bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lateral-aspect, target-strength measurements of in situ herring (Clupea harengus)
Authors: Pedersen Geir , Handegard Nils Olav , Ona Egil 
Published: May 2009

Abstract
Pedersen, G., Handegard, N. O., and Ona, E. 2009. Lateral-aspect, target-strength measurements of in situ herring (Clupea harengus). – ICES Journal of Marine Science, 66: 1191–1196. Surveys of schooling herring with the new multibeam sonar (Simrad MS70) pose new challenges when converting the echo energy to estimates of biomass. Because the sonar projects horizontally, data and models of lateral-aspect, herring target strength (TS) are needed. In this study, the TS of herring is measured with a horizontally projecting, split-beam echosounder (Simrad EK60). Target-tracking methods are used to estimate swimming angles relative to the horizontal (θ) of individual herring within schools and layers and to evaluate how θ and TS change with depth (z). Measurements of θ and TS are used as inputs for a model describing TS as a function of θ and z. The results indicate that the mean lateral-aspect TS of in situ herring depends on z. Moreover, the mean lateral-aspect TS is more sensitive to z than the mean dorsal-aspect TS predicted by a published model. At z = 50 m, the mean lateral-aspect TS is nearly 2.5 dB higher than the mean dorsal-aspect TS. Conversely, at z = 350 m, the lateral-aspect TS is 5 dB lower. These results suggest that herring swimbladders do not compress uniformly with increasing pressure, but compress dorsoventrally more than laterally.
Calibration methods for two scientific multibeam systems
Authors: Ona Egil , Mazauric Valerie , Andersen Lars Nonboe 
Published: May 2009

Abstract
Ona, E., Mazauric, V., and Andersen, L. N. 2009. Calibration methods for two scientific multibeam systems. – ICES Journal of Marine Science, 66: 1326–1334. The new Simrad scientific multibeam systems, the MS70 sonar and the ME70 echosounder, each transmit over many electronically formed beams with centre frequencies spanning from 70 to 120 kHz. Calibrations of these systems are therefore more complex than for conventional split-beam echosounder systems. Two large tungsten-carbide spheres (75 and 84 mm diameter) were designed and manufactured to facilitate accurate field calibrations over the entire operational bandwidth. These are heavy and therefore stable when suspended beneath a ship, and have target strengths much larger than those of biological targets potentially within the measurement volume. This paper presents procedures for calibrating each system in the field and the results from two such experiments. Detailed inspections of the results for individual beams indicate that minor adjustments in the described procedures might further improve the reported calibration accuracy.
High-frequency acoustics and bio-optics in ecosystems research
Authors: Holliday D. V. , Donaghay P. L. , Greenlaw C. F. , Napp J. M. , Sullivan J. M. 
Published: May 2009

Abstract
Holliday, D. V., Donaghay, P. L., Greenlaw, C. F., Napp, J. M., and Sullivan, J. M. 2009. High-frequency acoustics and bio-optics in ecosystems research. – ICES Journal of Marine Science, 66: 974–980. The propagation of light and sound in the ocean’s interior is modified by the presence of phytoplankton, zooplankton, fish, gas bubbles, and dissolved and suspended material. Information is encoded in the levels and spectral characteristics of acoustic and optical scattering and absorption. Using acoustics and optics allows us to study the distribution of marine life and learn about ecosystem-relevant processes. Two studies are highlighted. In the first, multifrequency, upward-looking echosounders deployed near autonomous, bio-optical profilers were used to track vertical migration and the formation and size structure of <1 m thick, zooplankton layers in relation to the biomass and size structure of thin phytoplankton layers. In the second, a multifrequency sonar was used to track the temporal (seasonal) evolution of zooplankton biomass and size structure in the Bering Sea at intervals of 20 min. This paper focuses on how advanced technologies are being used to observe processes, distributions, and behaviour of marine life that have, until now, been hidden, as it were, from biological oceanographers.
Evaluating the uncertainty of abundance estimates from acoustic surveys using geostatistical simulations
Authors: Woillez Mathieu , Rivoirard Jacques , Fernandes Paul G. 
Published: May 2009

