2,061 research outputs found
Unsupervised correspondence with combined geometric learning and imaging for radiotherapy applications
The aim of this study was to develop a model to accurately identify
corresponding points between organ segmentations of different patients for
radiotherapy applications. A model for simultaneous correspondence and
interpolation estimation in 3D shapes was trained with head and neck organ
segmentations from planning CT scans. We then extended the original model to
incorporate imaging information using two approaches: 1) extracting features
directly from image patches, and 2) including the mean square error between
patches as part of the loss function. The correspondence and interpolation
performance were evaluated using the geodesic error, chamfer distance and
conformal distortion metrics, as well as distances between anatomical
landmarks. Each of the models produced significantly better correspondences
than the baseline non-rigid registration approach. The original model performed
similarly to the model with direct inclusion of image features. The best
performing model configuration incorporated imaging information as part of the
loss function which produced more anatomically plausible correspondences. We
will use the best performing model to identify corresponding anatomical points
on organs to improve spatial normalisation, an important step in outcome
modelling, or as an initialisation for anatomically informed registrations. All
our code is publicly available at
https://github.com/rrr-uom-projects/Unsup-RT-Corr-NetComment: Accepted in 3rd Workshop on Shape in Medical Imaging (ShapeMI 2023).
This preprint has not undergone peer review or any post-submission
improvements or correction
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Knowledge practices in design: The role of visual representations as 'epistemic objects'
We use a detailed study of the knowledge work around visual representations to draw attention to the multidimensional nature of `objects'. Objects are variously described in the literatures as relatively stable or in flux; as abstract or concrete; and as used within or across practices. We clarify these dimensions, drawing on and extending the literature on boundary objects, and connecting it with work on epistemic and technical objects. In particular, we highlight the epistemic role of objects, using our observations of knowledge work on an architectural design project to show how, in this setting, visual representations are characterized by a `lack' or incompleteness that precipitates unfolding. The conceptual design of a building involves a wide range of technical, social and aesthetic forms of knowledge that need to be developed and aligned. We explore how visual representations are used, and how these are meaningful to different stakeholders, eliciting their distinct contributions. As the project evolves and the drawings change, new issues and needs for knowledge work arise. These objects have an `unfolding ontology' and are constantly in flux, rather than fully formed. We discuss the implications for wider understandings of objects in organizations and for how knowledge work is achieved in practice
Complete Genome Sequence and Comparative Metabolic Profiling of the Prototypical Enteroaggregative Escherichia coli Strain 042
Background \ud
Escherichia coli can experience a multifaceted life, in some cases acting as a commensal while in other cases causing intestinal and/or extraintestinal disease. Several studies suggest enteroaggregative E. coli are the predominant cause of E. coli-mediated diarrhea in the developed world and are second only to Campylobacter sp. as a cause of bacterial-mediated diarrhea. Furthermore, enteroaggregative E. coli are a predominant cause of persistent diarrhea in the developing world where infection has been associated with malnourishment and growth retardation. \ud
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Methods \ud
In this study we determined the complete genomic sequence of E. coli 042, the prototypical member of the enteroaggregative E. coli, which has been shown to cause disease in volunteer studies. We performed genomic and phylogenetic comparisons with other E. coli strains revealing previously uncharacterised virulence factors including a variety of secreted proteins and a capsular polysaccharide biosynthetic locus. In addition, by using Biolog™ Phenotype Microarrays we have provided a full metabolic profiling of E. coli 042 and the non-pathogenic lab strain E. coli K-12. We have highlighted the genetic basis for many of the metabolic differences between E. coli 042 and E. coli K-12. \ud
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Conclusion \ud
This study provides a genetic context for the vast amount of experimental and epidemiological data published thus far and provides a template for future diagnostic and intervention strategies
Developing and enhancing biodiversity monitoring programmes: a collaborative assessment of priorities
1.Biodiversity is changing at unprecedented rates, and it is increasingly important that these changes are quantified through monitoring programmes. Previous recommendations for developing or enhancing these programmes focus either on the end goals, that is the intended use of the data, or on how these goals are achieved, for example through volunteer involvement in citizen science, but not both. These recommendations are rarely prioritized.
