An architecture for trustworthy open data services

This paper addresses the development of trust in the use of Open Data through incorporation of appropriate authentication and integrity parameters for use by end user Open Data application developers in an architecture for trustworthy Open Data Services. The advantages of this architecture scheme is that it is far more scalable, not another certificate-based hierarchy that has problems with certificate revocation management. With the use of a Public File, if the key is compromised: it is a simple matter of the single responsible entity replacing the key pair with a new one and re-performing the data file signing process. Under this proposed architecture, the the Open Data environment does not interfere with the internal security schemes that might be employed by the entity. However, this architecture incorporates, when needed, parameters from the entity, e.g. person who authorized publishing as Open Data, at the time that datasets are created/added.

Alive SMC^2: Bayesian model selection for low-count time series models with intractable likelihoods

In this paper we present a new method for performing Bayesian parameter inference and model choice for low count time series models with intractable likelihoods. The method involves incorporating an alive particle filter within a sequential Monte Carlo (SMC) algorithm to create a novel pseudo-marginal algorithm, which we refer to as alive SMC^2. The advantages of this approach over competing approaches is that it is naturally adaptive, it does not involve between-model proposals required in reversible jump Markov chain Monte Carlo and does not rely on potentially rough approximations. The algorithm is demonstrated on Markov process and integer autoregressive moving average models applied to real biological datasets of hospital-acquired pathogen incidence, animal health time series and the cumulative number of poison disease cases in mule deer.

Toward making inroads in reducing the disparity of lung health in Australian Indigenous and New Zealand Maori children

Globally, Indigenous populations, which include Aboriginal and Torres Strait islanders in Australia and Māori people in New Zealand (NZ), have poorer health than their non-Indigenous counterparts (1). Indigenous peoples worldwide face substantial challenges in poverty, education, employment, housing, and disconnection from ancestral lands (1). While addressing social determinants of health is a priority, solving clinical issues is equally important. Indeed, ignoring the latter until social issues improve risks further disparity as this may take generations. A systematic overview of interventions addressing social determinants of health found a striking lack of reliable evaluations (2). Where evidence was available, health improvement associated with interventions was modest or uncertain (2). Thus, advances in healthcare remain essential and these require the best evidence available in preventing and managing common illnesses, including respiratory illnesses

Does Australia need laws for 'Biotrespass' to protect organic farmers?

The supreme court of Western Australia handed down a landmark decision yesterday, on genetically modified crop liability. The ruling in Marsh v Baxter is an enormous win for the agricultural biotechnology industry, and has disappointed organic farmers and their advocates.

Intravascular device administration sets: Replacement after standard versus prolonged use in hospitalised patients--a study protocol for a randomised controlled trial (The RSVP Trial)

Introduction Vascular access devices (VADs), such as peripheral or central venous catheters, are vital across all medical and surgical specialties. To allow therapy or haemodynamic monitoring, VADs frequently require administration sets (AS) composed of infusion tubing, fluid containers, pressure-monitoring transducers and/or burettes. While VADs are replaced only when necessary, AS are routinely replaced every 3–4 days in the belief that this reduces infectious complications. Strong evidence supports AS use up to 4 days, but there is less evidence for AS use beyond 4 days. AS replacement twice weekly increases hospital costs and workload. Methods and analysis This is a pragmatic, multicentre, randomised controlled trial (RCT) of equivalence design comparing AS replacement at 4 (control) versus 7 (experimental) days. Randomisation is stratified by site and device, centrally allocated and concealed until enrolment. 6554 adult/paediatric patients with a central venous catheter, peripherally inserted central catheter or peripheral arterial catheter will be enrolled over 4 years. The primary outcome is VAD-related bloodstream infection (BSI) and secondary outcomes are VAD colonisation, AS colonisation, all-cause BSI, all-cause mortality, number of AS per patient, VAD time in situ and costs. Relative incidence rates of VAD-BSI per 100 devices and hazard rates per 1000 device days (95% CIs) will summarise the impact of 7-day relative to 4-day AS use and test equivalence. Kaplan-Meier survival curves (with log rank Mantel-Cox test) will compare VAD-BSI over time. Appropriate parametric or non-parametric techniques will be used to compare secondary end points. p Values of <0.05 will be considered significant.

A time and motion study of peripheral venous catheter flushing practice using manually prepared and prefilled flush syringes

Peripheral venous catheters (PVCs) are the simplest and most frequently used method for drug, fluid, and blood product administration in the hospital setting. It is estimated that up to 90% of patients in acute care hospitals require a PVC; however, PVCs are associated with inherent complications, which can be mechanical or infectious. There have been a range of strategies to prevent or reduce PVC-related complications that include optimizing patency through the use of flushing. Little is known about the current status of flushing practice. This observational study quantified preparation and administration time and identified adherence to principles of Aseptic Non-Touch Technique and organizational protocol on PVC flushing by using both manually prepared and prefilled syringes.

