bluuebunny/crossref_metadata_2025_split huggingface dataset:
A roadmap of strain in doped anatase TiO2
Authors: Kelaidis N. , Kordatos A. , Christopoulos S.-R. G. , Chroneos A. 
Published: August 2018

AbstractAnatase titanium oxide is important for its high chemical stability and photocatalytic properties, however, the latter are plagued by its large band gap that limits its activity to only a small percentage of the solar spectrum. In that respect, straining the material can reduce its band gap increasing the photocatalytic activity of titanium oxide. We apply density functional theory with the introduction of the Hubbard + U model, to investigate the impact of stress on the electronic structure of anatase in conjunction with defect engineering by intrinsic defects (oxygen/titanium vacancies and interstitials), metallic dopants (iron, chromium) and non-metallic dopants (carbon, nitrogen). Here we show that both biaxial and uniaxial strain can reduce the band gap of undoped anatase with the use of biaxial strain being marginally more beneficial reducing the band gap up to 2.96 eV at a tensile stress of 8 GPa. Biaxial tensile stress in parallel with doping results in reduction of the band gap but also in the introduction of states deep inside the band gap mainly for interstitially doped anatase. Dopants in substitutional positions show reduced deep level traps. Chromium-doped anatase at a tensile stress of 8 GPa shows the most significant reduction of the band gap as the band gap reaches 2.4 eV.
Integrative epigenomic analysis in differentiated human primary bronchial epithelial cells exposed to cigarette smoke
Authors: Glass Kimberly , Thibault Derek , Guo Feng , Mitchel Jennifer A. , Pham Betty , Qiu Weiliang , Li Yan , Jiang Zhiqiang , Castaldi Peter J. , Silverman Edwin K. , Raby Benjamin , Park Jin-Ah , Yuan Guo-Cheng , Zhou Xiaobo 
Published: August 2018

AbstractCigarette smoke (CS) is one of the major risk factors for many pulmonary diseases, including chronic obstructive pulmonary disease (COPD) and lung cancer. The first line of defense for CS exposure is the bronchial epithelial cells. Elucidation of the epigenetic changes during CS exposure is key to gaining a mechanistic understanding into how mature and differentiated bronchial epithelial cells respond to CS. Therefore, we performed epigenomic profiling in conjunction with transcriptional profiling in well-differentiated human bronchial epithelial (HBE) cells cultured in air-liquid interface (ALI) exposed to the vapor phase of CS. The genome-wide enrichment of histone 3 lysine 27 acetylation was detected by chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq) in HBE cells and suggested the plausible binding of specific transcription factors related to CS exposure. Additionally, interrogation of ChIP-Seq data with gene expression profiling of HBE cells after CS exposure for different durations (3 hours, 2 days, 4 days) suggested that earlier epigenetic changes (3 hours after CS exposure) may be associated with later gene expression changes induced by CS exposure (4 days). The integration of epigenetics and gene expression data revealed signaling pathways related to CS-induced epigenetic changes in HBE cells that may identify novel regulatory pathways related to CS-induced COPD.
PR-LncRNA signature regulates glioma cell activity through expression of SOX factors
Authors: Torres-Bayona Sergio , Aldaz Paula , Auzmendi-Iriarte Jaione , Saenz-Antoñanzas Ander , Garcia Idoia , Arrazola Mariano , Gerovska Daniela , Undabeitia Jose , Querejeta Arrate , Egaña Larraitz , Villanúa Jorge , Ruiz Irune , Sarasqueta Cristina , Urculo Enrique , Araúzo-Bravo Marcos J. , Huarte Maite , Samprón Nicolas , Matheu Ander 
Published: August 2018

