A Subset of the CERN Virtual Machine File System: Fast Delivering of Complex Software Stacks for Supercomputing Resources

Delivering a reproducible environment along with complex and up-to-date software stacks on thousands of distributed and heterogeneous worker nodes is a critical task. The CernVM-File System (CVMFS) has been designed to help various communities to deploy software on worldwide distributed computing infrastructures by decoupling the software from the Operating System. However, the installation of this file system depends on a collaboration with system administrators of the remote resources and an HTTP connectivity to fetch dependencies from external sources. Supercomputers, which offer tremendous computing power, generally have more restrictive policies than grid sites and do not easily provide the mandatory conditions to exploit CVMFS. Different solutions have been developed to tackle the issue, but they are often specific to a scientific community and do not deal with the problem in its globality. In this paper, we provide a generic utility to assist any community in the installation of complex software dependencies on supercomputers with no external connectivity. The approach consists in capturing dependencies of applications of interests, building a subset of dependencies, testing it in a given environment, and deploying it to a remote computing resource. We experiment this proposal with a real use case by exporting Gauss-a Monte-Carlo simulation program from the LHCb experiment-on Mare Nostrum, one of the top supercomputers of the world. We provide steps to encapsulate the minimum required files and deliver a light and easy-to-update subset of CVMFS: 12.4 Gigabytes instead of 5.2 Terabytes for the whole LHCb repository

Estimating fall risk with inertial sensors using gait stability measures that do not require step detection

Falls have major consequences both at societal (health-care and economy) and individual (physical and psychological) levels. Questionnaires to assess fall risk are commonly used in the clinic, but their predictive value is limited. Objective methods, suitable for clinical application, are hence needed to obtain a quantitative assessment of individual fall risk. Falls in older adults often occur during walking and trunk position is known to play a critical role in balance control. Therefore, analysis of trunk kinematics during gait could present a viable approach to the development of such methods. In this study, nonlinear measures such as harmonic ratio (HR), index of harmonicity (IH), multiscale entropy (MSE) and recurrence quantification analysis (RQA) of trunk accelerations were calculated. These measures are not dependent on step detection, a potentially critical source of error. The aim of the present study was to investigate the association between the aforementioned measures and fall history in a large sample of subjects (42 fallers and 89 non-fallers) aged 50 or older. Univariate associations with fall history were found for MSE and RQA parameters in the AP direction; the best classification results were obtained for MSE with scale factor τ = 2 and for maximum length of diagonals in RQA (72.5% and 71% correct classifications, respectively). MSE and RQA were found to be positively associated with fall history and could hence represent useful tools in the identification of subjects for fall prevention programs. © 2013 Elsevier B.V

Low- and intermediate-temperature ammonia/hydrogen oxidation in a flow reactor: Experiments and a wide-range kinetic modeling

Understanding the chemistry behind the oxidation of ammonia/hydrogen mixtures is crucial for ensuring the flexible use of such mixtures in several applications, related to propulsion systems and power generation. In this work, the oxidation of ammonia/hydrogen blends was investigated through an experimental and kinetic-modeling study, where the low- and intermediate-temperature conditions were considered. An experimental campaign was performed in a flow reactor, at stoichiometric conditions and near-atmospheric pressure (126.7 kPa). The mole fraction of fuels, oxidizer and final products was measured. At the same time, a comprehensive kinetic model was set up, following a modular and hierarchical approach, and implementing the recently-available elementary rates. Such a model was used to interpret the experimental results, and to extend the analysis to literature data, covering several oxidation features. The reactivity boost provided by H2 addition was found to be approximately linear with its mole fraction in both flow- and jet-stirred-reactor conditions (except for the smallest H2 amounts in the flow reactor), in contrast with the more-than-linear increase in the laminar flame speed. The key role of HO2 in regulating fuel conversion and autoignition at low temperature was confirmed for binary mixtures, with H2NO being the bottleneck to the low-temperature oxidation of NH3-rich blends. On the other hand, the nitrogen fate was found to be mostly regulated by NHx + NO propagation and termination channels

Long-term effect of neonatal inhibition of APP gamma-secretase on hippocampal development in the Ts65Dn mouse model of Down syndrome

Neurogenesis impairment is considered a major determinant of the intellectual disability that characterizes Down syndrome (DS), a genetic condition caused by triplication of chromosome 21. Previous evidence obtained in the Ts65Dn mouse model of DS showed that the triplicated gene APP (amyloid precursor protein) is critically involved in neurogenesis alterations. In particular, excessive levels of AICD (amyloid precursor protein intracellular domain) resulting from APP cleavage by gamma-secretase increase the transcription of Ptch1, a Sonic Hedgehog (Shh) receptor that keeps the mitogenic Shh pathway repressed. Previous evidence showed that neonatal treatment with ELND006, an inhibitor of gamma-secretase, reinstates the Shh pathway and fully restores neurogenesis in Ts65Dn pups. In the framework of potential therapies for DS, it is extremely important to establish whether the positive effects of early intervention are retained after treatment cessation. Therefore, the goal of the current study was to establish whether early treatment with ELND006 leaves an enduring trace in the brain of Ts65Dn mice. Ts65Dn and euploid pups were treated with ELND006 in the postnatal period P3-P15 and the outcome of treatment was examined at ~ one month after treatment cessation. We found that in treated Ts65Dn mice the pool of proliferating cells in the hippocampal dentate gyrus (DG) and total number of granule neurons were still restored as was the number of pre- and postsynaptic terminals in the stratum lucidum of CA3, the site of termination of the mossy fibers from the DG. Accordingly, patch-clamp recording from field CA3 showed functional normalization of the input to CA3. Unlike in field CA3, the number of pre- and postsynaptic terminals in the DG of treated Ts65Dn mice was no longer fully restored. The finding that many of the positive effects of neonatal treatment were retained after treatment cessation provides proof of principle demonstration of the efficacy of early inhibition of gamma-secretase for the improvement of brain development in DS

