Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of HIV-1 Near Full-Length Proviral Genome Quasispecies from Patients with Undetectable Viral Load Undergoing First-Line HAART Therapy

Increased access to highly active antiretroviral therapy (HAART) by human immunodeficiency virus postive (HIV+) individuals has become a reality worldwide. In Brazil, HAART currently reaches over half of HIV-infected subjects. In the context of a remarkable HIV-1 genetic variability, highly related variants, called quasispecies, are generated. HIV quasispecies generated during infection can influence virus persistence and pathogenicity, representing a challenge to treatment. However, the clinical relevance of minority quasispecies is still uncertain. In this study, we have determined the archived proviral sequences, viral subtype and drug resistance mutations from a cohort of HIV+ patients with undetectable viral load undergoing HAART as first-line therapy using next-generation sequencing for near full-length virus genome (NFLG) assembly. HIV-1 consensus sequences representing NFLG were obtained for eleven patients, while for another twelve varying genome coverage rates were obtained. Phylogenetic analysis showed the predominance of subtype B (83%; 19/23). Considering the minority variants, 18 patients carried archived virus harboring at least one mutation conferring antiretroviral resistance; for six patients, the mutations correlated with the current ARVs used. These data highlight the importance of monitoring HIV minority drug resistant variants and their clinical impact, to guide future regimen switches and improve HIV treatment success.
Genotyping and Coalescent Phylogenetic Analysis of Pneumocystis jiroveci from South Africa

ABSTRACT Sequence analysis of Pneumocystis jiroveci internal transcribed spacer (ITS) regions has become an important epidemiological tool. The objectives of the present study were to investigate sequence variations in the ITS1-5.8S ribosomal DNA (rDNA)-ITS2 regions; determine the P. jiroveci genotypes present in Cape Town, South Africa; and resolve the lineage evolution of the types by use of the coalescent theory. ITS regions were amplified from samples collected from 19 patients. PCR products were cloned, and four to five clones were sequenced from each specimen. Statistical parsimony was applied for coalescence-based network genotype analysis. The most prevalent type was Eg (14 of 19 patients, 33 of 83 clones), followed by Gg (4 of 19 patients, 7 of 83 clones), Eu (3 of 19 patients, 5 of 83 clones), and Gh (2 of 19 patients, 2 of 83 clones). Four new combinations (Eo, Je, Ge, and No), 11 new ITS1 sequences, and 13 new ITS2 sequences were identified. A new ITS2 type was detected in three patients and was designated type u. Coinfection appeared to be common, with 15 of 19 patients harboring more than one type and with up to six types per specimen. The resultant parsimony network identified Eg as the most probable ancestral haplotype and supported the occurrence of recombinational events within the population studied. Although the 5.8S rDNA region revealed only 13 clones containing one to two nucleotide polymorphisms, it may assist in defining types. Coalescent theory proposed that Eg is an ancestral type from which microevolutionary subtypes radiate.
Modulation of Human Visual Evoked Potentials in 3-Dimensional Perception After Stimuli Produced With an Integral Imaging Method

We investigated the neurophysiological correlates of stereoscopic 3-dimensional (3-D) depth perception by studying human visual evoked potentials (VEPs) with an integral imaging method characterized by horizontal but not vertical disparity. The VEPs were recorded in 10 healthy men under 4 conditions. In condition I, stimuli A (flat, 2-dimensional [2-D] image) and B (concave 3-D image) were presented at random. In condition II, stimuli A and C (convex 3-D image) were presented at random. In condition III, stimuli B and C were presented at random. In condition IV, stimuli A, B, and C were presented at random. The data for flat VEPs to stimulus A were combined in conditions I and II. The data for concave VEPs to stimulus B were combined in conditions I and III. The data for convex VEPs to stimulus C were combined in conditions II and III. When 2-way analysis of variance (ANOVA) for 2 factors, stimulus conditions (flat VEPs, concave VEPs, and convex VEPs) and electrode positions, was applied for VEP data, the N1 and N2 peak amplitudes differed significantly among the 3 stimulus conditions. In condition IV, the N1 peak amplitudes differed significantly among the 3 stimuli. Multiple comparisons followed by Bonferroni adjustment did not detect differences in the N1 peak amplitude between stimuli A and B, between stimuli A and C, or between stimuli B and C. We concluded that VEPs to concave or convex 3-D stimuli were significantly different from VEPs to flat 2-D stimuli. This is the first report showing modulation of human VEPs in 3-D perception with an integral imaging method.
Using English for work: situations, forms, difficulties and attitudes

