Miracle-dz/UniFAR-FTUs huggingface dataset:
The polymorphisms and haplotypes of WWOX gene are associated with the risk of lung cancer in southern and eastern chinese populations

The WW domain‐containing oxidoreductase (WWOX) gene is an identified tumor suppressor gene, of which several single nucleotide polymorphisms have been reported to contribute to cancer susceptibility. We hypothesized that genetic variations in WWOX are associated with lung cancer risk. In two independent case–control studies conducted in southern and eastern Chinese, we genotyped five tagSNPs of WWOX gene (rs10220974C > T, rs3764340C > G, rs12918952G > A, rs383362G > T, and rs12828G > A) in 1,559 lung cancer cases and 1,679 controls. Logistic regression analysis showed that two tagSNPs (rs3764340C > G; rs383362G > T) were significantly associated with lung cancer risk in dominant model (rs3764340C > G, GC/GG vs. CC: adjust OR = 1.35, 95% CI = 1.11–1.65; rs383362G > T, TG + TT vs. GG: adjust OR = 1.33, 95% CI = 1.14–1.55). The haplotype analysis further shown that the haplotype “G‐T” was associated with the highest increased risk of lung cancer (OR = 2.20; 95% CI = 1.43–3.37). After combined these two loci, the number of the risk genotypes was associated with increased cancer risk in a dose–response manner (Ptrend = 3.16 × 10−6). In addition, a gene‐based association analysis by using VEGAS software suggested the WWOX as a susceptible gene for lung cancer (P = 0.009). However, for rs10220974C > T, rs12918952G > A, and rs12828G > A, no significant association was observed for lung cancer risk. Taken together, our data suggested that genetic variants in WWOX may be genetic biomarkers for susceptibility to lung cancer. Copyright © 2012 Wiley Periodicals, Inc.
Is the neutrophil-lymphocyte ratio an indicator of progression in patients with benign prostatic hyperplasia?

PURPOSE The aim of this study was to evaluate inflammation parameters and assess the utility of the neutrophil- lymphocyte ratio (NLR) as a simple and readily available predictor for clinical disease activity in patients with nenign prostate hyperplasia BPH. We also aimed to investigate the relationship between inflammatory parameters with α-blocker therapy response, and evaluate the potential association between NLR and the progression of benign prostatic hyperplasia (BPH). MATERIALS AND METHODS We examined 320 consecutive patients (July 2013-December 2013) admitted to our outpatient clinic with symptoms of the lower urinary tract at Bozok University. The mean age was 60 (range, 51-75) years. Complete blood count (CBC), prostate-specific antigen (PSA), erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) were assessed. Correlations between PSA, CRP, ESR, prostate volume, International Prostate Symptom Score (IPPS), maximum urinary flow rate (Qmax), and NLR were assessed statistically. Patients were divided into two groups: high and low risk of progression. RESULTS NLR was positively correlated with IPSS (p=0.001, r=0.265), PSA (p=0.001, r=0.194), and negatively correlated with Qmax (p<0.001, r=-0.236). High-risk patients a had a higher NLR compared with low-risk patients, based on IPSS (p<0.001), PSA (p=0.013), and Qmax (p<0.001); however, there were no significant differences between the groups in terms of age (p>0.05), and prostate volume (p>0.05). CONCLUSIONS NLR can predict BPH progression. We propose that increased inflammation is negatively associated with clinical status in BPH patients and suggest that NLR can give information along with LUTS severity which may be used as a readikly accessible marker for patient follow-up.
Is apathy a valid and meaningful symptom or syndrome in Parkinson's disease? A critical review.

