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Results for “parameter identification”

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PubMed1999

High-throughput tissue microarray analysis to evaluate genes uncovered by cDNA microarray screening in renal cell carcinoma.

Many genes and signaling pathways are involved in renal cell carcinoma (RCC) development. However, genetic tumor markers have not gained use in RCC diagnostics and prognosis prediction. Identification and evaluation of new molecular parameters are of utmost importance in cancer research and cancer treatment. Here we present a novel approach to rapidly identify clinically relevant molecular changes in cancer. To identify genes with relevance to RCC, a cDNA array analysis was first performed on 5184 cDNA clones on a filter to screen for genes with differential expression between the renal cancer cell line CRL-1933 and normal kidney tissue. There were 89 differentially expressed genes in the cancer cell line, one of them coding for vimentin, a cytoplasmic intermediate filament. In a second step, a renal cancer tissue microarray containing 532 RCC specimen was used to determine vimentin expression by immunohistochemistry. Vimentin expression was seen frequently in clear cell (51%) and papillary RCC (61%), but rarely in chromophobe RCC (4%) and oncocytomas (12%). Furthermore, vimentin expression was significantly associated with poor patient prognosis (P < 0.007) independent of grade and stage. These results obtained from minute arrayed tumor samples match well with previous findings on vimentin expression in renal tumors. It is concluded that the combination of tumor arrays and cDNA arrays is a powerful approach to rapidly identify and further evaluate genes that play a role in tumor biology.

Carcinoma, Renal Cell↗

PubMed2003

Seminal infection with Ralstonia picketti and cytolysosomal spermophagy in a previously fertile man.

OBJECTIVE: To determine the origin of large plaque-like cellular and acellular masses of debris found in the semen of a patient with otherwise normal semen quality and secondary infertility. DESIGN: A prospective case study. SETTINGS: Academic andrology laboratory. PATIENT(S): Secondary infertility patient presenting for routine semen evaluation. INTERVENTION(S): Following diagnosis of a seminal infection, the patient was treated with an antibiotic. MAIN OUTCOME MEASURE(S): Semen quality parameters, semen culture, and electron microscopy identification of cytolysosomal spermophagy. RESULT(S): Semen culture identified a rare infection with Ralstonia picketti and electron microscopy showed massive neutrophil and cytolysosomal spermophagy. Both were eliminated after antibiotic therapy. CONCLUSION(S): This case study documents a rare infection of the reproductive tract with Ralstonia picketti. Analysis of large seminal masses determined their origin to be primarily from acellular cytolysosomes. The presence of such masses in semen should be further evaluated, including semen culture.

Adult↗

PubMed1996

Techniques for improving overall consistency of serial ECG analysis.

The techniques that improve the overall repeatability of computer interpretation of electrocardiograms (ECGs) that have been recorded several minutes apart from patients in a clinically stable condition are described. Estimates of the normal amounts of variability present in many ECG parameters that are used in the identification of a variety of cardiac abnormalities have been adopted in conjunction with smoothing techniques to form the basis of the new methodology. When applied to the Glasgow ECG analysis program, these new methods improve overall repeatability by about 31% when tested on a set of 263 pairs of ECGs. Randomly generated noise was added to the test set and an additional technique aimed at removing noise from the ECG tracings was used in conjunction with the smoothing methods. The observed improvement over the original repeatability was 63%.

Adult↗

PubMed2000

Automatic analysis for amperometrical recordings of exocytosis.

Amperometry is a widely used technique for monitoring the secretion of catecholamines (CA) by exocytosis. The use of carbon fibre microelectrodes allows the on-line recording of CA released from a single secretory vesicle. Amperometric signals are generated by oxidation of the quantally released CA close to the electrode tip. Each event of exocytosis is called a secretory spike. Here we describe a program written for IGOR (Wavemetrics, Lake Oswego, OR, USA), which may be used to analyze amperometric signals off-line. The procedures allow, (i) digital filtering and analysis of the current noise, spike identification and calculation of spike kinetic parameters; (ii) spike review; (iii) pooling spikes and data to create galleries, tables and histograms of measured parameters which can be exported to a graphic format or files for further analysis.

