Synapse at CAp 2017 NER challenge: Fasttext CRF

We present our system for the CAp 2017 NER challenge which is about named entity recognition on French tweets. Our system leverages unsupervised learning on a larger dataset of French tweets to learn features feeding a CRF model. It was ranked first without using any gazetteer or structured external data, with an F-measure of 58.89\%. To the best of our knowledge, it is the first system to use fasttext embeddings (which include subword representations) and an embedding-based sentence representation for NER

Can consumers learn to ask three questions to improve shared decision making? A feasibility study of the ASK (AskShareKnow) Patient–Clinician Communication Model® intervention in a primary health-care setting

Funded by Informed Medical Decisions Foundation. Grant Number: #0175-1 National Health and Medical Research Council Public Health Training Fellowship. Grant Number: 568962Peer reviewedPublisher PD

Recurrent mutualism breakdown events in a legume rhizobia metapopulation.

Bacterial mutualists generate major fitness benefits for eukaryotes, reshaping the host phenotype and its interactions with the environment. Yet, microbial mutualist populations are predicted to generate mutants that defect from providing costly services to hosts while maintaining the capacity to exploit host resources. Here, we examined the mutualist service of symbiotic nitrogen fixation in a metapopulation of root-nodulating Bradyrhizobium spp. that associate with the native legume Acmispon strigosus. We quantified mutualism traits of 85 Bradyrhizobium isolates gathered from a 700 km transect in California spanning 10 sampled A. strigosus populations. We clonally inoculated each Bradyrhizobium isolate onto A. strigosus hosts and quantified nodulation capacity and net effects of infection, including host growth and isotopic nitrogen concentration. Six Bradyrhizobium isolates from five populations were categorized as ineffective because they formed nodules but did not enhance host growth via nitrogen fixation. Six additional isolates from three populations failed to form root nodules. Phylogenetic reconstruction inferred two types of mutualism breakdown, including three to four independent losses of effectiveness and five losses of nodulation capacity on A. strigosus. The evolutionary and genomic drivers of these mutualism breakdown events remain poorly understood

CD40L Deficiency Attenuates Diet-Induced Adipose Tissue Inflammation by Impairing Immune Cell Accumulation and Production of Pathogenic IgG-Antibodies

BACKGROUND: Adipose tissue inflammation fuels the metabolic syndrome. We recently reported that CD40L--an established marker and mediator of cardiovascular disease--induces inflammatory cytokine production in adipose cells in vitro. Here, we tested the hypothesis that CD40L deficiency modulates adipose tissue inflammation in vivo. METHODOLOGY/PRINCIPAL FINDINGS: WT or CD40L(-/-) mice consumed a high fat diet (HFD) for 20 weeks. Inflammatory cell recruitment was impaired in mice lacking CD40L as shown by a decrease of adipose tissue macrophages, B-cells, and an increase in protective T-regulatory cells. Mechanistically, CD40L-deficient mice expressed significantly lower levels of the pro-inflammatory chemokine MCP-1 both, locally in adipose tissue and systemically in plasma. Moreover, levels of pro-inflammatory IgG-antibodies against oxidized lipids were reduced in CD40L(-/-) mice. Also, circulating low-density lipoproteins and insulin levels were lower in CD40L(-/-) mice. However, CD40L(-/-) mice consuming HFD were not protected from the onset of diet-induced obesity (DIO), insulin resistance, and hepatic steatosis, suggesting that CD40L selectively limits the inflammatory features of diet-induced obesity rather than its metabolic phenotype. Interestingly, CD40L(-/-) mice consuming a low fat diet (LFD) showed both, a favorable inflammatory and metabolic phenotype characterized by diminished weight gain, improved insulin tolerance, and attenuated plasma adipokine levels. CONCLUSION: We present the novel finding that CD40L deficiency limits adipose tissue inflammation in vivo. These findings identify CD40L as a potential mediator at the interface of cardiovascular and metabolic disease

Programa de intervención en representaciones de creatividad y motivación académica de adolescentes

