Variation in the OC locus of Acinetobacter baumannii genomes predicts extensive structural diversity in the Lipooligosaccharide

Lipooligosaccharide (LOS) is a complex surface structure that is linked to many pathogenic properties of Acinetobacter baumannii. In A. baumannii, the genes responsible for the synthesis of the outer core (OC) component of the LOS are located between ilvE and aspS. The content of the OC locus is usually variable within a species, and examination of 6 complete and 227 draft A. baumannii genome sequences available in GenBank non-redundant and Whole Genome Shotgun databases revealed nine distinct new types, OCL4-OCL12, in addition to the three known ones. The twelve gene clusters fell into two distinct groups, designated Group A and Group B, based on similarities in the genes present. OCL6 (Group B) was unique in that it included genes for the synthesis of L-Rhamnosep. Genetic exchange of the different configurations between strains has occurred as some OC forms were found in several different sequence types (STs). OCL1 (Group A) was the most widely distributed being present in 18 STs, and OCL6 was found in 16 STs. Variation within clones was also observed, with more than one OC locus type found in the two globally disseminated clones, GC1 and GC2, that include the majority of multiply antibiotic resistant isolates. OCL1 was the most abundant gene cluster in both GC1 and GC2 genomes but GC1 isolates also carried OCL2, OCL3 or OCL5, and OCL3 was also present in GC2. As replacement of the OC locus in the major global clones indicates the presence of sub-lineages, a PCR typing scheme was developed to rapidly distinguish Group A and Group B types, and to distinguish the specific forms found in GC1 and GC2 isolates.

Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1

Acinetobacter baumannii isolate A1 was recovered in the United Kingdom in 1982 and belongs to global clone 1 (GC1). Here, we present its complete 3.91-Mbp genome sequence, generated via a combination of short-read sequencing (Illumina), long-read sequencing (PacBio), and manual finishing.

7-point Subjective Global Assessment is more time sensitive than conventional Subjective Global Assessment in detecting nutrition changes

Background: It is important for nutrition intervention in malnourished patients to be guided by accurate evaluation and detection of small changes in the patient’s nutrition status over time. However, the current Subjective Global Assessment (SGA) is not able to detect changes in a short period of time. The aim of the study was to determine whether 7-point SGA is more time sensitive to nutrition changes than the conventional SGA. Methods: In this prospective study, 67 adult inpatients assessed as malnourished using both the 7-point SGA and conventional SGA were recruited. Each patient received nutrition intervention and was followed up post-discharge. Patients were reassessed using both tools at 1, 3 and 5 months from baseline assessment. Results: It took significantly shorter time to see a one-point change using 7-point SGA compared to conventional SGA (median: 1 month vs. 3 months, p = 0.002). The likelihood of at least a one-point change is 6.74 times greater in 7-point SGA compared to conventional SGA after controlling for age, gender and medical specialties (odds ratio = 6.74, 95% CI 2.88-15.80, p<0.001). Fifty-six percent of patients who had no change in SGA score had changes detected using 7-point SGA. The level of agreement was 100% (k = 1, p < 0.001) between 7-point SGA and 3-point SGA and 83% (k=0.726, p<0.001) between two blinded assessors for 7-point SGA. Conclusion: The 7-point SGA is more time sensitive in its response to nutrition changes than conventional SGA. It can be used to guide nutrition intervention for patients.

Choose wisely: Network, ontology and annotation resources for the analysis of Staphylococcus aureus omics data

Staphylococcus aureus (S. aureus) is a prominent human and livestock pathogen investigated widely using omic technologies. Critically, due to availability, low visibility or scattered resources, robust network and statistical contextualisation of the resulting data is generally under-represented. Here, we present novel meta-analyses of freely-accessible molecular network and gene ontology annotation information resources for S. aureus omics data interpretation. Furthermore, through the application of the gene ontology annotation resources we demonstrate their value and ability (or lack-there-of) to summarise and statistically interpret the emergent properties of gene expression and protein abundance changes using publically available data. This analysis provides simple metrics for network selection and demonstrates the availability and impact that gene ontology annotation selection can have on the contextualisation of bacterial omics data.

