bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser
Authors: Hunter Mark S. , Yoon Chun Hong , DeMirci Hasan , Sierra Raymond G. , Dao E. Han , Ahmadi Radman , Aksit Fulya , Aquila Andrew L. , Ciftci Halilibrahim , Guillet Serge , Hayes Matt J. , Lane Thomas J. , Liang Meng , Lundström Ulf , Koglin Jason E. , Mgbam Paul , Rao Yashas , Zhang Lindsey , Wakatsuki Soichi , Holton James M. , Boutet Sébastien 
Published: November 2016

AbstractStructural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity and wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.
Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions
Authors: Matsunami Hideyuki , Barker Clive S. , Yoon Young-Ho , Wolf Matthias , Samatey Fadel A. 
Published: November 2016

AbstractThe bacterial flagellar hook is a tubular helical structure made by the polymerization of multiple copies of a protein, FlgE. Here we report the structure of the hook fromCampylobacter jejuniby cryo-electron microscopy at a resolution of 3.5 Å. On the basis of this structure, we show that the hook is stabilized by intricate inter-molecular interactions between FlgE molecules. Extra domains in FlgE, found only inCampylobacterand in related bacteria, bring more stability and robustness to the hook. Functional experiments suggest thatCampylobacterrequires an unusually strong hook to swim without its flagella being torn off. This structure reveals details of the quaternary organization of the hook that consists of 11 protofilaments. Previous study of the flagellar filament ofCampylobacterby electron microscopy showed its quaternary structure made of seven protofilaments. Therefore, this study puts in evidence the difference between the quaternary structures of a bacterial filament and its hook.
Hydrogen bonding: a mechanism for tuning electronic and optical properties of hybrid organic–inorganic frameworks
Authors: El-Mellouhi Fedwa , Bentria El Tayeb , Marzouk Asma , Rashkeev Sergey N , Kais Sabre , Alharbi Fahhad H 
Published: November 2016

AbstractThe field of hybrid inorganic–organic framework materials is one of the fastest growing fields in materials science because their enormous structural and chemical diversity presents great opportunities for creating many technologically relevant properties. One of the most important issues is controlling and tuning the structural, optical, thermal, mechanical and electronic properties of these complex materials by varying their chemistry, fabrication techniques and preparation conditions. Here we demonstrate that significant progress in this area may be achieved by introducing structural elements that form hydrogen bonds with the environment. Considering hybrid framework materials with different structural ordering containing protonated sulfonium cation H3S+and electronegative halogen anions (I−, Br−, Cl−and F−), we found that hydrogen bonding increases the structural stability of the material and may be used for tuning electronic states near the bandgap. We suggest that such a behaviour has a universal character and should be observed in hybrid inorganic–organic framework materials containing protonated cations. This effect may serve as a viable route for optoelectronic and photovoltaic applications.
USP21 deubiquitylates Nanog to regulate protein stability and stem cell pluripotency
Authors: Liu Xingyu , Yao Yuying , Ding Huiguo , Han Chuanchun , Chen Yuhan , Zhang Yuan , Wang Chanjuan , Zhang Xin , Zhang Yiling , Zhai Yun , Wang Ping , Wei Wenyi , Zhang Jing , Zhang Lingqiang 
Published: November 2016

AbstractThe homeobox transcription factor Nanog has a vital role in maintaining pluripotency and self-renewal of embryonic stem cells (ESCs). Stabilization of Nanog proteins is essential for ESCs. The ubiquitin–proteasome pathway mediated by E3 ubiquitin ligases and deubiquitylases is one of the key ways to regulate protein levels and functions. Although ubiquitylation of Nanog catalyzed by the ligase FBXW8 has been demonstrated, the deubiquitylase that maintains the protein levels of Nanog in ESCs yet to be defined. In this study, we identify the ubiquitin-specific peptidase 21 (USP21) as a deubiquitylase for Nanog, but not for Oct4 or Sox2. USP21 interacts with Nanog protein in ESCs in vivo and in vitro. The C-terminal USP domain of USP21 and the C-domain of Nanog are responsible for this interaction. USP21 deubiquitylates the K48-type linkage of the ubiquitin chain of Nanog, stabilizing Nanog. USP21-mediated Nanog stabilization is enhanced in mouse ESCs and this stabilization is required to maintain the pluripotential state of the ESCs. Depletion of USP21 in mouse ESCs leads to Nanog degradation and ESC differentiation. Overall, our results demonstrate that USP21 maintains the stemness of mouse ESCs through deubiquitylating and stabilizing Nanog.
High-quality AlN epitaxy on nano-patterned sapphire substrates prepared by nano-imprint lithography
Authors: Zhang Lisheng , Xu Fujun , Wang Jiaming , He Chenguang , Guo Weiwei , Wang Mingxing , Sheng Bowen , Lu Lin , Qin Zhixin , Wang Xinqiang , Shen Bo 
Published: November 2016

