Description and critical appraisal of principal components analysis (PCA) methodology applied to pulsed-field gel electrophoresis profiles of methicillin-resistant Staphylococcus aureus isolates

Principal components analysis (PCA) has been described for over 50 years; however, it is rarely applied to the analysis of epidemiological data. In this study PCA was critically appraised in its ability to reveal relationships between pulsed-field gel electrophoresis (PFGE) profiles of methicillin- resistant Staphylococcus aureus (MRSA) in comparison to the more commonly employed cluster analysis and representation by dendrograms. The PFGE type following SmaI chromosomal digest was determined for 44 multidrug-resistant hospital-acquired methicillin-resistant S. aureus (MR-HA-MRSA) isolates, two multidrug-resistant community-acquired MRSA (MR-CA-MRSA), 50 hospital-acquired MRSA (HA-MRSA) isolates (from the University Hospital Birmingham, NHS Trust, UK) and 34 community-acquired MRSA (CA-MRSA) isolates (from general practitioners in Birmingham, UK). Strain relatedness was determined using Dice band-matching with UPGMA clustering and PCA. The results indicated that PCA revealed relationships between MRSA strains, which were more strongly correlated with known epidemiology, most likely because, unlike cluster analysis, PCA does not have the constraint of generating a hierarchic classification. In addition, PCA provides the opportunity for further analysis to identify key polymorphic bands within complex genotypic profiles, which is not always possible with dendrograms. Here we provide a detailed description of a PCA method for the analysis of PFGE profiles to complement further the epidemiological study of infectious disease. © 2005 Elsevier B.V. All rights reserved.

An evaluation of task analysis techniques for industrial process control

The concept of a task is fundamental to the discipline of ergonomics. Approaches to the analysis of tasks began in the early 1900's. These approaches have evolved and developed to the present day, when there is a vast array of methods available. Some of these methods are specific to particular contexts or applications, others more general. However, whilst many of these analyses allow tasks to be examined in detail, they do not act as tools to aid the design process or the designer. The present thesis examines the use of task analysis in a process control context, and in particular the use of task analysis to specify operator information and display requirements in such systems. The first part of the thesis examines the theoretical aspect of task analysis and presents a review of the methods, issues and concepts relating to task analysis. A review of over 80 methods of task analysis was carried out to form a basis for the development of a task analysis method to specify operator information requirements in industrial process control contexts. Of the methods reviewed Hierarchical Task Analysis was selected to provide such a basis and developed to meet the criteria outlined for such a method of task analysis. The second section outlines the practical application and evolution of the developed task analysis method. Four case studies were used to examine the method in an empirical context. The case studies represent a range of plant contexts and types, both complex and more simple, batch and continuous and high risk and low risk processes. The theoretical and empirical issues are drawn together and a method developed to provide a task analysis technique to specify operator information requirements and to provide the first stages of a tool to aid the design of VDU displays for process control.

Analysis of organisational climate to improve the adequacy of primary health care in the State of Kuwait

This study covers two areas of contribution to the knowledge, firstly it tried to investigate rigourously the relationships of a number of factors believed that they may affect the climate perception, classified into three types to arrive to prove a hypothesis of the important role that qualification and personal factors play in shaping the climate perception, this is in contrast with situational factors. Secondly, the study tries to recluster the items of a wide-range applied scale for the measurement of climate named HAY in order to overcome the cross-cultural differences between the Kuwaiti and the American society, and to achieve a modified dimensions of climate for a civil service organisation in Kuwait. Furthermore, the study attempts to carry out a diagnostic test for the climate of the Ministry of Public Health in Kuwait, aiming to diagnose the perceived characteristics of the MoPH organisation, and suggests a number of areas to be given attention if an improvement is to be introduced. The study used extensively the statistical and the computer facilities to make the analysis more representing the field data, on the other hand this study is characterised by the very highly responsive rate of the main survey which would affect the findings reliability. Three main field studies are included, the first one was to conduct the main questionnaire where the second was to measure the "should be" climate by the experts of MoPH using the DELPHI technique, and the third was to conduct an extensive meeting with the very top management team in MoPH. Results of the first stage were subject to CLUSTER analysis for the reconstruction of the HAY tool, whereas comparative analysis was carried on between the results of the second and third stages on one side, the first from the other.

