bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calculating SPR distances between trees
Authors: Goloboff Pablo A. 
Published: November 2007

AbstractThe SPR distance between two trees is the minimum number of SPR moves required to convert one tree into the other. It has been proven as an NP‐complete problem. A heuristic to calculate SPR distances between trees is described. It performs favorably when compared with other existing heuristics, RIATA‐HGT and EEEP. Compared with RIATA‐HGT, the new method tends to produce better estimations when the trees are relatively similar, and worse estimations when the trees are very different (e.g., random trees); it produces results rather similar to those of EEEP, but orders of magnitude faster. A measure of tree‐similarity based on SPR distances is proposed, obtained by calculating the minimum number of weighted SPR moves (with moves to closer nodes being less costly). The resulting measure of similarity is symmetric (i.e., Dij = Dji, for any two trees i,j).© The Willi Hennig Society 2007.
Home range size, spatial distribution and habitat use of elephants in two enclosed game reserves in the Eastern Cape Province, South Africa
Authors: Roux C. , Bernard R. T. F. 
Published: November 2007

AbstractWe studied space use and habitat selection by elephants in two enclosed reserves in the Eastern Cape Province (South Africa) that conserve components of the regionally important and poorly conserved Thicket Biome. Home ranges of bulls and herds occupied most of the reserves, and core areas were significantly smaller and centred on permanent water. There was no significant difference in home range size of bulls and herds and both were significantly smaller in winter than summer. Components of the Thicket Biome occurred in the home ranges and core areas of all elephants where it was either used according to its abundance or avoided. However, this should not be interpreted as indicating that elephants will not affect plants of the Thicket Biome since change will be cumulative and monitoring should be ongoing to ensure the conservation of this regionally important Biome.
Family studies in chronic lymphocytic leukaemia and other lymphoproliferative tumours
Authors: Goldin Lynn R. , Caporaso Neil E. 
Published: November 2007

SummaryFamilies with multiple individuals affected with chronic lymphocytic leukaemia (CLL) and other related B‐cell tumours have been described in the literature. Familial CLL does not appear to differ from sporadic CLL in terms of prognostic markers and clinical outcome. Large, population‐based case–control and cohort studies have also shown significant familial aggregation of CLL and related conditions, including non‐Hodgkin and Hodgkin lymphoma. Monoclonal B‐cell lymphocytosis also aggregates in CLL families. However, the clinical implication of familial aggregation is minimal given the overall rarity of CLL. Linkage studies have been conducted in high‐risk CLL families to screen the whole genome for loci that contribute to susceptibility but no gene mutations have yet been identified by this method. Association studies of candidate genes have implicated immune function and other genes but more studies are needed to verify these findings. The ability to conduct large scale genomic studies will play an important role in detecting susceptibility genes for CLL over the next few years and thereby help to delineate aetiological pathways.
Chronic lymphocytic leukaemia: an overview of aetiology in light of recent developments in classification and pathogenesis
Authors: Linet Martha S. , Schubauer‐Berigan Mary K. , Weisenburger Dennis D. , Richardson David B. , Landgren Ola , Blair Aaron , Silver Sharon , Field R. William , Caldwell Glyn , Hatch Maureen , Dores Graça M. 
Published: November 2007

SummaryThis overview of the epidemiology of chronic lymphocytic leukaemia (CLL) summarizes the evolution of classification and coding systems and describes the intersection of pathogenesis and aetiology. The role of the putative precursor to CLL, monoclonal B‐cell lymphocytosis (MBL), is considered, and ideas for future investigations of the MBL‐CLL relationship are outlined. We discuss the epidemiology of CLL, focusing on descriptive patterns and methodological considerations. Postulated risk factors are reviewed including the role of ionizing and non‐ionizing radiation, occupational and environmental chemical exposures, medical conditions and treatments, and lifestyle and genetic factors. We conclude by raising key questions that need to be addressed to advance our understanding of CLL aetiology. Recommendations for future epidemiological studies are given, including the standardization of reporting of CLL across cancer registries, the clarification of the natural history of MBL, and the circumvention of the methodological shortcomings of prior epidemiological investigations in relation to radiation, chemical exposures and infectious agents.
Overview of monoclonal gammopathies of undetermined significance
Authors: Vogt Robert F. , Marti Gerald E. 
Published: November 2007

