Biomedical subjects

W de Vries

Publications and source records attributed to W de Vries.

At least 19 recordsLinked to original sources

PubMed2007

Water balances in intensively monitored forest ecosystems in Europe.

A soil hydrological model based on Darcy's law was used to calculate hydrological fluxes for 245 intensively monitored forest plots in Europe. Local measured input data for the model were rather limited and input was partly based on generic data. To obtain the best results, the model was calibrated on measured throughfall at the plots. Median transpiration fluxes are 350 mm; median leaching fluxes are 150 mm yr(-1) with the highest values in areas with high rainfall. Uncertainty analyses indicate that the use of local meteorological data instead of generic data leads to lower leaching fluxes at 70% of the plots due to an overestimation of the wind speed on basis of main meteorological stations. The underestimation of the leaching fluxes is confirmed by the median Cl fluxes which were slightly positive for the considered plots.

Adsorption↗

PubMed2006

Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA.

Inhibition of virus replication by means of RNA interference has been reported for several important human pathogens, including human immunodeficiency virus type 1 (HIV-1). RNA interference against these pathogens has been accomplished by introduction of virus-specific synthetic small interfering RNAs (siRNAs) or DNA constructs encoding short-hairpin RNAs (shRNAs). Their use as therapeutic antiviral against HIV-1 is limited, because of the emergence of viral escape mutants. In order to solve this durability problem, we tested DNA constructs encoding virus-specific long-hairpin RNAs (lhRNAs) for their ability to inhibit HIV-1 production. Expression of lhRNAs in mammalian cells may result in the synthesis of many siRNAs targeting different viral sequences, thus providing more potent inhibition and reducing the chance of viral escape. The lhRNA constructs were compared with in vitro diced double-stranded RNA and a DNA construct encoding an effective nef-specific shRNA for their ability to inhibit HIV-1 production in cells. Our results show that DNA constructs encoding virus-specific lhRNAs are capable of inhibiting HIV-1 production in a sequence-specific manner, without inducing the class I interferon genes.

Animals↗

PubMed2005

Interlaboratory comparison of three methods for the determination of the radon exhalation rate of building materials.

In this study three methods for the determination of the radon (222Rn) exhalation rate of building materials are compared. All three are so-called purge-and-trap methods in which the sample is enclosed in a container from which the exhaled radon is continuously purged by a constant flow of nitrogen gas. The outflowing radon is directed through a trapping agent, and the radon exhalation rate is subsequently calculated from the trapped activity. The main differences between the three methods are the trapping agent (silica gel, charcoal), trapping temperature (liquid nitrogen, room temperature), trapping period (30 min to 10 d), analytical method to determine the trapped activity (liquid scintillation counting, gamma ray spectrometry, total gamma counting) and the sample counting times (1 to 16 h). The repeatability and intralaboratory reproducibility are determined for one of the methods and amount to 3.1% and 4.3%, respectively. The intralaboratory reproducibility, derived from five samples with a radon release rate up to 450 microBq s(-1), was found to be 5.6% on average (range 3 to 8%). These figures are close to the combined standard uncertainty of the individual results that vary between 3 to 6%, depending on the method and method variables such as trapping period and the uncertainty of the calibration source. Furthermore, another 10 commercially available building materials were analyzed to investigate the correlation between the applied methods. Using linear regression analysis, it was found that the slope deviated not more than 10% from the one to one correspondence line. The results show that measurements of the exhalation rate can be carried out with a large degree of accuracy provided sufficient care is taken for a well-documented standard method.

Calibration↗

PubMed2004

Visual scoring versus histogram subtraction of in vivo binding of immunoglobulins against platelets after transfusion.

BACKGROUND: We developed a technique, in vivo binding of immunoglobulins in the platelet immunofluorescence test (IVBI-PIFT), that detects immunoglobulins bound in vivo to transfused platelets. The visually scored results of this technique, however, are susceptible to interobserver variation. We describe a more objective method to generate results in IVBI-PIFT. METHODS: We studied 201 samples in 120 patients with hematologic malignancies in the IVBI-PIFT. Histogram subtraction, i.e., fluorescence (anti-immunoglobulin G and fluorescein isothiocyanate) histogram before platelet transfusion subtracted from the histogram after platelet transfusion, was compared with visual scoring (pattern 1: no enhanced fluorescence before and after transfusion; pattern 2: enhanced fluorescence before and after platelet transfusion; pattern 3: enhanced fluorescence before transfusion; pattern 4: enhanced fluorescence after transfusion, interpreted as alloimmunization). After histogram subtraction, the number of remaining events (events post substraction, EPS) and the mean amount of fluorescence of these remaining events (mean channel post substraction, MCPS) were used and compared with the visual scoring and with platelet survival after transfusion. RESULTS: In 26 (13%) of the 201 samples studied in the IVBI-PIFT, fewer than three of five observers agreed on the visually scored pattern. In the 175 (87%) remaining samples, histogram subtraction showed a significant differentiation between pattern 4 and patterns 1 and 2 by using EPS, whereas patterns 4 and 3 were distinguished by using MCPS. The combination of EPS and MCPS differentiated best between pattern 4 and patterns 1, 2, and 3 (73% sensitivity, 96% specificity, 79% positive predictive value, and 95% negative predictive value). In contrast, the predictive value for platelet recovery after 1 and 16 h of pattern 4 from the visual scoring method and the results of histogram subtraction were poor. CONCLUSION: This objective method of histogram subtraction correlated well with the visual scoring method of IVBI-PIFT.

