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PubMed1979

A funny thing happened to us on the way to the latent entities.

Inferred latent entities, whether those of psychoanalysis, factor analysis, or cluster analysis, have declined in value for many clinical psychologists, both as tools of practice and as objects of theoretical interest. Behavior modification, rational-emotive therapy, crisis intervention, psycho-pharmacology, and actuarial prediction all tend to minimize reliance on latent entities in favor of purely dispositional concepts. Behavior genetics is, however, a powerful movement to the contrary. As regards categorical entities (types, taxa, syndromes, diseases), history reveals no impressive examples of their discovery by cluster algorithms; whereas organic medicine and psychopathology have both discovered many taxonic entities without reliance on formal (statistical) cluster methods. I offer eight reasons for this strange condition, with associated suggestions for ameliorating it. Adopting a realist instead of a fictionist approach to taxonomy, I give high priority to theory-based mathematical derivation of quantitative consistency tests for all taxometric results. I urge a large scale cooperative survey of taxometric methods based on Monte Carlo runs, biological pseudoproblems where the true axon is independently known, and live problem in genetics, organic medicine, and psychopathology. An empirical example of taxometric bootstrapping and consistency testing was presented from my own current research on schizotypy.

Humans↗

PubMedDate not supplied

Measuring stage of change for assessing readiness to increase fruit and vegetable intake among 18- to 24-year-olds.

PURPOSE: To examine the appropriateness of the five-stage schema developed for addictive behaviors when applied to nonaddictive behaviors such as fruit and vegetable consumption. DESIGN: A cross-sectional mail survey was conducted. SETTING: Self-administered questionnaires were mailed to the home addresses of respondents recruited in 10 states and returned upon completion. SUBJECTS: In all, 116 male and 185 female young adults (response rate = 70%) completed the questionnaires. Most respondents were Caucasian (74.4%) and college students (62.2%). MEASURES: Statistical analyses included analysis of variance with Scheffe's test, Pearson correlation and Cronbach's alpha coefficients, factor analysis, and cluster analysis. RESULTS: Staging algorithms for fruits and vegetables were developed according to the five-stage schema, and their construct validity was verified by the incremental trend of food intakes. The algorithms identified more than 80% of the subjects as precontemplators, preparers, or maintainers for both food groups. This distribution pattern agreed well with the three-factor solution generated from the stages of change questionnaire, for which internal reliability and validity were confirmed. Seven cluster profiles of the respondents were derived based on the three generated factors and appeared to represent stage subgroupings of those factors. The two food groups shared marked similarities regarding the profiling of the clusters, which was validated by comparing food intake. The results, however, cannot be generalized because of limitations involved in the current sample. CONCLUSIONS: The original five stages of change and traditional staging measures may need to be adapted and/or extended for dietary change.

Adolescent↗

PubMedDate not supplied

[Health status, use of health services and reported morbidity: application of correspondence analysis].

BACKGROUND: The study of the relationship between self-reported morbidity, health status and health care utilization presents methodological problems due to the variety of illnesses and medical conditions that one individual may report. In this article, correspondence analysis was use to analyse these relationships. METHODS: Data from the Spanish National Health Survey pertaining to the region of Catalonia was studied. Statistical analysis included multi-way correspondence analysis (MCA) followed by cluster analysis. RESULTS: The first factor extracted is defined by self-assessed health perception; the second, by limitation of activities, and the third is related to self-reported morbidity caused by chronic and acute health problems. Fourth and fifth factors, capture residual variability and missing values. Acute problems are more related to perception of poor health while chronic problems are related to perception of fair health. Also, it may be possible to distinguish self-reported morbidity due to relapses of chronic diseases from true acute health problems. Cluster analysis classified individuals into four groups: 1) healthy people; 2) people who assess their health as being poor and those with acute health problems; 3) people with chronic health problems, limited activity and a perception of fair health; and 4) missing values. CONCLUSIONS: Correspondence analysis is a useful tool when analyzing qualitative variables like those in a health survey.