Magyar egyetemi hallgatók vállalkozási attitűdjei és az attitűdöket befolyásoló tényezők elemzése a GUESSS-felmérés adatai alapján - Kik is akarnak ténylegesen vállalkozni? (Entrepreneurial attitudes of the Hungarian students and the analysis of the factors influencing attitudes based on the datas of GUESSS survey – Who want to undertake really?)

A vállalkozóvá válás meghatározó tényezőinek kutatása szakmai berkekben leginkább a Szent Grál keresésére emlékeztet: már lassan azt sem tudjuk, hogy egyáltalán léteznek-e ilyen tényezők. A kutatást nehezítik a többnyire önbevallásos kérdésekre adott torzított válaszok, a szóba jöhető tényezők számossága és a vállalkozói motivációk heterogenitása a különböző demográfiai karakterisztikákkal rendelkező népesség körében. Az egyetemi hallgatók körében némileg egyszerűbb a vizsgálat, hiszen ez egy relatíve homogén minta. Ugyanakkor itt a leginkább áttételesek a hatások, és ráadásul nem a tényleges vállalkozóvá válás, hanem többnyire csak a szándékok tesztelhetők. A vállalkozóvá válás szándékát Bandura társadalmi megismerés-elmélete, Shapero elmozduláselmélete és az Ajzen-féle tervezett magatartás elmélet alapján felállított koncepcionális modell keretén belül vizsgálják és elemzik a szerzők. Arra keresik a választ, hogy az egyes vállalkozói tulajdonságok, az egyetemi környezeti tényezők és a családi háttér hogyan hatnak a vállalkozóvá válásra. A teszteléshez a 21 országra kiterjedő 2011-es GUESSS-felmérésből a magyar egyetemi/ főiskolai hallgatók 5224-es erősségű mintáját használták fel. A multimoniális regressziós vizsgálat eredményei megerősítik, hogy a vállalkozói tulajdonságok és a családban levő vállalkozó megléte mellett a vállalkozói oktatás is pozitívan befolyásolják a vállalkozásindítási szándékot. A klaszterelemzés rámutatott arra, hogy a vállalkozói szándékok, az erre ható tényezők, továbbá a választott szak és más demográfiai tényezők szempontjából a hallgatók meglehetősen heterogének. _______ The search for the determining factors to become an entrepreneur is something like searching for the Holy Grail: After many decades we do not even know if these factors exist or not. The research is difficult because the questionnaires are self esteem, the potential influential factors are numerous, and the motivations do vary across the different cohorts of population. It is easier to conduct a survey amongst university students since this sample is relatively homogenous. At the same times, the determining factors to become an entrepreneur cannot be really tested; the authors can examine mostly the attitudes and the intentions. The conceptual model of entrepreneurial intentions, developed in the paper, based on Bandura, Shaper and Ajzen. The paper is testing eight hypotheses about the influential factors of entrepreneurial intentions such as entrepreneurial traits, the university environment, and the family background. For testing the hypothesis they use a sample of 5224 Hungarian students from the GUESSS 2011 survey. According to the multinomial regression, entrepreneurial intentions are positively influenced by certain entrepreneurial traits, entrepreneur in the family, and entrepreneurship courses at the higher education institutions. The cluster analysis results underline the heterogeneity of the students in terms of entrepreneurial intentions, gender, and the major field of studies

Use of conjoint analysis to examine beliefs related to the practice of early literacy instruction

