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PubMed1996

Automation of selective assays for on-line bioprocess monitoring by flow-injection analysis.

On-line analysis of one component in a complex media used for bioprocesses requires the application of selective tests such as enzymes assays. Because these assays are susceptible to interference by other medium components and have a limited detection range, automatic sample pretreatment is a prerequisite. The progress made with automatic sample pretreatment in flow-injection analysis makes this technique particularly suitable for on-line monitoring of bioprocesses. Moreover, newly developed software control systems may improve the necessary robustness of flow-infection analysis systems.

Animals↗

PubMed2004

Tracking of target motion using physically based modelling of organs.

In this paper, we describe a general methodology for the realistic reconstruction and animation of anatomic organs. In fact, in the scope of conformal radiotherapy and hadron therapy applications, we want to simulate the motion and the shape alteration of the internal anatomical objects and to input this knowledge to treatment planning. For the reconstruction, particle systems are used: firstly, surface shape of the considered organ is computed from a set of CT scan sections. Next, the volume defined by this surface is filled with particles. The coherency of the object is maintained due to the use of the classical Lennard-Jones inter particles force. This work permits to study the impact of the organs movement on the treatment of prostate and lung cancer. Our particle system has been suitably integrated in a radiation dose evaluation software, developed within an European BIOMED2 project and is currently supported by the French ETOILE project.

Humans↗

PubMed1997

A new data-acquisition system for the measurement of the net water flux across epithelia.

We describe a computer-based data-acquisition system designed for the measurement of net water flux across epithelia. It is based on the detection of a liquid meniscus position in a capillary tube using an electro-optical device. Then the data are digitized, transferred to the computer main memory and saved in a file. The advantages of the system are: (a) to measure net water transfer with an accuracy of 50 nl; (b) to switch from absorptive to secretory conditions in real time; (c) data are directly digitized to be analytically, graphically and statistically treated; (d) the specially developed software allows change of time intervals for data acquirement and the scale in graphic events; (e) the software also allows recall to the monitor screen of graphics from previous tests or to print them on paper; (f) a simple mechanical structure, saving maintenance and time; and (g) high reliability.

Animals↗

PubMed2000

Photopatch testing: the 12-year experience of the German, Austrian, and Swiss photopatch test group.

BACKGROUND: In 1984, the German, Austrian, and Swiss Photopatch Test Group was founded to standardize the photopatch test procedure and to investigate photoallergic reactions, as well as the epidemiology of photoallergy, in central Europe. Therefore in a first test period from 1985-1990, 32 test substances were applied on the backs of patients suspected to be photosensitive. After evaluation of these data, some substances were dismissed, and others were additionally integrated into the test tray. Thus a modified test tray comprising 26 test substances was used for the second test period (1991-1997). OBJECTIVE: According to the standard photopatch test procedure defined in the first test period, the aim of this multicenter study was to apply compounds from the modified second test tray to a large group of photosensitive patients. After evaluation of the second test period (1991-1997), the outcome was compared with the results of the first period. On the basis of these results and influenced by concurrently published case reports, a third modified photopatch test tray has been established. METHODS: After the application of a duplicate test tray for 24 hours, one test site was irradiated with 10 J/cm(2) UVA, and the other test site served as the control area. Readings were performed immediately and 24, 48, and 72 hours after irradiation. Test reactions were qualitatively graded according to a 4-point scale and classified by the investigators of the participating centers. In 49 participating clinics 1261 photopatch tests were performed. All data were subjected to computer-assisted analysis by using a specially developed software to classify all positive test reactions as plain contact or photoinduced reactions (nonspecific, toxic, or allergic photoreactions) and to define substance-specific reaction patterns. RESULTS: In test period 1 data of 1129 patients were evaluated. From 2859 positive test reactions, 28.6% were excluded as plain contact reactions, 71.4% were found to be photoinduced reactions, and 3.8% were classified as photoallergic. In test period 2 data of 1261 patients were evaluated. One thousand four hundred fifteen positive test reactions were observed, and of these, 28.7% were excluded as plain contact reactions, 71.3% were classified as photoinduced reactions, and 8.1% were classified as photoallergic reactions. In both test periods nonsteroidal anti-inflammatory drugs, disinfectants, and phenothiazines represented the leading photoallergens in the evaluated central European region. By using computer-assisted reaction pattern analysis, substance-specific reaction patterns could be distinguished. These substance-specific reaction patterns comprised 4 main categories: the well-known decrescendo (phototoxic) and crescendo (photoallergic) reaction patterns, as well as a combined and a plateau pattern. CONCLUSION: The test modification after the first test period led to a notably reduced number of positive (mainly nonphotoallergic and thus nonrelevant) test reactions per patient in the second test period (from 2.6 to 1.1). In contrast, the percentage of photoallergic reactions increased significantly from 3.8% to 8.1% of all positive test reactions. Test modifications after the first test period led to a remarkably improved specificity of the photopatch test. Furthermore, substance-specific reaction patterns observed in test period 1 were confirmed in test period 2.

