Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient Algorithms for Array Redistribution

Dynamic redistribution of arrays is required very often in programs on distributed presents efficient algorithms for redistribution between different cyclic(k) distributions, as defined in High Performance Fortran. We first propose special optimized algorithms for a cyclic(x) to cyclic(y) redistribution when x is a multiple of y, or y is a multiple of x. We then propose two algorithms, called the GCD method and the LCM method, for the general cyclic(x) to cyclic(y) redistribution when there is no particular relation between x and y. We have implemented these algorithms on the Intel Touchstone Delta, and find that they perform well for different array sizes and number of processors.
A New Approach to Calibrate Range Image and Color Image from Kinect

Kinect, as a new type of human-machine interaction sensor, is able to capture range images and color images of the scene simultaneously, but there is space parallax between them. A stereo calibration is expected to overcome it. Much different from the previous approaches, we introduced a new method in this paper to solve this problem which uses the range image directly. The method obtains the range calibration images of a newly designed calibration board and extracts calibration point pairs by an algorithm developed in this paper. Our experiments show that the method can complete calibration of the Kinect successfully.
Climate change impact on salmonid spawning in low-gradient streams in central Idaho, USA

Climate change is often predicted to cause a significant perturbation to watershed hydrology. It has been generally associated with negative impacts on natural systems, especially in conjunction with conservation and protection of sensitive ecosystems. In the U.S., spawning habitats of threatened and endangered salmonid species are important areas that are potentially vulnerable to climate change through variations in flood timing and magnitude, water temperature, and sediment input. In this work, we used a numerical model to investigate whether changes in flow regime, of the type predicted by some climate change scenarios for mountain streams in the western U.S.A. , would affect spawning site stability. We ran a two dimensional hydraulic model that simulated several flow regimes from low to bankfull stage and mapped grain mobility. We defined the model boundary conditions with high-resolution airborne bathymetric lidar surveys of an important spawning stream in central Idaho, USA. Our analyses showed that such unconfined low-gradient streams have not a great danger of extensive bed mobility, even at high flows. Consequently, in this landscape, alterations in flood timing due to climate change are unlikely to decrease the success rate of salmonid egg incubation by the mechanism of increased channel bed scour.
A systematic literature review of green software metrics

Green IT is getting increasing attention in software engineering research. Nevertheless energy eﬃciency studies have mostly focused on the hardware side of IT, the software role still requires deepening in terms of methods and techniques. Furthermore, it is necessary to understand how to assess the software“greenness”for stimulating the energy eﬃciency awareness, since early phases of the software lifecycle. The main goal of this study is to describe and to classify metrics related to software “greenness” present in the software engineering literature. Furthermore, this study analyzes the evolution of those metrics, in terms of type, context, and evaluation methods. To achieve this goal, a systematic literature review has been performed surveying the metrics claimed in the last decade. After examined 960 publications, we selected 23 of them as primary studies, from which we isolated extracting 96 dif-ferent green metrics. Therefore, we analyzed search results in order to show what is the trend of research about green software metrics, how metrics perform measurement on resources, and what type of metrics are more appealing for deﬁned contexts.
Molecular Mechanisms of Selenium Tolerance and Hyperaccumulation in Stanleya pinnata1[W][OA]

