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Hierarchical Cluster Analysis (hierarchical + cluster_analysis)
Selected AbstractsThe past, present, and future of chemometrics worldwide: some etymological, linguistic, and bibliometric investigations,JOURNAL OF CHEMOMETRICS, Issue 6-7 2006R. Kiralj Abstract Internet surfing for the word chemometrics in national languages and, in the Science Citation Index (SCI), searching for articles containing chemometr * were performed. The bibliometric, webometric, and country development descriptors from literature were then treated by Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA). In total, 82 written and 127 pronunciation forms of chemometrics were found in 48 languages worldwide. The forms ending in ,- y' (chemometry) and ,- ics' (chemometrics) can be grouped into at least three groups (I, J, K). Scientific collaboration, country development, geography, history, and language were shown to be important determinants in creation of form(s) of chemometrics in a particular country or language. PCA and HCA show that tradition in chemometrics, level of country development, and its scientific production are important for the existence of chemometric societies and laboratories worldwide. Today, the world tends toward becoming more homogeneous with respect to chemometric activity, and will reach a corresponding normal distribution in about 70 years from now. Copyright © 2007 John Wiley & Sons, Ltd. [source] QSAR of Progestogens: Use of a Priori and Computed Molecular Descriptors and Molecular GraphicsMOLECULAR INFORMATICS, Issue 4 2003Rudolf Kiralj Abstract Quantitative Structure-Activity Relationship (QSAR) study of two sets of oral progestogens was carried out by using Principal Component Analysis (PCA), Hierarchical Cluster Analysis (HCA) and Partial Least Squares (PLS). A priori, computed (at DFT 6-31G** level) and molecular graphics and modeling descriptors were employed. Molecular graphics and modeling studies of crystal structures of complexes progesterone receptor (PR)-progesterone, Fab,-progesterone and PR-metribolone have been performed. QSAR of progestogens is a three-dimensional phenomenon (over 96% of information is explained by the first three Principal Components), which can be, although it exhibits significant non-linearity, treated well with linear methods such as PLS. Progestogen activity depends primarily on double bond contents and resonance effects which define the skeletal conformation, and also on substituent characteristics (size, conformational and electronic properties). Sterical relationships between a substituent at C6(sp2) or C6(sp3)-, and sulfur atom from Met 801 residue of PR are important for progesterone binding to the protein and can be quantified. Basically the same was observed for substituents at ,-C10 with respect to residue Met759. [source] Personality variable differences between disease clustersEUROPEAN JOURNAL OF PERSONALITY, Issue 2 2003G. Matthews Previous studies of personality and health have focused mainly on the influence of psychological factors on single diseases such as cancer and coronary heart disease (CHD), thereby neglecting the problem of comorbidity (i.e. the combination of different diseases). The main focus of the present study was the discrimination between single- and multiple-disease conditions on the basis of personality traits. An extensive battery of personality scales implicated in health was administered to a sample of n=5133 individuals of both genders between the ages of 40 and 65. Subjects also reported their health or illness status. A factor analysis of the personality scales yielded five dimensions clearly interpretable as "Emotional Lability", "Type A Behaviour", "Behavioural Control", "Locus of Control over Diseases", and "Psychoticism". Hierarchical cluster analyses of the subsample of participants who reported suffering from more than one disease led to eight clusters representing individuals with different combinations of diseases. Generally, there were very few significant differences between healthy and single-disease participants with regard to personality. However, mean factor scores calculated for "Emotional Lability" were higher across the multiple-disease groups than in the healthy and single-disease groups. No other personality factor showed this trend. In general the results reported here show the important role negative affectivity (e.g. Emotional Lability, Neuroticism, Depression) plays in differentiating between single and multiple diseases. Copyright © 2003 John Wiley & Sons, Ltd. [source] Identification of differentially expressed genes in psoriasis using expression profiling approachesEXPERIMENTAL DERMATOLOGY, Issue 9 2005K. Itoh Abstract:, To identify differentially expressed genes which play causal roles in pathogenesis and maintenance for psoriasis, we used BodyMapping and introduced amplified fragment length polymorphism approaches. From the BodyMap database, we selected 2007 genes which specifically expressed in epithelial tissues. Among 2007 genes, we surveyed genes which differentially expressed in involved or uninvolved psoriatic lesional skin samples compared with atopic dermatitis, mycosis fungoides, and normal skin samples. As a result of surveying 2007 genes, 241 genes were differentially expressed only in involved psoriatic skin but not in the other samples. Hierarchical cluster analysis of gene expression profiles showed that 13 independent psoriatic-involved skin samples clustered tightly together, reflecting highly similar expression profiles. Using the same 2007 gene set, we examined gene expression levels in five serial lesions from distal uninvolved psoriatic skin to involved psoriatic plaque. We identified seven genes such as alpha-1-microglobulin/bikunin precursor, calnexin, claudin 