A general and scalable solution for heterogeneous workflow invocation and nesting

Several widely utilized, grid workflow management systems emerged in the last decade. These systems were developed by different scientific communities for various purposes. Enhancing these systems with the capability of invoking and nesting the workflows of other systems within their native workflows makes these communities to be able to carry out cross-organizational experiments and share non-native workflows. The novel solution described in this paper allows the integration of different workflow engines and makes them accessible for workflow systems in order to achieve this goal. The solution is based on an application repository and submitter, which exposes different workflow engines and executes them using the computational resources of the grid. In contrast with other approaches, our solution is scalable in terms of both number of workflows and amount of data, easily extendable in the sense that the integration of a new workflow engine does not require code re-engineering, and general, since it can be adopted by numerous workflow systems

Interoperability of heterogeneous large-scale scientific workflows and data resources

Workflow allows e-Scientists to express their experimental processes in a structured way and provides a glue to integrate remote applications. Since Grid provides an enormously large amount of data and computational resources, executing workflows on the Grid results in significant performance improvement. Several workflow management systems, which are widely used by different scientific communities, were developed for various purposes. Therefore, they differ in several aspects. This thesis outlines two major problems of existing workflow systems: workflow interoperability and data access. On the one hand, existing workflow systems are based on different technologies. Therefore, to achieve interoperability between their workflows at any level is a challenging task. In spite of the fact that there is a clear demand for interoperable workflows, for example, to enable scientists to share workflows, to leverage existing work of others, and to create multi-disciplinary workflows; currently, there are only limited, ad-hoc workflow interoperability solutions available for scientists. Existing solutions only realise workflow interoperability between a small set of workflow systems and do not consider performance issues that arise in the case of large-scale (computational and/or data intensive) scientific workflows. Scientific workflows are typically computation and/or data intensive and are executed in a distributed environment to speed up their execution time. Therefore, their performance is a key issue. Existing interoperability solutions bottleneck the communication between workflows in most scenarios dramatically increasing execution time. On the other hand, many scientific computational experiments are based on data that reside in data resources which can be of different types and vendors. Many workflow systems support access to limited subsets of such data resources preventing data level workflow interoperation between different systems. Therefore, there is a demand for a general solution that provides access to a wide range of data resources of different types and vendors. If such a solution is general, in the sense that it can be adopted by several workflow systems, then it also enables workflows of different systems to access the same data resources and therefore interoperate at data level. Note that data semantics are out of the scope of this work. For the same reasons as described above, the performance characteristics of such a solution are inevitably important. Although in terms of functionality, there are solutions which could be adopted by workflow systems for this purpose, they provide poor performance. For that reason, they did not gain wide acceptance by the scientific workflow community. Addressing these issues, a set of architectures is proposed to realise heterogeneous data access and heterogeneous workflow execution solutions. The primary goal was to investigate how such solutions can be implemented and integrated with workflow systems. The secondary aim was to analyse how such solutions can be implemented and utilised by single applications

p-species integrable reaction-diffusion processes

We consider a process in which there are p-species of particles, i.e. A_1,A_2,...,A_p, on an infinite one-dimensional lattice. Each particle $A_i$ can diffuse to its right neighboring site with rate $D_i$, if this site is not already occupied. Also they have the exchange interaction A_j+A_i --> A_i+A_j with rate $r_{ij}.$ We study the range of parameters (interactions) for which the model is integrable. The wavefunctions of this multi--parameter family of integrable models are found. We also extend the 2--species model to the case in which the particles are able to diffuse to their right or left neighboring sites.Comment: 16 pages, LaTe

