30472 research outputs found
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Understanding computation time: a critical discussion of time as a computational performance metric
No full textComputation time is an important performance metric that scientists and software engineers use to determine whether an algorithm is capable of running within a reasonable time frame. We provide an accessible critical review of the factors that influence computation time, highlighting problems in its reporting in current research and the negative practical impact that this has on developers, recommending best practice for its measurement and reporting. Discussing how computers and coders measure time, a discrepancy is exposed between best practice in the primarily theoretical field of computational complexity, and the difficulty for non-specialists in applying such theoretical findings. We therefore recommend establishing a better reporting practice, highlighting future work needed to expose the effects of poor reporting. Freely shareable templates are provided to help developers and researchers report this information more accurately, helping others to build upon their work, and thereby reducing the needless global duplication of computational and human effort.
Arkadiusz , Paul A. , and Jo Alyso
Opening the Future
No full textA talk to Australia's Group of 8 Libraries about the Opening the Future model for open access
Dissecting OCT4 defines the role of nucleosome binding in pluripotency
No full textPioneer transcription factors such as OCT4 can target silent genes embedded in nucleosome-dense regions. How nucleosome interaction enables transcription factors to target chromatin and determine cell identity remains elusive. Here, we systematically dissect OCT4 to show that nucleosome binding is encoded within the DNA-binding domain and yet can be uncoupled from free-DNA binding. Furthermore, accelerating the binding kinetics of OCT4 to DNA enhances nucleosome binding. In cells, uncoupling nucleosome binding diminishes the ability of OCT4 to individually access closed chromatin, while more dynamic nucleosome binding results in expansive genome scanning within closed chromatin. However, both uncoupling and enhancing nucleosome binding are detrimental to inducing pluripotency from differentiated cells. Remarkably, stable interactions between OCT4 and nucleosomes are continuously required for maintaining the accessibility of pluripotency enhancers in stem cells. Our findings reveal how the affinity and residence time of OCT4–nucleosome complexes modulate chromatin accessibility during cell fate changes and maintenance
The debate on screen time: an empirical case study in infant-directed video
Get PDFThis chapter presents data on how infants interact with educational videos, collected using sensitive eye-tracking measures of attention. It describes the ongoing Toddler Attentional Behaviours and Learning with Touchscreens (TABLET) Project, developed by Annette Karmiloff-Smith with Rachael Bedford and Tim J. Smith. The chapter presents some detailed empirical work that illustrates the kinds of methods Annette believed were needed to ground an evidence-based approach to understanding the impact of screen time on infant development. Annette was a great pragmatist who understood the importance of working with parents, media producers, and policy-makers, to find the best ways for infants to benefit from scientific insights into development. She decided to collaborate with Abbey Media to develop infant-directed DVD content designed specifically with infant cognitive research in mind. TABLET is ongoing project aiming to test whether infant exposure to touchscreen devices at 12 months-of-age is associated with long-term developmental differences at 18 and 42 months-of-age in domains including attention, temperament, developmental milestones, language, executive function and sleep
Assessment of protein-protein interfaces in cryo-EM derived assemblies
Get PDFStructures of macromolecular assemblies derived from cryo-EM maps often contain errors that become more abundant with decreasing resolution. Despite efforts in the cryo-EM community to develop metrics for map and atomistic model validation, thus far, no specific scoring metrics have been applied systematically to assess the interface between the assembly subunits. Here, we comprehensively assessed protein–protein interfaces in macromolecular assemblies derived by cryo-EM. To this end, we developed Protein Interface-score (PI-score), a density-independent machine learning-based metric, trained using the features of protein–protein interfaces in crystal structures. We evaluated 5873 interfaces in 1053 PDB-deposited cryo-EM models (including SARS-CoV-2 complexes), as well as the models submitted to CASP13 cryo-EM targets and the EM model challenge. We further inspected the interfaces associated with low-scores and found that some of those, especially in intermediate-to-low resolution (worse than 4 Å) structures, were not captured by density-based assessment scores. A combined score incorporating PI-score and fit-to-density score showed discriminatory power, allowing our method to provide a powerful complementary assessment tool for the ever-increasing number of complexes solved by cryo-EM
