bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased expression of NAF1 contributes to malignant phenotypes of glioma cells through promoting protein synthesis and associates with poor patient survival
Authors: Wei Jing , Yang Qi , Shi Jing , Shi Bingyin , Ji Meiju , Hou Peng 
Published: April 2019

AbstractThe H/ACA ribonucleoprotein (RNP) complex noncore subunit NAF1 is an indispensable factor during H/ACA RNP maturation, and one of the widely known functions of H/ACA RNP is modulating ribosome biosynthesis. However, the specific biological role and exact mechanism of NAF1 in human cancers including glioma remain largely unclear. In this study, we found that NAF1 was highly expressed in gliomas relative to normal brain tissues, and demonstrated that increased expression of NAF1 was strongly correlated with poor patient survival. Further studies revealed that NAF1 was transcriptionally regulated by c-Myc, NRF2, and telomerase reverse transcriptase (TERT), which are the key molecules associated with malignant progression of gliomas. Moreover, we demonstrated that NAF1 was a functional oncogene in glioma cells through promoting cell growth in vitro and in vivo, survival, migration, and invasion. Mechanistically, NAF1 acted as a rate-limiting controller of cell growth and invasiveness through enhancing 40S subunit assembly and protein synthesis including c-Myc, NRF2, TERT, POLR1A, and POLR2A. These molecules in turn enhanced the transcription and translation of NAF1, thereby forming positive feedback loops between them to promote malignant phenotypes of glioma cells. In addition, our data also showed that NAF1 depletion could trigger ribosome stress, not only impairing ribosomal biosynthesis but also reactivating p53 signaling via blocking MDM2. Taken together, we demonstrated that NAF1 promotes the tumorigenesis and progression of glioma through modulating ribosome assembly and protein synthesis, and predicted that NAF1 may be a potential therapeutic target and valuable prognostic biomarker in gliomas.
Structural basis for the recognition of K48-linked Ub chain by proteasomal receptor Rpn13
Authors: Liu Zhu , Dong Xu , Yi Hua-Wei , Yang Ju , Gong Zhou , Wang Yi , Liu Kan , Zhang Wei-Ping , Tang Chun 
Published: April 2019

AbstractThe interaction between K48-linked ubiquitin (Ub) chain and Rpn13 is important for proteasomal degradation of ubiquitinated substrate proteins. Only the complex structure between the N-terminal domain of Rpn13 (Rpn13NTD) and Ub monomer has been characterized, while it remains unclear how Rpn13 specifically recognizes K48-linked Ub chain. Using single-molecule FRET, here we show that K48-linked diubiquitin (K48-diUb) fluctuates among distinct conformational states, and a preexisting compact state is selectively enriched by Rpn13NTD. The same binding mode is observed for full-length Rpn13 and longer K48-linked Ub chain. Using solution NMR spectroscopy, we have determined the complex structure between Rpn13NTD and K48-diUb. In this structure, Rpn13NTD simultaneously interacts with proximal and distal Ub subunits of K48-diUb that remain associated in the complex, thus corroborating smFRET findings. The proximal Ub interacts with Rpn13NTD similarly as the Ub monomer in the known Rpn13NTD:Ub structure, while the distal Ub binds to a largely electrostatic surface of Rpn13NTD. Thus, a charge-reversal mutation in Rpn13NTD weakens the interaction between Rpn13 and K48-linked Ub chain, causing accumulation of ubiquitinated proteins. Moreover, physical blockage of the access of the distal Ub to Rpn13NTD with a proximity-attached Ub monomer can disrupt the interaction between Rpn13 and K48-diUb. Taken together, the bivalent interaction of K48-linked Ub chain with Rpn13 provides the structural basis for Rpn13 linkage selectivity, which opens a new window for modulating proteasomal function.
Lattice strain-enhanced exsolution of nanoparticles in thin films
Authors: Han Hyeon , Park Jucheol , Nam Sang Yeol , Kim Kun Joong , Choi Gyeong Man , Parkin Stuart S. P. , Jang Hyun Myung , Irvine John T. S. 
Published: April 2019

