bluuebunny/crossref_metadata_2025 huggingface dataset:
Loss of and damage to scallops due to storms in the Sea of Okhotsk
Authors: MIYAKE HIDEO , MATSUOKA MITSUAKI , FURUYA KUNIO
Published: October 2007

In the coastal zone of the Sea of Okhotsk off Hokkaido, Japan, the giant ezo scallop (Patinopecten yessoensis) is widely cultivated on the sea bed, making its fishery a major industry. However, the area experiences intense cyclones, including typhoons, about once a decade and the scallop resources appear to have received severe damage from the storms. Such an event occurred on 29 October 1988. The storm caused 12‐m‐high wind waves, which appeared to be fully developed sea waves. The water above the sea bed repeatedly moved back and forth at speeds of 1∼2 m s‐1 causing damage to the scallops due to collisions and rubbing with gravel and other scallops. From a comparison of wind data with the annual catch of scallops, intense cyclones seem to play an important role on the year‐to‐year fluctuations in the scallop fishery.
A three‐dimensional numerical model for a mariculture nitrogen cycle: case study in Shizugawa Bay, Japan
Authors: KISHI MICHIO J. , UCHIYAMA MASATO
Published: October 2007

A numerical model is developed for mariculture management, which consists of: (1) calculation of spatial distribution of PON (particulate organic nitrogen) using simulated current, (2) calculation of spatial distribution of DO (dissolved oxygen), (3) calculation of DON (dissolved organic nitrogen), (4) calculation of spatial distribution of DIN (dissolved inorganic nitrogen), and (5) calculation of the horizontal distribution of accumulated matter which is supplied by deposits from the mariculture of fish. This model is capable of calculating the detailed spatial distribution of PON, DON, DIN and DO by dividing the bay into many grid points. It also takes into consideration the effects of feed and fish in each raft, and the loading of DIN from rivers. The model is applied to Shizugawa Bay, in Miyagi Prefecture, Japan. The model elucidated the oxygen cycle among ecological compartments. The amount of dissolved oxygen supplied by photosynthesis is much greater than the consumption through respiration by fish and all other conditions for mariculture of fish are favourable in this bay.
Recruitment strategy of swimming crab, Portunus trituberculatus, in Hiuchi‐Nada, Japan
Authors: YANAGI TETSUO , TSUKAMOTO HIDESHI , IGAWA SHUJO , SHIOTA KOHJI
Published: October 2007

The recruitment strategy of swimming crabs, Portunus trituberculatus, was investigated by field observations and numerical experiments in Hiuchi‐Nada, Japan. Calculated dispersal patterns of zoeal and megalopal stages in a three‐dimensional numerical model reproduce observed patterns accurately. The temporal change of vertical migration patterns between the 1st and 2nd zoeas and the 3rd and 4th zoeas plays an important role in the process of recruitment of P. trituberculatus from spawning ground to nursery ground.
Stability of water masses‐impact on cod recruitment off West Greenland
Authors: LLORET M. STEIN AND J.
Published: October 2007

Based upon the hypothesis of Meyer (1968: Hansa, 16:2–4) that periods of low stability of the water column in autumn should parallel good cod year‐classes in the following year, the paper analyzes available time series of cod recruitment, subsurface oceanographic stability data and wind stress data off West Greenland. No significant correlations were found between stability, wind stress and recruitment when considering the entire. length of available time series. However, splitting the autumn‐based oceanographic data set into a pre‐ 1970s part (when warm climatic conditions and high recruitment prevailed), and a recent part (for the past 20 years of cooling climate) yields significant coherence of recruitment and environmental conditions for the cold climate period. For the warm climate period, only occasional consistency is shown. The possible influence of the Great Salinity Anomaly on recruitment of cod is discussed. It is suggested that during the past 20 years a new correlation mechanism, an advective coupling instead of low stability coupling, may explain the variability of recruitment.
Possible mechanisms underlying fluctuations in the Far Eastern sardine population inferred from time series of two biological traits
Authors: KAWASAKI TSUYOSHI , OMORI MICHIO
Published: October 2007

A cycle of fluctuation in the Far Eastern sardine, Sardinops sagax, population is accompanied by an abrupt drop and recovery of fish size and lipid content of parent fish, which may reflect a phase variation from coastal to oceanic and its reverse. The cycle begins with the survival success of a smaller number of eggs produced by high‐quality parents, which is triggered by a global climate change (density‐independent process), and finally ends in the survival failure resulting from an overexpansion of an enormous number of fish produced by low‐quality parents (density‐dependent process).
Declines in chinook salmon catches in the Strait of Georgia in relation to shifts in the marine environment
Authors: BEAMISH RICHARD J. , RIDDELL BRIAN E. , NEVILLE CHRYS‐ELLEN M. , THOMSON BARBARA L. , ZHANG ZIYANG
Published: October 2007

Chinook, Oncurhynchus tshawytscha, catches in the Strait of Georgia increased in the 1970s and reached maximum levels from 1976 to 1978. Catches then declined until they stabilized through regulation at levels approximately one‐quarter of the 1976 to 1978 levels. The timing of the decline in catch was synchronous with an increase in the mean temperature of the Strait of Georgia, a decline in annual Fraser River flows, and an abrupt decrease in the marine survival of hatchery‐reared chinook released into the Strait of Georgia. Surprisingly, the number of young chinook salmon (smolts) more than doubled over the period of declining catches compared with the number produced during the period of high catches. The increase in smolt abundance was a consequence of the production from hatcheries that was approximately equal to wild production.

