Efficient OpenCL-based concurrent tasks offloading on accelerators

Current heterogeneous platforms with CPUs and accelerators have the ability to launch several independent tasks simultaneously, in order to exploit concurrency among them. These tasks typically consist of data transfer commands and kernel computation commands. In this paper we develop a runtime approach to optimize the concurrency between data transfers and kernel computation commands in a multithreaded scenario where each CPU thread offloads tasks to the accelerator. It deploys a heuristic based on a temporal execution model for concurrent tasks. It is able to establish a near-optimal task execution order that significantly reduces the total execution time, including data transfers. Our approach has been evaluated employing five different benchmarks composed of dominant kernel and dominant transfer real tasks. In these experiments our heuristic achieves speedups up to 1.5x in AMD R9 and NVIDIA K20c accelerators and 1.3x in an Intel Xeon Phi (KNC) device.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Determination of heat wave definition temperatures in Spain at an isoclimatic level: time trend of heat wave duration and intensity across the decade 2009–2018

Background: In line with WHO guidelines for the implementation of public health prevention plans targeted at the impacts of high temperatures, a heat wave defnition temperature (Tthreshold) was calculated for 182 so called “isoclimatic zones” (IZ) in Spain. As the dependent variable for determining this Tthreshold, we analysed daily all-cause mortality data (ICD-10: A00-R99) for each IZ across the period 2009–2018. The independent variable used was the mean value of the maximum daily temperature of the summer months recorded at meteorological observatories in each IZ. We used Box–Jenkins models to ascertain mortality anomalies, and scatterplots to link these anomalies to the temperatures at which they occurred, thereby determining the Tthreshold for each IZ. We then calculated how many heat waves had occurred in each IZ, as well as their intensity, and analysed their time trend over this period. Results: The results showed that in 52.5% of the IZ, the percentile of the maximum temperatures series of the summer months to which Tthreshold corresponded was below the 95th percentile of the meteorological heat wave defnition in Spain: indeed, it only coincided in 30.7% of cases. The geographical distribution of these percentiles displayed great heterogeneity as a consequence of the local factors that infuence the temperature–mortality relationship. The trend in the number of heat waves analysed indicated an overall increase in Spain at a rate of 3.9 heat waves per decade, and a similar rise in mean annual intensity of 9.5 °C/decade. These time-trend values were higher than those yielded by analysing the trend in meteorological heat waves based on the 95th percentile. Conclusions: The results obtained in this study indicate the need to use a heat wave defnition based on epidemiological temperature–mortality studies, rather than on values based on meteorological percentiles. This could be minimising estimated health impacts in analyses of future impacts attributable to heat.Acknowledgements and funding The authors would like to express their gratitude for the following grants from the Carlos III Institute of Health (Instituto de Salud Carlos III/ISCIII) for the ENPY 304/20, and ENPY 436/21 projects.S

Effects of local factors on adaptation to heat in Spain (1983-2018)

The European Union is currently immersed in policy development to address the effects of climate change around the world. Key plans and processes for facilitating adaptation to high temperatures and for reducing the adverse effects on health are among the most urgent measures. Therefore, it is necessary to understand those factors that influence adaptation. The aim of this study was to provide knowledge related to the social, climate and economic factors that are related to the evolution of minimum mortality temperatures (MMT) in Spain in the rural and urban contexts, during the 1983-2018 time period. For this purpose, local factors were studied regarding their relationship to levels of adaptation to heat. MMT is an indicator that allows for establishing a relationship to between mortality and temperature, and is a valid indicator to assess the capacity of adaptation to heat of a certain population. MMT is obtained through the maximum daily temperature and daily mortality of the study period. The evolution of MMT values for Spain was established in a previous paper. An ecological, longitudinal and retrospective study was carried out. Generalized linear models (GLM) were performed to identify the variables that appeared to be related to adaptation. The adaptation was calculated as the difference in variation in MMT based on the average increase in maximum daily temperatures. In terms of adaptation to heat, urban populations have adapted more than non-urban populations. Seventy-nine percent (n = 11) of urban provinces have adapted to heat, compared to twenty-one percent (n = 3) of rural provinces that have not adapted. In terms of urban zones, income level and habituation to heat (values over the 95th percentile) were variables shown to be related to adaptation. In contrast, among non-urban provinces, a greater number of housing rehabilitation licenses and a greater number of health professionals were variables associated with higher increases in MMT, and therefore, with adaptation. These results highlight the need to carry out studies that allow for identifying the local factors that are most relevant and influential in population adaptation. More studies carried out at a small scale are needed.The authors gratefully acknowledge the grants for projects ENPY107/18; ENPY 376/18, ENPY 470/19 and ENPY 340/20 from the Carlos III Institute of Health, and is supported by the Biodiversity Foundation of the Ministry for Ecological Transition and Demographic Challenge. Likewise, to the UNED for the financing for the publication in Open Access.S

