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PubMed2005

TmaDB: a repository for tissue microarray data.

BACKGROUND: Tissue microarray (TMA) technology has been developed to facilitate large, genome-scale molecular pathology studies. This technique provides a high-throughput method for analyzing a large cohort of clinical specimens in a single experiment thereby permitting the parallel analysis of molecular alterations (at the DNA, RNA, or protein level) in thousands of tissue specimens. As a vast quantity of data can be generated in a single TMA experiment a systematic approach is required for the storage and analysis of such data. DESCRIPTION: To analyse TMA output a relational database (known as TmaDB) has been developed to collate all aspects of information relating to TMAs. These data include the TMA construction protocol, experimental protocol and results from the various immunocytological and histochemical staining experiments including the scanned images for each of the TMA cores. Furthermore the database contains pathological information associated with each of the specimens on the TMA slide, the location of the various TMAs and the individual specimen blocks (from which cores were taken) in the laboratory and their current status i.e. if they can be sectioned into further slides or if they are exhausted. TmaDB has been designed to incorporate and extend many of the published common data elements and the XML format for TMA experiments and is therefore compatible with the TMA data exchange specifications developed by the Association for Pathology Informatics community. Finally the design of the database is made flexible such that TMA experiments from several types of cancer can be stored in a single database, which incorporates the national minimum data set required for pathology reports supported by the Royal College of Pathologists (UK). CONCLUSION: TmaDB will provide a comprehensive repository for TMA data such that a large number of results from the numerous immunostaining experiments can be efficiently compared for each of the TMA cores. This will allow a systematic, large-scale comparison of tumour samples to facilitate the identification of gene products of clinical importance such as therapeutic or prognostic markers. In addition this work will contribute to the establishment of a standard for reporting TMA data analogous to MIAME in the description of microarray data.

Data Interpretation, Statistical↗

PubMed2006

Tell me a story: MMPI responses and personal biography in the case of a serial killer.

The interpretation of MMPI (Hathaway & McKinley, 1943) profiles has emphasized a language of pathological attribution that often serves the interests of clinical description and actuarial prediction better than those of individual case formulation and an understanding of the adaptive forces involved in the production of symptomatic behavior. In this article, I illustrate a contrasting approach, one that emphasizes MMPI items and scales as instruments of personal biography, with the case of the serial murderer Jeffrey Dahmer.

Adult↗

PubMed2004

Reproducibility of mammographic classifications for non-palpable suspect lesions with microcalcifications.

Observer variability in interpretation of mammograms is a well-known problem, especially for microcalcifications. The classification of the mammographic findings depends upon this interpretation. We performed an intraobserver study to evaluate a breast imaging reporting and data system (BI-RADS) based method for description and classification of non-palpable lesions with microcalcifications. A set of 100 non-palpable mammographic lesions mainly consisting of microcalcifications was described and classified on two occasions, by two radiologists at an interval of 6 months. The intraobserver variability was evaluated with kappa statistics. The overall agreement for the classification was moderate (kappa 0.54). The lowest kappa values were observed for the categories "probably benign (BI-RADS 3, kappa 0.59)" and "suspicious abnormality (BI-RADS 4, kappa 0.44)". The clinical management (follow-up or biopsy) of non-palpable lesions consisting of microcalcifications depending upon radiological classification in the groups BI-RADS 3 (follow-up) and BI-RADS 4 (biopsy) is therefore debatable.

Biopsy, Needle↗

PubMed1992

Home health care classification.

This article is the second in a series on the Home Health Care Classification research study conducted at Georgetown University School of Nursing (see the March 1992 CARING). The purpose of the study was to develop a method to assess and classify home health Medicare patients in order to predict their need for nursing and other home care services, including their outcomes of care. To accomplish this goal, data on actual resource use that could be objectively measured were used to predict resource requirements. A third article will provide more detail on the descriptive findings, statistical analyses, and the Preliminary Classification System.

Aged↗

PubMed1991

The choice of statistical tests.