AbstractNanoparticles formed on oxide surfaces are of key importance in many fields such as catalysis and renewable energy. Here, we control B-site exsolution via lattice strain to achieve a high degree of exsolution of nanoparticles in perovskite thin films: more than 1100 particles μm−2 with a particle size as small as ~5 nm can be achieved via strain control. Compressive-strained films show a larger number of exsolved particles as compared with tensile-strained films. Moreover, the strain-enhanced in situ growth of nanoparticles offers high thermal stability and coking resistance, a low reduction temperature (550 °C), rapid release of particles, and wide tunability. The mechanism of lattice strain-enhanced exsolution is illuminated by thermodynamic and kinetic aspects, emphasizing the unique role of the misfit-strain relaxation energy. This study provides critical insights not only into the design of new forms of nanostructures but also to applications ranging from catalysis, energy conversion/storage, nano-composites, nano-magnetism, to nano-optics.
USP8 maintains embryonic stem cell stemness via deubiquitination of EPG5
Authors: Gu Haifeng , Shi Xingxing , Liu Chao , Wang Chaoqun , Sui Ning , Zhao Yu , Gong Jiaqi , Wang Fuping , Zhang Hong , Li Wei , Zhao Tongbiao 
Published: April 2019

AbstractEmbryonic stem cells (ESCs) can propagate in an undifferentiated state indefinitely in culture and retain the potential to differentiate into any somatic lineage as well as germ cells. The catabolic process autophagy has been reported to be involved in ESC identity regulation, but the underlying mechanism is still largely unknown. Here we show that EPG5, a eukaryotic-specific autophagy regulator which mediates autophagosome/lysosome fusion, is highly expressed in ESCs and contributes to ESC identity maintenance. We identify that the deubiquitinating enzyme USP8 binds to the Coiled-coil domain of EPG5. Mechanistically, USP8 directly removes non-classical K63-linked ubiquitin chains from EPG5 at Lysine 252, leading to enhanced interaction between EPG5 and LC3. We propose that deubiquitination of EPG5 by USP8 guards the autophagic flux in ESCs to maintain their stemness. This work uncovers a novel crosstalk pathway between ubiquitination and autophagy through USP8-EPG5 interaction to regulate the stemness of ESCs.
Multiple low-temperature skyrmionic states in a bulk chiral magnet
Authors: Bannenberg Lars J. , Wilhelm Heribert , Cubitt Robert , Labh Ankit , Schmidt Marcus P. , Lelièvre-Berna Eddy , Pappas Catherine , Mostovoy Maxim , Leonov Andrey O. 
Published: April 2019

AbstractMagnetic skyrmions are topologically protected nanoscale spin textures with particle-like properties. In bulk cubic helimagnets, they appear under applied magnetic fields and condense spontaneously into a lattice in a narrow region of the phase diagram just below the magnetic ordering temperature, the so-called A-phase. Theory, however, predicts skyrmions to be locally stable in a wide range of magnetic fields and temperatures. Our neutron diffraction measurements reveal the formation of skyrmion states in large areas of the magnetic phase diagram, from the lowest temperatures up to the A-phase. We show that nascent and disappearing spiral states near critical lines catalyze topological charge changing processes, leading to the formation and destruction of skyrmionic states at low temperatures, which are thermodynamically stable or metastable depending on the orientation and strength of the magnetic field. Skyrmions are surprisingly resilient to high magnetic fields: the memory of skyrmion lattice states persists in the field polarized state, even when the skyrmion lattice signal has disappeared. These findings highlight the paramount role of magnetic anisotropies in stabilizing skyrmionic states and open up new routes for manipulating these quasi-particles towards energy-efficient spintronics applications.
The survey and reference assisted assembly of the Octopus vulgaris genome
Authors: Zarrella Ilaria , Herten Koen , Maes Gregory E. , Tai Shuaishuai , Yang Ming , Seuntjens Eve , Ritschard Elena A. , Zach Michael , Styfhals Ruth , Sanges Remo , Simakov Oleg , Ponte Giovanna , Fiorito Graziano 
Published: April 2019

