Miracle-dz/UniFAR-FTUs huggingface dataset:
Variational Bayesian Sparse Kernel-Based Blind Image Deconvolution With Student's-t Priors

In this paper, we present a new Bayesian model for the blind image deconvolution (BID) problem. The main novelty of this model is the use of a sparse kernel-based model for the point spread function (PSF) that allows estimation of both PSF shape and support. In the herein proposed approach, a robust model of the BID errors and an image prior that preserves edges of the reconstructed image are also used. Sparseness, robustness, and preservation of edges are achieved by using priors that are based on the Student's-t probability density function (PDF). This pdf, in addition to having heavy tails, is closely related to the Gaussian and, thus, yields tractable inference algorithms. The approximate variational inference methodology is used to solve the corresponding Bayesian model. Numerical experiments are presented that compare this BID methodology to previous ones using both simulated and real data.
Process-level power estimation in VM-based systems

Power estimation of software processes provides critical indicators to drive scheduling or power capping heuristics. State-of-the-art solutions can perform coarse-grained power estimation in virtualized environments, typically treating virtual machines (VMs) as a black box. Yet, VM-based systems are nowadays commonly used to host multiple applications for cost savings and better use of energy by sharing common resources and assets. In this paper, we propose a fine-grained monitoring middleware providing real-time and accurate power estimation of software processes running at any level of virtualization in a system. In particular, our solution automatically learns an application-agnostic power model, which can be used to estimate the power consumption of applications. Our middleware implementation, named BitWatts, builds on a distributed actor implementation to collect process usage and infer fine-grained power consumption without imposing any hardware investment (e.g., power meters). BitWatts instances use high-throughput communication channels to spread the power consumption across the VM levels and between machines. Our experiments, based on CPU- and memory-intensive benchmarks running on different hardware setups, demonstrate that BitWatts scales both in number of monitored processes and virtualization levels. This non-invasive monitoring solution therefore paves the way for scalable energy accounting that takes into account the dynamic nature of virtualized environments.
BRCA1 Gene Mutations in Breast Cancer Patients from Kerman Province, Iran

Background Breast cancer is the most common malignancy in Iranian women. Mutations in BRCA1 gene is one of the important genetic predisposing factors in breast cancer. This gene is a tumor suppressor that plays an important role in regulating the functions of RAD51 protein for strand invasion in homologous recombination repair. Methods The BRCA1 gene has amplified in the DNA isolated from breast cancer patients' leukocytes, using Polymerase Chain Reaction technique. The PCR products have sequenced using an automated DNA sequencer and subsequently obtained data have aligned with the human BRCA1 DNA sequences available online. Results In this study, we have considered nine different mutations on 60 examined chromosomes from 30 patients, living in Kerman province. A deletion of one adenine (c.1017delA) and insertion of one cytosine (c.969InsC) have found as the most frequent (20%) mutation in this survey. A substitution of thymine for adenine (c.999T>A) has detected as the second common BRCA1 gene defect (6.7%). The other mutations have identified as single nucleotide replacement including: c.792A>C, c.825G>C, c.822T>A, c.1068A>G, c.969A>T and c.966T>C. Conclusion The identified BRCA1 mutations were in accordance with the previous reports. To our knowledge, four mutations: (c.969InsC, c.792A>C, c.825G>C, c.822T>A) which have identified in this study, have not been previously reported in the literature. A larger cohort study would help identifying all relevant BRCA1 mutations in this population.
KernelHive: a new workflow‐based framework for multilevel high performance computing using clusters and workstations with CPUs and GPUs

