The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation.

A large repertoire of gene-centric data has been generated in the field of zebrafish biology. Although the bulk of these data are available in the public domain, most of them are not readily accessible or available in nonstandard formats. One major challenge is to unify and integrate these widely scattered data sources. We tested the hypothesis that active community participation could be a viable option to address this challenge. We present here our approach to create standards for assimilation and sharing of information and a system of open standards for database intercommunication. We have attempted to address this challenge by creating a community-centric solution for zebrafish gene annotation. The Zebrafish GenomeWiki is a 'wiki'-based resource, which aims to provide an altruistic shared environment for collective annotation of the zebrafish genes. The Zebrafish GenomeWiki has features that enable users to comment, annotate, edit and rate this gene-centric information. The credits for contributions can be tracked through a transparent microattribution system. In contrast to other wikis, the Zebrafish GenomeWiki is a 'structured wiki' or rather a 'semantic wiki'. The Zebrafish GenomeWiki implements a semantically linked data structure, which in the future would be amenable to semantic search. Database URL: http://genome.igib.res.in/twiki

Serum biomarkers in Acute Respiratory Distress Syndrome an ailing prognosticator

The use of biomarkers in medicine lies in their ability to detect disease and support diagnostic and therapeutic decisions. New research and novel understanding of the molecular basis of the disease reveals an abundance of exciting new biomarkers who present a promise for use in the everyday clinical practice. The past fifteen years have seen the emergence of numerous clinical applications of several new molecules as biologic markers in the research field relevant to acute respiratory distress syndrome (translational research). The scope of this review is to summarize the current state of knowledge about serum biomarkers in acute lung injury and acute respiratory distress syndrome and their potential value as prognostic tools and present some of the future perspectives and challenges

Growth, optical transmission and X-ray photoemission studies of BaB2O4 single crystals

Beta barium borate (beta-BBO) crystals have been grown by the top seeded solution growth technique (TSSG) using Na2O as a flux. The crystals exhibited high transparency and the absence of inclusions and found to have sodium contamination in the range 150 to 230 p.p.m. The effect of this contamination on some crystal properties of interest has been investigated. The presence of impurities causes optical absorption below 550 nm in BBO crystals of both alpha and beta-phases. X-ray photo emission spectroscopy (XPS) measurements performed on these crystals show that sodium gives rise to a measurable shift in the binding energies of the constituent ions. Further, the results show that Na+ ions enter into the lattice substitutionally and provide charge trapping sites close to the band edge

Sputter deposition of gallium nitride films using a GaAs target

GaAs was used as the target material for the deposition of GaN films by reactive sputtering. The films were grown at different compositions of the sputtering gas mixture (0-100% nitrogen in argon) at substrate temperatures of 450 and 550 degrees C. The films were studied using XRD and XPS techniques. Even a small quantity of nitrogen in the sputtering medium was found to prevent the formation of GaAs on the substrate. Films grown at 550 degrees C using 100% nitrogen as the sputtering-reactive gas were found to be single phase (0002) oriented hexagonal gallium nitride and revealed complete absence of arsenic. (C) 1998 Elsevier Science S.A.

The prevalence of low left atrial appendage emptying velocity and thrombus in patients undergoing catheter ablation for atrial fibrillation on uninterrupted peri-procedural Warfarin therapy

