bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kurt Weill'sThe River Is Blue: “Film-Opera” and Politics in 1930s Hollywood
Authors: GRABER NAOMI 
Published: August 2017

AbstractIn early 1937, Kurt Weill and playwright Clifford Odets collaborated on a Spanish Civil War film that they hoped would lead to a new kind of political–musical picture. Originally titledThe River Is Blue, the film was eventually released in 1938 asBlockadewithout the involvement of either Odets or Weill, but recently uncovered archival material of the abandoned project reveals new facets of Weill's musico-dramatic thought. The discovery of Odets's first draft of the screenplay shows an extraordinarily close collaboration between composer and screenwriter as the shot numbers in the script align exactly with numbers in Weill's score. Read together, these two documents show Weill attempting to combine different paradigms of film scoring that were popular in the 1930s. There are moments of typical Golden Age–style scoring with mickey-mousing and leitmotifs, but there is also evidence of older practices such as the use of popular songs. Weill's score also displays the influence of the Popular Front, elements of Eisensteinian montage, and anti-Wagnerianism. These show Weill working toward what he termed “film-opera,” not a filmed version of an opera but an entirely new genre that combined elements of musical theatre and movies.
Probing the crystallographic orientation of two-dimensional atomic crystals with supramolecular self-assembly
Authors: Wang Jinghui , Yu Hongde , Zhou Xu , Liu Xiaozhi , Zhang Renjie , Lu Zhixing , Zheng Jingying , Gu Lin , Liu Kaihui , Wang Dong , Jiao Liying 
Published: August 2017

AbstractProbing the crystallographic orientation of two-dimensional (2D) materials is essential to understand and engineer their properties. However, the nondestructive identification of the lattice orientations of various 2D materials remains a challenge due to their very thin nature. Here, we identify the crystallographic structures of various 2D atomic crystals using molecules as probes by utilizing orientation-dependent molecule–substrate interactions. We discover that the periodic atomic packing of 2D materials guides oleamide molecules to assemble into quasi-one-dimensional nanoribbons with specific alignments which precisely indicate the lattice orientations of the underlying materials. Using oleamide molecules as probes, we successfully identify the crystallographic orientations of ~12 different 2D materials without degrading their intrinsic properties. Our findings allow for the nondestructive identification of the lattice structure of various 2D atomic crystals and shed light on the functionalization of these 2D materials with supramolecular assembly.
VEGF amplifies transcription through ETS1 acetylation to enable angiogenesis
Authors: Chen Jiahuan , Fu Yi , Day Daniel S. , Sun Ye , Wang Shiyan , Liang Xiaodong , Gu Fei , Zhang Fang , Stevens Sean M. , Zhou Pingzhu , Li Kai , Zhang Yan , Lin Ruei-zeng , Smith Lois E. H. , Zhang Jin , Sun Kun , Melero-Martin Juan M. , Han Zeguang , Park Peter J. , Zhang Bing , Pu William T. 
Published: August 2017

AbstractRelease of promoter-proximally paused RNA polymerase II (RNAPII) is a recently recognized transcriptional regulatory checkpoint. The biological roles of RNAPII pause release and the mechanisms by which extracellular signals control it are incompletely understood. Here we show that VEGF stimulates RNAPII pause release by stimulating acetylation of ETS1, a master endothelial cell transcriptional regulator. In endothelial cells, ETS1 binds transcribed gene promoters and stimulates their expression by broadly increasing RNAPII pause release.
34
VEGF enhances ETS1 chromatin occupancy and increases ETS1 acetylation, enhancing its binding to BRD4, which recruits the pause release machinery and increases RNAPII pause release. Endothelial cell angiogenic responses in vitro and in vivo require ETS1-mediated transduction of VEGF signaling to release paused RNAPII. Our results define an angiogenic pathway in which VEGF enhances ETS1–BRD4 interaction to broadly promote RNAPII pause release and drive angiogenesis.
Asymmetric dynamics of DNA entering and exiting a strongly confining nanopore
Authors: Bell Nicholas A. W. , Chen Kaikai , Ghosal Sandip , Ricci Maria , Keyser Ulrich F. 
Published: August 2017

