bluuebunny/crossref_metadata_2025_split huggingface dataset:
In situ observation of oscillatory redox dynamics of copper
Authors: Cao Jing , Rinaldi Ali , Plodinec Milivoj , Huang Xing , Willinger Elena , Hammud Adnan , Hieke Stefan , Beeg Sebastian , Gregoratti Luca , Colbea Claudiu , Schlögl Robert , Antonietti Markus , Greiner Mark , Willinger Marc 
Published: July 2020

AbstractHow a catalyst behaves microscopically under reaction conditions, and what kinds of active sites transiently exist on its surface, is still very much a mystery to the scientific community. Here we present an in situ study on the red-ox behaviour of copper in the model reaction of hydrogen oxidation. Direct imaging combined with on-line mass spectroscopy shows that activity emerges near a phase boundary, where complex spatio-temporal dynamics are induced by the competing action of simultaneously present oxidizing and reducing agents. Using a combination of in situ imaging with in situ X-ray absorption spectroscopy and scanning photoemission microscopy, we reveal the relation between chemical and morphological dynamics and demonstrate that a static picture of active sites is insufficient to describe catalytic function of redox-active metal catalysts. The observed oscillatory redox dynamics provide a unique insight on phase-cooperation and a convenient and general mechanism for constant re-generation of transient active sites.
A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron
Authors: Ryan Daniel , Jenniches Laura , Reichardt Sarah , Barquist Lars , Westermann Alexander J. 
Published: July 2020

AbstractBacteria of the genus Bacteroides are common members of the human intestinal microbiota and important degraders of polysaccharides in the gut. Among them, the species Bacteroides thetaiotaomicron has emerged as the model organism for functional microbiota research. Here, we use differential RNA sequencing (dRNA-seq) to generate a single-nucleotide resolution transcriptome map of B. thetaiotaomicron grown under defined laboratory conditions. An online browser, called ‘Theta-Base’ (www.helmholtz-hiri.de/en/datasets/bacteroides), is launched to interrogate the obtained gene expression data and annotations of ~4500 transcription start sites, untranslated regions, operon structures, and 269 noncoding RNA elements. Among the latter is GibS, a conserved, 145 nt-long small RNA that is highly expressed in the presence of N-acetyl-D-glucosamine as sole carbon source. We use computational predictions and experimental data to determine the secondary structure of GibS and identify its target genes. Our results indicate that sensing of N-acetyl-D-glucosamine induces GibS expression, which in turn modifies the transcript levels of metabolic enzymes.
Direct observation of a Feshbach resonance by coincidence detection of ions and electrons in Penning ionization collisions
Authors: Margulis Baruch , Narevicius Julia , Narevicius Edvardas 
Published: July 2020

AbstractObservation of molecular dynamics with quantum state resolution is one of the major challenges in chemical physics. Complete characterization of collision dynamics leads to the microscopic understanding and unraveling of different quantum phenomena such as scattering resonances. Here we present an experimental approach for observing molecular dynamics involving neutral particles and ions that is capable of providing state-to-state mapping of the dynamics. We use Penning ionization reaction between argon and metastable helium to generate argon ion and ground state helium atom pairs at separation of several angstroms. The energy of an ejected electron carries the information about the initial electronic state of an ion. The coincidence detection of ionic products provides a state resolved description of the post-ionization ion-neutral dynamics. We demonstrate that correlation between the electron and ion energy spectra enables us to directly observe the spin-orbit excited Feshbach resonance state of HeAr+. We measure the lifetime of the quasi-bound HeAr+A2 state and discuss possible applications of our method.
Unexpected complexity of everyday manual behaviors
Authors: Yan Yuke , Goodman James M. , Moore Dalton D. , Solla Sara A. , Bensmaia Sliman J. 
Published: July 2020

AbstractHow does the brain control an effector as complex and versatile as the hand? One possibility is that neural control is simplified by limiting the space of hand movements. Indeed, hand kinematics can be largely described within 8 to 10 dimensions. This oft replicated finding has been construed as evidence that hand postures are confined to this subspace. A prediction from this hypothesis is that dimensions outside of this subspace reflect noise. To address this question, we track the hand of human participants as they perform two tasks—grasping and signing in American Sign Language. We apply multiple dimension reduction techniques and replicate the finding that most postural variance falls within a reduced subspace. However, we show that dimensions outside of this subspace are highly structured and task dependent, suggesting they too are under volitional control. We propose that hand control occupies a higher dimensional space than previously considered.
Finding flows of a Navier–Stokes fluid through quantum computing
Authors: Gaitan Frank 
Published: July 2020

