bluuebunny/crossref_metadata_2025_split huggingface dataset:
A quantitative analysis of the direct and indirect costs of nitrogen fixation: a model based on Azotobacter vinelandii
Authors: Inomura Keisuke , Bragg Jason , Follows Michael J 
Published: October 2016

Abstract
Nitrogen fixation is advantageous in microbial competition when bioavailable nitrogen is scarce, but has substantial costs for growth rate and growth efficiency. To quantify these costs, we have developed a model of a nitrogen-fixing bacterium that constrains mass, electron and energy flow at the scale of the individual. When tested and calibrated with laboratory data for the soil bacterium Azotobacter vinelandii, the model reveals that the direct energetic cost of nitrogen fixation is small relative to the cost of managing intracellular oxygen. It quantifies the costs and benefits of several potential oxygen protection mechanisms present in nature including enhanced respiration (respiratory protection) as well as the production of extracellular polymers as a barrier to O2 diffusion, and increasing cell size. The latter mechanisms lead to higher growth efficiencies relative to respiratory protection alone. This simple, yet mechanistic framework provides a quantitative model of nitrogen fixation, which can be applied in ecological simulations.
Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock
Authors: Bagnoud Alexandre , Chourey Karuna , Hettich Robert L. , de Bruijn Ino , Andersson Anders F. , Leupin Olivier X. , Schwyn Bernhard , Bernier-Latmani Rizlan 
Published: October 2016

AbstractThe Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.
Massive and parallel expression profiling using microarrayed single-cell sequencing
Authors: Vickovic Sanja , Ståhl Patrik L. , Salmén Fredrik , Giatrellis Sarantis , Westholm Jakub Orzechowski , Mollbrink Annelie , Navarro José Fernández , Custodio Joaquin , Bienko Magda , Sutton Lesley-Ann , Rosenquist Richard , Frisén Jonas , Lundeberg Joakim 
Published: October 2016

AbstractSingle-cell transcriptome analysis overcomes problems inherently associated with averaging gene expression measurements in bulk analysis. However, single-cell analysis is currently challenging in terms of cost, throughput and robustness. Here, we present a method enabling massive microarray-based barcoding of expression patterns in single cells, termed MASC-seq. This technology enables both imaging and high-throughput single-cell analysis, characterizing thousands of single-cell transcriptomes per day at a low cost (0.13 USD/cell), which is two orders of magnitude less than commercially available systems. Our novel approach provides data in a rapid and simple way. Therefore, MASC-seq has the potential to accelerate the study of subtle clonal dynamics and help provide critical insights into disease development and other biological processes.
CaMKII induces permeability transition through Drp1 phosphorylation during chronic β-AR stimulation
Authors: Xu Shangcheng , Wang Pei , Zhang Huiliang , Gong Guohua , Gutierrez Cortes Nicolas , Zhu Weizhong , Yoon Yisang , Tian Rong , Wang Wang 
Published: October 2016

AbstractMitochondrial permeability transition pore (mPTP) is involved in cardiac dysfunction during chronic β-adrenergic receptor (β-AR) stimulation. The mechanism by which chronic β-AR stimulation leads to mPTP openings is elusive. Here, we show that chronic administration of isoproterenol (ISO) persistently increases the frequency of mPTP openings followed by mitochondrial damage and cardiac dysfunction. Mechanistically, this effect is mediated by phosphorylation of mitochondrial fission protein, dynamin-related protein 1 (Drp1), by Ca2+/calmodulin-dependent kinase II (CaMKII) at a serine 616 (S616) site. Mutating this phosphorylation site or inhibiting Drp1 activity blocks CaMKII- or ISO-induced mPTP opening and myocyte death in vitro and rescues heart hypertrophy in vivo. In human failing hearts, Drp1 phosphorylation at S616 is increased. These results uncover a pathway downstream of chronic β-AR stimulation that links CaMKII, Drp1 and mPTP to bridge cytosolic stress signal with mitochondrial dysfunction in the heart.
cAMP-PKA-CaMKII signaling pathway is involved in aggravated cardiotoxicity during Fuzi and Beimu Combination Treatment of Experimental Pulmonary Hypertension
Authors: Zhuang Pengwei , Huang Yingying , Lu Zhiqiang , Yang Zhen , Xu Liman , Sun Fengjiao , Zhang Yanjun , Duan Jinao 
Published: October 2016