OBJECTIVE To review the nearly 30 papers suggesting that apathy may occur frequently in Parkinson's disease (PD) and that it may be a symptom or syndrome that is separate from depression. METHOD Literature review. RESULTS The review revealed three possible explanations for the high rates of apathy found in PD. First, there is much interest in an endogenous explanation of apathy because the basal ganglia and dopamine are implicated in both PD and apathy. Researchers have suggested links between apathy, dopamine depletion, and basal ganglia dysfunction in PD. Second, apathy in PD may be exogenous, resulting from disability and activity restriction. Third, apathy findings are inflated due to conceptual problems and methodological confounds. Indeed, apathy may be consistently confounded with symptoms of PD, including expressive masking, depression, disability, and cognitive decline. CONCLUSION Because apathy has not yet been found to relate to meaningful patient outcomes, and it appears that other factors such as depression and cognition are more strongly related to quality of life than apathy, there is not enough evidence to conclude that apathy is a clinically meaningful syndrome in PD. The role of PD in motivation is of theoretical and practical interest and deserves further research.
Aseptic non-touch technique and catheter-related bloodstream infection in children receiving parenteral nutrition at home

Objectives Parenteral nutrition (PN) at home is an acceptable form of delivering long-term PN for children with intestinal failure. Catheter-related bloodstream infection (CRBSI) is one of the serious complications of long-term PN and can lead to increasing morbidity and mortality. Using aseptic non-touch technique (ANTT) was proven to decrease the incidence of CRBSI in hospital patients. In this study we aimed to review the incidence of CRBSI in children receiving PN at home in our institution using the ANTT and a simplified training programme for parents and carers. Methods We retrospectively collected clinical and microbiological data on all children with intestinal failure (IF) who were on treatment with PN at home under our specialist IF rehabilitation service between November 2012 and November 2013. Results Thirty-five children were included, 16 of whom did not have any infection recorded during the study period. The overall CRBSI rate was 1.3 infections per 1000 line-days, with Staphylococcus being the commonest organism. Twenty-one children did not require catheter change and the overall catheter changes were 1.8 per 1000 line-days. Conclusion In this article, we report a low incidence of CRBSI in a single institution by using the principle of ANTT for accessing central venous catheters combined with a simplified, nurse-led, two-week standardised training programme for parents of children going home on PN.
Unbiased, Genome-Wide In Vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-Specific Liver Gene Expression

ABSTRACT We have used a simple and efficient method to identify condition-specific transcriptional regulatory sites in vivo to help elucidate the molecular basis of sex-related differences in transcription, which are widespread in mammalian tissues and affect normal physiology, drug response, inflammation, and disease. To systematically uncover transcriptional regulators responsible for these differences, we used DNase hypersensitivity analysis coupled with high-throughput sequencing to produce condition-specific maps of regulatory sites in male and female mouse livers and in livers of male mice feminized by continuous infusion of growth hormone (GH). We identified 71,264 hypersensitive sites, with 1,284 showing robust sex-related differences. Continuous GH infusion suppressed the vast majority of male-specific sites and induced a subset of female-specific sites in male livers. We also identified broad genomic regions (up to ∼100 kb) showing sex-dependent hypersensitivity and similar patterns of GH responses. We found a strong association of sex-specific sites with sex-specific transcription; however, a majority of sex-specific sites were >100 kb from sex-specific genes. By analyzing sequence motifs within regulatory regions, we identified two known regulators of liver sexual dimorphism and several new candidates for further investigation. This approach can readily be applied to mapping condition-specific regulatory sites in mammalian tissues under a wide variety of physiological conditions.
THERMAL AND FLEXURAL PROPERTIES OF REGENERATED CELLULOSE(RC)/POLY(3-HYDROXYBUTYRATE)(PHB)BIOCOMPOSITES

Regenerated cellulose (RC)/ poly(3-hydroxybutyrate) (PHB) composite was prepared via melt compounding with different RC contents from 1 to 7 wt. %. Regenerated cellulose fiber was prepared in NaOH/urea aqueous solution. The properties of the cellulose and the regenerated cellulose were compared using Fourier Transform Infrared Spectroscopy (FTIR), Thermogravimetric analysis (TGA), and Differential Scanning Calorimetry (DSC). The results of TGA and DSC revealed that the regenerated cellulose had lower thermal properties than cellulose. Meanwhile, the FTIR of regenerated cellulose showed that the intensity portrayed by a few peaks had reduced or disappeared as compared to cellulose. Besides, PHB composites were characterized using TGA and flexural testing. Moreover, thermal stability of the composites insignificantly changed with the incorporation of RC. Improvement in flexural strength and modulus were observed, whereas 3 wt. % was found to be the optimum RC content.
Radiative Hydrodynamic Models of the Optical and Ultraviolet Emission from Solar Flares