2.We used a collaborative approach, involving 52 experts in biodiversity monitoring in the UK, to develop a list of attributes of relevance to any biodiversity monitoring programme and to order these attributes by their priority. We also ranked the attributes according to their importance in monitoring biodiversity in the UK. Experts involved included data users, funders, programme organizers and participants in data collection. They covered expertise in a wide range of taxa.
3.We developed a final list of 25 attributes of biodiversity monitoring schemes, ordered from the most elemental (those essential for monitoring schemes; e.g. articulate the objectives and gain sufficient participants) to the most aspirational (e.g. electronic data capture in the field, reporting change annually). This ordered list is a practical framework which can be used to support the development of monitoring programmes.
4.People's ranking of attributes revealed a difference between those who considered attributes with benefits to end users to be most important (e.g. people from governmental organizations) and those who considered attributes with greatest benefit to participants to be most important (e.g. people involved with volunteer biological recording schemes). This reveals a distinction between focussing on aims and the pragmatism in achieving those aims.
5.Synthesis and applications. The ordered list of attributes developed in this study will assist in prioritizing resources to develop biodiversity monitoring programmes (including citizen science). The potential conflict between end users of data and participants in data collection that we discovered should be addressed by involving the diversity of stakeholders at all stages of programme development. This will maximize the chance of successfully achieving the goals of biodiversity monitoring programmes
Respiratory and Bronchitic Symptoms Predict Intention to Quit Smoking among Current Smokers with, and at Risk for, Chronic Obstructive Pulmonary Disease
Rationale: Smoking cessation is the most important intervention for patients with chronic obstructive pulmonary disease (COPD). What leads smokers with COPD to quit smoking remains unknown
Planet Hunters NGTS: New Planet Candidates from a Citizen Science Search of the Next Generation Transit Survey Public Data
We present the results from the first two years of the Planet Hunters Next Generation Transit Survey (NGTS) citizen science project, which searches for transiting planet candidates in data from the NGTS by enlisting the help of members of the general public. Over 8000 registered volunteers reviewed 138,198 light curves from the NGTS Public Data Releases 1 and 2. We utilize a user weighting scheme to combine the classifications of multiple users to identify the most promising planet candidates not initially discovered by the NGTS team. We highlight the five most interesting planet candidates detected through this search, which are all candidate short-period giant planets. This includes the TIC-165227846 system that, if confirmed, would be the lowest-mass star to host a close-in giant planet. We assess the detection efficiency of the project by determining the number of confirmed planets from the NASA Exoplanet Archive and TESS Objects of Interest (TOIs) successfully recovered by this search and find that 74% of confirmed planets and 63% of TOIs detected by NGTS are recovered by the Planet Hunters NGTS project. The identification of new planet candidates shows that the citizen science approach can provide a complementary method to the detection of exoplanets with ground-based surveys such as NGTS
Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression
Associations between single nucleotide polymorphisms (SNPs) at 5p15 and multiple cancer types have been reported. We have previously shown evidence for a strong association between prostate cancer (PrCa) risk and rs2242652 at 5p15, intronic in the telomerase reverse transcriptase (TERT) gene that encodes TERT. To comprehensively evaluate the association between genetic variation across this region and PrCa, we performed a fine-mapping analysis by genotyping 134 SNPs using a custom Illumina iSelect array or Sequenom MassArray iPlex, followed by imputation of 1094 SNPs in 22 301 PrCa cases and 22 320 controls in The PRACTICAL consortium. Multiple stepwise logistic regression analysis identified four signals in the promoter or intronic regions of TERT that independently associated with PrCa risk. Gene expression analysis of normal prostate tissue showed evidence that SNPs within one of these regions also associated with TERT expression, providing a potential mechanism for predisposition to disease
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