Publishing and sharing multi-dimensional image data with OMERO

Imaging data are used in the life and biomedical sciences to measure the molecular and structural composition and dynamics of cells, tissues, and organisms. Datasets range in size from megabytes to terabytes and usually contain a combination of binary pixel data and metadata that describe the acquisition process and any derived results. The OMERO image data management platform allows users to securely share image datasets according to specific permissions levels: data can be held privately, shared with a set of colleagues, or made available via a public URL. Users control access by assigning data to specific Groups with defined membership and access rights. OMERO’s Permission system supports simple data sharing in a lab, collaborative data analysis, and even teaching environments. OMERO software is open source and released by the OME Consortium at www.openmicroscopy.org

Abrasive water jet drilling of advanced sustainable bio-fibre-reinforced polymer/hybrid composites : a comprehensive analysis of machining-induced damage responses

This paper aims at investigating the effects of variable traverse speeds on machining-induced damage of fibre-reinforced composites, using the abrasive water jet (AWJ) drilling. Three different types of epoxy-based composites laminates fabricated by vacuum bagging technique containing unidirectional (UD) flax, hybrid carbon-flax and carbon fibre-reinforced composite were used. The drilling parameters used were traverse speeds of 20, 40, 60 and 80 mm/min, constant water jet pressure of 300 MPa and a hole diameter of 10 mm. The results obtained depict that the traverse speed had a significant effect with respect to both surface roughness and delamination drilling-induced damage responses. Evidently, an increase in water jet traverse speed caused an increase in both damage responses of the three samples. Significantly, the CFRP composite sample recorded the lowest surface roughness damage response, followed by C-FFRP, while FFRP exhibited the highest. However, samples of FFRP and hybrid C-FFRP recorded lowest and highest delamination damage responses, respectively. The discrepancy in both damage responses, as further validated with micrographs of colour video microscopy (CVM), scanning electron microscopy (SEM) and X-ray micro-computed tomography (X-ray μCT), is attributed to the different mechanical properties of the reinforced fibres, fibre orientation/ply stacking and hybridisation of the samples.Peer reviewe

Mass distribution in our Galaxy

This article summarizes recent work on the luminosity and mass distribution of the Galactic bulge and disk, and on the mass of the Milky Way's dark halo. A new luminosity model consistent with the COBE NIR data and the apparent magnitude distributions of bulge clump giant stars has bulge/bar length of \simeq 3.5\kpc, axis ratios of 1:(0.3-0.4):0.3, and short disk scale-length (\simeq 2.1\kpc). Gas-dynamical flows in the potential of this model with constant M/L fit the terminal velocities in $10\deg\le |l| \le 50\deg$ very well. The luminous mass distribution with this M/L is consistent with the surface density of known matter near the Sun, but still underpredicts the microlensing optical depth towards the bulge. Together, these facts argue strongly for a massive, near-maximal disk in our $\sim L^\ast$, Sbc spiral Galaxy. While the outer rotation curve and global mass distribution are not as readily measured as in similar spiral galaxies, the dark halo mass estimated from satellite velocities is consistent with a flat rotation curve continuing on from the luminous mass distribution

Evidence and argument in policymaking: development of workplace smoking legislation

<p>Abstract</p> <p>Background</p> <p>We sought to identify factors that affect the passage of public health legislation by examining the use of arguments, particularly arguments presenting research evidence, in legislative debates regarding workplace smoking restrictions.</p> <p>Methods</p> <p>We conducted a case-study based content analysis of legislative materials used in the development of six state workplace smoking laws, including written and spoken testimony and the text of proposed and passed bills and amendments. We coded testimony given before legislators for arguments used, and identified the institutional affiliations of presenters and their position on the legislation. We compared patterns in the arguments made in testimony to the relative strength of each state's final legislation.</p> <p>Results</p> <p>Greater discussion of scientific evidence within testimony given was associated with the passage of workplace smoking legislation that provided greater protection for public health, regardless of whether supporters outnumbered opponents or vice versa.</p> <p>Conclusion</p> <p>Our findings suggest that an emphasis on scientific discourse, relative to other arguments made in legislative testimony, might help produce political outcomes that favor public health.</p

Safety and efficacy of bexarotene in patients with relapsing-remitting multiple sclerosis (CCMR One): a randomised, double-blind, placebo-controlled, parallel-group, phase 2a study

