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 Quinone Degradation as a Triggering Event for Intense Pulsed Light-Elicited Metabolic Changes in Escherichia coli by Metabolomic Fingerprinting

Intense pulsed light (IPL) is becoming a new technical platform for disinfecting food against pathogenic bacteria. Metabolic changes are deemed to occur in bacteria as either the causes or the consequences of IPL-elicited bactericidal and bacteriostatic effects. However, little is known about the influences of IPL on bacterial metabolome. In this study, the IPL treatment was applied to E. coli K-12 for 0–20 s, leading to time- and dose-dependent reductions in colony-forming units (CFU) and morphological changes. Both membrane lipids and cytoplasmic metabolites of the control and IPL-treated E. coli were examined by the liquid chromatography-mass spectrometry (LC-MS)-based metabolomic fingerprinting. The results from multivariate modeling and marker identification indicate that the metabolites in electron transport chain (ETC), redox response, glycolysis, amino acid, and nucleotide metabolism were selectively affected by the IPL treatments. The time courses and scales of these metabolic changes, together with the biochemical connections among them, revealed a cascade of events that might be initiated by the degradation of quinone electron carriers and then followed by oxidative stress, disruption of intermediary metabolism, nucleotide degradation, and morphological changes. Therefore, the degradations of membrane quinones, especially the rapid depletion of menaquinone-8 (MK-8), can be considered as a triggering event in the IPL-elicited metabolic changes in E. coli

Identification of Quinone Degradation as a Triggering Event for Intense Pulsed Light-Elicited Metabolic Changes in <i>Escherichia coli</i> by Metabolomic Fingerprinting

Intense pulsed light (IPL) is becoming a new technical platform for disinfecting food against pathogenic bacteria. Metabolic changes are deemed to occur in bacteria as either the causes or the consequences of IPL-elicited bactericidal and bacteriostatic effects. However, little is known about the influences of IPL on bacterial metabolome. In this study, the IPL treatment was applied to E. coli K-12 for 0–20 s, leading to time- and dose-dependent reductions in colony-forming units (CFU) and morphological changes. Both membrane lipids and cytoplasmic metabolites of the control and IPL-treated E. coli were examined by the liquid chromatography-mass spectrometry (LC-MS)-based metabolomic fingerprinting. The results from multivariate modeling and marker identification indicate that the metabolites in electron transport chain (ETC), redox response, glycolysis, amino acid, and nucleotide metabolism were selectively affected by the IPL treatments. The time courses and scales of these metabolic changes, together with the biochemical connections among them, revealed a cascade of events that might be initiated by the degradation of quinone electron carriers and then followed by oxidative stress, disruption of intermediary metabolism, nucleotide degradation, and morphological changes. Therefore, the degradations of membrane quinones, especially the rapid depletion of menaquinone-8 (MK-8), can be considered as a triggering event in the IPL-elicited metabolic changes in E. coli

Changes of Enterocyte Morphology and Enterocyte: Goblet Cell Ratios in Dogs with Protein-Losing and Non-Protein-Losing Chronic Enteropathies

This study aimed to assess the morphometry of enterocytes as well as the goblet cell-to-enterocyte ratio in different intestinal segments of dogs with chronic enteropathies (CE). Histopathological intestinal samples from 97 dogs were included in the study (19 healthy juveniles, 21 healthy adults, 24 dogs with protein-losing enteropathy (PLE), and 33 CE dogs without PLE). Healthy adult small intestinal enterocytes showed progressively reduced epithelial cell height in the aboral direction, while juvenile dogs showed progressively increased epithelial cell height in the aboral direction. CE dogs had increased epithelial cell height in the duodenum, while PLE dogs had decreased epithelial cell heights compared to healthy adult dogs. Both the CE and PLE dogs showed decreased enterocyte width in the duodenal segment, and the ileal and colonic enterocytes of CE dogs were narrower than those of healthy adult dogs. CE dogs had a lower goblet cell-to-enterocyte ratio in the colon segment compared to healthy dogs. This study provides valuable morphometric information on enterocytes during canine chronic enteropathies, highlighting significant morphological enterocyte alterations, particularly in the small intestine, as well as a reduced goblet cell-to-enterocyte ratio in the colon of CE cases compared to healthy adult dogs.This article is published as Díaz-Regañón D, Gabriel V, Livania V, Liu D, Ahmed BH, Lincoln A, Wickham H, Ralston A, Merodio MM, Sahoo DK, et al. Changes of Enterocyte Morphology and Enterocyte: Goblet Cell Ratios in Dogs with Protein-Losing and Non-Protein-Losing Chronic Enteropathies. Veterinary Sciences. 2023; 10(7):417. https://doi.org/10.3390/vetsci10070417. Posted with permission.This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/)