1, leucine zipper down-regulated in cancer 1, tyrosinase-related protein 1, Yes-associated protein 1, and unc-13-like protein (Coleonyx elegans) which show high-expression levels only in uninvolved psoriatic lesions. These seven genes, which were reported to be related to apoptosis or antiproliferation, might have causal roles in pathophysiology in psoriasis. [source] Chemical Differences Are Observed in Children's Versus Adults' Latent Fingerprints as a Function of Time,JOURNAL OF FORENSIC SCIENCES, Issue 2 2010Kimone M. Antoine B.S. Abstract:, The identification of aged latent fingerprints is often difficult, especially for those of children. To understand this phenomenon, the chemical composition of children's versus adults' latent fingerprints was examined over time using Fourier transform infrared microscopy. Hierarchical cluster analysis revealed that children's and adults' prints were distinguishable for up to 4 weeks after deposition, based on differences in sebum composition. Specifically, adults had a higher lipid content than children, but both decreased over time, attributable to the volatility of free fatty acids. The aliphatic CH3, aliphatic CH2, and carbonyl ester compositions changed differently in adults versus children over time, consistent with higher cholesterol and cholesteryl esters in children's prints and wax esters and glycerides in adults' prints. Thus, fingerprint composition changes with time differently in children versus adults, making it a sensitive metric to estimate the age of an individual, especially when the age of the print is known. [source] Level of trace elements in Pteridophytes growing on serpentine and metalliferous soilsJOURNAL OF PLANT NUTRITION AND SOIL SCIENCE, Issue 6 2007Laura Cornara Abstract A screening of Pteridophytes growing on serpentine and metalliferous soils in Northern Italy was carried out to assess the ability of these plants to tolerate or accumulate trace elements of toxicological interest. Few data are available on metal tolerance/accumulation of terrestrial ferns growing in the Mediterranean region, and several species presented here have never been investigated for this purpose. The trace-element composition (As, Cd, Cr, Cu, Fe, Ni, Pb, Zn) and P content of aerial parts of plants (12 fern and 2 horsetail species) and of their associated soils were measured. An analysis of the relationship between element concentrations in soil and in shoot revealed a significant correlation only for Zn (p < 0.05). Hierarchical cluster analysis based on element concentrations in plant aerial parts showed two outliers, viz. Equisetum ramosissimum Desf., showing the highest levels of Cr, Fe, Cu, Ni, and As, and Nephrolepis cordifolia C. Presl., showing the highest Pb value. The bioaccumulation factor exceeded 1 only for Cd in two species, Athyrium filix-femina and Dryopteris filix-mas. However, also in these cases the corresponding values of the metal in the shoots were below the thresholds for hyperaccumulators. The examined Pteridophytes seem to have developed their adaptation prevalently through mechanisms of tolerance based on metal exclusion. None of these plant species seem suitable for phytoextraction, but N. cordifolia, Pteridium aquilinum ssp. aquilinum, and E. ramosissimum have potential to be used for stabilization and restoration of soils rich in heavy metals. [source] Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cinctaMOLECULAR ECOLOGY, Issue 15 2009DICK ROELOFS Abstract Field-selected tolerance to heavy metals has been reported for Orchesella cincta (Arthropoda: Collembola) populations occurring at metal-contaminated mining sites. This tolerance correlated with heritable increase in metal excretion efficiency, less pronounced cadmium (Cd)-induced growth reduction and overexpression of the metallothionein gene. We applied transcriptomics to determine differential gene expression caused by this abiotic stress in reference and Cd-tolerant populations. Many cDNAs responded to Cd exposure in the reference population. Significantly fewer clones were Cd responsive in tolerant animals. Analysis of variance revealed transcripts that interact between Cd exposure and population. Hierarchical cluster analysis of these clones identified two major groups. The first one contained cDNAs that were up-regulated by Cd in the reference culture but non-responsive or down-regulated in tolerant animals. This cluster was also characterized by elevated constitutive expression in the tolerant population. Gene ontology analysis revealed that these cDNAs were involved in structural integrity of the cuticle, anti-microbial defence, calcium channel-blocking, sulphur assimilation and chromatin remodelling. The second group consisted of cDNAs down-regulated in reference animals but not responding or slightly up-regulated in tolerant animals. Their functions involved carbohydrate metabolic processes, Ca2+ -dependent stress signalling, redox state, proteolysis and digestion. The reference population showed a strong signature of stress-induced genome-wide perturbation of gene expression, whereas the tolerant animals maintained normal gene expression upon Cd exposure. We confirmed the micro-evolutionary processes occurring in soil arthropod populations and suggest a major contribution of gene regulation to the evolution of a stress-adapted phenotype. [source] The meaning of clinical remission in polyarticular juvenile idiopathic arthritis: Gene expression profiling in peripheral blood mononuclear cells identifies distinct disease statesARTHRITIS & RHEUMATISM, Issue 3 2009Nicholas Knowlton Objective The development of biomarkers to predict response to therapy in polyarticular juvenile idiopathic arthritis (JIA) is an important issue in pediatric rheumatology. A critical step in this