Simultaneous analysis of large INTEGRAL/SPI datasets: optimizing the computation of the solution and its variance using sparse matrix algorithms

International audienceNowadays, analyzing and reducing the ever larger astronomical datasets is becoming a crucial challenge, especially for long cumulated observation times. The INTEGRAL/SPI X/γ-ray spectrometer is an instrument for which it is essential to process many exposures at the same time in order to increase the low signal-to-noise ratio of the weakest sources. In this context, the conventional methods for data reduction are inefficient and sometimes not feasible at all. Processing several years of data simultaneously requires computing not only the solution of a large system of equations, but also the associated uncertainties. We aim at reducing the computation time and the memory usage. Since the SPI transfer function is sparse, we have used some popular methods for the solution of large sparse linear systems; we briefly review these methods. We use the Multifrontal Massively Parallel Solver (MUMPS) to compute the solution of the system of equations. We also need to compute the variance of the solution, which amounts to computing selected entries of the inverse of the sparse matrix corresponding to our linear system. This can be achieved through one of the latest features of the MUMPS software that has been partly motivated by this work. In this paper we provide a brief presentation of this feature and evaluate its effectiveness on astrophysical problems requiring the processing of large datasets simultaneously, such as the study of the entire emission of the Galaxy. We used these algorithms to solve the large sparse systems arising from SPI data processing and to obtain both their solutions and the associated variances. In conclusion, thanks to these newly developed tools, processing large datasets arising from SPI is now feasible with both a reasonable execution time and a low memory usage

The SFA Business Review Vol. 3 No. 3

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Complete mtDNA genomes of Anopheles darlingi and an approach to anopheline divergence time

Abstract Background The complete sequences of the mitochondrial genomes (mtDNA) of members of the northern and southern genotypes of Anopheles (Nyssorhynchus) darlingi were used for comparative studies to estimate the time to the most recent common ancestor for modern anophelines, to evaluate differentiation within this taxon, and to seek evidence of incipient speciation. Methods The mtDNAs were sequenced from mosquitoes from Belize and Brazil and comparative analyses of structure and base composition, among others, were performed. A maximum likelihood approach linked with phylogenetic information was employed to detect evidence of selection and a Bayesian approach was used to date the split between the subgenus Nyssorhynchus and other Anopheles subgenera. Results The comparison of mtDNA sequences within the Anopheles darlingi taxon does not provide sufficient resolution to establish different units of speciation within the species. In addition, no evidence of positive selection in any protein-coding gene of the mtDNA was detected, and purifying selection likely is the basis for this lack of diversity. Bayesian analysis supports the conclusion that the most recent ancestor of Nyssorhynchus and Anopheles+Cellia was extant ~94 million years ago. Conclusion Analyses of mtDNA genomes of Anopheles darlingi do not provide support for speciation in the taxon. The dates estimated for divergence among the anopheline groups tested is in agreement with the geological split of western Gondwana (95 mya), and provides additional support for explaining the absence of Cellia in the New World, and Nyssorhynchus in the Afro-Eurasian continents

Molecular Analysis of Serum and Bronchoalveolar Lavage in a Mouse Model of Influenza Reveals Markers of Disease Severity That Can Be Clinically Useful in Humans

Background: Management of influenza, a major contributor to the worldwide disease burden, is complicated by lack of reliable methods for early identification of susceptible individuals. Identification of molecular markers that can augment existing diagnostic tools for prediction of severity can be expected to greatly improve disease management capabilities. Methodology/Principal Findings: We have analyzed cytokines, proteome flux and protein adducts in bronchoalveolar lavage (BAL) and sera from mice infected with influenza A virus (PR8 strain) using a previously established non-lethal model of influenza infection. Through detailed cytokine and protein adduct measurements of murine BAL, we first established the temporal profile of innate and adaptive responses as well as macrophage and neutrophil activities in response to influenza infection. A similar analysis was also performed with sera from a longitudinal cohort of influenza patients. We then used an iTRAQ-based, comparative serum proteome analysis to catalog the proteome flux in the murine BAL during the stages correlating with “peak viremia,” “inflammatory damage,” as well as the “recovery phase.” In addition to activation of acute phase responses, a distinct class of lung proteins including surfactant proteins was found to be depleted from the BAL coincident with their “appearance” in the serum, presumably due to leakage of the protein following loss of the integrity of the lung/epithelial barrier. Serum levels of at least two of these proteins were elevated in influenza patients during the febrile phase of infection compared to healthy controls or to the same patients at convalescence. Conclusions/Significance: The findings from this study provide a molecular description of disease progression in a mouse model of influenza and demonstrate its potential for translation into a novel class of markers for measurement of acute lung injury and improved case management.Singapore. National Research FoundationSingapore-MIT Alliance for Research and Technology (ID-IRG research program

