TaNF-YC11, one of the light-upregulated NF-YC members in Triticum aestivum, is co-regulated with photosynthesis-related genes

NF-Y is a heterotrimeric transcription factor complex. Each of the NF-Y subunits (NF-YA, NF-YB and NF-YC) in plants is encoded by multiple genes. Quantitative RT-PCR analysis revealed that five wheat NF-YC members (TaNF-YC5, 8, 9, 11 & 12) were upregulated by light in both the leaf and seedling shoot. Co-expression analysis of Affymetrix wheat genome array datasets revealed that transcript levels of a large number of genes were consistently correlated with those of the TaNF-YC11 and TaNF-YC8 genes in 3-4 separate Affymetrix array datasets. TaNF-YC11-correlated transcripts were significantly enriched with the Gene Ontology term photosynthesis. Sequence analysis in the promoters of TaNF-YC11-correlated genes revealed the presence of putative NF-Y complex binding sites (CCAAT motifs). Quantitative RT-PCR analysis of a subset of potential TaNF-YC11 target genes showed that ten out of the thirteen genes were also light-upregulated in both the leaf and seedling shoot and had significantly correlated expression profiles with TaNF-YC11. The potential target genes for TaNF-YC11 include subunit members from all four thylakoid membrane bound complexes required for the conversion of solar energy into chemical energy and rate limiting enzymes in the Calvin cycle. These data indicate that TaNF-YC11 is potentially involved in regulation of photosynthesis-related genes.

The Chilean wheat market and its price support mechanism : a spatial market integration analysis

This research investigates the spatial market integration of the Chilean wheat market in relation with its most representative international markets by using a vector error correction model (VECM) and how a price support policy, as a price band, affect it. The international market was characterized by two relevant wheat prices: PAN from Argentina and Hard Red Winter from the United States. The spatial market integration level, expressed in the error correction term (ECT), allowed concluding that there is a high integration degree among these markets with a variable influence of the price band mechanism mainly related with its estimation methodology. Moreover, this paper showed that Chile can be seen as price taker as long as the speed of its adjustment to international shocks, being these reactions faster than in the United States and Argentina. Finally, the results validated the "Law of the One Price", which assumes price equalization across all local markets in the long run.

A transcription factor map as revealed by a genome-wide gene expression analysis of whole-blood mRNA transcriptome in multiple sclerosis

Background Several lines of evidence suggests that transcription factors are involved in the pathogenesis of Multiple Sclerosis (MS) but a complete mapping the whole network has been elusive. One of the reasons is that there are several clinical subtypes of MS and transcription factors which may be involved in one subtype may not be in others. We investigated the possibility that this network could be mapped using microarray technologies and modern bioinformatics methods on a dataset from whole blood in 99 untreated MS patients (36 Relapse Remitting MS, 43 Primary Progressive MS, and 20 Secondary Progressive MS) and 45 age-matched healthy controls, Methodology/Principal Findings We have used two different analytical methodologies: a differential expression analysis and a differential co-expression analysis, which have converged on a significant number of regulatory motifs that seem to be statistically overrepresented in genes which are either differentially expressed (or differentially co-expressed) in cases and controls (e.g. V$KROX_Q6, p-value < 3.31E-6; V$CREBP1_Q2, p-value < 9.93E-6, V$YY1_02, p-value < 1.65E-5). Conclusions/significance: Our analysis uncovered a network of transcription factors that potentially dysregulate several genes in MS or one or more of its disease subtypes. Analysing the published literature we have found that these transcription factors are involved in the early T-lymphocyte specification and commitment as well as in oligodendrocytes dedifferentiation and development. The most significant transcription factors motifs were for the Early Growth response EGR/KROX family, ATF2, YY1 (Yin and Yang 1), E2F-1/DP-1 and E2F-4/DP-2 heterodimers, SOX5, and CREB and ATF families.

Mixed data types and the use of pattern analysis on the Australian groundnut germplasm data

Data in germplasm collections contain a mixture of data types; binary, multistate and quantitative. Given the multivariate nature of these data, the pattern analysis methods of classification and ordination have been identified as suitable techniques for statistically evaluating the available diversity. The proximity (or resemblance) measure, which is in part the basis of the complementary nature of classification and ordination techniques, is often specific to particular data types. The use of a combined resemblance matrix has an advantage over data type specific proximity measures. This measure accommodates the different data types without manipulating them to be of a specific type. Descriptors are partitioned into their data types and an appropriate proximity measure is used on each. The separate proximity matrices, after range standardisation, are added as a weighted average and the combined resemblance matrix is then used for classification and ordination. Germplasm evaluation data for 831 accessions of groundnut (Arachis hypogaea L.) from the Australian Tropical Field Crops Genetic Resource Centre, Biloela, Queensland were examined. Data for four binary, five ordered multistate and seven quantitative descriptors have been documented. The interpretative value of different weightings - equal and unequal weighting of data types to obtain a combined resemblance matrix - was investigated by using principal co-ordinate analysis (ordination) and hierarchical cluster analysis. Equal weighting of data types was found to be more valuable for these data as the results provided a greater insight into the patterns of variability available in the Australian groundnut germplasm collection. The complementary nature of pattern analysis techniques enables plant breeders to identify relevant accessions in relation to the descriptors which distinguish amongst them. This additional information may provide plant breeders with a more defined entry point into the germplasm collection for identifying sources of variability for their plant improvement program, thus improving the utilisation of germplasm resources.