The paper presents a new open‐source framework called KernelHive for multilevel parallelization of computations among various clusters, cluster nodes, and finally, among both CPUs and GPUs for a particular application. An application is modeled as an acyclic directed graph with a possibility to run nodes in parallel and automatic expansion of nodes (called node unrolling) depending on the number of computation units available. A methodology is proposed for parallelization and mapping of an application to the environment that includes selection of devices using a chosen optimizer, selection of best grid configurations for compute devices, optimization of data partitioning and the execution. One of possibly many scheduling algorithms can be selected considering execution time, power consumption, and so on. An easy‐to‐use GUI is provided for modeling and monitoring with a repository of ready‐to‐use constructs and computational kernels. The methodology, execution times, and scalability have been demonstrated for a distributed and parallel password‐breaking example run in a heterogeneous environment with a cluster and servers with different numbers of nodes and both CPUs and GPUs. Additionally, performance of the framework has been compared with an MPI + OpenCL implementation using a parallel geospatial interpolation application employing up to 40 cluster nodes and 320 cores. Copyright © 2015 John Wiley & Sons, Ltd.
Environmental Health

This chapter describes the adverse impact of social injustice on environmental health. Environmental pollution is a social injustice for all people, with a disproportionate impact on low- and middle-income countries and, within countries, low-income people, minority groups, and other marginalized populations. The chapter describes the evolution of the environmental justice movement and the studies that have demonstrated disproportionate exposures and the disproportionate occurrence of pollution-related diseases among low-income people, minority groups, and other marginalized populations. A separate section describes the environmental and health consequences of global climate change. Three text boxes focus on childhood lead poisoning, the impact of natural disasters on social justice, and on the new interdiscipilinary field of planetary health.
Mass spectrometry in proteomics.

4. Automated Interpretation of CID Spectra 282 5. Accurate Mass Tags 282 C. Protein Identification in Complex Mixtures 282 D. Analysis of Protein Expression 284 III. Proteomes and Post-Translational Modifications 285 A. Proteomes 285 1. The Analytical Challenge 285 2. Analysis of Protein−Protein Complexes 286 B. Post-Translational Modifications 286 1. Background 286 2. Detection and Purification of Phosphoproteins 288
Characterizing Vancomycin-Resistant Enterococcus Strains with Various Mechanisms of Daptomycin Resistance Developed in an In Vitro Pharmacokinetic/Pharmacodynamic Model

ABSTRACT Two daptomycin (DAP) regimens were evaluated in a pharmacokinetic/pharmacodynamic (PK/PD) model, and the mutants recovered were examined for changes in phenotypic characteristics. Three Enterococcus faecium strains (vancomycin-resistant Enterococcus [VRE] ATCC 51559, VRE 12311, and VRE SF 12047) were utilized in a 7-day, 1-compartment in vitro PK/PD model. The simulated dosing regimens were DAP at 6 mg/kg/day (free Cmax [fCmax] = 7.9 μg/ml, half-life [t1/2] = 8 h) and DAP at 10 mg/kg/day (fCmax = 13.17 μg/ml, t1/2 = 8 h). Samples were plated daily on Mueller-Hinton agar containing DAP at 16 μg/ml and 50 mg/liter Ca2+ to assess the emergence of DAP resistance. For each strain, the mutant with the highest DAP MIC was then evaluated for changes in relative surface charge, cell wall thickness, and cytoplasmic membrane depolarization induced by DAP. The initial DAP MICs were 4 μg/ml for all 3 strains. A dose-dependent response and regrowth were observed for DAP 6 mg/kg/day and DAP 10 mg/kg/day against all 3 strains. Mutants of VRE ATCC 51559 (MIC = 128 and 64 μg/ml) and VRE 12311 (MIC = 256 and 32 μg/ml) were recovered from the DAP 6 mg and DAP 10 mg regimen, respectively. For VRE SF 12047, a mutant (MIC = 64 μg/ml) was recovered from the DAP 6 mg model. All mutants displayed an increase in relative surface charge compared to those of their respective parent strains. The DAP-resistant mutants displayed a 43 to 58% increase in cell wall thickness (P < 0.0001), while DAP membrane depolarization decreased by 53 to 65% compared to that of the susceptible strains. VRE with DAP resistance displayed increased surface charge, increased cell wall thickness, and decreased depolarization induced by DAP, consistent with previous observations in Staphylococcus aureus with reduced DAP susceptibility. Further characterization of DAP-resistant VRE is warranted.
Evaluation of Aging for Thermally Upgraded Paper in Mineral Oil

