bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide analyses of the bZIP family reveal their involvement in the development, ripening and abiotic stress response in banana
Authors: Hu Wei , Wang Lianzhe , Tie Weiwei , Yan Yan , Ding Zehong , Liu Juhua , Li Meiying , Peng Ming , Xu Biyu , Jin Zhiqiang 
Published: July 2016

AbstractThe leucine zipper (bZIP) transcription factors play important roles in multiple biological processes. However, less information is available regarding the bZIP family in the important fruit crop banana. In this study, 121 bZIP transcription factor genes were identified in the banana genome. Phylogenetic analysis showed that MabZIPs were classified into 11 subfamilies. The majority of MabZIP genes in the same subfamily shared similar gene structures and conserved motifs. The comprehensive transcriptome analysis of two banana genotypes revealed the differential expression patterns of MabZIP genes in different organs, in various stages of fruit development and ripening and in responses to abiotic stresses, including drought, cold and salt. Interaction networks and co-expression assays showed that group A MabZIP-mediated networks participated in various stress signaling, which was strongly activated in Musa ABB Pisang Awak. This study provided new insights into the complicated transcriptional control of MabZIP genes and provided robust tissue-specific, development-dependent and abiotic stress-responsive candidate MabZIP genes for potential applications in the genetic improvement of banana cultivars.
Lutein acts via multiple antioxidant pathways in the photo-stressed retina
Authors: Kamoshita Mamoru , Toda Eriko , Osada Hideto , Narimatsu Toshio , Kobayashi Saori , Tsubota Kazuo , Ozawa Yoko 
Published: July 2016

AbstractLutein slows the progression of age-related macular degeneration (AMD), a leading cause of blindness in ageing societies. However, the underlying mechanisms remain elusive. Here, we evaluated lutein’s effects on light-induced AMD-related pathological events. Balb/c mice exposed to light (2000 lux, 3 h) showed tight junction disruption in the retinal pigment epithelium (RPE) at 12 h, as detected by zona occludens-1 immunostaining. Substantial disruption remained 48 h after light exposure in the vehicle-treated group; however, this was ameliorated in the mice treated with intraperitoneal lutein at 12 h, suggesting that lutein promoted tight junction repair. In the photo-stressed RPE and the neighbouring choroid tissue, lutein suppressed reactive oxygen species and increased superoxide dismutase (SOD) activity at 24 h and produced sustained increases in sod1 and sod2 mRNA levels at 48 h. SOD activity was induced by lutein in an RPE cell line, ARPE19. We also found that lutein suppressed upregulation of macrophage-related markers, f4/80 and mcp-1, in the RPE-choroid tissue at 18 h. In ARPE19, lutein reduced mcp-1 mRNA levels. These findings indicated that lutein promoted tight junction repair and suppressed inflammation in photo-stressed mice, reducing local oxidative stress by direct scavenging and most likely by induction of endogenous antioxidant enzymes.
Individual language experience modulates rapid formation of cortical memory circuits for novel words
Authors: Kimppa Lilli , Kujala Teija , Shtyrov Yury 
Published: July 2016

AbstractMastering multiple languages is an increasingly important ability in the modern world; furthermore, multilingualism may affect human learning abilities. Here, we test how the brain’s capacity to rapidly form new representations for spoken words is affected by prior individual experience in non-native language acquisition. Formation of new word memory traces is reflected in a neurophysiological response increase during a short exposure to novel lexicon. Therefore, we recorded changes in electrophysiological responses to phonologically native and non-native novel word-forms during a perceptual learning session, in which novel stimuli were repetitively presented to healthy adults in either ignore or attend conditions. We found that larger number of previously acquired languages and earlier average age of acquisition (AoA) predicted greater response increase to novel non-native word-forms. This suggests that early and extensive language experience is associated with greater neural flexibility for acquiring novel words with unfamiliar phonology. Conversely, later AoA was associated with a stronger response increase for phonologically native novel word-forms, indicating better tuning of neural linguistic circuits to native phonology. The results suggest that individual language experience has a strong effect on the neural mechanisms of word learning and that it interacts with the phonological familiarity of the novel lexicon.
Functional and Proteomic Investigations Reveal Major Royal Jelly Protein 1 Associated with Anti-hypertension Activity in Mouse Vascular Smooth Muscle Cells
Authors: Fan Pei , Han Bin , Feng Mao , Fang Yu , Zhang Lan , Hu Han , Hao Yue , Qi Yuping , Zhang Xiaozhen , Li Jianke 
Published: July 2016

