bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional activation of follistatin by Nrf2 protects pulmonary epithelial cells against silica nanoparticle-induced oxidative stress
Authors: Lin Chen , Zhao Xinyuan , Sun Desen , Zhang Lingda , Fang Wenpan , Zhu Tingjia , Wang Qiang , Liu Botao , Wei Saisai , Chen Guangdi , Xu Zhengping , Gao Xiangwei 
Published: February 2016

AbstractSilica nanoparticles (SiO2 NPs) cause oxidative stress in respiratory system. Meanwhile, human cells launch adaptive responses to overcome SiO2 NP toxicity. However, besides a few examples, the regulation of SiO2 NP-responsive proteins and their functions in SiO2 NP response remain largely unknown. In this study, we demonstrated that SiO2 NP induced the expression of follistatin (FST), a stress responsive gene, in mouse lung tissue as well as in human lung epithelial cells (A549). The levels of Ac-H3(K9/18) and H3K4me2, two active gene markers, at FST promoter region were significantly increased during SiO2 NP treatment. The induction of FST transcription was mediated by the nuclear factor erythroid 2-related factor 2 (Nrf2), as evidenced by the decreased FST expression in Nrf2-deficient cells and the direct binding of Nrf2 to FST promoter region. Down-regulation of FST promoted SiO2 NP-induced apoptosis both in cultured cells and in mouse lung tissue. Furthermore, knockdown of FST increased while overexpression of FST decreased the expression level of NADPH oxidase 1 (NOX1) and NOX5 as well as the production of cellular reactive oxygen species (ROS). Taken together, these findings demonstrated a protective role of FST in SiO2 NP-induced oxidative stress and shed light on the interaction between SiO2 NPs and biological systems.
Low c-Met expression levels are prognostic for and predict the benefits of temozolomide chemotherapy in malignant gliomas
Authors: Li Ming-Yang , Yang Pei , Liu Yan-Wei , Zhang Chuan-Bao , Wang Kuan-Yu , Wang Yin-Yan , Yao Kun , Zhang Wei , Qiu Xiao-Guang , Li Wen-Bin , Peng Xiao-Xia , Wang Yong-Zhi , Jiang Tao 
Published: February 2016

AbstractAberrant c-Met has been implicated in the development of many cancers. The objective of this study was to identify an unfavorable prognostic marker that might guide decisions regarding clinical treatment strategies for high-grade gliomas. C-Met expression was measured using immunohistochemistry in 783 gliomas, and we further analyzed c-Met mRNA levels using the Agilent Whole Genome mRNA Microarray in 286 frozen samples. In vitro, we performed cell migration and invasion assays. Cell sensitivity to temozolomide (TMZ) chemotherapy was determined using MTT assays. Both mRNA and protein levels of c-Met were significantly associated with tumor grade progression and inversely correlated with overall and progression-free survival in high-grade gliomas (all P < 0.0001). These findings were nearly consistent at the mRNA level across 3 independent cohorts. Multivariable analysis indicated that c-Met was an independent prognostic marker after adjusting for age, preoperative Karnofsky Performance Status (KPS) score, the extent of resection, radiotherapy, TMZ chemotherapy, and O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status. Further analysis in vitro revealed that downregulating the expression of c-Met dramatically inhibited cell migration and invasion capacities, enhanced sensitivity to TMZ chemotherapy in H4 and U87 glioma cells. Our results suggest that c-Met may serve as a potential predictive maker for clinical decision making.
Identification of different mechanisms leading to PAX6 down-regulation as potential events contributing to the onset of Hirschsprung disease
Authors: Enguix-Riego María Valle , Torroglosa Ana , Fernández Raquel María , Moya-Jiménez María José , de Agustín Juan Carlos , Antiñolo Guillermo , Borrego Salud 
Published: February 2016

