Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk of Bias in Systematic Reviews of Non-Randomized Studies of Adverse Cardiovascular Effects of Thiazolidinediones and Cyclooxygenase-2 Inhibitors: Application of a New Cochrane Risk of Bias Tool

Background Systematic reviews of the effects of healthcare interventions frequently include non-randomized studies. These are subject to confounding and a range of other biases that are seldom considered in detail when synthesizing and interpreting the results. Our aims were to assess the reliability and usability of a new Cochrane risk of bias (RoB) tool for non-randomized studies of interventions and to determine whether restricting analysis to studies with low or moderate RoB made a material difference to the results of the reviews. Methods and Findings We selected two systematic reviews of population-based, controlled non-randomized studies of the relationship between the use of thiazolidinediones (TZDs) and cyclooxygenase-2 (COX-2) inhibitors and major cardiovascular events. Two epidemiologists applied the Cochrane RoB tool and made assessments across the seven specified domains of bias for each of 37 component studies. Inter-rater agreement was measured using the weighted Kappa statistic. We grouped studies according to overall RoB and performed statistical pooling for (a) all studies and (b) only studies with low or moderate RoB. Kappa scores across the seven bias domains ranged from 0.50 to 1.0. In the COX-2 inhibitor review, two studies had low overall RoB, 14 had moderate RoB, and five had serious RoB. In the TZD review, six studies had low RoB, four had moderate RoB, four had serious RoB, and two had critical RoB. The pooled odds ratios for myocardial infarction, heart failure, and death for rosiglitazone versus pioglitazone remained significantly elevated when analyses were confined to studies with low or moderate RoB. However, the estimate for myocardial infarction declined from 1.14 (95% CI 1.07–1.24) to 1.06 (95% CI 0.99–1.13) when analysis was confined to studies with low RoB. Estimates of pooled relative risks of cardiovascular events with COX-2 inhibitors compared with no nonsteroidal anti-inflammatory drug changed little when analyses were confined to studies with low or moderate RoB. The exception was a rise in the relative risk associated with ibuprofen from 1.07 (95% CI 0.97–1.18) to 1.14 (95% CI 1.03–1.26). The main limitation of our study was testing the instrument on a narrow range of pharmacoepidemiological studies; we cannot assume our findings extend to a broader range of interventions and settings. Conclusions The Cochrane RoB tool highlighted a wide range of risks of bias in studies included in two widely cited reviews and had the potential to change the conclusions of the reviews. Systematic reviews that incorporate non-randomized studies of medical interventions should include a detailed assessment of RoB for each included study.
Layer-by-Layer Technology and Its Implications in the Field of Glucose Nanobiosensors:

Diabetes is the seventh leading cause of deaths in the US with almost 439 million people worldwide expected to be diabetic by 2030. The need for continuous, non-invasive monitoring is a top priority. Earlier devices that utilized electroenzymatic sensing technique were minimally invasive and had major pitfalls. Advancements in various non-invasive, especially fluorescence-based, sensing along with developments in LBL assembly have resulted in a new breed of micro/nanosensors that are implantable, reliable, reproducible, mechanically and functionally stable, responsive, and miniaturized. In this chapter, the authors discuss the history of glucose sensors, evolution over the past four decades, methods employed to detect glucose levels in fluorescent biosensors, and assays that can be fabricated on to the sensor membrane, immobilized into the membrane as multilayers, or encapsulated within micro/nanocapsules using LBL assembly technology. The authors briefly review the various materials available and currently implemented for fabrication of glucose biosensors using LBL assembly.
Breastfeeding and reduced risk of childhood obesity : will randomized trials on breastfeeding promotion give the definite answer ?