The molecular mechanisms responsible for selenium (Se) tolerance and hyperaccumulation were studied in the Se hyperaccumulator Stanleya pinnata (Brassicaceae) by comparing it with the related secondary Se accumulator Stanleya albescens using a combination of physiological, structural, genomic, and biochemical approaches. S. pinnata accumulated 3.6-fold more Se and was tolerant to 20 μm selenate, while S. albescens suffered reduced growth, chlorosis and necrosis, impaired photosynthesis, and high levels of reactive oxygen species. Levels of ascorbic acid, glutathione, total sulfur, and nonprotein thiols were higher in S. pinnata, suggesting that Se tolerance may in part be due to increased antioxidants and up-regulated sulfur assimilation. S. pinnata had higher selenocysteine methyltransferase protein levels and, judged from liquid chromatography-mass spectrometry, mainly accumulated the free amino acid methylselenocysteine, while S. albescens accumulated mainly the free amino acid selenocystathionine. S. albescens leaf x-ray absorption near-edge structure scans mainly detected a carbon-Se-carbon compound (presumably selenocystathionine) in addition to some selenocysteine and selenate. Thus, S. albescens may accumulate more toxic forms of Se in its leaves than S. pinnata. The species also showed different leaf Se sequestration patterns: while S. albescens showed a diffuse pattern, S. pinnata sequestered Se in localized epidermal cell clusters along leaf margins and tips, concentrated inside of epidermal cells. Transcript analyses of S. pinnata showed a constitutively higher expression of genes involved in sulfur assimilation, antioxidant activities, defense, and response to (methyl)jasmonic acid, salicylic acid, or ethylene. The levels of some of these hormones were constitutively elevated in S. pinnata compared with S. albescens, and leaf Se accumulation was slightly enhanced in both species when these hormones were supplied. Thus, defense-related phytohormones may play an important signaling role in the Se hyperaccumulation of S. pinnata, perhaps by constitutively up-regulating sulfur/Se assimilation followed by methylation of selenocysteine and the targeted sequestration of methylselenocysteine.
Exploring deep neural networks and deep autoencoders in reverberant speech recognition

We propose an approach to reverberant speech recognition adopting deep learning in front end as well as back end of the system. At the front end, we adopt a deep autoencoder (DAE) for enhancing the speech feature parameters, and speech recognition is performed using a DNN-HMM acoustic models at the back end. The system was evaluated on simulated and real reverberant speech data sets. On average, the DNN-HMM system trained on the multi-condition training data outperformed the MLLR-adapted GMM-HMM system trained on the same data. The feature enhancement with the DAE contributed to the improvement of recognition accuracy especially in more adverse conditions. We also performed an unsupervised adaptation of the DNN-HMM models to the test data enhanced by the DAE and achieved improvements in word accuracies in all reverberation conditions of the test data.
Robust Maximum Likelihood Acoustic Energy Based Source Localization in Correlated Noisy Sensing Environments

Acoustic energy based localization with wireless sensor networks is an interesting solution to locate sources and targets. For simplicity, localization formulation based on the maximum likelihood (ML) approach considers that the source and noise samples are uncorrelated and represented by a Gaussian distribution. However, the acoustic background noise can severely affect the accuracy of the location estimation. This paper proposes an accurate error estimate in which the correlation of the received signals at each wireless sensor is represented by a Hurst exponent and modeled by a fractional Gaussian noise (fGn). The experimental results show that the proposed solution is more appropriate for the source localization estimation under real acoustic noises and even for highly non-stationary sources.
Measuring node importance on Twitter microblogging

Social Networks (SN) are created whenever people interact with other people in online social networks, such as Twitter, Google+, Facebook and etc. Twitter is a social networking and micro-blogging service; it creates several new interesting social network structures. In this sense, our main goal is to investigate the power of retweet mechanism. The findings suggest that relations of "friendship" at Twitter are important but not enough. Still, the centrality measures of a node importance do not show how important users are. We uncovered some other principles that must be studied like, homophily phenomenon, the tendency of individuals to associate and bond with similar others.
Crystal Structure of Cytomegalovirus IE1 Protein Reveals Targeting of TRIM Family Member PML via Coiled-Coil Interactions