AbstractAconiti Lateralis Radix Praeparata (Fuzi) and Fritillariae Thunbergii bulbus (Beimu) have been widely used clinically to treat cardiopulmonary related diseases in China. However, according to the classic rules of traditional Chinese medicine, Fuzi and Beimu should be prohibited to use as a combination for their incompatibility. Therefore, it is critical to elucidate the paradox on the use of Fuzi and Beimu combination therapy. Monocrotaline-induced pulmonary hypertension rats were treated with either Fuzi, Beimu, or their combination at different stages of PH. We demonstrated that at the early stage of PH, Fuzi and Beimu combination significantly improved lung function and reduced pulmonary histopathology. However, as the disease progressed, when Fuzi and Beimu combination were used at the late stage of PH, right ventricular chamber dilation was histologically apparent and myocardial apoptosis was significantly increased compared with each drug alone. Western-blotting results indicated that the main chemical ingredient of Beimu could down-regulate the protein phosphorylation levels of Akt and PDE4D, whereas the combination of Fuzi and Beimu could up-regulate PKA and CaMKII signaling pathways. Therefore, we concluded that Fuzi and Beimu combination potentially aggravated the heart injury due to the inhibition of PDK1/Akt/PDE4D axis and subsequent synergistic activation of βAR-Gs-PKA/CaMKII signaling pathway.
Chiral Separation by Flows: The Role of Flow Symmetry and Dimensionality
Authors: Ro Sunghan , Yi Juyeon , Kim Yong Woon 
Published: October 2016

AbstractSeparation of enantiomers by flows is a promising chiral resolution method using cost-effective microfluidics. Notwithstanding a number of experimental and numerical studies, a fundamental understanding still remains elusive, and an important question as to whether it is possible to specify common physical properties of flows that induce separation has not been addressed. Here, we study the separation of rigid chiral objects of an arbitrary shape induced by a linear flow field at low Reynolds numbers. Based on a symmetry property under parity inversion, we show that the rate-of-strain field is essential to drift the objects in opposite directions according to chirality. From eigenmode analysis, we also derive an analytic expression for the separation conditions which shows that the flow field should be quasi-two-dimensional for the precise and efficient resolutions of microscopic enantiomers. We demonstrate this prediction by Langevin dynamics simulations with hydrodynamic interactions fully implemented. Finally, we discuss the practical feasibility of the linear flow analysis, considering separations by a vortex flow or an extensional flow under a confining potential.
Enhancement of ferromagnetism by oxygen isotope substitution in strontium ruthenate SrRuO3
Authors: Kawanaka Hirofumi , Aiura Yoshihiro , Hasebe Takayuki , Yokoyama Makoto , Masui Takahiko , Nishihara Yoshikazu , Yanagisawa Takashi 
Published: October 2016

AbstractThe oxygen isotope effect of the ferromagnetic transition in itinerant ferromagnet strontium ruthenate SrRuO3 with a Curie temperature Tc of 160 K is studied. We observed for the first time a shift of ∆Tc ~ 1 K by oxygen isotope substitution of 16O → 18O in SrRuO3 by precise measurements of DC and AC magnetizations. The results surprisingly lead to the noteworthy inverse isotope effect with negative coefficient α = −∂ lnTc/∂ lnM. The Raman spectra indicate that the main vibration frequency of 16O at 363 cm−1 shifts to 341 cm−1 following oxygen isotope substitution 18O. This shift is remarkably consistent with the Debye frequency being proportional to ∝ 1√M where M is the mass of an oxygen atom. The positive isotope shift of ∆Tc can be understood by taking account of the electron-phonon interaction.
In vivo dendritic cell targeting cellular vaccine induces CD4+ Tfh cell-dependent antibody against influenza virus
Authors: Yamasaki Satoru , Shimizu Kanako , Kometani Kohei , Sakurai Maki , Kawamura Masami , Fujii Shin-ichiro 
Published: October 2016