AbstractVascular smooth muscle cells (VSMCs) are a major cell type of the arterial wall and their functionality is associated with blood pressure regulation. Although royal jelly (RJ) has reported effects on anti-hypertension, the mechanism of blood pressure regulation by major royal jelly protein 1 (MRJP1), the most abundant RJ protein, is still unknown. The mrjp1 gene was inserted into mouse VSMCs to investigate how MRJP1 influences VSMC functionality by functional and proteomic analysis. The expression of MRJP1 in VSMCs significantly reduced cell contraction, migration and proliferation, suggesting a potential role in decreasing hypertension via action on VSMCs. These anti-hypertension activities were further observed in the changes of the proteome setting of mouse VSMCs. Among 675 different proteins after MRJP1 expression, 646 were down-regulated and significantly enriched in pathways implicated in VSMC contraction and migration, which suggest MRJP1 lowers VSMC contraction and migration by inhibiting muscle filament movement. The down-regulated proteins also enriched pathways in proliferation, indicating that MRJP1 hinders VSMC proliferation by reducing the supply of energy and genetic material. This is the first report integrating MRJP1 into VSMC, revealing the function and mechanism correlated with anti-hypertensive activity. This offers a therapeutic potential to control hypertension by gene-therapy using bee-products.
Demonstration of a robust magnonic spin wave interferometer
Authors: Kanazawa Naoki , Goto Taichi , Sekiguchi Koji , Granovsky Alexander B. , Ross Caroline A. , Takagi Hiroyuki , Nakamura Yuichi , Inoue Mitsuteru 
Published: July 2016

AbstractMagnonics is an emerging field dealing with ultralow power consumption logic circuits, in which the flow of spin waves, rather than electric charges, transmits and processes information. Waves, including spin waves, excel at encoding information via their phase using interference. This enables a number of inputs to be processed in one device, which offers the promise of multi-input multi-output logic gates. To realize such an integrated device, it is essential to demonstrate spin wave interferometers using spatially isotropic spin waves with high operational stability. However, spin wave reflection at the waveguide edge has previously limited the stability of interfering waves, precluding the use of isotropic spin waves, i.e., forward volume waves. Here, a spin wave absorber is demonstrated comprising a yttrium iron garnet waveguide partially covered by gold. This device is shown experimentally to be a robust spin wave interferometer using the forward volume mode, with a large ON/OFF isolation value of 13.7 dB even in magnetic fields over 30 Oe.
Knocking down of heat-shock protein 27 directs differentiation of functional glutamatergic neurons from placenta-derived multipotent cells
Authors: Cheng Yu-Che , Huang Chi-Jung , Lee Yih-Jing , Tien Lu-Tai , Ku Wei-Chi , Chien Raymond , Lee Fa-Kung , Chien Chih-Cheng 
Published: July 2016

AbstractThis study presents human placenta-derived multipotent cells (PDMCs) as a source from which functional glutamatergic neurons can be derived. We found that the small heat-shock protein 27 (HSP27) was downregulated during the neuronal differentiation process. The in vivo temporal and spatial profiles of HSP27 expression were determined and showed inverted distributions with neuronal proteins during mouse embryonic development. Overexpression of HSP27 in stem cells led to the arrest of neuronal differentiation; however, the knockdown of HSP27 yielded a substantially enhanced ability of PDMCs to differentiate into neurons. These neurons formed synaptic networks and showed positive staining for multiple neuronal markers. Additionally, cellular phenomena including the absence of apoptosis and rare proliferation in HSP27-silenced PDMCs, combined with molecular events such as cleaved caspase-3 and the loss of stemness with cleaved Nanog, indicated that HSP27 is located upstream of neuronal differentiation and constrains that process. Furthermore, the induced neurons showed increasing intracellular calcium concentrations upon glutamate treatment. These differentiated cells co-expressed the N-methyl-D-aspartate receptor, vesicular glutamate transporter, and synaptosomal-associated protein 25 but did not show expression of tyrosine hydroxylase, choline acetyltransferase or glutamate decarboxylase 67. Therefore, we concluded that HSP27-silenced PDMCs differentiated into neurons possessing the characteristics of functional glutamatergic neurons.
Simulated microgravity inhibits osteogenic differentiation of mesenchymal stem cells via depolymerizing F-actin to impede TAZ nuclear translocation
Authors: Chen Zhe , Luo Qing , Lin Chuanchuan , Kuang Dongdong , Song Guanbin 
Published: July 2016