We conclude that there was a change in the carrying capacity for chinook salmon in the Strait of Georgia in the late 1970s that contributed to the declines in abundance and that rebuilding stocks to the high abundance of the late 1970s is unlikely until the carrying capacity for chinook salmon changes either naturally or through manipulation. Although we did not separate density‐dependent and density‐independent effects on marine survival, the current total number of chinook smolts produced appears larger than required for the current marine carrying capacity.
Characterization of the pelagic ecosystem in surface waters of the northern Gulf of St, Lawrence in early summer: the larval redfish‐Calanus‐microplankton interaction
Authors: RUNGE JEFFREY A. , LAFONTAINE YVES DE
Published: October 2007

In June 1989, the water column along a transect in the north‐central Gulf of St Lawrence was thermally stratified (10–14oC at the surface; 0‐loC at 30 m). In the surface layer, nitrate and chlorophyll concentrations were very low; the mean concentration of chlorophyll a > 5 μm in the subsurface maximum was 0.26 μg1‐1. Autotrophic and (presumably) heterotrophic flagellates and dinoflagellates were the most abundant micro‐plankton. In this system, redfish (Sebastes spp.) larvae and the planktonic copepod Calanus finmarchicus overwhelmingly dominated the ichthyoplankton and zoo‐plankton, respectively. Redfish larvae, Calanus females and Calanus eggs were most abundant in the surface layer (0–25 m) day and night. Daily specific egg production rates of Calanus, calculated from shipboard incubations of females, approached the predicted maximal level for this species at the ambient temperature of the surface layer, indicating no or little food limitation. The redfish larvae were feeding almost exclusively on the Calanus eggs and were found in greatest abundance along the transect where Calanus egg production rates (eggs m‐2 day‐1), calculated from the product of the specific egg production rate and female concentration, were highest. The mono‐specificity of the larval redfish diet and the codom‐
Locations of early fishing grounds of saury in the northwestern Pacific
Authors: YASUDA ICHIRO , KITAGAWA DAIJI
Published: October 2007

In the north‐western Pacific, we found that locations of early fishing grounds of Pacific saury, Cololabis saira, are affected by two factors, the size composition and the meridional shift of the offshore Oyashio Front (OOF). Early fishing grounds are formed nearshore from the central Kuril Islands to Hokkaido in northward OOF years. In southward OOF years, they are far from the coasts. There also exists a tendency that early fishing grounds are formed south‐westward (north‐eastward) in years when a large (medium or small) size class of saury is dominant and when the OOF shifts north (south). These results support the hypothesis that saury migration is considerably influenced by oceanographic conditions, and that a large size class of saury leads to migration that can reach the vicinity of Japan early in the fishing season.
Population Production and Regulation in the Sea: a fisheries perspective
Authors: RICE JAKE
Published: October 2007

Population Production and Regulation in the Sea: a fisheries perspective
Interannual variability of the early life history of walleye pollock near Shelikof Strait as inferred from a spatially explicit, individual‐based model
Authors: HERMANN ALBERT J. , HINCKLEY SARAH , MEGREY BERNARD A. , STABENO PHYLLIS J.
Published: October 2007

A coupled biophysical model is used to hindcast the early life history of a population of walleye pollock (Theragra chalcogramma), to assess possible physical causes of interannual variability in recruitment. The modelling approach combines a primitive equation, rigid'lid hydrodynamic model with a probabilistic, individual‐based biological model of growth, development, and mortality. Individuals are tracked through space using daily velocity fields generated from the hydrodynamic model, along with self‐directed vertical migrations appropriate to each life stage in the biological model. The hydrodynamic model is driven with wind and runoff time series appropriate to each year. Biological model output compares favourably with observed spatial distributions for specific years. Lloyd's index of patchiness, calculated from model output, was similar to values calculated from field data. Five noncontiguous years were chosen for hindcasts to span a wide range of meteorological conditions (winds, runoff) and recruitment success. Interannual comparisons suggest that two years of above average recruitment (1978 and 1988), and one year of below average recruitment (1991), experienced flow fields which carried many individuals into the Alaskan Stream. At the same time, the vigorous flow fields generated in each of these years carried some individuals onto the shelf area to the south‐west of the spawning site. A year with low runoff and weak winds (1989) exhibited weak circulation, with extended retention of larvae near the spawning site. A year with high runoff (1987) was notable for the strength and frequency of mesoscale eddy activity. Eddies appear capable of both enhancing patchiness of early larvae (through retention) and dissipating patchiness of juveniles (through mesoscale mixing). Larvae retained in an eddy feature exhibit a narrower range of sizes than the population outside that feature.
Acoustic detection of mesoscale biophysical features in the Shelikof sea valley, and their relevance to pollock larvae in the Gulf of Alaska
Authors: BRODEUR RICHARD D. , NAPP JEFFREY M. , WILSON MATTHEW T. , BOGRAD STEVEN J. , COKELET EDWARD D. , SCHUMACHER JAMES D.
Published: October 2007

