bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanoscale kinetics of asymmetrical corrosion in core-shell nanoparticles
Authors: Shan Hao , Gao Wenpei , Xiong Yalin , Shi Fenglei , Yan Yucong , Ma Yanling , Shang Wen , Tao Peng , Song Chengyi , Deng Tao , Zhang Hui , Yang Deren , Pan Xiaoqing , Wu Jianbo 
Published: March 2018

AbstractDesigning new materials and structure to sustain the corrosion during operation requires better understanding on the corrosion dynamics. Observation on how the corrosion proceeds in atomic scale is thus critical. Here, using a liquid cell, we studied the real-time corrosion process of palladium@platinum (Pd@Pt) core-shell nanocubes via transmission electron microscopy (TEM). The results revealed that multiple etching pathways operatively contribute to the morphology evolution during corrosion, including galvanic etching on non-defected sites with slow kinetics and halogen-induced etching at defected sites at faster rates. Corners are the preferential corrosion sites; both etching pathways are mutually restricted during corrosion. Those insights on the interaction of nanostructures with reactive liquid environments can help better engineer the surface structure to improve the stability of electrocatalysts as well as design a new porous structure that may provide more active sites for catalysis.
Cation vacancy stabilization of single-atomic-site Pt1/Ni(OH)x catalyst for diboration of alkynes and alkenes
Authors: Zhang Jian , Wu Xi , Cheong Weng-Chon , Chen Wenxing , Lin Rui , Li Jia , Zheng Lirong , Yan Wensheng , Gu Lin , Chen Chen , Peng Qing , Wang Dingsheng , Li Yadong 
Published: March 2018

AbstractDevelopment of single-atomic-site catalysts with high metal loading is highly desirable but proved to be very challenging. Although utilizing defects on supports to stabilize independent metal atoms has become a powerful method to fabricate single-atomic-site catalysts, little attention has been devoted to cation vacancy defects. Here we report a nickel hydroxide nanoboard with abundant Ni2+ vacancy defects serving as the practical support to achieve a single-atomic-site Pt catalyst (Pt1/Ni(OH)x) containing Pt up to 2.3 wt% just by a simple wet impregnation method. The Ni2+ vacancies are found to have strong stabilizing effect of single-atomic Pt species, which is determined by X-ray absorption spectrometry analyses and density functional theory calculations. This Pt1/Ni(OH)x catalyst shows a high catalytic efficiency in diboration of a variety of alkynes and alkenes, yielding an overall turnover frequency value upon reaction completion for phenylacetylene of ~3000 h−1, which is much higher than other reported heterogeneous catalysts.
Design and validation of a foldable and photovoltaic wide-field epiretinal prosthesis
Authors: Ferlauto Laura , Airaghi Leccardi Marta Jole Ildelfonsa , Chenais Naïg Aurelia Ludmilla , Gilliéron Samuel Charles Antoine , Vagni Paola , Bevilacqua Michele , Wolfensberger Thomas J. , Sivula Kevin , Ghezzi Diego 
Published: March 2018

AbstractRetinal prostheses have been developed to fight blindness in people affected by outer retinal layer dystrophies. To date, few hundred patients have received a retinal implant. Inspired by intraocular lenses, we have designed a foldable and photovoltaic wide-field epiretinal prosthesis (named POLYRETINA) capable of stimulating wireless retinal ganglion cells. Here we show that within a visual angle of 46.3 degrees, POLYRETINA embeds 2215 stimulating pixels, of which 967 are in the central area of 5 mm, it is foldable to allow implantation through a small scleral incision, and it has a hemispherical shape to match the curvature of the eye. We demonstrate that it is not cytotoxic and respects optical and thermal safety standards; accelerated ageing shows a lifetime of at least 2 years. POLYRETINA represents significant progress towards the improvement of both visual acuity and visual field with the same device, a current challenging issue in the field.
An HDAC9-MALAT1-BRG1 complex mediates smooth muscle dysfunction in thoracic aortic aneurysm
Authors: Lino Cardenas Christian L. , Kessinger Chase W. , Cheng Yisha , MacDonald Carolyn , MacGillivray Thomas , Ghoshhajra Brian , Huleihel Luai , Nuri Saifar , Yeri Ashish S. , Jaffer Farouc A. , Kaminski Naftali , Ellinor Patrick , Weintraub Neal L. , Malhotra Rajeev , Isselbacher Eric M. , Lindsay Mark E. 
Published: March 2018

