Miracle-dz/UniFAR-FTUs huggingface dataset:
Java Tools and Technologies for Cluster Computing

The Java language and its associated libraries and environment provide a powerful and flexible platform for programming computer clusters. Java tools and technologies enable experimentation in both management aspects as well as performance aspects of cluster systems. We discuss the current interesting problems in cluster computing including those derived from distributed computing as well as the more performance-related ones derived from the discipline of parallel computing. We describe our experiments in building meta-computing management software in Java and message-passing high performance support software also written in pure Java. Our DISCWorld meta-computing system allows cluster applications to be embedded as services in a problem-solving environment. Our JUMP message-passing system allows users to develop conventional stand-alone Java applications that use the message-passing model of parallelism on cluster systems. JUMP applications are also compatible with DISCWorld and can be launched as component tasks in a dataflow-style task graph as managed by DISCWorld. In addition we discuss the support of multiple paradigms for parallelism, such as regular domain decomposition; irregular or scattered spatial decomposition; task farming; and dynamic and adaptive mesh support, that we are building into JUMP. We believe these higher level facilities make parallel computing on clusters easier for users to exploit. We review some of the Java tools and technologies available now and becoming available and discuss the contributions they make to cluster computing. We also describe experiments with these and how they influenced our design decisions for JUMP.
Mining security changes in FreeBSD

Current research on historical project data is rarely touching on the subject of security related information. Learning how security is treated in projects and which parts of a software are historically security relevant or prone to security changes can enhance the security strategy of a software project. We present a mining methodology for security related changes by modifying an existing method of software repository analysis. We use the gathered security changes to find out more about the nature of security in the FreeBSD project and we try to establish a link between the identified security changes and a tracker for security issues (security advisories). We give insights how security is presented in the FreeBSD project and show how the mined data and known security problems are connected.
Efficacy of Glass Ionomer Cements for Prevention of White Spot Lesions During Orthodontic Banding: A Randomized Clinical Trial

Objectives: This study aimed to compare the incidence of white spot lesions (WSLs) around orthodontic bands following the application of two glass ionomer (GI) cements namely GC Gold Label and GC Fuji Plus for six to 12 months. Materials and Methods: A total of 186 permanent first molars of orthodontic patients requiring banding of at least two permanent first molars were chosen. The teeth were examined for caries and presence of WSLs by visual inspection and by DIAGNOdent (scores 0–29). Orthodontic bands were randomly cemented to the right or left molars using GC Gold Label or GC Fuji Plus GI cements. Samples were randomly divided into three groups and bands were removed after six, nine and 12 months in groups 1, 2 and 3, respectively. The teeth were then examined for caries and presence of WSLs by visual inspection. DIAGNOdent was used on the buccal and lingual surfaces to determine the presence of WSLs. The data were statistically analyzed using one-way ANOVA, multivariate repeated measures ANOVA, the Kruskal Wallis and the Mann-Whitney tests. Results: Totally 174 teeth were evaluated. DIAGNOdent scores were not significantly different before cementation and after removal of bands in buccal and lingual surfaces of the teeth in the two cement groups. Lesions simulating WSLs were seen in 21 out of 174 teeth but DIAGNOdent scores were not indicative of caries. Conclusion: Remarkable WSLs were not detected visually or by DIAGNOdent at six, nine or 12 months following the cementation of bands with two GI cements.
mazEF: a chromosomal toxin-antitoxin module that triggers programmed cell death in bacteria

mazEF is a toxin-antitoxin module located on the Escherichia coli chromosome and that of some other bacteria, including pathogens. mazF specifies for a stable toxin, MazF, and mazE specifies for a labile antitoxin, MazE, that antagonizes MazF. MazF is a sequence-specific mRNA endoribonuclease that initiates a programmed cell death pathway in response to various stresses. The mazEF-mediated death pathway can act as a defense mechanism that prevents the spread of bacterial phage infection, allowing bacterial populations to behave like multicellular organisms.
Multivalued Geodesic Ray-Tracing for Computing Brain Connections Using Diffusion Tensor Imaging

