bluuebunny/crossref_metadata_2025_split huggingface dataset:
The High‐Pressure Characterization of Melt‐Castable Energetic Materials: 3,3′‐Bis‐Oxadiazole‐5,5′‐Bis‐Methylene Dinitrate
Authors: Bennion Jonathan C. , Batyrev Iskander G. , Ciezak‐Jenkins Jennifer A. 
Published: October 2018

AbstractThe high‐pressure behavior of 3,3′‐bis‐oxadiazole‐5,5′‐bis‐methylene dinitrate (BODN) was studied at room temperature to 25 GPa by Raman spectroscopy and powder X‐ray diffraction. The Raman spectra, powder patterns, and calculated unit‐cell volumes at selected pressures show qualitative agreement with first‐principles density function theory calculations. Over this pressure range, no evidence of polymorphism was observed which suggests that this energetic material can be formulated without the concern of forming lower‐density phases at elevated pressures. Vibrational measurements suggest a reversible deformation of the C−C linkage between the oxadiazole rings with increased pressure.
Spectral and structural analysis of a red fluorescent protein from Acropora digitifera
Authors: Kim So Eun , Hwang Kwang Yeon , Nam Ki Hyun 
Published: October 2018

AbstractFluorescent proteins (FPs) possess a wide variety of spectral properties that make them of widespread interest as optical markers. These proteins can be applied as pH indicators or metal biosensors. The discovery and characterization of new fluorescent proteins is expected to further extend their application. Here, we report the spectral and structural analysis of a red fluorescent protein from Acropora digitifera (designated AdRed). This protein shows a tetrameric state and is red emitting, with excitation and emission maxima at 567 and 612 nm, respectively. Its crystal structure shows the tetrameric interface stabilized by hydrogen bonding and salt bridges. The electron density map of the chromophore, consisting of Asp66–Tyr67–Gly68, shows the decarboxylated side chain of Asp66. Ser223, located near the chromophore, has the role of bridging His202 and Glu221, and is part of the hydrogen bond network. Mutated AdRed with Cys148Ser reveals a blue shift in fluorescence excitation and emission. Our results provide insights into understanding the molecular function of AdRed and other FPs.
Crystallographic evidence for two‐metal‐ion catalysis in human pol η
Authors: Wang Jimin , Smithline Zachary B. 
Published: October 2018

AbstractExtensive evidence exists that DNA polymerases use two metal ions to catalyze the phosphoryl transfer reaction. Recently, competing evidence emerged, suggesting that a third metal ion, known as MnC, may be involved in catalysis. The binding of MnC was observed in crystal structures of the replication complexes of human polymerase (pol) η, pol β, and pol μ. Its occupancy (qMnC) in the pol η replication complexes exhibited a strong correlation with the occupancy of the formed product pyrophosphate (qPPi), i.e., qMnC ∝ qPPi. However, a key piece of information was missing that is needed to distinguish between two possible sequences of events: (i) the chemical reaction occurs first with only two meal ions, followed by the binding of MnC in a “catch‐the‐product” mode; and (ii) MnC binds first, followed by the chemical reaction with all three metal ions in a “push‐the‐reaction‐forward” mode. Both mechanisms can lead to a strong correlation between qMnC and qPPi. However, qMnC ≤ qPPi in the first scenario, whereas qMnC ≥ qPPi in the second. In this study, an analysis of crystallographic data published recently for pol η complexes shows that the formation of the product pyrophosphate definitely precedes the binding of MnC. Therefore, just like all other DNA polymerases, human pol η employs a two‐metal‐ion catalytic mechanism. Rather than help to catalyze the reaction, MnC stabilizes the formed product, which remains trapped inside the crystals, before it slowly diffuses out.
Solution NMR structure of CHU_1110 from Cytophaga hutchinsonii, an AHSA1 protein potentially involved in metal ion stress response
Authors: Liang Chunjie , Zhu Jiang , Ramelot Theresa A. , Kennedy Michael A. , Yue Xiali , Li Xuegang , Liu Maili , He Ting , Yang Yunhuang 
Published: October 2018