process is determining whether there is biologic meaning to clinically derived terms such as "active disease" and "remission." The aim of this study was to use a systems biology approach to address this question. Methods We performed gene transcriptional profiling on children who fulfilled the criteria for specific disease states as defined by the consensus criteria developed by Wallace and colleagues. The study group comprised children with active disease (n = 14), children with clinical remission on medication (CRM; n = 9), children with clinical remission off medication (CR; n = 6), and healthy control children (n = 13). Transcriptional profiles in peripheral blood mononuclear cells (PBMCs) were obtained using Affymetrix U133 Plus 2.0 arrays. Results Hierarchical cluster analysis and predictive modeling demonstrated that the clinically derived criteria represent biologically distinct states. Minimal differences were seen between children with active disease and those with disease in CRM. Thus, underlying immune/inflammatory abnormalities persist despite a response to therapy. The PBMC transcriptional profiles of children whose disease was in remission did not return to normal but revealed networks of proinflammatory and antiinflammatory genes, suggesting that remission is a state of homeostasis, not a return to a normal state. Conclusion Gene transcriptional profiling of PBMCs revealed that clinically derived criteria for JIA disease states reflect underlying biology. We also demonstrated that neither CRM nor CR status results in resolution of the underlying inflammatory process, but that these conditions are more likely to be states of balanced homeostasis between proinflammatory and antiinflammatory mechanisms. [source] Unsupervised immunophenotypic profiling of chronic lymphocytic leukemiaCYTOMETRY, Issue 3 2006Luzette K. Habib Abstract Background Proteomics and functional genomics have revolutionized approaches to disease classification. Like proteomics, flow cytometry (FCM) assesses concurrent expression of many proteins, with the advantage of using intact cells that may be differentially selected during analysis. However, FCM has generally been used for incremental marker validation or construction of predictive models based on known patterns, rather than as a tool for unsupervised class discovery. We undertook a retrospective analysis of clinical FCM data to assess the feasibility of a cell-based proteomic approach to FCM by unsupervised cluster analysis. Methods Multicolor FCM data on peripheral blood (PB) and bone marrow (BM) lymphocytes from 140 consecutive patients with B-cell chronic lymphoproliferative disorders (LPDs), including 81 chronic lymphocytic leukemia (CLLs), were studied. Expression was normalized for CD19 totals, and recorded for 10 additional B-cell markers. Data were subjected to hierarchical cluster analysis using complete linkage by Pearson's correlation. Analysis of CLL in PB samples (n = 63) discovered three major clusters. One cluster (14 patients) was skewed toward "atypical" CLL and was characterized by high CD20, CD22, FMC7, and light chain, and low CD23. The remaining two clusters consisted almost entirely (48/49) of cases recorded as typical BCLL. The smaller "typical" BCLL cluster differed from the larger cluster by high CD38 (P = 0.001), low CD20 (P = 0.001), and low CD23 (P = 0.016). These two typical BCLL clusters showed a trend toward a difference in survival (P = 0.1090). Statistically significant cluster stability was demonstrated by expanding the dataset to include BM samples, and by using a method of random sampling with replacement. Conclusions This study supports the concept that unsupervised immunophenotypic profiling of FCM data can yield reproducible subtypes of lymphoma/chronic leukemia. Expanded studies are warranted in the use of FCM as an unsupervised class discovery tool, akin to other proteomic methods, rather than as a validation tool. © 2006 International Society for Analytical Cytology [source] Comparing agglomerative clustering and three weed classification frameworks to assess the invasiveness of alien species across spatial scalesDIVERSITY AND DISTRIBUTIONS, Issue 6 2006Roger A. Lawes ABSTRACT To prioritize weed management at the catchment scale, information is required on the species present, their relatively frequency, abundance, and likely spread and impact. The objective of this study was to classify the invasiveness of alien species that have invaded the Upper Burdekin Catchment in Queensland, Australia, at three spatial scales. A combination of three published weed classification frameworks and multivariate techniques were employed to classify species based on their frequency and cover at a range of spatial scales. We surveyed the Upper Burdekin Catchment for alien species, and for each species determined the following distribution indices , site frequency, total cover, transect frequency per site frequency and quadrat frequency per site frequency, cover per quadrat when present, cover per transect when present, and cover per site when present. These indices capture the effect of species abundance and frequency between sites (site frequency and total cover), within sites (transect frequency per site and cover per transect when present), and within transects (quadrat frequency per site frequency and cover per site). They were used to classify the species into seven groups using a hierarchical cluster analysis. The relationship between the indices was explored to determine how effective the small scale, site-specific indices were at predicting the broader, landscape-scale patterns. Strong correlations were observed between transect frequency per site and frequency (r2 = 0.89) and cover per transect when present and total cover (r2 = 0.62). This suggests that