The purpose of the study was to examine the relationship between teacher beliefs and actual classroom practice in early literacy instruction. Conjoint analysis was used to measure teachers' beliefs on four early literacy factors—phonological awareness, print awareness, graphophonic awareness, and structural awareness. A collective case study format was then used to measure the correspondence of teachers' beliefs with their actual classroom practice. ^ Ninety Project READS participants were given twelve cards in an orthogonal experimental design describing students that either met or did not meet criteria on the four early literacy factors. Conjoint measurements of whether the student is an efficient reader were taken. These measurements provided relative importance scores for each respondent. Based on the relative important scores, four teachers were chosen to participate in a collective case study. ^ The conjoint results enabled the clustering of teachers into four distinct groups, each aligned with one of the four early literacy factors. K-means cluster analysis of the relative importance measurements showed commonalities among the ninety respondents' beliefs. The collective case study results were mixed. Implications for researchers and practitioners include the use of conjoint analysis in measuring teacher beliefs on the four early literacy factors. Further, the understanding of teacher preferences on these beliefs may assist in the development of curriculum design and therefore increase educational effectiveness. Finally, comparisons between teachers' beliefs on the four early literacy factors and actual instructional practices may facilitate teacher self-reflection thus encouraging positive teacher change. ^

Modelagem estatística e atribuições dos eventos de precipitação extrema na Amazônia brasileira

Intense precipitation events (IPE) have been causing great social and economic losses in the affected regions. In the Amazon, these events can have serious impacts, primarily for populations living on the margins of its countless rivers, because when water levels are elevated, floods and/or inundations are generally observed. Thus, the main objective of this research is to study IPE, through Extreme Value Theory (EVT), to estimate return periods of these events and identify regions of the Brazilian Amazon where IPE have the largest values. The study was performed using daily rainfall data of the hydrometeorological network managed by the National Water Agency (Agência Nacional de Água) and the Meteorological Data Bank for Education and Research (Banco de Dados Meteorológicos para Ensino e Pesquisa) of the National Institute of Meteorology (Instituto Nacional de Meteorologia), covering the period 1983-2012. First, homogeneous rainfall regions were determined through cluster analysis, using the hierarchical agglomerative Ward method. Then synthetic series to represent the homogeneous regions were created. Next EVT, was applied in these series, through Generalized Extreme Value (GEV) and the Generalized Pareto Distribution (GPD). The goodness of fit of these distributions were evaluated by the application of the Kolmogorov-Smirnov test, which compares the cumulated empirical distributions with the theoretical ones. Finally, the composition technique was used to characterize the prevailing atmospheric patterns for the occurrence of IPE. The results suggest that the Brazilian Amazon has six pluvial homogeneous regions. It is expected more severe IPE to occur in the south and in the Amazon coast. More intense rainfall events are expected during the rainy or transitions seasons of each sub-region, with total daily precipitation of 146.1, 143.1 and 109.4 mm (GEV) and 201.6, 209.5 and 152.4 mm (GPD), at least once year, in the south, in the coast and in the northwest of the Brazilian Amazon, respectively. For the south Amazonia, the composition analysis revealed that IPE are associated with the configuration and formation of the South Atlantic Convergence Zone. Along the coast, intense precipitation events are associated with mesoscale systems, such Squall Lines. In Northwest Amazonia IPE are apparently associated with the Intertropical Convergence Zone and/or local convection.

X-ray diffraction analysis, binocular component analysis and radiocarbon dating of sediment cores from the NW Iberian shelf system

Based on a well-established stratigraphic framework and 47 AMS-14C dated sediment cores, the distribution of facies types on the NW Iberian margin is analysed in response to the last deglacial sea-level rise, thus providing a case study on the sedimentary evolution of a high-energy, low-accumulation shelf system. Altogether, four main types of sedimentary facies are defined. (1) A gravel-dominated facies occurs mostly as time-transgressive ravinement beds, which initially developed as shoreface and storm deposits in shallow waters on the outer shelf during the last sea-level lowstand; (2) A widespread, time-transgressive mixed siliceous/biogenic-carbonaceous sand facies indicates areas of moderate hydrodynamic regimes, high contribution of reworked shelf material, and fluvial supply to the shelf; (3) A glaucony-containing sand facies in a stationary position on the outer shelf formed mostly during the last-glacial sea-level rise by reworking of older deposits as well as authigenic mineral formation; and (4) A mud facies is mostly restricted to confined Holocene fine-grained depocentres, which are located in mid-shelf position. The observed spatial and temporal distribution of these facies types on the high-energy, low-accumulation NW Iberian shelf was essentially controlled by the local interplay of sediment supply, shelf morphology, and strength of the hydrodynamic system. These patterns are in contrast to high-accumulation systems where extensive sediment supply is the dominant factor on the facies distribution. This study emphasises the importance of large-scale erosion and material recycling on the sedimentary buildup during the deglacial drowning of the shelf. The presence of a homogenous and up to 15-m thick transgressive cover above a lag horizon contradicts the common assumption of sparse and laterally confined sediment accumulation on high-energy shelf systems during deglacial sea-level rise. In contrast to this extensive sand cover, laterally very confined and maximal 4-m thin mud depocentres developed during the Holocene sea-level highstand. This restricted formation of fine-grained depocentres was related to the combination of: (1) frequently occurring high-energy hydrodynamic conditions; (2) low overall terrigenous input by the adjacent rivers; and (3) the large distance of the Galicia Mud Belt to its main sediment supplier.

