FabSim3: An automation toolkit for verified simulations using high performance computing

A common feature of computational modelling and simulation research is the need to perform many tasks in complex sequences to achieve a usable result. This will typically involve tasks such as preparing input data, pre-processing, running simulations on a local or remote machine, post-processing, and performing coupling communications, validations and/or optimisations. Tasks like these can involve manual steps which are time and effort intensive, especially when it involves the management of large ensemble runs. Additionally, human errors become more likely and numerous as the research work becomes more complex, increasing the risk of damaging the credibility of simulation results. Automation tools can help ensure the credibility of simulation results by reducing the manual time and effort required to perform these research tasks, by making more rigorous procedures tractable, and by reducing the probability of human error due to a reduced number of manual actions. In addition, efficiency gained through automation can help researchers to perform more research within the budget and effort constraints imposed by their projects. This paper presents the main software release of FabSim3, and explains how our automation toolkit can improve and simplify a range of tasks for researchers and application developers. FabSim3 helps to prepare, submit, execute, retrieve, and analyze simulation workflows. By providing a suitable level of abstraction, FabSim3 reduces the complexity of setting up and managing a large-scale simulation scenario, while still providing transparent access to the underlying layers for effective debugging. The tool also facilitates job submission and management (including staging and curation of files and environments) for a range of different supercomputing environments. Although FabSim3 itself is application-agnostic, it supports a provably extensible plugin system where users automate simulation and analysis workflows for their own application domains. To highlight this, we briefly describe a selection of these plugins and we demonstrate the efficiency of the toolkit in handling large ensemble workflows.EPSRC under grant agreement EP/W007711/1, as well as by the VECMA and HiDALGO projects, which have received funding from the European Union Horizon 2020 research and innovation programme under grant agreement nos 800925 and 824115. In addition, FabFlee was supported by the ITFLOWS project and FabCovid19 by the STAMINA project, both of which have received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 882986 and No 883441 respectivel

Photostability studies of ketoconazole: isolation and structural elucidation of the main photodegradation products

The purpose of this study was to obtain information on the photochemical properties of ketoconazole, an antifungal agent. Photodegradation of ketoconazole in solution and shampoo under exposure to UV-C (254 nm) and UV-A (352 nm) radiations as well as daylight was monitored by HPLC. Separation of ketoconazole from its degradation products was obtained with monoisopropylamine - methanol (2:500 v/v) and amonium acetate- water (1:200 w/v) (7:3 v/v) as mobile phase on a LiChrospher® 100 column RP-8, 5 μm (150 mm x 4.6 mm) and a flow rate of 1 ml/min. The main protodegradation products: (cis-1-acetyl-4-{4-[[2-(2-chlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3- dioxolan-4-yl]methoxy]phenyl}piperazine and (cis-1-acetyl-4-{4-[[2-(4-chlorophenyl)-2-(1H-imidazol- 1-ylmethyl)-1,3-dioxolan-4-yl]methoxy]phenyl} piperazine, were isolated and characterized by HPLC-MS and NMR spectrometry. The results indicated photodechlorination of ketoconazole when exposed to light and a significant decrease in antifungal activity.Colegio de Farmacéuticos de la Provincia de Buenos Aire

BMJ Open

INTRODUCTION: Antineoplastic drugs (AD) are potentially carcinogenic and/or reprotoxic molecules. Healthcare professionals are increasingly exposed to these drugs and can be potentially contaminated by them. Internal contamination of professionals is a key concern for occupational physicians in the assessment and management of occupational risks in healthcare settings. Objectives of this study are to report AD internal contamination rate in nursing staff and to identify factors associated with internal contamination. METHODS AND ANALYSIS: This trial will be conducted in two French hospital centres: University Hospital of Bordeaux and IUCT-Oncopole of Toulouse. The target population is nurses practicing in one of the fifteen selected care departments where at least one of the five studied AD is handled (5-fluorouracil, cyclophosphamide, doxorubicin, ifosfamide, methotrexate). The trial will be conducted with the following steps: (1) development of analytical methods to quantify AD urine biomarkers, (2) study of the workplace and organization around AD in each care department (transport and handling, professional practices, personal and collective protection equipments available) (3) development of a self-questionnaire detailing professional activities during the day of inclusion, (4) nurses inclusion (urine samples and self-questionnaire collection), (5) urine assays, (6) data analysis. ETHICS AND DISSEMINATION: The study protocol has been approved by the French Advisory Committee on the Treatment of Information in Health Research (CCTIRS) and by the French Data Protection Authority (CNIL). Following the opinion of the Regional Committee for the Protection of Persons, this study is outside the scope of the provisions governing biomedical research and routine care (n degrees 2014/87). The results will be submitted to peer-reviewed journals and reported at suitable national and international meetings. TRIAL REGISTRATION NUMBER: NCT03137641