The basic principles of statistical analysis and statistical tests are presented. Test for the two-sample problem (e.g. comparison of two treatments) are extensively explained for qualitative (categorial), quantitative and ordinal response variables. As a powerful tool to derive significance probabilities independent from distributional assumptions (distribution free tests, nonparametric tests) the conditioning principle (conditional significance probability) is explained and its application demonstrated by examples. Some final remarks concern the role of significance tests in data description, data analysis and decisions as well as alternative decision procedures.

Data Interpretation, Statistical↗

PubMed1982

[Depression in black Africa. Review of the literature].

The first two chapters of the present review of literature about depression in Black Africa deal with epidemiological data and semiological items. The epidemiological approach rises up the same difficulties as those raised in similar researches carried out in Western Countries, and others linked with the sociological field being studied. We find in the clinical descriptions some basic symptoms classically described in the West. Yet, the expression of the depressive experience gives way to cultural persecutive interpretations, the meaning of which is treated in the third chapter.

Africa↗

PubMed1982

Functional alterations in the membrane of motile polymorphonuclear leukocytes.

We have applied microdocumentary techniques to the study of movement of human PMN's and their behavioral response to a chemoattractant. We discuss here findings which suggest a different interpretation from currently accepted theory. Videotape recordings were made on the movement of human PMN's. A slide modified from previous descriptions was designed to predict a straight-line gradient which could be maintained for periods up to 60 minutes. PMN suspensions were placed on the bridge of the slide with the chemoattractant N-formylmethionylleucyl-phenylalanine (F-Met-Leu-Phe) placed in one wall and PMN suspension medium in the well on the other side of the bridge. Videotapes were traced on the monitor screen at 15-second intervals. A lack of consistent orientation and "head-tail" polarity of any individual PMN was observed. Apparent polarity was observed less than 10% of the time. The net movement of cells in a given field was always toward the direction of the approaching and maintained gradient, but any individual cell failed to show a sustained directional orientation or movement toward the gradient. Individual cells constantly reoriented. Analysis of time-dependent characteristics of the chemotactic response is essential to the ultimate understanding of PMN motility.

Cell Membrane↗

PubMed1995

[The classification and therapeutical methods of cataract on Chinese medicine in the modern times].

We investigated cataract-related description on the medical literatures written at China in modern times. In those days, the cataract was classified by the shapes of clouds on the crystalline lens. In present Chinese medicine, it has been interpreted that the senilecataract was showed Eneinaisyo. Hyoei-naisyo, Katsuei-naisyo, Zyuei-naisyo, Sanei-naysyo, Fuei-naisyo, Tinei-naisyo, Ohei-naisyo, Engetsuei-naisyo, Soukaei-naisyo, Hakueiohsin-naisyo and Kokusuigyoei-naisyo; these words were old names for cataract. We separately rethought about their symptoms from the description in the original literatures; however, they showed some symptoms which generally were not found on the senilecataract. On the other hand, the therapeutic methods mainly existed pharmacotherapy, surgical methods and treatments with acupuncture and moxibustion and their applications were each different according to the shapes of the clouds.

Cataract↗

PubMed2004

Single-neuron discharge properties and network activity in dissociated cultures of neocortex.

Cultures of neurons from rat neocortex exhibit spontaneous, temporally patterned, network activity. Such a distributed activity in vitro constitutes a possible framework for combining theoretical and experimental approaches, linking the single-neuron discharge properties to network phenomena. In this work, we addressed the issue of closing the loop, from the identification of the single-cell discharge properties to the prediction of collective network phenomena. Thus, we compared these predictions with the spontaneously emerging network activity in vitro, detected by substrate arrays of microelectrodes. Therefore, we characterized the single-cell discharge properties to Gauss-distributed noisy currents, under pharmacological blockade of the synaptic transmission. Such stochastic currents emulate a realistic input from the network. The mean (m) and variance (s(2)) of the injected current were varied independently, reminiscent of the extended mean-field description of a variety of possible presynaptic network organizations and mean activity levels, and the neuronal response was evaluated in terms of the steady-state mean firing rate (f). Experimental current-to-spike-rate responses f(m, s(2)) were similar to those of neurons in brain slices, and could be quantitatively described by leaky integrate-and-fire (IF) point neurons. The identified model parameters were then used in numerical simulations of a network of IF neurons. Such a network reproduced a collective activity, matching the spontaneous irregular population bursting, observed in cultured networks. We finally interpret such a collective activity and its link with model details by the mean-field theory. We conclude that the IF model is an adequate minimal description of synaptic integration and neuronal excitability, when collective network activities are considered in vitro.

