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PubMed2004

[A multidisciplinary mModule for oncological documentation within a hospital information system].

The follow-up documentation of oncological patients in Germany is inadequate in many cases: it is usually limited to a minimal dataset mandated by the epidemiological tumor registers; it is carried out in a paper-based fashion and rarely in a multi-disciplinary context. Parallel documentation efforts can result in redundant or erroneous data and excess work. The introduction of hospital information systems (HIS) allows the implementation of digital oncological documentation systems integrated in surrounding clinical workflows that can provide access to existing data sources as well as data entry and presentation across departmental boundaries. This concept enables the integration of tumor documentation, quality assurance and process optimization within HIS. Feasibility requirements include a high flexibility and adaptability of the underlying HIS to reach a seamless integration of oncological documentation forms within routine clinical workflows. This paper presents the conceptual design and implementation of a modular oncological documentation system at the Muenster University Hospital that is capable of integrating the documentation requirements of multiple departments within the hospital.

Computer Systems↗

PubMed2001

Quantitative microbiological risk assessment.

The production of safe food is being increasingly based on the use of risk analysis, and this process is now in use to establish national and international food safety objectives. It is also being used more frequently to guarantee that safety objectives are met and that such guarantees are achieved in a cost-effective manner. One part of the overall risk analysis procedure-risk assessment-is the scientific process in which the hazards and risk factors are identified, and the risk estimate or risk profile is determined. Risk assessment is an especially important tool for governments when food safety objectives have to be developed in the case of 'new' contaminants in known products or known contaminants causing trouble in 'new' products. Risk assessment is also an important approach for food companies (i) during product development, (ii) during (hygienic) process optimalization, and (iii) as an extension (validation) of the more qualitative HACCP-plan. This paper discusses these two different types of risk assessment, and uses probability distribution functions to assess the risks posed by Escherichia coli O157:H7 in each case. Such approaches are essential elements of risk management, as they draw on all available information to derive accurate and realistic estimations of the risk posed. The paper also discusses the potential of scenario-analysis in simulating the impact of different or modified risk factors during the consideration of new or improved control measures.

Animals↗

PubMed2004

Structural elucidation of catechin and epicatechin in sorrel leaf extracts using liquid-chromatography coupled to diode array-, fluorescence-, and mass spectrometric detection.

Flavonoids are natural compounds in medicinal herbs and posses several biological activities important in plant drug design. Especially strong antioxidant effects play an important role against radical oxidative stress causing pathological processes, such as arteriosclerosis or cancer. The aim of this work was to investigate unknown analytes found in sorrel leaf (Rumex acetosa) extracts in order to discover new leading compounds to enable quality control in phytopharmaceuticals made thereof. Therefore compounds of interest were separated after methanolic extraction by reversed-phase liquid chromatography (RP-LC) employing silica-C18 as stationary phase using gradient elution with water (10 mM H3PO4) and acetonitrile as mobile phase. Structural elucidation was carried out by diode array, fluorescence, and mass spectroscopic detection. Photodiode-array detection allowed the extraction of UV-absorbance spectra from the peaks of interest. Absorbance maxima were found at 203 and 279 nm with a shoulder at 230 nm. Additionally fluorescence emission and excitation spectra were recorded from the analytes using a fluorescence detector (FLD) after stop flow (lambdaex = 279 nm, lambdaem = 307 nm). The chromatographic reversed-phase system was coupled to an ion-trap mass spectrometer (LC-MS) by using an electrospray ionization interface (ESI). After optimization processes the separation was carried out using an ammonium acetate buffer at pH 5.5. Mass spectrometric detection turned out to be more sensitive in negative mode. Collisionally induced dissociation (CID) was used to obtain fragment ions of structural relevance (LC-MS/MS). Finally, compounds of interest coming from sorrel leaf (Rumex acetosa) eluting at low acetonitrile concentrations were confirmed to be catechin and epicatechin.

Catechin↗

PubMed2004

Temperature effect on Listeria monocytogenes growth in the event of contamination of cooked pork products.