We report on radiative hydrodynamic simulations of moderate and strong solar flares. The flares were simulated by calculating the atmospheric response to a beam of nonthermal electrons injected at the apex of a one-dimensional closed coronal loop and include heating from thermal soft X-ray, extreme ultraviolet, and ultraviolet (XEUV) emission. The equations of radiative transfer and statistical equilibrium were treated in non-LTE and solved for numerous transitions of hydrogen, helium, and Ca II, allowing the calculation of detailed line profiles and continuum emission. This work improves on previous simulations by incorporating more realistic nonthermal electron beam models and includes a more rigorous model of thermal XEUV heating. We find that XEUV back-warming contributes less than 10% of the heating, even in strong flares. The simulations show elevated coronal and transition region densities resulting in dramatic increases in line and continuum emission in both the UV and optical regions. The optical continuum reaches a peak increase of several percent, which is consistent with enhancements observed in solar white-light flares. For a moderate flare (~M class), the dynamics are characterized by a long gentle phase of near balance between flare heating and radiative cooling, followed by an explosive phase with beam heating dominating over cooling and characterized by strong hydrodynamic waves. For a strong flare (~X class), the gentle phase is much shorter, and we speculate that for even stronger flares the gentle phase may be essentially nonexistent. During the explosive phase, synthetic profiles for lines formed in the upper chromosphere and transition region show blueshifts corresponding to a plasma velocity of ~120 km s-1, and lines formed in the lower chromosphere show redshifts of ~40 km s-1.
Biochronology of Triassic bivalves

Abstract Substantial advances by numerous researchers over the past 20 years have made it possible to develop a composite biochronological scheme for the Triassic based on the bivalves Claraia, Peribositria, Enteropleura, Daonella, Halobia, Eomonotis and Monotis. These bivalves exhibit temporal durations nearly equal to ammonoids and conodonts. Widely distributed across the Tethys, Panthalassa and Boreal regions, these bivalves occur in a wide variety of marine facies and water depths, but are most notable for their thick shell accumulation in deeper-water oxygen deficient environments. They were most likely resting or reclining benthos, may have housed chemosymbionts, and were part of episodic opportunistic palaeocommunities in or near oxygen deficient settings. A new biochronological zonation for bivalves is presented that encompasses the entire Triassic and is integrated with standard ammonoid schemes. The Lower Triassic is characterized by 2–3 zones of Claraia, most notably from the eastern Tethys representing the entire Induan and lower portion of the Olenekian. Later in the Olenekian, and most notably from the Boreal realm, species of Peribositria (included by some workers within Bositra) provide useful zonal indexes. The Middle Triassic is well represented by Enteropleura (Middle Anisian) and Daonella (Upper Anisian through Ladinian) in the Tethys and North America with significant occurrences throughout the circum-Pacific and Boreal realms. The Upper Triassic can be subdivided into 8–13 bivalve zones based on the succession of Halobia, Eomonotis and Monotis sensu lato species with best representation in the Tethys, Boreal and eastern Panthalassa regions.
Detecting V-Storms using Meteosat Second Generation SEVIRI image and its applications: A case study over Western Turkey

The present study focused on storm top observations utilizing the Meteosat Second Generation (MSG) data. The Spinning Enhanced Visible and Infrared Imager (SEVIRI) instrument aboard MSG provides image data with high spatial resolution (approximately 3 km) and high temporal resolution (15 minutes). This study used the thunderstorm event of 5 November 2007 over the C¿ameli town in Western Turkey to provide an analysis of the enhanced-V satellite signature using MSG data. This signature was an important indicator of severe weather which can be used during weather warning operations to augment radar information.
MECHANICAL PROPERTIES RELATED TO USE OF GLASS WASTE AS A RAW MATERIAL IN PORCELAIN STONEWARE TILE MIXTURES

