Living deep-water Lophelia and Madrepora corals in Maltese waters (Strait of Sicily, Mediterranean Sea)

The occurrence of living deep-water corals, Lophelia pertusa and Madrepora oculata, from stations 21-42 km off the southern and south-western coast of Malta is reported. Fragments of living colonies of both species, as well as some large pieces of Lophelia frameworks were recovered from depths of 390-617 m together with the solitary coral Desmophyllum dianthus (= cristagalli). The accompanying biota included the barnacle Pachylasma giganteum, the gastropod Coralliophila richardi, the bivalves Asperarca nodulosa and Spondylus gussonii, and the polychaete Eunice norvegicus, all of which are frequently associated with deep-water corals. The occurrence of the Lophelia-Madrepora- Desmophyllum triad, the large pieces of coral frameworks consisting predominantly of live, healthy polyps, and the associated biota, suggest that coral patches may be present in at least some of the investigated localities, rather than just fragmented remains or isolated colonies.peer-reviewe

Rethinking the assessment of risk of bias due to selective reporting:a cross-sectional study

BACKGROUND: Selective reporting is included as a core domain of Cochrane’s tool for assessing risk of bias in randomised trials. There has been no evaluation of review authors’ use of this domain. We aimed to evaluate assessments of selective reporting in a cross-section of Cochrane reviews and to outline areas for improvement. METHODS: We obtained data on selective reporting judgements for 8434 studies included in 586 Cochrane reviews published from issue 1–8, 2015. One author classified the reasons for judgements of high risk of selective reporting bias. We randomly selected 100 reviews with at least one trial rated at high risk of outcome non-reporting bias (non-/partial reporting of an outcome on the basis of its results). One author recorded whether the authors of these reviews incorporated the selective reporting assessment when interpreting results. RESULTS: Of the 8434 studies, 1055 (13 %) were rated at high risk of bias on the selective reporting domain. The most common reason was concern about outcome non-reporting bias. Few studies were rated at high risk because of concerns about bias in selection of the reported result (e.g. reporting of only a subset of measurements, analysis methods or subsets of the data that were pre-specified). Review authors often specified in the risk of bias tables the study outcomes that were not reported (84 % of studies) but less frequently specified the outcomes that were partially reported (61 % of studies). At least one study was rated at high risk of outcome non-reporting bias in 31 % of reviews. In the random sample of these reviews, only 30 % incorporated this information when interpreting results, by acknowledging that the synthesis of an outcome was missing data that were not/partially reported. CONCLUSIONS: Our audit of user practice in Cochrane reviews suggests that the assessment of selective reporting in the current risk of bias tool does not work well. It is not always clear which outcomes were selectively reported or what the corresponding risk of bias is in the synthesis with missing outcome data. New tools that will make it easier for reviewers to convey this information are being developed. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13643-016-0289-2) contains supplementary material, which is available to authorized users

Assessing risk of bias:a proposal for a unified framework for observational studies and randomized trials

BACKGROUND: Evidence based medicine aims to integrate scientific evidence, clinical experience, and patient values and preferences. Individual health care professionals need to appraise the evidence from randomized trials and observational studies when guidelines are not yet available. To date, tools for assessment of bias and terminologies for bias are specific for each study design. Moreover, most tools appeal only to methodological knowledge to detect bias, not to subject matter knowledge, i.e. in-depth medical knowledge about a topic. We propose a unified framework that enables the coherent assessment of bias across designs. METHODS: Epidemiologists traditionally distinguish between three types of bias in observational studies: confounding, information bias, and selection bias. These biases result from a common cause, systematic error in the measurement or common effect of the intervention and outcome respectively. We applied this conceptual framework to randomized trials and show how it can be used to identify bias. The three sources of bias were illustrated with graphs that visually represent researchers' assumptions about the relationships between the investigated variables (causal diagrams). RESULTS: Critical appraisal of evidence started with the definition of the research question in terms of the population of interest, the compared interventions and the main outcome. Next, we used causal diagrams to illustrate how each source of bias can lead to over- or underestimated treatment effects. Then, we discussed how randomization, blinded outcome measurement and intention-to-treat analysis minimize bias in trials. Finally, we identified study aspects that can only be appraised with subject matter knowledge, irrespective of study design. CONCLUSIONS: The unified framework encompassed the three main sources of bias for the effect of an assigned intervention on an outcome. It facilitated the integration of methodological and subject matter knowledge in the assessment of bias. We hope that graphical diagrams will help clarify debate among professionals by reducing misunderstandings based on different terminology for bias

On Neural Networks as Infinite Tree-Structured Probabilistic Graphical Models

Deep neural networks (DNNs) lack the precise semantics and definitive probabilistic interpretation of probabilistic graphical models (PGMs). In this paper, we propose an innovative solution by constructing infinite tree-structured PGMs that correspond exactly to neural networks. Our research reveals that DNNs, during forward propagation, indeed perform approximations of PGM inference that are precise in this alternative PGM structure. Not only does our research complement existing studies that describe neural networks as kernel machines or infinite-sized Gaussian processes, it also elucidates a more direct approximation that DNNs make to exact inference in PGMs. Potential benefits include improved pedagogy and interpretation of DNNs, and algorithms that can merge the strengths of PGMs and DNNs

Identifying a core set of outcome domains to measure in clinical trials for shoulder disorders:a modified Delphi study

