ERDMAS: An exemplar-driven institutional research data management and analysis strategy

Devising fit-for-purpose research data management strategies within a university is challenging. This is because the five ‘Vs’ for generated research data; its Volume, Variety, Velocity, Veracity and its Value must be constantly considered. Invariably, a combination of data V's for any given research endeavour determine how best to manage it appropriately addressing archiving, compliance, security, privacy, sharing, reuse and so forth. As such, institutions are faced with defining, shaping and refining strategies and practicies to ensure there are consistent and adequate research data management polices and guidelines in place for their researchers. FAIR data principles are very important for embracing open data opportunities, but more broadly, research data management practices need to be established in a comprehensive way. Additionally, new ICT options have rapidly become available where institutions can make considered choices on whether to continue to use ‘on prem’, private Cloud or public Cloud infrastructure. If a hybrid approach is adopted, then the potential impact on existing institutional research data management strategies must be continually assessed and revised accordingly. Getting the balance right between developing a relevant institutional policy on the one hand yet also dynamically catering for the eclectic research data management and analytics needs of researchers and their evolving interactions with external collaborators on the other, must be continually navigated. In this manuscript, an exemplar-driven research data management and analytics conceptual framework is introduced. A key feature of this framework is that it is couched in two dimensions. On one axis is the ‘standard’ linear approach of developing the research data management policy, guidelines, procedures, audit and risk assessment and an options matrix. Importantly, a second axis comprising a researcher-driven focus is introduced where exemplar research activities are used to define ‘classes’ of research data management and analysis requirements. This exemplar-driven dimension enables an ongoing system-wide comparative review to occur in parallel that can continually inform policy and guidelines refinement

The genetics of symbiotic nitrogen fixation: comparative genomics of 14 Rhizobia Strains by resolution of protein clusters.

The symbiotic relationship between legumes and nitrogen fixing bacteria is critical for agriculture, as it may have profound impacts on lowering costs for farmers, on land sustainability, on soil quality, and on mitigation of greenhouse gas emissions. However, despite the importance of the symbioses to the global nitrogen cycling balance, very few rhizobial genomes have been sequenced so far, although there are some ongoing efforts in sequencing elite strains. In this study, the genomes of fourteen selected strains of the order Rhizobiales, all previously fully sequenced and annotated, were compared to assess differences between the strains and to investigate the feasibility of defining a core ?symbiome??the essential genes required by all rhizobia for nodulation and nitrogen fixation. Comparison of these whole genomes has revealed valuable information, such as several events of lateral gene transfer, particularly in the symbiotic plasmids and genomic islands that have contributed to a better understanding of the evolution of contrasting symbioses. Unique genes were also identified, as well as omissions of symbiotic genes that were expected to be found. Protein comparisons have also allowed the identification of a variety of similarities and differences in several groups of genes, including those involved in nodulation, nitrogen fixation, production of exopolysaccharides, Type I to Type VI secretion systems, among others, and identifying some key genes that could be related to host specificity and/or a better saprophytic ability. However, while several significant differences in the type and number of proteins were observed, the evidence presented suggests no simple core symbiome exists. A more abstract systems biology concept of nitrogen fixing symbiosis may be required. The results have also highlighted that comparative genomics represents a valuable tool for capturing specificities and generalities of each genome.bitstream/item/74069/1/ID-34062.pd

An Overview of the Adaptive Behaviour Profile in Young Children with Angelman Syndrome: Insights from the Global Angelman Syndrome Registry

Objectives: Angelman syndrome (AS) is a rare genetic disorder that affects the expression of the UBE3A gene within the central nervous system that profoundly impacts neurodevelopment. Individuals with AS experience significant challenges across multiple adaptive behaviour domains including communication, motor skills, and the ability to independently perform daily functions such as feeding, and toileting. Furthermore, persons with AS can demonstrate specific behaviours that limit their ability to participate within their social environment that vary with age. The aim of this paper is to explore the adaptive behaviour profile through parent report from the Global Angelman Syndrome Registry. Methods: Specific parent report data from the Global Angelman Syndrome Registry were analysed to explore the adaptive profile of 204 young children, under the age of 6 years old, with formal diagnoses of AS. Analysis of data focused on communication skills, gross and fine motor skills, daily self-care skills (feeding, toileting, and dressing), and behavioural characteristics. Several relationships were explored: (a) the age at which certain skills were first performed based on genotype; (b) abilities in motor and adaptive behaviours, according to age and genotype, and (c) the frequency at which children performed specific communication skills and the presence and frequency of challenging behaviours, across age and genotype. Results: We visually present the ages at which frequent speech, walking, and independent dressing and toileting were first mastered by children. Additionally, we provide in-depth descriptives of expressive and receptive communication skills (including the use of alternative communication forms), fine and gross motor skills, eating, dressing, toileting, anxiety, aggression, and other behavioural characteristics. Conclusions: This cross-sectional profile of adaptive skills in 204 young children with AS showcases that although many communication, motor and adaptive skills were determined by age, children with a non-deletion aetiology exhibited advantages in communication skills, which may have impacted upon subsequent adaptive skills. The use of parent report in the present study provides valuable insight into the adaptive behaviour profile of young children with AS