Adult↗

PubMed1998

Antisense homology box-derived peptides represent a new class of endothelin receptor inhibitors.

Several peptides encoded by the sense and corresponding antisense DNA have been found to recognize and bind to each other. We developed software to search for sense-antisense regions within proteins taking into account the degeneracy of the genetic code, i.e., one amino acid can have several "antisense" counterparts. Using this approach, we searched endothelin receptor type A for intramolecular regions related in sense-antisense fashion. After locating these regions (termed "antisense homology boxes"), several corresponding peptides were synthesized. The four new ET(A) receptor fragment peptides ETR-P1 ("CALSVDRYRAVASW"), ETR-P3 ("QGIGPLITAIEI"), ETR-P4 ("IADNAERYSANLSSHV") and ETR-P6 ("LNRRNGSLRIALSEHLKNRREVA") reported here can inhibit ET-1 activity.

3T3 Cells↗

PubMed2002

A decision support system for wet soil cleaning.

Newly developed software can predict the essential characteristics of the sand product resulting from the ex-situ washing of contaminated soil, dredging sludge or breaker sand. The system was designed for the Dutch situation and it works on the basis of readily available information. The primary output of the system is an assessment of the reusability of the sand product, which is obtained by comparing the prediction of the residual contamination and engineering quality with accepted levels and standards for building materials. The system also provides a ranking of potential applications for the sand with respect to treatment cost, the amount of recycled material or the environmental quality of the product. The software integrates soil cleaning expertise and unit process modelling in a way that allows varying levels of refinement of input data, ranging from a simple identification of the pollution source to a detailed particle size distribution of the contaminated soil. Tests on a database containing information on 117 processed batches of soil, dredging sludge and breaker sand show an 80% success rate in predicting cleanability, even though the input contamination levels were predominantly taken from (relatively inaccurate) in-situ data.

Decision Support Techniques↗

PubMed1999

Increased accuracy of echocardiographic measurement of flow using automated spherical integration of multiple plane velocity vectors.

The calculation of blood flow in the heart by surface integration of velocity vectors (SIVV) using Doppler ultrasound is independent of the angle. Flow is normally calculated from velocity in a spherical thick shell with its center located at the ultrasound transducer. In a numerical simulation, we have shown that the ratio between minor and major axes of an elliptic flow area substantially influences the accuracy of the estimation of flow in a single scan plane. The accuracy of flow measurements by SIVV can be improved by calculating the mean of the values from more than one scan plane. We have produced an automated computer program that includes an antialiasing procedure. We confirmed an improvement of flow measurements in a pulsatile hydraulic flow model, the 95% confidence interval for single estimations being reduced from 20% to 10% (p < 0.05) using the newly developed software. We think that the SIVV method has important implications for clinical transthoracic echocardiography.

Algorithms↗

PubMed2000

Consequence analysis in LPG installation using an integrated computer package.

