bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glycerol-3-phosphate acyltransferase-1 upregulation by O-GlcNAcylation of Sp1 protects against hypoxia-induced mouse embryonic stem cell apoptosis via mTOR activation
Authors: Lee H J , Ryu J M , Jung Y H , Lee K H , Kim D I , Han H J 
Published: March 2016

AbstractOxygen signaling is critical for stem cell regulation, and oxidative stress-induced stem cell apoptosis decreases the efficiency of stem cell therapy. Hypoxia activates O-linked β-N-acetyl glucosaminylation (O-GlcNAcylation) of stem cells, which contributes to regulation of cellular metabolism, as well as cell fate. Our study investigated the role of O-GlcNAcylation via glucosamine in the protection of hypoxia-induced apoptosis of mouse embryonic stem cells (mESCs). Hypoxia increased mESCs apoptosis in a time-dependent manner. Moreover, hypoxia also slightly increased the O-GlcNAc level. Glucosamine treatment further enhanced the O-GlcNAc level and prevented hypoxia-induced mESC apoptosis, which was suppressed by O-GlcNAc transferase inhibitors. In addition, hypoxia regulated several lipid metabolic enzymes, whereas glucosamine increased expression of glycerol-3-phosphate acyltransferase-1 (GPAT1), a lipid metabolic enzyme producing lysophosphatidic acid (LPA). In addition, glucosamine-increased O-GlcNAcylation of Sp1, which subsequently leads to Sp1 nuclear translocation and GPAT1 expression. Silencing of GPAT1 by gpat1 siRNA transfection reduced glucosamine-mediated anti-apoptosis in mESCs and reduced mammalian target of rapamycin (mTOR) phosphorylation. Indeed, LPA prevented mESCs from undergoing hypoxia-induced apoptosis and increased phosphorylation of mTOR and its substrates (S6K1 and 4EBP1). Moreover, mTOR inactivation by rapamycin (mTOR inhibitor) increased pro-apoptotic proteins expressions and mESC apoptosis. Furthermore, transplantation of non-targeting siRNA and glucosamine-treated mESCs increased cell survival and inhibited flap necrosis in mouse skin flap model. Conversely, silencing of GPAT1 expression reversed those glucosamine effects. In conclusion, enhancing O-GlcNAcylation of Sp1 by glucosamine stimulates GPAT1 expression, which leads to inhibition of hypoxia-induced mESC apoptosis via mTOR activation.
Poly-ADP-ribosylation-mediated degradation of ARTD1 by the NLRP3 inflammasome is a prerequisite for osteoclast maturation
Authors: Wang C , Qu C , Alippe Y , Bonar S L , Civitelli R , Abu-Amer Y , Hottiger M O , Mbalaviele G 
Published: March 2016

AbstractEvidence implicates ARTD1 in cell differentiation, but its role in skeletal metabolism remains unknown. Osteoclasts (OC), the bone-resorbing cells, differentiate from macrophages under the influence of macrophage colony-stimulating factor (M-CSF) and receptor-activator of NF-κB ligand (RANKL). We found that M-CSF induced ADP-ribosyltransferase diphtheria toxin-like 1 (ARTD1) auto-ADP-ribosylation in macrophages, a modification that marked ARTD1 for cleavage, and subsequently, for degradation upon RANKL exposure. We established that ARTD1 proteolysis was NLRP3 inflammasome-dependent, and occurred via the proteasome pathway. Since ARTD1 is cleaved at aspartate214, we studied the impact of ARTD1 rendered uncleavable by D214N substitution (ARTD1D214N) on skeletal homeostasis. ARTD1D214N, unlike wild-type ARTD1, was resistant to cleavage and degradation during osteoclastogenesis. As a result, ARTD1D214N altered histone modification and promoted the abundance of the repressors of osteoclastogenesis by interfering with the expression of B lymphocyte-induced maturation protein 1 (Blimp1), the master regulator of anti-osteoclastogenic transcription factors. Importantly, ARTD1D214N-expressing mice exhibited higher bone mass compared with controls, owing to decreased osteoclastogenesis while bone formation was unaffected. Thus, unless it is degraded, ARTD1 represses OC development through transcriptional regulation.
Nanoelectromechanical resonant narrow-band amplifiers
Authors: Ramezany Alireza , Mahdavi Mohammad , Pourkamali Siavash 
Published: March 2016

