Miracle-dz/UniFAR-FTUs huggingface dataset:
A Decoupled Predictor-Directed Stream Prefetching Architecture

An effective method for reducing the effect of load latency in modern processors is data prefetching. One form of hardware-based data prefetching, stream buffers, has been shown to be particularly effective due to its ability to detect data streams and run ahead of them, prefetching as it goes. Unfortunately, in the past, the applicability of streaming was limited to stride intensive code. In this paper, we propose predictor-directed stream buffers (PSB), which allows the stream buffer to follow a general address prediction stream instead of a fixed stride. A general address prediction stream complicates the allocation of both stream buffer and memory resources because the predictions generated will not be as reliable as prior sequential next-line and stride-based stream buffer implementations. To address this, we examine using confidence-based techniques to guide the allocation and prioritization of stream buffers and their prefetch requests. Our results show, when using PSB on a benchmark suite heavy in pointer-based applications, that PSB provides a 23 percent speedup on average over the best previous stream buffer implementation, and an improvement of 75 percent over using no prefetching at all.
Coded Unitary Space–Time Modulation With Iterative Decoding: Error Performance and Mapping Design

This paper studies the bit error probability of coded unitary space-time modulation with iterative decoding where neither the transmitter nor the receiver knows the channel fading coefficients. The tight error bound with respect to the asymptotic performance is first analytically derived for any given unitary constellation and mapping rule. Design criteria regarding the choice of unitary constellation and mapping are then established. Furthermore, using the unitary constellation obtained from orthogonal design with quadrature phase-shift keying (QPSK or 4-PSK) and 8-PSK, two different mapping rules are proposed. The first mapping rule gives the most suitable mapping for systems that do not implement iterative processing, which is similar to a Gray mapping in coherent channels. The second mapping rule yields the best mapping for systems with iterative decoding. In particular, analytical and simulation results show that with the proposed mappings of the unitary constellations obtained from orthogonal designs, the asymptotic error performance of the iterative systems can closely approach a lower bound which is applicable to any unitary constellation and mapping
Mitochondrial Fusion in Yeast Requires the Transmembrane GTPase Fzo1p

Membrane fusion is required to establish the morphology and cellular distribution of the mitochondrial compartment. In Drosophila, mutations in the fuzzy onions (fzo) GTPase block a developmentally regulated mitochondrial fusion event during spermatogenesis. Here we report that the yeast orthologue of fuzzy onions, Fzo1p, plays a direct and conserved role in mitochondrial fusion. A conditional fzo1 mutation causes the mitochondrial reticulum to fragment and blocks mitochondrial fusion during yeast mating. Fzo1p is a mitochondrial integral membrane protein with its GTPase domain exposed to the cytoplasm. Point mutations that alter conserved residues in the GTPase domain do not affect Fzo1p localization but disrupt mitochondrial fusion. Suborganellar fractionation suggests that Fzo1p spans the outer and is tightly associated with the inner mitochondrial membrane. This topology may be required to coordinate the behavior of the two mitochondrial membranes during the fusion reaction. We propose that the fuzzy onions family of transmembrane GTPases act as molecular switches to regulate a key step in mitochondrial membrane docking and/or fusion.
Follow-Up Analysis of Genome-Wide Association Data Identifies Novel Loci for Type 1 Diabetes