PML nuclear bodies (PML-NBs) are enigmatic structures of the cell nucleus that act as key mediators of intrinsic immunity against viral pathogens. PML itself is a member of the E3-ligase TRIM family of proteins that regulates a variety of innate immune signaling pathways. Consequently, viruses have evolved effector proteins to modify PML-NBs; however, little is known concerning structure-function relationships of viral antagonists. The herpesvirus human cytomegalovirus (HCMV) expresses the abundant immediate-early protein IE1 that colocalizes with PML-NBs and induces their dispersal, which correlates with the antagonization of NB-mediated intrinsic immunity. Here, we delineate the molecular basis for this antagonization by presenting the first crystal structure for the evolutionary conserved primate cytomegalovirus IE1 proteins. We show that IE1 consists of a globular core (IE1CORE) flanked by intrinsically disordered regions. The 2.3 Å crystal structure of IE1CORE displays an all α-helical, femur-shaped fold, which lacks overall fold similarity with known protein structures, but shares secondary structure features recently observed in the coiled-coil domain of TRIM proteins. Yeast two-hybrid and coimmunoprecipitation experiments demonstrate that IE1CORE binds efficiently to the TRIM family member PML, and is able to induce PML deSUMOylation. Intriguingly, this results in the release of NB-associated proteins into the nucleoplasm, but not of PML itself. Importantly, we show that PML deSUMOylation by IE1CORE is sufficient to antagonize PML-NB-instituted intrinsic immunity. Moreover, co-immunoprecipitation experiments demonstrate that IE1CORE binds via the coiled-coil domain to PML and also interacts with TRIM5α We propose that IE1CORE sequesters PML and possibly other TRIM family members via structural mimicry using an extended binding surface formed by the coiled-coil region. This mode of interaction might render the antagonizing activity less susceptible to mutational escape.
In Vitro Studies Evaluating Leaching of Mercury from Mine Waste Calcine Using Simulated Human Body Fluids

In vitro bioaccessibility (IVBA) studies were carried out on samples of mercury (Hg) mine-waste calcine (roasted Hg ore) by leaching with simulated human body fluids. The objective was to estimate potential human exposure to Hg due to inhalation of airborne calcine particulates and hand-to-mouth ingestion of Hg-bearing calcines. Mine waste calcines collected from Hg mines at Almadén, Spain, and Terlingua, Texas, contain Hg sulfide, elemental Hg, and soluble Hg compounds, which constitute primary ore or compounds formed during Hg retorting. Elevated leachate Hg concentrations were found during calcine leaching using a simulated gastric fluid (as much as 6200 μg of Hg leached/g sample). Elevated Hg concentrations were also found in calcine leachates using a simulated lung fluid (as much as 9200 μg of Hg leached/g), serum-based fluid (as much as 1600 μg of Hg leached/g), and water of pH 5 (as much as 880 μg of Hg leached/g). The leaching capacity of Hg is controlled by calcine mineralogy; thus, calcines containing soluble Hg compounds contain higher leachate Hg concentrations. Results indicate that ingestion or inhalation of Hg mine-waste calcine may lead to increased Hg concentrations in the human body, especially through the ingestion pathway.
Achievable secrecy rate of the relay-eavesdropper channel with generalized feedback

We consider the relay-eavesdropper channel with generalized feedback at the source node. In the presence of a wire-tapper, the source can send confidential messages to an intended receiver with the help of the trusted relay. With a generalized feedback from the relay to the source node, the cooperation between the source node and relay node may be enhanced. The achievable secrecy rate region for this channel is derived by using rate splitting strategy and decode-and-forward (DF) strategy at the source node and compress-and-forward (CF) strategy at the relay node.
Suicide during Perinatal Period: Epidemiology, Risk Factors, and Clinical Correlates

Perinatal period may pose a great challenge for the clinical management and treatment of psychiatric disorders in women. In fact, several mental illnesses can arise during pregnancy and/or following childbirth. Suicide has been considered a relatively rare event during the perinatal period. However, in some mental disorders (i.e., postpartum depression, bipolar disorder, postpartum psychosis, etc.) have been reported a higher risk of suicidal ideation, suicide attempt, or suicide. Therefore, a complete screening of mothers’ mental health should also take into account thoughts of suicide and thoughts about harming infants as well. Clinicians should carefully monitor and early identify related clinical manifestations, potential risk factors, and alarm symptoms related to suicide. The present paper aims at providing a focused review about epidemiological data, risk factors, and an overview about the main clinical correlates associated with the suicidal behavior during the pregnancy and postpartum period. Practical recommendations have been provided as well.
Dietary patterns in pregnancy and respiratory and atopic outcomes in childhood

