Miracle-dz/UniFAR-FTUs huggingface dataset:
Warped-Shield: Tolerating Hard Faults in GPGPUs

Graphics processing units (GPUs) are rapidly becoming the parallel accelerators of choice to run general purpose applications. GPUs that run general purpose applications are termed as GPGPUs. Many mission-critical and long-running scientific application are being ported to run on GPGPUs. These applications demand strong computational integrity. GPGPUs, like many other digital components, face imminent reliability threats due to technology scaling. Of particular concern is the infield hard faults that are persistent and irreversible. GPGPUs comprise of dozens of streaming processors where each streaming processor employs tens of execution units, organized as single instruction multiple thread (SIMT) lanes to deliver massive parallel computational power. In this paper we exploit the massive replication of SIMT lanes to tolerate infield hard faults. First, we introduce thread shuffling to reroute threads, originally mapped to faulty SIMT lanes, to idle healthy lanes. Thread shuffling is insufficient when the number of healthy SIMT lanes is fewer than the number of active threads. To broaden the reach of thread shuffling, we propose dynamic warp deformation to split the warp into multiple sub-warps, each sub-warp uses fewer SIMT lanes thereby providing more opportunities to avoid using a faulty SIMT lane. Finally, we propose warp shuffling which exploits non-uniform degradation of different streaming processors by scheduling a warp to a streaming processor that requires fewer warp splits. Hence, warp shuffling helps to reduce the performance overhead associated with dynamic warp deformation. By deploying the proposed techniques, we can tolerate the worst case scenario of having up to three hard faults per four SIMT lane cluster with at most 36%performance degradation.
Cloud-centric application tracing and user monitoring intrusion prevention system

This paper presents first theoretical model of IDPS which combines application tracing and user decisions for building user profiles. This novel idea is based on fact that we have seen nearly all kind of malware since Intrusion Detection System was widely deployed. Our solution presents “deny any” policy as default action. Thus all behavior that we have not seen before is considered as malicious. This paper presents several novel approaches, such as building four various databases used for software description and one profile database for describing user behavior, opposite existing solutions which mainly uses just one database for specifying malware. Presented architecture of this approach outlines predispositions to use this solution with crowd sourcing.
Incidence, causes, and outcomes of dilated cardiomyopathy in children.

CONTEXT Dilated cardiomyopathy (DCM) is the most common form of cardiomyopathy and cause of cardiac transplantation in children. However, the epidemiology and clinical course of DCM in children are not well established. OBJECTIVE To provide a detailed description of the incidence, causes, outcomes, and related risk factors for DCM in children. DESIGN AND SETTING Longitudinal study based on a population-based, prospective cohort of children diagnosed as having DCM since January 1, 1996, at 89 pediatric cardiac centers and a retrospectively collected cohort of patients seen primarily at large tertiary care centers in North America and who had diagnoses between January 1, 1990, and December 31, 1995, and were enrolled through February 2003. PARTICIPANTS A total of 1426 children from the United States and Canada diagnosed as having DCM at younger than 18 years. Primary DCM was determined by strict echocardiographic and/or pathologic criteria. Patients with disease due to endocrine, immunologic, drug toxicity, and other causes were excluded. MAIN OUTCOME MEASURES Annual incidence per 100,000 children; mortality; cardiac transplantation. RESULTS The annual incidence of DCM in children younger than 18 years was 0.57 cases per 100,000 per year overall. The annual incidence was higher in boys than in girls (0.66 vs 0.47 cases per 100,000; P<.001), in blacks than in whites (0.98 vs 0.46 cases per 100,000; P<.001), and in infants (<1 year) than in children (4.40 vs 0.34 cases per 100,000; P<.001). The majority of children (66%) had idiopathic disease. The most common known causes were myocarditis (46%) and neuromuscular disease (26%). The 1- and 5-year rates of death or transplantation were 31% and 46%, respectively. Independent risk factors at DCM diagnosis for subsequent death or transplantation were older age, congestive heart failure, lower left ventricular fractional shortening Z score, and cause of DCM (P<.001 for all). CONCLUSIONS In children, DCM is a diverse disorder with outcomes that depend largely on cause, age, and heart failure status at presentation. Race, sex, and age affect the incidence of disease. Most children do not have a known cause of DCM, which limits the potential for disease-specific therapies.
Contribution of the rest–activity circadian rhythm to quality of life in cancer patients

