Publishing and sharing multi-dimensional image data with OMERO

Imaging data are used in the life and biomedical sciences to measure the molecular and structural composition and dynamics of cells, tissues, and organisms. Datasets range in size from megabytes to terabytes and usually contain a combination of binary pixel data and metadata that describe the acquisition process and any derived results. The OMERO image data management platform allows users to securely share image datasets according to specific permissions levels: data can be held privately, shared with a set of colleagues, or made available via a public URL. Users control access by assigning data to specific Groups with defined membership and access rights. OMERO’s Permission system supports simple data sharing in a lab, collaborative data analysis, and even teaching environments. OMERO software is open source and released by the OME Consortium at www.openmicroscopy.org

Characterization of the Sos Enattos site for the Einstein Telescope

In this work we report the ongoing characterization of the Sos Enattos former mine (Sardinia, Italy), one of the two candidate sites for the Einstein Telescope (ET), the European third-generation underground interferometric detector of Gravitational Waves. The Sos Enattos site lies on a crystalline basement, made of rocks with good geomechanical properties, characterized by negligible groundwater. In addition, the site has a very low seismic background noise due to the absence of active tectonics involving Sardinia. Finally, the area has a low population density, resulting in a reduced anthropic noise even at the ground level. This location was already studied in 2012-2014 as a promising site for an underground detector. More recently, in March 2019, we deployed a new network of surface and underground seismometers at the site, that is currently monitoring the local seismic noise. Most of the energy carried by the seismic waves is due to the microseisms below 1 Hz, showing a significant correlation with the waves of the west Mediterranean sea. Above 1 Hz the seismic noise in the underground levels of the mine approaches the Peterson's low noise model. Exploiting mine blasting works into the former mine, we were also able to perform active seismic measurements to evaluate the seismic waves propagation across the area. In conclusion we also give a first assessment about the acoustic and magnetic noise in this underground site

Quantification of milk yield and composition changes as affected by subclinical mastitis during the current lactation in sheep

[EN] The aim of this work was to quantify, on a half-udder basis, the changes in ewe milk yield and composition caused by unilateral subclinical mastitis within the current lactation. Fluctuations due to production level, infection severity, time from the onset of infection, and lactation curves were also studied. Yield and composition of milk from half-udders of unilateral infected ewes were compared between them and with a set of healthy halves using a mixed model. The experiment was completed with a whole-udder approach on the same animals. To test the effect of intramammary infection (IMI) in the 7 wk following the onset of infection, 20 ewes that acquired unilateral subclinical mastitis during lactation and 40 healthy ewes were used. Another group of 20 unilaterally infected ewes from wk 1 of lactation and other 40 healthy ewes were studied to test the effect of IMI on lactational milk yield and composition. The individual milk loss in ewes infected during lactation was 15% for the 7 wk following the onset of infection, and 6.6% more milk was produced by the uninfected half to compensate milk lost by the infected half. Lactational milk yield loss in ewes infected from wk 1 postpartum was 17%. The changes in milk yield were noticed from the week of infection diagnosis. The production level of animals influenced the milk yield changes caused by IMI in such a way that the more productive ewes lost more milk, although these losses were proportional to their production level. On the other hand, infection severity affected milk loss between glands, being more pronounced as somatic cell count increased. A clear decrease of lactose content and casein:protein ratio due to subclinical IMI was observed and it remained throughout the postinfection period. Improving udder health status is necessary to maintain milk production and quality in dairy ewes during lactationThe authors thank the regional government of Valencia ("Generalitat Valenciana") for its support by means of a research fellowship.Martí De Olives, AM.; Díaz, J.; Molina Pons, MP.; Peris Ribera, CJ. (2013). Quantification of milk yield and composition changes as affected by subclinical mastitis during the current lactation in sheep. Journal of Dairy Science. 96(12):7698-7708. doi:10.3168/jds.2013-6998S76987708961

Tools and data services registry: a community effort to document bioinformatics resources.

