bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stratification and therapeutic potential of PML in metastatic breast cancer
Authors: Martín-Martín Natalia , Piva Marco , Urosevic Jelena , Aldaz Paula , Sutherland James D. , Fernández-Ruiz Sonia , Arreal Leire , Torrano Verónica , Cortazar Ana R. , Planet Evarist , Guiu Marc , Radosevic-Robin Nina , Garcia Stephane , Macías Iratxe , Salvador Fernando , Domenici Giacomo , Rueda Oscar M. , Zabala-Letona Amaia , Arruabarrena-Aristorena Amaia , Zúñiga-García Patricia , Caro-Maldonado Alfredo , Valcárcel-Jiménez Lorea , Sánchez-Mosquera Pilar , Varela-Rey Marta , Martínez-Chantar Maria Luz , Anguita Juan , Ibrahim Yasir H. , Scaltriti Maurizio , Lawrie Charles H. , Aransay Ana M. , Iovanna Juan L. , Baselga Jose , Caldas Carlos , Barrio Rosa , Serra Violeta , dM Vivanco Maria , Matheu Ander , Gomis Roger R. , Carracedo Arkaitz 
Published: August 2016

AbstractPatient stratification has been instrumental for the success of targeted therapies in breast cancer. However, the molecular basis of metastatic breast cancer and its therapeutic vulnerabilities remain poorly understood. Here we show that PML is a novel target in aggressive breast cancer. The acquisition of aggressiveness and metastatic features in breast tumours is accompanied by the elevated PML expression and enhanced sensitivity to its inhibition. Interestingly, we find that STAT3 is responsible, at least in part, for the transcriptional upregulation of PML in breast cancer. Moreover, PML targeting hampers breast cancer initiation and metastatic seeding. Mechanistically, this biological activity relies on the regulation of the stem cell gene SOX9 through interaction of PML with its promoter region. Altogether, we identify a novel pathway sustaining breast cancer aggressiveness that can be therapeutically exploited in combination with PML-based stratification.
The aryl hydrocarbon receptor controls cyclin O to promote epithelial multiciliogenesis
Authors: Villa Matteo , Crotta Stefania , Dingwell Kevin S. , Hirst Elizabeth M. A. , Gialitakis Manolis , Ahlfors Helena , Smith James C. , Stockinger Brigitta , Wack Andreas 
Published: August 2016

AbstractEpithelia function as barriers against environmental insults and express the transcription factor aryl hydrocarbon receptor (AhR). However, AhR function in these tissues is unknown. Here we show that AhR regulates multiciliogenesis in both murine airway epithelia and in Xenopus laevis epidermis. In air-exposed airway epithelia, induction of factors required for multiciliogenesis, including cyclin O (Ccno) and Multicilin (Mcidas), is AhR dependent, and air exposure induces AhR binding to the Ccno promoter. Submersion and hypoxic conditions impede AhR-dependent Ccno induction. This is mediated by the persistence of Notch signalling, as Notch blockade renders multiciliogenesis and Ccno induction by AhR independent from air exposure. In contrast to Ccno induction, air exposure does not induce the canonical AhR target cytochrome P450 1a1 (Cyp1a1). Inversely, exposure to AhR ligands induces Cyp1a1 but not Ccno and impeded ciliogenesis. These data indicate that AhR involvement in detoxification of environmental pollutants may impede its physiological role, resulting in respiratory pathology.
Assessing the utility of autofluorescence-based pulmonary optical endomicroscopy to predict the malignant potential of solitary pulmonary nodules in humans
Authors: Seth Sohan , Akram Ahsan R. , McCool Paul , Westerfeld Jody , Wilson David , McLaughlin Stephen , Dhaliwal Kevin , Williams Christopher K. I. 
Published: August 2016

AbstractSolitary pulmonary nodules are common, often incidental findings on chest CT scans. The investigation of pulmonary nodules is time-consuming and often leads to protracted follow-up with ongoing radiological surveillance, however, clinical calculators that assess the risk of the nodule being malignant exist to help in the stratification of patients. Furthermore recent advances in interventional pulmonology include the ability to both navigate to nodules and also to perform autofluorescence endomicroscopy. In this study we assessed the efficacy of incorporating additional information from label-free fibre-based optical endomicrosopy of the nodule on assessing risk of malignancy. Using image analysis and machine learning approaches, we find that this information does not yield any gain in predictive performance in a cohort of patients. Further advances with pulmonary endomicroscopy will require the addition of molecular tracers to improve information from this procedure.
A novel transcription factor-like gene SbSDR1 acts as a molecular switch and confers salt and osmotic endurance to transgenic tobacco
Authors: Singh Vijay Kumar , Mishra Avinash , Haque Intesaful , Jha Bhavanath 
Published: August 2016

