bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theophylline controllable RNAi-based genetic switches regulate expression of lncRNA TINCR and malignant phenotypes in bladder cancer cells
Authors: Chen Zhicong , Liu Yuchen , He Anbang , Li Jianfa , Chen Mingwei , Zhan Yonghao , Lin Junhao , Zhuang Chengle , Liu Li , Zhao Guoping , Huang Weiren , Cai Zhiming 
Published: September 2016

AbstractTINCR is a well-known lncRNA which acts as a master regulator in somatic differentiation development. However, it is still unclear whether TINCR is also involved in caner occurrence and progression. In this study, we observed that TINCR was up-regulated in bladder cancer tissues and cells and contributed to oncogenesis and cancer progression. Silencing TINCR expression inhibited cell proliferation and promoted apoptosis in vitro, indicating that TINCR may be the potential therapeutic target for treating bladder urothelial carcinoma. Thus we used the synthetic biology approach to create theophylline controllable RNAi-based genetic switches which silenced TINCR in a dosage-dependent manner. Both RNAi-OFF and ON switches can be used to quantitatively control the expression of TINCR in bladder cancer to suppress the progression of bladder cancer. These findings suggest that lncRNA-TINCR could promote bladder cancer development and progression and artificial control of its expression through inducible RNAi may represent a new kind of therapeutic strategy for treating human bladder cancer.
Inhibitory Effect of Bone Morphogenetic Protein 4 in Retinal Pigment Epithelial-Mesenchymal Transition
Authors: Yao Haipei , Li Hui , Yang Shuai , Li Min , Zhao Chun , Zhang Jingfa , Xu Guotong , Wang Fang 
Published: September 2016

AbstractProliferative vitreoretinopathy (PVR), a serious vision-threatening complication of retinal detachment (RD), is characterized by the formation of contractile fibrotic membranes, in which epithelial-mesenchymal transition (EMT) of the retinal pigment epithelium (RPE) is a major event. Recent studies suggest an important role of bone morphogenetic protein 4 (BMP4) in the suppression of fibrosis. In this study, we aimed to investigate the role of BMP4 in the pathological process of PVR, particularly in the EMT of RPE cells. We found that BMP4 and its receptors were co-labelled with cytokeratin and α-SMA positive cells within the PVR membrane. Moreover, the mRNA and protein expression levels of BMP4 were decreased whereas BMP4 receptors ALK2, ALK3 and ALK6 were increased during TGF-β-induced EMT in primary RPE cells. Exogenous BMP4 inhibited TGF-β-induced epithelial marker down-regulation, as well as mesenchymal marker up-regulation at both the mRNA and protein levels in RPE cells. In addition, BMP4 treatment attenuated the TGF-β-induced gel contraction, cell migration and Smad2/3 phosphorylation. However, knockdown of endogenous BMP4 stimulated changes in EMT markers. Our results confirm the hypothesis that BMP4 might inhibit TGF-β-mediated EMT in RPE cells via the Smad2/3 pathway and suppress contraction. This might represent a potential treatment for PVR.
Enhanced immune response of MAIT cells in tuberculous pleural effusions depends on cytokine signaling
Authors: Jiang Jing , Chen Xinchun , An Hongjuan , Yang Bingfen , Zhang Fuping , Cheng Xiaoxing 
Published: September 2016

AbstractThe functions of MAIT cells at the site of Mycobacterium tuberculosis infection in humans are still largely unknown. In this study, the phenotypes and immune response of MAIT cells from tuberculous pleural effusions and peripheral blood were investigated. MAIT cells in tuberculous pleural effusions had greatly enhanced IFN-γ, IL-17F and granzyme B response compared with those in peripheral blood. The level of IFN-γ response in MAIT cells from tuberculous pleural effusions was inversely correlated with the extent of tuberculosis infection (p = 0.0006). To determine whether cytokines drive the immune responses of MAIT cells at the site of tuberculosis infection, the role of IL-1β, IL-2, IL-7, IL-12, IL-15 and IL-18 was investigated. Blockade of IL-2, IL-12 or IL-18 led to significantly reduced production of IFN-γ and/or granzyme B in MAIT cells from tuberculous pleural effusions. Majority of IL-2-producing cells (94.50%) in tuberculous pleural effusions had phenotype of CD3+CD4+, and most IL-12p40-producing cells (91.39%) were CD14+ cells. MAIT cells had significantly elevated expression of γc receptor which correlated with enhanced immune responses of MAIT cells. It is concluded that MAIT cells from tuberculous pleural effusions exhibited highly elevated immune response to Mtb antigens, which are controlled by cytokines produced by innate/adaptive immune cells.
Bifunctional Luminomagnetic Rare-Earth Nanorods for High-Contrast Bioimaging Nanoprobes
Authors: Gupta Bipin Kumar , Singh Satbir , Kumar Pawan , Lee Yean , Kedawat Garima , Narayanan Tharangattu N. , Vithayathil Sajna Antony , Ge Liehui , Zhan Xiaobo , Gupta Sarika , Martí Angel A. , Vajtai Robert , Ajayan Pulickel M. , Kaipparettu Benny Abraham 
Published: September 2016

