bluuebunny/crossref_metadata_2025_split huggingface dataset:
EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model
Authors: Hädicke Oliver , Klamt Steffen 
Published: January 2017

AbstractGenome-scale metabolic modeling has become an invaluable tool to analyze properties and capabilities of metabolic networks and has been particularly successful for the model organism Escherichia coli. However, for several applications, smaller metabolic (core) models are needed. Using a recently introduced reduction algorithm and the latest E. coli genome-scale reconstruction iJO1366, we derived EColiCore2, a model of the central metabolism of E. coli. EColiCore2 is a subnetwork of iJO1366 and preserves predefined phenotypes including optimal growth on different substrates. The network comprises 486 metabolites and 499 reactions, is accessible for elementary-modes analysis and can, if required, be further compressed to a network with 82 reactions and 54 metabolites having an identical solution space as EColiCore2. A systematic comparison of EColiCore2 with its genome-scale parent model iJO1366 reveals that several key properties (flux ranges, reaction essentialities, production envelopes) of the central metabolism are preserved in EColiCore2 while it neglects redundancies along biosynthetic routes. We also compare calculated metabolic engineering strategies in both models and demonstrate, as a general result, how intervention strategies found in a core model allow the identification of valid strategies in a genome-scale model. Overall, EColiCore2 holds promise to become a reference model of E. coli’s central metabolism.
Low serum 25-hydroxyvitamin D is associated with higher risk of frequent headache in middle-aged and older men
Authors: Virtanen Jyrki K. , Giniatullin Rashid , Mäntyselkä Pekka , Voutilainen Sari , Nurmi Tarja , Mursu Jaakko , Kauhanen Jussi , Tuomainen Tomi-Pekka 
Published: January 2017

AbstractVitamin D has been suggested to have a role in various neurovascular diseases, but the data regarding headache is inconclusive. Our aim was to investigate the associations between serum 25-hydroxyvitamin D [25(OH)D], a marker for vitamin D status, and risk of frequent headache. The study population consisted of 2601 men from the population-based Kuopio Ischaemic Heart Disease Risk Factor Study (KIHD) from eastern Finland, aged 42–60 years in 1984–1989. The cross-sectional associations with prevalence of self-reported frequent headache (defined as weekly or daily headaches) were estimated with multivariable-adjusted odds ratios. The average serum 25(OH) concentration was 43.4 nmol/L (SD 18.9, min-max 7.8–136.1 nmol/L). A total of 250 men (9.6%) reported frequent headache. The average serum 25(OH)D concentration among those with frequent headache was 38.3 nmol/L (SD 18.8) and 43.9 nmol/L (SD 18.9) among those without frequent headache, after adjustment for age and year and month of blood draw (P for difference <0.001). After multivariable adjustments, those in the lowest vs. the highest serum 25(OH)D quartile had 113% (95% CI 42, 218%; P for trend <0.001) higher odds for frequent headache. In conclusion, low serum 25(OH)D concentration was associated with markedly higher risk of frequent headache in men.
Nucleocapsid Interacts with NPM1 and Protects it from Proteolytic Cleavage, Enhancing Cell Survival, and is Involved in PEDV Growth
Authors: Shi Da , Shi Hongyan , Sun Dongbo , Chen Jianfei , Zhang Xin , Wang Xiaobo , Zhang Jialin , Ji Zhaoyang , Liu Jianbo , Cao Liyan , Zhu Xiangdong , Yuan Jing , Dong Hui , Wang Xin , Chang Tiecheng , Liu Ye , Feng Li 
Published: January 2017

AbstractPorcine epidemic diarrhea virus (PEDV) replicates in the cytoplasm of infected cells, but its nucleocapsid (N) protein localizes specifically to the nucleolus. The mechanism of nuclear translocation, and whether N protein associates with particular nucleolar components, is unknown. In this study, we confirm that a nucleolar phosphoprotein nucleophosmin (NPM1) interacts and co-localizes with the N protein in the nucleolus. In vitro binding studies indicated that aa 148–294 of N and aa 118–188 of NPM1 were required for binding. Interestingly, N protein importation into the nucleolus is independent of the ability of NPM1 to shuttle between the nucleus and the cytoplasm. Furthermore, overexpression of NPM1 promoted PEDV growth, while knockdown of NPM1 suppressed PEDV growth. In addition, binding of N protein to NPM1 protects it from proteolytic degradation by caspase-3, leading to increased cell survival. Taken together, our studies demonstrate a specific interaction of the N protein with the host cell protein NPM1 in the nucleolus. The results suggest potential linkages among viral strategies for the regulation of cell survival activities, possibly through an interaction of N protein with NPM1 which prevents its proteolytic cleavage and enhances cell survival, thus ultimately promoting the replication of PEDV.
Tin Compensation for the SnS Based Optoelectronic Devices
Authors: Wang S. F. , Wang W. , Fong W. K. , Yu Y. , Surya C. 
Published: January 2017

