bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomass estimation from surveys with likelihood-based geostatistics
Authors: Roa-Ureta Rubén , Niklitschek Edwin 
Published: October 2007

AbstractRoa-Ureta, R., and Niklitschek, E. 2007. Biomass estimation from surveys with likelihood-based geostatistics. – ICES Journal of Marine Science, 64. A likelihood-based geostatistical method for estimating fish biomass from survey data is presented. Biomass estimates from analysis of a positive random variable with an additional discrete probability mass at zero means that the method accommodates null observations and positive fish density. The positive fish density data were used to estimate mean fish density in the subareas where the stock was present. A presence/absence representation of the data in the survey area was modelled with a generalized linear spatial model of the binomial family, leading to an estimate of the area effectively occupied by the stock. As an extension, a procedure is proposed to accommodate extra sources of correlation, such as multiple surveys or multiple vessels. The new methodology was applied to three cases. The simplest case is a scallop trawl survey for which only the positive density data need to be analysed. The intermediate case is a trawl survey of highly mobile squid where the stock area and the mean density inside the stock area are analysed. The most complex case is in estimating the biomass of very localized orange roughy, for which repeat surveys create dependence in the data in addition to spatial correlation.
Phase I trial of personalized peptide vaccination for cytokine‐refractory metastatic renal cell carcinoma patients
Authors: Suekane Shigetaka , Nishitani Masaaki , Noguchi Masanori , Komohara Yoshihiro , Kokubu Takako , Naitoh Masayasu , Honma Shigenori , Yamada Akira , Itoh Kyogo , Matsuoka Kei , Kanayama Hiroomi 
Published: October 2007

The aim of this clinical trial was to investigate the toxicity and immunological responses of personalized peptide vaccination for cytokine‐refractory metastatic renal cell carcinoma patients. Patients were confirmed to be human leukocyte antigen (HLA)‐A24 or HLA‐A2 positive and had histologically confirmed renal cell carcinoma. Ten patients were enrolled in the present study. The peptides to be administered were determined based on the presence of peptide‐specific cytotoxic T lymphocyte precursors in peripheral blood mononuclear cells (PBMC) and peptide‐specific IgG in the plasma of cancer patients. Patients received subcutaneous injections of four different peptides (3 mg/peptide) every 2 weeks. Vaccinations were well tolerated without any major adverse events. A minimal increase in peptide‐specific interferon‐γ production in postvaccination PBMC was observed, regardless of higher levels of cytotoxic T lymphocyte activity in prevaccination PBMC. In contrast, an increase in peptide‐specific IgG levels of postvaccination (sixth) plasma was observed in the majority of patients. After progression, five patients received interleukin‐2 therapy and continuous vaccination, with survival of 31, 25, 23, 17, and 15 months, but interleukin‐2 did not impede humoral responses boosted by the vaccination. These results encourage further clinical trials of personalized peptide vaccinations. (Cancer Sci 2007; 98: 1965–1968)
Residential exposure to mould and dampness is associated with adverse respiratory health
Authors: Hagmolen of ten Have W. , Van Den Berg N. J. , Van Der Palen J. , Van Aalderen W. M. C. , Bindels P. J. E. 
Published: October 2007

SummaryBackground
Indoor exposure to mould and dampness is frequently associated with asthma symptoms with and without lung function changes. However, the mechanisms contributing to this threat to respiratory health are only partly understood.Objective
To investigate the contribution of recent exposure to mould and dampness in the living room or bedroom to respiratory health in a general practice‐based cohort of 526 asthmatic children.Methods
Parents were questioned about home characteristics, including moulds and dampness. The level of asthma control was evaluated in their participating children by means of asthma symptoms, peak expiratory flow (PEF) variability, severity of airway hyperresponsiveness (AHR), and medication usage.Results
Children exposed to indoor moulds and dampness more often had severe AHR compared with non‐exposed (42% vs. 16%; P0.001). They also showed an increased PEF variability (11.3% vs. 8.4%; P=0.03) and, however, not significant, more frequent asthma symptoms. The use of controller medication was not significantly different between exposed and non‐exposed children. After adjustment for gender, age, smoking, exposure to parental smoking, parental education, pet ownership, presence of inhalant allergy, use of controller medication, health care center, and season of study assessment, the odds ratio for severe AHR in exposed children was 3.95 [95% confidence interval (CI): 1.82–8.57].Conclusion
We found a consistent association between reported moulds and dampness in the living room or the child's bedroom and an increased risk for severe AHR in a general practice‐based cohort of asthmatic children, even after adjustment for gender, presence of inhalant allergy, and use of controller medication.
Interannual differences in prey taken by capelin, herring, and red salmon relative to zooplankton abundance during the spring bloom in a southeast Alaskan embayment
Authors: COYLE K. O. , PAUL A. J. 
Published: October 2007

