OpenCL Actors - Adding Data Parallelism to Actor-based Programming with CAF

The actor model of computation has been designed for a seamless support of concurrency and distribution. However, it remains unspecific about data parallel program flows, while available processing power of modern many core hardware such as graphics processing units (GPUs) or coprocessors increases the relevance of data parallelism for general-purpose computation. In this work, we introduce OpenCL-enabled actors to the C++ Actor Framework (CAF). This offers a high level interface for accessing any OpenCL device without leaving the actor paradigm. The new type of actor is integrated into the runtime environment of CAF and gives rise to transparent message passing in distributed systems on heterogeneous hardware. Following the actor logic in CAF, OpenCL kernels can be composed while encapsulated in C++ actors, hence operate in a multi-stage fashion on data resident at the GPU. Developers are thus enabled to build complex data parallel programs from primitives without leaving the actor paradigm, nor sacrificing performance. Our evaluations on commodity GPUs, an Nvidia TESLA, and an Intel PHI reveal the expected linear scaling behavior when offloading larger workloads. For sub-second duties, the efficiency of offloading was found to largely differ between devices. Moreover, our findings indicate a negligible overhead over programming with the native OpenCL API.Comment: 28 page

Study of the bivariate survival data using frailty models based on Lévy processes

Frailty models allow us to take into account the non-observable inhomogeneity of individual hazard functions. Although models with time-independent frailty have been intensively studied over the last decades and a wide range of applications in survival analysis have been found, the studies based on the models with time-dependent frailty are relatively rare. In this paper, we formulate and prove two propositions related to the identifiability of the bivariate survival models with frailty given by a nonnegative bivariate Lévy process. We discuss parametric and semiparametric procedures for estimating unknown parameters and baseline hazard functions. Numerical experiments with simulated and real data illustrate these procedures. The statements of the propositions can be easily extended to the multivariate case

Facilitative parenting and children's social, emotional and behavioural adjustment

Facilitative parenting (FP) supports the development of children’s social and emotional competence and effective peer relationships. Previous research has shown that FP discriminates between children bullied by peers from children who are not bullied, according to reports of teachers. This study investigates the association between FP and children’s social, emotional and behavioral problems, over and above the association with dysfunctional parenting (DP). 215 parents of children aged 5–11 years completed questionnaires about parenting and child behavior, and children and teachers completed measures of child bullying victimization. As predicted, FP accounted for variance in teacher reports of children’s bullying victimization as well as parent reports of children’s social and emotional problems and prosocial behavior better than that accounted for by DP. However for children’s reports of peer victimization the whole-scale DP was a better predictor than FP. Contrary to predictions, FP accounted for variance in conduct problems and hyperactivity better than DP. When analyses were replicated substituting subscales of dysfunctional and FP, a sub-set of FP subscales including Warmth, Supports Friendships, Not Conflicting, Child Communicates and Coaches were correlated with low levels of problems on a broad range of children’s adjustment problems. Parent–child conflict accounted for unique variance in children’s peer victimization (teacher report), peer problems, depression, emotional problems, conduct problems and hyperactivity. The potential relevance of FP as a protective factor for children against a wide range of adjustment problems is discussed

Konzeption und Implementierung eines Zertifizierungssystems zur Qualitätssicherung der Cochlea-Implantat-Versorgung in Deutschland

A standardized and structured process is indispensable for optimal hearing rehabilitation with cochlear implants (CI). The Executive Committee of the German Society of Otorhinolaryngology, Head and Neck Surgery (DGHNO-KHC), initiated the conception of a certification program and a Whitepaper based on the Association of the Scientific Medical Societies in Germany (AWMF) clinical practice guideline (CPG) describing the current medical standards of CI care in Germany. The goal was to independently confirm implementation of this CPG and make this information publicly available. With the support of an independent certification organization, successful implementation of the CI-CPG by a hospital would then be verified and confirmed by awarding the “Cochlear implant-provision institution” ( Cochlea-Implantat-versorgende Einrichtung , CIVE) quality certificate. A structure for implementation of a certification system was developed based on the CI-CPG. The following steps were required: 1) conception of a quality control system for certification of hospitals working in accordance with the CI-CPG; 2) development of required structures for an independent review of quality-relevant structure, process, and result parameters; 3) development of a standard procedure for independent certification of hospitals; 4) development of a certificate and a logo to demonstrate successful certification; 5) practical implementation of the certification. Following design of the certification program and the required organizational structure, the certification system was successfully launched in 2021. Applications for the quality certificate could be formally submitted from September 2021. A total of 51 off-site evaluations were performed by December 2022. In the first 16 months from introduction, 47 hospitals were successfully certified as CIVE. In this period, 20 experts were trained as auditors, who have since then carried out 18 on-site audits in hospitals. In summary, the conceptual design, structure, and practical implementation of a certification program for quality control in CI care was successfully implemented in Germany

Struktur und Einrichtung des Deutschen Cochlea-Implantat-Registers (DCIR)