SummaryAmong the B‐cell lymphoproliferative disorders, monoclonal gammopathy of undetermined significance (MGUS) is the humoral counterpart to monoclonal B‐cell lymphocytosis. This review introduces the papers from the section devoted to MGUS at the International Workshop entitled ‘Monoclonal B‐cell lymphocytosis and chronic lymphocytic leukaemia: environmental and genetic risk factors.’
Monoclonal B‐cell lymphocytosis as a biomarker in environmental health studies
Authors: Vogt Robert F. , Shim Youn K. , Middleton Dannie C. , Buffler Patricia A. , Campolucci Sharon S. , Lybarger Jeffrey A. , Marti Gerald E. 
Published: November 2007

SummaryThe first studies of monoclonal B‐cell lymphocytosis (MBL) in the general population were conducted as part of environmental health investigations that began in 1991. MBL was observed as an unexpected finding when blood samples were immunophenotyped by two‐colour flow cytometric methods in common use at that time. The initial observations led to a workshop in 1995, at which case definitions were considered and medical follow‐up investigations were recommended. Medical follow‐ups were conducted in 1997 and 2003. A total of eight cases of confirmed MBL and three cases of presumptive MBL were identified. This review summarizes the findings from those investigations and discusses the issues related to using MBL as a biomarker in environmental health research and population‐based studies.
Multiple myeloma, chronic lymphocytic leukaemia and associated precursor diseases
Authors: Landgren Ola , Kyle Robert A. 
Published: November 2007

SummaryMultiple myeloma and chronic lymphocytic leukaemia share common biological and clinical features including the presence of defined precursor conditions (monoclonal gammopathy of undetermined significance and monoclonal B‐cell lymphocytosis respectively). Here, we discuss evidence from the literature on the potential aetiological roles for genetic and chronic immune stimulatory factors on the pathway from precursor to malignancy. Also, we speculate on the relationship between precursor and malignancy and talk about future directions and gaps in the literature.
MicroRNAs in the pathogeny of chronic lymphocytic leukaemia
Authors: Nicoloso Milena S. , Kipps Thomas J. , Croce Carlo M. , Calin George A. 
Published: November 2007

SummaryMicroRNAs (miRNAs) have been linked to the initiation and progression of chronic lymphocytic leukaemia (CLL). The main molecular alterations are represented by variations in gene expression, usually mild and with consequences for a vast number of target protein‐coding genes. Recent studies have shown that miRNAs are the main candidates for the elusive class of CLL predisposing genes. These discoveries could be exploited for the development of useful markers for diagnosis and prognosis, as well as for the development of new RNA‐based cancer therapies.
Susceptibility genes and B‐chronic lymphocytic leukaemia
Authors: Slager Susan L. , Kay Neil E. , Fredericksen Zachary S. , Wang Alice H. , Liebow Mark , Cunningham Julie M. , Vachon Celine M. , Call Timothy G. , Cerhan James R. 
Published: November 2007

SummaryCommon genetic variants are thought to increase the risk of chronic lymphocytic leukaemia (CLL), and case–control studies provide an approach to detect these variants. There have been multiple candidate gene studies published to date, but relatively few disease pathway studies or large genomic association studies. We summarize the results of these previous studies, as well as present results from our recent large pathway study of 9412 single nucleotide polymorphisms from 1253 immunity and inflammation genes in a study of 126 CLL cases and 484 frequency‐matched controls. Several promising genes have been identified as susceptibility genes for risk of CLL across all of these association studies. However, a number of candidate gene studies have not been replicated in follow‐up studies, whereas the results from disease pathway and large genomic studies have yet to be replicated in an independent sample. The challenge of future studies of this type will be overcoming study design issues, including definition of CLL, sample size limitations and multiple testing issues.
Investigation of the interleukin (IL)‐4/IL‐4 receptor system in promyelocytic leukaemia PLB‐985 cells during differentiation toward neutrophil‐like phenotype: mechanism involved in IL‐4‐induced SOCS3 protein expression
Authors: Ratthé Claude , Girard Denis 
Published: November 2007

