Tapadoir: developing a statistical machine translation engine and associated resources for Irish

Tapadoir (from the Irish ´ tapa ‘fast’ and the nominal suffix -oir ´ ) is a statistical machine translation (SMT) project, funded by the Irish government. This work was commissioned to help government translators meet the translation demands which have arisen from the Irish language’s status as an official EU and national language. The development of this system, which translates English into Irish (a morphologically rich, low-resourced minority language), has produced an interesting set of challenges. These challenges have inspired a creative response to the lack of data and NLP tools available for the Irish language and have also resulted in the development of new resources for the Irish linguistic and NLP community. We show that our SMT system out-performs Google TranslateTM (a widely used general-domain SMT system) as a result of steps we have taken to tailor translation output to the user’s specific needs

Revealing Genomic Insights of the Unexplored Porcine Pathogen Actinobacillus pleuropneumoniae Using Whole Genome Sequencing

Actinobacillus pleuropneumoniae (APP) is the causative agent of pleuropneumonia in pigs, one of the most relevant bacterial respiratory diseases in the swine industry. To date, 19 serotypes have been described based on capsular polysaccharide typing with significant virulence dissimilarities. In this study, 16 APP isolates from Spanish origin were selected to perform antimicrobial susceptibility tests and comparative genomic analysis using whole genome sequencing (WGS). To obtain a more comprehensive worldwide molecular epidemiologic analyses, all APP whole genome assemblies available at the National Center for Biotechnology Information (NCBI) at the time of the study were also included. An in-house in silico PCR approach enabled the correct serotyping of unserotyped or incorrectly serotyped isolates and allowed for the discrimination between serotypes 9 and 11. A pangenome analysis identified the presence or absence of gene clusters to be serotype specific, as well as virulence profile analyses targeting the apx operons. Antimicrobial resistance genes were correlated to the presence of specific plasmids. Altogether, this study provides new insights into the genetic variability within APP serotypes, correlates phenotypic tests with bioinformatic analyses and manifests the benefits of populated databases for a better assessment of diversity and variability of relatively unknown pathogens. Overall, genomic comparative analysis enhances the understanding of transmission and epidemiological patterns of this species and suggests vertical transmission of the pathogen, including the resistance genes, within the Spanish integrated systems.info:eu-repo/semantics/publishedVersio

Phylogenetic analyses of Salmonella detected along the broiler production chain in Trinidad and Tobago

This study was conducted to determine the phylogenies of Salmonella strains isolated from cross-sectional studies conducted at hatcheries, broiler farms, processing plants, and retail outlets (broiler production chain) in Trinidad and Tobago over 4 yr (2016–2019). Whole-genome sequencing (WGS) was used to characterize Salmonella isolates. Core genome phylogenies of 8 serovars of public health significance were analyzed for similarities in origin and relatedness. In addition, Salmonella strains isolated from human salmonellosis cases in Trinidad were analyzed for their relatedness to the isolates detected along the broiler production chain. The common source of these isolates of diverse serovars within farms, within processing plants, between processing plants and retail outlets, and among farm-processing plant-retail outlet continuum was well-supported (bootstrap value >70%) by the core genome phylogenies for the respective serovars. Also, genome analyses revealed clustering of Salmonella serovars of regional (intra-Caribbean) and international (extra-Caribbean) origin. Similarly, strains of S. Enteritidis and S. Infantis isolated from human clinical salmonellosis in 2019 from Trinidad and Tobago clustered with our processing plant isolates recovered in 2018. This study is the first phylogenetic analysis of Salmonella isolates using WGS from the broiler industry in the Caribbean region. The use of WGS confirmed the genetic relatedness and transmission of Salmonella serovars contaminating chickens in broiler processing, and retailing in the country, with zoonotic and food safety implications for humans.The University of the West Indies, St. Augustine Campus Research and Publication Funds Committee.https://www.journals.elsevier.com/poultry-sciencehj2023Production Animal Studie

Transitioning to more sustainable, low-emissions agriculture in Brazil

KEY FINDINGS Cattle producers joined sustainability initiatives primarily to increase production, reduce production costs, learn new practices and access innovations, and because of their interest in sustainability. Farmers who shifted to sustainable intensification practices increased their productivity. Some also accessed new markets and a minority earned higher prices. Producers sought farming advice mostly from nearby farmers and technicians promoting sustainability initiatives. The cost of changing farm practices, insufficient technical assistance or capacity, and difficulty in complying with legal standards were the major barriers preventing other cattle producers from participating in sustainability initiatives. The greenhouse gas (GHG) emissions per kg of beef of cattle farmers in sustainable intensification programs were 18% lower compared to neighboring farms not in the programs. Early life-cycle cattle ranching (e.g. calving, early rearing), commonly associated with deforestation, has been more engaged with NGO initiatives providing support and agronomic outreach rather than formal standards and reporting. Coffee Coffee farmers joined a certification program because of requests from buyers, potential for receiving price premiums on their coffee, and to access new markets with certified products. Coffee farmers producing certified coffee increased their economic efficiency, mainly due to higher productivity, compared to before they certified. Coffee producers' connections to technicians and access to information mostly revolved around their participation in cooperatives.POLICY RECOMMENDATIONS Build on market development lessons from the coffee sector to enhance sustainability, quality, traceability, and branding in the cattle sector. Expand sustainability initiatives’ capacity to deliver market access, technical assistance, and finance services to more cattle farmers. Continue support to producers in sustainability initiatives over multiple years, as they are likely to increase the sustainability of their practices with time. Expand agronomic outreach and sustainability initiatives to calving and early rearing operations to reduce associated deforestation and GHG emissions

