Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of blood cultures in a children's hospital located in Southeastern Anatolia.

AIM Bloodstream infections in hospitalized patients are one of the most important causes of morbidity and mortality despite antimicrobial therapy. Early diagnosis and treatment of these infections is crucial. The aim of this study was to evaluate the distribution and antibiotic susceptibility of bacteria isolated from blood cultures in a children's hospital in the Southeastern Anatolia during an 18-month period. MATERIAL AND METHODS 7 040 blood cultures which were sent from hospitalized patients in Gaziantep Children's Hospital between 01.07. 2010 and 01.01. 2012 were evaluated. RESULTS A total of 7 040 blood cultures were evaluated in this study. Microbial growth was detected in 2075 (29.47%) blood cultures. The most frequently isolated bacteria were coagulase-negative staphylococci (%45.97) which were followed by Salmonella spp. (%7.8). 12.12% of enterococcal isolates were resistant to glycopeptide antibiotics. The most frequently isolated gram negative bacterium was Salmonella spp. 15.43% of Salmonella spp. showed decreased susceptibility against quinolones. The ESBL positivity rate of E. coli and K. pneumoniae strains was found to be 35.08% and 57.14%, respectively. The imipenem resistance rate of P. aeruginosa was found to be 33.33%. The most common nonfermentative bacterium was S. maltophilia. CONCLUSIONS The distribution of bacteria isolated from blood cultures and antibiotic resistance rates differ among different regions of Turkey. Different results obtained in our study may be related with regional tendencies to infections and patient population. Distribution of infectious agents and antibiotic resistance rates should be evaluated at regular intervals. This will lead to establishment of proper antibiotic usage policies in our country.
Clinical significance of hepatitis B virion and SVP productivity: relationships between intrahepatic and serum markers in chronic hepatitis B patients

Background Clinical use of hepatitis B viral (HBV) quantitative seromarker\s remains questionable since it is not precisely known whether they represent intrahepatic viral replication. Covalently closed circular DNA (cccDNA), relaxed circular DNA (rcDNA), and pregenomic RNA (pgRNA) are more likely to represent active HBV replication and their measurement can be used to derive virion productivity (VP; rcDNA/cccDNA), subviral particle (SVP) productivity (quantitative HBsAg/cccDNA), and replicative activity (RA; pgRNA/cccDNA). These can be used to compare relative HBV replication between HBeAg-negative and -positive patients. Objective To study the clinical significance of intrahepatic HBV replication phenomenon between HBeAg-negative and -positive patients and its correlation with quantitative HBV seromarkers. Method This was a prospective study between January 2010 and December 2011. Study subjects were naive chronic hepatitis B patients from Cipto Mangunkusumo and Medistra Hospitals. All patient samples underwent liver biochemistry and HBV seromarkers testing (HBeAg, quantitative HBsAg and HBV DNA levels), and patients underwent liver biopsy. Stored liver specimens were analysed for intrahepatic rcDNA, cccDNA, and pgRNA with quantification performed by real-time PCR. Comparison of HBV markers between HBsAg-positive and -negative patients was carried out using the Mann–Whitney U-test. Pearson’s correlation test was performed among HBV intrahepatic and seromarkers using their log-transformed values. Results A total of 104 patients were enrolled in this study; 54 (51.9%) were male. Patients’ mean age was 41.9 ± 11.63 years (range 19–70 years). Sixty-one patients (58.7%) were HBeAg-negative. All HBV markers were significantly higher in HBeAg-positive than HBeAg-negative patients, except for SVP productivity and RA. Serum HBV DNA was strongly correlated with intrahepatic total HBV DNA (r = 0.771), cccDNA (r = 0.774), and rcDNA (r = 0.780) while serum quantitative HBsAg showed only moderate correlation with intrahepatic total DNA (r = 0.671), cccDNA (r = 0.632), rcDNA (r = 0.675), and SVP productivity (r = 0.557). Conclusions Serum HBV DNA concentration and quantitative HBsAg might not accurately predict intrahepatic viral activity. Virion and SVP production do not occur in parallel with replicative activity.
Patterning of sexually dimorphic neurogenesis in the Caenorhabditis elegans ventral cord by Hox and TALE homeodomain transcription factors