Action Potentials↗

PubMed1988

Descriptive epidemiology of skin cancer in the Swiss Canton of Vaud.

Incidence registration and survival data for non-melanocytic skin neoplasms and cutaneous melanoma have been abstracted from the population-based system of the Cancer Registry of the Swiss Canton of Vaud, which has been operating in a particularly favourable environment, since the large majority of cutaneous lesions resected in the area are examined by a pathologist. Among the 5,712 cases registered, 66.7% were basal-cell carcinomas, 20.6% squamous-cell cancers, 9.3% cutaneous melanomas and 3.4% other miscellaneous histological types. The distribution by histological type did not differ appreciably in the 2 sexes, but there were marked inter-sex differences as regards anatomical site. In both sexes, head and neck was by far the commonest localization for non-melanomatous neoplasms (69 to 81% of all incident cases), followed by trunk for basal-cell cancers (18% in males, 15% in females) and upper limb for squamous-cell (10% in males, 17% in females). The distribution of skin melanomas differed considerably between the 2 sexes, by far the commonest site being the trunk for males (45% of cases) and lower limbs for females (40%), followed by head and neck (22% in both sexes). Incidence rates for both basal- and squamous-cell cancers increased with age, and rates were higher in males for each localization except the lower limb. In contrast, incidence for melanoma was higher in females, and incidence rates did not increase with age above 55 years for all sites except head and neck. This can be interpreted in terms of cohort effect, since mortality from melanoma has substantially increased in Switzerland across subsequent birth cohorts. Although this study is essentially descriptive, accurate inspection of these data provides some support for the major aetiological hypotheses of skin carcinogenesis, i.e., the observation that the large majority of basal- and squamous-cell cancers arise on the head and neck confirms the importance of long-term ultraviolet exposure; the relative excess of squamous-cell as compared to basal-cell neoplasms on the upper limb may suggest the role of exposure to other (chemical) carcinogens; and the proportional excess of melanomas on the trunk in males and lower limb in females further indicates that intermittent exposure to sunlight is probably the relevant aetiologic factor for melanocytic skin neoplasms.

Adult↗

PubMed2004

The description of physical signs of illness in photographs by physicians with abnormal colour vision.

BACKGROUND: Physicians with congenital colour vision deficiency (CCVD) have reported difficulties recognising certain physical signs of illness, for example, jaundice, red rashes and pallor, and interpreting coloured charts, diagrams and slide projections. However, there has been little study of the effects of CCVD on the performance of medical practitioners. AIM: The aim of this study was to look for evidence of the effect of CCVD on the ability of physicians to recognise and describe physical signs of illness that have colour as either the main or an important feature. METHOD: Twenty-three general practitioners with CCVD were shown 11 colour photographs depicting colour signs of illness and were asked to describe the signs they saw and rate their confidence in making their descriptions. Their responses were compared to those of 23 age-matched general practitioners with normal colour vision. RESULT: General practitioners with CCVD compared to those with normal colour vision had less ability and confidence in detecting physical signs in the photographs and naming the colours. CONCLUSIONS: The results of this study support other evidence that physicians with CCVD have difficulties detecting some colour signs of illness and naming the colours. Because of the use of photographs the extent of the problem in clinical practice is unknown but medical practitioners with CCVD should be aware of the possibility of failing to detect or correctly assess physical signs that are characterised by colour.

Color Vision Defects↗

PubMed1993

Interpreting the mammogram report.

