bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elicitors Derived from Hazel (Corylus avellana L.) Cell Suspension Culture Enhance Growth and Paclitaxel Production of Epicoccum nigrum
Authors: Salehi Mina , Moieni Ahmad , Safaie Naser 
Published: August 2018

AbstractThe microbial fermentation is considered as the potential source for large-scale production of paclitaxel. Since co-cultivation/mixed fermentation strategy has been reported as a yield enhancement strategy for paclitaxel production, investigation of fungal endophyte response to plant culture medium, plant cell extract (CE) and medium filtrate (MF) of plant cell suspension culture in terms of growth and paclitaxel production is interesting. In this study, 35 endophytic fungi were isolated from Taxus baccata and Corylus avellana grown in Iran. The analysis of high-performance liquid chromatography and mass spectrometry showed that one isolate (YEF2) produced paclitaxel. The isolate YEF2 was identified as Epicoccum nigrum by sequencing of ITS1-5.8S-ITS2 rDNA region and actin gene. YEF2 was slow-growing in Murashige and Skoog medium, but the synergistic interaction of gibberellic acid (GA3) and CE of C. avellana enhanced the growth of YEF2. The highest total yield of paclitaxel (314.7 µg/l; 11.5-folds) of E. nigrum strain YEF2 was obtained by using 28% (v/v) filter sterilized CE of C. avellana and 2 µg ml−1 GA3 that was significantly higher than the control. In this study, the effects of the plant cell extract on growth and paclitaxel production of paclitaxel producing endophytic fungus were studied for the first time.
New aspects of longitudinal instabilities in electron storage rings
Authors: Blednykh A. , Bacha B. , Bassi G. , Cheng W. , Chubar O. , Derbenev A. , Lindberg R. , Rakitin M. , Smaluk V. , Zhernenkov M. , Chen-Wiegart Yu-chen Karen , Wiegart L. 
Published: August 2018

AbstractNovel features of the longitudinal instability of a single electron bunch circulating in a low-emittance electron storage ring are discussed. Measurements and numerical simulations, performed both in time and frequency domain, show a non-monotonic increase of the electron beam energy spread as a function of single bunch current, characterized by the presence of local minima and maxima, where a local minimum of the energy spread is interpreted as a higher-order microwave instability threshold. It is also shown that thresholds related to the same zero-intensity bunch length depend linearly on the accelerating radio frequency voltage. The observed intensity-dependent features of the energy spread, confirmed by measurements with two independent diagnostics methods, i.e. horizontal beam profile measurements by a synchrotron light monitor and photon energy spectrum measurements of undulator radiation, are given a theoretical interpretation by applying a novel eigenvalue analysis based on the linearized Vlasov equation.
Profile distribution of CO2 in an arid saline-alkali soil with gypsum and wheat straw amendments: a two-year incubation experiment
Authors: Wang Junyi , Wang Xiujun , Wang Jiaping 
Published: August 2018

AbstractAdding gypsum and/or straw is a common practice for ameliorating saline-alkali soils. However, the effect of amendment on soil CO2 is poorly known. An incubation experiment was conducted for over two years in a saline-alkali soil of Yanqi Basin, which included four treatments: control, gypsum addition (Ca), wheat straw addition (S) and gypsum-wheat straw combination (Ca+S). We continuously monitored soil CO2 concentration, temperature and moisture at 15, 30, 45 and 60 cm. There was a clear seasonality in soil CO2 under all four treatments, which was generally similar to those in soil temperature and moisture. Straw addition led to a significant increase in soil CO2 over 0–60 cm in summer. While there was a significant increase of soil CO2 with gypsum addition only, soil CO2 significantly decreased with the addition of gypsum and straw (relative to straw addition only) during autumn and winter in 2014. Interestingly, integrated soil CO2 was lowest in soil profile under the Ca+S treatment during winter and spring. Our study implies that different amendments of organic matter and gypsum may result in various responses and interactions of biological, chemical and physical processes, with implications for the carbon cycle in saline-alkaline soils of arid region.
Iterative and discrete reconstruction in the evaluation of the rabbit model of osteoarthritis
Authors: Ketola Juuso H. , Karhula Sakari S. , Finnilä Mikko A. J. , Korhonen Rami K. , Herzog Walter , Siltanen Samuli , Nieminen Miika T. , Saarakkala Simo 
Published: August 2018

