bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hazardous thunderstorm intensification over Lake Victoria
Authors: Thiery Wim , Davin Edouard L. , Seneviratne Sonia I. , Bedka Kristopher , Lhermitte Stef , van Lipzig Nicole P. M. 
Published: September 2016

AbstractWeather extremes have harmful impacts on communities around Lake Victoria, where thousands of fishermen die every year because of intense night-time thunderstorms. Yet how these thunderstorms will evolve in a future warmer climate is still unknown. Here we show that Lake Victoria is projected to be a hotspot of future extreme precipitation intensification by using new satellite-based observations, a high-resolution climate projection for the African Great Lakes and coarser-scale ensemble projections. Land precipitation on the previous day exerts a control on night-time occurrence of extremes on the lake by enhancing atmospheric convergence (74%) and moisture availability (26%). The future increase in extremes over Lake Victoria is about twice as large relative to surrounding land under a high-emission scenario, as only over-lake moisture advection is high enough to sustain Clausius–Clapeyron scaling. Our results highlight a major hazard associated with climate change over East Africa and underline the need for high-resolution projections to assess local climate change.
Disparate acidification and calcium carbonate desaturation of deep and shallow waters of the Arctic Ocean
Authors: Luo Yiming , Boudreau Bernard P. , Mucci Alfonso 
Published: September 2016

AbstractThe Arctic Ocean is acidifying from absorption of man-made CO2. Current predictive models of that acidification focus on surface waters, and their results argue that deep waters will acidify by downward penetration from the surface. Here we show, with an alternative model, the rapid, near simultaneous, acidification of both surface and deep waters, a prediction supported by current, but limited, saturation data. Whereas Arctic surface water responds directly by atmospheric CO2 uptake, deeper waters will be influenced strongly by intrusion of mid-depth, pre-acidified, Atlantic Ocean water. With unabated CO2 emissions, surface waters will become undersaturated with respect to aragonite by 2105 AD and could remain so for ∼600 years. In deep waters, the aragonite saturation horizon will rise, reaching the base of the surface mixed layer by 2140 AD and likely remaining there for over a millennium. The survival of aragonite-secreting organisms is consequently threatened on long timescales.
A bead-based western for high-throughput cellular signal transduction analyses
Authors: Treindl Fridolin , Ruprecht Benjamin , Beiter Yvonne , Schultz Silke , Döttinger Anette , Staebler Annette , Joos Thomas O. , Kling Simon , Poetz Oliver , Fehm Tanja , Neubauer Hans , Kuster Bernhard , Templin Markus F. 
Published: September 2016

AbstractDissecting cellular signalling requires the analysis of large number of proteins. The DigiWest approach we describe here transfers the western blot to a bead-based microarray platform. By combining gel-based protein separation with immobilization on microspheres, hundreds of replicas of the initial blot are created, thus enabling the comprehensive analysis of limited material, such as cells collected by laser capture microdissection, and extending traditional western blotting to reach proteomic scales. The combination of molecular weight resolution, sensitivity and signal linearity on an automated platform enables the rapid quantification of hundreds of specific proteins and protein modifications in complex samples. This high-throughput western blot approach allowed us to identify and characterize alterations in cellular signal transduction that occur during the development of resistance to the kinase inhibitor Lapatinib, revealing major changes in the activation state of Ephrin-mediated signalling and a central role for p53-controlled processes.
Two-dimensional flow nanometry of biological nanoparticles for accurate determination of their size and emission intensity
Authors: Block Stephan , Fast Björn Johansson , Lundgren Anders , Zhdanov Vladimir P. , Höök Fredrik 
Published: September 2016

AbstractBiological nanoparticles (BNPs) are of high interest due to their key role in various biological processes and use as biomarkers. BNP size and composition are decisive for their functions, but simultaneous determination of both properties with high accuracy remains challenging. Optical microscopy allows precise determination of fluorescence/scattering intensity, but not the size of individual BNPs. The latter is better determined by tracking their random motion in bulk, but the limited illumination volume for tracking this motion impedes reliable intensity determination. Here, we show that by attaching BNPs to a supported lipid bilayer, subjecting them to hydrodynamic flows and tracking their motion via surface-sensitive optical imaging enable determination of their diffusion coefficients and flow-induced drifts, from which accurate quantification of both BNP size and emission intensity can be made. For vesicles, the accuracy of this approach is demonstrated by resolving the expected radius-squared dependence of their fluorescence intensity for radii down to 15 nm.
Faceted interfaces: a key feature to quantitative understanding of transformation morphology
Authors: Zhang Wen-Zheng , Gu Xin-Fu , Dai Fu-Zhi 
Published: September 2016

