Reflecting to Rebuild and Strengthen Professional Development A Collection of ‘Post-Online’ Conversations

The file attached to this record is the author's versionThis monograph is a multi-authored collection consisting of our faculty’s post-online reflections. The objective was to gather thoughts and discussion around teaching and research during COVID-19. We aim to build and explore around ‘lived experiences’ to provide a reference point to help Continuous Professional Learning and Development (CPLD) activities. The section on ‘digital diaries’ consists of dialogues from staff categorised into varied themes. In the testimonies, staff have reflected around their challenges, targets, strengths, familiarity and how they managed to overcome difficulties and achieve goals. A special section, from the Centre for Urban Research on Austerity (CURA), is devoted to identifying how pandemic has intensified research challenges, highlighting the funding, time and location constraints on academic research

Gata6 regulates aspartoacylase expression in resident peritoneal macrophages and controls their survival

The transcription factor Gata6 regulates proliferation and differentiation of epithelial and endocrine cells and cancers. Among hematopoietic cells, Gata6 is expressed selectively in resident peritoneal macrophages. We thus examined whether the loss of Gata6 in the macrophage compartment affected peritoneal macrophages, using Lyz2-Cre x Gata6flox/flox mice to tackle this issue. In Lyz2-Cre x Gata6flox/flox mice, the resident peritoneal macrophage compartment, but not macrophages in other organs, was contracted, with only a third the normal number of macrophages remaining. Heightened rates of death explained the marked decrease in peritoneal macrophage observed. The metabolism of the remaining macrophages was skewed to favor oxidative phosphorylation and alternative activation markers were spontaneously and selectively induced in Gata6-deficient macrophages. Gene expression profiling revealed perturbed metabolic regulators, including aspartoacylase (Aspa), which facilitates generation of acetyl CoA. Mutant mice lacking functional Aspa phenocopied the higher propensity to death and led to a contraction of resident peritoneal macrophages. Thus, Gata6 regulates differentiation, metabolism, and survival of resident peritoneal macrophages

Mapping Obscured Star Formation in the Host Galaxy of FRB 20201124A

We present high-resolution 1.5--6 GHz Karl G. Jansky Very Large Array (VLA) and $\textit{Hubble Space Telescope}$ ($\textit{HST}$) optical and infrared observations of the extremely active repeating fast radio burst (FRB) FRB$\,$20201124A and its barred spiral host galaxy. We constrain the location and morphology of star formation in the host and search for a persistent radio source (PRS) coincident with FRB$\,$20201124A. We resolve the morphology of the radio emission across all frequency bands and measure a star formation rate SFR $\approx 8.9\,M_{\odot}$ yr$^{-1}$, a factor of $\approx 4-6$ larger than optically-inferred SFRs, demonstrating dust-obscured star formation throughout the host. Compared to a sample of all known FRB hosts with radio emission, the host of FRB$\,$20201124A has the most significant obscured star formation. While ${\it HST}$ observations show the FRB to be offset from the bar or spiral arms, the radio emission extends to the FRB location. We propose that the FRB progenitor could have formed $\textit{in situ}$ (e.g., a magnetar central engine born from the explosion of a massive star). It is still plausible, although less likely, that the progenitor of FRB$\,$20201124A migrated from the central bar of the host, e.g., via a runaway massive star. We further place a limit on the luminosity of a putative PRS at the FRB position of $L_{\rm 6.0 \ GHz}$$\lesssim$2.6$\times$$10^{27}$erg s$^{-1}$Hz$^{-1}$, two orders of magnitude below any PRS known to date. However, this limit is still broadly consistent with both magnetar nebulae and hypernebulae models assuming a constant energy injection rate of the magnetar and an age of$\gtrsim 10^{5}$ yr in each model, respectively.Comment: 21 pages, 6 figures, 3 tables, Submitte

Short GRB Host Galaxies I: Photometric and Spectroscopic Catalogs, Host Associations, and Galactocentric Offsets

We present a comprehensive optical and near-infrared census of the fields of 90 short gamma-ray bursts (GRBs) discovered in 2005-2021, constituting all short GRBs for which host galaxy associations are feasible ($\approx$ 60% of the total Swift short GRB population). We contribute 245 new multi-band imaging observations across 49 distinct GRBs and 25 spectra of their host galaxies. Supplemented by literature and archival survey data, the catalog contains 335 photometric and 40 spectroscopic data sets. The photometric catalog reaches $3\sigma$ depths of $\gtrsim 24-27$ mag and $\gtrsim 23-26$ mag for the optical and near-infrared bands, respectively. We identify host galaxies for 84 bursts, in which the most robust associations make up 54% (49/90) of events, while only a small fraction, 6.7%, have inconclusive host associations. Based on new spectroscopy, we determine 17 host spectroscopic redshifts with a range of $z\approx 0.15-1.6$ and find that $\approx$ 25-44% of Swift short GRBs originate from $z>1$. We also present the galactocentric offset catalog for 83 short GRBs. Taking into account the large range of individual measurement uncertainties, we find a median of projected offset of $\approx 7.9$ kpc, for which the bursts with the most robust associations have a smaller median of $\approx 4.9$ kpc. Our catalog captures more high-redshift and low-luminosity hosts, and more highly-offset bursts than previously found, thereby diversifying the population of known short GRB hosts and properties. In terms of locations and host luminosities, the populations of short GRBs with and without detectable extended emission are statistically indistinguishable. This suggests that they arise from the same progenitors, or from multiple progenitors which form and evolve in similar environments. All of the data products are available on the BRIGHT website.Comment: 53 pages, 9 figures, 6 tables, submitte

Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth ∼20×). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types (∼94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination

Beyond BRAFV600: Clinical Mutation Panel Testing by Next-Generation Sequencing in Advanced Melanoma

The management of melanoma has evolved owing to improved understanding of its molecular drivers. To augment the current understanding of the prevalence, patterns, and associations of mutations in this disease, the results of clinical testing of 699 advanced melanoma patients using a pan-cancer next-generation sequencing (NGS) panel of hotspot regions in 46 genes were reviewed. Mutations were identified in 43 of the 46 genes on the panel. The most common mutations were BRAFV600 (36%), NRAS (21%), TP53 (16%), BRAFNon-V600 (6%), and KIT (4%). Approximately one-third of melanomas had >1 mutation detected, and the number of mutations per tumor was associated with melanoma subtype. Concurrent TP53 mutations were the most frequent events in tumors with BRAFV600and NRAS mutations. Melanomas with BRAFNon-V600mutations frequently harbored concurrent NRAS mutations (18%), which were rare in tumors with BRAFV600 mutations (1.6%). The prevalence of BRAFV600 and KIT mutations were significantly associated with melanoma subtypes, and BRAFV600 and TP53 mutations were significantly associated with cutaneous primary tumor location. Multiple potential therapeutic targets were identified in metastatic unknown primary and cutaneous melanomas that lacked BRAFV600and NRAS mutations. These results enrich our understanding of the patterns and clinical associations of oncogenic mutations in melanoma

TBVAC2020 : advancing tuberculosis vaccines from discovery to clinical development

TBVAC2020 is a research project supported by the Horizon 2020 program of the European Commission (EC). It aims at the discovery and development of novel tuberculosis (TB) vaccines from preclinical research projects to early clinical assessment. The project builds on previous collaborations from 1998 onwards funded through the EC framework programs FP5, FP6, and FP7. It has succeeded in attracting new partners from outstanding laboratories from all over the world, now totaling 40 institutions. Next to the development of novel vaccines, TB biomarker development is also considered an important asset to facilitate rational vaccine selection and development. In addition, TBVAC2020 offers portfolio management that provides selection criteria for entry, gating, and priority settings of novel vaccines at an early developmental stage. The TBVAC2020 consortium coordinated by TBVI facilitates collaboration and early data sharing between partners with the common aim of working toward the development of an effective TB vaccine. Close links with funders and other consortia with shared interests further contribute to this goal

TBVAC2020: Advancing tuberculosis vaccines from discovery to clinical development

TBVAC2020 is a research project supported by the Horizon 2020 program of the European Commission (EC). It aims at the discovery and development of novel tuberculosis (TB) vaccines from preclinical research projects to early clinical assessment. The project builds on previous collaborations from 1998 onwards funded through the EC framework programs FP5, FP6, and FP7. It has succeeded in attracting new partners from outstanding laboratories from all over the world, now totaling 40 institutions. Next to the development of novel vaccines, TB biomarker development is also considered an important asset to facilitate rational vaccine selection and development. In addition, TBVAC2020 offers portfolio management that provides selection criteria for entry, gating, and priority settings of novel vaccines at an early developmental stage. The TBVAC2020 consortium coordinated by TBVI facilitates collaboration and early data sharing between partners with the common aim of working toward the development of an effective TB vaccine. Close links with funders and other consortia with shared interests further contribute to this goal

Validation of the Body Concealment Scale for Scleroderma (BCSS): Replication in the Scleroderma Patient-centered Intervention Network (SPIN) Cohort

© 2016 Elsevier Ltd Body concealment is an important component of appearance distress for individuals with disfiguring conditions, including scleroderma. The objective was to replicate the validation study of the Body Concealment Scale for Scleroderma (BCSS) among 897 scleroderma patients. The factor structure of the BCSS was evaluated using confirmatory factor analysis and the Multiple-Indicator Multiple-Cause model examined differential item functioning of SWAP items for sex and age. Internal consistency reliability was assessed via Cronbach's alpha. Construct validity was assessed by comparing the BCSS with a measure of body image distress and measures of mental health and pain intensity. Results replicated the original validation study, where a bifactor model provided the best fit. The BCSS demonstrated strong internal consistency reliability and construct validity. Findings further support the BCSS as a valid measure of body concealment in scleroderma and provide new evidence that scores can be compared and combined across sexes and ages