bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic value of a 25-gene assay in patients with gastric cancer after curative resection
Authors: Wang Xiaohong , Liu Yiqiang , Niu Zhaojian , Fu Runjia , Jia Yongning , Zhang Li , Shao Duanfang , Du Hong , Hu Ying , Xing Xiaofang , Cheng Xiaojing , Li Lin , Guo Ting , Li Ziyu , Ji Qunsheng , Zhang Lianhai , Ji Jiafu 
Published: August 2017

AbstractThis study aimed to develop and validate a practical, reliable assay for prognosis and chemotherapy benefit prediction compared with conventional staging in Gastric cancer (GC). Twenty-three candidate genes with significant correlation between quantitative hybridization and microarray results plus 2 reference genes were selected to form a 25-gene prognostic classifier, which can classify patients into 3 distinct groups of different risk of mortality obtained by analyzing microarray data from 78 frozen tumor specimens. The 25-gene assay was associated with overall survival in both training (P = 0.017) and testing cohort (P = 0.005) (462 formalin-fixed paraffin-embedded samples). The risk prediction in stages I + II is significantly better than that in stages III. Analysis demonstrated that this 25-gene signature is an independent prognostic predictor and show higher prognostic accuracy than conventional TNM staging in early stage patients. Moreover, only high-risk patients in stage I + II were found benefit from adjuvant chemotherapy (P = 0.043), while low-risk patients in stage III were not found benefit from adjuvant chemotherapy. In conclusion, our results suggest that this 25-gene assay can reliably identify patients with different risk for mortality after surgery, especially for stage I + II patients, and might be able to predict patients who benefit from chemotherapy.
Strategic tradeoffs in competitor dynamics on adaptive networks
Authors: Hébert-Dufresne Laurent , Allard Antoine , Noël Pierre-André , Young Jean-Gabriel , Libby Eric 
Published: August 2017

AbstractRecent empirical work highlights the heterogeneity of social competitions such as political campaigns: proponents of some ideologies seek debate and conversation, others create echo chambers. While symmetric and static network structure is typically used as a substrate to study such competitor dynamics, network structure can instead be interpreted as a signature of the competitor strategies, yielding competition dynamics on adaptive networks. Here we demonstrate that tradeoffs between aggressiveness and defensiveness (i.e., targeting adversaries vs. targeting like-minded individuals) creates paradoxical behaviour such as non-transitive dynamics. And while there is an optimal strategy in a two competitor system, three competitor systems have no such solution; the introduction of extreme strategies can easily affect the outcome of a competition, even if the extreme strategies have no chance of winning. Not only are these results reminiscent of classic paradoxical results from evolutionary game theory, but the structure of social networks created by our model can be mapped to particular forms of payoff matrices. Consequently, social structure can act as a measurable metric for social games which in turn allows us to provide a game theoretical perspective on online political debates.
Oleate but not stearate induces the regulatory phenotype of myeloid suppressor cells
Authors: Wu Hao , Weidinger Carl , Schmidt Franziska , Keye Jacqueline , Friedrich Marie , Yerinde Cansu , Willimsky Gerald , Qin Zhihai , Siegmund Britta , Glauben Rainer 
Published: August 2017

AbstractTumor infiltrating myeloid cells play contradictory roles in the tumor development. Dendritic cells and classical activated macrophages support anti-tumor immune activity via antigen presentation and induction of pro-inflammatory immune responses. Myeloid suppressor cells (MSCs), for instance myeloid derived suppressor cells (MDSCs) or tumor associated macrophages play a critical role in tumor growth. Here, treatment with sodium oleate, an unsaturated fatty acid, induced a regulatory phenotype in the myeloid suppressor cell line MSC-2 and resulted in an increased suppression of activated T cells, paralleled by increased intracellular lipid droplets formation. Furthermore, sodium oleate potentiated nitric oxide (NO) production in MSC-2, thereby increasing their suppressive capacity. In primary polarized bone marrow cells, sodium oleate (C18:1) and linoleate (C18:2), but not stearate (C18:0) were identified as potent FFA to induce a regulatory phenotype. This effect was abrogated in MSC-2 as well as primary cells by specific inhibition of droplets formation while the inhibition of de novo FFA synthesis proved ineffective, suggesting a critical role for exogenous FFA in the functional induction of MSCs. Taken together our data introduce a new unsaturated fatty acid-dependent pathway shaping the functional phenotype of MSCs, facilitating the tumor escape from the immune system.
Asynchronous pulse responses of soil carbon and nitrogen mineralization to rewetting events at a short-term: Regulation by microbes
Authors: Song Xiaoli , Zhu Jianxing , He Nianpeng , Huang Jianhui , Tian Jing , Zhao Xiang , Liu Yuan , Wang Changhui 
Published: August 2017

