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Hierarchical Analysis (hierarchical + analysis)
Selected AbstractsGenetic and behavioural evidence for a city-wide supercolony of the invasive Argentine ant Linepithema humile (Mayr) (Hymenoptera: Formicidae) in southeastern AustraliaAUSTRALIAN JOURNAL OF ENTOMOLOGY, Issue 1 2009Elissa L Suhr Abstract The success of invasive ants is frequently attributed to genetic and behavioural shifts in colony structure during or after introduction. The Argentine ant (Linepithema humile), a global invader, differs in colony genetic structure and behaviour between native populations in South America and introduced populations in Europe, Japan, New Zealand and North America. However, little is known about its colony structure in Australia. We investigated the genetic structure and behaviour of L. humile across Melbourne, Victoria by quantifying variation at four microsatellite loci and assaying intraspecific aggression at neighbourhood (30,200 m), fine (1,3.3 km) and regional (5,82 km) spatial scales. Hierarchical analyses across these scales revealed that most genetic variation occurred among workers within nests (,98%). However, although low genetic differentiation occurred among workers between nests at the fine and regional scales (,2%), negligible differentiation was detected among workers from neighbouring nests. Spatial genetic autocorrelation analysis confirmed that neighbouring nests were genetically more similar to each other. Lack of aggression within and across these scales supported the view that L. humile is unicolonial and forms a large supercolony across Melbourne. Comparisons of genetic structure of L. humile among single nests sampled from Adelaide, Brisbane, Hobart and Perth with Melbourne showed no greater levels of genetic differentiation or dissimilar spatial structure, suggesting an Australia-wide supercolony. [source] Variation in Ancillary Testing among Pediatric Asthma Patients Seen in Emergency DepartmentsACADEMIC EMERGENCY MEDICINE, Issue 6 2007MHSA, Rachel M. Stanley MD Background:Variation in the management of acute pediatric asthma within emergency departments is largely unexplored. Objectives:To investigate whether ancillary testing for patients with asthma would be associated with patient, physician, and hospital characteristics. Methods:The authors performed an analysis of a subset of patients from an extensive retrospective chart review of randomly selected charts at all 25 member emergency departments of the Pediatric Emergency Care Applied Research Network. Patients with a diagnosis of asthma were selected for supplemental review and included in this study. Ancillary tests analyzed were chest radiographs and selected blood tests. Hierarchical analyses were performed to describe the associations between ancillary testing and the variables of interest. Results:A total of 12,744 chart abstractions were completed, of which 734 (6%) were patients with acute exacerbations of asthma. Overall, 302 patients with asthma (41%) had ancillary testing. Of the 734 patients with asthma, 198 (27%) had chest radiographs and 104 (14%) had blood tests. Chest radiographs were more likely to be ordered in patients with fever. Less blood testing was associated with physician subspecialty training in pediatric emergency medicine, patients treated at children's hospitals, higher patient oxygen saturation, and patient disposition to home. Conclusions:Ancillary testing occurred in more than one third of children with asthma, with chest radiographs ordered most frequently. Efforts to reduce the use of chest radiographs should target the management of febrile patients with asthma, whereas efforts to reduce blood testing should target providers without subspecialty training in pediatric emergency medicine and patients treated in nonchildren's hospitals who are more ill. [source] Hierarchical analysis of large-scale two-dimensional gel electrophoresis experimentsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 10 2003Amit Rubinfeld Abstract Large-scale two-dimensional gel experiments have the potential to identify proteins that play an important role in elucidating cell mechanisms and in various stages of drug discovery. Such experiments, typically including hundreds or even thousands of related gels, are notoriously difficult to perform, and analysis of the gel images has until recently been virtually impossible. In this paper we describe a scalable computational model that permits the organization and analysis of a large gel collection. The model is implemented in Compugen's Z4000Ô system. Gels are organized in a hierarchical, multidimensional data structure that allow the user to view a large-scale experiment as a tree of numerous simpler experiments, and carry out the analysis one step at a time. Analyzed sets of gels form processing units that can be combined into