Online gas- and particle-phase measurements of organosulfates, organosulfonates and nitrooxy organosulfates in Beijing utilizing a FIGAERO ToF-CIMS

Abstract. A Time of Flight Chemical Ionisation Mass spectrometer (CIMS) utilizing the Fast Inlet for Gas and AEROsol (FIGAERO) was deployed at a regional site 40 km north west of Beijing and successfully identified and measured 17 sulfur containing organics (SCOs = organo/nitrooxyorgano sulfates and sulfonates) with biogenic and anthropogenic precursors. The SCOs were quantified using laboratory synthesized standards of lactic acid sulfate and nitrophenol organosulfate (NP OS). The mean total (of the 17 identified by CIMS) SCO particle mass concentration was 207 &amp;amp;pm; 106 ng m−3 and had a maxima of 542 ng m−3, although contributed to only 2 &amp;amp;pm; 2.8 % of the organic aerosol (OA). SCO contribution to submicron mass (PM1) indicates a dominant secondary production of SCO due to the low contribution of SCOs to PM1 during periods of high mass loading. The CIMS identified a persistent gas phase presence of SCOs in the ambient air, which was further supported by post campaign vapour pressure measurements of NP OS. An increase in RH appeared to promote partitioning to the particle phase whereas higher temperatures favored higher gas phase concentrations. On average 12 % of the total SCOs were observed in the gas phase with C10H16NSO7 having just 5 % and IEPOX OS having 44 % on average in the gas phase. Biogenic emissions contributed to only 19 % of total SCOs detected. C10H16NSO7, an alpha-pinene derived SCO, representing the highest fraction (10 %) followed by an isoprene-derived SCO. Anthropogenic SCOs with PAH and aromatic precursors dominated the SCO mass loading (51 % total SCOs) with C11H11SO7, derived from methyl napthalene oxidation, contributing to 40 ng m−3 and 0.3 % of the OA mass. Biomass burning was also identified as a potential anthropogenic and biogenic source of SCOs, based on nitrophenol (NP) and acetonitrile time series via secondary production of NP OS. Gas and particle phase measurements of glycolic acid suggest that partitioning towards the particle phase promotes glycolic acid sulfate production, contrary to the current formation mechanism suggested in the literature. Highly oxidised multifunctional organic compounds (HOMS) and RO2 radical diurnal profiles, as measured by the iodide ToF-CIMS, are similar to that of total SCOs, supporting results that indicate HOMS are able to play a role in SCO production. Anthropogenic related SCOs correlated well with benzene, although their abundance depended highly on the photochemical age of the air mass, tracked using the ratio between pinonic acid and its oxidation product, acting as a qualitative photochemical clock. The HSO4.H2SO4− cluster measured by the CIMS was utilized as a qualitative marker for acidity and provides further evidence that the production rate of total SCOs is efficient in highly acidic aerosols with high SO42− and organic content. This dependency becomes more complex when observing individual SCOs due to variability of specific VOC precursors. </jats:p

The enhanced x-ray timing and polarimetry mission – eXTP: an update on its scientific cases, mission profile and development status

The enhanced x-ray timing and polarimetry mission (eXTP) is a flagship observatory for x-ray timing, spectroscopy and polarimetry developed by an international consortium. Thanks to its very large collecting area, good spectral resolution and unprecedented polarimetry capabilities, eXTP will explore the properties of matter and the propagation of light in the most extreme conditions found in the universe. eXTP will, in addition, be a powerful x-ray observatory. The mission will continuously monitor the x-ray sky, and will enable multi-wavelength and multi-messenger studies. The mission is currently in phase B, which will be completed in the middle of 2022

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 science. © The Author(s) 2019. Published by Oxford University Press