The aim of this study was to describe the effect of temperature on the growth of Listeria monocytogenes in the event of postprocess contamination of packaged pork meats. This study was carried out in two steps. In the first step, the effect of temperature on L. monocytogenes growth rates was determined in duplicates at 13 temperatures between 2 and 43 degrees C by turbidimetric methods and adjusted by a quantitative secondary model. Then, seven sets of growth kinetics were collected by challenge testing in white pudding and roulade, both cooked pork products prepared according to an industrial process and stored at suboptimal temperatures ranging from 2 to 20 degrees C. In the second step, objectives were to (i) collect direct information on the temperature effect of L. monocytogenes on the two pork products, (ii) compare the two products regarding L. monocytogenes exposure, and (iii) compare results given by modeling (step i) with results obtained independently and then evaluate the model application domain. Each kinetic was built with at least 10 experimental data and two replicates. Comparison between L. monocytogenes behavior at 4 degrees C on white pudding and roulade indicated that both meat products were affected by food safety problems. Indeed, after contamination and storage for 10 days at 4 degrees C, the bacterial population increased by 2 log CFU/g in both products. Comparison between growth kinetic simulations and experimental data obtained separately gave satisfactory conclusions; the difference between observed and predicted bacterial population values was always less than 1 log CFU/g and a bias factor of 1.18 when growth rates were compared. These results applied to L. monocytogenes contamination of white pudding or roulade can now be used either in the management of optimal process and distribution networks or in risk assessment (exposure assessment).

Animals↗

PubMed2004

Effect of multislice scanners on patient dose from routine CT examinations in East Anglia.

As part of the dose optimization process, the Ionising Radiation (Medical Exposure) Regulations 2000 include requirements relating to the assessment of patient dose, and the setting and subsequent review of diagnostic reference levels. In East Anglia, audits of effective dose in CT have been carried out in 1996, 1999 and 2002. In the 2002 audit, nine of the 14 scanners assessed had been replaced since the previous audit. Eight of the new scanners were multislice scanners, acquiring up to 16 slices in a single rotation. The objective of the 2002 audit was to investigate the effect of the introduction of these multislice scanners on patient doses from routine CT examinations. Exposure parameters were collected for 10 different types of routine CT examination. In excess of 550 sets of patient data were obtained. For each of these, effective doses were calculated using the results of Monte Carlo simulations published by the National Radiological Protection Board. Averaged across all 10 examinations, regional mean effective doses are 34% higher than in 1999. The multislice scanners in the region give, on average, 35% more effective dose than the single-slice scanners. The effect of collimation in multislice scanners makes these effective dose differences most notable for examinations that use narrow slice widths. Further optimization of exposures on multislice scanners has the potential to reduce the differences observed between single-slice and multislice doses. However, when taken in combination with the increased use of CT in many hospitals, the effective dose increases observed are likely to result in a significant increase in the already substantial collective radiation dose from CT.

England↗

PubMed1992

Geostatistical and morphological methods applied to three-dimensional microscopy.

Three-dimensional (3-D) images of osteocyte lacunae were examined on a confocal microscope. Both geostatistical and morphological processing techniques were used to improve and to analyse them. By a geostastical approach, this study aims at improving 3-D confocal images before any further image processing. Optimized linear filters, which take account of the second-order statistics and the 3-D structure of the data, allow for the removal of imperfections such as noise and/or blur due to the axial convolution, and interpolate voxels on a face-centred cubic grid from an initial cubic grid. An application of this technique to 3-D biological images is demonstrated. In a second step, a 3-D binary image is digitized and cleaned with 3-D morphological filters. The standard 3-D measurements cannot be applied in this case, since all osteocytes cut the border of the field. For this reason a 3-D Boolean model has been adjusted, from which it is possible to derive all useful information on the repartition and the morphology of the osteocytes.

Humans↗

PubMed1996

Infective endocarditis: ten-year review of medical and surgical therapy.

BACKGROUND: Infective endocarditis is a complex disease process. Optimal outcome often requires both medical and surgical expertise. The need for and timing of surgical intervention is controversial and continues to evolve in parallel to advancements in diagnosis and treatment. Our experience with the treatment of infective endocarditis is reviewed herein. METHODS: A retrospective review was compiled of 140 consecutive patients who fulfilled the modified von Reyn criteria for the diagnosis of endocarditis between January 1982 and April 1992. RESULTS: Patient characteristics, symptoms, and risk factors are described. Follow-up averaged 3.5 +/- 0.8 years and totaled 491 patient-years. New York Heart Association functional class at presentation had a significant influence on survival (p < 0.0001). Long-term survival was significantly greater (p = 0.036) in patients treated medically/surgically than those treated with medical therapy alone (75% versus 54% at 5 years). Medical treatment of aortic and prosthetic endocarditis was associated with higher mortality (58% and 67%, respectively) when compared with combined medical/surgical treatment (28% and 38%, respectively). Among the survivors, New York Heart Association class at follow-up was better (p < 0.0001) in the medical/surgical group (1.05 +/- 0.04) versus the medical treatment group (1.70 +/- 0.14). CONCLUSIONS: Combined medical/surgical treatment for infective endocarditis is associated with improved survival. Patients with aortic or prosthetic endocarditis are identified as subgroups that benefit most from surgical intervention. Valvular dysfunction incited by the infective process is an important factor that should be weighed carefully in the therapeutic decision.

