bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geometric tuning of self-propulsion for Janus catalytic particles
Authors: Michelin Sébastien , Lauga Eric 
Published: February 2017

AbstractCatalytic swimmers have attracted much attention as alternatives to biological systems for examining collective microscopic dynamics and the response to physico-chemical signals. Yet, understanding and predicting even the most fundamental characteristics of their individual propulsion still raises important challenges. While chemical asymmetry is widely recognized as the cornerstone of catalytic propulsion, different experimental studies have reported that particles with identical chemical properties may propel in opposite directions. Here, we show that, beyond its chemical properties, the detailed shape of a catalytic swimmer plays an essential role in determining its direction of motion, demonstrating the compatibility of the classical theoretical framework with experimental observations.
AlkB homolog 3-mediated tRNA demethylation promotes protein synthesis in cancer cells
Authors: Ueda Yuko , Ooshio Ikumi , Fusamae Yasuyuki , Kitae Kaori , Kawaguchi Megumi , Jingushi Kentaro , Hase Hiroaki , Harada Kazuo , Hirata Kazumasa , Tsujikawa Kazutake 
Published: February 2017

AbstractThe mammalian AlkB homolog (ALKBH) family of proteins possess a 2-oxoglutarate- and Fe(II)-dependent oxygenase domain. A similar domain in the Escherichia coli AlkB protein catalyzes the oxidative demethylation of 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) in both DNA and RNA. AlkB homolog 3 (ALKBH3) was also shown to demethylate 1-meA and 3-meC (induced in single-stranded DNA and RNA by a methylating agent) to reverse the methylation damage and retain the integrity of the DNA/RNA. We previously reported the high expression of ALKBH3 in clinical tumor specimens and its involvement in tumor progression. In this study, we found that ALKBH3 effectively demethylated 1-meA and 3-meC within endogenously methylated RNA. Moreover, using highly purified recombinant ALKBH3, we identified N6-methyladenine (N6-meA) in mammalian transfer RNA (tRNA) as a novel ALKBH3 substrate. An in vitro translation assay showed that ALKBH3-demethylated tRNA significantly enhanced protein translation efficiency. In addition, ALKBH3 knockdown in human cancer cells impaired cellular proliferation and suppressed the nascent protein synthesis that is usually accompanied by accumulation of the methylated RNAs. Thus, our data highlight a novel role for ALKBH3 in tumor progression via RNA demethylation and subsequent protein synthesis promotion.
Crystalline Structure, Defect Chemistry and Room Temperature Colossal Permittivity of Nd-doped Barium Titanate
Authors: Sun Qiaomei , Gu Qilin , Zhu Kongjun , Jin Rongying , Liu Jinsong , Wang Jing , Qiu Jinhao 
Published: February 2017

AbstractDielectric materials with high permittivity are strongly demanded for various technological applications. While polarization inherently exists in ferroelectric barium titanate (BaTiO3), its high permittivity can only be achieved by chemical and/or structural modification. Here, we report the room-temperature colossal permittivity (~760,000) obtained in xNd: BaTiO3 (x = 0.5 mol%) ceramics derived from the counterpart nanoparticles followed by conventional pressureless sintering process. Through the systematic analysis of chemical composition, crystalline structure and defect chemistry, the substitution mechanism involving the occupation of Nd3+ in Ba2+ -site associated with the generation of Ba vacancies and oxygen vacancies for charge compensation has been firstly demonstrated. The present study serves as a precedent and fundamental step toward further improvement of the permittivity of BaTiO3-based ceramics.
Predicting antimicrobial peptides with improved accuracy by incorporating the compositional, physico-chemical and structural features into Chou’s general PseAAC
Authors: Meher Prabina Kumar , Sahu Tanmaya Kumar , Saini Varsha , Rao Atmakuri Ramakrishna 
Published: February 2017

