Metrical Venn diagrams.
A type of Venn diagram is described which enables the observed frequencies in a 2x2x2 contingency table to be compared with their expectations on the hypothesis of no associations.
Gene Frequency↗
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The proportional Venn diagram of obstructive lung disease in the Italian general population.
STUDY OBJECTIVES: The Venn diagram of obstructive lung disease (OLD) has been recently quantified. We aimed to quantify the proportion of the general population with OLD, and the intersections of physician-diagnosed asthma, chronic bronchitis (CB), and emphysema in two Italian general population samples, in relationship to airflow obstruction (AO) determined through spirometry. DESIGN AND PARTICIPANTS: We analyzed data from two prospective studies (4,353 patients) carried out in the rural area of Po River delta from 1988 to 1991 and in the urban area of Pisa from 1991 to 1993. RESULTS: Prevalence rates of asthma, CB, and emphysema were 5.3%, 1.5%, and 1.2% in the Po delta, and 6.5%, 2.5%, and 3.6% in Pisa. A double Venn diagram, which was used to quantify the distribution of CB, emphysema, and asthma in relation to the presence/absence of AO, identified 15 categories. Isolated AO was the most frequent category (Po delta, 11.0%; Pisa, 6.7%), followed by asthma only without AO (Po delta, 3.3%; Pisa, 4.3%). The combination of the three OLD conditions was the only category that always showed higher prevalence rates for those with AO (Po delta, 0.20%; Pisa, 0.16%) than for those without AO (Po delta, 0.04%; Pisa, 0.05%). Of those with either OLD or AO, there were 61.4% in Po delta and 38.2% in Pisa with isolated AO, 24.8% and 41.9%, respectively, with an OLD without AO, and 13.8% and 19.9%, respectively, with simultaneous OLD and AO. For both genders, the frequency of isolated asthma decreased with age, while that of isolated AO, CB-emphysema, and the combination of asthma and CB-emphysema increased. CONCLUSION: About 18% of the Italian general population samples either reported the presence of OLD or showed spirometric signs of AO. We confirmed that the Venn diagram of OLD can be quantified in the general population by extending the mutually exclusive disease categories (including a concomitant diagnosis of asthma, CB, or emphysema) to 15.
Adolescent↗
Generalized Venn diagrams: a new method of visualizing complex genetic set relations.
MOTIVATION: Microarray experiments generate vast amounts of data. The unknown or only partially known functional context of differentially expressed genes may be assessed by querying the Gene Ontology database via GOMiner. Resulting tree representations are difficult to interpret and are not suited for visualization of this type of data. Methods are needed to effectively visualize these complex set relationships. RESULTS: We present a visualization approach for set relationships based on Venn diagrams. The proposed extension enhances the usual notion of Venn diagrams by incorporating set size information. The cardinality of the sets and intersection sets is represented by their corresponding circle (polygon) sizes. To avoid local minima, solutions to this problem are sought by evolutionary optimization. This generalized Venn diagram approach has been implemented as an interactive Java application (VennMaster) specifically designed for use with GOMiner in the context of the Gene Ontology database. AVAILABILITY: VennMaster is platform-independent (Java 1.4.2) and has been tested on Windows (XP, 2000), Mac OS X, and Linux. Supplementary information and the software (free for non-commercial use) are available at http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/vennm together with a user documentation. CONTACT: hans.kestler@medizin.uni-ulm.de.
Algorithms↗
The proportional Venn diagram of Behçet's disease-related manifestations among young adult men in Turkey.
