A model of horse mussel reef formation in the Bay of Fundy based on population growth and geological processes

From a total of 14 geological sediment provinces recognized in the Bay of Fundy only five: sand with bioherms, gravel/cobble, gravel /scallop bed, mottled gravel and glacio-marine mud were found to have significant populations of the horse mussel, Modiolus modiolus. Valve increment measures of annual growth rings in the early years of life of populations of these Bay of Fundy horse mussels, suggest that growth rates vary with the geological province where they are found. Horse mussel populations grow fastest on sand with bioherms, closely followed by those growing on gravel/scallop bed; the slowest growing are found on gravel/ cobble and mottled gravel geological provinces. Multibeam bathymetry and backscatter data have been collected in an area of mussel reefs in the central part of the Bay of Fundy. The data indicates that the mussel reefs (bioherms) tend to occur on the eastern side of small, gravel covered, glacial ridges on the seabed and form a variety of single and multiple, long and short reefs that rise above the seabed up to 3 m high. They are always associated with sand in transport at the seabed in a variety of bedforms. A conceptual model of formation and location is presented that considers: current velocity and turbulence, well-mixed water masses, seabed morphology, sediment distribution and sediment transport, as causative factors. RÉSUMÉ D’un total de 14 classes de sédiments géologiques reconnues dans la baie de Fundy, seulement cinq (biohermes, gravier/galets, gravier/fond de pétoncle, gravier tacheté et boue glacio-marine) renfermaient des populations importantes de modiole Modiolus modiolus. Les mesures de l’augmentation valvaire des cernes d’accroissement annuels durant les premières années de vie des populations de modioles dans la baie de Fundy indiqueraient que les taux de croissance varient selon la classe de sédiment géologique où ils se trouvent. Les populations de modioles croissent plus rapidement dans le sable renfermant des biohermes, et la croissance est presque aussi grande chez les modioles présents dans les classes de sédiments composées de gravier/fond de pétoncles; la croissance la plus lente a été observée dans les classes de sédiments géologiques composées de gravier/galets et de gravier tacheté. Des données ont été recueillies au moyen de la bathymétrie par secteurs et de la rétrodiffusion dans une zone de récifs de moules de la partie centrale de la baie de Fundy. Les données indiquent que les récifs de moules (biohermes) semblent se former sur le côté est de petites crêtes glaciaires recouvertes de gravier sur le plancher sous‑marin, et qu’ils forment divers récifs uniques et multiples, longs et courts, qui s’élèvent sur le plancher sous-marin jusqu’à une hauteur de trois mètres. Ils sont toujours associés avec le sable déplacé sur le plancher sous-marin dans diverses morphologies de fond. On présente un modèle conceptuel de la formation et de l’emplacement qui considère comme facteurs de causalité les éléments suivants : la vitesse et la turbulence actuelles, les masses d’eau homogènes, la morphologie du plancher sous-marin, la répartition des sédiments et les transports sédimentaires. [Traduit par la redaction

Exploring relation types for literature-based discovery

Objective Literature-based discovery (LBD) aims to identify “hidden knowledge” in the medical literature by: (1) analyzing documents to identify pairs of explicitly related concepts (terms), then (2) hypothesizing novel relations between pairs of unrelated concepts that are implicitly related via a shared concept to which both are explicitly related. Many LBD approaches use simple techniques to identify semantically weak relations between concepts, for example, document co-occurrence. These generate huge numbers of hypotheses, difficult for humans to assess. More complex techniques rely on linguistic analysis, for example, shallow parsing, to identify semantically stronger relations. Such approaches generate fewer hypotheses, but may miss hidden knowledge. The authors investigate this trade-off in detail, comparing techniques for identifying related concepts to discover which are most suitable for LBD. Materials and methods A generic LBD system that can utilize a range of relation types was developed. Experiments were carried out comparing a number of techniques for identifying relations. Two approaches were used for evaluation: replication of existing discoveries and the “time slicing” approach.1 Results Previous LBD discoveries could be replicated using relations based either on document co-occurrence or linguistic analysis. Using relations based on linguistic analysis generated many fewer hypotheses, but a significantly greater proportion of them were candidates for hidden knowledge. Discussion and Conclusion The use of linguistic analysis-based relations improves accuracy of LBD without overly damaging coverage. LBD systems often generate huge numbers of hypotheses, which are infeasible to manually review. Improving their accuracy has the potential to make these systems significantly more usabl

BLOC-1 and BLOC-3 regulate VAMP7 cycling to and from melanosomes via distinct tubular transport carriers.

