bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves
Authors: Ryffel Florian , Helfrich Eric J N , Kiefer Patrick , Peyriga Lindsay , Portais Jean-Charles , Piel Jörn , Vorholt Julia A 
Published: August 2015

Abstract
The phyllosphere, which is defined as the parts of terrestrial plants above the ground, is a large habitat for different microorganisms that show a high extent of adaption to their environment. A number of hypotheses were generated by culture-independent functional genomics studies to explain the competitiveness of specialized bacteria in the phyllosphere. In contrast, in situ data at the metabolome level as a function of bacterial colonization are lacking. Here, we aimed to obtain new insights into the metabolic interplay between host and epiphytes upon colonization of Arabidopsis thaliana leaves in a controlled laboratory setting using environmental metabolomics approaches. Quantitative nuclear magnetic resonance (NMR) and imaging high-resolution mass spectrometry (IMS) methods were used to identify Arabidopsis leaf surface compounds and their possible involvement in the epiphytic lifestyle by relative changes in compound pools. The dominant carbohydrates on the leaf surfaces were sucrose, fructose and glucose. These sugars were significantly and specifically altered after epiphytic leaf colonization by the organoheterotroph Sphingomonas melonis or the phytopathogen Pseudomonas syringae pv. tomato, but only to a minor extent by the methylotroph Methylobacterium extorquens. In addition to carbohydrates, IMS revealed surprising alterations in arginine metabolism and phytoalexin biosynthesis that were dependent on the presence of bacteria, which might reflect the consequences of bacterial activity and the recognition of not only pathogens but also commensals by the plant. These results highlight the power of environmental metabolomics to aid in elucidating the molecular basis underlying plant–epiphyte interactions in situ.
Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections
Authors: Dearlove Bethany L , Cody Alison J , Pascoe Ben , Méric Guillaume , Wilson Daniel J , Sheppard Samuel K 
Published: August 2015

Abstract
Campylobacter jejuni and Campylobacter coli are the biggest causes of bacterial gastroenteritis in the developed world, with human infections typically arising from zoonotic transmission associated with infected meat. Because Campylobacter is not thought to survive well outside the gut, host-associated populations are genetically isolated to varying degrees. Therefore, the likely origin of most strains can be determined by host-associated variation in the genome. This is instructive for characterizing the source of human infection. However, some common strains, notably isolates belonging to the ST-21, ST-45 and ST-828 clonal complexes, appear to have broad host ranges, hindering source attribution. Here whole-genome sequencing has the potential to reveal fine-scale genetic structure associated with host specificity. We found that rates of zoonotic transmission among animal host species in these clonal complexes were so high that the signal of host association is all but obliterated, estimating one zoonotic transmission event every 1.6, 1.8 and 12 years in the ST-21, ST-45 and ST828 complexes, respectively. We attributed 89% of clinical cases to a chicken source, 10% to cattle and 1% to pig. Our results reveal that common strains of C. jejuni and C. coli infectious to humans are adapted to a generalist lifestyle, permitting rapid transmission between different hosts. Furthermore, they show that the weak signal of host association within these complexes presents a challenge for pinpointing the source of clinical infections, underlining the view that whole-genome sequencing, powerful though it is, cannot substitute for intensive sampling of suspected transmission reservoirs.
Wet-chemical synthesis and applications of non-layer structured two-dimensional nanomaterials
Authors: Tan Chaoliang , Zhang Hua 
Published: August 2015

AbstractNon-layer structured nanomaterials with single- or few-layer thickness have two-dimensional sheet-like structures and possess intriguing properties. Recent years have seen major advances in development of a host of non-layer structured ultrathin two-dimensional nanomaterials such as noble metals, metal oxides and metal chalcogenides. The wet-chemical synthesis has emerged as the most promising route towards high-yield and mass production of such nanomaterials. These nanomaterials are now finding increasing applications in a wide range of areas including catalysis, energy production and storage, sensor and nanotherapy, to name but a few.
Acoustic metamaterial for subwavelength edge detection
Authors: Molerón Miguel , Daraio Chiara 
Published: August 2015