AbstractHirschsprung disease (HSCR) is attributed to a failure of neural crest derived cells to migrate, proliferate, differentiate or survive in the bowel wall during embryonic Enteric Nervous System (ENS) development. This process requires a wide and complex variety of molecules and signaling pathways which are activated by transcription factors. In an effort to better understand the etiology of HSCR, we have designed a study to identify new transcription factors participating in different stages of the colonization process. A differential expression study has been performed on a set of transcription factors using Neurosphere-like bodies from both HSCR and control patients. Differential expression levels were found for CDYL, MEIS1, STAT3 and PAX6. A significantly lower expression level for PAX6 in HSCR patients, would suit with the finding of an over-representation of the larger tandem (AC)m(AG)n repeats within the PAX6 promoter in HSCR patients, with the subsequent loss of protein P300 binding. Alternatively, PAX6 is a target for DNMT3B-dependant methylation, a process already proposed as a mechanism with a role in HSCR. Such decrease in PAX6 expression may influence in the proper function of signaling pathways involved in ENS with the confluence of additional genetic factors to the manifestation of HSCR phenotype.
Three-dimensional Organotypic Culture Models of Human Hepatocellular Carcinoma
Authors: Takai Atsushi , Fako Valerie , Dang Hien , Forgues Marshonna , Yu Zhipeng , Budhu Anuradha , Wang Xin Wei 
Published: February 2016

AbstractThree-dimensional cell culture methods are viable in vitro approaches that facilitate the examination of biological features cancer cells present in vivo. In this study, we demonstrate that hepatocellular carcinoma (HCC) cells in porous alginate scaffolds can generate organoid-like spheroids that mimic numerous features of glandular epithelium in vivo, such as acinar morphogenesis and apical expression patterns of EpCAM, a hepatic stem/progenitor cell marker highly expressed in a subset of HCC with stemness features. We show that the activation of Wnt/β-catenin signaling, an essential pathway for maintaining HCC stemness, is required for EpCAM+ HCC spheroid formation as well as the maintenance of the acinous structure. Furthermore, we demonstrate that EpCAM+ HCC cells cultured as spheroids are more sensitive to TGF/β-induced epithelial-mesenchymal transition with highly tumorigenic and metastatic potential in vivo compared to conventional two-dimensional (2D) culture. In addition, HCC cells in EpCAM+ spheroids are more resistant to chemotherapeutic agents than 2D-cultured cells. The alginate scaffold-based organotypic culture system is a promising, reliable and easy system that can be configured into a high throughput fashion for the identification of critical signaling pathways and screening of molecular drug targets specific for HCC.
Regulatory role of hexosamine biosynthetic pathway on hepatic cancer stem cell marker CD133 under low glucose conditions
Authors: Lin Shu-Hai , Liu Tengfei , Ming Xiaoyan , Tang Zhi , Fu Li , Schmitt-Kopplin Philippe , Kanawati Basem , Guan Xin-Yuan , Cai Zongwei 
Published: February 2016

AbstractCancer was hypothesized to be driven by cancer stem cells (CSCs), but the metabolic determinants of CSC-like phenotype still remain elusive. Here, we present that hexosamine biosynthetic pathway (HBP) at least in part rescues cancer cell fate with inactivation of glycolysis. Firstly, metabolomic analysis profiled cellular metabolome in CSCs of hepatocellular carcinoma using CD133 cell-surface marker. The metabolic signatures of CD133-positive subpopulation compared to CD133-negative cells highlighted HBP as one of the distinct metabolic pathways, prompting us to uncover the role of HBP in maintenance of CSC-like phenotype. To address this, CSC-like phenotypes and cell survival were investigated in cancer cells under low glucose conditions. As a result, HBP inhibitor azaserine reduced CD133-positive subpopulation and CD133 expression under high glucose condition. Furthermore, treatment of N-Acetylglucosamine in part restores CD133-positive subpopulation when either 2.5 mM glucose in culture media or glycolytic inhibitor 2-deoxy-D-glucose in HCC cell lines was applied, enhancing CD133 expression as well as promoting cancer cell survival. Together, HBP might be a key metabolic determinant in the functions of hepatic CSC marker CD133.
Intranasal Insulin Prevents Anesthesia-Induced Spatial Learning and Memory Deficit in Mice
Authors: Zhang Yongli , Dai Chun-ling , Chen Yanxing , Iqbal Khalid , Liu Fei , Gong Cheng-Xin 
Published: February 2016

