Curating Digital Pedagogy in the Humanities

This is the published introduction to the born-digital, open-access, peer-reviewed *Digital Pedagogy in the Humanities*. More a rationale and scholarly study of both Digital Pedagogy and DPiH in general, this introduces articulates the uses, theory, rationale about digital pedagogy as it has been shaped in U.S. institutions since the explosion of Digital Humanities in 2009. As a separate field now, Digital Pedagogy is built on the generosity of its practitioners, but saving the *stuff* of teaching and pedagogy is difficult. The introduction historicizes this now-published project, its open peer review process, and its development in the early years (starting in 2010) in addition to offering multiple pathways into using DPiH for both experienced practitioners and anyone curious about how to use the 500+ pedagogical artifacts among the 59 keywords. By defining digital pedagogy, articulating the 5 key concepts that surfaced with the creation of this project, and discussing potential obstacles about engaging in Digital Pedagogy (including an enumerated step-by-step process for getting started in using Digital Pedagogy strategies), this introduction invites all levels of engagement. In addition, the introduction provides an analysis of the types of content, contributors, and curators as well as early network analysis about the connections among all of the keywords, curators, and the shared pedagogical artifacts. Finally, the authors assess the project\u27s infrastructure, open access, and open peer review publishing process over the 10 years it took to bring this project to fruition, luckily, right at the moment that all higher education institutions were forced to grapple with a sudden move to online learning during March 2020. The concluding sections discuss the shifting role of published and publisher with this born-digital project and considers the use of new forms of infrastructure for a scholarly work that values pedagogy above all else

Introduction to The State of the Syllabus Special Edition

Positioning the syllabus as a key artifact in the modern academy, one that encapsulates many elements of intellectual, scholarly, social, cultural, political, and institutional contexts in which it is enmeshed, we offer in this special issue of Syllabus a set of provocations on the syllabus and its many roles. Including perspectives from full-time and part-time faculty, graduate students, and librarians, the issue offers a multifaceted take on how the syllabus is presently used and might be reimagined

Network + Publication + Ecosystem: Curating Digital Pedagogy, Fostering Community

We are excited to share our work on Digital Pedagogy in the Humanities (DPiH), which was published on the Humanities Commons in 2020 by the Modern Language Association after almost a decade of work. DPiH is a large-scale scholarly project that presents the stuff of teaching (syllabi, assignments, and resources) through a curated set of keywords such as “Poetry,” “Disability,” “Queer,” and “Annotation,” among many others. For each keyword, a curator or set of curators has selected and annotated ten pedagogical artifacts; created a curator’s selection statement; and presented a list of related resources. With a lengthy introduction to DPiH that historicizes and contextualizes the project, the edited collection, as a whole, presents a broad array of pedagogical practices that engage technology and offer concrete resources to faculty who would like to expand their existing teaching practices. In this piece, we would like to consider how the project, in its design and implementation, challenges existing ideas about scholarship, pedagogy, and our shared ecosystem of scholarly communication

Curating Digital Pedagogy in the Humanities

This is the published introduction to the born-digital, open-access, peer-reviewed Digital Pedagogy in the Humanities. More a rationale and scholarly study of both Digital Pedagogy and DPiH in general, this introduces articulates the uses, theory, rationale about digital pedagogy as it has been shaped in U.S. institutions since the explosion of Digital Humanities in 2009. As a separate field now, Digital Pedagogy is built on the generosity of its practitioners, but saving the stuff of teaching and pedagogy is difficult. The introduction historicizes this now-published project, its open peer review process, and its development in the early years (starting in 2010) in addition to offering multiple pathways into using DPiH for both experienced practitioners and anyone curious about how to use the 500+ pedagogical artifacts among the 59 keywords. By defining "digital pedagogy," articulating the 5 key concepts that surfaced with the creation of this project, and discussing potential obstacles about engaging in Digital Pedagogy (including an enumerated step-by-step process for getting started in using Digital Pedagogy strategies), this introduction invites all levels of engagement. In addition, the introduction provides an analysis of the types of content, contributors, and curators as well as early network analysis about the connections among all of the keywords, curators, and the shared pedagogical artifacts. Finally, the authors assess the project's infrastructure, open access, and open peer review publishing process over the 10 years it took to bring this project to fruition, luckily, right at the moment that all higher education institutions were forced to grapple with a sudden move to online learning during March 2020. The concluding sections discuss the shifting role of "published" and "publisher" with this born-digital project and considers the use of new forms of infrastructure for a scholarly work that values pedagogy above all else

