Realistic Data Enrichment for Robust Image Segmentation in Histopathology

Poor performance of quantitative analysis in histopathological Whole Slide Images (WSI) has been a significant obstacle in clinical practice. Annotating large-scale WSIs manually is a demanding and time-consuming task, unlikely to yield the expected results when used for fully supervised learning systems. Rarely observed disease patterns and large differences in object scales are difficult to model through conventional patient intake. Prior methods either fall back to direct disease classification, which only requires learning a few factors per image, or report on average image segmentation performance, which is highly biased towards majority observations. Geometric image augmentation is commonly used to improve robustness for average case predictions and to enrich limited datasets. So far no method provided sampling of a realistic posterior distribution to improve stability, e.g. for the segmentation of imbalanced objects within images. Therefore, we propose a new approach, based on diffusion models, which can enrich an imbalanced dataset with plausible examples from underrepresented groups by conditioning on segmentation maps. Our method can simply expand limited clinical datasets making them suitable to train machine learning pipelines, and provides an interpretable and human-controllable way of generating histopathology images that are indistinguishable from real ones to human experts. We validate our findings on two datasets, one from the public domain and one from a Kidney Transplant study.Comment: 11 pages, 2 figures, 1 tabl

Contractile function of detrusor smooth muscle from children with posterior urethral valves – the role of fibrosis

IntroductionPosterior urethral valves (PUV) is the most common cause of congenital bladder outflow obstruction with persistent lower urinary tract and renal morbidities. There is a spectrum of functional bladder disorders ranging from hypertonia to bladder underactivity, but the aetiology of these clinical conditions remains unclear.Aims and objectivesWe tested the hypothesis that replacement of detrusor muscle with non-muscle cells and excessive deposition of connective tissue is an important factor in bladder dysfunction with PUV. We used isolated detrusor samples from children with PUV and undergoing primary or secondary procedures in comparison to age-matched data from children with functionally normal bladders. In vitro contractile properties, as well as passive stiffness, were measured and matched to histological assessment of muscle and connective tissue. We examined if a major pathway for fibrosis was altered in PUV tissue samples.MethodsIsometric contractions were measured in vitro in response to either stimulation of motor nerves to detrusor or exposure to cholinergic and purinergic receptor agonists. Passive mechanical stiffness was measured by rapid stretching of the tissue and recording changes to muscle tension. Histology measured the relative amounts of detrusor muscle and connective tissue. Multiplex quantitative immunofluorescence labelling using five epitope markers was designed to determine cellular pathways, in particular the Wnt-signalling pathway, responsible for any changes to excessive deposition of connective tissue.Results and DiscussionPUV tissue showed equally reduced contractile function to efferent nerve stimulation or exposure to contractile agonists. Passive muscle stiffness was increased in PUV tissue samples. The smooth muscle:connective tissue ratio was also diminished and mirrored the reduction of contractile function and the increase of passive stiffness. Immunofluorescence labelling showed in PUV samples increased expression of the matrix metalloproteinase, MMP-7; as well as cyclin-D1 expression suggesting cellular remodelling. However, elements of a fibrosis pathway associated with Wnt-signalling were either reduced (β-catenin) or unchanged (c-Myc). The accumulation of extracellular matrix, containing collagen, will contribute to the reduced contractile performance of the bladder wall. It will also increase tissue stiffness that in vivo would lead to reduced filling compliance.ConclusionsReplacement of smooth muscle with fibrosis is a major contributory factor in contractile dysfunction in the hypertonic PUV bladder. This suggests that a potential strategy to restore normal contractile and filling properties is development of the effective use of antifibrotic agents

願書留（正月より十二月まで、名主上野新右衛門外）

Few quantifiable tissue biomarkers for the diagnosis and prognosis of prostate cancer exist. Using an unbiased, quantitative approach, this study evaluates the potential of three proteins of the 40S ribosomal protein complex as putative biomarkers of malignancy in prostate cancer. Prostate tissue arrays, constructed from 82 patient samples (245 tissue cores, stage pT3a or pT3b), were stained for antibodies against three ribosomal proteins, RPS19, RPS21 and RPS24. Semi-automated Ox-DAB signal quantification using ImageJ software revealed a significant change in expression of RPS19, RPS21 and RPS24 in malignant vs non-malignant tissue (p<0.0001). Receiver operating characteristics curves were calculated to evaluate the potential of each protein as a biomarker of malignancy in prostate cancer. Positive likelihood ratios for RPS19, RPS21 and RPS24 were calculated as 2.99, 4.21, and 2.56 respectively, indicating that the overexpression of the protein is correlated with the presence of disease. Triple-labelled, quantitative, immunofluorescence (with RPS19, RPS21 and RPS24) showed significant changes (p<0.01) in the global intersection coefficient, a measure of how often two fluorophore signals intersect, for RPS19 and RPS24 only. No change was observed in the co-localization of any other permutations of the three proteins. Our results show that RPS19, RPS21 or RPS24 are upregulated in malignant tissue and may serve as putative biomarkers for prostate cancer

Quantitative Expression and Co-Localization of Wnt Signalling Related Proteins in Feline Squamous Cell Carcinoma.

