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Adaptive strategies of soil viruses in oligotrophic arid environments
No full textIn natural environments, viruses must adapt to changing conditions such as variations in nutrient and water availability. However, our understanding of viral adaptation to different soil conditions remains limited. We compared soil viral adaptations in nutrient-limited arid inland regions versus nutrient-rich humid coastal regions using viromics. Our results provide new evidence that viruses employed diverse strategies to persist in oligotrophic arid environments. These strategies include (i) a higher prevalence of potential lysogenic viruses; (ii) a broader host range to enhance infection chances; (iii) encoding specific auxiliary metabolic genes to enhance viral fitness by boosting host resilience against nutrient limitation and aridity; and (iv) maintaining higher micro-diversity and more genes under positive selection to improve viral responses to inhospitable conditions
The Banksia plot: a method for visually comparing point estimates and confidence intervals across datasets
No full textOBJECTIVES: In research evaluating statistical analysis methods, a common aim is to compare point estimates and CIs calculated from different analyses. This can be challenging when the outcomes (and their scale ranges) differ across datasets. We therefore developed a graphical method, the "Banksia plot", to facilitate pairwise comparisons of different statistical analysis methods by plotting and comparing point estimates and CIs from each analysis method, both within and across datasets. STUDY DESIGN AND SETTING: The plot is constructed in three stages. Stage 1: To compare the results of two statistical analysis methods, for each dataset, the point estimate from the reference analysis method is centered on zero, and its confidence limits are scaled to range from -0.5 to 0.5. The same centering and scale adjustment values are then applied to the corresponding comparator analysis point estimate and confidence limits. Stage 2: A Banksia plot is constructed by plotting the centered and scaled point estimates from the comparator method for each dataset on a rectangle centered at zero, ranging from -0.5 to 0.5, which represents the reference method results. Stage 3: Optionally, a matrix of Banksia plots is graphed, showing all pairwise comparisons from multiple analysis methods. We illustrate the Banksia plot using two examples. RESULTS: Illustration of the Banksia plot demonstrates how the plot makes it immediately apparent whether there are differences in point estimates and CIs when using different analysis methods (example 1) or different data extractors (example 2). Furthermore, we demonstrate how different bases for ordering the CIs can be used to highlight particular differences (ie, in point estimates or CI widths). CONCLUSION: The Banksia plot provides a visual summary of pairwise comparisons of different analysis methods, allowing patterns and trends in the point estimates and CIs to be easily identified
Spatial Transcriptomics of CD8+ T cells within Breast Cancer
No full text© 2025 Justine SeowTumour-infiltrating CD8+ T lymphocytes (TILs) play a pivotal role in breast cancer immunity, making them key targets for immunotherapy. However, TILs exist in distinct functional states: exhausted T (TEX) cells, which lose their ability to combat tumours, and tissue-resident memory T (TRM) cells, which remain functionally active and correlate with improved patient survival. Despite the therapeutic potential of TRM cells, their spatial distribution and interactions within the tumour microenvironment (TME) remain poorly understood. This study integrates single-cell RNA sequencing (scRNA-seq) and panel-based spatial imaging (Visium and Xenium) to map the niches occupied by TRM and TEX cells in breast cancer. The TME is a highly heterogeneous landscape, where immune cells interact with malignant, stromal, and endothelial populations in spatially organised patterns. Recent studies highlight that structured immune cell arrangements are linked to better immunotherapy responses, reinforcing the importance of spatial context.
