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Recent Submissions

  • Antibiotics reduce bacterial load in Exaiptasia diaphana, but biofilms hinder its development as a gnotobiotic coral model

    Hartman, Leon M.; Blackall, Linda L.; van Oppen, Madeleine J. H. (Access Microbiology, Microbiology Society, 2022-01-17) [Article]
    Coral reefs are declining due to anthropogenic disturbances, including climate change. Therefore, improving our understanding of coral ecosystems is vital, and the influence of bacteria on coral health has attracted particular interest. However, a gnotobiotic coral model that could enhance studies of coral–bacteria interactions is absent. To address this gap, we tested the ability of treatment with seven antibiotics for 3 weeks to deplete bacteria in Exaiptasia diaphana, a sea anemone widely used as a coral model. Digital droplet PCR (ddPCR) targeting anemone Ef1-α and bacterial 16S rRNA genes was used to quantify bacterial load, which was found to decrease six-fold. However, metabarcoding of bacterial 16S rRNA genes showed that alpha and beta diversity of the anemone-associated bacterial communities increased significantly. Therefore, gnotobiotic E. diaphana with simplified, uniform bacterial communities were not generated, with biofilm formation in the culture vessels most likely impeding efforts to eliminate bacteria. Despite this outcome, our work will inform future efforts to create a much needed gnotobiotic coral model.
  • Giant valley-polarized spin splittings in magnetized Janus Pt dichalcogenides

    Sattar, Shahid; Larsson, J. Andreas; Canali, C. M.; Roche, Stephan; Garcia, Jose H. (Physical Review B, American Physical Society (APS), 2022-01-07) [Article]
  • Rare-Earth Doping in Nanostructured Inorganic Materials

    Zheng, Bingzhu; Fan, Jingyue; Chen, Bing; Qin, Xian; Wang, Juan; Wang, Feng; Deng, Renren; Liu, Xiaogang (Chemical Reviews, American Chemical Society (ACS), 2022-01-06) [Article]
  • Rumen Inoculum Enhances Cathode Performance in Single-Chamber Air-Cathode Microbial Fuel Cells

    Vargas, Ignacio T.; Tapia, Natalia; Regan, John M. (Materials, MDPI AG, 2022-01-05) [Article]
    During the last decade, bioprospecting for electrochemically active bacteria has included the search for new sources of inoculum for microbial fuel cells (MFCs). However, concerning power and current production, a Geobacter-dominated mixed microbial community derived from a wastewater inoculum remains the standard. On the other hand, cathode performance is still one of the main limitations for MFCs, and the enrichment of a beneficial cathodic biofilm emerges as an alternative to increase its performance. Glucose-fed air-cathode reactors inoculated with a rumen-fluid enrichment and wastewater showed higher power densities and soluble chemical oxygen demand (sCOD) removal (Pmax = 824.5 mWm−2; ΔsCOD = 96.1%) than reactors inoculated only with wastewater (Pmax = 634.1 mWm−2; ΔsCOD = 91.7%). Identical anode but different cathode potentials suggest that differences in performance were due to the cathode. Pyrosequencing analysis showed no significant differences between the anodic community structures derived from both inocula but increased relative abundances of Azoarcus and Victivallis species in the cathodic rumen enrichment. Results suggest that this rarely used inoculum for single-chamber MFCs contributed to cathodic biofilm improvements with no anodic biofilm effects.
  • Reinterpretation and Extension of Entropy Correction Terms for Residual Distribution and Discontinuous Galerkin Schemes: Application to Structure Preserving Discretization

