bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of co-expression genes and integrative analysis of gene microarray and proteomics profile of Keshan disease
Authors: Wang Sen , Yan Rui , Wang Bin , Du Peiru , Tan Wuhong , Lammi Mikko J. , Guo Xiong 
Published: January 2018

AbstractKeshan disease (KD) is a kind of endemic cardiomyopathy which has a high mortality. However, molecular mechanism in the pathogenesis of KD remains poorly understood. Serum samples were collected from 112 KD patients and 112 normal controls. Gene microarray was used to screen differently expressed genes. Genevestigator was applied to forecast co-expression genes of significant gene. iTRAQ proteomics analysis was used to verify significant genes and their co-expression genes. GO, COG, IPA and STRING were applied to undertake function categorization, pathway and network analysis separately. We identified 32 differentially expressed genes; IDH2, FEM1A, SSPB1 and their respective 30 co-expression genes; 68 differential proteins in KD. Significant proteins were categorized into 23 biological processes, 16 molecular functions, 16 cellular components, 15 function classes, 13 KD pathways and 1 network. IDH2, FEM1A, SSBP1, CALR, NDUFS2, IDH3A, GAPDH, TCA Cycle II (Eukaryotic) pathway and NADP repair pathway may play important roles in the pathogenesis of KD.
COX-2 induces oncogenic micro RNA miR655 in human breast cancer
Authors: Majumder Mousumi , Dunn Leanna , Liu Ling , Hasan Asma , Vincent Krista , Brackstone Muriel , Hess David , Lala Peeyush K. 
Published: January 2018

AbstractWe show that Cyclooxygenase-2 over-expression induces an oncogenic microRNA miR655 in human breast cancer cells by activation of EP4. MiR655 expression positively correlated with COX-2 in genetically disparate breast cancer cell lines and increased in all cell lines when grown as spheroids, implicating its link with stem-like cells (SLCs). Ectopic miR655 over-expression in MCF7 and SKBR3 cells resulted in increased proliferation, migration, invasion, spheroid formation and Epithelial to Masenchymal transition (EMT). Conversely, knocking down miR655 in aggressive MCF7-COX2 and SKBR3-COX2 cells reverted these phenotypes. MCF7-miR655 cells displayed upregulated NOTCH/WNT genes; both pathway inhibitors abrogated miR655-induced spheroid formation, linking miR655 with SLC-related pathways. MiR655 expression was dependent on EP4 activity and EP4 downstream signaling pathways PI3K/AKT, ERK and NF-kB and led to TGFβ resistance for Smad3 phosphorylation. Tail vein injection of MCF7-miR655 and SKBR3-miR655 cells in NOD/SCID/GUSB-null mice revealed increased lung colony growth and micrometastases to liver and spleen. MiR655 expression was significantly high in human breast tumors (n = 105) compared to non-tumor tissues (n = 20) and associated with reduced patient survival. Thus miR655 could serve as a prognostic breast cancer biomarker.
Role of diffusion-weighted imaging in the discrimination of benign and metastatic parotid area lymph nodes in patients with nasopharyngeal carcinoma
Authors: Chen Chuanben , Lin Zhizhong , Xiao Youping , Bai Penggang , Yue Qiuyuan , Chen Yunbin , Chen Lisha 
Published: January 2018

AbstractTo assess the utility of apparent diffusion coefficient (ADC) determined on diffusion-weighted MR imaging (DWI) to differentiate between benign and malignant parotid area lymph nodes (PLN) in nasopharyngeal carcinoma (NPC) patients. Thirty-nine consecutive NPC patients with a total of 40 enlarged, biopsied PLNs underwent DWI examination. ADC values for benign and malignant PLNs were measured and compared. Receiver operating characteristic (ROC) curve analysis was to evaluate the optimal threshold level of ADC values for metastatic PLNs. The kappa was to assess the degree of agreement between histopathological diagnoses and ADC values, or imaging features of PLNs on MRI. We found the mean ADC value for benign PLNs was markedly higher than malignant PLNs. A threshold ADC of 1.01 × 10−3 mm2/s was associated with a sensitivity of 85.7% and a specificity of 72.7% (area under the curve: 0.84). A moderate agreement was observed between the histopathological diagnosis and the threshold of ADC value (k value: 0.483). However, short axis diameter, necrosis, extranodal extension, and regional grouping of PLNs on MRI showed only a fair agreement with the histopathological diagnosis (k value: 0.257, 0.305, 0.276, and 0.205, respectively). Therefore, DWI may be a promising technique to differentiate metastatic from benign PLNs.
Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture
Authors: Khan Nymul , Maezato Yukari , McClure Ryan S. , Brislawn Colin J. , Mobberley Jennifer M. , Isern Nancy , Chrisler William B. , Markillie Lye Meng , Barney Brett M. , Song Hyun-Seob , Nelson William C. , Bernstein Hans C. 
Published: January 2018

