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New Science Gateways for Advanced Computing Simulations and Visualization Using Vine Toolkit in PL-Grid

A Science Gateway is a connection between scientists and their computational tools in the form of web portal. It creates a space for communities, collaboration and data sharing and visualization in a comprehensive and efficient manner. The main purpose of such a solution is to allow users to access the computational resources, process and analyze their data and get the results in a uniform and user friendly way. In this paper we propose a complex solution based on the Rich Internet Application (RIA) approach consisting of a web portal powered by Vine Toolkit with Adobe Flex/BlazeDs technologies. There are two Science Gateways described in detail one for engineers to manage computationally intensive workflows used in advanced airplane construction simulations, and one for nanotechnology scientists to manage experiments in nano-science field calculated with Density Functional Theory (DFT). In both cases the results show how modern web solution can help scientists in their work. &nbsp

A Primer on Data Analytics in Functional Genomics:How to Move from Data to Insight?

High-throughput technologies are now widely used in the life sciences field and are producing ever-increasing amounts and diversity of data. While many laboratories and even undergraduate students generate high-throughput data, analyzing these results requires a skill set that is traditionally reserved for bioinformaticians. Learning to program using languages such as R and Python and making sense of the vast amounts of available omics data have become easier, thanks to the multitude of available resources. This can empower bench-side researchers to perform more complex computational analyses. Tools such as KNIME or Galaxy (together with a growing number of tutorials and courses) have been crucial in providing simple user interfaces to conduct complex analyses under the hood, making the ‘big data’ revolution accessible to biologists. High-throughput methodologies and machine learning have been central in developing systems-level perspectives in molecular biology. Unfortunately, performing such integrative analyses has traditionally been reserved for bioinformaticians. This is now changing with the appearance of resources to help bench-side biologists become skilled at computational data analysis and handling large omics data sets. Here, we show an entry route into the field of omics data analytics. We provide information about easily accessible data sources and suggest some first steps for aspiring computational data analysts. Moreover, we highlight how machine learning is transforming the field and how it can help make sense of biological data. Finally, we suggest good starting points for self-learning and hope to convince readers that computational data analysis and programming are not intimidating

NT-proBNP increase during stress echocardiography predicts significant changes in ischemic mitral regurgitation severity in patients qualified for surgical revascularization

Background: In many patients, significant changes in ischemic mitral regurgitation (IMR) severity during exercise can be observed independent of the degree of IMR at rest. This study aimed to investigate the correlations between N-terminal fragment B-type natriuretic peptide (NT-proBNP) and echocardiography measurements at rest and at peak exercise in patients with moderate IMR who qualified for surgical revascularization. Methods: A total of 100 patients eligible for coronary artery bypass grafting, were included in this prospective study. All patients underwent exercise echocardiography. Additionally, the levels of NT-proBNP were measured at rest and after peak exercise. Results: A positive correlation of absolute NT-proBNP levels with effective regurgitant orifice area (EROA) were observed and with tricuspid regurgitant peak gradient (TRPG) at peak exercise. Absolute ∆NT-proBNP during exercise and the tenting area at rest were independent predictors of severe IMR at peak exercise. The level of absolute ∆NT-proBNP during exercise and coaptation height at rest were the most important predictors of significant increases in TRPG. The best cutoff value for ∆NT-proBNP as a predictor for increases in EROA at peak exercise was 68.9 pg/mL and to predict an increase in TRPG ≥ 50 mmHg at peak exercise was 68 pg/mL. Conclusions: The level of ∆NT-proBNP during exercise was the most important parameter in predicting significant changes in IMR severity and pulmonary pressure. Based on the present data, it can be speculated that integration of the assessment of NT-proBNP at rest and at exercise might improve patient selection for valve surgery

Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data

Subcellular localization is an important aspect of protein function, but the protein composition of many intracellular compartments is poorly characterized. For example, many nuclear bodies are challenging to isolate biochemically and thus remain inaccessible to proteomics. Here, we explore covariation in proteomics data as an alternative route to subcellular proteomes. Rather than targeting a structure of interest biochemically, we target it by machine learning. This becomes possible by taking data obtained for one organelle and searching it for traces of another organelle. As an extreme example and proof-of-concept we predict mitochondrial proteins based on their covariation in published interphase chromatin data. We detect about 1/3 of the known mitochondrial proteins in our chromatin data, presumably most as contaminants. However, these proteins are not present at random. We show covariation of mitochondrial proteins in chromatin proteomics data. We then exploit this covariation by multiclassifier combinatorial proteomics to define a list of mitochondrial proteins. This list agrees well with different databases on mitochondrial composition. This benchmark test raises the possibility that, in principle, covariation proteomics may also be applicable to structures for which no biochemical isolation procedures are available

DNA barcoding of Chironomidae from the Lake Skadar region: Reference library and a comparative analysis of the European fauna

Aims: The main aim of this study was to fill a gap in barcoding data of the European Chironomidae of the Balkan region, developing and testing the efficiency of a reference DNA barcode library for ancient Lake Skadar basin species (Montenegro/Albania), a region of Europe never before subjected to barcoding studies on Chironomidae. Another aim was to test the efficiency of DNA barcoding for the identification of European Chironomidae, including the estimation of optimal identification thresholds, using >12,000 barcodes. Location: Lake Skadar basin and adjacent area (Montenegro/Albania). Methods: Through this study, 770 individuals of Chironomidae from the Lake Skadar region were barcoded, both at adult and pre-imaginal stages. Adults were morphologically identified, while larvae were assigned to species by molecular identification, using different methods, of which the efficiency was tested, for a total of 97 different barcoded species. Results: The identification efficiency of the reference dataset developed for the Lake Skadar region was 98.6%, a value in line with that obtained when the identification efficiency for European Chironomidae was evaluated (95.8%), which confirms the accuracy of DNA barcoding for the identification of these insects. Moreover, we found that the optimal threshold for the molecular identification of the family is 1.6% nucleotide distance, though more specific thresholds are suggested for the identification of species belonging to Chironomidae subfamilies, since they are related to lower identification errors than to the use of a general threshold. The analysis of inconsistency between molecular and morphological identification shed light on taxonomic issues within European Chironomidae. Previously postulated species synonyms were confirmed, and also further cases requiring deeper investigation were detected. Main conclusions: Our de novo DNA barcode library was shown to have a high identification efficiency. Taxon-specific thresholds increase the efficacy of molecular identification. Hypothesized species synonyms could be validated through molecular techniques

Administration of oral anticoagulants in periprocedural complications based on case report series

The use of dabigatran, a non-vitamin K antagonist (VKA) oral anticoagulant, is still increasing. Dabigatran has a good efficacy and safety ratio, as well as a more predictable anticoagulation effect compared with VKA. On the other hand, there is acenocoumarol/warfarin, a VKA which was evaluated in numerous clinical trials and is a drug of choice in a valve-related atrial fibrillation (AF).Based on the real clinical cases, we attempted to summarize current recommendations on how to manage periprocedural complications on oral anticoagulant treatment.In the first case we presented a patient on dabigatran, undergoing pulmonary vein isolation (PVI) of AF, who developed a right groin hematoma after the procedure and hence required several blood transfusions. In the second case we showed a patient on acenocoumarol, with high bleeding risk, who developed a pocket hematoma after an implantable cardioverter-defibrillator (ICD) implantation. We also reported a patient on dabigatran, who developed a femoral artery pseudoaneurysm (FAP) following PVI of AF.Periprocedural oral anticoagulation depends on the anticoagulant type and requires individual assessment of thepatient’s thromboembolic and bleeding risk factors. Our case reports showed that in case of a bleeding, dabigatranmay be quickly stopped and then restarted recently after reaching hemostasis, in contrast to acenocoumarol. They also confirm a possibility of successful pseudoaneurysm closure without dabigatran suspension.The use of dabigatran, a non-vitamin K antagonist (VKA) oral anticoagulant, is still increasing. Dabigatran has a good efficacy and safety ratio, as well as a more predictable anticoagulation effect compared with VKA. On the other hand, there is acenocoumarol/warfarin, a VKA which was evaluated in numerous clinical trials and is a drug of choice in a valve-related atrial fibrillation (AF).Based on the real clinical cases, we attempted to summarize current recommendations on how to manage periprocedural complications on oral anticoagulant treatment.In the first case we presented a patient on dabigatran, undergoing pulmonary vein isolation (PVI) of AF, who developed a right groin hematoma after the procedure and hence required several blood transfusions. In the second case we showed a patient on acenocoumarol, with high bleeding risk, who developed a pocket hematoma after an implantable cardioverter-defibrillator (ICD) implantation. We also reported a patient on dabigatran, who developed a femoral artery pseudoaneurysm (FAP) following PVI of AF.Periprocedural oral anticoagulation depends on the anticoagulant type and requires individual assessment of thepatient’s thromboembolic and bleeding risk factors. Our case reports showed that in case of a bleeding, dabigatranmay be quickly stopped and then restarted recently after reaching hemostasis, in contrast to acenocoumarol. They also confirm a possibility of successful pseudoaneurysm closure without dabigatran suspension

