Miracle-dz/UniFAR-FTUs huggingface dataset:
High inbreeding in the Faroe Islands does not appear to constitute a risk factor for multiple sclerosis

Background: Large population-based genome-wide association studies have identified several multiple sclerosis (MS) genetic risk variants, but the existing missing heritability warrants different strategies. Isolated populations offer an alternative way of searching for rare genetic variants and evaluating the possible role of consanguinity in the development of MS. Studies of consanguinity and MS risk have yielded conflicting results. Objectives: In this study we investigated the role of consanguinity on MS risk in the relatively isolated Faroe Islands, which have a presumed high level of inbreeding. Methods: A total of 29 cases and 28 matched controls were genotyped and assessed for inbreeding coefficients, number of runs of homozygosity (ROH) at different lengths and observed number of homozygotes as measures of relatedness. Parametric and non-parametric statistical models were applied. Results: Both cases and controls exhibited considerable relatedness demonstrated by very high inbreeding coefficients, large number of observed homozygotes and many long ROH. However, apart from the number of ROH ≥ 2.5 mega base pairs, no significant differences between the two groups were observed. Conclusions: Overall, no significant difference between cases and controls were found, indicating that consanguinity in itself does not appear to be an important risk factor for MS in the population of the Faroe Islands.
A join point for loops in AspectJ

The current AspectJ join points represent locations in the code that are the interface of the Java objects. However, not all the "things that happen" happen at the interfaces. In particular, loops are a key place that could be advised for parallelisation. This article presents a loop join point model, which allows AspectJ to intervene directly in loops. More generally, this demonstrates the need for, and provides, a more complex join point in AspectJ.The approach used for recognising loops is based on a control-flow analysis at the bytecode level; this avoids ambiguities due to alternative forms of source-code that would effectively produce identical loops. This model is also enhanced with a mechanism for context exposure, which is pivotal for giving a meaning to the use of this join point, and with additional information through join point reflection. The context exposure is particularly useful for writing pointcuts that select specific loops only, and the problem of loop selection is also presented in the paper.Finally, LoopsAJ, an extension for the abc compiler that provides AspectJ with a loop join point, is presented. It is shown how to use this extension for writing aspects that parallelise loops.
Reactor Baffle Cooling CFD Framework for Swelling Assessment

This Paper presents an improved estimation of reactor core baffle temperature distribution, during operation, at the nominal power level to address swelling problems of the reactor internals. Swelling is the main limiting factor in the reactor core internals long term operation of VVER-1000 nuclear units. The material irradiation-induced swelling and creep models are very sensitive to temperature distribution in metal, thus a more detailed analysis of the core baffle metal thermohydraulic cooling characteristics is required. A framework for CFD analysis of VVER-1000 reactor baffle cooling is presented. Firstly, an analytical model was developed to obtain boundary conditions and simplify CFD analysis, i.e. the real geometry of the cooling channels was replaced by equivalent elements, the core was presented as porous body with the appropriate characteristics. Secondly, the CFD analysis was performed using 60–degree symmetry, which included: core, baffle and core barrel, it is limited by the height of the baffle. Core is simplified as a homogeneous body with considering of spatial volumetric energy release. Core baffle is presented as monolithic body with considering of gamma-ray heat generation. Model includes a simplified geometry of connecting studs, considering cooling flow of the coolant through the nuts grooves. Calculated convection coefficient and temperature are in good agreement with analytical model, and give a more convenient result comparing to RELAP5/mod3.2. Obtained results were used to estimate baffle swelling process. Due to the less conservative results in temperature distribution swelling and creep deformations significantly decreased.
Fibroblast growth factor receptor 4 as a potential prognostic and therapeutic marker in colorectal cancer