Action Potentials↗

PubMed2002

Fundamental issues, recent advances, and future directions in myodynamics.

A state-of-the-art report is presented on recent progress in selected areas of myodynamics, but also on problems that severely hamper the further development of the discipline. Significant advances have been made in elucidating the force-producing interaction between actin and the myosin-S1-subunit, including the localization of the most probable molecular site of power stroke initiation. Concerning the architecture of the myostructures, strong experimental evidence has accumulated for numerous intra-, inter-, and extramuscular pathways for lateral force transmission in addition to the serial sarcomere-to-sarcomere myotendinous path. It is shown that contemporary muscle models are inadequate in most respects and lag far behind the requirements an appropriate myodynamic model should fulfil. A similar comment applies to the current approaches designed to solve the myoskeletal indeterminacy problem. These formulations neglect myodynamic properties and do not allow for the implementation of biologically realistic objective functions. The solutions currently obtained are highly unsatisfactory. New research directions to rectify these situations are suggested, also with regard to the identification of subject-specific myodynamic parameters.

Adenosine Triphosphate↗

PubMed2000

Expediting the method development and quality control of reversed-phase liquid chromatography electrospray ionization mass spectrometry for pharmaceutical analysis by using an LC/MS performance test mix.

Mass spectrometry combined with liquid chromatography (LC/MS) has become an important analytical methodology in both pharmaceutical and biomolecule analyses. LC/MS, especially with reversed-phase HPLC (RP-LC), is extensively used in the separation and structural identification of pharmaceutical samples. However, many parameters have to be considered when a new LC/MS method is developed for either separation and structural analysis of unknown mixtures or quantitative analysis of a set of known compounds in an assay. The optimization of a new LC/MS method can be a time-consuming process. A novel kit-LC/MS performance test mix-composed of aspartame, cortisone, reserpine, and dioctyl phthalate has been developed to accelerate the process of establishing a new RP-LC/MS method. The LC/MS mix makes the evaluation and validation of an LC/MS method more efficient and easier. It also simplifies the quality control procedure for an LC/MS method in use.

Chromatography, High Pressure Liquid↗

PubMed2005

Development and validation of a fluorescence polarization-based competitive peptide-binding assay for HLA-A*0201--a new tool for epitope discovery.

Various approaches are currently proposed to successfully develop therapies for the prevention and treatment of infectious diseases and cancer. One of the most promising approaches is the development of vaccines that elicit cytotoxic T lymphocyte (CTL) responses. Consequently, identification and exact definition of molecular parameters involved in peptide-MHC class-I interactions of putative CTL epitopes are of prime importance for the development of immunomodulating compounds. To better facilitate epitope discovery, we developed and validated a novel state-of-the-art biochemical HLA-A0201 assay, which is comprised of technologically advanced cutting edge reagents. The technique is based on competition and uses a FITC-labeled reference peptide and highly purified soluble HLA-A0201 molecules to quantitatively measure the binding capacity of nonlabeled peptide candidates. Detection by fluorescence polarization allows real-time measurement of binding ratios without separation steps. During standardization, the problem of assay parameter variation is discussed, showing the dramatic influence of HLA and reference peptide concentrations as well as the choice of the reference peptide itself on IC(50) determinations. For validation, a panel of 15 well-defined HLA-A0201 ligands from various sources covering a broad range of binding affinities was tested. Binding data were used to compare against pre-existing quantitative assay systems. The results obtained demonstrated significant correlation among assay procedures, suggesting that the application of fluorescence polarization in combination with recombinant sHLA molecules is highly advantageous for the accurate assessment of peptide binding. Furthermore, the assay also features high-throughput screening capacity, providing uniquely efficient means of identifying and evaluating immune target molecules.

