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Abstract Glaucoma is a sight threatening neurodegenerative condition of the optic nerve head associated with ageing and marked by the loss of retinal ganglion cells. Mitochondrial dysfunction plays a crucial role in the pathogenesis of neurodegeneration in the most prevalent type of glaucoma: primary open angle glaucoma (POAG). All previous mitochondrial genome sequencing studies in POAG analyzed mitochondrial DNA (mtDNA) isolated from peripheral blood leukocytes and have not evaluated cells derived from ocular tissue, which better represent the glaucomatous disease context. In this study, we evaluated mitochondrial genome variation and heteroplasmy using massively parallel sequencing of mtDNA in a cohort of patients with POAG, and in a subset assess the role of somatic mitochondrial genome mutations in disease pathogenesis using paired samples of peripheral blood leukocytes and ocular tissue (Tenon’s ocular fibroblasts). An enrichment of potentially pathogenic nonsynonymous mtDNA variants was identified in Tenon’s ocular fibroblasts from participants with POAG. The absence of oxidative DNA damage and predominance of transition variants support the concept that errors in mtDNA replication represent the predominant mutation mechanism in Tenon’s ocular fibroblasts from patients with POAG. Pathogenic somatic mitochondrial genome mutations were observed in people with POAG. This supports the role of somatic mitochondrial genome variants in the etiology of glaucoma.

Summary: Background: BC2001 showed combining chemotherapy (5-FU + mitomycin-C) with radiotherapy improves loco-regional disease-free survival in patients with muscle-invasive bladder cancer (MIBC). We previously showed a 24-gene hypoxia-associated signature predicted benefit from hypoxia-modifying radiosensitisation in BCON and hypothesised that only patients with low hypoxia scores (HSs) would benefit from chemotherapy in BC2001. BC2001 allowed conventional (64Gy/32 fractions) or hypofractionated (55Gy/20 fractions) radiotherapy. An exploratory analysis tested an additional hypothesis that hypofractionation reduces reoxygenation and would be detrimental for patients with hypoxic tumours. Methods: RNA was extracted from pre-treatment biopsies (298 BC2001 patients), transcriptomic data generated (Affymetrix Clariom-S arrays), HSs calculated (median expression of 24-signature genes) and patients stratified as hypoxia-high or -low (cut-off: cohort median). Primary endpoint: invasive loco-regional control (ILRC); secondary overall survival. Findings: Hypoxia affected overall survival (HR = 1.30; 95% CI 0.99–1.70; p = 0.062): more uncertainty for ILRC (HR = 1.29; 95% CI 0.82–2.03; p = 0.264). Benefit from chemotherapy was similar for patients with high or low HSs, with no interaction between HS and treatment arm. High HS associated with poor ILRC following hypofractionated (n = 90, HR 1.69; 95% CI 0.99–2.89 p = 0.057) but not conventional (n = 207, HR 0.70; 95% CI 0.28–1.80, p = 0.461) radiotherapy. The finding was confirmed in an independent cohort (BCON) where hypoxia associated with a poor prognosis for patients receiving hypofractionated (n = 51; HR 14.2; 95% CI 1.7–119; p = 0.015) but not conventional (n = 24, HR 1.04; 95% CI 0.07–15.5, p = 0.978) radiotherapy. Interpretation: Tumour hypoxia status does not affect benefit from BC2001 chemotherapy. Hypoxia appears to affect fractionation sensitivity. Use of HSs to personalise treatment needs testing in a biomarker-stratified trial. Funding: Cancer Research UK, NIHR, MRC.

Abstract Glaucoma is a complex neurodegenerative disease resulting in progressive optic neuropathy and is a leading cause of irreversible blindness worldwide. Primary open angle glaucoma (POAG) is the predominant form affecting 65.5 million people globally. Despite the prevalence of POAG and the identification of over 120 glaucoma related genetic loci, the underlaying molecular mechanisms are still poorly understood. The transforming growth factor beta (TGF-β) signalling pathway is implicated in the molecular pathology of POAG. To gain a better understanding of the role TGF-β2 plays in the glaucomatous changes to the molecular pathology in the trabecular meshwork, we employed RNA-Seq to delineate the TGF-β2 induced changes in the transcriptome of normal primary human trabecular meshwork cells (HTM). We identified a significant number of differentially expressed genes and associated pathways that contribute to the pathogenesis of POAG. The differentially expressed genes were predominantly enriched in ECM regulation, TGF-β signalling, proliferation/apoptosis, inflammation/wound healing, MAPK signalling, oxidative stress and RHO signalling. Canonical pathway analysis confirmed the enrichment of RhoA signalling, inflammatory-related processes, ECM and cytoskeletal organisation in HTM cells in response to TGF-β2. We also identified novel genes and pathways that were affected after TGF-β2 treatment in the HTM, suggesting additional pathways are activated, including Nrf2, PI3K-Akt, MAPK and HIPPO signalling pathways. The identification and characterisation of TGF-β2 dependent differentially expressed genes and pathways in HTM cells is essential to understand the patho-physiology of glaucoma and to develop new therapeutic agents.