AbstractThoracic aortic aneurysm (TAA) has been associated with mutations affecting members of the TGF-β signaling pathway, or components and regulators of the vascular smooth muscle cell (VSMC) actomyosin cytoskeleton. Although both clinical groups present similar phenotypes, the existence of potential common mechanisms of pathogenesis remain obscure. Here we show that mutations affecting TGF-β signaling and VSMC cytoskeleton both lead to the formation of a ternary complex comprising the histone deacetylase HDAC9, the chromatin-remodeling enzyme BRG1, and the long noncoding RNA MALAT1. The HDAC9–MALAT1–BRG1 complex binds chromatin and represses contractile protein gene expression in association with gain of histone H3-lysine 27 trimethylation modifications. Disruption of Malat1 or Hdac9 restores contractile protein expression, improves aortic mural architecture, and inhibits experimental aneurysm growth. Thus, we highlight a shared epigenetic pathway responsible for VSMC dysfunction in both forms of TAA, with potential therapeutic implication for other known HDAC9-associated vascular diseases.
An accurate and robust imputation method scImpute for single-cell RNA-seq data
Authors: Li Wei Vivian , Li Jingyi Jessica 
Published: March 2018

AbstractThe emerging single-cell RNA sequencing (scRNA-seq) technologies enable the investigation of transcriptomic landscapes at the single-cell resolution. ScRNA-seq data analysis is complicated by excess zero counts, the so-called dropouts due to low amounts of mRNA sequenced within individual cells. We introduce scImpute, a statistical method to accurately and robustly impute the dropouts in scRNA-seq data. scImpute automatically identifies likely dropouts, and only perform imputation on these values without introducing new biases to the rest data. scImpute also detects outlier cells and excludes them from imputation. Evaluation based on both simulated and real human and mouse scRNA-seq data suggests that scImpute is an effective tool to recover transcriptome dynamics masked by dropouts. scImpute is shown to identify likely dropouts, enhance the clustering of cell subpopulations, improve the accuracy of differential expression analysis, and aid the study of gene expression dynamics.
Expansion of functional personalized cells with specific transgene combinations
Authors: Lipps Christoph , Klein Franziska , Wahlicht Tom , Seiffert Virginia , Butueva Milada , Zauers Jeannette , Truschel Theresa , Luckner Martin , Köster Mario , MacLeod Roderick , Pezoldt Jörn , Hühn Jochen , Yuan Qinggong , Müller Peter Paul , Kempf Henning , Zweigerdt Robert , Dittrich-Breiholz Oliver , Pufe Thomas , Beckmann Rainer , Drescher Wolf , Riancho Jose , Sañudo Carolina , Korff Thomas , Opalka Bertram , Rebmann Vera , Göthert Joachim R. , Alves Paula M. , Ott Michael , Schucht Roland , Hauser Hansjörg , Wirth Dagmar , May Tobias 
Published: March 2018

