bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-throughput search of ternary chalcogenides for p-type transparent electrodes
Authors: Shi Jingming , Cerqueira Tiago F. T. , Cui Wenwen , Nogueira Fernando , Botti Silvana , Marques Miguel A. L. 
Published: March 2017

AbstractDelafossite crystals are fascinating ternary oxides that have demonstrated transparent conductivity and ambipolar doping. Here we use a high-throughput approach based on density functional theory to find delafossite and related layered phases of composition ABX2, where A and B are elements of the periodic table, and X is a chalcogen (O, S, Se, and Te). From the 15 624 compounds studied in the trigonal delafossite prototype structure, 285 are within 50 meV/atom from the convex hull of stability. These compounds are further investigated using global structural prediction methods to obtain their lowest-energy crystal structure. We find 79 systems not present in the materials project database that are thermodynamically stable and crystallize in the delafossite or in closely related structures. These novel phases are then characterized by calculating their band gaps and hole effective masses. This characterization unveils a large diversity of properties, ranging from normal metals, magnetic metals, and some candidate compounds for p-type transparent electrodes.
Commensal gut bacteria modulate phosphorylation-dependent PPARγ transcriptional activity in human intestinal epithelial cells
Authors: Nepelska Malgorzata , de Wouters Tomas , Jacouton Elsa , Béguet-Crespel Fabienne , Lapaque Nicolas , Doré Joël , Arulampalam Velmurugesan , Blottière Hervé M. 
Published: March 2017

AbstractIn healthy subjects, the intestinal microbiota interacts with the host’s epithelium, regulating gene expression to the benefit of both, host and microbiota. The underlying mechanisms remain poorly understood, however. Although many gut bacteria are not yet cultured, constantly growing culture collections have been established. We selected 57 representative commensal bacterial strains to study bacteria-host interactions, focusing on PPARγ, a key nuclear receptor in colonocytes linking metabolism and inflammation to the microbiota. Conditioned media (CM) were harvested from anaerobic cultures and assessed for their ability to modulate PPARγ using a reporter cell line. Activation of PPARγ transcriptional activity was linked to the presence of butyrate and propionate, two of the main metabolites of intestinal bacteria. Interestingly, some stimulatory CMs were devoid of these metabolites. A Prevotella and an Atopobium strain were chosen for further study, and shown to up-regulate two PPARγ-target genes, ANGPTL4 and ADRP. The molecular mechanisms of these activations involved the phosphorylation of PPARγ through ERK1/2. The responsible metabolites were shown to be heat sensitive but markedly diverged in size, emphasizing the diversity of bioactive compounds found in the intestine. Here we describe different mechanisms by which single intestinal bacteria can directly impact their host’s health through transcriptional regulation.
Abnormalities in A-to-I RNA editing patterns in CNS injuries correlate with dynamic changes in cell type composition
Authors: Gal-Mark Nurit , Shallev Lea , Sweetat Sahar , Barak Michal , Billy Li Jin , Levanon Erez Y. , Eisenberg Eli , Behar Oded 
Published: March 2017

AbstractAdenosine to Inosine (A-to-I) RNA editing is a co- or post-transcriptional mechanism that modifies genomically encoded nucleotides at the RNA level. A-to-I RNA editing is abundant in the brain, and altered editing levels have been reported in various neurological pathologies and following spinal cord injury (SCI). The prevailing concept is that the RNA editing process itself is dysregulated by brain pathologies. Here we analyzed recent RNA-seq data, and found that, except for few mammalian conserved editing sites, editing is significantly higher in neurons than in other cell populations of the brain. We studied A-to-I RNA editing in stab wound injury (SWI) and SCI models and showed that the apparent under-editing observed after injury correlates with an approximately 20% reduction in the relative density of neurons, due to cell death and immune cell infiltration that may account for the observed under-editing. Studies of neuronal and astrocyte cultures and a computational analysis of SCI RNA-seq data further supported the possibility that a reduction in neuronal density is responsible for alterations in the tissue-wide editing patterns upon injury. Thus, our data suggest that the case for a mechanistic linkage between A-to-I RNA editing and brain pathologies should be revisited.
Hydrogen peroxide in deep waters from the Mediterranean Sea, South Atlantic and South Pacific Oceans
Authors: Hopwood Mark J. , Rapp Insa , Schlosser Christian , Achterberg Eric P. 
Published: March 2017

