Modelling the ability of legumes to suppress weeds

The ability of different legume cover crops to suppress annual weeds during the early establishment phase was compared using a simulation model of inter-plant competition and field observations. Height, partitioning parameters, extinction coefficients, crop density and time of emergence were recorded for 11 species sown in monocultures. A naturally occurring population of fat hen (Chenopodium album) was present on the experiment. The competition model was run to compare the expected suppressive ability of the different species on this weed. Samples of C. album were also taken from each plot immediately prior to cutting to provide some empirical observations. Predicted suppressive ability was correlated with seed size and height with large seeded, tall species such as white sweet clover being the most competitive. However, these species may recover poorly from mowing compromising their potential to suppress perennial weeds and a mixture of contrasting species may provide the optimum weed control

Adjustment with aphasia after stroke: study protocol for a pilot feasibility randomised controlled trial for SUpporting wellbeing through PEeR Befriending (SUPERB)

Background: Despite the high prevalence of mood problems after stroke, evidence on effective interventions particularly for those with aphasia is limited. There is a pressing need to systematically evaluate interventions aiming to improve wellbeing for people with stroke and aphasia. This study aims to evaluate the feasibility of a peer-befriending intervention. Methods/design: SUPERB is a single blind, parallel group feasibility trial of peer befriending for people with aphasia post-stroke and low levels of psychological distress. The trial includes a nested qualitative study and pilot economic evaluation and it compares usual care (n = 30) with usual care + peer befriending (n = 30). Feasibility outcomes include proportion screened who meet criteria, proportion who consent, rate of consent, number of missing/incomplete data on outcome measures, attrition rate at follow-up, potential value of conducting main trial using value of information analysis (economic evaluation), description of usual care, and treatment fidelity of peer befriending. Assessments and outcome measures (mood, wellbeing, communication, and social participation) for participants and significant others will be administered at baseline, with outcome measures re-administered at 4 and 10 months post-randomisation. Peer befrienders will complete outcome measures before training and after they have completed two cycles of befriending. The qualitative study will use semi-structured interviews of purposively sampled participants (n = 20) and significant others (n = 10) from both arms of the trial, and all peer befrienders to explore the acceptability of procedures and experiences of care. The pilot economic evaluation will utilise the European Quality of life measure (EQ-5D-5 L) and a stroke-adapted version of the Client Service Receipt Inventory (CSRI). Discussion: This study will provide information on feasibility outcomes and an initial indication of whether peer befriending is a suitable intervention to explore further in a definitive phase III randomised controlled trial. Trial registration: ClinicalTrials.gov identifier NCT02947776, registered 28th October 2016

Antinuclear antibodies (ANA) in chronic hepatitis C virus infection: correlates of positivity and clinical relevance.

We examined correlates of antinuclear antibody (ANA) positivity (ANA+) in individuals with chronic hepatitis C virus (HCV) infection and the effect of positivity on clinical outcome of HCV. Pretreatment sera from 645 patients from three centres in Sweden (n = 225), the UK (n = 207) and Italy (n = 213) were evaluated by indirect immunofluorescence on Hep-2 cells for ANA pattern and titre by a single laboratory. Liver biopsies were all scored by one pathologist. A total of 258 patients were subsequently treated with interferon monotherapy. There was a significant difference in the prevalence of ANA (1:40) by geographic location: Lund 4.4%, London 8.7%, Padova 10.3% [odds ratio (OR) = 0.66; 95% CI: 0.46-0.94; P = 0.023]. Duration of HCV infection, age at infection, current age, route of infection, viral genotype, alcohol consumption, fibrosis stage and inflammatory score were not correlated with ANA+ or ANA pattern. Female gender was correlated with ANA+ and this association persisted in multivariable analyses (OR = 3.0; P = 0.002). Increased plasma cells were observed in the liver biopsies of ANA-positive individuals compared with ANA-negative individuals, while a trend towards decreased lymphoid aggregates was observed [hazard ratio (HR) = 9.0, P = 0.037; HR = 0.291, P = 0.118, respectively]. No correlations were observed between ANA positivity and nonresponse to therapy (OR = 1.4; P = 0.513), although ANA+ was correlated with faster rates of liver fibrosis, this was not statistically significant (OR = 1.8; P = 0.1452). Low titre ANA+ should not be a contraindication for interferon treatment. Our observation of increased plasma cells in ANA+ biopsies might suggest B-cell polyclonal activity with a secondary clinical manifestation of increased serum immunoglobulins

