models
using Stan for Bayesian Inference | 29 pages, 15 figures | null | null | null | q-bio.QM stat.AP | http://creativecommons.org/licenses/by/4.0/ | Hidden Markov models (HMMs) are popular time series model in many fields
including ecology, economics and genetics. HMMs can be defined over discrete or
continuous time, though here we only cover the former. In the field of movement
ecology in particular, HMMs have become a popular tool for the analysis of
movement d... | [
{
"created": "Wed, 27 Jun 2018 18:41:15 GMT",
"version": "v1"
}
] | 2018-06-29 | [
[
"Leos-Barajas",
"Vianey",
""
],
[
"Michelot",
"Théo",
""
]
] | Hidden Markov models (HMMs) are popular time series model in many fields including ecology, economics and genetics. HMMs can be defined over discrete or continuous time, though here we only cover the former. In the field of movement ecology in particular, HMMs have become a popular tool for the analysis of movement dat... |
2203.14964 | Jianhua Xing | Jianhua Xing | Reconstructing data-driven governing equations for cell phenotypic
transitions: integration of data science and systems biology | 38 pages, 3 figures | null | 10.1088/1478-3975/ac8c16 | null | q-bio.QM physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Cells with the same genome can exist in different phenotypes. and can change
between distinct phenotypes when subject to specific stimuli and
microenvironments. Some examples include cell differentiation during
development, reprogramming for induced pluripotent stem cells and
transdifferentiation, cancer metastasis a... | [
{
"created": "Sat, 26 Mar 2022 18:24:44 GMT",
"version": "v1"
},
{
"created": "Mon, 1 Aug 2022 12:19:06 GMT",
"version": "v2"
}
] | 2022-09-28 | [
[
"Xing",
"Jianhua",
""
]
] | Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming for induced pluripotent stem cells and transdifferentiation, cancer metastasis and... |
0805.2288 | Marco Cosentino Lagomarsino | A.L. Sellerio, B. Bassetti, H. Isambert, M. Cosentino Lagomarsino | A comparative evolutionary study of transcription networks | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a comparative analysis of large-scale topological and evolutionary
properties of transcription networks in three species, the two distant bacteria
E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the
global aspects of feedback and hierarchy in transcriptional regulatory
pathways. ... | [
{
"created": "Thu, 15 May 2008 13:19:03 GMT",
"version": "v1"
}
] | 2008-05-16 | [
[
"Sellerio",
"A. L.",
""
],
[
"Bassetti",
"B.",
""
],
[
"Isambert",
"H.",
""
],
[
"Lagomarsino",
"M. Cosentino",
""
]
] | We present a comparative analysis of large-scale topological and evolutionary properties of transcription networks in three species, the two distant bacteria E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the global aspects of feedback and hierarchy in transcriptional regulatory pathways. Wh... |
2308.01362 | James Lu | Mark Laurie and James Lu | Explainable Deep Learning for Tumor Dynamic Modeling and Overall
Survival Prediction using Neural-ODE | 33 pages, 4 Figures and 2 Tables. Includes Supplementary Materials | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | While tumor dynamic modeling has been widely applied to support the
development of oncology drugs, there remains a need to increase predictivity,
enable personalized therapy, and improve decision-making. We propose the use of
Tumor Dynamic Neural-ODE (TDNODE) as a pharmacology-informed neural network to
enable model ... | [
{
"created": "Wed, 2 Aug 2023 18:08:27 GMT",
"version": "v1"
},
{
"created": "Sun, 15 Oct 2023 05:00:53 GMT",
"version": "v2"
},
{
"created": "Fri, 20 Oct 2023 20:10:10 GMT",
"version": "v3"
}
] | 2023-10-24 | [
[
"Laurie",
"Mark",
""
],
[
"Lu",
"James",
""
]
] | While tumor dynamic modeling has been widely applied to support the development of oncology drugs, there remains a need to increase predictivity, enable personalized therapy, and improve decision-making. We propose the use of Tumor Dynamic Neural-ODE (TDNODE) as a pharmacology-informed neural network to enable model di... |
1205.2318 | Soumen Roy | Soumen Roy | Systems biology beyond degree, hubs and scale-free networks: the case
for multiple metrics in complex networks | To appear in Systems and Synthetic Biology (Springer) | Systems and Synthetic Biology (2012) 6:31-34 | 10.1007/s11693-012-9094-y | null | q-bio.QM cond-mat.stat-mech cs.SI physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modeling and topological analysis of networks in biological and other complex