AbstractHydrogen peroxide (H2O2) is present ubiquitously in marine surface waters where it is a reactive intermediate in the cycling of many trace elements. Photochemical processes are considered the dominant natural H2O2source, yet cannot explain nanomolar H2O2concentrations below the photic zone. Here, we determined the concentration of H2O2in full depth profiles across three ocean basins (Mediterranean Sea, South Atlantic and South Pacific Oceans). To determine the accuracy of H2O2measurements in the deep ocean we also re-assessed the contribution of interfering species to ‘apparent H2O2’, as analysed by the luminol based chemiluminescence technique. Within the vicinity of coastal oxygen minimum zones, accurate measurement of H2O2was not possible due to interference from Fe(II). Offshore, in deep (>1000 m) waters H2O2concentrations ranged from 0.25 ± 0.27 nM (Mediterranean, Balearics-Algeria) to 2.9 ± 2.2 nM (Mediterranean, Corsica-France). Our results indicate that a dark, pelagic H2O2production mechanism must occur throughout the deep ocean. A bacterial source of H2O2is the most likely origin and we show that this source is likely sufficient to account for all of the observed H2O2in the deep ocean.
Parasitism perturbs the mucosal microbiome of Atlantic Salmon
Authors: Llewellyn M. S. , Leadbeater S. , Garcia C. , Sylvain F.-E. , Custodio M. , Ang K. P. , Powell F. , Carvalho G. R. , Creer S. , Elliot J. , Derome N. 
Published: March 2017

AbstractInteractions between parasite, host and host-associated microbiota are increasingly understood as important determinants of disease progression and morbidity. Salmon lice, including the parasitic copepod Lepeophtheirus salmonis and related species, are perhaps the most important problem facing Atlantic Salmon aquaculture after feed sustainability. Salmon lice parasitize the surface of the fish, feeding off mucus, scales and underlying tissue. Secondary bacterial infections are a major source of associated morbidity. In this study we tracked the diversity and composition of Salmo salar skin surface microbiota throughout a complete L. salmonis infection cycle among 800 post-smolts as compared to healthy controls. Among infected fish we observed a significant reduction in microbial richness (Chao1, P = 0.0136), raised diversity (Shannon, P < 7.86e-06) as well as highly significant destabilisation of microbial community composition (Pairwise Unifrac, beta-diversity, P < 1.86e-05; P = 0.0132) by comparison to controls. While undetectable on an individual level, network analysis of microbial taxa on infected fish revealed the association of multiple pathogenic genera (Vibrio, Flavobacterium, Tenacibaculum, Pseudomonas) with high louse burdens. We discuss our findings in the context of ecological theory and colonisation resistance, in addition to the role microbiota in driving primary and secondary pathology in the host.
Identifying ionic interactions within a membrane using BLaTM, a genetic tool to measure homo- and heterotypic transmembrane helix-helix interactions
Authors: Schanzenbach Christoph , Schmidt Fabian C. , Breckner Patrick , Teese Mark G. , Langosch Dieter 
Published: March 2017

AbstractThe assembly of integral membrane protein complexes is frequently supported by transmembrane domain (TMD) interactions. Here, we present the BLaTM assay that measures homotypic as well as heterotypic TMD-TMD interactions in a bacterial membrane. The system is based on complementation of β-lactamase fragments genetically fused to interacting TMDs, which confers ampicillin resistance to expressing cells. We validated BLaTM by showing that the assay faithfully reports known sequence-specific interactions of both types. In a practical application, we used BLaTM to screen a focussed combinatorial library for heterotypic interactions driven by electrostatic forces. The results reveal novel patterns of ionizable amino acids within the isolated TMD pairs. Those patterns indicate that formation of heterotypic TMD pairs is most efficiently supported by closely spaced ionizable residues of opposite charge. In addition, TMD heteromerization can apparently be driven by hydrogen bonding between basic or between acidic residues.
Nitrification inhibitors can increase post-harvest nitrous oxide emissions in an intensive vegetable production system
Authors: Scheer Clemens , Rowlings David , Firrell Mary , Deuter Peter , Morris Stephen , Riches David , Porter Ian , Grace Peter 
Published: March 2017

