Description: Background: Although cardiovascular disease is the major cause of premature death among Indigenous peoples in several advanced economies, no acute coronary syndrome (ACS) risk models have been validated in Indigenous populations. We tested the validity and calibration of three Global Registry of Acute Coronary Events (GRACE) scores among Aboriginal and non-Aboriginal Australians. Methods: GRACE scores were calculated at admission or discharge using clinical data, with all-cause deaths obtained from data linkage. Scores for GRACE models were validated for; 1) in-hospital death, 2) death within 6 months from admission or 3) death within 6 months of discharge (this also for 1 and 5-years mortality). Results: Aboriginal patient were younger (62 % aged

Description: Background: Aboriginal people have a disproportionately higher incidence rate of ischaemic heart disease (IHD) than non-Aboriginal people. The findings on Aboriginal disparity in receiving coronary artery procedures are inconclusive. We describe the profile and transfers of IHD patients admitted to rural hospitals as emergency admissions and investigate determinants of transfers and coronary angiography. Methods: Person-linked hospital and mortality records were used to identify 28-day survivors of IHD events commencing at rural hospitals in Western Australia. Outcome measures were receipt of coronary angiography, transfer to a metropolitan hospital, and coronary angiography if transferred to a metropolitan hospital. Results: Compared to non-Aboriginal patients, Aboriginal patients with IHD were more likely to be younger, have more co-morbidities, reside remotely, but less likely to have private insurance. After adjusting for demographic characteristics, Aboriginal people with MI were less likely to be transferred to a metropolitan hospital, and if transferred were less likely to receive coronary angiography. These disparities were not significant after adjusting for comorbidities and private insurance. In the full multivariate model age, comorbidities and private insurance were adversely associated with transfer to a metropolitan hospital and coronary angiography. Conclusion: Disparity in receiving coronary angiography following emergency admission for IHD to rural hospitals is mediated through the lower likelihood of being transferred to metropolitan hospitals where this procedure is performed. The likelihood of a transfer is increased if the patient has private insurance, however, rural Aboriginal people have a lower rate of private insurance than their non-Aboriginal counterparts. Health practitioners and policy makers can continue to claim that they treat Aboriginal and non-Aboriginal people alike based upon clinical indications, as private insurance is acting as a filter to reduce rural residents accessing interventional cardiology. If health practitioners and policy makers are truly committed to reducing health disparities, they must reflect upon the broader systems in which disparity is perpetuated and work towards a systems improvement.

Description: A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share 〉95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), 〉95% identity based on multiple alignment genes, 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups.

Description: Background: Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat. Results: Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages. Conclusions: Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale.

Description: Background: Salinivibrios are moderately halophilic bacteria found in salted meats, brines and hypersaline environments. We obtained three novel conspecific Salinivibrio strains closely related to S. costicola, from Socompa Lake, a high altitude hypersaline Andean lake (approx. 3,800 meters above the sea level). Results: The three novel Salinivibrio spp. were extremely resistant to arsenic (up to 200 mM As), NaCl (up to 15%), and UV-B radiation (19 KJ/m2, corresponding to 240 minutes of exposure) by means of phenotypic tests. Our subsequent draft genome ionsequencing and RAST-based genome annotation revealed the presence of genes related to arsenic, NaCl, and UV radiation resistance. The three novel Salinivibrio genomes also had the xanthorhodopsin gene cluster phylogenetically related to Marinobacter and Spiribacter. The genomic taxonomy analysis, including multilocus sequence analysis, average amino acid identity, and genome-to-genome distance revealed that the three novel strains belong to a new Salinivibrio species. Conclusions: Arsenic resistance genes, genes involved in DNA repair, resistance to extreme environmental conditions and the possible light-based energy production, may represent important attributes of the novel salinivibrios, allowing these microbes to thrive in the Socompa Lake.

Description: Sequential biopsy of breast cancer is used to assess biomarker effects and drug efficacy. The preoperative “window of opportunity” setting is advantageous to test biomarker changes in response to therapeutic a...

Description: © 2008 Riley et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 9 (2008): 210, doi:10.1186/1471-2164-9-210.

Description: The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins, at least one more than other bacteria, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3) there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4) one of the previously unseen clusters of proteins has a high proportion of "orphan" hypothetical proteins, raising the possibility these are cold-specific proteins. Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2) P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3) P. ingrahamii has a large number (11) of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4) Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5) Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study. The results of this genomic analysis provide a springboard for further investigations into mechanisms of psychrophily. Focus on the role of asparagine excess in proteins, targeted phenotypic characterizations and gene expression investigations are needed to ascertain if and how the organism regulates various proteins in response to growth at lower temperatures.