Adolescent↗

PubMed1996

Implications of 3-dimensional target shape and motion in aperture design.

To determine the shape of a radiation beam aperture a margin is typically applied to the clinical target volume (CTV) to yield the planning target volume (PTV), and the aperture is then determined from the projection of the PTV onto the aperture plane. This margin accounts for setup variability and organ motion originating from respiration or other physiologic processes. The use of either a uniform margin, or alternatively one which takes into account only the expected magnitude and direction of target motion, fails to account for the three-dimensional nature of the target; such a method neglects the volumetric effect of target shape on the fractional target volume irradiated when the target shifts partially out of the aperture. A mathematical framework is developed to analyze and illustrate the consequences of irradiating an irregular target shape in the presence of target motion. The effect of target shape on volume coverage is demonstrated for selected cases involving conventional BEV aperture design techniques. The volumetric implications of target shape are considered from two complementary points of view. The first involves transformation into a "displacement space," which isolates the volumetric effect of the shape of the target allowing it to be studied independently of the probability distribution of target motion. The second point of view combines the effects of the 3D target shape and the probability distribution of motion in a manner independent of beam direction to yield a 3D "target distribution." The two points of view represent distinct starting points for computation of the expected value of fractional target volume coverage in the presence of target motion. In certain cases it may be beneficial to (1) employ "target distributions" for the target and normal tissues in place of the conventional static PTV and, (2) include the aperture shape, on equal footing with parameters such as beam weights and energies, into a quantitative optimization process explicitly accounting for uncertainties in the position of the target volume and critical structures.

Equipment Design↗

PubMed1998

Influence of physical exercise on aging rats. III. Life-long exercise modifies the aging changes of the mechanical properties of limb muscle tendons.

We have previously shown that long-term regular physical exercise has a systemic influence on the rat by slowing the aging of its connective tissues, measured as thermal stability and biomechanical properties of tail tendons. This paper analyses whether the properties of limb muscle tendons are influenced not only by the aging process and the systemic effects of exercise but also from direct mechanical stimuli from long-term physical exercise. Male Sprague-Dawley rats were trained in a treadmill from the age of 5 to 23 months. The effects of training on muscle tendons were analyzed with respect to biomechanical properties. Also, the viscoelastic activation energies for interactions between collagen and the proteoglycan gel as well as between collagen fibrils were measured. Finally the asymptotes from the creep curves were calculated in order to estimate the magnitude of the viscoelastic creep. The effects of aging were analyzed with respect to the same parameters by comparing the group of 23-month-old sedentary rats with a 5-month-old baseline group. The biomechanical parameters did not change significantly with physical exercise. Neither did the activation energies change, but the asymptotes of the creep curves decreased, showing that there was less viscoelastic creep. Aging rendered the tendons significantly stronger and stiffer, increased the energy-absorbing capacity and decreased the strain values. The activation energies did not change with aging, but the high creep curve asymptote for the flexor tendons decreased. We conclude that aging rendered both types of tendons stiffer, and decreased their strain values at breaking point. Aging also increased the stress value, the energy absorption and the dry weight for the flexor tendon. Further, while physical exercise has a systemic delaying effect on age changes in connective tissues, in tendons subjected to substantial mechanical loads this effect as measured with biomechanical methods is counteracted by the optimization process elicited by the same physical exercise.

Aging↗

PubMed1996

Structure optimization of an artificial neural filter detecting membrane-spanning amino acid sequences.

