A study on the performance of distributed training of data-driven CFD simulations Iserte, Sergio; González-Barberá, Alejandro; Barreda, Paloma ...
International journal of high performance computing applications/The international journal of high performance computing applications,
09/2023, Letnik:
37, Številka:
5
Journal Article
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Data-driven methods for computer simulations are blooming in many scientific areas. The traditional approach to simulating physical behaviors relies on solving partial differential equations (PDEs). ...Since calculating these iterative equations is highly both computationally demanding and time-consuming, data-driven methods leverage artificial intelligence (AI) techniques to alleviate that workload. Data-driven methods have to be trained in advance to provide their subsequent fast predictions; however, the cost of the training stage is non-negligible. This article presents a predictive model for inferencing future states of a specific fluid simulation that serves as a use case for evaluating different training alternatives. Particularly, this study compares the performance of only CPU, multi-GPU, and distributed approaches for training a time series forecasting deep learning model. With some slight code adaptations, results show and compare, in different implementations, the benefits of distributed GPU-enabled training for predicting high-accuracy states in a fraction of the time needed by the computational fluid dynamics solver.
Patients with end-stage renal disease have very high mortality. In individuals on hemodialysis, cardiovascular deaths account for ~50% of all deaths in this population, mostly due to arrhythmia. To ...determine the causes of these arrhythmic deaths is essential in order to adopt preventive strategies. The main objective of this study was to investigate whether, the presence of QTc interval alterations, from electrolyte abnormalities or presence of rare genetic variants, could have a relationship with sudden arrhythmogenic deaths in end-stage renal disease patients.
We recorded the pre- and post-dialysis QTc interval in 111 patients undergoing hemodialysis. In 47 of them, we analyzed 24 SCD-related genes including the most prevalent genes associated with long QT syndrome using a custom resequencing panel.
We found a positive although not significant association between the presence of long QTc and mortality in a subset of end-stage renal disease patients. In addition, in five patients with long QTc only after dialysis (21.7%) we detected rare potentially pathogenic genetic variants. Three out of these five carriers subsequently died suddenly.
Genetic background may be determinant in the risk of sudden cardiac death in these patients. We recommend evaluating the QTc interval before and after hemodialysis, and performing a genetic analysis of individuals with long QTc after hemodialysis.
El incremento en el número de pacientes en lista de espera de trasplante renal ha llevado a intentar aumentar el número de posibles donantes incorporando candidatos que anteriormente no se habrían ...considerado óptimos, incluyendo entre estos a los donantes de pacientes de asistolia (DA) y aquellos con criterios «expandidos» (DCE). Los receptores de injertos de DA controlada (DAc) sufren más función retrasada del injerto, pero presentan una evolución a largo plazo equiparable a los de donantes de muerte encefálica, lo que ha permitido un aumento en el número de trasplantes de DAc en distintos países en los últimos años. De forma paralela, el uso de DAc con criterios expandidos (DAc/DCE) se ha incrementado en los últimos años en diferentes países, permitiendo acortar la lista de espera del trasplante renal. El uso de estos injertos, aunque se relaciona con una mayor frecuencia de función retrasada del injerto, ofrece supervivencias del injerto a largo plazo similares o solo ligeramente inferiores a las de los donantes de muerte encefálica con criterios expandidos. Distintos estudios han observado que los receptores de injertos DAc/DCE tienen peor función renal que los DAc/estándar y que los donantes de muerte encefálica/DCE. La mortalidad asociada al trasplante de injertos de DAc/DCE se relaciona principalmente con la elevada edad del receptor. Los pacientes que reciben un trasplante renal de DAc/≥ 60 años presentan mejor supervivencia que los que continúan en la lista de espera, aunque este hecho no se ha demostrado en los receptores de DAc/> 65 años. La utilización de este tipo de órganos debe llevar pareja la optimización de los tiempos quirúrgicos y el menor tiempo de isquemia fría posible.
