The Paradata Information Model

Presentation at the North American Data Documentation Conference (NADDI) 2013Paradata is data on study processes and the collection of study data. Here we describe the development of a Paradata Information Model (PIM) in support of the National Children¹s Study (NCS) of the Eunice Kennedy Shriver National Institute of Child Health and Development. We propose that paradata can be recorded with accompanying metadata informed by the General Longitudinal Business Process Model (GLBPM) developed by the Data Documentation Initiative (DDI) and the General Statistical Business Process Model (GSBPM). The PIM is be constructed in a joint top-down and bottom-up approach, appropriating broad verbs from DDI, HL7, LS-DAM, and CDISC, while incorporating study-specific processes involved in collecting NCS operational data elements (ODEs). The hope of paradata in longitudinal studies is that the collection of paradata will ensure that future researchers can integrate disparate data sets collected by a variety of technologies, especially in rapidly-evolving fields like genomics. Additionally, by giving PIM elements preconditions and postconditions, we can develop software agents which use paradata metadata as well as other information to assist humans in conducting biomedical research, ultimately facilitating more rapid collection and analysis of information and enabling a broader subset of researchers to discover and extract relevant information from study data sets.Institute for Policy & Social Research, University of Kansas; University of Kansas Libraries; Alfred P. Sloan Foundation; Data Documentation Initiative Alliance, Booz Allen Hamilto

Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity

Background Salivary amylase in humans is encoded by the copy variable gene AMY1 in the amylase gene cluster on chromosome 1. Although the role of salivary amylase is well established, the consequences of the copy number variation (CNV) at AMY1 on salivary amylase protein production are less well understood. The amylase gene cluster is highly structured with a fundamental difference between odd and even AMY1 copy number haplotypes. In this study, we aimed to explore, in samples from 119 unrelated individuals, not only the effects of AMY1 CNV on salivary amylase protein expression and amylase enzyme activity but also whether there is any evidence for underlying difference between the common haplotypes containing odd numbers of AMY1 and even copy number haplotypes. Results AMY1 copy number was significantly correlated with the variation observed in salivary amylase production (11.7% of variance, P < 0.0005) and enzyme activity (13.6% of variance, P < 0.0005) but did not explain the majority of observed variation between individuals. AMY1-odd and AMY1-even haplotypes showed a different relationship between copy number and expression levels, but the difference was not statistically significant (P = 0.052). Conclusions Production of salivary amylase is correlated with AMY1 CNV, but the majority of interindividual variation comes from other sources. Long-range haplotype structure may affect expression, but this was not significant in our data

The Engaged Department Initiative: GVSU, GRCC, and Aquinas Join Forces for Place-Based Impact

The Engaged Department Initiative (EDI) is a place-based cross-institutional collaboration located in the Grand Rapids region. Participating organizations include Michigan Campus Compact (MiCC), Grand Valley State University (GVSU), Grand Rapids Community College (GRCC), and Aquinas College (AQ). This innovative ethnographic case study is focused on evaluating how well the initiative completes their goals of increasing faculty knowledge and skills, expanding students’ community engagement, fostering intra- and inter- collaborations between the three institutions of higher education, and enhancing community partnerships. The hopes of this initiative is to make a real difference in the community and to create engaged citizens. By disseminating this research, we aspire to offer recommendations for people interested in spanning boundaries and working on place-based change in their own region

Accurate measurement of gene copy number for human alpha-defensin DEFA1A3

Background: Multi-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this variation, and analysis of its impact on function, has been hampered by the technical difficulty of large-scale but accurate typing of genomic copy number. The copy-variable alpha-defensin locus DEFA1A3 on human chromosome 8 commonly varies between 4 and 10 copies per diploid genome, and presents considerable challenges for accurate high-throughput typing. Results: In this study, we developed two paralogue ratio tests and three allelic ratio measurements that, in combination, provide an accurate and scalable method for measurement of DEFA1A3 gene number. We combined information from different measurements in a maximum-likelihood framework which suggests that most samples can be assigned to an integer copy number with high confidence, and applied it to typing 589 unrelated European DNA samples. Typing the members of three-generation pedigrees provided further reassurance that correct integer copy numbers had been assigned. Our results have allowed us to discover that the SNP rs4300027 is strongly associated with DEFA1A3 gene copy number in European samples. Conclusions: We have developed an accurate and robust method for measurement of DEFA1A3 copy number. Interrogation of rs4300027 and associated SNPs in Genome-Wide Association Study SNP data provides no evidence that alpha-defensin copy number is a strong risk factor for phenotypes such as Crohn’s disease, type I diabetes, HIV progression and multiple sclerosis

