Whole-genome functional characterization of RE1 silencers using a modified massively parallel reporter assay.

Transcriptional silencers are under- studied compared with activating elements. By using MPRAduo, Mouri et al. perform a whole-genome functional characterization screen of RE1 silencers and identify REST-binding motif characteristics and cofactor localization required for a functional silencer. They also identify human genetic variants that impact RE1 activity

Integrating Machine Learning for Planetary Science: Perspectives for the Next Decade

Machine learning (ML) methods can expand our ability to construct, and draw insight from large datasets. Despite the increasing volume of planetary observations, our field has seen few applications of ML in comparison to other sciences. To support these methods, we propose ten recommendations for bolstering a data-rich future in planetary science.Comment: 10 pages (expanded citations compared to 8 page submitted version for decadal survey), 3 figures, white paper submitted to the Planetary Science and Astrobiology Decadal Survey 2023-203

Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA.

The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%-80% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with public health programs from all six states in New England in the United States. We compare logistic growth rates during each variant\u27s respective emergence period, finding that Delta emerged 1.37-2.63 times faster than Alpha (range across states). We compute variant-specific effective reproductive numbers, estimating that Delta is 63%-167% more transmissible than Alpha (range across states). Finally, we estimate that Delta infections generate on average 6.2 (95% CI 3.1-10.9) times more viral RNA copies per milliliter than Alpha infections during their respective emergence. Overall, our evidence suggests that Delta\u27s enhanced transmissibility can be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on underlying population attributes and sequencing data availability

Comparative Transmissibility of SARS-CoV-2 Variants Delta and Alpha in New England, USA

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% more transmissible than Alpha, allowing Delta to become the globally dominant variant. However, it was unclear if the ostensible difference in relative transmissibility was due mostly to innate properties of Delta\u27s infectiousness or differences in the study populations. To investigate, we formed a partnership with SARS-CoV-2 genomic surveillance programs from all six New England US states. By comparing logistic growth rates, we found that Delta emerged 37-163% faster than Alpha in early 2021 (37% Massachusetts, 75% New Hampshire, 95% Maine, 98% Rhode Island, 151% Connecticut, and 163% Vermont). We next computed variant-specific effective reproductive numbers and estimated that Delta was 58-120% more transmissible than Alpha across New England (58% New Hampshire, 68% Massachusetts, 76% Connecticut, 85% Rhode Island, 98% Maine, and 120% Vermont). Finally, using RT-PCR data, we estimated that Delta infections generate on average ∼6 times more viral RNA copies per mL than Alpha infections. Overall, our evidence indicates that Delta\u27s enhanced transmissibility could be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on the underlying immunity and behavior of distinct populations

QCD and strongly coupled gauge theories : challenges and perspectives

We highlight the progress, current status, and open challenges of QCD-driven physics, in theory and in experiment. We discuss how the strong interaction is intimately connected to a broad sweep of physical problems, in settings ranging from astrophysics and cosmology to strongly coupled, complex systems in particle and condensed-matter physics, as well as to searches for physics beyond the Standard Model. We also discuss how success in describing the strong interaction impacts other fields, and, in turn, how such subjects can impact studies of the strong interaction. In the course of the work we offer a perspective on the many research streams which flow into and out of QCD, as well as a vision for future developments.Peer reviewe

The Future of Precision Medicine : Potential Impacts for Health Technology Assessment