AbstractAn induction of long-term cellular and humoral immunity is for the goal of vaccines, but the combination of antigens and adjuvant remain unclear. Here, we show, using a cellular vaccine carrying foreign protein antigen plus iNKT cell glycolipid antigen, designated as artificial adjuvant vector cells (aAVCs), that mature XCR1− DCs in situ elicit not only ordinal antigen-specific CD4+T cells, but also CD4+ Tfh and germinal center, resulted in inducing long-term antibody production. As a mechanism for leading the long-term antibody production by aAVC, memory CD4+ Tfh cells but not iNKTfh cells played an important role in a Bcl6 dependent manner. To develop it for influenza infection, we established influenza hemagglutinin-carrying aAVC (aAVC-HA) and found that all the mice vaccinated with aAVC-HA were protected from life-threatening influenza infection. Thus, the in vivo DC targeting therapy by aAVC would be useful for protection against viral infection.
Soil microbial C:N ratio is a robust indicator of soil productivity for paddy fields
Authors: Li Yong , Wu Jinshui , Shen Jianlin , Liu Shoulong , Wang Cong , Chen Dan , Huang Tieping , Zhang Jiabao 
Published: October 2016

AbstractMaintaining good soil productivity in rice paddies is important for global food security. Numerous methods have been developed to evaluate paddy soil productivity (PSP), most based on soil physiochemical properties and relatively few on biological indices. Here, we used a long-term dataset from experiments on paddy fields at eight county sites and a short-term dataset from a single field experiment in southern China, and aimed at quantifying relationships between PSP and the ratios of carbon (C) to nutrients (N and P) in soil microbial biomass (SMB). In the long-term dataset, SMB variables generally showed stronger correlations with the relative PSP (rPSP) compared to soil chemical properties. Both correlation and variation partitioning analyses suggested that SMB N, P and C:N ratio were good predictors of rPSP. In the short-term dataset, we found a significant, negative correlation of annual rice yield with SMB C:N (r = −0.99), confirming SMB C:N as a robust indicator for PSP. In treatments of the short-term experiment, soil amendment with biochar lowered SMB C:N and improved PSP, while incorporation of rice straw increased SMB C:N and reduced PSP. We conclude that SMB C:N ratio does not only indicate PSP but also helps to identify management practices that improve PSP.
Optically induced effective mass renormalization: the case of graphite image potential states
Authors: Montagnese M. , Pagliara S. , Galimberti G. , Dal Conte S. , Ferrini G. , van Loosdrecht P. H. M. , Parmigiani F. 
Published: October 2016

AbstractMany-body interactions with the underlying bulk electrons determine the properties of confined electronic states at the surface of a metal. Using momentum resolved nonlinear photoelectron spectroscopy we show that one can tailor these many-body interactions in graphite, leading to a strong renormalization of the dispersion and linewidth of the image potential state. These observations are interpreted in terms of a basic self-energy model, and may be considered as exemplary for optically induced many-body interactions.
Competing magnetic ground states and their coupling to the crystal lattice in CuFe2Ge2
Authors: May Andrew F. , Calder Stuart , Parker David S. , Sales Brian C. , McGuire Michael A. 
Published: October 2016

AbstractIdentifying and characterizing systems with coupled and competing interactions is central to the development of physical models that can accurately describe and predict emergent behavior in condensed matter systems. This work demonstrates that the metallic compound CuFe2Ge2 has competing magnetic ground states, which are shown to be strongly coupled to the lattice and easily manipulated using temperature and applied magnetic fields. Temperature-dependent magnetization M measurements reveal a ferromagnetic-like onset at 228 (1) K and a broad maximum in M near 180 K. Powder neutron diffraction confirms antiferromagnetic ordering below TN ≈ 175 K, and an incommensurate spin density wave is observed below ≈125 K. Coupled with the small refined moments (0.5–1 μB/Fe), this provides a picture of itinerant magnetism in CuFe2Ge2. The neutron diffraction data also reveal a coexistence of two magnetic phases that further highlights the near-degeneracy of various magnetic states. These results demonstrate that the ground state in CuFe2Ge2 can be easily manipulated by external forces, making it of particular interest for doping, pressure, and further theoretical studies.
Mitogenomes from type specimens, a genotyping tool for morphologically simple species: ten genomes of agar-producing red algae
Authors: Boo Ga Hun , Hughey Jeffery R. , Miller Kathy Ann , Boo Sung Min 
Published: October 2016