Introduction: The 2012 HRS/EHRA/ECAS guidelines encourage pre-procedural transesophageal echocardiography (TEE) prior to ablation for atrial fibrillation (AF), but acknowledge a lack of consensus in patients maintained on therapeutic warfarin before, during and after the procedure. This is partly because the incidence of left atrial appendage (LAA) thrombus is so low, that it is hard to draw clear conclusion regarding the characteristics of patients who develop thrombus. We hypothesize that the presence of low LAA emptying velocities, which predisposes to thrombus, and/or thrombus itself can be predicted in patients undergoing ablation, based upon clinical characteristics and transthoracic echocardiography (TTE). Methods: In this multicentre study, we undertook TTE and transesophageal echocardiograms (TEE) in 586 patients (age 59.9±0.4 years old, 64.5% male) undergoing catheter ablation for AF who were anticoagulated on warfarin (target international normalized ratio 2-3.5) for ≥3 consecutive weeks prior to procedure and maintained on warfarin for the procedure. Results: Low peak LAA emptying velocities (4.6cm on TTE (2.40 [2.13-5.41]), or persistent AF (2.60 [1.63-4.14]) compared to those with a higher LAA velocity without thrombus. Conclusion: In patients on uninterrupted warfarin therapy, a CHA 2DS2-VASc score ≥1 or LA diameter >4.6cm on TTE identifies 91.5% of those at risk of developing thrombus with LAA emptying velocity of <40 cm/s and 100% of those with thrombus in our cohort

Percutaneous cryoablation for the treatment of osteoid osteoma in the adult population

International audienceTo evaluate the technical feasibility and efficacy of percutaneous cryoablation for the treatment of osteoid osteoma (OO) in adults. 21 patients (12 male and nine female; mean age, 29.9 years) who underwent CT-guided percutaneous cryoablation for the treatment of OO were retrospectively evaluated. Procedures were carried out under local anaesthesia and conscious sedation in 13 patients, and under general anaesthesia in eight patients. Then, the ablation zone was evaluated with post-procedure magnetic resonance imaging at 6 weeks. Clinical outcome was assessed using a visual analogue scale (VAS) to evaluate severity of pain before procedure, as well as at primary (6 weeks) and secondary follow-up (6-40 months). All procedures were technically successful. Median VAS scores were: 8 (range, 5-10) before procedure and after procedure, respectively, 0 (range, 0-2; p < .0001) and 0 (range, 0-7; p < .0001) at primary and secondary follow-up. There were three minor complications (14.3%) and no major complication. A single patient reported symptom recurrence (4.8%) at secondary follow-up and successfully underwent a second cryoablation procedure. CT-guided percutaneous cryoablation is safe and effective in the treatment of OO in adults, and can be accomplished without general anaesthesia in selected cases. aEuro cent CT-guided percutaneous cryoablation of osteoid osteoma is safe and effective aEuro cent Cryoablation allows precise visual control of the aggregated iceball during procedure aEuro cent Percutaneous cryoablation can be accomplished without general anaesthesia in selected cases aEuro cent Another advantage of cryoablation is reduction of immediate postprocedural pain aEuro cent Post-procedure MRI is helpful in the evaluation of technical success

O⁶-methylguanine-DNA methyltransferase depletion and DNA damage in patients with melanoma treated with temozolomide alone or with lomeguatrib

We evaluated the pharmacodynamic effects of the O⁶-methylguanine-DNA methyltransferase (MGMT) inactivator lomeguatrib (LM) on patients with melanoma in two clinical trials. Patients received temozolomide (TMZ) for 5 days either alone or with LM for 5, 10 or 14 days. Peripheral blood mononuclear cells (PBMCs) were isolated before treatment and during cycle 1. Where available, tumour biopsies were obtained after the last drug dose in cycle 1. Samples were assayed for MGMT activity, total MGMT protein, and O⁶-methylguanine (O⁶-meG) and N7-methylguanine levels in DNA. MGMT was completely inactivated in PBMC from patients receiving LM, but detectable in those on TMZ alone. Tumours biopsied on the last day of treatment showed complete inactivation of MGMT but there was recovery of activity in tumours sampled later. Significantly more O⁶-meG was present in the PBMC DNA of LM/TMZ patients than those on TMZ alone. LM/TMZ leads to greater MGMT inactivation, and higher levels of O⁶-meG than TMZ alone. Early recovery of MGMT activity in tumours suggested that more protracted dosing with LM is required. Extended dosing of LM completely inactivated PBMC MGMT, and resulted in persistent levels of O⁶-meG in PBMC DNA during treatment