AbstractLong non-coding RNAs (LncRNAs) have emerged as a relevant class of genome regulators involved in a broad range of biological processes and with important roles in tumor initiation and malignant progression. We have previously identified a p53-regulated tumor suppressor signature of LncRNAs (PR-LncRNAs) in colorectal cancer. Our aim was to identify the expression and function of this signature in gliomas. We found that the expression of the four PR-LncRNAs tested was high in human low-grade glioma samples and diminished with increasing grade of disease, being the lowest in glioblastoma samples. Functional assays demonstrated that PR-LncRNA silencing increased glioma cell proliferation and oncosphere formation. Mechanistically, we found an inverse correlation between PR-LncRNA expression and SOX1, SOX2 and SOX9 stem cell factors in human glioma biopsies and in glioma cells in vitro. Moreover, knock-down of SOX activity abolished the effect of PR-LncRNA silencing in glioma cell activity. In conclusion, our results demonstrate that the expression and function of PR-LncRNAs are significantly altered in gliomagenesis and that their activity is mediated by SOX factors. These results may provide important insights into the mechanisms responsible for glioblastoma pathogenesis.
Mutant KLF1 in Adult Anemic Nan Mice Leads to Profound Transcriptome Changes and Disordered Erythropoiesis
Authors: Nébor Danitza , Graber Joel H. , Ciciotte Steven L. , Robledo Raymond F. , Papoin Julien , Hartman Emily , Gillinder Kevin R. , Perkins Andrew C. , Bieker James J. , Blanc Lionel , Peters Luanne L. 
Published: August 2018

AbstractAnemic Nan mice carry a mutation (E339D) in the second zinc finger of erythroid transcription factor KLF1. Nan-KLF1 fails to bind a subset of normal KLF1 targets and ectopically binds a large set of genes not normally engaged by KLF1, resulting in a corrupted fetal liver transcriptome. Here, we performed RNAseq using flow cytometric-sorted spleen erythroid precursors from adult Nan and WT littermates rendered anemic by phlebotomy to identify global transcriptome changes specific to the Nan Klf1 mutation as opposed to anemia generally. Mutant Nan-KLF1 leads to extensive and progressive transcriptome corruption in adult spleen erythroid precursors such that stress erythropoiesis is severely compromised. Terminal erythroid differentiation is defective in the bone marrow as well. Principle component analysis reveals two major patterns of differential gene expression predicting that defects in basic cellular processes including translation, cell cycle, and DNA repair could contribute to disordered erythropoiesis and anemia in Nan. Significant erythroid precursor stage specific changes were identified in some of these processes in Nan. Remarkably, however, despite expression changes in large numbers of associated genes, most basic cellular processes were intact in Nan indicating that developing red cells display significant physiological resiliency and establish new homeostatic set points in vivo.
K+ binding and proton redistribution in the E2P state of the H+, K+-ATPase
Authors: Dubey Vikas , Han Minwoo , Kopec Wojciech , Solov’yov Ilia A. , Abe Kazuhiro , Khandelia Himanshu 
Published: August 2018

AbstractThe H+, K+-ATPase (HKA) uses ATP to pump protons into the gastric lumen against a million-fold proton concentration gradient while counter-transporting K+ from the lumen. The mechanism of release of a proton into a highly acidic stomach environment, and the subsequent binding of a K+ ion necessitates a network of protonable residues and dynamically changing protonation states in the cation binding pocket dominated by five acidic amino acid residues E343, E795, E820, D824, and D942. We perform molecular dynamics simulations of spontaneous K+ binding to all possible protonation combinations of the acidic amino acids and carry out free energy calculations to determine the optimal protonation state of the luminal-open E2P state of the pump which is ready to bind luminal K+. A dynamic pKa correlation analysis reveals the likelihood of proton transfer events within the cation binding pocket. In agreement with in-vitro measurements, we find that E795 is likely to be protonated, and that E820 is at the center of the proton transfer network in the luminal-open E2P state. The acidic residues D942 and D824 are likely to remain protonated, and the proton redistribution occurs predominantly amongst the glutamate residues exposed to the lumen. The analysis also shows that a lower number of K+ ions bind at lower pH, modeled by a higher number of protons in the cation binding pocket, in agreement with the ‘transport stoichiometry variation’ hypothesis.
RNAm expression profile of cancer marker genes in HepG2 cells treated with different concentrations of a new indolin-3-one from Pseudomonas aeruginosa
Authors: Benicio Lucas Milanez , Simionato Ane Stefano , Novello Cláudio Roberto , Guimarães Jeconias Rocha , Felicidade Ingrid , de Oliveira Admilton Gonçalves , de Mello João Carlos Palazzo , Mantovani Mário Sérgio , Chryssafidis Andreas Lazaros , Andrade Galdino , de Syllos Colus Ilce Mara , de Oliveira Marcelo Tempesta 
Published: August 2018

