bluuebunny/crossref_metadata_2025_split huggingface dataset:
Even harmonic generation in isotropic media of dissociating homonuclear molecules
Authors: Silva R. E. F. , Rivière P. , Morales F. , Smirnova O. , Ivanov M. , Martín F. 
Published: September 2016

AbstractIsotropic gases irradiated by long pulses of intense IR light can generate very high harmonics of the incident field. It is generally accepted that, due to the symmetry of the generating medium, be it an atomic or an isotropic molecular gas, only odd harmonics of the driving field can be produced. Here we show how the interplay of electronic and nuclear dynamics can lead to a marked breakdown of this standard picture: a substantial part of the harmonic spectrum can consist of even rather than odd harmonics. We demonstrate the effect using ab-initio solutions of the time-dependent Schrödinger equation for "Equation missing" and its isotopes in full dimensionality. By means of a simple analytical model, we identify its physical origin, which is the appearance of a permanent dipole moment in dissociating homonuclear molecules, caused by light-induced localization of the electric charge during dissociation. The effect arises for sufficiently long laser pulses and the region of the spectrum where even harmonics are produced is controlled by pulse duration. Our results (i) show how the interplay of femtosecond nuclear and attosecond electronic dynamics, which affects the charge flow inside the dissociating molecule, is reflected in the nonlinear response, and (ii) force one to augment standard selection rules found in nonlinear optics textbooks by considering light-induced modifications of the medium during the generation process.
CLARITY-compatible lipophilic dyes for electrode marking and neuronal tracing
Authors: Jensen Kristian H. R. , Berg Rune W. 
Published: September 2016

AbstractFluorescent lipophilic dyes, such as DiI, stain cellular membranes and are used extensively for retrograde/anterograde labeling of neurons as well as for marking the position of extracellular electrodes after electrophysiology. Convenient histological clearing techniques, such as CLARITY, enable immunostaining and imaging of large volumes for 3D-reconstruction. However, such clearing works by removing lipids and, as an unintended consequence, also removes lipophilic dyes. To remedy this wash-out, the molecular structure of the dye can be altered to adhere to both membranes and proteins so the dye remains in the tissue after lipid–clearing. Nevertheless, the capacity of such modified dyes to remain in tissue has not yet been tested. Here, we test dyes with molecular modifications that make them aldehyde-fixable to proteins. We use three Dil–analogue dyes, CM-DiI, SP-DiI and FM 1–43FX that are modified to be CLARITY-compatible candidates. We use the challenging adult, myelin-rich spinal cord tissue, which requires prolonged lipid–clearing, of rats and mice. All three dyes remained in the tissue after lipid–clearing, but CM-DiI had the sharpest and FM 1–43FX the strongest fluorescent signal.
Effects of zirconium element on the microstructure and deuterium retention of W–Zr/Sc2O3 composites
Authors: Chen Hongyu , Luo Laima , Chen Jingbo , Zan Xiang , Zhu Xiaoyong , Xu Qiu , Luo Guangnan , Chen Junling , Wu Yucheng 
Published: September 2016

AbstractDense W and W–Zr composites reinforced with Sc2O3 particles were produced through powder metallurgy and subsequent spark plasma sintering (SPS) at 1700 °C and 58 MPa. Results showed that the W–1vol.%Zr/2vol.%Sc2O3 composites exhibited optimal performance with the best relative density of up to 98.93% and high Vickers microhardness of approximately 583 Hv. The thermal conductivity of W–Zr/Sc2O3 composites decreased initially and then increased as the Zr content increased. The moderate Zr alloying element could combine well with Sc2O3 particles and W grains and form a solid solution. However, excess Zr element leads to agglomeration in the grain boundaries. W–1vol.%Zr/2vol.%Sc2O3 composite had a good deuterium irradiation resistance very closing to pure tungsten compared with the other Zr element contents of composites. Under 500 K, D2 retention and release of them were similar to those of commercial tungsten, even lower between 400 K to 450 K. Pre-irradiation with 5 keV-He+ ions to a fluence of 1 × 1021 He+/m2 resulted in an increase in deuterium retention (deuterium was implanted after He+ irradiation), thereby shifting the desorption peak to a high temperature from 550 K to 650 K for the W–1vol.%Zr/2vol.%Sc2O3 composite.
Lysyl oxidase-like 4 involvement in retinoic acid epithelial wound healing
Authors: Comptour Aurélie , Rouzaire Marion , Belville Corinne , Bonnin Nicolas , Daniel Estelle , Chiambaretta Frédéric , Blanchon Loïc , Sapin Vincent 
Published: September 2016