Aged↗

PubMed1990

Effects of immunoneutralization of corticotropin-releasing hormone on ultradian rhythms of plasma adrenocorticotropin.

ACTH, like other anterior pituitary peptide hormones, is secreted episodically and demonstrates both circadian and ultradian rhythms. CRH is the major regulator of ACTH release from the pituitary corticotroph. To determine the dependence of ACTH ultradian rhythms on CRH, passive immunoneutralization was used to block the activity of endogenous CRH in rats with indwelling venous catheters. Blood was sampled at 2- and 15-min intervals while blood volume was replaced. Plasma ACTH was measured by RIA. Time-series analysis of plasma ACTH concentrations was performed with PULSAR and Cluster Analysis. The 2 min data demonstrated secretory bursts approximately every 20 min. CRH immunoneutralization had no effect on the frequency of these pulses, but significantly reduced their amplitude. This was the case for raw data as well as data in which lower frequency variation had been filtered out. The 15 min data demonstrated pulsatile secretion, with a secretory episode approximately every 100 min. This lower frequency rhythm was also observed when high frequency components were filtered out of the 2 min data series. Analysis of the 15 min and the filtered 2 min time series showed this rhythm to be almost totally ablated by CRH immunoneutralization. These results suggest that CRH is responsible for amplitude modulation of an underlying CRH-independent rhythm and that through intermittent amplitude modulation of this rhythm a lower frequency rhythm is generated. Comparison between treatment groups of pulses identified by PULSAR or Cluster Analysis yielded similar results, but the programs were discordant with each other. This is the first in vivo evidence of pulsatile ACTH secretion independent of CRH, the first report demonstrating that different ultradian rhythms of ACTH may be regulated by different mechanisms, and the first comparison of PULSAR and Cluster Analysis on plasma ACTH time series.

Activity Cycles↗

PubMed2004

Screening of urban aerosol particulate composites for selected metal distribution and their dependence on meteorological parameters.

Local atmospheric aerosol particulate samples, collected as composites on daily 6-12 hour basis, at Quaid-i-Azam University campus, Islamabad, Pakistan, using high volume sampling technique, were analysed for Pb, Na, K, Fe, Mn, Cd, Cr, Ni, Zn and Co by FAAS method. The monitoring period ran from October, 2001 through March, 2002, with a total of 105 samples collected on cellulose filters, treated in part with the HNO3-based wet digestion method for metal quantification, and for particle size distribution separately. The metal content of the aerosols was examined in relation to dependence on meteorological parameters, such as temperature, relative humidity, wind speed, sun shine and pan evaporation. Statistical correlation analysis was conducted for multiple metal pairs in aerosols, and the data were examined in relation to meteorological parameters and relevant aerosol particle size fractions. The study revealed no viable strong correlation between the meteorological parameters and metal levels; in general, however, a significant positive correlation was found for temperature. A strong positive correlation was observed for PM<25 and PM2.5-10. For coarse particles (PM10-100 and PM>100), however, a negative correlation was observed. The levels of Na, K, Fe and Zn were found in the range of 1-5 microg/m3 while those for the rest of the metals in the sub microg/m3 range. Principal component analysis and cluster analysis were performed on dataset for source identification and appointment. Largest contribution (33%) was shown by the industrial emissions followed by traffic/road dust (16.7%).

Aerosols↗

PubMedDate not supplied

Interaction of carboxymethyl-gamma-cyclodextrin with anticancer drugs studied by charge-transfer thin-layer chromatography.

The interaction between 22 anticancer drugs and carboxymethyl-gamma-cyclodextrin (CM-gamma-CD) was studied by reversed-phase charge-transfer thin-layer chromatography and the relative strength of interaction was calculated. CM-gamma-CD formed inclusion complexes with 11 compounds, the complex always being more hydrophilic than the uncomplexed drug. The inclusion forming capacity of drugs differed considerably according to their chemical structure. Both principal component analysis and cluster analysis found a relationship between the inclusion complex forming capacity and hydrophobicity parameters of anticancer drugs. This result suggests that the preponderant role of hydrophobic interactions is in inclusion complex formation.

