bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of influenza vaccinations on immune response and serum eotaxin level in patients with allergic bronchial asthma
Authors: Jahnz-Różyk Karina , Brydak Lidia B. , Targowski Tomasz , Machała Magdalena , Płusa Tadeusz 
Published: August 2004

BACKGROUND: One of the most promising markers of allergic inflammation is eotaxin, which has a selective influence on the migration of eosinophils. Its serum content significantly correlates with the intensity of allergic symptoms, so it might be interesting to know whether vaccination has any influence on serum expression of this chemokine.Aims: Comparison of the humoral response to influenza vaccine and post‐vaccination changes in the serum eotaxin level in patients with allergic bronchial asthma and healthy controls.Methods: Forty‐two asthmatics and 45 healthy individuals were vaccinated with a single dose of influenza subunit vaccine (Influvac). The serum eotaxin level and the antibody response to haemagglutinin (HI) and neuraminidase (NI) glycoproteins were measured before and after vaccination.Results: A significant increase of geometric mean titres of HI and NI was observed in both groups. There were no significant differences between the groups in meanfold increase of HI and NI titres, response rate and protective level of HI. After vaccination, a significant decrease of the mean serum eotaxin value was observed in patients with asthma (149.4±71.0 versus 125.1±67.0, p = 0.0017), while no similar effect was present in healthy individuals (153.4±56.9 versus 159.3±54.4, p = 0.5).Conclusions: The results indicate that in patients with allergic bronchial asthma influenza vaccinations assure efficient protective antibody level and modulate the serum level of eotaxin.
Production of anti‐Candida antibodies in mice with gut colonization of Candida albicans
Authors: Tansho Shigeru , Abe Shigeru , Ishibashi Hiroko , Mitsuya Masayasu , Wada Kayoko , Ikeda Tatsuo , Suegara Nobuo , Koshio Osamu , Ono Yasuo , Yamaguchi Hideyo 
Published: August 2004

BACKGROUND: Production of antibodies that are specific for allergens is an important pathological process in inflammatory allergic diseases. These contain the antibodies against antigens of Candida albicans, one of the normal microbial flora in an intestinal tract. We studied the effects of the prednisolone administration on the production of anti‐Candida antibodies in the gastrointestinally C. albicans‐colonized mice.Methods and Materials: BALB/c mice, treated with antibacterial antibiotics to decontaminate indigenous intestinal bacterial flora, were inoculated intragastrically with C. albicans. The mice, in which C. albicans grows intestinally, were administered prednisolone to induce temporary immunosuppression. The Candida growth in their intestinal tract and their antibody response to Candida were examined.Results: Antibiotic treatment allowed establishment of C. albicans gastrointestinal colonization, but did not cause subsequent systemic dissemination of C. albicans in all the animals. When these animals received an additional treatment with prednisolone, they showed a significantly higher population of C. albicans in their feces than those of animals treated with antibiotics alone, and the organisms were recovered even from their kidney. This systemic dissemination by C. albicans appeared to be temporal, because all the mice survived without any symptoms for more than 2 months. Examination of the serum titers of total immunoglobulin (Ig)E antibodies and specific IgE and IgG antibodies against Candida antigens demonstrated that titers of total IgE increased, partially by day 14 and clearly at day 27, in prednisolone‐treated Candida‐colonized mice. Without prednisolone treatment, an increment of the serum titer was scarcely observed. By day 27, corresponding to the increase of total IgE, the anti‐Candida IgE and IgG titer increased in mice of the prednisolone‐treated group.Conclusion: Administration of prednisolone to Candida‐colonized mice can induce production of the IgG, IgE antibodies against Candida antigens, perhaps through temporal systemic dissemination of Candida from the intestinal tract.
Gene clustering by Latent Semantic Indexing of MEDLINE abstracts
Authors: Homayouni Ramin , Heinrich Kevin , Wei Lai , Berry Michael W. 
Published: August 2004