Quality of life (QoL) is estimated from patients scores to items related to everyday life, including rest and activity. The rest–activity rhythm reflects endogenous circadian clock function. The relation between the individual rhythm in activity and QoL was investigated in 200 patients with metastatic colorectal cancer. Patients wore a wrist actigraph (Ambulatory Monitoring Inc., New York, NY) for 3–5 d before chronotherapy, and completed a QoL questionnaire developed by the European Organization for Research and Treatment of Cancer (QLQ-C30) plus the Hospital Anxiety and Depression Scale. The rest–activity circadian rhythm was characterized by the mean activity level (m), autocorrelation coefficient at 24h (r24), and the dichotomy index (I<O), a ratio between the amount of activity while in and out of bed. The distribution of the rest–activity cycle parameters and that of QoL scores was independent of sex, age, primary tumor, number of metastatic sites, and prior treatment. Both the 24h rhythm indicators were positively correlated with global QoL score as well as physical, emotional, and social functioning. Negative correlations were found between m, r24, or I<O and fatigue, appetite loss, and nausea. The rest–activity circadian rhythm appeared to be an objective indicator of physical welfare and QoL. This analysis suggests that circadian function may be one of the biological determinants of QoL in cancer patients.
Bayesian cluster ensembles

Cluster ensembles provide a framework for combining multiple base clusterings of a dataset to generate a stable and robust consensus clustering. There are important variants of the basic cluster ensemble problem, notably including cluster ensembles with missing values, row‐ or column‐distributed cluster ensembles. Existing cluster ensemble algorithms are applicable only to a small subset of these variants. In this paper, we propose Bayesian cluster ensemble (BCE), which is a mixed‐membership model for learning cluster ensembles, and is applicable to all the primary variants of the problem. We propose a variational approximation based algorithm for learning Bayesian cluster ensembles. BCE is further generalized to deal with the case where the features of original data points are available, referred to as generalized BCE (GBCE). We compare BCE extensively with several other cluster ensemble algorithms, and demonstrate that BCE is not only versatile in terms of its applicability but also outperforms other algorithms in terms of stability and accuracy. Moreover, GBCE can have higher accuracy than BCE, especially with only a small number of available base clusterings. © 2011 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 54–70 2011
Usefulness of Succinate dehydrogenase B (SDHB) immunohistochemistry in guiding mutational screening among patients with pheochromocytoma‐paraganglioma syndromes

Genetic testing of pheochromocytomas (PCC) and paragangliomas (PGL), although expensive, is gradually becoming a part of the routine laboratory investigation for patients with PCC‐PGL syndrome. Recently, Succinate dehydrogenase B (SDHB) immunochemistry has been shown to be an excellent indicator of germline mutations in the SDH genes and could help significantly reduce cost. This study assesses the utility of SDHB immunohistochemical analysis when used to guide genetic analysis, with emphasis on cost benefits it could provide in a resource‐limited setting. Forty‐four cases of PCC/PGL characterized by genetic analysis were included to determine their SDHB expression pattern by immunohistochemistry. SDHB antibody expression was negative among three cases each, with SDHB and SDHD mutations. Immunohistochemistry results were positive for all three cases of RET, a single case of neurofibromatosis and for two cases with Von Hippel‐Lindau (VHL) mutations while the remaining two cases with VHL mutations showed a diffuse ‘cytoplasmic blush’. Thirty of the remaining 31 samples demonstrated positive staining and were negative for mutations, while a lone sample that was negative for staining and mutation was not included in the final analysis as the internal control for the sample was not adequately stained. Cost analysis in our settings showed that triaging with SDHB immunohistochemistry could potentially reduce costs by USD 320–500 per patient. SDHB immunohistochemistry, when used as a guide to genetic testing, can significantly reduce the effort, time and costs of testing among patients with PCC‐PGL, a huge benefit in resource limited settings.
Analysis of the Relationship between Helicobacter pylori Infection and Diabetic Gastroparesis

