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  • Articles  (6,101)
  • Oxford University Press  (6,101)
  • 2010-2014  (6,101)
  • ICES Journal of Marine Science  (560)
  • Computer Journal  (440)
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  • Articles  (6,101)
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  • Oxford University Press  (6,101)
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  • 1
    Publication Date: 2013-10-02
    Description: We proposed two multiparty quantum secret sharing schemes based on n -particle Greenberger–Horne–Zeilinger-states (GHZ states), which are transformed from Einstein–Podolsky–Rosen pairs by entanglement swapping. In our schemes, the dealer imposes messages by performing local unitary operations ( I, x, i y, z ) on the n -particle GHZ state she holds, and the agents collaborate to deduce the dealer's messages by performing local unitary operations on their own qubit. The amount of dealer's secret message is positively related with the number of agents. The need of qubits is one-third less than the former schemes and, also, they can be reused for the next new round. The scheme (II) does not have to pre-share the code table, which increases the security without the risk of being stolen.
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  • 2
    Publication Date: 2013-10-02
    Description: Automatic fare collection (AFC) systems calculate the fare that the users must pay depending on the time of service (time-based) or the points of entrance and exit of the system (distance-based). The progressive introduction of Information and Communication Technologies allows the use of electronic tickets, which helps us to reduce costs and improve the control of the infrastructures. Nevertheless, these systems must be secure against possible fraud and they must also preserve users’ privacy. Therefore, we have studied the security requirements for the time-based and distance-based systems and we have proposed a protocol for each of the AFC systems. 1 The protocols offer strong privacy for honest users, i.e. the service provider is not able to disclose the identity of its users and, moreover, different journeys of the same user are not linkable between them. However, anonymity for users could be revoked if they misbehave. The protocols have been implemented in Android and its performance has been evaluated in two Android smartphones. The results remark that protocols are suitable to be used on an AFC system with a medium class mobile device although they offer a better experience with a high-class smartphone. The appearance in the market of more powerful mobile devices suggests a better usability of our proposal in a near future.
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  • 3
    Publication Date: 2013-10-02
    Description: Accurately locating unknown nodes is a critical issue in the study of wireless sensor networks (WSNs). Many localization approaches have been proposed based on anchor nodes, which are assumed to know their locations by manual placement or additional equipments such as global positioning system. However, none of these approaches can work properly under the adversarial scenario. In this paper, we propose a novel scheme called two-step secure localization (TSSL) stand against many typical malicious attacks, e.g. wormhole attack and location spoofing attack. TSSL detects malicious nodes step by step. First, anchor nodes collaborate with each other to identify suspicious nodes by checking their coordinates, identities and time of sending information. Then, by using a modified mesh generation scheme, malicious nodes are isolated and the WSN is divided into areas with different trust grades. Finally, a novel localization algorithm based on the arrival time difference of localization information is adopted to calculate locations of unknown nodes. Simulation results show that the TSSL detects malicious nodes effectively and the localization algorithm accomplishes localization with high localization accuracy.
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  • 4
    Publication Date: 2013-10-02
    Description: Distance-bounding protocols form a family of challenge–response authentication protocols that have been introduced to thwart relay attacks. They enable a verifier to authenticate and to establish an upper bound on the physical distance to an untrusted prover. We provide a detailed security analysis of a family of such protocols. More precisely, we show that the secret key shared between the verifier and the prover can be leaked after a number of nonce repetitions. The leakage probability, while exponentially decreasing with the nonce length, is only weakly dependent on the key length. Our main contribution is a high probability bound on the number of sessions required for the attacker to discover the secret, and an experimental analysis of the attack under noisy conditions. Both of these show that the attack's success probability mainly depends on the length of the used nonces rather than the length of the shared secret key. The theoretical bound could be used by practitioners to appropriately select their security parameters. While longer nonces can guard against this type of attack, we provide a possible countermeasure which successfully combats these attacks even when short nonces are used.
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  • 5
    Publication Date: 2013-10-02
    Description: In threshold public-key encryption (TPKE), the decryption key is divided into n shares, each one of which is given to a different decryption user in order to avoid single points of failure. A robust TPKE is that if threshold decryption of a valid ciphertext fails, the combiner can identify the decryption users that supplied invalid partial decryption shares. In this paper, we propose a practical and efficient TPKE scheme which is robust and non-interactive. Security against chosen-ciphertext attacks (CCAs) can be proved in the standard model under the hashed Diffie–Hellman assumption in bilinear groups. The security reduction is tight and simple. We use an instantiation hash function of the Kiltz's key encapsulation mechanism and Lai et al. 's chosen-ciphertext secure technique to construct a TPKE scheme. Moreover, our scheme is more simple and shown to be more efficient than currently existing CCA-secure TPKE schemes.
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  • 6
    Publication Date: 2013-10-02
    Description: The advances in the digital world (e.g. the Internet, Communications, etc.) are closing the gap between consumers and providers, in both Business to Consumer and Business to Business environments. Through the Internet, providers can offer their products directly to consumers, which increase their choices and allow them to contract a set of different services/products from different providers. But sometimes the consumer needs an all-or-nothing exchange with these providers: an atomic exchange. The consumer has negotiated/obtained a set of conditions that are only met if she acquires all the services/products. Thus, we need an Atomic Multi-Two-Party contract signing protocol. Even though digital signature of contracts is a topic that has been widely studied, it lacks a solution when applied to Atomic Multi-Two-Party scenarios. Here, we propose the first solution to solve this problem.
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  • 7
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    Oxford University Press
    Publication Date: 2013-10-02
    Description: Key-evolving cryptography is intended to mitigate the damage in case of a secret key compromise, one of the severest security threats to actual cryptographic schemes. In the public-key setting, the essential idea of key-evolving lies in updating the private key with time, while maintaining the same public key. Key evolution in encryption and signing has been well studied, especially in the identity-based (ID-based) setting where an entity's public key can be derived from that entity's identity information. From a more practical standpoint, however, one would like to use the primitive signcryption in the hierarchical ID-based setting. In this paper, we propose the first key-evolving hierarchical ID-based signcryption scheme that is scalable and joining-time-oblivious and allows secret keys to be updated autonomously. The security proofs of our construction depend on the bilinear Diffie–Hellman assumption and the computational Diffie–Hellman assumption in the random oracle model. To be specific, our proposal not only achieves the fundamental goals of confidentiality and authenticity, but also enjoys desirable properties of non-repudiation, ciphertext anonymity and strong forward security. Compared with the conventional sign-then-encrypt approach, our construction provides better efficiency in terms of the computation cost and the communication overhead.
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  • 8
    Publication Date: 2013-10-02
    Description: Cooperative Intelligent Transportation Systems (ITS) will turn up to us with safer and more efficient driving environments as well as convenient and infotainment features for future ITS stations. ETSI and ISO are completing the standardization of the building blocks of a reference communication architecture for cooperative ITS. Future ITS stations complying with this set of standards deployed in vehicles, at the roadside infrastructures and within the Internet are expected to communicate with each other through a combination of ITS dedicated communication protocols and legacy Internet protocols. However, in spite of the wide adoption of IPv6 for cooperative ITS communications, relatively little attention has been paid to the security issues related to IPv6 signaling and IPv6 transport communications. In this paper, we present our position on the emerging and urgent IPv6-related security issues that occur in communications between ITS stations complying with the ITS station reference architecture under standardization within ETSI TC ITS and ISO TC204.
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  • 9
    Publication Date: 2013-10-02
    Description: The objectives of this special issue are advanced security technologies and services for future computing environments, including, but not limited to, security primitives, protocols and security applications and services. Recent advances in security technologies and services for future computing environments have created a new class of the following: (i) Wireless sensor networks and radio-frequency identification security and privacy; (ii) security architectures for distributed network systems, P2P systems, cloud and grid systems; and (iii) security in e-commerce, mobile and wireless networks, and finally, security standards and assurance methods. All papers are expected to focus on novel approaches for advanced security technologies and services for future computing environments and to present high-quality results for tackling problems arising from the ever-growing advanced security technologies and services for future computing environments.
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  • 10
    Publication Date: 2013-10-02
    Description: In this paper, we present a statistical analysis of six traffic features based on entropy and distinct feature number at the packet level, and we find that, although these traffic features are unstable and show seasonal patterns like traffic volume in a long-time period, they are stable and consistent with Gaussian distribution in a short-time period. However, this equilibrium property will be violated by some anomalies. Based on this observation, we propose a Multi-dimensional Box plot method for Short-time scale Traffic (MBST) to classify abnormal and normal traffic. We compare our new method with the MCST method proposed in our prior work and the well-known wavelet-based and A Short-Timescale Uncorrelated-Traffic Equilibrium (ASTUTE) techniques. The detection result on synthetic anomaly traffic shows that MBST can better detect the low-rate attacks than wavelet-based and MCST methods, and detection result on real traffic demonstrates that MBST can detect more anomalies with lower false alarm rate than the two methods. Especially compared with ASTUTE, MBST performs much better for detecting anomalies involving a few large flows despite a little poor for detecting anomalies involving large number of small flows.
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  • 11
    Publication Date: 2011-12-08
    Description: Greenstreet, S. P. R., Fraser, H. M., Rogers, S. I., Trenkel, V. M., Simpson, S. D., and Pinnegar, J. K. 2012. Redundancy in metrics describing the composition, structure, and functioning of the North Sea demersal fish community. – ICES Journal of Marine Science, 69: 8–22. Broader ecosystem management objectives for North Sea demersal fish currently focus on restoring community size structure. However, most policy drivers explicitly concentrate on restoring and conserving biodiversity, and it has not yet been established that simply restoring demersal fish size composition will be sufficient to reverse declines in biodiversity and ensure a generally healthy community. If different aspects of community composition, structure, and function vary independently, then to monitor all aspects of community general health will require application of a suite of metrics. This assumes low redundancy among the metrics used in any such suite and implies that addressing biodiversity issues specifically will require explicit management objectives for particular biodiversity metrics. This issue of metric redundancy is addressed, and 15 metrics covering five main attributes of community composition, structure, and function are applied to groundfish survey data. Factor analysis suggested a new interpretation of the metric information and indicated that a minimum suite of seven metrics was necessary to ensure that all changes in the general health of the North Sea demersal fish community were monitored properly. Covariance among size-based and species-diversity metrics was low, implying that restoration of community size structure would not necessarily reverse declines in species diversity.
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  • 12
    Publication Date: 2011-12-08
    Description: Dankel, D. J., Aps, R., Padda, G., Röckmann, C., van der Sluijs, J. P., Wilson, D. C., and Degnbol, P. 2012. Advice under uncertainty in the marine system. – ICES Journal of Marine Science, 69: 3–7. There is some uncertainty in the fisheries science–policy interface. Although progress has been made towards more transparency and participation in fisheries science in ICES Areas, routine use of state-of-the-art quantitative and qualitative tools to address uncertainty systematically is still lacking. Fisheries science that gives advice to policy-making is plagued by uncertainties; the stakes of the policies are high and value-laden and need therefore to be treated as an example of "post-normal science" (PNS). To achieve robust governance, understanding of the characteristics and implications of the scientific uncertainties for management strategies need to come to the centre of the table. This can be achieved using state-of-the-art tools such as pedigree matrices and uncertainty matrices, as developed by PNS scholars and used in similar science–policy arenas on other complex issues. An explicit extension of the peer community within maritime systems will be required to put these new tools in place. These new competences become even more important as many countries within the ICES Area are now embarking on new policies.
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  • 13
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    Oxford University Press
    Publication Date: 2011-12-08
    Description: Browman, H.I. 2012. Quo Vadimus. – ICES Journal of Marine Science, 69: 1–2.