AbstractRewetting after precipitation events plays an important role in regulating soil carbon (C) and nitrogen (N) turnover processes in arid and semiarid ecosystems. Here, we conducted a 48-h rewetting simulation experiment with measurements of soil C and N mineralization rates (RC and RN, respectively) and microbial biomass N (MBN) at high temporal resolution to explore the pulse responses of R
C
and RN. RC and RN responded strongly and rapidly to rewetting over the short term. The maximum RC value (because of pulse effects) ranged from 16.53 to 19.33 µg C gsoil−1 h−1, observed 10 min after rewetting. The maximum RN varied from 22.86 to 40.87 µg N gsoil−1 h−1, appearing 5–6 h after rewetting. The responses of soil microbial growth to rewetting were rapid, and the maximum MBN was observed 2–3 h after rewetting. Unexpectedly, there was no correlation between RC, RN, and MBN during the process of rewetting, and RC and RN were uncoupled. In sum, the pulse responses of RC, RN, and microbial growth to simulated rewetting were rapid, strong, and asynchronous, which offers insights into the different responses of microbes to rewetting and mechanisms behind microbes.
Spiral Form of the Human Cochlea Results from Spatial Constraints
Authors: Pietsch M. , Aguirre Dávila L. , Erfurt P. , Avci E. , Lenarz T. , Kral A. 
Published: August 2017

AbstractThe human inner ear has an intricate spiral shape often compared to shells of mollusks, particularly to the nautilus shell. It has inspired many functional hearing theories. The reasons for this complex geometry remain unresolved. We digitized 138 human cochleae at microscopic resolution and observed an astonishing interindividual variability in the shape. A 3D analytical cochlear model was developed that fits the analyzed data with high precision. The cochlear geometry neither matched a proposed function, namely sound focusing similar to a whispering gallery, nor did it have the form of a nautilus. Instead, the innate cochlear blueprint and its actual ontogenetic variants were determined by spatial constraints and resulted from an efficient packing of the cochlear duct within the petrous bone. The analytical model predicts well the individual 3D cochlear geometry from few clinical measures and represents a clinical tool for an individualized approach to neurosensory restoration with cochlear implants.
Group association and vocal behaviour during foraging trips in Gentoo penguins
Authors: Choi Noori , Kim Jeong-Hoon , Kokubun Nobuo , Park Seongseop , Chung Hosung , Lee Won Young 
Published: August 2017

AbstractIn contrast to their terrestrial call, the offshore call of penguins during their foraging trips has been poorly studied due to the inaccessibility of the foraging site—the open ocean—to researchers. Here, we present the first description of the vocal behaviour of penguins in the open ocean and discuss the function of their vocal communication. We deployed an animal-borne camera on gentoo penguins (Pygoscelis papua) and recorded their foraging behaviour during chick guarding. From the video recordings, we collected 598 offshore calls from 10 individuals in two breeding seasons (2014–2015 and 2015–2016), and we analysed the acoustic characteristics and behavioural contexts of these calls, including diving patterns, group association events, and foraging behaviour. The offshore calls varied in their dominant frequency and length, and penguins produced calls of different lengths in succession. Group associations were observed within one minute following an offshore call in almost half of the instances (43.18%). Penguins undertook dives of shallower depths and shorter durations after producing an offshore call than those before producing an offshore call. Our findings show that penguins may use vocal communication in the ocean related with group association during foraging trips.
Double-stranded RNA induces chicken T-cell lymphoma apoptosis by TRIF and NF-κB
Authors: Zou Haitao , Su Ruixue , Ruan Jing , Shao Hongxia , Qian Kun , Ye Jianqiang , Yao Yongxiu , Nair Venugopal , Qin Aijian 
Published: August 2017

