Evidence of overfishing in small-scale fisheries in Madagascar

This is the final version. Available from the publisher via the DOI in this record.The datasets generated for this study are available on request to the corresponding authorSmall-scale fisheries are an important source of food, income and cultural identity to millions of people worldwide. Despite many fisher people observing declining catches, a lack of data remains a barrier to understanding the status of small-scale fisheries and their effective management in many places. Where data exist, complex analyses and stock assessments are often beyond the capacity and budgets of local managers. Working with small-scale fisheries in western Madagascar, we analyze landings data to provide a description of the fishery and evaluate the top twenty most commonly caught species for evidence of overfishing. Using length composition data, we use Froese’s three simple rules: Let them spawn, let them grow and let the mega-spawners live, as well as Cope and Punt’s decision tree to infer if spawning biomass is less than target reference points. We then use length-based parameters to calculate fishing mortality and compare with published estimates of natural mortality to assess overfishing (F > M). Over 17,000 fishing trips were registered over a 2-year period (2010–2012), landing just short of 2 million individual fish. Length data were recorded for a sample of over 120,000 individuals. Fish comprised 95% of landings, with the remainder comprised of other groups including crustaceans (mostly shrimp, crab, and lobster), cephalopods, and holothurians. We provide some of the first evidence that fish species caught in the small-scale fisheries of the Menabe region of Madagascar are experiencing overfishing. The most notable result is that for 13 of the 20 most common species, fishing mortality exceeds natural mortality. Many species had a large proportion of individuals (in some cases 100%) being caught before they reached maturity. Very few species were fished at their optimal size, and there were low numbers of large individuals (mega-spawners) in catches. Overfishing in western Madagascar presents a serious threat to the income, food security and well-being of some of the most vulnerable people in the world. The results of this paper support the call for improved management. However, management approaches should take account of overlapping fisheries and be inclusive to ensure the impacts of management do not undermine the rights of small-scale fishers. Further data are needed to better understand the trends and to improve management but should not hinder pragmatic action.European Union’s Regional Coastal Management Programme of the Indian Ocean Countrie

The Future of Qualitative Research in Psychology: Accentuating the Positive.

In this paper we reflect on current trends and anticipate future prospects regarding qualitative research in Psychology. We highlight various institutional and disciplinary obstacles to qualitative research diversity, complexity and quality. At the same time, we note some causes for optimism, including publication breakthroughs and vitality within the field. The paper is structured into three main sections which consider: 1) the positioning of qualitative research within Psychology; 2) celebrating the different kinds of knowledge produced by qualitative research; and 3) implementing high quality qualitative research. In general we accentuate the positive, recognising and illustrating innovative qualitative research practices which generate new insights and propel the field forward. We conclude by emphasising the importance of research training: for qualitative research to flourish within Psychology (and beyond), students and early career researchers require more sophisticated, in-depth instruction than is currently offered

A framework for protein structure classification and identification of novel protein structures

BACKGROUND: Protein structure classification plays a central role in understanding the function of a protein molecule with respect to all known proteins in a structure database. With the rapid increase in the number of new protein structures, the need for automated and accurate methods for protein classification is increasingly important. RESULTS: In this paper we present a unified framework for protein structure classification and identification of novel protein structures. The framework consists of a set of components for comparing, classifying, and clustering protein structures. These components allow us to accurately classify proteins into known folds, to detect new protein folds, and to provide a way of clustering the new folds. In our evaluation with SCOP 1.69, our method correctly classifies 86.0%, 87.7%, and 90.5% of new domains at family, superfamily, and fold levels. Furthermore, for protein domains that belong to new domain families, our method is able to produce clusters that closely correspond to the new families in SCOP 1.69. As a result, our method can also be used to suggest new classification groups that contain novel folds. CONCLUSION: We have developed a method called proCC for automatically classifying and clustering domains. The method is effective in classifying new domains and suggesting new domain families, and it is also very efficient. A web site offering access to proCC is freely available a

The mechanisms of humic substances self-assembly with biological molecules: The case study of the prion protein

