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To address the rapid growth of scientific publications and data in biomedical research, knowledge graphs (KGs) have become a critical tool for integrating large volumes of heterogeneous data to enable efficient information retrieval and automated knowledge discovery. However, transforming unstructured scientific literature into KGs remains a significant challenge, with previous methods unable to achieve human-level accuracy. Here we used an information extraction pipeline that won first place in the LitCoin Natural Language Processing Challenge (2022) to construct a large-scale KG named iKraph using all PubMed abstracts. The extracted information matches human expert annotations and significantly exceeds the content of manually curated public databases. To enhance the KG’s comprehensiveness, we integrated relation data from 40 public databases and relation information inferred from high-throughput genomics data. This KG facilitates rigorous performance evaluation of automated knowledge discovery, which was infeasible in previous studies. We designed an interpretable, probabilistic-based inference method to identify indirect causal relations and applied it to real-time COVID-19 drug repurposing from March 2020 to May 2023. Our method identified around 1,200 candidate drugs in the first 4 months, with one-third of those discovered in the first 2 months later supported by clinical trials or PubMed publications. These outcomes are very challenging to attain through alternative approaches that lack a thorough understanding of the existing literature. A cloud-based platform (https://biokde.insilicom.com) was developed for academic users to access this rich structured data and associated tools. 

Abstract There have been significant advances in biosignal extraction techniques to drive external biomechatronic devices or to use as inputs to sophisticated human machine interfaces. The control signals are typically derived from biological signals such as myoelectric measurements made either from the surface of the skin or subcutaneously. Other biosignal sensing modalities are emerging. With improvements in sensing modalities and control algorithms, it is becoming possible to robustly control the target position of an end-effector. It remains largely unknown to what extent these improvements can lead to naturalistic human-like movement. In this paper, we sought to answer this question. We utilized a sensing paradigm called sonomyography based on continuous ultrasound imaging of forearm muscles. Unlike myoelectric control strategies which measure electrical activation and use the extracted signals to determine the velocity of an end-effector; sonomyography measures muscle deformation directly with ultrasound and uses the extracted signals to proportionally control the position of an end-effector. Previously, we showed that users were able to accurately and precisely perform a virtual target acquisition task using sonomyography. In this work, we investigate the time course of the control trajectories derived from sonomyography. We show that the time course of the sonomyography-derived trajectories that users take to reach virtual targets reflect the trajectories shown to be typical for kinematic characteristics observed in biological limbs. Specifically, during a target acquisition task, the velocity profiles followed a minimum jerk trajectory shown for point-to-point arm reaching movements, with similar time to target. In addition, the trajectories based on ultrasound imaging result in a systematic delay and scaling of peak movement velocity as the movement distance increased. We believe this is the first evaluation of similarities in control policies in coordinated movements in jointed limbs, and those based on position control signals extracted at the individual muscle level. These results have strong implications for the future development of control paradigms for assistive technologies. 

Atmospheric oxidation of monoterpenes (C₁₀H₁₆) contributes to ambient particle number and mass concentrations due, in part, to the resulting peroxy radicals undergoing auto-oxidation to low-volatility highly oxygenated molecules (HOMs). 

Abstract. We present an updated mechanism for tropospheric halogen (Cl + Br + I) chemistry in the GEOS-Chem global atmospheric chemical transportmodel and apply it to investigate halogen radical cycling and implications for tropospheric oxidants. Improved representation of HOBr heterogeneouschemistry and its pH dependence in our simulation leads to less efficient recycling and mobilization of bromine radicals and enables the model toinclude mechanistic sea salt aerosol debromination without generating excessive BrO. The resulting global mean tropospheric BrO mixingratio is 0.19 ppt (parts per trillion), lower than previous versions of GEOS-Chem. Model BrO shows variable consistency and biases in comparison tosurface and aircraft observations in marine air, which are often near or below the detection limit. The model underestimates the daytimemeasurements of Cl2 and BrCl from the ATom aircraft campaign over the Pacific and Atlantic, which if correct would imply a very largemissing primary source of chlorine radicals. Model IO is highest in the marine boundary layer and uniform in the free troposphere, with a globalmean tropospheric mixing ratio of 0.08 ppt, and shows consistency with surface and aircraft observations. The modeled global meantropospheric concentration of Cl atoms is 630 cm−3, contributing 0.8 % of the global oxidation of methane, 14 % of ethane,8 % of propane, and 7 % of higher alkanes. Halogen chemistry decreases the global tropospheric burden of ozone by 11 %,NOx by 6 %, and OH by 4 %. Most of the ozone decrease is driven by iodine-catalyzed loss. The resulting GEOS-Chem ozonesimulation is unbiased in the Southern Hemisphere but too low in the Northern Hemisphere. 

