bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian-based deconvolution fluorescence microscopy using dynamically updated nonstationary expectation estimates
Authors: Wong Alexander , Wang Xiao Yu , Gorbet Maud 
Published: June 2015

AbstractFluorescence microscopy is widely used for the study of biological specimens. Deconvolution can significantly improve the resolution and contrast of images produced using fluorescence microscopy; in particular, Bayesian-based methods have become very popular in deconvolution fluorescence microscopy. An ongoing challenge with Bayesian-based methods is in dealing with the presence of noise in low SNR imaging conditions. In this study, we present a Bayesian-based method for performing deconvolution using dynamically updated nonstationary expectation estimates that can improve the fluorescence microscopy image quality in the presence of noise, without explicit use of spatial regularization.
Contrasting environmental drivers of adult and juvenile growth in a marine fish: implications for the effects of climate change
Authors: Ong Joyce Jia Lin , Nicholas Rountrey Adam , Jane Meeuwig Jessica , John Newman Stephen , Zinke Jens , Gregory Meekan Mark 
Published: June 2015

AbstractMany marine fishes have life history strategies that involve ontogenetic changes in the use of coastal habitats. Such ontogenetic shifts may place these species at particular risk from climate change, because the successive environments they inhabit can differ in the type, frequency and severity of changes related to global warming. We used a dendrochronology approach to examine the physical and biological drivers of growth of adult and juvenile mangrove jack (Lutjanus argentimaculatus) from tropical north-western Australia. Juveniles of this species inhabit estuarine environments and adults reside on coastal reefs. The Niño-4 index, a measure of the status of the El Niño-Southern Oscillation (ENSO) had the highest correlation with adult growth chronologies, with La Niña years (characterised by warmer temperatures and lower salinities) having positive impacts on growth. Atmospheric and oceanographic phenomena operating at ocean-basin scales seem to be important correlates of the processes driving growth in local coastal habitats. Conversely, terrestrial factors influencing precipitation and river runoff were positively correlated with the growth of juveniles in estuaries. Our results show that the impacts of climate change on these two life history stages are likely to be different, with implications for resilience and management of populations.
Analysis of the human diseasome using phenotype similarity between common, genetic and infectious diseases
Authors: Hoehndorf Robert , Schofield Paul N. , Gkoutos Georgios V. 
Published: June 2015

AbstractPhenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are signs and symptoms of human Mendelian diseases in databases such as OMIM and Orphanet. Exploiting these resources, several computational methods have been developed for integration and analysis of phenotype data to identify the genetic etiology of diseases or suggest plausible interventions. A similar resource would be highly useful not only for rare and Mendelian diseases, but also for common, complex and infectious diseases. We apply a semantic text-mining approach to identify the phenotypes (signs and symptoms) associated with over 6,000 diseases. We evaluate our text-mined phenotypes by demonstrating that they can correctly identify known disease-associated genes in mice and humans with high accuracy. Using a phenotypic similarity measure, we generate a human disease network in which diseases that have similar signs and symptoms cluster together and we use this network to identify closely related diseases based on common etiological, anatomical as well as physiological underpinnings.
Dietary proanthocyanidins modulate BMAL1 acetylation, Nampt expression and NAD levels in rat liver
Authors: Ribas-Latre Aleix , Baselga-Escudero Laura , Casanova Ester , Arola-Arnal Anna , Salvadó M-Josepa , Bladé Cinta , Arola Lluís 
Published: June 2015

AbstractMetabolism follows circadian rhythms, which are driven by peripheral clocks. Clock genes in the liver are entrained by daytime meals and food components. Proanthocyanidins (PAs), the most abundant flavonoids in the human diet, modulate lipid and glucose metabolism. The aim of this study was to determine whether PAs could adjust the clock system in the liver. Male Wistar rats were orally gavaged with 250 mg grape seed proanthocyanidin extract (GSPE)/kg body weight at zeitgeber time (ZT) 0 (light turned on), at ZT12 (light turned off), or before a 6 hour jet-lag and sacrificed at different times. The 24 hour rhythm of clock-core and clock-controlled gene expression indicated that nicotinamide phosphoribosyltransferase (Nampt) was the most sensitive gene to GSPE. However, Nampt was repressed or overexpressed after GSPE administration at ZT0 or ZT12, respectively. NAD levels, which are controlled by Nampt and also exhibit circadian rhythm, decreased or increased according to Nampt expression. Moreover, the ratio of acetylated Bmal1, that directly drives Nampt expression, only increased when GSPE was administered at ZT12. Therefore, GSPE modulated the clock system in the liver, suggesting that PAs can regulate lipid and glucose metabolism by adjusting the circadian rhythm in the liver.
Large increase in fracture resistance of stishovite with crack extension less than one micrometer
Authors: Yoshida Kimiko , Wakai Fumihiro , Nishiyama Norimasa , Sekine Risako , Shinoda Yutaka , Akatsu Takashi , Nagoshi Takashi , Sone Masato 
Published: June 2015

