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Kinds of Groupings Selected AbstractsContent and distribution of arsenic in soils, sediments and groundwater environments of the southern Pampa region, ArgentinaENVIRONMENTAL TOXICOLOGY, Issue 6 2006M. del C. Blanco Abstract The health of a large rural population in the southern Pampa (Argentina) is at risk owing to newly detected areas where As-groundwater exceeds 0.01 mg/L standard (WHO (1995) Guidelines for drinking water quality, 2nd edition. pp 43,45). Currently, devitrification of volcanic glass is invoked to interpret the origin of arsenic in the aquifers hosted in a sequence of pampean loess (Plio-Pleistocene) juxtaposed with postpampean loess (Holocene). Our data suggest that arsenic is not specifically associated with volcanic glass and that other minerals contribute to As-release into groundwater. The goals were (1) to understand As-groundwater spatial variability, (2) to explore soils/sediments/water relationships and to identify the probable As-provenance. Comparable As concentrations of the light and the heavy sand fractions suggest that though detrital glass is a major light constituent, other existing primary minerals are As-bearers that contribute to As-release into groundwater. Grouping of materials according to their As-content indicated spatial variability in the sedimentary distribution pattern leading to differences in the frequencies of occurrence of As-bearing minerals. Phreatic waters were Ca + Mg bicarbonate and devoid of As in the intake areas (Ventania System) and Na-carbonate but As-rich towards the discharge (Atlantic coast and local depressions). As-groundwater reflects a patchy distribution within the pampean landscape. A correspondence between As-high groundwater, EC >1 dSm, CO3H,, alkaline pH and a longer water residence time do exist triggering As extraction from the loess sand fraction and desorption from charged fine particles which lead to As-toxicity towards groundwater discharge. © 2006 Wiley Periodicals, Inc. Environ Toxicol 21: 561,574, 2006. [source] Invertebrate community structure in streams of the Manawatu,Wanganui region, New Zealand: the roles of catchment versus reach scale influencesFRESHWATER BIOLOGY, Issue 8 2004Russell G. Death Summary 1. Invertebrate communities at 187 least impacted streams in the Manawatu,Wanganui region of New Zealand were sampled between February and May 2000 to investigate the relative influence of catchment and reach scale environmental influences on community structure. 2. Of the 138 biological (fish and periphyton), local habitat and catchment scale descriptors used to examine invertebrate community patterns, alkalinity and conductivity were the most consistently influential predictors. 3. Of the 52 geographical information system (GIS)-derived catchment variables (catchment geology, catchment land use, rainfall and topography) only per cent catchment in pasture, indigenous forest, coastal sand, crushed argillite and wind blown sand were associated with any measures of the invertebrate communities. 4. Grouping of communities based on GIS data in general, did not generate distinct community types. Groupings based on river catchment, conductivity and alkalinity however, did produce distinct communities. 5. Streams with very low alkalinity were dominated by Ephemeroptera, Plecoptera and Trichoptera that were gradually replaced by Mollusca, Crustacea and Chironomidae as alkalinity increases. 6. Habitat characteristics measured at the scale of the reach were more closely linked with measures of invertebrate community structure than any GIS derived variables or river classifications. [source] Principles and practical grouping for the use of drill and practice programsJOURNAL OF COMPUTER ASSISTED LEARNING, Issue 2 2001A. Jackson Abstract A previous paper showed that young children performed better when working as individuals rather than in pairs on a drill and practice program. This paper reports an analysis of behaviour and talk for individuals and single sex pairs using a computer-based drill and practice activity to explain differences in performance. Results indicated that individuals were more likely to be task-focused and to complete tasks successfully than children working in pairs. Differences were found in off-task activity, behaviours and type of talk. Grouping and verbal interaction are discussed in relation to the type of task/program that children are asked to undertake, and how both task and peer presence may constrain the child's task focus and performance when reinforcing pre-existing knowledge. [source] The tick Ixodes ricinus: distribution and climate preferences in the western PalaearcticMEDICAL AND VETERINARY ENTOMOLOGY, Issue 2 2006A. ESTRADA-PEÑA Abstract In this study, multivariate spatial clustering on monthly normalized difference vegetation index (NDVI) maps is used to classify ecological regions over the western Palaearctic. This classification is then used to delineate the distribution and climate preferences of populations (clades) of the tick Ixodes ricinus L. (Acari: Ixodidae) from a geographically extensive dataset of tick records and a gridded 2.5-km resolution climate dataset. Using monthly layers of the NDVI, regions of similar ecological attributes were defined and nine populations with significant differences in critical climate parameters (P < 0.005) were detected. Grouping of tick records according to other categories, such as political divisions, a 4°× 4° grid overlying the study area, or the CORINE) and USGS) vegetation classification schemes did not provided significantly separated populations (P= 0.094,0.304). Factor analysis and hierarchical tree clustering provided an ecological overview of these tick clades: two Mediterranean and one Scandinavian (western) clades are clearly separated from a node that includes clades of different parts of central Europe and the British Isles, with contrasting affinities between the different clades. The capture records of these ecologically separated clades produce a clear bias when bioclimate envelope modelling is applied to the