bluuebunny/crossref_metadata_2025_split huggingface dataset:
CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types
Authors: Meng X , Wang J , Yuan C , Li X , Zhou Y , Hofestädt R , Chen M 
Published: December 2015

AbstractProtein–protein interactions (PPIs) and microRNA (miRNA)–target interactions are important for deciphering the mechanisms of tumorigenesis. However, current PPI databases do not support cancer-specific analysis. Also, no available databases can be used to retrieve cancer-associated miRNA–target interactions. As the pathogenesis of human cancers is affected by several miRNAs rather than a single miRNA, it is needed to uncover miRNA synergism in a systems level. Here for each cancer type, we constructed a miRNA–miRNA functionally synergistic network based on the functions of miRNA targets and their topological features in that cancer PPI network. And for the first time, we report the cancer-specific database CancerNet (http://bis.zju.edu.cn/CancerNet), which contains information about PPIs, miRNA–target interactions and functionally synergistic miRNA–miRNA pairs across 33 human cancer types. In addition, PPI information across 33 main normal tissues and cell types are included. Flexible query methods are allowed to retrieve cancer molecular interactions. Network viewer can be used to visualize interactions that users are interested in. Enrichment analysis tool was designed to detect significantly overrepresented Gene Ontology categories of miRNA targets. Thus, CancerNet serves as a comprehensive platform for assessing the roles of proteins and miRNAs, as well as their interactions across human cancers.
The Roles of MicroRNA-122 Overexpression in Inhibiting Proliferation and Invasion and Stimulating Apoptosis of Human Cholangiocarcinoma Cells
Authors: Liu Ning , Jiang Fan , He Tian-Lin , Zhang Jun-Kuan , Zhao Juan , Wang Chun , Jiang Gui-Xing , Cao Li-Ping , Kang Peng-Cheng , Zhong Xiang-Yu , Lin Tian-Yu , Cui Yun-Fu 
Published: December 2015

AbstractOur study investigated whether microRNA-122 (miR-122) played important roles in the proliferation, invasion and apoptosis of human cholangiocarcinoma (CC) cells. QBC939 and RBE cells lines were chosen and divided into five groups: miR-122 mimic group, anti-miR-122 group, negative control (NC) group, mock group and blank group. MiR-122 expression was measured by qRT-PCR. Roles of miR-122 in cell proliferation, apoptosis and invasion were investigated using MTT assay, flow cytometer and Transwell invasion assay, respectively. MiR-122 expression was lower in CC tissues and QBC939 cell than that in normal bile duct tissues, HCCC-9810 and RBE cells. In both QBC939 and RBE cells lines, miR-122 expression was higher in miR-122 mimic group than that in NC group, mock group and blank group; opposite results were found in anti-miR-122 group. Cell proliferation and invasion were remarkably inhibited in miR-122 mimic group after 48 h/72 h transfection, while apoptotic cells numbers were much greater in miR-122 mimic group; the opposite results were obtained from anti-miR-122 group (all P < 0.05). MiR-122 expression was significantly weaker in CC tissues and miR-122 overexpression might play pivotal roles in inhibiting proliferation, stimulating apoptosis and suppressing invasion of CC cells, suggesting a new target for CC diagnosis and treatment.
Fast non-Abelian geometric gates via transitionless quantum driving
Authors: Zhang J. , Kyaw Thi Ha , Tong D. M. , Sjöqvist Erik , Kwek Leong-Chuan 
Published: December 2015

AbstractA practical quantum computer must be capable of performing high fidelity quantum gates on a set of quantum bits (qubits). In the presence of noise, the realization of such gates poses daunting challenges. Geometric phases, which possess intrinsic noise-tolerant features, hold the promise for performing robust quantum computation. In particular, quantum holonomies, i.e., non-Abelian geometric phases, naturally lead to universal quantum computation due to their non-commutativity. Although quantum gates based on adiabatic holonomies have already been proposed, the slow evolution eventually compromises qubit coherence and computational power. Here, we propose a general approach to speed up an implementation of adiabatic holonomic gates by using transitionless driving techniques and show how such a universal set of fast geometric quantum gates in a superconducting circuit architecture can be obtained in an all-geometric approach. Compared with standard non-adiabatic holonomic quantum computation, the holonomies obtained in our approach tends asymptotically to those of the adiabatic approach in the long run-time limit and thus might open up a new horizon for realizing a practical quantum computer.
PI3K/Akt signaling pathway triggers P2X7 receptor expression as a pro-survival factor of neuroblastoma cells under limiting growth conditions
Authors: Gómez-Villafuertes Rosa , García-Huerta Paula , Díaz-Hernández Juan Ignacio , Miras-Portugal Mª Teresa 
Published: December 2015

