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Recent Submissions

  • Exploring Highly Functionalized Tetrahydropyridine as a Dual Inhibitor of Monoamine Oxidase A and B: Synthesis, Structural Analysis, Single Crystal XRD, Supramolecular Assembly Exploration by Hirshfeld Surface Analysis, and Computational Studies

    Khan, Bilal Ahmad; Ashfaq, Muhammad; Muhammad, S.; Munawar, Khurram Shahzad; Tahir, Muhammad Nawaz; Al-Sehemi, A. G.; Alarfaji, Saleh S. (ACS Omega, American Chemical Society (ACS), 2022-08-11) [Article]
    Ethyl 4-(4-fluorophenylamino)-2,6-bis(4-(trifluoromethyl)phenyl)-1-(4-fluoro-phenyl)-1,2,5,6-tetrahydropyridine-3-carboxylate (FTEAA) has been synthesized efficiently in an iodine-catalyzed five-component reaction of 4-fluoroaniline, 4-trifluoromethyl benzaldehyde, and ethyl acetoacetate in methanol at 55 °C for 12 h. Various spectro-analytical techniques such as 1H and 13C NMR and Fourier-transform infrared spectroscopy have validated the structure of FTEAA. Further confirmation of the structure of FTEAA has been established on the basis of single-crystal X-ray diffraction analysis. The supramolecular assembly of FTEAA in terms of strong and comparatively weak noncovalent interactions is fully investigated by Hirshfeld surface analysis, the interaction energy between pairs of molecules, and energy frameworks. The void analysis is conducted to explore the strength and stability of the crystal structure. Furthermore, molecular docking analysis was computationally performed to see the potential intermolecular interactions between the selected proteins and FTEAA. The binding interaction energies are found to be −8.8 and −9.6 kcal/mol for the proteins MAO-B (PDB ID: 2V5Z) and MAO-A (PDB ID: 2Z5X), respectively. These reasonably good binding energies (more negative values) indicate the efficient associations between the FTEAA and target proteins. The proteins and FTEAA were also analyzed for intermolecular interactions. FTEAA and proteins interact in a variety of ways, like conventional hydrogen bonds, carbon–hydrogen bonds, alkyl, π-alkyl, and halide interactions.
  • Millennia-old coral holobiont DNA provides insight into future adaptive trajectories

    Scott, Carly B.; Cárdenas, Anny; Mah, Matthew; Narasimhan, Vagheesh M.; Rohland, Nadin; Toth, Lauren T.; Voolstra, Christian R.; Reich, David; Matz, Mikhail V. (Molecular Ecology, Wiley, 2022-08-09) [Article]
    Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we leverage aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE - 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence ancient DNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.
  • High-resolution soil moisture data reveal complex multi-scale spatial variability across the United States

    Vergopolan, Noemi; Sheffield, Justin; Chaney, Nathaniel W.; Pan, Ming; Beck, Hylke E.; Ferguson, Craig R.; Torres-Rojas, Laura; Eigenbrod, Felix; Crow, Wade; Wood, Eric F. (Geophysical Research Letters, American Geophysical Union (AGU), 2022-08-04) [Article]
    Soil moisture (SM) spatiotemporal variability critically influences water resources, agriculture, and climate. However, besides site-specific studies, little is known about how SM varies locally (1–100-m scale). Consequently, quantifying the SM variability and its impact on the Earth system remains a long-standing challenge in hydrology. We reveal the striking variability of local-scale SM across the United States using SMAP-HydroBlocks — a novel satellite-based surface SM dataset at 30-m resolution. Results show how the complex interplay of SM with landscape characteristics and hydroclimate is primarily driven by local variations in soil properties. This local-scale complexity yields a remarkable and unique multi-scale behavior at each location. However, very little of this complexity persists across spatial scales. Experiments reveal that on average 48% and up to 80% of the SM spatial information is lost at the 1-km resolution, with complete loss expected at the scale of current state-of-the-art SM monitoring and modeling systems (1–25 km).
  • Highly Stable Lead-Free Perovskite Single Crystals with NIR Emission Beyond 1100 nm