N-labeled internal standards (4). Using this method, Tsikas (4) reported endogenous plasma nitrite concentrations in the order of 12 lM compared with our value of 4 lM. Apart from dietary intake of nitrate/nitrite, there are likely to be other factors that could affect the accurate measurement of plasma nitrite, eg, its short half-life of 110 s in human blood (5). Standardization of dietary sources of nitrate and nitrite will be an important factor to consider in future work in this area.
Ultrasonographic Measurement of the Biceps Femoris Long‐Head Muscle Architecture

Biceps femoris long‐head architectural assessment using ultrasonography (US) has not been previously described in detail for both acquisition (image capture) and digitization (image measurement) processes, and the effect of the US window width is unknown. This study aimed to describe the reliability and test‐retest minimum detectable difference of US‐based biceps femoris architectural measurements.
Genomewide mechanisms of chronological longevity by dietary restriction in budding yeast

Dietary restriction is arguably the most promising nonpharmacological intervention to extend human life and health span. Yet, only few genetic regulators mediating the cellular response to dietary restriction are known, and the question remains which other regulatory factors are involved. Here, we measured at the genomewide level the chronological lifespan of Saccharomyces cerevisiae gene deletion strains under two nitrogen source regimens, glutamine (nonrestricted) and γ‐aminobutyric acid (restricted). We identified 473 mutants with diminished or enhanced extension of lifespan. Functional analysis of such dietary restriction genes revealed novel processes underlying longevity by the nitrogen source quality, which also allowed us to generate a prioritized catalogue of transcription factors orchestrating the dietary restriction response. Importantly, deletions of transcription factors Msn2, Msn4, Snf6, Tec1, and Ste12 resulted in diminished lifespan extension and defects in cell cycle arrest upon nutrient starvation, suggesting that regulation of the cell cycle is a major mechanism of chronological longevity. We further show that STE12 overexpression is enough to extend lifespan, linking the pheromone/invasive growth pathway with cell survivorship. Our global picture of the genetic players of longevity by dietary restriction highlights intricate regulatory cross‐talks in aging cells.
Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat

Stem rust (caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn.), is a major disease in wheat (Triticum aestivium L.). However, in recent years it occurs rarely in Nebraska due to weather and the effective selection and gene pyramiding of resistance genes. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, we applied genome-wide association study (GWAS) on a set of 270 winter wheat genotypes (A-set). Genotyping was carried out using genotyping-by-sequencing and ∼35,000 high-quality SNPs were identified. The tested genotypes were evaluated for their resistance to the common stem rust race in Nebraska (QFCSC) in two replications. Marker-trait association identified 32 SNP markers, which were significantly (Bonferroni corrected P < 0.05) associated with the resistance on chromosome 2D. The chromosomal location of the significant SNPs (chromosome 2D) matched the location of Sr6 gene which was expected in these genotypes based on pedigree information. A highly significant linkage disequilibrium (LD, r2) was found between the significant SNPs and the specific SSR marker for the Sr6 gene (Xcfd43). This suggests the significant SNP markers are tagging Sr6 gene. Out of the 32 significant SNPs, eight SNPs were in six genes that are annotated as being linked to disease resistance in the IWGSC RefSeq v1.0. The 32 significant SNP markers were located in nine haplotype blocks. All the 32 significant SNPs were validated in a set of 60 different genotypes (V-set) using single marker analysis. SNP markers identified in this study can be used in marker-assisted selection, genomic selection, and to develop KASP (Kompetitive Allele Specific PCR) marker for the Sr6 gene. Highlights Novel SNPs for Sr6 gene, an important stem rust resistant gene, were identified and validated in this study. These SNPs can be used to improve stem rust resistance in wheat.
G-KNN: an efficient document classification algorithm for sparse datasets on GPUs using KNN

In nowadays we observe that there is more data than that can be effectively analyzed. Organizing this data has become one of the biggest problems in Computer Science. Many algorithms have been proposed for this purpose, highlighting those related to the Data Mining area, specifically the automatic document classification (ADC) algorithms. However, these algorithms are still a computational challenge because of the volume of data that needs to be processed. We found in the literature some proposals related to parallelization on graphics processing units (GPUs) to make these algorithms feasible. Still, most of the available parallel solutions ignore specific ADC challenges, such as high dimensionality and heterogeneity in the representation of the documents. In this context, we here present G-KNN, a GPU-based parallel version of the nearest neighbors algorithm (KNN), one of the most widely used ADC algorithms. In our evaluation using five different document collections, we show that the G-KNN can maintain the same classification effectiveness while increasing the efficiency by up to 12x faster than its sequential version using CPU and up to 3x faster than a CPU-based parallel implementation running with 6 threads. Moreover, our algorithm has a much lower memory consumption, enabling its use with large datasets.
Metabolomic responses to sublethal contaminant exposure in neonate and adult Daphnia magna