AbstractFaceted interfaces are a typical key feature of the morphology of many microstructures generated from solid-state phase transformations. Interpretation, prediction and simulation of this faceted morphology remain a challenge, especially for systems where irrational orientation relationships (ORs) between two phases and irrational interface orientations (IOs) are preferred. In terms of structural singularities, this work suggests an integrated framework, which possibly encompasses all candidates of faceted interfaces. The structural singularities are identified from a matching pattern, a dislocation structure and/or a ledge structure. The resultant singular interfaces have discrete IOs, described with low-index g’s (rational orientations) and/or Δg’s (either rational or irrational orientations). Various existing models are grouped according to their determined results regarding the OR and IO, and the links between the models are clarified in the integrated framework. Elimination of defect types as far as possible in a dominant singular interface often exerts a central restriction on the OR. An irrational IO is usually due to the elimination of dislocations in one direction, i.e., an O-line interface. Analytical methods using both three-dimensional and two-dimensional models for quantitative determinations of O-line interfaces are reviewed, and a detailed example showing the calculation for an irrational interface is given. The association between structural singularities and local energy minima is verified by atomistic calculations of interfacial energies in fcc/bcc alloys where it is found that the calculated equilibrium cross-sections are in a good agreement with observations from selected alloys.
Multipath Effects in Millimetre-Wave Wireless Communication using Orbital Angular Momentum Multiplexing
Authors: Yan Yan , Li Long , Xie Guodong , Bao Changjing , Liao Peicheng , Huang Hao , Ren Yongxiong , Ahmed Nisar , Zhao Zhe , Wang Zhe , Ashrafi Nima , Ashrafi Solyman , Talwar Shilpa , Sajuyigbe Soji , Tur Moshe , Molisch Andreas F. , Willner Alan E. 
Published: September 2016

AbstractElectromagnetic waves carrying orbital angular momentum (OAM) have been used for mode division multiplexing in free-space communication systems to increase both the capacity and the spectral efficiency. In the case of conventional wireless communication links using non-OAM beams, multipath effects caused by beam spreading and reflection from the surrounding objects affect the system performance. This paper presents the results of analysis, simulations, and measurements of multipath effects in a millimetre-wave communication link using OAM multiplexing at 28 GHz. Multipath-induced intra- and inter-channel crosstalk, which are caused by specular reflection from a plane parallel to the propagation path, are analysed and measured. Both the simulation and the experimental results show that an OAM channel with a high OAM number ℓ tends to suffer from both strong intra-channel crosstalk and strong inter-channel crosstalk with other OAM channels. Results of the analysis show that this observation can be explained on the basis of both the properties of OAM beam divergence and the filtering effect at the receiver, which is associated with the spiral wavefront of OAM beams.
Downregulation of angiotensin type 1 receptor and nuclear factor-κB by sirtuin 1 contributes to renoprotection in unilateral ureteral obstruction
Authors: Yang Shao-Yu , Lin Shuei-Liong , Chen Yung-Ming , Wu Vin-Cent , Yang Wei-Shiung , Wu Kwan-Dun 
Published: September 2016

AbstractActivation of sirtuin 1 (Sirt1) attenuates unilateral ureteral obstruction (UUO)-induced inflammation and fibrosis, suggesting that Sirt1 may prevent tubulointerstitial fibrosis. In this study, we explored changes in the expression of Sirt1 in the kidneys of UUO-treated rats and evaluated the effects of Sirt1 activation or inhibition on renal pathology and mediators of UUO pathogenesis, especially angiotensin II and nuclear factor (NF)-κB, in rats and rat renal fibroblasts. Sirt1 expression increased in the obstructed kidney but not in the contralateral kidney and was mainly detected in tubulointerstitial cells. Resveratrol, a Sirt1 activator, decreased UUO-induced inflammation and fibrosis, while sirtinol, a Sirt1 inhibitor, enhanced UUO-induced inflammation. UUO increased renal angiotensin type 1 receptor (AT1R), NF-κB, monocyte chemotactic protein 1 (MCP-1) and fibronectin expression. Resveratrol attenuated these UUO-induced changes, whereas sirtinol enhanced them, with the exception of fibronectin. In renal fibroblasts, Sirt1 overexpression reduced AT1R and NF-κB levels, while Sirt1 knockdown had the opposite effects. Sirtinol increased the levels of AT1R, NF-κB, MCP-1 and connective tissue growth factor (CTGF), while resveratrol reduced AT1R levels. Our results suggested that Sirt1 inhibited AT1R and NF-κB expression in renal fibroblasts and that these mechanisms may play roles in alleviating UUO-induced damages.
Novel and Neuroprotective Tetranortriterpenoids from Chinese Mangrove Xylocarpus granatum Koenig
Authors: Zhou Zhen-Fang , Kurtán Tibor , Mándi Attila , Gu Yu-Cheng , Yao Li-Gong , Xin Guo-Rong , Li Xu-Wen , Guo Yue-Wei 
Published: September 2016

