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

Surgical training tools for dermatology trainees: porcine vs. synthetic skin for excision and repair

Since dermatologists routinely perform surgery in an outpatient setting, ensuring that dermatology trainees are provided with opportunities to develop sufficient proficiency in excisional surgery and suture technique is paramount. The objectives of this study are to assess trainee preference for silicone-based synthetic skin compared with porcine skin as a surgical training medium and to assess the ability of trainees to successfully demonstrate basic surgical skills using the simulated skin model. Participants were a convenience sample of dermatology residents from the greater Chicago area, who were asked to perform an elliptical excision and bilayered repair on a silicone-based synthetic skin model. Residents were then surveyed regarding their satisfaction with the model. Four blinded dermatologist raters evaluated digital photographs obtained during the performance of the procedures and graded the execution of each maneuver using a surgical task checklist. Nineteen residents were enrolled. Residents were more likely to prefer pig skin to simulated skin for overall use (p = 0.040) and tissue repair (p = 0.018), but the nominal preference for tissue handling was nonsignificant (p = 0.086). There was no significant difference between satisfaction with pig skin versus synthetic skin with regard to excision experience (p = 0.82). The majority of residents (10/19) performed all surgical checklist tasks correctly. Of those residents who did not perform all steps correctly, many had difficulty obtaining adequate dermal eversion and wound approximation. Synthetic skin may be conveniently and safely utilized for hands-on surgical practice. Further refinement may be necessary to make synthetic skin comparable in feel and use to animal skin

Skin cancer discovery during total body skin examinations

Background: Patients presenting with a site-specific skin complaint may receive a total body skin examination (TBSE) or a more focused examination. A TBSE may be time-consuming but can potentially detect unsuspected or early stage skin cancers. The purpose of this study was to assess the detection of skin cancers associated with dermatologist-initiated TBSE performed immediately after a focused skin examination on the same patients. Methods: The dermatology records of patients with biopsy-proven melanoma, basal cell carcinoma (BCC), or squamous cell carcinoma (SCC) during a 2-year period were reviewed. Generalized linear mixed-effects models were used to estimate the odds of a lesion being identified by a dermatologist (rather than the patient or the patient\u27s primary health care provider). Results: A total 1563 biopsy-proven cutaneous malignancies were found on 1010 patients. Of these, 797 cancers (51%) were first identified by a dermatologist on TBSE and 764 (48.9%) by the patient or the referring provider. Among tumors first identified by dermatologists (n = 797), 553 (69%) were BCCs, 220 (28%) were SCCs, and 24 (3%) were melanomas. The mean Breslow depth was 0.53 mm (standard deviation: 0.31 mm) for melanomas found on TBSE versus 1.04 mm (standard deviation: 1.68 mm) if identified by patients or referring providers. BCCs were more likely to be identified by a dermatologist during a TBSE (n = 553 [56%] vs. n = 434 [44%]; odds ratio: 1.79; p \u3c .001). Tumors ultimately diagnosed as SCCs were more often identified by patients or patients\u27 primary care providers (n = 302 [58%]; odds ratio: 0.56; p \u3c .001). However, 220 otherwise undetected SCCs were found during dermatologist-performed TBSE. Conclusion: Dermatologist-performed TBSEs identified numerous cutaneous malignancies that might otherwise have remained undiagnosed. Early detection of melanoma or nonmelanoma skin cancer by TBSEs may spare patients significant morbidity and mortality