bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graphitic carbon nitride nanosheet electrode-based high-performance ionic actuator
Authors: Wu Guan , Hu Ying , Liu Yang , Zhao Jingjing , Chen Xueli , Whoehling Vincent , Plesse Cédric , Nguyen Giao T. M. , Vidal Frédéric , Chen Wei 
Published: June 2015

AbstractIonic actuators have attracted attention due to their remarkably large strain under low-voltage stimulation. Because actuation performance is mainly dominated by the electrochemical and electromechanical processes of the electrode layer, the electrode material and structure are crucial. Here, we report a graphitic carbon nitride nanosheet electrode-based ionic actuator that displays high electrochemical activity and electromechanical conversion abilities, including large specific capacitance (259.4 F g−1) with ionic liquid as the electrolyte, fast actuation response (0.5±0.03% in 300 ms), large electromechanical strain (0.93±0.03%) and high actuation stability (100,000 cycles) under 3 V. The key to the high performance lies in the hierarchical pore structure with dominant size <2 nm, optimal pyridinic nitrogen active sites (6.78%) and effective conductivity (382 S m−1) of the electrode. Our study represents an important step towards artificial muscle technology in which heteroatom modulation in electrodes plays an important role in promoting electrochemical actuation performance.
Identification of new susceptibility loci for IgA nephropathy in Han Chinese
Authors: Li Ming , Foo Jia-Nee , Wang Jin-Quan , Low Hui-Qi , Tang Xue-Qing , Toh Kai-Yee , Yin Pei-Ran , Khor Chiea-Chuen , Goh Yu-Fen , Irwan Ishak D. , Xu Ri-Cong , Andiappan Anand K. , Bei Jin-Xin , Rotzschke Olaf , Chen Meng-Hua , Cheng Ching-Yu , Sun Liang-Dan , Jiang Geng-Ru , Wong Tien-Yin , Lin Hong-Li , Aung Tin , Liao Yun-Hua , Saw Seang-Mei , Ye Kun , Ebstein Richard P. , Chen Qin-Kai , Shi Wei , Chew Soo-Hong , Chen Jian , Zhang Fu-Ren , Li Sheng-Ping , Xu Gang , Shyong Tai E. , Wang Li , Chen Nan , Zhang Xue-Jun , Zeng Yi-Xin , Zhang Hong , Liu Zhi-Hong , Yu Xue-Qing , Liu Jian-Jun 
Published: June 2015

AbstractIgA nephropathy (IgAN) is one of the most common primary glomerulonephritis. Previously identified genome-wide association study (GWAS) loci explain only a fraction of disease risk. To identify novel susceptibility loci in Han Chinese, we conduct a four-stage GWAS comprising 8,313 cases and 19,680 controls. Here, we show novel associations at ST6GAL1 on 3q27.3 (rs7634389, odds ratio (OR)=1.13, P=7.27 × 10−10), ACCS on 11p11.2 (rs2074038, OR=1.14, P=3.93 × 10−9) and ODF1-KLF10 on 8q22.3 (rs2033562, OR=1.13, P=1.41 × 10−9), validate a recently reported association at ITGAX-ITGAM on 16p11.2 (rs7190997, OR=1.22, P=2.26 × 10−19), and identify three independent signals within the DEFA locus (rs2738058, P=1.15 × 10−19; rs12716641, P=9.53 × 10−9; rs9314614, P=4.25 × 10−9, multivariate association). The risk variants on 3q27.3 and 11p11.2 show strong association with mRNA expression levels in blood cells while allele frequencies of the risk variants within ST6GAL1, ACCS and DEFA correlate with geographical variation in IgAN prevalence. Our findings expand our understanding on IgAN genetic susceptibility and provide novel biological insights into molecular mechanisms underlying IgAN.
Direct observation of TALE protein dynamics reveals a two-state search mechanism
Authors: Cuculis Luke , Abil Zhanar , Zhao Huimin , Schroeder Charles M. 
Published: June 2015

AbstractTranscription activator-like effector (TALE) proteins are a class of programmable DNA-binding proteins for which the fundamental mechanisms governing the search process are not fully understood. Here we use single-molecule techniques to directly observe TALE search dynamics along DNA templates. We find that TALE proteins are capable of rapid diffusion along DNA using a combination of sliding and hopping behaviour, which suggests that the TALE search process is governed in part by facilitated diffusion. We also observe that TALE proteins exhibit two distinct modes of action during the search process—a search state and a recognition state—facilitated by different subdomains in monomeric TALE proteins. Using TALE truncation mutants, we further demonstrate that the N-terminal region of TALEs is required for the initial non-specific binding and subsequent rapid search along DNA, whereas the central repeat domain is required for transitioning into the site-specific recognition state.
Chemical reaction mechanisms in solution from brute force computational Arrhenius plots
Authors: Kazemi Masoud , Åqvist Johan 
Published: June 2015

AbstractDecomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to whether these are calibrated by quantum mechanical calculations or experimental data. The thermodynamic activation parameters are in remarkable agreement with experiment results and allow discrimination among alternative mechanisms, as well as rationalization of their different activation enthalpies and entropies.
‘I still don’t know diddly’: a longitudinal qualitative study of patients’ knowledge and distress while undergoing evaluation of incidental pulmonary nodules
Authors: Sullivan Donald R , Golden Sara E , Ganzini Linda , Hansen Lissi , Slatore Christopher G 
Published: June 2015

Abstract
Background:
Hundreds of thousands of incidental pulmonary nodules are detected annually in the United States, and this number will increase with the implementation of lung cancer screening. The lengthy period for active pulmonary nodule surveillance, often several years, is unique among cancer regimens. The psychosocial impact of longitudinal incidental nodule follow-up, however, has not been described.

Aims:
We sought to evaluate the psychosocial impact of longitudinal follow-up of incidental nodule detection on patients.

Methods:
Veterans who participated in our previous study had yearly follow-up qualitative interviews coinciding with repeat chest imaging. We used conventional content analysis to explore their knowledge of nodules and the follow-up plan, and their distress.

Results:
Seventeen and six veterans completed the year one and year two interviews, respectively. Over time, most patients continued to have inadequate knowledge of pulmonary nodules and the nodule follow-up plan. They desired and appreciated more information directly from their primary care provider, particularly about their lung cancer risk. Distress diminished over time for most patients, but it increased around the time of follow-up imaging for some, and a small number reported severe distress.

Conclusions:
In settings in which pulmonary nodules are commonly detected, including lung cancer screening programmes, resources to optimise patient-centred communication strategies that improve patients’ knowledge and reduce distress should be developed.
Nuclear accumulation of CDH1 mRNA in hepatocellular carcinoma cells
Authors: Ghafoory S , Mehrabi A , Hafezi M , Cheng X , Breitkopf-Heinlein K , Hick M , Huichalaf M , Herbel V , Saffari A , Wölfl S 
Published: June 2015

AbstractExpression of E-cadherin has a central role in maintaining epithelial morphology. In solid tumors, reduction of E-cadherin results in disruption of intercellular contacts. Consequently, cells lose adhesive properties and gain more invasive mesenchymal properties. Nevertheless, the mechanism of E-cadherin regulation is not completely elucidated. Here we analyzed the distribution of E-cadherin expression at the cell level in human hepatocellular carcinoma, in which human liver paraffin blocks from 25 hepatocellular carcinoma patients were prepared from cancerous (CA) and noncancerous areas (NCA). In situ hybridization (ISH) was performed to detect E-cadherin and hypoxia-induced factor-1α (HIF1α) mRNAs and immunohistochemistry to stain E-cadherin protein. In parallel, RNA was extracted from CA and NCA, and E-cadherin and HIF1α were quantified by quantitative reverse transcription PCR. ISH revealed abundant E-cadherin mRNA in nuclei of hepatocellular carcinoma cells (HCCs), whereas immunohistochemistry showed depletion of E-cadherin protein from these areas. In sections of NCA, E-cadherin mRNA was also found in the cytosol, and E-cadherin protein was detected on the membrane of cells. Experiments in cell lines confirmed E-cadherin mRNA in nuclei of cells negative for E-cadherin protein. HIF1α expression is elevated in CAs, which is associated with a clear cytosolic staining for this mRNA. Our results demonstrate that E-caderhin mRNA is selectively retained in nuclei of HCCs, whereas other mRNAs are still exported, suggesting that translocation of E-cadherin mRNA from nuclei to cytoplasm has a role in regulating E-cadherin protein levels during epithelial mesenchymal transition.
Real-time and simultaneous monitoring of the phosphorylation and enhanced interaction of p53 and XPC acidic domains with the TFIIH p62 subunit
Authors: Okuda M , Nishimura Y 
Published: June 2015

