bluuebunny/crossref_metadata_2025_split huggingface dataset:
MALDI-Imaging Mass Spectrometry: a step forward in the anatomopathological characterization of stenotic aortic valve tissue
Authors: Mourino-Alvarez Laura , Iloro Ibon , de la Cuesta Fernando , Azkargorta Mikel , Sastre-Oliva Tamara , Escobes Iraide , Lopez-Almodovar Luis F. , Sanchez Pedro L. , Urreta Harkaitz , Fernandez-Aviles Francisco , Pinto Angel , Padial Luis R. , Akerström Finn , Elortza Felix , Barderas Maria G. 
Published: June 2016

AbstractAortic stenosis (AS) is the most common form of valve disease. Once symptoms develop, there is an inexorable deterioration with a poor prognosis; currently there are no therapies capable of modifying disease progression and aortic valve replacement is the only available treatment. Our goal is to study the progression of calcification by matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS) and get new insights at molecular level that could help in the understanding of this disease. In this work, we analyzed consecutive slices from aortic valve tissue by MALDI-IMS, to establish the spatial distribution of proteins and peptides directly from the surface of the histological sections. The analysis showed different structures corresponding to regions observed in conventional histology, including large calcification areas and zones rich in collagen and elastic fibers. Peptide extraction from the tissue, followed by liquid chromatography mass spectrometry analysis, provided the identification of collagen VI α-3 and NDRG2 proteins which correlated with the masses obtained by MALDI-IMS and were confirmed by immunohistochemistry. These results highlighted the molecular mechanism implied in AS using MALDI-IMS, a novel technique never used before in this pathology. In addition, we can define specific regions proving a complementary resolution of the molecular histology.
Long-Range Coulomb Effect in Intense Laser-Driven Photoelectron Dynamics
Authors: Quan Wei , Hao XiaoLei , Chen YongJu , Yu ShaoGang , Xu SongPo , Wang YanLan , Sun RenPing , Lai XuanYang , Wu ChengYin , Gong QiHuang , He XianTu , Liu XiaoJun , Chen Jing 
Published: June 2016

AbstractIn strong field atomic physics community, long-range Coulomb interaction has for a long time been overlooked and its significant role in intense laser-driven photoelectron dynamics eluded experimental observations. Here we report an experimental investigation of the effect of long-range Coulomb potential on the dynamics of near-zero-momentum photoelectrons produced in photo-ionization process of noble gas atoms in intense midinfrared laser pulses. By exploring the dependence of photoelectron distributions near zero momentum on laser intensity and wavelength, we unambiguously demonstrate that the long-range tail of the Coulomb potential (i.e., up to several hundreds atomic units) plays an important role in determining the photoelectron dynamics after the pulse ends.
A novel suicide shuttle plasmid for Streptococcus suis serotype 2 and Streptococcus equi ssp. zooepidemicus gene mutation
Authors: Liu Rui , Zhang Ping , Su Yiqi , Lin Huixing , Zhang Hui , Yu Lei , Ma Zhe , Fan Hongjie 
Published: June 2016

AbstractThe mariner-based Himar1 system has been utilized for creating mutant libraries of many Gram-positive bacteria. Streptococcus suis serotype 2 (SS2) and Streptococcus equi ssp. zooepidemicus (SEZ) are primary pathogens of swine that threaten the swine industry in China. To provide a forward-genetics technology for finding virulent phenotype-related genes in these two pathogens, we constructed a novel temperature-sensitive suicide shuttle plasmid, pMar4s, which contains the Himar1 system transposon, TnYLB-1, and the Himar1 C9 transposase from pMarA and the repTAs temperature-sensitive fragment from pSET4s. The kanamycin (Kan) resistance gene was in the TnYLB-1 transposon. Temperature sensitivity and Kan resistance allowed the selection of mutant strains and construction of the mutant library. The SS2 and SEZ mutant libraries were successfully constructed using the pMar4s plasmid. Inverse-Polymerase Chain Reaction (Inverse-PCR) results revealed large variability in transposon insertion sites and that the library could be used for phenotype alteration screening. The thiamine biosynthesis gene apbE was screened for its influence on SS2 anti-phagocytosis; likewise, the sagF gene was identified to be a hemolytic activity-related gene in SEZ. pMar4s was suitable for mutant library construction, providing more information regarding SS2 and SEZ virulence factors and illustrating the pathogenesis of swine streptococcosis.
Predicting the outcomes for out-of-hospital cardiac arrest patients using multiple biomarkers and suspension microarray assays
Authors: Huang Chien-Hua , Tsai Min-Shan , Chien Kuo-Liong , Chang Wei-Tien , Wang Tzung-Dau , Chen Shyr-Chyr , Ma Matthew Huei-Ming , Hsu Hsin-Yun , Chen Wen-Jone 
Published: June 2016