AbstractThis study demonstrates amplification of electrical signals using a very simple nanomechanical device. It is shown that vibration amplitude amplification using a combination of mechanical resonance and thermal-piezoresistive energy pumping, which was previously demonstrated to drive self-sustained mechanical oscillation, can turn the relatively weak piezoresistivity of silicon into a viable electronic amplification mechanism with power gains of >20 dB. Various functionalities ranging from frequency selection and timing to sensing and actuation have been successfully demonstrated for microscale and nanoscale electromechanical systems. Although such capabilities complement solid-state electronics, enabling state-of-the-art compact and high-performance electronics, the amplification of electronic signals is an area where micro-/nanomechanics has not experienced much progress. In contrast to semiconductor devices, the performance of the proposed nanoelectromechanical amplifier improves significantly as the dimensions are reduced to the nanoscale presenting a potential pathway toward deep-nanoscale electronics. The nanoelectromechanical amplifier can also address the need for ultranarrow-band filtering along with the amplification of low-power signals in wireless communications and certain sensing applications, which is another need that is not efficiently addressable using semiconductor technology.
Sequence features accurately predict genome-wide MeCP2 binding in vivo
Authors: Rube H. Tomas , Lee Wooje , Hejna Miroslav , Chen Huaiyang , Yasui Dag H. , Hess John F. , LaSalle Janine M. , Song Jun S. , Gong Qizhi 
Published: March 2016

AbstractMethyl-CpG binding protein 2 (MeCP2) is critical for proper brain development and expressed at near-histone levels in neurons, but the mechanism of its genomic localization remains poorly understood. Using high-resolution MeCP2-binding data, we show that DNA sequence features alone can predict binding with 88% accuracy. Integrating MeCP2 binding and DNA methylation in a probabilistic graphical model, we demonstrate that previously reported genome-wide association with methylation is in part due to MeCP2’s affinity to GC-rich chromatin, a result replicated using published data. Furthermore, MeCP2 co-localizes with nucleosomes. Finally, MeCP2 binding downstream of promoters correlates with increased expression in Mecp2-deficient neurons.
CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil
Authors: Almqvist Helena , Axelsson Hanna , Jafari Rozbeh , Dan Chen , Mateus André , Haraldsson Martin , Larsson Andreas , Molina Daniel Martinez , Artursson Per , Lundbäck Thomas , Nordlund Pär 
Published: March 2016

AbstractTarget engagement is a critical factor for therapeutic efficacy. Assessment of compound binding to native target proteins in live cells is therefore highly desirable in all stages of drug discovery. We report here the first compound library screen based on biophysical measurements of intracellular target binding, exemplified by human thymidylate synthase (TS). The screen selected accurately for all the tested known drugs acting on TS. We also identified TS inhibitors with novel chemistry and marketed drugs that were not previously known to target TS, including the DNA methyltransferase inhibitor decitabine. By following the cellular uptake and enzymatic conversion of known drugs we correlated the appearance of active metabolites over time with intracellular target engagement. These data distinguished a much slower activation of 5-fluorouracil when compared with nucleoside-based drugs. The approach establishes efficient means to associate drug uptake and activation with target binding during drug discovery.
Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells
Authors: Grover Amit , Sanjuan-Pla Alejandra , Thongjuea Supat , Carrelha Joana , Giustacchini Alice , Gambardella Adriana , Macaulay Iain , Mancini Elena , Luis Tiago C. , Mead Adam , Jacobsen Sten Eirik W. , Nerlov Claus 
Published: March 2016

AbstractAged haematopoietic stem cells (HSCs) generate more myeloid cells and fewer lymphoid cells compared with young HSCs, contributing to decreased adaptive immunity in aged individuals. However, it is not known how intrinsic changes to HSCs and shifts in the balance between biased HSC subsets each contribute to the altered lineage output. Here, by analysing HSC transcriptomes and HSC function at the single-cell level, we identify increased molecular platelet priming and functional platelet bias as the predominant age-dependent change to HSCs, including a significant increase in a previously unrecognized class of HSCs that exclusively produce platelets. Depletion of HSC platelet programming through loss of the FOG-1 transcription factor is accompanied by increased lymphoid output. Therefore, increased platelet bias may contribute to the age-associated decrease in lymphopoiesis.
Jack-of-all-trades effects drive biodiversity–ecosystem multifunctionality relationships in European forests
Authors: van der Plas Fons , Manning Peter , Allan Eric , Scherer-Lorenzen Michael , Verheyen Kris , Wirth Christian , Zavala Miguel A. , Hector Andy , Ampoorter Evy , Baeten Lander , Barbaro Luc , Bauhus Jürgen , Benavides Raquel , Benneter Adam , Berthold Felix , Bonal Damien , Bouriaud Olivier , Bruelheide Helge , Bussotti Filippo , Carnol Monique , Castagneyrol Bastien , Charbonnier Yohan , Coomes David , Coppi Andrea , Bastias Cristina C. , Muhie Dawud Seid , De Wandeler Hans , Domisch Timo , Finér Leena , Gessler Arthur , Granier André , Grossiord Charlotte , Guyot Virginie , Hättenschwiler Stephan , Jactel Hervé , Jaroszewicz Bogdan , Joly François-Xavier , Jucker Tommaso , Koricheva Julia , Milligan Harriet , Müller Sandra , Muys Bart , Nguyen Diem , Pollastrini Martina , Raulund-Rasmussen Karsten , Selvi Federico , Stenlid Jan , Valladares Fernando , Vesterdal Lars , Zielínski Dawid , Fischer Markus 
Published: March 2016