AbstractNanoparticles exhibiting both magnetic and luminescent properties are need of the hour for many biological applications. A single compound exhibiting this combination of properties is uncommon. Herein, we report a strategy to synthesize a bifunctional luminomagnetic Gd2−xEuxO3 (x = 0.05 to 0.5) nanorod, with a diameter of ~20 nm and length in ~0.6 μm, using hydrothermal method. Gd2O3:Eu3+ nanorods have been characterized by studying its structural, optical and magnetic properties. The advantage offered by photoluminescent imaging with Gd2O3:Eu3+ nanorods is that this ultrafine nanorod material exhibits hypersensitive intense red emission (610 nm) with good brightness (quantum yield more than 90%), which is an essential parameter for high-contrast bioimaging, especially for overcoming auto fluorescent background. The utility of luminomagnetic nanorods for biological applications in high-contrast cell imaging capability and cell toxicity to image two human breast cancer cell lines T47D and MDA-MB-231 are also evaluated. Additionally, to understand the significance of shape of the nanostructure, the photoluminescence and paramagnetic characteristic of Gd2O3:Eu3+ nanorods were compared with the spherical nanoparticles of Gd2O3:Eu3+.
Identification and functional characterization of the miRNA-gene regulatory network in chronic myeloid leukemia lineage negative cells
Authors: Agatheeswaran S. , Pattnayak N. C. , Chakraborty S. 
Published: September 2016

AbstractChronic myeloid leukemia (CML) is maintained by leukemic stem cells (LSCs) which are resistant to the existing TKI therapy. Hence a better understanding of the CML LSCs is necessary to eradicate these cells and achieve complete cure. Using the miRNA-gene interaction networks from the CML lin(−) cells we identified a set of up/down-regulated miRNAs and corresponding target genes. Association studies (Pearson correlation) from the miRNA and gene expression data showed that miR-1469 and miR-1972 have significantly higher number of target genes, 75 and 50 respectively. We observed that miR-1972 induces G2-M cell cycle arrest and miR-1469 moderately arrested G1 cell cycle when overexpressed in KCL22 cells. We have earlier shown that a combination of imatinib and JAK inhibitor I can significantly bring down the proliferation of CML lineage negative cells. Here we observed that imatinib and JAK inhibitor I combination restored the expression pattern of the down-regulated miRNAs in primary CML lin(−) cells. Thus effective manipulation of the deregulated miRNAs can restore the miRNA-mRNA networks that can efficiently inhibit CML stem and progenitor cells and alleviate the disease.
A theoretical study on predicted protein targets of apple polyphenols and possible mechanisms of chemoprevention in colorectal cancer
Authors: Scafuri Bernardina , Marabotti Anna , Carbone Virginia , Minasi Paola , Dotolo Serena , Facchiano Angelo 
Published: September 2016

AbstractWe investigated the potential role of apple phenolic compounds in human pathologies by integrating chemical characterization of phenolic compounds in three apple varieties, computational approaches to identify potential protein targets of the compounds, bioinformatics analyses on data from public archive of gene expression data, and functional analyses to hypothesize the effects of the selected compounds in molecular pathways. Starting by the analytic characterization of phenolic compounds in three apple varieties, i.e. Annurca, Red Delicious, and Golden Delicious, we used computational approaches to verify by reverse docking the potential protein targets of the identified compounds. Direct docking validation of the potential protein-ligand interactions has generated a short list of human proteins potentially bound by the apple phenolic compounds. By considering the known chemo-preventive role of apple antioxidants’ extracts against some human pathologies, we performed a functional analysis by comparison with experimental gene expression data and interaction networks, obtained from public repositories. The results suggest the hypothesis that chemo-preventive effects of apple extracts in human pathologies, in particular for colorectal cancer, may be the interference with the activity of nucleotide metabolism and methylation enzymes, similarly to some classes of anticancer drugs.
Application of subtracted gDNA microarray-assisted Bulked Segregant Analysis for rapid discovery of molecular markers associated with day-neutrality in strawberry (Fragaria x ananassa)
Authors: Gor Mian Chee , Mantri Nitin , Pang Edwin 
Published: September 2016

