Functional evaluation of out-of-the-box text-mining tools for data-mining tasks

Objective The trade-off between the speed and simplicity of dictionary-based term recognition and the richer linguistic information provided by more advanced natural language processing (NLP) is an area of active discussion in clinical informatics. In this paper, we quantify this trade-off among text processing systems that make different trade-offs between speed and linguistic understanding. We tested both types of systems in three clinical research tasks: phase IV safety profiling of a drug, learning adverse drug–drug interactions, and learning used-to-treat relationships between drugs and indications.Materials We first benchmarked the accuracy of the NCBO Annotator and REVEAL in a manually annotated, publically available dataset from the 2008 i2b2 Obesity Challenge. We then applied the NCBO Annotator and REVEAL to 9 million clinical notes from the Stanford Translational Research Integrated Database Environment (STRIDE) and used the resulting data for three research tasks.Results There is no significant difference between using the NCBO Annotator and REVEAL in the results of the three research tasks when using large datasets. In one subtask, REVEAL achieved higher sensitivity with smaller datasets.Conclusions For a variety of tasks, employing simple term recognition methods instead of advanced NLP methods results in little or no impact on accuracy when using large datasets. Simpler dictionary-based methods have the advantage of scaling well to very large datasets. Promoting the use of simple, dictionary-based methods for population level analyses can advance adoption of NLP in practice.     

“We have to ask and only then do”: Unpacking agency and autonomy in women's reproductive health in urban India

The limited autonomy and agency of women in developing countries is recognized as a key barrier to improving their reproductive health. Using an existing perinatal cohort in urban South India, we interviewed 36 women who had recently been through childbirth, and we carried out observations of family life and clinic encounters. Critical domains involved in women's agency and autonomy were women's participation in employment and group action and their mobility. Household decision making was considered a joint rather than individual responsibility. We call for a more nuanced understanding of these domains and their relationship to women's reproductive health, particularly for urban populations.     

Enhancement of paclitaxel and carboplatin therapies by CCL2 blockade in ovarian cancers

Ovarian cancer is associated with a leukocyte infiltrate and high levels of chemokines such as CCL2. We tested the hypothesis that CCL2 inhibition can enhance chemotherapy with carboplatin and paclitaxel. Elevated CCL2 expression was found in three non‐MDR paclitaxel resistant ovarian cancer lines ES‐2/TP, MES‐OV/TP and OVCAR‐3/TP, compared to parental cells. Mice xenografted with these cells were treated with the anti‐human CCL2 antibody CNTO 888 and the anti‐mouse MCP‐1 antibody C1142, with and without paclitaxel or carboplatin. Our results show an additive effect of CCL2 blockade on the efficacy of paclitaxel and carboplatin. This therapeutic effect was largely due to inhibition of mouse stromal CCL2. We show that inhibition of CCL2 can enhance paclitaxel and carboplatin therapy of ovarian cancer.     

Salivary Epithelial Cells as Model to Study Immune Response Against Cutaneous Pathogens

The human skin not only provides passive protection as a physical barrier against external injury, but also mediates active surveillance via epidermal cell surface receptors that recognize and respond to potential invaders. Primary keratinocytes and immortalized cell lines, the commonly used sources to investigate immune responses of cutaneous epithelium are often difficult to obtain and/or potentially exhibit changes in cellular genetic make‐up. Here we investigated the possibility of using salivary epithelial cells (SEC) to evaluate the host response to cutaneous microbes. Elevated secretion of IFN‐γ and IL‐12 was observed in the SEC stimulated with Staphylococcus aureus, a transient pathogen of the skin, as mono species biofilm as compared to SEC stimulated with a commensal microbe, the Staphylococcus epidermidis. Co‐culture of the SEC with both microbes as dual species biofilm elicited maximum cytokine response. Stimulation with S. aureus alone but not with S. epidermidis alone induced maximum toll‐like receptor‐2 (TLR‐2) expression in the SEC. Exposure to dual species biofilm induced a sustained upregulation of TLR‐2 in the SEC for up to an hour. The data support novel application of the SEC as efficient biospecimen that may be used to investigate personalized response to cutaneous microflora.