Diffusion tensor imaging (DTI) is a magnetic resonance technique used to explore anatomical fibrous structures, like brain white matter. Fiber-tracking methods use the diffusion tensor (DT) field to reconstruct the corresponding fibrous structure. A group of fiber-tracking methods trace geodesics on a Riemannian manifold whose metric is defined as a function of the DT. These methods are more robust to noise than more commonly used methods where just the main eigenvector of the DT is considered. Until now, geodesic-based methods were not able to resolve all geodesics, since they solved the Eikonal equation, and therefore were not able to deal with multivalued solutions. Our algorithm computes multivalued solutions using an Euler–Lagrange form of the geodesic equations. The multivalued solutions become relevant in regions with sharp anisotropy and complex geometries, or when the first arrival time does not describe the geodesic close to the anatomical fibrous structure. In this paper, we compare our algorit.
Policy Gradients Beyond Expectations: Conditional Value-at-Risk

Conditional Value at Risk (CVaR) is a prominent risk measure that is being used extensively in various domains such as finance. In this work we present a new formula for the gradient of the CVaR in the form of a conditional expectation. Our result is similar to policy gradients in the reinforcement learning literature. Based on this formula, we propose novel sampling-based estimators for the CVaR gradient, and a corresponding gradient descent procedure for CVaR optimization. We evaluate our approach in learning a risk-sensitive controller for the game of Tetris, and propose an importance sampling procedure that is suitable for such domains.
Evidence of a Functional Relationship between the Nucleus Accumbens Shell and Lateral Hypothalamus Subserving the Control of Feeding Behavior

Inhibition of neurons in the nucleus accumbens shell (AcbSh) with local injections of GABA agonists or glutamate antagonists elicits an intense, but specific, feeding response resembling that seen after stimulation of the lateral hypothalamus (LH). To help characterize the contribution of the LH to the expression of AcbSh-mediated feeding, we used the immunohistochemical detection of the nuclear protein Fos to determine whether inhibition of AcbSh cells results in an activation of LH neurons. Injections of the GABAA agonist muscimol into the AcbSh greatly increased the number of cells exhibiting Fos-like immunoreactivity in the LH, as well as in the lateral septum, paraventricular hypothalamic nucleus, ventral tegmental area, substantia nigra pars compacta, and nucleus of the solitary tract. Blocking activation of LH neurons with the selective NMDA receptor blocker d(−)-AP-5 is known to suppress deprivation-induced feeding. We found that injections ofd(−)-AP5 into the LH also dose-dependently suppressed AcbSh-mediated feeding. It is likely that inhibition of GABAergic neurons in the AcbSh is responsible for eliciting this feeding. If a behaviorally relevant GABAergic projection terminates in the LH, we should be able to mimic the effects seen after inhibition of the projection neurons by applying a GABA receptor blocker to the area. However, injections of the GABAA receptor blocker bicuculline or the GABABreceptor blocker saclofen did not significantly affect food intake. Thus, it appears that the expression of the feeding response depends on an NMDA-preferring receptor-mediated activation of LH neurons and is not the result of disinhibiting LH cells by disrupting transmission at GABA synapses.
A Novel Approach For Diversity And Multiplexing Gain Using SM-OSTBC

Spatial Modulation (SM) provides a multiplexing gain with respect to single-antenna systems by avoiding inter-channel interference. The aim of this paper is to design multiple-antenna wireless systems that exploit the SM concept and analyse e a SM-OSTBC (Orthogonal Space-Time Block Codes) and Alamouti STBC technology. By using analysis and simulation, we would compare the result.
Birth defects in children conceived by ICSI compared with children conceived by other IVF-methods; a meta-analysis.

BACKGROUND Intracytoplasmic sperm injection (ICSI) is a method of assisted reproductive technology that involves the selection of a single sperm cell and the manual injection of this cell into the egg. The lack of relevant experimental studies, the nature of the technology involving non-natural selection of the fertilizing sperm, and possible damage to the egg have caused concern that ICSI could increase the risk of birth defects. Data from available cohort studies comparing ICSI with standard in vitro fertilization (IVF) should be combined to evaluate the risks involved with ICSI. METHODS We reviewed more than 2500 titles and abstracts containing keywords related to ICSI and identified 22 scientific articles with data on birth defects among ICSI-births. A total of four peer-reviewed, non-overlapping prospective cohort studies provided reliable and comparable data on birth defects both for children conceived by ICSI and children conceived by standard IVF. These studies included a total of 5395 children born after ICSI. RESULTS The pooled estimate of the risk of a major birth defect was a 1.12-fold increase after ICSI when compared with standard IVF (risk ratio = 1.12, 95% confidence interval (CI): 0.97-1.28, P = 0.12). There was no marked heterogeneity of risk ratios between these studies (P = 0.10). We found no significantly increased risks after ICSI for any of the categories cardiovascular defects, musculoskeletal defects, hypospadias, neural tube defects, or oral clefts. CONCLUSIONS Our analysis does not indicate that the ICSI-procedure represents significant additional risks of major birth defects in addition to the risk involved in standard IVF. The data was limited, particularly on risks of specific categories of defects.
Traffic control under scarce resources in wireless networks - a game-based approach

