bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmentally friendly method to grow wide-bandgap semiconductor aluminum nitride crystals: Elementary source vapor phase epitaxy
Authors: Wu PeiTsen , Funato Mitsuru , Kawakami Yoichi 
Published: November 2015

AbstractAluminum nitride (AlN) has attracted increasing interest as an optoelectronic material in the deep ultraviolet spectral range due to its wide bandgap of 6.0 eV (207 nm wavelength) at room temperature. Because AlN bulk single crystals are ideal device substrates for such applications, the crystal growth of bulky AlN has been extensively studied. Two growth methods seem especially promising: hydride vapor phase epitaxy (HVPE) and sublimation. However, the former requires hazardous gases such as hydrochloric acid and ammonia, while the latter needs extremely high growth temperatures around 2000 °C. Herein we propose a novel vapor-phase-epitaxy-based growth method for AlN that does not use toxic materials; the source precursors are elementary aluminum and nitrogen gas. To prepare our AlN, we constructed a new growth apparatus, which realizes growth of AlN single crystals at a rate of ~18 μm/h at 1550 °C using argon as the source transfer via the simple reaction Al + 1/2N2 → AlN. This growth rate is comparable to that by HVPE and the growth temperature is much lower than that in sublimation. Thus, this study opens up a novel route to achieve environmentally friendly growth of AlN.
Therapeutic effect of baicalin on experimental autoimmune encephalomyelitis is mediated by SOCS3 regulatory pathway
Authors: Zhang Yuan , Li Xing , Ciric Bogoljub , Ma Cun-Gen , Gran Bruno , Rostami Abdolmohamad , Zhang Guang-Xian 
Published: November 2015

AbstractNatural compounds derived from medicinal plants have long been considered a rich source of novel therapeutic agents. Baicalin (Ba) is a bioactive flavonoid compound derived from the root of Scutellaria baicalensis, an herb widely used in traditional medicine for the treatment of various inflammatory diseases. In this study, we investigate the effects and mechanism of action of Ba in experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS). Ba treatment effectively ameliorated clinical disease severity in myelin oligodendrocyte glycoprotein (MOG)35–55 peptide-induced EAE and reduced inflammation and demyelination of the central nervous system (CNS). Ba reduced infiltration of immune cells into the CNS, inhibited expression of proinflammatory molecules and chemokines and prevented Th1 and Th17 cell differentiation via STAT/NFκB signaling pathways. Further, we showed that SOCS3 induction is essential to the effects of Ba, given that the inhibitory effect of Ba on pathogenic Th17 responses was largely abolished when SOCS3 signaling was knocked down. Taken together, our findings demonstrate that Ba has significant potential as a novel anti-inflammatory agent for therapy of autoimmune diseases such as MS.
Transcriptome analysis of human OXR1 depleted cells reveals its role in regulating the p53 signaling pathway
Authors: Yang Mingyi , Lin Xiaolin , Rowe Alexander , Rognes Torbjørn , Eide Lars , Bjørås Magnar 
Published: November 2015

AbstractThe oxidation resistance gene 1 (OXR1) is crucial for protecting against oxidative stress; however, its molecular function is unknown. We employed RNA sequencing to examine the role of human OXR1 for genome wide transcription regulation. In total, in non-treated and hydrogen peroxide exposed HeLa cells, OXR1 depletion resulted in down-regulation of 554 genes and up-regulation of 253 genes. These differentially expressed genes include transcription factors (i.e. HIF1A, SP6, E2F8 and TCF3), antioxidant genes (PRDX4, PTGS1 and CYGB) and numerous genes of the p53 signaling pathway involved in cell-cycle arrest (i.e. cyclin D, CDK6 and RPRM) and apoptosis (i.e. CytC and CASP9). We demonstrated that OXR1 depleted cells undergo cell cycle arrest in G2/M phase during oxidative stress and increase protein expression of the apoptosis initiator protease CASP9. In summary, OXR1 may act as a sensor of cellular oxidative stress to regulate the transcriptional networks required to detoxify reactive oxygen species and modulate cell cycle and apoptosis.
Compact Optical Fiber 3D Shape Sensor Based on a Pair of Orthogonal Tilted Fiber Bragg Gratings
Authors: Feng Dingyi , Zhou Wenjun , Qiao Xueguang , Albert Jacques 
Published: November 2015