AbstractThe fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized – and confirmed – that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.
Synthesis of Wurtzite Cu2ZnSnS4 Nanosheets with Exposed High-Energy (002) Facets for Fabrication of Efficient Pt-Free Solar Cell Counter Electrodes
Authors: Zhang Xiaoyan , Xu You , Zhang Junjie , Dong Shuai , Shen Liming , Gupta Arunava , Bao Ningzhong 
Published: January 2018

AbstractTwo-dimensional (2D) semiconducting nanomaterials have generated much interest both because of fundamental scientific interest and technological applications arising from the unique properties in two dimensions. However, the colloidal synthesis of 2D quaternary chalcogenide nanomaterials remains a great challenge owing to the lack of intrinsic driving force for its anisotropic growth. 2D wurtzite Cu2ZnSnS4 nanosheets (CZTS-NS) with high-energy (002) facets have been obtained for the first time via a simple one-pot thermal decomposition method. The CZTS-NS exhibits superior photoelectrochemical activity as compared to zero-dimensional CZTS nanospheres and comparable performance to Pt counter electrode for dye sensitized solar cells. The improved catalytic activity can be attributed to additional reactive catalytic sites and higher catalytic reactivity in high-energy (002) facets of 2D CZTS-NS. This is in accordance with the density functional theory (DFT) calculations, which indicates that the (002) facets of wurtzite CZTS-NS possess higher surface energy and exhibits remarkable reducibility for I3− ions. The developed synthetic method and findings will be helpful for the design and synthesis of 2D semiconducting nanomaterials, especially eco-friendly copper chalcogenide nanocrystals for energy harvesting and photoelectric applications.
Probiotic activities of Rhizobium laguerreae on growth and quality of spinach
Authors: Jiménez-Gómez Alejandro , Flores-Félix José David , García-Fraile Paula , Mateos Pedro F. , Menéndez Esther , Velázquez Encarna , Rivas Raúl 
Published: January 2018

AbstractThe growing interest in a healthy lifestyle and in environmental protection is changing habits regarding food consumption and agricultural practices. Good agricultural practice is indispensable, particularly for raw vegetables, and can include the use of plant probiotic bacteria for the purpose of biofertilization. In this work we analysed the probiotic potential of the rhizobial strain PEPV40, identified as Rhizobium laguerreae through the analysis of the recA and atpD genes, on the growth of spinach plants. This strain presents several in vitro plant growth promotion mechanisms, such as phosphate solubilisation and the production of indole acetic acid and siderophores. The strain PEPV40 produces cellulose and forms biofilms on abiotic surfaces. GFP labelling of this strain showed that PEPV40 colonizes the roots of spinach plants, forming microcolonies typical of biofilm initiation. Inoculation with this strain significantly increases several vegetative parameters such as leaf number, size and weight, as well as chlorophyll and nitrogen contents. Therefore, our findings indicate, for the first time, that Rhizobium laguerreae is an excellent plant probiotic, which increases the yield and quality of spinach, a vegetable that is increasingly being consumed raw worldwide.
Spin-coupling-induced Improper Polarizations and Latent Magnetization in Multiferroic BiFeO3
Authors: Jang Hyun Myung , Han Hyeon , Lee Jung-Hoon 
Published: January 2018

