Patterns of resistance to angular leaf spot, anthracnose and common bacterial blight in common bean germplasm

Diseases and insect pests are major causes of low yields of common bean (Phaseolus vulgaris L.) in Latin America and Africa. Anthracnose, angular leaf spot and common bacterial blight are widespread foliar diseases of common bean that also infect pods and seeds. One thousand and eighty-two accessions from a common bean core collection from the primary centres of origin were investigated for reaction to these three diseases. Angular leaf spot and common bacterial blight were evaluated in the field at Santander de Quilichao, Colombia, and anthracnose was evaluated in a screenhouse in Popayan, Colombia. By using the 15-group level from a hierarchical clustering procedure, it was found that 7 groups were formed with mainly Andean common bean accessions (Andean gene pool), 7 groups with mainly Middle American accessions (Middle American gene pool), while 1 group contained mixed accessions. Consistent with the theory of co-evolution, it was generally observed that accessions from the Andean gene pool were resistant to Middle American pathogen isolates causing anthracnoxe, while the Middle American accessions were resistant to pathogen isolates from the Andes. Different combinations of resistance patterns were found, and breeders can use this information to select a specific group of accessions on the basis of their need.

Direct visualization of Ras proteins in spatially distinct cell surface microdomains

Localization of signaling complexes to specific micro-domains coordinates signal transduction at the plasma membrane. Using immunogold electron microscopy of plasma membrane sheets coupled with spatial point pattern analysis, we have visualized morphologically featureless microdomains including lipid rafts, in situ and at high resolution. We find that an inner-plasma membrane lipid raft marker displays cholesterol-dependent clustering in microdomains with a mean diameter of 44 nm that occupy 35% of the cell surface. Cross-linking an outer-leaflet raft protein results in the redistribution of inner leaflet rafts, but they retain their modular structure. Analysis of Ras microlocalization shows that inactive H-ras is distributed between lipid rafts and a cholesterol-independent micro-domain. Conversely, activated H-ras and K-ras reside predominantly in nonoverlapping, cholesterol-independent microdomains. Galectin-1 stabilizes the association of activated H-ras with these nonraft microdomains, whereas K-ras clustering is supported by farnesylation, but not geranylgeranylation. These results illustrate that the inner plasma membrane comprises a complex mosaic of discrete microdomains. Differential spatial localization within this framework can likely account for the distinct signal outputs from the highly homologous Ras proteins.

Discovering coordination patterns

A large and growing amount of software systems rely on non-trivial coordination logic for making use of third party services or components. Therefore, it is of outmost importance to understand and capture rigorously this continuously growing layer of coordination as this will make easier not only the veri cation of such systems with respect to their original speci cations, but also maintenance, further development, testing, deployment and integration. This paper introduces a method based on several program analysis techniques (namely, dependence graphs, program slicing, and graph pattern analysis) to extract coordination logic from legacy systems source code. This process is driven by a series of pre-de ned coordination patterns and captured by a special purpose graph structure from which coordination speci cations can be generated in a number of di erent formalisms

Spatio-temporal analyses of the relationship between armed conflict and climate change in the eastern Africa

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Past/present and future worries: na fMRI study

For the past decade, numerous imaging techniques gave rise to remarka-ble progresses in the understanding of brain’s structure and function. Amongst the wide variety of studies onto the field of neuroscience, neuropsychiatric re-searches with resource to neuroimaging have attracted increasing attention. The present study will focus on the identification of brain areas recruited while normative subjects read sentences related to past/present or future wor-ries. Our main aim was to accurately characterize these brain areas while providing them with a time-stamp that would hopefully help us understand the implications of past/present memories and future envisioning in worrying episodes. With that purpose, functional magnetic resonance imaging data was collected from ten healthy individuals. The obtained data was processed and statistically treated using the General Linear Model and both Fixed and Ran-dom Effects Analysis for group-level results. Thereafter, a Multi-Voxel Pattern Analysis with Searchlight Mapping was performed in order to find patterns of activation that allow differentiation between conditions. The obtained results indicate higher brain activation while reading sen-tences related to past/present worries when compared to future worry or neu-tral sentences. The main areas include frontal cortex, posterior parietal, occipital and temporal areas. Worrying, per se, was characterized by activation of the medial posterior parietal cortex, left posterior occipital lobe and left central temporal lobe. With the searchlight mapping approach we were able to further identify patterns of distinction between conditions, which were located in the parietal, limbic and frontal lobes.

