Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Biomechanical evaluation and comparison of clinically relevant versus non-relevant leg length inequalities

Abstract Background Leg length inequalities are a frequent condition in every population. It is common clinical practice to consider LLIs of 2 cm and more as relevant and to treat those. However, the amount of LLIs that need treatment is not clearly defined in literature and the effect of real LLIs on the musculoskeletal system above and below 2 cm have not been studied biomechanically before. Methods By using surface topography, we evaluated 32 patients (10 females, 22 male) with real LLIs of ≥ 2 cm (mean: 2.72 cm; n = 10) and compared their pelvic position and spinal posture to patients with LLIs < 2 cm (mean: 1.24 cm; n = 22) while standing and walking. All patients were measured with a surface topography system during standing and while walking on a treadmill. To compare patient groups, we used Student t-tests for independent samples. Results Pelvic obliquity was significantly higher in patients with LLI ≥ 2 cm during the standing trial (p = 0.045) and during the midstance phase of the longer leg (p = 0.023) while walking. Further measurements did not reveal any significant differences (p = 0.06–0.706). Conclusions The results of our study suggest that relevant LLIs of ≥ 2 cm mostly affect pelvic obliquity and do not lead to significant alterations in the spinal posture during a standing trial. Additionally, we demonstrated that LLIs are better compensated when walking, showing almost no significant differences in pelvic and spinal posture between patients with LLIs smaller and greater than 2 cm. This study shows that LLIs ≥ 2 cm can still be compensated; however, we do not know if the compensation mechanisms may lead to long-term clinical pathologies

Creation and Evaluation of a Severity Classification of Hyperkyphosis and Hypolordosis for Exercise Therapy

The rise in the occurrence of musculoskeletal disorders, such as thoracic hyperkyphosis (THK) or lumbar hypolordosis (LHL), is a result of demographic changes. Exercise therapy is an effective approach that can reduce related disabilities and costs. To ensure successful therapy, an individualized exercise program adapted to the severity of the disorder is expedient. Nevertheless, appropriate classification systems are scarce. This project aimed to develop and evaluate a severity classification focused on exercise therapy for patients with THK or LHL. A multilevel severity classification was developed and evaluated by means of an online survey. Reference limits of spinal shape angles were established by data from video rasterstereography of 201 healthy participants. A mean kyphosis angle of 50.03° and an average lordosis angle of 40.72° were calculated as healthy references. The strength of the multilevel classification consisting of the combination of subjective pain and objective spinal shape factors was confirmed by the survey (70% agreement). In particular, the included pain parameters were considered relevant by 78% of the experts. Even though the results of the survey provide important evidence for further analyses and optimization options of the classification system, the current version is still acceptable as therapeutic support

Heterotopia and structuralism

The concept of heterotopia was introduced and immediately abandoned by Michel Foucault in 1966 – 67, but it quickly diffused across human geography, urban theory, and cultural studies during the 1990s. Notwithstanding the deserved impact of Foucault’s overall work on these fields, there are some conceptual problems with the heterotopia concept. While the desire for a single term to probe spatial difference is understandable, the author takes issue with the kind of space envisioned in heterotopology. From a close reading of Foucault’s notes, and with the help of Deleuze, Derrida, and Althusser, it is suggested that the spatiality of Foucault’s heterotopology repeats certain flaws of the structuralism in vogue in 1960s France. In order for heterotopias to be ‘absolutely different’ from ‘all the rest’ of space, Foucault needs to posit a totality to society and to perform a ‘slice of time’. The author ends by briefly examining how the structuralist tendency of heterotopology has pervaded some recent Anglophone adoptions of Foucault. As both geography and postcolonial theory have shown, slicing time often conceals particularist suppositions and is therefore inadequate to account for the multiplicity and unevenness of geographical change

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press