Creativity and its promotion are widespread concerns in education. However, few efforts have been made to implement intervention programs designed to promote creativity and other related aspects (e.g., academic motivation). The Future Problem Solving Program International (FPSPI), aimed for training creativity representations and creative problem solving skills in young people, has been one of the most implemented programs. This intervention’s materials and activities were adapted for Portuguese students, and a longitudinal study was conducted. The program was implemented during four months, in weekly sessions, by thirteen teachers. Teachers received previous training for the program and during the program’s implementation. Intervention participants included 77 Basic and Secondary Education students, and control participants included 78 equivalent students. Pretest-posttest measures of academic motivation and creativity representations were collected. Results suggest a significant increase, in the intervention group, in motivation and the appropriate representations of creativity. Practical implications and future research perspectives are presented.A criatividade e sua promoção geram grande preocupação em educação. Contudo, poucos esforços têm existido para implementar programas destinados a sua promoção e de outros aspetos relacionados (e.g., motivação acadêmica). O Future Problem Solving Program International (FPSPI), criado para melhorar as representações de criatividade e a resolução criativa de problemas em jovens, tem sido um dos mais implementados. Os seus materiais e atividades foram adaptados para estudantes portugueses, efetuando-se um estudo longitudinal. O programa foi implementado durante quatro meses, semanalmente, por treze professores, que receberam formação antes e durante a implementação. O grupo experimental incluiu 77 estudantes do Ensino Básico e Secundário, apresentando o grupo de controlo 78 estudantes com características equivalentes. Os dados sobre a motivação e criatividade foram recolhidos num pré e pós-teste. Os resultados sugerem um aumento significativo na motivação e crenças apropriadas de criatividade no grupo experimental. Implicações práticas e perspectivas para investigações futuras são apresentadas.La creatividad y su promoción generan gran preocupación en educación. Sin embargo, han sido llevados a cabo pocos esfuerzos para implementar programas de promoción de la creatividad y otros aspectos (e.g., motivación académica). El Future Problem Solving Program International (FPSPI), creado para mejorar las representaciones de creatividad y la solución creativa de problemas en jóvenes, ha sido bastante implementado. Se adaptaron sus materiales y actividades para estudiantes portugueses, y se desarrolló un estudio longitudinal. El programa se implementó semanalmente durante cuatro meses por trece profesores, que recibieron formación antes y durante la implementación. El grupo experimental incluyó 77 estudiantes de Educación Primaria y Secundaria y el grupo de control incluyó 78 estudiantes con características semejantes. Los datos de motivación y creatividad fueron recogidos en un pre y post-test, sugiriendo un aumento significativo de motivación y creencias apropiadas sobre la creatividad en el grupo experimental. Se presentan implicaciones prácticas y perspectivas para futuras investigaciones.Fundação para a Ciência e a Tecnologia (FCT) - SFRH/BPD/80825/201

Managing for ecological resilience of pinyon–juniper ecosystems during an era of woodland contraction

Abstract Dryland woodland ecosystems worldwide have experienced widespread drought‐ and heat‐related tree mortality events coupled with extreme wildfire behavior. In contrast to other forest types where the emphasis has been on the silvicultural enhancement of ecosystem resilience and restoration of structural heterogeneity, limited frameworks are available for management to improve drought resilience in semiarid woodlands. This challenge is especially acute in pinyon–juniper woodlands, a dominant vegetation type across western North America that has experienced extensive tree die‐off over the past several decades while simultaneously undergoing expansion in portions of its range. In this paper, we describe the critical and urgent need to manage for future drought resilience in these highly vulnerable ecosystems and synthesize the current state of knowledge on how to enhance woodland resilience to drought coupled with high temperatures and associated disturbances. We present a landscape prioritization framework for guiding management goals and practices that requires prioritization of efforts based on the need for action and the probability of a positive outcome. Four guiding factors include historical woodland structure and drivers of long‐term landscape change, current vegetation structure and composition, future climate suitability, and habitat and resource value. In summarizing the strength of evidence supporting our recommendations, we identify critical knowledge gaps and highlight the importance of adaptive management strategies that reflect current uncertainties. This will ultimately allow for improved management of diverse semiarid woodland ecosystems that are undergoing substantial changes due to past and present land use, biological invasions, and climate change

Dynamic Interactions Between Mega Symbiosis ICEs and Bacterial Chromosomes Maintain Genome Architecture.