    Liu, Zhuang; Qin, Xian; Chen, Qihao; Chen, Qiushui; Jing, Yuhang; Zhou, Zhonghao; Zhao, Yong Sheng; Chen, Jingsheng; Liu, Xiaogang (Advanced Optical Materials, Wiley, 2022-08-04) [Article]
    Materials that emit in the near-infrared (NIR) region are at the forefront of both research and industry, mainly due to their wide applications in national security, nondestructive bioimaging, long-wave communications, and photothermal conversion for medical care. As a key member of the luminescent materials family, metal halide perovskites have been intensively demonstrated to emit light in ultraviolet and visible regions. However, NIR-emitting perovskites suffer from severe limitations, such as low photoluminescence quantum yield and poor chemical/optical stability, thereby preventing them from practical applications. Herein, the synthesis and growth of Cs2MoCl6 and Cs2WCl6 perovskite single crystals with ultrahigh chemical and optical resistance to heat, moisture, polar solvents, and high-energy radiation is reported. Upon ultraviolet or blue excitation, these lead-free single crystals emit light beyond 1100 nm, the longest wavelength ever reported for perovskite hosts. Mechanistic studies indicate that self-trapped excitons are responsible for the NIR emission. The authors fabricate optoelectronic devices using these single crystals and demonstrate their broad applications in noninvasive palm vein imaging, night vision, and nondestructive food analysis. These results may stimulate research in the development of high-efficiency NIR perovskite phosphors for fast, accurate biometric identification and food inspection.
  • Variations in size specific effective dose with patient stature and beam width for kV cone beam CT imaging in radiotherapy

    Martin, Colin John; Abuhaimed, Abdullah (Journal of Radiological Protection, IOP Publishing, 2022-08-02) [Article]
    Facilities now available on linear accelerators for external beam radiotherapy enable radiation fields to be conformed to shapes of tumours with a high level of precision. However, in order for the treatment delivered to take advantage of this, the patient must be positioned on the couch with the same degree of accuracy. Kilovoltage cone beam computed tomography (CBCT) systems are now incorporated into radiotherapy linear accelerators to allow imaging to be performed at the time of treatment, and image guided radiation therapy (IGRT) is now standard in most radiotherapy departments throughout the world. However, because doses from imaging are much lower than therapy doses, less effort has been put into optimising radiological protection of imaging protocols. Standard imaging protocols supplied by the equipment vendor are often used with little adaptation to statures of individual patients, and exposure factors and field sizes are frequently larger than necessary. In this study, the impact of using standard protocols for imaging anatomical phantoms of varying size from a 193 adult phantom library has been evaluated. Monte Carlo simulations were used to calculate doses for organs and tissues for each phantom, and results combined in terms of size specific effective dose (SED). Values of SED from pelvic scans ranged from 11 mSv to 22 mSv for males and 8 mSv to 18 mSv for females, and for chest scans from 3.8 mSv to 7.6 mSv for males and 4.6 mSv to 9.5 mSv for females. Analysis of the results showed that if the same exposure parameters and field sizes are used, a person who is 5 cm shorter will receive a size specific effective dose that is 3% to 10% greater, while a person who is 10 kg lighter will receive a dose that is 10% to 14% greater as compared to the average size.
  • Landslide susceptibility maps of Italy: Lesson learnt from dealing with multiple landslide types and the uneven spatial distribution of the national inventory