AbstractMotivation: A major challenge in the interpretation of high-throughput genomic data is understanding the functional associations between genes. Previously, several approaches have been described to extract gene relationships from various biological databases using term-matching methods. However, more flexible automated methods are needed to identify functional relationships (both explicit and implicit) between genes from the biomedical literature. In this study, we explored the utility of Latent Semantic Indexing (LSI), a vector space model for information retrieval, to automatically identify conceptual gene relationships from titles and abstracts in MEDLINE citations.Results: We found that LSI identified gene-to-gene and keyword-to-gene relationships with high average precision. In addition, LSI identified implicit gene relationships based on word usage patterns in the gene abstract documents. Finally, we demonstrate here that pairwise distances derived from the vector angles of gene abstract documents can be effectively used to functionally group genes by hierarchical clustering. Our results provide proof-of-principle that LSI is a robust automated method to elucidate both known (explicit) and unknown (implicit) gene relationships from the biomedical literature. These features make LSI particularly useful for the analysis of novel associations discovered in genomic experiments.Availability: The 50-gene document collection used in this study can be interactively queried at http://shad.cs.utk.edu/sgo/sgo.htmlContact: rhomayouni@utmem.eduSupplementary information: http://shad.cs.utk.edu/sgo/pubs.html
Outcome signature genes in breast cancer: is there a unique set?
Authors: Ein-Dor Liat , Kela Itai , Getz Gad , Givol David , Domany Eytan 
Published: August 2004

Abstract
Motivation: Predicting the metastatic potential of primary malignant tissues has direct bearing on the choice of therapy. Several microarray studies yielded gene sets whose expression profiles successfully predicted survival. Nevertheless, the overlap between these gene sets is almost zero. Such small overlaps were observed also in other complex diseases, and the variables that could account for the differences had evoked a wide interest. One of the main open questions in this context is whether the disparity can be attributed only to trivial reasons such as different technologies, different patients and different types of analyses.
Results: To answer this question, we concentrated on a single breast cancer dataset, and analyzed it by a single method, the one which was used by van't Veer et al. to produce a set of outcome-predictive genes. We showed that, in fact, the resulting set of genes is not unique; it is strongly influenced by the subset of patients used for gene selection. Many equally predictive lists could have been produced from the same analysis. Three main properties of the data explain this sensitivity: (1) many genes are correlated with survival; (2) the differences between these correlations are small; (3) the correlations fluctuate strongly when measured over different subsets of patients. A possible biological explanation for these properties is discussed.
Contact: eytan.domany@weizmann.ac.il
Supplementary information: http://www.weizmann.ac.il/physics/complex/compphys/downloads/liate/
A rapid method for computationally inferring transcriptome coverage and microarray sensitivity
Authors: Reverter A. , McWilliam S. M. , Barris W. , Dalrymple B. P. 
Published: August 2004

Abstract
Motivation: There are many different gene expression technologies, including cDNA and oligo-based microarrays, SAGE and MPSS. For each organism of interest, coverage of the transcriptome and the genome will be different. We address the question of what level of coverage is required to exploit the sensitivity of the different technologies, and what is the sensitivity of the different approaches in the experimental study.
Results: We estimate the transcriptome coverage by randomly sampling transcripts from a pre-defined tag-to-gene mapping function. For a given microarray experiment, we locate the thresholds in intensities that define the distribution of transcript abundance. These values are compared against the distribution obtained by applying the same thresholds to the intensities from differentially expressed genes. The ratio of these two distributions meets at the equilibrium defining sensitivity. We conclude that a collection of ∼340 000 sequences is adequate for microarrays, but not large enough for maximum utilization of tag-based technologies. In the absence of large-scale sequencing, the majority of the tags detected by the latter approaches will remain unidentified until the genome sequence is available.
Contact: Tony.Reverter-Gomez@csiro.au
Origins of introns based on the definition of exon modules and their conserved interfaces
Authors: de Roos Albert D. G. 
Published: August 2004

