Standardizing clinical trials workflow representation in UML for international site comparison.

BACKGROUND: With the globalization of clinical trials, a growing emphasis has been placed on the standardization of the workflow in order to ensure the reproducibility and reliability of the overall trial. Despite the importance of workflow evaluation, to our knowledge no previous studies have attempted to adapt existing modeling languages to standardize the representation of clinical trials. Unified Modeling Language (UML) is a computational language that can be used to model operational workflow, and a UML profile can be developed to standardize UML models within a given domain. This paper's objective is to develop a UML profile to extend the UML Activity Diagram schema into the clinical trials domain, defining a standard representation for clinical trial workflow diagrams in UML. METHODS: Two Brazilian clinical trial sites in rheumatology and oncology were examined to model their workflow and collect time-motion data. UML modeling was conducted in Eclipse, and a UML profile was developed to incorporate information used in discrete event simulation software. RESULTS: Ethnographic observation revealed bottlenecks in workflow: these included tasks requiring full commitment of CRCs, transferring notes from paper to computers, deviations from standard operating procedures, and conflicts between different IT systems. Time-motion analysis revealed that nurses' activities took up the most time in the workflow and contained a high frequency of shorter duration activities. Administrative assistants performed more activities near the beginning and end of the workflow. Overall, clinical trial tasks had a greater frequency than clinic routines or other general activities. CONCLUSIONS: This paper describes a method for modeling clinical trial workflow in UML and standardizing these workflow diagrams through a UML profile. In the increasingly global environment of clinical trials, the standardization of workflow modeling is a necessary precursor to conducting a comparative analysis of international clinical trials workflows.

Parallel implementation of the recurrence method for computing the power-spectral density of thin avalanche photodiodes

A simulation program has been developed to calculate the power-spectral density of thin avalanche photodiodes, which are used in optical networks. The program extends the time-domain analysis of the dead-space multiplication model to compute the autocorrelation function of the APD impulse response. However, the computation requires a large amount of memory space and is very time consuming. We describe our experiences in parallelizing the code using both MPI and OpenMP. Several array partitioning schemes and scheduling policies are implemented and tested Our results show that the OpenMP code is scalable up to 64 processors on an SGI Origin 2000 machine and has small average errors.

Parallel bandwidth characteristics calculations for thin avalanche photodiodes on a SGI Origin 2000 supercomputer

An important factor for high-speed optical communication is the availability of ultrafast and low-noise photodetectors. Among the semiconductor photodetectors that are commonly used in today’s long-haul and metro-area fiber-optic systems, avalanche photodiodes (APDs) are often preferred over p-i-n photodiodes due to their internal gain, which significantly improves the receiver sensitivity and alleviates the need for optical pre-amplification. Unfortunately, the random nature of the very process of carrier impact ionization, which generates the gain, is inherently noisy and results in fluctuations not only in the gain but also in the time response. Recently, a theory characterizing the autocorrelation function of APDs has been developed by us which incorporates the dead-space effect, an effect that is very significant in thin, high-performance APDs. The research extends the time-domain analysis of the dead-space multiplication model to compute the autocorrelation function of the APD impulse response. However, the computation requires a large amount of memory space and is very time consuming. In this research, we describe our experiences in parallelizing the code in MPI and OpenMP using CAPTools. Several array partitioning schemes and scheduling policies are implemented and tested. Our results show that the code is scalable up to 64 processors on a SGI Origin 2000 machine and has small average errors.

Coccolithophore bloom size variation in response to the regional environment of the subarctic North Atlantic

Several environmental/physical variables derived from satellite and in situ data sets were used to understand the variability of coccolithophore abundance in the subarctic North Atlantic. The 7-yr (1997–2004) time-series analysis showed that the combined effects of high solar radiation, shallow mixed layer depth (<20 m), and increased temperatures explained >89% of the coccolithophore variation. The June 1998 bloom, which was associated with high light intensity, unusually high sea-surface temperature, and a very shallow mixed layer, was found to be one of the most extensive (>995,000 km2) blooms ever recorded. There was a pronounced sea-surface temperature shift in the mid-1990s with a peak in 1998, suggesting that exceptionally large blooms are caused by pronounced environmental conditions and the variability of the physical environment strongly affects the spatial extent of these blooms. Consequently, if the physical environment varies, the effects of these blooms on the atmospheric and oceanic environment will vary as well.