Network + Publication + Ecosystem: Curating Digital Pedagogy, Fostering Community

We are excited to share our work on Digital Pedagogy in the Humanities (DPiH), which was published on the Humanities Commons in 2020 by the Modern Language Association after almost a decade of work. DPiH is a large-scale scholarly project that presents the stuff of teaching (syllabi, assignments, and resources) through a curated set of keywords such as “Poetry,” “Disability,” “Queer,” and “Annotation,” among many others. For each keyword, a curator or set of curators has selected and annotated ten pedagogical artifacts; created a curator’s selection statement; and presented a list of related resources. With a lengthy introduction to DPiH that historicizes and contextualizes the project, the edited collection, as a whole, presents a broad array of pedagogical practices that engage technology and offer concrete resources to faculty who would like to expand their existing teaching practices. In this piece, we would like to consider how the project, in its design and implementation, challenges existing ideas about scholarship, pedagogy, and our shared ecosystem of scholarly communication

Escape from Autologous Neutralizing Antibodies in Acute/Early Subtype C HIV-1 Infection Requires Multiple Pathways

One aim for an HIV vaccine is to elicit neutralizing antibodies (Nab) that can limit replication of genetically diverse viruses and prevent establishment of a new infection. Thus, identifying the strengths and weaknesses of Nab during the early stages of natural infection could prove useful in achieving this goal. Here we demonstrate that viral escape readily occurred despite the development of high titer autologous Nab in two subjects with acute/early subtype C infection. To provide a detailed portrayal of the escape pathways, Nab resistant variants identified at multiple time points were used to create a series of envelope (Env) glycoprotein chimeras and mutants within the background of a corresponding newly transmitted Env. In one subject, Nab escape was driven predominantly by changes in the region of gp120 that extends from the beginning of the V3 domain to the end of the V5 domain (V3V5). However, Nab escape pathways in this subject oscillated and at times required cooperation between V1V2 and the gp41 ectodomain. In the second subject, escape was driven by changes in V1V2. This V1V2-dependent escape pathway was retained over time, and its utility was reflected in the virus's ability to escape from two distinct monoclonal antibodies (Mabs) derived from this same patient via introduction of a single potential N-linked glycosylation site in V2. Spatial representation of the sequence changes in gp120 suggested that selective pressure acted upon the same regions of Env in these two subjects, even though the Env domains that drove escape were different. Together the findings argue that a single mutational pathway is not sufficient to confer escape in early subtype C HIV-1 infection, and support a model in which multiple strategies, including potential glycan shifts, direct alteration of an epitope sequence, and cooperative Env domain conformational masking, are used to evade neutralization

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Background: The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England in March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. It is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (B.1.1.7) variant. We aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes. Methods: This cohort study was done among all patients with COVID-19 in England between March 29 and May 23, 2021, who were identified as being infected with either the alpha or delta SARS-CoV-2 variant through whole-genome sequencing. Individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from Public Health England's Second Generation Surveillance System and COVID-19-associated deaths dataset; the National Immunisation Management System; and NHS Digital Secondary Uses Services and Emergency Care Data Set). The risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. Stratified Cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status. Findings: Individual-level data on 43 338 COVID-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years [IQR 17–43]) were included in our analysis. 196 (2·3%) patients with the delta variant versus 764 (2·2%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio [HR] 2·26 [95% CI 1·32–3·89]). 498 (5·7%) patients with the delta variant versus 1448 (4·2%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted HR 1·45 [1·08–1·95]). Most patients were unvaccinated (32 078 [74·0%] across both groups). The HRs for vaccinated patients with the delta variant versus the alpha variant (adjusted HR for hospital admission 1·94 [95% CI 0·47–8·05] and for hospital admission or emergency care attendance 1·58 [0·69–3·61]) were similar to the HRs for unvaccinated patients (2·32 [1·29–4·16] and 1·43 [1·04–1·97]; p=0·82 for both) but the precision for the vaccinated subgroup was low. Interpretation: This large national study found a higher hospital admission or emergency care attendance risk for patients with COVID-19 infected with the delta variant compared with the alpha variant. Results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant. Funding: Medical Research Council; UK Research and Innovation; Department of Health and Social Care; and National Institute for Health Research