Animals↗

PubMed2004

Calibration of dosemeters used in mammography with different X ray qualities: EUROMET project no. 526.

The effect of different X ray radiation qualities on the calibration of mammographic dosemeters was investigated within the framework of a EUROMET (European Collaboration in Measurement Standards) project. The calibration coefficients for two ionization chambers and two semiconductor detectors were established in 13 dosimetry calibration laboratories for radiation qualities used in mammography. They were compared with coefficients for other radiation qualities, including those defined in ISO 4037-1, with first half value layers in the mammographic range. The results indicate that the choice of the radiation quality is not crucial for instruments with a small energy dependence of the response. However, the radiation quality has to be chosen carefully if instruments with a marked dependence of their response to the radiation energy are calibrated.

Calibration↗

PubMed2004

The value of crossmatch tests and panel tests as a screening tool to predict the outcome of platelet transfusion in a non-selected haematological population of patients.

BACKGROUND AND OBJECTIVES: Alloantibodies against platelets can be detected by using different laboratory tests. Most of these tests, which use panel cells or antigens as a target, perform poorly in non-selected haematological patients. In relation to these tests, a crossmatch test of transfused platelets and patient's serum may be viewed as the standard and may be superior in predicting donor platelet destruction by alloimmunization. MATERIALS AND METHODS: In 95 randomly selected thrombocytopenic patients with haematological malignancies, who were receiving leucodepleted blood products, 184 serum samples were studied in an in vitro crossmatch test by using the technique of the platelet immunofluorescence test (crossmatch-PIFT), in an in vivo crossmatch test detecting in vivo binding of immunoglobulins to transfused platelets according to the PIFT technique (in vivo-PIFT), in the indirect PIFT using five random donors as a target (panel-PIFT) and in an enzyme linked immunosorbent assay using immobilized human leucocyte antigens (HLAs) of 100 standardized donors (ELIHLA). The results of all these methods were related to the recovery at 1 and 16 h post-transfusion. RESULTS: The results of the crossmatch-PIFT were not associated with platelet recovery at 1 and 16 h after transfusion. Even in a subgroup of patients, in whom predefined clinical factors were excluded, no association with platelet recovery was found. The results of the crossmatch-PIFT correlated with those of the in vivo-PIFT (P = 0.02); however, 35 (19%) discrepant results were identified between these tests. The results of the crossmatch-PIFT were not related to the panel-PIFT (P = 0.25), but did relate to those of the ELIHLA (P = 0.02), still revealing 36 (20%) discrepant results. None of the in vivo-PIFT, the panel-PIFT or the ELIHLA was associated with platelet recovery after 1 h, whilst only a positive panel-PIFT was associated with poor platelet recovery at 16 h after transfusion (P = 0.03). CONCLUSIONS: In a population at low risk for alloimmunization, the correlation of test outcome and platelet recovery is poor. None of these crossmatch tests or screening tests was identified as superior to any other in this population.

Antigen-Antibody Reactions↗

PubMed2001

Assessments of impacts of nitrogen deposition on beech forests: results from the Pan-European Monitoring Programme.

The article reviews effects of nitrogen (N) deposition on beech forest ecosystems in Europe. On the basis of beech plots of the Pan-European Monitoring Programme of ICP Forests and the EU, the deposition of N compounds as well as input-output budgets are listed and compared with studies in North America. The authors also discuss the critical threshold for N leaching. At present, N is leached in 10% of the plots evaluated. An in-depth evaluation of a beech plot in central Germany is presented. The high N leaching results in a considerable increase (four times higher N content in 2000 compared to 1965) in the export of nitrate from the beech forests from a nearby source. Finally, ecophysiological indicators (N content in beech leaves, fine root system, N content, root/shoot ratios) are discussed as a result of high N input.

