bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial distribution and risk factors associated withSalmonella entericain pigs
Authors: PARADA J. , CARRANZA A. , ALVAREZ J. , PICHEL M. , TAMIOZZO P. , BUSSO J. , AMBROGI A. 
Published: November 2016

SUMMARYThe importance of pork in the transmission ofSalmonellaspp. to humans has led to the development of control programmes worldwide. For this, knowledge on the epidemiology of the infection in the production system is fundamental to the efficacy of the regulations. Our objective was to determine the prevalence and spatial distribution ofSalmonella-infected farms in the central region of Argentina, and to identify the predominant serotypes and epidemiological factors associated with an increased risk of infection.Salmonellawas isolated from 22 of 52 sampled farms, for a farm prevalence of 42·3% (95% confidence interval 28·4–56·1). The most frequent serotypes isolated wereS. Typhimurium andS. Derby, which have often been considered of public health concern in the region. Limited evidences of global and local clustering in the region under study were found, and the type of feed and presence of diarrhoeic pigs were significantly associated with havingSalmonellashedders in the farm. This highlights the need to evaluate microbiological controls at the farm level, and demonstrates the usefulness of the spatial tools to identify areas of greatest risk when processing pork at slaughterhouse, which could contribute to increasing the food safety of pork products.
Is “not just right experience” (NJRE) in obsessive-compulsive disorder part of an autistic phenotype?
Authors: Hellriegel Josselyn , Barber Caroline , Wikramanayake Maheshi , Fineberg Naomi A. , Mandy William 
Published: November 2016

ObjectiveHarm avoidance (HA) and “not just right experience” (NJRE) have been proposed to be 2 core motivational processes underlying obsessive-compulsive disorder (OCD). The objective of this study was to explore whether NJRE demarcates a neurodevelopmental OCD subgroup distinct from HA related to autistic traits and/or to a broader phenotype of cognitive rigidity and sensory processing difficulties associated with an earlier age of OCD onset.MethodsA correlational design investigated whether NJRE and HA are distinct entities in OCD and explored their relationship to autism spectrum disorder (ASD) traits measured by the Autism Quotient (AQ), sensory processing, set-shifting, and age of OCD onset in an OCD sample (N=25).ResultsNJRE was only moderately (r=.34) correlated to HA and not significant in this study. Consistent with predictions, NJRE was associated with sensory processing difficulties and an earlier age of OCD onset. No significant relationships were found between NJRE and ASD traits as measured by the AQ or set-shifting difficulties.ConclusionsThese preliminary findings suggest a lack of evidence demonstrating NJRE as a manifestation of core autistic traits as measured by the AQ. However, NJRE was associated with sensory abnormalities and an earlier age of OCD onset. The role of NJRE as a developmental, and possibly neurodevelopmental, risk factor for OCD possibly warrants further investigation.
Notch regulates BMP responsiveness and lateral branching in vessel networks via SMAD6
Authors: Mouillesseaux Kevin P. , Wiley David S. , Saunders Lauren M. , Wylie Lyndsay A. , Kushner Erich J. , Chong Diana C. , Citrin Kathryn M. , Barber Andrew T. , Park Youngsook , Kim Jun-Dae , Samsa Leigh Ann , Kim Jongmin , Liu Jiandong , Jin Suk-Won , Bautch Victoria L. 
Published: November 2016

