Miracle-dz/UniFAR-FTUs huggingface dataset:
Copy number variation detection using SNP genotyping arrays in three Chinese pig breeds.

We performed genome-wide CNV detection based on SNP genotyping data of 96 Chinese-native Tibetan, Dahe and Wuzhishan pigs. These pigs are particularly interesting because of their excellent adaptation to hypoxia or small body size, which facilitates the use of them as models of different human diseases in addition to valuable agricultural animals. A total of 105 CNV regions (CNVRs) were identified, encompassing 16.71 Mb of the pig genome. Seven of 10 (70%) CNVRs selected randomly were validated by quantitative real-time PCR. Comparison with previous studies revealed 25 (23.81%) novel CNVRs, indicating that CNV coverage of the pig genome is still incomplete and there exists large diversity between pig breeds. Functional analysis of genes located in these CNVRs confirmed the high representation of genes involved in sensory perception, neurological system processes and other basic metabolic processes. In addition, the majority of these CNVRs were detected to span reported pig QTL that affect various traits, which highlighted three biologically interesting genes with copy number changes (i.e., ANKRD34B, FAM110B and ABCG1). These genes may have economic importance in pig breeding and are worth being further investigated. We also obtained some CNVRs harboring genes that had human orthologs involved in human diseases such as cardiovascular disease and Alzheimer's disease. The findings of this study are a significant extension of the coverage of CNVRs in the pig genome and provide valuable resources for follow-up-associated studies of CNVs in pig complex traits as well as important implications of human diseases.
Microstructured Topography Enhanced the Responsiveness of Voltage-Gated Calcium Channels in H945RB.3 Human Neural Progenitor Cells

A topographical substrate with a packed polystyrene microbead (1.98 plusmn 0.20 mum in diameter) array was fabricated for the development of cell-based assay systems targeting voltage-gated calcium channels (VGCCs). We found that the microbead arrayed substrates enhanced the attachment and spreading of the cultured human neural progenitor cells (H945RB.3) as compared to the flat polystyrene surfaces. Microbead arrayed substrates also facilitated the development of higher VGCC responsiveness upon neuronal differentiation than flat substrates. The enhancement of both VGCC responsiveness and cell spreading were most significant until day 14 into differentiation.
RETARDED GROWTH OF EMBRYO1, a New Basic Helix-Loop-Helix Protein, Expresses in Endosperm to Control Embryo Growth1[W]

We have isolated two dominant mutants from screening approximately 50,000 RIKEN activation-tagging lines that have short inflorescence internodes. The activation T-DNAs were inserted near a putative basic helix-loop-helix (bHLH) gene and expression of this gene was increased in the mutant lines. Overexpression of this bHLH gene produced the original mutant phenotype, indicating it was responsible for the mutants. Specific expression was observed during seed development. The loss-of-function mutation of the RETARDED GROWTH OF EMBRYO1 (RGE1) gene caused small and shriveled seeds. The embryo of the loss-of-function mutant showed retarded growth after the heart stage although abnormal morphogenesis and pattern formation of the embryo and endosperm was not observed. We named this bHLH gene RGE1. RGE1 expression was determined in endosperm cells using the β-glucuronidase reporter gene and reverse transcription-polymerase chain reaction. Microarray and real-time reverse transcription-polymerase chain reaction analysis showed specific down-regulation of putative GDSL motif lipase genes in the rge1-1 mutant, indicating possible involvement of these genes in seed morphology. These data suggest that RGE1 expression in the endosperm at the heart stage of embryo development plays an important role in controlling embryo growth.
The Effect of Camellia Seed Oil Intake on Lipid Metabolism in Mice