The use of consumer products and pharmaceuticals that act as contaminants entering waterways through runoff and wastewater effluents alters aquatic ecosystem health. Traditional toxicological endpoints may underestimate the toxicity of contaminants, as lethal concentrations are often orders of magnitude higher than those found within freshwater ecosystems. While newer techniques examine the metabolic responses of sublethal contaminant exposure, there has been no direct comparison with ontogeny in Daphnia. It was hypothesized that Daphnia magna would have distinct metabolic changes after 3 different sublethal contaminant exposures, because of differences in the toxic mode of action and ontogeny. To test this hypothesis, the proton nuclear magnetic resonance metabolomic profiles were measured in D. magna aged day 0 and 18 after exposure to 28% of the lethal concentration of 50% of organisms tested (LC50) of atrazine, propranolol, and perfluorooctanesulfonic acid (PFOS) for 48 h. Principal component analysis revealed significant separation of contaminants from the control daphnids in both neonates and adults exposed to propranolol and PFOS. In contrast, atrazine exposure caused separation from the controls in only the adult D. magna. Minimal ontogenetic changes in the targeted metabolites were seen after exposure to propranolol. For both atrazine and PFOS exposures ontogeny exhibited unique changes in the targeted metabolites. These results indicate that, depending on the contaminant studied, neonates and adults respond uniquely to sublethal contaminant exposure. Environ Toxicol Chem 2017;36:938–946. © 2016 SETAC
Influence of Pesticide Residues on Honey Bee (Hymenoptera: Apidae) Colony Health in France

ABSTRACT A 3-yr field survey was carried out in France, from 2002 to 2005, to study honey bee (Apis mellifera L.) colony health in relation to pesticide residues found in the colonies. This study was motivated by recent massive losses of honey bee colonies, and our objective was to examine the possible relationship between low levels of pesticide residues in apicultural matrices (honey, pollen collected by honey bees, beeswax) and colony health as measured by colony mortality and adult and brood population abundance. When all apicultural matrices were pooled together, the number of pesticide residue detected per sampling period (four sampling periods per year) and per apiary ranged from 0 to 9, with the most frequent being two (29.6%). No pesticide residues were detected during 12.7% of the sampling periods. Residues of imidacloprid and 6- chloronicotinic acid were the most frequently detected in pollen loads, honey, and honey bee matrices. Several pairs of active ingredients were present concurrently within honey bees and in pollen loads but not in beeswax and honey samples. No statistical relationship was found between colony mortality and pesticide residues. When pesticide residues from all matrices were pooled together, a mixed model analysis did not show a significant relationship between the presence of pesticide residues and the abundance of brood and adults, and no statistical relationship was found between colony mortality and pesticide residues. Thus, although certain pesticide residues were detected in apicultural matrices and occasionally with another pesticide residual, more work is needed to determine the role these residues play in affecting colony health.
Odour assessment with piezoelectric quartz crystal sensor arrays, a suitable tool for quality control in food technology?