AbstractMicro-computed tomography (µCT) is a standard method for bone morphometric evaluation. However, the scan time can be long and the radiation dose during the scan may have adverse effects on test subjects, therefore both of them should be minimized. This could be achieved by applying iterative reconstruction (IR) on sparse projection data, as IR is capable of producing reconstructions of sufficient image quality with less projection data than the traditional algorithm requires. In this work, the performance of three IR algorithms was assessed for quantitative bone imaging from low-resolution data in the evaluation of the rabbit model of osteoarthritis. Subchondral bone images were reconstructed with a conjugate gradient least squares algorithm, a total variation regularization scheme, and a discrete algebraic reconstruction technique to obtain quantitative bone morphometry, and the results obtained in this manner were compared with those obtained from the reference reconstruction. Our approaches were sufficient to identify changes in bone structure in early osteoarthritis, and these changes were preserved even when minimal data were provided for the reconstruction. Thus, our results suggest that IR algorithms give reliable performance with sparse projection data, thereby recommending them for use in µCT studies where time and radiation exposure are preferably minimized.
Yu-Shiba-Rusinov bound states induced by a spin flipper in the vicinity of a s-wave superconductor
Authors: Pal Subhajit , Benjamin Colin 
Published: August 2018

AbstractWe theoretically study the formation and characteristics of Yu-Shiba-Rusinov bound states within the superconducting gap using a BTK approach in presence of a spin flipper (high spin magnetic impurity). We focus on the zero energy in the conductance spectra and show how a peak is formed at E = 0 due to flipping of the magnetic impurity spin, but for no flip case a dip forms at E = 0 in the conductance spectra. This E = 0 conductance peak is almost quantized at 2e2/h values, however it arises due to non-topological reasons in contrast to the E = 0 peak formed due to Majorana states.
Neural network identification of people hidden from view with a single-pixel, single-photon detector
Authors: Caramazza Piergiorgio , Boccolini Alessandro , Buschek Daniel , Hullin Matthias , Higham Catherine F. , Henderson Robert , Murray-Smith Roderick , Faccio Daniele 
Published: August 2018

AbstractLight scattered from multiple surfaces can be used to retrieve information of hidden environments. However, full three-dimensional retrieval of an object hidden from view by a wall has only been achieved with scanning systems and requires intensive computational processing of the retrieved data. Here we use a non-scanning, single-photon single-pixel detector in combination with a deep convolutional artificial neural network: this allows us to locate the position and to also simultaneously provide the actual identity of a hidden person, chosen from a database of people (N = 3). Artificial neural networks applied to specific computational imaging problems can therefore enable novel imaging capabilities with hugely simplified hardware and processing times.
The functional relations among motor-based prediction, sensory goals and feedback in learning non-native speech sounds: Evidence from adult Mandarin Chinese speakers with an auditory feedback masking paradigm
Authors: Liu Xiaoluan , Tian Xing 
Published: August 2018

AbstractPrevious studies in speech production and acquisition have mainly focused on how feedback vs. goals and feedback vs. prediction regulate learning and speech control. The present study investigated the less studied mechanism–prediction vs. goals in the context of adult Mandarin speakers’ acquisition of non-native sounds, using an auditory feedback masking paradigm. Participants were asked to learn two types of non-native vowels: /ø/ and /ɵ/—the former being less similar than the latter to Mandarin vowels, either in feedback available or feedback masked conditions. The results show that there was no significant improvement in learning the two targets when auditory feedback was masked. This suggests that motor-based prediction could not directly compare with sensory goals for adult second language acquisition. Furthermore, auditory feedback can help achieve learning only if the competition between prediction and goals is minimal, i.e., when target sounds are distinct from existing sounds in one’s native speech. The results suggest motor-based prediction and sensory goals may share a similar neural representational format, which could result in a competing relation in neural recourses in speech learning. The feedback can conditionally overcome such interference between prediction and goals. Hence, the present study further probed the functional relations among key components (prediction, goals and feedback) of sensorimotor integration in speech learning.
Differential association of ezetimibe-simvastatin combination with major adverse cardiovascular events in patients with or without diabetes: a retrospective propensity score-matched cohort study
Authors: Lee Yong-ho , Hong Namki , Lee Chan Joo , Park Sung Ha , Lee Byung-Wan , Cha Bong-Soo , Kang Eun Seok 
Published: August 2018