AbstractMicrogravity induces observed bone loss in space flight and reduced osteogenesis of bone mesenchymal stem cells (BMSCs) partly contributes to this phenomenon. Abnormal regulation or functioning of the actin cytoskeleton induced by microgravity may cause the inhibited osteogenesis of BMSCs, but the underlying mechanism remains obscure. In this study, we demonstrated that actin cytoskeletal changes regulate nuclear aggregation of the transcriptional coactivator with PDZ-binding motif (TAZ), which is indispensable for osteogenesis of bone mesenchymal stem cells (BMSCs). Moreover, we utilized a clinostat to model simulated microgravity (SMG) and demonstrated that SMG obviously depolymerized F-actin and hindered TAZ nuclear translocation. Interestingly, stabilizing the actin cytoskeleton induced by Jasplakinolide (Jasp) significantly rescued TAZ nuclear translocation and recovered the osteogenic differentiation of BMSCs in SMG, independently of large tumor suppressor 1(LATS1, an upstream kinase of TAZ). Furthermore, lysophosphatidic acid (LPA) also significantly recovered the osteogenic differentiation of BMSCs in SMG through the F-actin-TAZ pathway. Taken together, we propose that the depolymerized actin cytoskeleton inhibits osteogenic differentiation of BMSCs through impeding nuclear aggregation of TAZ, which provides a novel connection between F-actin cytoskeleton and osteogenesis of BMSCs and has important implications in bone loss caused by microgravity.
Familial bias and auditory feedback regulation of vocal babbling patterns during early song development
Authors: Sato Daisuke , Mori Chihiro , Sawai Azusa , Wada Kazuhiro 
Published: July 2016

AbstractLearned vocalizations are a crucial acoustic biosignal conveying individual traits in many species. Songbirds learn song patterns by listening to a tutor song and performing vocal practice during a sensitive developmental period. However, when and how individual differences in song patterns develop remain unknown. Here, we report that individual differences in vocal output exist even at the earliest song development stage, called subsong. Experiments involving the manipulation of both breeding pairs and song tutoring conditions revealed that the parental pair combination contributes to generating familial differences in syllable duration and variability in the subsong of offspring. Furthermore, after deafening, juveniles immediately changed their subsong by shortening the syllable durations but maintained the individual variability of their subsong temporal patterns, suggesting both auditory-sensitive modification and independent intrinsic regulation of vocal output. These results indicate that the temporal patterns of subsong are not merely disordered vocalization but are regulated by familial bias with sensitivity to auditory feedback, thus generating individual variability at the initiation of vocal development.
The influence of porosity and structural parameters on different kinds of gas hydrate dissociation
Authors: Misyura S. Y. 
Published: July 2016

AbstractMethane hydrate dissociation at negative temperatures was studied experimentally for different artificial and natural samples, differing by macro- and micro-structural parameters. Four characteristic dissociation types are discussed in the paper. The internal kinetics of artificial granule gas hydrates and clathrate hydrates in coal is dependent on the porosity, defectiveness and gas filtration rate. The density of pores distribution in the crust of formed ice decreases by the several orders of magnitude and this change significantly the rate of decay. Existing models for describing dissociation at negative temperatures do not take into account the structural parameters of samples. The dissociation is regulated by internal physical processes that must be considered in the simulation. Non-isothermal dissociation with constant external heat flux was simulated numerically. The dissociation is simulated with consideration of heat and mass transfer, kinetics of phase transformation and gas filtering through a porous medium of granules for the negative temperatures. It is shown that the gas hydrate dissociation in the presence of mainly microporous structures is fundamentally different from the disintegration of gas hydrates containing meso and macropores.
Dynamic mineral clouds on HD 189733b
Authors: Lee E. , Dobbs-Dixon I. , Helling Ch. , Bognar K. , Woitke P. 
Published: July 2016

