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PubMed1996

NMR spectral quantitation by principal-component analysis. II. Determination of frequency and phase shifts.

This paper extends the use of principal-component analysis in spectral quantification to the estimation of frequency and phase shifts in a single resonant peak across a series of spectra. The estimated parameters can be used to correct the spectra accordingly, resulting in more accurate peak-area estimation. Further, the removal of the variations in phase and frequency cause by instrumental and experimental fluctuations makes it possible to determine more accurately the remaining variations, which bear biological significance. The procedure is demonstrated on simulated data, a 3D chemical-shift-imaging dataset acquired from a cylinder of inorganic phosphate (Pi), and a set of 736 31P NMR in vivo spectra taken from a kinetic study of rate muscle energetics. In all cases, the procedure rapidly and automatically identifies the frequency and phase shifts present in the individual spectra. In the kinetic study, the procedure is used twice, first to adjust the phase and frequency of a reference peak (phosphocreatine) and then to determine the individual frequencies of the Pi peak in each of the spectra which further can be used for estimation of pH changes during the experiment.

Computer Simulation↗
PubMed1999

B-SPID: an object-relational database architecture to store, retrieve, and manipulate neuroimaging data.

We propose a hardware and software architecture to respond to crucial problems in the neuroimaging field: storage, retrieval, and processing of large datasets. The B-SPID project, here discussed, concerns the processing of neuroimages and attached components stored in an object-relational multimedia database management system (DBMS). Advanced bioinformation concepts are exploited in this project such as large scale data storage, high level graphical user interfaces and 3D graphical processing and display of data. Our database implementation is based on standard programming components, runs on several UNIX platforms and is written to be evolutive. Queries on this database are designed to obtain and display from neuroimaging data several types of results (pictures, text, or 3D graphical shapes) on heterogeneous systems.

Brain Mapping↗
PubMed1999

Molecular phylogeny and evolutionary history of the tit-tyrants (Aves: Tyrannidae).

Tit-tyrants of the genus Anairetes presently consist of six species; five inhabit various regions along the Andean cordillera of South America and one is endemic to the Juan Fernandez Islands off the coast of Chile. Data from mtDNA ND2 and Cyt b sequences were used to construct a phylogeny for all Anairetes species as well as Uromyias agilis, a closely related genus, and Stigmatura as an outgroup, to determine their relationships and history of radiation in South America. Results strongly supported the following paired relationships: A. nigrocristatus-A. reguloides, A. flavirostris-A. alpinus, and A. parulus-A. fernandezianus. This dataset, however, could not resolve basal nodes; therefore relationships among these pairs remains obscure. Moreover the genus Uromyias, controversially separated on morphological criteria from Anairetes, fell within the Anairetes clade, although its exact position could not be ascertained with confidence. The molecular data indicate that this group probably radiated within the past 2 million years, concomitant with highly accentuated cycles of global climatic change. Certain high altitude areas within the Andes may have been stable during global climatic changes and may have served as refugia during the Plio-Pleistocene.

Animals↗
PubMed1994

Comparison of chemotherapy and bone marrow transplants using two independent clinical databases.

Comparing the outcome of chemotherapy and bone marrow transplants in the absence of a randomized trial is difficult but necessary for diseases where small numbers of patients make such trials difficult if not impossible. To address this issue for adults with acute lymphoblastic leukemia in first remission, we created an empirical database using two separate datasets, one from the International Bone Marrow Transplant Registry and the other from two multicenter chemotherapy studies. Prior to combining the datasets, a study protocol was developed to define inclusion criteria, outcomes to be compared and statistical methods. The main problems of a non-randomized comparison are biases potentially introduced by differences in baseline composition of the two cohorts and differences in time-to-treatment. The source of the latter bias is different distributions of waiting times between achieving complete remission and receiving post-remission therapy. Several techniques to control these biases were evaluated; each gave qualitatively similar results. These methods can easily be applied to other clinical situations where randomized trials are not available.

Adolescent↗
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↗
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↗
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↗
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↗
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↗
PubMed1995

Analysis of the CD3 gene region and type 1 diabetes: application of fluorescence-based technology to linkage disequilibrium mapping.

The CD3 gene region on chromosome 11q23 has been implicated in susceptibility to type 1 (insulin-dependent) diabetes mellitus. Using semi-automated fluorescence-based technology, we have undertaken association and linkage analysis of a dinucleotide microsatellite in the CD3 delta (CD3D) gene. We have also performed a large case-control analysis of a restriction fragment length polymorphism (RFLP) in the CD3 epsilon (CD3E) gene, 26 kb from CD3D. We found no evidence for the previously reported association between the 8 kb allele of the RFLP and disease in a UK dataset of 403 diabetic patients and 446 nondiabetic controls. Furthermore, the use of the transmission/disequilibrium test (TDT) showed no evidence of linkage or association to type 1 diabetes at either marker locus. We conclude that the CD3 gene region does not contribute significantly to IDDM susceptibility. We have successfully applied semi-automated, fluorescence-based technology to undertake association analysis on the CD3D microsatellite. Moreover, by analysing 94 other dinucleotide repeat markers, we conclude that fluorescence-based methodology can generally be applied to large-scale, semi-automated association studies with most microsatellite markers.

Adolescent↗
PubMed1996

A clinical evaluation of flurbiprofen LAT and piroxicam gel: a multicentre study in general practice.