AbstractToll-like receptor-3 (TLR3), a member of the pathogen recognition receptor family, has been reported to activate immune response and to exhibit pro-apoptotic activity against some tumor cells. However it is unclear whether TLR3 has same function against chicken lymphoma. In this paper we investigated the effect of TLR3 activation on a Marek’s disease lymphoma-derived chicken cell line, MDCC-MSB1. The TLR3 agonist poly (I:C) activated TLR3 pathway and inhibited tumor cells proliferation through caspase-dependent apoptosis. Using pharmacological approaches, we found that an interferon-independent mechanism involving Toll-IL-1-receptor domain-containing adapter-inducing IFN-α (TRIF) and nuclear factor κB (NF-κB) causes the apoptosis of MDCC-MSB1 cells. This is the first report about the function of TLR3 in chicken T-cell lymphoma, especially in signal pathway. The mechanisms underlying TLR3-mediated apoptosis may contribute to the development of new drug to treat lymphomas and oncovirus infections.
Small molecule-mediated tribbles homolog 3 promotes bone formation induced by bone morphogenetic protein-2
Authors: Fan Jiabing , Pi-Anfruns Joan , Guo Mian , Im Dan C. S. , Cui Zhong-Kai , Kim Soyon , Wu Benjamin M. , Aghaloo Tara L. , Lee Min 
Published: August 2017

AbstractAlthough bone morphogenetic protein-2 (BMP2) has demonstrated extraordinary potential in bone formation, its clinical applications require supraphysiological milligram-level doses that increase postoperative inflammation and inappropriate adipogenesis, resulting in well-documented life-threatening cervical swelling and cyst-like bone formation. Recent promising alternative biomolecular strategies are toward promoting pro-osteogenic activity of BMP2 while simultaneously suppressing its adverse effects. Here, we demonstrated that small molecular phenamil synergized osteogenesis and bone formation with BMP2 in a rat critical size mandibular defect model. Moreover, we successfully elicited the BMP2 adverse outcomes (i.e. adipogenesis and inflammation) in the mandibular defect by applying high dose BMP2. Phenamil treatment significantly improves the quality of newly formed bone by inhibiting BMP2 induced fatty cyst-like structure and inflammatory soft-tissue swelling. The observed positive phenamil effects were associated with upregulation of tribbles homolog 3 (Trib3) that suppressed adipogenic differentiation and inflammatory responses by negatively regulating PPARγ and NF-κB transcriptional activities. Thus, use of BMP2 along with phenamil stimulation or Trib3 augmentation may be a promising strategy to improve clinical efficacy and safety of current BMP therapeutics.
Extreme absorption enhancement in ZnTe:O/ZnO intermediate band core-shell nanowires by interplay of dielectric resonance and plasmonic bowtie nanoantennas
Authors: Nie Kui-Ying , Li Jing , Chen Xuanhu , Xu Yang , Tu Xuecou , Ren Fang-Fang , Du Qingguo , Fu Lan , Kang Lin , Tang Kun , Gu Shulin , Zhang Rong , Wu Peiheng , Zheng Youdou , Tan Hark Hoe , Jagadish Chennupati , Ye Jiandong 
Published: August 2017

AbstractIntermediate band solar cells (IBSCs) are conceptual and promising for next generation high efficiency photovoltaic devices, whereas, IB impact on the cell performance is still marginal due to the weak absorption of IB states. Here a rational design of a hybrid structure composed of ZnTe:O/ZnO core-shell nanowires (NWs) with Al bowtie nanoantennas is demonstrated to exhibit strong ability in tuning and enhancing broadband light response. The optimized nanowire dimensions enable absorption enhancement by engineering leaky-mode dielectric resonances. It maximizes the overlap of the absorption spectrum and the optical transitions in ZnTe:O intermediate-band (IB) photovoltaic materials, as verified by the enhanced photoresponse especially for IB states in an individual nanowire device. Furthermore, by integrating Al bowtie antennas, the enhanced exciton-plasmon coupling enables the notable improvement in the absorption of ZnTe:O/ZnO core-shell single NW, which was demonstrated by the profound enhancement of photoluminescence and resonant Raman scattering. The marriage of dielectric and metallic resonance effects in subwavelength-scale nanowires opens up new avenues for overcoming the poor absorption of sub-gap photons by IB states in ZnTe:O to achieve high-efficiency IBSCs.
Impact of minocycline on vascularization and visual function in an immature mouse model of ischemic retinopathy
Authors: Xu Wenqin , Yin Jie , Sun Lijuan , Hu Zhicha , Dou Guorui , Zhang Zifeng , Wang Haiyan , Guo Changmei , Wang Yusheng 
Published: August 2017

