Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor

The presence of different transcripts of a gene across samples can be analysed by whole-transcriptome microarrays. Reproducing results from published microarray data represents a challenge due to the vast amounts of data and the large variety of pre-processing and filtering steps employed before the actual analysis is carried out. To guarantee a firm basis for methodological development where results with new methods are compared with previous results it is crucial to ensure that all analyses are completely reproducible for other researchers. We here give a detailed workflow on how to perform reproducible analysis of the GeneChip Human Exon 1.0 ST Array at probe and probeset level solely in R/Bioconductor, choosing packages based on their simplicity of use. To exemplify the use of the proposed workflow we analyse differential splicing and differential gene expression in a publicly available dataset using various statistical methods. We believe this study will provide other researchers with an easy way of accessing gene expression data at different annotation levels and with the sufficient details needed for developing their own tools for reproducible analysis of the GeneChip Human Exon 1.0 ST Array

Level of muscle regeneration in limb-girdle muscular dystrophy type 2I relates to genotype and clinical severity

<p>Abstract</p> <p>Background</p> <p>The balance between muscle regeneration and ongoing degeneration is a relationship that greatly influences the progression of muscular dystrophy. Numerous factors may influence the muscle regeneration, but more information about the relationship between genotype, clinical severity and the ability to regenerate is needed.</p> <p>Methods</p> <p>Muscle biopsies were obtained from the tibialis anterior muscle, and frozen sections were stained for general histopathological and immunohistological evaluation. Differences between groups were considered statistical significant at <it>P </it>< 0.05 using Student's unpaired <it>t</it>-test.</p> <p>Results</p> <p>We found that all patients with limb-girdle muscular dystrophy type 2I (LGMD2I) had a large number of internally nucleated fibers, a sign of previous regeneration. The level of expression of muscle-specific developmental proteins, such as neonatal myosin heavy chain (nMHC) and myogenin, was related to the clinical severity. Additionally, we found that the majority of nMHC-positive fibers did not stain positively for utrophin in patients who were compound heterozygous for the L276I mutation, suggesting that the predominant form of regeneration in these patients is fiber repair rather than formation of new fibers. Double staining showed that many smaller nMHC-positive fibers were positive for antibodies against the glycosylation on α-dystroglycan, suggesting that such glycosylation may be a result of muscle regeneration.</p> <p>Conclusion</p> <p>Severely affected patients with LGMD2I have a high level of muscle degeneration, which leads to a high rate of regeneration, but this is insufficient to change the imbalance between degeneration and regeneration, ultimately leading to progressive muscle wasting. Detailed information regarding the level and rate of muscle regeneration and potential obstructions of the regenerative pathway should be of use for future therapies involving satellite-cell activation.</p

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Objective: Through manual review of clinical notes for patients with type 2 diabetes mellitus attending a Danish diabetes center, the aim of the study was to identify adverse drug reactions (ADRs) associated with three classes of glucose-lowering medicines: "Combinations of oral blood-glucose lowering medicines" (A10BD), "dipeptidyl peptidase-4 (DDP-4) inhibitors" (A10BH), and "other blood glucose lowering medicines" (A10BX). Specifically, we aimed to describe the potential of clinical notes to identify new ADRs and to evaluate if sufficient information can be obtained for causality assessment. Methods: For observed adverse events (AEs) we extracted time to onset, outcome, and suspected medicine(s). AEs were assessed according to World Health Organization-Uppsala Monitoring Centre causality criteria and analyzed with respect to suspected medicines, type of ADR (system organ class), seriousness and labeling status. Findings: A total of 207 patients were included in the study leading to the identification of 163 AEs. 14% were categorized as certain, 60% as probable/likely, and 26% as possible. 15 (9%) ADRs were unlabeled of which two were serious: peripheral edema associated with sitagliptin and stomach ulcer associated with liraglutide. Of the unlabeled ADRs, 13 (87%) were associated with "other blood glucose lowering medications," the remaining 2 (13%) with "DDP-4 inhibitors." Conclusion: Clinical notes could potentially reveal unlabeled ADRs associated with prescribed medicines and sufficient information is generally available for causality assessment. However, manual review of clinical notes is too time-consuming for routine use and hence there is a need for developing information technology (IT) tools for automatic screening of patient records with the purpose to detect information about potentially serious and unlabeled ADRs

Technical report:a novel porcine model of acute pyelonephritis

A porcine model of acute Escherichia coli pyelonephritis is described. Nine female pigs with a mean weight  of 19 kg were included in the study. Following laparotomy and ureterotomy, catheters were placed bilaterally  in the renal pelvis. A culture of a porcine E. coli strain (109 CFU/mL, volume 3.25 mL) was inoculated  unilaterally in the renal pelvis. Following bacterial inoculation, the catheter was occluded for 20 min. The  inoculation procedure was repeated after two and four hrs. The contralateral kidneys served as controls  and were inoculated with sterile saline. Six hrs after the first inoculation pigs were euthanized and samples  of blood, abdominal swabs, urine and specimens from kidney, liver and spleen were cultured. The inflammatory  response in the kidneys, renal lymph nodes, liver and spleen was evaluated both macroscopically  and histologically and E. coli was identified by immunohistochemistry. E. coli was reisolated from all the  inoculated kidneys and was detected immunohistochemically in all inoculated kidneys, in four renal lymph  nodes from inoculated sides and in four spleens. Evidence of systemic bacterial spread was observed in five  pigs. Gross and histological lesions of acute pyelonephritis comparable to human cases were demonstrated  in all but one inoculated kidney. In conclusion, a novel porcine model for evaluating the pathogenesis of  acute pyelonephritis was established.

Exposure time independent summary statistics for assessment of drug dependent cell line growth inhibition

BACKGROUND: In vitro generated dose-response curves of human cancer cell lines are widely used to develop new therapeutics. The curves are summarised by simplified statistics that ignore the conventionally used dose-response curves’ dependency on drug exposure time and growth kinetics. This may lead to suboptimal exploitation of data and biased conclusions on the potential of the drug in question. Therefore we set out to improve the dose-response assessments by eliminating the impact of time dependency. RESULTS: First, a mathematical model for drug induced cell growth inhibition was formulated and used to derive novel dose-response curves and improved summary statistics that are independent of time under the proposed model. Next, a statistical analysis workflow for estimating the improved statistics was suggested consisting of 1) nonlinear regression models for estimation of cell counts and doubling times, 2) isotonic regression for modelling the suggested dose-response curves, and 3) resampling based method for assessing variation of the novel summary statistics. We document that conventionally used summary statistics for dose-response experiments depend on time so that fast growing cell lines compared to slowly growing ones are considered overly sensitive. The adequacy of the mathematical model is tested for doxorubicin and found to fit real data to an acceptable degree. Dose-response data from the NCI60 drug screen were used to illustrate the time dependency and demonstrate an adjustment correcting for it. The applicability of the workflow was illustrated by simulation and application on a doxorubicin growth inhibition screen. The simulations show that under the proposed mathematical model the suggested statistical workflow results in unbiased estimates of the time independent summary statistics. Variance estimates of the novel summary statistics are used to conclude that the doxorubicin screen covers a significant diverse range of responses ensuring it is useful for biological interpretations. CONCLUSION: Time independent summary statistics may aid the understanding of drugs’ action mechanism on tumour cells and potentially renew previous drug sensitivity evaluation studies