RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays

<p>Abstract</p> <p>Background</p> <p>Reverse Phase Protein Arrays (RPPA) are convenient assay platforms to investigate the presence of biomarkers in tissue lysates. As with other high-throughput technologies, substantial amounts of analytical data are generated. Over 1000 samples may be printed on a single nitrocellulose slide. Up to 100 different proteins may be assessed using immunoperoxidase or immunoflorescence techniques in order to determine relative amounts of protein expression in the samples of interest.</p> <p>Results</p> <p>In this report an RPPA Information Management System (RIMS) is described and made available with open source software. In order to implement the proposed system, we propose a metadata format known as reverse phase protein array markup language (RPPAML). RPPAML would enable researchers to describe, document and disseminate RPPA data. The complexity of the data structure needed to describe the results and the graphic tools necessary to visualize them require a software deployment distributed between a client and a server application. This was achieved without sacrificing interoperability between individual deployments through the use of an open source semantic database, S3DB. This data service backbone is available to multiple client side applications that can also access other server side deployments. The RIMS platform was designed to interoperate with other data analysis and data visualization tools such as Cytoscape.</p> <p>Conclusion</p> <p>The proposed RPPAML data format hopes to standardize RPPA data. Standardization of data would result in diverse client applications being able to operate on the same set of data. Additionally, having data in a standard format would enable data dissemination and data analysis.</p

The clinical features of the piriformis syndrome: a systematic review

Piriformis syndrome, sciatica caused by compression of the sciatic nerve by the piriformis muscle, has been described for over 70 years; yet, it remains controversial. The literature consists mainly of case series and narrative reviews. The objectives of the study were: first, to make the best use of existing evidence to estimate the frequencies of clinical features in patients reported to have PS; second, to identify future research questions. A systematic review was conducted of any study type that reported extractable data relevant to diagnosis. The search included all studies up to 1 March 2008 in four databases: AMED, CINAHL, Embase and Medline. Screening, data extraction and analysis were all performed independently by two reviewers. A total of 55 studies were included: 51 individual and 3 aggregated data studies, and 1 combined study. The most common features found were: buttock pain, external tenderness over the greater sciatic notch, aggravation of the pain through sitting and augmentation of the pain with manoeuvres that increase piriformis muscle tension. Future research could start with comparing the frequencies of these features in sciatica patients with and without disc herniation or spinal stenosis

The effect of obesity on spirometry tests among healthy non-smoking adults

<p>Abstract</p> <p>Introduction</p> <p>The effects of obesity on pulmonary functions have not been addressed previously among Saudi population. We aim to study the effects of obesity on spirometry tests among healthy non-smoking adults.</p> <p>Methods</p> <p>A cross sectional study conducted among volunteers healthy non-smoking adults Subjects. We divided the subjects into two groups according to their BMI. The first group consisted of non-obese subjects with BMI of 18 to 24.9 kg/m2 and the second group consisted of obese subjects with BMI of 30 kg/m2 and above. Subjects underwent spirometry tests according to American thoracic society standards with measurement of the following values: the forced vital capacity (FVC), forced expiratory volume in one second (FEV1), peak expiratory flow rate (PEF) and forced mid-expiratory flow (FEF25-75).</p> <p>Results</p> <p>The total subjects were 294 with a mean age of 32 years. There were 178 males and 116 females subjects. We found no significant differences in FEV1 (p value = 0.686), FVC (p value = 0.733), FEV1/FVC Ratio (p value = 0.197) and FEF25-75 (p value = 0.693) between the obese and non-obese subjects. However, there was significantly difference in PEF between the two groups (p value < 0.020).</p> <p>Conclusion</p> <p>Obesity does not have effect on the spirometry tests (except PEF) among health non-smoking adults. We recommend searching for alternative diagnosis in case of findings abnormal spirometry tests results among obese subjects.</p

New physical characterization of the Fontana Lapilli basaltic Plinian eruption, Nicaragua

