Examining Perceptions of Participation in a Pediatric IBD Collaborative: Analyzing the Sustainability of Quality Improvement Activities

In 2007, pediatric gastroenterologists from ten practice sites across the U.S. created a quality improvement collaborative, now known as ImproveCareNow, to improve the quality of care provided to children with inflammatory bowel disease. Despite the face validity and great potential of quality improvement collaboratives, investigators do not fully understand how improvement happens, including the variables contributing to quality measures and the necessary components needed to sustain quality improvement. The purpose of this project was to explore perceptions of collaborative participants to identify elements of sustainability. We performed qualitative interviews with 16 ImproveCareNow participants as one method in a triangulated strategy of measuring collaborative participants‟ perceptions. We selected informants from a diverse list of practice types and geographic locations, and asked open-ended questions, which we then transcribed and coded. For this master‟s paper‟s focus on sustainability, I extracted participant views of the collaborative‟s most valuable aspects, obstacles to participation, and perceptions of variables affecting outcome measures. New site participants found practice standardization to be most valuable; existing sites named a patient tracking, collaboration, and quality improvement training. New and existing sites mentioned time as the biggest obstacle to collaborative participation; existing sites, with more experience, also named persuading non-ICN providers to support the effort, and other challenges varied by particular ICN activities. Finally, 9 of 12 (75%) informants said that collaborative activities were responsible for improved inactive disease rates, and 3 of 12 (25%) said the ICN collaborative was partially responsible. When asked if other factors were affecting outcomes, 4 of 12 (33%) said no; 2 of 12 (17%) said yes; and 6 of 12 (50%) were uncertain. Analyzing in-depth interviews of ICN participants is the first step in understanding what health care providers perceive as the value from, benefits of, and challenges to initiating and sustaining collaborative quality improvement activities.Master of Public Healt

Blood levels of lead and dental caries in permanent teeth

ObjectivesThe purpose of this study was to determine whether there is an association between lead exposure within the ages of 1- 4- years and dental caries in the permanent dentition between ages 9- 17 among Mexican youth.MethodsData were collected for the Early Life Exposures in Mexico to Environmental Toxicants (ELEMENT) cohort from a group of 490 children born and reared in Mexico City. Among ages 1- 4- years, blood lead levels were measured in micrograms of lead per deciliter of blood (μg/dL) and the presence of caries in adolescence was determined using the International Caries and Detection and Assessment System (ICDAS). The relationship between blood levels of lead and decayed, missing, or filled surfaces (DMFS) was examined using negative binomial regression. Covariates were selected based on previous studies and included age, gender, socioeconomic status, oral hygiene, body mass index, and diet. The nonlinear relationship between lead and DMFS was examined using smoothing splines.ResultsThe mean overall blood lead level (BLL) was 4.83- μg/dL (S.D. of 2.2). The mean overall caries level (DMFS) was 4.1. No statistically significant association was found between early childhood blood lead levels and dental caries in adolescence.ConclusionThis study shows a lack of association between exposure to lead between the ages of 1- 4- years of age and dental caries in permanent dentition later in life. Other covariates, such as age and sugar consumption, appeared to play a more prominent role in caries development.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/163870/1/jphd12384.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163870/2/jphd12384_am.pd

Oral microbiome in HIV-associated periodontitis

M.N-J, J.R, Y.G. and R.P acknowledge funds from the Gala contra la SIDA 2013 and 2014 editions, the Nit per la Recerca a la Catalunya Central 2015 edition and the Red de investigación en SIDA.Supplemental Digital Content is available in the text HIV-associated periodontal diseases (PD) could serve as a source of chronic inflammation. Here, we sought to characterize the oral microbial signatures of HIV+ and HIV- individuals at different levels of PD severity. This cross-sectional study included both HIV+ and HIV- patients with varying degrees of PD. Two tooth, 2 cheek, and 1 saliva samples were obtained for microbiome analysis. Mothur/SILVADB were used to classify sequences. R/Bioconductor (Vegan, PhyloSeq, and DESeq2) was employed to assess overall microbiome structure differences and differential abundance of bacterial genera between groups. Polychromatic flow cytometry was used to assess immune activation in CD4 and CD8 cell populations. Around 250 cheek, tooth, and saliva samples from 50 participants (40 HIV+ and 10 HIV-) were included. Severity of PD was classified clinically as None/Mild (N), Moderate (M), and Severe (S) with 18 (36%), 16 (32%), and 16 (32%) participants in each category, respectively. Globally, ordination analysis demonstrated clustering by anatomic site (R 2 = 0.25, P < 0.001). HIV status and PD severity showed a statistically significant impact on microbiome composition but only accounted for a combined 2% of variation. HIV+ samples were enriched in genera Abiotrophia, Neisseria, Kingella, and unclassified Neisseriaceae and depleted in Leptotrichia and Selenomonas. The Neisseria genus was consistently enriched in HIV+ participants regardless of sampling site and PD level. Immune markers were altered in HIV+ participants but did not show association with the oral microbiome. HIV-associated changes in oral microbiome result in subtle microbial signatures along different stages of PD that are common in independent oral anatomic sites

Novel Bacterial Taxa in the Human Microbiome

The human gut harbors thousands of bacterial taxa. A profusion of metagenomic sequence data has been generated from human stool samples in the last few years, raising the question of whether more taxa remain to be identified. We assessed metagenomic data generated by the Human Microbiome Project Consortium to determine if novel taxa remain to be discovered in stool samples from healthy individuals. To do this, we established a rigorous bioinformatics pipeline that uses sequence data from multiple platforms (Illumina GAIIX and Roche 454 FLX Titanium) and approaches (whole-genome shotgun and 16S rDNA amplicons) to validate novel taxa. We applied this approach to stool samples from 11 healthy subjects collected as part of the Human Microbiome Project. We discovered several low-abundance, novel bacterial taxa, which span three major phyla in the bacterial tree of life. We determined that these taxa are present in a larger set of Human Microbiome Project subjects and are found in two sampling sites (Houston and St. Louis). We show that the number of false-positive novel sequences (primarily chimeric sequences) would have been two orders of magnitude higher than the true number of novel taxa without validation using multiple datasets, highlighting the importance of establishing rigorous standards for the identification of novel taxa in metagenomic data. The majority of novel sequences are related to the recently discovered genus Barnesiella, further encouraging efforts to characterize the members of this genus and to study their roles in the microbial communities of the gut. A better understanding of the effects of less-abundant bacteria is important as we seek to understand the complex gut microbiome in healthy individuals and link changes in the microbiome to disease

Host Genes Related to Paneth Cells and Xenobiotic Metabolism Are Associated with Shifts in Human Ileum-Associated Microbial Composition

The aim of this study was to integrate human clinical, genotype, mRNA microarray and 16 S rRNA sequence data collected on 84 subjects with ileal Crohn’s disease, ulcerative colitis or control patients without inflammatory bowel diseases in order to interrogate how host-microbial interactions are perturbed in inflammatory bowel diseases (IBD). Ex-vivo ileal mucosal biopsies were collected from the disease unaffected proximal margin of the ileum resected from patients who were undergoing initial intestinal surgery. Both RNA and DNA were extracted from the mucosal biopsy samples. Patients were genotyped for the three major NOD2 variants (Leufs1007, R702W, and G908R) and the ATG16L1T300A variant. Whole human genome mRNA expression profiles were generated using Agilent microarrays. Microbial composition profiles were determined by 454 pyrosequencing of the V3–V5 hypervariable region of the bacterial 16 S rRNA gene. The results of permutation based multivariate analysis of variance and covariance (MANCOVA) support the hypothesis that host mucosal Paneth cell and xenobiotic metabolism genes play an important role in host microbial interactions

Construction of 3D models of the CYP11B family as a tool to predict ligand binding characteristics

Aldosterone is synthesised by aldosterone synthase (CYP11B2). CYP11B2 has a highly homologous isoform, steroid 11β-hydroxylase (CYP11B1), which is responsible for the biosynthesis of aldosterone precursors and glucocorticoids. To investigate aldosterone biosynthesis and facilitate the search for selective CYP11B2 inhibitors, we constructed three-dimensional models for CYP11B1 and CYP11B2 for both human and rat. The models were constructed based on the crystal structure of Pseudomonas Putida CYP101 and Oryctolagus Cuniculus CYP2C5. Small steric active site differences between the isoforms were found to be the most important determinants for the regioselective steroid synthesis. A possible explanation for these steric differences for the selective synthesis of aldosterone by CYP11B2 is presented. The activities of the known CYP11B inhibitors metyrapone, R-etomidate, R-fadrazole and S-fadrazole were determined using assays of V79MZ cells that express human CYP11B1 and CYP11B2, respectively. By investigating the inhibitors in the human CYP11B models using molecular docking and molecular dynamics simulations we were able to predict a similar trend in potency for the inhibitors as found in the in vitro assays. Importantly, based on the docking and dynamics simulations it is possible to understand the enantioselectivity of the human enzymes for the inhibitor fadrazole, the R-enantiomer being selective for CYP11B2 and the S-enantiomer being selective for CYP11B1

Medulloblastoma Exome Sequencing Uncovers Subtype-Specific Somatic Mutations

Medulloblastomas are the most common malignant brain tumors in children1. Identifying and understanding the genetic events that drive these tumors is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. Recently, our group and others described distinct molecular subtypes of medulloblastoma based on transcriptional and copy number profiles2–5. Here, we utilized whole exome hybrid capture and deep sequencing to identify somatic mutations across the coding regions of 92 primary medulloblastoma/normal pairs. Overall, medulloblastomas exhibit low mutation rates consistent with other pediatric tumors, with a median of 0.35 non-silent mutations per megabase. We identified twelve genes mutated at statistically significant frequencies, including previously known mutated genes in medulloblastoma such as CTNNB1, PTCH1, MLL2, SMARCA4 and TP53. Recurrent somatic mutations were identified in an RNA helicase gene, DDX3X, often concurrent with CTNNB1 mutations, and in the nuclear co-repressor (N-CoR) complex genes GPS2, BCOR, and LDB1, novel findings in medulloblastoma. We show that mutant DDX3X potentiates transactivation of a TCF promoter and enhances cell viability in combination with mutant but not wild type beta-catenin. Together, our study reveals the alteration of Wnt, Hedgehog, histone methyltransferase and now N-CoR pathways across medulloblastomas and within specific subtypes of this disease, and nominates the RNA helicase DDX3X as a component of pathogenic beta-catenin signaling in medulloblastoma