AbstractElderly individuals are at increased risk of cognitive decline after anesthesia. General anesthesia is believed to be a risk factor for Alzheimer’s disease (AD). At present, there is no treatment that can prevent anesthesia-induced postoperative cognitive dysfunction. Here, we treated mice with daily intranasal administration of insulin (1.75 U/day) for one week before anesthesia induced by intraperitoneal injection of propofol and maintained by inhalation of sevoflurane for 1 hr. We found that the insulin treatment prevented anesthesia-induced deficit in spatial learning and memory, as measured by Morris water maze task during 1–5 days after exposure to anesthesia. The insulin treatment also attenuated anesthesia-induced hyperphosphorylation of tau and promoted the expression of synaptic proteins and insulin signaling in the brain. These findings show a therapeutic potential of intranasal administration of insulin before surgery to reduce the risk of anesthesia-induced cognitive decline and AD.
Allosteric coupling between proximal C-terminus and selectivity filter is facilitated by the movement of transmembrane segment 4 in TREK-2 channel
Authors: Zhuo Ren-Gong , Peng Peng , Liu Xiao-Yan , Yan Hai-Tao , Xu Jiang-Ping , Zheng Jian-Quan , Wei Xiao-Li , Ma Xiao-Yun 
Published: February 2016

AbstractTREK-2, a member of two-pore-domain potassium channel family, regulates cellular excitability in response to diverse stimuli. However, how such stimuli control channel function remains unclear. Here, by characterizing the responses of cytosolic proximal C-terminus deletant (ΔpCt) and transmembrane segment 4 (M4)-glycine hinge mutant (G312A) to 2-Aminoethoxydiphenyl borate (2-APB), an activator of TREK-2, we show that the transduction initiated from pCt domain is allosterically coupled with the conformation of selectivity filter (SF) via the movements of M4, without depending on the original status of SF. Moreover, ΔpCt and G312A also exhibited blunted responses to extracellular alkalization, a model to induce SF conformational transition. These results suggest that the coupling between pCt domain and SF is bidirectional and M4 movements are involved in both processes. Further mechanistic exploration reveals that the function of Phe316, a residue close to the C-terminus of M4, is associated with such communications. However, unlike TREK-2, M4-hinge of TREK-1 only controls the transmission from pCt to SF, rather than SF conformational changes triggered by pHo changes. Together, our findings uncover the unique gating properties of TREK-2 and elucidate the mechanisms for how the extracellular and intracellular stimuli harness the pore gating allosterically.
Identification of a prostaglandin D2 metabolite as a neuritogenesis enhancer targeting the TRPV1 ion channel
Authors: Shibata Takahiro , Takahashi Katsuhiro , Matsubara Yui , Inuzuka Emi , Nakashima Fumie , Takahashi Nobuaki , Kozai Daisuke , Mori Yasuo , Uchida Koji 
Published: February 2016

AbstractMast cells play important roles in allergic inflammation by secreting various mediators. In the present study, based on the finding that the medium conditioned by activated RBL-2H3 mast cells enhanced the nerve growth factor (NGF)-induced neuritogenesis of PC12 cells, we attempted to isolate an active compound from the mast cell conditioned culture medium. Our experiment identified 15-deoxy-Δ12,14-PGJ2 (15d-PGJ2), one of the PGD2 metabolites, as a potential enhancer of neuritogenesis. 15d-PGJ2 strongly enhanced the neuritogenesis elicited by a low-concentration of NGF that alone was insufficient to induce the neuronal differentiation. This 15d-PGJ2 effect was exerted in a Ca2+-dependent manner, but independently of the NGF receptor TrkA. Importantly, 15d-PGJ2 activated the transient receptor potential vanilloid-type 1 (TRPV1), a non-selective cation channel, leading to the Ca2+ influx. In addition, we observed that (i) NGF promoted the insertion of TRPV1 into the cell surface membrane and (ii) 15d-PGJ2 covalently bound to TRPV1. These findings suggest that the NGF/15d-PGJ2-induced neuritogenesis may be regulated by two sets of mechanisms, one for the translocation of TRPV1 into the cell surface by NGF and one for the activation of TRPV1 by 15d-PGJ2. Thus, there is most likely a link between allergic inflammation and activation of the neuronal differentiation.
Copying hierarchical leaders’ voices? Acoustic plasticity in female Japanese macaques
Authors: Lemasson Alban , Jubin Ronan , Masataka Nobuo , Arlet Malgorzata 
Published: February 2016

