Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic association of PRDM1-ATG5 intergenic region and autophagy with systemic lupus erythematosus in a Chinese population

Objective Recent genome-wide association studies suggested the PRDM1-ATG5 gene region as a systemic lupus erythematosus (SLE)-associated locus both in Caucasian and Chinese populations; however, the candidate gene was still obscure and the possible functional significance needed to be determined. Methods In this study, by a multistage integrative strategy, the authors first performed a case–control association study involving 1745 individuals in the Chinese population by genotyping nine single nucleotide polymorphisms within this region, and a meta-analysis was conducted. Correlation between associated genotypes and expression levels of messenger RNA in B-cell lines from 210 unrelated HapMap data was examined, and was validated in vitro. To determine the biological significance, a genetic association study was also checked in a pathway-based manner and the significant associations were validated in a second 844 Chinese cohort. Results A peak of association was found in the intergenic region (p=0.036–3.26×10−4). Meta-analysis consolidated the association between rs548234 and SLE (OR 1.254, p=1.28×10−16). Significant positive correlations with ATG5 expression were identified, suggesting ATG5 as a candidate gene in the region. Epstein–Barr virus B-cell-based downstream gene expression analysis supported a functional effect of rs548234 and rs6937876, and in-vitro experiments confirmed the regulatory effect of rs6937876 in B-cell populations. Finally, an autophagy pathway-based genetic association study identified ATG7 (p=1.12×10−4) and IRGM (p=0.015) as novel candidate genes, and gene–gene interactions were observed between ATG5, ATG7 and IRGM. Conclusion These data may demonstrate that autophagy is involved in the pathogenesis of SLE and imply a common biological pathway in autoimmunity.
Use of Electronic Health Data to Estimate Heart Failure Events in a Population-Based Cohort with CKD.

BACKGROUND AND OBJECTIVES Studies that use electronic health data typically identify heart failure (HF) events from hospitalizations with a principal diagnosis of HF. This approach may underestimate the total burden of HF among persons with CKD. We assessed the accuracy of algorithms for identifying validated HF events from hospitalizations and outpatient encounters, and we used this validation information to estimate the rate of HF events in a large CKD population. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We identified a cohort of 15,141 adults age 18-89 years with an eGFR<60 ml/min per 1.73 m2 from 2008 to 2011. Potential HF events during follow-up were randomly sampled for validation with medical record review. Positive predictive values from the validation study were used to estimate the rate of validated HF events in the full cohort. RESULTS A total of 1864 participants had at least one health care encounter that qualified as a potential HF event during 2.7 years of mean follow-up. Among 313 potential events that were randomly sampled for validation, positive predictive values were 92% for hospitalizations with a principal diagnosis of HF, 32% for hospitalizations with a secondary diagnosis of HF, and 70% for qualifying outpatient HF encounters. Through use of this validation information in the full cohort, the rate of validated HF events estimated from the most comprehensive algorithm that included principal and secondary diagnosis hospitalizations and outpatient encounters was 35.2 events/1000 person-years (95% confidence interval, 33.1 to 37.4), compared with 9.5 events/1000 person-years (95% confidence interval, 8.7 to 10.5) from the algorithm that included only principal diagnosis hospitalizations. Outpatient encounters accounted for 20% of the total number of validated HF events. CONCLUSIONS In studies that rely on electronic health data, algorithms that include hospitalizations with a secondary diagnosis of HF and outpatient HF encounters more fully capture the burden of HF, although validation of HF events may be necessary with this approach.
Septicemia with Streptococcus pseudopneumoniae: report of three cases with an apparent hepatic or bile duct association