AbstractWe report epitaxial growth of AlN films with atomically flat surface on nano-patterned sapphire substrates (NPSS) prepared by nano-imprint lithography. The crystalline quality can be greatly improved by using the optimized 1-μm-period NPSS. The X-ray diffraction ω-scan full width at half maximum values for (0002) and (10"Equation missing"2) reflections are 171 and 205 arcsec, respectively. The optimized NPSS contribute to eliminating almost entirely the threading dislocations (TDs) originating from the AlN/sapphire interface via bending the dislocations by image force from the void sidewalls before coalescence. In addition, reducing the misorientations of the adjacent regions during coalescence adopting the low lateral growth rate is also essential for decreasing TDs in the upper AlN epilayer.
In vivo online magnetic resonance quantification of absolute metabolite concentrations in microdialysate
Authors: Glöggler Stefan , Rizzitelli Silvia , Pinaud Noël , Raffard Gérard , Zhendre Vanessa , Bouchaud Véronique , Sanchez Stéphane , Radecki Guillaume , Ciobanu Luisa , Wong Alan , Crémillieux Yannick 
Published: November 2016

AbstractIn order to study metabolic processes in animal models of diseases and in patients, microdialysis probes have evolved as powerful tools that are minimally invasive. However, analyses of microdialysate, performed remotely, do not provide real-time monitoring of microdialysate composition. Microdialysate solutions can theoretically be analyzed online inside a preclicinal or clinical MRI scanner using MRS techniques. Due to low NMR sensitivity, acquisitions of real-time NMR spectra on very small solution volumes (μL) with low metabolite concentrations (mM range) represent a major issue. To address this challenge we introduce the approach of combining a microdialysis probe with a custom-built magnetic resonance microprobe that allows for online metabolic analysis (1H and 13C) with high sensitivity under continuous flow conditions. This system is mounted inside an MRI scanner and allows performing simultaneously MRI experiments and rapid MRS metabolic analysis of the microdialysate. The feasibility of this approach is demonstrated by analyzing extracellular brain cancer cells (glioma) in vitro and brain metabolites in an animal model in vivo. We expect that our approach is readily translatable into clinical settings and can be used for a better and precise understanding of diseases linked to metabolic dysfunction.
A compact time reversal emitter-receiver based on a leaky random cavity
Authors: Luong Trung-Dung , Hies Thomas , Ohl Claus-Dieter 
Published: November 2016