AbstractIn this work, a compact fiber-optic 3D shape sensor consisting of two serially connected 2° tilted fiber Bragg gratings (TFBGs) is proposed, where the orientations of the grating planes of the two TFBGs are orthogonal. The measurement of the reflective transmission spectrum from the pair of TFBGs was implemented by Fresnel reflection of the cleaved fiber end. The two groups of cladding mode resonances in the reflection spectrum respond differentially to bending, which allows for the unique determination of the magnitude and orientation of the bend plane (i.e. with a ± 180 degree uncertainty). Bending responses ranging from −0.33 to + 0.21 dB/m−1 (depending on orientation) are experimentally demonstrated with bending from 0 to 3.03 m−1. In the third (axial) direction, the strain is obtained directly by the shift of the TFBG Bragg wavelengths with a sensitivity of 1.06 pm/με.
Observed deep energetic eddies by seamount wake
Authors: Chen Gengxin , Wang Dongxiao , Dong Changming , Zu Tingting , Xue Huijie , Shu Yeqiang , Chu Xiaoqing , Qi Yiquan , Chen Hui 
Published: November 2015

AbstractDespite numerous surface eddies are observed in the ocean, deep eddies (a type of eddies which have no footprints at the sea surface) are much less reported in the literature due to the scarcity of their observation. In this letter, from recently collected current and temperature data by mooring arrays, a deep energetic and baroclinic eddy is detected in the northwestern South China Sea (SCS) with its intensity, size, polarity and structure being characterized. It remarkably deepens isotherm at deep layers by the amplitude of ~120 m and induces a maximal velocity amplitude about 0.18 m/s, which is far larger than the median velocity (0.02 m/s). The deep eddy is generated in a wake when a steering flow in the upper layer passes a seamount, induced by a surface cyclonic eddy. More observations suggest that the deep eddy should not be an episode in the area. Deep eddies significantly increase the velocity intensity and enhance the mixing in the deep ocean, also have potential implication for deep-sea sediments transport.
Drug target prioritization by perturbed gene expression and network information
Authors: Isik Zerrin , Baldow Christoph , Cannistraci Carlo Vittorio , Schroeder Michael 
Published: November 2015

AbstractDrugs bind to their target proteins, which interact with downstream effectors and ultimately perturb the transcriptome of a cancer cell. These perturbations reveal information about their source, i.e., drugs’ targets. Here, we investigate whether these perturbations and protein interaction networks can uncover drug targets and key pathways. We performed the first systematic analysis of over 500 drugs from the Connectivity Map. First, we show that the gene expression of drug targets is usually not significantly affected by the drug perturbation. Hence, expression changes after drug treatment on their own are not sufficient to identify drug targets. However, ranking of candidate drug targets by network topological measures prioritizes the targets. We introduce a novel measure, local radiality, which combines perturbed genes and functional interaction network information. The new measure outperforms other methods in target prioritization and proposes cancer-specific pathways from drugs to affected genes for the first time. Local radiality identifies more diverse targets with fewer neighbors and possibly less side effects.
Migratory Restlessness and the Role of Androgen for Increasing Behavioral Drive in the Spawning Migration of the Japanese eel
Authors: Sudo Ryusuke , Tsukamoto Katsumi 
Published: November 2015

AbstractMigratory restlessness refers to a type of locomotor activity observed just before the onset of a migration. This behavior is primarily known in birds, where it is considered to be an indicator of the urge for migration. In contrast, little is known about migratory restlessness in fishes. To confirm migratory restlessness in a fish, we measured the locomotor activity of the Japanese eel, Anguilla japonica during its migration season. Migratory-phase silver eels showed higher locomotor activity in aquaria than yellow eels at the non-migratiory growth-phase. Silver eels stayed outside of their shelters for longer durations in dark periods than yellow eels and were active even in light periods when yellow eels were inactive in the shelters. Silver eels had higher levels of the androgen hormone 11-ketotestosterone at the end of experiment than yellow eels. Administration of 11-ketotesosterone to yellow eels induced higher levels of locomotor activity than that observed in non-treated controls. These findings suggest that anguillid eels exhibit migratory restlessness just before their spawning migration and that 11-ketotestosterone may be involved in the onset of this behavior.
In situ fabrication of high-performance Ni-GDC-nanocube core-shell anode for low-temperature solid-oxide fuel cells
Authors: Yamamoto Kazuhiro , Qiu Nan , Ohara Satoshi 
Published: November 2015

