An Intelligent Editor for Natural Language Processing of Unrestricted Text

The understanding of natural language by computational methods has been a continuing and elusive problem in artificial intelligence. In recent years there has been a resurgence in natural language processing research. Much of this work has been on empirical or corpus-based methods which use a data-driven approach to train systems on large amounts of real language data. Using corpus-based methods, the performance of part-of-speech (POS) taggers, which assign to the individual words of a sentence their appropriate part of speech category (e.g., noun, verb, preposition), now rivals human performance levels, achieving accuracies exceeding 95%. Such taggers have proved useful as preprocessors for such tasks as parsing, speech synthesis, and information retrieval. Parsing remains, however, a difficult problem, even with the benefit of POS tagging. Moreover, as sentence length increases, there is a corresponding combinatorial explosion of alternative possible parses. Consider the following sentence from a New York Times online article: After Salinas was arrested for murder in 1995 and lawyers for the bank had begun monitoring his accounts, his personal banker in New York quietly advised Salinas\u27 wife to move the money elsewhere, apparently without the consent of the legal department. To facilitate parsing and other tasks, we would like to decompose this sentence into the following three shorter sentences which, taken together, convey the same meaning as the original: Salinas was arrested for murder in 1995. Lawyers for the bank had begun monitoring his accounts. His personal banker in New York quietly advised Salinas\u27 wife to move the money elsewhere, apparently without the consent of the legal department. This study investigates the development of heuristics for decomposing such long sentences into sets of shorter sentences without affecting the meaning of the original sentences. Without parsing or semantic analysis, heuristic rules were developed based on: (1) the output of a POS tagger (Brill\u27s tagger); (2) the punctuation contained in the input sentences; and (3) the words themselves. The heuristic algorithms were implemented in an intelligent editor program which first augmented the POS tags and assigned tags to punctuation, and then tested the rules against a corpus of 25 New York Times online articles containing approximately 1,200 sentences and over 32,000 words, with good results. Recommendations are made for improving the algorithms and for continuing this line of research

Characterising the gene regulatory landscape of CD4+ T cells

Despite the high prevalence of immune-mediated diseases, the molecular mechanisms by which they arise and the influence of genetic variation in the predisposition to disease are not well understood. Immune susceptibility loci identified by genome wide association studies (GWAS) overlap with active regulatory elements in CD4+ T cells, and particularly in regulatory T cells (Tregs). CD4+ T cells are the orchestrators of the adaptive immune response and their dysfunction has been associated with immune-mediated disorders through uncontrolled activation and resistance to downregulation, which is usually mediated by Tregs. T cell activation requires the combination of T cell receptor (TCR) recognition of an antigen and CD28 co-stimulation. The role of CD28 co-stimulation requirement in the activation of different T cell subsets has been understudied. Here, I assessed the role of immune disease variants in modulating pathways underlying T cell activation and Treg function. For that, I activated CD4+ T cells using different intensities of CD28 and TCR signals, followed by genome-wide transcriptome and chromatin profiling of naive and memory cells. I observed that CD28 plays a critical role in the expression of genes involved in effector functions, cell cycle regulation in memory T cells and in disease susceptibility. I profiled the gene expression regulatory landscape in Tregs using a combination of genomic assays. Due to the scarce Treg numbers in peripheral blood I first optimised the ChIPmentation (ChM) sequencing protocol to profile H3K4me3 and H3K27ac histone modifications in Tregs. I combined it with chromatin accessibility and gene expression profiling in resting and stimulated Tregs from ten donors. I observed cases of alternative transcription, such as alternative splicing and promoter, induced by stimulation, which could be predicted by changes in the chromatin landscape. Finally, I assessed how genetic variability impacts the function of Tregs and how this can lead to autoimmunity. I carried a quantitative trait locus (QTL) mapping using RNA-seq, ATAC-seq, H3K4me3 and H3K27ac ChM-seq data from Tregs isolated from 100 individuals. Additionally, I processed publicly available data from naive T cells to distinguish the Treg specific effects from generic CD4+ T cell signals. I recapitulated known colocalisations between QTLs and immune GWAS loci, and identified previously unknown Treg specific colocalisations. My findings highlight the value of carrying QTL studies in rare immune cell types relevant to the disease

Genomic profiling of T-cell activation suggests increased sensitivity of memory T cells to CD28 costimulation

T-cell activation is a critical driver of immune responses. The CD28 costimulation is an essential regulator of CD4 T-cell responses, however, its relative importance in naive and memory T cells is not fully understood. Using different model systems, we observe that human memory T cells are more sensitive to CD28 costimulation than naive T cells. To deconvolute how the T-cell receptor (TCR) and CD28 orchestrate activation of human T cells, we stimulate cells using varying intensities of TCR and CD28 and profiled gene expression. We show that genes involved in cell cycle progression and division are CD28-driven in memory cells, but under TCR control in naive cells. We further demonstrate that T-helper differentiation and cytokine expression are controlled by CD28. Using chromatin accessibility profiling, we observe that AP1 transcriptional regulation is enriched when both TCR and CD28 are engaged, whereas open chromatin near CD28- sensitive genes is enriched for NF-kB motifs. Lastly, we show that CD28-sensitive genes are enriched in GWAS regions associated with immune diseases, implicating a role for CD28 in disease development. Our study provides important insights into the differential role of costimulation in naive and memory T-cell responses and disease susceptibility

Who lives there? About native and exotic Trees. An educational proposal to know the ecological importance of native forests and the problem of biological invasions

