bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oscillatory vapour shielding of liquid metal walls in nuclear fusion devices
Authors: van Eden G. G. , Kvon V. , van de Sanden M. C. M. , Morgan T. W. 
Published: July 2017

AbstractProviding an efficacious plasma facing surface between the extreme plasma heat exhaust and the structural materials of nuclear fusion devices is a major challenge on the road to electricity production by fusion power plants. The performance of solid plasma facing surfaces may become critically reduced over time due to progressing damage accumulation. Liquid metals, however, are now gaining interest in solving the challenge of extreme heat flux hitting the reactor walls. A key advantage of liquid metals is the use of vapour shielding to reduce the plasma exhaust. Here we demonstrate that this phenomenon is oscillatory by nature. The dynamics of a Sn vapour cloud are investigated by exposing liquid Sn targets to H and He plasmas at heat fluxes greater than 5 MW m−2. The observations indicate the presence of a dynamic equilibrium between the plasma and liquid target ruled by recombinatory processes in the plasma, leading to an approximately stable surface temperature.
Pan-urologic cancer genomic subtypes that transcend tissue of origin
Authors: Chen Fengju , Zhang Yiqun , Bossé Dominick , Lalani Aly-Khan A. , Hakimi A. Ari , Hsieh James J. , Choueiri Toni K. , Gibbons Don L. , Ittmann Michael , Creighton Chad J. 
Published: July 2017

AbstractUrologic cancers include cancers of the bladder, kidney, prostate, and testes, with common molecular features spanning different types. Here, we show that 1954 urologic cancers can be classified into nine major genomic subtypes, on the basis of multidimensional and comprehensive molecular characterization (including DNA methylation and copy number, and RNA and protein expression). Tissue dominant effects are first removed computationally in order to define these subtypes, which reveal common processes—reflecting in part tumor microenvironmental influences—driving cellular behavior across tumor lineages. Six of the subtypes feature a mixture of represented cancer types as defined by tissue or cell of origin. Differences in patient survival and in the manifestation of specific pathways—including hypoxia, metabolism, NRF2-ARE, Hippo, and immune checkpoint—can further distinguish the subtypes. Immune checkpoint markers and molecular signatures of macrophages and T cell infiltrates are relatively high within distinct subsets of each cancer type studied. The pan-urologic cancer genomic subtypes would facilitate information sharing involving therapeutic implications between tissue-oriented domains.
Construction of ground-state preserving sparse lattice models for predictive materials simulations
Authors: Huang Wenxuan , Urban Alexander , Rong Ziqin , Ding Zhiwei , Luo Chuan , Ceder Gerbrand 
Published: July 2017

AbstractFirst-principles based cluster expansion models are the dominant approach in ab initio thermodynamics of crystalline mixtures enabling the prediction of phase diagrams and novel ground states. However, despite recent advances, the construction of accurate models still requires a careful and time-consuming manual parameter tuning process for ground-state preservation, since this property is not guaranteed by default. In this paper, we present a systematic and mathematically sound method to obtain cluster expansion models that are guaranteed to preserve the ground states of their reference data. The method builds on the recently introduced compressive sensing paradigm for cluster expansion and employs quadratic programming to impose constraints on the model parameters. The robustness of our methodology is illustrated for two lithium transition metal oxides with relevance for Li-ion battery cathodes, i.e., Li2x
Fe2(1−x)O2 and Li2x
Ti2(1−x)O2, for which the construction of cluster expansion models with compressive sensing alone has proven to be challenging. We demonstrate that our method not only guarantees ground-state preservation on the set of reference structures used for the model construction, but also show that out-of-sample ground-state preservation up to relatively large supercell size is achievable through a rapidly converging iterative refinement. This method provides a general tool for building robust, compressed and constrained physical models with predictive power.
Rewritable ferroelectric vortex pairs in BiFeO3
Authors: Li Yang , Jin Yaming , Lu Xiaomei , Yang Jan-Chi , Chu Ying-Hao , Huang Fengzhen , Zhu Jinsong , Cheong Sang-Wook 
Published: July 2017

