Yuchun Ding

Yuchun Ding
University of Cambridge | Cam · Department of Haematology

PhD

About

43
Publications
5,252
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377
Citations
Introduction
I'm a computer scientist who often work with pathologists to develop practical solutions in digital pathology. Apart from this, I spent my spare time created XWOW Ltd (twitter.com/X_WowCom) to minimise turnaround time in cancer diagnosis by making microscopic equipment easier to access. So far my greatest achievement has appeared on several media including ChronicleLive and Royal College of Pathologist Bulletin. I also enjoy making home-made biomedical experiments, check out my tweet for more. https://twitter.com/Dingdingading

Publications

Publications (43)
Article
Full-text available
Mutations in pre-mRNA processing factors (PRPFs) cause autosomal-dominant retinitis pigmentosa (RP), but it is unclear why mutations in ubiquitously expressed genes cause non-syndromic retinal disease. Here, we generate transcriptome profiles from RP11 (PRPF31-mutated) patient-derived retinal organoids and retinal pigment epithelium (RPE), as well...
Article
Full-text available
Statement of significance: The expression and the role of many extracellular matrix (ECM) components during human retinal development is not fully understood. In this study, expression of key ECM components (Collagen IV, Fibronectin, Brevican, Versican, IMPG1 and IMPG2) was investigated during human retinal ontogenesis. Collagen IV and Fibronectin...
Article
Full-text available
Metabolite profiling is an important tool that may better capture the multiple features of neurodegeneration. With the considerable parallels between mouse and human metabolism, the use of metabolomics in mouse models with neurodegenerative pathology provides mechanistic insight and ready translation into aspects of human disease. Using 400 MHz nuc...
Article
Simbiotics is a spatially explicit multi-scale modeling platform for the design, simulation and analysis of bacterial populations. Systems ranging from planktonic cells and colonies, to biofilm formation and development may be modeled. Representation of biological systems in Simbiotics is flexible, user-defined processes may be in a variety of form...
Article
β-cell dysfunction in type 2 diabetes (T2D) is associated with loss of cellular identity and mis-expression of alternative islet hormones, including glucagon. The molecular basis for these cellular changes has been attributed to dysregulation of core β-cell transcription factors, which regulate β-cell identity through activating and repressive mech...
Article
Context: Although diabetes affects 40-50% of adults with cystic fibrosis, remarkably little is known regarding the underlying mechanisms leading to impaired pancreatic β-cell insulin secretion. Efforts towards improving the functional β-cell deficit in cystic fibrosis related diabetes (CFRD) have been hampered by an incomplete understanding of whet...
Article
Full-text available
Cell replacement therapy is a promising treatment for irreversible retinal cell death in diverse diseases such as Stargardt's disease, age-related macular degeneration, and retinitis pigmentosa. The final impact of all retinal dystrophies is the loss of photoreceptors; hence, there is a pressing need for research into replacement. Seminal work has...
Article
Full-text available
Systemic inflammation enhances the risk and progression of Alzheimer's disease (AD). Lipopolysaccharide (LPS), a potent pro-inflammatory endotoxin produced by the gut, is found in excess levels in AD where it associates with neurological hallmarks of pathology. Sex differences in susceptibility to inflammation and AD progression have been reported,...
Article
Full-text available
Tissue specific extracellular matrices (ECM) provide structural support and enable access to molecular signals and metabolites, which are essential for directing stem cell renewal and differentiation. To mimic this phenomenon in vitro, tissue decellularisation approaches have been developed, resulting in the generation of natural ECM scaffolds that...
Article
Full-text available
Neuroinflammation plays an important role in the pathogenesis of a range of brain disorders. Non-invasive imaging of neuroinflammation is critical to help improve our understanding of the underlying disease mechanisms, monitor therapies and guide drug development. Generally, MRI lacks specificity to molecular imaging biomarkers, but molecular MR im...
Data
Response to LPS. Histology was used to divide animals into Iba1+ and Iba1- to the LPS intervention. Shown here are a larger view of an example histology slide (A) with the corresponding CEST signal (B) for an Iba1+ animal with higher levels of microglial response on the LPS injection site, compared with the contralateral vehicle injection site. (EP...
Data
