Every animal matters! Evaluating the selectivity of a Mediterranean bottom trawl fishery from a species community perspective

Bottom trawl fisheries often catch several species simultaneously. However, most studies addressing the catch performance and selectivity of a specific trawl focus on a few commercially important or most vulnerable species requiring management measures. By contrast, the present study considers the multispecies nature of Mediterranean bottom trawl fisheries through a holistic approach that accounts for the full species community in the catches. Specifically, we evaluated and compared the catch performance of the two codends allowed for this fishery, made of 40 mm square (SM40) and 50 mm diamond (DM50) meshes. Results showed that 50 and 80% of the catch in weight and count numbers, respectively, consisted of species without commercial value, demonstrating that large proportions of the catch are not considered when using the existing approach to evaluate the ecological impact of the fishing activity. Significant differences in catch profiles between the two codends were observed, especially for two commercial flatfish species, Arnoglossus laterna and Citharus linguatula, with larger contributions in the SM40. Further, the SM40 codend had a significantly higher retention, compared to DM50 codend, for specific sizes of Merluccius merluccius and Mullus barbatus. The outcomes of the study can be useful for the Mediterranean bottom trawl fisheries management

An overview of bottom trawl selectivity in the Mediterranean Sea

In the Mediterranean Sea, where bottom trawling for demersal species is the most important fishery in terms of landings, around 75% of the assessed fish stocks are overfished. Its status as one of the world’s most heavily exploited seas and the one subject to the highest trawling pressure has become a global concern. An extensive overview of bottom trawl selectivity studies was performed to assess the sustainability of this fishery in the Mediterranean. The selectivity parameters were collected from 93 peer-reviewed publications from 10 countries, totalling 742 records and 65 species. Our review highlighted that i) the catch of the bottom trawls commonly employed in the Mediterranean, although they comply with current codend mesh regulations, still includes immature individuals of 64-68% of the species investigated, and individuals under the minimum conservation reference size (MCRS) of 78% of the species investigated, and that ii) the MCRS set for 59% of the species analysed is well below their length at first maturity and is therefore ecologically inadequate. Although square-mesh codends are slightly more selective, the models developed herein demonstrate that improving size and species selectivity would require considerably larger meshes, which may significantly reduce profitability. The urgent need to mitigate the biological impacts of bottom trawling in the Mediterranean should be addressed by promoting the adoption of more ecologically sustainable fishing gears through the introduction of more selective meshes or of gear modifications

IMPROvER : the Integral Membrane Protein Stability Selector

Identifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein Stability Selector (IMPROvER) provides a rational approach to variant selection by employing three independent approaches: deep-sequence, model-based and data-driven. In silico tests using known stability data, and in vitro tests using three membrane protein targets with 7, 11 and 16 transmembrane helices provided measures of success. In vitro, individual approaches alone all identified stabilising variants at a rate better than expected by random selection. Low numbers of overlapping predictions between approaches meant a greater success rate was achieved (fourfold better than random) when approaches were combined and selections restricted to the highest ranked sites. The mix of information IMPROvER uses can be extracted for any helical membrane protein. We have developed the first general-purpose tool for selecting stabilising variants of alpha -helical membrane proteins, increasing efficiency and reducing workload. IMPROvER can be accessed at http://improver.ddns.net/IMPROvER/.Peer reviewe

Social presence and dishonesty in retail

Self-service checkouts (SCOs) in retail can benefit consumers and retailers, providing control and autonomy to shoppers independent from staff, together with reduced queuing times. Recent research indicates that the absence of staff may provide the opportunity for consumers to behave dishonestly, consistent with a perceived lack of social presence. This study examined whether a social presence in the form of various instantiations of embodied, visual, humanlike SCO interface agents had an effect on opportunistic behaviour. Using a simulated SCO scenario, participants experienced various dilemmas in which they could financially benefit themselves undeservedly. We hypothesised that a humanlike social presence integrated within the checkout screen would receive more attention and result in fewer instances of dishonesty compared to a less humanlike agent. This was partially supported by the results. The findings contribute to the theoretical framework in social presence research. We concluded that companies adopting self-service technology may consider the implementation of social presence in technology applications to support ethical consumer behaviour, but that more research is required to explore the mixed findings in the current study.<br/

ReCoil - an algorithm for compression of extremely large datasets of dna data

The growing volume of generated DNA sequencing data makes the problem of its long term storage increasingly important. In this work we present ReCoil - an I/O efficient external memory algorithm designed for compression of very large collections of short reads DNA data. Typically each position of DNA sequence is covered by multiple reads of a short read dataset and our algorithm makes use of resulting redundancy to achieve high compression rate

Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.

