bluuebunny/crossref_metadata_2025_split huggingface dataset:
An O2-sensing stressosome from a Gram-negative bacterium
Authors: Jia Xin , Wang Jian-bo , Rivera Shannon , Duong Duc , Weinert Emily E. 
Published: August 2016

AbstractBacteria have evolved numerous pathways to sense and respond to changing environmental conditions, including, within Gram-positive bacteria, the stressosome complex that regulates transcription of general stress response genes. However, the signalling molecules recognized by Gram-positive stressosomes have yet to be identified, hindering our understanding of the signal transduction mechanism within the complex. Furthermore, an analogous pathway has yet to be described in Gram-negative bacteria. Here we characterize a putative stressosome from the Gram-negative bacterium Vibrio brasiliensis. The sensor protein RsbR binds haem and exhibits ligand-dependent control of the stressosome complex activity. Oxygen binding to the haem decreases activity, while ferrous RsbR results in increased activity, suggesting that the V. brasiliensis stressosome may be activated when the bacterium enters anaerobic growth conditions. The findings provide a model system for investigating ligand-dependent signalling within stressosome complexes, as well as insights into potential pathways controlled by oxygen-dependent signalling within Vibrio species.
Atomistic material behavior at extreme pressures
Authors: Béland Laurent Karim , Osetsky Yuri N , Stoller Roger E 
Published: August 2016

AbstractComputer simulations are routinely performed to model the response of materials to extreme environments, such as neutron (or ion) irradiation. The latter involves high-energy collisions from which a recoiling atom creates a so-called atomic displacement cascade. These cascades involve coordinated motion of atoms in the form of supersonic shockwaves. These shockwaves are characterized by local atomic pressures >15 GPa and interatomic distances <2 Å. Similar pressures and interatomic distances are observed in other extreme environment, including short-pulse laser ablation, high-impact ballistic collisions and diamond anvil cells. Displacement cascade simulations using four different force fields, with initial kinetic energies ranging from 1 to 40 keV, show that there is a direct relationship between these high-pressure states and stable defect production. An important shortcoming in the modeling of interatomic interactions at these short distances, which in turn determines final defect production, is brought to light.
Oxidized Low-density Lipoprotein (ox-LDL) Cholesterol Induces the Expression of miRNA-223 and L-type Calcium Channel Protein in Atrial Fibrillation
Authors: He Fengping , Xu Xin , Yuan Shuguo , Tan Liangqiu , Gao Lingjun , Ma Shaochun , Zhang Shebin , Ma Zhanzhong , Jiang Wei , Liu Fenglian , Chen Baofeng , Zhang Beibei , Pang Jungang , Huang Xiuyan , Weng Jiaqiang 
Published: August 2016

AbstractAtrial fibrillation (AF) is the most common sustained arrhythmia causing high morbidity and mortality. While changing of the cellular calcium homeostasis plays a critical role in AF, the L-type calcium channel α1c protein has suggested as an important regulator of reentrant spiral dynamics and is a major component of AF-related electrical remodeling. Our computational modeling predicted that miRNA-223 may regulate theCACNA1Cgene which encodes the cardiac L-type calcium channel α1c subunit. We found that oxidized low-density lipoprotein (ox-LDL) cholesterol significantly up-regulates both the expression of miRNA-223 and L-type calcium channel protein. In contrast, knockdown of miRNA-223 reduced L-type calcium channel protein expression, while genetic knockdown of endogenous miRNA-223 dampened AF vulnerability. Transfection of miRNA-223 by adenovirus-mediated expression enhanced L-type calcium currents and promoted AF in mice while co-injection of aCACNA1C-specific miR-mimic counteracted the effect. Taken together, ox-LDL, as a known factor in AF-associated remodeling, positively regulates miRNA-223 transcription and L-type calcium channel protein expression. Our results implicate a new molecular mechanism for AF in which miRNA-223 can be used as an biomarker of AF rheumatic heart disease.
Experimental Identification of Electric Field Excitation Mechanisms in a Structural Transition of Tokamak Plasmas
Authors: Kobayashi T. , Itoh K. , Ido T. , Kamiya K. , Itoh S.-I. , Miura Y. , Nagashima Y. , Fujisawa A. , Inagaki S. , Ida K. , Hoshino K. 
Published: August 2016

