bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assay to visualize specific protein oxidation reveals spatio-temporal regulation of SHP2
Authors: Tsutsumi Ryouhei , Harizanova Jana , Stockert Rabea , Schröder Katrin , Bastiaens Philippe I. H. , Neel Benjamin G. 
Published: August 2017

AbstractReactive oxygen species are produced transiently in response to cell stimuli, and function as second messengers that oxidize target proteins. Protein-tyrosine phosphatases are important reactive oxygen species targets, whose oxidation results in rapid, reversible, catalytic inactivation. Despite increasing evidence for the importance of protein-tyrosine phosphatase oxidation in signal transduction, the cell biological details of reactive oxygen species-catalyzed protein-tyrosine phosphatase inactivation have remained largely unclear, due to our inability to visualize protein-tyrosine phosphatase oxidation in cells. By combining proximity ligation assay with chemical labeling of cysteine residues in the sulfenic acid state, we visualize oxidized Src homology 2 domain-containing protein-tyrosine phosphatase 2 (SHP2). We find that platelet-derived growth factor evokes transient oxidation on or close to RAB5+/ early endosome antigen 1− endosomes. SHP2 oxidation requires NADPH oxidases (NOXs), and oxidized SHP2 co-localizes with platelet-derived growth factor receptor and NOX1/4. Our data demonstrate spatially and temporally limited protein oxidation within cells, and suggest that platelet-derived growth factor-dependent “redoxosomes,” contribute to proper signal transduction.
Tilt-less 3-D electron imaging and reconstruction of complex curvilinear structures
Authors: Oveisi Emad , Letouzey Antoine , Alexander Duncan T. L. , Jeangros Quentin , Schäublin Robin , Lucas Guillaume , Fua Pascal , Hébert Cécile 
Published: August 2017

AbstractThe ability to obtain three-dimensional (3-D) information about morphologies of nanostructures elucidates many interesting properties of materials in both physical and biological sciences. Here we demonstrate a novel method in scanning transmission electron microscopy (STEM) that gives a fast and reliable assessment of the 3-D configuration of curvilinear nano﻿structures, all without needing to tilt the sample through an arc. Using one-dimensional crystalline defects known as dislocations as a prototypical example of a complex curvilinear object, we demonstrate their 3-D reconstruction two orders of magnitude faster than by standard tilt-arc TEM tomographic techniques, from data recorded by selecting different ray paths of the convergent STEM probe. Due to its speed and immunity to problems associated with a tilt arc, the tilt-less 3-D imaging offers important advantages for investigations of radiation-sensitive, polycrystalline, or magnetic materials. Further, by using a segmented detector, the total electron dose is reduced to a single STEM raster scan acquisition; our tilt-less approach will therefore open new avenues for real-time 3-D electron imaging of dynamic processes.
Erratum: Solitonic conduction of electrotonic signals in neuronal branchlets with polarized microstructure
Authors: Poznanski R. R. , Cacha L. A. , Al-Wesabi Y. M. S. , Ali J. , Bahadoran M. , Yupapin P. P. , Yunus J. 
Published: August 2017

AbstractA correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.
Lack of Evidence for Vasoactive and Inflammatory Mediators in the Promotion of Macular Edema Associated with Epiretinal Membranes
Authors: Applewhite Brooks P. , Babapoor-Farrokhran Savalan , Poon David , Hassan Syed Junaid , Wellmann Elizabeth , Ying Howard S. , Semenza Gregg L. , Montaner Silvia , Sodhi Akrit 
Published: August 2017

AbstractThe development of symptoms in patients with epiretinal membranes (ERMs) often corresponds with the accumulation of interstitial fluid in the retina [i.e., the development of macular edema, (ME)]. To explore the potential value of pharmacologic therapeutic options to treat ME in patients with ERMs, we examine here the expression of vasoactive and inflammatory mediators in the vitreous of patients with idiopathic ERMs. We observed that vitreous concentrations of classic vasoactive factors (e.g., vascular endothelial growth factor) were similar in ERM patients with ME compared to controls. Using an array assessing the expression of 102 inflammatory cytokines we similarly did not observe a marked difference in cytokine expression in the vitreous of most ERM patients with ME compared to control patients. While the array data did implicate a group of inflammatory cytokines that were elevated in a subset of ERM patients who had severe ME (central subfield thickness ≥450 μm on spectral domain optical coherence tomography), expression of 3 of these inflammatory cytokines, all previously implicated in the promotion of ME in ischemic retinal disease, were not elevated by quantitative enzyme-linked immunosorbent assay. We conclude that therapies modulating vasoactive mediators or inflammatory cytokines may not affect ME in ERM patients.
Increased TCR signal strength in DN thymocytes promotes development of gut TCRαβ(+)CD8αα(+) intraepithelial lymphocytes
Authors: Grandjean Capucine L. , Sumaria Nital , Martin Stefania , Pennington Daniel J. 
Published: August 2017