Psychosocial effects of the COVID-19 pandemic and mental health among LGBTQ+ young adults: a cross-cultural comparison across six nations
Get PDFAcross the world people have seen their lives interrupted by the COVID-19 pandemic. Using an online survey, we explored how the psychosocial effects of the pandemic affected the mental health of LGBTQ+ young adults who were confined with their parents during the lockdown period (N = 1,934), from six countries: Portugal, UK, Italy, Brazil, Chile, and Sweden. South American participants experienced more negative psychosocial effects of the pandemic. Depression and anxiety were higher among participants who were younger, not working, living in Europe and who reported feeling more emotionally affected by the pandemic, uncomfortable at home, or isolated from non-LGBTQ friends. Not attending higher education predicted depression while not being totally confined at home, residing habitually with parents, and fearing more future infection predicted anxiety. LGBTQ+ community groups, as well as health and educational services should remain particularly attentive to the needs of LGBTQ+ young adults during health crises
Bioinformation worlds and futures
No full textThis book sets out to define and consolidate the field of bioinformation studies in its transnational and global dimensions, drawing on debates in science and technology studies, anthropology and sociology. It provides situated analyses of bioinformation journeys across domains and spheres of interpretation. As unprecedented amounts of data relating to biological processes and lives are collected, aggregated, traded and exchanged, infrastructural systems and machine learners produce real consequences as they turn indeterminate data into actionable decisions for states, companies, scientific researchers and consumers. Bioinformation accrues multiple values as it transverses multiple registers and domains, and as it is transformed from bodies to becoming a subject of analysis tied to particular social relations, promises, desires and futures. The volume harnesses the anthropological sensibility for situated, fine-grained, ethnographically grounded analysis to develop an interdisciplinary dialogue on the conceptual, political, social and ethical dimensions posed by bioinformation
Teacher enthusiasm and students’ social-behavioral learning engagement: the mediating role of student enjoyment and boredom in Chinese EFL classes
Get PDFTeacher enthusiasm is attracting growing attention in educational and learner psychology research. There is evidence that teacher enthusiasm is contagious in class and positively affects student emotions. Their fundamental role in shaping student engagement has also been well documented. However, the links—between teacher enthusiasm and student emotions, and between student emotions and engagement—remain underexplored in instructed second language acquisition. The present study adopted a mixed-method approach to examine the complex relationships between perceived teacher enthusiasm, emotions (enjoyment and boredom), and social-behavioral learning engagement among 2002 EFL learners from 11 universities in China. Quantitative analyses showed small to large correlations between perceived teacher enthusiasm, enjoyment, boredom, and social-behavioral learning engagement. In addition, student enjoyment and boredom were found to co-mediate the relationship between perceptions of teacher enthusiasm and student social-behavioral engagement in English classes. Qualitative interviews with nine students provided insights into the potential causes of the statistical patterns. Theoretical and pedagogical implications are discussed, followed by directions for future research
An investigation of the three-way joint coaching alliance: a social identity theory perspective
Get PDFThis study builds upon the previous research that recognised coaching as a triangular political space generating power relationships. We integrate social identity theory into this power negotiation process and consider that the ultimate purpose of coaching is to facilitate a shared coaching identity among all related collaborators. To gain in-depth understanding of factors that promote a three-way joint coaching identity; we conducted 25 critical incident interviews and two levels of Q-sorting (n = 10) with coaches, coachees and organisational stakeholders. The research results indicated that a workplace coaching identity is a flexible space underpinned by coaches’ attitude, all collaborators’ positions and the contracting process. Coaches’ accommodated communication techniques determine the relationship climate (instrumental or influential). Coaches’ position in the coaching space regulates their self-interests and motivation to change. Moreover, a transparent contracting process encourages communication flows and psychological exchanges among all collaborators that may gain more support from stakeholders
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