AbstractThe development of strong, tough and damage-tolerant ceramics requires nano/microstructure design to utilize toughening mechanisms operating at different length scales. The toughening mechanisms so far known are effective in micro-scale, then, they require the crack extension of more than a few micrometers to increase the fracture resistance. Here, we developed a micro-mechanical test method using micro-cantilever beam specimens to determine the very early part of resistance-curve of nanocrystalline SiO2 stishovite, which exhibited fracture-induced amorphization. We revealed that this novel toughening mechanism was effective even at length scale of nanometer due to narrow transformation zone width of a few tens of nanometers and large dilatational strain (from 60 to 95%) associated with the transition of crystal to amorphous state. This testing method will be a powerful tool to search for toughening mechanisms that may operate at nanoscale for attaining both reliability and strength of structural materials.
Moisture-responsive films of cellulose stearoyl esters showing reversible shape transitions
Authors: Zhang Kai , Geissler Andreas , Standhardt Michaela , Mehlhase Sabrina , Gallei Markus , Chen Longquan , Marie Thiele Christina 
Published: June 2015

AbstractMoisture-responsive materials are gaining greater interest for their potentially wide applications and the readily access to moisture. In this study, we show the fabrication of moisture-responsive, self-standing films using sustainable cellulose as starting material. Cellulose was modified by stearoyl moieties at first, leading to cellulose stearoyl esters (CSEs) with diverse degrees of substitution (DSs). The films of CSE with a low DS of 0.3 (CSE0.3) exhibited moisture-responsive properties, while CSEs with higher DSs of 1.3 or 3 (CSE1.3 and CSE3) not. The CSE0.3 films could reversibly fold and unfold as rhythmical bending motions within a local moisture gradient due to the ab- and desorption of water molecules at the film surface. By spray-coating CSE3 nanoparticles (NPs) onto CSE0.3 films, moisture-responsive films with non-wetting surface were obtained, which can perform quick reversible bending movements and continuous shape transition on water. Furthermore, bilayer films containing one layer of CSE0.3 at one side and one layer of CSE3 at the other side exhibited combined responsiveness to moisture and temperature. By varying the thickness of CSE0.3 films, the minimal bending extent can be adjusted due to altered mechanical resistances, which allows a bending movement preferentially beginning with the thinner side.
Attolitre-sized lipid bilayer chamber array for rapid detection of single transporters
Authors: Soga Naoki , Watanabe Rikiya , Noji Hiroyuki 
Published: June 2015

AbstractWe present an attolitre-sized arrayed lipid bilayer chamber system (aL-ALBiC) for rapid and massively parallel single-molecule assay of membrane transporter activity. Because of the small reaction volume (200 aL), the aL-ALBiC performed fast detection of single transporter activity, thereby enhancing the sensitivity, throughput and accuracy of the analysis. Thus, aL-ALBiC broadens the opportunities for single-molecule analysis of various membrane transporters and can be used in pharmaceutical applications such as drug screening.
A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Glucometers
Authors: Du Yan , Hughes Randall A. , Bhadra Sanchita , Jiang Yu Sherry , Ellington Andrew D. , Li Bingling 
Published: June 2015