AbstractMultiferroic BiFeO3 (BFO) that exhibits a gigantic off-centering polarization (OCP) is the most extensively studied material among all multiferroics. In addition to this gigantic OCP, the BFO having R3c structural symmetry is expected to exhibit a couple of parasitic improper polarizations owing to coexisting spin-polarization coupling mechanisms. However, these improper polarizations are not yet theoretically quantified. Herein, we show that there exist two distinct spin-coupling-induced improper polarizations in the R3c BFO on the basis of the Landau-Lifshitz-Ginzburg theory: ΔP
LF
arising from the Lifshitz gradient coupling in a cycloidal spin-density wave, and ΔP
ms
originating from the biquadratic magnetostrictive interaction. With the help of ab initio calculations, we have numerically evaluated magnitudes of these improper polarizations, in addition to the estimate of all three relevant coupling constants. We further predict that the magnetic susceptibility increases substantially upon the transition from the bulk R3c BFO to the homogeneous canted spin state in a constrained epitaxial film, which satisfactorily accounts for the experimental observation. The present study will help us understand the magnetoelectric coupling and shed light on design of BFO-based materials with improved multiferroic properties.
Transfer of a bla
CTX-M-1-carrying plasmid between different Escherichia coli strains within the human gut explored by whole genome sequencing analyses
Authors: Knudsen Per Kristian , Gammelsrud Karianne Wiger , Alfsnes Kristian , Steinbakk Martin , Abrahamsen Tore G. , Müller Fredrik , Bohlin Jon 
Published: January 2018

AbstractHorizontal transfer of antibiotic resistance determinants contributes to dissemination of antibiotic resistance. Such transfer of resistance genes within the human gut has been documented in some in vivo studies. The present study investigated seven blaCTX-M-1-carrying Escherichia coli isolates from three consecutive faecal samples collected from one cystic fibrosis patient in a nine-months period, by analysing whole genome sequencing data. The analyses showed that the seven E. coli isolates represented three genetically diverse strains. All isolates contained blaCTX-M-1-carrying Incl1 plasmids that shared a common 101 kb backbone differing by only four SNPs. The plasmids harboured by the three different E. coli strains varied within limited regions suggestive of recombination events, according to the phylogenetic topology of the genomes of the isolates harbouring them. The findings strongly suggest that horizontal transfer of a blaCTX-M-1-carrying plasmid had occurred within the patient´s gut. The study illustrates the within-host diversity of faecally carried resistant E. coli isolates and highlights the value of collecting multiple bacterial colonies from longitudinally collected samples to assess faecal carriage of resistant enterobacteria. The clustering of the plasmids with the corresponding E. coli strains carrying them indicates that the plasmids appear to have adapted to their respective E. coli hosts.
Respiratory Syncytial Virus Infection Changes Cargo Composition of Exosome Released from Airway Epithelial Cells
Authors: Chahar Harendra Singh , Corsello Tiziana , Kudlicki Andrzej S. , Komaravelli Narayana , Casola Antonella 
Published: January 2018

AbstractExosomes are microvesicles known to carry biologically active molecules, including RNA, DNA and proteins. Viral infections can induce profound changes in exosome composition, and exosomes have been implicated in viral transmission and pathogenesis. No information is current available regarding exosome composition and function during infection with Respiratory Syncytial Virus (RSV), the most important cause of lower respiratory tract infections in children. In this study, we characterized exosomes released from RSV-infected lung carcinoma-derived A549 cells. RNA deep sequencing revealed that RSV exosomes contain a diverse range of RNA species like messenger and ribosomal RNA fragments, as well as small noncoding RNAs, in a proportion different from exosomes isolated from mock-infected cells. We observed that both RNA and protein signatures of RSV were present in exosomes, however, they were not able to establish productive infection in uninfected cells. Exosomes isolated from RSV-infected cells were able to activate innate immune response by inducing cytokine and chemokine release from human monocytes and airway epithelial cells. These data suggest that exosomes may play an important role in pathogenesis or protection against disease, therefore understating their role in RSV infection may open new avenues for target identification and development of novel therapeutics.
Analysis of Combined Transcriptomes Identifies Gene Modules that Differentially Respond to Pathogenic Stimulation of Vascular Smooth Muscle and Endothelial Cells
Authors: Pan Xiaokang , Wang Bowen , Yuan Tiezheng , Zhang Mengxue , Kent K. Craig , Guo Lian-Wang 
Published: January 2018