Unravelling Hominin Activities in the Zooarchaeological Assemblage of Barranco Leon (Orce, Granada, Spain)

Little is known about the subsistence practices of the first European settlers, mainly due to the shortage of archaeological sites in Europe older than a million years. This article contributes to the knowledge of the subsistence of the first Europeans with new zooarchaeology and taphonomic data from the Palaeolithic site of Barranco Leon (Orce, Granada, Spain). We present the results of the analysis of the faunal assemblages retrieved in the context of new excavations undertaken between 2016 and 2020. We have followed a standard methodology for the identification and quantification of species, mortality profiles, skeletal representation and taphonomic analysis. With regard to the taphonomic evidence, we have documented the extent of rounding, abrasion and other alterations. Finally, we examined traces from the activities of carnivores and hominins that led to the accumulation and alteration of the bone assemblages. Results indicate that the archaeo-paleontological deposits from Barranco Leon present a dual-patterned mixed taphonomic origin. The first phase primarily involved waterborne processes (BL-D1), which led to the accumulation of lithic raw materials, a few archaeological stone tools, and some faunal remains with percussion and cutmarks. The second phase (BL-D2) contains several stone tools associated with faunal remains with more anthropogenic alterations, such as cutmarks and percussion marks. After analysing the Barranco Leon zooarchaeological assemblage, the present study concludes that hominins had access to the meat and within-bone nutrients of animals of diverse sizes. However, the specific carcass acquisition mechanisms that hominins followed are less certain because the presence of tooth marks suggests that carnivores also played a role in the accumulation and modification of the Barranco Leon faunal assemblage.Peer reviewe

Gender differences in adaptation to heat in Spain (1983-2018)

In Spain the average temperature has increased by 1.7 °C since pre-industrial times. There has been an increase in heat waves both in terms of frequency and intensity, with a clear impact in terms of population health. The effect of heat waves on daily mortality presents important territorial differences. Gender also affects these impacts, as a determinant that conditions social inequalities in health. There is evidence that women may be more susceptible to extreme heat than men, although there are relatively few studies that analyze differences in the vulnerability and adaptation to heat by sex. This could be related to physiological causes. On the other hand, one of the indicators used to measure vulnerability to heat in a population and its adaptation is the minimum mortality temperature (MMT) and its temporal evolution. The aim of this study was to analyze the values of MMT in men and women and its temporal evolution during the 1983-2018 period in Spain's provinces. An ecological, longitudinal retrospective study was carried out of time series data, based on maximum daily temperature and daily mortality data corresponding to the study period. Using cubic and quadratic fits between daily mortality rates and the temperature, the minimum values of these functions were determined, which allowed for determining MMT values. Furthermore, we used an improved methodology that provided for the estimation of missing MMT values when polynomial fits were inexistent. This analysis was carried out for each year. Later, based on the annual values of MMT, a linear fit was carried out to determine the rate of evolution of MMT for men and for women at the province level. Average MMT for all of Spain's provinces was 29.4 °C in the case of men and 28.7 °C in the case of women. The MMT for men was greater than that of women in 86 percent of the total provinces analyzed, which indicates greater vulnerability among women. In terms of the rate of variation in MMT during the period analyzed, that of men was 0.39 °C/decade, compared to 0.53 °C/decade for women, indicating greater adaptation to heat among women, compared to men. The differences found between men and women were statistically significant. At the province level, the results show great heterogeneity. Studies carried out at the local level are needed to provide knowledge about those factors that can explain these differences at the province level, and to allow for incorporating a gender perspective in the implementation of measures for adaptation to high temperatures.The authors wish to thank the funding provided by the ENPY 304/20, ENPY 376/18 and ENPY 107/18 projects of the Carlos III Health Institute III (ISCIII). They also wish to thank the UNED for funding this publication in open access.S

Wolbachia and DNA barcoding insects: patterns, potential and problems

Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region

Arabidopsis metacaspase MC1 localizes in stress granules, clears protein aggregates and delays senescence