if a weed is abundant at the site level, it has the potential to occupy large areas of the catchment. The species groupings derived from the application of the three published weed classification frameworks were compared graphically to the groupings derived from the cluster analysis. One of the frameworks classified species into three groups. The other two frameworks classified species into four groups. There was a high degree of subjectivity in applying the frameworks to the survey data. Some of the data were of no relevance to the classification frameworks and were therefore ignored. We suggest that the weed classification frameworks should be used in conjunction with existing multivariate techniques to ensure that classifications capture important natural variations in observed data that may reflect invasion processes. The combined use of the frameworks and multivariate techniques enabled us to aggregate species into categories appropriate for management. [source] Phytogeographical evidence for post-glacial dispersal limitation of European beech forest speciesECOGRAPHY, Issue 6 2009Wolfgang Willner The post-glacial migration of European beech Fagus sylvatica has been addressed by many studies using either genetic or fossil data or a combination of both. In contrast to this, only little is known about the migration history of beech forest understorey species. In a review of phytosociological literature, we identified 110 plant species which are closely associated with beech forest. We divided the distribution range of European beech forests into 40 geographical regions, and the presence or absence of each species was recorded for each region. We compared overall species numbers per region and numbers of narrow-range species (species present in <10 regions). A multiple regression model was used to test for the explanatory value of three potential diversity controls: range in elevation, soil type diversity, and distance to the nearest potential refuge area. A hierarchical cluster analysis of the narrow-range species was performed. The frequency of range sizes shows a U-shaped distribution, with 42 species occurring in <10 regions. The highest number of beech forest species is found in the southern Alps and adjacent regions, and species numbers decrease with increasing distance from these regions. With only narrow-range species taken into consideration, secondary maxima are found in Spain, the southern Apennines, the Carpathians, and Greece. Distance to the nearest potential refuge area is the strongest predictor of beech forest species richness, while altitudinal range and soil type diversity had little or no predictive value. The clusters of narrow-range species are in good concordance with the glacial refuge areas of beech and other temperate tree species as estimated in recent studies. These findings support the hypothesis that the distribution of many beech forest species is limited by post-glacial dispersal rather than by their environmental requirements. [source] Children and adults with acute lymphoblastic leukaemia have similar gene expression profilesEUROPEAN JOURNAL OF HAEMATOLOGY, Issue 6 2005E. Kuchinskaya Abstract:,Objectives:,To compare the gene expression pattern in children and adults with acute lymphoblastic leukaemia (ALL) in order to improve our understanding of the difference in disease biology and prognosis. Methods:,The gene expression profiles in diagnostic samples from 29 children and 15 adults with ALL were analysed using the oligonucleotide chip Hu95ver2a, produced by Affymetrix. Results:,Unsupervised hierarchical cluster analysis revealed that, in spite of differences in outcome, patients clustered irrespective of age, first by T-cell or B-precursor immunophenotype, and second by cytogenetic changes within the B-precursor group. The expression pattern analysis allowed the reclassification of some samples into the proper cytogenetic group. We also showed that separate clustering of samples with the BCR/ABL translocation could be explained by different breakpoint regions in the BCR. No significant difference in gene expression was observed between samples with and without CDKN2A deletion within the B-precursor group. Analysis of different age groups revealed a similarity in expression profiles when infants with the MLL translocation and adults over 40 yr of age were compared irrespective of karyotype. Conclusions:,In spite of the difference in clinical outcome, the gene expression pattern in children and adults with ALL is very similar and is primarily dependent on immunophenotype and cytogenetic aberrations. However, when age groups are compared, the expression patterns of infants and adults over 40 show a remarkable similarity. [source] Groundfish species diversity and assemblage structure in Icelandic waters during recent years of warmingFISHERIES OCEANOGRAPHY, Issue 1 2010LILJA STEFANSDOTTIR Abstract Elevated ocean temperatures have been predicted to lead to a poleward shift in the latitudinal distribution ranges of fish species. Different responses of fish species to increased temperatures might lead to changes in assemblage structure and local species richness. In this study, the assemblage structure and diversity of groundfish in Icelandic waters were examined using data from a standardized groundfish survey conducted annually in 1996,2007. We used hierarchical cluster analysis to define assemblages in two time periods and canonical correspondence analysis to explore the relationships between the assemblages and temperature, depth, latitude, longitude and year. We further used two estimates of diversity, species richness and the Shannon index. Four major species assemblages were identified. Assemblages in the hydrographically stable deep waters north of the country were consistent during the