Quality assurance of assessment and moderation discourses involving sessional staff

Quality assurance is a major agenda in tertiary education. The casualisation of academic work, especially in teaching, is also a quality assurance issue. Casual or sessional staff members teach and assess more than 50% of all university courses in Australia, and yet the research in relation to the role sessional staff play in quality assurance of student assessment outcomes is scarce. Moderation processes are a pivotal part of robust quality assurance measures. Drawing upon previous work surrounding four discourses of moderation, this pilot project reports the results of research into the role and impact of sessional staff in moderation processes at tertiary level. Qualitative data were gathered through focus interviews. Results, in the form of various moderation discourses, indicate that sessional staff impact the formal quality assurance processes in numerous ways.

Comparison of Body Composition Assessment Methods in Breast Cancer Survivors

Purpose/Objectives: To examine and compare the reliability of four body composition methods commonly used in assessing breast cancer survivors. Design: Cross-sectional. Setting: A rehabilitation facility at a university-based comprehensive cancer center in the southeastern United States. Sample: 14 breast cancer survivors aged 40-71 years. Methods: Body fat (BF) percentage was estimated via bioelectric impedance analysis (BIA), air displacement plethysmography (ADP), and skinfold thickness (SKF) using both three- and seven-site algorithms, where reliability of the methods was evaluated by conducting two tests for each method (test 1 and test 2), one immediately after the other. An analysis of variance was used to compare the results of BF percentage among the four methods. Intraclass correlation coefficient (ICC) was used to test the reliability of each method. Main Research Variable: BF percentage. Findings: Significant differences in BF percentage were observed between BIA and all other methods (three-site SKF, p < 0.001; seven-site SKF, p < 0.001; ADP, p = 0.002). No significant differences (p > 0.05) in BF percentage between three-site SKF, seven-site SKF, and ADP were observed. ICCs between test 1 and test 2 for each method were BIA = 1, ADP = 0.98, three-site SKF = 0.99, and seven-site SKF = 0.94. Conclusions: ADP and both SKF methods produce similar estimates of BF percentage in all participants, whereas BIA overestimated BF percentage relative to the other measures. Caution is recommended when using BIA as the body composition method for breast cancer survivors who have completed treatment but are still undergoing adjuvant hormonal therapy. Implications for Nursing: Measurements of body composition can be implemented very easily as part of usual care and should serve as an objective outcome measure for interventions designed to promote healthy behaviors among breast cancer survivors. - See more at: https://onf.ons.org/onf/38/4/comparison-body-composition-assessment-methods-breast-cancer-survivors#sthash.5djfTS1Q.dpuf

Geography and international assessment: Opportunity or distraction

Assessments of students in primary and secondary education are debated among practitioners, policy-makers, and parents. In some countries, assessment scores serve a criterion for passage between levels of education, for example, from secondary school to post-secondary education. Those practices are often traditions and while they come under criticism, they are a long-accepted part of the educational practices within a country. In those countries, the students’ assessment and examination scores are posted in public places or published in local news media. In other countries, assessments are used for the periodic checks on individual student progress. The results of assessments may be used for rating schools, and in some cases, they are used for evaluating the performance of teachers. Assessments are used less often to analyze student performance and make judgments regarding the performance of the curriculum. Even less often, assessments serve to critically establish strategies for the improvement of student learning and educational practices. The ends on the continuum of the assessment debate often focus on the opportunities that assessments present to improve education on one end. The other end is that assessments serve as a major distraction from the important work of teachers by removing classroom room time from instruction. The debate on those issues continues.

Assessment of temperature effects on childhood pneumonia and diarrhoea

This thesis has identified the high risk areas of childhood pneumonia and diarrhoea in Queensland and quantified the effects of temperature on emergency department visits for childhood pneumonia and diarrhoea. It adds to the increasing evidence about the impacts of climate variability and change on children's health and may have significant implications for developing climate change adaptation strategies and paediatric care policies.

Non-destructive structural integrity assessment of a decommissioned rail wagon system

This paper presents a multi-criteria based approach for nondestructive diagnostic structural integrity assessment of a decommissioned flatbed rail wagon (FBRW) used for road bridge superstructure rehabilitation and replacement applications. First, full-scale vibration and static test data sets are employed in a FE model of the FBRW to obtain the best ‘initial’ estimate of the model parameters. Second, the ‘final’ model parameters are predicted using sensitivity-based perturbation analysis without significant difficulties encountered. Consequently, the updated FBRW model is validated using the independent sets of full-scale laboratory static test data. Finally, the updated and validated FE model of the FBRW is used for structural integrity assessment of a single lane FBRW bridge subjected to the Australian bridge design traffic load.