Porcelain represents one of the most complex ceramics, formulated from a mix of clay, feldspar and quartz are sintered to conform a glass-ceramic composite. Porcelain stoneware tile has excellent technical characteristics. Nowadays, research of new materials, for example non-hazardous wastes, that are able to replace the traditional fluxing agent with out changing the process or quality of the final products has been realized. The aim of this work is to study the possibility of the use of glass powder waste, in ceramic mixtures, for manufacturing of porcelain stoneware tiles. It was prepared by mixtures containing different amount of fireclay, glass waste, feldspar and quartz. The samples were fired reaching different maximum temperatures in the range 900-1200 0 C, with a soaking time of 1 hour. The fired samples were characterized and the use of small amounts of glass powder in addition with feldspar and quartz showed good results of mechanical technological properties. The 10F5Q5G was the only product that can be classified as a porcelain stoneware tile due to its properties.
Characterization of Fluorescence Lifetime of Photofrin and Delta-Aminolevulinic Acid Induced Protoporphyrin IX in Living Cells Using Single- and Two-Photon Excitation

Photodynamic therapy (PDT) is an effective treatment option for various types of invasive tumors. The efficacy of PDT treatment depends strongly on selective cell uptake and selective excitation of the tumor. The characterization of fluorescence lifetimes of photosensitizers localized inside living cells may provide the basis for further investigation of in vivo PDT dosage measurements using time-domain spectroscopy and imaging. In this communication, we investigated the fluorescence lifetime of localized Photofrin and delta-aminolevulinic acid (ALA) induced protoporphyrin IX (PpIX) in living MAT-LyLu (MLL) rat prostate adenocarcinoma cells. The MLL cells were incubated with the photosensitizers, and then treated with light under well-oxygenated conditions using a two-photon fluorescence lifetime imaging microscope (FLIM). Fluorescence lifetime images of these cells were recorded with average lifetimes of 5.5 plusmn 1.2 ns for Photofrin and 6.3 plusmn 1.2 ns for ALA-induced PpIX. When localized in cells, the lifetimes of both photosensitizers were found to be significantly shorter than those measured in organic solutions. The result for PpIX is consistent with literature values, while the lifetime of Photofrin is shorter than what has been reported. These results suggest that time-domain methods measuring photosensitizer lifetime changes may be good candidates for in vivo PDT dosage monitoring.
Recursive segmentation and recognition templates for image parsing

In this paper, we propose a Hierarchical Image Model (HIM) which parses images to perform segmentation and object recognition. The HIM represents the image recursively by segmentation and recognition templates at multiple levels of the hierarchy. This has advantages for representation, inference, and learning. First, the HIM has a coarse-to-fine representation which is capable of capturing long-range dependency and exploiting different levels of contextual information (similar to how natural language models represent sentence structure in terms of hierarchical representations such as verb and noun phrases). Second, the structure of the HIM allows us to design a rapid inference algorithm, based on dynamic programming, which yields the first polynomial time algorithm for image labeling. Third, we learn the HIM efficiently using machine learning methods from a labeled data set. We demonstrate that the HIM is comparable with the state-of-the-art methods by evaluation on the challenging public MSRC and PASCAL VOC 2007 image data sets.
Hypoxia Reduces the Efficiency of Elisidepsin by Inhibiting Hydroxylation and Altering the Structure of Lipid Rafts

The mechanism of action of elisidepsin (PM02734, Irvalec®) is assumed to involve membrane permeabilization via attacking lipid rafts and hydroxylated lipids. Here we investigate the role of hypoxia in the mechanism of action of elisidepsin. Culturing under hypoxic conditions increased the half-maximal inhibitory concentration and decreased the drug’s binding to almost all cell lines which was reversed by incubation of cells with 2-hydroxy palmitic acid. The expression of fatty acid 2-hydroxylase was strongly correlated with the efficiency of the drug and inversely correlated with the effect of hypoxia. Number and brightness analysis and fluorescence anisotropy experiments showed that hypoxia decreased the clustering of lipid rafts and altered the structure of the plasma membrane. Although the binding of elisidepsin to the membrane is non-cooperative, its membrane permeabilizing effect is characterized by a Hill coefficient of ~3.3. The latter finding is in agreement with elisidepsin-induced clusters of lipid raft-anchored GFP visualized by confocal microscopy. We propose that the concentration of elisidepsin needs to reach a critical level in the membrane above which elisidepsin induces the disruption of the cell membrane. Testing for tumor hypoxia or the density of hydroxylated lipids could be an interesting strategy to increase the efficiency of elisidepsin.
Misfolding and aggregation of newly synthesized proteins in the endoplasmic reticulum

