The Use of Ethnography in Maternity Care.

While the value of ethnography in health research is recognized, the extent to which it is used is unclear. The aim of this review was to map the use of ethnography in maternity care, and identify the extent to which the key principles of ethnographies were used or reported. We systematically searched the literature over a 10-year period. Following exclusions we analyzed 39 studies. Results showed the level of detail between studies varied greatly, highlighting the inconsistencies, and poor reporting of ethnographies in maternity care. Over half provided no justification as to why ethnography was used. Only one study described the ethnographic approach used in detail, and covered the key features of ethnography. Only three studies made reference to the underpinning theoretical framework of ethnography as seeking to understand and capture social meanings. There is a need to develop reporting guidelines to guide researchers undertaking and reporting on ethnographic research

Transposon and deletion mutagenesis of genes involved in perchlorate reduction in Azospira suillum PS.

UnlabelledAlthough much work on the biochemistry of the key enzymes of bacterial perchlorate reduction, chlorite dismutase, and perchlorate reductase has been published, understanding of the molecular mechanisms of this metabolism has been somewhat hampered by the lack of a clear model system amenable to genetic manipulation. Using transposon mutagenesis and clean deletions, genes important for perchlorate reduction in Azospira suillum PS have been identified both inside and outside the previously described perchlorate reduction genomic island (PRI). Transposon mutagenesis identified 18 insertions in 11 genes that completely abrogate growth via reduction of perchlorate but have no phenotype during denitrification. Of the mutants deficient in perchlorate reduction, 14 had insertions that were mapped to eight different genes within the PRI, highlighting its importance in this metabolism. To further explore the role of these genes, we also developed systems for constructing unmarked deletions and for complementing these deletions. Using these tools, every core gene in the PRI was systematically deleted; 8 of the 17 genes conserved in the PRI are essential for perchlorate respiration, including 3 genes that comprise a unique histidine kinase system. Interestingly, the other 9 genes in the PRI are not essential for perchlorate reduction and may thus have unknown functions during this metabolism. We present a model detailing our current understanding of perchlorate reduction that incorporates new concepts about this metabolism.ImportanceAlthough perchlorate is generated naturally in the environment, groundwater contamination is largely a result of industrial activity. Bacteria capable of respiring perchlorate and remediating contaminated water have been isolated, but relatively little is known about the biochemistry and genetics of this process. Here we used two complementary approaches to identify genes involved in perchlorate reduction. Most of these genes are located on a genomic island, which is potentially capable of moving between organisms. Some of the genes identified are known to be directly involved in the metabolism of perchlorate, but other new genes likely regulate the metabolism in response to environmental signals. This work has uncovered new questions about the regulation, energetics, and evolution of perchlorate reduction but also presents the tools to address them

Structure and evolution of chlorate reduction composite transposons.

UnlabelledThe genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. A newly isolated chlorate-reducing bacterium (Shewanella algae ACDC) and three previously isolated strains (Ideonella dechloratans, Pseudomonas sp. strain PK, and Dechloromarinus chlorophilus NSS) were genome sequenced and compared to published sequences (Alicycliphilus denitrificans BC plasmid pALIDE01 and Pseudomonas chloritidismutans AW-1). De novo assembly of genomes failed to join regions adjacent to genes involved in chlorate reduction, suggesting the presence of repeat regions. Using a bioinformatics approach and finishing PCRs to connect fragmented contigs, we discovered that chlorate reduction genes are flanked by insertion sequences, forming composite transposons in all four newly sequenced strains. These insertion sequences delineate regions with the potential to move horizontally and define a set of genes that may be important for chlorate reduction. In addition to core metabolic components, we have highlighted several such genes through comparative analysis and visualization. Phylogenetic analysis places chlorate reductase within a functionally diverse clade of type II dimethyl sulfoxide (DMSO) reductases, part of a larger family of enzymes with reactivity toward chlorate. Nucleotide-level forensics of regions surrounding chlorite dismutase (cld), as well as its phylogenetic clustering in a betaproteobacterial Cld clade, indicate that cld has been mobilized at least once from a perchlorate reducer to build chlorate respiration.ImportanceGenome sequencing has identified, for the first time, chlorate reduction composite transposons. These transposons are constructed with flanking insertion sequences that differ in type and orientation between organisms, indicating that this mobile element has formed multiple times and is important for dissemination. Apart from core metabolic enzymes, very little is known about the genetic factors involved in chlorate reduction. Comparative analysis has identified several genes that may also be important, but the relative absence of accessory genes suggests that this mobile metabolism relies on host systems for electron transport, regulation, and cofactor synthesis. Phylogenetic analysis of Cld and ClrA provides support for the hypothesis that chlorate reduction was built multiple times from type II dimethyl sulfoxide (DMSO) reductases and cld. In at least one case, cld has been coopted from a perchlorate reduction island for this purpose. This work is a significant step toward understanding the genetics and evolution of chlorate reduction

