Interaction of ENSO-driven Flood Variability and Anthropogenic Changes in Driving Channel Evolution: Corryong/ Nariel Creek, Australia

This is an Accepted Manuscript of an article published by Taylor & Francis in Australian Geographer on 03/09/2015, available online: 10.1080/00049182.2015.1048595Understanding the relative contributions of climatic and anthropogenic drivers of channel change are important to inform river management, especially in the context of environmental change. This global debate is especially pertinent in Australia as catchments have been severely altered since recent European settlement, and there is also strong evidence of cyclical climate variability controlling environmental systems. Corryong/Nariel Creek is an ideal setting to further study the interaction between climate and anthropogenic changes on channel evolution as it has experienced both significant periods of flood and drought, controlled by the El Niño Southern Oscillation (ENSO), and extensive anthropogenic changes. Since European settlement the floodplain has been completely cleared, the riparian zone almost entirely invaded by willows, and every reach of the channel has experienced some form of direct channel modification. Through the combined analysis of channel evolution, climate changes and anthropogenic history of the river it was found that both the ENSO-driven climate and anthropogenic drivers are significant, although at different scales of channel change. Significant straightening in response to land clearing in the early twentieth century occurred before any records of direct channel modifications. Following this, most river management works were in response to instabilities created in the clearing period, or to instabilities created by flooding triggering a new phase of instability in reaches which had already undergone stabilisation works. Overall, human activities triggered channel instability via land clearing, and management works since then generally exacerbated erosion during high flows that are driven by climate fluctuations. This research raises the interesting question of whether rivers in Australia have become more responsive to the ENSO cycle since the clearing of catchment and riparian vegetation, or whether the past response to climate variability was different

Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines

Publisher Copyright: © 2022We combined functional genomics and human genetics to investigate processes that affect type 1 diabetes (T1D) risk by mediating beta cell survival in response to proinflammatory cytokines. We mapped 38,931 cytokine-responsive candidate cis-regulatory elements (cCREs) in beta cells using ATAC-seq and snATAC-seq and linked them to target genes using co-accessibility and HiChIP. Using a genome-wide CRISPR screen in EndoC-βH1 cells, we identified 867 genes affecting cytokine-induced survival, and genes promoting survival and up-regulated in cytokines were enriched at T1D risk loci. Using SNP-SELEX, we identified 2,229 variants in cytokine-responsive cCREs altering transcription factor (TF) binding, and variants altering binding of TFs regulating stress, inflammation, and apoptosis were enriched for T1D risk. At the 16p13 locus, a fine-mapped T1D variant altering TF binding in a cytokine-induced cCRE interacted with SOCS1, which promoted survival in cytokine exposure. Our findings reveal processes and genes acting in beta cells during inflammation that modulate T1D risk.Peer reviewe

Visualization of Shared Genomic Regions and Meiotic Recombination in High-Density SNP Data

A fundamental goal of single nucleotide polymorphism (SNP) genotyping is to determine the sharing of alleles between individuals across genomic loci. Such analyses have diverse applications in defining the relatedness of individuals (including unexpected relationships in nominally unrelated individuals, or consanguinity within pedigrees), analyzing meiotic crossovers, and identifying a broad range of chromosomal anomalies such as hemizygous deletions and uniparental disomy, and analyzing population structure.We present SNPduo, a command-line and web accessible tool for analyzing and visualizing the relatedness of any two individuals using identity by state. Using identity by state does not require prior knowledge of allele frequencies or pedigree information, and is more computationally tractable and is less affected by population stratification than calculating identity by descent probabilities. The web implementation visualizes shared genomic regions, and generates UCSC viewable tracks. The command-line version requires pedigree information for compatibility with existing software and determining specified relationships even though pedigrees are not required for IBS calculation, generates no visual output, is written in portable C++, and is well-suited to analyzing large datasets. We demonstrate how the SNPduo web tool identifies meiotic crossover positions in siblings, and confirm our findings by visualizing meiotic recombination in synthetic three-generation pedigrees. We applied SNPduo to 210 nominally unrelated Phase I / II HapMap samples and, consistent with previous findings, identified six undeclared pairs of related individuals. We further analyzed identity by state in 2,883 individuals from multiplex families with autism and identified a series of anomalies including related parents, an individual with mosaic loss of chromosome 18, an individual with maternal heterodisomy of chromosome 16, and unexplained replicate samples.SNPduo provides the ability to explore and visualize SNP data to characterize the relatedness between individuals. It is compatible with, but distinct from, other established analysis software such as PLINK, and performs favorably in benchmarking studies for the analyses of genetic relatedness

Call volume, triage outcomes, and protocols during the first wave of the COVID-19 pandemic in the United Kingdom: Results of a national survey

Objectives During the first wave of the COVID-19 pandemic in the United Kingdom (UK), to describe volume and pattern of calls to emergency ambulance services, proportion of calls where an ambulance was dispatched, proportion conveyed to hospital, and features of triage used. Methods Semistructured electronic survey of all UK ambulance services (n = 13) and a request for routine service data on weekly call volumes for 22 weeks (February 1–July 3, 2020). Questionnaires and data request were emailed to chief executives and research leads followed by email and telephone reminders. The routine data were analyzed using descriptive statistics, and questionnaire data using thematic analysis. Results Completed questionnaires were received from 12 services. Call volume varied widely between services, with a UK peak at week 7 at 13.1% above baseline (service range -0.5% to +31.4%). All services ended the study period with a lower call volume than at baseline (service range -3.7% to -25.5%). Suspected COVID-19 calls across the UK totaled 604,146 (13.5% of all calls), with wide variation between services (service range 3.7% to 25.7%), and in service peaks of 11.4% to 44.5%. Ambulances were dispatched to 478,638 (79.2%) of these calls (service range 59.0% to 100.0%), with 262,547 (43.5%) resulting in conveyance to hospital (service range 32.0% to 53.9%). Triage models varied between services and over time. Two primary call triage systems were in use across the UK. There were a large number of products and arrangements used for secondary triage, with services using paramedics, nurses, and doctors to support decision making in the call center and on scene. Frequent changes to triage processes took place. Conclusions Call volumes were highly variable. Case mix and workload changed significantly as COVID-19 calls displaced other calls. Triage models and prehospital outcomes varied between services. We urgently need to understand safety and effectiveness of triage models to inform care during further waves and pandemics.Additional co-authors: Andy Newton, Alison Porter, Tom Quinn, Andy Rosser, Aloysius Niroshan Siriwardena, Robert Spaight, Victoria William