Abstract
Woillez, M., Rivoirard, J., and Fernandes, P. G. 2009. Evaluating the uncertainty of abundance estimates from acoustic surveys using geostatistical simulations. – ICES Journal of Marine Science, 66: 1377–1383. Geostatistical simulations, which can reproduce the spatial variability of a variable, are particularly helpful in estimating the uncertainty associated with the combination of different sources of variability. Acoustic surveys offer an example of such complex situations, where different data (e.g. acoustic backscatter, fish length, and fish age) must be combined to estimate abundance and its associated uncertainty. In this paper, the uncertainty of Scottish herring acoustic-survey estimates is investigated using these techniques. A specific multivariate, geostatistical model is used to describe the structural relationships, which includes highly skewed distributions of the acoustic-backscatter data and incorporates relationships between depth, mean length, and proportions-at-age. Conditional simulations, i.e. geostatistical simulations that honour the data values known at the data points, are used to generate multiple realizations of acoustic backscatter, mean length, and proportions-at-age. These are combined to produce multiple realizations of herring density over the sampled domain. Multiple realizations of total abundance and abundance-at-age are then provided. The uncertainty is assessed using basic statistics to track the significant variations of these values over the period 1989–2005. Higher coefficients of variation (CVs) are found on average for extreme ages (ages 1, 2i, 8, and 9+); otherwise, CVs are mostly around 12% for abundance-at-age and around 10% for total abundance.
Parabolic flight primes cytotoxic capabilities of polymorphonuclear leucocytes in humans
Authors: Kaufmann I. , Schachtner T. , Feuerecker M. , Schelling G. , Thiel M. , Choukèr A. 
Published: May 2009

AbstractBackground  Previously performed in vitro studies suggested that gravitational stress may alter functions of immune cells. This study investigated the in vivo effects of parabolic flight manoeuvres as a short‐term model of micro‐ and hypergravity on the cytotoxic and microbicidal polymorphonuclear leucocyte (PMN) functions as the key element of innate immunity.Material and methods  Twenty‐one healthy male volunteers underwent 30 subsequent parabolic flight manoeuvres. Each manoeuvre produced 22‐s periods of nearly weightlessness close to «0g», with each parabola starting with a pull‐up and ending with a pull‐out (hypergravity) at 1·8 g for about 20 s each. Blood samples were drawn 24 h prior to take off (T0), after 25–30 parabolas (T1), and 24 h (T2) and 48 h (T3) after flight for determination of (i) leucocyte number and subpopulations, (ii) PMNs’ capabilities to produce hydrogen peroxide (H2O2) and to adhere and phagocytose particles and (iii) plasma cytokines known to prime PMN functions [interleukin‐8 (IL‐8), tumour necrosis factor‐α (TNF‐α), granulocyte‐colony stimulating factor (G‐CSF) and granulocyte‐macrophage colony stimulating factor (GM‐CSF)].Results  Parabolic flight induced an increase in leucocyte number with a significant elevation of the PMN fraction. The spontaneous H2O2 production by PMNs did not change; however, the capability of PMNs to produce H2O2 in response to soluble stimuli [N‐formyl‐methionyl‐leucyl‐phenylalanine (fMLP), fMLP and TNF‐α, calcium ionophore (A23187), phorbol myristate acetate (PMA)] was increased. Adhesive and phagocytic properties of PMNs were not altered. Regarding priming cytokines, IL‐8 and G‐CSF were significantly elevated.Conclusions  Our data indicate that parabolic flight induces priming of the cytotoxic capabilities of PMNs without affecting microbicidal functions.
Brachial artery diameter is related to cardiovascular risk factors and intima‐media thickness
Authors: Holewijn S. , Den Heijer M. , Swinkels D. W. , Stalenhoef A. F. H. , De Graaf J. 
Published: May 2009

