bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photonic Quantum Networks formed from NV− centers
Authors: Nemoto Kae , Trupke Michael , Devitt Simon J. , Scharfenberger Burkhard , Buczak Kathrin , Schmiedmayer Jörg , Munro William J. 
Published: May 2016

AbstractIn this article we present a simple repeater scheme based on the negatively-charged nitrogen vacancy centre in diamond. Each repeater node is built from modules comprising an optical cavity containing a single NV−, with one nuclear spin from 15N as quantum memory. The module uses only deterministic processes and interactions to achieve high fidelity operations (>99%) and modules are connected by optical fiber. In the repeater node architecture, the processes between modules by photons can be in principle deterministic, however current limitations on optical components lead the processes to be probabilistic but heralded. Our resource-modest repeater architecture contains two modules at each node and the repeater nodes are then connected by entangled photon pairs. We discuss the performance of such a quantum repeater network with modest resources and then incorporate more resource-intense strategies step by step. Our architecture should allow large-scale quantum information networks with existing or near future technology.
Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene
Authors: Schobel Seth A. , Stucker Karla M. , Moore Martin L. , Anderson Larry J. , Larkin Emma K. , Shankar Jyoti , Bera Jayati , Puri Vinita , Shilts Meghan H. , Rosas-Salazar Christian , Halpin Rebecca A. , Fedorova Nadia , Shrivastava Susmita , Stockwell Timothy B. , Peebles R. Stokes , Hartert Tina V. , Das Suman R. 
Published: May 2016

AbstractRespiratory Syncytial Virus (RSV) is responsible for considerable morbidity and mortality worldwide and is the most important respiratory viral pathogen in infants. Extensive sequence variability within and between RSV group A and B viruses and the ability of multiple clades and sub-clades of RSV to co-circulate are likely mechanisms contributing to the evasion of herd immunity. Surveillance and large-scale whole-genome sequencing of RSV is currently limited but would help identify its evolutionary dynamics and sites of selective immune evasion. In this study, we performed complete-genome next-generation sequencing of 92 RSV isolates from infants in central Tennessee during the 2012–2014 RSV seasons. We identified multiple co-circulating clades of RSV from both the A and B groups. Each clade is defined by signature N- and O-linked glycosylation patterns. Analyses of specific RSV genes revealed high rates of positive selection in the attachment (G) gene. We identified RSV-A viruses in circulation with and without a recently reported 72-nucleotide G gene sequence duplication. Furthermore, we show evidence of convergent evolution of G gene sequence duplication and fixation over time, which suggests a potential fitness advantage of RSV with the G sequence duplication.
Interferon-γ and Tumor Necrosis Factor-α Polarize Bone Marrow Stromal Cells Uniformly to a Th1 Phenotype
Authors: Jin Ping , Zhao Yuanlong , Liu Hui , Chen Jinguo , Ren Jiaqiang , Jin Jianjian , Bedognetti Davide , Liu Shutong , Wang Ena , Marincola Francesco , Stroncek David 
Published: May 2016

AbstractActivated T cells polarize mesenchymal stromal cells (MSCs) to a proinflammatory Th1 phenotype which likely has an important role in amplifying the immune response in the tumor microenvironment. We investigated the role of interferon gamma (IFN-γ) and tumor necrosis factor alpha (TNF-α), two factors produced by activated T cells, in MSC polarization. Gene expression and culture supernatant analysis showed that TNF-α and IFN-γ stimulated MSCs expressed distinct sets of proinflammatory factors. The combination of IFN-γ and TNF-α was synergistic and induced a transcriptome most similar to that found in MSCs stimulated with activated T cells and similar to that found in the inflamed tumor microenvironment; a Th1 phenotype with the expression of the immunosuppressive factors IL-4, IL-10, CD274/PD-L1 and indoleamine 2,3 dioxygenase (IDO). Single cell qRT-PCR analysis showed that the combination of IFN-γ and TNF-α polarized uniformly to this phenotype. The combination of IFN-γ and TNF-α results in the synergist uniform polarization of MSCs toward a primarily Th1 phenotype. The stimulation of MSCs by IFN-γ and TNF-α released from activated tumor infiltrating T cells is likely responsible for the production of many factors that characterize the tumor microenvironment.
Vasoactive Intestinal Peptide modulates trophoblast-derived cell line function and interaction with phagocytic cells through autocrine pathways
Authors: Vota Daiana , Paparini Daniel , Hauk Vanesa , Toro Ayelén , Merech Fatima , Varone Cecilia , Ramhorst Rosanna , Pérez Leirós Claudia 
Published: May 2016