AbstractThe present study tested the effects of a newly identified indolin-3-one compound (compound 1), produced by Pseudomonas aeruginosa, on HepG2 cells. The MTT assays demonstrated decreased metabolic activities in HepG2 cells treated with compound 1, with dose- and time-dependent intensifying effect, starting at a concentration of 40 µM. The IC50 after 24, 48, 72, and 96 h treatments were 41.35, 52.7, 92.79 and 66.65 μM of compound 1, respectively. Below 80 µM, no significative damage on erythrocytes membranes was observed by the hemolytic assays. The RT-qPCR revealed that the compound modulated key genes involved in carcinogenesis process, indicating possible indolin-3-one mechanisms of action. The data showed that gene expression alterations promoted by compound 1, in concentrations up to 60 μM after 48 h, led to a decrease in cellular progression and there was no direct cellular damage. In addition, non-cytotoxic concentrations of compound 1 halved the concentration of the chemotherapeutic doxorubicin, maintaining similar therapeutic effect against HepG2 cells. The novelty of the molecule and the biological activities observed in the present study emphasize the potential of the compound 1 in cancer therapy research.
PSD-95-nNOS Coupling Regulates Contextual Fear Extinction in the Dorsal CA3
Authors: Cai Cheng-Yun , Chen Chen , Zhou Ying , Han Zhou , Qin Cheng , Cao Bo , Tao Yan , Bian Xin-Lan , Lin Yu-Hui , Chang Lei , Wu Hai-Yin , Luo Chun-Xia , Zhu Dong-Ya 
Published: August 2018

AbstractFear extinction depends on N-methyl-D-aspartate glutamate receptors (NMDARs) and brain-derived neurotrophic factor (BDNF) activation in the limbic system. However, postsynaptic density-95 (PSD-95) and neuronal nitric oxide synthase (nNOS) coupling, the downstream signaling of NMDARs activation, obstructs the BDNF signaling transduction. Thus, we wondered distinct roles of NMDAR activation and PSD-95-nNOS coupling on fear extinction. To explore the mechanisms, we detected protein-protein interaction using coimmunoprecipitation and measured protein expression by western blot. Contextual fear extinction induced a shift from PSD-95-nNOS to PSD-95-TrkB association in the dorsal hippocampus and c-Fos expression in the dorsal CA3. Disrupting PSD-95-nNOS coupling in the dorsal CA3 up-regulated phosphorylation of extracellular signal-regulates kinase (ERK) and BDNF, enhanced the association of BDNF-TrkB signaling with PSD-95, and promoted contextual fear extinction. Conversely, blocking NMDARs in the dorsal CA3 down-regulated BDNF expression and hindered contextual fear extinction. NMDARs activation and PSD-95-nNOS coupling play different roles in modulating contextual fear extinction in the hippocampus. Because inhibitors of PSD-95-nNOS interaction produce antidepressant and anxiolytic effect without NMDAR-induced side effects, PSD-95-nNOS could be a valuable target for PTSD treatment.
Event-related potentials of automatic imitation are modulated by ethnicity during stimulus processing, but not during motor execution
Authors: Rauchbauer Birgit , Pfabigan Daniela M. , Lamm Claus 
Published: August 2018

AbstractThis study investigated neural processes underlying automatic imitation and its modulation by ethnically diverse hand stimuli (Black, White) using event-related brain potentials (ERPs). Automatic imitation relies on motor stimulus-response compatibility (SRC), i.e., response conflict caused by motoric (in)congruency between task-irrelevant hand stimuli and the required response. Our novel task aimed to separate two distinct neuro-cognitive processing stages of automatic imitation and its modulation by ethnicity: the stage of stimulus processing (i.e. perception), comprising presentation of stimulus ethnicity and SRC, and the stage of response execution (i.e. action). Effects of ethnicity were observed in ERPs of different stages of stimulus processing - during presentation of ethnicity (LPP) and SRC (N190, P3). ERPs at response execution, Pre-Motion Positivity (PMP) and Reafferent Potential (RAP), were only sensitive to congruency. The N190 results may index visual self-other distinction, while the neural timecourse of P3 and PMP variation could reflect a dynamical decision process linking perception to action, with motor initiation reflected in the PMP component. The PMP might further index motor-related self-other distinction regardless of ethnicity. Importantly, overt motor execution was not influenced by ethnically diverse stimuli, which suggests generalizability of the automatic imitation effect across ethnicities.
Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions
Authors: Crespo-Piazuelo Daniel , Estellé Jordi , Revilla Manuel , Criado-Mesas Lourdes , Ramayo-Caldas Yuliaxis , Óvilo Cristina , Fernández Ana I. , Ballester Maria , Folch Josep M. 
Published: August 2018