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools

Factors affecting adherence to guidelines for antithrombotic therapy in elderly patients with atrial fibrillation admitted to internal medicine wards

Current guidelines for ischemic stroke prevention in atrial fibrillation or flutter (AFF) recommend Vitamin K antagonists (VKAs) for patients at high-intermediate risk and aspirin for those at intermediate-low risk. The cost-effectiveness of these treatments was demonstrated also in elderly patients. However, there are several reports that emphasize the underuse of pharmacological prophylaxis of cardio-embolism in patients with AFF in different health care settings. AIMS: To evaluate the adherence to current guidelines on cardio-embolic prophylaxis in elderly (> 65 years old) patients admitted with an established diagnosis of AFF to the Italian internal medicine wards participating in REPOSI registry, a project on polypathologies/polytherapies stemming from the collaboration between the Italian Society of Internal Medicine and the Mario Negri Institute of Pharmacological Research; to investigate whether or not hospitalization had an impact on guidelines adherence; to test the role of possible modifiers of VKAs prescription. METHODS: We retrospectively analyzed registry data collected from January to December 2008 and assessed the prevalence of patients with AFF at admission and the prevalence of risk factors for cardio-embolism. After stratifying the patients according to their CHADS(2) score the percentage of appropriateness of antithrombotic therapy prescription was evaluated both at admission and at discharge. Univariable and multivariable logistic regression models were employed to verify whether or not socio-demographic (age >80years, living alone) and clinical features (previous or recent bleeding, cranio-facial trauma, cancer, dementia) modified the frequency and modalities of antithrombotic drugs prescription at admission and discharge. RESULTS: Among the 1332 REPOSI patients, 247 were admitted with AFF. At admission, CHADS(2) score was ≥ 2 in 68.4% of patients, at discharge in 75.9%. Among patients with AFF 26.5% at admission and 32.8% at discharge were not on any antithrombotic therapy, and 43.7% at admission and 40.9% at discharge were not taking an appropriate therapy according to the CHADS(2) score. The higher the level of cardio-embolic risk the higher was the percentage of antiplatelet- but not of VKAs-treated patients. At admission or at discharge, both at univariable and at multivariable logistic regression, only an age >80 years and a diagnosis of cancer, previous or active, had a statistically significant negative effect on VKAs prescription. Moreover, only a positive history of bleeding events (past or present) was independently associated to no VKA prescription at discharge in patients who were on VKA therapy at admission. If heparin was considered as an appropriate therapy for patients with indication for VKAs, the percentage of patients admitted or discharged on appropriate therapy became respectively 43.7% and 53.4%. CONCLUSION: Among elderly patients admitted with a diagnosis of AFF to internal medicine wards, an appropriate antithrombotic prophylaxis was taken by less than 50%, with an underuse of VKAs prescription independently of the level of cardio-embolic risk. Hospitalization did not improve the adherence to guideline

Physical mechanical consolidation and protection of Miocenic limestone used on Mediterranean historical monuments: the case study of Pietra Cantone (southern Sardinia, Italy)

The present work aims to study the consolidating and protective chemical treatments of the Pietra Cantone, a Miocenic (lower Tortonian) limestone widely used in important monuments and historical buildings of Cagliari (southern Sardinia, Italy). Similar limestones of the same geological period have also been used in several important monuments of Mediterranean area, i.e., Malta and Gozo Islands, Matera (central Basilicata, Italy), Lecce (southern Puglia, Italy) and Balearic Islands (Spain). The Pietra Cantone limestone shows problems of chemical–physical decay, due to their petrophysical and compositional char- acteristics: high porosity (on average 28–36 vol%), low cemented muddy-carbonate matrix, presence of phyllosil- icates and sindepositional sea salts (\3%). So, after placed in the monument, this stone is easily alterable by weath- ering chemical processes (e.g., carbonate dissolution and sulfation) and also by cyclic mechanisms of crystalliza- tion/solubilization of salts and hydration/dehydration of hygroscopic phases of the clay component. To define the mineralogical-petrographic features (composition, texture) of limestone, the clay and salt crystalline phases, the optical microscope in polarized light and diffraction anal- ysis were used. To define the petrophysical characteristics (i.e., shape and size distribution of porosity, surface area(SBET), matrix microstructures, rock composition) and interactions of chemical treatments with rock, SEM–EDS analysis and N2 porosimetry with BET and BJH methods were used. To evaluate the efficacy of Na/K-silicates, ethyl silicate consolidants and protective nano-molecular silane monomer water repellent, the mechanical strengths (uni- axial compressive strength, point load and flexural resis- tance), water/helium open porosity, water absorption and vapour permeability data determined before and after the chemical treatments of the Pietra Cantone samples from monument were compared