study, while assemblage structure in the more variable shallow waters underwent some changes. For this period of generally increasing sea temperature, the canonical correspondence analysis also revealed a shift towards species representative of warmer temperatures. Diversity was shown to be highly variable both temporally and spatially, and also to vary with depth and temperature. Species richness increased with temperature and time southwest of the country, but decreased northeast of the country. The different trends detected between the northern and southern areas illustrate the importance of performing analyses at the most appropriate scale. [source] Molecular classification of borderline ovarian tumors using hierarchical cluster analysis of protein expression profilesINTERNATIONAL JOURNAL OF CANCER, Issue 6 2002Ayodele A. Alaiya Abstract Ovarian tumors range from benign to aggressive malignant tumors, including an intermediate class referred to as borderline carcinoma. The prognosis of the disease is strongly dependent on tumor classification, where patients with borderline tumors have much better prognosis than patients with carcinomas. We here describe the use of hierarchical clustering analysis of quantitative protein expression data for classification of this type of tumor. An accurate classification was not achieved using an unselected set of 1,584 protein spots for clustering analysis. Different approaches were used to select spots that were differentially expressed between tumors of different malignant potential and to use these sets of spots for classification. When sets of proteins were selected that differentiated benign and malignant tumors, borderline tumors clustered in the benign group. This is consistent with the biologic properties of these tumors. Our results indicate that hierarchical clustering analysis is a useful approach for analysis of protein profiles and show that this approach can be used for differential diagnosis of ovarian carcinomas and borderline tumors. © 2002 Wiley-Liss, Inc. [source] Multienzyme Profiling of Thermophilic Microorganisms with a Substrate Cocktail AssayADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 7-8 2005Renaud Sicard Abstract Labeled substrates for 16 different catalytic activities were combined into a cocktail reagent for multienzyme functional profiling, called PHENOZYMTM. The assay involves a single reaction followed by determination of substrate consumption by HPLC-analysis. The method allows a rapid identification of multiple enzyme activities, and is compatible with a diversity of growth media and reaction conditions (pH, temperature). The PHENOZYMTM cocktail was used to analyze the activity of 16 enzyme activities in a series of microbial strains, including thermophilic microorganisms. The functional profiles were used for a functional classification of the different microbial strains tested by hierarchical cluster analysis. The resulting "phylo-enzymatic" tree revealed associations consistent with the known phylogenetic classification of the strains. The influence of the culture medium on the enzyme activity profiles was also apparent. [source] Direct analysis of clinical relevant single bacterial cells from cerebrospinal fluid during bacterial meningitis by means of micro-Raman spectroscopyJOURNAL OF BIOPHOTONICS, Issue 1-2 2009Michaela Harz Abstract Bacterial meningitis is a relevant public health concern. Despite the availability of modern treatment strategies it is still a life-threatening disease that causes significant morbidity and mortality. Therefore, an initial treatment approach plays an important role. For in-time identification of specific bacterial pathogens of the cerebrospinal fluid (CSF) and emerged antimicrobial and adjunctive treatment, microbiological examination is of major importance. This contribution spotlights the potential of micro-Raman spectroscopy as a biomedical assay for direct analysis of bacteria in cerebrospinal fluid of patients with bacterial meningitis. The influence of miscellaneous artificial environments on several bacterial species present during bacterial meningitis was studied by means of Raman spectroscopy. The application of chemometric data interpretation via hierarchical cluster analysis (HCA) allows for the differentiation of in vitro cultured bacterial cells and can also be achieved on a single cell level. Moreover as proof of principle the investigation of a CSF sample obtained from a patient with meningococcal meningitis showed that the cerebrospinal fluid matrix does not mask the Raman spectrum of a bacterial cell notably since via chemometric analysis with HCA an identification of N. meningitidis cells from patients with bacterial meningitis could be achieved. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Multiple Justiciable Problems: Common Clusters and Their Social and Demographic IndicatorsJOURNAL OF EMPIRICAL LEGAL STUDIES, Issue 2 2004Pascoe Pleasence Justiciable problems do not always occur in isolation. However, little empirical research has examined multiple problems in depth by identifying common clusters of problems, their extent, and those who experience them. The Legal Services Research Centre's Periodic Survey of Justiciable Problems is a large-scale survey undertaken in England and Wales, documenting 5,611 respondents' experience of 21 discrete problem categories. Having assessed the overall incidence and overlap of problem types, hierarchical cluster analysis, based on each respondent's experience of these categories, was used to identify clusters. We then established social and demographic predictors of each cluster using mixed-effects Poisson regression and examined each problem type's likelihood of overlapping with further problems, both within and between identified clusters. We