AbstractDNA sequences from type specimens provide independent, objective characters that enhance the value of type specimens and permit the correct application of species names to phylogenetic clades and specimens. We provide mitochondrial genomes (mitogenomes) from archival type specimens of ten species in agar-producing red algal genera Gelidium and Pterocladiella. The genomes contain 43–44 genes, ranging in size from 24,910 to 24,970 bp with highly conserved gene synteny. Low Ka/Ks ratios of apocytochrome b and cytochrome oxidase genes support their utility as markers. Phylogenies of mitogenomes and cox1+rbcL sequences clarified classification at the genus and species levels. Three species formerly in Gelidium and Pterocladia are transferred to Pterocladiella: P. media comb. nov., P. musciformis comb. nov., and P. luxurians comb. and stat. nov. Gelidium sinicola is merged with G. coulteri because they share identical cox1 and rbcL sequences. We describe a new species, Gelidium millariana sp. nov., previously identified as G. isabelae from Australia. We demonstrate that mitogenomes from type specimens provide a new tool for typifying species in the Gelidiales and that there is an urgent need for analyzing mitogenomes from type specimens of red algae and other morphologically simple organisms for insight into their nomenclature, taxonomy and evolution.
Prognostic value of platelet to lymphocyte ratio in hepatocellular carcinoma: a meta-analysis
Authors: Ma Wencong , Zhang Ping , Qi Jun , Gu Litong , Zang Mingcui , Yao Haochen , Shi Xiaoju , Wang Chunli , Jiang Ying 
Published: October 2016

AbstractThis study was designed to evaluate the prognostic value of platelet to lymphocyte ratio (PLR) in hepatocellular carcinoma (HCC). A comprehensive literature search for relevant studies was performed in Web of science, Embase and Pubmed. A total of nine studies with 2017 patients were included in this meta-analysis, and combined hazard ratio (HR) or odds ratio (OR) and 95% confidence intervals (95%CIs) were served as effect measures. Pooled results showed that elevated PLR was associated with poor overall survival (OS) (HR = 1.63, 95%CI: 1.42–1.88, p = 0.000; I2 = 0.0%, Ph = 0.637) and poor disease-free survival (DFS)/recurrence-free survival (RFS) (HR=1.32, 95%CI: 1.15–1.52, p = 0.000; I2 = 19.3%, Ph = 0.287) in HCC patients. In addition, high PLR was not significantly correlated with the presence of vascular invasion, tumor multifocality, poor tumor grade or high level of serum AFP (>400 ng/ml). In conclusion, elevated PLR indicated a poor prognosis for patients with HCC. PLR may be a reliable, easily-obtained, and low cost biomarker with prognostic potential for HCC.
Chronic Sleep Disruption Alters Gut Microbiota, Induces Systemic and Adipose Tissue Inflammation and Insulin Resistance in Mice
Authors: Poroyko Valeriy A. , Carreras Alba , Khalyfa Abdelnaby , Khalyfa Ahamed A. , Leone Vanessa , Peris Eduard , Almendros Isaac , Gileles-Hillel Alex , Qiao Zhuanhong , Hubert Nathaniel , Farré Ramon , Chang Eugene B. , Gozal David 
Published: October 2016

AbstractChronic sleep fragmentation (SF) commonly occurs in human populations, and although it does not involve circadian shifts or sleep deprivation, it markedly alters feeding behaviors ultimately promoting obesity and insulin resistance. These symptoms are known to be related to the host gut microbiota. Mice were exposed to SF for 4 weeks and then allowed to recover for 2 weeks. Taxonomic profiles of fecal microbiota were obtained prospectively, and conventionalization experiments were performed in germ-free mice. Adipose tissue insulin sensitivity and inflammation, as well as circulating measures of inflammation, were assayed. Effect of fecal water on colonic epithelial permeability was also examined. Chronic SF-induced increased food intake and reversible gut microbiota changes characterized by the preferential growth of highly fermentative members of Lachnospiraceae and Ruminococcaceae and a decrease of Lactobacillaceae families. These lead to systemic and visceral white adipose tissue inflammation in addition to altered insulin sensitivity in mice, most likely via enhanced colonic epithelium barrier disruption. Conventionalization of germ-free mice with SF-derived microbiota confirmed these findings. Thus, SF-induced metabolic alterations may be mediated, in part, by concurrent changes in gut microbiota, thereby opening the way for gut microbiome-targeted therapeutics aimed at reducing the major end-organ morbidities of chronic SF.
Clinical and genetic analyses reveal novel pathogenic ABCA4 mutations in Stargardt disease families
Authors: Lin Bing , Cai Xue-Bi , Zheng Zhi-Li , Huang Xiu-Feng , Liu Xiao-Ling , Qu Jia , Jin Zi-Bing 
Published: October 2016

