Miracle-dz/UniFAR-FTUs huggingface dataset:
Observer bias in randomised clinical trials with binary outcomes: systematic review of trials with both blinded and non-blinded outcome assessors

Objective To evaluate the impact of non-blinded outcome assessment on estimated treatment effects in randomised clinical trials with binary outcomes. Design Systematic review of trials with both blinded and non-blinded assessment of the same binary outcome. For each trial we calculated the ratio of the odds ratios—the odds ratio from non-blinded assessments relative to the corresponding odds ratio from blinded assessments. A ratio of odds ratios <1 indicated that non-blinded assessors generated more optimistic effect estimates than blinded assessors. We pooled the individual ratios of odds ratios with inverse variance random effects meta-analysis and explored reasons for variation in ratios of odds ratios with meta-regression. We also analysed rates of agreement between blinded and non-blinded assessors and calculated the number of patients needed to be reclassified to neutralise any bias. Data Sources PubMed, Embase, PsycINFO, CINAHL, Cochrane Central Register of Controlled Trials, HighWire Press, and Google Scholar. Eligibility criteria for selecting studies Randomised clinical trials with blinded and non-blinded assessment of the same binary outcome. Results We included 21 trials in the main analysis (with 4391 patients); eight trials provided individual patient data. Outcomes in most trials were subjective—for example, qualitative assessment of the patient’s function. The ratio of the odds ratios ranged from 0.02 to 14.4. The pooled ratio of odds ratios was 0.64 (95% confidence interval 0.43 to 0.96), indicating an average exaggeration of the non-blinded odds ratio by 36%. We found no significant association between low ratios of odds ratios and scores for outcome subjectivity (P=0.27); non-blinded assessor’s overall involvement in the trial (P=0.60); or outcome vulnerability to non-blinded patients (P=0.52). Blinded and non-blinded assessors agreed in a median of 78% of assessments (interquartile range 64-90%) in the 12 trials with available data. The exaggeration of treatment effects associated with non-blinded assessors was induced by the misclassification of a median of 3% of the assessed patients per trial (1-7%). Conclusions On average, non-blinded assessors of subjective binary outcomes generated substantially biased effect estimates in randomised clinical trials, exaggerating odds ratios by 36%. This bias was compatible with a high rate of agreement between blinded and non-blinded outcome assessors and driven by the misclassification of few patients.
Vascular complications following coronary intervention correlate with long‐term cardiac events

We aimed to study the consequences and late outcomes of patients who experienced peripheral vascular complications (PVCs) following percutaneous coronary interventions (PCI). A retrospective analysis of the medical records of 10,669 patients who underwent PCI and experienced PVC between 1995 and 2002 was conducted. One thousand ninety‐six patients (10.27% of the study cohort) had PVC post‐PCI. After PCI, patients with PVC had higher rates of in‐hospital complications (P < 0.001) when compared to patients without PVC, including Q‐wave myocardial infarction (MI; 1.2% vs. 0.3%), coronary artery bypass grafting (CABG; 3.8% vs. 0.6%), and death (4.0% vs. 1.0%). At 1‐year follow‐up, late complications of MI (37.4% vs. 25.4%), non‐Q‐wave MI (34.9% vs. 22.7%), death (12.9% vs. 5.9%), and CABG (5.7% vs. 4.5%) were higher (< 0.001) in patients with PVC compared to those without. Multivariate analysis identified PVC as a significant predictor of 1‐year mortality (P = 0.045). This study underscores the need to make diligent efforts to minimize PVC and follow up these patients for future coronary events. Cardiovasc Interv 2004;62:181–185. © 2004 Wiley‐Liss, Inc.
Adherence of Borrelia burgdorferi

