On the Distribution and Fishery Potential of the Japanese Red Crab Chaceon granulatus in the Palauan Archipelago, Western Caroline Islands

A deep-water trapping survey in the Palauan archipelago, Western Caroline Islands, has revealed an abundance of the Japanese red crab, Chaceon granulatus. The recorded depth range (250-900 m) is similar to that of other geryonids, but the large numbers of females caught below 700 m is atypical. Mean yields in excess of 5 kg crabs plus 1 kg shrimp, Heterocarpus laevigatus, by-catch per trap-night were attainable at optimum depths. Chaceon granulatus is apparently a very large geryonid, with maximum weights of 2.02 kg and 1.51 kg recorded for male and female specimens, respectively. A range of body colors was observed: Orange-red shades appear to dominate the deeper waters (below 500 m) while yellow-tan colors are more abundant in the upper reaches. Preliminary evidence suggests that Chaceon granulatus is highly marketable, and the infrastructure in Palau is such that crabs could either be marketed fresh locally or airfreighted to Japan as a quick-frozen product. The high post-trapping survival rates observed indicate that maintaining crabs in live-holding tanks may be a feasible option. The large catches and quality of deep-water crabs taken suggests that the Palauan population of Chaceon granulatus may be able to support a small-scale fishery. It is not yet known whether this population is unusually large or whether these findings typify the deep forereef fauna of the region

Infection levels and species diversity of ascaridoid nematodes in Atlantic cod, Gadus morhua, are correlated with geographic area and fish size

Atlantic cod (Gadus morhua) is among the most important commercial fish species on the world market. Its infection by ascaridoid nematodes has long been known, Pseudoterranova even being named cod worm. In the present study, 755 individuals were sampled in the Barents, Baltic and North Seas during 2012–2014. Prevalences for Anisakis in whole fish and in fillets in the different fishing areas varied from 16 to 100% and from 12 to 90% respectively. Abundance was also greatly influenced by the sampling area. Generalized additive model results indicate higher numbers of Anisakis in the North Sea, even after the larger body size was accounted for. Numbers and prevalence of Anisakis were positively related to fish length or weight. The prevalence of parasites in whole fish and in fillets was also influenced by the season, with the spring displaying a peak for the prevalence in whole fish and, at the same time, a drop for the prevalence in fillets. Whereas 46% of cod had Anisakis larvae in their fillets, the majority (39%) had parasites mainly in the ventral part of the fillet and only 12% had parasites in their dorsal part. This observation is of importance for the processing of the fish. Indeed, the trimming of the ventral part of the cod fillet would allow the almost total elimination of ascaridoids except for cod from the Baltic Sea where there was no difference between the dorsal and the ventral part. The presence of other ascaridoid genera was also noticeable in some areas. For Pseudoterranova, the highest prevalence (45%) in whole fish was observed in the Northern North Sea, whereas the other areas had prevalences between 3 and 16%. Contracaecum was present in every commercial size cod sampled in the Baltic Sea with an intensity of up to 96 worms but no Contracaecum was isolated from the Central North Sea. Non-zoonotic Hysterothylacium was absent from the Baltic Sea but with a prevalence of 83% in the Barents and the Northern North Sea. A subsample of worms was identified with genetic-molecular tools and assigned to the species A. simplex (s.s.), A. pegreffii, P. decipiens (s.s.), P. krabbei, C. osculatum and H. aduncum. In addition to high prevalence and abundance values, the cod sampled in this study presented a diversity of ascaridoid nematodes with a majority of fish displaying a co-infection. Out of 295 whole infected fish, 269 were co-infected by at least 2 genera

A General Optimization Technique for High Quality Community Detection in Complex Networks

Recent years have witnessed the development of a large body of algorithms for community detection in complex networks. Most of them are based upon the optimization of objective functions, among which modularity is the most common, though a number of alternatives have been suggested in the scientific literature. We present here an effective general search strategy for the optimization of various objective functions for community detection purposes. When applied to modularity, on both real-world and synthetic networks, our search strategy substantially outperforms the best existing algorithms in terms of final scores of the objective function; for description length, its performance is on par with the original Infomap algorithm. The execution time of our algorithm is on par with non-greedy alternatives present in literature, and networks of up to 10,000 nodes can be analyzed in time spans ranging from minutes to a few hours on average workstations, making our approach readily applicable to tasks which require the quality of partitioning to be as high as possible, and are not limited by strict time constraints. Finally, based on the most effective of the available optimization techniques, we compare the performance of modularity and code length as objective functions, in terms of the quality of the partitions one can achieve by optimizing them. To this end, we evaluated the ability of each objective function to reconstruct the underlying structure of a large set of synthetic and real-world networks.Comment: MAIN text: 14 pages, 4 figures, 1 table Supplementary information: 19 pages, 8 figures, 5 table

