bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exact invariant solution reveals the origin of self-organized oblique turbulent-laminar stripes
Authors: Reetz Florian , Kreilos Tobias , Schneider Tobias M. 
Published: May 2019

AbstractWall-bounded shear flows transitioning to turbulence may self-organize into alternating turbulent and laminar regions forming a stripe pattern with non-trivial oblique orientation. Different experiments and flow simulations identify oblique stripe patterns as the preferred solution of the well-known Navier-Stokes equations, but the origin of stripes and their oblique orientation remains unexplained. In concluding his lectures, Feynman highlights the unexplained stripe pattern hidden in the solution space of the Navier-Stokes equations as an example demonstrating the need for improved theoretical tools to analyze the fluid flow equations. Here we exploit dynamical systems methods and demonstrate the existence of an exact equilibrium solution of the fully nonlinear 3D Navier-Stokes equations that resembles oblique stripe patterns in plane Couette flow. The stripe equilibrium emerges from the well-studied Nagata equilibrium and exists only for a limited range of pattern angles. This suggests a mechanism selecting the non-trivial oblique orientation angle of turbulent-laminar stripes.
Rationally engineered active sites for efficient and durable hydrogen generation
Authors: Xue Yurui , Hui Lan , Yu Huidi , Liu Yuxin , Fang Yan , Huang Bolong , Zhao Yingjie , Li Zhibo , Li Yuliang 
Published: May 2019

AbstractThe atomic-level understanding of the electrocatalytic activity is pivotal for developing new metal-free carbon electrocatalysts towards efficient renewable energy conversion. Here, by utilizing the amidated-carbon fibers, we demonstrate a rational surface modulation strategy on both structural and electronic properties, which will significantly boost the hydrogen evolution reaction activity of electrocatalysts. Theoretical calculations reveal the amidation decorated surface will promote significantly more 2D electrons towards the localization at the C=O branch. The modified surface displays a self-activated electron-extraction characteristic that was actualized by a fast reversible bond-switching between HO-C=Ccatalyst and O=C-Ccatalyst. Experimentally, this metal-free electrode exhibits outstanding hydrogen evolution reaction activities and long-term stabilities in both acidic and alkaline media, even surpassing the commercial 20 wt% Pt/C catalyst. Thus, this strategy can extend to a general blueprint for achieving precise tuning on highly efficient electron-transfer of hydrogen evolution reaction for broad applications under universal pH conditions.
Li@C60 as a multi-state molecular switch
Authors: Chandler Henry J. , Stefanou Minas , Campbell Eleanor E. B. , Schaub Renald 
Published: May 2019

AbstractThe field of molecular electronics aims at advancing the miniaturization of electronic devices, by exploiting single molecules to perform the function of individual components. A molecular switch is defined as a molecule that displays stability in two or more states (e.g. “on” and “off” involving conductance, conformation etc.) and upon application of a controlled external perturbation, electric or otherwise, undergoes a reversible change such that the molecule is altered. Previous work has shown multi-state molecular switches with up to four and six distinct states. Using low temperature scanning tunnelling microscopy and spectroscopy, we report on a multi-state single molecule switch using the endohedral fullerene Li@C60 that displays 14 molecular states which can be statistically accessed. We suggest a switching mechanism that relies on resonant tunnelling via the superatom molecular orbitals (SAMOs) of the fullerene cage as a means of Li activation, thereby bypassing the typical vibronic excitation of the carbon cage that is known to cause molecular decomposition.
Emergence of active nematics in chaining bacterial biofilms
Authors: Yaman Yusuf Ilker , Demir Esin , Vetter Roman , Kocabas Askin 
Published: May 2019

AbstractGrowing tissue and bacterial colonies are active matter systems where cell divisions and cellular motion generate active stress. Although they operate in the non-equilibrium regime, these biological systems can form large-scale ordered structures. How mechanical instabilities drive the dynamics of active matter systems and form ordered structures are not well understood. Here, we use chainingBacillus subtilis, also known as a biofilm, to study the relation between mechanical instabilities and nematic ordering. We find that bacterial biofilms have intrinsic length scales above which a series of mechanical instabilities occur. Localized stress and friction drive buckling and edge instabilities which further create nematically aligned structures and topological defects. We also observe that topological defects control stress distribution and initiate the formation of sporulation sites by creating three-dimensional structures. In this study we propose an alternative active matter platform to study the essential roles of mechanics in growing biological tissue.
A neural circuit model of decision uncertainty and change-of-mind
Authors: Atiya Nadim A. A. , Rañó Iñaki , Prasad Girijesh , Wong-Lin KongFatt 
Published: May 2019