Predicting Pro-Environmental Values and Behaviors with the Supernumerary Personality Inventory and Hope

This research examinesthe role ofpersonality traits beyond the Five-Factor Model (FFM) frameworkin predicting pro-environmental values and behaviors. A sample of 410participants completed personality scalesand reported both their environmental values and the extent to which they had engaged in a series of pro-environmental behaviors in the preceding 24 hours. Small positive correlations were found between environmental values and behaviors with integrityand femininityand negative correlations with religiosity. Overall, the results show limited evidence supporting the personality dimensions measured in predicting pro-environmentalvalues and behaviors.Implications of the findings are discussed

Revealing Genomic Insights of the Unexplored Porcine Pathogen Using Whole Genome Sequencing

(APP) is the causative agent of pleuropneumonia in pigs, one of the most relevant bacterial respiratory diseases in the swine industry. To date, 19 serotypes have been described based on capsular polysaccharide typing with significant virulence dissimilarities. In this study, 16 APP isolates from Spanish origin were selected to perform antimicrobial susceptibility tests and comparative genomic analysis using whole genome sequencing (WGS). To obtain a more comprehensive worldwide molecular epidemiologic analyses, all APP whole genome assemblies available at the National Center for Biotechnology Information (NCBI) at the time of the study were also included. An in-house in silico PCR approach enabled the correct serotyping of unserotyped or incorrectly serotyped isolates and allowed for the discrimination between serotypes 9 and 11. A pangenome analysis identified the presence or absence of gene clusters to be serotype specific, as well as virulence profile analyses targeting the apx operons. Antimicrobial resistance genes were correlated to the presence of specific plasmids. Altogether, this study provides new insights into the genetic variability within APP serotypes, correlates phenotypic tests with bioinformatic analyses and manifests the benefits of populated databases for a better assessment of diversity and variability of relatively unknown pathogens. Overall, genomic comparative analysis enhances the understanding of transmission and epidemiological patterns of this species and suggests vertical transmission of the pathogen, including the resistance genes, within the Spanish integrated systems. IMPORTANCE Pleuropneumonia is one of the most relevant respiratory infections in the swine industry. Despite (APP) being one of the most important pathogens in the pig production, this is the first comparative study including all available whole genome sequencing data from NCBI. Moreover, this study also includes 16 APP isolates of Spanish origin with known epidemiological relationships through vertical integrated systems. Genomic comparisons provided a deeper understanding of molecular and epidemiological knowledge between different APP serotypes. Furthermore, determination of resistance and toxin profiles allowed correlation with the presence of mobile genetic elements and specific serotype, respectively

Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water.

Shiga toxin-producing Escherichia coli (STEC) contamination of agricultural water might be an important factor to recent foodborne illness and outbreaks involving leafy greens. Closed bacterial genomes from whole genome sequencing play an important role in source tracking. We aimed to determine the limits of detection and classification of STECs by qPCR and nanopore sequencing using 24 hour enriched irrigation water artificially contaminated with E. coli O157:H7 (EDL933). We determined the limit of STEC detection by qPCR to be 30 CFU/reaction, which is equivalent to 105 CFU/ml in the enrichment. By using Oxford Nanopore's EPI2ME WIMP workflow and de novo assembly with Flye followed by taxon classification with a k-mer analysis software (Kraken2), E. coli O157:H7 could be detected at 103 CFU/ml (68 reads) and a complete fragmented E. coli O157:H7 metagenome-assembled genome (MAG) was obtained at 105-108 CFU/ml. Using a custom script to extract the E. coli reads, a completely closed MAG was obtained at 107-108 CFU/ml and a complete, fragmented MAG was obtained at 105-106 CFU/ml. In silico virulence detection for E. coli MAGs for 105-108 CFU/ml showed that the virulotype was indistinguishable from the spiked E. coli O157:H7 strain. We further identified the bacterial species in the un-spiked enrichment, including antimicrobial resistance genes, which could have important implications to food safety. We propose this workflow provides proof of concept for faster detection and complete genomic characterization of STECs from a complex microbial sample compared to current reporting protocols and could be applied to determine the limit of detection and assembly of other foodborne bacterial pathogens

Molecular Characterization of Salmonella Detected along the Broiler Production Chain in Trinidad and Tobago

This cross-sectional study determined the serovars, antimicrobial resistance genes, and virulence factors of Salmonella isolated from hatcheries, broiler farms, processing plants, and retail outlets in Trinidad and Tobago. Salmonella in silico serotyping detected 23 different serovars where Kentucky 20.5% (30/146), Javiana 19.2% (28/146), Infantis 13.7% (20/146), and Albany 8.9% (13/146) were the predominant serovars. There was a 76.0% (111/146) agreement between serotyping results using traditional conventional methods and whole-genome sequencing (WGS) in in silico analysis. In silico identification of antimicrobial resistance genes conferring resistance to aminoglycosides, cephalosporins, peptides, sulfonamides, and antiseptics were detected. Multidrug resistance (MDR) was detected in 6.8% (10/146) of the isolates of which 100% originated from broiler farms. Overall, virulence factors associated with secretion systems and fimbrial adherence determinants accounted for 69.3% (3091/4463), and 29.2% (1302/4463) counts, respectively. Ten of 20 isolates of serovar Infantis (50.0%) showed MDR and contained the blaCTX-M-65 gene. This is the first molecular characterization of Salmonella isolates detected along the entire broiler production continuum in the Caribbean region using WGS. The availability of these genomes will help future source tracking during epidemiological investigations associated with Salmonella foodborne outbreaks in the region and worldwide