This paper presents the prototype of the computer code, Atlantide, developed to assess the consequences associated with accidental events that can occur in a LPG storage plant. The characteristic of Atlantide is to be simple enough but at the same time adequate to cope with consequence analysis as required by Italian legislation in fulfilling the Seveso Directive. The application of Atlantide is appropriate for LPG storage/transferring installations. The models and correlations implemented in the code are relevant to flashing liquid releases, heavy gas dispersion and other typical phenomena such as BLEVE/Fireball. The computer code allows, on the basis of the operating/design characteristics, the study of the relevant accidental events from the evaluation of the release rate (liquid, gaseous and two-phase) in the unit involved, to the analysis of the subsequent evaporation and dispersion, up to the assessment of the final phenomena of fire and explosion. This is done taking as reference simplified Event Trees which describe the evolution of accidental scenarios, taking into account the most likely meteorological conditions, the different release situations and other features typical of a LPG installation. The limited input data required and the automatic linking between the single models, that are activated in a defined sequence, depending on the accidental event selected, minimize both the time required for the risk analysis and the possibility of errors. Models and equations implemented in Atlantide have been selected from public literature or in-house developed software and tailored with the aim to be easy to use and fast to run but, nevertheless, able to provide realistic simulation of the accidental event as well as reliable results, in terms of physical effects and hazardous areas. The results have been compared with those of other internationally recognized codes and with the criteria adopted by Italian authorities to verify the Safety Reports for LPG installations. A brief of the theoretical basis of each model implemented in Atlantide and an example of application are included in the paper.

Accidents, Occupational↗

PubMed2002

Spatial segregation within the sacral parasympathetic nucleus of neurons innervating the bladder or the penis of the rat as revealed by three-dimensional reconstruction.

The purpose of the present investigations was (1) to examine the spatial organization of preganglionic neurons of the sacral parasympathetic nucleus in the lumbosacral spinal cord of male adult rats and (2) to search, in this nucleus, for a possible segregation of sub-populations of neurons innervating the penis or the bladder, respectively. To estimate their spatial organization, neurons of the sacral parasympathetic nucleus were retrogradely labeled by wheat germ agglutinin coupled to horseradish peroxidase applied to the central end of the sectioned pelvic nerve. The sub-populations of lumbosacral neurons innervating the corpus cavernosum of the penis or the dome of the bladder were identified using transsynaptic retrograde labeling by pseudorabies virus injected into these organs in different rats. In both wheat germ agglutinin-labeled and pseudorabies virus-labeled rats, serial coronal sections were cut through the spinal L5-S1 segments. Labeled neurons were revealed by histochemistry (peroxidase experiments) or immunohistochemistry (pseudorabies virus experiments). By means of a three-dimensional reconstruction software developed in our laboratory, three-dimensional models were calculated from each spinal section image series. They revealed the spatial organization of (i) preganglionic neurons and (ii) neurons innervating the bladder or the penis. The different three-dimensional models were subsequently merged into a single one which revealed the segregation, within the sacral parasympathetic nucleus, of the sub-populations of neurons. Neurons labeled by virus injected into the penis extended predominantly from the rostral part of the L6 segment to the rostral part of the S1 segment while those labeled by bladder injections were distributed predominantly from the caudal part of the L6 segment to the caudal part of the S1 segment. These results support the hypothesis of a viscerotopic organization of sacral neurons providing the spinal control of pelvic organs.

Animals↗

PubMed1999

Three-dimensional distribution of nigrostriatal neurons in the rat: relation to the topography of striatonigral projections.

Functional regions of the rat striatum related to identified cortical territories were injected ionophoretically with wheat germ agglutinin coupled to horseradish peroxidase. Coronal serial sections were cut throughout the substantia nigra. The distributions of labelled striatal projections and nigrostriatal neurons were studied. Using software developed in our laboratory, three-dimensional reconstructions were calculated which confirmed and extended the organizational scheme of striatonigral projections already reported by our group. These projections were organized as a set of longitudinal lamellae spatially organized so as to segregate the flow of information emanating from striatal regions affiliated to sensorimotor and associative-limbic cortical areas. In addition, the relationship between the striatonigral projections and the nigrostriatal neurons was studied by three-dimensional reconstruction. For each striatal injection site, two populations of retrogradely labelled nigral neurons could be discriminated by their position with respect to the striatal projection field. The first one occupied a proximal position, in register with the labelled striatal projections, while the second was more distal. The populations of proximal neurons which innervate different functional striatal sectors were segregated both mediolaterally, dorsoventrally and rostrocaudally, while the populations of distal neurons were more scattered and showed a lesser degree of spatial segregation. The organization of these two populations with respect to the striatal projection fields suggests that the substantia nigra might control the flow of cortical information through the striatum via two different modalities, based respectively on a closed nigrostriatal loop involving the proximal neurons, and an open loop involving the distal ones.