AbstractWe report the solution nuclear magnetic resonance (NMR) structure of CHU_1110 from Cytophaga hutchinsonii. CHU_1110 contains three α‐helices and one antiparallel β‐sheet, forming a large cavity in the center of the protein, which are consistent with the structural characteristics of AHSA1 protein family. This protein shows high structural similarities to the prokaryotic proteins RHE_CH02687 from Rhizobium etli and YndB from Bacillus subtilis, which can bind with flavinoids. Unlike these two homologs, CHU_1110 shows no obvious interaction with flavonoids in NMR titration experiments. In addition, no direct interaction has been observed between CHU_1110 and ATP, although many homologous sequences of CHU_1110 have been annotated as ATPase. Combining the analysis of structural similarity of CHU_1110 and genomic context of its encoding gene, we speculate that CHU_1110 may be involved in the stress response of bacteria to heavy metal ions, even though its specific biological functions that need to be further investigated.
Exploiting graphical processing units to enable quantum chemistry calculation of large solvated molecules with conductor‐like polarizable continuum models
Authors: Liu Fang , Sanchez David M. , Kulik Heather J. , Martínez Todd J. 
Published: October 2018

AbstractThe conductor‐like polarizable continuum model (C‐PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in quantum chemistry. We have previously implemented C‐PCM solvation for Hartree‐Fock (HF) and density functional theory (DFT) on graphical processing units (GPUs), enabling the quantum mechanical treatment of large solvated biomolecules. Here, we first propose a GPU‐based algorithm for the PCM conjugate gradient linear solver that greatly improves the performance for very large molecules. The overhead for PCM‐related evaluations now consumes less than 15% of the total runtime for DFT calculations on large molecules. Second, we demonstrate that our algorithms tailored for ground state C‐PCM are transferable to excited state properties. Using a single GPU, our method evaluates the analytic gradient of the linear response PCM time‐dependent density functional theory energy up to 80× faster than a conventional central processing unit (CPU)‐based implementation. In addition, our C‐PCM algorithms are transferable to other methods that require electrostatic potential (ESP) evaluations. For example, we achieve speed‐ups of up to 130× for restricted ESP‐based atomic charge evaluations, when compared to CPU‐based codes. We also summarize and compare the different PCM cavity discretization schemes used in some popular quantum chemistry packages as a reference for both users and developers.
Ab initio simulations of liquid electrolytes for energy conversion and storage
Authors: Pham Tuan Anh 
Published: October 2018

AbstractUnderstanding physicochemical properties of liquid electrolytes is essential for predicting and optimizing device performance for a wide variety of emerging energy technologies, including photoelectrochemical water splitting, supercapacitors, and batteries. In this work, we review recent progress and open challenges in predicting structural, dynamical, and electronic properties of the liquids using first‐principles approaches. We briefly summarize the basic concepts of first‐principles molecular dynamics (FPMD), and we discuss how FPMD methods have enriched our understanding of a number of liquids, including aqueous solutions, organic electrolytes and ionic liquids. We also discuss technical challenges in extending FPMD simulations to the study of liquid electrolytes in more complex environments, including the interface between electrolytes and electrodes, which is a key component in many energy storage and conversion systems.
An update on enterovirus 71 infection and interferon type I response
Authors: Rasti Mojtaba , Khanbabaei Hashem , Teimoori Ali 
Published: October 2018

SummaryEnteroviruses are members of Pichornaviridae family consisting of human enterovirus group A, B, C, and D as well as nonhuman enteroviruses. Hand, foot, and mouth disease (HFMD) is a serious disease which is usually seen in the Asia‐Pacific region in children. Enterovirus 71 and coxsackievirus A16 are two important viruses responsible for HFMD which are members of group A enterovirus. IFN α and β are two cytokines, which have a major activity in the innate immune system against viral infections. Most of the viruses have some weapons against these cytokines. EV71 has two main proteases called 2A and 3C, which are important for polyprotein processing and virus maturation. Several studies have indicated that they have a significant effect on different cellular pathways such as interferon production and signaling pathway. The aim of this study was to investigate the latest findings about the interaction of 2A and 3C protease of EV71 and IFN production/signaling pathway and their inhibitory effects on this pathway.
Robust neural network–based tracking control and stabilization of a wheeled mobile robot with input saturation
Authors: Huang Hantao , Zhou Jingye , Di Qing , Zhou Jiawei , Li Jiawang 
Published: October 2018

