1,588 research outputs found
Towards Logical Specification of Statistical Machine Learning
We introduce a logical approach to formalizing statistical properties of
machine learning. Specifically, we propose a formal model for statistical
classification based on a Kripke model, and formalize various notions of
classification performance, robustness, and fairness of classifiers by using
epistemic logic. Then we show some relationships among properties of
classifiers and those between classification performance and robustness, which
suggests robustness-related properties that have not been formalized in the
literature as far as we know. To formalize fairness properties, we define a
notion of counterfactual knowledge and show techniques to formalize conditional
indistinguishability by using counterfactual epistemic operators. As far as we
know, this is the first work that uses logical formulas to express statistical
properties of machine learning, and that provides epistemic (resp.
counterfactually epistemic) views on robustness (resp. fairness) of
classifiers.Comment: SEFM'19 conference paper (full version with errors corrected
Vortex deformation and breaking in superconductors: A microscopic description
Vortex breaking has been traditionally studied for nonuniform critical
current densities, although it may also appear due to nonuniform pinning force
distributions. In this article we study the case of a
high-pinning/low-pinning/high-pinning layered structure. We have developed an
elastic model for describing the deformation of a vortex in these systems in
the presence of a uniform transport current density for any arbitrary
orientation of the transport current and the magnetic field. If is above a
certain critical value, , the vortex breaks and a finite effective
resistance appears. Our model can be applied to some experimental
configurations where vortex breaking naturally exists. This is the case for
YBaCuO (YBCO) low angle grain boundaries and films on vicinal
substrates, where the breaking is experienced by Abrikosov-Josephson vortices
(AJV) and Josephson string vortices (SV), respectively. With our model, we have
experimentally extracted some intrinsic parameters of the AJV and SV, such as
the line tension and compared it to existing predictions based on
the vortex structure.Comment: 11 figures in 13 files; minor changes after printing proof
On the complexity of acyclic modules in automata networks
Modules were introduced as an extension of Boolean automata networks. They
have inputs which are used in the computation said modules perform, and can be
used to wire modules with each other. In the present paper we extend this new
formalism and study the specific case of acyclic modules. These modules prove
to be well described in their limit behavior by functions called output
functions. We provide other results that offer an upper bound on the number of
attractors in an acyclic module when wired recursively into an automata
network, alongside a diversity of complexity results around the difficulty of
deciding the existence of cycles depending on the number of inputs and the size
of said cycle.Comment: 21 page
Caspase-Dependent Inhibition of Mousepox Replication by gzmB
BACKGROUND: Ectromelia virus is a natural mouse pathogen, causing mousepox. The cytotoxic T (Tc) cell granule serine-protease, granzyme B, is important for its control, but the underlying mechanism is unknown. Using ex vivo virus immune Tc cells, we have previously shown that granzyme B is able to activate several independent pro-apoptotic pathways, including those mediated by Bid/Bak/Bax and caspases-3/-7, in target cells pulsed with Tc cell determinants. METHODS AND FINDINGS: Here we analysed the physiological relevance of those pro-apoptotic pathways in ectromelia infection, by incubating ectromelia-immune ex vivo Tc cells from granzyme A deficient (GzmB(+) Tc cells) or granzyme A and granzyme B deficient (GzmAxB(-/-) Tc cell) mice with ectromelia-infected target cells. We found that gzmB-induced apoptosis was totally blocked in ectromelia infected or peptide pulsed cells lacking caspases-3/-7. However ectromelia inhibited only partially apoptosis in cells deficient for Bid/Bak/Bax and not at all when both pathways were operative suggesting that the virus is able to interfere with apoptosis induced by gzmB in case not all pathways are activated. Importantly, inhibition of viral replication in vitro, as seen with wild type cells, was not affected by the lack of Bid/Bak/Bax but was significantly reduced in caspase-3/-7-deficient cells. Both caspase dependent processes were strictly dependent on gzmB, since Tc cells, lacking both gzms, neither induced apoptosis nor reduced viral titers. SIGNIFICANCE: Out findings present the first evidence on the biological importance of the independent gzmB-inducible pro-apoptotic pathways in a physiological relevant virus infection model
Mesoscopic organization reveals the constraints governing C. elegans nervous system
One of the biggest challenges in biology is to understand how activity at the
cellular level of neurons, as a result of their mutual interactions, leads to
the observed behavior of an organism responding to a variety of environmental
stimuli. Investigating the intermediate or mesoscopic level of organization in
the nervous system is a vital step towards understanding how the integration of
micro-level dynamics results in macro-level functioning. In this paper, we have
considered the somatic nervous system of the nematode Caenorhabditis elegans,
for which the entire neuronal connectivity diagram is known. We focus on the
organization of the system into modules, i.e., neuronal groups having
relatively higher connection density compared to that of the overall network.