Endomembrane organelle maturation requires cargo delivery via fusion with membrane transport intermediates and recycling of fusion factors to their sites of origin. Melanosomes and other lysosome-related organelles obtain cargoes from early endosomes, but the fusion machinery involved and its recycling pathway are unknown. Here, we show that the v-SNARE VAMP7 mediates fusion of melanosomes with tubular transport carriers that also carry the cargo protein TYRP1 and that require BLOC-1 for their formation. Using live-cell imaging, we identify a pathway for VAMP7 recycling from melanosomes that employs distinct tubular carriers. The recycling carriers also harbor the VAMP7-binding scaffold protein VARP and the tissue-restricted Rab GTPase RAB38. Recycling carrier formation is dependent on the RAB38 exchange factor BLOC-3. Our data suggest that VAMP7 mediates fusion of BLOC-1-dependent transport carriers with melanosomes, illuminate SNARE recycling from melanosomes as a critical BLOC-3-dependent step, and likely explain the distinct hypopigmentation phenotypes associated with BLOC-1 and BLOC-3 deficiency in Hermansky-Pudlak syndrome variants.This work was supported by grants from the National Institutes of Health, National Eye Institute (R01 EY015625, to M.S. Marks and G.  Raposo), National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01 AR048155, to M.S. Marks, and F32 AR062476, to M.K. Dennis), National Institute of General Medical Sciences (R01 GM108807, to M.S. Marks); Fondation pour la Recherche Médicale (to T.  Galli); the UK Medical Research Council (G0900113, to J.P. Luzio); and the Wellcome Trust (108429, to E.V. Sviderskaya and D.C. Bennett). This work was also supported by a Canadian Institutes of Health Research Fellowship (to G.G.  Hesketh) and a Fondation pour la Recherche Médicale grant from Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Curie, and Fondation pour la Recherche Médicale (DEQ20140329491 Team label, to G. Raposo).This is the final version of the article. It first appeared from Rockefeller University Press via http://dx.doi.org/10.1083/jcb.20160509

TReatIng Urinary symptoms in Men in Primary Healthcare using non-pharmacological and non-surgical interventions (TRIUMPH) compared with usual care: Study protocol for a cluster randomised controlled trial

Background: Lower urinary tract symptoms (LUTS) can relate to urinary storage or voiding. In men, the prevalence and severity of LUTS increases with age, with a significant impact on quality of life. The majority of men presenting with LUTS are managed by their general practitioner (GP) in the first instance, with conservative therapies recommended as the initial treatment. However, the provision of conservative therapies in primary care is variable and can be time and resource limited. GPs require practical resources to enhance patient engagement with such interventions. TRIUMPH aims to determine whether a standardised and manualised care intervention delivered in primary care achieves superior symptomatic outcome for LUTS versus usual care.Methods/design: TRIUMPH is a two-arm, cluster randomised controlled trial (RCT) being conducted in 30 National Health Service (NHS) general practices in England. The TRIUMPH intervention comprises a standardised LUTS advice booklet developed for the trial with patient and healthcare professional (HCP) consultation. The booklet is delivered to patients by nurses/healthcare assistants following assessment of their urinary symptoms. Patients are directed to relevant sections of the booklet, providing the manualised element of the intervention. To encourage adherence, HCPs provide follow-up contacts over 12 weeks. Practices are randomised 1:1 to either deliver the TRIUMPH intervention or a usual care pathway. The patient-reported International Prostate Symptom Score (IPSS) at 12 months post consent is the primary outcome. Secondary outcomes include cost-effectiveness, patient-reported outcomes on LUTS, quality of life, and patient and HCP acceptability and experience of the intervention. Primary analyses will be conducted on an intention-to-treat basis.Discussion: It is unclear whether conservative therapies for male LUTS are effectively delivered in primary care using current approaches. This can lead to men being inappropriately referred to secondary care or experiencing persistent symptoms. Primary care, therefore, holds the key to effective treatment for these men. The TRIUMPH intervention, through its standardised and manualised approach, has been developed to support GP practices in delivering effective conservative care. This pragmatic, cluster RCT should provide robust evidence in a primary-care setting to inform future guidelines

Treatment of lower urinary tract symptoms in men in primary care using a conservative intervention: Cluster randomised controlled trial