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  • 14
    Publication Date: 2011-12-08
    Description: Hüssy, K., Coad, J. O., Farrell, E. D., Clausen, L. A. W., and Clarke, M. W. 2012. Age verification of boarfish ( Capros aper ) in the Northeast Atlantic. – ICES Journal of Marine Science, 69: 34–40. The boarfish ( Capros aper ) is a pelagic species of recent interest to the fishing industry, with landings increasing by 〉500% over the past 3 years. The objective of the study was to provide a method for age determination based on whole sagittal otoliths, with the results to be used in stock assessment. Translucent zones laid down at regular intervals are identified by marginal increment analysis as seasonally recurring. Translucent zones are formed between September/October and March/April, regardless of fish age. The occurrence of the first annulus is validated by analysis of presumed daily growth increments. Subsequent annulus deposition is homogenous between individuals and allows general guidelines to be derived for interpreting the age of boarfish using their otoliths.
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  • 15
    Publication Date: 2011-12-08
    Description: Kim, D., Yang, E. J., Kim, K. H., Shin, C-W., Park, J., Yoo, S., and Hyun, J-H. 2012. Impact of an anticyclonic eddy on the summer nutrient and chlorophyll a distributions in the Ulleung Basin, East Sea (Japan Sea). – ICES Journal of Marine Science, 69: 23–29. The impact of the anticyclonic Ulleung Warm Eddy (UWE) on the vertical distributions of nutrient and chlorophyll a (Chl a ) concentrations in the Ulleung Basin (UB) was investigated during the contrasting summers of 2005 and 2007. The physical structure of the water column was characterized by an intrathermocline eddy (ITE) in 2005, whereas the UWE remained distant from the sampling transect in 2007. Water column structures appeared to be highly stratified, and nutrients in the surface waters were totally depleted at all stations. In 2005, an exceptionally high concentration of Chl a (5.5 mg m –3 ) was measured below the surface mixed layer in the eddy core (station D3), and values of ~2.5 mg m –3 were observed at the eddy edge (stations D2 and D4). Formation of an ITE efficiently mixed surface and deep-ocean waters, the latter supplying sufficient nutrients to generate an extremely high concentration of Chl a at the base of the subsurface layer. Overall, the results indicated that the anticyclonic UWE plays a key ecological role in supporting substantial phytoplankton biomass in the nutrient-depleted surface waters in summer and maintaining high benthic mineralization in the deep-sea sediments of the UB.
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  • 16
    Publication Date: 2011-12-08
    Description: Franchini, P., Sola, L., Crosetti, D., Milana, V., and Rossi, A. R. 2012. Low levels of population genetic structure in the gilthead sea bream, Sparus aurata , along the coast of Italy. – ICES Journal of Marine Science, 69: 41–50. The gilthead sea bream, Sparus aurata , is a coastal, commercially important fish. Contrasting results concerning the genetic structure of the species at different geographic scales have been reported. Here, an investigation is made into the population genetic structure of S. aurata along the coast of Italy, using samples analysed previously and material from new sampling sites (12) and using different microsatellite loci (10). One sample from the eastern Atlantic and three temporal replicates from one site were also included. The presence of a weak (overall F ST = 0.0072), but significant, genetic population subdivision was detected by F -statistics. Temporal replicates indicate genetic data consistency over time. Isolation by distance between the Atlantic and the coast of Italy is suggested by a Mantel test. The distributional pattern of genetic variance obtained by analysis of molecular variation reflects the geographic sampling areas, but is only partially congruent with the results obtained with fewer sites and loci. The dispersal of passive eggs/larvae by the main currents appears to contribute to shaping the gene flow. Given the intensity of sea bream aquaculture activities in Italy, the possibility that aquaculture may have partially contributed to the population genetic pattern detected cannot be excluded.
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  • 17
    Publication Date: 2011-12-08
    Description: Charrier, F., Mazel, V., Caraguel, J-M., Abdallah, Y., Le Gurun, L. L., Legault, A., and Laffaille, P. 2012. Escapement of silver-phase European eels, Anguilla anguilla , determined from fishing activities in a Mediterranean lagoon (Or, France). – ICES Journal of Marine Science, 69: 30–33. Escapement of silver eels from a Mediterranean lagoon was estimated by a capture–tagging–recapture and automated tag-reading study. The population of silver-phase eels in the lagoon was estimated to be 13.2 kg ha –1 , with an escapement rate from the commercial fishery of 76.8%.
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  • 18
    Publication Date: 2011-12-08
    Description: Jennings, S., and Lee, J. 2012. Defining fishing grounds with vessel monitoring system data. – ICES Journal of Marine Science, 69: 51–63. Methods for defining fishing grounds to support marine spatial planning and management are developed, applied, and compared. The methods are broadly applicable and repeatable because they use vessel monitoring system (VMS) data that are archived and increasingly accessible. For several fleets at regional and national scales, an attempt is made to assess how the choice of criteria for defining grounds influences (i) size, shape, and location, (ii) overlap among grounds, and (iii) the extent to which annual and multi-annual patterns of fishing activity describe grounds used seasonally or by individual vessels. The results show that grounds defined by excluding infrequently fished margins (areas with 〈10% of total fishing activity) are typically 50% smaller than total fished area. However, landings weight or value (LWV) per unit activity can be higher at the margins, with 10% of activity usually accounting for 10–20% of LWV. The removal of fishing activity in the margins, as a consequence of regulation or fleet behaviour, would lead to disproportionately greater reductions in interactions with other fisheries, sectors, and the environment. Accessible high-resolution information on the "anatomy" of all fishing grounds would better inform debates on the allocation and the use of marine space and the integration of fisheries and environmental management.
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  • 19
    Publication Date: 2011-12-08
    Description: Bentley, N., Kendrick, T. H., Starr, P. J., and Breen, P. A. 2012. Influence plots and metrics: tools for better understanding fisheries catch-per-unit-effort standardizations. – ICES Journal of Marine Science, 69: 84–88. Standardization of catch per unit effort using generalized linear models (GLMs) is a common procedure that attempts to remove the confounding effects of variables other than abundance. Simple plots and metrics are described to assist understanding the standardization effects of explanatory variables included in GLMs, illustrated with an example based on New Zealand trevally ( Caranx lutescens ) data.
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  • 20
    Publication Date: 2011-12-08
    Description: Aldrin, M., Mortensen, B., Storvik, G., Nedreaas, K., Aglen, A., and Aanes, S. 2012. Improving management decisions by predicting fish bycatch in the Barents Sea shrimp fishery. – ICES Journal of Marine Science, 69: 64–74. When the bycatch of juvenile fish within the Barents Sea shrimp fishery is too large, the area is closed to fishing for a certain period. Bycatch is estimated from sampled trawl hauls, for which the shrimp yield is recorded, along with the total number of various bycatch fish species. At present, bycatch estimation is based on a simple estimator, the sum of the number of fish caught within the area of interest within a small time window, divided by the corresponding shrimp yield (in weight). No historical data are used. A model-based estimation is proposed in which spatio-temporal models are constructed for the variation in both the yield of shrimp and the amount of bycatch in space and time. The main effects are described through generalized additive models, and local dependence structures are specified through correlated random effects. Model estimation includes historical and recent data. Experiments with both simulated and real data show that the model-based estimator outperforms the present simple estimator when a low or moderate number of samples (e.g. 〈20) is available, whereas the two estimators are equally good when the number of samples is high.
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  • 21
    Publication Date: 2011-12-08
    Description: Jiao, Y., Smith, E. P., O'Reilly, R., and Orth, D. J. 2012. Modelling non-stationary natural mortality in catch-at-age models. – ICES Journal of Marine Science, 69: 105–118. Non-stationarity in the natural mortality of many species has been discussed among research scientists, but no generally applicable models/methods have been developed where a statistical catch-at-age (SCA) model framework is used. Using the Atlantic weakfish ( Cynoscion regalis ) fishery as an example, several SCA models are developed to assess the population dynamics, then compared. Models used included (i) an SCA with constant natural mortality, (ii) an SCA with unknown natural mortality, but with a hierarchical prior distribution from a mixture of distributions based on life-history information, (iii) an SCA with age-specific unknown natural mortality, (iv) an SCA with time-varying natural mortality, following a random-walk process, and (v) an SCA with age-specific time-varying natural mortality. The last two models imply that the population dynamics are not stationary. A Bayesian approach was used to estimate parameters, and performance of the models was compared through goodness-of-fit and the retrospective patterns of the models. A simulation study was then conducted to test the uncertainty resulting from model selection, the efficiency of using the best model selected based on deviance information criterion, and whether changes in natural mortality could be detected. An SCA with time-varying natural mortality, following a random-walk process, is proposed for the example fishery here. The estimated non-stationary temporal patterns in natural mortality were linked further to climate–ocean oscillation indices, to diagnose possible mechanisms/linkages to these temporal variations in natural mortality.
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  • 22
    Publication Date: 2011-12-08
    Description: Juntunen, T., Vanhatalo, J., Peltonen, H., and Mäntyniemi, S. 2012. Bayesian spatial multispecies modelling to assess pelagic fish stocks from acoustic- and trawl-survey data. – ICES Journal of Marine Science, 69: 95–104. A Bayesian spatial model was constructed to estimate the abundance of multiple fish species in a pelagic environment. Acoustic- and trawl-survey data were combined with environmental data to predict the spatial distribution of (i) the acoustic backscattering of fish, (ii) the relative proportion of each species, and (iii) their mean length in the Gulf of Finland in the northeastern Baltic Sea. By combining the three spatial model layers, the spatial distribution of the biomass of each species was estimated. The model consists of a linear predictor on environmental variables and a spatial random effect given by a Gaussian process. A Bayesian approach is a natural choice for the task because it provides a theoretically justified means of summarizing the uncertainties from various model layers. In the study area, three species dominate pelagic waters: sprat ( Sprattus sprattus ), herring ( Clupea harengus ), and three-spined stickleback ( Gasterosteus aculeatus ). Results are presented for each model layer and for estimated total biomass for each species in 2 x 2 km lattices. The posterior mean and central 95% credible intervals of total biomass were sprat 45.7 kt (27.7–71.6), herring 24.6 kt (9.7–41.3), and three-spined stickleback 1.9 kt (0.9–3.2).
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  • 23
    Publication Date: 2011-12-08
    Description: Smith, W. K., and Solow, A. R. 2012. Missing and presumed lost: extinction in the ocean and its inference. – ICES Journal of Marine Science, 69: 89–94. The number of modern extinctions in the ocean is unknown. The actual demise of the last individual of a species is essentially unobservable, so extinction can only be inferred. Statistical methods are described for inferring extinction from sighting records, species–area considerations, and taxonomic samples collected at two different times. The methods are illustrated using a variety of real datasets, including a sighting record of the Caribbean monk seal and results from three surveys of benthic invertebrates.
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  • 24
    Publication Date: 2011-12-08
    Description: Delavenne, J., Metcalfe, K., Smith, R. J., Vaz, S., Martin, C. S., Dupuis, L., Coppin, F., and Carpentier, A. 2012. Systematic conservation planning in the eastern English Channel: comparing the Marxan and Zonation decision-support tools. – ICES Journal of Marine Science, 69: 75–83. The systematic conservation approach is now commonly used for the design of efficient marine protected area (MPA) networks, and identifying these priority areas often involves using specific conservation-planning software. Several such software programmes have been developed in recent years, each differing in the underlying algorithms used. Here, an investigation is made into whether the choice of software influences the location of priority areas by comparing outputs from Marxan and Zonation, two widely used conservation-planning, decision-support tools. Using biological and socio-economic data from the eastern English Channel, outputs are compared and it is shown that the two software packages identified similar sets of priority areas, although the relatively wide distribution of habitat types and species considered offered much flexibility. Moreover, the similarity increased with increasing spatial constraint, especially when using real-world cost data, suggesting that the choice of cost metric has a greater influence on conservation-planning analyses than the choice of software. However, Marxan generally produced more efficient results and Zonation produced results with greater connectivity, so the most appropriate software package will depend on the overall goals of the MPA planning process.
