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Comprehensive Comparison (comprehensive + comparison)
Selected AbstractsComprehensive comparison of FISH, RT-PCR, and RQ-PCR for monitoring the BCR-ABL gene after hematopoietic stem cell transplantation in CMLEUROPEAN JOURNAL OF HAEMATOLOGY, Issue 5 2002Yoo-Jin Kim Abstract: The reverse transcriptase-polymerase chain reaction (RT-PCR) was compared with fluorescence in situ hybridization (FISH) and real-time quantitative RT-PCR (RQ-PCR) for minimal residual disease (MRD) monitoring in 266 post-transplant bone marrow samples from 78 patients with chronic myelogenous leukemia (CML). The sensitivities of FISH to BCR-ABL positive samples determined by first-round (1st) RT-PCR, second-round (2nd) RT-PCR, and RQ-PCR were 64.2%, 25.8%, and 20.7%, respectively. The BCR-ABL/ABL ratio by RQ-PCR had a mean of 0.000,13 in the 1st RT-PCR-negative samples and 1.42 in the 1st RT-PCR-positive samples (P<0.001), and means of 0.000,39 and 0.51 in the 2nd RT-PCR-negative and -positive samples (P< 0.001). The mean ratios of BCR-ABL/ABL by RQ-PCR were significantly different in N/N (1st/2nd RT-PCR) or N/P and P/P (P<0.001), but not in N/N and N/P, which showed that the discriminative power of RQ-PCR is confined to the 1st RT-PCR level. In this respect, monitoring of the 1st RT-PCR might be useful for estimating normalized BCR-ABL levels after transplantation. Nested RT-PCR was of limited use, as RQ-PCR quantified the BCR-ABL transcripts in 60 (91%) of 66 samples determined to be negative by 2nd RT-PCR. FISH was significantly correlated with RQ-PCR in FISH-positive samples (n=24, r=0.79, P=0.001). An increase of FISH preceded that of RQ-PCR in a few cases with molecular relapse. By analyzing a large number of samples post-transplant, we found that RQ-PCR might be the most useful assay for MRD monitoring; however, FISH and RT-PCR were found to be useful complementary tools. [source] Study of electronic spectra of free-base porphin and Mg-porphin: Comprehensive comparison of variety of ab initio, DFT, and semiempirical methodsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2005Josef Abstract SAC (symmetry adapted cluster)/SAC-CI and CASPT2 (multiconfigurational second-order perturbation theory) electron excitation spectra of free-base porphin and magnesium-porphin were determined using basis set functions augmented by both the polarization and diffuse functions,6-31+G(d). Such basis is recommended for correct description of the spectra because diffuse functions play fundamental roles in the formation of Rydberg MOs. The obtained results indicated that already the lowest roots in Au, B1u, B2g, and B3g irreducible representations display Rydberg character. The calculated spectra are in a good agreement with both experimental and recently calculated electronic transitions. It is concluded that the SAC/SAC-CI level spectral lines are significantly affected by configuration selection when energy thresholds 5.0 × 10,6 and 5.0 × 10,7 a.u. are used for the determination of ground and excited state properties. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 294,303, 2005 [source] Steerable catheters in minimally invasive vascular surgeryTHE INTERNATIONAL JOURNAL OF MEDICAL ROBOTICS AND COMPUTER ASSISTED SURGERY, Issue 4 2009Yili Fu Abstract Background Remote-controlled catheter navigation systems have recently been introduced into minimally invasive vascular surgery and some of them have already been applied in clinical practice. Steerable catheters with improved manoeuvrability play an important role in these innovations for conventional catheterization. Methods This review details the development of various steerable catheters, both in use clinically and under investigation. Comprehensive comparison and analysis in several key aspects are followed to reveal both the advantages and limitations of these catheters, as well as the requirements for relevant techniques. Results Steerable catheters are able to select direction in the distal end, and superior to conventional counterparts in many aspects. Differences between magnetic and active catheters mainly lie in function, safety, configuration of operating room and cost. They have similar requirements for miniaturization and slave insertion mechanisms. Conclusions Steerable catheters are rapidly evolving and still require technological refinements to extend current capabilities. Copyright © 2009 John Wiley & Sons, Ltd. [source] Methods to account for spatial autocorrelation in the analysis of species distributional data: a reviewECOGRAPHY, Issue 5 2007Carsten F. Dormann Species distributional or trait data based on range map (extent-of-occurrence) or atlas survey data often display spatial autocorrelation, i.e. locations close to each other exhibit more similar values than those further