OBJECTIVE—Two recent genome-wide association (GWA) studies have revealed novel loci for type 1 diabetes, a common multifactorial disease with a strong genetic component. To fully utilize the GWA data that we had obtained by genotyping 563 type 1 diabetes probands and 1,146 control subjects, as well as 483 case subject–parent trios, using the Illumina HumanHap550 BeadChip, we designed a full stage 2 study to capture other possible association signals. RESEARCH DESIGN AND METHODS—From our existing datasets, we selected 982 markers with P < 0.05 in both GWA cohorts. Genotyping these in an independent set of 636 nuclear families with 974 affected offspring revealed 75 markers that also had P < 0.05 in this third cohort. Among these, six single nucleotide polymorphisms in five novel loci also had P < 0.05 in the Wellcome Trust Case-Control Consortium dataset and were further tested in 1,303 type 1 diabetes probands from the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) plus 1,673 control subjects. RESULTS—Two markers (rs9976767 and rs3757247) remained significant after adjusting for the number of tests in this last cohort; they reside in UBASH3A (OR 1.16; combined P = 2.33 × 10−8) and BACH2 (1.13; combined P = 1.25 × 10−6). CONCLUSIONS—Evaluation of a large number of statistical GWA candidates in several independent cohorts has revealed additional loci that are associated with type 1 diabetes. The two genes at these respective loci, UBASH3A and BACH2, are both biologically relevant to autoimmunity.
Falling sex ratios and emerging evidence of sex-selective abortion in Nepal: evidence from nationally representative survey data

Objectives To quantify trends in changing sex ratios of births before and after the legalisation of abortion in Nepal. While sex-selective abortion is common in some Asian countries, it is not clear whether the legal status of abortion is associated with the prevalence of sex-selection when sex-selection is illegal. In this context, Nepal provides an interesting case study. Abortion was legalised in 2002 and prior to that, there was no evidence of sex-selective abortion. Changes in the sex ratio at birth since legalisation would suggest an association with legalisation, even though sex-selection is expressly prohibited. Design Analysis of data from four Demographic and Health Surveys, conducted in 1996, 2001, 2006 and 2011. Setting Nepal. Participants 31 842 women aged 15–49. Main outcome measure Conditional sex ratios (CSRs) were calculated, specifically the CSR for second-born children where the first-born was female. This CSR is where the evidence of sex-selective abortion will be most visible. CSRs were looked at over time to assess the impact of legalisation as well as for population sub-groups in order to identify characteristics of women using sex-selection. Results From 2007 to 2010, the CSR for second-order births where the first-born was a girl was found to be 742 girls per 1000 boys (95% CI 599 to 913). Prior to legalisation of abortion (1998–2000), the same CSR was 1021 (906–1150). After legalisation, it dropped most among educated and richer women, especially in urban areas. Just 325 girls were born for every 1000 boys among the richest urban women. Conclusions The fall in CSRs witnessed post-legalisation indicates that sex-selective abortion is becoming more common. This change is very likely driven by both supply and demand factors. Falling fertility has intensified the need to bear a son sooner, while legal abortion services have reduced the costs and risks associated with obtaining an abortion.
Cyclophilin inhibitors in hepatitis C viral infection

Cyclophilins (Cyps) are proteins that are ubiquitously present with peptidyl-prolyl cis-trans isomerase activity and play an important role in de novo protein folding and in isomerization of native proteins in several cellular systems. There is growing evidence that indicates CypB is a positive modulator of the HCV RNA-dependent RNA polymerase in the replication complex. Early in vitro and animal data with selective Cyp inhibitors show a potent anti-HCV effect. This anti-HCV effect was confirmed in the first patient study with the selective Cyp inhibitor Debio-025. Preclinical data suggest that Cyp inhibitors may present a higher barrier to the selection of resistance than protease and polymerase inhibitors and that a combination of Cyp inhibitors with either of these drugs or interferon results in additive or synergistic anti-HCV activity. By interfering at the level of host–viral interaction, Cyp inhibition may open the way for a novel approach to anti-HCV treatment that could be complementary, not only to interferon-based treatment, but also to future treatments that directly target HCV replication enzymes such as protease and polymerase inhibitors.
The Temporal and Spatial Invasion Genetics of the Western Corn Rootworm (Coleoptera: Chrysomelidae) in Southern Europe