mapping of habitat suitability for the tick in the western Palaearctic. The best-performing methods (Cohen's kappa = 0.834,0.912) use partial models developed with data from each ecoregion, which are then overlapped over the region of study. It is concluded that the use of ecologically derived ecoregions is an objective step in assessing the presence of ecologically different clades, and provides a guide in the development of data partitioning for habitat suitability modelling. [source] Mitochondrial DNA reveals multiple Northern Hemisphere introductions of Caprella mutica (Crustacea, Amphipoda)MOLECULAR ECOLOGY, Issue 5 2008GAIL V. ASHTON Abstract Caprella mutica (Crustacea, Amphipoda) has been widely introduced to non-native regions in the last 40 years. Its native habitat is sub-boreal northeast Asia, but in the Northern Hemisphere, it is now found on both coasts of North America, and North Atlantic coastlines of Europe. Direct sequencing of mitochondrial DNA (cytochrome c oxidase subunit I gene) was used to compare genetic variation in native and non-native populations of C. mutica. These data were used to investigate the invasion history of C. mutica and to test potential source populations in Japan. High diversity (31 haplotypes from 49 individuals), but no phylogeographical structure, was identified in four populations in the putative native range. In contrast, non-native populations showed reduced genetic diversity (7 haplotypes from 249 individuals) and informative phylogeographical structure. Grouping of C. mutica populations into native, east Pacific, and Atlantic groups explained the most among-region variation (59%). This indicates independent introduction pathways for C. mutica to the Pacific and Atlantic coasts of North America. Two dominant haplotypes were identified in eastern and western Atlantic coastal populations, indicating several dispersal routes within the Atlantic. The analysis indicated that several introductions from multiple sources were likely to be responsible for the observed global distribution of C. mutica, but the pathways were least well defined among the Atlantic populations. The four sampled populations of C. mutica in Japan could not be identified as the direct source of the non-native populations examined in this study. The high diversity within the Japan populations indicates that the native range needs to be assessed at a far greater scale, both within and among populations, to accurately assess the source of the global spread of C. mutica. [source] Grouping Pavement Condition Variables for Performance Modeling Using Self-Organizing MapsCOMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 2 2001Nii O. Attoh-Okine Different modeling techniques have been employed for the evaluation of pavement performance, determination of structural capacity, and performance predictions. The evaluation of performance involves the functional analysis of pavements based on the history of the riding quality. The riding comfort and pavement performance can be conveniently defined in terms of roughness and pavement distresses. Thus different models have been developed relating roughness with distresses to predict pavement performance. These models are too complex and require parsimonious equations involving fewer variables. Artificial neural networks have been used successfully in the development of performance-prediction models. This article demonstrates the use of an artificial intelligence neural networks self-organizing maps for the grouping of pavement condition variables in developing pavement performance models to evaluate pavement conditions on the basis of pavement distresses. [source] Should an obsessive,compulsive spectrum grouping of disorders be included in DSM-V?,DEPRESSION AND ANXIETY, Issue 6 2010Katharine A. Phillips M.D. Abstract The obsessive,compulsive (OC) spectrum has been discussed in the literature for two decades. Proponents of this concept propose that certain disorders characterized by repetitive thoughts and/or behaviors are related to obsessive,compulsive disorder (OCD), and suggest that such disorders be grouped together in the same category (i.e. grouping, or "chapter") in DSM. This article addresses this topic and presents options and preliminary recommendations to be considered for DSM-V. The article builds upon and extends prior reviews of this topic that were prepared for and discussed at a DSM-V Research Planning Conference on Obsessive,Compulsive Spectrum Disorders held in 2006. Our preliminary recommendation is that an OC-spectrum grouping of disorders be included in DSM-V. Furthermore, we preliminarily recommend that consideration be given to including this group of disorders within a larger supraordinate category of "Anxiety and Obsessive,Compulsive Spectrum Disorders." These preliminary recommendations must be evaluated in light of recommendations for, and constraints upon, the overall structure of DSM-V. Depression and Anxiety, 2010. © 2010 Wiley-Liss, Inc. [source] Posttraumatic stress disorder and the structure of common mental disordersDEPRESSION AND ANXIETY, Issue 4 2002Brian J. Cox Ph.D. Abstract Krueger [1999: Arch Gen Psychiatry 56:921,926] identified a three-factor structure of psychopathology that explained the covariation or grouping of common mental disorders found in the U.S. National Comorbidity Survey (NCS) [Kessler et al., 1994: Arch Gen Psychiatry 51:8,19]. These three fundamental groupings included an externalizing disorders factor and two internalizing disorders factors (anxious-misery and fear). We extended this research through the examination of additional data from a large subsample of the NCS (n=5,877) that contained diagnostic information on posttraumatic stress disorder (PTSD). Factor analytic findings revealed that PTSD showed no affinity with the fear factor defined by panic and phobic disorders, and instead loaded on the anxious-misery factor defined primarily by mood disorders. An identical pattern of results emerged for both lifetime PTSD and 12-month PTSD prevalence figures. Implications of these findings for the classification of PTSD and