Englisch als Lingua franca (EFL) ist die wichtigste Rolle, die die englische Sprache heutzutage spielt. Diese wird in unterschiedlichsten Kontexten benutzt wie sonst keine andere Sprache. Ein besonderer Kontext in dem EFL benutzt wird ist die internationale Wirtschaft. Die multinationalen Korporationen, die international arbeiten, bestimmen in ihren Sprachrichtlinien ELF als ihre ubliche korporative Sprache. Diese Masterarbeit ist eine empirische Fallstudie in einer multinationalen Korporation, Bank Austria, und in ihren Filialen in Bulgarien, Tschechen, Slowakei, Ungarn, Rumanien, Serbien und Slowenien. Die Studie setzt Ihren Schwerpunkt auf die Formen und Situationen in welchen ELF benutzt wird, sowie auf die Schwierigkeiten der Angestellten zu verstehen und verstanden zu werden. Die kommunikativen Schwierigkeiten uber die kommunikativen Kanale hinweg werden auch untersucht (Email, Telefonate, Telekonferenzen, offizielle Dokumente und Sitzungen). Des Weiteren werden die Einstellungen gegenuber Benutzung der ELF in der Arbeit der Angestellten der Bank Austria untersucht. Insbesondere, berichteten die Teilnehmer der Studie uber den Einfluss der Nutzung der ELF auf ihre Leistung und Kariere. Die Ergebnisse deuten darauf hin, dass die Angestellten in Bank Austria aktive, fortgeschrittene Kommunikatoren sind, deren kommunikative Interaktionen mittels ELF in der Arbeit problemfrei sind. Zusatzlich, die Angestellten berichten allgemein positive Einstellungen uber die Nutzung der ELF in ihrem Arbeitsleben, ohne dass ELF ihre Leistung und Kariere negativ beeinflussen wurde. Sie nehmen ELF eher als eine Voraussetzung wahr.
Microbial dynamics in glacier forefield soils show succession is not just skin deep

All over the world, glaciers are receding. One key consequence of glacier area loss is the creation of new terrestrial habitats. This presents an experimental opportunity to study both community formation and the implications of glacier loss for terrestrial ecosystems. In this issue of Molecular Ecology, Rime et al. ( ) describe how microbial communities are structured according to soil depth and development in the forefield of Damma glacier in Switzerland. The study provides insights into the contrasting structures of microbial communities at different stages of soil development. An important strength of the study is the integration of soil depth into the paradigm of primary succession, a feature which has rarely been considered by other studies. These findings underscore the importance of studying the interactions between microbial communities and glaciers at a time when Earth's glacial systems are experiencing profound change.
Educational Benefits of Diversity in Medical School: A Survey of Students

Purpose Many U.S. medical schools have abandoned affirmative action, limiting the recruitment and reducing the admission of underrepresented minority (URM) students even though research supports the premise that the public benefits from an increase in URM physicians and that URM physicians are likely to serve minority, poor, and Medicaid populations. Faculty and students commonly assume they benefit from peer cultural exchange, and the published evidence for the past two decades supports this notion. This research examined the students' perceptions of the educational merits of a diverse student body by surveying medical students at two schools. Method In 2000, medical students from all four years at Harvard Medical School and the University of California, San Francisco, School of Medicine were enrolled in a telephone survey about the relevance of racial diversity (among students) in their medical education. Students responded to the interviewer's questions on a five-point Likert-type scale. Results Of the 55% of students who could be located, 97% responded to the survey. Students reported having little intercultural contact during their formative years but significantly more interactions during higher education years, especially in medical school. Students reported contacts with diverse peers greatly enhanced their educational experience. They strongly supported strengthening or maintaining current affirmative action policies in admissions. The responses and demography of the Harvard and UCSF students did not differ significantly, nor did they differ for majority students and URM students—all groups overwhelmingly thought that racial and ethnic diversity among their peers enhanced their education. Conclusions Diversity in the student body enhanced the educational experiences of students in two U.S. medical schools.
Influence of Soil Use on Prevalence of Tetracycline, Streptomycin, and Erythromycin Resistance and Associated Resistance Genes

