Enrichment of the NLST and NSCLC-Radiomics computed tomography collections with AI-derived annotations

Public imaging datasets are critical for the development and evaluation of automated tools in cancer imaging. Unfortunately, many do not include annotations or image-derived features, complicating their downstream analysis. Artificial intelligence-based annotation tools have been shown to achieve acceptable performance and thus can be used to automatically annotate large datasets. As part of the effort to enrich public data available within NCI Imaging Data Commons (IDC), here we introduce AI-generated annotations for two collections of computed tomography images of the chest, NSCLC-Radiomics, and the National Lung Screening Trial. Using publicly available AI algorithms we derived volumetric annotations of thoracic organs at risk, their corresponding radiomics features, and slice-level annotations of anatomical landmarks and regions. The resulting annotations are publicly available within IDC, where the DICOM format is used to harmonize the data and achieve FAIR principles. The annotations are accompanied by cloud-enabled notebooks demonstrating their use. This study reinforces the need for large, publicly accessible curated datasets and demonstrates how AI can be used to aid in cancer imaging

Cardiac magnetic resonance predictors of left ventricular remodelling following acute ST elevation myocardial infarction: The VavirimS study

Left ventricular (LV) remodelling (REM) ensuing after ST-elevation myocardial infarction (STEMI), has typically been studied by echocardiography, which has limitations, or cardiac magnetic resonance (CMR) in early phase that may overestimate infarct size (IS) due to tissue edema and stunning. This prospective, multicenter study investigated LV-REM performing CMR in the subacute phase, and 6 months after STEMI

Diversity and ethics in trauma and acute care surgery teams: results from an international survey

Background Investigating the context of trauma and acute care surgery, the article aims at understanding the factors that can enhance some ethical aspects, namely the importance of patient consent, the perceptiveness of the ethical role of the trauma leader, and the perceived importance of ethics as an educational subject. Methods The article employs an international questionnaire promoted by the World Society of Emergency Surgery. Results Through the analysis of 402 fully filled questionnaires by surgeons from 72 different countries, the three main ethical topics are investigated through the lens of gender, membership of an academic or non-academic institution, an official trauma team, and a diverse group. In general terms, results highlight greater attention paid by surgeons belonging to academic institutions, official trauma teams, and diverse groups. Conclusions Our results underline that some organizational factors (e.g., the fact that the team belongs to a university context or is more diverse) might lead to the development of a higher sensibility on ethical matters. Embracing cultural diversity forces trauma teams to deal with different mindsets. Organizations should, therefore, consider those elements in defining their organizational procedures. Level of evidence Trauma and acute care teams work under tremendous pressure and complex circumstances, with their members needing to make ethical decisions quickly. The international survey allowed to shed light on how team assembly decisions might represent an opportunity to coordinate team member actions and increase performance

3D visualization and analysis of HI in and around galaxies

Toekomstige surveys in de 21-cm lijn van neutraal atomair waterstof (HI) met de nieuwe ontvanger, Apertif, op de Westerbork Synthese Radio Telescoop zullen van vele duizenden melkwegstelsels de verdeling en de bewegingen van het atomaire waterstofgas in kaart brengen. Apertif geeft de telescoop een twintig keer groter gezichtsveld en maakt het mogelijk in korte tijd grote delen van de hemel waar te nemen. De hoeveelheid gegevens die voor onderzoek beschikbaar komen wordt hierdoor dermate groot dat goede visualisatie en analyse technieken meer dan ooit tevoren onmisbaar zijn om in de HI gegevens de vaak subtiele aanwijzingen te vinden voor gas dat de melkwegstelsels instroomt (of juist ontsnapt, gedreven door b.v. sterrewinden en exploderende sterren). Deze informatie is van belang voor het begrijpen van de levenscyclus van melkwegstelsels. Het zal heel moeilijk zijn om op een volledig geautomatizeerde manier deze aanwijzingen in de gegevens te vinden, zelfs als slim gebruikk wordt gemaakt van de samenhang van de gegevens in zowel de ruimtelijke dimensie (positie aan de hemel) alsook in de gemeten radële snelheid. We hebben daarom onderzoek gedaan naar state-of-the-art technieken voor interactieve 3-dimensionale visualisatie, filtering en selectie van gegevens in 3D om hiermee de ontdekking en analyse van bovengenoemde subtiele aanwijzingen in de HI gegevens van melkwegstelsels te vergemakkelijken en te versnellen. We hebben hiervoor SlicerAstro ontwikkeld, een 3D sofware module met alle hierbovengenoemde mogelijkheden. SlicerAstro is een geheel nieuwe module die speciaal ontwikkeld is voor radiosterrenkundige HI gegevens en die is ingebed in het voor medische visualisatie doeleinden ontwikkelde software pakket 3DSlicer. AstroSlicer biedt de mogelijkheden om snel en efficient HI gegevens in drie dimensies goed te visualiseren, slimme filtering en selectie toe te passen, en ook een directe vergelijking te maken met modellen van de regelmatige gasverdeling in de waargenomen melkwegstelsels

HiGPUs: Hermite's N-body integrator running on Graphic Processing Units

HiGPUs is an implementation of the numerical integration of the classical, gravitational, N-body problem, based on a 6th order Hermite's integration scheme with block time steps, with a direct evaluation of the particle-particle forces. The main innovation of this code is its full parallelization, exploiting both OpenMP and MPI in the use of the multicore Central Processing Units as well as either Compute Unified Device Architecture (CUDA) or OpenCL for the hosted Graphic Processing Units. We tested both performance and accuracy of the code using up to 256 GPUs in the supercomputer IBM iDataPlex DX360M3 Linux Infiniband Cluster provided by the italian supercomputing consortium CINECA, for values of N ≤ 8 millions. We were able to follow the evolution of a system of 8 million bodies for few crossing times, task previously unreached by direct summation codes. HiGPUs is also available as part of the AMUSE project

The role of 3-D interactive visualization in blind surveys of H I in galaxies

Upcoming H I surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize H I objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. We discuss how Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain. The requirements for a fully interactive visualization tool are: coupled 1-D/2-D/3-D visualization, quantitative and comparative capabilities, combined with supervised semi-automated analysis. Moreover, the source code must have the following characteristics for enabling collaborative work: open, modular, well documented, and well maintained. We review four state of-the-art, 3-D visualization packages assessing their capabilities and feasibility for use in the case of 3-D astronomical data

A Pseudouridine Isoxazolidinyl Nucleoside Analogue Structural Analysis: A Morphological Approach

An in silico study has been conducted upon (3′RS,5′SR)-5-[2′-benzyl-5′-hydroxymethyl-1′,2′-isoxazolidin-3′-yl]uracil through a molecular dynamics/docking approach that highlights its potential inhibitory activity upon the wild-type pseudouridine 5′-monophosphate glycosidase. The crystal structure of this compound has been solved by means of X-ray single crystal diffraction and the data inferred were used to predict its crystal morphology. These data were compared with optical microscopy images and confirmed the validity of the computed models. This robust approach, already used for several other different compounds, provides a fast and reliable tool to standardize a crystallization method in order to get similar and good quality crystals. As different crystal shapes could be associated with different polymorphic forms, this method could be considered a fast and cheap screening to choose among different and coexistent polymorphic forms. Furthermore, a match with the original crystal structure of pseudouridine 5′-monophosphate is provided