AbstractFunctional blood vessel growth depends on generation of distinct but coordinated responses from endothelial cells. Bone morphogenetic proteins (BMP), part of the TGFβ superfamily, bind receptors to induce phosphorylation and nuclear translocation of SMAD transcription factors (R-SMAD1/5/8) and regulate vessel growth. However, SMAD1/5/8 signalling results in both pro- and anti-angiogenic outputs, highlighting a poor understanding of the complexities of BMP signalling in the vasculature. Here we show that BMP6 and BMP2 ligands are pro-angiogenic in vitro and in vivo, and that lateral vessel branching requires threshold levels of R-SMAD phosphorylation. Endothelial cell responsiveness to these pro-angiogenic BMP ligands is regulated by Notch status and Notch sets responsiveness by regulating a cell-intrinsic BMP inhibitor, SMAD6, which affects BMP responses upstream of target gene expression. Thus, we reveal a paradigm for Notch-dependent regulation of angiogenesis: Notch regulates SMAD6 expression to affect BMP responsiveness of endothelial cells and new vessel branch formation.
Competition among networks highlights the power of the weak
Authors: Iranzo Jaime , Buldú Javier M. , Aguirre Jacobo 
Published: November 2016

AbstractThe unpreventable connections between real networked systems have recently called for an examination of percolation, diffusion or synchronization phenomena in multilayer networks. Here we use network science and game theory to explore interactions in networks-of-networks and model these as a game for gaining importance. We propose a viewpoint where networks choose the connection strategies, in contrast with classical approaches where nodes are the active players. Specifically, we investigate how creating paths between networks leads to different Nash equilibria that determine their structural and dynamical properties. In a wide variety of cases, selecting adequate connections leads to a cooperative solution that allows weak networks to overcome the strongest opponent. Counterintuitively, each weak network can induce a global transition to such cooperative configuration regardless of the actions of the strongest network. This power of the weak reveals a critical dominance of the underdogs in the fate of networks-of-networks.
tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence
Authors: Chionh Yok Hian , McBee Megan , Babu I. Ramesh , Hia Fabian , Lin Wenwei , Zhao Wei , Cao Jianshu , Dziergowska Agnieszka , Malkiewicz Andrzej , Begley Thomas J. , Alonso Sylvie , Dedon Peter C. 
Published: November 2016

AbstractMicrobial pathogens adapt to the stress of infection by regulating transcription, translation and protein modification. We report that changes in gene expression in hypoxia-induced non-replicating persistence in mycobacteria—which models tuberculous granulomas—are partly determined by a mechanism of tRNA reprogramming and codon-biased translation. Mycobacterium bovis BCG responded to each stage of hypoxia and aerobic resuscitation by uniquely reprogramming 40 modified ribonucleosides in tRNA, which correlate with selective translation of mRNAs from families of codon-biased persistence genes. For example, early hypoxia increases wobble cmo5U in tRNAThr(UGU), which parallels translation of transcripts enriched in its cognate codon, ACG, including the DosR master regulator of hypoxic bacteriostasis. Codon re-engineering of dosR exaggerates hypoxia-induced changes in codon-biased DosR translation, with altered dosR expression revealing unanticipated effects on bacterial survival during hypoxia. These results reveal a coordinated system of tRNA modifications and translation of codon-biased transcripts that enhance expression of stress response proteins in mycobacteria.
Modulated phases of graphene quantum Hall polariton fluids
Authors: Pellegrino Francesco M. D. , Giovannetti Vittorio , MacDonald Allan H. , Polini Marco 
Published: November 2016

AbstractThere is a growing experimental interest in coupling cavity photons to the cyclotron resonance excitations of electron liquids in high-mobility semiconductor quantum wells or graphene sheets. These media offer unique platforms to carry out fundamental studies of exciton-polariton condensation and cavity quantum electrodynamics in a regime, in which electron–electron interactions are expected to play a pivotal role. Here, focusing on graphene, we present a theoretical study of the impact of electron–electron interactions on a quantum Hall polariton fluid, that is a fluid of magneto-excitons resonantly coupled to cavity photons. We show that electron–electron interactions are responsible for an instability of graphene integer quantum Hall polariton fluids towards a modulated phase. We demonstrate that this phase can be detected by measuring the collective excitation spectra, which is often at a characteristic wave vector of the order of the inverse magnetic length.
A two-dimensional spin field-effect switch
Authors: Yan Wenjing , Txoperena Oihana , Llopis Roger , Dery Hanan , Hueso Luis E. , Casanova Fèlix 
Published: November 2016

