bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell transcriptome and epigenomic reprogramming of cardiomyocyte-derived cardiac progenitor cells
Authors: Chen Xin , Chakravarty Tushar , Zhang Yiqiang , Li Xiaojin , Zhong Jiang F. , Wang Charles 
Published: September 2016

AbstractThe molecular basis underlying the dedifferentiation of mammalian adult cardiomyocytes (ACMs) into myocyte-derived cardiac progenitor cells (mCPCs) during cardiac tissue regeneration is poorly understood. We present data integrating single-cell transcriptome and whole-genome DNA methylome analyses of mouse mCPCs to understand the epigenomic reprogramming governing their intrinsic cellular plasticity. Compared to parental cardiomyocytes, mCPCs display epigenomic reprogramming with many differentially-methylated regions, both hypermethylated and hypomethylated, across the entire genome. Correlating well with the methylome, our single-cell transcriptomic data show that the genes encoding cardiac structure and function proteins are remarkably down-regulated in mCPCs, while those for cell cycle, proliferation, and stemness are significantly up-regulated. In addition, implanting mCPCs into infarcted mouse myocardium improves cardiac function with augmented left ventricular ejection fraction. This dataset suggests that the cellular plasticity of mammalian cardiomyocytes is the result of a well-orchestrated epigenomic reprogramming and a subsequent global transcriptomic alteration. Understanding cardiomyocyte epigenomic reprogramming may enable the design of future clinical therapies that induce cardiac regeneration, and prevent heart failure.
Novel O-GlcNAcylation on Ser40 of canonical H2A isoforms specific to viviparity
Authors: Hirosawa Mitsuko , Hayakawa Koji , Yoneda Chikako , Arai Daisuke , Shiota Hitoshi , Suzuki Takehiro , Tanaka Satoshi , Dohmae Naoshi , Shiota Kunio 
Published: September 2016

AbstractWe report here newly discovered O-linked-N-acetylglucosamine (O-GlcNAc) modification of histone H2A at Ser40 (H2AS40Gc). The mouse genome contains 18 H2A isoforms, of which 13 have Ser40 and the other five have Ala40. The combination of production of monoclonal antibody and mass spectrometric analyses with reverse-phase (RP)-high performance liquid chromatography (HPLC) fractionation indicated that the O-GlcNAcylation is specific to the Ser40 isoforms. The H2AS40Gc site is in the L1 loop structure where two H2A molecules interact in the nucleosome. Targets of H2AS40Gc are distributed genome-wide and are dramatically changed during the process of differentiation in mouse trophoblast stem cells. In addition to the mouse, H2AS40Gc was also detected in humans, macaques and cows, whereas non-mammalian species possessing only the Ala40 isoforms, such as silkworms, zebrafish and Xenopus showed no signal. Genome database surveys revealed that Ser40 isoforms of H2A emerged in Marsupialia and persisted thereafter in mammals. We propose that the emergence of H2A Ser40 and its O-GlcNAcylation linked a genetic event to genome-wide epigenetic events that correlate with the evolution of placental animals.
Evolutionary robotics simulations help explain why reciprocity is rare in nature
Authors: André Jean-Baptiste , Nolfi Stefano 
Published: September 2016

AbstractThe relative rarity of reciprocity in nature, contrary to theoretical predictions that it should be widespread, is currently one of the major puzzles in social evolution theory. Here we use evolutionary robotics to solve this puzzle. We show that models based on game theory are misleading because they neglect the mechanics of behavior. In a series of experiments with simulated robots controlled by artificial neural networks, we find that reciprocity does not evolve, and show that this results from a general constraint that likely also prevents it from evolving in the wild. Reciprocity can evolve if it requires very few mutations, as is usually assumed in evolutionary game theoretic models, but not if, more realistically, it requires the accumulation of many adaptive mutations.
Hippopotamus (H. amphibius) diet change indicates herbaceous plant encroachment following megaherbivore population collapse
Authors: Chritz Kendra L. , Blumenthal Scott A. , Cerling Thure E. , Klingel Hans 
Published: September 2016

