bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a New Broadly Cross-reactive Epitope within Domain III of the Duck Tembusu Virus E Protein
Authors: Li Chenxi , Bai Xiaofei , Meng Runze , Shaozhou Wulin , Zhang Qingshan , Hua Ronghong , Liu Jyung-Hurng , Liu Ming , Zhang Yun 
Published: November 2016

AbstractIn 2010, a pathogenic flavivirus termed duck Tembusu virus (DTMUV) caused widespread outbreak of egg-drop syndrome in domesticated ducks in China. Although the glycoprotein E of DTMUV is an important structural component of the virus, the B-cell epitopes of this protein remains uncharacterized. Using phage display and mutagenesis, we identified a minimal B-cell epitope, 374EXE/DPPFG380, that mediates binding to a nonneutralizing monoclonal antibody. DTMUV-positive duck serum reacted with the epitope, and amino acid substitutions revealed the specific amino acids that are essential for antibody binding. Dot-blot assays of various flavivirus-positive sera indicated that EXE/DPPFG is a cross-reactive epitope in most flaviviruses, including Zika, West Nile, Yellow fever, dengue, and Japanese encephalitis viruses. These findings indicate that the epitope sequence is conserved among many strains of mosquito-borne flavivirus. Protein structure modeling revealed that the epitope is located in domain III of the DTMUV E protein. Together, these results provide new insights on the broad cross-reactivity of a B-cell binding site of the E protein of flaviviruses, which can be exploited as a diagnostic or therapeutic target for identifying, studying, or treating DTMUV and other flavivirus infections.
Oncometabolite D-2-Hydroxyglurate Directly Induces Epithelial-Mesenchymal Transition and is Associated with Distant Metastasis in Colorectal Cancer
Authors: Colvin Hugh , Nishida Naohiro , Konno Masamitsu , Haraguchi Naotsugu , Takahashi Hidekazu , Nishimura Junichi , Hata Taishi , Kawamoto Koichi , Asai Ayumu , Tsunekuni Kenta , Koseki Jun , Mizushima Tsunekazu , Satoh Taroh , Doki Yuichiro , Mori Masaki , Ishii Hideshi 
Published: November 2016

AbstractDeranged metabolism is a hallmark of cancer, playing a significant role in driving the disease process. One such example is the induction of carcinogenesis by the oncometabolite D-2 hydroxyglutarate (D-2HG), which is produced by the mutated enzyme isocitrate dehydrogenase (IDH) occurring in subsets of leukaemias and brain tumours. The oncogenic property of D-2HG appears to stem from its ability to interfere with the activities of α-ketoglutarate-dependent dioxygenases, including the Jumonji family histone demethylases. Here, we find in colorectal cancer cells that even in the absence of IDH mutation, the levels of D-2HG and its enantiomer L-2HG were elevated through glutamine anaplerosis. D-2HG, but not L-2HG, increased the trimethylation of histone H3 lysine 4 of the promoter region of ZEB1, a master regulator of epithelial-mesenchymal transition (EMT), and increased the expression of the ZEB1 gene to directly induce EMT in colorectal cancer cells. EMT promotes the ability of cancer cells to invade the local tissue and enter into the bloodstream, leading to distant organ metastasis. D-2HG levels were elevated in colorectal cancer specimens, particularly in those associated with distant metastasis, supporting the observations in vitro and implicating the contribution of D-2HG in metastasis, the major cause of death in this disease.
Transcriptional changes during ovule development in two genotypes of litchi (Litchi chinensis Sonn.) with contrast in seed size
Authors: Pathak Ashish K. , Singh Sudhir P. , Gupta Yogesh , Gurjar Anoop K. S. , Mantri Shrikant S. , Tuli Rakesh 
Published: November 2016

