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The lightning talk and poster included here were presented at the 28th Annual Lorne Proteomics Symposium, February 2023. Traditional high performance computational infrastructure in Australia has not been designed for bioinformatics, and this presents challenges to many researchers in the life sciences, including proteomics. The Australian BioCommons has been engaging with members of the national proteomics community, including the Australasian Core Facilities group, since 2020 to understand the specific bioinformatics challenges facing researchers. Challenges noted include a lack of sufficient compute (memory, cores), an imbalance between the software available for model and non-model organisms, the constant tension presented by the need for both open source and proprietary software, and the presence of high intellectual barriers that prevent the community from adopting new solutions to their challenges, whether these solutions are software, hardware or policy based. In this presentation we will introduce the current scope of activities that the Australian BioCommons is coordinating in consultation with the Australian proteomics community that are aimed at addressing the challenges noted above. These activities range from development of discovery services for tools and workflows on local systems, deployment of tailored software and infrastructure that address proteomics requirements, establishing processes to allow information sharing with the broader community, and the beginnings of a collective national informatics training effort that supports the proteomics community. Specific examples include creating reusable/scalable DIA-NN workflows for use on a variety of computational infrastructures, and work with the freely accessible Galaxy Australia online bioinformatics workbench (https://usegalaxy.org.au/) to increase the size and complexity of possible MaxQuant analyses, make popular interactive tools like LFQanalyst available and expand the proteomics tool set available. Finally we are collectively exploring the use of the ARDC Nectar Cloud (https://ardc.edu.au/services/ardc-nectar-research-cloud/) for proteomics and development of a hosted proteomics-specific instance of Galaxy Australia. We invite the Australian proteomics community to join us in the on-going effort to make sure that they have a fit-for-purpose and meaningful slice of the computational pie: the right tools, workflows and reference data, accessible on suitable compute systems, so that we can collectively empower both experts and end users within Australian proteomics. If you would like to join the conversation, you are welcome at our new quarterly meeting series, where we discuss current community challenges and feature presentations from both local and international proteomics researchers. You can also join our Google Group: https://www.biocommons.org.au/proteomics

Please see attached file for experiment information.

The visual world provides a myriad of cues every instance that can be used to direct information processing. How does the brain integrate predictive information from disparate sources to modify visual priorities, and are combination strategies consistent across individuals? Previous evidence shows that sensory cues that are predictive of the value of a visually guided task (incentive value) and cues that signal where task-relevant stimuli may occur (spatial certainty) act independently to bias attention. Anticipatory accounts propose that both cues are comparably encoded into an attentional priority map, whereas the counterfactual account argues that incentive value cues instead induce a reactive encoding of losses based on the direction of attention. Here we adjudicate between these alternatives and further determine whether there are individual differences in how attentional cues are encoded. 149 participants viewed two coloured placeholders that specified the potential value of correctly identifying an imminent target if it appeared in that specific placeholder. Prior to the target’s presentation, an endogenous spatial cue indicated the target’s more likely location. The anticipatory and counterfactual accounts were used to motivate parametric regressors that were compared in their explanatory power of the observed data, at the group level and on data stratified by a clustering algorithm applied to identify individual differences. The algorithm revealed 2 subtypes in the population; whereas all individuals use spatial certainty cues a subset does not use incentive value cues. However, when used, the influence of incentive value cues reflects a counterfactual loss function. The data show that spatial certainty and incentive value act independently to influence visual priorities because they act at distinct points in information processing, and that theories of motivated attention must account for the non-uniform influence of incentive value on visual priorities.

Aims We aimed to determine how white blood cell (WBC) telomeres and telomere length change over time are associated with health status in type 1 diabetes. Methods Relative telomere length (rTL) was measured in WBC DNA from two time-points (median 6.8 years apart) in 618 individuals from the Finnish Diabetic Nephropathy Study by quantitative PCR, with interassay CV ≤ 4%. Results Baseline rTL correlated inversely with age and was shorter in men. Individuals in the shortest vs. longest rTL tertile had adverse cardiometabolic profiles, worse renal function, and were prescribed more antihypertensive and lipid-lowering drugs. While overall rTL tended to decrease during the median 6.8-years of follow-up, telomeres shortened in 55.3% of subjects, lengthened in 40.0%, and did not change in 4.7%. Baseline rTL correlated inversely with rTL change. Telomere lengthening was associated with higher HDL-Cholesterol (HDL-C), HDL-C/ApoA1, and with antihypertensive drug and (inversely) with lipid-lowering drug commencement during follow-up. Correlates of rTL percentage change per-annum (adjusted model) were baseline BMI, eGFR, previous retinal laser treatment, HDL-C, and HDL-C/ApoA1. Conclusions Telomere length measurements may facilitate the treatment and monitoring of the health status of individuals with type 1 diabetes.

Supplemental material, sj-pdf-2-las-10.1177_0023830920969735 for Intonational Variation in the North-West of England: The Origins of a Rising Contour in Liverpool by Claire Nance, Sam Kirkham, Kate Lightfoot and Luke Carroll in Language and Speech