AbstractMetamaterials have demonstrated the possibility to produce super-resolved images by restoring propagative and evanescent waves. However, for efficient information transfer, for example, in compressed sensing, it is often desirable to visualize only the fast spatial variations of the wave field (carried by evanescent waves), as the one created by edges or small details. Image processing edge detection algorithms perform such operation, but they add time and complexity to the imaging process. Here we present an acoustic metamaterial that transmits only components of the acoustic field that are approximately equal to or smaller than the operating wavelength. The metamaterial converts evanescent waves into propagative waves exciting trapped resonances, and it uses periodicity to attenuate the propagative components. This approach achieves resolutions ∼5 times smaller than the operating wavelength and makes it possible to visualize independently edges aligned along different directions.
Tuning of Ranvier node and internode properties in myelinated axons to adjust action potential timing
Authors: Ford Marc C. , Alexandrova Olga , Cossell Lee , Stange-Marten Annette , Sinclair James , Kopp-Scheinpflug Conny , Pecka Michael , Attwell David , Grothe Benedikt 
Published: August 2015

AbstractAction potential timing is fundamental to information processing; however, its determinants are not fully understood. Here we report unexpected structural specializations in the Ranvier nodes and internodes of auditory brainstem axons involved in sound localization. Myelination properties deviated significantly from the traditionally assumed structure. Axons responding best to low-frequency sounds had a larger diameter than high-frequency axons but, surprisingly, shorter internodes. Simulations predicted that this geometry helps to adjust the conduction velocity and timing of action potentials within the circuit. Electrophysiological recordings in vitro and in vivo confirmed higher conduction velocities in low-frequency axons. Moreover, internode length decreased and Ranvier node diameter increased progressively along the distal axon segments, which simulations show was essential to ensure precisely timed depolarization of the giant calyx of Held presynaptic terminal. Thus, individual anatomical parameters of myelinated axons can be tuned to optimize pathways involved in temporal processing.
Atomically controlled substitutional boron-doping of graphene nanoribbons
Authors: Kawai Shigeki , Saito Shohei , Osumi Shinichiro , Yamaguchi Shigehiro , Foster Adam S. , Spijker Peter , Meyer Ernst 
Published: August 2015

AbstractBoron is a unique element in terms of electron deficiency and Lewis acidity. Incorporation of boron atoms into an aromatic carbon framework offers a wide variety of functionality. However, the intrinsic instability of organoboron compounds against moisture and oxygen has delayed the development. Here, we present boron-doped graphene nanoribbons (B-GNRs) of widths ofN=7, 14 and 21 by on-surface chemical reactions with an employed organoboron precursor. The location of the boron dopant is well defined in the centre of the B-GNR, corresponding to 4.8 atom%, as programmed. The chemical reactivity of B-GNRs is probed by the adsorption of nitric oxide (NO), which is most effectively trapped by the boron sites, demonstrating the Lewis acid character. Structural properties and the chemical nature of the NO-reacted B-GNR are determined by a combination of scanning tunnelling microscopy, high-resolution atomic force microscopy with a CO tip, and density functional and classical computations.
Materials Prediction via Classification Learning
Authors: Balachandran Prasanna V. , Theiler James , Rondinelli James M. , Lookman Turab 
Published: August 2015

AbstractIn the paradigm of materials informatics for accelerated materials discovery, the choice of feature set (i.e. attributes that capture aspects of structure, chemistry and/or bonding) is critical. Ideally, the feature sets should provide a simple physical basis for extracting major structural and chemical trends and furthermore, enable rapid predictions of new material chemistries. Orbital radii calculated from model pseudopotential fits to spectroscopic data are potential candidates to satisfy these conditions. Although these radii (and their linear combinations) have been utilized in the past, their functional forms are largely justified with heuristic arguments. Here we show that machine learning methods naturally uncover the functional forms that mimic most frequently used features in the literature, thereby providing a mathematical basis for feature set construction without a priori assumptions. We apply these principles to study two broad materials classes: (i) wide band gap AB compounds and (ii) rare earth-main group RM intermetallics. The AB compounds serve as a prototypical example to demonstrate our approach, whereas the RM intermetallics show how these concepts can be used to rapidly design new ductile materials. Our predictive models indicate that ScCo, ScIr and YCd should be ductile, whereas each was previously proposed to be brittle.
Glyceraldehyde caused Alzheimer’s disease-like alterations in diagnostic marker levels in SH-SY5Y human neuroblastoma cells
Authors: Koriyama Yoshiki , Furukawa Ayako , Muramatsu Michiru , Takino Jun-ichi , Takeuchi Masayoshi 
Published: August 2015