Multiple Cone Visual Pigments and the Potential for Trichromatic Colour Vision in Two Species of Elasmobranch

Elasmobranchs (sharks, skates and rays) are the modern descendents of the first jawed vertebrates and, as apex predators, often occupy the highest trophic levels of aquatic (predominantly marine) ecosystems. However, despite their crucial role in the structure of marine communities, their importance both to commercial and to recreational fisheries, and the inherent interest in their role in vertebrate evolution, very little is known about their visual capabilities, especially with regard to whether or not they have the potential for colour vision. Using microspectrophotometry, we show that the retinae of the giant shovelnose ray (Rhinobatos typus) and the eastern shovelnose ray (Aptychotrema rostrata) contain three spectrally distinct cone visual pigments with wavelengths of maximum absorbance (lamda_max) at 477, 502 and 561 nm and at 459, 492 and 553 nm, respectively. The retinae of R. typus and A. rostrata also contain a single type of rod visual pigment with lamda_max at 504 and 498 nm, respectively. R. typus, living in the same estuarine waters as A. rostrata, were found to have identical visual pigments to R. typus inhabiting coral reef flats, despite a considerable difference in habitat spectral radiance. This is the first time that multiple cone visual pigments have been measured directly in an elasmobranch. The finding raises the possibility that some species are able to discriminate colour - a visual ability traditionally thought to be lacking in this vertebrate class - and it is evident that the visual ecology of elasmobranchs is far more complex than once thought

Random Effects Logistic Models for Analyzing Efficacy of a Longitudinal Randomized Treatment With Non-Adherence

We present a random effects logistic approach for estimating the efficacy of treatment for compliers in a randomized trial with treatment non-adherence and longitudinal binary outcomes. We use our approach to analyse a primary care depression intervention trial. The use of a random effects model to estimate efficacy supplements intent-to-treat longitudinal analyses based on random effects logistic models that are commonly used in primary care depression research. Our estimation approach is an extension of Nagelkerke et al.\u27s instrumental variables approximation for cross-sectional binary outcomes. Our approach is easily implementable with standard random effects logistic regression software. We show through a simulation study that our approach provides reasonably accurate inferences for the setting of the depression trial under model assumptions. We also evaluate the sensitivity of our approach to model assumptions for the depression trial

RETROCAM: A Versatile Optical Imager for Synoptic Studies

We present RETROCAM, an auxiliary CCD camera that can be rapidly inserted into the optical beam of the MDM 2.4m telescope. The speed and ease of reconfiguring the telescope to use the imager and a straightforward user interface permit the camera to be used during the course of other observing programs. This in turn encourages RETROCAM's use for a variety of monitoring projects.Comment: 6 pages, 6 figures, Accepted by A

Blinding participants and assessors in a feasibility randomised controlled trial of peer-befriending for people with aphasia post-stroke

