bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the effect of the North Atlantic Oscillation on temperature and salinity of the subpolar North Atlantic intermediate and deep waters
Authors: Sarafanov Artem 
Published: April 2009

Abstract
Sarafanov, A. 2009. On the effect of the North Atlantic Oscillation on temperature and salinity of the subpolar North Atlantic intermediate and deep waters. – ICES Journal of Marine Science, 66: 1448–1454. The close relationship between the observed water mass properties and the winter North Atlantic Oscillation (NAO) index (1950–2000s; r2 ≈ 0.65) implies that changes in the NAO-related atmospheric forcing may account for up to two-thirds of thermohaline changes at the intermediate and deep levels in the subpolar North Atlantic on a decadal time-scale. Persistent NAO decline (amplification) results in increase (decrease) in temperature and salinity in the intermediate–deep water column. A general mechanism explaining the close link between the NAO and coherent decadal changes in the intermediate and deep-water temperature and salinity in the region is inferred from the observed changes in the regional circulation and water mass properties. Two factors dominate this link: (i) intensity of convection in the Labrador Sea controlling injection of relatively cold freshwater into the intermediate layer, and (ii) zonal extension of the Subpolar Gyre that regulates the relative contribution of cold fresh subpolar water and warm saline subtropical water to the deep-water formation.
Empirical analyses of the length, weight, and condition of adult Atlantic salmon on return to the Scottish coast between 1963 and 2006
Authors: Bacon P. J. , Palmer S. C. F. , MacLean J. C. , Smith G. W. , Whyte B. D. M. , Gurney W. S. C. , Youngson A. F. 
Published: April 2009

Abstract
Bacon, P. J., Palmer, S. C. F., MacLean, J. C., Smith, G. W., Whyte, B. D. M., Gurney, W. S. C., and Youngson, A. F. 2009. Empirical analyses of the length, weight, and condition of adult Atlantic salmon on return to the Scottish coast between 1963 and 2006. – ICES Journal of Marine Science, 66: 844–859. Sea age, size, and condition of adult Atlantic salmon (Salmo salar) are prime determinants of individual, and hence population, productivity. To elucidate potential mechanisms, 151 000 records of salmon returning to six Scottish coastal sites over 44 years were analysed for length, weight, and condition, by site, sex, sea age, and river age. After correcting for capture effort biases, all sites showed seasonal increases in length and weight for both 1 sea winter (1SW) and 2SW fish. However, whereas condition increased slightly with season for 2SW, it decreased notably for 1SW. Sites showed common decadal trends in length, weight, and condition. Within years, length and weight residuals from trends were coherent across sites, but residuals from condition trends were not. Rates of seasonal condition change also showed decadal trends, dramatically different between sea ages, but common across sites within sea-age groups. Longer salmon were disproportionately heavy in all seasons. 1SW condition was markedly lower in 2006. Detrended correlations with oceanic environmental variables were generally not significant, and always weak. A published correlation between the condition of 1SW salmon caught at a single site and sea surface temperatures in the Northeast Atlantic could not be substantiated for any of the six fisheries over the wider time-scales examined.
Application of a generalized additive model (GAM) to reveal relationships between environmental factors and distributions of pelagic fish and krill: a case study in Sendai Bay, Japan
Authors: Murase Hiroto , Nagashima Hiroshi , Yonezaki Shiroh , Matsukura Ryuichi , Kitakado Toshihide 
Published: April 2009

