Biomedical subjects

Paul H C Eilers

Publications and source records attributed to Paul H C Eilers.

At least 19 recordsLinked to original sources

PubMed2007

Data exploration in meta-analysis with smooth latent distributions.

Meta-analysis with discrete outcomes is interpreted as the estimation (in one or two dimensions) of a non-parametric smooth latent distribution of event probabilities (or rates). A simple but efficient EM algorithm is presented. A fine grid is used and fast smoothing is done by penalized least squares. Data exploration is the primary goal, but the estimated distribution can also be used to compute useful statistics of treatment effects.

Algorithms↗

PubMed2007

Role of tumor-derived proinflammatory cytokines GM-CSF, TNF-alpha, and IL-12 in the migration and differentiation of antigen-presenting cells in cervical carcinoma.

BACKGROUND: Proinflammatory cytokines are important in modifying the activity, differentiation, and migration of antigen-presenting cells and may influence the survival of cancer patients. The study assessed whether GM-CSF, TNF-alpha, and IL-12, produced by cervical cancer cells, are important for the activity, differentiation, and migration of antigen-presenting cells. METHODS: In 90 patients with cervical carcinoma the number of monocytes/tumor-associated macrophages (TAM), mature dendritic cells (DC), and Langerhans cells (LHC) was determined using immunohistochemistry. An RNA in situ hybridization technique was used to measure the expression level of GM-CSF, TNF-alpha, IL-12p35, and IL-12p40. RESULTS: TAM were detected intraepithelial as well as in the stroma of the tumor. LHC were only detected intraepithelial and mature DC only in the tumor stroma. The number of TAM correlated positively with the number of mature DC. The expression levels of GM-CSF and TNF-alpha correlated positively with the number of TAM and DC. TNF-alpha showed a negative correlation with the number of LHC. A significant correlation between the expression of functional IL-12 (IL-12p40) and stromal TAM was found. The expression of GM-CSF, TNF-alpha, and IL-12p40 did not correlate significantly with disease-free survival. However, high IL-12p40 expression was associated with a favorable cumulative overall survival. CONCLUSIONS: The results suggest that GM-CSF as well as TNF-alpha, produced by cervical carcinoma cells, may play a role in the differentiation of monocytes into mature DC. Furthermore, TNF-alpha may influence the migration of LHC from the tumor.

Adenocarcinoma↗

PubMed2006

Gastric accommodation and motility are influenced by the barostat device: Assessment with magnetic resonance imaging.

The barostat is considered the gold standard for evaluation of proximal gastric motility especially for the accommodation response to a meal. The procedure is invasive because it involves the introduction of an intragastric catheter and bag and is not always well tolerated. Moreover, the barostat bag itself may influence motility. Nowadays magnetic resonance imaging (MRI) is able to measure several aspects of gastric motility noninvasively. To evaluate whether the accommodation response of the stomach, observed with the barostat, is present during MRI and whether the barostat interferes with gastric physiology, gastric accommodation, motility, and emptying were studied twice in 14 healthy subjects with MRI using three-dimensional volume scans and two-dimensional dynamic scans once in the presence of a barostat bag and once when the barostat bag was not present. Fasting and postprandial intragastric volumes were significantly higher in the experiment with barostat vs. without barostat (fasting: 350 +/- 132 ml vs. 37 +/- 21 ml, P < 0.0001; postprandial: 852 +/- 126 ml vs. 361 +/- 62 ml, P < 0.0001). No significant differences were found in gastric emptying (88 +/- 41 vs. 97 +/- 40 ml/h, not significant) and contraction frequency between both experiments. The accommodation response observed in the presence of the barostat bag was not observed in the absence of the barostat bag. In conclusion, the presence of an intragastric barostat bag does not interfere with gastric emptying or motility, but the accommodation response measured with the barostat in situ is not observed without the barostat bag in situ. Gastric accommodation is a nonphysiological barostat-induced phenomenon.

Adult↗

PubMed2006

Hypercholesterolemia reduces collateral artery growth more dominantly than hyperglycemia or insulin resistance in mice.