AbstractMegaherbivores (>1000 kg) are critical for ecosystem health and function, but face population collapse and extinction globally. The future of these megaherbivore-impoverished ecosystems is difficult to predict, though many studies have demonstrated increasing representation of C3 woody plants. These studies rely on direct observational data, however, and tools for assessing decadal-scale changes in African ecology without observation are lacking. We use isotopic records of historical common hippopotamus (Hippopotamus amphibius) canines to quantify herbaceous vegetation change in Queen Elizabeth National Park, Uganda following a period of civil unrest and poaching. This poaching event led to population collapse of two threatened African megaherbivore species: hippopotamus and African elephants (Loxodonta africana). Serial carbon isotope ratios (δ13C) in canine enamel from individuals that lived between 1960–2000 indicated substantial increases in C3 herbaceous plants in their diet (<20% C3 in the 1960s to 30–45% C3 in the 80s and 90s), supported by other observational and ecological data. These data indicate megaherbivore loss results in succession of both woody and herbaceous C3 vegetation and further reaching effects, such as decreased grazing capacity and herbivore biodiversity in the area. Given multiple lines of evidence, these individuals appear to accurately capture herbaceous vegetation change in Mweya.
A novel method for the injection and manipulation of magnetic charge states in nanostructures
Authors: Gartside J. C. , Burn D. M. , Cohen L. F. , Branford W. R. 
Published: September 2016

AbstractRealising the promise of next-generation magnetic nanotechnologies is contingent on the development of novel methods for controlling magnetic states at the nanoscale. There is currently demand for simple and flexible techniques to access exotic magnetisation states without convoluted fabrication and application processes. 360° domain walls (metastable twists in magnetisation separating two domains with parallel magnetisation) are one such state, which is currently of great interest in data storage and magnonics. Here, we demonstrate a straightforward and powerful process whereby a moving magnetic charge, provided experimentally by a magnetic force microscope tip, can write and manipulate magnetic charge states in ferromagnetic nanowires. The method is applicable to a wide range of nanowire architectures with considerable benefits over existing techniques. We confirm the method’s efficacy via the injection and spatial manipulation of 360° domain walls in Py and Co nanowires. Experimental results are supported by micromagnetic simulations of the tip-nanowire interaction.
Salvage Intensity-Modulated Radiation Therapy (IMRT) for Locally Recurrent Nasopharyngeal Cancer after Definitive IMRT: A Novel Scenario of the Modern Era
Authors: Kong Lin , Wang Lei , Shen Chunying , Hu Chaosu , Wang Lei , Lu Jiade J. 
Published: September 2016

AbstractLocally recurrent nasopharyngeal carcinoma (rNPC) after definitive IMRT occurs in 10% of all cases and represents a distinct clinical entity that has been selectively enriched by radio-resistant cancer cells. Therefore, we report of the outcomes of 77 patients who had repeat salvage-IMRT for rNPC after only a definitive course of IMRT. Various clinical outcomes were measured. Log-rank tests were used to detect differences in the survival outcomes between factor-defined subgroups. Multivariable analysis was performed using the Cox proportional hazard model. The median follow-up time was 25.7 months (range 3.0–75.7 months), measured from the time of recurrence. The median OS time and PFS time of the entire cohort was 37.0 and 20.5 months, respectively. Thirty-four patients (44.2%) died. Approximately 35% of these patients died from disease progression, but 53% were from treatment-induced severe adverse effects (SAEs) without evidence of disease progression. Higher T-classification of the recurrent tumor and the development of SAEs were found to be the only independent and significant adverse prognostic factors on multivariable analysis. These outcomes underscore the particularly virulent characteristics of rNPC after definitive IMRT. Concerning is the impact of re-irradiation toxicity on patient mortality.
Scalable Differentiation of Human iPSCs in a Multicellular Spheroid-based 3D Culture into Hepatocyte-like Cells through Direct Wnt/β-catenin Pathway Inhibition
Authors: Pettinato Giuseppe , Ramanathan Rajesh , Fisher Robert A , Mangino Martin J. , Zhang Ning , Wen Xuejun 
Published: September 2016