Objective: To achieve consensus on the most important outcome domains to measure across all clinical trials for shoulder disorders. Methods: We performed an online modified Delphi study with an international, multidisciplinary and multistakeholder panel. A literature review and the OMERACT Filter 2.0 framework was used to generate a list of potential core domains, which were presented to patients, clinicians and researchers in two Delphi rounds. Participants were asked to judge the importance of each potential core domain and provide a rationale for their response. A core domain was defined a priori as a domain that at least 67% of participants considered core. Results: In both rounds, 335 individuals were invited to participate (268 clinicians/researchers and 67 patients); response rates were 27% (n=91) and 29% (n=96), respectively. From a list of 41 potential core domains, four domains met our criteria for inclusion: 'pain', 'physical functioning', 'global assessment of treatment success' and 'health-related quality of life'. Two additional domains, 'sleep functioning' and 'psychological functioning', met the criteria for inclusion by some, but not all stakeholder groups. There was consensus that 'number of deaths' was not a core domain, but insufficient agreement on whether or not several other domains, including 'range of motion' and 'muscle strength', were core domains. Conclusions: Based on international consensus from patients, clinicians and researchers, 'pain', 'physical functioning', 'global assessment of treatment success' and 'health-related quality of life' were considered core outcome domains for shoulder disorder trials. The value of several other domains needs further consideration

Outcome Reporting in Randomized Trials for Shoulder Disorders: Literature Review to Inform the Development of a Core Outcome Set

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141827/1/acr23254_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141827/2/acr23254.pd

Singlet oxygen initiates a plastid signal controlling photosynthetic gene expression.

Retrograde signals from the plastid regulate photosynthesis-associated nuclear genes and are essential to successful chloroplast biogenesis. One model is that a positive haem-related signal promotes photosynthetic gene expression in a pathway that is abolished by the herbicide norflurazon. Far-red light (FR) pretreatment and transfer to white light also results in plastid damage and loss of photosynthetic gene expression. Here, we investigated whether norflurazon and FR pretreatment affect the same retrograde signal. We used transcriptome analysis and real-time reverse transcription-polymerase chain reaction (RT-PCR) to analyse the effects of these treatments on nuclear gene expression in various Arabidopsis (Arabidopsis thaliana) retrograde signalling mutants. Results showed that the two treatments inhibited largely different nuclear gene sets, suggesting that they affected different retrograde signals. Moreover, FR pretreatment resulted in singlet oxygen (1 O2 ) production and a rapid inhibition of photosynthetic gene expression. This inhibition was partially blocked in the executer1executer2 mutant, which is impaired in 1 O2 signalling. Our data support a new model in which a 1 O2 retrograde signal, generated by chlorophyll precursors, inhibits expression of key photosynthetic and chlorophyll synthesis genes to prevent photo-oxidative damage during de-etiolation. Such a signal would provide a counterbalance to the positive haem-related signal to fine tune regulation of chloroplast biogenesis.This work was funded by BBSRC grants 51/P17214 and BB/ J018139/1 to M.J.T. and BB/J018694/1 to A.G.S

Employment transitions and mental health in a cohort of 45 years and older Australians

Background: This study investigated the associations between employment transitions and psychological distress among a cohort of 45 years and older Australians. Methods: This study was based on the 45 and Up Study, a large prospective cohort of participants aged 45 years and older (N = 267,153), followed up over the period 2006–2015. The risk of psychological distress was compared between various employment transitions categories by specifying an ordered logistic regression model adjusting for confounders. Results: Compared to participants who remained employed at baseline and follow-up, higher psychological distress was found among those who transitioned from being employed to unemployed (OR = 2.68, 95%CI 2.13–3.33) and to not being in the labour force or retired (OR = 2.21, 95%CI 1.85–2.62). Higher psychological distress was also evident among those who remained unemployed from baseline to follow-up (OR = 2.00, 95%CI 1.10–3.43), and those who transitioned from being retired to being unemployed (OR = 1.55, 95%CI 1.03–2.27). Conversely, lower psychological distress was found among those who transitioned from being unemployed to being employed (OR = 0.35, 95%CI 0.25–0.51). In general, lower psychological distress was found among ‘positive’ employment transitions (transitioning to being employed or retired). Conclusions: Policies focussing on re-employment in older age, as well as unemployment schemes, might be helpful in reducing psychological distress among middle-and old-age Australians

Overexpression of chloroplast-targeted ferrochelatase 1 results in a genomes uncoupled chloroplast-to-nucleus retrograde signalling phenotype.

Chloroplast development requires communication between the progenitor plastids and the nucleus, where most of the genes encoding chloroplast proteins reside. Retrograde signals from the chloroplast to the nucleus control the expression of many of these genes, but the signalling pathway is poorly understood. Tetrapyrroles have been strongly implicated as mediators of this signal with the current hypothesis being that haem produced by the activity of ferrochelatase 1 (FC1) is required to promote nuclear gene expression. We have tested this hypothesis by overexpressing FC1 and specifically targeting it to either chloroplasts or mitochondria, two possible locations for this enzyme. Our results show that targeting of FC1 to chloroplasts results in increased expression of the nuclear-encoded chloroplast genes GUN4, CA1, HEMA1, LHCB2.1, CHLH after treatment with Norflurazon (NF) and that this increase correlates to FC1 gene expression and haem production measured by feedback inhibition of protochlorophyllide synthesis. Targeting FC1 to mitochondria did not enhance the expression of nuclear-encoded chloroplast genes after NF treatment. The overexpression of FC1 also increased nuclear gene expression in the absence of NF treatment, demonstrating that this pathway is operational in the absence of a stress treatment. Our results therefore support the hypothesis that haem synthesis is a promotive chloroplast-to-nucleus retrograde signal. However, not all FC1 overexpression lines enhanced nuclear gene expression, suggesting there is still a lot we do not understand about the role of FC1 in this signalling pathway. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.BBRS