Integration of multi-scale biosimulation models via light-weight semantics

Currently, biosimulation researchers use a variety of computational environments and languages to model biological processes. Ideally, researchers should be able to semi- automatically merge models to more effectively build larger, multi-scale models. How- ever, current modeling methods do not capture the underlying semantics of these models sufficiently to support this type of model construction. In this paper, we both propose a general approach to solve this problem, and we provide a specific example that demon- strates the benefits of our methodology. In particular, we describe three biosimulation models: (1) a cardio-vascular fluid dynamics model, (2) a model of heart rate regulation via baroreceptor control, and (3) a sub-cellular-level model of the arteriolar smooth mus- cle. Within a light-weight ontological framework, we leverage reference ontologies to match concepts across models. The light-weight ontology then helps us combine our three models into a merged model that can answer questions beyond the scope of any single model

The TNG Near Infrared Camera Spectrometer

NICS (acronym for Near Infrared Camera Spectrometer) is the near-infrared cooled camera-spectrometer that has been developed by the Arcetri Infrared Group at the Arcetri Astrophysical Observatory, in collaboration with the CAISMI-CNR for the TNG (the Italian National Telescope Galileo at La Palma, Canary Islands, Spain). As NICS is in its scientific commissioning phase, we report its observing capabilities in the near-infrared bands at the TNG, along with the measured performance and the limiting magnitudes. We also describe some technical details of the project, such as cryogenics, mechanics, and the system which executes data acquisition and control, along with the related software.Comment: 7 pages, 5 figures, compiled with A&A macros. A&A in pres

Discovery of strong CIV absorption in the highest redshift quasar

We report the near-IR detection of a prominent CIV absorption in the rest-frame UV spectrum of the most distant known QSO, SDSS J104433.04-012502.2, at z=5.80. This QSO was recently observed with XMM-Newton and it was found to be notably X-ray weak. The equivalent width of the CIV absorption feature (~10 A) strongly supports the idea that the X-ray faintness of this QSO is due to heavy absorption by gas with a column density N_H > 10^{24} cm^-2. The shape of the CIV feature suggests that this is a Broad Absorption Line QSO. Although absorbed by a huge column of gas, the observed continuum in the 0.9-2.4um range (~1300-3500 A rest frame) exactly matches the template of unabsorbed QSOs without invoking any reddening (E(B-V)<0.08 mag), indicating that dust in the absorbing gas is either absent or composed of large grains.Comment: 4 pages, 2 figures, accepted for publication in A&A Letter

The ATLAS barrel level-1 Muon Trigger Sector-Logic/RX off-detector trigger and acquisition board

The ATLAS experiment uses a system of three concentric layers of Resistive Plate Chambers (RPC) detector for the Level-1 Muon Trigger in the air-core barrel toroid region. The trigger algorithm looks for hit coincidences within different detector layers inside the programmable geometrical road which defines the transverse momentum cut. The on-detector electronics that provides the trigger and detector readout functionalities collects input signals coming from the RPC front-end. Trigger and readout data are then sent via optical fibres to the off-detector electronics. Six or seven optical fibres from one of the 64 trigger sectors go to one Sector-Logic/RX module, that later elaborates the collected trigger and readout data, and sends data respectively to the Read-Out Driver modules and to the Central Level-1 Trigger. We present the functionality and the implementation of the VME Sector-Logic/RX module, and the configuration of the system for the first cosmic ray data collected using this module

Radiation test and application of FPGAs in the ATLAS Level 1 Trigger

The front-end system of the Silicon Drift Detectors (SDDs) of the ALICE experiment is made of two ASICs. The first chip performs the preamplification, temporary analogue storage and analogue-to-digital conversion of the detector signals. The second chip is a digital buffer that allows for a significant reduction of the connection from the front-end module to the outside world. In this paper, the results achieved on the first complete prototype of the front-end system for the SDDs of ALICE are presented

Role of Advanced Glycation End-Products and Oxidative Stress in Type-2-Diabetes-Induced Bone Fragility and Implications on Fracture Risk Stratification

Type 2 diabetes (T2D) and osteoporosis (OP) are major causes of morbidity and mortality that have arelevant health and economic burden. Recent epidemiological evidence suggests that both of these disorders are often associated with each other and that T2D patients have an increased risk of fracture, making bone an additional target of diabetes. As occurs for other diabetic complications, the increased accumulation of advanced glycation end-products (AGEs) and oxidative stress represent the major mechanisms explaining bone fragility in T2D. Both of these conditions directly and indirectly (through the promotion of microvascular complications) impair the structural ductility of bone and negatively affect bone turnover, leading to impaired bone quality, rather than decreased bone density. This makes diabetes-induced bone fragility remarkably different from other forms of OP and represents a major challenge for fracture risk stratification, since either the measurement of BMD or the use of common diagnostic algorithms for OP have a poor predictive value. We review and discuss the role of AGEs and oxidative stress on the pathophysiology of bone fragility in T2D, providing some indications on how to improve fracture risk prediction in T2D patients

May car washing represent a risk for Legionella infection?

