Responding to the cuts in UK AID to neglected tropical diseases control programmes in Africa.

The early termination of the Accelerating the Sustainable Control and Elimination of Neglected Tropical Diseases (Ascend) programme by the UK government in June 2021 was a bitter blow to countries in East and West Africa where no alternative source of funding existed. Here we assess the potential impact the cuts may have had if alternative funding had not been made available by new development partners and outline new strategies developed by affected countries to mitigate current and future disruptions to neglected tropical disease control programmes.

Modelling the impact of school reopening and contact tracing strategies on Covid-19 dynamics in different epidemiologic settings in Brazil.

We simulate the impact of school reopening during the COVID-19 pandemic in three major urban centers in Brazil to identify the epidemiological indicators and the best timing for the return of in-school activities and the effect of contact tracing as a mitigation measure. Our goal is to offer guidelines for evidence-based policymaking. We implement an extended SEIR model stratified by age and considering contact networks in different settings - school, home, work, and community, in which the infection transmission rate is affected by various intervention measures.

Mâmawihitowin (bringing the camps together): Perinatal healthcare provider and staff participation in an Indigenous-led experiential intervention for enhancing culturally informed care-a mixed methods study.

Background: In partnership with a Nehiyawak (Plains Cree) community of Maskwacîs,central Alberta (Canada), we implemented an Indigenous-led intervention to provide experiential learning opportunities for perinatal health care providers (HCPs) and staff. Our objective was to capture the impact of participating in cultural safety learning opportunities on perceived self-awareness for HCPs and staff to provide enhanced culturally informed care.

Methods: Perinatal HCPs and staff who work regularly with Indigenous women from our partnering community took part in a series of experiential learning activities designed by a Community Advisory Committee.

The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA.

The raw material for viral evolution is provided by intra-host mutations occurring during replication, transcription or post-transcription. Replication and transcription of proceed through the synthesis of negative-sense 'antigenomes' acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences.

Androgen receptor function and targeted therapeutics across breast cancer subtypes.

Despite significant progress in breast cancer (BC) therapy, it is globally the most commonly diagnosed cancer and leads to the death of over 650,000 women annually. Androgen receptor (AR) is emerging as a potential new therapeutic target in BC. While the role of AR is well established in prostate cancer (PCa), its function in BC remains incompletely understood.

Low Blood Levels of LRG1 Before Radical Prostatectomy Identify Patients with High Risk of Progression to Castration-resistant Prostate Cancer.

Background: After radical prostatectomy (RP), depending on stage, up to 40% of patients with prostate cancer (PCa) will experience biochemical failure (BF). Despite salvage therapy, approximately one-third of these patients will need permanent hormone therapy (pHT) and are at risk of progression to castration-resistant PCa (CRPC). Prognostic markers herald the need for neoadjuvant, adjuvant, or multimodal treatment.

Considering equity in priority setting using transmission models: Recommendations and data needs.

Objectives: Disease transmission models are used in impact assessment and economic evaluations of infectious disease prevention and treatment strategies, prominently so in the COVID-19 response. These models rarely consider dimensions of equity relating to the differential health burden between individuals and groups. We describe concepts and approaches which are useful when considering equity in the priority setting process, and outline the technical choices concerning model structure, outputs, and data requirements needed to use transmission models in analyses of health equity.

The Chromatin Regulator HMGA1a Undergoes Phase Separation in the Nucleus.

The protein high mobility group A1 (HMGA1) is an important regulator of chromatin organization and function. However, the mechanisms by which it exerts its biological function are not fully understood. Here, we report that the HMGA isoform, HMGA1a, nucleates into foci that display liquid-like properties in the nucleus, and that the protein readily undergoes phase separation to form liquid condensates in vitro.

BLMM: Parallelised computing for big linear mixed models.

Within neuroimaging large-scale, shared datasets are becoming increasingly commonplace, challenging existing tools both in terms of overall scale and complexity of the study designs. As sample sizes grow, researchers are presented with new opportunities to detect and account for grouping factors and covariance structure present in large experimental designs. In particular, standard linear model methods cannot account for the covariance and grouping structures present in large datasets, and the existing linear mixed models (LMM) tools are neither scalable nor exploit the computational speed-ups afforded by vectorisation of computations over voxels.

Application of a convolutional neural network to the quality control of MRI defacing.

Large-scale neuroimaging datasets present unique challenges for automated processing pipelines. Motivated by a large clinical trials dataset with over 235,000 MRI scans, we consider the challenge of defacing - anonymisation to remove identifying facial features. The defacing process must undergo quality control (QC) checks to ensure that the facial features have been removed and that the brain tissue is left intact.

Getting the most out of maths: How to coordinate mathematical modelling research to support a pandemic, lessons learnt from three initiatives that were part of the COVID-19 response in the UK.

In March 2020 mathematics became a key part of the scientific advice to the UK government on the pandemic response to COVID-19. Mathematical and statistical modelling provided critical information on the spread of the virus and the potential impact of different interventions. The unprecedented scale of the challenge led the epidemiological modelling community in the UK to be pushed to its limits.