AbstractLitchi chinensis is a subtropical fruit crop, popular for its nutritional value and taste. Fruits with small seed size and thick aril are desirable in litchi. To gain molecular insight into gene expression that leads to the reduction in the size of seed in Litchi chinensis, transcriptomes of two genetically closely related genotypes, with contrasting seed size were compared in developing ovules. The cDNA library constructed from early developmental stages of ovules (0, 6, and 14 days after anthesis) of bold- and small-seeded litchi genotypes yielded 303,778,968 high quality paired-end reads. These were de-novo assembled into 1,19,939 transcripts with an average length of 865 bp. A total of 10,186 transcripts with contrast in expression were identified in developing ovules between the small- and large- seeded genotypes. A majority of these differences were present in ovules before anthesis, thus suggesting the role of maternal factors in seed development. A number of transcripts indicative of metabolic stress, expressed at higher level in the small seeded genotype. Several differentially expressed transcripts identified in such ovules showed homology with Arabidopsis genes associated with different stages of ovule development and embryogenesis.
Three-waveform bidirectional pumping of single electrons with a silicon quantum dot
Authors: Tanttu Tuomo , Rossi Alessandro , Tan Kuan Yen , Mäkinen Akseli , Chan Kok Wai , Dzurak Andrew S. , Möttönen Mikko 
Published: November 2016

AbstractSemiconductor-based quantum dot single-electron pumps are currently the most promising candidates for the direct realization of the emerging quantum standard of the ampere in the International System of Units. Here, we discuss a silicon quantum dot single-electron pump with radio frequency control over the transparencies of entrance and exit barriers as well as the dot potential. We show that our driving protocol leads to robust bidirectional pumping: one can conveniently reverse the direction of the quantized current by changing only the phase shift of one driving waveform with respect to the others. We anticipate that this pumping technique may be used in the future to perform error counting experiments by pumping the electrons into and out of a reservoir island monitored by a charge sensor.
Genomic continuity of Argentinean Mennonites
Authors: Pardo-Seco Jacobo , Llull Cintia , Berardi Gabriela , Gómez Andrea , Andreatta Fernando , Martinón-Torres Federico , Toscanini Ulises , Salas Antonio 
Published: November 2016

AbstractMennonites are Anabaptist communities that originated in Central Europe about 500 years ago. They initially migrated to different European countries, and in the early 18th century they established their first communities in North America, from where they moved to other American regions. We aimed to analyze an Argentinean Mennonite congregation from a genome-wide perspective by way of investigating >580.000 autosomal SNPs. Several analyses show that Argentinean Mennonites have European ancestry without signatures of admixture with other non-European American populations. Among the worldwide datasets used for population comparison, the CEU, which is the best-subrogated Central European population existing in The 1000 Genome Project, is the dataset showing the closest genome affinity to the Mennonites. When compared to other European population samples, the Mennonites show higher inbreeding coefficient values. Argentinean Mennonites show signatures of genetic continuity with no evidence of admixture with Americans of Native American or sub-Saharan African ancestry. Their genome indicates the existence of an increased endogamy compared to other Europeans most likely mirroring their lifestyle that involve small communities and historical consanguineous marriages.
Photoswitchable non-fluorescent thermochromic dye-nanoparticle hybrid probes
Authors: Harrington Walter N. , Haji Mwafaq R. , Galanzha Ekaterina I. , Nedosekin Dmitry A. , Nima Zeid A. , Watanabe Fumiya , Ghosh Anindya , Biris Alexandru S. , Zharov Vladimir P. 
Published: November 2016

AbstractPhotoswitchable fluorescent proteins with controllable light–dark states and spectral shifts in emission in response to light have led to breakthroughs in the study of cell biology. Nevertheless, conventional photoswitching is not applicable for weakly fluorescent proteins and requires UV light with low depth penetration in bio-tissue. Here we introduce a novel concept of photoswitchable hybrid probes consisting of thermochromic dye and absorbing nanoparticles, in which temperature-sensitive light–dark states and spectral shifts in absorption can be switched through controllable photothermal heating of doped nanoparticles. The proof-of-concept is demonstrated through the use of two different types of temperature-sensitive dyes doped with magnetic nanoparticles and reversibly photoswitched by a near-infrared laser. Photoacoustic imaging revealed the high contrast of these probes, which is sufficient for their visualization in cells and deep tissue. Our results suggest that these new photoswitchable multicolour probes can be used for multimodal cellular diagnostics and potentially for magnetic and photothermal therapy.
Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein
Authors: Vestergaard Mike , Chan Siu Hung Joshua , Jensen Peter Ruhdal 
Published: November 2016