Background: Progressive disability in multiple sclerosis occurs because CNS axons degenerate as a late consequence of demyelination. In animals, retinoic acid receptor RXR-gamma agonists promote remyelination. We aimed to assess the safety and efficacy of a non-selective retinoid X receptor agonist in promoting remyelination in people with multiple sclerosis. Methods: This randomised, double-blind, placebo-controlled, parallel-group, phase 2a trial (CCMR One) recruited patients with relapsing-remitting multiple sclerosis from two centres in the UK. Eligible participants were aged 18–50 years and had been receiving dimethyl fumarate for at least 6 months. Via a web-based system run by an independent statistician, participants were randomly assigned (1:1), by probability-weighted minimisation using four binary factors, to receive 300 mg/m2 of body surface area per day of oral bexarotene or oral placebo for 6 months. Participants, investigators, and outcome assessors were masked to treatment allocation. MRI scans were done at baseline and at 6 months. The primary safety outcome was the number of adverse events and withdrawals attributable to bexarotene. The primary efficacy outcome was the patient-level change in mean lesional magnetisation transfer ratio between baseline and month 6 for lesions that had a baseline magnetisation transfer ratio less than the within-patient median. We analysed the primary safety outcome in the safety population, which comprised participants who received at least one dose of their allocated treatment. We analysed the primary efficacy outcome in the intention-to-treat population, which comprised all patients who completed the study. This study is registered in the ISRCTN Registry, 14265371, and has been completed. Findings: Between Jan 17, 2017, and May 17, 2019, 52 participants were randomly assigned to receive either bexarotene (n=26) or placebo (n=26). Participants who received bexarotene had a higher mean number of adverse events (6·12 [SD 3·09]; 159 events in total) than did participants who received placebo (1·63 [SD 1·50]; 39 events in total). All bexarotene-treated participants had at least one adverse event, which included central hypothyroidism (n=26 vs none on placebo), hypertriglyceridaemia (n=24 vs none on placebo), rash (n=13 vs one on placebo), and neutropenia (n=10 vs none on placebo). Five (19%) participants on bexarotene and two (8%) on placebo discontinued the study drug due to adverse events. One episode of cholecystitis in a placebo-treated participant was the only serious adverse event. The change in mean lesional magnetisation transfer ratio was not different between the bexarotene group (0·25 percentage units [pu; SD 0·98]) and the placebo group (0·09 pu [0·84]; adjusted bexarotene–placebo difference 0·16 pu, 95% CI –0·39 to 0·71; p=0·55). Interpretation: We do not recommend the use of bexarotene to treat patients with multiple sclerosis because of its poor tolerability and negative primary efficacy outcome. However, statistically significant effects were seen in some exploratory MRI and electrophysiological analyses, suggesting that other retinoid X receptor agonists might have small biological effects that could be investigated in further studies. Funding: Multiple Sclerosis Society of the United Kingdom

Assessing Natural Resource Use by Forest-Reliant Communities in Madagascar Using Functional Diversity and Functional Redundancy Metrics

Biodiversity plays an integral role in the livelihoods of subsistence-based forest-dwelling communities and as a consequence it is increasingly important to develop quantitative approaches that capture not only changes in taxonomic diversity, but also variation in natural resources and provisioning services. We apply a functional diversity metric originally developed for addressing questions in community ecology to assess utilitarian diversity of 56 forest plots in Madagascar. The use categories for utilitarian plants were determined using expert knowledge and household questionnaires. We used a null model approach to examine the utilitarian (functional) diversity and utilitarian redundancy present within ecological communities. Additionally, variables that might influence fluctuations in utilitarian diversity and redundancy—specifically number of felled trees, number of trails, basal area, canopy height, elevation, distance from village—were analyzed using Generalized Linear Models (GLMs). Eighteen of the 56 plots showed utilitarian diversity values significantly higher than expected. This result indicates that these habitats exhibited a low degree of utilitarian redundancy and were therefore comprised of plants with relatively distinct utilitarian properties. One implication of this finding is that minor losses in species richness may result in reductions in utilitarian diversity and redundancy, which may limit local residents' ability to switch between alternative choices. The GLM analysis showed that the most predictive model included basal area, canopy height and distance from village, which suggests that variation in utilitarian redundancy may be a result of local residents harvesting resources from the protected area. Our approach permits an assessment of the diversity of provisioning services available to local communities, offering unique insights that would not be possible using traditional taxonomic diversity measures. These analyses introduce another tool available to conservation biologists for assessing how future losses in biodiversity will lead to a reduction in natural resources and provisioning services from forests

Survival of HIV-Infected Adolescents on Antiretroviral Therapy in Uganda: Findings from a Nationally Representative Cohort in Uganda