AbstractSelf-regulation between structure and turbulence, which is a fundamental process in the complex system, has been widely regarded as one of the central issues in modern physics. A typical example of that in magnetically confined plasmas is the Low confinement mode to High confinement mode (L-H) transition, which is intensely studied for more than thirty years since it provides a confinement improvement necessary for the realization of the fusion reactor. An essential issue in the L-H transition physics is the mechanism of the abrupt “radial” electric field generation in toroidal plasmas. To date, several models for the L-H transition have been proposed but the systematic experimental validation is still challenging. Here we report the systematic and quantitative model validations of the radial electric field excitation mechanism for the first time, using a data set of the turbulence and the radial electric field having a high spatiotemporal resolution. Examining time derivative of Poisson’s equation, the sum of the loss-cone loss current and the neoclassical bulk viscosity current is found to behave as the experimentally observed radial current that excites the radial electric field within a few factors of magnitude.
Transition from two-dimensional photonic crystals to dielectric metasurfaces in the optical diffraction with a fine structure
Authors: Rybin Mikhail V. , Samusev Kirill B. , Lukashenko Stanislav Yu. , Kivshar Yuri S. , Limonov Mikhail F. 
Published: August 2016

AbstractWe study experimentally a fine structure of the optical Laue diffraction from two-dimensional periodic photonic lattices. The periodic photonic lattices with the C4v square symmetry, orthogonal C2v symmetry and hexagonal C6v symmetry are composed of submicron dielectric elements fabricated by the direct laser writing technique. We observe surprisingly strong optical diffraction from a finite number of elements that provides an excellent tool to determine not only the symmetry but also exact number of particles in the finite-length structure and the sample shape. Using different samples with orthogonal C2v symmetry and varying the lattice spacing, we observe experimentally a transition between the regime of multi-order diffraction, being typical for photonic crystals to the regime where only the zero-order diffraction can be observed, being is a clear fingerprint of dielectric metasurfaces characterized by effective parameters.
Broadband multiple responses of surface modes in quasicrystalline plasmonic structure
Authors: Yuan Haiming , Jiang Xiangqian , Huang Feng , Sun Xiudong 
Published: August 2016

AbstractWe numerically study the multiple excitation of surface modes in 2D photonic quasicrystal/metal/substrate structure. An improved rigorous coupled wave analysis method that can handle the quasicrystalline structure is presented. The quasicrystalline lattice, which refers to Penrose tiling in this paper, is generated by the cut-and-project method. The normal incidence spectrum presents a broadband multiple responses property. We find that the phase matching condition determines the excitation frequency for a given incident angle, while the depth of the reflection valley depends on the incident polarization. The modes will split into several sub-modes at oblique incidence, which give rise to the appearance of more responses on the spectrum.
Highly stable tandem solar cell monolithically integrating dye-sensitized and CIGS solar cells
Authors: Chae Sang Youn , Park Se Jin , Joo Oh-Shim , Jun Yongseok , Min Byoung Koun , Hwang Yun Jeong 
Published: August 2016

AbstractA highly stable monolithic tandem solar cell was developed by combining the heterogeneous photovoltaic technologies of dye-sensitized solar cell (DSSC) and solution-processed CuInxGa1-xSeyS1-y (CIGS) thin film solar cells. The durability of the tandem cell was dramatically enhanced by replacing the redox couple from "Equation missing" to [Co(bpy)3]2+ /[Co(bpy)3]3+), accompanied by a well-matched counter electrode (PEDOT:PSS) and sensitizer (Y123). A 1000 h durability test of the DSSC/CIGS tandem solar cell in ambient conditions resulted in only a 5% decrease in solar cell efficiency. Based on electrochemical impedance spectroscopy and photoelectrochemical cell measurement, the enhanced stability of the tandem cell is attributed to minimal corrosion by the cobalt-based polypyridine complex redox couple.
Predictive Immunohistochemical Markers Related to Drug Selection for Patients Treated with Sunitinib or Sorafenib for Metastatic Renal Cell Cancer
Authors: Ma Xin , Wang Lei , Li Hongzhao , Zhang Yu , Gao Yu , Guo Gang , Liu Kan , Meng Qingyu , Zhao Chaofei , Wang Dianjun , Song Zhigang , Zhang Xu 
Published: August 2016

