Conditional and Unconditional Simulation of Healthy Patients' Visual Fields

This paper describes a simulation problem, motivated by the study of glaucoma, a very serious and widespread ocular illness. To ascertain whether a patient suffers from glaucoma, a perimetric test is done, but the evolution of the disease is very slow, and large longitudinal sets of tests taken on the same patient are needed to study its evolution, to analyze the efficiency of existing methods to detect the progression of glaucoma and to develop new ones. Simulation can be a very useful procedure to get appropriate data sets to work with. Our aim in this work is to simulate several VFs in a healthy patient to reflect his evolution in time. We use a spatio‐temporal model to simulate from, taking into account the correlation existing between the observed (or simulated) values in space and time. Two different simulation procedures (unconditional and conditional) are studied, and applied to obtain the simulations we are interested in. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Reaction mechanism of surfactant‐sensitized chemiluminescence of bis(2,4,6‐trichlorophyenyl) oxalate and hydrogen peroxide induced by gold nanoparticles

The chemiluminescence (CL) of bis(2,4,6‐trichlorophyenyl) oxalate with hydrogen peroxide in the present of cationic surfactant and gold nanoparticles was studied. The CL emission was obviously enhanced in the presence of surfactant at a suitable concentration, with a synergetic catalysis effect exhibited. Different sizes of gold nanoparticles (15 and 50 nm) showed different effects on CL intensity. Mechanisms of the CL reaction and sensitization effect are discussed. Copyright © 2008 John Wiley & Sons, Ltd.     

Describing Ordinal Odds Ratios for Stratified r × c Tables

For an r × ctable with ordinal responses, odds ratios are commonly used to describe the relationship between the row and column variables. This article shows two types of ordinal odds ratios where local‐global odds ratios are used to compare several groups on a c‐category ordinal response and a global odds ratio is used to measure the global association between a pair of ordinal responses. When there is a stratification factor, we consider Mantel‐Haenszel (MH) type estimators of these odds ratios to summarize the association from several strata. Like the ordinary MH estimator of the common odds ratio for several 2 × 2 contingency tables, the estimators are used when the association is not expected to vary drastically among the strata. Also, the estimators are consistent under the ordinary asymptotic framework in which the number of strata is fixed and also under sparse asymptotics in which the number of strata grows with the sample size. Compared to the maximum likelihood estimators, simulations find that the MH type estimators perform better especially when each stratum has few observations. This article provides variances and covariances formulae for the local‐global odds ratios estimators and applies the bootstrap method to obtain a standard error for the global odds ratio estimator. At the end, we discuss possible ways of testing the homogeneity assumption.     

INCIDENTAL MORTALITY OF NORTHERN SEA LIONS IN SHELIKOF STRAIT, ALASKA

The incidental catch of northern sea lions ( Eumetopias jubatus ) in the walleye pollock ( Theragra chalcogramma ) joint-venture fishery in Shelikof Strait, Alaska, was studied during 1982–1984 to assess the nature and magnitude of the catch. Data were obtained by placing U.S. observers on foreign processing vessels. Dead sea lions recovered from trawl nets were counted, sexed and measured, teeth were removed for age determination by dental laminae; and stomach contents were analyzed. Although the fishery has continued to expand both in number of boats and estimated total catch (74,136 metric tons [t] in 1982 to 171,539 t in 1984), the estimated incidental catch of northern sea lions has declined (ranging from 958 to 1,436 in 1982, 216 to 324 in 1983 and 237 to 355 in 1984). Of the sea lions processed, 73 percent were caught between 2000 and 0500 h, probably during net retrieval. Most caught sea lions were females ranging in age from 1–25 yr with a mean age of 6.43 yr; 79 percent of the females were sexually mature and probably part of the reproducing population. Males had a mean age of 4.8 yr and only 12 percent were old enough to obtain and defend territories. Analysis of stomach contents showed that the sea lions consumed pollock the same size as that taken by the commercial fishery. The impact of the incidental catch on the Gulf of Alaska sea lion population is unknown.     

Validation of age readings from otoliths of juvenile roundnose grenadier, Coryphaenoides rupestris, a deep-water macrourid fish

Validation of the ageing of deep-water fish is difficult and there are only a few instances where the rings on the otoliths have been shown to be laid down annually. Roundnose grenadier have been fished commercially in the North Atlantic since the 1960s and the adult fish have frequently been aged by counting the rings in otoliths or scales. All the ageing was done on the assumption that the rings in the otoliths or scales were annual. Between 1975 and 1992, the Scottish Association for Marine Science carried out seasonal trawling surveys in the Rockall Trough using a fine-meshed trawl, and collected otoliths from a wide size range of roundnose grenadier. An examination of the growing edge of otoliths from juvenile fish from these collections suggests that the rings in the otoliths are laid down annually. The broader, opaque zones which represent the growth phase were dominant between September and March. The thinner, hyaline zones were dominant between April and July. The apparent delay in the growth phase compared with most shallow-water species is discussed in relation to the availability of mesopelagic prey.     