Acquisition of mobile genetic elements can confer novel traits to bacteria. Some integrative and conjugative elements confer upon members of Bradyrhizobium the capacity to fix nitrogen in symbiosis with legumes. These so-called symbiosis integrative conjugative elements (symICEs) can be extremely large and vary as monopartite and polypartite configurations within chromosomes of related strains. These features are predicted to impose fitness costs and have defied explanation. Here, we show that chromosome architecture is largely conserved despite diversity in genome composition, variations in locations of attachment sites recognized by integrases of symICEs, and differences in large-scale chromosomal changes that occur upon integration. Conversely, many simulated nonnative chromosome-symICE combinations are predicted to result in lethal deletions or disruptions to architecture. Findings suggest that there is compatibility between chromosomes and symICEs. We hypothesize that the size and structural flexibility of symICEs are important for generating combinations that maintain chromosome architecture across a genus of nitrogen-fixing bacteria with diverse and dynamic genomes

Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome

Contact with poison ivy plants is widely dreaded because they produce a natural product called urushiol that is responsible for allergenic contact delayed-dermatitis symptoms lasting for weeks. For this reason, the catchphrase most associated with poison ivy is “leaves of three, let it be”, which serves the purpose of both identification and an appeal for avoidance. Ironically, despite this notoriety, there is a dearth of specific knowledge about nearly all other aspects of poison ivy physiology and ecology. As a means of gaining a more molecular-oriented understanding of poison ivy physiology and ecology, Next Generation DNA sequencing technology was used to develop poison ivy root and leaf RNA-seq transcriptome resources. De novo assembled transcriptomes were analyzed to generate a core set of high quality expressed transcripts present in poison ivy tissue. The predicted protein sequences were evaluated for similarity to SwissProt homologs and InterProScan domains, as well as assigned both GO terms and KEGG annotations. Over 23,000 simple sequence repeats were identified in the transcriptome, and corresponding oligo nucleotide primer pairs were designed. A pan-transcriptome analysis of existing Anacardiaceae transcriptomes revealed conserved and unique transcripts among these species

Re-evaluation of a Tn5::gacA mutant of Pseudomonas syringae pv. tomato DC3000 uncovers roles for uvrC and anmK in promoting virulence.

Pseudomonas syringae is a taxon of plant pathogenic bacteria that can colonize and proliferate within the interior space of leaf tissue. This process requires P. syringae to rapidly upregulate the production of virulence factors including a type III secretion system (T3SS) that suppress host defenses. GacS/A is a two-component system that regulates virulence of many plant and animal pathogenic bacteria including P. syringae. We recently investigated the virulence defect of strain AC811, a Tn5::gacA mutant of P. syringae pv. tomato DC3000 that is less virulent on Arabidopsis. We discovered that decreased virulence of AC811 is not caused by loss of GacA function. Here, we report the molecular basis of the virulence defect of AC811. We show that AC811 possesses a nonsense mutation in anmK, a gene predicted to encode a 1,6-anhydromuramic acid kinase involved in cell wall recycling. Expression of a wild-type allele of anmK partially increased growth of AC811 in Arabidopsis leaves. In addition to the defective anmK allele, we also show that the Tn5 insertion in gacA exerts a polar effect on uvrC, a downstream gene encoding a regulator of DNA damage repair. Expression of the wild-type anmK allele together with increased expression of uvrC fully restored the virulence of AC811 during infection of Arabidopsis. These results demonstrate that defects in anmK and uvrC are together sufficient to account for the decreased virulence of AC811, and suggest caution is warranted in assigning phenotypes to GacA function based on insertional mutagenesis of the gacA-uvrC locus

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria

Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/