Abstract The purpose of the study was to explore the significance of FGFR4 protein expression in colorectal cancer. Immunohistochemistry showed 46.8% (148/316) tumors positive for FGFR4 and 7.3% (23/316) for adjacent normal specimens. FGFR4 positivity was correlated with shortened disease free survival (DFS) and overall survival (OS). Multivariate analysis revealed that FGFR4 was an independent prognostic factor. FGFR4 silencing markedly reduced the migration and invasion capacity of colorectal cancer cell lines. These results suggest FGFR4 is a potential prognostic and therapeutic marker for colorectal cancer.
Multiscale Sharpening and Smoothing in Besov Spaces with Applications to Image Enhancement

In this paper we use multiscale characteristics of wavelet decompositions and their relationship to smoothness spaces such as Besov spaces to derive a framework for smoothing and sharpening of signals and images. As a result, we derive a multiscale generalization of traditional techniques, such as unsharp masking, while using the smoothness parameter α in the Besov space Bαq(Lp) to provide a unifying framework for the two operations sharpening and smoothing. As a result multiscale smoothing or sharpening is defined as a switching between different smoothness spaces. The degree of sharpening or smoothing is linked to the Besov space parameter α. Combined with wavelet denoising the nonlinear image enhancement in Besov spaces via wavelets provides a tool for high-quality low-cost image processing. For the example of a document, that has been blurred by a scanning process, we demonstrate how information on the smoothing properties of an input device combined with an image model provide enough information to determine the right amount of multiscale sharpening, i.e., for inverting the smoothing process, that is suitable to obtain a deblurred image. Multiscale sharpening then leads to a switching from a Besov space with large degree of smoothness to the one with a lower degree of smoothness. This technique combined with wavelet denoising provides visually pleasant images with crisp text.
Human Cancer Xenografts in Outbred Nude Mice Can Be Confounded by Polymorphisms in a Modifier of Tumorigenesis

Tumorigenicity studies often employ outbred nude mice, in the absence of direct evidence that this mixed genetic background will negatively affect experimental outcome. Here we show that outbred nude mice carry two different alleles of Pla2g2a, a genetic modifier of intestinal tumorigenesis in mice. Here, we identify previous unreported linked polymorphisms in the promoter, noncoding and coding sequences of Pla2g2a and show that outbred nude mice from different commercial providers are heterogeneous for this polymorphic Pla2g2a allele. This heterogeneity even extends to mice obtained from a single commercial provider, which display mixed Pla2g2a genotypes. Notably, we demonstrated that the polymorphic Pla2g2a allele affects orthotopic xenograft establishment of human colon cancer cells in outbred nude mice. This finding establishes a non-cell-autonomous role for Pla2g2a in suppressing intestinal tumorigenesis. Using in vitro reporter assays and pharmacological inhibitors, we show promoter polymorphisms and nonsense-mediated RNA decay (NMD) as underlying mechanisms that lead to low Pla2g2a mRNA levels in tumor-sensitive mice. Together, this study provides mechanistic insight regarding Pla2g2a polymorphisms and demonstrates a non-cell-autonomous role for Pla2g2a in suppressing tumors. Moreover, our direct demonstration that mixed genetic backgrounds of outbred nude mice can significantly affect baseline tumorigenicity cautions against future use of outbred mice for tumor xenograft studies.
Functional anatomy of human social cognition