Background. Legionella is a ubiquitous Gram-negative bacterium naturally found in aquatic environments. It can pose a health problem when it grows and spreads in man-made water systems. Legionella pneumophila is the most common cause of Legionnaires\u2019 disease nowadays, a community-acquired pneumonia with pulmonary symptoms and chest radiography no different from any other form of infectious pneumonia. Legionella monitoring is important for public health reasons, including the identification of unusual environmental sources of Legionella. Methods. We report two cases of Legionnaires\u2019 disease associated with two different car wash installations in the province of Vicenza, in the Veneto region, northeastern Italy. Patients were not employees of the car wash installations, but users of the service. In both cases, Legionella antigen was detected in urine using the Alere BinaxNOW\uae Legionella Urinary Antigen, and Legionella antibodies were detected in serum using SERION ELISA classic Legionella pneumophila 1-7 IgG and IgM. Water samples were also analyzed as part of the surveillance program for Legionella prevention and control in compliance with the Italian guidelines. Results. Both patients had clinical symptoms and chest radiography compatible with pneumonia, and only one of them had diabetes as a risk factor. Legionella urinary antigen and serological test on serum samples were positive for Legionella in both patients, even if much slighter in the case A due to the retrospective serological investigation performed a year later the episode and after the second clinical case occurred in the same district. The environmental investigations highlighted two different car wash plants as potential source of infection. A certified company using shock hyperchlorination was asked to disinfect the two plants and, subsequently, control samples resulted negative for Legionella pneumophila. Conclusions. Any water source producing aerosols should be considered at risk for the transmission of Legionella bacteria, including car wash installations frequently used by a large number of customers and where poor maintenance probably creates favorable conditions for Legionella overgrowth and spreading. Additional research is needed to ascertain optimal strategies for Legionella monitoring and control, but environmental surveillance, paying careful attention to possible unconventional sources, should remain an important component of any Legionnaires\u2019 disease prevention program. Additionally, all available diagnostic methods would be recommended for the confirmation of all cases even in the event of non-serogroup 1 Legionella pneumophila infection, probably underestimated at this time

Efficacy of adalimumab as second-line therapy in a pediatric cohort of crohn’s disease patients who failed infliximab therapy: The Italian society of pediatric gastroenterology, hepatology, and nutrition experience

Background: Adalimumab (Ada) treatment is an available option for pediatric Crohn’s disease (CD) and the published experience as rescue therapy is limited. Objectives: We investigated Ada efficacy in a retrospective, pediatric CD cohort who had failed previous infliximab treatment, with a minimum follow-up of 6 months. Methods: In this multicenter study, data on demographics, clinical activity, growth, laboratory values (CRP) and adverse events were collected from CD patients during follow-up. Clinical remission (CR) and response were defined with Pediatric CD Activity Index (PCDAI) score ≤10 and a decrease in PCDAI score of ≥12.5 from baseline, respectively. Results: A total of 44 patients were consecutively recruited (mean age 14.8 years): 34 of 44 (77%) had active disease (mean PCDAI score 24.5) at the time of Ada administration, with a mean disease duration of 3.4 (range 0.3–11.2) years. At 6, 12, and 18 months, out of the total of the enrolled population, CR rates were 55%, 78%, and 52%, respectively, with a significant decrease in PCDAI scores (P&lt;0.01) and mean CRP values (mean CRP 5.7 and 2.4 mL/dL, respectively; P&lt;0.01) at the end of follow-up. Steroid-free remission rates, considered as the total number of patients in CR who were not using steroids at the end of this study, were 93%, 95%, and 96% in 44 patients at 6, 12, and 18 months, respectively. No significant differences in growth parameters were detected. In univariate analysis of variables related to Ada efficacy, we found that only a disease duration &gt;2 years was negatively correlated with final PCDAI score (P&lt;0.01). Two serious adverse events were recorded: 1 meningitis and 1 medulloblastoma. Conclusion: Our data confirm Ada efficacy in pediatric patients as second-line biological therapy after infliximab failure. Longer-term prospective data are warranted to define general effectiveness and safety in pediatric CD patients