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PubMed1999

An assessment of the Nam Pehchan computer program for the identification of names of south Asian ethnic origin.

BACKGROUND: An assessment was made of the usefulness and accuracy of a computer program for the identification of the south Asian population through the classification of names on a disease register. METHODS: The computer program, Nam Pehchan, was used to classify names as either south Asian or non south Asian. The results were compared with a reference standard, which combined use of the program with visual inspection. The latter was facilitated by a computer-generated dictionary of common non south Asian names. The data set consisted of 356,555 cases of incident cancer (ICD9: 140-208) registered between 1990 and 1992 by Thames, Trent, West Midlands and Yorkshire cancer registries. RESULTS: Nam Pehchan classified 5506 cases as south Asian. Visual inspection identified 2024 false positives (36.8 per cent of all cases identified as south Asian by Nam Pehchan) and 363 false negatives (9.5 per cent of those identified by the reference standard). Compared with the reference standard, Nam Pehchan had a sensitivity of 90.5 per cent and a positive predictive value of 63.2 per cent. CONCLUSION: The Nam Pehchan program quickly identified a high proportion of the names classified as south Asian by the reference standard, but the high false positive rate means that the program alone is not an adequate single strategy. The time-consuming process of inspection of program negatives for large data sets can be substantially reduced by comparison with dictionaries of common non south Asian names.

Asia↗

PubMed1997

3-D biomechanical analysis of sprint hurdles at different competitive levels.

Four different competition sessions were examined using three-dimensional video techniques to study the hurdle clearance at different levels of performance in male and female athletes. In total, 28 trials were digitized (50 Hz) using the "Kine Analysis" software package. The Direct Linear Transformation algorithm and cross-validated quintic spline were carried out for the data. This study showed that the better female group performed with a greater take-off distance (P = 0.0006), making a lower take-off angle possible. This results in a greater horizontal velocity (P = 0.0002) than the lower level female group. Relative to the horizontal displacement of the CM from take-off to landing, the CM parabola peak occurred at 54 +/- 4% and 55 +/- 6% from take-off for the two male groups and 54 +/- 7% and 51 +/- 3% for the two female groups. There were no statistically significant differences between either the male groups or the female groups or the sexes. This would indicate that the relative peaks are at a similar point in the different parabolic paths. However, in absolute terms the peak occurred at different positions in the different groups. The reason for this is unclear and will need further investigation.

Biomechanical Phenomena↗

PubMed2004

A preliminary survey of the health behaviors of community leaders.

The purpose of this study was to investigate the health behavior of a town ' s community leaders and other issues associated with that behavior. Structured questionnaires designed by the researchers were used to collect data at a meeting for the announcement of community building; they were filled out in the 10 or 20 minutes before the meeting began and 70 valid responses were received. The SPSS for Window version 10.0 software package was used for data analysis. The results of the study showed that the community leaders demonstrated higher standards of health-protective behaviors (i.e. elder/adult checkups, Pap smear exam and breast self-examination) than others living in the community. Variables such as gender, educational level, self-perceived health status, number of chronic illnesses were correlated with different types of dietary behavior. Subjects who were 40 years old and over, educated to junior high school or lower, who had performed less than one year of community service and were free of chronic illness engaged in relatively regular exercise. Subjects who had performed more than one year of community service were more likely to utilize the preventive services provided by national health insurance. It is recommended that public health nurses improve their cooperation with community leaders over providing health -related activities in order to promote better health behavior on the part of such leaders.

Adult↗

PubMed2003

Two-dimensional SPICE-linked multiresolution impedance method for low-frequency electromagnetic interactions.

A multiresolution impedance method for the solution of low-frequency electromagnetic interaction problems typically encountered in bioelectromagnetics is presented. While the impedance method in its original form is based on the discretization of the scattering objects into equal-sized cells, our formulation decreases the number of unknowns by using an automatic mesh generation method that does not yield equal-sized cells in the modeling space. Results indicate that our multiresolution mesh generation scheme can provide a 50%-80% reduction in cell count, providing new opportunities for the solution of low-frequency bioelectromagnetic problems that require a high level of detail only in specific regions of the modeling space. Furthermore, linking the mesh generator to a circuit simulator such as SPICE permits the addition of arbitrarily complex passive and active circuit elements to the generated impedance network, opening the door to significant advances in the modeling of bioelectromagnetic phenomena.