AbstractCD4(+)CD8(+)“double positive” (DP) thymocytes differentiate into diverse αβ T cell sub-types using mechanistically distinct programs. For example, conventional αβ T cells develop from DP cells after partial-agonist T cell receptor (TCR) interactions with self-peptide/MHC, whereas unconventional αβ T cells, such as TCRαβ(+)CD8αα(+)intraepithelial lymphocytes (IELs), require full-agonist TCR interactions. Despite this, DP cells appear homogeneous, and it remains unclear how distinct TCR signalling instructs distinct developmental outcomes. Moreover, whether TCR signals at earlier stages of development, for example in CD4(−)CD8(−)double negative (DN) cells, impact on later fate decisions is presently unknown. Here, we assess four strains of mice that display altered TCR signal strength in DN cells, which correlates with altered generation of unconventional TCRαβ(+)CD8αα(+)IELs. FVB/n mice (compared to C57BL/6 animals) and mice with altered preTCRα (pTα) expression, both displayed weaker TCR signalling in DN cells, an inefficient DN-to-DP transition, and reduced contribution of TCRαβ(+)CD8αα(+)IELs to gut epithelium. Conversely, TCRαβ(+)CD8αα(+)IEL development was favoured in mice with increased TCR signal strength in DN cells. Collectively, these data suggest TCR signal strength in DN cells directly impacts on subsequent DP cell differentiation, fundamentally altering the potential of thymocyte progenitors to adopt conventional versus unconventional T cell fates.
Impact of biology knowledge on the conservation and management of large pelagic sharks
Authors: Yokoi Hiroki , Ijima Hirotaka , Ohshimo Seiji , Yokawa Kotaro 
Published: August 2017

AbstractPopulation growth rate, which depends on several biological parameters, is valuable information for the conservation and management of pelagic sharks, such as blue and shortfin mako sharks. However, reported biological parameters for estimating the population growth rates of these sharks differ by sex and display large variability. To estimate the appropriate population growth rate and clarify relationships between growth rate and relevant biological parameters, we developed a two-sex age-structured matrix population model and estimated the population growth rate using combinations of biological parameters. We addressed elasticity analysis and clarified the population growth rate sensitivity. For the blue shark, the estimated median population growth rate was 0.384 with a range of minimum and maximum values of 0.195–0.533, whereas those values of the shortfin mako shark were 0.102 and 0.007–0.318, respectively. The maturity age of male sharks had the largest impact for blue sharks, whereas that of female sharks had the largest impact for shortfin mako sharks. Hypotheses for the survival process of sharks also had a large impact on the population growth rate estimation. Both shark maturity age and survival rate were based on ageing validation data, indicating the importance of validating the quality of these data for the conservation and management of large pelagic sharks.
Association of the resolvin precursor 17-HDHA, but not D- or E- series resolvins, with heat pain sensitivity and osteoarthritis pain in humans
Authors: Valdes Ana M. , Ravipati Srinivasarao , Menni Cristina , Abhishek Abhishek , Metrustry Sarah , Harris Juliette , Nessa Ayrun , Williams Frances M. K. , Spector Tim D. , Doherty Michael , Chapman Victoria , Barrett David A. 
Published: August 2017

