Miracle-dz/UniFAR-FTUs huggingface dataset:
Data-Locality Aware Dynamic Schedulers for Independent Tasks with Replicated Inputs

In this paper we concentrate on a crucial parameter for efficiency in Big Data and HPC applications: data locality. We focus on the scheduling of a set of independant tasks, each depending on an input file. We assume that each of these input files has been replicated several times and placed in local storage of different nodes of a cluster, similarly of what we can find on HDFS system for example. We consider two optimization problems, related to the two natural metrics: makespan optimization (under the constraint that only local tasks are allowed) and communication optimization (under the constraint of never letting a processor idle in order to optimize makespan). For both problems we investigate the performance of dynamic schedulers, in particular the basic greedy algorithm we can for example find in the default MapReduce scheduler. First we theoretically study its performance, with probabilistic models, and provide a lower bound for communication metric and asymptotic behaviour for both metrics. Second we propose simulations based on traces from a Hadoop cluster to compare the different dynamic schedulers and assess the expected behaviour obtained with the theoretical study.
Differential Dual-Polarized Filtering Dielectric Resonator Antenna

This communication presents a differential dual-polarized filtering dielectric resonator antenna (DRA). In this antenna, a four-leaf-clover-shaped dielectric resonator is excited with two groups of out-of-phase modes. The novel configuration and differential feeding provide the DRA with high isolation for input ports, and the elaborately designed feeding strips ensure controllable input impedances for integration applications. After integrating with a pair of filtering baluns on the opposite side of the reflecting ground, the proposed DRA also exhibits good out-of-band rejection for each port with a wide stopband and two radiation nulls at band edges. A prototype has been designed and implemented, and reasonable agreement between the measured and simulated results can be observed.
A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction

Rhodopsins are seven α-helical membrane proteins that are of great importance in chemistry, biology, and modern biotechnology. Any in silico study on rhodopsin properties and functioning requires a high-quality three-dimensional structure. Due to particular difficulties with obtaining membrane protein structures from the experiment, in silico prediction of the three-dimensional rhodopsin structure based only on its primary sequence is an especially important task. For the last few years, significant progress was made in the field of protein structure prediction, especially for methods based on comparative modeling. However, the majority of this progress was made for soluble proteins and further investigations are needed to achieve similar progress for membrane proteins. In this paper, we evaluate the performance of modern protein structure prediction methodologies (implemented in the Medeller, I-TASSER, and Rosetta packages) for their ability to predict rhodopsin structures. Three widely used methodologies were considered: two general methodologies that are commonly applied to soluble proteins and a methodology that uses constraints that are specific for membrane proteins. The test pool consisted of 36 target-template pairs with different sequence similarities that was constructed on the basis of 24 experimental rhodopsin structures taken from the RCSB database. As a result, we showed that all three considered methodologies allow obtaining rhodopsin structures with the quality that is close to the crystallographic one (root mean square deviation (RMSD) of the predicted structure from the corresponding X-ray structure up to 1.5 Å) if the target-template sequence identity is higher than 40%. Moreover, all considered methodologies provided structures of average quality (RMSD < 4.0 Å) if the target-template sequence identity is higher than 20%. Such structures can be subsequently used for further investigation of molecular mechanisms of protein functioning and for the development of modern protein-based biotechnologies.
Access to injectable biologic medications by medicare beneficiaries: geographic distribution of US dermatologist prescribers

Abstract Purpose: Injectable biologics (IB) are important in dermatology and we sought to examine the distribution of US IB-prescribing dermatologists. Materials and methods: We used Centers for Medicare and Medicaid Services Medicare Provider Utilization and Payment Data: Part D for 2013–2015. The density of dermatologists who prescribe IB (etanercept, adalimumab, ustekinumab, secukinumab) in each US county, represented as number of dermatologists per 100,000 Medicare Part D beneficiaries, was calculated. Results: 2,992 dermatologists (26.3% of dermatologists) prescribed IB in this study. The national density of IB-prescribing dermatologists was 7.22. Only 778 counties (24.8%) have at least one IB-prescribing dermatologist. The densities of IB-prescribing dermatologists in metropolitan counties were 8.07–8.12. The densities of IB-prescribing dermatologists were 4.55 and 6.51 for urban populations of greater than 20,000 people adjacent and non-adjacent to metropolitan areas, respectively. Urban counties with populations between 2,500–19,999 and adjacent to a metropolitan area had a density of 2.03 and urban counties with the same population and not adjacent to a metropolitan area had a density of 2.84. Completely rural or urban counties with populations under 2,500 people had densities between 2.31–2.35. Conclusions: There are disparities in the availability of IB-prescribing dermatologists across urban-rural geographic settings in the US.
Aberrant imprinting in mouse trophoblast stem cells established from somatic cell nuclear transfer-derived embryos