OBJECTIVES: To determine the frequency of the features associated with Behçet's disease (BD) in a young men population and generate a proportional Venn diagram of those features. METHODS: Data was collected from 3714 otherwise healthy men recruited for military service at the entrance. Study was conducted in a two-step procedure. Firstly, all participants were questioned by a general practitioner via using visual Behçet's questionnaire. Those participants, in whom at least one BD-related manifestation of the disease (oral ulcer, genital ulcer, folliculitis, erythema nodosum, uveitis, venous involvement of the lower extremities) have been demonstrated, were further examined by a rheumatologist at the second-stage of the study. RESULTS: The areas of intersection among the 6 individual BD-related manifestations produced 63 mutually exclusive symptom groups. Sixteen out 63 of these groups were functionally operative in our study population. Forty-seven (1.2%) of the all participants were considered to have at least 1 of the BD-related manifestation after examined by rheumatologist. The prevalence rates of the individual manifestations among the study population were as follows; oral ulcer 29 (0.78%), folliculitis 31 (0.83%), genital ulcer 9 (0.24%), venous involvement 13 (0.35%), erythema nodosum 4 (0.10%) and uveitis 3 (0.08%). The group consisting of oral ulcer with folliculitis was the largest proportion of participants followed by the group having oral ulcer only, accounting for 0.29% and 0.18%, respectively. Four (0.1%) of the participants were fulfilled the International Study Group for BD criteria following rheumatologic and ophthalmologic examinations. After excluding the group having oral ulcer with folliculitis, additional 12 cases had features suggesting BD though they didn't fulfill the International Study Group for BD criteria. CONCLUSION: The Venn diagram of this study demonstrates that International Study Group for BD criteria can detect almost the quarter of 16 cases suspected as having BD. We suggest that the application of information regarding the frequencies of individual BD-related manifestations and their association with each other in a general population might serve as a helpful tool for physicians while making diagnosis.
Adult↗
A Venn diagram model that allows triple-label immunophenotypic analysis of cells based upon double-label measurements.
Using Venn diagrams derived from set theory, a mathematic model is presented that allows triple-label immunophenotypic analysis of cells based upon double-label measurements. Practical applications of this method are illustrated and discussed. Using this model, triple-label data concerning Leu-8 and Leu-9 (CD7) antigen co-expression by Leu-4+ (CD3+) leukocytes were derived from double-label measurements obtained with a single laser flow cytometer. Mean values were as follows: Leu-4+8+9+ (62%), Leu-4+8-9+ (36%), Leu-4+8+9- (0%), and Leu-4+8-9- (0%). Examples are given of additional models based upon similar principles.
Adult↗
The proportional Venn diagram of obstructive lung disease: two approximations from the United States and the United Kingdom.
STUDY OBJECTIVES: The nonproportional Venn diagram of obstructive lung disease (OLD) produced for the 1995 American Thoracic Society guidelines has not been quantified. We aim to quantify the proportion of the general population with OLD and the intersections of physician-diagnosed asthma, chronic bronchitis, and emphysema in the United States and the United Kingdom, and to examine the relationship to obstructive spirometry. DESIGN AND PARTICIPANTS: We analyzed data from the US National Health and Nutrition Examination (NHANES) III survey (1988 to 1994) and the UK General Practice Research Database for the year 1998. RESULTS: The areas of intersection among the three OLD conditions produced seven mutually exclusive disease groups. The asthma-only group was the largest proportion of OLD patients, accounting for 50.3% and 79.4% of all OLD patients in the United States and the United Kingdom, respectively, and decreased with increasing age. Overall, 17% and 19% of OLD patients in the United States and in the United Kingdom, respectively, reported more than one OLD condition, and this percentage increased with age. According to the spirometry data from NHANES III, only 37.4% of emphysema-only patients had objective airflow obstruction. The prevalence of airflow obstruction was significantly higher among participants with combinations of emphysema and chronic bronchitis (57.7%), with emphysema and asthma (51.9%), and with all three OLD diseases concomitantly (52.0%). CONCLUSION: Concomitant diagnosis of asthma, chronic bronchitis, or emphysema is common among OLD patients from the general population, particularly in adults aged > or = 50 years.
Adult↗
Venn diagrams and neuronal vulnerability.
Greenamyre and Young note that there is poor correlation between which hippocampal regions are damaged in Alzheimer's disease and which have the highest concentrations of NMDA receptors. They conclude that EAAs can thus only be necessary, but not sufficient to explain Alzheimer's damage. We note that this is in fact probably the rule rather than the exception: some of the most credible agents which damage neurons are merely necessary, but not sufficient to explain selective neuronal vulnerability.
