Statistical tests for intra-tumour clonal co-occurrence and exclusivity

Tumour progression is an evolutionary process in which different clones evolve over time, leading to intra-tumour heterogeneity. Interactions between clones can affect tumour evolution and hence disease progression and treatment outcome. Intra-tumoural pairs of mutations that are overrepresented in a co-occurring or clonally exclusive fashion over a cohort of patient samples may be suggestive of a synergistic effect between the different clones carrying these mutations. We therefore developed a novel statistical testing framework, called GeneAccord, to identify such gene pairs that are altered in distinct subclones of the same tumour. We analysed our framework for calibration and power. By comparing its performance to baseline methods, we demonstrate that to control type I errors, it is essential to account for the evolutionary dependencies among clones. In applying GeneAccord to the single-cell sequencing of a cohort of 123 acute myeloid leukaemia patients, we find 1 clonally co-occurring and 8 clonally exclusive gene pairs. The clonally exclusive pairs mostly involve genes of the key signalling pathways

Multicenter Qualitative Study Exploring the Patient Experience of Digital Ulcers in Systemic Sclerosis

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154886/1/acr24127.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154886/2/acr24127_am.pd

Intra-and inter-observer reliability of nailfold videocapillaroscopy - A possible outcome measure for systemic sclerosis-related microangiopathy

OBJECTIVES: Our aim was to assess the reliability of nailfold capillary assessment in terms of image evaluability, image severity grade ('normal', 'early', 'active', 'late'), capillary density, capillary (apex) width, and presence of giant capillaries, and also to gain further insight into differences in these parameters between patients with systemic sclerosis (SSc), patients with primary Raynaud's phenomenon (PRP) and healthy control subjects.METHODS: Videocapillaroscopy images (magnification 300×) were acquired from all 10 digits from 173 participants: 101 patients with SSc, 22 with PRP and 50 healthy controls. Ten capillaroscopy experts from 7 European centres evaluated the images. Custom image mark-up software allowed extraction of the following outcome measures: overall grade ('normal', 'early', 'active', 'late', 'non-specific', or 'ungradeable'), capillary density (vessels/mm), mean vessel apical width, and presence of giant capillaries.RESULTS: Observers analysed a median of 129 images each. Evaluability (i.e. the availability of measures) varied across outcome measures (e.g. 73.0% for density and 46.2% for overall grade in patients with SSc). Intra-observer reliability for evaluability was consistently higher than inter- (e.g. for density, intra-class correlation coefficient [ICC] was 0.71 within and 0.14 between observers). Conditional on evaluability, both intra- and inter-observer reliability were high for grade (ICC 0.93 and 0.78 respectively), density (0.91 and 0.64) and width (0.91 and 0.85).CONCLUSIONS: Evaluability is one of the major challenges in assessing nailfold capillaries. However, when images are evaluable, the high intra- and inter-reliabilities suggest that overall image grade, capillary density and apex width have potential as outcome measures in longitudinal studies

Programming moir\'e patterns in 2D materials by bending

Moir\'e superlattices in twisted two-dimensional materials have generated tremendous excitement as a platform for achieving quantum properties on demand. However, the moir\'e pattern is highly sensitive to the interlayer atomic registry, and current assembly techniques suffer from imprecise control of the average twist angle, spatial inhomogeneity in the local twist angle, and distortions due to random strain. Here, we demonstrate a new way to manipulate the moir\'e patterns in hetero- and homo-bilayers through in-plane bending of monolayer ribbons, using the tip of an atomic force microscope. This technique achieves continuous variation of twist angles with improved twist-angle homogeneity and reduced random strain, resulting in moir\'e patterns with highly tunable wavelength and ultra-low disorder. Our results pave the way for detailed studies of ultra-low disorder moir\'e systems and the realization of precise strain-engineered devices

Three-dimensional optoacoustic imaging of nailfold capillaries in systemic sclerosis and its potential for disease differentiation using deep learning

From Springer Nature via Jisc Publications RouterHistory: received 2020-05-07, accepted 2020-09-09, registration 2020-09-16, pub-electronic 2020-10-05, online 2020-10-05, collection 2020-12Publication status: PublishedFunder: Helmholtz Association; doi: http://dx.doi.org/10.13039/501100009318; Grant(s): i3 (ExNet-0022-Phase2-3)Funder: University of Manchester; doi: http://dx.doi.org/10.13039/501100000770; Grant(s): MC_PC_16053Funder: Manchester Biomedical Research Centre; doi: http://dx.doi.org/10.13039/100014653Funder: H2020 European Research Council; doi: http://dx.doi.org/10.13039/100010663; Grant(s): No 694968 (PREMSOT)Funder: Arthritis Research UK,United Kingdom; Grant(s): 19465Abstract: The autoimmune disease systemic sclerosis (SSc) causes microvascular changes that can be easily observed cutaneously at the finger nailfold. Optoacoustic imaging (OAI), a combination of optical and ultrasound imaging, specifically raster-scanning optoacoustic mesoscopy (RSOM), offers a non-invasive high-resolution 3D visualization of capillaries allowing for a better view of microvascular changes and an extraction of volumetric measures. In this study, nailfold capillaries of patients with SSc and healthy controls are imaged and compared with each other for the first time using OAI. The nailfolds of 23 patients with SSc and 19 controls were imaged using RSOM. The acquired images were qualitatively compared to images from state-of-the-art imaging tools for SSc, dermoscopy and high magnification capillaroscopy. The vascular volume in the nailfold capillaries were computed from the RSOM images. The vascular volumes differ significantly between both cohorts (0.216 ± 0.085 mm3 and 0.337 ± 0.110 mm3; p < 0.0005). In addition, an artificial neural network was trained to automatically differentiate nailfold images from both cohorts to further assess whether OAI is sensitive enough to visualize anatomical differences in the capillaries between the two cohorts. Using transfer learning, the model classifies images with an area under the ROC curve of 0.897, and a sensitivity of 0.783 and specificity of 0.895. In conclusion, this study demonstrates the capabilities of RSOM as an imaging tool for SSc and establishes it as a modality that facilitates more in-depth studies into the disease mechanisms and progression