6 research outputs found

    Rendering co-author graphs using linked-open-data fromWikidata

    No full text
    Wikidata is the linked-open-data graph of the Wikimedia foundation with its most known sibling Wikipedia (Vrandečić, 2012). What Wikipedia is to text, Wikidata is to data. Like in Wikipedia linked-data can be added for everyone, by everyone. This makes Wikidata a very rich source of data. A substantial part of the data on Wikidata is about scientific publications and the authors of these publications (Taraborelli et al., 2016). Scholia is a tool that uses this data to create a profile page for authors and publications (Nielsen et al., 2017). This report describes a workflow to create co-author graphs using the data from Scholia

    MoodBar: increasing new user retention in Wikipedia through lightweight socialization

    No full text
    Socialization in online communities allows existing members to welcome and recruit newcomers, introduce them to com-munity norms and practices, and sustain their early participa-tion. However, socializing newcomers does not come for free: in large communities, socialization can result in a significant workload for mentors and is hard to scale. In this study we present results from an experiment that measured the effect of a lightweight socialization tool on the activity and reten-tion of newly registered users attempting to edit for the first time Wikipedia. Wikipedia is struggling with the retention of newcomers and our results indicate that a mechanism to elicit lightweight feedback and to provide early mentoring to new-comers improves their chances of becoming long-term con-tributors. Author Keywords Wikipedia, online community, socialization, user retention

    Enlace entre imagem e palavra: o livro ilustrado criado por mulheres

    No full text
    Esta dissertação investiga o enlace narrativo entre as linguagens verbal e visual em livros ilustrados criados por mulheres. Pretende-se, com a pesquisa, enfocar na visualidade tendo como material de análise a criação de mulheres. O objetivo é analisar a articulação entre imagem e palavra presente nas narrativas de livros ilustrados brasileiros elaborados por mulheres e selecionados pelo PNLD Literário de 2018 do Ensino Fundamental (1º a 3º ano). A pesquisa justifica-se pela relevância do livro ilustrado na formação literária e humana das crianças, pela importância das imagens na construção narrativa do livro ilustrado e pela pertinência da autoria feminina na literatura infantil. A pesquisa, de caráter analítico, ocorreu por meio da seleção de obras do PNLD Literário de 2018 escritas e ilustradas pela mesma autora: As cores dos pássaros, de Lúcia Hiratsuka, Dona Nenê e o sumiço do brinco, de Rita Taraborelli e Claro Cleusa. Claro, Clóvis, de Raquel Matsushita. Ao longo da dissertação, objetivos específicos nortearam o trabalho, tais como investigar o percurso da literatura infantil e do livro ilustrado e o lugar da autora nesse cenário; descrever o percurso formativo das autoras das obras selecionadas; analisar a relação entre a imagem e a palavra presente em livros ilustrados produzidos por mulheres e selecionados pelo PNLD Literário 2018 do Ensino Fundamental (1º a 3º ano) e refletir como a imagem representa elementos do texto verbal (tempo, espaço e personagens). A fundamentação teórica voltada à literatura baseia-se em Bakhtin (2011), Barthes (2011), Coelho (2000), Hunt (2013), Lajolo e Zilberman (2007), Ramos e Panozzo (2011), Zilberman (2003, 2005, 2012) e outros autores. Para o recorte histórico da mulher na sociedade, a pesquisa foi embasada em Beauvoir (1970), Dalcastagnè (2007), Duarte (2010), Knapp (2021), Louro (2001), Wollstonecraft (2016), Woolf (2014), Zinani (2014, 2021) e outras autoras. Por fim, na análise da narrativa verbal e visual, os estudos de Adam (2008), Dondis (1997), Linden (2018), Heller (2013), Nikolajeva e Scott (2011), Oliveira (2008) e outros serviram de aporte teórico à pesquisa. Para a discussão do corpus, foi realizado o estudo dos paratextos de cada obra, da construção da narrativa verbal e visual e da relação entre palavra e imagem na condução do enredo. O estudo demonstra a relevância da imagem, muitas vezes tida como secundária, na geração de sentidos e na polissemia das obras literárias para as infâncias. Por meio da pesquisa, foi possível analisar as nuances de cada uma