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  • 25
    Publication Date: 2011-12-08
    Description: Andersen, B. S., Ulrich, C., Eigaard, O. R., and Christensen, A-S. 2012. Short-term choice behaviour in a mixed fishery: investigating métier selection in the Danish gillnet fishery. – ICES Journal of Marine Science, 69: 131–143. The study presents a short-term effort allocation modelling approach based on a discrete choice random utility model combined with a survey questionnaire to examine the selection of métiers (a combination of fishing area and target species) in the Danish North Sea gillnet fishery. Key decision variables were identified from the survey questionnaire, and relevant proxies for the decision function were identified based on available landings and effort information. Additional variables from the survey questionnaire were further used to validate and verify the outcome of the choice model. Commercial fishers in a mixed fishery make use of a number of decision variables used previously in the literature, but also a number of decision parameters rarely explicitly accounted for, such as price, weather, and management regulation. The seasonal availability of individual target species and within-year changes in monthly catch ration were the main explanatory drivers, but gillnetters were also responsive to information on the whole fishery, fish prices, and distance travelled to fishing grounds. Heterogeneous responses were evident from geographic differences in home harbour, which underpins the need to understand alternative fishing strategies among individual gillnetters better.
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  • 26
    Publication Date: 2011-12-08
    Description: Calise, L., and Knutsen, T. 2012. Multifrequency target strength of northern krill ( Meganyctiphanes norvegica ) swimming horizontally. – ICES Journal of Marine Science, 69: 119–130. Multifrequency acoustic measurements on ex situ horizontally swimming krill were made in a novel experimental setting. An ensemble of northern krill ( Meganyctiphanes norvegica ) was introduced to a large enclosure (a mesocosm), and acoustic backscatter was sampled using a multifrequency (70, 120, and 200 kHz) echosounder (Simrad EK60). Two submerged lamps were placed at opposite sides of the mesocosm and switched on and off to induce the krill, by light attraction, to swim horizontally through the acoustic beams. By tracking echoes, animal displacement, swimming speed, and target strength ( TS ) by frequency were estimated. The dominant and secondary modes of the total-length distribution were 21.8 ± 3.0 and 27.8 ± 2.7 mm, respectively. Although krill orientation was assumed stable and the ping rate was high, the range and inter-ping variability of the average TS values were large, decreasing and increasing with frequency, respectively. The overall TS frequency response observed and concurrent measurements at 120 and 200 kHz confirm the theoretical expectation that the acoustic backscatter from the investigated organisms were confined to the Rayleigh and Geometric scattering regions, a finding that might both aid acoustic identification and size-group separation of in situ northern krill.
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  • 27
    Publication Date: 2012-02-02
    Description: This paper presents a benchmarking, performance analysis and optimization study of the OP2 ‘active’ library, which provides an abstraction framework for the parallel execution of unstructured mesh applications. OP2 aims to decouple the scientific specification of the application from its parallel implementation, and thereby achieve code longevity and near-optimal performance through re-targeting the application to execute on different multi-core/many-core hardware. Runtime performance results are presented for a representative unstructured mesh application on a variety of many-core processor systems, including traditional X86 architectures from Intel (Xeon based on the older Penryn and current Nehalem micro-architectures) and GPU offerings from NVIDIA (GTX260, Tesla C2050). Our analysis demonstrates the contrasting performance between the use of CPU (OpenMP) and GPU (CUDA) parallel implementations for the solution of an industrial-sized unstructured mesh consisting of about 1.5 million edges. Results show the significance of choosing the correct partition and thread-block configuration, the factors limiting the GPU performance and insights into optimizations for improved performance.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
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  • 28
    Publication Date: 2012-02-02
    Description: In this paper, we describe the integrated power, area and thermal modeling framework in the structural simulation toolkit (SST) for large-scale high performance computer simulation. It integrates various power and thermal modeling tools and computes run-time energy dissipation for core, network on chip, memory controller and shared cache. It also provides functionality to update the leakage power as temperature changes. We illustrate the utilization of the framework by applying it to explore interconnect options in manycore systems with consideration of temperature variation and leakage feedback. We compare power, energy-delay-area product (EDAP) and energy-delay product (EDP) of four manycore configurations-1 core, 2 cores, 4 cores and 8 cores per cluster. Results from simulation with or without consideration of temperature variation both show that the 4-core per cluster configuration has the best EDAP and EDP. Even so, considering that temperature variation increases total power dissipation, we demonstrate the importance of considering temperature variation in the design flow. With this power, area and thermal modeling capability, the SST can be used for hardware/software co-design of future exascale systems.
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  • 29
    Publication Date: 2012-02-02
    Description: With the advent of heterogeneous computing systems consisting of multi-core central processing units (CPUs) and many-core graphics processing units (GPUs), robust methods are needed to facilitate fair benchmark comparisons between different systems. In this paper, we present a benchmarking methodology for measuring a number of performance metrics for heterogeneous systems. Methods for comparing performance and energy efficiency are included. Consideration is given to further metrics, such as associated running costs and carbon emissions. We give a case study for these metrics applied to Bristol University Docking engine, a molecular mechanics-based docking application that has been ported to open computing language at the University of Bristol. Results are included for both AMD and NVIDIA GPUs, and for a highly optimized code on the latest x86 CPUs.
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  • 30
    Publication Date: 2012-02-02
    Description: Java embedded systems often include Java middleware classes installed on the client device. For higher performance, they can be compiled into machine code before runtime using an ahead-of-time compiler (AOTC). There are many approaches to AOTC, yet a bytecode-to-C (b-to-C) AOTC which translates the bytecode into the C code and then compiles it using an existing optimizing compiler such as gcc would be the most straightforward one. This paper explores a few important design and optimization issues of a b-to-C AOTC, including the compilation form for the translated C code, the call interfaces among translated and interpreted Java methods, and Java-specific optimizations by the AOTC that can complement the gcc optimizations. We evaluate these issues with our b-to-C AOTC implemented on the MIPS platform for the Sun's CDC VM to understand their performance impact.
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  • 31
    Publication Date: 2012-02-02
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  • 32
    Publication Date: 2012-02-17
    Description: Rosen, S., Engås, A., Fernö, A., and Jörgensen, T. 2012. The reactions of shoaling adult cod to a pelagic trawl: implications for commercial trawling. – ICES Journal of Marine Science, 69: 303–312. The reactions of shoaling adult Atlantic cod to a pelagic trawl were measured during fishing off the north coast of Norway. Cod remaining in the trawl track dived at rates as fast as 0.35 m s –1 following vessel passage and swam away from the vessel, in the direction of the approaching trawl, at an average rate of 0.6 m s –1 . They did not attempt to swim ahead of the trawl as documented previously, but passed into the lower half of the trawl entrance and swam slowly in the direction of trawling at a rate of 0.2–0.5 m s –1 as the trawl's greater speed through water carried them deeper into the trawl. Shoals compressed vertically once inside the trawl, suggesting that packing density increased at least fourfold. Fish remained in the lower part of the trawl as they moved through its tapered section towards the codend, with little to no clearance above the bottom panel, but significant clearance beneath the top panel. Catches were sufficient to support commercial harvest, and the behaviour observed suggests that changes in trawl design and fishing strategy might improve fuel economy and species selectivity.
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  • 33
    Publication Date: 2012-02-17
    Description: Shackell, N. L., Bundy, A., Nye, J. A., and Link, J. S. 2012. Common large-scale responses to climate and fishing across Northwest Atlantic ecosystems. – ICES Journal of Marine Science, 69: 151–152. Investigating whether there were common biological responses to climate and fishing across seven Northwest Atlantic ecosystems, a minimum/maximum autocorrelation factor analysis of biological indicators for each region revealed a common primary multivariate trend of a rapid change during the 1980s and early 1990s. There was a strong common pattern in the biological indicators responsible for the primary multivariate temporal trend in the five more northerly regions: an increase in the abundance of phytoplankton, an increase in biomass at mid-trophic levels, and a decline in predatory groundfish size. The common associations between patterns and drivers were fishing indices and the Atlantic Multidecadal Oscillation, but all associations weakened when co-varying drivers were held constant. The results are consistent with known long-term effects of intense fishing, such as a decline in average fish size and changes in species composition. Less fishing pressure has allowed some regions to recover to former predatory biomass levels since the late 1990s, but the bulk of the biomass consists of fewer species. However, fishing was not the only driver, and a more mechanistic understanding of how the climate affects lower trophic levels is needed to contextualize climate effects in heavily fished ecosystems.
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  • 34
    Publication Date: 2012-02-17
    Description: Deporte, N., Ulrich, C., Mahévas, S., Demanèche, S., and Bastardie, F. 2012. Regional métier definition: a comparative investigation of statistical methods using a workflow applied to international otter trawl fisheries in the North Sea. – ICES Journal of Marine Science, 69: 331–342. The European Common Fisheries Policy recognizes the importance of accounting for heterogeneity in fishing practices, and métier-based sampling is now at the core of the EU Data Collection Framework. The implementation of such an approach would require Member States to agree on the standard regional métier definitions and on practical rules to categorize logbook records into métiers. Several alternative approaches have been used in the past to categorize landings profiles, but no consensus has yet emerged. A generic open-source workflow is developed to test and compare a selection of methods, including principal components analysis (PCA), hierarchical agglomerative clustering (HAC), K -means, and Clustering LARge Applications (CLARA), and to provide simple allocation rules. This workflow is applied to a unique regional dataset consisting of bottom-trawl logbooks of five North Sea countries. No method proved to be infallible, but combining PCA with either CLARA or HAC performed best. For 2008, a hierarchical classification with 14 species assemblages is proposed. Discriminant analysis proved more robust than simple ordination methods for allocating a new logbook record into an existing métier. The whole approach is directly operational and could contribute to defining more objective and consistent métiers across European fisheries.
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  • 35
    Publication Date: 2012-02-17
    Description: Greenstreet, S. P. R., Rogers, S. I., Rice, J. C., Piet, G. J., Guirey, E. J., Fraser, H. M., and Fryer, R. J. 2012. A reassessment of trends in the North Sea Large Fish Indicator and a re-evaluation of earlier conclusions. – ICES Journal of Marine Science, 69: 343–345. Previous analysis of the Large Fish Indicator, the basis for the North Sea "fish communities" EcoQO, suggested a strong recovery between 2001 and 2008. Discovery of a mistake in this earlier analysis now suggests that this recovery is not as strong as first thought, but reanalysis of the corrected data still supports the majority of conclusions drawn in the original paper.