AbstractBackground  Previous reports showed inconsistent results about the potential role of flow‐mediated dilatation (FMD) in cardiovascular(CV) risk prediction. Few data are available about the role of nitroglycerin‐mediated dilatation (NMD), but recently, brachial artery diameter(BAD) appeared to have predictive value in CV risk prediction.We determined the relation of FMD, BAD and NMD with known CV risk factors and intima‐media thickness (IMT), a well‐established surrogate marker of atherosclerosis, in a community‐based population, the Nijmegen Biomedical Study (NBS).Materials and methods  FMD, BAD and NMD were measured in the brachial, and IMT in the common carotid artery ultrasononically in 337 participants, aged 50–70 years. Traditional clinical and biochemical parameters were determined.Results  Both FMD and NMD were not correlated with most CV risk factors or prevalent CVD. However, both IMT and BAD did show significant correlations with CV risk factors. In accordance, both IMT and BAD were significantly correlated with prevalent CVD (r = 0·62 and r = −0·37, respectively) . Furthermore, FMD was not correlated with IMT and did hardly (R2 = 1·1%) improve the prediction of IMT by CV risk factors in regression analysis. However, both BAD and NMD did correlate with IMT (r = −0·29 and r = 0·25, respectively).Conclusion  In our study, FMD and NMD were not related to known CV risk factors and prevalent CVD, and FMD was not correlated with IMT, a surrogate marker of atherosclerosis. Most intriguingly, BAD was significantly correlated with some CV risk factors, prevalent CVD and IMT. So, BAD is a potential valuable tool in CV risk prediction in middle‐aged low‐risk populations, whereas FMD is not.
Towards an understanding of resilience in isolated coral reefs
Authors: HALFORD ANDREW R. , CALEY M. JULIAN 
Published: May 2009

AbstractIn 1998, seawater temperature anomalies led to unprecedented levels of coral bleaching on reefs worldwide. We studied the direct effects of this thermal event on benthic communities and its indirect effects on their associated coral reef fish communities at a group of remote reefs off NW Australia. Long‐term monitoring of benthic and fish assemblages on these reefs allowed us to compare the responses of these communities to coral bleaching using a data series that included 4 years before, and 6 years following, this bleaching event. While bleaching mortality was evident to >30 m depth, it was patchy among the shallower survey sites with decreases in live coral cover ranging from 30% to 90% across seven surveyed locations Within 2 years of the bleaching, hard coral recovery had begun at all sites and by 2003 reef‐wide coral cover had increased to ∼39% of its preimpact levels. We exploited this pattern of differential survival of corals among sites, the associated changes in these benthic communities, and their patterns of recovery, to better understand links between benthic community dynamics and their associated fish communities. Temporal changes in the resident fish communities strongly reflected the differential shifts in the benthic communities, but were lagged by 12–18 months. Five years after the bleaching event, the fish communities on five of the seven surveyed locations showed evidence of recovery, however, none had regained their preimpact structures. Analyses of these communities by taxonomic family revealed a range of responses to the disturbance reflective of their life‐histories and trophic and habitat affiliations. The slow but recognizable recovery of this isolated reef system has parallels with other relatively isolated systems that displayed resilience to the 1998 bleaching event, e.g. the Chagos archipelago, but it also contrasts sharply with low levels of resilience documented in other isolated reef systems subject to the same disturbance, e.g. the Seychelles. In this context, our results highlight the significant knowledge gaps remaining in understanding the resilience of these ecosystems to disturbance.
Assessment of bioactive and bio‐adhesive therapies to enhance stem cell attachment to root surface dentine
Authors: Elseed M. A. , Murray P. E. , Garcia‐Godoy F. , Namerow K. N. 
Published: May 2009

AbstractAim  To compare bioactive and bio‐adhesive therapies to enhance stem cell attachment to the root dentine of human teeth.Methodology  Dentine slabs (n = 72) were cut from the lower 3 mm of the roots of extracted human permanent teeth. The root dentine slabs were untreated, or coated with bio‐adhesive, or human recombinant transforming growth factor‐beta1 (hrTGF‐B1), or human recombinant bone morphogenic protein‐2 (hrBMP‐2). The dentine slabs were placed with the root surface in contact with confluent periodontal stem cell (PSC) cultures using aseptic techniques. The cells and dentine slabs were submerged in culture media for 4, 24 and 72 h. The specimens were fixed in formalin, dehydrated and processed for scanning electron microscopy (SEM).Results  SEM micrographs at ×2000 magnification revealed PSC extensive adherence to root dentine for all of the bio‐adhesive and bioactive treatments. The addition of bioactive molecules did not improve PSC attachment. Few cells attached to the negative control treatments.Conclusions  Bio‐adhesive and bioactive growth factors were not needed to promote PSC attachment to the root dentine of human teeth, because it already appears to have good natural properties to promote PSC attachment. This suggests PSC can be used for the clinical replantation of avulsed teeth without the need for bio‐adhesive and bioactive treatments.
The upregulation of oncostatin M in inflamed human dental pulps
Authors: Huang F‐M , Tsai C‐H , Yang S‐F , Chang Y‐C 
Published: May 2009