AbstractTrophoblast cells migrate and invade the decidual stroma in a tightly regulated process to maintain immune homeostasis at the maternal-placental interface during the first weeks of pregnancy. Locally synthesized factors modulate trophoblast cell function and their interaction with maternal leukocytes to promote the silent clearance of apoptotic cells. The vasoactive intestinal peptide (VIP) is a pleiotropic polypeptide with trophic and anti-inflammatory effects in murine pregnancy models. We explored the effect of VIP on two human first trimester trophoblast cell lines, particularly on their migration, invasiveness and interaction with phagocytic cells, and the signalling and regulatory pathways involved. We found that VIP enhanced trophoblast cell migration and invasion through the activation of high affinity VPAC receptors and PKA-CRE signalling pathways. VIP knocked-down trophoblast cells showed reduced migration in basal and leukemic inhibitor factor (LIF)-elicited conditions. In parallel, VIP-silenced trophoblast cells failed to induce the phagocytosis of apoptotic bodies and the expression of immunosuppressant markers by human monocytes. Our results suggest that VIP-mediated autocrine pathways regulate trophoblast cell function and contribute to immune homeostasis maintenance at placentation and may provide new clues for therapeutic intervention in pregnancies complicated by defective deep placentation.
Spider web and silk performance landscapes across nutrient space
Authors: Blamires Sean J. , Tseng Yi-Hsuan , Wu Chung-Lin , Toft Søren , Raubenheimer David , Tso I.-Min 
Published: May 2016

AbstractPredators have been shown to alter their foraging as a regulatory response to recent feeding history, but it remains unknown whether trap building predators modulate their traps similarly as a regulatory strategy. Here we fed the orb web spider Nephila pilipes either live crickets, dead crickets with webs stimulated by flies, or dead crickets without web stimulation, over 21 days to enforce spiders to differentially extract nutrients from a single prey source. In addition to the nutrients extracted we measured web architectures, silk tensile properties, silk amino acid compositions, and web tension after each feeding round. We then plotted web and silk “performance landscapes” across nutrient space. The landscapes had multiple peaks and troughs for each web and silk performance parameter. The findings suggest that N. pilipes plastically adjusts the chemical and physical properties of their web and silk in accordance with its nutritional history. Our study expands the application of the geometric framework foraging model to include a type of predatory trap. Whether it can be applied to other predatory traps requires further testing.
Implementation of Outstanding Electronic Transport in Polar Covalent Boron Nitride Atomic Chains: another Extraordinary Odd-Even Behaviour
Authors: Xu Xiaodong , Li Weiqi , Liu Linhua , Feng Jikang , Jiang Yongyuan , Tian Wei Quan 
Published: May 2016

AbstractA theoretical investigation of the unique electronic transport properties of the junctions composed of boron nitride atomic chains bridging symmetric graphene electrodes with point-contacts is executed through non-equilibrium Green’s function technique in combination with density functional theory. Compared with carbon atomic chains, the boron nitride atomic chains have an alternative arrangement of polar covalent B-N bonds and different contacts coupling electrodes, showing some unusual properties in functional atomic electronic devices. Remarkably, they have an extraordinary odd-even behavior of conductivity with the length increase. The rectification character and negative differential resistance of nonlinear current-voltage characteristics can be achieved by manipulating the type of contacts between boron nitride atomic chains bridges and electrodes. The junctions with asymmetric contacts have an intrinsic rectification, caused by stronger coupling in the C-N contact than the C-B contact. On the other hand, for symmetric contact junctions, it is confirmed that the transport properties of the junctions primarily depend on the nature of contacts. The junctions with symmetric C-N contacts have higher conductivity than their C-B contacts counterparts. Furthermore, the negative differential resistances of the junctions with only C-N contacts is very conspicuous and can be achieved at lower bias.
Overexpression of spinach non-symbiotic hemoglobin in Arabidopsis resulted in decreased NO content and lowered nitrate and other abiotic stresses tolerance
Authors: Bai Xuegui , Long Juan , He Xiaozhao , Yan Jinping , Chen Xuanqin , Tan Yong , Li Kunzhi , Chen Limei , Xu Huini 
Published: May 2016