AbstractIt has been historically claimed that call production in nonhuman primates has been shaped by genetic factors, although, recently socially-guided plasticity and cortical control during vocal exchanges have been observed. In humans, context-dependent vocal convergence with relatives, friends or leaders’ voices can be found. Comparative studies with monkeys and apes presenting tolerant social organizations have demonstrated that affiliative bonding is the determining factor of convergence. We tested whether vocal copying could also exist in a primate species with a despotic social organization. We compared the degree of inter-individual similarity of contact calls in two groups of Japanese macaques as a function of age, dominance rank, maternal kin and affiliative bonds. We found a positive relationship between dyadic acoustic similarity and female rank differences. Since most call exchanges were initiated by dominant females and since this species is known for the ability of responders to acoustically match initiators’ calls, we conclude that high social status may motivate vocal convergence in this despotic society. Accordingly, intra-individual comparisons showed that isolated calls were more stereotyped than exchanged calls and that dominants had more stereotyped voices than subordinates. This opens new lines of research with regard to social motivation guiding acoustic plasticity in primates.
Imperfection works: Survival, transmission and persistence in the system of Heliothis virescens ascovirus 3h (HvAV-3h), Microplitis similis and Spodoptera exigua
Authors: Li Shun-Ji , Hopkins Richard J. , Zhao Yi-Pei , Zhang Yun-Xuan , Hu Jue , Chen Xu-Yang , Xu Zhi , Huang Guo-Hua 
Published: February 2016

AbstractAscoviruses are insect-specific large DNA viruses that mainly infect noctuid larvae, and are transmitted by parasitoids in the fields. Heliothis virescens ascovirus 3h (HvAV-3h) has been recently isolated from Spodoptera exigua, without parasitoid vector identified previously. Here we report that Microplitis similis, a solitary endoparasitoid wasp, could transmit HvAV-3h between S. exigua larvae in the laboratory. When the female parasitoid wasp acquired the virus and served as a vector, the period of virion viability on the ovipositor was 4.1 ± 1.4 days. Infected host larvae were still acceptable for egg laying by parasitoids, and the parasitoids thereafter transmitted virus to healthy hosts. Virus acquisition occurred only from donor hosts between 3 and 9 days post infection. The peak of virus acquisition (80.9 ± 6.3%) was found when M. similis wasps oviposited in larvae that had been inoculated with the virus 7 days previously. When virus infection of the host took place during the life cycle of the parasitoid wasp, it caused 1- to 4-day-old immature parasitoids death in the host, whilst a small proportion of 5- to 6-day-old and the majority of 7-day-old parasitoids larvae survived from the virus-infected hosts. Viral contamination did not reduce the life span or fecundity of female M. similis.
EPR Steering inequalities with Communication Assistance
Authors: Nagy Sándor , Vértesi Tamás 
Published: February 2016

AbstractIn this paper, we investigate the communication cost of reproducing Einstein-Podolsky-Rosen (EPR) steering correlations arising from bipartite quantum systems. We characterize the set of bipartite quantum states which admits a local hidden state model augmented with c bits of classical communication from an untrusted party (Alice) to a trusted party (Bob). In case of one bit of information (c = 1), we show that this set has a nontrivial intersection with the sets admitting a local hidden state and a local hidden variables model for projective measurements. On the other hand, we find that an infinite amount of classical communication is required from an untrusted Alice to a trusted Bob to simulate the EPR steering correlations produced by a two-qubit maximally entangled state. It is conjectured that a state-of-the-art quantum experiment would be able to falsify two bits of communication this way.
Cobalt Sulfide/Graphene Composite Hydrogel as Electrode for High-Performance Pseudocapacitors
Authors: Meng Xiaoqian , Deng Jin , Zhu Junwu , Bi Huiping , Kan Erjun , Wang Xin 
Published: February 2016