AbstractThere is considerable evidence that biodiversity promotes multiple ecosystem functions (multifunctionality), thus ensuring the delivery of ecosystem services important for human well-being. However, the mechanisms underlying this relationship are poorly understood, especially in natural ecosystems. We develop a novel approach to partition biodiversity effects on multifunctionality into three mechanisms and apply this to European forest data. We show that throughout Europe, tree diversity is positively related with multifunctionality when moderate levels of functioning are required, but negatively when very high function levels are desired. For two well-known mechanisms, ‘complementarity’ and ‘selection’, we detect only minor effects on multifunctionality. Instead a third, so far overlooked mechanism, the ‘jack-of-all-trades’ effect, caused by the averaging of individual species effects on function, drives observed patterns. Simulations demonstrate that jack-of-all-trades effects occur whenever species effects on different functions are not perfectly correlated, meaning they may contribute to diversity–multifunctionality relationships in many of the world’s ecosystems.
Towards controlled polymer brushes via a self-assembly-assisted-grafting-to approach
Authors: Zhou Tian , Qi Hao , Han Lin , Barbash Dmitri , Li Christopher Y. 
Published: March 2016

AbstractPrecise synthesis of polymer brushes to modify the surface of nanoparticles and nanodevices for targeted applications has been one of the major focuses in the community for decades. Here we report a self-assembly-assisted-grafting-to approach to synthesize polymer brushes on flat substrates. In this method, polymers are pre-assembled into two-dimensional polymer single crystals (PSCs) with functional groups on the surface. Chemically coupling the PSCs onto solid substrates leads to the formation of polymer brushes. Exquisite control of the chain folding in PSCs allows us to obtain polymer brushes with well-defined grafting density, tethering points and brush conformation. Extremely high grafting density (2.12 chains per nm2) has been achieved in the synthesized single-tethered polymer brushes. Moreover, polymer loop brushes have been successfully obtained using oddly folded PSCs from telechelic chains. Our approach combines some of the important advantages of conventional ‘grafting-to’ and ‘grafting-from’ methods, and is promising for tailored synthesis of polymer brushes.
Magnetic nanoparticle film reconstruction modulated by immersion within DMSA aqueous solution
Authors: Xiang Qing , Borges Teixeira Cimei , Sun Li , Morais Paulo Cesar 
Published: March 2016

AbstractThe process of reconstruction of pre-fabricated films comprising maghemite nanoparticles deposited onto flat glass substrates triggered by immersion into aqueous solutions of meso-2,3-dimercaptosuccinic acid (DMSA) at increasing concentration (0.025, 0.050 and 0.100 mol/L) is herein reported. The evolution of this process was assessed by measuring the time (t) dependence of the particle analysis histogram width (W) extracted from atomic force microscopy images. Furthermore, a physical picture to model the film reconstruction which provides reconstruction time constants associated to single particles (τ1) and small agglomerates (τn), the key units associated to the process, ranging from τ1 = 2.9 and τn = 3.4 hour (0.025 mol/L) to τ1 = 5.1 and τn = 4.6 hour (0.100 mol/L) is proposed. The nanoparticle-based film reconstruction triggered by an exogenous stimulus, the use of the W versus t data to describe the process and the model picture accounting for the recorded data have not been previously reported.
Rashba Torque Driven Domain Wall Motion in Magnetic Helices
Authors: Pylypovskyi Oleksandr V. , Sheka Denis D. , Kravchuk Volodymyr P. , Yershov Kostiantyn V. , Makarov Denys , Gaididei Yuri 
Published: March 2016