Abstract In the quest of identifying newer molecular targets for the management of glucocorticoid-induced ocular hypertension (GC-OHT) and glaucoma (GCG), several microarray studies have attempted to investigate the genome-wide transcriptome profiling of primary human trabecular meshwork (TM) cells in response to dexamethasone (DEX). However, no studies are reported so far to demonstrate the temporal changes in the expression of genes in the cultured human TM cells in response to DEX treatment. Therefore, in the present study, the time-dependent changes in the genome-wide expression of genes in primary human TM cells after short (16 hours: 16 h) and long exposure (7 days: 7 d) of DEX was investigated using RNA sequencing. There were 199 (118 up-regulated; 81 down-regulated) and 525 (119 up-regulated; 406 down-regulated) DEGs in 16 h and 7 d treatment groups respectively. The unique genes identified in 16 h and 7 d treatment groups were 152 and 478 respectively. This study found a distinct gene signature and pathways between two treatment regimes. Longer exposure of DEX treatment showed a dys-regulation of Wnt and Rap1 signaling and so highlighted potential therapeutic targets for pharmacological management of GC-OHT/glaucoma.

Abstract Hypoxia is common in non-small cell lung cancer (NSCLC) and an attractive therapeutic target. As hypoxia-targeting treatments are effective in patients with the most hypoxic tumours, we aimed to develop a lung adenocarcinoma (LUAD) hypoxia-related gene expression signature. RNAseq was used to identify genes significantly differentially expressed under hypoxia (1% O2) in four LUAD cell lines. Identified genes were used for unsupervised clustering of a TCGA-LUAD training dataset (n = 252) and in a machine learning approach to build a hypoxia-related signature. Thirty-five genes were upregulated in common in three of the four lines and reduced in the training cohort to a 28-gene signature. The signature was prognostic in the TCGA training (HR 2.12, 95% CI 1.34–3.37, p = 0.0011) and test (n = 250; HR 2.13, 95% CI 1.32–3.45, p = 0.0016) datasets. The signature was prognostic for overall survival in a meta-analysis of nine other datasets (n = 1257; HR 2.08, 95% CI 1.60–2.70, p

Objectives To understand the views and motivations of healthcare workers at a vaccination hub who received a COVID-19 vaccination in March–May 2021.Study design This is an observational study via an anonymous electronic survey of seven questions focus on where survey recipients received information about the vaccine roll-out, their motivations for receiving the vaccine and their level of comfort in receiving the vaccine.Setting The Liverpool Vaccination Hub is located in South Western Sydney.Participants Participants were healthcare workers who received the first dose of a COVID-19 vaccine in the Australian Government’s Phase 1a and 1b priority categories. The majority of survey respondents (70%) were female (median aged between 35 and 44 years). The majority of survey respondents were clinical workers, such as nurse, paramedics and doctors.Outcome measures χ2 analysis was used for analysis of survey responses in univariate analysis. Logistic regression was used to analyse survey responses, adjusting for week, type of health worker and age.Results 4746 healthcare workers responded to the survey after receiving their first vaccine dose, a response rate of 23%. Over 90% of respondents said that COVID-19 vaccination information from their organisation was easily available. Most of them reported that they were comfortable receiving a COVID-19 vaccine. The majority of respondents were motivated to receive the vaccine due to concern about contracting COVID-19 themselves (75%), or concerns about transmitting it to other people such as patients (52%), family members (65%) or other community members (54%). Younger respondents were more likely to have preferred more information on vaccine safety (p