ABSTRACT This study examined differences in antibiotic-resistant soil bacteria and the presence and quantity of resistance genes in soils with a range of management histories. We analyzed four soils from agricultural systems that were amended with manure from animals treated with erythromycin and exposed to streptomycin and/or oxytetracycline, as well as non-manure-amended compost and forest soil. Low concentrations of certain antibiotic resistance genes were detected using multiplex quantitative real-time PCR (qPCR), with tet(B), aad(A), and str(A) each present in only one soil and tet(M) and tet(W) detected in all soils. The most frequently detected resistance genes were tet(B), tet(D), tet(O), tet(T), and tet(W) for tetracycline resistance, str(A), str(B), and aac for streptomycin resistance, and erm(C), erm(V), erm(X), msr(A), ole(B), and vga for erythromycin resistance. Transposon genes specific for Tn916, Tn1549, TnB1230, Tn4451, and Tn5397 were detected in soil bacterial isolates. The MIC ranges of isolated bacteria for tetracycline, streptomycin, and erythromycin were 8 to >256 μg/ml, 6 to >1,024 μg/ml, and 0.094 to >256 μg/ml, respectively. Based on 16S rRNA gene similarity, isolated bacteria showed high sequence identity to genera typical of soil communities. Bacteria with the highest MICs were detected in manure-amended soils or soils from agricultural systems with a history of antibiotic use. Non-manure-amended soils yielded larger proportions of antibiotic-resistant bacteria, but these had lower MICs, carried fewer antibiotic resistance genes, and did not display multidrug resistance (MDR).
Induction of Long-Term Glycemic Control in Newly Diagnosed Type 2 Diabetic Patients by Transient Intensive Insulin Treatment

OBJECTIVE Type 2 diabetes is a slowly progressive disease, in which the gradual deterioration of glucose tolerance is associated with the progressive decrease in β-cell function. Hyperglycemia per se has deleterious effects on both beta-cell function and insulin action, which are partially reversible by the short-term control of blood glucose levels. We hypothesized that the induction of euglycemia, using intensive insulin therapy at the time of clinical diagnosis, could lead to a significant improvement in insulin secretion and action and thus alter the clinical course of the disease. RESEARCH DESIGN AND METHODS Thirteen newly diagnosed diet-unresponsive type 2 diabetic patients were treated with continuous subcutaneous insulin infusion (CSII) for 2 weeks and followed longitudinally while being treated with diet alone. RESULTS Four patients were considered therapeutic failures since CSII failed to induce euglycemia (n = 1) or glucose control deteriorated within 6 months after CSII (n = 3). The remaining nine patients were maintained on diet alone with adequate control from 9 to > 50 months (median ± SE, 26 ± 4.8 months). In five patients, glycemic control deteriorated after 9–36 months, but a repeat 2-week CSII treatment reestablished control in four patients. One of these patients underwent a third CSII treatment 13 months later. At the time this article was written, six patients of the initial group were still controlled without medication 16–59 months (median ± SE, 45.5 ± 6.6 months) after the initiation of treatment. Body weight remained unchanged in all patients. CONCLUSIONS These findings suggest that in a significant proportion of type 2 diabetic patients who fail to respond to dietary measures, short-term intensive insulin treatment can effectively establish responsiveness, allowing long-term glycemic control without medication. Further studies are required to establish whether simpler treatment regimens could be equally effective. If the hypothesis offered here finds support, present approaches to the management of newly diagnosed type 2 diabetes may need to be revised.
Expression of epidermal growth factor receptor in the goat cumulus–oocyte complex