Alzheimer Disease↗
The Venn diagram: a metaphor for life.
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Chronic Disease↗
Venn diagrams in drug abuse education.
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Antisocial Personality Disorder↗
Knee arthroplasty rating.
A number of rating systems used to evaluate the results of total knee arthroplasty exist. Many of these systems are based on different concepts, and might be expected to give divergent results. To see if this was so, the authors examined a consecutive series of 235 posterior stabilized knee arthroplasties recording the results according to five rating systems: HSS (The Hospital for Special Surgery), Brigham, Freeman, BOA (British Orthopaedic Association), and the VENN diagram. In spite of their apparent differences, all point systems and the BOA gave almost identical results, while the VENN diagram proved to be the most stringent. The authors suggest that any of the current point systems may be used to "score" arthroplasties, but the results should also be rated with the VENN diagram in order to see the quality of the arthroplasty and a comparison between the different series.
Aged↗
How does an enzyme evolved in vitro compare to naturally occurring homologs possessing the targeted function? Tyrosine aminotransferase from aspartate aminotransferase.
Aspartate aminotransferase (AATase) and tyrosine aminotransferase (TATase) are Escherichia coli paralogs that share 43% sequence identity. A plausible model posits that TATase arose from a duplication of an ancestral AATase-like enzyme. Directed evolution of AATase to an enzyme having TATase activity was undertaken in order to compare the evolved AATase variants with homologous TATases. Eight rounds of DNA shuffling and in vivo selection followed by a backcross with WT AATase produced enzymes that exhibited 100-270-fold increases in k(cat)/K(m)(Phe) and had as much as 11% of the tyrosine aminotransferase activity of WT E.coli TATase. Amino acid substitutions in 11 clones from rounds 7 and 8 were compared with conserved residues in AATases and TATases. The findings are conveniently and compactly illustrated by the use of Venn diagrams and set theory notation. A statistically significant (0.001 or=75% identical) in AATases and variable (<75% identical) in TATases. Very few mutations occur in the intersection (set AAT intersection TAT) of amino acid residues that are conserved in both enzyme types. Seven mutations from set AAT-TAT were combined by site-directed mutagenesis to give a construct that is 60% as active as the best round 8 enzyme, which has 13 amino acid replacements. The Venn diagrams may provide a generally useful tool to highlight the most important specificity determinants for rational redesign. Amino acid replacements were mapped onto the crystal structure of a hydrocinnamate complex of a designed TATase. Five of the seven positions most frequently substituted in the evolved clones are within 15 A of the phenyl side-chain, but only six of the 48 positions that were mutated once or twice are within that radius. Context dependence, neutral mutations, different selective pressures, and stochastic components provide explanations for the observation that many of the substitutions found in the directly evolved enzymes differ from the corresponding amino acids found in the modern natural TATases.
Amino Acid Sequence↗
Nosography of X-ray negative dyspepsia.
The clinical pictures of 109 patients with X-ray negative dyspepsia (XND) are described, and a comparison is made with the clinical pictures of 39 gastric ulcer patients and 61 duodenal ulcer patients. In addition it has been attempted to subdivide XND into clinically relevant subgroups by means of a Venn diagram. The XND patients were characterized by an equal sex distribution and, in comparison with the ulcer patients, a shorter length of history. The upper abdominal pain was less frequently relieved by eating and more frequently provoked by eating in XND than in ulcer disease. The XND patients also suffered more frequently from irritable colon symptoms. Endoscopy only revealed an ulcer in 11 patients with XND, and the clinical pictures of these patients differed from those of patients with radiologically demonstrated ulcers. The clinical pictures of XND are further analysed in the context of current hypotheses, and it is concluded that Venn diagrams are useful for the analysis of heterogeneous clinical syndromes.
Abdomen↗
Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds.