AbstractClinical trials suggested that the benefits of ezetimibe-statin combination therapy on major adverse cardiovascular events (MACE) might be greater in patients with diabetes. We aimed to investigate the differential association of ezetimibe-statin combination with incident MACE by presence of diabetes. In this retrospective cohort study, subjects treated with simvastatin 20 mg plus ezetimibe 10 mg (S + E) or simvastatin 20 mg alone (S) between 2005 and 2015 were 1:1 matched using propensity score as stratified by diabetes. Primary outcome was newly-developed MACE composed of cardiovascular death, ACS, coronary revascularization, or non-hemorrhagic stroke. During 5,077 and 12,439 person-years, the incidence rates of MACE were 24.9, 20.1, 35.3, and 22.8/1000 person-years among no diabetes S, no diabetes S + E, diabetes S, and diabetes S + E, respectively. Relative to no diabetes S, adjusted HR (aHR) for MACE in diabetes S was 1.23 (p = 0.086), whereas S + E was associated with a lower risk of MACE in both non-diabetic patients (aHR 0.76, p = 0.047) and diabetic patients (aHR 0.60, p = 0.007) with significant difference (relative excess risk due to interaction = −0.39, p = 0.044). In conclusion, reduction of MACE risk associated with ezetimibe plus simvastatin therapy relative to simvastatin alone was greater in patients with diabetes than in patients without diabetes.
Schistosoma mansoni infection is associated with quantitative and qualitative modifications of the mammalian intestinal microbiota
Authors: Jenkins Timothy P. , Peachey Laura E. , Ajami Nadim J. , MacDonald Andrew S. , Hsieh Michael H. , Brindley Paul J. , Cantacessi Cinzia , Rinaldi Gabriel 
Published: August 2018

AbstractIn spite of the extensive contribution of intestinal pathology to the pathophysiology of schistosomiasis, little is known of the impact of schistosome infection on the composition of the gut microbiota of its mammalian host. Here, we characterised the fluctuations in the composition of the gut microbial flora of the small and large intestine, as well as the changes in abundance of individual microbial species, of mice experimentally infected with Schistosoma mansoni with the goal of identifying microbial taxa with potential roles in the pathophysiology of infection and disease. Bioinformatic analyses of bacterial 16S rRNA gene data revealed an overall reduction in gut microbial alpha diversity, alongside a significant increase in microbial beta diversity characterised by expanded populations of Akkermansia muciniphila (phylum Verrucomicrobia) and lactobacilli, in the gut microbiota of S. mansoni-infected mice when compared to uninfected control animals. These data support a role of the mammalian gut microbiota in the pathogenesis of hepato-intestinal schistosomiasis and serves as a foundation for the design of mechanistic studies to unravel the complex relationships amongst parasitic helminths, gut microbiota, pathophysiology of infection and host immunity.
High-resolution synchrotron-based X-ray microtomography as a tool to unveil the three-dimensional neuronal architecture of the brain
Authors: Fonseca Matheus de Castro , Araujo Bruno Henrique Silva , Dias Carlos Sato Baraldi , Archilha Nathaly Lopes , Neto Dionísio Pedro Amorim , Cavalheiro Esper , Westfahl Harry , da Silva Antônio José Roque , Franchini Kleber Gomes 
Published: August 2018

AbstractThe assessment of neuronal number, spatial organization and connectivity is fundamental for a complete understanding of brain function. However, the evaluation of the three-dimensional (3D) brain cytoarchitecture at cellular resolution persists as a great challenge in the field of neuroscience. In this context, X-ray microtomography has shown to be a valuable non-destructive tool for imaging a broad range of samples, from dense materials to soft biological specimens, arisen as a new method for deciphering the cytoarchitecture and connectivity of the brain. In this work we present a method for imaging whole neurons in the brain, combining synchrotron-based X-ray microtomography with the Golgi-Cox mercury-based impregnation protocol. In contrast to optical 3D techniques, the approach shown here does neither require tissue slicing or clearing, and allows the investigation of several cells within a 3D region of the brain.
Identification and characterization of a novel β-D-galactosidase that releases pyruvylated galactose
Authors: Higuchi Yujiro , Matsufuji Hitomi , Tanuma Masanari , Arakawa Takatoshi , Mori Kazuki , Yamada Chihaya , Shofia Risa , Matsunaga Emiko , Tashiro Kosuke , Fushinobu Shinya , Takegawa Kaoru 
Published: August 2018