higher level units in an iterative framework. The different conditions at the core of the experiment design, termed the dimensions of the experiment, are transformed from a multidimensional structure to a single hierarchy. The higher level comparison is performed with the aid of a synthetic "adaptor" gel image, called a Raw Master Gel (RMG). The RMG allows the inclusion of data from an entire set of gels to be presented as a gel image, thereby enabling the iterative process. Our model includes a flexible experimental design approach that allows the researcher to choose the condition to be analyzed a posteriori. It also enables data reuse, the performing of several different analysis designs on the same experimental data. The stability and reproducibility of a protein can be analyzed by tracking it up or down the hierarchical dimensions of the experiment. [source] Staff- and School-Level Predictors of School Organizational Health: A Multilevel AnalysisJOURNAL OF SCHOOL HEALTH, Issue 6 2007Katherine Bevans PhD ABSTRACT Background:, An organizationally healthy school environment is associated with favorable student and staff outcomes and thus is often targeted by school improvement initiatives. However, few studies have differentiated staff-level from school-level predictors of organizational health. Social disorganization theory suggests that school-level factors, such as faculty turnover, student mobility, and concentration of student poverty, would be negatively associated with school organizational health, but these relationships may be moderated by staff-level factors. Methods:, The present study examined the association among school- and staff-level predictors of staff-perceived school organizational health (eg, academic emphasis, collegial leadership, and staff affiliation), as measured by the Organizational Health Inventory. Results:, Multilevel analyses on data from 1395 staff across 37 elementary schools indicated that school membership accounted for between 26% and 35% of the variance in different components of staff-perceived organizational health. Two-level hierarchical analyses indicated that both school- and staff-level characteristics are important predictors of organizational health. Furthermore, some school and staff characteristics interacted to predict staff affiliation and collegial leadership. Conclusions:, Findings suggest that factors at both the school and staff level are important potential targets for school improvement. Administrators aiming to improve relationships among staff members should be cognizant of staff-level characteristics (race, age, and role in school) associated with less favorable perceptions of the school environment, whereas efforts to enhance student work ethic and discipline should target schools with specific school-level characteristics (high rates of faculty turnover and student mobility). [source] Study of GM immunoglobulin allotypic system in Berbers and Arabs from MoroccoAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 1 2006C. Coudray The GM immunoglobulin allotype polymorphism was investigated in four Moroccan populations: three Berber groups from Khenifra (Middle Atlas), Amizmiz (High Atlas), and Bouhria (Beni Snassen) and one Arabic-speaking sample from the Doukkala area (Abda, Chaouia, Doukkali, and Tadla districts in south-central Morocco). In order to characterize the genetic relationships between the populations, our results were compared with those obtained for other North African groups (from Morocco, Algeria, Tunisia, and Niger) and for Middle-East Africans, sub-Saharans, and Southwest Europeans. Based on GM haplotype frequencies, Factorial Correspondence Analyses, FST significance testing, and hierarchical analyses of variance were performed. Our results reveal that Moroccan populations have heterogeneous GM profiles with high frequencies of GM haplotypes in Europeans (from 76% for Doukkala to 88% for Bouhria) and relatively high frequencies of GM haplotypes in sub-Saharans (from 11% for Bouhria to 23% for Amizmiz). The genetic diversity observed among Moroccans is not significantly correlated with either geographic or linguistic differentiation. In spite of their cultural and historical differentiation, we did not discover any significant genetic differences between Berbers and Arabic-speakers from Morocco. However, when large geographical areas are considered, our population samples are integrated in the North African GM variation, significantly distant from sub-Saharan groups but with a close relationship with Southwest European populations. Am. J. Hum. Biol. 18:23,34, 2006. © 2005 Wiley-Liss, Inc. [source] Scales of association: hierarchical linear models and the measurement of ecological systemsECOLOGY LETTERS, Issue 6 2007Sean M. McMahon Abstract A fundamental challenge to understanding patterns in ecological systems lies in employing