Background: Reproduction in animals requires development of distinct neurons in each sex. In C. elegans, most ventral cord neurons (VCNs) are present in both sexes, with the exception of six hermaphrodite‐specific neurons (VCs) and nine pairs of male‐specific neurons (CAs and CPs) that arise from analogous precursor cells. How are the activities of sexual regulators and mediators of neuronal survival, division, and fate coordinated to generate sex‐specificity in VCNs? Results: To address this, we have developed a toolkit of VCN markers that allows us to examine sex‐specific neurogenesis, asymmetric fates of daughters of a neuroblast division, and regional specification on the anteroposterior axis. Here, we describe the roles of the Hox transcription factors LIN‐39 and MAB‐5 in promoting survival, differentiation, and regionalization of VCNs. We also find that the TALE class homeodomain proteins CEH‐20 and UNC‐62 contribute to specification of neurotransmitter fate in males. Furthermore, we identify that VCN sex is determined during the L1 larval stage. Conclusions: These findings, combined with future analyses made possible by the suite of VCN markers described here, will elucidate how Hox‐mediated cell fate decisions and sex determination intersect to influence development of neuronal sex differences. Developmental Dynamics 243:159–171, 2014. © 2013 Wiley Periodicals, Inc.
Influence of basiliximab induction therapy on long term outcome after liver transplantation, a prospectively randomised trial.

BACKGROUND In OLT induction therapy with interleukin-2-receptor antibodies is often applied as part of the standard immunosuppression protocol. It was the aim of this study to determine if Basilixirnab mduction therapy serves to reduce the incidence of acute rejection episodes and improves graft function and survival in the long term after OLT. MATERIAL/METHODS We prospectively analysed 99 patients transplanted at our institution (1997-2000). Patients were randomised to two study groups: 51 patients received Basiliximab induction combined with Calcineurin inhibitors and steroids, 48 patients received CNIs and steroids only. Incidence and severity of rejection, graft and patient survival and intensity of long-term immunosuppression were analysed. Frequency of CNI and steroid induced adverse effects were recorded. RESULTS In our patient collective we could not detect a significant impact of Basiliximab induction therapy on the fre queny of acute or chronic rejection. CNI levels were almost identical in both groups; graft and patient survival rates were not influenced by the application of induction therapy. CONCLUSIONS In our patient collective induction therapy does not have a general positive influence on the post transplant course. A slight improvement in long term renal function could be detected for Basiliximab treated patients.
The role of research training during higher medical education in the promotion of academic medicine in the UK

Objectives: To examine the research activities and perceived barriers to research among higher specialist trainees in geriatric medicine and to show how trainees active in research might have a role in assisting their peers in getting started in research. Design: Cross-sectional questionnaire survey on research activities, attitudes to doing research and perceived difficulties in doing research. Setting and participants: Trainee members of the British Geriatrics Society (BGS) in the UK. Results: A total of 122 responses (30% response rate) were received after a single mailing and a follow-up questionnaire to trainees attending the BGS national conference. Although 64% (67/104) of respondents would like to undertake a period of research, many perceived barriers preventing them from planning, funding and executing a research project. Among those who had not undertaken research, the majority (70%, 42/60) indicated that they have no clear idea of a topic to research, 64% (39/61) did not know how to develop an idea and 62% (38/61) indicated that they did not know how to get funding. Trainees motivated to do research were faced with particular difficulties with regards to funding and selection of a project topic. Conclusions: One useful method would be systematically to provide basic information to trainees on how to enter into the early stages of research. This would help to overcome some of the unnecessary uncertainty that many trainees keen to do research seem to have.
Induction of Multifunctional Human Immunodeficiency Virus Type 1 (HIV-1)-Specific T Cells Capable of Proliferation in Healthy Subjects by Using a Prime-Boost Regimen of DNA- and Modified Vaccinia Virus Ankara-Vectored Vaccines Expressing HIV-1 Gag Coupled to CD8+ T-Cell Epitopes