AbstractClinical evidence has implicated diabetes mellitus as one of the risk factors for the development and progression of Alzheimer’s disease (AD). However, the neurotoxic pathway activated due to abnormalities in glucose metabolism has not yet been identified in AD. In order to investigate the relationship between impaired cerebral glucose metabolism and the pathophysiology of AD, SH-SY5Y human neuroblastoma cells were exposed to glyceraldehyde (GA), an inhibitor of glycolysis. GA induced the production of GA-derived advanced glycation end-products (GA-AGEs) and cell apoptosis, glycolytic inhibition, decreases in the medium concentrations of diagnostic markers of AD, such as amyloid β 1-42 (Aβ42) and increases in tau phosphorylation. These results suggest that the production of GA-AGEs and/or inhibition of glycolysis induce AD-like alterations and this model may be useful for examining the pathophysiology of AD.
Glycosyltransferase ST6GAL1 contributes to the regulation of pluripotency in human pluripotent stem cells
Authors: Wang Yu-Chieh , Stein Jason W. , Lynch Candace L. , Tran Ha T. , Lee Chia-Yao , Coleman Ronald , Hatch Adam , Antontsev Victor G. , Chy Hun S. , O’Brien Carmel M. , Murthy Shashi K. , Laslett Andrew L. , Peterson Suzanne E. , Loring Jeanne F. 
Published: August 2015

AbstractMany studies have suggested the significance of glycosyltransferase-mediated macromolecule glycosylation in the regulation of pluripotent states in human pluripotent stem cells (hPSCs). Here, we observed that the sialyltransferase ST6GAL1 was preferentially expressed in undifferentiated hPSCs compared to non-pluripotent cells. A lectin which preferentially recognizes α-2,6 sialylated galactosides showed strong binding reactivity with undifferentiated hPSCs and their glycoproteins and did so to a much lesser extent with differentiated cells. In addition, downregulation of ST6GAL1 in undifferentiated hPSCs led to a decrease in POU5F1 (also known as OCT4) protein and significantly altered the expression of many genes that orchestrate cell morphogenesis during differentiation. The induction of cellular pluripotency in somatic cells was substantially impeded by the shRNA-mediated suppression of ST6GAL1, partially through interference with the expression of endogenous POU5F1 and SOX2. Targeting ST6GAL1 activity with a sialyltransferase inhibitor during cell reprogramming resulted in a dose-dependent reduction in the generation of human induced pluripotent stem cells (hiPSCs). Collectively, our data indicate that ST6GAL1 plays an important role in the regulation of pluripotency and differentiation in hPSCs and the pluripotent state in human cells can be modulated using pharmacological tools to target sialyltransferase activity.
Left brain cortical activity modulates stress effects on social behavior
Authors: Lee Eunee , Hong Jiso , Park Young-Gyun , Chae Sujin , Kim Yong , Kim Daesoo 
Published: August 2015

AbstractWhen subjected to stress, some individuals develop maladaptive symptoms whereas others retain normal behavior. The medial prefrontal cortex (mPFC) is known to control these adaptive responses to stress. Here, we show that mPFC neurons in the left hemisphere control stress effects on social behavior. Mice made socially avoidant by the stress of chronic social defeats showed depressed neural activity in the left mPFC. Photoactivation of these neurons reversed social avoidance and restored social activity. Despite social defeats, resilient mice with normal sociability showed normal firing rates in the left mPFC; however, photoinhibition of these neurons induced social avoidance. The same photomodulation administered to the right mPFC caused no significant effects. These results explain how stressed individuals develop maladaptive behaviors through left cortical depression, as reported in mood and anxiety disorders.
Wave trains induced by circularly polarized electric fields in cardiac tissues
Authors: Feng Xia , Gao Xiang , Tang Juan-Mei , Pan Jun-Ting , Zhang Hong 
Published: August 2015