AbstractIn addition to its value in meat production, the pig is an interesting animal model for human digestive tract studies due to its physiological similarities. The aim of this study was to describe the microbiome composition, distribution and interaction along the Iberian pig intestinal tract and its role in whole-body energy homeostasis. The V3-V4 region of the 16S rRNA gene was amplified and sequenced from the microbiomes of five gut sections (duodenum, jejunum, ileum, and proximal and distal colon) in thirteen castrated male pigs. A total of 1,669 operational taxonomic units distributed in 179 genera were found among all samples. The two most abundant genera in the small intestine wereLactobacillusandClostridium, whilePrevotellawas predominant in the colon. The colon samples were more similar among the pigs and richer in species than the small intestine samples were. In the small intestine, the metagenome prediction pointed to rapid internalization and conversion of the available simple carbohydrates for microbial proliferation and maintenance. In the colon, a competition among anaerobic bacteria for plant polysaccharide degradation to produce short chain fatty acids was found. This study confirms that the energy pathways of the gut microbiome differ along its sections and provides a description of the correlations between genera.
Targeted next-generation sequencing-based molecular diagnosis of congenital hand malformations in Chinese population
Authors: Qin Litao , Lou Guiyu , Guo Liangjie , Zhang Yuwei , Wang Hongdan , Wang Li , Hou Qiaofang , Liu Hongyan , Li Xichuan , Liao Shixiu 
Published: August 2018

AbstractCongenital hand malformations is rare and characterized by hand deformities. It is highly heterogeneous, both clinically and genetically, which complicates the identification of causative genes and mutations. Recently, targeted next-generation (NGS) sequencing has been successfully used for the detection of heterogeneous diseases, and the use of NGS also has contributed significantly in evaluating the etiology of heterogeneous disease. Here, we employed targeted NGS to screen 248 genes involved in genetic skeletal disorders, including congenital hand malformations. Three pathogenic mutations located in the GJA1, ROR2 and TBX5 genes were detected in three large Chinese families with congenital hand malformations. Two novel mutations were reported, and a known causative mutation was verified in this Chinese population. This is also the first report that the same panel of targeted NGS was employed to perform molecular diagnosis of different subtypes of congenital hand malformations. Our study supported the application of a targeted NGS panel as an effective tool to detect the genetic cause for heterogeneous diseases in clinical diagnosis.
A versatile open-source analysis of the limiting efficiency of photo electrochemical water-splitting
Authors: Holmes-Gentle Isaac , Hellgardt Klaus 
Published: August 2018

AbstractUnderstanding the fundamental thermodynamic limits of photo-electrochemical (PEC) water splitting is of great scientific and practical importance. In this work, a ‘detailed balance’ type model of solar quantum energy converters and non-linear circuit analysis is used to calculate the thermodynamic limiting efficiency of various configurations of PEC design. This model is released as freely accessible open-source (GNU GPL v3) code written in MATLAB with a graphical user interface (GUI). The capabilities of the model are demonstrated by simulating selected permutations of PEC design and results are validated against previous literature. This tool will enable solar fuel researchers to easily compare experimental results to theoretical limits to assess its realised performance using the GUI. Furthermore, the code itself is intended to be extendable and so can be modified to include non-ideal losses such as the over-potential required or complex optical phenomena.
Phase Modulators Based on High Mobility Ambipolar ReSe2 Field-Effect Transistors
Authors: Pradhan Nihar R. , Garcia Carlos , Isenberg Bridget , Rhodes Daniel , Feng Simin , Memaran Shahriar , Xin Yan , McCreary Amber , Walker Angela R. Hight , Raeliarijaona Aldo , Terrones Humberto , Terrones Mauricio , McGill Stephen , Balicas Luis 
Published: August 2018