Objective Precision medicine allows health care interventions to be tailored to groups of patients based on their disease susceptibility, diagnostic or prognostic information or treatment response. We analyse what developments are expected in precision medicine over the next decade and consider the implications for health technology assessment (HTA) agencies. Methods We perform a pragmatic review of the literature on the health economic challenges of precision medicine, and conduct interviews with representatives from HTA agencies, research councils and researchers from a variety of fields, including digital health, health informatics, health economics and primary care research. Results Three types of precision medicine are highlighted as likely to emerge in clinical practice and impact upon HTA agencies: complex algorithms, digital health applications and ‘omics’-based tests. Defining the scope of an evaluation, identifying and synthesizing the evidence and developing decision analytic models will more difficult when assessing more complex and uncertain treatment pathways. Stratification of patients will result in smaller subgroups, higher standard errors and greater decision uncertainty. Equity concerns may present in instances where biomarkers correlate with characteristics such as ethnicity, whilst fast-paced innovation may reduce the shelf-life of guidance and necessitate more frequent reviewing. Discussion Innovation in precision medicine promises substantial benefits to patients, but will also change the way in which some health services are delivered and evaluated. As biomarker discovery accelerates and AI-based technologies emerge, the technical expertise and processes of HTA agencies will need to adapt if the objective of value for money is to be maintained

Reactive iron, not fungal community, drives organic carbon oxidation potential in floodplain soils

Wetlands host ∼20% of terrestrial organic carbon and serve as a major sink for atmospheric carbon. Anoxic soils and sediments accrue soil organic carbon (SOC) partly by hampering the activity of extracellular oxidative enzymes that break down phenolic polymers. Upon aeration, fungal-driven oxidative enzymatic depolymerization and microbial respiration of released monomers ensue. Redox-active metals can simultaneously catalyze abiotic nonspecific oxidation of SOC, notable examples including Mn(III) or Fe(II) through Fenton-like, hydrogen peroxide-catalyzed oxidative radical production. However, the extent of reactive metal contributions to biotic and abiotic SOC degradation is not understood in the context of natural environments with diverse redox chemistry. We tested the relative contributions of fungi, Mn(III) and Fe(II) to phenolic substrate (L-DOPA) oxidation in floodplain soils representing a range of transient redox conditions driven by permanent vs. periodic flooding. Phenol oxidative potential was highest in permanently flooded soils with fewer fungal taxa known for observed (per)oxidase activity and instead correlated with HCl-extractable Fe(II), Fe(total) and Fe(II)/Fe(total), suggesting a specific role of Fe(II). Fe(II) additions enhanced phenol oxidative potential in sterilized and non-sterilized soils in the presence of hydrogen peroxide, indicating abiotic Fe-mediated radical chemistry could significantly enhance wetland SOC oxidative depolymerization throughout redox-active floodplain soils. Fungal community composition did not correlate to phenol oxidative potential overall and only more oxic soils adjacent to the river with diverse fungal communities showed declining oxidative potential after sterilization. Mn(III) addition did not significantly enhance phenol oxidative potential across all soils, although it appeared to drive fungal-mediated oxidative potential in the most aerated floodplain soils. Understanding how metals mediate SOC depolymerization as abiotic oxidants or microbially-harnessed enzyme cofactors and substrates in soils under variable hydrologic controls will improve our ability to represent depolymerization in terrestrial carbon models in wetland and other frequently saturated soils

Massive Open Online Courses (MOOCs) and their impact on academic library services: exploring the issues and challenges

2012 was a year of rapid change for education with the advent of MOOCs—Massive Open Online Courses—available for the world to use to learn for free. But what does this mean for the role of the librarian? How has the landscape in education changed, and what are the issues and challenges that librarians now face? This article reviews the position of libraries in the emergence of MOOCs and the role that a librarian could undertake within the research, production, and presentation of MOOCs

'The art of democracy': young people's democratic learning in gallery contexts

In this article the authors report on research which aimed to explore the opportunities for democratic action and learning in a number of artist-led gallery education projects in the south-west of England. The research takes an approach to citizenship learning and democracy that is less focused on citizenship as a specific subject in the formal school curriculum and the achievement of specific citizenship outcomes that can follow from it. Rather, it is more focused upon understanding how democratic practices that are embedded in the day-to-day lives of young people contribute to their democratic learning and participation as citizens. Drawing upon conceptual categories and concepts that illuminate the process, the authors demonstrate the nature and character of young people’s democratic learning. An implication arising from this is the need for practice-orientated research in other contexts (e.g. work, leisure and home) to fully understand the nature of democratic learning