Miracle-dz/UniFAR-FTUs huggingface dataset:
Bayesian computation for statistical models with intractable normalizing constants

This paper deals with some computational aspects in the Bayesian analysis of statistical models with intractable normalizing constants. In the presence of intractable normalizing constants in the likelihood function, traditional MCMC methods cannot be applied. We propose an approach to sample from such posterior distributions. The method can be thought as a Bayesian version of the MCMC-MLE approach of Geyer and Thompson (1992). To the best of our knowledge, this is the first general and asymptotically consistent Monte Carlo method for such problems. We illustrate the method with examples from image segmentation and social network modeling. We study as well the asymptotic behavior of the algorithm and obtain a strong law of large numbers for empirical averages.
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.

We present here a simple and fast method allowing the isolation of DNA binding sites for transcription factors from families of coregulated genes, with results illustrated in Saccharomyces cerevisiae. Although conceptually simple, the algorithm proved efficient for extracting, from most of the yeast regulatory families analyzed, the upstream regulatory sequences which had been previously found by experimental analysis. Furthermore, putative new regulatory sites are predicted within upstream regions of several regulons. The method is based on the detection of over-represented oligonucleotides. A specificity of this approach is to define the statistical significance of a site based on tables of oligonucleotide frequencies observed in all non-coding sequences from the yeast genome. In contrast with heuristic methods, this oligonucleotide analysis is rigorous and exhaustive. Its range of detection is however limited to relatively simple patterns: short motifs with a highly conserved core. These features seem to be shared by a good number of regulatory sites in yeast. This, and similar methods, should be increasingly required to identify unknown regulatory elements within the numerous new coregulated families resulting from measurements of gene expression levels at the genomic scale. All tools described here are available on the web at the site http://copan.cifn. unam.mx/Computational_Biology/ yeast-tools
Characterization of a Novel Two-Partner Secretion System in Escherichia coli O157:H7

ABSTRACT Gram-negative bacteria contain multiple secretion pathways that facilitate the translocation of proteins across the outer membrane. The two-partner secretion (TPS) system is composed of two essential components, a secreted exoprotein and a pore-forming β barrel protein that is thought to transport the exoprotein across the outer membrane. A putative TPS system was previously described in the annotation of the genome of Escherichia coli O157:H7 strain EDL933. We found that the two components of this system, which we designate OtpA and OtpB, are not predicted to belong to either of the two major subtypes of TPS systems (hemolysins and adhesins) based on their sequences. Nevertheless, we obtained direct evidence that OtpA and OtpB constitute a bona fide TPS system. We found that secretion of OtpA into the extracellular environment in E. coli O157:H7 requires OtpB and that when OtpA was produced in an E. coli K-12 strain, its secretion was strictly dependent on the production of OtpB. Furthermore, using OtpA/OtpB as a model system, we show that protein secretion via the TPS pathway is extremely rapid.
Who is Punished? How Voters Evaluate Male and Female Legislators Who Do Not Compromise

A record high number of women currently serve in the U.S. Congress. This increase has led many people to speculate that more female legislators will mean more legislative compromise and consensus building. Given these types of expectations – perpetuated by media, politicians and even political science research – what happens when female politicians refuse to compromise? Previous research suggests conflicting possibilities. While some research on gender suggests that women who break with gender stereotypes (for example, by refusing to compromise) can face a backlash, other research shows that gender stereotypes have a minimal effect on how the public perceives female politicians. In this manuscript, we examine how people respond to female lawmakers who do not compromise. Relying on two national experiments, we demonstrate that female lawmakers may face a heavier punishment for not compromising, but only under certain conditions. In fact, we show that under other conditions it is male legislators who are disproportionately punished for refusing to compromise.
Machine learning approaches for the discovery of gene-gene interactions in disease data

Because of the complexity of gene-phenotype relationships machine learning approaches have considerable appeal as a strategy for modelling interactions. A number of such methods have been developed and applied in recent years with some modest success. Progress is hampered by the challenges presented by the complexity of the disease genetic data, including phenotypic and genetic heterogeneity, polygenic forms of inheritance and variable penetrance, combined with the analytical and computational issues arising from the enormous number of potential interactions. We review here recent and current approaches focusing, wherever possible, on applications to real data (particularly in the context of genome-wide association studies) and looking ahead to the further challenges posed by next generation sequencing data.
Network Synthesis with Non-Simultaneous Multicommodity Flow Requirements: Bounds and Heuristics

