Estuarine behaviour of European silver eel (<i>Anguilla anguilla</i>) in the Scheldt estuary

Estuaries are among the most productive ecosystems in the world and are characterised by high habitat diversity. As transition areas between inland rivers and the open sea, they function as transport zones for diadromous species like the European eel (Anguilla anguilla), a catadromous fish species that migrates to the Sargasso Sea for spawning. However, information on the migratory behaviour of eel in estuaries is scarce. Therefore, more insight is needed to efficiently restore and conserve the species. We tracked 47 eels with acoustic telemetry between July 2012 and October 2015 and analysed their behaviour from the Braakman creek into the Scheldt Estuary, separated by a tidal barrier. Eels arrived in the Braakman between mid-summer and early winter and stayed there on average 44 days (0 - 578 days). As such, arrival in the Scheldt Estuary was much later: between early autumn and early winter. The average residence time in the Scheldt Estuary was considerably shorter than in the Braakman, and was only five days (0 - 64 days). The long residence time in the Braakman was probably due to the discontinuous operation of the tidal barrier, which is used to control the water level in the upstream wetland area. This resulted in a discontinuous flow conditions, leading to searching behaviour in eels. Eventually 37 eels did pass the sluice and reached the Scheldt Estuary; the 10 eels which did not pass the sluice were probably caught by a commercial eel fisherman in the Braakman creek. In the Scheldt Estuary, 26 eels migrated towards the sea, whereas eight took the opposite direction and three were only detected at the first receivers downstream of the sluice. The eight eels that did not migrate towards the sea showed estuarine retention behaviour. They could have been injured by the tidal barrier or missed the right moment to migrate, and could be waiting in the estuary until favourable conditions are met to proceed their journey. Our results indicate that eel migration is obstructed by a tidal barrier, which resulted in delayed eel migration. As the migratory period occurred from mid-summer to early winter, this information can be implemented in management plans such as environmental windows to open the sluice during eel migration if circumstances allow such measurements

Extracting causal rules from spatio-temporal data

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-23374-1_2This paper is concerned with the problem of detecting causality in spatiotemporal data. In contrast to most previous work on causality, we adopt a logical rather than a probabilistic approach. By defining the logical form of the desired causal rules, the algorithm developed in this paper searches for instances of rules of that form that explain as fully as possible the observations found in a data set. Experiments with synthetic data, where the underlying causal rules are known, show that in many cases the algorithm is able to retrieve close approximations to the rules that generated the data. However, experiments with real data concerning the movement of fish in a large Australian river system reveal significant practical limitations, primarily as a consequence of the coarse granularity of such movement data. In response, instead of focusing on strict causation (where an environmental event initiates a movement event), further experiments focused on perpetuation (where environmental conditions are the drivers of ongoing processes of movement). After retasking to search for a different logical form of rules compatible with perpetuation, our algorithm was able to identify perpetuation rules that explain a significant proportion of the fish movements. For example, approximately one fifth of the detected long-range movements of fish over a period of six years were accounted for by 26 rules taking account of variations in water-level alone.EPSRCAustralian Research Council (ARC) under the Discovery Projects Schem

Scraping the Social? Issues in live social research

What makes scraping methodologically interesting for social and cultural research? This paper seeks to contribute to debates about digital social research by exploring how a ‘medium-specific’ technique for online data capture may be rendered analytically productive for social research. As a device that is currently being imported into social research, scraping has the capacity to re-structure social research, and this in at least two ways. Firstly, as a technique that is not native to social research, scraping risks to introduce ‘alien’ methodological assumptions into social research (such as an pre-occupation with freshness). Secondly, to scrape is to risk importing into our inquiry categories that are prevalent in the social practices enabled by the media: scraping makes available already formatted data for social research. Scraped data, and online social data more generally, tend to come with ‘external’ analytics already built-in. This circumstance is often approached as a ‘problem’ with online data capture, but we propose it may be turned into virtue, insofar as data formats that have currency in the areas under scrutiny may serve as a source of social data themselves. Scraping, we propose, makes it possible to render traffic between the object and process of social research analytically productive. It enables a form of ‘real-time’ social research, in which the formats and life cycles of online data may lend structure to the analytic objects and findings of social research. By way of a conclusion, we demonstrate this point in an exercise of online issue profiling, and more particularly, by relying on Twitter to profile the issue of ‘austerity’. Here we distinguish between two forms of real-time research, those dedicated to monitoring live content (which terms are current?) and those concerned with analysing the liveliness of issues (which topics are happening?)

Distributed Contact and Identity Management

Contact management is a twofold problem involving a local and global level where the separation between them is rather fuzzy. Locally, users need to deal with contact management, which refers to a local need to store, organize, maintain up to date, and find information that will allow them contacting or reaching other people, organizations, etc. Globally, users deal with identity management that refers to peers having multiple identities (i.e., profiles) and the need of staying in control of them. In other words, they should be able to manage what information is shared and with whom. We believe many existing applications try to deal with this problem looking only at the data level and without analyzing the underlying complexity. Our approach focus on the complex social relations and interactions between users, identifying three main subproblem: (i) management of identity, (ii) search, and (iii) privacy. The solution we propose concentrates on the models that are needed to address these problems. In particular, we propose a Distributed Contact Management System (DCM System) that: Models and represents the knowledge of peers about physical or abstract objects through the notion of entities that can be of different types (e.g., locations, people, events, facilities, organizations, etc.) and are described by a set of attributes; By representing contacts as entities, allows peers to locally organize their contacts taking into consideration the semantics of the contact’s characteristics; By describing peers as entities allows them to manage their different identities in the network, by sharing different views of themselves (showing possibly different in- formation) with different people. The contributions of this thesis are, (i) the definition of a reference architecture that allows dealing with the diversity in relation with the partial view that peers have of the world, (ii) an approach to search entities based on identifiers, (iii) an approach to search entities based on descriptions, and (iv) the definition of the DCM system that instantiates the previously mentioned approaches and architecture to address concrete usage scenarios