AbstractTreatment of acute liver failure by cell transplantation is hindered by a shortage of human hepatocytes. Current protocols for hepatic differentiation of human induced pluripotent stem cells (hiPSCs) result in low yields, cellular heterogeneity, and limited scalability. In the present study, we have developed a novel multicellular spheroid-based hepatic differentiation protocol starting from embryoid bodies of hiPSCs (hiPSC-EBs) for robust mass production of human hepatocyte-like cells (HLCs) using two novel inhibitors of the Wnt pathway. The resultant hiPSC-EB-HLCs expressed liver-specific genes, secreted hepatic proteins such as Albumin, Alpha Fetoprotein, and Fibrinogen, metabolized ammonia, and displayed cytochrome P450 activities and functional activities typical of mature primary hepatocytes, such as LDL storage and uptake, ICG uptake and release, and glycogen storage. Cell transplantation of hiPSC-EB-HLC in a rat model of acute liver failure significantly prolonged the mean survival time and resolved the liver injury when compared to the no-transplantation control animals. The transplanted hiPSC-EB-HLCs secreted human albumin into the host plasma throughout the examination period (2 weeks). Transplantation successfully bridged the animals through the critical period for survival after acute liver failure, providing promising clues of integration and full in vivo functionality of these cells after treatment with WIF-1 and DKK-1.
Diameter Dependence of Planar Defects in InP Nanowires
Authors: Wang Fengyun , Wang Chao , Wang Yiqian , Zhang Minghuan , Han Zhenlian , Yip SenPo , Shen Lifan , Han Ning , Pun Edwin Y. B. , Ho Johnny C. 
Published: September 2016

AbstractIn this work, extensive characterization and complementary theoretical analysis have been carried out on Au-catalyzed InP nanowires in order to understand the planar defect formation as a function of nanowire diameter. From the detailed transmission electron microscopic measurements, the density of stacking faults and twin defects are found to monotonically decrease as the nanowire diameter is decreased to 10 nm, and the chemical analysis clearly indicates the drastic impact of In catalytic supersaturation in Au nanoparticles on the minimized planar defect formation in miniaturized nanowires. Specifically, during the chemical vapor deposition of InP nanowires, a significant amount of planar defects is created when the catalyst seed sizes are increased with the lower degree of In supersaturation as dictated by the Gibbs-Thomson effect, and an insufficient In diffusion (or Au-rich enhancement) would lead to a reduced and non-uniform In precipitation at the NW growing interface. The results presented here provide an insight into the fabrication of “bottom-up” InP NWs with minimized defect concentration which are suitable for various device applications.
Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity
Authors: Rabbi S. M. F. , Daniel H. , Lockwood P. V. , Macdonald C. , Pereg L. , Tighe M. , Wilson B. R. , Young I. M. 
Published: September 2016

AbstractAggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250–2000 μm) and micro-aggregates (53–250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes.
Ultrahigh Purcell factor in low-threshold nanolaser based on asymmetric hybrid plasmonic cavity
Authors: Wei Wei , Yan Xin , Zhang Xia 
Published: September 2016

AbstractA low-threshold nanolaser with all three dimensions at the subwavelength scale is proposed and investigated. The nanolaser is constructed based on an asymmetric hybrid plasmonic F-P cavity with Ag-coated end facets. Lasing characteristics are calculated using finite element method at the wavelength of 1550 nm. The results show that owing to the low modal loss, large modal confinement factor of the asymmetric plasmonic cavity structure, in conjunction with the high reflectivity of the Ag reflectors, a minimum threshold gain of 240 cm−1 is predicted. Furthermore, the Purcell factor as large as 2518 is obtained with optimized structure parameters to enhance rates of spontaneous and stimulated emission.
PMMA-Etching-Free Transfer of Wafer-scale Chemical Vapor Deposition Two-dimensional Atomic Crystal by a Water Soluble Polyvinyl Alcohol Polymer Method
Authors: Van Ngoc Huynh , Qian Yongteng , Han Suk Kil , Kang Dae Joon 
Published: September 2016

