Miracle-dz/UniFAR-FTUs huggingface dataset:
Study on the detection and correction of software based on UML

We have proposed an approach to the correction of anti-patterns; we believe that before attempting such corrections it is important to have confirmation from the developer. Assumptions are made when identifying or correcting certain anti-patterns; however, these assumptions that we recognize as the causes of the anti-pattern may be the behavior the developer actually intended with the design, or may not be the most optimal correction for the anti pattern. We propose these transformations as a guide for the improvement of the design; nevertheless the decision of applying the changes should be left to the user.
Inactivation of the Tricarboxylic Acid Cycle Aconitase Gene from Streptomyces viridochromogenesTü494 Impairs Morphological and Physiological Differentiation

ABSTRACT The tricarboxylic acid (TCA) cycle aconitase gene acnAfrom Streptomyces viridochromogenes Tü494 was cloned and analyzed. AcnA catalyzes the isomerization of citrate to isocitrate in the TCA cycle, as indicated by the ability of acnA to complement the aconitase-deficient Escherichia coli mutant JRG3259. An acnA mutant was unable to develop aerial mycelium and to sporulate, resulting in a bald phenotype. Furthermore, the mutant did not produce the antibiotic phosphinothricin tripeptide, demonstrating that AcnA also affects physiological differentiation.
Micro hydraulic system using slim artificial muscles for a wearable haptic glove

Over the past few decades, various haptic gloves have been developed for use in virtual environments. The actuating systems for most existing haptic gloves require lots of external auxiliary equipment. Because of this, the motion of the user is restricted by the length of the electric wires or pneumatic tubes attached to this equipment. A compact actuation system, including related equipment, is thus indispensable for a wearable haptic glove to be truly effective. To resolve the problem of hampered motion and reach, a micro hydraulic actuating system was developed in this research. It was composed of a slim, flexible artificial muscle, a compact hydraulic module for actuating the muscle, and a micro pressure sensor for measuring without flux loss. The characteristics of the muscle were investigated for their control capacity. The step and sinusoidal responses were analyzed to evaluate the performance of the micro hydraulic system. Once these analyses were completed, a lightweight and compact actuation system was built incorporating a wearable haptic glove. By virtue of the developed micro hydraulic system, the wearable haptic glove was able to operate independently of any external equipment, and movement was completely free of any restrictions from wires or tubes.
EFFECT OF POTENTIATION AND STRETCHING ON MAXIMAL FORCE,RATE OF FORCE DEVELOPMENT, AND RANGE OF MOTION

The purpose of this investigation was to compare the effects of stretching vs. potentiation on subsequent maximal force and rate of force development capabilities of subjects in an isometric squat. Ten male collegiate athletes participated as subjects in this study. Subjects were tested during 3 separate sessions that involved joint range of motion (ROM) measurements of the lower body and isometric squat trials on a force plate to determine peak force (PF) and rate of force development (RFD) values. One testing session was preceded by 10 minutes of quiet sitting (C), 1 by a 30-minute lower-body stretching protocol (S), and 1 by 3 sets of a leg press exercise using 90% of the subjects' previously determined 1 repetition maximum (P). Three repetitions were performed for each set of the leg press, with a 3-minute rest period between each set. PF during the isometric squat was not significantly different following any of the 3 conditions (C: 100.0 ± 0.0%, S: 101.2 ± 6.5%, P: 98.6 ± 6.2%). However, RFD was significantly lower in P (87.5 ± 12.8%) compared with both C (100.0 ± 0.0%) and S (102.6 ± 18.5%). Significant improvement in ROM occurred only following P. It appears the potentiation protocol used in the current investigation may actually have had fatiguing effects instead of potentiating effects, but it did result in significant increases in ROM.
Assessment of Serum Vitamin D Levels in Women with Polycystic Ovary Syndrome

Background: Polycystic ovary syndrome (PCOS) is a common endocrinopathy in women ofreproductive age with primary features of infertility, menstrual irregularity, and clinical or biochemicalevidence of hyperandrogenism (hirsutism, acne and high androgen level). Vitamin D has a role in thedevelopment of metabolic and endocrine abnormalities in PCOS mediated by insulin resistance.Objective: Measure serum 25-hydroxy vitamin D levels in women with polycystic ovary syndrome andcompare their levels with age and body mass index matched healthy controls. Also, assess thecorrelation between insulin resistance and 25-hydroxy vitamin D among women with PCOS.Subjects and Methods: Eighty eight women were involved in this study with age range (18-34 years). Subjects were divided into two groups: Group 1- forty five women with PCOS and Group 2- forty threewomen without PCOS (as controls). Serum 25-hydroxy vitamin D, insulin, free testosterone, Luteinizing hormone (LH), Follicle stimulatinghormone (FSH) were measured by enzyme linked immunosorbent assay (ELISA), while serum calciumand fasting serum glucose were measured by spectrophotometer.Results: Significant increase in mean value of fasting serum glucose, insulin, homeostatic modelassessment of insulin resistance (HOMA-IR), LH, LH/FSH ratio, and free testosterone with significantdecrease in mean value of serum FSH, 25-hydroxy vitamin D, and calcium for patients with PCOScomparing to age and body mass index match controls. Additionally, significant negative correlationswere found between serum 25-hydroxy vitamin D levels with fasting serum glucose (r= -0.484, p=0.01),fasting serum insulin (r= -0.422, p=0.04), and HOMA-IR (r= -0.542, p=0.0001) in women with PCOS.Conclusion: Vitamin D has a role in metabolic and hormonal disturbance seen in PCOS through impactof vitamin D on insulin releasing and function.
CUSTOMIZABLE EMBEDDED SYSTEM ARCHITECTURES

We outline a framework for dynamic application customization for low-power and real-time embedded systems. The framework implements a cross-layer application-customizable embedded systems platform, in which the hardware, the system software, and the application tasks are fine-tuned in their interaction and functionality to the requirements of the program under execution. The traditional design approach has been to put together a set of general-purpose embedded processor cores, deploy a domain specific or a general operating system (OS) and map on it the set of program tasks. In all such systems, the main culprit for the energy inefficiency and the poor real-time guarantees is the general-purpose nature of the hardware architecture, the system software layer, and the interaction between them. The proposed architecture is capable of utilizing application information to boost the performance and lower the power consumption of the most important microarchitectural components such as instruction/data caches and the memory subsystem. We outline a design framework, including CAD support infrastructure and reprogrammable hardware support, for a dynamically customizable embedded system. We outline the underlying algorithms for compile-time extraction of the utilized application properties and we present the architectural principles of the hardware support. Experimental results confirm the efficacy of this novel embedded system architecture.
Primate color vision: A comparative perspective

Abstract Thirty years ago virtually everything known about primate color vision derived from psychophysical studies of normal and color-defective humans and from physiological investigations of the visual system of the macaque monkey, the most popular of human surrogates for this purpose. The years since have witnessed much progress toward the goal of understanding this remarkable feature of primate vision. Among many advances, investigations focused on naturally occurring variations in color vision in a wide range of nonhuman primate species have proven to be particularly valuable. Results from such studies have been central to our expanding understanding of the interrelationships between opsin genes, cone photopigments, neural organization, and color vision. This work is also yielding valuable insights into the evolution of color vision.
Rights or Identity? Naturalization Processes among “Labor Migrants” in Germany

The determinants of the decision to naturalize for first and second generation “labor migrants” in Germany are examined. We assume that Turkish migrants’ comparatively high naturalization rate cannot be explained by the legal advantages they gain by naturalizing. We argue instead that naturalization offers an opportunity for individual upward mobility to Turkish migrants who have achieved a high level of individual assimilation. Using data from the GSOEP, we show that individual assimilation does in fact promote naturalization for Turkish migrants, but not for members of other ethnic groups, which generally have higher status within German society.
Asymptotic cohomological functions on projective varieties