Context.Observations of exoplanet atmospheres have revealed the presence of cloud particles in their atmospheres. 3D modelling of cloud formation in atmospheres of extrasolar planets coupled to the atmospheric dynamics has long been a challenge.Aims.We investigate the thermo-hydrodynamic properties of cloud formation processes in the atmospheres of hot Jupiter exoplanets.Methods.We simulate the dynamic atmosphere of HD 189733b with a 3D model that couples 3D radiative-hydrodynamics with a kinetic, microphysical mineral cloud formation module designed for RHD/GCM exoplanet atmosphere simulations. Our simulation includes the feedback effects of cloud advection and settling, gas phase element advection and depletion/replenishment and the radiative effects of cloud opacity. We model the cloud particles as a mix of mineral materials which change in size and composition as they travel through atmospheric thermo-chemical environments. All local cloud properties such as number density, grain size and material composition are time-dependently calculated. Gas phase element depletion as a result of cloud formation is included in the model. In situ effective medium theory and Mie theory is applied to calculate the wavelength dependent opacity of the cloud component.Results.We present a 3D cloud structure of a chemically complex, gaseous atmosphere of the hot Jupiter HD 189733b. Mean cloud particle sizes are typically sub-micron (0.01−0.5μm) at pressures less than 1 bar with hotter equatorial regions containing the smallest grains. Denser cloud structures occur near terminator regions and deeper (~1 bar) atmospheric layers. Silicate materials such as MgSiO3[s] are found to be abundant at mid-high latitudes, while TiO2[s] and SiO2[s] dominate the equatorial regions. Elements involved in the cloud formation can be depleted by several orders of magnitude.Conclusions.The interplay between radiative-hydrodynamics and cloud kinetics leads to an inhomogeneous, wavelength dependent opacity cloud structure with properties differing in longitude, latitude and depth. This suggests that transit spectroscopy would sample a variety of cloud particles properties (sizes, composition, densities).
Kinetically guided colloidal structure formation
Authors: Hecht Fabian M. , Bausch Andreas R. 
Published: July 2016

Significance
The well-studied self-organization of colloidal particles is predicted to result in a variety of fascinating applications. Yet, whereas self-assembly techniques are extensively explored, designing and producing mesoscale-sized objects remains a major challenge, as equilibration times and thus structure formation timescales become prohibitively long. Asymmetric mesoscopic objects, without prior introduction of asymmetric particles with all its complications, are out of reach––due to the underlying principle of thermal equilibration. In the present article, we introduce a strategy to overcome these limitations on the mesoscale. By controlling and stirring the process of diffusion-limited cluster aggregation introducing DNA hybridization-mediated heteroparticle aggregation, we are able to produce finite-sized anisotropic structures on the mesoscale.
Heterometallic antenna−reactor complexes for photocatalysis
Authors: Swearer Dayne F. , Zhao Hangqi , Zhou Linan , Zhang Chao , Robatjazi Hossein , Martirez John Mark P. , Krauter Caroline M. , Yazdi Sadegh , McClain Michael J. , Ringe Emilie , Carter Emily A. , Nordlander Peter , Halas Naomi J. 
Published: July 2016

Significance
Plasmon-enhanced photocatalysis holds significant promise for controlling chemical reaction rates and outcomes. Unfortunately, traditional plasmonic metals have limited surface chemistry, while conventional catalysts are poor optical absorbers. By placing a catalytic reactor particle adjacent to a plasmonic antenna, the highly efficient and tunable light-harvesting capacities of plasmonic nanoparticles can be exploited to drastically increase absorption and hot-carrier generation in the reactor nanoparticles. We demonstrate this antenna−reactor concept by showing that plasmonic aluminum nanocrystal antennas decorated with small catalytic palladium reactor particles exhibit dramatically increased photocatalytic activity over their individual components. The modularity of this approach provides for independent control of chemical and light-harvesting properties and paves the way for the rational, predictive design of efficient plasmonic photocatalysts.
Virtual lexicogrammar
Authors: Glaz Adam 
Published: July 2016

In this chapter, a proposal is made to anchor considerations on the lexicon-grammar continuity in the notions of metonymy and virtuality. In cognitive linguistics, as discussed subsequently in the chapter, metonymy is viewed as operating at the very heart of language, i.e. within the linguistic sign. But rather than being an ultimate prime, it is shown here to derive from a more fundamental phenomenon of the virtual as real – this is linked with Ronald Langacker’s idea of the indeterminacy of grammatical coding. Following this, a view of lexicogrammar is proposed such that metonymy-qua-virtuality operates at all levels of linguistic complexity because it operates within the very network of relationships between linguistic form, conceptualization, and the real world.
A New Look at Bronchopulmonary Dysplasia: Postcapillary Pathophysiology and Cardiac Dysfunction
Authors: Sehgal Arvind , Malikiwi Andra , Paul Eldho , Tan Kenneth , Menahem Samuel 
Published: July 2016