AbstractResolvins are omega-3 fatty acid derived potent bioactive lipids that resolve inflammation and modulate transient receptor potential channels. Exogenous administration of the resolvin precursor 17-HDHA shows a strong analgesic effect in animal models of osteoarthritis and acute inflammatory pain, but has not been studied in humans. Our aim was to assess the role of 17-HDHA and resolvins in heat pain sensitivity and in osteoarthritis pain in humans. Resolvins D1, D2, D3, D5, E1 and 17-HDHA, were measured by liquid chromatography-mass spectrometry and tested for association with heat pain thresholds in 250 healthy volunteers who had undergone quantitative sensory testing. Resolvins D1, D2 and 17-HDHA were then tested in 62 individuals affected with knee osteoarthritis and 52 age matched controls and tested for association with knee pain. Circulating levels of docosahexaenoic acid (DHA) were also measured. Levels of 17-HDHA, but not those of the other 5 resolvins tested, were associated with increased heat pain thresholds (beta = 0.075; 95% CI 0.024, 0.126; p < 0.0046). 17-HDHA was associated with lower pain scores in OA patients (beta −0.41; 95% CI-0.69, −0.12; p < 0.005; adjusted for covariates) but not with radiographic osteoarthritis. The associations of 17-HDHA with heat pain sensitivity and osteoarthritis pain were independent of DHA levels.
Compensated Row-Column Ultrasound Imaging System Using Multilayered Edge Guided Stochastically Fully Connected Random Fields
Authors: Ben Daya Ibrahim , Chen Albert I. H. , Shafiee Mohammad Javad , Wong Alexander , Yeow John T. W. 
Published: August 2017

AbstractThe row-column method received a lot of attention for 3-D ultrasound imaging. By reducing the number of connections required to address the 2-D array and therefore reducing the amount of data to handle, this addressing method allows for real time 3-D imaging. Row-column still has its limitations: the issues of sparsity, speckle noise inherent to ultrasound, the spatially varying point spread function, and the ghosting artifacts inherent to the row-column method must all be taken into account when building a reconstruction framework. In this research, we build on a previously published system and propose an edge-guided, compensated row-column ultrasound imaging system that incorporates multilayered edge-guided stochastically fully connected conditional random fields to address the limitations of the row-column method. Tests carried out on simulated and real row-column ultrasound images show the effectiveness of our proposed system over other published systems. Visual assessment show our proposed system’s potential at preserving edges and reducing speckle. Quantitative analysis shows that our proposed system outperforms previously published systems when evaluated with metrics such as Peak Signal-to-Noise Ratio, Coefficient of Correlation, and Effective Number of Looks. These results show the potential of our proposed system as an effective tool for enhancing 3-D row-column imaging.
Interactive effect of gibberellic acid and NPK fertilizer combinations on ramie yield and bast fibre quality
Authors: Ullah Sana , Anwar Sumera , Rehman Muzammal , Khan Shahbaz , Zafar Sara , Liu Lijun , Peng Dingxiang 
Published: August 2017

AbstractUnderstanding the effects of different combinations of nitrogen (N), phosphorus (P) and potassium (K) fertilizers and the effects of GA3 (gibberellic acid) foliar spray on the fiber quality and yield of ramie are important for maximizing the economic value of these plants. Three pot experiments were conducted using low NPK (140:70:140 kg/ha), normal NPK (280:140:280 kg/ha), and low NPK + GA3 (10 mg/L) treatments. In each experiment, following fertilizers were applied: no fertilizer (control), N, P, K, NP, NK, PK, and NPK. Ramie was harvested three times from each plant; ramie grown without fertilizers had significantly lower biomass and yield than plants grown with fertilizers. At both normal and low fertilization rates, application of NPK resulted in greater growth and yield than application of N, P, K, NP, NK, or PK. Unfertilized plants produced the thinnest fibres (22-24 µm), with lowest elongation rate (3.0–3.1%) and breaking strength (22.7–23.3 cN). Fibre yield and fibre quality were improved by application of GA3 + fertilizers. Maximum fibre yield was obtained at low NPK + GA3 treatment, resulting in 65–81% more yield than low NPK alone. GA3 with low NPK treatment significantly improved fibre diameter, fibre elongation, and breaking strength compared to both NPK alone and control treatment.
Growth of the northeastern margin of the Tibetan Plateau by squeezing up of the crust at the boundaries
Authors: Shi Jianyu , Shi Danian , Shen Yang , Zhao Wenjin , Xue Guangqi , Su Heping , Song Yang 
Published: August 2017

AbstractIn classic orogenic models, the mountain range is underlain by a deep crustal root. Here we present the crustal and upper mantle structures along two receiver function profiles across Qilian, an orogen experiencing recent growth at the northern margin of the Tibetan plateau. Opposite to an expected crustal root beneath the orogen, the Moho beneath Qilian is arch-like, shallower beneath the center and deepens by up to 10 km beneath its southern and northern boundaries. Additional velocity interfaces sub-parallel to the Moho are observed in the lower crust of the basins south of Qilian, which we interpret as the top of a mechanically strong lower crust thrusting several tens of kilometers underneath Qilian. In the north, the small lateral offset between the surface and mantle traces of the thrust system reveals a steep boundary, indicating that the North China cratonic crust acts as a strong resistance to the northward growth of the plateau, forcing the development of the left-lateral strike-slip Haiyuan fault south of the northern Qilian suture. The young Qilian orogen thus has been rising and growing progressively from the boundaries to the center, squeezed up by more rigid tectonic blocks in the north and south.
Angiotensin II induces cholesterol accumulation and injury in podocytes
Authors: Yang Yingjie , Yang Qian , Yang Jian , Ma Yiqiong , Ding Guohua 
Published: August 2017