Mesoscale features such as fronts and eddies can act to retain larval walleye pollock (Theragra chalcogramma) within the continental shelf zone in the western Gulf of Alaska. During two May cruises, we observed unusual patterns of backscattering with a 38 kHz acoustic system. Characteristics of this signal were a strong scattering layer at the surface and in midwater, with the water column between nearly void of sound scattering organisms. This signal appeared in several transects where satellite remote sensing indicated the presence of an eddy. Analysis of concomitant water properties and ADCP (153 kHz) data confirmed the existence of an anomalous physical feature at this location. Biological properties (chlorophyll and zooplankton) showed marked changes across the edge of the feature. Larval pollock densities were estimated to be an order of magnitude higher within this feature compared to those outside. Acoustic backscatter signals can be used to identify and characterize mesoscale biophysical features in the ocean, thereby enabling real‐time studies of these features.
Variations in larval walleye pollock feeding and condition: a synthesis
Authors: THEILACKER GAIL H. , BAILEY KEVIN M. , CANINO MICHAEL F. , PORTER STEVEN M.
Published: October 2007

There was a strong association among concentrations of microzooplankton prey sampled from the walleye pollock, Theragra chalcogramma, larval habitat, gut contents of larvae, and their nutritional condition. Subsequently, hypothesized survival potentials linked to food availability were validated by independently determined mortality rates. We present evidence that a significant number of walleye pollock larvae were starving in 1991 but that fewer were starving in 1992. At some stations where prey levels were anomalously low in 1991, up to 40% of the larvae were in poor condition. There appears to be a 2‐week period after first feeding when walleye pollock are vulnerable to starvation.
Interannual variability in growth of larval and juvenile walleye pollock Theragra chalcogramma in the western Gulf of Alaska, 1983–91
Authors: BAILEY KEVIN M. , BROWN ANNETTE L. , YOKLAVICH MARY M. , MIER KATHRYN L.
Published: October 2007

Interannual variability in growth of larval walleye pollock Theragra chalcogramma was examined from 1983 to 1991 and of juveniles from 1985 to 1990. ANCOVA was used to assess differences in population growth rates, and an alternate method was developed to examine variations between annual length‐at‐age data and average ‘expected’ values over different age groupings. For larvae, the years 1986, 1987, 1989 and 1990 had higher than average length‐at‐age, and 1988 and 1991 had lower than average values. Relationships between growth and SST and larval density were not clear. A tentative relationship between copepod nauplii abundance and larval length‐at‐age was noted. The consequence of larval growth to larval mortality, late larval abundance or recruitment was not clear. We conclude that larval mortality rates are highly variable and tend to mask effects of moderate variability in growth on later abundance. For juveniles, 1987 had significantly lower than average length‐at‐age and 1988 had higher than average values. Although there are few years of data, they tend to support the importance of juvenile growth in the recruitment process. Conditions for the large 1988 year class are documented and discussed, including warm SST, calm winds, relatively low larval growth rates, low abundances of potential predators on larvae, low larval mortality rates, and high juvenile growth rates.
Behavioural determinants of distribution and survival in early stages of walleye pollock, Theragra chalcogrammai a synthesis of experimental studies
Authors: OLLA BORI L. , DAVIS MICHAEL W. , RYER CLIFFORD H. , SOGARD SUSAN M.
Published: October 2007

This review summarizes results of an extensive series of laboratory studies on the behavioural responses of early life stages of walleye pollock, Theragra chakogramma to key environmental factors including light, temperature, gravity, turbulence, food availability and predator presence. Experiments focused on vertical distribution of egg through 0‐age stages, and social interactions of age‐0 juveniles. Key factors were modified either singly or in concert to determine their direct and indirect influence on fish behaviour. The observed results suggest that the behaviour of individual fish depends on the integration of a continually changing hierarchy of both intrinsic and extrinsic factors, with the relative importance of a specific factor varying with ontogeny and over time and space. The broad range of responses displayed by early life stages suggests that behaviour plays an important role in determining the consequences of environmental variability on walleye pollock populations. In general, results from our laboratory experiments are consistent with patterns observed in field studies, supporting the efficacy of using experimental behavioural research to define some of the underlying mechanisms controlling distribution and survival in the field, and eventual recruitment to adult populations.
Contributions of FOCI research to forecasts of year‐class strength of walleye pollock in Shelikof Strait, Alaska
Authors: MEGREY BERNARD A. , HOLLOWED ANNE B. , HARE STEVEN R. , MACKLIN S. ALLEN , STABENO PHYLLIS J.
Published: October 2007

NOAA's Fisheries Oceanography Coordinated Investigations (FOCI) contributes information to help forecast year‐class strength of walleye pollock (Theragra chalcogramma) in the Gulf of Alaska. Quantitative estimates of recruitment are obtained from models of stock assessment and stock projection employing information supplied by FOCI. To generate its information, FOCI convenes specialists in marine biology, physical and fisheries oceanography, meteorology, and statistics to assemble and analyse relevant biological and physical time series with respect to recruitment and processes hypothesized to influence fish survival. Statistical methods encompass linear and nonlinear regression, stochastic simulation modelling, transfer function time series modelling, and tree‐modelling regression. The current database consists of 31 years of data, and analyses have identified factors that affect ocean stratification and circulation during spring and summer of the fish's birth year as being important to recruitment. A conceptual model of the recruitment process serves as the framework for a recruitment forecast scheme. A stochastic mathematical simulation model of the conceptual model produces similarities between simulated and observed recruitment time series. FOCI has successfully forecast recruitment observed over the past several years.
Spatial variations in feeding and condition of juvenile pink and chum salmon off Vancouver Island, British Columbia
Authors: PERRY R. IAN , HARGREAVES N. BRENT , WADDELL BRENDA J. , MACKAS DAVID L.
Published: October 2007