Cox-2 Promotes Chromogranin A Expression and Bioactivity: Evidence for a PGE2-Dependent Mechanism and the Involvement of a Proximal cAMP-Responsive Element.

Abstract The prostanoid biosynthetic enzyme cyclooxygenase-2 (Cox-2) is upregulated in several neuroendocrine tumors. The aim of the current study was to employ a neuroendocrine cell (PC12) model of Cox-2 over-expression to identify gene products that might be implicated in the oncogenic and/or inflammatory actions of this enzyme in the setting of neuroendocrine neoplasia. Expression array and real-time PCR analysis demonstrated that levels of the neuroendocrine marker chromogranin A (CGA) were 2-fold and 3.2-fold higher, respectively, in Cox-2 over-expressing cells (PCXII) vs their control (PCMT) counterparts. Immunocytochemical and immunoblotting analyses confirmed that both intracellular and secreted levels of CGA were elevated in response to Cox-2 induction. Moreover, exogenous addition of prostaglandin E2 (1u�­M), mimicked this effect in PCMT cells, while treatment of PCXII cells with the Cox-2 selective inhibitor NS-398 (100 nM) reduced CGA expression levels, thereby confirming the biospecificity of this finding. Levels of neurone specific enolase (NSE) were similar in the two cell lines, suggesting that the effect of Cox-2 on CGA expression was specific and not due to a global enhancement of neuroendocrine marker expression/differentiation. Cox-2-dependent CGA upregulation was associated with significantly increased chromaffin granule number and intracellular and secreted levels of dopamine. CGA promoter-driven reporter gene expression studies provided evidence that prostaglandin E2-dependent upregulation required a proximal cAMP-responsive element (CRE; -71 - -64 bp). This study is the first to demonstrate that Cox-2 upregulates both CGA expression and bioactivity in a neuroendocrine cell line and has major implications for the role of this polypeptide in the pathogenesis of neuroendocrine cancers in which Cox-2 is upregulated.

Quasiexperimental Study of the Effects of Antibiotic Use, Gastric Acid-Suppressive Agents, and Infection Control Practices on the Incidence of Clostridium difficile-Associated Diarrhea in Hospitalized Patients

The objective of this study was to evaluate the effects of antimicrobial drug use, gastric acid-suppressive agent use, and infection control practices on the incidence of Clostridium difficile-associated diarrhea (CDAD) in a 426-bed general teaching hospital in Northern Ireland. The study was retrospective and ecological in design. A multivariate autoregressive integrated moving average (time-series analysis) model was built to relate CDAD incidence with antibiotic use, gastric acid-suppressive agent use, and infection control practices within the hospital over a 5-year period (February 2002 to March 2007). The findings of this study showed that temporal variation in CDAD incidence followed temporal variations in expanded-spectrum cephalosporin use (average delay = 2 months; variation of CDAD incidence = 0.01/100 bed-days), broad-spectrum cephalosporin use (average delay = 2 months; variation of CDAD incidence = 0.02/100 bed-days), fluoroquinolone use (average delay = 3 months; variation of CDAD incidence = 0.004/100 bed-days), amoxicillin-clavulanic acid use (average delay = 1 month; variation of CDAD incidence = 0.002/100 bed-days), and macrolide use (average delay = 5 months; variation of CDAD incidence = 0.002/100 bed-days). Temporal relationships were also observed between CDAD incidence and use of histamine-2 receptor antagonists (H2RAs; average delay = 1 month; variation of CDAD incidence = 0.001/100 bed-days). The model explained 78% of the variance in the monthly incidence of CDAD. The findings of this study highlight a temporal relationship between certain classes of antibiotics, H2RAs, and CDAD incidence. The results of this research can help hospitals to set priorities for restricting the use of specific antibiotic classes, based on the size-effect of each class and the delay necessary to observe an effect.