apart. If this pattern remains present in the residuals of a statistical model based on such data, one of the key assumptions of standard statistical analyses, that residuals are independent and identically distributed (i.i.d), is violated. The violation of the assumption of i.i.d. residuals may bias parameter estimates and can increase type I error rates (falsely rejecting the null hypothesis of no effect). While this is increasingly recognised by researchers analysing species distribution data, there is, to our knowledge, no comprehensive overview of the many available spatial statistical methods to take spatial autocorrelation into account in tests of statistical significance. Here, we describe six different statistical approaches to infer correlates of species' distributions, for both presence/absence (binary response) and species abundance data (poisson or normally distributed response), while accounting for spatial autocorrelation in model residuals: autocovariate regression; spatial eigenvector mapping; generalised least squares; (conditional and simultaneous) autoregressive models and generalised estimating equations. A comprehensive comparison of the relative merits of these methods is beyond the scope of this paper. To demonstrate each method's implementation, however, we undertook preliminary tests based on simulated data. These preliminary tests verified that most of the spatial modeling techniques we examined showed good type I error control and precise parameter estimates, at least when confronted with simplistic simulated data containing spatial autocorrelation in the errors. However, we found that for presence/absence data the results and conclusions were very variable between the different methods. This is likely due to the low information content of binary maps. Also, in contrast with previous studies, we found that autocovariate methods consistently underestimated the effects of environmental controls of species distributions. Given their widespread use, in particular for the modelling of species presence/absence data (e.g. climate envelope models), we argue that this warrants further study and caution in their use. To aid other ecologists in making use of the methods described, code to implement them in freely available software is provided in an electronic appendix. [source] Systemic IFN-, drives kidney nephritis in B6.Sle123 miceEUROPEAN JOURNAL OF IMMUNOLOGY, Issue 7 2008Anna-Marie Fairhurst Abstract The impact of IFN-, secretion on disease progression was assessed by comparing phenotypic changes in the lupus-prone B6.Sle1Sle2Sle3 (B6.Sle123) strain and the parental C57BL/6 (B6) congenic partner using an adenovirus (ADV) expression vector containing a recombinant IFN-, gene cassette (IFN-ADV). A comprehensive comparison of cell lineage composition and activation in young B6 and B6.Sle123 mice revealed a variety of cellular alterations in the presence and absence of systemic IFN-,. Most IFN-,-induced phenotypes were similar in B6 and B6.Sle123 mice; however, B6.Sle123 mice uniquely exhibited increased B1 and plasma cells after IFN-, exposure, although both strains had an overall loss of mature B cells in the bone marrow, spleen and periphery. Although most of the cellular effects of IFN-, were identical in both strains, severe glomerulonephritis occurred only in B6.Sle123 mice. Mice injected with IFN-ADV showed an increase in immune complex deposition in the kidney, together with an unexpected decrease in serum anti-nuclear antibody levels. In summary, the predominant impact of systemic IFN-, in this murine model is an exacerbation of mechanisms mediating end organ damage. [source] Fast set-up of doxycycline-inducible protein expression in human cell lines with a single plasmid based on Epstein,Barr virus replication and the simple tetracycline repressorFEBS JOURNAL, Issue 3 2007Markus Bach We have developed a novel plasmid vector, pEBTetD, for full establishment of doxycycline-inducible protein expression by just a single transfection. pEBTetD contains an Epstein,Barr virus origin of replication for stable and efficient episomal propagation in human cell lines, a cassette for continuous expression of the simple tetracycline repressor, and a cytomegalovirus-type 2 tetracycline operator (tetO2)-tetO2 promoter. As there is no integration of vector into the genome, clonal isolation of transfected cells is not necessary. Cells are thus ready for use 1 week after transfection; this contrasts with 3,12 weeks for other systems. Adequate regulation of protein expression was accomplished by abrogation of mRNA polyadenylation. In northern analysis of seven cDNAs coding for transport proteins, pools of transfected human embryonic kidney 293 cells showed on/off mRNA ratios in the order of 100 : 1. Cell pools were also analyzed for regulation of protein function. With