AbstractThe life of a transformer is limited by the degradation of its solid insulation. Winding conductors and other solid insulation materials in oil-immersed transformers have been insulated using cellulose products. For many years, manufacturers have met the needs of special applications by designing transformers using thermally upgraded materials to achieve lighter weight, higher power density and increased life. Recently, the effects of thermally upgraded insulation on diagnostic techniques such as gas-in-oil analysis, and indicators of their insulation degradation, have been reviewed. This paper describes evaluations of amine-impregnated thermally upgraded paper insulation's thermal degradation characteristics and decomposition reactions in mineral transformer oil. The thermal resistance of the thermally upgraded paper is evaluated by comparison with Kraft paper insulation. Further, aging degradation mechanisms of decompositional degradation of the thermally upgraded paper due to aging in mineral t.
Activation of human monocytes/macrophages by hypo‐osmotic shock

Phagocytosis and secretion of interleukins and growth factors put the macrophage in the centre of the wound healing process. For the last four years over 400 human ulcers have been treated in elderly and paraplegic patients by local application of monocytes prepared from a blood unit, in a unique, closed, sterile system. The process of preparation includes a step of hypo‐osmotic shock, which induces monocyte/macrophage activation. This is different from any other known method of activation. In the present study we evaluated the efficacy of the hypo‐osmotic shock. We found enhanced levels of IL‐1 (P = 0·004) and IL‐6 (P = 0·001) in the incubation medium (100% autologous serum) of the activated cells, as compared with controls, prepared in the same system. The IL‐1 reached a plateau after 6 and 12 h incubation at 37°C, in both experimental and control incubation medium. The level of IL‐6 was further elevated after 12 and 24 h incubation in experimental and control incubation mediums (P = 0·001). The phagocytosis of fluorescent beads was markedly enhanced after hypo‐osmotic shock (P = 0·005).
An efficient approach of backup reprovisioning for multiple link failures in WDM optical networks

This paper investigates an approach for Backup re-provisioning using Shared Path Protection to combat against concurrent multiple failures scenarios. The MSPP approach used, considers the cost related to selection of a backup resource and tries to provide backup to maximum number of vulnerable connections. Secondly, MBR and GBR policies have been used interchangeably based upon the value of Re-provisioning Success Rate (RSR) to ensure optimal resource utilization. Results show that the new approach performs well in terms of Protection Efficiency, Resource Overbuild, Re-provisioning Success Rate and Service Disruption Ratio.
Evaluation of Immunoglobulin A1 (IgA1) Protease and IgA1 Protease-Inhibitory Activity in Human Female Genital Infection with Neisseria gonorrhoeae

ABSTRACT Immunoglobulin A1 (IgA1) protease, an enzyme that selectively cleaves human IgA1, may be a virulence factor for pathogenic organisms such as Neisseria gonorrhoeae. Host protection from the effects of IgA1 protease includes antibody-mediated inhibition of IgA1 protease activity, and it is believed that the relative balance between IgA1 protease and inhibitory antibodies contributes to the pathogenesis of disease caused by IgA1 protease-producing organisms. We have examined the levels of these two opposing factors in genital tract secretions and sera from women with uncomplicated infection withN. gonorrhoeae. When IgA1 in cervical mucus was examined by Western blotting, no evidence of cleavage fragments characteristic of IgA1 protease activity was seen in gonococcus-infected or control patients. Cleavage fragments typical of IgA1 protease were detected, however, after the addition of exogenous IgA1 protease to cervical mucus. Degraded IgA1 was detected in some vaginal wash samples, but the fragment pattern was not typical of IgA1 protease activity. AllN. gonorrhoeae isolates from the infected patients produced IgA1 protease in vitro. All but two serum samples and 16 of 65 cervical mucus samples displayed inhibitory activity against gonococcal IgA1 protease, but there was no significant difference in the level of inhibitory activity between gonococcus-infected and noninfected patients in either cervical mucus or serum. There was no difference in the levels of IgA1 protease-inhibitory activity in serum or cervical mucus collected from patients at recruitment and 2 weeks later. These results suggest that cleavage of IgA1 by gonococcal IgA1 protease within the lumen of the female lower genital tract is unlikely to be a significant factor in the pathogenesis of infections by N. gonorrhoeae.
Implementation of BT-trees