research on its etiology are briefly discussed. © 2002 Wiley-Liss, Inc. [source] Toddlers can adaptively change how they categorize: same objects, same session, two different categorical distinctionsDEVELOPMENTAL SCIENCE, Issue 1 2009Jessica S. Horst Two experiments demonstrate that 14- to 18-month-old toddlers can adaptively change how they categorize a set of objects within a single session, and that this ability is related to vocabulary size. In both experiments, toddlers were presented with a sequential touching task with objects that could be categorized either according to some perceptually salient dimension corresponding to a taxonomic distinction (e.g. animals vs. vehicles) or to some less obvious dimension (e.g. rigid vs. deformable). In each experiment, children with larger productive vocabularies responded to both dimensions, showing evidence of sensitivity to each way of categorizing the items. Children with smaller productive vocabularies attended only to the taxonomically related categorical grouping. These experiments confirm that toddlers can adaptively shift the basis of their categorization and highlight the dynamic interaction between the child and the current task in early categorization. [source] Latent Separability: Grouping Goods without Weak SeparabilityECONOMETRICA, Issue 1 2000Richard Blundell This paper develops a new concept of separability with overlapping groups,latent separability. This is shown to provide a useful empirical and theoretical framework for investigating the grouping of goods and prices. It is a generalization of weak separability in which goods are allowed to enter more than one group and where the composition of groups is identified by the choice of group specific exclusive goods. Latent separability is shown to be equivalent to weak separability in latent rather than purchased goods and provides a relationship between separability and household production theory. For the popular class of linear, almost ideal and translog demand models and their generalizations, we provide a method for choosing the number of homothetic separable groups. A detailed method for exploring the composition of the separable groups is also presented. These methods are applied to a long time series of British individual household data on the consumption of twenty two nondurable and service goods. [source] Capillary electrophoresis-time of flight-mass spectrometry using noncovalently bilayer-coated capillaries for the analysis of amino acids in human urineELECTROPHORESIS, Issue 12 2008Rawi Ramautar Abstract A capillary electrophoresis-time of flight-mass spectrometry (CE-TOF-MS) method for the analysis of amino acids in human urine was developed. Capillaries noncovalently coated with a bilayer of Polybrene (PB) and poly(vinyl sulfonate) (PVS) provided a considerable EOF at low pH, thus facilitating the fast separation of amino acids using a BGE of 1,M formic acid (pH,1.8). The PB,PVS coating proved to be very consistent yielding stable CE-MS patterns of amino acids in urine with favorable migration time repeatability (RSDs <2%). The relatively low sample loading capacity of CE was circumvented by an in-capillary preconcentration step based on pH-mediated stacking allowing 100-nL sample injection (i.e. ca. 4% of capillary volume). As a result, LODs for amino acids were down to 20,nM while achieving satisfactory separation efficiencies. Preliminary validation of the method with urine samples showed good linear responses for the amino acids (R2 >0.99), and RSDs for peak areas were <10%. Special attention was paid to the influence of matrix effects on the quantification of amino acids. The magnitude of ion suppression by the matrix was similar for different urine samples. The CE-TOF-MS method was used for the analysis of urine samples of patients with urinary tract infection (UTI). Concentrations of a subset of amino acids were determined and compared with concentrations in urine of healthy controls. Furthermore, partial least squares,discriminant analysis (PLS,DA) of the CE-TOF-MS dataset in the 50,450,m/z region showed a distinctive grouping of the UTI samples and the control samples. Examination of score and loadings plot revealed a number of compounds, including phenylalanine, to be responsible for grouping of the samples. Thus, the CE-TOF-MS method shows good potential for the screening of body fluids based on the analysis of endogenous low-molecular weight metabolites such as amino acids and related compounds. [source] Australasian emergency physicians: A learning and educational needs analysis.EMERGENCY MEDICINE AUSTRALASIA, Issue 2 2008Part Three: Participation by FACEM in available CPD: What do they do, do they like it? Abstract Objective: To determine the participation of Emergency Physicians (EP) in currently available continuing professional development opportunities (CPD), their perception of the usefulness of available CPD and their preferred format or method of CPD desired in the future. Method: A mailed survey of Fellows of the Australasian College for Emergency Medicine with 17 Likert type options on educational methods and qualitative analysis grouping volunteered free text responses. Results: The most frequent learning methods reported by EP are on the job contact with other clinicians, formal ED based teaching and reading journals, which were also perceived as useful or very useful learning methods by more than 90% of EP. Less than 15% often or always participate on hospital grand rounds, high fidelity simulation, computer programmes or commercially sponsored events. Increased exposure was desired to high-fidelity simulation center skills training by 58% of respondents with nearly 49% of fellows also wanting more participation in international conferences with around 44% of fellows also wanting more participation in international conferences with around 44% desiring more formal teaching in the ED, more formal feedback on performance, and more meetings with other hospital departments. Over 50% of EP want less or no exposure to commercially sponsored dinners or events. Conclusion: Whilst emergency