bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping RNA–RNA interactome and RNA structure in vivo by MARIO
Authors: Nguyen Tri C. , Cao Xiaoyi , Yu Pengfei , Xiao Shu , Lu Jia , Biase Fernando H. , Sridhar Bharat , Huang Norman , Zhang Kang , Zhong Sheng 
Published: June 2016

AbstractThe pervasive transcription of our genome presents a possibility of revealing new genomic functions by investigating RNA interactions. Current methods for mapping RNA–RNA interactions have to rely on an ‘anchor’ protein or RNA and often require molecular perturbations. Here we present the MARIO (Mapping RNA interactome in vivo) technology to massively reveal RNA–RNA interactions from unperturbed cells. We mapped tens of thousands of endogenous RNA–RNA interactions from mouse embryonic stem cells and brain. We validated seven interactions by RNA antisense purification and one interaction using single-molecule RNA–FISH. The experimentally derived RNA interactome is a scale-free network, which is not expected from currently perceived promiscuity in RNA–RNA interactions. Base pairing is observed at the interacting regions between long RNAs, including transposon transcripts, suggesting a class of regulatory sequences acting in trans. In addition, MARIO data reveal thousands of intra-molecule interactions, providing in vivo data on high-order RNA structures.
A high-throughput technique for determining grain boundary character non-destructively in microstructures with through-thickness grains
Authors: Seita Matteo , Volpi Marco , Patala Srikanth , McCue Ian , Schuh Christopher A , Diamanti Maria Vittoria , Erlebacher Jonah , Demkowicz Michael J 
Published: June 2016

AbstractGrain boundaries (GBs) govern many properties of polycrystalline materials. However, because of their structural variability, our knowledge of GB constitutive relations is still very limited. We present a novel method to characterise the complete crystallography of individual GBs non-destructively, with high-throughput, and using commercially available tools. This method combines electron diffraction, optical reflectance and numerical image analysis to determine all five crystallographic parameters of numerous GBs in samples with through-thickness grains. We demonstrate the technique by measuring the crystallographic character of about 1,000 individual GBs in aluminum in a single run. Our method enables cost- and time-effective assembly of crystallography–property databases for thousands of individual GBs. Such databases are essential for identifying GB constitutive relations and for predicting GB-related behaviours of polycrystalline solids.
Function-specific virtual screening for GPCR ligands using a combined scoring method
Authors: Kooistra Albert J. , Vischer Henry F. , McNaught-Flores Daniel , Leurs Rob , de Esch Iwan J. P. , de Graaf Chris 
Published: June 2016

AbstractThe ability of scoring functions to correctly select and rank docking poses of small molecules in protein binding sites is highly target dependent, which presents a challenge for structure-based drug discovery. Here we describe a virtual screening method that combines an energy-based docking scoring function with a molecular interaction fingerprint (IFP) to identify new ligands based on G protein-coupled receptor (GPCR) crystal structures. The consensus scoring method is prospectively evaluated by: 1) the discovery of chemically novel, fragment-like, high affinity histamine H1 receptor (H1R) antagonists/inverse agonists, 2) the selective structure-based identification of ß2-adrenoceptor (ß2R) agonists and 3) the experimental validation and comparison of the combined and individual scoring approaches. Systematic retrospective virtual screening simulations allowed the definition of scoring cut-offs for the identification of H1R and ß2R ligands and the selection of an optimal ß-adrenoceptor crystal structure for the discrimination between ß2R agonists and antagonists. The consensus approach resulted in the experimental validation of 53% of the ß2R and 73% of the H1R virtual screening hits with up to nanomolar affinities and potencies. The selective identification of ß2R agonists shows the possibilities of structure-based prediction of GPCR ligand function by integrating protein-ligand binding mode information.
Severest crisis overlooked—Worst disruption of terrestrial environments postdates the Permian–Triassic mass extinction
Authors: Hochuli Peter A. , Sanson-Barrera Anna , Schneebeli-Hermann Elke , Bucher Hugo 
Published: June 2016