We show that this mesoscopic feature cannot be explained exclusively in terms
of considerations, such as optimizing for resource constraints (viz., total
wiring cost) and communication efficiency (i.e., network path length).
Comparison with other complex networks designed for efficient transport (of
signals or resources) implies that neuronal networks form a distinct class.
This suggests that the principal function of the network, viz., processing of
sensory information resulting in appropriate motor response, may be playing a
vital role in determining the connection topology. Using modular spectral
analysis, we make explicit the intimate relation between function and structure
in the nervous system. This is further brought out by identifying functionally
critical neurons purely on the basis of patterns of intra- and inter-modular
connections. Our study reveals how the design of the nervous system reflects
several constraints, including its key functional role as a processor of
information.Comment: Published version, Minor modifications, 16 pages, 9 figure
The Genomic Signature of Crop-Wild Introgression in Maize
The evolutionary significance of hybridization and subsequent introgression
has long been appreciated, but evaluation of the genome-wide effects of these
phenomena has only recently become possible. Crop-wild study systems represent
ideal opportunities to examine evolution through hybridization. For example,
maize and the conspecific wild teosinte Zea mays ssp. mexicana, (hereafter,
mexicana) are known to hybridize in the fields of highland Mexico. Despite
widespread evidence of gene flow, maize and mexicana maintain distinct
morphologies and have done so in sympatry for thousands of years. Neither the
genomic extent nor the evolutionary importance of introgression between these
taxa is understood. In this study we assessed patterns of genome-wide
introgression based on 39,029 single nucleotide polymorphisms genotyped in 189
individuals from nine sympatric maize-mexicana populations and reference
allopatric populations. While portions of the maize and mexicana genomes were
particularly resistant to introgression (notably near known
cross-incompatibility and domestication loci), we detected widespread evidence
for introgression in both directions of gene flow. Through further
characterization of these regions and preliminary growth chamber experiments,
we found evidence suggestive of the incorporation of adaptive mexicana alleles
into maize during its expansion to the highlands of central Mexico. In
contrast, very little evidence was found for adaptive introgression from maize
to mexicana. The methods we have applied here can be replicated widely, and
such analyses have the potential to greatly informing our understanding of
evolution through introgressive hybridization. Crop species, due to their
exceptional genomic resources and frequent histories of spread into sympatry
with relatives, should be particularly influential in these studies
Association between Type 2 Diabetes Loci and Measures of Fatness
Background: Type 2 diabetes (T2D) is a metabolic disorder characterized by disturbances of carbohydrate, fat and protein metabolism and insulin resistance. The majority of T2D patients are obese and obesity by itself may be a cause of insulin resistance. Our aim was to evaluate whether the recently identified T2D risk alleles are associated with human measures of fatness as characterized with Dual Energy X-ray Absorptiometry (DEXA). Methodology/Principal Findings: Genotypes and phenotypes of approximately 3,000 participants from cross-sectional ERF study were analyzed. Nine single nucleotide polymorphisms (SNPs) in CDKN2AB, CDKAL1, FTO, HHEX, IGF2BP2, KCNJ11, PPARG, SLC30A8 and TCF7L2 were genotyped. We used linear regression to study association between individual SNPs and the combined allelic risk score with body mass index (BMI), fat mass index (FMI), fat percentage (FAT), waist circumference (WC) and waist to hip ratio (WHR). Significant association was observed between rs8050136 (FTO) and BMI (p = 0.003), FMI (p = 0.007) and WC (p = 0.03); fat percentage was borderline significant (p = 0.053). No other SNPs alone or combined in a risk score demonstrated significant association to the measures of fatness. Conclusions/Significance: From the recently identified T2D risk variants only the risk variant of the FTO gene (rs8050136) showed statistically significant association with BMI, FMI, and WC
The CS1 segment of fibronectin is involved in human OSCC pathogenesis by mediating OSCC cell spreading, migration, and invasion