AbstractWe have explored a facile technique to transfer large area 2-Dimensional (2D) materials grown by chemical vapor deposition method onto various substrates by adding a water-soluble Polyvinyl Alcohol (PVA) layer between the polymethyl-methacrylate (PMMA) and the 2D material film. This technique not only allows the effective transfer to an arbitrary target substrate with a high degree of freedom, but also avoids PMMA etching thereby maintaining the high quality of the transferred 2D materials with minimum contamination. We applied this method to transfer various 2D materials grown on different rigid substrates of general interest, such as graphene on copper foil, h-BN on platinum and MoS2 on SiO2/Si. This facile transfer technique has great potential for future research towards the application of 2D materials in high performance optical, mechanical and electronic devices.
An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase
Authors: Matthes Dirk , Gapsys Vytautas , Brennecke Julian T. , de Groot Bert L. 
Published: September 2016

AbstractThe formation of well-defined filamentous amyloid structures involves a polydisperse collection of oligomeric states for which relatively little is known in terms of structural organization. Here we use extensive, unbiased explicit solvent molecular dynamics (MD) simulations to investigate the structural and dynamical features of oligomeric aggregates formed by a number of highly amyloidogenic peptides at atomistic resolution on the μs time scale. A consensus approach has been adopted to analyse the simulations in multiple force fields, yielding an in-depth characterization of pre-fibrillar oligomers and their global and local structure properties. A collision cross section analysis revealed structurally heterogeneous aggregate ensembles for the individual oligomeric states that lack a single defined quaternary structure during the pre-nucleation phase. To gain insight into the conformational space sampled in early aggregates, we probed their substructure and found emerging β-sheet subunit layers and a multitude of ordered intermolecular β-structure motifs with growing aggregate size. Among those, anti-parallel out-of-register β-strands compatible with toxic β-barrel oligomers were particularly prevalent already in smaller aggregates and formed prior to ordered fibrillar structure elements. Notably, also distinct fibril-like conformations emerged in the oligomeric state and underscore the notion that pre-nucleated oligomers serve as a critical intermediate step on-pathway to fibrils.
Pressurized brines in continental Antarctica as a possible analogue of Mars
Authors: Forte Emanuele , Dalle Fratte Michele , Azzaro Maurizio , Guglielmin Mauro 
Published: September 2016

AbstractInterest in brines in extreme and cold environments has recently increased after they have been found on Mars. Those brines can be potential new subsurface habitats for peculiar ecosystems. In the McMurdo Dry Valleys of the Antarctic, the best analogue for Mars conditions, only a few cases of brines have been identified in some perennially frozen lakes and in one case in an underground aquifer. Here, we present the occurrence of pressurized brines in a shallow perennially ice-covered lake south of 70°S in an ice-free area of Victoria Land, Antarctica. For the first time, we also imaged, by means of ground penetrating radar data, the existence of a pingo-like-feature (PLF) formed by the extrusion of brines, which has also been confirmed by borehole evidence. Those brines are fed by an underground talik external to the lake basin, enhancing the possibility of unexploited ecosystems that could find an analogue in Martian environments.
The Role of Climate Covariability on Crop Yields in the Conterminous United States
Authors: Leng Guoyong , Zhang Xuesong , Huang Maoyi , Asrar Ghassem R. , Leung L. Ruby 
Published: September 2016

AbstractThe covariability of temperature (T), precipitation (P) and radiation (R) is an important aspect in understanding the climate influence on crop yields. Here, we analyze county-level corn and soybean yields and observed climate for the period 1983–2012 to understand how growing-season (June, July and August) mean T, P and R influence crop yields jointly and in isolation across the CONterminous United States (CONUS). Results show that nationally averaged corn and soybean yields exhibit large interannual variability of 21% and 22%, of which 35% and 32% can be significantly explained by T and P, respectively. By including R, an additional of 5% in variability can be explained for both crops. Using partial regression analyses, we find that studies that ignore the covariability among T, P, and R can substantially overestimate the sensitivity of crop yields to a single climate factor at the county scale. Further analyses indicate large spatial variation in the relative contributions of different climate variables to the variability of historical corn and soybean yields. The structure of the dominant climate factors did not change substantially over 1983–2012, confirming the robustness of the findings, which have important implications for crop yield prediction and crop model validations.
Mycobacterium tuberculosis exploits the formation of new blood vessels for its dissemination
Authors: Polena Helena , Boudou Frédéric , Tilleul Sylvain , Dubois-Colas Nicolas , Lecointe Cécile , Rakotosamimanana Niaina , Pelizzola Mattia , Andriamandimby Soa Fy , Raharimanga Vaomalala , Charles Patricia , Herrmann Jean-Louis , Ricciardi-Castagnoli Paola , Rasolofo Voahangy , Gicquel Brigitte , Tailleux Ludovic 
Published: September 2016