Abstract. We present a comprehensive simulation of tropospheric chlorinewithin the GEOS-Chem global 3-D model of oxidant–aerosol–halogen atmosphericchemistry. The simulation includes explicit accounting of chloridemobilization from sea salt aerosol by acid displacement of HCl and by otherheterogeneous processes. Additional small sources of tropospheric chlorine(combustion, organochlorines, transport from stratosphere) are also included.Reactive gas-phase chlorine Cl*, including Cl, ClO, Cl2, BrCl, ICl,HOCl, ClNO3, ClNO2, and minor species, is produced by theHCl+OH reaction and by heterogeneous conversion of sea salt aerosolchloride to BrCl, ClNO2, Cl2, and ICl. The modelsuccessfully simulates the observed mixing ratios of HCl in marine air(highest at northern midlatitudes) and the associated HNO3decrease from acid displacement. It captures the high ClNO2 mixingratios observed in continental surface air at night and attributes thechlorine to HCl volatilized from sea salt aerosol and transported inlandfollowing uptake by fine aerosol. The model successfully simulates thevertical profiles of HCl measured from aircraft, where enhancements in thecontinental boundary layer can again be largely explained by transport inlandof the marine source. It does not reproduce the boundary layer Cl2mixing ratios measured in the WINTER aircraft campaign (1–5 ppt in thedaytime, low at night); the model is too high at night, which could be due touncertainty in the rate of the ClNO2+Cl- reaction, but we haveno explanation for the high observed Cl2 in daytime. The globalmean tropospheric concentration of Cl atoms in the model is 620 cm−3and contributes 1.0 % of the global oxidation of methane, 20 % ofethane, 14 % of propane, and 4 % of methanol. Chlorine chemistryincreases global mean tropospheric BrO by 85 %, mainly through theHOBr+Cl- reaction, and decreases global burdens of troposphericozone by 7 % and OH by 3 % through the associated bromine radicalchemistry. ClNO2 chemistry drives increases in ozone of up to8 ppb over polluted continents in winter. 

The evolution of organic aerosol (OA) and brown carbon (BrC) in wildfire plumes, including the relative contributions of primary versus secondary sources, has been uncertain in part because of limited knowledge of the precursor emissions and the chemical environment of smoke plumes. We made airborne measurements of a suite of reactive trace gases, particle composition, and optical properties in fresh western US wildfire smoke in July through August 2018. We use these observations to quantify primary versus secondary sources of biomass-burning OA (BBPOA versus BBSOA) and BrC in wildfire plumes. When a daytime wildfire plume dilutes by a factor of 5 to 10, we estimate that up to one-third of the primary OA has evaporated and subsequently reacted to form BBSOA with near unit yield. The reactions of measured BBSOA precursors contribute only 13 ± 3% of the total BBSOA source, with evaporated BBPOA comprising the rest. We find that oxidation of phenolic compounds contributes the majority of BBSOA from emitted vapors. The corresponding particulate nitrophenolic compounds are estimated to explain 29 ± 15% of average BrC light absorption at 405 nm (BrC Abs₄₀₅) measured in the first few hours of plume evolution, despite accounting for just 4 ± 2% of average OA mass. These measurements provide quantitative constraints on the role of dilution-driven evaporation of OA and subsequent radical-driven oxidation on the fate of biomass-burning OA and BrC in daytime wildfire plumes and point to the need to understand how processing of nighttime emissions differs. 

Abstract. Airborne and ground-based measurements of aerosol concentrations, chemicalcomposition, and gas-phase precursors were obtained in three valleys innorthern Utah (USA). The measurements were part of the Utah Winter FineParticulate Study (UWFPS) that took place in January–February 2017. Totalaerosol mass concentrations of PM₁ were measured from a Twin Otteraircraft, with an aerosol mass spectrometer (AMS). PM₁ concentrationsranged from less than 2µgm⁻³ during clean periods to over100µgm⁻³ during the most polluted episodes, consistent withPM_2.5 total mass concentrations measured concurrently at groundsites. Across the entire region, increases in total aerosol mass above∼2µgm⁻³ were associated with increases in theammonium nitrate mass fraction, clearly indicating that the highest aerosolmass loadings in the region were predominantly attributable to an increase inammonium nitrate. The chemical composition was regionally homogenous fortotal aerosol mass concentrations above 17.5µgm⁻³, with 74±5% (average±standard deviation) ammonium nitrate, 18±3%organic material, 6±3% ammonium sulfate, and 2±2%ammonium chloride. Vertical profiles of aerosol mass and volume in the regionshowed variable concentrations with height in the polluted boundary layer.Higher average mass concentrations were observed within the first few hundredmeters above ground level in all three valleys during pollution episodes. Gas-phase measurements of nitric acid (HNO₃) and ammonia (NH₃) duringthe pollution episodes revealed that in the Cache and Utah valleys, partitioningof inorganic semi-volatiles to the aerosol phase was usually limited by theamount of gas-phase nitric acid, with NH₃ being in excess. The inorganicspecies were compared with the ISORROPIA thermodynamic model. Total inorganicaerosol mass concentrations were calculated for various decreases in totalnitrate and total ammonium. For pollution episodes, our simulations of a50% decrease in total nitrate lead to a 46±3% decrease in totalPM₁ mass. A simulated 50% decrease in total ammonium leads to a36±17%µgm⁻³ decrease in total PM₁ mass, over the entirearea of the study. Despite some differences among locations, ourresults showed a higher sensitivity to decreasing nitric acid concentrationsand the importance of ammonia at the lowest total nitrate conditions. In theSalt Lake Valley, both HNO₃ and NH₃ concentrations controlledaerosol formation.