bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Historical Sketch of the Landscape of the Red River Delta
Authors: Li Tana 
Published: June 2016

AbstractThis article is an attempt to stand back and re-imagine the landscape of the Red River over the last two millennia. The only static components of the Red River valley and delta are its mountains and geological deposits, everything else has changed over time. By marrying historical records with recent scientific findings on the Red River, this article outlines aspects of these changes; including changes to the climate and landscape, the possibility of shifting river courses, the movement of historical trade routes, and the rise of Thang Long–Hanoi.
Internal guide RNA interactions interfere with Cas9-mediated cleavage
Authors: Thyme Summer B. , Akhmetova Laila , Montague Tessa G. , Valen Eivind , Schier Alexander F. 
Published: June 2016

AbstractThe CRISPR/Cas system uses guide RNAs (gRNAs) to direct sequence-specific DNA cleavage. Not every gRNA elicits cleavage and the mechanisms that govern gRNA activity have not been resolved. Low activity could result from either failure to form a functional Cas9–gRNA complex or inability to recognize targets in vivo. Here we show that both phenomena influence Cas9 activity by comparing mutagenesis rates in zebrafish embryos with in vitro cleavage assays. In vivo, our results suggest that genomic factors such as CTCF inhibit mutagenesis. Comparing near-identical gRNA sequences with different in vitro activities reveals that internal gRNA interactions reduce cleavage. Even though gRNAs containing these structures do not yield cleavage-competent complexes, they can compete with active gRNAs for binding to Cas9. These results reveal that both genomic context and internal gRNA interactions can interfere with Cas9-mediated cleavage and illuminate previously uncharacterized features of Cas9–gRNA complex formation.
Crystal structure of NOD2 and its implications in human disease
Authors: Maekawa Sakiko , Ohto Umeharu , Shibata Takuma , Miyake Kensuke , Shimizu Toshiyuki 
Published: June 2016

AbstractNucleotide-binding oligomerization domain-containing protein 2 (NOD2), a member of the NOD-like receptors family, are crucial for innate immune responses. Mutations of NOD2 have been associated with chronic inflammatory disorders such as Crohn’s disease (CD), Blau syndrome (BS) and early-onset sarcoidosis (EOS), but little is known about its signalling mechanism and the role it plays in these diseases. Here, we report the crystal structure of rabbit NOD2 in an ADP-bound state. The structure reveals an inactive closed conformation in which the subdomains in the NOD domain are closely packed by ADP-mediated and inter-domain interactions. Mapping of the BS- or EOS-associated gain-of-function mutations reveals that most of these mutations are located in the NOD subdomain interfaces, and are likely to disrupt the inner domain interactions, facilitating a conformational change to the active form. Conversely, mutations associated with CD are distributed throughout the protein, some of which may affect oligomer formation and ligand binding.
Integration of metal-organic frameworks into an electrochemical dielectric thin film for electronic applications
Authors: Li Wei-Jin , Liu Juan , Sun Zhi-Hua , Liu Tian-Fu , Lü Jian , Gao Shui-Ying , He Chao , Cao Rong , Luo Jun-Hua 
Published: June 2016

AbstractThe integration of porous metal-organic frameworks onto the surface of materials, for use as functional devices, is currently emerging as a promising approach for gas sensing and flexible displays. However, research focused on potential applications in electronic devices is in its infancy. Here we present a facile strategy by which interpenetrated, crystalline metal-organic framework films are deposited onto conductive metal-plate anodes via in situ temperature-controlled electrochemical assembly. The nanostructure of the surface as well as the thickness and uniformity of the film are well controlled. More importantly, the resulting films exhibit enhanced dielectric properties compared to traditional inorganic or organic gate dielectrics. This study demonstrates the successful implementation of the rational design of metal-organic framework thin films on conductive supports with high-performance dielectric properties.
Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes
Authors: Ai Rizi , Hammaker Deepa , Boyle David L. , Morgan Rachel , Walsh Alice M. , Fan Shicai , Firestein Gary S. , Wang Wei 
Published: June 2016

