bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stability and complexity in model meta-ecosystems
Authors: Gravel Dominique , Massol François , Leibold Mathew A. 
Published: August 2016

AbstractThe diversity of life and its organization in networks of interacting species has been a long-standing theoretical puzzle for ecologists. Ever since May’s provocative paper challenging whether ‘large complex systems [are] stable’ various hypotheses have been proposed to explain when stability should be the rule, not the exception. Spatial dynamics may be stabilizing and thus explain high community diversity, yet existing theory on spatial stabilization is limited, preventing comparisons of the role of dispersal relative to species interactions. Here we incorporate dispersal of organisms and material into stability–complexity theory. We find that stability criteria from classic theory are relaxed in direct proportion to the number of ecologically distinct patches in the meta-ecosystem. Further, we find the stabilizing effect of dispersal is maximal at intermediate intensity. Our results highlight how biodiversity can be vulnerable to factors, such as landscape fragmentation and habitat loss, that isolate local communities.
Anisotropic etching of platinum electrodes at the onset of cathodic corrosion
Authors: Hersbach Thomas J. P. , Yanson Alexei I. , Koper Marc T. M. 
Published: August 2016

AbstractCathodic corrosion is a process that etches metal electrodes under cathodic polarization. This process is presumed to occur through anionic metallic reaction intermediates, but the exact nature of these intermediates and the onset potential of their formation is unknown. Here we determine the onset potential of cathodic corrosion on platinum electrodes. Electrodes are characterized electrochemically before and after cathodic polarization in 10 M sodium hydroxide, revealing that changes in the electrode surface start at an electrode potential of −1.3 V versus the normal hydrogen electrode. The value of this onset potential rules out previous hypotheses regarding the nature of cathodic corrosion. Scanning electron microscopy shows the formation of well-defined etch pits with a specific orientation, which match the voltammetric data and indicate a remarkable anisotropy in the cathodic etching process, favouring the creation of (100) sites. Such anisotropy is hypothesized to be due to surface charge-induced adsorption of electrolyte cations.
A predictive nondestructive model for the covariation of tree height, diameter and stem volume scaling relationships
Authors: Zhang Zhongrui , Zhong Quanlin , Niklas Karl J. , Cai Liang , Yang Yusheng , Cheng Dongliang 
Published: August 2016

AbstractMetabolic scaling theory (MST) posits that the scaling exponents among plant height H, diameter D, and biomass M will covary across phyletically diverse species. However, the relationships between scaling exponents and normalization constants remain unclear. Therefore, we developed a predictive model for the covariation of H, D and stem volume V scaling relationships and used data from Chinese fir (Cunninghamia lanceolata) in Jiangxi province, China to test it. As predicted by the model and supported by the data, normalization constants are positively correlated with their associated scaling exponents for D vs. V and H vs. V, whereas normalization constants are negatively correlated with the scaling exponents of H vs. D. The prediction model also yielded reliable estimations of V (mean absolute percentage error = 10.5 ± 0.32 SE across 12 model calibrated sites). These results (1) support a totally new covariation scaling model, (2) indicate that differences in stem volume scaling relationships at the intra-specific level are driven by anatomical or ecophysiological responses to site quality and/or management practices and (3) provide an accurate non-destructive method for predicting Chinese fir stem volume.
Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations
Authors: Oikonomopoulos Spyros , Wang Yu Chang , Djambazian Haig , Badescu Dunarel , Ragoussis Jiannis 
Published: August 2016

AbstractTo assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration. cDNA libraries were generated using a template switching protocol to facilitate the direct comparison between different sequencing platforms. The MinION performance was assessed for its ability to sequence the cDNAs directly with good accuracy in terms of abundance and full length. The abundance of the ERCC cDNA molecules sequenced by MinION agreed with their expected concentration. No length or GC content bias was observed. The majority of cDNAs were sequenced as full length. Additionally, a complex cDNA population derived from a human HEK-293 cell line was sequenced on an Illumina HiSeq 2500, PacBio RS II and ONT MinION platforms. We observed that there was a good agreement in the measured cDNA abundance between PacBio RS II and ONT MinION (rpearson = 0.82, isoforms with length more than 700bp) and between Illumina HiSeq 2500 and ONT MinION (rpearson = 0.75). This indicates that the ONT MinION can sequence quantitatively both long and short full length cDNA molecules.
A Generalized Lossy Transmission-Line Model for Tunable Graphene-Based Transmission Lines with Attenuation Phenomenon
Authors: Wu Yongle , Qu Meijun , Liu Yuanan 
Published: August 2016

