University of Leeds
  • Leeds, W.Yorkshire, United Kingdom
Recent publications
Different 2,4-thiazolidinedione-tethered coumarins 5a–b, 10a–n and 11a–d were synthesised and evaluated for their inhibitory action against the cancer-associated hCAs IX and XII, as well as the physiologically dominant hCAs I and II to explore their selectivity. Un-substituted phenyl-bearing coumarins 10a, 10 h, and 2-thienyl/furyl-bearing coumarins 11a–c exhibited the best hCA IX (KIs between 0.48 and 0.93 µM) and hCA XII (KIs between 0.44 and 1.1 µM) inhibitory actions. Interestingly, none of the coumarins had any inhibitory effect on the off-target hCA I and II isoforms. The sub-micromolar compounds from the biochemical assay, coumarins 10a, 10 h and 11a–c, were assessed in an in vitro antiproliferative assay, and then the most potent antiproliferative agent 11a was tested to explore its impact on the cell cycle phases and apoptosis in MCF-7 breast cancer cells to provide more insights into the anticancer activity of these compounds.
Ulcerative colitis (UC) is a complex immune-mediated disease in which the gut microbiota plays a central role, and may determine prognosis and disease progression. We aimed to assess whether a specific microbiota profile, as measured by a machine learning approach, can be associated with disease severity in patients with UC. In this prospective pilot study, consecutive patients with active or inactive UC and healthy controls (HCs) were enrolled. Stool samples were collected for fecal microbiota assessment analysis by 16S rRNA gene sequencing approach. A machine learning approach was used to predict the groups' separation. Thirty-six HCs and forty-six patients with UC (20 active and 26 inactive) were enrolled. Alpha diversity was significantly different between the three groups (Shannon index: p-values: active UC vs HCs = 0.0005; active UC vs inactive UC = 0.0273; HCs vs inactive UC = 0.0260). In particular, patients with active UC showed the lowest values, followed by patients with inactive UC, and HCs. At species level, we found high levels of Bifidobacterium adolescentis and Haemophilus parainfluenzae in inactive UC and active UC, respectively. A specific microbiota profile was found for each group and was confirmed with sparse partial least squares discriminant analysis, a machine learning-supervised approach. The latter allowed us to observe a perfect class prediction and group separation using the complete information (full Operational Taxonomic Unit table), with a minimal loss in performance when using only 5% of features. A machine learning approach to 16S rRNA data identifies a bacterial signature characterizing different degrees of disease activity in UC. Follow-up studies will clarify whether such microbiota profiling are useful for diagnosis and management.
Context: The osteogenic potential of the human dental pulp stromal cells (hDPSCs) was reduced in the state of oxidative stress. Resveratrol (RSV) possesses numerous biological properties, including osteogenic potential, growth-promoting and antioxidant activities. Objective: This study investigates the osteogenic potential of RSV by activating the Sirt1/Nrf2 pathway on oxidatively stressed hDPSCs and old mice. Materials and methods: The hDPSCs were subjected to reactive oxygen species (ROS) fluorescence staining, cell proliferation assay, ROS activity assay, superoxide dismutase (SOD) enzyme activity, the glutathione (GSH) concentration assay, alkaline phosphatase staining, real-time polymerase chain reaction (RT-PCR) and Sirt1 immunofluorescence labelling to assess the antioxidant stress and osteogenic ability of RSV. Forty female Kunming mice were divided into Old, Old-RSV, Young and Young-RSV groups to assess the repair of calvarial defects of 0.2 mL RSV of 20 mg/kg/d for seven days by injecting intraperitoneally at 4 weeks after surgery using micro-computed tomography, nonlinear optical microscope and immunohistochemical analysis. Results: RSV abates oxidative stress by alleviating the proliferation, mitigating the ROS activity, increasing the SOD enzyme activity and ameliorating the GSH concentration (RSV IC50 in hDPSCs is 67.65 ± 9.86). The antioxidative stress and osteogenic capabilities of RSV were confirmed by the up-regulated gene expression of SOD1, xCT, RUNX2 and OCN, as well as Sirt1/Nrf2. The collagen, bone matrix formation and Sirt1 expression, are significantly increased after RSV treatment in mice. Discussion and conclusions: For elderly or patients with oxidative stress physiological states such as hypertension, heart disease, diabetes, etc., RSV may potentially improve bone augmentation surgery in regenerative medicine.