AbstractFundamental research and drug development for personalized medicine necessitates cell cultures from defined genetic backgrounds. However, providing sufficient numbers of authentic cells from individuals poses a challenge. Here, we present a new strategy for rapid cell expansion that overcomes current limitations. Using a small gene library, we expanded primary cells from different tissues, donors, and species. Cell-type-specific regimens that allow the reproducible creation of cell lines were identified. In depth characterization of a series of endothelial and hepatocytic cell lines confirmed phenotypic stability and functionality. Applying this technology enables rapid, efficient, and reliable production of unlimited numbers of personalized cells. As such, these cell systems support mechanistic studies, epidemiological research, and tailored drug development.
The oxidized phospholipid oxPAPC protects from septic shock by targeting the non-canonical inflammasome in macrophages
Authors: Chu Lan H. , Indramohan Mohanalaxmi , Ratsimandresy Rojo A. , Gangopadhyay Anu , Morris Emily P. , Monack Denise M. , Dorfleutner Andrea , Stehlik Christian 
Published: March 2018

AbstractLipopolysaccharide (LPS) of Gram-negative bacteria can elicit a strong immune response. Although extracellular LPS is sensed by TLR4 at the cell surface and triggers a transcriptional response, cytosolic LPS binds and activates non-canonical inflammasome caspases, resulting in pyroptotic cell death, as well as canonical NLRP3 inflammasome-dependent cytokine release. Contrary to the highly regulated multiprotein platform required for caspase-1 activation in the canonical inflammasomes, the non-canonical mouse caspase-11 and the orthologous human caspase-4 function simultaneously as innate sensors and effectors, and their regulation is unclear. Here we show that the oxidized phospholipid 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphorylcholine (oxPAPC) inhibits the non-canonical inflammasome in macrophages, but not in dendritic cells. Aside from a TLR4 antagonistic role, oxPAPC binds directly to caspase-4 and caspase-11, competes with LPS binding, and consequently inhibits LPS-induced pyroptosis, IL-1β release and septic shock. Therefore, oxPAPC and its derivatives might provide a basis for therapies that target non-canonical inflammasomes during Gram-negative bacterial sepsis.
Mutual potentiation drives synergy between trimethoprim and sulfamethoxazole
Authors: Minato Yusuke , Dawadi Surendra , Kordus Shannon L. , Sivanandam Abiram , Aldrich Courtney C. , Baughn Anthony D. 
Published: March 2018

AbstractTrimethoprim (TMP)-sulfamethoxazole (SMX) is a widely used synergistic antimicrobial combination to treat a variety of bacterial and certain fungal infections. These drugs act by targeting sequential steps in the biosynthetic pathway for tetrahydrofolate (THF), where SMX inhibits production of the THF precursor dihydropteroate, and TMP inhibits conversion of dihydrofolate (DHF) to THF. Consequently, SMX potentiates TMP by limiting de novo DHF production and this mono-potentiation mechanism is the current explanation for their synergistic action. Here, we demonstrate that this model is insufficient to explain the potent synergy of TMP-SMX. Using genetic and biochemical approaches, we characterize a metabolic feedback loop in which THF is critical for production of the folate precursor dihydropterin pyrophosphate (DHPPP). We reveal that TMP potentiates SMX activity through inhibition of DHPPP synthesis. Our study demonstrates that the TMP-SMX synergy is driven by mutual potentiation of the action of each drug on the other.
Sedimentary noise and sea levels linked to land–ocean water exchange and obliquity forcing
Authors: Li Mingsong , Hinnov Linda A. , Huang Chunju , Ogg James G. 
Published: March 2018

AbstractIn ancient hothouses lacking ice sheets, the origins of large, million-year (myr)-scale sea-level oscillations remain a mystery, challenging current models of sea-level change. To address this mystery, we develop a sedimentary noise model for sea-level changes that simultaneously estimates geologic time and sea level from astronomically forced marginal marine stratigraphy. The noise model involves two complementary approaches: dynamic noise after orbital tuning (DYNOT) and lag-1 autocorrelation coefficient (ρ1). Noise modeling of Lower Triassic marine slope stratigraphy in South China reveal evidence for global sea-level variations in the Early Triassic hothouse that are anti-phased with continental water storage variations in the Germanic Basin. This supports the hypothesis that long-period (1-2 myr) astronomically forced water mass exchange between land and ocean reservoirs is a missing link for reconciling geological records and models for sea-level change during non-glacial periods.
Aberrant GlyRS-HDAC6 interaction linked to axonal transport deficits in Charcot-Marie-Tooth neuropathy
Authors: Mo Zhongying , Zhao Xiaobei , Liu Huaqing , Hu Qinghua , Chen Xu-Qiao , Pham Jessica , Wei Na , Liu Ze , Zhou Jiadong , Burgess Robert W. , Pfaff Samuel L. , Caskey C. Thomas , Wu Chengbiao , Bai Ge , Yang Xiang-Lei 
Published: March 2018