methods that can analyse, test and draw inference from measured associations between variables across scales. Hierarchical linear models (HLM) use advanced estimation algorithms to measure regression relationships and variance,covariance parameters in hierarchically structured data. Although hierarchical models have occasionally been used in the analysis of ecological data, their full potential to describe scales of association, diagnose variance explained, and to partition uncertainty has not been employed. In this paper we argue that the use of the HLM framework can enable significantly improved inference about ecological processes across levels of organization. After briefly describing the principals behind HLM, we give two examples that demonstrate a protocol for building hierarchical models and answering questions about the relationships between variables at multiple scales. The first example employs maximum likelihood methods to construct a two-level linear model predicting herbivore damage to a perennial plant at the individual- and patch-scale; the second example uses Bayesian estimation techniques to develop a three-level logistic model of plant flowering probability across individual plants, microsites and populations. HLM model development and diagnostics illustrate the importance of incorporating scale when modelling associations in ecological systems and offer a sophisticated yet accessible method for studies of populations, communities and ecosystems. We suggest that a greater coupling of hierarchical study designs and hierarchical analysis will yield significant insights on how ecological processes operate across scales. [source] Fine scale genetic population structure of the freshwater and Omono types of nine-spined stickleback Pungitius pungitius (L.) within the Omono River system, JapanJOURNAL OF FISH BIOLOGY, Issue 2006T. Tsuruta The fine scale geographic population structure of two types of nine-spined stickleback Pungitius pungitius (the widely distributed freshwater type and a local endemic, the Omono type) within the Omono River system, Japan, was investigated. A principal components analysis of allele frequencies and neighbour-joining tree for pair-wise FST values, based on 10 allozyme loci, revealed that the Omono type was comprised of four regional groups with relatively high genetic divergence. This grouping was also supported by hierarchical analysis of molecular variance (AMOVA) with a higher variance component among the regional groups, and by an exact test with significant genotypic differentiation for all sample pairs among the regional groups. Moreover, in the clustering of individuals using the Bayesian method, most of individuals in each regional group were assigned the corresponding cluster. On the other hand, there were less pronounced regional groups of the freshwater type, although AMOVA, exact test for genotypic differentiation and Bayesian analysis indicated genetic divergence between two sampling sites in lower reach of the Omono River and other sites. The results suggest that the Omono type represented an earlier colonization, with subsequent invasion of the freshwater type. [source] Detection of bacteria aided by immuno-nanoparticlesJOURNAL OF RAMAN SPECTROSCOPY, Issue 11 2007Ghinwa Naja Abstract Magnetic immuno-nanorice particles were used for the capture and detection of Escherichia coli (E. coli) bacteria. The selectivity of the method was attained by attaching a specific anti- E. coli antibody on the surface of the nanorice, binding exclusively to E. coli. The antibody attachment to the nanorice (60% sorption efficiency) took place through protein-A molecules (82% uptake). Once E. coli was captured, the immuno-nanorice-bacteria complex was separated from the solution using the magnetic property of the nanorice. The detection of bacteria sorbed onto the immuno-nanorice was accomplished using the ultra-violet resonance Raman (UVRR) method, detecting single bacterial cells. Specific information concerning the aromatic residues tyrosine (Tyr), phenylalanine (Phe) and tryptophan (Trp) was derived. The discriminant function and cluster hierarchical analysis confirmed the specific and reliable bacteria-detection capabilities. Copyright © 2007 John Wiley & Sons, Ltd. [source] Taxonomic revision of Mecyclothorax Sharp (Coleoptera, Carabidae) of Hawaii Island: abundant genitalic variation in a nascent island radiationMITTEILUNGEN AUS DEM MUSEUM FUER NATURKUNDE IN BERLIN-DEUTSCHE ENTOMOLOGISCHE ZEITSCHRIFT, Issue 1 2008James K. Liebherr Abstract The Hawaii Island fauna of Mecyclothorax Sharp, 1903 is taxonomically revised and found to comprise 30 species, 18 newly described: M. gagnei sp. n., M. nitidus sp. n., M. maunakukini sp. n., M. punakukini sp. n., M. kaukukini sp. n., M. perivariipes sp. n., M. aa sp. n., M. giffini sp. n., M. hephaestus sp. n., M. funebris sp. n., M. granulipennis