AbstractStratifying patients on the basis of molecular signatures could facilitate development of therapeutics that target pathways specific to a particular disease or tissue location. Previous studies suggest that pathogenesis of rheumatoid arthritis (RA) is similar in all affected joints. Here we show that distinct DNA methylation and transcriptome signatures not only discriminate RA fibroblast-like synoviocytes (FLS) from osteoarthritis FLS, but also distinguish RA FLS isolated from knees and hips. Using genome-wide methods, we show differences between RA knee and hip FLS in the methylation of genes encoding biological pathways, such as IL-6 signalling via JAK-STAT pathway. Furthermore, differentially expressed genes are identified between knee and hip FLS using RNA-sequencing. Double-evidenced genes that are both differentially methylated and expressed include multiple HOX genes. Joint-specific DNA signatures suggest that RA disease mechanisms might vary from joint to joint, thus potentially explaining some of the diversity of drug responses in RA patients.
First-principles quantum dynamical theory for the dissociative chemisorption of H2O on rigid Cu(111)
Authors: Zhang Zhaojun , Liu Tianhui , Fu Bina , Yang Xueming , Zhang Dong H. 
Published: June 2016

AbstractDespite significant progress made in the past decades, it remains extremely challenging to investigate the dissociative chemisorption dynamics of molecular species on surfaces at a full-dimensional quantum mechanical level, in particular for polyatomic-surface reactions. Here we report, to the best of our knowledge, the first full-dimensional quantum dynamics study for the dissociative chemisorption of H2O on rigid Cu(111) with all the nine molecular degrees of freedom fully coupled, based on an accurate full-dimensional potential energy surface. The full-dimensional quantum mechanical reactivity provides the dynamics features with the highest accuracy, revealing that the excitations in vibrational modes of H2O are more efficacious than increasing the translational energy in promoting the reaction. The enhancement of the excitation in asymmetric stretch is the largest, but that of symmetric stretch becomes comparable at very low energies. The full-dimensional characterization also allows the investigation of the validity of previous reduced-dimensional and approximate dynamical models.
Mechanochemical spinodal decomposition: a phenomenological theory of phase transformations in multi-component, crystalline solids
Authors: Rudraraju Shiva , Van der Ven Anton , Garikipati Krishna 
Published: June 2016

AbstractWe present a phenomenological treatment of diffusion-driven martensitic phase transformations in multi-component crystalline solids that arise from non-convex free energies in mechanical and chemical variables. The treatment describes diffusional phase transformations that are accompanied by symmetry-breaking structural changes of the crystal unit cell and reveals the importance of a mechanochemical spinodal, defined as the region in strain–composition space, where the free-energy density function is non-convex. The approach is relevant to phase transformations wherein the structural order parameters can be expressed as linear combinations of strains relative to a high-symmetry reference crystal. The governing equations describing mechanochemical spinodal decomposition are variationally derived from a free-energy density function that accounts for interfacial energy via gradients of the rapidly varying strain and composition fields. A robust computational framework for treating the coupled, higher-order diffusion and nonlinear strain gradient elasticity problems is presented. Because the local strains in an inhomogeneous, transforming microstructure can be finite, the elasticity problem must account for geometric nonlinearity. An evaluation of available experimental phase diagrams and first-principles free energies suggests that mechanochemical spinodal decomposition should occur in metal hydrides such as ZrH2−2c. The rich physics that ensues is explored in several numerical examples in two and three dimensions, and the relevance of the mechanism is discussed in the context of important electrode materials for Li-ion batteries and high-temperature ceramics.
Speedup of quantum evolution of multiqubit entanglement states
Authors: Zhang Ying-Jie , Han Wei , Xia Yun-Jie , Tian Jian-Xiang , Fan Heng 
Published: June 2016