AbstractFerroelectric vortex in multiferroic materials has been considered as a promising alternative to current memory cells for the merit of high storage density. However, the formation of regular natural ferroelectric vortex is difficult, restricting the achievement of vortex memory device. Here, we demonstrated the creation of ferroelectric vortex-antivortex pairs in BiFeO3 thin films by using local electric field. The evolution of the polar vortex structure is studied by piezoresponse force microscopy at nanoscale. The results reveal that the patterns and stability of vortex structures are sensitive to the poling position. Consecutive writing and erasing processes cause no influence on the original domain configuration. The Z4 proper coloring vortex-antivortex network is then analyzed by graph theory, which verifies the rationality of artificial vortex-antivortex pairs. This study paves a foundation for artificial regulation of vortex, which provides a possible pathway for the design and realization of non-volatile vortex memory devices and logical devices.
An extended model for culture-dependent heterogenous gene expression and proliferation dynamics in mouse embryonic stem cells
Authors: Godwin Simon , Ward Daniel , Pedone Elisa , Homer Martin , Fletcher Alexander G. , Marucci Lucia 
Published: July 2017

AbstractDuring development, pluripotency is a transient state describing a cell’s ability to give rise to all three germ layers and germline. Recent studies have shown that, in vitro, pluripotency is highly dynamic: exogenous stimuli provided to cultures of mouse embryonic stem cells, isolated from pre-implantation blastocysts, significantly affect the spectrum of pluripotency. 2i/LIF, a recently defined serum-free medium, forces mouse embryonic stem cells into a ground-state of pluripotency, while serum/LIF cultures promote the co-existence of ground-like and primed-like mouse embryonic stem cell subpopulations. The latter heterogeneity correlates with temporal fluctuations of pluripotency markers, including the master regulator Nanog, in single cells. We propose a mathematical model of Nanog dynamics in both media, accounting for recent experimental data showing the persistence of a small Nanog Low subpopulation in ground-state pluripotency mouse embryonic stem cell cultures. The model integrates into the core pluripotency Gene Regulatory Network both inhibitors present in 2i/LIF (PD and Chiron), and feedback interactions with genes found to be differentially expressed in the two media. Our simulations and bifurcation analysis show that, in ground-state cultures, Nanog dynamics result from the combination of reduced noise in gene expression and the shift of the system towards a monostable, but still excitable, regulation. Experimental data and agent-based modelling simulations indicate that mouse embryonic stem cell proliferation dynamics vary in the two media, and cannot be reproduced by accounting only for Nanog-dependent cell-cycle regulation. We further demonstrate that both PD and Chiron play a key role in regulating heterogeneity in transcription factor expression and, ultimately, mouse embryonic stem cell fate decision.
Interaction between von Hippel-Lindau Protein and Fatty Acid Synthase Modulates Hypoxia Target Gene Expression
Authors: Sun Wendi , Kato Hiroyuki , Kitajima Shojiro , Lee Kian Leong , Gradin Katarina , Okamoto Takashi , Poellinger Lorenz 
Published: July 2017

AbstractHypoxia-inducible factors (HIFs) play a central role in the transcriptional response to changes in oxygen availability. Stability of HIFs is regulated by multi-step reactions including recognition by the von Hippel-Lindau tumour suppressor protein (pVHL) in association with an E3 ligase complex. Here we show that pVHL physically interacts with fatty acid synthase (FASN), displacing the E3 ubiquitin ligase complex. This results in HIF-α protein stabilization and activation of HIF target genes even in normoxia such as during adipocyte differentiation. 25-hydroxycholesterol (25-OH), an inhibitor of FASN expression, also inhibited HIF target gene expression in cultured cells and in mouse liver. Clinically, FASN is frequently upregulated in a broad variety of cancers and has been reported to have an oncogenic function. We found that upregulation of FASN correlated with induction of many HIF target genes, notably in a malignant subtype of prostate tumours. Therefore, pVHL-FASN interaction plays a regulatory role for HIFs and their target gene expression.
Phytoextraction of cadmium-contaminated soil and potential of regenerated tobacco biomass for recovery of cadmium
Authors: Yang Yang , Ge Yichen , Zeng Hongyuan , Zhou Xihong , Peng Liang , Zeng Qingru 
Published: July 2017