AbstractAn increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used to explore the feasibility of recombinant Bovine Alpha Lactalbumin production coupled with market prices of utilized materials. We found that recombinant protein production could be a feasible food source and an alternative to traditional sources.
Thymic exosomes promote the final maturation of thymocytes
Authors: Lundberg Vanja , Berglund Martin , Skogberg Gabriel , Lindgren Susanne , Lundqvist Christina , Gudmundsdottir Judith , Thörn Karolina , Telemo Esbjörn , Ekwall Olov 
Published: November 2016

AbstractExtensive knowledge has been gained the last years concerning mechanisms underlying the selection of single positive thymocytes in the thymic medulla. Less is known regarding other important processes in the thymic medulla such as the regulation of late stage thymocyte maturation. We have previously reported that exosomes are abundant in the thymus with a phenotype that indicates an epithelial cell origin and immunoregulatory properties. In this study we use an in vitro system to investigate the effects of thymic exosomes on the maturation of single positive thymocytes as well as effects on nTreg formation. We show that thymic exosomes promote the maturation of single positive CD4+CD25− cells into mature thymocytes with S1P1+Qa2+ and CCR7+Qa2+ phenotypes. Furthermore, we show that thymic exosomes reduce the formation of CD4+CD25+FoxP3+ thymocytes and that these exosome effects are independent of dendritic cell co-stimulation but require intact exosomal RNA content and surface proteins. An efficient direct uptake of exosomes by both thymocytes and thymic DC’s is also demonstrated. In conclusion, this study demonstrates that exosomes may represent a new route of communication within the thymus.
LRBA is Essential for Allogeneic Responses in Bone Marrow Transplantation
Authors: Park Mi Young , Sudan Raki , Srivastava Neetu , Neelam Sudha , Youngs Christie , Wang Jia-Wang , Engelman Robert W. , Kerr William G. 
Published: November 2016

AbstractThe PH-BEACH-WD40 (PBW) protein family members play a role in coordinating receptor signaling and intracellular vesicle trafficking. LPS-Responsive-Beige-like Anchor (LRBA) is a PBW protein whose immune function remains elusive. Here we show that LRBA-null mice are viable, but exhibit compromised rejection of allogeneic, xenogeneic and missing self bone-marrow grafts. Further, we demonstrate that LRBA-null Natural Killer (NK) cells exhibit impaired signaling by the key NK activating receptors, NKp46 and NKG2D. However, induction of IFN-γ by cytokines remains intact, indicating LRBA selectively facilitates signals by receptors for ligands expressed on the surface of NK targets. Surprisingly, LRBA limits immunoregulatory cell numbers in tissues where GvHD is primed or initiated, and consistent with this LRBA-null mice also demonstrate resistance to lethal GvHD. These findings demonstrate that LRBA is redundant for host longevity while being essential for both host and donor-mediated immune responses and thus represents a unique and novel molecular target in transplant immunology.
Fibroblast miR-210 overexpression is independently associated with clinical failure in Prostate Cancer – a multicenter (in situ hybridization) study
Authors: Andersen Sigve , Richardsen Elin , Moi Line , Donnem Tom , Nordby Yngve , Ness Nora , Holman Marte Eilertsen , Bremnes Roy M. , Busund Lill-Tove 
Published: November 2016