AbstractAs is well known, quantum speed limit time (QSLT) can be used to characterize the maximal speed of evolution of quantum systems. We mainly investigate the QSLT of generalized N-qubit GHZ-type states and W-type states in the amplitude-damping channels. It is shown that, in the case N qubits coupled with independent noise channels, the QSLT of the entangled GHZ-type state is closely related to the number of qubits in the small-scale system. And the larger entanglement of GHZ-type states can lead to the shorter QSLT of the evolution process. However, the QSLT of the W-type states are independent of the number of qubits and the initial entanglement. Furthermore, by considering only M qubits among the N-qubit system respectively interacting with their own noise channels, QSLTs for these two types states are shorter than in the case N qubits coupled with independent noise channels. We therefore reach the interesting result that the potential speedup of quantum evolution of a given N-qubit GHZ-type state or W-type state can be realized in the case the number of the applied noise channels satisfying M < N.
Lysophosphatidylcholine plays critical role in allergic airway disease manifestation
Authors: Bansal Preeti , Gaur Shailendera Nath , Arora Naveen 
Published: June 2016

AbstractPhospholipase A2 (sPLA2), pivotal for allergic and inflammatory response, hydrolyses phosphatidylcholine (PC) to lysophosphatidylcholine (LPC). In present study, the role of LPC in allergic airway disease manifestation was studied using mouse model. Balb/c mice were immunized using cockroach extract (CE) and LPC release was blocked by sPLA2 inhibitor. Airway hyperresponse (AHR), lung-histology, total and differential leukocyte count (TLC&DLC), Th2 type cytokines, sPLA2 activity and LPC levels in bronchoalveolar lavage fluid (BALF) were measured. Exogenous LPC was given to the mice with or without CE sensitization, to demonstrate its role in allergic airway disease manifestation. Anti-CD1d antibody was given to study the involvement of natural killer T (NKT) cells in LPC induced response. AHR, lung-inflammation, TLC, DLC, Th2 type cytokines, sPLA2 activity and LPC levels were increased on CE challenge. sPLA2 activity and LPC release was blocked by sPLA2-inhibitor, which decreased AHR, and inflammatory parameters. Exogenous LPC with or without CE sensitization increased above parameters. CE challenge or LPC exposure increased LY49C+TCRβ+ NKT cells in BALF and spleen, which was reduced by anti-CD1d antibody, accompanied with reduction in AHR and allergic airway inflammation parameters. Conclusively, LPC induces allergic airway disease manifestation and it does so probably via CD1d-restricted LY49C+TCRβ+ NKT cells.
Interoccurrence time statistics in fully-developed turbulence
Authors: Manshour Pouya , Anvari Mehrnaz , Reinke Nico , Sahimi Muhammad , Tabar M. Reza Rahimi 
Published: June 2016

AbstractEmergent extreme events are a key characteristic of complex dynamical systems. The main tool for detailed and deep understanding of their stochastic dynamics is the statistics of time intervals of extreme events. Analyzing extensive experimental data, we demonstrate that for the velocity time series of fully-developed turbulent flows, generated by (i) a regular grid; (ii) a cylinder; (iii) a free jet of helium, and (iv) a free jet of air with the Taylor Reynolds numbers Reλ from 166 to 893, the interoccurrence time distributions P(τ) above a positive threshold Q in the inertial range is described by a universal q- exponential function, P(τ) = β(2 − q)[1 − β(1 − q)τ]1/(1−q), which may be due to the superstatistical nature of the occurrence of extreme events. Our analysis provides a universal description of extreme events in turbulent flows.
Nifurtimox Is Effective Against Neural Tumor Cells and Is Synergistic with Buthionine Sulfoximine
Authors: Du Michael , Zhang Linna , Scorsone Kathleen A. , Woodfield Sarah E. , Zage Peter E. 
Published: June 2016

