A framework for evaluating semantic metadata

Because poor quality semantic metadata can destroy the effectiveness of semantic web technology by hampering applications from producing accurate results, it is important to have frameworks that support their evaluation. However, there is no such framework developedto date. In this context, we proposed i) an evaluation reference model, SemRef, which sketches some fundamental principles for evaluating semantic metadata, and ii) an evaluation framework, SemEval, which provides a set of instruments to support the detection of quality problems and the collection of quality metrics for these problems. A preliminary case study of SemEval shows encouraging results.

Enhancing enterprise knowledge processes via cross-media extraction

In large organizations the resources needed to solve challenging problems are typically dispersed over systems within and beyond the organization, and also in different media. However, there is still the need, in knowledge environments, for extraction methods able to combine evidence for a fact from across different media. In many cases the whole is more than the sum of its parts: only when considering the different media simultaneously can enough evidence be obtained to derive facts otherwise inaccessible to the knowledge worker via traditional methods that work on each single medium separately. In this paper, we present a cross-media knowledge extraction framework specifically designed to handle large volumes of documents composed of three types of media text, images and raw data and to exploit the evidence across the media. Our goal is to improve the quality and depth of automatically extracted knowledge.

KnoFuss:a comprehensive architecture for knowledge fusion

We propose a knowledge fusion architecture KnoFuss based on the application of problem-solving methods technology, which allows methods for subtasks of the fusion process to be combined and the best methods to be selected, depending on the domain and task at hand.

Assessing walking limitations in stroke survivors:are self-reports and proxy-reports interchangeable?

Objective: To examine the extent to which proxy-report measures adequately assess walking limitations and are interchangeable with self-report measures in stroke survivors. Design and Participants: Self-report, proxy-report, and observed performance measures of walking limitations were compared cross-sectionally on 3 occasions following the discharge from hospital of 101 stroke survivors. Correlations between measures, differences between mean scores, and agreement of self- and proxy reports were analyzed. Results and Conclusions: Self- and proxy-report measures correlated significantly with each other and with observed performance measures; differences between mean scores were not found. Agreement between individual self- and proxy-report pairs was poor, however, indicating that freely substituting proxy-report data for self-report data when self-report data are unavailable is inappropriate.

Habits and attitudes towards retinoscopy and the relative accuracy of dedicated and combined retinoscopes

The studies presented in this thesis were carried out because of a lack of previous research with respect to (a) the habits and attitudes towards retinoscopy and (b) the relative accuracy of dedicated retinoscopes compared to combined types in which changing the bulb allows use in spot or streak mode. An online British survey received responses from 298 optometrists. Decision tree analyses revealed that optometrists working in multiple practices tended to rely less on retinoscopy than those in the independent sector. Only half of the respondents used dynamic retinoscopy. The majority, however, agreed that retinoscopy was an important test. The University attended also influenced the type of retinoscope used and the use of autorefractors. Combined retinoscopes were used most by the more recently qualified optometrists and few agreed that combined retinoscopes were less accurate. A trial indicated that combined and dedicated retinoscopes were equally accurate. Here, 4 optometrists (2 using spot and 2 using streak retinoscopes) tested one eye of 6 patients using combined and dedicated retinoscopes. This trial also demonstrated the utility of the relatively unknown ’15 degrees of freedom’ rule that exploits replication in factorial ANOVA designs to achieve sufficient statistical power when recruitment is limited. An opportunistic international survey explored the use of retinoscopy by 468 practitioners (134 ophthalmologists, 334 optometrists) attending contact related courses. Decision tree analyses found (a) no differences in the habits of optometrists and ophthalmologists, (b) differences in the reliance on retinoscopy and use of dynamic techniques across the participating countries and (c) some evidence that younger practitioners were using static and dynamic retinoscopy least often. In conclusion, this study has revealed infrequent use of static and dynamic retinoscopy by some optometrists, which may be the only means of determining refractive error and evaluating accommodation in patients with communication difficulties.

Market value, R&D and intellectual property:an empirical analysis of large Australian firms

This paper considers the value of innovation to large Australian firms. Specifically, we investigate how R&D and intellectual property activity influences the market value of firms, using a Tobin’s q approach. R&D data are available for the period 1994–96 and data on patent, trade mark and design applications for 1996. The findings suggest that R&D and patent activity are positively and significantly associated with market value. The results also suggest that private returns to R&D in Australia are low by international standards.