two transport proteins of the plasma membrane, the on/off activity ratios were 24 : 1 and 34 : 1, respectively. With enhanced green fluorescent protein, a 23 : 1 ratio was observed based on fluorescence intensity data from flow cytometry. The unique advantage of our system rests on the unmodified tetracycline repressor, which is less likely, by relocation upon binding of doxycycline, to cause cellular disturbances than chimera of tetracycline repressor and eukaryotic transactivation domains. Thus, in a comprehensive comparison of on- and off-states, a steady cellular background is provided. Finally, in contrast to a system based on Flp recombinase, the set-up of our system is inherently reliable. [source] Polyaniline Entrapped in Silver: Structural Properties and Electrical ConductivityADVANCED FUNCTIONAL MATERIALS, Issue 8 2009Guy Nesher Abstract By employing the new methodology of entrapment of organic molecules within metals, we demonstrate the ability to modify the conductivity of a metal by suitable polymer entrapment. Specifically, polyaniline (PANI) in two molecular weights was entrapped in silver at different concentrations and a comprehensive comparison was preformed for a range of the composite properties, characterized by XRD, SEM, BET, TGA, and density measurements. Pressed films were utilized to measure the electrical conductivity of the composites in order to study the PANI-silver interactions at the molecular level and to establish a correlation between the microscopic morphology and the film conduction. Such correlations have been identified, and are interpreted. This work extends the functional applications of the new metallic composites and offers insight on the polymer-metal molecular level interactions. [source] Performance comparison between fixed length switching and variable length switchingINTERNATIONAL JOURNAL OF COMMUNICATION SYSTEMS, Issue 5 2008Chengchen Hu Abstract Fixed length switching (FLS) and variable length switching (VLS) are two main types of switching architecture in high-speed input-queued switches. FLS is based on a cell-by-cell scheduling algorithm, while VLS operates on the variable packet granularity. This paper aims to make a comprehensive comparison between these two switching modes to guide the industrial design and academic research. We use stochastic models, Petri net models, analysis and simulations to investigate various performance measures of interest. Average packet latency, bandwidth utilization, segmentation and reassembly overhead, as well as packet loss are the identified key parameters that influence the outcome of the comparison. The results achieved in this paper are twofold. On one hand, it is shown that FLS enables smaller packet loss and lower packet delay in case of a short packet. On the other hand, VLS favors better bandwidth utilization, reduced implementation complexity and lower average packet delay. We recommend VLS in the conclusion since its disadvantages can be compensated by some methods, while the problems in FLS are difficult to be solved. Copyright © 2007 John Wiley & Sons, Ltd. [source] Review and comparison of tropospheric scintillation prediction models for satellite communicationsINTERNATIONAL JOURNAL OF SATELLITE COMMUNICATIONS AND NETWORKING, Issue 4 2006P. Yu Abstract An overview of the origin and characteristics of tropospheric scintillation is presented and a measurement database against which scintillation models are to be tested is described. Maximum likelihood log-normal and gamma distributions are compared with the measured distribution of scintillation intensity. Eleven statistical models of monthly mean scintillation intensity are briefly reviewed and their predictions compared with measurements. RMS error, correlation, percentage error bias, RMS percentage error and percentage error skew are used in a comprehensive comparison of these models. In the context of our measurements, the ITU-R model has the best overall performance. Significant difference in the relative performance of the models is apparent when these results are compared with those from a similar study using data measured in Italy. Copyright © 2006 John Wiley & Sons, Ltd. [source] Production of Shiga toxin by Shiga toxin-expressing Escherichia coli (STEC) in broth media: from divergence to definitionLETTERS IN APPLIED MICROBIOLOGY, Issue 4 2007L.B. Rocha Abstract Aims:, To determine the suitability of eight different commercial broth media for Shiga toxin (Stx) production. Methods and Results:, Shiga toxin-producing Escherichia coli (STEC) strains producing Stx1 or Stx2 were grown at 37°C (250 rev min,1) for 24 h in brain heart infusion broth, E. coli broth, Evans medium, Luria-Bertani broth, Penassay broth, buffered-peptone water, syncase broth and trypticase soy broth. Toxin production was measured by