AbstractAim  To compare oncostatin M (OSM) expression in clinically healthy and inflamed specimened human pulp tissue.Methodology  Thirty pulpal tissue specimens (15 clinically healthy and 15 inflamed) were obtained from extracted third molars with informed consent from patients. The levels of OSM were compared between clinically healthy pulp and inflamed pulp tissues using the semi‐quantitative reverse‐transcriptase polymerase chain reaction. In addition, immunohistochemistry was used to identify the in situ localization of OSM expression in pulp specimens. For testing of differences in the OSM between the clinically healthy and inflamed human dental pulps, the Wilcoxon–Mann–Whitney rank sum test was applied. Differences in OSM expression between tissue with low and high levels of inflammation were subsequently analysed by Fisher’s exact test.Results  Inflamed pulps exhibited significantly higher OSM mRNA gene expression than clinically healthy pulps (P < 0.05). Immunohistochemistry demonstrated that OSM expression was significantly higher in inflamed than clinically healthy pulps (P < 0.05). OSM staining was detected in odontoblasts, fibroblasts, inflammatory infiltrates and endothelial cells.Conclusions  Oncostatin M expression was elevated in inflamed pulp tissue. OSM is potentially involved in the disease process of pulpal inflammation.
Predictive value of on‐treatment response during full‐dose antiviral therapy of patients with hepatitis C virus cirrhosis and portal hypertension
Authors: Giannini E. G. , Basso M. , Savarino V. , Picciotto A. 
Published: May 2009

Abstract.Objective.  Therapy with full‐dose pegylated interferon (PEG‐IFN) and weight‐based ribavirin has been evaluated in limited series of patients with hepatitis C virus (HCV) and advanced disease. In this study, we evaluated the efficacy and tolerability of full‐dose antiviral therapy in patients with compensated, fully developed cirrhosis, and assessed the predictive value of on‐treatment virological response.Design and subjects.  We studied 85 HCV‐positive cirrhotic patients (82 Child‐Pugh class A; 41 treatment‐naïve) who were treated with PEG‐IFN α‐2a (1.5 μg kg−1week−1) or α‐2b (180 μg week−1) and weight‐based ribavirin for 24 (genotype 2–3) or 48 (genotype 1–4) weeks. Forty‐three patients were genotype 1 (51%), and HCV‐RNA was >600 000 IU mL−1 in 53 patients (62%). Prevalence of portal hypertension and diabetes was 81% and 18% respectively.Results.  Sustained virological response (SVR) was obtained in 22 patients (26%). Positive serum HCV‐RNA at week 4 and week 12 of therapy predicted nonresponse (NR) in 85% (52/61) and 100% (38/38) of patients, respectively. Treatment was discontinued due to adverse events in 14 patients (16%). Genotype 1–4 (P = 0.02) and HCV‐RNA >600 000 IU mL−1 (P = 0.02) were the baseline parameters significantly associated with lack of SVR, whilst positive serum HCV‐RNA at week 12 was the only parameter independently associated with NR (100% negative predictive value).Conclusion.  Full‐dose antiviral therapy with PEG‐IFN and ribavirin can be safely carried out even in patients with compensated, fully established cirrhosis and portal hypertension. Selecting patients on the basis of HCV genotype and viral load, and application of on‐treatment stopping rule may help rationalize treatment in patients who are unlikely to obtain SVR.
Analysing laser‐scanned digital terrain models of gravel bed surfaces: linking morphology to sediment transport processes and hydraulics
Authors: HODGE REBECCA , BRASINGTON JAMES , RICHARDS KEITH 
Published: May 2009

AbstractThe grain‐scale topography of a sediment surface is a key component of a fluvial system, affecting aspects including sediment transport, flow resistance and ecology. However, its effect is hard to quantify because of the need for grain‐scale elevation data from in situ fluvial gravel surfaces which are difficult to collect. The sediment surface properties are, therefore, commonly estimated as a function of the sediment grain‐size distribution; however, because of additional factors, such as grain packing and shape, there is not necessarily a unique relationship between the two. A new methodology has been developed that uses terrestrial laser scanning to collect grain‐scale topographic data from in situ fluvial gravel surfaces, from which digital terrain models are created. This paper investigates methods of analysing such digital terrain models, and possible sedimentological interpretations that can be drawn from the analysis. Eleven digital terrain models from exposed gravel surfaces in two contrasting rivers (the River Feshie and Bury Green Brook) were analysed by calculating: the distribution of surface elevations, semivariograms, surface inclinations, surface slopes and aspects and grain orientation. The distribution of surface elevations and surface slope and aspect analysis were found to be most informative. In the River Feshie, grain‐size was interpreted as being a dominant control on sediment surface structure and gravel imbrication was identified. In Bury Green Brook, the location of the digital terrain models within the riffle–pool sequence was the dominant control on surface structure and grain orientation. Such digital terrain models therefore provide a new approach to measuring and quantifying the topography of fluvial sediment surfaces.
Aeolian dune‐field development in a water table‐controlled system: Skeiđarársandur, Southern Iceland
Authors: MOUNTNEY NIGEL P. , RUSSELL ANDREW J. 
Published: May 2009