This study describes the genetics of the western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte in southern Europe during the introduction (1996–2001) and establishment/spread (2002–2011) phases of its invasion. The Diabrotica microsatellite core-set was used to perform traditional population genetics analyses. Our results indicated that during the introduction phase genetic diversity and population genetic structure were lower overall as compared to the establishment/spread phase. Unusually high genetic differentiation was found between the Italy and southern Europe comparisons, including high differentiation between Italian populations separated by a short distance during the establishment/spread phase. STRUCTURE analysis revealed two genetic clusters during the introduction phase and two genetic clusters during the establishment/spread phase. However, bottlenecked populations were only detected during the invasion phase. A small but significant isolation by distance effect was noted in both phases. Serbia was the geographic source of WCR to Croatia and Hungary in the introduction phase, while the United States of America was the possible source of WCR to Italy in 2001. These introductory populations were the subsequent source of individuals sampled during the establishment/spread phase. Repeated introductions and admixture events in southern Europe may have resulted in genetically diverse WCR populations that have attained 83% of all known alleles worldwide.
Interactive Level-of-Detail Rendering of Large Graphs

We propose a technique that allows straight-line graph drawings to be rendered interactively with adjustable level of detail. The approach consists of a novel combination of edge cumulation with density-based node aggregation and is designed to exploit common graphics hardware for speed. It operates directly on graph data and does not require precomputed hierarchies or meshes. As proof of concept, we present an implementation that scales to graphs with millions of nodes and edges, and discuss several example applications.
A robust foreground segmentation method by temporal averaging multiple video frames

Foreground segmentation in videos by background subtraction methods are widely used in video surveillance applications. Adaptive single or mixture Gaussian models have been adopted for modeling nonstationary temporal distributions of background pixels. However, a challenge for this approach is that it is hard to choose a threshold to separate foreground from background accurately because of the so-called camouflage problem. This paper proposes a simple and effective scheme to alleviate the problem. It is achieved by averaging the frames in video sequences temporally, which reduces the variances of background models. Thus the background model is squeezed to a very narrow region and the probability of camouflage is reduced dramatically, which helps to improve the sensitivity and reliability. Significant improvements are shown on real video data. Incorporating this algorithm into a statistical framework for background subtraction leads to an improved foreground segmentation performance compared to a standard method.
Text entry on handheld computers by older users

Small pocket computers offer great potential in workplaces where mobility is needed to collect data or access reference information while carrying out tasks such as maintenance or customer support. This paper reports on three studies examining the hypothesis that data entry by older workers is easier when the pocket computer has a physical keyboard, albeit a small one, rather than a touchscreen keyboard. Using a counter-balanced, within-subjects design the accuracy and speed with which adults over 55 years of age could make or modify short text entries was measured for both kinds of pocket computer. The keyboard computer was the Hewlett Packard 360LX (HP), but the touch-screen computers varied across studies (experiment 1: Apple Newton™ and PalmPilot™; experiment 2: Philips Nino™; experiment 3: Casio E10™). All studies showed significant decrements in accuracy and speed when entering text via the touch-screen. Across studies, most participants preferred using the HP's small physical keyboard. Even after additional practice with the touch screen (experiments 2 and 3) many entries still contained errors. Experiment 3 showed that younger people were faster but not more accurate than older people at using the touch-screen keyboard. It is concluded that satisfactory text entry on palm-size computers awaits improvements to the touch-screen keyboard or alternative input methods such as handwriting or voice. Interface developments that assist older people typically benefit younger users too.
Enhanced Microglial Clearance of Myelin Debris in T Cell-Infiltrated Central Nervous System

Acute multiple sclerosis lesions are characterized by accumulation of T cells and macrophages, destruction of myelin and oligodendrocytes, and axonal damage. There is, however, limited information on neuroimmune interactions distal to sites of axonal damage in the Tcell-infiltrated central nervous system. We investigated T-cell infiltration, myelin clearance, microglial activation, and phagocytic activity distal to sites of axonal transection through analysis of the perforant pathway deafferented dentate gyrus in SJL mice that had received T cells specific for myelin basic protein (TMBP) or ovalbumin (TOVA). The axonal lesion of TMBP-recipient mice resulted in lesion-specific recruitment of large numbers of T cells in contrast to very limited T-cell infiltration in TOVA-recipient and -naïve perforant pathway-deafferented mice. By double immunofluorescence and confocal microscopy, infiltration with TMBP but not TOVA enhanced the microglial response to axonal transection and microglial phagocytosis of myelin debris associated with the degenerating axons. Because myelin antigen-specific immune responses may provoke protective immunity, increased phagocytosis of myelin debris might enhance regeneration after a neural antigen-specific T cell-mediated immune response in multiple sclerosis.
Monensin Turns on Microtubule‐Associated Translocation of Secretory Granules in Cultured Rat Atrial Myocytes