ABSTRACTCapelin, herring, and red salmon diets were examined in relation to zooplankton abundance and biomass in the water column and surface layer of Auke Bay, Alaska, during the spring bloom period, 1987 and 1988 (April through mid‐June). Euphausiid eggs were the dominant prey of capelin in mid‐May 1987. Pseu‐docalanus spp. and barnacle nauplii dominated during the rest of the season. Capelin consumed Calanus spp. and Metridia spp. in April and Pseudocaknus and Cen‐tropages abdominalis in May and June 1988. During May and June 1987, herring were eating primarily barnacle larvae and Oikopleura spp. During April 1988, herring consumed primarily Calanus spp. and barnacle nauplii. In late April and early May they shifted to Pseudocalanus and Thysanoessa raschii, and in late May and June they consumed Centropages abdominalis and barnacle cyprids. Outmigrating red salmon fry consumed primarily Oikopleura during both years, along with substantial quantities of barnacle larvae. These dietary changes roughly correspond with variations in the abundance of prey taxa in the plankton samples. Likelihood measures of niche breadth indicated that capelin sometimes consume prey in approximately equal proportions to its abundance. Niche overlap between the herring and capelin was greatest in April and early May. Niche overlap was also high between herring and red salmon during June, when herring were in shallow water to breed.
Pacific sand lance of the Port Moller estuary, southeastern Bering Sea: an estuarine^dependent early life history
Authors: McGURK MICHAEL D. , WARBURTON H. DAVID 
Published: October 2007

ABSTRACTThree waves of spawning Pacific sand lance (Ammo‐dytes hexapterus) entered the Port Moller estuary from mid‐January to late May 1990. Each wave laid its eggs on sand in lower Moller Bay with the center of egg distribution about 14 km inside the estuary. After incubation for 45 to 94 d, each cohort of eggs hatched out over a 41‐ to 63‐d period. Larvae moved at a rate of 0.21 knvd“1 toward a deep fjordlike basin at the head of Herendeen Bay inside the estuary about 20 km southwest of the center of hatch. The basin has the lowest flushing rate of the estuary, and unlike the rest of Port Moller, it is vertically stratified, which allows the development of a spring‐summer zooplankton community with greater biomass than any other location in the estuary. Larvae may have moved to the basin to enhance growth or to avoid offshore transport to areas of low food abundance, but we cannot demonstrate a direct link between growth and habitat. We conclude that the Port Moller sand lance stock has an estuarine early life history that evolved in response to the unique physical conditions of the Port Moller estuary–a shallow, well‐mixed site with sandy substrate that is suitable for incubation of demersal eggs next to a deep, vertically stratified fjord with a rich zooplankton community that is suitable for rearing of larvae.
Global climate change and ocean upwelling
Authors: HSIEH WILLIAM W. , BOER GEORGE J. 
Published: October 2007

ABSTRACTThe influence of global greenhouse warming on the ocean's biological productivity may be more complicated and weaker than that proposed by Bakun (1990). A doubled carbon dioxide simulation made with the Canadian Climate Centre atmospheric general circulation model coupled to a simplified mixed layer ocean model suggests that the midlatitude continents do not all follow the Bakun scenario in developing anomalous low pressure in summer and enhancing coastal winds favorable to upwelling. In the open ocean the equatorial and subpolar zonal upwelling bands and the subtropical downwelling bands generally weaken as winds diminish owing to the weakening of the equator‐to‐pole temperature gradient in the lower troposphere under global warming. With a weakening of open ocean upwelling and an absence of enhanced coastal upwelling, the overall effect of global warming could be to decrease the global biological productivity.
A microcomputer program for stimulating effects of physical transport processes on fish larvae
Authors: WALTERS CARL J. , HANNAH CHARLES G. , THOMSON KEITH 
Published: October 2007

