Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring Fine-Grained Task-Based Execution on Multi-GPU Systems

Using multi-GPU systems, including GPU clusters, is gaining popularity in scientific computing. However, when using multiple GPUs concurrently, the conventional data parallel GPU programming paradigms, e.g., CUDA, cannot satisfactorily address certain issues, such as load balancing, GPU resource utilization, overlapping fine grained computation with communication, etc. In this paper, we present a fine-grained task-based execution framework for multi-GPU systems. By scheduling finer-grained tasks than what is supported in the conventional CUDA programming method among multiple GPUs, and allowing concurrent task execution on a single GPU, our framework provides means for solving the above issues and efficiently utilizing multi-GPU systems. Experiments with a molecular dynamics application show that, for nonuniform distributed workload, the solutions based on our framework achieve good load balance, and considerable performance improvement over other solutions based on the standard CUDA programming methodologies.
Responsible Integration of Biological and Psychosocial Models

Despite research demonstrating that gene expression differs in response to social environmental circumstances, deterministic views of biology are common. Stuart and colleagues (2014) encourage readers to think about genetic factors in the same dynamic and probabilistic manner that they consider other causes of intimate partner violence. Given that participants had co-occurring alcohol problems, future studies should evaluate how different genetic polymorphisms uniquely and synergistically contribute to heavy drinking and aggression under different socio-environmental conditions. Psychological expectancies have a powerful impact on behavior, thus extreme caution is required before labeling people as genetically predisposed to violence.
Data and Activity Representation for Grid Computing

Computational grids are becoming increasingly popular as an infrastructure for computa- tional science research. The demand for high-level tools and problem solving environments has prompted active research in Grid Computing Environments (GCEs). Many GCEs have been one-o development e orts. More recently, there have been many e orts to de ne component ar- chitectures for constructing important pieces of a GCE. This paper examines another approach, based on a `data-centric' framework for building powerful, context-aware GCEs spanning mul- tiple layers of abstraction. We describe a scheme for representing data and activities in a GCE and outline various tools under development which use this representation.
Tips and Tricks in Pediatric Vitreoretinal Surgery

Pediatric vitreoretinopathies pose unique challenges to the retinal surgeon because of the distinct anatomic and physiological differences from adult retinal diseases. The pars plana, through which the vitreoretinal instrumentation may be safely introduced, is not fully formed until approximately the age of 8 or 9 months, thereby necessitating entry through the pars plicata when a posterior approach is desired in the newborn eye. The vitreous gel, which is well formed and firm in normal newborn eyes, may be optically empty or abnormally syneretic in various pediatric diseases. The vitreoretinal adhesion is stronger in children than in adults, making the surgical induction of posterior vitreous detachment relatively difficult. The biochemistry of the newborn eye is in flux, with rising and falling levels of vascular endothelial growth factor (VEGF), insulin-like growth factor-1, tumor growth factor-b, and other cytokines, which may affect the progression or stabilization of pediatric vitreoretinopathies. To operate safely, the pediatric vitreoretinal surgeon must understand the characteristics that define diseases, such as retinopathy of prematurity (ROP), familial exudative vitreoretinopathy (FEVR), persistent fetal vasculature syndrome (PFVS), congenital x-linked retinoschisis (CXLRS), and Coats disease. We discuss below several common pitfalls and misunderstandings in the surgical approach to pediatric vitreoretinopathies.
High-Throughput Sequencing and Mutagenesis to Accelerate the Domestication of Microlaena stipoides as a New Food Crop