ABSTRACT A double-blind randomized phase I trial was conducted in human immunodeficiency virus type 1 (HIV-1)-negative subjects receiving vaccines vectored by plasmid DNA and modified vaccinia virus Ankara (MVA) expressing HIV-1 p24/p17 gag linked to a string of CD8+ T-cell epitopes. The trial had two groups. One group received either two doses of MVA.HIVA (2× MVA.HIVA) (n = 8) or two doses of placebo (2× placebo) (n = 4). The second group received 2× pTHr.HIVA followed by one dose of MVA.HIVA (n = 8) or 3× placebo (n = 4). In the pTHr.HIVA-MVA.HIVA group, HIV-1-specific T-cell responses peaked 1 week after MVA.HIVA vaccination in both ex vivo gamma interferon (IFN-γ) ELISPOT (group mean, 210 spot-forming cells/106 cells) and proliferation (group mean stimulation index, 37), with assays detecting positive responses in four out of eight and five out of eight subjects, respectively. No HIV-1-specific T-cell responses were detected in either assay in the 2× MVA.HIVA group or subjects receiving placebo. Using a highly sensitive and reproducible cultured IFN-γ ELISPOT assay, positive responses mainly mediated by CD4+ T cells were detected in eight out of eight vaccinees in the pTHr.HIVA-MVA.HIVA group and four out of eight vaccinees in the 2× MVA.HIVA group. Importantly, no false-positive responses were detected in the eight subjects receiving placebo. Of the 12 responders, 11 developed responses to previously identified immunodominant CD4+ T-cell epitopes, with 6 volunteers having responses to more than one epitope. Five out of 12 responders also developed CD8+ T-cell responses to the epitope string. Induced T cells produced a variety of anti-viral cytokines, including tumor necrosis factor alpha and macrophage inflammatory protein 1β. These data demonstrate that prime-boost vaccination with recombinant DNA and MVA vectors can induce multifunctional HIV-1-specific T cells in the majority of vaccinees.
Efficacy of an implanted neuroprosthesis for restoring hand grasp in tetraplegia: a multicenter study.

OBJECTIVE To evaluate an implanted neuroprosthesis that allows tetraplegic users to control grasp and release in 1 hand. DESIGN Multicenter cohort trial with at least 3 years of follow-up. Function for each participant was compared before and after implantation, and with and without the neuroprosthesis activated. SETTING Tertiary spinal cord injury (SCI) care centers, 8 in the United States, 1 in the United Kingdom, and 1 in Australia. PARTICIPANTS Fifty-one tetraplegic adults with C5 or C6 SCIs. INTERVENTION An implanted neuroprosthetic system, in which electric stimulation of the grasping muscles of 1 arm are controlled by using contralateral shoulder movements, and concurrent tendon transfer surgery. Assessed participants' ability to grasp, move, and release standardized objects; degree of assistance required to perform activities of daily living (ADLs), device usage; and user satisfaction. MAIN OUTCOME MEASURES Pinch force; grasp and release tests; ADL abilities test and ADL assessment test; and user satisfaction survey. RESULTS Pinch force was significantly greater with the neuroprosthesis in all available 50 participants, and grasp-release abilities were improved in 49. All tested participants (49/49) were more independent in performing ADLs with the neuroprosthesis than they were without it. Home use of the device for regular function and exercise was reported by over 90% of the participants, and satisfaction with the neuroprosthesis was high. CONCLUSIONS The grasping ability provided by the neuroprosthesis is substantial and lasting. The neuroprosthesis is safe, well accepted by users, and offers improved independence for a population without comparable alternatives.
Public Sector Audit in Contemporary Society: A Short Review and Introduction