Curriculum reform in testing and accountability contexts

Recent international educational developments have important implications for the skills and understandings in curriculum and assessment that teachers develop, both in pre-service and in practice. Global developments in curriculum and assessment reform require teachers to utilise a network of knowledges and develop a repertoire of assessment skills and understandings. In a context of testing, accountability and auditing, data analysis skills are increasingly required to examine pedagogic practices for the development of intervention teaching and learning strategies to improve learning outcomes for all students (Marsh, 2009). However, too often the data are used predominantly for accountability purposes that serve at national levels as a catalyst for measurement, comparison and allocation of funding (Lingard and Sellar, 2013). With increased accountability demands brought about by global competitiveness and programs for international measurement of educational attainment, there has also emerged an increase in the use of testing, which in some countries has become the dominant form of assessment. For example in Australia, national testing of students in Years 3, 5, 7 and 9 began in 2008 under the National Australia Program – Literacy and Numeracy (NAPLAN). The results from this program for each school are published on the My School website (www.myschool.edu.au), increasing the competitive nature of the testing and intensifying the demands on teachers and schools. In particular, there has been a shift in the enacted curriculum in Australia to a focus on literacy and numeracy because the curriculum is tested.

A Chlamydia trachomatis strain with a chemically generated amino acid substitution (P370L) in the cthtrA gene shows reduced elementary body production

Background Chlamydia (C.) trachomatis is the most prevalent bacterial sexually transmitted infection worldwide and the leading cause of preventable blindness. Genetic approaches to investigate C. trachomatis have been only recently developed due to the organism’s intracellular developmental cycle. HtrA is a critical stress response serine protease and chaperone for many bacteria and in C. trachomatis has been previously shown to be important for heat stress and the replicative phase of development using a chemical inhibitor of the CtHtrA activity. In this study, chemically-induced SNVs in the cthtrA gene that resulted in amino acid substitutions (A240V, G475E, and P370L) were identified and characterized. Methods SNVs were initially biochemically characterized in vitro using recombinant protein techniques to confirm a functional impact on proteolysis. The C. trachomatis strains containing the SNVs with marked reductions in proteolysis were investigated in cell culture to identify phenotypes that could be linked to CtHtrA function. Results The strain harboring the SNV with the most marked impact on proteolysis (cthtrAP370L) was detected to have a significant reduction in the production of infectious elementary bodies. Conclusions This provides genetic evidence that CtHtrA is critical for the C. trachomatis developmental cycle.

Lung disease in indigenous children

Children in indigenous populations have substantially higher respiratory morbidity than non-indigenous children. Indigenous children have more frequent respiratory infections that are, more severe and, associated with long-term sequelae. Post-infectious sequelae such as chronic suppurative lung disease and bronchiectasis are especially prevalent among indigenous groups and have lifelong impact on lung function. Also, although estimates of asthma prevalence among indigenous children are similar to non-indigenous groups the morbidity of asthma is higher in indigenous children. To reduce the morbidity of respiratory illness, best-practice medicine is essential in addition to improving socio-economic factors, (eg household crowding), tobacco smoke exposure, and access to health care and illness prevention programs that likely contribute to these issues. Although each indigenous group may have unique health beliefs and interfaces with modern health care, a culturally sensitive and community-based comprehensive care system of preventive and long term care can improve outcomes for all these conditions. This article focuses on common respiratory conditions encountered by indigenous children living in affluent countries where data is available.

Reclassification of [Pasteurella] trehalosi as Bibersteinia trehalosi gen. nov., comb. nov.