AbstractThere is a need for better prognostication in prostate cancer (PC). “The micromanager of hypoxia”, microRNA-210 (miR-210) is directly linked to hypoxia, is overexpressed in PC and has been implied in tumor cell-fibroblast crosstalk. We investigated the prognostic impact of miR-210 in tumor cells and fibroblasts in PC. Tumor and stromal samples from a multicenter PC cohort of 535 prostatectomy patients were inserted into tissue microarrays. To investigate the expression of miR-210, we used in situ hybridization and two pathologists semiquantitatively scored its expression. Overexpression of miR-210 in tumor cells was not associated to biochemical failure-free survival (BFFS, p = 0.85) or clinical failure-free survival (CFFS, p = 0.09). However, overexpression of miR-210 in fibroblasts was significantly associated to a poor CFFS (p = 0.001), but not BFFS (p = 0.232). This feature was validated in both cohorts. Overexpression of miR-210 was independently associated with a reduced CFFS (HR = 2.76, CI 95% 1.25–6.09, p = 0.012). Overexpression of miR-210 in fibroblasts is independently associated with a poor CFFS. This highlights the importance of fibroblasts and cellular compartment crosstalk in PC. miR-210 is a candidate prognostic marker and potential therapeutic target in PC.
Evidences for redox reaction driven charge transfer and mass transport in metal-assisted chemical etching of silicon
Authors: Kong Lingyu , Dasgupta Binayak , Ren Yi , Mohseni Parsian K. , Hong Minghui , Li Xiuling , Chim Wai Kin , Chiam Sing Yang 
Published: November 2016

AbstractIn this work, we investigate the transport processes governing the metal-assisted chemical etching (MacEtch) of silicon (Si). We show that in the oxidation of Si during the MacEtch process, the transport of the hole charges can be accomplished by the diffusion of metal ions. The oxidation of Si is subsequently governed by a redox reaction between the ions and Si. This represents a fundamentally different proposition in MacEtch whereby such transport is understood to occur through hole carrier conduction followed by hole injection into (or electron extraction from) Si. Consistent with the ion transport model introduced, we showed the possibility in the dynamic redistribution of the metal atoms that resulted in the formation of pores/cracks for catalyst thin films that are ≲30 nm thick. As such, the transport of the reagents and by-products are accomplished via these pores/cracks for the thin catalyst films. For thicker films, we show a saturation in the etch rate demonstrating a transport process that is dominated by diffusion via metal/Si boundaries. The new understanding in transport processes described in this work reconcile competing models in reagents/by-products transport, and also solution ions and thin film etching, which can form the foundation of future studies in the MacEtch process.
Infliximab and Dexamethasone Attenuate the Ductular Reaction in Mice
Authors: Verhulst Stefaan , Best Jan , Syn Wing-Kin , Reynaert Hendrik , Hellemans Karine H. , Canbay Ali , Dolle Laurent , van Grunsven Leo A. 
Published: November 2016

AbstractChronic hepatic injury is accompanied by a ductular response that is strongly correlated with disease severity and progression of fibrosis. To investigate whether anti-inflammatory drugs can modulate the ductular response, we treated mice suffering from a steatotic or cholestatic injury with anti-TNF-α antibodies (Infliximab) or glucocorticoids (Dexamethasone). We discovered that Dexamethasone and Infliximab can both modulate the adaptive remodeling of the biliary architecture that occurs upon liver injury and limit extracellular matrix deposition. Infliximab treatment, at least in these steatotic and cholestatic mouse models, is the safer approach since it does not increase liver injury, allows inflammation to take place but inhibits efficiently the ductular response and extracellular matrix deposition. Infliximab-based therapy could, thus, still be of importance in multiple chronic liver disorders that display a ductular response such as alcoholic liver disease or sclerosing cholangitis.
Conspecific injury raises an alarm in medaka
Authors: Mathuru Ajay S. 
Published: November 2016

