bluuebunny/crossref_metadata_2025_split huggingface dataset:
An investigation of seawater and sediment depth using a prototype airborne electromagnetic instrumentation system – a case study in Broken Bay, Australia
Authors: Vrbancich Julian 
Published: December 2008

ABSTRACTPrevious studies using commercial airborne electromagnetic equipment that is not optimized for marine surveying have demonstrated the use of airborne electromagnetic methods for measuring water depth and estimating sediment thickness. A new prototype helicopter time‐domain airborne electromagnetic system, SeaTEM(0), is now under development for bathymetric surveying. The first sea trial of the SeaTEM(0) system took place over Broken Bay, New South Wales, Australia, in shallow water up to ∼30 m in depth. Broken Bay was chosen because the separate paleodrainage systems for the Hawkesbury River, Brisbane Water and Pittwater, which join in Broken Bay give rise to paleovalleys infilled with unconsolidated sediments, ranging in thickness between 0 m (bedrock outcrop) and ∼200 m. The survey area also included a tombolo with a beach either side, which provided the opportunity to measure water depth through a surf zone. Sediment thickness and water depth is predicted from stitched layered‐earth inversion of data based on a simplified two‐layer model that represents seawater and sediment overlying a resistive half‐space basement (bedrock). The resulting bathymetric profiles show agreement typically to within ∼±1 m and ∼±0.5 m with known water depths in areas less than 20 and 6 m deep respectively. The inverted depth profile of the second (sediment) layer is noisy; however, the profiles reveal coarse topographic features of paleovalleys to depth limits of ∼60 to 80 m below sea level in 20 to 30 m water depth, as well as resolving bedrock ridges and exposed reefs in shallow waters.
Cytolytic mechanisms and T‐cell receptor Vβ usage by ex vivo generated Epstein–Barr virus‐specific cytotoxic T lymphocytes
Authors: Vanhoutte Victoria J. , McAulay Karen A. , McCarrell Erin , Turner Marc , Crawford Dorothy H. , Haque Tanzina 
Published: December 2008

Summary Ex‐vivo‐generated Epstein–Barr virus (EBV)‐specific cytotoxic T lymphocytes (CTL) have been used for cellular adoptive immunotherapy of EBV‐associated lymphomas. Here we investigated the phenotypes, cytolytic mechanisms, polyfunctionality and T‐cell receptor (TCR) usage in growing and established CTL, generated by weekly stimulation with an EBV‐transformed autologous lymphoblastoid cell line (LCL). Our results showed that phenotypically mature CTL developed within the first 4 weeks of culture, with an increase in CD45RO and CD69, and a decrease in CD45RA, CD62L, CD27 and CD28 expression. Spectratyping analysis of the variable β‐chain of the TCR revealed that TCR repertoire remained diverse during the course of culture. Cytotoxicity of CTL was significantly inhibited by concanamycin A (P < 0·0001) and ethylene glycol‐bis tetraacetic acid (P < 0·0001), indicating that a calcium and perforin‐mediated exocytosis pathway with the release of granzyme B was the principal cytotoxic mechanism. The CTL mainly produced interferon‐γ (IFN‐γ) or tumour necrosis factor‐α (TNF‐α) upon restimulation with autologous LCL, although there were some polyfunctional cells producing IFN‐γ and TNF‐α. Granzyme B, perforin and Fas ligand were detected in CD8+ and CD4+ cells in all CTL; however, a greater proportion of CD8+ than CD4+ T cells expressed granzyme B (P < 0·0001) and more granzyme B was detected in CD8+ T cells than in CD4+ T cells (P = 0·001). This difference was not observed with Fas ligand or perforin expression. Our results provide insight into the basic characteristics of ex‐vivo‐generated CTL.
Do all stoneflies nymphs have respiratory proteins? Further data on the presence of hemocyanin in the larval stages of plecoptera species
Authors: Amore V. , Belardinelli M. , Guerra L. , Buonocore F. , Fausto A. M. , Ubero‐Pascal N. , Fochetti R. 
Published: December 2008