AbstractVitamin A and its active forms (retinoic acids/RAs) are known to have pro-healing properties, but their mechanisms of action are still poorly understood. This work aimed to identify the cellular and molecular processes by which atRA (all-trans RA) improves wound healing, using an in vivo model of mouse corneal alkali burns and an in vitro cellular human corneal epithelial injury model. Regulation by atRA has been studied on most of the cellular events that occur in wound healing. We investigated the direct influence of atRA on a specific target gene known to be involved in the extracellular matrix (ECM) dynamics, one of the pathways contributing to epithelial repair. Our results demonstrate that atRA promotes corneal epithelial wound healing by acting preferentially on migration. The induction of lysyl oxidase-like 4 (LOXL4) expression by atRA in the corneal epithelium environment was established as essential in the mechanism of atRA-dependent wound healing. Our study describes for the first time a direct link between a retinoic-induced gene and protein, LOXL4, and its general clinical pro-healing properties in ECM dynamics.
On the interplay between neoclassical tearing modes and nonlocal transport in toroidal plasmas
Authors: Ji X. Q. , Xu Y. , Hidalgo C. , Diamond P. H. , Liu Yi , Pan O. , Shi Z. B. , Yu D. L. 
Published: September 2016

AbstractThis Letter presents the first observation on the interplay between nonlocal transport and neoclassical tearing modes (NTMs) during transient nonlocal heat transport events in the HL-2A tokamak. The nonlocality is triggered by edge cooling and large-scale, inward propagating avalanches. These lead to a locally enhanced pressure gradient at the q = 3/2 (or 2/1) rational surface and hence the onset of the NTM in relatively low β plasmas (βN < 1). The NTM, in return, regulates the nonlocal transport by truncation of avalanches by local sheared toroidal flows which develop near the magnetic island. These findings have direct implications for understanding the dynamic interaction between turbulence and large-scale mode structures in fusion plasmas.
Polysaccharide enhances Radix Saposhnikoviae efficacy through inhibiting chromones decomposition in intestinal tract
Authors: Yang Jing-Ming , Jiang Hua , Dai Hong-Liang , Wang Zi-Wei , Jia Gui-Zhi , Meng Xiang-Cai 
Published: September 2016

AbstractVegetative but not reproductive stage of Saposhnikovia divaricate (Turxz.) schischk possesses pharmacological activities. However, our recent study showed that reproductive S. divaricate supplemented with polysaccharide showed evidently elevated pharmacological activities and increased cimifugin content in rat serum. The aims of present study were to assess the influence of polysaccharides on the chromones pharmacological activities in Radix Saposhnikoviae (RS), the dried root of vegetative stage of S. divaricate, and to explore the underlying mechanisms. Only cimifugin was detected in the plasma of chromone treated animals and RS polysaccharide significantly increased the plasma content of cimifugin. It was shown that neither cimifugin absorption nor glycoside components transformation in simulated digestive fluid was affected by RS polysaccharide. However, a significant promotion of transformation of cimifugin to more stable prime-O-glucosylcimifugin (PGCN) by RS polysaccharide, and a protective effect of polysaccharide on chromone components were observed in small intestine solutions. Meanwhile, RS polysaccharide produced a significant elevation of cimifugin and PGCN concentration in vivo. Based on these findings, we concluded that RS polysaccharide could greatly increase the content of cimifugin, which might be related to its degradation-proof effect on cimifugin, via transforming cimifugin to comparatively more stable PGCN and spatial structure protection.
Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments
Authors: Adel Mustafa , Elbehery Ali H. A. , Aziz Sherry K. , Aziz Ramy K. , Grossart Hans-Peter , Siam Rania 
Published: September 2016

