INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens

Abstract In response to the EFSA call New approaches in identifying and characterizing microbial and chemical hazards, the project INNUENDO (https://sites.google.com/site/theinnuendoproject/) aimed to design an analytical platform and standard procedures for the use of whole-genome sequencing in surveillance and outbreak investigation of food-borne pathogens. The project firstly attempted to identify existing flaws and needs, and then to provide applicable cross-sectorial solutions. The project focused in developing a platform for small countries with limited economical and personnel resources. To achieve these goals, we applied a user-centered design strategy involving the end-users, such as microbiologists in public health and veterinary authorities, in every step of the design, development and implementation phases. As a result, we delivered the INNUENDO Platform V1.0 (https://innuendo.readthedocs.io/en/latest/), a stand-alone, portable, open-source, end-to-end system for the management, analysis, and sharing of bacterial genomic data. The platform uses Nextflow workflow manager to assemble analytical software modules in species-specific protocols that can be run using a user-friendly interface. The reproducibility of the process is ensured by using Docker containers and throught the annotation of the whole process using an ontology. Several modules, available at https://github.com/TheInnuendoProject, have been developed including: genome assembly and species confirmation; fast genome clustering; in silico typing; standardized species-specific phylogenetic frameworks for Campylobacter jejuni, Yersinia enterocolitica, Salmonella enterica and Escherichia coli based on an innovative gene-by-gene methodology; quality control measures from raw reads to allele calling; reporting system; a built-in communication protocols and a strain classification system enabling smooth communication during outbreak investigation. As proof-of-concepts, the proposed solutions have been thoroughly tested in simulated outbreak conditions by several public health and veterinary agencies across Europe. The results have been widely disseminated through several channels (web-sites, scientific publications, organization of workshops). The INNUENDO Platform V1.0 is effectively one of the models for the usage of open-source software in genomic epidemiology.Peer reviewe

Steering a Tractor by Means of an EMG-Based Human-Machine Interface

An electromiographic (EMG)-based human-machine interface (HMI) is a communication pathway between a human and a machine that operates by means of the acquisition and processing of EMG signals. This article explores the use of EMG-based HMIs in the steering of farm tractors. An EPOC, a low-cost human-computer interface (HCI) from the Emotiv Company, was employed. This device, by means of 14 saline sensors, measures and processes EMG and electroencephalographic (EEG) signals from the scalp of the driver. In our tests, the HMI took into account only the detection of four trained muscular events on the driver’s scalp: eyes looking to the right and jaw opened, eyes looking to the right and jaw closed, eyes looking to the left and jaw opened, and eyes looking to the left and jaw closed. The EMG-based HMI guidance was compared with manual guidance and with autonomous GPS guidance. A driver tested these three guidance systems along three different trajectories: a straight line, a step, and a circumference. The accuracy of the EMG-based HMI guidance was lower than the accuracy obtained by manual guidance, which was lower in turn than the accuracy obtained by the autonomous GPS guidance; the computed standard deviations of error to the desired trajectory in the straight line were 16 cm, 9 cm, and 4 cm, respectively. Since the standard deviation between the manual guidance and the EMG-based HMI guidance differed only 7 cm, and this difference is not relevant in agricultural steering, it can be concluded that it is possible to steer a tractor by an EMG-based HMI with almost the same accuracy as with manual steering

Genetic landscape of 6089 inherited retinal dystrophies affected cases in Spain and their therapeutic and extended epidemiological implications

Inherited retinal diseases (IRDs), defined by dysfunction or progressive loss of photoreceptors, are disorders characterized by elevated heterogeneity, both at the clinical and genetic levels. Our main goal was to address the genetic landscape of IRD in the largest cohort of Spanish patients reported to date. A retrospective hospital-based cross-sectional study was carried out on 6089 IRD affected individuals (from 4403 unrelated families), referred for genetic testing from all the Spanish autonomous communities. Clinical, demographic and familiar data were collected from each patient, including family pedigree, age of appearance of visual symptoms, presence of any systemic findings and geographical origin. Genetic studies were performed to the 3951 families with available DNA using different molecular techniques. Overall, 53.2% (2100/3951) of the studied families were genetically characterized, and 1549 different likely causative variants in 142 genes were identified. The most common phenotype encountered is retinitis pigmentosa (RP) (55.6% of families, 2447/4403). The most recurrently mutated genes were PRPH2, ABCA4 and RS1 in autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL) NON-RP cases, respectively; RHO, USH2A and RPGR in AD, AR and XL for non-syndromic RP; and USH2A and MYO7A in syndromic IRD. Pathogenic variants c.3386G > T (p.Arg1129Leu) in ABCA4 and c.2276G > T (p.Cys759Phe) in USH2A were the most frequent variants identified. Our study provides the general landscape for IRD in Spain, reporting the largest cohort ever presented. Our results have important implications for genetic diagnosis, counselling and new therapeutic strategies to both the Spanish population and other related populations.This work was supported by the Instituto de Salud Carlos III (ISCIII) of the Spanish Ministry of Health (FIS; PI16/00425 and PI19/00321), Centro de Investigación Biomédica en Red Enfermedades Raras (CIBERER, 06/07/0036), IIS-FJD BioBank (PT13/0010/0012), Comunidad de Madrid (CAM, RAREGenomics Project, B2017/BMD-3721), European Regional Development Fund (FEDER), the Organización Nacional de Ciegos Españoles (ONCE), Fundación Ramón Areces, Fundación Conchita Rábago and the University Chair UAM-IIS-FJD of Genomic Medicine. Irene Perea-Romero is supported by a PhD fellowship from the predoctoral Program from ISCIII (FI17/00192). Ionut F. Iancu is supported by a grant from the Comunidad de Madrid (CAM, PEJ-2017-AI/BMD7256). Marta del Pozo-Valero is supported by a PhD grant from the Fundación Conchita Rábago. Berta Almoguera is supported by a Juan Rodes program from ISCIII (JR17/00020). Pablo Minguez is supported by a Miguel Servet program from ISCIII (CP16/00116). Marta Corton is supported by a Miguel Servet program from ISCIII (CPII17/00006). The funders played no role in study design, data collection, data analysis, manuscript preparation and/or publication decisions

La producción científica sobre América Latína a través de las revistas españolas de ciencias sociales y humanidades

[ES] Se presenta un análisis cuantitativo bibliográfica sobre la producción científica de temática latinoamericana aparecida en revistas españolas de Ciencias Sociales y Humanidades durante el periodo 1975-1986. El trabajo se complementa con los datos obtenidos en el Servicio de Acceso al Documento Primario del ISOC para loa años 1984-1987, El análisis realizado permite conocer datos globales sobre el número de artículos y revistas, asi como las materias y los países preferidos por los americanistas españoles. Se recogen conclusiones sobre el distinto comportamiento de las revistas de Humanidades en relación con las de Ciencia y Tecnología, carencias y modas coyunturales de la literatura y problemática que aboga por una mayor cooperación entre loa Centros de Documentación de habla española.[EN] This paper gives a quantitative bibliographic analysis of scientific production on Lationameriean subjects as published in Spanish Social Sciences and Humanities journals during the period 1975-1986. The data obtained from the "Document Retrieval and Supply Service" of tbe ISOC for the period 1984-87 completes the study. The resulta of the analysis provide global numerical information on the articles and journala, and an the subjects preferred by the Spanish expeits on Latin America. The conclusions show the lack of bibliometric studies in Humanities journals compared with those in Seientific and Technological ones, and the need for greater cooperation between Spanish-speaking documentation C entres.Peer reviewe