Global food demand, climatic variability and reduced land availability are driving the need for domestication of new crop species. The accelerated domestication of a rice-like Australian dryland polyploid grass, Microlaena stipoides (Poaceae), was targeted using chemical mutagenesis in conjunction with high throughput sequencing of genes for key domestication traits. While M. stipoides has previously been identified as having potential as a new grain crop for human consumption, only a limited understanding of its genetic diversity and breeding system was available to aid the domestication process. Next generation sequencing of deeply-pooled target amplicons estimated allelic diversity of a selected base population at 14.3 SNP/Mb and identified novel, putatively mutation-induced polymorphisms at about 2.4 mutations/Mb. A 97% lethal dose (LD97) of ethyl methanesulfonate treatment was applied without inducing sterility in this polyploid species. Forward and reverse genetic screens identified beneficial alleles for the domestication trait, seed-shattering. Unique phenotypes observed in the M2 population suggest the potential for rapid accumulation of beneficial traits without recourse to a traditional cross-breeding strategy. This approach may be applicable to other wild species, unlocking their potential as new food, fibre and fuel crops.
GATA-3 Expression in Breast Cancer Has a Strong Association with Estrogen Receptor but Lacks Independent Prognostic Value

Background: GATA-3 is a transcription factor involved in human growth and differentiation. Gene expression profiling has shown that GATA-3 is highly expressed in the Luminal A subtype of breast cancer. A recent study found GATA-3 to be associated with favorable breast cancer pathologic features, including negative lymph node and positive estrogen receptor (ER) status. GATA-3 levels were also found to be an independent prognostic marker, with low expression predicting for breast cancer recurrence. Materials and Methods: Our case series consists of 3,119 cases of invasive breast cancer in which GATA-3 expression was assessed by immunohistochemistry on tissue microarrays. We considered >5% nuclear staining to be a positive result for GATA-3. Results: Thirty-two percent of cases were GATA-3 positive. GATA-3 is almost exclusively expressed in ER+ patients and is also associated with lower tumor grade, older age at diagnosis, and the absence of Her2 overexpression. In univariate analysis, the presence of GATA-3 is a marker of good prognosis and predicted for superior breast cancer–specific survival, relapse-free survival, and overall survival. However, in multivariate models including patient age, tumor size, histologic grade, nodal status, ER status, and Her2 status, GATA-3 was not independently prognostic for these same outcomes. In the subgroups of ER+ patients treated with or without tamoxifen, GATA-3 was again nonprognostic for all outcomes. Discussion: GATA-3 is a molecular marker that is highly associated with ER expression, but it does not seem to have prognostic value independent of ER, nor does it predict for response to tamoxifen among ER-positive patients. (Cancer Epidemiol Biomarkers Prev 2008;17(2):365–73)
ESBL-Producing Escherichia coli from Cows Suffering Mastitis in China Contain Clinical Class 1 Integrons with CTX-M Linked to ISCR1

The prevalence of pathogenic multi-drug resistant (MDR) extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is rapidly increasing, becoming a global concern. In a veterinary context, ESBL-producing E. coli are mostly reported in poultry and pigs. Here, we report on the prevalence and characterize ESBL-producing E. coli isolated from diverse dairy farms in China. Overall, 36 (23.53%) out of 153 E. coli isolates from mastitic milk samples (n = 1252) were confirmed as ESBL-producers by double-disc synergy testing and PCR. Nucleotide analysis of PCR amplicons revealed that blaCTX-M was the predominant ESBL gene detected in 28 (77.78%) isolates, with blaCTX-M-15 being the major (78.57%) allele encoding for ESBLs. Also, 20 (55.56%) and 6 (16.67%) of the ESBL isolates were carrying blaTEM and blaSHV genes, respectively, in singlet or in combination. The majority of these isolates belonged to phylo-group A (69.44%) and D (16.67%). Strikingly, all these isolates were found to be MDR showing high resistance to cephalosporins including the fourth generation cefepime and common non β-lactams. Additionally, class 1 integrons (intI1) were found in 30 (83.33%) isolates. Analysis of the class 1 integrons variable regions indicated that they were carrying up to five different gene cassettes conferring resistance to various drugs with a predominant combination of dfrA17-aadA5 genes in tandem, conferring resistance to aminoglycosides and trimethoprim. However, no ESBL encoding genes were found in the cassettes. Interestingly, 22 (66.11%) of the ESBL isolates were also carrying insertion sequence common region 1 (ISCR1) which was found to be associated with most of the CTX-M genes. Altogether, the current study reports on the high prevalence of ESBL-positive E. coli, particularly CTX-M-15, carrying clinical class 1 integrons and ISCR1 elements are likely indicative of their rapid and wider dissemination, posing threats to veterinary and public health. To the best of our knowledge, this is the first comprehensive study to report on the alarming high occurrence of ESBL-producing E. coli from mastitic cows in China.
Prevalence of metabolic syndrome in the indigenous population, aged 19 to 69 years, from Jaguapiru Village, Dourados (MS), Brazil.

