Multi-Criteria Decision Analysis as a tool to extract fishing footprints and estimate fishing pressure: application to small scale coastal fisheries and implications for management in the context of the Maritime Spatial Planning Directive

In the context of the Maritime Spatial Planning Directive and with the intention of contributing to the implementation of a future maritime spatial plan, it was decided to analyze data from the small scale coastal fisheries sector of Greece and estimate the actual extent of its activities, which is largely unknown to date. To this end we identified the most influential components affecting coastal fishing: fishing capacity, bathymetry, distance from coast, Sea Surface Chlorophyll (Chl-a) concentration, legislation, marine traffic activity, trawlers and purse seiners fishing effort and no-take zones. By means of Multi-Criteria Decision Analysis (MCDA) conducted through a stepwise procedure, the potential fishing footprint with the corresponding fishing intensity was derived. The method provides an innovative and cost-effective way to assess the impact of the, notoriously hard to assess, coastal fleet. It was further considered how the inclusion of all relevant anthropogenic activities (besides fishing) could provide the background needed to plan future marine activities in the framework of Marine Spatial Planning (MSP) and form the basis for a more realistic management approach

The Picard-Fuchs equations for complete hyperelliptic integrals of even order curves, and the actions of the generalized Neumann system

We consider a family of genus 2 hyperelliptic curves of even order and obtain explicitly the systems of 5 linear ordinary differential equations for periods of the corresponding Abelian integrals of first, second, and third kind, as functions of some parameters of the curves. The systems can be regarded as extensions of the well-studied Picard-Fuchs equations for periods of complete integrals of first and second kind on odd hyperelliptic curves. The periods we consider are linear combinations of the action variables of several integrable systems, in particular the generalized Neumann system with polynomial separable potentials. Thus the solutions of the extended Picard-Fuchs equations can be used to study various properties of the actions. (C) 2014 AIP Publishing LLC.Peer ReviewedPostprint (published version

Intercomparison of five nets used for mesozooplankton sampling

Intercomparison of nets commonly used for mesozooplankton sampling in the Black and Mediterranean seas was attempted within SESAME (Southern European Seas: Assessing and Modelling Ecosystem Changes) project. Five nets were compared: three Juday nets equipped with 150 μm, 180 μm and 200 μm mesh size, Nansen net (100 μm mesh size) and WP2 (200 μm mesh size). Replicated samples were collected at one station in the western Black Sea offshore waters in April 2009. Collected samples were analyzed at species level (except for meroplankton), stages (for copepods) and size length. A decrease of total abundance values was observed with increasing mesh size, due to the significantly higher numbers of animals smaller than 1 mm in the samples obtained by fine mesh size than with coarser nets. Few comparisons were revealed significant for the abundance of animals with 1-2 mm length, while no significance was detected for specimens larger than 2 mm. The above differences resulted in discripancies between nets regarding species and stages composition. Biomass values did not differ significantly between nets, due to the strong contribution to total biomass of the large animals fraction (Calanus euxinus). The smallest and the largest animals revealed high variability between replicates collected by Nansen, Juday- 200 μm and WP2 nets. Correction factors were calculated for the conversion of abundance values between each couple of nets. The detected differences between nets regarding the abundance and biomass, the community taxonomic composition and size structure, as well as the estimated correction factors, provide useful information for the harmonization of data obtained by the above nets in the Black Sea

Cyclin-dependent kinase 9 as a potential target for anti-TNF resistant inflammatory bowel disease