Camellia seed oil has mainly been applied to the production of cosmetics, and research into its dietary effects is required. Alterations in lipid metabolism by the intake of camellia seed oil were investigated. Health parameters such as diet intake, weight gain, fat mass, and plasma cholesterol and triglyceride levels were measured in mice fed a high fat diet containing camellia seed oil; comparisons were made to a normal diet and a high fat diet containing either soybean oil or olive oil as controls. No significant differences in weight gain and diet intake were observed between the groups. However, the camellia seed oil diet suppressed epididymal fat weight similarly to the olive oil diet. In total cholesterol and HDL (high density lipoprotein) cholesterol levels, the soybean oil, olive oil and camellia seed oil diet groups showed significant increases compared with the normal diet. However, increases in LDL (low density lipoprotein) cholesterol levels were inhibited by the camellia seed oil diet similarly to the olive oil diet. As the high oleic acid content of camellia seed oil is similar to that of olive oil, it is proposed that its presence mitigated fat accumulation and plasma cholesterol levels.
Evaluation of an Atlas-Based PET Head Attenuation Correction Using PET/CT & MR Patient Data

The goal of this study was to compare MR-based PET patient attenuation correction (AC) to CT-based AC in the head using clinical whole-body FDG-PET patient data obtained from a tri-modality PET/CT & MR setup. The MR-based AC utilizes an atlas-based approach, registering the patient's MR images to a CT-based atlas, producing `pseudoCT' images. Thirteen clinical whole-body FDG patients were included in this study. PET mean activity concentration values were measured and compared in six ~ 15 ml volumes-of-interest throughout the brain tissue. The AC methods compared to CT-based AC were segmentation of the CT (air, fat, soft tissue) and atlas-based MR-AC. Results: PET activity concentration was systematically under-estimated on average by 1.32 kBq/ml (4.9%) when using the segmented CT-based AC, mainly due to lack of attenuation correction for skull bone. Using the atlas-based method, the error was reduced to 0.03 kBq/ml (0.2%) on average. PET image visualization demonstrated spatial variations in activity concentration accuracy induced by the AC methods that were consistent with the approximations in each method. Conclusion: The results demonstrate that the atlas-based AC in the head provides adequate PET quantitation and image quality as compared to methods that do not account for bone.
Modelling, design and control of wind diesel hybrid power system using bond graph

This paper illustrates the use of diesel electricity generator set and Dispatch Controller to adapt the number of running engines to a given electrical load that is partly met by wind turbines. Control coordination among the system components is established with a view to regulate the system voltage and frequency while extracting maximum power from wind. This paper utilized the bond graph approach in the modelling of such a wind/diesel hybrid power system for a stand-alone unit in a remote location. This design allows for the addition of wind energy inputs in conjunction with the diesel generators for fuel saving.
Electrophilic Prostaglandins and Lipid Aldehydes Repress Redox-sensitive Transcription Factors p53 and Hypoxia-inducible Factor by Impairing the Selenoprotein Thioredoxin Reductase*

Tumor suppressor p53 exhibits an enigmatic phenotype in cells exposed to electrophilic, cyclopentenone prostaglandins of the A and J series. Namely, cells harboring a wild-type p53 gene accumulate p53 protein that is conformationally and functionally impaired. This occurs via an unknown molecular mechanism. We report that electrophilic cyclopentenone prostaglandins covalently modify and inhibit thioredoxin reductase, a selenoprotein that governs p53 and other redox-sensitive transcription factors. This mechanism accounts fully for the unusual p53 phenotype in cells exposed to electrophilic prostaglandins. Based on this mechanism we derived, tested, and affirmed several predictions regarding the kinetics of p53 inactivation; the protective effects of selenium; the structure-activity relationships for inhibition of thioredoxin reductase and impairment of p53 by electrophilic lipids; the susceptibility of hypoxia-inducible factor to inactivation by electrophilic lipids; and the equivalence of chemical inactivation of p53 to deletion of a p53 allele. Chemical precepts dictate that other electrophilic agents should also inhibit thioredoxin reductase and impair its governance of redox-sensitive proteins. Our results provide a novel framework to understand how endogenous and exogenous electrophiles might participate in carcinogenesis; how selenoproteins and selenium might confer protection against cancer; how certain tumors might acquire their paradoxical p53 phenotype; and how chronic inflammation might heighten the risk for cancer.
Posterior brain damage and cognitive impairment in pediatric multiple sclerosis