AbstractTime reversal acoustics (TRA) has gained widespread applications for communication and measurements. In general, a scattering medium in combination with multiple transducers is needed to achieve a sufficiently large acoustical aperture. In this paper, we report an implementation for a cost-effective and compact time reversal emitter-receiver driven by a single piezoelectric element. It is based on a leaky cavity with random 3-dimensional printed surfaces. The random surfaces greatly increase the spatio-temporal focusing quality as compared to flat surfaces and allow the focus of an acoustic beam to be steered over an angle of 41°. We also demonstrate its potential use as a scanner by embedding a receiver to detect an object from its backscatter without moving the TRA emitter.
Long-term exposure to Myozyme results in a decrease of anti-drug antibodies in late-onset Pompe disease patients
Authors: Masat Elisa , Laforêt Pascal , De Antonio Marie , Corre Guillaume , Perniconi Barbara , Taouagh Nadjib , Mariampillai Kuberaka , Amelin Damien , Mauhin Wladimir , Hogrel Jean-Yves , Caillaud Catherine , Ronzitti Giuseppe , Puzzo Francesco , Kuranda Klaudia , Colella Pasqualina , Mallone Roberto , Benveniste Olivier , Mingozzi Federico ,   French Pompe Registry Study Group, Bassez G. , Bedat-Millet A. L. , Behin A. , Eymard B. , Leonard-Louis S. , Stojkovic T. , Canal A. , Decostre V. , Bouhour F. , Boyer F. , Castaing Y. , Chapon F. , Cintas P. , Durieu I. , Echaniz-Laguna A. , Feasson L. , Furby A. , Hamroun D. , Ferrer X. , Solé G. , Froissart R. , Piraud M. , Germain D. , Benistan K. , Guffon-Fouilhoux N. , Journel H. , Labauge P. , Lacour A. , Levy A. , Magot A. , Péréon Y. , Minot-Myhié M. -C. , Nadaj-Pakleza A. , Nathier C. , Orlikowski D. , Pellegrini N. , Petiot P. , Praline J. , Lofaso F. , Prigent H. , Dutry A. , Renard D. , Sacconi S. , Desnuelle C. , Salort-Campana E. , Pouget J. , Tiffreau V. , Vincent D. , Zagnoli F. 
Published: November 2016

AbstractImmunogenicity of recombinant human acid-alpha glucosidase (rhGAA) in enzyme replacement therapy (ERT) is a safety and efficacy concern in the management of late-onset Pompe disease (LOPD). However, long-term effects of ERT on humoral and cellular responses to rhGAA are still poorly understood. To better understand the impact of immunogenicity of rhGAA on the efficacy of ERT, clinical data and blood samples from LOPD patients undergoing ERT for >4 years (n = 28) or untreated (n = 10) were collected and analyzed. In treated LOPD patients, anti-rhGAA antibodies peaked within the first 1000 days of ERT, while long-term exposure to rhGAA resulted in clearance of antibodies with residual production of non-neutralizing IgG. Analysis of  T cell responses to rhGAA showed detectable T cell reactivity only after in vitro restimulation. Upregulation of several cytokines and chemokines was detectable in both treated and untreated LOPD subjects, while IL2 secretion was detectable only in subjects who received ERT. These results indicate that long-term ERT in LOPD patients results in a decrease in antibody titers and residual production of non-inhibitory IgGs. Immune responses to GAA following long-term ERT do not seem to affect efficacy of ERT and are consistent with an immunomodulatory effect possibly mediated by regulatory T cells.
Photoelectron Holographic Atomic Arrangement Imaging of Cleaved Bimetal-intercalated Graphite Superconductor Surface
Authors: Matsui Fumihiko , Eguchi Ritsuko , Nishiyama Saki , Izumi Masanari , Uesugi Eri , Goto Hidenori , Matsushita Tomohiro , Sugita Kenji , Daimon Hiroshi , Hamamoto Yuji , Hamada Ikutaro , Morikawa Yoshitada , Kubozono Yoshihiro 
Published: November 2016

AbstractFrom the C 1s and K 2p photoelectron holograms, we directly reconstructed atomic images of the cleaved surface of a bimetal-intercalated graphite superconductor, (Ca, K)C8, which differed substantially from the expected bulk crystal structure based on x-ray diffraction (XRD) measurements. Graphene atomic images were collected in the in-plane cross sections of the layers 3.3 Å and 5.7 Å above the photoelectron emitter C atom and the stacking structures were determined as AB- and AA-type, respectively. The intercalant metal atom layer was found between two AA-stacked graphenes. The K atomic image revealing 2 × 2 periodicity, occupying every second centre site of C hexagonal columns, was reconstructed, and the Ca 2p peak intensity in the photoelectron spectra of (Ca, K)C8 from the cleaved surface was less than a few hundredths of the K 2p peak intensity. These observations indicated that cleavage preferentially occurs at the KC8 layers containing no Ca atoms.
Large enhancement of superconducting transition temperature in single-element superconducting rhenium by shear strain
Authors: Mito Masaki , Matsui Hideaki , Tsuruta Kazuki , Yamaguchi Tomiko , Nakamura Kazuma , Deguchi Hiroyuki , Shirakawa Naoki , Adachi Hiroki , Yamasaki Tohru , Iwaoka Hideaki , Ikoma Yoshifumi , Horita Zenji 
Published: November 2016