AbstractTargeted drug decisions in metastatic renal cell carcinoma are exclusively made on the basis of clinical criteria. We investigated whether these biomarkers (HIF-1α, HIF-2α, CAIX, VEGF, VEGFR1, VEGFR2, VEGFR3, PDGFB, PDGFRA, PDGFRB, CD31, CD44, bcl-xL, KIT, p21, CXCR4, PTEN, (CSF)-1R, RET, and FLT-3) can predictive the different effects between sunitinib and sorafenib treatments and are available to guide targeted drug selection. We enrolled all patients who underwent nephrectomy with postoperative sunitinib- or sorafenib-treatment at our institution from 2007 to 2012. Immunohistochemical approach was applied to assess the potential differential effects of immunostainings between sunitinib- and sorafenib-treated groups. We found that patients with high HIF-2α, CD31 expression showed greater relative PFS and OS benefit and patients with high CAIX expression presented greater relative OS benefit from sunitinib than from sorafenib, patients with high VEGFR1 or PDGFRB expression levels exhibited worse relative PFS benefit from sunitinib than from sorafenib. Namely high HIF-2α, CD31, and CAIX expression levels along with low VEGFR1 and PDGFRB expression levels improved the benefit of sunitinib treatment compared with sorafenib treatment. These results can identify whether patients can benefit more from sunitinib or sorafenib for drug selection guidance, eventually with precision medicine.
Hypoxic Preconditioning Inhibits Hypoxia-induced Apoptosis of Cardiac Progenitor Cells via the PI3K/Akt-DNMT1-p53 Pathway
Authors: Xu Rongfeng , Sun Yuning , Chen Zhongpu , Yao Yuyu , Ma Genshan 
Published: August 2016

AbstractResearch has demonstrated that hypoxic preconditioning (HP) can enhance the survival and proliferation of cardiac progenitor cells (CPCs); however, the underlying mechanisms are not fully understood. Here, we report that HP of c-kit (+) CPCs inhibits p53 via the PI3K/Akt-DNMT1 pathway. First, CPCs were isolated from the hearts of C57BL/6 mice and further purified by magnetic-activated cell sorting. Next, these cells were cultured under either normoxia (H0) or HP for 6 hours (H6) followed by oxygen–serum deprivation for 24 hours (24h). Flow cytometric analysis and MTT assays revealed that hypoxia-preconditioned CPCs exhibited an increased survival rate. Western blot and quantitative real-time PCR assays showed that p53 was obviously inhibited, while DNMT1 and DNMT3β were both significantly up-regulated by HP. Bisulphite sequencing analysis indicated that DNMT1 and DNMT3β did not cause p53 promoter hypermethylation. A reporter gene assay and chromatin immunoprecipitation analysis further demonstrated that DNMT1 bound to the promoter locus of p53 in hypoxia-preconditioned CPCs. Together, these observations suggest that HP of CPCs could lead to p53 inhibition by up-regulating DNMT1 and DNMT3β, which does not result in p53 promoter hypermethylation and that DNMT1 might directly repress p53, at least in part, by binding to the p53 promoter locus.
Expression of Cystic Fibrosis Transmembrane Conductance Regulator in Ganglia of Human Gastrointestinal Tract
Authors: Xue Ruiqi , Gu Huan , Qiu Yamei , Guo Yong , Korteweg Christine , Huang Jin , Gu Jiang 
Published: August 2016

AbstractCF is caused by mutations of the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) which is an anion selective transmembrane ion channel that mainly regulates chloride transport, expressed in the epithelia of various organs. Recently, we have demonstrated CFTR expression in the brain, the spinal cord and the sympathetic ganglia. This study aims to investigate the expression and distribution of CFTR in the ganglia of the human gastrointestinal tract. Fresh tissue and formalin-fixed paraffin-embedded normal gastrointestinal tract samples were collected from eleven surgical patients and five autopsy cases. Immunohistochemistry, in situ hybridization, laser-assisted microdissection and nested reverse transcriptase polymerase chain reaction were performed. Expression of CFTR protein and mRNA was detected in neurons of the ganglia of all segments of the human gastrointestinal tract examined, including the stomach, duodenum, jejunum, ileum, cecum, appendix, colon and rectum. The extensive expression of CFTR in the enteric ganglia suggests that CFTR may play a role in the physiology of the innervation of the gastro-intestinal tract. The presence of dysfunctional CFTRs in enteric ganglia could, to a certain extent, explain the gastrointestinal symptoms frequently experienced by CF patients.
Electroretinographic evaluations of retinal function before, just after and after intravitreal injections
Authors: Yagura Kazuma , Shinoda Kei , Matsumoto Soiti , Terauchi Gaku , Kawashima Makoto , Watanabe Emiko , Matsumoto Harue , Iwata Takeshi , Mizota Atsushi , Miyake Yozo 
Published: August 2016

