Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data

Abstract Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the de novo assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided de novo assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs. In this study, we evaluated 10 long-read assemblers using a variety of metrics on Pacific Biosciences (PacBio) data sets from different taxonomic categories with considerable differences in genome size. The results allowed us to narrow down the list to a few assemblers that can be effectively applied to eukaryotic assembly projects. Moreover, we highlight how best to use limited genomic resources for effectively evaluating the genome assemblies of non-model organisms.
Frequency of Helicobacter pylori infection in dyspeptic patients in Libya.

OBJECTIVE Helicobacter pylori infection is a very common infection worldwide particularly in the developing countries. The organism plays an important role in peptic ulcer diseases. The aim of the study was to detect and correlate the prevalence of Helicobacter pylori with such diseases and to evaluate the histopathological grading of gastritis. METHODS One hundred thirty two patients of 15-83 years of age (average 38) attending the endoscopy unit at the El-Jamahiria Hospital, Binghazi, Libya, mainly complaining from epigastric pain were randomly selected. Three antral biopsies for rapid urease test, direct smear stain and histology together with serum samples were obtained from each patient. Grading of gastritis and the presence of Helicobacter pylori was scored according to the Sydney system. RESULTS Patients were considered infected when 2 of the biopsy-based tests were positive. Helicobacter pylori was detected in 108 (82%) of 132 patients examined (86% by rapid urease test, 77% by direct smear stain, 95% by histology). The endoscopic findings revealed that 77 (77%) of 100 patients with non-ulcer dyspepsia, 26 (96%) of 27 with duodenal ulcer, 4 (100%) of 4 with gastric ulcer and in one patient with gastric cancer were Helicobacter pylori positive. The enzyme-linked immunosorbent assay test showed 94% sensitivity and 88% specificity. Histopathological sections from the majority of duodenal ulcer and gastric ulcer patients revealed higher grade (II and III) of gastritis than non-ulcer dyspepsia patients. CONCLUSION Helicobacter pylori infection is significantly correlated with peptic ulcer diseases than with non-ulcer dyspepsia. Patients with duodenal ulcer and gastric ulcer had a significantly higher grade of gastritis than patients with non-ulcer dyspepsia.
Adverse Life Experience and Psychological Distress in Adolescence: Moderating and Mediating Effects of Emotion Regulation and Rumination.

The current study tested whether emotion regulation and rumination moderated and/or mediated the relationship between accumulated adverse life experience and psychological distress in adolescence. In class, Australian high school students (n = 2637, 12-18 years, 68% female) from 41 schools completed well-validated measures of adverse life experience, emotion regulation, rumination and psychological distress, and were followed up 1 year later (n = 1973, 75% retention rate). Adjusting for age, gender and baseline psychological distress, adverse life experience predicted psychological distress 1 year later. Expressive suppression and rumination were positively associated with psychological distress. Cognitive reappraisal was negatively associated with psychological distress and moderated the relationship between adverse life experience and psychological distress. This relationship was also partially mediated by cognitive reappraisal, expressive suppression and rumination. Promoting cognitive reappraisal and minimizing expressive suppression and rumination may be useful strategies to improve mental health for adolescents who have experienced adverse life events. Future research should examine whether adolescents who have experienced adverse life events can be trained in effective emotion regulation strategies and whether this training can prevent development of psychological maladjustment. Copyright © 2015 John Wiley & Sons, Ltd.
Transcription of hepatitis B virus by RNA polymerase II

We employed an in vitro cell-free transcription system to locate RNA polymerase II promoters on the hepatitis B virus genome. The strongest promoter precedes the surface antigen (HBsAg) gene, which is comprised of a long (500 base pairs) presurface region as well as the mature HBsAg coding sequence. The origin of this transcript was localized by using truncated templates and S1 endonuclease mapping. The activity of the promoter was confirmed in transfection experiments in which the complete HBsAg gene was introduced into monkey kidney cells via a simian virus 40 expression vector. A second RNA polymerase II promoter preceding the HBcAg gene was also active in the cell-free system. The presence of multiple promoters in the hepatitis B virus genome suggests that the relative levels of viral-specific proteins detected in liver and serum may reflect differential or regulated promoter efficiency.
Environmental Disclosure of Chemical Industry:Evidence from Chinese A-share Market

Environmental pollution and environmental information disclosure have increasingly drawn the attention of the countries around the world.The article selects A-share listed companies of chemical industry in China.Using Logistic model,we research the impact of financial performance of listed companies upon environmental reporting.The conclusion of the study shows that the total number of enterprises which disclosed environmental information has increased year by year,and environmental information content and volume which heavy pollution corporations disclosed have increased annually.And the more profitability the listed companies attain,the more environmental information they incline to disclose.Moreover,companies will have ability to disclose environmental information so as to reduce the agency costs arising from information asymmetry.Furthermore,the development capacity of companies is negative correlation to environmental reporting,and the liabilities degree of listed companies is negative correlation to environmental information disclosure,but it is not significant.This article also offers policy recommendations that enhance environmental information transparency and regulate environmental information reporting of listed companies.
Rab13-dependent Trafficking of RhoA Is Required for Directional Migration and Angiogenesis*