Abstract Streptococcus pseudopneumoniae was described in 2004 as a new human pathogen, acknowledged in a range of clinical infections typically associated to the respiratory tract. This report demonstrates that S. pseudopneumoniae has the potential to cause invasive infection. In blood cultures from three patients, growth of an atypical Streptococcus pneumoniae (non-capsular, non-serotypeable, optochin susceptible under ambient atmosphere and bile-intermediately soluble) was recovered. All three patients had a history of a haematological disease (myelodysplastic syndrome and multiple myeloma) and an apparent origin of infection related to the liver or bile duct. All isolates were genome sequenced and subsequently identified as S. pseudopneumoniae by multi-locus sequence analysis (MLSA). Multi-locus sequence typing (MLST) based on the S. pneumoniae scheme revealed unknown sequence types and the antibiogram and resistome revealed no antibiotic resistance.
Evaluation of the Brain 5-HT2A Receptor Binding Index in Dogs with Anxiety Disorders, Measured with 123I-5I-R91150 and SPECT

The serotonergic system has been implicated in emotional and cognitive functions since early work. In particular, an important role has been attributed to the 5-HT2A receptor in schizophrenia, depression, eating disorders, and anxiety. The aim of the study was to evaluate the involvement of the brain 5-HT2A receptor in dogs with severe anxiety disorder, using 123I-5I-R91150 and SPECT. Methods: SPECT was performed with the 5-HT2A receptor-specific radioligand 123I-5I-R91150 to determine the 5-HT2A receptor binding index (BI) in the brains of dogs. Sixteen dogs with pathologic anxiety problems were compared with 22 normal-behaving reference dogs. Results: Lower 5-HT2A receptor BI was found in the left (P = 0.001) and right (P = 0.002) frontal cortices in the group of dogs with anxiety disorders than in the reference group. Right (P = 0.022) and left (P = 0.048) temporocortical BIs were also significantly lower in the dogs with anxiety disorders. Finally, the BI was significantly lower in the right occipital cortex (P = 0.038) of dogs with anxiety disorders than in the reference dogs. After correction for multiple comparisons (P < 0.0056), only the bilateral frontocortical lower BI remained significant. Conclusion: The findings in this study indicate that the 5-HT2A receptor is involved in the pathophysiology of anxiety disorders in dogs. The affected brain regions are in concordance with the brain regions involved in human anxiety disorders. The acquired data confirm the potential of using the dog as a natural model for investigation of the different mechanisms of anxiety disorders. In this regard, the use of dogs may contribute to the development of novel treatment approaches and new drugs for veterinary and human use.
A comparative transcriptomic analysis of astrocytes differentiation from human neural progenitor cells

Astrocytes are a morphologically and functionally heterogeneous population of cells that play critical roles in neurodevelopment and in the regulation of central nervous system homeostasis. Studies of human astrocytes have been hampered by the lack of specific molecular markers and by the difficulties associated with purifying and culturing astrocytes from adult human brains. Human neural progenitor cells (NPCs) with self‐renewal and multipotent properties represent an appealing model system to gain insight into the developmental genetics and function of human astrocytes, but a comprehensive molecular characterization that confirms the validity of this cellular system is still missing. Here we used an unbiased transcriptomic analysis to characterize in vitro culture of human NPCs and to define the gene expression programs activated during the differentiation of these cells into astrocytes using FBS or the combination of CNTF and BMP4. Our results demonstrate that in vitro cultures of human NPCs isolated during the gliogenic phase of neurodevelopment mainly consist of radial glial cells (RGCs) and glia‐restricted progenitor cells. In these cells the combination of CNTF and BMP4 activates the JAK/STAT and SMAD signaling cascades, leading to the inhibition of oligodendrocytes lineage commitment and activation of astrocytes differentiation. On the other hand, FBS‐derived astrocytes have properties of reactive astrocytes. Our work suggests that in vitro culture of human NPCs represents a valuable cellular system to study human disorders characterized by impairment of astrocytes development and function. Our datasets represent an important resource for researchers studying human astrocytes development and might set the basis for the discovery of novel human‐specific astrocyte markers.
Prevalence of Helicobacter pylori in patients with gastro-oesophageal reflux disease: systematic review

