A semantic Grid for molecular science

Proceedings of the 2003 UK e-Science All Hands Meeting, 31st August - 3rd September, Nottingham UKThe properties of molecules have very well defined semantics and allow the creation of a semantic GRID. Markup languages (CML - Chemical Markup Language) and dictionary-based ontologies have been designed to support a wide range of applications, including chemical supply, publication and the safety of compounds. Many properties can be computed by Quantum Mechanical (QM) programs and we have developed a "black-box" system based on XML wrappers for all components. This is installed on a Condor system on which we have computed properties for 250, 000 compounds. The results of this will be available in an OpenData/OpenSource peer-to-peer (P2P) system (WorldWide Molecular Matrix - WWMM)

Strong ground motion characteristics of 2016 Central Italy earthquakes and implications for ground motion modeling

The 2016 Central Italy earthquake sequence produced three mainshocks: (1) M6.1 24 August, (2) M5.9 26 October, and (3) M6.5 30 October. Each mainshock was followed by many aftershocks, some of which with M > 5.0. All earthquake events occurred on southeast-northwest trending normal faults. As part of reconnaissance activities of these events performed by the Geotechnical Extreme Events Reconnaissance Association (GEER), ground motion data was processed and analyzed. After processing all data using procedures developed during the latest Next Generation Attenuation (NGA-West2) project, we analyze strong motion characteristics of all three mainshocks, two selected large aftershocks (M5.3 24 August and M4.8 26 August) and a foreshock (M5.4 26 October). Our analysis shows that stations near the hanging wall, exhibit fling-step in some cases but no obvious rupture directivity effects. We compare ground motion intensity measures (including peak ground acceleration and velocity, PGA and PGV, respectively) to Italy-specific and global ground motion models. Overall, the data exhibit fast attenuation at large distance (>100 km), which is captured by Italy-adjusted global models, but not by Italy-specific models. We also found that global models tend to over-predict ground motions at short periods. Both features were also observed from the 2009 L’Aquila earthquake data and may represent regional features. We estimate the spatial distribution of PGA for the three mainshocks by means of a Kriging analysis performed on within-event residuals using a global semi-variogram model. We found that the ground motion is most intense south-west of the Mt.Vettore - Mt.Bove normal fault. Given the importance of Italian normal fault earthquakes in worldwide ground motion databases, this data set is of global significance for studies of normal fault ground motions

Non-ergodic site response model based on local recordings for Menta Dam site

The paper describes the development of a non-ergodic site response model for a strategic site in the Aspromonte mountains, in Southern Italy. Fractured metamorphic rocks belonging to Calabrian complex outcrop in this area, located in a region where Southern Apennines crustal faults and subduction of the Calabrian Arc contribute to the seismic hazard. At the site, three accelerometers are installed since 2016 as part of the monitoring system of the Menta Dam, a bituminous-faced rockfill dam constructed for the water supply of the region. Ground motions recorded at the site and elsewhere from regional crustal and subduction earthquakes have been used to evaluate region-specific source and path adjustment to global ground motion models (GMMs). Those regionally adjusted GMMs have, in turn, been used to evaluate the mean bias of site-specific recordings, which is used to estimate non-ergodic site response for the dam site. This analysis highlights that site-specific site response is appreciably larger than the global average prediction of GMMs for periods lower than 0.4s. A non-ergodic GMM is developed that accounts for these effects to be used in subsequent Probabilistic Site Hazard Analysis (PSHA)

Decitabine impact on the endocytosis regulator RhoA, the folate carriers RFC1 and FOLR1, and the glucose transporter GLUT4 in human tumors.

BackgroundIn 31 solid tumor patients treated with the demethylating agent decitabine, we performed tumor biopsies before and after the first cycle of decitabine and used immunohistochemistry (IHC) to assess whether decitabine increased expression of various membrane transporters. Resistance to chemotherapy may arise due to promoter methylation/downregulation of expression of transporters required for drug uptake, and decitabine can reverse resistance in vitro. The endocytosis regulator RhoA, the folate carriers FOLR1 and RFC1, and the glucose transporter GLUT4 were assessed.ResultsPre-decitabine RhoA was higher in patients who had received their last therapy >3 months previously than in patients with more recent prior therapy (P = 0.02), and varied inversely with global DNA methylation as assessed by LINE1 methylation (r = -0.58, P = 0.006). Tumor RhoA scores increased with decitabine (P = 0.03), and RFC1 also increased in patients with pre-decitabine scores ≤150 (P = 0.004). Change in LINE1 methylation with decitabine did not correlate significantly with change in IHC scores for any transporter assessed. We also assessed methylation of the RFC1 gene (alias SLC19A1). SLC19A1 methylation correlated with tumor LINE1 methylation (r = 0.45, P = 0.02). There was a small (statistically insignificant) decrease in SLC19A1 methylation with decitabine, and there was a trend towards change in SLC19A1 methylation with decitabine correlating with change in LINE1 methylation (r = 0.47, P <0.15). While SLC19A1 methylation did not correlate with RFC1 scores, there was a trend towards an inverse correlation between change in SLC19A1 methylation and change in RFC1 expression (r = -0.45, P = 0.19).ConclusionsIn conclusion, after decitabine administration, there was increased expression of some (but not other) transporters that may play a role in chemotherapy uptake. Larger patient numbers will be needed to define the extent to which this increased expression is associated with changes in DNA methylation

XSEDE Campus Bridging – Cluster software distribution strategy and tactics

This document is both a public document and an internal working document intended to define XSEDE strategies related to XSEDE’s cluster build software distribution project. This is part a strategy document, part tactical.XSEDE is supported by National Science Foundation Grant 1053575 (XSEDE: eXtreme Science and Engineering Discovery Environment)

The Relationship Between HR Practices and Firm Performance: Examining Causal Order

Significant research attention has been devoted to examining the relationship between HR practices and firm performance, and the research support has assumed HR as the causal variable. Using data from 45 business units (with 62 data points), this study examines how measures of HR practices correlate with past, concurrent, and future operational performance measures. The results indicate that correlations with performance measures at all three times are both high and invariant, and that controlling for past or concurrent performance virtually eliminates the correlation of HR with future performance. Implications are discussed