AbstractA Fragaria Discovery Panel (FDP; strawberry-specific SDA) containing 287 features was constructed by subtracting the pooled gDNA of nine non-angiosperm species from the pooled gDNA of five strawberry genotypes. This FDP was used for Bulk Segregant Analysis (BSA) to enable identification of molecular markers associated with day-neutrality. Analysis of hybridisation patterns of a short day (SD) DNA bulk and three day-neutral (DN) DNA bulks varying in flowering strength allowed identification of a novel feature, FaP2E11, closely linked toCYTOKININ OXIDASE 1(CKX1) gene possibly involved in promoting flowering under non-inductive condition. The signal intensities of FaP2E11 feature obtained from the strong DN bulk (DN1) is three fold higher than the short day bulk (SD), indicating that the putative marker may linked to aCKX1variant allele with lower enzyme activity. We propose a model for flowering regulation based on the hypothesis that flowering strength may be regulated by the copy number of FaP2E11-linkedCKX1alleles. This study demonstrates the feasibility of the SDA-based BSA approach for the identification of molecular markers associated with day-neutrality in strawberry. This innovative strategy is an efficient and cost-effective approach for molecular marker discovery.
The influence of personality and perceived stress on the development of breast cancer: 20-year follow-up of 29,098 Japanese women
Authors: Sawada Takayuki , Nishiyama Takeshi , Kikuchi Norimasa , Wang Chaochen , Lin Yingsong , Mori Mitsuru , Tanno Kozo , Tamakoshi Akiko , Kikuchi Shogo 
Published: September 2016

AbstractBreast cancer is the most common cancer in women. However, it remains unproven whether psychological factors have an influence on breast cancer incidence. In our earlier study, subjects possessing two personality traits, decisiveness and “ikigai” (a Japanese word meaning something that makes one’s life worth living), showed a significantly lower risk of developing breast cancer, although no psychological factors have been convincingly demonstrated to have an influence on breast cancer development in other studies. Therefore, we conducted this follow-up analysis to confirm the association between breast cancer incidence and psychological traits, using the final dataset of a large-scale prospective cohort study in Japan. We identified 209 cases of incident breast cancer out of a maximum 21-year follow-up of 29,098 Japanese women. Cox proportional hazard regression analysis, adjusted for the same potential confounders used in our previous study, did not reveal any significant relationships between breast cancer incidence and four psychological traits: having “ikigai”, decisiveness, ease of anger arousal and perceived stress. Our finding is consistent with previous studies and suggests that the psychological traits are unlikely to be an important risk factor for breast cancer.
The Effect of Next-Nearest Neighbour Hopping in the One, Two, and Three Dimensional Holstein Model
Authors: Chandler Carl J. , Prosko Christian , Marsiglio F. 
Published: September 2016

AbstractAllowing a single electron to hop to next-nearest neighbours (NNN) in addition to the closest atomic sites in the Holstein model, a modified Trugman method is applied to exactly calculate the effect on the polaronic effective mass in one, two, and three dimensions, building on the previous study of the one-dimensional NNN Holstein model. We also present perturbative calculations and a heuristic scaling factor for the coupling strength and ion frequency to nearly map the NNN Holstein model back onto the original Holstein model. When account is taken of the modified electronic bandwidth near the electron energy, we find that including NNN hopping effectively increases the polaron effective mass.
Noninvasive mapping of the redox status of dimethylnitrosamine-induced hepatic fibrosis using in vivo dynamic nuclear polarization-magnetic resonance imaging
Authors: Kawano Takahito , Murata Masaharu , Hyodo Fuminori , Eto Hinako , Kosem Nuttavut , Nakata Ryosuke , Hamano Nobuhito , Piao Jing Shu , Narahara Sayoko , Akahoshi Tomohiko , Hashizume Makoto 
Published: September 2016

