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PubMed1985

The classification of subjects with joint complaints on incomplete biochemical and haematological datasets.

We performed a retrospective study on 163 subjects suffering from rheumatic fever (16), rheumatoid arthritis (36), lupus erythematosus (17), gout (21), arthrosis (50) and osteomyelitis (23). The number of variables evaluated was 39. These were all of a general biochemical and haematological nature. A feature reduction resulted in sixteen variables that matched well with those known from the literature. Linear discriminant analysis yielded poor results in classifying the six disease categories (with 18 variables 61.8%). A reduction to three disease categories improved the classification results remarkably. This, and the excellent discriminating power between patients and the reference group, shows that the selected variables are illustrative only for general clinical pictures, such as infection, and not for the desired differential diagnosis.

Arthritis, Rheumatoid↗
PubMed2004

Multi-species assessment of electrical resistance as a skin integrity marker for in vitro percutaneous absorption studies.

Assessment of percutaneous absorption in vitro provides key information when predicting dermal absorption in vivo. Confirmation of skin membrane integrity is an essential component of the in vitro method, as described in test guideline OECD 428. Historically, assessment of the membrane's permeability to tritiated water (T2O) and the generation of a permeability coefficient (Kp) were used to confirm that the skin membrane was intact prior to application of the test penetrant. Measuring electrical resistance (ER) across the membrane is a simpler, quicker, safer and more cost effective method. To investigate the robustness of the ER integrity measure, the Kp values for T2O for a range of human and animal skin membranes were compared with corresponding ER data. Overall, for human, rat, pig, mouse, rabbit and guinea pig skin, the ER data gave a good inverse association with the corresponding Kp values; the higher the Kp the lower the ER values. In addition, the distribution across a large dataset for individual skin samples was similar for Kp and ER, allowing a cut-off value for ER to be established for each skin type. Based on CTL's (Syngenta Central Toxicology Laboratory) standard static diffusion cells and databridge, we propose that intact skin should have an ER equal to or above (in kOmega): human (10), mouse (5) guinea pig (5), pig (4) rat (3), and rabbit (0.8). We conclude that measurement of ER across in vitro skin membranes provides a robust measurement of skin barrier integrity and is an appropriate alternative to Kp for T2O in order to identify intact membranes that have acceptable permeability characteristics for in vitro percutaneous absorption studies.

Administration, Topical↗
PubMed2003

Serotonergic brainstem abnormalities in Northern Plains Indians with the sudden infant death syndrome.

The rate of the sudden infant death syndrome (SIDS) among American Indian infants in the Northern Plains is almost 6 times higher than in U.S. white infants. In a study of infant mortality among Northern Plains Indians, we tested the hypothesis that receptor binding abnormalities to the neurotransmitter serotonin (5-HT) in SIDS cases, compared with autopsied controls, occur in regions of the medulla oblongata that contain 5-HT neurons and that are critical for the regulation of cardiorespiration and central chemosensitivity during sleep, i.e. the medullary 5-HT system. Tritiated-lysergic acid diethylamide binding to 5-HT(1A-D) and 5-HT2 receptors was measured in 19 brainstem nuclei in 23 SIDS and 6 control infants using tissue receptor autoradiography. Binding in the arcuate nucleus, a part of the medullary 5-HT system along the ventral surface, in the SIDS infants (mean age-adjusted binding 7.1 +/- 0.8 fmol/mg tissue, n = 23) was significantly lower than in controls (mean age-adjusted binding 13.1 +/- 1.6 fmol/mg tissue, n = 5) (p = 0.003). Binding also demonstrated significant diagnosis x age interactions (p < 0.04) in 4 other nuclei that are components of the 5-HT system. These data suggest that medullary 5-HT dysfunction can lead to sleep-related, sudden death in affected SIDS infants, and confirm the same binding abnormalities reported by us in a larger dataset of non-American Indian SIDS and control infants. This study also links 5-HT abnormalities in the arcuate nucleus with exposure to adverse prenatal exposures, i.e. cigarette smoking (p = 0.011) and alcohol (p = 0.075), during the periconceptional period or throughout pregnancy. Prenatal exposure to cigarette smoke and/or alcohol may contribute to abnormal fetal medullary 5-HT development in SIDS infants.

Age Factors↗
PubMed2001

Design and analysis of trials with quality of life as an outcome: a practical guide.

