bluuebunny/crossref_metadata_2025_split huggingface dataset:
The triterpenoid CDDO-imidazolide ameliorates mouse liver ischemia-reperfusion injury through activating the Nrf2/HO-1 pathway enhanced autophagy
Authors: Xu Dongwei , Chen Lili , Chen Xiaosong , Wen Yankai , Yu Chang , Yao Jufang , Wu Hailong , Wang Xin , Xia Qiang , Kong Xiaoni 
Published: August 2017

AbstractNuclear factor erythroid 2-related factor 2 (Nrf2)-mediated induction of antioxidants has been implicated to have protective roles in ischemia-reperfusion (I/R) injury in many animal models. However, the in vivo effects of CDDO-imidazole (CDDO-Im) (1-[2-cyano-3-,12-dioxooleana-1,9(11)-dien-28-oyl] imidazole), a Nrf2 activator, in hepatic I/R injury is lacking and its exact molecular mechanisms are still not very clear. The goals of this study were to determine whether CDDO-Im can prevent liver injury induced by I/R in the mouse, and to elucidate the molecular target of drug action. Mice were randomly equally divided into two groups and administered intraperitoneally with either DMSO control or CDDO-Im (2 mg/kg) 3 h before subjected to 90-min hepatic 70% ischemia followed by reperfusion. Subsequently, the Liver and blood samples of these mice were collected to evaluate liver injury. CDDO-Im pretreatment markedly improve hepatic I/R injury by attenuating hepatic necrosis and apoptosis, reducing reactive oxygen species (ROS) levels and inflammatory responses, and ameliorating mitochondrial dysfunction. Mechanistically, by using Nrf2 Knockout mice and hemeoxygenase 1 (HO-1) inhibitor, we found that these CDDO-Im protection effects are attributed to enhanced autophagy, which is mediated by activating Nrf2/HO-1 pathway. By accelerating autophagy and clearance of damaged mitochondria, CDDO-Im reduced the mtDNA release and ROS overproduction, and in turn decreased damage-associated molecular patterns induced inflammatory responses and the following secondary liver injury. These results indicate that by enhancing autophagy, CDDO-Im-mediated activation of Nrf2/HO-1 signaling could be a novel therapeutic strategy to minimize the adverse effects of hepatic I/R injury.
Specialized odorant receptors in social insects that detect cuticular hydrocarbon cues and candidate pheromones
Authors: Pask Gregory M. , Slone Jesse D. , Millar Jocelyn G. , Das Prithwiraj , Moreira Jardel A. , Zhou Xiaofan , Bello Jan , Berger Shelley L. , Bonasio Roberto , Desplan Claude , Reinberg Danny , Liebig Jürgen , Zwiebel Laurence J. , Ray Anandasankar 
Published: August 2017

AbstractEusocial insects use cuticular hydrocarbons as components of pheromones that mediate social behaviours, such as caste and nestmate recognition, and regulation of reproduction. In ants such as Harpegnathos saltator, the queen produces a pheromone which suppresses the development of workers’ ovaries and if she is removed, workers can transition to a reproductive state known as gamergate. Here we functionally characterize a subfamily of odorant receptors (Ors) with a nine-exon gene structure that have undergone a massive expansion in ants and other eusocial insects. We deorphanize 22 representative members and find they can detect cuticular hydrocarbons from different ant castes, with one (HsOr263) that responds strongly to gamergate extract and a candidate queen pheromone component. After systematic testing with a diverse panel of hydrocarbons, we find that most Harpegnathos saltator Ors are narrowly tuned, suggesting that several receptors must contribute to detection and discrimination of different cuticular hydrocarbons important in mediating eusocial behaviour.
Tree height strongly affects estimates of water-use efficiency responses to climate and CO2 using isotopes
Authors: Brienen R. J. W. , Gloor E. , Clerici S. , Newton R. , Arppe L. , Boom A. , Bottrell S. , Callaghan M. , Heaton T. , Helama S. , Helle G. , Leng M. J. , Mielikäinen K. , Oinonen M. , Timonen M. 
Published: August 2017