AbstractGenerally Early Triassic floras are believed to be depauperate, suffering from protracted recovery following the Permian–Triassic extinction event. Here we present palynological data of an expanded East Greenland section documenting recovered floras in the basal Triassic (Griesbachian) and a subsequent fundamental floral turnover, postdating the Permian–Triassic boundary extinction by about 500 kyrs. This event is marked by a swap in dominating floral elements, changing from gymnosperm pollen-dominated associations in the Griesbachian to lycopsid spore-dominated assemblages in the Dienerian. This turnover coincides with an extreme δ13Corg negative shift revealing a severe environmental crisis, probably induced by volcanic outbursts of the Siberian Traps, accompanied by a climatic turnover, changing from cool and dry in the Griesbachian to hot and humid in the Dienerian. Estimates of sedimentation rates suggest that this environmental alteration took place within some 1000 years. Similar, coeval changes documented on the North Indian Margin (Pakistan) and the Bowen Basin (Australia) indicate the global extent of this crisis. Our results evidence the first profound disruption of the recovery of terrestrial environments about 500kyrs after the Permian–Triassic extinction event. It was followed by another crisis, about 1myrs later thus, the Early Triassic can be characterised as a time of successive environmental crises.
A portable trap with electric lead catches up to 75% of an invasive fish species
Authors: Johnson Nicholas S. , Miehls Scott , O’Connor Lisa M. , Bravener Gale , Barber Jessica , Thompson Henry , Tix John A. , Bruning Tyler 
Published: June 2016

AbstractA novel system combining a trap and pulsed direct current electricity was able to catch up to 75% of tagged invasive sea lamprey Petromyzon marinus in free-flowing streams. Non-target mortality was rare and impacts to non-target migration were minimal; likely because pulsed direct current only needed to be activated at night (7 hours of each day). The system was completely portable and the annual cost of the trapping system was low ($4,800 U.S. dollars). Use of the technology is poised to substantially advance integrated control of sea lamprey, which threaten a fishery valued at 7 billion U.S. dollars annually, and help restore sea lamprey populations in Europe where they are native, but imperiled. The system may be broadly applicable to controlling invasive fishes and restoring valued fishes worldwide, thus having far reaching effects on ecosystems and societies.
The association between polyomavirus BK strains and BKV viruria in liver transplant recipients
Authors: Wang Robert Y. L. , Li Yi-Jung , Lee Wei-Chen , Wu Hsin-Hsu , Lin Chan-Yu , Lee Cheng-Chia , Chen Yung-Chang , Hung Cheng-Chieh , Yang Chih-Wei , Tian Ya-Chung 
Published: June 2016

AbstractBK virus (BKV) is a polyomavirus that cause of allograft dysfunction among kidney transplant recipients. The role of BKV infection in non-renal solid organ transplant recipients is not well understood neither for the relationship between various BKV strains with occurrence of BKV viral viruria. This study aimed to understand the prevalence of BKV infection and identified of BKV various strains in the urine of liver transplant recipients. There was not significant difference of renal outcome between high BKV viruria and low BKV viruria in the liver transplant recipients. The WW-non-coding control region (NCCR) BKV detected in urine was associated with higher urinary BKV load, whereas the Dunlop-NCCR BKV was detected in the urine of low urinary BKV load. Anin vitrocultivation system demonstrated that WW-BKV strain exhibiting the higher viral DNA replication efficiency and higher BKV load. Altogether, this is the first study to demonstrate the impact of BKV strains on the occurrence of BK viruria in the liver transplant recipients.
Prostacyclin reverses the cigarette smoke-induced decrease in pulmonary Frizzled 9 expression through miR-31
Authors: Tennis M. A. , New M. L. , McArthur D. G. , Merrick D. T. , Dwyer-Nield L. D. , Keith R. L. 
Published: June 2016

AbstractHalf of lung cancers are diagnosed in former smokers, leading to a significant treatment burden in this population. Chemoprevention in former smokers using the prostacyclin analogue iloprost reduces endobronchial dysplasia, a premalignant lung lesion. Iloprost requires the presence of the WNT receptor Frizzled 9 (Fzd9) for inhibition of transformed growth in vitro. To investigate the relationship between iloprost, cigarette smoke and Fzd9 expression, we used human samples, mouse models and in vitro studies. Fzd9 expression was low in human lung tumors and in progressive dysplasias. In mouse models and in vitro studies, tobacco smoke carcinogens reduced expression of Fzd9 while prostacyclin maintained or increased expression. Expression of miR-31 repressed Fzd9 expression, which was abrogated by prostacyclin. We propose a model where cigarette smoke exposure increases miR-31 expression, which leads to decreased Fzd9 expression and prevents response to iloprost. When smoke is removed miR-31 is reduced, prostacyclin can increase Fzd9 expression and progression of dysplasia is inhibited. Fzd9 and miR-31 are candidate biomarkers for precision application of iloprost and monitoring of treatment progress. As we continue to investigate the mechanisms of prostacyclin chemoprevention and identify biomarkers for its use, we will facilitate clinical trials and speed implementation of this valuable prevention approach.
Large Bandgap Shrinkage from Doping and Dielectric Interface in Semiconducting Carbon Nanotubes
Authors: Comfort Everett , Lee Ji Ung 
Published: June 2016