Multiscale analysis of factors that affect the distribution of sharks throughout the northern Gulf of Mexico

Identification of the spatial scale at which marine communities are organized is critical to proper management, yet this is particularly difficult to determine for highly migratory species like sharks. We used shark catch data collected during 2006–09 from fishery-independent bottom-longline surveys, as well as biotic and abiotic explanatory data to identify the factors that affect the distribution of coastal sharks at 2 spatial scales in the northern Gulf of Mexico. Centered principal component analyses (PCAs) were used to visualize the patterns that characterize shark distributions at small (Alabama and Mississippi coast) and large (northern Gulf of Mexico) spatial scales. Environmental data on temperature, salinity, dissolved oxygen (DO), depth, fish and crustacean biomass, and chlorophyll-a (chl-a) concentration were analyzed with normed PCAs at both spatial scales. The relationships between values of shark catch per unit of effort (CPUE) and environmental factors were then analyzed at each scale with co-inertia analysis (COIA). Results from COIA indicated that the degree of agreement between the structure of the environmental and shark data sets was relatively higher at the small spatial scale than at the large one. CPUE of Blacktip Shark (Carcharhinus limbatus) was related positively with crustacean biomass at both spatial scales. Similarly, CPUE of Atlantic Sharpnose Shark (Rhizoprionodon terraenovae) was related positively with chl-a concentration and negatively with DO at both spatial scales. Conversely, distribution of Blacknose Shark (C. acronotus) displayed a contrasting relationship with depth at the 2 scales considered. Our results indicate that the factors influencing the distribution of sharks in the northern Gulf of Mexico are species specific but generally transcend the spatial boundaries used in our analyses.

The vibrational spectra and the normal coordinate analysis of thiocarbonye halides /|nby C. R. Subramaniam. -- 260 St. Catharines, Ont. : [s. n.],

The infrared and the Raman spectra of eSelF has been obtained for the first time and has been analysed to give the in-plane normal vibrational frequencies of the molecule, in the ground state. A normal co-ordinate analysis has been carried out for the molecules CSF2, CSClF and eSel 2 using a Urey-Bradley type of potential function and the elements of the [L] matrix elements, the distribution of the potential energy in Urey-Bradley space, and the displacement vector diagrams for the normal modes of vibration for these molecules, have been obtained. The bond for~e constants obtained through the normal co-ordinate analysis, have given some interesting results. The stretching force constant, Kes ' varies markedly with halogen substitution and the force constants KeF and Keel also vary with substitution.

Perfil de mercado de la Unión Europea y los países de la EFTA

El presente trabajo de grado busca evaluar el perfil del mercado de la Unión Europea y los países de la EFTA para identificar las oportunidades comerciales de Colombia, más específicamente en los siguientes países: Suiza, Noruega, Liechtenstein, Islandia, Republica Checa, Rumania y Suecia. A través de esta investigación se realizó un análisis de los 25 productos más exportados de Colombia a cada uno de los países estudiados, tomando en cuenta sus códigos arancelarios. Adicionalmente, se evaluaron las balanzas comerciales de cada uno de los países, las tendencias de las exportaciones Colombianas de los últimos años, y las posibles oportunidades de mercados teniendo en cuenta las necesidades de importaciones detalladas de cada país europeo. A partir de la información encontrada la investigación se concentró en la proveniencia exacta del departamento Colombiano que hacia las exportaciones de los 25 productos más representativos a cada uno de los países evaluados. Teniendo en cuenta esta información, se evaluó por departamento, las oportunidades y perfiles de mercado de exportación hacia Suiza, Noruega, Liechtenstein, Islandia, Republica Checa, Rumania y Suecia. Finalmente se identificaron los 10 productos más exportados de Colombia a cada uno de los países analizados, con el fin de enfocar las mejoras y potencializar las exportaciones de estos productos a los países europeos evaluados. Adicionalmente durante la investigación se realizan recomendaciones específicas por país y al final del documento se encuentran las conclusiones generales y recomendaciones principales para futuras exportaciones de Colombia a los países de la EFTA, República Checa, Rumania y Suecia.