AbstractA core–shell anode consisting of nickel–gadolinium-doped-ceria (Ni–GDC) nanocubes was directly fabricated by a chemical process in a solution containing a nickel source and GDC nanocubes covered with highly reactive {001} facets. The cermet anode effectively generated a Ni metal framework even at 500 °C with the growth of the Ni spheres. Anode fabrication at such a low temperature without any sintering could insert a finely nanostructured layer close to the interface between the electrolyte and the anode. The maximum power density of the attractive anode was 97 mW cm–2, which is higher than that of a conventional NiO–GDC anode prepared by an aerosol process at 55 mW cm–2 and 600 °C, followed by sintering at 1300 °C. Furthermore, the macro- and microstructure of the Ni–GDC-nanocube anode were preserved before and after the power-generation test at 700 °C. Especially, the reactive {001} facets were stabled even after generation test, which served to reduce the activation energy for fuel oxidation successfully.
Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response
Authors: Khraiwesh Basel , Qudeimat Enas , Thimma Manjula , Chaiboonchoe Amphun , Jijakli Kenan , Alzahmi Amnah , Arnoux Marc , Salehi-Ashtiani Kourosh 
Published: November 2015

AbstractChanges in the environment, such as those caused by climate change, can exert stress on plant growth, diversity and ultimately global food security. Thus, focused efforts to fully understand plant response to stress are urgently needed in order to develop strategies to cope with the effects of climate change. Because Physcomitrella patens holds a key evolutionary position bridging the gap between green algae and higher plants and because it exhibits a well-developed stress tolerance, it is an excellent model for such exploration. Here, we have used Physcomitrella patens to study genome-wide responses to abiotic stress through transcriptomic analysis by a high-throughput sequencing platform. We report a comprehensive analysis of transcriptome dynamics, defining profiles of elicited gene regulation responses to abiotic stress-associated hormone Abscisic Acid (ABA), cold, drought and salt treatments. We identified more than 20,000 genes expressed under each aforementioned stress treatments, of which 9,668 display differential expression in response to stress. The comparison of Physcomitrella patens stress regulated genes with unicellular algae, vascular and flowering plants revealed genomic delineation concomitant with the evolutionary movement to land, including a general gene family complexity and loss of genes associated with different functional groups.
The fish diversity in the upper reaches of the Salween River, Nujiang River, revealed by DNA barcoding
Authors: Chen Weitao , Ma Xiuhui , Shen Yanjun , Mao Yuntao , He Shunping 
Published: November 2015

AbstractNujiang River (NR), an essential component of the biodiversity hotspot of the Mountains of Southwest China, possesses a characteristic fish fauna and contains endemic species. Although previous studies on fish diversity in the NR have primarily consisted of listings of the fish species observed during field collections, in our study, we DNA-barcoded 1139 specimens belonging to 46 morphologically distinct fish species distributed throughout the NR basin by employing multiple analytical approaches. According to our analyses, DNA barcoding is an efficient method for the identification of fish by the presence of barcode gaps. However, three invasive species are characterized by deep conspecific divergences, generating multiple lineages and Operational Taxonomic Units (OTUs), implying the possibility of cryptic species. At the other end of the spectrum, ten species (from three genera) that are characterized by an overlap between their intra- and interspecific genetic distances form a single genetic cluster and share haplotypes. The neighbor-joining phenogram, Barcode Index Numbers (BINs) and Automatic Barcode Gap Discovery (ABGD) identified 43 putative species, while the General Mixed Yule-coalescence (GMYC) identified five more OTUs. Thus, our study established a reliable DNA barcode reference library for the fish in the NR and sheds new light on the local fish diversity.
Acute and additive toxicity of ten photosystem-II herbicides to seagrass
Authors: Wilkinson Adam D. , Collier Catherine J. , Flores Florita , Negri Andrew P. 
Published: November 2015

