ProbCD: enrichment analysis accounting for categorization uncertainty

As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. We developed an open-source R package to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table for
the enrichment problem is built using the expectation of a Bernoulli Scheme stochastic process given the categorization probabilities. An on-line interface was created to allow usage by non-programmers and is available at: http://xerad.systemsbiology.net/ProbCD/. We present an analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques and (ii) probabilistic gene annotation

Quark zero modes in intersecting center vortex gauge fields

The zero modes of the Dirac operator in the background of center vortex gauge field configurations in $\R^2$ and $\R^4$ are examined. If the net flux in D=2 is larger than 1 we obtain normalizable zero modes which are mainly localized at the vortices. In D=4 quasi-normalizable zero modes exist for intersecting flat vortex sheets with the Pontryagin index equal to 2. These zero modes are mainly localized at the vortex intersection points, which carry a topological charge of $\pm 1/2$. To circumvent the problem of normalizability the space-time manifold is chosen to be the (compact) torus \T^2 and \T^4, respectively. According to the index theorem there are normalizable zero modes on \T^2 if the net flux is non-zero. These zero modes are localized at the vortices. On \T^4 zero modes exist for a non-vanishing Pontryagin index. As in $\R^4$ these zero modes are localized at the vortex intersection points.Comment: 20 pages, 4 figures, LaTeX2e, references added, treatment of ideal vortices on the torus shortene

Оптимизация технологических показателей на стадии падения добычи нефти в процессе разработки нефтяных месторождений

Объектом исследования являются технологические процессы на стадии падения добычи нефти. Цель исследования – анализ эффективности технологических процессов при разработке нефтяных месторождений на стадии падения добычи нефти. В процессе исследования были разобраны геолого-технологические проблемы разработки месторождений на стадии падения добычи нефти, произведен обзор современных методов к решению задач по оптимизации процессов добычи. В результате исследования выявлен положительный эффект от проведения оптимизационных мероприятий, а также описан комплексный подход к оптимизации процессов добычи.The object of research is technological processes at the stage of oil production decline. The purpose of the study is to analyze the efficiency of technological processes in the development of oil fields at the stage of a decline in oil production. In the course of the study, the geological and technological problems of field development at the stage of the decline in oil production were analyzed, and a review of modern methods for solving problems of optimizing production processes was made. As a result of the study, a positive effect from the implementation of optimization measures was revealed, and an integrated approach to the optimization of production processes was described

Are language production problems apparent in adults who no longer meet diagnostic criteria for attention-deficit/hyperactivity disorder?

In this study, we examined sentence production in a sample of adults (N = 21) who had had attention-deficit/hyperactivity disorder (ADHD) as children, but as adults no longer met DSM-IV diagnostic criteria (APA, 2000). This “remitted” group was assessed on a sentence production task. On each trial, participants saw two objects and a verb. Their task was to construct a sentence using the objects as arguments of the verb. Results showed more ungrammatical and disfluent utterances with one particular type of verb (i.e., participle). In a second set of analyses, we compared the remitted group to both control participants and a “persistent” group, who had ADHD as children and as adults. Results showed that remitters were more likely to produce ungrammatical utterances and to make repair disfluencies compared to controls, and they patterned more similarly to ADHD participants. Conclusions focus on language output in remitted ADHD, and the role of executive functions in language production

Human Galectins Induce Conversion of Dermal Fibroblasts into Myofibroblasts and Production of Extracellular Matrix: Potential Application in Tissue Engineering and Wound Repair