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  • 36
    Publication Date: 2012-02-17
    Description: Xie, Y., Michielsens, C. G. J., and Martens, F. J. 2012. Classification of fish and non-fish acoustic tracks using discriminant function analysis. – ICES Journal of Marine Science, 69: 313–322. Hydroacoustic data acquired for estimating fish populations contain information on both fish and non-fish targets, so sonar technicians traditionally rely on their knowledge of fish behaviour and experience with hydroacoustics to remove non-fish targets from the hydroacoustic data. This process is often labour-intensive and time-consuming, making real-time assessment of fish populations difficult. Simple solutions are not always available for all circumstances. However, the split-beam sonar data collected in the lower Fraser River, British Columbia, Canada, showed distinct signatures between actively swimming fish and non-fish objects such as drifting debris, surface bubbles, and stationary objects in the water column and off the river bottom. Acoustic tracks of fish and non-fish targets were characterized by differentiable statistical patterns that were amenable to discriminant function analysis (DFA). An application of DFA to segregate fish and non-fish targets detected by a split-beam sonar system in the lower Fraser River is presented, characteristics of user-identified fish and non-fish acoustic tracks being utilized as learning samples for the DFA. Also, a method to rank the discriminating power of individual variables is presented, providing guidance for constructing efficient and effective discriminant functions with variables that offer high discriminating power. The DFA yielded classification accuracies of 96% for fish and 91% for non-fish tracks and reduced the manual sorting time by 50–75%.
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  • 37
    Publication Date: 2012-02-17
    Description: Rey, F. 2012. Declining silicate concentrations in the Norwegian and Barents Seas. – ICES Journal of Marine Science, 69: 208–212. Since 1990, a decline in silicate concentrations together with increasing salinities has been observed in the Atlantic water of the Norwegian and Barents Seas. This decline in silicate has been found to be related to the relative proportion in which eastern and western source water masses from the northeastern North Atlantic enter the Norwegian Sea.
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  • 38
    Publication Date: 2012-02-17
    Description: Zhou, S., Milton, D. A., and Fry, G. C. 2012. Integrated risk analysis for rare marine species impacted by fishing: sustainability assessment and population trend modelling. – ICES Journal of Marine Science, 69: 271–280. Risk assessment and conservation management of rare species are challenging due to a lack of data. We developed an integrated risk assessment approach to assess human impact on population sustainability of rare species. The approach involved two components: a quantitative sustainability assessment coupled with modelling trends in relative abundance. Both components took nil catches into account through zero-inflated statistical distributions that simultaneously modelled the zero and non-zero catches separately in submodels. The sustainability assessment used detection–non-detection data for population estimation and linked sustainability to easily collected life-history traits. This component provides an assessment of population sustainability at one point in time. The trend modelling applied zero-inflated negative binomial models to temporal trends in density and dispersion of species. It provided a complement to the static sustainability assessment. We applied this integrated approach to assess the risk to 14 species of rare, protected sea snakes incidentally caught in the Australian Northern Prawn Fishery. This approach can be applicable for risk assessment of many species with limited abundance data, a large number of absences and some presence–absence information only.
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  • 39
    Publication Date: 2012-02-17
    Description: Frid, C. L. J., and Paramor, O. A. L. 2012. Feeding the world: what role for fisheries? – ICES Journal of Marine Science, 69: 145–150. Fisheries (wild capture and aquaculture) deliver more than 110 million tonnes of food and around 15% of the dietary protein to the 7 billion people currently living on the planet. With the global population expected to peak at 9 billion by 2050, and 〉80% of global fish stocks currently fully or overexploited (and aquaculture is at least in part dependent on capture fisheries), the contribution of fisheries looks set to decline. The challenge is therefore determining how better management, an ecosystem perspective, and more efficient utilization of fisheries waste can support fisheries products continuing to contribute significantly to "feeding the world" up to and beyond the population peak.
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  • 40
    Publication Date: 2012-02-17
    Description: Boström, M. K., Östman, Ö., Bergenius, M. A. J., and Lunneryd, S-G. 2012. Cormorant diet in relation to temporal changes in fish communities. – ICES Journal of Marine Science, 69: 175–183. The stomach contents of 229 great cormorants ( Phalacrocorax carbo sinensis ) shot between March and October 2009 along the Swedish east coast were analysed for differences in diet between gender, age, and breeding phase. Sticklebacks ( Gasterosteus aculeatus and Pungitius pungitius ) were the most common prey, followed by eelpout ( Zoarces viviparus ), herring ( Clupea harengus membras ), and cyprinids (Cyprinidae). Diet did not differ between age and gender, but changed over the breeding season. The different phases explained around 10% of the total variation in stomach content between cormorants, suggesting no major shift in diet over the breeding season. The diet of cormorants in 2009 was compared with the results of a study conducted in the same area in 1992. There were evident changes in the diet between 1992 and 2009, with less perch ( Perca fluviatilis ) and cyprinids and more eelpout and herring in 2009. This change in diet could partly be related to changes in the fish community. The seasonal changes in diet composition of whole stomachs were less notable than in many previous studies, but long-term changes in the fish communities may induce changes in cormorant diet. It is clearly important to use stomach contents in areas with many small fish species for a comprehensive assessment of cormorant diet.
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  • 41
    Publication Date: 2012-02-17
    Description: Cañás, L., Stransky, C., Schlickeisen, J., Sampedro, M. P., and Fariña, A. C. 2012. Use of the otolith shape analysis in stock identification of anglerfish ( Lophius piscatorius ) in the Northeast Atlantic. – ICES Journal of Marine Science, 69: 250–256. The geographical variability in the anglerfish Lophius piscatorius otolith shape was investigated to examine biological evidence for the current separation into Northern and Southern stocks of L. piscatorius established in the Southwest European waters (Southern Shelf area) by the International Council for the Exploration of the Sea (ICES). In all, 629 otoliths of L. piscatorius (12–90 cm total length) from commercial fishing and research surveys were collected in two consecutive years, 2008 and 2009. The otolith shape was compared between stocks for differences in univariate descriptors using non-parametric analysis of covariance, as well as elliptical Fourier shape descriptors, through a metric multidimensional scaling and a linear discriminant analysis (LDA). The differences found in the otolith shape between Northern and Southern stocks were not large enough to hold the current status of L. piscatorius regarding stock definition in the Southern Shelf area, although homogeneous mixing between both stocks is not expected as there were significant differences between three univariate descriptors and the LDA was significant. These results are in agreement with the previous L. piscatorius stock identification studies (genetics, body morphology, and migratory behaviour), which do not support the current separation of these stocks but found substructures within the area.
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  • 42
    Publication Date: 2013-02-21
    Description: Bachiller, E., Cotano, U., Boyra, G., and Irigoien, X. 2013. Spatial distribution of the stomach weights of juvenile anchovy ( Engraulis encrasicolus L.) in the Bay of Biscay. – ICES Journal of Marine Science, 70: 362–378. Previous studies have shown that the survival of larval and juvenile anchovy off the continental shelf in the Bay of Biscay is not significantly different from that observed on the shelf, even though the food concentration is significantly higher on the shelf. In this paper we investigate the causes for the lack of relationship between food and survival for anchovy juvenile through analyses of feeding activity versus zooplankton distribution (in the transition from summer to fall from 2003 to 2010). The spatial distribution of the stomach weights of juvenile anchovy in relation to body size on and off the shelf revealed higher stomach fullness in areas off the shelf, where less zooplankton biomass was available. This result indicates that the food concentration is not always the main factor determining ingestion in fish. A situation of comparatively lesser prey abundance may provide better feeding conditions when combined with lower predation risk and lower light attenuation. In addition, the relatively heavier stomachs found in anchovies caught in years of higher recruitment indices suggest a large stomach content may be a symptom of good biological condition that may favour the winter survival of a larger fraction of the juvenile stock.
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  • 43
    Publication Date: 2013-02-21
    Description: Van Hoof, L. 2013. Design or pragmatic evolution: applying ITQs in EU fisheries management. – ICES Journal of Marine Science, 70: 462–470. Among the proposals for the 2012 revision of the EU Common Fisheries Policy, a strong case is made for the introduction of a system of rights-based management. The EU perceives individual fishing concessions as an important instrument for capacity management. We will use the introduction of individual tradable quotas in the management of the Dutch North Sea beam trawl fisheries as a case for exploring the effect of the introduction of such an instrument. The effect will be assessed in terms of reduction of fishing capacity in the Dutch beam trawl fleet and its economic and social impact. These Dutch experiences will be translated to the current debate on the reform of the EU Common Fisheries Policy. Especially, we will focus on the issues of "relative stability", the concentration of rights, and the effects on the small-scale fisheries sector. Some of the negative effects associated with individual tradable rights can be addressed through design. However, trying to maintain stability and counter perceived negative impacts on fishing communities will modify the effect of introducing individual fishing concessions.
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  • 44
    Publication Date: 2013-02-21
    Description: Spitz, J., Chouvelon, T., Cardinaud, M., Kostecki, C., and Lorance, P. 2013. Prey preferences of adult sea bass Dicentrarchus labrax in the northeastern Atlantic: implications for bycatch of common dolphin Delphinus delphis – ICES Journal of Marine Science, 70: 452–461. In the northeastern Atlantic, adult sea bass ( Dicentrarchus labrax ) is one of largest fish living on the shelf, and this species has important commercial value. However, pelagic trawl fisheries that target sea bass have negative operational interactions with common dolphins ( Delphinus delphis ). Our goal was to determine the diet of adult sea bass in the Bay of Biscay from stomach-content and stable-isotope analyses, and explore the dietary overlap between sea bass and common dolphins. We found that sea bass primarily target small pelagic fish, most notably mackerel ( Scomber scombrus ), scads ( Trachurus spp.), anchovy ( Engraulis encrasicolus ), and sardine ( Sardina pilchardus ). These four species also dominated the diets of common dolphins. This overlap in feeding preferences could increase the risk of dolphins being caught by trawl fisheries while feeding among sea bass, and may be an underlying mechanism to explain the high rate of common dolphin bycatch observed in the pelagic trawl fishery for sea bass in the Bay of Biscay. Understanding the foraging ecology and trophic interactions of predator species is an essential step for identifying and resolving management issues in the northeastern Atlantic and other marine ecosystems.
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  • 45
    Publication Date: 2013-02-21
    Description: Lassen, H., Pedersen, S. A., Frost, H., and Hoff. A. 2013. Fishery management advice with ecosystem considerations. – ICES Journal of Marine Science, 70: 471–479. The European Union Marine Strategy Framework Directive (MSFD) includes four descriptors of Good Environmental Status (GES) which are affected by fishing activity. These descriptors are: biodiversity, fish stocks, foodweb, and seabed integrity. This paper shows how these descriptors can be related to variables within an ecological model and how an ecological model can be used to analyse whether the fishing pressure that is estimated based on bioeconomic criteria is within general sustainable limits. The paper presents an example of such an analysis of the Eastern Baltic cod fishery using two models: a bioeconomic model and an ecological model. The models are calibrated based on historic data. The mapping between the descriptors specified by MSFD and variables available for analysis in the models is incomplete, e.g. genetics and spatial structures are not included in the models. The models can be used strategically, providing a qualitative understanding of the anticipated relative changes.
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  • 46
    Publication Date: 2013-02-21
    Description: Finley, C. and Oreskes, N. 2013. Maximum sustained yield: a policy disguised as science. – ICES Journal of Marine Science, 70: 245–250. Overfishing is most commonly explained as an example of the tragedy of the commons, where individuals are unable to control their activities, leading to the destruction of the resource they are dependent on. The historical record suggests otherwise. Between1949 and 1958, the US State Department used fisheries science, and especially the concept of maximum sustained yield (MSY) as a political tool to achieve its foreign policy objectives. During the Cold War, the Department thought that if countries were allowed to restrict fishing in their waters, it might lead to restrictions on passage of military vessels. While there has been much criticism of MSY and its failure to conserve fish stocks, there has been little attention paid to the political context in which MSY was adopted.
