Stakeholder Perceptions of Point-of-Care Ultrasound Implementation in Resource-Limited Settings

Nearly half of the world lacks access to diagnostic imaging. Point of care ultrasound (POCUS) is a versatile and relatively affordable imaging modality that offers promise as a means of bridging the radiology gap and improving care in low resource settings. Methods: We performed semi-structured interviews of key stakeholders at two diverse hospitals where POCUS implementation programs had recently been conducted: one in a rural private hospital in Haiti and the other in a public referral hospital in Malawi. Questions regarding the clinical utility of POCUS, as well as barriers and facilitators of its implementation, were asked of study participants. Using the Framework Method, analysis of interview transcripts was guided by the WHO ASSURED criteria for point of care diagnostics. Results: Fifteen stakeholders with diverse roles in POCUS implementation were interviewed. Interviewees from both sites considered POCUS a valuable diagnostic tool that improved clinical decisions. They perceived barriers to adequate training as one of the most important remaining barriers to POCUS implementation. Conclusions: In spite of the increasing affordability and portability of ultrasounds devices, there are still important barriers to the implementation of POCUS in resource-limited settings

End-user involvement in a systematic review of quantitative and qualitative research of non-pharmacological interventions for attention deficit hyperactivity disorder delivered in school settings: reflections on the impacts and challenges.

JOURNAL ARTICLEBACKGROUND: The benefits of end-user involvement in health-care research are widely recognized by research agencies. There are few published evaluations of end-user involvement in systematic reviews. OBJECTIVES: (i) Describe end-user involvement in a complex mixed-methods systematic review of ADHD in schools, (ii) reflect on the impact of end-user involvement, (iii) highlight challenges and benefits experienced and (iv) provide suggestions to inform future involvement. METHODS: End-users were involved in all stages of the project, both as authors and as members of an advisory group. In addition, several events were held with groups of relevant end-users during the project. RESULTS: End-user input (i) guided the direction of the research, (ii) contributed to a typology of interventions and outcomes, (iii) contributed to the direction of data analysis and (iv) contributed to the robustness of the syntheses by demonstrating the alignment of interim findings with lived experiences. Challenges included (i) managing expectations, (ii) managing the intensity of emotion, (iii) ensuring that involvement was fruitful for all not just the researcher, (iv) our capacity to communicate and manage the process and (v) engendering a sense of involvement amongst end-users. CONCLUSIONS: End-user involvement was an important aspect of this project. To minimize challenges in future projects, a recognition by the project management team and the funding provider that end-user involvement even in evidence synthesis projects is resource intensive is essential to allow appropriate allocation of time and resources for meaningful engagement.NIHR HTA programmeNIHRExeter NHS Foundation Trus

Factor VIII gene inversions causing severe hemophilia A originate almost exclusively in male germ cells

The factor VIII gene, which is defective In hemophilia A, is located in the last megabase of the long arm of the X chromosome. Inversions due to intrachromosomal homologous recombination between mispaired copies of gene A located within intron 22 of the gene and about 500 kb telomeric to it account for nearly half of all cases of severe hemophilia A. We hypothesized that pairing of Xq with its homolog inhibits the Inversion process, and that, therefore, the event originates predominantly in male germ cells. In all 20 informative cases In which the inversion originated in a maternal grandparent, DNA polymorphism analysis determined that it occurred in the male germline. In addition, all but one of 50 mothers of sporadic cases due to an Inversion were carriers. Thus, these data support the hypothesis and Indicate that factor VIII gene inversions leading to severe hemophilia A occur almost exclusively In male germ cell

Mercury cycling in restored coastal wetlands.