Social cognitive processes Humans and their ancestors have lived in social groups for millions of years. This history has provided selection pressures for the ability to predict conspe-cifics' actions (Cosmides & Tooby, 1992). Though it might be possible to predict people's behavior directly by extrapolating from past observations, doing so on the basis of inferred mental states and traits—including intentions and goals, emotions, personality traits, and beliefs—is more economical and may yield more accurate predictions, especially in complex social contexts (Dennett, 1987; Humphrey, 1984). Evidence from social and developmental psychology shows that humans are very sensitive, from an early age, to cues that can enable predictions about behavior. In fact, our propensity to attribute mental states extends to inanimate objects, appearing as a tendency towards anthropomorphism (Boyer, 2003; Scholl & Tremoulet, 2000). In the present chapter, we will focus on the neural circuitry subserving the attribution of animacy and intention (that an object is alive and that it is a mental object), emotional states, personality traits, and intentional or belief states (" theory of mind " [ToM]) to others. This focus is consistent with Brothers' (Brothers, 1990) definition of social cognition as " the processing of any information which culminates in the accurate perception of the dispositions and intentions of other individuals " (p. 28). Some processes that fall under the rubric of social cognition appear to be perceptual, in that they are fast and apparently automatic, and seem to be relatively little influenced by top-down processes. Others appear to rely more on conceptual knowledge, and thus might more properly be called attributional. In this chapter, we will distinguish between these terms as follows. When processes appear to be primarily stimulus-driven, and to rely little or not at all on context or top-down contributions, we will refer to them as perception. When processes appear to be equal parts bottom-up and top-down, we will refer to them as recognition. Finally, when processes appear to be largely top-down, or when it is unclear how to categorize a given process or set of processes, we will refer to them as attribution. A bit about organization: Though this chapter is organized in terms of different social cognitive processes, it could have been organized in at least two other ways; that is, by anatomical structure (for example, a section reviewing all the social cognitive processes in which the amygdala is implicated) and by levels of …
Cardiovascular , Pulmonary and Renal Pathology Tubular Overexpression of Transforming Growth Factor-1 Induces Autophagy and Fibrosis but Not Mesenchymal Transition of Renal Epithelial Cells

From the Institute of Human Genetics,* University of Heidelberg, Heidelberg, Germany; UMR_S 702, INSERM/University of Paris 6 (UPMC), Hopital Tenon, Paris, France; the Institute of Anatomy, University of Zurich, Zurich, Switzerland; the Institute of Vegetative Anatomy, Charité, University of Berlin, Berlin, Germany; the Institute of Biochemistry, Medical Faculty, University of Leipzig, Leipzig, Germany; the Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania; the Abteilung: Anatomie und Entwicklungsbiologie,** Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; and the Division of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany
Convection Problems on Anisotropic Meshes

Abstract. The Galerkin and SDFEM methods are compared for a steady state convection problem. The theoretical part of this work deals with the development of approximation results for continuous solutions on the unit square containing an edge singularity. In the numerical part we verify those approximation results by considering continuous as well as discontinuous solutions to the transport problem on an annular domain with a singularity at the inner circle.
Fast transform for decoding both errors and erasures of Reed-Solomon codes over GF(2/sup m/) for 8/spl les/m/spl les/10

In this letter, it is shown that a fast, prime-factor discrete Fourier transform (DFT) algorithm can be modified to compute Fourier-like transforms of long sequences of 2/sup m/-1 points over GF(2/sup m/), where 8/spl les/m/spl les/10. Using these transforms, together with the Berlekamp-Massey algorithm, the complexity of the transform-domain decoder for correcting both errors and erasures of the Reed-Solomon codes of block length 2/sup m/-1 over GF(2/sup m/) for 8/spl les/m/spl les/10 is reduced substantially from the previous time-domain decoder. A computer simulation verifies these new results.
Discovery of the 198 Second X-Ray Pulsar GRO J2058+42

GRO J2058+42, a transient 198 s X-ray pulsar, was discovered by the Burst and Transient Source Experiment (BATSE) on the Compton Gamma Ray Observatory (CGRO) during a "giant" outburst in 1995 September-October. The total flux peaked at about 300 mcrab (20-50 keV) as measured by Earth occultation. The pulse period decreased from 198 to 196 s during the 46 day outburst. The pulse shape evolved over the course of the outburst and exhibited energy-dependent variations. BATSE observed five additional weak outbursts from GRO J2058+42, each with a 2 week duration and a peak-pulsed flux of about 15 mcrab (20-50 keV), that were spaced by about 110 days. An observation of the 1996 November outburst by the Rossi X-Ray Timing Explorer (RXTE) proportional counter array (PCA) localized the source to within a 4' radius error circle (90% confidence) centered on R.A. = 20h59. ͫ0, decl. = 41°43' (J2000). Additional shorter outbursts with peak-pulsed fluxes of about 8 mcrab were detected by BATSE halfway between the first four 15 mcrab outbursts. The RXTE All-Sky Monitor detected all eight weak outbursts with approximately equal durations and intensities. GRO J2058+42 is most likely a Be/X-ray binary that appears to outburst at periastron and apastron. No optical counterpart has been identified to date, and no X-ray source was present in the error circle in archival ROSAT observations.
Distribution of Can1p into stable domains reflects lateral protein segregation within the plasma membrane of living S. cerevisiae cells