Abstract
Murase, H., Nagashima, H., Yonezaki, S., Matsukura, R., and Kitakado, T. 2009. Application of a generalized additive model (GAM) to reveal relationships between environmental factors and distributions of pelagic fish and krill: a case study in Sendai Bay, Japan. – ICES Journal of Marine Science, 66: 1417–1424. A generalized additive model (GAM) was applied to fishery-survey data to reveal the influences of environmental factors on the distribution patterns of Japanese anchovy (Engraulis japonicus), sand lance (Ammodytes personatus), and krill (Euphausia pacifica). Echosounder and physical-oceanographic data were collected in Sendai Bay, Japan, in spring 2005. A hierarchical model was used with two spatial strata: (i) presence and absence of each species; and (ii) biomass density of each species, given its presence; and six environmental covariates (surface water temperature, salinity, and chlorophyll, and near-seabed water temperature, salinity, and depth). The results indicate non-linear responses of the two indices to the environmental covariates. In addition, the biomasses estimated by the GAMs were comparable with estimates based on conventional, stratified-random sampling for each species. GAMs are very useful for (i) investigating the effects of environmental factors on the distributions of biological organisms, and (ii) predicting the distributions of animal densities in unsurveyed areas.
Identifying New Components Participating in the Secondary Cell Wall Formation of Vessel Elements in Zinnia and Arabidopsis
Authors: Endo Satoshi , Pesquet Edouard , Yamaguchi Masatoshi , Tashiro Gen , Sato Mayuko , Toyooka Kiminori , Nishikubo Nobuyuki , Udagawa-Motose Makiko , Kubo Minoru , Fukuda Hiroo , Demura Taku 
Published: April 2009

Abstract
Xylem vessel elements are hollow cellular units that assemble end-to-end to form a continuous vessel throughout the plant body; the xylem vessel is strengthened by the xylem elements' reinforced secondary cell walls (SCWs). This work aims to unravel the contribution of unknown actors in xylem vessel differentiation using the model in vitro cell culture system of Zinnia elegans differentiating cell cultures and the model in vivo system of Arabidopsis thaliana plants. Tracheary Element Differentiation-Related6 (TED6) and TED7 were selected based on an RNA interference (RNAi) screen in the Zinnia system. RNAi reduction of TED6 and 7 delayed tracheary element (TE) differentiation and co-overexpression of TED6 and 7 increased TE differentiation in cultured Zinnia cells. Arabidopsis TED6 and 7 were expressed preferentially in differentiating vessel elements in seedlings. Aberrant SCW formation of root vessel elements was induced by transient RNAi of At TED7 alone and enhanced by inhibition of both TED6 and 7. Protein–protein interactions were demonstrated between TED6 and a subunit of the SCW-related cellulose synthase complex. Our strategy has succeeded in finding two novel components in SCW formation and has opened the door for in-depth analysis of their molecular functions.
The WD40 Repeat Protein NEDD1 Functions in Microtubule Organization during Cell Division inArabidopsis thaliana
Authors: Zeng C.J. Tracy , Lee Y.-R. Julie , Liu Bo 
Published: April 2009

AbstractAlthough cells of flowering plants lack a structurally defined microtubule-organizing center like the centrosome, organization of the spindles and phragmoplasts in mitosis is known to involve the evolutionarily conserved γ-tubulin complex. We have investigated the function of Arabidopsis thaliana NEDD1, a WD40 repeat protein related to the animal NEDD1/GCP-WD protein, which interacts with the γ-tubulin complex. The NEDD1 protein decorates spindle microtubules (MTs) preferentially toward spindle poles and phragmoplast MTs toward their minus ends. A T-DNA insertional allele of the single NEDD1 gene was isolated and maintained in heterozygous sporophytes, and NEDD1's function in cell division was analyzed in haploid microspores produced by the heterozygote. In approximately half of the dividing microspores exhibiting aberrant MT organization, spindles were no longer restricted to the cell periphery and became abnormally elongated. After mitosis, MTs aggregated between reforming nuclei but failed to appear in a bipolar configuration. Consequently, defective microspores did not form a continuous cell plate, and two identical nuclei were produced with no differentiation into generative and vegetative cells. Our results support the notion that the plant NEDD1 homolog plays a critical role in MT organization during mitosis, and its function is likely linked to that of the γ-tubulin complex.
Discovery, characterization and validation of single nucleotide polymorphisms within 206 bovine genes that may be considered as candidate genes for beef production and quality
Authors: Williams J. L. , Dunner S. , Valentini A. , Mazza R. , Amarger V. , Checa M. L. , Crisà A. , Razzaq N. , Delourme D. , Grandjean F. , Marchitelli C. , García D. , Pérez Gomez R. , Negrini R. , Ajmone Marsan P. , Levéziel H. 
Published: April 2009

