bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome sequencing data and de novo draft assemblies for 66 teleost species
Authors: Malmstrøm Martin , Matschiner Michael , Tørresen Ole K. , Jakobsen Kjetill S. , Jentoft Sissel 
Published: January 2017

AbstractTeleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9–39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context. We further present a nuclear marker set used for phylogenetic inference and evaluate each gene tree in relation to the species tree to test for homogeneity in the phylogenetic signal. Collectively, these analyses illustrate the robustness of this highly diverse data set and enable extensive reuse of the selected phylogenetic markers and the genomic data in general. This data set covers all major teleost lineages and provides unprecedented opportunities for comparative studies of teleosts.
Unraveling the enhanced Oxygen Vacancy Formation in Complex Oxides during Annealing and Growth
Authors: Hensling Felix V. E. , Xu Chencheng , Gunkel Felix , Dittmann Regina 
Published: January 2017

AbstractThe reduction of oxides during annealing and growth in low pressure processes is a widely known problem. We hence investigate the influence of mere annealing and of growth in vacuum systems to shed light on the reasons behind the reduction of perovskites. When comparing the existing literature regarding the reduction of the perovskite model material SrTiO3 it is conspicuous that one finds different oxygen pressures required to achieve reduction for vacuum annealing and for chemically controlled reducing atmospheres. The unraveling of this discrepancy is of high interest for low pressure physical vapor depositions of thin films heterostructures to gain further understanding of the reduction of the SrTiO3. For thermal annealing, our results prove the attached measurement devices (mass spectrometer/ cold cathode gauge) to be primarily responsible for the reduction of SrTiO3 in the deposition chamber by shifting the thermodynamic equilibrium to a more reducing atmosphere. We investigated the impact of our findings on the pulsed laser deposition growth at low pressure for LaAlO3/SrTiO3. During deposition the reduction triggered by the presence of the laser plume dominates and the impact of the measurement devices plays a minor role. During post annealing a complete reoxidization of samples is inhibited by an insufficient supply of oxygen.
Apelin receptor homodimer-oligomers revealed by single-molecule imaging and novel G protein-dependent signaling
Authors: Cai Xin , Bai Bo , Zhang Rumin , Wang Chunmei , Chen Jing 
Published: January 2017

AbstractThe apelin receptor (APJ) belongs to family A of the G protein-coupled receptors (GPCRs) and is a potential pharmacotherapeutic target for heart failure, hypertension, and other cardiovascular diseases. There is evidence APJ heterodimerizes with other GPCRs; however, the existence of APJ homodimers and oligomers remains to be investigated. Here, we measured APJ monomer-homodimer-oligomer interconversion by monitoring APJ dynamically on cells and compared their proportions, spatial arrangement, and mobility using total internal reflection fluorescence microscopy, resonance energy transfer, and proximity biotinylation. In cells with <0.3 receptor particles/μm2, approximately 60% of APJ molecules were present as dimers or oligomers. APJ dimers were present on the cell surface in a dynamic equilibrium with constant formation and dissociation of receptor complexes. Furthermore, we applied interference peptides and MALDI-TOF mass spectrometry to confirm APJ homo-dimer and explore the dimer-interfaces. Peptides corresponding to transmembrane domain (TMD)1, 2, 3, and 4, but not TMD5, 6, and 7, disrupted APJ dimerization. APJ mutants in TMD1 and TMD2 also decreased bioluminescence resonance energy transfer of APJ dimer. APJ dimerization resulted in novel functional characteristics, such as a distinct G-protein binding profile and cell responses after agonist stimulation. Thus, dimerization may serve as a unique mechanism for fine-tuning APJ-mediated functions.
Perceived Stress and Colorectal Cancer Incidence: The Japan Collaborative Cohort Study
Authors: Kikuchi Norimasa , Nishiyama Takeshi , Sawada Takayuki , Wang Chaochen , Lin Yingsong , Watanabe Yoshiyuki , Tamakoshi Akiko , Kikuchi Shogo 
Published: January 2017