AbstractFinding a physical approach for increasing the superconducting transition temperature (Tc) is a challenge in the field of material science. Shear strain effects on the superconductivity of rhenium were investigated using magnetic measurements, X-ray diffraction, transmission electron microscopy, and first-principles calculations. A large shear strain reduces the grain size and simultaneously expands the unit cells, resulting in an increase inTc. Here we show that this shear strain approach is a new method for enhancingTcand differs from that using hydrostatic strain. The enhancement ofTcis explained by an increase in net electron–electron coupling rather than a change in the density of states near the Fermi level. The shear strain effect in rhenium could be a successful example of manipulating Bardeen–Cooper–Schrieffer-type Cooper pairing, in which the unit cell volumes are indeed a key parameter.
Graded Mirror Self-Recognition by Clark’s Nutcrackers
Authors: Clary Dawson , Kelly Debbie M. 
Published: November 2016

AbstractThe traditional ‘mark test’ has shown some large-brained species are capable of mirror self-recognition. During this test a mark is inconspicuously placed on an animal’s body where it can only be seen with the aid of a mirror. If the animal increases the number of actions directed to the mark region when presented with a mirror, the animal is presumed to have recognized the mirror image as its reflection. However, the pass/fail nature of the mark test presupposes self-recognition exists in entirety or not at all. We developed a novel mirror-recognition task, to supplement the mark test, which revealed gradation in the self-recognition of Clark’s nutcrackers, a large-brained corvid. To do so, nutcrackers cached food alone, observed by another nutcracker, or with a regular or blurry mirror. The nutcrackers suppressed caching with a regular mirror, a behavioural response to prevent cache theft by conspecifics, but did not suppress caching with a blurry mirror. Likewise, during the mark test, most nutcrackers made more self-directed actions to the mark with a blurry mirror than a regular mirror. Both results suggest self-recognition was more readily achieved with the blurry mirror and that self-recognition may be more broadly present among animals than currently thought.
Association of Mannose-binding Lectin Polymorphisms with Tuberculosis Susceptibility among Chinese
Authors: Liu Cheng , He Tao , Rong Yanxiao , Du Fengjiao , Ma Dongxing , Wei Yujie , Mei Zhiqin , Wang Yuling , Wang Haibin , Zhu Yuehua , Zhang Zongde , Zheng Li , Wu Xueqiong , Liu Huiliang , Ding Wenjun 
Published: November 2016

AbstractTuberculosis (TB) is caused by infection of Mycobacterium tuberculosis. Host genetic variability is an important determinant of the risk of developing TB in humans. Although the association between MBL2 polymorphisms and TB has been studied in various populations, the results are controversial. In this study four functional single-nucleotide polymorphisms (SNPs, H/L, X/Y, P/Q and A/B) across the MBL2 gene were genotyped by direct DNA sequencing of PCR products in a case-control population of Chinese Han origin, consisting of 1,020 patients with pulmonary TB and 1,020 controls. We found that individuals carrying variant allele at A/B (namely BB or AB genotypes) was associated with increased susceptibility to TB (odds ratios [OR] = 1.57, 95% confidence interval [CI] 1.30–1.91, P = 1.3 × 10−6). Additionally, LYPB haplotype showed a significant association with increased risk of TB (OR = 1.54, 95% CI 1.27–1.87, P = 4.2 × 10−6; global haplotype association P = 3.5 × 10−5). Furthermore, individuals bearing low- or medium- MBL expression haplotype pairs had an increased risk of TB (OR = 1.56, 95% CI 1.29–1.90, P = 1.4 × 10−6). Thus, the reduced expression of functional MBL secondary to having MBL2 variants may partially mediate the increased susceptibility to TB risk.
The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis
Authors: Hotterbeekx An , Xavier Basil B. , Bielen Kenny , Lammens Christine , Moons Pieter , Schepens Tom , Ieven Margareta , Jorens Philippe G , Goossens Herman , Kumar-Singh Samir , Malhotra-Kumar Surbhi 
Published: November 2016