Background: Studies of the relation between maternal diet in pregnancy and respiratory and atopic outcomes in the offspring have focused on the effects of individual nutrients and foods rather than dietary patterns. A study was undertaken to determine whether dietary patterns in pregnancy are related to childhood asthma and related outcomes. Methods: In a population-based birth cohort, the Avon Longitudinal Study of Parents and Children (ALSPAC), dietary patterns in pregnancy previously identified using principal components analysis (“health conscious”, “traditional”, “processed”, “vegetarian” and “confectionery”) were related to early wheezing phenotypes and eczema; wheezing, hay fever, eczema, doctor-diagnosed asthma, atopy and total IgE at 7 years; lung function and bronchial responsiveness at 8–9 years. In regression models, confounders were controlled for using propensity scores. Results: Univariately, the “health conscious” pattern was positively associated with eczema, total IgE, forced expiratory volume in 1 s and forced expiratory flow and negatively associated with early wheezing and asthma (unadjusted odds ratios per standard deviation increase in pattern score for early persistent wheeze and asthma: 0.78 (95% CI 0.70 to 0.87), p = 7.3×10−6, N = 8886 and 0.90 (95% CI 0.84 to 0.97), p = 0.007, N = 7625, respectively). The “processed” pattern was positively associated with early wheezing and negatively associated with atopy and forced vital capacity. On controlling for confounders, the effects were substantially attenuated and became non-significant (adjusted odds ratios for the associations of the “health conscious” pattern with early persistent wheeze and asthma: 1.00 (0.86 to 1.16), p = 0.99 and 0.95 (0.86 to 1.04), p = 0.27, respectively). Conclusions: In this cohort, dietary patterns in pregnancy did not predict asthma and related outcomes in the offspring after controlling for confounders.
A systematic review and meta-analysis of case–control trials

The extracellular matrix is important for tumor invasion and metastasis. Normal function of the extracellular matrix depends on the balance between matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs). The objective of this metaanalysis was to assess the relationship between expression of MMP-9, MMP-2, and TIMP-2 and invasion of pituitary adenomas. We searched Pubmed, Embase, and the Chinese Biomedical Database up to October 2015. RevMan 5.1 software (Cochrane Collaboration, Copenhagen, Denmark) was used for statistical analysis. We calculated the standardized mean difference (SMD) for data expressed as mean±standard deviation because of the difference in the detection method. Twenty-four studies (1320 patients) were included. MMP-9 expression was higher in the patients with invasive pituitary adenomas (IPAs) thanpatientswith noninvasivepituitary adenomas (NIPAs)with detectionmethodsof IHC [odds ratio (OR)=5.48, 95%confidence interval (CI)=2.61–11.50, P<0.00001), and reverse transcriptase-polymerase chain reaction (SMD=2.28, 95% CI=0.91–3.64, P= 0.001). MMP-2 expressionwas also increased in patientswith IPAs at the protein level (OR=3.58, 95%CI=1.63–7.87,P=0.001), and RNA level (SMD=3.91, 95% CI=1.52–6.29, P=0.001). Meta-analysis showed that there was no difference in TIMP-2 expression between invasive and NIPAs at the protein level (OR=0.38, 95% CI=0.06–2.26, P=0.29). MMP-9 expression in prolactinomas and nonfunctioning pituitary adenomas was also no difference (OR=1.03, 95% CI=0.48–2.20, P=0.95). The results indicated that MMP-9 and -2 may be correlated with invasiveness of pituitary adenomas, although their relationship with functional status of pituitary adenomas is still not clear. TIMP-2 expression in IPAs needs to be investigated further. Abbreviations:CBM =Chinese Biomedical Database, ECM = The extracellular matrix, IHC = immunohistochemical staining, IPAs = invasive pituitary adenomas, MMPs = matrix metalloproteinases, MVD = microvessel density, NIPAs = noninvasive pituitary adenomas, OR = odds ratio, PAs = Pituitary adenomas, RT-PCR = reverse transcriptase-polymerase chain reaction, SD = standard deviation, SMD = standardized mean difference, TIMPs = tissue inhibitors of metalloproteinases.
Decision under Uncertainty: an Islamic Perspective

