bluuebunny/crossref_metadata_2025_split huggingface dataset:
Striped nanoscale phase separation at the metal–insulator transition of heteroepitaxial nickelates
Authors: Mattoni G. , Zubko P. , Maccherozzi F. , van der Torren A.J.H. , Boltje D. B. , Hadjimichael M. , Manca N. , Catalano S. , Gibert M. , Liu Y. , Aarts J. , Triscone J.-M. , Dhesi S. S. , Caviglia A. D. 
Published: November 2016

AbstractNucleation processes of mixed-phase states are an intrinsic characteristic of first-order phase transitions, typically related to local symmetry breaking. Direct observation of emerging mixed-phase regions in materials showing a first-order metal–insulator transition (MIT) offers unique opportunities to uncover their driving mechanism. Using photoemission electron microscopy, we image the nanoscale formation and growth of insulating domains across the temperature-driven MIT in NdNiO3 epitaxial thin films. Heteroepitaxy is found to strongly determine the nanoscale nature of the phase transition, inducing preferential formation of striped domains along the terraces of atomically flat stepped surfaces. We show that the distribution of transition temperatures is a local property, set by surface morphology and stable across multiple temperature cycles. Our data provide new insights into the MIT of heteroepitaxial nickelates and point to a rich, nanoscale phenomenology in this strongly correlated material.
Engineering and optimising deaminase fusions for genome editing
Authors: Yang Luhan , Briggs Adrian W. , Chew Wei Leong , Mali Prashant , Guell Marc , Aach John , Goodman Daniel Bryan , Cox David , Kan Yinan , Lesha Emal , Soundararajan Venkataramanan , Zhang Feng , Church George 
Published: November 2016

AbstractPrecise editing is essential for biomedical research and gene therapy. Yet, homology-directed genome modification is limited by the requirements for genomic lesions, homology donors and the endogenous DNA repair machinery. Here we engineered programmable cytidine deaminases and test if we could introduce site-specific cytidine to thymidine transitions in the absence of targeted genomic lesions. Our programmable deaminases effectively convert specific cytidines to thymidines with 13% efficiency in Escherichia coli and 2.5% in human cells. However, off-target deaminations were detected more than 150 bp away from the target site. Moreover, whole genome sequencing revealed that edited bacterial cells did not harbour chromosomal abnormalities but demonstrated elevated global cytidine deamination at deaminase intrinsic binding sites. Therefore programmable deaminases represent a promising genome editing tool in prokaryotes and eukaryotes. Future engineering is required to overcome the processivity and the intrinsic DNA binding affinity of deaminases for safer therapeutic applications.
Towards first-principles molecular design of liquid crystal-based chemoresponsive systems
Authors: Roling Luke T. , Scaranto Jessica , Herron Jeffrey A. , Yu Huaizhe , Choi Sangwook , Abbott Nicholas L. , Mavrikakis Manos 
Published: November 2016

AbstractNematic liquid crystals make promising chemoresponsive systems, but their development is currently limited by extensive experimental screening. Here we report a computational model to understand and predict orientational changes of surface-anchored nematic liquid crystals in response to chemical stimuli. In particular, we use first-principles calculations to evaluate the binding energies of benzonitrile, a model for 4′-pentyl-4-biphenylcarbonitrile, and dimethyl methylphosphonate to metal cation models representing the substrate chemical sensing surface. We find a correlation between these quantities and the experimental response time useful for predicting the response time of cation–liquid crystal combinations. Consideration of charge donation from chemical species in the surface environment is critical for obtaining agreement between theory and experiment. Our model may be extended to the design of improved chemoresponsive liquid crystals for selectively detecting other chemicals of practical interest by choosing appropriate combinations of metal cations with liquid crystals of suitable molecular structure.
The ethanopharmacological aspect of carbon nanodots in turmeric smoke
Authors: Chun Sechul , Muthu Manikandan , Gansukh Enkhtaivan , Thalappil Pradeep , Gopal Judy 
Published: November 2016