AbstractTo investigate the effect of nitrification inhibitors (NIs) 3,4-dimethylpyrazole phosphate (DMPP) and 3-methylpyrazole 1,2,4-triazole (3MP + TZ), on N2O emissions and yield from a typical vegetable rotation in sub-tropical Australia we monitored soil N2O fluxes continuously over an entire year using an automated greenhouse gas measurement system. The temporal variation of N2O fluxes showed only low emissions over the vegetable cropping phases, but significantly higher emissions were observed post-harvest accounting for 50–70% of the annual emissions. NIs reduced N2O emissions by 20–60% over the vegetable cropping phases; however, this mitigation was offset by elevated N2O emissions from the NIs treatments over the post-harvest fallow period. Annual N2O emissions from the conventional fertiliser, the DMPP treatment, and the 3MP + TZ treatment were 1.3, 1.1 and 1.6 (sem = 0.2) kg-N ha−1 year−1, respectively. This study highlights that the use of NIs in vegetable systems can lead to elevated N2O emissions by storing N in the soil profile that is available to soil microbes during the decomposition of the vegetable residues. Hence the use of NIs in vegetable systems has to be treated carefully and fertiliser rates need to be adjusted to avoid an oversupply of N during the post-harvest phase.
Effects of biophysical constraints, climate and phylogeny on forest shrub allometries along an altitudinal gradient in Northeast China
Authors: Sun Han , Wang Xiangping , Fan Yanwen , Liu Chao , Wu Peng , Li Qiaoyan , Yin Weilun 
Published: March 2017

AbstractWhether there is a general allometry law across plant species with different sizes and under different environment has long been controversial and shrubs are particularly useful to examine these questions. Here we sampled 939 individuals from 50 forest shrub species along a large altitudinal gradient. We tested several allometry models with four relationships simultaneously (between stem diameter, height, leaf, stem and aboveground biomass), including geometric, elastic and stress similarity, and metabolic scaling theory’s predictions on small plants (MSTs) and trees (MSTt). We also tested if allometric exponents change markedly with climate and phylogeny. The predicted exponents of MSTt, elastic similarity and stress similarity (models for trees) were not supported by our data, while MSTs and geometric similarity gained more support, suggesting the finite size effect is more important for shrub allometries than being a woody plant. The influence of climate and phylogeny on allometric exponents were not significant or very weak, again suggesting strong biophysical constraints on shrub allometries. Our results reveal clear differences of shrub allometries from previous findings on trees (e.g. much weaker climatic and phylogenic control). Comparisons of herbs, shrubs and trees along a same climatic gradient are needed for better understanding of plant allometries.
Microbiota alteration is associated with the development of stress-induced despair behavior
Authors: Marin Ioana A. , Goertz Jennifer E. , Ren Tiantian , Rich Stephen S. , Onengut-Gumuscu Suna , Farber Emily , Wu Martin , Overall Christopher C. , Kipnis Jonathan , Gaultier Alban 
Published: March 2017

AbstractDepressive disorders often run in families, which, in addition to the genetic component, may point to the microbiome as a causative agent. Here, we employed a combination of behavioral, molecular and computational techniques to test the role of the microbiota in mediating despair behavior. In chronically stressed mice displaying despair behavior, we found that the microbiota composition and the metabolic signature dramatically change. Specifically, we observed reduced Lactobacillus and increased circulating kynurenine levels as the most prominent changes in stressed mice. Restoring intestinal Lactobacillus levels was sufficient to improve the metabolic alterations and behavioral abnormalities. Mechanistically, we identified that Lactobacillus-derived reactive oxygen species may suppress host kynurenine metabolism, by inhibiting the expression of the metabolizing enzyme, IDO1, in the intestine. Moreover, maintaining elevated kynurenine levels during Lactobacillus supplementation diminished the treatment benefits. Collectively, our data provide a mechanistic scenario for how a microbiota player (Lactobacillus) may contribute to regulating metabolism and resilience during stress.
Actual fusion efficiency in the lipid mixing assay - Comparison between nanodiscs and liposomes
Authors: François-Martin Claire , Pincet Frédéric 
Published: March 2017