AbstractFuture development in spintronic devices will require an advanced control of spin currents, for example by an electric field. Here we demonstrate an approach that differs from previous proposals such as the Datta and Das modulator, and that is based on a van de Waals heterostructure of atomically thin graphene and semiconducting MoS2. Our device combines the superior spin transport properties of graphene with the strong spin–orbit coupling of MoS2 and allows switching of the spin current in the graphene channel between ON and OFF states by tuning the spin absorption into the MoS2 with a gate electrode. Our proposal holds potential for technologically relevant applications such as search engines or pattern recognition circuits, and opens possibilities towards electrical injection of spins into transition metal dichalcogenides and alike materials.
Reader domain specificity and lysine demethylase-4 family function
Authors: Su Zhangli , Wang Fengbin , Lee Jin-Hee , Stephens Kimberly E. , Papazyan Romeo , Voronina Ekaterina , Krautkramer Kimberly A. , Raman Ana , Thorpe Jeremy J. , Boersma Melissa D. , Kuznetsov Vyacheslav I. , Miller Mitchell D. , Taverna Sean D. , Phillips George N. , Denu John M. 
Published: November 2016

AbstractThe KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an extensive histone peptide microarray analysis uncovers trimethyl-lysine histone-binding preferences among the closely related KDM4 double tudor domains (DTDs). KDM4A/B DTDs bind strongly to H3K23me3, a poorly understood histone modification recently shown to be enriched in meiotic chromatin of ciliates and nematodes. The 2.28 Å co-crystal structure of KDM4A-DTD in complex with H3K23me3 peptide reveals key intermolecular interactions for H3K23me3 recognition. Furthermore, analysis of the 2.56 Å KDM4B-DTD crystal structure pinpoints the underlying residues required for exclusive H3K23me3 specificity, an interaction supported by in vivo co-localization of KDM4B and H3K23me3 at heterochromatin in mammalian meiotic and newly postmeiotic spermatocytes. In vitro demethylation assays suggest H3K23me3 binding by KDM4B stimulates H3K36 demethylation. Together, these results provide a possible mechanism whereby H3K23me3-binding by KDM4B directs localized H3K36 demethylation during meiosis and spermatogenesis.
Arabidopsis seed germination speed is controlled by SNL histone deacetylase-binding factor-mediated regulation of AUX1
Authors: Wang Zhi , Chen Fengying , Li Xiaoying , Cao Hong , Ding Meng , Zhang Cun , Zuo Jinghong , Xu Chaonan , Xu Jimei , Deng Xin , Xiang Yong , Soppe Wim J. J. , Liu Yongxiu 
Published: November 2016

AbstractHistone acetylation is known to affect the speed of seed germination, but the molecular regulatory basis of this remains ambiguous. Here we report that loss of function of two histone deacetylase-binding factors, SWI-INDEPENDENT3 (SIN3)-LIKE1 (SNL1) and SNL2, results in accelerated radicle protrusion and growth during seed germination. AUXIN RESISTANT 1 (AUX1) is identified as a key factor in this process, enhancing germination speed downstream of SNL1 and SNL2. AUX1 expression and histone H3 acetylation at lysines 9 and 18 is regulated by SNL1 and SNL2. The D-type cyclins encoding genes CYCD1;1 and CYCD4;1 display increased expression in AUX1 over-expression lines and the snl1snl2 double mutant. Accordingly, knockout of CYCD4;1 reduces seed germination speed of AUX1 over-expression lines and snl1snl2 suggesting the importance of cell cycling for radicle protrusion during seed germination. Together, our work identifies AUX1 as a link between histone acetylation mediated by SNL1 and SNL2, and radicle growth promoted by CYCD1;1 and CYCD4;1 during seed germination.
In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075
Authors: Wu Xia , Chavez Juan D. , Schweppe Devin K. , Zheng Chunxiang , Weisbrod Chad R. , Eng Jimmy K. , Murali Ananya , Lee Samuel A. , Ramage Elizabeth , Gallagher Larry A. , Kulasekara Hemantha D. , Edrozo Mauna E. , Kamischke Cassandra N. , Brittnacher Mitchell J. , Miller Samuel I. , Singh Pradeep K. , Manoil Colin , Bruce James E. 
Published: November 2016