It has been previously reported that epidermal growth factor (EGF) influences meiotic maturation and development competence of oocytes in various mammalian species. The present study was undertaken to analyze the expression of the gene encoding the EGF‐receptor (EGF‐R) in the goat cumulus–oocyte complex during meiotic competence acquisition. Expression of EGF‐R mRNA was evaluated by PCR on reverse transcribed mRNA from follicular cells and oocytes, using EGF‐R specific primers designed from human cDNA. The presence of the EGF‐R transcript was evidenced in follicular cells as well as in meiotically competent and incompetent oocytes. Western blot analysis performed with specific anti EGF‐R antibody revealed in meiotically competent and incompetent oocytes and in follicular cells a 170 kD polypeptide corresponding to the goat EGF‐R protein. In oocytes the amount of EGF‐R increased with meiotic competence acquisition. EGF‐R distribution was examined by indirect immunofluorescence on frozen sections of cumulus–oocyte complexes (COCs). EGF‐R immunoreactivity was observed in cumulus cells and in oocytes. Staining appeared to be confined to the periphery of the cells for both oocytes and cumulus cells. In this study, we identified the main component required for signaling via EGF‐R in the goat oocyte and in follicular cells. These results suggest a possible involvement of EGF in the regulation of follicular growth and oocyte maturation in goat. Mol. Reprod. Dev. 67: 439–445, 2004. © 2004 Wiley‐Liss, Inc.
The Influence of Phenobarbital on Biotransformation of 25‐Hydroxycholecalciferol

Altered vitamin D metabolism has been implicated as a cause of anticonvulsant-induced osteomalacia. Previous studies have demonstrated accelerated biotransformation of vitamin D3 to 25-hydroxycholecalciferol (25-OHD3). However, it is not known whether the 25-OHD3 is metabolized to 1,25-dihydroxycholecalciferol (1,25-(OH)2D3), the tissue-active metabolite of vitamin D3. This study using rats was undertaken to study the influence of phenobarbital on the biotransformation of 25-OHD3 to 1,25-(OH)2D3. The disappearance rate of 25-OHD3 was virtually the same in the pheno-barbital-treated group (re = 0.0615 pmole/min) and the control group (re - 0.0549 pmole/min). Similarly, the appearance rate of 1,25-(OH)2D3 was virtually the same in the treated group (ra = 0.0133 pmole/min) and the control group (ra = 0.0134 pmole/min). These data suggest that phenobarbital does not affect the biotransformation of 25-OHD3 to 1,25-(OH)2D3. The implication of this observation is that altered vitamin D metabolism does not account for phenobarbital-induced osteomalacia.
Combined evaluation of risk factors predicting poor ovarian responders in Chinese patients undergoing in vitro fertilization

Abstract This study aimed to explore the parameters associated with poor ovarian response (POR) to develop an early warning score model (EWSM) for detecting POR in Chinese women undergoing in vitro fertilization, in order to improve the outcomes. Between 2005 and 2011, we recruited 736 patients with POR after IVF and 736 individuals with normal ovarian response after IVF as controls. Clinical parameters were determined to evaluate the ovarian reserve. We then compared the clinical parameters between the POR and control groups, and performed a multivariate analysis to determine the independent factors associated with ovarian response. Receiver-operator characteristic (ROC) was used to analyze the predicted values of individual and combined risk factors. The predicted values were further tested in another cohort of 957 patients. Age, basal follicle-stimulating hormone (bFSH), antral follicle count (AFC), and FSH/luteinizing hormone (LH) ratio were identified as independent factors associated with ovarian response. The EWSM was established using a combination of these parameters. The sensitivity and specificity of the EWSM were 74.6% and 93.6%, respectively. In conclusion, combination of individual risk factors could predict POR with high specificity. The EWSM may help in the evaluation of IVF treatment at an early stage.
Escaping unintended collusion in MBA programmes in China

The purpose of this article is to examine the problem of possible but unintended collusion between business schools and their Master of Business Administration (MBA) students, specifically as it relates to the recent need to promote ethical behaviour in business practice in a global context. The focal point of the article is on the relationship between MBA programmes and candidates in the context of guanxi in modern business and political environments. The article revisits the concept of guanxi philosophically and connects it to social responsibility and moral obligation in business education. The authors contend that guanxi may have been interpreted too loosely as networking, thus fostering an approach that ignores the important moral dimensions of the concept. The more philosophical approach, which includes such concepts as moral obligation, is recommended to safeguard the integrity of recruiting, student–teacher development, and the coursework of MBA programmes in the People’s Republic of China. In considering the practical implications, the article covers the re-examination of guanxi as a moral concept, the judicious application of caution when considering applicants based on their work experience, the use of free and independent academic judgment when questionable decisions and behaviours occur, and the open discussion of ethical decision-making in course activities.
Axonal transport of neurotrophins by visceral afferent and efferent neurons of the vagus nerve of the rat

