Phylogenetic position of Riemerella anatipestifer based on 16S rRNA gene sequences

Riemerella anatipestifer, the causative agent of septicemia anserum exsudativa (also called new duckling disease), belongs to the family Flavobacteriaceae of gram-negative bacteria. We determined the DNA sequences of the rrs genes encoding the 16S rRNAs of four R. anatipestifer strains by directly sequencing PCR-amplified rrs genes. A sequence similarity analysis confirmed the phylogenetic position of R. anatipestifer in the family Flavobacteriaceae in rRNA superfamily V and allowed fine mapping of R. anatipestifer on a separate rRNA branch comprising the most closely related species, Bergeyella zoohelcum, as well as Chryseobacterium balustinum, Chryseobacterium indologenes, and Chryseobacterium gleum. The sequences of the rrs genes of the four R. anatipestifer strains varied between 0.5 and 1.0%, but all of the strains occupied the same position on the phylogenetic tree. In general, differences in rrs genes were observed among R. anatipestifer strains, even within a given serotype, as shown by restriction fragment length polymorphism of PCR-amplified rrs genes.

Phylogenetic positions of Clostridium chauvoei and Clostridium septicum based on 16S rRNA gene sequences

The sequences of the 16S rRNA genes (rrs genes) of Clostridium chauvoei, the causative agent of blackleg in cattle, and the phenotypically related organism Clostridium septicum were determined. After amplification of 1,507-bp PCR fragments from the corresponding rrs genes, the sequences were determined in a single round of sequencing by using conserved region primers. A sequence similarity analysis of the sequences revealed the close phylogenetic relationship of C. chauvoei and C. septicum in Clostridium cluster I (M. D. Collins, P. A. Lawson, A. Willems, J. J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J. A. E. Farrow, Int. J. Syst. Bacteriol. 44:812-826, 1994), which includes Clostridium carnis, Clostridium perfringens, Clostridium botulinum, and Clostridium tetani. We found that 99.3% of the nucleotides in the genes of C. chauvoei and C. septicum are identical.

Counts of harpacticoid copepods associated with cold-water coral substrates obtained from several Belgica cruises, Porcupine Seabight (North-East Atlantic)

The influence of microhabitat type on the diversity and community structure of the harpacticoid copepod fauna associated with a cold-water coral degradation zone was investigated in the Porcupine Seabight (North-East Atlantic). Three substrate types were distinguished: dead fragments of the cold-water coral Lophelia pertusa, skeletons of the glass sponge Aphrocallistes bocagei and the underlying sediment. At the family level, it appears that coral fragments and underlying sediment do not harbour distinctly diVerent assemblages, with Ectinosomatidae, Ameiridae, Pseudotachidiidae, Argestidae and Miraciidae as most abundant. Conclusions on assemblage structure and diversity of the sponge skeletons are limited as only two samples were available. Similarity analysis at species level showed a strong variation in the sediment samples, which did not harbour a distinctly different assemblage in opposition to the coral and sponge samples. Several factors (sediment infill on the hard substrates, mobility of the copepods, limited sample sizes) are proposed to explain this apparent lack of a distinct difference between the microhabitats. Coral fragments and sediment were both characterised by high species diversity and low species dominance, which might indicate that copepod diversity is not substantially influenced by hydrodynamic stress. The additive partitioning of species diversity showed that by adding locations species richness was greatly enhanced. The harpacticoid community in the cold-water coral degradation zone is highly diverse and includes 157 species, 62 genera and 19 families. Information from neighbouring soft-bottom regions is necessary to assess whether total species diversity is increased by the presence of these complex habitatproviding substrates.