Recently, lipid-raft-based subdomains within the plasma membrane of living Saccharomyces cerevisiae cells were visualized using green fluorescent protein fusions, and non-overlapping subdomains containing either Pma1p or Can1p were distinguished. In this study, the long-term stability of the subdomains was investigated. Experiments with latrunculin A and nocodazole ruled out the involvement of cytoskeletal components in the stabilization of the subdomains. Also a putative role of the cell wall was excluded, because protoplasting of the cells changed neither the pattern nor the stability of the subdomains. By contrast, the expected inner dynamics of the membrane subdomains was documented by FRAP experiments. Finally, two other proteins were localized within the frame of the Can1p/Pma1p plasma-membrane partition. We show that Fur4p (another H+ symporter) and Sur7p (a protein of unknown function) occupy the Can1p subdomain.
Investigation of reinforcing flexible pavements with waste plastic fibers in Ras Al Khaimah, UAE

With the increase of solid wastes, officials in Ras Al Khaimah (RAK), United Arab Emirates (UAE) are evaluating reuses of these materials rather than being dumped in landfills. Furthermore, asphalt pavements in RAK are failing prematurely due to heavy and slow traffic accompanied with high temperatures during the summer. To assist in the efforts of solving these problems, this study was conducted to investigate the effects of adding waste plastic fibers to Hot Mix Asphalt (HMA). Tests were conducted on a standard HMA with two asphalt binder grades and two waste plastic fiber contents (0.5 and 1% by weight of mix). Results showed that HMA fracture resistance at −10 and 21.1°C temperatures and rutting resistance at a 54.4°C temperature increased by the addition of waste plastic fibers. For an overall improvement in performance of asphalt pavement, the optimum waste plastic fiber content was found to be 0.5% by weight of mix. Thus, by adding waste plastic fibers to HMA, an improvement of performance (rutting and cracking resistances) of asphalt pavements and a positive effect on the environment could be achieved by the reuse of discarded plastic waste.
Bioinformatics tools toward GC-MS and LC-MS data analysis, management and visualization

cancer (CRC) is one of the most diffuse cancers worldwide; evidences showed that Adenomatous Polyposis Coli (APC) is a multifunctional tumor suppressor gene that regulates and controls many biological functions; mutations in this gene has been reported in many cases of CRC. SNPs contribute to gene mutations and expression variations justifying phenotypic variations among population and hence such SNPs would be potential biological targets for identification and analysis; therefore this work focused on analysis of SNPs in the coding regions of APC gene found as non-synonymous variants (nsSNP) and those in the 3'un-translated region (3'UTR) affecting miRNA binding using computational methods. 333 nsSNPs were analyzed by tools that concerning structural and functional aberrations and measure degrees and scores of alterations; and then the protein variants were subjected to structural modeling to highlight the impact of amino acid substitution upon protein phenotype. Analysis with Sift and Polyphen resulted in 15 damaging nsSNPs out of a total and marked 5 amino acid substitutions (E142G, R99W, R24N, L680S and W157T) with probably high deleterious scores, while analysis of 51 3'UTR SNPs by its special tool PolymiRTS resulted in no single nucleotide variant at that region could disturb the conserved sites of miRNA. It has been found that the use of such computational analysis tools was highly valuable and critical to highlight life threatening mutations and early sounds for APC gene aberrations causing truncated products with adverse outcomes.
Toward Multilingual Neural Machine Translation with Universal Encoder and Decoder

