Comparison of sampling adequacy between OPD based pipelle biopsy and in- patient conventional D&C, presented with abnormal uterine bleeding

Objective: To determine agreement on adequacy of sample by pipelle biopsy and conventional dilatation and curettage in patients with abnormal uterine bleeding. Study design: Cross sectional studySetting and Duration of Study: Department of Obstetrics and Gyneacology, Islamic International Medical College Trust, Railway Hospital Rawalpindi. Study was carried out over a period of six months (11-07-2012 to 14-01-2013). Patients and Methods: 84 patients presented with abnormal uterine bleeding age 45 years and older, attended Gynecology department of Railway Hospital Rawalpindi. Who qualified the inclusion criteria were enrolled in this study by non-probability consecutive sampling technique. The diagnostic intervention for endometrial sampling was by pipelle device and by conventional D&C. Both procedures were performed in the OT at the same time.First the pipelle sample was taken and was labeled as “A” then conventional D&C was performed and was labeled as “B”. Both samples were sent to the pathologist, who was blinded as to the method of sample collection for histopathology assessment. Adequacy of the sample was assessed as per operational definition. A data base was made in SPSS version 17. Kappa statistics was applied to assess the agreement. Results: Out of 84 patients, 80 (98.8%) of the patients had adequate sample with Pipelle Biopsy as compared to conventional curettage and dilatation (D & C). We therefore recommend the use of pipelle biopsy as a first line tool for endometrial assessment for our setups instead of D&C. Conclusion: Our study concluded that the Pipelle biopsy is a useful and convenient method to the patients and physicians as ompared to D&C performed in the operating theatre. It is useful in obese and high-risk patients with minimum chances of perforation of uterus due to its soft flexible tip

The Human Microbiome and Recurrent Abdominal Pain in Children

This project explores the nature of the human intestinal microbiome in healthy children and children with recurrent abdominal pain. The overall goal is to obtain a robust knowledge base of the intestinal microbiome in children without evidence of pain or gastrointestinal disease and in those with recurrent abdominal pain (functional abdominal pain (FAP) and FAP associated with changes in bowel habits, i.e., irritable bowel syndrome or IBS). Specific aims include: 1. Characterize the composition of the gut microbiome in healthy children by DNA sequencing. 2. Determine the presence of disease-specific organism signatures of variable gut microbiomes in children with recurrent abdominal pain. 3. Perform functional gut metagenomics by evaluation of whole community gene expression profiles and discovery of disease-specific pathway signatures. Multiple strategies have been deployed to navigate and understand the nature of the intestinal microbiome in childhood. These strategies included 454 pyrosequencing-based strategies to sequence 16S rRNA genes and understand the detailed composition of microbes in healthy and disease groups. Microarray-based hybridization with the PhyloChip and quantitative real-time PCR (qPCR) probes were applied as complementary strategies to gain an understanding of the intestinal microbiome from various perspectives. Data collected and analyzed during the HMP UH2 Demo project, from a set of healthy and IBS children (7-12 yo) may enable the identification of core microbiomes in children, in addition to variable components that may distinguish healthy from diseased pediatric states. Twenty-two children with IBS and twenty-two healthy children were enrolled and analyzed in the UH2 phase of this study. The planned enrollment targets for the UH2/3 phases include 50 healthy children, 50 children with FAP and 50 children with IBS (minimum of 3 time points per child). We are currently analyzing the dataset for the presence of disease-specific signatures in the human microbiome, and correlating these microbial signatures with pediatric health or IBS disease status in addition to IBS subtype (e.g., diarrhea-vs constipation-predominant). In the next phase, whole genome shotgun sequencing and metatranscriptomics will be performed with a subset of children in each group. This study explores the nature of core and variable human microbiome in pre-adolescent healthy children and children with IBS. 
&#xa

Taking the Initiative? TLRP and Educational Research

Evaluating the effects of known subject traits on pediatric GI community structure and function. PCoA of the GI microbial communities of healthy children as a function of Bray-Curtis dissimilarities and 16S-based OTUs (A–D), WGS-based species (E–H), KO groups (I–L), and KEGG pathway profiles (M–P). Variation among profiles was evaluated with respect to known traits, and the percent variation captured by each axis is indicated in parenthesis. Adonis analysis results describe the significance of each trait to overall community variation. (TIF 1.58 kb

It’s not which school but which set you’re in that matters: the influence of ability-grouping practices on student progress in mathematics