AbstractPosttranslational modifications have critical roles in diverse biological processes through interactions. Tumor-suppressor protein p53 and nucleotide excision repair factor XPC each contain an acidic region, termed the acidic transactivation domain (TAD) and acidic fragment (AF), respectively, that binds to the pleckstrin homology (PH) domain of the p62 subunit of the transcription factor TFIIH. Human p53-TAD contains seven serine and two threonine residues, all of which can be phosphorylated. Similarly, XPC-AF contains six serine and two threonine residues, of which Thr117, Ser122 and Ser129 have been reported as phosphorylation sites in vivo, although their phosphorylation roles are unknown. Phosphorylation of Ser46 and Thr55 of p53-TAD increases its binding ability; however, the role of XPC-AF phosphorylation remains elusive. Here we describe a system for real-time and simultaneous monitoring of the phosphorylation and p62-PH affinity of p53-TAD and XPC-AF using nuclear magnetic resonance (NMR) spectroscopy. Unexpectedly, among seven reported kinases that presumably phosphorylate Ser46 and/or Thr55 of p53-TAD, only two specific and high-efficiency enzymes were identified: JNK2α2 for Ser46 and GRK5 for Thr55. During interaction with p62-PH, four different affinity complexes resulting from various phosphorylation states of p53-TAD by the kinases were identified. The kinetics of the site-specific phosphorylation reaction of p53-TAD and its affinity for p62-PH were monitored in real-time using the NMR system. Isothermic calorimetry showed that phosphorylation of Ser129 of XPC-AF increases binding to p62-PH. Although CK2 was predicted to phosphorylate Ser122, Ser129 and Ser140 from its sequence context, it specifically and efficiently phosphorylated only Ser129. Simultaneous monitoring of the phosphorylation and augmentation in p62-PH binding identified a key residue of p62-PH for contacting phosphorylated Ser129. In summary, we have established an NMR system for real-time and simultaneous monitoring of site-specific phosphorylation and enhancement of affinity between phosphorylation domains and their target. The system is also applicable to other posttranslational modifications.
Compensatory angiogenesis and tumor refractoriness
Authors: Gacche R N 
Published: June 2015

AbstractSince the establishment of tumor angiogenesis as a therapeutic target, an excitement in developing the anti-angiogenic agents was resulted in tailoring a humanized monoclonal antibody (Bevacizumab) against vascular endothelial growth factor (VEGF): a key factor in recruiting angiogenesis. The past three decades’ research in the area of angiogenesis also invented a series of novel and effective anti-angiogenic agents targeting the VEGF signaling axis. Despite the demonstrable clinical benefits of anti-angiogenic therapy, the preclinical and clinical data of the current therapeutic settings clearly indicate the transient efficacy, restoration of tumor progression and aggressive recurrence of tumor invasion after the withdrawal of anti-angiogenic therapy. Therefore, the impact of this therapeutic regime on improving overall survival of patients has been disappointing in clinic. The recent advances in pathophysiology of tumor angiogenesis and related molecular and cellular underpinnings attributed the conspiracy of compensatory angiogenic pathways in conferring evasive and intrinsic tumor resistance to anti-angiogenic agents. The understandings of how these pathways functionally cross-talk for sustaining tumor angiogenesis during VEGF blockade is essential and perhaps may act as a basic prerequisite for designing novel therapeutic strategies to combat the growing arrogance of tumors toward anti-angiogenic agents. The present review offers a discourse on major compensatory angiogenic pathways operating at cellular and molecular levels and their attributes with resistance to anti-angiogenic agents along with strategic opinions on future setting in targeting tumor angiogenesis.
Mutations of the functional ARH1 allele in tumors from ARH1 heterozygous mice and cells affect ARH1 catalytic activity, cell proliferation and tumorigenesis
Authors: Kato J , Vekhter D , Heath J , Zhu J , Barbieri J T , Moss J 
Published: June 2015