Spatial variations in feeding and condition of juvenile pink (Oncorhynchus gorbuscha) and chum (Oncorhynchus keta) salmon, and their implications for growth, were examined on the Vancouver Island continental shelf in early summer 1992. Juvenile pink salmon off northern Vancouver Island had more material in their stomachs, were in better condition, and had higher potential growth rates (from a bioenergetics model) than pink salmon off southern Vancouver Island. These variations were consistent with spatial differences in zoo‐plankton biomass, there being more plankton in the northern region. There was a significant positive relationship between condition of pinks and the amount of material in their stomachs, suggesting a positive feedback on feeding success. Juvenile chum in the north also had more material in their stomachs than chum to the south. However, condition factor was not significantly different between southern and northern regions nor was there a significant relationship between condition factor and the weight of stomach contents for chum on the southern shelf. A bioenergetics model suggests that chum in the south were food limited. Stable carbon isotope data also indicated different feeding histories for some chum in the southern region, which may have been recent migrants onto the continental shelf from near‐shore areas, or possibly a nearby hatchery. Estimation of the energy required by juvenile salmon to migrate north in a continental shelf area with low zooplankton biomass and a weak northerly current (inner shelf), compared with an area with higher zooplankton biomass but a strong southerly current (outer shelf), indicated sufficient surplus energy only in the inner shelf, consistent with observations of northward migrations predominantly through this area. Spatial variations in current velocity and zooplankton biomass can affect feeding, condition, and potential growth of juvenile pink and chum salmon off Vancouver Island.
Skipjack velocity, dwell time and migration
Authors: GAULDIE R. W. , SHARP G. D.
Published: October 2007

Apparent velocities (distance travelled/time at liberty) of tagged Pacific skipjack tuna, Katsuwonus pelamis, observed over the 1978 to 1982 Skipjack Survey and Assessment Program (SSAP) of the South Pacific Commission (SPC) were very low (less than 10 cm s‐1in 90% of observations) compared with the minimum swimming speed of skipjack tunas of 70–100 cm s‐1. Such low apparent velocities are not biologically meaningful and therefore the extrapolation of biological properties from mathematical models, such as diffusion and advection models, based on the tagging data is difficult, if not impossible. This paper explores alternative approaches to the 1978 to 1982 SSAP data set. Dwell time and migration analysis indicate a north to south seasonal migratory pattern with the skipjack home range located along an arc from the Solomon Islands, through Fiji and Samoa, to the Marquesas. Ancillary evidence supports a purposeful rather than advective migration pattern that oscillates between southern feeding areas and northern breeding areas. many hands. Most of the previous analyses have focused on the issue of interactions between fisheries for K. pelamis that are in different political jurisdictions (Kleiber et al., 1984) and estimates of the size of the standing crop of K. pelamis (Kleiber et al., 1983; Kearney et al., 1984). Models of interactions between fisheries for K. pelamis in different jurisdictions (Sibert, 1984; Hilborn, 1990) have pointed towards the use of diffusion and advection models in studying fish movements (Sibert and Fournier, 1994; Sibert et al., 1995).
The distribution of sea birds relative to their fish prey off Vancouver Island: opposing results at large and small spatial scales
Authors: LOGERWELL ELIZABETH A. , HARGREAVES N. BRENT
Published: October 2007

We investigated the distribution of common murres, Uria aalge, and shearwaters, Puffinus griseus and P. tenuirostris, relative to their fish prey at two spatial scales, one of hundreds of kilometres and the other of kilometres. Data on oceanographic conditions, the distribution of sea birds and the distribution of fish in the upper water column were collected during three research surveys off Vancouver Island (British Columbia, Canada). At the large spatial scale, we found that both murres and shearwaters were more abundant inshore than offshore of the shelf break and that their fish prey were likewise more abundant in the inshore habitat. At the smaller scale, we investigated the relative importance of fronts and fish density. In contrast to what we expected based on our finding at the large spatial scale, there was a significant negative relationship between fish and both murre and shearwater density. We found that fronts, independent of fish density, did not have an effect on small‐scale murre density and had only a weak effect on small‐scale shearwater density. We suggest that the negative relationship between fish and sea bird density at the scale of kilometres may have been due to fish diving to escape foraging sea birds and thus avoiding capture in the near‐surface trawl used in this study. If this avoidance behaviour is common in pelagic fish, then sea birds may affect fish populations by driving fish away from plankton‐rich surface waters and thus negatively affecting the feeding and growth rates of their fish prey.
Transport and settlement mechanisms of larval stone flounder, Kareius bicoloratus, into nursery grounds
Authors: YAMASHITA YOH , TSURUTA YOSHINARI , YAMADA HIDEAKI
Published: October 2007