AbstractWe fabricated ambipolar field-effect transistors (FETs) from multi-layered triclinic ReSe2, mechanically exfoliated onto a SiO2 layer grown on p-doped Si. In contrast to previous reports on thin layers (~2 to 3 layers), we extract field-effect carrier mobilities in excess of 102 cm2/Vs at room temperature in crystals with nearly ~10 atomic layers. These thicker FETs also show nearly zero threshold gate voltage for conduction and high ON to OFF current ratios when compared to the FETs built from thinner layers. We also demonstrate that it is possible to utilize this ambipolarity to fabricate logical elements or digital synthesizers. For instance, we demonstrate that one can produce simple, gate-voltage tunable phase modulators with the ability to shift the phase of the input signal by either 90° or nearly 180°. Given that it is possible to engineer these same elements with improved architectures, for example on h-BN in order to decrease the threshold gate voltage and increase the carrier mobilities, it is possible to improve their characteristics in order to engineer ultra-thin layered logic elements based on ReSe2.
Polyphenols (S3) Isolated from Cone Scales of Pinus koraiensis Alleviate Decreased Bone Formation in Rat under Simulated Microgravity
Authors: Diao Yan , Chen Bin , Wei Lijun , Wang Zhenyu 
Published: August 2018

AbstractIn order to screen out an effective bone loss protectant from natural plant polyphenol and to elucidate the mechanism of the plant polyphenols that alleviate bone loss under simulated microgravity, the proliferation activities of 9 total polyphenol extracts from natural product (TPENP) on osteoblasts were measured. Polyphenols (S3) was isolated from total polyphenols of cone scales from pinus koraiensis (Korean pine). ALP activity in osteoblasts and MDA level in femur were measured. Mechanical properties and microstructure of the distal cancellous region of the femur in rat were tested. Various bone metabolism markers, enzymes activity and genes expression were also analyzed. The results showed that S3 has the highest activity of osteoblast proliferation. S3 promoted ALP activity in osteoblasts, enhanced mechanical properties and microstructure of the distal cancellous region of femur in rat, decreased MDA level, elevated the serum concentration of BALP, PINP and activities of SOD, CAT, GSH-Px in femur under simulated microgravity. In addition, S3 enhanced the expression of NRF-2, β-catenin, p-GSK3-β, OSX, RUNX2, Osteonectin, Osteocalcin, ALP and collagen I. These results indicated that S3 can alleviated bone loss induced by simulated microgravity through abate the inhibition of the oxidative stress on Wnt/β-catenin signaling pathway.
High-pressure Raman scattering in bulk HfS2: comparison of density functional theory methods in layered MS2 compounds (M = Hf, Mo) under compression
Authors: Ibáñez J. , Woźniak T. , Dybala F. , Oliva R. , Hernández S. , Kudrawiec R. 
Published: August 2018

AbstractWe report high-pressure Raman-scattering measurements on the transition-metal dichalcogenide (TMDC) compound HfS2. The aim of this work is twofold: (i) to investigate the high-pressure behavior of the zone-center optical phonon modes of HfS2 and experimentally determine the linear pressure coefficients and mode Grüneisen parameters of this material; (ii) to test the validity of different density functional theory (DFT) approaches in order to predict the lattice-dynamical properties of HfS2 under pressure. For this purpose, the experimental results are compared with the results of DFT calculations performed with different functionals, with and without Van der Waals (vdW) interaction. We find that DFT calculations within the generalized gradient approximation (GGA) properly describe the high-pressure lattice dynamics of HfS2 when vdW interactions are taken into account. In contrast, we show that DFT within the local density approximation (LDA), which is widely used to predict structural and vibrational properties at ambient conditions in 2D compounds, fails to reproduce the behavior of HfS2 under compression. Similar conclusions are reached in the case of MoS2. This suggests that large errors may be introduced if the compressibility and Grüneisen parameters of bulk TMDCs are calculated with bare DFT-LDA. Therefore, the validity of different approaches to calculate the structural and vibrational properties of bulk and few-layered vdW materials under compression should be carefully assessed.