Faced with physical and energy density limitations on clock speed, contemporary microprocessor designers have increasingly turned to on-chip parallelism for performance gains. Algorithms should ...accordingly be designed with ample amounts of fine-grained parallelism if they are to realize the full performance of the hardware. This requirement can be challenging for algorithms that are naturally expressed as a sequence of small-matrix operations, such as the Kalman filter methods widely in use in high-energy physics experiments. In the High-Luminosity Large Hadron Collider (HL-LHC), for example, one of the dominant computational problems is expected to be finding and fitting charged-particle tracks during event reconstruction; today, the most common track-finding methods are those based on the Kalman filter. Experience at the LHC, both in the trigger and offline, has shown that these methods are robust and provide high physics performance. Previously we reported the significant parallel speedups that resulted from our efforts to adapt Kalman-filter-based tracking to many-core architectures such as Intel Xeon Phi. Here we report on how effectively those techniques can be applied to more realistic detector configurations and event complexity.
In the High-Luminosity Large Hadron Collider (HL-LHC), one of the most challenging computational problems is expected to be finding and fitting charged-particle tracks during event reconstruction. ...The methods currently in use at the LHC are based on the Kalman filter. Such methods have shown to be robust and to provide good physics performance, both in the trigger and offline. In order to improve computational performance, we explored Kalman-filter-based methods for track finding and fitting, adapted for many-core SIMD (single instruction, multiple data) and SIMT (single instruction, multiple thread) architectures. Our adapted Kalman-filter-based software has obtained significant parallel speedups using such processors, e.g., Intel Xeon Phi, Intel Xeon SP (Scalable Processors) and (to a limited degree) NVIDIA GPUs. Recently, an effort has started towards the integration of our software into the CMS software framework, in view of its exploitation for the Run III of the LHC. Prior reports have shown that our software allows in fact for some significant improvements over the existing framework in terms of computational performance with comparable physics performance, even when applied to realistic detector configurations and event complexity. Here, we demonstrate that in such conditions physics performance can be further improved with respect to our prior reports, while retaining the improvements in computational performance, by making use of the knowledge of the detector and its geometry.
Abstract One of the main objectives of the Spanish and Portuguese-Speaking Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and ...dissemination of scientific knowledge in the area of forensic genetics. Due to this fact, GHEP-ISFG holds different working commissions that are set up to develop activities in scientific aspects of general interest. One of them, the Mixture Commission of GHEP-ISFG, has organized annually, since 2009, a collaborative exercise on analysis and interpretation of autosomal short tandem repeat (STR) mixture profiles. Until now, three exercises have been organized (GHEP-MIX01, GHEP-MIX02 and GHEP-MIX03), with 32, 24 and 17 participant laboratories respectively. The exercise aims to give a general vision by addressing, through the proposal of mock cases, aspects related to the edition of mixture profiles and the statistical treatment. The main conclusions obtained from these exercises may be summarized as follows. Firstly, the data show an increased tendency of the laboratories toward validation of DNA mixture profiles analysis following international recommendations (ISO/IEC 17025:2005). Secondly, the majority of discrepancies are mainly encountered in stutters positions (53.4%, 96.0% and 74.9%, respectively for the three editions). On the other hand, the results submitted reveal the importance of performing duplicate analysis by using different kits in order to reduce errors as much as possible. Regarding the statistical aspect (GHEP-MIX02 and 03), all participants employed the likelihood ratio (LR) parameter to evaluate the statistical compatibility and the formulas employed were quite similar. When the hypotheses to evaluate the LR value were locked by the coordinators (GHEP-MIX02) the results revealed a minor number of discrepancies that were mainly due to clerical reasons. However, the GHEP-MIX03 exercise allowed the participants to freely come up with their own hypotheses to calculate the LR value. In this situation the laboratories reported several options to explain the mock cases proposed and therefore significant differences between the final LR values were obtained. Complete information concerning the background of the criminal case is a critical aspect in order to select the adequate hypotheses to calculate the LR value. Although this should be a task for the judicial court to decide, it is important for the expert to account for the different possibilities and scenarios, and also offer this expertise to the judge. In addition, continuing education in the analysis and interpretation of mixture DNA profiles may also be a priority for the vast majority of forensic laboratories.
Abstract The GHEP-ISFG Working Group performed a collaborative exercise to monitor the current practice of mitochondrial (mt)DNA reporting. The participating laboratories were invited to evaluate a ...hypothetical case example and assess the statistical significance of a match between the haplotypes of a case (hair) sample and a suspect. A total of 31 forensic laboratories participated of which all but one used the EMPOP database. Nevertheless, we observed a tenfold range of reported LR values (32–333.4), which was mainly due to the selection of different reference datasets in EMPOP but also due to different applied formulae. The results suggest the need for more standardization as well as additional research to harmonize the reporting of mtDNA evidence.
In 1989, the association between Cftr (the gene) and cystic fibrosis or CF (the disease) was first reported. Since then, more than 500 mutations in Cftr have been identified. CFTR (the Cftr product) ...has been well characterised and shown to be involved in cAMP-dependent transmembrane Cl super(-) transport. Subsequently, several mouse Cftr knock-outs have been obtained and shown to lead to a deficiency in epithelial cell Cl super(-) transport. Transfer of Cftr into either CFTR-deficient or CFTR-mutant cells both in vitro and in vivo has been shown to restore a normal CFTR-dependent Cl super(-) transport. Moreover, a number of clinical studies have shown that gene transfer of wild-type human CFTR cDNA into the airways of CF patients leads to the transient restoration of the Cl super(-) transport function and/or the transmembrane potential difference across the airway epithelium.
Cystic fibrosis (CF) is a lethal genetic disorder affecting secretory epithelia, caused by mutations on the CFTR gene. In this paper we study the interactivity between the CFTR gene and CF disease ...over the time course of CF.
Cross-sectional analysis of CF patient population data from Latin-America, Canada, and The Netherlands, under the assumption that they represent stationary populations, was used to determined and correlates hazard rates, average cores and CF progression rates.
Results suggests the existence of two phases throughout the course of CF.
While the initial phase was related to the CFTR genotype, the kinetics of the second phase seems to be common to all groups considered. The hypothesis that the interactivity between the CFTR gene and CF disease would be limited in time is presented, suggesting that mutant CFTR would trigger a disease that evolves to become independent from the CFTR gene itself.
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