Miracle-dz/UniFAR-FTUs huggingface dataset:
Human papillomavirus associated with oesophageal cancer

Aim: To study the prevalence and the different types of human papillomavirus (HPV) in patients with oesophageal cancer from a high risk area of South Africa (Transkei). Methods: DNA samples from 50 paraffin wax embedded tissue sections were analysed by nested polymerase chain reaction (PCR) using the degenerate HPV L1 consensus primer pairs MY09/MY11 and GP5+/GP6+. Positive PCR samples were subjected to DNA sequence analysis. Results: HPV DNA was detected in 23 of the 50 samples. Sequence analysis revealed that most patients (11) harboured DNA to HPV type 11, whereas other types included DNA HPV type 39 (seven patients), type 16 (two patients), and type 52 (one patient). HPV type 39 has not previously been shown to be associated with oesophageal cancer. In contrast to earlier studies that have found HPV type 16 to be more frequently associated with oesophageal cancer, HPV type 11 was the predominant subtype in this study. Conclusions: The high frequency of occurrence of HPV in oesophageal tumours (23 of 50 patients; 46%) implicates HPV as one of the possible aetiological factors in this disease. The finding that the low risk HPV subtypes predominate indicates that transformation may be effected via the E6 and E7 proteins.
von Willebrand factor cleaving protease (ADAMTS‐13) and ADAMTS‐13 neutralizing autoantibodies in 100 patients with thrombotic thrombocytopenic purpura

The congenital or acquired deficiency of the von Willebrand factor (VWF) cleaving protease, ADAMTS‐13 has been specifically associated with a diagnosis of thrombotic thrombocytopenic purpura (TTP), a microangiopathy characterized by the formation of occlusive platelet thrombi. The mechanisms of TTP were investigated in 100 patients diagnosed on the basis of the presence of at least three of the following: thrombocytopenia, haemolytic anaemia, elevated serum levels of lactate dehydrogenase and neurological symptoms. Plasma levels of ADAMTS‐13 were severely reduced (<10% of normal) in 48%, moderately reduced (between 10% and 46%) in 24% and normal (>46%) in 28%. A neutralizing antibody was the cause of the deficiency in 38% of the cases, with a higher prevalence of this mechanism (87%) in the 48 patients with severely reduced ADAMTS‐13. Double heterozygosity for a 29 base pair (bp) deletion and a nucleotide insertion and homozygosity for a 6 bp deletion in the ADAMTS13 gene were identified only in two patients born from consanguineous marriages. In conclusion, this study indicated that ADAMTS‐13 was normal in nearly one‐third of patients with TTP and that ADAMTS‐13 deficiency was not associated with the presence of neutralizing antibodies in more than half of the patients.
Coach perceptions of psychological characteristics and behaviors of male and female athletes and their impact on coach behaviors

An interpretive investigation was conducted to gain an in-depth understanding of (1) coach perceptions of psychological characteristics and behaviors of male and female athletes and (2) how these perceptions impact coach behavior. The participants were fourteen collegiate head cross country coaches (1 female, 13 male) who were identified by their peers as having knowledge and experience in coaching males and females. They have been coaching an average of 23.2 years (range = 8-29) and have coached both females and males an average of 15.7 years (range = 3-28). A semi-structured interview format was used to achieve the investigative purposes. More specifically, the interview consisted of three parts. In the first part, coaches were asked to identify and describe characteristics and behaviors or their male and female athletes. Content analyses were conducted on the identified raw data themes to aid in describing and interpreting coaches' perceptions of their female and male athletes. The following themes emerged as characteristic of female athletes: emotional / sensitive; need from coach; coachable; feel expectations / want to please; competitive with teammates; weight conscious / eating disorders; academically conscious and; additional attributes conducive to athletic success. Themes emerging as characteristic of male athletes included the following: know it all attitude / challenge coach; tend to get off track; ego-involved / struggle with not winning; team emphasis; less emotional than female / hide feelings and; additional attributes conducive to athletic success.
Recruiting Mechanism of the AAA Peroxins, Pex1p and Pex6p, to Pex26p on the Peroxisomal Membrane