systems, must venture beyond the limited consideration of very few network
metrics like degree, betweenness or assortativity. A proper identification of
informative and redundant entities from many different metrics, using recently
demonstr... | [
{
"created": "Thu, 10 May 2012 17:26:02 GMT",
"version": "v1"
},
{
"created": "Sun, 3 Jun 2012 07:32:22 GMT",
"version": "v2"
}
] | 2012-09-25 | [
[
"Roy",
"Soumen",
""
]
] | Modeling and topological analysis of networks in biological and other complex systems, must venture beyond the limited consideration of very few network metrics like degree, betweenness or assortativity. A proper identification of informative and redundant entities from many different metrics, using recently demonstrat... |
1812.10050 | Moo K. Chung | Shih-Gu Huang, S. Balqis Samdin, Chee-Ming Ting, Hernando Ombao, Moo
K. Chung | Statistical Model for Dynamically-Changing Correlation Matrices with
Application to Brain Connectivity | Accepted for publication in Journal of Neuroscience Methods | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Recent studies have indicated that functional connectivity is
dynamic even during rest. A common approach to modeling the dynamic functional
connectivity in whole-brain resting-state fMRI is to compute the correlation
between anatomical regions via sliding time windows. However, the direct use of
the samp... | [
{
"created": "Tue, 25 Dec 2018 06:23:33 GMT",
"version": "v1"
},
{
"created": "Sun, 3 Nov 2019 16:28:17 GMT",
"version": "v2"
}
] | 2019-11-05 | [
[
"Huang",
"Shih-Gu",
""
],
[
"Samdin",
"S. Balqis",
""
],
[
"Ting",
"Chee-Ming",
""
],
[
"Ombao",
"Hernando",
""
],
[
"Chung",
"Moo K.",
""
]
] | Background: Recent studies have indicated that functional connectivity is dynamic even during rest. A common approach to modeling the dynamic functional connectivity in whole-brain resting-state fMRI is to compute the correlation between anatomical regions via sliding time windows. However, the direct use of the sample... |
2307.00635 | Jacob Luber | Jai Prakash Veerla, Jillur Rahman Saurav, Michael Robben, Jacob M
Luber | Analyzing Lack of Concordance Between the Proteome and Transcriptome in
Paired scRNA-Seq and Multiplexed Spatial Proteomics | null | null | null | null | q-bio.TO q-bio.GN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In this study, we analyze discordance between the transcriptome and proteome
using paired scRNA-Seq and multiplexed spatial proteomics data from HuBMAP. Our
findings highlight persistent transcripts in key immune markers, including
CD45-RO, Ki67, CD45, CD20, and HLA-DR. CD45-RO is consistently expressed in
memory T c... | [
{
"created": "Sun, 2 Jul 2023 18:43:03 GMT",
"version": "v1"
}
] | 2023-07-04 | [
[
"Veerla",
"Jai Prakash",
""
],
[
"Saurav",
"Jillur Rahman",
""
],
[
"Robben",
"Michael",
""
],
[
"Luber",
"Jacob M",
""
]
] | In this study, we analyze discordance between the transcriptome and proteome using paired scRNA-Seq and multiplexed spatial proteomics data from HuBMAP. Our findings highlight persistent transcripts in key immune markers, including CD45-RO, Ki67, CD45, CD20, and HLA-DR. CD45-RO is consistently expressed in memory T cel... |
2309.04057 | Mitchel Colebank | Mitchel J. Colebank, Naomi C. Chesler | Efficient Uncertainty Quantification in a Multiscale Model of Pulmonary
Arterial and Venous Hemodynamics | 10 Figures, 2 tables | null | null | null | q-bio.TO physics.med-ph | http://creativecommons.org/licenses/by-sa/4.0/ | Computational hemodynamics models are becoming increasingly useful in the
management and prognosis of complex, multiscale pathologies, including those
attributed to the development of pulmonary vascular disease. However, diseases
like pulmonary hypertension are heterogeneous, and affect both the proximal
arteries and... | [
{
"created": "Fri, 8 Sep 2023 01:09:17 GMT",
"version": "v1"
}
] | 2023-09-11 | [
[
"Colebank",
"Mitchel J.",
""
],
[
"Chesler",
"Naomi C.",
""
]
] | Computational hemodynamics models are becoming increasingly useful in the management and prognosis of complex, multiscale pathologies, including those attributed to the development of pulmonary vascular disease. However, diseases like pulmonary hypertension are heterogeneous, and affect both the proximal arteries and v... |
1511.00673 | Karol Bacik | Karol A. Bacik, Michael T. Schaub, Mariano Beguerisse-D\'iaz, Yazan N.