Illness Management and Recovery: A Review of the Literature

OBJECTIVE: Illness Management and Recovery (IMR) is a standardized psychosocial intervention that is designed to help people with severe mental illness manage their illness and achieve personal recovery goals. This literature review summarizes the research on consumer-level effects of IMR and articles describing its implementation. METHODS: In 2011, the authors conducted a literature search of Embase, MEDLINE, PsycINFO, CINAHL, and the Cochrane Library by using the key words “illness management and recovery,” “wellness management and recovery,” or “IMR” AND (“schizophrenia” OR “bipolar” OR “depression” OR “recovery” OR “mental health”). Publications that cited two seminal IMR articles also guided further exploration of sources. Articles that did not deal explicitly with IMR or a direct adaptation were excluded. RESULTS: Three randomized-controlled trials (RCTs), three quasi-controlled trials, and three pre-post trials have been conducted. The RCTs found that consumers receiving IMR reported significantly more improved scores on the IMR Scale (IMRS) than consumers who received treatment as usual. IMRS ratings by clinicians and ratings of psychiatric symptoms by independent observers were also more improved for the IMR consumers. Implementation studies (N=16) identified several important barriers to and facilitators of IMR, including supervision and agency support. Implementation outcomes, such as participation rates and fidelity, varied widely. CONCLUSIONS: IMR shows promise for improving some consumer-level outcomes. Important issues regarding implementation require additional study. Future research is needed to compare outcomes of IMR consumers and active control groups and to provide a more detailed understanding of how other services utilized by consumers may affect outcomes of IMR

An interacting spin flip model for one-dimensional proton conduction

A discrete asymmetric exclusion process (ASEP) is developed to model proton conduction along one-dimensional water wires. Each lattice site represents a water molecule that can be in only one of three states; protonated, left-pointing, and right-pointing. Only a right(left)-pointing water can accept a proton from its left(right). Results of asymptotic mean field analysis and Monte-Carlo simulations for the three-species, open boundary exclusion model are presented and compared. The mean field results for the steady-state proton current suggest a number of regimes analogous to the low and maximal current phases found in the single species ASEP [B. Derrida, Physics Reports, {\bf 301}, 65-83, (1998)]. We find that the mean field results are accurate (compared with lattice Monte-Carlo simulations) only in the certain regimes. Refinements and extensions including more elaborate forces and pore defects are also discussed.Comment: 13pp, 6 fig

A randomized controlled trial of Illness Management and Recovery with an active control condition

Objective The purpose of the study was to rigorously test Illness Management and Recovery (IMR) against an active control group in a sample that included veterans. Methods A total of 118 participants with schizophrenia spectrum disorders, 56 of whom were veterans, were recruited from a Department of Veterans Affairs medical center and a community mental health center in the same city and were randomly assigned to an IMR group (N=60) or a weekly problem-solving group intervention (N=58). Groups met weekly for nine months. Blinded assessments were conducted at baseline, nine months, and 18 months on measures of symptoms, functioning, illness self-management, medication adherence, subjective recovery experiences, and service utilization. Results No significant differences were found between IMR and problem-solving groups. Participants in both groups improved significantly over time in symptom severity, illness management, and quality of life and had fewer emergency department visits. Participation rates in both interventions were low. Only 28% of consumers assigned to IMR and 17% of those assigned to the problem-solving group participated in more than half the scheduled groups, and 23% and 34%, respectively, attended no sessions. Conclusions This is the first randomized controlled trial of IMR to report negative findings. Given the inclusion of an active control group and the low participation rates, further research is needed to understand factors affecting IMR effectiveness. Increased attention may need to be paid to facilitate more active participation in IMR, such as individual follow-up with consumers and the integration of IMR with ongoing treatment

Two interacting diffusing particles on low-dimensional discrete structures

In this paper we study the motion of two particles diffusing on low-dimensional discrete structures in presence of a hard-core repulsive interaction. We show that the problem can be mapped in two decoupled problems of single particles diffusing on different graphs by a transformation we call 'diffusion graph transform'. This technique is applied to study two specific cases: the narrow comb and the ladder lattice. We focus on the determination of the long time probabilities for the contact between particles and their reciprocal crossing. We also obtain the mean square dispersion of the particles in the case of the narrow comb lattice. The case of a sticking potential and of 'vicious' particles are discussed.Comment: 9 pages, 6 postscript figures, to appear in 'Journal of Physics A',-January 200