We consider certain cohomological invariants called asymptotic cohomological functions, which are associated to irreducible projective varieties. Asymptotic cohomological functions are generalizations of the concept of the volume of a line bundle-the asymptotic growth of the number of global sections-to higher cohomology. We establish that they give a notion invariant under the numerical equivalence of divisors, and extend uniquely to continuous functions on the real Neron-Severi space. To illustrate the theory, we work out these invariants for abelian varieties, smooth surfaces, and certain homogeneous spaces.
AN EXPOSITION ON THE TIME-AVERAGED ACCURACY OF APPROXIMATE DE-CONVOLUTION , LARGE EDDY SIMULATION MODELS OF TURBULENCE

The purpose of this report is to give a self-contained and detailed mathematical introduction to the analysis in the report [LL04c] of the accuracy of some predictive model’s of turbulence. The models are based on approximate de-convolution methods and were introduced into LES by Stolz and Adams. We recall the development of the models, review the known theory of the models and expand the proof from [LL04c] that the time averaged consistency error of the Nth approximate deconvolution LES model converges to zero uniformly in the kinematic viscosity and in the Reynolds number as the cube root of the averaging radius. We also give a higher order but non-uniform consistency error bound for the zeroth order model directly from the Navier-Stokes equations and study the distribution of consistency errors among length-scales.
Applying Multi- and Cross-Lingual Stochastic Phone Space Transformations to Non-Native Speech Recognition

In the context of hybrid HMM/MLP Automatic Speech Recognition (ASR), this paper describes an investigation into a new type of stochastic phone space transformation, which maps “source” phone (or phone HMM state) posterior probabilities (as obtained at the output of a Multilayer Perceptron/MLP) into “destination” phone (HMM phone state) posterior probabilities. The resulting stochastic matrix transformation can be used within the same language to automatically adapt to different phone formats (e.g., IPA) or across languages. Additionally, as shown here, it can also be applied successfully to non-native speech recognition. In the same spirit as MLLR adaptation, or MLP adaptation, the approach proposed here is directly mapping posterior distributions, and is trained by optimizing on a small amount of adaptation data a Kullback-Leibler based cost function, along a modified version of an iterative EM algorithm. On a non-native English database (HIWIRE), and comparing with multiple setups (monophone and triphone mapping, MLLR adaptation) we show that the resulting posterior mapping yields state-of-the-art results using very limited amounts of adaptation data in mono-, cross- and multi-lingual setups. We also show that “universal” phone posteriors, trained on a large amount of multilingual data, can be transformed to English phone posteriors, resulting in an ASR system that significantly outperforms a system trained on English data only. Finally, we demonstrate that the proposed approach outperforms alternative data-driven, as well as a knowledge-based, mapping techniques.
Bacterial genomic DNA isolation using sonication for microarray analysis.

Isolation of high-quality genomic DNA is a crucial step in bacterial comparative genomic studies using microarrays. Numerous procedures employing either physical or detergent/ enzyme-based cell lysing followed by phenol extraction, chaotropic-based fractionation, or size exclusion column purification can be used (1–4). However, few of them can be easily adapted for high-throughput operation at low cost. Despite the use of multiple time-consuming steps, DNA preparation remains a manageable task, since only a limited number of strains are used in most microarray experiments. We recently developed a new application of microarray technology, Library on a Slide, for bacterial comparative genomics studies (5). This platform combines the approach of dot blot hybridization with the technology of microarrays, resulting in glass slides arrayed with thousands of bacterial genomes (up to 15,000). Thus, libraries of entire genomes rather than the sequence of a single genome or set of genes are printed on the slides, which are used to screen these libraries for the presence of specific genetic elements of interest. An effective high-throughput procedure for DNA isolation from numerous samples is necessary for array printing. We previously used an UltraClean-htp™ 96-well microbial DNA isolation kit (Mobio, Carlsbad, CA, USA) to isolate DNA. While good-quality DNA was obtained, this time-consuming multistep protocol with relative low yield and high cost made it difficult to implement in preparing thousands of samples. This paper describes a new and simple method for preparing highly concentrated and fragmented bacterial DNA based on sonication and heat treatment. We have applied this new method with good success to a number of Gram negative and positive bacteria, including Escherichia coli, Hemophilus influenzae, Salmonella typhimurium, Klebsiella pneumoniae, Streptococcus agalactiae, Staphylococcus epidermidis, Staphylococcus aureus, Streptococcus mutans, and Enterococcus faecalis. Bacterial strains were grown overnight in 3–8 mL of the liquid medium of choice in 10-mL culture tubes for small batch processing or in 96-deep-well plates (two plates with 1.5 mL/well inoculants were later combined) for high-throughput processing. Bacteria were pelleted by centrifugation at 2000× g for 20 min and resuspended in 80 μL sonication buffer (50 mM Tris and 10 mM EDTA, pH 7.5, with optional 100 ng/μL RNase A). The suspension was transferred to a 0.5-mL thin wall PCR tube or a fully skirted 96-well PCR plate (Greiner Bio-One, Longwood, FL, USA). Then the tube/plate was placed in a plate horn (Misonix, Farmingdale, NY, USA) filled with a water and ice mixture and treated with …
Massive Withdrawal Symptoms and Affective Vulnerability Are Associated with Variants of the CHRNA4 Gene in a Subgroup of Smokers

