Object oriented data analysis in ALEPH

This article describes the status of the ALPHA^{++} project of the ALEPH collaboration. The ALEPH data have been converted from Fortran data structures (BOS banks) into C^{++} objects and stored in a object oriented database (Objectivity/DB), using tools provided by the RD45 collaboration and the LHC^{++} software project at CERN. A description of the database setup and of a preliminary version of an object oriented analysis program is given.This article describes the status of the ALPHA^{++} project of the ALEPH collaboration. The ALEPH data have been converted from Fortran data structures (BOS banks) into C^{++} objects and stored in a object oriented database (Objectivity/DB), using tools provided by the RD45 collaboration and the LHC^{++} software project at CERN. A description of the database setup and of a preliminary version of an object oriented analysis program is given

In situ visualization of large-scale turbulence simulations in Nek5000 with ParaView Catalyst

In situ visualization on high-performance computing systems allows us to analyze simulation results that would otherwise be impossible, given the size of the simulation data sets and offline post-processing execution time. We develop an in situ adaptor for Paraview Catalyst and Nek5000, a massively parallel Fortran and C code for computational fluid dynamics. We perform a strong scalability test up to 2048 cores on KTH’s Beskow Cray XC40 supercomputer and assess in situ visualization’s impact on the Nek5000 performance. In our study case, a high-fidelity simulation of turbulent flow, we observe that in situ operations significantly limit the strong scalability of the code, reducing the relative parallel efficiency to only ≈ 21 % on 2048 cores (the relative efficiency of Nek5000 without in situ operations is ≈ 99 %). Through profiling with Arm MAP, we identified a bottleneck in the image composition step (that uses the Radix-kr algorithm) where a majority of the time is spent on MPI communication. We also identified an imbalance of in situ processing time between rank 0 and all other ranks. In our case, better scaling and load-balancing in the parallel image composition would considerably improve the performance of Nek5000 with in situ capabilities. In general, the result of this study highlights the technical challenges posed by the integration of high-performance simulation codes and data-analysis libraries and their practical use in complex cases, even when efficient algorithms already exist for a certain application scenario

Cellular localization of the potassium channel Kir7.1 in guinea pig and human kidney

Cellular localization of the potassium channel Kir7.1 in guinea pig and human kidney.BackgroundK+ channels have important functions in the kidney, such as maintenance of the membrane potential, volume regulation, recirculation, and secretion of potassium ions. The aim of this study was to obtain more information on the localization and possible functional role of the inwardly rectifying K+ channel, Kir7.1.MethodsKir7.1 cDNA (1114 bp) was isolated from guinea pig kidney (gpKir7.1), and its tissue distribution was analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR). In addition, a genomic DNA fragment (6153 bp) was isolated from a genomic library. cRNA was expressed in Xenopus laevis oocytes for functional studies. Immunohistochemistry and RT-PCR were used to localize Kir7.1 in guinea pig and human kidney.ResultsThe expression of gpKir7.1 in Xenopus laevis oocytes revealed inwardly rectifying K+ currents. The reversal potential was strongly dependent on the extracellular K+ concentration, shifting from -14 mV at 96 mmol/L K+ to -90 mV at 1 mmol/L K+. gpKir7.1 showed a low affinity for Ba2+. Significant expression of gpKir7.1 was found in brain, kidney, and lung, but not in heart, skeletal muscle, liver, or spleen. Immunocytochemical detection in guinea pig identified the gpKir7.1 protein in the basolateral membrane of epithelial cells of the proximal tubule. RT-PCR analysis identified strong gpKir7.1 expression in the proximal tubule and weak expression in glomeruli and thick ascending limb. In isolated human tubule fragments, RT-PCR showed expression in proximal tubule and thick ascending limb.ConclusionOur results suggest that Kir7.1 may contribute to basolateral K+ recycling in the proximal tubule and in the thick ascending limb

Breeding season of the South American fur seal (Arctocephalus Australis, Otariidae: Carnivora): new data for establishing independent evolutionary histories?

The South American fur seal (SAFS) is distributed from Peru (Pacific Ocean) to Uruguay (Atlantic Ocean). However, there is a section of coastline of about 2,300 km along the Chilean coast where no SAFS are recorded. Based on morphological comparisons 3 geographic forms have been reported (Peruvian, South Chilean, Atlantic), whereas preliminary genetic studies suggest the presence of 3 distinct genetic types (Peruvian, South Chile, Atlantic). However, both of these approaches are support only the existence of 2 independent evolutionary histories for SAFS (Peruvian, Atlantic), in which case, we would also expect to find some differences in the species’ life histories among these locals populations (e.g., in the timing of the breeding season). In this study, we compare the breeding seasons of SAFS at Punta Pichalo (19°36’S-Chile), Isla Guafo (43°33’S-Chile), and Isla de Lobos (35°01’S-Uruguay) with data published for Punta San Juan (15°21’S-Peru). The periods for establishing territories, pupping, and mating took place on similar dates at Isla Guafo and Isla de Lobos, but occurred about a month earlier at Punta Pichalo and Punta San Juan. Pupping peaked at Isla Guafo on 15-December, at Isla de Lobos on 17-December, and at Punta Pichalo on 27-November. These differences in timing were not related to demographic, oceanographic or photoperiod conditions of the breeding sites under study, neither is related with the latitudinal effects on the breeding phenology. Based on results, we suggest that certain characteristics of life history can help identify species with independent evolutionary historie

Impact of central surgical review in a study of malignant germ cell tumors

BACKGROUND: Verification of surgical staging has received little attention in clinical oncology trials. Central surgical review was undertaken during a study of malignant pediatric germ cell tumors. METHODS: Children's Oncology Group study AGCT0132 included central surgical review during the study. Completeness of submitted data and confirmation of assigned stage were assessed. Review responses were: assigned status confirmed, assignment withheld pending review of additional information requested, or institutional assignment of stage disputed with explanation given. Changes in stage assignment were at the discretion of the enrolling institution. RESULTS: A total of 206 patients underwent central review. Failure to submit required data elements or need for clarification was noted in 40%. Disagreement with stage assignment occurred in 10% with 17/21 discordant patients reassigned to stage recommended by central review. Four ovarian tumor patients not meeting review criteria for Stage I remained in that stratum by institutional decision. Two-year event free survival in Stage I ovarian patients was 25% for discordant patients compared to 57% for those meeting Stage I criteria by central review. CONCLUSIONS: Central review of stage assignment improved complete data collection and assignment of correct tumor stage at study entry, and allowed for prompt initiation of chemotherapy in patients determined not to have Stage I disease

Individual Rights, Economic Transactions, and Recognition: A Legal Approach to Social Economics

Modernity brought the idea of individual property rights as a com- plex phenomenon. However, economics adopted a simplistic view of property as a fundamental institution, understating the complex interaction of different rights and obligations that frame the legal environment of economic processes with an insufficiently elaborated tool. Here, a more elaborate view of legal elements will be propose