    Loche, Marco; Alvioli, Massimiliano; Marchesini, Ivan; Bakka, Haakon; Lombardo, Luigi (Earth-Science Reviews, Elsevier BV, 2022-07-30) [Article]
    Landslide susceptibility corresponds to the probability of landslide occurrence across a given geographic space. This probability is usually estimated by using a binary classifier which is informed of landslide presence/absence data and associated landscape characteristics. Here, we consider the Italian national landslide inventory to prepare slope-unit based landslide susceptibility maps. These maps are prepared for the eight types of mass movements existing in the inventory, (Complex, Deep Seated Gravitational Slope Deformation, Diffused Fall, Fall, Rapid Flow, Shallow, Slow Flow, Translational) and we build one susceptibility map for each type. The analysis – carried out by using a Bayesian version of a Generalized Additive Model with a multiple intercept for each Italian region – revealed that the inventory may have been compiled with different levels of detail. This would be consistent with the dataset being assembled from twenty sub–inventories, each prepared by different administrations of the Italian regions. As a result, this spatial heterogeneity may lead to biased national–scale susceptibility maps. On the basis of these considerations, we further analyzed the national database to confirm or reject the varying quality hypothesis on the basis of the model equipped with multiple regional intercepts. For each landslide type, we then tried to build unbiased susceptibility models by removing regions with a poor landslide inventory from the calibration stage, and used them only as a prediction target of a simulation routine. We analyzed the resulting eight maps finding out a congruent dominant pattern in the Alpine and Apennine sectors. The whole procedure is implemented in R–INLA. This allowed to examine fixed (linear) and random (nonlinear) effects from an interpretative standpoint and produced a full prediction equipped with an estimated uncertainty. We propose this overall modeling pipeline for any landslide datasets where a significant mapping bias may influence the susceptibility pattern over space.
  • Space-time landslide susceptibility modelling in Taiwan

    Fang, Zhice; Wang, Yi; van Westen, C.J.; Lombardo, Luigi (California Digital Library (CDL), 2022-07-27) [Preprint]
    Portraying spatiotemporal variations in landslide susceptibility patterns is crucial for landslide prevention and management. In this study, we implement a space-time modeling approach to predict the landslide susceptibility on a yearly basis across the main island of Taiwan, from 2004 to 2018. We use a Bayesian version of a binomial generalized additive model, which assumes that landslide occurrences follow a Bernoulli distribution. We generate 46,074 slope units to partition the island of Taiwan and divided the time domain into 14 annual units. The binary landslide label assigned to each slope unit and their temporal replicates come from an available landslide database, that contains an inventory for every year. We only consider new landslides or reactivations of previous mass movements in the yearly inventories. This information and its absence counterpart are regressed against a set of static and dynamic covariates. Our modeling strategy features an initial explanatory model to test the goodness-of-fit and interpret the effect of covariates. Then, five cross-validation (CV) schemes are tested to provide a full spectrum of the predictive capacity of our model. Specifically, we implement a fully randomized 10-fold CV, a spatially constrained CV, two temporal CV (a leave one year out and a sequential temporal aggregation), together with a spatio-temporal CV. We summarize the performance in each of these tests, through their pure numerical expression as well as their residual representation in space and time. Overall, our space-time model produces excellent and interpretable results. We consider this type of dynamic prediction the new direction to take to finally move away from the static view provided by traditional susceptibility models. And, we consider such analyses just a stepping stone for further improvements, the most natural of which would lead to statistical simulations for future scenarios.
  • Spatial and environmental variables structure sponge symbiont communities