AbstractThere is great interest in using quantum computers to efficiently simulate a quantum system’s dynamics as existing classical computers cannot do this. Little attention, however, has been given to quantum simulation of a classical nonlinear continuum system such as a viscous fluid even though this too is hard for classical computers. Such fluids obey the Navier–Stokes nonlinear partial differential equations, whose solution is essential to the aerospace industry, weather forecasting, plasma magneto-hydrodynamics, and astrophysics. Here we present a quantum algorithm for solving the Navier–Stokes equations. We test the algorithm by using it to find the steady-state inviscid, compressible flow through a convergent-divergent nozzle when a shockwave is (is not) present. We find excellent agreement between numerical simulation results and the exact solution, including shockwave capture when present. Finally, we compare the algorithm’s computational cost to deterministic and random classical algorithms and show that a significant speed-up is possible. Our work points to a large new application area for quantum computing with substantial economic impact, including the trillion-dollar aerospace industry, weather-forecasting, and engineered-plasma technologies.
Facile synthesis of Pd@graphene nanocomposites with enhanced catalytic activity towards Suzuki coupling reaction
Authors: Khan Mujeeb , Shaik Mohammed Rafi , Adil Syed Farooq , Kuniyil Mufsir , Ashraf Muhammad , Frerichs Hajo , Sarif Massih Ahmad , Siddiqui Mohammed Rafiq H. , Al–Warthan Abdulrahman , Labis Joselito P. , Islam Mohammad Shahidul , Tremel Wolfgang , Tahir Muhammad Nawaz 
Published: July 2020

AbstractA facile and chemical specific method to synthesize highly reduced graphene oxide (HRG) and Pd (HRG@Pd) nanocomposite is presented. The HRG surfaces are tailored with amine groups using 1-aminopyrene (1-AP) as functionalizing molecules. The aromatic rings of 1-AP sit on the basal planes of HRG through π–π interactions, leaving amino groups outwards (similar like self-assembled monolayer on 2D substrates). The amino groups provide the chemically specific binding sites to the Pd nucleation which subsequently grow into nanoparticles. HRG@Pd nanocomposite demonstrated both uniform distribution of Pd nanoparticles on HRG surface as well as excellent physical stability and dispersibility. The surface functionalization was confirmed using, ultraviolet–visible (UV–Vis), Fourier transform infra-red and Raman spectroscopy. The size and distribution of Pd nanoparticles on the HRG and crystallinity were confirmed using high-resolution transmission electron microscopy and powder X-ray diffraction and X-ray photoelectron spectroscopy. The catalytic efficiency of highly reduced graphene oxide-pyrene-palladium nanocomposite (HRG-Py-Pd) is tested towards the Suzuki coupling reactions of various aryl halides. The kinetics of the catalytic reaction (Suzuki coupling) using HRG-Py-Pd nanocomposite was monitored using gas chromatography (GC).
Study on the 3D printability of poly(3-hydroxybutyrate-co-3-hydroxyvalerate)/poly(lactic acid) blends with chain extender using fused filament fabrication
Authors: Vigil Fuentes Miguel A. , Thakur Suman , Wu Feng , Misra Manjusri , Gregori Stefano , Mohanty Amar K. 
Published: July 2020

AbstractIn this study, the 3D printability of a series of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)/poly(lactic acid) (PLA) blends were investigated using fused filament fabrication (FFF). The studied blends suffered from poor 3D printability due to differences in compatibility and low thermal resistance. These shortcomings were addressed by incorporating a functionalized styrene-acrylate copolymer with oxirane moieties as a chain extender (CE). To enhance mechanical properties, the synergistic effect of 3D printing parameters such as printing temperature and speed, layer thickness and bed temperature were explored. Rheological analysis showed improvement in the 3D printability of PHBV:PLA:CE blend by allowing a higher printing temperature (220 °C) and sufficient printing speed (45 mm s−1). The surface morphology of fractured tensile specimens showed good bonding between layers when a bed temperature of 60 °C was used and a layer thickness of 0.25 mm was designed. The optimized printing samples shown higher storage modulus and strength, resulting in stiffer and stronger parts. The crystallinity, morphology and performance of the 3D printed products were correlated to share key methods to improve the 3D printability of PHBV:PLA based blends which may be implemented in other biopolymer blends, and further highlight how process parameters enhance the mechanical performance of 3D printed products.
Species traits predict the aryl hydrocarbon receptor 1 (AHR1) subtypes responsible for dioxin sensitivity in birds
Authors: Bianchini Kristin , Morrissey Christy A. 
Published: July 2020