SummaryThis paper presents a robust neural network–based control scheme to deal with the problem of tracking and stabilization simultaneously for a wheeled mobile robot subject to parametric uncertainties, external disturbances, and input saturation. At first, a new error‐state transformation scheme is designed by introducing some auxiliary variables as an additional virtual control signals to reduce the adverse effect caused by the underactuation. These variables can change their structures for different desired trajectories to be tracked. Then, a robust control law is proposed combining with a kinematic controller and a dynamic controller, while a three‐layer neural network system is applied to approximate model uncertainties. Stability analysis via the Lyapunov theory shows that the proposed controller can make tracking errors converge to bounded neighborhoods of the origin. Finally, some simulation results are illustrated to verify the effectiveness of the proposed control strategy.
Underwater place recognition using forward‐looking sonar images: A topological approach
Authors: Santos Matheus M. , Zaffari Guilherme B. , Ribeiro Pedro O. C. S. , Drews‐Jr Paulo L. J. , Botelho Silvia S. C. 
Published: October 2018

AbstractAutonomous underwater vehicles are a prominent tool for underwater exploration because they can access dangerous places avoiding the risks for the human beings. However, the autonomous navigation still a challenge due to the characteristics of the environment that decrease the performance of the sensor and the robot perception. In this context, this paper proposes a loop closure detector addressed to the simultaneous localization and mapping problem at semistructured environments using acoustic images acquired by forward‐looking sonars. The images are segmented by an adaptative approach based on the acoustic beams analysis. A pose‐invariant topological graph is build to represent the relationship between image features. The loop closure detection is achieved using a graph comparison. The approach is evaluated in a real environment at a marina. The results reveal all loop closures of the data set are detected with a high precision and present an invariant to image rotation.
Looking to the past to ensure the future of the world's oldest living vertebrate: Isotopic evidence for multi‐decadal shifts in trophic ecology of the Australian lungfish
Authors: Olden Julian D. , Fallon Stewart J. , Roberts David T. , Espinoza Tom , Kennard Mark J. 
Published: October 2018

AbstractMeeting the conservation challenges of long‐lived animal species necessitate long‐term assessments of trophic ecology. The use of dietary proxies, such as ratios of naturally occurring stable isotopes in animal tissues demonstrating progressive growth, has shown considerable promise to reconstruct trophic histories of long‐lived organisms experiencing environmental change. Here, we combine innovative radiocarbon scale‐ageing techniques with stable isotope analysis of carbon and nitrogen from cross sections of scale to reconstruct the trophic ecology of Australian lungfish (Neoceratodus forsteri) across its remaining global distribution. Over a 65‐year period, we found pronounced temporal shifts in the δ13C and δ15N isotopic ratios of lungfish that coincided with a period of hydrological modification by dams and land‐use intensification associated with agriculture and livestock grazing. In the Brisbane and Burnett Rivers, whose hydrology is substantially regulated by large dams, lungfish showed consistent trends of δ13C depletion and δ15N enrichment over time. This may indicate anthropogenic changes in background isotopic levels of basal energy sources and/or that additional seston exported downstream from impoundments represent a carbon source that was previously unavailable, thus shifting lungfish diet from benthic‐dominated primary production typical of unmodified river systems, to pelagic carbon sources. By contrast, δ13C ratios of lungfish in the unregulated Mary River were more stable through time, whereas δ15N ratios increased during a period of dairy industry expansion and increased application of nitrogen fertilization and then subsequently decreased at the same time that rates of pasture development declined and nutrient inputs presumably decreased. In conclusion, we provide evidence for human‐caused alterations in background isotopic levels and potential changes in availability of benthic versus pelagic energy resources supporting Australian lungfish and demonstrate how detectable trophic signals in long‐lived fish scales can reveal long‐term anthropogenic changes in riverine ecosystems.
Barriers to dispersal: The effect of a weir on stream insect drift
Authors: Brooks Andrew J. , Wolfenden Benjamin , Downes Barbara J. , Lancaster Jill 
Published: October 2018