AbstractStargardt disease (STGD1) is a juvenile macular degeneration predominantly inherited in an autosomal recessive pattern, characterized by decreased central vision in the first 2 decades of life. The condition has a genetic basis due to mutation in the ABCA4 gene, and arises from the deposition of lipofuscin-like substance in the retinal pigmented epithelium (RPE) with secondary photoreceptor cell death. In this study, we describe the clinical and genetic features of Stargardt patients from four unrelated Chinese cohorts. The targeted exome sequencing (TES) was carried out in four clinically confirmed patients and their family members using a gene panel comprising 164 known causative inherited retinal dystrophy (IRD) genes. Genetic analysis revealed eight ABCA4 mutations in all of the four pedigrees, including six mutations in coding exons and two mutations in adjacent intronic areas. All the affected individuals showed typical manifestations consistent with the disease phenotype. We disclose two novel ABCA4 mutations in Chinese patients with STGD disease, which will expand the existing spectrum of disease-causing variants and will further aid in the future mutation screening and genetic counseling, as well as in the understanding of phenotypic and genotypic correlations.
Fabrication of a silver particle-integrated silicone polymer-covered metal stent against sludge and biofilm formation and stent-induced tissue inflammation
Authors: Lee Tae Hoon , Jang Bong Seok , Jung Min Kyo , Pack Chan Gi , Choi Jun-Ho , Park Do Hyun 
Published: October 2016

AbstractTo reduce tissue or tumor ingrowth, covered self-expandable metal stents (SEMSs) have been developed. The effectiveness of covered SEMSs may be attenuated by sludge or stone formation or by stent clogging due to the formation of biofilm on the covering membrane. In this study, we tested the hypothesis that a silicone membrane containing silver particles (Ag-P) would prevent sludge and biofilm formation on the covered SEMS. In vitro, the Ag-P-integrated silicone polymer-covered membrane exhibited sustained antibacterial activity, and there was no definite release of silver ions from the Ag-P-integrated silicone polymer membrane at any time point. Using a porcine stent model, in vivo analysis demonstrated that the Ag-P-integrated silicone polymer-covered SEMS reduced the thickness of the biofilm and the quantity of sludge formed, compared with a conventional silicone-covered SEMS. In vivo, the release of silver ions from an Ag-P-integrated silicone polymer-covered SEMS was not detected in porcine serum. The Ag-P-integrated silicone polymer-covered SEMS also resulted in significantly less stent-related bile duct and subepithelium tissue inflammation than a conventional silicone polymer-covered SEMS. Therefore, the Ag-P-integrated silicone polymer-covered SEMS reduced sludge and biofilm formation and stent-induced pathological changes in tissue. This novel SEMS may prolong the stent patency in clinical application.
Selective detection of viable seed-borne Acidovorax citrulli by real-time PCR with propidium monoazide
Authors: Tian Qian , Feng Jian-jun , Hu Jie , Zhao Wen-jun 
Published: October 2016

AbstractIn recent years, use of the DNA-intercalating dye propidium monoazide (PMA) in real-time PCR has been reported as a novel method to detect viable bacteria in different types of samples, such as food, environmental, and microbiological samples. In this study, viable cells of Acidovorax citrulli, the causal agent of bacterial seedling blight and fruit blotch, were selectively detected and differentiated from dead cells by real-time fluorescent polymerase chain reaction amplification after the bacterial solution was treated with the DNA-binding dye PMA. The primers and TaqMan probe were based on the A. citrulli genome (Aave_1909, Gene ID: 4669443) and were highly specific for A. citrulli. The detection threshold of this assay was 103 colony-forming units per mL (CFU/mL) in pure cell suspensions containing viable and dead cells and infected watermelon seeds. Application of this assay enables the selective detection of viable cells of A. citrulli and facilitates monitoring of the pathogen in watermelon and melon seeds.