Too much knowledge for a nurse? Use of physical assessment by final-semester nursing students

There is debate around the scope of physical assessment skills that should be taught in undergraduate nursing programs. Yet this debate is largely uninformed by evidence on what is learned and practiced by nursing students. This study examined the pattern and correlates of physical assessment skill utilization by 208 graduating nursing students at an Australian university, including measures of knowledge, frequency of use and perceived barriers to physical assessment skills during clinical practice. Of the 126 skills surveyed, on average only five were used every time students practiced. Core skills reflected inspection or general observation of the patient; none involved complex palpation, percussion or auscultation. Skill utilization was also shaped by specialty area. Most skills (70%) were, on average, never performed or learned and students perceived nursing physical assessment was marginalized in both university and workplace contexts. Lack of confidence was thus a significant barrier to use of skills. Based on these findings we argue that the current debate must shift to how we might best support students to integrate comprehensive physical assessment into nursing practice.

International trends in the implementation of assessment for learning: Implications for policy and practice

This paper discusses the emergence of assessment for learning (AfL) across the globe with particular attention given to Western educational jurisdictions. Authors from Australia, Canada, Ireland, Israel, New Zealand, Norway, and the USA explain the genesis of AfL, its evolution and impact on school systems, and discuss current trends in policy directions for AfL within their respective countries. The authors also discuss the implications of these various shifts and the ongoing tensions that exist between AfL and summative forms of assessment within national policy initiatives.

A laboratory assessment of the choice of vessel size under individual transferable quota regimes

This paper examines the effect of individual transferable quota regimes on technology choice, such as choice of vessel size, by using the laboratory experiment method. We find that even if vessel sizes change over time, the quota price can converge to the fundamental value conditioned on the vessels chosen. We also find that subjects choose their vessel type to maximise their profits based on the quota trading prices in the previous period. This result implies that the efficiency of quota markets in the beginning period is important because any inefficiency in quota markets may affect vessel sizes in ensuing periods. Moreover, we find that the initial allocations may significantly influence vessel sizes through two channels: first, a higher initial allocation to a subject increases the likelihood that the subject invests in a large-sized vessel; second, the quota price may be higher and more unstable under unequal allocation than under equal allocation; thus, whether the allocation is equal influences subjects' choice of vessel type. © 2014 Australian Agricultural and Resource Economics Society Inc.

SECA: SNP effect concordance analysis using genome-wide association summary results

The genomics era provides opportunities to assess the genetic overlap across phenotypes at the measured genotype level; however, current approaches require individual-level genome-wide association (GWA) single nucleotide polymorphism (SNP) genotype data in one or both of a pair of GWA samples. To facilitate the discovery of pleiotropic effects and examine genetic overlap across two phenotypes, I have developed a user-friendly web-based application called SECA to perform SNP effect concordance analysis using GWA summary results. The method is validated using publicly available summary data from the Psychiatric Genomics Consortium.

Genetic variants underlying risk of endometriosis: Insights from meta-analysis of eight genome-wide association and replication datasets

BACKGROUND Endometriosis is a heritable common gynaecological condition influenced by multiple genetic and environmental factors. Genome-wide association studies (GWASs) have proved successful in identifying common genetic variants of moderate effects for various complex diseases. To date, eight GWAS and replication studies from multiple populations have been published on endometriosis. In this review, we investigate the consistency and heterogeneity of the results across all the studies and their implications for an improved understanding of the aetiology of the condition. METHODS Meta-analyses were conducted on four GWASs and four replication studies including a total of 11 506 cases and 32 678 controls, and on the subset of studies that investigated associations for revised American Fertility Society (rAFS) Stage III/IV including 2859 cases. The datasets included 9039 cases and 27 343 controls of European (Australia, Belgium, Italy, UK, USA) and 2467 cases and 5335 controls of Japanese ancestry. Fixed and Han and Elkin random-effects models, and heterogeneity statistics (Cochran's Q test), were used to investigate the evidence of the nine reported genome-wide significant loci across datasets and populations. RESULTS Meta-analysis showed that seven out of nine loci had consistent directions of effect across studies and populations, and six out of nine remained genome-wide significant (P < 5 × 10(-8)), including rs12700667 on 7p15.2 (P = 1.6 × 10(-9)), rs7521902 near WNT4 (P = 1.8 × 10(-15)), rs10859871 near VEZT (P = 4.7 × 10(-15)), rs1537377 near CDKN2B-AS1 (P = 1.5 × 10(-8)), rs7739264 near ID4 (P = 6.2 × 10(-10)) and rs13394619 in GREB1 (P = 4.5 × 10(-8)). In addition to the six loci, two showed borderline genome-wide significant associations with Stage III/IV endometriosis, including rs1250248 in FN1 (P = 8 × 10(-8)) and rs4141819 on 2p14 (P = 9.2 × 10(-8)). Two independent inter-genic loci, rs4141819 and rs6734792 on chromosome 2, showed significant evidence of heterogeneity across datasets (P < 0.005). Eight of the nine loci had stronger effect sizes among Stage III/IV cases, implying that they are likely to be implicated in the development of moderate to severe, or ovarian, disease. While three out of nine loci were inter-genic, the remaining were in or near genes with known functions of biological relevance to endometriosis, varying from roles in developmental pathways to cellular growth/carcinogenesis. CONCLUSIONS Our meta-analysis shows remarkable consistency in endometriosis GWAS results across studies, with little evidence of population-based heterogeneity. They also show that the phenotypic classifications used in GWAS to date have been limited. Stronger associations with Stage III/IV disease observed for most loci emphasize the importance for future studies to include detailed sub-phenotype information. Functional studies in relevant tissues are needed to understand the effect of the variants on downstream biological pathways.