An artificial neural network has been developed for the recognition and prediction of transmembrane regions in the amino acid sequences of human integral membrane proteins. It provides an additional prediction method besides the common hydrophobicity analysis by statistical means. Membrane/nonmembrane transition regions are predicted with 92% accuracy in both training and independent test data. The method used for the development of the neural filter is the algorithm of structure evolution. It subjects both the architecture and parameters of the system to a systematical optimization process and carries out local search in the respective structure and parameter spaces. The training technique of incomplete induction as part of the structure evolution provides for a comparatively general solution of the problem that is described by input-output relations only. Seven physiochemical side-chain properties were used to encode the amino acid sequences. It was found that geometric parameters like side-chain volume, bulkiness, or surface area are of minor importance. The properties polarity, refractivity, and hydrophobicity, however, turned out to support feature extraction. It is concluded that membrane transition regions in proteins are encoded in sequences as a characteristic feature based on the respective side-chain properties. The method of structure evolution is described in detail for this particular application and suggestions for further development of amino acid sequence filters are made.

Algorithms↗

PubMed1999

The Design of Leadlike Combinatorial Libraries.

The optimization of low-potency leads into drugs is often accompanied by an increase in molecular weight (M(r)) and lipophilicity, as a consequence of affinity enhancement. Hits with affinity at µM levels discovered by screening leadlike libraries allow scope for this optimization process, as shown schematically by the distributions of M(r) for a leadlike library (1), oral drugs (2), and a typical combinatorial chemistry library (3). y=percentage with a particular molecular weight.

Journal Article↗

PubMed2000

Green fluorescent protein in Saccharomyces cerevisiae: real-time studies of the GAL1 promoter.

Green fluorescent protein (GFP) was used to study the regulation of the galactose-inducible GAL1 promoter in yeast Saccharomyces cerevisiae strains. GFP was cloned into the pGAL110 vector and transformed into the yeast strains. Time course studies comparing culture fluorescence intensity and GFP concentration were conducted along with on-line monitoring of GFP expression. Our results demonstrated that GFP fluorescence could be used as a quantifiable on-line reporter gene in yeast strains. The effect of an integrated GAL10p-GAL4 transcription cassette was investigated. Induction time studies showed that there was no significant difference in GFP expression level by adding galactose at different culture times. A wide range of galactose concentrations was used to study the initial galactose concentration effect on GFP expression kinetics. A minimum of 0.05 g/L galactose doubled the GFP fluorescence signal as compared to the control, whereas 0.1 g/L gave the highest specific GFP yield. A simple analytical model was proposed to describe GFP expression kinetics based on the experimental results. In addition, this GFP-based approach was shown to have potential use for high-throughput studies. The use of GFP as a generic tool provided important insights to the GAL expression system and has great potential for further process optimization applications.

Blotting, Western↗

PubMed2001

An evaluation of the detection limits possible for competitive capillary electrophoretic immunoassays.

Using a high-affinity antibody for estradiol, thermodynamic and experimental limitations on detection limits for competitive capillary electrophoretic immunoassays were examined. Theoretical modeling of the dose-response curves for such assays allowed for optimization of experimental conditions. Through the examination of experimental and theoretical results generalizations could be made as to the ability of capillary electrophoretic immunoassays to achieve low detection limits. An experimental detection limit of 310 pM, corresponding to 2100 molecules, was achieved. A minimum theoretical detection limit for the antibody of interest was approximated to be 125-525 pM depending on the standard deviation. An overview of the optimization process is given as well as commentary on theoretical predictions.

Antibodies↗

PubMed2004

Morphologically structured model for antitumoral retamycin production during batch and fed-batch cultivations of Streptomyces olindensis.

A morphologically structured model is proposed to describe trends in biomass growth, substrate consumption, and antitumoral retamycin production during batch and fed-batch cultivations of Streptomyces olindensis. Filamentous biomass is structured into three morphological compartments (apical, subapical, and hyphal), and the production of retamycin, a secondary metabolite, is assumed to take place in the subapical cell compartment. Model accounts for the effect of glucose as well as complex nitrogen source on both the biomass growth and retamycin production. Laboratory data from bench-scale batch and fed-batch fermentations were used to estimate some model parameters by nonlinear regression. The predictive capability of the model was then tested for additional fed-batch and continuous experiments not used in the previous fitting procedure. The model predictions show fair agreement to the experimental data. The proposed model can be useful for further studies on process optimization and control.

Anthracyclines↗

PubMed2004

Fed-batch optimization of alpha-amylase and protease-producing Bacillus subtilis using Markov chain methods.