Smart Contracts in Insurance: A Law and Futurology Perspective

Smart contracts are innovative contracts that differ from traditional ones in that they are self-executing, as they entail the possibility of representing contract terms in programming code that gets automatically executed on a blockchain or other distributed ledgers. Following the latest developments in blockchain technology, smart contracts have been the focus of growing attention and are currently among the major innovations that are taking place in financial services. This paper investigates the scope for their application in insurance both in the near and longer term, exploring the legal challenges that they pose. The analysis shows that in the near term smart contracts will be mainly exploited to automate underwriting, claims handling and payouts. It considers how the automation of these processes will operate at law and emphasises the impact that smart contracts can have especially on the reduction of transaction costs and on the very essence of the insurance contract—the insurer's promise to pay. Building on current technological developments, the paper then turns to role that smart contracts can play in insurance in the longer term, advancing the prospect of the automation of the entire insurance contract. In particular, it argues that the interaction between smart contracts and artificial intelligence and machine learning can challenge traditional frameworks of thought such as incomplete contracting and, in the farther-distant future, will culminate in contracts that will both self-interpret and self-enforce their terms—what can be called the true smart contracts. The analysis identifies and addresses the main legal issues that can arise in this context, exploring how to strike a balance between the goal of fostering innovation and the need to ensure policyholder and investor protection

Overexpression of the Cytokine BAFF and Autoimmunity Risk

$\textbf{BACKGROUND}$: Genomewide association studies of autoimmune diseases have mapped hundreds of susceptibility regions in the genome. However, only for a few association signals has the causal gene been identified, and for even fewer have the causal variant and underlying mechanism been defined. Coincident associations of DNA variants affecting both the risk of autoimmune disease and quantitative immune variables provide an informative route to explore disease mechanisms and drug-targetable pathways. $\textbf{METHODS}$: Using case-control samples from Sardinia, Italy, we performed a genomewide association study in multiple sclerosis followed by TNFSF13B locus-specific association testing in systemic lupus erythematosus (SLE). Extensive phenotyping of quantitative immune variables, sequence-based fine mapping, cross-population and cross-phenotype analyses, and gene-expression studies were used to identify the causal variant and elucidate its mechanism of action. Signatures of positive selection were also investigated. $\textbf{RESULTS}$: A variant in TNFSF13B, encoding the cytokine and drug target B-cell activating factor (BAFF), was associated with multiple sclerosis as well as SLE. The disease-risk allele was also associated with up-regulated humoral immunity through increased levels of soluble BAFF, B lymphocytes, and immunoglobulins. The causal variant was identified: an insertion-deletion variant, GCTGT→A (in which A is the risk allele), yielded a shorter transcript that escaped microRNA inhibition and increased production of soluble BAFF, which in turn up-regulated humoral immunity. Population genetic signatures indicated that this autoimmunity variant has been evolutionarily advantageous, most likely by augmenting resistance to malaria. $\textbf{CONCLUSIONS}$: A TNFSF13B variant was associated with multiple sclerosis and SLE, and its effects were clarified at the population, cellular, and molecular levels. (Funded by the Italian Foundation for Multiple Sclerosis and others.).Supported by grants (2011/R/13 and 2015/R/09, to Dr. Cucca) from the Italian Foundation for Multiple Sclerosis; contracts (N01-AG-1-2109 and HHSN271201100005C, to Dr. Cucca) from the Intramural Research Program of the National Institute on Aging, National Institutes of Health (NIH); a grant (FaReBio2011 “Farmaci e Reti Biotecnologiche di Qualità,” to Dr. Cucca) from the Italian Ministry of Economy and Finance; a grant (633964, to Dr. Cucca) from the Horizon 2020 Research and Innovation Program of the European Union; a grant (U1301.2015/AI.1157.BE Prat. 2015-1651, to Dr. Cucca) from Fondazione di Sardegna; grants (“Centro per la ricerca di nuovi farmaci per malattie rare, trascurate e della povertà” and “Progetto collezione di composti chimici ed attività di screening,” to Dr. Cucca) from Ministero dell’Istruzione, dell’Università e della Ricerca; grants (HG005581, HG005552, HG006513, and HG007022, to Dr. Abecasis) from the National Human Genome Research Institute; a grant (9-2011-253, to Dr. Todd) from JDRF; a grant (091157, to Dr. Todd) from the Wellcome Trust; a grant (to Dr. Todd) from the National Institute for Health Research (NIHR); and the NIHR Cambridge Biomedical Research Centre. Dr. Idda was a recipient of a Master and Back fellowship from the Autonomous Region of Sardinia