A New Clustering Methodology for the Analysis of Sorted or Categorized Stimuli

This paper introduces a new stochastic clustering methodology devised for the analysis of categorized or sorted data. The methodology reveals consumers' common category knowledge as well as individual differences in using this knowledge for classifying brands in a designated product class. A small study involving the categorization of 28 brands of U.S. automobiles is presented where the results of the proposed methodology are compared with those obtained from KMEANS clustering. Finally, directions for future research are discussed.

Surface thermal analysis of North Brabant cities and neighbourhoods during heat waves

The urban heat island effect is often associated with large metropolises. However, in the Netherlands even small cities will be affected by the phenomenon in the future (Hove et al., 2011), due to the dispersed or mosaic urbanisation patterns in particularly the southern part of the country: the province of North Brabant. This study analyses the average night time land surface temperature (LST) of 21 North-Brabant urban areas through 22 satellite images retrieved by Modis 11A1 during the 2006 heat wave and uses Landsat 5 Thematic Mapper to map albedo and normalized difference temperature index (NDVI) values. Albedo, NDVI and imperviousness are found to play the most relevant role in the increase of nighttime LST. The surface cover cluster analysis of these three parameters reveals that the 12 “urban living environment” categories used in the region of North Brabant can actually be reduced to 7 categories, which simplifies the design guidelines to improve the surface thermal behaviour of the different neighbourhoods thus reducing the Urban Heat Island (UHI) effect in existing medium size cities and future developments adjacent to those cities.

Whole Genome Analysis of Gene Expression Reveals Coordinated Activation of Signaling and Metabolic Pathways during Pollen-Pistil Interactions in Arabidopsis

Plant reproduction depends on the concerted activation of many genes to ensure correct communication between pollen and pistil. Here, we queried the whole transcriptome of Arabidopsis (Arabidopsis thaliana) in order to identify genes with specific reproductive functions. We used the Affymetrix ATH1 whole genome array to profile wild-type unpollinated pistils and unfertilized ovules. By comparing the expression profile of pistils at 0.5, 3.5, and 8.0 h after pollination and applying a number of statistical and bioinformatics criteria, we found 1,373 genes differentially regulated during pollen-pistil interactions. Robust clustering analysis grouped these genes in 16 time-course clusters representing distinct patterns of regulation. Coregulation within each cluster suggests the presence of distinct genetic pathways, which might be under the control of specific transcriptional regulators. A total of 78% of the regulated genes were expressed initially in unpollinated pistil and/or ovules, 15% were initially detected in the pollen data sets as enriched or preferentially expressed, and 7% were induced upon pollination. Among those, we found a particular enrichment for unknown transcripts predicted to encode secreted proteins or representing signaling and cell wall-related proteins, which may function by remodeling the extracellular matrix or as extracellular signaling molecules. A strict regulatory control in various metabolic pathways suggests that fine-tuning of the biochemical and physiological cellular environment is crucial for reproductive success. Our study provides a unique and detailed temporal and spatial gene expression profile of in vivo pollen-pistil interactions, providing a framework to better understand the basis of the molecular mechanisms operating during the reproductive process in higher plants.