AbstractContrary to what was assumed regarding the presence of respiratory proteins in insects, a functional hemocyanin was recently found in larvae and adults of the stoneflies species Perla marginata, whereas in the close species Perla grandis, hemocyanin functionality was deduced from sequence data. In order to verify if the presence of this ancient trait is widespread within the order and to investigate why stoneflies have maintained it, we have extended the search for hemocyanin to species of other Plecoptera families. In particular, we assessed the presence of hemocyanin in the larval stage of nine Plecoptera species, belonging to six of the seven families of the European stonefly‐fauna, and analyzed its potential functionality as deduced by sequence data. We cloned and sequenced the corresponding cDNAs and studied their expression with RT‐PCR technique. Moreover, we performed homology studies using the deduced amino acid sequences. On the basis of our analysis, we hypothesized a functional role of the hemocyanin only for two species: Dinocras cephalotes and Isoperla grammatica (Perloidea). In all the investigated Nemouroidea and in Siphonoperla torrentium (Perloidea), this protein may have been lost. Larval size, life‐cycle length, trophic role and environmental induction are discussed as possible explanations of these different physiological requirements.
Surviving glacial ages within the Biotic Gap: phylogeography of the New Zealand cicada Maoricicada campbelli
Authors: Hill Kathy B. R. , Simon Chris , Marshall David C. , Chambers Geoffrey K. 
Published: December 2008

AbstractAim  New Zealand is an ideal location in which to investigate the roles of landscape and climate change on speciation and biogeography. An earlier study of the widespread endemic cicada Maoricicada campbelli (Myers) found two phylogeographically distinguishable major clades – northern South Island plus North Island (northern‐SI + NI) and Otago. These two clades appeared to have diverged on either side of an area of the South Island known as the Biotic Gap. We sampled more intensively to test competing theories for this divergence. We aimed to discover if M. campbelli had survived within the Biotic Gap during recent glacial maxima, and if predicted areas of secondary contact between the two major clades existed.Location  New Zealand.Methods  We analysed mitochondrial DNA sequences (1520 bp; 212 individuals; 91 populations) using phylogenetic (maximum likelihood, Bayesian), population genetic (analysis of molecular variance) and molecular dating methods (Bayesian relaxed clock with improved priors).Results  We found strong geographical structuring of genetic variation. Our dating analyses suggest that M. campbelli originated 1.83–2.58 Ma, and split into the two major clades 1.45–2.09 Ma. The main subclades in the northern‐SI + NI clade arose almost simultaneously at 0.69–1.03 Ma. Most subclades are supported by long internal branches and began to diversify 0.40–0.78 Ma. We found four narrow areas of secondary contact between the two major clades. We also found a difference between calling songs of the Otago vs. northern‐SI + NI clades.Main conclusions  Phylogeographical patterns within M. campbelli indicate an early Pleistocene split into two major clades, followed by late Pleistocene range expansion and in situ population differentiation of subclades. The northern‐SI + NI clade diversified so rapidly that the main subclade relationships cannot be resolved, and we now have little evidence for a disjunction across the Biotic Gap. Structure within the main subclades indicates rapid divergence after a common bottlenecking event, perhaps attributable to an extremely cold glacial maximum at c. 0.43 Ma. Clade structure and dating analyses indicate that M. campbelli survived in many refugia during recent glacial maxima, including within the Biotic Gap. The narrow overlap between the two major clades is attributed to recent contact during the current interglacial and slow gene diffusion. The two major clades appear to be in the early stages of speciation based on genetic and behavioural differences.
Clusterings should not be compared by visual inspection: response to Gagné & Proulx
Authors: Heikinheimo H. , Fortelius M. , Eronen J. , Mannila H. 
Published: December 2008

AbstractIn Heikinheimo et al. (Journal of Biogeography, 2007, 34, 1053–1064) we used clustering to analyse European land mammal fauna. Gagné & Proulx criticized our choice of the Euclidean distance measure in the analysis, and advocated the use of the Hellinger distance measure, claiming that this leads to very different clustering results. The criticism fails to take into account the probabilistic nature of the methods used and the fact that in this case the similarity measures correlate strongly. Gagné & Proulx used subjective inspection as the criterion of similarity between clusterings. We show that this is insufficient and misleading. Namely, owing to the local minimum problem, two clustering runs rarely give identical results. In the case of our study, the measured similarity (using the kappa statistic) between the Euclidean‐ and Hellinger‐based clusterings is roughly equal to the similarity between two clusterings that both use the Hellinger distance but different random initialization points.
Ezetimibe monotherapy for cholesterol lowering in 2,722 people: systematic review and meta‐analysis of randomized controlled trials
Authors: Pandor A. , Ara R. M. , Tumur I. , Wilkinson A. J. , Paisley S. , Duenas A. , Durrington P. N. , Chilcott J. 
Published: December 2008