AbstractIntravitreal injections (IVI) have become a part of daily practice for a growing number of procedures. We evaluated the retinal function by recording intraoperative photopic electroretinograms (ERGs) before an injection (T1), just after the injection (T2) and after the aspiration of the anterior chamber fluid (T3) of 19 eyes of 19 patients (mean age 70.6 years; men = 11) who received an IVI of an anti-vascular endothelial growth factor. The mean amplitudes of the b-wave, photopic negative responses (PhNR) and oscillatory potentials (OPs) 1 and 2 at T2 were significantly smaller than that at T1, but no significant difference was observed between T3 and T1. The mean implicit times of the a-wave and OP1, 2 and 3 at T2 and the a-wave and the OP2 at T3 were significantly longer than that at T1. The mean intraocular pressure (IOP) at T2 (49.32 mm Hg) was significantly higher and the IOP at T3 (8.74 mm Hg) was significantly lower than that at T1 (21.05 mm Hg). The retinal function was reduced and the IOP elevated just after the IVI. The response of each ERG component was different suggesting a different sensitivity of each type of retinal neuron to IVI.
Conditional Deletion of Smad1 Ameliorates Glomerular Injury in Progressive Glomerulonephritis
Authors: Araki Makoto , Matsubara Takeshi , Abe Hideharu , Torikoshi Kazuo , Mima Akira , Iehara Noriyuki , Fukatsu Atsushi , Kita Toru , Arai Hidenori , Doi Toshio 
Published: August 2016

AbstractMatrix expansion and cell proliferation are concomitantly observed in various glomerular injuries. However, the molecular mechanisms responsible for these changes have not been fully elucidated. We have reported that Smad1 is a key signalling molecule that regulates the transcription of type IV collagen (Col4) in mesangial matrix expansion and is thereby involved in glomerular injury in an acute model of glomerulonephritis. In this study, we addressed the role of Smad1 signalling in accelerated nephrotoxic nephritis (NTN), a model of progressive glomerulonephritis, using conditional deletion of Smad1 in Rosa26CreERT2 mice (Smad1-CKO). Mesangial matrix expansion in the Smad1-CKO mice with NTN was significantly inhibited compared with that in wild type mice with NTN, which was consistent with the decrease in Col4 expression level. On the other hand, STAT3 activation and cell proliferation were not influenced by Smad1 deletion in the NTN model. Therefore, we investigated another factor that activates cell proliferation in the absence of Smad1. Id2 induced VEGF secretion and subsequent STAT3 activation, independently of Smad1 expression in mouse mesangial cells. Here we show that Smad1 plays an important role in the development of glomerular injury without affecting cell proliferation, in progressive glomerulonephritis.
UWB to 30 narrow sub‐bands frequency reconfigurable antipodal Vivaldi antenna
Authors: Bitchikh M. , Ghanem F. 
Published: August 2016

An antipodal Vivaldi antenna is presented that can be switched between an UWB mode and a tuneable very narrowband mode where the 3.3–10.6 GHz band can be covered by 30 different sub‐bands. To achieve this high‐frequency resolution, a gap is inserted in the Vivaldi feedline and a split‐ring‐resonator (SRR) is disposed close to it to serve as a coupling‐bridge. By doing so, only frequencies whose quarter‐wavelengths correspond to the SRR electrical length get coupled, before being coupled again to the other side of the feedline causing thus the antenna operation. Moreover, by capacitively loading the SRR and varying the load, the frequencies that can bridge the gap are varied, which allows tuning the antenna operating band. Now, to be able to efficiently cover the whole UWB, two SRRs of different sizes are alternatively used. Each SRR can be deactivated by disrupting its structure by means of switches. Finally, to operate the antenna in the UWB mode, the two SRR's are deactivated and the gap in the feedline is closed by means of a switch. To present the Letter, simulated and measured results are presented and discussed.
Joint interpolation for LTE downlink channel estimation in very high‐mobility environments with support vector machine regression
Authors: Charrada Anis , Samet Abdelaziz 
Published: August 2016