Humic substances (HS) are the largest constituent of soil organic matter and are considered as a key component of the terrestrial ecosystem. HS may facilitate the transport of organic and inorganic molecules, as well as the sorption interactions with environmentally relevant proteins such as prions. Prions enter the environment through shedding from live hosts, facilitating a sustained incidence of animal prion diseases such as Chronic Wasting Disease and scrapie in cervid and ovine populations, respectively. Changes in prion structure upon environmental exposure may be significant as they can affect prion infectivity and disease pathology. Despite its relevance, the mechanisms of prion interaction with HS are still not completely understood. The goal of this work is to advance a structural-level picture of the encapsulation of recombinant, non-infectious, prion protein (PrP) into different natural HS. We observed that PrP precipitation upon addition of HS is mainly driven by a mechanism of “salting-out” whereby PrP molecules are rapidly removed from the solution and aggregate in insoluble adducts with humic molecules. Importantly, this process does not alter the protein folding since insoluble PrP retains its α-helical content when in complex with HS. The observed ability of HS to promote PrP insolubilization without altering its secondary structure may have potential relevance in the context of “prion ecology”. These results suggest that soil organic matter interacts with prions possibly without altering the protein structures. This may facilitate prions preservation from biotic and abiotic degradation leading to their accumulation in the environment

Evaluation of a text supported weight maintenance programme ‘Lighten Up Plus’ following a weight reduction programme: randomised controlled trial

Background Many overweight people find it difficult to maintain weight loss after attending a weight reduction programme. Self-weighing and telephone support are known to be useful methods for self-monitoring for weight loss. We examined the effectiveness of an SMS-text messaging based weight maintenance programme to encourage regular self-weighing in adults who had completed a 12 week commercial weight loss programme. Methods Randomised controlled trial of 380 obese or overweight men and women. The intervention group (n=190) received a single maintenance support phone call and SMS-text based weight maintenance messages over 12 weeks to encourage regular self-weighing after completing their weight loss programme. The primary outcome was change in weight at nine months follow up. Results Our sample (N=380) had a mean age of 47.4 years (SD 13.4), mean baseline weight and BMI of 93.1kg (16.1) and 34.4 kg/m2 (5.0) respectively, as well as majority female (87.3%) and White British (80.0%). Using intention to treat analysis both groups regained weight at nine months follow up; the intervention group regained an average of 1.36 kg while the control group regained 1.81 kg. Adjusting for covariates resulted in a mean difference of 0.45 kg (95% CI -0.78, 1.67) favouring the intervention group at nine month follow up. Conclusions We found no evidence that an SMS based weight maintenance intervention encouraging adults to weigh themselves weekly prevented weight regain at three or nine months after completing a commercial weight loss programme. <br/

Considering methodological options for reviews of theory: illustrated by a review of theories linking income and health

Background: Review of theory is an area of growing methodological advancement. Theoretical reviews are particularly useful where the literature is complex, multi-discipline, or contested. It has been suggested that adopting methods from systematic reviews may help address these challenges. However, the methodological approaches to reviews of theory, including the degree to which systematic review methods can be incorporated, have received little discussion in the literature. We recently employed systematic review methods in a review of theories about the causal relationship between income and health. Methods: This article discusses some of the methodological issues we considered in developing the review and offers lessons learnt from our experiences. It examines the stages of a systematic review in relation to how they could be adapted for a review of theory. The issues arising and the approaches taken in the review of theories in income and health are considered, drawing on the approaches of other reviews of theory. Results: Different approaches to searching were required, including electronic and manual searches, and electronic citation tracking to follow the development of theories. Determining inclusion criteria was an iterative process to ensure that inclusion criteria were specific enough to make the review practical and focused, but not so narrow that key literature was excluded. Involving subject specialists was valuable in the literature searches to ensure principal papers were identified and during the inductive approaches used in synthesis of theories to provide detailed understanding of how theories related to another. Reviews of theory are likely to involve iterations and inductive processes throughout, and some of the concepts and techniques that have been developed for qualitative evidence synthesis can be usefully translated to theoretical reviews of this kind. Conclusions: It may be useful at the outset of a review of theory to consider whether the key aim of the review is to scope out theories relating to a particular issue; to conduct in-depth analysis of key theoretical works with the aim of developing new, overarching theories and interpretations; or to combine both these processes in the review. This can help decide the most appropriate methodological approach to take at particular stages of the review