Genetic algorithm for shipping route estimation with long-range tracking data : automatic reconstruction of shipping routes based on the historical ship positions for maritime safety applications

Ship tracking systems allow Maritime Organizations that are concerned with the Safety at Sea to obtain information on the current location and route of merchant vessels. Thanks to Space technology in recent years the geographical coverage of the ship tracking platforms has increased significantly, from radar based near-shore traffic monitoring towards a worldwide picture of the maritime traffic situation. The long-range tracking systems currently in operations allow the storage of ship position data over many years: a valuable source of knowledge about the shipping routes between different ocean regions. The outcome of this Master project is a software prototype for the estimation of the most operated shipping route between any two geographical locations. The analysis is based on the historical ship positions acquired with long-range tracking systems. The proposed approach makes use of a Genetic Algorithm applied on a training set of relevant ship positions extracted from the long-term storage tracking database of the European Maritime Safety Agency (EMSA). The analysis of some representative shipping routes is presented and the quality of the results and their operational applications are assessed by a Maritime Safety expert.

reale Strahlenbild bei einer Röntgenthoraxaufnahme

Digital radiography, thoracic imaging, micro-dosimetry, high-resolution x-ray film, drum scanner, x-ray intensity pattern, analysis of frequency components

Donor's and organ representations in liver, kidney, heart and lung transplantation : a qualitative longitudinal study

Purpose: Organ transplantation is a biological and psychological challenge and graft acceptance is an important achievement for patients. Patients' concerns toward the deceased donor and the organ may contribute to this process. Method: Forty-seven patients involved in heart (N=9), liver (N=8), lung (N=14) and kidney (N=16) transplantation participated in IRB-approved longitudinal semi-structured interviews: (T1) registered on the waiting-list, (T2) six months and (T3) twelve months after transplantation. Qualitative pattern analysis (QUAPA) was carried out on the verbatim transcripts and concerns about the donor and the organ were then analysed. Results: - Donor's representation: At T1, patients were reluctant to talk about the donor: 27% expressed culpability and 19% accepted the clause of anonymity. At T2, intense emotions were associated with the reminiscing about the donor and 45% highlighted the generosity of his/her act. In addition, heart, lung and kidney recipients were concerned about the donor's identity: 42% challenged the clause of anonymity. Liver recipients complained about anonymity, but could nevertheless cope with it. At T3, 47% of heart, lung and kidney recipients thought daily of the donor and 33% were still looking for information about him/her. Liver recipients rarely have thoughts about the donor. - Organ representation: At T1, organ descriptions were biomedical (49% of the interviewees) and more rarely, mainly heart candidates, referred to the symbolic meaning of the organ. After transplantation (T2-T3), function was underlined. Acceptance and organ integration were associated with post-operative outcomes (23%) and psychological well-being (45%). Some patients (32%) inferred the donor's personality from the organ quality and felt privileged having received an organ in such a good state. Conclusion: Donor's representations should be explored during the transplantation process as they play an important role in the psychological acceptance of the graft.

A novel tool to analyze MRI recurrence patterns in glioblastoma.

At least 10% of glioblastoma relapses occur at distant and even contralateral locations. This disseminated growth limits surgical intervention and contributes to neurological morbidity. Preclinical data pointed toward a role for temozolomide (TMZ) in reducing radiotherapy-induced glioma cell invasiveness. Our objective was to develop and validate a new analysis tool of MRI data to examine the clinical recurrence pattern of glioblastomas. MRIcro software was used to map the location and extent of initial preoperative and recurrent tumors on MRI of 63 patients in the European Organisation for Research and Treatment of Cancer (EORTC) 26981/22981/National Cancer Institute of Canada (NCIC) CE.3 study into the same stereotaxic space. This allowed us to examine changes of site and distance between the initial and the recurrent tumor on the group level. Thirty of the 63 patients were treated using radiotherapy, while the other patients completed a radiotherapy-plus-TMZ treatment. Baseline characteristics (median age, KPS) and outcome data (progression-free survival, overall survival) of the patients included in this analysis resemble those of the general study cohort. The patient groups did not differ in the promoter methylation status of methyl guanine methyltransferase (MGMT). Overall frequency of distant recurrences was 20%. Analysis of recurrence patterns revealed no difference between the groups in the size of the recurrent tumor or in the differential effect on the distance of the recurrences from the preoperative tumor location. The data show the feasibility of groupwise recurrence pattern analysis. An effect of TMZ treatment on the recurrence pattern in the EORTC 26981/22981/NCIC CE.3 study could not be demonstrated.

Mycobacterium bovis identification by a molecular method from post-mortem inspected cattle obtained in abattoirs of Mato Grosso do Sul, Brazil

The presence of Mycobacterium bovis in bovine carcasses with lesions suggestive of tuberculosis was evaluated. Seventy-two carcass samples were selected during slaughter inspection procedures in abattoirs in the state of Mato Grosso do Sul, Brazil. Seventeen (23.6%) of samples showed colonies suggestive of mycobacteria that were confirmed to be acid-fast bacilli by Ziehl-Neelsen staining. Polymerase chain reaction (PCR) using primers specific for M. bovis identified M. bovis in 13 (76.5%) isolates. The PCR-restriction enzyme pattern analysis using gene encoding for the 65-kDa protein and two restriction enzymes identified the remaining four isolates that were represented by two M. tuberculosis complex and two nontuberculous mycobacteria. The results are indicative of infection of slaughter cattle by M. bovis and other mycobacteria in the state of Mato Grosso do Sul.