AbstractAntimicrobial peptides (AMPs) are important components of the innate immune system that have been found to be effective against disease causing pathogens. Identification of AMPs through wet-lab experiment is expensive. Therefore, development of efficient computational tool is essential to identify the best candidate AMP prior to the in vitro experimentation. In this study, we made an attempt to develop a support vector machine (SVM) based computational approach for prediction of AMPs with improved accuracy. Initially, compositional, physico-chemical and structural features of the peptides were generated that were subsequently used as input in SVM for prediction of AMPs. The proposed approach achieved higher accuracy than several existing approaches, while compared using benchmark dataset. Based on the proposed approach, an online prediction server iAMPpred has also been developed to help the scientific community in predicting AMPs, which is freely accessible at http://cabgrid.res.in:8080/amppred/. The proposed approach is believed to supplement the tools and techniques that have been developed in the past for prediction of AMPs.
Extracellular protonation modulates cell-cell interaction mechanics and tissue invasion in human melanoma cells
Authors: Hofschröer Verena , Koch Alexander , Ludwig Florian Timo , Friedl Peter , Oberleithner Hans , Stock Christian , Schwab Albrecht 
Published: February 2017

AbstractDetachment of cells from the primary tumour precedes metastatic progression by facilitating cell release into the tissue. Solid tumours exhibit altered pH homeostasis with extracellular acidification. In human melanoma, the Na+/H+ exchanger NHE1 is an important modifier of the tumour nanoenvironment. Here we tested the modulation of cell-cell-adhesion by extracellular pH and NHE1. MV3 tumour spheroids embedded in a collagen matrix unravelled the efficacy of cell-cell contact loosening and 3D emigration into an environment mimicking physiological confinement. Adhesive interaction strength between individual MV3 cells was quantified using atomic force microscopy and validated by multicellular aggregation assays. Extracellular acidification from pHe7.4 to 6.4 decreases cell migration and invasion but increases single cell detachment from the spheroids. Acidification and NHE1 overexpression both reduce cell-cell adhesion strength, indicated by reduced maximum pulling forces and adhesion energies. Multicellular aggregation and spheroid formation are strongly impaired under acidification or NHE1 overexpression. We show a clear dependence of melanoma cell-cell adhesion on pHe and NHE1 as a modulator. These effects are opposite to cell-matrix interactions that are strengthened by protons extruded via NHE1. We conclude that these opposite effects of NHE1 act synergistically during the metastatic cascade.
Heteroaryldihydropyrimidine (HAP) and Sulfamoylbenzamide (SBA) Inhibit Hepatitis B Virus Replication by Different Molecular Mechanisms
Authors: Zhou Zheng , Hu Taishan , Zhou Xue , Wildum Steffen , Garcia-Alcalde Fernando , Xu Zhiheng , Wu Daitze , Mao Yi , Tian Xiaojun , Zhou Yuan , Shen Fang , Zhang Zhisen , Tang Guozhi , Najera Isabel , Yang Guang , Shen Hong C. , Young John A. T. , Qin Ning 
Published: February 2017

AbstractHeteroaryldihydropyrimidine (HAP) and sulfamoylbenzamide (SBA) are promising non-nucleos(t)ide HBV replication inhibitors. HAPs are known to promote core protein mis-assembly, but the molecular mechanism of abnormal assembly is still elusive. Likewise, the assembly status of core protein induced by SBA remains unknown. Here we show that SBA, unlike HAP, does not promote core protein mis-assembly. Interestingly, two reference compounds HAP_R01 and SBA_R01 bind to the same pocket at the dimer-dimer interface in the crystal structures of core protein Y132A hexamer. The striking difference lies in a unique hydrophobic subpocket that is occupied by the thiazole group of HAP_R01, but is unperturbed by SBA_R01. Photoaffinity labeling confirms the HAP_R01 binding pose at the dimer-dimer interface on capsid and suggests a new mechanism of HAP-induced mis-assembly. Based on the common features in crystal structures we predict that T33 mutations generate similar susceptibility changes to both compounds. In contrast, mutations at positions in close contact with HAP-specific groups (P25A, P25S, or V124F) only reduce susceptibility to HAP_R01, but not to SBA_R01. Thus, HAP and SBA are likely to have distinctive resistance profiles. Notably, P25S and V124F substitutions exist in low-abundance quasispecies in treatment-naïve patients, suggesting potential clinical relevance.
Adaptability of small brown planthopper to four rice cultivars using life table and population projection method
Authors: Zheng Xiao-Min , Tao Yun-Li , Chi Hsin , Wan Fang-Hao , Chu Dong 
Published: February 2017

