A formal architecture-centric and model driven approach for the engineering of science gateways

From n-Tier client/server applications, to more complex academic Grids, or even the most recent and promising industrial Clouds, the last decade has witnessed significant developments in distributed computing. In spite of this conceptual heterogeneity, Service-Oriented Architecture (SOA) seems to have emerged as the common and underlying abstraction paradigm, even though different standards and technologies are applied across application domains. Suitable access to data and algorithms resident in SOAs via so-called ‘Science Gateways’ has thus become a pressing need in order to realize the benefits of distributed computing infrastructures.In an attempt to inform service-oriented systems design and developments in Grid-based biomedical research infrastructures, the applicant has consolidated work from three complementary experiences in European projects, which have developed and deployed large-scale production quality infrastructures and more recently Science Gateways to support research in breast cancer, pediatric diseases and neurodegenerative pathologies respectively. In analyzing the requirements from these biomedical applications the applicant was able to elaborate on commonly faced issues in Grid development and deployment, while proposing an adapted and extensible engineering framework. Grids implement a number of protocols, applications, standards and attempt to virtualize and harmonize accesses to them. Most Grid implementations therefore are instantiated as superposed software layers, often resulting in a low quality of services and quality of applications, thus making design and development increasingly complex, and rendering classical software engineering approaches unsuitable for Grid developments.The applicant proposes the application of a formal Model-Driven Engineering (MDE) approach to service-oriented developments, making it possible to define Grid-based architectures and Science Gateways that satisfy quality of service requirements, execution platform and distribution criteria at design time. An novel investigation is thus presented on the applicability of the resulting grid MDE (gMDE) to specific examples and conclusions are drawn on the benefits of this approach and its possible application to other areas, in particular that of Distributed Computing Infrastructures (DCI) interoperability, Science Gateways and Cloud architectures developments

Understanding salinity tolerance of a bread wheat landrace Mocho de Espiga Branca

Salinity is one of the major abiotic stresses severely affecting cereal crop yields worldwide. Improving salinity tolerance of the most widely cultivated cereal, bread wheat (Triticum aestivum L.), is essential to increase grain yields on saline agricultural lands. Shoot sodium (Na⁺) exclusion is often reported as a major salinity tolerance mechanism in bread wheat. This process enables plants to reduce root-to-shoot Na⁺ transport by retrieving Na⁺ from the xylem and prevent toxic concentrations of Na⁺ from accumulating in the shoot. However, a Portuguese bread wheat landrace Mocho de Espiga Branca was recently identified with up to 10× higher leaf Na⁺ concentrations and yet maintained similar salinity tolerance compared to other bread wheat cultivars. The first focus of this PhD study was to understand how Mocho de Espiga Branca accumulates high concentrations of Na⁺ in the leaf compared to Gladius and Scout under salinity. DNA sequencing of a major Na⁺ exclusion gene TaHKT1;5-D revealed that a naturally occurring single nucleotide substitution resulted in a L190P amino acid residue change. This variation was found to disrupt the capability of TaHKT1;5-D to retrieve Na⁺ from the xylem and hence causing the high leaf Na⁺ accumulation in Mocho de Espiga Branca. A CAPS marker was developed to enable plant breeders to select for this allele in bread wheat. The second focus of this study was to identify novel genetic loci linked to salinity tolerance of Mocho de Espiga Branca. 19 salinity tolerance sub-traits were phenotyped in an F₂ population derived from Mocho de Espiga Branca and Gladius for quantitative trait loci (QTL) analysis. Genomic regions significantly associated with salinity tolerance were detected on chromosomes 1A, 1D, 4A, 4B and 5A for the sub-traits of plant growth, and on chromosome 2A, 2B, 4D and 5D for Na⁺, potassium (K⁺) and chloride (Cl⁻) accumulation. A number of candidate genes that encode proteins associated with plant salinity tolerance were identified. These include Na⁺/H⁺ antiporters, K⁺ channels, Na⁺/calcium (Ca²⁺) transporter, H⁺-ATPase, calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs). The third focus of this study was to investigate whether any difference(s) in accumulation of five known compatible solutes (glycine betaine, proline, sucrose, glucose and fructose) associated with osmotic adjustment were present in Mocho de Espiga Branca compared to Gladius and Scout under salinity. The concentrations of the detected compatible solutes in Mocho de Espiga Branca were found to respond similarly compared to Gladius and Scout in response to salinity, suggesting these organic solutes are not contributing to the ability of Mocho de Espiga Branca to maintain growth while accumulating high concentration of leaf Na⁺ salinity. Overall, in this PhD study, a SNP linked to impairment of the Na⁺ transporter TaHKT1;5-D was identified and shown to be responsible for the increased shoot Na⁺ concentration in Mocho de Espiga Branca. The findings highlight the importance of other mechanisms that are independent from Na⁺ exclusion in salinity tolerance of bread wheat and the need to investigate these further in the future.Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 202

Shale instability of deviated wellbores in southern Iraqi fields

Wellbore instability problems are the cause for the majority of nonproductive time in the southern Iraqi fields\u27 developments. The most severe problem in terms of effort and disbursement which is referred to a pipe sticking in Tanuma shale formation. Examining the drilling data revealed that this phenomenon was mostly related to the shear failure of the wellbore. Thus, a geomechanical analysis and drilling parameters/ practice optimization analysis were performed on a field in southern Iraq based on data from 45 deviated wells. The geomechanics analysis predicted the suitable drilling fluid density to prevent onset shear failure by using the Mogi-Coulomb failure criterion, including thermally and chemically induced stresses and the bedding related failure of the wellbore. While the drilling parameters optimization was conducted by DROPS simulator and multi-regression analysis and resulted in a significant reduction in the shale exposure time to the drilling fluid. The drilling practice analysis was derived based on drilling data from stuck-free well also facilitated in preventing the drilling fluid density reduction by tripping processes. These analyses identified the following areas of improvement. First, the mud weight being used was not changed properly with respect to variation in wells azimuth and inclination. Secondly, anisotropic effects of the stress and strength parameters for this shale formation should be considered in wells trajectory design. Thirdly, the time depended-failure of wellbore was observed in even though the drilling fluid density was appropriately selected. Fourthly, the swabbing effect while tripping was negatively contributed to wellbore stability. Due to limited of published studies regarding wellbore problems in southern Iraqi fields; this research could serve as a significant case history for similar fields --Abstract, page iii