AbstractDams and weirs degrade river ecosystems, reducing diversity and altering the assemblage composition of aquatic biota. These structures may damage rivers by disrupting longitudinal connectivity, fragmenting rivers, and isolating populations. We tested whether a weir could impede the downstream dispersal of stream insects by comparing drift rates through natural pools and through a weir pool. For three of four of our study taxa (Offadens spp., Austrosimulium spp., and Simsonia spp.), we found the numbers of drifters were consistently reduced by the weir across multiple occasions (reduction ranging from 68 to 98%) to a higher degree than natural pools (reduction ranging from 24 to 41%). Drift of Cheumatopsyche spp. through the weir was greatly reduced in December (−95%) compared with natural pools, but the weir had little effect during April (−9%). There were size‐related patterns in drift through the weir pool for some taxa. In the weir pool, emigrating individuals of Austrosimulium spp. were significantly smaller than immigrating individuals, which was not observed in natural pools. In contrast, significant reductions of Cheumatopsyche spp. drifters through the weir only occurred when individuals were small (December). Within the weir pool, the combined effects of lower average water velocity, multiple large low velocity areas, and the weir wall were likely to be the cause of the reduction in stream insect drift through the weir. The impediment of drift of some taxa by weirs may affect dispersal and colonisation processes. This obstruction of downstream movement could undermine the outcomes of river restoration projects.
Nucleation, morphology, and structure of sub‐nm thin ceria islands on Rh(111)
Authors: Flege Jan Ingo , Höcker Jan , Sadowski Jerzy T. , Senanayake Sanjaya D. , Falta Jens 
Published: October 2018

The early stages of ceria growth on Rh(111) at high temperature have been investigated by low‐energy electron microscopy and photoemission electron microscopy. Ceria was deposited by reactive Ce deposition at substrate temperatures between 700°C and 900°C in an oxygen ambient of 5 × 10−7 Torr. At 700°C, we observe a high nucleation density of 100‐nm‐sized islands. With elevated temperature, the average island size increases, and the nucleation density decreases. Triangularly shaped islands nucleate preferentially at step edges, with seemingly abrupt interfaces between Ce and Rh. At 900°C, the island edges are still straight, but during growth the islands lose their triangular form. Instead, growth along the substrate step edges becomes favorable, leading to a maze‐like morphology. Atomic force microscopy reveals islands of 0.3 to 0.6‐nm height, consistent with ceria islands formed by one or two trilayers (O―Ce―O) of ceria. Moreover, the second layer of the islands is also triangularly shaped, with lateral dimensions of 50 nm and similar step heights. IV‐LEEM analysis leads to the conclusion that the rhodium surface is covered by a layer of reduced cerium oxide, which is partially overgrown by smaller islands of CeO2.
Silica Nanowire Growth on Coscinodiscus Species Diatom Frustules via Vapor–Liquid–Solid Process
Authors: Li Aobo , Zhao Xiaoguang , Anderson Stephan , Zhang Xin 
Published: October 2018

AbstractDiatom frustules are a type of porous silicon dioxide microparticle that has long been used in applications ranging from biomedical sensors to dye‐sensitized solar cells. The favorable material properties, enormous surface area, and enhanced light scattering capacity support the promise of diatom frustules as candidates for next generation biomedical devices and energy applications. In this study, the vapor–liquid–solid (VLS) method is employed to incorporate silica nanowires on the surface of diatom frustules. Compared to the original frustule structures, the frustule–nanowire composite material's surface area increases over 3‐fold, and the light scattering ability increases by 10%. By varying the gold catalyst thickness during the VLS process, tuning of the resultant nanowire length/density is achieved. Through material characterization, it is determined that both float growth and root growth processes jointly result in the growth of the silica nanowires. From a thermodynamics point of view, the preferential growth of the silica nanowires on frustules is found to have resulted from the enormous partial surface area of gold nanoparticles on the diatom frustules. The frustule–nanowire composite materials have potential applications in the development of novel biomedical sensing devices and may greatly enhance next generation solar cell performance.
Enhancement of Thermoelectric Performance in CuSbSe2 Nanoplate‐Based Pellets by Texture Engineering and Carrier Concentration Optimization
Authors: Luo Yubo , Du Chengfeng , Liang Qinghua , Zheng Yun , Zhu Beibei , Hu Huanlong , Khor Khiam Aik , Xu Jianwei , Yan Qingyu , Kanatzidis Mercouri G. 
Published: October 2018