BACKGROUND AND AIMS: Resistance to single cytokine blockade, namely anti-TNF therapy, is a growing concern for patients with inflammatory bowel disease (IBD). The transcription factor T-bet is a critical regulator of intestinal homeostasis, is genetically linked to mucosal inflammation and controls the expression of multiples genes such as the pro-inflammatory cytokines IFN-γ and TNF. Inhibiting T-bet may therefore offer a more attractive prospect for treating IBD but remains challenging to target therapeutically. In this study, we evaluate the effect of targeting the transactivation function of T-bet using inhibitors of P-TEFb (CDK9-cyclin T), a transcriptional elongation factor downstream of T-bet. METHODS: Using an adaptive immune-mediated colitis model, human colonic lymphocytes from IBD patients and multiple large clinical datasets, we investigate the effect of CDK9 inhibitors on cytokine production and gene expression in colonic CD4+ T cells and link these genetic modules to clinical response in patients with IBD. RESULTS: Systemic CDK9 inhibition led to histological improvement of immune-mediated colitis and was associated with targeted suppression of colonic CD4+ T cell-derived IFN-γ and IL-17A. In colonic lymphocytes from IBD patients, CDK9 inhibition potently repressed genes responsible for pro-inflammatory signalling, and in particular genes regulated by T-bet. Remarkably, CDK9 inhibition targeted genes that were highly expressed in anti-TNF resistant IBD and that predicted non-response to anti-TNF therapy. CONCLUSION: Collectively, our findings reveal CDK9 as a potential target for anti-TNF resistant IBD, which has the potential for rapid translation to the clinic

An objective framework to test the quality of candidate indicators of good environmental status

This is the final version. Available from the publisher via the DOI in this record.Large efforts are on-going within the EU to prepare the Marine Strategy Framework Directive's (MSFD) assessment of the environmental status of the European seas. This assessment will only be as good as the indicators chosen to monitor the 11 descriptors of good environmental status (GEnS). An objective and transparent framework to determine whether chosen indicators actually support the aims of this policy is, however, not yet in place. Such frameworks are needed to ensure that the limited resources available to this assessment optimize the likelihood of achieving GEnS within collaborating states. Here, we developed a hypothesis-based protocol to evaluate whether candidate indicators meet quality criteria explicit to the MSFD, which the assessment community aspires to. Eight quality criteria are distilled from existing initiatives, and a testing and scoring protocol for each of them is presented. We exemplify its application in three worked examples, covering indicators for three GEnS descriptors (1, 5, and 6), various habitat components (seaweeds, seagrasses, benthic macrofauna, and plankton), and assessment regions (Danish, Lithuanian, and UK waters). We argue that this framework provides a necessary, transparent and standardized structure to support the comparison of candidate indicators, and the decision-making process leading to indicator selection. Its application could help identify potential limitations in currently available candidate metrics and, in such cases, help focus the development of more adequate indicators. Use of such standardized approaches will facilitate the sharing of knowledge gained across the MSFD parties despite context-specificity across assessment regions, and support the evidence-based management of European seas.European Union: 7th Framework ProgrammeNatural Environment Research Council (NERC)UK Department for Environment, Food and Rural Affair

Habitat Selection and Temporal Abundance Fluctuations of Demersal Cartilaginous Species in the Aegean Sea (Eastern Mediterranean)

Predicting the occurrence of keystone top predators in a multispecies marine environment, such as the Mediterranean Sea, can be of considerable value to the long-term sustainable development of the fishing industry and to the protection of biodiversity. We analysed fisheries independent scientific bottom trawl survey data of two of the most abundant cartilaginous fish species (Scyliorhinus canicula, Raja clavata) in the Aegean Sea covering an 11-year sampling period. The current findings revealed a declining trend in R. clavata and S. canicula abundance from the late ′90 s until 2004. Habitats with the higher probability of finding cartilaginous fish present were those located in intermediate waters (depth: 200–400 m). The present results also indicated a preferential species' clustering in specific geographic and bathymetric regions of the Aegean Sea. Depth appeared to be one of the key determining factors for the selection of habitats for all species examined. With cartilaginous fish species being among the more biologically sensitive fish species taken in European marine fisheries, our findings, which are based on a standardized scientific survey, can contribute to the rational exploitation and management of their stocks by providing important information on temporal abundance trends and habitat preferences