A peroxisomal C‐tail‐anchored type‐II membrane protein, Pex26p, recruits AAA ATPase Pex1p–Pex6p complexes to peroxisomes. We herein attempted to gain mechanistic insight into Pex26p function. Pex26pΔ33‐40 truncated in amino‐acid residues at 33‐40 abolishes the recruiting of Pex1p–Pex6p complex to peroxisomes and fails to complement the impaired phenotype of pex26 CHO cell mutant ZP167, thereby suggesting that peroxisomal localization of Pex1p and Pex6p is indispensable for the transport of matrix proteins. In in vitro transport assay using semipermeabilized CHO cells, Pex1p is targeted to peroxisomes in a manner dependent on ATP hydrolysis, while Pex6p targeting requires ATP but not its hydrolysis. This finding is confirmed by the assay using Walker‐motif mutants. Transport of Pex1p and Pex6p is temperature‐dependent. In vitro binding assays with glutathione‐S‐transferase‐fused Pex26p, Pex1p and Pex6p bind to Pex26p in a manner dependent on ATP binding but not ATP hydrolysis. These results suggest that ATP hydrolysis is required for stable localization of Pex1p to peroxisomes, but not for binding to Pex26p. Moreover, Pex1p and Pex6p are altered to a more compact conformation upon binding to ATP, as verified by limited proteolysis. Taken together, Pex1p and Pex6p are most likely regulated in their peroxisomal localization onto Pex26p via conformational changes by the ATPase cycle.
du CRSN : le point sur la dépression , première partie Impact of substance P receptor antagonism on the serotonin and norepinephrine systems : relevance to the antidepressant / anxiolytic response

Rev Psychiatr Neurosci 2004;29(3) © 2004 Canadian Medical Association Substance P (neurokinin-1 [NK1]) receptor antagonists appear to be effective antidepressant and anxiolytic agents, as indicated in 3 double-blind clinical trials. In laboratory animals, they promptly attenuate the responsiveness of serotonin (5-hydroxytryptamine [5-HT]) and norepinephrine (NE) neurons to agonists of their cell-body autoreceptors, as is the case for some antidepressant drugs that are currently in clinical use. Long-term, but not subacute, antagonism of NK1 receptors in rats increases 5-HT transmission in the hippocampus, a property common to all antidepressant treatments tested thus far. This enhancement seems to be mediated by a time-dependent increase in the firing rate of 5-HT neurons. Mice with the NK1 receptor deleted from their genetic code also have an increased firing rate of 5-HT neurons. Taken together, these observations strongly suggest that NK1 antagonists could become a new class of antidepressant and anxiolytic agents.
Noise speech wavelet analyzing in special time ranges

speech analyzing in special periods of time has been presented in this paper. One of the most important periods in signal processing is near to Zero. By this paper, we analyze noise speech signals when these signals are near to Zero. Our strategy is defining some subfunctions and compress histograms when a noise speech signal is in a special period. It can be so useful for wavelet signal processing and spoken systems analyzing.
Lymphocyte Oxidative Stress/Genotoxic Effects Are Related to Serum IgG and IgA Levels in Coke Oven Workers

