bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the impact of PSC inspectors’ professional profile: a case study of the Spanish Maritime Administration
Authors: Ravira Francisco J. , Piniella Francisco 
Published: January 2016

Abstract
Full-scale globalisation of trade has been accompanied by a progressive liberalisation of maritime transport. The proliferation of open registries has created a situation in which Port State Control (PSC) has become much more effective than the feeble or non-existent control exercised by those States. This study has been conducted on the influence of the professional profile of inspectors on inspection results. The objective of our paper was to evaluate the impact of PSC inspectors’ professional profile by conducting a case study of the Spanish Maritime Administration. The paper concludes with a discussion of the correlation between deficiencies detected and professional profiles.
The effects of using axial magnetic field in extreme ultraviolet photon sources for nanolithography – recent integrated simulation
Authors: Sizyuk V. , Hassanein A. 
Published: January 2016

AbstractWe developed a comprehensive model for simulating laser/target interaction in the presence of external axial magnetic fields. The model was integrated into the framework of the HEIGHTS-LPP computer simulation package and benchmarked with recent experimental results. The package was then used to study the angular distribution of extreme ultraviolet (EUV) photon output in plasmas produced in tin planar targets by a Nd:YAG laser. A moderate (0.5 T) permanent magnetic field does not affect EUV source evolution and output. More effective control of plasma plume expansion should be based on magnetic field gradients, that is, on the temporary varying magnetic fields as a magnetic pinch. Analysis of angular EUV output showed strong anisotropy of photon emissions. We found that the correct monitoring angle (i.e., at which the measured EUV flux corresponds to the averaged value after the correctly integrated angular distribution) does not depend on laser irradiance in the studied range and is equivalent to ~60°. We recommend arranging the EUV sensors accordingly in experiments with planar tin targets.
BAP1/ASXL1 recruitment and activation for H2A deubiquitination
Authors: Sahtoe Danny D. , van Dijk Willem J. , Ekkebus Reggy , Ovaa Huib , Sixma Titia K. 
Published: January 2016

AbstractThe deubiquitinating enzyme BAP1 is an important tumor suppressor that has drawn attention in the clinic since its loss leads to a variety of cancers. BAP1 is activated by ASXL1 to deubiquitinate mono-ubiquitinated H2A at K119 in Polycomb gene repression, but the mechanism of this reaction remains poorly defined. Here we show that the BAP1 C-terminal extension is important for H2A deubiquitination by auto-recruiting BAP1 to nucleosomes in a process that does not require the nucleosome acidic patch. This initial encounter-like complex is unproductive and needs to be activated by the DEUBAD domains of ASXL1, ASXL2 or ASXL3 to increase BAP1’s affinity for ubiquitin on H2A, to drive the deubiquitination reaction. The reaction is specific for Polycomb modifications of H2A as the complex cannot deubiquitinate the DNA damage-dependent ubiquitination at H2A K13/15. Our results contribute to the molecular understanding of this important tumor suppressor.
Exosomes as nanocarriers for systemic delivery of the Helicobacter pylori virulence factor CagA
Authors: Shimoda Asako , Ueda Koji , Nishiumi Shin , Murata-Kamiya Naoko , Mukai Sada-atsu , Sawada Shin-ichi , Azuma Takeshi , Hatakeyama Masanori , Akiyoshi Kazunari 
Published: January 2016

AbstractCagA, encoded by cytotoxin-associated gene A (cagA), is a major virulence factor of Helicobacter pylori, a gastric pathogen involved in the development of upper gastrointestinal diseases. Infection with cagA-positive H. pylori may also be associated with diseases outside the stomach, although the mechanisms through which H. pylori infection promotes extragastric diseases remain unknown. Here, we report that CagA is present in serum-derived extracellular vesicles, known as exosomes, in patients infected with cagA-positive H. pylori (n = 4). We also found that gastric epithelial cells inducibly expressing CagA secrete exosomes containing CagA. Addition of purified CagA-containing exosomes to gastric epithelial cells induced an elongated cell shape, indicating that the exosomes deliver functional CagA into cells. These findings indicated that exosomes secreted from CagA-expressing gastric epithelial cells may enter into circulation, delivering CagA to distant organs and tissues. Thus, CagA-containing exosomes may be involved in the development of extragastric disorders associated with cagA-positive H. pylori infection.
Functional inhibition of urea transporter UT-B enhances endothelial-dependent vasodilatation and lowers blood pressure via L-arginine-endothelial nitric oxide synthase-nitric oxide pathway
Authors: Sun Yi , Lau Chi-Wai , Jia Yingli , Li Yingjie , Wang Weiling , Ran Jianhua , Li Fei , Huang Yu , Zhou Hong , Yang Baoxue 
Published: January 2016