The mathematics achievement of a cohort of 955 students in 42 classes in six schools in London was followed over a four-year period, until they took their GCSEs in the summer of 2000. All six schools were regarded by Ofsted as providing a good standard of education, and all were involved in teacher-training partnerships with universities. Matched data on key stage 3 test scores and GCSE grades were available for 709 students, and these data were analysed in terms of the progress from key stage 3 test scores to GCSE grades. Although there were wide differences between schools in terms of overall GCSE grades, the average progress made by students was similar in all six schools. However, within each school, the progress made during key stage 4 varied greatly from set to set. Comparing students with the same key stage 3 scores, students placed in top sets averaged nearly half a GCSE grade higher than those in the other upper sets, who in turn averaged a third of a grade higher than those in lower sets, who in turn averaged around a third of a grade higher than those students placed in bottom sets. In the four schools that used formal whole-class teaching, the difference in GCSE grades between top and bottom sets, taking key stage 3 scores into account, ranged from just over 1 grade at GCSE to nearly 3 grades. At the schools using small-group and individualised teaching, the differences in value-added between sets were not significant. In two of the schools, a significant proportion of working class students were placed into lower sets than would be indicated by their key stage 3 test scores

A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy

While current major national research efforts (i.e., the NIH Human Microbiome Project) will enable comprehensive metagenomic characterization of the adult human microbiota, how and when these diverse microbial communities take up residence in the host and during reproductive life are unexplored at a population level. Because microbial abundance and diversity might differ in pregnancy, we sought to generate comparative metagenomic signatures across gestational age strata. DNA was isolated from the vagina (introitus, posterior fornix, midvagina) and the V5V3 region of bacterial 16S rRNA genes were sequenced (454FLX Titanium platform). Sixty-eight samples from 24 healthy gravidae (18 to 40 confirmed weeks) were compared with 301 non-pregnant controls (60 subjects). Generated sequence data were quality filtered, taxonomically binned, normalized, and organized by phylogeny and into operational taxonomic units (OTU); principal coordinates analysis (PCoA) of the resultant beta diversity measures were used for visualization and analysis in association with sample clinical metadata. Altogether, 1.4 gigabytes of data containing >2.5 million reads (averaging 6,837 sequences/sample of 493 nt in length) were generated for computational analyses. Although gravidae were not excluded by virtue of a posterior fornix pH >4.5 at the time of screening, unique vaginal microbiome signature encompassing several specific OTUs and higher-level clades was nevertheless observed and confirmed using a combination of phylogenetic, non-phylogenetic, supervised, and unsupervised approaches. Both overall diversity and richness were reduced in pregnancy, with dominance of Lactobacillus species (L. iners crispatus, jensenii and johnsonii, and the orders Lactobacillales (and Lactobacillaceae family), Clostridiales, Bacteroidales, and Actinomycetales. This intergroup comparison using rigorous standardized sampling protocols and analytical methodologies provides robust initial evidence that the vaginal microbial 16S rRNA gene catalogue uniquely differs in pregnancy, with variance of taxa across vaginal subsite and gestational age

Global phylogenetic trees after AbundantOTU and QIIME denoising.

<p>Global phylogenetic trees show the distribution of taxonomy among all the pregnant and non-pregnant subject samples. The internal cluster dendrograms are colored by taxa Family level projections (annotated in figure legend), while the mid-circle is colored by the majority origins of OTUs from pregnant or non-pregnant subject samples (pregnant-magenta; non-pregnant-brown). Outermost circle using text to indicates OTU projection to Order level (Bacteroidales-red, Actinomycetales-yellow, Lactobacillales-green, Clostridiales-blue). OTU tables and representative sequences generated from AbundantOTU (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036466#pone-0036466-g004" target="_blank"><b>Figure 4A</b></a>) and QIIME denoised (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036466#pone-0036466-g004" target="_blank"><b>Figure 4B</b></a>) datasets were employed in generating these global phylogenetic trees.</p

Additional file 9: Table S7. of Structure and function of the healthy pre-adolescent pediatric gut microbiome

Genera differing in the 16S profiles of healthy child and adult GI communities. Between-group differences were evaluated with two-tailed White’s non-parametric t-tests with Storey’s FDR corrections. (XLSX 14.6 kb

Subclassification of microbial community structure by vaginal subsite and week of gestation.

<p>(A) Pregnancy clusters vaginal microbial communities, while site of vaginal sampling minimally contributes to within cluster formation. Canberra beta diversity metric with PCoA plot clustering. Each dots represents one sample from the distinct vaginal subsites (mid vagina, posterior fornix, and vaginal introitus) of individual subjects from pregnant (green shades) and non-pregnant (blue and purple shades). (B) Among gravid subjects, microbial community richness and diversity (Shannon indices) vary by week of gestation and proximity to the uterus. Community richness and Shannon diversity indices by gestational age and vaginal sampling site against normalized abundance values from both OTU and phylogeny based analysis charted by vaginal site (posterior fornix, mid vagina, introitus) and gestational age. Richness - Black; Diversity – Dark Red; Left panel designates OTU based; Right panel designates Phylogeny based. Gestational age interval shown in weeks, or designated as non-pregnant (NP). Error bars denote variance (standard error of the mean, s.e.m.). In each of the gestational age intervals, an equivalent number of gravidae were sampled and compared (n = 6 per strata).</p