AbstractPredicting the prognosis for cardiac arrest is still challenging. Combining biomarkers from diverse pathophysiological pathways may provide reliable indicators for the severity of injury and predictors of long-term outcomes. We investigated the feasibility of using a multimarker strategy with key independent biomarkers to improve the prediction of outcomes in cardiac arrest. Adult out-of-hospital cardiac arrest patients with sustained return of spontaneous circulation were prospectively enrolled in this study. Blood samples were taken at 2 and 24 hours after cardiac arrest. Suspension microarray assays were used to test 21 different biomarkers. A total of 99 patients were enrolled, 45 of whom survived to hospital discharge. We identified 11 biomarkers that, when combined with clinical variables and factors of APACHE II score and history of arrhythmia, were independent determinants for outcome of in-hospital mortality (concordance = 0.9249, standard error = 0.0779). Three biomarkers combined with APACHE II and age were independent determinants for favorable neurological outcome at hospital discharge (area under the receiver-operator characteristic curve, 0.938; 95% confidence interval, 0.854 ~ 1.0). In conclusion, a systemic multiple biomarker approach using suspension microarray assays can identify independent predictors and model the outcomes of cardiac arrest patients during the post-cardiac arrest period.
Identification of key metabolic changes in renal interstitial fibrosis rats using metabonomics and pharmacology
Authors: Zhao Liangcai , Dong Minjian , Liao Shixian , Du Yao , Zhou Qi , Zheng Hong , Chen Minjiang , Ji Jiansong , Gao Hongchang 
Published: June 2016

AbstractRenal fibrosis is one of the important pathways involved in end-stage renal failure. Investigating the metabolic changes in the progression of disease may enhance the understanding of its pathogenesis and therapeutic information. In this study, 1H-nuclear magnetic resonance (NMR)-based metabonomics was firstly used to screen the metabolic changes in urine and kidney tissues of renal interstitial fibrotic rats induced by unilateral ureteral obstruction (UUO), at 7, 14, 21 and 28 days after operation, respectively. The results revealed that reduced levels of bioenergy synthesis and branched chain amino acids (BCAAs), as well as elevated levels of indoxyl sulfate (IS) are involved in metabolic alterations of renal fibrosis rats. Next, by pharmacological treatment we found that reduction of IS levels could prevent the renal fibrotic symptoms. Therefore, we suggested that urinary IS may be used as a potential biomarker for the diagnosis of renal fibrosis and a therapeutic target for drugs. Novel attempt combining metabonomics and pharmacology was established that have ability to provide more systematic diagnostic and therapeutic information of diseases.
Retrieving orbital angular momentum distribution of light with plasmonic vortex lens
Authors: Zhou Hailong , Dong Jianji , Zhang Jihua , Zhang Xinliang 
Published: June 2016

AbstractWe utilize a plasmonic vortex lens (PVL) to retrieve the orbital angular momentum (OAM) distribution of light. The OAM modes are coupled to the surface plasmon polaritons (SPPs) in the form of various Bessel functions respectively. By decomposing the interference pattern of SPPs into these Bessel functions, we can retrieve the relative amplitude and the relative phase of input OAM modes simultaneously. Our scheme shows advantage in integration and can measure hybrid OAM states by one measurement.
Purifying selection shapes the coincident SNP distribution of primate coding sequences
Authors: Chen Chia-Ying , Hung Li-Yuan , Wu Chan-Shuo , Chuang Trees-Juen 
Published: June 2016