AbstractIn this paper we report the growth of high quality SnS thin films with good crystallinity deposited on two-dimensional (2D) mica substrates. It is believed that the 2D nature of SnS, with strong intra-layer covalent bonds and weak inter-layer van der Waals interactions, is responsible for its relative insensitivity to lattice mismatch. We also investigated the reduction of Sn vacancies in the material using Sn-compensation technique during the material growth process. The experimental results clearly demonstrated substantial enhancements in the electrical and structural properties for films deposited using Sn-compensation technique. A mobility of 51 cm2 V−1 s−1 and an XRD rocking curve full width at half maximum of 0.07° were obtained. Sn-compensated SnS/GaN:Si heterojunctions were fabricated and significant improvement in both the I-V characteristics and the spectral responsivities of the devices were characterized.
Plasmonic bio-sensing for the Fenna-Matthews-Olson complex
Authors: Chen Guang-Yin , Lambert Neill , Shih Yen-An , Liu Meng-Han , Chen Yueh-Nan , Nori Franco 
Published: January 2017

AbstractWe study theoretically the bio-sensing capabilities of metal nanowire surface plasmons. As a specific example, we couple the nanowire to specific sites (bacteriochlorophyll) of the Fenna-Matthews-Olson (FMO) photosynthetic pigment protein complex. In this hybrid system, we find that when certain sites of the FMO complex are subject to either the suppression of inter-site transitions or are entirely disconnected from the complex, the resulting variations in the excitation transfer rates through the complex can be monitored through the corresponding changes in the scattering spectra of the incident nanowire surface plasmons. We also find that these changes can be further enhanced by changing the ratio of plasmon-site couplings. The change of the Fano lineshape in the scattering spectra further reveals that “site 5” in the FMO complex plays a distinct role from other sites. Our results provide a feasible way, using single photons, to detect mutation-induced, or bleaching-induced, local defects or modifications of the FMO complex, and allows access to both the local and global properties of the excitation transfer in such systems.
Loss-tolerant measurement-device-independent quantum private queries
Authors: Zhao Liang-Yuan , Yin Zhen-Qiang , Chen Wei , Qian Yong-Jun , Zhang Chun-Mei , Guo Guang-Can , Han Zheng-Fu 
Published: January 2017

AbstractQuantum private queries (QPQ) is an important cryptography protocol aiming to protect both the user’s and database’s privacy when the database is queried privately. Recently, a variety of practical QPQ protocols based on quantum key distribution (QKD) have been proposed. However, for QKD-based QPQ the user’s imperfect detectors can be subjected to some detector- side-channel attacks launched by the dishonest owner of the database. Here, we present a simple example that shows how the detector-blinding attack can damage the security of QKD-based QPQ completely. To remove all the known and unknown detector side channels, we propose a solution of measurement-device-independent QPQ (MDI-QPQ) with single- photon sources. The security of the proposed protocol has been analyzed under some typical attacks. Moreover, we prove that its security is completely loss independent. The results show that practical QPQ will remain the same degree of privacy as before even with seriously uncharacterized detectors.
Positive association between physical activity and PER3 expression in older adults
Authors: Takahashi Masaki , Haraguchi Atsushi , Tahara Yu , Aoki Natsumi , Fukazawa Mayuko , Tanisawa Kumpei , Ito Tomoko , Nakaoka Takashi , Higuchi Mitsuru , Shibata Shigenobu 
Published: January 2017