AbstractGraphene and its composite hydrogels with interconnected three-dimensional (3D) structure have raised continuous attention in energy storage. Herein, we describe a simple hydrothermal strategy to synthesize 3D CoS/graphene composite hydrogel (CGH), which contains the reduction of GO sheets and anchoring of CoS nanoparticles on graphene sheets. The formed special 3D structure endows this composite with high electrochemical performance. Remarkably, the obtained 3D CGH exhibits high specific capacitance (Cs) of 564 F g−1 at a current density of 1 A g−1 (about 1.3 times higher than pure CoS), superior rate capability and high stability. It is worth mentioning that this methodology is readily adaptable to decorating CoS nanoparticles onto graphene sheets and may be extended to the preparation of other pseudocapacitive materials based on graphene hydrogels for electrochemical applications.
Side coupling of multiple optical channels by spiral patterned zinc oxide coatings on large core plastic optical fibers
Authors: Rahim Hazli Rafis Bin Abdul , Manjunath Somarapalli , Fallah Hoorieh , Thokchom Siddharth , Harun Sulaiman Wadi , Mohammed Waleed Soliman , Hornyak Louis Gabor , Dutta Joydeep 
Published: February 2016

Improved optical side coupling efficiency was demonstrated for spiral patterned zinc oxide (ZnO) nanorods coated large core plastic optic fibers (POFs) as opposed to unpatterned continuous coatings. ZnO nanorods were grown by the hydrothermal method directly onto POF surfaces. Nanorods coating enhanced coupling inside the fiber by scattering light but were also capable of causing leakage. Structuring the growth to specific regions allows scattering from different segments along the fiber to contribute to the total coupled power. ZnO nanorods growth time of 12 h and temperature of 90 °C provided the best coupling voltage. Side coupling was measured to be a factor of 2.2 times better for spiral patterned coatings as opposed to unpatterned coatings. The formation of multiple segments was as well used for multiple‐wavelength channels excitation where different bands were side coupled from different segments.
Isolation and identification of berberine and berberrubine metabolites by berberine-utilizing bacterium Rhodococcus sp. strain BD7100
Authors: Ishikawa Kazuki , Takeda Hisashi , Wakana Daigo , Sato Fumihiko , Hosoe Tomoo 
Published: February 2016

Abstract
Based on the finding of a novel berberine (BBR)-utilizing bacterium, Rhodococcus sp. strain BD7100, we investigated the degradation of BBR and its analog berberrubine (BRU). Resting cells of BD7100 demethylenated BBR and BRU, yielding benzeneacetic acid analogs. Isolation of benzeneacetic acid analogs suggested that BD7100 degraded the isoquinoline ring of the protoberberine skeleton. This work represents the first report of cleavage of protoberberine skeleton by a microorganism.
Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins
Authors: Salim José Augusto , Borro Luiz , Mazoni Ivan , Yano Inácio , Jardine José G. , Neshich Goran 
Published: February 2016

Abstract
Motivation: A graphical representation of physicochemical and structural descriptors attributed to amino acid residues occupying the same topological position in different, structurally aligned proteins can provide a more intuitive way to associate possible functional implications to identified variations in structural characteristics. This could be achieved by observing selected characteristics of amino acids and of their corresponding nano environments, described by the numerical value of matching descriptor. For this purpose, a web-based tool called multiple structure single parameter (MSSP) was developed and here presented.
Results: MSSP produces a two-dimensional plot of a single protein descriptor for a number of structurally aligned protein chains. From a total of 150 protein descriptors available in MSSP, selected of &gt;1500 parameters stored in the STING database, it is possible to create easily readable and highly informative XY-plots, where X-axis contains the amino acid position in the multiple structural alignment, and Y-axis contains the descriptor’s numerical values for each aligned structure. To illustrate one of possible MSSP contributions to the investigation of changes in physicochemical and structural properties of mutants, comparing them with the cognate wild-type structure, the oncogenic mutation of M918T in RET kinase is presented. The comparative analysis of wild-type and mutant structures shows great changes in their electrostatic potential. These variations are easily depicted at the MSSP-generated XY-plot.
Availability and Implementation: The web server is freely available at http://www.cbi.cnptia.embrapa.br/SMS/STINGm/MPA/index.html. Web server implemented in Perl, Java and JavaScript and JMol or Protein Viewer as structure visualizers.
Contact: goran.neshich@embrapa.br or gneshich@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.