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

Role of ribavirin in the treatment of hepatitis C virus-associated mixed cryoglobulinemia with interferon-free regimens

Mixed cryoglobulinemia (MC) is the most common extrahepatic manifestation of chronic hepatitis C (CHC), with the presence of symptoms in 10-15% of cases. There have been encouraging data regarding immunological and clinical responses in patients treated with the novel combinations of direct-acting antivirals (DAAs), but the role of ribavirin (RBV) in the treatment of MC has not yet been demonstrated. We prospectively enrolled 132 patients affected by MC and CHC, and virological, immunological and clinical responses were evaluated at 12\ua0weeks after completion of treatment. All subjects were treated with interferon (IFN)-free regimens according to clinical guidelines, with or without RBV. All patients achieved a virological response. A complete immunological response (CR) was observed in 71 subjects (53.8%), a partial response in 44 (33.3%), and no response in 17 (12.8%). Ten patients showed a complete resolution of symptoms (7.6%), and 31 showed a significant improvement (23.5%). CR was significantly higher in patients taking RBV (71.1 vs. 44.8%, p\ua0<\ua00.001) and in treatment-na\uefve patients (62.5 vs. 43.3%, p\ua0<\ua00.001). In logistic regression analysis, duration of HCV infection of less than 20\ua0years (OR 2.448; 95% IC 1.335-6.202; p\ua0=\ua00.019), treatment-na\uefve status (OR 2.885; 95% IC 1.404-9.660; p\ua0=\ua00.025) and the use of RBV (OR 6.961; 95% IC 3.912-26.885; p\ua0<\ua00.001) were predictors of CR. In MC patients, IFN-free regimens are effective and well tolerated, and RBV seems to significantly increase the immunological response and promote a decline in cryocrit

Treatment with PEG-IFN and ribavirin in patients with chronic hepatitis C, low grade of hepatic fibrosis, genotype 1 and 4 and favorable IFNL3 genotype: A pharmacogenetic prospective study

The new direct-acting antivirals agents (DAAs) rapidly changed the treatment approach in chronic hepatitis C (CHC); however, the interferon (IFN)-free therapies availability is currently different in some countries, due to higher costs of these drugs. Na\uefve treated patients, who are not eligible for IFN-free therapies, could be selected for standard dual treatment with pegylated (PEG)-IFN and ribavirin (RBV), through IFN lambda 3 gene polymorphisms and fibrosis stage evaluation. Inclusion criteria were: na\uefve treated CHC patients with GT1 or GT4, without major contraindication to PEG-IFN or RBV, with fibrosis stage F0-F2 and IFNL3 rs8099917/rs12979860 TT/CC genotypes. 65 patients were included in the study. Overall SVR was observed in 50 patients (76.9%); SVR rates among different genotypes were as follows: 15 with GT1a (71.4%), 27 with GT1b (79.4%) and 8 for GT4 (80%). The RBV cutoff at 2weeks of 1800ng/mL, predictor of RVR, was determined (p=0.003; sensibility=60.4%, specificity=88.2%, positive predictive value=88.9%, negative predictive value=100%). In multivariate analysis, factors significantly associated with treatment failure were living alone condition (OR=4.302; 95%IC=1.254-16.257; p=0.034) and RBV plasma level <1800ng/mL at 2weeks (OR=4.970; 95%IC=1.405-17.565; p=0.009). Considering a pharmacogenetic-guided approach, dual therapy with PEG-IFN and RBV can be considered a reliable option for patients ineligible for IFN-free treatments, who are motivated and well informed about all the aspects related to PEG-IFN administration

Daclatasvir Plasma Levels in a Cohort of Patients with Hepatitis C Virus Infection Taking Methadone: A Prospective Analysis

Backround: The effect of methadone (MET) during therapy with novel direct-acting antiviral agents is still not fully understood. Currently, no data are available about the influence of MET on daclatasvir (DCV) plasma levels in patients affected by chronic hepatitis C (CHC). The aim of this study was to assess the DCV plasma concentrations in patients treated with sofosbuvir (SOF) plus DCV, with or without ribavirin (RBV) and with or without MET

Vitamin D pathway gene polymorphisms affecting daclatasvir plasma concentration at 2 weeks and 1 month of therapy

Vitamin D (VD) influences genetic expression through its receptor (VDR). VD pathway gene polymorphisms seem to influence antiviral drug pharmacokinetics and therapeutic outcome/toxicity. We investigated the association between daclatasvir (DCV) plasma concentrations and genetic variants (SNPs) associated with the VD pathway

Pharmacogenetics of the anti-HCV drug sofosbuvir: a preliminary study

Sofosbuvir is a potent nucleotide HCV NS5B polymerase inhibitor that is also a P-glycoprotein (encoded by the ABCB1 gene) and breast cancer resistance protein (encoded by the ABCG2 gene) substrate. Concerning previous anti-HCV therapies, pharmacogenetics had a significant impact, particularly considering the association of interleukin28B polymorphisms with dual-therapy (ribavirin\u200a+\u200apegylated IFN) outcomes