La creciente pérdida de bosques nativos y la invasión por especies de plantas exóticas en las Sierras de Córdoba constituyen problemas que conllevan serias consecuencias ambientales, sociales y económicas. Aquí presentamos una propuesta didáctica dirigida a alumnos del nivel primario, basada en el uso de actividades lúdicas y del Ciclo de Indagación. A través del juego, el contacto directo con el entorno natural y la indagación de primera mano se buscó que los alumnos conozcan las plantas leñosas nativas y exóticas presentes en la zona, así como también que perciban la importancia ecológica del bosque nativo y comprendan la problemática de las invasiones biológicas. Esta propuesta se centra en la interacción de los árboles nativos y exóticos con otros seres vivos a los que brindan refugio, sostén o alimento, entre otras funciones.The increasing loss of native forests and the invasion of exotic plant species in the mountains of Cordoba are serious problems involving environmental, social and economic consequences. We hereby present an educational proposal directed to primary school students, based on the use of recreational activities and the Inquiry Cycle. By means of games, direct contact with the natural environment, and frst-hand inquiry we sought students to know the native and exotic woody plants present in the area, as well as to perceive the ecological importance of native forests and understand the problem of biological invasions. This proposal focuses on the interaction of native and exotic trees with other living beings to which they provide refuge, support, or food, among other functions.Fil: Baranzelli, Matias Cristian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Córdoba, Silvina Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Ferreiro, Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Glinos, Evangelina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Maubecin, Constanza Clara. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Paiaro, Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Renny, Mauricio Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentin

Managing intra-EU mobility—do WHO principles of ethical recruitment have relevance?

BACKGROUND: The WHO Global Code of Practice on the International Recruitment of Health Personnel provides for guidance in health workforce management and cooperation in the international context. This article aims to examine whether the principles of the voluntary WHO Global Code of Practice can be applied to trigger health policy decisions within the EU zone of free movement of persons. METHODS: In the framework of the Joint Action on European Health Workforce Planning and Forecasting project (Grant Agreement: JA EUHWF 20122201 (see healthworkforce.eu)), focus group discussions were organised with over 30 experts representing ministries, universities and professional and international organisations. Ideas were collected about the applicability of the principles and with the aim to find EU law compatible, relevant solutions using a qualitative approach based on a standardised, semi-structured interview guide and pre-defined statements. RESULTS: Based on implementation practices summarised, focus group experts concluded that positive effects of adhering to the Code can be identified and useful ideas-compatible with EU law-exist to manage intra-EU mobility. The most relevant areas for intervention include bilateral cooperations, better use of EU financial resources, improved retention and integration policies and better data flow and monitoring. Improving retention is of key importance; however, ethical considerations should also apply within the EU. Compensation of source countries can be a solution to further elaborate on when developing EU financial mechanisms. Intra-EU circular mobility might be feasible and made more transparent if directed by tailor-made, institutional-level bilateral cooperations adjusted to different groups and profiles of health professionals. Integration policies should be improved as discrimination still exists when offering jobs despite the legal environment facilitating the recognition of professional qualifications. A system of feedback on registration/licencing data should be promoted providing for more evidence on intra-EU mobility and support its management. CONCLUSIONS: Workforce planning in EU Member States can be supported, and more equitable distribution of the workforce can be provided by building policy decisions on the principles of the WHO Code. Political commitment has to be strengthened in EU countries to adopt implementation solutions for intra-EU problems. Long-term benefits of respecting global principles of the Code should be better demonstrated in order to incentivise all parties to follow such long-term objectives

Daily fluctuations in pollination effectiveness explain higher efficiency of native over exotic bees in Lepechinia floribunda (Lamiaceae)

Despite Stebbins’ principle of the most efficient pollinator being proposed decades ago, the most important pollinators are still mainly identified using the frequency of visits to flowers. This shortcoming results in a gap between the characterization of the flower visitors of a plant species and a reliable estimation of the plant fitness consequences of the mutualistic interaction. The performance of a mutualistic visitor depends on its abundance, behaviour, effectiveness (pollen removal and deposition per unit time) and efficiency (seed set per unit time) conditioned by the temporal matching between pollinator activity and temporal patterns of maturation of the sexual functions of flowers. Although there have been recent attempts to provide a conceptual and methodological framework to characterize pollinators’ performance, few have combined all key elements of visitors and plants to provide an accurate estimation of pollinators’ performance under natural conditions.Fil: Baranzelli, Matias Cristian. Universidad Nacional Autónoma de México; México. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Benitez-Vieyra, Santiago Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Glinos, Evangelina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Trenchi, Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Córdoba, Silvina Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Camina, Julia Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Ashworth, Lorena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Sersic, Alicia Noemi. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Cocucci, Andrea Aristides. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Fornoni, Juan Enrique. Universidad Nacional Autónoma de México; Méxic

Can genetically based clines in plant defence explain greater herbivory at higher latitudes?

Greater plant defence is predicted to evolve at lower latitudes in response to increased herbivore pressure. However, recent studies question the generality of this pattern. In this study, we tested for genetically based latitudinal clines in resistance to herbivores and underlying defence traits of Oenothera biennis. We grew plants from 137 populations from across the entire native range of O. biennis. Populations from lower latitudes showed greater resistance to multiple specialist and generalist herbivores. These patterns were associated with an increase in total phenolics at lower latitudes. A significant proportion of the phenolics were driven by the concentrations of two major ellagitannins, which exhibited opposing latitudinal clines. Our analyses suggest that these findings are unlikely to be explained by local adaptation of herbivore populations or genetic variation in phenology. Rather greater herbivory at high latitudes can be explained by latitudinal clines in the evolution of plant defences.</p