This document presents the full implementation details of BT-trees, a highly efficient ordered map, and an evaluation which compares BT-trees with unordered maps. BT- trees are often much faster than other ordered maps, and have comparable performance to unordered map implementations. However, in benchmarks which favor unordered maps, BT-trees are not faster than the fastest unordered map implementations we know of.
Cardiac Troponin I and Troponin T: Recent Players in the Field of Myocardial Markers

Abstract The troponin (Tn) complex consists of three subunits referred to as TnT, TnI and TnC. Myocardium contains TnT and TnI isoforms which are not present in skeletal muscles and which can be separated from the muscular isoforms by immunological techniques. Using commercially available immunoassays, clinical laboratories are able to determine cardiac TnT and TnI (cTnT and cTnI) quickly and reliably as classical cardiac markers. After acute myocardial infarction, cTnT and cTnI concentrations start to increase in serum in a rather similar way than CK-MB, but return to normal after longer periods of time (approximately one week). Because of their excellent cardiac specificity, Tn subunits appear ideally suited for the differential diagnosis of myocardial and muscular damage, for example in noncardiac surgery patients, in patients with muscular trauma or with chronic muscular diseases, or after intense physical exercise. cTnT and cTnI may also be used for detecting evidence of minor myocardial damage: therefore they have found new clinical applications, in particular risk stratification in patients with unstable angina. In spite of the possible reexpression of cTnT in human skeletal muscles, and of the lack of standardization of cTnI assays, Tn subunits are not far to meet the criteria of ideal markers for acute myocardial injury. Only an insufficient sensitivity in the first hours following the acute coronary syndroms requiries to maintain an early myocardial marker in the cardiac panel for routine laboratory testing.
Polyadenylation site prediction using interesting emerging patterns

This paper presents a study on polyadenylation site prediction in mRNA sequences. We describe a method, called PolyA-EP, that we developed for predicting polyadenylation sites and we present a systematic study of the problem of recognizing mRNA 3' ends which contain a polyadenylation site using the proposed method. PolyA-EP exploits the advantages of emerging patterns, namely high understandability and discriminating power and can be used for both descriptive and predictive analysis. In particular, PolyA-EP is a parameterizable tool that can be used in order to extract interesting emerging patterns for describing or predicting polyadenylation sites. Moreover, the extracted emerging patterns can span across many elements around the polyadenylation site. We discuss the results of the experiments we conducted with Arabidopsis thaliana sequences drawing important conclusions and finally we propose a framework that improves the accuracy of polyadenylation site prediction.
Protein data representation and query using optimized data decomposition

MOTIVATION To provide data management tools to maintain and query efficiently experimental and derived protein data with the goal of providing new insights into structure-function relationships. The tools should be portable, extensible, and accessible locally, or via the World Wide Web, providing data that would not otherwise be available. RESULTS The initial phase of the work, the data representation and query of all available macromolecular structure data, including real-time access to complex property patterns based on the amino acid sequence, is reported. protein structure data taken from the Protein Data Bank (PDB) are decomposed into native and derived elementary properties, and represented as compact indexed objects minimizing storage requirements and query time for select types of query. In addition, collections of indices representing a particular property are maintained and can be queried for specific property patterns found across the whole database. The approach is proving applicable to a wide variety of data available on specific protein families.
Refactoring Tools: Fitness for Purpose

Refactoring is the process of changing software's structure while preserving its external behavior. Refactoring tools can improve the speed and accuracy with which developers create and maintain software-but only if they are used. In practice, tools are not used as much as they could be; this seems to be because sometimes they do not align with the refactoring tactic preferred by most programmers, a tactic the authors call "floss refactoring. " They propose five principles that characterize successful floss-refactoring tools - principles that can help programmers to choose the most appropriate refactoring tools and also help toolsmiths to design tools that fit the programmer's purpose.
A molecular dynamics study of the tensile behaviour of ultrathin gold nanowires