A new web-based genomics resource for bioinformatics analysis of Rhipicephalus (Boophilus) microplus: CattleTickBase

No abstract availabl

Microarray evidence for off target effects in tick RNA interference experiments, and the lack of strong correlation between DSRNA and antibody phenotypes in tick In vitro treatments for vaccine candidate screening

No abstract availabl

RDM+PM Checklist: Towards a Measure of Your Institution’s Preparedness for the Effective Planning of Research Data Management

A review at our institution and a number of other Australian universities was conducted to identify an optimal institutional-wide approach to Research Data Management (RDM). We found, with a few notable exceptions, a lack of clear policies and processes across institutes and no harmonisation in the approaches taken. We identified limited methods in place to cater for the development of Research Data Management Plans (RDMPs) across different disciplines, project types and no identifiable business intelligence (BI) for auditing or oversight. When interviewed, many researchers were not aware of their institution’s RDM policy, whilst others did not understand how it was relevant to their research. It was also discovered that primary materials (PM), which are often directly linked to the effective management of research data, were not well covered. Additionally, it was unclear in understanding who was the data custodian responsible for overall oversight, and there was a lack of clear guidance on the roles and responsibilities of researchers and their supervisors. These findings indicate that institutions are at risk in terms of meeting regulatory requirements and managing data effectively and safely. In this paper, we outline an alternative approach focusing on RDM ‘Planning’ rather than on RDMPs themselves. We developed simple-to-understand guidance for researchers on the redeveloped RDM policy, which was implemented via an online ‘RDM+PM Checklist’ tool that guides researchers and students. Moreover, as it is a structured tool, it provides real-time business intelligence that can be used to measure how compliant the organisation is and ideally identify opportunities for continuous improvement

Association between early and current gastro-intestinal symptoms and co-morbidities in children and adolescents with Angelman syndrome

Background Angelman syndrome (AS) is a neurogenetic disorder that causes severe intellectual disability, expressive language deficits, motor impairment, ataxia, sleep problems, epileptic seizures and a happy disposition. People with AS frequently experience gastrointestinal (GI) symptoms. Method This study used data from the Global Angelman Syndrome Registry to explore the relationship between early and current GI symptoms and co-morbidity in children and adolescents with AS (\u1d62f = 173). Two groups that experienced a high (\u1d62f = 91) and a low (\u1d62f = 82) frequency of GI symptoms were examined in relation to feeding and GI history in infancy, sleep and toileting problems, levels of language and communication and challenging behaviours. Predictors of GI symptoms were then investigated using a series of logistic regressions. Results This analysis found that constipation and gastroesophageal reflux affected 84% and 64%, of the sample, respectively. The high frequency of GI symptoms were significantly associated with: ‘refusal to nurse’, ‘vomiting’, ‘arching’, ‘difficulty gaining weight’, gastroesophageal reflux, ‘solid food transition’, frequency of night-time urinary continence and sleep hyperhidrosis during infancy. GI symptoms were not significantly associated with sleep, toileting, language or challenging behaviours. Significant predictors of high frequency GI symptoms were gastroesophageal reflux and sleep hyperhidrosis. Conclusions Future research needs to investigate the association between AS and GI co-morbidity in adults with AS

Exploring the transcriptomic data of the Australian paralysis tick, Ixodes holocyclus

