Specifying and Analysing SOC Applications with COWS

COWS is a recently defined process calculus for specifying and combining service-oriented applications, while modelling their dynamic behaviour. Since its introduction, a number of methods and tools have been devised to analyse COWS specifications, like e.g. a type system to check confidentiality properties, a logic and a model checker to express and check functional properties of services. In this paper, by means of a case study in the area of automotive systems, we demonstrate that COWS, with some mild linguistic additions, can model all the phases of the life cycle of service-oriented applications, such as publication, discovery, negotiation, orchestration, deployment, reconfiguration and execution. We also provide a flavour of the properties that can be analysed by using the tools mentioned above

Veterinary decision making in relation to metritis - a qualitative approach to understand the background for variation and bias in veterinary medical records

<p>Abstract</p> <p>Background</p> <p>Results of analyses based on veterinary records of animal disease may be prone to variation and bias, because data collection for these registers relies on different observers in different settings as well as different treatment criteria. Understanding the human influence on data collection and the decisions related to this process may help veterinary and agricultural scientists motivate observers (veterinarians and farmers) to work more systematically, which may improve data quality. This study investigates qualitative relations between two types of records: 1) 'diagnostic data' as recordings of metritis scores and 2) 'intervention data' as recordings of medical treatment for metritis and the potential influence on quality of the data.</p> <p>Methods</p> <p>The study is based on observations in veterinary dairy practice combined with semi-structured research interviews of veterinarians working within a herd health concept where metritis diagnosis was described in detail. The observations and interviews were analysed by qualitative research methods to describe differences in the veterinarians' perceptions of metritis diagnosis (scores) and their own decisions related to diagnosis, treatment, and recording.</p> <p>Results</p> <p>The analysis demonstrates how data quality can be affected during the diagnostic procedures, as interaction occurs between diagnostics and decisions about medical treatments. Important findings were when scores lacked consistency within and between observers (variation) and when scores were adjusted to the treatment decision already made by the veterinarian (bias). The study further demonstrates that veterinarians made their decisions at 3 different levels of focus (cow, farm, population). Data quality was influenced by the veterinarians' perceptions of collection procedures, decision making and their different motivations to collect data systematically.</p> <p>Conclusion</p> <p>Both variation and bias were introduced into the data because of veterinarians' different perceptions of and motivations for decision making. Acknowledgement of these findings by researchers, educational institutions and veterinarians in practice may stimulate an effort to improve the quality of field data, as well as raise awareness about the importance of including knowledge about human perceptions when interpreting studies based on field data. Both recognitions may increase the usefulness of both within-herd and between-herd epidemiological analyses.</p

Dairy cattle ruminal resistome: characterisation and association with productive traits