AbstractADP-ribosylation results from transfer of the ADP-ribose moiety of nicotinamide adenine dinucleotide (NAD) to an acceptor with ADP-ribose-acceptor content determined by the activities of ADP-ribosyltransferases, which modify the acceptor, and ADP-ribose-acceptor hydrolase (ARH), which cleave the ADP-ribose-acceptor bond. ARH1 was discovered as an ADP-ribose(arginine)protein hydrolase. Previously, we showed that ARH1-knockout and ARH1 heterozygous mice spontaneously developed tumors. Further, ARH1-knockout and ARH1 heterozygous mouse embryonic fibroblasts (MEFs) produced tumors when injected into nude mice. In tumors arising in ARH1 heterozygous mice and MEFs, we found both loss of heterozygosity (LOH) of the ARH1 gene and ARH1 gene mutations. In the present report, we found that these mutant ARH1 genes encode proteins with reduced ARH1 enzymatic activity. Moreover, MEFs transformed with ARH1 mutant genes exhibiting different levels of ARH1 activity showed altered rates of proliferation, anchorage-independent colony growth in soft agar, and tumorigenesis in nude mice. MEFs transformed with the wild-type (WT) gene, but expressing low levels of hydrolase activity were also tumorigenic. However, transformation with the WT gene was less likely to yield tumors than transformation with a mutant gene exhibiting similar hydrolase activity. Thus, control of protein-ADP-ribosylation by ARH1 is critical for tumorigenesis. In the human cancer database, LOH and mutations of the ARH1 gene were observed. Further, ARH1 gene mutations were located in exons 3 and 4, comparable to exons 2 and 3 of the murine ARH1 gene, which comprise the catalytic site. Thus, human ARH1 gene mutations similar to their murine counterparts may be involved in human cancers.
The infection of turkeys and chickens by reassortants derived from pandemic H1N1 2009 and avian H9N2 influenza viruses
Authors: Sun Honglei , Kong Weili , Liu Litao , Qu Yi , Li Chong , Shen Ye , Zhou Yu , Wang Yu , Wu Sizhe , Pu Juan , Liu Jinhua , Sun Yipeng 
Published: June 2015

AbstractOutbreaks of pandemic H1N1 2009 (pH1N1) in turkeys have been reported in several countries. Co-infection of pH1N1 and avian H9N2 influenza viruses in turkeys provide the opportunity for their reassortment and novel reassortant viruses might further be transmitted to other avian species. However, virulence and transmission of those reassortant viruses in poultry remain unclear. In the present study, we generated 16 single-gene reassortant influenza viruses including eight reassortants on the pH1N1 background by individual replacement with a corresponding gene segment from H9N2 and eight reassortants on the H9N2 background replaced individually with corresponding gene from pH1N1 and characterized reassortants viruses in turkeys and chickens. We found that the pH1N1 virus dramatically increased its infectivity and transmissibility in turkeys and chickens after introducing any gene (except for PB2) from H9N2 virus and H9N2 virus acquired single gene (except for HA) of pH1N1 almost did not influence its replication and transmission in turkeys and chickens. Additionally, 13 reassortant viruses transmitted from turkeys to chickens. Our results indicate that turkeys and chickens are susceptible to pH1N1-H9N2 reassortant viruses and mixing breeding of different avian species would facilitate the transmission of these reassortant viruses.
Placement of oppositely charged aminoacids at a polypeptide termini determines the voltage-controlled braking of polymer transport through nanometer-scale pores
Authors: Asandei Alina , Chinappi Mauro , Lee Jong-kook , Ho Seo Chang , Mereuta Loredana , Park Yoonkyung , Luchian Tudor 
Published: June 2015

AbstractProtein and solid-state nanometer-scale pores are being developed for the detection, analysis and manipulation of single molecules. In the simplest embodiment, the entry of a molecule into a nanopore causes a reduction in the latter’s ionic conductance. The ionic current blockade depth and residence time have been shown to provide detailed information on the size, adsorbed charge and other properties of molecules. Here we describe the use of the nanopore formed by Staphylococcus aureus α-hemolysin and polypeptides with oppositely charged segments at the N- and C-termini to increase both the polypeptide capture rate and mean residence time of them in the pore, regardless of the polarity of the applied electrostatic potential. The technique provides the means to improve the signal to noise of single molecule nanopore-based measurements.
Automated Detection of Leakage in Fluorescein Angiography Images with Application to Malarial Retinopathy
Authors: Zhao Yitian , J. C. MacCormick Ian , G. Parry David , Leach Sophie , A. V. Beare Nicholas , P. Harding Simon , Zheng Yalin 
Published: June 2015