Existential values transformation in all organ transplantation: A qualitative prospective study.

Organ transplantation offers a treatment of choice for patients suffering from end stage illnesses. The aim of this IRB approved prospective qualitative study was to analyze patients’ psychological concerns from their inclusion on the waiting list for first organ transplantation (TX) (T1; N=71; kidney, K=30; liver, Li=11; lung, Lu=15; heart, H=15) and six months after TX (T2; N=49; K=15; Li=10; Lu=14; H=10). Semi-structured interviews were conducted at home or in a place selected by patients. Qualitative pattern analysis (QUAPA) of the verbatim transcriptions was applied. T1 (K) Patients maintained an apparent normality (87%), building emotional protection (23%), and developing a fatalist attitude towards life (43%). (Li) Physical limits were set to spare energy until TX (73%). Illness led to reevaluation of life values (66%). (Lu) Physical and psychological self-protection was prioritized when health declined (67%). Modified life values, fatalism (33%) and spirituality (27 %) were mentioned. (H) Patients husbanded physical (80%) and psychological (67%) resources and self-protection. Modified life values and fatalist attitude towards life were reported (40%). T2 (K) New perspective on life was described, with increase of empathy towards others (20%). (Li) Positive identity and life values modifications (60%), greater openness towards others, closeness to significant ones (30%) and a more self-centered attitude (30%) prioritizing the essential (20%) were reported. Lack of respect of life values generated anger (40%). (Lu) Setting existential priorities and increase in spirituality (64%), along with the development of new life values, greater openness to others (57%) and closeness to significant ones (21%) were underlined. Lack of respect of human values induced negative feelings (36%). Self-centered attitudes, setting limits to other people were mentioned (29%). (H) Change in life values with setting life priorities was reported (70%) with increase in spirituality, and the lack of respect of life values generated anger (50%). Self-centered attitudes were reported (60%). TX not only comes with positive physical benefits, but also with positive existential values and psychological transformation, and the development of a more altruistic attitude and humanistic values.

Evaluer la peur de tomber chez les personnes âgées à domicile: Un modèle qualitatif

Cet article (2006) décrit la démarche qui a fondé le développement de l'instrument d'évaluation de la peur de tomber à travers des "portraits" chez des personnes âgées vivant à domicile "chuteuses ou non chuteuses" (non publiés). Une analyse qualitative originale a été développée dans ce contexte la QUAPA (QUAlitative Pattern Analysis): une analyse des patterns permettant de décrire les différents degrés d'intensité auxquels la peur de tomber est décrites par les personnes âgées elles-mêmes. Cet instrument se base sur une validité "écologique". Il s'ancre dans le vécu des personnes âgées tel qu'il est rapporté et décrit par elles. L'évaluation de la peur de tomber réalisée à l'aide de ces portraits doit être confrontée à celle effectuée à l'aide d'autres instruments validés et largement utilisés dans le domaine de l'évaluation de la peur de tomber: FES, FES-I. Autres références publiées: Piot-Ziegler C (2002). La peur de tomber: comment l'évaluer ? Actualités Psychologiques, 12, 51-68. In C. Piot-Ziegler, (Vol. Ed.), Actualités Psychologiques: Vol. 12. Les chutes chez les personnes âgées: une approche interdisciplinaire (pp. 1-120). Piot-Ziegler C, Cuttelod T et Santiago M (2007). Définir la "peur de tomber" chez les personnes âgées à domicile. Etude qualitative. Bulletin de psychologie, 60(6), nov-déc, 515-525. Références non publiées: Piot-Ziegler C, Cuttelod T (2004). Evaluation de la peur de tomber: portraits issus du vécu des patients (questionnaire-portraits pour évaluer la peur de tomber chez des personnes âgées « chuteuses et non chuteuses ». Piot-Ziegler C, Cuttelod T (2004). Evaluation de la peur de tomber: portraits issus du vécu des patients (Guide de l'utilisateur).L'objectif de cet article (rédigé en 2006) est de dégager un modèle permettant d'évaluer l'intensité de la peur de tomber chez des personnes âgées vivant à domicile sur la base de données qualitatives récoltées dans une première étude (étude publiée: Piot-Ziegler et al. 2007).Dans cette étude qualitative, 58 entretiens semi-structurés ont été réalisés chez des personnes âgées vivant à domicile. Les thèmes abordés par les personnes âgées montrent que la peur de tomber se définit transversalement à travers les conséquences fonctionnelles, sociales et psychologiques consécutives à leur(s) chute(s).Afin d'explorer la possible existence de patterns, permettant de rendre compte de l'intensité de la peur de tomber, une méthode originale d'analyse qualitative (non informatisée) a été développée: la QUAPA (QUAlitative Patterns Analysis).Les résultats de cette analyse montrent l'existence d'une cohérence interne transversale (patterns) dans les trois dimensions définissant la peur de tomber (fonctionnelles, sociales et psychologiques) en fonction de l'intensité de la peur de tomber. Quatre patterns différents ont été mis en évidence. Ils débouchent sur une modélisation rendant compte des différents degrés d'intensité à laquelle la peur de tomber s'exprime chez les personnes âgées.Ce modèle en "patterns" permet d'évaluer la peur de tomber ressentie par une personne âgée en fonction des conséquences fonctionnelles, sociales et psychologiques à long terme consécutives à une ou plusieurs chutes. Ce modèle devra être mis à l'épreuve sur un grand échantillon de personnes âgées vivant à domicile ou dans d'autres espaces de vie (institutions), mais il constitue une alternative originale aux questionnaires utilisés actuellement qui se basent principalement sur le concept d'efficacité personnelle. Surtout il se base sur le vécu tel qu'il est rapporté par les personnes âgées elles-mêmes.Pour obtenir le questionnaire d'évaluation par "portraits" de la peur de tomber (e.mail: Chantal.Piot-Ziegler@unil.ch). Les documents suivants seront mis à disposition.Piot-Ziegler et C, Cuttelod T (2004). Evaluation de la peur de tomber: portraits issus du vécu des patients (questionnaire-portraits pour évaluer la peur de tomber chez des personnes âgées « chuteuses et non chuteuses » (Questionnaire).Piot-Ziegler et C, Cuttelod T (2004). Evaluation de la peur de tomber: portraits issus du vécu des patients (Guide de l'utilisateur).Mots-clés : chute ; peur de tomber ; personne âgée ; domicile ; recherche; approche compréhensive ; évaluation ; méthode qualitative ; pattern, QUAPA.