physicians currently participate in a wide variety of learning methods, the results of this survey suggest EP most appreciate ED based teaching, would like more contact with other departments, along with increased opportunities for simulation based learning and attendance at international conferences. [source] Diagnosis Clusters for Emergency MedicineACADEMIC EMERGENCY MEDICINE, Issue 12 2003Debbie A. Travers RN Objectives: Aggregated emergency department (ED) data are useful for research, ED operations, and public health surveillance. Diagnosis data are widely available as The International Classification of Diseases, version, 9, Clinical Modification (ICD-9-CM) codes; however, there are over 24,000 ICD-9-CM code-descriptor pairs. Standardized groupings (clusters) of ICD-9-CM codes have been developed by other disciplines, including family medicine (FM), internal medicine (IM), inpatient care (Agency for Healthcare Research and Quality [AHRQ]), and vital statistics (NCHS). The purpose of this study was to evaluate the coverage of four existing ICD-9-CM cluster systems for emergency medicine. Methods: In this descriptive study, four cluster systems were used to group ICD-9-CM final diagnosis data from a southeastern university tertiary referral center. Included were diagnoses for all ED visits in July 2000 and January 2001. In the comparative analysis, the authors determined the coverage in the four cluster systems, defined as the proportion of final diagnosis codes that were placed into clusters and the frequencies of diagnosis codes in each cluster. Results: The final sample included 7,543 visits with 19,530 diagnoses. Coverage of the ICD-9-CM codes in the ED sample was: AHRQ, 99%; NCHS, 88%; FM, 71%; IM, 68%. Seventy-six percent of the AHRQ clusters were small, defined as grouping <1% of the diagnosis codes in the sample. Conclusions: The AHRQ system provided the best coverage of ED ICD-9-CM codes. However, most of the clusters were small and not significantly different from the raw data. [source] Evaluation of estrogenic activity of phthalate esters by gene expression profiling using a focused microarray (estrarray®),ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 6 2008Meher Parveen Abstract Phthalates are used industrially as plasticizers and are known to contaminate natural environments, mostly as di-ester or mono-ester complexes. Because they are structurally similar to natural estrogens, they could act as endocrine disruptors. Here, we used a DNA microarray containing estrogen responsive genes (EstrArray®) to examine gene expression profiles in MCF-7 cells treated with 10 ,M butylbenzyl phthalate (BBP), dibutyl phthalate (DBP), diethyl phthalate (DEP), and diisopropyl phthalate (DIP) along with the natural estrogen 17,-estradiol ([E2], 10 nM). The profiles for phthalate esters and E2 were examined by correlation analysis using correlation coefficients (r -values) and cluster analysis. We found that BBP showed the highest correlation with E2 (r = 0.85), and DEP and DIP showed moderate r -values (r = 0.52 and r = 0.49, respectively). Dibutyl phthalate exhibited the lowest (but still significant) correlation with E2 (r = 0.36). Furthermore, among the pairs of chemicals, DEP-DIP and DIP-DBP showed very high correlations (r = 0.90 and r = 0.80, respectively), and the other pairs showed moderate relationships, which reflected how structurally close they are to each other. The analysis of six functional groups of genes (enzymes, signaling, proliferation, transcription, transport, and others) indicated that the genes belonging to the enzyme, transcription, and other functional groups showed common responses to phthalate esters and E2. Although the effect of BBP was similar to that of E2, the other phthalate esters showed different types of effects. These results indicate that the structure of estrogenic chemicals is strongly related to their estrogenic activity and can be evaluated by appropriate grouping of the responsive genes by focused microarray analysis. [source] Stepwise geographical traceability of virgin olive oils by chemical profiles using artificial neural network modelsEUROPEAN JOURNAL OF LIPID SCIENCE AND TECHNOLOGY, Issue 10 2009Diego L. García-González Abstract The geographical traceability of virgin olive oils implies the use of analytical methods that allow the identification of the origin of the oil and the authentication of the information boasted on the labels. In this work, the geographical identification of the virgin olive oils has been addressed by complete chemical characterisation of samples (64 compounds analysed by GC and HPLC) and the design of artificial neural network (ANN) models for each one of the levels of a proposed classification scheme. A high number of samples (687) from Spain, Italy and Portugal served as training and test sets for the ANN models. The highest classification level, focused on the grouping of samples by country, was achieved through analysis of fatty acids, with 99.9% of samples classified. Other levels (region, province, Protected Designations of Origin or PDO) were focused on Spanish oils and required additional series of compounds (sterols, alcohols, hydrocarbons) as well as the fatty acids to obtain classification rates higher than 90%. The classification of oils into different PDOs , the last and most difficult level of classification , showed the highest root mean square errors. The classification percentages, however, were still higher than 90% in the test set, which proves the application of the traceability methodology for a chemical verification of PDO claims. [source] Gene expression signatures in chronic and aggressive periodontitis: a pilot studyEUROPEAN JOURNAL OF ORAL SCIENCES, Issue 3 2004Panos N. Papapanou This pilot study examined gene expression signatures in pathological gingival tissues of subjects with chronic or aggressive periodontitis, and explored whether new subclasses of periodontitis can be identified based on gene expression profiles. A total of 14 patients, seven with chronic and seven with aggressive periodontitis, were examined with respect