AbstractLipid exchange occurs between membranes during fusion or active lipid transfer. These processes are necessary in vivo for the homeostasis of the cell at the level of the membranes, the organelles and the cell itself. They are also used by the cell to interact with the surrounding medium. Several assays have been developed to characterize in vitro these processes on model systems. The most common one, relying on fluorescence dequenching, measures lipid mixing between small membranes such as liposomes or nanodiscs in bulk. Usually, relative comparisons of the rate of lipid exchange are made between measurements performed in parallel. Here, we establish a quantitative standardization of this assay to avoid any bias resulting from the temperatures, the chosen fluorescent lipid fractions and from the various detergents used to normalize the measurements. We used this standardization to quantitatively compare the efficiency of SNARE-induced fusion in liposome-liposome and liposome-nanodisc configurations having similar collision frequency. We found that the initial yield of fusion is comparable in both cases, 1 per 2–3 million collisions in spite of a much larger dequenching signal with nanodiscs. Also, the long-term actual fusion rate is slightly lower with nanodiscs than in the liposome-liposome assay.
Ultrathin (<1 μm) Substrate-Free Flexible Photodetector on Quantum Dot-Nanocellulose Paper
Authors: Wu Jingda , Lin Lih Y. 
Published: March 2017

AbstractConventional approaches to flexible optoelectronic devices typically require depositing the active materials on external substrates. This is mostly due to the weak bonding between individual molecules or nanocrystals in the active materials, which prevents sustaining a freestanding thin film. Herein we demonstrate an ultrathin freestanding ZnO quantum dot (QD) active layer with nanocellulose structuring, and its corresponding device fabrication method to achieve substrate-free flexible optoelectronic devices. The ultrathin ZnO QD-nanocellulose composite is obtained by hydrogel transfer printing and solvent-exchange processes to overcome the water capillary force which is detrimental to achieving freestanding thin films. We achieved an active nanocellulose paper with ~550 nm thickness, and >91% transparency in the visible wavelength range. The film retains the photoconductive and photoluminescent properties of ZnO QDs and is applied towards substrate-free Schottky photodetector applications. The device has an overall thickness of ~670 nm, which is the thinnest freestanding optoelectronic device to date, to the best of our knowledge, and functions as a self-powered visible-blind ultraviolet photodetector. This platform can be readily applied to other nano materials as well as other optoelectronic device applications.
D-Glutamate is metabolized in the heart mitochondria
Authors: Ariyoshi Makoto , Katane Masumi , Hamase Kenji , Miyoshi Yurika , Nakane Maiko , Hoshino Atsushi , Okawa Yoshifumi , Mita Yuichiro , Kaimoto Satoshi , Uchihashi Motoki , Fukai Kuniyoshi , Ono Kazunori , Tateishi Syuhei , Hato Daichi , Yamanaka Ryoetsu , Honda Sakiko , Fushimura Yohei , Iwai-Kanai Eri , Ishihara Naotada , Mita Masashi , Homma Hiroshi , Matoba Satoaki 
Published: March 2017

AbstractD-Amino acids are enantiomers of L-amino acids and have recently been recognized as biomarkers and bioactive substances in mammals, including humans. In the present study, we investigated functions of the novel mammalian mitochondrial protein 9030617O03Rik and showed decreased expression under conditions of heart failure. Genomic sequence analyses showed partial homology with a bacterial aspartate/glutamate/hydantoin racemase. Subsequent determinations of all free amino acid concentrations in 9030617O03Rik-deficient mice showed high accumulations of D-glutamate in heart tissues. This is the first time that a significant amount of D-glutamate was detected in mammalian tissue. Further analysis of D-glutamate metabolism indicated that 9030617O03Rik is a D-glutamate cyclase that converts D-glutamate to 5-oxo-D-proline. Hence, this protein is the first identified enzyme responsible for mammalian D-glutamate metabolism, as confirmed in cloning analyses. These findings suggest that D-glutamate and 5-oxo-D-proline have bioactivities in mammals through the metabolism by D-glutamate cyclase.
Mirolydidae, a new family of Jurassic pamphilioid sawfly (Hymenoptera) highlighting mosaic evolution of lower Hymenoptera
Authors: Wang Mei , Rasnitsyn Alexandr P. , Yang Zhongqi , Shih Chungkun , Wang Hongbin , Ren Dong 
Published: March 2017