highlight policy implications of our findings, particularly concerning developing "joined-up" solutions to multiple "joined-up" problems. [source] Sources of knowledge in clinical practice in postgraduate medical students and faculty members: a conceptual mapJOURNAL OF EVALUATION IN CLINICAL PRACTICE, Issue 4 2007Reza Yousefi-Nooraie MD Abstract Objectives, To determine the most important knowledge sources that can influence clinical practice and to cluster them in conceptual groups based on their relative importance. Methods, Faculty members, fellows and residents of a large teaching tertiary care hospital were asked to rate the importance of different resources in their daily clinical practice and their understanding of some common terms from evidence-based medicine. The knowledge sources were distributed in a two-dimensional map using multidimensional scaling and hierarchical cluster analysis. Results, A total of 250 of 320 recruited hospital staff returned the questionnaires. The most important resources in daily practice were English journals, text books and literature searching for faculty members, experience, text books and English journals for fellows and text books, experience and peers for residents. Regional journals were the least important resources for all study groups. About 62.7% of residents did not know the meaning of ,number needed to treat', 36.8%,confidence interval', 54.9%,confounding factor' and 44.6%,meta-analysis'. The percentages for faculty members were 41.3%, 37%, 42.2% and 39.1%. The knowledge sources were placed in four clusters in a point map derived from the multidimensional scaling process. Conclusion, The dominance of the traditional information resources and experience-based medicine debate which is the consequence of traditional approaches to medical education may be one of the considerable barriers to the dissemination of evidence-based medicine in developing countries. The evidence-based clinical practice guidelines could be used as a useful passive-predigested source for busy clinicians to make informed decisions. A considerable Western bias may undermine the local research in developing world. [source] Determination of Total Protein Content in Gelatin Solutions with the Lowry or Biuret AssayJOURNAL OF FOOD SCIENCE, Issue 8 2006P. Zhou ABSTRACT:, Gelatins can be obtained from different sources and prepared using different processes, and the end product gelatin may vary in amino acid composition and molecular weight distribution. In the present study, the variation in "protein color" development among gelatins in colorimetric total protein content measurements was investigated at 540 nm using the Biuret assay and at 650 nm using the Lowry assay, with bovine serum albumin as the reference protein. In both the Biuret and Lowry assays, the color response varied significantly among gelatins. The difference in imino acid content was the major factor responsible for this variation, which probably influenced the gelatin helix , coil phase transition and resulted in the difference in gelatin associate state. Based on their "protein color" development abilities in both Biuret and Lowry, gelatins were classified into 2 major groups with the hierarchical cluster analysis: 1 group included all cold water fish gelatins, while the other included gelatins from warm water fish, avian, and mammalian species. [source] Differentiation of eight tea (Camellia sinensis) cultivars in China by elemental fingerprint of their leavesJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 14 2009Yingxu Chen Abstract BACKGROUND: Tea is an infusion made from dried leaves of tea (Camellia sinensis) and can be a good dietary source of essential trace metals for humans. Therefore, it is necessary to consider variations in element content of tea leaves among tea cultivars. Thus, elemental fingerprint techniques, based on elemental contents (Al, B, Ca, Cd, Co, Cr, Cu, Fe, K, Mg, Mn, Na, P, Pb, and Zn) determined by inductively coupled plasma atomic emission spectrometry (ICP-AES) and multivariate statistical analysis, have been used to differentiate eight tea cultivars. RESULTS: The ranges of element concentrations in leaves of the eight cultivars were in good agreement with those obtained in previous studies and the level of most elements in tea leaves was significantly different among cultivars. The classifications of eight tea cultivars were 100% accurate in total by principal component analysis (PCA), hierarchical cluster analysis (HCA), linear discriminant analysis (LDA), and back-propagation neural network (BPNN) analysis. CONCLUSION: Each cultivar presented a distinctive element fingerprint and the elements in tea leaves can be significant predictors in differentiating tea cultivars. Copyright © 2009 Society of Chemical Industry [source] Phenotypical characterization of indigenous freshwater crayfish populationsJOURNAL OF ZOOLOGY, Issue 2 2007D. Sint Abstract The morphology of an animal is known to reflect both genetic variation and adaptation to the environment. Thus, phenotypic criteria have been used to characterize indigenous crayfish populations. Twenty-one morphometric parameters were measured on crayfish from 25 waterbodies in the Austrian and Italian parts of Tyrol. They were analysed with hierarchical cluster analysis to obtain the population structure based on morphological similarity between and within the freshwater crayfish species Astacus astacus (noble crayfish), Austropotamobius torrentium (stone crayfish) and Austropotamobius pallipes (white-clawed crayfish). Furthermore, a stepwise discriminant analysis was applied to the morphometric data to test their differentiating power between populations. Both analyses resulted in a clear differentiation of species and populations, and reflected geographic