CITATION: Bakanda, C. et al. 2011. Survival of HIV-infected adolescents on antiretroviral therapy in Uganda : findings from a nationally representative cohort in Uganda. PLoS ONE, 6(4): e19261, doi:10.1371/journal.pone.0019261.The original publication is available at http://journals.plos.org/plosoneBackground: Adolescents have been identified as a high-risk group for poor adherence to and defaulting from combination antiretroviral therapy (cART) care. However, data on outcomes for adolescents on cART in resource-limited settings remain scarce. Methods: We developed an observational study of patients who started cART at The AIDS Service Organization (TASO) in Uganda between 2004 and 2009. Age was stratified into three groups: children (≤10 years), adolescents (11-19 years), and adults (≥20 years). Kaplan-Meier survival curves were generated to describe time to mortality and loss to follow-up, and Cox regression used to model associations between age and mortality and loss to follow-up. To address loss to follow up, we applied a weighted analysis that assumes 50% of lost patients had died. Findings: A total of 23,367 patients were included in this analysis, including 810 (3.5%) children, 575 (2.5%) adolescents, and 21 982 (94.0%) adults. A lower percentage of children (5.4%) died during their cART treatment compared to adolescents (8.5%) and adults (10%). After adjusting for confounding, other features predicted mortality than age alone. Mortality was higher among males (p<0.001), patients with a low initial CD4 cell count (p<0.001), patients with advanced WHO clinical disease stage (p<0.001), and shorter duration of time receiving cART (p<0.001). The crude mortality rate was lower for children (22.8 per 1000 person-years; 95% CI: 16.1, 29.5), than adolescents (36.5 per 1000 person-years; 95% CI: 26.3, 46.8) and adults (37.5 per 1000 person-years; 95% CI: 35.9, 39.1). Interpretation: This study is the largest assessment of adolescents receiving cART in Africa. Adolescents did not have cART mortality outcomes different from adults or children. © 2011 Bakanda et al.http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019261Publisher's versio

A Novel Microfluidic Dielectrophoresis Technology to Enable Rapid Diagnosis of Mycobacteria tuberculosis in Clinical Samples

To achieve the global efforts to end tuberculosis, affordable diagnostics suitable for true point-of-care implementation are required to reach the missing millions. In addition, diagnostics with increased sensitivity and expanded drug susceptibility testing are needed to address drug resistance and to diagnose low-bacterial burden cases. The laboratory-on-a-chip technology described herein used dielectrophoresis to selectively isolate Mycobacterium tuberculosis from sputum samples, purifying the bacterial population ahead of molecular confirmation by multiplex real-time quantitative PCR. After optimization using a panel of 50 characterized sputum samples, the performance of the prototype was assessed against the current gold standards, screening 100 blinded sputum samples using characterized and biobanked sputum provided by Foundation for Innovative New Diagnostics. Concordance with culture diagnosis was 100% for smear-negative samples and 87% for smear-positive samples. Of the smear-positive samples, the high burden sample concordance was 100%. Samples were diagnosed on the basis of visual assessment of the dielectrophoresis array and by multiplex real-time quantitative PCR assay. The results described herein demonstrate the potential of the CAPTURE-XT technology to provide a powerful sample preparation tool that could function as a front-end platform for molecular detection. This versatile tool could equally be applied as a visual detection diagnostic, potentially associated with bacterial identification for low-cost screening or coupled with an expanded PCR assay for genotypic drug susceptibility testing

Dialysis and pediatric acute kidney injury: choice of renal support modality

Dialytic intervention for infants and children with acute kidney injury (AKI) can take many forms. Whether patients are treated by intermittent hemodialysis, peritoneal dialysis or continuous renal replacement therapy depends on specific patient characteristics. Modality choice is also determined by a variety of factors, including provider preference, available institutional resources, dialytic goals and the specific advantages or disadvantages of each modality. Our approach to AKI has benefited from the derivation and generally accepted defining criteria put forth by the Acute Dialysis Quality Initiative (ADQI) group. These are known as the risk, injury, failure, loss, and end-stage renal disease (RIFLE) criteria. A modified pediatrics RIFLE (pRIFLE) criteria has recently been validated. Common defining criteria will allow comparative investigation into therapeutic benefits of different dialytic interventions. While this is an extremely important development in our approach to AKI, several fundamental questions remain. Of these, arguably, the most important are “When and what type of dialytic modality should be used in the treatment of pediatric AKI?” This review will provide an overview of the limited data with the aim of providing objective guidelines regarding modality choice for pediatric AKI. Comparisons in terms of cost, availability, safety and target group will be reviewed