Adipose-targeted SWELL1 deletion exacerbates obesity- and age-related nonalcoholic fatty liver disease

Healthy expansion of adipose tissue is critical for the maintenance of metabolic health, providing an optimized reservoir for energy storage in the form of triacylglycerol-rich lipoproteins. Dysfunctional adipocytes that are unable to efficiently store lipid can result in lipodystrophy and contribute to nonalcoholic fatty liver disease (NAFLD) and metabolic syndrome. Leucine-rich repeat containing protein 8a/SWELL1 functionally encodes the volume-regulated anion channel complex in adipocytes, is induced in early obesity, and is required for normal adipocyte expansion during high-fat feeding. Adipose-specific SWELL1 ablation (Adipo KO) leads to insulin resistance and hyperglycemia during caloric excess, both of which are associated with NAFLD. Here, we show that Adipo-KO mice exhibited impaired adipose depot expansion and excess lipolysis when raised on a variety of high-fat diets, resulting in increased diacylglycerides and hepatic steatosis, thereby driving liver injury. Liver lipidomic analysis revealed increases in oleic acid-containing hepatic triacylglycerides and injurious hepatic diacylglyceride species, with reductions in hepatocyte-protective phospholipids and antiinflammatory free fatty acids. Aged Adipo-KO mice developed hepatic steatosis on a regular chow diet, and Adipo-KO male mice developed spontaneous, aggressive hepatocellular carcinomas (HCCs). These data highlight the importance of adipocyte SWELL1 for healthy adipocyte expansion to protect against NAFLD and HCC in the setting of overnutrition and with aging

Nitric Oxide-Releasing Silica Nanoparticle-Doped Polyurethane Electrospun Fibers

Electrospun polyurethane fibers doped with nitric oxide (NO)-releasing silica particles are presented as novel macromolecular scaffolds with prolonged NO-release and high porosity. Fiber diameter (119–614 nm) and mechanical strength (1.7–34.5 MPa of modulus) were varied by altering polyurethane type and concentration, as well as the NO-releasing particle composition, size, and concentration. The resulting NO-releasing electrospun nanofibers exhibited ~83% porosity with flexible plastic or elastomeric behavior. The use of N-diazeniumdiolate- or S-nitrosothiol-modified particles yielded scaffolds exhibiting a wide range of NO release totals and durations (7.5 nmol mg−1–0.12 μmol mg−1 and 7 h to 2 weeks, respectively). The application of NO-releasing porous materials as coating for subcutaneous implants may improve tissue biocompatibility by mitigating the foreign body response and promoting cell integration

Jaundice: an important, poorly recognized risk factor for diminished survival in patients with adenocarcinoma of the head of the pancreas

AbstractObjectivesJaundice impairs cellular immunity, an important defence against the dissemination of cancer. Jaundice is a common mode of presentation in pancreatic head adenocarcinoma. The purpose of this study was to determine whether there is an association between preoperative jaundice and survival in patients who have undergone resection of such tumours.MethodsThirty possible survival risk factors were evaluated in a database of over 400 resected patients. Univariate analysis was used to determine odds ratio for death. All factors for which a P‐value of <0.30 was obtained were entered into a multivariate analysis using the Cox model with backward selection.ResultsPreoperative jaundice, age, positive node status, poor differentiation and lymphatic invasion were significant indicators of poor outcome in multivariate analysis. Absence of jaundice was a highly favourable prognostic factor. Interaction emerged between jaundice and nodal status. The benefit conferred by the absence of jaundice was restricted to patients in whom negative node status was present. Five‐year overall survival in this group was 66%. Jaundiced patients who underwent preoperative stenting had a survival advantage.ConclusionsPreoperative jaundice is a negative risk factor in adenocarcinoma of the pancreas. Additional studies are required to determine the exact mechanism for this effect