Background: A food and fluid intake program is essential for ultraendurance athletes to maximize performance and avoid possible gastrointestinal symptoms (GIS). However, the ability to follow such a program during a race has been under-assessed. We thus investigated the fluctuations of food and fluid intake during the 24-h run World Championship of 12 elite athletes (6 men and 6 women; age: 46 ± 7 years, height: 170 ± 9 cm, weight: 61.1 ± 9.6 kg, total distance run: 193-272 km) and assessed their ability to follow their nutritional program. Methods: Real-time overall intake (fluids, energy, and macronutrients) was recorded and compared to that of their program. The temporal difference in absolute values and the degree of divergence from their program were assessed, divided into four 6-h periods. GIS were recorded during the race. A questionnaire identifying the details of their nutritional program and the self-assessed causes of their inability to follow it was completed by the participants the day after the race. Results: Water, total fluid, carbohydrates (CHO), and energy intake decreased during the last quarter of the 24-h ultramarathon relative to the first half (p = 0.024, 0.022, 0.009, and 0.042). However, the differences were no longer significant after these values were normalized by the number of passages in front of the supply tent. The participants progressively failed to follow their nutritional program, with the intake of their planned items dropping to approximately 50% during the last quarter. However, this was adequately compensated by increases in unplanned foods allowing them to match their expected targets. GIS, lack of appeal of the planned items, and attractivity of unplanned items were the main explanations given for their deviation from the program (64, 27, and 27%, respectively). Conclusion: Despite evident difficulty in following their nutritional programs (mostly attributed to GIS), elite ultraendurance runners managed to maintain high rates of fluid and food intake during a 24-h ultramarathon and therefore still met their planned elevated nutritional objectives.Abbreviations: CHO: carbohydrates, GIS: gastrointestinal symptoms.
Objectives: This study aimed to investigate oral microbial signatures associated with hyper- glycaemia, by correlating the oral microbiome with three glycaemic markers. Potential association between clinical parameters and oral bacterial taxa that could be modulating the hyperglycaemic microbiome was also explored. Methods: Twenty-three individuals diagnosed with type 2 Diabetes Mellitus (T2D) and presenting periodontitis were included, as well as 25 systemically and periodontally healthy ones. Fasting blood glucose, glycated haemoglobin, salivary glucose, periodontitis classifica- tion, caries experience and activity and salivary pH were evaluated. The V4 region of the 16S rRNA gene was amplified from total salivary DNA, and amplicons were sequenced (Illumina MiSeq). Results: Hyperglycaemia was correlated with proportions of Treponema, Desulfobulbus, Phocaiecola and Saccharimonadaceae. Desulfobulbus was ubiquitous and the most enriched organism in T2D individuals (log2FC = 4). The Firmicutes/Bacteroidetes ratio was higher at alkali salivary pH than acidic pH. In the network analysis, Desulfobulbus was clustered in a negative association with caries-associated and butyrate-producing bacteria. Conclusion: The salivary microbiome is shaped by systemic hyperglycaemia, as well as changes in the salivary pH, which may be linked to local hyperglycaemia. The enrichment of predictive biomarkers of gut dysbiosis in the salivary microbiome can reflect its capacity for impairment of hyperglycaemia.
Localisation, as it aims to shift power in the humanitarian system, will involve the increased inclusion of local faith actors, those national and local faith-affiliated groups and organisations that are often first, and last, responders in crises and have been responding in humanitarian contexts for many years, but often in parallel to humanitarian coordination mechanisms. In primary research in South Sudan with local faith actors and international humanitarian actors, this article aims to examine the inroads and barriers to local faith actor involvement in the humanitarian system and the realisation of localisation with local actors such as these. The research is based on an ethnographic study in which researchers were imbedded in a humanitarian project that aimed to help bridge divides between local faith actors and the international humanitarian system. The findings are based on one-on-one and group interviews with 89 participants from a range of international and local, and faith and secular, organisations. Findings indicate that local faith actors are active in responding to crises and want to be linked to the humanitarian system, but they feel distanced from it and pigeonholed as local faith actors. Formalisation through the appropriate registration systems and then training and networking with the humanitarian system helped them build legitimacy and feel confident to participate in humanitarian coordination. International humanitarian actors can help bridge barriers by understanding and connecting with the local faith actors and challenging their own assumptions about who local faith actors are.