The transport mechanism of stone flounder,Kareius bicoloratus, larvae from the central area of Sendai Bay to inshore areas and their settlement in shallow nursery grounds during winter‐early spring were studied in 1991 and 1992. Stone flounder eggs were abundant in the central area of Sendai Bay at depths of 25–50 m, and their larvae are thought to be transported inshore by warm offshore waters entering into the Bay through its central part. Settling larvae consisted primarily of stages G through I1. These stages correspond to the metamorphosing period and showed behaviour related to selective tidal‐stream transport, occurring on and near the bottom during the daytime and ascending at night, especially on flood tides, enabling migration to inshore and estuarine nursery habitats. This diel vertical migration is also considered to play an important role in avoiding predation by diurnal piscivorous fishes and nocturnal benthic sand shrimp. Settling flounder were abundant in deeper waters in February, and with inshore movement, densities peaked in late March in estuaries. In exposed inshore areas of Sendai Bay with no easily accessible estuaries, settling and settled flounder concentrated in inshore areas at depths of around 10 m. The mechanisms by which selective tidal‐stream transport occurs are discussed.
The Bering Sea Green Belt: shelf‐edge processes and ecosystem production
Authors: SPRINGER ALAN M. , McROY C. PETER , FLINT MIKHAIL V.
Published: October 2007

The concept of a highly productive habitat, or Green Belt, along the edge of the continental shelf in the Bering Sea is based upon compelling but fragmentary and often anecdotal observations of a variety of physical and biological features acquired from many sources over many years. Enhanced production at continental margins is not a novel concept, but in the case of the Bering Sea its importance has been overlooked during studies of the unusually broad continental shelf. The limited data reported from the vicinity of the shelf edge in the Bering Sea indicate that annual primary production can be as high as 175 to 275 g C m˜ year‐, or approximately 60% greater than production in the adjacent outer shelf domain and 270% greater than in the oceanic domain. Estimates of annual secondary production at the eastern shelf edge also average approximately 60% higher than estimates for the outer domain and 260% higher than those for the oceanic domain. Physical processes at the shelf edge, such as intensive tidal mixing and transverse circulation and eddies in the Bering Slope Current, bring nutrients into the euphoric zone and contribute to enhanced primary and secondary production and elevated biomass of phytoplankton and zooplankton. Fishes and squids concentrate in this narrow corridor because of favourable feeding conditions and because of a thermal refuge from cold shelf‐bottom temperatures that can be found at the shelf edge from fall to spring. The abundance of zooplankton, fishes and squids, in turn, attracts large numbers of marine birds and mammals. In aggregate, the observations suggest that sustained primary productivity, intense food web exchange and high transfer efficiency at the shelf edge are important to biomass yield at numerous trophic levels and to ecosystem production of the Bering Sea.
Effects of pheasant management on vegetation and birds in lowland woodlands
Authors: Draycott Roger A. H. , Hoodless Andrew N. , Sage Rufus B.
Published: October 2007

Releasing pheasants in woodlands for game shooting is a widespread practice in the British countryside. Apart from changes to ground flora in woodland release pens, the effects of pheasant releasing on woodland biodiversity are poorly understood.

We surveyed 159 lowland broad‐leaved woods in southern and eastern England during spring–summer 2004 to determine the impact of pheasant management on vegetation structure and composition and on bird populations. Eighty‐one of the woods contained pheasant release pens with annual releases of pheasants and associated gamebird management such as supplementary feeding in winter. In the remaining 78 woods there had been no pheasant management for at least 25 years.

We found that the pheasant‐managed woods had a more open structure, with between 2% and 7% less canopy cover and a denser field layer with between 5% and 58% more ground vegetation cover, including grasses and bramble Rubus fruticosus.

We recorded approximately 40% more birds in woods in southern England and between 22% and 32% more birds were observed in pheasant‐managed woods than control woods. Woodpigeons and warblers were more abundant in pheasant‐managed woods.

Synthesis and applications: We conclude that the impacts of pheasant releasing on vegetation structure and bird communities in woodlands are benign or positive. This study demonstrates that some aspects of woodland management for pheasants, including reducing the extent of canopy cover can encourage growth of understorey vegetation which helps create favourable conditions for some woodland bird species.
Cognitive‐behavioural treatment for men with intellectual disabilities and sexually abusive behaviour: a pilot study
Authors: Murphy Glynis , Powell Simon , Guzman Ana‐Maria , Hays Sarah‐Jane
Published: October 2007

Background  Cognitive‐behaviour therapy (CBT) seems to be becoming the treatment of choice for non‐disabled sex offenders. Nevertheless, there have been relatively few evaluations of such treatment for men with intellectual disabilities (ID) and sexually abusive behaviour.

Method  A pilot study providing CBT for two groups of men with ID is described. Measures of change in sexual knowledge, victim empathy and cognitive distortions were collected, together with a log of further sexually abusive behaviour.

Results  Fifteen men were offered treatment but some dropped out and some declined to take part in the research. The results for the eight men who consented to the research and completed treatment showed significant positive changes in sexual knowledge and victim empathy (two men completed both groups, making 10 sets of data in all). Cognitive distortions showed significant change on only one of the two measures. Some men showed further sexually abusive behaviour either during or after the treatment group (all had been previously diagnosed as on the autistic spectrum).