A prospective, randomized, multicentre, open, crossover study of the comparative efficacy, tolerability and acceptability of two topical nonsteroidal anti-inflammatory drug (NSAID) therapies, flurbiprofen local-action transcutaneous (LAT) patch (40 mg b.d.) and piroxicam gel (3 cm, 0.5% q.d.s), was conducted in general practice in the UK in 137 men and women with soft-tissue rheumatism of the shoulder or elbow (e.g. epicondylitis, tendinitis, bursitis and adhesive capsulitis). Patients received one therapy for 4 days before crossing over to the other NSAID for a further 4 days, followed by 6 days of their preferred therapy. Clinical assessment of severity of pain, tenderness and overall clinical condition was carried out at baseline and after 4, 8 and 14 days. Patients self-assessed the severity of pain during the day and at night, and also the quality of their sleep during each treatment phase. More patients showed a greater improvement in all of the clinical assessments of efficacy following treatment with flurbiprofen LAT during the crossover phase. There was a statistically significant reduction in the severity of pain, the principal measure of efficacy, in favour of flurbiprofen LAT: 42% of patients showed greater improvement with flurbiprofen LAT compared with 26% who showed a greater improvement with piroxicam gel (p = 0.012; n = 131, intent-to-treat). Eligible dataset (n = 126) analysis revealed statistically significant differences in favour of flurbiprofen LAT in the severity of lesion tenderness (p = 0.03) and the overall change in clinical condition (p = 0.04) compared with baseline status. Superior efficacy for flurbiprofen LAT was also indicated in the patients' assessment at the end of the crossover phase (day 8), at which 69% chose to continue treatment with flurbiprofen LAT compared with only 31% of patients who chose piroxicam gel (n = 126; p < 0.001). There were, in addition, statistically significant differences in favour of flurbiprofen LAT in assessments for night pain (p < 0.001), quality of sleep (p = 0.004) and the patients' overall opinion of treatment (p < 0.001). Both treatments were well tolerated with a low incidence of mainly local adverse events. These results showed that flurbiprofen LAT had a greater efficacy than piroxicam gel, and was also preferred by patients in the treatment of painful soft-tissue rheumatism of the shoulder and elbow.

Administration, Cutaneous↗
PubMed1999

Transparent image access in a distributed picture archiving and communications system: the Master Database broker.

A distributed design is the most cost-effective system for small-to medium-scale picture archiving and communications systems (PACS) implementations. However, the design presents an interesting challenge to developers and implementers: to make stored image data, distributed throughout the PACS network, appear to be centralized with a single access point for users. A key component for the distributed system is a central or master database, containing all the studies that have been scanned into the PACS. Each study includes a list of one or more locations for that particular dataset so that applications can easily find it. Non-Digital Imaging and Communications in Medicine (DICOM) clients, such as our worldwide web (WWW)-based PACS browser, query the master database directly to find the images, then jump to the most appropriate location via a distributed web-based viewing system. The Master Database Broker provides DICOM clients with the same functionality by translating DICOM queries to master database searches and distributing retrieval requests transparently to the appropriate source. The Broker also acts as a storage service class provider, allowing users to store selected image subsets and reformatted images with the original study, without having to know on which server the original data are stored.

CD-ROM↗
PubMed1999

Tetanus toxoid and congenital abnormalities.

OBJECTIVE: To study the human teratogenic potential of tetanus vaccination during pregnancy. METHODS: Pair analysis of cases with congenital abnormalities and matched healthy controls was performed in the large population-based dataset of the Hungarian Case-Control Surveillance of Congenital Abnormalities, 1980-1994. RESULTS: Of 35 727 pregnant women who had babies without any defects in the study period (control group), 33 (0.09%) were vaccinated with tetanus. Of 21563 pregnant women who had offspring with congenital abnormalities, 25 (0.12%) had tetanus vaccination. This difference was not significant (P = 0.39). The case-control pair analysis confirmed the safety of tetanus vaccination during pregnancy, particularly in the second and third months of gestation, i.e. during the critical period for congenital abnormalities. CONCLUSION: Tetanus vaccination during pregnancy appears not be teratogenic to the fetus. Thus, there is no contraindication, if the use of tetanus toxoid is necessary during pregnancy.

Abnormalities, Drug-Induced↗
PubMedDate not supplied

Scientific and cost-effectiveness criteria in selecting batteries of short-term tests.

The scientific and cost-effectiveness criteria introduced in this paper can be applied to published datasets and current and proposed batteries of short-term tests. The reports in the current volume will provide a wealth of additional material for such evaluations, but more systematically obtained information will be necessary to assess both the internal and external validity of these tests. Individual tests and batteries of tests should be standardized, employ positive controls, generate results capable of quantitative analyses that may make dichotomous classification as "positive" and "negative" obsolete, be interpreted in light of mechanisms of action, and be cost-effective on a grand scale. For regulatory purposes our long-term goal should be to replace the whole animal lifetime bioassay with an appropriate and cost-effective set of short-term tests.

Animals↗
PubMed1992

Distributed data analysis in a multicenter study: the CARDIA Study.

Unlike distributed data entry, which is used in many large epidemiologic studies and multicenter clinical trials, distributed data analysis is a relatively new concept. This paper reports on the usefulness of such a system in the Coronary Artery Risk Development in Young Adults (CARDIA) Study. CARDIA distributes the entire examination dataset to participating centers soon after completion of each round of data collection. The process was designed to encourage more numerous, diverse, and rapid publications, and to allow for more efficient use of the manpower and expertise in centers. Responsibilities of the coordinating center have changed from a conventional coordinating center but remain substantial due to the need for collating, monitoring, verifying, and documenting the distributed data analysis (DDA) system. DDA is successful from the standpoint of implementation and operation--21 manuscripts representing work analyzed at six participating centers had been submitted for publication within 3.5 years of the completion of the baseline examination.

Adolescent↗