AbstractA salt- and drought-responsive novel geneSbSDR1is predominantly localised to the nucleus, up-regulated under abiotic stresses and is involved in the regulation of metabolic processes.SbSDR1 showed DNA-binding activity to genomic DNA, microarray analysis revealed the upregulation of host stress-responsive genes and the results suggest thatSbSDR1 acts as a transcription factor. Overexpression ofSbSDR1did not affect the growth and yield of transgenic plants in non-stress conditions. Moreover, the overexpression ofSbSDR1stimulates the growth of plants and enhances their physiological status by modulating the physiology and inhibiting the accumulation of reactive oxygen species under salt and osmotic stress. Transgenic plants that overexpressedSbSDR1had a higher relative water content, membrane integrity and concentration of proline and total soluble sugars, whereas they showed less electrolyte leakage and lipid peroxidation than wild type plants under stress conditions. In field conditions,SbSDR1plants recovered from stress-induced injuries and could complete their life cycle. This study suggests thatSbSDR1functions as a molecular switch and contributes to salt and osmotic tolerance at different growth stages. Overall,SbSDR1is a potential candidate to be used for engineering salt and drought tolerance in crops without adverse effects on growth and yield.
Missing gene identification using functional coherence scores
Authors: Chitale Meghana , Khan Ishita K. , Kihara Daisuke 
Published: August 2016

AbstractReconstructing metabolic and signaling pathways is an effective way of interpreting a genome sequence. A challenge in a pathway reconstruction is that often genes in a pathway cannot be easily found, reflecting current imperfect information of the target organism. In this work, we developed a new method for finding missing genes, which integrates multiple features, including gene expression, phylogenetic profile and function association scores. Particularly, for considering function association between candidate genes and neighboring proteins to the target missing gene in the network, we used Co-occurrence Association Score (CAS) and PubMed Association Score (PAS), which are designed for capturing functional coherence of proteins. We showed that adding CAS and PAS substantially improve the accuracy of identifying missing genes in the yeast enzyme-enzyme network compared to the cases when only the conventional features, gene expression, phylogenetic profile, were used. Finally, it was also demonstrated that the accuracy improves by considering indirect neighbors to the target enzyme position in the network using a proper network-topology-based weighting scheme.
Single-electron Spin Resonance in a Quadruple Quantum Dot
Authors: Otsuka Tomohiro , Nakajima Takashi , Delbecq Matthieu R. , Amaha Shinichi , Yoneda Jun , Takeda Kenta , Allison Giles , Ito Takumi , Sugawara Retsu , Noiri Akito , Ludwig Arne , Wieck Andreas D. , Tarucha Seigo 
Published: August 2016

AbstractElectron spins in semiconductor quantum dots are good candidates of quantum bits for quantum information processing. Basic operations of the qubit have been realized in recent years: initialization, manipulation of single spins, two qubit entanglement operations and readout. Now it becomes crucial to demonstrate scalability of this architecture by conducting spin operations on a scaled up system. Here, we demonstrate single-electron spin resonance in a quadruple quantum dot. A few-electron quadruple quantum dot is formed within a magnetic field gradient created by a micro-magnet. We oscillate the wave functions of the electrons in the quantum dots by applying microwave voltages and this induces electron spin resonance. The resonance energies of the four quantum dots are slightly different because of the stray field created by the micro-magnet and therefore frequency-resolved addressable control of each electron spin resonance is possible.
Tunable magnetism in metal adsorbed fluorinated nanoporous graphene
Authors: Kumar Pankaj , Sharma Vinit , Reboredo Fernando A. , Yang Li-Ming , Pushpa Raghani 
Published: August 2016