AbstractDifferences in avian sensitivity to dioxin-like compounds (DLCs) are directly attributable to the identities of amino acids at two sites within the ligand binding domain (LBD) of the aryl hydrocarbon receptor 1 (AHR1). Recent work suggests that by influencing avian exposure to naturally occurring dioxins, differences in diet, habitat, and migration may have influenced the evolution of three AHR1 LBD genotypes in birds: type 1 (high sensitivity), type 2 (moderate sensitivity), and type 3 (low sensitivity). Using a boosted regression tree (BRT) analysis, we built on previous work by examining the relationship between a comprehensive set of 17 species traits, phylogeny, and the AHR1 LBD across 89 avian species. The 17 traits explained a combined 74% of the model deviance, while phylogenetic relatedness explained only 26%. The strongest predictors of AHR1 LBD were incubation period and habitat type. We found that type 3 birds tended to occupy aquatic habitats, and, uniquely, we also found that type 3 birds tended to have slower developmental rates. We speculate that this reflects higher evolutionary exposure to naturally occurring dioxins in waterbirds and species with K-selected life histories. This study highlights the value of trait-based approaches in helping to understand differing avian species sensitivities to environmental contaminants.
Exploiting defective RRAM array as synapses of HTM spatial pooler with boost-factor adjustment scheme for defect-tolerant neuromorphic systems
Authors: Woo Jiyong , Van Nguyen Tien , Kim Jeong Hun , Im Jong-Pil , Im Solyee , Kim Yeriaron , Min Kyeong-Sik , Moon Seung Eon 
Published: July 2020

AbstractA crossbar array architecture employing resistive switching memory (RRAM) as a synaptic element accelerates vector–matrix multiplication in a parallel fashion, enabling energy-efficient pattern recognition. To implement the function of the synapse in the RRAM, multilevel resistance states are required. More importantly, a large on/off ratio of the RRAM should be preferentially obtained to ensure a reasonable margin between each state taking into account the inevitable variability caused by the inherent switching mechanism. The on/off ratio is basically adjusted in two ways by modulating measurement conditions such as compliance current or voltage pulses modulation. The latter technique is not only more suitable for practical systems, but also can achieve multiple states in low current range. However, at the expense of applying a high negative voltage aimed at enlarging the on/off ratio, a breakdown of the RRAM occurs unexpectedly. This stuck-at-short fault of the RRAM adversely affects the recognition process based on reading and judging each column current changed by the multiplication of the input voltage and resistance of the RRAM in the array, degrading the accuracy. To address this challenge, we introduce a boost-factor adjustment technique as a fault-tolerant scheme based on simple circuitry that eliminates the additional process to identify specific locations of the failed RRAMs in the array. Spectre circuit simulation is performed to verify the effect of the scheme on Modified National Institute of Standards and Technology dataset using convolutional neural networks in non-ideal crossbar arrays, where experimentally observed imperfective RRAMs are configured. Our results show that the recognition accuracy can be maintained similar to the ideal case because the interruption of the failure is suppressed by the scheme.
A strong preference for the TA/TA dinucleotide step discovered for an acridine-based, potent antitumor dsDNA intercalator, C-1305: NMR-driven structural and sequence-specificity studies
Authors: Laskowski Tomasz , Andrałojć Witold , Grynda Jakub , Gwarda Paulina , Mazerski Jan , Gdaniec Zofia 
Published: July 2020