[ES] El resistoma ruminal está compuesto por todos los genes de resistencia antimicrobiana (ARG) presentes en los microorganismos que habitan en el rumen. La Organización Mundial de la Salud advirtió sobre el problema de los patógenos resistentes a antimicrobianos (AMR), ya que se prevé que para 2050 las bacterias multirresistentes dejarán 10 millones de víctimas al año, superando al cáncer como nuestro principal problema de salud. Entre las 1,461 enfermedades reconocidas en humanos, el 60% de ellas son causadas por patógenos de múltiples huéspedes capaces de moverse a través de especies. Aproximadamente el 75% de las enfermedades infecciosas recientemente detectadas han sido zoonóticas. Aquí radica la importancia de caracterizar el resistoma ruminal, ya que los ARG podrían saltar de las heces y la saliva tanto inter como intra-especies, llegando a los humanos por contacto directo, a través de la cadena alimentaria o diseminados en el medio ambiente (por ejemplo, estiércol). Un buen enfoque para reducir los riesgos de la aparición de AMR es comprender cómo aparecen, su relación con el huésped, cómo interactúan o cómo se transmiten a los humanos. Este es uno de los objetivos de la Iniciativa Una Única Salud (One Health Initiative) que busca la integración de la salud humana, animal y ambiental bajo el mismo marco. Esta tesis tiene como objetivo caracterizar el resistoma ruminal y determinar la la heredabilidad de la composición de este resistoma en el vacuno lechero. Para ello, el metagenoma ruminal de 472 vacas frisonas de 14 granjas comerciales españolas fue secuenciado usando el dispositivo MinION de Oxford Nanopore Technologies. Después del control de calidad, las lecturas de ADN se analizaron con la herramienta SQMreads de SqueezeMeta (Tamames y Puente-Sánchez, 2019), una pipeline para metagenómica, que alinea cada lectura con una base de datos de referencia de genes y proporcionando el número de copias de cada gen presente en la muestra. Implementamos una integración personalizada de la base de datos integral de resistencia a antibióticos (CARD). El pipeline se implementó en el centro de supercomputación CESGA. Como resultado, se determinaron los 69 ARG más prevalentes. La heredabilidad de la abundancia relativa de los ARG más abundantes osciló entre 0,10 (mupA) y 0,49 (tetW). Las correlaciones más notables se encontraron entre msbA y metano (- 0.45), rpoB2 y rendimiento de grasa (-0.62) y macB y emisión de metano (- 0.40). Se analizaron 25 de estos genes individualmente y se calculó la correlación fenotípica entre su abundancia fenotípica y las de los bacteriófagos, observando altas correlaciones. Esto puede explicarse por la presencia de plásmidos resistente a múltiples fármacos y a una alta transferencia horizontal de genes mediada por bacteriófagos. Como conclusión, pudimos determinar los ARG más prevalentes en el ecosistema ruminal, que mostraron una alta heredabilidad de su abundancia relativa, con una fuerte correlación genética con carácteres productivos de importancia económica. Se necesitan más estudios para obtener información sobre el papel de estos genes en el metagenoma ruminal.[EN] The rumen resistome is the compound of all the antimicrobial resistance genes (ARGs) present in the microbes that inhabit the rumen. The World Health Organization (WHO) warned about the issue with antimicrobial resistant (AMRs) pathogens, as it is predicted that by 2050 multi-resistant bacteria will kill 10 million people per year, surpassing cancer as our main health concern. Among the 1,461 diseases recognised in humans, 60% of them are caused by multi- host pathogens capable of moving across species. And roughly 75% of the newly detected infective diseases over the last 30 years have been zoonotic. Here lies the importance of characterizing the rumen resistome, as ARGs could jump from faeces and saliva within and across species, arriving to humans via direct contact, through the food chain or disseminated in the environment (e.g. manure). A good approach to reduce the risks of the emergence of AMR is to understand how they appear, their relationship with the host, how they interact or how they are transmitted to humans. This is one of the goals of the One Health Initiative, which is the integration of human, animal and environmental health under the same framework. This thesis aims to contribute to this Initiative by characterizing the rumen resistome and estimating the host genetic control over thereof. The ruminal metagenome of 472 Friesian cows from 14 commercial Spanish farms were sequenced using the MinION device from Oxford Nanopore Technologies. After quality control, the DNA reads were analysed with the SQMreads tool from SqueezeMeta (Tamames and Puente-Sánchez, 2019), a pipeline for metagenomics. Aligning each read to a gene reference database and providing the number of copies of each gene present in the sample. We implemented a custom integration of the Comprehensive Antibiotic Resistance Database (CARD). The pipeline was implemented in the CESGA super-computing centre in Galicia. As a result, the 69 most prevalent ARGs were determined. The heritability