AbstractGenome-wide analysis has observed an excess of coincident single nucleotide polymorphisms (coSNPs) at human-chimpanzee orthologous positions and suggested that this is due to cryptic variation in the mutation rate. While this phenomenon primarily corresponds with non-coding coSNPs, the situation in coding sequences remains unclear. Here we calculate the observed-to-expected ratio of coSNPs (coSNPO/E) to estimate the prevalence of human-chimpanzee coSNPs and show that the excess of coSNPs is also present in coding regions. Intriguingly, coSNPO/E is much higher at zero-fold than at nonzero-fold degenerate sites; such a difference is due to an elevation of coSNPO/E at zero-fold degenerate sites, rather than a reduction at nonzero-fold degenerate ones. These trends are independent of chimpanzee subpopulation, population size, or sequencing techniques; and hold in broad generality across primates. We find that this discrepancy cannot fully explained by sequence contexts, shared ancestral polymorphisms, SNP density and recombination rate and that coSNPO/E in coding sequences is significantly influenced by purifying selection. We also show that selection and mutation rate affect coSNPO/E independently and coSNPs tend to be less damaging and more correlated with human diseases than non-coSNPs. These suggest that coSNPs may represent a “signature” during primate protein evolution.
Nutrient shortage triggers the hexosamine biosynthetic pathway via the GCN2-ATF4 signalling pathway
Authors: Chaveroux Cédric , Sarcinelli Carmen , Barbet Virginie , Belfeki Sofiane , Barthelaix Audrey , Ferraro-Peyret Carole , Lebecque Serge , Renno Toufic , Bruhat Alain , Fafournoux Pierre , Manié Serge N. 
Published: June 2016

AbstractThe hexosamine biosynthetic pathway (HBP) is a nutrient-sensing metabolic pathway that produces the activated amino sugar UDP-N-acetylglucosamine, a critical substrate for protein glycosylation. Despite its biological significance, little is known about the regulation of HBP flux during nutrient limitation. Here, we report that amino acid or glucose shortage increase GFAT1 production, the first and rate-limiting enzyme of the HBP. GFAT1 is a transcriptional target of the activating transcription factor 4 (ATF4) induced by the GCN2-eIF2α signalling pathway. The increased production of GFAT1 stimulates HBP flux and results in an increase in O-linked β-N-acetylglucosamine protein modifications. Taken together, these findings demonstrate that ATF4 provides a link between nutritional stress and the HBP for the regulation of the O-GlcNAcylation-dependent cellular signalling.
Using metabarcoding to reveal and quantify plant-pollinator interactions
Authors: Pornon André , Escaravage Nathalie , Burrus Monique , Holota Hélène , Khimoun Aurélie , Mariette Jérome , Pellizzari Charlène , Iribar Amaia , Etienne Roselyne , Taberlet Pierre , Vidal Marie , Winterton Peter , Zinger Lucie , Andalo Christophe 
Published: June 2016

AbstractGiven the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number oftrnLand ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number oftrnLand ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 andtrnLsequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole.
Pro-apoptotic Bax molecules densely populate the edges of membrane pores
Authors: Kuwana Tomomi , Olson Norman H. , Kiosses William B. , Peters Bjoern , Newmeyer Donald D. 
Published: June 2016

AbstractHow the pro-apoptotic Bax protein permeabilizes the mitochondrial outer membrane is not fully understood. Previously, using cryo-electron microscopy (cryo-EM), we showed that activated Bax forms large, growing pores. Whether formed in liposomes or in mitochondrial outer membranes, Bax-induced pores exhibit the same morphology, with negative curvature flanking the edges and with no visible protein structure protruding from the membranes. Here we used cryo-EM to show that gold-labeled Bax molecules, after activation by Bid, became localized strictly at pore edges. This argues that Bax acts at short range to deform the membrane. Also, Bax molecules populated the walls of both small and large pores at the same density, implying that Bax is continuously recruited to the pores as they widen. Moreover, because all Bax molecules became oligomerized after membrane insertion, we infer that Bax oligomers are present at pore edges. We suggest that oligomerization may promote pore enlargement.
Mutation of the Traj18 gene segment using TALENs to generate Natural Killer T cell deficient mice
Authors: Zhang Jingjing , Bedel Romain , Krovi S. Harsha , Tuttle Kathryn D. , Zhang Bicheng , Gross James , Gapin Laurent , Matsuda Jennifer L. 
Published: June 2016