    Cleary, D F R; Polónia, Ana R. M.; Swierts, Thomas; Coelho, Francisco J. R. C.; de Voogd, Nicole J.; Gomes, Newton C. M. (Molecular Ecology, Wiley, 2022-07-26) [Article]
    Understanding the maintenance and origin of beta diversity is a central topic in ecology. However, the factors that drive diversity patterns and underlying processes remain unclear, particularly for host-prokaryotic associations. Here, beta diversity patterns were studied in five prokaryotic biotopes, namely, two high microbial abundance (HMA) sponge taxa (Xestospongia spp. and Hyrtios erectus), one low microbial abundance (LMA) sponge taxon (Stylissa carteri), sediment and seawater sampled across thousands of kilometers. Using multiple regression on distance matrices (MRM), spatial (geographic distance) and environmental (sea surface temperature and chlorophyll a concentrations) variables proved significant predictors of beta diversity in all five biotopes and together explained from 54% to 82% of variation in dissimilarity of both HMA species, 27% to 43% of variation in sediment and seawater, but only 20% of variation of the LMA S. carteri. Variance partitioning was subsequently used to partition the variation into purely spatial, purely environmental and spatially-structured environmental components. The amount of variation in dissimilarity explained by the purely spatial component was lowest for S. carteri at 11% and highest for H. erectus at 55%. The purely environmental component, in turn, only explained from 0.15 to 2.83% of variation in all biotopes. In addition to spatial and environmental variables, a matrix of genetic differences between pairs of sponge individuals also proved a significant predictor of variation in prokaryotic composition of the Xestospongia species complex. We discuss the implications of these results for the HMA-LMA dichotomy and compare the MRM results with results obtained using constrained ordination and zeta diversity.
  • Multiplex Chemical Imaging Based on Broadband Stimulated Raman Scattering Microscopy

    Cadena, Alejandro De la; Vernuccio, Federico; Talone, Benedetta; Bresci, Arianna; Ceconello, Chiara; Das, Subir; Vanna, Renzo; Cerullo, Giulio; Polli, Dario (Journal of Visualized Experiments, MyJove Corporation, 2022-07-25) [Article]
    Stimulated Raman scattering (SRS) microscopy is a nonlinear optical technique for label-free chemical imaging. This analytical tool delivers chemical maps at high speed, and high spatial resolution of thin samples by directly interrogating their molecular vibrations. In its standard implementation, SRS microscopy is narrowband and forms images with only a single vibrational frequency at a time. However, this approach not only hinders the chemical specificity of SRS but also neglects the wealth of information encoded within vibrational spectra. These limitations can be overcome by broadband SRS, an implementation capable of extracting a vibrational spectrum per pixel of the image in parallel. This delivers hyperspectral data that, when coupled with chemometric analysis, maximizes the amount of information retrieved from the specimen. Thus, broadband SRS improves the chemical specificity of the system, allowing the quantitative determination of the concentration of the different constituents of a sample. Here, we report a protocol for chemical imaging with broadband SRS microscopy, based on a home-built SRS microscope operating with a custom differential multichannel-lock-in amplifier detection. It discusses the sample preparation, alignment of the SRS apparatus, and chemometric analysis. By acquiring vibrational Raman spectra, the protocol illustrates how to identify different chemical species within a mixture, determining their relative concentrations.
  • Reconfigurable beam-steerable leaky-wave antenna loaded with metamaterial apertures using liquid crystal-based delay lines

    Torabi, Elahehsadat; Erricolo, Danilo; Chen, Pai-Yen; Fuscaldo, Walter; Beccherelli, Romeo (Optics Express, Optica Publishing Group, 2022-07-22) [Article]
    An original liquid crystal (LC)-based substrate integrated waveguide (SIW) leaky-wave antenna is proposed. Inside the SIW, there is an embedded stripline sandwiched between an LC pool and another dielectric slab. The antenna couples the guided quasi-TEM mode into free space through a periodic set of complementary electric inductive-capacitive (cELC) resonators. Simulation results show that the antenna performs fixed-frequency continuous beam steering of 52° from backward −28° to forward 24° at 25.85 GHz. This relatively wide beam scan angle is achieved by tuning the LC permittivity through an applied quasi-DC bias voltage to the stripline. Simulation results show that the antenna has high realized gain through the entire scanning range (less than 1 dB degradation), relatively wide bandwidth, and good tolerance to frequency drift and fabrication errors.
  • Highly sensitive graphene oxide leaf wetness sensor for disease supervision on medicinal plants