Heterogeneous phenotypes of complex disorders pose a great challenge for genetic association studies and for the development of personalized treatment strategies. Cluster analysis of phenotypic data has been recently proposed as a reliable auxiliary method for such studies. A cohort of 236 treatment-seeking smokers was investigated after overnight nicotine abstinence. Alpha4 nicotinic acetylcholine receptor (nAChR) subunit-related phenotypes were assessed by the Fagerström Test for Nicotine Dependence (FTND), exhaled carbon monoxide (CO) measurements, the Minnesota Nicotine Withdrawal Scale (MNWS) and the Zung Self-Rating Depression Scale (ZSDS). Seven tag SNPs (single-nucleotide polymorphisms) across CHRNA4 (the gene encoding alpha4 subunit of the nicotinic acetylcholine receptor) were genotyped and two-step cluster analysis was used for phenotypic cluster characterization. Haplotype estimation was determined by HapStat module of R 2.0 software. Three different phenotypic clusters were identified and the C3 cluster was characterized by the highest ZSDS and MNWS scores compared to others. Furthermore, lifetime prevalence of major depression was significantly higher in the C3 cluster (p = 0.019). In genetic association tests, this cluster was also significantly associated with rs3787138 genotypes (p = 0.004) while haplotype analyses of three SNPs (rs3787138, rs1044396, rs3787140) revealed that the risk for C3 phenotype was almost three times higher in GCC haplotype carriers compared to others (pperm = 0.013). This is the first report on a significant association between CHRNA4 variants and a subgroup of smokers characterized by massive withdrawal symptoms and affective vulnerability. Identification of such a phenotypic cluster can be a pivotal step for further pharmacogenetic studies on ligands of the alpha4 nAChR subunit. Our results suggest that performing cluster analysis in genetic association studies can be proposed for complex disorders.
Overview of image security techniques with applications in multimedia systems

The growth of networked multimedia system has created a need for the copyright protection of digital images and video. Copyright protection involves the authentication of image content and/or ownership. This can be used to identify illegal copies of an image. One approach is to mark an image by adding an invisible structure known as a digital watermark to the image. Techniques of incorporating such a watermark into digital images include spatial-domain techniques, transform-domain algorithms and sub-band filtering approaches.
GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications

Interpreting the genetic variants located in the regulatory regions, such as enhancers and promoters, is an indispensable step to understand molecular mechanism of complex traits. Recent studies show that genetic variants detected by genome-wide association study (GWAS) are significantly enriched in the regulatory regions. Therefore, detecting, annotating and prioritizing of genetic variants affecting gene regulation are critical to our understanding of genotype–phenotype relationships. Here, we developed a web server GWAS3D to systematically analyze the genetic variants that could affect regulatory elements, by integrating annotations from cell type-specific chromatin states, epigenetic modifications, sequence motifs and cross-species conservation. The regulatory elements are inferred from the genome-wide chromosome interaction data, chromatin marks in 16 different cell types and 73 regulatory factors motifs from the Encyclopedia of DNA Element project. Furthermore, we used these function elements, as well as risk haplotype, binding affinity, conservation and P-values reported from the original GWAS to reprioritize the genetic variants. Using studies from low-density lipoprotein cholesterol, we demonstrated that our reprioritizing approach was effective and cell type specific. In conclusion, GWAS3D provides a comprehensive annotation and visualization tool to help users interpreting their results. The web server is freely available at http://jjwanglab.org/gwas3d.
Rapid clearance of epigenetic protein reporters from wound edge cells in Drosophila larvae does not depend on the JNK or PDGFR/VEGFR signaling pathways