[Pasteurella] trehalosi is an important pathogen of sheep, being primarily associated with serious systemic infections in lambs but also having an association with pneumonia. The aim of the present investigation was to characterize a broad collection of strains tentatively identified as [P.] trehalosi in order to reclassify and rename this taxon to support improvements in our understanding of the pathogenesis and epidemiology of this important organism. The type strain for [P.] trehalosi, strain NCTC 10370T, was included along with 42 field isolates from sheep (21), cattle (14), goats (1), roe deer (3) and unknown sources (3). An extended phenotypic characterization was performed on all 43 strains. Amplified fragment length polymorphism (AFLP) was also performed on the isolates. Two of the field isolates were subjected to 16S rRNA gene sequencing. These sequences, along with five existing sequences for [P.] trehalosi strains and 12 sequences for other taxa in the family Pasteurellaceae, were subjected to a phylogenetic analysis. All the isolates and the reference strains were identified as [P.] trehalosi. A total of 17 out of 22 ovine isolates produced acid from all glycosides, while only four out of 14 bovine isolates produced acid from all glycosides. All 22 ovine isolates were haemolytic and CAMP-positive, while no other isolate was haemolytic and only two bovine isolates were CAMP-positive. Nineteen AFLP types were found within the [P.] trehalosi isolates. All [P.] trehalosi isolates shared at least 70% similarity in AFLP patterns. The largest AFLP type included the type strain and 7 ovine field isolates. Phylogenetic analysis indicated that the seven strains studied (two field isolates and the five serovar reference strains) are closely related, with 98.6% or higher 16S rRNA gene sequence similarity. As both genotypic and phenotypic testing support the separate and distinct nature of these organisms, we propose the transfer of [P.] trehalosi to a new genus, Bibersteinia, as Bibersteinia trehalosi comb. nov. The type strain is NCTC 10370T (=ATCC 29703T). Bibersteinia trehalosi can be distinguished from the existing genera of the family by the observation of only nine characteristics; catalase, porphyrin, urease, indole, phosphatase, acid from dulcitol, (+)-D-galactose, (+)-D mannose and (+)-D-trehalose.

Incorporating dugong habitats into the marine protected area design for the Great Barrier Reef Marine Park, Queensland, Australia.

Dugong habitats were considered in the design for the new zoning network for the Great Barrier Reef Marine Park as part of the Representative Areas Program. One of the specific design guidelines developed as part of the biophysical operational principles recommended that 50% of all high priority dugong habitats should be incorporated in the network of no-take areas. The high priority dugong habitat incorporated in no-take protection increased from 1396 to 3476 km2 (or 16.9-42.0% of all identified sites). Although this increase in protection fell short of the recommended 50%, overall the level of protection afforded by the Great Barrier Reef Marine Park Zoning Plan 2003 increased for all the locations identified.

Naiset rajalla : Kyöpeli, Nainen, Naara(s), Neitsyt, Morsian, Akka ja Ämmä Suomen paikannimissä

Women at the boundary. Kyöpeli ( ghost, devil, elf, fairy, enchantress, witch ), Nainen ( woman ), Naara(s) ( female animal, derogatory term for a woman ), Neitsyt ( young, [virgin] woman ), Morsian ( bride ), Akka ( old woman, wife, grandmother ) and Ämmä ( [old] woman, wife, grandmother ) in Finnish place names This study examines a total of about 4,000 Finnish place names which include a specific that refers to a woman: Kyöpeli, Nainen, Naara(s), Neitsyt, Morsian, Akka or Ämmä. The study has two main objectives. First, to interpret the place names in the data, that is, to examine the words included in the data and establish their background and to differentiate names of different ages. In establishing the background of a name, the type of place (e.g. lake, hill or marsh) and its location, as well as the semantics of the feminine specific, are taken into account. The connotations of words referring to a woman are also studied. Words that refer to a woman are often affective and susceptible to changes in meaning, which is reflected in the history of place names. The second main objective is to recognise and highlight mythological place names. Mythology is pivotal for the interpretation of many place names with a feminine specific. The criteria for mythological names have not been explicitly discussed in Finnish onomastics until now, and I seek to determine such criteria in this study with the help of the data. Mythological place names often refer to large and significant natural localities, which are in many cases important boundaries for the community. Names for smaller localities may also be mythological if they refer to a place with a key location or a special topography (e.g. steep or rocky places). I also discuss the stories involved with specific places in the data, such as stories about supernatural beings. Each of the name groups discussed in the study has its own profile. For example, Naara(s) names are so old that naara is no longer understood to refer to a woman. These names have thus often been misinterpreted in onomastics. Names beginning with Morsian, on the other hand, appear to be of fairly recent origin and may be attributed to an international cautionary tale. Names beginning with Nais, Neitsyt, Akka and Ämmä highlight the duality of the data. They include both old names for important natural localities or boundaries and more recent names for modest dwellings, small cultivated areas and useless marshy ponds. This distribution of place names may reflect a cultural shift that changed the status of women in the community.