AbstractVarious studies report substantial increases in intrinsic water-use efficiency (W
i
), estimated using carbon isotopes in tree rings, suggesting trees are gaining increasingly more carbon per unit water lost due to increases in atmospheric CO2. Usually, reconstructions do not, however, correct for the effect of intrinsic developmental changes in W
i
as trees grow larger. Here we show, by comparing W
i
across varying tree sizes at one CO2 level, that ignoring such developmental effects can severely affect inferences of trees’ W
i
. W
i
doubled or even tripled over a trees’ lifespan in three broadleaf species due to changes in tree height and light availability alone, and there are also weak trends for Pine trees. Developmental trends in broadleaf species are as large as the trends previously assigned to CO2 and climate. Credible future tree ring isotope studies require explicit accounting for species-specific developmental effects before CO2 and climate effects are inferred.
Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
Authors: Collins Ben C. , Hunter Christie L. , Liu Yansheng , Schilling Birgit , Rosenberger George , Bader Samuel L. , Chan Daniel W. , Gibson Bradford W. , Gingras Anne-Claude , Held Jason M. , Hirayama-Kurogi Mio , Hou Guixue , Krisp Christoph , Larsen Brett , Lin Liang , Liu Siqi , Molloy Mark P. , Moritz Robert L. , Ohtsuki Sumio , Schlapbach Ralph , Selevsek Nathalie , Thomas Stefani N. , Tzeng Shin-Cheng , Zhang Hui , Aebersold Ruedi 
Published: August 2017

AbstractQuantitative proteomics employing mass spectrometry is an indispensable tool in life science research. Targeted proteomics has emerged as a powerful approach for reproducible quantification but is limited in the number of proteins quantified. SWATH-mass spectrometry consists of data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics (accuracy, sensitivity, and selectivity) of targeted proteomics at large scale. While previous SWATH-mass spectrometry studies have shown high intra-lab reproducibility, this has not been evaluated between labs. In this multi-laboratory evaluation study including 11 sites worldwide, we demonstrate that using SWATH-mass spectrometry data acquisition we can consistently detect and reproducibly quantify >4000 proteins from HEK293 cells. Using synthetic peptide dilution series, we show that the sensitivity, dynamic range and reproducibility established with SWATH-mass spectrometry are uniformly achieved. This study demonstrates that the acquisition of reproducible quantitative proteomics data by multiple labs is achievable, and broadly serves to increase confidence in SWATH-mass spectrometry data acquisition as a reproducible method for large-scale protein quantification.
Landscape of submitochondrial protein distribution
Authors: Vögtle F.-Nora , Burkhart Julia M. , Gonczarowska-Jorge Humberto , Kücükköse Cansu , Taskin Asli Aras , Kopczynski Dominik , Ahrends Robert , Mossmann Dirk , Sickmann Albert , Zahedi René P. , Meisinger Chris 
Published: August 2017

AbstractThe mitochondrial proteome comprises ~1000 (yeast)–1500 (human) different proteins, which are distributed into four different subcompartments. The sublocalization of these proteins within the organelle in most cases remains poorly defined. Here we describe an integrated approach combining stable isotope labeling, various protein enrichment and extraction strategies and quantitative mass spectrometry to produce a quantitative map of submitochondrial protein distribution in S. cerevisiae. This quantitative landscape enables a proteome-wide classification of 986 proteins into soluble, peripheral, and integral mitochondrial membrane proteins, and the assignment of 818 proteins into the four subcompartments: outer membrane, inner membrane, intermembrane space, or matrix. We also identified 206 proteins that were not previously annotated as localized to mitochondria. Furthermore, the protease Prd1, misannotated as intermembrane space protein, could be re-assigned and characterized as a presequence peptide degrading enzyme in the matrix.
Giant onsite electronic entropy enhances the performance of ceria for water splitting
Authors: Naghavi S. Shahab , Emery Antoine A. , Hansen Heine A. , Zhou Fei , Ozolins Vidvuds , Wolverton Chris 
Published: August 2017

AbstractPrevious studies have shown that a large solid-state entropy of reduction increases the thermodynamic efficiency of metal oxides, such as ceria, for two-step thermochemical water splitting cycles. In this context, the configurational entropy arising from oxygen off-stoichiometry in the oxide, has been the focus of most previous work. Here we report a different source of entropy, the onsite electronic configurational entropy, arising from coupling between orbital and spin angular momenta in lanthanide f orbitals. We find that onsite electronic configurational entropy is sizable in all lanthanides, and reaches a maximum value of ≈4.7 kB per oxygen vacancy for Ce4+/Ce3+ reduction. This unique and large positive entropy source in ceria explains its excellent performance for high-temperature catalytic redox reactions such as water splitting. Our calculations also show that terbium dioxide has a high electronic entropy and thus could also be a potential candidate for solar thermochemical reactions.
Mass production of bulk artificial nacre with excellent mechanical properties
Authors: Gao Huai-Ling , Chen Si-Ming , Mao Li-Bo , Song Zhao-Qiang , Yao Hong-Bin , Cölfen Helmut , Luo Xi-Sheng , Zhang Fu , Pan Zhao , Meng Yu-Feng , Ni Yong , Yu Shu-Hong 
Published: August 2017

