98 research outputs found
Biomechanical Morphing for Personalized Fitting of Scoliotic Torso Skeleton Models
The use of patient-specific biomechanical models offers many opportunities in the treatment of adolescent idiopathic scoliosis, such as the design of personalized braces. The first step in the development of these patient-specific models is to fit the geometry of the torso skeleton to the patient’s anatomy. However, existing methods rely on high-quality imaging data. The exposure to radiation of these methods limits their applicability for regular monitoring of patients. We present a method to fit personalized models of the torso skeleton that takes as input biplanar low-dose radiographs. The method morphs a template to fit annotated points on visible portions of the spine, and it relies on a default biomechanical model of the torso for regularization and robust fitting of hardly visible parts of the torso skeleton, such as the rib cage. The proposed method provides an accurate and robust solution to obtain personalized models of the torso skeleton, which can be adopted as part of regular management of scoliosis patients. We have evaluated the method on ten young patients who participated in our study. We have analyzed and compared clinical metrics on the spine and the full torso skeleton, and we have found that the accuracy of the method is at least comparable to other methods that require more demanding imaging methods, while it offers superior robustness to artifacts such as interpenetration of ribs. Normal-dose X-rays were available for one of the patients, and for the other nine we acquired low-dose X-rays, allowing us to validate that the accuracy of the method persisted under less invasive imaging modalities
Valentine: Evaluating Matching Techniques for Dataset Discovery
Data scientists today search large data lakes to discover and integrate
datasets. In order to bring together disparate data sources, dataset discovery
methods rely on some form of schema matching: the process of establishing
correspondences between datasets. Traditionally, schema matching has been used
to find matching pairs of columns between a source and a target schema.
However, the use of schema matching in dataset discovery methods differs from
its original use. Nowadays schema matching serves as a building block for
indicating and ranking inter-dataset relationships. Surprisingly, although a
discovery method's success relies highly on the quality of the underlying
matching algorithms, the latest discovery methods employ existing schema
matching algorithms in an ad-hoc fashion due to the lack of openly-available
datasets with ground truth, reference method implementations, and evaluation
metrics. In this paper, we aim to rectify the problem of evaluating the
effectiveness and efficiency of schema matching methods for the specific needs
of dataset discovery. To this end, we propose Valentine, an extensible
open-source experiment suite to execute and organize large-scale automated
matching experiments on tabular data. Valentine includes implementations of
seminal schema matching methods that we either implemented from scratch (due to
absence of open source code) or imported from open repositories. The
contributions of Valentine are: i) the definition of four schema matching
scenarios as encountered in dataset discovery methods, ii) a principled dataset
fabrication process tailored to the scope of dataset discovery methods and iii)
the most comprehensive evaluation of schema matching techniques to date,
offering insight on the strengths and weaknesses of existing techniques, that
can serve as a guide for employing schema matching in future dataset discovery
methods
Local Embeddings for Relational Data Integration
Deep learning based techniques have been recently used with promising results
for data integration problems. Some methods directly use pre-trained embeddings
that were trained on a large corpus such as Wikipedia. However, they may not
always be an appropriate choice for enterprise datasets with custom vocabulary.
Other methods adapt techniques from natural language processing to obtain
embeddings for the enterprise's relational data. However, this approach blindly
treats a tuple as a sentence, thus losing a large amount of contextual
information present in the tuple.
We propose algorithms for obtaining local embeddings that are effective for
data integration tasks on relational databases. We make four major
contributions. First, we describe a compact graph-based representation that
allows the specification of a rich set of relationships inherent in the
relational world. Second, we propose how to derive sentences from such a graph
that effectively "describe" the similarity across elements (tokens, attributes,
rows) in the two datasets. The embeddings are learned based on such sentences.
Third, we propose effective optimization to improve the quality of the learned
embeddings and the performance of integration tasks. Finally, we propose a
diverse collection of criteria to evaluate relational embeddings and perform an
extensive set of experiments validating them against multiple baseline methods.
Our experiments show that our framework, EmbDI, produces meaningful results for
data integration tasks such as schema matching and entity resolution both in
supervised and unsupervised settings.Comment: Accepted to SIGMOD 2020 as Creating Embeddings of Heterogeneous
Relational Datasets for Data Integration Tasks. Code can be found at
https://gitlab.eurecom.fr/cappuzzo/embd
HER2 and TOP2A in high-risk early breast cancer patients treated with adjuvant epirubicin-based dose-dense sequential chemotherapy
<p>Abstract</p> <p>Background</p> <p>HER2 and TOP2A parameters (gene status, mRNA and protein expression) have individually been associated with the outcome of patients treated with anthracyclines. The aim of this study was to comprehensively evaluate the prognostic/predictive significance of the above parameters in early, high-risk breast cancer patients treated with epirubicin-based, dose-dense sequential adjuvant chemotherapy.</p> <p>Methods</p> <p>In a series of 352 breast carcinoma tissues from patients that had been post-operatively treated with epirubicin-CMF with or without paclitaxel, we assessed HER2 and TOP2A gene status (chromogenic in situ hybridization), mRNA expression (quantitative reverse transcription PCR), as well as HER2 and TopoIIa protein expression (immunohistochemistry).</p> <p>Results</p> <p>HER2 and TOP2A amplification did not share the same effects on their downstream molecules, with consistent patterns observed in HER2 mRNA and protein expression according to HER2 amplification (all parameters strongly inter-related, p values < 0.001), but inconsistent patterns in the case of TOP2A. TOP2A gene amplification (7% of all cases) was not related to TOP2A mRNA and TopoIIa protein expression, while TOP2A mRNA and TopoIIa protein were strongly related to each other (p < 0.001). Hence, TOP2A amplified tumors did not correspond to tumors with high TOP2A mRNA or TopoIIa protein expression, while the latter were characterized by high Ki67 scores (p = 0.003 and p < 0.001, respectively). Multivariate analysis adjusted for nodal involvement, hormone receptor status, Ki67 score and HER2/TOP2A parameters revealed HER2/TOP2A co-amplification (21.2% of HER2 amplified tumors) as an independent favorable prognostic factor for DFS (HR = 0.13, 95% CI: 0.02-0.96, p = 0.046); in contrast, increased HER2/TOP2A mRNA co-expression was identified as an independent adverse prognostic factor for both DFS (HR = 2.41, 95% CI: 1.31-4.42, p = 0.005) and OS (HR = 2.83, 95% CI: 1.42-5.63, p = 0.003), while high TOP2A mRNA expression was an independent adverse prognostic factor for OS (HR = 2.06, 95% CI: 1.23-3.46, p = 0.006). None of the parameters tested was associated with response to paclitaxel.</p> <p>Conclusions</p> <p>This study confirms the favorable prognostic value of HER2/TOP2A co-amplification and the adverse prognostic value of high TOP2A mRNA expression extending it to the adjuvant treatment setting in early high-risk breast cancer. The strong adverse prognostic impact of high HER2/TOP2A mRNA co-expression needs further validation in studies designed to evaluate markers predictive for anthracyclines.</p> <p>Trial registration</p> <p>Australian New Zealand Clinical Trials Registry <a href="http://www.anzctr.org.au/ACTRN12611000506998">ACTRN12611000506998</a>.</p
Association of osteopontin with specific prognostic factors and survival in adjuvant breast cancer trials of the Hellenic Cooperative Oncology Group
Additional file 1. OPN supplementary data
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