Supporting systematic reviews using LDA-based document representations

BACKGROUND: Identifying relevant studies for inclusion in a systematic review (i.e. screening) is a complex, laborious and expensive task. Recently, a number of studies has shown that the use of machine learning and text mining methods to automatically identify relevant studies has the potential to drastically decrease the workload involved in the screening phase. The vast majority of these machine learning methods exploit the same underlying principle, i.e. a study is modelled as a bag-of-words (BOW). METHODS: We explore the use of topic modelling methods to derive a more informative representation of studies. We apply Latent Dirichlet allocation (LDA), an unsupervised topic modelling approach, to automatically identify topics in a collection of studies. We then represent each study as a distribution of LDA topics. Additionally, we enrich topics derived using LDA with multi-word terms identified by using an automatic term recognition (ATR) tool. For evaluation purposes, we carry out automatic identification of relevant studies using support vector machine (SVM)-based classifiers that employ both our novel topic-based representation and the BOW representation. RESULTS: Our results show that the SVM classifier is able to identify a greater number of relevant studies when using the LDA representation than the BOW representation. These observations hold for two systematic reviews of the clinical domain and three reviews of the social science domain. CONCLUSIONS: A topic-based feature representation of documents outperforms the BOW representation when applied to the task of automatic citation screening. The proposed term-enriched topics are more informative and less ambiguous to systematic reviewers. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13643-015-0117-0) contains supplementary material, which is available to authorized users

A spectroscopic study of the structure of amorphous hydrogenated carbon

A range of amorphous hydrogenated carbon (a-C:H) samples have been studied using inelastic neutron spectroscopy (INS) and Fourier transform infrared (FTIR) spectroscopy. Using these complementary techniques, the bonding environments of both carbon and hydrogen can be probed in some detail, with the INS data providing not only qualitative but also quantitative information. By comparing the data from each of the samples we have been able to examine the effects of different deposition conditions, i.e. precursor gas, deposition energy and deposition method, on the atomic-scale structure of a-C:H

Reduction of claustrophobia during magnetic resonance imaging: methods and design of the "CLAUSTRO" randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>Magnetic resonance (MR) imaging has been described as the most important medical innovation in the last 25 years. Over 80 million MR procedures are now performed each year and on average 2.3% (95% confidence interval: 2.0 to 2.5%) of all patients scheduled for MR imaging suffer from claustrophobia. Thus, prevention of MR imaging by claustrophobia is a common problem and approximately 2,000,000 MR procedures worldwide cannot be completed due to this situation. Patients with claustrophobic anxiety are more likely to be frightened and experience a feeling of confinement or being closed in during MR imaging. In these patients, conscious sedation and additional sequences (after sedation) may be necessary to complete the examinations. Further improvements in MR design appear to be essential to alleviate this situation and broaden the applicability of MR imaging. A more open scanner configuration might help reduce claustrophobic reactions while maintaining image quality and diagnostic accuracy.</p> <p>Methods/Design</p> <p>We propose to analyze the rate of claustrophobic reactions, clinical utility, image quality, patient acceptance, and cost-effectiveness of an open MR scanner in a randomized comparison with a recently designed short-bore but closed scanner with 97% noise reduction. The primary aim of this study is thus to determine whether an open MR scanner can reduce claustrophobic reactions, thereby enabling more examinations of claustrophobic patients without incurring the safety issues associated with conscious sedation. In this manuscript we detail the methods and design of the prospective "CLAUSTRO" trial.</p> <p>Discussion</p> <p>This randomized controlled trial will be the first direct comparison of open vertical and closed short-bore MR systems in regards to claustrophobia and image quality as well as diagnostic utility.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov: <a href="http://www.clinicaltrials.gov/ct2/show/NCT00715806">NCT00715806</a></p

Exploiting Learning Technologies for World Wide Web Agents

Postprin

Identifying semi-invariant features on mouse contours

This paper addresses the problem of reliably fitting an orientated model to video data of laboratory mice assays by specifically locating semi-invariant points on an extracted outline. In the case of mice, the rapid changes in direction and shape often lead to failure when using explicit models. Here we employ a standard background subtraction algorithm in order to derive contour information from a well defined top-down view of the assay. Using this contour, we compare three different approaches at locating head, tail-tip and tail-base features that allow us to constrain orientation. We validate each approach against an annotated gold-standard data-set, and conclude that a composite method delivers the best results. This ultimately has benefits for analysing higher-level behaviour where it is crucial to retain orientation.

Deoxygenation of graphene oxide : reduction or cleaning?

We show that the two-component model of graphene oxide (GO), that is, composed of highly oxidized carbonaceous debris complexed to oxygen functionalized graphene sheets, is a generic feature of the synthesis of GO, independent of oxidant or protocol used. The debris present, roughly one-third by mass, can be removed by a base wash. A number of techniques, including solid state NMR, demonstrate that the properties of the base-washed material are independent of the base used and that it contains similar functional groups to those present in the debris but at a lower concentration. Removal of the oxidation debris cleans the GO, revealing its true monolayer nature and in the process increases the C/O ratio (i.e., a deoxygenation). By contrast, treating GO with hydrazine both removes the debris and reduces (both deoxygenations) the graphene sheets