Background: Whether Helicobacter pylori infection is associated with diabetic gastroparesis (DGP) is unclear. This study aimed to investigate the potential correlation between H. pylori infection and DGP. Methods: In this study, 163 patients with type 2 diabetes mellitus and 175 nondiabetic patients who were treated in our department were divided into DGP, simple diabetes, non-DGP (NDG), and normal groups based on their conditions. The H. pylori infection rate in each group was calculated. H. pylori eradication therapy was performed for patients with H. pylori infection in each group. The eradication rates were compared between the groups, and the improvements in gastroparesis-associated symptoms were compared before and after treatment in patients with DGP. Results: The H. pylori infection rate was 74.6% in the DGP group, which was significantly higher than that in the simple diabetes (51.1%, P < 0.01), NDG (57.7%, P < 0.05), and normal groups (48.0%, P < 0.01). With increased disease course, the incidence of DGP and the H. pylori infection rate gradually increased (P < 0.05). In the DGP group, the incidences of upper abdominal pain and distention, early satiety, and anorexia were 75.5%, 66.0%, and 67.9%, respectively, before eradication treatment; and 43.4%, 35.8%, and 39.6%, respectively, after eradication treatment, and the difference was statistically significant (P < 0.01). In patients with DGP with successful H. pylori eradication, the number of barium strips discharged after eradication was 5.9 ± 1.0, which was significantly larger than that before treatment (4.1 ± 0.7, P < 0.01). In addition, the number of barium strips discharged was significantly larger in patients with DGP with successful H. pylori eradication than those with failed H. pylori eradication (P < 0.01). Conclusions: DGP development might be associated with H. pylori infection. H. pylori eradication can effectively improve dyspepsia-associated symptoms and delayed gastric emptying in patients with DGP.
The Basic Region of the Diaphanous-autoregulatory Domain (DAD) Is Required for Autoregulatory Interactions with the Diaphanous-related Formin Inhibitory Domain*

Mammalian diaphanous-related (mDia) formins act as Rho GTPase effectors during cytoskeletal remodeling. Rho binding to mDia amino-terminal GTPase-binding domains (GBDs) causes the adjacent Dia-inhibitory domain (DID) to release the carboxyl-terminal Dia-autoregulatory (DAD) domain that flanks the formin homology-2 (FH2) domain. The release of DAD allows the FH2 domain to then nucleate and elongate nonbranched actin filaments. DAD, initially discovered as a region of homology shared between a phylogenetically divergent set of formin proteins, is comprised of a core motif, MDXLLXL, and an adjacent region is comprised of numerous basic residues, typically RRKR in the mDia family. Here, we show that these specific amino acids within the basic region of DAD contribute to the binding of DID and therefore the maintenance of the mDia autoregulatory mechanism. In addition, expression of full-length versions of mDia2 containing amino acid substitutions in either the DAD core or basic regions causes profound changes in the F-actin architecture, including the formation of filopodia-like structures that rapidly elongate from the cell edge. These studies further refine our understanding of the molecular contribution of DAD to mDia control and the role of mDia2 in the assembly of membrane protrusions.
Control of shape memory alloy actuators

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Visual correlation of host processes and network traffic

Anomalous communication patterns are one of the leading indicators of computer system intrusions according to the system administrators we have interviewed. But a major problem is being able to correlate across the host/network boundary to see how network connections are related to running processes on a host. This paper introduces Portall, a visualization tool that gives system administrators a view of the communicating processes on the monitored machine correlated with the network activity in which the processes participate. Portall is a prototype of part of the Network Eye framework we have introduced in an earlier paper (Ball, et al., 2004). We discuss the Portall visualization, the supporting infrastructure it requires, and a formative usability study we conducted to obtain administrators' reactions to the tool.
Accurate Diagnostics for Bovine tuberculosis Based on High-Throughput Sequencing

Background Bovine tuberculosis (bTB) is an enduring contagious disease of cattle that has caused substantial losses to the global livestock industry. Despite large-scale eradication efforts, bTB continues to persist. Current bTB tests rely on the measurement of immune responses in vivo (skin tests), and in vitro (bovine interferon-γ release assay). Recent developments are characterized by interrogating the expression of an increasing number of genes that participate in the immune response. Currently used assays have the disadvantages of limited sensitivity and specificity, which may lead to incomplete eradication of bTB. Moreover, bTB that reemerges from wild disease reservoirs requires early and reliable diagnostics to prevent further spread. In this work, we use high-throughput sequencing of the peripheral blood mononuclear cells (PBMCs) transcriptome to identify an extensive panel of genes that participate in the immune response. We also investigate the possibility of developing a reliable bTB classification framework based on RNA-Seq reads. Methodology/Principal Findings Pooled PBMC mRNA samples from unaffected calves as well as from those with disease progression of 1 and 2 months were sequenced using the Illumina Genome Analyzer II. More than 90 million reads were splice-aligned against the reference genome, and deposited to the database for further expression analysis and visualization. Using this database, we identified 2,312 genes that were differentially expressed in response to bTB infection (p<10−8). We achieved a bTB infected status classification accuracy of more than 99% with split-sample validation on newly designed and learned mixtures of expression profiles. Conclusions/Significance We demonstrated that bTB can be accurately diagnosed at the early stages of disease progression based on RNA-Seq high-throughput sequencing. The inclusion of multiple genes in the diagnostic panel, combined with the superior sensitivity and broader dynamic range of RNA-Seq, has the potential to improve the accuracy of bTB diagnostics. The computational pipeline used for the project is available from http://code.google. com/p/bovine-tb-prediction.
Validation of a short-term memory test for the recognition of people and faces