Estudio de la diversidad genética de Botrytis sp en orquídeas y la resistencia al ataque del hongo

En la actualidad la mayoría de plantas sufren pérdidas debido a las enfermedades que les provocan los hongos. Uno de estos grupos amenazado por el ataque de los hongos son las especies de la familia Orchidaceae, especies que se encuentran amenazadas y con numerosas especies en peligro de extinción. Uno de los problemas sanitarios más destacados es Botrytis cinerea, hongo patógeno cosmopolita, causante de enfermedades importantes en muchas plantas tales como frutas, verduras, accesiones de viveros, plantas ornamentales y huertos cultivos (Jarvis 1977; Elad et al., 2007). Este género es uno de los grupos de hongos más ampliamente conocido y distribuido. Contiene 22 especies (Hennebert 1973; Yohalem et al., 2003) y un híbrido (B. allii) (Yohalem & Alabama, 2003) vinculado a las etapas sexuales y un amplio número de huéspedes específicos (Beever y Weds, 2000); infecta más de 200 especies vegetales distintas (Williamson et al., 2007). Dada la importancia de este patógeno se realiza un estudio de caracterización morfológica y molecular del hongo, aislado de plantas de orquídeas cultivadas en condiciones de invernadero, de hortalizas y plantas frutales, con síntomas de necrosis, atizonamientos y pudriciones. El análisis de las características morfológicas (presencia de esclerocios, tamaño de conidios, presencia de estructuras sexuales in vitro) y fenotípicas (crecimiento micelial a diferentes temperaturas, germinación de esporas), nos permitió determinar características importantes del comportamiento del hongo y establecer cuáles son las mejores condiciones para su patogenicidad. Se afianzo este trabajo con estudios moleculares a través del análisis de la región ribosomal ITS1-ITS4. Entre los aislados estudiados se identificaron dos especies diferentes, Botrytis cinerea y B. fabiopsis, esta última conocida como especifica de Vicia faba, se lo aisló de una planta de Pelargonium sp. Se hizo un análisis filogenético para comparar estas dos especies, encontrándose que B. fabiopsis está estrechamente relacionada con B. cinerea y B. elliptica, pero lejanamente relacionado con B. fabae. Además, se analizó las poblaciones de los aislados de Botrytis, para ello se seleccionaron tres parejas de cebadores microsatelites con altos porcentajes de polimorfismo. Al analizar la similaridad entre los aislados se determinaron tres grupos de poblaciones de B. cinerea entre los cuales Botrytis fabiopsis comparte un grupo grande con B. cinerea. La diferenciación genética no fue significativa entre la población de aislados de orquídeas y hortalizas, la diferencia génica que fue muy baja, lo que sugiere que la especificidad de Botrytis no está dada por los hospederos, aunque la posibilidad de la especificidad con algún cultivo no puede descartarse. ABSTRACT Most plants suffer diseases caused by fungi. Orchidaceae is one of the threatened groups with many endangered species. Included into the most important problems in plant health is Botrytis cinerea, a cosmopolitan pathogen which causes major diseases in many plants of agronomic interest such as fruits, vegetables, planthouses accessions and ornamental plants (Jarvis, 1977; Elad et al, 2007). The genus Botrytis is one of the most widely and disseminated fungi. The genus contains 22 species (Hennebert 1973; Yohalem et al, 2003) and a hybrid (B. allii) (Yohalem & Alabama, 2003) linked to the sexual stages of a large number of specific hosts (Beever & Weds, 2000); infects over 200 different plant species (Williamson et al., 2007). Due to the importance of this pathogen, a study of morphological and molecular characterization of the fungus was carried out. Fungi samples were isolated from orchid plants grown in greenhouse conditions, vegetables and fruits with signs of necrosis, blight and rottening. To establish the best conditions for pathogenicity, behavioral characteristics of the fungus were studied through the analysis of morphological characteristics (presence of sclerotia, conidia size, sexual structures in vitro) and mycelial growth at different temperatures. To complete the characterization of the fungi, a molecular study was performed via the analysis of ribosomal ITS1-ITS4 region. Two different species were identified: Botrytis cinerea and Botrytis fabiopsis (known by specificity to Vicia faba). B. fabiopsis was isolated from a plant of the genus Pelargonium. A phylogenetic analysis was carried out to compare these two species leading to the conclusion that B. fabiopsis is closely related to B. cinerea and B. elliptica, but distantly related to B. fabae. The populations of Botrytis isolates were also analyzed. Three pairs of microsatellite primers with high percentages of polymorphism were selected. A similarity analysis showed three groups of populations of B. cinerea, including Botrytis fabiopsis. The genetic differentiation was not significant among the populations of isolates from orchids and vegetables; genetic differences were very low, suggesting that the specificity of Botrytis species is not given by the hosts.