BACKGROUND: Gene expression studies increasingly compare expression responses between different experimental backgrounds (genetic, physiological, or phylogenetic). By focusing on dynamic responses rather than a direct comparison of static expression levels, this type of study allows a finer dissection of primary and secondary regulatory effects in the various backgrounds. Usually, results of such experiments are presented in the form of Venn diagrams, which are intuitive and visually appealing, but lack a statistical foundation. RESULTS: Here we introduce Vector Analysis (VA) as a simple, yet principled, approach to comparing expression responses in different experimental backgrounds. VA enables the automatic assignment of genes to response prototypes and provides statistical significance estimates to eliminate spurious response patterns. The application of VA to a real dataset, comparing nutrient starvation responses in wild type and mutant Arabidopsis plants, reveals that consistent patterns of expression behavior are present in the data and are reliably detected by the algorithm. CONCLUSION: Vector analysis is a flexible, easy-to-use technique to compare gene expression patterns in different experimental backgrounds. It compares favorably with the classical Venn diagram approach and can be implemented manually using spreadsheets, such as Excel, or automatically by using the supplied software.
Algorithms↗
Topology and graph theory applied to cortical anatomy may help explain working memory capacity for three or four simultaneous items.
Cognitive experimentation suggests that at any single instant only three or four items ("chunks") are simultaneously prominent as a working memory (WM) trace, if we disregard the rehearsal component of WM. The reason for small WM capacity may concern combinatorial manageability. How might the neural representations of these few coactive chunks occupy a spatially distributed set of areas of the sheet-like cortex, while providing both order and flexibility to associate items in WM? Each attribute of each simultaneously active WM item must have broad access to the representational facilities of the cortical sheet, comprising tens of thousands of modular "cortical columns." The two hypothesized neural levels of WM during any moment of cognition comprise (a) "binding" together of many distributed attribute representations within each respective WM chunk, and (b) combinatorial play among three or four WM chunk-representations. Anatomical and functional evidence of cortical unity through its depth suggests that cortex may be viewed as essentially planar in its distribution of activations. Thus, a moment's WM is hypothesized here to reside in myriad activated cortical planar "patches," each subdivided into up to four amoeboid "subpatches." Two different lines of topological reasoning suggest orderly associations of such representations. (1) The four-color principle of map topology, and the related K(4) is planar theorem of graph theory, imply that if a small cortical area is dynamically subdivided into no more than four, discretely bounded planar subareas, then each such segment has ample free access to each of the others. (2) A hypothetical alternative to such associative adjacency of simultaneously active cortical representations of chunk-attributes is associative overlap, whereby, in dense cortical neuropil, activated subpatches behave like Venn diagrams of intersecting sets. As the number of Venn-like coactive subpatches within a patch increases, maintaining ad hoc associativity among all combinations requires exponentially proliferating intersections. Beyond four, serpentine subpatch shapes are required, which could easily lead to pathologies of omission or commission. As hypothesized by many researchers, the binding of the widely distributed cortical modules that represent a given chunk may involve synchrony or coherence of a single EEG frequency. Elsewhere, I have conjectured that such a binding frequency for a single chunk may bear a harmonic relationship with the additional EEG frequencies that are simultaneously binding the other WM chunks. Other possible mechanisms of binding have also been hypothesized. Whatever the mechanism, the many attributes of a moment's complement of three or four WM chunks must generally have an accidental relationship with the spatial distribution of the cortical feature analyzers that must be activated to represent those attributes. Therefore, the cortex may need, and have, comprehensive anatomical connections of each of its modules for representing an attribute (or of small redundant module groupings) with every other. If such whole-part cortico-cortical connections are somehow exploited not only to fully represent each cognitive chunk in its bound-together attributes, but also to bring the major business of intensive WM information processing down to the level of local circuits, in the sorts of topological patterning hypothesized here, there may be two adaptive results: (1) Time and other economies would be achieved in the reduction of activity in distant cortico-cortical connections to lower-energy global orchestration, or binding processes. (2) The piecemeal local topological limit to four subpatches would be writ large, across the entire cortex, preventing an unconstrained combinatorial explosion of associations among all attributes of all three or four simultaneously active chunks. Such hypothetical convergence to foci in local subpatch interactions might take place primarily in association cortex, and/or it might involve temporary shifts in response properties in some cortical subpat might involve temporary shifts in response properties in some cortical subpatches. Quantitative studies of the densely packed cortical fine structure, by Braitenberg and Schüz, and others, seem potentially consistent with this vision of cortical function in cognition.