OBJECTIVE: Collateral artery development (arteriogenesis), a vital compensatory mechanism in patients with arterial obstructive disease, may be deregulated by vascular risk factors, eg, diabetes or hypercholesterolemia. Here, we compared the effects of either disturbed glucose metabolism or disturbed lipid metabolism on arteriogenesis. METHODS AND RESULTS: Femoral artery occlusion was performed in streptozotocin(STZ)-treated mice, nonobese diabetic (NOD) mice, and insulin-resistant Ob/Ob mice on regular diet, and APOE3*Leiden mice on different hypercholesterolemic diets. Angiography and laser Doppler perfusion analysis of hindlimbs were performed postoperatively. Surprisingly, angiographic arteriogenesis was not impaired in diabetic and insulin-resistant mice. Perfusion recovery in STZ-treated and Ob/Ob mice was only decreased by 19% and 16%, respectively (P<0.05). Furthermore, perfusion recovery was unchanged between high-glycemic and mild-glycemic NOD mice. Angiographic arteriogenesis in APOE3*Leiden mice, however, was markedly impaired at 7 days and 14 days (P< or =0.01). Correspondingly, perfusion recovery was 41% decreased in APOE3*Leiden mice (P<0.05). There was an inverse correlation of perfusion recovery with plasma cholesterol (P=0.02), but not with triglyceride, free fatty acid, glucose, or insulin levels. CONCLUSIONS: Hypercholesterolemia reduces arteriogenesis more dominantly than hyperglycemia or hyperinsulinemia in mice. This suggests that a disturbed lipid metabolism as observed in diabetic patients might be crucial for the impairment of collateral formation.

Acute Disease↗

PubMed2006

Vascular endothelial growth factor a in eyes with uveal melanoma.

OBJECTIVES: To determine the presence of vascular endothelial growth factor A (VEGF-A) in the aqueous humor of eyes with uveal melanoma and to identify its source. METHODS: The VEGF-A concentrations were determined in aqueous humor samples obtained after enucleation from 74 eyes with untreated uveal melanoma and from 8 eyes with treated uveal melanoma. Patient survival and clinical and histopathological tumor variables were compared. In situ hybridization, Western blot analysis, and enzyme-linked immunosorbent assay were used to determine expression of VEGF-A in tumor tissue and in overlying retina. RESULTS: Aqueous VEGF-A concentrations ranged from 18 to 826 pg/mL in 74 untreated eyes, while concentrations in 30 control eyes were significantly lower (median, 50.1 pg/mL) (P<.001). Concentrations in 8 treated eyes were much higher (median, 364 pg/mL). In situ hybridization on tissue sections and Western blot analysis and enzyme-linked immunosorbent assay on tissue extracts revealed VEGF-A in uveal melanoma tissue and in retinal tissue. CONCLUSIONS: Uveal melanoma is associated with increased concentrations of VEGF-A in aqueous humor. Aqueous VEGF-A concentration correlates with largest basal tumor diameter and with the tumor height. In eyes with uveal melanoma, tumor and retinal tissues are sources of VEGF-A.

Adult↗

PubMed2006

Simple and multiple P-splines regression with shape constraints.

In many research areas, especially within social and behavioural sciences, the relationship between predictor and criterion variables is often assumed to have a particular shape, such as monotone, single-peaked or U-shaped. Such assumptions can be transformed into (local or global) constraints on the sign of the nth-order derivative of the functional form. To check for such assumptions, we present a non-parametric regression method, P-splines regression, with additional asymmetric discrete penalties enforcing the constraints. We show that the corresponding loss function is convex and present a Newton-Raphson algorithm to optimize. Constrained P-splines are illustrated with an application on monotonicity-constrained regression with both one and two predictor variables, using data from research on the cognitive development of children.

Algorithms↗

PubMed2005

Bayesian proportional hazards model with time-varying regression coefficients: a penalized Poisson regression approach.

One can fruitfully approach survival problems without covariates in an actuarial way. In narrow time bins, the number of people at risk is counted together with the number of events. The relationship between time and probability of an event can then be estimated with a parametric or semi-parametric model. The number of events observed in each bin is described using a Poisson distribution with the log mean specified using a flexible penalized B-splines model with a large number of equidistant knots. Regression on pertinent covariates can easily be performed using the same log-linear model, leading to the classical proportional hazard model. We propose to extend that model by allowing the regression coefficients to vary in a smooth way with time. Penalized B-splines models will be proposed for each of these coefficients. We show how the regression parameters and the penalty weights can be estimated efficiently using Bayesian inference tools based on the Metropolis-adjusted Langevin algorithm.

Bayes Theorem↗

PubMed2005

Sign constraints improve the detection of differences between complex spectral data sets: LC-IR as an example.