AbstractThe bandgap of a semiconductor is one of its most important electronic properties. It is often considered to be a fixed property of the semiconductor. As the dimensions of semiconductors reduce, however, many-body effects become dominant. Here, we show that doping and dielectric, two critical features of semiconductor device manufacturing, can dramatically shrink (renormalize) the bandgap. We demonstrate this in quasi-one-dimensional semiconducting carbon nanotubes. Specifically, we use a four-gated device, configured as a p-n diode, to investigate the fundamental electronic structure of individual, partially supported nanotubes of varying diameter. The four-gated construction allows us to combine both electrical and optical spectroscopic techniques to measure the bandgap over a wide doping range.
Far-Infrared and Raman Spectroscopy Investigation of Phonon Modes in Amorphous and Crystalline Epitaxial GeTe-Sb2Te3 Alloys
Authors: Bragaglia V. , Holldack K. , Boschker J. E. , Arciprete F. , Zallo E. , Flissikowski T. , Calarco R. 
Published: June 2016

AbstractA combination of far-infrared and Raman spectroscopy is employed to investigate vibrational modes and the carrier behavior in amorphous and crystalline ordered GeTe-Sb2Te3 alloys (GST) epitaxially grown on Si(111). The infrared active GST mode is not observed in the Raman spectra and vice versa, indication of the fact that inversion symmetry is preserved in the metastable cubic phase in accordance with the F"Equation missing"m3 space group. For the trigonal phase, instead, a partial symmetry break due to Ge/Sb mixed anion layers is observed. By studying the crystallization process upon annealing with both the techniques, we identify temperature regions corresponding to the occurrence of different phases as well as the transition from one phase to the next. Activation energies of 0.43 eV and 0.08 eV for the electron conduction are obtained for both cubic and trigonal phases, respectively. In addition a metal-insulator transition is clearly identified to occur at the onset of the transition between the disordered and the ordered cubic phase.
Genetic polymorphisms of IL-17A, IL-17F, TLR4 and miR-146a in association with the risk of pulmonary tuberculosis
Authors: Wang Min , Xu Guisheng , Lü Lingshuang , Xu Kun , Chen Yongzhong , Pan Hongqiu , Burstrom Bo , Burstrom Kristina , Wang Jianming 
Published: June 2016

AbstractGenetic factors affect host susceptibility to pathogens. In this population-based case control study, we explored the genetic polymorphisms of IL-17, TLR4 and miR-146a in association with pulmonary tuberculosis in a Chinese Han population. We recruited 1601 pulmonary tuberculosis patients matched with 1526 healthy controls and genotyped twelve functional single nucleotide polymorphisms (SNPs). After the correction for multiple comparisons, two SNPs (rs10759932 and rs2737190) in the TLR4 gene remained significant. Individuals carrying the rs2737190-AG genotype (vs. AA) had a significantly increased risk of either clinical tuberculosis (OR: 1.31, 95% CI: 1.11–1.53) or sputum smear-positive tuberculosis (OR: 1.35, 95% CI: 1.13–1.61). Stratification analysis revealed that the effects of genetic variations on tuberculosis were more evident among non-smokers. People with haplotype TLR4 rs10983755G–rs10759932C had a significantly increased risk of tuberculosis (OR: 3.43, 95% CI: 2.34–5.05). Moreover, we found that SNPs of rs3819024 in IL-17A and rs763780 in IL-17F were weakly related to a prognosis of tuberculosis. Our results suggest that genetic polymorphisms of IL-17 and TLR4 may play a role in host susceptibility to tuberculosis in the Chinese Han population. More work is necessary to identify specific causative variants of tuberculosis underlying the observed associations.
Paternal overweight is associated with increased breast cancer risk in daughters in a mouse model
Authors: Fontelles Camile Castilho , Carney Elissa , Clarke Johan , Nguyen Nguyen M. , Yin Chao , Jin Lu , Cruz M. Idalia , Ong Thomas Prates , Hilakivi-Clarke Leena , de Assis Sonia 
Published: June 2016