AbstractThe central rift of the Red Sea has 25 brine pools with different physical and geochemical characteristics. Atlantis II (ATIID), Discovery Deeps (DD) and Chain Deep (CD) are characterized by high salinity, temperature and metal content. Several studies reported microbial communities in these brine pools, but few studies addressed the brine pool sediments. Therefore, sediment cores were collected from ATIID, DD, CD brine pools and an adjacent brine-influenced site. Sixteen different lithologic sediment sections were subjected to shotgun DNA pyrosequencing to generate 1.47 billion base pairs (1.47 × 109 bp). We generated sediment-specific reads and attempted to annotate all reads. We report the phylogenetic and biochemical uniqueness of the deepest ATIID sulfur-rich brine pool sediments. In contrary to all other sediment sections, bacteria dominate the deepest ATIID sulfur-rich brine pool sediments. This decrease in virus-to-bacteria ratio in selected sections and depth coincided with an overrepresentation of mobile genetic elements. Skewing in the composition of viruses-to-mobile genetic elements may uniquely contribute to the distinct microbial consortium in sediments in proximity to hydrothermally active vents of the Red Sea and possibly in their surroundings, through differential horizontal gene transfer.
Na2CO3-responsive mechanisms in halophyte Puccinellia tenuiflora roots revealed by physiological and proteomic analyses
Authors: Zhao Qi , Suo Jinwei , Chen Sixue , Jin Yudan , Ma Xiaolin , Yin Zepeng , Zhang Yuhong , Wang Tai , Luo Ji , Jin Wenhai , Zhang Xia , Zhou Zhiqiang , Dai Shaojun 
Published: September 2016

AbstractSoil alkalization severely affects crop growth and agricultural productivity. Alkali salts impose ionic, osmotic, and high pH stresses on plants. The alkali tolerance molecular mechanism in roots from halophyte Puccinellia tenuiflora is still unclear. Here, the changes associated with Na2CO3 tolerance in P. tenuiflora roots were assessed using physiological and iTRAQ-based quantitative proteomic analyses. We set up the first protein dataset in P. tenuiflora roots containing 2,671 non-redundant proteins. Our results showed that Na2CO3 slightly inhibited root growth, caused ROS accumulation, cell membrane damage, and ion imbalance, as well as reduction of transport and protein synthesis/turnover. The Na2CO3-responsive patterns of 72 proteins highlighted specific signaling and metabolic pathways in roots. Ca2+ signaling was activated to transmit alkali stress signals as inferred by the accumulation of calcium-binding proteins. Additionally, the activities of peroxidase and glutathione peroxidase, and the peroxiredoxin abundance were increased for ROS scavenging. Furthermore, ion toxicity was relieved through Na+ influx restriction and compartmentalization, and osmotic homeostasis reestablishment due to glycine betaine accumulation. Importantly, two transcription factors were increased for regulating specific alkali-responsive gene expression. Carbohydrate metabolism-related enzymes were increased for providing energy and carbon skeletons for cellular metabolism. All these provide new insights into alkali-tolerant mechanisms in roots.
Tissue-specific Co-expression of Long Non-coding and Coding RNAs Associated with Breast Cancer
Authors: Wu Wenting , Wagner Erin K. , Hao Yangyang , Rao Xi , Dai Hongji , Han Jiali , Chen Jinhui , Storniolo Anna Maria V. , Liu Yunlong , He Chunyan 
Published: September 2016

AbstractInference of the biological roles of lncRNAs in breast cancer development remains a challenge. Here, we analyzed RNA-seq data in tumor and normal breast tissue samples from 18 breast cancer patients and 18 healthy controls and constructed a functional lncRNA-mRNA co-expression network. We revealed two distinctive co-expression patterns associated with breast cancer, reflecting different underlying regulatory mechanisms: (1) 516 pairs of lncRNA-mRNAs have differential co-expression pattern, in which the correlation between lncRNA and mRNA expression differs in tumor and normal breast tissue; (2) 291 pairs have dose-response co-expression pattern, in which the correlation is similar, but the expression level of lncRNA or mRNA differs in the two tissue types. We further validated our findings in TCGA dataset and annotated lncRNAs using TANRIC. One novel lncRNA, AC145110.1 on 8p12, was found differentially co-expressed with 127 mRNAs (including TOX4 and MAEL) in tumor and normal breast tissue and also highly correlated with breast cancer clinical outcomes. Functional enrichment and pathway analyses identified distinct biological functions for different patterns of co-expression regulations. Our data suggested that lncRNAs might be involved in breast tumorigenesis through the modulation of gene expression in multiple pathologic pathways.
Active Thermal Extraction and Temperature Sensing of Near-field Thermal Radiation
Authors: Ding D. , Kim T. , Minnich A. J. 
Published: September 2016