The increase in the number of patients on the kidney transplant waiting list has led to an attempt to increase the number of potential donors by incorporating candidates that previously would not have been considered optimal, including donors after cardiac death (DCD) and those with “expanded” criteria (ECD). Recipients of controlled DCD (cDCD) grafts suffer more delayed graft function (DGF), but have a long-term evolution comparable to those of brain-dead donors, which has allowed an increase in the number of cDCD transplants in different countries in recent years. In parallel, the use of cDCD with expanded criteria (cDCD/ECD) has increased in recent years in different countries, allowing the waiting list for kidney transplantation to be shortened. The use of these grafts, although associated with a higher frequency of DGF, offers similar or only slightly lower long-term graft survival than those of brain death donors with expanded criteria. Different studies have observed that cDCD/ECD graft recipients have worse kidney function than cDCD/standard and brain death/ECD. Mortality associated with cDCD/ECD graft transplantation mostly relates to the recipient age. Patients who receive a cDCD/≥60 graft have better survival than those who continue on the waiting list, although this fact has not been demonstrated in recipients of cDCD/>65 years. The use of this type of organ should be accompanied by the optimization of surgical times and the shortest possible cold ischemia.
The increase in the number of patients on the kidney transplant waiting list has led to an attempt to increase the number of potential donors by incorporating candidates that previously would not ...have been considered optimal, including donors after cardiac death (DCD) and those with “expanded” criteria (ECD). Recipients of controlled DCD (cDCD) grafts suffer more delayed graft function (DGF), but have a long-term evolution comparable to those of brain-dead donors, which has allowed an increase in the number of cDCD transplants in different countries in recent years. In parallel, the use of cDCD with expanded criteria (cDCD/ECD) has increased in recent years in different countries, allowing the waiting list for kidney transplantation to be shortened. The use of these grafts, although associated with a higher frequency of DGF, offers similar or only slightly lower long-term graft survival than those of brain death donors with expanded criteria. Different studies have observed that cDCD/ECD graft recipients have worse kidney function than cDCD/standard and DBD/ECD. Mortality associated with cDCD/ECD graft transplantation mostly relates to the recipient age. Patients who receive a cDCD/≥60 graft have better survival than those who continue on the waiting list, although this fact has not been demonstrated in recipients of cDCD/>65 years. The use of this type of organ should be accompanied by the optimization of surgical times and the shortest possible cold ischemia.
El incremento en el número de pacientes en lista de espera de trasplante renal ha llevado a intentar aumentar el número de posibles donantes incorporando candidatos que anteriormente no se habrían considerado óptimos, incluyendo entre estos a los donantes de pacientes de asistolia (DA) y aquellos con criterios “expandidos” (DCE). Los receptores de injertos de DA controlada (cDCD) sufren más función retrasada del injerto, pero presentan una evolución a largo plazo equiparable a los de donantes de muerte encefálica, lo que ha permitido un aumento en el número de trasplantes de cDCD en distintos países en los últimos años. De forma paralela, el uso de cDCD con criterios expandidos (cDCD/DCE) se ha incrementado en los últimos años en diferentes países, permitiendo acortar la lista de espera del trasplante renal. El uso de estos injertos, aunque se relaciona con una mayor frecuencia de función retrasada del injerto, ofrece supervivencias del injerto a largo plazo similares o solo ligeramente inferiores a las de los donantes de muerte encefálica con criterios expandidos. Distintos estudios han observado que los receptores de injertos cDCD/DCE tienen peor función renal que los cDCD/estándar y que los donantes de muerte encefálica/DCE. La mortalidad asociada al trasplante de injertos de cDCD/DCE se relaciona principalmente con la elevada edad del receptor. Los pacientes que reciben un trasplante renal de cDCD/≥60 años presentan mejor supervivencia que los que continúan en la lista de espera, aunque este hecho no se ha demostrado en los receptores de cDCD/>65 años. La utilización de este tipo de órganos debe llevar pareja la optimización de los tiempos quirúrgicos y el menor tiempo de isquemia fría posible.
The movements of the affected upper limb in infantile hemiplegia are slower and clumsy. This leads to a decrease in the use of the affected hand. The visual effect obtained using the mirror box and ...the observation of actions in another individual can activate the same structural neuronal cells responsible for the execution of these actions. This research will study the affected upper limb functionality in hemiplegia infantile from 6 to 12 years old after the application of two intervention protocols: observation action therapy and mirror therapy combined with observation action therapy. Children with a diagnose of congenital infantile hemiplegia will be recruited to participate in a randomized controlled trial with two intervention protocols during four weeks (1 h per/day; 5 sessions per/week): Mirror Therapy Action Observation (MTAO) or Action Observation Therapy (AOT). The study variables will be: spontaneous use, measured with the Assisting Hand Assessment (AHA); manual ability measured with the Jebsen Taylor Hand Function Test (JTHFT); surface electromyography of the flexors and extensors muscles of the wrist and grasp strength through a grip dynamometer. Four assessments will be performed: At baseline situation, at the end of treatment, 3 and 6 months after treatment (follow-up assessments). This study will study the effects of these therapies on the use of the affected upper limb in children with hemiplegia.