AbstractHepatic fibrosis is a chronic disorder caused by viral infection and/or metabolic, genetic and cholestatic disorders. A noninvasive procedure that enables the detection of liver fibrosis based on redox status would be useful for disease identification and monitoring, and the development of treatments. However, an appropriate technique has not been reported. This study describes a novel method for assessing the redox status of the liver using in vivo dynamic nuclear polarization-magnetic resonance imaging (DNP-MRI) with the nitroxyl radical carbamoyl-PROXYL as a molecular imaging probe, which was tested in dimethylnitrosamine-treated mice as a model of liver fibrosis. Based on the pharmacokinetics of carbamoyl-PROXYL in control livers, reduction rate mapping was performed in fibrotic livers. Reduction rate maps demonstrated a clear difference between the redox status of control and fibrotic livers according to the expression of antioxidants. These findings indicate that in vivo DNP-MRI with a nitroxyl radical probe enables noninvasive detection of changes in liver redox status.
Construction of a high-density genetic map and QTL mapping for pearl quality-related traits in Hyriopsis cumingii
Authors: Bai Zhi-Yi , Han Xue-Kai , Liu Xiao-Jun , Li Qing-Qing , Li Jia-Le 
Published: September 2016

AbstractA high-density genetic map is essential for quantitative trait locus (QTL) fine mapping. In this study, 4,508 effective single nucleotide polymorphism markers (detected using specific-locus amplified fragment sequencing) and 475 microsatellites were mapped to 19 linkage groups (LGs) using a family with 157 individuals. The map spanned 2,713 cM, with an average of 259 markers and 79 loci per LG and an average inter-marker distance of 1.81 cM. To identify QTLs for pearl quality traits, 26 putatively significant QTLs were detected for 10 traits, including, three for shell width, seven for body weight, two for shell weight, two for margin mantle weight, five for inner mantle weight, and seven for shell nacre colour. Among them, five QTLs associated with shell nacre colour were mapped to LG17 and explained 19.7% to 22.8% of the trait variation; this suggests that some important genes or loci determine shell nacre colour in LG17. The linkage map and mapped QTLs for shell nacre colour would be useful for improving the quality ofHyriopsis cumingiivia marker-assisted selection.
High Density Crossbar Arrays with Sub- 15 nm Single Cells via Liftoff Process Only
Authors: Khiat Ali , Ayliffe Peter , Prodromakis Themistoklis 
Published: September 2016

AbstractEmerging nano-scale technologies are pushing the fabrication boundaries at their limits, for leveraging an even higher density of nano-devices towards reaching 4F2/cell footprint in 3D arrays. Here, we study the liftoff process limits to achieve extreme dense nanowires while ensuring preservation of thin film quality. The proposed method is optimized for attaining a multiple layer fabrication to reliably achieve 3D nano-device stacks of 32 × 32 nanowire arrays across 6-inch wafer, using electron beam lithography at 100 kV and polymethyl methacrylate (PMMA) resist at different thicknesses. The resist thickness and its geometric profile after development were identified to be the major limiting factors, and suggestions for addressing these issues are provided. Multiple layers were successfully achieved to fabricate arrays of 1 Ki cells that have sub- 15 nm nanowires distant by 28 nm across 6-inch wafer.
Guidelines to electrode positioning for human and animal electrical impedance myography research
Authors: Sanchez Benjamin , Pacheck Adam , Rutkove Seward B. 
Published: September 2016

AbstractThe positioning of electrodes in electrical impedance myography (EIM) is critical for accurately assessing disease progression and effectiveness of treatment. In human and animal trials for neuromuscular disorders, inconsistent electrode positioning adds errors to the muscle impedance. Despite its importance, how the reproducibility of resistance and reactance, the two parameters that define EIM, are affected by changes in electrode positioning remains unknown. In this paper, we present a novel approach founded on biophysical principles to study the reproducibility of resistance and reactance to electrode misplacements. The analytical framework presented allows the user to quantify a priori the effect on the muscle resistance and reactance using only one parameter: the uncertainty placing the electrodes. We also provide quantitative data on the precision needed to position the electrodes and the minimum muscle length needed to achieve a pre-specified EIM reproducibility. The results reported here are confirmed with finite element model simulations and measurements on five healthy subjects. Ultimately, our data can serve as normative values to enhance the reliability of EIM as a biomarker and facilitate comparability of future human and animal studies.
3′-hydroxy-3,4,5,4′-tetramethoxystilbene, the metabolite of resveratrol analogue DMU-212, inhibits ovarian cancer cell growth in vitro and in a mice xenograft model
Authors: Piotrowska-Kempisty Hanna , Ruciński Marcin , Borys Sylwia , Kucińska Małgorzata , Kaczmarek Mariusz , Zawierucha Piotr , Wierzchowski Marcin , Łażewski Dawid , Murias Marek , Jodynis-Liebert Jadwiga 
Published: September 2016

