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

Case-control Indian buffet process identifies biomarkers of response to Codrituzumab

Abstract Background Codrituzumab, a humanized monoclonal antibody against Glypican-3 (GPC3), which is expressed in hepatocellular carcinoma (HCC), was tested in a randomized phase II trial in advanced HCC patients who had failed prior systemic therapy. Biomarker analysis was performed to identify a responder population that benefits from treatment. Methods A novel statistical method based on the Indian buffet process (IBP) was used to identify biomarkers predictive of response to treatment with Codrituzumab. The IBP is a novel method that allows flexibility in analysis design, and which is sensitive to slight, but meaningful between-group differences in biomarkers in very complex datasets Results The IBP model identified several subpopulations of patients having defined biomarker values. Tumor necrosis and viable cell content in the tumor were identified as prognostic markers of disease progression, as were the well-known HCC prognostic markers of disease progression, alpha-fetoprotein and Glypican-3 expression. Predictive markers of treatment response included natural killer (NK) cell surface markers and parameters influencing NK cell activity, all related to the mechanism of action of this drug Conclusions The Indian buffet process can be effectively used to detect statistically significant signals with high sensitivity in complex and noisy biological data Trial registration NCT01507168, January 6, 201

Predicting arbuscular mycorrhizal fungal colonization of soybean in farmers’ fields by using infection unit density

Estimating arbuscular mycorrhizal (AM) fungal activity to colonize crop root before cultivation is prerequisite for effective utilization of their functions which enhance growth and yield of the plant especially under low fertilizer input. We have hypothesized that the infection unit (IU) density formed on test plant roots grown for short period (12 days) with soil sampled from soybean production fields would be an effective indicator to predict AM fungal colonization intensity to the plant. In order to test this hypothesis, three-year farmland survey was conducted, in which soil samples before sowing soybean and the plant root samples at third trifoliate (V3) and full bloom (R2) stage were collected from farmers’ fields in two regions in Hokkaido, Iwamizawa and Tokachi. For each sampling spot, IU density was determined by using test plants, and intensity of AM fungal colonization of soybean root was measured. Before pursuing field survey, laboratory experiments were conducted to find out proper soil storage condition that keeps IU density unchanged while handling many soil samples. Our results indicated that IU density was almost comparable to the original value after six-month storage if soil samples were kept in a refrigerator, although storing at ambient temperature significantly decreased the measurement. Air drying also had negative impact on IU density. According to the field survey, IU densities determined using field soil were positively and significantly correlated with AM fungal colonization of soybean roots at both V3 and R2 stages. Differences in climate, soil type, and style of agriculture between Iwamizawa and Tokachi seemed to have little effect on IU density-AM fungal colonization relationship. Other than IU density, soil pH and soil penetration resistance at 10 cm depth were selected as significant explanatory variables for predicting AM fungal colonization by multiple regression analysis. However, IU density was the most influential factor among three. Therefore, IU density is recognized as an effective measure to evaluate AM fungal colonizing activity in field soil.</p

Evaluating Clinical And Prognostic Implications Of Glypican-3 In Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is one of the most deadly cancers worldwide. In patients with HCC, histopathogical differentiation is an important indicator of prognosis; however, because determination of HCC differentiation is difficult, the recently described immunohistochemical (IHC) marker glypican3 (GPC3) might assist in HCC prognostication.The goal of our study was to investigate GPC3's IHC staining pattern and define the relationship between its expression and patients' clinicopathologic features and overall survival. We retrieved clinical parameters from 101 pathologically diagnosed HCC patients' medical records and classified these patients into 4 clinical score categories (0–3) based on increasing GPC3 staining intensity and the percentage of stained tumor cells in their resection and biopsy specimens. Histopathological samples were well, moderately, and poorly differentiated in 33, 22, and 12 patients, respectively, and the GPC3 expression rate was 63%, 86%, and 92%,respectively. The median overall survival was 49.9 months (confidence interval (CI): 35.3–64.6 months) for clinical scores 0–1 and 30.7 months (CI: 19.4–41.9 months) for clinical scores 2–3. This difference was not statistically significant (P = .06) but showed a strong trend. In conclusion, a greater GPC3 expression is associated with a worse HCC prognosis and may be a promising prognostic marker.PubMedWoSScopu

I-124 codrituzumab imaging and biodistribution in patients with hepatocellular carcinoma

Abstract Background I-124 codrituzumab (aka GC33), an antibody directed at Glypican 3, was evaluated in patients with hepatocellular carcinoma (HCC). Fourteen patients with HCC underwent baseline imaging with I-124 codrituzumab (~ 185 MBq, 10 mg). Seven of these patients undergoing sorafenib/immunotherapy with 2.5 or 5 mg/kg of cold codrituzumab had repeat imaging, with co-infusion of I-124 codrituzumab, as part of their immunotherapy treatment. Three patients who progressed while on sorafenib/immunotherapy were re-imaged after a 4-week washout period to assess for the presence of antigen. Serial positron emission tomography (PET) imaging and pharmacokinetics were performed following I-124 codrituzumab. An ELISA assay was used to determine “cold” codrituzumab serum pharmacokinetics and compare it to that of I-124 codrituzumab. Correlation of imaging results was performed with IHC. Short-term safety assessment was also evaluated. Results Thirteen patients had tumor localization on baseline I-124 codrituzumab; heterogeneity in tumor uptake was noted. In three patients undergoing repeat imaging while on immunotherapy/sorafenib, evidence of decreased I-124 codrituzumab uptake was noted. All three patients who underwent imaging after progression while on immunotherapy continued to have I-124 codrituzumab tumor uptake. Pharmacokinetics of I-124 codrituzumab was similar to that of other intact IgG. No significant adverse events were observed related to the I-124 codrituzumab. Conclusions I-124 codrituzumab detected tumor localization in most patients with HCC. Pharmacokinetics was similar to that of other intact iodinated humanized IgG. No visible cross-reactivity with normal organs was observed