We have studied the effect of monensin on microtubule-associated translocation of atrial secretory granules in 5-7-day-old cultures of atrial myocytes from adult rats. Atrial granules and microtubules were localized by immunofluorescent microscopy of myocytes double-labeled with primary antibodies against atrial natriuretic polypeptide (ANP) and α-tubulin. In control myocytes, fluorescence due to atrial granules was predominantly localized to the perinuclear region containing the Golgi complex. After exposure for 30 minutes to monensin (0.5−5.0 μM), myocytes transiently contained conspicuous linear arrays of atrial granules associated with cytoplasmic microtubules. Thereafter, ANP fluorescence accumulated in subsarcolemmal foci at the cell periphery, while perinuclear ANP fluorescence faded. The monensin-induced redistribution of atrial granules was observable in both serum-containing and serum-free media and was unaffected by reducing external Ca2+ to low values, by inhibition of sarcoplasmic reticulum Ca2+ release with ryanodine, or by both. The redistribution was prevented by pretreatment with nocodazole, which fragmented microtubules and scattered Golgi complexes and the associated atrial granules throughout the cytoplasm. Radioimmunoassay showed that monensin seemingly decreased the rate of ANP secretion into the medium from 0.15 to 0.11 fmol/(hr±myocyte). These results suggest that monensin turns on microtubule-associated translocation of atrial granules from the perinuclear areas to the cell periphery by modifying the interaction between microtubules and atrial granules. Monensin also promotes movement of atrial granules along the microtubules but does not accelerate the release of ANP.
Apoptosis of CD4+ and CD8+ T Cells Isolated Immediately ex Vivo Correlates with Disease Severity in Human Immunodeficiency Virus Type 1 Infection

Apoptosis of CD4+ and CD8+ T cells has been shown in peripheral blood mononuclear cells (PBMCs) from HIV-infected adults analyzed after overnight culture. Because cell death may be an artifact of in vitro culture, and because there is little information on apoptosis in pediatric HIV disease, we undertook a cross-sectional analysis of apoptosis in PBMCs analyzed immediately ex vivo in HIV-infected children and adults. PBMCs from 22 children, four adolescents, and nine adults and seronegative age-matched control subjects were stained for CD4 and CD8 surface markers. Apoptotic cells were detected in a newly characterized flow cytometric assay by diminished forward and increased side scatter. Children with the most advanced disease had 9.9% (SEM 1.8) apoptotic CD4+ T cells above control, significantly higher than in asymptomatic patients [0.4% (SEM 2.3)], those with mild disease [2.2% (SEM 1.83)], and those with moderate disease [2.5 (SEM 3.6)] (p = 0.015). The percentages of both CD4+ and CD8+ T cell apoptosis were directly related to CD4+ T cell depletion (R2 = 0.23; p = 0.006; n = 32 and R2 = 0.2; p = 0.012; n = 30, respectively). Patients who responded to antiretroviral therapy with the greatest increase in CD4+ T cell percentage had the least CD4+ T cell apoptosis (R2 = 0.15; p = 0.1; n = 19). These findings show that the rate or extent of T cell death by apoptosis percentage of T cell apoptosis is significantly increased in HIV-infected children. The observed correlation of both CD4+ and CD8+ T cell apoptosis with CD4+ T cell depletion suggests that apoptosis plays a role in HIV pathogenesis and may be a useful marker of disease activity.
A Web Search Engine-Based Approach to Measure Semantic Similarity between Words