Abstract
Summary: Central to the unraveling of the early evolution of the genome is the origin and role of introns. The evolution of the genome can be characterized by a continuous expansion of functional modules that occurs without the interruption of existing processes. The design-by-contract methodology of software development offers a modular approach to design that seeks to increase flexibility by focusing on the design of constant interfaces between functional modules. Here, it is shown that design-by-contract can offer a framework for genome evolution. The definition of an ancient exon module with identical splice sites leads to a relatively simple sequence of events that explains the role of introns, intron phase differences and the evolution of multi-exon proteins in an RNA world. An interaction of the experimentally defined six-nucleotide splicing consensus sequence together with a limited number of primitive ribozymes can account for a rapid creation of protein diversity.
Contact: albert.de.roos@thebeaglearmada.nl
Structure of nanometre‐sized Xe particles embedded in Al crystals
Authors: SONG M. , MITSUISHI K. , FURUYA K. , ALLEN C. W. , BIRTCHER R. C. , DONNELLY S. E. 
Published: August 2004

SummaryThe structure and lattice parameters of Xe particles about 1 nm to about 6 nm in size embedded in Al were investigated with off‐Bragg condition high‐resolution transmission electron microscopy. An Xe particle about 1 nm in size had different structural properties from those 2–6 nm in sizes. Some 1‐nm Xe particles had an face‐centred cubic (f.c.c.) structure with the same orientation as the Al matrix, whereas others of the same size had a non‐f.c.c. structure. The lattice parameters of a 1‐nm f.c.c. Xe particle were about 20% smaller than the average value obtained from electron diffraction, i.e. the particle was compressed by about 80%. The lattice parameters of Xe crystals about 2 nm to about 6 nm in size were almost the same as those obtained from diffraction results. One of the reasons for the extra compression seen with a 1‐nm Xe particle is the increase in pressure inside an Xe particle with decreasing particle size.
Near‐field imaging of organic nanofibres
Authors: VOLKOV V. S. , BOZHEVOLNYI S. I. , BORDO V. G. , RUBAHN H.‐G. 
Published: August 2004

SummaryThe optical near‐field of orientated nanofibres of para‐hexaphenyl was investigated by a combination of localized far‐field ultraviolet excitation and scanning near‐field fluorescence detection. Morphological inhomogeneities of the nanofibres together with selective incoupling into the near‐field probe resulted in a detection sensitivity was dependent on individual nanoaggregates. Strongest near‐field intensity and radiation into the far‐field were observed at the crossing points of nanofibres. The near‐field observation of a distance‐dependent damping of the waveguiding along the nanofibres allowed us to determine the imaginary part of the dielectric function of the nanofibres, in quantitative agreement with far‐field optical data.
Atomic force microscopy study of DNA deposited on poly l‐ornithine‐coated mica
Authors: PODESTÀ A. , IMPERADORI L. , COLNAGHI W. , FINZI L. , MILANI P. , DUNLAP D. 
Published: August 2004

SummaryAnalyses of individual biomolecules, like DNA, or DNA–protein complexes, via atomic force microscopy, require ‘gentle’ methods to immobilize DNA on surfaces, which allow the ensemble of molecules to adopt conformations dictated primarily by their physical characteristics, and which possibly permit the use of a wide selection of buffers. We show that poly‐l‐ornithine‐coated mica is a good substrate for fast, reliable deposition of DNA for wet or dry imaging. The surface firmly secures DNA, which retains the B‐form helical rise (0.34 nm bp−1). The conformations of DNA that result are reminiscent of three‐dimensional random coils projected on to a plane. The contrast is good, especially in solution, and buffers with physiological concentrations of salt with or without divalent cations may be used. This is important for comparison of scanning probe microscopy results with those obtained by different techniques.
Combining Ar ion milling with FIB lift‐out techniques to prepare high quality site‐specific TEM samples
Authors: HUANG Z. 
Published: August 2004