AbstractSmoke manifested ever since our ancient’s lit fire; today it has evolved to become an environmental concern. However, medicinal smoke is still part of man’s natural remedies, religious and cultural practices too. The Asiatic household practice of burning turmeric rhizomes to relieve nose and chest congestion is a well known yet never scientifically authenticated or studied practice. For the first time we investigate the components of these turmeric smudges, validate their antimicrobial and anticancer properties and their cell compatibility. With smoke there is always nanoparticulate carbon and turmeric smoke is no exception. If so, what is the role of the nano carbon (NC) in the turmeric smudge effect? This study isolated, characterized and exposed these secret natural NC undercover agents in turmeric smoke. Their unequivocal role in the ethanopharmocological activity of turmeric smudging has been demonstrated. This work opens a new avenue for use of such nano components of smoke for harnessing the ethanopharmacological property of various medicinal smokes, by excluding the smoke factor, through extracting the nano carbon material in them. This is a possibility to realizing the use of such naturally available nanomaterial, as an eco friendly substitute for the notorious anthropogenic nanomaterials.
Staurosporines decrease ORMDL proteins and enhance sphingomyelin synthesis resulting in depletion of plasmalemmal phosphatidylserine
Authors: Maekawa Masashi , Lee Minhyoung , Wei Kuiru , Ridgway Neale D. , Fairn Gregory D. 
Published: November 2016

AbstractAccumulation of phosphatidylserine in the inner leaflet of the plasma membrane is a hallmark of eukaryotes. Sublethal levels of staurosporine and related compounds deplete phosphatidylserine from the plasma membrane and abrogate K-Ras signaling. Here, we report that low-dose staurosporine and related compounds increase sphingomyelin mass. Mass-spectrometry and metabolic tracer analysis revealed an increase in both the levels and rate of synthesis of sphingomyelin in response to sublethal staurosporine. Mechanistically, it was determined that the abundance of the ORMDL proteins, which negatively regulate serine-palmitoyltransferase, are decreased by low-dose staurosporine. Finally, inhibition of ceramide synthesis, and thus sphingomyelin, prevented the displacement of phosphatidylserine and cholesterol from the inner leaflet of the plasma membrane. The results establish that an optimal level of sphingomyelin is required to maintain the distribution of phosphatidylserine and cholesterol in the plasma membrane and further demonstrate a complex relationship between the trafficking of phosphatidylserine and sphingomyelin.
Novel identified associations of RGS1 and RASGRP1 variants in IgA Nephropathy
Authors: Zhou Xu-Jie , Nath Swapan K , Qi Yuan-Yuan , Sun Celi , Hou Ping , Zhang Yue-Miao , Lv Ji-Cheng , Shi Su-Fang , Liu Li-Jun , Chen Ruoyan , Yang Wanling , He Kevin , Li Yanming , Zhang Hong 
Published: November 2016

AbstractKnown susceptibility loci together can only explain about 6–8% of the disease heritability of IgA nephropathy (IgAN), suggesting that there are still a large number of genetic variants remained to be discovered. We previously identified IgAN and systemic lupus erythematosus (SLE)/lupus nephritis (LN) shared many loci based on GWAS on Chinese populations. The more recent study with high-density genotyping of immune-related loci in individuals with Asian ancestry identified 10 new and 6 suggestive loci in SLE. In the current study, we thus included all the lead SNPs from these 16 loci reported, and firstly tested their associations in 1,248 patients with sporadic IgAN, 737 patients with LN and 1,187 controls. Significant associations identified in IgAN were replicated in additional 500 patients and 2372 controls. rs12022418 in RGS1 (p = 3.0 × 10−6) and rs7170151 in RASGRP1 (p = 1.9 × 10−5) showed novel associations in IgAN. Compared to SNPs that were in LD with them, the associated variants showed higher potential of regulatory features by affecting gene expression. And systemic evaluation of GWAS data supported the pleiotropic effects of RGS1 and RASGRP1 variants in mediating human complex diseases. In conclusion, novel risk loci shared between IgAN and SLE/LN were identified, which may shed new light to exploit the potential pathogenesis for those two diseases.
Distinct roles for primate caudate dopamine D1 and D2 receptors in visual discrimination learning revealed using shRNA knockdown
Authors: Takaji Masafumi , Takemoto Atsushi , Yokoyama Chihiro , Watakabe Akiya , Mizukami Hiroaki , Ozawa Keiya , Onoe Hirotaka , Nakamura Katsuki , Yamamori Tetsuo 
Published: November 2016