Binding Sites↗

PubMed2002

[Immunotherapy: new insights].

Immunotherapy of cancer, autoimmune diseases, and chronic viral infections is still in the early stages of development. This review deals with new immunotherapeutic approaches against tumors. Until now, a variety of specific and unspecific immunostimulatory strategies have been applied with only modest clinical success. The molecular characterization of novel human tumor antigens and the increased understanding of the immunological pathways involved in tumor immunity, however, have paved the way for the design of promising gene-based cellular cancer immune vaccines. Tumor antigens are readily available now and several ways to deliver antigen have been developed. The most important and widely used approaches consist of whole-cell vaccines, dendritic cell-based immunotherapy, and peptide vaccines. Clinical trials have, in general, demonstrated the safety of such strategies. There is, however, an important lack of information regarding to the correlation of clinical responses and analysis of the antitumoral immune effectors. Recently, exciting new immunological techniques and tools have been developed which allow to characterize antigen specific T cells at a single-cell level. In future, tumor rejection antigens have to be identified using new approaches such as reverse immunology which can be targeted therapeutically. A better quality control of the different immunotherapeutic approaches is mandatory if used in patients and the different therapeutic modalities need to be compared directly. This standardization of immunotherapeutic clinical trials may allow the identification of patient sub-groups responding favourably to treatment. The precise definition of immune parameters will ultimately result in optimised therapeutic approaches. Finally, the identification of antigen specific T and B cells by new assessment tools may result in novel surrogate markers for clinical diagnostic immunotherapy.

Animals↗

PubMed2002

Alteration of reaction and substrate specificity of a bacterial type III polyketide synthase by site-directed mutagenesis.

RppA, which belongs to the type III polyketide synthase family, catalyses the synthesis of 1,3,6,8-tetrahydroxynaphthalene (THN), which is the key intermediate of melanin biosynthesis in the bacterium Streptomyces griseus. The reaction of THN synthesis catalysed by RppA is unique in the type III polyketide synthase family, in that it selects malonyl-CoA as a starter substrate. The Cys-His-Asn catalytic triad is also present in RppA, as in plant chalcone synthases, as revealed by analyses of active-site mutants having amino acid replacements at Cys(138), His(270) and Asn(303) of RppA. Site-directed mutagenesis of the amino acid residues that are likely to form the active-site cavity revealed that the aromatic ring of Tyr(224) is essential for RppA to select malonyl-CoA as a starter substrate, since substitution of Tyr(224) by amino acids other than Phe and Trp abolished the ability of RppA to accept malonyl-CoA as a starter, whereas the mutant enzymes Y224F and Y224W were capable of synthesizing THN via the malonyl-CoA-primed reaction. Of the site-directed mutants generated, A305I was found to produce only a triketide pyrone from hexanoyl-CoA as starter substrate, although wild-type RppA synthesizes tetraketide and triketide pyrones in the hexanoyl-CoA-primed reaction. The kinetic parameters of Ala(305) mutants and identification of their products showed that the substitution of Ala(305) by bulky amino acid residues restricted the number of elongations of the growing polyketide chain. Both Tyr(224) (important for starter substrate selection) and Ala(305) (important for intermediate elongation) were found to be conserved in three other RppAs from Streptomyces antibioticus and Streptomyces lividans.

Acyl Coenzyme A↗

PubMed1999

Amount and organization of the heterochromatin in Olea europaea and related species.