Selective in vitro glycosylation of recombinant proteins:semi-synthesis of novel homogeneous glycoforms of human erythropoietin

Background: A natural glycoprotein usually exists as a spectrum of glycosylated forms, where each protein molecule may be associated with an array of oligosaccharide structures. The overall range of glycoforms can have a variety of different biophysical and biochemical properties, although details of structure–function relationships are poorly understood, because of the microheterogeneity of biological samples. Hence, there is clearly a need for synthetic methods that give access to natural and unnatural homogeneously glycosylated proteins. The synthesis of novel glycoproteins through the selective reaction of glycosyl iodoacetamides with the thiol groups of cysteine residues, placed by site-directed mutagenesis at desired glycosylation sites has been developed. This provides a general method for the synthesis of homogeneously glycosylated proteins that carry saccharide side chains at natural or unnatural glycosylation sites. Here, we have shown that the approach can be applied to the glycoprotein hormone erythropoietin, an important therapeutic glycoprotein with three sites of N-glycosylation that are essential for in vivo biological activity. Results: Wild-type recombinant erythropoietin and three mutants in which glycosylation site asparagine residues had been changed to cysteines (His10-WThEPO, His10-Asn24Cys, His10-Asn38Cys, His10-Asn83CyshEPO) were overexpressed and purified in yields of 13 mg l−1 from Escherichia coli. Chemical glycosylation with glycosyl-β-N-iodoacetamides could be monitored by electrospray MS. Both in the wild-type and in the mutant proteins, the potential side reaction of the other four cysteine residues (all involved in disulfide bonds) were not observed. Yield of glycosylation was generally about 50% and purification of glycosylated protein from non-glycosylated protein was readily carried out using lectin affinity chromatography. Dynamic light scattering analysis of the purified glycoproteins suggested that the glycoforms produced were monomeric and folded identically to the wild-type protein. Conclusions: Erythropoietin expressed in E. coli bearing specific Asn→Cys mutations at natural glycosylation sites can be glycosylated using β-N-glycosyl iodoacetamides even in the presence of two disulfide bonds. The findings provide the basis for further elaboration of the glycan structures and development of this general methodology for the synthesis of semi-synthetic glycoproteins. Results: Wild-type recombinant erythropoietin and three mutants in which glycosylation site asparagine residues had been changed to cysteines (His10-WThEPO, His10-Asn24Cys, His10-Asn38Cys, His10-Asn83CyshEPO) were overexpressed and purified in yields of 13 mg l−1 from Escherichia coli. Chemical glycosylation with glycosyl-β-N-iodoacetamides could be monitored by electrospray MS. Both in the wild-type and in the mutant proteins, the potential side reaction of the other four cysteine residues (all involved in disulfide bonds) were not observed. Yield of glycosylation was generally about 50% and purification of glycosylated protein from non-glycosylated protein was readily carried out using lectin affinity chromatography. Dynamic light scattering analysis of the purified glycoproteins suggested that the glycoforms produced were monomeric and folded identically to the wild-type protein. Conclusions: Erythropoietin expressed in E. coli bearing specific Asn→Cys mutations at natural glycosylation sites can be glycosylated using β-N-glycosyl iodoacetamides even in the presence of two disulfide bonds. The findings provide the basis for further elaboration of the glycan structures and development of this general methodology for the synthesis of semi-synthetic glycoproteins

All-optical OFDM and distributed Raman amplification:challenges to enable high capacities and extend reach

We review recent advances in all-optical OFDM technologies and discuss the performance of a field trial of a 2 Tbit/s Coherent WDM over 124 km with distributed Raman amplification. The results indicate that careful optimisation of the Raman pumps is essential. We also consider how all-optical OFDM systems perform favourably against energy consumption when compared with alternative coherent detection schemes. We argue that, in an energy constrained high-capacity transmission system, direct detected all-optical OFDM with `ideal' Raman amplification is an attractive candidate for metro area datacentre interconnects with ~100 km fibre spans, with an overall energy requirement at least three times lower than coherent detection techniques.

Insulin therapy in people with type 2 diabetes:opportunities and challenges?

Given the continued interest in defining the optimal management of individuals with type 2 diabetes, the Editor of Diabetes Care convened a working party of diabetes specialists to examine this topic in the context of insulin therapy. This was prompted by recent new evidence on the use of insulin in such people. The group was aware of evidence that the benefits of insulin therapy are still usually offered late, and thus the aim of the discussion was how to define the optimal timing and basis for decisions regarding insulin and to apply these concepts in practice. It was noted that recent evidence had built upon that of the previous decades, together confirming the benefits and safety of insulin therapy, albeit with concerns about the potential for hypoglycemia and gain in body weight. Insulin offers a unique ability to control hyperglycemia, being used from the time of diagnosis in some circumstances, when metabolic control is disturbed by medical illness, procedures, or therapy, as well as in the longer term in ambulatory care. For those previously starting insulin, various other forms of therapy can be added later, which offer complementary effects appropriate to individual needs. Here we review current evidence and circumstances in which insulin can be used, consider individualized choices of alternatives and combination regimens, and offer some guidance on personalized targets and tactics for glycemic control in type 2 diabetes. © 2014 by the American Diabetes Association.