Aluminum↗

PubMed2001

Modeled impacts of farming practices and structural agricultural changes on nitrogen fluxes in the Netherlands.

In the Netherlands, nutrient emissions from intensive animal husbandry have contributed to decreased species diversity in (semi) natural terrestrial and aquatic ecosystems, pollution of groundwater, and possibly global warming due to N2O emissions. This paper presents the results of a modelling study presenting the impacts of both structural measures and improved farming practices on major nitrogen (N) fluxes, including NH3 and N2O emission, uptake, leaching, and runoff, in the Netherlands, using input data for the year 2000. Average annual fluxes (Gg N year(-1)) for the year 2000 were estimated at 132 for NH3 emission (160 Gg NH 3 year(-1)), 28 for N2O emission, 50 for N inflow to groundwater, and 15 for N inflow to surface water at a total N input of 1046. At this input, nitrate (NO3) concentrations in groundwater often exceeded the target of 50 mg NO3 l(-1), specifically in well-drained sandy soils. The ammonia (NH3) emissions exceeded emission targets that were set to protect the biodiversity of nonagricultural land. Improved farming practices were calculated to lead to a significant reduction in NH3 emissions to the atmosphere and N leaching and runoff to groundwater and surface water, but these improvements were not enough to reach all the targets set for those fluxes. Only strong structural measures clearly improved the situation. The NH3 emission target of 30 Gg NH3 year(-1), suggested for the year 2030, could not be attained, however, unless pig and poultry farming is completely banned in the Netherlands and all cattle stay almost permanently in low emission stables.

Agriculture↗

PubMed2001

Assessment of nitrogen ceilings for Dutch agricultural soils to avoid adverse environmental impacts.

In the Netherlands, high traffic density and intensive animal husbandry have led to high emissions of reactive nitrogen (N) into the environment. This leads to a series of environmental impacts, including: (1) nitrate (NO3) contamination of drinking water, (2) eutrophication of freshwater lakes, (3) acidification and biodiversity impacts on terrestrial ecosystems, (4) ozone and particle formation affecting human health, and (5) global climate change induced by emissions of N2O. Measures to control reactive N emissions were, up to now, directed towards those different environmental themes. Here we summarize the results of a study to analyse the agricultural N problem in the Netherlands in an integrated way, which means that all relevant aspects are taken into account simultaneously. A simple N balance model was developed, representing all crucial processes in the N chain, to calculate acceptable N inputs to the farm (so-called N ceiling) and to the soil surface (application in the field) by feed concentrates, organic manure, fertiliser, deposition, and N fixation. The N ceilings were calculated on the basis of critical limits for NO 3 concentrations in groundwater, N concentrations in surface water, and ammonia (NH3) emission targets related to the protection of biodiversity of natural areas. Results show that in most parts of the Netherlands, except the western and the northern part, the N ceilings are limited by NH 3 emissions, which are derived from critical N loads for nature areas, rather than limits for both ground- and surface water. On the national scale, the N ceiling ranges between 372 and 858 kton year(-1) depending on the choice of critical limits. The current N import is 848 kton year(-1). A decrease of nearly 60% is needed to reach the ceilings that are necessary to protect the environment against all adverse impacts of N pollution from agriculture.

Agriculture↗

PubMed2001

A review of the calculation procedure for critical acid loads for terrestrial ecosystems.

Target loads for acid deposition in the Netherlands, as formulated in the Dutch environmental policy plan, are based on critical load calculations at the end of the 1980s. Since then knowledge on the effect of acid deposition on terrestrial ecosystems has substantially increased. In the early 1990s a simple mass balance model was developed to calculate critical loads. This model was evaluated and the methods were adapted to represent the current knowledge. The main changes in the model are the use of actual empirical relationships between Al and H concentrations in the soil solution, the addition of a constant base saturation as a second criterion for soil quality and the use of tree species-dependant critical Al/base cation (BC) ratios for Dutch circumstances. The changes in the model parameterisation and in the Al/BC criteria led to considerably (50%) higher critical loads for root damage. The addition of a second criterion in the critical load calculations for soil quality caused a decrease in the critical loads for soils with a median to high base saturation such as loess and clay soils. The adaptation hardly effected the median critical load for soil quality in the Netherlands, since only 15% of the Dutch forests occur on these soils. On a regional scale, however, critical loads were (much) lower in areas where those soils are located.

Acid Rain↗

PubMed2000

Evidence against a redshift z > 6 for the galaxy STIS123627+621755.

