A critical analysis of disability policy and practice in Flanders : toward differentiated manifestations of interdependency

Notions of citizenship and disability rights denote abstract, ambiguous, and contested principles, and realizing these ideas entails complexity in practice. This is particularly the case since the welfare state is no longer conceived as the principal provider of welfare services and resources in many European welfare states. In that vein, we critically analyze the underlying principles, rationales, values, and potential implications of the White Paper "Perspective 2020: a new support policy for disabled people" in Flanders (the Dutch speaking part of Belgium). We tease out which understanding of the disabled human subject is promoted by this so-called innovative social policy and excavate how policy makers and a diversity of actors involved in the policy implementation process consider the provision of care and support. Our main argument entails that the welfare state should acknowledge and vindicate differentiated manifestations of interdependency rather than reinforcing a dichotomy that is based on notions of in/dependent human subjects

Thorough in silico and in vitro cDNA analysis of 21 putative BRCA1 and BRCA2 splice variants and a complex tandem duplication in BRCA2 allowing the identification of activated cryptic splice donor sites in BRCA2 exon 11

For 21 putative BRCA1 and BRCA2 splice site variants, the concordance between mRNA analysis and predictions by in silico programs was evaluated. Aberrant splicing was confirmed for 12 alterations. In silico prediction tools were helpful to determine for which variants cDNA analysis is warranted, however, predictions for variants in the Cartegni consensus region but outside the canonical sites, were less reliable. Learning algorithms like Adaboost and Random Forest outperformed the classical tools. Further validations are warranted prior to implementation of these novel tools in clinical settings. Additionally, we report here for the first time activated cryptic donor sites in the large exon 11 of BRCA2 by evaluating the effect at the cDNA level of a novel tandem duplication (5 breakpoint in intron 4; 3 breakpoint in exon 11) and of a variant disrupting the splice donor site of exon 11 (c.6841+1G>C). Additional sites were predicted, but not activated. These sites warrant further research to increase our knowledge on cis and trans acting factors involved in the conservation of correct transcription of this large exon. This may contribute to adequate design of ASOs (antisense oligonucleotides), an emerging therapy to render cancer cells sensitive to PARP inhibitor and platinum therapies

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Etiology of knee pain in elite cyclists A 14-month consecutive case series

Overuse injuries of the knee are a common cause of missed training and competition days in elite cyclists, however the underlying conditions causing this knee pain are not well defined. We conducted a diagnostic study, investigating a consecutive series of 53 high level cyclists with non-traumatic knee pain over a 14 month period. Demographic data on the participants’ cycling specialty and training level was noted. Clinical information concerning knee pain intensity, location and occurrence were collected using a questionnaire. Our results show 7 different overuse injuries were identified. The prepatellar friction syndrome accounted for the majority of these overuse injuries (46%), while medial plica syndrome (15%), biceps femoris tendinopathy (7.5%), patellar tendinopathy (9.4%), infrapatellar plica friction syndrome (7.5%), infrapatellar fat pad impingement (5.7%) and iliotibial band syndrome (3.7%) were other causes of knee pain in these athletes. In contrast to current belief, our results show that instead of patellofemoral cartilage overload, friction related overuse injuries are the most frequent and underestimated cause of knee pain in high level cyclists

Dealing with pseudogenes in in the next generation sequencing era

Presence of pseudogenes is a dreadful issue in next generation sequencing (NGS), because their contamination can interfere with the detection of variants in the genuine gene and generate false positive and false negative variants. In this chapter we focus on issues related to the application of NGS strategies for analysis of genes with pseudogenes in a clinical setting. The degree to which a pseudogene impacts the ability to accurately detect and map variants in its parent gene depends on the degree of similarity (homology) with the parent gene itself. Hereby, target enrichment and mapping strategies are crucial factors to avoid “contaminating” pseudogene sequences. For target enrichment, we describe advantages and disadvantages of PCR- and capture-based strategies. For mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some examples of genes associated with Mendelian disorders, for which interesting NGS approaches are described to avoid interference with pseudogene sequences

Deep Diamond Re-ID.

Re-identification neural networks are widely used in numerous applications such as crowd control, crime investi- gations, safety systems and even in most smartphones to unlock the phone with a picture of the owner. These techniques are mostly used to re-identify faces or persons but in this paper we investigate the possibility to adapt these to also re-identify similar looking objects such as diamonds. Since polished diamonds are very similar to the naked eye, it is difficult to distinguish one diamond from another. We have indications that diamonds are sometimes switched by trained switchers with fake or less expensive stones, while they pretend to inspect the stone. A solution to this is diamond fingerprinting. We therefore propose a technique to generate a unique ID for each stone, which allows to re-identify the diamond solely based on an image of the gem. Since each diamond is assigned a unique ID it is even possible to keep track of the diamonds over time. This allows the seller to verify his stones before and after trading while switchers don’t stand a chance. For this task we trained and adapted a classification network optimized for both speed and accuracy.status: submitte