AbstractThe common octopus, Octopus vulgaris, is an active marine predator known for the richness and plasticity of its behavioral repertoire, and remarkable learning and memory capabilities. Octopus and other coleoid cephalopods, cuttlefish and squid, possess the largest nervous system among invertebrates, both for cell counts and body to brain size. O. vulgaris has been at the center of a long-tradition of research into diverse aspects of its biology. To leverage research in this iconic species, we generated 270 Gb of genomic sequencing data, complementing those available for the only other sequenced congeneric octopus, Octopus bimaculoides. We show that both genomes are similar in size, but display different levels of heterozygosity and repeats. Our data give a first quantitative glimpse into the rate of coding and non-coding regions and support the view that hundreds of novel genes may have arisen independently despite the close phylogenetic distance. We furthermore describe a reference-guided assembly and an open genomic resource (CephRes-gdatabase), opening new avenues in the study of genomic novelties in cephalopods and their biology.
Cyclone avoidance behaviour by foraging seabirds
Authors: Weimerskirch Henri , Prudor Aurélien 
Published: April 2019

AbstractIn the context of climate change, how extreme climatic events, such as cyclones, will affect the foraging abilities of marine vertebrates is still poorly known. During the course of a study on the foraging behaviour of two tropical seabirds, red-footed boobies and great frigatebirds, several cyclones have affected their breeding grounds and foraging zones, allowing us to study their response to extreme wind conditions. We examined whether adults and young naïve birds were able to predict the arrival of a cyclone and behave accordingly to reduce mortality risks and optimise foraging. We show that when a cyclone approached, juveniles and adults of the two species differed in their decisions to leave the colony for the sea. When the winds reached gale force, the juveniles of both species and adult frigatebirds remained at the colony, whereas adult boobies continued their foraging routine. The mortality of the individuals remaining on land remained limited. When encountering at-sea gale conditions, adult birds were able to avoid the centre of the low pressure systems and moved westward to bypass the route of the cyclones and circumvent the moving cyclone. Frigatebirds climb to high altitudes when close to the eye of the cyclone to bypass it at high speeds. These movements likely reduce the mortality risk at sea but can temporarily cause birds to move outside their normal range at sea or over land masses. We discuss the potential consequences of an increase in cyclonic conditions on seabird populations.
A decade of sustained selection pressure on two surface sites of the VP1 protein of Enterovirus A71 suggests that immune evasion may be an indirect driver for virulence
Authors: Roberts Ryan , Yee Pinn Tsin Isabel , Mujawar Shama , Lahiri Chandrajit , Poh Chit Laa , Gatherer Derek 
Published: April 2019

AbstractEnterovirus A71 (EV-A71) is an emerging pathogen in the Enterovirus A species group. EV-A71 causes hand, foot and mouth disease (HFMD), with virulent variants exhibiting polio-like acute flaccid paralysis and other central nervous system manifestations. We analysed all enterovirus A71 complete genomes with collection dates from 2008 to mid-2018. All sub-genotypes exhibit a strong molecular clock with omega (dN/dS) suggesting strong purifying selection. In sub-genotypes B5 and C4, positive selection can be detected at two surface sites on the VP1 protein, also detected in positive selection studies performed prior to 2008. Toggling of a limited repertoire of amino acids at these positively selected residues over the last decade suggests that EV-A71 may be undergoing a sustained frequency-dependent selection process for immune evasion, raising issues for vaccine development. These same sites have also been previously implicated in virus-host binding and strain-associated severity of HFMD, suggesting that immune evasion may be an indirect driver for virulence (154 words).
Effect of cell culture density on dental pulp-derived mesenchymal stem cells with reference to osteogenic differentiation
Authors: Noda Sonoko , Kawashima Nobuyuki , Yamamoto Mioko , Hashimoto Kentaro , Nara Keisuke , Sekiya Ichiro , Okiji Takashi 
Published: April 2019

AbstractDental pulp stem cells (DPSCs) are a good source for tissue regeneration, however, the number of DPSCs in the pulp tissue is limited. Cell propagation is essential for tissue engineering using DPSCs and the cell culture conditions may affect the properties of DPSCs. The purpose of this study was to analyze the effect of cell culture condition, especially dense culture condition, on the property and differentiation pathway of DPSCs. We cultured DPSCs under sparse (sDPSCs; 5 × 103 cells/cm2) or dense (dDPSCs; 1 × 105 cells/cm2) conditions for 4 days and compared their properties. The populations of CD73+ and CD105+ cells were significantly decreased in dDPSCs. Both groups showed multi-differentiation potential, but mineralized nodule formation was enhanced in dDPSCs. The phosphorylation of focal adhesion kinase (FAK) and phosphoinositide 3-kinase (PI3K) proteins was promoted in dDPSCs, and alkaline phosphatase (ALP) mRNA expression in dDPSCs was abolished in the presence of pan-PI3K and FAK inhibitors. dDPSCs implanted into mouse bone cavities induced more mineralized tissue formation than sDPSCs and control. These findings indicate that dense culture conditions modified the properties of DPSCs and gave rise to osteogenic-lineage commitment via integrin signaling and suggest that dense culture conditions favor the propagation of DPSCs to be used for mineralized tissue regeneration.
Modeling the Effects of Morphine-Altered Virus Specific Antibody Responses on HIV/SIV Dynamics
Authors: Mutua Jones M. , Perelson Alan S. , Kumar Anil , Vaidya Naveen K. 
Published: April 2019