Angiogenesis requires concomitant remodeling of cell junctions and migration, as exemplified by recent observations of extensive endothelial cell movement along growing blood vessels. We report that a protein complex that regulates cell junctions is required for VEGF-driven directional migration and for angiogenesis in vivo. The complex consists of RhoA and Syx, a RhoA guanine exchange factor cross-linked by the Crumbs polarity protein Mupp1 to angiomotin, a phosphatidylinositol-binding protein. The Syx-associated complex translocates to the leading edge of migrating cells by membrane trafficking that requires the tight junction recycling GTPase Rab13. In turn, Rab13 associates with Grb2, targeting Syx and RhoA to Tyr1175-phosphorylated VEGFR2 at the leading edge. Rab13 knockdown in zebrafish impeded sprouting of intersegmental vessels and diminished the directionality of their tip cells. These results indicate that endothelial cell mobility in sprouting vessels is facilitated by shuttling the same protein complex from disassembling junctions to the leading edges of cells.
Man-to-woman sexual transmission of HIV: longitudinal study of 343 steady partners of infected men.

To study incidence and risk factors of heterosexually transmitted HIV infection, we followed a cohort of 343 seronegative women, stable, monogamous partners of infected men whose only risk of acquiring HIV was sexual exposure to the infected partner. Nineteen seroconversions occurred in 529.6 person years (py) of observation, yielding an incidence rate of 3.6 per 100 py. The incidence rate was 7.2 per 100 py among women who did not always use or never used condoms and 1.1 among those who always used them [relative risk (RR) 6.6, 95% confidence interval (CI) 1.9-21.9]. Anal sex was associated with a risk increase in only those women not always using condoms (RR 1.4, 95% CI 0.4-4.8). No seroconversions were observed among 22 women using oral contraceptives. One of the women using intrauterine devices seroconverted. In couples who did not always use condoms, seroconversions occurred more frequently in partners of men with symptomatic diseases, with a low CD4+ cell number (< 400 per mm3) or with a detectable p24 antigen. In couples not always using condoms and where the man had a low CD4+ cell count, the joint presence of blood viral antigens and AIDS symptoms conditioned a fivefold increased risk of seroconversion of the woman (RR 5.4, CI 1.4-20.3). At multivariate analysis, women with longer relationships (> or = 1 year) showed a lower risk of seroconversion (RR 0.3, CI 0.1-0.8), and those partners of men positive for p24 antigen in serum had an increased risk of seroconversion (RR = 4.0, CI 0.1-0.8).
Microglia dysfunction in schizophrenia: an integrative theory.

Schizophrenia is a devastating illness of unknown etiology. It is characterized by increased brain ventricular volume, suggesting a progressive neurodevelopmental condition. There is evidence suggesting a correlation between in utero viral exposure and subsequent occurrence of schizophrenia. Many neurotransmitter systems have been implicated as being dysfunctional in schizophrenia. There are also data suggesting immune system dysfunction in schizophrenia, and a negative correlation between schizophrenia and rheumatoid arthritis. Microglia are phagocytic immune cells in the central nervous system (CNS) derived from peripheral blood monocytes. They are involved in brain development, neuroproliferative and neurodegenerative activities, several CNS illnesses, and CNS viral immunity. They may also be involved in neurotransmitter regulation. The current theory postulates microglial dysfunction initiated by early CNS viral exposure results in the abnormal neural development and neurotransmitter dysfunction seen in schizophrenia.
Privatizing or Socializing Corporate Responsibility

This article explores why companies choose some Corporate Responsibility initiatives over others. The focus is on competing voluntary programs to oversee and protect labor standards. These programs may differ with regard to two aspects: the governance of the program and the financial and managerial responsibility for compliance. These aspects are crucial to distinguish “socializing” or “privatizing” types of voluntary labor regulation. The article explores the conditions under which companies in apparel production choose different types of governance and responsibility, based on qualitative and quantitative evidence of the European industry. The study shows that corporate preference for multi-stakeholder governed programs is positively affected by societal pressure orchestrated by NGOs, through both public campaigns and informal efforts, together with pressures from consumers and media. Second, the position of the firm in the value chain affects preference for taking financial and managerial responsibility for compliance.
An Analysis of the Financial Performance of Selected Savings and Credit Co-Operative Societies in Botswana