AbstractThe circadian clock regulates many physiological functions including physical activity and feeding patterns. In addition, scheduled exercise and feeding themselves can affect the circadian clock. The purpose of the present study was to investigate the relationship between physical/feeding activity and expression of clock genes in hair follicle cells in older adults. Twenty adult men (age, 68 ± 7 years, mean ± SE) were examined in this cross-sectional study. Prior to hair follicle cell collection, the participants were asked to wear a uniaxial accelerometer for one week. The timings of breakfast, lunch, and dinner were also recorded. Hair follicle cells were then collected over a 24 h period at 4 h intervals. The amplitude of PER3 expression was positively correlated with moderate and vigorous physical activity (r = 0.582, p = 0.007) and peak oxygen uptake (r = 0.481, p = 0.032), but these correlations were not observed for NR1D1 or NR1D2. No association was noted between meal times and the amplitude or the acrophase for any of these three clock genes. These findings suggest that rhythmic expression of the circadian clock gene PER3 is associated with the amount of daily physical activity and physical fitness in older adults.
High-Quality Metal–Organic Framework ZIF-8 Membrane Supported on Electrodeposited ZnO/2-methylimidazole Nanocomposite: Efficient Adsorbent for the Enrichment of Acidic Drugs
Authors: Wu Mian , Ye Huili , Zhao Faqiong , Zeng Baizhao 
Published: January 2017

AbstractMetal–organic framework (MOF) membranes have received increasing attention as adsorbents, yet the defects in most membrane structures greatly thwart their capacity performance. In this work, we fabricated a novel ZnO/2-methylimidazole nanocomposite with multiple morphology by electrochemical method. The nanocomposite provided sufficient and strong anchorages for the zeolitic imidazolate frameworks-8 (ZIF-8) membrane. Thus, a crack-free and uniform MOF membrane with high performance was successfully obtained. In this case, 2-methylimidazole was believed to react with ZnO to form uniform ZIF nuclei, which induced and guided the growth of ZIF-8 membrane. The as-prepared ZIF-8 membrane had large surface area and good thermal stability. As expected, it displayed high adsorption capacity for acidic drugs (e.g., ibuprofen, ketoprofen and acetylsalicylic acid) as they could interact through hydrophobic, hydrogen bonding and π-π stacking interaction. Accordingly, by coupling with gas chromatography the ZIF-8 membrane was successfully applied to the real-time dynamic monitoring of ibuprofen in patient’s urine.
Enhancement effect of mass imbalance on Fulde-Ferrell-Larkin-Ovchinnikov type of pairing in Fermi-Fermi mixtures of ultracold quantum gases
Authors: Wang Jibiao , Che Yanming , Zhang Leifeng , Chen Qijin 
Published: January 2017

AbstractUltracold two-component Fermi gases with a tunable population imbalance have provided an excellent opportunity for studying the exotic Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) states, which have been of great interest in condensed matter physics. However, the FFLO states have not been observed experimentally in Fermi gases in three dimensions (3D), possibly due to their small phase space volume and extremely low temperature required for an equal-mass Fermi gas. Here we explore possible effects of mass imbalance, mainly in a 6Li–40K mixture, on the one-plane-wave FFLO phases for a 3D homogeneous case at the mean-field level. We present various phase diagrams related to the FFLO states at both zero and finite temperatures, throughout the BCS-BEC crossover, and show that a large mass ratio may enhance substantially FFLO type of pairing.
Nitrogen-doped Carbon Derived from ZIF-8 as a High-performance Metal-free Catalyst for Acetylene Hydrochlorination
Authors: Chao Songlin , Zou Fang , Wan Fanfan , Dong Xiaobin , Wang Yanlin , Wang Yuxuan , Guan Qingxin , Wang Guichang , Li Wei 
Published: January 2017

AbstractAcetylene hydrochlorination is a major industrial technology for manufacturing vinyl chloride monomer in regions with abundant coal resources; however, it is plagued by the use of mercury(II) chloride catalyst. The development of a nonmercury catalyst has been extensively explored. Herein, we report a N-doped carbon catalyst derived from ZIF-8 with both high activity and quite good stability. The acetylene conversion reached 92% and decreased slightly during a 200 h test at 220 °C and atmospheric pressure. Experimental studies and theoretical calculations indicate that C atoms adjacent to the pyridinic N are the active sites, and coke deposition covering pyridinic N is the main reason for catalyst deactivation. The performance of those N-doped carbons makes it possible for practical applications with further effort. Furthermore, the result also provides guidance for designing metal-free catalysts for similar reactions.
Continuous fabrication of nanostructure arrays for flexible surface enhanced Raman scattering substrate
Authors: Zhang Chengpeng , Yi Peiyun , Peng Linfa , Lai Xinmin , Chen Jie , Huang Meizhen , Ni Jun 
Published: January 2017