AbstractDominant mutations in glycyl-tRNA synthetase (GlyRS) cause a subtype of Charcot-Marie-Tooth neuropathy (CMT2D). Although previous studies have shown that GlyRS mutants aberrantly interact with Nrp1, giving insight into the disease’s specific effects on motor neurons, these cannot explain length-dependent axonal degeneration. Here, we report that GlyRS mutants interact aberrantly with HDAC6 and stimulate its deacetylase activity on α-tubulin. A decrease in α-tubulin acetylation and deficits in axonal transport are observed in mice peripheral nerves prior to disease onset. An HDAC6 inhibitor used to restore α-tubulin acetylation rescues axonal transport deficits and improves motor functions of CMT2D mice. These results link the aberrant GlyRS-HDAC6 interaction to CMT2D pathology and suggest HDAC6 as an effective therapeutic target. Moreover, the HDAC6 interaction differs from Nrp1 interaction among GlyRS mutants and correlates with divergent clinical presentations, indicating the existence of multiple and different mechanisms in CMT2D.
Genomics of habitat choice and adaptive evolution in a deep-sea fish
Authors: Gaither Michelle R. , Gkafas Georgios A. , de Jong Menno , Sarigol Fatih , Neat Francis , Regnier Thomas , Moore Daniel , Grӧcke Darren R. , Hall Neil , Liu Xuan , Kenny John , Lucaci Anita , Hughes Margaret , Haldenby Sam , Hoelzel A. Rus 
Published: March 2018

AbstractIntraspecific diversity promotes evolutionary change, and when partitioned among geographic regions or habitats can form the basis for speciation. Marine species live in an environment that can provide as much scope for diversification in the vertical as in the horizontal dimension. Understanding the relevant mechanisms will contribute significantly to our understanding of eco-evolutionary processes and effective biodiversity conservation. Here, we provide an annotated genome assembly for the deep-sea fishCoryphaenoides rupestrisand re-sequencing data to show that differentiation at non-synonymous sites in functional loci distinguishes individuals living at different depths, independent of horizontal spatial distance. Our data indicate disruptive selection at these loci; however, we find no clear evidence for differentiation at neutral loci that may indicate assortative mating. We propose that individuals with distinct genotypes at relevant loci segregate by depth as they mature (supported by survey data), which may be associated with ecotype differentiation linked to distinct phenotypic requirements at different depths.
Mechanical dyssynchrony and diastolic dysfunction are common in LVH: a pilot correlation study using Doppler echocardiography and CZT gated-SPECT MPI
Authors: Tsai Szu-Ying , Wang Shan-Ying , Shiau Yu-Chien , Wu Yen-Wen 
Published: March 2018