    Patle, Kamlesh S.; Dehingia, Biswajit; Kalita, Hemen; Palaparthy, Vinay S. (Computers and Electronics in Agriculture, Elsevier BV, 2022-07-21) [Article]
    Plant disease prediction plays a pivotal role to abate the crop loss. For this purpose, early disease prediction models have been explored, where information about leaf wetness duration (LWD) is one of the important factors. The leaf wetness duration is measured with the help of leaf wetness sensors (LWS). Here, the LWS is fabricated on the polyamide flexible substrate where graphene oxide (GO) is used as the sensing film to detect the water molecules on the leaf canopy. Fabricated GO LWS has been tested under laboratory conditions, we exposed the entire sensing film with water molecule and we observed that it offers response of about 45000 % with respect to the air. Subsequently, observed response time of the fabricated sensor is around 400 s with recovery time of about 100 s. Further, the fabricated sensor shows only 2 % change in the response when exposed to the temperature ranging from 20 0C to 65 0C. Under field conditions, to explore the efficacy of the fabricated LWS, we benchmarked the LWD measured using the GO LWS with commercial LWS (Phytos 31). We have deployed the fabricated GO LWS along with Phytos 31 on the Tulsi (Ocimum tenuiflorum) medical plant. The on-field testing of the GO LWS indicates that maximum difference in LWD value using fabricated GO LWS and Phytos 31 is around ± 30 min.
  • A high-order Lagrange-Galerkin scheme for a class of Fokker-Planck equations and applications to mean field games

    Calzola, Elisa; Carlini, Elisabetta; Silva, Francisco J. (arXiv, 2022-07-18) [Preprint]
    In this paper we propose a high-order numerical scheme for linear Fokker-Planck equations with a constant diffusion term. The scheme, which is built by combining Lagrange-Galerkin and semi-Lagrangian techniques, is explicit, conservative, consistent, and stable for large time steps compared with the space steps. We provide a convergence analysis for the exactly integrated Lagrange-Galerkin scheme, and we propose an implementable version with inexact integration. Our main application is the construction of a high-order scheme to approximate solutions of time dependent mean field games systems.
  • Synthesis, spectral characterization, crystal structure and computational investigation of 2-formyl-6-methoxy-3-carbethoxy quinoline as potential SARS-CoV inhibitor

    Franklin Ebenazer, A.; Saravanabhavan, M.; Ramesh, K.S.; Muhammad, Shabbir; Al-Sehemi, Abdullah G.; Sampathkumar, N. (The Journal of physics and chemistry of solids, Elsevier BV, 2022-07-16) [Article]
    The recent COVID-19 outbreak caused by the novel coronavirus SARS-CoV-2 has an immense impact on global health and economy. Although vaccines are being used, urgent need of drugs based on natural products with high efficacy and safety is a pressing priority. Quinoline alkaloids are well known for their therapeutic action against malaria; initially, it was tried against Coronaviruses. It is a basic vital scaffold to design drugs with required biological and pharmacological activities. In this present study, a new quinoline compound was synthesized and characterized by spectroscopy techniques. Crystal structure was established by SCXRD analysis and data is used as an input to perform various computations. Additionally, using state-of-the-art quantum computational techniques, the geometry optimization and calculation of UV–Vis spectrum of 2F6M3CQ were performed at B3LYP/6-311G* level of theory. The optimized molecular geometric parameters as well as UV–Vis spectrum values are found to be in good agreement with their respective experimental results. The visualization of 3-D plots of FMO and MEP indicated the structure and reactivity trends of 2F6M3CQ molecule. Molecular docking methods were utilized to find the drug ability of 2F6M3CQ with Mproprotein of SARS-CoV-2. There were many intermolecular interactions between Mpro protein and 2F6M3CQ molecule which lead to good binding energy (−5.5 kcal/mol) between them which was found to be better than the binding energy of chloroquinine molecule (−4.5 kcal/mol) as studied under same docking protocols. Finally, drug likeness and ADME properties of 2F6M3CQ were also analyzed. There is no violation found for RO5 in our 2F6M3CQ compound. ADME analysis shows drug like properties of compound 2F6M3CQ which predicts that it might be a potential candidate for inhibition of SARS-CoV-2.
  • Multi-hazard susceptibility mapping of cryospheric hazards in a high-Arctic environment: Svalbard Archipelago