Antineoplastic Agents↗

PubMed1985

Subclassification of neurons in the ventrobasal complex of the dog: quantitative Golgi study using principal components analysis.

The neuronal architecture of the ventrobasal complex (VB) in dog is examined in coronal and horizontal brain sections processed by Golgi- and Nissl-staining methods. Presumed projection and intrinsic neurons are identified by differences in soma size and shape, dendritic branch pattern, the morphology and distribution of appendages, and the appearance of axons. Forty-five projection neurons are examined by quantifying (1) soma cross-sectional area, (2) dendritic field extent and shape, (3) appendages on the soma, primary dendrites, and in a defined major dendritic branch zone, and (4) location in the VB. When considered independently, each variable offers little evidence for separation into morphological classes. However, several of the variables have wide ranges and show significant correlation with other parameters. Using the multivariate descriptive methods of principal components analysis and cluster analysis, a separation of the projection neurons into three morphological classes designated as large, medium, and small neurons is indicated. The features most critical in distinguishing between the groups are, in descending order of importance: (1) dendritic field extent; (2) number of primary dendrites; (3) soma cross-sectional area; (4) number of appendages per major branch point (MBP); (5) number of appendages on the soma; and, (6) number of appendages on the primary dendrites. Dendritic field shape and neuron location have little influence in determining classification.

Analysis of Variance↗

PubMed1989

Morphology of Golgi-impregnated neurons in hyperstriatum ventralis, pars caudalis in adult male and female canaries.

Golgi-impregnated neurons in the song control nucleus hyperstriatum ventralis, pars caudalis (HVc) in male and female canaries (Serinus canarius) have been divided into classes, primarily on the basis of interneuronal variability in spine density and dendritic branching pattern. At least four neuronal classes are found in HVc: aspinous neurons and three classes of spiny neurons. The "furry" dendrite (FD) cell class consists of neurons with long dendrites that are densely packed with spines. Their cell bodies are between 10 and 15 microns in diameter. Neurons of the thick dendrite (TD) cell class also have long dendrites but only about half as many spines along their dendritic branches. Their cell bodies are between 12 and 18 microns in diameter. Neurons of the short dendrite (SD) cell class are characterized by a low spin density, very thin dendrites, and a small dendritic field. Their cell bodies are between 9 and 13 microns in diameter. The TD class can be divided into two subclasses on the basis of the shape of the dendritic field. Principal component factor analysis and cluster analysis provide objective support for this classification scheme. Neurons of subclass TD2 are sexually dimorphic. Neurons from males have dendritic trees that are about 70% larger and have 40% more dendritic endings than do neurons from females. There may also be small sex differences in dendritic morphology in the SD class and in the remainder of the TD class. There are clearly no sex differences in the dendritic morphology of neurons from the FD class. The direct pathway which is believed responsible for dimorphic song production in canaries is from HVc to nucleus robustus archistriatalis (RA) and then to the motor neurons which control the avian vocal organ. It is surprising that the most striking dimorphism in the present data occurs in neurons which, on morphological grounds, are unlikely to project to RA.

Animals↗

PubMed1994

Structure and function of gustatory neurons in the nucleus of the solitary tract. I. A classification of neurons based on morphological features.