AbstractEight new tetranortriterpenoids (1–8) were isolated from the twigs and leaves of the Chinese mangrove plantXylocarpus granatum, together with four related known ones (9–12). The structures of new compounds were elucidated by detailed spectroscopic analysis. The absolute configuration of 9-epixylogranatin A (1) was determined by time-dependent density functional theory-electronic circular dichroism (TDDFT-ECD) calculations of the solution conformers. Xylogranatumin A (2) represents the first example of the 9, 10-secolimonoid with an unprecedented oxygen-bridged B ring (2,7-dioxabicyclo[2.2.1]-heptane). All the isolates were evaluated for thein vitroneuroprotective activity, both compounds 11 and 12 displayed moderate effects against H2O2-induced neurotoxicity in PC12 cells at the concentration of 10μM, with an increase in cell viability of 12.0% and 11.6%, respectively.
Origin of multi-level switching and telegraphic noise in organic nanocomposite memory devices
Authors: Song Younggul , Jeong Hyunhak , Chung Seungjun , Ahn Geun Ho , Kim Tae-Young , Jang Jingon , Yoo Daekyoung , Jeong Heejun , Javey Ali , Lee Takhee 
Published: September 2016

AbstractThe origin of negative differential resistance (NDR) and its derivative intermediate resistive states (IRSs) of nanocomposite memory systems have not been clearly analyzed for the past decade. To address this issue, we investigate the current fluctuations of organic nanocomposite memory devices with NDR and the IRSs under various temperature conditions. The 1/f noise scaling behaviors at various temperature conditions in the IRSs and telegraphic noise in NDR indicate the localized current pathways in the organic nanocomposite layers for each IRS. The clearly observed telegraphic noise with a long characteristic time in NDR at low temperature indicates that the localized current pathways for the IRSs are attributed to trapping/de-trapping at the deep trap levels in NDR. This study will be useful for the development and tuning of multi-bit storable organic nanocomposite memory device systems.
Expression of the aryl hydrocarbon receptor contributes to the establishment of intestinal microbial community structure in mice
Authors: Murray Iain A. , Nichols Robert G. , Zhang Limin , Patterson Andrew D. , Perdew Gary H. 
Published: September 2016

AbstractEnvironmental and genetic factors represent key components in the establishment/maintenance of the intestinal microbiota. The aryl hydrocarbon receptor (AHR) is emerging as a pleiotropic factor, modulating pathways beyond its established role as a xenobiotic sensor. The AHR is known to regulate immune surveillance within the intestine through retention of intraepithelial lymphocytes, functional redistribution of Th17/Treg balance. Consequently, environmental/genetic manipulation of AHR activity likely influences host-microbe homeostasis. Utilizing C57BL6/J Ahr−/+ and Ahr−/− co-housed littermates followed by 18 days of genotypic segregation, we examined the influence of AHR expression upon intestinal microbe composition/functionality and host physiology. 16S sequencing/quantitative PCR (qPCR) revealed significant changes in phyla abundance, particularly Verrucomicrobia together with segmented filamentous bacteria and an increase in species diversity in Ahr−/− mice following genotypic segregation. Metagenomics/metabolomics indicate microbial composition is associated with functional shifts in bacterial metabolism. Analysis identified Ahr−/−-dependent increases in ileal gene expression, indicating increased inflammatory tone. Transfer of Ahr−/− microbiota to wild-type germ-free mice recapitulated the increase Verrucomicrobia and inflammatory tone, indicating Ahr−/−-microbial dependence. These data suggest a role for the AHR in influencing the community structure of the intestinal microbiota.
Predicted structure of a Minus-C OBP from Batocera horsfieldi (Hope) suggests an intermediate structure in evolution of OBPs
Authors: Zheng Zhi-Chuan , Li Dong-Zhen , Zhou Aiming , Yi Shan-Cheng , Liu Hao , Wang Man-Qun 
Published: September 2016