AbstractManipulation of the domain wall propagation in magnetic wires is a key practical task for a number of devices including racetrack memory and magnetic logic. Recently, curvilinear effects emerged as an efficient mean to impact substantially the statics and dynamics of magnetic textures. Here, we demonstrate that the curvilinear form of the exchange interaction of a magnetic helix results in an effective anisotropy term and Dzyaloshinskii–Moriya interaction with a complete set of Lifshitz invariants for a one-dimensional system. In contrast to their planar counterparts, the geometrically induced modifications of the static magnetic texture of the domain walls in magnetic helices offer unconventional means to control the wall dynamics relying on spin-orbit Rashba torque. The chiral symmetry breaking due to the Dzyaloshinskii–Moriya interaction leads to the opposite directions of the domain wall motion in left- or right-handed helices. Furthermore, for the magnetic helices, the emergent effective anisotropy term and Dzyaloshinskii–Moriya interaction can be attributed to the clear geometrical parameters like curvature and torsion offering intuitive understanding of the complex curvilinear effects in magnetism.
Reproducibility of radiomics for deciphering tumor phenotype with imaging
Authors: Zhao Binsheng , Tan Yongqiang , Tsai Wei-Yann , Qi Jing , Xie Chuanmiao , Lu Lin , Schwartz Lawrence H. 
Published: March 2016

AbstractRadiomics (radiogenomics) characterizes tumor phenotypes based on quantitative image features derived from routine radiologic imaging to improve cancer diagnosis, prognosis, prediction and response to therapy. Although radiomic features must be reproducible to qualify as biomarkers for clinical care, little is known about how routine imaging acquisition techniques/parameters affect reproducibility. To begin to fill this knowledge gap, we assessed the reproducibility of a comprehensive, commonly-used set of radiomic features using a unique, same-day repeat computed tomography data set from lung cancer patients. Each scan was reconstructed at 6 imaging settings, varying slice thicknesses (1.25 mm, 2.5 mm and 5 mm) and reconstruction algorithms (sharp, smooth). Reproducibility was assessed using the repeat scans reconstructed at identical imaging setting (6 settings in total). In separate analyses, we explored differences in radiomic features due to different imaging parameters by assessing the agreement of these radiomic features extracted from the repeat scans reconstructed at the same slice thickness but different algorithms (3 settings in total). Our data suggest that radiomic features are reproducible over a wide range of imaging settings. However, smooth and sharp reconstruction algorithms should not be used interchangeably. These findings will raise awareness of the importance of properly setting imaging acquisition parameters in radiomics/radiogenomics research.
Net-Immobilization of β-glucosidase on Nonwoven Fabrics to Lower the Cost of “Cellulosic Ethanol” and Increase Cellulose Conversions
Authors: Zhu Xing , He Bin , Zhao Changwen , Fan Rong , Zhang Lihua , Wang Guan , Ma Yuhong , Yang Wantai 
Published: March 2016

AbstractThe main limitation preventing the use of enzymatic cellulosic ethanol in industrial production is its higher cost which is mainly due to the elevated price of β-glucosidase (BG). Herein, we report on a simple strategy for the in-situ encapsulation of BG for repeated cellulosic ethanol production. In this strategy, BG was net-immobilized into a poly(ethylene glycol) (PEG) net-cloth layer on a PP nonwoven fabric by way of the visible light-induced surface controlled/living graft cross-linking polymerization. The visible light and mild reaction conditions could ensure the activity retention of BG during immobilization, while the non-swelling uniform net-mesh formed by living cross-linking polymerization could prevent the leakage of BG effectively (at the immobilization rate of more than 98.6% and the leakage rate of only 0.4%). When the BG-loaded fabric was used in combination with free cellulase (CEL), the results of the catalytic reaction demonstrated that these BG-loaded fabrics could not only give a 40% increase in cellulose conversions but also be reused for more than fifteen batches without losing the activity. These BG-loaded fabrics with characteristics including easy separation, excellent operation stability, a low cost of the polymeric matrix and a simple fabrication process are particularly interesting for a future bio-fuel production strategy.
Spin-Current and Spin-Splitting in Helicoidal Molecules Due to Spin-Orbit Coupling
Authors: Caetano R. A. 
Published: March 2016