Prior investigations in other laboratories have provided convincing evidence that the neurons of the rostral nucleus of the solitary tract (rNST) can be grouped according to their physiological response properties or morphologic features. The present study is based on the premise that the response properties of gustatory neurons are related to, and perhaps governed by, their morphology and connectivity. In this first phase of our ongoing investigation of structure-function relationships in the rNST of the rat, we have used intracellular injection of neurobiotin to label individual physiologically characterized gustatory neurons. A total of 63 taste-sensitive neurons were successfully labeled and subjected to three-dimensional quantitative and qualitative analysis. A cluster analysis using six morphologic features (total cell volume, soma area, mean segment length, swelling density, spine density, and number of primary dendrites) was used to identify six cell groups. Subsequent analyses of variance and posthoc comparisons verified that each of these six groups differed from all others with respect to at least one variable, so each group was "typified" by at least one of the six morphologic features. Neurons in group A were found to be the smallest neurons in the sample. The cells in group B had small somata and exhibited the highest swelling density of any group. Group C neurons were distinguished by dendrites with long, spine-free branches. These dendrites were significantly longer than those of any other group except Group F. The neurons in group D had more primary dendrites than any other group. Group E neurons possessed dendrities with the lowest swelling density but the most spines of any group. The cells in group F were the largest neurons in our sample and possessed the largest somata of any group. Thus overall cell size and density of dendritic spines and swellings were found to be particularly important variables in this classification scheme. Our preliminary results suggest that the number and density of dendritic spines (as well as other morphologic features) may be related to a given neuron's most effective stimulus, indicating that it will indeed be possible to use the criteria established in the present investigation to derive structure-function relationships for gustatory neurons in the rNST.

Animals↗

PubMed2006

Classifications of ovarian cancer tissues by proteomic patterns.

Ovarian cancer is a morphologically and biologically heterogeneous disease. The identification of type-specific protein markers for ovarian cancer would provide the basis for more tailored treatments, as well as clues for understanding the molecular mechanisms governing cancer progression. In the present study, we used a novel approach to classify 24 ovarian cancer tissue samples based on the proteomic pattern of each sample. The method involved fractionation according to pI using chromatofocusing with analytical columns in the first dimension followed by separation of the proteins in each pI fraction using nonporous RP HPLC, which was coupled to an ESI-TOF mass analyzer for molecular weight (MW) analysis. A 2-D mass map of the protein content of each type of ovarian cancer tissue samples based upon pI versus intact protein MW was generated. Using this method, the clear cell and serous ovarian carcinoma samples were histologically distinguished by principal component analysis and clustering analysis based on their protein expression profiles and subtype-specific biomarker candidates of ovarian cancers were identified, which could be further investigated for future clinical study.

Adenocarcinoma, Clear Cell↗

PubMed1996

Evaluation of Osilinus attratus as a bioindicator organism to monitor oil pollution in the Canary Islands.

Concentrations of n-alkanes and PAHs in the visceral mass of the marine winkle Osilinus attratus taken from three locations on the southeast coast of Tenerife (Canary Islands, Spain) over a two-year period, were evaluated at monthly intervals in order to assess if this small marine winkle may be used as bioindicador organism. Factor analysis and cluster analysis were applied in order to determine if it was possible to relate sampling areas to potential sources of petroleum contamination.

Animals↗

PubMed1985

Prediction of long-term outcome of tibial osteotomy in medial gonarthrosis.

To predict the long-term outcome after tibial osteotomy for medial gonarthrosis, multivariate statistical techniques were used and prognostic equations were defined. A comparison between different evaluation systems was also performed. Clinical and radiographic data from 81 patients followed up for more than 7 years were used. Twenty-eight preoperative variables were analysed in relation to the outcome at 7 years with the multivariate procedures discriminant analysis and cluster analysis. Among the variables, knee flexion and walking capacity were found to be the most dominant factors. Excluding the undercorrected osteotomies, preoperative walking capacity was now the dominating variable for prediction. Seven years postoperatively only small differences were found between the evaluation criteria of pain relief, London Hospital score, and HSS score. The discriminant functions for the highest ranked evaluation criteria are given in the text, as are dendrograms showing the patterns of interdependence between the evaluation criteria. Thus it was possible to transform clinical entities into factors suitable for determination and calculation of postoperative evaluation. The most commonly used evaluation systems had very similar discriminant functions showing good agreement.