Objective: We combined structural and functional MRI to better understand the mechanisms responsible for cognitive impairment in pediatric patients with multiple sclerosis (MS). Methods: Brain dual-echo, diffusion tensor, 3D T1-weighted, and resting-state (RS) fMRI scans were acquired from 35 consecutive pediatric patients with MS and 16 sex- and age-matched healthy controls. Patients with abnormalities in ≥2 neuropsychological tests were classified as cognitively impaired. The regional distribution of white matter (WM) and gray matter (GM) damage was assessed using voxel-wise analyses. Default mode network (DMN) RS functional connectivity (FC) was also measured. Results: Sixteen patients (45%) were classified as cognitively impaired. Compared to cognitively preserved (CP) patients, cognitively impaired patients with MS had higher occurrence of T2 lesions as well as more severe damage to the WM and GM, as measured by atrophy and diffusivity abnormalities, in the posterior regions of the parietal lobes close to the midline (precuneus, posterior cingulum, and corpus callosum). Compared to the other study groups, they also showed reduced RS FC of the precuneus, whereas CP patients experienced an increased RS FC of the anterior cingulate cortex. A multivariable model identified diffusivity abnormalities of the cingulum and corpus callosum and RS FC of the precuneus as the covariates more strongly associated with cognitive impairment (C-index = 0.99). Conclusions: In pediatric patients with MS, cognitive dysfunction is associated with structural and functional abnormalities of the posterior core regions of the DMN. WM structural abnormalities co-occurring at this level are likely to be the substrate of such modifications.
Diel Variation in the Sizes of Larvae of Bugula neritina in Field Populations

Abstract. The scale of planktonic larval dispersal affects a variety of ecological and evolutionary processes. Recent work suggests that the dispersal ability of obligately lecithotrophic larvae is influenced by the amount of energy supplied to each larva: larger larvae may stay in the plankton longer and thus travel greater distances than smaller larvae. We examined a prediction of this hypothesis in the bryozoan Bugula neritina, which each morning releases brooded larvae that settle within a few hours. If larger larvae stay in the plankton longer than smaller larvae, than larger larvae should increase in frequency in the planktonic population as the day progresses. However, field surveys revealed a negative relationship between time of day and the sizes of planktonic larvae. Because these results may have been complicated by prolonged larval release, we sequestered groups of brooding colonies in field mesocosms to examine release patterns. Larvae were released over a period of 8–9 h, with smaller larvae increasing in frequency as the day progressed. We conclude that populations of larvae of B. neritina may not be homogenous in energetic content throughout the day; this must be taken into consideration when designing studies of many aspects of larval biology.
Ineffectiveness of Latex Condoms in Preventing Contamination of the Transvaginal Ultrasound Transducer Head

The efficacy of condoms in preventing contamination of the transvaginal ultrasound transducer head and possible transmission of blood-borne pathogens is unknown. Our objective was to determine the rate of contamination of the transvaginal ultrasound probe after use in the emergency department. After indicated transvaginal ultrasound scans, the latex condom was removed and the transducer head was inspected for contamination. The presence of vaginal bleeding and the duration of the ultrasound scan were noted. Ten milliliters of hydrogen peroxide (H2O2) was placed in the condom. Bubbling, which occurs in the presence of blood or cervicovaginal secretions, was considered a positive test. Exposure of a clean condom or coupling gel to H2O2 did not cause bubbling. Two-tailed Fisher's Exact and Student's t tests were used for statistical analysis. Of 173 cases, 8 (5%) had a positive H2O2 test for contamination. In only 3 of these 8 cases was gross contamination seen. Latex condoms are ineffective in preventing contamination of the transvaginal ultrasound transducer head. Visual inspection of the transducer head often fails to identify the presence of blood or body fluids. This suggests that additional measures should be taken to prevent transmission of blood-borne pathogens.
Plastic adherent stromal cells from the bone marrow of commonly used strains of inbred mice: Variations in yield, growth, and differentiation