Ixodes holocyclus is the paralysis tick commonly found in Australia. I. holocyclus does not cause paralysis in the primary host – bandicoots, but markedly affects secondary hosts such as companion animals, livestock and humans. Holocyclotoxins are the neurotoxin molecules in I. holocyclus responsible for paralysis symptoms. There is a limited understanding of holocyclotoxins due to the difficulties in purifying and expressing these toxins in vitro. Next-generation sequencing technologies were utilised for the first time to generate transcriptome data from two cDNA samples –salivary glands samples collected from female adult ticks engorged on paralysed companion animals and on bandicoots. Contigencoded proteins in each library were annotated according to their best BLAST match against several databases and functionally assigned into six protein categories: housekeeping, transposable elements, pathogen-related, hypothetical, secreted and novel. The “secreted protein” category is comprised of ten protein families: enzymes, protease inhibitors, antigens, mucins, immunity-related, lipocalins, glycinerich, putative secreted, salivary and toxin-like. Comparisons of contig representation between the two libraries reveal the differential expression of tick proteins collected from different hosts. This study provides a preliminary description of the I. holocyclus tick salivary gland transcriptome

A platform in the use of medicines to treat chronic hepatitis C (PLATINUM C) protocol for a prospective treatment registry of real world o

Background Safe, highly curative, short course, direct acting antiviral (DAA) therapies are now available to treat chronic hepatitis C. DAA therapy is freely available to all adults chronically infected with the hepatitis C virus (HCV) in Australia. If left untreated, hepatitis C may lead to progressive hepatic fibrosis, cirrhosis and hepatocellular carcinoma. Australia is committed to eliminating hepatitis as a public health threat by 2030 set by the World Health Organization. However, since the introduction of funded DAA treatment, uptake has been suboptimal. Australia needs improved strategies for testing, treatment uptake and treatment completion to address the persisting hepatitis C public health problem. PLATINUM C is a HCV treatment registry and research platform for assessing the comparative effectiveness of alternative interventions for achieving virological cure. Methods PLATINUM C will prospectively enrol people with active HCV infection confirmed by recent detection of HCV ribonucleic acid (RNA) in blood. Those enrolled will agree to allow standardised collection of demographic, lifestyle, treatment, virological outcome and other relevant clinical data to better inform the future management of HCV infection. The primary outcome is virological cure evidenced by sustained virological response (SVR), which is defined as a negative HCV PCR result 6 to 18 months after initial prescription of DAA therapy and no less than 12 weeks after the completion of treatment. Study participants will be invited to opt-in to medication adherence monitoring and quality of life assessments using validated self-reported instruments (EQ-5D-5L). Discussion PLATINUM C is a treatment registry and platform for nesting pragmatic trials. Data collected will inform the design, development and implementation of pragmatic trials. The digital infrastructure, study procedures and governing systems established by the registry will allow PLATINUM C to support a wider research platform in the management of hepatitis C in primary care. Trial registration The trial is registered with the Australia and New Zealand Clinical Trials Register (ACTRN12619000023156). Date of registration: 10/01/2019

BarleyVarDB: a database of barley genomic variation

Barley (Hordeum vulgare L.) is one of the first domesticated grain crops and represents the fourth most important cereal source for human and animal consumption. BarleyVarDB is a database of barley genomic variation. It can be publicly accessible through the website at http://146.118.64.11/BarleyVar. This database mainly provides three sets of information. First, there are 57 754 224 single nuclear polymorphisms (SNPs) and 3 600 663 insertions or deletions (InDels) included in BarleyVarDB, which were identified from high-coverage whole genome sequencing of 21 barley germplasm, including 8 wild barley accessions from 3 barley evolutionary original centers and 13 barley landraces from different continents. Second, it uses the latest barley genome reference and its annotation information publicly accessible, which has been achieved by the International Barley Genome Sequencing Consortium (IBSC). Third, 522 212 whole genome-wide microsatellites/simple sequence repeats (SSRs) were also included in this database, which were identified in the reference barley pseudo-molecular genome sequence. Additionally, several useful web-based applications are provided including JBrowse, BLAST and Primer3. Users can design PCR primers to asses polymorphic variants deposited in this database and use a user-friendly interface for accessing the barley reference genome. We envisage that the BarleyVarDB will benefit the barley genetic research community by providing access to all publicly available barley genomic variation information and barley reference genome as well as providing them with an ultra-high density of SNP and InDel markers for molecular breeding and identification of functional genes with important agronomic traits in barley. Database URL: http://146.118.64.11/BarleyVa