AbstractInvariant Natural Killer T (iNKT) cells are a unique subset of T lymphocytes that have been implicated in both promoting and suppressing a multitude of immune responses. In mice, iNKT cells express T cell antigen receptors (TCRs) comprising a unique TCRα rearrangement between the Trav11 and Traj18 gene segments. When paired with certain Trbv TCRβ chains, these TCRs recognize lipid antigens presented by the major histocompatibility complex (MHC) class I-like molecule, CD1d. Until recently, the sole model of iNKT deficiency targeted the Jα18, which is absolutely required to form the TCR with the appropriate antigenic specificity. However, these mice were demonstrated to have a large reduction in TCR repertoire diversity, which could confound results arising from studies using these mice. Here, we have created a new NKT-deficient mouse strain using transcription activator-like effector nuclease (TALEN) technology to only disrupt the expression of Jα18, leaving the remaining Jα repertoire unperturbed. We confirm that these mice lack iNKT cells and do not respond to lipid antigen stimulation while the development of conventional T cells, regulatory T cells, and type Ib NKT cells is normal. This new mouse strain will serve as a new model of iNKT cell deficiency to facilitate our understanding of iNKT biology.
Patterns of Gesture Use in Adolescents With Autism Spectrum Disorder
Authors: Braddock Barbara A. , Gabany Christina , Shah Meera , Armbrecht Eric S. , Twyman Kimberly A. 
Published: June 2016

Purpose
The purpose of this study was to examine patterns of spontaneous gesture use in a sample of adolescents with autism spectrum disorder (ASD).

Method
Thirty-five adolescents with ASD ages 11 to 16 years participated (mean age = 13.51 years; 29 boys, 6 girls). Participants' spontaneous speech and gestures produced during a narrative task were later coded from videotape. Parents were also asked to complete questionnaires to quantify adolescents' general communication ability and autism severity.

Results
No significant subgroup differences were apparent between adolescents who did not gesture versus those who produced at least 1 gesture in general communication ability and autism severity. Subanalyses including only adolescents who produced gesture indicated a statistically significant negative association between gesture rate and general communication ability, specifically speech and syntax subscale scores. Adolescents who gestured produced higher proportions of iconic gestures and used gesture mostly to add information to speech.

Conclusions
The findings relate spontaneous gesture use to underlying strengths and weaknesses in adolescents' speech and syntactical language development. More research examining cospeech gesture in fluent speakers with ASD is needed.
Research on a current commutation drive circuit for hybrid dc circuit breaker and its optimisation design
Authors: Wen Weijie , Huang Yulong , Cheng Tiehan , Gao Shutong , Chen Zhengyu , Zhang Xiangyu , Yu Zhanqing , Zeng Rong , Liu Weidong 
Published: June 2016

Hybrid direct current circuit breakers (DCCBs) have great prospects for the isolation of dc faults in multi‐terminal dc grids. Current commutation from the mechanical switch branch to the static DCCB branch is the precondition to interrupt fault currents successfully for the hybrid DCCBs. A current commutation drive circuit (CCDC) is presented in this study, and it has features of low cost, low operating losses and free maintenance. Experiments have been carried out on a unidirectional 44 kV hybrid DCCB prototype with CCDC. The results show the current of 3.4 kA can be commutated by CCDC within 130 μs, and be interrupted successfully within 2 ms. For a bidirectional 80 kV hybrid DCCB cell, the effectiveness of CCDC is validated with simulations carried out in PACAD. Then, an index is defined to represent the current commutation capability of CCDC and a mathematical model for CCDC is established to calculate the index. To reduce the cost of CCDC with certain current commutation capability, an optimisation method based on genetic algorithm is proposed in this study. According to the optimisation results of CCDC suitable for bidirectional 80 kV hybrid DCCB cell, the cost of CCDC has been reduced by optimisation.
Plug‐in repetitive control of single‐phase grid‐connected inverter for AC module applications
Authors: Evran Fatih 
Published: June 2016