The amount and spatial organization of the heterochromatin in nuclei of the shoot meristem and the frequency in the nuclear DNA of sequences belonging to a family of tandem repeats were investigated in cultivars of Olea europaea and related species. Significant differences between Olea species and between cultivars of O. europaea were observed: (i) in the spatial organization of the heterochromatin in interphase nuclei as determined by the number and surface area of the chromocentres; (ii) in genome size; and (iii) in the amount of condensed chromatin as measured by cytophotometry carried out at different thresholds of optical density. DNA elements belonging to a family of tandem repeats about 80 bp in length (OeTaq80 repeats) were isolated from the genomic DNA of an olive cultivar. It was shown: (i) by nucleotide sequence comparisons, that these repeats display variability in structure even within the same array, where different elements may share no more than 74% homology; (ii) by in situ hybridization, that OeTaq80-related DNA sequences are mainly localized in the heterochromatin at the chromosome ends; (iii) by dot-blot hybridization experiments, that these sequences are highly represented in the genome of all the olive cultivars and the majority of Olea species studied, and that their frequency may differ significantly even between olive cultivars; and (iv) by calculating the copy number of OeTaq80-related sequences per haploid (1C) genome, that the redundancy of these DNA elements may differ significantly between the genomes tested. It is suggested that the inter- and intraspecific changes in the nuclear and genomic traits observed can contribute to the understanding of the phylogenetic relationships between Olea species and in defining parameters to be exploited in varietal identification within cultivated olives.

Base Sequence↗

PubMed2003

Validation of the Hendrich II Fall Risk Model: a large concurrent case/control study of hospitalized patients.

This large case/control study of fall and non-fall patients, in an acute care tertiary facility, was designed to concurrently test the Hendrich Fall Risk Model. Cases and controls (355/780) were randomly enrolled and assessed for more than 600 risk factors (intrinsic/extrinsic). Standardized instruments were used for key physical attributes as well as clinician assessments. A risk factor model was developed through stepwise logistic regression. Two-way interactions among the risk factors were tested for significance. The best fitting model included 2 Log L chi square statistic as well as sensitivity and specificity values retrospectively. The result of the study is an easy to use validated Hendrich Fall Risk Model with eight assessment parameters for high-risk fall identification tested in acute care environments.

Accidental Falls↗

PubMedDate not supplied

[Narcissism inventory-90 (NI-90). Empirically-based reduction and identification of items sensitive for change--a questionnaire particularly suited for measuring self-regulatory parameters].

By analysing Narcissism Inventories [1] gathered by the admission from 639 consecutive in-patients, as well as a related sample of inventories gathered from 397 consecutive patients (7/93-7/96) by admission and discharge, we examined the possibility of reducing the number of items of the Narcissism Inventory without losing significant information. This examination shows that reducing the inventory to a total of 5 items per scale is reasonable, without a relevant loss of metric quality in the item-reduced scales. In addition, items particularly sensitive to change could be identified and pointedly kept in the new, reduced scales. Through the deliberate selection of these items, it was possible to produce an empirically-guided short-version of the Narcissism Inventory, suited particularly for the examination of clinical process and regulatory parameters. With persistence of the original 18 scales proposed by the authors of the original test, a reduction to a total of 90 items results. The name "Narcissism Inventory-90 (NI-90)" is, therefore, suggested for this new version.

Adult↗

PubMed2005

Osteoprotegerin and bone mineral density in hemodiafiltration patients.