MLCut: exploring multi-level cuts in dendrograms for biological data.

Choosing a single similarity threshold for cutting dendrograms is not sufficient for performing hierarchical clustering analysis of heterogeneous data sets. In addition, alternative automated or semi-automated methods that cut dendrograms in multiple levels make assumptions about the data in hand. In an attempt to help the user to find patterns in the data and resolve ambiguities in cluster assignments, we developed MLCut: a tool that provides visual support for exploring dendrograms of heterogeneous data sets in different levels of detail. The interactive exploration of the dendrogram is coordinated with a representation of the original data, shown as parallel coordinates. The tool supports three analysis steps. Firstly, a single-height similarity threshold can be applied using a dynamic slider to identify the main clusters. Secondly, a distinctiveness threshold can be applied using a second dynamic slider to identify “weak-edges” that indicate heterogeneity within clusters. Thirdly, the user can drill-down to further explore the dendrogram structure - always in relation to the original data - and cut the branches of the tree at multiple levels. Interactive drill-down is supported using mouse events such as hovering, pointing and clicking on elements of the dendrogram. Two prototypes of this tool have been developed in collaboration with a group of biologists for analysing their own data sets. We found that enabling the users to cut the tree at multiple levels, while viewing the effect in the original data, is a promising method for clustering which could lead to scientific discoveries.

Optimization of the Ion Source-Mass Spectrometry Parameters in Non-Steroidal Anti-Inflammatory and Analgesic Pharmaceuticals Analysis by a Design of Experiments Approach

The flow rates of drying and nebulizing gas, heat block and desolvation line temperatures and interface voltage are potential electrospray ionization parameters as they may enhance sensitivity of the mass spectrometer. The conditions that give higher sensitivity of 13 pharmaceuticals were explored. First, Plackett-Burman design was implemented to screen significant factors, and it was concluded that interface voltage and nebulizing gas flow were the only factors that influence the intensity signal for all pharmaceuticals. This fractionated factorial design was projected to set a full 2(2) factorial design with center points. The lack-of-fit test proved to be significant. Then, a central composite face-centered design was conducted. Finally, a stepwise multiple linear regression and subsequently an optimization problem solving were carried out. Two main drug clusters were found concerning the signal intensities of all runs of the augmented factorial design. p-Aminophenol, salicylic acid, and nimesulide constitute one cluster as a result of showing much higher sensitivity than the remaining drugs. The other cluster is more homogeneous with some sub-clusters comprising one pharmaceutical and its respective metabolite. It was observed that instrumental signal increased when both significant factors increased with maximum signal occurring when both codified factors are set at level +1. It was also found that, for most of the pharmaceuticals, interface voltage influences the intensity of the instrument more than the nebulizing gas flowrate. The only exceptions refer to nimesulide where the relative importance of the factors is reversed and still salicylic acid where both factors equally influence the instrumental signal. Graphical Abstract ᅟ.

RELATIONSHIP BETWEEN COLUMN DENSITY AND SURFACE MIXING RATIO FOR O3 AND NO2: IMPLICATIONS FOR SATELLITE OBSERVATIONS AND THE IMPACTS OF VERTICAL MIXING

