Facilitating High Performance Code Parallelization

With the surge of social media on one hand and the ease of obtaining information due to cheap sensing devices and open source APIs on the other hand, the amount of data that can be processed is as well vastly increasing. In addition, the world of computing has recently been witnessing a growing shift towards massively parallel distributed systems due to the increasing importance of transforming data into knowledge in today’s data-driven world. At the core of data analysis for all sorts of applications lies pattern matching. Therefore, parallelizing pattern matching algorithms should be made efficient in order to cater to this ever-increasing abundance of data. We propose a method that automatically detects a user’s single threaded function call to search for a pattern using Java’s standard regular expression library, and replaces it with our own data parallel implementation using Java bytecode injection. Our approach facilitates parallel processing on different platforms consisting of shared memory systems (using multithreading and NVIDIA GPUs) and distributed systems (using MPI and Hadoop). The major contributions of our implementation consist of reducing the execution time while at the same time being transparent to the user. In addition to that, and in the same spirit of facilitating high performance code parallelization, we present a tool that automatically generates Spark Java code from minimal user-supplied inputs. Spark has emerged as the tool of choice for efficient big data analysis. However, users still have to learn the complicated Spark API in order to write even a simple application. Our tool is easy to use, interactive and offers Spark’s native Java API performance. To the best of our knowledge and until the time of this writing, such a tool has not been yet implemented

Alterations of gait kinematics depend on the deformity type in the setting of adult spinal deformity

Purpose : To evaluate 3D kinematic alterations during gait in Adult Spinal Deformity (ASD) subjects with different deformity presentations. Methods : One hundred nineteen primary ASD (51 ± 19y, 90F), age and sex-matched to 60 controls, underwent 3D gait analysis with subsequent calculation of 3D lower limb, trunk and segmental spine kinematics as well as the gait deviation index (GDI). ASD were classified into three groups: 51 with sagittal malalignment (ASD-Sag: SVA > 50 mm, PT > 25°, and/or PI-LL > 10°), 28 with only frontal deformity (ASD-Front: Cobb > 20°) and 40 with only hyperkyphosis (ASD-HyperTK: TK > 60°). Kinematics were compared between groups. Results ASD-Sag had a decreased pelvic mobility compared to controls with a decreased ROM of hips (38 vs. 45°) and knees (51 vs. 61°). Furthermore, ASD-Sag exhibited a decreased walking speed (0.8 vs. 1.2 m/s) and GDI (80 vs. 95, all p < 0.05) making them more prone to falls. ASD-HyperTK showed similar patterns but in a less pronounced way. ASD-Front had normal walking patterns. GDI, knee flex/extension and walking speed were significantly associated with SVA and PT (r = 0.30–0.65). Conclusion Sagittal spinal malalignment seems to be the driver of gait alterations in ASD. Patients with higher GT, SVA, PT or PI-LL tended to walk slower, with shorter steps in order to maintain stability with a limited flexibility in the pelvis, hips and knees. These changes were found to a lesser extent in ASD with only hyperkyphosis but not in those with only frontal deformity. 3D gait analysis is an objective tool to evaluate functionality in ASD patients depending on their type of spinal deformity

Effect of carbapenem resistance on outcomes of bloodstream infection caused by Enterobacteriaceae in low-income and middle-income countries (PANORAMA): a multinational prospective cohort study