AbstractIn nanopore sensing, changes in ionic current are used to analyse single molecules in solution. The translocation dynamics of polyelectrolytes is of particular interest given potential applications such as DNA sequencing. In this paper, we determine how the dynamics of voltage driven DNA translocation can be affected by the nanopore geometry and hence the available configurational space for the DNA. Using the inherent geometrical asymmetry of a conically shaped nanopore, we examine how DNA dynamics depends on the directionality of transport. The total translocation time of DNA when exiting the extended conical confinement is significantly larger compared to the configuration where the DNA enters the pore from the open reservoir. By using specially designed DNA molecules with positional markers, we demonstrate that the translocation velocity progressively increases as the DNA exits from confinement. We show that a hydrodynamic model can account for these observations.
Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes
Authors: Balasubramanian Suganthi , Fu Yao , Pawashe Mayur , McGillivray Patrick , Jin Mike , Liu Jeremy , Karczewski Konrad J. , MacArthur Daniel G. , Gerstein Mark 
Published: August 2017

AbstractVariants predicted to result in the loss of function of human genes have attracted interest because of their clinical impact and surprising prevalence in healthy individuals. Here, we present ALoFT (annotation of loss-of-function transcripts), a method to annotate and predict the disease-causing potential of loss-of-function variants. Using data from Mendelian disease-gene discovery projects, we show that ALoFT can distinguish between loss-of-function variants that are deleterious as heterozygotes and those causing disease only in the homozygous state. Investigation of variants discovered in healthy populations suggests that each individual carries at least two heterozygous premature stop alleles that could potentially lead to disease if present as homozygotes. When applied to de novo putative loss-of-function variants in autism-affected families, ALoFT distinguishes between deleterious variants in patients and benign variants in unaffected siblings. Finally, analysis of somatic variants in >6500 cancer exomes shows that putative loss-of-function variants predicted to be deleterious by ALoFT are enriched in known driver genes.
Improved split fluorescent proteins for endogenous protein labeling
Authors: Feng Siyu , Sekine Sayaka , Pessino Veronica , Li Han , Leonetti Manuel D. , Huang Bo 
Published: August 2017

AbstractSelf-complementing split fluorescent proteins (FPs) have been widely used for protein labeling, visualization of subcellular protein localization, and detection of cell–cell contact. To expand this toolset, we have developed a screening strategy for the direct engineering of self-complementing split FPs. Via this strategy, we have generated a yellow–green split-mNeonGreen21–10/11 that improves the ratio of complemented signal to the background of FP1–10-expressing cells compared to the commonly used split GFP1–10/11; as well as a 10-fold brighter red-colored split-sfCherry21–10/11. Based on split sfCherry2, we have engineered a photoactivatable variant that enables single-molecule localization-based super-resolution microscopy. We have demonstrated dual-color endogenous protein tagging with sfCherry211 and GFP11, revealing that endoplasmic reticulum translocon complex Sec61B has reduced abundance in certain peripheral tubules. These new split FPs not only offer multiple colors for imaging interaction networks of endogenous proteins, but also hold the potential to provide orthogonal handles for biochemical isolation of native protein complexes.
An allosteric ligand-binding site in the extracellular cap of K2P channels
Authors: Luo Qichao , Chen Liping , Cheng Xi , Ma Yuqin , Li Xiaona , Zhang Bing , Li Li , Zhang Shilei , Guo Fei , Li Yang , Yang Huaiyu 
Published: August 2017

AbstractTwo-pore domain potassium (K2P) channels generate leak currents that are responsible for the maintenance of the resting membrane potential, and they are thus potential drug targets for treating diseases. Here, we identify N-(4-cholorphenyl)-N-(2-(3,4-dihydrosioquinolin-2(1H)-yl)-2-oxoethyl)methanesulfonamide (TKDC) as an inhibitor of the TREK subfamily, including TREK-1, TREK-2 and TRAAK channels. Using TKDC as a chemical probe, a study combining computations, mutagenesis and electrophysiology reveals a K2P allosteric ligand-binding site located in the extracellular cap of the channels. Molecular dynamics simulations suggest that ligand-induced allosteric conformational transitions lead to blockage of the ion conductive pathway. Using virtual screening approach, we identify other inhibitors targeting the extracellular allosteric ligand-binding site of these channels. Overall, our results suggest that the allosteric site at the extracellular cap of the K2P channels might be a promising drug target for these membrane proteins.
Differential dynamic microscopy of bidisperse colloidal suspensions
Authors: Safari Mohammad S. , Poling-Skutvik Ryan , Vekilov Peter G. , Conrad Jacinta C. 
Published: August 2017