AbstractThe striatum plays important motor, associative and cognitive roles in brain functions. However, the rodent dorsolateral (the primate putamen) and dorsomedial (the primate caudate nucleus) striatum are not anatomically separated, making it difficult to distinguish their functions. By contrast, anatomical separation exists between the caudate nucleus and putamen in primates. Here, we successfully decreased dopamine D1 receptor (D1R) or D2R mRNA expression levels selectively in the marmoset caudate using shRNA knockdown techniques, as determined using positron emission tomography imaging with specific D1R and D2R ligands and postmortem in situ hybridization analysis. We then conducted a voxel-based correlation analysis between binding potential values of PET imaging and visual discrimination learning task performance in these genetically modified marmosets to find a critical role for the caudate D2R but no apparent role for the caudate D1R. This latter finding challenges the current understanding of the mechanisms underlying D1R activation in the caudate.
Coral Reef Resilience, Tipping Points and the Strength of Herbivory
Authors: Holbrook Sally J. , Schmitt Russell J. , Adam Thomas C. , Brooks Andrew J. 
Published: November 2016

AbstractCoral reefs increasingly are undergoing transitions from coral to macroalgal dominance. Although the functional roles of reef herbivores in controlling algae are becoming better understood, identifying possible tipping points in the herbivory-macroalgae relationships has remained a challenge. Assessment of where any coral reef ecosystem lies in relation to the coral-to-macroalgae tipping point is fundamental to understanding resilience properties, forecasting state shifts, and developing effective management practices. We conducted a multi-year field experiment in Moorea, French Polynesia to estimate these properties. While we found a sharp herbivory threshold where macroalgae escape control, ambient levels of herbivory by reef fishes were well above that needed to prevent proliferation of macroalgae. These findings are consistent with previously observed high resilience of the fore reef in Moorea. Our approach can identify vulnerable coral reef systems in urgent need of management action to both forestall shifts to macroalgae and preserve properties essential for resilience.
Systems-wide analysis of manganese deficiency-induced changes in gene activity of Arabidopsis roots
Authors: Rodríguez-Celma Jorge , Tsai Yi-Hsiu , Wen Tuan-Nan , Wu Yu-Ching , Curie Catherine , Schmidt Wolfgang 
Published: November 2016

AbstractManganese (Mn) is pivotal for plant growth and development, but little information is available regarding the strategies that evolved to improve Mn acquisition and cellular homeostasis of Mn. Using an integrated RNA-based transcriptomic and high-throughput shotgun proteomics approach, we generated a comprehensive inventory of transcripts and proteins that showed altered abundance in response to Mn deficiency in roots of the model plant Arabidopsis. A suite of 22,385 transcripts was consistently detected in three RNA-seq runs; LC-MS/MS-based iTRAQ proteomics allowed the unambiguous determination of 11,606 proteins. While high concordance between mRNA and protein expression (R = 0.87) was observed for transcript/protein pairs in which both gene products accumulated differentially upon Mn deficiency, only approximately 10% of the total alterations in the abundance of proteins could be attributed to transcription, indicating a large impact of protein-level regulation. Differentially expressed genes spanned a wide range of biological functions, including the maturation, translation, and transport of mRNAs, as well as primary and secondary metabolic processes. Metabolic analysis by UPLC-qTOF-MS revealed that the steady-state levels of several major glucosinolates were significantly altered upon Mn deficiency in both roots and leaves, possibly as a compensation for increased pathogen susceptibility under conditions of Mn deficiency.
Kisspeptin and RFRP-3 differentially regulate food intake and metabolic neuropeptides in the female desert jerboa
Authors: Talbi Rajae , Laran-Chich Marie-Pierre , Magoul Rabia , El Ouezzani Seloua , Simonneaux Valérie 
Published: November 2016

AbstractJerboas are wild rodents exhibiting exceptional adaptation to their desert environment. Under harsh autumn conditions, they shut down reproduction, increase body weight and hibernate, while during spring they become sexually active even under negative energy-balance. We recently reported that these rhythms are associated with synchronized changes in genes expressing reproductive (Kiss1, Rfrp) and metabolic (Npy and Pomc) peptides, raising the hypothesis of coordinated seasonal regulation of both functions. Here we analyzed whether kisspeptin and RFRP-3 regulate food-intake in parallel to their established reproductive functions. Intracerebroventricular administration of kisspeptin inhibited food intake by 1.5-fold in fasted, but not ad-libitum fed, female jerboas captured in spring, an effect associated with an increase in Pomc and decrease in Rfrp mRNA levels. By contrast, intracerebroventricular injection of RFRP-3 induced a 4-fold increase in food-intake in ad-libitum female jerboas, together with a decrease in Pomc and increase in Npy mRNA levels. This orexigenic effect of RFRP-3 was observed in both spring and autumn, whereas kisspeptin’s anorexigenic effect was only observed in spring. Altogether, this study reports opposite metabolic effects of kisspeptin and RFRP-3 in the female jerboa and strengthens our hypothesis of a coordinated, season-dependent, regulation of reproductive activity and food intake through interactions of these hypothalamic peptides.
Passively synchronized Q-switched and mode-locked dual-band Tm3+:ZBLAN fiber lasers using a common graphene saturable absorber
Authors: Jia Chenglai , Shastri Bhavin J. , Abdukerim Nurmemet , Rochette Martin , Prucnal Paul R. , Saad Mohammed , Chen Lawrence R. 
Published: November 2016