pH regulation in anoxic rice coleoptiles at pH 3.5: biochemical pHstats and net H+ influx in the absence and presence of NO3−

During anoxia, cytoplasmic pH regulation is crucial. Mechanisms of pH regulation were studied in the coleoptile of rice exposed to anoxia and pH 3.5, resulting in H+ influx. Germinating rice seedlings survived a combination of anoxia and exposure to pH 3.5 for at least 4 d, although development was retarded and net K+ efflux was continuous. Further experiments used excised coleoptile tips (7–10 mm) in anoxia at pH 6.5 or 3.5, either without or with 0.2 mM NO3−, which distinguished two processes involved in pH regulation. Net H+ influx (μmol g−1 fresh weight h−1) for coleoptiles with NO3− was ∼1.55 over the first 24 h, being about twice that in the absence of NO3−, but then decreased to 0.5–0.9 as net NO3− uptake declined from ∼1.3 to 0.5, indicating reduced uptake via H+–NO3− symports. NO3− reduction presumably functioned as a biochemical pHstat. A second biochemical pHstat consisted of malate and succinate, and their concentrations decreased substantially with time after exposure to pH 3.5. In anoxic coleoptiles, K+ balancing the organic anions was effluxed to the medium as organic anions declined, and this efflux rate was independent of NO3− supply. Thus, biochemical pHstats and reduced net H+ influx across the plasma membrane are important features contributing to pH regulation in anoxia-tolerant rice coleoptiles at pH 3.5

Operant Sensation Seeking Requires Metabotropic Glutamate Receptor 5 (mGluR5)

Pharmacological and genetic studies have suggested that the metabotropic glutamate receptor 5 (mGluR5) is critically involved in mediating the reinforcing effects of drugs of abuse, but not food. The purpose of this study was to use mGluR5 knockout (KO), heterozygous (Het), and wildtype (WT) mice to determine if mGluR5 modulates operant sensation seeking (OSS), an operant task that uses varied sensory stimuli as a reinforcer. We found that mGluR5 KO mice had significantly reduced OSS responding relative to WT mice, while Het mice displayed a paradoxical increase in OSS responding. Neither KO nor Het mice exhibited altered operant responding for food as a reinforcer. Further, we assessed mGluR5 KO, Het and WT mice across a battery of cocaine locomotor, place preference and anxiety related tests. Although KO mice showed expected differences in some locomotor and anxiety measures, Het mice either exhibited no phenotype or an intermediate one. In total, these data demonstrate a key role for mGluR5 in OSS, indicating an important role for this receptor in reinforcement-based behavior

Non-absorbable disaccharides versus placebo/no intervention and lactulose versus lactitol for the prevention and treatment of hepatic encephalopathy in people with cirrhosis