Description: MR acknowledges support from DE-FG02-04ER63940. JTS acknowledges the support from the University of Washington NASA NAI program and the NSF Astrobiology IGERT program. TZW acknowledges support from a grant from the Fondation Fourmentin-Guilbert and AD acknowledges support from the European Union BioSapiens Network of Excellence, Grant LSHG CT-2003-503265

Description: Background: The number of patients with advanced chronic kidney disease opting for conservative management rather than dialysis is unknown but likely to be growing as increasingly frail patients with advanced renal disease present to renal services. Conservative kidney management includes ongoing medical input and support from a multidisciplinary team. There is limited evidence concerning patient and carer experience of this choice. This study will explore quality of life, symptoms, cognition, frailty, performance decision making, costs and impact on carers in people with advanced chronic kidney disease managed without dialysis and is funded by the National Institute of Health Research in the UK. Methods: In this prospective, multicentre, longitudinal study, patients will be recruited in the UK, by renal research nurses, once they have made the decision not to embark on dialysis. Carers will be asked to ‘opt-in’ with consent from patients. The approach includes longitudinal quantitative surveys of quality of life, symptoms, decision making and costs for patients and quality of life and costs for carers, with questionnaires administered quarterly over 12 months. Additionally, the decision making process will be explored via qualitative interviews with renal physicians/clinical nurse specialists.DiscussionThe study is designed to capture patient and carer profiles when conservative kidney management is implemented, and understand trajectories of care-receiving and care-giving with the aim of optimising palliative care for this population. It will explore the interactions that lead to clinical care decisions and the impact of these decisions on informal carers with the intention of improving clinical outcomes for patients and the experiences of care givers.

Description: Background: In Australia, the two major pathways of refugee entry are the United Nations High Commissioner for Refugees resettlement programme and irregular maritime arrivals (IMAs) seeking asylum. The Australian Government’s policies towards IMAs since July 2013 are controversial, uncompromising and consistently harsh, with asylum seekers held in detention centres for prolonged periods. Refugees and asylum seekers have distinct and unique stressors that make resettlement difficult. Methods: This exploratory study examines resettlement experiences for refugee youth in Western Australia using the psychosocial conceptual framework and qualitative methods. Focus group discussions and key informant interviews were undertaken with verbatim transcripts analysed using thematic analysis to identify themes. Results: Themes documented that language and its impact, and experience with education, health, and social activities, support structures provided to youth and supporting future aspirations as critical to successful resettlement. This exploratory study contributes to developing a broader understanding of the resettlement experiences of refugee youth, drawing on their current and past experiences, cultural differences and mechanisms for coping. Conclusion: Fluency in English language, especially spoken, was a facilitator of successful resettlement. Our results align with previous studies documenting that support programs are vital for successful resettlement. Although faced with immense difficulties refugee youth are resilient, want to succeed and have aspirations for the future. Strategies and recommendations suggested by refugee youth themselves could be used for developing interventions to assist successful resettlement.

Description: Background: It is often recommended that behaviour-change interventions be tailored to barriers. There is a scarcity of research into the best method of barrier identification, although combining methods has been suggested to be beneficial. This paper compares the feasibility and costs of three different methods of barrier identification used in three implementation projects conducted in primary care. Methods: Underpinned by a theory-base, project one used a questionnaire and interviews; project two used a single focus group and questionnaire, and project three used a literature review of published barriers. The feasibility of each project, as experienced by the research team, and labour costs are summarised. Results: The literature review of published barriers was the least costly and most feasible method, being quick to conduct and avoiding the challenges of recruitment experienced when using interviews or a questionnaire. The feasibility of using questionnaires was further reduced by the time taken to develop the instruments. Conducting a single focus group was also found to be a more feasible method, taking less time than interviews to collect and analyse the barriers. Conclusions: Considering the ease of recruitment, time required and cost of the different methods to collect barriers is crucial at the start of implementation studies. The literature review method is the least costly and most feasible method. Use of a single focus group was found to be more feasible than conducting individual interviews or administering a questionnaire, with less recruitment challenges experienced, and quicker data collection. Future research would benefit from comparing the robustness of the methods in terms of the comprehensiveness of barriers identified.