The standardization of imaging techniques, interpretation and reporting has become an important issue as the use of mammographic screening has increased. Each mammogram report should indicate whether the breast is fatty or consists of dense glandular tissue. A brief description of abnormalities should be followed by the conclusion and recommendations. Well-circumscribed lesions have a 98 percent benign rate; these lesions generally do not require biopsy but can be followed at six-month intervals for a period of time. The overall rate of malignancy for biopsies prompted by mammography is 20 to 35 percent. Lesions interpreted as highly suspicious are malignant in 75 to 90 percent of cases. Mammographically detected tumors are generally smaller than palpable tumors at the time of diagnosis. In addition, patients who have mammographically detected lesions are more often node-negative and therefore have a better prognosis than patients with palpable lesions.

Breast Diseases↗

PubMedDate not supplied

The steady-state dipole-flow test for characterization of hydraulic conductivity statistics in a highly permeable aquifer: Horkheimer Insel site, Germany.

Over the last decade the dipole-flow test (DFT) evolved from the general idea of using recirculatory flow to evaluate aquifer properties, to the development of prototype instrumentation and feasibility studies, to a reliable tool for characterization of aquifer heterogeneity. The DFT involves the interpretation of head in recirculatory flow between injection and extraction sections (chambers) in a single well isolated from each other by a multipacker system. In this study, the steady-state dipole flow test (DFT) has been used to characterize the statistics of horizontal hydraulic conductivity (Kr) of the highly permeable, heterogeneous, and thin aquifer at the Horkheimer Insel site, Germany. In previous studies, Kr estimates were based on the steady-state head difference between chambers. A new by-chamber interpretation is proposed that is based on drawdown within each individual chamber. This interpretation yields more detailed information on structure of heterogeneity of the aquifer without introducing complexity into the analysis. The DFT results indicate that Kr ranges from 49 to 6000 m/day (mean ln Kr [(m/s)] approximately -4, and variance of ln Kr [(m/s)] approximately 1-2). Descriptive statistics from the DFT compare well with those from previous field and laboratory tests (pumping, borehole flowmeter, and permeameter tests and grain-size analysis) at this site. It is shown that the role of confining boundaries in the DFT interpretation is negligible even in this case of a thin (< 4 m thick) aquifer. This study demonstrates the flexibility of the DFT and expands the potential application of this method to a wide range of hydrogeologic settings.

Environmental Monitoring↗

PubMed2004

Measurement of perception and interpretation skills during radiology training: utility of the script concordance approach.

Imaging specialties require both perceptual and interpretation skills. Except in very simple cases, data perception and interpretation vary among clinicians. This variability makes for difficulty in measuring these skills with traditional assessment tools. The script concordance approach is conceived to allow standardized assessment in contexts of uncertainty. In this exploratory study, the authors tested the usefulness of the approach for assessment of perceptual and interpretation skills in radiology. A perception test (PT) and an interpretation test (IT) were designed according to the approach. Both tests used plain chest X-rays. Three groups were tested: clerkship students (20), junior residents (R1-R3; 20), senior residents (R4-R5; 20). Eleven certified radiologists, all currently appointed to chest reading, provided the answers by aggregate scoring method. Statistics included descriptive, ANOVA, regression analysis, Pearson and Spearman correlation coefficients. Cronbach alpha values were 0.79 and 0.81 for the PT and IT respectively. Score progression was statistically significant in both tests. Perception scores progressed more rapidly than interpretation scores during training. Effect size was large in discriminating low versus higher level of expertise, 2.2 (PT) and 1.6 (IT). The Pearson correlation coefficient between both tests was 0.58. Cronbach alpha coefficient values indicate reasonable reliability for both tests. The linear progression of scores, each at its own pace, and the positive and moderate magnitude of the Pearson correlation coefficient are arguments suggesting measurement of two different skills. More studies are necessary to document the approach usefulness for assessment in radiology training.

Clinical Competence↗

PubMed2005

Design, validation, and application of a seven-strain Staphylococcus aureus PCR product microarray for comparative genomics.