ABSTRACT Although phenotypic abnormalities frequently appear in the placenta following somatic cell nuclear transfer (SCNT), mouse trophoblast stem cells (TSCs) established from SCNT embryos reportedly show no distinct abnormalities compared with those derived from normal fertilization. In this study, we reexamined SCNT–TSCs to identify their imprinting statuses. Placenta-specific maternally imprinted genes (Gab1, Slc38a4, and Sfmbt2) consistently showed biallelic expression in SCNT–TSCs, suggesting their loss of imprinting (LOI). The LOI of Gab1 was associated with decreased DNA methylation, and that of Sfmbt2 was associated with decreased DNA methylation and histone H3K27 trimethylation. The maternal allele of the intergenic differentially methylated region (IG–DMR) was aberrantly hypermethylated following SCNT, even though this region was prone to demethylation in TSCs when established in a serum-free chemically defined medium. These findings indicate that the development of cloned embryos is associated with imprinting abnormalities specifically in the trophoblast lineage from its initial stage, which may affect subsequent placental development.
Exploring the Vision Processing Unit as Co-Processor for Inference

The success of the exascale supercomputer is largely debated to remain dependent on novel breakthroughs in technology that effectively reduce the power consumption and thermal dissipation requirements. In this work, we consider the integration of co-processors in high-performance computing (HPC) to enable low-power, seamless computation offloading of certain operations. In particular, we explore the so-called Vision Processing Unit (VPU), a highly-parallel vector processor with a power envelope of less than 1W. We evaluate this chip during inference using a pre-trained GoogLeNet convolutional network model and a large image dataset from the ImageNet ILSVRC challenge. Preliminary results indicate that a multi-VPU configuration provides similar performance compared to reference CPU and GPU implementations, while reducing the thermal-design power (TDP) up to 8x in comparison.
Sexual Assault Prevention for Heavy Drinking College Men: Development and Feasibility of an Integrated Approach

Despite the prevalence of sexual assault on college campuses, few interventions aimed at decreasing college men’s proclivity to perpetrate sexual aggression have been developed and tested. This article details the theoretical framework, content, and piloting of a sexual assault prevention program for college men who engage in heavy drinking, a high-risk group who may be particularly well positioned to intervene as proactive bystanders in drinking environments. In an open trial, male facilitators delivered the three-session Sexual Assault and Alcohol Feedback and Education (SAFE) program to 25 heavy drinking college men. Session 1 was a 90-min review of personalized normative feedback regarding alcohol use, sexual activity, alcohol-related sexual consequences, understanding of consent, and engagement in bystander intervention, delivered individually in a motivational interviewing style. Session 2 was a 2½-hr group-based sexual assault prevention workshop focusing on social norms, empathy, masculinity, consent, and bystander intervention. Session 3 was a 90-min booster group session that reviewed previous topics and included the active practice of bystander intervention skills. Analyses of postsession assessments of utility, therapeutic alliance, and satisfaction and examination of alcohol use and sexual assault–related outcomes from baseline to the 2-month assessment support the preliminary feasibility and acceptability of the SAFE program.
How to influence the mesenchymal stem cells fate? Emerging role of ectoenzymes metabolizing nucleotides

Extracellular purines, principally adenosine triphosphate and adenosine, are among the oldest evolutionary and widespread chemical messengers. The integrative view of purinergic signaling as a multistage coordinated cascade involves the participation of nucleotides/nucleosides, their receptors, enzymes metabolizing extracellular nucleosides and nucleotides as well as several membrane transporters taking part in the release and/or uptake of these molecules. In view of the emerging data, it is evident and widely accepted that an extensive network of diverse enzymatic activities exists in the extracellular space. The enzymes regulate the availability of nucleotide and adenosine receptor agonists, and consequently, the course of signaling events. The current data indicate that mesenchymal stem cells (MSCs) and cells induced to differentiate exhibit different sensitivity to purinergic ligands as well as a distinct activity and expression profiles of ectonucleotidases than mature cells. In the proposed review, we postulate for a critical role of these enzymatic players which, by orchestrating a fine‐tune regulation of nucleotides concentrations, are integrally involved in modulation and diversification of purinergic signals. This specific hallmark of the MSC purinome should be linked with cell‐specific biological potential and capacity for tissue regeneration. We anticipate this publication to be a starting point for scientific discussion and novel approach to the in vitro and in vivo regulation of the MSC properties.
OAS1 and OAS3 negatively regulate the expression of chemokines and interferon-responsive genes in human macrophages