Spectroscopy is a fast and rich analytical tool. On many occasions, spectra are acquired of two or more sets of samples that differ only slightly. These data sets then need to be compared and analyzed, but sometimes it is difficult to find the differences. We present a simple and effective method that detects and extracts new spectral features in a spectrum coming from one set with respect to spectra of another set on the basis of the fact that these new spectral features are essentially positive quantities. The proposed procedure (i) characterizes the spectra of the reference set by a component model and (ii) uses asymmetric least squares (ASLS) to find differences with respect to this component model. It should be stressed that the method only focuses on new features and does not trace relative changes of spectral features that occur in both sets of spectra. A comparison is made with the conventional ordinary least squares (OLS) approach. Both methods (OLS and ASLS) are illustrated with simulations and are tested for size-exclusion chromatography with infrared detection (SEC-IR) of mixtures of polymer standards. Both methods are able to provide information about new spectral features. It is shown that the ASLS-based procedure yields the best recovery of new features in the simulations and in the SEC-IR experiments. Band positions and band shapes of new spectral features are better retrieved with the ASLS than with the OLS method, even those which could hardly be detected visually. Depending on the spectroscopic technique used, the ASLS-based method facilitates identification of the new chemical compounds.

Chromatography, Liquid↗

PubMed2005

Reliability of human serum protein profiles generated with C8 magnetic beads assisted MALDI-TOF mass spectrometry.

Protein profiling with mass spectrometry is a promising approach for classification and identification of biomarkers; however, there is debate about measurement quality and reliability. Here, we present a pipeline for preprocessing, statistical data analysis and presentation. Serum samples of 16 healthy individuals are used to generate protein profiles with high-resolution MALDI-TOF after isolation of peptides with C8 magnetic beads. Analysis of variance was performed after binning, baseline correction and normalization of the mean spectra. Relative variations in the spectra are expressed as coefficient of variation, which depending on the respective preanalytical variation parameter investigated, was found to range between 0.15 and 0.67 in this study. With this novel method, the reproducibility of our protein profiling procedure could be quantified. We showed that circadian rhythm and the number of freeze-thaw cycles had relatively limited influence on serum protein profiles, whereas the period between collection and serum centrifugation had a more pronounced effect.

Carbon↗

PubMed2005

Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single nucleotide polymorphism arrays.

Most human cancers show genetic instabilities leading to allelic imbalances, including loss of heterozygosity (LOH). Single nucleotide polymorphism (SNP) arrays can be used to detect LOH. Currently, these arrays require intact genomic DNA as obtained from frozen tissue; however, for most cancer cases, only low-quality DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is available. In this study, we tested Illumina BeadArrays to genotype FFPE tissue and detect LOH/allelic imbalances in matched colorectal tumor and normal tissue. Genotypes were compared between leukocyte and FFPE normal tissue as well as between frozen and FFPE tumor tissue. Identical genotypes and LOH profiles were obtained from normal and tumor isolates. LOH was mainly observed on chromosomes 4, 5q, 12q, 14q, 15q, 17p, 18, and 20p, which are commonly detected regions in colorectal cancer. LOH profiles of the BeadArrays were compared with profiles obtained by Affymetrix GeneChip 10K arrays, showing identical LOH patterns. These data show that genome-wide genotyping of FFPE tissue with the BeadArray gives reliable results and is a powerful technique for LOH analysis.

Colorectal Neoplasms↗

PubMed2005

Macrodissection versus microdissection of rectal carcinoma: minor influence of stroma cells to tumor cell gene expression profiles.

BACKGROUND: The molecular determinants of carcinogenesis, tumor progression and patient prognosis can be deduced from simultaneous comparison of thousands of genes by microarray analysis. However, the presence of stroma cells in surgically excised carcinoma tissues might obscure the tumor cell-specific gene expression profiles of these samples. To circumvent this complication, laser microdissection can be performed to separate tumor epithelium from the surrounding stroma and healthy tissue. In this report, we compared RNAs isolated from macrodissected, of which only surrounding healthy tissue had been removed, and microdissected rectal carcinoma samples by microarray analysis in order to determine the most reliable approach to detect the expression of tumor cell-derived genes by microarray analysis. RESULTS: As microdissection yielded low tissue and RNA quantities, extra rounds of mRNA amplification were necessary to obtain sufficient RNA for microarray experiments. These second rounds of amplification influenced the gene expression profiles. Moreover, the presence of stroma cells in macrodissected samples had a minor contribution to the tumor cell gene expression profiles, which can be explained by the observation that more RNA is extracted from tumor epithelial cells than from stroma. CONCLUSION: These data demonstrate that the more convenient procedure of macrodissection can be adequately used and yields reliable data regarding the identification of tumor cell-specific gene expression profiles.

Carcinoma↗

PubMed2005

Substantial changes in gene expression of Wnt, MAPK and TNFalpha pathways induced by TGF-beta1 in cervical cancer cell lines.

