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

Systemic treatments and outcomes in CIC-rearranged Sarcoma: A national multi-centre clinicopathological series and literature review

UNLABELLED: CIC-rearranged sarcoma is a recently established, ultra-rare, molecularly defined sarcoma subtype. We aimed to further characterise clinical features of CIC-rearranged sarcomas and explore clinical management including systemic treatments and outcomes. METHODS: A multi-centre retrospective cohort study of patients diagnosed between 2014-2019. RESULTS: Eighteen patients were identified. The median age was 27 years (range 13-56), 10 patients were male (56%), 11 patients (61%) had localised disease and 7 patients had advanced (metastatic or unresectable) disease at diagnosis. Of 11 patients with localised disease at diagnosis, median overall survival (OS) was 40.6 months and the 1-, 2- and 5-year OS estimates were 82%, 64% and 34% respectively. Nine patients (82%) underwent surgery (all had R0 resections), 8 (73%) patients received radiotherapy to the primary site (median dose 57Gy in 28 fractions), and 8 (73%) patients received chemotherapy (predominantly Ewing-based regimens). Metastases developed in 55% with a median time to recurrence of 10.5 months. In patients with advanced disease at diagnosis, median OS was 12.6 months (95% CI 5.1-20.1), 1-year OS was 57%. Median progression-free survival was 5.8 months (95% CI 4.5-7.2). Durable systemic therapy responses occurred infrequently with a median duration of systemic treatment response of 2.1 months. One durable complete response of metastatic disease to VDC/IE chemotherapy was seen. Responses to pazopanib (n = 1) and pembrolizumab (n = 1) were not seen. CONCLUSION: In this series, CIC-rearranged sarcomas affected young adults and had a high incidence of presenting with, or developing, metastatic disease. The prognosis overall was poor. In advanced disease, durable systemic therapy responses were infrequent

Combined Orofacial Aspergillosis and Mucormycosis: Fatal Complication of a Recurrent Paediatric Glioma—Case Report and Review of Literature

9noMucormycosis and aspergillosis are two opportunistic fungal infections, which can evolve into life-threatening complications. They generally affect patients with relevant risk factors such as immunocompromisation or long-term use of antibiotics or corticosteroids. Treatment usually combines medical and surgical approaches, often including extended necrosectomies, although the prognosis of generalized fungal infections is very poor. In this paper, we present the case of a 17-year-old girl affected by combined aspergillosis and mucormycosis, following treatment of a recurrent glioma. The patient was hospitalized for a suspected cellulitis of the right hemi-face, involving frontal maxillary area and the upper airways and was immediately put on intravenous antibiotic therapies; after performing nasal septum and maxillary biopsies, concomitant mucormycosis and aspergillosis were diagnosed and antimycotic therapy with liposomal B-amphotericin was administered. After evaluation by the oral surgeon and otolaryngologist, surgical cranio-facial necrosectomy was suggested, but refused by the parents of the patient. The girl died only few days later, due to a respiratory arrest. Awareness of this pathology with prompt diagnosis and early treatment may improve the outcome of these infections and reduce the mortality.reservedmixedChermetz, Maddalena; Gobbo, Margherita; Rupel, Katia; Ottaviani, Giulia; Tirelli, Giancarlo; Bussani, Rossana; Luzzati, Roberto; Di Lenarda, Roberto; Biasotto, MatteoChermetz, Maddalena; Gobbo, Margherita; Rupel, Katia; Ottaviani, Giulia; Tirelli, GIAN CARLO; Bussani, Rossana; Luzzati, Roberto; DI LENARDA, Roberto; Biasotto, Matte