Animals↗

PubMed1997

The bivariate probit model of uncomplicated control of tumor: a heuristic exposition of the methodology.

PURPOSE: To describe the concept, models, and methods for the construction of estimates of joint probability of uncomplicated control of tumors in radiation oncology. Interpolations using this model can lead to the identification of more efficient treatment regimens for an individual patient. The requirement to find the treatment regimen that will maximize the joint probability of uncomplicated control of tumors suggests a new class of evolutionary experimental designs--Response Surface Methods--for clinical trials in radiation oncology. METHODS AND MATERIALS: The software developed by Lesaffre and Molenberghs is used to construct bivariate probit models of the joint probability of uncomplicated control of cancer of the oropharynx from a set of 45 patients for each of whom the presence/absence of recurrent tumor (the binary event E1/E1) and the presence/absence of necrosis (the binary event E2/E2) of the normal tissues of the target volume is recorded, together with the treatment variables dose, time, and fractionation. RESULTS: The bivariate probit model can be used to select a treatment regime that will give a specified probability, say P(S) = 0.60, of uncomplicated control of tumor by interpolation within a set of treatment regimens with known outcomes of recurrence and necrosis. The bivariate probit model can be used to guide a sequence of clinical trials to find the maximum probability of uncomplicated control of tumor for patients in a given prognostic stratum using Response Surface Methods by extrapolation from an initial set of treatment regimens. CONCLUSIONS: The design of treatments for individual patients and the design of clinical trials might be improved by use of a bivariate probit model and Response Surface Methods.

Dose-Response Relationship, Radiation↗

PubMed1999

Assessment of the uncertainties in dose delivery of a commercial system for linac-based stereotactic radiosurgery.

PURPOSE: Linac-based stereotactic radiosurgery (SRS) was introduced in our department in 1992, and since then, more than 200 patients have been treated with this method. An in-house-developed algorithm for target localization and dose calculation has recently been replaced with a commercially available system. In this study, both systems have been compared, and positional accuracy, as well as dose calculation, have been verified experimentally. METHODS AND MATERIALS: The in-house-developed software for target localization and dose calculation is an extension to George Sherouse's GRATIS(R) software for radiotherapy treatment planning, and has been replaced by a commercial (BrainSCAN version 3.1; BrainLAB, Germany) treatment planning system (TPS) for SRS. The positional accuracy for the entire SRS procedure (from image acquisition to treatment) has been investigated by treatment of simulated targets in the form of 0.2-cm lead beads inserted into an anthropomorphic phantom. Both dose calculation algorithms have been verified against manual calculations (based on basic beam data and CT data from phantom and patients), and measurements with the anthropomorphic phantom applying ionization chamber, thermoluminescent detectors, and radiographic film. This analysis has been performed on a variety of experimental situations, starting with static beams and simple one-arc treatments, to more complex and clinical relevant applications. Finally, 11 patients have been evaluated with both TPS in parallel for comparison and continuity of clinical experience. RESULTS: Phantom studies evaluating the entire SRS procedure have shown that a target, localized by CT, can be irradiated with a positional accuracy of 0.08 cm in any direction with 95% confidence. Neglecting the influence of dose perturbation when the beam passes through bone tissue or air cavities, the calculated dose values obtained from both TPSs agreed within 1% (SD 1%) for phantom and patient studies. The application of a one-dimensional path length correction for tissue heterogeneity influences the treatment prescription 4% on average (SD 1%), which is in compliance with theoretical predictions. The phantom measurements confirmed the predicted dose at isocenter within uncertainty for the different treatment schedules in this study. CONCLUSION: The full SRS procedure applied to an anthropomorphic phantom has been used as a comprehensive method to assess the uncertainties involved in dose delivery and target positioning. The results obtained with both TPSs are in agreement with AAPM Report 54, TG 42 and clinical continuity is assured. However, the use of a one-dimensional path length correction will result in an increase of 4% in dose prescription, which is slightly more than that predicted in the literature.

Algorithms↗

PubMed1999

Volumetric visualization of head and neck CT data for treatment planning.