AbstractA class 1 non-symbiotic hemoglobin family gene, SoHb, was isolated from spinach. qRT-PCR showed that SoHb was induced by excess nitrate, polyethylene glycol, NaCl, H2O2, and salicylic acid. Besides, SoHb was strongly induced by application of nitric oxide (NO) donor, while was suppressed by NO scavenger, nitrate reductase inhibitor, and nitric oxide synthase inhibitor. Overexpression of SoHb in Arabidopsis resulted in decreased NO level and sensitivity to nitrate stress, as shown by reduced root length, fresh weight, the maximum photosystem II quantum ratio of variable to maximum fluorescence (Fv/Fm), and higher malondialdehyde contents. The activities and gene transcription of superoxide dioxidase, and catalase decreased under nitrate stress. Expression levels of RD22, RD29A, DREB2A, and P5CS1 decreased after nitrate treatment in SoHb-overexpressing plants, while increased in the WT plants. Moreover, SoHb-overexpressing plants showed decreased tolerance to NaCl and osmotic stress. In addition, the SoHb-overexpression lines showed earlier flower by regulating the expression of SOC, GI and FLC genes. Our results indicated that the decreasing NO content in Arabidopsis by overexpressing SoHb might be responsible for lowered tolerance to nitrate and other abiotic stresses.
QSAR Accelerated Discovery of Potent Ice Recrystallization Inhibitors
Authors: Briard Jennie G. , Fernandez Michael , De Luna Phil , Woo Tom. K. , Ben Robert N. 
Published: May 2016

AbstractIce recrystallization is the main contributor to cell damage and death during the cryopreservation of cells and tissues. Over the past five years, many small carbohydrate-based molecules were identified as ice recrystallization inhibitors and several were shown to reduce cryoinjury during the cryopreservation of red blood cells (RBCs) and hematopoietic stems cells (HSCs). Unfortunately, clear structure-activity relationships have not been identified impeding the rational design of future compounds possessing ice recrystallization inhibition (IRI) activity. A set of 124 previously synthesized compounds with known IRI activities were used to calibrate 3D-QSAR classification models using GRid INdependent Descriptors (GRIND) derived from DFT level quantum mechanical calculations. Partial least squares (PLS) model was calibrated with 70% of the data set which successfully identified 80% of the IRI active compounds with a precision of 0.8. This model exhibited good performance in screening the remaining 30% of the data set with 70% of active additives successfully recovered with a precision of ~0.7 and specificity of 0.8. The model was further applied to screen a new library of aryl-alditol molecules which were then experimentally synthesized and tested with a success rate of 82%. Presented is the first computer-aided high-throughput experimental screening for novel IRI active compounds.
Whole genome sequencing of Gyeongbuk Araucana, a newly developed blue-egg laying chicken breed, reveals its origin and genetic characteristics
Authors: Jeong Hyeonsoo , Kim Kwondo , Caetano-Anollés Kelsey , Kim Heebal , Kim Byung-ki , Yi Jun-Koo , Ha Jae-Jung , Cho Seoae , Oh Dong Yep 
Published: May 2016

AbstractChicken, Gallus gallus, is a valuable species both as a food source and as a model organism for scientific research. Here, we sequenced the genome of Gyeongbuk Araucana, a rare chicken breed with unique phenotypic characteristics including flight ability, large body size, and laying blue-shelled eggs, to identify its genomic features. We generated genomes of Gyeongbuk Araucana, Leghorn, and Korean Native Chicken at a total of 33.5, 35.82, and 33.23 coverage depth, respectively. Along with the genomes of 12 Chinese breeds, we identified genomic variants of 16.3 million SNVs and 2.3 million InDels in mapped regions. Additionally, through assembly of unmapped reads and selective sweep, we identified candidate genes that fall into heart, vasculature and muscle development and body growth categories, which provided insight into Gyeongbuk Araucana’s phenotypic traits. Finally, genetic variation based on the transposable element insertion pattern was investigated to elucidate the features of transposable elements related to blue egg shell formation. This study presents results of the first genomic study on the Gyeongbuk Araucana breed; it has potential to serve as an invaluable resource for future research on the genomic characteristics of this chicken breed as well as others.
Controlling Octahedral Rotations in a Perovskite via Strain Doping
Authors: Herklotz A. , Wong A. T. , Meyer T. , Biegalski M. D. , Lee H. N. , Ward T. Z. 
Published: May 2016