AbstractDecision-making is often accompanied by a degree of confidence on whether a choice is correct. Decision uncertainty, or lack in confidence, may lead to change-of-mind. Studies have identified the behavioural characteristics associated with decision confidence or change-of-mind, and their neural correlates. Although several theoretical accounts have been proposed, there is no neural model that can compute decision uncertainty and explain its effects on change-of-mind. We propose a neuronal circuit model that computes decision uncertainty while accounting for a variety of behavioural and neural data of decision confidence and change-of-mind, including testable model predictions. Our theoretical analysis suggests that change-of-mind occurs due to the presence of a transient uncertainty-induced choice-neutral stable steady state and noisy fluctuation within the neuronal network. Our distributed network model indicates that the neural basis of change-of-mind is more distinctively identified in motor-based neurons. Overall, our model provides a framework that unifies decision confidence and change-of-mind.
Extracellular DNA release, quorum sensing, and PrrF1/F2 small RNAs are key players in Pseudomonas aeruginosa tobramycin-enhanced biofilm formation
Authors: Tahrioui Ali , Duchesne Rachel , Bouffartigues Emeline , Rodrigues Sophie , Maillot Olivier , Tortuel Damien , Hardouin Julie , Taupin Laure , Groleau Marie-Christine , Dufour Alain , Déziel Eric , Brenner-Weiss Gerald , Feuilloley Marc , Orange Nicole , Lesouhaitier Olivier , Cornelis Pierre , Chevalier Sylvie 
Published: May 2019

AbstractBiofilms are structured microbial communities that are the leading cause of numerous chronic infections which are difficult to eradicate. Within the lungs of individuals with cystic fibrosis (CF), Pseudomonas aeruginosa causes persistent biofilm infection that is commonly treated with aminoglycoside antibiotics such as tobramycin. However, sublethal concentrations of this aminoglycoside were previously shown to increase biofilm formation by P. aeruginosa, but the underlying adaptive mechanisms still remain elusive. Herein, we combined confocal laser scanning microscope analyses, proteomics profiling, gene expression assays and phenotypic studies to unravel P. aeruginosa potential adaptive mechanisms in response to tobramycin exposure during biofilm growth. Under this condition, we show that the modified biofilm architecture is related at least in part to increased extracellular DNA (eDNA) release, most likely as a result of biofilm cell death. Furthermore, the activity of quorum sensing (QS) systems was increased, leading to higher production of QS signaling molecules. We also demonstrate upon tobramycin exposure an increase in expression of the PrrF small regulatory RNAs, as well as expression of iron uptake systems. Remarkably, biofilm biovolumes and eDNA relative abundances in pqs and prrF mutant strains decrease in the presence of tobramycin. Overall, our findings offer experimental evidences for a potential adaptive mechanism linking PrrF sRNAs, QS signaling, biofilm cell death, eDNA release, and tobramycin-enhanced biofilm formation in P. aeruginosa. These specific adaptive mechanisms should be considered to improve treatment strategies against P. aeruginosa biofilm establishment in CF patients’ lungs.
Lattice frustration in spin-orbit Mott insulator Sr3Ir2O7 at high pressure
Authors: Zhang Jianbo , Yan Dayu , Yesudhas Sorb , Deng Hongshan , Xiao Hong , Chen Bijuan , Sereika Raimundas , Yin Xia , Yi Changjiang , Shi Youguo , Liu Zhenxian , Pärschke Ekaterina M. , Chen Cheng-Chien , Chang Jun , Ding Yang , Mao Ho-kwang 
Published: May 2019