Memorising and processing faces is a short-term memory dependent task of utmost importance in the security domain, in which constant and high performance is a must. Especially in access or passport control-related tasks, the timely identification of performance decrements is essential, margins of error are narrow and inadequate performance may have grave consequences. However, conventional short-term memory tests frequently use abstract settings with little relevance to working situations. They may thus be unable to capture task-specific decrements. The aim of the study was to devise and validate a new test, better reflecting job specifics and employing appropriate stimuli. After 1.5 s (short) or 4.5 s (long) presentation, a set of seven portraits of faces had to be memorised for comparison with two control stimuli. Stimulus appearance followed 2 s (first item) and 8 s (second item) after set presentation. Twenty eight subjects (12 male, 16 female) were tested at seven different times of day, 3 h apart. Recognition rates were above 60% even for the least favourable condition. Recognition was significantly better in the ‘long’ condition (+10%) and for the first item (+18%). Recognition time showed significant differences (10%) between items. Minor effects of learning were found for response latencies only. Based on occupationally relevant metrics, the test displayed internal and external validity, consistency and suitability for further use in test/retest scenarios. In public security, especially where access to restricted areas is monitored, margins of error are narrow and operator performance must remain high and level. Appropriate schedules for personnel, based on valid test results, are required. However, task-specific data and performance tests, permitting the description of task specific decrements, are not available. Commonly used tests may be unsuitable due to undue abstraction and insufficient reference to real-world conditions. Thus, tests are required that account for task-specific conditions and neurophysiological characteristics.
Safe-commit analysis to facilitate team software development

Software development teams exchange source code in shared repositories. These repositories are kept consistent by having developers follow a commit policy, such as “Program edits can be committed only if all available tests succeed. ” Such policies may result in long intervals between commits, increasing the likelihood of duplicative development and merge conflicts. Furthermore, commit policies are generally not automatically enforceable. We present a program analysis to identify committable changes that can be released early, without causing failures of existing tests, even in the presence of failing tests in a developer's local workspace. The algorithm can support relaxed commit policies that allow early release of changes, reducing the potential for merge conflicts. In experiments using several versions of a non-trivial software system with failing tests, 3 newly enabled commit policies were shown to allow a significant percentage of changes to be committed.
RAT selection based on association probability in 5G heterogeneous networks

The use of multiple radio access technologies (RATs) is inevitable in future heterogeneous cellular networks. Various RATs can offer different throughputs, and thus RAT selection plays an important role in quality of service provisioning. In this paper, considering a heterogeneous network with two throughput classes, we introduce a new practical probabilistic RAT selection approach. In contrary to the common deterministic approaches, in this scheme, each user performs the RAT selection periodically in a random manner using an association probability determined by a central unit in the network. The user remains connected to the selected RAT for a specific amount of time and then again performs the selection. To find the association probabilities, the network throughput maximization is formulated. Since the resulting problem is not convex, we propose two alternatives, one with sub-optimal solution but lower complexity and one with the use of change of variables with optimal solution. Finally, numerical simulations demonstrate the superior performance of our proposed schemes in comparison to several possible approaches. Also, these numerical investigations indicate that our sub-optimal method works very close to the optimal one.
Music and Geography: Content Description of Musical Audio from Different Parts of the World

This paper analyses how audio features related to different musical facets can be useful for the comparative analysis and classification of music from diverse parts of the world. The music collection under study gathers around 6,000 pieces, including traditional music from different geographical zones and countries, as well as a varied set of Western musical styles. We achieve promising results when trying to automatically distinguish music from Western and non-Western traditions. A 86.68% of accuracy is obtained using only 23 audio features, which are representative of distinct musical facets (timbre, tonality, rhythm), indicating their complementarity for music description. We also analyze the relative performance of the different facets and the capability of various descriptors to identify certain types of music. We finally present some results on the relationship between geographical location and musical features in terms of extracted descriptors. All the reported outcomes demonstrate that automatic description of audio signals together with data mining techniques provide means to characterize huge music collections from different traditions, complementing ethnomusicological manual analysis and providing a link between music and geography.