Quantitative histology measures vs CEST signal. In addition to the classification into Iba1+ and Iba1-, which was based on the judgement of an experienced pathologist, we correlated a quantitative, morphometric marker of microglia activation (soma size) with the CEST response. The difference between the LPS injection side and the contralateral vehi...
Data
CEST signal variability in control animals. To improve field homogeneity, we applied a gel cap to the top of the skull, which improved B0 homogeneity across the brain: (A) After shimming but without gel cap the B0 map, CEST map and the asymmetry spectrum from an ROI on the hippocampus; (B) with the 3% agarose gel cap. The CEST spectrum showed less...
Data
Details of experiment and resulting classification into iba1+ animals (responders) or Iba1—Non-responders, with contributing factors experimenter and genotype). In highlighted animals, there was at least a 20% change in CEST signal between LPS and PBS side. (PDF)
Data
Contribution of different metabolites to CEST signal. While the drug (LPS) itself does not have a measurable effect in the CEST MRI acquisition, several metabolites overlap and contribute to the CEST effect around 0.6 ppm. (A) Z spectrum and asymmetry spectrum of LPS in saline solution (5ng/μL concentration, pH 7.4). (B) Z-spectrum of several brain...
Data
T2 weighted images. T2 weighted images were acquired for all animals, while T2 maps were acquired for a subset of n = 6 animals. A) Representative T2 weighted image, with no visible effect from the injections (edema or hemorrhage). B) Both injections were visible in T2 maps (increased contrast in injection sites), however T2 values did not differ s...
Article
Full-text available
uthors and contributions as published: Jonathan Naylor, Harold Fellermann, Yuchun Ding, Waleed K. Mohammed, Nicholas S. Jakubovics, Joy Mukherjee, Catherine A. Biggs, Phillip C. Wright, and Natalio Krasnogor. JN wrote the manuscript, developed the software and models and performed data analysis. HF supervised the work, designed the overall study, s...
Preprint
Full-text available
Mutations in pre-mRNA processing factors (PRPFs) cause 40% of autosomal dominant retinitis pigmentosa (RP), but it is unclear why mutations in ubiquitously expressed PRPFs cause retinal disease. To understand the molecular basis of this phenotype, we have generated RP type 11 (PRPF31-mutated) patient-specific retinal organoids and retinal pigment e...
Thesis
Imaging has become an essential component in many fields of medical and clinical research. The availability of medical imaging provides an excellent opportunity for monitoring and diagnosis of diseases. Automatic analysis of medical images can help with these processes. To date, automatic medical image analysis is still a difficult job in the field...
Article
Full-text available
Segmentation and analysis of histological images provides a valuable tool to gain insight into the biology and function of microglial cells in health and disease. Common image segmentation methods are not suitable for inhomogeneous histology image analysis and accurate classification of microglial activation states has remained a challenge. In this...
Article
Full-text available
Microglia activation has emerged as a potential key factor in the pathogenesis of Alzheimer’s disease. Metabolite levels assessed by magnetic resonance spectroscopy (MRS) are used as markers of neuroinflammation in neurodegenerative diseases, but how they relate to microglial activation in health and chronic disease is incompletely understood. Usin...
Article
Full-text available
Retinal blood vessels have been implicated in a large number of diseases including diabetic retinopathy and cardiovascular diseases, which cause damages to retinal blood vessels. The availability of retinal vessel imaging provides an excellent opportunity for monitoring and diagnosis of retinal diseases, and automatic analysis of retinal vessels wi...
Conference Paper
Full-text available
A second order Mumford-Shah model is proposed for image denoising. Unlike the original Mumford-Shah model, the proposed new model uses second order derivatives defined in bounded Hessian space as its regulariser. This model is capable of eliminating the undesirable staircase effect associated with the original Mumford-Shah model with a total variat...
Article
Blood vessel segmentation is of great importance in medical diagnostic applications. Filter based methods that make use of Hessian matrices have been found to be very useful for blood vessel segmentation in both 2D and 3D medical images. However, these methods often fail on images that contain high density microvessels and background noise. The err...
Conference Paper
Full-text available
Vessel segmentation algorithms play a very important role in vascular disease diagnosis and prediction. Current vessel segmentation research uses mostly images of large vessels, which are relatively easy to extract, but segmenting microvasculature is more challenging and very important for analysing vascular disease such as Alzheimer's Diseases. Th...

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