This article gives a short review of recent research on public sector audit, and then introduces six articles in a special issue on public sector audit in contemporary society. Many countries have developed their audit institutions and expanded the audit activities in particular since the 1980s. New public management and the theory of the &#8216;audit society&#8217; explain much of this development well, also in some international organizations, but some countries have also experienced a contraction in the audit activities in the public sector. Moreover, literature on public sector audit outside the Anglo&#8208;American and North European contexts, and especially from Africa, Asia and Latin&#8208;America, is limited. There are big variations in how audit institutions are organized, in what they produce, in their relations to stakeholders and media, and in their impacts on organizations and society. Overall, auditors are little active in the fight against corruption, and the Napoleonic court system for organizing supreme audit institutions seems to be little effective. The audit institutions in the Anglo&#8208;American and Nordic accountability regimes seem to be relatively effective, but the recent research show that auditors' independence and relevance are persistent challenging issues in public sector audit.
Two distinct endothelial lineages in ontogeny, one of them related to hemopoiesis.

We have shown previously by means of quail/chick transplantations that external and visceral organs, i.e., somatopleural and splanchnopleural derivatives, acquire their endothelial network through different mechanisms, namely immigration (termed angiogenesis) versus in situ emergence of precursors (or vasculogenesis). We have traced the distribution of QH1-positive cells in chick hosts after replacement of the last somites by quail somites (orthotopic grafts) or lateral plate mesoderm (heterotopic grafts). The results lead to the conclusion that the embryo becomes vascularized by endothelial precursors from two distinct regions, splanchnopleural mesoderm and paraxial mesoderm. The territories respectively vascularized are complementary, precursors from the paraxial mesoderm occupy the body wall and kidney, i.e., they settle along with the other paraxial mesoderm derivatives and colonize the somatopleure. The precursors from the two origins have distinct recognition and potentialities properties: endothelial precursors of paraxial origin are barred from vascularizing visceral organs and from integrating into the floor of the aorta, and are never associated with hemopoiesis; splanchnopleural mesoderm grafted in the place of somites, gives off endothelial cells to body wall and kidney but also visceral organs. It gives rise to hemopoietic precursors in addition to endothelial cells.
Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection

HIV adaptation to a host in chronic infection is simulated by means of a Monte-Carlo algorithm that includes the evolutionary factors of mutation, positive selection with varying strength among sites, random genetic drift, linkage, and recombination. By comparing two sensitive measures of linkage disequilibrium (LD) and the number of diverse sites measured in simulation to patient data from one-time samples of pol gene obtained by single-genome sequencing from representative untreated patients, we estimate the effective recombination rate and the average selection coefficient to be on the order of 1% per genome per generation (10−5 per base per generation) and 0.5%, respectively. The adaptation rate is twofold higher and fourfold lower than predicted in the absence of recombination and in the limit of very frequent recombination, respectively. The level of LD and the number of diverse sites observed in data also range between the values predicted in simulation for these two limiting cases. These results demonstrate the critical importance of finite population size, linkage, and recombination in HIV evolution.
Randomized controlled double-blind trial of optimal dose methylphenidate in children and adolescents with severe attention deficit hyperactivity disorder and intellectual disability.