As a part of our studies on the folding of glycoproteins in the ER, we analyzed the fate of viral glycoproteins that have misfolded either spontaneously or through inhibition of N-linked glycosylation. Newly synthesized Semliki Forest virus spike glycoproteins E1 and p62 and influenza hemagglutinin were studied in infected and transfected tissue culture cells. Misfolded proteins aggregated in less than 1 min after release from polysomes and aberrant interchain disulfide bonds were formed immediately. When more than one protein was misfolded, mixed aggregates were generated. This indicated that the formation of complexes was nonspecific, random, and not restricted to products from single polysomes. The size of the aggregates varied from small oligomers to complexes of several million daltons. BiP was associated noncovalently with the aggregates and with some of the nonaggregated products. We conclude that aggregation reflects the poor solubility of incompletely folded polypeptide chains.
A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase—extensive moonlighting in mitochondrial tRNA biogenesis

Transfer RNAs (tRNAs) reach their mature functional form through several steps of processing and modification. Some nucleotide modifications affect the proper folding of tRNAs, and they are crucial in case of the non-canonically structured animal mitochondrial tRNAs, as exemplified by the apparently ubiquitous methylation of purines at position 9. Here, we show that a subcomplex of human mitochondrial RNase P, the endonuclease removing tRNA 5′ extensions, is the methyltransferase responsible for m1G9 and m1A9 formation. The ability of the mitochondrial tRNA:m1R9 methyltransferase to modify both purines is uncommon among nucleic acid modification enzymes. In contrast to all the related methyltransferases, the human mitochondrial enzyme, moreover, requires a short-chain dehydrogenase as a partner protein. Human mitochondrial RNase P, thus, constitutes a multifunctional complex, whose subunits moonlight in cascade: a fatty and amino acid degradation enzyme in tRNA methylation and the methyltransferase, in turn, in tRNA 5′ end processing.
Transport activity and presence of ClC‐7/Ostm1 complex account for different cellular functions

Loss of the lysosomal ClC‐7/Ostm1 2Cl−/H+ exchanger causes lysosomal storage disease and osteopetrosis in humans and additionally changes fur colour in mice. Its conversion into a Cl− conductance in Clcn7unc/unc mice entails similarly severe lysosomal storage, but less severe osteopetrosis and no change in fur colour. To elucidate the basis for these phenotypical differences, we generated Clcn7td/td mice expressing an ion transport‐deficient mutant. Their osteopetrosis was as severe as in Clcn7−/− mice, suggesting that the electric shunt provided by ClC‐7unc can partially rescue osteoclast function. The normal coat colour of Clcn7td/td mice and their less severe neurodegeneration suggested that the ClC‐7 protein, even when lacking measurable ion transport activity, is sufficient for hair pigmentation and that the conductance of ClC‐7unc is harmful for neurons. Our in vivo structure‐function analysis of ClC‐7 reveals that both protein‐protein interactions and ion transport must be considered in the pathogenesis of ClC‐7‐related diseases.
A methodology of human factors analysis for systems engineering: theory and applications

This paper discusses a methodology for studying human erroneous behavior that comprises four modeling phases, namely: (1) a paradigm of human behavior; (2) a taxonomy and related tables for human erroneous actions; (3) a set of data and correlations from the real working environment; and (4) a procedure for application of the methodology to different types of analysis, at different levels of complexity. The methodology has been developed to support possible applications of human factors to design and safety assessment of technological systems. The results of some applications are presented for prospective and retrospective studies in the domains of nuclear reactors and civil aviation.