AbstractMammalian urea transporters (UTs), UT-A and UT-B, are best known for their role in urine concentration. UT-B is especially distributed in multiple extrarenal tissues with abundant expression in vascular endothelium, but little is known about its role in vascular function. The present study investigated the physiological significance of UT-B in regulating vasorelaxations and blood pressure. UT-B deletion in mice or treatment with UT-B inhibitor PU-14 in Wistar-Kyoto rats (WKYs) and spontaneous hypertensive rats (SHRs) reduced blood pressure. Acetylcholine-induced vasorelaxation was significantly augmented in aortas from UT-B null mice. PU-14 concentration-dependently produced endothelium-dependent relaxations in thoracic aortas and mesenteric arteries from both mice and rats and the relaxations were abolished by Nω-nitro-L-arginine methyl ester. Both expression and phosphorylation of endothelial nitric oxide synthase (eNOS) were up-regulated and expression of arginase I was down-regulated when UT-B was inhibited both in vivo and in vitro. PU-14 induced endothelium-dependent relaxations to a similar degree in aortas from 12 weeks old SHRs or WKYs. In summary, here we report for the first time that inhibition of UT-B plays an important role in regulating vasorelaxations and blood pressure via up-regulation of L-arginine-eNOS-NO pathway and it may become another potential therapeutic target for the treatment of hypertension.
Coral mucus fuels the sponge loop in warm- and cold-water coral reef ecosystems
Authors: Rix Laura , de Goeij Jasper M. , Mueller Christina E. , Struck Ulrich , Middelburg Jack J. , van Duyl Fleur C. , Al-Horani Fuad A. , Wild Christian , Naumann Malik S. , van Oevelen Dick 
Published: January 2016

AbstractShallow warm-water and deep-sea cold-water corals engineer the coral reef framework and fertilize reef communities by releasing coral mucus, a source of reef dissolved organic matter (DOM). By transforming DOM into particulate detritus, sponges play a key role in transferring the energy and nutrients in DOM to higher trophic levels on Caribbean reefs via the so-called sponge loop. Coral mucus may be a major DOM source for the sponge loop, but mucus uptake by sponges has not been demonstrated. Here we used laboratory stable isotope tracer experiments to show the transfer of coral mucus into the bulk tissue and phospholipid fatty acids of the warm-water sponge Mycale fistulifera and cold-water sponge Hymedesmia coriacea, demonstrating a direct trophic link between corals and reef sponges. Furthermore, 21–40% of the mucus carbon and 32–39% of the nitrogen assimilated by the sponges was subsequently released as detritus, confirming a sponge loop on Red Sea warm-water and north Atlantic cold-water coral reefs. The presence of a sponge loop in two vastly different reef environments suggests it is a ubiquitous feature of reef ecosystems contributing to the high biogeochemical cycling that may enable coral reefs to thrive in nutrient-limited (warm-water) and energy-limited (cold-water) environments.
Comparative transcriptome analysis reveals insights into the streamlined genomes of haplosclerid demosponges
Authors: Guzman Christine , Conaco Cecilia 
Published: January 2016

AbstractSponges (Porifera) are one of the most ancestral metazoan groups. They are characterized by a simple body plan lacking the true tissues and organ systems found in other animals. Members of this phylum display a remarkable diversity of form and function and yet little is known about the composition and complexity of their genomes. In this study, we sequenced the transcriptomes of two marine haplosclerid sponges belonging to Demospongiae, the largest and most diverse class within phylum Porifera and compared their gene content with members of other sponge classes. We recovered 44,693 and 50,067 transcripts expressed in adult tissues of Haliclona amboinensis and Haliclona tubifera, respectively. These transcripts translate into 20,280 peptides in H. amboinensis and 18,000 peptides in H. tubifera. Genes associated with important signaling and metabolic pathways, regulatory networks, as well as genes that may be important in the organismal stress response, were identified in the transcriptomes. Futhermore, lineage-specific innovations were identified that may be correlated with observed sponge characters and ecological adaptations. The core gene complement expressed within the tissues of adult haplosclerid demosponges may represent a streamlined and flexible genetic toolkit that underlies the ecological success and resilience of sponges to environmental stress.
The nature of Ordovician limestone-marl alternations in the Oslo-Asker District (Norway): witnesses of primary glacio-eustasy or diagenetic rhythms?
Authors: Amberg Chloé E. A. , Collart Tim , Salenbien Wout , Egger Lisa M. , Munnecke Axel , Nielsen Arne T. , Monnet Claude , Hammer Øyvind , Vandenbroucke Thijs R. A. 
Published: January 2016

