A comparison of Australian and European Union research performance profiles

"Governments worldwide face the challenge of how best to prioritise their international science and innovation (S&I) cooperation activities. This involves balancing the intrinsic benefits that may arise from international S&I cooperation with extrinsic considerations – diplomacy, trade, national security etc. The interplay of these intrinsic and extrinsic considerations means that complex and often ambiguous tradeoffs need to be addressed by policymakers. In some cases international S&I cooperation priorities will reflect extrinsic diplomatic and geopolitical goals. In other cases the objectives will relate more closely to balancing the costs, risks and benefits of particular bilateral and multilateral S&I cooperation opportunities. Given the limited financial resources available to support international S&I cooperation it is useful for policymakers to have access to appropriate decision-support tools and information. This should help to avoid wasteful resource allocations caused by a lack of access to relevant information.This paper seeks to contribute to the evolving policy framework in this area by considering ways of characterising and mapping international imbalances in research performance." - page 2Australian National Universit

Structure and Expression of the Actin Gene Family of Drosophila melanogaster

We have isolated the six actin genes of Drosophila melanogaster from a Drosophila genomic DNA library and have compared structural features of the genes by restriction mapping, electron microscopy and DNA sequencing. We found that at least two of the actin genes contain intervening sequences which interrupt the genes at different positions. Several of the genes were shown to be lacking intervening sequences in the analogous positions. This nonconservation of intron position is in striking contrast to the strong conservation of intron positions seen in other gene families. The DNA sequences of the protein coding regions of the genes are highly conserved while the intron and untranslated sequences are not. The primary sequences of all the Drosophila actins resemble mammalian cytoplasmic actins more than mammalian muscle actins. We studied the distribution of actin mRNAs in different developmental stages and in different dissected body parts with the use of gene specific hybridization probes which we isolated from the 3' untranslated portions of the genes. We found that the genes fall into three main categories with respect to their patterns of expression in Drosophila. Trancripts from two of the genes are found throughout Drosophila development. They are expressed at higher levels in ovaries and embryonic cultured cells than in muscle containing tissue and are thought to be cytoplasmic actins. Two others encode thoracic muscle actins. Their transcripts accumulate predominantly in the thoracic regions of the adult where the flight and jump muscles are found. The other two genes are most active in larvae and in adult abdomens. They are thought to encode actins used in the larval, pupal, and adult intersegmental muscles. We studied the structure of the cytoplasmic actin gene, act5C, in detail and found that it encodes at least six different mRNAs. At the 5' end there are two nonhomologous leader exons which are alternately spliced to the remainder of the gene. At the 3' end of the gene, three sites of polyadenylation are used. The 3' variation is the principal cause of the transcript length heterogeneity observed in the transcripts. In whole animal RNA, the two leader exons are expressed with the same pattern through development and with all three polyadenylation sites. There is some developmental variability in the use of the three polyadenylation sites. In order to determine if each exon is preceded by a functional promoter and to identify sequences important for transcription initiation from each exon, we made fusions between act5C promoter fragments and the bacterial chloramphenicol acetyltransferase (CAT) gene and tested these for promoter activity in transient assays in Kc cells. We found that each exon is preceded by a separate, functional promoter. At least two regions of DNA sequences are necessary for optimal expression from exon 1. One of these lies greater than 1.9 kb upstream from the exon 1 cap site. All of the sequences required for exon 2 transcription lie within 450 bases of its cap site. There is evidence from some constructions that transcription initiation from exon 1 may inhibit transcription initiation from ex on 2.</p

A bibliometric analysis of Australia's international research collaboration in science and technology: analytical methods and initial findings

This paper presents the initial findings from an exploratory bibliometric analysis of Australia's international collaboration in science and technology. This paper is focusses on: (a) Assessing the methodological challenges faced in comprehensively mapping Australia's science and technology research activity from an international engagement perspective; (b) Suggesting solutions to these challenges; (c) Providing some policy-relevant findings of potential use to the Australian Government and the European Commission

Mapping Australia's research strengths from an international perspective

Deliverable lead: ANUThe Forum for European-Australian Science and Technology cooperation (known as FEAST) was an Australia-EU joint initiative that highlighted and promoted international research collaboration between Australia and Europe. It operated from 2001 until 2012The key outcomes of the paper are as yet undefined as this aspect awaits feedback from stakeholders following circulation of this paper.AUS-ACCESS4EU project no. 244485Project funded under EU FP7, Capacities Programme, International Cooperation; Project number: FP7-244485Project funded by the European Commission under the International cooperation activity of the Capacities Programme of the 7th European Framework Programme for RTD.Version