AbstractThe intertwined charge, spin, orbital, and lattice degrees of freedom could endow 5d compounds with exotic properties. Current interest is focused on electromagnetic interactions in these materials, whereas the important role of lattice geometry remains to be fully recognized. For this sake, we investigate pressure-induced phase transitions in the spin-orbit Mott insulator Sr3Ir2O7 with Raman, electrical resistance, and x-ray diffraction measurements. We reveal an interesting magnetic transition coinciding with a structural transition at 14.4 GPa, but without a concurrent insulator-metal transition. The conventional correlation between magnetic and Mott insulating states is thereby absent. The observed softening of the one-magnon mode can be explained by a reduced tetragonal distortion, while the actual magnetic transition is associated with tilting of the IrO6 octahedra. This work highlights the critical role of lattice frustration in determining the high-pressure phases of Sr3Ir2O7. The ability to control electromagnetic properties via manipulating the crystal structure with pressure promises a new way to explore new quantum states in spin-orbit Mott insulators.
Mapping connections in signaling networks with ambiguous modularity
Authors: Lill Daniel , Rukhlenko Oleksii S. , Mc Elwee Anthony James , Kashdan Eugene , Timmer Jens , Kholodenko Boris N. 
Published: May 2019

AbstractModular Response Analysis (MRA) is a suite of methods that under certain assumptions permits the precise reconstruction of both the directions and strengths of connections between network modules from network responses to perturbations. Standard MRA assumes that modules are insulated, thereby neglecting the existence of inter-modular protein complexes. Such complexes sequester proteins from different modules and propagate perturbations to the protein abundance of a downstream module retroactively to an upstream module. MRA-based network reconstruction detects retroactive, sequestration-induced connections when an enzyme from one module is substantially sequestered by its substrate that belongs to a different module. Moreover, inferred networks may surprisingly depend on the choice of protein abundances that are experimentally perturbed, and also some inferred connections might be false. Here, we extend MRA by introducing a combined computational and experimental approach, which allows for a computational restoration of modular insulation, unmistakable network reconstruction and discrimination between solely regulatory and sequestration-induced connections for a range of signaling pathways. Although not universal, our approach extends MRA methods to signaling networks with retroactive interactions between modules arising from enzyme sequestration effects.
Longitudinal 16S rRNA data derived from limb regenerative tissue samples of axolotl Ambystoma mexicanum
Authors: Demircan Turan , İlhan Ayşe Elif , Ovezmyradov Guvanch , Öztürk Gürkan , Yıldırım Süleyman 
Published: May 2019

AbstractThe Mexican axolotl (Ambystoma mexicanum) is a critically endangered species and a fruitful amphibian model for regenerative biology. Despite growing body of research on the cellular and molecular biology of axolotl limb regeneration, microbiological aspects of this process remain poorly understood. Here, we describe bacterial 16S rRNA amplicon dataset derived from axolotl limb tissue samples in the course of limb regeneration. The raw data was obtained by sequencing V3–V4 region of 16S rRNA gene and comprised 14,569,756 paired-end raw reads generated from 21 samples. Initial data analysis using DADA2 pipeline resulted in amplicon sequence variant (ASV) table containing a total of ca. 5.9 million chimera-removed, high-quality reads and a median of 296,971 reads per sample. The data constitute a useful resource for the research on the microbiological aspects of axolotl limb regeneration and will also broadly facilitate comparative studies in the developmental and conservation biology of this critically endangered species.
Multi-omics Analysis of Liver Infiltrating Macrophages Following Ethanol Consumption
Authors: Marentette John O. , Wang Meng , Michel Cole R. , Powell Roger , Zhang Xing , Reisdorph Nichole , Fritz Kristofer S. , Ju Cynthia 
Published: May 2019