Abstract
BACKGROUND AND AIMS
Tacrolimus is the main immunosuppressive drug in the vast majority of kidney transplants, but it is a drug with a narrow therapeutic margin. Each centre must establish ...therapeutic ranges to optimize its efficacy and minimize its toxic effects. Maintaining levels in the appropriate range is difficult due to its inherent inter- and intra-patient variability. In the monitoring of transplants, in addition to assessing the drug levels at each visit, the measurement of time in therapeutic range (TTR) allows us to measure how long the patient has been exposed to the appropriate doses. Currently, it is not known which are the optimal ranges of time or of blood levels that are better related to the subsequent evolution of kidney transplantation.
METHOD
We performed a single centre, observational study of 215 consecutive kidney transplant recipients performed in our centre from October/2014 to January/2020 who received uninterrupted treatment with tacrolimus during the first year, excluding hypersensitized recipients. TTR was calculated using the Rosendaal method between months 3 and 12 (TTR-M3-12) or 6 and 12 (TTR-M6-12) with a target for blood levels >6 ng/mL (TTR-M3-12-T > 6, TTR-M6-12-T > 6) or between 6 and 10 ng/mL (TTR-M3-12-T6-10, TTR-M6-12-T6-10).
RESULTS
The mean follow-up time was 4.1 ± 2.0 years. The TTR that had a greater capacity to discriminate the risk of rejection {TTR-M3-12-T > 6: AUC-ROC 0.614, 95% confidence interval (95% CI) 0.513–0.714; P = .018; TTR-M6-12-T > 6: AUC-ROC 0.607, 95% CI 0.502–0.713, P = .029; TTR-M3-12-T6-10: AUC-ROC 0.610, 95% CI 0.516–0.703, P = .023; TTR-M6-12-T6-10; AUC-ROC 0.596, 95% CI 0.495–0.696, P = .051} during the first year and of having a glomerular filtration rate of <30 mL/min/1.73 m2 at the first year (TTR-M3-12-T > 6: AUC-ROC 0.676, 95% CI 0.542–0.811; P = .014; TTR-M6-12-T > 6: AUC-ROC 0.623, 95% CI 0.511–0.795; P = .037; TTR-M3-12-T6-10: AUC-ROC 0.566, 95% CI 0.429–0.703; P = .358; TTR-M6-12-T6-10: AUC-ROC 0.575, 95% CI 0.446–0.703; P = .310) was TTR-M3-12-T > 6. By Cox regression, the TTR that was significantly related to death censored graft loss of the kidney graft censoring for death was TTR-M3-12-T > 6 (TTR-M3-12-T > 6: HR = 0.972, 95% CI 0.949–0.995; P = .079; TTR-M6-12-T > 6: HR = 0.980, 95% CI 0.961–0.998; P = .033; TTR-M3-12-T6-10: HR = 0.985, 95% CI 0.962–1.009; P = .230; TTR-M6-12-T6-10: HR = 0.987, 95% CI 0.968–1.007; P = .199). By multivariate Cox regression analysis, patients in the lower tertile of TTR (HR = 10.027, 95% CI 1.244–81.447; P = .031) had worse survival than those in the upper tertiles, regardless of kidney function in the first year (Fig. 1).
CONCLUSION
The measurement of TTR after kidney transplantation makes possible to easily estimate the time of exposure to adequate levels of tacrolimus, relating it to the risk of acute rejection, kidney function in the first year, and death-censored graft survival. Among the possible TTR measures, the one that is best related to post-transplant outcome is taking into account tacrolimus blood levels between month 3 and 12 and those >6 ng/mL (TTR-M3-12-T > 6).
•Individual tacrolimus blood levels are the usual way to monitor the immunosuppressive effect in solid organ transplant.•A greater variability throughout a determined period of time has been related ...to a worse kidney graft outcome, but variability does not consider the therapeutic range goal.•Determining the time in therapeutic range using the Rosendaal method allows dose optimization by considering the adverse events associated with both supratherapeutic and subtherapeutic doses.•In our population of kidney transplant recipients, a lower time in the therapeutic range of tacrolimus levels relates to higher risk of acute rejection, worse 1-year kidney function, and worse long-term death-censored graft survival.•We suggest incorporating the measurement of therapeutic range after kidney transplant as an easy way to estimate the time of exposure to adequate levels of tacrolimus that also relates to kidney graft outcome.