    Nicu, Ionut Cristi; Elia, Letizia; Rubensdotter, Lena; Tanyas, Hakan; Lombardo, Luigi (Copernicus GmbH, 2022-07-14) [Preprint]
    The Svalbard Archipelago represents the northernmost place on Earth where cryospheric hazards, such as thaw slumps (TS) and thermo-erosion gullies (TEG) could take place and rapidly develop under the influence of climatic variations. Svalbard permafrost is specifically sensitive to rapidly occurring warming and therefore, a deeper understanding of TS and TEG is necessary to understand and foresee the dynamics behind local cryospheric hazards' occurrences and their global implications. We present the latest update of two polygonal inventories where the extent of TS and TEG is recorded across Nordenskiöld Land (Svalbard Archipelago), over a surface of approximately 4000 km2. This area was chosen because it represents the most concentrated ice-free area of the Svalbard Archipelago and, at the same time, where most of the current human settlements are concentrated. The inventories were created through visual interpretation of high-resolution aerial photographs, as part of our ongoing effort toward creating a pan-Arctic repository of TS and TEG. Overall, we mapped 562 TS and 908 TEG, from which we separately generated two susceptibility maps using a Generalized Additive Modelling (GAM) approach, under the assumption that TS and TEG manifest across Nordenskiöld Land, according to a Bernoulli probability distribution. Once validating the modelling results, the two susceptibility patterns were combined into the first multi-hazard cryospheric susceptibility map of the area.
  • Intra C-RAN Two-Way Multi-Pair Computation under Total Power and Fronthaul Capacity Constraints

    Hasabelnaby, Mahmoud A.; Chaaban, Anas (IEEE, 2022-07-14) [Conference Paper]
    Most existing works on cloud radio-access networks (C-RANs) investigate the uplink or the downlink transmissions separately. However, joint uplink and downlink design can bring additional advantages, especially in intra-cloud C-RAN communications scenarios. In this paper, a two-way multi-pair computation strategy is proposed, where message source-destination information is taken into account in our design. The achievble end-to-end rate of this scheme is derived, optimized, and evaluated numerically under total power and fronthaul capacity constraints. Numerical results reveal that significant improvement in the achievable end-to-end sum-rate can be obtained using the proposed scheme compared to conventional ones.
  • High Current Density Oxygen Evolution in Carbonate Buffered Solution Achieved by Active Site Densification and Electrolyte Engineering

    Nishimoto, Takeshi; Shinagawa, Tatsuya; Naito, Takahiro; Harada, Kazuki; Yoshida, Masaaki; Takanabe, Kazuhiro (Elsevier BV, 2022-07-13) [Preprint]
    High current density reaching 1 A cm −2 for efficient oxygen evolution reaction (OER) is demonstrated by interactively optimizing electrolyte and electrode at non-extreme pH levels. Careful electrolyte assessment revealed that the state-of-the-art nickel-iron oxide electrocatalyst in alkaline solution maintained its high OER performance with a small Tafel slope in K-carbonate solution at pH 10.5 at 353 K. The OER performance was improved when Cu or Au was introduced into the iron oxide (FeO x ) as a third element during the preparation of electrode by electrodeposition. The resultant OER achieved 1 A cm −2 at 1.53 V vs. reversible hydrogen electrode (RHE) stably for 90 h, comparable to those in extreme alkaline conditions. Constant Tafel slopes, apparent activation energy, and the same signatures from operando X-ray absorption spectroscopy among these samples suggest that this improvement seems solely correlated with enhanced electrochemical surface area caused by adding the third element.
  • Population Genomics and Haplotype Analysis in Bread Wheat Identify a Gene Regulating Glume Pubescence

