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Next-generation sequencing (NGS) represents a significant advancement in clinical genetics. However, its use creates several technical, data interpretation and management challenges. It is essential to follow a consistent data analysis pipeline to achieve the highest possible accuracy and avoid false variant calls. Herein, we aimed to compare the performance of twenty-eight combinations of NGS data analysis pipeline compartments, including short-read mapping (BWA-MEM, Bowtie2, Stampy), variant calling (GATK-HaplotypeCaller, GATK-UnifiedGenotyper, SAMtools) and interval padding (null, 50bp, 100bp) methods, along with a commercially available pipeline (BWA Enrichment, Illumina®). C59 chemical structure Fourteen germline DNA samples from breast cancer patients were sequenced using a targeted NGS panel approach and subjected to data analysis.

We highlight that interval padding is required for the accurate detection of intronic variants including spliceogenic pathogenic variants (PVs). In addition, using nearly default parameters, tormatics personnel might not always be available. The results also reveal the necessity of improving the existing tools and/or at the same time developing new pipelines to generate more reliable and more consistent data.Complex cascades of RNA-binding proteins regulate the mRNA metabolism and influence gene expression. Several distinct proteins act at different stages of mRNA life cycle. SR family proteins in yeast are implicated in mRNA processing and nuclear export. In this report, we uncover the role of an SR/RGG-motif containing mRNA export factor Gbp2 in mRNA translation regulation. We demonstrate that Gbp2 localizes to cytoplasmic granules upon heat shock and oxidative stress. Our pull-down assays demonstrate that Gbp2 directly binds to the conserved translation factor eIF4G1 via its RGG motif. We further mapped the region on eIF4G1 to which Gbp2 binds and observed that the binding region overlaps with another translation repressor Sbp1. We found that the RGG-motif deletion mutant is defective in localizing to polysome fractions. Upon tethering Gbp2 to a GFP reporter mRNA in vivo, translation of GFP reporter decreased significantly indicating that Gbp2 acts as a translation repressor. Consistent with these results, we show that Gbp2 can directly repress mRNA translation in the in vitro translation systems in an RGG-motif dependent manner. Taken together, our results establish that the mRNA export factor Gbp2 has a vital role in repressing translation of mRNA. We propose that Gbp2 is a multifaceted RGG-motif protein responsible for translational repression without affecting mRNA levels.Defining protein complexes in the cell is important for learning about cellular processes mechanisms as they perform many of the molecular functions in these processes. Most of the proposed algorithms predict a complex as a dense area in a Protein-Protein Interaction (PPI) network. Others, on the other hand, weight the network using gene expression or geneontology (GO). These approaches, however, eliminate the proteins and their edges that offer no gene expression data. This can lead to the loss of important topological relations. Therefore, in this study, a method based on the Gene Expression and Core-Attachment (GECA) approach was proposed for addressing these limitations. GECA is a new technique to identify core proteins using common neighbor techniques and biological information. Moreover, GECA improves the attachment technique by adding the proteins that have low closeness but high similarity to the gene expression of the core proteins. GECA has been compared with several existing methods and proved in most datasets to be able to achieve the highest F-measure. The evaluation of complexes predicted by GECA shows high biological significance.

Postoperative complications are associated with prolonged hospital stay and a rise in costs of treatment. The Comprehensive Complication Index (CCI) was developed as a scoring system that does not only take the most severe complication into account but all complications after surgery. Our aim was to compare the Clavien-Dindo scoring system with the CCI in predicting length of hospital stay (LOHS) and in-hospital costs after colorectal resections.

Complications occurring after surgical procedures, performed between October 2012 and September 2013, were prospectively recorded. During this period 164 patients developed complication(s). Only patients that underwent a colorectal resection were included. Multivariable linear regression analysis was performed to find independent predictors of in-hospital costs and LOHS.

64 patients (age (range) 69 (10-91) years, M/F 36/28) were retained. 46 (71.9%) patients had a Clavien-Dindo score ≥ IIIb. Median (IQR) CCI was 40 (30.2-53.9). Mean (±SD) in-hospitals costs for all patients were €12,920 ± €10,229. The adjusted difference (95% CI,

-value) in in-hospital costs for minor and major (Clavien-Dindo ≥ IIIb) complications was 10,021 (€4283 to €15,759,

 = 0.001). A 10 point increase in CCI increased in-hospital costs by €2040. Multivariable analysis retained CCI > 40 as the only independent risk factor for increased in-hospital costs (Standard Beta Coeffic (

-value) 8063 (

 = 0.022).

CCI is a better predictor of in-hospital costs than Clavien-Dindo score to classify complications after colorectal resections, as it captures all complications. Further research is warranted to extrapolate our findings to other sub-specialities of surgery.

CCI is a better predictor of in-hospital costs than Clavien-Dindo score to classify complications after colorectal resections, as it captures all complications. Further research is warranted to extrapolate our findings to other sub-specialities of surgery.The term "menstrual health" has seen increased use across advocacy, programming, policy, and research, but has lacked a consistent, self-contained definition. As a rapidly growing field of research and practice a comprehensive definition is needed to (1) ensure menstrual health is prioritised as a unified objective in global health, development, national policy, and funding frameworks, (2) elucidate the breadth of menstrual health, even where different needs may be prioritised in different sectors, and (3) facilitate a shared vocabulary through which stakeholders can communicate across silos to share learning. To achieve these aims, we present a definition of menstrual health developed by the Terminology Action Group of the Global Menstrual Collective. We describe the definition development process, drawing on existing research and terminology, related definitions of health, and consultation with a broad set of stakeholders. Further, we provide elaboration, based on current evidence, to support interpretation of the definition.