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

Small bugs, big appetites: experimental quantification of duckweed-herbivore interactions

The role of herbivores in driving the structure of freshwater macrophyte communities remains poorly understood in comparison with terrestrial ecosystems. For instance, although duckweed (subfamily Lemnoideae) are globally distributed, can be ecologically dominant, and are of growing economic importance, their interactions with herbivores remain understudied. It remains unknown if herbivores could strongly impact duckweed’s rapid population growth and how they could influence species composition of macrophyte communities. We here test whether the water-lily aphid (Rhopalosiphum nymphaeae) exhibits a preference between species of duckweed and how duckweed and aphids reciprocally affect each other’s performance. Our two-way choice experiments reveal that aphids display preference for Spirodela polyrhiza > Landoltia punctata = Lemna minor >> Wolffia brasiliensis. By evaluating the growth of aphid populations on each duckweed species we found that preference may be adaptive in certain ecological conditions when high growth rate is advantageous. Quantifying the population growth rate of duckweed in the presence and absence of aphids revealed differential tolerance of herbivory across duckweed species. These results suggest that a single herbivore could have a significant impact on duckweed populations and species composition in nature. We pursued this possibility with a manipulative field experiment. Using exclosures in natural ponds, we manipulated the presence of herbivores. We found that herbivory impacts species composition of duckweed communities in a complex manner. Species are differently affected in ambient herbivory and herbivore addition treatments, and there is considerable variation in herbivore effect between sites due to difference in local herbivore communities. After finding interspecific variation in duckweed response to herbivory, we tested the possibility of intraspecific variation in plant defenses against herbivores. We found that resistance and tolerance vary between duckweed genotypes, and herbivory could be a potential driver of duckweed evolution. We here highlight the importance of quantifying the plant-herbivore interactions in aquatic ecosystems in the lab and the field

Role of sudarshan kriya and pranayam on lipid profile and blood cell parameters during exam stress: A randomized controlled trial

Background: Yoga is a science practiced in India over thousands of years. It produces constituent physiological changes and has sound scientific basis. Aim: Since exam stress modifies lipid profile and hematological parameters, we conducted an investigation on the effect of sudarshan kriya (SK and P) program on these parameters. Materials and Methods: Blood samples of 43 engineering students were collected at four intervals namely baseline (BL), exam stress (ES), three and six weeks practice of SK and P during exam stress. Lipid profile and hematological parameters were measured at all four intervals. Results: ES elevated total cholesterol (TC), triglycerides (TGL) and very low density lipoprotein (VLDL) levels. Hematological parameters affected by ES included neutrophil, lymphocytes, platelet count, packed cell volume (PCV) and mean cell volume (MCV). Three and six weeks practice of SK and P reduced the elevated lipid profile, hematological parameters and improved lymphocyte levels. Conclusion: Our study indicates that SK and P practice has the potential to overcome ES by improving lipid profile and hematological parameters

Distance saturation product predicts health–related quality of life among sarcoidosis patients

<p>Abstract</p> <p>Background</p> <p>Sarcoidosis is a chronic disease with different phenotypic manifestations. Health-related quality of life is an important aspect in sarcoidosis, yet difficult to measure. The objective of this study was to identify clinical markers predictive of poor quality of life in sarcoidosis patients that can be followed over time and targeted for intervention.</p> <p>Methods</p> <p>We assessed the quality of life of 162 patients with confirmed sarcoidosis in a prospective, cross-sectional study using the Sarcoidosis Health Questionnaire (SHQ) and Short Form-36 Health Survey (SF-36). We evaluated the validity of these questionnaires and sought to identify variables that would best explain the performance scores of the patients.</p> <p>Results</p> <p>On multivariate regression analyses, the very best composite model to predict total scores from both surveys was a model containing the distance-saturation product and Borg Dyspnea Scale score at the end of a 6-min walk test. This model could better predict SF-36 scores (R² = 0.33) than SHQ scores (R² = 0.24). Substitution of distanced walked in 6 min for the distance-saturation product in this model resulted in a lesser ability to predict both scores (R² = 0.26 for SF-36; R² = 0.22 for SHQ).</p> <p>Conclusions</p> <p>Both the SHQ and SF-36 surveys are valuable tools in the assessment of health-related quality of life in sarcoidosis patients. The best model to predict quality of life among these patients, as determined by regression analyses, included the distance-saturation product and Borg score after the 6-min walk test. Both variables represent easily obtainable clinical parameters that can be followed over time and targeted for intervention.</p

A multivariate view of the speciation continuum

The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model