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Single-cell RNA-Sequencing (scRNA-Seq) has undergone major technological advances in recent years, enabling the conception of various organism-level cell atlassing projects. With increasing numbers of datasets being deposited in public archives, there is a need to address the challenges of enabling the reproducibility of such data sets. Here, we describe guidelines for a minimum set of metadata to sufficiently describe scRNA-Seq experiments, ensuring reproducibility of data analyses.

Exposure based exercises are a common element of many gold standard treatments for anxiety disorders and post-traumatic stress disorder and virtual reality simulations have been evaluated as a platform for providing clients with opportunities for repeated exposure during treatment. Although research on virtual reality exposure therapy (VRET) indicates effectiveness and high levels of user satisfaction, VRETs require a participant to complete exposure exercises in-offices with specialized equipment. The current exploratory case method study evaluates the experience and outcomes of one student veteran with social anxiety disorder and PTSD completing twelve sessions of VRET exposure using a mobile phone simulation of a virtual grocery store. The participant reported decreases in psychological symptoms, improvements in neurological connectivity, and better sleep quality upon completing the trial. Results suggest that VRET using a mobile application is feasible and warrants further research to evaluate effectiveness more fully. Implications include the use of a mobile based virtual reality simulation for intervening in social anxiety for student veterans.

Museums reflect the practices of the dominant culture within the particular society in which they are located. This article examines the effects of museums offering texts, cultural artifacts and experiences in English only, which function to exclude patrons, often visiting in family groups, from culturally and linguistically diverse backgrounds. This article includes explanations of various theoretical frameworks that help to explain how the construction and dynamism of social boundaries impact museum participation and guide considerations about designing and implementing bilingual and multilingual practices. Examples of successful institutional implementation are included. Recent research findings indicate that positive results for museums and visitors are supported when multilingual practices are central to mission statements and institutional sustainability goals.

Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants. Data from large-scale RNA sequencing studies including Blueprint, PCAWG, ENCODE, GTEx and HipSci can be visualized next to each other. In Expression Atlas, users can query genes or gene-sets of interest and explore their expression across or within species, tissues, developmental stages in a constitutive or differential context, representing the effects of diseases, conditions or experimental interventions. All processed data matrices are available for direct download in tab-delimited format or as R-data. In addition to the web interface, data sets can now be searched and downloaded through the Expression Atlas R package. Novel features and visualizations include the on-the-fly analysis of gene set overlaps and the option to view gene co-expression in experiments investigating constitutive gene expression across tissues or other conditions.

Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations. Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks. Specifically, it uses curated rice reference pathways to derive pathway projections for an additional 66 species based on gene orthology, and facilitates display of gene expression, gene–gene interactions, and user-defined omics data in the context of these pathways. As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes periodic data and software upgrades. Via powerful, intuitive search interfaces, users can easily query across various portals and interactively analyze search results by clicking on diverse features such as genomic context, highly augmented gene trees, gene expression anatomograms, associated pathways, and external informatics resources. All data in Gramene are accessible through both visual and programmatic interfaces.

Motivation The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer. Results The RNASeq-er API (Application Programming Interface) enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices (Fragments Per Kilobase Of Exon Per Million Fragments Mapped, Transcripts Per Million, raw counts) as well as sample attributes annotated with ontology terms. To date over 270 00 RNA-Seq runs in nearly 10 000 studies (1PB of raw FASTQ data) in 264 species in ENA have been processed and made available via the API. Availability and Implementation The RNASeq-er API can be accessed at http://www.ebi.ac.uk/fg/rnaseq/api. The commands used to analyse the data are available in supplementary materials and at https://github.com/nunofonseca/irap/wiki/iRAP-single-library. Supplementary information Supplementary data are available at Bioinformatics online.

