96 research outputs found

    A closer look at the Sci-Hub corpus: what is being downloaded and from where?

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    Sci-Hub remains among the most common sites via which readers circumvent article paywalls and access scholarly literature. But where exactly are its download requests coming from? And just what is being downloaded? Bastian Greshake has analysed the full Sci-Hub corpus and its request data, and found that articles are being downloaded from all over the world, more recently published papers are among the most requested, and there is a marked overrepresentation of requested articles from journals publishing on chemistry

    Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges

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    Background: There is a lack of understanding the evolutionary forces driving niche segregation of closely related organisms. In addition, pinpointing the genes driving ecological divergence is a key goal in molecular ecology. Here, larval transcriptome sequences obtained by next-generation-sequencing are used to address these issues in a morphologically cryptic sister species pair of non-biting midges (Chironomus riparius and C. piger). Results: More than eight thousand orthologous open reading frames were screened for interspecific divergence and intraspecific polymorphisms. Despite a small mean sequence divergence of 1.53% between the sister species, 25.1% of 18,115 observed amino acid substitutions were inferred by α statistics to be driven by positive selection. Applying McDonald-Kreitman tests to 715 alignments of gene orthologues identified eleven (1.5%) genes driven by positive selection. Conclusions: Three candidate genes were identified as potentially responsible for the observed niche segregation concerning nitrite concentration, habitat temperature and water conductivity. Additionally, signs of positive selection in the hydrogen sulfide detoxification pathway were detected, providing a new plausible hypothesis for the species’ ecological differentiation. Finally, a divergently selected, nuclear encoded mitochondrial ribosomal protein may contribute to reproductive isolation due to cytonuclear coevolution

    Open sharing of genomic data: Who does it and why?

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    We explored the characteristics and motivations of people who, having obtained their genetic or genomic data from Direct-To-Consumer genetic testing (DTC-GT) companies, voluntarily decide to share them on the publicly accessible web platform openSNP. The study is the first attempt to describe open data sharing activities undertaken by individuals without institutional oversight. In the paper we provide a detailed overview of the distribution of the demographic characteristics and motivations of people engaged in genetic or genomic open data sharing. The geographical distribution of the respondents showed the USA as dominant. There was no significant gender divide, the age distribution was broad, educational background varied and respondents with and without children were equally represented. Health, even though prominent, was not the respondents' primary or only motivation to be tested. As to their motivations to openly share their data, 86.05% indicated wanting to learn about themselves as relevant, followed by contributing to the advancement of medical research (80.30%), improving the predictability of genetic testing (76.02%) and considering it fun to explore genotype and phenotype data (75.51%). Whereas most respondents were well aware of the privacy risks of their involvement in open genetic data sharing and considered the possibility of direct, personal repercussions troubling, they estimated the risk of this happening to be negligible. Our findings highlight the diversity of DTC-GT consumers who decide to openly share their data. Instead of focusing exclusively on health-related aspects of genetic testing and data sharing, our study emphasizes the importance of taking into account benefits and risks that stretch beyond the health spectrum. Our results thus lend further support to the call for a broader and multi-faceted conceptualization of genomic utility

    An investigation of the Movimento da Escola Moderna (MEM) pedagogy and its contribultion to learning to learn in Portuguese pre-schools

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    This study identifies how the Movimento da Escola Moderna model for pre-school education works in practice, and how it has supported (or constrained) effective learning processes associated with 'learning to learn'. The conceptual framework combines socio-cultural theories of learning with literature on learning to learn and the role of interactions in teaching-learning processes to identify effective learning processes in the early years. Adopting an interpretative approach to research, the study involves an in depth casestudy approach with ethnographic elements. Two classrooms, purposefully selected, provide detailed illustrative cases of the MEM pedagogy. Data included observations (participant observations and video recording), interviews (adults and children), and documents. The analysis combined a theoretically driven framework with grounded analysis. This research showed that relationships between the MEM model, its practice and the children's participation in processes that promote 'learning to learn', are not straightforward. Both classrooms provided 'communities of learning' where children were encouraged to self-regulate their learning and engage in collaborative activities, transforming their identity from 'child' to 'leamer', and their leading activity from 'playing with others' to 'learning with others' . It was found that the structural and dynamic quality of day-to-day practices sometimes had contradictory effects, which led to the identification of some conditions required to guarantee such change for all the children including the youngest and those less participative. The implications for further development of the MEM model and teachers' practices are discussed. These findings contribute to understand the role of pedagogy in mediating, from an early age, the development of a life-long learner