AbstractThe mechanisms by which the airborne pathogen Mycobacterium tuberculosis spreads within the lung and leaves its primary niche to colonize other organs, thus inducing extrapulmonary forms of tuberculosis (TB) in humans, remains poorly understood. Herein, we used a transcriptomic approach to investigate the host cell gene expression profile in M. tuberculosis–infected human macrophages (ΜΦ). We identified 33 genes, encoding proteins involved in angiogenesis, for which the expression was significantly modified during infection, and we show that the potent angiogenic factor VEGF is secreted by M. tuberculosis-infected ΜΦ, in an RD1-dependent manner. In vivo these factors promote the formation of blood vessels in murine models of the disease. Inhibiting angiogenesis, via VEGF inactivation, abolished mycobacterial spread from the infection site. In accordance with our in vitro and in vivo results, we show that the level of VEGF in TB patients is elevated and that endothelial progenitor cells are mobilized from the bone marrow. These results strongly strengthen the most recent data suggesting that mycobacteria take advantage of the formation of new blood vessels to disseminate.
The Mechanism of Hsp90 ATPase Stimulation by Aha1
Authors: Wolmarans Annemarie , Lee Brian , Spyracopoulos Leo , LaPointe Paul 
Published: September 2016

AbstractHsp90 is a dimeric molecular chaperone responsible for the folding, maturation, and activation of hundreds of substrate proteins called ‘clients’. Numerous co-chaperone proteins regulate progression through the ATP-dependent client activation cycle. The most potent stimulator of the Hsp90 ATPase activity is the co-chaperone Aha1p. Only one molecule of Aha1p is required to fully stimulate the Hsp90 dimer despite the existence of two, presumably identical, binding sites for this regulator. Using ATPase assays with Hsp90 heterodimers, we find that Aha1p stimulates ATPase activity by a three-step mechanism via the catalytic loop in the middle domain of Hsp90. Binding of the Aha1p N domain to the Hsp90 middle domain exerts a small stimulatory effect but also drives a separate conformational rearrangement in the Hsp90 N domains. This second event drives a rearrangement in the N domain of the opposite subunit and is required for the stimulatory action of the Aha1p C domain. Furthermore, the second event can be blocked by a mutation in one subunit of the Hsp90 dimer but not the other. This work provides a foundation for understanding how post-translational modifications regulate co-chaperone engagement with the Hsp90 dimer.
Freestanding bacterial cellulose-graphene oxide composite membranes with high mechanical strength for selective ion permeation
Authors: Fang Qile , Zhou Xufeng , Deng Wei , Zheng Zhi , Liu Zhaoping 
Published: September 2016

AbstractGraphene oxide (GO) based membranes have been widely applied in molecular separation based on the size exclusion effect of the nanochannels formed by stacked GO sheets. However, it’s still a challenge to prepare a freestanding GO-based membrane with high mechanical strength and structural stability which is prerequisite for separation application in aqueous solution. Here, a freestanding composite membrane based on bacterial cellulose (BC) and GO is designed and prepared. BC network provides a porous skeleton to spread GO sheets and uniformly incorporates into the GO layers, which endows the BC + GO composite membrane with well water-stability, excellent tensile strength, as well as improved toughness, guaranteeing its separation applicability in water environment. The resulting BC + GO membrane exhibits obviously discrepant permeation properties for different inorganic/organic ions with different size, and in particular, it can quickly separate ions in nano-scale from angstrom-scale. Therefore, this novel composite membrane is considered to be a promising candidate in the applications of water purification, food industry, biomedicine, and pharmaceutical and fuel separation.