SummaryFocused ion beam (FIB) techniques can prepare site‐specific transmission electron microscopy (TEM) cross‐section samples very quickly but they suffer from beam damage by the high energy Ga+ ion beam. An amorphous layer about 20–30 nm thick on each side of the TEM lamella and the supporting carbon film makes FIB‐prepared samples inferior to the traditional Ar+ thinned samples for some investigations such as high resolution transmission electron microscopy (HRTEM) and electron energy loss spectroscopy (EELS). We have developed techniques to combine broad argon ion milling with focused ion beam lift‐out methods to prepare high‐quality site‐specific TEM cross‐section samples. Site‐specific TEM cross‐sections were prepared by FIB and lifted out using a Narishige micromanipulator onto a half copper‐grid coated with carbon film. Pt deposition by FIB was used to bond the lamellae to the Cu grid, then the coating carbon film was removed and the sample on the bare Cu grid was polished by the usual broad beam Ar+ milling. By doing so, the thickness of the surface amorphous layers is reduced substantially and the sample quality for TEM observation is as good as the traditional Ar+ milled samples.
Minimizing photobleaching during confocal microscopy of fluorescent probes bound to chromatin: role of anoxia and photon flux
Authors: BERNAS T. , ZARȨBSKI M. , COOK R. R. , DOBRUCKI J. W. 
Published: August 2004

SummaryExposure to light can destroy the ability of a molecule to fluoresce. Such photobleaching limits the use of fluorescence and confocal microscopy in biological studies. Loss of fluorescence decreases the signal‐to‐noise ratio and so image resolution; it also prevents the acquisition of meaningful data late during repeated scanning (e.g. when collecting three‐dimensional images). The aim of this work was to investigate the role of oxygen in the photobleaching of fluorophores bound to DNA in fixed cells, and to explore whether anoxia could minimize such bleaching. Anoxia significantly reduced bleaching rates and changed the order of reaction of both propidium iodide (an intercalator) and chromomycin A3 (a minor‐groove binder) bound to DNA; it afforded the greatest protection at low photon fluxes. However, it had no effect on the bleaching of the green fluorescent protein (GFP) covalently attached to a histone and so bound to DNA, probably because the protein shielded the chromophore from oxygen. Bleaching of all three fluorophores depended on photon flux. Practical ways of minimizing bleaching were examined, and examples of three‐dimensional images of DNA marked by propidium and GFP (collected under standard and optimized conditions) are presented.
Direct atomic force microscopy observations of monovalent ion induced binding of DNA to mica
Authors: ELLIS J. S. , ABDELHADY H. G. , ALLEN S. , DAVIES M. C. , ROBERTS C. J. , TENDLER S. J. B. , WILLIAMS P. M. 
Published: August 2004

SummaryMultivalent ions in solution are known to mediate attraction between two like‐charged molecules. Such attraction has proved useful in atomic force microscopy (AFM) where DNA may be immobilized to a mica surface facilitating direct imaging in liquid. Theories of DNA immobilization suggest that either ‘salt bridging’ or fluctuation in the positions of counter ions about both the mica surface and DNA backbone secure DNA to the mica substrate. Whilst both theoretical and experimental evidence suggest that immobilization is possible in the presence of divalent ions, very few studies identify that such immobilization is possible with monovalent ions. Here we present direct AFM evidence of DNA immobilized to mica in the presence of only monovalent ions. Our data depict E. coli plasmid pBR322 adsorbed onto the negatively charged mica both after short (10 min) and long (24 h) incubation periods. These data suggest the need to re‐explore current theories of like‐charge attraction to include the possibility of monovalent interactions. We suggest that this DNA immobilization strategy may offer the potential to image natural processes with limited immobilization forces and hence enable maximum conformational freedom of the immobilized biomolecule.
Microwave exposure increases bone demineralization rate independent of temperature
Authors: TINLING S. P. , GIBERSON R. T. , KULLAR R. S. 
Published: August 2004