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  • 47
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    Oxford University Press
    Publication Date: 2013-02-21
    Description: The sharing of the Northeast Atlantic mackerel ( Scomber scombrus ) stock is analysed as a game between four parties: the European Union, Norway, the Faroe Islands, and Iceland. Consideration is given to how the outcome depends on the nature of the stock's migrations. Two types of migrations are considered: (i) density-dependent, where the mackerel migrates into the Icelandic economic zone only if it exceeds 3.5 million t, and (ii) stochastic migrations, where the said migrations are stochastic. It is determined that the Faroe Islands would never accept a cooperative solution wherein they can only fish with the globally optimal fishing mortality within their own zone. This is also true for Iceland when the migrations into her zone are stochastic, but not if they are density-dependent. In the latter case, the other players have incentives to retaliate to Icelandic overfishing by fishing harder, which greatly reduces the number of years when mackerel are available in the Icelandic zone. It is assumed that the objective is maximization of the catch volume over a time-horizon of 50 years.
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  • 48
    Publication Date: 2013-02-21
    Description: Harris, P. T., Bridge, T. C. L., Beaman, R. J., Webster, J. M., Nichol, S. L., and Brooke, B. P. 2013. Submerged banks in the Great Barrier Reef, Australia, greatly increase available coral reef habitat. – ICES Journal of Marine Science, 70: 284–293. Anthropogenic global ocean warming is predicted to cause bleaching of many near-sea-surface (NSS) coral reefs, placing increased importance on deeper reef habitats to maintain coral reef biodiversity and ecosystem function. However, the location and spatial extent of many deep reef habitats is poorly known. The question arises: how common are deep reef habitats in comparison with NSS reefs? We used a dataset from the Great Barrier Reef (GBR) to show that only about 39% of available seabed on submerged banks is capped by NSS coral reefs (16 110 km 2 ); the other 61% of bank area (25 600 km 2 ) is submerged at a mean depth of around 27 m and represents potential deep reef habitat that is spatially distributed along the GBR continental shelf in the same latitudinal distribution as NSS reefs. Out of 25 600 km 2 of submerged bank area, predictive habitat modelling indicates that more than half (around 14 000 km 2 ) is suitable habitat for coral communities.
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  • 49
    Publication Date: 2013-02-21
    Description: Dutertre, M., Hamon D., Chevalier C., and Ehrhold, A. 2013. The use of the relationships between environmental factors and benthic macrofaunal distribution in the establishment of a baseline for coastal management – ICES Journal of Marine Science, 70: 294–308. Relationships between benthic macrofauna and natural abiotic factors were studied along the coastal fringe of South Brittany, situated north of the Gulf of Biscay on the French Atlantic continental shelf. Within the framework of the REBENT network, sediment characteristics, depth, and macrofaunal abundance were determined for 95 stations spread over five subtidal sectors, using a combination of seabed acoustic remote sensing systems and grab sampling. The physico-chemical properties of the water column and the hydrodynamic conditions were generated by validated three-dimensional environmental models which take into account variations over shorter temporal scales. Multivariate analyses ranked 16 natural abiotic variables according to the significance of their influence on the macrofauna. Together these variables explained 51% of spatial variation in the macrofauna, with morpho-sedimentological and hydrological factors contributing 22% and 26%, respectively. The outputs from validated three-dimensional environmental models appear to be useful interpretational tools for benthic ecology studies, especially in estuarine and coastal ecosystems with high environmental variability due to regular freshwater inputs. Ten major species assemblages were identified using biological and physical characteristics. The results provide important baseline knowledge for future ecosystem and resource management.
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  • 50
    Publication Date: 2013-02-21
    Description: Prigge, E., Marohn, L., Oeberst R., and Hanel, R. 2013. Model prediction vs. reality—testing the predictions of a European eel ( Anguilla anguilla ) stock dynamics model against the in situ observation of silver eel escapement in compliance with the European eel regulation – ICES Journal of Marine Science, 70: 309–318. A direct monitoring of European silver eel ( Anguilla anguilla , L) escapement from rivers and estuaries has been proven to be challenging, and a Europe-wide documentation of escaping silver eel numbers therefore hardly seems realistic. To reinforce management decisions, policy-makers are thus widely reliant on the accuracy of escapement models. A 3-year programme of silver eel escapement monitoring was undertaken to compile model input data and revise an eel population model (German Eel Model II; GEM II) already used in the decision-making process of management authorities. By compiling necessary input data and analysing vital system-specific population characteristics, it was possible to compare the documented silver eel escapement with the modelled potential silver eel escapement. Resulting model predictions were close to actually monitored escapement numbers, which were distinctly lower than reference escapement values for the same freshwater system given in the implementation report of the German Eel Management Plans. Applying different commercial and recreational catch scenarios revealed the sensitivity of the model. The results show the potential of the GEM II and highlight the importance of high-quality input data to use model predictions as the basis for management measures.
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  • 51
    Publication Date: 2013-02-21
    Description: Sumaila, U. R. 2013. How to make progress in disciplining overfishing subsidies. ICES Journal of Marine Science, 70: 251–258. The World Trade Organization (WTO) has been working for more than seven years now to discipline overfishing subsidies, as mandated by the global community, without success. I argue that this failure is partly because WTO negotiators aim for an all-inclusive deal, i.e. negotiations are conducted as a "single undertaking", whereby results must be achieved in all areas. Negotiators are required to broker an all-inclusive deal for all maritime WTO member countries and for all fisheries, whether domestic or international; small or large scale; developing or developed country fisheries. It is argued here that this commitment to a "single undertaking" does not align the incentive to remove subsidies with national interests, and therefore needs to be changed by splitting the world's fisheries into domestic and international fisheries. In this way, the battle for eliminating overfishing subsidies for some stocks would shift to home countries, and for others this would still rest with the international community. This split, it is argued, would align the incentives and improve the chances of eliminating overfishing subsidies.
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  • 52
    Publication Date: 2013-02-21
    Description: Morgan, M. J., Garabana, D., Rideout, R. M., Román, E., Pérez-Rodriguez, A. and Saborido-Rey, F. 2013. Changes in distribution of Greenland halibut in a varying environment. – ICES Journal of Marine Science, 70: 352–361. Fish are expected to respond to changing oceanographic temperature by altering their distribution. Off the coast of Newfoundland, Canada, there have been major changes in oceanographic temperature over the last several decades, with both record cold and record warm years being observed. Greenland halibut is an important flatfish species in the area, and is distributed in deep waters over a very wide geographic range. Thus, it might be buffered from temperature change in the overall area by reduced temperature variation at depth, and the diverse temperature conditions over its wide range. We examined intrapopulation variation in temperature and depth distribution, and the biological changes in relation to changes in available temperature. On the Flemish Cap, variation in available temperature was limited, and changes in depth were related to changing age composition and the differential depth distribution with age/size. In other areas there was a larger decline in available temperature, and associated with this, Greenland halibut moved to deeper waters and occupied warmer temperatures than they had previously. Concurrently, growth declined and condition increased. This study shows that shifts in distribution may not result in maintenance of homogeneous environmental conditions, and that resulting biological changes will be difficult to predict.
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  • 53
    Publication Date: 2013-02-21
    Description: Hufnagl, M., Huebert, K. B., and Temming, A. 2013. How does seasonal variability in growth, recruitment, and mortality affect the performance of length-based mortality and asymptotic length estimates in aquatic resources? – ICES Journal of Marine Science, 70: 329–341. We tested the sensitivity of eight methods for estimating total mortality from size frequencies (modified Wetherall; Powell; Beverton and Holt; Jones and van Zalinge; Hoenig; Ssentongo and Larkin; seasonal and non-seasonal Length Converted Catch Curve) to violations of basic assumptions, such as seasonal growth, mortality, recruitment and variable asymptotic length L or growth parameter K . For each method, bias was estimated by simulating length frequency distributions with different combinations of known L , Z and K values, calculating ( Z / K ) and L estimates, and comparing the true input with the estimated output values. Input mortality was generally underestimated by all methods and in 27% of all simulations no method provided estimates within ± 1. Spring recruitment especially negatively influenced the mortality estimate. A decision tree was developed that provides general guidance in selecting appropriate methods despite violated assumptions, but species-specific case studies are recommended. An example of a species-specific study is provided for the brown shrimp, Crangon crangon. Despite inherent limitations for all methods, the results illustrate that estimates of and Z for brown shrimp can be improved substantially by selecting suitable methods and correcting for observed bias.
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  • 54
    Publication Date: 2013-02-21
    Description: Brunel, T., and Piet, G. J. 2013. Is age structure a relevant criterion for the health of fish stocks? – ICES Journal of Marine Science, 70: 270–283. The age and size structure of exploited fish stocks is one of the criteria for Good Environmental Status of commercial fish. However, two underlying assumptions to this criterion remain to be tested: first, that a well-balanced age structure is indeed indicative of a "healthier" stock, and second, that managers can exert a control on the age structure, independently from the regulation of stock abundance. This study investigates these questions using simulations from a population model in which recruitment is based on egg production, which is more sensitive to age structure variations than the traditionally used spawning stock biomass (SSB) and that was parameterized to represent the population dynamics of North Sea cod, plaice, and herring. Our results show that (i) the age structure is highly dependent on the selection pattern, as well as on the level of fishing mortality; (ii) the selection pattern determines the ability of fish stocks to withstand, and recover from, external perturbation; and (iii) the selection pattern determines the output of the fishery providing the management option to balance stable but relatively low yields vs strongly fluctuating high yields. Therefore, we propose to make the selection pattern, for which clear management targets can be set, a policy goal instead of the age structure that is currently in place.
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  • 55
    Publication Date: 2013-02-21
    Description: Bréchon, A. L., Coombs S. H., Sims D. W., and Griffiths A. M. 2013. Development of a rapid genetic technique for the identification of clupeid larvae in the Western English Channel and investigation of mislabelling in processed fish products – ICES Journal of Marine Science, 70: 399–407. A novel genetic technique, involving real-time polymerase chain reaction (PCR) and high-resolution melt (HRM) analysis was developed, which successfully identified four species of clupeid larvae from the Western English Channel and revealed the presence of herring ( Clupea harengus ). This was unexpected in a context of global warming as herring are at the southern limit of their range off southwest England, where the larvae are generally very rare. The application of the method in cases of degraded DNA, such as in processed fishery products, was also assessed, revealing a low level of misidentification or equivocal identity (8.3%). Eight-year-old formalin-preserved samples were also analysed successfully. This highlights the potentially broad applications for HRM-based approaches to species identification in marine science.
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  • 56
    Publication Date: 2013-02-21
    Description: Quetglas, A., Ordines, F., Hidalgo, M., Monserrat, S., Ruiz, S., Amores, Á., Moranta, J., and Massutí, E. 2013. Synchronous combined effects of fishing and climate within a demersal community. – ICES Journal of Marine Science, 70: 319–328. Accumulating evidence shows that fishing exploitation and environmental variables can synergistically affect the population dynamics of exploited populations. Here, we document an interaction between fishing impact and climate variability that triggered a synchronic response in the population fluctuations of six exploited species in the Mediterranean from 1965–2008. Throughout this period, the fishing activity experienced a sharp increase in fishing effort, which caused all stocks to shift from an early period of underexploitation to a later period of overexploitation. This change altered the population resilience of the stocks and brought about an increase in the sensitivity of its dynamics to climate variability. Landings increased exponentially when underexploited but displayed an oscillatory behaviour once overexploited. Climatic indices, related to the Mediterranean mesoscale hydrography and large-scale north Atlantic climatic variability, seemed to affect the species with broader age structure and longer lifespan, while the global-scale El Niño Southern Oscillation index (ENSO) positively influenced the population abundances of species with a narrow age structure and short lifespan. The species affected by ENSO preferentially inhabit the continental shelf, suggesting that Mediterranean shelf ecosystems are sensitive to the hydroclimatic variability linked to global climate.