AbstractSurface-enhanced Raman spectroscopy (SERS) has been a powerful tool for applications including single molecule detection, analytical chemistry, electrochemistry, medical diagnostics and bio-sensing. Especially, flexible SERS substrates are highly desirable for daily-life applications, such as real-time and in situ Raman detection of chemical and biological targets, which can be used onto irregular surfaces. However, it is still a major challenge to fabricate the flexible SERS substrate on large-area substrates using a facile and cost-effective technique. The roll-to-roll ultraviolet nanoimprint lithography (R2R UV-NIL) technique provides a solution for the continuous fabrication of flexible SERS substrate due to its high-speed, large-area, high-resolution and high-throughput. In this paper, we presented a facile and cost-effective method to fabricate flexible SERS substrate including the fabrication of polymer nanostructure arrays and the metallization of the polymer nanostructure arrays. The polymer nanostructure arrays were obtained by using R2R UV-NIL technique and anodic aluminum oxide (AAO) mold. The functional SERS substrates were then obtained with Au sputtering on the surface of the polymer nanostructure arrays. The obtained SERS substrates exhibit excellent SERS and flexibility performance. This research can provide a beneficial direction for the continuous production of the flexible SERS substrates.
Transgenerational epimutations induced by multi-generation drought imposition mediate rice plant’s adaptation to drought condition
Authors: Zheng Xiaoguo , Chen Liang , Xia Hui , Wei Haibin , Lou Qiaojun , Li Mingshou , Li Tiemei , Luo Lijun 
Published: January 2017

AbstractEpigenetic mechanisms are crucial mediators of appropriate plant reactions to adverse environments, but their involvement in long-term adaptation is less clear. Here, we established two rice epimutation accumulation lines by applying drought conditions to 11 successive generations of two rice varieties. We took advantage of recent technical advances to examine the role of DNA methylation variations on rice adaptation to drought stress. We found that multi-generational drought improved the drought adaptability of offspring in upland fields. At single-base resolution, we discovered non-random appearance of drought-induced epimutations. Moreover, we found that a high proportion of drought-induced epimutations maintained their altered DNA methylation status in advanced generations. In addition, genes related to transgenerational epimutations directly participated in stress-responsive pathways. Analysis based on a cluster of drought-responsive genes revealed that their DNA methylation patterns were affected by multi-generational drought. These results suggested that epigenetic mechanisms play important roles in rice adaptations to upland growth conditions. Epigenetic variations have morphological, physiological and ecological consequences and are heritable across generations, suggesting that epigenetics can be considered an important regulatory mechanism in plant long-term adaptation and evolution under adverse environments.
Direct coupling: a possible strategy to control fruit production in alternate bearing
Authors: Prasad Awadhesh , Sakai Kenshi , Hoshino Yoshinobu 
Published: January 2017

AbstractWe investigated the theoretical possibility of applying phenomenon of synchronization of coupled nonlinear oscillators to control alternate bearing in citrus. The alternate bearing of fruit crops is a phenomenon in which a year of heavy yield is followed by an extremely light one. This phenomenon has been modeled previously by the resource budget model, which describes a typical nonlinear oscillator of the tent map type. We have demonstrated how direct coupling, which could be practically realized through grafting, contributes to the nonlinear dynamics of alternate bearing, especially phase synchronization. Our results show enhancement of out-of-phase synchronization in production, which depends on initial conditions obtained under the given system parameters. Based on these numerical experiments, we propose a new method to control alternate bearing, say in citrus, thereby enabling stable fruit production. The feasibility of validating the current results through field experimentation is also discussed.
Cerebrospinal fluid lens-free microscopy: a new tool for the laboratory diagnosis of meningitis
Authors: Delacroix Robin , Morel Sophie Nhu An , Hervé Lionel , Bordy Thomas , Dinten Jean-Marc , Drancourt Michel , Allier Cédric 
Published: January 2017