Animals↗

PubMed2004

A new automated cell washer device for thawed cord blood units.

BACKGROUND: The current available techniques to wash out DMSO from thawed umbilical cord blood (UCB) units are based essentially on standard centrifugation in an open system with various degrees of cell loss. STUDY DESIGN AND METHODS: We evaluated the capacity of a new automated closed device (Cytomate, Baxter, IL) to wash out the DMSO from thawed UCB units, saving at the same time the progenitor and accessory cells in terms of CD34+ cells and MNCs. We modified the standard software of the device and calculated the cell recovery on 25 UCB units. Moreover, we set up a new gas chromatographic method to exactly detect the DMSO removal rate. RESULTS: To evaluate the efficiency of the Cytomate device, we considered the postthawing (prewashing) versus postwashing cell recovery. The average recovery (%) in terms of total nucleated cells was 63.30 (range, 40.12-89.00), CD34+ cells was 70.20 (range, 11.51-89.01), CD3+ cells was 61.01 (range, 28.80-87.08), CD4+ cells was 62.53 (range, 30.62-96.73), CD8+ cells was 57.4 (range, 26.87-94.72), CD19+ cells was 63.33 (range, 39.10-90.33), CD16+/56+ cells was 70.67 (range, 8.91-98.40), CFU-GM was 74.33 (range, 20.23-98.60), total CFUs was 82.34 (range, 14.83-247.12), and viability was 89.67(range, 70.74-98.30). The total working time required was, on average, 15 minutes (range, 7-20). CONCLUSIONS: The Cytomate device demonstrated a satisfying efficiency in cell recovery and in maintaining the clonogenic power of the UCB graft. The removal rate of DMSO was practically complete with evident advantages for the recipient. Finally, the entire manipulation performed in a closed system revealed to be safe, maintaining the sterility of the graft.

Automation↗

PubMed2005

Modulation of IMPDH2, survivin, topoisomerase I and vimentin increases sensitivity to methotrexate in HT29 human colon cancer cells.

We determined differentially expressed genes in HT29 human colon cancer cells, both after short treatment with methotrexate (MTX) and after the resistance to MTX had been established. Screening was performed using Atlas Human Cancer 1.2K cDNA arrays. The analysis was carried out using Atlas image 2.01 and genespring 6.1 software. Among the differentially expressed genes we chose for further validation were inosine monophosphate dehydrogenase type II (IMPDH2), inosine monophosphate cyclohydrolase and survivin as up-regulated genes, and topoisomerase I (TOP1) and vimentin as down-regulated genes. Changes in mRNA levels were validated by quantitative RT-PCR. Additionally, functional analyses were performed inhibiting the products of the selected genes or altering their expression to test if these genes could serve as targets to modify MTX cytotoxicity. Inhibition of IMPDH or TOP1 activity, antisense treatment against survivin, or overexpression of vimentin, sensitized resistant HT29 cells to MTX. Therefore, these proteins could constitute targets to develop modulators in MTX chemotherapy.

Antimetabolites, Antineoplastic↗

PubMed2003

A dose delivery verification method for conventional and intensity-modulated radiation therapy using measured field fluence distributions.

Treatment verification has been a weak link in external beam radiation therapy. As new and more complicated treatment techniques, such as intensity-modulated radiation therapy (IMRT), are implemented into clinical practice, verifying the accuracy of treatment delivery becomes increasingly important. Existing methods for treatment verification are highly labor intensive. We have developed a method for verifying the delivery of external beam radiotherapy and implemented the methodology into a system consisting of both hardware and software components. The system uses grayscale images acquired on the treatment machine from the planned treatment beams. From these images, the photon fluence distribution of each beam is derived. These measured photon fluence maps are then used as input to a separate dose calculation engine to compute the delivered absolute dose and the dose distribution in the same patient, assuming that the patient is set up as required by the treatment plan. The dose distribution generated from the measured fluence maps can then be compared to that of the treatment plan. Software tools, such as overlaying isodose curves generated with this method on those imported from the plan, dose difference maps, dose difference volume histograms, and three-dimensional perspective views of the dose differences, have also been developed. The system thus provides a means to verify the dose, the dose prescription, and the monitor units applied. The potential exists with a suitable electronic portal imaging system to reduce the quality assurance efforts, especially for IMRT.

Algorithms↗

PubMed2005

Virtual micro MLC commissioning.