Managing Risk: From Regulation to the Reintegration of Sexual Offenders

In the last number of years the management of the dangerous in the community, particularly sex offenders, has generated enormous concern. This concern has been reflected at a number of different levels - in media and popular responses to the risk posed by released sex offenders in the community and in official discourses where an abundance of legislation and policy reforms have been enacted within a relatively short period of time. This analysis seeks to critically evaluate these developments within the context of contemporary criminal justice policy and practice in relation to the management of sex offenders in the community. The article analyses the contemporary focus on risk management or preventative governance which underpins the current regulatory framework and has been reflected in both the sentencing options and in control in the community initiatives for sex offenders. In this respect, the article highlights the gap between policy and practice in terms of the effective risk management of sex offenders. Given the failure of the traditional justice system with respect to these types of offences, it will be argued that the retributive framework could usefully be supplemented by the theory and practice of reintegrative or restorative community justice, and public education in particular, in order to better manage the risk presented by sex offenders in the community.

Maximum likelihood estimation of higher-order integer-valued autoregressive processes

In this article, we extend the earlier work of Freeland and McCabe [Journal of time Series Analysis (2004) Vol. 25, pp. 701–722] and develop a general framework for maximum likelihood (ML) analysis of higher-order integer-valued autoregressive processes. Our exposition includes the case where the innovation sequence has a Poisson distribution and the thinning is binomial. A recursive representation of the transition probability of the model is proposed. Based on this transition probability, we derive expressions for the score function and the Fisher information matrix, which form the basis for ML estimation and inference. Similar to the results in Freeland and McCabe (2004), we show that the score function and the Fisher information matrix can be neatly represented as conditional expectations. Using the INAR(2) speci?cation with binomial thinning and Poisson innovations, we examine both the asymptotic e?ciency and ?nite sample properties of the ML estimator in relation to the widely used conditional least
squares (CLS) and Yule–Walker (YW) estimators. We conclude that, if the Poisson assumption can be justi?ed, there are substantial gains to be had from using ML especially when the thinning parameters are large.

Maximum likelihood estimation of higher-order integer-valued autoregressive processes

Corrigendum Vol. 30, Issue 2, 259, Article first published online: 15 MAR 2009 to correct the order of authors names: Bu R., K. Hadri, and B. McCabe.

Long-term return reversals-Value and growth or tax? UK evidence

This paper examines (i) whether value-growth characteristics have more power than past performance in predicting return reversals; and (ii) whether typical rational behaviour such as incentives to delay paying capital gain taxes can better explain long-term reversals than past performance. We find that value-growth characteristics generally provide better explanations for long-term stock returns than past performance. The evidence also shows that winners identified by capital gains dominate past performance winners in predicting reversals in the cross-sectional comparison. However, in the time-series analysis, when returns on capital gain winners are adjusted by the Fama and French (1996) risk factors, the predictive power of capital gain winners disappears. Our results show that capital gain winners are heavily featured as growth stocks. Return reversals in capital gain winners potentially reflect market price corrections for growth stocks. We conclude that investors’ incentives to delay paying capital gain taxes cannot fully rationalise long-term reversals in the UK market. Our results also imply that the long-term return pattern potentially reflects a mixture of investor rational and irrational behaviour.

Cytotoxicity of 1-alkylquinolinium bromide ionic liquids in murine fibroblast NIH 3T3 cells

Minimal toxicity data are available for 1-alkylquinolinium bromide ionic liquids. Here, their toxicity to NIH 3T3 murine fibroblast cells, of relevance to their potential antimicrobial application, is presented. Toxicity data, presented by time-point analysis with a particular focus on the immediate toxicity upon short term cellular exposure, indicate a link between the length of the alkyl chain substituent and resultant biological toxicity. 1-Tetradecylquinolinium bromide was found to exhibit cellular toxicity comparable to benzalkonium chloride over all time points tested. By comparison, 1-octylquinolinium bromide initially exerted significantly lower cytotoxicity at one hour; however, toxicity was found to have a cumulative effect over time-course analysis up to three days. This illustrates that alkyl chain components may govern not only overall toxicity, but also the rate of toxicity. Fluorescence microscopy was utilised to examine destabilisation of the plasma membrane by 1 tetradecylquinolinium bromide and benzalkonium chloride after one hour, with membrane destabilisation not observed for 1-octylquinolinium bromide, or the base constituent quinoline.