Background and aims: In behavioural interventions, blinding participants to intervention versus control conditions is problematic, as is blinding assessors to participants’ group allocation. When participants are provided with information about the intervention to be tested, they will know whether they are in the intervention or the control arm of the study. This is particularly problematic in psychological interventions where people who may already be distressed or anxious are likely to become even more distressed when they realise they are in the control arm of a study. To minimise potential threats to validity and maintain lack of bias, we took a number of steps in the SUpporting well-being through PEeR-Befriending (SUPERB) feasibility trial for people with aphasia to ensure blinding. This presentation will report on these steps and evaluate their effectiveness. Methods: SUPERB is a single blind, mixed methods, parallel group phase II randomised controlled trial (RCT) comparing usual care+peer-befriending (n = 30) versus usual care (n = 30), starting at discharge from hospital. Little is known about what usual care for psychological support after stroke-aphasia constitutes, and this study will document the services the participants receive in their area for both groups. A modified two-stage consent design has been adopted (Campbell, Peters, Grant, Quilty, & Dieppe, 2005; Torgerson & Roland, 1998), as highlighted in the Medical Research Council framework for complex interventions (Craig et al., 2008). In the first stage, all participants consent to take part in a study on adjustment post-stroke and have their data collected at three time points (i.e., baseline, 4 months, and 10 months). They know they may be compared to other people in the study receiving different packages of care, but are blind to the fact that the study tests a specific intervention (peer-befriending). Following baseline assessments, participants are randomised to either usual care+peer-befriending or usual care. At this point, a second stage consent to take part in the intervention is completed with those participants allocated to the peer-befriending arm. Rate of consent at both stages is monitored. Blinded researchers (assessors) complete assessments for both groups at 4 months and 10 months. Strategies to maintain blinding of assessors include the following: the use of scripts during assessments and asking the participants not to reveal what care they have received; unblinded researcher organising post-randomisation appointments, so that assessors cannot become unblinded by partners/carers of people with aphasia revealing information; and management of the work environment (separate office space, different telephones, and no physical or electronic access to sensitive data). Instances of unblinding are recorded. Results: The trial is currently underway. Thirty-eight of 60 participants have been recruited and 27 have been randomised. The two-stage consent process has been largely successful. No instances of unblinding by participants or researchers have been recorded. Near misses (n = 4) have been recorded for the blinded researchers. These are unrelated to the assessments with participants but rather workplace factors (e.g., use of email, shared calendars, and overhearing telephone conversations). Conclusions: Blinding of participants and researchers is critical to the success of a RCT. This paper raises and discusses a range of processes including a modified two-stage consent process and careful preparation and monitoring of participants, researchers, and workplace factors – which are all important steps to reducing the possibility of unblinding

Machine learning reduced workload with minimal risk of missing studies: development and evaluation of an RCT classifier for Cochrane Reviews

BACKGROUND: To describe the development, calibration and evaluation of a machine learning classifier designed to reduce study identification workload in Cochrane for producing systematic reviews. METHODS: A machine learning classifier for retrieving RCTs was developed (the ‘Cochrane RCT Classifier’), with the algorithm trained using a dataset of title-abstract records from Embase, manually labelled by the Cochrane Crowd. The classifier was then calibrated using a further dataset of similar records manually labelled by the Clinical Hedges team, aiming for 99% recall. Finally, the recall of the calibrated classifier was evaluated using records of RCTs included in Cochrane Reviews that had abstracts of sufficient length to allow machine classification. RESULTS: The Cochrane RCT Classifier was trained using 280,620 records (20,454 of which reported RCTs). A classification threshold was set using 49,025 calibration records (1,587 of which reported RCTs) and our bootstrap validation found the classifier had recall of 0.99 (95% CI 0.98 to 0.99) and precision of 0.08 (95% CI 0.06 to 0.12) in this dataset. The final, calibrated RCT classifier correctly retrieved 43,783 (99.5%) of 44,007 RCTs included in Cochrane Reviews but missed 224 (0.5%). Older records were more likely to be missed than those more recently published. CONCLUSIONS: The Cochrane RCT Classifier can reduce manual study identification workload for Cochrane reviews, with a very low and acceptable risk of missing eligible RCTs. This classifier now forms part of the Evidence Pipeline, an integrated workflow deployed within Cochrane to help improve the efficiency of the study identification processes that support systematic review production