    Abgrall, Rémi; Öffner, Philipp; Ranocha, Hendrik (Journal of Computational Physics, Elsevier BV, 2022-01) [Article]
    For the general class of residual distribution (RD) schemes, including many finite element (such as continuous/discontinuous Galerkin) and flux reconstruction methods, an approach to construct entropy conservative/ dissipative semidiscretizations by adding suitable correction terms has been proposed by Abgrall ((2018) [1]). In this work, the correction terms are characterized as solutions of certain optimization problems and are adapted to the SBP-SAT framework, focusing on discontinuous Galerkin methods. Novel generalizations to entropy inequalities, multiple constraints, and kinetic energy preservation for the Euler equations are developed and tested in numerical experiments. For all of these optimization problems, explicit solutions are provided. Additionally, the correction approach is applied for the first time to obtain a fully discrete entropy conservative/dissipative RD scheme. Here, the application of the deferred correction (DeC) method for the time integration is essential. This paper can be seen as describing a systematic method to construct structure preserving discretization, at least for the considered example.
  • Dynamic Persistent Homology for Brain Networks via Wasserstein Graph Clustering

    Chung, Moo K.; Huang, Shih-Gu; Carroll, Ian C.; Calhoun, Vince D.; Goldsmith, H. Hill (arXiv, 2022-01-01) [Preprint]
    We present the novel Wasserstein graph clustering for dynamically changing graphs. The Wasserstein clustering penalizes the topological discrepancy between graphs. The Wasserstein clustering is shown to outperform the widely used k-means clustering. The method applied in more accurate determination of the state spaces of dynamically changing functional brain networks.
  • The effect of side chain engineering on conjugated polymers in organic electrochemical transistors for bioelectronic applications

    He, Yifei; Kukhta, Nadzeya A.; Marks, Adam; Luscombe, Christine K. (Journal of Materials Chemistry C, Royal Society of Chemistry (RSC), 2022) [Article]
    The versatile synthetic side chain toolbox assists in tuning the OECT parameters by controlling material properties of organic mixed conductors. In this review we critically summarise and evaluate various side chains used throughout OECT materials.
  • Host-cell recognition through Cs-GRP78 is enhanced in the new Omicron variant of SARS-CoV-2, in silico structural point of view

    Elfiky, Abdo A.; Ibrahim, Ibrahim M (Journal of Infection, Elsevier BV, 2022-01) [Article]
  • Hydrotreating and oxidative desulfurization of heavy fuel oil into low sulfur marine fuel over dual function NiMo/γ–Al2O3 catalyst

    Vedachalam, Sundaramurthy; Dalai, Ajay K. (Catalysis Today, Elsevier BV, 2022-01) [Article]
  • Using Neural Networks to Perform Rapid High-Dimensional Kilonova Parameter Inference

    Almualla, Mouza; Ning, Yuhong; Bulla, Mattia; Dietrich, Tim; Coughlin, Michael W.; Guessoum, Nidhal (arXiv, 2021-12-31) [Preprint]
    On the 17th of August, 2017 came the simultaneous detections of GW170817, a gravitational wave that originated from the coalescence of two neutron stars, along with the gamma-ray burst GRB170817A, and the kilonova counterpart AT2017gfo. Since then, there has been much excitement surrounding the study of neutron star mergers, both observationally, using a variety of tools, and theoretically, with the development of complex models describing the gravitational-wave and electromagnetic signals. In this work, we improve upon our pipeline to infer kilonova properties from observed light-curves by employing a Neural-Network framework that reduces execution time and handles much larger simulation sets than previously possible. In particular, we use the radiative transfer code POSSIS to construct 5-dimensional kilonova grids where we employ different functional forms for the angular dependence of the dynamical ejecta component. We find that incorporating an angular dependence improves the fit to the AT2017gfo light-curves by up to ~50% when quantified in terms of the weighted Mean Square Error.
  • Virtual Screening of TADF Emitters for Single-Layer OLEDs