    An Annotated Draft Genome for Radix auricularia (Gastropoda, Mollusca)

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    Molluscs are the second most species-rich phylum in the animal kingdom, yet only 11 genomes of this group have been published so far. Here, we present the draft genome sequence of the pulmonate freshwater snail Radix auricularia. Six whole genome shotgun libraries with different layouts were sequenced. The resulting assembly comprises 4,823 scaffolds with a cumulative length of 910 Mb and an overall read coverage of 72×. The assembly contains 94.6% of a metazoan core gene collection, indicating an almost complete coverage of the coding fraction. The discrepancy of ∼690 Mb compared with the estimated genome size of R. auricularia (1.6 Gb) results from a high repeat content of 70% mainly comprising DNA transposons. The annotation of 17,338 protein coding genes was supported by the use of publicly available transcriptome data. This draft will serve as starting point for further genomic and population genetic research in this scientifically important phylum

    Open Humans:A platform for participant-centered research and personal data exploration

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    Background Many aspects of our lives are now digitized and connected to the internet. As a result, individuals are now creating and collecting more personal data than ever before. This offers an unprecedented chance for human-participant research ranging from the social sciences to precision medicine. With this potential wealth of data comes practical problems (e.g., how to merge data streams from various sources), as well as ethical problems (e.g., how best to balance risks and benefits when enabling personal data sharing by individuals). Results To begin to address these problems in real time, we present Open Humans, a community-based platform that enables personal data collections across data streams, giving individuals more personal data access and control of sharing authorizations, and enabling academic research as well as patient-led projects. We showcase data streams that Open Humans combines (e.g., personal genetic data, wearable activity monitors, GPS location records, and continuous glucose monitor data), along with use cases of how the data facilitate various projects. Conclusions Open Humans highlights how a community-centric ecosystem can be used to aggregate personal data from various sources, as well as how these data can be used by academic and citizen scientists through practical, iterative approaches to sharing that strive to balance considerations with participant autonomy, inclusion, and privacy.publishedVersio

    Implementing the co-immune open innovation program to address vaccination hesitancy and access to vaccines : retrospective study

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    Background: The rise of major complex public health problems, such as vaccination hesitancy and access to vaccination, requires innovative, open, and transdisciplinary approaches. Yet, institutional silos and lack of participation on the part of nonacademic citizens in the design of solutions hamper efforts to meet these challenges. Against this background, new solutions have been explored, with participatory research, citizen science, hackathons, and challenge-based approaches being applied in the context of public health. Objective: Our aim was to develop a program for creating citizen science and open innovation projects that address the contemporary challenges of vaccination in France and around the globe. Methods: We designed and implemented Co-Immune, a program created to tackle the question of vaccination hesitancy and access to vaccination through an online and offline challenge-based open innovation approach. The program was run on the open science platform Just One Giant Lab. Results: Over a 6-month period, the Co-Immune program gathered 234 participants of diverse backgrounds and 13 partners from the public and private sectors. The program comprised 10 events to facilitate the creation of 20 new projects, as well as the continuation of two existing projects, to address the issues of vaccination hesitancy and access, ranging from app development and data mining to analysis and game design. In an open framework, the projects made their data, code, and solutions publicly available. Conclusions: Co-Immune highlights how open innovation approaches and online platforms can help to gather and coordinate noninstitutional communities in a rapid, distributed, and global way toward solving public health issues. Such initiatives can lead to the production and transfer of knowledge, creating novel solutions in the public health sector. The example of Co-Immune contributes to paving the way for organizations and individuals to collaboratively tackle future global challenges
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