A stoichiometry-based model for the fed-batch culture of the recombinant bacterium Bacillus subtilis ATCC 6051a, producing extracellular alpha-amylase as a desirable product and proteases as undesirable products, was developed and verified. The model was then used for optimizing the feeding schedule in fed-batch culture. To handle higher-order model equations (14 state variables), an optimization methodology for the dual-enzyme system is proposed by integrating Pontryagin's optimum principle with fermentation measurements. Markov chain Monte Carlo (MCMC) procedures were appropriate for model parameter and decision variable estimation by using a priori parameter distributions reflecting the experimental results. Using a simplified Metropolis-Hastings algorithm, the specific productivity of alpha-amylase was maximized and the optimum path was confirmed by experimentation. The optimization process predicted a further 14% improvement of alpha-amylase productivity that could not be realized because of the onset of sporulation. Among the decision variables, the switching time from batch to fed-batch operation (t(s)) was the most sensitive decision variable.

Algorithms↗

PubMed2026

Engineering the Vero Cell Lineage: Toward a Programmable Vaccine Manufacturing Platform.

Vero cells remain an indispensable continuous substrate for human viral vaccine manufacturing. Despite decades of empirical process optimization, intrinsic genomic instability, including segmental aneuploidy and dynamic chromatin rearrangements, continues to limit the durability of engineered phenotypes under sustained viral burden and bioreactor stress. Here, we review the expanding engineering toolkit for the Vero lineage across a three-layered functional framework: the membrane interface, cytoplasmic foundry, and nuclear blueprint, evaluating translational prospects at each level. Receptor transplantation and morphological reprogramming have broadened viral entry range and enabled suspension-adapted culture formats, while metabolic flux management and temporally controlled apoptosis modulation have addressed intracellular production bottlenecks, albeit often with trade-offs between productivity, biosafety, and long-term population stability. At the genomic level, targeted perturbations of transcriptional regulators and emerging epigenetic interventions offer more durable gains, yet expression drift, clonal heterogeneity, and karyotypic instability during extended passaging highlight the need for locus-level precision rather than constitutive trait installation. Looking forward, infection-responsive dynamic logic circuits and the systematic identification of Vero-specific genomic safe harbors could shift the paradigm toward a conditionally responsive manufacturing architecture. Collectively, these advances suggest a pathway for transitioning the Vero lineage from a passive, empirically optimized biological substrate into a conditionally responsive, genomically stable, and programmable platform for modern vaccine preparedness.

Vero cells↗

PubMed1987

Promoter recognition and promoter strength in the Escherichia coli system.

The strength of Escherichia coli promoters in vivo as well as the rates of association between RNA polymerase and promoter sequences differ by more than an order of magnitude. Since efficient promoter recognition and rapid binding of the enzyme might be a prerequisite for exceptional promoter strength we have determined the forward rate constants kon (as well as koff) for nine promoters including PL, PA1, and PN25 from phages lambda, T7, and T5, respectively as well as Pbla and PlacUV5 from E. coli. The second order forward rate constants span a 30-fold range from 1 X 10(7) M-1 s-1 for Pbla and PL up to 2.9 X 10(8) M-1 S-1 for PN25. Little correlation between 'promoter recognition' as defined by the rate of complex formation of a promoter sequence with RNA polymerase and its strength in vivo as defined by the rate of RNA synthesis has been found. This adds to the evidence that the complex functional pathway encoded in a promoter sequence can be limited at various levels and that promoter strength in vivo is the result of an optimization process involving more than just one functional parameter.

Bacteriophage lambda↗

PubMed2004

Analysis of immobilized L-cysteine on polymers.

Recently, we reported that L-cysteine attached to polymeric biomaterials, without prior nitrosation, enhances the hemocompatibility of biomaterials via exploiting endogenous nitric oxide (NO). As part of the polymer optimization process to further enhance platelet inhibition, a kinetic model is being developed to predict the release rate of NO. A key model parameter is the immobilized concentration of L-cysteine. This article demonstrates how several chemiluminescence-based assays, previously utilized for measuring thiols in solution, were successfully adapted to quantify immobilized L-cysteine. The assays showed that the immobilized L-cysteine on the modified PET sample is within the range of 4.1 to 6.5 nmol/cm(2). An advantage of using the more successful chemiluminescence-based assay is that it can accurately measure molar concentrations of any thiol-containing compound with a detection limit in the pmol range. The major disadvantage is that L-cysteine must first be broken off of the polymer and released into solution prior to measurement, therefore leaving the sample unable to be reused. Other thiol-measuring techniques, such as fluorescence microscopy and X-ray photoelectron spectroscopy (XPS), were used to provide qualitative and semiquantitative analysis to substantiate the polymer development.

Cysteine↗