Stress granules (SGs) are highly conserved cytoplasmic condensates that assemble in response to stress and contribute to maintaining protein homeostasis. These membraneless organelles are dynamic, disassembling once the stress is no longer present. Persistence of SGs due to mutations or chronic stress has been often related to age-dependent protein-misfolding diseases in animals. Here, we find that the metacaspase MC1 is dynamically recruited into SGs upon proteotoxic stress in Arabidopsis (Arabidopsis thaliana). Two predicted disordered regions, the prodomain and the 360 loop, mediate MC1 recruitment to and release from SGs. Importantly, we show that MC1 has the capacity to clear toxic protein aggregates in vivo and in vitro, acting as a disaggregase. Finally, we demonstrate that overexpressing MC1 delays senescence and this phenotype is dependent on the presence of the 360 loop and an intact catalytic domain. Together, our data indicate that MC1 regulates senescence through its recruitment into SGs and this function could potentially be linked to its remarkable protein aggregate-clearing activity

Short- and Long-Term Prognosis of Patients With Takotsubo Syndrome Based on Different Triggers: Importance of the Physical Nature

Background Takotsubo syndrome (TTS) is an acute reversible heart condition initially believed to represent a benign pathology attributable to its self-limiting clinical course; however, little is known about its prognosis based on different triggers. This study compared short- and long-term outcomes between TTS based on different triggers, focusing on various physical triggering events. Methods and Results We analyzed patients with a definitive TTS diagnosis recruited for the Spanish National Registry on TTS (RETAKO [Registry on Takotsubo Syndrome]). Short- and long-term outcomes were compared between different groups according to triggering factors. A total of 939 patients were included. An emotional trigger was detected in 340 patients (36.2%), a physical trigger in 293 patients (31.2%), and none could be identified in 306 patients (32.6%). The main physical triggers observed were infections (30.7%), followed by surgical procedures (22.5%), physical activities (18.4%), episodes of severe hypoxia (18.4%), and neurological events (9.9%). TTS triggered by physical factors showed higher mortality in the short and long term, and within this group, patients whose physical trigger was hypoxia were those who had a worse prognosis, in addition to being triggered by physical factors, including age >70 years, diabetes mellitus, left ventricular eyection fraction <30% and shock on admission, and increased long-term mortality risk. Conclusions TTS triggered by physical factors could present a worse prognosis in terms of mortality. Under the TTS label, there could be as yet undiscovered very different clinical profiles, whose differentiation could lead to individual better management, and therefore the perception of TTS as having a benign prognosis should be generally ruled out

Novel deep targeted sequencing method for minimal residual disease monitoring in acute myeloid leukemia

A high proportion of patients with acute myeloid leukemia who achieve minimal residual disease (MRD) negative status ultimately relapse because a fraction of pathological clones remains undetected by standard methods. We designed and validated a high-throughput sequencing method for MRD assessment of cell clonotypes with mutations of NPM1, IDH1/2 and/or FLT3-SNVs. For clinical validation, 106 follow-up samples from 63 patients in complete remission were studied by NGS, evaluating the level of mutations detected at diagnosis. The predictive value of MRD status by NGS, multiparameter flow cytometry, or quantitative PCR was determined by survival analysis. The method achieved a sensitivity of 10-4 for SNV mutations and 10-5 for insertions/deletions and could be used in acute myeloid leukemia patients who carry any mutation (86% in our diagnosis data set). NGS-determined MRD positive status was associated with lower disease-free survival (hazard ratio [HR] 3.4, p=0.005) and lower overall survival (HR 4.2, p<0.001). Multivariate analysis showed that MRD positive status by NGS was an independent factor associated with risk of death (HR 4.54, p =0.005) and the only independent factor conferring risk of relapse (HR 3.76, p =0.012). This NGS based method simplifies and standardizes MRD evaluation, with high applicability in acute myeloid leukemia. It also improves upon flow cytometry and quantitative PCR to predict acute myeloid leukemia outcome and could be incorporated in clinical settings and clinical trials.This study was supported by the Subdirección General de Investigación Sanitaria (Instituto de Salud Carlos III, Spain) grants PI13/02387 and PI16/01530, and the CRIS against Cancer foundation grant 2014/0120. M.L. holds a postdoctoral fellowship of the Spanish Ministry of Economy and Competitiveness (FPDI-2013-16409). P.R.P. holds a postdoctoral fellowship of the Spanish of Instituto de Salud Carlos III: Contrato Predoctoral de Formación en Investigación en Salud i-PFIS (IFI 14/00008).S

Corrigendum to 'Editor's Choice - European Society for Vascular Surgery (ESVS) 2020 Clinical Practice Guidelines on the Management of Vascular Graft and Endograft Infections' [European Journal of Vascular &amp; Endovascular Surgery 59/3 (2020) 339-384]

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