OBJECTIVE To evaluate the prevalence of metabolic syndrome in an indigenous Brazilian population. METHODS Indigenous Brazilians aged 18-69 years from Jaguapiru Village, Dourados, MS were studied. Participants were selected by simple random sampling of 360 houses in the village. The abdominal circumference of the population was evaluated, and measurements <80 cm for females or <90 cm for males were considered normal. Capillary blood glucose levels by glucometer and oral glucose tolerance tests were measured, and, when necessary, total cholesterol, HDL cholesterol and triglyceride levels were assessed. RESULTS Of the 632 indigenous Brazilians in the study, 281 were males. We observed that 287 (45.4%) presented abdominal circumference values greater than normal; of those, 199 were women (43.4% of all women in the study) and 88 were men (26.1% of all men in the study). CONCLUSION Metabolic syndrome is common in the Indian Jaguapiru Village.
Optimization and fabrication by 3D printing of a volcano smoke antenna for UWB applications

Ultra-Wideband (UWB) technology is a low power and high data rate technology for applications like radar imaging, sensor data collection, position localization and medical imaging. In UWB systems, antennas plays a critical role as they are required to be compact and wideband with minimal pulse distortion. This paper present a small three-dimensional volcano smoke antenna, designed and optimized in a FDTD full-wave simulator and then fabricated by 3D printing. The antenna has a simulated 10 dB impedance bandwidth from 3.2 GHz to 12.6 GHz, suitable for the UWB band. The measured return-loss for the 3D printed antenna shows a good agreement with the simulations. Hence, 3D printing can be used as an alternative method for fabricating complex shaped three-dimensional antennas.
Expression of growth control and differentiation genes in human lens epithelial cells with extended life span.

PURPOSE Peptide growth factors including hepatocyte growth factor (HGF), platelet-derived growth factor (PDGF), and epidermal growth factor (EGF) are mitogens for many cell types and may act as regulators of lens epithelial cell growth and differentiation. The present study was undertaken to investigate the expression of growth factor receptors and crystallin genes in the human lens epithelial cell line HLE B-3, created by infection with Adeno12-simian virus 40 (Ad12-SV40) hybrid virus. METHODS Reverse transcriptase-polymerase chain reaction (RT-PCR) with gene-specific primers was used to detect transcripts, and Southern and western blot analyses were used for identification of gene products. Functional analysis of PDGF receptor was performed by measuring the effect of PDGF-BB on Ca2+ release, cell growth, and western blot analysis, by using an antiphosphotyrosine antibody. RESULTS Human lens epithelial B-3 cells expressed the growth factor receptors HGF-R, EGF-R, and PDGF-Rbeta, but not PDGF-Ralpha, and also expressed the oncogenes H-ras and raf and the growth inhibitor transforming growth factor-beta1. Stimulation of PDGF-Rbeta with PDGF-BB in HLE B-3 cells increased phosphorylation of the receptor, was associated with an increase in intracellular Ca2+ levels, and produced a small increase in cell growth. In addition, HLE B-3 cells expressed transcripts for alphaA-, alphaB-, and betaB2-crystallins, and expressed the corresponding proteins. The transcripts for alphaA-crystallin decreased markedly at higher passages. CONCLUSIONS The above findings suggest that the increased growth potential of human lens epithelial cells by Ad12-SV40 infection maintained certain lens-specific properties and response to PDGF.
Concomitant Tumor Immunity to a Poorly Immunogenic Melanoma Is Prevented by Regulatory T Cells