Moving from laboratory to real life conditions: Influence on the assessment of variability and stability of gait

The availability of wearable sensors allows shifting gait analysis from the traditional laboratory settings, to daily life conditions. However, limited knowledge is available about whether alterations associated to different testing environment (e.g. indoor or outdoor) and walking protocols (e.g. free or controlled), result from actual differences in the motor behaviour of the tested subjects or from the sensitivity to these changes of the indexes adopted for the assessment. In this context, it was hypothesized that testing environment and walking protocols would not modify motor control stability in the gait of young healthy adults, who have a mature and structured gait pattern, but rather the variability of their motor pattern. To test this hypothesis, data from trunk and shank inertial sensors were collected from 19 young healthy participants during four walking tasks in different environments (indoor and outdoor) and in both controlled (i.e. following a predefined straight path) and free conditions. Results confirmed what hypothesized: variability indexes (Standard deviation, Coefficient of variation and Poincaré plots) were significantly influenced by both environment and walking conditions. Stability indexes (Harmonic ratio, Short term Lyapunov exponents, Recurrence quantification analysis and Sample entropy), on the contrary, did not highlight any change in the motor control. In conclusion, this study highlighted an influence of environment and testing condition on the assessment of specific characteristics of gait (i.e. variability and stability). In particular, for young healthy adults, both environment and testing conditions affect gait variability indexes, whereas neither affect gait stability indexes

Obstructive sleep apneas naturally occur in mice during REM sleep and are highly prevalent in a mouse model of Down syndrome

Study objectives: The use of mouse models in sleep apnea study is limited by the belief that central (CSA) but not obstructive sleep apneas (OSA) occur in rodents. We aimed to develop a protocol to investigate the presence of OSAs in wild-type mice and, then, to apply it to a validated model of Down syndrome (Ts65Dn), a human pathology characterized by a high incidence of OSAs. Methods: In a pilot study, nine C57BL/6J wild-type mice were implanted with electrodes for electroencephalography (EEG), neck electromyography (nEMG), and diaphragmatic activity (DIA), and then placed in a whole-body-plethysmographic (WBP) chamber for 8 h during the rest (light) phase to simultaneously record sleep and breathing activity. CSA and OSA were discriminated on the basis of WBP and DIA signals recorded simultaneously. The same protocol was then applied to 12 Ts65Dn mice and 14 euploid controls. Results: OSAs represented about half of the apneic events recorded during rapid-eye-movement-sleep (REMS) in each experimental group, while the majority of CSAs were found during non-rapid eye movement sleep. Compared with euploid controls, Ts65Dn mice had a similar total occurrence rate of apneic events during sleep, but a significantly higher occurrence rate of OSAs during REMS, and a significantly lower occurrence rate of CSAs during NREMS. Conclusions: Mice physiologically exhibit both CSAs and OSAs. The latter appear almost exclusively during REMS, and are highly prevalent in Ts65Dn. Mice may, thus, represent a useful model to accelerate the understanding of the pathophysiology and genetics of sleep-disordered breathing and to help the development of new therapies

The Additional Representative Images for Legacy (ARI-L) project for the ALMA Science Archive

The Additional Representative Images for Legacy (ARI-L) project is a European Development project for ALMA Upgrade approved by the Joint ALMA Observatory (JAO) and the European Southern Observatory (ESO), started in June 2019. It aims to increase the legacy value of the ALMA Science Archive (ASA) by bringing the reduction level of ALMA data from Cycles 2-4 close to that of data from more recent Cycles processed for imaging with the ALMA Pipeline. As of mid-2021 more than 150000 images have been returned to the ASA for public use. At its completion in 2022, the project will have provided enhanced products for at least 70% of the observational data from Cycles 2-4 processable with the ALMA Pipeline. In this paper we present the project rationale, its implementation, and the new opportunities offered to ASA users by the ARI-L products. The ARI-L cubes and images complement the much limited number of archival image products generated during the data quality assurance stages (QA2), which cover only a small fraction of the available data for those Cycles. ARI-L imaging products are highly relevant for many science cases and significantly enhance the possibilities for exploiting archival data. Indeed, ARI-L products facilitate archive access and data usage for science purposes even for non-expert data miners, provide a homogeneous view of all data for better dataset comparisons and download selections, make the archive more accessible to visualization and analysis tools, and enable the generation of preview images and plots similar to those possible for subsequent Cycles.Comment: 15 pages. Accepted for publication in PAS