Global variations and time trends in the prevalence of childhood myopia, a systematic review and quantitative meta-analysis:implications for aetiology and early prevention

The aim of this review was to quantify the global variation in childhood myopia prevalence over time taking account of demographic and study design factors. A systematic review identified population-based surveys with estimates of childhood myopia prevalence published by February 2015. Multilevel binomial logistic regression of log odds of myopia was used to examine the association with age, gender, urban versus rural setting and survey year, among populations of different ethnic origins, adjusting for study design factors. 143 published articles (42 countries, 374 349 subjects aged 1- 18 years, 74 847 myopia cases) were included. Increase in myopia prevalence with age varied by ethnicity. East Asians showed the highest prevalence, reaching 69% (95% credible intervals (CrI) 61% to 77%) at 15 years of age (86% among Singaporean-Chinese). Blacks in Africa had the lowest prevalence; 5.5% at 15 years (95% CrI 3% to 9%). Time trends in myopia prevalence over the last decade were small in whites, increased by 23% in East Asians, with a weaker increase among South Asians. Children from urban environments have 2.6 times the odds of myopia compared with those from rural environments. In whites and East Asians sex differences emerge at about 9 years of age; by late adolescence girls are twice as likely as boys to be myopic. Marked ethnic differences in age-specific prevalence of myopia exist. Rapid increases in myopia prevalence over time, particularly in East Asians, combined with a universally higher risk of myopia in urban settings, suggest that environmental factors play an important role in myopia development, which may offer scope for prevention.

Towards the knowledge-based design of universal influenza epitope ensemble vaccines

Motivation: Influenza A viral heterogeneity remains a significant threat due to unpredictable antigenic drift in seasonal influenza and antigenic shifts caused by the emergence of novel subtypes. Annual review of multivalent influenza vaccines targets strains of influenza A and B likely to be predominant in future influenza seasons. This does not induce broad, cross protective immunity against emergent subtypes. Better strategies are needed to prevent future pandemics. Cross-protection can be achieved by activating CD8+ and CD4+ T cells against highly-conserved regions of the influenza genome. We combine available experimental data with informatics-based immunological predictions to help design vaccines potentially able to induce cross-protective T-cells against multiple influenza subtypes. Results: To exemplify our approach we designed two epitope ensemble vaccines comprising highly-conserved and experimentally-verified immunogenic influenza A epitopes as putative non-seasonal influenza vaccines; one specifically targets the US population and the other is a universal vaccine. The USA-specific vaccine comprised 6 CD8+ T cell epitopes (GILGFVFTL, FMYSDFHFI, GMDPRMCSL, SVKEKDMTK, FYIQMCTEL, DTVNRTHQY) and 3 CD4+ epitopes (KGILGFVFTLTVPSE, EYIMKGVYINTALLN, ILGFVFTLTVPSERG). The universal vaccine comprised 8 CD8+ epitopes: (FMYSDFHFI, GILGFVFTL, ILRGSVAHK, FYIQMCTEL, ILKGKFQTA, YYLEKANKI, VSDGGPNLY, YSHGTGTGY) and the same 3 CD4+ epitopes. Our USA-specific vaccine has a population protection coverage (portion of the population potentially responsive to one or more component epitopes of the vaccine, PPC) of over 96% and 95% coverage of observed influenza subtypes. The universal vaccine has a PPC value of over 97% and 88% coverage of observed subtypes.

Top down control in a relatively pristine seagrass ecosystem

The loss of large-bodied herbivores and/or top predators has been associated with large-scale changes in terrestrial, freshwater, and marine ecosystems around the world. Understanding the consequences of these declines has been hampered by a lack of studies in relatively pristine systems. To fill this gap, I investigated the dynamics of the relatively pristine seagrass ecosystem of Shark Bay, Australia. I began by examining the seagrass species distributions, stoichiometry, and patterns of nutrient limitation across the whole of Shark Bay. Large areas were N-limited, P-limited, or limited by factors other than nutrients. Phosphorus-limitation was centered in areas of restricted water exchange with the ocean. Nutrient content of seagrasses varied seasonally, but the strength of seasonal responses were species-specific. Using a cafeteria-style experiment, I found that fast-growing seagrass species, which had higher nutrient content experienced higher rates of herbivory than slow-growing species that are dominant in the bay but have low nutrient content. Although removal rates correlated well with nutrient content at a broad scale, within fast-growing species removal rates were not closely tied to N or P content. Using a combination of stable isotope analysis and animal borne video, I found that green turtles (Chelonia mydas)—one of the most abundant large-bodied herbivores in Shark Bay—appear to assimilate little energy from seagrasses at the population level. There was, however, evidence of individual specialization in turtle diets with some individuals foraging largely on seagrasses and others feeding primarily on macroalgae and gelatinous macroplankton. Finally, I used exclusion cages, to examine whether predation-sensitive habitat shifts by megagrazers (green turtles, dugongs) transmitted a behavior-mediated trophic cascade (BMTC) between sharks and seagrasses. In general, data were consistent with predictions of a behavior-mediated trophic cascade. Megaherbivore impacts on seagrasses were large only in the microhabitat where megaherbivores congregate to reduce predation risk. My study highlights the importance of large herbivores in structuring seagrass communities and, more generally, suggests that roving top predators likely are important in structuring communities—and possibly ecosystems—through non-consumptive pathways.