Health Related Quality of Life (HRQoL) measures are becoming more frequently used in clinical trials, as both primary and secondary endpoints. Investigators are now asking statisticians for advice on how to plan (e.g., sample size) and analyze studies using HRQoL measures. HRQoL measures such as the SF-36 are usually measured on an ordered categorical (ordinal) scale. In the designing stages and when analyzing, the scales are often scored and the scores treated as if they were continuous and normally distributed. However the ordinal scaling of HRQoL measures leads to problems in determining sample size, and conventional parametric methods of estimation and hypothesis testing may not be appropriate for such outcomes. We present practical guidelines for the design and analysis of trials with HRQoL measures as outcomes. We used conventional statistical methods (i.e., t-tests and multiple regression), various ordinal regression models (proportional odds, continuation ratio, polytomous and stereotype) and bootstrap methods to analyze an HRQoL dataset. To illustrate the various methods we used HRQoL data on the SF-36 Role Limitations Emotional dimension for two groups of patients with leg ulcers. The bootstrap, t-test, and multiple regression methods gave similar results. The various ordinal regression models also gave similar results. If the HRQoL measure has a large number of ordered categories, most of which are occupied, and the underlying scale really is continuous but measured imperfectly by an instrument with a limited number of discrete values, then an informal rule of thumb is that this discrete scale should be treated as continuous if it has seven or more categories and as ordinal otherwise.

Algorithms↗
PubMed2001

Use of narrative analysis for comparisons of the causes of fatal accidents in three countries: New Zealand, Australia, and the United States.

OBJECTIVES: To investigate the utility of narrative analysis of text information for describing the mechanism of injury and to compare the patterns of the mechanism of injury for work related fatalities in three countries. METHODS: Three national collections of data on work related fatalities were used in this study including those for New Zealand, 1985-94 (n=723), for Australia, 1989-92 (n=1,220), and for the United States, 1989-92 (16,383). The New Zealand and Australian collections used the type of occurrence standard code for the mechanism of injury, however the United States collection did not. All three databases included a text description of the circumstances of the fatality so a text based analysis was developed to enable a comparison of the mechanisms of injury in each of the three countries. A test set of 200 cases from each country dataset was used to develop the narrative analysis and to allow comparison of the narrative and standard approaches to mechanism coding. RESULTS: The narrative coding was more useful for some types of injury than others. Differences in coding the narrative codes compared with the standard code were mainly due to lack of sensitivity in detecting cases for all three datasets, although specificity was always high. The pattern of causes was very similar between the two coding methods and between the countries. Hit by moving objects, falls, and rollovers were among the five most common mechanisms of workplace fatalities for all countries. More common mechanisms that distinguished the three countries were electrocutions for Australia, drowning for New Zealand, and gunshot for the United States. CONCLUSION: Narrative analysis shows some promise as an alternative approach for investigating the causes of fatalities.

Accidents, Occupational↗
PubMed1999

A new multiparameter flow cytometer: optical and electrical cell analysis in combination with video microscopy in flow.

BACKGROUND: Flow cytometers, which are commercially available, do not necessarily meet all demands of actual biomedical research. This is the case for the investigation of mechanisms involved in cell volume regulation, which requires electrical volume measurement and ratiometric multichannel fluorescence analysis for the simultaneous assessment of different physiologic parameters (intracellular pH and the intracellular concentration of calcium ions, etc). METHODS AND RESULTS: We describe the construction of a new nonsorting flow cytometer designed for the simultaneous acquisition of seven parameters including fluorescence signals, forward and perpendicular light scatter, cell volume according to the electrical Coulter principle, and flow cytometric imaging. The instrument is equipped with three different light sources. A tunable argon-ion laser generates efficient excitation of the most standard fluorescent probes in the visible spectral range, and an arc lamp provides the means for ultraviolet excitation at low cost. Because of the spatial filtering by the excitation and detection optics, two independent sets of dual fluorescence measurements can be performed, a prerequisite for flexible ratiometric fluorescence analysis. A flow video microscope integrated into the optical system optionally generates either brightfield or phase images of selected flowing particles. Only particles whose individual datasets meet predefined gating conditions are imaged in real time. To avoid smear effects, the motion of the object to be imaged (speed approximately 8 m/s) is frozen on the target of a CCD camera by flash illumination. For this purpose, a high radiance gas discharge lamp with 25-mJ electric pulse energy provides an illumination time of 18 ns (full width half maximum). Test results obtained from latex spheres and cells are shown. CONCLUSIONS: Test results indicate that our instrument can perform Coulter measurements in combination with flexible optical analysis. Moreover, integration of an adapted video microscope into a flow cytometer is an approach to overcome the gap between flow and image cytometry.