AbstractThe role of microglia in the pathophysiology of ischemic retinal diseases has been extensively studied. Retinal microglial activation may be correlated with retinal neovascularization in oxygen-induced retinopathy (OIR), an animal model that has been widely used in retinopathy of prematurity (ROP) research. Minocycline is an antibiotic that decreases microglial activation following hyperoxic and hypoxic-ischemic phases in neonatal rodents. Here, we investigated the effects of minocycline on vascularization and visual function. In our results, we found that after the administration of minocycline, microglial reactivity was reduced in the retina, which was accompanied by an increase in the avascular area at P12, P14 and P17. Although microglial reactivity was reduced at P17, minocycline treatment did not attenuate retinal neovascularization. A changing trend in microglial number was observed, and the apoptosis and proliferation states on different days partly contributed to this change. Further study also revealed that although minocycline downregulated the levels of proinflammatory factors, visual function appeared to be significantly worsened. Collectively, we demonstrated that minocycline disturbed the physiological vascularization of the avascular area and exacerbated visual dysfunction, indicating that minocycline may not be an effective drug and may even be detrimental for the treatment of ischemic retinopathy in immature mammals.
Hypoxia impairs agonist-induced integrin αIIbβ3 activation and platelet aggregation
Authors: Kiouptsi Klytaimnistra , Gambaryan Stepan , Walter Elena , Walter Ulrich , Jurk Kerstin , Reinhardt Christoph 
Published: August 2017

AbstractUnder ischemic conditions, tissues are exposed to hypoxia. Although human physiology, to a certain extent, can adapt to hypoxic conditions, the impact of low oxygen levels on platelet function is unresolved. Therefore, we explored how reduction of atmospheric oxygen levels to 1% might affect agonist-induced aggregation and static adhesion of isolated human platelets. We uncovered that isolated, washed human platelets exposed to hypoxic conditions show reduced thrombin receptor-activating peptide-6 (TRAP-6) and convulxin-induced aggregation. Of note, this hypoxia-triggered effect was not observed in platelet-rich plasma. Independent of the agonist used (TRAP-6, ADP), activation of the platelet fibrinogen receptor integrin αIIbβ3 (GPIIbIIIa, CD41/CD61) was strongly reduced at 1% and 8% oxygen. The difference in agonist-induced integrin αIIbβ3 activation was apparent within 5 minutes of stimulation. Following hypoxia, re-oxygenation resulted in the recovery of integrin αIIbβ3 activation. Importantly, platelet secretion was not impaired by hypoxia. Static adhesion experiments revealed decreased platelet deposition to fibrinogen coatings, but not to collagen or vitronectin coatings, indicating that specifically the function of the integrin subunit αIIb is impaired by exposure of platelets to reduced oxygen levels. Our results reveal an unexpected effect of oxygen deprivation on platelet aggregation mediated by the fibrinogen receptor integrin αIIbβ3.
Penetration depth and nonlocal manipulation of quantum spin hall edge states in chiral honeycomb nanoribbons
Authors: Xu Yong , Uddin Salah , Wang Jun , Wu Jiansheng , Liu Jun-Feng 
Published: August 2017

AbstractWe have studied numerically the penetration depth of quantum spin hall edge states in chiral honeycomb nanoribbons based on the Green’s function method. The changing of edge orientation from armchair to zigzag direction decreases the penetration depth drastically. The penetration depth is used to estimate the gap opened for the finite-size effect. Beside this, we also proposed a nonlocal transistor based on the zigzag-like chiral ribbons in which the current is carried at one edge and the manipulation is by the edge magnetization at the other edge. The difficulty that the edge magnetization is unstable in the presence of a ballistic current can be removed by this nonlocal manipulation.
Adenoviral E4 34K protein interacts with virus packaging components and may serve as the putative portal
Authors: Ahi Yadvinder S. , Hassan Ahmed O. , Vemula Sai V. , Li Kunpeng , Jiang Wen , Zhang Guang Jun , Mittal Suresh K. 
Published: August 2017