AbstractVentilator-associated pneumonia (VAP) is one of the commonest hospital-acquired infections associated with high mortality. VAP pathogenesis is closely linked to organisms colonizing the endotracheal tube (ETT) such as Staphylococcus epidermidis and Pseudomonas aeruginosa, the former a common commensal with pathogenic potential and the latter a known VAP pathogen. However, recent gut microbiome studies show that pathogens rarely function alone. Hence, we determined the ETT microbial consortium co-colonizing with S. epidermidis or P. aeruginosa to understand its importance in the development of VAP and for patient prognosis. Using bacterial 16S rRNA and fungal ITS-II sequencing on ETT biomass showing presence of P. aeruginosa and/or S. epidermidis on culture, we found that presence of P. aeruginosa correlated inversely with patient survival and with bacterial species diversity. A decision tree, using 16S rRNA and patient parameters, to predict patient survival was generated. Patients with a relative abundance of Pseudomonadaceae <4.6% and of Staphylococcaceae <70.8% had the highest chance of survival. When Pseudomonadaceae were >4.6%, age of patient <66.5 years was the most important predictor of patient survival. These data indicate that the composition of the ETT microbiome correlates with patient prognosis, and presence of P. aeruginosa is an important predictor of patient outcome.
An Investigation of the Differences and Similarities between Generated Small-World Networks for Right- and Left-Hand Motor Imageries
Authors: Zhang Jiang , Li Yuyao , Chen Huafu , Ding Jurong , Yuan Zhen 
Published: November 2016

AbstractIn this study, small-world network analysis was performed to identify the similarities and differences between functional brain networks for right- and left-hand motor imageries (MIs). First, Pearson correlation coefficients among the nodes within the functional brain networks from healthy subjects were calculated. Then, small-world network indicators, including the clustering coefficient, the average path length, the global efficiency, the local efficiency, the average node degree, and the small-world index, were generated for the functional brain networks during both right- and left-hand MIs. We identified large differences in the small-world network indicators between the functional networks during MI and in the random networks. More importantly, the functional brain networks underlying the right- and left-hand MIs exhibited similar small-world properties in terms of the clustering coefficient, the average path length, the global efficiency, and the local efficiency. By contrast, the right- and left-hand MI brain networks showed differences in small-world characteristics, including indicators such as the average node degree and the small-world index. Interestingly, our findings also suggested that the differences in the activity intensity and range, the average node degree, and the small-world index of brain networks between the right- and left-hand MIs were associated with the asymmetry of brain functions.
Thermoelectric properties of in-situ plasma spray synthesized sub-stoichiometry TiO2−x
Authors: Lee Hwasoo , Han Su Jung , Chidambaram Seshadri Ramachandran , Sampath Sanjay 
Published: November 2016

AbstractThe thermoelectric properties of sub-stoichiometric TiO2−xdeposits produced by cascaded-plasma spray process are investigated from room-temperature to 750 K. Sub-stoichiometric TiO2−xdeposits are formed throughin-situreaction of the TiO1.9within the high temperature plasma flame and manipulated through introduction of varying amounts of hydrogen in the plasma. Although the TiO2−xparticles experience reduction within plasma, it can also re-oxidize through interaction with the surrounding ambient atmosphere, resulting in a complex interplay between process conditions and stoichiometry. The deposits predominantly contain rutile phase with presence of Magneli phases especially under significantly reducing plasma conditions. The resultant deposits show sensitivity to thermoelectric properties and under certain optimal conditions repeatedly show Seebeck coefficients reaching values of −230 μV K−1at temperatures of 750 K while providing an electrical conductivity of 5.48 × 103 S m−1, relatively low thermal conductivity in the range of 1.5 to 2 W m−1K−1resulting in power factor of 2.9 μW cm−1K−2. The resultant maximum thermoelectric figure of merit value reached 0.132 under these optimal conditions. The results point to a potential pathway for a large-scale fabrication of low-cost oxide based thermoelectric with potential applicability at moderate to high temperatures.