PURPOSE: To demonstrate the utility of volume rendering, an alternative visualization technique to surface rendering, in the practice of CT based radiotherapy planning for the head and neck. METHODS AND MATERIALS: Rendo-avs, a volume visualization tool developed at the University of Chicago, was used to volume render head and neck CT scans from two cases. Rendo-avs is a volume rendering tool operating within the graphical user interface environment of AVS (Application Visualization System). Users adjust the opacity of various tissues by defining the opacity transfer function (OTF), a function which preclassifies voxels by opacity prior to rendering. By defining the opacity map (OTF), the user selectively enhances and suppresses structures of various intensity. Additional graphics tools are available within the AVS network, allowing for the manipulation of perspective, field of view, data orientation. Users may draw directly on volume rendered images, create a partial surface, and thereby correlate objects in the 3D scene to points on original axial slices. Information in volume rendered images is mapped into the original CT slices via a Z buffer, which contains the depth information (Z coordinate) for each pixel in the rendered view. Locally developed software was used to project conventionally designed GTV contours onto volume rendered images. RESULTS: The lymph nodes, salivary glands, vessels, and airway are visualized in detail without prior manual segmentation. Volume rendering can be used to explore the finer anatomic structures that appear on consecutive axial slices as "points." Rendo-avs allowed for acceptable interactivity, with a processing time of approximately 5 seconds per 256 x 256 pixel output image. CONCLUSIONS: Volume rendering is a useful alternative to surface rendering, offering high-quality visualization, 3D anatomic delineation, and time savings to the user, due to the elimination of manual segmentation as a preprocessing step. Volume rendered images can be merged with conventional treatment planning images to add anatomic information to the treatment planning process.

Head↗

PubMed2002

ORF-FINDER: a vector for high-throughput gene identification.

We have developed a simple and efficient system (ORF-FINDER) for selecting open reading frames (ORFs) from randomly fragmented genomic DNA fragments. The ORF-FINDER vectors are plasmids that contain a translational start site out of frame with respect to the gene for green fluorescent protein (GFP). Insertion of DNA fragments that bring the initiating ATG in frame with GFP and that contain no stop codons (that is, ORFs) results in the expression of ORF-GFP fusion proteins. In addition, we have developed software (GeneWorks and GenomeAnalyzer) to predict the optimal insert size for maximizing the number of gene-coding ORFs and minimizing unintentionally selected non-coding ORFs. To demonstrate the feasibility of using the ORF-FINDER system to screen genomes for ORFs, we cloned yeast genomic DNA and succeeded in enriching for ORFs by 25-fold. Furthermore, we have shown that the vector can effectively isolate ORFs from the more complex genomes of eukaryotic parasites. We envision that ORF-FINDER will have several applications including genome sequencing projects, gene building from oligonucleotides and construction of expression libraries enriched for ORFs.

Animals↗

PubMed1997

Computerized optimization of the high-performance liquid chromatographic enantioseparation of a mixture of 4-dinitrophenyl amino acids on a quinine carbamate-type chiral stationary phase using DRYLAB.

A method is proposed for the sensitive chiral analysis of amino acid enantiomers by high-performance liquid chromatography (HPLC). Thus the enantiomers of a mixture of seven racemic amino acids were resolved as their DNP derivatives from each other and from the peak of the hydrolyzed reagent, employing a quinine carbamate-based chiral anion exchange-type chiral stationary phase (CSP) and aqueous buffered mobile phases. However, the initial isocratic chromatogram yielded many peak overlaps although the corresponding enantiomers were well resolved. Therefore, the separation of the complex mixture had to be optimized; we utilized the commercial computer method development software DRYLAB. First, the influence of the manifold mobile phase parameters and chromatographic conditions (pH, type and content of organic modifier, buffer concentration, temperature, type of co-ion, etc.) on retention and resolution was studied by isocratic elution. Furthermore, with such optimized conditions linear and multi-segmented organic modifier and buffer salt gradients, respectively, were simulated with the computer program and experimentally verified. Average errors of prediction of retention times lay between 2 and 8%. Finally, a highly improved HPLC gradient method resulted in almost all components being baseline separated and equally spaced and accelerated by a factor of more than 3 compared to the initial run.

Amino Acids↗

PubMed2002

An automated method for volumetric quantification of magnetization transfer of the brain.