das histórias selecionadas e apontar o quanto a aproximação e o distanciamento entre as palavras e as imagens podem agregar sentidos às narrativas. Destaca-se ainda o papel fundamental do design gráfico, que propicia a união entre as duas instâncias e constrói a materialidade do livro. Por fim, salienta-se a importância de uma educação para as imagens, visto que, no livro ilustrado, ler as palavras é insuficiente para entender as possibilidades de sentido oferecidas pela narrativa. [resumo fornecido pelo autor]This dissertation investigates the narrative link between verbal and visual languages in picture books created by women. The research intends to focus on visuality, having as material for analysis the creation of women. The objective is to analyze the articulation between image and word present in the narratives of Brazilian picture books written by women and selected by PNLD Literário of Elementary School (1st to 3rd year) in 2018. The research is justified by the relevance of the picture book in the literary and human formation of children, by the importance of images in the narrative construction of the picture book and by the pertinence of female authorship in children's literature. The dissertation, that has an analytical character, took place through the selection of the books from PNLD Literário written and illustrated by the same author: As cores dos pássaros, by Lúcia Hiratsuka, Dona Nenê e o sumiço do brinco, by Rita Taraborelli and Claro Cleusa. Claro, Clovis, by Raquel Matsushita. Throughout the research, specific objectives guided the work, such as to investigate the path of children's literature and picture books and also the place of the author in this scenario; to describe the educational path of the female authors of the selected books; to analyze the relationship between the image and the word present in picture books produced by women and selected by PNLD Literário 2018 of Elementary School (1st to 3rd year) and to reflect how the image represents elements of the verbal text (like time, space and characters). The theoretical approach focused on literature is based on Bakhtin (2011), Barthes (2011), Coelho (2000), Hunt (2013), Lajolo and Zilberman (2007), Ramos and Panozzo (2011), Zilberman (2003, 2005, 2012) and other authors. For the historical cut of women in society, the research was based on Beauvoir (1970), Dalcastagnè (2007), Duarte (2010), Knapp (2021), Louro (2001), Wollstonecraft (2016), Woolf (2014), Zinani (2014, 2021) and other authors. For the analysis of verbal and visual narrative, the studies of Adam (2008), Dondis (1997), Linden (2018), Heller (2013), Nikolajeva and Scott (2011), Oliveira (2008) and others served as input. For the discussion of the corpus, the paratexts, the construction of the verbal and visual narrative and the relationship between word and image were analyzed in each book. The study demonstrates the relevance of the image, often seen as secondary, in the generation of meanings and in the polysemy of literary books for childhood. Through the research, it was possible to analyze the nuances of each of the selected stories and point out how the approximation and distance between words and images can add meaning to the narratives. The fundamental role of graphic design is also highlighted, which provides the union between the two instances and builds the materiality of the book. Finally, the importance of education for the images is highlighted, since, in the picture book, reading the words is insufficient to understand the possibilities of meaning offered by the narrative.[resumo fornecido pelo autor

    Enacting conflict, controversy, and aggression in online spaces

    No full text
    Online spaces have been the sites of conflict and aggressive behavior since the earliest days of the internet, from Usenet, Internet Relay Chat and web forums to Facebook and Twitter (Danet, 1998; Donath, 1999; Herring et al, 2002). While flaming and trolling in digital environments have in the past been the subject of research in a wide range of different fields (communication, anthropology, political science, psychology) attempts to systematically describe and compare different forms of communicative aggression across online spaces and trace their immediate and long-term impacts on the negotiation of power relations and community dynamics remain incomplete and are