AbstractTriazoloacridinone C-1305, a potent antitumor agent recommended for Phase I clinical trials, exhibits high activity towards a wide range of experimental colon carcinomas, in many cases associated with complete tumor regression. C-1305 is a well-established dsDNA intercalator, yet no information on its mode of binding into DNA is available to date. Herein, we present the NMR-driven and MD-refined reconstruction of the 3D structures of the d(CGATATCG)2:C-1305 and d(CCCTAGGG)2:C-1305 non-covalent adducts. In both cases, the ligand intercalates at the TA/TA site, forming well-defined dsDNA:drug 1:1 mol/mol complexes. Orientation of the ligand within the binding site was unambiguously established by the DNA/ligand proton-proton NOE contacts. A subsequent, NMR-driven study of the sequence-specificity of C-1305 using a series of DNA duplexes, allowed us to confirm a strong preference towards TA/TA dinucleotide steps, followed by the TG/CA steps. Interestingly, no interaction at all was observed with duplexes containing exclusively the AT/AT, GG/CC and GA/TC steps.
Sine ventilation in lung injury models: a new perspective for lung protective ventilation
Authors: Spassov Sashko , Wenzel Christin , Lozano-Zahonero Sara , Boycheva Dimona , Streicher Lea , Schmidt Johannes , Schumann Stefan 
Published: July 2020

AbstractMechanical ventilation is associated with the risk of ventilator induced lung injury. For reducing lung injury in mechanically ventilated patients, the application of small tidal volumes and positive end-expiratory pressures has become clinical standard. Recently, an approach based on linear airway pressure decline and decelerated expiratory flow during expiration implied lung protective capacities. We assumed that ventilation with a smoothed, i.e. sinusoidal airway pressure profile may further improve ventilation efficiency and lung protection. We compared the effects of mechanical ventilation with sinusoidal airway pressure profile (SINE) regarding gas exchange, respiratory system compliance and histology to conventional volume and pressure controlled ventilation (VCV and PCV) and to VCV with flow-controlled expiration (FLEX) in two rat models of lung injury, tween induced surfactant depletion and high tidal volume mechanical ventilation. In both lung injury models ventilation with SINE showed more efficient CO2 elimination and blood oxygenation, improved respiratory system compliance and resulted in lower alveolar wall thickness, compared to VCV, PCV and FLEX. Optimization of the airway pressure profile may provide a novel means of lung protective mechanical ventilation.
Large-scale microlens arrays on flexible substrate with improved numerical aperture for curved integral imaging 3D display
Authors: Wang Wenwen , Chen Guixiong , Weng Yalian , Weng Xuyang , Zhou Xiongtu , Wu Chaoxing , Guo Tailiang , Yan Qun , Lin Zhixian , Zhang Yongai 
Published: July 2020

AbstractCurved integral imaging 3D display could provide enhanced 3D sense of immersion and wider viewing angle, and is gaining increasing interest among discerning users. In this work, large scale microlens arrays (MLAs) on flexible PMMA substrate were achieved based on screen printing method. Meanwhile, an inverted reflowing configuration as well as optimization of UV resin’s viscosity and substrate’s surface wettability were implemented to improved the numerical aperture (NA) of microlenses. The results showed that the NA values of MLAs could be increased effectively by adopting inverted reflowing manner with appropriate reflowing time. With decreasing the substrate’s wettability, the NA values could be increased from 0.036 to 0.096, when the UV resin contact angles increased from 60.1° to 88.7°. For demonstration, the fabricated MLAs was combined to a curved 2D monitor to realize a 31-inch curved integral imaging 3D display system, exhibiting wider viewing angle than flat integral imaging 3D display system.
VOC fingerprints: metabolomic signatures of biothreat agents with and without antibiotic resistance
Authors: Dailey Allyson , Saha Jessica , Zaidi Fatima , Abdirahman Hafsa , Haymond Amanda , Alem Farhang , Hakami Ramin , Couch Robin 
Published: July 2020

AbstractCategory A and B biothreat agents are deemed to be of great concern by the US Centers for Disease Control and Prevention (CDC) and include the bacteria Francisella tularensis, Yersinia pestis, Burkholderia mallei, and Brucella species. Underscored by the impact of the 2020 SARS-CoV-2 outbreak, 2016 Zika pandemic, 2014 Ebola outbreak, 2001 anthrax letter attacks, and 1984 Rajneeshee Salmonella attacks, the threat of future epidemics/pandemics and/or terrorist/criminal use of pathogenic organisms warrants continued exploration and development of both classic and alternative methods of detecting biothreat agents. Volatile organic compounds (VOCs) comprise a large and highly diverse group of carbon-based molecules, generally related by their volatility at ambient temperature. Recently, the diagnostic potential of VOCs has been realized, as correlations between the microbial VOC metabolome and specific bacterial pathogens have been identified. Herein, we describe the use of microbial VOC profiles as fingerprints for the identification of biothreat-relevant microbes, and for differentiating between a kanamycin susceptible and resistant strain. Additionally, we demonstrate microbial VOC profiling using a rapid-throughput VOC metabolomics method we refer to as ‘simultaneous multifiber headspace solid-phase microextraction’ (simulti-hSPME). Finally, through VOC analysis, we illustrate a rapid non-invasive approach to the diagnosis of BALB/c mice infected with either F. tularensis SCHU S4 or Y. pestis CO92.
Caspofungin induces the release of Ca2+ ions from internal stores by activating ryanodine receptor-dependent pathways in human tracheal epithelial cells
Authors: Müller Sabrina , Koch Christian , Weiterer Sebastian , Weigand Markus A. , Sander Michael , Henrich Michael 
Published: July 2020