AbstractStrand exchange nucleic acid circuitry can be used to transduce isothermal nucleic acid amplification products into signals that can be readable on an off-the-shelf glucometer. Loop-mediated isothermal amplification (LAMP) is limited by the accumulation of non-specific products, but nucleic acid circuitry can be used to probe and distinguish specific amplicons. By combining this high temperature isothermal amplification method with a thermostable invertase, we can directly transduce Middle-East respiratory syndrome coronavirus and Zaire Ebolavirus templates into glucose signals, with a sensitivity as low as 20–100 copies/μl, equating to atto-molar (or low zepto-mole). Virus from cell lysates and synthetic templates could be readily amplified and detected even in sputum or saliva. An OR gate that coordinately triggered on viral amplicons further guaranteed fail-safe virus detection. The method describes has potential for accelerating point-of-care applications, in that biological samples could be applied to a transducer that would then directly interface with an off-the-shelf, approved medical device.
An Effective Way to Optimize the Functionality of Graphene-Based Nanocomposite: Use of the Colloidal Mixture of Graphene and Inorganic Nanosheets
Authors: Jin Xiaoyan , Adpakpang Kanyaporn , Young Kim In , Mi Oh Seung , Lee Nam-Suk , Hwang Seong-Ju 
Published: June 2015

AbstractThe best electrode performance of metal oxide–graphene nanocomposite material for lithium secondary batteries can be achieved by using the colloidal mixture of layered CoO2 and graphene nanosheets as a precursor. The intervention of layered CoO2 nanosheets in-between graphene nanosheets is fairly effective in optimizing the pore and composite structures of the Co3O4–graphene nanocomposite and also in enhancing its electrochemical activity via the depression of interaction between graphene nanosheets. The resulting CoO2 nanosheet-incorporated nanocomposites show much greater discharge capacity of ~1750 mAhg−1 with better cyclability and rate characteristics than does CoO2-free Co3O4–graphene nanocomposite (~1100 mAhg−1). The huge discharge capacity of the present nanocomposite is the largest one among the reported data of cobalt oxide–graphene nanocomposite. Such a remarkable enhancement of electrode performance upon the addition of inorganic nanosheet is also observed for Mn3O4–graphene nanocomposite. The improvement of electrode performance upon the incorporation of inorganic nanosheet is attributable to an improved Li+ ion diffusion, an enhanced mixing between metal oxide and graphene and the prevention of electrode agglomeration. The present experimental findings underscore an efficient and universal role of the colloidal mixture of graphene and redoxable metal oxide nanosheets as a precursor for improving the electrode functionality of graphene-based nanocomposites.
Multifunctional glucose biosensors from Fe3O4 nanoparticles modified chitosan/graphene nanocomposites
Authors: Zhang Wenjing , Li Xiaojian , Zou Ruitao , Wu Huizi , Shi Haiyan , Yu Shanshan , Liu Yong 
Published: June 2015

AbstractNovel water-dispersible and biocompatible chitosan-functionalized graphene (CG) has been prepared by a one-step ball milling of carboxylic chitosan and graphite. Presence of nitrogen (from chitosan) at the surface of graphene enables the CG to be an outstanding catalyst for the electrochemical biosensors. The resulting CG shows lower ID/IG ratio in the Raman spectrum than other nitrogen-containing graphene prepared using different techniques. Magnetic Fe3O4 nanoparticles (MNP) are further introduced into the as-synthesized CG for multifunctional applications beyond biosensors such as magnetic resonance imaging (MRI). Carboxyl groups from CG is used to directly immobilize glucose oxidase (GOx) via covalent linkage while incorporation of MNP further facilitated enzyme loading and other unique properties. The resulting biosensor exhibits a good glucose detection response with a detection limit of 16 μM, a sensitivity of 5.658 mA/cm2/M and a linear detection range up to 26 mM glucose. Formation of the multifunctional MNP/CG nanocomposites provides additional advantages for applications in more clinical areas such as in vivo biosensors and MRI agents.
Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil
Authors: Banning Natasha C. , Maccarone Linda D. , Fisk Louise M. , Murphy Daniel V. 
Published: June 2015