AbstractTo investigate the frequency shift phenomenon by inserting graphene, a generalized lossy transmission-line model and the related electrical parameter-extraction theory are proposed in this paper. Three kinds of graphene-based transmission lines with attenuation phenomenon including microstrip line, double-side parallel strip line and uniplanar coplanar waveguide are analyzed under the common conditions where different chemical potentials are loaded on graphene. The values of attenuation constant and phase constant and the real and imaginary parts of the characteristic impedance of transmission lines are extracted to analyze in details. When the attenuation constant and the reactance part of the characteristic impedance are approximately equal to zero, this kind of transmission line has low or zero insertion loss. On the contrary, the transmission line is under the radiation mode with obvious insertion loss. The phase constant changes linearly under the transmission mode and can be varied with changing of chemical potentials which attributes to the property of frequency tunability. Furthermore, a bandwidth reconfigurable uniplanar coplanar waveguide power divider is simulated to demonstrate that this theory can be applied to the design of three-port devices. In summary, this work provides a strong potential approach and design theory to help design other kinds of terahertz and mid-infrared reconfigurable devices.
Electric field control of magnon-induced magnetization dynamics in multiferroics
Authors: Risinggård Vetle , Kulagina Iryna , Linder Jacob 
Published: August 2016

AbstractWe consider theoretically the effect of an inhomogeneous magnetoelectric coupling on the magnon-induced dynamics of a ferromagnet. The magnon-mediated magnetoelectric torque affects both the homogeneous magnetization and magnon-driven domain wall motion. In the domains, we predict a reorientation of the magnetization, controllable by the applied electric field, which is almost an order of magnitude larger than that observed in other physical systems via the same mechanism. The applied electric field can also be used to tune the domain wall speed and direction of motion in a linear fashion, producing domain wall velocities several times the zero field velocity. These results show that multiferroic systems offer a promising arena to achieve low-dissipation magnetization rotation and domain wall motion by exciting spin-waves.
Quantitative profiling of spreading-coupled protein tyrosine phosphorylation in migratory cells
Authors: Xie Yajun , Wang Jinlong , Zhang Yuanya , Liu Xiaofei , Wang Xiaorong , Liu Kehui , Huang Xiahe , Wang Yingchun 
Published: August 2016

AbstractProtein tyrosine phosphorylation is an important mechanism that regulates cytoskeleton reorganization and cell spreading of migratory cells. A number of cytoskeletal proteins are known to be tyrosine phosphorylated (pY) in different cellular processes. However, the profile of pY proteins during different stages of cell spreading has not been available. Using immunoafffinity enrichment of pY proteins coupled with label free quantitative proteomics, we quantitatively identified 447 pY proteins in the migratory ECV-304 cells at the early spreading (adhesion) and the active spreading stages. We found that pY levels of the majority of the quantified proteins were significantly increased in the active spreading stage compared with the early spreading stage, suggesting that active cell spreading is concomitant with extra tyrosine phosphorylation. The major categories of proteins impacted by tyrosine phosphorylation are involved in cytoskeleton and focal adhesion regulation, protein translation and degradation. Our findings, for the first time, dissect the cell spreading-specific pY signals from the adhesion induced pY signals and provide a valuable resource for the future mechanistic research regarding the regulation of cell spreading.
Low-dose ticagrelor yields an antiplatelet efficacy similar to that of standard-dose ticagrelor in healthy subjects: an open-label randomized controlled trial
Authors: Li Pan , Gu Ying , Yang Yawei , Chen Lizhi , Liu Junmei , Gao Lihong , Qin Yongwen , Cai Quancai , Zhao Xianxian , Wang Zhuo , Ma Liping 
Published: August 2016