AbstractClinically, cardiac fibrillation caused by spiral and turbulent waves can be terminated by globally resetting electric activity in cardiac tissues with a single high-voltage electric shock, but it is usually associated with severe side effects. Presently, a promising alternative uses wave emission from heterogeneities induced by a sequence of low-voltage uniform electric field pulses. Nevertheless, this method can only emit waves locally near obstacles in turbulent waves and thereby requires multiple obstacles to globally synchronize myocardium and thus to terminate fibrillation. Here we propose a new approach using wave emission from heterogeneities induced by a low-voltage circularly polarized electric field (i.e., a rotating uniform electric field). We find that, this approach can generate circular wave trains near obstacles and they propagate outwardly. We study the characteristics of such circular wave trains and further find that, the higher-frequency circular wave trains can effectively suppress spiral turbulence.
Quantum Nonlocality of Arbitrary Dimensional Bipartite States
Authors: Li Ming , Zhang Tinggui , Hua Bobo , Fei Shao-Ming , Li-Jost Xianqing 
Published: August 2015

AbstractWe study the nonlocality of arbitrary dimensional bipartite quantum states. By computing the maximal violation of a set of multi-setting Bell inequalities, an analytical and computable lower bound has been derived for general two-qubit states. This bound gives the necessary condition that a two-qubit state admits no local hidden variable models. The lower bound is shown to be better than that from the CHSH inequality in judging the nonlocality of some quantum states. The results are generalized to the case of high dimensional quantum states and a sufficient condition for detecting the non-locality has been presented.
Role of initial system-bath correlation on coherence trapping
Authors: Zhang Ying-Jie , Han Wei , Xia Yun-Jie , Yu Yan-Mei , Fan Heng 
Published: August 2015

AbstractWe study the coherence trapping of a qubit correlated initially with a non-Markovian bath in a pure dephasing channel. By considering the initial qubit-bath correlation and the bath spectral density, we find that the initial qubit-bath correlation can lead to a more efficient coherence trapping than that of the initially separable qubit-bath state. The stationary coherence in the long time limit can be maximized by optimizing the parameters of the initially correlated qubit-bath state and the bath spectral density. In addition, the effects of this initial correlation on the maximal evolution speed for the qubit trapped to its stationary coherence state are also explored.
High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea
Authors: Gaur Rashmi , Jeena Ganga , Shah Niraj , Gupta Shefali , Pradhan Seema , Tyagi Akhilesh K , Jain Mukesh , Chattopadhyay Debasis , Bhatia Sabhyata 
Published: August 2015

AbstractThis study presents genome-wide discovery of SNPs through next generation sequencing of the genome of Cicer reticulatum. Mapping of the C. reticulatum sequenced reads onto the draft genome assembly of C. arietinum (desi chickpea) resulted in identification of 842,104 genomic SNPs which were utilized along with an additional 36,446 genic SNPs identified from transcriptome sequences of the aforementioned varieties. Two new chickpea Oligo Pool All (OPAs) each having 3,072 SNPs were designed and utilized for SNP genotyping of 129 Recombinant Inbred Lines (RILs). Using Illumina GoldenGate Technology genotyping data of 5,041 SNPs were generated and combined with the 1,673 marker data from previously published studies, to generate a high resolution linkage map. The map comprised of 6698 markers distributed on eight linkage groups spanning 1083.93 cM with an average inter-marker distance of 0.16 cM. Utility of the present map was demonstrated for improving the anchoring of the earlier reported draft genome sequence of desi chickpea by ~30% and that of kabuli chickpea by 18%. The genetic map reported in this study represents the most dense linkage map of chickpea , with the potential to facilitate efficient anchoring of the draft genome sequences of desi as well as kabuli chickpea varieties.
Histone demethylase JMJD3 is required for osteoblast differentiation in mice
Authors: Zhang Feng , Xu Longyong , Xu Longxia , Xu Qing , Karsenty Gerard , Chen Charlie Degui 
Published: August 2015

AbstractJMJD3 (KDM6B) is an H3K27me3 demethylases and emerges as an important player in developmental processes. Although some evidence indicated the involvement of JMJD3 in osteoblast differentiation in vitro, its role as a whole in osteoblast differentiation and bone formation in vivo remains unknown. Here we showed that homozygous deletion of Jmjd3 resulted in severe delay of osteoblast differentiation and bone ossification in mice. By biochemical and genetical methods, we demonstrated that JMJD3 mediated RUNX2 transcriptional activity and cooperated with RUNX2 to promote osteoblast differentiation and bone formation in vivo. These results strongly demonstrated that JMJD3 is required for osteoblast differentiation and bone formation in mice.
UCP-3 uncoupling protein confers hypoxia resistance to renal epithelial cells and is upregulated in renal cell carcinoma
Authors: Braun Norbert , Klumpp Dominik , Hennenlotter Jörg , Bedke Jens , Duranton Christophe , Bleif Martin , Huber Stephan M. 
Published: August 2015