AbstractThe use of organic materials in spintronic devices has been seriously considered after recent experimental works have shown unexpected spin-dependent electrical properties. The basis for the confection of any spintronic device is ability of selecting the appropriated spin polarization. In this direction, DNA has been pointed out as a potential candidate for spin selection due to the spin-orbit coupling originating from the electric field generated by accumulated electrical charges along the helix. Here, we demonstrate that spin-orbit coupling is the minimum ingredient necessary to promote a spatial spin separation and the generation of spin-current. We show that the up and down spin components have different velocities that give rise to a spin-current. By using a simple situation where spin-orbit coupling is present, we provide qualitative justifications to our results that clearly point to helicoidal molecules as serious candidates to integrate spintronic devices.
Hedgehog associated to microparticles inhibits adipocyte differentiation via a non-canonical pathway
Authors: Fleury Audrey , Hoch Lucile , Martinez M. Carmen , Faure Hélène , Taddei Maurizio , Petricci Elena , Manetti Fabrizio , Girard Nicolas , Mann André , Jacques Caroline , Larghero Jérôme , Ruat Martial , Andriantsitohaina Ramaroson , Le Lay Soazig 
Published: March 2016

AbstractHedgehog (Hh) is a critical regulator of adipogenesis. Extracellular vesicles are natural Hh carriers, as illustrated by activated/apoptotic lymphocytes specifically shedding microparticles (MP) bearing the morphogen (MPHh+). We show that MPHh+ inhibit adipocyte differentiation and orientate mesenchymal stem cells towards a pro-osteogenic program. Despite a Smoothened (Smo)-dependency, MPHh+ anti-adipogenic effects do not activate a canonical Hh signalling pathway in contrast to those elicited either by the Smo agonist SAG or recombinant Sonic Hedgehog. The Smo agonist GSA-10 recapitulates many of the hallmarks of MPHh+ anti-adipogenic effects. The adipogenesis blockade induced by MPHh+ and GSA-10 was abolished by the Smo antagonist LDE225. We further elucidate a Smo/Lkb1/Ampk axis as the non-canonical Hh pathway used by MPHh+ and GSA-10 to inhibit adipocyte differentiation. Our results highlight for the first time the ability of Hh-enriched MP to signal via a non-canonical pathway opening new perspectives to modulate fat development.
Quantifying the influence of Bessel beams on image quality in optical coherence tomography
Authors: Curatolo Andrea , Munro Peter R. T. , Lorenser Dirk , Sreekumar Parvathy , Singe C. Christian , Kennedy Brendan F. , Sampson David D. 
Published: March 2016

AbstractLight scattered by turbid tissue is known to degrade optical coherence tomography (OCT) image contrast progressively with depth. Bessel beams have been proposed as an alternative to Gaussian beams to image deeper into turbid tissue. However, studies of turbid tissue comparing the image quality for different beam types are lacking. We present such a study, using numerically simulated beams and experimental OCT images formed by Bessel or Gaussian beams illuminating phantoms with optical properties spanning a range typical of soft tissue. We demonstrate that, for a given scattering parameter, the higher the scattering anisotropy the lower the OCT contrast, regardless of the beam type. When focusing both beams at the same depth in the sample, we show that, at focus and for equal input power and resolution, imaging with the Gaussian beam suffers less reduction of contrast. This suggests that, whilst Bessel beams offer extended depth of field in a single depth scan, for low numerical aperture (NA < 0.1) and typical soft tissue properties (scattering coefficient, μs = 3.7 mm−1 and high scattering anisotropy, g > 0.95), superior contrast (by up to ~40%) may be obtained over an extended depth range by a Gaussian beam combined with dynamic focusing.
The origin of the criticality in meme popularity distribution on complex networks
Authors: Kim Yup , Park Seokjong , Yook Soon-Hyung 
Published: March 2016

AbstractPrevious studies showed that the meme popularity distribution is described by a heavy-tailed distribution or a power-law, which is a characteristic feature of the criticality. Here, we study the origin of the criticality on non-growing and growing networks based on the competition induced criticality model. From the direct Mote Carlo simulations and the exact mapping into the position dependent biased random walk (PDBRW), we find that the meme popularity distribution satisfies a very robust power- law with exponent α = 3/2 if there is an innovation process. On the other hand, if there is no innovation, then we find that the meme popularity distribution is bounded and highly skewed for early transient time periods, while it satisfies a power-law with exponent α ≠ 3/2 for intermediate time periods. The exact mapping into PDBRW clearly shows that the balance between the creation of new memes by the innovation process and the extinction of old memes is the key factor for the criticality. We confirm that the balance for the criticality sustains for relatively small innovation rate. Therefore, the innovation processes with significantly influential memes should be the simple and fundamental processes which cause the critical distribution of the meme popularity in real social networks.