AbstractRecently, we proposed an active thermal extraction (ATX) scheme that enables thermally populated surface phonon polaritons to escape into the far-field. The concept is based on a fluorescence upconversion process that also occurs in laser cooling of solids (LCS). Here, we present a generalized analysis of our scheme using the theoretical framework for LCS. We show that both LCS and ATX can be described with the same mathematical formalism by replacing the electron-phonon coupling parameter in LCS with the electron-photon coupling parameter in ATX. Using this framework, we compare the ideal efficiency and power extracted for the two schemes and examine the parasitic loss mechanisms. This work advances the application of ATX to manipulate near-field thermal radiation for applications such as temperature sensing and active radiative cooling.
Luteolin Attenuates Airway Mucus Overproduction via Inhibition of the GABAergic System
Authors: Shen Mei-Lin , Wang Chen-Hung , Lin Ching-Huei , Zhou Ning , Kao Shung-Te , Wu Dong Chuan 
Published: September 2016

AbstractAirway mucus overproduction is one of the most common symptoms of asthma that causes severe clinical outcomes in patients. Despite the effectiveness of general asthma therapies, specific treatments that prevent mucus overproduction in asthma patients remain lacking. Recent studies have found that activation of GABAA receptors (GABAAR) is important for promoting mucus oversecretion in lung airway epithelia. Here, we report that luteolin, a natural flavonoid compound, suppresses mucus overproduction by functionally inhibiting the GABAergic system. This hypothesis was investigated by testing the effects of luteolin on goblet cell hyperplasia, excessive mucus secretion, and GABAergic transmission using histological and electrophysiological approaches. Our results showed that 10 mg/kg luteolin significantly decreased the number of goblet cells in the lung tissue and inhibited mucus overproduction in an in vivo asthma model induced by ovalbumin (OVA) in mice. Patch-clamp recordings showed that luteolin inhibited GABAAR-mediated currents in A549 cells. Furthermore, the inhibitory effects of luteolin on OVA-induced goblet cell hyperplasia and mucus overproduction were occluded by the GABAAR antagonist picrotoxin. In conclusion, our observations indicate that luteolin effectively attenuates mucus overproduction at least partially by inhibiting GABAARs, suggesting the potential for therapeutic administration of luteolin in the treatment of mucus overproduction in asthma patients.
Next-generation sequencing-based molecular diagnosis of 35 Hispanic retinitis pigmentosa probands
Authors: Zhang Qi , Xu Mingchu , Verriotto Jennifer D. , Li Yumei , Wang Hui , Gan Lin , Lam Byron L. , Chen Rui 
Published: September 2016

AbstractRetinitis pigmentosa (RP) is a heterogeneous group of inherited retinal diseases. The prevalence of RP and the mutation spectrum vary across populations. Hispanic people account for approximately 17% of the United States population, and the genetic etiologies of RP of this ethnic group still remain not well defined. Utilizing next-generation sequencing (NGS), we screened mutations in known retinal disease-causing genes in an RP cohort of 35 unrelated Hispanic probands from the Miami area. We achieved a solving rate of 66% and identified 15 novel putative pathogenic mutations, including a frequent founder mutation disrupting PRPF31 splicing. Our data show that the mutation spectrum of Hispanic RP receives a significant impact from disease-causing alleles of Spanish origin and may also contain population-specific alleles.
Preservation and phylogeny of Cambrian ecdysozoans tested by experimental decay of Priapulus
Authors: Sansom Robert S. 
Published: September 2016

AbstractThe exceptionally preserved Cambrian fossil record provides unique insight into the early evolutionary history of animals. Understanding of the mechanisms of exceptional soft tissue preservation frames all interpretations of the fauna and its evolutionary significance. This is especially true for recent interpretations of preserved nervous tissues in fossil ecdysozoans. However, models of soft tissue preservation lack empirical support from actualistic studies. Here experimental decay of the priapulid Priapulus reveal consistent bias towards rapid loss of internal non-cuticular anatomy compared with recalcitrant cuticular anatomy. This is consistent with models of Burgess Shale-type preservation and indicates that internal tissues are unlikely to be preserved with fidelity if organically preserved. This pattern, along with extreme body margin distortion, is consistent with onychophoran decay, and is therefore resolved as general for early ecdysozoans. Application of these patterns to phylogenetic data finds scalidophoran taxa to be very sensitive to taphonomically informed character coding, but not panarthropodan taxa. Priapulid decay also have unexpected relevance for interpretation of myomeres in fossil chordates. The decay data presented serve not only as a test of models of preservation but also a framework with which to interpret ecdysozoan fossil anatomies, and the subsequent evolutionary inferences drawn from them.
Fungicidal activities of soil humic/fulvic acids as related to their chemical structures in greenhouse vegetable fields with cultivation chronosequence
Authors: Wu Meng , Song Mengya , Liu Ming , Jiang Chunyu , Li Zhongpei 
Published: September 2016

