Prediction of Disease Severity in Patients with Early Rheumatoid Arthritis by Gene Expression Profiling

In order to test the ability of peripheral blood gene expression profiles to predict future disease severity in patients with early rheumatoid arthritis (RA), a group of 17 patients (1 ± 0.2 years disease duration) was evaluated at baseline for gene expression profiles. Disease status was evaluated after a mean of 5 years using an index combining pain, global and recoded MHAQ scores. Unsupervised and supervised algorithms identified “predictor genes” whose combined expression levels correlated with follow-up disease severity scores. Unsupervised clustering algorithms separated patients into two branches. The only significant difference between these two groups was the disease severity score; demographic variables and medication usage were not different. Supervised T-Test analysis identified 19 “predictor genes” of future disease severity. Results were validated in an independent cohort of subjects of established RA with using Support Vector Machines and K-Nearest-Neighbor Classification. Our study demonstrates that peripheral blood gene expression profiles may be a useful tool to predict future disease severity in patients with early and established RA

Using gene expression data to identify certain gastro-intestinal diseases

BACKGROUND: Inflammatory bowel diseases, ulcerative colitis and Crohn’s disease are considered to be of autoimmune origin, but the etiology of irritable bowel syndrome remains elusive. Furthermore, classifying patients into irritable bowel syndrome and inflammatory bowel diseases can be difficult without invasive testing and holds important treatment implications. Our aim was to assess the ability of gene expression profiling in blood to differentiate among these subject groups. METHODS: Transcript levels of a total of 45 genes in blood were determined by quantitative real-time polymerase chain reaction (RT-PCR). We applied three separate analytic approaches; one utilized a scoring system derived from combinations of ratios of expression levels of two genes and two different support vector machines. RESULTS: All methods discriminated different subject cohorts, irritable bowel syndrome from control, inflammatory bowel disease from control, irritable bowel syndrome from inflammatory bowel disease, and ulcerative colitis from Crohn’s disease, with high degrees of sensitivity and specificity. CONCLUSIONS: These results suggest these approaches may provide clinically useful prediction of the presence of these gastro-intestinal diseases and syndromes

Regulating and Deregulating the Public Utilities 1830-2010

History can provide invaluable insights into important issues of the economic and social regulation of utilities, and offer lessons towards future debates. But the history of utility regulation – which speaks of changing, diverse and complex experiences around the world – was, unfortunately, sidelined or marginalised when economists and policymakers enthusiastically embraced the question of how to reform the utilities from the 1970s. This paper provides an overview of the three, overarching, `waves' of utility regulation from the nineteenth century to the present, documenting how, when and why the ways in which the roles of the state, the market and firms altered over time. It then contextualises and explains the main contributions of each of the papers included in this special issue of Business History, which cover energy, communications, water, transportation and other urban infrastructure regulation, across Western Europe, the United States and Australia

Is consuming yoghurt associated with weight management outcomes? Results from a systematic review.

BACKGROUND: Yoghurt is part of the diet of many people worldwide and is commonly recognised as a 'health food'. Epidemiological studies suggest that yoghurt may be useful as part of weight management programs. In the absence of comprehensive systematic reviews, this systematic review investigated the effect of yoghurt consumption by apparently healthy adults on weight-related outcomes. METHODS: An extensive literature search was undertaken, as part of a wider scoping review, to identify yoghurt studies. A total of 13 631 records were assessed for their relevance to weight-related outcomes. RESULTS: Twenty-two publications were eligible according to the review protocol. Cohort studies (n=6) and cross-sectional studies (n=7) all showed a correlation between yoghurt and lower or improved body weight/composition. Six randomised controlled trials (RCTs) and one controlled trial had various limitations, including small size and short duration. One RCT showed significant effects of yoghurt on weight loss, but was confounded by differences in calcium intake. One trial showed nonsignificant weight gain and the remaining five trials showed nonsignificant weight losses that were greater in yoghurt consumers. CONCLUSIONS: Yoghurt consumption is associated with lower body mass index, lower body weight/weight gain, smaller waist circumference and lower body fat in epidemiological studies. RCTs suggest weight reduction effects, but do not permit determination of a cause-effect relationship. Well-controlled, adequately powered trials in research and community settings appear likely to identify a modest but beneficial effect of yoghurt consumption for prevention of weight gain and management of obesity. The ready availability of yoghurt (a nutrient-dense food) and its ease of introduction to most diets suggests that educating the public to eat yoghurt as part of a balanced and healthy diet may potentially contribute to improved public health. Future carefully designed RCTs could provide proof of principle and large community-based studies could determine the practical impact of yoghurt on body weight/composition