AbstractDrugs of abuse, such as opiates, have been widely associated with enhancing HIV replication, accelerating disease progression and diminishing host-immune responses, thereby making it harder to effectively manage HIV infection. It is thus important to study the effects of drugs of abuse on HIV-infection and immune responses. Here, we develop mathematical models that incorporate the effects of morphine-altered antibody responses on HIV/SIV dynamics. Based on fitting the model to experimental data from simian immunodeficiency virus (SIV) infections in control and morphine-addicted macaques, we found that two of the most significant effects of virus specific antibodies are neutralizing viral particles and enhancing viral clearance. Using our model, we quantified how morphine alters virus-specific antibody responses, and how this alteration affects the key components of virus dynamics such as infection rate, virus clearance, viral load, CD4+T cell count, and CD4+T cell loss in SIV-infected macaques under conditioning with morphine. We found that in a subpopulation of SIV-infected morphine addicted macaques, the presence of drugs of abuse may cause significantly diminished antibody responses, resulting in more severe infection with increased SIV infectivity, a decreased viral clearance rate, increased viral load, and higher CD4+T cell loss.
Theory for spin torque in Weyl semimetal with magnetic texture
Authors: Kurebayashi Daichi , Nomura Kentaro 
Published: April 2019

AbstractThe spin-transfer torque is a fundamental physical quantity to operate the spintronics devices such as racetrack memory. We theoretically study the spin-transfer torque and analyze the dynamics of the magnetic domain walls in magnetic Weyl semimetals. Owing to the strong spin-orbit coupling in Weyl semimetals, the spin-transfer torque can be significantly enhanced, because of which they can provide a more efficient means of controlling magnetic textures. We derive the analytical expression of the spin-transfer torque and find that the velocity of the domain wall is one order of magnitude greater than that of conventional ferromagnetic metals. Furthermore, due to the suppression of longitudinal conductivity in the thin domain-wall configuration, the dissipation due to Joule heating for the spin-transfer torque becomes much smaller than that in bulk metallic ferromagnets. Consequently, the fast-control of the domain wall can be achieved with smaller dissipation from Joule heating in the Weyl semimetals as required for application to low-energy-consumption spintronics devices.
Reproductive interference in live-bearing fish: the male guppy is a potential biological agent for eradicating invasive mosquitofish
Authors: Tsurui-Sato K. , Fujimoto S. , Deki O. , Suzuki T. , Tatsuta H. , Tsuji K. 
Published: April 2019

AbstractThe eradication of invasive exotic species is desirable but often infeasible. Here, we show that male guppies are a potential biological agent for eradicating invasive mosquitofish through the mechanism of reproductive interference, which is defined as any sexual behavior erratically directed at a different species that damages female and/or male fitness. Together with decades of data on species distribution, our field surveys suggest that mosquitofish initially became established on Okinawa Island before being replaced by the more recently introduced guppies. More importantly, our laboratory experiments suggest that reproductive interference was one of the mechanisms underlying this species exclusion, and that in this case, the negative effects were asymmetric, i.e., they only impacted mosquitofish. Reproductive interference may offer a safer and more convenient method of biological control than the traditional sterile male release method because radiation is not necessary.
Means and Long-Term Trends of Global Coastal Zone Precipitation
Authors: Curtis Scott 
Published: April 2019