The abilities and limitations of a piezoelectric quartz crystal sensor array (quartz crystal micro balance sensors (QMB's) coated with different polar chromatographic phases: CW1500, CW20M, OV17, SE54, OV1) were investigated after automated headspace sampling by simultaneous sensor-GC-Analysis. Sensor responses were measured considering polarity of reference compounds and humidity of samples. QMB sensors show good linearity and good reproducibility in a wide range of concentration. Ginger and pepper samples of different geographical origin as well as spice mixtures with varying contents of the ingredients could be discriminated by the QMB sensor array system. Nevertheless, the QMB array is not able to recognize the distinct odour of a sample, especially if it is caused by trace volatiles, or less volatile odoriferous compounds like vanillin. It could be useful if major headspace compounds are responsible for distinct properties of samples to be discriminated.
Ataluren stimulates ribosomal selection of near-cognate tRNAs to promote nonsense suppression

Significance The drug ataluren restores activity to otherwise nonfunctional nonsense alleles, a capability possibly reflecting the insertion of near-cognate aminoacyl tRNAs at premature termination codons during protein synthesis. Because nonsense alleles comprise a significant fraction of all alleles causing inherited disorders, drugs that promote such nonsense codon readthrough have broad therapeutic potential. However, the effectiveness of therapeutic nonsense suppression depends on the nature of the amino acids inserted at each of the three nonsense codons. Here we demonstrate that ataluren does indeed promote insertion of near-cognate tRNAs at nonsense codons, that the latter process yields functional proteins, and that specific codon:anticodon base pairings are critical to this process. These results should enable predictions of better clinical outcomes with therapeutic nonsense suppression. A premature termination codon (PTC) in the ORF of an mRNA generally leads to production of a truncated polypeptide, accelerated degradation of the mRNA, and depression of overall mRNA expression. Accordingly, nonsense mutations cause some of the most severe forms of inherited disorders. The small-molecule drug ataluren promotes therapeutic nonsense suppression and has been thought to mediate the insertion of near-cognate tRNAs at PTCs. However, direct evidence for this activity has been lacking. Here, we expressed multiple nonsense mutation reporters in human cells and yeast and identified the amino acids inserted when a PTC occupies the ribosomal A site in control, ataluren-treated, and aminoglycoside-treated cells. We find that ataluren’s likely target is the ribosome and that it produces full-length protein by promoting insertion of near-cognate tRNAs at the site of the nonsense codon without apparent effects on transcription, mRNA processing, mRNA stability, or protein stability. The resulting readthrough proteins retain function and contain amino acid replacements similar to those derived from endogenous readthrough, namely Gln, Lys, or Tyr at UAA or UAG PTCs and Trp, Arg, or Cys at UGA PTCs. These insertion biases arise primarily from mRNA:tRNA mispairing at codon positions 1 and 3 and reflect, in part, the preferred use of certain nonstandard base pairs, e.g., U-G. Ataluren’s retention of similar specificity of near-cognate tRNA insertion as occurs endogenously has important implications for its general use in therapeutic nonsense suppression.
ViPTree: the viral proteomic tree server

Summary ViPTree is a web server provided through GenomeNet to generate viral proteomic trees for classification of viruses based on genome-wide similarities. Users can upload viral genomes sequenced either by genomics or metagenomics. ViPTree generates proteomic trees for the uploaded genomes together with flexibly selected reference viral genomes. ViPTree also serves as a platform to visually investigate genomic alignments and automatically annotated gene functions for the uploaded viral genomes, thus providing virus researchers the first choice for classifying and understanding newly sequenced viral genomes. Availability and Implementation ViPTree is freely available at: http://www.genome. jp/viptree . Contact goto@kuicr.kyoto-u.ac. jp. Supplementary information Supplementary data are available at Bioinformatics online.
Parenteral Vaccination with Heat‐Inactivated Mycobacterium Bovis Reduces the Prevalence of Tuberculosis‐Compatible Lesions in Farmed Wild Boar