AbstractHypertrophic cardiomyopathy (HCM) is an often under-diagnosed cause of left ventricular hypertrophy (LVH). It affects 1/500 of the population, is the most commonly inherited cardiovascular disorder, and can present in apical, concentric, or septal forms. Although most patients are asymptomatic, sudden cardiac death can be the initial presentation of HCM. By retrospectively enrolling patients suspected of having three different types of HCM in the absence of epicardial coronary stenosis, we aimed to examine systolic and diastolic dysfunction and perfusion abnormalities using both Doppler echocardiography and state-of-the-art gated single-photon emission computerized tomography (SPECT) myocardial perfusion imaging (MPI) with a cadmium-zinc-telluride camera and thallium-201. Both regional perfusion and gated SPECT parameters were collected in addition to diastolic parameters from Doppler echocardiography. The results showed that mild ischemia was common in patients suspected of having HCM, with a mean summed stress score of 4.7 ± 4.9 (score 0–4 in 17-segment model). The patients with HCM were associated with discernible left ventricular mechanical dyssynchrony, especially those with the apical form. In addition, diastolic dysfunction was prevalent and early to late ventricular filling velocity ratios were significantly different between groups. By combining gated-MPI and Doppler data, the trivial functional changes in HCM may be identified.
Modulating the water channel AQP4 alters miRNA expression, astrocyte connectivity and water diffusion in the rodent brain
Authors: Jullienne Amandine , Fukuda Andrew M. , Ichkova Aleksandra , Nishiyama Nina , Aussudre Justine , Obenaus André , Badaut Jérôme 
Published: March 2018

AbstractAquaporins (AQPs) facilitate water diffusion through the plasma membrane. Brain aquaporin-4 (AQP4) is present in astrocytes and has critical roles in normal and disease physiology. We previously showed that a 24.9% decrease in AQP4 expression after in vivo silencing resulted in a 45.8% decrease in tissue water mobility as interpreted from magnetic resonance imaging apparent diffusion coefficients (ADC). Similar to previous in vitro studies we show decreased expression of the gap junction protein connexin 43 (Cx43) in vivo after intracortical injection of siAQP4 in the rat. Moreover, siAQP4 induced a loss of dye-coupling between astrocytes in vitro, further demonstrating its effect on gap junctions. In contrast, silencing of Cx43 did not alter the level of AQP4 or water mobility (ADC) in the brain. We hypothesized that siAQP4 has off-target effects on Cx43 expression via modification of miRNA expression. The decreased expression of Cx43 in siAQP4-treated animals was associated with up-regulation of miR224, which is known to target AQP4 and Cx43 expression. This could be one potential molecular mechanism responsible for the effect of siAQP4 on Cx43 expression, and the resultant decrease in astrocyte connectivity and dramatic effects on ADC values and water mobility.
Genetic and metabolic regulation of Mycobacterium tuberculosis acid growth arrest
Authors: Baker Jacob J. , Abramovitch Robert B. 
Published: March 2018

AbstractMycobacterium tuberculosis (Mtb) senses and adapts to acidic environments during the course of infection. Acidic pH-dependent adaptations include the induction of metabolic genes associated with anaplerosis and growth arrest on specific carbon sources. Here we report that deletion of isocitrate lyase or phosphoenolpyruvate carboxykinase results in reduced growth at acidic pH and altered metabolite profiles, supporting that remodeling of anaplerotic metabolism is required for pH-dependent adaptation. Mtb cultured at pH 5.7 in minimal medium containing glycerol as a single carbon source exhibits an acid growth arrest phenotype, where the bacterium is non-replicating but viable and metabolically active. The bacterium assimilates and metabolizes glycerol and maintains ATP pools during acid growth arrest and becomes tolerant to detergent stress and the antibiotics isoniazid and rifampin. A forward genetic screen identified mutants that do not arrest their growth at acidic pH, including four enhanced acid growth (eag) mutants with three distinct mutations in the proline-proline-glutamate (PPE) gene MT3221 (also named ppe51). Overexpression of the MT3221(S211R) variant protein in wild type Mtb results in enhanced acid growth and reduced drug tolerance. These findings support that acid growth arrest is a genetically controlled, adaptive process and not simply a physiological limitation associated with acidic pH.
Metaboloptics: Visualization of the tumor functional landscape via metabolic and vascular imaging
Authors: Martinez Amy F. , McCachren Samuel S. , Lee Marianne , Murphy Helen A. , Zhu Caigang , Crouch Brian T. , Martin Hannah L. , Erkanli Alaattin , Rajaram Narasimhan , Ashcraft Kathleen A. , Fontanella Andrew N. , Dewhirst Mark W. , Ramanujam Nirmala 
Published: March 2018