A newly identified cytokine, osteoprotegerin (OPG) appears to be involved in the regulation of bone remodeling. In vitro studies suggest that OPG, a soluble member of the TNF receptor family of proteins, inhibits osteoclastogenesis by interrupting the intercellular signaling between osteoblastic stromal cells and osteoclast progenitors. As patients with chronic renal failure (CRF) often have renal osteodystrophy (ROD), we investigated the role of osteoprotegerin (OPG) in ROD, and investigated whether there was any relationship between serum OPG, intact parathyroid (PTH) (iPTH), vitamin D, and trabecular bone. Serum OPG combined with iPTH might be a useful tool in the noninvasive diagnosis of ROD, at least in cases in which the range of PTH values compromises reliable diagnosis. Thirty-six patients on maintenance hemodiafiltration (HDF) and a control group of 36 age and sex matched healthy subjects with no known metabolic bone disease were studied. The following assays were made on serum: iPTH, osteocalcin (BGP), bone alkaline phosphatase, 25(OH)-cholecalciferol, calcium, phosphate, OPG, IGF-1, estradiol, and free testosterone. Serum Ca++, P, B-ALP, BGP, IGF-1, iPTH, and OPG levels were significantly higher in HDF patients than in controls, while DXA measurements and quantitative ultrasound (QUS) parameters were significantly lower. On grouping patients according to their mean OPG levels, we observed significantly lower serum IGF-1, vitamin D3 concentrations, and lumbar spine and hip bone mineral density in the high OPG groups. No correlation was found between OPG and bone turnover markers, whereas a negative correlation was found between serum OPG and IGF-1 levels (r=-0.64, p=0.032). Serum iPTH concentrations were positively correlated with bone alkaline phosphatase (B-ALP) (r=0.69, p=0.038) and BGP (r=0.92, p<0.001). The findings made suggest that an increase in OPG levels may be a compensatory response to elevated bone loss. The low bone mineral density (BMD) levels found in the high OPG group might have been due to the significant decrease in serum IGF-1 and vitamin D3 observed. In conclusion, the findings made in the present study demonstrate that increased OPG in hemodiafiltration patients is only partly due to decreased renal clearance. As it may partly reflect a compensatory response to increased bone loss, this parameter might be helpful in the identification of patients with a marked reduction in trabecular BMD.

Absorptiometry, Photon↗

PubMed2005

Infection in social networks: using network analysis to identify high-risk individuals.

Simulation studies using susceptible-infectious-recovered models were conducted to estimate individuals' risk of infection and time to infection in small-world and randomly mixing networks. Infection transmitted more rapidly but ultimately resulted in fewer infected individuals in the small-world, compared with the random, network. The ability of measures of network centrality to identify high-risk individuals was also assessed. "Centrality" describes an individual's position in a population; numerous parameters are available to assess this attribute. Here, the authors use the centrality measures degree (number of contacts), random-walk betweenness (a measure of the proportion of times an individual lies on the path between other individuals), shortest-path betweenness (the proportion of times an individual lies on the shortest path between other individuals), and farness (the sum of the number of steps between an individual and all other individuals). Each was associated with time to infection and risk of infection in the simulated outbreaks. In the networks examined, degree (which is the most readily measured) was at least as good as other network parameters in predicting risk of infection. Identification of more central individuals in populations may be used to inform surveillance and infection control strategies.

Community-Acquired Infections↗

PubMed2006

EMERALD, AIMI, and PROMISE: is there still a potential for embolic protection in primary PCI?

The recent trials of routine use of embolic protection devices for primary percutaneous coronary interventions (PCI) (the EMERALD, PROMISE, and AIMI trials) have demonstrated neutral or even negative effects of these devices on myocardial reperfusion and final infarct size. Despite these results, there is still ground to believe that PCI-induced embolization may be clinically relevant in specific subsets of patients with acute myocardial infarction (AMI). Significant clinical consequences may be expected when embolization is quantitatively relevant and/or is qualitatively characterized by lipid-rich athero-embolism (as is the case of lipid core embolization through the ruptured cap of a fibro-atheroma). Future trials on embolic protection devices in primary PCI should adopt a selective, rather than a routine strategy, through the identification, by angiographic or intravascular imaging parameters, of patients at highest risk of clinically relevant embolization. Such trials should also adopt specific endpoints able to evaluate the effect of micro-embolization, which is currently far from optimally assessed by the standard markers of myocardial reperfusion.

Angioplasty, Balloon, Coronary↗

PubMed2000

Joint effects of genetic hitchhiking and background selection on neutral variation.

