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

Cellular Dynamics: Cellular Systems in the Time Domain

Plant cells are the fundamental building blocks of growth and development. For each cell type, the size, shape, and mechanical properties of the cell wall are customized for particular physiological functions (Szymanski and Cosgrove, 2009; Winship et al., 2011). The morphogenesis of highly polarized cell types such as trichoblasts and pollen tubes is internally programmed and occurs largely in the absence of a neighbor. Most cell types differentiate in the context of a tissue. Therefore, their growth and shape change can operate at larger spatial scales to influence tissue- and organ-level processes. Because plant cells grow symplastically and are mechanically coupled to their neighboring cells, growth properties and information flow within and between tissues can feed back on and influence cell behaviors. Plant cells are also metabolically specialized. Within a single tissue or organ, cell types can differ greatly in terms of how central metabolism is fueled, the types of metabolites that accumulate, and where in the cell they are stored. Despite the structural and biochemical diversity of different cell types, their cell biology and development can be considered as a similar set of integrated systems-level processes. For example, the metabolic activity and energy status of a cell varies as a function of light levels or developmental stage. The biosynthesis and transport activities of the cytosol and endomembrane systems are integrated with metabolism over time. Cellular systems are also integrated across wide spatial scales. Proteins and protein complexes at the approximately 10- to 100-nm scale can use the cytoskeleton to position organelles and organize the cytoplasm at the approximately 1- to 10-μm spatial scale, to influence cell behaviors. Discovering and unraveling the complexity of these multiscale systems level interactions is a grand challenge in plant research. In recent years, progress has been rapid and is being driven in large part by the widespread use of multichannel quantitative time-lapse imaging. Using this approach, it is possible to create a spatial and temporal coordinate system in which multiple parameters can be measured and cross-correlated, and the effects of mutations or other experimental manipulations can be more deeply analyzed.This editorial is published as Szymanski, Dan, Diane Bassham, Teun Munnik, and Wataru Sakamoto. "Cellular Dynamics: Cellular Systems in the Time Domain." Plant Physiology (2018): 12-15. doi: 10.1104/pp.17.01777. Copyright American Society of Plant Biologists. Posted with permission. .</p

Objectification in Virtual Romantic Contexts: Perceived Discrepancies Between Self and Partner Ideals Differentially Affect Body Consciousness in Women and Men

The current study examined whether exposure to sexually objectifying images in a potential romantic partner's virtual apartment affects discrepancies between people's perception of their own appearance (i.e., self-perceptions) and their perception of the body ideal that is considered desirable to a romantic partner (i.e., partner-ideals). Participants were 114 heterosexual undergraduate students (57 women and 57 men) from a northeastern U.S. university. The study used a 2 (Participant Gender) x 2 (Virtual Environment: Sexualized vs. Non-Sexualized) between-subjects design. We predicted that women exposed to sexually objectifying images in a virtual environment would report greater discrepancies between their self-perceptions and partner-ideals than men, which in turn would contribute to women's body consciousness. Findings support this hypothesis and show that perceived discrepancies account for the relationship between exposure to sexually objectifying images and body consciousness for women but not men. We also found gender asymmetries in objectification responses when each component of perceived discrepancies, i.e., self-perceptions versus perceptions of a romantic partner's body ideal, were examined separately. For men, exposure to muscular sexualized images was significantly associated with their self-perceptions but not their perceptions of the body size that is considered desirable to a romantic partner. For women, exposure to thin sexualized images was significantly associated with their perceptions that a romantic partner preferred a woman with a smaller body size. However, exposure to these images did not affect women's self-perceptions. Implications for gender asymmetries in objectification responses and perceived discrepancies that include a romantic partner's perceptions are discussed