Bone marrow stroma contains a unique cell population, referred to as marrow stromal cells (MSCs), capable of differentiating along multiple mesenchymal cell lineages. A standard liquid culture system has been developed to isolate MSCs from whole marrow by their adherence to plastic wherein the cells grow as clonal populations derived from a single precursor termed the colony‐forming‐unit fibroblast (CFU‐F). Using this liquid culture system, we demonstrate that the relative abundance of MSCs in the bone marrow of five commonly used inbred strains of mice varies as much as 10‐fold, and that the cells also exhibit markedly disparate levels of alkaline phosphatase expression, an early marker of osteoblast differentiation. For each strain examined, the method of isolating MSCs by plastic adherence yields a heterogeneous cell population. These plastic adherent cells also exhibit widely varying growth kinetics between the different strains. Importantly, of three inbred strains commonly used to prepare transgenic mice that we examined, only cells derived from FVB/N marrow readily expand in culture. Further analysis of cultures derived from FVB/N marrow showed that most plastic adherent cells express CD11b and CD45, epitopes of lymphohematopoietic cells. The later consists of both pre‐B‐cell progenitors, granulocytic and monocytic precursors, and macrophages. However, a subpopulation of the MSCs appear to represent bona fide mesenchymal progenitors, as cells can be induced to differentiate into osteoblasts and adipocytes after exposure to dexamethasone and into myoblasts after exposure to amphotericin B. Our results point to significant strain differences in the properties of MSCs and indicate that standard methods cannot be applied to murine bone marrow to isolate relatively pure populations of MSCs. J. Cell. Biochem. 72:570–585, 1999. © 1999 Wiley‐Liss, Inc.
ON MEASURING ABSOLUTE TECHNICAL AND ALLOCATIVE EFFICIENCIES

SUMMARY. This paper describes how absolute measurement of technical and syste matic allocative efficiencies can be done by estimating a stochastic profit frontier. This method is illustrated by an application to micro-level data for Indian farm production, and uses a maxi mum likelihood procedure for estimating the frontier. The empirical results indicate that the average restricted real profit for the sample is about 41% below the estimated frontier. The empirical flexibility of the model yields estimates of technical efficiencies for individual sample participants. These are used to identify factors causing variations in farm? specific technical efficiency across sample farms. The advantage of the empirical specification of the model is that it provides policy relevant elasticity estimates with respect to fixed endownments and prices of variable factors of production and output.
An Overview of Portfolio Insurances: CPPI and CPDO

Derivative instruments attempt to protect a portfolio against failure events. Constant proportion portfolio insurance (CPPI) and constant proportion debt obligations (CPDO) strategies are recent innovations and have only been adopted in the credit market for the last couple of years. Since their introduction, CPPI strategies have been popular because they provide protection while at the same time they offer high yields. CPDOs were only introduced into the market in 2006 and can be considered as a variation of the CPPI with as main difference the fact that CPDOs do not provide principal protection. Both CPPI and CPDO strategies take investment positions in a risk-free bond and a risky portfolio (often one or more credit default swaps). At each step, the portfolio is rebalanced and the level of risk taken will depend on the distance between the current value of the portfolio and the necessary amount needed to full all the future obligations. In a first step the functioning of both products is studied in depth concluding with drawing some conclusions on their risky-ness. How to obtain EU publications Our priced publications are available from EU Bookshop (http://bookshop.europa.eu), where you can place an order with the sales agent of your choice. The Publications Office has a worldwide network of sales agents. You can obtain their contact details by sending a fax to (352) 29 29-42758. The mission of the JRC is to provide customer-driven scientific and technical support for the conception, development, implementation and monitoring of EU policies. As a service of the European Commission, the JRC functions as a reference centre of science and technology for the Union. Close to the policy-making process, it serves the common interest of the Member States, while being independent of special interests, whether private or national. LB -N A -2376-EN -C
A viable mutation in cauliflower mosaic virus, a retroviruslike plant virus, separates its capsid protein and polymerase genes