Abstract The drastic cellular changes required for epidermal cells to dedifferentiate and become motile during wound closure are accompanied by changes in gene transcription, suggesting corresponding alterations in chromatin. However, the epigenetic changes that underlie wound‐induced transcriptional programs remain poorly understood partly because a comprehensive study of epigenetic factor expression during wound healing has not been practical. To determine which chromatin modifying factors might contribute to wound healing, we screened publicly available fluorescently tagged reporter lines in Drosophila for altered expression at the wound periphery during healing. Thirteen reporters tagging seven different proteins showed strongly diminished expression at the wound edge. Three downregulated proteins, Osa, Kismet, and Spt6, are generally associated with active chromatin, while four others, Sin3A, Sap130, Mi‐2, and Mip120, are associated with repressed chromatin. In all cases reporter downregulation was independent of the Jun N‐terminal kinase and Pvr pathways, suggesting that novel signals control reporter clearance. Taken together, our results suggest that clearance of chromatin modifying factors may enable wound edge cells to rapidly and comprehensively change their transcriptional state following tissue damage.
N-gram Adaptation with Dynamic Interpolation Coefficient Using Information Retrieval Technique

This study presents an N-gram adaptation technique when additional text data for the adaptation do not exist. We use a language modeling approach to the information retrieval (IR) technique to collect the appropriate adaptation corpus from baseline text data. We propose to use a dynamic interpolation coefficient to merge the N-gram, where the interpolation coefficient is estimated from the word hypotheses obtained by segmenting the input speech. Experimental results show that the proposed adapted N-gram always has better performance than the background N-gram.
TEXTO PARA DISCUSSÃO N ° 1245 a COMPARING MODELS FOR FORECASTING THE YIELD CURVE

The evolution of the yields of different maturities is related and can be described by a reduced number of commom latent factors. Multifactor interest rate models of the finance literature, common factor models of the time series literature and others use this property. Each model has advantages and disadvantages, and it is an empirical matter to evaluate the performance of the approaches. This exercise compares 4 alternative models for the term structure using 3 different markets: the Brazilian domestic and sovereign market and the US market.
Elevated serum neopterin predicts future adverse cardiac events in patients with chronic stable angina pectoris.

AIMS Serum levels of neopterin, an immune modulator secreted by activated macrophages, are elevated in patients with acute coronary syndromes compared with stable angina patients and control subjects. In unstable angina, serum neopterin levels correlate with the presence of vulnerable coronary stenosis, multiple complex coronary lesions, and patient outcome. The present study assessed the prognostic significance of raised serum neopterin concentrations in patients with stable angina pectoris. METHODS AND RESULTS We carried out a 1-year follow-up prospective study in 297 patients with chronic stable chest pain undergoing diagnostic coronary angiography. The primary study endpoint was the composite of non-fatal myocardial infarction, unstable angina, and cardiac death. Fifty-one patients (17.2%) had adverse coronary events during follow-up. Mean serum neopterin levels were significantly higher in patients with events compared with those without (P=0.02). On multiple regression analysis, neopterin levels (P=0.021), severity of coronary artery disease (P=0.009), and a history of previous myocardial infarction (P=0.001) were independent predictors of adverse events. CONCLUSIONS Serum neopterin is an independent predictor of major adverse coronary events in patients with chronic stable angina pectoris. This marker of macrophage activation may be useful for risk stratification in patients with chronic stable angina.