AbstractDeveloping nanostructures with tunable magnetic states is crucial for designing novel data storage and quantum information devices. Using density functional theory, we investigate the thermodynamic stability and magnetic properties of tungsten adsorbed tri-vacancy fluorinated (TVF) graphene. We demonstrate a strong structure-property relationship and its response to external stimuli via defect engineering in graphene-based materials. Complex interplay between defect states and the chemisorbed atom results in a large magnetic moment of 7 μB along with high in-plane magneto-crystalline anisotropy energy (MAE) of 17 meV. Under the influence of electric field, spin crossover effect accompanied by a change in the MAE is observed. The ascribed change in spin-configuration is caused by the modification of exchange coupling between defect states and a change in the occupation of d-orbitals of the metal complex. Our predictions open a promising way towards controlling the magnetic properties in graphene based spintronic and non-volatile memory devices.
Central chronic apelin infusion decreases energy expenditure and thermogenesis in mice
Authors: Drougard Anne , Fournel Audren , Marlin Alysson , Meunier Etienne , Abot Anne , Bautzova Tereza , Duparc Thibaut , Louche Katie , Batut Aurelie , Lucas Alexandre , Le-Gonidec Sophie , Lesage Jean , Fioramonti Xavier , Moro Cedric , Valet Philippe , Cani Patrice D. , Knauf Claude 
Published: August 2016

AbstractApelin is a bioactive peptide involved in the control of energy metabolism. In the hypothalamus, chronic exposure to high levels of apelin is associated with an increase in hepatic glucose production, and then contributes to the onset of type 2 diabetes. However, the molecular mechanisms behind deleterious effects of chronic apelin in the brain and consequences on energy expenditure and thermogenesis are currently unknown. We aimed to evaluate the effects of chronic intracerebroventricular (icv) infusion of apelin in normal mice on hypothalamic inflammatory gene expression, energy expenditure, thermogenesis and brown adipose tissue functions. We have shown that chronic icv infusion of apelin increases the expression of pro-inflammatory factors in the hypothalamus associated with an increase in plasma interleukin-1 beta. In parallel, mice infused with icv apelin exhibit a significant lower energy expenditure coupled to a decrease in PGC1alpha, PRDM16 and UCP1 expression in brown adipose tissue which could explain the alteration of thermogenesis in these mice. These data provide compelling evidence that central apelin contributes to the development of type 2 diabetes by altering energy expenditure, thermogenesis and fat browning.
Monolithic integration of room-temperature multifunctional BaTiO3-CoFe2O4 epitaxial heterostructures on Si(001)
Authors: Scigaj Mateusz , Dix Nico , Gázquez Jaume , Varela María , Fina Ignasi , Domingo Neus , Herranz Gervasi , Skumryev Vassil , Fontcuberta Josep , Sánchez Florencio 
Published: August 2016

AbstractThe multifunctional (ferromagnetic and ferroelectric) response at room temperature that is elusive in single phase multiferroic materials can be achieved in a proper combination of ferroelectric perovskites and ferrimagnetic spinel oxides in horizontal heterostructures. In this work, lead-free CoFe2O4/BaTiO3 bilayers are integrated with Si(001) using LaNiO3/CeO2/YSZ as a tri-layer buffer. They present structural and functional properties close to those achieved on perovskite substrates: the bilayers are fully epitaxial with extremely flat surface and exhibit robust ferromagnetism and ferroelectricity at room temperature.
Magnetic-flux-driven topological quantum phase transition and manipulation of perfect edge states in graphene tube
Authors: Lin S. , Zhang G. , Li C. , Song Z. 
Published: August 2016

AbstractWe study the tight-binding model for a graphene tube with perimeter N threaded by a magnetic field. We show exactly that this model has different nontrivial topological phases as the flux changes. The winding number, as an indicator of topological quantum phase transition (QPT) fixes at N/3 if N/3 equals to its integer part [N/3], otherwise it jumps between [N/3] and [N/3] + 1 periodically as the flux varies a flux quantum. For an open tube with zigzag boundary condition, exact edge states are obtained. There exist two perfect midgap edge states, in which the particle is completely located at the boundary, even for a tube with finite length. The threading flux can be employed to control the quantum states: transferring the perfect edge state from one end to the other, or generating maximal entanglement between them.
Tyrosine phosphorylation and protein degradation control the transcriptional activity of WRKY involved in benzylisoquinoline alkaloid biosynthesis
Authors: Yamada Yasuyuki , Sato Fumihiko 
Published: August 2016