to clinical periodontal status, composition of subgingival bacterial plaque assessed by checkerboard hybridizations, and levels of serum IgG antibodies to periodontal bacteria assayed by checkerboard immunoblotting. In addition, at least two pathological pockets/patient were biopsied, processed for RNA extraction, amplification and labeling, and used to study gene expression using Affymetrix U-133 A arrays. Based on a total of 35 microarrays, no significantly different gene expression profiles appeared to emerge between chronic and aggressive periodontitis. However, a de novo grouping of the 14 subjects into two fairly robust clusters was possible based on similarities in gene expression. These two groups had similar clinical periodontal status and subgingival bacterial profiles, but differed significantly with respect to serum IgG levels against the important periodontal pathogens Porphyromonas gingivalis, Tannerella forsythensis and Campylobacter rectus. These early data point to the usefulness of gene expression profiling techniques in the identification of subclasses of periodontitis with common pathobiology. [source] Evolution of astacin-like metalloproteases in animals and their function in developmentEVOLUTION AND DEVELOPMENT, Issue 2 2006Frank Möhrlen SUMMARY Astacin-like metalloproteases are ubiquitous in the animal kingdom but their phylogenetic relationships and ancient functions within the Metazoa are unclear. We have cloned and characterized four astacin-like cDNAs from the marine hydroid Hydractinia echinata and performed a database search for related genes in the draft genome sequence of the sea anemone Nematostella vectensis. These sequences and those of higher animals' astacins were subjected to phylogenetic analysis revealing five clusters within the Eumetazoa. The bone morphogenetic protein-1/tolloid-like astacins were represented in all eumetazoan phyla studied. The meprins were only found in vertebrates and cnidarians. Two clusters were taxon-specific, and one cluster represented astacins, which probably evolved after the split of the Cnidaria. Interestingly, grouping of astacins according to the protease catalytic domain alone resulted in clusters of proteins with similar overall domain architecture. The Hydractinia astacins were expressed in distinct cells during metamorphosis and some also during wound healing. Previously characterized cnidarian astacins also act during development. Based on our phylogeny, however, we propose that the developmental function of most of them is not homologous to the developmental function assigned to higher animals' astacins. [source] Fuzzy based fast dynamic programming solution of unit commitment with ramp constraintsEXPERT SYSTEMS, Issue 4 2009S. Patra Abstract: A fast dynamic programming technique based on a fuzzy based unit selection procedure is proposed in this paper for the solution of the unit commitment problem with ramp constraints. The curse of dimensionality of the dynamic programming technique is eliminated by minimizing the number of prospective solution paths to be stored at each stage of the search procedure. Heuristics like priority ordering of the units, unit grouping, fast economic dispatch based on priority ordering, and avoidance of repeated economic dispatch through memory action have been employed to make the algorithm fast. The proposed method produced comparable results with the best performing methods found in the literature. [source] Delimiting morphologically identical varieties of soybean [Glycine max (L.) Merr.] using lipoxygenase activitity levelFEDDES REPERTORIUM, Issue 3-4 2005M. S. Ayodele The occurrence of beany flavour resulting from lipoxygenase activity in soybeans was sufficiently manifested in all the 22 varieties of soybean investigated. There were significant differences in the level of lipoxygenase activity among varieties. A positive correlation was observed between lipoxygenase activity and beany flavour. Lipoxygenase activity level was found reliable in delimiting the varieties. A considerable degree of overlaps and associations were observed among the varietal grouping based on lip- oxygenase activity values. Such overlaps corroborate the reported closeness of plant morphological attributes of the varieties. Lipoxygenase activity was therefore, considered a reliable chemotaxonomic tool that could be useful for taxa delimitation, where there are very similar morphological attributes that may hinder easy delimitation. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) Abgrenzung von morphologisch identischen Varietäten der Soyabohne [Glycine max (L.) Merr.] mittels aktiver Lipoxygenase Das Auftreten eines bohnenähnlichen Geruchs (soybean flavour) als Ergebnis der Lipoxygenase-Aktivität wurde in allen untersuchten 22 Sojabohnen-Sorten eindeutig nachgewiesen. Im Niveau der Lipoxygenase-Aktivität treten zwischen den einzelnen Sorten manifeste Unterschiede auf. Zwischen der Lipoxygenase-Aktivität und dem bohnenartigen Geruch wurde eine positive Korrelation beobachtet. Die Höhe der Lipoxygenase-Aktivität trennt die Sorten zuverlässig. Ein beträchtlicher Grad an Überschneidungen und von Gemeinsamkeiten wurde zwischen den auf Grund der Lipoxygenase-Aktivitätswerte gebildeten Sortengruppen gefunden. Die Überschneidungen bestätigen die Nähe der morphologischen Merkmale der Sorten. Die Lipoxygenase-Aktivität wird daher als eine verlässliche taxonomische Hilfe für die Trennung der Sippen angesehen, deren große morphologische Nähe eine leichte Trennung erschwert. [source] Genetic differences among the LPS biosynthetic loci of serovars of Leptospira interrogans and Leptospira borgpeterseniiFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 1 2001Alejandro de la Peña-Moctezuma Abstract The gene organization in the lipopolysaccharide biosynthetic (rfb) locus was analyzed in seven Leptospira interrogans serovars within serogroup Icterohemorrhagiae, seven non-Icterohemorrhagiae serovars and one Leptospira borgpetersenii serovar. Two groups of loci were delineated based on DNA hybridization and sequence analysis. Group 1 contained the two