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

Obtention et culture de protoplastes de Sequoia sempervirens (D. Don.) Endl. et Sequoiadendron giganteum (Lindl.) Buchholz

CNRS T Bordereau / INIST-CNRS - Institut de l'Information Scientifique et TechniqueSIGLEFRFranc

Phenology and frost hardiness of sugar maple populations

International audienc

A Functional GM-CSF Receptor on Dendritic Cells Is Required for Efficient Protective Anti-Tumor Immunity

Dendritic cells (DC) play a major role during the priming phase of anti-tumor immunization, as they are required for an efficient tumor-associated antigens presentation. At least one dendritic cell-based therapy has already been successfully approved by regulators for clinical application in prostate cancer patients. Moreover, DC development is dependent on the granulocyte macrophage colony stimulating factor (GM-CSF), a cytokine that has been successfully used as a potent inducer of anti-tumoral immunity. To better understand the relation between DC and GM-CSF in anti-tumor immunity, we studied the DC function in mice lacking the cytokine receptor common subunit beta (βc-/-) for GM-CSF, IL-3 and IL-5 and immunized with irradiated tumor cells. Such immunization induces a protective, specific tumor immunization in wild-type mice, while βc-/- mice failed to mount an immune response. Upon in vitro stimulation, DC from βc-/- mice (DCβc-/-) are unable to undergo a full maturation level. In vivo experiments show that they lack the ability to prevent tumor growth, in contrast to DCWT. Moreover, matured DCWT rescued immunization in βc-/- mice. DC maturation is dependent on a functional pathway involving GM-CSF signaling through a biologically functional receptor. These findings may contribute to new strategies for efficient anti-tumor immunotherapies

The early bud gets the cold: spring phenology drives exposure to late frost

International audienc

The early bud gets the cold: Diverging spring phenology drives exposure to late frost in a Picea mariana [(Mill.) BSP ] common garden

Under climate change, the increasing occurrence of late frost combined with advancing spring phenology can increase the risk of frost damage in trees. In this study, we tested the link between intra-specific variability in bud phenology and frost exposure and damages. We analysed the effects of the 2021 late frost event in a black spruce (Picea mariana (Mill.) BSP) common garden in Québec, Canada. We hypothesised that the timing of budbreak drives the exposure of vulnerable tissues and explains differences in frost damage. Budbreak was monitored from 2015 to 2021 in 371 trees from five provenances originating between 48°and 53°N and planted in a common garden at 48°N. Frost damages were assessed on the same trees through the pro-portion of damaged buds per tree and related to the phenological phases by ordinal regressions. After an unusually warm spring, minimum temperatures fell to -1.9°Con May 28 and 29, 2021. At this moment, trees from the northern provenances were more advanced in their phenology and showed more frost damage. Provenances with earlier budbreak had a higher probability of damage occurrence according to ordinal regression. Our study highlights the importance of intra-specific variability of pheno-logical traits on the risk of frost exposure. We provide evidence that the timings of bud phenology affect sensitivity to frost, leading to damages at temperatures of -1.9°C. Under the same conditions, the earlier growth reactivation observed in the northern provenances increases the risks of late frost damage on the developing buds

Efficacy of FOLFOX Chemotherapy in Metastatic Enteropancreatic Neuroendocrine Tumors

International audienceBackground/Aim: FOLFOX (5-Fluorouracile and oxaliplatin) exhibits promising activity in advanced welldifferentiated neuroendocrine tumors (NETs). This retrospective study aimed to analyze the outcome of metastatic enteropancreatic NETs patients treated with FOLFOX. Patients and Methods: We retrospectively identified patients treated with FOLFOX for NETs of enteropancreatic or unknown origin among those referred to our Regional Multidisciplinary Tumor Board. Results: Among 48 patients, most often pancreatic NETs (n=33, 68.8%), the median Ki67 index was 10%. The median number cycle of FOLFOX was 6 and median follow-up was 34.8 months. Disease control rate (DCR) was 83.3%. Median PFS and OS were 12.6 and 29.4 months respectively. Median chemotherapy break was 14.1 months. No significant difference was observed between PFS and the following criteria: Ki67 index, primary tumor site, alkaline phosphatase levels, primary tumor surgery and 18 F-FDG PET positivity. Conclusion: FOLFOX exhibits a high DCR and a short duration of treatment with a relative long chemotherapy break in patients with metastatic enteropancreatic NETs

Demonstration of immunomodulatory properties for the human MuStem cell population, a promising candidate for cell therapy of muscular dystrophies

Demonstration of immunomodulatory properties for the human MuStem cell population, a promising candidate for cell therapy of muscular dystrophies. 2nd annual meeting of French Society for Stem Cell Researc