Animals↗
Displaying clinical data relationships using scaled rectangle diagrams.
A method is presented to draw rectangles to represent categorical data relationships. The idea is an adaptation of a scaled Venn diagram. Rectangles are drawn with area proportional to the frequency of categories and the rectangles are positioned to overlap each other so that the areas of overlap are in proportion to the joint frequencies of the characteristics. The diagrams are especially useful to illustrate symptom co-occurrence.
Arthritis, Rheumatoid↗
Scaled rectangle diagrams can be used to visualize clinical and epidemiological data.
OBJECTIVE: To illustrate scaled rectangle diagrams as a method for displaying clinical and epidemiological attributes (such as symptoms, signs, results of marker tests, disease, or risk factors). These are quantitative Venn diagrams, but using rectangles instead of circles. STUDY DESIGN AND SETTING: The method is illustrated through examples from various data sets with different types of clinical information. RESULTS: Examples drawing on studies of lung disease, rheumatic fever, blood pressure, lipid levels, sudden infant death syndrome, and low birth weight illustrate the different types of relationships between variables that the scaled rectangle approach can reveal (e.g., high- and low-risk groups; dependent, independent, or co-occurring attributes; effects from choice of cutoff; cumulative distributions; and case-control attributes). CONCLUSION: Scaled rectangle diagrams are a novel way to display clinical data. They show clearly the relative frequency of clinical attributes and the extent to which they are shared characteristics. Features are revealed that might otherwise not have been appreciated.
Case-Control Studies↗
A scaled sample space cube used to illustrate attributable fractions.
A three-dimensional graphic method is proposed for displaying the association structure between multiple explanatory variables and their relation to a categorical response. The method combines the techniques of mosaic displays and scaled Venn diagrams, and is especially useful for illustrating attributable fractions in epidemiology. The primary purpose is to show the reduction of disease risk in a population if the joint exposure distribution or the conditional risk function is modified, and the method can be extended to illustrate the potential effects of successive removal of exposures on the overall risk of disease. The scaled sample space cube may be used for communicating the difficult concept of attributable fraction to statisticians, the medical community and the general public in an easily understandable way. Demonstrations of the method use theoretical models as well as data from the Hordaland study on the effect of smoking and occupational exposure on obstructive lung disease. Also, the general principle of adding a third dimension to a mosaic display, instead of using shading or colouring, to show an attribute of a cell in a multiway contingency table, can be helpful for other purposes, as in residual analysis of a loglinear model fitting.
Algorithms↗
Familial endocrine myxolentiginosis.
We present an unusual case of a left atrial myxoma as a feature of a familial mesoectodermal disorder and review the literature. The new term "familial endocrine myxolentiginosis" is proposed, which is descriptive of the major clinical components of the syndrome. Myriad features of this disorder include (1) cardiac myxomas; (2) cutaneous myxomas; (3) multiple lentigines or blue nevi, particularly of the head and neck; (4) bilateral primary pigmented nodular adrenocortical hyperplasia; (5) unusual testicular tumors; (6) pituitary tumors; (7) myxoid fibroadenomas of the breast; (8) myxomatous disorder of the stroma of the breast; (9) ductal adenoma of the breast; and (10) psammomatous melanotic schwannoma. A tentative diagnosis is suggested by identifying two features and a definitive diagnosis is made by three or more features. The clinical and pathologic features of cardiac myxoma in familial endocrine myxolentiginosis are identical to those of familial cardiac myxoma: age < 40 years, atypical locations, multicentric origins, and recurrent presentations. A Venn diagram classification for cardiac myxomas is proposed. We include photographic, echocardiographic, biopsy, and adrenal computerized tomography documentation in our patient. Recognition of this disorder is important because of its clinical, surgical, and genetic implications. The availability of transesophageal echocardiographic technology should allow early diagnosis of this underdiagnosed entity. Clinicians should consider this entity in the differential diagnosis of their patients with any one of these manifestations.
Adult↗