Automatic categorization of diverse experimental information in the bioscience literature

Background: Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. Results: We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Conclusions: Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort

A maximum likelihood estimation procedure for binary data from cross-over studies

A maximum likelihood estimation procedure is presented for the expected frequencies when modelling binary data from two-period cross-over studies. This procedure provides a simple approach to parameter estimation in models for binary data from cross-over experiments, and in particular for a log-nonlinear model proposed by Becker and Balagtas (1993).http://www.sastat.org.za/journal.ht

Ensuring an Essential Supply of Allied Health Professions (AHP) Placements: Using Crowdsourcing to Develop a National Call to Action

Sustainable growth in the Allied Health Professions (AHP) workforce is an ambition of the United Kingdom’s NHS Long Term Plan. However historically, access to good quality placements has been a barrier to increasing pre-registration training numbers. This article focuses on work carried out by Health Education England (HEE) to gain insights on the impact of the COVID-19 pandemic on capacity. Using a pragmatic, embedded mixed-methods approach, insights were gathered using an online workshop, crowdsourcing, open for two weeks in the summer of 2020. AHP placement stakeholders could vote, share ideas or comment. Descriptive data were extracted, and comments made were analysed using inductive thematic analysis. Participants (N = 1,800) made over 8,500 comments. The themes identified included: diversity of placement opportunity, improved placement coordination, a more joined-up system, supervision models and educator capacity. Alongside considering the challenges to placement capacity, several areas of innovative practice owing to the pandemic were highlighted. Generated insights have shaped the aims and objectives of the Health Education (HEE) pre-registration AHP student practice learning programme for 2020/2021 and beyond. The COVID-19 pandemic has disrupted the delivery of AHP placements. In the absence of face-to-face activities, crowdsourcing provided an online data collection tool offering stakeholders an opportunity to engage with the placement capacity agenda and share learning. Findings have shaped the HEE approach to short-term placement recovery and long-term growth

Cytochrome oxidase subunit VI of Trypanosoma brucei is imported without a cleaved presequence and is developmentally regulated at both RNA and protein levels

Mitochondrial respiration in the African trypanosome undergoes dramatic developmental stage regulation. This requires co-ordinated control of components encoded by both the nuclear genome and the kinetoplast, the unusual mitochondrial genome of these parasites. As a model for understanding the co-ordination of these genomes, we have examined the regulation and mitochondrial import of a nuclear-encoded component of the cytochrome oxidase complex, cytochrome oxidase subunit VI (COXVI). By generating transgenic trypanosomes expressing intact or mutant forms of this protein, we demonstrate that COXVI is not imported using a conventional cleaved presequence and show that sequences at the N-terminus of the protein are necessary for correct mitochondrial sorting. Analyses of endogenous and transgenic COXVI mRNA and protein expression in parasites undergoing developmental stage differentiation demonstrates a temporal order of control involving regulation in the abundance of, first, mRNA and then protein. This represents the first dissection of the regulation and import of a nuclear-encoded protein into the cytochrome oxidase complex in these organisms, which were among the earliest eukaryotes to possess a mitochondrion

Exploring FlyBase Data Using QuickSearch.

FlyBase (flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This unit describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2016 by John Wiley & Sons, Inc

FlyBase 2.0: the next generation.

FlyBase (flybase.org) is a knowledge base that supports the community of researchers that use the fruit fly, Drosophila melanogaster, as a model organism. The FlyBase team curates and organizes a diverse array of genetic, molecular, genomic, and developmental information about Drosophila. At the beginning of 2018, 'FlyBase 2.0' was released with a significantly improved user interface and new tools. Among these important changes are a new organization of search results into interactive lists or tables (hitlists), enhanced reference lists, and new protein domain graphics. An important new data class called 'experimental tools' consolidates information on useful fly strains and other resources related to a specific gene, which significantly enhances the ability of the Drosophila researcher to design and carry out experiments. With the release of FlyBase 2.0, there has also been a restructuring of backend architecture and a continued development of application programming interfaces (APIs) for programmatic access to FlyBase data. In this review, we describe these major new features and functionalities of the FlyBase 2.0 site and how they support the use of Drosophila as a model organism for biological discovery and translational research