AbstractOdorant binding proteins (OBPs) transport hydrophobic odorants from the environment to odorant receptors and play an important role in specific recognition of volatiles. Here, we expressed and purified a minus-C OBP, BhorOBPm2, fromBatocera horsfieldi, a major pest ofPopolus, to determine its binding characteristics with 58 candidate volatiles using a fluorescence competition-binding assay. We showed that BhorOBPm2 exhibited high binding affinity with chain volatiles and that ligands were selected based on chain length. In order to elucidate the binding mechanism, homology modeling and molecular-docking experiments were performed to investigate interactions between BhorOBPm2 and volatiles. The predicted structure with only two disulfide bonds showed one continuous channel for ligand binding, similar to classic OBPs AgamOBP1 and CquiOBP1. Unexpectedly, we observed a larger binding pocket for BhorOBPm2 and broader specificity for ligands than classic OBPs due to the expansive flexibility of BhorOBPm2 resulting from a lack of disulfide bonds. These findings suggested that BhorOBPm2 might present an intermediate structure in the evolution of OBPs. Furthermore, we designed two mutant proteins to simulate and verify functions of the C-terminal region. The changes in binding affinity observed here indicated a novel action differing from that of the “lid” described in previous studies.
N-doped graphene layers encapsulated NiFe alloy nanoparticles derived from MOFs with superior electrochemical performance for oxygen evolution reaction
Authors: Feng Yi , Yu Xin-Yao , Paik Ungyu 
Published: September 2016

AbstractWater splitting, an efficient approach for hydrogen production, is often hindered by unfavorable kinetics of oxygen evolution reaction (OER). In order to reduce the overpotential, noble metal oxides-based electrocatalysts like RuO2 and IrO2 are usually utilized. However, due to their scarcity, the development of cost-effective non-precious OER electrocatalysts with high efficiency and good stability is urgently required. Herein, we report a facile one-step annealing of metal-organic frameworks (MOFs) strategy to synthesize N-doped graphene layers encapsulated NiFe alloy nanoparticles (NiFe@C). Through tuning the nanoparticle size and calcination temperature, NiFe@C with an average size of around 16 nm obtained at 700 °C exhibits superior OER performance with an overpotential of only 281 mV at 10 mA cm−2 and high durability. The facile synthesis method and excellent electrochemical performance show great potential of NiFe@C in replacing the precious metal-based electrocatalysts in the OER.
Key clinical beam parameters for nanoparticle-mediated radiation dose amplification
Authors: Detappe Alexandre , Kunjachan Sijumon , Drané Pascal , Kotb Shady , Myronakis Marios , Biancur Douglas E. , Ireland Thomas , Wagar Matthew , Lux Francois , Tillement Olivier , Berbeco Ross 
Published: September 2016

AbstractAs nanoparticle solutions move towards human clinical trials in radiation therapy, the influence of key clinical beam parameters on therapeutic efficacy must be considered. In this study, we have investigated the clinical radiation therapy delivery variables that may significantly affect nanoparticle-mediated radiation dose amplification. We found a benefit for situations which increased the proportion of low energy photons in the incident beam. Most notably, “unflattened” photon beams from a clinical linear accelerator results in improved outcomes relative to conventional “flat” beams. This is measured by significant DNA damage, tumor growth suppression, and overall improvement in survival in a pancreatic tumor model. These results, obtained in a clinical setting, clearly demonstrate the influence and importance of radiation therapy parameters that will impact clinical radiation dose amplification with nanoparticles.
The UPR inducer DPP23 inhibits the metastatic potential of MDA-MB-231 human breast cancer cells by targeting the Akt–IKK–NF-κB–MMP-9 axis
Authors: Shin Soon Young , Kim Chang Gun , Jung You Jung , Lim Yoongho , Lee Young Han 
Published: September 2016

