BioPatML.NET – a bioinformatic pattern search engine

In the present paper, we introduce BioPatML.NET, an application library for the Microsoft Windows .NET framework [2] that implements the BioPatML pattern definition language and sequence search engine. BioPatML.NET is integrated with the Microsoft Biology Foundation (MBF) application library [3], unifying the parsers and annotation services supported or emerging through MBF with the language, search framework and pattern repository of BioPatML. End users who wish to exploit the BioPatML.NET engine and repository without engaging the services of a programmer may do so via the freely accessible web-based BioPatML Editor, which we describe below.

Assessing the effectiveness of the child safety net : linkage of hospital and child protection services data on ‘maltreated’ and ‘unintentionally injured' children

-International recognition of need for public health response to child maltreatment -Need for early intervention at health system level -Important role of health professionals in identifying, reporting, documenting suspician of maltreatment -Up to 10% of all children presenting at ED’s are victims and without identification, 35% reinjured and 5% die -In Qld, mandatory reporting requirement for doctors and nurses for suspected abuse or neglect

The new normativity : the innovation imperative

At a quite fundamental level, the very way in which Public Service Broadcasting (PSB) may envisage its future usually captured in the semantic shift from PSB to Public Service Media (PSM) is at stake when considering the recent history of public value discourse and the public value test. The core Reithian PSB idea assumed that public value would be created through the application of core principles of universality of availability and appeal, provision for minorities, education of the public, distance from vested interests, quality programming standards, program maker independence, and fostering of national culture and the public sphere. On the other hand, the philosophical import of the public value test is that potentially any excursion into the provision of new media services needs to be justified ex ante. In this era of New Public Management, greater transparency and accountability, and the proposition that resources for public value deliverables be contestable and not sequestered in public sector institutions, what might be the new Archimedean point around which a contemporised normativity for PSM be built? This paper will argue for the innovation imperative as an organising principle for contemporary PSM. This may appear counterintuitive, as it is precisely PSB’s predilection for innovating in new media services (in online, mobile, and social media) that has produced the constraining apparatus of the ex ante/public value/Drei-Stufen-Test in Europe, based on principles of competitive neutrality and transparency in the application of public funds for defined and limited public benefit. However, I argue that a commitment to innovation can define as complementary to, rather than as competitive ‘crowding out’, the new products and services that PSM can, and should, be delivering into a post-scarcity, superabundant all-media marketplace. The evidence presented in this paper for this argument is derived mostly from analysis of PSM in the Australian media ecology. While no PSB outside Europe is subject to a formal public value test, the crowding out arguments are certainly run in Australia, particularly by powerful commercial interests for whom free news is a threat to monetising quality news journalism. Take right wing opinion leader, herself a former ABC Board member, Judith Sloan: ‘… the recent expansive nature of the ABC – all those television stations, radio stations and online offerings – is actually squeezing activity that would otherwise be undertaken by the private sector. From partly correcting market failure, the ABC is now causing it. We are now dealing with a case of unfair competition and wasted taxpayer funds’ (The Drum, 1 August http://www.abc.net.au/unleashed/2818220.html). But I argue that the crowding out argument is difficult to sustain in Australia because of the PSB’s non-dominant position and the fact that much of innovation generated by the two PSBs, the ABC and the SBS, has not been imitated by or competed for by the commercials. The paper will bring cases forward, such as SBS’ Go Back to Where you Came From (2011) as an example of product innovation, and a case study of process and organisational innovation which also has resulted in specific product and service innovation – the ABC’s Innovation Unit. In summary, at least some of the old Reithian dicta, along with spectrum scarcity and market failure arguments, have faded or are fading. Contemporary PSM need to justify their role in the system, and to society, in terms of innovation.