AbstractThe expression of purinergic P2X7 receptor (P2X7R) in neuroblastoma cells is associated to accelerated growth rate, angiogenesis, metastasis and poor prognosis. Noticeably, P2X7R allows the survival of neuroblastoma cells under restrictive conditions, including serum and glucose deprivation. Previously we identified specificity protein 1 (Sp1) as the main factor involved in the transcriptional regulation of P2rx7 gene, reporting that serum withdrawal triggers the expression of P2X7R in Neuro-2a (N2a) neuroblastoma cell line. Here we demonstrate that PI3K/Akt pathway is crucial for the upregulation of P2X7R expression in serum-deprived neuroblastoma cells, circumstance that facilitates cell proliferation in the absence of trophic support. The effect exerted by PI3K/Akt is independent of both mTOR and GSK3, but requires the activation of EGF receptor (EGFR). Nuclear levels of Sp1 are strongly reduced by inhibition of PI3K/Akt pathway and blockade of Sp1-dependent transcription with mithramycin A prevents upregulation of P2rx7 gene expression following serum withdrawal. Furthermore, atypical PKCζ plays a key role in the regulation of P2X7R expression by preventing phosphorylation and, consequently, activation of Akt. Altogether, these data indicate that activation of EGFR enhanced the expression of P2X7R in neuroblastoma cells lacking trophic support, being PI3K/Akt/PKCζ signaling pathway and Sp1 mediating this pro-survival outcome.
Non-Faradaic Electrochemical Detection of Exocytosis from Mast and Chromaffin Cells Using Floating-Gate MOS Transistors
Authors: Jayant Krishna , Singhai Amit , Cao Yingqiu , Phelps Joshua B. , Lindau Manfred , Holowka David A. , Baird Barbara A. , Kan Edwin C. 
Published: December 2015

AbstractWe present non-faradaic electrochemical recordings of exocytosis from populations of mast and chromaffin cells using chemoreceptive neuron MOS (CνMOS) transistors. In comparison to previous cell-FET-biosensors, the CνMOS features control (CG), sensing (SG) and floating gates (FG), allows the quiescent point to be independently controlled, is CMOS compatible and physically isolates the transistor channel from the electrolyte for stable long-term recordings. We measured exocytosis from RBL-2H3 mast cells sensitized by IgE (bound to high-affinity surface receptors FcεRI) and stimulated using the antigen DNP-BSA. Quasi-static I-V measurements reflected a slow shift in surface potential ("Equation missing") which was dependent on extracellular calcium ([Ca]o) and buffer strength, which suggests sensitivity to protons released during exocytosis. Fluorescent imaging of dextran-labeled vesicle release showed evidence of a similar time course, while un-sensitized cells showed no response to stimulation. Transient recordings revealed "Equation missing" fluctuations with a rapid rise and slow decay. Chromaffin cells stimulated with high KCl showed both slow "Equation missing" shifts and extracellular action potentials exhibiting biphasic and inverted capacitive waveforms, indicative of varying ion-channel distributions across the cell-transistor junction. Our approach presents a facile method to simultaneously monitor exocytosis and ion channel activity with high temporal sensitivity without the need for redox chemistry.
Caspase-11 and caspase-1 differentially modulate actin polymerization via RhoA and Slingshot proteins to promote bacterial clearance
Authors: Caution Kyle , Gavrilin Mikhail A. , Tazi Mia , Kanneganti Apurva , Layman Daniel , Hoque Sheshadri , Krause Kathrin , Amer Amal O. 
Published: December 2015