AbstractVarious methods have been exploited to replicate nacre features into artificial structural materials with impressive structural and mechanical similarity. However, it is still very challenging to produce nacre-mimetics in three-dimensional bulk form, especially for further scale-up. Herein, we demonstrate that large-sized, three-dimensional bulk artificial nacre with comprehensive mimicry of the hierarchical structures and the toughening mechanisms of natural nacre can be facilely fabricated via a bottom-up assembly process based on laminating pre-fabricated two-dimensional nacre-mimetic films. By optimizing the hierarchical architecture from molecular level to macroscopic level, the mechanical performance of the artificial nacre is superior to that of natural nacre and many engineering materials. This bottom-up strategy has no size restriction or fundamental barrier for further scale-up, and can be easily extended to other material systems, opening an avenue for mass production of high-performance bulk nacre-mimetic structural materials in an efficient and cost-effective way for practical applications.
Evidence that Listeria innocua modulates its membrane’s stored curvature elastic stress, but not fluidity, through the cell cycle
Authors: Furse Samuel , Jakubec Martin , Rise Frode , Williams Huw E. , Rees Catherine E. D. , Halskau Øyvind 
Published: August 2017

AbstractThis paper reports that the abundances of endogenous cardiolipin and phosphatidylethanolamine halve during elongation of the Gram-positive bacterium Listeria innocua. The lyotropic phase behaviour of model lipid systems that describe these modulations in lipid composition indicate that the average stored curvature elastic stress of the membrane is reduced on elongation of the cell, while the fluidity appears to be maintained. These findings suggest that phospholipid metabolism is linked to the cell cycle and that changes in membrane composition can facilitate passage to the succeding stage of the cell cycle. This therefore suggests a means by which bacteria can manage the physical properties of their membranes through the cell cycle.
Genetic predisposition to lung cancer: comprehensive literature integration, meta-analysis, and multiple evidence assessment of candidate-gene association studies
Authors: Wang Junjun , Liu Qingyun , Yuan Shuai , Xie Weijia , Liu Yuan , Xiang Ying , Wu Na , Wu Long , Ma Xiangyu , Cai Tongjian , Zhang Yao , Sun Zhifu , Li Yafei 
Published: August 2017

AbstractMore than 1000 candidate-gene association studies on genetic susceptibility to lung cancer have been published over the last two decades but with few consensuses for the likely culprits. We conducted a comprehensive review, meta-analysis and evidence strength evaluation of published candidate-gene association studies in lung cancer up to November 1, 2015. The epidemiological credibility of cumulative evidence was assessed using the Venice criteria. A total of 1018 publications with 2910 genetic variants in 754 different genes or chromosomal loci were eligible for inclusion. Main meta-analyses were performed on 246 variants in 138 different genes. Twenty-two variants from 21 genes (APEX1 rs1130409 and rs1760944, ATM rs664677, AXIN2 rs2240308, CHRNA3 rs6495309, CHRNA5 rs16969968, CLPTM1L rs402710, CXCR2 rs1126579, CYP1A1 rs4646903, CYP2E1 rs6413432, ERCC1 rs11615, ERCC2 rs13181, FGFR4 rs351855, HYKK rs931794, MIR146A rs2910164, MIR196A2 rs11614913, OGG1 rs1052133, PON1 rs662, REV3L rs462779, SOD2 rs4880, TERT rs2736098, and TP53 rs1042522) showed significant associations with lung cancer susceptibility with strong cumulative epidemiological evidence. No significant associations with lung cancer risk were found for other 150 variants in 98 genes; however, seven variants demonstrated strong cumulative evidence. Our findings provided the most updated summary of genetic risk effects on lung cancer and would help inform future research direction.
A Flexible Electret Membrane with Persistent Electrostatic Effect and Resistance to Harsh Environment for Energy Harvesting
Authors: Huiming Xiao , Gangjin Chen , Xumin Chen , Zhi Chen 
Published: August 2017