A viable strain of cauliflower mosaic virus is described which arose by illegitimate recombination of two lethal parents. In this strain, the normally overlapping open reading frames IV and V, corresponding to the retrovirus gag and pol genes, are separated by a short intergenic region, suggesting that in this virus and in contrast to retroviruses, fusion of gag and pol gene products is not obligatory.
The Impact of Benzodiazepines on Safe Driving

Objective. Benzodiazepines are prescribed to relieve anxiety and aid sleep. Studies demonstrate that benzodiazepines increase odds of crash involvement, but little evidence exists regarding their impact on crash responsibility. We examined the impact of benzodiazepines on crash responsibility by drug half-life and driver age, using a case-control design with drivers aged 20 and over involved in fatal crashes in the United States from 1993–2006. Methods. Drivers (all with BAC = 0) were classified as having no benzodiazepines detected versus short, intermediate, or long half-life benzodiazepines. Cases were drivers with at least one potentially unsafe driving action (UDA) in relation to the crash (e.g., speeding), a proxy measure for crash responsibility; controls had no UDAs recorded. Odds ratios (ORs) of any UDA by benzodiazepines half-life exposure were calculated, with adjustment for age, sex, other medication usage, and prior driving record. Results. Compared with drivers not using benzodiazepines, drivers taking intermediate or long half-life benzodiazepines demonstrated increased odds of an UDA from ages 25 (intermediate OR: 1.59; 95% CI = 1.08, 2.33; long OR: 1.68; 95% CI = 1.34, 2.12) to 55 (intermediate OR: 1.50; 95% CI = 1.09, 2.06; long OR: 1.33; 95% CI = 1.12, 1.57). Drivers taking short half-life benzodiazepines did not demonstrate increased odds compared to drivers not using benzodiazepines. Conclusions. Given the potential impact of benzodiazepines on driver safety, further experimental research is needed to better understand the effect of benzodiazepines on crash responsibility.
Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds

ABSTRACT The purple sulfur bacterium Allochromatium vinosum DSM 180T is one of the best-studied sulfur-oxidizing anoxygenic phototrophic bacteria, and it has been developed into a model organism for laboratory-based studies of oxidative sulfur metabolism. Here, we took advantage of the organism's high metabolic versatility and performed whole-genome transcriptional profiling to investigate the response of A. vinosum cells upon exposure to sulfide, thiosulfate, elemental sulfur, or sulfite compared to photoorganoheterotrophic growth on malate. Differential expression of 1,178 genes was observed, corresponding to 30% of the A. vinosum genome. Relative transcription of 551 genes increased significantly during growth on one of the different sulfur sources, while the relative transcript abundance of 627 genes decreased. A significant number of genes that revealed strongly enhanced relative transcription levels have documented sulfur metabolism-related functions. Among these are the dsr genes, including dsrAB for dissimilatory sulfite reductase, and the sgp genes for the proteins of the sulfur globule envelope, thus confirming former results. In addition, we identified new genes encoding proteins with appropriate subcellular localization and properties to participate in oxidative dissimilatory sulfur metabolism. Those four genes for hypothetical proteins that exhibited the strongest increases of mRNA levels on sulfide and elemental sulfur, respectively, were chosen for inactivation and phenotypic analyses of the respective mutant strains. This approach verified the importance of the encoded proteins for sulfur globule formation during the oxidation of sulfide and thiosulfate and thereby also documented the suitability of comparative transcriptomics for the identification of new sulfur-related genes in anoxygenic phototrophic sulfur bacteria.
Resistive Bridge fault model evolution from conventional to ultra deep submicron

We present three resistive bridging fault models valid for different CMOS technologies. The models are partitioned into a general framework (which is shared by all three models) and a technology-specific part. The first model is based on Shockley equations and is valid for conventional but not deep submicron CMOS. The second model is obtained by fitting SPICE data. The third resistive bridging fault model uses Berkeley predictive technology model and BSIM4; it is valid for CMOS technologies with feature sizes of 90nm and below, accurately describing non-trivial electrical behavior in that technologies. Experimental results for ISCAS circuits show that the test patterns obtained for the Shockley model are still valid for the fitted model, but lead to coverage loss under the predictive model.