High-risk, high-stake relationships: building effective industry-university partnerships for Work Integrated Learning (WIL)

Many industry peak and professional bodies advocate students undertake professional work placements as a key work integrated learning (WIL) experience in accredited university degree courses. However, mismatched expectations and gaps in the way industry partners (IPs) are supported during these work placements can place these high-stake alliances at risk. A review of models and strategies supporting industry partners indicates many are contingent on the continued efforts of well-networked individuals in both universities and IP organisations to make these connections work. It is argued that whilst these individuals are highly valued they often end up representing a whole course or industry perspective, not just their area of expertise. Sustainable partnership principles and practices with shared responsibility across stakeholder groups are needed instead. This paper provides an overview of work placement approaches in the disciplines of business, engineering and urban development at an Australian, metropolitan university. Employing action research and participatory focus group methodologies, it gathers and articulates recommendations from associated IPs on practical suggestions and strategies to improve relationships and the resultant quality of placements.

Complete genomic sequence of a Rubus yellow net virus isolate and detection of genome-wide pararetrovirus-derived small RNAs

Rubus yellow net virus (RYNV) was cloned and sequenced from a red raspberry (Rubus idaeus L.) plant exhibiting symptoms of mosaic and mottling in the leaves. Its genomic sequence indicates that it is a distinct member of the genus Badnavirus, with 7932. bp and seven ORFs, the first three corresponding in size and location to the ORFs found in the type member Commelina yellow mottle virus. Bioinformatic analysis of the genomic sequence detected several features including nucleic acid binding motifs, multiple zinc finger-like sequences and domains associated with cellular signaling. Subsequent sequencing of the small RNAs (sRNAs) from RYNV-infected R. idaeus leaf tissue was used to determine any RYNV sequences targeted by RNA silencing and identified abundant virus-derived small RNAs (vsRNAs). The majority of the vsRNAs were 22-nt in length. We observed a highly uneven genome-wide distribution of vsRNAs with strong clustering to small defined regions distributed over both strands of the RYNV genome. Together, our data show that sequences of the aphid-transmitted pararetrovirus RYNV are targeted in red raspberry by the interfering RNA pathway, a predominant antiviral defense mechanism in plants. © 2013.

Prevalence of asymptomatic malaria and bed net ownership and use in Bhutan, 2013 : a country earmarked for malaria elimination

Background With dwindling malaria cases in Bhutan in recent years, the government of Bhutan has made plans for malaria elimination by 2016. This study aimed to determine coverage, use and ownership of LLINs, as well as the prevalence of asymptomatic malaria at a single time-point, in four sub-districts of Bhutan. Methods A cross-sectional study was carried out in August 2013. Structured questionnaires were administered to a single respondent in each household (HH) in four sub-districts. Four members from 25 HH, randomly selected from each sub-district, were tested using rapid diagnostic tests (RDT) for asymptomatic Plasmodium falciparum and Plasmodium vivax infection. Multivariable logistic regression models were used to identify factors associated with LLIN use and maintenance. Results All blood samples from 380 participants tested negative for Plasmodium infections. A total of 1,223 HH (92.5% of total HH) were surveyed for LLIN coverage and use. Coverage of LLINs was 99.0% (1,203/1,223 HH). Factors associated with decreased odds of sleeping under a LLIN included: washing LLINs nine months compared to washing LLINs every six months; HH in the least poor compared to the most poor socio-economic quintile; a HH income of Nu 5,001-10,000 (US$1 = Nu 59.55), and Nu >10,000, compared to HH with income of

Mapping of adult plant resistance to net form of net blotch in three Australian barley populations

Net form of net blotch (NFNB), caused by Pyrenophora teres Drechs. f. teres Smedeg., is a serious disease problem for the barley industry in Australia and other parts of the world. Three doubled haploid barley populations, Alexis/Sloop, WI2875-1/Alexis, and Arapiles/Franklin, were used to identify genes conferring adult plant resistance to NFNB in field trials. Quantitative trait loci (QTLs) identified were specific for adult plant resistance because seedlings of the parental lines were susceptible to the NFNB isolates used in this study. QTLs were identified on chromosomes 2H, 3H, 4H, and 7H in both the Alexis/Sloop and WI2875-1/Alexis populations and on chromosomes 1H, 2H, and 7H in the Arapiles/Franklin population. Using QTLNetwork, epistatic interactions were identified between loci on chromosomes 3H and 6H in the Alexis/Sloop population, between 2H and 4H in the WI2875-1/Alexis population, and between 5H and 7H in the Arapiles/Franklin population. Comparisons with earlier studies of NFNB resistance indicate the pathotype-dependent nature of many resistance QTLs and the importance of establishing an international system of pathotype nomenclature and differential testing.