AbstractWhile many studies have shown that maternal weight and nutrition in pregnancy affects offspring’s breast cancer risk, no studies have investigated the impact of paternal body weight on daughters’ risk of this disease. Here, we show that diet-induced paternal overweight around the time of conception can epigenetically reprogram father’s germ-line and modulate their daughters’ birth weight and likelihood of developing breast cancer, using a mouse model. Increased body weight was associated with changes in the miRNA expression profile in paternal sperm. Daughters of overweight fathers had higher rates of carcinogen-induced mammary tumors which were associated with delayed mammary gland development and alterations in mammary miRNA expression. The hypoxia signaling pathway, targeted by miRNAs down-regulated in daughters of overweight fathers, was activated in their mammary tissues and tumors. This study provides evidence that paternal peri-conceptional body weight may affect daughters’ mammary development and breast cancer risk and warrants further studies in other animal models and humans.
Myeloid-Specific Blockade of Notch Signaling Attenuates Choroidal Neovascularization through Compromised Macrophage Infiltration and Polarization in Mice
Authors: Dou Guo-Rui , Li Na , Chang Tian-Fang , Zhang Ping , Gao Xiang , Yan Xian-Chun , Liang Liang , Han Hua , Wang Yu-Sheng 
Published: June 2016

AbstractMacrophages have been recognized as an important inflammatory component in choroidal neovascularization (CNV). However, it is unclear how these cells are activated and polarized, how they affect angiogenesis and what the underlining mechanisms are during CNV. Notch signaling has been implicated in macrophage activation. Previously we have shown that inducible disruption of RBP-J, the critical transcription factor of Notch signaling, in adult mice results in enhanced CNV, but it is unclear what is the role of macrophage-specific Notch signaling in the development of CNV. In the current study, by using the myeloid specific RBP-J knockout mouse model combined with the laser-induced CNV model, we show that disruption of Notch signaling in macrophages displayed attenuated CNV growth, reduced macrophage infiltration and activation, and alleviated angiogenic response after laser induction. The inhibition of CNV occurred with reduced expression of VEGF and TNF-α in infiltrating inflammatory macrophages in myeloid specific RBP-J knockout mice. These changes might result in direct inhibition of EC lumen formation, as shown in an in vitro study. Therefore, clinical intervention of Notch signaling in CNV needs to pinpoint myeloid lineage to avoid the counteractive effects of global inhibition.
HTRA1 promoter variant differentiates polypoidal choroidal vasculopathy from exudative age-related macular degeneration
Authors: Ng Tsz Kin , Liang Xiao Ying , Lai Timothy Y. Y. , Ma Li , Tam Pancy O. S. , Wang Jian Xiong , Chen Li Jia , Chen Haoyu , Pang Chi Pui 
Published: June 2016

AbstractExudative age-related macular degeneration (AMD) and polypoidal choroidal vasculopathy (PCV) share similar abnormal choroidal vasculature, but responses to treatments are different. In this study, we sequenced the whole HTRA1 gene and its promoter by direct sequencing in a Hong Kong Chinese PCV cohort. We identified rs11200638, c.34delCinsTCCT, c.59C>T, rs1049331 and rs2293870 significantly associated with PCV. Notably, rs2672598 was significantly associated with exudative AMD (p = 1.31 × 10−4) than PCV (p = 0.11). Logistic regression indicated that rs2672598 (p = 2.27 × 10−3) remained significant after adjusting for rs11200638 in exudative AMD. Moreover, the rs11200638-rs2672598 joint genotype AA-CC conferred higher risk to exudative AMD (43.11 folds) than PCV (3.68 folds). Promoter analysis showed that rs2672598 C-allele showed higher luciferase expression than wildtype T-allele (p = 0.026), independent of rs11200638 genotype (p = 0.621). Coherently, vitreous humor HTRA1 expression with rs2672598 CC genotype was significantly higher than that with TT genotype by 2.56 folds (p = 0.02). Furthermore, rs2672598 C-allele was predicted to alter the transcription factor binding sites, but not rs11200638 A-allele. Our results revealed that HTRA1 rs2672598 is more significantly associated with exudative AMD than PCV in ARMS2/HTRA1 region, and it is responsible for elevated HTRA1 transcriptional activity and HTRA1 protein expression.
Kinetics and Mechanisms of γ′ Reprecipitation in a Ni-based Superalloy
Authors: Masoumi F. , Shahriari D. , Jahazi M. , Cormier J. , Devaux A. 
Published: June 2016