AbstractDual-band fiber lasers are emerging as a promising technology to penetrate new industrial and medical applications from their dual-band properties, in addition to providing compactness and environmental robustness from the waveguide structure. Here, we demonstrate the use of a common graphene saturable absorber and a single gain medium (Tm3+:ZBLAN fiber) to implement (1) a dual-band fiber ring laser with synchronized Q-switched pulses at wavelengths of 1480 nm and 1840 nm, and (2) a dual-band fiber linear laser with synchronized mode-locked pulses at wavelengths of 1480 nm and 1845 nm. Q-switched operation at 1480 nm and 1840 nm is achieved with a synchronized repetition rate from 20 kHz to 40.5 kHz. For synchronous mode-locked operation, pulses with full-width at half maximum durations of 610 fs and 1.68 ps at wavelengths of 1480 nm and 1845 nm, respectively, are obtained at a repetition rate of 12.3 MHz. These dual-band pulsed sources with an ultra-broadband wavelength separation of ~360 nm will add new capabilities in applications including optical sensing, spectroscopy, and communications.
Image analysis-derived metrics of histomorphological complexity predicts prognosis and treatment response in stage II-III colon cancer
Authors: Mezheyeuski Artur , Hrynchyk Ina , Karlberg Mia , Portyanko Anna , Egevad Lars , Ragnhammar Peter , Edler David , Glimelius Bengt , Östman Arne 
Published: November 2016

AbstractThe complexity of tumor histomorphology reflects underlying tumor biology impacting on natural course and response to treatment. This study presents a method of computer-aided analysis of tissue sections, relying on multifractal (MF) analyses, of cytokeratin-stained tumor sections which quantitatively evaluates of the morphological complexity of the tumor-stroma interface. This approach was applied to colon cancer collection, from an adjuvant treatment randomized study. Metrics obtained with the method acted as independent markers for natural course of the disease, and for benefit of adjuvant treatment. Comparative analyses demonstrated that MF metrics out-performed standard histomorphological features such as tumor grade, budding and configuration of invasive front. Notably, the MF analyses-derived “αmax” –metric constitutes the first response-predictive biomarker in stage II-III colon cancer showing significant interactions with treatment in analyses using a randomized trial-derived study population. Based on these results the method appears as an attractive and easy-to-implement tool for biomarker identification.
A Low-loss Metasurface Antireflection Coating on Dispersive Surface Plasmon Structure
Authors: Jeon Jiyeon , Bhattarai Khagendra , Kim Deok-Kee , Kim Jun Oh , Urbas Augustine , Lee Sang Jun , Ku Zahyun , Zhou Jiangfeng 
Published: November 2016

AbstractOver the years, there has been increasing interest in the integration of metal hole array (MHA) with optoelectronic devices, as a result of enhanced coupling of incident light into the active layer of devices via surface plasmon polariton (SPP) resonances. However, not all incident light contributes to the SPP resonances due to significant reflection loss at the interface between incident medium and MHA. Conventional thin-film antireflection (AR) coating typically does not work well due to non-existing material satisfying the AR condition with strong dispersion of MHA’s effective impedances. We demonstrate a single-layer metasurface AR coating that completely eliminates the refection and significantly increases the transmission at the SPP resonances. Operating at off-resonance wavelengths, the metasurface exhibits extremely low loss and does not show resonant coupling with the MHA layer. The SPP resonance wavelengths of MHA layer are unaffected whereas the surface wave is significantly increased, thereby paving the way for improved performance of optoelectronic devices. With an improved retrieval method, the metasurface is proved to exhibit a high effective permittivity ("Equation missing") and extremely low loss (tan δ ~ 0.005). A classical thin-film AR coating mechanism is identified through analytical derivations and numerical simulations.
Sulforaphane, a natural component of broccoli, inhibits vestibular schwannoma growth in vitro and in vivo
Authors: Kim Bo Gyung , Fujita Takeshi , Stankovic Konstantina M. , Welling D. Bradley , Moon In Seok , Choi Jae Young , Yun Jieun , Kang Jong Soon , Lee Jong Dae 
Published: November 2016