In 2012, a wild boar (Sus scrofa) tuberculosis (TB) control programme was set up in a wild boar farm by means of intramuscular (IM) vaccination with a heat-inactivated Mycobacterium bovis vaccine (IV). The goal was to assess safety and efficacy of the parenterally administered IV in a large farm setting with natural M. bovis circulation. Based on preceding results under laboratory conditions, we hypothesized that vaccinated piglets would show smaller scores of TB-compatible lesions (TBCL) than unvaccinated controls. After vaccination, no adverse reactions were detected by visual inspection or at post-mortem examination (n = 668 and 97, respectively). Post-mortem data on TBCL were available for 97 vaccinated wild boar and 182 controls. The observed TBCL prevalence was 4.1% (95% CI = 0.2-8%) and 12.1% (95% CI = 7.1-17.1%) for vaccinated and control wild boar, respectively (P < 0.05). Among those animals with TBCL, no difference in the mean lesion score was found (P > 0.05). The results show that IV administered intramuscularly to wild boar piglets is safe and protects vaccinated individuals (66% reduction in TBCL prevalence) against natural challenge in a low-prevalence setting. In a context of increasing TB prevalence in wild boar in Mediterranean habitats, vaccination achieved a progressive though slow decline in lesion prevalence since the onset of the vaccination scheme. Hence, vaccination might contribute, along with other tools, to TB control in wild boar and in pigs.
A widely conserved bacterial cytoskeletal component influences unique helical shape and motility of the spirochete Leptospira biflexa

Leptospires and other members of the evolutionarily ancient phylum of Spirochaetes are bacteria often characterized by long, highly motile spiral‐ or wave‐shaped cells. Morphology and motility are critical factors in spirochete physiology, contributing to the ability of these bacteria to successfully colonize diverse environments. However, the mechanisms conferring the helical structure of Leptospira spp. have yet to be fully elucidated. We have identified five Leptospira biflexa bactofilin proteins, a recently characterized protein family with cytoskeletal properties. These five bactofilins are conserved in all species of the Leptospiraceae, indicating that these proteins arose early in the evolution of this family. One member of this protein family, LbbD, confers the optimal pitch distance in the helical structure of L. biflexa. Mutants lacking lbbD display a unique compressed helical morphology, a reduced motility and a decreased ability to tolerate cell wall stressors. The change in the helical spacing, combined with the motility and cell wall integrity defects, showcases the intimate relationship and coevolution between shape and motility in these spirochetes.
Study on multi-network traffic modeling in distribution communication network access service

Network traffic model is the basis for network performance analysis, dynamic allocation of network bandwidth and network planning and construction. A good traffic model and prediction method is great significance for the design of a new generation of network protocols, network management and diagnosis, design of high performance routers, load balancers Network hardware equipment and improving the quality of the network services. With the construction of energy smart grid, especially in the distribution network is particularly evident. Increasing the variety of electrical equipment, which make distribution and communication network structure more complex and changeable, including a variety of communication systems, more Equipment, a larger scale and communication traffic characteristics. It can cause a great impact on the backbone network capacity. Considering the reliability and security of the power grid, this paper analyzes the characteristics of conventional traffic model based on the traffic characteristics of the distribution network and establishes a multi-convergence traffic prediction model to be used in the distribution network to improve the accuracy of network traffic prediction. Provide a reliable theoretical basis.
Activation of Magnesium Lignosulfonate and Kraft Lignin: Influence on the Properties of Phenolic Resin-Based Composites for Potential Applications in Abrasive Materials

Magnesium lignosulfonate and kraft lignin were activated by different oxidizing agents for use in phenolic resin composites used for the production of abrasive components. The physicochemical properties of the oxidized materials were analyzed by Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), dynamic mechanical-thermal analysis (DMTA) and inverse gas chromatography (IGC). The homogeneity of the model abrasive composites containing the studied products was assessed based on observations obtained using a scanning electron microscope (SEM). FTIR and XPS analysis of the oxidized products indicated that the activation process leads mainly to the formation of carbonyl groups. The IGC technique was used to assess changes in the surface energy and the acid–base properties of the studied biopolymers. The changes in the acid–base properties suggest that more groups acting as electron donors appear on the oxidized surface of the materials. DMTA studies showed that the model composites with 5% magnesium lignosulfonate oxidized by H2O2 had the best thermomechanical properties. Based on the results it was possible to propose a hypothetical mechanism of the oxidation of the natural polymers. The use of such oxidized products may improve the thermomechanical properties of abrasive articles.