Panel-based spatial transcriptomics is inherently limited by gene selection, which impacts its ability to accurately resolve specific immune populations. Current pre-designed panels may not fully capture the genes necessary for distinguishing functionally distinct CD8+ T cell subsets. To address this challenge, we developed Xenium Panel Generation (XPG) - a computational tool for optimising gene panels, allowing researchers to tailor gene selection to their specific biological questions. This tool along with recent improvements in Xenium technologies, improved the identification of TRM and TEX cells within spatial datasets, enabling higher-resolution mapping of immune-tumour interactions. T cells infiltrate the TME, where local cellular interactions and spatial positioning shape their function and drive their differentiation. Currently, no panel-based spatial transcriptomics studies have mapped TRM and TEX cells in breast cancer. These subsets are transcriptionally similar, and conventional protein-based imaging techniques like immunofluorescence, which rely on small antibody panels, lack the resolution to reliably distinguish between them. This research aims to fill this gap by identifying the distinct spatial niches and cell type enrichment within the neighbourhood of TRM and TEX population that shapes their function. By elucidating the localisation and signalling environments of these cells, this study will enhance patient stratification and inform targeted immunotherapies
Development and Validation of the Intimate Partner Sexual Violence Scale (IPSVS): A Multi-Dimensional Scale to Measure Sexual Violence in Intimate Relationships
No full textIntimate partner sexual violence (IPSV) is defined as any non-consensual sexual behavior perpetrated within an intimate relationship. It is overwhelmingly perpetrated by men against women and causes significant harm to the health and wellbeing of victim/survivors. Although it is generally accepted that IPSV is globally prevalent, to date, comprehensive instruments to measure IPSV have been lacking. Moreover, existing measurement tools have largely failed to capture the diversity of perpetrator tactics, the deeply degrading and dehumanizing nature of many IPSV behaviors, and the role of perpetrator intent. As a result, there is a dearth of robust quantitative data to help understand the nature and magnitude of the problem. This article describes the development of a new multi-dimensional measurement tool-the Intimate Partner Sexual Violence Scale (IPSVS). The IPSVS is grounded in qualitative evidence from victim/survivors and examines IPSV as a multi-dimensional phenomenon with perpetrator intent as a central organizing principle. Following consultation with experts, a representative sample of 702 women victim/survivors in Australia completed an online survey including 34 IPSV behaviors to establish reliability and validity of the items. Exploratory factor analysis revealed 20 items across 3 factors-"Dominance and humiliation," "Emotional coercion," and "Aggressive indifference"-explaining 52.681% of the variance. Cronbach's alphas ranged from .741 to .890. These domains highlight that different perpetrator motivations may underlie different types of IPSV, challenging the predominant classification of IPSV according to severity or level of physical harm. The IPSVS has the potential to dramatically improve measurement of sexual violence in intimate relationships and has important implications for future research and practice
Myeloid cell genome-wide screen identifies variants associated with Mycobacterium tuberculosis–induced cytokine transcriptional responses
No full textImmune and clinical outcomes to Mycobacterium tuberculosis (Mtb) infection vary greatly between individuals, yet the underlying genetic and cellular mechanisms driving this heterogeneity remain poorly understood. We performed a cellular genome-wide association study to identify genetic variants associated with Mtb-induced monocyte transcriptional expression of IL1B, IL6, TNF, and IFNB1 via RNA-Seq in a Ugandan cohort. Significantly associated variants were assessed for transferability in an independent Seattle cohort, further validated in vitro, and assessed for clinical phenotype associations. We identified 77 loci suggestively associated with Mtb-induced cytokine expression in monocytes in Uganda. SNPs associated with Mtb-induced TNF were enriched within α-linolenic acid metabolism pathway genes, which was validated in vitro using PLA2 inhibitors. Four loci maintained significant associations in Seattle. We validated a cytokine effect with siRNA knockdown for two of these loci, which mapped to the genes SLIT3 and SLC1A1. Furthermore, exogenous treatment of macrophages with SLIT3 enhanced Mtb intracellular replication. Finally, SLC1A1 and SLIT3 variants were associated with susceptibility to tuberculous meningitis and subsequent survival, respectively, in a Vietnamese cohort. In summary, we identified multiple variants and pathways associated with Mtb-induced cytokine transcriptional responses that were validated in vitro and were associated with clinical tuberculosis susceptibility
Bacterivorous Nematodes Drive Ammonification and Bacterial Community Growth in a Strongly Acidic Soil
No full textNematodes, the most abundant animals on Earth, play a vital role in the soil biosphere by regulating microbial communities and influencing nutrient cycling. However, their grazing impact on soil nitrogen (N) cycling and microbial communities remains insufficiently understood. In this study, we addressed this knowledge gap through a microcosm experiment using gamma-sterilised acidic soil (pH < 4.5), inoculated with either microbial suspension alone or in combination with low or high concentrations of nematodes. Our results revealed that nematodes significantly increased soil NH₄⁺–N content and bacterial abundance, with bacterivorous nematodes increasingly dominating the microcosm environment. This study provides new evidence that bacterivorous nematodes significantly enhance ammonification in acidic soil, with implications for soil N availability and agricultural productivity