AbstractTicagrelor has a greater antiplatelet efficacy than clopidogrel but may be accompanied by an increased risk of bleeding. This study evaluated the antiplatelet effect and pharmacokinetic profile of low-dose ticagrelor in healthy Chinese volunteers. Thirty healthy subjects were randomized to receive standard-dose ticagrelor (180-mg loading dose, 90-mg twice daily [bid] [n = 10]), low-dose ticagrelor (90-mg loading dose, 45-mg bid [n = 10]), or clopidogrel (600-mg loading dose, 75-mg once daily [n = 10]). Platelet reactivity was assessed by using the VerifyNow P2Y12 assay at baseline and 0.5, 1, 2, 4, 8, 24, 48 and 72 hours post-dosing. The ticagrelor and AR-C124910XX concentrations were measured for pharmacokinetic analysis. The percentage inhibition of P2Y12 reaction units was higher in the low-dose and standard-dose ticagrelor group than in the clopidogrel group at 0.5, 1, 2, 4, 8 and 48 hours post-dosing (P < 0.05 for all), but did not differ significantly between the two ticagrelor doses at any time-point (P > 0.05). The plasma ticagrelor and ARC124910XX concentrations were approximately 2-fold higher with standard-dose versus low-dose ticagrelor. No serious adverse events were reported. In conclusion, low-dose ticagrelor achieved faster and higher inhibition of platelet functions in healthy Chinese subjects than did clopidogrel, with an antiplatelet efficacy similar to that of standard-dose ticagrelor.
A new method for assessing plant lodging and the impact of management options on lodging in canola crop production
Authors: Wu Wei , Ma Bao–Luo 
Published: August 2016

AbstractLodging, defined as the permanent displacement of aboveground parts, is a common problem to cause yield loss, deterioration in seed quality and difficult to harvest in canola (Brassica napus L.) crop production. This study aimed to develop a method for assessing crop lodging, to examine how agronomic practices affected the relationships between root lodging and electrical capacitance traits. Canola plants were more susceptible to root lodging than stem lodging. The electrical measurements were more closely related with anchorage strength (Sp) than stem bending strength (Ss). Among the three electrical measurements, the root capacitance (C) displayed the most consistent and significant relationships with Sp in all three field experiments (R2 = 0.88–0.56; P ≤ 0.01). This study indicates that the risk of lodging can be reduced by using appropriate management practices and variety selection. Enhancing root Sp was advocated as a priority over enhancing stem Ss in cultivar improvement. Electrical measurements, especially of root C, can be considered as a non–invasive technique that could partially replace the intrusive methods used for the in situ assessment of lodging resistance among various agronomic practices or can be applied in breeding programs for selecting genotypes with high yield potentials and strong Sp values.
Individual aggregates of amyloid beta induce temporary calcium influx through the cell membrane of neuronal cells
Authors: Drews Anna , Flint Jennie , Shivji Nadia , Jönsson Peter , Wirthensohn David , De Genst Erwin , Vincke Cécile , Muyldermans Serge , Dobson Chris , Klenerman David 
Published: August 2016

AbstractLocal delivery of amyloid beta oligomers from the tip of a nanopipette, controlled over the cell surface, has been used to deliver physiological picomolar oligomer concentrations to primary astrocytes or neurons. Calcium influx was observed when as few as 2000 oligomers were delivered to the cell surface. When the dosing of oligomers was stopped the intracellular calcium returned to basal levels or below. Calcium influx was prevented by the presence in the pipette of the extracellular chaperone clusterin, which is known to selectively bind oligomers, and by the presence a specific nanobody to amyloid beta. These data are consistent with individual oligomers larger than trimers inducing calcium entry as they cross the cell membrane, a result supported by imaging experiments in bilayers, and suggest that the initial molecular event that leads to neuronal damage does not involve any cellular receptors, in contrast to work performed at much higher oligomer concentrations.
Normalization of human RNA-seq experiments using chimpanzee RNA as a spike-in standard
Authors: Yu Hannah , Hahn Yoonsoo , Park Sang-Ryoul , Chung Sun-Ku , Jeong Sangkyun , Yang Inchul 
Published: August 2016

AbstractNormalization of human RNA-seq experiments employing chimpanzee RNA as a spike-in standard is reported. Human and chimpanzee RNAs exhibit single nucleotide variations (SNVs) in average 210-bp intervals. Spike-in chimpanzee RNA would behave the same as the human counterparts during the whole NGS procedures owing to the high sequence similarity. After discrimination of species origins of the NGS reads based on SNVs, the chimpanzee reads were used to read-by-read normalize biases and variations of human reads. By this approach, as many as 10,119 transcripts were simultaneously normalized for the entire NGS procedures leading to accurate and reproducible quantification of differential gene expression. In addition, incomparable data sets from different in-process degradations or from different library preparation methods were made well comparable by the normalization. Based on these results, we expect that the normalization approaches using near neighbor genomes as internal standards could be employed as a standard protocol, which will improve both accuracy and comparability of NGS results across different sample batches, laboratories and NGS platforms.
Nitrogen fixation and nifH diversity in human gut microbiota
Authors: Igai Katsura , Itakura Manabu , Nishijima Suguru , Tsurumaru Hirohito , Suda Wataru , Tsutaya Takumi , Tomitsuka Eriko , Tadokoro Kiyoshi , Baba Jun , Odani Shingo , Natsuhara Kazumi , Morita Ayako , Yoneda Minoru , Greenhill Andrew R. , Horwood Paul F. , Inoue Jun-ichi , Ohkuma Moriya , Hongoh Yuichi , Yamamoto Taro , Siba Peter M. , Hattori Masahira , Minamisawa Kiwamu , Umezaki Masahiro 
Published: August 2016

AbstractIt has been hypothesized that nitrogen fixation occurs in the human gut. However, whether the gut microbiota truly has this potential remains unclear. We investigated the nitrogen-fixing activity and diversity of the nitrogenase reductase (NifH) genes in the faecal microbiota of humans, focusing on Papua New Guinean and Japanese individuals with low to high habitual nitrogen intake. A 15N2 incorporation assay showed significant enrichment of 15N in all faecal samples, irrespective of the host nitrogen intake, which was also supported by an acetylene reduction assay. The fixed nitrogen corresponded to 0.01% of the standard nitrogen requirement for humans, although our data implied that the contribution in the gut in vivo might be higher than this value. The nifH genes recovered in cloning and metagenomic analyses were classified in two clusters: one comprising sequences almost identical to Klebsiella sequences and the other related to sequences of Clostridiales members. These results are consistent with an analysis of databases of faecal metagenomes from other human populations. Collectively, the human gut microbiota has a potential for nitrogen fixation, which may be attributable to Klebsiella and Clostridiales strains, although no evidence was found that the nitrogen-fixing activity substantially contributes to the host nitrogen balance.
H3.3 demarcates GC-rich coding and subtelomeric regions and serves as potential memory mark for virulence gene expression in Plasmodium falciparum
Authors: Fraschka Sabine Anne-Kristin , Henderson Rob Wilhelmus Maria , Bártfai Richárd 
Published: August 2016

AbstractHistones, by packaging and organizing the DNA into chromatin, serve as essential building blocks for eukaryotic life. The basic structure of the chromatin is established by four canonical histones (H2A, H2B, H3 and H4), while histone variants are more commonly utilized to alter the properties of specific chromatin domains. H3.3, a variant of histone H3, was found to have diverse localization patterns and functions across species but has been rather poorly studied in protists. Here we present the first genome-wide analysis of H3.3 in the malaria-causing, apicomplexan parasite, P. falciparum, which revealed a complex occupancy profile consisting of conserved and parasite-specific features. In contrast to other histone variants, PfH3.3 primarily demarcates euchromatic coding and subtelomeric repetitive sequences. Stable occupancy of PfH3.3 in these regions is largely uncoupled from the transcriptional activity and appears to be primarily dependent on the GC-content of the underlying DNA. Importantly, PfH3.3 specifically marks the promoter region of an active and poised, but not inactive antigenic variation (var) gene, thereby potentially contributing to immune evasion. Collectively, our data suggest that PfH3.3, together with other histone variants, indexes the P. falciparum genome to functionally distinct domains and contribute to a key survival strategy of this deadly pathogen.
Strains of the Propionibacterium acnes type III lineage are associated with the skin condition progressive macular hypomelanosis
Authors: Barnard Emma , Liu Jared , Yankova Eliza , Cavalcanti Silvana M. , Magalhães Marcelo , Li Huiying , Patrick Sheila , McDowell Andrew 
Published: August 2016

AbstractProgressive macular hypomelanosis (PMH) is a common skin disorder that causes hypopigmentation in a variety of skin types. Although the underlying aetiology of this condition is unclear, there is circumstantial evidence that links the skin bacterium Propionibacterium acnes to the condition. We now describe the first detailed population genetic analysis of P. acnes isolates recovered from paired lesional and non-lesional skin of PMH patients. Our results demonstrate a strong statistical association between strains from the type III phylogenetic lineage and PMH lesions (P = 0.0019), but not those representing other phylogroups, including those associated with acne (type IA1). We also demonstrate, based on in silico 16S rDNA analysis, that PMH isolates previously recovered from patients in Europe are also consistent with the type III lineage. Using comparative genome analysis, we identified multiple genomic regions that are specific for, or absent from, type III strains compared to other phylogroups. In the former case, these include open reading frames with putative functions in metabolism, transport and transcriptional regulation, as well as predicted proteins of unknown function. Further study of these genomic elements, along with transcriptional and functional analyses, may help to explain why type III strains are associated with PMH.
Mesenchymal Stem Cells Reversed Morphine Tolerance and Opioid-induced Hyperalgesia
Authors: Hua Zhen , Liu LiPing , Shen Jun , Cheng Kathleen , Liu Aijun , Yang Jing , Wang Lina , Qu Tingyu , Yang HongNa , Li Yan , Wu Haiyan , Narouze John , Yin Yan , Cheng Jianguo 
Published: August 2016

AbstractMore than 240 million opioid prescriptions are dispensed annually to treat pain in the US. The use of opioids is commonly associated with opioid tolerance (OT) and opioid-induced hyperalgesia (OIH), which limit efficacy and compromise safety. The dearth of effective way to prevent or treat OT and OIH is a major medical challenge. We hypothesized that mesenchymal stem cells (MSCs) attenuate OT and OIH in rats and mice based on the understanding that MSCs possess remarkable anti-inflammatory properties and that both OT and chronic pain are associated with neuroinflammation in the spinal cord. We found that the development of OT and OIH was effectively prevented by either intravenous or intrathecal MSC transplantation (MSC-TP), which was performed before morphine treatment. Remarkably, established OT and OIH were significantly reversed by either intravenous or intrathecal MSCs when cells were transplanted after repeated morphine injections. The animals did not show any abnormality in vital organs or functions. Immunohistochemistry revealed that the treatments significantly reduced activation level of microglia and astrocytes in the spinal cord. We have thus demonstrated that MSC-TP promises to be a potentially safe and effective way to prevent and reverse two of the major problems of opioid therapy.
Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass
Authors: Liu Peng , Wang Le , Wong Sek-Man , Yue Gen Hua 
Published: August 2016

AbstractAsian seabass has suffered from viral nervous necrosis (VNN) disease. Our previous study has mapped quantitative trait loci (QTL) for resistance to VNN disease. To fine map these QTL and identify causative genes, we identified 6425 single nucleotide polymorphisms (SNPs) from 85 dead and 94 surviving individuals. Combined with 155 microsatellites, we constructed a genetic map consisting of 24 linkage groups (LGs) containing 3000 markers, with an average interval of 1.27 cM. We mapped one significant and three suggestive QTL with phenotypic variation explained (PVE) of 8.3 to 11.0%, two significant and two suggestive QTL with PVE of 7.8 to 10.9%, for resistance in three LGs and survival time in four LGs, respectively. Further analysis one QTL with the largest effect identified protocadherin alpha-C 2-like (Pcdhac2) as the possible candidate gene. Association study in 43 families with 1127 individuals revealed a 6 bp insertion-deletion was significantly associated with disease resistance. qRT-PCR showed the expression ofPcdhac2was significantly induced in the brain, muscle and skin after nervous necrosis virus (NNV) infection. Our results could facilitate marker-assisted selection (MAS) for resistance to NNV in Asian seabass and set up the basis for functional analysis of the potential causative gene for resistance.