VMD: a community annotation database for oomycetes and microbial genomes

The VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two plant pathogens Phytophthora sojae and Phytophthora ramorum. With the completion of the draft genome sequences of these pathogens in collaboration with the DOE Joint Genome Institute (JGI), we have created this resource to make the sequences publicly available. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with ∼19 000 and ∼16 000 gene models, respectively. We used two different statistical methods to validate these gene models, Fickett's and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, we could assign putative functions to 17 694 genes in P.sojae and 14 700 genes in P.ramorum. We created an easy-to-use genome browser to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are ∼ 1600 gene models for P.sojae and ∼700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs. The database is publicly available at

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Autosomal Recessive Cerebellar Atrophy and Spastic Ataxia in Patients With Pathogenic Biallelic Variants in GEMIN5

The hereditary ataxias are a heterogenous group of disorders with an increasing number of causative genes being described. Due to the clinical and genetic heterogeneity seen in these conditions, the majority of such individuals endure a diagnostic odyssey or remain undiagnosed. Defining the molecular etiology can bring insights into the responsible molecular pathways and eventually the identification of therapeutic targets. Here, we describe the identification of biallelic variants in the GEMIN5 gene among seven unrelated families with nine affected individuals presenting with spastic ataxia and cerebellar atrophy. GEMIN5, an RNA-binding protein, has been shown to regulate transcription and translation machinery. GEMIN5 is a component of small nuclear ribonucleoprotein (snRNP) complexes and helps in the assembly of the spliceosome complexes. We found that biallelic GEMIN5 variants cause structural abnormalities in the encoded protein and reduce expression of snRNP complex proteins in patient cells compared with unaffected controls. Finally, knocking out endogenous Gemin5 in mice caused early embryonic lethality, suggesting that Gemin5 expression is crucial for normal development. Our work further expands on the phenotypic spectrum associated with GEMIN5-related disease and implicates the role of GEMIN5 among patients with spastic ataxia, cerebellar atrophy, and motor predominant developmental delay.The C57BL/6NTac-Gemin5em1(IMPC)H/H mice and phenotypes were generated at the MRC Harwell Institute. The knockout mouse generation protocol has been approved as per MRC Harwell Institute guidelines. The MRC Harwell Institute generated the mice as part of the International Mouse Phenotyping Consortium (IMPC) and has received funding from the National Institutes for Health for generating and/or phenotyping (5UM1HG006348-08) the C57BL/6NTac-Gemin5em1(IMPC)H/H mice. The research reported in this publication is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Funding and associated primary phenotypic information may be found at www.mousephenotype.org

The Role of Trust in Public Attitudes toward Invasive Species Management on Guam: A Case Study

Public attitudes toward invasive alien species management and trust in managers’ ability to effectively manage non-native species can determine public support for conservation action. Guam has experienced widespread species loss and ecosystem transformation due to invasive species. Despite Guam’s long history with invasives and efforts to eradicate them, we know little about the sociological context of invasive species. Using focused group discussions, we explore public attitudes toward invasive species management. Respondents expressed support for management activities and a desire to participate directly in conservation actions. Participants also expressed frustration with government institutions and lack of confidence in managers’ abilities to control invasive species. Perceptions of managers’ trustworthiness, communication with managers, and positive personal experiences with managers were related to positive attitudes about management and support for existing initiatives

Contenidos audiovisuales y plataformas VoD en España: estudios de caso

Este libro editado en formato PDF forma parte de la colección iniciada en el año 2012 a partir de la compilación de los trabajos de investigación más destacados realizados por el estudiantado de la asignatura Estructura del mercado audiovisual, en el grado de Comunicación Audiovisual de la Universidad de Málaga. Aquí se abordan objetos de estudio relacionados con la producción y el consumo de contenidos audiovisuales desde diversas metodologías que analizan los diferentes sectores del audiovisual desde una perspectiva industrial y económica. En una disciplina en la que se estima necesaria una mayor actualización en la investigación académica, los trabajos aquí presentados presentan casos de estudio paradigmáticos del estado de la industria del audiovisual en España. Dichos textos, presentados aquí como capítulos, suponen la introducción en la investigación de estudiantes que combinan su formación académica e investigadora con su formación como profesionales en el área de la Comunicación Audiovisual. Ofrecemos aquí una selección de aquellas investigaciones que destacan por su interés, su capacidad analítica y crítica, su actualidad, su pertinencia y su disciplinada adecuación a una metodología de investigación apropiada dentro de las Ciencias Sociales. En el año 2022, a las puertas de lo que parece una inminente recesión económica, las industrias audiovisuales han recuperado parte del volumen de negocio perdido durante los años de pandemia de Covid-19. Las plataformas OTT han dejado de constituir una novedad y se han integrado y consolidado dentro del mercado, como medio de comercialización de contenidos audiovisuales prioritario en los hogares

First Very Long Baseline Interferometry Detections at 870 μm

The first very long baseline interferometry (VLBI) detections at 870 μm wavelength (345 GHz frequency) are reported, achieving the highest diffraction-limited angular resolution yet obtained from the surface of the Earth and the highest-frequency example of the VLBI technique to date. These include strong detections for multiple sources observed on intercontinental baselines between telescopes in Chile, Hawaii, and Spain, obtained during observations in 2018 October. The longest-baseline detections approach 11 Gλ, corresponding to an angular resolution, or fringe spacing, of 19 μas. The Allan deviation of the visibility phase at 870 μm is comparable to that at 1.3 mm on the relevant integration timescales between 2 and 100 s. The detections confirm that the sensitivity and signal chain stability of stations in the Event Horizon Telescope (EHT) array are suitable for VLBI observations at 870 μm. Operation at this short wavelength, combined with anticipated enhancements of the EHT, will lead to a unique high angular resolution instrument for black hole studies, capable of resolving the event horizons of supermassive black holes in both space and time