SummaryThere is a long‐standing controversy regarding an effect of microwaves, independent of increasing temperature, on the rate of bone demineralization. In this study, we exposed standardized samples of gerbil femur to constant microwave exposure while maintaining the demineralizing solution (ethylenediamine tetraacetic acid, EDTA) at 20 °C. Random samples were selected at 3 h intervals, embedded in plastic and sectioned for histological evaluation to determine the extent of demineralization. The time to complete demineralization was significantly faster with microwave exposure (33 h) compared to non‐exposure on a tissue rotator (45 h) in a limited amount (5 mL/24 h) of EDTA. The presence of bone marrow was a significant barrier to the rate of demineralization and resulted in an asymmetrical pattern of mineral extraction. Samples without bone marrow were completely demineralized after 21 h of exposure to microwaves and EDTA. Additional comparisons were made between samples exposed to an effectively infinite supply of demineralizing agent (bone marrow intact). There was a significant increase in rate with unlimited demineralizing agent with (24 h) or without (30 h) microwaves when compared to tissue demineralized on the rotator. Our results establish a positive effect of microwaves on the rate of bone demineralization which is independent of temperature.
Peace and Progress? Political and Social Change Among Young Loyalists in Northern Ireland
Authors: McAuley James W. 
Published: August 2004

Politics in Northern Ireland remain dominated by the search for an enduring settlement resting on an agreed set of political values and arrangements, between Ulster Unionists and loyalists on the one side, and Irish nationalists and republicans, on the other. Sectarian divisions continue to emphasize the persistence of conflictual social relationships between these gropings. Central to any possibility of a resolution to conflict is the awareness of how conflictual or reconciliatory values are transmitted from one generation to another, and how young people reconstruct their understandings of society. This article examines processes of political socialization and political identity formation around children and young people in Northern Ireland. It focuses in particular on those growing up within the Ulster loyalist tradition.“North Belfast is witnessing the creation of the next wave of paramilitary gunmen. Today they are aged eight, their stones bouncing harmlessly off the army and police Land Rovers… . But give them a decade and, unless things change remarkably in the meantime many of these children will know how to fire a rifle or revolver, will have learnt to manufacture and use blast‐bombs, and know exactly how much sugar is needed in a petrol bomb.”          — McKittrick, 2001, p. 14“Young people in Northern Ireland are heir to a historical legacy of sectarian social division. On the ethnic frontier these manifest themselves in the territorialization of economic, residential and cultural life.”          — Bell, 1990, p. 96
Teachers' and Ppils' Educational Experiences and School‐Based Responses to the Conflict in Northern Ireland
Authors: Kilpatrick Rosemary , Leitch Ruth 
Published: August 2004

This article describes a study which examined (a) the impact of the political conflict on teachers' and ppils' experiences of education in Northern Ireland and (b) the impact of curricular‐based interventions designed to support the ppils and reduce prejudice. The focus of the second part of the article is on the prejudice reduction initiatives identified. A total of 44 staff and 78 ppils spread across 8 schools participated and both teachers' and ppils' perspectives were identified, the latter being an extremely important dimension which has rarely been addressed in previous studies of this area. The findings, which highlight the complexity of the impact of the political conflict, are considered to have both practical and theoretical implications for prejudice reduction programs.
“Young people are asked to ‘voice’ their views not only because it is seen as beneficial to them personally, but because people believe they can learn from what they are saying.”

—Hadfield and Hawe, 2001, p. 94
Herpes simplex virus‐based vectors
Authors: Lachmann Robin 
Published: August 2004

SummaryHerpes simplex virus (HSV)‐based vectors have primarily been developed for neuronal gene delivery, taking advantage of the virus' natural neurotropism. Two types of vector are available: replication defective viruses, whose cytotoxicity has been abolished by deleting viral gene products, and amplicon vectors, which are plasmids packaged into HSV particles with the aid of a helper virus. In this review I discuss how the cytotoxicity of the wild‐type virus has been abolished, the progress which has been made toward defining promoter elements capable of directing long‐term transgene expression form the latent viral genome and some of the potential clinical uses of these versatile vectors.