AbstractBenzylisoquinoline alkaloids (BIQ) are among the most structurally diverse and pharmaceutically valuable secondary metabolites. A plant-specific WRKY-type transcription factor, CjWRKY1, was isolated from Coptis japonica and identified as a transcriptional activator of BIQ biosynthesis. However, the expression of CjWRKY1 gene alone was not sufficient for the activation of genes encoding biosynthetic enzymes. Here, we report the importance of post-translational regulation of CjWRKY1 in BIQ biosynthesis. First, we detected the differential accumulation of CjWRKY1 protein in two cell lines with similar CjWRKY1 gene expression but different levels of accumulated alkaloids. Further investigation of the WRKY protein identified the phosphorylation of the WRKYGQK core domain at Y115. The CjWRKYY115E phosphorylation-mimic mutant showed loss of nuclear localization, DNA-binding activity and transactivation activity compared to wild-type CjWRKY1. Rapid degradation of the CjWRKY1 protein was also confirmed following treatment with inhibitors of the 26S proteasome and protease inhibitors. The existence of two independent degradation pathways as well as protein phosphorylation suggests the fine-tuning of CjWRKY1 activities is involved in the regulation of biosynthesis of BIQs.
Modulation of IL-6 induced RANKL expression in arthritic synovium by a transcription factor SOX5
Authors: Feng Xiaoke , Shi Yumeng , Xu Lingxiao , Peng Qiuyue , Wang Fang , Wang Xiaoxi , Sun Wei , Lu Yan , Tsao Betty P. , Zhang Miaojia , Tan Wenfeng 
Published: August 2016

AbstractReceptor activator of nuclear factor κB ligand (RANKL) is critically involved in bone erosion of rheumatoid arthritis (RA). We previously reported association between younger age at onset of RA and a RANKL promoter SNP that conferred an elevated promoter activity via binding to a transcription factor SOX5. Here we study the regulation of SOX5 levels in relation to RANKL expression in RA synovial fibroblasts (SF) and the development of bone erosion in the collagen-induced arthritis (CIA) mouse. Our data indicated SOX5 levels were higher in synovium and synovial fluid from RA compared to osteoarthritis patients. Pro-inflammatory cytokines upregulated SOX5 and RANKL expression in both primary RA SF and the rheumatoid synovial fibroblast cell line, MH7A. Overexpression of SOX5 resulted in significantly increased RANKL levels, while knockdown of SOX5 resulted in diminished IL-6 mediated RANKL upregulation in MH7A cells. Chromatin immunoprecipitation (ChIP) showed approximately 3-fold enrichment of RANKL-specific DNA in anti-SOX5 immunoprecipitate in IL-6 treated MH7A cells as compared to untreated cells. Locally silencing SOX5 gene significantly diminished RANKL positive cells and bone erosion in CIA mice. These findings suggest SOX5 is an important regulator of IL-6-induced RANKL expression in RA SF.
Analysis of Photoluminescence Thermal Quenching: Guidance for the Design of Highly Effective p-type Doping of Nitrides
Authors: Liu Zhiqiang , Huang Yang , Yi Xiaoyan , Fu Binglei , Yuan Guodong , Wang Junxi , Li Jinmin , Zhang Yong 
Published: August 2016

AbstractA contact-free diagnostic technique for examining position of the impurity energy level of p-type dopants in nitride semiconductors was proposed based on photoluminescence thermal quenching. The Mg ionization energy was extracted by the phenomenological rate-equation model we developed. The diagnostic technique and analysis model reported here are priorities for the design of highly effective p-doping of nitrides and could also be used to explain the abnormal and seldom analyzed low characteristic temperature T0 (about 100 K) of thermal quenching in p-type nitrides systems. An In-Mg co-doped GaN system is given as an example to prove the validity of our methods. Furthermore, a hole concentration as high as 1.94 × 1018 cm−3 was achieved through In-Mg co-doping, which is nearly one order of magnitude higher than typically obtained in our lab.
The Role of Prostate Apoptosis Response-4 (Par-4) in Mycobacterium tuberculosis Infected Macrophages
Authors: Han Ji-Ye , Lim Yun-Ji , Choi Ji-Ae , Lee Jung-hwan , Jo Sung-Hee , Oh Sung-Man , Song Chang-Hwa 
Published: August 2016