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  • 57
    Publication Date: 2013-02-21
    Description: Papetti, C., Di Franco, A., Zane, L., Guidetti, P., De Simone, V., Spizzotin, M., Zorica, B., Cikes Kec, V. and Mazzoldi, C. 2013. Single population and common natal origin for Adriatic Scomber scombrus stocks: evidence from an integrated approach – ICES Journal of Marine Science, 70: 387–398. In order to implement proper fishery management strategies aimed at avoiding stock declines, information about connectivity among stocks and populations is critically required. In this perspective, the present study investigated population structure of the Atlantic mackerel Scomber scombrus in the northern–central Adriatic Sea by integrating multiple approaches (analysis of fisheries data, population genetics, and otolith chemistry). Monthly data of fishery landings indicate a latitudinal trend along the western Adriatic coast, with Atlantic mackerel disappearing from the northern waters in winter, corresponding to the reproductive season. Population genetic analyses by genotyping of eight microsatellites clearly point to the presence of a single panmictic population in the northern–central Adriatic Sea. Otolith cores of samples from the northern–central Adriatic were chemically homogeneous, suggesting a common spawning ground. These results strongly suggest that Atlantic mackerel perform an autumn–winter migration in the northern–central Adriatic Sea, from the northern to the central sector, to reach a single spawning ground, and that a single population is present in this area. Considering that S. scombrus has shown a marked decline in the last 40 years in the Adriatic, this study highlights a potential high vulnerability to collapse by overfishing for the Atlantic mackerel stocks in this geographic area.
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  • 58
    Publication Date: 2013-02-21
    Description: Uusitalo, L., Fleming-Lehtinen, V., Hällfors, H., Jaanus A., Hällfors, S., and London, L. 2013. A novel approach for estimating phytoplankton biodiversity – ICES Journal of Marine Science, 70: 408–417. Maintaining biodiversity is one of the main priorities in environmental protection. The biodiversity of phytoplankton, the key primary producers in the marine ecosystem, is, however, often very difficult to estimate, since the phytoplankton assemblage includes a vast number of taxa, many of which occur in such small quantities that they may not be recorded in routine sampling. Moreover, many taxa cannot be identified to species level by routine methods such as light microscopy of preserved samples, even by a skilled taxonomist. This means that, in general, we cannot assume to have a complete list of species in the ecosystem at any given point in time. In this paper, we present an approach for evaluating phytoplankton biodiversity in spite of this challenge. Since eutrophication, which increases phytoplankton biomass, has been identified as the most important factor causing degradation of the Baltic Sea ecosystem, the proposed approach was evaluated against total phytoplankton biomass. When phytoplankton biomass was low, both low and high biodiversity values were observed, and, as the phytoplankton biomass increased, the high biodiversity values disappeared. These results were consistent both using data based on individual samples and using yearly sampling station averages.
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  • 59
    Publication Date: 2013-02-21
    Description: Frie, A. K., Hammill, M. O., Hauksson, E., Lind, Y., Lockyer, C., Stenman, O., and Svetocheva, O. 2013. Error patterns in age estimation and tooth readability assignment of grey seals ( Halichoerus grypus ): results from a transatlantic, image-based, blind-reading study using known-age animals – ICES Journal of Marine Science, 70: 418–430. We analysed error patterns in a first interlaboratory grey seal ( Halichoerus grypus ) age-reading experiment. The experiment involved ten readers, who estimated age using images of cementum growth layers from teeth of 68 known-age seals (0–22 years). The percentages of correct estimates ranged from 32.4% to 60.3% among readers, and 89.3% of all errors were by ±1–2 years. Six readers showed increasing underageing with increasing seal age. An elevated risk of underestimation by 1 year occurred in teeth collected 0–5 months after breeding and was attributed to more frequent absence of a distinct growth layer for the new year and lack of information on months between the last birthday and the date of sample collection (plusmonths). For plusmonths 6–11, positive bias was predominant, suggesting that overestimation is the more common error when plusmonth information is available. Readers assigned readability scores to the tooth sections, and 79.1% of all ageing errors occurred in sections of low or intermediate readability. Excluding these sections would, however, also exclude 43.0% of all correct estimates. Neither levels of age estimation error nor predictive values of readability assignments were associated with reader experience levels. Analyses of image markings identified common errors in delineations of annual increment layers.
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  • 60
    Publication Date: 2013-02-21
    Description: Domínguez-Petit, R., Ouellet, P., and Lambert, Y. 2013. Reproductive strategy, egg characteristics and embryonic development of Greenland halibut ( Reinhardtius hippoglossoides ). – ICES Journal of Marine Science, 70: 342–351. Despite the commercial importance of Greenland halibut (GH), important gaps exist in our knowledge of the reproductive and early life stage biology for this species. The present study examined through laboratory experiments the spawning strategy, realized fecundity, egg characteristics, biochemical composition, and embryonic development of GH. The results confirmed the hypothesis that GH is a single-batch spawner producing large eggs, resulting in low realized fecundity. Embryonic development and hatching time are highly dependent on incubation temperature; 50% hatching occurred after 46, 30, and 24 days at 2, 4, and 6°C, respectively. Few changes in the biochemical composition of the eggs are observed during embryonic development. Newly hatched larvae are not well developed, having a large yolk sac, no pigmentation and incomplete development of the jaws. Egg specific density confirmed the mesopelagic distribution of the eggs at sea. However, important buoyancy changes occurring in the last 3–4 days before hatching indicate that larvae hatch higher in the water column. These results are important for understanding advection and dispersion processes of GH eggs and larvae and the connectivity between spawning grounds and nursery areas.
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  • 61
    Publication Date: 2013-02-21
    Description: Johnsen, E., and Harbitz, A. 2013. Small-scale spatial structuring of burrowed sandeels and the catching properties of the dredge – ICES Journal of Marine Science, 70: 379–386. The lesser sandeel ( Ammodytes marinus ) remains burrowed for long periods in the seabed in sandy areas, and its habitat preference is reflected in a large-scale (10 km) patchy distribution in the North Sea. The small-scale spatial structure of sandeels in the seabed is less known. In this study, it was found that sandeel catches in grabs and dredges fit gamma distributions with a common shape parameter on both a 10 m and a 100 m scale. These spatial models were used to examine the catching properties of the dredge, which, in the new ICES sandeel assessment, is used to estimate recruitment and maturity curves. Analyses of the empirical data and simulations of the dredge and grab catch rates show very low dredge catchability (~5%), but no length-dependent catchability in the dredge was found. However, analyses of the catch rates of parallel dredge hauls indicated increasing dredge catchability with sandeel density. The observed small-scale patchiness and the low and seemingly density-dependent dredge catchability result in biased abundance estimates with low precision. Therefore, we recommend a joint international effort to develop a more catch-efficient sampling dredge, where the effect of density on catchability is further examined.
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  • 62
    Publication Date: 2013-02-21
    Description: Rousi, H., Laine, A. O., Peltonen, H., Kangas, P., Andersin, A-B., Rissanen, J., Sandberg-Kilpi, E., and Bonsdorff, E. 2013. Long-term changes in coastal zoobenthos in the northern Baltic Sea: the role of abiotic environmental factors – ICES Journal of Marine Science, 70: 440–451. We investigated site-specific changes in a coastal zoobenthic community during 1964–2007 in the northern Baltic Sea. Multivariate analysis indicated that the community structure had changed. The amphipods Monoporeia affinis and Pontoporeia femorata decreased drastically in the late 1970s–early 1980s, and by the early 1990s P. femorata vanished and M. affinis abundance was low. The decline of M . affinis and P . femorata was followed by an increase of the bivalve Macoma balthica and the arrival of the polychaete genus Marenzelleria in the 1990s. Trend analyses showed a rising trend for near-bottom temperature from the late 1960s. There was a significant decline in salinity during the early 1980s, which stabilized during the early 1990s. A negative trend was observed for oxygen concentration during the entire study period. There were interannual variations in the phosphorus and nitrogen concentrations, and a step-like increase in phosphorus concentration at the beginning of the 21st century. The correlations of temperature, salinity, oxygen, total phosphorus and nitrogen with zoobenthic communities were examined using Constrained Correspondence Analysis. Temperature was the most highly correlated explanatory variable for the benthic species. The study highlights the importance of long-term data sets in assessing the state and ecological processes of zoobenthic systems.
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  • 63
    Publication Date: 2013-02-21
    Description: O'Driscoll, R. L., Oeffner, J., and Dunford, A. J. 2013. In situ target strength estimates of optically verified southern blue whiting ( Micromesistius australis ) – ICES Journal of Marine Science, 70: 431–439. Estimates of the acoustic target strength (TS) of southern blue whiting ( Micromesistius australis ) at 38 kHz were obtained using an autonomous acoustic–optical system (AOS) mounted on a demersal trawl. Data were collected from aggregations of spawning adult [mean fork length (FL) 34.4 cm] and immature (mean FL 24.6 cm) southern blue whiting south of New Zealand. Mean TS was estimated from 162 tracks containing 695 echoes from targets identified from video as southern blue whiting. The mean TS was –37.9 dB with a 95% confidence interval ( CI ) of –39.7 to –36.6 dB for 21 immature fish and –34.6 dB (95% CI –35.4 to –34.0 dB) for 141 adults. A logarithmic fit through the mean TS values produced a TS–fork length (FL) relationship from optically verified targets of TS = 22.06 log 10 FL – 68.54. This new relationship gives TS values within 1 dB of those estimated using the relationship recently adopted by ICES for blue whiting ( Micromesistius poutassou ) of TS = 20 log 10 TL – 65.2 (where TL is total length) obtained from in situ measurements, but higher values than those estimated from the previous relationship for southern blue whiting of TS = 38 log 10 FL – 97, which was based on swimbladder modelling.
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  • 64
    Publication Date: 2013-02-21
    Description: De Robertis, A., Wilson, C. D., Furnish, S. R., and Dahl, P. H. 2013. Underwater radiated noise measurements of a noise-reduced fisheries research vessel. – ICES Journal of Marine Science, 70: 480–484. Vessel-radiated noise is traditionally measured at naval acoustic ranges, but lower-cost options are desirable for routine monitoring of research vessels. Measurements of a noise-reduced research vessel made at a naval noise range are compared to those made using an experimental mooring equipped with commercially available instrumentation. The measurements from the mooring were precise and within 2.5 dB of those from the noise range at third-octave bands 〈500 Hz. At higher frequencies, direct comparisons were precluded by an intermittent shaft-related noise present only during the mooring measurements, but previously observed at the navy range. The agreement between the two methods suggests that simplified, field-deployable hydrophone systems can be used to accurately characterize the noise signatures of research vessels.
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  • 65
    Publication Date: 2013-02-24
    Description: Gaussian processes are widely used in nonparametric regression, classification and spatiotemporal modelling, facilitated in part by a rich literature on their theoretical properties. However, one of their practical limitations is expensive computation, typically on the order of n 3 where n is the number of data points, in performing the necessary matrix inversions. For large datasets, storage and processing also lead to computational bottlenecks, and numerical stability of the estimates and predicted values degrades with increasing n . Various methods have been proposed to address these problems, including predictive processes in spatial data analysis and the subset-of-regressors technique in machine learning. The idea underlying these approaches is to use a subset of the data, but this raises questions concerning sensitivity to the choice of subset and limitations in estimating fine-scale structure in regions that are not well covered by the subset. Motivated by the literature on compressive sensing, we propose an alternative approach that involves linear projection of all the data points onto a lower-dimensional subspace. We demonstrate the superiority of this approach from a theoretical perspective and through simulated and real data examples.