Abstract.Objectives.  To study the evidence on the efficacy and safety of ezetimibe monotherapy for the treatment of primary (heterozygous familial and non‐familial) hypercholesterolaemia.Design.  Systematic review and meta‐analysis of randomized controlled trials (RCTs).Methods.  Eleven electronic bibliographic databases covering the biomedical, scientific and grey literature were searched from inception and supplemented by contact with experts in the field. Two reviewers independently determined the eligibility of RCTs, with a minimum treatment duration of 12 weeks, which compared ezetimibe monotherapy (10 mg per day) with placebo.Results.  In the absence of data from clinical outcome trials, surrogate endpoints such as changes in lipid concentrations were used as indicators of clinical outcomes. A meta‐analysis of eight randomized, double‐blind, placebo‐controlled trials (all 12 weeks) showed that ezetimibe monotherapy was associated with a statistically significant mean reduction in LDL cholesterol (from baseline to endpoint) of −18.58%, (95% CI: −19.67 to −17.48, P < 0.00001) compared with placebo. Significant (P < 0.00001) changes were also found in total cholesterol (−13.46%, 95% CI: −14.22 to −12.70), HDL cholesterol (3.00%, 95% CI: 2.06–3.94) and triglyceride levels (−8.06%, 95% CI: −10.92 to −5.20). Ezetimibe monotherapy appeared to be well tolerated with a safety profile similar to placebo.Conclusions.  In a meta‐analysis restricted to short‐term trials in hypercholesterolaemia, significant potentially favourable changes in lipid and lipoprotein levels relative to baseline occurred with ezetimibe monotherapy. Further long‐term studies with cardiovascular and other clinical outcome data are needed to assess the efficacy and safety of ezetimibe more fully.
Genetic diversity and differentiation processes in the ploidy series of Olea europaea L.: a multiscale approach from subspecies to insular populations
Authors: GARCÍA‐VERDUGO C. , FAY M. F. , GRANADO‐YELA C. , DE CASAS R. RUBIO , BALAGUER L. , BESNARD G. , VARGAS P. 
Published: December 2008

AbstractGeographical isolation and polyploidization are central concepts in plant evolution. The hierarchical organization of archipelagos in this study provides a framework for testing the evolutionary consequences for polyploid taxa and populations occurring in isolation. Using amplified fragment length polymorphism and simple sequence repeat markers, we determined the genetic diversity and differentiation patterns at three levels of geographical isolation in Olea europaea: mainland‐archipelagos, islands within an archipelago, and populations within an island. At the subspecies scale, the hexaploid ssp. maroccana (southwest Morocco) exhibited higher genetic diversity than the insular counterparts. In contrast, the tetraploid ssp. cerasiformis (Madeira) displayed values similar to those obtained for the diploid ssp. guanchica (Canary Islands). Geographical isolation was associated with a high genetic differentiation at this scale. In the Canarian archipelago, the stepping‐stone model of differentiation suggested in a previous study was partially supported. Within the western lineage, an east‐to‐west differentiation pattern was confirmed. Conversely, the easternmost populations were more related to the mainland ssp. europaea than to the western guanchica lineage. Genetic diversity across the Canarian archipelago was significantly correlated with the date of the last volcanic activity in the area/island where each population occurs. At the island scale, this pattern was not confirmed in older islands (Tenerife and Madeira), where populations were genetically homogeneous. In contrast, founder effects resulted in low genetic diversity and marked genetic differentiation among populations of the youngest island, La Palma.
Parts exchange: tuning the flagellar motor to fit the conditions
Authors: Delalez Nicolas , Armitage Judith P. 
Published: December 2008

SummaryMany cellular activities are driven by complex protein machines. By measuring the behaviour of fluorescent protein fusions in real time in living cells it has become apparent that many of these complexes are not fixed, but are dynamic. To some extent this might be expected, for example, for cell division complexes, as defining mid‐cell is linked to growth and cell cycle, but perhaps comes as more of a surprise with a complex anchored machine like the bacterial flagellar motor. The assumption has been that once made it remains intact. However, the dynamics of this structure is strongly supported in two manuscripts in this issue of Molecular Microbiology. The stator units which form a peptioglycan anchored ring around the rotor, generating torque in response to the ion motive force, clearly disengage when conditions change. The driving ion is shown to be important in both engagement of the stator to the rotor and the selection of the type of stator unit. These new results provide an insight into the mechanisms underlying motor function, which might rely on dynamic processes, and clearly illustrate the need to move away from a static view of cellular structures.
Production, characterization and determination of the real catalytic properties of the putative ‘succinate dehydrogenase’ from Wolinella succinogenes
Authors: Juhnke Hanno D. , Hiltscher Heiko , Nasiri Hamid R. , Schwalbe Harald , Lancaster C. Roy D. 
Published: December 2008