of the relative abundance of the more abundant ARGs ranged between 0.10 (mupA) and 0.49 (tetW). The most remarkable correlations were found between msbA and methane emissions(- 0.45), rpoB2 and fat yield (-0.62) and macB and methane emission (-0.40). Twenty-five of these genes were analysed individually and their phenotypic correlation with bacteriophages was calculated, showing that their relative abundances are highly correlated between them and with the bacteriophages. This can be explained by the presence of a multidrug resistant plasmid and a high horizontal gene transfer mediated by bacteriophages. As a conclusion, we were able to determine the most prevalent ARGs in the ruminal ecosystem, and their relative abundance in the rumen resulted to be highly heritable, with strong genetic correlation with economically important traits. Further studies are needed to gain insights on the role of these genes in the rumen metagenome.[CA] El resistoma ruminal està compost per tots els gens de resistència antimicrobiana (ARG) presents en els microorganismes que habiten en el rumen. L'Organització Mundial de la Salut va advertir sobre el problema dels patògens resistents a antimicrobians (AMR), ja que es preveu que per a 2050 els bacteris multirresistentes deixaran 10 milions de matesal any, superant al càncer com el nostre principal problema de salut. Entre les 1,461 malalties reconegudes en humans, el 60% d'elles són causades per patògens de múltiples hostes capaços de moure's a través d'espècies. Aproximadament el 75% de les malalties infeccioses recentment detectades han sigut zoonóticas. Ací radica la importància de caracteritzar el resistoma ruminal, ja que els ARG podrien botar de les excrements i la saliva tant entre com intra espècies, arribant als humans per contacte directe, a través de la cadena alimentària o disseminats en el medi ambient (per exemple, fem) . Un bon enfocament per a reduir els riscos de l'aparició d'AMR és comprendre com apareixen, la seua relació amb l'hoste, com interactuen o com es transmeten als humans. Este és un dels objectius de la Iniciativa Una Única Salut (One Health Initiative) que busca la integració de la salut humana, animal i ambiental davall el mateix marc. El metagenoma ruminal de 472 vaques frisones de 14 granges comercials espanyoles va ser seqüenciat usant el dispositiu miniàs d'Oxford Nanopore Technologies. Després del control de qualitat, les lectures d'ADN es van analitzar amb la ferramenta SQMreads de SqueezeMeta (Tamames i Puente-Sánchez, 2019), una pipeline per a metagenómica. Alineant cada lectura amb una base de dades de referència de gens i proporcionant el nombre de còpies de cada gen present en la mostra. Implementem una integració personalitzada de la Base de dades integral de resistència a antibiòtics (CARD). La pipeline es va implementar en el centre de supercomputació CESGA. Com resultat, es van determinar els 69 ARG més prevalents. L'heredabilidad de l'abundància relativa dels ARG més abundants va oscil·lar entre 0,10 (mupA) i 0,49 (tetW) . Les correlacions més notables es van trobar entre msbA i metà (- 0.45) , rpoB2 i rendiment de greix (- 0.62) i macB i emissió de metà (-0.40). Es van analitzar 25 d'estos gens individualment i es va calcular la seua correlació fenotípica amb bacteriòfags, la qual cosa va demostrar que estan altament correlacionats entre ells i amb els propis bacteriòfags. Açò pot explicar-se per la presència d'un plasmidi resistent a múltiples fàrmacs i a una alta transferència horitzontal de gens mediada per bacteriòfags. Com a conclusió, vam poder determinar els ARG més prevalents en l'ecosistema ruminal, que van mostrar una alta heredabilidad de la seua abundància relativa, amb una forta correlació genètica amb trets econòmicament importants. Es necessiten més estudis per a obtindre informació sobre el paper d'estos gens en el metagenoma ruminal.López Catalina, A. (2020). Dairy cattle ruminal resistome: characterisation and association with productive traits. http://hdl.handle.net/10251/150876TFG

Agroecological Transitions: From Theory to Practice in Local Participatory Design

This Open Access book presents feedback from the ‘Territorial Agroecological Transition in Action’- TATA-BOX research project, which was devoted to these specific issues. The multidisciplinary and multi-organisation research team steered a four-year action-research process in two territories of France. It also presents: i) the key dimensions to be considered when dealing with agroecological transition: diversity of agriculture models, management of uncertainties, polycentric governance, autonomies, and role of actors’ networks; ii) an operational and original participatory process and associated boundary tools to support local stakeholders in shifting from a shared diagnosis to a shared action plan for transition, and in so doing developing mutual understanding and involvement; iii) an analysis of the main effects of the methodology on research organisation and on stakeholders’ development and application; iv) critical analysis and foresights on the main outcomes of TATA-BOX, provided by external researchers