AbstractColorectal cancer is the third most common cancer worldwide, and many risk factors for colorectal cancer have been established. However, it remains uncertain whether psychological stress contributes to the onset of colorectal cancer. Therefore, we conducted a large-scale prospective cohort study to confirm the association between perceived stress and colorectal cancer incidence. We identified 680 cases of colon cancer and 330 cases of rectal cancer during a maximum of 21-year follow-up of 61,563 Japanese men and women. Cox regression analysis adjusted for potential confounders revealed a significant association of perceived stress with rectal cancer incidence but not with colon cancer incidence. This finding is partly consistent with that from only one previous study that addressed an association between perceived stress and the risk of colorectal cancer. However, studies on this topic are sparse and warrant further exploration.
Binding of N-methylscopolamine to the extracellular domain of muscarinic acetylcholine receptors
Authors: Jakubík Jan , Randáková Alena , Zimčík Pavel , El-Fakahany Esam E. , Doležal Vladimír 
Published: January 2017

AbstractInteraction of orthosteric ligands with extracellular domain was described at several aminergic G protein-coupled receptors, including muscarinic acetylcholine receptors. The orthosteric antagonists quinuclidinyl benzilate (QNB) and N-methylscopolamine (NMS) bind to the binding pocket of the muscarinic acetylcholine receptor formed by transmembrane α-helices. We show that high concentrations of either QNB or NMS slow down dissociation of their radiolabeled species from all five subtypes of muscarinic acetylcholine receptors, suggesting allosteric binding. The affinity of NMS at the allosteric site is in the micromolar range for all receptor subtypes. Using molecular modelling of the M2 receptor we found that E172 and E175 in the second extracellular loop and N419 in the third extracellular loop are involved in allosteric binding of NMS. Mutation of these amino acids to alanine decreased affinity of NMS for the allosteric binding site confirming results of molecular modelling. The allosteric binding site of NMS overlaps with the binding site of some allosteric, ectopic and bitopic ligands. Understanding of interactions of NMS at the allosteric binding site is essential for correct analysis of binding and action of these ligands.
Imbalance of Th17/Treg cells in pathogenesis of patients with human leukocyte antigen B27 associated acute anterior uveitis
Authors: Zhuang Zhenchao , Wang Yuqin , Zhu Gejing , Gu Yunfeng , Mao Liping , Hong Meng , Li Yali , Zheng Meiqin 
Published: January 2017

AbstractTh17 and regulatory T cells, involved in the pathogenesis of several autoimmune diseases, are new lineages of CD4+ T helper cells. However, the role of their imbalance in human leukocyte antigen B27-associated acute anterior uveitis has not been elucidated. In our study, the percentages of Th17 and Treg cells, their molecular markers and related factors in peripheral blood of patients and healthy controls were measured by flow cytometry, real-time RT-PCR and ELISA. We observed a remarkable increase of CD4+ and CD4+IL-17+ T cells in peripheral blood of patients compared to controls. The molecular markers and related factors of Th17 cell were also showed a distinct elevation. Interestingly, we observed an obvious decrease of CD4+CD25+Foxp3+ T cells and Foxp3 mRNA level in patients. The ratio of Th17/Treg in patients was dramatically higher than controls. Moreover, the ratio of Th17/Treg cells had a more significantly positive correlation with the disease activity score than Th17 cells whereas Treg cells had a negative correlation. Our findings demonstrated a distinct increase of Th17 cells and a significant decrease of Treg cells in patients compared to controls. The imbalance of Th17 and Treg cells may play a vital role in the pathogenesis of the disease.
Simple, Efficient and Controllable Synthesis of Iodo/Di-iodoarenes via Ipsoiododecarboxylation/Consecutive Iodination Strategy
Authors: Yang Yun , Zhang Lijuan , Deng Guo-Jun , Gong Hang 
Published: January 2017

AbstractA practical, efficient, and operationally simple strategy for the ipsoiododecarboxylation and di-iodination of aromatic carboxylic acids using the low-cost commercial reagent succinimide (NIS) as iodine source is reported. This iodination or di-iodination process can be easily controlled through reaction conditions, thereby providing corresponding iodination or di-iodination products with high yields. Furthermore, these two reactions can be easily scaled up to gram-scale by using palladium catalyst (0.66 mol%), which provides high isolated yield.
Reversible Martensitic Transformation under Low Magnetic Fields in Magnetic Shape Memory Alloys
Authors: Bruno N. M. , Wang S. , Karaman I. , Chumlyakov Y. I. 
Published: January 2017