Animals↗
PubMed1997

A population needs assessment profile for dementia.

The Tayside Profile for Dementia Planning is an instrument designed to obtain data for population needs assessment and planning. It provides a brief tool to collect a minimum dataset by non-specialists. Third-party informants-informal carers or involved professionals-are used as data sources. The key concept is the use of a descriptive profile rather than a summative score or categorization. The profile consists of a set of needs indicators, information on current service response and demographic and background data. Key levels of dependency are measured by time interval dependency. Validity, reliability, acceptability and usability are satisfactory, with the crucial exception that informal carers and professionals appear to perceive needs differently. Further research is needed to assess which type of informant provides the more useful data.

Caregivers↗
PubMed2002

Publishing large proteome datasets: scientific policy meets emerging technologies.

Currently, there are various approaches to proteomic analyses based on either 2D gel or HPLC separation platforms, generating data of different formats, structures and types. Identification of these separated proteins or peptide fragments is typically achieved by mass spectrometry (MS) measurements that use either accurate mass measurements or fragmentation (MS-MS) information. Integrating the information generated from these different platforms is essential if proteomics is to succeed. A further challenge lies in generating standards that can accept the hundreds-of-thousands of mass spectra produced per analysis based on threshold or probability measurements. Finally, peer review and electronic publication processes will be crucial to the dissemination and use of proteomic information. Merging the policy requirements of data-intensive research with information technology will enable scientists to gain real value from global proteomics information.

Chromatography, Liquid↗
PubMed1999

Quantification of 99Tcm-HMPAO brain SPET in two series of healthy volunteers using different triple-headed SPET configurations: normal databases and methodological considerations.

We evaluated the methodological issues underlying the assessment of normal confidence intervals, as used in clinically based region-of-interest (ROI) semi-quantification of 99Tcm-HMPAO brain SPET. At two different centres equipped with high-resolution, triple-headed gamma cameras, HMPAO SPET scans were performed on two groups of 24 and 15 healthy volunteers respectively. Together with an operator-defined analysis (ODA), a semi-automated analysis (SAA) was conducted on the normal datasets in one centre. Tests of intra- and inter-observer variability were performed. Repeat scans were performed within 72 h after the first to analyse short-term regional inter-study variations. The overall regional uptake showed significant differences in most regions between both normal datasets. Intra-observer and inter-observer reproducibility were on average within 4% for the ODA, while for the SAA it was less than 1%. Inter-study variations were excellent for both centres, ranging from -4% to +3% for most regions studied. The variability in clinical brain perfusion studies largely depends on the reproducibility of the data analysis technique. A semi-automated approach shows clear advantages over an entirely operator-defined approach. Intra-subject repeat studies show enough stability for use as reliable baseline measurements in the construction of a normal database or to allow activation studies with high sensitivity.

Adult↗
PubMed1997

Evaluation of a novel infrared range vibration-based descriptor (EVA) for QSAR studies. 1. General application.

A novel molecular descriptor (EVA) based upon calculated infrared range vibrational frequencies is evaluated for use in QSAR studies. The descriptor is invariant to both translation and rotation of the structures concerned. The method was applied to 11 QSAR datasets exhibiting both a range of biological endpoints and various degrees of structural diversity. This study demonstrates that robust QSAR models can be obtained using the EVA descriptor and examines the effect of EVA parameter changes on these models; recommendations are made as to the appropriate choice of parameters. The performance of EVA was found to be comparable in statistical terms to that of CoMFA, despite the fact that EVA does not require the generation of a structural alignment. Models derived using semiempirical (MOPAC AM1 and PM3) and AMBER mechanics calculated normal mode frequencies are compared, with the overall conclusion that the semiempirical methods perform equally well and both outperform the AMBER-based models.

Computer Simulation↗
PubMed1999

Comparison of alternative methods for assessing injury severity based on anatomic descriptors.