Concomitant tumor immunity describes immune responses in a host with a progressive tumor that rejects the same tumor at a remote site. In this work, concomitant tumor immunity was investigated in mice bearing poorly immunogenic B16 melanoma. Progression of B16 tumors did not spontaneously elicit concomitant immunity. However, depletion of CD4+ T cells in tumor-bearing mice resulted in CD8+ T cell–mediated rejection of challenge tumors given on day 6. Concomitant immunity was also elicited by treatment with cyclophosphamide or DTA-1 monoclonal antibody against the glucocorticoid-induced tumor necrosis factor receptor. Immunity elicited by B16 melanoma cross-reacted with a distinct syngeneic melanoma, but not with nonmelanoma tumors. Furthermore, CD8+ T cells from mice with concomitant immunity specifically responded to major histocompatibility complex class I–restricted epitopes of two melanocyte differentiation antigens. RAG1 −/− mice adoptively transferred with CD8+ and CD4+ T cells lacking the CD4+CD25+ compartment mounted robust concomitant immunity, which was suppressed by readdition of CD4+CD25+ cells. Naturally occurring CD4+CD25+ T cells efficiently suppressed concomitant immunity mediated by previously activated CD8+ T cells, demonstrating that precursor regulatory T cells in naive hosts give rise to effective suppressors. These results show that regulatory T cells are the major regulators of concomitant tumor immunity against this weakly immunogenic tumor.
Use of the All Patient Refined-Diagnosis Related Group (APR-DRG) Risk of Mortality Score as a Severity Adjustor in the Medical ICU

Objective To evaluate the performance of APR-DRG (All Patient Refined—Diagnosis Related Group) Risk of Mortality (ROM) score as a mortality risk adjustor in the intensive care unit (ICU). Design Retrospective analysis of hospital mortality. Setting Medical ICU in a university hospital located in metropolitan New York. Patients 1213 patients admitted between February 2004 and March 2006. Main results Mortality rate correlated significantly with increasing APR-DRG ROM scores (p < 0.0001). Multiple logistic regression analysis demonstrated that, after adjusting for patient age and disease group, APR-DRG ROM was significantly associated with mortality risk in patients, with a one unit increase in APR-DRG ROM associated with a 3-fold increase in mortality. Conclusions APR-DRG ROM correlates closely with ICU mortality. Already available for many hospitalized patients around the world, it may provide a readily available means for severity-adjustment when physiologic scoring is not available.
Diagnostics of active galaxies I. Modeling the infrared properties of dusty cores of starburst galaxies

Aims. Despite extensive observations over the last decades, the central questions regarding the power source of the large IR luminosity of Ultra Luminous Infra Red Galaxies (ULIRGs), and their evolution, are still not fully answered. In this paper we will focus on massive star formation as a central engine and present an evolutionary model for these dust-enshrouded star formation regions. Methods. An evolutionary model was created using existing star formation and radiative transfer codes (STARBURST99, RADMC and RADICAL) as building blocks. The results of the simulations are compared to data from two IRAS catalogs. Results. From the simulations it is found that the dust surrounding the starburst region is made up from two components. There is a low optical depth (tau = 0.1, which corresponds to 0.1% of the total dust mass), hot (T similar to 400 K) non-grey component close to the starburst (scale size 10 pc) and a large scale, colder grey component (100 pc, 75 K) with a much larger column (tau = 10). The simulations also show that starburst galaxies can be powered by massive star formation. The parameters for this star forming region are difficult to determine, since the IR continuum luminosity is only sensitive to the total UV input. Therefore, there is a degeneracy between the total starburst mass and the initial mass function (IMF) slope. A less massive star formation with a shallower IMF will produce the same amount of OB stars and therefore the same amount of irradiating UV flux. Assuming the stars are formed according to a Salpeter IMF (Psi(M) proportional to M(-2.35)), the star formation region should produce 10(9) M(circle dot) of stars (either in one instantaneous burst, or in a continuous process) in order to produce enough IR radiation. Conclusions. Our models confirm that massive star formation is a valid power source for ULIRGs. In order to remove degeneracies and further determine the parameters of the physical environment also IR spectral features and molecular emissions need to be included.
Perinatal growth failure: the road to obesity, insulin resistance and cardiovascular disease in adults.