Analysis Scheme in the Ensemble Kalman Filter

This paper discusses an important issue related to the implementation and interpretation of the analysis scheme in the ensemble Kalman filter . I t i s shown that the obser vations must be treated as random variables at the analysis steps. That is, one should add random perturbations with the correct statistics to the obser vations and generate an ensemble of obser vations that then is used in updating the ensemble of model states. T raditionally , this has not been done in previous applications of the ensemble Kalman filter and, as will be shown, this has resulted in an updated ensemble with a variance that is too low . This simple modification of the analysis scheme results in a completely consistent approach if the covariance of the ensemble of model states is interpreted as the prediction error covariance, and there are no further requirements on the ensemble Kalman filter method, except for the use of an ensemble of sufficient size. Thus, there is a unique correspondence between the error statistics from the ensemble Kalman filter and the standard Kalman filter approach

Lobectomia por carcinoma brônquico : análise das co-morbidades e o seu impacto na morbi-mortalidade pós-operatória

Objetivo: Analisar o impacto das co-morbidades no desempenho pós-operatório de lobectomia por carcinoma brônquico. Pacientes e Métodos: Entre Janeiro de 1998 e Dezembro de 2004, foram estudados retrospectivamente 493 pacientes submetidos à lobectomia por carcinoma brônquico, dentre os quais 305 preencheram os critérios de inclusão. Todos os pacientes foram submetidos à lobectomias com técnica cirúrgica semelhante. Foi realizada análise das co-morbidades de forma a categorizar os pacientes nas escalas de Torrington-Henderson (PORT) e de Charlson, estabelecendo-se assim grupos de risco para complicações e óbito. Resultados: a mortalidade operatória foi 2,9% e o índice de complicações de 44%. O escape aéreo prolongado foi a complicação mais freqüente (20.6%). A análise univariada mostrou que sexo, idade, tabagismo, terapia neoadjuvante e diabetes apresentaram impacto significativo na incidência de complicações. O índice de massa corporal (23,8 ± 4,4), o VEF1 (74,1±24%), bem como a relação VEF1/CVF (0,65 ± 0,1) foram fatores preditivos da ocorrência de complicações. Ambas as escalas de Charlson e PORT foram eficazes na identificação de grupos de risco e na relação com a morbi-mortalidade (p=0,001 e p<0,001). A análise multivariada identificou que o IMC e o índice de Charlson foram os principais determinantes de complicações, enquanto que o escape aéreo prolongado foi o principal fator envolvido na mortalidade (p=0,01). Conclusão: Valores reduzidos de VEF1, VEF1/CVF e IMC baixo, assim como graus 3-4 de Charlson, e 3 de PORT estão associados a maior número de complicações após lobectomias por carcinoma brônquico. Nesta amostra, o escape aéreo persistente esteve fortemente associado à mortalidade.

Análise do modelo de gestão implantado no Centro de Atenção Psicossocial CAPS II OESTE de 1995 a 2005, situado no distrito sanitário Oeste do município de Natal/RN, à luz da Co-gestão

This dissertation has as aim the praxis of co-management of the health service of CAPS II OESTE of Natal-RN, where health workers, family members got to materialize guidelines and principles of psychiatric Brazilian reform in real possibilities of subjectivity construction, whereas they changed social relations in daily life. The path chosen to record was from testimonials and contributions of those who meant their done. Redeeming this story from social representations of the majority of their builders was an instigating, delicate and rewarding task, emphasizing the living memory, rebuilt in a line of time which could not be found in simple documentary collections. Mainly, by knowing that service routine was intense and had as characteristic the singular mobility itself from a creation process and therefore not always its dynamic allowed adequate records. At the same time, from this occurred the field and bibliographic research which allowed the detailed information from the prior milestones and motivated to the practice here reported. The rereading of concepts in an interface with the reports of the interviewees enabled the verification that the model of mental health advocated by psychiatric reform was understood. Once noticed the presence of the beliefs and values of people in motivating energy for the progress of reform, it has gone to fetch theoretical subsidies of administrative order to understand how they saw this building and that uniqueness has been printed. The theoretical way and praxis have tracked here has allowed to analyze how occurred such a process of production and subjectivity and collectives that when organize enabled themselves for analysis and intervention, including in crisis situations. Therefore, it was revealed that ethical and multi-disciplinarity, the humanitarian sense, the coresponsibility, co-production and horizontal management were the key factors for spread from a changing protagonist. One can thus conclude that co-management from that collective has been multi-disciplinary weaving a cross

Uso de recursos e padrão de co-ocorrência com insetos predadores em comunidades sub-tropicais de girinos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudos de Análise de Cocitação de Autores: uma abordagem teórico-metodológica para a compreensão de um domínio