Whenever an edge failure occurs in a telecommunications network, the amount of traac using the faulty edge has to be rerouted on some other paths through the network thus requiring the presence of reserve capacity in the network. This leads to the design of a network of extra capacities suucient to independently reroute the ow on each arc and having minimum cost. This problem is known as a network synthesis problem with non-simultaneous multicommodity ow requirements. Here we propose to use a surrogate duality method based on a model formulation containing several blocks of constraints to compute lower bounds on the linear relaxation of the problem. This bound is then considered as input to a greedy heuristic to nd integer feasible solutions. Finally, a tabu search procedure based on this greedy heuristic is developed and tested on a wide set of problem instances. 1 duality, lower bounds, tabu search.
Using a Formal Language Constructs for Software Model Evolution

In this paper we present an automated support for software model evolution using a formal language constructs. For this, we extended Object Constraint Language (OCL) with actions to define a new language - CAL (Constraint with Action Language), which gives users the ability to evaluate objects change a-priori. We have added a data type, directed acyclic graph (DAG) to CAL to automate model evolution. DAG has been annotated (ADAG) with dependency weights based on an improved graph labeling scheme. Rules are designed to translate a UML model into CAL data structure (ADAG). CAL contains a small set of constructs, but is powerful enough to be used efficiently for typical software evolution management operations like impact analysis, correction, improvement and enhancement of models. A prototype tool VCAL (visual CAL), for dependency analysis of UML Class Diagrams is presented.
Dietary macronutrient composition affects b cell responsiveness but not insulin sensitivity 1 – 3

Background: Altering dietary carbohydrate or fat content may have chronic effects on insulin secretion and sensitivity, which may vary with individual metabolic phenotype. Objective: The objective was to evaluate the contribution of tightly controlled diets differing in carbohydrate and fat content for 8 wk to insulin sensitivity and b cell responsiveness and whether effects of diet would vary with race, free-living diet, or insulin response. Design: Healthy overweight men and women (36 European Americans, 33 African Americans) were provided with food for 8 wk and received either a eucaloric standard diet (55% carbohydrate, 27% fat) or a eucaloric reduced-carbohydrate (RedCHO)/higher-fat diet (43% carbohydrate, 39% fat). Insulin sensitivity and b cell responsiveness were assessed at baseline and 8 wk by using a liquid meal
Assessment of Energy Intake and Energy Expenditure of Male Adolescent Academy-Level Soccer Players during a Competitive Week

This study investigated the energy intake and expenditure of professional adolescent academy-level soccer players during a competitive week. Over a seven day period that included four training days, two rest days and a match day, energy intake (self-reported weighed food diary and 24-h recall) and expenditure (tri-axial accelerometry) were recorded in 10 male players from a professional English Premier League club. The mean macronutrient composition of the dietary intake was 318 ± 24 g·day−1 (5.6 ± 0.4 g·kg−1 BM) carbohydrate, 86 ± 10 g·day−1 (1.5 ± 0.2 g·kg−1 BM) protein and 70 ± 7 g·day−1 (1.2 ± 0.1 g·kg−1 BM) fats, representing 55% ± 3%, 16% ± 1%, and 29% ± 2% of mean daily energy intake respectively. A mean daily energy deficit of −1302 ± 1662 kJ (p = 0.035) was observed between energy intake (9395 ± 1344 kJ) and energy expenditure (10679 ± 1026 kJ). Match days (−2278 ± 2307 kJ, p = 0.012) and heavy training days (−2114 ± 2257 kJ, p = 0.016) elicited the greatest deficits between intake and expenditure. In conclusion, the mean daily energy intake of professional adolescent academy-level soccer players was lower than the energy expended during a competitive week. The magnitudes of these deficits were greatest on match and heavy training days. These findings may have both short and long term implications on the performance and physical development of adolescent soccer players.
Geographical seroprevalence of Anaplasma marginale infection (anaplasmosis) by ELISA in Ovis aries, in district Peshawar, Pakistan

Geographical seroprevalence of Anaplasma marginale(T) in sheep, Ovis aries (L) was done from January-May, 2012 in district Peshawar which is a crowded area of Pakistan. In this area sheep’s infection with A. marginale is not reported before. For this purpose, 376 serum samples were obtained conveniently from 4 different breeds of sheep, from different geographical areas of Peshawar. An indirect ELISA using recombinant MSP-5 as antigen of A. marginale, was performed. Totally, 92/376 (24.47%) of the overall sheep sera were positive. In 6 areas of Peshawar, Peshthakhara and Mashokhel area were found highly infected i.e. 32.00% and 32.00% respectively, while Ghazi baba area was less infected comparatively. This is the first record of A. marginale showing high rate infection in sheep in Peshawar, Pakistan, This research should be useful in epidemiological applications.
Guidelines for the use of spiral computed tomography in screening for lung cancer