AbstractInflammasomes are multiprotein complexes that include members of the NOD-like receptor family and caspase-1. Caspase-1 is required for the fusion of the Legionella vacuole with lysosomes. Caspase-11, independently of the inflammasome, also promotes phagolysosomal fusion. However, it is unclear how these proteases alter intracellular trafficking. Here, we show that caspase-11 and caspase-1 function in opposing manners to phosphorylate and dephosphorylate cofilin, respectively upon infection with Legionella. Caspase-11 targets cofilin via the RhoA GTPase, whereas caspase-1 engages the Slingshot phosphatase. The absence of either caspase-11 or caspase-1 maintains actin in the polymerized or depolymerized form, respectively and averts the fusion of pathogen-containing vacuoles with lysosomes. Therefore, caspase-11 and caspase-1 converge on the actin machinery with opposing effects to promote vesicular trafficking.
A lipasin/Angptl8 monoclonal antibody lowers mouse serum triglycerides involving increased postprandial activity of the cardiac lipoprotein lipase
Authors: Fu Zhiyao , Abou-Samra Abdul B. , Zhang Ren 
Published: December 2015

AbstractLipasin/Angptl8 is a feeding-induced hepatokine that regulates triglyceride (TAG) metabolism; its therapeutical potential, mechanism of action and relation to the lipoprotein lipase (LPL), however, remain elusive. We generated five monoclonal lipasin antibodies, among which one lowered the serum TAG level when injected into mice and the epitope was determined to be EIQVEE. Lipasin-deficient mice exhibited elevated postprandial activity of LPL in the heart and skeletal muscle, but not in white adipose tissue (WAT), suggesting that lipasin suppresses the activity of LPL specifically in cardiac and skeletal muscles. Consistently, mice injected with the effective antibody or with lipasin deficiency had increased postprandial cardiac LPL activity and lower TAG levels only in the fed state. These results suggest that lipasin acts, at least in part, in an endocrine manner. We propose the following model: feeding induces lipasin, activating the lipasin-Angptl3 pathway, which inhibits LPL in cardiac and skeletal muscles to direct circulating TAG to WAT for storage; conversely, fasting induces Angptl4, which inhibits LPL in WAT to direct circulating TAG to cardiac and skeletal muscles for oxidation. This model suggests a general mechanism by which TAG trafficking is coordinated by lipasin, Angptl3 and Angptl4 at different nutritional statuses.
Identification of Nα-acetyl-α-lysine as a probable thermolyte and its accumulation mechanism in Salinicoccus halodurans H3B36
Authors: Jiang Kai , Xue Yanfen , Ma Yanhe 
Published: December 2015

AbstractSalinicoccus halodurans H3B36 is a moderate halophile that was isolated from a 3.2-m-deep sediment sample in Qaidam Basin, China. Our results suggest that Nα-acetyl-α-lysine can accumulate and act as a probable thermolyte in this strain. The accumulation mechanism and biosynthetic pathway for this rare compatible solute were also elucidated. We confirmed that the de novo synthesis pathway of Nα-acetyl-α-lysine in this strain starts from aspartate and passes through lysine. Through RNA sequencing, we also found an 8-gene cluster (orf_1582–1589) and another gene (orf_2472) that might encode the biosynthesis of Nα-acetyl-α-lysine in S. halodurans H3B36. Orf_192, orf_193 and orf_1259 might participate in the transportation of precursors for generating Nα-acetyl-α-lysine under the heat stress. The transcriptome reported here also generated a global view of heat-induced changes and yielded clues for studying the regulation of Nα-acetyl-α-lysine accumulation. Heat stress triggered a global transcriptional disturbance and generated a series of actions to adapt the strain to heat stress. Furthermore, the transcriptomic results showed that the regulon of RpoN (orf_2534) may be critical to conferring heat stress tolerance and survival to S. halodurans.
Comparison of catch per unit effort among four minnow trap models in the three-spined stickleback (Gasterosteus aculeatus) fishery
Authors: Budria Alexandre , DeFaveri Jacquelin , Merilä Juha 
Published: December 2015