SummaryThe interleukin 4 (IL‐4)/IL‐4 receptor (IL‐4R) system in promyelocytes is not well documented. Here, we used promyelocytic leukaemia PLB‐985 cells differentiated with dimethylsulfoxide (PLB‐985D) toward neutrophil‐like phenotype to investigate the IL‐4/IL‐4R system. PLB‐985 cells did not express CD132 (γc) but expressed the complete IL‐4 type II receptor (IL‐4Rα and IL‐13Rα1). Moreover, PLB‐985 cells lost surface expression of IL‐13Rα1 during differentiation, resulting in PLB‐985D cells expressing only IL‐4Rα fully responsive to IL‐4, as judged by activation of mitogen‐activated protein (MAP) kinases and Janus kinase 1. IL‐4 also increased suppressor of cytokine signalling 3 (SOCS3) protein level in the presence of the proteasome inhibitor MG132 exclusively in PLB‐985D cells. As the IL‐4Rα chain has been associated with a component of the phagocyte NADPH oxidase, we used PLB‐985‐gp91phox deficient cells (mimicking chronic granulomatous disease, X‐CGD), to investigate the IL‐4/IL‐4R system in X‐CGD‐D cells. IL‐4 was found to activate MAP kinases in X‐CGD‐D cells but did not up‐regulate SOCS3, in contrast to granulocyte colony‐stimulating factor, granulocyte‐macrophage colony‐stimulating factor and IL‐6. Utilization of catalase, cycloheximide and genistein inhibitors showed that IL‐4 induced SOCS3 by a mechanism dependent on a complete NADPH oxidase complex, protein synthesis and tyrosine phosphorylation, but independent of production of reactive oxygen species. We conclude that IL‐4 induces cell signalling in promyelocytes expressing only IL‐4Rα.
Differential effects of BMP‐2 and TGF‐β1 on chondrogenic differentiation of adipose derived stem cells
Authors: Mehlhorn A. T. , Niemeyer P. , Kaschte K. , Muller L. , Finkenzeller G. , Hartl D. , Sudkamp N. P. , Schmal H. 
Published: November 2007

Abstract.  Objectives: This article addresses the interaction of transforming growth factor β1 (TGF‐β1) and bone morphogenic protein 2 (BMP‐2) during osteo‐chondrogenic differentiation of adipose‐derived adult stem cells (ASC). TGF‐β1 was expected to modulate the BMP‐2‐induced effects through transcriptional regulation of Dlx‐5, Msx‐2 and Runx‐2. Materials and Methods: Encapsulated ASC were cultured for 14 days in medium containing TGF‐β1 and/or BMP‐2. mRNA expression of the extracellular matrix molecules col2a1, cartilage oligomeric matrix protein, col10a1, alkaline phosphatase (AP) and transcription factors Msx‐2, Dlx‐5 and Runx‐2 was analysed. Release of glycosaminoglycans, collagen types II and X into the extracellular matrix was demonstrated. Results: BMP‐2 and TGF‐β1 induced a chondrogenic phenotype in ASC. Combined growth factor treatment had a synergistic effect on col10a1 and an additive effect on col2a1 mRNA expression. Synthesis of glycosaminoglycans was enhanced by combined growth factor treatment. Addition of TGF‐β1 inhibited BMP‐2 induced AP expression and activity and both proteins promoted chondrogenic maturation. Conclusions: Prevention of BMP‐2‐induced osteogenic transdifferentiation by TGF‐β1 seemed not to be mediated by transcriptional regulation of Dlx‐5. Due to these findings, simultaneous stimulation of ASC with BMP‐2 and TGF‐β1 seemed to be beneficial for complete differentiation of ASC into chondrocytes.
The linkage between riparian predators and aquatic insects across a stream‐resource spectrum
Authors: BURDON FRANCIS J. , HARDING JON S. 
Published: November 2007