Cerebral white matter damages can be detected and characterized using magnetization transfer (MT) imaging. In this study a fully automated method of measuring and analyzing the MT of the whole human brain is presented and assessed. A 3D-FLASH sequence with off-resonance RF pulse was optimized for fast, volumetric MT measurements. The postprocessing software developed for this purpose includes a SPM99-based segmentation algorithm, a visualization tool, and a histogram-based MT parameter analysis. The reproducibility of the method was tested with phantom measures and in studies on nine healthy volunteers. Small variances (0-1.6%) and therefore, a high reproducibility of MT parameter measurements were found in vitro, slightly higher variances in volunteer investigations (0.7-4.0%). With our technique, we expect to be able to better recognize and follow up the progression of white matter diseases. Due to the high reproducibility, this volumetric approach is specifically suitable for longitudinal MT studies.

Adult↗

PubMed2001

Changes in posterior capsule opacification after poly(methyl methacrylate), silicone, and acrylic intraocular lens implantation.

PURPOSE: To prospectively evaluate the progression of posterior capsule opacification (PCO) after poly(methyl methacrylate) (PMMA), silicone, and acrylic intraocular lens (IOL) implantation. SETTING: Hayashi Eye Hospital, Fukuoka, Japan. METHODS: Three hundred eyes of 300 patients scheduled to have IOL implantation were initially randomized into 3 groups based on IOL type: PMMA, silicone, or acrylic. Of the 300 eyes, 269 completed the follow-up. The PCO density in these eyes was measured 1 week and 3, 6, 12, 18, and 24 months postoperatively using special computer software developed for the Scheimpflug videophotography system. Visual acuity and the incidence of neodymium:YAG (Nd:YAG) laser capsulotomy were also examined. RESULTS: Three months postoperatively and later, the mean PCO value in the PMMA group increased significantly (P <.0001); the increase in the silicone and acrylic groups was not significant. The PCO value in the PMMA group was significantly greater than in the silicone or acrylic group (P <.0001). The PCO value in the acrylic group was slightly less than in the silicone group at 18 and 24 months, but the difference was marginal. The survival rate not requiring Nd:YAG capsulotomy was least in the PMMA group, followed by the silicone and acrylic groups in that order (P <.0001). The mean logMAR visual acuity in the PMMA group increased postoperatively and was worse than in the silicone or acrylic group. CONCLUSIONS: The degree of PCO after PMMA IOL implantation progressed significantly with time, while the progression after silicone and acrylic IOL implantation was slight. Therefore, PCO in eyes with a PMMA IOL was significantly more extensive than in those with a silicone or acrylic IOL and resulted in marked impairment of visual acuity.

Acrylic Resins↗

PubMed1999

Posterior capsule opacification after phacoemulsification in patients with diabetes mellitus.

PURPOSE: To compare posterior capsule opacification (PCO) after phacoemulsification and implantation of heparin-surface-modified (HSM) poly(methyl methacrylate) (PMMA) intraocular lenses (IOLs) in the capsular bag in patients with diabetes mellitus with that in a control group. SETTING: St. Erik's Eye Hospital, Stockholm, Sweden. METHODS: This prospective study comprised 26 patients with diabetes mellitus and 26 control patients without diabetes. Those with glaucoma, exfoliation syndrome, uveitis, and pupil size smaller than 6.0 mm after dilation were excluded. All patients received the same standardized phacoemulsification procedure with implantation of an HSM PMMA IOL in the capsular bag. Posterior capsule opacification was scored 1 and 2 years after surgery by evaluating retroillumination images taken with a Scheimpflug camera (Nidek Anterior Eye Segment Analysis System) after pupil dilation with phenylephrine 10% and cyclopentolate 1%. The PCO density behind the IOL optic was graded clinically from 0 to 4 (0 = none, 1 = minimal, 2 = mild, 3 = moderate, 4 = severe) and scored using the Evaluation of Posterior Capsule Opacification medical software developing system. RESULTS: No differences in PCO were found between the diabetic and control groups 1 year after surgery. The total PCO score was significantly less in diabetic than in control eyes 2 years after surgery (P < .05, Mann-Whitney). In addition, progression of PCO from 1 year to 2 years after surgery was significantly less in diabetic groups with different stages of diabetic retinopathy than in the control group (P < or = .05, Kruskal-Wallis analysis of variance and multiple comparisons). CONCLUSION: The rate of PCO after phacoemulsification was statistically significantly lower in patients with diabetes mellitus than in those without diabetes.

Aged↗