AbstractResearch tasks in microgravity include monitoring the dynamics of constituents of varying size and mobility in processes such as aggregation, phase separation, or self-assembly. We use differential dynamic microscopy, a method readily implemented with equipment available on the International Space Station, to simultaneously resolve the dynamics of particles of radius 50 nm and 1 μm in bidisperse aqueous suspensions. Whereas traditional dynamic light scattering fails to detect a signal from the larger particles at low concentrations, differential dynamic microscopy exhibits enhanced sensitivity in these conditions by accessing smaller wavevectors where scattering from the large particles is stronger. Interference patterns due to scattering from the large particles induce non-monotonic decay of the amplitude of the dynamic correlation function with the wavevector. We show that the position of the resulting minimum contains information on the vertical position of the particles. Together with the simple instrumental requirements, the enhanced sensitivity of differential dynamic microscopy makes it an appealing alternative to dynamic light scattering to characterize samples with complex dynamics.
Model-Based Therapy Planning Allows Prediction of Haemodynamic Outcome after Aortic Valve Replacement
Authors: Kelm M. , Goubergrits L. , Bruening J. , Yevtushenko P. , Fernandes J. F. , Sündermann S. H. , Berger F. , Falk V. , Kuehne T. , Nordmeyer S. ,   CARDIOPROOF group, Morley-Fletcher E. , De Maldè M. , Muthurangu V. , Khushnood A. , Chinali M. , Pongiglione G. , Hennemuth A. , Mirzae H. , Neugebauer M. , Ecabert O. , Neumann D. , Groenenboom P. , Plank G. , Manset D. , McGuire A. , Naci H. , Salcher M. 
Published: August 2017

AbstractOptimizing treatment planning is essential for advances in patient care and outcomes. Precisely tailored therapy for each patient remains a yearned-for goal. Cardiovascular modelling has the potential to simulate and predict the functional response before the actual intervention is performed. The objective of this study was to proof the validity of model-based prediction of haemodynamic outcome after aortic valve replacement. In a prospective study design virtual (model-based) treatment of the valve and the surrounding vasculature were performed alongside the actual surgical procedure (control group). The resulting predictions of anatomic and haemodynamic outcome based on information from magnetic resonance imaging before the procedure were compared to post-operative imaging assessment of the surgical control group in ten patients. Predicted vs. post-operative peak velocities across the valve were comparable (2.97 ± 1.12 vs. 2.68 ± 0.67 m/s; p = 0.362). In wall shear stress (17.3 ± 12.3 Pa vs. 16.7 ± 16.84 Pa; p = 0.803) and secondary flow degree (0.44 ± 0.32 vs. 0.49 ± 0.23; p = 0.277) significant linear correlations (p < 0.001) were found between predicted and post-operative outcomes. Between groups blood flow patterns showed good agreement (helicity p = 0.852, vorticity p = 0.185, eccentricity p = 0.333). Model-based therapy planning is able to accurately predict post-operative haemodynamics after aortic valve replacement. These validated virtual treatment procedures open up promising opportunities for individually targeted interventions.
Regulation of Orai1/STIM1 mediated ICRAC by intracellular pH
Authors: Gavriliouk D. , Scrimgeour N. R. , Grigoryev S. , Ma L. , Zhou F. H. , Barritt G. J. , Rychkov G. Y. 
Published: August 2017

AbstractCa2+ release activated Ca2+ (CRAC) channels composed of two cellular proteins, Ca2+-sensing stromal interaction molecule 1 (STIM1) and pore-forming Orai1, are the main mediators of the Ca2+ entry pathway activated in response to depletion of intracellular Ca2+ stores. Previously it has been shown that the amplitude of CRAC current (ICRAC) strongly depends on extracellular and intracellular pH. Here we investigate the intracellular pH (pHi) dependence of ICRAC mediated by Orai1 and STIM1ectopically expressed in HEK293 cells. The results indicate that pHi affects not only the amplitude of the current, but also Ca2+ dependent gating of CRAC channels. Intracellular acidification changes the kinetics of ICRAC, introducing prominent re-activation component in the currents recorded in response to voltage steps to strongly negative potentials. ICRAC with similar kinetics can be observed at normal pHi if the expression levels of Orai1 are increased, relative to the expression levels of STIM1. Mutations in the STIM1 inactivation domain significantly diminish the dependence of ICRAC kinetics on pHi, but have no effect on pHi dependence of ICRAC amplitude, implying that more than one mechanism is involved in CRAC channel regulation by intracellular pH.
2 + 1 dimensional de Sitter universe emerging from the gauge structure of a nonlinear quantum system
Authors: Kam Chon-Fai , Liu Ren-Bao 
Published: August 2017