Abstract(E)-3-(3,5-dimethoxyphenyl)-1-(2-methoxyphenyl)prop-2-en-1-one (DPP23) is a synthetic polyphenol derivative that selectively induces apoptosis in cancer cells through the unfolded protein response pathway. In the present study, we evaluated the effect of DPP23 on tumour invasion and metastasis. Here, we show that DPP23 inhibited tumour necrosis factor alpha (TNFα)-induced motility, F-actin formation, and the invasive capability of MDA-MB-231 cells. DPP23 inhibited NF-κB-dependent MMP-9 expression at the transcriptional level. Akt is involved in the activation of IKK, an upstream regulator of NF-κB. DPP23 inhibited IKK and Akt, and knockdown of Akt2 significantly inhibited TNFα-induced IKK phosphorylation. We found that DPP23 bound to the catalytic domain of Akt2, as revealed by an in silico molecular docking analysis. These results suggest that DPP23 prevents TNFα-induced invasion of highly metastatic MDA-MB-231 breast cancer cells by inhibiting Akt–IKK–NF-κB axis-mediated MMP-9 gene expression. In addition, DPP23 attenuated experimental liver metastasis in a syngenic intrasplenic transplantation model using 4T1 mouse mammary carcinoma cells. Collectively, these results suggest that DPP23 could be used as a potential platform for the prevention of invasion and metastasis of early-stage breast cancer or as an adjuvant for chemo/radiotherapy.
CIBZ Regulates Mesodermal and Cardiac Differentiation of by Suppressing T and Mesp1 Expression in Mouse Embryonic Stem Cells
Authors: Kotoku Tomomi , Kosaka Koji , Nishio Miki , Ishida Yasumasa , Kawaichi Masashi , Matsuda Eishou 
Published: September 2016

AbstractThe molecular mechanisms underlying mesodermal and cardiac specification from embryonic stem cells (ESCs) are not fully understood. Here, we showed that the BTB domain-containing zinc finger protein CIBZ is expressed in mouse ESCs but is dramatically downregulated during ESC differentiation. CIBZ deletion in ESCs induced specification toward mesoderm phenotypes and their differentiation into cardiomyocytes, whereas overexpression of CIBZ delayed these processes. During ESC differentiation, CIBZ loss-and-gain-of-function data indicate that CIBZ negatively regulates the expressions of Brachyury (T) and Mesp1, the key transcriptional factors responsible for the specification of mammalian mesoderm and cardiac progenitors, respectively. Chromatin immunoprecipitation assays showed that CIBZ binds to T and Mesp1 promoters in undifferentiated ESCs and luciferase assays indicate that CIBZ suppresses T and Mesp1 promoters. These findings demonstrate that CIBZ is a novel regulator of mesodermal and cardiac differentiation of ESCs and suggest that CIBZ-mediated cardiac differentiation depends on the regulation of these two genes.
Low accumulation of chlorogenic acids represses reddening during flesh browning in Japanese peach “Okayama PEH7”
Authors: Yokotani Naoki , Uraji Misugi , Hara Miyuki , Hihara Seisuke , Hatanaka Tadashi , Oda Kenji 
Published: September 2016

Abstract
In peaches, fruit flesh browns unattractively after peeling or cutting. A recently developed cultivar, Okayama PEH7, was distinct from other Japanese cultivars, including Okayama PEH8, with respect to its reduced browning potential. Homogenate prepared from Okayama PEH7 flesh had significantly less reddening during the browning reaction. Okayama PEH7 had less soluble phenolic compounds and higher polyphenol oxidase activity than Okayama PEH8. Reduced browning was observed even when phenols prepared from Okayama PEH7 were incubated with crude extract from Okayama PEH8, suggesting that phenols lower the browning potential of Okayama PEH7. In Okayama PEH7, contents of chlorogenic acid and its isomers were about one-tenth compared to Okayama PEH8. Exogenous addition of chlorogenic acid to Okayama PEH7 homogenate increased the browning potential and visibly enhanced reddening. These results indicate that the reduced browning of Okayama PEH7 flesh is due to a defect in chlorogenic acid accumulation.
TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes
Authors: Minkin Ilia , Pham Son , Medvedev Paul 
Published: September 2016

Abstract

Motivation
de Bruijn graphs have been proposed as a data structure to facilitate the analysis of related whole genome sequences, in both a population and comparative genomic settings. However, current approaches do not scale well to many genomes of large size (such as mammalian genomes).

Results
In this article, we present TwoPaCo, a simple and scalable low memory algorithm for the direct construction of the compacted de Bruijn graph from a set of complete genomes. We demonstrate that it can construct the graph for 100 simulated human genomes in less than a day and eight real primates in &lt; 2 h, on a typical shared-memory machine. We believe that this progress will enable novel biological analyses of hundreds of mammalian-sized genomes.

Availability and Implementation
Our code and data is available for download from github.com/medvedevgroup/TwoPaCo.

Supplementary information
Supplementary data are available at Bioinformatics online.