Summary1. Spatial subsidies, defined as the flow of energy, nutrients, organisms or pollutants from one habitat to another, have been shown to affect the food–web dynamics in a wide range of ecosystems. An important subsidy to riparian communities is the contribution of adult stream insects to terrestrial predators such as birds, bats and lizards, but also invertebrates including ground and web‐building spiders.2. We surveyed 37 first‐ and second‐order forest streams across differing environmental gradients in the Central South Island, New Zealand, to investigate the relationship between potential aquatic prey subsidies and predatory riparian arachnids. We anticipated that stream‐insect biomass would be positively associated with riparian arachnids, as a result of emergent adult aquatic insect subsidies to the adjacent habitat.3. We confirmed positive associations between stream‐insect biomass as a predictor variable and riparian arachnid biomass (R2 = 0.42, F1,34 = 25.2, P < 0.001) and web densities (R2 = 0.45, F1,14 = 11.5, P < 0.01) respectively as dependent variables after adjusting for the confounding effects of environmental variables. Hierarchical partitioning confirmed the importance of stream insect biomass as a statistically significant contributor to the total explained variance in analyses calculated for arachnid biomass, abundance and web density.4. A concurrent survey of spider‐web density along 20‐m transects from the stream edge into the forest indicated a strong decline in web‐building spider density moving away from the stream (R2 = 0.41, F1,158 = 109, P < 0.001), with stream‐insect biomass as a significant covariate (F1,149 = 17.7, P < 0.001).5. Our results suggest that productivity gradients present in the donor system affect the magnitude of the interaction between adjacent habitats. Productivity gradients may lead to increased reciprocal subsidies through a positive feedback loop involving the predation of spiders and other predatory terrestrial invertebrates by aquatic predators. However, terrestrial insectivores such as birds, bats and lizards that are not readily used as prey by aquatic predators may circumvent the feedback cycle by consuming a large proportion of emergent aquatic‐insect biomass. This may lead to asymmetry in the strength of food–web linkages between aquatic and terrestrial habitats.
Influence of aquatic macrophyte habitat complexity on invertebrate abundance and richness in tropical lagoons
Authors: THOMAZ SIDINEI M. , DIBBLE ERIC D. , EVANGELISTA LUIZ R. , HIGUTI JANET , BINI LUIS M. 
Published: November 2007

Summary1. Aquatic plants are a key component of spatial heterogeneity in a waterscape, contributing to habitat complexity and helping determine diversity at various spatial scales. Theoretically, the more complex a habitat, the higher the number of species present.2. Few empirical data are available to test the hypothesis that complexity increases diversity in aquatic communities (e.g. Jeffries, 1993). Fractal dimension has become widely applied in ecology as a tool to quantify the degree of complexity at different scales.3. We investigated the hypothesis that complexity in vegetated habitat in two tropical lagoons mediates littoral invertebrate number of taxa (S) and density (N). Aquatic macrophyte habitat complexity was defined using a fractal dimension and a gradient of natural plant complexities. We also considered plant area, plant identity and, only for S, invertebrate density as additional explanatory variables.4. Our results indicate that habitat complexity provided by the different architectures of aquatic plants, significantly affects both S and total N. However, number of individuals (as a result of passive sampling) also helps to account for S and, together with plant identity and area, contributes to the determination of N. We suggest that measurements of structural complexity, measured through fractal geometry, should be included in studies aimed at explaining attributes of attached invertebrates at small (e.g. plant or leaf) scales.
Assessing mate size in the red swamp crayfish Procambarus clarkii: effects of visual versus chemical stimuli
Authors: AQUILONI LAURA , GHERARDI FRANCESCA 
Published: November 2007

Summary1. Mate assessment requires an efficient system of information exchange between the sexes and often relies on several forms of communication. Both sexes of the crayfish, Procambarus clarkii, select a mate on the basis of its body size, independently of chelar size/symmetry and dominance status, large size being a proxy for a high quality partner. Here, we explored the effects that visual and chemical stimuli, emitted alone or in combination, exert on the assessment of size of a potential mate.2. We followed a binary choice test paradigm, in which two male or female ‘targets’, of either large or small size, were simultaneously presented to a female or a male ‘chooser’. We recorded the first target visited, the total duration of the visits per target, and the behaviour of the chooser when approaching the target area.3. Our results show that females require a combination of visual and chemical stimuli to select the larger male. A more complex pattern was found when males were the choosers. While visual and chemical cues together rendered them willing to mate with the larger female, their initial choice and the total time spent near her depended only on smell. In mate assessment by P. clarkii, visual and chemical information seem to act as ‘non‐redundant signals’.
P‐ and S‐wave velocities of consolidated sediments from a seafloor seismic survey in the North Celtic Sea Basin, offshore Ireland
Authors: Shillington Donna J. , Minshull Timothy A. , Peirce Christine , O'Sullivan John M. 
Published: November 2007