Objective: To determine whether a standardised and manualised care intervention in men in primary care could achieve superior improvement of lower urinary tract symptoms (LUTS) compared with usual care. Design: Cluster randomised controlled trial. Setting: 30 National Health Service general practice sites in England. Participants: Sites were randomised 1:1 to the intervention and control arms. 1077 men (≥18 years) with bothersome LUTS recruited between June 2018 and August 2019: 524 were assigned to the intervention arm (n=17 sites) and 553 were assigned to the usual care arm (n=13 sites). Intervention: Standardised information booklet developed with patient and expert input, providing guidance on conservative and lifestyle interventions for LUTS in men. After assessment of urinary symptoms (manualised element), general practice nurses and healthcare assistants or research nurses directed participants to relevant sections of the manual and provided contact over 12 weeks to assist with adherence. Main outcome measures: The primary outcome was patient reported International Prostate Symptom Score (IPSS) measured 12 months after participants had consented to take part in the study. The target reduction of 2.0 points on which the study was powered reflects the minimal clinically important difference where baseline IPSS is <20. Secondary outcomes were patient reported quality of life, urinary symptoms and perception of LUTS, hospital referrals, and adverse events. The primary intention-to-treat analysis included 887 participants (82% of those recruited) and used a mixed effects multilevel linear regression model adjusted for site level variables used in the randomisation and baseline scores. Results: Participants in the intervention arm had a lower mean IPSS at 12 months (adjusted mean difference −1.81 points, 95% confidence interval −2.66 to −0.95) indicating less severe urinary symptoms than those in the usual care arm. LUTS specific quality of life, incontinence, and perception of LUTS also improved more in the intervention arm than usual care arm at 12 months. The proportion of urology referrals (intervention 7.3%, usual care 7.9%) and adverse events (intervention seven events, usual care eight events) were comparable between the arms. Conclusions: A standardised and manualised intervention in primary care showed a sustained reduction in LUTS in men at 12 months. The mean difference of −1.81 points (95% confidence interval −0.95 to −2.66) on the IPSS was less than the predefined target reduction of 2.0 points. Trial registration: ISRCTN Registry ISRCTN11669964

Lower urinary tract symptoms in men: The TRIUMPH cluster RCT

Conservative therapies are recommended as initial treatment for male lower urinary tract symptoms. However, there is a lack of evidence on effectiveness and uncertainty regarding approaches to delivery. The objective was to determine whether or not a standardised and manualised care intervention delivered in primary care achieves superior symptomatic outcome for lower urinary tract symptoms to usual care. This was a two-arm cluster randomised controlled trial. The trial was set in 30 NHS general practice sites in England. Participants were adult men (aged ≥ 18 years) with bothersome lower urinary tract symptoms. Sites were randomised 1 : 1 to deliver the TReatIng Urinary symptoms in Men in Primary Health care using non-pharmacological and non-surgical interventions trial intervention or usual care to all participants. The TReatIng Urinary symptoms in Men in Primary Health care using non-pharmacological and non-surgical interventions intervention comprised a standardised advice booklet developed for the trial from the British Association of Urological Surgeons' patient information sheets, with patient and expert input. Patients were directed to relevant sections by general practice or research nurses/healthcare assistants following urinary symptom assessment, providing the manualised element. The healthcare professional provided follow-up contacts over 12 weeks to support adherence to the intervention. The primary outcome was the validated patient-reported International Prostate Symptom Score 12 months post consent. Rather than the minimal clinically important difference of 3.0 points for overall International Prostate Symptom Score, the sample size aimed to detect a difference of 2.0 points, owing to the recognised clinical impact of individual symptoms. A total of 1077 men consented to the study: 524 in sites randomised to the intervention arm ( = 17) and 553 in sites randomised to the control arm ( = 13). A difference in mean International Prostate Symptom Score at 12 months was found (adjusted mean difference of -1.81 points, 95% confidence interval -2.66 to -0.95 points), with a lower score in the intervention arm, indicating less severe symptoms. Secondary outcomes of patient-reported urinary symptoms, quality of life specific to lower urinary tract symptoms and perception of lower urinary tract symptoms all showed evidence of a difference between the arms favouring the intervention. No difference was seen between the arms in the proportion of urology referrals or adverse events. In qualitative interviews, participants welcomed the intervention, describing positive effects on their symptoms, as well as on their understanding of conservative care and their attitude towards the experience of lower urinary tract symptoms. The interviews highlighted that structured, in-depth self-management is insufficiently embedded within general practitioner consultations. From an NHS perspective, mean costs and quality-adjusted life-years were similar between trial arms. The intervention arm had slightly lower mean costs (adjusted mean difference of -£29.99, 95% confidence interval -£109.84 to £22.63) than the usual-care arm, and a small gain in quality-adjusted life-years (adjusted mean difference of 0.001, 95% confidence interval -0.011 to 0.014). The intervention showed a small, sustained benefit for men's lower urinary tract symptoms and quality of life across a range of outcome measures in a UK primary care setting. Qualitative data showed that men highly valued the intervention. Intervention costs were marginally lower than usual-care costs. Limitations of the study included that trial participants were unmasked, with limited diversity in ethnicity and deprivation level. Additional research is needed to assess the applicability of the intervention for a more ethnically diverse population.. This trial is registered as ISRCTN11669964. This award was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme (NIHR award ref: 16/90/03) and is published in full in ; Vol. 28, No. 13. See the NIHR Funding and Awards website for further award information