Abstract Objectives: To ascertain the prevalence of Helicobacter pylori in patients with gastro-oesophageal reflux disease and its association with the disease. Design: Systematic review of studies reporting the prevalence of H pylori in patients with and without gastro-oesophageal reflux disease. Data sources: Four electronic databases, searched to November 2001, experts, pharmaceutical companies, and journals. Main outcome measure: Odds ratio for prevalence of H pylori in patients with gastro-oesophageal reflux disease. Results: 20 studies were included. The pooled estimate of the odds ratio for prevalence of H pylori was 0.60 (95% confidence interval 0.47 to 0.78), indicating a lower prevalence in patients with gastro-oesophageal reflux disease. Substantial heterogeneity was observed between studies. Location seemed to be an important factor, with a much lower prevalence of H pylori in patients with gastro-oesophageal reflux disease in studies from the Far East, despite a higher overall prevalence of infection than western Europe and North America. Year of study was not a source of heterogeneity. Conclusion: The prevalence of H pylori infection was significantly lower in patients with than without gastro-oesophageal reflux, with geographical location being a strong contributor to the heterogeneity between studies. Patients from the Far East with reflux disease had a lower prevalence of H pylori infection than patients from western Europe and North America, despite a higher prevalence in the general population. What is already known on this topic The relation between H pylori infection and gastro-oesophageal reflux disease is controversial Studies on the prevalence of H pylori in patients with gastro-oesophageal reflux disease have given conflicting results Recent guidelines recommend eradication of H pylori in patients requiring long term proton pump inhibitors, essentially for reflux disease What this study adds Despite heterogeneity between studies, the prevalence of H pylori was significantly lower in patients with than without gastro-oesophageal reflux disease Further well designed studies are required to establish the clinical relevance of the findings, particularly in eradication therapy
Cyclic AMP-Rap 1 A signaling activates RhoA to induce 2 c-adrenoceptor translocation to the cell surface of microvascular smooth muscle cells

Selvi C. Jeyaraj, Nicholas T. Unger, Ali H. Eid, Srabani Mitra, N. Paul El-Dahdah, Lawrence A. Quilliam, Nicholas A. Flavahan, and Maqsood A. Chotani Center for Cardiovascular and Pulmonary Research, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio; Department of Biological and Environmental Sciences, Qatar University, Doha, Qatar; Davis Heart and Lung Research Institute, Ohio State University, Columbus, Ohio; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana; Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, Maryland; and Department of Pediatrics, Ohio State University, Columbus, Ohio
Leading zero anticipation for latency improvement in floating-point fused multiply-add units

The leading zero anticipation (LZA) is vital in the floating-point fused multiply-add (FMA) units. The general LZA algorithms can only deal with 2 operands. It increases the critical path delay of high performance floating-point FMA units. The paper presents a novel LZA algorithm to deal with 3 operands directly and implemented the 106-bit leading zero anticipator in the high performance floating-point FMA with the general LZA algorithm and the proposed LZA algorithm respectively. Compared with the general leading zero anticipator, the proposed leading zero anticipator can reduce the delay of the critical path by 16.67% and reduce the area by 19.63% approximately.
Damage Potential of Rose Chafer and Japanese Beetle (Coleoptera: Scarabaeidae) in Michigan Vineyards

Responses of young non-fruiting grapevines, Vitis labrusca (L.) var. 'Niagara', to defoliation were examined at two stages of vine growth when beetles typically infest vineyards. In the first experiment, vines were caged and subjected to two weeks of feeding by 0,10, 20, or 40 adult Macrodactylus subspinosus Fabricius (Scarabaeidae: Macrodactylini) during bloom, or to the same range of adult Popillia japonica Newman (Scarabaeidae: Anomalini) during veraison, when berries begin changing color. Leaf area removed increased with beetle density, but less than 1% of the leaf area was removed at the highest density of M. subspinosus, and less than 7% at the highest density of P. japonica. Vine growth measurements taken during the year of injury and prior to bloom during the following season indicated no significant impacts of this leaf injury on vegetative growth. In the second experiment, mechanical injury was induced by removing 0, 10, 20, or 30% of the total leaf area of every fully expanded leaf at bloom or veraison. A significant effect of mechanical injury at bloom was found on cane diameters when measured at veraison, indicating that a carbon source limitation was induced in these vines. By the time of leaf loss, cane diameters were not significantly different across treatments, indicating that vines may have been able to compensate for the earlier defoliation. Injury at veraison had no significant effect on vine growth parameters. These results suggest that young 'Niagara' vines are able to tolerate foliar injury far exceeding that caused by two weeks of exposure to 40 beetles of either species. Surveys of Michigan vineyards containing different grape varieties indicated that although both beetle species could be found in high abundance, leaf injury levels were low. The implications for management of beetle foliar herbivory in vineyards are discussed.
Life-history diversity and its importance to population stability and persistence of a migratory fish: steelhead in two large North American watersheds.