    Lin, Kun-Han; Wetzelaer, Gert-Jan A. H.; Blom, Paul W. M.; Andrienko, Denis (Frontiers in Chemistry, Frontiers Media SA, 2021-12-16) [Article]
    Thermally-activated delayed fluorescence (TADF) is a concept which helps to harvest triplet excitations, boosting the efficiency of an organic light-emitting diode. TADF can be observed in molecules with spatially separated donor and acceptor groups with a reduced triplet-singlet energy level splitting. TADF materials with balanced electron and hole transport are attractive for realizing efficient single-layer organic light emitting diodes, greatly simplifying their manufacturing and improving their stability. Our goal here is to computationally screen such materials and provide a comprehensive database of compounds with a range of emission wavelengths, ionization energies, and electron affinities.
  • Molecular Design Strategies toward Improvement of Charge Injection and Ionic Conduction in Organic Mixed Ionic–Electronic Conductors for Organic Electrochemical Transistors

    Kukhta, Nadzeya A.; Marks, Adam; Luscombe, Christine K. (Chemical Reviews, American Chemical Society (ACS), 2021-12-13) [Article]
    Expanding the toolbox of the biology and electronics mutual conjunction is a primary aim of bioelectronics. The organic electrochemical transistor (OECT) has undeniably become a predominant device for mixed conduction materials, offering impressive transconduction properties alongside a relatively simple device architecture. In this review, we focus on the discussion of recent material developments in the area of mixed conductors for bioelectronic applications by means of thorough structure–property investigation and analysis of current challenges. Fundamental operation principles of the OECT are revisited, and characterization methods are highlighted. Current bioelectronic applications of organic mixed ionic–electronic conductors (OMIECs) are underlined. Challenges in the performance and operational stability of OECT channel materials as well as potential strategies for mitigating them, are discussed. This is further expanded to sketch a synopsis of the history of mixed conduction materials for both p- and n-type channel operation, detailing the synthetic challenges and milestones which have been overcome to frequently produce higher performing OECT devices. The cumulative work of multiple research groups is summarized, and synthetic design strategies are extracted to present a series of design principles that can be utilized to drive figure-of-merit performance values even further for future OMIEC materials.
  • Asymmetrical carbon nanotubes exhibit opposing thermal rectification behaviors under different heat baths

    Chen, Wei-Jen; Feng, Biao; Shao, Cheng; Yang, Jin; Fan, Liwu; Ong, Wee-Liat; Chang, I-Ling (International Journal of Heat and Mass Transfer, Elsevier BV, 2021-12-11) [Article]
    Asymmetrical nanostructures are leading candidates to create efficient thermal rectifiers critical in thermal management and energy conversion systems. Due to their nanoscale size and inherent non-equilibrium nature, their working principles are commonly elucidated through non-equilibrium molecular dynamic simulations. Using asymmetrical carbon nanotubes, the resulting thermal rectification under different heat baths is found to differ in magnitude and direction. We find that nanotubes with the Langevin baths have a higher thermal conductivity in one heat flow direction due to the low-frequency phonons, resulting in a positive rectification. On the other hand, nanotubes with the Nose-Hoover baths show similar thermal conductivity contributions in both heat flow directions across the whole phonon frequency range, culminating in a negative rectification. Our work highlights how asymmetrical carbon nanostructures can rectify heat flow differently under different heat baths and provides strong evidence for the need to consider their non-equilibrium phonon spectrum before analyzing any associated nanoscale thermal transport phenomena.
  • Magnetic Sensitivity Distribution of Hall Devices in Antiferromagnetic Switching Experiments

    Schreiber, F.; Meer, H.; Schmitt, C.; Ramos, R.; Saitoh, E.; Baldrati, L.; Kläui, Mathias (Physical Review Applied, American Physical Society (APS), 2021-12-09) [Article]
    We analyze the complex impact of the local magnetic spin texture on the transverse Hall-type voltage in device structures utilized to measure magnetoresistance effects. We find a highly localized and asymmetric magnetic sensitivity in the eight-terminal geometries that are frequently used in current-induced switching experiments, for instance, to probe antiferromagnetic materials. Using current-induced switching of antiferromagnetic NiO/Pt as an example, we estimate the change in the spin Hall magnetoresistance signal associated with switching events based on the domain-switching patterns observed via direct imaging. This estimate correlates with the actual electrical data after subtraction of a nonmagnetic contribution. Here, the consistency of the correlation across three measurement geometries with fundamentally different switching patterns strongly indicates a magnetic origin of the measured and analyzed electrical signals.
  • Exploring Sentiment as a Potential Indicator of Bias in Disease Ontologies