AbstractIn this study, we evaluated the adaptability of the small brown planthopper (SBPH), Laodelphax striatellus (Hemiptera: Delphacidae) to four rice cultivars including Shengdao13 (SD13), Shengdao14 (SD14), Shengdao15 (SD15), and Zixiangnuo (ZXN) using the age-stage, two-sex life table with a simplified method for recording egg production (i.e., every five days vs. daily). The intrinsic rate of increase (r) of the SBPH was the highest (0.1067 d−1) on cultivar SD15, which was similar to the rate on SD14 (0.1029 d−1), but was significantly higher than that occurring on ZXN (0.0897 d−1) and SD13 (0.0802 d−1). The differences of the finite rate of increase (λ) on the four rice cultivars were consistent with the r values. Population projection predicted an explosive population growth of the SBPH occurring in a relatively short time when reared on SD14 and SD15. These findings demonstrated that the SBPH can successfully survive on the four rice cultivars, although there were varying host adaptabilities.
Connexin30.3 is expressed in mouse embryonic stem cells and is responsive to leukemia inhibitory factor
Authors: Saito Mikako , Asai Yuma , Imai Keiichi , Hiratoko Shoya , Tanaka Kento 
Published: February 2017

AbstractThe expression of 19 connexin (Cx) isoforms was observed in the mouse embryonic stem (ES) cell line, EB3. Their expression patterns could be classified into either pluripotent state-specific, differentiating stage-specific, or non-specificCxs. We focused onCx30.3as typical of the first category.Cx30.3was pluripotent state-specific and upregulated by leukemia inhibitory factor (LIF), a specific cytokine that maintains the pluripotent state of ES cell, via a Jak signaling pathway. Cx30.3 protein was localized to both the cell membrane and cytosol. The dynamic movement of Cx30.3 in the cell membrane was suggested by the imaging analysis by means of overexpressed Cx30.3-EGFP fusion protein. The cytosolic portion was postulated to be a ready-to-use Cx pool. TheCx30.3expression level in ES cell colonies dramatically decreased immediately after their separation into single cells. It was suggested that mRNA forCx30.3and Cx30.3 protein might be decomposed more rapidly than mRNA for Cx43 and Cx43 protein, respectively. These indicate possible involvement of Cx30.3 in the rapid formation and/or decomposition of gap junctions; implying a functional relay between Cx30.3 and other systems such as adhesion proteins.
A high sensitive fiber-optic strain sensor with tunable temperature sensitivity for temperature-compensation measurement
Authors: Hu Jie , Huang Hui , Bai Min , Zhan TingTing , Yang ZhiBo , Yu Yan , Qu Bo 
Published: February 2017

AbstractA high sensitive fiber-optic strain sensor, which consists of a cantilever, a tandem rod and a fiber collimator, was proposed. The tandem rod, which transfer the applied strain to the cantilever, was used for tuning the temperature sensitivity from −0.15 to 0.19 dB/°C via changing the length ratio of the rods. Moreover, due to the small beam divergence of the collimator, high strain sensitivity can be realized via incident-angle sensitive detection-mechanism. A strain detection-range of 1.1 × 103 με (with a sensing length of 21.5 mm), a detection limit of 5.7 × 10−3 με, and a maximum operating frequency of 1.18 KHz were demonstrated. This sensor is promising for compensating the thermal-expansion of various target objects.
Network growth models: A behavioural basis for attachment proportional to fitness
Authors: Bell Michael , Perera Supun , Piraveenan Mahendrarajah , Bliemer Michiel , Latty Tanya , Reid Chris 
Published: February 2017

AbstractSeveral growth models have been proposed in the literature for scale-free complex networks, with a range of fitness-based attachment models gaining prominence recently. However, the processes by which such fitness-based attachment behaviour can arise are less well understood, making it difficult to compare the relative merits of such models. This paper analyses an evolutionary mechanism that would give rise to a fitness-based attachment process. In particular, it is proven by analytical and numerical methods that in homogeneous networks, the minimisation of maximum exposure to node unfitness leads to attachment probabilities that are proportional to node fitness. This result is then extended to heterogeneous networks, with supply chain networks being used as an example.
Subthalamic Neurons Encode Both Single- and Multi-Limb Movements in Parkinson’s Disease Patients
Authors: Tankus Ariel , Strauss Ido , Gurevich Tanya , Mirelman Anat , Giladi Nir , Fried Itzhak , Hausdorff Jeffrey M. 
Published: February 2017