Life-history strategies can buffer individuals and populations from environmental variability. For instance, it is possible that asynchronous dynamics among different life histories can stabilize populations through portfolio effects. Here, we examine life-history diversity and its importance to stability for an iconic migratory fish species. In particular, we examined steelhead (Oncorhynchus mykiss), an anadromous and iteroparous salmonid, in two large, relatively pristine, watersheds, the Skeena and Nass, in north-western British Columbia, Canada. We synthesized life-history information derived from scales collected from adult steelhead (N = 7227) in these watersheds across a decade. These migratory fishes expressed 36 different manifestations of the anadromous life-history strategy, with 16 different combinations of freshwater and marine ages, 7·6% of fish performing multiple spawning migrations, and up to a maximum of four spawning migrations per lifetime. Furthermore, in the Nass watershed, various life histories were differently prevalent through time - three different life histories were the most prevalent in a given year, and no life history ever represented more than 45% of the population. These asynchronous dynamics among life histories decreased the variability of numerical abundance and biomass of the aggregated population so that it was > 20% more stable than the stability of the weighted average of specific life histories: evidence of a substantial portfolio effect. Year of ocean entry was a key driver of dynamics; the median correlation coefficient of abundance of life histories that entered the ocean the same year was 2·5 times higher than the median pairwise coefficient of life histories that entered the ocean at different times. Simulations illustrated how different elements of life-history diversity contribute to stability and persistence of populations. This study provides evidence that life-history diversity can dampen fluctuations in population abundances and biomass via portfolio effects. Conserving genetic integrity and habitat diversity in these and other large watersheds can enable a diversity of life histories that increases population and biomass stability in the face of environmental variability.
Plasma Lipoproteins, Apolipoproteins, and Triglyceride Metabolism in Familial Hypertriglyceridemia

Several parameters of lipoprotein metabolism were examined in 38 men with primary hypertriglyceridemia (phenotype IV). Family investigation showed that 17 men had familial combined hyperlipidemia (FCH), seven had familial hypertriglyceridemia (FHT), and 14 had unclassified hypertriglyceridemia (UNC). In all three groups, plasma high density lipoprotein (HDL) cholesterol and the concentrations of apolipoprotein A-l and A-I1 were decreased, and apolipoprotein B was increased, each to the same extent. These results are compatible with an increased risk of cardiovascular disease in both FCH and FHT patients. The mean concentration of LDL cholesterol and the ratio of LDL to HDL cholesterol were significantly higher in FCH subjects, which could explain their increased risk. Postheparin lipoprotein lipase and hepatic lipase were the same in both groups. Determination of apolipoprotein C composition, which may modulate lipoprotein lipase activity, did not reveal any abnormalities in the different groups. In both FCH and FHT, the mean turnover rate of plasma triglycerides was almost twice normal, indicating that overproduction of plasma triglyceride plays an important role in both disorders. However, there was an overlap with normal controls, indicating impaired triglyceride removal in some subjects. The underlying mechanism of hypertriglyceridemia in FCH and FHT therefore seems to be heterogeneous.
Colonoscopy and the Management of Polyps Containing Invasive Carcinoma

