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

Identification of lake trout Salvelinus namaycush spawning habitat in northern Lake Huron using high-resolution satellite imagery

© 2015 International Association for Great Lakes Research. The availability and quality of spawning habitat may limit lake trout recovery in the Great Lakes, but comprehensive maps of current spawning habitats are unavailable at the basin scale. Current methods used to identify lake trout spawning locations are time- and labor-intensive and spatially limited. Due to the observation that some lake trout spawning sites are relatively clean of overlaying algae compared to adjacent areas not used for spawning, we hypothesized that spawning sites could be identified using satellite imagery. Satellite imagery collected just before and after the spawning season in 2013 was used to assess whether lake trout spawning habitat could be identified based on its spectral characteristics. Results indicated that Pléiades high-resolution multispectral satellite imagery can be successfully used to estimate the vegetative cover of substrates and temporal changes in vegetative coverage, and that models developed from processed imagery can be used to identify potential shallow water lake trout spawning sites based on comparison of sites where lake trout eggs were and were not observed after spawning. Satellite imagery is a new potential tool for identifying nearshore lake trout spawning habitat across broad areas of the Great Lakes

Exercise Oscillatory Ventilation: Interreviewer Agreement and a Novel Determination

INTRODUCTION: Determination of exercise oscillatory ventilation (EOV) is subjective, and the interreviewer agreement has not been reported. The purposes of this study were, among patients with heart failure (HF), as follows: 1) to determine the interreviewer agreement for EOV and 2) to describe a novel, objective, and quantifiable measure of EOV. METHODS: This was a secondary analysis of the HEART Camp: Promoting Adherence to Exercise in Patients with Heart Failure study. EOV was determined through a blinded review by six individuals on the basis of their interpretation of the EOV literature. Interreviewer agreement was assessed using Fleiss kappa (κ). Final determination of EOV was based on agreement by four of the six reviewers. A new measure (ventilation dispersion index; VDI) was calculated for each test, and its ability to predict EOV was assessed with the receiver operator characteristics curve. RESULTS: Among 243 patients with HF (age, 60 ± 12 yr; 45% women), the interreviewer agreement for EOV was fair (κ = 0.303) with 10-s discrete data averages and significantly better, but only moderate (κ = 0.429) with 30-s rolling data averages. Prevalence rates of positive and indeterminate EOVs were 18% and 30% with the 10-s discrete averages and 14% and 13% with the 30-s rolling averages, respectively. VDI was strongly associated with EOV, with areas under the receiver operator characteristics curve of 0.852 to 0.890. CONCLUSIONS: Interreviewer agreement for EOV in patients with HF is fair to moderate, which can negatively affect risk stratification. VDI has strong predictive validity with EOV; as such, it might be a useful measure of prognosis in patients with HF

Encapsulation of a Nerve Agent Detoxifying Enzyme by a Mesoporous Zirconium Metal–Organic Framework Engenders Thermal and Long-Term Stability

Immobilized enzymes typically have greater thermal and operational stability than their soluble form. Here we report that for the first time, a nerve agent detoxifying enzyme, organophosphorus acid anhydrolase (OPAA), has been successfully encapsulated into a water-stable zirconium metal–organic framework (MOF). This MOF features a hierarchical mesoporous channel structure and exhibits a 12 wt % loading capacity of OPAA. The thermal and long-term stabilities of OPAA are both significantly enhanced after immobilization

Prostate Cancer with Peritoneal Carcinomatosis: A robotic-assisted radical prostatectomy-based Case Series

OBJECTIVE: To aid in the diagnosis and treatment of patients with metastatic tumor seeding, an exceedingly phenomenon following minimally invasive urological surgery, additional case reports are needed. MATERIALS AND METHODS: We report our experience with patients determined to have peritoneal carcinomatosis following robotic-assisted radical prostatectomy (RARP) and provide a descriptive summary of these unique cases. RESULTS: Five cases of peritoneal carcinomatosis were identified, all of which occurred relatively late - between 8-13 years - following RARP. Four of the five cases had T3 disease at the time of prostatectomy. CONCLUSIONS: Certain clinical factors, such as advanced pathologic stage at the time of prostatectomy, may predict risk for carcinomatosis following RARP. Additionally, next generation imaging modalities, such as PSMA PET, may aid in identifying these metastases and are likely to identify increasing numbers of these patients as next generation imaging becomes more widely available. Continued documentation and classification of this atypical presentation are needed to improve our understanding and management of this phenomenon

Nanosizing a Metal–Organic Framework Enzyme Carrier for Accelerating Nerve Agent Hydrolysis

