The role of octreotide in preventing complications after pancreatoduodenectomy for cancer

Background Although the mortality rate of pancreatoduodenectomy has fallen sharply over the last two decades, there is still a risk of serious complications resulting from leakage at the site of anastomosis between the pancreatic remnant and the gastrointestinal tract. Numerous techniques have been described to minimise the risk of these anastomotic leaks, but they can be difficult to avoid if the distal pancreas is unobstructed with a soft parenchyma and a non-dilated duct. The risk of leakage is largely dependent upon the presence of activated pancreatic enzymes, and this fact provides a rationale for the perioperative use of the somatostatin analogue octreotide to inhibit exocrine pancreatic secretion. Discussion Six prospective randomised controlled trials have been published on the use of prophylactic octreotide in pancreatic surgery, five from Europe and one from the USA. The five (multicentre) European studies have consistently shown that octreotide reduces the postoperative complication rate, but the American study does not confirm this benefit. Methodological differences may explain the discrepancy, notably the fact that most of the US patients had received preoperative chemoradiation which is likely to have reduced enzyme secretion. A meta-analysis of four of these studies showed that octreotide lowered the rate of postoperative complications from 37 to 21%, chiefly by reducing the risk of pancreatic fistula. Prophylactic octreotide therapy is cost effective and should be used at least in patients with normal pancreatic parenchyma

Genomic organization and cytokine-mediated inducibility of the human TRIM-8/Gerp gene.

Cytokine signaling is negatively regulated by a set of SH2 domain-containing proteins, the Suppressors of Cytokine Signaling (SOCS) acting as intracellular modulators. Experimental evidence indicates that SOCS gene expression is induced by cytokines and pro-inflammatory stimuli and is highly controlled both at transcription and translation level. Furthermore, SOCS proteins appear rapidly degraded inside the cells, mostly controlling their stability by interacting with specific molecules such as elongin B and C. It has been shown that SOCS-1/JAB, a member of the SOCS family, interacts with TRIM-8/Gerp, a new ring protein specifically binding SOCS-1 recombinant polypeptide in-vitro and in-vivo. Trim-8/Gerp, transcribes a 3.0-kb mRNA, spans 551 AA and is highly conserved during evolution. In addition, it can be induced by IFN-γ in epithelial and lymphoid cells and is expressed mostly ubiquitously in murine and human tissues. Here in this report we present the genomic organization of this new SOCS-1 interactor, and we add new tools for extending investigation of the complex mechanism that undergoes negatively regulation of cytokine signaling

NF-κB: blending metabolism, immunity, and inflammation

The procurement and management of nutrients and ability to fight infections are fundamental requirements for survival. These defense responses are bioenergetically costly, requiring the immune system to balance protection against pathogens with the need to maintain metabolic homeostasis. NF-κB transcription factors are central regulators of immunity and inflammation. Over the last two decades, these factors have emerged as a pivotal node coordinating the immune and metabolic systems in physiology and the etiopathogenesis of major threats to human health, including cancer, autoimmunity, chronic inflammation, and others. In this review, we discuss recent advances in understanding how NF-κB-dependent metabolic programs control inflammation, metabolism, and immunity and how improved knowledge of them may lead to better diagnostics and therapeutics for widespread human diseases

HPC-REDItools: A novel HPC-aware tool for improved large scale RNA-editing analysis

Background: RNA editing is a widespread co-/post-transcriptional mechanism that alters primary RNA sequences through the modification of specific nucleotides and it can increase both the transcriptome and proteome diversity. The automatic detection of RNA-editing from RNA-seq data is computational intensive and limited to small data sets, thus preventing a reliable genome-wide characterisation of such process. Results: In this work we introduce HPC-REDItools, an upgraded tool for accurate RNA-editing events discovery from large dataset repositories. Availability: https://github.com/BioinfoUNIBA/REDItools2. Conclusions: HPC-REDItools is dramatically faster than the previous version, REDItools, enabling big-data analysis by means of a MPI-based implementation and scaling almost linearly with the number of available cores