The UK House of Commons Science and Technology Committee has called for evidence on the roles that different stakeholders play in reproducibility and research integrity. Of central priority are proposals for improving research integrity and quality, as well as guidance and support for researchers. In response to this, we argue that there is one important component of research integrity that is often absent from discussion: the pedagogical consequences of how we teach, mentor, and supervise students through open scholarship. We justify the need to integrate open scholarship principles into research training within higher education and argue that pedagogical communities play a key role in fostering an inclusive culture of open scholarship. We illustrate these benefits by presenting the Framework for Open and Reproducible Research Training (FORRT) , an international grassroots community whose goal is to provide support, resources, visibility, and advocacy for the adoption of principled, open teaching and mentoring practices, whilst generating conversations about the ethics and social impact of higher-education pedagogy. Representing a diverse group of early-career researchers and students across specialisms, we advocate for greater recognition of and support for pedagogical communities, and encourage all research stakeholders to engage with these communities to enable long-term, sustainable change.
Background Despite decades of accruing evidence supporting the clinical utility of cardiovascular magnetic resonance (CMR), adoption of CMR in routine cardiovascular practice remains limited in many regions of the world. Persistent use of long scan times of 60 min or more contributes to limited adoption, though techniques available on most scanners afford routine CMR examination within 30 min. Incorporating such techniques into standardize protocols can answer common clinical questions in daily practice, including those related to heart failure, cardiomyopathy, ventricular arrhythmia, ischemic heart disease, and non-ischemic myocardial injury. Body In this white paper, we describe CMR protocols of 30 min or shorter duration with routine techniques with or without stress perfusion, plus specific approaches in patient and scanner room preparation for efficiency. Minimum requirements for the scanner gradient system, coil hardware and pulse sequences are detailed. Recent advances such as quantitative myocardial mapping and other add-on acquisitions can be incorporated into the proposed protocols without significant extension of scan duration for most patients. Conclusion Common questions in clinical cardiovascular practice can be answered in routine CMR protocols under 30 min; their incorporation warrants consideration to facilitate increased access to CMR worldwide.
Background Inherited vitreoretinopathies arise as a consequence of congenital retinal vascularisation abnormalities. They represent a phenotypically and genetically heterogeneous group of disorders that can have a major impact on vision. Several genes encoding proteins and effectors of the canonical Wnt/β-catenin pathway have been associated and precise diagnosis, although difficult, is essential for proper clinical management including syndrome specific management where appropriate. This work aimed to investigate the molecular basis of disease in a single proband born to consanguineous parents, who presented with microphthalmia, persistent foetal vasculature, posterior lens vacuoles, vitreoretinal dysplasia, microcephaly, hypotelorism and global developmental delay, and was registered severely visually impaired by 5 months of age. Methods Extensive genomic pre-screening, including microarray comparative genomic hybridisation and sequencing of a 114 gene panel associated with cataract and congenital ophthalmic disorders was conducted by an accredited clinical laboratory. Whole exome sequencing (WES) was undertaken on a research basis and in vitro TOPflash transcriptional reporter assay was utilised to assess the impact of the putative causal variant. Results In the proband, WES revealed a novel, likely pathogenic homozygous mutation in the cadherin-associated protein beta-1 gene ( CTNNB1), c.884C>G; p.(Ala295Gly), which encodes a co-effector molecule of the Wnt/β-catenin pathway. The proband’s parents were shown to be heterozygous carriers but ophthalmic examination did not detect any abnormalities. Functional assessment of the missense variant demonstrated significant reduction of β-catenin activity. Conclusions This is the first report of a biallelic disease-causing variation in CTNNB1 . We conclude that this biallelic, transcriptional inactivating mutation of CTNNB1 causes a severe, syndromic form of microphthalmia, persistent foetal vasculature and vitreoretinal dysplasia that results in serious visual loss in infancy.
Background Measurement of cardiac structure and function from images (e.g. volumes, mass and derived parameters such as left ventricular (LV) ejection fraction [LVEF]) guides care for millions. This is best assessed using cardiovascular magnetic resonance (CMR), but image analysis is currently performed by individual clinicians, which introduces error. We sought to develop a machine learning algorithm for volumetric analysis of CMR images with demonstrably better precision than human analysis. Methods A fully automated machine learning algorithm was trained on 1923 scans (10 scanner models, 13 institutions, 9 clinical conditions, 60,000 contours) and used to segment the LV blood volume and myocardium. Performance was quantified by measuring precision on an independent multi-site validation dataset with multiple pathologies with n = 109 patients, scanned twice. This dataset was augmented with a further 1277 patients scanned as part of routine clinical care to allow qualitative assessment of generalization ability by identifying mis-segmentations. Machine learning algorithm (‘machine’) performance was compared to three clinicians (‘human’) and a commercial tool (cvi42, Circle Cardiovascular Imaging). Findings Machine analysis was quicker (20 s per patient) than human (13 min). Overall machine mis-segmentation rate was 1 in 479 images for the combined dataset, occurring mostly in rare pathologies not encountered in training. Without correcting these mis-segmentations, machine analysis had superior precision to three clinicians (e.g. scan-rescan coefficients of variation of human vs machine: LVEF 6.0% vs 4.2%, LV mass 4.8% vs. 3.6%; both P < 0.05), translating to a 46% reduction in required trial sample size using an LVEF endpoint. Conclusion We present a fully automated algorithm for measuring LV structure and global systolic function that betters human performance for speed and precision.