In this study, the estimation of fast‐fading long term evolution (LTE) downlink channels in high‐speed applications of LTE advanced is investigated by the authors. A robust channel estimation and interpolation algorithm is essential in order to adequately track the fast time‐varying channel response. In this contribution, the multipath fast‐fading channel is modelled as a discrete, tapped‐delay and finite impulse response filter. Using support vector machine regression (SVR), they develop an extended algorithm to jointly estimate the complex‐valued channel frequency response in time and frequency domains, in the presence of fading and non‐linear noise from the transmission of known pilot symbols. Furthermore, the channel estimates at the known pilot symbols are interpolated to the unknown data symbols by using the non‐linear SVR approach exploiting kernel features. This study integrates both channel estimation at pilot symbols and interpolation at data symbol into the complex SVR interpolation method. The bit error rate and mean square error performances of the authors’ fast‐fading channel estimation scheme is demonstrated via simulation for LTE downlink with 64‐QAM modulation and 500 km/h velocity under non‐linearities.
Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway
Authors: Bisaria Namita , Greenfeld Max , Limouse Charles , Pavlichin Dmitri S. , Mabuchi Hideo , Herschlag Daniel 
Published: August 2016

Significance
Many biological processes, including splicing, translation, and genome maintenance, require structured RNAs to fold into complex three-dimensional shapes. Our current understanding of these processes is based on distilling principles from descriptive folding studies. Moving toward predictive models will require coupling observed structural changes with kinetic and thermodynamic measurements. We have dissected P4-P6 RNA folding through distinct structural states and measured the rate and equilibrium constants for transitions between these states. Common kinetics found for RNA tertiary elements embedded in different structural contexts may help develop predictive folding models. Also, our results suggest that RNA folding may be well described by a model analogous to the diffusion-collision model for protein folding.
Crystal structure of a human neuronal nAChR extracellular domain in pentameric assembly: Ligand-bound α2 homopentamer
Authors: Kouvatsos Nikolaos , Giastas Petros , Chroni-Tzartou Dafni , Poulopoulou Cornelia , Tzartos Socrates J. 
Published: August 2016

Significance
Nicotinic acetylcholine receptors (nAChRs) are pentameric ligand-gated ion channels involved in fast neurotransmission. Here, we present the crystal structure of the homopentameric assembly of the extracellular domain (ECD) of α2 nAChR subunit in complex with an agonist. The structure provides a unique opportunity to probe the interactions involved in the formation of the ligand binding site of a WT nAChR and their role in stabilizing an agonist. Furthermore, functional studies revealed the role of additional residues in the activation and desensitization of the α2β2 nAChRs. High sequence identity of α2 ECD with other neuronal subunits signifies the importance of the structure as a template for modeling several neuronal nAChR ECDs and for designing nAChR subtype-specific drugs against related diseases.
From fire whirls to blue whirls and combustion with reduced pollution
Authors: Xiao Huahua , Gollner Michael J. , Oran Elaine S. 
Published: August 2016

Significance
The growing worldwide demand to reduce emissions from combustion calls for development of alternative technologies for high-efficiency and low-emission combustion. Whereas fire whirls are known for their intense and disastrous threat to life and surrounding environments, their swirl properties and thus higher combustion efficiency imply an unexploited potential for highly efficient, low-emission combustion. In studying fire whirls over water for oil-spill cleanup, we discovered a beautiful, swirling flame phenomenon, the “blue whirl,” which evolves from a fire whirl and burns with nearly soot-free combustion. Understanding and control of the blue whirl and its predecessor, the fire whirl, will suggest new ways for fuel-spill remediation, reduced-pollution combustion, and fluid mechanics research.
The politics of office design
Authors: Roderick Ian 
Published: August 2016

AbstractRecent changes in open plan office design are intended to facilitate flexible and collaborative work practices. Though promoted in terms of aesthetics and functionality, these changes in layout and furnishing communicate a great deal about how work and the workers that perform them are understood. Drawing upon the semiotics of framing and the chronotope, the open plan office is analyzed as a multimodal realization of neoliberal discourses on the flexibilization and deregulation of work. As such, the collaborative open plan office does more than represent or give expression to neoliberal ideologies, it normalizes and makes durable the work processes, identities and temporalities of neoliberalized labour.