AbstractPyruvyl modification of oligosaccharides is widely seen in both prokaryotes and eukaryotes. Although the biosynthetic mechanisms of pyruvylation have been investigated, enzymes that metabolize and degrade pyruvylated oligosaccharides are not well known. Here, we searched for a pyruvylated galactose (PvGal)-releasing enzyme by screening soil samples. We identified a Bacillus strain, as confirmed by the 16S ribosomal RNA gene analysis, that exhibited PvGal-ase activity toward p-nitrophenyl-β-D-pyruvylated galactopyranose (pNP-β-D-PvGal). Draft genome sequencing of this strain, named HMA207, identified three candidate genes encoding potential PvGal-ases, among which only the recombinant protein encoded by ORF1119 exhibited PvGal-ase activity. Although ORF1119 protein displayed broad substrate specificity for pNP sugars, pNP-β-D-PvGal was the most favorable substrate. The optimum pH for the ORF1119 PvGal-ase was determined as 7.5. A BLAST search suggested that ORF1119 homologs exist widely in bacteria. Among two homologs tested, BglC from Clostridium but not BglH from Bacillus showed PvGal-ase activity. Crystal structural analysis together with point mutation analysis revealed crucial amino acids for PvGal-ase activity. Moreover, ORF1119 protein catalyzed the hydrolysis of PvGal from galactomannan of Schizosaccharomyces pombe, suggesting that natural polysaccharides might be substrates of the PvGal-ase. This novel PvGal-catalyzing enzyme might be useful for glycoengineering projects to produce new oligosaccharide structures.
Post-Deposition Wetting and Instabilities in Organic Thin Films by Supersonic Molecular Beam Deposition
Authors: Chiarella Fabio , Perroni Carmine Antonio , Chianese Federico , Barra Mario , De Luca Gabriella Maria , Cataudella Vittorio , Cassinese Antonio 
Published: August 2018

AbstractWe discuss the formation and post-deposition instability of nanodrop-like structures in thin films of PDIF-CN2 (a perylene derivative) deposited via supersonic molecular beam deposition technique on highly hydrophobic substrates at room temperature. The role of the deposition rate on the characteristic lengths of the organic nanodrops has been investigated by a systematic analysis of atomic force microscope images of the thin films and through the use of the height-height correlation function. The nanodrops appear to be a metastable configuration for the freshly-deposited films. For this reason, post-deposition wetting effect has been examined with unprecedented accuracy throughout a year of experimental observations. The observed time scales, from few hours to months, are related to the growth rate, and characterize the thin films morphological reordering from three-dimensional nanodrops to a well-connected terraced film. While the interplay between adhesion and cohesion energies favors the formation of 3D-mounted structures during the growth, wetting phenomenon following the switching off of the molecular flux is found to be driven by an instability. A slow rate downhill process survives at the molecular flux shutdown and it is accompanied and maybe favored by the formation of a precursor layer composed of more lying molecules. These results are supported by simulations based on a non-linear stochastic model. The instability has been simulated, for both the growth and the post-growth evolution. To better reproduce the experimental data it is needed to introduce a surface equalizer term characterized by a relaxation time taking into account the presence of a local mechanism of molecular correlation.
The landscape of the A-to-I RNA editome from 462 human genomes
Authors: Ouyang Zhangyi , Ren Chao , Liu Feng , An Gaole , Bo Xiaochen , Shu Wenjie 
Published: August 2018

AbstractA-to-I editing, as a post-transcriptional modification process mediated by ADAR, plays a crucial role in many biological processes in metazoans. However, how and to what extent A-to-I editing diversifies and shapes population diversity at the RNA level are largely unknown. Here, we used 462 mRNA-sequencing samples from five populations of the Geuvadis Project and identified 16,518 A-to-I editing sites, with false detection rate of 1.03%. These sites form the landscape of the RNA editome of the human genome. By exploring RNA editing within and between populations, we revealed the geographic restriction of rare editing sites and population-specific patterns of edQTL editing sites. Moreover, we showed that RNA editing can be used to characterize the subtle but substantial diversity between different populations, especially those from different continents. Taken together, our results demonstrated that the nature and structure of populations at the RNA level are illustrated well by RNA editing, which provides insights into the process of how A-to-I editing shapes population diversity at the transcriptomic level. Our work will facilitate the understanding of the landscape of the RNA editome at the population scale and will be helpful for interpreting differences in the distribution and prevalence of disease among individuals and across populations.
A Low-Cost Non-explosive Synthesis of Graphene Oxide for Scalable Applications
Authors: Ranjan Pranay , Agrawal Shweta , Sinha Apurva , Rao T. Rajagopala , Balakrishnan Jayakumar , Thakur Ajay D. 
Published: August 2018