Typically, in order to organize the traffic in networks, some routing protocol is involved to establish and maintain paths for data flow. In the light of routing limitations in wireless environments, particularly restrictive when low power nodes are involved in a dynamic environment, the paper presents a different approach to organize the network traffic. In the proposed solution each node takes an independent and selfish decision about forwarding the data as a result of a game between the nodes.
A Financial Decision Supporting System Based on Fuzzy Candlestick Patterns

A financial decision supporting system based on the fuzzy candlestick pattern is proposed and developed. We model Japanese candlestick patterns by using fuzzy linguistic variables. Japanese candlestick theory is an empirical model of investment decision. The theory assumes that the trend of financial time series could be predicted by identifying specific candlestick patterns in the candlestick charts. In our system, the investment expertise is represented in fuzzy candlestick patterns and can be stored in a pattern base. The investors can make their investment decisions based on the identified candlestick patterns. A knowledge based pattern recognition method for candlestick pattern is implemented in the system, and the investor can edit, validate, and share the imprecise and vague candlestick patterns through the graphical interface of the proposed system.
Change in human brain functional network based on Granger causality analysis

In recent years, the emergence of the fMRI provides a possibility of further exploration for the human brain. The complex workings of the brain are composed of a plurality of brain functional networks. To further explore the change affected by task in human brain functional network, the efficiency of a method of effective connectivity is examined by comparing the two resting state fMRI data before and after a task. Distinguished from the view of the brain network as a whole in previous studies, the method of Granger causality analysis (GCA) we used is focused on the internal organization within a brain network. Also, the method of functional connectivity is used to compare the efficiency of Granger causality analysis. The results show that taking the default mode network (DMN) as an example, the method of Granger causality analysis can be more sensitive to the functional re-organization in a human brain network after a task compared with functional connectivity. And the target of incoming causal influences area changed from rPCu to BG after task.
Handling Concept Drift in a Text Data Stream Constrained by High Labelling Cost

In many real-world classification problems the concept being modelled is not static but rather changes over time - a situation known as concept drift. Most techniques for handling concept drift rely on the true classifications of test instances being available shortly after classification so that classifiers can be retrained to handle the drift. However, in applications where labelling instances with their true class has a high cost this is not reasonable. In this paper we present an approach for keeping a classifier up-to-date in a concept drift domain which is constrained by a high cost of labelling. We use an active learning type approach to select those examples for labelling that are most useful in handling changes in concept. We show how this approach can adequately handle concept drift in a text filtering scenario requiring just 15% of the documents to be manually categorised and labelled.
Metabolic syndrome among HIV-infected patients: prevalence, characteristics, and related factors.

OBJECTIVE To assess the prevalence in HIV-infected patients of the metabolic syndrome as defined by the National Cholesterol Education Program, i.e., three or more of the following components: abdominal obesity, hypertriglyceridemia, low HDL cholesterol, high blood pressure, and high fasting glucose. RESEARCH DESIGN AND METHODS In this cross-sectional study, 710 HIV-infected patients managed at the outpatient clinic of a tertiary hospital during 2003 completed the study protocol consisting of a medical examination and laboratory analysis after a 12-h overnight fast. RESULTS Metabolic syndrome prevalence was 17% and increased from 5.1% among HIV-infected patients under age 30 years to 27.0% for those aged 50-59 years. Age (per 10-year increment) (odds ratio [OR] 1.41 [95% CI 1.12-1.77]), BMI (1.27 [1.19-1.36]), past and present protease inhibitor exposure (2.96 [1.03-3.55] and 4.18 [1.4-12.5], respectively) were independently associated with the metabolic syndrome on logistic regression analysis. Furthermore, only stavudine (d4T) (1.74 [1.01-2.98]) and lopinavir/ritonavir (2.46 [1.28-4.71]) were associated with the metabolic syndrome after adjustment for age and BMI. CONCLUSIONS The prevalence of metabolic syndrome among these HIV-infected patients is similar to that previously reported in uninfected individuals. Of specific concern is the association of protease inhibitor exposure with the metabolic syndrome and, more specifically, with exposure to stavudine and lopinavir/ritonavir when individual antiretroviral drugs were analyzed.
Human Immunodeficiency Virus Type 1 Replication Is Modulated by Host Cyclophilin A Expression Levels