Conclusion  There is a need for a larger multi‐site trial of treatment with a broad set of measures and the ability to analyse who benefits from such treatments and who does not.
Dual‐mode reflectance and fluorescence near‐video‐rate confocal microscope for architectural, morphological and molecular imaging of tissue
Authors: CARLSON ALICIA L. , COGHLAN LEZLEE G. , GILLENWATER ANN M. , RICHARDS‐KORTUM REBECCA R.
Published: October 2007

We have developed a near‐video‐rate dual‐mode reflectance and fluorescence confocal microscope for the purpose of imaging ex vivo human specimens and in vivo animal models. The dual‐mode confocal microscope (DCM) has light sources at 488, 664 and 784 nm, a frame rate of 15 frames per second, a maximum field of view of 300 × 250 μm and a resolution limit of 0.31 μm laterally and 1.37 μm axially. The DCM can image tissue architecture and cellular morphology, as well as molecular properties of tissue, using reflective and fluorescent molecular‐specific optical contrast agents.

Images acquired with the DCM demonstrate that the system has the sub‐cellular resolution needed to visualize the morphological and molecular changes associated with cancer progression and has the capability to image animal models of disease in vivo. In the hamster cheek pouch model of oral carcinogenesis, the DCM was used to image the epithelium and stroma of the cheek pouch; blood flow was visible and areas of dysplasia could be distinguished from normal epithelium using 6% acetic acid contrast. In human oral cavity tissue slices, DCM reflectance images showed an increase in the nuclear‐to‐cytoplasmic ratio and density of nuclei in neoplastic tissues as compared to normal tissue. After labelling tissue slices with fluorescent contrast agents targeting the epidermal growth factor receptor, an increase in epidermal growth factor receptor expression was detected in cancerous tissue as compared to normal tissue. The combination of reflectance and fluorescence imaging in a single system allowed imaging of two different parameters involved in neoplastic progression, providing information about both the morphological and molecular expression changes that occur with cancer progression.

The dual‐mode imaging capabilities of the DCM allow investigation of both morphological changes as well as molecular changes that occur in disease processes. Analyzing both factors simultaneously may be advantageous when trying to detect and diagnose disease. The DCM's high resolution and near‐video‐rate image acquisition and the growing inventory of molecular‐specific contrast agents and disease‐specific molecular markers holds significant promise for in vivo studies of disease processes such as carcinogenesis.
Quantitative STEM mass measurement of biological macromolecules in a 300 kV TEM
Authors: SOUSA ALIOSCKA A. , LEAPMAN RICHARD D.
Published: October 2007

For almost four decades, the scanning transmission electron microscope (STEM) has made significant contributions to structural biology by providing accurate determinations of the molecular masses of large protein assemblies that have arbitrary shapes and sizes. Nevertheless, STEM mass mapping has been implemented in very few laboratories, most of which have employed cold field‐emission gun (FEG) electron sources operating at acceleration voltages of 100 kV and lower. Here we show that a 300 kV commercial transmission electron microscope (TEM) equipped with a thermally assisted Shottky FEG can also provide accurate STEM mass measurements. Using the recently published database of elastic‐scattering cross sections from the National Institute of Standards and Technology, we show that the measured absolute mass values for tobacco mosaic virus and limpet hemocyanin didecamers agree with the known values to within better than 10%. Applying the established approach, whereby tobacco mosaic virus is added to a specimen as a calibration standard, we find that the measured molecular weight of the hemocyanin assemblies agrees with the known value to within 3%. This accuracy is achievable although only a very small fraction (∼0.002) of the incident probe current of 300 kV electrons is scattered onto the annular dark‐field STEM detector. FEG TEMs operating at intermediate voltages (200–400 kV) are becoming common tools for determining the structure of frozen hydrated protein assemblies. The ability to perform mass determination with the same instrument can provide important complementary information about the numbers of subunits comprising the protein assemblies whose structure is being studied.
Improved correction of axial geometrical distortion in index‐mismatched fluorescent confocal microscopic images using high‐aperture objective lenses
Authors: VAN ELBURG H.J. , KUYPERS L.C. , DECRAEMER W.F. , DIRCKX J.J.J.
Published: October 2007

Extracting quantitative data from microscopic volume images is straightforward when the refractive indices of the immersion medium and the mounting medium are equal. The readings of the position of the specimen stage can be directly used to measure depth and width. Imperfectly matched immersion and mounting media result in axial geometrical distortion. Linear correction of the axial distortion using the paraxial estimate of the axial scaling factor yields results that may differ as much as 4% from the actual values. From calculations based on a theoretical expression of the 3‐D point‐spread function in the focal region of a high‐aperture microscope focussing into a mismatched mounting medium, we derived axial scaling factors that result in quantitative results accurate to better than 1%. From a non‐linear correction procedure, an improved formula for the paraxial estimate of the axial scaling factor is derived.
Quantitative investigation of murine cytomegalovirus nucleocapsid interaction
Authors: BUSER CHRISTOPHER , FLEISCHER FRANK , MERTENS THOMAS , MICHEL DETLEF , SCHMIDT VOLKER , WALTHER PAUL
Published: October 2007