AbstractIn the background of rapid expansion of plastic greenhouse vegetable production in China, many environmental risks have emerged in recent years. In this study, the soils with a chronosequence in greenhouse vegetable fields were collected and the soil humic acids (HAs) and fluvic acids (FAs) were extracted and purified. The soil HAs and FAs were found to show inhibition activities against phytopathogenic fungi for the first time. Fourier transform infrared spectroscopy was performed to investigate the chemical structures of HAs and FAs. The variation of relative peak areas indicated the chemical structure of HAs become more complex and stable under continuous cultivation. The PCA analysis showed HAs and FAs could be distinctly separated from each other and cultivation years mainly determined the variation. Mantel test and RDA analysis indicated the active components (aliphatic peaks for HAs and COOH, OH peaks for FAs) had positive correlation with the inhibition rates of HAs and FAs against phytopathogenic fungi. According to our research, the active fungicidal components in soil HAs and FAs decreased along with the extension of cultivation years, which made the soil suffer more risk to phytopathogenic fugi. So we believe continuous cultivation too many years in PGVP systems is inadvisable.
Alteration of interleaflet coupling due to compounds displaying rapid translocation in lipid membranes
Authors: Reigada Ramon 
Published: September 2016

AbstractThe spatial coincidence of lipid domains at both layers of the cell membrane is expected to play an important role in many cellular functions. Competition between the surface interleaflet tension and a line hydrophobic mismatch penalty are conjectured to determine the transversal behavior of laterally heterogeneous lipid membranes. Here, by a combination of molecular dynamics simulations, a continuum field theory and kinetic equations, I demonstrate that the presence of small, rapidly translocating molecules residing in the lipid bilayer may alter its transversal behavior by favoring the spatial coincidence of similar lipid phases.
MicroRNA in sperm from Duroc, Landrace and Yorkshire boars
Authors: Kasimanickam Vanmathy , Kastelic John 
Published: September 2016

AbstractSperm contain microRNAs (miRNAs), which may have roles in epigenetic control. Regarding phylogenetic relationships among various swine breeds, Yorkshire and Landrace, are considered phenotypically and genetically very similar, but distinctly different from Duroc. The objective of the present study was to compare abundance of boar sperm miRNAs in these three breeds. Overall, 252 prioritized miRNAs were investigated using real-time PCR; relative expression of miRNAs in sperm was similar in Yorkshire and Landrace boars, but significantly different compared to Duroc. Seventeen miRNAs (hsa-miR-196a-5p, hsa-miR-514a-3p, hsa-miR-938, hsa-miR-372-3p, hsa-miR-558, hsa-miR-579-3p, hsa-miR-595, hsa-miR-648, hsa-miR-524-3p, hsa-miR-512-3p, hsa-miR-429, hsa-miR-639, hsa-miR-551a, hsa-miR-624-5p, hsa-miR-585-3p, hsa-miR-508-3p and hsa-miR-626) were down-regulated (P < 0.05; fold regulation ≤−2) in Yorkshire and Landrace sperm, compared to Duroc sperm. Furthermore, three miRNAs (hsa-miR-9-5p, hsa-miR-150-5p, and hsa-miR-99a-5p) were significantly up-regulated in Yorkshire and Landrace sperm compared to Duroc sperm, However, 240 miRNAs were not significantly different (within + 2 fold) between Yorkshire and Landrace sperm. We concluded that miRNAs in sperm were not significantly different between Yorkshire and Landrace boars, but there were significant differences between those two breeds and Duroc boars. Furthermore, integrated target genes for selected down-regulated miRNAs (identified via an in-silico method) appeared to participate in spermatogenesis and sperm functions.