AbstractAeolian dune fields characterized by partly vegetated bedforms undergoing active construction and with interdune depressions that lie at or close to the water table are widespread on Skeiđarársandur, Southern Iceland. The largest aeolian dune complex on the sandur covers an area of 80 km2 and is characterized by four distinct landform types: (i) spatially isolated aeolian dunes; (ii) extensive areas of damp and wet (flooded) interdune flat with small fluvial channels; (iii) small aeolian dune fields composed of assemblages of bedforms with simple morphologies and small, predominantly damp, interdune corridors; and (iv) larger aeolian dune fields composed of assemblages of complex bedforms floored by older aeolian dune deposits that are themselves raised above the level of the surrounding wet sandur plain. The morphology of each of these landform areas reflects a range of styles of interaction between aeolian dune, interdune and fluvial processes that operate coevally on the sandur surface. The geometry, scale, orientation and facies composition of sets of strata in the cores of the aeolian dunes, and their relationship to adjoining interdune strata, have been analysed to explain the temporal behaviour of the dunes in terms of their mode of initiation, construction, pattern of migration, style of accumulation and nature of preservation. Seasonal and longer‐term flooding‐induced changes in water table level have caused episodic expansion and contraction of the wet interdune ponds. Most of the dunes are currently undergoing active construction and migration and, although sediment availability is limited because of the high water table, substantial aeolian transport must occur, especially during winter months when the surface of the wet interdune ponds is frozen and sand can be blown across the sandur without being trapped by surface moisture. Bedforms within the larger dune fields have grown to a size whereby formerly damp interdune flats have been reduced to dry enclosed depressions and dry aeolian system accumulation via bedform climb is ongoing. Despite regional uplift of the proximal sandur surface in response to glacial retreat and unloading over the past century, sediment compaction‐induced subsidence of the distal sandur is progressively placing aeolian deposits below the water table and is enabling the accumulation of wet aeolian systems and increasing the likelihood of their long‐term preservation. Wet, dry and stabilizing aeolian system types all co‐exist on Skeiđarársandur and the dunes are variously undergoing coeval construction, accumulation, bypass, stabilization and destruction as a result of interactions between localized factors.
Experimental insights into laser diffraction particle sizing of fine‐grained sediments for use in palaeoceanography
Authors: JONKERS LUKAS , PRINS MAARTEN A. , BRUMMER GEERT‐JAN A. , KONERT MARTIN , LOUGHEED BRYAN C. 
Published: May 2009

AbstractGrain‐size measurements of fine‐grained sediments based on laser diffraction may contain spurious information due to the over‐estimation of the size and proportion of platy particles. Consequently, some regard the use of laser diffraction particle sizing in palaeoceanography inappropriate. Here, it is shown experimentally that such concerns are not warranted. Laser diffraction particle sizing is known to be fast, precise and allows for detailed particle sizing over a broad size range; it is therefore potentially a very powerful technique if the complications associated with it can be overcome. As most sediments are mixtures of different components transported by different mechanisms, inferences of past environmental parameters require decomposition of the grain‐size record in question. Useful decomposition can only be performed if changes in the contribution of the components are registered predictably by the measuring device. This study reports on mixing experiments which show that the Fritsch A22 laser diffraction particle sizer does indeed register small changes in the contribution of the mixing components in a predictable way. Mixing proportions estimated from the measurements do, however, differ from the initial mixing proportions, but these can be converted with only small errors. Application of the conversion equations to a North Atlantic grain‐size record that showed consistent slowdown of deep‐ocean circulation in response to millennial scale ice‐rafting events during the last glacial does not quantitatively affect the original inferences. Laser diffraction particle sizing of fine‐grained sediments therefore yields reproducible and useful data for palaeoceanographic reconstructions.