AbstractTumor cells can adapt to a hostile environment with reduced oxygen supply. The present study aimed to identify mechanisms that confer hypoxia resistance. Partially hypoxia/reoxygenation (H/R)-resistant proximal tubular (PT) cells were selected by exposing PT cultures to repetitive cycles of H/R. Thereafter, H/R-induced changes in mRNA and protein expression, inner mitochondrial membrane potential (ΔΨm), formation of superoxide and cell death were compared between H/R-adapted and control PT cultures. As a result, H/R-adapted PT cells exhibited lower H/R-induced hyperpolarization of ΔΨm and produced less superoxide than the control cultures. Consequently, H/R triggered ΔΨm break-down and DNA degradation in a lower percentage of H/R-adapted than control PT cells. Moreover, H/R induced upregulation of mitochondrial uncoupling protein-3 (UCP-3) in H/R-adapted PT but not in control cultures. In addition, ionizing radiation killed a lower percentage of H/R-adapted as compared to control cells suggestive of an H/R-radiation cross-resistance developed by the selection procedure. Knockdown of UCP-3 decreased H/R- and radioresitance of the H/R-adapted cells. Finally, UCP-3 protein abundance of PT-derived clear cell renal cell carcinoma and normal renal tissue was compared in human specimens indicating upregulation of UCP-3 during tumor development. Combined, our data suggest functional significance of UCP-3 for H/R resistance.
Localized Tail States and Electron Mobility in Amorphous ZnON Thin Film Transistors
Authors: Lee Sungsik , Nathan Arokia , Ye Yan , Guo Yuzheng , Robertson John 
Published: August 2015

AbstractThe density of localized tail states in amorphous ZnON (a-ZnON) thin film transistors (TFTs) is deduced from the measured current-voltage characteristics. The extracted values of tail state density at the conduction band minima (Ntc) and its characteristic energy (kTt) are about 2 × 1020 cm−3eV−1 and 29 meV, respectively, suggesting trap-limited conduction prevails at room temperature. Based on trap-limited conduction theory where these tail state parameters are considered, electron mobility is accurately retrieved using a self-consistent extraction method along with the scaling factor ‘1/(α + 1)’ associated with trapping events at the localized tail states. Additionally, it is found that defects, e.g. oxygen and/or nitrogen vacancies, can be ionized under illumination with hv ≫ Eg, leading to very mild persistent photoconductivity (PPC) in a-ZnON TFTs.
HCRP-1 regulates cell migration and invasion via EGFR-ERK mediated up-regulation of MMP-2 with prognostic significance in human renal cell carcinoma
Authors: Chen Feifei , Deng Junpeng , Liu Xin , Li Wang , Zheng Junnian 
Published: August 2015

AbstractPrevious studies indicated a role of hepatocellular carcinoma-related protein-1(HCRP-1) in human cancers, however, its expression pattern in renal cell carcinoma (RCC) and the molecular mechanism of HCRP-1 on cancer progression have not been characterized. In the present study, HCRP-1 expression was examined in a RCC tissue microarray. The negative expression of HCRP-1 was significantly correlated with tumor grade (P = 0.002), TNM stage (P = 0.001) and pT status (P = 0.003). Furthermore, we showed a strong correlation between negative HCRP-1 expression and worse overall and disease-specific survival (P = 0.0003 and P = 0.0012, respectively). Knockdown of HCRP-1 promoted cell migration and invasion in 786-O and OS-RC-2 cell lines. HCRP-1 depletion increased matrix metalloproteinase (MMP)-2 protein level, with increased extracellular signal-regulatedkinase (ERK) phosphorylation, which could be reversed by ERK siRNA or ERK inhibitor, PD98059. Further analysis showed that HCRP-1 knockdown induced epidermal growth factor receptor (EGFR) phosphorylation. Treatment with EGFR inhibitor or EGFR siRNA blocked HCRP-1-mediated up-regulation of EGFR, ERK phosphorylation and MMP-2 expression. In summary, our results showed that negative HCRP-1 expression is an independent prognostic factor for RCC patients and promotes migration and invasion by EGFR-ERK-mediated up-regulation of MMP-2. HCRP-1 may serve as a therapeutic target for RCC.