The Fontana Lapilli deposit was erupted in the late Pleistocene from a vent, or multiple vents, located near Masaya volcano (Nicaragua) and is the product of one of the largest basaltic Plinian eruptions studied so far. This eruption evolved from an initial sequence of fluctuating fountain-like events and moderately explosive pulses to a sustained Plinian episode depositing fall beds of highly vesicular basaltic-andesite scoria (SiO2 > 53 wt%). Samples show unimodal grain size distribution and a moderate sorting that are uniform in time. The juvenile component predominates (> 96 wt%) and consists of vesicular clasts with both sub-angular and fluidal, elongated shapes. We obtain a maximum plume height of 32 km and an associated mass eruption rate of 1.4 × 108 kg s−1 for the Plinian phase. Estimates of erupted volume are strongly sensitive to the technique used for the calculation and to the distribution of field data. Our best estimate for the erupted volume of the majority of the climactic Plinian phase is between 2.9 and 3.8 km3 and was obtained by applying a power-law fitting technique with different integration limits. The estimated eruption duration varies between 4 and 6 h. Marine-core data confirm that the tephra thinning is better fitted by a power-law than by an exponential trend

Can Simply Answering Research Questions Change Behaviour? Systematic Review and Meta Analyses of Brief Alcohol Intervention Trials

BACKGROUND: Participant reports of their own behaviour are critical for the provision and evaluation of behavioural interventions. Recent developments in brief alcohol intervention trials provide an opportunity to evaluate longstanding concerns that answering questions on behaviour as part of research assessments may inadvertently influence it and produce bias. The study objective was to evaluate the size and nature of effects observed in randomized manipulations of the effects of answering questions on drinking behaviour in brief intervention trials. METHODOLOGY/PRINCIPAL FINDINGS: Multiple methods were used to identify primary studies. Between-group differences in total weekly alcohol consumption, quantity per drinking day and AUDIT scores were evaluated in random effects meta-analyses. Ten trials were included in this review, of which two did not provide findings for quantitative study, in which three outcomes were evaluated. Between-group differences were of the magnitude of 13.7 (-0.17 to 27.6) grams of alcohol per week (approximately 1.5 U.K. units or 1 standard U.S. drink) and 1 point (0.1 to 1.9) in AUDIT score. There was no difference in quantity per drinking day. CONCLUSIONS/SIGNIFICANCE: Answering questions on drinking in brief intervention trials appears to alter subsequent self-reported behaviour. This potentially generates bias by exposing non-intervention control groups to an integral component of the intervention. The effects of brief alcohol interventions may thus have been consistently under-estimated. These findings are relevant to evaluations of any interventions to alter behaviours which involve participant self-report

Novel image analysis approach for quantifying expression of nuclear proteins assessed by immunohistochemistry: application to measurement of oestrogen and progesterone receptor levels in breast cancer

INTRODUCTION: Manual interpretation of immunohistochemistry (IHC) is a subjective, time-consuming and variable process, with an inherent intra-observer and inter-observer variability. Automated image analysis approaches offer the possibility of developing rapid, uniform indicators of IHC staining. In the present article we describe the development of a novel approach for automatically quantifying oestrogen receptor (ER) and progesterone receptor (PR) protein expression assessed by IHC in primary breast cancer. METHODS: Two cohorts of breast cancer patients (n = 743) were used in the study. Digital images of breast cancer tissue microarrays were captured using the Aperio ScanScope XT slide scanner (Aperio Technologies, Vista, CA, USA). Image analysis algorithms were developed using MatLab 7 (MathWorks, Apple Hill Drive, MA, USA). A fully automated nuclear algorithm was developed to discriminate tumour from normal tissue and to quantify ER and PR expression in both cohorts. Random forest clustering was employed to identify optimum thresholds for survival analysis. RESULTS: The accuracy of the nuclear algorithm was initially confirmed by a histopathologist, who validated the output in 18 representative images. In these 18 samples, an excellent correlation was evident between the results obtained by manual and automated analysis (Spearman\u27s rho = 0.9, P \u3c 0.001). Optimum thresholds for survival analysis were identified using random forest clustering. This revealed 7% positive tumour cells as the optimum threshold for the ER and 5% positive tumour cells for the PR. Moreover, a 7% cutoff level for the ER predicted a better response to tamoxifen than the currently used 10% threshold. Finally, linear regression was employed to demonstrate a more homogeneous pattern of expression for the ER (R = 0.860) than for the PR (R = 0.681). CONCLUSIONS: In summary, we present data on the automated quantification of the ER and the PR in 743 primary breast tumours using a novel unsupervised image analysis algorithm. This novel approach provides a useful tool for the quantification of biomarkers on tissue specimens, as well as for objective identification of appropriate cutoff thresholds for biomarker positivity. It also offers the potential to identify proteins with a homogeneous pattern of expression