This piece of research aims at analyzing the absolute and relative co-citation indicators, especially Salton’s Cosine and comparing the contribution of these indicators to the understanding of a domain, applying them to the universe of "Metric Studies" at the BRAPCI base. It also aims at presenting the co-citation network generated from the absolute frequencies and highlighting the groupings of co-cited authors, depending on the relative values, integrating and explaining the information from the two indexes. The domain analysis, by means of its 11 approaches, including “Bibliometric Studies”, focuses on the science characterization and evaluation, in that it allows us to identify and to analyze the conditions under which the scientific knowledge is constructed and socialized. In these studies, the contribution of citation and co-citation analysis is highlighted. Of the total of 147 articles retrieved at BRAPCI base, the authors cited in at least 11 articles, in a total of 38 researchers, were selected. The 38 x 38 symmetric matrix with the absolute frequencies of co-citation and the matrix with the relative values of Salton’s Cosine were generated. The co-citation network with absolute frequency values were constructed, through Ucinet software. Cluster analysis of data with relative values wer performed, using the SPSS software. Significant differences between the absolute and relative indexes, with some high absolute values of co-citation were observed; when considered in relation to the presence of each author, their significance is decreased. As to the generated network, seven groups were determined, in which only one is established for close themes and comes from co-citations in the original sense of the term. Five groups present closeness in absolute and relative indicators. It can be concluded about the importance of the studies of authors' co-citation analysis, which associate the two indexes, absolute and relative, in order to visualize and understand the underlying structures of a scientific domain.

Analysis of Phenotypic Variation in Childhood Wheezing Disorders

Recurrent wheezing or asthma is a common problem in children that has increased considerably in prevalence in the past few decades. The causes and underlying mechanisms are poorly understood and it is thought that a numb er of distinct diseases causing similar symptoms are involved. Due to the lack of a biologically founded classification system, children are classified according to their observed disease related features (symptoms, signs, measurements) into phenotypes. The objectives of this PhD project were a) to develop tools for analysing phenotypic variation of a disease, and b) to examine phenotypic variability of wheezing among children by applying these tools to existing epidemiological data. A combination of graphical methods (multivariate co rrespondence analysis) and statistical models (latent variables models) was used. In a first phase, a model for discrete variability (latent class model) was applied to data on symptoms and measurements from an epidemiological study to identify distinct phenotypes of wheezing. In a second phase, the modelling framework was expanded to include continuous variability (e.g. along a severity gradient) and combinations of discrete and continuo us variability (factor models and factor mixture models). The third phase focused on validating the methods using simulation studies. The main body of this thesis consists of 5 articles (3 published, 1 submitted and 1 to be submitted) including applications, methodological contributions and a review. The main findings and contributions were: 1) The application of a latent class model to epidemiological data (symptoms and physiological measurements) yielded plausible pheno types of wheezing with distinguishing characteristics that have previously been used as phenotype defining characteristics. 2) A method was proposed for including responses to conditional questions (e.g. questions on severity or triggers of wheezing are asked only to children with wheeze) in multivariate modelling.ii 3) A panel of clinicians was set up to agree on a plausible model for wheezing diseases. The model can be used to generate datasets for testing the modelling approach. 4) A critical review of methods for defining and validating phenotypes of wheeze in children was conducted. 5) The simulation studies showed that a parsimonious parameterisation of the models is required to identify the true underlying structure of the data. The developed approach can deal with some challenges of real-life cohort data such as variables of mixed mode (continuous and categorical), missing data and conditional questions. If carefully applied, the approach can be used to identify whether the underlying phenotypic variation is discrete (classes), continuous (factors) or a combination of these. These methods could help improve precision of research into causes and mechanisms and contribute to the development of a new classification of wheezing disorders in children and other diseases which are difficult to classify.

Species interactions and random dispersal rather than habitat filtering drive community assembly during early plant succession

Theory on plant succession predicts a temporal increase in the complexity of spatial community structure and of competitive interactions: initially random occurrences of early colonising species shift towards spatially and competitively structured plant associations in later successional stages. Here we use long-term data on early plant succession in a German post mining area to disentangle the importance of random colonisation, habitat filtering, and competition on the temporal and spatial development of plant community structure. We used species co-occurrence analysis and a recently developed method for assessing competitive strength and hierarchies (transitive versus intransitive competitive orders) in multispecies communities. We found that species turnover decreased through time within interaction neighbourhoods, but increased through time outside interaction neighbourhoods. Successional change did not lead to modular community structure. After accounting for species richness effects, the strength of competitive interactions and the proportion of transitive competitive hierarchies increased through time. Although effects of habitat filtering were weak, random colonization and subsequent competitive interactions had strong effects on community structure. Because competitive strength and transitivity were poorly correlated with soil characteristics, there was little evidence for context dependent competitive strength associated with intransitive competitive hierarchies.