AbstractA novel flexible electret membrane, exhibiting persistent electrostatic effect, distinctive temperature stability and outstanding capability of resistance to harsh environment and fatigue, is demonstrated by experiment. Its excellent electret performance is correlated to the synergy of three factors, which are space charge injection, dipole orientation and interfacial polarization according to the analysis of charge storage mechanism. This electret membrane is provided with sandwich configuration PTFE/THV/PTFE, prepared by hot pressing method and thermal charging technology. After wiped its surface with alcohol, its surface potential declines to zero from −550 V, then recovers rapidly to −310 V and finally maintains constant for 800 hours, which shows that its electret performance distinctly precedes traditional electret material such as single PTFE, FEP electret membrane. The measurement of thermal stimulating potentials displays that its surface potential reaches maximum about 5 times initial value at 125 °C. A micro-vibration energy harvester is assembled with this membrane. Its maximum output power reaches 4.66 μW at tapping frequency 5 Hz and keeps stable during over 2000 tapping tests within 100 days, which indicates the long-life service and resistance to harsh environment and fatigue of this electret membrane.
Seasonal total methane depletion in limestone caves
Authors: Waring Chris L. , Hankin Stuart I. , Griffith David W. T. , Kertesz Michael A. , Kobylski Victoria , Wilson Neil L. , Coleman Nicholas V. , Kettlewell Graham , Zlot Robert , Bosse Michael , Bell Graham 
Published: August 2017

AbstractMethane concentration in caves is commonly much lower than the external atmosphere, yet the cave CH4 depletion causal mechanism is contested and dynamic links to external diurnal and seasonal temperature cycles unknown. Here, we report a continuous 3-year record of cave methane and other trace gases in Jenolan Caves, Australia which shows a seasonal cycle of extreme CH4 depletion, from ambient ~1,775 ppb to near zero during summer and to ~800 ppb in winter. Methanotrophic bacteria, some newly-discovered, rapidly consume methane on cave surfaces and in external karst soils with lifetimes in the cave of a few hours. Extreme bacterial selection due to the absence of alternate carbon sources for growth in the cave environment has resulted in an extremely high proportion 2–12% of methanotrophs in the total bacteria present. Unexpected seasonal bias in our cave CH4 depletion record is explained by a three-step process involving methanotrophy in aerobic karst soil above the cave, summer transport of soil-gas into the cave through epikarst, followed by further cave CH4 depletion. Disentangling cause and effect of cave gas variations by tracing sources and sinks has identified seasonal speleothem growth bias, with implied palaeo-climate record bias.
Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken
Authors: Hussain Hafiz I. , Iqbal Zahid , Seleem Mohamed N. , Huang Deyu , Sattar Adeel , Hao Haihong , Yuan Zonghui 
Published: August 2017

AbstractNumerous studies have examined the prevalence of pathogenic Escherichia coli in poultry and poultry products; however, limited data are available regarding their resistance- and virulence-associated gene expression profiles. This study was designed to examine the resistance and virulence of poultry E. coli strains in vitro and in vivo via antibiotic susceptibility, biofilm formation and adhesion, and invasion and intracellular survivability assays in Caco-2 and Raw 264.7 cell lines as well as the determination of the median lethal dose in two-day old chickens. A clinical pathogenic multidrug-resistant isolate, E. coli 381, isolated from broilers, was found to be highly virulent in cell culture and 1000-fold more virulent in a chicken model than other strains; accordingly, the isolate was subsequently selected for transcriptome analysis. The comparative gene expression profile of MDR E. coli 381 and the reference human strain E. coli ATCC 25922 was completed with Illumina HiSeq. 2500 transcriptome analysis. Differential gene expression analysis indicates that there are multiple pathways involved in the resistance and virulence of this highly virulent strain. The results garnered from this study provide critical information about the highly virulent MDR E. coli strain of poultry origin and warrant further investigation due to its significant threat to public health.
Compound A influences gene regulation of the Dexamethasone-activated glucocorticoid receptor by alternative cofactor recruitment
Authors: Desmet S. J. , Bougarne N. , Van Moortel L. , De Cauwer L. , Thommis J. , Vuylsteke M. , Ratman D. , Houtman R. , Tavernier J. , De Bosscher K. 
Published: August 2017