The resolution of multileaf collimators (MLCs) is limited by their finite leaf width. A commercial package (HD-270) uses 3D couch translation and leaf adjustments to emulate smaller leaf widths. In this paper, we report on the commissioning of this feature using software testing, dial gauge measurements, and film dosimetry. We also identify a variety of limitations: software bugs and truncation artifacts, MLC leaf positioning uncertainties (random variations, systematic gantry dependence and backlash), and uncertainties in couch positioning. These reduce the capabilities of this implementation below that achievable theoretically.

Equipment Design↗

PubMed2003

Evaluation of breast cancer risk assessment packages in the family history evaluation and screening programme.

INTRODUCTION: Accurate individualised breast cancer risk assessment is essential to provide risk-benefit analysis prior to initiating interventions designed to lower breast cancer risk. Several mathematical models for the estimation of individual breast cancer risk have been proposed. However, no single model integrates family history, hormonal factors, and benign breast disease in a comprehensive fashion. A new model by Tyrer and Cuzick has addressed these deficiencies. Therefore, this study has assessed the goodness of fit and discriminatory value of the Tyrer-Cuzick model against established models namely Gail, Claus, and Ford. METHODS: The goodness of fit and discriminatory accuracy of the models was assessed using data from 1933 women attending the Family History Evaluation and Screening Programme, of whom 52 developed cancer. All models were applied to these women over a mean follow up of 5.27 years to estimate risk of breast cancer. RESULTS: The ratios (95% confidence intervals) of expected to observed numbers of breast cancers were 0.48 (0.37 to 0.64) for Gail, 0.56 (0.43 to 0.75) for Claus, 0.49 (0.37 to 0.65) for Ford, and 0.81 (0.62 to 1.08) for Tyrer-Cuzick. The accuracy of the models for individual cases was evaluated using ROC curves. These showed that the area under the curve was 0.735 for Gail, 0.716 for Claus, 0.737 for Ford, and 0.762 for Tyrer-Cuzick. CONCLUSION: The Tyrer-Cuzick model is the most consistently accurate model for prediction of breast cancer. The Gail, Claus, and Ford models all significantly underestimate risk, although the accuracy of the Claus model may be improved by adjustments for other risk factors.

Adult↗

PubMed2004

Logos: a modular bayesian model for de novo motif detection.

The complexity of the global organization and internal structure of motifs in higher eukaryotic organisms raises significant challenges for motif detection techniques. To achieve successful de novo motif detection, it is necessary to model the complex dependencies within and among motifs and to incorporate biological prior knowledge. In this paper, we present LOGOS, an integrated LOcal and GlObal motif Sequence model for biopolymer sequences, which provides a principled framework for developing, modularizing, extending and computing expressive motif models for complex biopolymer sequence analysis. LOGOS consists of two interacting submodels: HMDM, a local alignment model capturing biological prior knowledge and positional dependency within the motif local structure; and HMM, a global motif distribution model modeling frequencies and dependencies of motif occurrences. Model parameters can be fit using training motifs within an empirical Bayesian framework. A variational EM algorithm is developed for de novo motif detection. LOGOS improves over existing models that ignore biological priors and dependencies in motif structures and motif occurrences, and demonstrates superior performance on both semi-realistic test data and cis-regulatory sequences from yeast and Drosophila genomes with regard to sensitivity, specificity, flexibility and extensibility.

Algorithms↗

PubMed2004

Expression profiles of a human pancreatic cancer cell line upon induction of apoptosis search for modulators in cancer therapy.

We analyzed the differential gene expression in the pancreatic cancer cell line NP-18 upon induction of apoptosis caused by cyclin-dependent kinase inhibition triggered by either overexpression of the tumor suppressor gene p16(INK4A)using an adenoviral construction or incubation with the chemical inhibitors, roscovitine or olomoucine. Screening was performed using cDNA arrays from Clontech that allowed the determination of the expression of 1,176 genes specifically related with cancer. The analysis was carried out using the Atlas Image 2.01 (Clontech) and GeneSpring 4.2 (Silicon Genetics) softwares. Among the differentially expressed genes, we chose for further validation histone deacetylase 1 (HDAC1), von Hippel Lindau and decorin as upregulated genes, and Sp1, hypoxia-inducible factor-1 alpha and DNA primase as downregulated genes. The changes in the expression of these genes to mRNA were validated by quantitative RT-PCR and the final translation into protein by Western blot analysis. Inhibition of HDAC activity, Sp1 binding and DNA primase expression led to an increase in the level of apoptosis, both in parental cells and in doxorubicin-resistant cells. Therefore, these proteins could constitute possible targets to develop modulators in cancer chemotherapy that would increase or restore apoptosis.