Profile of consumers and their partners of a perinatal and infant mental health (PIMH) service in Australia

© 2017 John Wiley & Sons Ltd The perinatal period is a time of great vulnerability for many women, in particular those with a range of psychosocial vulnerabilities and mental health risk factors. This paper outlines the psychosocial and mental health profile of consumers and their partners of a perinatal and infant mental health (PIMH) service in Australia. To establish the consumer profile, we analysed client vulnerabilities and demographical information maintained over a 6-year period for 406 consumers. Consumer information, including mental health problems, psychosocial vulnerabilities and demographical information, was entered into a standalone database by the allocated clinicians upon service allocation and throughout treatment. The women accepted by PIMH presented with an average of nine different vulnerabilities. Frequently endorsed risk factors included depression (72.66%), anxiety (71.43%), comorbid depression and anxiety (58.13%), self-harm (past, 7.88%, present, 16.26%), a history of family mental health issues (39.66%), childhood trauma (57.88%), limited support (68.84%), relationship conflict with partners (38.92%) and financial stress (47.29%). The women's partners also presented with a range of vulnerabilities, in particular childhood trauma (34.11%) and mental health issues (30.81%). This study contributes to our understanding of the profile of vulnerable women in the perinatal period, and in particular contributes to the literature by highlighting that in addition to depression, anxiety, self-harm and trauma are also significant in PIMH service delivery

Mental Health Attitudes and Beliefs in a Community Sample on the Central Coast in Australia: Barriers to Help Seeking

© 2018, Springer Science+Business Media, LLC, part of Springer Nature. There continues to be call for greater community awareness actions and strategies to reduce stigma and enhance mental health literacy nationally and internationally. To identify local barriers to help-seeking and perceptions around stigma, we developed a ‘mental health attitudes and beliefs’ survey which was administered at a range of community events on the Central Coast in New South Wales, Australia. The aim was for the results of this survey to inform the development of strategies that enhance local help-seeking behaviours that are sensitive to the role of age, gender and Indigenous status. People who approached our Mental Health Information stall were invited to complete the survey and 282 individuals completed the survey. The data was analysed descriptively with a focus on comparing subgroups based on age, gender, Indigenous status, and previous service access or experience of mental illness. Cost, stigma and mental health literacy were found to be prominent barriers to help-seeking for the overall cohort; however, the ways in which or extent to which these barriers impact on help seeking varied between subgroups. A discussion of these differences and their implications for practice is the focus of this paper

Cost-effectiveness of voluntary HIV-1 counseling and testing in reducing sexual transmission of HIV-1 in Kenya and Tanzania.