Upon viral infection, the 2′, 5′-oligoadenylate synthetase (OAS)-ribonuclease L (RNaseL) system works to cleave viral RNA, thereby blocking viral replication. However, it is unclear whether OAS proteins have a role in regulating gene expression. Here, we show that OAS1 and OAS3 act as negative regulators of the expression of chemokines and interferon-responsive genes in human macrophages. Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 nuclease (Cas9) technology was used to engineer human myeloid cell lines in which the OAS1 or OAS3 gene was deleted. Neither OAS1 nor OAS3 was exclusively responsible for the degradation of rRNA in macrophages stimulated with poly(I:C), a synthetic surrogate for viral double-stranded (ds)RNA. An mRNA sequencing analysis revealed that genes related to type I interferon signaling and chemokine activity were increased in OAS1−/− and OAS3−/− macrophages treated with intracellular poly(I:C). Indeed, retinoic-acid-inducible gene (RIG)-I- and interferon-induced helicase C domain-containing protein (IFIH1 or MDA5)-mediated induction of chemokines and interferon-stimulated genes was regulated by OAS3, but Toll-like receptor 3 (TLR3)- and TLR4-mediated induction of those genes was modulated by OAS1 in macrophages. However, stimulation of these cells with type I interferons had no effect on OAS1- or OAS3-mediated chemokine secretion. These data suggest that OAS1 and OAS3 negatively regulate the expression of chemokines and interferon-responsive genes in human macrophages.
Poor plant performance under simulated climate change is linked to mycorrhizal responses in a semi‐arid shrubland

Warmer and drier conditions associated with ongoing climate change will increase abiotic stress for plants and mycorrhizal fungi in drylands world‐wide, thereby potentially reducing vegetation cover and productivity and increasing the risk of land degradation and desertification. Rhizosphere–microbial interactions and feedbacks are critical processes that could either mitigate or aggravate the vulnerability of dryland vegetation to forecasted climate change. We conducted a 4‐year manipulative study in a semi‐arid shrubland in the Iberian Peninsula to assess the effects of warming (c. 2.5°C; W), rainfall reduction (c. 30%; RR) and their combination (W+RR) on the performance of native shrubs (Helianthemum squamatum) and their associated mycorrhizal fungi. Warming (W and W+RR) decreased the net photosynthetic rates of H. squamatum shrubs by c. 31% despite concurrent increases in stomatal conductance (c. 33%), leading to sharp decreases (c. 50%) in water use efficiency. Warming also advanced growth phenology, decreased leaf nitrogen and phosphorus contents per unit area, reduced shoot biomass production by c. 36% and decreased survival during a dry year in both W and W+RR plants. Plants under RR showed more moderate decreases (c. 10%–20%) in photosynthesis, stomatal conductance and shoot growth. Warming, RR and W+RR altered ectomycorrhizal fungal (EMF) community structure and drastically reduced the relative abundance of EMF sequences obtained by high‐throughput sequencing, a response associated with decreases in the leaf nitrogen, phosphorus and dry matter contents of their host plants. In contrast to EMF, the community structure and relative sequence abundances of other non‐mycorrhizal fungal guilds were not significantly affected by the climate manipulation treatments. Synthesis. Our findings highlight the vulnerability of both native plants and their symbiotic mycorrhizal fungi to climate warming and drying in semi‐arid shrublands, and point to the importance of a deeper understanding of plant–soil feedbacks to predict dryland vegetation responses to forecasted aridification. The interdependent responses of plants and ectomycorrhizal fungi to warming and rainfall reduction may lead to a detrimental feedback loop on vegetation productivity and nutrient pool size, which could amplify the adverse impacts of forecasted climate change on ecosystem functioning in EMF‐dominated drylands.
Effectiveness of Community Treatment Order in Patients with a First Episode of Psychosis: A Mirror-Image Study

Objective: Poor adherence to antipsychotic medications is strongly associated with psychotic relapses and hospitalizations. This may hinder patients’ ability to function, particularly in a first episode of psychosis (FEP). Poor adherence to treatment may be due to poor insight that can alter the capacity to consent to care, including pharmacotherapy. When patients are judged legally lacking the capacity to consent to care, treatment can be mandated through community treatment orders (CTOs). This naturalistic study examines the effects of CTOs in FEP patients. Method: This study examines 38 FEP patients legally deemed unable to consent to care during their follow-up. Using a naturalistic mirror-image approach, we compare clinical (Scale for the Assessment of Positive Symptoms [SAPS], Scale for the Assessment of Negative Symptoms [SANS]), functional (Global Assessment of Functioning Scale [GAF], Social and Occupational Functioning Assessment Scale [SOFAS]), and service use (number of emergency room visits, length of hospitalizations) indicators before and after CTO. Results: After the CTO, 37 of 38 patients complied with treatment. Statistically significant improvements in clinical (▵SAPS = –6.3; 95% CI, 4.5 to 8.1 and ▵SANS = –2.2; 95% CI, 0.9 to 3.4, P < 0.01) and functional (▵GAF = +15.0; 95% CI, 8.4 to 21.6, ▵SOFAS = +18.6; 95% CI, 12.8 to 24.4, P < 0.01) outcomes were observed. Significant reduction in emergency room visits (P = 0.016) and days of hospitalization per month in acute care units (P < 0.05) were identified with no difference in hospital days per month in short-stay units. Moreover, encounters with case managers (P = 0.008) and attendance of cognitive therapy sessions (P = 0.031) were significantly higher. However, patients’ weight significantly increased after CTO (▵weight = +8.0 kg, P < 0.01). Conclusions: In FEP patients, CTOs improve compliance to treatment, which contributes to reducing positive and negative symptoms, shortening hospital stays, and improving functioning.
Lymphocyte Autophagy in Homeostasis, Activation, and Inflammatory Diseases