AbstractMagnetic field-induced, reversible martensitic transformations in NiCoMnIn meta-magnetic shape memory alloys were studied under constant and varying mechanical loads to understand the role of coupled magneto-mechanical loading on the transformation characteristics and the magnetic field levels required for reversible phase transformations. The samples with two distinct microstructures were tested along the [001] austenite crystallographic direction using a custom designed magneto-thermo-mechanical characterization device while carefully controlling their thermodynamic states through isothermal constant stress and stress-varying magnetic field ramping. Measurements revealed that these meta-magnetic shape memory alloys were capable of generating entropy changes of 14 J kg−1 K−1 or 22 J kg −1 K−1, and corresponding magnetocaloric cooling with reversible shape changes as high as 5.6% under only 1.3 T, or 3 T applied magnetic fields, respectively. Thus, we demonstrate that this alloy is suitable as an active component in near room temperature devices, such as magnetocaloric regenerators, and that the field levels generated by permanent magnets can be sufficient to completely transform the alloy between its martensitic and austenitic states if the loading sequence developed, herein, is employed.
Improvement of thermoelectric properties and their correlations with electron effective mass in Cu1.98SxSe1−x
Authors: Zhao Lanling , Fei Frank Yun , Wang Jun , Wang Funing , Wang Chunlei , Li Jichao , Wang Jiyang , Cheng Zhenxiang , Dou Shixue , Wang Xiaolin 
Published: January 2017

AbstractSulphur doping effects on the crystal structures, thermoelectric properties, density-of-states, and effective mass in Cu1.98SxSe1−x were studied based on the electrical and thermal transport property measurements, and first-principles calculations. The X-ray diffraction patterns and Rietveld refinements indicate that room temperature Cu1.98SxSe1−x (x = 0, 0.02, 0.08, 0.16) and Cu1.98SxSe1−x (x = 0.8, 0.9, 1.0) have the same crystal structure as monoclinic-Cu2Se and orthorhombic-Cu2S, respectively. Sulphur doping can greatly enhance zT values when x is in the range of 0.8≤ × ≤1.0. Furthermore, all doped samples show stable thermoelectric compatibility factors over a broad temperature range from 700 to 1000 K, which could greatly benefit their practical applications. First-principles calculations indicate that both the electron density-of-sates and the effective mass for all the compounds exhibit non-monotonic sulphur doping dependence. It is concluded that the overall thermoelectric performance of the Cu1.98SxSe1−x system is mainly correlated with the electron effective mass and the density-of-states.
Corydalis edulis Maxim. Promotes Insulin Secretion via the Activation of Protein Kinase Cs (PKCs) in Mice and Pancreatic β Cells
Authors: Zheng Jiao , Zhao Yunfang , Lun Qixing , Song Yuelin , Shi Shepo , Gu Xiaopan , Pan Bo , Qu Changhai , Li Jun , Tu Pengfei 
Published: January 2017

AbstractCorydalis edulisMaxim., a widely grown plant in China, had been proposed for the treatment for type 2 diabetes mellitus. In this study, we found thatC. edulisextract (CE) is protective against diabetes in mice. The treatment of hyperglycemic and hyperlipidemic apolipoprotein E (ApoE)−/− mice with a high dose of CE reduced serum glucose by 28.84% and serum total cholesterol by 17.34% and increased insulin release. We also found that CE significantly enhanced insulin secretion in a glucose-independent manner in hamster pancreatic β cell (HIT-T15). Further investigation revealed that CE stimulated insulin exocytosis by a protein kinase C (PKC)-dependent signaling pathway and that CE selectively activated novel protein kinase Cs (nPKCs) and atypical PKCs (aPKCs) but not conventional PKCs (cPKCs) in HIT-T15 cells. To the best of our knowledge, our study is the first to identify the PKC pathway as a direct target and one of the major mechanisms underlying the antidiabetic effect of CE. Given the good insulinotropic effect of this herbal medicine, CE is a promising agent for the development of new drugs for treating diabetes.
MircoRNA-145 promotes activation of hepatic stellate cells via targeting krüppel-like factor 4
Authors: Men Ruoting , Wen Maoyao , Zhao Mingyue , Dan Xuelian , Yang Zongze , Wu Wenchao , Wang Maggie Haitian , Liu Xiaojing , Yang Li 
Published: January 2017