Background Access to HIV-1 voluntary counseling and testing (VCT) is severely limited in less-developed countries. We undertook a multisite trial of HIV-1 VCT to assess its impact, cost, and cost-effectiveness in less-developed country settings.\ud Methods\ud The cost-effectiveness of HIV-1 VCT was estimated for a hypothetical cohort of 10 000 people seeking VCT in urban east Africa. Outcomes were modelled based on results from a randomised controlled trial of HIV-1 VCT in Tanzania and Kenya. Our main outcome measures included programme cost, number of HIV-1 infections averted, cost per HIV-1 infection averted, and cost per disability-adjusted life-year (DALY) saved. We also modelled the impact of targeting VCT by HIV-1 prevalence of the client population, and the proportion of clients who receive VCT as a couple compared with as individuals. Sensitivity analysis was done on all model parameters.\ud Findings\ud HIV-1 VCT was estimated to avert 1104 HIV-1 infections in Kenya and 895 in Tanzania during the subsequent year. The cost per HIV-1 infection averted was US$249 and$346, respectively, and the cost per DALY saved was $12·77 and$17·78. The intervention was most cost-effective for HIV-1-infected people and those who received VCT as a couple. The cost-effectiveness of VCT was robust, with a range for the average cost per DALY saved of $5·16-27·36 in Kenya, and$6·58-45·03 in Tanzania. Analysis of targeting showed that increasing the proportion of couples to 70% reduces the cost per DALY saved to $10·71 in Kenya and$13·39 in Tanzania, and that targeting a population with HIV-1 prevalence of 45% decreased the cost per DALY saved to $8·36 in Kenya and$11·74 in Tanzania.\ud Interpretation\ud HIV-1 VCT is highly cost-effective in urban east African settings, but slightly less so than interventions such as improvement of sexually transmitted disease services and universal provision of nevirapine to pregnant women in high-prevalence settings. With the targeting of VCT to populations with high HIV-1 prevalence and couples the cost-effectiveness of VCT is improved significantly

Synthetic and Evolutionary Construction of a Chlorate-Reducing Shewanella oneidensis MR-1.

UnlabelledDespite evidence for the prevalence of horizontal gene transfer of respiratory genes, little is known about how pathways functionally integrate within new hosts. One example of a mobile respiratory metabolism is bacterial chlorate reduction, which is frequently encoded on composite transposons. This implies that the essential components of the metabolism are encoded on these mobile elements. To test this, we heterologously expressed genes for chlorate reduction from Shewanella algae ACDC in the non-chlorate-reducing Shewanella oneidensis MR-1. The construct that ultimately endowed robust growth on chlorate included cld, a cytochrome c gene, clrABDC, and two genes of unknown function. Although strain MR-1 was unable to grow on chlorate after initial insertion of these genes into the chromosome, 11 derived strains capable of chlorate respiration were obtained through adaptive evolution. Genome resequencing indicated that all of the evolved chlorate-reducing strains replicated a large genomic region containing chlorate reduction genes. Contraction in copy number and loss of the ability to reduce chlorate were also observed, indicating that this phenomenon was extremely dynamic. Although most strains contained more than six copies of the replicated region, a single strain with less duplication also grew rapidly. This strain contained three additional mutations that we hypothesized compensated for the low copy number. We remade the mutations combinatorially in the unevolved strain and determined that a single nucleotide polymorphism (SNP) upstream of cld enabled growth on chlorate and was epistatic to a second base pair change in the NarP binding sequence between narQP and nrfA that enhanced growth.ImportanceThe ability of chlorate reduction composite transposons to form functional metabolisms after transfer to a new host is an important part of their propagation. To study this phenomenon, we engineered Shewanella oneidensis MR-1 into a chlorate reducer. We defined a set of genes sufficient to endow growth on chlorate from a plasmid, but found that chromosomal insertion of these genes was nonfunctional. Evolution of this inoperative strain into a chlorate reducer showed that tandem duplication was a dominant mechanism of activation. While copy number changes are a relatively rapid way of increasing gene dosage, replicating almost 1 megabase of extra DNA is costly. Mutations that alleviate the need for high copy number are expected to arise and eventually predominate, and we identified a single nucleotide polymorphism (SNP) that relieved the copy number requirement. This study uses both rational and evolutionary approaches to gain insight into the evolution of a fascinating respiratory metabolism