AbstractThe aim of this study was to estimate the influence of regenerated tobacco on the extraction of Cd from two acidic soils as well as to address the problem of how to deal with contaminated leaves following phytoextraction. Results showed that a coppicing tobacco led to a decline in Cd concentration in regenerated leaves and stalks when plants were grown in pots, but increased concentrations in regenerated lower and middle leaves when plants were grown under field conditions. The highest recorded bioconcentration factors in Chaling and Guanxi soil were 37.53 and 19.21 in lower leaves in the field, respectively. Total Cd extraction efficiency in practice (9.43% for Chaling soil and 6.24% for Guanxi soil) under field conditions confirmed our theoretical calculations (10.0% for Chaling soil and 6.73% for Guanxi soil). Use of a 0.5% hydrochloric acid(HCl) solution was sufficient to reduce Cd (98.4%) in tobacco leaves to permissible levels as required by the Hygienic Standard for Feeds in China (≤0.5 mg kg−1). Regenerated tobacco has the potential to allow cultivation of Cd contaminated farmland to produce animal feed, assist in lowering total Cd content of soil, and allow income generation for farmers.
Selection and characterization of DNA aptamer against glucagon receptor by cell-SELEX
Authors: Wang Guodong , Liu Jun , Chen Ke , Xu Yiling , Liu Bo , Liao Jie , Zhu Lei , Hu Xiaoxiao , Li Jianglin , Pu Ying , Zhong Wen , Fu Ting , Liu Huixia , Tan Weihong 
Published: July 2017

AbstractExcessive secretion of glucagon, a functional insulin antagonist, significantly contributes to hyperglycemia. Glucagon exerts its physiological functions through activation of the glucagon receptor (GCGR). Inhibition of GCGR activity represents a potential therapeutic approach for reducing excess glucose production in diabetes mellitus. Aptamers are short DNA or RNA oligonucleotides evolved from systematic evolution of ligands by exponential enrichment (SELEX). Here, we have successfully selected a DNA aptamer against GCGR by cell-SELEX, which can specifically bind membrane protein of CHO-GCGR cells with a K
d
of 52.7 ± 5.1 nM. Aptamer-mediated pull-down and gcgr knockdown assay verified that GCGR was the target of aptamer GR-3. Binding analysis revealed that GR-3 could recognize other cells with different affinity according to the level of GCGR protein expressed in these cells. Hepatic tissue imaging suggested that GR-3 could bind the cell membrane of hepatic tissues. With the advantages of small size, high binding affinity, good stability, lack of immunogenicity, and easy synthesis, aptamer GR-3 against GCGR can be a promising tool with the potential to attenuate hyperglycemia in diabetes mellitus.
Auditory environmental context affects visual distance perception
Authors: Etchemendy Pablo E. , Abregú Ezequiel , Calcagno Esteban R. , Eguia Manuel C. , Vechiatti Nilda , Iasi Federico , Vergara Ramiro O. 
Published: July 2017

AbstractIn this article, we show that visual distance perception (VDP) is influenced by the auditory environmental context through reverberation-related cues. We performed two VDP experiments in two dark rooms with extremely different reverberation times: an anechoic chamber and a reverberant room. Subjects assigned to the reverberant room perceived the targets farther than subjects assigned to the anechoic chamber. Also, we found a positive correlation between the maximum perceived distance and the auditorily perceived room size. We next performed a second experiment in which the same subjects of Experiment 1 were interchanged between rooms. We found that subjects preserved the responses from the previous experiment provided they were compatible with the present perception of the environment; if not, perceived distance was biased towards the auditorily perceived boundaries of the room. Results of both experiments show that the auditory environment can influence VDP, presumably through reverberation cues related to the perception of room size.
Transition metal alloying effect on the phosphoric acid adsorption strength of Pt nanoparticles: an experimental and density functional theory study
Authors: Park Hee-Young , Lim Dong-Hee , Yoo Sung Jong , Kim Hyoung-Juhn , Henkensmeier Dirk , Kim Jin Young , Ham Hyung Chul , Jang Jong Hyun 
Published: July 2017