Transforming growth factor-beta 1 (TGF-beta1) is a potent inhibitor of epithelial cell proliferation. During the development of cervical carcinoma however, an increase in production of TGF-beta1 is accompanied by decreased sensitivity for the growth-limiting effect of TGF-beta1. TGF-beta1 has an anti-proliferative effect on cells of the immune system and thus can be advantageous for tumor progression. The aim of the present study was to determine the effect of TGF-beta1 on mRNA expression profile of genes in pathways involved in cell growth and cell death, in cervical carcinoma cell lines with different sensitivity to TGF-beta1. For this purpose, we have investigated changes in gene expression in TGF-beta1 stimulated cervical cancer cell lines with high (CC10B), intermediate (SiHa) and low (HeLa) sensitivity to the anti-proliferative effect of TGF-beta1, at timepoints 0, 6, 12 and 24 h. Microarray analysis, using Affymetrics focus arrays, representing 8973 genes, was used to measure gene expression. In our study novel target genes involved in tumor necrosis factor alpha (TNFalpha), mitogen-activated protein kinase (MAPK) and wingless type (Wnt) pathways in response to TGF-beta1 were found. Substantial differences in gene expression between TGF-beta1 sensitive and insensitive cell lines were observed involving genes in TNFalpha, MAPK, Wnt and Smad pathways. Since these pathways are implicated in cell proliferation and cell death, these pathways may play a role in determining the overall sensitivity of a cell to TGF-beta1 induced cell growth inhibition. The results were subsequently validated by quantitative real-time PCR. Increased resistance to TGF-beta1 induced cell growth inhibition was correlated with an elevated production of TGF-beta1 by the cell lines, as measured by enzyme linked immunosorbent assay. TGF-beta1 production did not inhibit cell growth, since blocking TGF-beta1 protein by anti-TGF-beta had no effect on cell proliferation. TGF-beta1 excretion by tumor cells more likely contributes to paracrine stimulation of tumor development.

Base Sequence↗

PubMed2005

The use of Bcl-2 and PTHLH immunohistochemistry in the diagnosis of peripheral chondrosarcoma in a clinicopathological setting.

Distinguishing osteochondroma from low-grade secondary peripheral chondrosarcoma can be difficult. In osteochondroma, growth-signalling pathways are thought to be downregulated through exostosin (EXT) inactivation. A previous pilot study focusing on expression of putative EXT downstream effectors indicated that progression of osteochondroma towards grade I chondrosarcoma was characterised by upregulation of Bcl-2 and parathyroid hormone-like hormone (PTHLH). We investigated their use as diagnostic markers in a large nationwide series of 71 osteochondromas and 34 chondrosarcomas. Bcl-2 immunohistochemistry proved to be a valuable diagnostic tool: scoring negative in 95% (specificity) of the osteochondromas and positive in 57% (sensitivity) of the chondrosarcomas, reaching a positive predictive value of 84% and negative predictive value of 82%. Positivity was not related to age, hereditary status, gender or thickness of the cartilage cap. Presence of internal controls and verification using mRNA in situ hybridisation strengthened the reliability of the immunohistochemical staining. PTHLH showed more variable staining, being positive in osteochondromas from females or adolescent males, suggesting age- and gender-dependent expression. Thus, in cases where the distinction between osteochondroma and chondrosarcoma is difficult, Bcl-2 is a valuable diagnostic marker for malignancy, regardless of tumour size, patient gender or age, and this can be extended with PTHLH for non-adolescent male patients.

Adolescent↗

PubMed2005

Chondromyxoid fibroma resembles in vitro chondrogenesis, but differs in expression of signalling molecules.

Chondromyxoid fibroma is a rare benign cartilaginous bone tumour characterized by morphological features that resemble different steps of chondrogenesis in terms of both cellular morphology, ranging from spindled to rounded cells, and the extracellular matrix formed, which ranges from fibrous to cartilaginous. The presence in chondromyxoid fibroma of signalling molecules that regulate the spatial expression of proteins involved in normal cartilage proliferation and differentiation was investigated in samples from 20 patients and compared with articular chondrocytes from 11 normal donors cultivated in 3D pellet culture. Sections were stained with safranin-O and H&E, and immunohistochemistry was performed for p16, cyclin D1, FGFR3, BCL2, p21, PTHLH, PTHR1 and N-cadherin. Expression patterns were analysed using hierarchical clustering. In chondromyxoid fibroma, specific morphological features correlated with a distinct pattern of expression. Comparison with normal chondrocytes in pellet culture showed a striking morphological resemblance, but with an unmistakably different pattern of expression. N-cadherin, PTHLH, and PTHR1 were expressed to a significantly higher level (p < 0.01) in articular chondrocyte pellets but, conversely, there was significantly lower expression of cyclin D1, p16 and BCL2 (p < 0.05) in these cells. Morphological similarities reflect common steps in cartilage differentiation, albeit driven by different molecular mechanisms. The proteins we have found to be differentially expressed seem crucial for neoplastic chondrogenesis.