AbstractKrüppel-like Factor 4 (KLF4), a target gene of miR-145, can negatively regulate lung fibrosis. However, the potential role of KLF4 and miR-145 in hepatic stellate cells (HSCs) activation or in hepatic fibrosis keeps unclear. This study aims to characterize miR-145 and KLF4 in activated HSCs and liver cirrhotic, and the underlying molecular basis. miR-145 was significantly up-regulated, while KLF4 was dramatically down-regulated during the activation of rat primary HSCs and TGF-βtreated HSCs. Furthermore, miR-145 mimics induced and inhibition of miR-145 reduced α-SMA and COL-I expression in primary HSCs. Additionally, the mRNA and protein levels of KLF4 in the liver of cirrhotic patients and rats were significantly down-regulated. α-SMA and COL-I were increased after inhibition of KLF4 by specific shRNA in primary HSCs. Forced KLF4 expression led to a reduction of α-SMA and COL-I expression in HSCs. miR-145 promotes HSC activation and liver fibrosis by targeting KLF4.
Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes
Authors: Delrieu-Trottin Erwan , Mona Stefano , Maynard Jeffrey , Neglia Valentina , Veuille Michel , Planes Serge 
Published: January 2017

AbstractDespite the unique nature of endemic species, their origin and population history remain poorly studied. We investigated the population history of 28 coral reef fish species, close related, from the Gambier and Marquesas Islands, from five families, with range size varying from widespread to small-range endemic. We analyzed both mitochondrial and nuclear sequence data using neutrality test and Bayesian analysis (EBSP and ABC). We found evidence for demographic expansions for most species (24 of 28), irrespective of range size, reproduction strategy or archipelago. The timing of the expansions varied greatly among species, from 8,000 to 2,000,000 years ago. The typical hypothesis for reef fish that links population expansions to the Last Glacial Maximum fit for 14 of the 24 demographic expansions. We propose two evolutionary processes that could lead to expansions older than the LGM: (a) we are retrieving the signature of an old colonization process for widespread, large-range endemic and paleoendemic species or (b) speciation; the expansion reflects the birth of the species for neoendemic species. We show for the first time that the demographic histories of endemic and widespread reef fish are not distinctly different and suggest that a number of processes drive endemism.
Pirfenidone controls the feedback loop of the AT1R/p38 MAPK/renin-angiotensin system axis by regulating liver X receptor-α in myocardial infarction-induced cardiac fibrosis
Authors: Li Chunmei , Han Rui , Kang Le , Wang Jianping , Gao Yonglin , Li Yanshen , He Jie , Tian Jingwei 
Published: January 2017

AbstractPirfenidone (PFD), an anti-fibrotic small molecule drug, is used to treat fibrotic diseases, but its effects on myocardial infarction (MI)-induced cardiac fibrosis are unknown. The aim of this study was to determine the effects of PFD on MI-induced cardiac fibrosis and the possible underlying mechanisms in rats. After establishment of the model, animals were administered PFD by gavage for 4 weeks. During the development of MI-induced cardiac fibrosis, we found activation of a positive feedback loop between the angiotensin II type 1 receptor (AT1R)/phospho-p38 mitogen-activated protein kinase (p38 MAPK) pathway and renin-angiotensin system (RAS), which was accompanied by down-regulation of liver X receptor-α (LXR-α) expression. PFD attenuated body weight, heart weight, left ventricular weight, left ventricular systolic pressure, and ±dp/dtmax changes induced by MI, which were associated with a reduction in cardiac fibrosis, infarct size, and hydroxyproline concentration. Moreover, PFD inhibited the AT1R/p38 MAPK pathway, corrected the RAS imbalance [decreased angiotensin-converting enzyme (ACE), angiotensin II, and angiotensin II type 1 receptor expression, but increased ACE2 and angiotensin (1-7) activity and Mas expression] and strongly enhanced heart LXR-α expression. These results indicate that the cardioprotective effects of PFD may be due, in large part, to controlling the feedback loop of the AT1R/p38 MAPK/RAS axis by activation of LXR-α.
Transcriptomic basis for drought-resistance in Brassica napus L.
Authors: Wang Pei , Yang Cuiling , Chen Hao , Song Chunpeng , Zhang Xiao , Wang Daojie 
Published: January 2017

