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Unexamined Beliefs: Understanding Teachers’ Reasoning about Poverty
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In: Nenadal, Lindsey. (2018). Unexamined Beliefs: Understanding Teachers’ Reasoning about Poverty. UCLA: Education 0249. Retrieved from: http://www.escholarship.org/uc/item/2nj116nf (2018)
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Lies of the reader: Disadvantages of the sociological research methods for the study of the reading
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In: ISSN: 2304-9650 ; EISSN: 2305-6746 ; European Journal of Contemporary Education ; https://hal.archives-ouvertes.fr/hal-01735434 ; European Journal of Contemporary Education, Academic Publishing House Researcher, 2018, 7 (1), pp.190 - 213. ⟨10.13187/ejced.2018.1.190⟩ (2018)
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The Effects of Self-Disclosure on Implicit Bias and Social Judgments of Disfluent Speech
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In: http://rave.ohiolink.edu/etdc/view?acc_num=kent1542362073730088 (2018)
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How do context awareness and listener experience taking the SPEAK test influence perceptions of non-native speaking proficiency?
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In: http://rave.ohiolink.edu/etdc/view?acc_num=miami1525275325263283 (2018)
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RACIAL CONTEXT: IMPACT ON STUDENTS’ UNDERSTANDING OF RACE, BIAS, AND TALKING WITH YOUNG CHILDREN ABOUT RACE
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From Big Data to Deep Learning: A Leap Towards Strong AI or ‘Intelligentia Obscura’?
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In: Big Data and Cognitive Computing ; Volume 2 ; Issue 3 (2018)
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Rising declaratives of the Quality-suspending kind
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In: Glossa: a journal of general linguistics; Vol 3, No 1 (2018); 121 ; 2397-1835 (2018)
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Conversational Time Travel: Evidence of a Retrospective Bias in Real Life Conversations
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In: Frontiers in Psychology, 9 (2018)
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Occurrence table after data filtering for Ion PGM and MiSeq sequencing ...
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Abundance table before data filtering for Ion PGM and MiSeq sequencing ...
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Detecting Media Bias in On-line News Articles: A Text Analytics Approach
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In: Electronic Theses and Dissertations (2018)
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Sentiment Bias in Predictive Text Recommendations Results in Biased Writing ...
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The influence of intelligence on the endorsement of the intelligence–attractiveness halo
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Name-Based Measures of Neighborhood Composition: How Telling Are Neighbors' Names
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In: Survey Research Methods ; 11 ; 4 ; 435-450 (2018)
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Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses
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Abstract:
Background: Viruses are key players regulating microbial ecosystems. Exploration of viral assemblages is now possible thanks to the development of metagenomics, the most powerful tool available for studying viral ecology and discovering new viruses. Unfortunately, several sources of bias lead to the misrepresentation of certain viruses within metagenomics workflows, hindering the shift from merely descriptive studies towards quantitative comparisons of communities. Therefore, benchmark studies on virus enrichment and random amplification protocols are required to better understand the sources of bias. Results: We assessed the bias introduced by viral enrichment on mock assemblages composed of seven DNA viruses, and the bias from random amplification methods on human saliva DNA viromes, using qPCR and deep sequencing, respectively. While iodixanol cushions and 0.45 μm filtration preserved the original composition of nuclease-protected viral genomes, low-force centrifugation and 0.22 μm filtration removed large viruses. Comparison of unamplified and randomly amplified saliva viromes revealed that multiple displacement amplification (MDA) induced stochastic bias from picograms of DNA template. However, the type of bias shifted to systematic using 1 ng, with only a marginal influence by amplification time. Systematic bias consisted of over-amplification of small circular genomes, and under-amplification of those with extreme GC content, a negative bias that was shared with the PCR-based sequence-independent, single-primer amplification (SISPA) method. MDA based on random priming provided by a DNA primase activity slightly outperformed those based on random hexamers and SISPA, which may reflect differences in ability to handle sequences with extreme GC content. SISPA viromes showed uneven coverage profiles, with high coverage peaks in regions with low linguistic sequence complexity. Despite misrepresentation of certain viruses after random amplification, ordination plots based on dissimilarities among contig profiles showed perfect overlapping of related amplified and unamplified saliva viromes and strong separation from unrelated saliva viromes. This result suggests that random amplification bias has a minor impact on beta diversity studies. Conclusions: Benchmark analyses of mock and natural communities of viruses improve understanding and mitigate bias in metagenomics surveys. Bias induced by random amplification methods has only a minor impact on beta diversity studies of human saliva viromes ; This work was supported by the Spanish Ministry of Economy and Competitiveness through grant SAF2012-38421 and a “Formación de Personal Investigador” Ph.D. studentship to MP-M. The funding sources had no role in the design and any other aspect of the development of the study
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Keyword:
Amplification protocols; Bias; Biología y Biomedicina / Biología; DNA; Saliva viromes; Viruses
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URL: https://doi.org/10.1186/s40168-018-0507-3 http://hdl.handle.net/10486/685034
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Introducing Registered Reports at Language Learning: Promoting Transparency, Replication, and a Synthetic Ethic in the Language Sciences
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Lies of the reader: Disadvantages of the sociological research methods for the study of the reading
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In: European Journal of Contemporary Education ; 7 ; 1 ; 190-213 (2018)
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