Female↗

PubMed2006

Introgression of genomic components from Chinese Brassica rapa contributes to widening the genetic diversity in rapeseed (B. napus L.), with emphasis on the evolution of Chinese rapeseed.

In spite of its short history of being an oil crop in China, the Chinese semi-winter rapeseed (Brassica napus L., 2n = 38, AACC) has been improved rapidly by intentional introgression of genomic components from Chinese B. rapa (2n = 20, AA). As a result, the Chinese semi-winter rapeseed has diversified genetically from the spring and winter rapeseed grown in the other regions such as Europe and North America. The objectives of this study were to investigate the roles of the introgression of the genomic components from the Chinese B. rapa in widening the genetic diversity of rapeseed and to verify the role of this introgression in the evolution of the Chinese rapeseed. Ten lines of the new type of rapeseed, which were produced by introgression of Chinese B. rapa to Chinese normal rapeseed, were compared for genetic diversity using amplified fragment length polymorphism (AFLP) with three groups of 35 lines of the normal rapeseed, including 9 semi-winter rapeseed lines from China, 9 winter rapeseed lines from Europe and 17 spring rapeseed lines from Northern Europe, Canada and Australia. Analysis of 799 polymorphic fragments revealed that within the groups, the new type rapeseed had the highest genetic diversity, followed by the semi-winter normal rapeseed from China. Spring and winter rapeseed had the lowest genetic diversity. Among the groups, the new type rapeseed group had the largest average genetic distance to the other three groups. Principal component analysis and cluster analysis, however, could not separate the new type rapeseed group from Chinese normal rapeseed group. Our data suggested that the introgression of Chinese B. rapa could significantly diversify the genetic basis of the rapeseed and play an important role in the evolution of Chinese rapeseed. The use of new genetic variation for the exploitation of heterosis in Brassica hybrid breeding is discussed.

Brassica napus↗

PubMed2007

CH-overtone regions as diagnostic markers for near-infrared spectroscopic diagnosis of primary cancers in human pancreas and colorectal tissue.

We have investigated the application of near-infrared spectroscopy for detection of human primary pancreatic and colorectal cancers. Spectra from cancerous and normal tissue were collected from a total of 37 surgically resected pancreatic and colorectal patient tissue specimens using a fibre-optic probe. Major spectral differences were observed in the CH-stretching first (6,000-5,400 cm(-1)) and second overtone (9,000-7,900 cm(-1)) regions. By use of artificial neural networks, linear discriminant analysis, and cluster analysis as pattern-recognition methods the spectra were classified into cancerous and normal tissue groups with accuracy up to 89%. We also explored differences between the spectra obtained from colorectal and pancreatic tissue. Spectral data from cancerous and normal tissue were classified organ-specifically into four groups with accuracy between 80 and 83%. Our results indicate that CH-overtone regions, besides serving as diagnostic markers for NIR spectroscopic diagnosis of primary human pancreas and colorectal cancers, are also useful for elucidating differences between the spectra obtained from colorectal and pancreatic cancerous tissue.

Adult↗

PubMed1996

Application of chemometric methods in Auger electron microanalysis of composites.

Principal component analysis and cluster analysis have been used in AES investigations of fibre-matrix interactions in alumina fibre reinforced MgLi-alloys prepared by high-pressure infiltration. The samples have been fractured in ultra high vacuum to expose surfaces and interfaces without contamination. All main components exhibit Auger valence band transitions which change their shape with the chemical state. Chemometric methods have been utilized to identify characteristic peak shapes and to classify the investigated areas by composition. Fibre fracture surfaces are characterized by Al, magnesia and Li oxide formed by a redox reaction of alumina with Mg and Li penetrating along grain boundaries. For samples with high silica content a thin interfacial oxide layer on matrix grain boundaries and matrix-fibre interfaces has been found.

Journal Article↗

PubMed2006

A synoptic climatology of pollen concentrations during the six warmest months in Sydney, Australia.