Fast stable direct fitting and smoothness selection for Generalized Additive Models

Existing computationally efficient methods for penalized likelihood GAM fitting employ iterative smoothness selection on working linear models (or working mixed models). Such schemes fail to converge for a non-negligible proportion of models, with failure being particularly frequent in the presence of concurvity. If smoothness selection is performed by optimizing `whole model' criteria these problems disappear, but until now attempts to do this have employed finite difference based optimization schemes which are computationally inefficient, and can suffer from false convergence. This paper develops the first computationally efficient method for direct GAM smoothness selection. It is highly stable, but by careful structuring achieves a computational efficiency that leads, in simulations, to lower mean computation times than the schemes based on working-model smoothness selection. The method also offers a reliable way of fitting generalized additive mixed models

Geo-additive models of Childhood Undernutrition in three Sub-Saharan African Countries

We investigate the geographical and socioeconomic determinants of childhood undernutrition in Malawi, Tanzania and Zambia, three neighboring countries in Southern Africa using the 1992 Demographic and Health Surveys. We estimate models of undernutrition jointly for the three countries to explore regional patterns of undernutrition that transcend boundaries, while allowing for country-specific interactions. We use semiparametric models to flexibly model the effects of selected so-cioeconomic covariates and spatial effects. Our spatial analysis is based on a flexible geo-additive model using the district as the geographic unit of anal-ysis, which allows to separate smooth structured spatial effects from random effect. Inference is fully Bayesian and uses recent Markov chain Monte Carlo techniques. While the socioeconomic determinants generally confirm what is known in the literature, we find distinct residual spatial patterns that are not explained by the socioeconomic determinants. In particular, there appears to be a belt run-ning from Southern Tanzania to Northeastern Zambia which exhibits much worse undernutrition, even after controlling for socioeconomic effects. These effects do transcend borders between the countries, but to a varying degree. These findings have important implications for targeting policy as well as the search for left-out variables that might account for these residual spatial patterns

Fast Primal-Dual Gradient Method for Strongly Convex Minimization Problems with Linear Constraints

In this paper we consider a class of optimization problems with a strongly convex objective function and the feasible set given by an intersection of a simple convex set with a set given by a number of linear equality and inequality constraints. A number of optimization problems in applications can be stated in this form, examples being the entropy-linear programming, the ridge regression, the elastic net, the regularized optimal transport, etc. We extend the Fast Gradient Method applied to the dual problem in order to make it primal-dual so that it allows not only to solve the dual problem, but also to construct nearly optimal and nearly feasible solution of the primal problem. We also prove a theorem about the convergence rate for the proposed algorithm in terms of the objective function and the linear constraints infeasibility.Comment: Submitted for DOOR 201

Finding rare objects and building pure samples: Probabilistic quasar classification from low resolution Gaia spectra

We develop and demonstrate a probabilistic method for classifying rare objects in surveys with the particular goal of building very pure samples. It works by modifying the output probabilities from a classifier so as to accommodate our expectation (priors) concerning the relative frequencies of different classes of objects. We demonstrate our method using the Discrete Source Classifier, a supervised classifier currently based on Support Vector Machines, which we are developing in preparation for the Gaia data analysis. DSC classifies objects using their very low resolution optical spectra. We look in detail at the problem of quasar classification, because identification of a pure quasar sample is necessary to define the Gaia astrometric reference frame. By varying a posterior probability threshold in DSC we can trade off sample completeness and contamination. We show, using our simulated data, that it is possible to achieve a pure sample of quasars (upper limit on contamination of 1 in 40,000) with a completeness of 65% at magnitudes of G=18.5, and 50% at G=20.0, even when quasars have a frequency of only 1 in every 2000 objects. The star sample completeness is simultaneously 99% with a contamination of 0.7%. Including parallax and proper motion in the classifier barely changes the results. We further show that not accounting for class priors in the target population leads to serious misclassifications and poor predictions for sample completeness and contamination. (Truncated)Comment: MNRAS accepte