In this work, we focus on the study of structural and electrical properties of vanadium oxide thin films synthesized by RF magnetron sputtering. The samples were deposited on glass at 0%, 5%, 10% and 20%, O2 concentration inside the vacuum of the chamber. The films were characterized by x-ray Photoelectron Spectroscopy (XPS), Scanning Electron Microscopy (SEM), Conventional and High Resolution Transmission Electron Microscopy (CTEM and HRTEM, respectively), UV–vis Spectroscopy and Cyclic Voltammetry (CV). The increase in oxygen concentration induces agglomeration behaviour atmospheric-deposition-dependent on film characteristic surface, this phenomenon in turn, influences its structural and electrical properties. A reducing atmosphere enabled the formation of V2O5 to VO2 phases, respectively, the mixed-valence of V5+ and V4+ related with V2O5 and VO2 system were established. The existence of V2O5 and VO2 on the surface film is supported by x-ray photoelectron spectroscopy analysis. The reduction process in substrate surface was detected from 10%, content of O2 which showed a local minimum associated with agglomeration of V-oxide in the surface substrate, and a possible heterostructure configuration. The electrochemical response showed a minimum in diffusion cathodic associated to kinetic phenomena of double layer. However, the diffusion anodic was constant, associated to rapid electronic transfer and maximum coloration efficiency during electrochromic experiment. The co-existence phases on the surface films generates electrochromic and thermochromic behaviour.

Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼ 200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials.

In this work, relationships between chemical and physical properties of fluorine doped tin oxide films prepared by the chemical spray pyrolysis technique have been studied. Changes in the structural, optical and electrical properties of these films in relation to their doping concentrations determined by the resonant nuclear reaction analysis and x-ray photoelectron spectroscopy (XPS) techniques have been correlated. By XPS measurements, it was found that the fluorine content in the tin oxide films does not induce any chemical shift of the Sn and O core levels. At the same time, XPS measurements are carried out at low binding energy, shown that the valence band of heavy doped tin oxide changes with respect to that determined in SnO2 powder, due to the influence of the fluorine doping. In addition, it was shown that the formation of F–Sn complexes provides a decrease in both the concentration and mobility of the carriers.

CcGA20ox1 is a gene encoding a GA 20-oxidase, a gibberellin (GA) biosynthetic enzyme, previously isolated from the citrus hybrid Carrizo citrange (Citrus sinensis (L.) Osbeck x Poncirus trifoliata (L.) Raf.). Southern blot analysis of genomic DNA of Carrizo citrange with CcGA20ox1 suggested the presence in the hybrid of another gene encoding another GA 20-oxidase. A cDNA clone from this new gene (CcGA20ox2) was isolated using RNA from the other parent C. sinensis. CcGA20ox2 encoded a protein of 372 amino acids that showed 67.1% identify with CcGA20ox1, and its expression product catalyzed the in vitro conversion of GA(12) to GA(9), confirming that it corresponds to another active GA20ox. Amplification of genomic DNA and isolation of genomic clones of CcGA20ox1 and CcGA20ox2 revealed that the parental sources these genes in the hybrid were P. trifolicata and C. sinensis, respectively. The sequences of CcGA20ox1 and CcGA20ox2 showed that both genes contained two introns, which are also conserved in GA20ox genes of other species like Arabidopsis thaliana L., Pisum sativum L. and Solanum lycopersicum L. Determination of transcript levels in the Carrizo citrange hybrid by quantitative real-time polymerase chain reaction showed that CcGA20ox1 and expressed mainly in internodes, leaves and seeds, and CcGA20ox2 in flower buds and flowers at anthesis, with the genes having similar transcript levels in young developing fruits.