A gene expression atlas for different kinds of stress in the mouse brain

Stressful experiences are part of everyday life and animals have evolved physiological and behavioral responses aimed at coping with stress and maintaining homeostasis. However, repeated or intense stress can induce maladaptive reactions leading to behavioral disorders. Adaptations in the brain, mediated by changes in gene expression, have a crucial role in the stress response. Recent years have seen a tremendous increase in studies on the transcriptional effects of stress. The input raw data are freely available from public repositories and represent a wealth of information for further global and integrative retrospective analyses. We downloaded from the Sequence Read Archive 751 samples (SRA-experiments), from 18 independent BioProjects studying the effects of different stressors on the brain transcriptome in mice. We performed a massive bioinformatics re-analysis applying a single, standardized pipeline for computing differential gene expression. This data mining allowed the identification of novel candidate stress-related genes and specific signatures associated with different stress conditions. The large amount of computational results produced was systematized in the interactive “Stress Mice Portal”

Symptoms and Surgical Management of a Distal Choledochal Cyst in a Patient with Pancreas Divisum: Case Report and Review of the Literature

We report the case of a 63-year-old woman who presented with the rare finding of a distal choledochocele in a pancreas divisum with recurrent abdominal pain and episodes of pancreatitis. She underwent successful resection with choledochectomy, papillectomy and reconstruction with a hepatico-jejunostomy and reinsertion of the uncinate pancreatic duct into the same jejunal loop. Comparable literature findings are discussed with regard to the presented case

Predictors of the need for an extracervical approach to intrathoracic goitre

Background: Sternotomy and lateral thoracotomy are required infrequently to remove an intrathoracic goitre (ITG). As few studies have explored the need for an extracervical approach (ECA), the aim of this study was to examine this in a large cohort of patients. Methods: A prospective database of all patients who had surgery for ITG between 2004 and 2016 was interrogated. Patient demographics, preoperative characteristics and type of operation were analysed to identify factors associated with an ECA. Results: Of 237 patients who had surgery for ITG, 29 (12·2 per cent) required an ECA. ITGs below the aortic arch (odds ratio (OR) 10·84; P = 0·004), those with an iceberg shape (OR 59·30; P < 0·001) and revisional surgery (OR 4·83; P = 0·022) were significant preoperative predictors of an ECA. Conclusion: The extent of intrathoracic extension in relation to the aortic arch, iceberg goitre shape and revisional surgery were independent risk factors for ECA. Careful preoperative assessment should take these factors into consideration when determining the optimal surgical approach to ITG

CoVaCS : a consensus variant calling system

Background: The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and precision medicine. The body of genome resequencing data is progressively increasing underlining the need for accurate and time-effective bioinformatics systems for genotyping - a crucial prerequisite for identification of candidate causal mutations in diagnostic screens. Results: Here we present CoVaCS, a fully automated, highly accurate system with a web based graphical interface for genotyping and variant annotation. Extensive tests on a gold standard benchmark data-set -the NA12878 Illumina platinum genome- confirm that call-sets based on our consensus strategy are completely in line with those attained by similar command line based approaches, and far more accurate than call-sets from any individual tool. Importantly our system exhibits better sensitivity and higher specificity than equivalent commercial software. Conclusions: CoVaCS offers optimized pipelines integrating state of the art tools for variant calling and annotation for whole genome sequencing (WGS), whole-exome sequencing (WES) and target-gene sequencing (TGS) data. The system is currently hosted at Cineca, and offers the speed of a HPC computing facility, a crucial consideration when large numbers of samples must be analysed. Importantly, all the analyses are performed automatically allowing high reproducibility of the results. As such, we believe that CoVaCS can be a valuable tool for the analysis of human genome resequencing studies. CoVaCS is available at: https://bioinformatics.cineca.it/covacs

PeachVar-DB : Curated Collection of Genetic Variations for the Interactive Analysis of Peach Genome Data

Applying next-generation sequencing (NGS) technologies to species of agricultural interest has the potential to accelerate the understanding and exploration of genetic resources. The storage, availability and maintenance of huge quantities of NGS-generated data remains a major challenge. The PeachVar-DB portal, available at http://hpc-bioinformatics.cineca.it/peach, is an open-source catalog of genetic variants present in peach (Prunus persica L. Batsch) and wild-related species of Prunus genera, annotated from 146 samples publicly released on the Sequence Read Archive (SRA). We designed a user-friendly web-based interface of the database, providing search tools to retrieve single nucleotide polymorphism (SNP) and InDel variants, along with useful statistics and information. PeachVar-DB results are linked to the Genome Database for Rosaceae (GDR) and the Phytozome database to allow easy access to other external useful plant-oriented resources. In order to extend the genetic diversity covered by the PeachVar-DB further, and to allow increasingly powerful comparative analysis, we will progressively integrate newly released data