Electrostatic steering and ionic tethering in enzyme–ligand binding: Insights from simulations

To bind at an enzyme’s active site, a ligand must diffuse or be transported to the enzyme’s surface, and, if the binding site is buried, the ligand must diffuse through the protein to reach it. Although the driving force for ligand binding is often ascribed to the hydrophobic effect, electrostatic interactions also influence the binding process of both charged and nonpolar ligands. First, electrostatic steering of charged substrates into enzyme active sites is discussed. This is of particular relevance for diffusion-influenced enzymes. By comparing the results of Brownian dynamics simulations and electrostatic potential similarity analysis for triose-phosphate isomerases, superoxide dismutases, and β-lactamases from different species, we identify the conserved features responsible for the electrostatic substrate-steering fields. The conserved potentials are localized at the active sites and are the primary determinants of the bimolecular association rates. Then we focus on a more subtle effect, which we will refer to as “ionic tethering.” We explore, by means of molecular and Brownian dynamics simulations and electrostatic continuum calculations, how salt links can act as tethers between structural elements of an enzyme that undergo conformational change upon substrate binding, and thereby regulate or modulate substrate binding. This is illustrated for the lipase and cytochrome P450 enzymes. Ionic tethering can provide a control mechanism for substrate binding that is sensitive to the electrostatic properties of the enzyme’s surroundings even when the substrate is nonpolar.

Benthic fauna of an offshore borrow area in Broward County, Florida /

Benthic fauna from two stations within a 5-year-old borrow area and two control stations off Hillsboro Beach (Broward County), Florida, were sampled quarterly from June 1977 to March 1978 to evaluate the long-term impact of offshore dredging. Generally enhanced productivities occurred within the borrow area, although there was much seasonal variation among stations. Species diversities were usually higher at the borrow stations than at the control stations. The single exception was due to a high concentration of the bivalve E. nitens at one of the control stations in June. Although faunal similarity analysis revealed a qualitative change in the fauna of the borrow area, this change is not considered detrimental. Conspicuous patterns of heterogeneous faunal distributions were evident in this study, particularly for the bivalve E. nitens. No lasting detrimental effects, in terms of numbers of species, faunal densities, or species diversity, resulted from the dredging operation. (Author).

Capparaceae: flora do Rio Grande do Norte e biogeografia no semiárido brasileiro

Capparaceae comprises 25 genera and 480 species, of which 110 are included in 18 genera in Neotropics. Its distribution is pantropical with high frequency in seasonally dry environments. Its representatives are woody, shrubs and rarely wines, with simple leave or compound 3-foliolate, shorts and deciduous floral bracts, tetramerous and nocturnal flowers with exserts and numerous stamens, ovary supero on a gynophore and fleshy fruits, dehiscents or indehiscentes. For Brazil, 12 genera and 28 species are recorded and 12 of that are endemic to the country, occurring preferentially in vegetation of savanna estépica s.str., seasonal semideciduos forest and restinga. This work shows two chapters. In the first chapter, the distributions patterns of the species occurring in the brazilian semi-arid region and their distribution intra Caatinga are discussed. The distribution patterns were determined from a review of the distribution of species in herbaria collections and supplemented with data obtained from specific bibliography about the family. A map containing 1 × 1 grid cells was used to evaluate the richness, collection efforts and floristic similarity of the species intra Caatinga. Six genera and eight species were registered in Caatinga. Four species are endemic to Brazil, with only one endemic to Caatinga, and the other four are widespread in Neotropics. Four distribution patterns were observed: restricted to the NE, broad and continuous in Brazil, disjunct and neotropical. All the species were recorded in Bahia, state with the highest species richness per grid cell and also remarkable sampling efforts species of the family. The state of Piauí presents priority areas for further collection of Capparaceae, due to low family representation in the state. The floristic similarity analysis intra Caatinga was low, 22 %, probably due to a few species of the family in the region and the wide distribution of the same. The second chapter presents the Capparaceae of flora to Rio Grande do Norte (RN), since the state has a little-known flora, with specific studies. Through collections in the state and herbaria review, five genera and six species of Capparaceae were recorded in RN: Capparidastrum (1 spp.); Crateva (1 spp.); Cynophalla (2 spp.); Mesocapparis (1 spp.) and Neocalyptrocalyx (1 spp.). Capparidastrum frondosum and Mesocapparis lineata are new records for the state. An identification key, descriptions and images, comments on the biology of the species and protected areas where they occur are showed.

