Challenges and opportunities for RISC-V architectures towards genomics-based workloads

The use of large-scale supercomputing architectures is a hard requirement for scientific computing Big-Data applications. An example is genomics analytics, where millions of data transformations and tests per patient need to be done to find relevant clinical indicators. Therefore, to ensure open and broad access to high-performance technologies, governments, and academia are pushing toward the introduction of novel computing architectures in large-scale scientific environments. This is the case of RISC-V, an open-source and royalty-free instruction-set architecture. To evaluate such technologies, here we present the Variant-Interaction Analytics use case benchmarking suite and datasets. Through this use case, we search for possible genetic interactions using computational and statistical methods, providing a representative case for heavy ETL (Extract, Transform, Load) data processing. Current implementations are implemented in x86-based supercomputers (e.g. MareNostrum-IV at the Barcelona Supercomputing Center (BSC)), and future steps propose RISC-V as part of the next MareNostrum generations. Here we describe the Variant Interaction Use Case, highlighting the characteristics leveraging high-performance computing, indicating the caveats and challenges towards the next RISC-V developments and designs to come from a first comparison between x86 and RISC-V architectures on real Variant Interaction executions over real hardware implementations.This work has been partially financed by the European Commission (EU-HORIZON NEARDATA GA.101092644, VITAMIN-V GA.101093062), the MEEP Project which received funding from the European High-Performance Computing Joint Undertaking (JU) under grant agreement No 946002. The JU receives support from the European Union’s Horizon 2020 research and innovation program and Spain, Croatia and Turkey. Also by the Spanish Ministry of Science (MICINN) under scholarship BES-2017-081635, the Research State Agency (AEI) and European Regional Development Funds (ERDF/FEDER) under DALEST grant agreement PID2021-126248OBI00, MCIN/AEI/10.13039/ 501100011033/FEDER and PID GA PID2019-107255GB-C21, and the Generalitat de Catalunya (AGAUR) under grant agreements 2021-SGR-00478, 2021-SGR-01626 and ”FSE Invertint en el teu futur”.Peer ReviewedPostprint (author's final draft

¿Qué factores hacen fallar un reimplante de cadera luego de una revisión en dos tiempos?

Introducción: El objetivo del estudio fue analizar la supervivencia sin recurrencia de infección en pacientes con reemplazo total de cadera tratados con revisión en dos tiempos, valorando el impacto del cultivo intraoperatorio y la congelación positiva en el reimplante. Materiales y Métodos: Estudio retrospectivo de 96 casos con infección periprotésica crónica, según los criterios de la MusculoSkeletal Infection Society, sometidos a los dos tiempos quirúrgicos en nuestra institución, entre 2008 y 2013. El seguimiento promedio fue 90 meses. La falla séptica se definió sobre la base de un consenso tipo Delphi modificado. La supervivencia sin falla séptica se definió sobre la base del estimador de Kaplan-Meier. Se compararon los resultados de supervivencia en función del cultivo intraoperatorio y de los estudios de anatomía patológica por congelación mediante la prueba del orden logarítmico. Resultados: La supervivencia sin falla séptica fue del 82,65% a los 2 años (IC95% 73,25-88,99%), 80,40% a los 5 años (IC95% 70,70-87,17%) y 77,32% a 6-10 años (IC95% 66,90-84,33%). Hubo significativamente más fallas en los pacientes con un cultivo positivo en el reimplante que en aquellos con un cultivo negativo (prueba del orden logarítmico, p = 0,0208), y en quienes tuvieron un estudio anatomopatológico por congelación positivo en el reimplante que en aquellos con un resultado negativo (prueba del orden logarítmico, p = 0,0154). Conclusiones: Los reimplantes sin recurrencias infecciosas por, al menos, 6 años tuvieron un riesgo de falla séptica muy bajo. Cuando se detectó un cultivo o una congelación positivos, la falla séptica fue significativamente mayor