AbstractSmooth muscle cells (SMCs) and endothelial cells (ECs) are vital cell types composing the vascular medial wall and the atheroprotective inner lining, respectively. Current treatments for cardiovascular disease inhibit SMC hyperplasia but compromise EC integrity, predisposing patients to thrombosis. Therapeutics targeting SMCs without collateral damage to ECs are highly desirable. However, differential (SMC versus EC) disease-associated regulations remain poorly defined. We conducted RNA-seq experiments to investigate SMC-versus-EC differential transcriptomic dynamics, following treatment of human primary SMCs and ECs with TNFα or IL-1β, both established inducers of SMC hyperplasia and EC dysfunction. As revealed by combined SMC/EC transcriptomes, after TNFα or IL-1β induction, 174 and 213 genes respectively showed greater up-regulation in SMCs than in ECs (SMC-enriched), while 117 and 138 genes showed greater up-regulation in ECs over SMCs (EC-enriched). Analysis of gene interaction networks identified central genes shared in the two SMC-enriched gene sets, and a distinct group of central genes common in the two EC-enriched gene sets. Significantly, four gene modules (subnetworks) were identified from these central genes, including SMC-enriched JUN and FYN modules and EC-enriched SMAD3 and XPO1 modules. These modules may inform potential intervention targets for selective blockage of SMC hyperplasia without endothelial damage.
Genome-wide association study in Asia-adapted tropical maize reveals novel and explored genomic regions for sorghum downy mildew resistance
Authors: Rashid Zerka , Singh Pradeep Kumar , Vemuri Hindu , Zaidi Pervez Haider , Prasanna Boddupalli Maruthi , Nair Sudha Krishnan 
Published: January 2018

AbstractGlobally, downy mildews are among the important foliar diseases of maize that cause significant yield losses. We conducted a genome-wide association study for sorghum downy mildew (SDM;Peronosclerospora sorghi) resistance in a panel of 368 inbred lines adapted to the Asian tropics. High density SNPs from Genotyping-by-sequencing were used in GWAS after controlling for population structure and kinship in the panel using a single locus mixed model. The study identified a set of 26 SNPs that were significantly associated with SDM resistance, with Bonferroni corrected P values ≤ 0.05. Among all the identified SNPs, the minor alleles were found to be favorable to SDM resistance in the mapping panel. Trend regression analysis with 16 independent genetic variants including 12 SNPs and four haplotype blocks identified SNP S2_6154311 on chromosome 2 with P value 2.61E-24 and contributing 26.7% of the phenotypic variation. Six of the SNPs/haplotypes were within the same chromosomal bins as the QTLs for SDM resistance mapped in previous studies. Apart from this, eight novel genomic regions for SDM resistance were identified in this study; they need further validation before being applied in the breeding pipeline. Ten SNPs identified in this study were co-located in reported mildew resistance genes.
Responses of Intrinsic Water-use Efficiency and Tree Growth to Climate Change in Semi-Arid Areas of North China
Authors: Weiwei L. U. , Xinxiao Y. U. , Guodong J. I. A. , Hanzhi L. I. , Ziqiang L. I. U. 
Published: January 2018

AbstractTree-level intrinsic water-use efficiency (iWUE) is derived from the tree-ring 13C isotope composition (δ13C) and is an important indicator of the adaptability for trees to climate change. However, there is still uncertainty regarding the relationship between long-term forest ecosystem carbon sequestration capacity and iWUE. To determine whether elevated atmospheric CO2 concentration (Ca) increase iWUE and tree growth (basal area increment, BAI), dendrochronological methods and stable isotope analyses were used to examine annual changes in the tree-ring width and carbon isotope composition (δ13C) of Platycladus orientalis in northern China. The iWUE derived from δ13C has increased significantly (p < 0.01). Long-term iWUE trend was largely and positively driven by the elevated atmospheric CO2 concentration and temperature. We observed a general increase in averaged BAI, which had significant positive correlation with iWUE (R2 = 0.3186, p < 0.01). Increases in iWUE indeed translated into enhanced P. orientalis growth in semi-arid areas of northern China. Elevated atmospheric CO2 concentration significantly (p < 0.01) stimulated P. orientalis biomass accumulation when Ca was less than approximately 320 ppm in the early phase; however, this effect was not pronounced when Ca exceeded 320 ppm.
Comparative analysis of low complexity regions in Plasmodia
Authors: Chaudhry S. R. , Lwin N. , Phelan D. , Escalante A. A. , Battistuzzi F. U. 
Published: January 2018