AbstractAngiotensin II (Ang II) is a risk factor for the initiation and progression of chronic kidney disease (CKD), as elevated Ang II levels can lead to podocyte injury. However, there have been no studies on the role of Ang II in lipid metabolism or on podocyte injury caused by lipid dysfunction. Our study showed that Ang II induced lipid droplet (LD) accumulation and expression of the LD marker adipose differentiation-related protein (ADRP) in podocytes, and the extent of lipid deposition could be alleviated by losartan. Our study also demonstrated that Ang II increased the content of cholesterol in podocytes, which is an LD component, and this change was accompanied by decreased expression of the cholesterol efflux-related molecule ATP-binding cassette transporter-1 (ABCA1) and increased expression of the cholesterol uptake-related molecule LDL receptor (LDLR) and the cholesterol synthesis-related molecules sterol regulatory element-binding protein (SREBP1 and SREBP2) and 3-hydroxy-3-methylglutaryl CoA reductase (HMGCR). Pretreating podocytes with methyl-β-cyclodextrin (CD), which induces cholesterol efflux, decreased Ang II-mediated cholesterol accumulation and Ang II-induced podocyte apoptosis and maintained the podocyte cytoskeleton and spreading. These results suggested that Ang II induced podocyte cholesterol accumulation by regulating the expression of cholesterol metabolism-related molecules and that the subsequent cholesterol metabolism dysfunction resulted in podocyte injury.
Contactless graphene conductivity mapping on a wide range of substrates with terahertz time-domain reflection spectroscopy
Authors: Lin Hungyen , Braeuninger-Weimer Philipp , Kamboj Varun S. , Jessop David S. , Degl’Innocenti Riccardo , Beere Harvey E. , Ritchie David A. , Zeitler J. Axel , Hofmann Stephan 
Published: August 2017

AbstractWe demonstrate how terahertz time-domain spectroscopy (THz-TDS) operating in reflection geometry can be used for quantitative conductivity mapping of large area chemical vapour deposited graphene films on sapphire, silicon dioxide/silicon and germanium. We validate the technique against measurements performed with previously established conventional transmission based THz-TDS and are able to resolve conductivity changes in response to induced back-gate voltages. Compared to the transmission geometry, measurement in reflection mode requires careful alignment and complex analysis, but circumvents the need of a terahertz transparent substrate, potentially enabling fast, contactless, in-line characterisation of graphene films on non-insulating substrates such as germanium.
Enhancement of the productivity of the potent bacteriocin avicin A and improvement of its stability using nanotechnology approaches
Authors: Fahim Hazem A. , Rouby Waleed M. A. El , El-Gendy Ahmed O. , Khairalla Ahmed S. , Naguib Ibrahim A. , Farghali Ahmed A. 
Published: August 2017

AbstractHerein, enhancements of the yield and antimicrobial activity duration of the bacteriocin avicin A were accomplished using fractional factorial design (FFD) and layered double hydroxide (LDH) nanoparticles. Firstly, potential factors affecting bacteriocin production were selected for preliminary study. By a 25-1 FFD, high pH was shown to have a positive effect on avicin A yield, while temperature and duration of incubation, as well as peptone nitrogen sources all had negative effects. The highest bacteriocin production and activity (2560 BU/ml) were observed after 30 h of incubation at 30 °C, with pH adjustment at 7, and in the presence of 2 g mannitol as carbon source and 2.2 g peptone as nitrogen source. Secondly, avicin A nanocomposites with different LDH precursors were tested. Only avicin A-ZnAl-CO3 LDH demonstrated a potent antimicrobial activity against Lactobacillus sakei LMGT 2313 that lasted for at least 24 days, as compared to the values of 6 and 15 days observed with the free avicin A that has been stored at room temperature and at 4 °C, respectively. In conclusion, avicin A production and stability can be improved by manipulating the growth conditions and media composition, together with conjugation to LDHs.
Atomic-scale engineering of ferroelectric-ferromagnetic interfaces of epitaxial perovskite films for functional properties
Authors: Hausmann Simon , Ye Jingfan , Aoki Toshihiro , Zheng Jian-Guo , Stahn Jochen , Bern Francis , Chen Binda , Autieri Carmine , Sanyal Biplab , Esquinazi Pablo D. , Böni Peter , Paul Amitesh 
Published: August 2017