difficult to generalize beyond specific contexts. Attempting such a description seems particularly relevant in light of efforts to use algorithmic and computational approaches to automatically assess aggressive behavior (Yasseri et al, 2012; Taraborelli and Ciampaglia, 2010) following into a similar direction as sentiment analysis in seeking to quantify particular communicative actions (Kennedy, 2012; Papacharissi & Oliveira, 2012). Such approaches raise serious questions about the heterogeneous and culturally specific nature of aggression, which is deeply rooted in different communities discourses and practices. Research from all areas of study is therefore essential in order to improve understanding of such actions and their implications. This panel brings together scholars from different disciplines using both qualitative and quantitative methods to study conflict in different online environments. It addresses some of the following questions in a series of five paper presentations: - What is considered aggressive behavior in different online environments? - What is the relation between aggressive behavior and controversy? - How is conflict enacted discursively and symbolically? - In what ways does the interaction between cultural and technological aspects shape the characterization of these behaviors? - What is the impact of aggressive behavior in different user communities? 2,2 , 2 , examines a single case of a long-term editor of the Arabic, English and Hebrew Wikipedias who was eventually blocked indefinitely from the English Wikipedia for edit warring and the evasion of Wikipedia arbitration committee sanctions against him. The author follows the story of the rise and fall of this model Wikipedian and discusses the impact of his experience on our understanding of what Wikipedians are like, why some Wikipedia conflicts can never be resolved and the increasing power of a selected group of arbitrators to administer “justice” on Wikipedia. 2,2 , 2 , focuses on how memes in Facebook reproduce symbolic violence through stigmatizing social stereotypes in humorous memes. The authors analyse three humor fanpages and their content and cross data with 394 online interviews. Results point to several strategies of reproduction of the stigma through humorous discourse, which are classified as a) legitimation, b) humurous allowance and c) discredit of the critics. The paper furthermore discusses the role that social network sites play in this process through their sociotechnical characteristics. 2,2 , 2 , presents an analysis of Facebook memorial page trolling, a tactic of self-identifying Facebook trolls who post abusive comments and images onto pages created for and dedicated to the deceased. It draws from extensive participant observation and discusses the complex relationship between platform, community and user behavior. The authors focus specifically on the ways in which trolls’ on-site behaviors both subverts and replicates the behavioral patterns of “legitimate” users — behaviors which are embedded within and necessitated by Facebook’s architecture. 2,2 , 2 , approaches an ongoing political debate on Twitter. The authors apply a combined quantitative and qualitative methodology to investigate the structural make-up and emotional content of tweeting activity around the hashtag #auspol (for Australian politics) in order to highlight the polarity and conservativism that characterise this highly active community of politically engaged individuals. They document the centralised structure of this particular community which is based around a deeply committed core of contributors, and explore the communicative tone, patterns of engagement and thematic drivers that shape the affective character of the community and its cohesiveness. 2,2 , 2 , assesses the discursive politics of a public debate that erupted in January 2013 in the German-speaking Twittersphere after a female journalist complained in an interview that a prominent German politician had commented on the size of her bust following a public event. Under the hashtag #aufschrei (#outcry) a group of Twitter users posted personal accounts of sexual harassment and violence they had experienced, providing countless first-hand examples of sexist and discriminatory behavior towards women and girls. The authors conduct a content analysis of a sample of the #aufschrei tweets to demonstrate how online environments can become a stage for the struggle of different actors to define gender as a relevant social category. 