SummaryA large number of putative single nucleotide polymorphisms (SNPs) have been identified from the bovine genome‐sequencing project. However, few of these have been validated and many will turn out to be sequencing artefacts or have low minor allele frequencies. In addition, there is little information available on SNPs within coding regions, which are likely to be responsible for phenotypic variation. Therefore, additional SNP discovery is necessary to identify and validate polymorphisms both in specific genes and genome‐wide. Sequence‐tagged sites within 286 genes were resequenced from a panel of animals representing a wide range of European cattle breeds. For 80 genes, no polymorphisms were identified, and 672 putative SNPs were identified within 206 genes. Fifteen European cattle breeds (436 individuals plus available parents) were genotyped with these putative SNPs, and 389 SNPs were confirmed to have minor allele frequencies above 10%. The genes containing SNPs were localized on chromosomes by radiation hybrid mapping and on the bovine genome sequence by Blast. Flanking microsatellite loci were identified, to facilitate the alignment of the genes containing the SNPs in relation to mapped quantitative trait loci. Of the 672 putative SNPs discovered in this work, only 11 were found among the validated SNPs and 100 were found among the approximately 2.3 million putative SNPs currently in dbSNP. The genes studied in this work could be considered as candidates for traits associated with beef production and the SNPs reported will help to assess the role of the genes in the genetic control of muscle development and meat quality. The allele frequency data presented allows the general utility of the SNPs to be assessed.
CMC‐544 (inotuzumab ozogamicin) shows less effect on multidrug resistant cells: analyses in cell lines and cells from patients with B‐cell chronic lymphocytic leukaemia and lymphoma
Authors: Takeshita Akihiro , Shinjo Kaori , Yamakage Nozomi , Ono Takaaki , Hirano Isao , Matsui Hirotaka , Shigeno Kazuyuki , Nakamura Satoki , Tobita Tadasu , Maekawa Masato , Ohnishi Kazunori , Sugimoto Yoshikazu , Kiyoi Hitoshi , Naoe Tomoki , Ohno Ryuzo 
Published: April 2009

SummaryThe effect of CMC‐544, a calicheamicin‐conjugated anti‐CD22 monoclonal antibody, was analysed in relation to CD22 and P‐glycoprotein (P‐gp) in B‐cell chronic lymphocytic leukaemia (CLL) and non‐Hodgkin lymphoma (NHL) in vitro. The cell lines used were CD22‐positive parental Daudi and Raji, and their P‐gp positive sublines, Daudi/MDR and Raji/MDR. Cells obtained from 19 patients with B‐cell CLL or NHL were also used. The effect of CMC‐544 was analysed by viable cell count, morphology, annexin‐V staining, and cell cycle distribution. A dose‐dependent, selective cytotoxic effect of CMC‐544 was observed in cell lines that expressed CD22. CMC‐544 was not effective on Daudi/MDR and Raji/MDR cells compared with their parental cells. The MDR modifiers, PSC833 and MS209, restored the cytotoxic effect of CMC‐544 in P‐gp‐expressing sublines. In clinical samples, the cytotoxic effect of CMC‐544 was inversely related to the amount of P‐gp (P = 0·003), and to intracellular rhodamine‐123 accumulation (P < 0·001). On the other hand, the effect positively correlated with the amount of CD22 (P = 0·010). The effect of CMC‐544 depends on the levels of CD22 and P‐gp. Our findings will help to predict the clinical effectiveness of this drug on these B‐cell malignancies, suggesting a beneficial effect with combined use of CMC‐544 and MDR modifiers.
Transforming growth factor‐β in allergic inflammatory disease of the upper airways: friend or foe?
Authors: Salib R. J. , Howarth P. H. 
Published: April 2009

SummaryTGF‐β is a multi‐functional cytokine with a huge array of effects on a variety of cell types. It is rapidly emerging as a key major player in the way the airway epithelium behaves and its ability to repair itself. This is not only of relevance to allergic airway diseases such as asthma and allergic rhinitis, which are increasing in prevalence worldwide, but in many other diseases. The full impact any disruption of TGF‐β signalling may have in the development and persistence of allergic inflammatory airway diseases is yet to be fully realized and remains the subject of ongoing research. There has been a recent revival of interest in the role of regulatory T cells in controlling allergic inflammation. Evidence is emerging of a significant contribution by TGF‐β to this regulatory process. This review aims to summarize current knowledge relating to TGF‐β in relation to allergic inflammatory upper airways disease, and attempts to clarify some of the discrepancies and inconsistencies in this area. It also considers the therapeutic implications of novel TGF‐β therapy, including potential future applications in the treatment of nasal polyposis and reduction of post‐operative scar tissue formation following endoscopic sinus surgery.
Non‐atopic intrinsic asthma and the ‘family tree’ of chronic respiratory disease syndromes
Authors: Holt P. G. , Sly P. D. 
Published: April 2009