¿As radiografias de perfil são necessárias para classificar corretamente as fraturas do colo do fêmur? Análise intra e interobservador usando o sistema de classificação de garden

INTRODUCCIÓN: Históricamente, el diagnóstico de una fractura medial de cadera requiere de una radiografía anteroposterior (AP) y de perfil (P). Nos propusimos analizar la importancia de la radiografía de perfil en la evaluación y planificación del tratamiento de las fracturas mediales de cadera, utilizando la clasificación de Garden. MATERIALES Y MÉTODOS: Se prepararon diapositivas con radiografías AP y de P de 100 pacientes con fracturas mediales de cadera admitidos en nuestra central de emergencias. Tres cirujanos de cadera evaluaron de forma independiente las incidencias AP únicamente y luego las vistas AP y P, utilizando la clasificación de Garden. RESULTADOS: Se utilizó el método de Kruskal Wallis para comparar los rangos en la clasificación de Garden después de ver la proyección de P y no se encontraron diferencias estadísticamente significativas (Kruskal Wallis 0, p=1). El acuerdo ponderado entre AP y el AP combinado con el P del Garden promedio fue de 81 % (p < 0.001). Se analizó el porcentaje de pacientes recategorizados entre fracturas no desplazadas y desplazadas, tras observar el perfil: 5% (n=5, IC 95% 1-11%). Para comparar el Garden AP con el Garden P, se utilizó el método kappa ponderado cuadrático. CONCLUSIONES: Existe una alta concordancia en la clasificación de Garden al comparar las observaciones de las radiografías AP, con las observaciones AP y P juntas. Cinco pacientes hubiesen recibido un tratamiento quirúrgico diferente dependiendo del especialista que interpretaba las radiografías. Esto permite destacar la importancia de solicitar la incidencia de perfil de rutina en pacientes con sospecha de fractura medial de cadera.INTRODUCTION: Femoral neck fractures have been historically diagnosed by anteroposterior (AP) and lateral (L) radiographic views. We analyzed the importance of the L view for management of femoral neck fractures, using the Garden's classification system. MATERIALS AND METHODS: Slides were elaborated with AP and L radiographic views of 100 patients with femoral neck fractures admitted to our emergency department. Three hip surgeons assessed independently AP views only and then AP and L views together using Garden's classification system. RESULTS: No statistically significant differences (Kruskal Wallis 0, p=1) were found while comparing categories among Garden's classification system, after assessing L views. There was an 81 % (p < 0.001) agreement of Garden category between AP and AP combined with L views. When analyzing patients with changing categories between displaced and non displaced after assessing L view images, we found a 5% (n=5, CI 95% 1-11%) of change. For comparing AP Garden with L view Garden, we used a quadratic weighted kappa method. CONCLUSIONS: There is a high agreement in the Garden category when comparing AP with combined AP and L observations. Five patients would have received a different surgical treatment dependent on the hip surgeon who assessed the radiographs. This highlights the relevance of routinely L radiographs whenever a femoral neck fracture is suspected.INTRODUÇÃO: Historicamente, o diagnóstico de uma fratura medial de quadril requer uma radiografia ântero-posterior (AP) e de perfil (P). Propusemo-nos a analisar a importância da radiografia de perfil na avaliação e planejamento do tratamento das fraturas mediais do quadril, utilizando a classificação de Garden. MATERIAIS E MÉTODOS: As lâminas foram preparadas com radiografias AP e P de 100 pacientes com fratura medial do quadril admitidos em nosso centro de emergência. Três cirurgiões de quadril avaliaram independentemente apenas os eventos AP e, em seguida, as visualizações AP e P, usando a classificação de Garden. RESULTADOS: O método de Kruskal Wallis foi usado para comparar as classificações na classificação de Garden após a visualização da projeção P e não foram encontradas diferenças estatisticamente significativas (Kruskal Wallis 0, p = 1). A concordância ponderada entre AP e AP combinada com a média do Garden P foi de 81% (p <0,001). Foi analisada a porcentagem de pacientes reclassificados em fraturas sem deslocamento e com deslocamento, após observação do perfil: 5% (n = 5, IC 95% 1-11%). Para comparar o Garden AP com o Garden P, foi utilizado o método kappa quadrático ponderado. CONCLUSÕES: Há alta concordância na classificação de Garden ao comparar as observações radiográficas AP com as observações AP e P juntas. Cinco pacientes teriam recebido um tratamento cirúrgico diferente dependendo do especialista que interpretou as radiografias. Isso destaca a importância de solicitar a incidência do perfil de rotina em pacientes com suspeita de fratura medial de quadril.Fil: Novillo, Matías. Hospital Italiano. Servicio de Ortopedia y Traumatología; ArgentinaFil: Díaz Dilernia, Fernando. Hospital Italiano. Servicio de Ortopedia y Traumatología; Argentina. Universidad de Buenos Aires; ArgentinaFil: García Barreiro, Gonzalo. Hospital Italiano. Servicio de Ortopedia y Traumatología; Argentina. Universidad de Buenos Aires; ArgentinaFil: Posadas Martinez, Maria Lourdes. Hospital Italiano. Departamento de Medicina. Servicio de Clínica Medica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Comba, Fernando. Hospital Italiano. Servicio de Ortopedia y Traumatología; ArgentinaFil: Buttaro, Martín Alejandro. Hospital Italiano. Servicio de Ortopedia y Traumatología; Argentin