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) Gag and the cellular protein cyclophilin A form an essential complex in the virion core: virions produced by proviruses encoding Gag mutants with decreased cyclophilin A affinity exhibit attenuated infectivity, as do virions produced in the presence of the competitive inhibitor cyclosporine. The A224E Gag mutant has no effect on cyclophilin A affinity but renders HIV-1 replication cyclosporine resistant in Jurkat T cells. In contrast, A224E mutant virus is dead in H9 T cells, although replication is rescued by cyclosporine or by expression in cis of a Gag mutant that decreases cyclophilin A-affinity. The observation that disruption of the Gag-cyclophilin A interaction rescues A224E mutant replication in H9 cells prompted experiments which revealed that, relative to Jurkat cells, H9 cells express greater quantities of cyclophilin A. The resulting larger quantity of cyclophilin A shown to be packaged into virions produced by H9 cells is presumably disruptive to the A224E mutant virion core. Further evidence that increased cyclophilin A expression in H9 cells is of functional relevance was provided by the finding that Gag mutants with decreased cyclophilin A affinity are dead in Jurkat cells but capable of replication in H9 cells. Similarly, cyclosporine concentrations which inhibit wild-type HIV-1 replication in Jurkat cells stimulate HIV-1 replication in H9 cells. These results suggest that HIV-1 virion infectivity imposes narrow constraints upon cyclophilin A stoichiometry in virions and that infectivity is finely tuned by host cyclophilin A expression levels.
Vector quantization of LSF parameters with a mixture of dirichlet distributions

Quantization of the linear predictive coding parameters is an important part in speech coding. Probability density function (PDF)-optimized vector quantization (VQ) has been previously shown to be more efficient than VQ based only on training data. For data with bounded support, some well-defined bounded-support distributions (e.g., the Dirichlet distribution) have been proven to outperform the conventional Gaussian mixture model (GMM), with the same number of free parameters required to describe the model. When exploiting both the boundary and the order properties of the line spectral frequency (LSF) parameters, the distribution of LSF differences LSF can be modelled with a Dirichlet mixture model (DMM). We propose a corresponding DMM based VQ. The elements in a Dirichlet vector variable are highly mutually correlated. Motivated by the Dirichlet vector variable's neutrality property, a practical non-linear transformation scheme for the Dirichlet vector variable can be obtained. Similar to the Karhunen-Loève transform for Gaussian variables, this non-linear transformation decomposes the Dirichlet vector variable into a set of independent beta-distributed variables. Using high rate quantization theory and by the entropy constraint, the optimal inter- and intra-component bit allocation strategies are proposed. In the implementation of scalar quantizers, we use the constrained-resolution coding to approximate the derived constrained-entropy coding. A practical coding scheme for DVQ is designed for the purpose of reducing the quantization error accumulation. The theoretical and practical quantization performance of DVQ is evaluated. Compared to the state-of-the-art GMM-based VQ and recently proposed beta mixture model (BMM) based VQ, DVQ performs better, with even fewer free parameters and lower computational cost
Discordant 16S and 23S rRNA Gene Phylogenies for the Genus Helicobacter: Implications for Phylogenetic Inference and Systematics

ABSTRACT Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31′ and 27′. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum.
Proximal methods for image restoration using a class of non-tight frame representations

The objective of this paper is to develop a convex optimization approach for solving image deconvolution problems involving frame representations. Until now, most of the proposed frame-based variational methods assumed either Lipschitz differentiability properties or tight representations. These assumptions are relaxed here, thus offering the possibility of considering a broader class of image restoration problems. The proposed algorithms allow us to solve both frame analysis and frame synthesis problems for various noise distributions. The proposed approach is proved to be effective for restoring data corrupted by Poisson noise by using (non-tight) discrete dual-tree wavelet representations.
Three Accounts of Literary Style

And this is precisely what happens in the opening sentence of Pride and Prejudice: “It is a truth universally acknowledged, that a single man in possession of a good fortune, must be in want of a wife” (Austen, 1). But how does this instant seduction operate? At first reading, the sentence appears to state a truth, of universal import, the kind of truth we assign to the proposition, “It is a truth that water boils at 100° Celsius. ” But it immediately weakens this assertion by stating that such truth is “universally acknowledged. ” Far from being an improvement, this is a retreat: a truth is a truth is a truth, and I need not add that its acknowledgment is “universal” —there would be something strange in the statement that “it is a truth, universally acknowledged, that water boils at 100° Celsius. ” And the situation gets even worse with the rest of