ABSTRACTA simple microcomputer program uses Lagrangian particle tracking to simulate the fates of individual larvae subject to wind‐ and tide‐driven advection fields and diffusion. Space/time advection patterns are provided to the program as inputs; thus, the program can use results from various hydrodynamic models. The program can simultaneously track several groups of larvae that are assigned varying attributes, including (1) body size, to allow simulation of effects of variation in growth rates; (2) spawning locations and times; (3) vertical migration behavior; and (4) settlement strategy (duration of larval period, depth conditions for settlement). The model is intended as an exploratory tool to help identify alternative hypotheses that might explain observed life history patterns and causes of inter‐annual variation in recruitment rate. For English sole in the Hecate Strait, B.C., the model leads us to hypothesize that observed spawning locations have resulted from a tradeoff between places that would provide the best feeding opportunities and places that would minimize risk of advective export to unfavorable rearing habitats.
Response of the Southern California current system to the mid‐latitude North Pacific coastal warming events of 1982–1983 and 1940–1941
Authors: SIMPSON JAMES J. 
Published: October 2007

ABSTRACTThe large‐scale structure of the California Current during the 1982–1983 mid‐latitude North Pacific coastal warming event showed several persistent (> 16 months), anomalous conditions: positive sea surface temperature anomalies (1–2.5oC), depression of the inshore thermocline by as much as 50 m greater than normal, anomalous high inshore steric heights (˜ 1.05 dyn. m) compared with normal values, anomalous high sea levels (˜ 25 cm), positive subsurface temperature anomalies (3–4oC), negative salinity anomalies (0.1‐0.3%), positive dissolved oxygen anomalies (0.5‐1.5 ml/1), and negative inshore nutrient anomalies. The magnitudes of the subsurface anomalies generally are much larger than those of the surface anomalies. The cross‐shelf length scales of the subsurface anomalies vary between 300 and 500 km. During this same period, pronounced negative sea surface temperature anomalies (2–3oC) developed in the central mid‐latitude North Pacific. The characteristic diagrams and sign reversals in the salinity, oxygen, and nutrient anomalies are consistent with enhanced onshore transport of Pacific subarctic water from the offshore California Current. The source of this water is primarily from the west‐northwest. The subsurface anomalies were produced dynamically by a depression of the inshore thermocline, which, at least in part, resulted from convergence of mass at the coastal boundary. The surface anomalies, however, were produced by a combination of dynamical and local thermodynami‐cal processes. Observed anomalous atmospheric forcing, as reflected in the 700 mb height anomaly and in negative upwelling indices, is consistent with enhanced onshore transport from offshore California Current. All the data support the conclusion that the expansion and intensification of the Aleutian Low and the decrease in strength of the North Pacific High produced an anomalous basin‐wide atmospheric circulation that, coupled directly with the large‐scale wind‐driven oceanic circulation, produced a major component of the North Pacific coastal warming response observed during 1982–1983. Nearly identical mid‐latitude atmospheric forcing and oceanic responses were observed during the 1940–1941 analog event. Anomalous phytoplankton and zooplankton distributions also were observed, and fish catch during this period decreased by about 40%, with nearshore pelagic species particularly affected. Not only was the abundance of single species affected, but also the community structure (i.e., rank order of abundance) was changed in response to the changing environmental conditions. The biological response appears to have been driven by the increased static stability, deeper thermocline, and reduced nutrient concentrations, which, in turn, resulted from the anomalous atmospheric circulation.
A review: Walleye pollock in the North Pacific–how much difference do they really make?
Authors: SPRINGER ALAN M. 
Published: October 2007