Hardjo subtypes, Hardjoprajitno and Hardjobovis. Group 2 (containing Copenhageni, Pomona, Naam, Mwogolo, Smithi, Lai, Canicola, Autumnalis, Pyrogenes, Australis and Icterohemorrhagiae) differed from Group 1 in its organization upstream of orf11, where five ORFs (32, 33, 34, 35, 37) were identified that were not contained in the Group 1 loci. These ORFs encoded a putative epimerase (orf32), a glycosyltransferase (orf33), two integral membrane proteins (orfs 34 and 35), and a galactosyltransferase (orf37). Serovars Australis, Pomona and Autumnalis did not contain orf37. Serovar Bataviae was excluded from the grouping because of its unique genetic organization upstream of orf13. In the Group 2 loci, comparison of the genetic layout at the 5, end revealed differences which included mutations disrupting reading frames in either or both orf34 and orf35 and apparent allelic differences between orf33 homologs that may be sufficient to account for the genetic basis of serovar identity. [source] Soil parent material is a key determinant of the bacterial community structure in arable soilsFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Andreas Ulrich Abstract The bacterial community composition in soil and rhizosphere taken from arable field sites, differing in soil parent material and soil texture, was analyzed using terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes. Nine sandy to silty soils from North-East Germany could clearly be distinguished from each other, with a relatively low heterogeneity in the community structure within the field replicates. There was a relationship between the soil parent material, i.e. different glacial and aeolian sediments, and the clustering of the profiles from different sites. A site-specific grouping of T-RFLP profiles was also found for the rhizosphere samples of the same field sites that were planted with potatoes. The branching of the rhizosphere profiles corresponded partly with the soil parent material, whereas the effect of the plant genotype was negligible. Selected terminal restriction fragments differing in their relative abundance within the nine soils were analyzed based on the cloning of the 16S rRNA genes of one soil sample. A high phylogenetic diversity observed to include Acidobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, and Gemmatimonadetes. The assignment of three out of the seven selected terminal restriction fragments to members of Acidobacteria suggested that this group seems to participate frequently in the shifting of community structures that result from soil property changes. [source] Characterisation of symbionts of entomopathogenic nematodes by universally primed-PCR (UP-PCR) and UP-PCR product cross-hybridisationFEMS MICROBIOLOGY LETTERS, Issue 1 2002O. Nielsen Abstract This work introduces and demonstrates the applicability of universally primed-PCR (UP-PCR) for differentiating bacterial symbionts of entomopathogenic nematodes. Furthermore, typing by UP-PCR product cross-hybridisation was successfully introduced to cluster the bacterial strains. The work was initiated by isolating 10 isolates of Photorhabdus temperata (S172) from the nematode host Heterorhabditis sp. (DK172) and 12 isolates of Xenorhabdus bovienii (S1) from the nematode Steinernema feltiae (DK1). The isolates were compared by UP-PCR using different primers. The two bacterial species (P. temperata and X. bovienii) could be distinguished on the basis of the banding pattern whereas isolates isolated from the same nematode host had identical banding patterns. Three isolates obtained from DK172 and DK1, respectively, were then selected along with a number of reference strains (Hb, HP88, C1, K122, HSH2, HL81, T228, 61, AN6, Q58) and further characterised by UP-PCR product cross-hybridisation. The Xenorhabdus strains (Q58, AN6, 61, T228, S1) represented three species and these species were separated by the hybridisation technique. The Photorhabdus strains (Hb, HP88, C1, K122, HSH2, HL81, S172) represented two species and were also separated according to this in the cross-hybridisation. Within each species of Photorhabdus, two subgroups were formed as a result of intensity of the hybridisation signals. This grouping was in agreement with previous studies in other laboratories. [source] Cell wall teichoic acids: structural diversity, species specificity in the genus Nocardiopsis, and chemotaxonomic perspectiveFEMS MICROBIOLOGY REVIEWS, Issue 3 2001Irina B Naumova Abstract Data on the structures of cell wall teichoic acids, the anionic carbohydrate-containing polymers, found in many Gram-positive bacteria have been summarized and the polymers of the actinomycete genus Nocardiopsis have been considered from the taxonomic standpoint. The structures of these polymers or their combinations have been demonstrated to be indicative of each of seven Nocardiopsis species and two subspecies, verified by the DNA,DNA relatedness data, and to correlate well with the grouping of the organisms based on 16S rDNA sequences. As each of the intrageneric taxa discussed is definable by the composition of teichoic acids, the polymers are considered to be valuable taxonomic markers for the Nocardiopsis species and subspecies. The 13C NMR spectra of the polymers, data on the products of their chemical degradation, and distinguishing constituents of whole cell walls derived from teichoic acids are discussed, which are useful for identification of certain polymers and members of the genus Nocardiopsis at the species and subspecies level in microbiological practice. [source] Incorporating covariates in mapping heterogeneous traits: a hierarchical model using empirical Bayes estimationGENETIC EPIDEMIOLOGY, Issue 7 2007Swati Biswas Abstract Complex genetic traits are inherently heterogeneous, i.e., they may be caused by different genes, or non-genetic factors, in different individuals. So, for mapping genes responsible for these diseases using linkage analysis, heterogeneity must be accounted for in the model. Heterogeneity across different families can be modeled using a mixture distribution by letting each family have its