We investigated oxidative stress/genotoxic effects levels, immunoglobulin levels, polycyclic aromatic hydrocarbons (PAHs) levels exposed in 126 coke oven workers and in 78 control subjects, and evaluated the association between oxidative stress/genotoxic effects levels and immunoglobulin levels. Significant differences were observed in biomarkers, including 1-hydroxypyrene levels, employment time, percentages of alcohol drinkers, MDA, 8-OHdG levels, CTL levels and CTM, MN, CA frequency, and IgG, IgA levels between the control and exposed groups. Slightly higher 1-OHP levels in smoking users were observed. For the dose-response relationship of IgG, IgA, IgM, and IgE by 1-OHP, each one percentage increase in urinary 1-OHP generates a 0.109%, 0.472%, 0.051%, and 0.067% decrease in control group and generates a 0.312%, 0.538%, 0.062%, and 0.071% decrease in exposed group, respectively. Except for age, alcohol and smoking status, IgM, and IgE, a significant correlation in urinary 1-OHP and other biomarkers in the total population was observed. Additionally, a significant negative correlation in genotoxic/oxidative damage biomarkers of MDA, 8-OH-dG, CTL levels, and immunoglobins of IgG and IgA levels, especially in coke oven workers, was found. These data suggest that oxidative stress/DNA damage induced by PAHs may play a role in toxic responses for PAHs in immunological functions.
Acceleration of Age-Associated Methylation Patterns in HIV-1-Infected Adults

Patients with treated HIV-1-infection experience earlier occurrence of aging-associated diseases, raising speculation that HIV-1-infection, or antiretroviral treatment, may accelerate aging. We recently described an age-related co-methylation module comprised of hundreds of CpGs; however, it is unknown whether aging and HIV-1-infection exert negative health effects through similar, or disparate, mechanisms. We investigated whether HIV-1-infection would induce age-associated methylation changes. We evaluated DNA methylation levels at >450,000 CpG sites in peripheral blood mononuclear cells (PBMC) of young (20-35) and older (36-56) adults in two separate groups of participants. Each age group for each data set consisted of 12 HIV-1-infected and 12 age-matched HIV-1-uninfected samples for a total of 96 samples. The effects of age and HIV-1 infection on methylation at each CpG revealed a strong correlation of 0.49, p<1 x10-200 and 0.47, p<1x10-200. Weighted gene correlation network analysis (WGCNA) identified 17 co-methylation modules; module 3 (ME3) was significantly correlated with age (cor=0.70) and HIV-1 status (cor=0.31). Older HIV-1+ individuals had a greater number of hypermethylated CpGs across ME3 (p=0.015). In a multivariate model, ME3 was significantly associated with age and HIV status (Data set 1: βage= 0.007088, p=2.08 x 10-9; βHIV= 0.099574, p=0.0011; Data set 2: βage= 0.008762, p=1.27x 10-5; βHIV= 0.128649, p= 0.0001). Using this model, we estimate that HIV-1 infection accelerates age-related methylation by approximately 13.7 years in data set 1 and 14.7 years in data set 2. The genes related to CpGs in ME3 are enriched for polycomb group target genes known to be involved in cell renewal and aging. The overlap between ME3 and an aging methylation module found in solid tissues is also highly significant (Fisher-exact p=5.6 x 10-6, odds ratio=1.91). These data demonstrate that HIV-1 infection is associated with methylation patterns that are similar to age-associated patterns and suggest that general aging and HIV-1 related aging work through some common cellular and molecular mechanisms. These results are an important first step for finding potential therapeutic targets and novel clinical approaches to mitigate the detrimental effects of both HIV-1-infection and aging.
A logic for conditional possibility

In this paper, we present a logical framework for integrating the quantitative and qualitative approaches to uncertainty management based on possibility theory. The semantics of the logic is based on the Dempster’s rule of conditioning for possibility theory. It is then shown that classical modal logic, conditional logic, possibilistic logic, quantitative modal logic and qualitative possibilistic logic are all sublogics of the present logical framework.
Evidence for liquid water during the high-density to low-density amorphous ice transition

Polymorphism of water has been extensively studied, but controversy still exists over the phase transition between high-density amorphous (HDA) and low-density amorphous (LDA) ice. We report the phase behavior of HDA ice inside high-pressure cryocooled protein crystals. Using X-ray diffraction, we demonstrate that the intermediate states in the temperature range from 80 to 170 K can be reconstructed as a linear combination of HDA and LDA ice, suggesting a first-order transition. We found evidence for a liquid state of water during the ice transition based on the protein crystallographic data. These observations open the possibility that the HDA ice induced by high-pressure cryocooling is a genuine glassy form of high-density liquid.
Molecular Characterization of the Acid-Inducible asr Gene of Escherichia coli and Its Role in Acid Stress Response