Remote sensing of sea surface and coastal features in the area of the Golfe d'Arguin,Mauritania

The analysis of a series of NOAA AVHRR satellite data recorded between July and September 1986 shows the interaction between northerly and southerly water masses during summer as well as the northern limit of the northward advance of water masses originating from the South Equatorial Current. Two upwelling situations analysed by means of NOAA data show the intrusion of suspended matter from the ocean into the Golfe d'Arguin and illustrate the water circulation within the coastal zone. This circulation pattern is detailed by LANDSAT and SPOT data. A SPOT picture from October 1987 shows the structure of the intertidal and coastal geomorphology.     

CryoRes: Local Resolution Estimation of Cryo-EM Density Maps by Deep Learning

Recent progress in cryo-EM research has ignited a revolution in biological macromolecule structure determination. Resolution is an essential parameter for quality assessment of a cryo-EM density map, and it is known that resolution varies in different regions of a map. Currently available methods for local resolution estimation require manual adjustment of parameters and in some cases necessitate acquisition or de novo generation of so-called “half maps”. Here, we developed CryoRes, a deep-learning algorithm to estimate local resolution directly from a single final cryo-EM density map, specifically by learning resolution-aware patterns of density map voxels through supervised training on a large dataset comprising 1,174 experimental cryo-EM density maps. CryoRes significantly outperforms all of the state-of-the-art competing resolution estimation methods, achieving an average RMSE of 2.26 Å for local resolution estimation relative to the currently most reliable FSC-based method blocres, yet requiring only the single final map as input. Further, CryoRes is able to generate a molecular mask for each map, with accuracy 12.12% higher than the masks generated by ResMap. CryoRes is ultra-fast, fully automatic, parameter-free, applicable to cryo-EM subtomogram data, and freely available at https://cryores.zhanglab.net.     

North Sea cod and climate change – modelling the effects of temperature on population dynamics

In order to examine the likely impacts of climate change on fish stocks, it is necessary to couple the output from large‐scale climate models to fisheries population simulations. Using projections of future North Sea surface temperatures for the period 2000–2050 from the Hadley General Circulation Model, we estimate the likely effects of climate change on the North Sea cod population. Output from the model suggests that increasing temperatures will lead to an increased rate of decline in the North Sea cod population compared with simulations that ignore environmental change. Although the simulation developed here is relatively simplistic, we demonstrate that inclusion of environmental factors in population models can markedly alter one's perception of how the population will behave. The development of simulations incorporating environment effects will become increasingly important as the impacts of climate change on the marine ecosystem become more pronounced.     

Induction of larval metamorphosis in the sea cucumber Stichopus japonicus by periphitic diatoms

The mass production of juvenile seeds of the sea cucumber,Stichopus japonicus has recently developed by the SeaFarming Center of Saga Prefecture. Methods for the culture ofperiphicic diatoms have been improved. There are three importantsteps in propagating the diatoms. The first step is theenrichment, with the addition of the nutrient salts, undercontrolled light intensity. The second step is washing withhigh pressure seawater and reversal of the plates. The laststep is elimination of copepods, which feed on diatoms, usinga pesticide. Small periphitic diatoms such as Navicula,Amphora, Achnanthes, and Nitzschia are easily culturedat a density of more than one million cells cm^–2, andthese diatoms are able to induce larval metamorphosis andserve as a food source for juvenile sea cucumbers.     

The encrustation of fossil and recent sea-urchin tests: ecological and taphonomic significance

A comparison of fossil ( Echitwlampas sp. from the Lower Miocene Zogelsdorf Formation, Austria) and Recent ( Schizaster canaliferus from the northern Adriatic Sea) irregular sea-urchin tests shows that, upon their death, burrowing echinoids can serve as a substrate for a dense epigrowth. Size, shape, stable orientation, and surface residence-time were identified as key factors governing encrustation. The encrusters on fossil Echinolampas were bryozoans, serpulid polychaetes, barnacles, and coralline algae, while the recent material was initially encrusted by serpulids and hydrozoan colonies, and ultimately covered by the full range of sessile, hemi-sessile, and vagile species characterizing the benthic community in the Adriatic. In Echinolampas , epigrowth was more abundant on the lower (oral) surface; this specific distribution was echoed in S. canaliferus , where epigrowth started on the bottom side and grew upward. This indicates that the tests have a stable orientation and a surface residence-time long enough to allow intense encrustation. A taphonomic model is developed, and the role of encrustation on such special substrates for overall community structure is discussed. The Recent/fossil comparison provides new insights for both fields of study: the recent material indicates the role of soft-bodied faunas as well as the complexity of small-scaled ecological processes; the fossil material reflects many of the above phenomena and adds important taphonomic details on the fate of encrusted biogenic structures and on encruster growth patterns and distributions.