AbstractMany cancers adeptly modulate metabolism to thrive in fluctuating oxygen conditions; however, current tools fail to image metabolic and vascular endpoints at spatial resolutions needed to visualize these adaptations in vivo. We demonstrate a high-resolution intravital microscopy technique to quantify glucose uptake, mitochondrial membrane potential (MMP), and SO2 to characterize the in vivo phentoypes of three distinct murine breast cancer lines. Tetramethyl rhodamine, ethyl ester (TMRE) was thoroughly validated to report on MMP in normal and tumor-bearing mice. Imaging MMP or glucose uptake together with vascular endpoints revealed that metastatic 4T1 tumors maintained increased glucose uptake across all SO2 (“Warburg effect”), and also showed increased MMP relative to normal tissue. Non-metastatic 67NR and 4T07 tumor lines both displayed increased MMP, but comparable glucose uptake, relative to normal tissue. The 4T1 peritumoral areas also showed a significant glycolytic shift relative to the tumor regions. During a hypoxic stress test, 4T1 tumors showed significant increases in MMP with corresponding significant drops in SO2, indicative of intensified mitochondrial metabolism. Conversely, 4T07 and 67NR tumors shifted toward glycolysis during hypoxia. Our findings underscore the importance of imaging metabolic endpoints within the context of a living microenvironment to gain insight into a tumor’s adaptive behavior.
Spatiotemporal Airy Ince–Gaussian wave packets in strongly nonlocal nonlinear media
Authors: Peng Xi , Zhuang Jingli , Peng Yulian , Li DongDong , Zhang Liping , Chen Xingyu , Zhao Fang , Deng Dongmei 
Published: March 2018

AbstractThe self-accelerating Airy Ince–Gaussian (AiIG) and Airy helical Ince–Gaussian (AihIG) wave packets in strongly nonlocal nonlinear media (SNNM) are obtained by solving the strongly nonlocal nonlinear Schrödinger equation. For the first time, the propagation properties of three dimensional localized AiIG and AihIG breathers and solitons in the SNNM are demonstrated, these spatiotemporal wave packets maintain the self-accelerating and approximately non-dispersion properties in temporal dimension, periodically oscillating (breather state) or steady (soliton state) in spatial dimension. In particular, their numerical experiments of spatial intensity distribution, numerical simulations of spatiotemporal distribution, as well as the transverse energy flow and the angular momentum in SNNM are presented. Typical examples of the obtained solutions are based on the ratio between the input power and the critical power, the ellipticity and the strong nonlocality parameter. The comparisons of analytical solutions with numerical simulations and numerical experiments of the AiIG and AihIG optical solitons show that the numerical results agree well with the analytical solutions in the case of strong nonlocality.
Design of broadband graphene-metamaterial absorbers for permittivity sensing at mid-infrared regions
Authors: Huang Hailong , Xia Hui , Xie Wenke , Guo Zhibo , Li Hongjian , Xie Ding 
Published: March 2018

AbstractIn this paper, a tunable broadband metamaterial absorber (MA) based on graphene is investigated theoretically and numerically at mid-infrared regions. Compared with the previously reported multiband graphene-based MAs, a broad bandwidth of 11.7 THz with the absorption over 90% is obtained in the proposed MA, which is composed of a Jerusalem cross (JC) metal encrusting into the slot graphene layer in the top layer. The results show that the origin of broadband absorption is caused by coupling effect between metal and graphene, and this effect is explained by the two-mode waveguide coupling theory. The tunability of MA is achieved via changing the external gate voltage to modify the Fermi energy of graphene. Further results show that the proposed MA can be used as the permittivity sensor with a high absorption. This work indicates that the proposed MA has the potential applications with respect to sensors and infrared absorbers.