enzyme-linked immunosorbent assay (ELISA) in polymyxin-treated cell pellets and/or supernatants of cultures, ELISA optical densities reached 1 when isolates were grown for 2,4 h in E. coli broth in the presence of antibiotic. Besides, a collection of STEC-expressing Stx strains was evaluated and the Stx production was assayed in the supernatants and in polymyxin-treated pellets of bacterial growth after 4 h of cultivation in E. coli broth in the presence of antibiotic. Conclusions:, The most suitable medium for Stx production was E. coli broth when the bacterial isolates were grown for 4 h in the presence of ciprofloxacin and the Stx production is detected in the supernatant. Significance and Impact of the Study:, This study presents the first comprehensive comparison of different broth media with regard to Stx production to establish optimal culture conditions for STEC detection in routine diagnostic laboratories. [source] Linnaeus' sexual system and flowering plant phylogenyNORDIC JOURNAL OF BOTANY, Issue 1-2 2007Birgitta Bremer Carl Linnaeus brought order to the knowledge of plants and animals by arranging all known species in encyclopaedic works. He proposed a system of plants, the sexual system, based on the number and arrangement of male and female organs. His artificial sexual system has since long been replaced by ,natural' or phylogenetic systems but there has never been a comprehensive comparison of the sexual system with modern plant classification. The currently most often used classification of flowering plants is the APG-system. It is based on comprehensive phylogenies of flowering plants, reconstructed by analyses of DNA data. The APG-system covers all flowering plants which are classified in 453 families and these are classified in 45 orders. Most of the species were not known at time of Linnaeus. Families and orders in the APG-system are arranged in larger informal groups representing major branches in the flowering plant phylogenetic tree. Three such groups are the monocots, the rosids, and the asterids. I have examined all genera published in Species plantarum (1753) and classified them according to order and major groups in the APG-system. All classes except one, number 15 Tetradynamia, comprises groups of unrelated plants. Not surprisingly, the sexual system does not display what we know today about plant relationships. As is evident from this analysis, there is little correspondence between the sexual system and the APG-system. This does not mean that the sexual system has been useless or misleading. When it was introduced, it formed the basis for much intensified research and increased knowledge of plants. [source] Changes of the hepatic proteome in murine models for toxically induced fibrogenesis and sclerosing cholangitisPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 24 2006Corinna Henkel Abstract We investigated the changes in the hepatic proteome in murine models for toxic-induced fibrogenesis and sclerosing cholangitis. A comprehensive comparison of protein changes observed is made and the mechanistical basis of the expression changes is discussed. Hepatic fibrosis was induced by repetitive intraperitoneal CCl4 treatment of BALB/c mice or developed spontaneously in BALB/c-ATP-binding cassette, subfamily B, member 4 (Abcb4) knock out mice. Fibrosis was verified by a morphometric score and assessment of hydroxyproline content of liver tissue, respectively. The innovative difference in-gel electrophoresis (DIGE) technique was used to analyse protein expression levels of the mouse proteome. Results were confirmed by Western blotting and real-time RT-PCR. In CCl4 -induced fibrosis 20 out of 40 and in BALB/c- Abcb4,/, mice 8 out of 28 differentially expressed proteins were identified utilizing DIGE. Only two proteins, selenium-binding protein (Sbp2) and carbonic anhydrase 3, have been unidirectionally expressed (i.e. down-regulated) in both models. Relevant differences in the pathogenesis of toxically induced liver fibrosis and sclerosing cholangitis exist. The only novel protein with regard to liver fibrosis depicting a unidirectional expression pattern in both animal models was Sbp2. An explicit protein function could not be clarified yet. [source] Expansion of circulating T cells resembling follicular helper T cells is a fixed phenotype that identifies a subset of severe systemic lupus erythematosusARTHRITIS & RHEUMATISM, Issue 1 2010Nicholas Simpson Objective In the sanroque mouse model of lupus, pathologic germinal centers (GCs) arise due to increased numbers of follicular helper T (Tfh) cells, resulting in high-affinity anti,double-stranded DNA antibodies that cause end-organ inflammation, such as glomerulonephritis. The purpose of this study was to examine the hypothesis that this pathway could account for a subset of patients with systemic