AbstractAlcoholic liver disease (ALD) is a significant health hazard and economic burden affecting approximately 10 million people in the United States. ALD stems from the production of toxic-reactive metabolites, oxidative stress and fat accumulation in hepatocytes which ultimately results in hepatocyte death promoting hepatitis and fibrosis deposition. Monocyte-derived infiltrating Ly6Chi and Ly6Clow macrophages are instrumental in perpetuating and resolving the hepatitis and fibrosis associated with ALD pathogenesis. In the present study we isolated liver infiltrating macrophages from mice on an ethanol diet and subjected them to metabolomic and proteomic analysis to provide a broad assessment of the cellular metabolite and protein differences between infiltrating macrophage phenotypes. We identified numerous differentially regulated metabolites and proteins between Ly6Chi and Ly6Clow macrophages. Bioinformatic analysis for pathway enrichment of the differentially regulated metabolites showed a significant number of metabolites involved in the processes of glycerophospholipid metabolism, arachidonic acid metabolism and phospholipid biosynthesis. From analysis of the infiltrating macrophage proteome, we observed a significant enrichment in the biological processes of antigen presentation, actin polymerization and organization, phagocytosis and apoptotic regulation. The data presented herein could yield exciting new research avenues for the analysis of signaling pathways regulating macrophage polarization in ALD.
Near-zero temperature coefficient of resistance of hybrid resistor fabricated with carbon nanotube and metal alloy
Authors: Lee Sunwoo , Kim Eun-Min , Lim Youngtaek 
Published: May 2019

AbstractA hybrid resistor has been fabricated by parallely connecting carbon nanotube (CNT) fiber with negative temperature coefficient of resistance (TCR) and metal alloy with positive TCR to achieve near zero TCR. The CNT fibers were prepared by yarning CNTs grown on the silicone substrate by chemical vapor deposition (CVD) method. The CNT fiber resistors were fabricated by winding CNT fiber on the ceramic rod. Metal terminals were connected at both ends of the CNT fiber wound on the ceramic rod. The metal alloy resistors were fabricated with copper (Cu) and nickel (Ni) with different weight compositions. Electrical resistance and thermal stability (in terms of TCR in this work) of the CNT fiber resistors, the metal alloy resistors, and the hybrid resistors were measured as 7.94 Ω and −870 ppm/°C, 7.94 Ω and 1100 ppm/°C, and 3.97 Ω and −2 ppm/°C, respectively. In case of parallelly connected resistors with suitable combination, the resistance was lower than that of resistor with lower value, and the TCR approached to near zero. Finally, we propose a theoretical approach for adjusting resistance and TCR of the hybrid resistor composed of metal alloy and CNT fibers.
MicroRNA-140-5p inhibits cell proliferation, migration and promotes cell apoptosis in gastric cancer through the negative regulation of THY1-mediated Notch signaling
Authors: Wu Kun , Zou Jun , Lin Chao , Jie Zhi-Gang 
Published: May 2019

Abstract
Studies have highlighted the importance of microRNAs (miRs) in the development of various cancers, including gastric cancer (GC), a commonly occurring malignancy, accompanied by high recurrence and metastasis rate. The aim of the current study was to investigate the role of miR-140-5p in GC. Microarray expression profiles were initially employed to screen the differentially expressed gene related to GC, and the miR regulating the gene was predicted accordingly. The data obtained indicated that thymus cell antigen 1 (THY1) was differentially expressed in GC and confirmed to be a target gene of miR-140-5p. Poorly expressed miR-140-5p and highly expressed THY1 were observed in the GC tissues. SGC-7901 cells were treated with miR-140-5p mimic/inhibitor, siRNA against THY1 and siRNA against Notch1 in order to determine their regulatory roles in GC cell activities. The relationship of miR-140-5p, THY1 and the Notch signaling pathway was subsequently identified. Moreover, cell proliferation, migration, invasion and apoptosis were determined using 3-(4,5-dimethylthiazol-2-yl)-5(3-carboxymethonyphenol)-2-(4-sulfophenyl)-2H-tetrazolium (MTS), wound-healing, transwell assay and flow cytometry, respectively. The overexpression of miR-140-5p and silencing of THY1 resulted in a diminished expression of the Notch signaling pathway-related proteins, as well as inhibited proliferation, migration and invasion of GC cells, enhanced expression of pro-apoptotic proteins in addition to elevated apoptosis rate. Taken together, the present study suggests that miR-140-5p directly targets and negatively regulates THY1 expression and inhibits activation of the Notch signaling pathway, whereby the up-regulation of miR-140-5p inhibits development of GC, highlighting the promise of miR-140-5p as a potential target for GC treatment.
CRISPR/Cas9 applications in gene therapy for primary immunodeficiency diseases
Authors: De Ravin Suk See , Brault Julie 
Published: May 2019