Success rate and safety of catheter ablation in preexcitation syndrome: A comparison between adult and pediatric patients

Background: In contrast to adults, in whom cardiac rhythm disorders are mainly conditioned by coronary artery disease, in children, arrhythmias are most often associated with inherited heart disorders. Catheter ablation (CA) has an important role in the management of cardiac arrhythmias, in adults and children. The aim of the study was to assess and compare the efficacy and safety of CA in children and adults with preexcitation syndrome. Methods: The study population comprised 43 adults and 43 children diagnosed with a Wolff-Parkinson-White syndrome (WPW). The mean age of the study population was 41 ± 15 years for adults and 14 ± 2.5 years for children. In all patients, an electrophysiological study and CA were performed. Analysis with respect to the procedure duration, fluoroscopy exposure time, location of accessory pathways (AP), immediate success rate and complications were performed. Results: Electrophysiological study revealed the most frequent presence of left-sided AP (56% in children and 70% in adults). The mean procedure duration was 96 ± 36 min and 106 ± 51 min in children and adults, respectively (p = NS). The mean fluoroscopy duration was 8.5 ± 4.3 min and 5.9 ± 5.8 min in children and adults, respectively p < 0.05. The CA procedure was successful in 40 out of 43 (93%) adults and in 36 out of 43 (83.7%) children (p = NS). In 2 (4%) children minor complications occurred. Conclusions: Ablation in children and adults are equally effective with respect to short-term clinical observation

The impact of subthalamic deep brain stimulation on polysomnographic sleep pattern in patients with Parkinson's disease – Preliminary report

Aim of the study We present the preliminary results of the study focused on the impact of subthalamic deep brain stimulation (DBS-STN) on sleep and other non-motor symptoms (NMS). Materials and methods Ten patients with advanced PD, underwent two-night polysomnography (PSG) mean 1.1 week before surgery and 6.2 months post DBS programming. NMS were assessed with a set of scales before surgery and 6 months and 12 months following DBS programming. Results Contrary to previous studies, we noted deterioration of sleep pattern in the follow-up PSG. We found a decrease in total sleep time, duration of the stage N2, with prolongation of stage N1 and wakefulness after sleep onset. We did not detect any impact of DBS-STN on subjective severity of restless legs syndrome. REM – sleep behavior disorder, however reported was not observed in any patient during PSG evaluations. We also found statistically significant correlations between severity of sleep disturbances and quality of life, as well as, between severity of motor symptoms and worse objective sleep quality. Conclusions We found that DBS-STN improved quality of life, subjective quality of sleep and sleepiness, however, contrary to the previous studies the objective parameters of sleep worsened after the surgery