Bone Neoplasms↗

PubMed2004

Quantile smoothing of array CGH data.

MOTIVATION: Plots of array Comparative Genomic Hybridization (CGH) data often show special patterns: stretches of constant level (copy number) with sharp jumps between them. There can also be much noise. Classic smoothing algorithms do not work well, because they introduce too much rounding. To remedy this, we introduce a fast and effective smoothing algorithm based on penalized quantile regression. It can compute arbitrary quantile curves, but we concentrate on the median to show the trend and the lower and upper quartile curves showing the spread of the data. Two-fold cross-validation is used for optimizing the weight of the penalties. RESULTS: Simulated data and a published dataset are used to show the capabilities of the method to detect the segments of changed copy numbers in array CGH data.

Algorithms↗

PubMed2004

New background correction method for liquid chromatography with diode array detection, infrared spectroscopic detection and Raman spectroscopic detection.

A new method to eliminate the background spectrum (EBS) during analyte elution in column liquid chromatography (LC) coupled to spectroscopic techniques is proposed. This method takes into account the shape and also intensity differences of the background eluent spectrum. This allows the EBS method to make a better estimation of the background eluent spectrum during analyte elution. This is an advantage for quantification as well as for identification of analytes. The EBS method uses a two-step procedure. First, the baseline spectra are modeled using a limited number of principal components (PCs). Subsequently, an asymmetric least squares (asLS) regression method is applied using these principal components to correct the measured spectra during elution for the background contribution. The asymmetric least squares regression needs one parameter, the asymmetry factor p. This asymmetry factor determines relative weight of positive and negative residuals. Simulations are performed to test the EBS method in well-defined situations. The effect of spectral noise on the performance and the sensitivity of the EBS method for the value of the asymmetry factorp is tested. Two applications of the EBS method are discussed. In the first application, the goal is to extract the analyte spectrum from an LC-Raman analysis. In this case, the EBS method facilitates easy identification of unknown analytes using spectral libraries. In a second application, the EBS method is used for baseline correction in LC-diode array detection (DAD) analysis of polymeric standards during a gradient elution separation. It is shown that the EBS method yields a good baseline correction, without the need to perform a blank chromatographic run.

Spectrophotometry, Infrared↗

PubMed2004

Gene expression of parathyroid tumors: molecular subclassification and identification of the potential malignant phenotype.

Parathyroid tumors are heterogeneous, and diagnosis is often difficult using histologic and clinical features. We have undertaken expression profiling of 53 hereditary and sporadic parathyroid tumors to better define the molecular genetics of parathyroid tumors. A class discovery approach identified three distinct groups: (1) predominantly hyperplasia cluster, (2) HRPT2/carcinoma cluster consisting of sporadic carcinomas and benign and malignant tumors from Hyperparathyroidism-Jaw Tumor Syndrome patients, and (3) adenoma cluster consisting mainly of primary adenoma and MEN 1 tumors. Gene sets able to distinguish between the groups were identified and may serve as diagnostic biomarkers. We demonstrated, by both gene and protein expression, that Histone 1 Family 2, amyloid beta precursor protein, and E-cadherin are useful markers for parathyroid carcinoma and suggest that the presence of a HRPT2 mutation, whether germ-line or somatic, strongly influences the expression pattern of these 3 genes. Cluster 2, characterized by HRPT2 mutations, was the most striking, suggesting that parathyroid tumors with somatic HRPT2 mutation or tumors developing on a background of germ-line HRPT2 mutation follow pathways distinct from those involved in mutant MEN 1-related parathyroid tumors. Furthermore, our findings likely preclude an adenoma to carcinoma progression model for parathyroid tumorigenesis outside of the presence of either a germ-line or somatic HRPT2 mutation. These findings provide insights into the molecular pathways involved in parathyroid tumorigenesis and will contribute to a better understanding, diagnosis, and treatment of parathyroid tumors.

Gene Expression Profiling↗

PubMed2004

Enhancing scatterplots with smoothed densities.

MOTIVATION: Scatterplots of microarray data generally contain a very large number of dots, making it difficult to get a good impression of their distribution in dense areas. RESULTS: We present a fast and simple algorithm for two-dimensional histogram smoothing, to visually enhance scatterplots. AVAILABILITY: Functions for Matlab and R are available from the corresponding author.

Algorithms↗