Autophagy is a catabolic mechanism, allowing the degradation of cytoplasmic content via lysosomal activity. Several forms of autophagy are described in mammals. Macroautophagy leads to integration of cytoplasmic portions into vesicles named autophagosomes that ultimately fuse with lysosomes. Chaperone-mediated autophagy is in contrast the direct translocation of protein in lysosomes. Macroautophagy is central to lymphocyte homeostasis. Although its role is controversial in lymphocyte development and in naive cell survival, it seems particularly involved in the maintenance of certain lymphocyte subtypes. Its importance in memory B and T cells biology has recently emerged. Moreover, some effector cells like plasma cells rely on autophagy for survival. Autophagy is central to glucose and lipid metabolism, and to the maintenance of organelles like mitochondria and endoplasmic reticulum. In addition macroautophagy, or individual components of its machinery, are also actors in antigen presentation by B cells, a crucial step to receive help from T cells, this crosstalk favoring their final differentiation into memory or plasma cells. Autophagy is deregulated in several autoimmune or autoinflammatory diseases like systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and Crohn’s disease. Some treatments used in these pathologies impact autophagic activity, even if the causal link between autophagy regulation and the efficiency of the treatments has not yet been clearly established. In this review, we will first discuss the mechanisms linking autophagy to lymphocyte subtype survival and the signaling pathways involved. Finally, potential impacts of autophagy modulation in lymphocytes on the course of these diseases will be approached.
Synergizing Appearance and Motion With Low Rank Representation for Vehicle Counting and Traffic Flow Analysis

Appearance and motion, which are complementary, account for a dominant proportion of visual information. We propose to synergize them using a low-rank representation framework for the estimation and analysis of traffic flow. Taking advantage of the downward-looking camera configuration, we do the processing only on the measure line, called virtual gantry, instead of dealing with the whole frame, resulting in much improved efficiency. Enforcing the low-rank constraint on the spatiotemporal image which is generated via stacking pixels on virtual gantry over time, we introduce the block-sparse robust principal component analysis algorithm, in which the motion cue is leveraged to highlight the foreground and realize vehicle detection with high accuracy. The motion flow is further exploited for size normalization to classify vehicles into lite, small, medium, and large categories. Benefiting from the low-rank representation, our method is parameter insensitive, robust to illumination changes, and requires no training. We perform extensive experiments on the 24/7 videos collected over the highways in China and Singapore, obtaining nearly 100% accuracy. Meanwhile, insightful observations on the obtained traffic information are given, which could be very valuable to the users, especially to the traffic management sectors.
Longitudinal Study of Transfusion Utilization in Hospitalized Veterans.

Objective Although transfusion guidelines have changed considerably over the past two decades, the adoption of patient blood management programs has not been fully realized across hospitals in the United States. Patients and Methods We evaluated trends in red blood cell (RBC), platelet and plasma transfusion at three Veterans Health Administration (VHA) hospitals from 2000 through 2010. Results There were 176,521 hospitalizations in 69,621 patients; of these, 13.6% of hospitalizations involved transfusion of blood products (12.7% RBCs, 1.4% platelets, 3.0% plasma). Transfusion occurred in 25.2% of surgical and 5.3% of medical hospitalizations. Transfusion use peaked in 2002 for surgical hospitalizations and declined afterwards (p<0.001). There was no significant change in transfusion use over time (p=0.126) for medical hospitalizations. In hospitalizations that involved transfusions, there was a 20.3% reduction in the proportion of hospitalizations in which ≥3 units of RBCs were given (from 51.7% to 41.1%; p<0.001) and a 73.6% increase when one RBC unit was given (from 8.0% to 13.8%; p<0.001) from 2000-2010. Of the hospitalizations with RBC transfusion, 9.6% involved the use of one unit over the entire study period. The most common principal diagnoses for medical patients receiving transfusion were anemia, malignancy, heart failure, pneumonia and renal failure. Over time, transfusion utilization increased in patients who were admitted for infection (p=0.009). Conclusion Blood transfusions in three VHA hospitals have decreased over time for surgical patients but remained the same for medical patients. Further study examining appropriateness of blood products in medical patients appears necessary.