Biodiversity of the Deep-Sea Continental Margin Bordering the Gulf of Maine (NW Atlantic): Relationships among Sub-Regions and to Shelf Systems

Background: In contrast to the well-studied continental shelf region of the Gulf of Maine, fundamental questions regarding the diversity, distribution, and abundance of species living in deep-sea habitats along the adjacent continental margin remain unanswered. Lack of such knowledge precludes a greater understanding of the Gulf of Maine ecosystem and limits development of alternatives for conservation and management. Methodology/Principal Findings: We use data from the published literature, unpublished studies, museum records and online sources, to: (1) assess the current state of knowledge of species diversity in the deep-sea habitats adjacent to the Gulf of Maine (39–43uN, 63–71uW, 150–3000 m depth); (2) compare patterns of taxonomic diversity and distribution of megafaunal and macrofaunal species among six distinct sub-regions and to the continental shelf; and (3) estimate the amount of unknown diversity in the region. Known diversity for the deep-sea region is 1,671 species; most are narrowly distributed and known to occur within only one sub-region. The number of species varies by sub-region and is directly related to sampling effort occurring within each. Fishes, corals, decapod crustaceans, molluscs, and echinoderms are relatively well known, while most other taxonomic groups are poorly known. Taxonomic diversity decreases with increasing distance from the continental shelf and with changes in benthic topography. Low similarity in faunal composition suggests the deep-sea region harbours faunal communities distinct from those of the continental shelf. Non-parametric estimators of species richness suggest a minimum of 50% of the deep-sea species inventory remains to be discovered. Conclusions/Significance: The current state of knowledge of biodiversity in this deep-sea region is rudimentary. Our ability to answer questions is hampered by a lack of sufficient data for many taxonomic groups, which is constrained by sampling biases, life-history characteristics of target species, and the lack of trained taxonomists

DEVELOPMENTAL, HORMONAL, AND ENZYMATIC ASPECTS OF BETA-ALANYL-L-TYROSINE HYDROLASE FROM THE FLESHFLY, SARCOPHAGA BULLATA PARKER.

Abstract not availabl

Environmental Geology of Halifax Harbour, Nova Scotia

This paper demonstrates the importance of integrated studies of marine geology and geochemistry in the environmental management of an urbanized coastal inlet, using Halifax Harbour, Nova Scotia, as an example. The harbour receives 170 million litres of raw sewage per day; other sources of contamination include landfills, industrial activity, surface runoff and dredging. The level of contamination by metals in surficial sediments in Halifax Harbour is among the highest anywhere recorded in marine harbours, and is a result of sediment trapping and lack of flushing. Geological and oceanographic conditions strongly influence the present environmental quality of the harbour; assessment of environmental quality, and the design of waste-water management systems in urban harbours, are fundamentally dependant on detailed knowledge of sediment transport, deposition and erosion. Résumé En prenant pour exemple le cas du Port de Halifax, le présent article montre l'importance de l'intégration d'études de géologie et de géochimie dans la gestion environnementale des bras de mer urbanisée. Quotidiennement, 170 millions de litres d'eaux d'égout sont déversés dans le port. Les décharges, les activités industrielles, les eaux de ruissellement et le dragage constituent d'autres sources de contamination. Le niveau de contamination des métaux des dépôts sédimentaires superficiels du Port de Halifax est parmi les plus élevés des ports marins étudiés dans le monde, et cela est la conséquence de la rétention des sédiments et du manque de chasse d'eau. Les conditions géologiques et océanographiques sont des facteurs lourds de la qualité actuelle de l'environnement du port; l'évaluation de la qualité de l'environnement et la conception de systèmes de gestion des eaux usées en port urbains dépendent d'abord des connaisances détaillées des modes de transport, de sédimentation et d'érosion des sédiments