AbstractOrdovician limestone-marl alternations in the Oslo-Asker District have been interpreted as signaling glacio-eustatic lowstands, which would support a prolonged “Early Palaeozoic Icehouse”. However, these rhythmites could alternatively reflect differential diagenesis, without sedimentary trigger. Here, we test both hypotheses through one Darriwilian and three Katian sections. Our methodology consists of a bed-by-bed analysis of palynological (chitinozoan) and geochemical (XRF) data, to evaluate whether the limestone/marl couplets reflect an original cyclic signal. The results reveal similar palynomorph assemblages in limestones and marls. Exceptions, which could be interpreted as reflecting palaeoclimatological fluctuations, exist at the species level:Ancyrochitina bornholmensisseems to be more abundant in the marl samples from the lower Frognerkilen Formation on Nakkholmen Island. However, these rare cases where chitinozoans differ between limestone/marl facies are deemed insufficient for the identification of original cyclicity. The geochemical data show a near-perfect correlation between insoluble elements in the limestone and the marls, which indicates a similar composition of the potential precursor sediment, also in the Frognerkilen Formation. This is consistent with the palynological data. Although an original cyclic pattern could still be recorded by other, uninvestigated parameters, our palaeontological and geochemical data combined do not support the presence of such a signal.
High Electron Mobility in Epitaxial Trilayer Graphene on Off-axis SiC(0001)
Authors: Hajlaoui Mahdi , Sediri Haikel , Pierucci Debora , Henck Hugo , Phuphachong Thanyanan , Silly Mathieu G. , de Vaulchier Louis-Anne , Sirotti Fausto , Guldner Yves , Belkhou Rachid , Ouerghi Abdelkarim 
Published: January 2016

AbstractThe van de Waals heterostructure formed by an epitaxial trilayer graphene is of particular interest due to its unique tunable electronic band structure and stacking sequence. However, to date, there has been a lack in the fundamental understanding of the electronic properties of epitaxial trilayer graphene. Here, we investigate the electronic properties of large-area epitaxial trilayer graphene on a 4° off-axis SiC(0001) substrate. Micro-Raman mappings and atomic force microscopy (AFM) confirmed predominantly trilayer on the sample obtained under optimized conditions. We used angle-resolved photoemission spectroscopy (ARPES) and Density Functional Theory (DFT) calculations to study in detail the structure of valence electronic states, in particular the dispersion of π bands in reciprocal space and the exact determination of the number of graphene layers. Using far-infrared magneto-transmission (FIR-MT), we demonstrate, that the electron cyclotron resonance (CR) occurs between Landau levels with a (B)1/2 dependence. The CR line-width is consistent with a high Dirac fermions mobility of ~3000 cm2·V−1·s−1 at 4 K.
MicroRNAs in Honey Bee Caste Determination
Authors: Ashby Regan , Forêt Sylvain , Searle Iain , Maleszka Ryszard 
Published: January 2016

AbstractThe cellular mechanisms employed by some organisms to produce contrasting morphological and reproductive phenotypes from the same genome remains one of the key unresolved issues in biology. Honeybees (Apis mellifera) use differential feeding and a haplodiploid sex determination system to generate three distinct organismal outcomes from the same genome. Here we investigate the honeybee female and male caste-specific microRNA and transcriptomic molecular signatures during a critical time of larval development. Both previously undetected and novel miRNAs have been discovered, expanding the inventory of these genomic regulators in invertebrates. We show significant differences in the microRNA and transcriptional profiles of diploid females relative to haploid drone males as well as between reproductively distinct females (queens and workers). Queens and drones show gene enrichment in physio-metabolic pathways, whereas workers show enrichment in processes associated with neuronal development, cell signalling and caste biased structural differences. Interestingly, predicted miRNA targets are primarily associated with non-physio-metabolic genes, especially neuronal targets, suggesting a mechanistic disjunction from DNA methylation that regulates physio-metabolic processes. Accordingly, miRNA targets are under-represented in methylated genes. Our data show how a common set of genetic elements are differentially harnessed by an organism, which may provide the remarkable level of developmental flexibility required.
HIV-1 gp120 induces type-1 programmed cell death through ER stress employing IRE1α, JNK and AP-1 pathway
Authors: Shah Ankit , Vaidya Naveen K. , Bhat Hari K. , Kumar Anil 
Published: January 2016