The co-operative sector plays an important role in a country’s socio-economic development. This paper evaluated the financial performance of 9 selected Savings and Credit Co-operative Societies (SACCOSs) in Botswana by analysing audited financial statements of a five-year period from 2008 to 2012. The analytical techniques used include descriptive statistics of financial aggregates and ratios, correlation, regression and common size analyses. The financial aggregates analysed included all items that impact income generation as well as items that represent the financial position of the selected societies. The findings underscored that the selected SACCOSs achieved good financial results and were in strong financial position. The results also indicated a significant relationship between Net Profit ratio and Capital Employed Ratio to inform that the Net Profit Ratio was the most important explainer of Return on Capital Employed. The 5 year common size analysis also revealed a growth in income and in the financial status of the selected societies. The capital structure of these societies was characterised by substantial share of internal funds. Conclusively, maintaining an optimal balance between the interest on loans and interest on members’ savings, and investing extra cash in diversified portfolio to reduce the risk levels would make the SACCOSs grow and function more productively and profitably. They would also then succeed in attracting more members and thereby significantly contribute towards poverty reduction and economic diversification drives in the country.
Subband image coding using entropy-coded quantization over noisy channels

The design and performance of two entropy-coded subband image coding schemes are studied. The difference between these schemes is the procedure used for encoding the lowest-frequency subband; predictive coding is used in one system and transform coding in the other. Other subbands are encoded using zero-memory quantization. It is shown that, in the absence of channel noise, both schemes perform better than other subband coding methods. The unacceptable sensitivity of these schemes to transmission noise is demonstrated, and a combined source/channel coding scheme in which rate-compatible punctured convolutional codes are used to provide protection against channel noise is developed. In the presence of channel noise, these channel-optimized schemes offer dramatic performance improvements over schemes designed based on a noiseless-channel assumption. <<ETX>>
Identification of adverse events occurring during hospitalization. A cross-sectional study of litigation, quality assurance, and medical records at two teaching hospitals.

STUDY OBJECTIVES To estimate the efficacy of a medical record review for identifying adverse events and negligent case suffered by hospitalized patients. DESIGN Cross-sectional study comparing an objective medical record review with information available from hospital quality assurance records as well as risk management and litigation records. SETTING Two metropolitan teaching hospitals in the northeastern United States. MEASUREMENTS AND MAIN RESULTS Using the litigation and risk management records as a criterion standard, we found that the medical record review had a sensitivity of 80% (93 of 116; 95% CI, 73% to 88%) for discovering adverse events and a sensitivity of 76% (51 of 67; 95% CI, 66% to 86%) for discovering negligent care. We estimated that record review of a random sample of hospitalizations across a geographic region would have even higher sensitivity (adverse-event sensitivity, 84%; negligence sensitivity, 80%). Moreover, we found that the adverse events we failed to discover led to less costly malpractice claims. A significant number of adverse events (20 of 172) among hospitalizations never gave rise to litigation or risk management investigation. Six of the twenty were due to negligent care. Quality assurance efforts at the level of the clinical departments in one hospital led to review of only 12 out of 82 risk management records. CONCLUSIONS The overwhelming majority of adverse events and episodes of negligent care are discoverable with the methods we used to evaluate medical records. Quality assurance efforts using similar record review methods should be further evaluated.
Impact of reduction in working hours for doctors in training on postgraduate medical education and patients’ outcomes: systematic review

Objectives To determine whether a reduction in working hours of doctors in postgraduate medical training has had an effect on objective measures of medical education and clinical outcome. Design Systematic review. Data sources Medline, Embase, ISI Web of Science, Google Scholar, ERIC, and SIGLE were searched without language restriction for articles published between 1990 and December 2010. Reference lists and citations of selected articles. Study selection Studies that assessed the impact of a change in duty hours using any objective measure of outcome related to postgraduate medical training, patient safety, or clinical outcome. Any study design was eligible for inclusion. Results 72 studies were eligible for inclusion: 38 reporting training outcomes, 31 reporting outcomes in patients, and three reporting both. A reduction in working hours from greater than 80 hours a week (in accordance with US recommendations) does not seem to have adversely affected patient safety and has had limited effect on postgraduate training. Reports on the impact of European legislation limiting working hours to less than 56 or 48 a week are of poor quality and have conflicting results, meaning that firm conclusions cannot be made. Conclusions Reducing working hours to less than 80 a week has not adversely affected outcomes in patient or postgraduate training in the US. The impact of reducing hours to less than 56 or 48 a week in the UK has not yet been sufficiently evaluated in high quality studies. Further work is required, particularly in the European Union, using large multicentre evaluations of the impact of duty hours’ legislation on objective educational and clinical outcomes.
Partial regeneration and long‐term survival of rat retinal ganglion cells after optic nerve crush is accompanied by altered expression, phosphorylation and distribution of cytoskeletal proteins