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  • 66
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2013-02-24
    Description: Karl Pearson edited Biometrika for the first 35 years of its existence. Not only did he shape the journal, he also contributed over 200 pieces and inspired, more or less directly, most of the other contributions. The journal could not be separated from the man.
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  • 67
    Publication Date: 2013-02-24
    Description: In the modelling of longitudinal data from several groups, appropriate handling of the dependence structure is of central importance. Standard methods include specifying a single covariance matrix for all groups or independently estimating the covariance matrix for each group without regard to the others, but when these model assumptions are incorrect, these techniques can lead to biased mean effects or loss of efficiency, respectively. Thus, it is desirable to develop methods for simultaneously estimating the covariance matrix for each group that will borrow strength across groups in a way that is ultimately informed by the data. In addition, for several groups with covariance matrices of even medium dimension, it is difficult to manually select a single best parametric model among the huge number of possibilities given by incorporating structural zeros and/or commonality of individual parameters across groups. In this paper we develop a family of nonparametric priors using the matrix stick-breaking process of Dunson et al. (2008) that seeks to accomplish this task by parameterizing the covariance matrices in terms of their modified Cholesky decompositions (Pourahmadi, 1999). We establish some theoretical properties of these priors, examine their effectiveness via a simulation study, and illustrate the priors using data from a longitudinal clinical trial.
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  • 68
    Publication Date: 2013-02-24
    Description: Full Bayesian computational inference for model determination in undirected graphical models is currently restricted to decomposable graphs or other special cases, except for small-scale problems, say up to 15 variables. In this paper we develop new, more efficient methodology for such inference, by making two contributions to the computational geometry of decomposable graphs. The first of these provides sufficient conditions under which it is possible to completely connect two disconnected complete subsets of vertices, or perform the reverse procedure, yet maintain decomposability of the graph. The second is a new Markov chainMonte Carlo sampler for arbitrary positive distributions on decomposable graphs, taking a junction tree representing the graph as its state variable. The resulting methodology is illustrated with numerical experiments on three models.
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  • 69
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2013-02-24
    Description: In longitudinal data analysis, statistical inference for sparse data and dense data could be substantially different. For kernel smoothing, the estimate of the mean function, the convergence rates and the limiting variance functions are different in the two scenarios. This phenomenon poses challenges for statistical inference, as a subjective choice between the sparse and dense cases may lead to wrong conclusions. We develop methods based on self-normalization that can adapt to the sparse and dense cases in a unified framework. Simulations show that the proposed methods outperform some existing methods.
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  • 70
    Publication Date: 2013-02-24
    Description: The problem of testing smooth components of an extended generalized additive model for equality to zero is considered. Confidence intervals for such components exhibit good across-the-function coverage probabilities if based on the approximate result , where f is the vector of evaluated values for the smooth component of interest and V f is the covariance matrix for f according to the Bayesian view of the smoothing process. Based on this result, a Wald-type test of f =0 is proposed. It is shown that care must be taken in selecting the rank used in the test statistic. The method complements previous work by extending applicability beyond the Gaussian case, while considering tests of zero effect rather than testing the parametric hypothesis given by the null space of the component’s smoothing penalty. The proposed p -values are routine and efficient to compute from a fitted model, without requiring extra model fits or null distribution simulation.
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  • 71
    Publication Date: 2013-02-24
    Description: Motivated by analysis of genetical genomics data, we introduce a sparse high-dimensional multivariate regression model for studying conditional independence relationships among a set of genes adjusting for possible genetic effects. The precision matrix in the model specifies a covariate-adjusted Gaussian graph, which presents the conditional dependence structure of gene expression after the confounding genetic effects on gene expression are taken into account. We present a covariate-adjusted precision matrix estimation method using a constrained 1 minimization, which can be easily implemented by linear programming. Asymptotic convergence rates in various matrix norms and sign consistency are established for the estimators of the regression coefficients and the precision matrix, allowing both the number of genes and the number of the genetic variants to diverge. Simulation shows that the proposed method results in significant improvements in both precision matrix estimation and graphical structure selection when compared to the standard Gaussian graphical model assuming constant means. The proposed method is applied to yeast genetical genomics data for the identification of the gene network among a set of genes in the mitogen-activated protein kinase pathway.
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  • 72
    Publication Date: 2013-02-24
    Description: This paper introduces, constructs and studies a new class of arrays, called strong orthogonal arrays, as suitable designs for computer experiments. A strong orthogonal array of strength t enjoys better space-filling properties than a comparable orthogonal array in all dimensions lower than t while retaining the space-filling properties of the latter in t dimensions. Latin hypercubes based on strong orthogonal arrays of strength t are more space-filling than comparable orthogonal array-based Latin hypercubes in all g dimensions for any 2 ≤ g ≤ t – 1.
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  • 73
    Publication Date: 2013-02-24
    Description: This paper considers the construction of blocked two-level regular designs with weak minimum aberration. We first obtain the minimum value of the number of two-factor interactions which are aliased with the block effects. Based on this result, two methods are then proposed in two different scenarios to construct weak minimum aberration blocked two-level designs with respect to some existing combined wordlength patterns.
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  • 74
    Publication Date: 2013-02-24
    Description: Rathbun et al. (2007) and Waagepetersen (2008) propose estimating functions for parameters of Poisson point process intensity that may be applied when space- and/or time-varying covariates are sampled from a probability-based sampling design. This paper demonstrates that Waageptersen’s estimating function is optimal in a class of weighted estimating functions.
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  • 75
    Publication Date: 2013-02-24
    Description: We show that the proportional likelihood ratio model proposed recently by Luo & Tsai (2012) enjoys model-invariant properties under certain forms of nonignorable missing mechanisms and randomly double-truncated data, so that target parameters in the population can be estimated consistently from those biased samples. We also construct an alternative estimator for the target parameters by maximizing a pseudolikelihood that eliminates a functional nuisance parameter in the model. The corresponding estimating equation has a U-statistic structure. As an added advantage of the proposed method, a simple score-type test is developed to test a null hypothesis on the regression coefficients. Simulations show that the proposed estimator has a small-sample efficiency similar to that of the nonparametric likelihood estimator and performs well for certain nonignorable missing data problems.
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  • 76
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    Oxford University Press
    Publication Date: 2013-02-24
    Description: This paper considers benchmarking issues in the context of small area estimation. We find optimal estimators within the class of benchmarked linear estimators under linear constraints. This extends existing results for external and internal benchmarking, and also links the two. Necessary and sufficient conditions for self-benchmarking are found for an augmented model. Most results of this paper are found using ideas of orthogonal projection
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  • 77
    Publication Date: 2013-02-24
    Description: Suppose we are interested in the effect of a binary treatment on an outcome where that relationship is confounded by an ordinal confounder. We assume that the true confounder is not observed but, rather, we observe a nondifferentially mismeasured version of it. We show that, under certain monotonicity assumptions about its effect on the treatment and on the outcome, an effect measure controlling for the mismeasured confounder will fall between the corresponding crude and true effect measures. We also present results for coarsened and, under further assumptions, multiple misclassified confounders.
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  • 78
    Publication Date: 2013-02-24
    Description: Applying concepts from partial identification to the domain of finite population sampling, we propose a method for interval estimation of a population mean when the probabilities of sample selection lie within a posited interval. The interval estimate is derived from sharp bounds on the Hajek (1971) estimator of the population mean. We demonstrate the method’s utility for sensitivity analysis by applying it to a sample of needles collected as part of a syringe tracking and testing programme in New Haven, Connecticut.
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  • 79
    Publication Date: 2013-02-24
    Description: Since many environmental processes are spatial in extent, a single extreme event may affect several locations, and the spatial dependence must be taken into account in an appropriate way. This paper proposes a framework for conditional simulation of max-stable processes and gives closed forms for the regular conditional distributions of Brown–Resnick and Schlather processes. We test the method on simulated data and present applications to extreme rainfall around Zurich and extreme temperatures in Switzerland. The proposed framework provides accurate conditional simulations and can handle problems of realistic size.
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  • 80
    Publication Date: 2013-02-24
    Description: We study the nonparametric estimation of the cumulative incidence function and the cause-specific hazard function for current status data with competing risks via kernel smoothing. A smoothed naive nonparametric maximum likelihood estimator and a smoothed full nonparametric maximum likelihood estimator are shown to have pointwise asymptotic normality and faster convergence rates than the corresponding unsmoothed nonparametric likelihood estimators. Using the smoothed estimators and the plug-in principle, we can estimate the cause-specific hazard function, which has not been studied previously. We also propose semi-smoothed estimators of the cause-specific hazard as an alternative to the smoothed estimator and demonstrate that neither is uniformly more efficient than the other. Numerical studies show that a smoothed bootstrap method works well for selecting the bandwidths in the smoothed nonparametric estimation. The use of the estimators is exemplified by an application to cumulative incidence and hazard of subtype-specific HIV infection from a sero-prevalence study in injecting drug users in Thailand.
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  • 81
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    Oxford University Press
    Publication Date: 2013-02-24
    Description: Highlights, trends and influences are identified associated with the pages of Biometrika subsequent to the editorship of Karl Pearson.
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  • 82
    Publication Date: 2013-02-24
    Description: Copy number variant is an important type of genetic structural variation appearing in germline DNA, ranging from common to rare in a population. Both rare and common copy number variants have been reported to be associated with complex diseases, so it is important to identify both simultaneously based on a large set of population samples. We develop a proportion adaptive segment selection procedure that automatically adjusts to the unknown proportions of the carriers of the segment variants. We characterize the detection boundary that separates the region where a segment variant is detectable by some method from the region where it cannot be detected. Although the detection boundaries are very different for the rare and common segment variants, it is shown that the proposed procedure can reliably identify both whenever they are detectable. Compared with methods for single-sample analysis, this procedure gains power by pooling information from multiple samples. The method is applied to analyse neuroblastoma samples and identifies a large number of copy number variants that are missed by single-sample methods.
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  • 83
    Publication Date: 2013-02-24
    Description: We derive sufficient conditions for the cross-correlation coefficient of a multivariate spatial process to vary with location when the spatial model is augmented with nugget effects. The derived class is valid for any choice of covariance functions, and yields substantial flexibility between multiple processes. The key is to identify the cross-correlation coefficient matrix with a contraction matrix, which can be either diagonal, implying a parsimonious formulation, or a fully general contraction matrix, yielding greater flexibility but added model complexity. We illustrate the approach with a bivariate minimum and maximum temperature dataset in Colorado, allowing the two variables to be positively correlated at low elevations and nearly independent at high elevations, while still yielding a positive definite covariance matrix.
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  • 84
    Publication Date: 2013-02-24
    Description: Variable screening techniques have been proposed to mitigate the impact of high dimensionality in classification problems, including t -test marginal screening (Fan & Fan, 2008) and maximum marginal likelihood screening (Fan & Song, 2010). However, these methods rely on strong modelling assumptions that are easily violated in real applications. To circumvent the parametric modelling assumptions, we propose a new variable screening technique for binary classification based on the Kolmogorov–Smirnov statistic. We prove that this so-called Kolmogorov filter enjoys the sure screening property under much weakened model assumptions. We supplement our theoretical study by a simulation study.
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  • 85
    Publication Date: 2013-02-24
    Description: Cumulative sum or cusum charts are typically used to detect a change in the distribution of a sequence of observations, e.g., shifts in the mean. Usually, after signalling, the chart is restarted by setting it to some value below the signalling threshold. We propose a non-restarting cusum chart which is able to detect periods during which the stream is out of control. Further, we advocate an upper boundary to prevent the cusum chart rising too high, which helps to detect a change back into control. We present an algorithm to control the false discovery rate when considering cusum charts based on multiple streams of data. We consider two definitions of a false discovery: signalling out-of-control when the observations have been in control since the start and signalling out-of-control when the observations have been in control since the last time the chart was at zero. We prove that the false discovery rate is controlled under both these definitions simultaneously. Simulations reveal the difference in false discovery rate control when using these and other desirable definitions of a false discovery.