In this study, we quantitatively investigate the role of the M97 protein for viral morphogenesis in murine cytomegalovirus (MCMV)‐infected fibroblast cells. For this purpose, a statistical analysis is performed for the spatial distribution of nuclear B‐capsids (devoid of DNA, containing the scaffold) and C‐capsids (filled with DNA). Cell nuclei infected with either wild‐type or an M97 deletion mutant were compared. Univariate and multivariate point process characteristics (like Ripley's K‐function, the L‐function and the nearest neighbour distance distribution function) are investigated in order to describe and quantify the effects that the deletion of M97 causes to the process of DNA packaging into nucleocapsids. The estimation of the function L(r) −r reveals that with respect to the wild type there is an increased frequency of point pairs at a very short distance (less than approximately 100 nm) for both the B‐capsids as well as for the C‐capsids. For the M97 deletion mutant type this is no longer true. Here only the C‐capsids show such a clustering behaviour, whereas for B‐capsids it is almost nonexistant. Estimations of functionals such as the nearest neighbour distance distribution function confirmed these results. Thereby, a quantification is provided for the effect that the deletion of M97 leads to a loss of typical nucleocapsid clustering in MCMV‐infected nuclei.
Regulation of fatty acid metabolism in bacteria
Authors: Fujita Yasutaro , Matsuoka Hiroshi , Hirooka Kazutake
Published: October 2007

In Escherichia coli, the main player in transcription regulation of fatty acid metabolism is the FadR protein, which is involved in negative regulation of fatty acid degradation and in positive and negative regulation of the cellular processes related to it, as well as in positive regulation of the biosynthesis of unsaturated fatty acids in a concerted manner with negative regulation of FabR. On the other hand, Bacillus subtilis possesses two global transcriptional regulators, FadR (YsiA) and FapR. B. subtilis FadR represses fatty acid degradation, whereas FapR represses almost all the processes in the biosynthesis of saturated fatty acids and phospholipids. Furthermore, Streptococcus pneumoniae FabT represses the genes of fatty acid biosynthesis that are clustered in its genome. Long‐chain acyl‐CoAs appear to be metabolic signals for fatty acid degradation by bacteria in general, and antagonize the FadR protein from either E. coli or B. subtilis. However, malonyl‐CoA is a metabolic signal for fatty acid and phospholipid biosynthesis by Gram‐positive low‐GC bacteria, and it antagonizes FapR. These would be the primary aspects for understanding the elaborate and complex regulation of fatty acid metabolism in bacteria to maintain membrane lipid homeostasis.
Glucosylceramide synthase is essential for alfalfa defensin‐mediated growth inhibition but not for pathogenicity of Fusarium graminearum
Authors: Ramamoorthy Vellaisamy , Cahoon Edgar B. , Li Jia , Thokala Mercy , Minto Robert E. , Shah Dilip M.
Published: October 2007

Antifungal defensins, MsDef1 and MtDef4, from Medicago spp., inhibit the growth of a fungal pathogen, Fusarium graminearum, at micromolar concentrations. However, molecular mechanisms by which they inhibit the growth of this fungus are not known. We have characterized a functional role of the fungal sphingolipid glucosylceramide in regulating sensitivity of the fungus to MsDef1 and MtDef4. A null mutation of the FgGCS1 gene encoding glucosylceramide synthase results in a mutant lacking glucosylceramide. The ΔFggcs1‐null mutant becomes resistant to MsDef1, but not to MtDef4. It shows a significant change in the conidial morphology and displays dramatic polar growth defect, and its mycelia are resistant to cell wall degrading enzymes. Contrary to its essential role in the pathogenicity of a human fungal pathogen, Cryptococcus neoformans, GCS1 is not required for the pathogenicity of F. graminearum. The ΔFggcs1 mutant successfully colonizes wheat heads and corn silk, but its ability to spread in these tissues is significantly reduced as compared with the wild‐type PH‐1 strain. In contrast, it retains full virulence on tomato fruits and Arabidopsis thaliana floral and foliar tissues. Based on our findings, we conclude that glucosylceramide is essential for MsDef1‐mediated growth inhibition of F. graminearum, but its role in fungal pathogenesis is host‐dependent.
Function of heterologous and truncated RNase P proteins in Bacillus subtilis
Authors: Gößringer Markus , Hartmann Roland K.
Published: October 2007

Bacterial RNase P is composed of an RNA subunit and a single protein (encoded by the rnpB and rnpA genes respectively). The Bacillus subtilis rnpA knockdown strain d7 was used to screen for functional conservation among bacterial RNase P proteins from a representative spectrum of bacterial subphyla. We demonstrate conserved function of bacterial RNase P (RnpA) proteins despite low sequence conservation. Even rnpA genes from psychrophilic and thermophilic bacteria rescued growth of B. subtilis d7 bacteria; likewise, terminal extensions and insertions between β strands 2 and 3, in the so‐called metal binding loop, were compatible with RnpA function in B. subtilis. A deletion analysis of B. subtilis RnpA defined the structural elements essential for bacterial RNase P function in vivo. We further extended our complementation analysis in B. subtilis strain d7 to the four individual RNase P protein subunits from three different Archaea, as well as to human Rpp21 and Rpp29 as representatives of eukaryal RNase P. None of these non‐bacterial RNase P proteins showed any evidence of being able to replace the B. subtilis RNase P protein in vivo, supporting the notion that archaeal/eukaryal RNase P proteins are evolutionary unrelated to the bacterial RnpA protein.
Deformation in the Neoproterozoic Smalfjord Formation, northern Norway: an indicator of glacial depositional conditions?
Authors: ARNAUD EMMANUELLE
Published: October 2007