AbstractMinnow traps are commonly used in the stickleback (Gasterostidae) fishery, but the potential differences in catch per unit effort (CPUE) among different minnow trap models are little studied. We compared the CPUE of four different minnow trap models in field experiments conducted with three-spined sticklebacks (Gasterosteus aculeatus). Marked (up to 26 fold) differences in median CPUE among different trap models were observed. Metallic uncoated traps yielded the largest CPUE (2.8 fish/h), followed by metallic black nylon-coated traps (1.3 fish/h). Collapsible canvas traps yielded substantially lower CPUEs (black: 0.7 fish/h; red: 0.1 fish/h) than the metallic traps. Laboratory trials further revealed significant differences in escape probabilities among the different trap models. While the differences in escape probability can explain at least part of the differences in CPUE among the trap models (e.g. high escape rate and low CPUE in red canvas traps), discrepancies between model-specific CPUEs and escape rates suggests that variation in entrance rate also contributes to the differences in CPUE. In general and in accordance with earlier data on nine-spined stickleback (Pungitius pungitius) trapping, the results suggest that uncoated metallic (Gee-type) traps are superior to the other commonly used minnow trap models in stickleback fisheries.
Did Large-Scale Vaccination Drive Changes in the Circulating Rotavirus Population in Belgium?
Authors: Pitzer Virginia E. , Bilcke Joke , Heylen Elisabeth , Crawford Forrest W. , Callens Michael , De Smet Frank , Van Ranst Marc , Zeller Mark , Matthijnssens Jelle 
Published: December 2015

AbstractVaccination can place selective pressures on viral populations, leading to changes in the distribution of strains as viruses evolve to escape immunity from the vaccine. Vaccine-driven strain replacement is a major concern after nationwide rotavirus vaccine introductions. However, the distribution of the predominant rotavirus genotypes varies from year to year in the absence of vaccination, making it difficult to determine what changes can be attributed to the vaccines. To gain insight in the underlying dynamics driving changes in the rotavirus population, we fitted a hierarchy of mathematical models to national and local genotype-specific hospitalization data from Belgium, where large-scale vaccination was introduced in 2006. We estimated that natural- and vaccine-derived immunity was strongest against completely homotypic strains and weakest against fully heterotypic strains, with an intermediate immunity amongst partially heterotypic strains. The predominance of G2P[4] infections in Belgium after vaccine introduction can be explained by a combination of natural genotype fluctuations and weaker natural and vaccine-induced immunity against infection with strains heterotypic to the vaccine, in the absence of significant variation in strain-specific vaccine effectiveness against disease. However, the incidence of rotavirus gastroenteritis is predicted to remain low despite vaccine-driven changes in the distribution of genotypes.
Identification, characterization and molecular analysis of the viable but nonculturable Rhodococcus biphenylivorans
Authors: Su Xiaomei , Sun Faqian , Wang Yalin , Hashmi Muhammad Zaffar , Guo Li , Ding Linxian , Shen Chaofeng 
Published: December 2015

AbstractNumerous bacteria, including pollutant-degrading bacteria can enter the viable but nonculturable state (VBNC) when they encounter harsh environmental conditions. VBNC bacteria, as a vast majority of potent microbial resource can be of great significance in environmental rehabilitation. It is necessary to study the VBNC state of pollutant-degrading bacteria under various stress conditions. The aim of this study was to determine whetherRhodococcus biphenylivoranscould enter the VBNC state under oligotrophic and low temperature conditions and to examine the changes of morphology, enzymatic activity and gene expressions that might underline such state. The obtained results indicated thatR.biphenylivoransTG9Tcould enter into the VBNC state and recover culturability under favorable environmental conditions. Results from Illumina high throughput RNA-sequencing revealed that the up-regulated genes related to ATP accumulation, protein modification, peptidoglycan biosynthesis and RNA polymerase were found in the VBNC cells and the down-regulated genes mainly encoded hypothetical protein, membrane protein and NADH dehydrogenase subunit, which render VBNC cells more tolerant to survive under inhospitable conditions. This study provides new insights into prevention and control of the VBNC state of pollutant-degrading bacteria for their better capabilities in environmental rehabilitation.
Controllable Growth of Large–Size Crystalline MoS2 and Resist-Free Transfer Assisted with a Cu Thin Film
Authors: Lin Ziyuan , Zhao Yuda , Zhou Changjian , Zhong Ren , Wang Xinsheng , Tsang Yuen Hong , Chai Yang 
Published: December 2015