AbstractPhotosystem II herbicides are transported to inshore marine waters, including those of the Great Barrier Reef and are usually detected in complex mixtures. These herbicides inhibit photosynthesis, which can deplete energy reserves and reduce growth in seagrass, but the toxicity of some of these herbicides to seagrass is unknown and combined effects of multiple herbicides on seagrass has not been tested. Here we assessed the acute phytotoxicity of 10 PSII herbicides to the seagrass Halophila ovalis over 24 and/or 48 h. Individual herbicides exhibited a broad range of toxicities with inhibition of photosynthetic activity (∆F/Fm′) by 50% at concentrations ranging from 3.5 μg l−1 (ametryn) to 132 μg l−1 (fluometuron). We assessed potential additivity using the Concentration Addition model of joint action for binary mixtures of diuron and atrazine as well as complex mixtures of all 10 herbicides. The effects of both mixture types were largely additive, validating the application of additive effects models for calculating the risk posed by multiple PSII herbicides to seagrasses. This study extends seagrass ecotoxicological data to ametryn, metribuzin, bromacil, prometryn and fluometuron and demonstrates that low concentrations of PSII herbicide mixtures have the potential to impact ecologically relevant endpoints in seagrass, including ∆F/Fm′.
Sample storage-induced changes in the quantity and quality of soil labile organic carbon
Authors: Sun Shou-Qin , Cai Hui-Ying , Chang Scott X. , Bhatti Jagtar S. 
Published: November 2015

AbstractEffects of sample storage methods on the quantity and quality of labile soil organic carbon are not fully understood even though their effects on basic soil properties have been extensively studied. We studied the effects of air-drying and frozen storage on cold and hot water soluble organic carbon (WSOC). Cold- and hot-WSOC in air-dried and frozen-stored soils were linearly correlated with those in fresh soils, indicating that storage proportionally altered the extractability of soil organic carbon. Air-drying but not frozen storage increased the concentrations of cold-WSOC and carbohydrate in cold-WSOC, while both increased polyphenol concentrations. In contrast, only polyphenol concentration in hot-WSOC was increased by air-drying and frozen storage, suggesting that hot-WSOC was less affected by sample storage. The biodegradability of cold- but not hot-WSOC was increased by air-drying, while both air-drying and frozen storage increased humification index and changed specific UV absorbance of both cold- and hot-WSOC, indicating shifts in the quality of soil WSOC. Our results suggest that storage methods affect the quantity and quality of WSOC but not comparisons between samples, frozen storage is better than air-drying if samples have to be stored and storage should be avoided whenever possible when studying the quantity and quality of both cold- and hot-WSOC.
Pivotal Role of the Chromatin Protein Nupr1 in Kras-Induced Senescence and Transformation
Authors: Grasso Daniel , Bintz Jennifer , Lomberk Gwen , Molejon Maria Ines , Loncle Celine , Garcia Maria Noé , Lopez Maria Belen , Urrutia Raul , Iovanna Juan L. 
Published: November 2015

AbstractNupr1 is a chromatin protein, which cooperates with KrasG12D to induce PanIN formation and pancreatic cancer development in mice, though the molecular mechanisms underlying this effect remain to be fully characterized. In the current study, we report that Nupr1 acts as a gene modifier of the effect of KrasG12D-induced senescence by regulating Dnmt1 expression and consequently genome-wide levels of DNA methylation. Congruently, 5-aza-2′-deoxycytydine, a general inhibitor of DNA methylation, reverses the KrasG12D-induced PanIN development by promoting senescence. This requirement of Nupr1 expression, however, is not restricted to the pancreas since in lung of Nupr1–/– mice the expression of KrasG12D induces senescence instead of transformation. Therefore, mechanistically this data reveals that epigenetic events, at least at the level of DNA methylation, modulate the functional outcome of common genetic mutations, such as KrasG12D, during carcinogenesis. The biomedical relevance of these findings lies in that they support the rational for developing similar therapeutic interventions in human aimed at controlling either the initiation or progression of cancer.
Inhibition of insulin fibrillation by osmolytes: Mechanistic Insights
Authors: Choudhary Sinjan , Kishore Nand , Hosur Ramakrishna V. 
Published: November 2015