Background Non-absorbable disaccharides (lactulose and lactitol) are recommended as first-line treatment for hepatic encephalopathy. The previous (second) version of this review included 10 randomised clinical trials (RCTs) evaluating non-absorbable disaccharides versus placebo/no intervention and eight RCTs evaluating lactulose versus lactitol for people with cirrhosis and hepatic encephalopathy. The review found no evidence to either support or refute the use of the non-absorbable disaccharides and no differences between lactulose versus lactitol. Objectives To assess the beneficial and harmful effects of i) non-absorbable disaccharides versus placebo/no intervention and ii) lactulose versus lactitol in people with cirrhosis and hepatic encephalopathy. Search methods We carried out electronic searches of the Cochrane Hepato-Biliary Group Controlled Trials Register, the Cochrane Central Register of Controlled Trials (CENTRAL 2015, Issue 10), MEDLINE, EMBASE, and Science Citation Index Expanded to 19 October 2015; manual searches of meetings and conference proceedings; checks of bibliographies; and correspondence with investigators and pharmaceutical companies. Selection criteria We included RCTs, irrespective of publication status, language, or blinding. Data collection and analysis Two review authors, working independently, retrieved data from published reports and correspondence with investigators. The primary outcomes were mortality, hepatic encephalopathy, and serious adverse events. We presented the results of meta-analyses as risk ratios (RR) and mean differences (MD) with 95% confidence intervals (CI). We assessed the quality of the evidence using 'Grading of Recommendations Assessment Development and Evaluation' (GRADE) and bias control using the Cochrane Hepato-Biliary Group domains. Our analyses included regression analyses of publication bias and other small study effects, Trial Sequential Analyses to detect type 1 and type 2 errors, and subgroup and sensitivity analyses. Main results We included 38 RCTs with a total of 1828 participants. Eight RCTs had a low risk of bias in the assessment of mortality. All trials had a high risk of bias in the assessment of the remaining outcomes. Random-effects meta-analysis showed a beneficial effect of non-absorbable disaccharides versus placebo/no intervention on mortality when including all RCTs with extractable data (RR 0.59, 95% CI 0.40 to 0.87; 1487 participants; 24 RCTs; I2 = 0%; moderate quality evidence) and in the eight RCTs with a low risk of bias (RR 0.63, 95% CI 0.41 to 0.97; 705 participants). The Trial Sequential Analysis with the relative risk reduction (RRR) reduced to 30% confirmed the findings when including all RCTs, but not when including only RCTs with a low risk of bias or when we reduced the RRR to 22%. Compared with placebo/no intervention, the non-absorbable disaccharides were associated with beneficial effects on hepatic encephalopathy (RR 0.58, 95% CI 0.50 to 0.69; 1415 participants; 22 RCTs; I2 = 32%; moderate quality evidence). Additional analyses showed that non-absorbable disaccharides can help to reduce serious adverse events associated with the underlying liver disease including liver failure, hepatorenal syndrome, and variceal bleeding (RR 0.47, 95% CI 0.36 to 0.60; 1487 participants; 24 RCTs; I2 = 0%; moderate quality evidence). We confirmed the results in Trial Sequential Analysis. Tests for subgroup differences showed no statistical differences between RCTs evaluating prevention, overt, or minimal hepatic encephalopathy. The evaluation of secondary outcomes showed a potential beneficial effect of the non-absorbable disaccharides on quality of life, but we were not able to include the data in an overall meta-analysis (very low quality evidence). Non-absorbable disaccharides were associated with non-serious (mainly gastrointestinal) adverse events (very low quality evidence). None of the RCTs comparing lactulose versus lactitol evaluated quality of life. The review found no differences between lactulose and lactitol for the remaining outcomes (very low quality evidence). Authors' conclusions This review includes a large number of RCTs evaluating the prevention or treatment of hepatic encephalopathy. The analyses found evidence that non-absorbable disaccharides may be associated with a beneficial effect on clinically relevant outcomes compared with placebo/no intervention. Plain language summary Are non-absorbable disaccharides associated with beneficial or harmful effects in people with cirrhosis and hepatic encephalopathy? Background Cirrhosis is a chronic disorder of the liver. People with cirrhosis may develop hepatic encephalopathy, a condition that results in poor brain functioning. Hepatic encephalopathy may be clinically obvious (overt) with changes including poor concentration, tremor, and alterations in consciousness. Others have no obvious clinical changes (minimal) but, when tested, some aspects of brain function such as attention and the ability to perform complex tasks are impaired. The reason why people develop hepatic encephalopathy is complex. The accumulation of ammonia plays a key role. The non-absorbable disaccharides, lactulose and lactitol, are indigestible sugars that reduce the levels of ammonia in the blood. Review question We investigated the use of non-absorbable disaccharides for the prevention and treatment of hepatic encephalopathy in people with cirrhosis by reviewing randomised clinical trials (RCTs). Search date The search date was October 2015. Study funding sources Seven RCTs received financial support and 11 RCTs received lactitol or inactive placebo free of charge from a pharmaceutical company. Study characteristics We included 29 RCTs comparing non-absorbable disaccharides with inactive placebo or no intervention and nine RCTs comparing lactulose with lactitol. Seven of the included RCTs evaluated the prevention of hepatic encephalopathy and 31 evaluated the treatment of hepatic encephalopathy. Sixteen of the treatment RCTs included people with overt hepatic encephalopathy while 15 included people with minimal hepatic encephalopathy. The duration of treatment varied depending on the type of hepatic encephalopathy from five days to one year. Key results People who received non-absorbable disaccharides were less likely to die than people given a placebo or no treatment. They were also less likely to develop serious complications of their liver disease such as liver failure, bleeding, and infections. The non-absorbable disaccharides were also effective in preventing the development of hepatic encephalopathy and increased the number of participants who recovered from hepatic encephalopathy. There was some evidence from a small number of trials that lactulose has a beneficial effect on the quality of life, but we were unable to include the data in an overall analysis. The non-absorbable disaccharides were associated with adverse events including diarrhoea, nausea, bloating, and flatulence. None of the RCTs comparing lactulose versus lactitol reported quality of life. The analyses showed no differences between the two interventions for the remaining outcomes. Quality of the evidence In the comparison of non-absorbable disaccharides versus placebo/no intervention, we found moderate quality evidence of benefit for the outcomes of death, hepatic encephalopathy, and serious complications. The evidence for the remaining outcomes was of very low quality