own heterogeneity parameter denoting the probability that its disease-causing gene is linked to the marker map under consideration. A substantial gain in power is expected if covariates that can discriminate between the families of linked and unlinked types are incorporated in this modeling framework. To this end, we propose a hierarchical Bayesian model, in which the families are grouped according to various (categorized) levels of covariate(s). The heterogeneity parameters of families within each group are assigned a common prior, whose parameters are further assigned hyper-priors. The hyper-parameters are obtained by utilizing the empirical Bayes estimates. We also address related issues such as evaluating whether the covariate(s) under consideration are informative and grouping of families. We compare the proposed approach with one that does not utilize covariates and show that our approach leads to considerable gains in power to detect linkage and in precision of interval estimates through various simulation scenarios. An application to the asthma datasets of Genetic Analysis Workshop 12 also illustrates this gain in a real data analysis. Additionally, we compare the performances of microsatellite markers and single nucleotide polymorphisms for our approach and find that the latter clearly outperforms the former. Genet. Epidemiol. 2007. © 2007 Wiley-Liss, Inc. [source] Evolutionary-based grouping of haplotypes in association analysisGENETIC EPIDEMIOLOGY, Issue 3 2005Jung-Ying Tzeng Abstract Haplotypes incorporate more information about the underlying polymorphisms than do genotypes for individual SNPs, and are considered as a more informative format of data in association analysis. To model haplotypes requires high degrees of freedom, which could decrease power and limit a model's capacity to incorporate other complex effects, such as gene-gene interactions. Even within haplotype blocks, high degrees of freedom are still a concern unless one chooses to discard rare haplotypes. To increase the efficiency and power of haplotype analysis, we adapt the evolutionary concepts of cladistic analyses and propose a grouping algorithm to cluster rare haplotypes to the corresponding ancestral haplotypes. The algorithm determines the cluster bases by preserving common haplotypes using a criterion built on the Shannon information content. Each haplotype is then assigned to its appropriate clusters probabilistically according to the cladistic relationship. Through this algorithm, we perform association analysis based on groups of haplotypes. Simulation results indicate power increases for performing tests on the haplotype clusters when compared to tests using original haplotypes or the truncated haplotype distribution. Genet. Epidemiol. © 2005 Wiley-Liss, Inc. [source] A Combined Cluster and Interaction Model: The Hierarchical Assignment ProblemGEOGRAPHICAL ANALYSIS, Issue 3 2005Mark W. Horner This article presents a new spatial modeling approach that deals with interactions between individual geographic entities. The developed model represents a generalization of the transportation problem and the classical assignment problem and is termed the hierarchical assignment problem (HAP). The HAP optimizes the spatial flow pattern between individual origin and destination locations, given that some grouping, or aggregation of individual origins and destinations is permitted to occur. The level of aggregation is user specified, and the aggregation step is endogenous to the model itself. This allows for the direct accounting of aggregation costs in pursuit of optimal problem solutions. The HAP is formulated and solved with several sample data sets using commercial optimization software. Trials illustrate how HAP solutions respond to changes in levels of aggregation, as well as reveal the diverse network designs and allocation schemes obtainable with the HAP. Connections between the HAP and the literature on the p-median problem, cluster analysis, and hub-and-spoke networks are discussed and suggestions for future research are made. [source] Exploratory Analysis of Similarities in Solar Cycle Magnetic Phases with Southern Oscillation Index Fluctuations in Eastern AustraliaGEOGRAPHICAL RESEARCH, Issue 4 2008ROBERT G.V. BAKER Abstract There is growing interest in the role that the Sun's magnetic field has on weather and climatic parameters, particularly the ~11 year sunspot (Schwab) cycle, the ~22 yr magnetic field (Hale) cycle and the ~88 yr (Gleissberg) cycle. These cycles and the derivative harmonics are part of the peculiar periodic behaviour of the solar magnetic field. Using data from 1876 to the present, the exploratory analysis suggests that when the Sun's South Pole is positive in the Hale Cycle, the likelihood of strongly positive and negative Southern Oscillation Index (SOI) values increase after certain phases in the cyclic ~22 yr solar magnetic field. The SOI is also shown to track the pairing of sunspot cycles in ~88 yr periods. This coupling of odd cycles, 23,15, 21,13 and 19,11, produces an apparently close charting in positive and negative SOI fluctuations for each grouping. This Gleissberg effect is also apparent for the southern hemisphere rainfall anomaly. Over the last decade, the SOI and rainfall fluctuations have been tracking similar values to that recorded in Cycle 15 (1914,1924). This discovery has important implications for future drought predictions in Australia and in countries in the northern and southern hemispheres which have been shown to be influenced by the sunspot cycle. Further, it provides a benchmark for long-term SOI behaviour. [source] Influences of species, latitudes and methodologies on estimates of phenological response to global warmingGLOBAL CHANGE BIOLOGY, Issue 9 2007CAMILLE PARMESANArticle first published online: 14 AUG 200 Abstract New analyses are presented addressing the global impacts of recent climate change on phenology of plant and animal species. A meta-analysis spanning 203 species was conducted on published datasets from the northern hemisphere. Phenological response was examined with respect to