sp. n., M. rufipennis sp. n., M. blackburnianus sp. n., M. swezeyi sp. n., M. sinuosus sp. n., M. williamsi sp. n., M. purpuripennis sp. n., and M. footei sp. n. New synonymies include: Mecyclothorax parvus Britton, 1948 = M. subunctus (Perkins), 1917; Thriscothorax munroi Perkins, 1937 = M. karschi (Blackburn), 1882; Thriscothorax gracilis Sharp, 1903 and Mecyclothorax proximus Britton, 1948 = M. konanus Sharp, 1903; Mecyclothorax terminalis Britton, 1948 = M. discedens (Sharp) 1903. Mecyclothorax vulcanus (Blackburn) was described from a mixed series, with the cryptic sibling species M. hephaestus newly described to correct the partial misidentification. Species delimitation for the highly variable M. konanus is achieved using a hierarchical analysis based on infraspecifically variable attributes. Extensive male genitalic variation is documented within M. konanus and M. deverilli (Blackburn), and also among the cryptic sibling species pair M. variipes (Blackburn) and M. perivariipes. The observed variation is consistent with various hypotheses of sexual selection, but not with the genitalic lock and key hypothesis. Areas of endemism are tentatively proposed based on the most restricted distributions of Hawaii Island Mecyclothorax, with various flanks of Mauna Kea and Mauna Loa volcanoes identified as distinctive areas. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Geological barriers and restricted gene flow in the holarctic skipper Hesperia comma (Hesperiidae)MOLECULAR ECOLOGY, Issue 11 2004M. L. FORISTER Abstract Patterns of genetic variation within a species may be a consequence of historical factors, such as past fragmentation, as well as current barriers to gene flow. Using sequence data from the mitochondrial cytochrome oxidase subunit II region (COII) and the nuclear gene wingless, we conducted a phylogeographical study of the holarctic skipper Hesperia comma to elucidate patterns of genetic diversity and to infer historical and contemporary processes maintaining genetic variation. One hundred and fifty-one individuals were sampled from throughout North America and Eurasia, focusing on California and adjacent regions in the western United States where morphological diversity is highest compared to the rest of the range. Analyses of sequence data obtained from both genes revealed a well-supported division between the Old and New World. Within western North America, wingless shows little geographical structure, while a hierarchical analysis of genetic diversity of COII sequences indicates three major clades: a western clade in Oregon and Northern California, an eastern clade including the Great Basin, Rocky Mountains and British Columbia, and a third clade in southern California. The Sierra Nevada and the Transverse Ranges appear to be the major barriers to gene flow for H. comma in the western United States. Relatively reduced haplotype diversity in Eurasia compared to North America suggests that populations on the two continents have been affected by different historical processes. [source] A hierarchical analysis of transcriptome alterations in intrauterine growth restriction (IUGR) reveals common pathophysiological pathways in mammals,THE JOURNAL OF PATHOLOGY, Issue 3 2007C Buffat Abstract Intra-uterine growth restriction (IUGR) is a frequent disease, affecting up to 10% of human pregnancies and responsible for increased perinatal morbidity and mortality. Moreover, low birth weight is an important cause of the metabolic syndrome in the adult. Protein depletion during the gestation of rat females has been widely used as a model for human IUGR. By transcriptome analysis of control and protein-deprived rat placentas, we were able to identify 2543 transcripts modified more than 2.5 fold (1347 induced and 1196 repressed). Automatic functional classification enabled us to identify clusters of induced genes affecting chromosome structure, transcription, intracellular transport, protein modifications and apoptosis. In particular, we suggest the existence of a complex balance regulating apoptosis. Among repressed genes, we noted several groups of genes involved in immunity, signalling and degradation of noxious chemicals. These observations suggest that IUGR placentas have a decreased resistance to external aggression. The promoters of the most induced and most repressed genes were contrasted for their composition in putative transcription factor binding sites. There was an over-representation of Znfinger (ZNF) proteins and Pdx1 (pancreatic and duodenal homeobox protein 1) putative binding sites. Consistently, Pdx1 and a high proportion of ZNF genes were induced at the transcriptional level. A similar analysis of ZNF promoters showed an increased presence of putative binding sites for the Tata box binding protein (Tbp). Consistently again, we showed that the Tbp and TBP-associated factors (Tafs) were up-regulated in IUGR placentas. Also, samples of human IUGR and control placentas showed that human orthologous ZNFs and PDX1 were transcriptionnally induced, especially in non-vascular IUGR. Immunohistochemistry revealed increased expression of PDX1 in IUGR human placentas. In conclusion, our approach permitted the proposition of hypotheses on a hierarchy of gene inductions/repressions leading to massive transcriptional alterations in the IUGR placenta, in humans and in rodents. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Testing hypotheses of speciation in the Plethodon jordani species complex with allozymes and mitochondrial DNA sequencesBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2006DAVID W. WEISROCK Salamander populations of the Plethodon jordani species complex form a challenging system for applying the general lineage concept of species to diagnose population-level lineages. The present study reports and analyses mitochondrial-DNA haplotypes (,1200 nucleotide bases from the genes encoding ND2, tRNATrp, and tRNAAla from 438 salamanders) from 100 populations representing six species of the P. jordani complex (Plethodon amplus, Plethodon cheoah, Plethodon jordani, Plethodon meridianus, Plethodon metcalfi, and Plethodon montanus) with comparative analyses of previously published allozymic data to reconstruct the evolutionary history of this group and to diagnose species lineages. Analyses of mitochondrial haplotypic data include nested-cladistic analysis of phylogeography, analysis of molecular variance, hierarchical analysis of nucleotide-diversity measures, and likelihood-based estimates of recent temporal changes in population size. New analyses of allozymic data include multidimensional scaling and principal component analyses, and both data sets are analysed and compared for congruent genetic structure using Mantel correlation tests. These analyses in combination identify the six named species as distinct evolutionary lineages despite sporadic genetic exchanges among them and some discordance between mitochondrial DNA and allozymic markers. Sexual isolation is not complete for any pair of these six species, but they replace each other geographically and appear to block the geographical spreading of their neighbours. The P. jordani complex is a strong study system for investigating the genetic and ecological processes responsible for vicariant speciation. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89, 25,51. [source] Influence of private practice setting and physician characteristics on the use of breast cancer adjuvant chemotherapy for elderly women,,CANCER, Issue 17 2009Dawn L. Hershman MD Abstract BACKGROUND: Although >70% of younger women with nonmetastatic breast cancer (BC) received adjuvant chemotherapy, only approximately 15% to 20% of elderly women with BC received chemotherapy. The decision to treat may be associated with nonmedical factors, such as patient, physician, or practice characteristics. In the current study, the association between oncologist characteristics and the receipt of chemotherapy in elderly women with BC was evaluated. METHODS: Women aged >65 years who were diagnosed with American Joint Committee on Cancer stages I to III BC between 1991 and 2002 were identified in the Surveillance, Epidemiology, and End Results-Medicare database. The Physician Unique Identification Number was linked to the American Medical Association Masterfile to obtain information on oncologists. Investigated was the association between demographic, tumor, and oncologist-related factors and the receipt of chemotherapy, using Generalized Estimating Equations to control for clustering. Patients were defined as low risk (estrogen/progesterone receptor positive, stage I/II disease) and high risk (estrogen/progesterone receptor-negative, stage II/III disease). RESULTS: Of 42,544 women identified, 8714 (20%) were treated with adjuvant chemotherapy. In a hierarchical analysis, women who underwent chemotherapy were more likely be treated by oncologists primarily employed in a private practice (odds ratio [OR], 1.40; 95% confidence interval [95% CI], 1.23-1.59) and who graduated after 1975 (OR, 1.12; 95% CI, 1.01-1.26) and were less likely to have an oncologist trained in the United States (OR, 0.83; 95% CI, 0.74-0.93). The association between a private practice setting and the receipt of chemotherapy was found to be similar for patients at high risk (OR, 1.55) and low risk (OR, 1.35) for cancer recurrence. CONCLUSIONS: Elderly women with BC treated by oncologists who were employed in a private practice were more likely to receive chemotherapy. Efforts to determine whether these associations reflected experience, practice setting, insurance type, or other economic incentives are warranted. Cancer 2009. Published 2009 by the American Cancer Society. [source] | ||||||||||||||||||||||||||||