AbstractPrecipitation in the coastal zone is important to the socio-economic and ecological well-being of the world. Meteorologically, precipitation is generated by unique mechanisms at the land-sea interface, which is why coastal zone precipitation is not well resolved by global climate models. Yet, to date, much more effort has been placed in analyzing global precipitation over the oceans and land. In this study, global coastal zone precipitation is quantified by selecting Global Precipitation Climatology Centre V2018 0.5° grid cells in 50 km zones from the shoreline into the interior. The transition from maritime to continental precipitation regimes is revealed in the long-term (1931–2010) average, as there is a pronounced coast-to-interior decline in rainfall from approximately 911.5 mm yr−1 within 50 km of the coast to 727.2 mm yr−1 from 100 to 150 km away from the coast. Globally, coastal zone precipitation peaks in boreal summer, extending into fall for precipitation at the coastline. Dividing the long-term record into early and late 40-year periods reveals an increasing trend in precipitation in the coastal zone, with the interior increasing faster than at the coastline. Averaging over 30-year climate normals from 1931–60 to 1981–2010 further confirms this result. A seasonal analysis reveals that the upward trends, and discrepancy between the coast and inland are maximized in the austral summer season. Interestingly, from May to September there is a declining trend in rainfall at the coastline, whereas the interior only shows minimal declines in August and September. Potential forcing mechanisms that could favor a wetter interior coastal zone include changes in the sea breeze circulation, urban heat island effect, or precipitation content associated with synoptic systems or monsoonal circulations.
A New Eye Dual-readout Method for MiRNA Detection based on Dissolution of Gold nanoparticles via LSPR by CdTe QDs Photoinduction
Authors: Borghei Yasaman-Sadat , Hosseini Morteza 
Published: April 2019

AbstractBreast cancer (BC) is the most frequent cancer that affects one in eight women worldwide. Recent advances in early cancer diagnosis anticipates more efficient treatment and prolong patient survival. MicroRNAs expression profiling plays a key role in diagnosis of cancer such as BC in early stages. For the first time we describe direct injection of hot electrons from plasmonic gold nanoparticles (AuNPs) to adsorbed water molecules with photoinduction of CdTe quantum dots (QDs) with emission wavelength at ~560 nm. As a result of hot electrons exiting from AuNPs with red color, gold cations (holes) are gradually discharged (AuNPs dissolution) leading to a colorless solution. Our group applied this phenomenon to propose a spectral method for miRNA recognition based on different responsive disaggregation and aggregation of CdTe QDs interacted with single strand DNA probes and DNA/RNA heteroduplex respectively resulting in a detection limit of 4.4 pM. This method has been applied also for the determination of miR-155 in the human breast carcinoma MCF-7 cells and normal human embryonic kidney cell line (HEK 293).
HLA-G 3′ untranslated region variants +3187G/G, +3196G/G and +3035T define diametrical clinical status and disease outcome in epithelial ovarian cancer
Authors: Schwich Esther , Rebmann Vera , Michita Rafael Tomoya , Rohn Hana , Voncken Jan Willem , Horn Peter A. , Kimmig Rainer , Kasimir-Bauer Sabine , Buderath Paul 
Published: April 2019

AbstractExpression of the non-classical human leukocyte antigen-G (HLA-G) promotes cancer progression in various malignancies including epithelial ovarian cancer (EOC). As single nucleotide polymorphisms (SNPs) in the HLA-G 3′ untranslated region (UTR) regulate HLA-G expression, we investigated HLA-G 3′UTR haplotypes arranged by SNPs in healthy controls (n = 75) and primary EOC patients (n = 79) and determined soluble HLA-G (sHLA-G) levels. Results were related to the clinical status and outcome. Although haplotype frequencies were similar in patients and controls, (i) sHLA-G levels were increased in EOC independent of the haplotype, (ii) homozygosity for UTR-1 or UTR-2 genotypes were significantly associated with metastases formation and presence of circulating tumor cells before therapy, whereas (iii) the UTR-5 and UTR-7 haplotypes were significantly associated with a beneficial clinical outcome regarding negative nodal status, early FIGO staging, and improved overall survival. Lastly, (iv) the ambivalent impact on clinical EOC aspects could be deduced to specific SNPs in the HLA-G 3′UTR: +3187G, +3196G and +3035T alleles. Our results give evidence that even if the genetic background of the HLA-G 3′UTR is identical between patients and controls, certain SNPs have the potential to contribute to diametrical clinical status/outcome in EOC.