two factors: distribution of species across latitudes and taxonomic affiliation or functional grouping of target species. Amphibians had a significantly stronger shift toward earlier breeding than all other taxonomic/functional groups, advancing more than twice as fast as trees, birds and butterflies. In turn, butterfly emergence or migratory arrival showed three times stronger advancement than the first flowering of herbs, perhaps portending increasing asynchrony in insect,plant interactions. Response was significantly stronger at higher latitudes where warming has been stronger, but latitude explained < 4% of the variation. Despite expectation, latitude was not yet an important predictor of climate change impacts on phenology. The only two previously published estimates of the magnitude of global response are quite different: 2.3 and 5.1 days decade,1 advancement. The scientific community has assumed this difference to be real and has attempted to explain it in terms of biologically relevant phenomena: specifically, differences in distribution of data across latitudes, taxa or time periods. Here, these and other possibilities are explored. All analyses indicate that the difference in estimated response is primarily due to differences between the studies in criteria for incorporating data. It is a clear and automatic consequence of the exclusion by one study of data on ,stable' (nonresponsive) species. Once this is accounted for, the two studies support each other, generating similar conclusions despite analyzing substantially nonoverlapping datasets. Analyses here on a new expanded dataset estimate an overall spring advancement across the northern hemisphere of 2.8 days decade,1. This is the first quantitative analysis showing that data-sampling methodologies significantly impact global (synthetic) estimates of magnitude of global warming response. [source] A comparison of published head and neck stage groupings in carcinomas of the oral cavityHEAD & NECK: JOURNAL FOR THE SCIENCES & SPECIALTIES OF THE HEAD AND NECK, Issue 8 2001Patti A. Groome PhD Abstract Background The combination of T, N, and M classifications into stage groupings is meant to facilitate a number of activities, including the estimation of prognosis and the comparison of therapeutic interventions among similar groups of cases. We tested the UICC/AJCC 5th edition stage grouping and seven other TNM-based groupings proposed for head and neck cancer for their ability to meet these expectations in a specific site: carcinomas of the oral cavity. Methods We defined four criteria to assess each grouping scheme: (1) the subgroups defined by T, N, and M that make up a given group within a grouping scheme have similar survival rates (hazard consistency); (2) the survival rates differ among the groups (hazard discrimination); (3) the prediction of cure is high (outcome prediction); and (4) the distribution of patients among the groups is balanced. We identified or derived a measure for each criterion, and the findings were summarized by use of a scoring system. The range of scores was from 0 (best) to 7 (worst). The data are population based from a prospectively gathered series in Southern Norway, with 556 patients diagnosed from 1983 through 1995. Clinical stage assignment was used, and the outcome of interest was cause-specific survival. Results Summary scores across the eight schemes ranged from 1.66 for TANIS-3 to 6.50 for UICC/AJCC-5. The TANIS-7 staging scheme performed best on the hazard consistency criterion. The Kiricuta scheme performed best on the hazard discrimination criterion. Synderman predicted outcome best overall and Berg produced the most balanced distribution of cases among its groups. Conclusions UICC/AJCC stage groupings were defined without empirical investigation. When tested, this scheme did not perform as well as any of seven empirically derived schemes we evaluated. Our results suggest that the usefulness of the TNM system could be enhanced by optimizing the design of stage groupings through empirical investigation. © 2001 John Wiley & Sons, Inc. Head Neck 23: 613,624, 2001. [source] The Diabetes Continuity of Care Scale: the development and initial evaluation of a questionnaire that measures continuity of care from the patient perspective,HEALTH & SOCIAL CARE IN THE COMMUNITY, Issue 6 2004Lisa R. Dolovich PharmD MSc Abstract The purpose of the present study was to develop and pilot test a questionnaire to assess continuity of care from the perspective of patients with diabetes. Seven patient and two healthcare-provider focus groups were conducted. These focus groups generated 777 potential items. This number was reduced to 56 items after item reduction, face validity testing and readability analysis, and to 47 items after a preliminary factor analysis. Readability was assessed as requiring 7,8 years of schooling. Sixty adult patients with diabetes completed the draft Diabetes Continuity of Care Scale (DCCS) at a single point in time to assess the validity of the instrument. Patients completed the draft DCCS again 2 weeks later to assess test,retest reliability. A provisional factor analysis and grouping according to clinical sense yielded five domains: access and getting care, care by doctor, care by other healthcare professionals, communication between healthcare professionals, and self-care. The internal consistency (Cronbach's alpha) for the whole scale was 0.89. The test,retest reliability was r = 0.73. The DCCS total score was moderately correlated with some of the measures used to establish construct validity. The DCCS could differentiate between patients who did and did not achieve specific process and clinical indicators of good diabetes care (e.g. Hba1c tested within 6 months). The development of the DCCS was centred on the patient's perspective and revealed that the patient perspective regarding continuity of care extends beyond the concept of seeing one doctor. Initial testing of this instrument demonstrates that it has promise as a reliable and valid measure in this area. [source] | ||||||||||||||||||||||||||||||||||||||||||||||||||||