Quantitative trait loci and epistatic interactions in barley conferring resistance to net type net blotch (Pyrenophora teres f. teres) isolates.

Net type net blotch (NTNB) is an important barley disease in Australia and elsewhere, with significant yield reduction. This trait is important in selection along with other traits of quality and agronomic value. Two-hundred doubled-haploid lines were generated through anther culture from a cross between 'Pompadour' and 'Stirling'. Quantitative trait loci (QTL) were identified against five isolates of Pyrenophora teres f. teres, which represent virulences across Australia. QTL were mapped on chromosomes 3H and 6H using simple sequence repeat (SSR) markers. The resistance locus on 6H was detected with all isolates while the 3H locus was detected with two isolates. The 6H QTL from 'Pompadour' contributed resistance to isolates 97NB1, 95NB100 and NB81, whereas 6H QTL from 'Stirling' contributed resistance to isolates NB50 and NB52B. The 3H QTL from 'Pompadour' contributed resistance to NB50 and NB52B. Significant epistatic interactions were detected between QTL on 3H and 6H. These resistance QTL are a useful resource and identifying closely linked SSR markers with allelic combinations will facilitate in marker-assisted selection to develop NTNB resistant breeding lines.

Net radiation dynamics: performance of 20 daily net radiation models as related to model structure and intricacy in two climates.

We compared daily net radiation (Rn) estimates from 19 methods with the ASCE-EWRI Rn estimates in two climates: Clay Center, Nebraska (sub-humid) and Davis, California (semi-arid) for the calendar year. The performances of all 20 methods, including the ASCE-EWRI Rn method, were then evaluated against Rn data measured over a non-stressed maize canopy during two growing seasons in 2005 and 2006 at Clay Center. Methods differ in terms of inputs, structure, and equation intricacy. Most methods differ in estimating the cloudiness factor, emissivity (e), and calculating net longwave radiation (Rnl). All methods use albedo (a) of 0.23 for a reference grass/alfalfa surface. When comparing the performance of all 20 Rn methods with measured Rn, we hypothesized that the a values for grass/alfalfa and non-stressed maize canopy were similar enough to only cause minor differences in Rn and grass- and alfalfa-reference evapotranspiration (ETo and ETr) estimates. The measured seasonal average a for the maize canopy was 0.19 in both years. Using a = 0.19 instead of a = 0.23 resulted in 6% overestimation of Rn. Using a = 0.19 instead of a = 0.23 for ETo and ETr estimations, the 6% difference in Rn translated to only 4% and 3% differences in ETo and ETr, respectively, supporting the validity of our hypothesis. Most methods had good correlations with the ASCE-EWRI Rn (r2 > 0.95). The root mean square difference (RMSD) was less than 2 MJ m-2 d-1 between 12 methods and the ASCE-EWRI Rn at Clay Center and between 14 methods and the ASCE-EWRI Rn at Davis. The performance of some methods showed variations between the two climates. In general, r2 values were higher for the semi-arid climate than for the sub-humid climate. Methods that use dynamic e as a function of mean air temperature performed better in both climates than those that calculate e using actual vapor pressure. The ASCE-EWRI-estimated Rn values had one of the best agreements with the measured Rn (r2 = 0.93, RMSD = 1.44 MJ m-2 d-1), and estimates were within 7% of the measured Rn. The Rn estimates from six methods, including the ASCE-EWRI, were not significantly different from measured Rn. Most methods underestimated measured Rn by 6% to 23%. Some of the differences between measured and estimated Rn were attributed to the poor estimation of Rnl. We conducted sensitivity analyses to evaluate the effect of Rnl on Rn, ETo, and ETr. The Rnl effect on Rn was linear and strong, but its effect on ETo and ETr was subsidiary. Results suggest that the Rn data measured over green vegetation (e.g., irrigated maize canopy) can be an alternative Rn data source for ET estimations when measured Rn data over the reference surface are not available. In the absence of measured Rn, another alternative would be using one of the Rn models that we analyzed when all the input variables are not available to solve the ASCE-EWRI Rn equation. Our results can be used to provide practical information on which method to select based on data availability for reliable estimates of daily Rn in climates similar to Clay Center and Davis.