Satellites have great potential for diagnosis of surface air quality conditions, though reduced sensitivity of satellite instrumentation to the lower troposphere currently impedes their applicability. One objective of the NASA DISCOVER-AQ project is to provide information relevant to improving our ability to relate satellite-observed columns to surface conditions for key trace gases and aerosols. In support of DISCOVER-AQ, this dissertation investigates the degree of correlation between O3 and NO2 column abundance and surface mixing ratio during the four DISCOVER-AQ deployments; characterize the variability of the aircraft in situ and model-simulated O3 and NO2 profiles; and use the WRF-Chem model to further investigate the role of boundary layer mixing in the column-surface connection for the Maryland 2011 deployment, and determine which of the available boundary layer schemes best captures the observations. Simple linear regression analyses suggest that O3 partial column observations from future satellite instruments with sufficient sensitivity to the lower troposphere may be most meaningful for surface air quality under the conditions associated with the Maryland 2011 campaign, which included generally deep, convective boundary layers, the least wind shear of all four deployments, and few geographical influences on local meteorology, with exception of bay breezes. Hierarchical clustering analysis of the in situ O3 and NO2 profiles indicate that the degree of vertical mixing (defined by temperature lapse rate) associated with each cluster exerted an important influence on the shapes of the median cluster profiles for O3, as well as impacted the column vs. surface correlations for many clusters for both O3 and NO2. However, comparisons to the CMAQ model suggest that, among other errors, vertical mixing is overestimated, causing too great a column-surface connection within the model. Finally, the WRF-Chem model, a meteorology model with coupled chemistry, is used to further investigate the impact of vertical mixing on the O3 and NO2 column-surface connection, for an ozone pollution event that occurred on July 26-29, 2011. Five PBL schemes were tested, with no one scheme producing a clear, consistent “best” comparison with the observations for PBLH and pollutant profiles; however, despite improvements, the ACM2 scheme continues to overestimate vertical mixing.

Statistical Analysis of the heavy neutral Atoms measured by IBEX

We investigate the directional distribution of heavy neutral atoms in the heliosphere by using heavy neutral maps generated with the IBEX-Lo instrument over three years from 2009 to 2011. The interstellar neutral (ISN) O&Ne gas flow was found in the first-year heavy neutral map at 601 keV and its flow direction and temperature were studied. However, due to the low counting statistics, researchers have not treated the full sky maps in detail. The main goal of this study is to evaluate the statistical significance of each pixel in the heavy neutral maps to get a better understanding of the directional distribution of heavy neutral atoms in the heliosphere. Here, we examine three statistical analysis methods: the signal-to-noise filter, the confidence limit method, and the cluster analysis method. These methods allow us to exclude background from areas where the heavy neutral signal is statistically significant. These methods also allow the consistent detection of heavy neutral atom structures. The main emission feature expands toward lower longitude and higher latitude from the observational peak of the ISN O&Ne gas flow. We call this emission the extended tail. It may be an imprint of the secondary oxygen atoms generated by charge exchange between ISN hydrogen atoms and oxygen ions in the outer heliosheath.

MORPHOLOGICAL DIVERSITY OF MANGO GERMPLASM FROM THE UPPER ATHI RIVER REGION OF EASTERN KENYA: AN ANALYSIS BASED ON NON- FRUIT DESCRIPTORS

Phenotypic variation in plants can be evaluated by morphological characterization using visual attributes. Fruits have been the major descriptors for identification of different varieties of fruit crops. However, even in their absence, farmers, breeders and interested stakeholders require to distinguish between different mango varieties. This study aimed at determining diversity in mango germplasm from the Upper Athi River (UAR) and providing useful alternative descriptors for the identification of different mango varieties in the absence of fruits. A total of 20 International Plant Genetic Resources Institute (IPGRI) descriptors for mango were selected for use in the visual assessment of 98 mango accessions from 15 sites of the UAR region of eastern Kenya. Purposive sampling was used to identify farmers growing diverse varieties of mangoes. Evaluation of the descriptors was performed on-site and the data collected were then subjected to multivariate analysis including Principal Component Analysis (PCA) and Cluster analysis, one- way analysis of variance (ANOVA) and Chi square tests. Results classified the accessions into two major groups corresponding to indigenous and exotic varieties. The PCA showed the first six principal components accounting for 75.12% of the total variance. A strong and highly significant correlation was observed between the color of fully grown leaves, leaf blade width, leaf blade length and petiole length and also between the leaf attitude, color of young leaf, stem circumference, tree height, leaf margin, growth habit and fragrance. Useful descriptors for morphological evaluation were 14 out of the selected 20; however, ANOVA and Chi square test revealed that diversity in the accessions was majorly as a result of variations in color of young leaves, leaf attitude, leaf texture, growth habit, leaf blade length, leaf blade width and petiole length traits. These results reveal that mango germplasm in the UAR has significant diversity and that other morphological traits apart from fruits can be useful in morphological characterization of mango.