    Slater, Luke T.; Williams, John A.; Schofield, Paul N.; Gkoutos, Georgios V. (IEEE, 2021-12-09) [Conference Paper]
    Ontologies are fundamental tools for the organisation and analysis of biomedical data. One of their roles is as controlled domain vocabularies, providing standardised language and categorisation for relevant domain concepts. As such, ontologies frequently include a wealth of natural language metadata including labels and definitions. Since these metadata are usually created by humans, there exists the possibility that conscious and unconscious biases may be reflected in them. Moreover, humans and computers engage directly with these metadata during the course of scientific practice, and therefore any biases or idiosyncrasies may influence work involving the use of these concepts. Previous work has exposed the possibility of bias in ontological representations of disease domains, however there have been no methods developed for automatic or semiautomatic guidance towards bias in ontology metadata. In this article, we develop an approach to explore sentiment analysis as a potential indicator of bias in ontology concept definitions. We evaluate its use on pairs of disease classes from MESH and Human Disease Ontology (DO), comparing and contrasting sentiment scores between them. We use these examples to identify and evaluate a number of outlying examples, relating them to existing literature. We discuss how our approach could be used to guide ontology developers towards outlying and potentially biased language, forming a tool that could be used to evaluate and improve normalisation of ontology metadata. We also discuss the applicability and appropriateness of general-purpose sentiment analysis applied to biomedical texts, and potential influences of bias on computational analysis, in the context of our results.
  • Chemical and Sooting Structures of Counterflow Diffusion Flames of Butanol Isomers: An Experimental and Modeling Study

    Zhang, Jizhou; Yan, Fuwu; Jiang, Peng; Zhou, Mengxiang; Wang, Yu (Combustion Science and Technology, Informa UK Limited, 2021-12-08) [Article]
    This work reports an experimental and numerical analysis on the sooting characteristics of butanol isomers. Light extinction and gas chromatography were used to measure soot and gas-phase species, respectively. Kinetic analysis of the tested flames was performed with detailed gas-phase mechanism and a sectional soot model. The present work aims to provide an understanding on the effects of butanol isomeric structures on sooting tendencies. For a comprehensive analysis, flames of both neat butanol fuels and butanol/hydrocarbon mixtures were studied. The results showed that the relative ranking of sooting tendencies among the butanol isomers were similar in neat butanol flames and in butanol-doped ethylene flames. In addition, we show that a small amount of butanol addition in ethylene flame enhanced soot formation. It was found that different isomeric structures mainly affected the formation of C3H3, which led to the different concentrations of important aromatic soot precursors. In the butanol-doped ethylene flames, the blending of the four butanol isomers increased the number of C3H3 formation pathways, which in turn significantly increased the production of benzene. Structural effects explaining for the differences in the sooting tendencies of the four butanol isomers in neat butanol flames and ethylene/butanol flames were found to be the same.
  • Machine Learning Prediction of Metal-Organic Framework Guest Accessibility from Linker and Metal Chemistry