SummaryBoth the genomes of the epsilonproteobacteria Wolinella succinogenes and Campylobacter jejuni contain operons (sdhABE) that encode for so far uncharacterized enzyme complexes annotated as ‘non‐classical’ succinate:quinone reductases (SQRs). However, the role of such an enzyme ostensibly involved in aerobic respiration in an anaerobic organism such as W. succinogenes has hitherto been unknown. We have established the first genetic system for the manipulation and production of a member of the non‐classical succinate:quinone oxidoreductase family. Biochemical characterization of the W. succinogenes enzyme reveals that the putative SQR is in fact a novel methylmenaquinol:fumarate reductase (MFR) with no detectable succinate oxidation activity, clearly indicative of its involvement in anaerobic metabolism. We demonstrate that the hydrophilic subunits of the MFR complex are, in contrast to all other previously characterized members of the superfamily, exported into the periplasm via the twin‐arginine translocation (tat)‐pathway. Furthermore we show that a single amino acid exchange (Ala86→His) in the flavoprotein of that enzyme complex is the only additional requirement for the covalent binding of the otherwise non‐covalently bound FAD. Our results provide an explanation for the previously published puzzling observation that the C. jejuni sdhABE operon is upregulated in an oxygen‐limited environment as compared with microaerophilic laboratory conditions.
Highly Arthritis‐susceptible DA Rats Express IL‐1β in Articular Cartilage
Authors: Weiss R. J. , Erlandsson Harris H. , Palmblad K. 
Published: December 2008

AbstractThere are genetically determined differences in susceptibility to arthritis among inbred rat strains. The aim of the present study was to elucidate phenotypical differences, by determining expression of TNF and IL‐1β, two pivotal mediators of arthritis, in the highly arthritis‐prone Dark Agouti (DA) rat compared to that of two arthritis‐resistant rat strains, the major histocompatibility complex‐homologous Piebald‐Viral‐Glaxo (PVG.1AV1) rat and the Brown Norway (BN) rat, assessed by immunohistochemistry. We demonstrate a distinct difference in articular cartilage, with chondrocytes expressing IL‐1β, not TNF, in the highly arthritis‐prone DA rat as opposed to the two arthritis‐resistant BN or PVG.1AV1 rat strains, where no cytokine expression was documented. The results were otherwise congruent among the rat strains. We observed TNF‐ and IL‐1β‐expressing cells within the synovial lining layer in all rat strains. Other tissues studied, auricular cartilage as well as muscle, lung, thyroid gland and kidney tissue, were devoid of cytokine expression. Constitutional expression of IL‐1β in chondrocytes might facilitate initiation and perpetuation of inflammation. This may offer one explanation of why erosive arthritides are so easily induced in the DA rat and also support the hypothesis that articular chondrocytes may themselves play a major role in cartilage matrix degradation.
Relationship between Circulating Levels of IFN‐γ, IL‐10, CXCL9 and CCL2 in Pulmonary and Extrapulmonary Tuberculosis is Dependent on Disease Severity
Authors: Hasan Z. , Jamil B. , Khan J. , Ali R. , Khan M. A. , Nasir N. , Yusuf M. S. , Jamil S. , Irfan M. , Hussain R. 
Published: December 2008