AbstractThe ER stress-mediated apoptosis has been implicated in several neurodegenerative diseases; however, its role in HIV/neuroAIDS remains largely unexplored. The present study was undertaken to assess the involvement and detailed mechanism of IRE1α pathway in HIV-1 gp120-mediated ER stress and its possible involvement in cell death. Various signaling molecules for IRE1α pathway were assessed using SVGA cells, primary astrocytes and gp120 transgenic mice, which demonstrated gp120-mediated increase in phosphorylated JNK, XBP-1 and AP-1 leading to upregulation of CHOP. Furthermore, HIV-1 gp120-mediated activation of IRE1α also increased XBP-1 splicing. The functional consequence of gp120-mediated ER stress was determined via assessment of gp120-mediated cell death using PI staining and MTT assay. The gp120-mediated cell death also involved caspase-9/caspase-3-mediated apoptosis. These findings were confirmed with the help of specific siRNA for IRE1α, JNK, AP-1, BiP and CHOP showing significant reduction in gp120-mediated CHOP expression. Additionally, silencing all the intermediates also reduced the gp120-mediated cell death and caspase-9/caspase-3 activation at differential levels. This study provides ER-stress as a novel therapeutic target in the management of gp120-mediated cell death and possibly in the treatment of neuroAIDS.
Chi and dLMO function antagonistically on Notch signaling through directly regulation of fng transcription
Authors: Han Hui , Fan Jialin , Xiong Yue , Wu Wenqing , Lu Yi , Zhang Lei , Zhao Yun 
Published: January 2016

AbstractGene apterous (ap), chip (chi) and beadex (bx) play important roles in the dorsal-ventral compartmentalization in Drosophila wing discs. Meanwhile, Notch signaling is essential to the same process. It has been reported that Ap and Chi function as a tetramer to regulate Notch signaling. At the same time, dLMO (the protein product of gene bx) regulates the activity of Ap by competing its binding with Chi. However, the detailed functions of Chi and dLMO on Notch signaling and the relevant mechanisms remain largely unknown. Here, we report the detailed functions of Chi and dLMO on Notch signaling. Different Chi protein levels in adjacent cells could activate Notch signaling mainly in the cells with higher level of Chi. dLMO could induce antagonistical phenotypes on Notch signaling compared to that induced by Chi. These processes depend on their direct regulation of fringe (fng) transcription.
Molecular hydrogen regulates gene expression by modifying the free radical chain reaction-dependent generation of oxidized phospholipid mediators
Authors: Iuchi Katsuya , Imoto Akemi , Kamimura Naomi , Nishimaki Kiyomi , Ichimiya Harumi , Yokota Takashi , Ohta Shigeo 
Published: January 2016

AbstractWe previously showed that H2 acts as a novel antioxidant to protect cells against oxidative stress. Subsequently, numerous studies have indicated the potential applications of H2 in therapeutic and preventive medicine. Moreover, H2 regulates various signal transduction pathways and the expression of many genes. However, the primary targets of H2 in the signal transduction pathways are unknown. Here, we attempted to determine how H2 regulates gene expression. In a pure chemical system, H2 gas (approximately 1%, v/v) suppressed the autoxidation of linoleic acid that proceeds by a free radical chain reaction and pure 1-palmitoyl-2-arachidonyl-sn-glycero-3-phosphocholine (PAPC), one of the major phospholipids, was autoxidized in the presence or absence of H2. H2 modified the chemical production of the autoxidized phospholipid species in the cell-free system. Exposure of cultured cells to the H2-dependently autoxidized phospholipid species reduced Ca2+ signal transduction and mediated the expression of various genes as revealed by comprehensive microarray analysis. In the cultured cells, H2 suppressed free radical chain reaction-dependent peroxidation and recovered the increased cellular Ca2+, resulting in the regulation of Ca2+-dependent gene expression. Thus, H2 might regulate gene expression via the Ca2+ signal transduction pathway by modifying the free radical-dependent generation of oxidized phospholipid mediators.
High-frequency chaotic dynamics enabled by optical phase-conjugation
Authors: Mercier Émeric , Wolfersberger Delphine , Sciamanna Marc 
Published: January 2016