Tesis doctoral del Departamento del Departamento de Biotecnología de la Universidad Politécnica de Valencia, realizada en el Instituto de Biología Molecular y Celular de Plantas., El cultivo de los cítricos representa la mayor producción de frutos en el mundo y España, en particular, ocupa una posición relevante siendo el quinto productor y primer exportador mundial de cítricos para su consumo en fresco. La obtención de variedades de alta calidad comercial y elevada producción, capaces de satisfacer las exigencias del mercado, constituye un objetivo esencial de la citricultura actual. El desarrollo vegetativo determina la forma y el comportamiento general de la planta, de modo que tiene una influencia decisiva en la cantidad y calidad del fruto, así como en las prácticas culturales. Sin embargo, el conocimiento de las señales que regulan el desarrollo vegetativo en cítricos es limitado. En este trabajo se han desarrollado nuevas herramientas de genómica funcional, en particular colecciones de ESTs y micromatrices de DNA, con las que hemos estudiado en detalle diversos aspectos del desarrollo vegetativo en cítricos. Mediante el análisis funcional de una colección de ESTs generada a partir de tejidos vegetativos hemos aislado los genes relacionados con la función principal de estos tejidos, la fotosíntesis. Adicionalmente, a partir de la colección de ESTs del Proyecto de Genómica Funcional de Cítricos (CFGP) hemos identificado genes implicados en el metabolismo de isoprenoides y flavonoides en cítricos. La mayoría de los genes de la biosíntesis de fitohormonas derivadas de isoprenoides, como giberelinas (GAs), brasinosteroides y ácido abscísico no habían sido aislados antes en cítricos. La identificación de los genes de biosíntesis de monoterpenos y sesquiterpenos, responsables del aroma tanto de las hojas como del fruto, ha mostrado que la familia de terpeno sintasas en cítricos es una de las más amplias y diversas en plantas. El análisis de la expresión génica mediante micromatrices de DNA nos ha permitido elaborar mapas de expresión génica en los tejidos reproductivos y en los tejidos vegetativos, incluida la raíz.

14 pages, 4 figures, 4 tables.-- PMID: 18684239 [PubMed].-- Supporting information (Suppl fig. S1, tables S1-S12) available at: http://www3.interscience.wiley.com/journal/121370890/suppinfo, The effect of gibberellins (GA) on internode transcriptome was investigated in transgenic Carrizo citrange (Citrus sinensis × Poncirus trifoliata) plants overexpressing endogenous CcGA20ox1 (encoding a GA biosynthetic gene), and in non-transformed explants treated with GA3, using a citrus cDNA microarray. Substantial modulation of gene expression was found in sense CcGA20ox plants. Extensive up-regulation of genes involved in photosynthesis and carbon utilization, and down-regulation of those involved in protein synthesis and ribosome biogenesis were shown for the first time in plants with higher GA content. Importantly, increase of net photosynthesis in attached leaves was also demonstrated. Expression of other genes belonging to functional groups not reported previously to be regulated by GA (mainly abiotic and biotic stresses, and cuticle biosynthesis), and genes involved in cell division and cell wall architecture were also differentially expressed. Culture of citrus explants for 24 h in GA3 solution produced much lower changes in the transcriptome compared with CcGA20ox plants (1.6% versus 16%, respectively, of total genes in the microarray), suggesting that most of the changes observed in CcGA20ox plants were a consequence of a long-standing GA effect. Interestingly, genes related to abiotic and biotic stresses were similarly modulated in transgenics and GA3-treated explants., This work was supported by grants from the Ministerio de Ciencia y Tecnología of Spain (GEN2001-4885-C05). L. Huerta was recipient of a research grant from the Universidad Politécnica de Valencia.

Carrizo citrange (Citrus sinensis x Poncirus trifoliata) is a citrus hybrid widely used as a rootstock, whose genetic manipulation to improve different growth characteristics is of high agronomic interest. In this work, transgenic Carrizo citrange plants have been produced overexpressing sense and antisense CcGA20ox1 (a key enzyme of GA biosynthesis) under control of the 35S promoter to modify plant architecture. As expected, taller (sense) and shorter (antisense) phenotypes correlated with higher and lower levels, respectively, of active GA(1) in growing shoots. In contrast, other phenotypic characteristics seemed to be specific to citrus, or different from those described for similar transgenics in other species. For instance, thorns, typical organs of citrus at juvenile stages, were much longer in sense and shorter in antisense plants, and xylem tissue was reduced in leaf and internode of sense plants. Antisense plants presented a bushy phenotype, suggesting a possible effect of GAs on auxin biosynthesis and/or transport. The main foliole of sense plants was longer, although total leaf area was reduced. Leaf thickness was smaller in sense and larger in antisense plants due to changes in the spongy parenchyma. Internode cell length was not altered in transgenic plants, indicating that, in citrus, GAs regulate cell division rather than cell elongation. Interestingly, the phenotypes described were not apparent when transgenic plants were grafted on non-transgenic rootstock. This suggests that roots contribute to the GA economy of aerial parts in citrus and opens the possibility of using the antisense plants as dwarfing rootstocks.