AbstractProtection against Mycobacterium tuberculosis infection is dependent on T cell and macrophage activation regulated by cytokines. Cytokines and chemokines produced at disease sites may be released into circulation. Data available on circulating cytokines in tuberculosis (TB) is mostly on pulmonary TB (PTB) with limited information on extrapulmonary disease (EPul‐TB). We measured interferon‐gamma (IFN‐γ), interkeukin‐10 (IL‐10), CXCL9 and CCL2 in sera of patients (n = 80) including; PTB (n = 42), EPul‐TB (n = 38) and BCG vaccinated healthy endemic controls (EC, n = 42). EPul‐TB patients comprised those with less severe (LNTB) or severe (SevTB) disease. Serum IFN‐γ, IL‐10 and CXCL9 levels were significantly greater while CCL2 was reduced in TB patients as compared with EC. IFN‐γ was significantly greater in PTB as compared with LNTB (P = 0.002) and SevTB (P = 0.029). CXCL9 was greater in PTB as compared with LNTB (P = 0.009). In contrast, CCL2 levels were reduced in PTB as compared with LNTB (P = 0.021) and SevTB (P = 0.024). A Spearman’s rank correlation analysis determined a positive association between IFN‐γ and IL‐10 (rho = 0.473, P = 0.002) and IFN‐γ and CXCL9 (rho = 0.403, P = 0.008) in the PTB group. However, in SevTB, only IFN‐γ and CXCL9 were positively associated (rho = 0.529, P = 0.016). Systemic levels of cytokines are reflective of local responses at disease sites. Therefore, our data suggests that in PTB increased IFN‐γ and CXCL9 balanced by IL‐10 may result in a more effective cell mediated response in the host. However, elevated inflammatory chemokines CXCL9 and CCL2 in severe EPul‐TB without concomitant down modulatory cytokines may exacerbate disease related pathology and hamper restriction of M. tuberculosis infection.
Effect of an Extract Based on the Medicinal Mushroom Agaricus blazei Murill on Release of Cytokines, Chemokines and Leukocyte Growth Factors in Human Blood Ex Vivo and In Vivo
Authors: Johnson E. , Førland D. T. , Sætre L. , Bernardshaw S. V. , Lyberg T. , Hetland G. 
Published: December 2008

AbstractAn immunostimulatory extract based on the medicinal mushroom Agaricus blazei Murill (AbM) has been shown to stimulate mononuclear phagocytes in vitro to produce pro‐inflammatory cytokines, and to protect against lethal peritonitis in mice. The present aim was to study the effect of AbM on release of several cytokines in human whole blood both after stimulation ex vivo and in vivo after oral intake over several days in healthy volunteers. The 17 signal substances examined were; T helper 1 (Th1) cytokines [interleukin (IL)‐2, interferon (IFN)‐γ and IL‐12], T helper 2 cytokines (IL‐4, IL‐5 and IL‐13), pleiotropic (IL‐7, IL‐17), pro‐inflammatory [IL‐1β, IL‐6, tumour necrosis factor (TNF)‐α (mainly produced by Th1 cells)] – and anti‐inflammatory (IL‐10) cytokines, chemokines [IL‐8, macrophage inhibitory protein (MIP)‐1β and monocyte chemoattractant protein (MCP)‐1] and leukocyte growth factors [granulocyte colony‐stimulating factor (G‐CSF), granulocyte/macrophage colony stimulating factor]. After stimulation of whole blood ex vivo with 0.5–5.0% of a mushroom extract, AndoSan™ mainly containing AbM, there was a dose‐dependent increase in all the cytokines studied, ranging from two to 399‐fold (TNF‐α). However, in vivo in the eight volunteers who completed the daily intake (60 ml) of this AbM extract for 12 days, a significant reduction was observed in levels of IL‐1β (97%), TNF‐α (84%), IL‐17 (50%) and IL‐2 (46%). Although not significant, there was a trend towards reduced levels for IL‐8, IFN‐γ and G‐CSF, whilst those of the remaining nine cytokines tested, were unaltered. The discrepant results on cytokine release ex vivo and in vivo may partly be explained by the antioxidant activity of AbM in vivo and limited absorption of its large, complex and bioactive β‐glucans across the intestinal mucosa to the reticuloendothelial system and blood.
Natural Immunity has Significant Impact on Immune Responses Against Cancer
Authors: Rubin B. 
Published: December 2008

AbstractThe immune system defends the host against pathogenic attacks by micro‐organisms and their products. It does not react against self‐components due to the relatively efficient negative selection of developing T lymphocytes in the thymus. This process does permit T cells with low avidity against self to be present in the T cell repertoire. Such cells play an important physiological role as the host needs so‐called autoimmune reactions in order to eliminate dying cells or transformed tumour cells. One of the mysteries in immunology is how the host maintains beneficial autoimmune reactions and avoids pathogenic autoimmune reactions. Activation of the adaptive T lymphocytes is mediated by the low avidity interaction between T‐cell antigen receptors and antigenic peptides associated with major histocompatibility complex class I or class II molecules. This interaction is strengthened by T‐cell co‐receptors such as CD2, CD4, CD8, CD28 and CD154, which react with ligands expressed by cells of the innate immune system. In recent years, the importance of pre‐activation of the innate immune system for initiation of adaptive T‐cell immune responses has been appreciated. In the present review, I will summarize our work on how natural immunity plays an important role in determining the level of beneficial autoimmune reactions against cancer.