AbstractBerry phases and gauge structures are fundamental quantum phenomena. In linear quantum mechanics the gauge field in parameter space presents monopole singularities where the energy levels become degenerate. In nonlinear quantum mechanics, which is an effective theory of interacting quantum systems, there can be phase transitions and hence critical surfaces in the parameter space. We find that these critical surfaces result in a new type of gauge field singularity, namely, a conic singularity that resembles the big bang of a 2 + 1 dimensional de Sitter universe, with the fundamental frequency of Bogoliubov excitations acting as the cosmic scale, and mode softening at the critical surface, where the fundamental frequency vanishes, causing a causal singularity. Such conic singularity may be observed in various systems such as Bose-Einstein condensates and molecular magnets. This finding offers a new approach to quantum simulation of fundamental physics.
Cu-chitosan nanoparticle boost defense responses and plant growth in maize (Zea mays L.)
Authors: Choudhary Ram Chandra , Kumaraswamy R. V. , Kumari Sarita , Sharma S. S. , Pal Ajay , Raliya Ramesh , Biswas Pratim , Saharan Vinod 
Published: August 2017

AbstractIn agriculture, search for biopolymer derived materials are in high demand to replace the synthetic agrochemicals. In the present investigation, the efficacy of Cu-chitosan nanoparticles (NPs) to boost defense responses against Curvularia leaf spot (CLS) disease of maize and plant growth promotry activity were evaluated. Cu-chitosan NPs treated plants showed significant defense response through higher activities of antioxidant (superoxide dismutase and peroxidase) and defense enzymes (polyphenol oxidase and phenylalanine ammonia-lyase). Significant control of CLS disease of maize was recorded at 0.04 to 0.16% of Cu-chitosan NPs treatments in pot and 0.12 to 0.16% of NPs treatments in field condition. Further, NPs treatments exhibited growth promotry effect in terms of plant height, stem diameter, root length, root number and chlorophyll content in pot experiments. In field experiment, plant height, ear length, ear weight/plot, grain yield/plot and 100 grain weight were enhanced in NPs treatments. Disease control and enhancement of plant growth was further enlightened through Cu release profile of Cu-chitosan NPs. This is an important development in agriculture nanomaterial research where biodegradable Cu-chitosan NPs are better compatible with biological control as NPs “mimic” the natural elicitation of the plant defense and antioxidant system for disease protection and sustainable growth.
Effect of fluoride treatment on gene expression in tea plant (Camellia sinensis)
Authors: Li Qing-Sheng , Lin Xiao-Ming , Qiao Ru-Ying , Zheng Xin-Qiang , Lu Jian-Liang , Ye Jian-Hui , Liang Yue-Rong 
Published: August 2017

AbstractTea plant is a typical fluorine (F) accumulator. F concentration in mature tea leaves is several hundred times higher than that in normal field crops. Long-term consumption of teas with high level F will increase the risks of dental and skeletal fluorosis. The mechanism of F accumulation in tea stands unclear. RNA-Seq and digital gene expression (DGE) techniques were used to investigate the effect of F on the differential expressions of transcriptome in tea plant. The results showed that F content in mature tea leaves was increased with increase in F concentration of cultural solution and duration of F treatment time. Based on comparison with data of GO, COG, KEGG and Nr databases, 144 differentially expressed unigenes with definite annotation were identified. Real-time reverse transcription PCR (qRT-PCR) was used to validate the effect of F on expression of 5 unigenes screened from the 144 unigenes. F treatment induced the expression of defense genes such as receptor-like kinases (RLKs) and U-box domain-containing protein. Based on the present study, F uptake is considered to be related to calcium-transporting ATPase, especially autoinhibited Ca2+ ATPase (ACAs) which was activated by the RLKs and worked as a carrier in uptake of F by tea plant.
Fluoroquinolone structure and translocation flux across bacterial membrane
Authors: Vergalli Julia , Dumont Estelle , Cinquin Bertrand , Maigre Laure , Pajovic Jelena , Bacqué Eric , Mourez Michael , Réfrégiers Matthieu , Pagès Jean-Marie 
Published: August 2017