AbstractTwo-dimensional MoS2 is a promising material for future nanoelectronics and optoelectronics. It has remained a great challenge to grow large-size crystalline and high surface coverage monolayer MoS2. In this work, we investigate the controllable growth of monolayer MoS2 evolving from triangular flakes to continuous thin films by optimizing the concentration of gaseous MoS2, which has been shown a both thermodynamic and kinetic growth factor. A single-crystal monolayer MoS2 larger than 300 μm was successfully grown by suppressing the nuclei density and supplying sufficient source. Furthermore, we present a facile process of transferring the centimeter scale MoS2 assisted with a copper thin film. Our results show the absence of observable residues or wrinkles after we transfer MoS2 from the growth substrates onto flat substrates using this technique, which can be further extended to transfer other two-dimensional layered materials.
Systemic treatment of patients with metachronous peritoneal carcinomatosis of colorectal origin
Authors: van Oudheusden T. R. , Razenberg L. G. , van Gestel Y. R. , Creemers G. J. , Lemmens V. E. , de Hingh I. H. 
Published: December 2015

AbstractCombining chemotherapy and targeted therapies has resulted in an enhanced survival in metastatic colorectal cancer (mCRC) patients. However, the result of this palliative treatment in patients with metachronous peritoneal carcinomatosis (PC) remains unknown. The current population-based study aims to investigate the use and effect of palliative systemic treatment in patients with metachronous PC of colorectal origin. Data on metachronous PC were collected between 2010 and 2011 for all patients who were diagnosed with M0 colorectal cancer between 2003 and 2008 in the Dutch Eindhoven Cancer Registry. Patient demographics and detailed data on chemotherapeutic treatment were collected and compared. Ninety-two patients with metachronous PC received chemotherapy in a palliative setting compared to 94 patients without treatment. In 36 patients, Bevacizumab was added to the treatment (39%). Overall survival was 3.4, 13 and 20.3 months in the no treatment, systemic treatment and systemic treatment + Bevacizumab respectively (P < 0.001). Male gender was a positive predictor and right sided primary tumor location a negative predictor of receiving bevacizumab. Approximately 40% of patients with metachronous PC received bevacizumab in addition to chemotherapy. Treatment with systemic chemotherapy in combination with bevacizumab may increase survival in a patients with metachronous colorectal PC.
Low temperature superplasticity and thermal stability of a nanostructured low-carbon microalloyed steel
Authors: Hu J. , Du L.-X. , Sun G.-S. , Xie H. , Misra R.D.K. 
Published: December 2015

AbstractWe describe here for the first time the low temperature superplasticity of nanostructured low carbon steel (microalloyed with V, N, Mn, Al, Si and Ni). Low carbon nanograined/ultrafine-grained (NG/UFG) bulk steel was processed using a combination of cold-rolling and annealing of martensite. The complex microstructure of NG/UFG ferrite and 50–80 nm cementite exhibited high thermal stability at 500 °C with low temperature elongation exceeding 100% (at less than 0.5 of the absolute melting point) as compared to the conventional fine-grained (FG) counterpart. The low temperature superplasticity is adequate to form complex components. Moreover, the low strength during hot processing is favorable for decreasing the spring back and minimize die loss.
Genome-wide association study reveals two loci for serum magnesium concentrations in European-American children
Authors: Chang Xiao , Glessner Joseph , Tin Adrienne , Li Jin , Guo Yiran , Wei Zhi , Liu Yichuan , Mentch Frank D. , Hou Cuiping , Zhao Yan , Wang Tiancheng , Qiu Haijun , Kim Cecilia , Sleiman Patrick M. A. , Hakonarson Hakon 
Published: December 2015

AbstractMagnesium ions are essential to the basic metabolic processes in the human body. Previous genetic studies indicate that serum magnesium levels are highly heritable and a few genetic loci have been reported involving regulation of serum magnesium in adults. In this study, we examined if additional loci influence serum magnesium levels in children. We performed a genome-wide association study (GWAS) on 2,267 European-American children genotyped on the Illumina HumanHap550 or Quad610 arrays, sharing over 500,000 markers, as the discovery cohort and 257 European-American children genotyped on the Illumina Human OmniExpress arrays as the replication cohort. After genotype imputation, the strongest associations uncovered were with imputed SNPs residing within theFGFR2(rs1219515,P = 1.1 × 10−5) andPAPSS2(rs1969821,P = 7.2 × 10−6) loci in the discovery cohort, both of which were robustly replicated in our independent patient cohort (rs1219515,P = 3.5 × 10−3; rs1969821,P = 1.2 × 10−2). The associations at theFGFR2locus were also weakly replicated in a dataset from a previous GWAS of serum magnesium in European adults. Our results indicate thatFGFR2andPAPSS2may play an important role in the regulation of magnesium homeostasis in children of European-American ancestry.