Using urea dilution to standardise cellular and non-cellular components of pleural and bronchoalveolar lavage (BAL) fluids in the cat

A technique to standardise the analysis of cellular and non-cellular components in epithelial lining fluid (ELF) collected during saline lavage of pulmonary and pleural cavities was developed using the urea dilution method. Bronchoalveolar lavage (BAL) and pleural lavage (PL) fluids were collected from 12 clinically healthy cats. Total and differential cell counts in BAL fluid were within normal ranges for the cat, while cell Counts in PL fluid were assumed to be normal based on clinical health during examination, auscultation and lactate dehydrogenase (LDH) activities being comparable with other species. The major clinical implication of this study was that nucleated cell counts within feline ELF could not be predicted from analysis of lavage fluid which suggests that calculation of the proportion of ELF in lavage fluid by the urea dilution method may be necessary to avoid misdiagnosis of health or disease in pulmonary or pleural cavities. (C) 2005 ESFM and AAFP. Published by Elsevier Ltd. All rights reserved.

Do process modelling techniques get better? A comparative ontological analysis of BPMN

Current initiatives in the field of Business Process Management (BPM) strive for the development of a BPM standard notation by pushing the Business Process Modeling Notation (BPMN). However, such a proposed standard notation needs to be carefully examined. Ontological analysis is an established theoretical approach to evaluating modelling techniques. This paper reports on the outcomes of an ontological analysis of BPMN and explores identified issues by reporting on interviews conducted with BPMN users in Australia. Complementing this analysis we consolidate our findings with previous ontological analyses of process modelling notations to deliver a comprehensive assessment of BPMN.

Applying a Systems Approach to the Analysis of the Benefits of Conversion to Organic Production

Although the current level of organic production in industrialised countries amounts to little more than 1-2 percent, it is recognised that one of the major issues shaping agricultural output over the next several decades will be the demand for organic produce (Dixon et al. 2001). In Australia, the issues of healthy food and environmental concern contribute to increasing demand and market volumes for organic produce. However, in Indonesia, using more economical inputs for organic production is a supply-side factor driving organic production. For individual growers and processors, conversion from conventional to organic agriculture is often a challenging step, entailing a thorough revision of established practices and heightened market insecurity. This paper examines the potential for a systems approach to the analysis of the conversion process, to yield insights for household and community decisions. A framework for applying farming systems research to investigate the benefits of organic production in both Australia and Indonesia is discussed. The framework incorporates scope for farmer participation, crucial to the understanding of farming systems; analysis of production; and relationships to resources, technologies, markets, services, policies and institutions in their local cultural context. A systems approach offers the potential to internalise the external effects that may be constraining decisions to convert to organic production, and for the design of decision-making tools to assist households and the community. Systems models can guide policy design and serve as a mechanism for predicting the impact of changes to the policy and market environments. The increasing emphasis of farming systems research on community and environment in recent years is in keeping with the proposed application to organic production, processing and marketing issues. The approach will also facilitate the analysis of critical aspects of the Australian production, marketing and policy environment, and the investigation of these same features in an Indonesian context.

Efficiency analysis of Islamic banks:a case of Gulf Cooperation Council (GCC)

Although considerable effort has been invested in the measurement of banking efficiency using Data Envelopment Analysis, hardly any empirical research has focused on comparison of banks in Gulf States Countries This paper employs data on Gulf States banking sector for the period 2000-2002 to develop efficiency scores and rankings for both Islamic and conventional banks. We then investigate the productivity change using Malmquist Index and decompose the productivity into technical change and efficiency change. Further, hypothesis testing and statistical precision in the context of nonparametric efficiency and productivity measurement have been used. Specially, cross-country analysis of efficiency and comparisons of efficiencies between Islamic banks and conventional banks have been investigated using Mann-Whitney test.

The development of an optimized system of narcotic and explosive contraband mimics for calibration and training of biological detectors