AbstractIn screening studies, the cytotoxic activity of four metabolites of resveratrol analogue 3,4,5,4′-tetramethoxystilbene (DMU-212) against A-2780 and SKOV-3 ovarian cancer cells was investigated. The most active metabolite, 3′-hydroxy-3,4,5,4′-tetramethoxystilbene (DMU-214), was chosen for further studies. The cytotoxicity of DMU-214 was shown to be higher than that of the parent compound, DMU-212, in both cell lines tested. Since DMU-212 was supposed to undergo metabolic activation through its conversion to DMU-214, an attempt was made to elucidate the mechanism of its anti-proliferative activity. We found that in SKOV-3 cells lacking p53, DMU-214 induced receptor-mediated apoptosis. In A-2780 cell line with expression of wild-type p53, DMU-214 modulated the expression pattern of p53-target genes driving intrinsic and extrinsic apoptosis pathways, as well as DNA repair and damage prevention. Regardless of the up-regulation of p48, p53R2, sestrins and Gaad45 genes involved in cancer cell DNA repair, we demonstrated the stronger anti-proliferative and pro-apoptotic effects of DMU-214 in A-2780 cells when compared to those in SKOV-3. Hence we verified DMU-214 activity in the xenograft model using SCID mice injected with A-2780 cells. The strong anti-proliferative activity of DMU-214 in the in vivo model allowed to suggest the tested compound as a potential therapeutic in ovarian cancer treatment.
Abrogation of CC chemokine receptor 9 ameliorates ventricular remodeling in mice after myocardial infarction
Authors: Huang Yan , Wang Dandan , Wang Xin , Zhang Yijie , Liu Tao , Chen Yuting , Tang Yanhong , Wang Teng , Hu Dan , Huang Congxin 
Published: September 2016

AbstractCC chemokine receptor 9 (CCR9), which is a unique receptor for CC chemokine ligand (CCL25), is mainly expressed on lymphocytes, dendritic cells (DCs) and monocytes/macrophages. CCR9 mediates the chemotaxis of inflammatory cells and participates in the pathological progression of inflammatory diseases. However, the role of CCR9 in the pathological process of myocardial infarction (MI) remains unexplored; inflammation plays a key role in this process. Here, we used CCR9 knockout mice to determine the functional significance of CCR9 in regulating post-MI cardiac remodeling and its underlying mechanism. MI was induced by surgical ligation of the left anterior descending coronary artery in CCR9 knockout mice and their CCR9+/+ littermates. Our results showed that the CCR9 expression levels were up-regulated in the hearts of the MI mice. Abrogation of CCR9 improved the post-MI survival rate and left ventricular (LV) dysfunction and decreased the infarct size. In addition, the CCR9 knockout mice exhibited attenuated inflammation, apoptosis, structural and electrical remodeling compared with the CCR9+/+ MI mice. Mechanistically, CCR9 mainly regulated the pathological response by interfering with the NF-κB and MAPK signaling pathways. In conclusion, the data reveal that CCR9 serves as a novel modulator of pathological progression following MI through NF-κB and MAPK signaling.
DDX3X promotes the biogenesis of a subset of miRNAs and the potential roles they played in cancer development
Authors: Zhao Luqing , Mao Yitao , Zhao Yuelong , He Yanong 
Published: September 2016

AbstractDDX3X, located on the X-chromosome, belongs to the DEAD-box RNA helicase family and acts as a key RNA-binding protein to exert its regulatory functions in various biological processes. In this paper, knock-down the expression of DDX3X can affect a subset of miRNA expression levels, especially for miR-1, miR-141, miR-145, miR-19b, miR-20a and miR-34a. Through adopting the immunoprecipitation (IP), RNA immunoprecipitation (RIP), dual luciferase reporter assays, we illustrate that DDX3X could interact with Drosha/DGCR8 complex, elevate the processing activity of Drosha/DGCR8 complex on pri-miRNAs, and increase mature miRNA expression levels. For the studies of potential roles and biological functions of DDX3X-dependent miRNAs and their downstream target genes in multiple cancers, we use the primary data from The Cancer Genome Atlas (TCGA), Ingenuity Pathway Analysis (IPA) and several miRNA target prediction databases, to systematically analyze the expression levels of DDX3X-dependent miRNAs in almost 14 kinds of cancers versus normal tissues, and the essential biological functions for their putative downstream target genes. All these findings will provide us novel insights and directions for thoroughly exploring the regulatory mechanisms of miRNA biogenesis, and shed light on effectively searching the clinical significances and biological roles of DDX3X-dependent miRNAs and their target genes in cancer development.