Borrelia burgdorferi, the causative agent of Lyme disease, expresses on its surface two decorin binding adhesins, DbpA and DbpB. Previous studies have demonstrated that vaccination of mice with DbpA provided protection against challenge with heterologous Borrelia strains despite considerable sequence variability among DbpA in these strains. We have now examined the importance of individual amino acid residues in DbpA for decorin binding. We demonstrated that chemical modification of lysine residues resulted in loss of ligand binding activity. Of the 27 lysine residues in native DbpA from strain 297, 6 are present in most and 5 are conserved in all 30 DbpA sequences examined so far. Analysis of recombinant DbpA in which individual lysine residues have been mutated to alanine suggested that three of the conserved residues distributed throughout the DbpA sequence are required for decorin binding. These mutants lost their ability to bind decorin in Western ligand blot assay and bound reduced amounts of decorin in an ELISA. Furthermore, these mutant DbpA proteins did not inhibit the adherence of B. burgdorferi to a decorin substrata, and they did not recognize decorin in an extracellular matrix established by human fibroblast cultures. We conclude that the three lysine residues Lys-82, Lys-163, and Lys-170 are crucial for the binding of DbpA to decorin.
Increased dietary iron and radiation in rats promote oxidative stress, induce localized and systemic immune system responses, and alter colon mucosal environment

Astronauts are exposed to increased body iron stores and radiation, both of which can cause oxidative damage leading to negative health effects. The purpose of this study was to investigate combined effects of high dietary iron (650 mg/kg diet) and radiation exposure (0.375 Gy cesium‐137 every other day for 16 d) on markers of oxidative stress, immune system function, and colon mucosal environment in male Sprague‐Dawley rats (n=8/group). Control rats consumed adequate iron (45 mg/kg diet) and were not irradiated. Combined treatments increased liver glutathione peroxidase, serum catalase, and colon myeloperoxidase while decreasing total fecal short‐chain fatty acid concentrations. The high‐iron diet alone increased leukocyte count. Radiation decreased the T‐cell CD4: CD8 ratio. Plasma iron was negatively correlated with cytokine production in activated monocytes. Genes involved in colon microbial signaling, immune response, and injury repair were altered by radiation. Genes involved with injury repair and pathogen recognition changed with dietary iron. These data demonstrate that dietary iron and radiation, alone and combined, contribute to oxidative stress that is related to immune system alterations in circulation and the colon. The model presented may help us better understand the changes to these systems that have been identified among astronauts. —Morgan, J. L. L. , Ritchie, L. E. , Crucian, B. E. , Theriot, C. , Wu, H. , Sams, C. , Smith, S. M. , Turner, N. D. , Zwart, S. R. Increased dietary iron and radiation in rats promote oxidative stress, induce localized and systemic immune system responses, and alter colon mucosal environment. FASEB J. 28, 1486–1498 (2014). www.fasebj. org
Long-Term Growth Scenarios for Bangladesh

Bangladesh has achieved robust economic growth over the past 10 years, with real GDP growing by more than 6 percent on average each year. This paper investigates whether the country will be able to maintain such high levels of growth going forward. A simple growth model calibrated to the Bangladesh economy is used to analyze various growth scenarios. The main finding of the paper is that it is crucial for the country to focus on reforms to raise total factor productivity (TFP) growth, to sustain the high real GDP growth seen in the recent past. The country will fail to achieve high growth in absence of strong TFP growth despite meeting the levels of investment as outlined in the Seventh Five Year Plan. The model is also used to gain insights on government debt sustainability given different growth scenarios. The analysis highlights the significance of meeting revenue targets in maintaining sustainability, considering the planned expansion in expenditures.
Design considerations for association studies of candidate genes in families