A simple approximate theory of snow machining is applied to modelling successive wedge turns of alpine skiing. The model involves predefined control functions describing skier’s control over the turns via angle of attack, edge angle and loading of the skis. To demonstrate the model’s potential, reasonable control functions with a small number of free parameters are designed and used in attempt to reproduce the data obtained in a previous field study by other researches. The results are in semi-quantitative agreement with the data. In particular, the model explains the nature of the abnormally high values for the “coefficient of friction” deduced in that study. Future field studies of wedge turns should aim at measuring the angle of attack, edge angle and loading of the skis. This will allow to determine the control functions from the experimental data and hence to conduct a more stringent verification of the model.
Background Pregnant women with type 1 diabetes strive for tight glucose targets (3.5-7.8 mmol/L) to minimise the risks of obstetric and neonatal complications. Despite using diabetes technologies including continuous glucose monitoring (CGM), insulin pumps and contemporary insulin analogues, most women struggle to achieve and maintain the recommended pregnancy glucose targets. This study aims to evaluate whether the use of automated closed-loop insulin delivery improves antenatal glucose levels in pregnant women with type 1 diabetes. Methods/design A multicentre, open label, randomized, controlled trial of pregnant women with type 1 diabetes and a HbA1c of ≥48 mmol/mol (6.5%) at pregnancy confirmation and ≤ 86 mmol/mol (10%) at randomization. Participants who provide written informed consent before 13 weeks 6 days gestation will be entered into a run-in phase to collect 96 h (24 h overnight) of CGM glucose values. Eligible participants will be randomized on a 1:1 basis to CGM (Dexcom G6) with usual insulin delivery (control) or closed-loop (intervention). The closed-loop system includes a model predictive control algorithm (CamAPS FX application), hosted on an android smartphone that communicates wirelessly with the insulin pump (Dana Diabecare RS) and CGM transmitter. Research visits and device training will be provided virtually or face-to-face in conjunction with 4-weekly antenatal clinic visits where possible. Randomization will stratify for clinic site. One hundred twenty-four participants will be recruited. This takes into account 10% attrition and 10% who experience miscarriage or pregnancy loss. Analyses will be performed according to intention to treat. The primary analysis will evaluate the change in the time spent in the target glucose range (3.5-7.8 mmol/l) between the intervention and control group from 16 weeks gestation until delivery. Secondary outcomes include overnight time in target, time above target (> 7.8 mmol/l), standard CGM metrics, HbA1c and psychosocial functioning and health economic measures. Safety outcomes include the number and severity of ketoacidosis, severe hypoglycaemia and adverse device events. Discussion This will be the largest randomized controlled trial to evaluate the impact of closed-loop insulin delivery during type 1 diabetes pregnancy. Trial registration ISRCTN 56898625 Registration Date: 10 April, 2018.