AbstractThe subthalamic nucleus (STN) is the main target for neurosurgical treatment of motor signs of Parkinson’s disease (PD). Despite the therapeutic effect on both upper and lower extremities, its role in motor control and coordination and its changes in Parkinson’s disease are not fully clear. We intraoperatively recorded single unit activity in ten patients with PD who performed repetitive feet or hand movements while undergoing implantation of a deep brain stimulator. We found both distinct and overlapping representations of upper and lower extremity movement kinematics in subthalamic units and observed evidence for re-routing to a multi-limb representation that participates in limb coordination. The well-known subthalamic somatotopy showed a large overlap of feet and hand representations in the PD patients. This overlap and excessive amounts of kinematics or coordination units may reflect pathophysiology or compensatory mechanisms. Our findings thus explain, at the single neuron level, the important subthalamic role in motor control and coordination and indicate the effect of PD on the neuronal representation of movement.
Metronomic capecitabine versus best supportive care as second-line treatment in hepatocellular carcinoma: a retrospective study
Authors: Casadei Gardini Andrea , Foca Flavia , Scartozzi Mario , Silvestris Nicola , Tamburini Emiliano , Faloppi Luca , Brunetti Oronzo , Rudnas Britt , Pisconti Salvatore , Valgiusti Martina , Marisi Giorgia , Foschi Francesco Giuseppe , Ercolani Giorgio , Tassinari Davide , Cascinu Stefano , Frassineti Giovanni Luca 
Published: February 2017

AbstractPreliminary studies suggest that capecitabine may be safe and effective in HCC patients. The aim of this study was to retrospectively evaluate the safety and efficacy of metronomic capecitabine as second-line treatment. This multicentric study retrospectively analyzed data of HCC patients unresponsive or intolerant to sorafenib treatment with metronomic capecitabine or best supportive care (BSC).Median progression free survival was 3.1 months in patients treated with capecitabine (95%CI: 2.7–3.5). Median overall survival was 12.0 months (95% CI: 10.7–15.8) in patients receiving capecitabine, while 9.0 months (95% CI: 6.5–13.9) in patients receiving BSC. The result of univariate unweighted Cox regression model shows a 46% reduction in death risk for patients on capecitabine (95%CI: 0.357–0.829; p =0.005) compared to patients receiving BSC alone. After weighting for potential confounders, death risk remained essentially unaltered (45%; 95%CI: 0.354–0.883; p = 0.013). Metronomic capecitabine seems a safe second-line treatment for HCC patients in terms of management of adverse events, showing a potential anti-tumour activity which needs further evaluation in phase III studies.
Link between plasminogen activator inhibitor-1 and cardiovascular risk in chronic hepatitis C after viral clearance
Authors: Chang Ming-Ling , Lin Yu-sheng , Pao Li-Heng , Huang Hsin-Chih , Chiu Cheng-Tang 
Published: February 2017

AbstractThe pathophysiological implications of plasminogen activator inhibitor-1 (PAI-1) in HCV infection remain obscure. This prospective study evaluated 669 HCV patients, of whom 536 had completed a course of anti-HCV therapy and had pre-, peri- and post-therapy measurements of various profiles, including PAI-1 levels. Multivariate analysis demonstrated, before anti-HCV-therapy, platelet count and PAI-1-rs1799889 genotype were associated with PAI-1 levels. Among patients with a sustained virological response (SVR, n = 445), platelet count was associated with PAI-1 level at 24 weeks post-therapy. GEE analysis showed that PAI-1-rs-1799889 and interferon-λ3-rs12979860 genotypes affected PAI-1 levels early and late in therapy, respectively. At 24 weeks post-therapy, higher lipid, brain natriuretic peptide, homocysteine and PAI-1 levels and PAI-1 activity were noted only in SVR patients compared with pre-therapy levels. Within 24 weeks post-therapy, 2.2% of the SVR (mean age: 57.8 yr; 8 smoking males; the 2 females had pre-therapy hypercholesteremia or cardiovascular family history of disease) and 0% of the non-SVR patients experienced a new cardiovascular event. Platelet counts consistently correlated with PAI-1 levels regardless of HCV infection. PAI-1-rs-1799889 and interferon-λ3-rs12979860 genotypes mainly affected PAI-1 levels longitudinally. Within 24 weeks post-anti-HCV therapy, the SVR patients showed increasing PAI-1 levels with accelerating cardiovascular risk, especially the vulnerable cases.
Eco-evolutionary feedbacks can rescue cooperation in microbial populations
Authors: Moreno-Fenoll Clara , Cavaliere Matteo , Martínez-García Esteban , Poyatos Juan F. 
Published: February 2017