Avaliação do cuidado de enfermagem na perspectiva da segurança do paciente em unidades de terapia intensiva: na visão de profissionais, pacientes e familiares

Technological advances combined with healthcare assistance bring increased risks related to patient safety, causing health institutions to be environments susceptible to losses in the provided care. Sectors of high complexity, such as Intensive Care Units have such characteristics highlighted due to being spaces designed for the care of patients in serious medical condition, when the use of advanced technological devices becomes a necessity. Thus, the aim of this study was to assess nursing care from the perspective of patient safety in intensive care units. This is an evaluative research, which combines various forms of data collection and analysis in order to conduct a deepened investigation. Data collection occurred in loco, from April to July 2014 in hospitals equipped with adult intensive care unit services. For this, a checklist instrument and semi-structured interviews conducted with patients, families, professionals were used in order to evaluate the structure-process-outcome triad. The instrument for nursing care assessment regarding Patient Safety included 97 questions related to structure and processes. Interviews provided data for outcome analysis. The selection of interviewees/participants was based on the willingness of potential participants. The following methods were used to collect data resulting from the instrument: statistical analysis of inter-rater reliability measure known as kappa (K); observations from judges resulting from the observation process; and added information obtained from the literature on the thematic. Data analysis from the interviews was carried out with IRAMUTEQ software, which used Descending Hierarchical Classification and Similarity analysis to aid in data interpretation. Research steps followed the ethical principles presented by Resolution No. 466 of December 12, 2012, and the results were presented in three manuscripts: 1) Evaluation of patient safety in Intensive Care Units: a focus on structure; 2) Health evaluation processes: a nursing care perspective on patient safety; 3) Patient safety in intensive care units: perception of nurses, family members and patients. The first article, related to the structure, refers to the use of 24 items of the employed instrument, showing that most of the findings were not aligned with the adequacy standards, which indicates poor conditions in structures offered in health services. The second article provides an analysis of the pillar of Processes, with the use of 73 items of the instrument, showing that 50 items did not meet the required standards for safe handling due to the absence of adequate scientific guidance and effective communication in nursing care process. For the third article, results indicate that intensive care units were safe places, yet urges for changes, especially in the physical structure and availability of materials and communication among professionals, patients and families. Therefore, our findings suggest that the nursing care being provided in the evaluated intensive care units contains troubling shortcomings with regards to patient safety, thereby evidencing an insecure setting for the assistance offered, in addition to a need for urgent measures to remedy the identified inadequacies with appropriate structures and implement protocols and care guidelines in order to consolidate an environment more favorable to patient safety.