Adenoviridae↗

PubMed2004

Optical methods--quantitative light fluorescence.

Considerable research during the past two decades has focused upon the development of new technologies for the detection of dental caries. Of these technologies, the method that has been most extensively studied is based upon the indirectly assessed changes in the fluorescence of enamel associated with the loss of mineral. The purpose of this presentation was to review the available information regarding the use of this technology, commonly known as quantitative light fluorescence, for caries detection, particularly early caries detection, and the potential for the routine use of this technology in clinical caries trials. This technology is unique in its ability to measure small changes in the mineral content of enamel lesions quantitatively. The results of recent small-scale clinical trials have indicated that the impact of caries-preventive measures can be determined within a six-month period. With current hardware and software refinements and the results of long-term clinical validation studies that are in progress, it may be that this technology will be the future method of choice for caries clinical trials.

Clinical Trials as Topic↗

PubMed2006

Evaluation of MetriGenix custom 4D arrays applied for detection of breast cancer subtypes.

BACKGROUND: Previously, a total of five breast cancer subtypes have been identified based on variation in gene expression patterns. These expression profiles were also shown to be associated with different prognostic value. In this study tumour samples from 27 breast cancer patients, previously subtyped by expression analysis using DNA microarrays, and four controls from normal breast tissue were included. A new MetriGenix 4D array proposed for diagnostic use was evaluated. METHODS: We applied MetriGenix custom 4D arrays for the detection of previously defined molecular subtypes of breast cancer. MetriGenix 4D arrays have special features including probe immobilization in microchannels with chemiluminescence detection that enable shorter hybridization time. RESULTS: The MetriGenix 4D array platform was evaluated with respect to both the accuracy in classifying the samples as well as the performance of the system itself. In a cross validation analysis using "Nearest Shrunken Centroid classifier" and the PAM software, 77% of the samples were classified correctly according to earlier classification results. CONCLUSION: The system shows potential for fast screening; however, improvements are needed.

Breast Neoplasms↗

PubMed2005

Quasi-analytic formalism for mode characteristics in highly overmoded rectangular dielectric waveguide bends.

A fast and simple quasi-analytic method to simulate mode characteristics in highly overmoded rectangular dielectric waveguide bends is presented. Fast mode-based bend models are necessary, since overmoded rectangular waveguides have become very popular in optical interconnects on printed circuit boards. The proposed method combines a simple mode solver with the formalism that was proposed by Melloni et al. [J. Lightwave Technol. 16, 571 (2001)], yielding to a very convenient and accurate quasi-analytic formalism for the bend transfer function based on matrix notation. For that purpose, a simple method to approximate leaky modes is introduced. The model offers the ability to predict individual modal phases and amplitudes within a given bend as well as the calculation of coupling losses and was validated using three-dimensional beam-propagation-method simulation software.

Journal Article↗

PubMed2003

Spectral depth profiling of arbitrary surfaces by thermal emission decay-Fourier transform infrared spectroscopy.

We report a new spectroscopic technique that combines step-scanning Fourier transform infrared spectroscopy with opto-thermal transient emission radiometry (OTTER) in order to provide near-surface depth-resolved spectra in the range 700-1800 cm(-1). It works nondestructively, without contact, with samples of arbitrary shape and size, without requiring prior preparation. The depth of surface probed depends on the thermal diffusivity of the sample; for organic materials it is approximately 10 microm. With homogeneous samples, absolute absorption coefficients can be measured. With two-layered samples, the technique proved able to distinguish between the spectral properties of the top layer and the substrate and to estimate the thickness of the top layer. We present a theoretical analysis with the main design features of the instrumentation and software, together with studies of homogeneous and layered samples, to validate the methods and illustrate the potential of the technique for practical applications.

Adhesives↗

PubMed2026

Digital and computational morphology in hematology: current platforms, clinical evidence, and future requirements.