In a screen to identify genes that are expressed differentially in the retina after partial optic nerve crush, we identified MAP1B as an up‐regulated transcript. Western blot analysis of inner retina protein preparations confirmed changes in the protein composition of the microtubule‐associated cytoskeleton of crushed vs. uncrushed nerve. MAP1B immunoreactivity and transcript levels were elevated for two weeks after crush. Immunostaining and Western blots with monoclonal antibodies directed against developmentally regulated phosphorylation sites on MAP1B revealed a gradient of MAP1B phosphorylation from the proximal optic nerve stump to the soma of retinal ganglion cells. Most interestingly, using antibodies directed against developmentally regulated phosphorylation sites on MAP1B, we observed that a significant number of crushed optic nerve axons develop MAP1B‐immunopositive growth cones, which cross the crush site and migrate along the distal nerve fragment. In parallel, an abnormal distribution of highly phosphorylated neurofilament protein (pNF‐H) in the cell soma and dendrites of presumably axotomized retinal ganglion cells was observed following partial nerve crush. This redistribution is present for the period between day 7 and 28 postcrush and is not seen in cells that stay connected to the superior colliculus. Axotomized ganglion cells, which contain pNF‐H in soma and dendrites appear to have been disconnected from the colliculus at an early stage but survive axonal trauma for long periods.
Intentional Topiramate Ingestion in an Adolescent Female

OBJECTIVE: To describe an intentional topiramate ingestion by an adolescent and warn of the potential for topiramate abuse. CASE SUMMARY: A 17-year-old female intentionally ingested approximately eight 100-mg topiramate tablets for the purpose of “getting high. ” Soon after ingestion, she was found at school obtunded and nonresponsive. Upon transfer to the emergency department, she became combative and aggressive with evolving neurologic abnormalities including incoherence, confusion, disorientation, and significant speech impairments including echolalia. Approximately 24 hours after ingestion, the patient had completely recovered without requiring specific treatment or experiencing sequelae. DISCUSSION: The clinical effects following acute topiramate intoxication appear consistent with the drug's known pharmacologic properties. There are few other reports of topiramate ingestions and most cases have had mild outcomes. CONCLUSIONS: Due to the multifactorial effects topiramate may have upon the central nervous system and its anorectic effect, abuse of this drug by adolescents should be considered upon presentation of an adolescent with mental status changes.
Effects of lupin kernel flour-enriched bread on blood pressure: a controlled intervention study.

BACKGROUND Available data suggest that substitution of refined carbohydrate in the diet with protein and fiber may benefit blood pressure. Lupin kernel flour is high in protein and fiber and low in carbohydrate. OBJECTIVE Our objective was to determine the effects on blood pressure of a diet moderately higher in dietary protein and fiber achieved by substituting lupin kernel flour for wheat flour in bread. DESIGN Overweight and obese men and women (n = 88) were recruited to a 16-wk parallel-design study. Participants were randomly assigned to replace 15-20% of their usual daily energy intake with white bread (control) or lupin kernel flour-enriched bread (lupin). Measurements, including 24-h ambulatory blood pressure, were taken at baseline and 16 wk. RESULTS Seventy-four participants (37 per group) completed the intervention. Baseline mean (+/-SD) systolic/diastolic blood pressures were 122.1 +/- 9.6/70.8 +/- 7.2 mm Hg (control) and 120.1 +/- 9.5/71.2 +/- 5.9 mm Hg (lupin). For lupin relative to control, the estimated mean (95% CI) net differences in protein, fiber, and carbohydrate intakes during the intervention were 13.7 g/d (95% CI: 2.3, 25.0 g/d), 12.5 g/d (95% CI: 8.8, 16.2 g/d), and -19.9 g/d (95% CI: -45.2, 5.5 g/d), respectively. Differences in systolic blood pressure, diastolic blood pressure, pulse pressure, and heart rate were -3.0 mm Hg (95% CI: -5.6, -0.3 mm Hg; P = 0.03), 0.6 mm Hg (95% CI: -1.0, 2.2 mm Hg; P = 0.47), -3.5 mm Hg (95% CI: -5.3, -1.8 mm Hg; P < 0.001), and 0.0 beats/min (95% CI: -1.7, 1.7 beats/min; P = 0.99), respectively. CONCLUSIONS Increasing protein and fiber in bread with lupin kernel flour may be a simple dietary approach to help reduce blood pressure and cardiovascular risk. This trial was registered at the Australian New Zealand Clinical Trials Registry at http://www.anzctr. org.au/trial_view. aspx? ID=1014 as ACTRN12606000034538 on 25 January 2006.