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  1. Beard, Daniel A (Ed.)
    The geometry of the blood vessel wall plays a regulatory role on the motion of red blood cells (RBCs). The overall topography of the vessel wall depends on many features, among which the endothelial lining of the endothelial surface layer (ESL) is an important one. The endothelial lining of vessel walls presents a large surface area for exchanging materials between blood and tissues. The ESL plays a critical role in regulating vascular permeability, hindering leukocyte adhesion as well as inhibiting coagulation during inflammation. Changes in the ESL structure are believed to cause vascular hyperpermeability and entrap immune cells during sepsis, which could significantly alter the vessel wall geometry and disturb interactions between RBCs and the vessel wall, including the wall-induced migration of RBCs and the thickening of a cell-free layer. To investigate the influence of the vessel wall geometry particularly changed by the ESL under various pathological conditions, such as sepsis, on the motion of RBCs, we developed two models to represent the ESL using the immersed boundary method in two dimensions. In particular, we used simulations to study how the lift force and drag force on a RBC near the vessel wall vary with different wall thickness, spatial variation,more »and permeability associated with changes in the vessel wall geometry. We find that the spatial variation of the wall has a significant effect on the wall-induced migration of the RBC for a high permeability, and that the wall-induced migration is significantly inhibited as the vessel diameter is increased.« less
    Free, publicly-accessible full text available July 17, 2024
  2. Free, publicly-accessible full text available April 1, 2024
  3. Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward amore »single taxon.« less
    Free, publicly-accessible full text available April 1, 2024
  4. Free, publicly-accessible full text available January 1, 2024
  5. Stewart, Frank J. (Ed.)
    ABSTRACT A nearly complete genome of an uncultured Mollicutes sp. was obtained from the metagenome of the gut of Limacina rangii (open-ocean snail), an important grazer and prey for higher trophic animals along the rapidly warming region of the western Antarctic Peninsula.
    Free, publicly-accessible full text available December 15, 2023
  6. Free, publicly-accessible full text available January 1, 2024
  7. Key Points The external radiative forcing is the primary driver of the 1979–2013 warming for April–September, with varying decadal warming rates The interdecadal Pacific and Atlantic multidecadal variability intensify/dampen the warming when transitioning to positive/negative phase The combined effects of these factors reproduce the observed varied pace of decadal Arctic troposphere warming during 1979–2013
    Free, publicly-accessible full text available December 16, 2023
  8. Mackelprang, Rachel (Ed.)
    ABSTRACT Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in nonmesophilic organisms, however, is currently missing. In this study, thermodynamically constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella psychrophila WP2, under suboptimal (4°C), optimal (15°C), and supraoptimal (20°C) growth temperatures. The models were calibrated with experimentally determined growth rates of WP2. Gibbs free energy change of reactions (Δ r G ′), metabolic fluxes, and metabolite concentrations were predicted using random simulations to characterize temperature-dependent changes in the metabolism. The modeling revealed the highest metabolic efficiency at the optimal temperature, and it suggested distinct patterns of ATP production and consumption that could lead to lower metabolic efficiency under suboptimal or supraoptimal temperatures. The modeling also predicted rearrangement of fluxes through multiple metabolic pathways, including the glycolysis pathway, Entner-Doudoroff pathway, tricarboxylic acid (TCA) cycle, and electron transport system, and these predictions were corroborated through comparisons to WP2 transcriptomes. Furthermore, predictions of metabolite concentrations revealed the potential conservation of reducing equivalents and ATP in the suboptimal temperature, consistent with experimental observations from other psychrophiles. Taken together, the WP2 models providedmore »mechanistic insights into the metabolism of a psychrophile in response to different temperatures. IMPORTANCE Metabolic flexibility is a central component of any organism’s ability to survive and adapt to changes in environmental conditions. This study represents the first application of thermodynamically constrained genome-scale models in simulating the metabolic responses of a deep-sea psychrophilic bacterium to various temperatures. The models predicted differences in metabolic efficiency that were attributed to changes in metabolic pathway utilization and metabolite concentration during growth under optimal and nonoptimal temperatures. Experimental growth measurements were used for model calibration, and temperature-dependent transcriptomic changes corroborated the model-predicted rearrangement of metabolic fluxes. Overall, this study highlights the utility of modeling approaches in studying the temperature-driven metabolic responses of an extremophilic organism.« less
  9. Abstract. The main drivers of the continental Northern Hemisphere snow cover are investigated in the 1979–2014 period. Four observational datasets are usedas are two large multi-model ensembles of atmosphere-only simulations with prescribed sea surface temperature (SST) and sea ice concentration (SIC). Afirst ensemble uses observed interannually varying SST and SIC conditions for 1979–2014, while a second ensemble is identical except for SIC witha repeated climatological cycle used. SST and external forcing typically explain 10 % to 25 % of the snow cover variance in modelsimulations, with a dominant forcing from the tropical and North Pacific SST during this period. In terms of the climate influence of the snow coveranomalies, both observations and models show no robust links between the November and April snow cover variability and the atmospheric circulation1 month later. On the other hand, the first mode of Eurasian snow cover variability in January, with more extended snow over western Eurasia, isfound to precede an atmospheric circulation pattern by 1 month, similar to a negative Arctic oscillation (AO). A decomposition of the variabilityin the model simulations shows that this relationship is mainly due to internal climate variability. Detailed outputs from one of the modelsindicate that the western Eurasia snow cover anomalies are precededmore »by a negative AO phase accompanied by a Ural blocking pattern and astratospheric polar vortex weakening. The link between the AO and the snow cover variability is strongly related to the concomitant role of thestratospheric polar vortex, with the Eurasian snow cover acting as a positive feedback for the AO variability in winter. No robust influence of theSIC variability is found, as the sea ice loss in these simulations only drives an insignificant fraction of the snow cover anomalies, with fewagreements among models.« less
    Free, publicly-accessible full text available January 1, 2024
  10. Abstract Objective . Neural decoding is an important tool in neural engineering and neural data analysis. Of various machine learning algorithms adopted for neural decoding, the recently introduced deep learning is promising to excel. Therefore, we sought to apply deep learning to decode movement trajectories from the activity of motor cortical neurons. Approach . In this paper, we assessed the performance of deep learning methods in three different decoding schemes, concurrent, time-delay, and spatiotemporal. In the concurrent decoding scheme where the input to the network is the neural activity coincidental to the movement, deep learning networks including artificial neural network (ANN) and long-short term memory (LSTM) were applied to decode movement and compared with traditional machine learning algorithms. Both ANN and LSTM were further evaluated in the time-delay decoding scheme in which temporal delays are allowed between neural signals and movements. Lastly, in the spatiotemporal decoding scheme, we trained convolutional neural network (CNN) to extract movement information from images representing the spatial arrangement of neurons, their activity, and connectomes (i.e. the relative strengths of connectivity between neurons) and combined CNN and ANN to develop a hybrid spatiotemporal network. To reveal the input features of the CNN in the hybrid networkmore »that deep learning discovered for movement decoding, we performed a sensitivity analysis and identified specific regions in the spatial domain. Main results . Deep learning networks (ANN and LSTM) outperformed traditional machine learning algorithms in the concurrent decoding scheme. The results of ANN and LSTM in the time-delay decoding scheme showed that including neural data from time points preceding movement enabled decoders to perform more robustly when the temporal relationship between the neural activity and movement dynamically changes over time. In the spatiotemporal decoding scheme, the hybrid spatiotemporal network containing the concurrent ANN decoder outperformed single-network concurrent decoders. Significance . Taken together, our study demonstrates that deep learning could become a robust and effective method for the neural decoding of behavior.« less