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  • 86
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    Oxford University Press
    Publication Date: 2012-11-16
    Description: In a matched observational study of treatment effects, a sensitivity analysis asks about the magnitude of the departure from random assignment that would need to be present to alter the conclusions of an analysis that assumes that matching for measured covariates removes all bias. The reported degree of sensitivity to unmeasured biases depends on both the process that generated the data and the chosen methods of analysis, so a poor choice of method may lead to an exaggerated report of sensitivity to bias. This suggests the possibility of performing more than one analysis with a correction for multiple inference, say testing one null hypothesis using two or three different tests. In theory and in an example, it is shown that, in large samples, the gains from testing twice will often be large, because testing twice has the larger of the two design sensitivities of the component tests, and the losses due to correcting for two tests will often be small, because two tests of one hypothesis will typically be highly correlated, so a correction for multiple testing that takes this into account will be small. An illustration uses data from the U.S. National Health and Nutrition Examination Survey concerning lead in the blood of cigarette smokers.
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  • 87
    Publication Date: 2012-11-16
    Description: Inferences related to the second-order properties of functional data, as expressed by covariance structure, can become unreliable when the data are non-Gaussian or contain unusual observations. In the functional setting, it is often difficult to identify atypical observations, as their distinguishing characteristics can be manifold but subtle. In this paper, we introduce the notion of a dispersion operator, investigate its use in probing the second-order structure of functional data, and develop a test for comparing the second-order characteristics of two functional samples that is resistant to atypical observations and departures from normality. The proposed test is a regularized M -test based on a spectrally truncated version of the Hilbert–Schmidt norm of a score operator defined via the dispersion operator. We derive the asymptotic distribution of the test statistic, investigate the behaviour of the test in a simulation study and illustrate the method on a structural biology dataset.
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  • 88
    Publication Date: 2012-11-16
    Description: Linear classifiers are very popular, but can have limitations when classes have distinct subpopulations. General nonlinear kernel classifiers are very flexible, but do not give clear interpretations and may not be efficient in high dimensions. We propose the bidirectional discrimination classification method, which generalizes linear classifiers to two or more hyperplanes. This new family of classification methods gives much of the flexibility of a general nonlinear classifier while maintaining the interpretability, and much of the parsimony, of linear classifiers. They provide a new visualization tool for high-dimensional, low-sample-size data. Although the idea is generally applicable, we focus on the generalization of the support vector machine and distance-weighted discrimination methods. The performance and usefulness of the proposed method are assessed using asymptotics and demonstrated through analysis of simulated and real data. Our method leads to better classification performance in high-dimensional situations where subclusters are present in the data.
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  • 89
    Publication Date: 2012-11-16
    Description: Two transformations are proposed that give orthogonal components with a one-to-one correspondence between the original vectors and the components. The aim is that each component should be close to the vector with which it is paired, orthogonality imposing a constraint. The transformations lead to a variety of new statistical methods, including a unified approach to the identification and diagnosis of collinearities, a method of setting prior weights for Bayesian model averaging, and a means of calculating an upper bound for a multivariate Chebychev inequality. One transformation has the property that duplicating a vector has no effect on the orthogonal components that correspond to nonduplicated vectors, and is determined using a new algorithm that also provides the decomposition of a positive-definite matrix in terms of a diagonal matrix and a correlation matrix. The algorithm is shown to converge to a global optimum.
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  • 90
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    Unknown
    Oxford University Press
    Publication Date: 2012-11-16
    Description: Scaled sparse linear regression jointly estimates the regression coefficients and noise level in a linear model. It chooses an equilibrium with a sparse regression method by iteratively estimating the noise level via the mean residual square and scaling the penalty in proportion to the estimated noise level. The iterative algorithm costs little beyond the computation of a path or grid of the sparse regression estimator for penalty levels above a proper threshold. For the scaled lasso, the algorithm is a gradient descent in a convex minimization of a penalized joint loss function for the regression coefficients and noise level. Under mild regularity conditions, we prove that the scaled lasso simultaneously yields an estimator for the noise level and an estimated coefficient vector satisfying certain oracle inequalities for prediction, the estimation of the noise level and the regression coefficients. These inequalities provide sufficient conditions for the consistency and asymptotic normality of the noise-level estimator, including certain cases where the number of variables is of greater order than the sample size. Parallel results are provided for least-squares estimation after model selection by the scaled lasso. Numerical results demonstrate the superior performance of the proposed methods over an earlier proposal of joint convex minimization.
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  • 91
    Publication Date: 2012-11-16
    Description: In this article, we propose a regression method for simultaneous supervised clustering and feature selection over a given undirected graph, where homogeneous groups or clusters are estimated as well as informative predictors, with each predictor corresponding to one node in the graph and a connecting path indicating a priori possible grouping among the corresponding predictors. The method seeks a parsimonious model with high predictive power through identifying and collapsing homogeneous groups of regression coefficients. To address computational challenges, we present an efficient algorithm integrating the augmented Lagrange multipliers, coordinate descent and difference convex methods. We prove that the proposed method not only identifies the true homogeneous groups and informative features consistently but also leads to accurate parameter estimation. A gene network dataset is analysed to demonstrate that the method can make a difference by exploring dependency structures among the genes.
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  • 92
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    Unknown
    Oxford University Press
    Publication Date: 2012-11-16
    Description: This article proposes a method of moments technique for estimating the sparsity of signals in a random sample. This involves estimating the largest eigenvalue of a large Hermitian trigonometric matrix under mild conditions. As illustration, the method is applied to two well-known problems. The first focuses on the sparsity of a large covariance matrix and the second investigates the sparsity of a sequence of signals observed with stationary, weakly dependent noise. Simulation shows that the proposed estimators can have significantly smaller mean absolute errors than their main competitors.
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  • 93
    Publication Date: 2012-11-16
    Description: We introduce a doubly stochastic marked point process model for supervised classification problems. Regardless of the number of classes or the dimension of the feature space, the model requires only 2–3 parameters for the covariance function. The classification criterion involves a permanental ratio for which an approximation using a polynomial-time cyclic expansion is proposed. The approximation is effective even if the feature region occupied by one class is a patchwork interlaced with regions occupied by other classes. An application to DNA microarray analysis indicates that the cyclic approximation is effective even for high-dimensional data. It can employ feature variables in an efficient way to reduce the prediction error significantly. This is critical when the true classification relies on nonreducible high-dimensional features.
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  • 94
    Publication Date: 2012-11-16
    Description: Researchers in the biological sciences nowadays often encounter the curse of dimensionality. To tackle this, sufficient dimension reduction aims to estimate the central subspace, in which all the necessary information supplied by the covariates regarding the response of interest is contained. Subsequent statistical analysis can then be made in a lower-dimensional space while preserving relevant information. Many studies are concerned with the transformed response rather than the original one, but they may have different central subspaces. When estimating the central subspace of the transformed response, direct methods will be inefficient. In this article, we propose a more efficient two-stage estimator of the central subspace of a transformed response. This approach is extended to censored responses and is applied to combining multiple biomarkers. Simulation studies and data examples support the superiority of the procedure.
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  • 95
    Publication Date: 2012-11-16
    Description: Transient semi-Markov processes have traditionally been used to describe the transitions of a patient through the various states of a multistate survival model. A survival distribution in this context is a sojourn through the states until passage to a fatal absorbing state or certain endpoint states. Using complete sojourn data, this paper shows how such survival distributions and associated hazard functions can be estimated nonparametrically and also how nonparametric bootstrap pointwise confidence bands can be constructed for them when patients are subject to independent right censoring from each state during the sojourn. Limitations to the estimability of such survival distributions that result from random censoring with bounded support are clarified. The methods are applicable to any sort of sojourn through any finite state process of arbitrary complexity involving feedback into previously occupied states.
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  • 96
    Publication Date: 2012-11-16
    Description: In some problems involving functional data, it is desired to undertake prediction or classification before the full trajectory of a function is observed. In such cases, it is often preferable to suffer somewhat greater error in return for making a decision relatively early. The prediction and classification problems can be treated similarly, using mean squared prediction error, or classification error, respectively, as the means for quantifying performance, so in this paper we focus principally on classification. We introduce a method for determining when an early decision can reasonably be made, using only part of the trajectory, and we show how to use the method to choose among data types. Our approach is fully nonparametric, and no specific model is required. Properties of error-rate are studied as functions of time and data type. The effectiveness of the proposed method is illustrated in both theoretical and numerical terms. The classification referred to in this paper would be termed supervised classification in machine learning, to distinguish it from unsupervised classification, or clustering.
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  • 97
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    Unknown
    Oxford University Press
    Publication Date: 2012-11-16
    Description: Linear mixed models cover a wide range of statistical methods, which have found many uses in the estimation for complex surveys. The purpose of this work is to consider methods by which linear mixed models may be used at the design stage of a survey to incorporate available auxiliary information. This paper reviews the ideas of balanced sampling and the cube algorithm, and proposes an implementation of the latter by which penalized balanced samples can be selected. Such samples can reduce or eliminate the need for linear mixed model weight adjustments, a result demonstrated theoretically and via simulation. Horvitz–Thompson estimators for such samples will be highly efficient for any responses well approximated by a linear mixed model in the auxiliary information. In Monte Carlo experiments using nonparametric and temporal linear mixed models, the strategy of penalized balanced sampling with Horvitz–Thompson estimation dominates a variety of standard strategies.
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  • 98
    Publication Date: 2012-11-16
    Description: Monte Carlo algorithms are commonly used to identify a set of models for Bayesian model selection or model averaging. Because empirical frequencies of models are often zero or one in high-dimensional problems, posterior probabilities calculated from the observed marginal likelihoods, renormalized over the sampled models, are often employed. Such estimates are the only recourse in several newer stochastic search algorithms. In this paper, we prove that renormalization of posterior probabilities over the set of sampled models generally leads to bias that may dominate mean squared error. Viewing the model space as a finite population, we propose a new estimator based on a ratio of Horvitz–Thompson estimators that incorporates observed marginal likelihoods, but is approximately unbiased. This is shown to lead to a reduction in mean squared error compared to the empirical or renormalized estimators, with little increase in computational cost.
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  • 99
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    Unknown
    Oxford University Press
    Publication Date: 2012-11-16
    Description: Many proper scoring rules such as the Brier and log scoring rules implicitly reward a probability forecaster relative to a uniform baseline distribution. Recent work has motivated weighted proper scoring rules, which have an additional baseline parameter. To date two families of weighted proper scoring rules have been introduced, the weighted power and pseudospherical scoring families. These families are compatible with the log scoring rule: when the baseline maximizes the log scoring rule over some set of distributions, the baseline also maximizes the weighted power and pseudospherical scoring rules over the same set. We characterize all weighted proper scoring families and prove a general property: every proper scoring rule is compatible with some weighted scoring family, and every weighted scoring family is compatible with some proper scoring rule.
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  • 100
    Publication Date: 2012-11-16
    Description: Projective shape consists of the information about a configuration of points that is invariant under projective transformations. It is an important tool in machine vision to pick out features that are invariant to the choice of camera view. The simplest example is the cross ratio for a set of four collinear points. Recent work involving ideas from multivariate robustness enables us to introduce here a natural preshape on projective shape space. This makes it possible to adapt the Procrustes analysis that forms the basis of much methodology in the simpler setting of similarity shape space.
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