Background Low-income and middle-income countries (LMICs) are under-represented in reports on the burden of antimicrobial resistance. We aimed to quantify the clinical effect of carbapenem resistance on mortality and length of hospital stay among inpatients in LMICs with a bloodstream infection due to Enterobacteriaceae. Methods The PANORAMA study was a multinational prospective cohort study at tertiary hospitals in Bangladesh, Colombia, Egypt, Ghana, India, Lebanon, Nepal, Nigeria, Pakistan, and Vietnam, recruiting consecutively diagnosed patients with carbapenem-susceptible Enterobacteriaceae (CSE) and carbapenem-resistant Entero-bacteriaceae (CRE) bloodstream infections. We excluded patients who had previously been enrolled in the study and those not treated with curative intent at the time of bloodstream infection onset. There were no age restrictions. Central laboratories in India and the UK did confirmatory testing and molecular characterisation, including strain typing. We applied proportional subdistribution hazard models with inverse probability weighting to estimate the effect of carbapenem resistance on probability of discharge alive and in-hospital death, and multistate modelling for excess length of stay in hospital. All patients were included in the analysis. Findings Between Aug 1, 2014, and June 30, 2015, we recruited 297 patients from 16 sites in ten countries: 174 with CSE bloodstream infection and 123 with CRE bloodstream infection. Median age was 46 years (IQR 15–61). Crude mortality was 20% (35 of 174 patients) for patients with CSE bloodstream infection and 35% (43 of 123 patients) for patients with CRE bloodstream infection. Carbapenem resistance was associated with an increased length of hospital stay (3·7 days, 95% CI 0·3–6·9), increased probability of in-hospital mortality (adjusted subdistribution hazard ratio 1·75, 95% CI 1·04–2·94), and decreased probability of discharge alive (0·61, 0·45–0·83). Multilocus sequence typing showed various clades, with marginal overlap between strains in the CRE and CSE clades. Interpretation Carbapenem resistance is associated with increased length of hospital stay and mortality in patients with bloodstream infections in LMICs. These data will inform global estimates of the burden of antimicrobial resistance and reinforce the need for better strategies to prevent, diagnose, and treat CRE infections in LMICs

Survey on worldwide trauma team activation requirement

PURPOSE : trauma team activation (TTA) is thought to be essential for advanced and specialized care of very severely injured patients. However, non-specific TTA criteria may result in overtriage that consumes valuable resources or endanger patients in need of TTA secondary to undertriage. Consequently, criterion standard definitions to calculate the accuracy of the various TTA protocols are required for research and quality assurance purposes. Recently, several groups suggested a list of conditions when a trauma team is considered to be essential in the initial care in the emergency room. The objective of the survey was to post hoc identify trauma-related conditions that are thought to require a specialized trauma team that may be widely accepted, independent from the country’s income level. METHODS : A set of questions was developed, centered around the level of agreement with the proposed post hoc criteria to define adequate trauma team activation. The participants gave feedback before they answered the survey to improve the quality of the questions. The finalized survey was conducted using an online tool and a word form. The income per capita of a country was rated according to the World Bank Country and Lending groups. RESULTS : The return rate was 76% with a total of 37 countries participating. The agreement with the proposed criteria to define post hoc correct requirements for trauma team activation was more than 75% for 12 of the 20 criteria. The rate of disagreement was low and varied between zero and 13%. The level of agreement was independent from the country’s level of income. CONCLUSIONS : The agreement on criteria to post hoc define correct requirements for trauma team activation appears high and it may be concluded that the proposed criteria could be useful for most countries, independent from their level of income. Nevertheless, more discussions on an international level appear to be warranted to achieve a full consensus to define a universal set of criteria that will allow for quality assessment of over- and undertriage of trauma team activation as well as for the validation of field triage criteria for the most severely injured patients worldwide.http://link.springer.com/journal/68am2022Surger

Comprehensive Fragment Screening of the SARS-CoV-2 Proteome Explores Novel Chemical Space for Drug Development

12 pags., 4 figs., 3 tabs.SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome.Work at BMRZ is supported by the state of Hesse. Work in Covid19-NMR was supported by the Goethe Corona Funds, by the IWBEFRE-program 20007375 of state of Hesse, the DFG through CRC902: “Molecular Principles of RNA-based regulation.” and through infrastructure funds (project numbers: 277478796, 277479031, 392682309, 452632086, 70653611) and by European Union’s Horizon 2020 research and innovation program iNEXT-discovery under grant agreement No 871037. BY-COVID receives funding from the European Union’s Horizon Europe Research and Innovation Programme under grant agreement number 101046203. “INSPIRED” (MIS 5002550) project, implemented under the Action “Reinforcement of the Research and Innovation Infrastructure,” funded by the Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and co-financed by Greece and the EU (European Regional Development Fund) and the FP7 REGPOT CT-2011-285950—“SEE-DRUG” project (purchase of UPAT’s 700 MHz NMR equipment). The support of the CERM/CIRMMP center of Instruct-ERIC is gratefully acknowledged. This work has been funded in part by a grant of the Italian Ministry of University and Research (FISR2020IP_02112, ID-COVID) and by Fondazione CR Firenze. A.S. is supported by the Deutsche Forschungsgemeinschaft [SFB902/B16, SCHL2062/2-1] and the Johanna Quandt Young Academy at Goethe [2019/AS01]. M.H. and C.F. thank SFB902 and the Stiftung Polytechnische Gesellschaft for the Scholarship. L.L. work was supported by the French National Research Agency (ANR, NMR-SCoV2-ORF8), the Fondation de la Recherche Médicale (FRM, NMR-SCoV2-ORF8), FINOVI and the IR-RMN-THC Fr3050 CNRS. Work at UConn Health was supported by grants from the US National Institutes of Health (R01 GM135592 to B.H., P41 GM111135 and R01 GM123249 to J.C.H.) and the US National Science Foundation (DBI 2030601 to J.C.H.). Latvian Council of Science Grant No. VPP-COVID-2020/1-0014. National Science Foundation EAGER MCB-2031269. This work was supported by the grant Krebsliga KFS-4903-08-2019 and SNF-311030_192646 to J.O. P.G. (ITMP) The EOSC Future project is co-funded by the European Union Horizon Programme call INFRAEOSC-03-2020—Grant Agreement Number 101017536. Open Access funding enabled and organized by Projekt DEALPeer reviewe

Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium’s collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Alteration of the sitting and standing movement in adult spinal deformity

International audienceAdults with spinal deformity (ASD) are known to have spinal malalignment affecting their quality of life and daily life activities. While walking kinematics were shown to be altered in ASD, other functional activities are yet to be evaluated such as sitting and standing, which are essential for patients’ autonomy and quality of life perception. In this cross-sectional study, 93 ASD subjects (50 ± 20 years; 71 F) age and sex matched to 31 controls (45 ± 15 years; 18 F) underwent biplanar radiographic imaging with subsequent calculation of standing radiographic spinopelvic parameters. All subjects filled HRQOL questionnaires such as SF36 and ODI. ASD were further divided into 34 ASD-sag (with PT > 25° and/or SVA >5 cm and/or PI-LL >10°), 32 ASD-hyperTK (with only TK >60°), and 27 ASD-front (with only frontal malalignment: Cobb >20°). All subjects underwent 3D motion analysis during the sit-to-stand and stand-to-sit movements. The range of motion (ROM) and mean values of pelvis, lower limbs, thorax, head, and spinal segments were calculated on the kinematic waveforms. Kinematics were compared between groups and correlations to radiographic and HRQOL scores were computed. During sit-to-stand and stand-to-sit movements, ASD-sag had decreased pelvic anteversion (12.2 vs 15.2°), hip flexion (53.0 vs 62.2°), sagittal mobility in knees (87.1 vs 93.9°), and lumbar mobility (L1L3-L3L5: −9.1 vs −6.8°, all p 2 = 0.44). Lumbar sagittal ROM was determined by PI-LL mismatch (adj. R2 = 0.13). In conclusion, the type of spinal deformity in ASD seems to determine the strategy used for sitting and standing. Future studies should evaluate whether surgical correction of the deformity could restore sitting and standing kinematics and ultimately improve quality of life

Analisi sensoriale e contenuto in stilbeni di vini a DOC 'Ruche di Castagnole Monferrato'

La ricerca ha considerato otto vini a DOC \u201cRuch\ue9 di Castagnole Monferrato\u201d delle vendemmie 2007 e 2008, dei quali \ue8 stato ottenuto il profilo sensoriale ed eseguito il dosaggio di alcuni stilbeni (trans- e cis-resveratrolo, \u3b5- e \u3b4-viniferina). I risultati hanno evidenziato differenze visive significative in entrambe le annate ed una maggiore variabilit\ue0 aromatica nel 2008. I vini del 2008, annata pi\uf9 fresca e molto pi\uf9 piovosa del 2007, hanno presentato maggior sapidit\ue0, maggiori note speziate e livelli pi\uf9 elevati di stilbeni. Particolarmente interessante \ue8 la presenza di \u3b4-viniferina, raramente dosata in altri vini del commercio, che ha raggiunto valori fino a 10 mg/L. Il trans-reseveratrolo \ue8 variato da 0,8 a 10,3 mg/L, il cis-resveratrolo da 0 a 20,2 mg/L e l\u2019\u3b5-viniferina da 0 e 2 mg/L