441 research outputs found
Quick Annotator: an open-source digital pathology based rapid image annotation tool.
Image-based biomarker discovery typically requires accurate segmentation of histologic structures (e.g. cell nuclei, tubules, and epithelial regions) in digital pathology whole slide images (WSIs). Unfortunately, annotating each structure of interest is laborious and often intractable even in moderately sized cohorts. Here, we present an open-source tool, Quick Annotator (QA), designed to improve annotation efficiency of histologic structures by orders of magnitude. While the user annotates regions of interest (ROIs) via an intuitive web interface, a deep learning (DL) model is concurrently optimized using these annotations and applied to the ROI. The user iteratively reviews DL results to either (1) accept accurately annotated regions or (2) correct erroneously segmented structures to improve subsequent model suggestions, before transitioning to other ROIs. We demonstrate the effectiveness of QA over comparable manual efforts via three use cases. These include annotating (1) 337,386 nuclei in 5 pancreatic WSIs, (2) 5,692 tubules in 10 colorectal WSIs, and (3) 14,187 regions of epithelium in 10 breast WSIs. Efficiency gains in terms of annotations per second of 102×, 9×, and 39× were, respectively, witnessed while retaining f-scores >0.95, suggesting that QA may be a valuable tool for efficiently fully annotating WSIs employed in downstream biomarker studies
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Influence of air injection on the liquefaction-induced deformation mechanisms beneath shallow foundations
Earthquake-induced liquefaction of soils frequently causes serious damage to structures with shallow foundations. Reducing the degree of saturation of liquefiable soils by air injection is offered as a cost-effective and reliable method of mitigating liquefaction hazards. Nevertheless, very little experimental research is available on the performance of this method. Particularly, the way that air injection influences the deformation mechanisms beneath shallow foundations is not well defined. Gaining a deeper insight into soil displacements during and after air injection can pave the way for developing effective guidelines for the use of this particular technique. For this purpose, a series of dynamic centrifuge tests are presented in this paper. The prevailing deformation mechanisms are identified in a novel way using displacement vector fields. The results indicate that air injection alters the deformation mechanisms that develop underneath and in the ground surrounding a shallow foundation, substantially reducing the average settlements.The first author wishes to acknowledge the financial assistance provided during the course of this study by the Ministry of National Education (M.E.B.) of Turkey
Successful transition from fed-batch to continuous manufacturing within a mAb process development cycle
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Physical modelling of air injection to remediate liquefaction
Seismic liquefaction of loosely packed, saturated soils poses a significant threat to the built environment. Recently, air injection into liquefiable soil deposits has been introduced as an innovative and cost-effective liquefaction mitigation technique. However, few effective guidelines are available to the engineers for its application and performance. The way that air should be injected appropriately, most particularly, in the presence of structures, is not clearly defined. The distribution of retained air bubbles within the saturated soil medium and its effect on the seismic response also need further investigation. In an effort to offer insights into this problem, an experimental programme consisting of a series of centrifuge and 1g shaking table tests was undertaken. The results have shown that the use of higher air injection pressure provides a much wider and a more uniform air-entrapped zone, but increases the risk of soil deformations developed under the foundations. The distance from the air injector and preferential flow pathways influence the distribution of the retained air bubbles and seismic response of the soil models. Moreover, it was shown in a novel way that the air injection technique is not very effective at low confining stresses to reduce liquefaction-induced deformations beneath shallow foundations. The first author extends his thanks to the Ministry of National Education
(MEB) of Turkey for their financial support
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Twenty-one years of heave monitoring in London Clay at Horseferry Road Basement
An 11 m-deep basement structure in London SW1 was left vacant from 1968 to 1989. The basement heaved significantly during this period due to the lack of a superstructure, providing a unique opportunity to study the development of long-term heave in London Clay. May (1975) presented the monitoring results from 1968-73 and excerpts of site data collected after 1973 have also been circulating informally in the industry since the 1990s. However, the full set of monitoring data remains hitherto unpublished.
This paper was initially drafted in the early 1990s when three of the authors (Nicholson, Chapman, and Solera) were working together with Arup. The paper somehow never got published as people and circumstances changed. More recently, the first author (Chan) started postgraduate research on heave and pressure beneath slabs in excavations in over-consolidated clays, using the heave monitoring data from the draft paper to complement centrifuge test results. For this reason, it was decided that the draft paper should be revised and published for the benefit of the wider industry.
This paper provides a comprehensive case history of the site, publishing further heave data to June 1989, giving a total of 21 years of heave monitoring. Further site investigation data and calculations are included for comparison. The data show that the presence of a basement did not significantly reduce the shear strength of the clay beneath it. The coefficient of consolidation of the clay was 38 – 52 m²/year and long-term heave was still ongoing 21 years after the end of excavation.EPSRC grant reference number EP/L016095/
Centrifuge Modelling of Earthquake Effects in Uniform Deposits of Saturated Sand
Centrifuge models representing level uniform saturated deposits of relatively loose and dense sand were tested at Cambridge University\u27s Schofield Centre to clarify the behaviour of these deposits under earthquake loading. The excess pore pressure, vertical propagation of the accelerations and ground surface settlements resulting from a model earthquake are presented and discussed. The results show that, for similar dynamic loading, the models undergo large shear stiffness degradation resulting from significant pore pressure build up, this taking place at a slower rate in the dense sand. As a result of the cyclic loading, the models suffer settlements, occurring mostly during the event, that are noticeably smaller in the dense model. The upwards propagation of the accelerations through the model depends on the relative density of the sand and changes during the seismic event, following degradation of sand mechanical properties. Large short-duration acceleration spikes are observed near the surface of the dense model, corresponding to large amplification of input acceleration. The results presented and discussed contribute to the understanding of the basic mechanisms of earthquake-induced liquefaction and the use of densification as a measure to mitigate its effects
Centrifuge testing to evaluate the liquefaction response of air-injected partially saturated soils beneath shallow foundations
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