Boolean versus ranked querying for biomedical systematic reviews

Background: The process of constructing a systematic review, a document that compiles the published evidence pertaining to a specified medical topic, is intensely time-consuming, often taking a team of researchers over a year, with the identification of relevant published research comprising a substantial portion of the effort. The standard paradigm for this information-seeking task is to use Boolean search; however, this leaves the user(s) the requirement of examining every returned result. Further, our experience is that effective Boolean queries for this specific task are extremely difficult to formulate and typically require multiple iterations of refinement before being finalized. Methods: We explore the effectiveness of using ranked retrieval as compared to Boolean querying for the purpose of constructing a systematic review. We conduct a series of experiments involving ranked retrieval, using queries defined methodologically, in an effort to understand the practicalities of incorporating ranked retrieval into the systematic search task. Results: Our results show that ranked retrieval by itself is not viable for this search task requiring high recall. However, we describe a refinement of the standard Boolean search process and show that ranking within a Boolean result set can improve the overall search performance by providing early indication of the quality of the results, thereby speeding up the iterative query-refinement process. Conclusions: Outcomes of experiments suggest that an interactive query-development process using a hybrid ranked and Boolean retrieval system has the potential for significant time-savings over the current search process in the systematic reviewing

Optimization of an efficient cell culture hepatitis B infection system for assessment of hepatitis B virus neutralizing monoclonal antibodies.

Background: Human polyclonal plasma-derived hepatitis B immunoglobulin (HBIG) is currently used for immunoprophylaxis of HBV infection. The development of virus-neutralizing monoclonal antibodies (MAbs) requires the use of optimized cell culture systems supporting HBV infection. Objective: This study aims to optimize the hepatitis B virus infectivity of NTCP-reconstituted HepG2 (HepG2-NTCP) cells to establish an efficient system to evaluate the HBV-neutralizing effect of anti-HBs MAbs. Methods: Serum-derived HBV (sHBV) and cell culture-derived HBV (ccHBV) were simultaneously used for the optimization of HBV infection in HepG2-NTCP cells by applying different modifications. Results: Our results for the first time showed that in addition to human serum, monkey serum could significantly improve ccHBV infection, while fetal and adult bovine serum as well as duck and sheep serum did not have a promotive effect. In addition, sHBV and ccHBV infectivity are largely similar except that adding 5% of PEG, which is commonly used to improve in vitro infection of ccHBV, significantly reduced sHBV infection. We showed that a combination of spinoculation, trypsinization, and also adding human or monkey serum to HBV inoculum could significantly improve the permissivity of HepG2-NTCP cells to HBV infection compared with individual strategies. All anti-HBs MAbs were able to successfully neutralize both ccHBV and sHBV infection in our optimized in vitro system. Conclusion: Our study suggests different strategies for improving ccHBV and sHBV infection in HepG2-NTCP cells. This cell culture-based system allows assessment of HBV neutralizing MAbs and may also prove to be valuable for the analysis of other HBV neutralizing therapeutics

Automatic Boolean query formulation for systematic review literature search

Formulating Boolean queries for systematic review literature search is a challenging task. Commonly, queries are formulated by information specialists using the protocol specified in the review and interactions with the research team. Information specialists have in-depth experience on how to formulate queries in this domain, but may not have in-depth knowledge about the reviews' topics. Query formulation requires a significant amount of time and effort, and is performed interactively; specialists repeatedly formulate queries, attempt to validate their results, and reformulate specific Boolean clauses. In this paper, we investigate the possibility of automatically formulating a Boolean query from the systematic review protocol. We propose a novel five-step approach to automatic query formulation, specific to Boolean queries in this domain, which approximates the process by which information specialists formulate queries. In this process, we use syntax parsing to derive the logical structure of high-level concepts in a query, automatically extract and map concepts to entities in order to perform entity expansion, and finally apply post-processing operations (such as stemming and search filters). Automatic query formulation for systematic review literature search has several benefits: (i) it can provide reviewers with an indication of the types of studies that will be retrieved, without the involvement of an information specialist, (ii) it can provide information specialists with an initial query to begin the formulation process, (iii) it can provide researchers that perform rapid reviews with a method to quickly perform searches

Blood transcriptional profiles distinguish different clinical stages of cutaneous leishmaniasis in humans

Cutaneous leishmaniasis (CL) is a neglected tropical disease with severe morbidity and socioeconomic sequelae. A better understanding of underlying immune mechanisms that lead to different clinical outcomes of CL could inform the rational design of intervention measures. While transcriptomic analyses of CL lesions were recently reported by us and others, there is a dearth of information on the expression of immune-related genes in the blood of CL patients. Herein, we investigated immune-related gene expression in whole blood samples collected from individuals with different clinical stages of CL along with healthy volunteers in an endemic CL region where Leishmania (L.) tropica is prevalent. Study participants were categorized into asymptomatic (LST+) and healthy uninfected (LST-) groups based on their leishmanin skin test (LST). Whole blood PAXgene samples were collected from volunteers, who had healed CL lesions, and patients with active L. tropica cutaneous lesions. Quality RNA extracted from 57 blood samples were subjected to Dual-color reverse-transcription multiplex ligation-dependent probe amplification (dcRT-MLPA) assay for profiling 144 immune-related genes. Results show significant changes in the expression of genes involved in interferon signaling pathway in the blood of active CL patients, asymptomatics and healed individuals. Nonetheless, distinct profiles for several immune-related genes were identified in the healed, the asymptomatic, and the CL patients compared to the healthy controls. Among others, IFI16 and CCL11 were found as immune transcript signatures for the healed and the asymptomatic individuals, respectively. These results warrant further exploration to pinpoint novel blood biomarkers for different clinical stages of CL.Immunogenetics and cellular immunology of bacterial infectious disease