separations. Thus, the developed morphometric methods were shown to be applicable to characterize the phenotype in freshwater crayfish and seem appropriate to be used for stock identification and the effective characterization of management units in decapod crustaceans. [source] BUBBLESTREAM WHISTLES ARE NOT REPRESENTATIVE OF A BOTTLENOSE DOLPHIN'S VOCAL REPERTOIREMARINE MAMMAL SCIENCE, Issue 1 2005Deborah Fripp Abstract Whistling bottlenose dolphins sometimes identify themselves with a concurrent bubblestream, and some researchers use these bubblestream whistles as their sole whistle sample. However, bubblestream whistles are not known to be representative of the entire repertoire. Bubblestreams and whistles were recorded from three captive female dolphins and their newborn calves. Bubblestreams were rare (0.13/min), with calves producing ten times as many as adults. Overall, 79% of bubblestreams were associated with whistles, but only 1 % of whistles were associated with bubblestreams. Bubblestream whistles were not independent: 49% occurred within 1 sec of another bubblestream, and 72% of these had the same contour as other bubblestream whistles in the bout. Bubblestream use was context-dependent: adults were more likely to bubblestream when caring for a calf (P < 0.001), and calves were more likely to bubblestream when other calves were present (P < 0.001). Bubblestreams were not associated with all whistle types. Bubblestream whistles were not evenly distributed across the clusters of a hierarchical cluster analysis of contour parameters using 300 randomly selected non-bubblestream whistles and 92 independent bubblestream whistles (10 clusters, P= 0.003). In conclusion, bubblestreams are rare visual cues that dolphins produce in association with certain whistles in certain contexts and are not representative of the dolphin's repertoire. [source] Genetic variation among populations of Pythium irregulare in southern AustraliaPLANT PATHOLOGY, Issue 5 2000P. R. Harvey Isolates of Pythium irregulare were sampled from seven cereal crops throughout South Australia to determine the extent of genetic diversity within this pathogen and the scale of genetic differentiation among populations. Data derived from 29 individual restriction fragment length polymorphism (RFLP) loci differentiated 54 DNA fingerprints among the 92 isolates analysed. Some isolates had two alleles at several RFLP loci and were scored as heterozygous. One such isolate was selfed in vitro and segregation ratios in the progeny were not significantly different from those expected for allelic variation in a diploid. These data provided evidence that outcrossing occurs within P. irregulare and may contribute to the high level of genetic variation within the species (DT = 0·502). Allelic frequencies were significantly different among all seven populations and GST values showed significant genetic differentiation between populations. The average genetic identity among populations was low and hierarchical cluster analysis provided no clear evidence that populations formed geographically related groups. These analyses indicate low levels of interpopulation gene flow within P. irregulare and imply that population differentiation results from genetic drift. [source] Medication adherence patterns in adult renal transplant recipients,RESEARCH IN NURSING & HEALTH, Issue 6 2006Cynthia L. Russell Abstract Patient adherence to immunosuppressive medications adherence is crucial to survival of the patient and a transplanted kidney, yet adherence is variable. Using a prospective, descriptive design, immunosuppressive medication adherence of 44 renal transplant recipients was followed for 6 months at a Midwestern transplant center using electronic monitoring. Four medication adherence patterns emerged from a hierarchical cluster analysis: those who took medications on time, those who took medications on time with late/missed doses, those who rarely took medications on time and who were late with morning and/or evening doses, and those who missed doses. This study is a step toward developing and implementing interventions targeted to specific patterns of poor adherence. © 2006 Wiley Periodicals, Inc. Res Nurs Health 29: 521,532, 2006 [source] Molecular characterization of the G,-globin-Tag transgenic mouse model of hormone refractory prostate cancer: Comparison to human prostate cancer,THE PROSTATE, Issue 6 2010Alfonso Calvo Abstract BACKGROUND Prostate cancer (PrCa) has a high incidence in Western countries and at present, there is no cure for hormone refractory prostate cancer. Transgenic mouse models have proven useful for understanding mechanisms of prostate carcinogenesis. The characterization of genetically modified mouse PrCa models using high-throughput genomic analyses provides important information to guide appropriate experiment applications for such model. METHODS We have analyzed the transcriptome of the hormone refractory and highly metastatic Fetal Globin-SV40/T-antigen (G,-globin-Tag) transgenic mouse model for PrCa compared to normal mouse prostate tissue. Gene expression patterns found in G,-globin-Tag mouse prostate tumors were compared with publicly available human localized and metastatic prostate tumors (GEO accession # GSE3325) through hierarchical cluster analysis, Pearson's rank correlation coefficient, and Self Organizing Feature Maps (SOM) analyses. RESULTS G,-globin-Tag tumors clustered closely with human metastatic tumors and gene expression patterns had a significant correlation (P,<,0.01), unlike human localized primary tumors (P,>,0.6). Bioinformatic analyses identified deregulated genetic pathways and networks in G,-globin-Tag tumors, which displayed similarities to alterations in human PrCa. Changes in the expression of genes involved in DNA replication