PhDSaltmarsh restoration is being implemented across Europe and North America yet, there is little understanding of the effects of de-embankment on Hg biogeochemical cycling. The aim of this thesis is to understand the controls upon Hg dynamics in coastal sites, with specific emphasis on the effects of ecosystem restoration on MeHg production. This is the first study in the UK to examine the effect of saltmarsh restoration on Hg methylation. Field observations were used to assess broad-scale Hg dynamics and physico-chemical controls on MeHg production. A laboratory experiment was conducted to explore the short-term effects of saline inundation on MeHg production. Recently de-embanked sites have lower MeHg concentrations, probably due to poor drainage and limited vegetation development. Physical sediment properties are less heterogeneous in restored sites, which are reflecting lower habitat and topographic heterogeneity. Previous land-use has a significant impact on physico-chemical sediment characteristics and these characteristics change over time to reflect saltmarsh development. There was evidence to show that it takes decades for restored sites to attain similar physico-chemical characteristics to their natural counterparts. This could have significant implications for wider biogeochemical cycling in restored saltmarshes, and long-term implications for the delivery of biogeochemical ecosystem services. This aspect of the research was completely novel, providing the first evidence of the spatial and temporal variation of Hg and MeHg concentrations in restored saltmarshes in the UK. Laboratory experiments showed that MeHg production was greatest in fluctuating saline conditions (cumulative exposure of 1830 pg g-1) compared to all other treatments. For example, the anoxic-saline treatment had a cumulative exposure of 460 pg g-1. Findings indicated that peaks of MeHg could be produced immediately following tidal inundation and that MeHg could potentially increase over time as the site develops to a tidal regime more comparable to a natural saltmarsh. Previous 3 studies have indicated that permanently flooded soils produce high MeHg concentration however this is the first study to show that fluctuating saline conditions could produce a large pulse of MeHg, an important consideration for coastal managers. Surface sediments in restored coastal wetlands appear to be areas of significant MeHg production. MeHg concentration was found to be well correlated with indicators of sulphate reducing bacteria (r=0.536, p<0.001), however most importantly, evidence was found for biogeochemical relationships with MeHg concentration, particularly the association of MeHg and indicators of iron reduction (r=0.561, p<0.001). Therefore, where MeHg is normally restricted by sulphide production, high levels of MeHg can be formed through other pathways. Coastal areas are not generally considered to be areas of concern for MeHg production because high chloride and sulphide concentrations have been shown to inhibit Hg methylation. However, this research shows that other pathways can also be responsible for Hg methylation (i.e. iron reduction) and therefore coastal sediment can be significant contributors to Hg methylation.PhD studentship from the Natural Environment Research Council (UK) (NE/J500331/1) and Queen Mary University of Londo

Can big data solve a big problem? Reporting the obesity data landscape in line with the Foresight obesity system map.

BACKGROUND: Obesity research at a population level is multifaceted and complex. This has been characterised in the UK by the Foresight obesity systems map, identifying over 100 variables, across seven domain areas which are thought to influence energy balance, and subsequent obesity. Availability of data to consider the whole obesity system is traditionally lacking. However, in an era of big data, new possibilities are emerging. Understanding what data are available can be the first challenge, followed by an inconsistency in data reporting to enable adequate use in the obesity context. In this study we map data sources against the Foresight obesity system map domains and nodes and develop a framework to report big data for obesity research. Opportunities and challenges associated with this new data approach to whole systems obesity research are discussed. METHODS: Expert opinion from the ESRC Strategic Network for Obesity was harnessed in order to develop a data source reporting framework for obesity research. The framework was then tested on a range of data sources. In order to assess availability of data sources relevant to obesity research, a data mapping exercise against the Foresight obesity systems map domains and nodes was carried out. RESULTS: A reporting framework was developed to recommend the reporting of key information in line with these headings: Background; Elements; Exemplars; Content; Ownership; Aggregation; Sharing; Temporality (BEE-COAST). The new BEE-COAST framework was successfully applied to eight exemplar data sources from the UK. 80% coverage of the Foresight obesity systems map is possible using a wide range of big data sources. The remaining 20% were primarily biological measurements often captured by more traditional laboratory based research. CONCLUSIONS: Big data offer great potential across many domains of obesity research and need to be leveraged in conjunction with traditional data for societal benefit and health promotion

Is adolescent body mass index and waist circumference associated with the food environments surrounding schools and homes? A longitudinal analysis

Background: There has been considerable interest in the role of access to unhealthy food options as a determinant of weight status. There is conflict across the literature as to the existence of such an association, partly due to the dominance of cross-sectional study designs and inconsistent definitions of the food environment. The aim of our study is to use longitudinal data to examine if features of the food environment are associated to measures of adolescent weight status. Methods: Data were collected from secondary schools in Leeds (UK) and included measurements at school years 7 (ages 11/12), 9 (13/14), and 11 (15/16). Outcome variables, for weight status, were standardised body mass index and standardised waist circumference. Explanatory variables included the number of fast food outlets, supermarkets and ‘other retail outlets’ located within a 1 km radius of an individual’s home or school, and estimated travel route between these locations (with a 500 m buffer). Multi-level models were fit to analyse the association (adjusted for confounders) between the explanatory and outcome variables. We also examined changes in our outcome variables between each time period. Results: We found few associations between the food environment and measures of adolescent weight status. Where significant associations were detected, they mainly demonstrated a positive association between the number of amenities and weight status (although effect sizes were small). Examining changes in weight status between time periods produced mainly non-significant or inconsistent associations. Conclusions: Our study found little consistent evidence of an association between features of the food environment and adolescent weight status. It suggests that policy efforts focusing on the food environment may have a limited effect at tackling the high prevalence of obesity if not supported by additional strategies

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts