bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial effects in meta-foodwebs
Authors: Barter Edmund , Gross Thilo 
Published: August 2017

AbstractIn ecology it is widely recognised that many landscapes comprise a network of discrete patches of habitat. The species that inhabit the patches interact with each other through a foodweb, the network of feeding interactions. The meta-foodweb model proposed by Pillaiet al. combines the feeding relationships at each patch with the dispersal of species between patches, such that the whole system is represented by a network of networks. Previous work on meta-foodwebs has focussed on landscape networks that do not have an explicit spatial embedding, but in real landscapes the patches are usually distributed in space. Here we compare the dispersal of a meta-foodweb on Erdős-Rényi networks, that do not have a spatial embedding, and random geometric networks, that do have a spatial embedding. We found that local structure and large network distances in spatially embedded networks, lead to meso-scale patterns of patch occupation by both specialist and omnivorous species. In particular, we found that spatial separations make the coexistence of competing species more likely. Our results highlight the effects of spatial embeddings for meta-foodweb models, and the need for new analytical approaches to them.
The Diagnostic Value of Global Longitudinal Strain (GLS) on Myocardial Infarction Size by Echocardiography: A Systematic Review and Meta-analysis
Authors: Diao Kai-yue , Yang Zhi-gang , Ma Min , He Yong , Zhao Qin , Liu Xi , Gao Yue , Xie Lin-jun , Guo Ying-kun 
Published: August 2017

AbstractA systematic review and meta-analysis of prospective randomized studies were performed to evaluate the diagnostic value of measuring global longitudinal strain (GLS) using speckle tracking echocardiography (STE) in determining myocardial infarction (MI) size, which is usually measured based on late gadolinium enhancement (LGE) by cardiovascular magnetic resonance (CMR). Eleven trials with a total of 765 patients were included. The pooled correlation was 0.70 (95% CI: 0.64, 0.74) between two-dimensional (2D) GLS and the LGE percentage, and it was 0.55 (95% CI: 0.19, 0.78) for three-dimensional (3D) GLS. Pooled diagnostic estimates for 2D GLS to differentiate an MI size >12% were as follows: sensitivity, 0.77 (95% CI: 0.61, 0.90); specificity, 0.86 (95% CI: 0.68, 0.96); positive likelihood ratio (PLR), 8.13 (95% CI: 1.90, 26.61); negative likelihood ratio (NLR), 0.28 (95% CI: 0.10, 0.54); and diagnostic odds ratio (DOR), 39.87 (95% CI: 4.12, 172.83). The estimated area under the curve (AUC) of the summary receiver operating characteristic (SROC) curve was 0.702. The 2D STE results positively correlated with the infarction size quantified by CMR for patients who had experienced their first MI. This approach can serve as a good diagnostic index for assessing infarction area. However, more consolidated STE studies are still needed to determine the value of 3D STE.
Molecular determinants of proton selectivity and gating in the red-light activated channelrhodopsin Chrimson
Authors: Vierock Johannes , Grimm Christiane , Nitzan Noam , Hegemann Peter 
Published: August 2017

AbstractChannelrhodopsins are light-gated ion channels of green algae used for the precise temporal and spatial control of transmembrane ion fluxes. The channelrhodopsin Chrimson from Chlamydomonas noctigama allows unprecedented deep tissue penetration due to peak absorption at 590 nm. We demonstrate by electrophysiological recordings and imaging techniques that Chrimson is highly proton selective causing intracellular acidification in HEK cells that is responsible for slow photocurrent decline during prolonged illumination. We localized molecular determinants of both high proton selectivity and red light activation to the extracellular pore. Whereas exchange of Glu143 only drops proton conductance and generates an operational Na-channel with 590 nm activation, exchange of Glu139 in addition increased the open state lifetime and shifted the absorption hypsochromic by 70 nm. In conjunction with Glu300 in the center and Glu124 and Glu125 at the intracellular end of the pore, Glu139 contributes to a delocalized activation gate and stabilizes by long-range interaction counterion configuration involving protonation of Glu165 that we identified as a key determinant of the large opsin shift in Chrimson.
Lipids, fatty acids and hydroxy-fatty acids of Euphausia pacifica
Authors: Yamada Hidetoshi , Yamazaki Yuya , Koike Seiji , Hakozaki Mayuka , Nagahora Nozomi , Yuki Sayaka , Yano Akira , Tsurumi Koichiro , Okumura Takuji 
Published: August 2017

AbstractEuphausia pacifica is a good candidate for a resource of marine n-3 PUFA. However, few reports exist of the lipid and fatty acid composition of E. pacifica. To examine the potential of E. pacifica as a resource of marine n-3 PUFA, we analyzed E. pacifica oil. We extracted lipids from E. pacifica harvested from the Pacific Ocean near Sanriku, Japan. Lipid classes of E. pacifica oil were analyzed by TLC-FID and the fatty acid composition of the oil was analyzed by GC/MS. Free fatty acids and hydroxy-fatty acids were analyzed by LC/QTOFMS. The lipid content of E. pacifica ranged from 1.30% to 3.57%. The ratios of triacylglycerols, phosphatidylcholine, phosphatidylethanolamine and free fatty acids in E. pacifica lipids were 5.3–23.0%, 32.6–53.4%, 8.5–25.4% and 2.5–7.0%, respectively. The content of n-3 PUFA in E. pacifica lipids was 38.6–46.5%. We also showed that E. pacifica contains unusual fatty acids and derivatives: C16-PUFAs (9,12-hexadecadienoic acid, 6,9,12-hexadecatrienoic acid and 6,9,12,15-hexadecatetraenoic acid) and hydroxy-PUFAs (8-HETE and 10-HDoHE). E. pacifica is a good resource of marine n-3 PUFA. Moreover, E. pacifica can provide C16-PUFA and hydroxy-PUFAs.
Establishment of the most comprehensive ITS2 barcode database to date of the traditional medicinal plant Rhodiola (Crassulaceae)
Authors: Zhu Ruo-Wei , Li Yuan-Cong , Zhong Da-Lv , Zhang Jian-Qiang 
Published: August 2017

AbstractThe roots and rhizomes of Rhodiola crenulata and R. rosea have been used worldwide as adaptogens for hundreds of years. However, rapid growth in demand has resulted in merchants using other species of Rhodiola as adulterants. Here, we surveyed 518 individuals representing 47 of the 55 species in the genus, including 253 R. crenulata individuals from 16 populations and 98 R. rosea individuals from 11 populations, to evaluate the utility of the internal transcribed spacer 2 (ITS2) barcode for identification of Rhodiola species. We detected six haplotypes in R. crenulata and only one haplotype in R. rosea. An obvious overlap between intra- and inter-specific distance was detected, and the authentication efficacy of ITS2, which was assessed by BLAST1, a nearest distance method, and a tree test, was much lower than in other groups. However, R. crenulata and R. rosea could be exactly identified. Analysis showed that the secondary structure of ITS2 differs in R. crenulata and its closest relatives. Our results demonstrated that both a mini barcode from ITS2 and the structure of ITS2 are effective markers for the identification of R. crenulata and R. rosea. This study represents the most comprehensive database of ITS2 barcodes in Rhodiola to date and will be useful in Rhodiola species identification.
Characterizing particulate polycyclic aromatic hydrocarbon emissions from diesel vehicles using a portable emissions measurement system
Authors: Zheng Xuan , Wu Ye , Zhang Shaojun , Hu Jingnan , Zhang K. Max , Li Zhenhua , He Liqiang , Hao Jiming 
Published: August 2017

AbstractParticulate polycyclic aromatic hydrocarbons (p-PAHs) emitted from diesel vehicles are of concern because of their significant health impacts. Laboratory tests, road tunnel and roadside experiments have been conducted to measure p-PAH emissions. While providing valuable information, these methods have limited capabilities of characterizing p-PAH emissions either from individual vehicles or under real-world conditions. We employed a portable emissions measurement (PEMS) to measure real-world emission factors of priority p-PAHs for diesel vehicles representative of an array of emission control technologies. The results indicated over 80% reduction in p-PAH emission factors comparing the China V and China II emission standard groups (113 μg kg−1 vs. 733 μg kg−1). The toxicity abatement in terms of Benzo[a]pyrene equivalent emissions was substantial because of the large reductions in highly toxic components. By assessing real traffic conditions, the p-PAH emission factors on freeways were lower than on local roads by 52% ± 24%. A significant correlation (R2~0.85) between the p-PAH and black carbon emissions was identified with a mass ratio of approximately 1/2000. A literature review indicated that diesel p-PAH emission factors varied widely by engine technology, measurement methods and conditions, and the molecular diagnostic ratio method for source apportionment should be used with great caution.
The effect of topical administration of cyclopentolate on ocular biometry: An analysis for mouse and human models
Authors: Huang Furong , Huang Shenghai , Xie Ruozhong , Yang Yanan , Yan Jiaofeng , Cao Xiaowen , Zhang Chunlan , Zhou Feng , Shen Meixiao , Qu Jia , Zhou Xiangtian 
Published: August 2017

AbstractMydriasis with muscarinic antagonists have been used routinely prior to retinal examination and sometimes prior to refractive measurements of the mouse eye. However, biometric changes during topical administration of muscarinic antagonists have not been fully investigated in mice and humans. We found that the mouse eyes treated with cyclopentolate developed a hyperopia with a reduction in both the vitreous chamber depth and axial length. In humans, prior to the cyclopentolate treatment, a 6D accommodative stimulus produced a myopic shift with a reduced anterior chamber depth, choroidal thickness and anterior lens radius of curvature and an increase in lens thickness. After the cyclopentolate treatment, human eyes developed a hyperopic shift with an increased anterior chamber depth and anterior lens radius of curvature and a reduced lens thickness. Therefore, the biometric changes associated with this hyperopic shift were mainly located in the posterior segment of the eye in mice. However, it is the anterior segment of the eye that plays a main role in the hyperopic shift in human subjects. These results further indicate that mouse eyes do not have accommodation which needs to be taken into account when they are used for the study of human refractive errors.
Targeted metabolome profiling by dual-probe microdialysis sampling and treatment using Gardenia jasminoides for rats with type 2 diabetes
Authors: Wang Lu , Pi Zifeng , Liu Shu , Liu Zhiqiang , Song Fengrui 
Published: August 2017

AbstractDiabetes causes a variety of end-stage organ complications, including diabetic nephropathy. Metabolomics offers an approach for characterizing biofluid metabolic changes, but studies focusing on diabetic nephropathy are limited due to the loss of tissue-specific metabolic information. A microdialysis application for the sampling of intact endogenous metabolites has been developed, utilizing two probes simultaneously inserted into the kidney tissues and jugular vein of rats with type 2 diabetes. The comprehensive and quantitative analysis of 20 diagnostic biomarkers closely realated to type 2 diabetes and its complications were performed. Results indicated that amino acid and nucleotide levels were lower in diabetic rats, revealing that the metabolic pathways of amino acid, as well as purine and pyrimidine, were disturbed. Targeted metabolomics using mass spectrometry was performed to find potential therapeutic biomarkers and related metabolic pathways of Gardenia jasminoides (G. jasminoides) for treating diabetes. Results suggested that seven biomarkers in the kidney and five biomarkers in the blood were related to G. jasminoides. In addition, the marked perturbations of pathways were regulated after treatment with G. jasminoides, including amino acid metabolism and purine metabolism. These biomarkers and metabolic pathways provided new understanding for molecular mechanisms of G. jasminoides for treating diabetes and its complications.
A comprehensive analysis of the association of common variants of ABCG2 with gout
Authors: Yu Kuang-Hui , Chang Pi-Yueh , Chang Shih-Cheng , Wu-Chou Yah-Huei , Wu Li-An , Chen Ding-Pin , Lo Fu-Sung , Lu Jang-Jih 
Published: August 2017

AbstractThe objective of the present study was to determine whether there was an association between single nucleotide polymorphisms (SNPs) in ABCG2 and gout. We recruited 333 participants including 210 patients with gout and 123 controls and genotyped 45 SNPs in both cohorts. We found that 24 SNPs in ABCG2 are susceptibility loci associated with gout. Haplotype analysis revealed five blocks across the ABCG2 locus were associated with an increased risk of gout with odds ratios (ORs) from 2.59–3.17 (all P < 0.0001). A novel finding in the present study was the identification of rs3114018 in block 3 and its association with increased gout risk. We found that the rs2231142T allele in block 2 and the rs3114018C-rs3109823T (C-T) risk haplotype in block 3 conferred the greatest evidence of association to gout risk (P = 1.19 × 10−12 and P = 9.20 × 10−11, respectively). Our study provides an improved understanding of ABCG2 variations in patients with gout and, as shown by haplotype analysis, that ABCG2 may have a role in gout susceptibility.
Universal scaling of the self-field critical current in superconductors: from sub-nanometre to millimetre size
Authors: Talantsev E. F. , Crump W. P. , Tallon J. L. 
Published: August 2017

AbstractUniversal scaling behaviour in superconductors has significantly elucidated fluctuation and phase transition phenomena in these materials. However, universal behaviour for the most practical property, the critical current, was not contemplated because prevailing models invoke nucleation and migration of flux vortices. Such migration depends critically on pinning, and the detailed microstructure naturally differs from one material to another, even within a single material. Through microstructural engineering there have been ongoing improvements in the field-dependent critical current, thus illustrating its non-universal behaviour. But here we demonstrate the universal size scaling of the self-field critical current for any superconductor, of any symmetry, geometry or band multiplicity. Key to our analysis is the huge range of sample dimensions, from single-atomic-layer to mm-scale. These have widely variable microstructure with transition temperatures ranging from 1.2 K to the current record, 203 K. In all cases the critical current is governed by a fundamental surface current density limit given by the relevant critical field divided by the penetration depth.
Quantitative and organisational changes in mature extracellular matrix revealed through high-content imaging of total protein fluorescently stained in situ
Authors: Holdsworth Gill , Bon Hélène , Bergin Marianne , Qureshi Omar , Paveley Ross , Atkinson John , Huang Linghong , Tewari Roohi , Twomey Breda , Johnson Timothy 
Published: August 2017

AbstractFibrosis is a common driver of end-stage organ failure in most organs. It is characterised by excessive accumulation of extracellular matrix (ECM) proteins. Therapeutic options are limited and novel treatments are urgently required, however current cell-based high-throughput screening (HTS) models to identify molecules affecting ECM accumulation are limited in their relevance or throughput. We report a novel sensitive approach which combines in situ fluorescent staining of accumulated decellularised ECM proteins with automated high-content microscopy. Using this method to measure ECM accumulation in a kidney cell model, we demonstrated good agreement with established radiolabelled amino acid incorporation assays: TGFβ1 delivered a potent pro-fibrotic stimulus, which was reduced by TGFβ antibody or the anti-fibrotic nintedanib. Importantly, our method also provides information about matrix organisation: the extent of ECM accumulation was unaffected by the BMP antagonist Gremlin-1 but a pronounced effect on matrix fibrillar organisation was revealed. This rapid, straightforward endpoint provides quantitative data on ECM accumulation and offers a convenient cross-species readout that does not require antibodies. Our method facilitates discovery of novel pro- and anti-fibrotic agents in 384-well plate format and may be widely applied to in vitro cell-based models in which matrix protein deposition reflects the underlying biology or pathology.
Deciphering Clostridium metabolism and its responses to bioreactor mass transfer during syngas fermentation
Authors: Wan Ni , Sathish Ashik , You Le , Tang Yinjie J. , Wen Zhiyou 
Published: August 2017

AbstractThis study used 13C tracers and dynamic labeling to reveal metabolic features (nutrients requirements, pathway delineation and metabolite turnover rates) of Clostridium carboxidivorans P7, a model strain for industrial syngas fermentation, and its implication with bioreactor mass transfer. P7 shows poor activity for synthesizing amino acids (e.g., phenylalanine) and thus, needs rich medium for cell growth. The strain has multiple carbon fixation routes (Wood-Ljungdahl pathway, pyruvate:ferredoxin oxidoreductase reaction and anaplerotic pathways) and Re-citrate synthase (Ccar_06155) was a key enzyme in its tricarboxylic acid cycle (TCA) pathway. High fluxes were observed in P7’s Wood-Ljungdahl pathway, right branch of TCA cycle, pyruvate synthesis, and sugar phosphate pathways, but the cells anabolic pathways were strikingly slow. In bioreactor culture, when syngas flowrate increased from 1 to 10 mL/min, P7 strain produced same amount of total extracellular products (acids and alcohols) but high flowrate favored alcohol accumulation. This observation was due to the mass transfer limitation influencing energy metabolism (CO/H2 oxidation for cofactor generations) more prominently than carbon fixation. When syngas flowrate increased from 10 of 20 mL/min, the alcohol productivity was not improved and the labeling rate (~0.03 h−1) of key metabolite acetyl-CoA reached to P7 strain’s metabolism limitation regime.
Morphine activation of mu opioid receptors causes disinhibition of neurons in the ventral tegmental area mediated by β-arrestin2 and c-Src
Authors: Bull Fiona A. , Baptista-Hon Daniel T. , Lambert Jeremy J. , Walwyn Wendy , Hales Tim G. 
Published: August 2017

AbstractThe tyrosine kinase, c-Src, participates in mu opioid receptor (MOP) mediated inhibition in sensory neurons in which β-arrestin2 (β-arr2) is implicated in its recruitment. Mice lacking β-arr2 exhibit increased sensitivity to morphine reinforcement; however, whether β-arr2 and/or c-Src participate in the actions of opioids in neurons within the reward pathway is unknown. It is also unclear whether morphine acts exclusively through MOPs, or involves delta opioid receptors (DOPs). We examined the involvement of MOPs, DOPs, β-arr2 and c-Src in the inhibition by morphine of GABAergic inhibitory postsynaptic currents (IPSCs) recorded from neurons in the mouse ventral tegmental area. Morphine inhibited spontaneous IPSC frequency, mainly through MOPs, with only a negligible effect remaining in MOP−/− neurons. However, a reduction in the inhibition by morphine for DOP−/− c.f. WT neurons and a DPDPE-induced decrease of IPSC frequency revealed a role for DOPs. The application of the c-Src inhibitor, PP2, to WT neurons also reduced inhibition by morphine, while the inactive PP3, and the MEK inhibitor, SL327, had no effect. Inhibition of IPSC frequency by morphine was also reduced in β-arr2−/− neurons in which PP2 caused no further reduction. These data suggest that inhibition of IPSCs by morphine involves a β-arr2/c-Src mediated mechanism.
Multiple origins of endosymbionts in Chlorellaceae with no reductive effects on the plastid or mitochondrial genomes
Authors: Fan Weishu , Guo Wenhu , Van Etten James L. , Mower Jeffrey P. 
Published: August 2017

AbstractAncient endosymbiotic relationships have led to extreme genomic reduction in many bacterial and eukaryotic algal endosymbionts. Endosymbionts in more recent and/or facultative relationships can also experience genomic reduction to a lesser extent, but little is known about the effects of the endosymbiotic transition on the organellar genomes of eukaryotes. To understand how the endosymbiotic lifestyle has affected the organellar genomes of photosynthetic green algae, we generated the complete plastid genome (plastome) and mitochondrial genome (mitogenome) sequences from three green algal endosymbionts (Chlorella heliozoae, Chlorella variabilis and Micractinium conductrix). The mitogenomes and plastomes of the three newly sequenced endosymbionts have a standard set of genes compared with free-living trebouxiophytes, providing no evidence for functional genomic reduction. Instead, their organellar genomes are generally larger and more intron rich. Intron content is highly variable among the members of Chlorella, suggesting very high rates of gain and/or loss of introns during evolution. Phylogenetic analysis of plastid and mitochondrial genes demonstrated that the three endosymbionts do not form a monophyletic group, indicating that the endosymbiotic lifestyle has evolved multiple times in Chlorellaceae. In addition, M. conductrix is deeply nested within the Chlorella clade, suggesting that taxonomic revision is needed for one or both genera.
Flexible regulation of DNA displacement reaction through nucleic acid-recognition enzyme and its application in keypad lock system and biosensing
Authors: Li Chao , Shi Liu , Tao Yaqin , Mao Xiaoxia , Xiang Yang , Li Genxi 
Published: August 2017

AbstractToehold-mediated DNA strand displacement reaction (SDR) plays pivotal roles for the construction of diverse dynamic DNA nanodevices. To date, many elements have been introduced into SDR system to achieve controllable activation and fine regulation. However, as the most relevant stimuli for nucleic acid involved reaction, nucleic acid-recognizing enzymes (NAEs) have received nearly no attention so far despite SDR often takes place in NAEs-enriched environment (i.e., biological fluids). Herein, we report a set of NAEs-controlled SDR strategies, which take full advantage of NAEs’ properties. In this study, three different kinds of enzymes belonging to several classes (i.e., exonuclease, endonuclease and polymerase) have been used to activate or inhibit SDR, and more importantly, some mechanisms behind these strategies on how NAEs affect SDR have also been revealed. The exploration to use NAEs as possible cues to operate SDR will expand the available toolbox to build novel stimuli-fueled DNA nanodevices and could open the door to many applications including enzyme-triggered biocomputing and biosensing.