Bushfire Impact on Drinking Water Distribution Networks and Investigation Methods: A Review
No full textAbstract
Bushfire events can directly and indirectly impact drinking water distribution networks. Water authorities around the world have experienced compromised water supply and quality in the aftermath of recent bushfires, necessitating costly investigation and repair. Future climate models predict an escalation of bushfire weather events with a significant increase in the severity and frequency in many regions, for which water authorities must now prepare. Currently, there is no systematic review on the impact that bushfires can have on drinking water networks and how these impacts can be evaluated and investigated. The current study provides a systematic review of academic literature, agency response, water operator reports and media releases on these two emerging topics. On bushfire impacts, the review focuses on the physical impact to water assets, potential risk to water quality in the distribution network, and possible interruptions to water supply. On evaluation and investigation methods, the review summarizes available testing methods for evaluating physical damages to assets, identification of chemical or biological contaminants that may compromise water quality, and the identification of, or elective, interruption of water service. Gaps in our knowledge on how drinking water assets are physically damaged and how services are interrupted due to water quality testing or results are also identified to inform water operators, government agencies and researchers. Further research into the impact of bushfire temperature and duration on various types of pipe materials exposed is discussed
Estimating the longitudinal association between pain characteristics and clinical outcomes in young people with mental ill-health
No full textBACKGROUND: Mental ill-health has a major impact on young people, with pain often co-occurring. We estimated the prevalence and impact of pain in young people with mental ill-health. METHODS: Longitudinal data (baseline and three-month follow-up) of 1,107 Australian young people (aged 12-25 years) attending one of five youth mental health services. Multi-level linear mixed models estimated associations between pain characteristics (frequency, intensity, and limitations) and outcomes with false discovery rate (FDR) adjustment. Pain characteristics were baseline-centered to estimate if the baseline score (between-participant effect) and/or change from baseline (within-participant effect) was associated with outcomes. RESULTS: At baseline, 16% reported serious pain more than 3 days, 51% reported at least moderate pain, and 25% reported pain-related activity limitations in the last week. Between participants, higher serious pain frequency was associated with greater anxiety symptoms (β[95%CI]: 0.90 [0.45, 1.35], FDR-p=0.001), higher pain intensity was associated with greater symptoms of depression (1.50 [0.71, 2.28], FDR-p=0.001), anxiety (1.22 [0.56, 1.89], FDR-p=0.002), and suicidal ideation (3.47 [0.98, 5.96], FDR-p=0.020), and higher pain limitations were associated with greater depressive symptoms (1.13 [0.63, 1.63], FDR-p<0.001). Within participants, increases in pain intensity were associated with increases in tobacco use risk (1.09 [0.48, 1.70], FDR-p=0.002), and increases in pain limitations were associated with increases in depressive symptoms (0.99 [0.54, 1.43], FDR-p<0.001) and decreases in social and occupational functioning (-1.08 [-1.78, -0.38], FDR-p=0.009). CONCLUSIONS: One-in-two young people seeking support for mental ill-health report pain. Youth mental health services should consider integrating pain management
Seven-year-old beginner cellists’ lived experiences of music performance
No full textMusic performance is a demanding activity requiring complex coordination of abilities from diverse domains. It can be perceived as a form of artistic expression and communication but experienced as a demonstration of personal competency with emotional ramifications that affect musicians’ ongoing interest and motivations. Participating in music performance is often a key part of musical development; however, children’s perspectives on formative experiences of music performance during early learning are largely unknown. Given the broad range of interacting factors and significant implications, understanding musicians’ performance experiences, particularly for child learners, is vital to support sustained engagement. The present study investigated 14 seven-year-old beginner cellists’ experiences of music performance during the first 18 months of tuition via a novel combination of Interpretative Phenomenological Analysis and Participatory Action Research methodologies. Three superordinate themes emerged: (1) feelings of arousal and emotional valence during performance, (2) the identification of four distinct performance environments, and (3) the impact of performance experiences in each environment on children’s personal development, including fostering autonomy, agency, confidence, altruism, and social connection. The findings have pedagogical implications for how educators and parents of novice musicians in middle childhood can provide safe music learning environments with varied means of engaging in a range of supportive performance opportunities