A spatial assessment of the risk to a mobile marine mammal from bycatch

Several species of marine mammals are at risk of extinction from being captured as bycatch in commercial fisheries. Various approaches have been developed and implemented to address this bycatch problem, including devices and gear changes, time and area closures and fisheries moratoria. Most of these solutions are difficult to implement effectively, especially for artisanal fisheries in developing countries and remote regions. Re-zoning of the Great Barrier Reef World Heritage Area (GBRWHA) in 2004 closed 33% of the region to extractive activities, including commercial fishing. However, the impact of re-zoning and the associated industry restructuring on a threatened marine mammal, the dugong (Dugong dugon), is difficult to quantify. Accurate information on dugong bycatch in commercial nets is unavailable because of the large geographic extent of the GBRWHA, the remoteness of the region adjacent to the Cape York Peninsula where most dugongs occur and the artisanal nature of the fishery. In the face of this uncertainty, a spatial risk-assessment approach was used to evaluate the re-zoning and associated industry restructuring for their ability to reduce the risk of dugong bycatch from commercial fisheries netting. The new zoning arrangements appreciably reduced the risk of dugong bycatch by reducing the total area where commercial netting is permitted. Netting is currently not permitted in 67% of dugong habitats of high conservation value, a 56% improvement over the former arrangements. Re-zoning and industry restructuring also contributed to a 22% decline in the spatial extent of conducted netting. Spatial risk assessment approaches that evaluate the risk of mobile marine mammals from bycatch are applicable to other situations where there is limited information on the location and intensity of bycatch, including remote regions and developing countries where resources are limited.

The effect of habitat and environmental history on otolith chemistry of barramundi Lates calcarifer in estuarine populations of a regulated tropical river

We examine the microchemistry of otoliths of cohorts of a fished shed population of the large catadromous fish, barramundi Lates calcarifer from the estuary of a large tropical river. Barramundi from the estuary of the large, heavily regulated Fitzroy River, north eastern Australia were analysed by making transects of 87Sr/86Sr isotope and trace metal/Ca ratios from the core to the outer edge. Firstly, we examined the Sr/Ca, Ba/Ca, Mg/Ca and Mn/Ca and 87Sr/86Sr isotope ratios in otoliths of barramundi tagged in either freshwater or estuarine habitats that were caught by the commercial fishery in the estuary. We used 87Sr/86Sr isotope ratios to identify periods of freshwater residency and assess whether trace metal/Ca ratios varied between habitats. Only Sr/Ca consistently varied between known periods of estuarine or freshwater residency. The relationships between trace metal/Ca and river flow, salinity, temperature were examined in fish tagged and recaptured in the estuary. We found weak and inconsistent patterns in relationships between these variables in the majority of fish. These results suggest that both individual movement history within the estuary and the scale of environmental monitoring were reducing our ability to detect any patterns. Finally, we examined fish in the estuary from two dominant age cohorts (4 and 7 yr old) before and after a large flood in 2003 to ascertain if the flood had enabled fish from freshwater habitats to migrate to the estuary. There was no difference in the proportion of fish in the estuary that had accessed freshwater after the flood. Instead, we found that larger individuals with each age cohort were more likely to have spent a period in freshwater. This highlights the need to maintain freshwater flows in rivers. About half the fish examined had accessed freshwater habitats before capture. Of these, all had spent at least their first two months in marine salinity waters before entering freshwater and some did not enter freshwater until four years of age. This contrasts with the results of several previous studies in other parts of the range that found that access to freshwater swamps by larval barramundi was important for enhanced population productivity and recruitment.

Dominant negative ATM mutations in breast cancer families

BACKGROUND: The ATM gene encoding a putative protein kinase is mutated in ataxia-telangiectasia (A-T), an autosomal recessive disorder with a predisposition for cancer. Studies of A-T families suggest that female heterozygotes have an increased risk of breast cancer compared with noncarriers. However, neither linkage analyses nor mutation studies have provided supporting evidence for a role of ATM in breast cancer predisposition. Nevertheless, two recurrent ATM mutations, T7271G and IVS10-6T-->G, reportedly increase the risk of breast cancer. We examined these two ATM mutations in a population-based, case-control series of breast cancer families and multiple-case breast cancer families. METHODS: Five hundred twenty-five or 262 case patients with breast cancer and 381 or 68 control subjects, respectively, were genotyped for the T7271G and IVS10-6T-->G ATM mutations, as were index patients from 76 non-BRCA1/2 multiple-case breast cancer families. Linkage and penetrance were analyzed. ATM protein expression and kinase activity were analyzed in lymphoblastoid cell lines from mutation carriers. All statistical tests were two-sided. RESULTS: In case and control subjects unselected for family history of breast cancer, one case patient had the T7271G mutation, and none had the IVS10-6T-->G mutation. In three multiple-case families, one of these two mutations segregated with breast cancer. The estimated average penetrance of the mutations was 60% (95% confidence interval [CI] = 32% to 90%) to age 70 years, equivalent to a 15.7-fold (95% CI = 6.4-fold to 38.0-fold) increased relative risk compared with that of the general population. Expression and activity analyses of ATM in heterozygous cell lines indicated that both mutations are dominant negative. CONCLUSION: At least two ATM mutations are associated with a sufficiently high risk of breast cancer to be found in multiple-case breast cancer families. Full mutation analysis of the ATM gene in such families could help clarify the role of ATM in breast cancer susceptibility.