A functional genomics project has been initiated to approach the molecular characterization of the main biological and agronomical traits of citrus. As a key part of this project, a citrus EST collection has been generated from 25 cDNA libraries covering different tissues, developmental stages and stress conditions. The collection includes a total of 22,635 high-quality ESTs, grouped in 11,836 putative unigenes, which represent at least one third of the estimated number of genes in the citrus genome. Functional annotation of unigenes which have Arabidopsis orthologues (68% of all unigenes) revealed gene representation in every major functional category, suggesting that a genome-wide EST collection was obtained. A Citrus clementina Hort. ex Tan. cv. Clemenules genomic library, that will contribute to further characterization of relevant genes, has also been constructed. To initiate the analysis of citrus transcriptome, we have developed a cDNA microarray containing 12,672 probes corresponding to 6875 putative unigenes of the collection. Technical characterization of the microarray showed high intra- and inter-array reproducibility, as well as a good range of sensitivity. We have also validated gene expression data achieved with this microarray through an independent technique such as RNA gel blot analysis.

Se llevaron a cabo seis recolectas ocasionales en la zona submareal e intermareal de Punta Arena y Cabo Pulmo, Baja California Sur, entre 1989 y 1994. Se registró la presencia de 115 especies, 66 de ellas pertenecientes a la clase Rhodophyceae, 23 a Phaeophyceae, 4 a Bacillariophyceae, 18 a Chlorophyceae y 4 a Cyanophyceae. En Punta Arena se localizaron 88 especies y en Cabo Pulmo 68. La lista florística se acompaña de datos sobre estacionalidad, estadio reproductivo, nivel de marea, sustrato, exposición al oleaje y el epifitismo asociado. La ficoflora de estas localidades es de afinidad tropical, encontrándose más diversificada en primavera. Se citan por primera vez para el Golfo de California a Pneophyllum conicum (E. Y. Dawson) Keats, Chamberlain et Baba, Hincksia rallsiae (Vickers) P.C. Silva y Acetabularia parvula Solms-Laubach.

Se llevaron a cabo 4 muestreos de algas marinas bentónicas en 3 localidades de las costas de Mazatlán, Sinaloa, mediante los cuales se determinó la presencia de 124 especies de algas marinas. Se identificaron 7 especies de Cyanophyceae, 72 de Rho­dophyceae, 12 de Phaeophyceae, 7 de Baci-llariophyceae y 26 de Chlorophyceae. Cada especie se acompaña de datos sobre su distribución en el área de estudio, el estado reproductivo, el nivel de marea, el modo, las facies y el epifitismo. Se comparó la diversidad de las especies entre la estación climática de lluvias y la de secas, durante 1971, 1983, 1987 y 1988. Rhodophyceae dominó en términos de diversidad en relación con las 4 clases restantes. La ficoflora de Mazatlán es tropical y es más diversa en la estación de lluvias.

Science in electronic and printed media allows the dissemination of knowledge among the various sectors of society, making scientific knowledge a stock of social knowledge. This stock of social knowledge can act as a typification or "recipe" for everyday life, and in the case of psychiatric and psychological knowledge, diagnoses of "mental illness" (psychopathology) can serve as a prescription both for behavior and for the definition of identity. Exploring the relationship between knowledge about mental disorders and the construction of identities highlights processes of social estrangement, stigmatization and negative definition of identity. RESUMEN La divulgacion de la ciencia en medios electronicos e impresos permite que el conocimiento se difunda con mayor alcance entre los diversos sectores de la sociedad, haciendo del conocimiento cientifico un acervo del conocimiento social. Este acervo puede funcionar como tipificacion o “receta” para la vida cotidiana, y en el caso del conocimiento psiquiatrico y psicologico, los diagnosticos de “enfermedades mentales” (psicopatologia), puede servir como prescripcion tanto para el comportamiento como para la definicion de la propia identidad. Explorar la relacion entre el conocimiento sobre los trastornos mentales y la construccion de las identidades pone de relieve procesos de extranamiento social, estigmatizacion y definicion negativa de la identidad.