Members of the galectin family of endogenous lectins are potent adhesion/growth-regulatory effectors. Their multi-functionality opens possibilities for their use in bioapplications. We studied whether human galectins induce the conversion of human dermal fibroblasts into myofibroblasts (MFBs) and the production of a bioactive extracellular matrix scaffold is suitable for cell culture. Testing a panel of galectins of all three subgroups, including natural and engineered variants, we detected activity for the proto-type galectin-1 and galectin-7, the chimera-type galectin-3 and the tandem-repeat-type galectin-4. The activity of galectin-1 required the integrity of the carbohydrate recognition domain. It was independent of the presence of TGF-beta 1, but it yielded an additive effect. The resulting MFBs, relevant, for example, for tumor progression, generated a matrix scaffold rich in fibronectin and galectin-1 that supported keratinocyte culture without feeder cells. Of note, keratinocytes cultured on this substratum presented a stem-like cell phenotype with small size and keratin-19 expression. In vivo in rats, galectin-1 had a positive effect on skin wound closure 21 days after surgery. In conclusion, we describe the differential potential of certain human galectins to induce the conversion of dermal fibroblasts into MFBs and the generation of a bioactive cell culture substratum. Copyright (C) 2011 S. Karger AG, Base

Initial determination of the spins of the gluino and squarks at LHC

In principle particle spins can be measured from their production cross sections once their mass is approximately known. The method works in practice because spins are quantized and cross sections depend strongly on spins. It can be used to determine, for example, the spin of the top quark. Direct application of this method to supersymmetric theories will have to overcome the challenge of measuring mass at the LHC, which could require high statistics. In this article, we propose a method of measuring the spins of the colored superpatners by combining rate information for several channels and a set of kinematical variables, without directly measuring their masses. We argue that such a method could lead to an early determination of the spin of gluino and squarks. This method can be applied to the measurement of spin of other new physics particles and more general scenarios.Comment: 23 pages, 8 figures, minor change

Testing the Gaussian expansion method in exactly solvable matrix models

The Gaussian expansion has been developed since early 80s as a powerful analytical method, which enables nonperturbative studies of various systems using `perturbative' calculations. Recently the method has been used to suggest that 4d space-time is generated dynamically in a matrix model formulation of superstring theory. Here we clarify the nature of the method by applying it to exactly solvable one-matrix models with various kinds of potential including the ones unbounded from below and of the double-well type. We also formulate a prescription to include a linear term in the Gaussian action in a way consistent with the loop expansion, and test it in some concrete examples. We discuss a case where we obtain two distinct plateaus in the parameter space of the Gaussian action, corresponding to different large-N solutions. This clarifies the situation encountered in the dynamical determination of the space-time dimensionality in the previous works.Comment: 30 pages, 15 figures, LaTeX; added references for section

Gene Function Classification Using Bayesian Models with Hierarchy-Based Priors

We investigate the application of hierarchical classification schemes to the annotation of gene function based on several characteristics of protein sequences including phylogenic descriptors, sequence based attributes, and predicted secondary structure. We discuss three Bayesian models and compare their performance in terms of predictive accuracy. These models are the ordinary multinomial logit (MNL) model, a hierarchical model based on a set of nested MNL models, and a MNL model with a prior that introduces correlations between the parameters for classes that are nearby in the hierarchy. We also provide a new scheme for combining different sources of information. We use these models to predict the functional class of Open Reading Frames (ORFs) from the E. coli genome. The results from all three models show substantial improvement over previous methods, which were based on the C5 algorithm. The MNL model using a prior based on the hierarchy outperforms both the non-hierarchical MNL model and the nested MNL model. In contrast to previous attempts at combining these sources of information, our approach results in a higher accuracy rate when compared to models that use each data source alone. Together, these results show that gene function can be predicted with higher accuracy than previously achieved, using Bayesian models that incorporate suitable prior information

Speaker- versus listener-oriented disfluency: A re-examination of arguments and assumptions from autism spectrum disorder

We re-evaluate conclusions about disfluency production in high-functioning forms of autism spectrum disorder (HFA). Previous studies examined individuals with HFA to address a theoretical question regarding speaker- and listener-oriented disfluencies. Individuals with HFA tend to be self-centric and have poor pragmatic language skills, and should be less likely to produce listener-oriented disfluency. However, previous studies did not account for individual differences variables that affect disfluency. We show that both matched and unmatched controls produce fewer repairs than individuals with HFA. For silent pauses, there was no difference between matched controls and HFA, but both groups produced more than unmatched controls. These results identify limitations in prior research and shed light on the relationship between autism spectrum disorders and disfluent speech