AbstractIn the late 1930s, Karl von Frisch reported that semiochemicals released upon injury, act as alarm substances (Schreckstoff) in fish. In Ostariophysi species, club cells in the epidermis are believed to contain cues related to alarm substance; however, the function of club cells, primarily as reservoirs of alarm substance has been debated. Here, I describe an alarm response in the Japanese rice fishOryzias latipes(medaka), a member of the order Beloniformes. The response to alarm substance (Schreckreaction) in medaka is characterized by bouts of immobility and an increase in cortisol levels within minutes of exposure to conspecific skin extract. Histological analysis, however, suggests that club cells are either rare or absent in the medaka epidermis. In addition to describing an uncharacterized behavior in a vertebrate popular for genetic and developmental studies, these results support the hypothesis that the primary function of epidermal club cells may be unrelated to a role as alarm substance cells. The existence of similar behavioral responses in two evolutionarily distant but well established laboratory models, the zebrafish and the medaka, offers the possibility of comparative analyses of neural circuits encoding innate fear.
Laser Printing of Superhydrophobic Patterns from Mixtures of Hydrophobic Silica Nanoparticles and Toner Powder
Authors: Ngo Chi-Vinh , Chun Doo-Man 
Published: November 2016

AbstractIn this work, a new and facile dry printing method was developed for the direct fabrication of superhydrophobic patterns based on silica nanoparticles. Mixtures of hydrophobic fumed silica nanoparticles and toner powder were printed on paper and polymer sheets using a commercial laser printer to produce the superhydrophobic patterns. The mixing ratio of the toner powder (for the laser printer) to hydrophobic silica was also investigated to optimize both the printing quality and the superhydrophobicity of the printed areas. The proper mixing ratio was then used to print various superhydrophobic patterns, including triangular, square, circular, and complex arrangements, to demonstrate that superhydrophobic surfaces with different patterns can be fabricated in a few seconds without any post-processing. The superhydrophobicity of each sample was evaluated by contact angle measurements, and all printed areas showed contact angles greater than 150°. The research described here opens the possibility of rapid production of superhydrophobic surfaces with various patterns. Ultimately, the obtained findings may have a significant impact on applications related to self-cleaning, control of water geometry and position, fluid mixing and fluid transport.
Dynamics of the photosphere along the solar cycle from SDO/HMI
Authors: Roudier Th. , Malherbe J. M. , Mirouh G. M. 
Published: November 2016

Context. As the global magnetic field of the Sun has an activity cycle, one expects to observe some variation of the dynamical properties of the flows visible in the photosphere.
Aims. We investigate the flow field during the solar cycle by analysing SDO/HMI observations of continuum intensity, Doppler velocity and longitudinal magnetic field.
Methods. We first picked data at disk center during 6 yr along the solar cycle with a 48-h time step in order to study the overall evolution of the continuum intensity and magnetic field. Then we focused on thirty 6-h sequences of quiet regions without any remnant of magnetic activity separated by 6 months, in summer and winter, when disk center latitude B0 is close to zero. The horizontal velocity was derived from the local correlation tracking technique over a field of view of 216.4 Mm × 216.4 Mm located at disk center.
Results. Our measurements at disk center show the stability of the flow properties between meso- and supergranular scales along the solar cycle.
Conclusions. The network magnetic field, produced locally at disk center independently from large scale dynamo, together with continuum contrast, vertical and horizontal flows, seem to remain constant during the solar cycle.
Urethral Duplication with Two Hypospadic Meati—An Unusual Variant
Authors: Davidson Joseph , Wright Naomi , Garriboli Massimo 
Published: November 2016

AbstractDuplication of the urethra is a rare congenital anomaly, with approximately 300 cases reported in the literature. We report a unique case of this condition in a male infant. This case differs from the classical Effman type II-A2 duplication because of the presence of two hypospadic urethral meati, as opposed to a ventral or dorsal accessory meatus with a normally positioned distal urethra. The patient underwent a single-stage repair consisting of a proximal urethra-urethral anastomosis and distal urethral tubularization at 21 months of age with excellent results in terms of both function and cosmesis.