AbstractThe effect of alloying with transition metals (Ni, Co, Fe) on the adsorption strength of phosphoric acid on Pt alloy surfaces was investigated using electrochemical analysis and first-principles calculations. Cyclic voltammograms of carbon-supported Pt3M/C (M = Ni, Co, and Fe) electrocatalysts in 0.1 M HClO4 with and without 0.01 M H3PO4 revealed that the phosphoric acid adsorption charge density near the onset potential on the nanoparticle surfaces was decreased by alloying with transition metals in the order Co, Fe, Ni. First-principles calculations based on density functional theory confirmed that the adsorption strength of phosphoric acid was weakened by alloying with transition metals, in the same order as that observed in the electrochemical analysis. The simulation suggested that the weaker phosphoric acid adsorption can be attributed to a lowered density of states near the Fermi level due to alloying with transition metals.
Ecological Effect of Arginine on Oral Microbiota
Authors: Zheng Xin , He Jinzhi , Wang Lin , Zhou Shuangshuang , Peng Xian , Huang Shi , Zheng Liwei , Cheng Lei , Hao Yuqing , Li Jiyao , Xu Jian , Xu Xin , Zhou Xuedong 
Published: July 2017

AbstractDental caries is closely associated with the microbial dybiosis between acidogenic/aciduric pathogens and alkali-generating commensal bacteria colonized in the oral cavity. Our recent studies have shown that arginine may represent a promising anti-caries agent by modulating microbial composition in an in vitro consortium. However, the effect of arginine on the oral microbiota has yet to be comprehensively delineated in either clinical cohort or in vitro biofilm models that better represent the microbial diversity of oral cavity. Here, by employing a clinical cohort and a saliva-derived biofilm model, we demonstrated that arginine treatment could favorably modulate the oral microbiota of caries-active individuals. Specifically, treatment with arginine-containing dentifrice normalized the oral microbiota of caries-active individuals similar to that of caries-free controls in terms of microbial structure, abundance of typical species, enzymatic activities of glycolysis and alkali-generation related enzymes and their corresponding transcripts. Moreover, we found that combinatory use of arginine with fluoride could better enrich alkali-generating Streptococcus sanguinis and suppress acidogenic/aciduric Streptococcus mutans, and thus significantly retard the demineralizing capability of saliva-derived oral biofilm. Hence, we propose that fluoride and arginine have a potential synergistic effect in maintaining an eco-friendly oral microbial equilibrium in favor of better caries management.
Niche-specific gene expression in a parasitic nematode; increased expression of immunomodulators in Teladorsagia circumcincta larvae derived from host mucosa
Authors: McNeilly Tom N. , Frew David , Burgess Stewart T. G. , Wright Harry , Bartley David J. , Bartley Yvonne , Nisbet Alasdair J. 
Published: July 2017

AbstractMetazoan parasites have to survive in many different niches in order to complete their life-cycles. In the absence of reliable methods to manipulate parasite genomes and/or proteomes, identification of the molecules critical for parasite survival within these niches has largely depended on comparative transcriptomic and proteomic analyses of different developmental stages of the parasite; however, changes may reflect differences associated with transition between developmental stages rather than specific adaptations to a particular niche. In this study, we compared the transcriptome of two fourth-stage larval populations of the nematode parasite,Teladorsagia circumcincta, which were of the same developmental stage but differed in their location within the abomasum, being either mucosal-dwelling (MD) or lumen-dwelling (LD). Using RNAseq, we identified 57 transcripts which were significantly differentially expressed between MD and LD larvae. Of these transcripts, the majority (54/57) were up-regulated in MD larvae, one of which encoded for an ShKT-domain containing protein, Tck6, capable of modulating ovine T cell cytokine responses. Other differentially expressed transcripts included homologues of ASP-like proteins, proteases, or excretory-secretory proteins of unknown function. Our study demonstrates the utility of niche- rather than stage-specific analysis of parasite transcriptomes to identify parasite molecules of potential importance for survival within the host.
Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins
Authors: Halakou Farideh , Kilic Emel Sen , Cukuroglu Engin , Keskin Ozlem , Gursoy Attila 
Published: July 2017

AbstractTraditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction but also helps us to find the mutual exclusive interactions. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different interactions, functions, and downstream signalling. In this study, we proposed a new representation for structural PPI networks inspecting the alternative conformations of proteins. We performed a large-scale study by creating breast cancer metastasis network and equipped it with different conformers of proteins. Our results showed that although 88% of proteins in our network has at least two structures in Protein Data Bank (PDB), only 22% of them have alternative conformations and the remaining proteins have different regions saved in PDB. However, using even this small set of alternative conformations we observed a considerable increase in our protein docking predictions. Our protein-protein interaction predictions increased from 54% to 76% using the alternative conformations. We also showed the benefits of investigating structural data and alternative conformations of proteins through three case studies.
Reaction dynamics of the chimeric channelrhodopsin C1C2
Authors: Hontani Yusaku , Marazzi Marco , Stehfest Katja , Mathes Tilo , van Stokkum Ivo H. M. , Elstner Marcus , Hegemann Peter , Kennis John T. M. 
Published: July 2017

AbstractChannelrhodopsin (ChR) is a key protein of the optogenetic toolkit. C1C2, a functional chimeric protein of Chlamydomonas reinhardtii ChR1 and ChR2, is the only ChR whose crystal structure has been solved, and thus uniquely suitable for structure-based analysis. We report C1C2 photoreaction dynamics with ultrafast transient absorption and multi-pulse spectroscopy combined with target analysis and structure-based hybrid quantum mechanics/molecular mechanics calculations. Two relaxation pathways exist on the excited (S1) state through two conical intersections CI1 and CI2, that are reached via clockwise and counter-clockwise rotations: (i) the C13=C14 isomerization path with 450 fs via CI1 and (ii) a relaxation path to the initial ground state with 2.0 ps and 11 ps via CI2, depending on the hydrogen-bonding network, hence indicating active-site structural heterogeneity. The presence of the additional conical intersection CI2 rationalizes the relatively low quantum yield of photoisomerization (30 ± 3%), reported here. Furthermore, we show the photoreaction dynamics from picoseconds to seconds, characterizing the complete photocycle of C1C2.
Scalable and Transfer-Free Fabrication of MoS2/SiO2 Hybrid Nanophotonic Cavity Arrays with Quality Factors Exceeding 4000
Authors: Hammer Sebastian , Mangold H. Moritz , Nguyen Ariana E. , Martinez-Ta Dominic , Naghibi Alvillar Sahar , Bartels Ludwig , Krenner Hubert J. 
Published: July 2017

AbstractWe report the fully-scalable fabrication of a large array of hybrid molybdenum disulfide (MoS2) - silicon dioxide (SiO2) one-dimensional, free-standing photonic-crystal cavities capable of enhancement of the MoS2 photoluminescence at the narrow cavity resonance. We demonstrate continuous tunability of the cavity resonance wavelength across the entire emission band of MoS2 simply by variation of the photonic crystal periodicity. Device fabrication started by substrate-scale growth of MoS2 using chemical vapor deposition (CVD) on non-birefringent thermal oxide on a silicon wafer; it was followed by lithographic fabrication of a photonic crystal nanocavity array on the same substrate at more than 50% yield of functional devices. Our cavities exhibit three dominant modes with measured linewidths less than 0.2 nm, corresponding to quality factors exceeding 4000. All experimental findings are found to be in excellent agreement with finite difference time domain (FDTD) simulations. CVD MoS2 provides scalable access to a direct band gap, inorganic, stable and efficient emitter material for on-chip photonics without the need for epitaxy and is at CMOS compatible processing parameters even for back-end-of-line integration; our findings suggest feasibility of cavity based line-narrowing in MoS2-based on-chip devices as it is required for instance for frequency-multiplexed operation in on-chip optical communication and sensing.