The identification of galaxies at extreme distances provides the most direct information about the earliest phases of galaxy formation. But at redshifts z > 5 even the most luminous galaxies appear faint; the interpretation of low signal-to-noise ratio data is difficult and misidentifications do occur. Here we report optical and near-infrared observations of the source STIS123627+621755, which was previously suggested to be at a redshift of 6.68 (ref. 1). At that redshift, and with the reported spectral energy distribution, the galaxy should be essentially invisible at wavelengths less than 9,300 A, because the intervening intergalactic medium absorbs almost all light energetic enough to ionize neutral hydrogen--that is, with wavelengths less than the redshifted Lyman limit of lambda = (1 + z) x 912A. At near-infrared wavelengths, however, the galaxy should be relatively bright. Here we report a detection of the galaxy at 6,700 A and a non-detection at a wavelength of 1.2 microm, contrary to expectations for z approximately 6.68. The data conservatively require that STIS123627+621755 has a redshift z < 6.

Journal Article↗

PubMed2000

Cloning and characterization of human histone deacetylase 8.

To date, seven different human histone deacetylases (HDACs) have been identified, which fall into two distinct classes. We have isolated and characterized a cDNA encoding a novel human HDAC, which we name HDAC8. HDAC8 shows a high degree of sequence similarity to HDAC1 and HDAC2 and thus belongs to the class I of HDACs. HDAC8 is expressed in a variety of tissues. Human cells overexpressing HDAC8 localize the protein in sub-nuclear compartments whereas HDAC1 shows an even nuclear distribution. In addition, the HDAC8 gene is localized on the X chromosome at position q13, which is close to the XIST gene and chromosomal breakpoints associated with preleukemia.

Amino Acid Sequence↗

PubMed1999

Platelet-bound immunogloblins before and after platelet transfusion: measurement of in vivo binding.

In routine tests to investigate immunological mechanisms as a cause for enhanced destruction of transfused platelets; serum from the patient is tested against a panel of donor lymphocytes and platelets to demonstrate the presence of antibodies against HLA or platelet specific antibodies. Here we describe a flow cytometric technique in which in vivo binding of immunoglobulins (Ig) is measured. By comparing the histograms of the platelet suspensions before and after transfusion, four different patterns were obtained: no Ig binding before and after transfusion (pattern 1), pre-existent Ig binding (patterns 2 and 3) or preferential Ig binding to the transfused platelets (pattern 4). This technique was tested in 164 random platelet transfusions and 34 HLA-matched platelet transfusions. A statistically significant association was found between pattern 1 and a negative result of the indirect platelet immunofluorescence test for the detection of antibodies in the serum taken before the transfusion studied or a good platelet recovery and between pattern 4 and a positive indirect platelet immunofluorescence test or a low platelet recovery.

Autoimmunity↗

PubMed1998

Correction factors for the NMi free-air ionization chamber for medium-energy x-rays calculated with the Monte Carlo method.

A new method is described for the determination of x-ray quality dependent correction factors for free-air ionization chambers. The method is based on weighting correction factors for mono-energetic photons, which are calculated using the Monte Carlo method, with measured air kerma spectra. With this method, correction factors for electron loss, scatter inside the chamber and transmission through the diaphragm and front wall have been calculated for the NMi free-air chamber for medium-energy x-rays for a wide range of x-ray qualities in use at NMi. The newly obtained correction factors were compared with the values in use at present, which are based on interpolation of experimental data for a specific set of x-ray qualities. For x-ray qualities which are similar to this specific set, the agreement between the correction factors determined with the new method and those based on the experimental data is better than 0.1%, except for heavily filtered x-rays generated at 250 kV. For x-ray qualities dissimilar to the specific set, differences up to 0.4% exist, which can be explained by uncertainties in the interpolation procedure of the experimental data. Since the new method does not depend on experimental data for a specific set of x-ray qualities, the new method allows for a more flexible use of the free-air chamber as a primary standard for air kerma for any x-ray quality in the medium-energy x-ray range.

Air↗

PubMed1998

Enterococcal endocarditis--a case treated with teicoplanin and amoxycillin.

The study aimed to determine the antibacterial therapy effective in the cure of endocarditis caused by Enterococcus faecalis resistant to clinically achievable levels of vancomycin. Isolation of the causative enterococcus had been achieved by direct inoculation of the resected valve into the culture medium in theatre. The patient was known to have had an aortic valve defect since childhood and had recently undergone splenectomy following trauma. Blood cultures were negative prior to valve replacement. A perivalvular abscess was noted at operation. In vitro minimal bactericidal results and serum activity were the basis of the postoperative choice of drugs. The minimal bactericidal level of teicoplanin was 250 micrograms/ml and that of amoxycillin 64 micrograms/ml. Neither is achievable with the advocated dosage. A combination of these two cell-wall-active agents successfully eliminated the infection. Acting at two different sites in the synthesis of the bacterial cell wall, teicoplanin and amoxycillin were found to be bactericidal in vitro at the trough levels of the antibiotics in the serum. The patient recovered fully.