Current commercially available mimics contain varying amounts of either the actual explosive/drug or the chemical compound of suspected interest by biological detectors. As a result, there is significant interest in determining the dominant chemical odor signatures of the mimics, often referred to as pseudos, particularly when compared to the genuine contraband material. This dissertation discusses results obtained from the analysis of drug and explosive headspace related to the odor profiles as recognized by trained detection canines. Analysis was performed through the use of headspace solid phase microextraction in conjunction with gas chromatography mass spectrometry (HS-SPME-GC-MS). Upon determination of specific odors, field trials were held using a combination of the target odors with COMPS. Piperonal was shown to be a dominant odor compound in the headspace of some ecstasy samples and a recognizable odor mimic by trained detection canines. It was also shown that detection canines could be imprinted on piperonal COMPS and correctly identify ecstasy samples at a threshold level of approximately 100ng/s. Isosafrole and/or MDP-2-POH show potential as training aid mimics for non-piperonal based MDMA. Acetic acid was shown to be dominant in the headspace of heroin samples and verified as a dominant odor in commercial vinegar samples; however, no common, secondary compound was detected in the headspace of either. Because of the similarities detected within respective explosive classes, several compounds were chosen for explosive mimics. A single based smokeless powder with a detectable level of 2,4-dinitrotoluene, a double based smokeless powder with a detectable level of nitroglycerine, 2-ethyl-1-hexanol, DMNB, ethyl centralite and diphenylamine were shown to be accurate mimics for TNT-based explosives, NG-based explosives, plastic explosives, tagged explosives, and smokeless powders, respectively. The combination of these six odors represents a comprehensive explosive odor kit with positive results for imprint on detection canines. As a proof of concept, the chemical compound PFTBA showed promise as a possible universal, non-target odor compound for comparison and calibration of detection canines and instrumentation. In a comparison study of shape versus vibration odor theory, the detection of d-methyl benzoate and methyl benzoate was explored using canine detectors. While results did not overwhelmingly substantiate either theory, shape odor theory provides a better explanation of the canine and human subject responses.

The Development of an Optimized System of Narcotic and Explosive Contraband Mimics for Calibration and Training of Biological Detectors

Current commercially available mimics contain varying amounts of either the actual explosive/drug or the chemical compound of suspected interest by biological detectors. As a result, there is significant interest in determining the dominant chemical odor signatures of the mimics, often referred to as pseudos, particularly when compared to the genuine contraband material. This dissertation discusses results obtained from the analysis of drug and explosive headspace related to the odor profiles as recognized by trained detection canines. Analysis was performed through the use of headspace solid phase microextraction in conjunction with gas chromatography mass spectrometry (HS-SPME-GC-MS). Upon determination of specific odors, field trials were held using a combination of the target odors with COMPS. Piperonal was shown to be a dominant odor compound in the headspace of some ecstasy samples and a recognizable odor mimic by trained detection canines. It was also shown that detection canines could be imprinted on piperonal COMPS and correctly identify ecstasy samples at a threshold level of approximately 100ng/s. Isosafrole and/or MDP-2-POH show potential as training aid mimics for non-piperonal based MDMA. Acetic acid was shown to be dominant in the headspace of heroin samples and verified as a dominant odor in commercial vinegar samples; however, no common, secondary compound was detected in the headspace of either. Because of the similarities detected within respective explosive classes, several compounds were chosen for explosive mimics. A single based smokeless powder with a detectable level of 2,4-dinitrotoluene, a double based smokeless powder with a detectable level of nitroglycerine, 2-ethyl-1-hexanol, DMNB, ethyl centralite and diphenylamine were shown to be accurate mimics for TNT-based explosives, NG-based explosives, plastic explosives, tagged explosives, and smokeless powders, respectively. The combination of these six odors represents a comprehensive explosive odor kit with positive results for imprint on detection canines. As a proof of concept, the chemical compound PFTBA showed promise as a possible universal, non-target odor compound for comparison and calibration of detection canines and instrumentation. In a comparison study of shape versus vibration odor theory, the detection of d-methyl benzoate and methyl benzoate was explored using canine detectors. While results did not overwhelmingly substantiate either theory, shape odor theory provides a better explanation of the canine and human subject responses.

Analysis of key predistribution schemes in wireless sensor networks

Combinatorial designs are used for designing key predistribution schemes that are applied to wireless sensor networks in communications. This helps in building a secure channel. Private-key cryptography helps to determine a common key between a pair of nodes in sensor networks. Wireless sensor networks using key predistribution schemes have many useful applications in military and civil operations. When designs are efficiently implemented on sensor networks, blocks with unique keys will be the result. One such implementation is a transversal design which follows the principle of simple key establishment. Analysis of designs and modeling the key schemes are the subjects of this project.