Abstract Hearing rehabilitation of patients with severe hearing loss or deafness using cochlear implants (CI) is a very successful but also complex and lifelong process that requires high quality standards for structure, process, and results. Medical registries represent an ideal tool for conducting quality control relevant to care while at the same time collecting scientific data. Therefore, at the initiative of the Executive Committee of the German Society of Oto-Rhino-Laryngology, Head and Neck Surgery (DGHNO-KHC), a Germany-wide CI registry (the German Cochlear Implant Register, DCIR) was to be established. The following goals were to be achieved: 1) legal and contractual basis for the register; 2) definition of the register contents; 3) development of evaluation standards (hospital-specific and national annual reports); 4) development of a logo; 5) practical operation of the registry. After defining a catalog of services that defines the content, structure, and operation of the DCIR, a registry operator with audiological expertise was sought. After considering various offers, the registry was technically implemented in cooperation with the provider INNOFORCE (Ruggell, Liechtenstein) as registry operator. This also included the realization of an interface for data transfer from previously existing databases and development of a data protection concept for productive operation of the DCIR under the scientific leadership of the DGHNO-KHC Executive Committee. Since January 2022, it has been possible for participating hospitals to enter pseudonymized data into the DCIR. To date, 75 hospitals in Germany have contractually agreed to participate in the registry. During the first 15 months, data from over 2500 implants in over 2000 patients were registered in the DCIR. The work presented here describes the structuring, development, and successful establishment of the DCIR. Introduction of the DCIR represents an important milestone of future scientifically based quality control in CI care. The registry presented here can therefore be considered as an example for other areas of medical care and thus also sets an international standard

Discovery of Potent, Selective, and Orally Bioavailable Small-Molecule Modulators of the Mediator Complex-Associated Kinases CDK8 and CDK19.

The Mediator complex-associated cyclin-dependent kinase CDK8 has been implicated in human disease, particularly in colorectal cancer where it has been reported as a putative oncogene. Here we report the discovery of 109 (CCT251921), a potent, selective, and orally bioavailable inhibitor of CDK8 with equipotent affinity for CDK19. We describe a structure-based design approach leading to the discovery of a 3,4,5-trisubstituted-2-aminopyridine series and present the application of physicochemical property analyses to successfully reduce in vivo metabolic clearance, minimize transporter-mediated biliary elimination while maintaining acceptable aqueous solubility. Compound 109 affords the optimal compromise of in vitro biochemical, pharmacokinetic, and physicochemical properties and is suitable for progression to animal models of cancer

Risk-adjusted CUSUM control charts for shared frailty survival models with application to hip replacement outcomes: a study using the NJR dataset

Background:  Continuous monitoring of surgical outcomes after joint replacement is needed to detect which brands’ components have a higher than expected failure rate and are therefore no longer recommended to be used in surgical practice. We developed a monitoring method based on cumulative sum (CUSUM) chart specifically for this application.  Methods:  Our method entails the use of the competing risks model with the Weibull and the Gompertz hazard functions adjusted for observed covariates to approximate the baseline time-to-revision and time-to-death distributions, respectively. The correlated shared frailty terms for competing risks, corresponding to the operating unit, are also included in the model. A bootstrap-based boundary adjustment is then required for risk-adjusted CUSUM charts to guarantee a given probability of the false alarm rates. We propose a method to evaluate the CUSUM scores and the adjusted boundary for a survival model with the shared frailty terms. We also introduce a unit performance quality score based on the posterior frailty distribution. This method is illustrated using the 2003-2012 hip replacement data from the UK National Joint Registry (NJR). Results:  We found that the best model included the shared frailty for revision but not for death. This means that the competing risks of revision and death are independent in NJR data. Our method was superior to the standard NJR methodology. For one of the two monitored components, it produced alarms four years before the increased failure rate came to the attention of the UK regulatory authorities. The hazard ratios of revision across the units varied from 0.38 to 2.28. Conclusions:  An earlier detection of failure signal by our method in comparison to the standard method used by the NJR may be explained by proper risk-adjustment and the ability to accommodate time-dependent hazards. The continuous monitoring of hip replacement outcomes should include risk adjustment at both the individual and unit level

Análise dos atributos dos cuidados primários em saúde utilizando os prontuários eletrônicos na cidade do Rio de Janeiro

Resumo A epidemiologia desempenha um papel estratégico neste estágio do ciclo de política, contribuindo para o estabelecimento de metas, alocação de recursos e uso de sistemas de informação. Em 2009, a Secretaria Municipal de Saúde do Rio de Janeiro iniciou uma reforma do modelo de atenção, utilizando como principal influência o conceito de Atenção Primária em Saúde. Este estudo avalia a tendência de indicadores selecionados do “pay-for-performance” que mensuram o processo de cuidado em saúde na APS da cidade. Estudo de painéis repetidos, a partir dos registros administrativos e clínicos dos prontuários eletrônicos no período de 2012 a 2016. Foram escolhidos sete indicadores que analisaram o desempenho longitudinal dentro da meta estabelecida, entre aqueles que representam acesso, longitudinalidade, coordenação do cuidado – atributos da APS, assim como outras características dos serviços como desempenho assistencial e eficiência econômica. Este estudo demonstrou que a descentralização da gestão para níveis mais próximos do usuário é potencialmente exitoso para o registro de dados clínicos, caso seja realizado um adequado monitoramento dos indicadores, auditorias clínicas frequentes e realizado periodicamente um “feedback” aos profissionais de saúde com os dados e indicadores acompanhados

Comparison of Parallelisation Approaches, Languages, and Compilers for Unstructured Mesh Algorithms on GPUs

Efficiently exploiting GPUs is increasingly essential in scientific computing, as many current and upcoming supercomputers are built using them. To facilitate this, there are a number of programming approaches, such as CUDA, OpenACC and OpenMP 4, supporting different programming languages (mainly C/C++ and Fortran). There are also several compiler suites (clang, nvcc, PGI, XL) each supporting different combinations of languages. In this study, we take a detailed look at some of the currently available options, and carry out a comprehensive analysis and comparison using computational loops and applications from the domain of unstructured mesh computations. Beyond runtimes and performance metrics (GB/s), we explore factors that influence performance such as register counts, occupancy, usage of different memory types, instruction counts, and algorithmic differences. Results of this work show how clang's CUDA compiler frequently outperform NVIDIA's nvcc, performance issues with directive-based approaches on complex kernels, and OpenMP 4 support maturing in clang and XL; currently around 10% slower than CUDA