AbstractBesides epitaxial mismatch that can be accommodated by lattice distortions and/or octahedral rotations, ferroelectric-ferromagnetic interfaces are affected by symmetry mismatch and subsequent magnetic ordering. Here, we have investigated La0.67 Sr0.33 MnO3 (LSMO) samples with varying underlying unit cells (uc) of BaTiO3 (BTO) layer on (001) and (110) oriented substrates in order to elucidate the role of symmetry mismatch. Lattice mismatch for 3 uc of BTO and symmetry mismatch for 10 uc of BTO, both associated with local MnO6 octahedral distortions of the (001) LSMO within the first few uc, are revealed by scanning transmission electron microscopy. Interestingly, we find exchange bias along the in-plane [110]/[100] directions only for the (001) oriented samples. Polarized neutron reflectivity measurements confirm the existence of a layer with zero net moment only within (001) oriented samples. First principle density functional calculations show that even though the bulk ground state of LSMO is ferromagnetic, a large lattice constant together with an excess of La can stabilize an antiferromagnetic LaMnO3-type phase at the interface region and explain the experimentally observed exchange bias. Atomic scale tuning of MnO6 octahedra can thus be made possible via symmetry mismatch at heteroepitaxial interfaces. This aspect can act as a vital parameter for structure-driven control of physical properties.
Non-autonomous multi-rogue waves for spin-1 coupled nonlinear Gross-Pitaevskii equation and management by external potentials
Authors: Li Li , Yu Fajun 
Published: August 2017

AbstractWe investigate non-autonomous multi-rogue wave solutions in a three-component(spin-1) coupled nonlinear Gross-Pitaevskii(GP) equation with varying dispersions, higher nonlinearities, gain/loss and external potentials. The similarity transformation allows us to relate certain class of multi-rogue wave solutions of the spin-1 coupled nonlinear GP equation to the solutions of integrable coupled nonlinear Schrödinger(CNLS) equation. We study the effect of time-dependent quadratic potential on the profile and dynamic of non-autonomous rogue waves. With certain requirement on the backgrounds, some non-autonomous multi-rogue wave solutions exhibit the different shapes with two peaks and dip in bright-dark rogue waves. Then, the managements with external potential and dynamic behaviors of these solutions are investigated analytically. The results could be of interest in such diverse fields as Bose-Einstein condensates, nonlinear fibers and super-fluids.
In Vivo Confocal Microscopy Evaluation of Ocular Surface with Graft-Versus-Host Disease-Related Dry Eye Disease
Authors: He Jingliang , Ogawa Yoko , Mukai Shin , Saijo-Ban Yumiko , Kamoi Mizuka , Uchino Miki , Yamane Mio , Ozawa Nobuhiro , Fukui Masaki , Mori Takehiko , Okamoto Shinichiro , Tsubota Kazuo 
Published: August 2017

AbstractDry eye disease (DED) is often elicited by graft-versus-host disease (GVHD), an extensive complication of hematopoietic stem cell transplantation (HSCT). To unravel the mechanism of this type of DED, in vivo confocal microscopy (IVCM) was used to investigate alterations in the state of the sub-basal nerves, dendritic cells (DCs) and globular immune cells (GICs) in the central cornea and limbal epithelia. In this study, we examined 12 HSCT recipients with GVHD-caused DED and 10 HSCT recipients without GVHD-associated DED and evaluated the clinical parameters in the 2 groups. Analysis of the central cornea and limbal epithelia using IVCM was conducted to investigate the density of the corneal sub-basal nerves, DCs and GICs as well as the tortuosity and branching of the sub-basal nerves. As suggested by our data, the clinical variables in the GVHD group were significantly different from those in the non-GVHD group. Additionally, GVHD-triggered DED conceivably increased the density of DCs and GICs in the central cornea and the density of DCs in limbal epithelia and altered the morphology of the sub-basal nerves. These phenomena are presumably correlated with the degree of inflammation. Thus, our findings may be translated into non-invasive diagnostic methods that indicate the severity of inflammation on the ocular surface in HSCT recipients.