<p>Abstract</p> <p>Background</p> <p>The alternatively spliced V region or type III connecting segment III (IIICS) of fibronectin is important in early development, wound healing, and tumorigenesis, however, its role in oral cancer has not been fully investigated. Thus, we investigated the role of CS-1, a key site within the CSIII region of fibronectin, in human oral squamous cell carcinoma (OSCC).</p> <p>Methods</p> <p>To determine the expression of CS-1 in human normal and oral SCC tissue specimens immunohistochemical analyses were performed. The expression of CS1 was then associated with clinicopathological factors. To investigate the role of CS-1 in regulating OSCC cell spreading, migration and invasion, OSCC cells were assayed for spreading and migration in the presence of a CS-1 peptide or a CS-1 blocking peptide, and for invasion using Matrigel supplemented with these peptides. In addition, integrin Îą4siRNA or a focal adhesion kinase (FAK) anti-sense oligonucleotide was transfected into OSCC cells to examine the mechanistic role of integrin Îą4 or FAK in CS1-mediated cell spreading and migration, respectively.</p> <p>Results</p> <p>CS-1 expression levels were significantly higher in OSCC tissues compared to normal tissues (p < 0.05). Also, although, high levels of CS-1 expression were present in all OSCC tissue samples, low-grade tumors stained more intensely than high grade tumors. OSCC cell lines also expressed higher levels of CS-1 protein compared to normal human primary oral keratinocytes. There was no significant difference in total fibronectin expression between normal and OSCC tissues and cells. Inclusion of CS-1 in the in vitro assays enhanced OSCC cell spreading, migration and invasion, whereas the CS1 blocking peptide inhibited these processes. Suppression of integrin Îą4 significantly inhibited the CS1-mediated cell spreading. Furthermore, this migration was mediated by focal adhesion kinase (FAK), since FAK suppression significantly blocked the CS1-induced cell migration.</p> <p>Conclusion</p> <p>These data indicate that the CS-1 site of fibronectin is involved in oral cancer pathogenesis and in regulating OSCC cell spreading, migration and invasion.</p
Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV
The performance of muon reconstruction, identification, and triggering in CMS
has been studied using 40 inverse picobarns of data collected in pp collisions
at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection
criteria covering a wide range of physics analysis needs have been examined.
For all considered selections, the efficiency to reconstruct and identify a
muon with a transverse momentum pT larger than a few GeV is above 95% over the
whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4,
while the probability to misidentify a hadron as a muon is well below 1%. The
efficiency to trigger on single muons with pT above a few GeV is higher than
90% over the full eta range, and typically substantially better. The overall
momentum scale is measured to a precision of 0.2% with muons from Z decays. The
transverse momentum resolution varies from 1% to 6% depending on pseudorapidity
for muons with pT below 100 GeV and, using cosmic rays, it is shown to be
better than 10% in the central region up to pT = 1 TeV. Observed distributions
of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO
Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV
The performance of muon reconstruction, identification, and triggering in CMS
has been studied using 40 inverse picobarns of data collected in pp collisions
at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection
criteria covering a wide range of physics analysis needs have been examined.
For all considered selections, the efficiency to reconstruct and identify a
muon with a transverse momentum pT larger than a few GeV is above 95% over the
whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4,
while the probability to misidentify a hadron as a muon is well below 1%. The
efficiency to trigger on single muons with pT above a few GeV is higher than
90% over the full eta range, and typically substantially better. The overall
momentum scale is measured to a precision of 0.2% with muons from Z decays. The
transverse momentum resolution varies from 1% to 6% depending on pseudorapidity
for muons with pT below 100 GeV and, using cosmic rays, it is shown to be
better than 10% in the central region up to pT = 1 TeV. Observed distributions
of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO
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