Screening should be considered in lung cancer, more than any other cancer. Not only is the disease highly fatal, essentially incurable, when diagnosed on the prompting of symptoms and/or clinical signs, but its occurrence is also highly concentrated in identifiably high-risk persons. The degree of usefulness of computed tomography (CT)-based screening for lung cancer must be thought of in reference to a particular, presumably optimal, regimen of pursuing early stage diagnosis. This is an algorithm that begins with the initial test (“screening CT”) and ends in either discontinuation of the diagnostic pursuit or in diagnosis of lung cancer. A carefully developed, extensively pilot tested and critically reviewed, updated protocol for CT-based screening for lung cancer is presented here. Its implementation is addressed, together with quality assurance. Finally, the associated curability rate for lung cancer is addressed in the light of what is known or can be surmised from evidence already available. However, recommendation for or against screening requires further information. Principally, the patients risk for lung cancer (in the near future) and the patients life expectancy (when spared of death from lung cancer). These two factors influence when, if ever, to begin screening, and if it is initiated, when to discontinue it. Finally, cost-effectiveness of the screening program should also be considered.
What the Third World Wants: An Interpretation of the Development and Meaning of the New International Economic Order Ideology

This article proposes one answer to the question of 'why Third World governments have adopted and supported the ideology underlying their proposals for a New International Economic Order'. While it may seem ambitious to try to assess what the Third World wants (many others have already tried), this attempt differs from some others in that it is particularly concerned with the ways beliefs (and beliefs about beliefs) affect conflict resolution.
Effects of silibinin and ethanol on skeletal muscle ischemia-reperfusion injury.

PURPOSE To investigate the potential beneficial effect of silibinin in ischemia-reperfusion injury (IRI) of skeletal muscle. METHODS Under urethane anesthesia, four experimental groups were established in Balb/c mice: I) Sham-control, II) IRI (Tourniquet-induced) (2+1 h), III) IRI+ethanol (10%), and IV) IRI+silibinin (50 mg/kg/IP). The viability of muscle (left) was evaluated by the triphenyltetrazolium chloride dye method and calculated as the percentage of the contralateral control muscle (right). Malondialdehyde, superoxide dismutase, and catalase were measured in the gastrocnemius muscle via a spectrophotometer. RESULTS The viability of gastrocnemius muscle in group II was significantly lower in comparison with that seen in group I. The administration of either ethanol or silibinin rendered the tissues to recover nearly to the baseline level. Additionally, malondialdehyde levels were higher in group II than those in group I. The application of silibinin prior to the reperfusion attenuated these to the control levels. However, malondialdehyde levels in the ethanol administrated group were reduced as well. The enhanced superoxide dismutase activity seen in the IRI group was not diminished in the animals treated with either silibinin or ethanol. Similarly, there were no differences between groups regarding the catalase activities. CONCLUSION Ethanol seems to be effective in attenuating IRI in skeletal muscle and no definite conclusion can be made on silibinin effect.
Unprecedented simultaneous enhancement in strain tolerance, toughness and strength of Al2O3 ceramic by multiwall-type failure of a high loading of carbon nanotubes

Carbon nanotubes (CNTs) have a remarkable load-bearing ability. Recently, however, multi-walled CNTs (MWCNTs) have been shown to possess dramatically higher load-bearing ability when intimately embedded in an oxide ceramic (Al2O3), because the load could be transferred not to only their outermost walls but also their generally unloaded inner walls via the strong interwall shear resistance originating from residual compressive stresses. This phenomenon is characterized by an uncommon, highly energy-dissipating, multiwall-type failure of individual MWCNTs during hybrid fracture, with no evidence of pullout. Here, we demonstrate that this nanoscale in-MWCNT load-transfer process, at an optimized, high loading of MWCNTs (10 vol%) and in a pore-free and uniform platform, leads to unprecedented, dramatic simultaneous enhancement in strain tolerance (81%), fracture toughness (52.2%), and flexural strength (22%) of the Al2O3 ceramic matrix. The extent of toughening by this mechanism is also the highest ever reported. This unprecedented performance by using a high loading of functional MWCNTs, namely, toughening, strengthening, softening and lightening, simultaneously and at this level, has implications for many functional and structural applications.
Detecting Intelligence - The Turing Test and Other Design Detection Methodologies

âCan machines think? â When faced with this âmeaninglessâ question, Alan Turing suggested we ask a different, more precise question: can a machine reliably fool a human interviewer into believing the machine is human? To answer this question, Turing outlined what came to be known as the Turing Test for artificial intelligence, namely, an imitation game where machines and humans interacted from remote locations and human judges had to distinguish between the human and machine participants. According to the test, machines that consistently fool human judges are to be viewed as intelligent. While popular culture champions the Turing Test as a scientific procedure for detecting artificial intelligence, doing so raises significant issues. First, a simple argument establishes the equivalence of the Turing Test to intelligent design methodology in several fundamental respects. Constructed with similar goals, shared assumptions and identical observational models, both projects attempt to detect intelligent agents through the examination of generated artifacts of uncertain origin. Second, if the Turing Test rests on scientifically defensible assumptions then design inferences become possible and cannot, in general, be wholly unscientific. Third, if passing the Turing Test reliably indicates intelligence, this implies the likely existence of a designing intelligence in nature.
Mental Health and Psychosocial Adjustment of Cuban Immigrants in South Florida