A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990–2010: A systematic analysis for the Global Burden of Disease Study 2010

BACKGROUND Quantification of the disease burden caused by different risks informs prevention by providing an account of health loss different to that provided by a disease-by-disease analysis. No complete revision of global disease burden caused by risk factors has been done since a comparative risk assessment in 2000, and no previous analysis has assessed changes in burden attributable to risk factors over time. METHODS We estimated deaths and disability-adjusted life years (DALYs; sum of years lived with disability [YLD] and years of life lost [YLL]) attributable to the independent effects of 67 risk factors and clusters of risk factors for 21 regions in 1990 and 2010. We estimated exposure distributions for each year, region, sex, and age group, and relative risks per unit of exposure by systematically reviewing and synthesising published and unpublished data. We used these estimates, together with estimates of cause-specific deaths and DALYs from the Global Burden of Disease Study 2010, to calculate the burden attributable to each risk factor exposure compared with the theoretical-minimum-risk exposure. We incorporated uncertainty in disease burden, relative risks, and exposures into our estimates of attributable burden. FINDINGS In 2010, the three leading risk factors for global disease burden were high blood pressure (7·0% [95% uncertainty interval 6·2-7·7] of global DALYs), tobacco smoking including second-hand smoke (6·3% [5·5-7·0]), and alcohol use (5·5% [5·0-5·9]). In 1990, the leading risks were childhood underweight (7·9% [6·8-9·4]), household air pollution from solid fuels (HAP; 7·0% [5·6-8·3]), and tobacco smoking including second-hand smoke (6·1% [5·4-6·8]). Dietary risk factors and physical inactivity collectively accounted for 10·0% (95% UI 9·2-10·8) of global DALYs in 2010, with the most prominent dietary risks being diets low in fruits and those high in sodium. Several risks that primarily affect childhood communicable diseases, including unimproved water and sanitation and childhood micronutrient deficiencies, fell in rank between 1990 and 2010, with unimproved water and sanitation accounting for 0·9% (0·4-1·6) of global DALYs in 2010. However, in most of sub-Saharan Africa childhood underweight, HAP, and non-exclusive and discontinued breastfeeding were the leading risks in 2010, while HAP was the leading risk in south Asia. The leading risk factor in Eastern Europe, most of Latin America, and southern sub-Saharan Africa in 2010 was alcohol use; in most of Asia, North Africa and Middle East, and central Europe it was high blood pressure. Despite declines, tobacco smoking including second-hand smoke remained the leading risk in high-income north America and western Europe. High body-mass index has increased globally and it is the leading risk in Australasia and southern Latin America, and also ranks high in other high-income regions, North Africa and Middle East, and Oceania. INTERPRETATION Worldwide, the contribution of different risk factors to disease burden has changed substantially, with a shift away from risks for communicable diseases in children towards those for non-communicable diseases in adults. These changes are related to the ageing population, decreased mortality among children younger than 5 years, changes in cause-of-death composition, and changes in risk factor exposures. New evidence has led to changes in the magnitude of key risks including unimproved water and sanitation, vitamin A and zinc deficiencies, and ambient particulate matter pollution. The extent to which the epidemiological shift has occurred and what the leading risks currently are varies greatly across regions. In much of sub-Saharan Africa, the leading risks are still those associated with poverty and those that affect children.