Immunoglobulin, glucocorticoid, or combination therapy for multisystem inflammatory syndrome in children: a propensity-weighted cohort study.

BACKGROUND: Multisystem inflammatory syndrome in children (MIS-C), a hyperinflammatory condition associated with SARS-CoV-2 infection, has emerged as a serious illness in children worldwide. Immunoglobulin or glucocorticoids, or both, are currently recommended treatments. METHODS: The Best Available Treatment Study evaluated immunomodulatory treatments for MIS-C in an international observational cohort. Analysis of the first 614 patients was previously reported. In this propensity-weighted cohort study, clinical and outcome data from children with suspected or proven MIS-C were collected onto a web-based Research Electronic Data Capture database. After excluding neonates and incomplete or duplicate records, inverse probability weighting was used to compare primary treatments with intravenous immunoglobulin, intravenous immunoglobulin plus glucocorticoids, or glucocorticoids alone, using intravenous immunoglobulin as the reference treatment. Primary outcomes were a composite of inotropic or ventilator support from the second day after treatment initiation, or death, and time to improvement on an ordinal clinical severity scale. Secondary outcomes included treatment escalation, clinical deterioration, fever, and coronary artery aneurysm occurrence and resolution. This study is registered with the ISRCTN registry, ISRCTN69546370. FINDINGS: We enrolled 2101 children (aged 0 months to 19 years) with clinically diagnosed MIS-C from 39 countries between June 14, 2020, and April 25, 2022, and, following exclusions, 2009 patients were included for analysis (median age 8·0 years [IQR 4·2-11·4], 1191 [59·3%] male and 818 [40·7%] female, and 825 [41·1%] White). 680 (33·8%) patients received primary treatment with intravenous immunoglobulin, 698 (34·7%) with intravenous immunoglobulin plus glucocorticoids, 487 (24·2%) with glucocorticoids alone; 59 (2·9%) patients received other combinations, including biologicals, and 85 (4·2%) patients received no immunomodulators. There were no significant differences between treatments for primary outcomes for the 1586 patients with complete baseline and outcome data that were considered for primary analysis. Adjusted odds ratios for ventilation, inotropic support, or death were 1·09 (95% CI 0·75-1·58; corrected p value=1·00) for intravenous immunoglobulin plus glucocorticoids and 0·93 (0·58-1·47; corrected p value=1·00) for glucocorticoids alone, versus intravenous immunoglobulin alone. Adjusted average hazard ratios for time to improvement were 1·04 (95% CI 0·91-1·20; corrected p value=1·00) for intravenous immunoglobulin plus glucocorticoids, and 0·84 (0·70-1·00; corrected p value=0·22) for glucocorticoids alone, versus intravenous immunoglobulin alone. Treatment escalation was less frequent for intravenous immunoglobulin plus glucocorticoids (OR 0·15 [95% CI 0·11-0·20]; p<0·0001) and glucocorticoids alone (0·68 [0·50-0·93]; p=0·014) versus intravenous immunoglobulin alone. Persistent fever (from day 2 onward) was less common with intravenous immunoglobulin plus glucocorticoids compared with either intravenous immunoglobulin alone (OR 0·50 [95% CI 0·38-0·67]; p<0·0001) or glucocorticoids alone (0·63 [0·45-0·88]; p=0·0058). Coronary artery aneurysm occurrence and resolution did not differ significantly between treatment groups. INTERPRETATION: Recovery rates, including occurrence and resolution of coronary artery aneurysms, were similar for primary treatment with intravenous immunoglobulin when compared to glucocorticoids or intravenous immunoglobulin plus glucocorticoids. Initial treatment with glucocorticoids appears to be a safe alternative to immunoglobulin or combined therapy, and might be advantageous in view of the cost and limited availability of intravenous immunoglobulin in many countries. FUNDING: Imperial College London, the European Union's Horizon 2020, Wellcome Trust, the Medical Research Foundation, UK National Institute for Health and Care Research, and National Institutes of Health