AbstractBacterial populations whose growth depends on the cooperative production of public goods are usually threatened by the rise of cheaters that do not contribute but just consume the common resource. Minimizing cheater invasions appears then as a necessary mechanism to maintain these populations. However, that invasions result instead in the persistence of cooperation is a prospect that has yet remained largely unexplored. Here, we show that the demographic collapse induced by cheaters in the population can actually contribute to the rescue of cooperation, in a clear illustration of how ecology and evolution can influence each other. The effect is made possible by the interplay between spatial constraints and the essentiality of the shared resource. We validate this result by carefully combining theory and experiments, with the engineering of a synthetic bacterial community in which the public compound allows survival to a lethal stress. The characterization of the experimental system identifies additional factors that can matter, like the impact of the lag phase on the tolerance to stress, or the appearance of spontaneous mutants. Our work explains the unanticipated dynamics that eco-evolutionary feedbacks can generate in microbial communities, feedbacks that reveal fundamental for the adaptive change of ecosystems at all scales.
Identification of Extracellular Segments by Mass Spectrometry Improves Topology Prediction of Transmembrane Proteins
Authors: Langó Tamás , Róna Gergely , Hunyadi-Gulyás Éva , Turiák Lilla , Varga Julia , Dobson László , Várady György , Drahos László , Vértessy Beáta G. , Medzihradszky Katalin F. , Szakács Gergely , Tusnády Gábor E. 
Published: February 2017

AbstractTransmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions. Here we report a method for the high-throughput determination of extracellular segments of transmembrane proteins based on the identification of surface labeled and biotin captured peptide fragments by LC/MS/MS. We show that reliable identification of extracellular protein segments increases the accuracy and reliability of existing topology prediction algorithms. Using the experimental topology data as constraints, our improved prediction tool provides accurate and reliable topology models for hundreds of human transmembrane proteins.
Electrical and photocatalytic properties of boron-doped ZnO nanostructure grown on PET–ITO flexible substrates by hydrothermal method
Authors: Wang Wei , Ai Taotao , Yu Qi 
Published: February 2017

AbstractBoron-doped zinc oxide sheet-spheres were synthesized on PET–ITO flexible substrates using a hydrothermal method at 90 °C for 5 h. The results of X-ray diffraction and X-ray photoelectron spectroscopy indicated that the B atoms were successfully doped into the ZnO lattice, the incorporation of B led to an increase in the lattice constant of ZnO and a change in its internal stress. The growth mechanism of pure ZnO nanorods and B-doped ZnO sheet-spheres was specifically investigated. The as-prepared BZO/PET–ITO heterojunction possessed obvious rectification properties and its positive turn-on voltage was 0.4 V. The carrier transport mechanisms involved three models such as hot carrier tunneling theory, tunneling recombination, and series-resistance effect were explored. The BZO/PET–ITO nanostructures were more effective than pure ZnO to degrade the RY 15, and the degradation rate reached 41.45%. The decomposition process with BZO nanostructure followed first-order reaction kinetics. The photocurrent and electrochemical impedance spectroscopy revealed that the B-doping could promote the separation of photo-generated electron-hole pairs, which was beneficial to enhance the photocatalytic activity. The photocurrent density of B-doped and pure ZnO/PET–ITO were 0.055 mA/cm2 and 0.016 mA/cm2, respectively. The photocatalytic mechanism of the sample was analyzed by the energy band theory.