    Hu, Xin; Zuo, Jianfang (Frontiers in plant science, Frontiers Media SA, 2022-07-13) [Article]
    Glume hairiness or pubescence is an important morphological trait with high heritability to distinguish/characterize wheat and is related to the resistance to biotic and abiotic stresses. Hg1 (formerly named Hg) on chromosome arm 1AS controlled glume hairiness in wheat. Its genetic analysis and mapping have been widely studied, yet more useful and accurate information for fine mapping of Hg1 and identification of its candidate gene is lacking. The cloning of this gene has not yet been reported for the large complex wheat genome. Here, we performed a GWAS between SNP markers and glume pubescence (Gp) in a wheat population with 352 lines and further demonstrated the gene expression and haplotype analysis approach for isolating the Hg1 gene. One gene, TraesCSU02G143200 (TaELD1-1A), encoding glycosyltransferase-like ELD1/KOBITO 1, was identified as the most promising candidate gene of Hg1. The gene annotation, expression pattern, function SNP variation, haplotype analysis, and co-expression analysis in floral organ (spike) development indicated that it is likely to be involved in the regulation of glume pubescence. Our study demonstrates the importance of high-quality reference genomes and annotation information, as well as bioinformatics analysis, for gene cloning in wheat.
  • Effect of Ligands on the Stability of Gold Nanoclusters

    Pensa, Evangelina; Azofra Mesa, Luis; Salvarezza, Roberto C.; Carro, Pilar (The Journal of Physical Chemistry Letters, American Chemical Society (ACS), 2022-07-11) [Article]
    Gold nanoclusters (AuNCs) are atomic architectures that can be precisely tailored for catalytic applications. In this work, we studied two benchmark AuNCs, Au25(SR)18 and Au144(SR)60, covered by aromatic and aliphatic ligands to envision how the 3D structure of the ligand impacts the stability of the nanomaterial. Surprisingly, we found that increasing the alkanethiol length has a poor or null effect on the stability of the AuNCs, a trend opposite to that on Au(111) surfaces. When considering the aromatic or aliphatic nature, the AuNC stability follows the same trend as on Au(111): the thermodynamical stability is dictated by the ligand density rather than its chemical nature, where the aliphatic ligand imparts more stability than the aromatic one. Our findings provide a tool to predict how an ultrasmall gold core can interact with the environment, substrate, and themselves according to the stability of its protecting ligand shell.
  • Catalytic Desaturation of Aliphatic Amides and Imides Enabled by Excited-State Base-Metal Catalysis

    Wang, Chenyang; Azofra Mesa, Luis; Dam, Phong; Sebek, Michael; Steinfeldt, Norbert; Rabeah, Jabor; El-Sepelgy, Osama (ACS Catalysis, American Chemical Society (ACS), 2022-07-10) [Article]
    Herein, we report a photoexcited base-metal-catalyzed selective desaturation of aliphatic amides and imides. The reaction is catalyzed by a base-metal cobalt complex under visible-light irradiation. This transformation can be efficiently processed at room temperature and enables the synthesis of valuable cyclic and acyclic enamides and enimides from abundant chemicals. Density functional theory (DFT) analysis, electron paramagnetic resonance (EPR), and UV–vis studies rationalized the discovered reactivity of the cobalt catalyst for the photochemical C(sp3)–H activation reaction. Finally, we demonstrated the potential of our process by scaling-up experiments using a continuous flow photoreactor.
  • Continuous Integration for HPC with Github Actions and Tapis

    Pachev, Benjamin; Stuart, Georgia; Dawson, Clint (ACM, 2022-07-08) [Conference Paper]
    Continuous integration and deployment (CICD) are fundamental to modern software development. While many platforms such as GitHub and Atlassian provide cloud solutions for CICD, these solutions don’t fully meet the unique needs of high performance computing (HPC) applications. These needs include, but are not limited to, testing distributed memory and scaling studies, both of which require an HPC environment. We propose a novel framework for running CICD workflows on supercomputing resources. Our framework directly integrates with GitHub Actions and leverages TACC’s Tapis API for communication with HPC resources. The framework is demonstrated for PYthon Ocean PArticle TRAcking (PYOPATRA), an HPC application for Lagrangian particle tracking.

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