AbstractBased on transcriptomic data from four experimental settings with drought-resistant and drought-sensitive cultivars under drought and well-watered conditions, statistical analysis revealed three categories encompassing 169 highly differentially expressed genes (DEGs) in response to drought in Brassica napus L., including 37 drought-resistant cultivar-related genes, 35 drought-sensitive cultivar-related genes and 97 cultivar non-specific ones. We provide evidence that the identified DEGs were fairly uniformly distributed on different chromosomes and their expression patterns are variety specific. Except commonly enriched in response to various stimuli or stresses, different categories of DEGs show specific enrichment in certain biological processes or pathways, which indicated the possibility of functional differences among the three categories. Network analysis revealed relationships among the 169 DEGs, annotated biological processes and pathways. The 169 DEGs can be classified into different functional categories via preferred pathways or biological processes. Some pathways might simultaneously involve a large number of shared DEGs, and these pathways are likely to cross-talk and have overlapping biological functions. Several members of the identified DEGs fit to drought stress signal transduction pathway in Arabidopsis thaliana. Finally, quantitative real-time PCR validations confirmed the reproducibility of the RNA-seq data. These investigations are profitable for the improvement of crop varieties through transgenic engineering.
Switch from sexual to parthenogenetic reproduction in a zebra shark
Authors: Dudgeon Christine L. , Coulton Laura , Bone Ren , Ovenden Jennifer R. , Thomas Severine 
Published: January 2017

AbstractParthenogenesis is a natural form of asexual reproduction in which embryos develop in the absence of fertilisation. Most commonly found in plants and invertebrate organisms, an increasing number of vertebrate species have recently been reported employing this reproductive strategy. Here we use DNA genotyping to report the first demonstration of an intra-individual switch from sexual to parthenogenetic reproduction in a shark species, the zebra shark Stegostoma fasciatum. A co-housed, sexually produced daughter zebra shark also commenced parthenogenetic reproduction at the onset of maturity without any prior mating. The demonstration of parthenogenesis in these two conspecific individuals with different sexual histories provides further support that elasmobranch fishes may flexibly adapt their reproductive strategy to environmental circumstances.
Efficient generation of hPSC-derived midbrain dopaminergic neurons in a fully defined, scalable, 3D biomaterial platform
Authors: Adil Maroof M. , Rodrigues Gonçalo M. C. , Kulkarni Rishikesh U. , Rao Antara T. , Chernavsky Nicole E. , Miller Evan W. , Schaffer David V. 
Published: January 2017

AbstractPluripotent stem cells (PSCs) have major potential as an unlimited source of functional cells for many biomedical applications; however, the development of cell manufacturing systems to enable this promise faces many challenges. For example, there have been major recent advances in the generation of midbrain dopaminergic (mDA) neurons from stem cells for Parkinson’s Disease (PD) therapy; however, production of these cells typically involves undefined components and difficult to scale 2D culture formats. Here, we used a fully defined, 3D, thermoresponsive biomaterial platform to rapidly generate large numbers of action-potential firing mDA neurons after 25 days of differentiation (~40% tyrosine hydroxylase (TH) positive, maturing into 25% cells exhibiting mDA neuron-like spiking behavior). Importantly, mDA neurons generated in 3D exhibited a 30-fold increase in viability upon implantation into rat striatum compared to neurons generated on 2D, consistent with the elevated expression of survival markers FOXA2 and EN1 in 3D. A defined, scalable, and resource-efficient cell culture platform can thus rapidly generate high quality differentiated cells, both neurons and potentially other cell types, with strong potential to accelerate both basic and translational research.