We report the synthesis and characterization of a water-stable zirconium metal–organic framework (MOF), <b>NU-1003</b>, featuring the largest mesoporous aperture known for a zirconium MOF. This material has been used to immobilize the nerve agent hydrolyzing enzyme, organophosphorus acid anhydrolase (OPAA). The catalytic efficiency of immobilized OPAA in <i>nanosized</i> <b>NU-1003</b> is significantly increased compared to that of OPAA immobilized in <i>microsized</i> <b>NU-1003</b> and even exceeds that of the free OPAA enzyme. This paper highlights a method for rapid and highly efficient hydrolysis of nerve agents using nanosized enzyme carriers

Fish avoidance of ships during acoustic surveys tested with quiet uncrewed surface vessels

Acoustic surveys to estimate fish biomass and abundance are a major component of many fisheries monitoring programs. An important bias in acoustic surveys is that fish may avoid the survey vessel. Here, we utilized quiet uncrewed surface vessels (USVs) equipped with 120 kHz split beam echosounders to evaluate fish responses to motorized survey vessels. Two of these USVs were deployed in Lakes Michigan and Huron in summer 2021 and compared against three motorized vessels used in conventional fisheries acoustic surveys. Paired comparisons employed vessel-drone passes that provided the opportunity to observe fish response as vessels approached and then overtook their quiet USV counterparts. Sound originating from the vessels was primarily in the 10–1000 Hz range. Overall received sound pressure levels for ships at the closest pass were 100 dB (re 1 µPa @ 1 m) for one and 133–134 dB for the other two vessels. In contrast, sound originating from the USV was not detectable over ambient noise. We examined acoustic data from the USVs for potential changes in total acoustic backscatter, average target depth, and average in situ target strength as vessels approached. We observed weak evidence of an avoidance response by fish to the vessel with the loudest noise profile and highest survey speed but not for the other two vessels. We also compared acoustic data from 33 2-km transects surveyed by both vessels and the USVs, finding few differences between vessel and USV data for water depths between 5 and 80 m. Results from this work suggest that acoustics estimates of fishes in Lakes Michigan and Huron (primarily alewife, rainbow smelt, and bloater) are largely consistent among the vessels used in these two lakes for standard acoustic surveys and that fish avoidance is minimal in water depths \u3e 5 meters

Nanosizing a Metal–Organic Framework Enzyme Carrier for Accelerating Nerve Agent Hydrolysis

We report the synthesis and characterization of a water-stable zirconium metal–organic framework (MOF), <b>NU-1003</b>, featuring the largest mesoporous aperture known for a zirconium MOF. This material has been used to immobilize the nerve agent hydrolyzing enzyme, organophosphorus acid anhydrolase (OPAA). The catalytic efficiency of immobilized OPAA in <i>nanosized</i> <b>NU-1003</b> is significantly increased compared to that of OPAA immobilized in <i>microsized</i> <b>NU-1003</b> and even exceeds that of the free OPAA enzyme. This paper highlights a method for rapid and highly efficient hydrolysis of nerve agents using nanosized enzyme carriers

Protein Intake at Twice the RDA in Older Men Increases Circulatory Concentrations of the Microbiome Metabolite Trimethylamine-N-Oxide (TMAO)

Higher dietary protein intake is increasingly recommended for the elderly; however, high protein diets have also been linked to increased cardiovascular disease (CVD) risk. Trimethylamine-N-oxide (TMAO) is a bacterial metabolite derived from choline and carnitine abundant from animal protein-rich foods. TMAO may be a novel biomarker for heightened CVD risk. The purpose of this study was to assess the impact of a high protein diet on TMAO. Healthy men (74.2 ± 3.6 years, n = 29) were randomised to consume the recommended dietary allowance of protein (RDA: 0.8 g protein/kg bodyweight/day) or twice the RDA (2RDA) as part of a supplied diet for 10 weeks. Fasting blood samples were collected pre- and post-intervention for measurement of TMAO, blood lipids, glucose tolerance, insulin sensitivity, and inflammatory biomarkers. An oral glucose tolerance test was also performed. In comparison with RDA, the 2RDA diet increased circulatory TMAO (p = 0.002) but unexpectedly decreased renal excretion of TMAO (p = 0.003). LDL cholesterol was increased in 2RDA compared to RDA (p = 0.049), but no differences in other biomarkers of CVD risk and insulin sensitivity were evident between groups. In conclusion, circulatory TMAO is responsive to changes in dietary protein intake in older healthy males.Education, Faculty ofNon UBCKinesiology, School ofReviewedFacult