Using an Electronic Lab Notebook System to Promote Data Management Plans

Presented at the 2019 Medical Library Association Annual Conference.Background: At an academic medical center, the rollout of an electronic lab notebook (ELN) system includes tailored support to develop functional data management plans for participating research labs. The office of research is sponsoring the adoption of the ELN and, while administrative drivers include improving lab efficiency and reducing institutional liability, the pilot primarily focuses on the benefits of ELN use. In particular, improving the collection of and access to experimental information for research projects. The creation of data management plans, in conjunction with the ELN adoption, allows participants to engage more holistically with the research processes of their laboratories. Description: Nine research labs are identified as “early adopters” for the 4-month pilot of the selected electronic lab notebook system. As participants in the pilot, these labs are expected to a) attend training on the ELN system and b) evaluate their current information and data management practices. To ensure these expectations are met, the institution's ELN implementation team meets with each lab prior to conducting the ELN training to discuss how they manage (i.e., organize, store, and share) research data. These consults result in a draft data management plan that reflect the labs’ current research data management processes and provides suggestions for potential areas of improvement/streamlining. The training on the functionality of the ELN follows this to encourage participating labs to develop concrete strategies for integrating the ELN into the research data/information management processes of the lab overall. Conclusion: As of this submission, the authors have worked directly with four of the “early adopter” labs (each with 6-10 members) to review their information and data management practices while onboarding them to the ELN. These labs receive an individualized data management plan in addition to training on the ELN. A primary outcome is to complete this process with the remaining five “early adopter” labs while gathering feedback on the ELN system itself and monitoring the adoption success of the ELN in these labs. A secondary outcome is to “scale up” this program for full rollout to the institution in 2019

(Per)chlorate-reducing bacteria can utilize aerobic and anaerobic pathways of aromatic degradation with (per)chlorate as an electron acceptor.

UnlabelledThe pathways involved in aromatic compound oxidation under perchlorate and chlorate [collectively known as (per)chlorate]-reducing conditions are poorly understood. Previous studies suggest that these are oxygenase-dependent pathways involving O2 biogenically produced during (per)chlorate respiration. Recently, we described Sedimenticola selenatireducens CUZ and Dechloromarinus chlorophilus NSS, which oxidized phenylacetate and benzoate, two key intermediates in aromatic compound catabolism, coupled to the reduction of perchlorate or chlorate, respectively, and nitrate. While strain CUZ also oxidized benzoate and phenylacetate with oxygen as an electron acceptor, strain NSS oxidized only the latter, even at a very low oxygen concentration (1%, vol/vol). Strains CUZ and NSS contain similar genes for both the anaerobic and aerobic-hybrid pathways of benzoate and phenylacetate degradation; however, the key genes (paaABCD) encoding the epoxidase of the aerobic-hybrid phenylacetate pathway were not found in either genome. By using transcriptomics and proteomics, as well as by monitoring metabolic intermediates, we investigated the utilization of the anaerobic and aerobic-hybrid pathways on different electron acceptors. For strain CUZ, the results indicated utilization of the anaerobic pathways with perchlorate and nitrate as electron acceptors and of the aerobic-hybrid pathways in the presence of oxygen. In contrast, proteomic results suggest that strain NSS may use a combination of the anaerobic and aerobic-hybrid pathways when growing on phenylacetate with chlorate. Though microbial (per)chlorate reduction produces molecular oxygen through the dismutation of chlorite (ClO2(-)), this study demonstrates that anaerobic pathways for the degradation of aromatics can still be utilized by these novel organisms.ImportanceS. selenatireducens CUZ and D. chlorophilus NSS are (per)chlorate- and chlorate-reducing bacteria, respectively, whose genomes encode both anaerobic and aerobic-hybrid pathways for the degradation of phenylacetate and benzoate. Previous studies have shown that (per)chlorate-reducing bacteria and chlorate-reducing bacteria (CRB) can use aerobic pathways to oxidize aromatic compounds in otherwise anoxic environments by capturing the oxygen produced from chlorite dismutation. In contrast, we demonstrate that S. selenatireducens CUZ is the first perchlorate reducer known to utilize anaerobic aromatic degradation pathways with perchlorate as an electron acceptor and that it does so in preference over the aerobic-hybrid pathways, regardless of any oxygen produced from chlorite dismutation. D. chlorophilus NSS, on the other hand, may be carrying out anaerobic and aerobic-hybrid processes simultaneously. Concurrent use of anaerobic and aerobic pathways has not been previously reported for other CRB or any microorganisms that encode similar pathways of phenylacetate or benzoate degradation and may be advantageous in low-oxygen environments