AbstractAmmonia-oxidising archaea (AOA) and bacteria (AOB) are responsible for the rate limiting step in nitrification; a key nitrogen (N) loss pathway in agricultural systems. Dominance of AOA relative to AOB in the amoA gene pool has been reported in many ecosystems, although their relative contributions to nitrification activity are less clear. Here we examined the distribution of AOA and AOB with depth in semi-arid agricultural soils in which soil organic matter content or pH had been altered and related their distribution to gross nitrification rates. Soil depth had a significant effect on gene abundances, irrespective of management history. Contrary to reports of AOA dominance in soils elsewhere, AOA gene copy numbers were four-fold lower than AOB in the surface (0–10 cm). AOA gene abundance increased with depth while AOB decreased and sub-soil abundances were approximately equal (10–90 cm). The depth profile of total archaea did not mirror that of AOA, indicating the likely presence of archaea without nitrification capacity in the surface. Gross nitrification rates declined significantly with depth and were positively correlated to AOB but negatively correlated to AOA gene abundances. We conclude that AOB are most likely responsible for regulating nitrification in these semi-arid soils.
Novel PI3K/AKT targeting anti-angiogenic activities of 4-vinylphenol, a new therapeutic potential of a well-known styrene metabolite
Authors: Yue Grace Gar-Lee , Lee Julia Kin-Ming , Kwok Hin-Fai , Cheng Ling , Wong Eric Chun-Wai , Jiang Lei , Yu Hua , Leung Hoi-Wing , Wong Yuk-Lau , Leung Ping-Chung , Fung Kwok-Pui , Lau Clara Bik-San 
Published: June 2015

AbstractThe pneumo- and hepato-toxicity of 4-vinylphenol (4VP), a styrene metabolite, has been previously reported. Nevertheless, the present study reported the novel anti-angiogenic activities of 4VP which was firstly isolated from the aqueous extract of a Chinese medicinal herb Hedyotis diffusa. Our results showed that 4VP at non-toxic dose effectively suppressed migration, tube formation, adhesion to extracellular matrix proteins, as well as protein and mRNA expressions of metalloproteinase-2 of human endothelial cells (HUVEC and HMEC-1). Investigation of the signal transduction revealed that 4VP down-regulated PI3K/AKT and p38 MAPK. Besides, 4VP interfered with the phosphorylation of ERK1/2, the translocation and expression of NFkappaB. In zebrafish embryo model, the new blood vessel growth was significantly blocked by 4VP (6.25–12.5 μg/mL medium). The VEGF-induced blood vessel formation in Matrigel plugs in C57BL/6 mice was suppressed by 4VP (20–100 μg/mL matrigel). In addition, the blood vessel number and tumor size were reduced by intraperitoneal 4VP (0.2–2 mg/kg) in 4T1 breast tumor-bearing BALB/c mice, with doxorubicin as positive control. Together, the in vitro and in vivo anti-angiogenic activities of 4VP were demonstrated for the first time. These findings suggest that 4VP has great potential to be further developed as an anti-angiogenic agent.
Automated Detection of Vessel Abnormalities on Fluorescein Angiogram in Malarial Retinopathy
Authors: Zhao Yitian , MacCormick Ian J. C. , Parry David G. , Beare Nicholas A. V. , Harding Simon P. , Zheng Yalin 
Published: June 2015

AbstractThe detection and assessment of intravascular filling defects is important, because they may represent a process central to cerebral malaria pathogenesis: neurovascular sequestration. We have developed and validated a framework that can automatically detect intravascular filling defects in fluorescein angiogram images. It first employs a state-of-the-art segmentation approach to extract the vessels from images and then divide them into individual segments by geometrical analysis. A feature vector based on the intensity and shape of saliency maps is generated to represent the level of abnormality of each vessel segment. An AdaBoost classifier with weighted cost coefficient is trained to classify the vessel segments into normal and abnormal categories. To demonstrate its effectiveness, we apply this framework to 6,358 vessel segments in images from 10 patients with malarial retinopathy. The test sensitivity, specificity, accuracy and area under curve (AUC) are 74.7%, 73.5%, 74.1% and 74.2% respectively when compared to the reference standard of human expert manual annotations. This performance is comparable to the agreement that we find between human observers of intravascular filling defects. Our method will be a powerful new tool for studying malarial retinopathy.
Investigation on Spin Dependent Transport Properties of Core-Shell Structural Fe3O4/ZnS Nanocomposites for Spintronic Application
Authors: Liu Er , Yuan Honglei , Kou Zhaoxia , Wu Xiumei , Xu Qingyu , Zhai Ya , Sui Yunxia , You Biao , Du Jun , Zhai Hongru 
Published: June 2015