AbstractCerebrospinal fluid cytology is performed by operator-dependant light microscopy as part of the routine laboratory work-flow diagnosis of meningitis. We evaluated operator-independent lens-free microscopy numeration of erythrocytes and leukocytes for the cytological diagnosis of meningitis. In a first step, prospective optical microscopy counts of leukocytes done by five different operators yielded an overall 16.7% misclassification of 72 cerebrospinal fluid specimens in meningitis/non-meningitis categories using a 10 leukocyte/μL cut-off. In a second step, the lens-free microscopy algorithm adapted for counting cerebrospinal fluid cells and discriminating leukocytes from erythrocytes was modified step-by-step in the prospective analysis of 215 cerebrospinal fluid specimens. The definite algorithm yielded a 100% sensitivity and a 86% specificity compared to confirmed diagnostics. In a third step, a blind lens-free microscopic analysis of 116 cerebrospinal fluid specimens, including six cases of microbiology-confirmed infectious meningitis, yielded a 100% sensitivity and a 79% specificity. Adapted lens-free microscopy is thus emerging as an operator-independent technique for the rapid numeration of leukocytes and erythrocytes in cerebrospinal fluid. In particular, this technique is well suited to the rapid diagnosis of meningitis at point-of-care laboratories.
Transforming growth factor β-activated kinase 1 transcriptionally suppresses hepatitis B virus replication
Authors: Pang Jinke , Zhang Geng , Lin Yong , Xie Zhanglian , Liu Hongyan , Tang Libo , Lu Mengji , Yan Ran , Guo Haitao , Sun Jian , Hou Jinlin , Zhang Xiaoyong 
Published: January 2017

AbstractHepatitis B Virus (HBV) replication in hepatocytes is restricted by the host innate immune system and related intracellular signaling pathways. Transforming growth factor β-activated kinase 1 (TAK1) is a key mediator of toll-like receptors and pro-inflammatory cytokine signaling pathways. Here, we report that silencing or inhibition of endogenous TAK1 in hepatoma cell lines leads to an upregulation of HBV replication, transcription, and antigen expression. In contrast, overexpression of TAK1 significantly suppresses HBV replication, while an enzymatically inactive form of TAK1 exerts no effect. By screening TAK1-associated signaling pathways with inhibitors and siRNAs, we found that the MAPK-JNK pathway was involved in TAK1-mediated HBV suppression. Moreover, TAK1 knockdown or JNK pathway inhibition induced the expression of farnesoid X receptor α, a transcription factor that upregulates HBV transcription. Finally, ectopic expression of TAK1 in a HBV hydrodynamic injection mouse model resulted in lower levels of HBV DNA and antigens in both liver and serum. In conclusion, our data suggest that TAK1 inhibits HBV primarily at viral transcription level through activation of MAPK-JNK pathway, thus TAK1 represents an intrinsic host restriction factor for HBV replication in hepatocytes.
Parametric Study of Amorphous High-Entropy Alloys formation from two New Perspectives: Atomic Radius Modification and Crystalline Structure of Alloying Elements
Authors: Hu Q. , Guo S. , Wang J.M. , Yan Y.H. , Chen S.S. , Lu D.P. , Liu K.M. , Zou J.Z. , Zeng X.R. 
Published: January 2017

AbstractChemical and topological parameters have been widely used for predicting the phase selection in high-entropy alloys (HEAs). Nevertheless, previous studies could be faulted due to the small number of available data points, the negligence of kinetic effects, and the insensitivity to small compositional changes. Here in this work, 92 TiZrHfM, TiZrHfMM, TiZrHfMMM (M = Fe, Cr, V, Nb, Al, Ag, Cu, Ni) HEAs were prepared by melt spinning, to build a reliable and sufficiently large material database to inspect the robustness of previously established parameters. Modification of atomic radii by considering the change of local electronic environment in alloys, was critically found out to be superior in distinguishing the formation of amorphous and crystalline alloys, when compared to using atomic radii of pure elements in topological parameters. Moreover, crystal structures of alloying element were found to play an important role in the amorphous phase formation, which was then attributed to how alloying hexagonal-close-packed elements and face-centered-cubic or body-centered-cubic elements can affect the mixing enthalpy. Findings from this work not only provide parametric studies for HEAs with new and important perspectives, but also reveal possibly a hidden connection among some important concepts in various fields.