AbstractWe have studied here using a number of biophysical tools the effects of osmolytes, betaine, citrulline, proline and sorbitol which differ significantly in terms of their physical characteristics such as, charge distribution, polarity, H-bonding abilities etc, on the fibrillation of insulin. Among these, betaine, citrulline and proline are very effective in decreasing the extent of fibrillation. Proline also causes a substantial delay in the onset of fibrillation in the concentration range (50–250 mM) whereas such an effect is seen for citrulline only at 250 mM and in case of betaine this effect is not seen at all in the whole concentration range. The enthalpies of interaction at various stages of fibrillation process have suggested that the preferential exclusion of the osmolyte and its polar interaction with the protein are important in inhibition. The results indicate that the osmolytes are most effective when added prior to the elongation stage of fibrillation. These observations have significant biological implications, since insulin fibrillation is known to cause injection amyloidosis and our data may help in designing lead drug molecules and development of potential therapeutic strategies.
Quantitative Profiling of the Effects of Vanoxerine on Human Cardiac Ion Channels and its Application to Cardiac Risk
Authors: Obejero-Paz Carlos A. , Bruening-Wright Andrew , Kramer James , Hawryluk Peter , Tatalovic Milos , Dittrich Howard C. , Brown Arthur M. 
Published: November 2015

AbstractVanoxerine has been in clinical trials for Parkinsonism, depression and cocaine addiction but lacked efficacy. Although a potent blocker of hERG, it produced no serious adverse events. We attributed the unexpected result to offsetting Multiple Ion Channel Effects (MICE). Vanoxerine’s effects were strongly frequency-dependent and we repositioned it for treatment of atrial fibrillation and flutter. Vanoxerine terminated AF/AFL in an animal model and a dose-ranging clinical trial. Reversion to normal rhythm was associated with QT prolongation yet absent proarrhythmia markers for Torsade de Pointes (TdP). To understand the QT/TdP discordance, we used quantitative profiling and compared vanoxerine with dofetilide, a selective hERG-blocking torsadogen used for intractable AF, verapamil, a non-torsadogenic MICE comparator and bepridil, a torsadogenic MICE comparator. At clinically relevant concentrations, verapamil blocked hCav1.2 and hERG, as did vanoxerine and bepridil both of which also blocked hNav1.5. In acute experiments and simulations, dofetilide produced early after depolarizations (EADs) and arrhythmias, whereas verapamil, vanoxerine and bepridil produced no proarrhythmia markers. Of the MICE drugs only bepridil inhibited hERG trafficking following overnight exposure. The results are consistent with the emphasis on MICE of the CiPA assay. Additionally we propose that trafficking inhibition of hERG be added to CiPA.
FPGA implementation of a high‐speed, real‐time, windowed standard deviation filter
Authors: Herbert J. , Wilson S. , Rakic A.D. , Taimre T. 
Published: November 2015

Characterisation of the standard deviation of a time‐series signal has uncommon, yet widespread applications. The usual requirement for a representation of signal standard deviation in real‐time implies a high computation speed. A method based on a field programmable gate array (FPGA) implementation is presented. The technique is benchmarked against conventional computational approaches and shows a single windowed standard deviation update calculation of a 16 bit sample can be achieved in 11 ns on a modern CPU. The FPGA implementation is found to be superior to all other approaches examined with an operation time of below 10 ns, and thus provides a useful tool for the real‐time measurement of the standard deviation of signals above 100 MHz.
Characterization of a new Lactobacillus salivarius strain engineered to express IBV multi-epitope antigens by chromosomal integration
Authors: Ma Bing-cun , Yang Xin , Wang Hong-ning , Cao Hai-peng , Xu Peng-wei , Ding Meng-die , Liu Hui 
Published: November 2015

Abstract
To obtain adhesive and safe lactic acid bacteria (LAB) strains for expressing heterologous antigens, we screened LAB inhabitants in intestine of Tibetan chickens by analyzing their adhesion and safety properties and the selected LAB was engineered to express heterologous antigen (UTEpi C-A) based on chromosomal integration strategy. We demonstrated that a new Lactobacillu salivarius TCMM17 strain is strongly adhesive to chicken intestinal epithelial cells, contains no endogenous plasmids, is susceptible to tested antimicrobials, and shows no toxicities. In order to examine the potential of TCMM17 strain as heterogenous antigen delivering vehicle, we introduced a UTEpi C-A expression cassette in its chromosome by constructing a non-replicative plasmid (pORI280-UUTEpi C-AD). The recombinant TCMM17 strain (∆TCMM17) stably was found to keep the gene cassette through 50 generations, and successfully displayed EpiC encoded by the cassette on its surface. This work provides a universal platform for development of novel oral vaccines and expression of further antigens of avian pathogens.