A hydro-wood net-energy approach to hydro project design

An integrated approach to energy planning, when applied to large hydroelectric projects, requires that the energy-opportunity cost of the land submerged under the reservoir be incorporated into the planning methodology. Biomass energy lost from the submerged land has to be compared to the electrical energy generated, for which we develop four alternative formulations of the net-energy function. The design problem is posed as an LP problem and is solved for two sites in India. Our results show that the proposed designs may not be viable in net-energy terms, whereas a marginal reduction in the generation capacity could lead to an optimal design that gives substantial savings in the submerged area. Allowing seasonal variations in the hydroelectric generation capacity also reduces the reservoir size. A mixed hydro-wood generation system is then examined and is found to be viable.

Spot Form of Net Blotch Resistance in a Diverse Set of Barley Lines in Australia and Canada.

The responses of 95 barley lines and cultivars to spot form of net blotch (SFNB) caused by Pyrenophora teres f. maculata were analyzed as seedlings and adults in Australia and Canada. Cluster analyses revealed complex reaction responses. Only 2 lines (Esperance Orge 289 and TR3189) were resistant to all isolates at the seedling stage, whereas 15 lines and cultivars (81-82/033, Arimont, BYDV-018, CBSS97M00855T-B2-M1-Y1-M2-Y-1M-0Y, C19776, Keel, Sloop, Torrens, TR326, VB0111, Yarra, VB0229, WI-2477, WI2553, and Wisconsin Pedigree) were resistant toward the two Canadian isolates and mixture of Australian isolates at the adult stages. In Australian field experiments, the effectiveness of SFNB resistance in three barley cultivars (Barque. Cowabbie, and Schooner) and one breeding line (VB9104) with a different source of resistance was tested. Barque, which possessed a resistance gene that provided complete resistance to SFNB, was the most effective and showed no effect on grain yield or quality in the presence of inoculum. Generally, cultivars with seedling or adult resistance had less disease and better grain quality than the susceptible control. Dash, but they were not as effective as Barque. A preliminary differential set of 19 barley lines and cultivars for P teres I. maculata is proposed.

Integrating biodiversity conservation into forestry : an empirical analysis of institutional adaptation

Integrating biodiversity conservation into forest management in non-industrial private forests requires changes in the practices of those public and private actors that have implementing responsibilities and whose strategic and operational opportunities are at stake. Understanding this kind of context-dependent institutional adaptation requires bridging between two analytical approaches: policy implementation and organizational adaptation, backed up with empirical analysis. The empirical analyses recapitulated in this thesis summary address organizational competences, specialization, professional judgment, and organizational networks. The analyses utilize qualitative and quantitative data from public and private sector organizations as well as associations. The empirical analyses produced stronger signals of policy implementation than of organizational adaptation. The organizations recognized the policy and social demand for integrating biodiversity conservation into forest management and their professionals were in favor of conserving biodiversity. However, conservation was integrated to forest management so tightly that it could be said to be subsumed by mainstream forestry. The organizations had developed some competences for conservation but the competences did not differentiate among the organizations other than illustrating the functional differences between industry, administration and associations. The networks that organizations depended on consisted of traditional forestry actors and peers both in planning policy and at the operational level. The results show that he demand for biodiversity conservation has triggered incremental changes in organizations. They can be considered inert regarding this challenge. Isomorphism is advanced by hierarchical guidance and standardization, and by professional norms. Analytically, this thesis contributes to the understanding of organizational behavior across the public and private sector boundaries. The combination of a policy implementation approach inherent in analysis of public policies in hierarchical administration settings, and organizational adaptation typically applied to private sector organizations, highlights the importance of institutional interpretation. Institutional interpretation serves the understanding of the empirically identified diversions from the basic tenets of the two approaches. Attention to institutions allows identification of the overlap of the traditionally segregated approaches.