Experiences with 565 colonoscopic polypectomies and 91 colonic and rectal resections containing infiltrating carcinoma in polyps are reviewed. A plan of management based on pathologic study of resected polyps is formulated to avoid further unnecessary surgery. It was concluded that: (1) Tubular adenomas containing invasive carcinomas have a low incidence of metastatic node involvement. This incidence is related to the depth of carcinomatous involvement. Resection of these polyps with a margin free of carcinoma constitutes definitive and adequate treatment, and that (2) Villous adenomas containing invasive carcinoma have a high incidence of metastatic nodal involvement, and operative resection of the involved area of the colon is recommended, and that (3) Pedunculated tubulovillous adenomas containing invasive carcinoma behave like tubular adenomas, and the recommendations for further surgery in the patient with tubular adenomas with carcinoma apply equally well for these lesions. Sessile tubulovillous polyps tend to behave like villous adenomas, and if invasive carcinoma is demonstrated, further operation is recommended.
Homogeneity Index: An objective tool for assessment of conformal radiation treatments

Homogeneity Index (HI) is an objective tool to analyz the uniformity of dose distribution in the target volume. Various formulae have been described in literature for its calculation but there is paucity of data regarding the ideal formula and the factors affecting this index. This study was undertaken to analyze HI in our patients using various formulae and to find out the co-relation between HI and prescribed dose, target volume and target location. A retrospective review of 99 patients was performed. HI was calculated using five different formulae (A-E). The patients were divided in five groups each, based on prescribed dose, target volume and target location and mean HI of each group was analysed to find the co-relation between these factors and HI. When there were multiple target volumes the primary target volume was studied. The statistical calculation was done using SPSS version 16.0. Ninety nine patients were found evaluable with 75 males and 24 females. Ninety five patients were treated with radical intent and four with palliative intent. The sites treated were head and neck (46.4%), Pelvis (17.1%), brain (15.1%), abdomen (12.1%), and thorax (6.1%). The mean prescribed dose was 4304 cGy (centiGray) and the mean target volume was 476.2 cc. The mean value of HI was 1.21, 2.08, 30.13, 21.51 and 1.27 with different formulae. There was considerable agreement between HI calculated using various formulae specially the formulae considering prescribed dose (C, D). On statistical analysis, there was no significant co-relation between the location and volume of target but there was a trend toward better HI with increasing prescribed dose. Future studies with more number of patients can confirm our results.
Molecular simulations of zeolites: adsorption, diffusion, and shape selectivity.

Note: Chevron, Energy Technology Company, 100 Chevron Way, Richmond, California 94802-0627 Reference EPFL-ARTICLE-200588doi:10.1021/cr8002642 URL: http://pubs3.acs. org/acs/journals/doilookup? in_doi=10.1021/cr8002642 URL: http://pubs.acs. org/doi/pdfplus/10.1021/cr8002642 Record created on 2014-08-14, modified on 2017-05-12
REFINED EDDY VISCOSITY SCHEMES AND LARGE EDDY SIMULATIONS FOR ASCENDING MIXED CONVECTION FLOWS

The present work is concerned with the modelling of ascending turbulent ('mixed convection') flow in a vertical heated pipe. All fluid properties are assumed to be constant and buoyancy is accounted for within the Boussinesq approximation. Four Eddy Viscosity Models (EVMs) are examined against experimental measurements and the direct numerical simulation data of You et al. (2003). The EVMs embody distinct physical refinements with respect to the parent high-Reynolds-number k-e model. Large Eddy Simulations (LES) employing the classical Smagorinsky sub-grid-scale model are also presented. Three different CFD codes have been employed in the study: 'CONVERT', 'Code_Saturne', and 'STAR-CD', which are respectively in- house, industrial, and commercial packages. In relation to forced convection Nusselt number and local friction coefficient, discrepancies are identified between 'reference' data sources, namely earlier DNS and experimental results and the present LES computations. The Launder-Sharma closure (Launder and Sharma, 1974) is in the closest agreement with DNS results for levels of heat transfer impairment in ascending mixed convection flow, although again there is a lack of consensus between reference sources.