Age at menarche is a marker of timing of puberty in females. It varies widely between individuals, is a heritable trait and is associated with risks for obesity, type 2 diabetes, cardiovascular disease, breast cancer and all-cause mortality. Studies of rare human disorders of puberty and animal models point to a complex hypothalamic-pituitary-hormonal regulation, but the mechanisms that determine pubertal timing and underlie its links to disease risk remain unclear. Here, using genome-wide and custom-genotyping arrays in up to 182,416 women of European descent from 57 studies, we found robust evidence (P < 5 × 10(-8)) for 123 signals at 106 genomic loci associated with age at menarche. Many loci were associated with other pubertal traits in both sexes, and there was substantial overlap with genes implicated in body mass index and various diseases, including rare disorders of puberty. Menarche signals were enriched in imprinted regions, with three loci (DLK1-WDR25, MKRN3-MAGEL2 and KCNK9) demonstrating parent-of-origin-specific associations concordant with known parental expression patterns. Pathway analyses implicated nuclear hormone receptors, particularly retinoic acid and γ-aminobutyric acid-B2 receptor signalling, among novel mechanisms that regulate pubertal timing in humans. Our findings suggest a genetic architecture involving at least hundreds of common variants in the coordinated timing of the pubertal transition

A guide for social science journal editors on easing into open science

Journal editors have a large amount of power to advance open science in their respective fields by incentivising and mandating open policies and practices at their journals. The Data PASS Journal Editors Discussion Interface (JEDI, an online community for social science journal editors: www.dpjedi.org) has collated several resources on embedding open science in journal editing (www.dpjedi.org/resources). However, it can be overwhelming as an editor new to open science practices to know where to start. For this reason, we created a guide for journal editors on how to get started with open science. The guide outlines steps that editors can take to implement open policies and practices within their journal, and goes through the what, why, how, and worries of each policy and practice. This manuscript introduces and summarizes the guide (full guide: https://doi.org/10.31219/osf.io/hstcx)

BRCA2 polymorphic stop codon K3326X and the risk of breast, prostate, and ovarian cancers

Background: The K3326X variant in BRCA2 (BRCA2*c.9976A&gt;T; p.Lys3326*; rs11571833) has been found to be associated with small increased risks of breast cancer. However, it is not clear to what extent linkage disequilibrium with fully pathogenic mutations might account for this association. There is scant information about the effect of K3326X in other hormone-related cancers. Methods: Using weighted logistic regression, we analyzed data from the large iCOGS study including 76 637 cancer case patients and 83 796 control patients to estimate odds ratios (ORw) and 95% confidence intervals (CIs) for K3326X variant carriers in relation to breast, ovarian, and prostate cancer risks, with weights defined as probability of not having a pathogenic BRCA2 variant. Using Cox proportional hazards modeling, we also examined the associations of K3326X with breast and ovarian cancer risks among 7183 BRCA1 variant carriers. All statistical tests were two-sided. Results: The K3326X variant was associated with breast (ORw = 1.28, 95% CI = 1.17 to 1.40, P = 5.9x10- 6) and invasive ovarian cancer (ORw = 1.26, 95% CI = 1.10 to 1.43, P = 3.8x10-3). These associations were stronger for serous ovarian cancer and for estrogen receptor–negative breast cancer (ORw = 1.46, 95% CI = 1.2 to 1.70, P = 3.4x10-5 and ORw = 1.50, 95% CI = 1.28 to 1.76, P = 4.1x10-5, respectively). For BRCA1 mutation carriers, there was a statistically significant inverse association of the K3326X variant with risk of ovarian cancer (HR = 0.43, 95% CI = 0.22 to 0.84, P = .013) but no association with breast cancer. No association with prostate cancer was observed. Conclusions: Our study provides evidence that the K3326X variant is associated with risk of developing breast and ovarian cancers independent of other pathogenic variants in BRCA2. Further studies are needed to determine the biological mechanism of action responsible for these associations

Breech presentation at term and associated obstetric risks factors-a nationwide population based cohort study

Purpose The aim of this study was to estimate whether breech presentation at term was associated with known individual obstetric risk factors for adverse fetal outcome. Methods This was a retrospective, nationwide Finnish population-based cohort study. Obstetric risks in all breech and vertex singleton deliveries at term were compared between the years 2005 and 2014. A multivariable logistic regression model was used to determine significant risk factors. Results The breech presentation rate at term for singleton pregnancies was 2.4%. The stillbirth rate in term breech presentation was significantly higher compared to cephalic presentation (0.2 vs 0.1%). The odds ratios (95% CIs) for fetal growth restriction, oligohydramnios, gestational diabetes, a history of cesarean section and congenital fetal abnormalities were 1.19 CI (1.07-1.32), 1.42 CI (1.27-1.57), 1.06 CI (1.00-1.13), 2.13 (1.98-2.29) and 2.01 CI (1.92-2.11). Conclusions The study showed that breech presentation at term on its own was significantly associated with antenatal stillbirth and a number of individual obstetric risk factors for adverse perinatal outcomes. The risk factors included oligohydramnios, fetal growth restriction, gestational diabetes, history of caesarean section and congenital anomalies.Peer reviewe