AbstractStudies on dsDNA bacteriophages have revealed that a DNA packaging complex assembles at a special vertex called the ‘portal vertex’ and consists of a portal, a DNA packaging ATPase and other components. AdV protein IVa2 is presumed to function as a DNA packaging ATPase. However, a protein that functions as a portal is not yet identified in AdVs. To identify the AdV portal, we performed secondary structure analysis on a set of AdV proteins and compared them with the clip region of the portal proteins of bacteriophages phi29, SPP1 and T4. Our analysis revealed that the E4 34K protein of HAdV-C5 contains a region of strong similarity with the clip region of the known portal proteins. E4 34K was found to be present in empty as well as mature AdV particles. In addition, E4 34K co-immunoprecipitates and colocalizes with AdV packaging proteins. Immunogold electron microscopy demonstrated that E4 34K is located at a single site on the virus surface. Finally, tertiary structure prediction of E4 34K and its comparison with that of single subunits of Phi29, SPP1 and T4 portal proteins revealed remarkable similarity. In conclusion, our results suggest that E4 34K is the putative AdV portal protein.
Interocularly merged face percepts eliminate binocular rivalry
Authors: Klink P. Christiaan , Boucherie Daphne , Denys Damiaan , Roelfsema Pieter R. , Self Matthew W. 
Published: August 2017

AbstractFaces are important visual objects for humans and other social animals. A complex network of specialized brain areas is involved in the recognition and interpretation of faces. This network needs to strike a balance between being sensitive enough to distinguish between different faces with similar features, and being tolerant of low-level visual changes so that a given face is stably perceived as a particular individual. Such stability may require feedback from higher brain regions down to the level where details are represented. Here, we describe a phenomenon in which interocular competition between face features is stabilized and eliminated when observers attend high-level face characteristics. Two different face images presented to the individual eyes do not cause the perceptual fluctuations that are typically observed in binocular rivalry. Instead, they merge into a stable percept of an intermediate face that combines features from both eyes’ images. The stability of the intermediate face percept depends on the observer attending holistic face properties such as identity or gender. It disappears when observers explicitly attend facial features, suggesting a crucial role of top-down stabilizing feedback from high-level areas that represent holistic faces back to lower processing levels where detailed face features compete for conscious representation.
A DNA-centered explanation of the DNA polymerase translocation mechanism
Authors: Arias-Gonzalez J. Ricardo 
Published: August 2017

AbstractDNA polymerase couples chemical energy to translocation along a DNA template with a specific directionality while it replicates genetic information. According to single-molecule manipulation experiments, the polymerase-DNA complex can work against loads greater than 50 pN. It is not known, on the one hand, how chemical energy is transduced into mechanical motion, accounting for such large forces on sub-nanometer steps, and, on the other hand, how energy consumption in fidelity maintenance integrates in this non-equilibrium cycle. Here, we propose a translocation mechanism that points to the flexibility of the DNA, including its overstretching transition, as the principal responsible for the DNA polymerase ratcheting motion. By using thermodynamic analyses, we then find that an external load hardly affects the fidelity of the copying process and, consequently, that translocation and fidelity maintenance are loosely coupled processes. The proposed translocation mechanism is compatible with single-molecule experiments, structural data and stereochemical details of the DNA-protein complex that is formed during replication, and may be extended to RNA transcription.
iTRAQ and virus-induced gene silencing revealed three proteins involved in cold response in bread wheat
Authors: Zhang Ning , Zhang Lingran , Zhao Lei , Ren Yan , Cui Dangqun , Chen Jianhui , Wang Yongyan , Yu Pengbo , Chen Feng 
Published: August 2017

AbstractBy comparing the differentially accumulated proteins from the derivatives (UC 1110 × PI 610750) in the F10 recombinant inbred line population which differed in cold-tolerance, altogether 223 proteins with significantly altered abundance were identified. The comparison of 10 cold-sensitive descendant lines with 10 cold-tolerant descendant lines identified 140 proteins that showed decreased protein abundance, such as the components of the photosynthesis apparatus and cell-wall metabolism. The identified proteins were classified into the following main groups: protein metabolism, stress/defense, carbohydrate metabolism, lipid metabolism, sulfur metabolism, nitrogen metabolism, RNA metabolism, energy production, cell-wall metabolism, membrane and transportation, and signal transduction. Results of quantitative real-time PCR of 20 differentially accumulated proteins indicated that the transcriptional expression patterns of 10 genes were consistent with their protein expression models. Virus-induced gene silencing of Hsp90, BBI, and REP14 genes indicated that virus-silenced plants subjected to cold stress had more severe drooping and wilting, an increased rate of relative electrolyte leakage, and reduced relative water content compared to viral control plants. Furthermore, ultrastructural changes of virus-silenced plants were destroyed more severely than those of viral control plants. These results indicate that Hsp90, BBI, and REP14 potentially play vital roles in conferring cold tolerance in bread wheat.