A continuum of increasing risk of adulthood diseases, such as cardiovascular disease, type 2 diabetes and hypertension, with decreasing size at birth is now well-reported and a number of different hypotheses have been proposed. Birthweight links with disease risk markers such as insulin resistance are apparent from childhood, particularly when low birthweight is followed by rapid postnatal weight gain and childhood obesity. Such growth patterns follow fetal growth restraint, associated with maternal-uterine factors such as primiparity, smoking, maternal genes or variations in maternal diet. The fetal metabolic and hormonal responses to intrauterine growth restraint and to rapid postnatal growth are likely to be key to the early pathogenesis of adulthood disease. Thrifty fetal genotypes may enhance these adaptations and improve perinatal survival but predispose to adulthood disease. Their historical selection could explain high prevalences of type 2 diabetes in some ethnic groups, and their identification could allow targeting of potential interventions.
Combination chemotherapy and radiotherapy for primary central nervous system lymphoma: Radiation Therapy Oncology Group Study 93-10.

PURPOSE Primary CNS lymphoma (PCNSL) is an aggressive primary brain tumor. Cranial irradiation alone rarely results in long-term disease control or prolonged survival. We prospectively studied the use of combination chemotherapy plus cranial irradiation in newly diagnosed patients with PCNSL. PATIENTS AND METHODS We enrolled 102 newly diagnosed, immunocompetent patients with PCNSL; 98 were assessable. Patients first received five cycles of methotrexate 2.5 g/m(2), vincristine, procarbazine, and intraventricular methotrexate (12 mg). Whole-brain radiotherapy (RT) was administered to a total dose of 45 Gy and all patients received high-dose cytarabine after RT. RESULTS Fifty-eight percent of patients with measurable disease had a complete response to preirradiation chemotherapy and 36% had a partial (> 50%) response, for a 94% response rate. Median progression-free survival was 24.0 months and overall survival was 36.9 months. Age was an important prognostic factor; median survival was 50.4 months in patients younger than 60 and only 21.8 months in those aged 60 or older (P <.001). Fifty-three percent of patients had grade 3 or 4 toxicity during induction chemotherapy, half of which was hematologic. However, 12 patients (15%) experienced severe delayed neurologic toxicity, eight of whom died. CONCLUSION This is the first multicenter trial demonstrating improved survival with the combination of chemotherapy plus RT compared with previous reports of RT alone. A high-dose methotrexate-based regimen produced a high response rate before RT was administered. High-dose methotrexate combined with cranial irradiation is an effective therapeutic approach to PCNSL, but neurotoxicity is a delayed risk of this approach.
The Brain Microvascular Endothelium Supports T Cell Proliferation and Has Potential for Alloantigen Presentation

Endothelial cells (EC) form the inner lining of blood vessels and are positioned between circulating lymphocytes and tissues. Hypotheses have formed that EC may act as antigen presenting cells based on the intimate interactions with T cells, which are seen in diseases like multiple sclerosis, cerebral malaria (CM) and viral neuropathologies. Here, we investigated how human brain microvascular EC (HBEC) interact with and support the proliferation of T cells. We found HBEC to express MHC II, CD40 and ICOSL, key molecules for antigen presentation and co-stimulation and to take up fluorescently labeled antigens via macropinocytosis. In co-cultures, we showed that HBEC support and promote the proliferation of CD4+ and CD8+ T cells, which both are key in CM pathogenesis, particularly following T cell receptor activation and co-stimulation. Our findings provide novel evidence that HBEC can trigger T cell activation, thereby providing a novel mechanism for neuroimmunological complications of infectious diseases.