Pulmonary hypertension (PH) and right ventricular function are the focus of cardiovascular effects of bronchopulmonary dysplasia (BPD). We assessed cardiac indexes reflecting systemic afterload and pulmonary venous back pressure as pathophysiologic factors. Cardiac parameters were measured by conventional echocardiography in 20 preterm infants with severe BPD and compared with those of 10 preterm infants with no BPD and 20 healthy term infants. In infants with severe BPD, PH was noted in 5 (25%) by tricuspid regurgitation Doppler jet ≥2.8 m/s and in 15 (75%) by time to peak velocity/right ventricular ejection time <0.34. Among systemic cardiac indexes, significant impairment of diastolic measures was noted in the BPD group compared with infants with no BPD and term infants. The significance persisted after adjusting for gestational age and birth weight. These included transmitral E/A ratio (1.07 ± 0.07 vs. 0.91 ± 0.04 vs. 0.89 ± 0.09; P < 0.0001), isovolumic relaxation time (68.8 ± 3.9 vs. 58.5 ± 7.8 vs. 54.2 ± 5.7 ms; P < 0.0001), mitral valve stroke volume (4.7 ± 0.7 vs. 5.6 ± 0.6 vs. 5.9 ± 0.1; P = 0.002), and myocardial performance index (0.33 ± 0.05 vs. 0.28 ± 0.01 vs. 0.27 ± 0.05; P = 0.03). Left ventricular output was significantly lower in the BPD cohort (183 ± 45 vs. 189 ± 9 vs. 191 ± 32 mL/kg/min; P = 0.03). Altered systemic (left‐sided) cardiac function was noted in infants with BPD, which may lead to pulmonary venous congestion contributing to a continued need for respiratory support.
Experimental investigation of the radial structure of energetic particle driven modes
Authors: Horváth L. , Papp G. , Lauber Ph. , Por G. , Gude A. , Igochine V. , Geiger B. , Maraschek M. , Guimarais L. , Nikolaeva V. , Pokol G.I. 
Published: July 2016

Abstract
Alfvén eigenmodes (AEs) and energetic particle modes (EPMs) are often excited by energetic particles (EPs) in tokamak plasmas. One of the main open questions concerning EP driven instabilities is the non-linear evolution of the mode structure. The aim of the present paper is to investigate the properties of beta-induced AEs (BAEs) and EP driven geodesic acoustic modes (EGAMs) observed in the ramp-up phase of off-axis NBI heated ASDEX Upgrade (AUG) discharges. This paper focuses on the changes in the mode structure of BAEs/EGAMs during the non-linear chirping phase. Our investigation has shown that in the case of the observed down-chirping BAEs the changes in the radial structure are smaller than the uncertainty of our measurement. This behaviour is most probably the consequence of the fact that BAEs are normal modes, thus their radial structure strongly depends on the background plasma parameters rather than on the EP distribution. In the case of rapidly upward chirping EGAMs the analysis consistently shows shrinkage of the mode structure. The proposed explanation is that the resonance in the velocity space moves towards more passing particles which have narrower orbit widths.
Exact calculation of the joint allele frequency spectrum for isolation with migration models
Authors: Kern Andrew D. , Hey Jody 
Published: July 2016

AbstractPopulation genomic datasets collected over the past decade have spurred interest in developing methods that can utilize massive numbers of loci for inference of demographic and selective histories of populations. The allele frequency spectrum (AFS) provides a convenient statistic for such analysis and accordingly much attention has been paid to predicting theoretical expectations of the AFS under a number of different models. However, to date, exact solutions for the joint AFS of two or more populations under models of migration and divergence have not been found. Here we present a novel Markov chain representation of the coalescent on the state space of the joint AFS that allows for rapid, exact calculation of the joint AFS under isolation with migration (IM) models. In turn, we show how our Markov chain method, in the context of composite likelihood estimation, can be used for accurate inference of parameters of the IM model using SNP data. Lastly, we apply our method to recent whole genome datasets from AfricanDrosophila melanogaster.