O uso da Divergência de Kullback-Leibler e da Divergência Generalizada como medida de similaridade em sistemas CBIR

The content-based image retrieval is important for various purposes like disease diagnoses from computerized tomography, for example. The relevance, social and economic of image retrieval systems has created the necessity of its improvement. Within this context, the content-based image retrieval systems are composed of two stages, the feature extraction and similarity measurement. The stage of similarity is still a challenge due to the wide variety of similarity measurement functions, which can be combined with the different techniques present in the recovery process and return results that aren’t always the most satisfactory. The most common functions used to measure the similarity are the Euclidean and Cosine, but some researchers have noted some limitations in these functions conventional proximity, in the step of search by similarity. For that reason, the Bregman divergences (Kullback Leibler and I-Generalized) have attracted the attention of researchers, due to its flexibility in the similarity analysis. Thus, the aim of this research was to conduct a comparative study over the use of Bregman divergences in relation the Euclidean and Cosine functions, in the step similarity of content-based image retrieval, checking the advantages and disadvantages of each function. For this, it was created a content-based image retrieval system in two stages: offline and online, using approaches BSM, FISM, BoVW and BoVW-SPM. With this system was created three groups of experiments using databases: Caltech101, Oxford and UK-bench. The performance of content-based image retrieval system using the different functions of similarity was tested through of evaluation measures: Mean Average Precision, normalized Discounted Cumulative Gain, precision at k, precision x recall. Finally, this study shows that the use of Bregman divergences (Kullback Leibler and Generalized) obtains better results than the Euclidean and Cosine measures with significant gains for content-based image retrieval.

Collaborative Filtering with Data Classification : A Combined Approach to Hotel Recommendation Systems

Recommendation systems aim to help users make decisions more efficiently. The most widely used method in recommendation systems is collaborative filtering, of which, a critical step is to analyze a user's preferences and make recommendations of products or services based on similarity analysis with other users' ratings. However, collaborative filtering is less usable for recommendation facing the "cold start" problem, i.e. few comments being given to products or services. To tackle this problem, we propose an improved method that combines collaborative filtering and data classification. We use hotel recommendation data to test the proposed method. The accuracy of the recommendation is determined by the rankings. Evaluations regarding the accuracies of Top-3 and Top-10 recommendation lists using the 10-fold cross-validation method and ROC curves are conducted. The results show that the Top-3 hotel recommendation list proposed by the combined method has the superiority of the recommendation performance than the Top-10 list under the cold start condition in most of the times.

Science-based entrepreneur project development process for pre-service science teachers: difficulties faced*

This study used a phenomenological research design to determine the difficulties faced in the science-based entrepreneur project development process for pre-service science teachers.. Qualitative data were obtained through interviews conducted with ten pre-service science teachers. The data were analysed using an inductive thematic analysis. The results indicated that pre-service science teachers have most difficulty ‘making decisions on one of the innovative ideas’ and ‘making predictions about unexpected situations’. They also have difficulties ‘calculating the cost as a result of design or work analysis’, ‘identifying if the idea already existed (similarity analysis)’ and ‘making decisions on the required materials, tools, services’. These results show the need for pre-service science teachers to communicate with other institutions and organisations.

Vulcanus 2.0: A Recommender System for Accessibility

Even though the use of recommender systems is already widely spread in several application areas, there is still a lack of studies for accessibility research field. One of these attempts to use recommender system benefits for accessibility needs is Vulcanus. The Vulcanus recommender system uses similarity analysis to compare user’s trails. In this way, it is possible to take advantage of the user’s past behavior and distribute personalized content and services. The Vulcanus combined concepts from ubiquitous computing, such as user profiles, context awareness, trails management, and similarity analysis. It uses two different approaches for trails similarity analysis: resources patterns and categories patterns. In this work we performed an asymptotic analysis, identifying Vulcanus’ algorithm complexity. Furthermore we also propose improvements achieved by dynamic programming technique, so the ordinary case is improved by using a bottom-up approach. With that approach, many unnecessary comparisons can be skipped and now Vulcanus 2.0 is presented with improvements in its average case scenario.