High-Precision Tuning of State for Memristive Devices by Adaptable Variation-Tolerant Algorithm

Using memristive properties common for the titanium dioxide thin film devices, we designed a simple write algorithm to tune device conductance at a specific bias point to 1% relative accuracy (which is roughly equivalent to 7-bit precision) within its dynamic range even in the presence of large variations in switching behavior. The high precision state is nonvolatile and the results are likely to be sustained for nanoscale memristive devices because of the inherent filamentary nature of the resistive switching. The proposed functionality of memristive devices is especially attractive for analog computing with low precision data. As one representative example we demonstrate hybrid circuitry consisting of CMOS summing amplifier and two memristive devices to perform analog multiply and accumulate computation, which is a typical bottleneck operation in information processing.Comment: 20 pages, 6 figure

An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery.

Despite major progress in defining the genetic basis of Mendelian disorders, the molecular etiology of many cases remains unknown. Patients with these undiagnosed disorders often have complex presentations and require treatment by multiple health care specialists. Here, we describe an integrated clinical diagnostic and research program using whole-exome and whole-genome sequencing (WES/WGS) for Mendelian disease gene discovery. This program employs specific case ascertainment parameters, a WES/WGS computational analysis pipeline that is optimized for Mendelian disease gene discovery with variant callers tuned to specific inheritance modes, an interdisciplinary crowdsourcing strategy for genomic sequence analysis, matchmaking for additional cases, and integration of the findings regarding gene causality with the clinical management plan. The interdisciplinary gene discovery team includes clinical, computational, and experimental biomedical specialists who interact to identify the genetic etiology of the disease, and when so warranted, to devise improved or novel treatments for affected patients. This program effectively integrates the clinical and research missions of an academic medical center and affords both diagnostic and therapeutic options for patients suffering from genetic disease. It may therefore be germane to other academic medical institutions engaged in implementing genomic medicine programs

Interleukin 6 increases production of cytokines by colonic innate lymphoid cells in mice and patients with chronic intestinal inflammation

Background & Aims: Innate lymphoid cells (ILCs) are a heterogeneous group of mucosal inflammatory cells that participate in chronic intestinal inflammation. We investigated the role of interleukin 6 (IL6) in inducing activation of ILCs in mice and in human beings with chronic intestinal inflammation. Methods: ILCs were isolated from colons of Tbx21-/- × Rag2-/- mice (TRUC), which develop colitis; patients with inflammatory bowel disease (IBD); and patients without colon inflammation (controls). ILCs were characterized by flow cytometry; cytokine production was measured by enzyme-linked immunosorbent assay and cytokine bead arrays. Mice were given intraperitoneal injections of depleting (CD4, CD90), neutralizing (IL6), or control antibodies. Isolated colon tissues were analyzed by histology, explant organ culture, and cell culture. Bacterial DNA was extracted from mouse fecal samples to assess the intestinal microbiota. Results: IL17A- and IL22-producing, natural cytotoxicity receptor-negative, ILC3 were the major subset of ILCs detected in colons of TRUC mice. Combinations of IL23 and IL1α induced production of cytokines by these cells, which increased further after administration of IL6. Antibodies against IL6 reduced colitis in TRUC mice without significantly affecting the structure of their intestinal microbiota. Addition of IL6 increased production of IL17A, IL22, and interferon-γ by human intestinal CD3-negative, IL7-receptor-positive cells, in a dose-dependent manner. Conclusions: IL6 contributes to activation of colonic natural cytotoxicity receptor-negative, CD4-negative, ILC3s in mice with chronic intestinal inflammation (TRUC mice) by increasing IL23- and IL1α-induced production of IL17A and IL22. This pathway might be targeted to treat patients with IBD because IL6, which is highly produced in colonic tissue by some IBD patients, also increased the production of IL17A, IL22, and interferon-γ by cultured human colon CD3-negative, IL7-receptor-positive cells