ABSTRACT Enterobacteria have developed numerous constitutive and inducible strategies to sense and adapt to an external acidity. These molecular responses require dozens of specific acid shock proteins (ASPs), as shown by genomic and proteomic analysis. Most of the ASPs remain poorly characterized, and their role in the acid response and survival is unknown. We recently identified an Escherichia coli gene, asr (acid shock RNA), encoding a protein of unknown function, which is strongly induced by high environmental acidity (pH < 5.0). We show here that Asr is required for growth at moderate acidity (pH 4.5) as well as for the induction of acid tolerance at moderate acidity, as shown by its ability to survive subsequent transfer to extreme acidity (pH 2.0). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western analysis of acid-shocked E. coli cells harboring a plasmid-borne asr gene demonstrated that the Asr protein is synthesized as a precursor with an apparent molecular mass of 18 kDa. Mutational studies of the asr gene also demonstrated the Asr preprotein contains 102 amino acids. This protein is subjected to an N-terminal cleavage of the signal peptide and a second processing event, yielding 15- and 8-kDa products, respectively. Only the 8-kDa polypeptide was detected in acid-shocked cells containing only the chromosomal copy of the asr gene. N-terminal sequencing and site-directed mutagenesis revealed the two processing sites in the Asr protein precursor. Deletion of amino acids encompassing the processing site required for release of the 8-kDa protein resulted in an acid-sensitive phenotype similar to that observed for the asr null mutant, suggesting that the 8-kDa product plays an important role in the adaptation to acid shock. Analysis of Asr:PhoA fusions demonstrated a periplasmic location for the Asr protein after removal of the signal peptide. Homologues of the asr gene from other Enterobacteriaceae were cloned and shown to be induced in E. coli under acid shock conditions.
Racing With and Against the Machine: Changes in Occupational Skill Composition in an Era of Rapid Technological Advance

Rapid advances in digital technologies have profound implications for work. Many middle and low skill jobs have disappeared, contributing to increasing inequality, falling labor force participation and stagnating median incomes. We examine changes in the skill content of jobs from 2006-2014 using comprehensive data on occupational skill requirements of 674 occupations to understand the effects of recent changes in automation. We identify seven distinct skill categories empirically and explain over 62% of the variation in the data. Consistent with theory, we find a significant reduction in skills that compete with machines, an increase in skills that complement machines, and an increase in skills where machines (thus far) have not made great in-roads. Complementarity across skills has increased, boosting the need for worker flexibility. The remarkable scale and scope of occupational skill changes that we document just since 2006 portend even bigger changes in coming years.
Changes in erythropoiesis in hereditary hemochromatosis are not mediated by HFE expression in nucleated red cells.

BACKGROUND AND OBJECTIVES The HFE protein interacts with the transferrin receptor (TfR) to regulate cellular iron uptake. Nucleated erythroid cells have the highest number of TfR and the greatest iron uptake. The aim of this study was to investigate whether erythroid iron uptake is directly affected by HFE mutations. DESIGN AND METHODS Iron status and erythropoiesis was investigated in sixty, asymptomatic HFE C282Y homozygotes. Reverse transcription-polymerase chain reaction, flow cytometry and immunocytochemistry were employed to investigate the HFE expression profile of normal peripheral blood, nucleated erythroid cells and several cultured cell lines. RESULTS The HFE C282Y homozygous subjects showed subtle erythropoietic changes with raised transferrin saturation and reticulocyte counts and low-normal serum transferrin receptor levels, but normal erythrocyte count and mean cell volume. HFE mRNA was detected in macrophages and monocytes and HFE protein was detected in granulocytes and at low levels in monocytes. Cultured primary human erythroid colonies did not express HFE mRNA or protein. INTERPRETATION AND CONCLUSIONS There is evidence that HFE C282Y homozygotes display increased plasma iron turnover and increased erythropoiesis, despite there being no evidence that HFE is expressed in erythroid colonies with a normal HFE genotype. It is likely that HFE mutations do not directly alter erythroid iron handling, but alter the supply of iron to the erythroid tissues.
Functional Connectivity of the Infant Human Brain