2Danet,B.(1998).Textasmask:Gender,play,andperformanceontheInternet.InS.G.Jones(Ed.),2 Danet, B. (1998). Text as mask: Gender, play, and performance on the Internet. In S. G. Jones (Ed.), 2 (pp. 129-158). Thousand Oaks; Ca: Sage. Donath, J. S. (1999). Identity and deception in the virtual community. In M. A. Smith and P. Kollock (Eds.), 2 (pp. 29-59). London: Routledge. Herring, S., Job-Sluder, K., Scheckler, R., & Barab, S. (2002). Searching for Safety Online: Managing “Trolling” in a Feminist Forum. 2 , 18(5), 371–384. doi:10.1080/01972240290108186 Kennedy, H. (2012). Perspectives on Sentiment Analysis. 2 , 435–450. doi:10.1080/08838151.2012.732141 Papacharissi, Z., & De Fatima Oliveira, M. (2012). Affective News and Networked Publics: The Rhythms of News Storytelling on #Egypt. 2 , 266–282. doi:10.1111/j.1460-2466.2012.01630.x Taraborelli, D., & Ciampaglia, G.L. (2010). Beyond Notability. Collective Deliberation on Content Inclusion in Wikipedia. Fourth IEEE International Conference on Self-Adaptive and Self-Organizing Systems Workshops (SASOW '10). Yasseri, T., Sumi, R., Rung, A., Kornai, A., & Kertész, J. (2012). Dynamics of conflicts in Wikipedia. $2 , e38869. doi:10.1371/journal.pone.003886

    Effects on the incidence of cardiovascular events of the addition of pioglitazone versus sulfonylureas in patients with type 2 diabetes inadequately controlled with metformin (TOSCA.IT): a randomised, multicentre trial

    No full text
    BACKGROUND: The best treatment option for patients with type 2 diabetes in whom treatment with metformin alone fails to achieve adequate glycaemic control is debated. We aimed to compare the long-term effects of pioglitazone versus sulfonylureas, given in addition to metformin, on cardiovascular events in patients with type 2 diabetes. METHODS: TOSCA.IT was a multicentre, randomised, pragmatic clinical trial, in which patients aged 50-75 years with type 2 diabetes inadequately controlled with metformin monotherapy (2-3 g per day) were recruited from 57 diabetes clinics in Italy. Patients were randomly assigned (1:1), by permuted blocks randomisation (block size 10), stratified by site and previous cardiovascular events, to add-on pioglitazone (15-45 mg) or a sulfonylurea (5-15 mg glibenclamide, 2-6 mg glimepiride, or 30-120 mg gliclazide, in accordance with local practice). The trial was unblinded, but event adjudicators were unaware of treatment assignment. The primary outcome, assessed with a Cox proportional-hazards model, was a composite of first occurrence of all-cause death, non-fatal myocardial infarction, non-fatal stroke, or urgent coronary revascularisation, assessed in the modified intention-to-treat population (all randomly assigned participants with baseline data available and without any protocol violations in relation to inclusion or exclusion criteria). This study is registered with ClinicalTrials.gov, number NCT00700856. FINDINGS: Between Sept 18, 2008, and Jan 15, 2014, 3028 patients were randomly assigned and included in the analyses. 1535 were assigned to pioglitazone and 1493 to sulfonylureas (glibenclamide 24 [2%], glimepiride 723 [48%], gliclazide 745 [50%]). At baseline, 335 (11%) participants had a previous cardiovascular event. The study was stopped early on the basis of a futility analysis after a median follow-up of 57·3 months. The primary outcome occurred in 105 patients (1·5 per 100 person-years) who were given pioglitazone and 108 (1·5 per 100 person-years) who were given sulfonylureas (hazard ratio 0·96, 95% CI 0·74-1·26, p=0·79). Fewer patients had hypoglycaemias in the pioglitazone group than in the sulfonylureas group (148 [10%] vs 508 [34%], p<0·0001). Moderate weight gain (less than 2 kg, on average) occurred in both groups. Rates of heart failure, bladder cancer, and fractures were not significantly different between treatment groups. INTERPRETATION: In this long-term, pragmatic trial, incidence of cardiovascular events was similar with sulfonylureas (mostly glimepiride and gliclazide) and pioglitazone as add-on treatments to metformin. Both of these widely available and affordable treatments are suitable options with respect to efficacy and adverse events, although pioglitazone was associated with fewer hypoglycaemia events