Abstract
Primary immunodeficiency diseases (PIDs) encompass a range of diseases due to mutations in genes that are critical for immunity. Haploinsufficiency and gain-of-function mutations are more complex than simple loss-of-function mutations; in addition to increased susceptibility to infections, immune dysregulations like autoimmunity and hyperinflammation are common presentations. Hematopoietic stem cell (HSC) gene therapy, using integrating vectors, provides potential cure of disease, but genome-wide transgene insertions and the lack of physiological endogenous gene regulation may yet present problems, and not applicable in PIDs where immune regulation is paramount. Targeted genome editing addresses these concerns; we discuss some approaches of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas system applicable for gene therapy in PIDs. Preclinical repair of gene mutations and insertion of complementary DNA restore endogenous gene regulation and they have shown very promising data for clinical application. However, ongoing studies to characterize off-target genotoxicity, careful donor designs to ensure physiological expression, and maneuvers to optimize engraftment potential are critical to ensure successful application of this next-gen targeted HSC gene therapy.
Modelling and kink correction of bulk CMOS at liquid helium temperature
Authors: Li Zhen , Luo Chao , Lu Tengteng , Xu Jun , Kong Weicheng , Guo Guoping 
Published: May 2019

Cryogenic characterisation and modelling of CMOS technology (1.8 and 5 V) is presented in this Letter. Several P‐type MOS and N‐type MOS transistors with different width to length ratios were extensively characterised under various bias conditions at temperatures ranging from 300 K down to 4.2 K. The authors extracted their fundamental physical parameters and developed a compact model based on BSIM3V3. A simple subcircuit was built to correct the kink effect. The RMS error of test results and modelling results is 3%.
Experimental study on low‐THz automotive radar signal attenuation during snowfall
Authors: Norouzian Fatemeh , Marchetti Emidio , Hoare Edward , Gashinova Marina , Constantinou Costas , Gardner Peter , Cherniakov Mikhail 
Published: May 2019

Experimental measurement results of automotive radar signal attenuation during various intensities of snowfall at the current automotive radar frequency (77 GHz) and low‐terahertz (THz) (100–300 GHz) frequencies are presented and compared in this study. The attenuation is characterised by measuring the ratio of the received power from a reference target through snow precipitation of various intensities and through the same path with no precipitation. Statistical analysis of the attenuation is presented. Higher attenuation is measured at a higher frequency, and also attenuation increases as snowfall rate and liquid water content in snowflakes increases. This study is fundamentally important to investigate the effect of adverse weather conditions on low‐THz radar performance in comparison with the current automotive radars operating in the traditional mm‐wave band. In addition, the effects of low‐THz wave attenuation and scattering due to typical contaminants formed on the radome of automotive radars and reflection from common objects on the road are presented.
Biodistribution of nanodiamonds in the body of mice using EPR spectrometry
Authors: Inzhevatkin Evgeny , Baron Alexey , Maksimov Nikolai , Volkova Marina , Puzyr Alexey , Ronzhin Nikita , Bondar Vladimir 
Published: May 2019

In vitro experiments proved the usefulness of electron paramagnetic resonance (EPR) spectrometry for detecting detonation nanodiamonds (NDs) in samples of biomaterials (blood and homogenates of organs of mice). A characteristic EPR signal (g = 2.003, ΔH ≃ 10 G) was detected in biomaterials containing NDs, and its intensity linearly increased at nanoparticle concentrations of between 1.6 and 200 µg/ml. In vivo experiments demonstrated that EPR spectrometry was effective for monitoring the inter‐organ distribution of NDs intravenously injected to mice. In 2.5 h after the injection of NDs, the nanoparticles mainly accumulated in the lungs and liver of the animals – about 25 and 20%, respectively, of the initially injected NDs. The amounts of NDs accumulated in the heart and kidneys were considerably lower. Also, EPR spectrometry did not detect NDs in the blood, spleen, brain, and femoral muscles of mice. Ten days after injection, EPR spectrometry detected redistribution of NDs in mice. The amounts of nanoparticles decreased approximately by a factor of 3.5 in the lungs and increased almost by a factor of 3 in the liver; NDs were detected in the spleen. This study suggests ways to use EPR spectrometry to study the distribution, accumulation, and elimination of detonation NDs injected into laboratory animals.