AbstractThe perovskite unit cell is the fundamental building block of many functional materials. The manipulation of this crystal structure is known to be of central importance to controlling many technologically promising phenomena related to superconductivity, multiferroicity, mangetoresistivity and photovoltaics. The broad range of properties that this structure can exhibit is in part due to the centrally coordinated octahedra bond flexibility, which allows for a multitude of distortions from the ideal highly symmetric structure. However, continuous and fine manipulation of these distortions has never been possible. Here, we show that controlled insertion of He atoms into an epitaxial perovskite film can be used to finely tune the lattice symmetry by modifying the local distortions, i.e., octahedral bonding angle and length. Orthorhombic SrRuO3 films coherently grown on SrTiO3 substrates are used as a model system. Implanted He atoms are confirmed to induce out-of-plane strain, which provides the ability to controllably shift the bulk-like orthorhombically distorted phase to a tetragonal structure by shifting the oxygen octahedra rotation pattern. These results demonstrate that He implantation offers an entirely new pathway to strain engineering of perovskite-based complex oxide thin films, useful for creating new functionalities or properties in perovskite materials.
Migration mechanism of a GaN bicrystalline grain boundary as a model system
Authors: Lee Sung Bo , Yoo Seung Jo , Kim Young-Min , Kim Jin-Gyu , Han Heung Nam 
Published: May 2016

AbstractUsing in situ high-resolution transmission electron microscopy, we have explored migration mechanism of a grain boundary in a GaN bicrystal as a model system. During annealing at 500 °C, the grain-boundary region underwent a decrease in thickness, which occurred by decomposition or sublimation of GaN during annealing at 500 °C coupled with electron-beam sputtering. The decrease in thickness corresponds to an increase in the driving force for migration, because the migration of the grain boundary was driven by the surface energy difference. As the driving force increased with annealing time, the grain-boundary morphology turned from atomically smooth to rough, which is characterized by kinetic roughening. The observations indicate that a grain boundary exhibits a nonlinear relationship between driving force for migration and migration velocity, in discord with the general presumption that a grain boundary follows a linear relationship.
Embryo Microinjection of Selenomethionine Reduces Hatchability and Modifies Oxidant Responsive Gene Expression in Zebrafish
Authors: Thomas J. K. , Janz D. M. 
Published: May 2016

AbstractIn previous studies we demonstrated that exposure to selenomethionine (SeMet) causes developmental toxicities in zebrafish (Danio rerio). The objectives of this study were to establish a dose-response relationship for developmental toxicities in zebrafish after embryo microinjection of Se (8, 16 or 32 μg/g dry mass of eggs) in the form of SeMet and to investigate potential underlying mechanism(s) of SeMet-induced developmental toxicities. A dose-dependent increase in frequencies of mortality and total deformities and reduced hatchability were observed in zebrafish exposed to excess Se via embryo microinjection. The egg Se concentration causing 20% mortality was then used to investigate transcript abundance of proteins involved in antioxidant protection and methylation. Excess Se exposure modified gene expression of oxidant-responsive transcription factors (nuclear factor erythroid 2-related factornrf2aandnrf2b) and enzymes involved in cellular methylation (methionine adenosyltransferasemat1aandmat2ab) in zebrafish larvae. Notably, excess Se exposure up-regulated transcript abundance of aryl hydrocarbon receptor 2 (ahr2), a signalling pathway involved in the toxicity of dioxin-related compounds. Our findings suggest that oxidative stress or modification of methylation, or a combination of these mechanisms, might be responsible for Se-induced developmental toxicities in fishes.
Proteomic profiling of small-molecule inhibitors reveals dispensability of MTH1 for cancer cell survival
Authors: Kawamura Tatsuro , Kawatani Makoto , Muroi Makoto , Kondoh Yasumitsu , Futamura Yushi , Aono Harumi , Tanaka Miho , Honda Kaori , Osada Hiroyuki 
Published: May 2016