Billeh, Mauricio Barahona | Flow-based network analysis of the Caenorhabditis elegans connectome | 28 pages including Supplementary Information, 8 figures and 12
figures in the SI | PLoS Comput Biol 12.8 (2016): e1005055 | 10.1371/journal.pcbi.1005055 | null | q-bio.NC physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We exploit flow propagation on the directed neuronal network of the nematode
Caenorhabditis elegans to reveal dynamically relevant features of its
connectome. We find flow-based groupings of neurons at different levels of
granularity, which we relate to functional and anatomical constituents of its
nervous system. A ... | [
{
"created": "Mon, 2 Nov 2015 20:50:27 GMT",
"version": "v1"
},
{
"created": "Thu, 10 Dec 2015 20:40:23 GMT",
"version": "v2"
},
{
"created": "Mon, 8 Aug 2016 10:07:59 GMT",
"version": "v3"
}
] | 2016-08-09 | [
[
"Bacik",
"Karol A.",
""
],
[
"Schaub",
"Michael T.",
""
],
[
"Beguerisse-Díaz",
"Mariano",
""
],
[
"Billeh",
"Yazan N.",
""
],
[
"Barahona",
"Mauricio",
""
]
] | We exploit flow propagation on the directed neuronal network of the nematode Caenorhabditis elegans to reveal dynamically relevant features of its connectome. We find flow-based groupings of neurons at different levels of granularity, which we relate to functional and anatomical constituents of its nervous system. A sy... |
1304.7393 | Mark Flegg | Mark B Flegg, Stefan Hellander, Radek Erban | Convergence of methods for coupling of microscopic and mesoscopic
reaction-diffusion simulations | null | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, three multiscale methods for coupling of mesoscopic
(compartment-based) and microscopic (molecular-based) stochastic
reaction-diffusion simulations are investigated. Two of the three methods that
will be discussed in detail have been previously reported in the literature;
the two-regime method (TRM) an... | [
{
"created": "Sat, 27 Apr 2013 18:06:39 GMT",
"version": "v1"
}
] | 2013-04-30 | [
[
"Flegg",
"Mark B",
""
],
[
"Hellander",
"Stefan",
""
],
[
"Erban",
"Radek",
""
]
] | In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and ... |
2306.06296 | Michael Shvartsman | Michael Shvartsman, Benjamin Letham, Stephen Keeley | Response Time Improves Choice Prediction and Function Estimation for
Gaussian Process Models of Perception and Preferences | 18 pages incl. references and supplement; 11 figures | null | null | null | q-bio.NC cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Models for human choice prediction in preference learning and psychophysics
often consider only binary response data, requiring many samples to accurately
learn preferences or perceptual detection thresholds. The response time (RT) to
make each choice captures additional information about the decision process,
howeve... | [
{
"created": "Fri, 9 Jun 2023 23:22:49 GMT",
"version": "v1"
}
] | 2023-06-13 | [
[
"Shvartsman",
"Michael",
""
],
[
"Letham",
"Benjamin",
""
],
[
"Keeley",
"Stephen",
""
]
] | Models for human choice prediction in preference learning and psychophysics often consider only binary response data, requiring many samples to accurately learn preferences or perceptual detection thresholds. The response time (RT) to make each choice captures additional information about the decision process, however ... |
1212.4745 | M. Angeles Serrano | M. \'Angeles Serrano, Manuel Jurado, Ramon Reigada | Negative-feedback self-regulation contributes to robust and
high-fidelity transmembrane signal transduction | null | null | null | null | q-bio.CB q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a minimal motif model for transmembrane cell signaling. The model
assumes signaling events taking place in spatially distributed nanoclusters
regulated by a birth/death dynamics. The combination of these spatio-temporal
aspects can be modulated to provide a robust and high-fidelity response
behavior withou... | [
{
"created": "Wed, 19 Dec 2012 17:06:07 GMT",
"version": "v1"
},
{
"created": "Sat, 20 Apr 2013 08:07:17 GMT",
"version": "v2"
}
] | 2013-04-23 | [
[
"Serrano",
"M. Ángeles",
""
],
[
"Jurado",
"Manuel",
""
],
[
"Reigada",
"Ramon",
""
]
] | We present a minimal motif model for transmembrane cell signaling. The model assumes signaling events taking place in spatially distributed nanoclusters regulated by a birth/death dynamics. The combination of these spatio-temporal aspects can be modulated to provide a robust and high-fidelity response behavior without ... |
1304.8009 | Sergiy Perepelytsya | S.M. Perepelytsya, S.N. Volkov | Dynamics of ion-phosphate lattice of DNA in left-handed double helix
form | 12 pages, 3 figures | Ukr. J. Phys. V. 58, 554-562 (2013) | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The conformational vibrations of Z-DNA with counterions are studied in
framework of phenomenological model developed. The structure of left-handed
double helix with counterions neutralizing the negatively charged phosphate
groups of DNA is considered as the ion-phosphate lattice. The frequencies and
Raman intensities... | [
{
"created": "Tue, 30 Apr 2013 14:27:08 GMT",
"version": "v1"
}
] | 2013-05-01 | [
[
"Perepelytsya",
"S. M.",
""
],
[
"Volkov",
"S. N.",
""
]
] | The conformational vibrations of Z-DNA with counterions are studied in framework of phenomenological model developed. The structure of left-handed double helix with counterions neutralizing the negatively charged phosphate groups of DNA is considered as the ion-phosphate lattice. The frequencies and Raman intensities f... |
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