AbstractThe antimycotic drug caspofungin is known to alter the cell function of cardiomyocytes and the cilia-bearing cells of the tracheal epithelium. The objective of this study was to investigate the homeostasis of intracellular Ca2+ concentration ([Ca2+]i) after exposure to caspofungin in isolated human tracheal epithelial cells. The [Ca2+]i was measured using the ratiometric fluoroprobe FURA-2 AM. We recorded two groups of epithelial cells with distinct responses to caspofungin exposure, which demonstrated either a rapid transient rise in [Ca2+]i or a sustained elevation of [Ca2+]i. Both patterns of Ca2+ kinetics were still observed when an influx of transmembraneous Ca2+ ions was pharmacologically inhibited. Furthermore, in extracellular buffer solutions without Ca2+ ions, caspofungin exposure still evoked this characteristic rise in [Ca2+]i. To shed light on the origin of the Ca2+ ions responsible for the elevation in [Ca2+]i we investigated the possible intracellular storage of Ca2+ ions. The depletion of mitochondrial Ca2+ stores using 25 µM 2,4-dinitrophenol (DNP) did not prevent the caspofungin-induced rise in [Ca2+]i, which was rapid and transient. However, the application of caffeine (30 mM) to discharge Ca2+ ions that were presumably stored in the endoplasmic reticulum (ER) prior to caspofungin exposure completely inhibited the caspofungin-induced changes in [Ca2+]i levels. When the ER-bound IP3 receptors were blocked by 2-APB (40 µM), we observed a delayed transient rise in [Ca2+]i as a response to the caspofungin. Inhibition of the ryanodine receptors (RyR) using 40 µM ryanodine completely prevented the caspofungin-induced elevation of [Ca2+]i. In summary, caspofungin has been shown to trigger an increase in [Ca2+]i independent from extracellular Ca2+ ions by liberating the Ca2+ ions stored in the ER, mainly via a RyR pathway.
Histological validation of in vivo assessment of cancer tissue inhomogeneity and automated morphological segmentation enabled by Optical Coherence Elastography
Authors: Plekhanov Anton A. , Sirotkina Marina A. , Sovetsky Alexander A. , Gubarkova Ekaterina V. , Kuznetsov Sergey S. , Matveyev Alexander L. , Matveev Lev A. , Zagaynova Elena V. , Gladkova Natalia D. , Zaitsev Vladimir Y. 
Published: July 2020

AbstractWe present a non-invasive (albeit contact) method based on Optical Coherence Elastography (OCE) enabling the in vivo segmentation of morphological tissue constituents, in particular, monitoring of morphological alterations during both tumor development and its response to therapies. The method uses compressional OCE to reconstruct tissue stiffness map as the first step. Then the OCE-image is divided into regions, for which the Young’s modulus (stiffness) falls in specific ranges corresponding to the morphological constituents to be discriminated. These stiffness ranges (characteristic "stiffness spectra") are initially determined by careful comparison of the "gold-standard" histological data and the OCE-based stiffness map for the corresponding tissue regions. After such pre-calibration, the results of morphological segmentation of OCE-images demonstrate a striking similarity with the histological results in terms of percentage of the segmented zones. To validate the sensitivity of the OCE-method and demonstrate its high correlation with conventional histological segmentation we present results obtained in vivo on a murine model of breast cancer in comparative experimental study of the efficacy of two antitumor chemotherapeutic drugs with different mechanisms of action. The new technique allowed in vivo monitoring and quantitative segmentation of (1) viable, (2) dystrophic, (3) necrotic tumor cells and (4) edema zones very similar to morphological segmentation of histological images. Numerous applications in other experimental/clinical areas requiring rapid, nearly real-time, quantitative assessment of tissue structure can be foreseen.