AbstractWideband chaos is of interest for applications such as random number generation or encrypted communications, which typically use optical feedback in a semiconductor laser. Here, we show that replacing conventional optical feedback with phase-conjugate feedback improves the chaos bandwidth. In the range of achievable phase-conjugate mirror reflectivities, the bandwidth increase reaches 27% when compared with feedback from a conventional mirror. Experimental measurements of the time-resolved frequency dynamics on nanosecond time-scales show that the bandwidth enhancement is related to the onset of self-pulsing solutions at harmonics of the external-cavity frequency. In the observed regime, the system follows a chaotic itinerancy among these destabilized high-frequency external-cavity modes. The recorded features are unique to phase-conjugate feedback and distinguish it from the long-standing problem of time-delayed feedback dynamics.
Insights on FXR selective modulation. Speculation on bile acid chemical space in the discovery of potent and selective agonists
Authors: Sepe Valentina , Festa Carmen , Renga Barbara , Carino Adriana , Cipriani Sabrina , Finamore Claudia , Masullo Dario , del Gaudio Federica , Monti Maria Chiara , Fiorucci Stefano , Zampella Angela 
Published: January 2016

AbstractBile acids are the endogenous modulators of the nuclear receptor FXR and the membrane receptor GPBAR1. FXR represents a promising pharmacological target for the treatment of cholestatic liver disorders. Currently available semisynthetic bile acid derivatives cover the same chemical space of bile acids and therefore they are poorly selective toward BA receptors, increasing patient risk for adverse side effects. In this report, we have investigated around the structure of CDCA describing the synthesis and the in vitro and in vivo pharmacological characterization of a novel family of compounds modified on the steroidal tetracyclic core and on the side chain. Pharmacological characterization resulted in the identification of several potent and selective FXR agonists. These novel agents might add utility in the treatment of cholestatic disorders by potentially mitigating side effects linked to unwanted activation of GPBAR1.
Reptile Toll-like receptor 5 unveils adaptive evolution of bacterial flagellin recognition
Authors: Voogdt Carlos G. P. , Bouwman Lieneke I. , Kik Marja J. L. , Wagenaar Jaap A. , van Putten Jos P. M. 
Published: January 2016

AbstractToll-like receptors (TLR) are ancient innate immune receptors crucial for immune homeostasis and protection against infection. TLRs are present in mammals, birds, amphibians and fish but have not been functionally characterized in reptiles despite the central position of this animal class in vertebrate evolution. Here we report the cloning, characterization and function of TLR5 of the reptile Anolis carolinensis (Green Anole lizard). The receptor (acTLR5) displays the typical TLR protein architecture with 22 extracellular leucine rich repeats flanked by a N- and C-terminal leucine rich repeat domain, a membrane-spanning region and an intracellular TIR domain. The receptor is phylogenetically most similar to TLR5 of birds and most distant to fish TLR5. Transcript analysis revealed acTLR5 expression in multiple lizard tissues. Stimulation of acTLR5 with TLR ligands demonstrated unique responsiveness towards bacterial flagellin in both reptile and human cells. Comparison of acTLR5 and human TLR5 using purified flagellins revealed differential sensitivity to Pseudomonas but not Salmonella flagellin, indicating development of species-specific flagellin recognition during the divergent evolution of mammals and reptiles. Our discovery of reptile TLR5 fills the evolutionary gap regarding TLR conservation across vertebrates and provides novel insights in functional evolution of host-microbe interactions.
Fabrication of 45 nm high In component metamorphic In0.7Ga0.3As/In0.6Ga0.4As composite‐channel high electron‐mobility transistors on GaAs substrates
Authors: Kang Weihua , Zhang Xiaodong , Ji Xian , Cai Yong , Zhou Jiahui , Xu Wenjun , Li Qi , Xiao Gongli , Zhang Baoshun , Li Haiou 
Published: January 2016

A 45 nm high In component metamorphic In0.7Ga0.3As/In0.6Ga0.4As composite‐channel high electron‐mobility transistor (mHEMT) on GaAs substrate with good DC and RF performance has been developed. The structure was grown by molecular beam epitaxy and exhibits a superior electron mobility of 10200 cm2/(V.s) and a sheet density of 3.5 × 1012 cm−2 at a room temperature. A combined optical and e‐beam lithography technology was used to achieve the nanometre mHEMT device. The mHEMT device shows an extrinsic transconductance of up to 990 mS/mm and a maximum current density of 910 mA/mm. The unity current gain cutoff frequency fT and the maximum oscillation frequency fmax are 187.94 and 258.62 GHz, respectively. These performances make the device well suited for millimetre‐wave applications.