Diversity and genetic structure in natural populations of Hancornia speciosa var. speciosa Gomes in northeastern Brazil

Hancornia speciosa Gomes is a fruit tree native from Brazil that belongs to Apocinaceae family, and is popularly known as Mangabeira. Its fruits are widely consumed raw or processed as fruit jam, juices and ice creams, which have made it a target of intense exploitation. The extractive activities and intense human activity on the environment of natural occurrence of H. speciosa has caused genetic erosion in the species and little is known about the ecology or genetic structure of natural populations. The objective of this research was the evaluation of the genetic diversity and genetic structure of H. speciosa var. speciosa. The genetic variability was assessed using 11 allozyme loci with a sample of 164 individuals distributed in six natural populations located in the States of Pernambuco and Alagoas, Northeastern Brazil. The results showed a high level of genetic diversity within the species (e= 0.36) seeing that the most of the genetic variability of H. speciosa var. speciosa is within its natural populations with low difference among populations ( or = 0.081). The inbreeding values within ( = -0.555) and among populations ( =-0.428) were low showing lacking of endogamy and a surplus of heterozygotes. The estimated gene flow ( m ) was high, ranging from 2.20 to 13.18, indicating to be enough to prevent the effects of genetic drift and genetic differentiation among populations. The multivariate analyses indicated that there is a relationship between genetic and geographical distances, which was confirmed by a spatial pattern analysis using Mantel test (r = 0.3598; p = 0.0920) with 1000 random permutations. The high genetic diversity index in these populations indicates potential for in situ genetic conservation.

Scene Classification Using a Hybrid Generative/Discriminative Approach

We investigate whether dimensionality reduction using a latent generative model is beneficial for the task of weakly supervised scene classification. In detail, we are given a set of labeled images of scenes (for example, coast, forest, city, river, etc.), and our objective is to classify a new image into one of these categories. Our approach consists of first discovering latent ";topics"; using probabilistic Latent Semantic Analysis (pLSA), a generative model from the statistical text literature here applied to a bag of visual words representation for each image, and subsequently, training a multiway classifier on the topic distribution vector for each image. We compare this approach to that of representing each image by a bag of visual words vector directly and training a multiway classifier on these vectors. To this end, we introduce a novel vocabulary using dense color SIFT descriptors and then investigate the classification performance under changes in the size of the visual vocabulary, the number of latent topics learned, and the type of discriminative classifier used (k-nearest neighbor or SVM). We achieve superior classification performance to recent publications that have used a bag of visual word representation, in all cases, using the authors' own data sets and testing protocols. We also investigate the gain in adding spatial information. We show applications to image retrieval with relevance feedback and to scene classification in videos