AbstractThe core-shell structural Fe3O4/ZnS nanocomposites with controllable shell thickness were well-fabricated via seed-mediate growth method. Structural and morphological characterizations reveal the direct deposition of crystalline II-VI compound semiconductor ZnS shell layer on Fe3O4 particles. Spin dependent electrical transport is studied on Fe3O4/ZnS nanocomposites with different shell thickness and a large magnetoresistance (MR) ratio is observed under the magnetic field of 1.0 T at room temperature and 100 K for the compacted sample by Fe3O4/ZnS nanocomposites, which is 50% larger than that of sample with pure Fe3O4 particles, indicating that the enhanced MR is contributed from the spin injection between Fe3O4 and ZnS layer.
11-GHz waveguide Nd:YAG laser CW mode-locked with single-layer graphene
Authors: Okhrimchuk Andrey G. , Obraztsov Petr A. 
Published: June 2015

AbstractWe report stable, passive, continuous-wave (CW) mode-locking of a compact diode-pumped waveguide Nd:YAG laser with a single-layer graphene saturable absorber. The depressed cladding waveguide in the Nd:YAG crystal is fabricated with an ultrafast laser inscription method. The saturable absorber is formed by direct deposition of CVD single-layer graphene on the output coupler. The few millimeter-long cavity provides generation of 16-ps pulses with repetition rates in the GHz range (up to 11.3 GHz) and 12 mW average power. Stable CW mode-locking operation is achieved by controlling the group delay dispersion in the laser cavity with a Gires–Tournois interferometer.
The actions of neurotensin in rat bladder detrusor contractility
Authors: Dong Xingyou , Bai Xinyu , Zhao Jiang , Wang Liang , Wang Qingqing , Li Longkun 
Published: June 2015

AbstractThis study assessed the expression, distribution and function of neurotensin (NTs) and two main neurotensin receptors (NTSR), NTSR1 and NTSR2 in normal rat urinary bladders. NTs is primarily located in the suburothelium and the interstitium of smooth muscle bundles. The NTSR1 and NTSR2 receptor subtypes are found to co-localize with smooth muscle cells (SMCs). NTs not only can directly act on bladder SMCs to induce intracellular calcium mobilization by activating the phospholipase C/inositol triphosphate (PLC/IP3) pathway, promoting extracellular calcium influx through a non-selective cation channels, but may be also involved in the modulation of the cholinergic system. Nowadays, the selective antimuscarinic drugs (solifenacin) and the selective beta 3-adrenergic agonist (mirabegron) are used as the first-line pharmacotherapy for overactive bladder (OAB), but without satisfactory treatment benefits in some patients. This study provided evidence suggesting that bladder NTs may play an important role in the regulation of micturition. Further research is needed to investigate the effects of NTs on bladder contractility and the underlying mechanism, which might reveal that the administration of NTSR antagonists can potentially relieve the symptoms of OAB by coordination with antimuscarinic pharmacotherapy.
Rapamycin protects against gentamicin-induced acute kidney injury via autophagy in mini-pig models
Authors: Cui Jing , Bai Xue-Yuan , Sun Xuefeng , Cai Guangyan , Hong Quan , Ding Rui , Chen Xiangmei 
Published: June 2015

AbstractGentamicin may cause acute kidney injury. The pathogenesis of gentamicin nephrotoxicity is unclear. Autophagy is a highly conserved physiological process involved in removing damaged or aged biological macromolecules and organelles from the cytoplasm. The role of autophagy in the pathogenesis of gentamicin nephrotoxicity is unclear. The miniature pigs are more similar to humans than are those of rodents and thus they are more suitable as human disease models. Here we established the first gentamicin nephrotoxicity model in miniature pigs, investigated the role of autophagy in gentamicin-induced acute kidney injury and determined the prevention potential of rapamycin against gentamicin-induced oxidative stress and renal dysfunction. At 0, 1, 3, 5, 7 and 10 days after gentamicin administration, changes in autophagy, oxidative damage, apoptosis and inflammation were assessed in the model group. Compared to the 0-day group, gentamicin administration caused marked nephrotoxicity in the 10-day group. In the kidneys of the 10-day group, the level of autophagy decreased and oxidative damage and apoptosis were aggravated. After rapamycin intervention, autophagy activity was activated, renal damage in proximal tubules was markedly alleviated and interstitium infiltration of inflammatory cells was decreased. These results suggest that rapamycin may ameliorate gentamicin-induced nephrotoxicity by enhancing autophagy.