AbstractThis work reports the thermoelectric properties of the CuSbSe2‐x mol% PtTe2 (x = 0, 0.5, 1.0, 1.5, and 2.0) pellets composed of highly oriented single crystalline nanoplates. CuSbSe2‐PtTe2 single crystalline nanoplates are prepared by a wet‐chemical process, and the pellets are prepared through a bottom‐up self‐assembly of the CuSbSe2‐PtTe2 nanoplates and spark plasma sintering (SPS) process. X‐ray diffraction and field emission scanning electron microscopic analyses show a highly textured nature with an orientation factor of ≈0.8 for (00l) facets along the primary surface of the pellets (in‐plane, perpendicular to the SPS pressure). By this way, bulk‐single‐crystal‐like electrical and thermal transport properties with a strong anisotropy are obtained, which results in an effective optimization on thermoelectric performance. The maximum in‐plane thermoelectric figure‐of‐merit ZT value reaches 0.50 at 673 K for CuSbSe2‐2.0 mol% PtTe2 pellet, which is about five times higher than the in‐plane ZT (0.10) for pure CuSbSe2.
Noninvasive Transdermal Delivery System of Lidocaine Using an Acoustic Droplet‐Vaporization Based Wearable Patch
Authors: Soto Fernando , Jeerapan Itthipon , Silva‐López Cristian , Lopez‐Ramirez Miguel Angel , Chai Ingrid , Xiaolong Lu , Lv Jian , Kurniawan Jonas F. , Martin Ian , Chakravarthy Krishnan , Wang Joseph 
Published: October 2018

AbstractCurrent technologies for managing acute and chronic pain have focused on reducing the time required for achieving high therapeutic efficiency. Herein a wearable transdermal patch is introduced, employing an acoustic droplet vaporization (ADV) methodology, as an effective noninvasive transdermal platform, for a fast local delivery of the anesthetic agent lidocaine. The skin‐worn patch consists of a flexible drug reservoir containing hundreds of micropores loaded with lidocaine, and mixed with the perfluorocarbon (PFC) emulsion. The ultrasound‐triggered vaporization of the PFC emulsion provides the necessary force to breach dermal barriers. The drug release kinetics of our model was investigated by measuring the amount of lidocaine that passed through phantom tissue and pigskin barriers. The ADV platform increases the payload skin penetration resulting in shorter treatment times compared to passive diffusion or ultrasound alone, holding considerable promise for addressing the delayed therapeutic action and slow pain relief of existing delivery protocols. It is envisioned that the integration of ADV‐based transdermal devices could be expanded to the depth‐dependent delivery of other pain management, vaccines, and gene therapy modalities.
Designable 3D Microshapes Fabricated at the Intersection of Structured Flow and Optical Fields
Authors: Yuan Rodger , Nagarajan Maxwell B. , Lee Jaemyon , Voldman Joel , Doyle Patrick S. , Fink Yoel 
Published: October 2018

Abstract3D structures with complex geometric features at the microscale, such as microparticles and microfibers, have promising applications in biomedical engineering, self‐assembly, and photonics. Fabrication of complex 3D microshapes at scale poses a unique challenge; high‐resolution methods such as two‐photon‐polymerization have print speeds too low for high‐throughput production, while top‐down approaches for bulk processing using microfabricated template molds have limited control of microstructure geometries over multiple axes. Here, a method for microshape fabrication is presented that combines a thermally drawn transparent fiber template with a masked UV‐photopolymerization approach to enable biaxial control of microshape fabrication. Using this approach, high‐resolution production of complex microshapes not producible using alternative methods is demonstrated, such as octahedrons, dreidels, and axially asymmetric fibers, at throughputs as high as 825 structures/minute. Finally, the fiber template is functionalized with conductive electrodes to enable hierarchical subparticle localization using dielectrophoretic forces.