A molecular dynamics simulation of ultrathin gold nanowires for tensile behaviour has been carried out. Ultrathin nanowires, unlike the bulk FCC structure, have a multi-shell helical structure. This work compares the mechanical properties of the 7-1 multi-shell helical structure with those of the FCC structure. The results reveal that the temperature and the strain rate influence the yielding stress. One atom chain was detected before the nanowire broke when the temperature was near absolute zero. At room temperature, severe interaction between atoms caused successive yielding and a cluster of three atoms in cross-section was formed before the nanowire broke.
Security considerations in blinded exposure experiments using electromagnetic waves

Whether exposure to electromagnetic fields well below accepted exposure limits has a cytogenetic effect on human cells has long been debated. It is widely published and generally accepted that the exposure unit invariably used in these experiments is capable of providing blinded exposure conditions. The following short report illustrates, however, that exposure conditions might not always be as effectively masked as is generally assumed. Bioelectromagnetics 29:658–659, 2008. © 2008 Wiley‐Liss, Inc.
An experiment to measure the usability of parallel programming systems

SUMMARY The growth of commercial and academic interest in parallel and distributed computing during the past fifteen years has been accompanied by a corresponding increase in the number of available parallel programming systems (PPS). However, little work has been done to evaluate their usability, or to develop criteria for such evaluations. As a result, the usability of a typical PPS is based on how easily a small set of trivially parallel algorithms can be implemented by its authors. This paper discusses the design and results of an experiment to objectively compare the usability of two PPSs. Half of the students in a graduate parallel and distributed computing course solved a problem using the Enterprise PPS while the other half used a PVM-like library of message-passing routines. The objective was to measure usability. This experiment provided valuable feedback as to what features of PPSs are useful and the benefits they provide during the development of parallel programs. Although many usability experiments have been conducted for sequential programming languages and environments, they are rare in the parallel programming domain. Such experiments are necessary to help narrow the gap between what parallel programmers want, and what current PPSs provide.
Predicting sickness impact profile at six months after stroke: further results from the European multi-center CERISE study

Abstract Purpose: To develop prognostic models and equations for predicting participation at six months after stroke. Methods: This European prospective cohort study recruited 532 consecutive patients from four rehabilitation centers. Participation was assessed at six months after stroke with the Sickness Impact Profile (SIP), which consists of a physical, psychosocial and independent dimension. Twenty-six independent variables on admission to the rehabilitation center and 13 additional variables measured at two months post stroke were included in the analysis. A multiple logistic regression analysis was conducted predicting good participation (SIP < 20%). Sensitivity, specificity, positive and negative predictive values were calculated. Results: The prognostic models for the three dimensions provided independent predictors containing demographics, complications, diagnostic, and disability measures. Sensitivity ranged from 64–84%, specificity 66–85%, positive predictive value 70–78%, and negative predictive value 76–87%. Barthel Index on admission, Euroqol Health State at two months and Caregiver Strain Index at two months were retained in all prediction models. Conclusions: A combination of variables was found in the prognostic models of the three dimensions of the SIP at six months after stroke. Already from the early beginning of stroke rehabilitation it seems important to focus on personal activities of daily living as well as caregivers' strain. Implications for Rehabilitation Prognostic factors predicting participation, measured by the three dimensions of the Sickness Impact Profile at six months post stroke include demographic variables, post-stroke complications, diagnostic parameters and disability measures. Significant prognostic variables for all three dimensions of the Sickness Impact Profile were a higher Barthel Index score on admission to the rehabilitation center, a higher Euroqol Health State score at two months post stroke and a lower Caregiver Strain Index score at two months post stroke. Early stroke therapy should therefore further emphasize rehabilitation of personal activities of daily living such as mobility, walking, feeding, dressing, and toilet use, as well as considering strategies to reduce caregiver strain such as giving support, providing information and training carers.