This study presents two‐stage inverter topology for single‐phase grid‐connected photovoltaic (PV) applications and its control implementations. The two‐stage systems are reliable and work well. Typically, the second stage inverts solar power into AC power, whereas the first stage which is used to increase low PV panel voltage can achieve maximum power point tracking. In this configuration, a boost or a flyback type DC/DC converter topology is usually employed. However, such converters have major drawbacks such as low efficiency and limited voltage gain due to power losses. In the proposed topology, a low‐voltage PV panel can be connected to power grid through solar inverter by using high‐gain DC/DC converter which has unique features such as galvanic isolation and continuous current for AC module applications. Conventional controller results in poor control performance due to the finite gain at desired frequencies. Hence, a plug‐in repetitive controller is proposed to obtain low total harmonic distortions (THDs). The performance of the proposed system is provided for the system which injects the PV panel current in the maximum power point voltage to a grid of 220 V(rms) at a power range of 150–300 W with a unity power factor and a low input current THD.
Correction of cavity absorptance measure method for cryogenic radiometer
Authors: Yi Xiaolong , Fang Wei , Luo Yang , Xia Zhiwei , Wang Yupeng 
Published: June 2016

As the reference detector of absolute radiance calibration primary radiometer (ARCPR) for space remote sensing, total solar irradiance (TSI) cavity is investigated to ensure the measurement accuracy. TSI cavity adopts a sloping bottom cavity. The geometrical parameters and paint material of sloping bottom cavity are both optimised to improve the invariance of absorptance in the environment of ground and space. The optimisation of substitution method is proposed to measure the average absorptance by two‐dimensional scan. The uniformity is evaluated by absorptance map. Experimental results illustrate that sloping bottom cavity has a super‐high absorptance of 0.999928 (wavelength is 632 nm), and the relative measure uncertainty is approximated to 6 ppm. Meanwhile, compared with the absorptance map of conical cavity, the sloping bottom design improves the uniformity of absorptance. Therefore, the sloping bottom cavity can be adopted as the reference detector of ARCPR. Furthermore, the optimised substitution method is suitable for the investigation of the blackbody cavity with super‐high absorptance.
Improvement of gas ultrasonic flowmeter measurement non‐linearity based on ray tracing method
Authors: Zheng Dandan , Mei Jianqiang , Wang Mi 
Published: June 2016

Gas ultrasonic flowmeters are widely used in natural gas industry. When flow velocity achieves to tens of meters per second, the measurement error may appear significant non‐linearity with flow velocity increased. In order to solve this problem, reasons of non‐linearity are discussed based on the ray acoustics theory. First, the two‐dimensional ray tracing method is introduced and realised by Matlab. Second, both DN100 and DN500 diametric single path gas ultrasonic flowmeters are simulated, respectively. The ultrasonic wave propagation trajectory, transit time, path angle and receiving position of transducer are analysed with increasing flow velocities 1–50 m/s. Third, it is noted that the assumption of traditional velocity measurement model is not consistent with the actual ultrasound propagation. Therefore, a corrected model is proposed. Through comparing results of traditional and corrected models, the measurement error is reduced up to 4%, and the measurement non‐linearity is improved.
Modelling and evaluation of HF‐RFID signal propagation characterisations under material properties variation
Authors: Yin Aijun , Ren Hongji 
Published: June 2016

Previous electromagnetic (EM) wave‐based approaches to evaluate material physical properties are focused on applications of GHz and THz. High‐frequency radio‐frequency identification (HF‐RFID, 13.56 MHz) is low‐cost and mostly used as communication solution. Material properties variation can be affected by damage (such as defects or fatigue). In this study, the authors present a preliminary study that applies HF‐RFID on non‐destructive testing and evaluation. The evaluation model of HF‐RFID signal propagation characterisations under material EM properties variation is demonstrated. Simulations and experiments for oil debris monitoring and metal surface defect detection are demonstrated and simulations are in good agreement with experiment results. (i) In oil debris monitoring experiment, as the debris amount in the 25 ml breaker increases from 0.0 to 2.0 g, penetration signal decreases by 7.8% and reflected signal increases by 174.3%. (ii) In metal surface defect experiment, as the defect size increases from 1 to 5 mm, reflected signal decreases by 1.0%. The authors’ work also presents a blueprint for non‐destructive testing method using other high‐frequency devices.