Tacrolimus has a narrow therapeutic margin. Maintaining tacrolimus blood levels in the appropriate range is difficult because of its intrapatient variability. In fact, greater blood level variability has been related to worse kidney graft outcome, but only measuring variability does not consider the therapeutic range goal. Determining the time in therapeutic range (TTR) using the Rosendaal method allows dose optimization by considering the adverse events associated with both supratherapeutic and subtherapeutic doses. Some previous studies in kidney and lung transplantation have shown that the measurement of TTR has been related to the subsequent graft outcome.
We performed a single-center, observational study including 215 consecutive kidney transplants performed in our center. The percentage of time that the patient remained with levels above 6 ng/mL between months 3 and 12 (%TTR3-12) was calculated using the Rosendaal method.
A lower %TTR3-12 was associated with a higher risk of acute rejection (area under the receiver operating characteristic curve, 0.614; 95% confidence interval CI, 0.513-0.714; P = .018) and with a higher risk of having a 1-year glomerular filtration rate < 30 mL/min/1.73 m2 (area under the receiver operating characteristic curve, 0.676; 95% CI, 0.542-0.811; P = .014). The lowest tertile of %TTR3-12 was independently associated with a higher risk of death-censored graft loss (hazard ratio, 10.773; 95% CI, 1.315-88.264; P = .027) after adjusting by 1-year glomerular filtration rate, expanded criteria donation, and acute rejection throughout the first year.
To conclude, measuring TTR after kidney transplant is an easy way to estimate the time of exposure to adequate levels of tacrolimus and relates to kidney graft outcome.
The pressure for Water Resource Recovery Facilities (WRRF) operators to efficiently treat wastewater is greater than ever because of the water crisis, produced by the climate change effects and more ...restrictive regulations. Technicians and researchers need to evaluate WRRF performance to ensure maximum efficiency. For this purpose, numerical techniques, such as CFD, have been widely applied to the wastewater sector to model biological reactors and secondary settling tanks with high spatial and temporal accuracy. However, limitations such as complexity and learning curve prevent extending CFD usage among wastewater modeling experts. This paper presents HydroSludge, a framework that provides a series of tools that simplify the implementation of the processes and workflows in a WRRF. This work leverages HydroSludge to preprocess existing data, aid the meshing process, and perform CFD simulations. Its intuitive interface proves itself as an effective tool to increase the efficiency of wastewater treatment. PRACTITIONER POINTS: This paper introduces a software platform specifically oriented to WRRF, named HydroSludge, which provides easy access to the most widespread and leading CFD simulation software, OpenFOAM. Hydrosludge is intended to be used by WRRF operators, bringing a more wizard-like, automatic, and intuitive usage. Meshing assistance, submersible mixers, biological models, and distributed parallel computing are the most remarkable features included in HydroSludge. With the provided study cases, HydroSludge has proven to be a crucial tool for operators, managers, and researchers in WRRF.
The number of kidney transplants obtained from controlled donations after circulatory death is increasing, with long-term outcomes similar to those obtained with donations after brain death. ...Extraction using normothermic regional perfusion can improve results with controlled donors after circulatory death; however, information on the histological impact and extraction procedure is scarce.
We retrospectively investigated all kidney transplants performed from October 2014 to December 2019, in which a follow-up kidney biopsy had been performed at 1-year follow-up, comparing controlled procedures with donors after circulatory death and normothermic regional perfusion versus donors after brain death. Interstitial fibrosis/tubular atrophy was assessed by adding the values of interstitial fibrosis and tubular atrophy, according to the Banff classification of renal allograft pathology.
When we compared histological data from 66 transplants with donations after brain death versus 24 transplants with donations after circulatory death and normothermic regional perfusion, no differences were found in the degree of fibrosis in the 1-year follow-up biopsy (1.7 ± 1.3 vs 1.7 ± 1.1; P = .971) or in the ratio of patients with increased fibrosis calculated as interstitial fibrosis/tubular atrophy >2 (18% vs 13%; P = .522). In our multivariate analysis, which included acute rejection, expanded criteria donation, and the type of donation, no variable was independently related to an increased risk of interstitial fibrosis/tubular atrophy >2.
The outcomes of kidney grafts procured in our center using controlled procedures with donors after circulatory death and normothermic regional perfusion were indistinguishable from those obtained from donors after brain death, showing the same degree of fibrosis in the 1-year posttransplant surveillance biopsy. Our data support the conclusion that normothermic regional perfusion should be the method of choice for extraction in donors after circulatory death.
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