    Pétuya, Rémi; Durdy, Samantha; Antypov, Dmytro; Gaultois, Michael W; Berry, Neil G; Darling, George R; Katsoulidis, Alexandros P; Dyer, Matthew S; Rosseinsky, Matthew J. (Angewandte Chemie, Wiley, 2021-12-08) [Article]
    The choice of metal and linker together define the structure and therefore the guest accessibility of a metal-organic framework (MOF), but the large number of possible metal-linker combinations makes the selection of components for synthesis challenging. We predict the guest accessibility of a MOF with 80.5% certainty based solely on the identity of these two components as chosen by the experimentalist, by decomposing reported experimental three-dimensional MOF structures in the Cambridge Structural Database into metal and linker and then learning the connection between the components’ chemistry and the MOF porosity. Pore dimensions of the guest-accessible space are classified into four ranges with three sequential models. Both the dataset and the predictive models are available to download and offer simple guidance in prioritization of the choice of the components for exploratory MOF synthesis for separation and catalysis based on guest accessibility considerations.
  • Observable variations in human sex ratio at birth

    Long, Yanan; Chen, Qi; Larsson, Henrik; Rzhetsky, Andrey (PLOS Computational Biology, Public Library of Science (PLoS), 2021-12-02) [Article]
    The human sex ratio at birth (SRB), defined as the ratio between the number of newborn boys to the total number of newborns, is typically slightly greater than 1/2 (more boys than girls) and tends to vary across different geographical regions and time periods. In this large-scale study, we sought to validate previously-reported associations and test new hypotheses using statistical analysis of two very large datasets incorporating electronic medical records (EMRs). One of the datasets represents over half (∼ 150 million) of the US population for over 8 years (IBM Watson Health MarketScan insurance claims) while another covers the entire Swedish population (∼ 9 million) for over 30 years (the Swedish National Patient Register). After testing more than 100 hypotheses, we showed that neither dataset supported models in which the SRB changed seasonally or in response to variations in ambient temperature. However, increased levels of a diverse array of air and water pollutants, were associated with lower SRBs, including increased levels of industrial and agricultural activity, which served as proxies for water pollution. Moreover, some exogenous factors generally considered to be environmental toxins turned out to induce higher SRBs. Finally, we identified new factors with signals for either higher or lower SRBs. In all cases, the effect sizes were modest but highly statistically significant owing to the large sizes of the two datasets. We suggest that while it was unlikely that the associations have arisen from sex-specific selection mechanisms, they are still useful for the purpose of public health surveillance if they can be corroborated by empirical evidences.
  • The Original Design Principles of the Y-Series Nonfullerene Acceptors, from Y1 to Y6

    Yang, Yang (ACS Nano, American Chemical Society (ACS), 2021-12-02) [Article]
    Since 2019, the power conversion efficiencies of organic photovoltaics have risen sharply from ∼13% to ∼19% because of the newly invented Y-series nonfullerene acceptors (Y-NFAs; mainly Y1 to Y6). However, comprehensive insights into the design principles behind these molecules have not been fully elucidated or explained in the literature. In this Perspective, I share our original insights into the understanding, prediction, and design principles of Y1 to Y6 and offer a brief history behind the discoveries of the Y-NFAs.
  • Effects of sour oilfield produced water on direct contact membrane distillation systems

    Marques, Debora Salomon; Raynel, Guillaume; Al-Saeed, Duaa; Al-Thabet, Mohammad (Materials Chemistry and Physics, Elsevier BV, 2021-12) [Article]
    A fully corrosion-resistant direct contact membrane distillation system has been built to test the viability of desalinating oil field produced water using fluorinated polyoxadiazole (F-POD) hollow fiber membranes. This highly hydrophobic membrane material was designed to endure the harsh conditions of Arabian oil field produced waters. These waters have high salinity, and the presence of dissolved organic compounds and gases - including hydrogen sulfide (H2S). The hazards associated with H2S require special safety controls. In this paper, the desalination of sour produced water with membrane distillation is compared with Gulf Sea water from the East Coast of Saudi Arabia. The effect of the produced water on the efficiency of the membrane distillation was evaluated in terms of distillation flux and salt rejection. The high salinity, the presence of H2S, and volatile organic compounds (VOC) are found to negatively impact the flux and salt rejection.

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