AbstractBacterial multidrug resistance is a worrying health issue. In Gram-negative antibacterial research, the challenge is to define the antibiotic permeation across the membranes. Passing through the membrane barrier to reach the inhibitory concentration inside the bacterium is a pivotal step for antibacterial molecules. A spectrofluorimetric methodology has been developed to detect fluoroquinolones in bacterial population and inside individual Gram-negative bacterial cells. In this work, we studied the antibiotic accumulation in cells expressing various levels of efflux pumps. The assays allow us to determine the intracellular concentration of the fluoroquinolones to study the relationships between the level of efflux activity and the antibiotic accumulation, and finally to evaluate the impact of fluoroquinolone structures in this process. This represents the first protocol to identify some structural parameters involved in antibiotic translocation and accumulation, and to illustrate the recently proposed “Structure Intracellular Concentration Activity Relationship” (SICAR) concept.
Simulated forward and backward self motion, based on realistic parameters, causes motion induced blindness
Authors: Thomas Victoria , Davidson Matthew , Zakavi Parisa , Tsuchiya Naotsugu , van Boxtel Jeroen 
Published: August 2017

AbstractMotion Induced Blindness (MIB) is a well-established visual phenomenon whereby highly salient targets disappear when viewed against a moving background mask. No research has yet explored whether contracting and expanding optic flow can also trigger target disappearance. We explored MIB using mask speeds corresponding to driving at 35, 50, 65 and 80 km/h in simulated forward (expansion) and backward (contraction) motion as well as 2-D radial movement, random, and static mask motion types. Participants (n = 18) viewed MIB targets against masks with different movement types, speed, and target locations. To understand the relationship between saccades, pupil response and perceptual disappearance, we ran two additional eye-tracking experiments (n = 19). Target disappearance increased significantly with faster mask speeds and upper visual field target presentation. Simulated optic flow and 2-D radial movement caused comparable disappearance, and all moving masks caused significantly more disappearance than a static mask. Saccades could not entirely account for differences between conditions, suggesting that self-motion optic flow does cause MIB in an artificial setting. Pupil analyses implied that MIB disappearance induced by optic flow is not subjectively salient, potentially explaining why MIB is not noticed during driving. Potential implications of MIB for driving safety and Head-Up-Display (HUD) technologies are discussed.
Significant association of the CHRNB3-CHRNA6 gene cluster with nicotine dependence in the Chinese Han population
Authors: Wen Li , Han Haijun , Liu Qiang , Su Kunkai , Yang Zhongli , Cui Wenyan , Yuan Wenji , Ma Yunlong , Fan Rongli , Chen Jiali , Jiang Keran , Jiang Xianzhong , Payne Thomas J. , Wang Jundong , Li Ming D. 
Published: August 2017

AbstractAlthough numerous studies have revealed significant associations between variants in the nicotinic acetylcholine receptors (nAChR) subunits and nicotine dependence (ND), only few studies were performed in Chinese subjects. Here, we performed association and interaction analysis for 20 single nucleotide polymorphisms (SNPs) in the CHRNB3-CHRNA6 gene cluster with ND in a Chinese Han population (N = 5,055). We found nominally significant associations for all tested SNPs with ND measured by the Fagerström Test for Nicotine Dependence score; of these, 11 SNPs remained significant after Bonferroni correction for multiple tests (p = 9 × 10−4~2 × 10−3). Further conditional analysis indicated that no other SNP was significantly associated with ND independent of the most-highly significant SNP, rs6474414. Also, our haplotype-based association analysis indicated that each haplotype block was significantly associated with ND (p < 0.01). Further, we provide the first evidence of the genetic interaction of these two genes in affecting ND in this sample with an empirical p-value of 0.0015. Finally, our meta-analysis of samples with Asian and European origins for five SNPs in CHRNB3 showed significant associations with ND, with p-values ranging from 6.86 × 10−14 for rs13280604 to 6.50 × 10−8 for rs4950. This represents the first study showing that CHRNB3/A6 are highly associated with ND in a large Chinese Han sample.