An MLSA-based online scheme for the rapid identification of Stenotrophomonas isolates

An online scheme to assign Stenotrophomonas isolates to genomic groups was developed using the multilocus sequence analysis (MLSA), which is based on the DNA sequencing of selected fragments of the housekeeping genes ATP synthase alpha subunit (atpA), the recombination repair protein (recA), the RNA polymerase alpha subunit (rpoA) and the excision repair beta subunit (uvrB). This MLSA-based scheme was validated using eight of the 10 Stenotrophomonas species that have been previously described. The environmental and nosocomial Stenotrophomonas strains were characterised using MLSA, 16S rRNA sequencing and DNA-DNA hybridisation (DDH) analyses. Strains of the same species were found to have greater than 95% concatenated sequence similarity and specific strains formed cohesive readily recognisable phylogenetic groups. Therefore, MLSA appeared to be an effective alternative methodology to amplified fragment length polymorphism fingerprint and DDH techniques. Strains of Stenotrophomonas can be readily assigned through the open database resource that was developed in the current study (www.steno.lncc.br/)

Lightweight Multilingual Software Analysis

Developer preferences, language capabilities and the persistence of older languages contribute to the trend that large software codebases are often multilingual, that is, written in more than one computer language. While developers can leverage monolingual software development tools to build software components, companies are faced with the problem of managing the resultant large, multilingual codebases to address issues with security, efficiency, and quality metrics. The key challenge is to address the opaque nature of the language interoperability interface: one language calling procedures in a second (which may call a third, or even back to the first), resulting in a potentially tangled, inefficient and insecure codebase. An architecture is proposed for lightweight static analysis of large multilingual codebases: the MLSA architecture. Its modular and table-oriented structure addresses the open-ended nature of multiple languages and language interoperability APIs. We focus here as an application on the construction of call-graphs that capture both inter-language and intra-language calls. The algorithms for extracting multilingual call-graphs from codebases are presented, and several examples of multilingual software engineering analysis are discussed. The state of the implementation and testing of MLSA is presented, and the implications for future work are discussed.Comment: 15 page

Feature extraction based on bio-inspired model for robust emotion recognition

Emotional state identification is an important issue to achieve more natural speech interactive systems. Ideally, these systems should also be able to work in real environments in which generally exist some kind of noise. Several bio-inspired representations have been applied to artificial systems for speech processing under noise conditions. In this work, an auditory signal representation is used to obtain a novel bio-inspired set of features for emotional speech signals. These characteristics, together with other spectral and prosodic features, are used for emotion recognition under noise conditions. Neural models were trained as classifiers and results were compared to the well-known mel-frequency cepstral coefficients. Results show that using the proposed representations, it is possible to significantly improve the robustness of an emotion recognition system. The results were also validated in a speaker independent scheme and with two emotional speech corpora.Fil: Albornoz, Enrique Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Milone, Diego Humberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Rufiner, Hugo Leonardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; Argentin

Lightweight Call-Graph Construction for Multilingual Software Analysis

Analysis of multilingual codebases is a topic of increasing importance. In prior work, we have proposed the MLSA (MultiLingual Software Analysis) architecture, an approach to the lightweight analysis of multilingual codebases, and have shown how it can be used to address the challenge of constructing a single call graph from multilingual software with mutual calls. This paper addresses the challenge of constructing monolingual call graphs in a lightweight manner (consistent with the objective of MLSA) which nonetheless yields sufficient information for resolving language interoperability calls. A novel approach is proposed which leverages information from a compiler-generated AST to provide the quality of call graph necessary, while the program itself is written using an Island Grammar that parses the AST providing the lightweight aspect necessary. Performance results are presented for a C/C++ implementation of the approach, PAIGE (Parsing AST using Island Grammar Call Graph Emitter) showing that despite its lightweight nature, it outperforms Doxgen, is robust to changes in the (Clang) AST, and is not restricted to C/C++.Comment: 10 page

Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us

Leishmaniasis is a complex parasitic disease from a taxonomic, clinical and epidemiological point of view. The role of genetic exchanges has been questioned for over twenty years and their recent experimental demonstration along with the identification of interspecific hybrids in natura has revived this debate. After arguing that genetic exchanges were exceptional and did not contribute to Leishmania evolution, it is currently proposed that interspecific exchanges could be a major driving force for rapid adaptation to new reservoirs and vectors, expansion into new parasitic cycles and adaptation to new life conditions. To assess the existence of gene flows between species during evolution we used MLSA-based (MultiLocus Sequence Analysis) approach to analyze 222 Leishmania strains from Africa and Eurasia to accurately represent the genetic diversity of this genus. We observed a remarkable congruence of the phylogenetic signal and identified seven genetic clusters that include mainly independent lineages which are accumulating divergences without any sign of recent interspecific recombination. From a taxonomic point of view, the strong genetic structuration of the different species does not question the current classification, except for species that cause visceral forms of leishmaniasis (L. donovani, L. infantum and L. archibaldi). Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles, they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago. These results should have practical consequences concerning the molecular identification of parasites and the subsequent therapeutic management of the disease