Cephalopods in the north-eastern Atlantic: Species, biogeography, ecology, exploitation and conservation

Cephalopods play a significant role in coastal and oceanic ecosystems, both as consumers of invertebrates and small fish and as the prey of some fish, seabirds and marine mammals and other large predators. Approximately 30 species of cephalopod have been recorded in the north-eastern Atlantic and adjacent waters, including 18 teuthid (squid), seven sepiolid (bobtail), three sepiid (cuttlefish) and 10 octopod (octopus) species. A number of these are exploited commercially and support important target and by-catch fisheries in Western Europe. During the past decade, annual landings of cephalopods from the north-eastern Atlantic (International Council for the Exploration of the Sea [ICES] area) have ranged from 40,000 to 55,000 t, including substantial catches of long-fin (loliginid) squid (7000–11,000 t per annum), short-fin (ommastrephid) squid (3000–10,000 t), cuttlefish (including sepiolids; 16,000–24,000 t) and octopods (12,000–18,000 t). The most important exploited species in the north-eastern Atlantic are Eledone cirrhosa, Illex coindetii, Loligo forbesi, Loligo vulgaris, Octopus vulgaris, Todarodes sagittatus, Todaropsis eblanae and Sepia officinalis. Other species including Alloteuthis subulata, Gonatus fabricii and certain sepiolids, appear to be abundant and may be marketable. Cephalopods tend to rapidly concentrate heavy metals and other toxic substances in their tissues and this plays an important role in the bioaccumulation of these pollutants in marine predators as well as having implications for human consumption. High levels of cadmium and mercury are often recorded in cephalopod tissues. Another important environmental issue concerns the potential impact of widespread human activity on cephalopod spawning areas, particularly bottom-fishing operations but also shipping, and oil exploration and production. In contrast to many finfish species that spawn annually over a number of years, most cephalopods live only 1–2 yr and die after spawning. Therefore, failure to reproduce and recruit adequately in any given year may seriously impact the long-term viability of cephalopod stocks. Climate change is expected to have a significant effect on many species in the north-eastern Atlantic. This review provides a detailed account of the zoogeography, biology and ecology of cephalopods in the north-eastern Atlantic, on a species-by-species basis. Important economic, ecological and conservation issues affecting cephalopods in this area are also discusse

Vestiges of the proto-Caribbean seaway: origin of the San Souci Volcanic Group, Trinidad

Outcrops of volcanic–hypabyssal rocks in Trinidad document the opening of the proto-Caribbean seaway during Jurassic–Cretaceous break-up of the Americas. The San Souci Group on the northern coast of Trinidad comprises the San Souci Volcanic Formation (SSVF) and passive margin sediments of the ~ 130–125 Ma Toco Formation. The Group was trapped at the leading edge of the Pacific-derived Caribbean Plate during the Cretaceous–Palaeogene, colliding with the para-autochthonous margin of Trinidad during the Oligocene–Miocene. In-situ U–Pb ion probe dating of micro-zircons from a mafic volcanic breccia reveal the SSVF crystallised at 135.0 ± 7.3 Ma. The age of the SSVF is within error of the age of the Toco Formation. Assuming a conformable contact, geodynamic models indicate a likely origin for the SSVF on the passive margin close to the northern tip of South America. Immobile element and Nd–Hf radiogenic isotope signatures of the mafic rocks indicate the SSVF was formed by ≪10% partial melting of a heterogeneous spinel peridotite source with no subduction or continental lithospheric mantle component. Felsic breccias within the SSVF are more enriched in incompatible elements, with isotope signatures that are less radiogenic than the mafic rocks of the SSVF. The felsic rocks may be derived from re-melting of mafic crust. Although geochemical comparisons are drawn here with proto-Caribbean igneous outcrops in Venezuela and elsewhere in the Caribbean more work is needed to elucidate the development of the proto-Caribbean seaway and its rifted margins. In particular, ion probe dating of micro-zircons may yield valuable insights into magmatism and metamorphism in the Caribbean, and in altered basaltic terranes more generally