INTRODUCTION: Morphologic examination of peripheral blood and bone marrow remains central to the diagnosis and classification of hematologic disorders. Conventional optical microscopy, however, is labor-intensive, dependent on operator expertise, and affected by interobserver variability. Digital morphology has developed from automated image acquisition and cell pre-classification into a broader field that includes whole-slide imaging, remote review, quantitative morphometry, and artificial intelligence-based analysis. CONTENT: This review examines current applications of digital morphology in peripheral blood, bone marrow aspirates, malaria detection, and body-fluid analysis. Commercial platforms are evaluated with particular attention to the distinction between raw automated pre-classification, expert digital post-classification, and comparison with independent optical microscopy. Digital systems generally perform well for common mature leukocyte populations but remain less reliable for rare or diagnostically critical cells, including blasts, abnormal lymphoid cells, plasma cells, and intermediate maturation stages. Research systems increasingly extend analysis from individual-cell classification to whole-slide, specimen-level, and patient-level assessment. SUMMARY: Digital morphology can improve standardization, image traceability, remote consultation, education, proficiency testing, quality assurance, and selected aspects of laboratory workflow. Its clinical value depends on appropriate validation, transparent reporting of reference methods, recognition of algorithm-specific failure modes, and clearly defined criteria for expert review and conventional microscopy. Human expertise remains essential not only for validating results but also for adapting cell taxonomies and interpretive rules to evolving classifications of hematologic diseases. OUTLOOK: Future progress will require representative multicenter datasets, harmonized morphologic terminology, external validation, interoperability with laboratory information systems, and continuous monitoring after software or hardware updates. Integration of morphology with quantitative hematology, flow cytometry, cytogenetics, genomics, and clinical data may support more comprehensive computational diagnosis. Digital platforms may also broaden access to specialist expertise, training, and quality programs in resource-limited institutions and regions, provided that infrastructure, governance, and professional competency are adequately supported.

artificial intelligence↗

PubMedDate not supplied

Comparison of single and dual platform methodologies for the estimation of CD34+ hematopoietic progenitor cells: correlation with colony assay.

In this study three assays for the enumeration of CD34+ progenitors were compared: 1) a modified version of the Milan protocol, used in the standard dual-platform format; 2) a dual-platform version of the ISHAGE protocol; 3) the ProCOUNT software version 2.0/ProCOUNT kit. The assays were compared to validate the accuracy of CD34+ cell counts in mobilized peripheral blood (PB), apheresis products (AP), and cord blood (CB). The ProCOUNT protocol uses reference beads for absolute CD34+ cell counting, whereas CD34 counts by other techniques are derived from a separate leukocyte count performed by a hematology analyzer. A good correlation between the ISHAGE and ProCOUNT methods was obtained for estimation of CD34+ counts in PB (n=42 samples analyzed) and AP (n=35)--except for samples having a leukocyte count >25 x 10(9)/L or a CD34 count <0.0025 x 10(9)/L)--while a suboptimal correlation between the methods was observed for CB (n=30). The ProCOUNT system proved to be effective in reducing the variability in CD34+ cell counting and appeared to be useful for intralaboratory methodology standardization. The main disadvantage of the ProCOUNT assay was its inability to calculate CD34 counts in leukopenic samples and in CB samples showing a high erythroblast count. As far as the correlation with hematopoietic colonies is concerned, data collected from apheresis samples showed a good correlation between the three flow cytometry methods and colony-forming unit granulocyte-macrophage (CFU-GM) counts, confirming the value of the flow cytometric test as a real-time, truly predictive test to measure the hematopoietic potential of the graft. In summary, all methods are suitable for enumeration of most PB samples, while the single-platform methodology should be preferred for the analysis of AP and CB. We also found the dual-platform format of the ISHAGE method precise and accurate for the estimation of CD34+ cells from CB samples. Based on these data it can be concluded that the single-platform flow cytometry assay format should be the preferred approach for CD34+ stem cell enumeration in different types of samples.

Adolescent↗

PubMed2003

AMID: autonomous modeler of intragenic duplication.

Intragenic duplication is an evolutionary process where segments of a gene become duplicated. While there has been much research into whole-gene or domain duplication, there have been very few studies of non-tandem intragenic duplication. The identification of intragenically replicated sequences may provide insight into the evolution of proteins, helping to link sequence data with structure and function. This paper describes a tool for autonomously modelling intragenic duplication. AMID provides: identification of modularly repetitive genes; an algorithm for identifying repeated modules; and a scoring system for evaluating the modules' similarity. An evaluation of the algorithms and use cases are presented.

Algorithms↗