In genetic epidemiologic studies, investigators often use generalized linear models to evaluate the relationships between a disease trait and covariates, such as one or more candidate genes or an environmental exposure. Recently, attention has turned to study designs that mandate the inclusion of family members in addition to a proband. Standard models for analysis assume independent observations, which is unlikely to be true for family data, and the usual standard errors for the regression parameter estimates may be too large or too small, depending on the distribution of the covariates within and between families. The consequences of familial correlation on the study efficiency can be measured by a design effect that is equivalent to the relative information in a sample of unrelated individuals compared to a sample of families with the same number of individuals. We examine design effects for studies in association, and illustrate how the design effect is influenced by the intra‐familial distribution of covariate values such as would be expected for a candidate gene. Typical design effects for a candidate gene range between 1.1 and 2.4, depending on the size of the family and the amount of unexplained familial correlation. These values correspond to a modest 10% increase in the required sample size up to more than doubling the requirements. Design effect values are useful in study design to compare the efficiency of studies that sample families versus independent individuals and to determine sample size requirements that account for familial correlation. Genet. Epidemiol. 20:149–174, 2001. © 2001 Wiley‐Liss, Inc.
The Cytomegalovirus-Encoded Chemokine Receptor US28 Can Enhance Cell-Cell Fusion Mediated by Different Viral Proteins

ABSTRACT The human cytomegalovirus (CMV) US28 gene encodes a functional CC chemokine receptor. However, this activity was observed in cells transfected to express US28 and might not correspond to the actual role of the protein in the CMV life cycle. Expression of US28 allows human immunodeficiency virus type 1 (HIV-1) entry into certain CD4+ cells and their fusion with cells expressing HIV-1 envelope (Env) proteins. Such properties were initially reported for the cellular chemokine receptors CCR5 and CXCR4, which behave as CD4-associated HIV-1 coreceptors. We found that coexpression of US28 and either CXCR4 or CCR5 in CD4+ cells resulted in enhanced synctium formation with HIV-1 Env+ cells. This positive effect of US28 on cell fusion seems to be distinct from its HIV-1 coreceptor activity. Indeed, enhancement of cell fusion was also observed when US28 was expressed on the HIV-1 Env+ cells instead of an CD4+ target cells. Furthermore, US28 could enhance cell fusion mediated by other viral proteins, in particular, the G protein of vesicular stomatitis virus (VSV-G). The HIV-1 coreceptor and fusion-enhancing activities could be affected by mutations in different domains of US28. The fusion-enhancing activity of US28 seems to be cell type dependent. Indeed, cells coexpressing VSV-G and US28 fused more efficiently with human, simian, or feline target cells, while US28 had no apparent effect on fusion with the three mouse or rat cell lines tested. The positive effect of US28 on cell fusion might therefore require its interaction with a cell-specific factor. We discuss a possible role for US28 in the fusion of the CMV envelope with target cells and CMV entry.
NOLLYWOOD AS A TOOL FOR RE-SHAPING NIGERIAN IMAGE AND DIPLOMACY

Nollywood has grown so strong in recent times to command both local and international audiences and also has the capacity to provide a platform for the positive promotion and projection of her image and values in the international community thereby influencing relationships among them. The study examines if nollywood can be used to re-shape and rebrand the image of Nigeria as well as help in boasting the relationships between her and the international community. Samples of 200 respondents were selected from Awka metropolis through non-probability sampling. The study found out that residents of Awka watch home movies and are of the view that the films can serve as an instrument for influencing the populace and determining the country’s relationship with the outside world. They also believe in the image of Nigeria as portrayed by these movies which can have negative effects to Nigeria’s image and diplomacy. The study therefore, recommends that movie makers and regulators should live up to their callings and generate positive themes that can be used to re-shape and rebrand Nigeria.
Impaired Expression of Glycogen Synthase mRNA in Skeletal Muscle of NIDDM Patients

