Detecting palindromes,patterns and borders in regular languages

Given a language L and a non-deterministic finite automaton M, we consider whether we can determine efficiently (in the size of M) if M accepts at least one word in L, or infinitely many words. Given that M accepts at least one word in L, we consider how long a shortest word can be. The languages L that we examine include the palindromes, the non-palindromes, the k-powers, the non-k-powers, the powers, the non-powers (also called primitive words), the words matching a general pattern, the bordered words, and the unbordered words.     

Parallel Implementation of a Low Order Algorithm for Dynamics of Multibody Systems on a Distributed Memory Computing System

In this paper, a new hybrid parallelisable low order algorithm, developed by the authors for multibody dynamics analysis, is implemented numerically on a distributed memory parallel computing system. The presented implementation can currently accommodate the general spatial motion of chain systems, but key issues for its extension to general tree and closed loop systems are discussed. Explicit algebraic constraints are used to increase coarse grain parallelism, and to study the influence of the dimension of system constraint load equations on the computational efficiency of the algorithm for real parallel implementation using the Message Passing Interface (MPI). The equation formulation parallelism and linear system solution strategies which are used to reduce communication overhead are addressed. Numerical results indicate that the algorithm is scalable, that significant speed-up can be obtained, and that a quasi-logarithmic relation exists between time needed for a function call and numbers of processors used. This result agrees well with theoretical performance predictions. Numerical comparisons with results obtained from independently developed analysis codes have validated the correctness of the new hybrid parallelisable low order algorithm, and demonstrated certain computational advantages.     

Query-driven visualization of time-varying adaptive mesh refinement data

The visualization and analysis of AMR-based simulations is integral to the process of obtaining new insight in scientific research. We present a new method for performing query-driven visualization and analysis on AMR data, with specific emphasis on time-varying AMR data. Our work introduces a new method that directly addresses the dynamic spatial and temporal properties of AMR grids that challenge many existing visualization techniques. Further, we present the first implementation of query-driven visualization on the GPU that uses a GPU-based indexing structure to both answer queries and efficiently utilize GPU memory. We apply our method to two different science domains to demonstrate its broad applicability.     

Service Science

This paper is a first exploration of the relationship between service science and Grid computing. Service science is the study of value co-creation interactions among entities, known as service systems. Within the emerging service science community, service is often defined as the application of competences (resources) for the benefit of another. Grid computing is the study of resource sharing among entities, known as virtual organizations, which solve complex business, societal, scientific, and engineering problems. Within the Grid computing community, service is sometimes defined as protocols plus behavior. Both Grid computing and service science are connecting academic, industry, government, and volunteer sector collaborators on a range of projects including eScience, healthcare, environmental sustainability, and more. This paper compares and contrasts the notions of resource, entity, service, interaction, and success criteria for the two areas of study. In conclusion, new areas for collaborative inquiry are proposed.     

A biomechanical analysis of anterior load carriage

Front load carriage is a common occupational task in some industries (e.g. agriculture, construction), but, as compared to lifting tasks, relatively little research has been conducted on the biomechanical loading during these activities. The focus of this study was to explore the low back biomechanics during these activities and, specifically, to examine the effects of load height and walking speed on trunk muscle activity and trunk posture. Eleven male participants participated in two separate front load-carriage experiments. The first experiment called for carrying a barbell (with weight corresponding to 20% of elbow flexion strength) at three heights (knuckle height, elbow height and shoulder height) at a constant horizontal distance from the spine. The second experiment called for participants to carry a bucket of potatoes weighing 14 kg at the same three heights, but with no further restrictions in technique. In both experiments, the participants performed this task while either standing still or walking at a self-selected speed. As they performed these tasks, the activity levels of the right-side muscle of the rectus abdominis, external oblique, biceps brachii, anterior deltoid and three levels (T9, T12 and L3) of the erector spinae were sampled. Mid-sagittal plane trunk posture was also quantified using three magnetic field-based motion sensors at T9, T12 and L3. The results showed a significant effect of both walking speed and load height on trunk posture and trunk muscle activity levels in both the barbell and bucket experiments. In the barbell experiment, the walking trials generated 43% more trunk muscle activity than the standing trials. Trials at shoulder height produced 11% more muscle activity than trials at elbow height in the T9 erector spinae muscles and 71% more muscle activity in the anterior deltoid. In the bucket experiment, trunk muscle activity responded in a similar fashion, but the key result here was the quantification of the natural hyperextension posture of the spine used to balance the bucket of potatoes. These results provide insight into muscle activation patterns in dynamic settings, especially (load) carrying biomechanics, and have implications in industrial settings that require workers to carry loads in front of their bodies.     