AbstractVestibular schwannoma (VS) is an intracranial tumor that causes significant morbidity, including hearing loss, tinnitus, dizziness, and possibly even death from brainstem compression. However, FDA-approved pharmacologic treatments for VS do not exist. Sulforaphane (SFN) is a naturally occurring isothiocyanate found in cruciferous vegetables, such as broccoli, with potent chemoprotective effects in several cell types. Our objective was to determine whether SFN is effective against VS in vitro and in vivo. Human primary VS cells, HEI-193 schwannoma cells, and SC4 Nf2−/− Schwann cells were used to investigate the inhibitory effects of SFN in vitro. Cell proliferation was assessed by bromodeoxyuridine (BrdU) incorporation, and cell viability and metabolic activity was calculated by MTT assay. Apoptosis was measured by flow cytometry, terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) staining, and Western blot for cleaved caspases. A mouse model with a murine schwannoma allograft was also used to examine the antitumor activity of SFN. SFN exhibited significant antiproliferative activity in schwannoma cells in vitro, via the inhibition of HDAC activity and the activation of ERK. SFN treatment induced apoptosis and cell cycle arrest at the G2/M phase. SFN also significantly inhibited schwannoma growth in vivo. Our preclinical studies motivate a future prospective clinical study of SFN for the treatment of VS.
Derepressing muscleblind expression by miRNA sponges ameliorates myotonic dystrophy-like phenotypes in Drosophila
Authors: Cerro-Herreros Estefania , Fernandez-Costa Juan M. , Sabater-Arcis María , Llamusi Beatriz , Artero Ruben 
Published: November 2016

AbstractMyotonic Dystrophy type 1 (DM1) originates from alleles of the DMPK gene with hundreds of extra CTG repeats in the 3′ untranslated region (3′ UTR). CUG repeat RNAs accumulate in foci that sequester Muscleblind-like (MBNL) proteins away from their functional target transcripts. Endogenous upregulation of MBNL proteins is, thus, a potential therapeutic approach to DM1. Here we identify two miRNAs, dme-miR-277 and dme-miR-304, that differentially regulate muscleblind RNA isoforms in miRNA sensor constructs. We also show that their sequestration by sponge constructs derepresses endogenous muscleblind not only in a wild type background but also in a DM1 Drosophila model expressing non-coding CUG trinucleotide repeats throughout the musculature. Enhanced muscleblind expression resulted in significant rescue of pathological phenotypes, including reversal of several mis-splicing events and reduced muscle atrophy in DM1 adult flies. Rescued flies had improved muscle function in climbing and flight assays, and had longer lifespan compared to disease controls. These studies provide proof of concept for a similar potentially therapeutic approach to DM1 in humans.
Interaction of benzo[a]pyrene diol epoxide isomers with human serum albumin: Site specific characterisation of adducts and associated kinetics
Authors: Motwani Hitesh V. , Westberg Emelie , Törnqvist Margareta 
Published: November 2016

AbstractCarcinogenicity of benzo[a]pyrene {B[a]P, a polycyclic aromatic hydrocarbon (PAH)} involves DNA-modification by B[a]P diol epoxide (BPDE) metabolites. Adducts to serum albumin (SA) are not repaired, unlike DNA adducts, and therefore considered advantageous in assessment of in vivo dose of BPDEs. In the present work, kinetic experiments were performed in relation to the dose (i.e. concentration over time) of different BPDE isomers, where human SA (hSA) was incubated with respective BPDEs under physiological conditions. A liquid chromatography (LC) tandem mass spectrometry methodology was employed for characterising respective BPDE-adducts at histidine and lysine. This strategy allowed to structurally distinguish between the adducts from racemic anti- and syn-BPDE and between (+)- and (−)-anti-BPDE, which has not been attained earlier. The adduct levels quantified by LC-UV and the estimated rate of disappearance of BPDEs in presence of hSA gave an insight into the reactivity of the diol epoxides towards the N-sites on SA. The structure specific method and dosimetry described in this work could be used for accurate estimation of in vivo dose of the BPDEs following exposure to B[a]P, primarily in dose response studies of genotoxicity, e.g. in mice, to aid in quantitative risk assessment of PAHs.