A comparison of genomic copy number calls by Partek Genomics Suite, Genotyping Console and Birdsuite algorithms to quantitative PCR

<p>Abstract</p> <p>Background</p> <p>Copy number variants are >1 kb genomic amplifications or deletions that can be identified using array platforms. However, arrays produce substantial background noise that contributes to high false discovery rates of variants. We hypothesized that quantitative PCR could finitely determine copy number and assess the validity of calling algorithms.</p> <p>Results</p> <p>Using data from 29 Affymetrix SNP 6.0 arrays, we determined copy numbers using three programs: Partek Genomics Suite, Affymetrix Genotyping Console 2.0 and Birdsuite. We compared array calls at 25 chromosomal regions to those determined by qPCR and found nearly identical calls in regions of copy number 2. Conversely, agreement differed in regions called variant by at least one method. The highest overall agreement in calls, 91%, was between Birdsuite and quantitative PCR. Partek Genomics Suite calls agreed with quantitative PCR 76% of the time while the agreement of Affymetrix Genotyping Console 2.0 with quantitative PCR was 79%.</p> <p>Conclusions</p> <p>In 38 independent samples, 96% of Birdsuite calls agreed with quantitative PCR. Analysis of three copy number calling programs and quantitative PCR showed Birdsuite to have the greatest agreement with quantitative PCR.</p

Householders’ Mental Models of Domestic Energy Consumption: Using a Sort-And-Cluster Method to Identify Shared Concepts of Appliance Similarity

If in-home displays and other interventions are to successfully influence people's energy consumption, they need to communicate about energy in terms that make sense to users. Here we explore householders' perceptions of energy consumption, using a novel combination of card-sorting and clustering to reveal shared patterns in the way people think about domestic energy consumption. The data suggest that, when participants were asked to group appliances which they felt naturally 'went together', there are relatively few shared ideas about which appliances are conceptually related. To the extent participants agreed on which appliances belonged together, these groupings were based on activities (e.g., entertainment) and location within the home (e.g., kitchen); energy consumption was not an important factor in people's categorisations. This suggests messages about behaviour change aimed at reducing energy consumption might better be tied to social practices than to consumption itself

Genome-Wide Analysis of Copy Number Variation in Type 1 Diabetes

Type 1 diabetes (T1D) tends to cluster in families, suggesting there may be a genetic component predisposing to disease. However, a recent large-scale genome-wide association study concluded that identified genetic factors, single nucleotide polymorphisms, do not account for overall familiality. Another class of genetic variation is the amplification or deletion of >1 kilobase segments of the genome, also termed copy number variations (CNVs). We performed genome-wide CNV analysis on a cohort of 20 unrelated adults with T1D and a control (Ctrl) cohort of 20 subjects using the Affymetrix SNP Array 6.0 in combination with the Birdsuite copy number calling software. We identified 39 CNVs as enriched or depleted in T1D versus Ctrl. Additionally, we performed CNV analysis in a group of 10 monozygotic twin pairs discordant for T1D. Eleven of these 39 CNVs were also respectively enriched or depleted in the Twin cohort, suggesting that these variants may be involved in the development of islet autoimmunity, as the presently unaffected twin is at high risk for developing islet autoimmunity and T1D in his or her lifetime. These CNVs include a deletion on chromosome 6p21, near an HLA-DQ allele. CNVs were found that were both enriched or depleted in patients with or at high risk for developing T1D. These regions may represent genetic variants contributing to development of islet autoimmunity in T1D