Erwinia oleae sp. nov., isolated from olive knots caused by Pseudomonas savastanoi pv. savastanoi

Three endophytic bacterial isolates were obtained in Italy from olive knots caused by Pseudomonas savastanoi pv. savastanoi. Phenotypic tests in combination with 16S rRNA gene sequence analysis indicated a phylogenetic position of these isolates in the genus Erwinia or Pantoea, and revealed two other strains with highly similar 16S rRNA gene sequences (> 99 %), CECT 5262 and CECT 5264, obtained in Spain from olive knots. Rep-PCR DNA fingerprinting of the five strains from olive knots with BOX, ERIC and REP primers revealed three groups of profiles that were highly similar to each other. Multilocus sequence analysis (MLSA) based on concatenated partial atpD, gyrB, infB and rpoB gene sequences, indicated that the strains constitute a single novel species in the genus Erwinia. The strains showed general phenotypic characteristic of Erwinia, and whole genome DNA-DNA hybridization data confirmed they represent a single novel Erwinia species. The strains showed a DNA G+C base composition ranging from 54.7 to 54.9 mol%. They could be discriminated from the phylogenetically related Erwinia species by their ability to utilise potassium gluconate, L-rhamnose and D-arabitol, but not glycerol, inositol and D-sorbitol. The name Erwinia oleae (type strain DAPP-PG 531T = LMG 25322T = DSM 23398T) is proposed for this new taxon

Resuscitation and quantification of stressed Escherichia coli K12 NCTC8797 in water samples

The aim of this study was to investigate the impact on numbers of using different media for the enumeration of Escherichia coli subjected to stress, and to evaluate the use of different resuscitation methods on bacterial numbers. E. coli was subjected to heat stress by exposure to 55 °C for 1 h or to light-induced oxidative stress by exposure to artificial light for up to 8 h in the presence of methylene blue. In both cases, the bacterial counts on selective media were below the limits of detection whereas on non-selective media colonies were still produced. After resuscitation in non-selective media, using a multi-well MPN resuscitation method or resuscitation on membrane filters, the bacterial counts on selective media matched those on non-selective media. Heat and light stress can affect the ability of E. coli to grow on selective media essential for the enumeration as indicator bacteria. A resuscitation method is essential for the recovery of these stressed bacteria in order to avoid underestimation of indicator bacteria numbers in water. There was no difference in resuscitation efficiency using the membrane filter and multi-well MPN methods. This study emphasises the need to use a resuscitation method if the numbers of indicator bacteria in water samples are not to be underestimated. False-negative results in the analysis of drinking water or natural bathing waters could have profound health effects

“If You Are Old Enough to Die for Your Country, You Should Be Able to Get a Pinch of Snuff”: Views of Tobacco 21 Among Appalachian Youth

Background: Multiple strategies have been utilized in attempts to decrease the prevalence of youth tobacco use. One strategy, raising the minimum legal sale age (MLSA) of tobacco products to 21, known as Tobacco 21, has recently gained popularity. Tobacco 21 legislation targets youth tobacco use by obstructing two main sources of youth tobacco products: stores and older friends. Although these sources are the most common for youth across the nation, regional differences have not been explored. Further, youth perspectives about raising the tobacco MLSA have not been considered. Youth may help identify potential challenges to implementing tobacco control measures, as well as suggest alternatives for intervention, thus helping to shape successful tobacco control policies. Study Aim: This study aimed to 1) examine youth perspectives on raising the tobacco minimum legal sale age to 21 and 2) identify common sources of tobacco products among middle and high school students living in rural, low-income Appalachian communities. Methods: A cross-sectional survey about perceptions and use of tobacco products was conducted with students in the Appalachian regions of Kentucky and North Carolina (N=426). Questions were asked concerning perspectives on the effect of Tobacco 21 implementation. Descriptive statistics characterized participants by Tobacco 21 perspectives. Participants were given the opportunity to further expand upon their opinions in an open-ended format. Results: The majority (58.7%) of participants responded that the same number of youth would use tobacco if the legal purchase age were raised, followed by responses that fewer would use (28.9%) and more would use (12.4%). Significant differences emerged based on tobacco use status (p\u3c.05), friends’ tobacco use (p\u3c.001), and whether participants identified family members as sources of youth tobacco products (p=.047). When given the opportunity to expand upon their views concerning the implementation of Tobacco 21 laws in their communities, many respondents cited poor enforcement of tobacco MLSAs at stores, continued access to tobacco products from family members and friends, and the overall abundance of tobacco in their communities as potential barriers to the successful implementation. Conclusion: Fewer than one-third of participants believed that Tobacco 21 legislation would succeed in reducing the prevalence of youth tobacco use. Perspectives on the effect of Tobacco 21 legislation were related to personal tobacco use, exposure to tobacco users, and beliefs that family members provide tobacco products to youth. Open-ended responses identify potential obstacles in implementing Tobacco 21 legislation in Appalachia. Future research should attempt to include youth perspectives when designing and implementing tobacco control policies and examine family members as sources of tobacco products for youth