AbstractChildren with aggressive neural tumors have poor survival rates and novel therapies are needed. Previous studies have identified nifurtimox and buthionine sulfoximine (BSO) as effective agents in children with neuroblastoma and medulloblastoma. We hypothesized that nifurtimox would be effective against other neural tumor cells and would be synergistic with BSO. We determined neural tumor cell viability before and after treatment with nifurtimox using MTT assays. Assays for DNA ladder formation and poly-ADP ribose polymerase (PARP) cleavage were performed to measure the induction of apoptosis after nifurtimox treatment. Inhibition of intracellular signaling was measured by Western blot analysis of treated and untreated cells. Tumor cells were then treated with combinations of nifurtimox and BSO and evaluated for viability using MTT assays. All neural tumor cell lines were sensitive to nifurtimox and IC50 values ranged from approximately 20 to 210 μM. Nifurtimox treatment inhibited ERK phosphorylation and induced apoptosis in tumor cells. Furthermore, the combination of nifurtimox and BSO demonstrated significant synergistic efficacy in all tested cell lines. Additional preclinical and clinical studies of the combination of nifurtimox and BSO in patients with neural tumors are warranted.
Unsaturated C3,5,7,9-Monocarboxylic Acids by Aqueous, One-Pot Carbon Fixation: Possible Relevance for the Origin of Life
Authors: Scheidler Christopher , Sobotta Jessica , Eisenreich Wolfgang , Wächtershäuser Günter , Huber Claudia 
Published: June 2016

AbstractAll scientific approaches to the origin of life share a common problem: a chemical path to lipids as main constituents of extant cellular enclosures. Here we show by isotope-controlled experiments that unsaturated C3,5,7,9-monocarboxylic acids form by one-pot reaction of acetylene (C2H2) and carbon monoxide (CO) in contact with nickel sulfide (NiS) in hot aqueous medium. The primary products are toto-olefinic monocarboxylic acids with CO-derived COOH groups undergoing subsequent stepwise hydrogenation with CO as reductant. In the resulting unsaturated monocarboxylic acids the double bonds are mainly centrally located with mainly trans-configuration. The reaction conditions are compatible with an origin of life in volcanic-hydrothermal sub-seafloor flow ducts.
Localization of PPAR isotypes in the adult mouse and human brain
Authors: Warden Anna , Truitt Jay , Merriman Morgan , Ponomareva Olga , Jameson Kelly , Ferguson Laura B. , Mayfield R. Dayne , Harris R. Adron 
Published: June 2016

AbstractPeroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that act as ligand-activated transcription factors. PPAR agonists have well-documented anti-inflammatory and neuroprotective roles in the central nervous system. Recent evidence suggests that PPAR agonists are attractive therapeutic agents for treating neurodegenerative diseases as well as addiction. However, the distribution of PPAR mRNA and protein in brain regions associated with these conditions (i.e. prefrontal cortex, nucleus accumbens, amygdala, ventral tegmental area) is not well defined. Moreover, the cell type specificity of PPARs in mouse and human brain tissue has yet to be investigated. We utilized quantitative PCR and double immunofluorescence microscopy to determine that both PPAR mRNA and protein are expressed ubiquitously throughout the adult mouse brain. We found that PPARs have unique cell type specificities that are consistent between species. PPARα was the only isotype to colocalize with all cell types in both adult mouse and adult human brain tissue. Overall, we observed a strong neuronal signature, which raises the possibility that PPAR agonists may be targeting neurons rather than glia to produce neuroprotection. Our results fill critical gaps in PPAR distribution and define novel cell type specificity profiles in the adult mouse and human brain.
Modelling Adaptive Learning Behaviours for Consensus Formation in Human Societies
Authors: Yu Chao , Tan Guozhen , Lv Hongtao , Wang Zhen , Meng Jun , Hao Jianye , Ren Fenghui 
Published: June 2016