Analysis of bio-derived platform chemicals in ionic liquid media by desorption/ionization mass spectrometry

In this work, desorption/ionization mass spectrometry was employed for the analysis of sugars and small platform chemicals that are common intermediates in biomass transformation reactions. Specifically, matrix-assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI) mass spectrometric techniques were employed as alternatives to traditional chromatographic methods. Ionic liquid matrices (ILMs) were designed based on traditional solid MALDI matrices (2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (CHCA)) and 1,3-dialkylimidazolium ionic liquids ([BMIM]Cl, [EMIM]Cl, and [EMIM]OAc) that have been employed as reaction media for biomass transformation reactions such as the conversion of carbohydrates to valuable platform chemicals. Although two new ILMs were synthesized ([EMIM][DHB] and [EMIM][CHCA] from [EMIM]OAc), chloride-containing ILs did not react with matrices and resulted in mixtures of IL and matrix in solution. Compared to the parent solid matrices, much less matrix interference was observed in the low mass region of the mass spectrum (< 500 Da) using each of the IL-matrices. Furthermore, the formation of a true ILM (i.e. a new ion pair) does not appear to be necessary for analyte ionization. MALDI sample preparation techniques were optimized based on the compatibility with analyte, IL and matrix. ILMs and IL-matrix mixtures of DHB allowed for qualitative analysis of glucose, fructose, sucrose and N-acetyl-D-glucosamine. Analogous CHCA-containing ILMs did not result in appreciable analyte signals under similar conditions. Small platform compounds such as 5-hydroxymethylfurfural (HMF) and levulinic acid were not detected by direct analysis using MALDI-MS. Furthermore, sugar analyte signals were only detected at relatively high matrix:IL:analyte ratios (1:1:1) due to significant matrix and analyte suppression by the IL ions. Therefore, chemical modification of analytes with glycidyltrimethylammonium chloride (GTMA) was employed to extend this method to quantitative applications. Derivatization was accomplished in aqueous IL solutions with fair reaction efficiencies (36.9 – 48.4 % glucose conversion). Calibration curves of derivatized glucose-GTMA yielded good linearity in all solvent systems tested, with decreased % RSDs of analyte ion signals in IL solutions as compared to purely aqueous systems (1.2 – 7.2 % and 4.2 – 8.7 %, respectively). Derivatization resulted in a substantial increase in sensitivity for MALDI-MS analyses: glucose was reliably detected at IL:analyte ratios of 100:1 (as compared to 1:1 prior to derivatization). Screening of all test analytes resulted in appreciable analyte signals in MALDI-MS spectra, including both HMF and levulinic acid. Using appropriate internal standards, calibration curves were constructed and this method was employed for monitoring a model dehydration reaction of fructose to HMF in [BMIM]Cl. Calibration curves showed wide dynamic ranges (LOD – 100 ng fructose/μg [BMIM]Cl, LOD – 75 ng HMF/μg [BMIM]Cl) with correlation coefficients of 0.9973 (fructose) and 0.9931 (HMF). LODs were estimated from the calibration data to be 7.2 ng fructose/μg [BMIM]Cl and 7.5 ng HMF/μg [BMIM]Cl, however relatively high S/N ratios at these concentrations indicate that these values are likely overestimated. Application of this method allowed for the rapid acquisition of quantitative data without the need for prior separation of analyte and IL. Finally, small molecule platform chemicals HMF and levulinic acid were qualitatively analyzed by DESI-MS. Both HMF and levulinic acid were easily ionized and the corresponding molecular ions were easily detected in the presence of 10 – 100 times IL, without the need for chemical modification prior to analysis. DESI-MS analysis of ILs in positive and negative ion modes resulted in few ions in the low mass region, showing great potential for the analysis of small molecules in IL media.

Rethinking Professional Practice: The Logic of Competition and the Crisis of Identity in Housing Practice

The relationship between professionalism, education and housing practice has become increasingly strained following the introduction of austerity measures and welfare reforms across a range of countries. Focusing on the development of UK housing practice, this article considers how notions of professionalism are being reshaped within the context of welfare retrenchment and how emerging tensions have both affected the identity of housing professionals and impacted on the delivery of training and education programmes. The article analyses the changing knowledges and skills valued in contemporary housing practice and considers how the sector has responded to the challenges of austerity. The central argument is that a dominant logic of competition has culminated in a crisis of identity for the sector. Although the focus of the article is on UK housing practice, the processes identified have a wider relevance for the analysis of housing and welfare delivery in developed economies.

Frequency of mutations and polymorphisms in borderline ovarian tumors of known cancer genes.