The receptor‐mediated axonal transport of [125I]‐labeled neurotrophins by afferent and efferent neurons of the vagus nerve was determined to predict the responsiveness of these neurons to neurotrophins in vivo. [125I]‐labeled neurotrophins were administered to the proximal stump of the transected cervical vagus nerve of adult rats. Vagal afferent neurons retrogradely transported [125I]neurotrophin‐3 (NT‐3), [125I]nerve growth factor (NGF), and [125I]neurotrophin‐4 (NT‐4) to perikarya in the ipsilateral nodose ganglion, and transganglionically transported [125I]NT‐3, [125I]NGF, and [125I]NT‐4 to the central terminal field, the nucleus tractus solitarius (NTS). Vagal afferent neurons showed minimal accumulation of [125I]brain‐derived neurotrophic factor (BDNF). In contrast, efferent (parasympathetic and motor) neurons located in the dorsal motor nucleus of the vagus and nucleus ambiguus retrogradely transported [125I]BDNF, [125I]NT‐3, and [125I]NT‐4, but not [125I]NGF.
Advertising and Consumer Welfare

Controversy has surrounded the welfare effects of advertising, mainly Concerning consumer welfare effects. Unfortunately, the measures of consumer Welfare effects in most studies have been ad hoc and incorrect. The consumer Welfare consequences of advertising can be measured consistently and accurately When consumer demand equations are derived from an expenditure function. This ls illustrated using the Almost Ideal Demand System, which is popular in econometric estimation of food demand systems. An empirical application uses data on Australian meat consumption to evaluate generic advertising of meats. The results from using a theoretically correct money-metric measure of consumer Welfare effects, taking account of cross-cotnmodity effects of advertising and price Changes, are compared with ad hoc approaches previous studies have proposed. In addition, the consumer welfare measures are combined with measures of Producer benefits in order to compute private and social returns.
Nerve growth factor activates the RARβ2 promoter by a Ras‐dependent mechanism

Nerve growth factor (NGF) and retinoic acid (RA) exert important actions on PC12 cells. We have previously shown that incubation with NGF induces retinoic acid receptor β (RARβ) binding to a hormone response element in PC12 cells. In this study we show that NGF increases RARβ protein levels by enhancing basal RARβ2 promoter activity, and potentiates stimulation by RA in transient transfection assays. The effect of RA is mediated by a RA response element (RARE) located at −37/−53 and mutation of this element abolishes activation by the retinoid, as well as cooperation with NGF. However, the action of NGF is independent of the RARE and is mediated by sequences overlapping the TATA box and the INR comprising nucleotides −59 to +14. NGF produces a strong decrease in some of the complexes that bind to the INR. These results suggest that the RARβ2 gene could be in a basal repressed state and NGF could increase RARβ2 transcription by inducing the release of some inhibitory factors from the INR. Functional Ras is required for RARβ2 promoter activation by NGF because expression of oncogenic Ras increases promoter activity and a dominant inhibitory Ras mutant blocks the effect of NGF. Oncogenic Raf also mimics the effect of NGF on the promoter. Other ligands of tyrosine kinase receptors that stimulate Ras also cause RARβ2 promoter activation and act cooperatively with RA. These results indicate the existence of cross‐coupling of the Ras–Raf signal transduction pathway with retinoid receptor pathways which could increase sensitivity to RA and be important for PC12 cell function.
Cognitive evoked potential (P300): a metric for cerebral concussion

ABSTRACT‐ Cognitive impairment has been reported to occur in minor head injury (concussion). The value of the P300 evoked potential as a measure of cerebral concussion was studied in 20 patients with minor head injury and compared with the data from 20 normal subjects. Significant abnormalities of the P300 latency and amplitude were noted in these patients in the post‐concussion period. The abnormalities improved completely on repeat testing. The correlation of the P300 to other parameters of head injury is discussed. The P300 constitutes a simple laboratory test that is a sensitive measure of cerebral dysfunction in concussive head injuries.