Prevention of COVID-19 transmission from deceased subject: A critical point of view

info:eu-repo/semantics/publishedVersio

INFN Cloud Users and Projects Support, Training and Communication

Having a long tradition in state-of-the-art distributed IT technologies, in the last couple of years INFN made available to its users “INFN Cloud”: a cloud infrastructure and related services portfolio dedicated to the scientific communities supported by INFN. Given the distributed nature of the infrastructure as well as the considerable number of technical solutions provided to the INFN users, it is important to have a reliable user support service aimed to properly interact both with INFN Cloud users and administrators. As an added value, proper training activities have been defined and differentiated to different types of users and the training courses are integrated with a rich set of user guides and technical documentation. In this article, an overview of the INFN Cloud, its evolution to DataCloud project, and the support and training activities will be provided and presented

Sequencing of 15 622 Gene-bearing BACs Clarifies the Gene-dense Regions of the Barley Genome

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley–Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant

Analysis of Italian requests for compensation in cases of responsibility for healthcare-related infections: A retrospective study

IntroductionThe aim of this study was to examine the type of compensation claims for alleged medical malpractice in the field of healthcare-related infections in Italy.MethodsIt was analyzed which was the most frequent clinical context, the characteristics of the disputes established, which were the alleged damages most often complained of, which were the possibly censurable behaviors of the health professionals, and which were the reasons for acceptance or rejection of the request for compensation.ResultsIn 90.2%, the issue questioned regarded surgical site infections. The most common pathogens involved were coagulase-negative Staphylococci (34.1%) and Staphylococcus aureus (24.4%). The lack or non-adherence to protocols of prophylaxis and/or prevention of healthcare-related infections was the most reported cause of acceptance of the request of compensation.DiscussionAccording to our data, a stronger effort should be made in terms of risk management perspective in order to ensure the develop and application of protocols for prevention of Gram-positive healthcare-related infections and strengthen infection control and antimicrobial stewardship programs

INDIGO-DataCloud: A data and computing platform to facilitate seamless access to e-infrastructures

This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud framework enhancements to manage the demanding requirements of scientific communities, either locally or through enhanced interfaces. The middleware developed allows to federate hybrid resources, to easily write, port and run scientific applications to the cloud. In particular, we have extended existing PaaS (Platform as a Service) solutions, allowing public and private e-infrastructures, including those provided by EGI, EUDAT, and Helix Nebula, to integrate their existing services and make them available through AAI services compliant with GEANT interfederation policies, thus guaranteeing transparency and trust in the provisioning of such services. Our middleware facilitates the execution of applications using containers on Cloud and Grid based infrastructures, as well as on HPC clusters. Our developments are freely downloadable as open source components, and are already being integrated into many scientific applications

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST: Barley provides facile access to BAC sequences and their annotations, along with the barley– Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.Keywords: Aegilops tauschii, Barley, centromere BACs, HarvEST:Barley, gene distribution, synteny, recombination frequency, Hordeum vulgare L., BAC sequencingThis is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. on behalf of the Society for Experimental Biology. The published article can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-313X. Supporting information is available online at: http://onlinelibrary.wiley.com/doi/10.1111/tpj.12959/abstrac

When less is more: ‘slicing’ sequencing data improves read decoding accuracy and de novo assembly quality

MotivationAs the invention of DNA sequencing in the 70s, computational biologists have had to deal with the problem of de novo genome assembly with limited (or insufficient) depth of sequencing. In this work, we investigate the opposite problem, that is, the challenge of dealing with excessive depth of sequencing.ResultsWe explore the effect of ultra-deep sequencing data in two domains: (i) the problem of decoding reads to bacterial artificial chromosome (BAC) clones (in the context of the combinatorial pooling design we have recently proposed), and (ii) the problem of de novo assembly of BAC clones. Using real ultra-deep sequencing data, we show that when the depth of sequencing increases over a certain threshold, sequencing errors make these two problems harder and harder (instead of easier, as one would expect with error-free data), and as a consequence the quality of the solution degrades with more and more data. For the first problem, we propose an effective solution based on 'divide and conquer': we 'slice' a large dataset into smaller samples of optimal size, decode each slice independently, and then merge the results. Experimental results on over 15 000 barley BACs and over 4000 cowpea BACs demonstrate a significant improvement in the quality of the decoding and the final assembly. For the second problem, we show for the first time that modern de novo assemblers cannot take advantage of ultra-deep sequencing data.Availability and implementationPython scripts to process slices and resolve decoding conflicts are available from http://goo.gl/YXgdHT; software Hashfilter can be downloaded from http://goo.gl/[email protected] or [email protected] informationSupplementary data are available at Bioinformatics online

Healthcare Liability and Thyroidectomy: When Is the Surgeon Wrong?

Thyroid surgeries can often lead to operative complications, sometimes with consequences on the patient’s health. This often leads to claims for compensation but the assessments of consultants and judges are not always objective. Based on these considerations, the authors analyzed forty-seven sentences issued between 2013 and 2022 regarding claims of alleged medical malpractice. This analysis aims to examine the cases presented in the sentences and the evaluations proposed by the judges to offer ideas for objective evaluation by the legislation in force in Italy