lupus erythematosus (SLE). Methods An expansion of Tfh cells is a causal, and therefore consistent, component of the sanroque mouse phenotype. We validated the enumeration of circulating T cells resembling Tfh cells as a biomarker of this expansion in sanroque mice, and we performed a comprehensive comparison of the surface phenotype of circulating and tonsillar Tfh cells in humans. This circulating biomarker was enumerated in SLE patients (n = 46), Sjögren's syndrome patients (n = 17), and healthy controls (n = 48) and was correlated with disease activity and end-organ involvement. Results In sanroque mice, circulating Tfh cells increased in proportion to their GC counterparts, making circulating Tfh cells a feasible human biomarker of this novel mechanism of breakdown in GC tolerance. In a subset of SLE patients (14 of 46), but in none of the controls, the levels of circulating Tfh cells (defined as circulating CXCR5+CD4+ cells with high expression of Tfh-associated molecules, such as inducible T cell costimulator or programmed death 1) were increased. This cellular phenotype did not vary with time, disease activity, or treatment, but it did correlate with the diversity and titers of autoantibodies and with the severity of end-organ involvement. Conclusion These findings in SLE patients are consistent with the autoimmune mechanism in sanroque mice and identify Tfh effector molecules as possible therapeutic targets in a recognizable subset of patients with SLE. [source] Direct comparison of four bacterial source tracking methods and use of composite data setsJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2007E.A. Casarez Abstract Aims:, Four bacterial source tracking (BST) methods, enterobacterial repetitive intergenic consensus sequence polymerase chain reaction (ERIC-PCR), automated ribotyping using HindIII, Kirby-Bauer antibiotic resistance analysis (KB-ARA) and pulsed-field gel electrophoresis (PFGE) were directly compared using the same collection of Escherichia coli isolates. The data sets from each BST method and from composite methods were compared for library accuracy and their ability to identify water isolates. Methods and Results:, Potential sources of faecal pollution were identified by watershed sanitary surveys. Domestic sewage and faecal samples from pets, cattle, avian livestock, other nonavian livestock, avian wildlife and nonavian wildlife sources were collected for isolation of E. coli. A total of 2275 E. coli isolates from 813 source samples were screened using ERIC-PCR to exclude clones and to maximize library diversity, resulting in 883 isolates from 745 samples selected for the library. The selected isolates were further analysed using automated ribotyping with HindIII, KB-ARA and PFGE. A total of 555 E. coli isolates obtained from 412 water samples were analysed by the four BST methods. A composite data set of the four BST methods gave the highest rates of correct classification (RCCs) with the fewest unidentified isolates than any single method alone. RCCs for the four-method composite data set and a seven-way split of source classes ranged from 22% for avian livestock to 83% for domestic sewage. Two-method composite data sets were also found to be better than individual methods, having RCCs similar to the four-method composite and identification of the same major sources of faecal pollution. Conclusions:, The use of BST composite data sets may be more beneficial than the use of single methods. Significance and Impact of the Study:, This is one of the first comprehensive comparisons using composite data from several BST methods. While the four-method approach provided the most desirable BST results, the use of two-method composite data sets may yield comparable BST results while providing for cost, labour and time savings. [source] Rethinking the Black Public Sphere: An Alternative Vocabulary for Multiple Public SpheresCOMMUNICATION THEORY, Issue 4 2002Catherine R. Squires Many theorists propose that there are multiple, coexisting "subaltern" counterpublic spheres. However, most discussions of these subaltern counterpublics rely on group identity markers to differentiate between these spheres and do not provide alternative means for distinguishing between subaltern public spheres. This essay presents an alternative vocabulary for multiple public spheres through an exploration of the history of the African American public sphere. Three types of marginal publics, enclave, counterpublic, and satellite, are defined as examples of how we might incorporate considerations of the kinds of resources different publics have available to them. This vocabulary facilitates more flexible descriptions of publics that are normally defined by identity and allows for more comprehensive comparisons across public spheres. [source] | |||||||||||||||||||