Asymmetric exclusion process with next-nearest-neighbor interaction: some comments on traffic flow and a nonequilibrium reentrance transition

We study the steady-state behavior of a driven non-equilibrium lattice gas of hard-core particles with next-nearest-neighbor interaction. We calculate the exact stationary distribution of the periodic system and for a particular line in the phase diagram of the system with open boundaries where particles can enter and leave the system. For repulsive interactions the dynamics can be interpreted as a two-speed model for traffic flow. The exact stationary distribution of the periodic continuous-time system turns out to coincide with that of the asymmetric exclusion process (ASEP) with discrete-time parallel update. However, unlike in the (single-speed) ASEP, the exact flow diagram for the two-speed model resembles in some important features the flow diagram of real traffic. The stationary phase diagram of the open system obtained from Monte Carlo simulations can be understood in terms of a shock moving through the system and an overfeeding effect at the boundaries, thus confirming theoretical predictions of a recently developed general theory of boundary-induced phase transitions. In the case of attractive interaction we observe an unexpected reentrance transition due to boundary effects.Comment: 12 pages, Revtex, 7 figure

Exact time-dependent correlation functions for the symmetric exclusion process with open boundary

As a simple model for single-file diffusion of hard core particles we investigate the one-dimensional symmetric exclusion process. We consider an open semi-infinite system where one end is coupled to an external reservoir of constant density $\rho^\ast$ and which initially is in an non-equilibrium state with bulk density $\rho_0$. We calculate the exact time-dependent two-point density correlation function $C_{k,l}(t)\equiv -$ and the mean and variance of the integrated average net flux of particles $N(t)-N(0)$ that have entered (or left) the system up to time $t$. We find that the boundary region of the semi-infinite relaxing system is in a state similar to the bulk state of a finite stationary system driven by a boundary gradient. The symmetric exclusion model provides a rare example where such behavior can be proved rigorously on the level of equal-time two-point correlation functions. Some implications for the relaxational dynamics of entangled polymers and for single-file diffusion in colloidal systems are discussed.Comment: 11 pages, uses REVTEX, 2 figures. Minor typos corrected and reference 17 adde

Two-dimensional X-ray diffraction as a tool for the rapid, non-destructive detection of low calcite quantities in aragonitic corals

Paleoclimate reconstructions based on reef corals require precise detection of diagenetic alteration. Secondary calcite can significantly affect paleotemperature reconstructions at very low amounts of ~1%. X-ray powder diffraction is routinely used to detect diagenetic calcite in aragonitic corals. This procedure has its limitations as single powder samples might not represent the entire coral heterogeneity. A conventional and a 2-D X-ray diffractometer were calibrated with gravimetric powder standards of high and low magnesium calcite (0.3% to 25% calcite). Calcite contents <1% can be recognized with both diffractometer setups based on the peak area of the calcite [104] reflection. An advantage of 2-D-XRD over convenient 1-D-XRD methods is the nondestructive and rapid detection of calcite with relatively high spatial resolution directly on coral slabs. The calcite detection performance of the 2-D-XRD setup was tested on thin sections from fossil Porites sp. samples that, based on powder XRD measurements, showed <1% calcite. Quantification of calcite contents for these thin sections based on 2-D-XRD and digital image analysis showed very similar results. This enables spot measurements with diameters of ∼4 mm, as well as systematic line scans along potential tracks previous to geochemical proxy sampling. In this way, areas affected by diagenetic calcite can be avoided and alternative sampling tracks can be defined. Alternatively, individual sampling positions that show dubious proxy results can later be checked for the presence of calcite. The presented calibration and quantification method can be transferred to any 2-D X-ray diffractometer