AbstractA low cost, non-explosive process for the synthesis of graphene oxide (GO) is demonstrated. Using suitable choice of reaction parameters including temperature and time, this recipe does not require expensive membranes for filtration of carbonaceous and metallic residues. A pre-cooling protocol is introduced to control the explosive nature of the highly exothermic reactions during the oxidation process. This alleviates the requirement for expensive membranes and completely eliminates the explosive nature of intermediate reaction steps when compared to existing methods. High quality of the synthesized GO is corroborated using a host of characterization techniques including X-ray diffraction, optical spectroscopy, X-ray photoemission spectroscopy and current-voltage characteristics. Simple reduction protocol using ultra-violet light is demonstrated for potential application in the area of photovoltaics. Using different reduction protocols together with the proposed inexpensive method, reduced GO samples with tunable conductance over a wide range of values is demonstrated. Density functional theory is employed to understand the structure of GO. We anticipate that this scalable approach will catalyze large scale applications of GO.
TNFR2 ligation in human T regulatory cells enhances IL2-induced cell proliferation through the non-canonical NF-κB pathway
Authors: Wang Jun , Ferreira Ricardo , Lu Wanhua , Farrow Samatha , Downes Kate , Jermutus Lutz , Minter Ralph , Al-Lamki Rafia S. , Pober Jordan S. , Bradley John R. 
Published: August 2018

AbstractHuman T regulatory cells (T regs) express high levels of TNF receptor 2 (TNFR2). Ligation of TNFR2 with TNF, which can recognise both TNFR1 and TNFR2, or with a TNFR2-selective binding molecule, DARPin 18 (D18) activates canonical NF-κB signalling, assessed by IκBα degradation, and the magnitude of the response correlates with the level of TNFR2 expression. RNA-seq analysis of TNF- or D18-treated human T regs revealed that TNFR2 ligation induces transcription of NFKB2 and RELB, encoding proteins that form the non-canonical NF-κB transcription factor. In combination with IL2, D18 treatment is specific for T regs in (1) stabilising NF-κB-inducing kinase protein, the activator of non-canonical NF-κB signalling, (2) inducing translocation of RelB from cytosol to nucleus, (3) increasing cell cycle entry, and (4) increasing cell numbers. However, the regulatory function of the expanded T regs is unaltered. Inhibition of RelB nuclear translocation blocks the proliferative response. We conclude that ligation of TNFR2 by D18 enhances IL2-induced T regs proliferation and expansion in cell number through the non-canonical NF-κB pathway.
A universal curve of apatite crystallinity for the assessment of bone integrity and preservation
Authors: Dal Sasso Gregorio , Asscher Yotam , Angelini Ivana , Nodari Luca , Artioli Gilberto 
Published: August 2018

AbstractThe reliable determination of bioapatite crystallinity is of great practical interest, as a proxy to the physico-chemical and microstructural properties, and ultimately, to the integrity of bone materials. Bioapatite crystallinity is used to diagnose pathologies in modern calcified tissues as well as to assess the preservation state of fossil bones. To date, infrared spectroscopy is one of the most applied techniques for bone characterisation and the derived infrared splitting factor (IRSF) has been widely used to practically assess bioapatite crystallinity. Here we thoroughly discuss and revise the use of the IRSF parameter and its meaning as a crystallinity indicator, based on extensive measurements of fresh and fossil bones, virtually covering the known range of crystallinity degree of bioapatite. A novel way to calculate and use the infrared peak width as a suitable measurement of true apatite crystallinity is proposed, and validated by combined measurement of the same samples through X-ray diffraction. The non-linear correlation between the infrared peak width and the derived ISRF is explained. As shown, the infrared peak width at 604 cm−1can be effectively used to assess both the average crystallite size and structural carbonate content of bioapatite, thus establishing a universal calibration curve of practical use.