Bacterial comparative genomics has been revolutionized by microarrays, but the power of any microarray is dependent on the number and diversity of gene reporters it contains. Staphylococcus aureus is an important human pathogen causing a wide range of invasive and toxin-mediated diseases, and more than 20% of the genome of any isolate consists of variable genes. Seven whole-genome sequences of S. aureus are available, and we exploited this rare opportunity to design, build, and validate a comprehensive, nonredundant PCR product microarray carrying reporters that represent every predicted open reading frame (3,623 probes). Such a comprehensive microarray necessitated a novel design strategy. Validation with the seven sequenced strains showed correct identification of 93.9% of genes present or absent/divergent but was dependent on the method of analysis chosen. Microarray data were highly reproducible, reducing the need for many replicate slides. Interpretation of microarray data was enhanced by focusing on the major areas of variation--the presence or absence of mobile genetic elements (MGEs). We compiled "composite genomes" of every individual MGE and visualized their distribution. This allowed the sensitive discrimination of related isolates, including the first clear description of how isolates of the same clone of epidemic methicillin-resistant S. aureus differ substantially in their carriage of MGEs. These MGEs carry virulence and resistance genes, suggesting differences in pathogenic potential. The novel methods of design and interpretation of data generated from this microarray will enable further studies of S. aureus evolution, epidemiology, and pathogenesis.

Bacterial Proteins↗

PubMed1980

[Investigation of demands in data and text processing by an ergonomic job description questionnaire (DT-EIJDQ) (author's transl)].

A questionnaire for Ergonomic Job Description is developed for the area of text and data processing. The contents and structure of the method are described and its applicability is demonstrated in a field study. To interprete the data, methods of cluster, profile, and factor analyses are used. The jobs for which the data have been collected are classified according to their specific demands by the use of factor analysis. Further applications of the method are outlined.

Ergonomics↗

PubMed1989

On the imperfect elasticity of lung tissue.

This paper deals with a unifying hypothesis addressed at lung tissue resistance and its responses to neurohumoral and biophysical stimuli. The hypothesis holds that dissipative and elastic processes within lung tissue are coupled at the level of the stress-bearing element. Such a description leads naturally to consideration of a readily measured attribute of organ-level dissipative behavior called lung tissue hysteresivity, eta. On preliminary analysis this attribute is found to be nearly frequency independent and numerically conserved across species. To the degree that the numerical value of eta might be conserved during an intervention in which tissue dynamic elastance changes, such behavior would be consistent with the notion that elastic energy storage and dissipative energy loss reside within the very same stress-bearing element and, moreover, that those processes within the stress-bearing element bear an approximately fixed relationship. Tissue hysteresivity is closely related to the parameter K used by Bachofen and Hildebrandt (J. Appl. Physiol. 30: 493-497, 1971) to describe energy dissipation per cycle, and both lend themselves directly to interpretation based on processes ongoing at the levels of microstructure and molecule. Intraparenchymal connective tissues, surface film, and contractile elements appear to submit individually to this description and, in doing so, yield respective hysteresivities that are relatively well matched; this suggests that such hysteretic matching may be a necessary condition for synchronous expansion of the alveolar duct. The overriding simplicity with which this description organizes diverse observations implies that it may capture some unifying attribute of underlying mechanism.

Airway Resistance↗

PubMed1999

Retaining the equilibrium point hypothesis as an abstract description of the neuromuscular system.

The lambda version of the equilibrium point (EP) hypothesis for motor control is examined in light of recent criticisms of its various instantiations. Four important assumptions that have formed the basis for recent criticism are analyzed: First, the assumption that intact muscles possess invariant force-length characteristics (ICs). Second, that these ICs are of the same form in agonist-antagonist pairs. Third, that muscle control is monoparametric and that the control parameter, lambda, can be given a neurophysiological interpretation. Fourth, that reflex loop time delays and the known, asymmetric, nonlinear mechanical properties of muscles can be ignored. Mechanical and neurophysiological investigations of the neuromuscular system suggests that none of these assumptions is likely to be correct. This has been taken to mean that the EP hypothesis is oversimplified and a new approach is needed. It is argued that such an approach can be provided without rejecting the EP hypothesis, rather to regard it as an input-output description of muscle and associated segmental circuits. The operation of the segmental circuitry can be interpreted as having the function, at least in part, of compensating for a variety of nonlinearities and asymmetries such that the overall system implements the lambda-EP model equations.

Eye Movements↗