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat

Correction to: Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

The original version of this article unfortunately contained a mistake

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat

Effect of Ischemia Duration and Protective Interventions on the Temporal Dynamics of Tissue Composition After Myocardial Infarction

The impact of cardioprotective strategies and ischemia duration on postischemia/reperfusion (I/R) myocardial tissue composition (edema, myocardium at risk, infarct size, salvage, intramyocardial hemorrhage, and microvascular obstruction) is not well understood. OBJECTIVE: To study the effect of ischemia duration and protective interventions on the temporal dynamics of myocardial tissue composition in a translational animal model of I/R by the use of state-of-the-art imaging technology. METHODS AND RESULTS: Four 5-pig groups underwent different I/R protocols: 40-minute I/R (prolonged ischemia, controls), 20-minute I/R (short-duration ischemia), prolonged ischemia preceded by preconditioning, or prolonged ischemia followed by postconditioning. Serial cardiac magnetic resonance (CMR)-based tissue characterization was done in all pigs at baseline and at 120 minutes, day 1, day 4, and day 7 after I/R. Reference myocardium at risk was assessed by multidetector computed tomography during the index coronary occlusion. After the final CMR, hearts were excised and processed for water content quantification and histology. Five additional healthy pigs were euthanized after baseline CMR as reference. Edema formation followed a bimodal pattern in all 40-minute I/R pigs, regardless of cardioprotective strategy and the degree of intramyocardial hemorrhage or microvascular obstruction. The hyperacute edematous wave was ameliorated only in pigs showing cardioprotection (ie, those undergoing short-duration ischemia or preconditioning). In all groups, CMR-measured edema was barely detectable at 24 hours postreperfusion. The deferred healing-related edematous wave was blunted or absent in pigs undergoing preconditioning or short-duration ischemia, respectively. CMR-measured infarct size declined progressively after reperfusion in all groups. CMR-measured myocardial salvage, and the extent of intramyocardial hemorrhage and microvascular obstruction varied dramatically according to CMR timing, ischemia duration, and cardioprotective strategy. CONCLUSIONS: Cardioprotective therapies, duration of index ischemia, and the interplay between these greatly influence temporal dynamics and extent of tissue composition changes after I/R. Consequently, imaging techniques and protocols for assessing edema, myocardium at risk, infarct size, salvage, intramyocardial hemorrhage, and microvascular obstruction should be standardized accordingly.Sin financiación15.211 JCR (2017) Q1, 4/128 Cardiac and Cardiovascular Systems, 1/71 Hematology, 2/65 Peripheral Vascular DiseaseUE