SummaryWe present a scheme below in which the most common forms of inflammatory diseases of the respiratory tract, notably atopic and non‐atopic asthma and COPD, are depicted as separate offshoots from a common ‘at‐risk’ pathway underpinned by genotypes related to aberrations in control of host defence and tissue repair mechanisms. We propose that entrance into this pathway is initially programmed by environmental experience during infancy and early childhood, in particular by severe lower respiratory tract infection, and that further progression towards expression of specific disease phenotype(s) is determined by the nature, timing and frequency of additional environmental insults subsequently encountered. At the one extreme, early sensitization of at‐risk subjects to aeroallergens can potentially drive rapid progression towards expression of the atopic asthmatic phenotype under the dual onslaught of inflammatory responses to allergens/pathogens. At the opposite end of the spectrum the drip‐feed effects of occasional infections on respiratory function(s) are amplified over a longer time frame by inflammation resulting from exposure to tobacco smoke and/or related chemical pollutants. Non‐atopic asthma is envisaged to fit between these two extremes, being driven essentially by the downstream effects of respiratory infections alone in at‐risk subjects. An important common factor in all three disease phenotypes is that acute exacerbations are typically driven by infections, the host responses to which display a characteristic T‐helper type 2‐like footprint, which in our view points to underlying genotype(s) which result in unbalanced host responses to respiratory pathogens.
γ‐aminobutyric acid nurtures allergic asthma
Authors: Lu W.‐Y. , Inman M. D. 
Published: April 2009

SummaryAsthma often occurs as a result of immune‐based inflammatory responses, which consequently cause pathological changes in airway structural cells. However, the underlying mechanisms of airway pathology in asthma are still not fully understood. Our recent studies revealed a critical role of γ‐aminobutyric acid (GABA) signalling pathway in the airway epithelium of allergic asthma through its ability to stimulate mucus production. This review briefly describes the GABAergic signalling system and its role in the regulation of mucus protein production in bronchial airway epithelial cells.
Phenotypic and functional markers for 1α,25-dihydroxyvitamin D3-modified regulatory dendritic cells
Authors: Pedersen A W , Holmstrøm K , Jensen S S , Fuchs D , Rasmussen S , Kvistborg P , Claesson M H , Zocca M-B 
Published: April 2009

SummaryThe clinical use of dendritic cells (DCs) to induce antigen-specific immune tolerance has been hampered by the lack of a widely acknowledged method for generating human regulatory DCs but even more so by the non-existence of reliable markers. Thus, we set out to find reliable markers that can be measured with simple methods to identify regulatory DCs that are applicable for future clinical studies. Human DCs were generated from peripheral blood monocytes in the presence of 1α,25-dihydroxyvitamin D3 (VD3), which gave rise to a phenotype that resembles immature DCs, with the exception of high CD14 and reduced CD1a on the cell surface. These VD3-treated DCs exert a long-lasting inefficient T cell stimulation and induce T cell hyporesponsiveness with regulatory potential. Importantly, such VD3-treated DCs were readily distinguishable from untreated DCs by low levels of interleukin-23 secretion and low expression of miR-155 upon exposure to maturation stimuli. Furthermore, VD3-treated DCs showed over-expression of miR-378. All these features can be used as robust markers for quality control of VD3-treated regulatory DCs in future clinical studies.
The effect of surface–solute interactions on the transport of solutes through porous materials
Authors: Rose D. A. , Abbas F. , Adey M. A. 
Published: April 2009

