An Optimized Data Structure for High Throughput 3D Proteomics Data: mzRTree

As an emerging field, MS-based proteomics still requires software tools for efficiently storing and accessing experimental data. In this work, we focus on the management of LC-MS data, which are typically made available in standard XML-based portable formats. The structures that are currently employed to manage these data can be highly inefficient, especially when dealing with high-throughput profile data. LC-MS datasets are usually accessed through 2D range queries. Optimizing this type of operation could dramatically reduce the complexity of data analysis. We propose a novel data structure for LC-MS datasets, called mzRTree, which embodies a scalable index based on the R-tree data structure. mzRTree can be efficiently created from the XML-based data formats and it is suitable for handling very large datasets. We experimentally show that, on all range queries, mzRTree outperforms other known structures used for LC-MS data, even on those queries these structures are optimized for. Besides, mzRTree is also more space efficient. As a result, mzRTree reduces data analysis computational costs for very large profile datasets.Comment: Paper details: 10 pages, 7 figures, 2 tables. To be published in Journal of Proteomics. Source code available at http://www.dei.unipd.it/mzrtre

Executive function abnormalities in pathological gamblers

doi:10.1186/1745-0179-4

Increased plasma homocysteine predicts arrhythmia recurrence after minimally invasive epicardial ablation for nonvalvular atrial fibrillation

ObjectiveMinimally invasive epicardial ablation via right minithoracotomy is an emerging option for patients with drug-refractory nonvalvular atrial fibrillation. To guide the development of rational treatment algorithms, factors predisposing to recurrence of arrhythmia need to be quantified and eventually treated. We addressed the association of the plasma levels of homocysteine and the recurrence of atrial fibrillation after minimally invasive ablation.MethodsWe obtained peripheral blood samples from 104 patients at follow-up after arrhythmia surgery; the homocysteine concentration was expressed as micromoles per liter. Prospective follow-up was conducted through electrocardiogram Holter monitoring (average 18.5 ± 5.8 months). Stratified analysis (high vs low homocysteine) was based on the cutoff value for the last quartile of homocysteine concentration (16 μmol/L). Time-to-event and diagnostic performance analyses were performed.ResultsThe rate of freedom from atrial fibrillation was 89.4% at the end of follow-up. Elevated circulating homocysteine level, persistent type of atrial fibrillation, and increased left atrial dimension independently predicted the recurrence of atrial fibrillation during the follow-up (adjusted Cox regression). Patients with a high homocysteine level were more likely to have atrial fibrillation recurrence (stratified Kaplan–Meier, P < .001). The cutoff value for elevated homocysteine (16 μmol/L) yielded a good diagnostic performance in the prediction of atrial fibrillation recurrence (area under the receiver operating characteristic curve, 0.807).ConclusionsThe homocysteine level measured during the follow-up reliably predicts the risk of recurrence after epicardial ablation of nonvalvular atrial fibrillation via minithoracotomy. Specific treatments to reduce plasma homocysteine could be considered in the future in these patients

Beta-Blocker Use in Older Hospitalized Patients Affected by Heart Failure and Chronic Obstructive Pulmonary Disease: An Italian Survey From the REPOSI Register

Beta (β)-blockers (BB) are useful in reducing morbidity and mortality in patients with heart failure (HF) and concomitant chronic obstructive pulmonary disease (COPD). Nevertheless, the use of BBs could induce bronchoconstriction due to β2-blockade. For this reason, both the ESC and GOLD guidelines strongly suggest the use of selective β1-BB in patients with HF and COPD. However, low adherence to guidelines was observed in multiple clinical settings. The aim of the study was to investigate the BBs use in older patients affected by HF and COPD, recorded in the REPOSI register. Of 942 patients affected by HF, 47.1% were treated with BBs. The use of BBs was significantly lower in patients with HF and COPD than in patients affected by HF alone, both at admission and at discharge (admission, 36.9% vs. 51.3%; discharge, 38.0% vs. 51.7%). In addition, no further BB users were found at discharge. The probability to being treated with a BB was significantly lower in patients with HF also affected by COPD (adj. OR, 95% CI: 0.50, 0.37-0.67), while the diagnosis of COPD was not associated with the choice of selective β1-BB (adj. OR, 95% CI: 1.33, 0.76-2.34). Despite clear recommendations by clinical guidelines, a significant underuse of BBs was also observed after hospital discharge. In COPD affected patients, physicians unreasonably reject BBs use, rather than choosing a β1-BB. The expected improvement of the BB prescriptions after hospitalization was not observed. A multidisciplinary approach among hospital physicians, general practitioners, and pharmacologists should be carried out for better drug management and adherence to guideline recommendations

