Disease classification from capillary electrophoresis: mass spectrometry

We investigate the possibility of using pattern recognition techniques to classify various disease types using data produced by a new form of rapid Mass Spectrometry. The data format has several advantages over other high-throughput technologies and as such could become a useful diagnostic tool. We investigate the binary and multi-class performances obtained using standard classifiers as the number of features is varied and conclude that there is potential in this technique and suggest research directions that would improve performance

The KOUNCIL Consortium: From Genetic Defects to Therapeutic Development for Nephronophthisis

Contains fulltext : 191425.pdf (publisher's version ) (Open Access

Dimensionality reduction of protein mass spectrometry data using random projection

Protein mass spectrometry (MS) pattern recognition has recently emerged as a new method for cancer diagnosis. Unfortunately, classification performance may degrade owing to the enormously high dimensionality of the data. This paper investigates the use of Random Projection in protein MS data dimensionality reduction. The effectiveness of Random Projection (RP) is analyzed and compared against Principal Component Analysis (PCA) by using three classification algorithms, namely Support Vector Machine, Feed-forward Neural Networks and K-Nearest Neighbour. Three real-world cancer data sets are employed to evaluate the performances of RP and PCA. Through the investigations, RP method demonstrated better or at least comparable classification performance as PCA if the dimensionality of the projection matrix is sufficiently large. This paper also explores the use of RP as a pre-processing step prior to PCA. The results show that without sacrificing classification accuracy, performing RP prior to PCA significantly improves the computational time.<br /

Non-invasive sources of cells with primary cilia from pediatric and adult patients

Contains fulltext : 153513.pdf (publisher's version ) (Open Access)BACKGROUND: Ciliopathies give rise to a multitude of organ-specific pathologies; obtaining relevant primary patient material is useful for both diagnostics and research. However, acquisition of primary ciliated cells from patients, particularly pediatric patients, presents multiple difficulties. Biopsies and blood samples are invasive, and patients (and their parents) may be reluctant to travel to medical centers, especially for research purposes. We sought to develop non-invasive methods of obtaining viable and ciliated primary cells from ciliopathy patients which could be obtained in the home environment. FINDINGS: We introduce two methods for the non-invasive acquisition of primary ciliated cells. In one approach, we collected spontaneously shed deciduous (milk) teeth from children. Fibroblast-like cells were observed after approximately 2 weeks of culture of fragmented teeth. Secondly, urine samples were collected from children or adults. Cellular content was isolated and after approximately 1 week, renal epithelial cells were observed. Both urine and tooth-derived cells ciliate and express ciliary proteins visible with immunofluorescence. Urine-derived renal epithelial cells (URECs) are amenable to 3D culturing, siRNA knockdown, and ex vivo drug testing. CONCLUSIONS: As evidence continues to accumulate showing that the primary cilium has a central role in development and disease, the need for readily available and ciliated patient cells will increase. Here, we introduce two methods for the non-invasive acquisition of cells with primary cilia. We believe that these cells can be used for further ex vivo study of ciliopathies and in the future, for personalized medicine

Den osynlige fotbollsspelaren : Redovisning av fotbollsspelare på balansräkningen

Problem: Genom Svenska Fotbollförbundets införande av elitlicensen får fotbollsklubbar redovisa inköpta spelare som en tillgång eller kostnadsföra utgiften direkt. Dock får ej icke förvärvade spelare aktiveras på balansräkningen. Syfte: Undersöka möjligheten att redovisa alla spelare i en fotbollsklubb ekonomiskt samt undersöka sätt att värdera spelare vilka saknar anskaffningspris. Även utreda om en sådan redovisning leder till en mer ekonomisk rättvisande bild av klubbarna och hur jämförbarheten mellan klubbarna påverkas. Vill väcka intresse kring problemen med spelarvärdering på balansräkningen. Genomförande: Studie av litteratur i ämnet, gällande lagar och Svenska Fotbollförbundets elitlicens. Material insamlades genom en kvalitativ undersökning i form av intervjuer av kunniga personer inom elitfotboll och redovisning. Materialet från litteratur och intervjuer sammankopplas och diskuteras. Slutsatser: Undersökningen visar att rådande regler för fotbollsklubbarnas redovisning är efter de möjligheter som finns utformade på ett bra sätt och att därmed endast förvärvade spelare kan aktiveras. Detta då objektiva värderingsmodeller för ej köpta spelare saknas och att detta krävs för att få ett korrekt värde på spelaren. Dagens regler ger inte en helt rättvisande bild av fotbollsklubbarna men dock så väl som är möjligt idag

Prioritization and burden analysis of rare variants in 208 candidate genes suggest they do not play a major role in CAKUT

The leading cause of end-stage renal disease in children is attributed to congenital anomalies of the kidney and urinary tract (CAKUT). Familial clustering and mouse models support the presence of monogenic causes. Genetic testing is insufficient as it mainly focuses on HNF1B and PAX2 mutations that are thought to explain CAKUT in 5-15% of patients. To identify novel, potentially pathogenic variants in additional genes, we designed a panel of genes identified from studies on familial forms of isolated or syndromic CAKUT and genes suggested by in vitro and in vivo CAKUT models. The coding exons of 208 genes were analyzed in 453 patients with CAKUT using next-generation sequencing. Rare truncating, splice-site variants, and non-synonymous variants, predicted to be deleterious and conserved, were prioritized as the most promising variants to have an effect on CAKUT. Previously reported disease-causing mutations were detected, but only five were fully penetrant causal mutations that improved diagnosis. We prioritized 148 candidate variants in 151 patients, found in 82 genes, for follow-up studies. Using a burden test, no significant excess of rare variants in any of the genes in our cohort compared with controls was found. Thus, in a study representing the largest set of genes analyzed in CAKUT patients to date, the contribution of previously implicated genes to CAKUT risk was significantly smaller than expected, and the disease may be more complex than previously assumed