SummaryWe have investigated the effect of differences in surface charge, valency of ion, solute concentration, solution flux and physical structure on the leaching and uptake of individual ions from simple solutions flowing through porous materials. We studied the miscible displacement of solutions of four salts (KBr, K2SO4, CaBr2 and CaSO4) having different cation : anion ratios separately through three inert materials (ballotini, pumice and ceramic) and two sizes of a reactive material (sepiolite) over several ranges of concentration (c) and at many pore‐water velocities (v) under steady vertical saturated flow. Breakthrough curves of individual effluent ions (K+, Br−, Ca2+ and SO42−) were analysed by CXTFIT 2.0 to optimize transport parameters (retardation factor, R; dispersion coefficient, K) assuming that transport was governed by the convective–dispersion equation. In the inert materials, R did not differ significantly from 1 irrespective of c. In sepiolite, R was < 1 for anions and > 1 for cations, and became more extreme as c decreased. R varied with the valency of the anions, as predicted by diffuse double layer theory, and with that of the cations by a simple charge balance. Freundlich isotherms, reconstructed from R values, described the sorption of the cations and exclusion of the anions. For the inert materials, K did not depend on the ion or c and increased monotonically with v. For sepiolite, K also increased with v and with small but non‐significant differences between ions and concentrations. The K(v) functions were consistent with Passioura’s theory of dispersion in aggregated media, and the transport was reversible as R and K values did not depend on whether the media were being leached or resalinized. The effective dispersion coefficient of an ion is K* = K/R so, although K(v) appears to be unaffected by ion or concentration of solute in sepiolite, K*(v) will be affected. Thus, the controlling factor of these surface–solute interactions is R.
Impact of stone content on water movement in water‐repellent sand
Authors: Urbanek E. , Shakesby R. A. 
Published: April 2009

SummarySoils are commonly stony, especially in steep upland or heavily degraded sites. The hydrological effect of large stone contents has been previously investigated in wettable but not in water‐repellent soils. For the latter, the focus has instead been on the impact of other soil characteristics (e.g. cracks and macropores) likely to promote water percolation. This paper investigates stone effects on water flow in water‐repellent sand under laboratory conditions. Seventy‐five experiments were performed on a water‐repellent sand mixed with a range of quantities of different‐sized wettable and water‐repellent stones. The time taken for water to pass through each sand–stone mix, the percolated water volumes and numbers of dry and wet stones following each 60‐minute experiment were recorded. At large stone contents (> 55% or > 65% by weight, depending on stone wettability), percolation occurred relatively quickly and in comparatively large quantities. At intermediate stone contents (45–65%) percolation response was variable and at stone contents < 45% for wettable and < 55% for water‐repellent soils no water percolation occurred. We argue that with large stone contents flow pathways develop along sand–stone interfaces and a continuous preferential flow path can form provided there are sufficient stone‐to‐stone connections. The distribution and alignment of the stones, especially at intermediate stone contents, are important for promoting water movement. Water repellency determinations based only on the fine sediment component in stony soils could therefore be misleading as regards determining their hydrological response: the influence of the clastic component must also be considered.
High concentrations of blue crab (Callinectes sapidus) larvae along the offshore edge of a coastal current: effects of convergent circulation
Authors: TILBURG CHARLES E. , DITTEL ANA I. , EPIFANIO CHARLES E. 
Published: April 2009

AbstractUsing a combination of observations and numerical modeling, we examined the distribution of blue crab (Callinectes sapidus) larvae along the edge of the buoyant plume emanating from the mouth of Delaware Bay along the east coast of the USA. Our observations consisted of larval sampling and hydrographic measurements taken along a series of transects that spanned the plume, the plume edge, and the coastal ocean. The numerical model is a realistic circulation model of Delaware Bay and the adjoining coastal ocean that includes daily wind forcing, daily river discharge, and tides. We tested the hypothesis that the offshore edges of coastal currents are regions of convergence and retention for larvae of estuary dependent species. Collected data showed a marked difference between the distribution of early and late stage larvae. Patches of early stage larvae occurred within lower salinities typical of the estuarine plume and higher salinities associated with the offshore edge of the plume. Late‐stage larvae occurred almost entirely in salinities characteristic of the offshore edge. The field study was followed by a modeling component that simulated larval distributions over the spawning season of 2005. Output from the model showed simulated larval distributions that were similar to the observations. This study provides new insight into the distribution of larvae and larval patches in Delaware Bay and any region with extensive buoyancy and tidally driven flow. Results indicate that larvae tend to congregate along the edges of plumes emanating from estuaries due solely to physical mechanisms, regardless of the initial spawning location.