This paper takes an air mass approach to investigating the influence of weather on pollen concentrations in the atmosphere in Sydney, Australia, by producing a synoptic classification of pollen concentrations measured in the Sydney Basin. This synoptic classification has been produced using multivariate statistical techniques including principal component analysis and cluster analysis, to assign days into meteorologically homogenous categories. Surface and upper air meteorological data for warm months (October-March) over a 10-year period were used as input into the statistical analyses. Eleven synoptic categories were found in Sydney during the warm months. Pollen concentrations for the total pollen load and five individual families measured over a 3.5-year period have been investigated for each of the synoptic categories. High pollen concentrations during the warm months in Sydney are found to be influenced by the presence of a region of low surface pressure located to the south of the continent, bringing fast dry westerly gradient winds to Sydney. It is envisaged that these results will be important from a pollen forecast and associated public health perspective.

Air Pollutants↗

PubMed2002

Two-year population-based molecular epidemiological study of tuberculosis transmission in the metropolitan area of Milan, Italy.

A 2-year, population-based, molecular epidemiological study was conducted in Milan, Italy, to determine the proportion of tuberculosis (TB) cases attributable to recent transmission. All strains were typed by restriction fragment length polymorphism (RFLP) analysis; clustering was considered indicative of recent transmission. Of the 581 cases, 239 (41.1%) belonged to clusters that consisted of 2 to 11 patients; 28.1% were attributable to recent transmission (number of clustered patients minus 1). Clustering was associated with multidrug-resistant Mycobacterium tuberculosis strains (74.2% of cases), AIDS (60.2%), and a history of incarceration (67.4%). The frequency of multidrug-resistant Mycobacterium tuberculosis was 5.3% overall (15.4% among AIDS patients). Among AIDS patients, infection with a resistant strain was independently associated with clustering (odds ratio, 1.32; 95% confidence interval, 1.07-1.163), while among non-AIDS patients, three factors were associated with clustering: history of incarceration (odds ratio, 2.03; 95% confidence interval, 1.41-2.92), age <30 years (odds ratio, 1.43; 95% confidence interval, 1.05-1.94), and native-born Italian nationality (odds ratio, 1.44; 95% confidence interval, 1.08-1.92). Of the 118 patients who belonged to either the smallest or the largest cluster, 19 (16.1%) reported an epidemiological link with another study patient. The results of this study highlight the need for control programs that focus on selected high-risk groups consisting primarily of HIV-infected individuals and persons with social and lifestyle risks for TB. These programs should be aimed at reducing the probability of transmission of drug-resistant TB through early identification of cases and provision of effective treatment until the individual is cured.

Adult↗

PubMed2006

Characterization of Escherichia coli isolates from different fecal sources by means of classification tree analysis of fatty acid methyl ester (FAME) profiles.

Microbial source tracking (MST) methods need to be rapid, inexpensive and accurate. Unfortunately, many MST methods provide a wealth of information that is difficult to interpret by the regulators who use this information to make decisions. This paper describes the use of classification tree analysis to interpret the results of a MST method based on fatty acid methyl ester (FAME) profiles of Escherichia coli isolates, and to present results in a format readily interpretable by water quality managers. Raw sewage E. coli isolates and animal E. coli isolates from cow, dog, gull, and horse were isolated and their FAME profiles collected. Correct classification rates determined with leaveone-out cross-validation resulted in an overall low correct classification rate of 61%. A higher overall correct classification rate of 85% was obtained when the animal isolates were pooled together and compared to the raw sewage isolates. Bootstrap aggregation or adaptive resampling and combining of the FAME profile data increased correct classification rates substantially. Other MST methods may be better suited to differentiate between different fecal sources but classification tree analysis has enabled us to distinguish raw sewage from animal E. coli isolates, which previously had not been possible with other multivariate methods such as principal component analysis and cluster analysis.

Animals↗