Adult↗

PubMed1996

Detection of static and dynamic activities using uniaxial accelerometers.

Rehabilitation treatment may be improved by objective analysis of activities of daily living. For this reason, the feasibility of distinguishing several static and dynamic activities (standing, sitting, lying, walking, ascending stairs, descending stairs, cycling) using a small set of two or three uniaxial accelerometers signals can be measured with a portable data acquisition system, which potentially makes it possible to perform online detection of static and dynamic activities in the home environment. However, the procedures described in this paper have yet to be evaluated in the home environment. Experiments were conducted on ten healthy subjects, with accelerometers mounted on several positions and orientations on the body, performing static and dynamic activities according to a fixed protocol. Specifically, accelerometers on the sternum and thigh were evaluated. These accelerometers were oriented in the sagittal plane, perpendicular to the long axis of the segment (tangential), or along this axis (radial). First, discrimination between the static or dynamic character of activities was investigated. This appeared to be feasible using an rms-detector applied on the signal of one sensor tangentially mounted on the thigh. Second, the distinction between static activities was investigated. Standing, sitting, lying supine, on a side and prone could be distinguished by observing the static signals of two accelerometers, one mounted tangentially on the thigh, and the second mounted radially on the sternum. Third, the distinction between the cyclical dynamic activities walking, stair ascent, stair descent and cycling was investigated. The discriminating potentials of several features of the accelerometer signals were assessed: the mean value, the standard deviation, the cycle time and the morphology. Signal morphology was expressed by the maximal cross-correlation coefficients with template signals for the different dynamic activities. The mean signal values and signal morphology of accelerometers mounted tangentially on the thigh and the sternum appeared to contribute to the discrimination of dynamic activities with varying detection performances. The standard deviation of the signal and the cycle time were primarily related to the speed of the dynamic activities, and did not contribute to the discrimination of the activities. Therefore, discrimination of dynamic activities on the basis of the combined evaluation of the mean signal value and signal morphology is proposed.

Activities of Daily Living↗

PubMed1993

Quantification of fluorescence properties of lymphocytes in peripheral blood mononuclear cell suspensions using a latent class model.

Lymphocytes, monocytes, granulocytes, and other blood cells can be distinguished on the basis of their forward (FSC) and sideward (SSC) light scatter properties and their expression of CD45 and CD14. A FSC,SSC gate can be set to include > 95% of the lymphocytes using a "back gating" procedure on the CD45+, CD14- cells. However, nonlymphoid cells such as monocytes have light scattering properties similar to lymphocytes. This problem occurs particularly in patient populations where the light scattering properties of lymphocyte subsets have changed (e.g., due to activation) and are similar to those of the monocytes. Thus, immunophenotyping using antibodies specific for other markers than CD45 and CD14 does not allow a direct assessment of the percentage of all lymphocytes positive for those markers. In order to optimize immunophenotyping we have developed analytic model in which the FSC,SSC dot plot is partitioned into six nonoverlapping light scatter regions. Each light scatter region contains a mixture population of different cell types, i.e., lymphocytes, monocytes, granulocytes, and other cells. The proportions of each cell type are known from the CD45,CD14 expression within each light scatter region. Under the assumption of independence of fluorescence and scatter properties conditional on cell type, the expression of markers other than CD45 or CD14 are derived from the cell type composition and the fluorescence properties on the other markers of each light scatter region. The underlying statistical model is a latent class model, and maximum likelihood estimates are computed using the expectation-maximization (EM) algorithm. The application of the model for immunophenotyping of lymphocytes of healthy individuals and cancer patients receiving immunotherapy is shown.

Antibodies, Monoclonal↗

PubMed1993

Acyclic directed graphs for automatic image analysis of lung parenchymal geometry.

We have developed a simple method for encoding pulmonary alveolar geometry suitable for morphometric analysis and modeling. The approach involves the use of 8-bit video microscopic images of lung which are thresholded to produce binary images. Each alveolar wall was thinned to its midline to produce a skeletonized image. We present an algorithm for converting such an image to an acyclic directed graph. Such a representation is quite suitable for mathematical treatment, lending itself to problems involving simulation or modeling. We present as an example application, the measurement of dihedral angles in rat lung using conventional histological sections.

Algorithms↗