£ 2 Although theories of choice tend to treat gambling as a prototypic situation of decision making under risk, decision makers distinguish between " risk taking " and gambling, saying that while they should take risks, they should never gamble. They react to variability more by trying actively to avoid it or control it than by treating it as a tradeoff with expected value in making a choice. Introduction Text book presentation of decision under uncertainty does not distinguish between investment and gambling. " We structure the uncertainty facing an agent by interpreting risky situations as gambles " (Jehle, 1991, p. 193). Writers start with how an entrepreneur chooses among different investment projects, and end up with lottery ticket as a " concrete example " of the problem (e.g. Sinn, 1983, pp. 4-5). After defining a lottery to be a prize received with a given probability, Varian (1992, p. 172) writes: " Most situations involving behavior under risk can be put into this lottery framework. " Allais (1976) reports that he started analyzing random choice by " thinking about a method for successful racecourse betting, based on the use of newspaper forecasts. " (p. 445) Thus decision under uncertainty is viewed as choosing among lotteries. Chance and skill appear to be treated equally in this framework. It is not clear how gambling differs from entrepreneurship, and why taking a risk in some instances is praised and in others is blamed. On the other hand, studies of decision under uncertainty from an Islamic perspective are quite rare, if any. Further, despite the central position of gharar and risk in Islamic principles of exchange, there is no framework for studying such transactions within an integral theme of decision under risk. This paper is an attempt to address these problems in a suggestive manner. Although it is far from providing a coherent theory of the subject, it points to some starting points that researchers in Islamic Economics might find relevant for developing such a theory.
Experimental estimation of the effects of all amino-acid mutations to HIV Env

HIV is notorious for its capacity to evade immunity and anti-viral drugs through rapid sequence evolution. Knowledge of the functional effects of mutations to HIV is critical for understanding this evolution. HIV’s most rapidly evolving protein is its envelope (Env). Here we use deep mutational scanning to experimentally estimate the effects of all amino-acid mutations to Env on viral replication in cell culture. Most mutations are under purifying selection in our experiments, although a few sites experience strong selection for mutations that enhance HIV’s growth in cell culture. We compare our experimental measurements of each site’s preference for each amino acid to the actual frequencies of these amino acids in naturally occurring HIV sequences. Our measured amino-acid preferences correlate with amino-acid frequencies in natural sequences for most sites. However, our measured preferences are less concordant with natural amino-acid frequencies at surface-exposed sites that are subject to pressures absent from our experiments such as antibody selection. We show that some regions of Env have a high inherent tolerance to mutation, whereas other regions (such as epitopes of broadly neutralizing antibodies) have a significantly reduced capacity to tolerate mutations. Overall, our results help disentangle the role of inherent functional constraints and external selection pressures in shaping Env’s evolution.
An analysis of transcription consistency in spontaneous speech from the buckeye corpus

We present a preliminary analysis of transcriber consistency in labeling and segmentation of words and phones in the Buckeye corpus of spontaneous, informal speech. We find that pairwise inter-transcriber agreement on exact phone label match was 76%, and segmentation agreement within 20% of phone pair length was 75%, though longer phones are more consistently segmented than shorter phones. Patterns of consistency variation in labeling are observed as a function of phonetic categories that are similar to patterns reported for read speech. More agreement is seen on consonants than on vowels, and on fricatives and labials than on other consonant classes. In general, we find that shorter, more reduced words and phones result in more transcriber disagreement.
Comparative summary of binning results obtained for simulated datasets generated using MetaSim and ART

This section provides a comparison of binning results obtained for simulated datasets generated using two read-simulators, namely MetaSim [1] and ART [2]. These simulated datasets were identical to each other with respect to their mean read length (~ 100bp) and dataset size (35,000 reads each). Both data sets were generated using the 454 error model. These simulated data sets were subsequently analyzed using six binning methods.
Competing collinear and noncollinear interactions in chirped quasi-phase-matched optical parametric amplifiers

Chirped quasi-phase-matched optical parametric amplifiers (chirped QPM OPAs) are investigated experimentally. The measured collinear gain is constant over a broad bandwidth, which makes these devices attractive candidates for use in femtosecond amplifier systems. The experiment also shows that chirped QPM OPAs support noncollinear gain-guided modes. These modes can dominate the desired collinear gain and generate intense parametric fluorescence. Design guidelines to mitigate these parasitic processes are discussed.