Characterization of a globin-coupled oxygen sensor with a gene-regulating function

Globin-coupled sensors (GCSs) are multiple-domain transducers, consisting of a regulatory globin-like heme-binding domain and a linked transducer domain(s). GCSs have been described in both Archaea and bacteria. They are generally assumed to bind O2 (and perhaps other gaseous ligands) and to transmit a conformational change signal through the transducer domain in response to fluctuating O2 levels. In this study, the heme-binding domain, AvGReg178, and the full protein, AvGReg of the Azotobacter vinelandii GCS, were cloned, expressed, and purified. After purification, the heme iron of AvGReg178 was found to bind O2. This form was stable over many hours. In contrast, the predominant presence of a bis-histidine coordinate heme in ferric AvGReg was revealed. Differences in the heme pocket structure were also observed for the deoxygenated ferrous state of these proteins. The spectra showed that the deoxygenated ferrous derivatives of AvGReg178 and AvGReg are characterized by a penta-coordinate and hexa-coordinate heme iron, respectively. O2 binding isotherms indicate that AvGReg178 and AvGReg show a high affinity for O2 with P50 values at 20 °C of 0.04 and 0.15 torr, respectively. Kinetics of CO binding indicate that AvGReg178 carbonylation conforms to a monophasic process, comparable with that of myoglobin, whereas AvGReg carbonylation conforms to a three-phasic reaction, as observed for several proteins with bis-histidine heme iron coordination. Besides sensing ligands, in vitro data suggest that AvGReg(178) may have a role in O2-mediated NO-detoxification, yielding metAvGReg(178) and nitrate. © 2007 by The American Society for Biochemistry and Molecular Biology, Inc

Lysosomal Disorders Drive Susceptibility to Tuberculosis by Compromising Macrophage Migration.

A zebrafish genetic screen for determinants of susceptibility to Mycobacterium marinum identified a hypersusceptible mutant deficient in lysosomal cysteine cathepsins that manifests hallmarks of human lysosomal storage diseases. Under homeostatic conditions, mutant macrophages accumulate undigested lysosomal material, which disrupts endocytic recycling and impairs their migration to, and thus engulfment of, dying cells. This causes a buildup of unengulfed cell debris. During mycobacterial infection, macrophages with lysosomal storage cannot migrate toward infected macrophages undergoing apoptosis in the tuberculous granuloma. The unengulfed apoptotic macrophages undergo secondary necrosis, causing granuloma breakdown and increased mycobacterial growth. Macrophage lysosomal storage similarly impairs migration to newly infecting mycobacteria. This phenotype is recapitulated in human smokers, who are at increased risk for tuberculosis. A majority of their alveolar macrophages exhibit lysosomal accumulations of tobacco smoke particulates and do not migrate to Mycobacterium tuberculosis. The incapacitation of highly microbicidal first-responding macrophages may contribute to smokers' susceptibility to tuberculosis.This work was supported by the National Institutes of Health (R37AI054503, LR, R01NS082567, CBM, 5F30HL110455, RB, 1DP2-OD008614, DMT), the Wellcome Trust (LR), the National Institute of Health Research Cambridge Biomedical Research Centre (LR), the Health Research Board of Ireland (HRA_POR/2013/387, MO’S and CSA/2012/16, JK), and The Royal City of Dublin Hospital Trust (Grant 146, JK).This is the final version of the article. It first appeared from Cell Press via http://dx.doi.org/10.1016/j.cell.2016.02.034

Sex- and age-specific trends in mortality from suicide and undetermined death in Germany 1991–2002

BACKGROUND: Over the last decade, significant downward linear time trends in suicide mortality were observed in most Western countries. To date, it is not established whether those favourable time trends developed homogeneously for sex and age groups and how they were affected by the number of undetermined deaths. METHODS: Data on suicide mortality and undetermined death from 1991 to 2002 in Germany were obtained from the German Federal Statistical Office. For each year, the age-standardised suicide rate (SR), undetermined death rate (UDR) and total rate (SR+UDR) was calculated by direct standardisation separately for men and women. Time trends were analyzed by Poisson regression estimating the average annual percentage change (AAPC) of the rates for sex and four age groups (15–24, 25–44, 45–74, ≥ 75 years). RESULTS: A significant decline of the SR was observed in all age groups but was less pronounced among the younger ages, particularly among men aged 15–24 years (AAPC -0.7%, p = 0.041). The SR in the oldest male age group (≥ 75 years) declined much stronger (AAPC -3.5%, p < 0.001). In women, the AAPC of the SR ranged from -1.7% to -4.6%. The average annual percentage changes in the age groups 25 – 74 years did not differ substantially for SR and SR+UDR. In contrast, due to an increase of undetermined deaths for subjects ≥ 75 years, time trends in this age group were affected by the number of undetermined deaths, especially in women. CONCLUSION: Observing downward trends in suicide mortality with lower declines for younger subjects, prevention strategies should focus in particular on younger subjects