Recent studies on Neoproterozoic climate change have prompted renewed interest in Neoproterozoic glacial deposits and renewed debate over the criteria used to identify the nature of glacial influence on sedimentation. Analyses of soft sediment deformation structures have provided important clues to distinguish between competing palaeoenvironmental interpretations of Quaternary glacial deposits; a similar approach is presented here in the analysis of Neoproterozoic glacial deposits of the Smalfjord Formation, northern Norway. A detailed sedimentological and structural analysis at several sites in the Varangerfjorden area reveals complex soft sediment deformation at various scales in conglomerate, sandstone and diamictite. Deformation is predominantly ductile and includes anticlinal and synclinal folding, flow noses, flame structures, recumbent folding and shear structures. The deformed sediments are associated predominantly with conglomerate and sandstone, which record glaciofluvial and deltaic depositional conditions. Some deformations can be attributed to rapid deposition and slumping, whereas others appear to record shear stress associated with overriding ice. The scale, style and range of deformation, together with the coarse‐grained nature of the deformed sediments and facies associations, suggest that these were unfrozen outwash sediments that were overridden by ice and resedimented in a dynamic ice‐proximal setting. Whereas recent studies of diamictite‐bearing strata of the Smalfjord Formation had revealed no clear evidence of glacial influence on deposition, deformation structures documented here suggest that glacial conditions prevailed on the basin margin during deposition of Smalfjord Formation sediments, with sedimentary facies and deformation structures typical of temperate ice‐proximal settings.
The Arabidopsis TALE homeobox gene ATH1 controls floral competency through positive regulation of FLC
Authors: Proveniers Marcel , Rutjens Bas , Brand Marco , Smeekens Sjef
Published: October 2007

Floral induction is controlled by a plethora of genes acting in different pathways that either repress or promote floral transition at the shoot apical meristem (SAM). During vegetative development high levels of floral repressors maintain the Arabidopsis SAM as incompetent to respond to promoting factors. Among these repressors, FLOWERING LOCUS C (FLC) is the most prominent. The processes underlying downregulation of FLC in response to environmental and developmental signals have been elucidated in considerable detail. However, the basal induction of FLC and its upregulation by FRIGIDA (FRI) are still poorly understood. Here we report the functional characterization of the ARABIDOPSIS THALIANA HOMEOBOX 1 (ATH1) gene. A function of ATH1 in floral repression is suggested by a gradual downregulation of ATH1 in the SAM prior to floral transition. Further evidence for such a function of ATH1 is provided by the vernalization‐sensitive late flowering of plants that constitutively express ATH1. Analysis of lines that differ in FRI and/or FLC allele strength show that this late flowering is caused by upregulation of FLC as a result of synergism between ATH1 overexpression and FRI. Lack of ATH1, however, results in attenuated FLC levels independently of FRI, suggesting that ATH1 acts as a general activator of FLC expression. This is further corroborated by a reduction of FLC‐mediated late flowering in fca‐1 and fve‐1 autonomous pathway backgrounds when combined with ath1. Since other floral repressors of the FLC clade are not significantly affected by ATH1, we conclude that ATH1 controls floral competency as a specific activator of FLC expression.
Overexpression of Arabidopsis MAP kinase kinase 7 leads to activation of plant basal and systemic acquired resistance
Authors: Zhang Xudong , Dai Ya , Xiong Yuqing , DeFraia Christopher , Li Jiayang , Dong Xinnian , Mou Zhonglin
Published: October 2007

There is a growing body of evidence indicating that mitogen‐activated protein kinase (MAPK) cascades are involved in plant defense responses. Analysis of the completed Arabidopsis thaliana genome sequence has revealed the existence of 20 MAPKs, 10 MAPKKs and 60 MAPKKKs, implying a high level of complexity in MAPK signaling pathways, and making the assignment of gene functions difficult. The MAP kinase kinase 7 (MKK7) gene of Arabidopsis has previously been shown to negatively regulate polar auxin transport. Here we provide evidence that MKK7 positively regulates plant basal and systemic acquired resistance (SAR). The activation‐tagged bud1 mutant, in which the expression of MKK7 is increased, accumulates elevated levels of salicylic acid (SA), exhibits constitutive pathogenesis‐related (PR) gene expression, and displays enhanced resistance to both Pseudomonas syringae pv. maculicola (Psm) ES4326 and Hyaloperonospora parasitica Noco2. Both PR gene expression and disease resistance of the bud1 plants depend on SA, and partially depend on NPR1. We demonstrate that the constitutive defense response in bud1 plants is a result of the increased expression of MKK7, and requires the kinase activity of the MKK7 protein. We found that expression of the MKK7 gene in wild‐type plants is induced by pathogen infection. Reducing mRNA levels of MKK7 by antisense RNA expression not only compromises basal resistance, but also blocks the induction of SAR. Intriguingly, ectopic expression of MKK7 in local tissues induces PR gene expression and resistance to Psm ES4326 in systemic tissues, indicating that activation of MKK7 is sufficient for generating the mobile signal of SAR.