AbstractThe detection and assessment of leakage in retinal fluorescein angiogram images is important for the management of a wide range of retinal diseases. We have developed a framework that can automatically detect three types of leakage (large focal, punctate focal and vessel segment leakage) and validated it on images from patients with malarial retinopathy. This framework comprises three steps: vessel segmentation, saliency feature generation and leakage detection. We tested the effectiveness of this framework by applying it to images from 20 patients with large focal leak, 10 patients with punctate focal leak and 5,846 vessel segments from 10 patients with vessel leakage. The sensitivity in detecting large focal, punctate focal and vessel segment leakage are 95%, 82% and 81%, respectively, when compared to manual annotation by expert human observers. Our framework has the potential to become a powerful new tool for studying malarial retinopathy and other conditions involving retinal leakage.
Carrier type inversion in quasi-free standing graphene: studies of local electronic and structural properties
Authors: Melios Christos , Panchal Vishal , Giusca Cristina E. , Strupiński Włodek , Silva S. Ravi P. , Kazakova Olga 
Published: June 2015

AbstractWe investigate the local surface potential and Raman characteristics of as-grown and ex-situ hydrogen intercalated quasi-free standing graphene on 4H-SiC(0001) grown by chemical vapor deposition. Upon intercalation, transport measurements reveal a change in the carrier type from n- to p-type, accompanied by a more than three-fold increase in carrier mobility, up to μh ≈ 4540 cm2 V−1 s−1. On a local scale, Kelvin probe force microscopy provides a complete and detailed map of the surface potential distribution of graphene domains of different thicknesses. Rearrangement of graphene layers upon intercalation to (n + 1)LG, where n is the number of graphene layers (LG) before intercalation, is demonstrated. This is accompanied by a significant increase in the work function of the graphene after the H2-intercalation, which confirms the change of majority carriers from electrons to holes. Raman spectroscopy and mapping corroborate surface potential studies.
The Wnt5a-Ror2 axis promotes the signaling circuit between interleukin-12 and interferon-γ in colitis
Authors: Sato Akira , Kayama Hisako , Shojima Kensaku , Matsumoto Shinji , Koyama Hirofumi , Minami Yasuhiro , Nojima Satoshi , Morii Eiichi , Honda Hiroaki , Takeda Kiyoshi , Kikuchi Akira 
Published: June 2015

AbstractWnt5a, which regulates various cellular functions in Wnt signaling, is involved in inflammatory responses, however the mechanism is not well understood. We examined the role of Wnt5a signaling in intestinal immunity using conditional knockout mice for Wnt5a and its receptor Ror2. Removing Wnt5a or Ror2 in adult mice suppressed dextran sodium sulfate (DSS)-induced colitis. It also attenuated the DSS-dependent increase in inflammatory cytokine production and decreased interferon-γ (IFN-γ)-producing CD4+ Th1 cell numbers in the colon. Wnt5a was highly expressed in stromal fibroblasts in ulcerative lesions in the DSS-treated mice and inflammatory bowel disease patients. Dendritic cells (DCs) isolated from the colon of Wnt5a and Ror2 deficient mice reduced the ability to differentiate naïve CD4+ T cells to IFN-γ-producing CD4+ Th1 cells. In vitro experiments demonstrated that the Wnt5a-Ror2 signaling axis augmented the DCs priming effect of IFN-γ, leading to enhanced lipopolysaccharide (LPS)-induced interleukin (IL)-12 expression. Taken together, these results suggest that Wnt5a promotes IFN-γ signaling, leading to IL-12 expression in DCs and thereby inducing Th1 differentiation in colitis.
Paracrine effects of haematopoietic cells on human mesenchymal stem cells
Authors: Zhou Shuanhu 
Published: June 2015

AbstractStem cell function decline during ageing can involve both cell intrinsic and extrinsic mechanisms. Bone and blood formation are intertwined in bone marrow, therefore haematopoietic cells and bone cells could be extrinsic factors for each other. In this study, we assessed the paracrine effects of extrinsic factors from haematopoietic cells on human mesenchymal stem cells (MSCs). Our data showed that haematopoietic cells stimulate proliferation, osteoblast differentiation and inhibit senescence of MSCs; TNF-α, PDGF-β, Wnt1, 4, 6, 7a and 10a, sFRP-3 and sFRP-5 are dominantly expressed in haematopoietic cells; the age-related increase of TNF-α in haematopoietic cells may perform as a negative factor in the interactions of haematopoietic cells on MSCs via TNF-α receptors and then activating NF-κB signaling or Wnt/β-catenin signaling to induce senescence and reduce osteoblast differentiation in MSCs. In conclusion, our data demonstrated that there are paracrine interactions of haematopoietic cells on human MSCs; immunosenescence may be one of the extrinsic mechanisms by which skeletal stem cell function decline during human skeletal ageing.