ABSTRACTPopulations of several species of marine birds and mammals in the Bering Sea and Gulf of Alaska have been declining since the mid‐1970s, with numbers of one, the Steller sea lion (Eumetopias jubatus), so depressed it was listed as threatened under the Endangered Species Act in spring 1990. All of the declining populations depend to an important extent on walleye pollock (Theragra chakogramma) for food, although they eat numerous other species as well. In contrast, certain animals that compete with pollock for common prey have been increasing in abundance. All of these changes could be related through food web connections mediated by pollock. Pollock is also important to people–it presently supports the largest single‐species commercial fishery in the world, in large part because of its great biomass, which has averaged about 15 × 106t in the Bering Sea over the past 15 years. Pollock consume an inordinate proportion of the pelagic production in the Bering Sea, which further supports the conclusion that it is a key species in the ecosystem. However, there are conflicting hypotheses about the importance of the roles played by pollock as predator and prey, and about the effect that changes in pollock abundance might have on biomass yield at higher trophic levels.
A context for recruitment correlations: why marine fisheries biologists should still look for them
Authors: TYLER A. V. 
Published: October 2007

ABSTRACTIn many cases when ecologists want to investigate a process, they often look for the best system on which to conduct the research, “best” meaning that the possibility of discovering mechanisms is optimized or made easier in some way. In fisheries we do it backwards. The species and system are given to us by economics, and we then fly in the face of the difficult circumstances to find mechanisms that are elusive anyway. These difficult circumstances constitute in some sense the first set of statistical problems. Using examples from the Northeast Pacific, I review the characteristics of cohort time series that make some species more tractable; propose a conscious process of conceptualization to assist in the formulation of clear, germane hypotheses; highlight the contrast between modeling in the sense of statistical fitting versus simulation models of processes; explore how the first round of models integrates with the second round of planning for new data collection at sea and in the lab; and, finally, propose how to judge success in terms of an operational approach.
The Fraser River plume: some preliminary observations on the distribution of juvenile salmon, herring, and their prey
Authors: JOHN MICHAEL A. ST. , MACDONALD J. STEVENSON , HARRISON PAUL J. , BEAMISH RICHARD J. , CHOROMANSKI EDWARD 
Published: October 2007

ABSTRACTZooplankton and fish densities in the southern Strait of Georgia were observed to coincide with variations in surface salinities resulting from the outflow of the Fraser River. Vertical net hauls in the euphotic zone revealed that copepods, amphipods, and euphausiids were significantly more abundant per m3 in the brackish estuarine plume (surface salinities ‐ 10–15 ppt) when compared to the area covered by the freshwater of the Fraser River plume (0–10 ppt) and the region of the Strait of Georgia (25–30 ppt) unaffected by the outflow of the Fraser River.The estuarine and riverine plumes had significantly higher fish densities (adult and juvenile herring, and juvenile salmonids [excluding chinook]) than the Strait of Georgia region, with no significant differences in densities of juvenile chinook salmon observed between regions. The highest catches of juvenile salmonids were at the boundary between the estuarine plume and the Strait of Georgia. Zooplankton found in the stomach contents of both adult and juvenile herring suggested that the herring were filter‐feeding on the zooplankton in the estuarine plume. Juvenile salmonids fed primarily on small unidentifiable juvenile fish. The existence of increased densities of prey items in the estuarine plume is proposed to be the primary mechanism resulting in increased residence time in this region by outmigrating juvenile salmonids. Utilization of aggregated zooplankton could lead to increased salmonid growth rates and therefore to enhanced survival of individuals utilizing the Fraser River plume environment.
The influence of ocean currents on latitude of landfall and migration speed of sockeye salmon returning to the Fraser River
Authors: THOMSON K. A. , INGRAHAM W. J. , HEALEY M. C. , LEBLOND P. H. , GROOT C. , HEALEY C. G. 
Published: October 2007