BACKGROUND: There is mounting confusion as to which anatomic scoring systems can be used to adequately control for trauma case mix when predicting patient survival. METHODS: Several Abbreviated Injury Scale (AIS) and International Classification of Disease Clinical (ICD-9CM)-based methods of scoring severity were compared by using data from the Pennsylvania Trauma Outcome Study. By using a design dataset, the probability of survival was modeled as a function of each score or profile. Resulting coefficients were used to derive expected probabilities in a test dataset; expected and observed probabilities were then compared by using standard measures of discrimination and calibration. RESULTS: The modified Anatomic Profile, Anatomic Profile, and New Injury Severity Score outperformed the International Classification of Disease-based Injury Severity Score. This finding remains true when AIS values are obtained by means of a conversion from International Classification of Disease to AIS. CONCLUSION: Results support the integrity of the AIS and argue for its continued use in research and evaluation. The modified Anatomic Profile, Anatomic Profile, and New Injury Severity Score, however, should be used in preference to the Injury Severity Score as an overall measure of severity.

Humans↗
PubMedDate not supplied

DMARD use in early rheumatoid arthritis. Lessons from observations in patients with established disease.

The concept of early and aggressive therapy of rheumatoid arthritis (RA) has been well documented in the past years. It includes immediate DMARD institution after diagnosis, the use of the most effective DMARDs, and rapid switching of regimens if a level of disease activity close to remission is not achieved. In this review we briefly explore to what degree this new concept has been implemented in routine clinical care. Based on an observational dataset comprising 3342 DMARD courses, we present evidence of a change in DMARD patterns in newly diagnosed RA patients towards a higher prescription rate of more aggressive drugs like methotrexate (MTX), as well as a decreasing lag time until MTX was instituted in RA patients over the years. One consequence of recent changes in therapeutic strategies is that comparative analyses of formerly versus recently employed DMARDs will be considerably biased in observational studies. By contrast to changes in DMARD usage, survey data show neither a shortening of referral time nor a change in the approach to diagnose early RA. These data indicate a need for more dissemination of the early arthritis concept.

Adult↗
PubMed1989

Diverse prognosis in metastatic breast cancer: who should be offered alternative initial therapies?

In an attempt to clarify appropriate treatment options for women with stage IV breast cancer, we studied the survival experience of a large dataset of patients treated on Cancer and Leukemia Group B (CALGB) protocols. The study, restricted to women who had had no prior chemotherapy for metastatic disease, demonstrated a surprisingly poor prognosis, with an estimated median survival of 1.6 years and only 26% alive at 3 years. Analysis of prognostic factors permitted the identification of subsets with even shorter survival, such as women with estrogen receptor negative tumor in more than one metastatic site and prior adjuvant chemotherapy. We feel that an evaluation of intensive investigational treatment approaches, such as trials using autologous bone marrow transplantation, is justified for most stage IV breast cancer patients, in view of their poor prognosis.

Biomarkers, Tumor↗
PubMed2002

Neural network based automated algorithm to identify joint locations on hand/wrist radiographs for arthritis assessment.

Arthritis is a significant and costly healthcare problem that requires objective and quantifiable methods to evaluate its progression. Here we describe software that can automatically determine the locations of seven joints in the proximal hand and wrist that demonstrate arthritic changes. These are the five carpometacarpal (CMC1, CMC2, CMC3, CMC4, CMC5), radiocarpal (RC), and the scaphocapitate (SC) joints. The algorithm was based on an artificial neural network (ANN) that was trained using independent sets of digitized hand radiographs and manually identified joint locations. The algorithm used landmarks determined automatically by software developed in our previous work as starting points. Other than requiring user input of the location of nonanatomical structures and the orientation of the hand on the film, the procedure was fully automated. The software was tested on two datasets: 50 digitized hand radiographs from patients participating in a large clinical study, and 60 from subjects participating in arthritis research studies and who had mild to moderate rheumatoid arthritis (RA). It was evaluated by a comparison to joint locations determined by a trained radiologist using manual tracing. The success rate for determining the CMC, RC, and SC joints was 87%-99%, for normal hands and 81%-99% for RA hands. This is a first step in performing an automated computer-aided assessment of wrist joints for arthritis progression. The software provides landmarks that will be used by subsequent image processing routines to analyze each joint individually for structural changes such as erosions and joint space narrowing.

Algorithms↗
PubMed2004

Long terminal repeat retrotransposons of Mus musculus.