Based on recent studies of the abnormal physiology and biochemistry of the glycogen synthesis in skeletal muscle of non-insulin-dependent diabetes mellitus (NIDDM) patients and their first-degree relatives, the key enzyme of this pathway, glycogen synthase (GS), is considered a candidate gene in the pathogenesis of insulin resistance. Comparing matched groups of 14 NIDDM patients with 14 control subjects, we found that impaired insulin-stimulated nonoxidative glucose metabolism of peripheral tissue (P < 0.02) and reduced total GS activity (P < 0.05) of vastus lateralis muscle from patients with NIDDM were accompanied by a 39% reduction (P < 0.02) in the steady state level of GS mRNA per microgram DNA of muscle. In both diabetic and control subjects, the mRNA expression of GS was unaffected after euglycemic-hyperinsulinemic clamp for 4 h. With single-stranded conformation polymorphism analysis of the entire coding sequence of the GS gene, we were unable to detect any genetic variants in a subset of eight NIDDM patients. We conclude that abnormal pretranslational regulation of the GS gene may contribute to impaired glycogen synthesis of muscle in NIDDM. Our studies give no evidence for structural changes in the coding region of the GS gene, and it is unknown if the decreased mRNA expression is due to impaired transcription or accelerated degradation of the transcript.
Optimization of Plasmid Maintenance in the Attenuated Live Vector Vaccine Strain Salmonella typhiCVD 908-htrA

ABSTRACT The broad objective of the research presented here is to develop a noncatalytic plasmid maintenance system for the stabilization of multicopy expression plasmids encoding foreign antigens in aSalmonella typhi live-vector vaccine strain such as CVD 908-htrA. We have enhanced the maintenance of expression plasmids at two independent levels. First, we removed dependence upon balanced-lethal maintenance systems that involve catalytic enzymes expressed from multicopy plasmids; we accomplished this through incorporation into expression plasmids of a postsegregational killing system based on the noncatalytic hok-sok plasmid addiction system from the antibiotic resistance factor pR1. We also included at least one naturally occurring plasmid partition function in our expression plasmids, which eliminates random segregation of these plasmids, thereby enhancing their inheritance and stability; to accomplish this, we incorporated either the par locus from pSC101, the parA locus from pR1, or both. We monitored the stability of optimized expression plasmids within CVD 908-htrA by quantitating expression of a variant of green fluorescent protein (GFPuv) by using flow cytometry. In this report, we demonstrate the utility of this novel plasmid maintenance system in enhancing the stability of our expression plasmids and go on to show that as the copy number of stabilized plasmids increases, the toxicity of GFPuv synthesis also increases. The implications of these observations for the rational design of immunogenic and protective bacterial live vector vaccines are discussed.
Benthic microbial metabolism in seagrass meadows along a carbonate gradient in Sulawesi, Indonesia

: Sediment carbon and nitrogen cycling were examined in tropical seagrass meadows across a gradient of increasing carbonate content during wet and dry seasons in Awerange Bay, Sulawesi, Indonesia. Coincident with an increase in seagrass and microalgal productivity, increases in rates of sulfate reduction, ammonification, O 2 consumption, nitrogen fixation, CH 4 release, carbonate dissolution, and pore water concentrations and fluxes of H 2 S were observed across the gradient. These increases occurred despite a decline in particulate nutrient and dissolved iron concentrations in the sediment. Sulfate reduction appeared to be the dominant decomposition pathway, with rates ranging from 27-68 mmol S m -2 d -1 inshore to 53-98 mmol S m -2 d -1 in the outer bay. Rapid rates of carbon oxidation were matched by rapid rates of N transformation, with ratios of C and N mineralization rates close to the sediment C:N ratio. Denitrification (range: 1022 to 1897 μmol N m -2 d -1 ) equated to -25% of ammonification, with the proportion decreasing from 19-53% inshore to 0.5-17% offshore. The patterns of increase in C and N cycling were attributed to greater water clarity along the gradient, allowing greater light levels to foster higher rates of seagrass productivity and, in turn, increased rates of mineralization and carbonate dissolution.
The Linkage between the Degree of Compliance with Corporate Governance Rules and Profitability: Evidence from Palestine Exchange Listed Firms