ABSTRACTA geophysical survey was conducted over a hydrocarbon prospect in the North Celtic Sea Basin using a small array of ocean‐bottom seismographs (OBSs). The purpose of this study was to determine the ratio of compressional (P)‐ to shear (S)‐wave velocity of consolidated sedimentary rocks in order to constrain possible subsurface variations in pore‐fluid content. The ratio of VP and VS is known to be particularly sensitive to lithology, porosity and pore‐fluid content, making it a useful parameter for evaluating hydrocarbon prospects. OBSs offer a relatively cheap and time‐effective means of acquiring multi‐component data compared with ocean‐bottom cables. In this contribution, we demonstrate the ability of an OBS survey comprising three pairs of two OBSs spaced at 1.6 km to recover lateral variations in the VP/VS ratio. A key requirement of this type of study is that S waves will be generated by mode conversions in the subsurface, since they cannot be generated in nor travel through fluids. In this survey, the contrast in physical properties of the hard seabed of the North Celtic Sea Basin provided a means of generating converted S waves. Two‐dimensional ray‐tracing and forward modelling was used to create both VP and VS models along a profile crossing the Blackrock prospect in the North Celtic Sea Basin. These models comprise four layers and extend to a maximum depth of 1.1 km. The observed northward decrease in the VP/VS ratio at depths of 500–1000 m below the seafloor in the study area is interpreted to represent lateral variation in the amount of gas present in the pore space of Upper Cretaceous chalks and shales overlying the prospective reservoir.
Modulation of diabetes in NOD mice by GAD65‐specific monoclonal antibodies is epitope specific and accompanied by anti‐idiotypic antibodies
Authors: Hall Tyler R. , Bogdani Marika , LeBoeuf Renee C. , Kirk Elizabeth A. , Maziarz Marlena , Banga J. Paul , Oak Shilpa , Pennington Christina A. , Hampe Christiane S. 
Published: November 2007

SummaryType 1 diabetes is caused by the autoimmune destruction of pancreatic beta cells. Here we show that administration of a human monoclonal antibody (b96·11) specific to the 65‐kDa isoform of glutamate decarboxylase (GAD65) to prediabetic non‐obese diabetic (NOD) mice significantly delays the onset of autoimmune diabetes. We found this effect to be epitope‐specific, as only b96·11 showed this therapeutic property, while a GAD65‐specific human monoclonal control antibody (b78) derived from the same patient, but specific to a different determinant of GAD65, had no significant effect on the progression of disease. Administration of b96·11 or b78 to NOD mice was accompanied by the generation of anti‐idiotypic antibodies. Importantly, the induced anti‐idiotypic antibodies were specific for the immunizing antibody and blocked the binding of GAD65 by the respective antibody. These findings suggest a potential role for the internal image of the GAD65 determinant recognized by b96·11 in the anti‐idiotypic antibody, supporting an immunomodulatory role for GAD65‐specific autoantibodies, as originally postulated by Jerne.
Isolation and characterization of dendritic cells from common marmosets for preclinical cell therapy studies
Authors: Ohta Shigeki , Ueda Yoko , Yaguchi Masae , Matsuzaki Yumi , Nakamura Masaya , Toyama Yoshiaki , Tanioka Yoshikuni , Tamaoki Norikazu , Nomura Tatsuji , Okano Hideyuki , Kawakami Yutaka , Toda Masahiro 
Published: November 2007

SummaryDendritic cells (DCs) have important functions as modulators of immune responses, and their ability to activate T cells is of great value in cancer immunotherapy. The isolation of DCs from the peripheral blood of rhesus and African green monkeys has been reported, but the immune system in the common marmoset remains poorly characterized, although it offers many potential advantages for preclinical studies. In the present study, we devised methods, based on techniques developed for mouse and human DC preparation, for isolating DCs from three major tissue sources in the common marmoset: bone marrow (BM), spleen and peripheral blood. Each set of separated cells was analysed using the cell surface DC‐associated markers CD11c, CD80, CD83, CD86 and human leucocyte antigen (HLA)‐DR, all of which are antibodies against human antigens, and the cells were further characterized both functionally and morphologically as antigen‐presenting cells. BM proved to be an excellent cell source for the isolation of DCs intended for preclinical studies on cell therapy, for which large quantities of cells are required. In the BM‐derived CD11c+ cell population, cells exhibiting the characteristic features of DCs were enriched, with the typical DC morphology and the abilities to undergo endocytosis, to secrete interleukin (IL)‐12, and to stimulate Xenogenic T cells. Moreover, BM‐derived DCs produced the neurotrophic factor NT‐3, which is also found in murine splenic DCs. These results suggest that BM‐derived DCs from the common marmoset may be useful for biological analysis and for preclinical studies on cell therapy for central nervous system diseases and cancer.