Screening of serum samples from Wegener's granulomatosis patients using antibody microarrays

Wegener's Granulomatosis (WG) is an idiopathic granulomatosis autoimmune vasculitis that primarily affects small vessels and is associated with glomerulonephritis and pulmonary granulomatous vasculitis. Anti‐neutrophil cytoplasmic auto‐antibodies (cANCA) against proteinase‐3 are used to identify WG, but ANCA titers are not present in some patients with the localized disease. The objective of this study was to develop an antibody array to help identify protein expression patterns in serum from patients with WG as compared to normals. The arrays were tested for limits of detection, background, and cross reactivity using standard proteins. The arrays were hybridized with either normal patient serum (n = 30) or with serum samples from a population of WG patients (n = 26) that were age and sex matched. Data analysis and curve fitting of the standard dilution series calculated r² values and determined a sensitivity of <50 pg/mL for the majority of proteins. A total of 24 proteins were assessed. Several statistically significant increases (p<0.05) were seen in the expression of: angiotensin converting enzyme‐I, IFN‐γ, IL‐8, s‐ICAM‐1 and s‐VCAM in WG patients as compared to controls. Utilizing the antibody microarray technology has led to the identification of potential biomarkers of vascular injury in the serum of WG patients.     

Analysis of factors contributing to success in a program of micromanipulation-assisted fertilization

OBJECTIVE: To determine factors important to clinical success in micromanipulation-assisted in vitro fertilization (IVF). DESIGN: Procedures invoked in two separate series of micromanipulation-assisted IVF cycles, one unsuccessful (series I) and the other successful (series II), were compared in an effort to identify changes that led to clinical success. SETTING: University-based IVF clinic. PATIENTS: In both IVF series involving micromanipulation, patients consisted of infertile couples who fit any of five categories of male-factor related infertility. The female patients underwent controlled hyperstimulation for oocyte retrieval and the oocytes were inseminated normally or were subjected either to partial zona dissection or subzonal sperm insertion to assist fertilization. Results in all groups were compared between the two patient series. RESULTS: In the successful series II, a noticeable improvement in fertilization rate and embryo quality was observed compared with series I. A significant increase in the percentage of patients reaching embryo transfer, the pregnancy rate per transfer, and the pregnancy rate per retrieval were noted in series II; a 25% ongoing pregnancy rate per retrieval was observed overall in this successful group, with "ongoing" defined as manifestation of at least a fetal sac on ultrasound with no detectable problems. Patients with a mixed transfer of embryos derived from manipulated and normally inseminated oocytes had a 75% rate of pregnancy per transfer in series II. Differences between the two series could not be attributed to patient selection or biases in selection of oocytes relegated to micromanipulation. However, oocyte handling, micromanipulation, and culture protocols differed significantly between the two series in that temperature and pH of oocytes was better controlled, and micromanipulation time was minimized in series II. CONCLUSION: Success in micromanipulation depends on maintenance of the oocyte in a stable and supportive environment throughout the micromanipulation procedure. It is also important to minimize trauma to the eggs by performing micromanipulation rapidly and with minimal distortion of the egg. Patients with a poor fertilization rate in standard IVF may experience a substantial increase in the likelihood of pregnancy when micromanipulation-assisted fertilization is performed on some eggs.     

Low temperature thermal conductivity of twinned and untwinned indium-thallium alloys

The low-temperature lattice thermal conductivity of twinned and untwinned, martensitic and non-martensitic, indium-thallium alloys has been measured to probe the effect of twin boundaries on phonon thermal transport. The phonon scattering by electrons, sample surfaces, dislocations, and thallium impurities is accounted for adequately by existing theoretical models. The reduced lattice thermal conductivity seen in twinned samples is attributed to additional phonon scattering by twin boundaries and, for the polycrystalline samples, by grain boundaries. Phonon scattering by twin boundaries is much weaker than that generally reported for grain boundaries, and is well represented by an acoustic-mismatch model.     

A new approach to defining a multidisciplinary field of science: The case of cardiovascular biology

This paper describes a new and objective method for tackling the problem of defining a multidisciplinary research area for bibliometric analysis. The test field was cardiovascular biology. A three stage process was adopted in setting a boundary around this research field:

1. Appropriate sections of a hierarchical subject classification scheme, Medical Subject Headings (MeSH), were developed into a “MeSH filter” through which papers indexed in MEDLINE were screened.
2. A panel of cardiovascular experts reviewed the core set of classification terms, identifying irrelevant and missing areas, facilitating the development of a more sophisticated “filter”.
3. The definition was validated using publication lists from research departments with a known interest in cardiovascular research.

This iterative process resulted in a definition of the field which captured basic and clinical research papers from the international biomedical research community and which was recognisable to experts in the field of cardiovascular research. Importantly, the field boundary also excluded publications which were not relevant to cardiovascular research. The process of involving experts in shaping the field definition also yielded two intangible, but key benefits: (a) it lent credibility to subsequent analyses, the results of which were to be presented to policy-makers in cardiovascular biology, and (b) it served to shape consensus among the cardiovascular experts on the full range of scientific disciplines that are relevant to their field. Analysis of international publishing in cardiovascular research revealed that whilst the UK and US dominate in total numbers of papers, the relative emphasis on cardiovascular research in these countries (as a proportion ofall biomedical publishing) is actually quite low, and declining. Japan and Germany in contrast appear to give greater emphasis to cardiovascular research in their national portfolios of biomedical science, and between 1988–1991 Japan established a marked increase in activity.