Borderline ovarian tumors represent an understudied subset of ovarian tumors. Most studies investigating aberrations in borderline tumors have focused on KRAS/BRAF mutations. In this study, we conducted an extensive analysis of mutations and single-nucleotide polymorphisms (SNPs) in borderline ovarian tumors. Using the Sequenom MassArray platform, we investigated 160 mutations/polymorphisms in 33 genes involved in cell signaling, apoptosis, angiogenesis, cell cycle regulation and cellular senescence. Of 52 tumors analyzed, 33 were serous, 18 mucinous and 1 endometrioid. KRAS c.35G>A p.Gly12Asp mutations were detected in eight tumors (six serous and two mucinous), BRAF V600E mutations in two serous tumors, and PIK3CA H1047Y and PIK3CA E542K mutations in a serous and an endometrioid BOT, respectively. CTNNB1 mutation was detected in a serous tumor. Potentially functional polymorphisms were found in vascular endothelial growth factor (VEGF), ABCB1, FGFR2 and PHLPP2. VEGF polymorphisms were the most common and detected at four loci. PHLPP2 polymorphisms were more frequent in mucinous as compared with serous tumors (P=0.04), with allelic imbalance in one case. This study represents the largest and most comprehensive analysis of mutations and functional SNPs in borderline ovarian tumors to date. At least 25% of borderline ovarian tumors harbor somatic mutations associated with potential response to targeted therapeutics.

Outlier effects on robust joint modelling of longitudinal and survival data

Robust joint modelling is an emerging field of research. Through the advancements in electronic patient healthcare records, the popularly of joint modelling approaches has grown rapidly in recent years providing simultaneous analysis of longitudinal and survival data. This research advances previous work through the development of a novel robust joint modelling methodology for one of the most common types of standard joint models, that which links a linear mixed model with a Cox proportional hazards model. Through t-distributional assumptions, longitudinal outliers are accommodated with their detrimental impact being down weighed and thus providing more efficient and reliable estimates. The robust joint modelling technique and its major benefits are showcased through the analysis of Northern Irish end stage renal disease patients. With an ageing population and growing prevalence of chronic kidney disease within the United Kingdom, there is a pressing demand to investigate the detrimental relationship between the changing haemoglobin levels of haemodialysis patients and their survival. As outliers within the NI renal data were found to have significantly worse survival, identification of outlying individuals through robust joint modelling may aid nephrologists to improve patient's survival. A simulation study was also undertaken to explore the difference between robust and standard joint models in the presence of increasing proportions and extremity of longitudinal outliers. More efficient and reliable estimates were obtained by robust joint models with increasing contrast between the robust and standard joint models when a greater proportion of more extreme outliers are present. Through illustration of the gains in efficiency and reliability of parameters when outliers exist, the potential of robust joint modelling is evident. The research presented in this thesis highlights the benefits and stresses the need to utilise a more robust approach to joint modelling in the presence of longitudinal outliers.

Analysis of surfaces for characterization of fungal burden: does it matter?

Objectives: Mycological contamination of occupational environments can be a result of fungal spores’ dispersion in the air and on surfaces. Therefore, it is very important to assess it in both types of the samples. In the present study we assessed fungal contamination in the air and in the surface samples to show relevance of surfaces sampling in complementing the results obtained in the air samples. Material and Methods: In total, 42 settings were assessed by the analysis of air and surfaces samples. The settings were divided into settings with a high fungal load (7 poultry farms and 7 pig farms, 3 cork industries, 3 waste management plants, 2 wastewater treatment plants and 1 horse stable) and a low fungal load (10 hospital canteens, 8 college canteens and 1 maternity hospital). In addition to culture-based methods, molecular tools were also applied to detect fungal burden in the settings with a higher fungal load. Results: From the 218 sampling sites, 140 (64.2%) presented different species in the examined surfaces when compared with the species identified in the air. A positive association in the high fungal load settings was found between the presence of different species in the air and surfaces. Wastewater treatment plants constituted the setting with the highest number of different species between the air and surface. Conclusions: We observed that surfaces sampling and application of molecular tools showed the same efficacy of species detection in high fungal load settings, corroborating the fact that surface sampling is crucial for a correct and complete analysis of occupational scenarios.

Phylodynamic modelling of foot-and-mouth disease virus sequence data

The under-reporting of cases of infectious diseases is a substantial impediment to the control and management of infectious diseases in both epidemic and endemic contexts. Information about infectious disease dynamics can be recovered from sequence data using time-varying coalescent approaches, and phylodynamic models have been developed in order to reconstruct demographic changes of the numbers of infected hosts through time. In this study I have demonstrated the general concordance between empirically observed epidemiological incidence data and viral demography inferred through analysis of foot-and-mouth disease virus VP1 coding sequences belonging to the CATHAY topotype over large temporal and spatial scales. However a more precise and robust relationship between the effective population size (