ABSTRACTWe hypothesize that the interannual variability of the Northeast Pacific Ocean circulation affects the latitude of landfall and migration speed of adult sockeye salmon (Oncorhynchus nerka) returning to the Fraser River. The Ocean Surface Current Simulations (OSCURS) model was used to simulate the return migration paths of compass‐orientated sockeye for two years: 1982, which had a weak Alaska Gyre circulation and low Northern Diversion Rate (defined as the percentage of sockeye returning around the north end of Vancouver Island instead of the south end); and 1983, with a strong circulation and high northern diversion rate. The majority of model sockeye made landfall further north in 1983 than in 1982. The difference in landfall between 1983 and 1982 depended on the migration start position, swim speed, direction of orientation, and migration start date. The currents assisted the shoreward migration of sockeye starting from south of 55o N and impeded the migration of sockeye starting from further north. The simulation results were consistent with our hypothesis and suggest that the effects of the Northeast Pacific currents must be included in sockeye migration models. We propose a conceptual model for the prediction of the Northern Diversion Rate that includes Blackbourn's (1987) temperature‐displacement model, enhanced to include the effects of currents during the ocean phase of migration, and the use of two predictive formulas for the coastal phase of migration: the formula of Xie and Hsieh (1989) for sockeye approaching Vancouver Island directly from the ocean, and a yet‐to‐be‐developed formula for sockeye approaching from within the Coastal Downwelling Domain directly to the north of Vancouver Island.
Recent changes in the trophic structure of the Black Sea
Authors: ZAITSEV YU. P. 
Published: October 2007

ABSTRACTDuring the past few decades, the Black Sea has been subjected to various human impacts that have led to changes in the ecology of this inland sea. River runoff has introduced high levels of certain heavy metals and other toxic substances as well as detergents. Ship traffic has led to the introduction of new species, and fishing pressures have also altered the ecology of the area.This paper reviews major ecological changes over the past 40 years. An increase in nutrients has caused eutrophication, with outbursts of phytoplankton blooms and changes in the species composition of these algae. Small‐sized zooplankton species and gelatinous zooplankton have become more common, while many of the herbivorous copepods have decreased in abundance or have disappeared. The introduction of the predatory ctenophore Mnemiopsis leidyi in the 1980s has had significant impact on the plankton community and has led to a sharp decline in anchovy stocks. Decreased water transparency has led to a loss of macrophytic algae, except in shallow waters, and to a subsequent decline in the zoobenthos associated with this flora. Eutrophication has also led to decreased oxygen concentrations in the near‐bottom water due to large amounts of decomposing phytoplankton, and regions of hypoxia and anoxia now appear on the shelf, with consequent reduction in benthic populations of invertebrates and demersal fish. The numbers of fish species harvested commercially have fallen from 26 to 5, but the total catch has increased, owing to increases in abundance of small fish (e.g., sprat) and horse mackerel, and to increased fishing effort.
Sampling error resulting from depth‐dependent plankton distributions and current differentials in a two‐layered system
Authors: ANDERSON JOHN T. , WEBSTER IAN T. 
Published: October 2007

ABSTRACTWe evaluate a source of error observed in standard ichthyoplankton bongo tows in which volumes of water filtered did not result in increased catches of red‐fish. Our analyses demonstrate that, under conditions where redfish larvae are distributed in surface waters in a two‐layered system, current differentials between surface and subsurface layers resulted in biased, standardized estimates of larval abundances as a result of filtering varying amounts of subsurface waters. Analysis of standard survey results on Flemish Cap demonstrated that this source of bias was limited to the May‐June period, after waters became stratified and before redfish passed from the larvae to pelagic juvenile stage. Correcting for this source of sampling bias wIII result in more accurate absolute estimates of ichthyoplankton abundance, and we estimate that variation (CV) for replicate samples may be reduced by 10%.
Are tidal fronts good recruitment areas for herbivorous copepods?
Authors: UYE SHIN‐ICHI , YAMAOKA TORU , FUJISAWA TOSHIRO 
Published: October 2007

ABSTRACTHorizontal distributions of phytoplankton biomass and numerical abundance of copepod nauplii were investigated across a tidal front in the northern part of Bungo Channel, the Inland Sea of Japan, in May and June 1988. The frontal area was characterized by abrupt changes in subsurface (3 m deep) temperature and salinity, and by an increased standing stock of phytoplankton. The density of copepod nauplii was lower in the frontal area than in adjacent stratified and mixed areas. The population egg production rate of a predominant copepod species (Paracakmus sp.) was higher due to elevated fecundity on an individual basis in response to increased chlorophyll concentrations, in the frontal zone. However, the frontal population was subjected to higher mortality, probably due to predation by carnivores that were mainly accumulated passively within the area. From these facts, we conclude that tidal fronts are not always good areas for recruitment of herbivorous copepods, although fronts give rise to high standing stocks of phytoplankton.