and repair (Rb1, p53, Myc, PCNA, DNMT3A) and growth factor signaling pathways (TGF,2, ERK1/2, NRas, and Notch1) are deregulated in the G,-globin-Tag tumors, suggesting their key role in the oncogenic process. Identification of an enrichment of putative binding sites for transcription factors revealed eight transcription factors that may be important in G,-globin-Tag carcinogenesis, including SP1, NF-Y, CREB, Elk1, and E2F. Novel genes related to microtubule regulation were also identified in G,-globin-Tag tumors as potentially important candidate targets for PrCa. Overexpression of stathmin-1, whose expression was increased in human metastatic prostate tumors, was validated in G,-globin-Tag tumors by immunohistochemistry. This protein belongs to the SV40/T-antigen cancer signature identified in previous studies in prostate, breast, and lung cancer mouse models. CONCLUSIONS Our results show that the G,-globin-Tag model for hormone refractory PrCa shares important features with aggressive, metastatic human PrCa. Given the role of stathmin-1 in the destabilization of microtubles and taxane resistance, the G,-globin-Tag model and other SV40/T-antigen driven transgenic models may be useful for testing potential therapies directed at stathmin-1 in human prostate tumors. Prostate 70: 630,645, 2010. Published 2010 Wiley-Liss, Inc. [source] The influence of dog ownership in childhood on the sociality of elderly Japanese menANIMAL SCIENCE JOURNAL, Issue 3 2010Miho NAGASAWA ABSTRACT In Japan, care for the elderly has been a serious social issue. The relationship between dog ownership and health of the elderly has attracted considerable attention, but it is still unclear whether dog ownership affects the health of owners. In this study, we focused on the experiences of dog ownership in the past. The questionnaire survey was conducted targeting elderly Japanese men and asking them to clarify whether the experience of dog ownership in the past influences their current mental and physical health. To examine the characteristics of the experience of dog ownership, we divided past dog owners by a hierarchical cluster analysis using the variables related to the experiences of dog ownership. We added the ,never owned a dog' group to the three groups that were provided by the cluster analysis, and conducted analysis of variance and multiple linear regression analysis using the variables of physical and mental health. The results showed that the group that owned their first dog at an early age and owned more dogs later scored higher in the companionship and social support scales. These results suggested that the experiences of dog ownership in childhood were related to the sociality of older men, such as the enhancement of their companionship with others. [source] Gene expression profiling of cranial sensory ganglia that transmit food intake stimuliBIOFACTORS, Issue 1-4 2004Ichiro Matsumoto Abstract Peripheral cranial sensory nerves projecting into the oral cavity receive food intake stimuli and transmit sensory signals to the central nervous system. They are derived from four cranial sensory ganglia, trigeminal, geniculate, petrosal, and nodose ganglia, each of which contains multiple kinds of sensory neurons with different cell morphologies and neuronal properties. We investigated the complex properties of these neurons from the viewpoint of gene expression using DNA microarrays. The 498 genes were selected from a total of 8,740 genes as showing tissue-dependent expression on the microarray by hierarchical cluster analysis, in which several genes known to be differentially expressed in cranial sensory ganglia are included. This suggests that DNA microarray cluster analysis revealed a number of characteristic genes for sensory neurons in these ganglia. Among the selected 498 genes, 44 genes are associated with neurotransmission, such as neuropeptides, their receptors, and vesicle transport, and 26 are ion channels regulating membrane potentials. The identification of a number of genes related directly to neural properties indicates that these sensory ganglia contain heterogeneous types of neurons with different neural properties. [source] High throughput comparative genomic hybridization array analysis of multifocal urothelial cancersCANCER SCIENCE, Issue 8 2006Hiroaki Kawanishi The purpose of this study was to examine genetic alterations occur during synchronous or metachronous multifocal development of urothelial cancers on the whole genome using a comparative genomic hybridization (CGH) array. We used 10 tumor pairs (2 tumors for each patient), in which we had previously defined a clonal relationship by microsatellite analysis. For CGH array analysis, Vysis GenoSensor Array 300 kit was used. An unsupervised hierarchical cluster analysis revealed that the tumors from one patient were clustered together independent of the tumors of all other patients. On the other hand, many genetic divergences among multifocal urothelial cancers were newly found by a CGH array analysis. The concordant genetic alteration patterns of the chromosomal arm in tumor pairs were most frequently observed in 9p, 9q, 8p, 7p, 7q and 11q, while discordant patterns were most frequently found in 15q, 20q, 2q, 10p and 11q. Investigation using a CGH array showed that genetically stable multifocal tumors were less frequent, and that a large percentage of urothelial cancers accumulate genetic alterations during multifocal development by clonal evolution. We might have to consider these genetic accumulations during multifocal development when designing strategies for prevention and detection of recurrent multifocal urothelial cancers. CGH array can be a powerful tool for genetic analysis of multifocal urothelial cancer. (Cancer Sci 2006; 97: 746,752) [source] | ||||||||||||||||||||||