Abstract Clear cell renal cell carcinoma (ccRCC) has been previously classified into putative discrete prognostic subtypes by gene expression profiling. To investigate the robustness of these proposed subtype classifications, we evaluated 12 public datasets, together with a new dataset of 265 ccRCC gene expression profiles. Consensus clustering showed unstable subtype and principal component analysis (PCA) showed a continuous spectrum both within and between datasets. Considering the lack of discrete delineation and continuous spectrum observed, we developed a continuous quantitative prognosis score (Continuous Linear Enhanced Assessment of RCC, or CLEAR score). Prognostic performance was evaluated in independent cohorts from The Cancer Genome Atlas (TCGA) (n = 414) and EMBL-EBI (n = 53), CLEAR score demonstrated both superior prognostic estimates and inverse correlation with anti-angiogenic tyrosine-kinase inhibition in comparison to previously proposed discrete subtyping classifications. Inverse correlation with high-dose interleukin-2 outcomes was also observed for the CLEAR score. Multiple somatic mutations (VHL, PBRM1, SETD2, KDM5C, TP53, BAP1, PTEN, MTOR) were associated with the CLEAR score. Application of the CLEAR score to independent expression profiling of intratumoral ccRCC regions demonstrated that average intertumoral heterogeneity exceeded intratumoral expression heterogeneity. Wider investigation of cancer biology using continuous approaches may yield insights into tumor heterogeneity; single cell analysis may provide a key foundation for this approach.

The communities of practice (COP) framework describes learning as a process of navigating one's position of membership within a community of professionals pursuing a set of common goals using established practices. As students navigate their membership within a community like a physics research group, they develop a mental model of the community of practice and use this model to guide their future career decisions. Drawing has been shown to illustrate students' perspectives and experiences, offering important benefits as a source of qualitative information. In this proof-of-concept paper, we explore how a drawing survey can be used to identify elements of a student's COP model in the context of a research group. We describe the development and validation of this drawing survey using the response process evaluation method. This method establishes the degree to which students interpret survey prompts as intended. We then review a sample of seven student drawings made in response to the survey to investigate the degree to which the survey generates sufficient data to examine a student's COP model. Finally, we demonstrate a use case examining N = 23 drawings that allow us to identify patterns and possible differences in responses from different student groups (physics majors and biology majors). We then reflect on this use of a drawing survey by highlighting important aspects of the process and discussing limitations.

Integrating computational thinking (CT) into STEM disciplines requires secondary teachers to develop their pedagogical content knowledge of computing and content integration. Experienced teachers who choose to integrate CT in their secondary STEM courses may struggle in the same ways as novice teachers as they learn about programming and its potential use within their content areas. This study describes these potential struggles as teacher re-novicing in the context of high school physics. The research team facilitated a week-long computing integration workshop for physics teachers (n = 24) from three countries. The teachers engaged with computational learning activities in Jupyter Notebooks with the goal of developing their capacity to integrate Python in physics applications. Qualitative analysis of teacher surveys supported our theorization of a pathway of CT integration knowledge development. We describe these professional learning needs in four illustrative cases, building a grounded theory for teacher re-novicing as a pathway beginning with computing knowledge, moving through physics applications of computing, and arriving at pedagogical knowledge for physics-CT integration.

We provide novel functional data that posttranscriptional silencing of gene RPL19 using RNAi not only abrogates the malignant phenotype of PC-3M prostate cancer cells but is selective with respect to transcription and translation of other genes. Reducing RPL19 transcription modulates a subset of genes, evidenced by gene expression array analysis and Western blotting, but does not compromise cell proliferation or apoptosis in-vitro. However, growth of xenografted tumors containing the knocked-down RPL19 in-vivo is significantly reduced. Analysis of the modulated genes reveals induction of the non-malignant phenotype principally to involve perturbation of networks of transcription factors and cellular adhesion genes. The data provide evidence that extra-ribosomal regulatory functions of RPL19, beyond protein synthesis, are critical regulators of cellular phenotype. Targeting key members of affected networks identified by gene expression analysis raises the possibility of therapeutically stabilizing a benign phenotype generated by modulating the expression of an individual gene and thereafter constraining a malignant phenotype while leaving non-malignant tissues unaffected.

The communities of practice (COP) framework is useful in understanding the effort to expand physics education into professional preparation. This framework prompts physics educators and physics education researchers to consider “what counts as doing physics” that we want to prepare students for and how we can model professional physics practice in our classrooms. We argue that this focus on community omits an important consideration of the student’s perceptions of the physics community, which informs how they navigate the community. We introduce the idea of a COP model to describe a student’s internal representation of the community’s goals and practices and their sense of membership within the community. The student develops their COP model in response to legitimate peripheral participation within the community and uses this model to extrapolate their experience of the local community to the global community. We describe how this construct shares similarities with other frameworks but retains distinct features that make it a helpful tool for analysis. We demonstrate the use of the COP model in the review of student interviews about the use of computational practices in the physics community. The COP model helps us interpret student responses in terms of their COP models’ alignment and misalignment with the physics community. We discuss implications for instruction and reflect on the utility of the COP-model construct.