AbstractWe describe Pamphilioidea: Mirolydidae Wang, Rasnitsyn et Ren, fam. n., containing Mirolyda hirta Wang, Rasnitsyn et Ren, gen. et sp. n., from the late Middle Jurassic Jiulongshan Formation of Daohugou, Inner Mongolia, China. The new taxon is characterized by unique forewing venation with the presence of forewing SC, 1-RS almost as long as 1-M, M + Cu straight, 2r-rs strongly reclival, and antenna with homonomous flagellum, revealing new and important details in antennal evolutionary transformations. Thus, M. hirta with a combination of primitive and more derived characters highlights its transitional state in the Pamphilioidea and complex mosaic evolution within Pamphilioidea in the late Middle Jurassic. The body of this species is densely covered with thin and long setae, suggesting its possible habit of visiting gymnosperm reproductive organs for pollen feeding and/or pollination during the late Middle Jurassic, much earlier than the appearance of angiosperm flowers.
Anomalous shear band characteristics and extra-deep shock-affected zone in Zr-based bulk metallic glass treated with nanosecond laser peening
Authors: Wei Yanpeng , Xu Guangyue , Zhang Kun , Yang Zhe , Guo Yacong , Huang Chenguang , Wei Bingchen 
Published: March 2017

AbstractThe effects of nanosecond laser peening on Zr41Ti14Cu12.5Ni10Be22.5 metallic glass were investigated in this study. The peening treatment produced an extra-deep shock-affected zone compared to crystal metal. As opposed to the conventional shear bands, numerous arc shear bands appeared and aggregated in the vertical direction of the laser beam, forming basic units for accommodating plastic deformation. The arc shear bands exhibited short and discrete features near the surface of the material, then grew longer and fewer at deeper peened layer depths, which was closely related to the laser shock wave attenuation. An energy dissipation model was established based on Hugoniot Elastic Limit and shear band characteristics to represent the formation of an extra-deep shock-affected zone. The results presented here suggest that the bulk modification of metallic glass with a considerable affected depth is feasible. Further, they reveal that nanosecond laser peening is promising as an effective approach to tuning shear bands for improved MGs ductility.
Cluster analysis: a new approach for identification of underlying risk factors for coronary artery disease in essential hypertensive patients
Authors: Guo Qi , Lu Xiaoni , Gao Ya , Zhang Jingjing , Yan Bin , Su Dan , Song Anqi , Zhao Xi , Wang Gang 
Published: March 2017

AbstractGrading of essential hypertension according to blood pressure (BP) level may not adequately reflect clinical heterogeneity of hypertensive patients. This study was carried out to explore clinical phenotypes in essential hypertensive patients using cluster analysis. This study recruited 513 hypertensive patients and evaluated BP variations with ambulatory blood pressure monitoring. Four distinct hypertension groups were identified using cluster analysis: (1) younger male smokers with relatively high BP had the most severe carotid plaque thickness but no coronary artery disease (CAD); (2) older women with relatively low diastolic BP had more diabetes; (3) non-smokers with a low systolic BP level had neither diabetes nor CAD; (4) hypertensive patients with BP reverse dipping were most likely to have CAD but had least severe carotid plaque thickness. In binary logistic analysis, reverse dipping was significantly associated with prevalence of CAD. Cluster analysis was shown to be a feasible approach for investigating the heterogeneity of essential hypertension in clinical studies. BP reverse dipping might be valuable for prediction of CAD in hypertensive patients when compared with carotid plaque thickness. However, large-scale prospective trials with more information of plaque morphology are necessary to further compare the predicative power between BP dipping pattern and carotid plaque.
Physics of chewing in terrestrial mammals
Authors: Virot Emmanuel , Ma Grace , Clanet Christophe , Jung Sunghwan 
Published: March 2017

AbstractPrevious studies on chewing frequency across animal species have focused on finding a single universal scaling law. Controversy between the different models has been aroused without elucidating the variations in chewing frequency. In the present study we show that vigorous chewing is limited by the maximum force of muscle, so that the upper chewing frequency scales as the −1/3 power of body mass for large animals and as a constant frequency for small animals. On the other hand, gentle chewing to mix food uniformly without excess of saliva describes the lower limit of chewing frequency, scaling approximately as the −1/6 power of body mass. These physical constraints frame the −1/4 power law classically inferred from allometry of animal metabolic rates. All of our experimental data stay within these physical boundaries over six orders of magnitude of body mass regardless of food types.