Origin discrimination and quality evaluation of Gastrodiae rhizoma (Orchidaceae) by high-performance liquid chromatographic fingerprint

Purpose: To develop a high-performance liquid chromatography (HPLC) fingerprint method for the quality control and origin discrimination of Gastrodiae rhizoma . Methods: Twelve batches of G. rhizoma collected from Sichuan, Guizhou and Shanxi provinces in china were used to establish the fingerprint. The chromatographic peak (gastrodin) was taken as the reference peak, and all sample separation was performed on a Agilent C18 (250 mm×4.6 mmx5 μm) column with a column temperature of 25 °C. The mobile phase was acetonitrile/0.8 % phosphate water solution (in a gradient elution mode) and the flow rate of 1 mL/min. The detection wavelength was 270 nm. The method was validated as per the guidelines of Chinese Pharmacopoeia. Results: The chromatograms of the samples showed 11 common peaks, of which no. 4 was identified as that of Gastrodin. Data for the samples were analyzed statistically using similarity analysis and hierarchical cluster analysis (HCA). The similarity index between reference chromatogram and samples’ chromatograms were all > 0.80. The similarity index of G. rhizoma from Guizhou, Shanxi and Sichuan is evident as follows: 0.854 - 0.885, 0.915 - 0.930 and 0.820 - 0.848, respectively. The samples could be divided into three clusters at a rescaled distance of 7.5: S1 - S4 as cluster 1; S5 - S8 cluster 2, and others grouped into cluster 3. Conclusion: The findings indicate that HPLC fingerprinting technology is appropriate for quality control and origin discrimination of G. rhizoma.

Dinâmica espaço-temporal em uma guilda de borboletas frugívoras no limite norte da Floresta Atlântica Nordestina

The extent of the Brazilian Atlantic rainforest, a global biodiversity hotspot, has been reduced to less than 7% of its original range. Yet, it contains one of the richest butterfly fauna in the world. Butterflies are commonly used as environmental indicators, mostly because of their strict association with host plants, microclimate and resource availability. This research describes diversity, composition and species richness of frugivorous butterflies in a forest fragment in the Brazilian Northeast. It compares communities in different physiognomies and seasons. The climate in the study area is classified as tropical rainy, with two well defined seasons. Butterfly captures were made with 60 Van Someren-Rydon traps, randomly located within six different habitat units (10 traps per unit) that varied from very open (e.g. coconut plantation) to forest interior. Sampling was made between January and December 2008, for five days each month. I captured 12090 individuals from 32 species. The most abundant species were Taygetis laches, Opsiphanes invirae and Hamadryas februa, which accounted for 70% of all captures. Similarity analysis identified two main groups, one of species associated with open or disturbed areas and a second by species associated with shaded areas. There was a strong seasonal component in species composition, with less species and lower abundance in the dry season and more species and higher abundance in the rainy season. K-means analysis indicates that choice of habitat units overestimated faunal perceptions, suggesting less distinct units. The species Taygetis virgilia, Hamadryas chloe, Callicore pygas e Morpho achilles were associated with less disturbed habitats, while Yphthimoides sp, Historis odius, H. acheronta, Hamadryas feronia e Siderone marthesia likey indicate open or disturbed habitats. This research brings important information for conservation of frugivorous butterflies, and will serve as baseline for future projects in environmental monitoring

An Artificial Intelligence Approach to Dyscalculia

Dyscalculia stands for a brain-based condition that makes it hard to make sense of numbers and mathematical concepts. Some adolescents with dyscalculia cannot grasp basic number concepts. They work hard to learn and memorize basic number facts. They may know what to do in mathematical classes but do not understand why they are doing it. In other words, they miss the logic behind it. However, it may be worked out in order to decrease its degree of severity. For example, disMAT, an app developed for android may help children to apply mathematical concepts, without much effort, that is turning in itself, a promising tool to dyscalculia treatment. Thus, this work focuses on the development of an Intelligent System to estimate children evidences of dyscalculia, based on data obtained on-the-fly with disMAT. The computational framework is built on top of a Logic Programming framework to Knowledge Representation and Reasoning, complemented with a Case-Based problem solving approach to computing, that allows for the handling of incomplete, unknown, or even contradictory information.