Measuring the semantic similarity between words is an important component in various tasks on the web such as relation extraction, community mining, document clustering, and automatic metadata extraction. Despite the usefulness of semantic similarity measures in these applications, accurately measuring semantic similarity between two words (or entities) remains a challenging task. We propose an empirical method to estimate semantic similarity using page counts and text snippets retrieved from a web search engine for two words. Specifically, we define various word co-occurrence measures using page counts and integrate those with lexical patterns extracted from text snippets. To identify the numerous semantic relations that exist between two given words, we propose a novel pattern extraction algorithm and a pattern clustering algorithm. The optimal combination of page counts-based co-occurrence measures and lexical pattern clusters is learned using support vector machines. The proposed method outperforms various baselines and previously proposed web-based semantic similarity measures on three benchmark data sets showing a high correlation with human ratings. Moreover, the proposed method significantly improves the accuracy in a community mining task.
Functional Impairment of the Brainstem in Infants With Bronchopulmonary Dysplasia

OBJECTIVES. To gain new insights into the influence of bronchopulmonary dysplasia on the immature brain and to detect abnormalities, we studied the functional integrity of the brainstem in infants with bronchopulmonary dysplasia. METHODS. Forty-one very preterm infants with bronchopulmonary dysplasia were studied at postconceptional ages of 37 to 42 weeks. Brainstem auditory evoked responses were recorded and analyzed by using the maximal length sequence technique. RESULTS. Compared with term control subjects, wave V latency in the maximal length sequence brainstem auditory evoked response of the infants with bronchopulmonary dysplasia increased significantly at all 91 to 910 clicks per second rates. Similarly, I–V and particularly III–V interpeak intervals increased significantly. The III–V/I–III interval ratio also increased significantly at all click rates. All of these abnormalities became more significant as the click rate was increased. Compared with healthy, very preterm control subjects, all of these maximal length sequence brainstem auditory evoked response variables increased significantly at all click rates, although the differences between the 2 groups were slightly smaller than those between the infants with bronchopulmonary dysplasia and the term control subjects. The wave I and III latencies and I–III interval in the infants with bronchopulmonary dysplasia did not show any abnormalities. The slopes of the wave V latency-rate function and I–V and particularly III–V interval-rate functions for the infants with bronchopulmonary dysplasia were significantly steeper than those for both term and healthy, very preterm control subjects. The slope of the III–V/I–III interval ratio-rate function for the infants with bronchopulmonary dysplasia was also significantly steeper than those for the 2 control groups. CONCLUSIONS. The results suggest poor myelination and synaptic function of the brainstem in infants with bronchopulmonary dysplasia, resulting in impaired functional integrity. In comparison, peripheral neural function was relatively intact.
Approximation Algorithms for Many-to-Many Traffic Grooming in Optical WDM Networks

A large number of network applications today allow several users to interact together using the many-to-many service mode. In many-to-many communication, also referred to as group communication, a session consists of a group of users (we refer to them as members), where each member transmits its traffic to all other members in the same group. In this paper, we address the problem of grooming subwavelength many-to-many traffic (e.g., OC-3) into high-bandwidth wavelength channels (e.g., OC-192) in optical wavelength division multiplexing (WDM) mesh networks. The cost of an optical WDM network is dominated by the cost of higher-layer electronic ports (i.e., transceivers). A transceiver is needed for each initiation and termination of a lightpath. Therefore, our objective is to minimize the total number of lightpaths established. Unfortunately, the grooming problem even with unicast traffic has been shown to be NP-hard. In this paper, we introduce two novel approximation algorithms for the many-to-many traffic grooming problem. We also consider the routing and wavelength assignment problem with the objective of minimizing the number of wavelengths used. Through extensive experiments, we show that the proposed algorithms use a number of lightpaths that is very close to that of a derived lower bound. Also, we compare the two algorithms on other important objectives such as the number of logical hops traversed by a traffic stream, total amount of electronic switching at a node, and Min-Max objectives.