Satellite Communications

This study is motivated by the need to give the reader a broad view of the developments, key concepts, and technologies related to information society evolution, with a focus on the wireless communications and geoinformation technologies and their role in the environment. Giving perspective, it aims at assisting people active in the industry, the public sector, and Earth science fields as well, by providing a base for their continued work and thinking

Combining SOA and BPM Technologies for Cross-System Process Automation

This paper summarizes the results of an industry case study that introduced a cross-system business process automation solution based on a combination of SOA and BPM standard technologies (i.e., BPMN, BPEL, WSDL). Besides discussing major weaknesses of the existing, custom-built, solution and comparing them against experiences with the developed prototype, the paper presents a course of action for transforming the current solution into the proposed solution. This includes a general approach, consisting of four distinct steps, as well as specific action items that are to be performed for every step. The discussion also covers language and tool support and challenges arising from the transformation

Design and pre-testing of lipid-based, ready-to-use foods for the prevention and treatment of malnutrition in low-resource settings

Background: Managing child and adult undernutrition is a global public health priority. In poor settings, improved specialised products are needed for treatment and prevention, including for chronic disease/HIV. Objective: To develop a method for the design and pre‐clinical testing of novel, low‐cost Ready‐to‐Use Therapeutic Foods (RUTF), to be also applied to supplementary/complementary feeding interventions. A method was developed and tested, using four sequential studies, with HIV‐positive Kenyan adults with severe acute malnutrition (case‐study). A qualitative study explored adherence and consumption barriers with the current UNstandard peanut/milk‐powder‐based therapeutic formulation (P‐RUTF). A study using Linear Programming (LP) designed an improved, cheaper formulation soy/maize/sorghum‐based (SMS‐RUTF), considered accurate if: its manufactured prototype, compared to calculated values; it had a measured energy density difference (EDD) <10%; a protein or lipid difference (P/LD) <5g/100g. An acceptability study (4‐weeks‐cross‐over design; washout one‐week) compared use of SMS‐RUTF against P‐RUTF (n=41), using 18 consumption/safety/preference criteria. Based on a literature review (28 randomized controlled trials of micronutrient supplementation; outcomes: increased survival and CD4 cell count, reduced viral load), four criteria to determine micronutrient specifications for the SMS‐RUTF fortification were developed and applied. The reported compliance with the prescribed RUTF was relatively low, and informed the necessary formulation improvements. The LP-determined formulation was accurate (EDD: 7%; PD and LD: 2.3 and 1.0g/100g). The LP-based prototype was acceptable and safe, but with an average number of days of nausea and vomit (0.16 and 0.04 d) occurred with a higher frequency (P < 0.05) than in the control (0.09 and 0.02 d). The existing evidence for determining micronutrient specifications for SMS�]RUTF posed some challenges for the development of manufacturing specifications. Twelve of the micronutrient specifications developed for SMS�]RUTF fortificant premix were equivalent to the UN minimum standards; eleven were 2 to 10 times higher. Conclusions: The proposed set of methods can be used to design and pre�]clinically test improved/cheaper RUTF products, targeting malnourished adults. Novel formulations should be clinically trialled before widespread�]use

The Variable Expression of Transitive Subject and Possesor in Wayuunaiki (Guajiro)

In Wayuunaiki, verbal affixes cross-reference clausal arguments in various ways. Most notably, there are two ways to express transitive subjects, and two ways to express possessors. Much like voice alternatives, the variable expression of subject and possessor impart different perspectives on a situation type, but unlike traditional voice categories, syntactic valence remains equal. This dissertation characterizes these constructions with a specific question in mind: what do these two cross-referencing alternations communicate and what influences their usage? To answer these questions, I consider the linguistic properties observed in the usage of these constructions in narratives (Jusayú 1986, 1994), and informal conversations. Mosonyi (1975) describes the Subjective and Objective transitive clauses as focus alternatives. Álvarez (1993) discovered that the O in the Objective clause must be definite. Despite the association of definiteness and focus as a central factors, the usage of the alternatives in discourse has has not received enough attention. I here conclude that the Subjective variant is the pragmatically marked option, whose primary function is to defocus a 3rd person O that is typically inanimate, new and non-topical. This clause type has the effect of retaining its syntactic valency, but expresseing semantically low transitivity. Álvarez (1990) documents possessor ascension as a construction that involves unrestricted noun incorporation. Matera (2001) adds that the possessor of an incorporated noun can only assume the role of transitive object or stative subject. In the present corpus exploration, I conclude that the External Possessor construction is the functionally marked clause, whose function is primarily to defocus a possessed nominal that is typically inalienable, inanimate, and non-topical information. Additionally, whole-part relationships frequently participate in incorporation, while kinship relations do so rarely. These two ways to cross-reference arguments are here interpreted as differential focus assignment on clausal arguments (Dixon & Aikhenvald 1997). They both involve the prefixation of a- referring to the transitive subject and the external possessor. I conclude that in these constructions this prefix has the effect of backgrounding an entity and consequently assigning undivided focus to the subject or the possessor