The underlying objective of this study is to empirically investigate the relationship between the degree of compliance with the rules of the code of Corporate Governance (CG) that became effective in 2009 and profitability of Palestine Exchange Listed firms. Compliance with CG rules is measured based on a criteria of ten corporate governance indicators identified in the study of Abdelkarim and Ijbarah (2010), while profitability is measured by the percentage of change in ROI reported in year 2008 and its average over the period 2009-2015. The Use of ROI as a dependent variable in this study is based on the theoretical assumption that CG should have positive impact on efficiency in terms of cost management and increase in sales due to increase in market share. Prior research in developed economies reported a significant impact of corporate governance on firm performance particularly if measured as a change in market value. However, in Palestine there was only one study that investigated the relationship between corporate governance measured as the level of ownership concentration and firm’s performance measured using Tobin’s Q (Abdelkarim and Alawneh, 2005). Using regression analysis, this study provides empirical evidence that there is no statistically significant relationship between the degree of compliance with the rules in the code of corporate governance and profitability of sample firms. Explanations for this key finding are provided in this study.
Knowledge Management in Process Improvement and Best Practices Sharing

Software process improvement involves complex decision-making activities and requires supporting tools to coordinate and optimize information exchange within organizations. This work presents the theoretical background for developing a framework capable of integrating decision levels in software development organizations. In addition, this framework aims to improve and coordinate information exchange among the different modeling paradigms/conventions. Semantic technologies, namely ontologies, stand for an opportunity to suggest the use of best practices based on the essentials of the enterprise such as size or process and business goals. This work relies on different standards, methodologies and models, which focus on process improvement and human resources management of processes related to software development. In this way, knowledge derived from the application of some of the most used technologies for process improvement is captured, allowing the use and reuse among different enterprises and processes and promoting transversal process-oriented management.
IMPACT OF ADOPTING IFRS STANDARD ON THE EQUITY COST OF BRAZILIAN OPEN CAPITAL COMPANIES

Purpose: This study aims to assess the impact of adopting IFRS standard on the equity cost of Brazilian open capital companies in the period of 2004-2013. Originality/gap/relevance/implications: The adoption of International Financial Reporting Standards aims to increase the quality of accounting information. Studies performed in Europe suggest that, after the adoption of the IFRS standard, there was a reduction in the equity cost of companies due to the reduction of information asymmetry and risk. Key methodological aspects: The equity cost was calculated using the capital asset pricing model (CAPM) adapted to the Brazilian case. The empirical strategy was the difference analysis in differences, comparing the results of companies that voluntarily adopted the IFRS with companies that adopted IFRS after the mandatory adoption period. Summary of key results: The results indicate that the adoption of the IFRS standard does not contribute to reduce the equity cost in Brazil. Key considerations/conclusions: Suggesting that the process of adopting the international accounting standard may take more time to impact the equity cost of Brazilian open capital companies, since the impact of IFRS is not related only with the adoption, but also with its use by companies and users.
Detecting source code plagiarism on introductory programming course assignments using a bytecode approach

Even though there are various source code plagiarism detection approaches, most of them only concern with low-level plagiarism attack with an assumption that plagiarism is only conducted by students who are not proficient in programming. However, plagiarism is often conducted not only due to student incapability, but also because of bad time management. Thus, high-level plagiarism attack should be detected and evaluated. This paper proposes source code plagiarism detection approach which can detect most introductory-programming-course plagiarism attacks at any level by utilizing low-level instructions instead of source code tokens. Several mechanisms are also introduced to improve its effectiveness such as instruction generalization, instruction reinterpretation, method-based comparison, and method linearization. Since low-level instruction is a language-dependent feature, Java is selected as target programming language with bytecode as its low-level instruction. Based on evaluation, it can be concluded that our approach is more effective to detect most plagiarism attack types than raw source code approach on introductory programming course. This evaluation is based on plagiarism attack types that are collected through controlled experiment.