Interventions to promote or maintain physical activity during and after the transition to retirement: an evidence synthesis

Background: It has been argued that transition points in life, such as the approach towards and early years of retirement, present key opportunities for interventions to improve the health of the population. Interventions that may change or preserve activity levels around the time of retirement have the potential to provide benefits in terms of increased health and well-being for people in later life. Research has highlighted health inequalities in health statuses in the retired population and in response to interventions. Objective: We aimed to conduct a systematic review and meta-synthesis of the types and effectiveness of interventions to increase physical activity among people around the time of retirement. We also aimed to identify factors that may underpin the effectiveness or acceptability of interventions, and how issues of health inequalities may be addressed. Data sources: The following electronic databases were searched: (1) MEDLINE; (2) Applied Social Sciences Index and Abstracts; (3) The Cochrane Library (including The Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, Database of Abstracts of Reviews of Effects, Health Technology Assessment Database); (4) Cumulative Index to Nursing and Allied Health Literature; (5) Science Citation Index; (6) Social Science Citation Index; (7) PsycINFO; (8) Evidence for Policy and Practice Information and Co-ordinating Centre; (9) SPORTDiscus; (10) Social Policy and Practice; (11) Health Management Information Consortium; and (12) Sociological Abstracts. We also searched for grey literature, checked reference lists of included papers and screened other reviews. Review methods: A systematic review of quantitative and qualitative literature was carried out between February 2014 and April 2015. The searches aimed to identify, first, evidence of effectiveness of interventions for older adults at the point of transition to retirement and, second, data relating to perceptions of barriers and facilitators to intervention effectiveness. A meta-synthesis of the two types of evidence was also carried out to provide further interpretation of the review findings. Results: A systematic search of the literature identified a large number of potentially relevant studies. Of these, 103 studies examining the effectiveness of interventions and 55 qualitative papers met the criteria for inclusion. A review of the effectiveness literature indicated a dearth of studies that investigate interventions that specifically examine the transition to retirement. More general studies in older adults indicated that a range of interventions might be effective for people around retirement age. The qualitative literature indicated the importance of considering the appeal and enjoyment, and social aspects, of interventions. Although there were a range of different measures in use, many were self-reported and few studies included an evaluation of sedentary time. A meta-synthesis across the data types indicated that elements reported as significant by participants did not always feature in the interventions. Limitations: Owing to the lack of evidence relating to the retirement transition, we examined the literature relating to older adults. The applicability of these data to people around retirement age may need consideration. Conclusions: Although the retirement transition is considered a significant point of life change, only a small volume of literature has reported interventions specifically in this period. The included literature suggests that interventions should take account of views and preferences of the target population and evaluate effectiveness by measuring meaningful outcomes and using a control group design. Study registration: This study is registered as PROSPERO CRD42014007446. Funding: The National Institute for Health Research Public Health Research programme

Special Libraries, April 1933

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