BACKGROUND: Long terminal repeat (LTR) retrotransposons make up a large fraction of the typical mammalian genome. They comprise about 8% of the human genome and approximately 10% of the mouse genome. On account of their abundance, LTR retrotransposons are believed to hold major significance for genome structure and function. Recent advances in genome sequencing of a variety of model organisms has provided an unprecedented opportunity to evaluate better the diversity of LTR retrotransposons resident in eukaryotic genomes. RESULTS: Using a new data-mining program, LTR_STRUC, in conjunction with conventional techniques, we have mined the GenBank mouse (Mus musculus) database and the more complete Ensembl mouse dataset for LTR retrotransposons. We report here that the M. musculus genome contains at least 21 separate families of LTR retrotransposons; 13 of these families are described here for the first time. CONCLUSIONS: All families of mouse LTR retrotransposons are members of the gypsy-like superfamily of retroviral-like elements. Several different families of unrelated non-autonomous elements were identified, suggesting that the evolution of non-autonomy may be a common event. High sequence similarity between several LTR retrotransposons identified in this study and those found in distantly-related species suggests that horizontal transfer has been a significant factor in the evolution of mouse LTR retrotransposons.

Animals↗
PubMed1994

From terminology to terminology services.

Terminologies have traditionally been considered as static datasets held in books or databases. The GALEN Terminology Server presents a prototype for a new view of terminologies delivered as a set of functions and services provided to other applications. This facilitates their development and integration as part of a strategy for sharing and re-using information and knowledge. The essential features of the Terminology server are the functions which it can perform; questions which it can answer and statements which it can be told. The GALEN Terminology Server supports these operations through a modular architecture and uniform applications programming interface which allows client applications to ignore the internal structure and simply use the Server for terminological, coding, and linguistic functions.

Computer Systems↗
PubMed2000

The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial of the National Cancer Institute: history, organization, and status.

The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial is enrolling 148,000 men and women ages 55-74 at ten screening centers nationwide with balanced randomization to intervention and control arms. For prostate cancer, men receive a digital rectal examination and a blood test for prostate-specific antigen. For lung cancer, men and women receive a posteroanterior view chest X-ray. For colorectal cancer, men and women undergo a 60-cm flexible sigmoidoscopy. For ovarian cancer, women receive a blood test for the CA125 tumor marker and transvaginal ultrasound. Members of the control arm continue with their usual care. Follow-up in both groups will continue for at least 13 years from randomization to assess health status and cause of death. The primary endpoint is mortality from the four PLCO cancers, which accounts for about 53% of all cancer deaths in men and 41% of cancer deaths in women in the United States each year. Blood specimens are collected from screened participants, buccal cell DNA from controls, and histology slides from cases; these are maintained in a biorepository. Participants complete a baseline questionnaire (covering health status and risk factors) and a dietary questionnaire. More than 12,000 participants were enrolled in the pilot phase (concluded in September 1994). Changes in the eligibility criteria followed. As of April 2000, enrollment exceeded 144,500. Data are scanned into designated on-site computers for uploading by participant identification number to the coordinating center for quality checks, archival storage, and preparation of analysis datasets for use by the National Cancer Institute (NCI). Scientific direction is provided by NCI scientists, trial investigators, external consultants, and an independent data safety and monitoring board. Performance and data quality are monitored via data edits, site visits, random record audits, and teleconferences. The PLCO trial is formally endorsed by the American Cancer Society and has been ranked by the American Urological Association as one of the most important prostate cancer studies being conducted. Special efforts to enroll black participants are cosponsored by the U.S. Centers for Disease Control and Prevention.

Aged↗
PubMed2001

yMGV: a database for visualization and data mining of published genome-wide yeast expression data.

The yeast Microarray Global Viewer (yMGV) is an on-line database providing a synthetic view of the transcriptional expression profiles of Saccharomyces cerevisiae genes in most of the published expression datasets. yMGV displays a one-screen graphical representation of gene expression variations for each published genome-wide experiment, allowing quick retrieval of experimental conditions affecting expression of this gene. yMGV also provides tools to isolate groups of genes sharing similar transcription profiles in a defined subset of experiments. Additionally, yMGV furnishes a set of statistical tools for critical assessment of published data. We therefore believe that yMGV is an efficient tool that affords a quick and comprehensive overview of microarray data and generates new gene classifications. As of 20 March 2001 the yMGV database contains 6 000 000 measurements, representing genome-wide expression comparisons of 932 experiments from 39 microarray publications. The yMGV interface is available at http://transcriptome.ens.fr/ymgv/.

Computational Biology↗