Due to relatively high rates of strongly selected deleterious mutations, directional selection on favorable alleles (causing hitchhiking effects on linked neutral polymorphisms) is expected to occur while a deleterious mutation-selection balance is present in a population. We analyze this interaction of directional selection and background selection and study their combined effects on neutral variation, using a three-locus model in which each locus is subjected to either deleterious, favorable, or neutral mutations. Average heterozygosity is measured by simulations (1) at the stationary state under the assumption of recurrent hitchhiking events and (2) as a transient level after a single hitchhiking event. The simulation results are compared to theoretical predictions. It is shown that known analytical solutions describing the hitchhiking effect without background selection can be modified such that they accurately predict the joint effects of hitchhiking and background on linked, neutral variation. Generalization of these results to a more appropriate multilocus model (such that background selection can occur at multiple sites) suggests that, in regions of very low recombination rates, stationary levels of nucleotide diversity are primarily determined by hitchhiking, whereas in regions of high recombination, background selection is the dominant force. The implications of these results on the identification and estimation of the relevant parameters of the model are discussed.

Alleles↗

PubMed2007

Effects of ring-porous and diffuse-porous stem wood anatomy on the hydraulic parameters used in a water flow and storage model.

Calibration of a recently developed water flow and storage model based on experimental data for a young diffuse-porous beech tree (Fagus sylvatica L.) and a young ring-porous oak tree (Quercus robur L.) revealed that differences in stem wood anatomy between species strongly affect the calibrated values of the hydraulic model parameters. The hydraulic capacitance (C) of the stem storage tissue was higher in oak than in beech (939.8 versus 212.3 mg MPa(-1)). Model simulation of the elastic modulus (epsilon) revealed that this difference was linked to the higher elasticity of the stem storage tissue of oak compared with beech. Furthermore, the hydraulic resistance (R (x)) of beech was about twice that of oak (0.1829 versus 0.1072 MPa s mg(-1)). To determine the physiological meaning of the R (x) parameter identified by model calibration, we analyzed the stem wood anatomy of the beech and oak trees. Calculation of stem specific hydraulic conductivity (k (s)) of beech and oak with the Hagen-Poiseuille equation confirmed the differences in R (x) predicted by the model. The contributions of different vessel diameter classes to the total hydraulic conductivity of the xylem were calculated. As expected, the few big vessels contributed much more to total conductivity than the many small vessels. Compared with beech, the larger vessels of oak resulted in a higher k (s) (10.66 versus 4.90 kg m(-1) s(-1) MPa(-1)). The calculated ratio of k (s) of oak to beech was 2, confirming the R (x) ratio obtained by model calibration. Thus, validation of the R (x) parameter of the model led to identification of its physiological meaning.

Fagus↗

PubMed1986

Intramammary lymphatic invasion in breast carcinomas. Evaluation using ABH isoantigens as endothelial markers.

Recent studies indicate that intramammary lymphatic invasion represents an important prognostic parameter in breast carcinomas. However, the identification of intramammary lymphatic invasion in tissue sections is a subjective procedure, frequently hampered by factors such as fixation artefacts and interobserver variations. In this study, monoclonal antibodies to ABH isoantigens were applied on formalin-fixed, paraffin-embedded breast carcinoma tissue by using the avidin-biotin-peroxidase complex technique. In addition, the H antigen was localized using the Ulex europeus agglutinin I lectin binding technique. Isoantigen localization provided excellent delineation of lymphatics and blood vessels, in general unhampered by the retention of isoantigen expression in some breast carcinomas. In comparison, Factor VIII-related antigen localization required prior trypsin enhancement and was less sensitive and less consistent. The staining for isoantigens was more intense in vascular than in lymphatic endothelium. ABH isoantigen localization of lymphatic channels identified lymphatic tumor emboli peripheral to and within the carcinomas, and distinguished bona fide intramammary lymphatic invasion from tissue shrinkage artefacts. The applicability to routinely processed tissue permits retrospective studies and renders the identification of intramammary lymphatic invasion a more objective procedure. Further studies are needed to assess the role of this technique in evaluating the prognostic value of intramammary lymphatic invasion; the technique may be extended also to the study of other neoplasms.

ABO Blood-Group System↗