How the Routine Use of Patient-Reported Outcome Measures for Hemodialysis Care Influences Patient-Clinician Communication: A Mixed-Methods Study.

Background And Objectives: Patient-reported outcome measures invite patients to self-report aspects of their quality of life and have been reported to enhance communication with clinicians. We aimed to examine how routine use of patient-reported outcome measures in in-center hemodialysis units influenced patient-clinician communication.

Design, Setting, Participants, & Measurements: A concurrent, longitudinal, mixed-methods approach was used.

Evolving polarisation of infiltrating and alveolar macrophages in the lung during metastatic progression of melanoma suggests CCR1 as a therapeutic target.

Metastatic tumour progression is facilitated by tumour associated macrophages (TAMs) that enforce pro-tumour mechanisms and suppress immunity. In pulmonary metastases, it is unclear whether TAMs comprise tissue resident or infiltrating, recruited macrophages; and the different expression patterns of these TAMs are not well established. Using the mouse melanoma B16F10 model of experimental pulmonary metastasis, we show that infiltrating macrophages (IM) change their gene expression from an early pro-inflammatory to a later tumour promoting profile as the lesions grow.

Evaluating and mitigating the potential indirect effect of COVID-19 on control programmes for seven neglected tropical diseases: a modelling study.

Background: In line with movement restrictions and physical distancing essential for the control of the COVID-19 pandemic, WHO recommended postponement of all neglected tropical disease (NTD) control activities that involve community-based surveys, active case finding, and mass drug administration in April, 2020. Following revised guidance later in 2020, and after interruptions to NTD programmes of varying lengths, NTD programmes gradually restarted in the context of an ongoing pandemic. However, ongoing challenges and service gaps have been reported.

Reliability of multi-site UK Biobank MRI brain phenotypes for the assessment of neuropsychiatric complications of SARS-CoV-2 infection: The COVID-CNS travelling heads study.

Introduction: Magnetic resonance imaging (MRI) of the brain could be a key diagnostic and research tool for understanding the neuropsychiatric complications of COVID-19. For maximum impact, multi-modal MRI protocols will be needed to measure the effects of SARS-CoV-2 infection on the brain by diverse potentially pathogenic mechanisms, and with high reliability across multiple sites and scanner manufacturers. Here we describe the development of such a protocol, based upon the UK Biobank, and its validation with a travelling heads study.

Demes: a standard format for demographic models.

Understanding the demographic history of populations is a key goal in population genetics, and with improving methods and data, ever more complex models are being proposed and tested. Demographic models of current interest typically consist of a set of discrete populations, their sizes and growth rates, and continuous and pulse migrations between those populations over a number of epochs, which can require dozens of parameters to fully describe. There is currently no standard format to define such models, significantly hampering progress in the field.

The long-term relation between physical activity and executive function in the Rotterdam Study.

Background: Research on the association between physical inactivity and cognitive decline and dementia is dominated by studies with short-term follow-up, that might be biased by reverse causality.

Objective: Investigate the long-term association between physical activity, cognition, and the rate of age-associated cognitive decline.

Methods: We investigated the association between late-life physical activity and executive functioning and rate of decline of executive abilities during follow-up of up to 16 years, in 3553 participants of the prospective Rotterdam Study cohort.

Patient and care provider inclusion in the development of an educational graphic novel for heart transplanted teenagers.

Purpose: Teenagers experience high rates of rejection and organ failure after heart transplantation due to non-adherence to medications, poor transition into adult care, and difficulties communicating with adults including healthcare providers. This project aimed to creatively bridge this gap-including teenage patients, their parents, and healthcare providers in the development of a new resource meant to motivate teenage heart-transplant-patients to take interest and ownership of their long-term health.

Methods: Four teenage heart-transplanted patients, four parents, and three healthcare providers provided insight into relevant content for an educational resource through semi-standardized questionnaires and interviews.

Excess deaths during the COVID-19 pandemic in Iran.

Background: The actual number of deaths during the COVID-19 pandemic is expected to be higher than the reported deaths. We aimed to estimate the number of deaths in Iran during the COVID-19 pandemic from December 22, 2019 to March 20, 2022.

Methods: We compared the number of age- and sex-specific deaths reported by Iran's Bureau of Vital Statistics with the predicted deaths estimated using an improved Lee-Carter model.

Determining the Relationship Between Blood Pressure, Kidney Function, and Chronic Kidney Disease: Insights From Genetic Epidemiology.

Background: It is well established that decreased kidney function can increase blood pressure (BP), but it is unproven whether moderately elevated BP causes chronic kidney disease (CKD) or glomerular hyperfiltration.

Methods: 311 119 White British UK Biobank participants were included in logistic regression analyses to estimate the odds of CKD (defined as long-term kidney replacement therapy, estimated glomerular filtration rate [eGFR]< 60mL/min/1.73m, or urinary albumin:creatinine ratio ≥3 mg/mmol) associated with higher genetically predicted BP using genetic risk scores comprising 219 systolic and 223 diastolic BP loci.