BACKGROUND Attention deficit hyperactivity disorder is increased in children with intellectual disability. Previous research has suggested stimulants are less effective than in typically developing children but no studies have titrated medication for individual optimal dosing or tested the effects for longer than 4 weeks. METHOD One hundred and twenty two drug-free children aged 7-15 with hyperkinetic disorder and IQ 30-69 were recruited to a double-blind, placebo-controlled trial that randomized participants using minimization by probability, stratified by referral source and IQ level in a one to one ratio. Methylphenidate was compared with placebo. Dose titration comprised at least 1 week each of low (0.5 mg/kg/day), medium (1.0 mg/kg/day) and high dose (1.5 mg/kg/day). Parent and teacher Attention deficit hyperactivity disorder (ADHD) index of the Conners Rating Scale-Short Version at 16 weeks provided the primary outcome measures. Clinical response was determined with the Clinical Global Impressions scale (CGI-I). Adverse effects were evaluated by a parent-rated questionnaire, weight, pulse and blood pressure. Analyses were by intention to treat. TRIAL REGISTRATION ISRCTN 68384912. RESULTS Methylphenidate was superior to placebo with effect sizes of 0.39 [95% confidence intervals (CIs) 0.09, 0.70] and 0.52 (95% CIs 0.23, 0.82) for the parent and teacher Conners ADHD index. Four (7%) children on placebo versus 24 (40%) of those on methylphenidate were judged improved or much improved on the CGI. IQ and autistic symptoms did not affect treatment efficacy. Active medication was associated with sleep difficulty, loss of appetite and weight loss but there were no significant differences in pulse or blood pressure. CONCLUSIONS Optimal dosing of methylphenidate is practical and effective in some children with hyperkinetic disorder and intellectual disability. Adverse effects typical of methylphenidate were seen and medication use may require close monitoring in this vulnerable group.
Genetic analysis of an invasion region by use of a Tn3-lac transposon and identification of a second positive regulator gene, invE, for cell invasion of Shigella sonnei: significant homology of invE with ParB of plasmid P1

We have previously cloned two distinct regions of the Shigella sonnei form I plasmid pSS120, a 37-kilobase-pair DNA region and a virF region, which were found to be essential for cell invasion in Escherichia coli K-12 (J. Kato, K. Ito, A. Nakamura, and H. Watanabe, Infect. Immun. 57:1391-1398, 1989). The 37-kilobase-pair DNA region was randomly inserted by use of transposon Tn3-lac. At least eight genes were found to be located within the region, as determined by analysis of Tn3-lac-generated lac fusions. Expression of six genes, ipaB, ipaC, invE, invG, invJ, and invK, was apparently regulated by the positive regulator virF. IpaB and IpaC proteins could not found in invE mutants even if the virF gene was present. This observation suggested that the invE region encoded a positive regulator different from the virF gene. The functional relationship between the invE and virF genes was then examined. Translational fusions ipaB::Tn3-lac and invJ::Tn3-lac were used as indicators for gene expression, and the following results were obtained. Full expression of the ipaB and invJ genes required the presence of both the invE and virF regions. virF positively regulated the expression of invE at the transcriptional level. An increase in the copy number of invE enhanced the expression of ipaB and invJ in the absence of virF. These findings strongly indicate that the invE gene product, whose expression is regulated by virF, acts positively on the invasion-associated genes. InvE is a 35,407-dalton protein and has significant homologies with ParB of plasmid P1 and SopB of plasmid F, which are DNA-binding proteins involved in plasmid partitioning.
Surveillance study of novobiocin and phenylbutazone residues in raw bovine milk using liquid chromatography-tandem mass spectrometry

A simple method permitting the simultaneous determination of trace residues of novobiocin and phenylbutazone in raw milk samples using liquid chromatography-tandem mass spectrometry was developed. Raw milk samples were mixed with acetonitrile to facilitate the concurrent precipitation of milk proteins and extraction of both veterinary drugs. Without additional clean-up or concentration of the resulting extract, the analytes could be quantified at concentrations as low as 0.0025 and 0.001 µg ml−1 for phenylbutazone and novobiocin, respectively. The analysis of a series of fortified raw milk samples at analyte concentrations ranging from 0.005 to 0.1 µg ml−1 and from 0.01 to 0.2 µg ml−1 for phenylbutazone and novobiocin, respectively, yielded average recoveries ranging from 89.2% to 104.3% with standard deviations below 7%. The analytical method was applied to the analysis of raw milk samples collected from transport trucks upon delivery at dairy-processing plants throughout Alberta, Canada. Novobiocin was detected in 13 of 1072 samples tested at concentrations ranging from 0.001 to 0.007 µg ml−1. Phenylbutazone was not detected in any of the samples tested.