The Yuan-Tseh Lee Array for Microwave Background Anisotropy

The Yuan-Tseh Lee Array for Microwave Background Anisotropy (AMiBA) is the first interferometer dedicated to studying the cosmic microwave background (CMB) radiation at 3mm wavelength. The choice of 3mm was made to minimize the contributions from foreground synchrotron radiation and Galactic dust emission. The initial configuration of seven 0.6m telescopes mounted on a 6-m hexapod platform was dedicated in October 2006 on Mauna Loa, Hawaii. Scientific operations began with the detection of a number of clusters of galaxies via the thermal Sunyaev-Zel'dovich effect. We compare our data with Subaru weak lensing data in order to study the structure of dark matter. We also compare our data with X-ray data in order to derive the Hubble constant.Comment: accepted for publication in ApJ (13 pages, 7 figures); a version with high resolution figures available at http://www.asiaa.sinica.edu.tw/~keiichi/upfiles/AMiBA7/pho_highreso.pd

FabSim3: An automation toolkit for verified simulations using high performance computing

A common feature of computational modelling and simulation research is the need to perform many tasks in complex sequences to achieve a usable result. This will typically involve tasks such as preparing input data, pre-processing, running simulations on a local or remote machine, post-processing, and performing coupling communications, validations and/or optimisations. Tasks like these can involve manual steps which are time and effort intensive, especially when it involves the management of large ensemble runs. Additionally, human errors become more likely and numerous as the research work becomes more complex, increasing the risk of damaging the credibility of simulation results. Automation tools can help ensure the credibility of simulation results by reducing the manual time and effort required to perform these research tasks, by making more rigorous procedures tractable, and by reducing the probability of human error due to a reduced number of manual actions. In addition, efficiency gained through automation can help researchers to perform more research within the budget and effort constraints imposed by their projects. This paper presents the main software release of FabSim3, and explains how our automation toolkit can improve and simplify a range of tasks for researchers and application developers. FabSim3 helps to prepare, submit, execute, retrieve, and analyze simulation workflows. By providing a suitable level of abstraction, FabSim3 reduces the complexity of setting up and managing a large-scale simulation scenario, while still providing transparent access to the underlying layers for effective debugging. The tool also facilitates job submission and management (including staging and curation of files and environments) for a range of different supercomputing environments. Although FabSim3 itself is application-agnostic, it supports a provably extensible plugin system where users automate simulation and analysis workflows for their own application domains. To highlight this, we briefly describe a selection of these plugins and we demonstrate the efficiency of the toolkit in handling large ensemble workflows

Brain Activation Patterns Characterizing Different Phases of Motor Action: Execution, Choice and Ideation.

Motor behaviour is controlled by a large set of interacting neural structures, subserving the different components involved in hierarchical motor processes. Few studies have investigated the neural substrate of higher-order motor ideation, i.e. the mental operation of conceiving a movement. The aim of this functional magnetic resonance imaging study was to segregate the neural structures involved in motor ideation from those involved in movement choice and execution. An index finger movement paradigm was adopted, including three different conditions: performing a pre-specified movement, choosing and executing a movement and ideating a movement of choice. The tasks involved either the right or left hand, in separate runs. Neuroimaging results were obtained by comparing the different experimental conditions and computing conjunction maps of the right and left hands for each contrast. Pre-specified movement execution was supported by bilateral fronto-parietal motor regions, the cerebellum and putamen. Choosing and executing finger movement involved mainly left fronto-temporal areas and the anterior cingulate. Motor ideation activated almost exclusively left hemisphere regions, including the inferior, middle and superior frontal regions, middle temporal and middle occipital gyri. These findings show that motor ideation is controlled by a cortical network mainly involved in abstract thinking, cognitive and motor control, semantic and visual imagery processes

Agrocombustibles: ¿Otro negocio es posible?

Hoy en día, los agrocombustibles (principalmente biodiesel y bioetanol) son objeto de políticas públicas e incentivos, y se ha acelerado su producción a gran escala, con la intención de reducir las emisiones de gases de efecto invernadero, y por tanto contribuir a la mitigación del cambio climático. Las y los autores de este libro integran el Grup de Bionegocis, un espacio multidisciplinario impulsado desde la Campaña “No te Comas el Mundo”, que investiga en Cataluña desde el año 2007 sobre la temática de los agrocombustibles. El principal objetivo de esta publicación se ubica en profundizar algunos aspectos con el objetivo de brindar herramientas de reflexión y de acción. Pretende responder a preguntas tales como: ¿Qué son los agrocombustibles? ¿Es positivo su rendimiento energético? ¿Cuál es la huella hídrica de estos carburantes? ¿Son realmente una respuesta ante el calentamiento global? ¿De dónde proviene la materia prima? ¿Mejoran las condiciones de vida en los países del Sur? ¿Cuáles son los intereses corporativos en este rubro? ¿Generarán los agrocombustibles una mayor Deuda ecológica? ¿Es la segunda generación una respuesta adecuada? ¿Qué perspectivas tenemos ante la Soberanía alimentaria y la Soberanía energética?Peer reviewe