AbstractSince recent publications suggested that the survival of cancer cells depends on MTH1 to avoid incorporation of oxidized nucleotides into the cellular DNA, MTH1 has attracted attention as a potential cancer therapeutic target. In this study, we identified new purine-based MTH1 inhibitors by chemical array screening. However, although the MTH1 inhibitors identified in this study targeted cellular MTH1, they exhibited only weak cytotoxicity against cancer cells compared to recently reported first-in-class inhibitors. We performed proteomic profiling to investigate the modes of action by which chemically distinct MTH1 inhibitors induce cancer cell death and found mechanistic differences among the first-in-class MTH1 inhibitors. In particular, we identified tubulin as the primary target of TH287 and TH588 responsible for the antitumor effects despite the nanomolar MTH1-inhibitory activity in vitro. Furthermore, overexpression of MTH1 did not rescue cells from MTH1 inhibitor–induced cell death and siRNA-mediated knockdown of MTH1 did not suppress cancer cell growth. Taken together, we conclude that the cytotoxicity of MTH1 inhibitors is attributable to off-target effects and that MTH1 is not essential for cancer cell survival.
QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts
Authors: Ribeiro João V. , Bernardi Rafael C. , Rudack Till , Stone John E. , Phillips James C. , Freddolino Peter L. , Schulten Klaus 
Published: May 2016

AbstractThe proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the efficiency and quality of their work by carrying out tedious or repetitive tasks while enabling easy control of every step. Whether carrying out simulations within the live view mode on a small laptop or performing complex and large simulations on supercomputers or Cloud computers, QwikMD uses the same steps and user interface. QwikMD is freely available by download on group and personal computers. It is also available on the cloud at Amazon Web Services.
Melting curve of SiO2 at multimegabar pressures: implications for gas giants and super-Earths
Authors: González-Cataldo Felipe , Davis Sergio , Gutiérrez Gonzalo 
Published: May 2016

AbstractUltrahigh-pressure phase boundary between solid and liquid SiO2 is still quite unclear. Here we present predictions of silica melting curve for the multimegabar pressure regime, as obtained from first principles molecular dynamics simulations. We calculate the melting temperatures from three high pressure phases of silica (pyrite-, cotunnite-, and Fe2P-type SiO2) at different pressures using the Z method. The computed melting curve is found to rise abruptly around 330 GPa, an increase not previously reported by any melting simulations. This is in close agreement with recent experiments reporting the α-PbO2–pyrite transition around this pressure. The predicted phase diagram indicates that silica could be one of the dominant components of the rocky cores of gas giants, as it remains solid at the core of our Solar System’s gas giants. These results are also relevant to model the interior structure and evolution of massive super-Earths.
Identification and functional analysis of two novel connexin 50 mutations associated with autosome dominant congenital cataracts
Authors: Yu Yinhui , Wu Menghan , Chen Xinyi , Zhu Yanan , Gong Xiaohua , Yao Ke 
Published: May 2016

AbstractAutosomal dominant congenital cataracts (ADCC) are clinically and genetically heterogeneous diseases. The present study recruited two Chinese families with bilateral nuclear cataract or zonular pulverulent phenotype. Direct sequencing of candidate genes identified two novel missense mutations of Cx50, Cx50P59A (c.175C > G) and Cx50R76H (c.227G > A), both co-segregated well with all affected individuals. Bioinformatics analysis predicted deleterious for both mutations. Functional and cellular behaviors of wild type and mutant Cx50 examined by stably transfecting recombinant systems revealed similar protein expression levels. Protein distribution pattern by fluorescence microscopy showed that Cx50R76H localized at appositional membranes forming gap junctions with enormous cytoplasmic protein accumulation, whereas the Cx50P59A mutation was found inefficient at forming detectable plaques. Cell growth test by MTT assay showed that induction of Cx50P59A decreased cell viability. Our study constitutes the first report that the Cx50P59A and Cx50R76H mutations are associated with ADCC and expands the mutation spectrum of Cx50 in association with congenital cataracts. The genetic, cellular, and functional data suggest that the altered intercellular communication governed by mutated Cx50 proteins may act as the molecular mechanism underlying ADCC, which further confirms the role of Cx50 in the maintenance of human lens transparency.