    Evidence of viable Helicobacter pylori and other bacteria of public health interest associated with free-living amoeba in lettuce samples by next generation sequencing and other molecular techniques

    No full text
    [EN] Vegetables are one of the sources from which Helicobacter pylori can be acquired. This bacterium infects > 50% of the global population and is a recognized type I human carcinogen. H. pylori enters into the viable but nonculturable state when it is in the environment, and therefore the use of molecular techniques is much convenient for its detection. Free-living amoebae (FLA) are protozoans found in vegetables. They are transmission vehicles for amoeba-resistant bacteria, among which H. pylori is included. The aim of this study is to study the occurrence and viability of H. pylori from lettuce samples, H. pylori internalized into FLA and the microbiome of FLA isolated from these samples. Special focus was pointed to human pathogenic bacteria. H. pylori was not directly detected in any lettuce sample by means of molecular techniques and neither by culture. However, intra-amoebic H. pylori DNA was detected by means of PMA-qPCR in 55% of the samples and viable intra-amoebic H. pylori cells in 25% of the samples by means of DVC-FISH technique. When FLA microbiome was studied, 21 bacterial genera were part of FLA microbiome in all samples. Helicobacter genus was detected as part of the FLA microbiome in two samples. Other bacteria of public health interest such as Aeromonas sp., Arcobacter sp., Legionella sp., Mycobacterium sp., Pseudomonas sp. and Salmonella sp. were detected as part of FLA microbiome along the analysed samples. This study demonstrates for the first time that H. pylori is internalized as well as alive inside FLA isolated from vegetables. Moreover, this study shows that FLA promote H. pylori detection in environmental samples. In addition, as far as we are aware, this is the first study which studies the microbiome of FLA isolated from vegetables. Among the FLA microbiome, bacteria of public health interest were detected, pointing out that FLA are carriers of these pathogens which can reach humans and cause a public health concern.This study has been supported by the Conselleria de Educacion, Investigacion, Cultura y Deporte, of the Community of Valencia, Spain, within the program of support for research under project AICO/2018/273. The author Laura Moreno-Mesonero is the recipient of a technician contract funded by the Consellerfa de Educacion, Investigacion, Cultura y Deporte, of the Community of Valencia, Spain, within the program of support for research under project AICO/2018/273.Moreno-Mesonero, L.; Hortelano, I.; Moreno Trigos, MY.; Ferrús Pérez, MA. (2020). Evidence of viable Helicobacter pylori and other bacteria of public health interest associated with free-living amoeba in lettuce samples by next generation sequencing and other molecular techniques. International Journal of Food Microbiology. 318:1-8. https://doi.org/10.1016/j.ijfoodmicro.2019.108477S18318Agustí, G., Codony, F., Fittipaldi, M., Adrados, B., & Morató, J. (2010). Viability Determination of Helicobacter pylori Using Propidium Monoazide Quantitative PCR. Helicobacter, 15(5), 473-476. doi:10.1111/j.1523-5378.2010.00794.xAndersen, A. P., Elliott, D. A., Lawson, M., Barland, P., Hatcher, V. B., & Puszkin, E. G. (1997). Growth and morphological transformations of Helicobacter pylori in broth media. Journal of Clinical Microbiology, 35(11), 2918-2922. doi:10.1128/jcm.35.11.2918-2922.1997Azevedo, N. F., Almeida, C., Cerqueira, L., Dias, S., Keevil, C. W., & Vieira, M. J. (2007). Coccoid Form of Helicobacter pylori as a Morphological Manifestation of Cell Adaptation to the Environment. Applied and Environmental Microbiology, 73(10), 3423-3427. doi:10.1128/aem.00047-07Bai, X., Xi, C., & Wu, J. (2016). Survival of Helicobacter pylori in the wastewater treatment process and the receiving river in Michigan, USA. Journal of Water and Health, 14(4), 692-698. doi:10.2166/wh.2016.259Barker, J., & Brown, M. R. W. (1994). Trojan Horses of the microbial world: protozoa and the survival of bacterial pathogens in the environment. Microbiology, 140(6), 1253-1259. doi:10.1099/00221287-140-6-1253Batra, P., Mathur, P., & Misra, M. C. (2016). Aeromonas spp.: An Emerging Nosocomial Pathogen. Journal of Laboratory Physicians, 8(01), 001-004. doi:10.4103/0974-2727.176234Burstein, D., Amaro, F., Zusman, T., Lifshitz, Z., Cohen, O., Gilbert, J. A., … Segal, G. (2016). Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires. Nature Genetics, 48(2), 167-175. doi:10.1038/ng.3481Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., … Knight, R. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5), 335-336. doi:10.1038/nmeth.f.303CELLINI, L., ROBUFFO, I., CAMPLI, E., BARTOLOMEO, S., TARABORELLI, T., & DAINELLI, B. (1998). Recovery ofHelicobacter pyloriATCC43504 from a viable but not culturable state: regrowth or resuscitation? APMIS, 106(1-6), 571-579. doi:10.1111/j.1699-0463.1998.tb01386.xCengiz, A., Harmis, N., & Stapleton, F. (2000). Co-incubation of Acanthamoeba castellanii with strains of Pseudomonas aeruginosa alters the survival of amoeba. Clinical and Experimental Ophthalmology, 28(3), 191-193. doi:10.1046/j.1442-9071.2000.00291.xChavatte, N., Lambrecht, E., Van Damme, I., Sabbe, K., & Houf, K. (2016). Abundance, diversity and community composition of free-living protozoa on vegetable sprouts. Food Microbiology, 55, 55-63. doi:10.1016/j.fm.2015.11.013Comeau, A. M., Douglas, G. M., & Langille, M. G. I. (2017). Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research. mSystems, 2(1). doi:10.1128/msystems.00127-16Delafont, V., Brouke, A., Bouchon, D., Moulin, L., & Héchard, Y. (2013). Microbiome of free-living amoebae isolated from drinking water. Water Research, 47(19), 6958-6965. doi:10.1016/j.watres.2013.07.047Di Rienzi, S. C., Sharon, I., Wrighton, K. C., Koren, O., Hug, L. A., Thomas, B. C., … Ley, R. E. (2013). The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife, 2. doi:10.7554/elife.01102Ferreira, S., Luís, Â., Oleastro, M., Pereira, L., & Domingues, F. C. (2019). A meta-analytic perspective on Arcobacter spp. antibiotic resistance. Journal of Global Antimicrobial Resistance, 16, 130-139. doi:10.1016/j.jgar.2018.12.018Gaze, W. H., Burroughs, N., Gallagher, M. P., & Wellington, E. M. H. (2003). Interactions between Salmonella typhimurium and Acanthamoeba polyphaga , and Observation of a New Mode of Intracellular Growth within Contractile Vacuoles. Microbial Ecology, 46(3), 358-369. doi:10.1007/s00248-003-1001-3Gellatly, S. L., & Hancock, R. E. W. (2013). Pseudomonas aeruginosa: new insights into pathogenesis and host defenses. Pathogens and Disease, 67(3), 159-173. doi:10.1111/2049-632x.12033Ghenghesh, K. S., Ghenghesh, K. S., Ahmed, S. F., El-Khalek, R. A., Al-Gendy, A., & Klena, J. (2008). Aeromonas-Associated Infections in Developing Countries. Journal of Infection in Developing Countries, 2(2), 81. doi:10.3855/t2.2.81Gourabathini, P., Brandl, M. T., Redding, K. S., Gunderson, J. H., & Berk, S. G. (2008). Interactions between Food-Borne Pathogens and Protozoa Isolated from Lettuce and Spinach. Applied and Environmental Microbiology, 74(8), 2518-2525. doi:10.1128/aem.02709-07Hooi, J. K. Y., Lai, W. Y., Ng, W. K., Suen, M. M. Y., Underwood, F. E., Tanyingoh, D., … Ng, S. C. (2017). Global Prevalence of Helicobacter pylori Infection: Systematic Review and Meta-Analysis. Gastroenterology, 153(2), 420-429. doi:10.1053/j.gastro.2017.04.022Hsueh, T.-Y., & Gibson, K. E. (2015). Transfer of Acanthamoeba spp. to fresh produce from water and environmental surfaces. Letters in Applied Microbiology, 61(2), 192-198. doi:10.1111/lam.12445Hug, L. A., Baker, B. J., Anantharaman, K., Brown, C. T., Probst, A. J., Castelle, C. J., … Banfield, J. F. (2016). A new view of the tree of life. Nature Microbiology, 1(5). doi:10.1038/nmicrobiol.2016.48Huse, S. M., Dethlefsen, L., Huber, J. A., Mark Welch, D., Relman, D. A., & Sogin, M. L. (2008). Correction: Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing. PLoS Genetics, 4(12). doi:10.1371/annotation/3d8a6578-ce56-45aa-bc71-05078355b851Iovieno, A., Ledee, D. R., Miller, D., & Alfonso, E. C. (2010). Detection of Bacterial Endosymbionts in Clinical Acanthamoeba Isolates. Ophthalmology, 117(3), 445-452.e3. doi:10.1016/j.ophtha.2009.08.033Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., & Glöckner, F. O. (2012). Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Research, 41(1), e1-e1. doi:10.1093/nar/gks808Kopylova, E., Noé, L., & Touzet, H. (2012). SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics, 28(24), 3211-3217. doi:10.1093/bioinformatics/bts611KUROKAWA, M., NUICINA, M., NAKANISHI, H., TOMITA, S., TAMURA, T., & SHIMOYAMA, T. (1999). Resuscitation from the Viable but Nonculturable State of Helicobacter pylori. Journal of the Japanese Association for Infectious Diseases, 73(1), 15-19. doi:10.11150/kansenshogakuzasshi1970.73.15Del Mar Lleò, M., Benedetti, D., Tafi, M. C., Signoretto, C., & Canepari, P. (2007). Inhibition of the resuscitation from the viable but non-culturable state in Enterococcus faecalis. Environmental Microbiology, 9(9), 2313-2320. doi:10.1111/j.1462-2920.2007.01345.xLyczak, J. B., Cannon, C. L., & Pier, G. B. (2000). Establishment of Pseudomonas aeruginosa infection: lessons from a versatile opportunist1*Address for correspondence: Channing Laboratory, 181 Longwood Avenue, Boston, MA 02115, USA. Microbes and Infection, 2(9), 1051-1060. doi:10.1016/s1286-4579(00)01259-4LYNCH, M. F., TAUXE, R. V., & HEDBERG, C. W. (2009). The growing burden of foodborne outbreaks due to contaminated fresh produce: risks and opportunities. Epidemiology and Infection, 137(3), 307-315. doi:10.1017/s0950268808001969Marshall, B. (2002). Helicobacter pylori: 20 years on. Clinical Medicine, 2(2), 147-152. doi:10.7861/clinmedicine.2-2-147José Maschio, V., Corção, G., & Rott, M. B. (2015). IDENTIFICATION OF Pseudomonas spp. AS AMOEBA-RESISTANT MICROORGANISMS IN ISOLATES OF Acanthamoeba. Revista do Instituto de Medicina Tropical de São Paulo, 57(1), 81-83. doi:10.1590/s0036-46652015000100012McLean, J. S., Lombardo, M.-J., Badger, J. H., Edlund, A., Novotny, M., Yee-Greenbaum, J., … Lasken, R. S. (2013). Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proceedings of the National Academy of Sciences, 110(26), E2390-E2399. doi:10.1073/pnas.1219809110Medina, G., Flores-Martin, S., Fonseca, B., Otth, C., & Fernandez, H. (2014). Mechanisms associated with phagocytosis of Arcobacter butzleri by Acanthamoeba castellanii. Parasitology Research, 113(5), 1933-1942. doi:10.1007/s00436-014-3842-8Moreno, Y., Ferrús, M. A., Alonso, J. L., Jiménez, A., & Hernández, J. (2003). Use of fluorescent in situ hybridization to evidence the presence of Helicobacter pylori in water. Water Research, 37(9), 2251-2256. doi:10.1016/s0043-1354(02)00624-3Moreno, Y., Moreno-Mesonero, L., & García-Hernández, J. (2019). DVC-FISH to identify potentially pathogenic Legionella inside free-living amoebae from water sources. Environmental Research, 176, 108521. doi:10.1016/j.envres.2019.06.002Moreno-Mesonero, L., Moreno, Y., Alonso, J. L., & Ferrús, M. A. (2016). DVC-FISH and PMA-qPCR techniques to assess the survival of Helicobacter pylori inside Acanthamoeba castellanii. Research in Microbiology, 167(1), 29-34. doi:10.1016/j.resmic.2015.08.002Moreno-Mesonero, L., Moreno, Y., Alonso, J. L., & Ferrús, M. A. (2017). Detection of viableHelicobacter pyloriinside free-living amoebae in wastewater and drinking water samples from Eastern Spain. Environmental Microbiology, 19(10), 4103-4112. doi:10.1111/1462-2920.13856Ng, C. G., Loke, M. F., Goh, K. L., Vadivelu, J., & Ho, B. (2017). Biofilm formation enhances Helicobacter pylori survivability in vegetables. Food Microbiology, 62, 68-76. doi:10.1016/j.fm.2016.10.010Nilsson, H.-O., Blom, J., Al-Soud, W. A., Ljungh, A., Andersen, L. P., & Wadström, T. (2002). Effect of Cold Starvation, Acid Stress, and Nutrients on Metabolic Activity of Helicobacter pylori. Applied and Environmental Microbiology, 68(1), 11-19. doi:10.1128/aem.68.1.11-19.2002Olofsson, J., Axelsson-Olsson, D., Brudin, L., Olsen, B., & Ellström, P. (2013). Campylobacter jejuni Actively Invades the Amoeba Acanthamoeba polyphaga and Survives within Non Digestive Vacuoles. PLoS ONE, 8(11), e78873. doi:10.1371/journal.pone.0078873Percival, S. L., & Thomas, J. G. (2009). Transmission of Helicobacter pylori and the role of water and biofilms. Journal of Water and Health, 7(3), 469-477. doi:10.2166/wh.2009.070Piqueres, P., Moreno, Y., Alonso, J. L., & Ferrús, M. A. (2006). A combination of direct viable count and fluorescent in situ hybridization for estimating Helicobacter pylori cell viability. Research in Microbiology, 157(4), 345-349. doi:10.1016/j.resmic.2005.09.003Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., … Glöckner, F. O. (2012). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41(D1), D590-D596. doi:10.1093/nar/gks1219Rahman, M., Abd, H., Romling, U., Sandstrom, G., & Möllby, R. (2008). Aeromonas–Acanthamoeba interaction and early shift to a viable but nonculturable state of Aeromonas by Acanthamoeba. Journal of Applied Microbiology, 104(5), 1449-1457. doi:10.1111/j.1365-2672.2007.03687.xRichards, C. L., Buchholz, B. J., Ford, T. E., Broadaway, S. C., Pyle, B. H., & Camper, A. K. (2011). Optimizing the growth of stressed Helicobacter pylori. Journal of Microbiological Methods, 84(2), 174-182. doi:10.1016/j.mimet.2010.11.015Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F., … Woyke, T. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499(7459), 431-437. doi:10.1038/nature12352Rognes, T., Flouri, T., Nichols, B., Quince, C., & Mahé, F. (2016). VSEARCH: a versatile open source tool for metagenomics. PeerJ, 4, e2584. doi:10.7717/peerj.2584Samba-Louaka, A., Robino, E., Cochard, T., Branger, M., Delafont, V., Aucher, W., … Héchard, Y. (2018). Environmental Mycobacterium avium subsp. paratuberculosis Hosted by Free-Living Amoebae. Frontiers in Cellular and Infection Microbiology, 8. doi:10.3389/fcimb.2018.00028Santiago, P., Moreno, Y., & Ferrús, M. A. (2015). Identification of ViableHelicobacter pyloriin Drinking Water Supplies by Cultural and Molecular Techniques. Helicobacter, 20(4), 252-259. doi:10.1111/hel.12205Sarem, M., & Corti, R. (2016). Rol de las formas cocoides de Helicobacter pylori en la infección y la recrudescencia. Gastroenterología y Hepatología, 39(1), 28-35. doi:10.1016/j.gastrohep.2015.04.009Signoretto, C., del Mar Lleò, M., Tafi, M. C., & Canepari, P. (2000). Cell Wall Chemical Composition of Enterococcus faecalis in the Viable but Nonculturable State. Applied and Environmental Microbiology, 66(5), 1953-1959. doi:10.1128/aem.66.5.1953-1959.2000Tezcan-Merdol, D., Ljungström, M., Winiecka-Krusnell, J., Linder, E., Engstrand, L., & Rhen, M. (2004). Uptake and Replication of Salmonella enterica in Acanthamoeba rhysodes. Applied and Environmental Microbiology, 70(6), 3706-3714. doi:10.1128/aem.70.6.3706-3714.2004Thomas, V., Loret, J.-F., Jousset, M., & Greub, G. (2008). Biodiversity of amoebae and amoebae-resisting bacteria in a drinking water treatment plant. Environmental Microbiology, 10(10), 2728-2745. doi:10.1111/j.1462-2920.2008.01693.xVaerewijck, M. J. M., Sabbe, K., Baré, J., & Houf, K. (2011). Occurrence and diversity of free-living protozoa on butterhead lettuce. International Journal of Food Microbiology, 147(2), 105-111. doi:10.1016/j.ijfoodmicro.2011.03.015Waite, D. W., Vanwonterghem, I., Rinke, C., Parks, D. H., Zhang, Y., Takai, K., … Hugenholtz, P. (2017). Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.). Frontiers in Microbiology, 8. doi:10.3389/fmicb.2017.00682White, C. I., Birtles, R. J., Wigley, P., & Jones, P. H. (2010). Mycobacterium avium subspecies paratuberculosis in free-living amoebae isolated from fields not used for grazing. Veterinary Record, 166(13), 401-402. doi:10.1136/vr.b4797Winiecka-Krusnell, J., Wreiber, K., Euler, A. von, Engstrand, L., & Linder, E. (2002). Free-living Amoebae Promote Growth and Survival of Helicobacter pylori. Scandinavian Journal of Infectious Diseases, 34(4), 253-256. doi:10.1080/00365540110080052Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N. N., … Eisen, J. A. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. doi:10.1038/nature08656Yahaghi, E., Khamesipour, F., Mashayekhi, F., Safarpoor Dehkordi, F., Sakhaei, M. H., Masoudimanesh, M., & Khameneie, M. K. (2014). Helicobacter pyloriin Vegetables and Salads: Genotyping and Antimicrobial Resistance Properties. BioMed Research International, 2014, 1-11. doi:10.1155/2014/757941Yeoh, Y. K., Sekiguchi, Y., Parks, D. H., & Hugenholtz, P. (2015). Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage. Molecular Biology and Evolution, 33(4), 915-927. doi:10.1093/molbev/msv281Yousuf, F. A., Siddiqui, R., & Khan, N. A. (2013). Acanthamoeba castellanii of the T4 genotype is a potential environmental host for Enterobacter aerogenes and Aeromonas hydrophila. Parasites & Vectors, 6(1). doi:10.1186/1756-3305-6-169Zhang, Y., & Sievert, S. M. (2014). Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria. Frontiers in Microbiology, 5. doi:10.3389/fmicb.2014.00110Zhang, J., Kobert, K., Flouri, T., & Stamatakis, A. (2013). PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics, 30(5), 614-620. doi:10.1093/bioinformatics/btt59
    corecore