AbstractThe glucocorticoid receptor (GR) is a transcription factor of which the underlying gene regulatory mechanisms are complex and incompletely understood. The non-steroidal anti-inflammatory Compound A (CpdA), a selective GR modulating compound in various cell models, has been shown to favour GR-mediated gene repression but not GR-mediated gene activation. Shifting balances towards only a particular subset of GR gene regulatory events may be of benefit in the treatment of inflammatory diseases. We present evidence to support that the combination of CpdA with Dexamethasone (DEX), a classic steroidal GR ligand, can shape GR function towards a unique gene regulatory profile in a cell type-dependent manner. The molecular basis hereof is a changed GR phosphorylation status concomitant with a change in the GR cofactor recruitment profile. We subsequently identified and confirmed the orphan nuclear receptor SHP as a coregulator that is specifically enriched at GR when CpdA and DEX are combined. Combining CpdA with DEX not only leads to stronger suppression of pro-inflammatory gene expression, but also enhanced anti-inflammatory GR target gene expression in epithelial cells, making ligand combination strategies in future a potentially attractive alternative manner of skewing and fine-tuning GR effects towards an improved therapeutic benefit.
TaiNi: Maximizing research output whilst improving animals’ welfare in neurophysiology experiments
Authors: Jiang Zhou , Huxter John R. , Bowyer Stuart A. , Blockeel Anthony J. , Butler James , Imtiaz Syed A. , Wafford Keith A. , Phillips Keith G. , Tricklebank Mark D. , Marston Hugh M. , Rodriguez-Villegas Esther 
Published: August 2017

AbstractUnderstanding brain function at the cell and circuit level requires representation of neuronal activity through multiple recording sites and at high sampling rates. Traditional tethered recording systems restrict movement and limit the environments suitable for testing, while existing wireless technology is still too heavy for extended recording in mice. Here we tested TaiNi, a novel ultra-lightweight (<2 g) low power wireless system allowing 72-hours of recording from 16 channels sampled at ~19.5 KHz (9.7 KHz bandwidth). We captured local field potentials and action-potentials while mice engaged in unrestricted behaviour in a variety of environments and while performing tasks. Data was synchronized to behaviour with sub-second precision. Comparisons with a state-of-the-art wireless system demonstrated a significant improvement in behaviour owing to reduced weight. Parallel recordings with a tethered system revealed similar spike detection and clustering. TaiNi represents a significant advance in both animal welfare in electrophysiological experiments, and the scope for continuously recording large amounts of data from small animals.
Drosophila protease ClpXP specifically degrades DmLRPPRC1 controlling mitochondrial mRNA and translation
Authors: Matsushima Yuichi , Hirofuji Yuta , Aihara Masamune , Yue Song , Uchiumi Takeshi , Kaguni Laurie S. , Kang Dongchon 
Published: August 2017

AbstractClpXP is the major protease in the mitochondrial matrix in eukaryotes, and is well conserved among species. ClpXP is composed of a proteolytic subunit, ClpP, and a chaperone-like subunit, ClpX. Although it has been proposed that ClpXP is required for the mitochondrial unfolded protein response, additional roles for ClpXP in mitochondrial biogenesis are unclear. Here, we found thatDrosophilaleucine-rich pentatricopeptide repeat domain-containing protein 1 (DmLRPPRC1) is a specific substrate of ClpXP. Depletion or introduction of catalytically inactive mutation of ClpP increases DmLRPPRC1 and causes non-uniform increases of mitochondrial mRNAs, accumulation of some unprocessed mitochondrial transcripts, and modest repression of mitochondrial translation inDrosophilaSchneider S2 cells. Moreover, DmLRPPRC1 over-expression induces the phenotypes similar to those observed when ClpP is depleted. Taken together, ClpXP regulates mitochondrial gene expression by changing the protein level of DmLRPPRC1 inDrosophilaSchneider S2 cells.
Invisible Trojan-horse attack
Authors: Sajeed Shihan , Minshull Carter , Jain Nitin , Makarov Vadim 
Published: August 2017

AbstractWe demonstrate the experimental feasibility of a Trojan-horse attack that remains nearly invisible to the single-photon detectors employed in practical quantum key distribution (QKD) systems, such as Clavis2 from ID Quantique. We perform a detailed numerical comparison of the attack performance against Scarani-Ac´ın-Ribordy-Gisin (SARG04) QKD protocol at 1924 nm versus that at 1536 nm. The attack strategy was proposed earlier but found to be unsuccessful at the latter wavelength, as reported in N. Jain et al., New J. Phys. 16, 123030 (2014). However at 1924 nm, we show experimentally that the noise response of the detectors to bright pulses is greatly reduced, and show by modeling that the same attack will succeed. The invisible nature of the attack poses a threat to the security of practical QKD if proper countermeasures are not adopted.