Feline oral squamous cell carcinoma (FOSCC) is an aggressive neoplasm in cats. Little is known about the possible molecular mechanisms that may be involved in the initiation, maintenance and progression of FOSCC. Wnt signalling is critical in development and disease, including many mammalian cancers. In this study, we have investigated the expression of Wnt signalling related proteins using quantitative immunohistochemical techniques on tissue arrays. We constructed tissue arrays with 58 individual replicate tissue samples. We tested for the expression of four key Wnt/ß-catenin transcription targets, namely Cyclin D1 (CCND1 or CD1), FRA1, c-Myc and MMP7. All antibodies showed cross reactivity in feline tissue except MMP7. Quantitative immunohistochemical analysis of single proteins (expressed as area fraction / amount of tissue for normal vs tumor, mean ± SE) showed that the expression of CD1 (3.9 ± 0.5 vs 12.2 ± 0.9), FRA1 (5.5 ± 0.6 vs 16.8 ± 1.1) and c-Myc (5.4 ± 0.5 vs 12.5 ± 0.9) was increased in FOSCC tissue by 2.3 to 3 fold compared to normal controls (p<0.0001). By using a multilabel, quantitative fluorophore technique we further investigated if the co-localization of these proteins (all transcription factors) with each other and in the nucleus (stained with 4',6-diamidino-2-phenylindole, DAPI) was altered in FOSCC compared to normal tissue. The global intersection coefficients, a measure of the proximity of two fluorophore labeled entities, showed that there was a significant change (p < 0.01) in the co-localization for all permutations (e.g. CD1/FRA1 etc), except for the nuclear localization of CD1. Our results show that putative targets of Wnt signalling transcription are up-regulated in FOSCC with alterations in the co-localization of these proteins and could serve as a useful marker for the disease.This research was funded by the Prostate Cancer Research Centre charity (registered UK charity no. 1156027), Grant Number AA1. A small financial contribution was also made through intra-mural funds from the Royal Veterinary College.This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.pone.016110

Coupled simulation of potential natural vegetation, terrestrial carbon balance and physical land-surface properties with the ALBIOC model

ALBIOC (ALbedo- BIOsphere- Carbon) is an integrated terrestrial biosphere model designed as a too] to explore the effects of climate and atmospheric CO, concentration on vegetation, land-surface characteristics and carbon storage. The model is based, although designed to be simple in structure and computationally fast, on biophysical and ecophysiological principles and simulates in a fully interactive manner the potential distribution of vegetation, terrestrial carbon storage and physical land-surface properties. Testing was extensive and focused on broad spatial patterns (5 degrees resolution) of biome distribution, and variables important for the surface energy balance and hydrological cycle (seasonal snow cover, surface albedo, runoff and evaporation) and for the global carbon cycle (seasonal canopy cover, primary production and carbon storage). Because ALBIOC simulates a range of physical and biogeochemical variables in an integrated way, it was possible to test the model against a more comprehensive range of indicators than has normally been the case for terrestrial biosphere models. The simulated vegetation distribution is as accurate as more specialised biogeography models taking into account the coarse resolution of the model. ALBIOC simulates a global NPP of 57 PgC/year, which is in the range of the values found in the literature and other model estimates. Land-surface albedo. snow depth, runoff, and FPAR showed a generally good agreement with observations within the known limits of available data sets of these variables. The model's mechanistic basis would allow extension to simulate, e.g. transient response to rapid climate change (vegetation dynamics) and carbon isotopic balances. while its computational efficiency renders it suitable for inclusion in Earth system models of intermediate complexity. (C) 2001 Elsevier Science B.V. All rights reserved

RPS19, RPS21, and RPS24 protein expression using immunofluorescence.

<p>Representative images of the co-expression of RPS19 (Cy3- Red), RPS21 (FITC- Green), and RPS24 (Cy5- Blue) which was analysed in both malignant (D, E, F) and non-malignant (A, B, C) prostate tissue. Whole tissue cores (A and D) were imaged on an Olympus IX81 confocal system at low magnification. Intensity of fluorescent signals were optimised at the beginning of each study to prevent oversaturation for each fluorophore. Quantification of co-localization was carried out on images gathered from a randomly selected area of the tissue core using a 40x objective zoom (E is malignant and B is non-malignant) on an Olympus IX81 confocal system. The image was further magnified using a 6x digital zoom. Each image was then deconvolved (C and F) and the GIC was calculated using Huygens software (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186047#sec003" target="_blank">Materials and methods</a>). Scale bar = 10 μm.</p