Protection Assessment using Reduced Power System Fault Data

Wavelet transforms provide basis functions for time-frequency analysis and have properties that are particularly useful for the compression of analogue point on wave transient and disturbance power system signals. This paper evaluates the compression properties of the discrete wavelet transform using actual power system data. The results presented in the paper indicate that reduction ratios up to 10:1 with acceptable distortion are achievable. The paper discusses the application of the reduction method for expedient fault analysis and protection assessment.

Chromospheric velocities of a C-class flare

Aims. We use high spatial and temporal resolution observations from the Swedish Solar Telescope to study the chromospheric velocities of a C-class flare originating from active region NOAA 10969.
Methods. A time-distance analysis is employed to estimate directional velocity components in Hα and Ca ii K image sequences. Also, imaging spectroscopy has allowed us to determine flare-induced line-of-sight velocities. A wavelet analysis is used to analyse the periodic nature of associated flare bursts.
Results. Time-distance analysis reveals velocities as high as 64 km s-1 along the flare ribbon and 15 km s-1 perpendicular to it. The velocities are very similar in both the Hα and Ca ii K time series. Line-of-sight Hα velocities are red-shifted with values up to 17 km s-1. The high spatial and temporal resolution of the observations have allowed us to detect velocities significantly higher than those found in earlier studies. Flare bursts with a periodicity of ≈60 s are also detected. These bursts are similar to the quasi-periodic oscillations observed at hard X-ray and radio wavelength data.
Conclusions. Some of the highest velocities detected in the solar atmosphere are presented. Line-of-sight velocity maps show considerable mixing of both the magnitude and direction of velocities along the flare path. A change in direction of the velocities at the flare kernel has also been detected which may be a signature of chromospheric evaporation.

Demonstration of saturation in a Ni-like Ag x-ray laser at 14 nm

We report the first demonstration of saturation in a Ni-like x-ray laser, specifically Ni-like Ag x-ray laser at 14 nm. Using high-resolution spatial imaging and angularly resolved streaking techniques, the output source size as well as the time history, divergence, energy, and spatial profile of the output beam have been fully characterized. The output intensity of the Ag laser was measured to be about 70 GWcm(-2) The narrow divergence, short pulse duration, high efficiency, and high brightness of the Ag laser make it an ideal candidate for many x-ray laser applications.

Non-radial pulsation, rotation and outburst in the Be star omega Orionis from the MuSiCoS 1998 campaign

omega Ori (HD37490, HR1934) is a Be star known to have presented variations. In order to investigate the nature and origin of its short-term and mid-term variability, a study is performed of several spectral lines (Halpha, Hdelta, HeI 4471, 4713, 4921, 5876, 6678, CII 4267, 6578, 6583, Mg II 4481, Si III 4553 and Si II 6347), based on 249 high signal-to-noise high-resolution spectra taken with 8 telescopes over 22 consecutive nights during the MuSiCoS (Multi SIte COntinuous Spectroscopy) campaign in November-December 1998. The stellar parameters are revisited and the projected rotational velocity (v sin i = 179 km s(-1)) is redetermined using several methods. With the MuSiCoS 98 dataset, a time series analysis of line-profile variations (LPVs) is performed using the Restricted Local Cleanest (RLC) algorithm and a least squares method. The behaviour of the velocity of the centroid of the lines, the equivalent widths and the apparent vsini for several lines, as well as Violet and Red components of photospheric lines affected by emission (red He i lines, Si II 6347, CII 6578, 6583) are analyzed. The non-radial pulsation (NRP) model is examined using phase diagrams and the Fourier-Doppler Imaging (FDI) method. The LPVs are consistent with a NRP mode with l = 2 or 3, \m\ = 2 with frequency 1.03 cd(-1). It is shown that an emission line outburst occurred in the middle of the campaign. Two scenarios are proposed to explain the behaviour of a dense cloud, temporarily orbiting around the star with a frequency 0.46 c d(-1), in relation to the outburst.