Infancy is a critical and immensely important period in human brain development. Subtle changes during this stage may be greatly amplified with the unfolding of different developmental processes, exerting far-reaching consequences. Studies of the structure and behavioral manifestations of the infant brain are fruitful. However, the specific functional brain mechanisms that enable the execution of different behaviors remained elusive until the advent of functional connectivity fMRI (fcMRI), which provides an unprecedented opportunity to probe the infant functional brain development in vivo. Since its inception, a burgeoning field of infant brain functional connectivity study has emerged and thrived during the past decade. In this review, we describe (1) findings of normal development of functional connectivity networks and their relationships to behaviors and (2) disruptions of the normative functional connectivity development due to identifiable genetic and/or environmental risk factors during the first 2 years of human life. Technical considerations of infant fcMRI are also provided. It is our hope to consolidate previous findings so that the field can move forward with a clearer picture toward the ultimate goal of fcMRI-based objective methods for early diagnosis/identification of risks and evaluation of early interventions to optimize developing functional connectivity networks in this critical developmental window.
Identification of single exon genes and their encoded proteins in rice (Oryza sativa L.) genome: an in silico approach

In this study, we predicted Single Exon Genes (SEGs) distributed in whole rice genome and their expressed proteins. Complete genome of rice was retrieved from TIGR. CDS annotation in the FEATURE (GenBank format) was used to predict SEGs sequences. Organelle gene sequences, pseudogenes, tRNA genes, rRNA genes and duplicated genes were eliminated through different bioinformatics tools. A sizeable number (8.1%) of SEGs in whole rice genome were detected. Predicted SEGs were further searched for their differential response under anoxia. Out of total detected SEGs, only 39.33% were anoxia responsive. Among the total detected anoxia-responsive SEG, only 23.48% encode the known proteins.
A Generic Scheme for Estimating the Size of a Group While Avoiding Feedback Implosion

We present a probabilistic polling scheme for estimating the size of a group of nodes affected by the same event. We analyze the bias of the proposed scheme and show how it can be completely eliminated. Our scheme differs from previouswork in several important ways. First, it is generic in the sense t hat it is not dependent on the physical properties of the underly ing network. Second, it uses a “one-shot” estimation techniquethat does not depend on the results of previous rounds. Finally, t he estimating nodes control the number of feedback messages, t hus allowing a good balance between the overhead imposed by the scheme and its precision. We compared our scheme to previous works and saw a notable performance improvement: our scheme reduced the number of response messages by 80-90% while obtaining the same precision.
Probing university students' adoption and utilization of social networking websites in Nigeria

This study was designed to examine the influence of socio-demographic variables, innovation characteristics, time and social systems, on university students’ adoption and use of social networking websites (SNWs). Survey design was adopted. A structured questionnaire was used for data collection from 600 respondents comprising undergraduate and postgraduate students in the two public universities. Frequency distribution, factor and regression analyses were performed on the data collected. Findings revealed that socio-demographic variables had positive influence on students’ adoption and use of SNWs. The three Diffusion of Innovation variables significantly contributed to the adoption and use of SNWs but innovation characteristics had the strongest influence, while time exerted the least. All the innovation characteristics had positive and significant correlation with the use of SNWs with relative advantage having the highest contribution and complexity the least. In view of these findings, university authorities need to design and develop appropriate social networking systems to serve as a cost-effective platform to deliver instructions to students.