In this paper, we present our first attempts in building a multilingual Neural Machine Translation framework under a unified approach in which the information shared among languages can be helpful in the translation of individual language pairs. We are then able to employ attention-based Neural Machine Translation for many-to-many multilingual translation tasks. Our approach does not require any special treatment on the network architecture and it allows us to learn minimal number of free parameters in a standard way of training. Our approach has shown its effectiveness in an under-resourced translation scenario with considerable improvements up to 2.6 BLEU points. In addition, we point out a novel way to make use of monolingual data with Neural Machine Translation using the same approach with a 3.15-BLEU-score gain in IWSLT’16 English→German translation task.
LC-MS-Based Metabolomics Study of Marine Bacterial Secondary Metabolite and Antibiotic Production in Salinispora arenicola

An LC-MS-based metabolomics approach was used to characterise the variation in secondary metabolite production due to changes in the salt content of the growth media as well as across different growth periods (incubation times). We used metabolomics as a tool to investigate the production of rifamycins (antibiotics) and other secondary metabolites in the obligate marine actinobacterial species Salinispora arenicola, isolated from Great Barrier Reef (GBR) sponges, at two defined salt concentrations and over three different incubation periods. The results indicated that a 14 day incubation period is optimal for the maximum production of rifamycin B, whereas rifamycin S and W achieve their maximum concentration at 29 days. A “chemical profile” link between the days of incubation and the salt concentration of the growth medium was shown to exist and reliably represents a critical point for selection of growth medium and harvest time.
Hypocholesterolaemic Activity of Lupin Peptides: Investigation on the Crosstalk between Human Enterocytes and Hepatocytes Using a Co-Culture System Including Caco-2 and HepG2 Cells

Literature indicates that peptic and tryptic peptides derived from the enzymatic hydrolysis of lupin protein are able to modulate cholesterol metabolism in human hepatic HepG2 cells and that part of these peptides are absorbed in a small intestine model based on differentiated human Caco-2 cells. In this paper, a co-culture system, including Caco-2 and HepG2 cells, was investigated with two objectives: (a) to verify whether cholesterol metabolism in HepG2 cells was modified by the peptides absorption through Caco-2 cells; (b) to investigate how lupin peptides influence cholesterol metabolism in Caco-2 cells. The experiments showed that the absorbed peptides, not only maintained their bioactivity on HepG2 cells, but that this activity was improved by the crosstalk of the two cells systems in co-culture. In addition, lupin peptides showed a positive influence on cholesterol metabolism in Caco-2 cells, decreasing the proprotein convertase subtilisin/kexin type 9 (PCSK9) secretion.
Assessment of Nutrient and Storage Stabilizing Potential of Ginger and Garlic on Composite Fruit Smoothies

Aims: The study aimed at demonstrating the influence of natural spices (ginger and garlic) and storage conditions on nutritional, microbial and organoleptic characteristics of composite fruit smoothies. Study Design: Completely Randomized General Factorial Design and Multivariate Pattern Recognition Technique were used to achieve the study. Results: Univariate data analysis results showed type spices as the most significant factor (p = 0.05) with respect to variables considered. There was a decline in vitamin C, titratable acidity and pH as storage time advanced. Total and reducing sugars and o Brix increased with storage while other chemical parameters did not change significantly. Garlic and ginger extracts enhanced microbial stability and contributed to better sensory acceptability of the samples. Principal component analysis (PCA) multivariate model further showed the distinct trends between the impacts of garlic and ginger on the score and loading plots. Smoothies enriched with garlic had comparatively higher TPC, crude fibre, pH, vitamin C, sodium and its ratios with potassium and magnesium, within the first week, total and reducing sugars on the third week. Conversely, ginger enriched smoothies were high in acidity, sensorial scores, magnesium and potassium in the first week of storage and o Brix afterward. Conclusion: Garlic and ginger are potent natural preservatives with additional nutritional benefits that could replace synthetic additives.