AbstractLearning is an important capability of humans and plays a vital role in human society for forming beliefs and opinions. In this paper, we investigate how learning affects the dynamics of opinion formation in social networks. A novel learning model is proposed, in which agents can dynamically adapt their learning behaviours in order to facilitate the formation of consensus among them, and thus establish a consistent social norm in the whole population more efficiently. In the model, agents adapt their opinions through trail-and-error interactions with others. By exploiting historical interaction experience, a guiding opinion, which is considered to be the most successful opinion in the neighbourhood, can be generated based on the principle of evolutionary game theory. Then, depending on the consistency between its own opinion and the guiding opinion, a focal agent can realize whether its opinion complies with the social norm (i.e., the majority opinion that has been adopted) in the population, and adapt its behaviours accordingly. The highlight of the model lies in that it captures the essential features of people’s adaptive learning behaviours during the evolution and formation of opinions. Experimental results show that the proposed model can facilitate the formation of consensus among agents, and some critical factors such as size of opinion space and network topology can have significant influences on opinion dynamics.
Ultra-doped n-type germanium thin films for sensing in the mid-infrared
Authors: Prucnal Slawomir , Liu Fang , Voelskow Matthias , Vines Lasse , Rebohle Lars , Lang Denny , Berencén Yonder , Andric Stefan , Boettger Roman , Helm Manfred , Zhou Shengqiang , Skorupa Wolfgang 
Published: June 2016

AbstractA key milestone for the next generation of high-performance multifunctional microelectronic devices is the monolithic integration of high-mobility materials with Si technology. The use of Ge instead of Si as a basic material in nanoelectronics would need homogeneous p- and n-type doping with high carrier densities. Here we use ion implantation followed by rear side flash-lamp annealing (r-FLA) for the fabrication of heavily doped n-type Ge with high mobility. This approach, in contrast to conventional annealing procedures, leads to the full recrystallization of Ge films and high P activation. In this way single crystalline Ge thin films free of defects with maximum attained carrier concentrations of 2.20 ± 0.11 × 1020 cm−3 and carrier mobilities above 260 cm2/(V·s) were obtained. The obtained ultra-doped Ge films display a room-temperature plasma frequency above 1,850 cm−1, which enables to exploit the plasmonic properties of Ge for sensing in the mid-infrared spectral range.
PDNAsite: Identification of DNA-binding Site from Protein Sequence by Incorporating Spatial and Sequence Context
Authors: Zhou Jiyun , Xu Ruifeng , He Yulan , Lu Qin , Wang Hongpeng , Kong Bing 
Published: June 2016

AbstractProtein-DNA interactions are involved in many fundamental biological processes essential for cellular function. Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. Subsequently, Latent Semantic Analysis (LSA) was applied to remove the redundancies in the feature space. Finally, a predictor (PDNAsite) was developed through the integration of the support vector machines (SVM) classifier and ensemble learning. Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. A web-server of our predictor (http://hlt.hitsz.edu.cn:8080/PDNAsite/) is made available for free public accessible to the biological research community.
Significant pharmacokinetic differences of berberine are attributable to variations in gut microbiota between Africans and Chinese
Authors: Alolga Raphael N. , Fan Yong , Chen Zhuo , Liu Li-Wei , Zhao Yi-Jing , Li Jin , Chen Yan , Lai Mao-De , Li Ping , Qi Lian-Wen 
Published: June 2016

AbstractWe investigated the influence of gut microbiotal metabolism on the pharmacokinetics of berberine in healthy male Africans and Chinese. The Cmax and AUC in the Africans were 2.67-fold and 2.0-fold higher than the Chinese, respectively. Microbiotal compositions by 16S rRNA pyrosequencing showed higher abundance of the genera Prevotella, Bacteroides and Megamonas (34.22, 13.88 and 10.68%, respectively) in the Chinese than the Africans (30.08, 9.43 and 0.48%, respectively). Scatter plot showed a strong negative correlation between the microbiotal abundance and the berberine AUC, especially for the genus Prevotella (r = −0.813) and its species. A more extensive metabolism was observed in Chinese with 1.83-fold higher metabolites, possibly contributing to the lower AUC than the Africans. In conclusion, significant PK differences of berberine were observed between Africans and Chinese, which is partly attributable to variations in gut microbiota and its corresponding metabolic capacity.