Given documented variation in pre-migration and migration-related experiences, Cuban immigrants in the U.S. who arrived during or subsequent to 1980 may be disadvantaged in mental health and psychosocial adjustment relative to earlier arrivals. Using wave 1 of the Physical Challenge and Health study, we compare earlier and later arriving immigrants in levels of depression, anxiety, and self-esteem and test whether adversity and social support, acculturationrelated factors, or pre-migration conditions account for any differences observed among a sample of adults living in South Florida (N=191). Bivariate analyses reveal that later arrivals are relatively disadvantaged in anxiety and self-esteem and marginally so in depression. While later arrivals do not report more adversity in the U.S., they have lower levels of family support to cope with any adversity experienced. Later arrivals are also less likely to interview in English or to have a strong American identity, and they were more likely to have arrived as adults. Relative disadvantages in anxiety and self-esteem are best explained by indicators of acculturation and family support. Policies and programs that address acculturation difficulties and increase family support could improve the health and adjustment of these and similar immigrants.
Procedural Interpretation: A Method of Working Between the Lines in the Nonverbal Realm

Throughout the last century, verbal interpretation has been an inseparable companion to the process of psychoanalysis, and the ability to interpret effectively continues to be highly valued by psychoanalysts. Today many of us can convincingly argue that a thoughtful, well-timed interpretation still constitutes the most significant therapeutic event that can occur in an analysis. Our acknowledgment of the importance of spoken interpretation can have its disadvantages, though. Efforts to fine-tune our ability to convey understanding by verbal means may run the risk of disavowing another essential aspect of our clinical work: namely that of nonverbal activities, which themselves can have a very powerful therapeutic impact. That we sometimes have difficulty finding the language to describe these activities and may occasionally neglect them shouldn’t surprise us—nonverbal issues seem to be the stuff of intuition, not objective discourse. In most relationships, much of what is going on nonverbally is usually not talked about directly— it is simply experienced between the lines. Regardless of any tendency to overlook them, these between-the-lines, nonverbal events can contribute significantly both in achieving understanding, and communicating that understanding to our patients. In fact, I believe that a therapist needs to demonstrate his thinking through his behavior as a necessary adjunct to communicating with words. In this way, I hope to elevate the realm of behavior to be equal to the realm of language in the interpretive process.
Treating young children's disruptive behavior problems: dissemination of an evidence- based parent management training program in the Netherlands

High levels of young children’s disruptive behavior problems are persistent, highly prevalent, and a serious public health concern. If left untreated, these behaviors can lead to serious difficulties in broad areas of child and family functioning, and economically impact the wider society. Therefore, early intervention is necessary to protect these children and their parents from a negative developmental trajectory. Reviews of treatment outcome literature for young children with disruptive behavior problems find that interventions involving parents as the primary agent of change remain the most consistently supported. The focus of this thesis was on the theme of dissemination of an evidence-based parent management training program to the Netherlands, and in particular the implementation of Parent-Child Interaction Therapy. The primary aim of this thesis was to study the effectiveness of PCIT in Dutch clinical practice and additionally other components related to dissemination and study of parent management training (PMT) programs were evaluated, including behavioral assessment techniques, treatment attrition, and therapists’ perspectives. The findings from the effectiveness studies on PCIT in this thesis show that PMT programs can be successfully transported to the Netherlands without the need for cultural adaptations and work well in real-world clinical practice. Findings on other implementation outcomes including the therapists’ perspectives on training and the treatment model, and good psychometric properties for the integral behavioral assessment techniques support this conclusion. In the general discussion recommendations are made for future research on long-term maintenance, effective elements, and treatment retention in order to understand how benefits of PMT programs for children, their families, and the greater society can be maximized.
A fast and compact quantum random number generator

We present the realization of a physical quantum random number generator based on the process of splitting a beam of photons on a beam splitter, a quantum mechanical source of true randomness. By utilizing either a beam splitter or a polarizing beam splitter, single photon detectors and high speed electronics the presented devices are capable of generating a binary random signal with an autocorrelation time of 11.8 ns and a continuous stream of random numbers at a rate of 1 Mbit/s. The randomness of the generated signals and numbers is shown by running a series of tests upon data samples. The devices described in this paper are built into compact housings and are simple to operate.