AbstractLow complexity regions (LCRs) are a common feature shared by many genomes, but their evolutionary and functional significance remains mostly unknown. At the core of the uncertainty is a poor understanding of the mechanisms that regulate their retention in genomes, whether driven by natural selection or neutral evolution. Applying a comparative approach of LCRs to multiple strains and species is a powerful approach to identify patterns of conservation in these regions. Using this method, we investigate the evolutionary history of LCRs in the genus Plasmodium based on orthologous protein coding genes shared by 11 species and strains from primate and rodent-infecting pathogens. We find multiple lines of evidence in support of natural selection as a major evolutionary force shaping the composition and conservation of LCRs through time and signatures that their evolutionary paths are species specific. Our findings add a comparative analysis perspective to the debate on the evolution of LCRs and harness the power of sequence comparisons to identify potential functionally important LCR candidates.
8u, a pro-apoptosis/cell cycle arrest compound, suppresses invasion and metastasis through HSP90α downregulating and PI3K/Akt inactivation in hepatocellular carcinoma cells
Authors: Wang Ning , Chen Shaopeng , Zhang Bin , Li Shangfu , Jin Feng , Gao Dan , Liu Hongxia , Jiang Yuyang 
Published: January 2018

Abstract8u, an acridine derivative, has been proved effective anti-hepatocarcinoma effect, while the underlying mechanism remains unclear. Here, metabolomics and proteomics approaches were applied to study its anti-cancer mechanism and explore its effect on HepG2 cells’ invasion and metastasis abilities. The results showed that 8u significantly suppressed HepG2 cells migration and enhanced cell-to-cell junctions. The inhibition effect of 8u on invasion and metastasis disappeared after HSP90α gene silencing, and was reversed after HSP90α overexpression. The biological experimental results indicated that 8u also blocked PI3K/Akt pathway, thereby reducing fatty acid synthase (FASN) protein expression and disordering intracellular lipid metabolism to inhibit cell invasion and metastasis. In addition, HSP90α protein and PI3K/Akt pathway could co-adjust to each other. These findings demonstrated that 8u could efficiently suppress the invasion and metastasis of HepG2 cells by decreasing the expression of HSP90α protein and inhibiting the PI3K/Akt signaling pathway, which could be used as a potential candidate for the treatment of HCC.
Exploring the consequences of social defeat stress and intermittent ethanol drinking on dopamine dynamics in the rat nucleus accumbens
Authors: Deal Alex L. , Konstantopoulos Joanne K. , Weiner Jeff L. , Budygin Evgeny A. 
Published: January 2018

AbstractThe current study aimed to explore how presynaptic dopamine (DA) function is altered following brief stress episodes and chronic ethanol self-administration and whether these neuroadaptations modify the acute effects of ethanol on DA dynamics. We used fast-scan cyclic voltammetry to evaluate changes in DA release and uptake parameters in rat nucleus accumbens brain slices by analyzing DA transients evoked through single pulse electrical stimulation. Adult male rats were divided into four groups: ethanol-naïve or ethanol drinking (six week intermittent two-bottle choice) and stressed (mild social defeat) or nonstressed. Results revealed that the mild stress significantly increased DA release and uptake in ethanol-naïve subjects, compared to nonstressed controls. Chronic ethanol self-administration increased the DA uptake rate and occluded the effects of stress on DA release dynamics. Bath-applied ethanol decreased stimulated DA efflux in a concentration-dependent manner in all groups; however, the magnitude of this effect was blunted by either stress or chronic ethanol, or by a combination of both procedures. Together, these findings suggest that stress and ethanol drinking may promote similar adaptive changes in accumbal presynaptic DA release measures and that these changes may contribute to the escalation in ethanol intake that occurs during the development of alcohol use disorder.