Background Right atrial (RA) area predicts mortality in patients with pulmonary hypertension, and is recommended by the European Society of Cardiology/European Respiratory Society pulmonary hypertension guidelines. The advent of deep learning may allow more reliable measurement of RA areas to improve clinical assessments. The aim of this study was to automate cardiovascular magnetic resonance (CMR) RA area measurements and evaluate the clinical utility by assessing repeatability, correlation with invasive haemodynamics and prognostic value. Methods A deep learning RA area CMR contouring model was trained in a multicentre cohort of 365 patients with pulmonary hypertension, left ventricular pathology and healthy subjects. Inter-study repeatability (intraclass correlation coefficient (ICC)) and agreement of contours (DICE similarity coefficient (DSC)) were assessed in a prospective cohort (n = 36). Clinical testing and mortality prediction was performed in n = 400 patients that were not used in the training nor prospective cohort, and the correlation of automatic and manual RA measurements with invasive haemodynamics assessed in n = 212/400. Radiologist quality control (QC) was performed in the ASPIRE registry, n = 3795 patients. The primary QC observer evaluated all the segmentations and recorded them as satisfactory, suboptimal or failure. A second QC observer analysed a random subcohort to assess QC agreement (n = 1018). Results All deep learning RA measurements showed higher interstudy repeatability (ICC 0.91 to 0.95) compared to manual RA measurements (1st observer ICC 0.82 to 0.88, 2nd observer ICC 0.88 to 0.91). DSC showed high agreement comparing automatic artificial intelligence and manual CMR readers. Maximal RA area mean and standard deviation (SD) DSC metric for observer 1 vs observer 2, automatic measurements vs observer 1 and automatic measurements vs observer 2 is 92.4 ± 3.5 cm ² , 91.2 ± 4.5 cm ² and 93.2 ± 3.2 cm ² , respectively. Minimal RA area mean and SD DSC metric for observer 1 vs observer 2, automatic measurements vs observer 1 and automatic measurements vs observer 2 was 89.8 ± 3.9 cm ² , 87.0 ± 5.8 cm ² and 91.8 ± 4.8 cm ² . Automatic RA area measurements all showed moderate correlation with invasive parameters (r = 0.45 to 0.66), manual (r = 0.36 to 0.57). Maximal RA area could accurately predict elevated mean RA pressure low and high-risk thresholds (area under the receiver operating characteristic curve artificial intelligence = 0.82/0.87 vs manual = 0.78/0.83), and predicted mortality similar to manual measurements, both p < 0.01. In the QC evaluation, artificial intelligence segmentations were suboptimal at 108/3795 and a low failure rate of 16/3795. In a subcohort (n = 1018), agreement by two QC observers was excellent, kappa 0.84. Conclusion Automatic artificial intelligence CMR derived RA size and function are accurate, have excellent repeatability, moderate associations with invasive haemodynamics and predict mortality.
This paper presents the results of an investigation into the long-term flexural behaviour of cracked reinforced recycled aggregate concrete (RAC) beams. Washed construction and demolition wastes (CDW) with a maximum size of 20 mm were used as the coarse recycled aggregate. The main variable in the research was the replacement ratio of recycled aggregate. Specimens with 0%, 50% and 100% recycled aggregate were cast and tested. The experimental results showed that samples with an increased amount of recycled aggregate had significantly reduced strength and a noticeable increase in both short-term and long-term deflection of RAC beams over equivalent normal concrete (NC) beams. Increased levels of RA resulted in greater creep and shrinkage of RAC and greater long-term loss of tension stiffening in RAC reinforced tension specimens. Prediction of long-term deflections using Eurocode 2, even after incorporating the experimental concrete properties within the Code method, underestimated the experimental deflections of the RAC beams. However, by modifying the tension stiffening factor, β used in Eurocode 2, deflections were predicted to within approximately 1%. From this investigation, it is recommended that the factor β be reduced from 0.5 (for NC) to 0.4 (for RAC @50% replacement) and 0.3 (for RAC @100% replacement).
The last decade has seen renewed concern within the scientific community over the reproducibility and transparency of research findings. This paper outlines some of the various responsibilities of stakeholders in addressing the systemic issues that contribute to this concern. In particular, this paper asserts that a united, joined-up approach is needed, in which all stakeholders, including researchers, universities, funders, publishers, and governments, work together to set standards of research integrity and engender scientific progress and innovation. Using two developments as examples: the adoption of Registered Reports as a discrete initiative, and the use of open data as an ongoing norm change, we discuss the importance of collaboration across stakeholders.
Clinical trial managers play a vital role in the design and conduct of clinical trials in the UK. There is a current recruitment and retention crisis for this specialist role due to a complex set of factors, most likely to have come to a head due to the COVID-19 pandemic. Academic clinical trial units and departments are struggling to recruit trial managers to vacant positions, and multiple influences are affecting the retention of this highly skilled workforce. Without tackling this issue, we face major challenges in the delivery on the Department of Health and Social Care’s Future of UK Clinical Research Delivery implementation plan. This article, led by a leading network of and for UK Trial Managers, presents some of the issues and ways in which national stakeholders may be able to address this.
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Krzysztof J Kubiak
  • School of Mechanical Engineering
Samit Chakrabarty
  • School of Biomedical Sciences; Chakrabarty group
Martin Zebracki
  • Citizenship and Belonging Group
Woodhouse Lane, LS2 9JT, Leeds, W.Yorkshire, United Kingdom
Head of institution
Professor Simone Buitendijk
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