AbstractProstate apoptosis response-4 (Par-4) is a tumor suppressor protein that forms a complex with glucose-regulated protein 78 (GRP78) to induce apoptosis. Previously, we reported that ER stress-induced apoptosis is a critical host defense mechanism against Mycobacterium tuberculosis (Mtb). We sought to understand the role of Par-4 during ER stress-induced apoptosis in response to mycobacterial infection. Par-4 and GRP78 protein levels increased in response Mtb (strain: H37Ra) infection. Furthermore, Par-4 and GRP78 translocate to the surface of Mtb H37Ra-infected macrophages and induce apoptosis via caspase activation. NF-κB activation, Mtb-mediated ER stress, and Par-4 production were significantly diminished in macrophages with inhibited ROS production. To test Par-4 function during mycobacterial infection, we analyzed intracellular survival of Mtb H37Ra in macrophages with Par-4 overexpression or knockdown. Mtb H37Ra growth was significantly reduced in Par-4 overexpressing macrophages and increased in knockdown macrophages. We also observed increased Par-4, GRP78, and caspases activation in Bacillus Calmette-Guérin (BCG)-infected prostate cancer cells. Our data demonstrate that Par-4 is associated with ER stress-induced apoptosis resulting in reduced intracellular survival of mycobacteria. BCG treatment increases Par-4-dependent caspase activation in prostate cancer cells. These results suggest ER stress-induced Par-4 acts as an important defense mechanism against mycobacterial infection and regulates cancer.
Characterization of a novel low-temperature-active, alkaline and sucrose-tolerant invertase
Authors: Zhou Junpei , He Limei , Gao Yajie , Han Nanyu , Zhang Rui , Wu Qian , Li Junjun , Tang Xianghua , Xu Bo , Ding Junmei , Huang Zunxi 
Published: August 2016

AbstractA glycoside hydrolase family 32 invertase from Bacillus sp. HJ14 was expressed in Escherichia coli. The purified recombinant enzyme (rInvHJ14) showed typical biochemical properties of low-temperature-active and alkaline enzymes: (i) rInvHJ14 was active and stable in the range of pH 7.0–9.5 with an apparent pH optimum of 8.0; (ii) rInvHJ14 was most active but not stable at 30–32.5 °C, with 19.7, 48.2 and 82.1% of its maximum activity when assayed at 0, 10 and 20 °C, respectively and the Ea, ΔG* (30 °C), Km (30 °C) and kcat (30 °C) values for hydrolysis of sucrose by rInvHJ14 was 47.6 kJ mol−1, 57.6 kJ mol−1, 62.9 mM and 746.2 s−1, respectively. The enzyme also showed strong sucrose tolerance. rInvHJ14 preserved approximately 50% of its highest activity in the presence of 2045.0 mM sucrose. Furthermore, potential factors for low-temperature-active and alkaline adaptations of rInvHJ14 were presumed. Compared with more thermostable homologs, rInvHJ14 has a higher frequency of glycine residues and a longer loop but a lower frequency of proline residues (especially in a loop) in the catalytic domain. The catalytic pockets of acid invertases were almost negatively charged while that of alkaline rInvHJ14 was mostly positively charged.
Welding of silver nanowire networks via flash white light and UV-C irradiation for highly conductive and reliable transparent electrodes
Authors: Chung Wan-Ho , Kim Sang-Ho , Kim Hak-Sung 
Published: August 2016

AbstractIn this work, silver nanowire inks with hydroxypropyl methylcellulose (HPMC) binders were coated on polyethylene terephthalate (PET) substrates and welded via flash white light and ultraviolet C (UV-C) irradiation to produce highly conductive transparent electrodes. The coated silver nanowire films were firmly welded and embedded into PET substrate successfully at room temperature and under ambient conditions using an in-house flash white light welding system and UV-C irradiation. The effects of light irradiation conditions (light energy, irradiation time, pulse duration and pulse number) on the silver nanowire networks were studied and optimized. Bending fatigue tests were also conducted to characterize the reliability of the welded transparent conductive silver nanowire films. The surfaces of the welded silver nanowire films were analyzed via scanning electron microscopy (SEM), while the transmittance of the structures was measured using a spectrophotometer. From the results, a highly conductive and transparent silver nanowire film with excellent reliability could be achieved at room temperature under ambient conditions via the combined flash white light and UV-C irradiation welding process.
New route for hollow materials
Authors: Rivaldo-Gómez C. M. , Ferreira F. F. , Landi G. T. , Souza J. A. 
Published: August 2016

AbstractHollow micro/nano structures form an important family of functional materials. We have used the thermal oxidation process combined with the passage of electric current during a structural phase transition to disclose a colossal mass diffusion transfer of Ti ions. This combination points to a new route for fabrication of hollow materials. A structural phase transition at high temperature prepares the stage by giving mobility to Ti ions and releasing vacancies to the system. The electric current then drives an inward delocalization of vacancies, condensing into voids and finally turning into a big hollow. This strong physical phenomenon leading to a colossal mass transfer through ionic diffusion is suggested to be driven by a combination of phase transition and electrical current followed by chemical reaction. We show this phenomenon for Ti leading to TiO2 microtube formation, but we believe that it can be used to other metals undergoing structural phase transition at high temperatures.