ECMO for COVID-19 patients in Europe and Israel

Since March 15th, 2020, 177 centres from Europe and Israel have joined the study, routinely reporting on the ECMO support they provide to COVID-19 patients. The mean annual number of cases treated with ECMO in the participating centres before the pandemic (2019) was 55. The number of COVID-19 patients has increased rapidly each week reaching 1531 treated patients as of September 14th. The greatest number of cases has been reported from France (n = 385), UK (n = 193), Germany (n = 176), Spain (n = 166), and Italy (n = 136) .The mean age of treated patients was 52.6 years (range 16–80), 79% were male. The ECMO configuration used was VV in 91% of cases, VA in 5% and other in 4%. The mean PaO2 before ECMO implantation was 65 mmHg. The mean duration of ECMO support thus far has been 18 days and the mean ICU length of stay of these patients was 33 days. As of the 14th September, overall 841 patients have been weaned from ECMO support, 601 died during ECMO support, 71 died after withdrawal of ECMO, 79 are still receiving ECMO support and for 10 patients status n.a. . Our preliminary data suggest that patients placed on ECMO with severe refractory respiratory or cardiac failure secondary to COVID-19 have a reasonable (55%) chance of survival. Further extensive data analysis is expected to provide invaluable information on the demographics, severity of illness, indications and different ECMO management strategies in these patients

Forensic microbiology and bioterrorism risk (Part II)

The letters containing anthrax, sent in 2001 in USA, showed that pathogens and toxins can be effectively used for terrorist purposes. A new subfield of forensic science, called &ldquo;microbial forensics&rdquo;, has been developed. It is a new scientific discipline dedicated to collect and analyze microbiological evidence from a scene of crime. In addition to collecting and analyzing traditional forensic evidences, the microbial forensic investigation will attempt to determine the identity of the causal agent, as so as epidemiologic investigation, but with higher-resolution characterization. The tools for a successful attribution include genetically based-assays to determine the exact strain of isolate, aiming the individualization of the source of the pathogen used in a biological weapon. Following the 2001 anthrax attacks, genotyping of B. anthracis was done on 8 variable number tandem repeats loci (VNTR polymorphisms), with multilocus variable number tandem repeats (MLVA) method. In recent years some research groups have increased the VNTR markers number to 25 loci, while other groups have identified single nucleotide repeat (SNR) polymorphisms, which display very high mutation rates. SNR marker system allows the distinguishing of isolates with extremely low levels of genetic diversity within the same MLVA genotype

SIMPLIFIED AND ADVANCED APPROACHES FOR EVACUATION ANALYSIS OF PASSENGER SHIPS IN THE EARLY STAGE OF DESIGN

In order to improve the survival capability of passenger and ro-ro ships in event of fire or flooding, in the last few years a set of international Regulations has been issued. In particular, the Regulation SOLAS \u201cSafe Return to Port\u201d is addressed towards design criteria able to guarantee adequate functionality of the ship when a casualty occurs. The Regulation requires the evacuation of the ship when a given threshold of damage (i.e., fire and flood) is exceeded. The evacuation analysis has become of primary importance even in the early-stage design. Indeed, the new amendments to SOLAS Regulation II-2/13.3.2.7 makes the evacuation analysis mandatory for both new and existing passenger and ro-ro ships since the early steps of the project. In this paper, the current IMO Guidelines have been analysed, and a case study for the evacuation of a 3600-person cruise ship has been carried out by means of both a simplified and an advanced method. To perform advanced calculations, two different software, based on virtual reality, have been used and the results have been compared with simplified method ones

Evacuation analysis for passenger ships: a new mandatory step for the early-stage design

Modern passenger ships must be safe in event of fire or flooding. On this basis, a set of stringent international Regulations has been issued to improve the intrinsic survival capability of a ship. Indeed, specific SOLAS Regulations, commonly known as "Safe Return to Port", are addressed towards design criteria able to guarantee adequate functionality of the ship when a casualty occurs. The main objective is to permit either a return to port by means of own propulsion system or an orderly evacuation of the persons on board. Since December 2006 IMO introduced the basic concepts on this topic, which has been subjected to continuous evolutions through the introduction of new specific requirements. Nowadays, this matter has become of primary importance even in the early-stage design. Indeed, the new amendments to SOLAS Regulation II-2/13.3.2.7 issued on May 2016 made the evacuation analysis mandatory for both new and existing passenger ships since the early steps in the project. In this paper, the new IMO revised Guidelines have been analyzed, and a case study for the evacuation of a 3600-person cruise ship has been carried out by means of both simplified and advanced methods

A Simulation Model for Hybrid-Electric Inland Waterway Passenger Vessels

The increasing focus on air pollution reduction for transportation systems requires to adopt new technologies and innovative solutions to limit vehicles emissions. In case of inland waterway transportation (IWT), once vessels have to operate close to urban areas or in natural reserves, the necessity to provide a \u2019green navigation\u2019 is of primary importance. With this specific aim, especially for small crafts, the adoption of an hybrid-electric power system grant a significant pollution reduction, leading also to a possible Zero Emission Mode (ZEM) navigation. However, the particular configuration of inland waterways makes the estimation of vessels\u2019 hydrodynamic performances harder compared to a seagoing ship, because of restricted waters effects, affecting both resistance and manoeuvring characteristics. For this purpose, time domain simulation program has been developed to estimate the effective power demand of an inland vessel during a specific route. The program has been tested on the specific case of a passenger vessel designed for the Grado lagoon, where all the reference route bathymetric data were available. By means of the simulations it has been possible to state whether the vessel is suitable to operate in ZEM mode during the service