AbstractThe reprecipitation mechanisms and kinetics of γ′ particles during cooling from supersolvus and subsolvus temperatures were studied in AD730TM Ni-based superalloy using Differential Thermal Analysis (DTA). The evolution in the morphology and distribution of reprecipitated γ′ particles was investigated using Field Emission Gun Scanning Electron Microscopy (FEG-SEM). Depending on the cooling rate, γ′ particles showed multi or monomodal distribution. The irregularity growth characteristics observed at lower cooling rates were analyzed in the context of Mullins and Sekerka theory, and allowed the determination of a critical size of γ′ particles above which morphological instability appears. Precipitation kinetics parameters were determined using a non-isothermal JMA model and DTA data. The Avrami exponent was determined to be in the 1.5–2.3 range, suggesting spherical or irregular growth. A methodology was developed to take into account the temperature dependence of the rate coefficient k(T) in the non-isothermal JMA equation. In that regard, a function for k(T) was developed. Based on the results obtained, reprecipitation kinetics models for low and high cooling rates are proposed to quantify and predict the volume fraction of reprecipitated γ′ particles during the cooling process.
Cloaking of solar cell contacts at the onset of Rayleigh scattering
Authors: San Román Etor , Vitrey Alan , Buencuerpo Jerónimo , Prieto Iván , Llorens José M. , García-Martín Antonio , Alén Benito , Chaudhuri Anabil , Neumann Alexander , Brueck S. R. J. , Ripalda José M. 
Published: June 2016

AbstractElectrical contacts on the top surface of solar cells and light emitting diodes cause shadow losses. The phenomenon of extraordinary optical transmission through arrays of subwavelength holes suggests the possibility of engineering such contacts to reduce the shadow using plasmonics, but resonance effects occur only at specific wavelengths. Here we describe instead a broadband effect of enhanced light transmission through arrays of subwavelength metallic wires, due to the fact that, in the absence of resonances, metal wires asymptotically tend to invisibility in the small size limit regardless of the fraction of the device area taken up by the contacts. The effect occurs for wires more than an order of magnitude thicker than the transparency limit for metal thin films. Finite difference in time domain calculations predict that it is possible to have high cloaking efficiencies in a broadband wavelength range, and we experimentally demonstrate contact shadow losses less than half of the geometric shadow.
In-situ Electric Field-Induced Modulation of Photoluminescence in Pr-doped Ba0.85Ca0.15Ti0.90Zr0.10O3 Lead-Free Ceramics
Authors: Sun Hai Ling , Wu Xiao , Chung Tat Hang , Kwok K. W. 
Published: June 2016

AbstractLuminescent materials with dynamic photoluminescence activity have aroused special interest because of their potential widespread applications. One proposed approach of directly and reversibly modulating the photoluminescence emissions is by means of introducing an external electric field in an in-situ and real-time way, which has only been focused on thin films. In this work, we demonstrate that real-time electric field-induced photoluminescence modulation can be realized in a bulk Ba0.85Ca0.15Ti0.90Zr0.10O3 ferroelectric ceramic doped with 0.2 mol% Pr3+, owing to its remarkable polarization reversal and phase evolution near the morphotropic phase boundary. Along with in-situ X-ray diffraction analysis, our results reveal that an applied electric field induces not only typical polarization switching and minor crystal deformation, but also tetragonal-to-rhombohedral phase transformation of the ceramic. The electric field-induced phase transformation is irreversible and engenders dominant effect on photoluminescence emissions as a result of an increase in structural symmetry. After it is completed in a few cycles of electric field, the photoluminescence emissions become governed mainly by the polarization switching and thus vary reversibly with the modulating electric field. Our results open a promising avenue towards the realization of bulk ceramic-based tunable photoluminescence activity with high repeatability, flexible controllability and environmental-friendly chemical process.