AbstractThe nosocomial pathogen Acinetobacter baumannii is a frequent cause of hospital-acquired infections worldwide and is a challenge for treatment due to its evolved resistance to antibiotics, including carbapenems. Here, to gain insight on A. baumannii antibiotic resistance mechanisms, we analyse the protein interaction network of a multidrug-resistant A. baumannii clinical strain (AB5075). Using in vivo chemical cross-linking and mass spectrometry, we identify 2,068 non-redundant cross-linked peptide pairs containing 245 intra- and 398 inter-molecular interactions. Outer membrane proteins OmpA and YiaD, and carbapenemase Oxa-23 are hubs of the identified interaction network. Eighteen novel interactors of Oxa-23 are identified. Interactions of Oxa-23 with outer membrane porins OmpA and CarO are verified with co-immunoprecipitation analysis. Furthermore, transposon mutagenesis of oxa-23 or interactors of Oxa-23 demonstrates changes in meropenem or imipenem sensitivity in strain AB5075. These results provide a view of porin-localized antibiotic inactivation and increase understanding of bacterial antibiotic resistance mechanisms.
Electrically Tunable Nd:YAG waveguide laser based on Graphene
Authors: Ma Linan , Tan Yang , Akhmadaliev Shavkat , Zhou Shengqiang , Chen Feng 
Published: November 2016

AbstractWe demonstrate a tunable hybrid Graphene-Nd:YAG cladding waveguide laser exploiting the electro-optic and the Joule heating effects of Graphene. A cladding Nd:YAG waveguide was fabricated by the ion irradiation. The multi-layer graphene were transferred onto the waveguide surface as the saturable absorber to get the Q-switched pulsed laser oscillation in the waveguide. Composing with appropriate electrodes, graphene based capacitance and heater were formed on the surface of the Nd:YAG waveguide. Through electrical control of graphene, the state of the hybrid waveguide laser was turned on or off. And the laser operation of the hybrid waveguide was electrically tuned between the continuous wave laser and the nanosecond pulsed laser.
Engineering yeast for high-level production of stilbenoid antioxidants
Authors: Li Mingji , Schneider Konstantin , Kristensen Mette , Borodina Irina , Nielsen Jens 
Published: November 2016

AbstractStilbenoids, including resveratrol and its methylated derivatives, are natural potent antioxidants, produced by some plants in trace amounts as defense compounds. Extraction of stilbenoids from natural sources is costly due to their low abundance and often limited availability of the plant. Here we engineered the yeast Saccharomyces cerevisiae for production of stilbenoids on a simple mineral medium typically used for industrial production. We applied a pull-push-block strain engineering strategy that included overexpression of the resveratrol biosynthesis pathway, optimization of the electron transfer to the cytochrome P450 monooxygenase, increase of the precursors supply, and decrease of the pathway intermediates degradation. Fed-batch fermentation of the final strain resulted in a final titer of 800 mg l−1 resveratrol, which is by far the highest titer reported to date for production of resveratrol from glucose. We further integrated heterologous methyltransferases into the resveratrol platform strain and hereby demonstrated for the first time de novo biosynthesis of pinostilbene and pterostilbene, which have better stability and uptake in the human body, from glucose.
Non-contact radio frequency shielding and wave guiding by multi-folded transformation optics method
Authors: Madni Hamza Ahmad , Zheng Bin , Yang Yihao , Wang Huaping , Zhang Xianmin , Yin Wenyan , Li Erping , Chen Hongsheng 
Published: November 2016

AbstractCompared with conventional radio frequency (RF) shielding methods in which the conductive coating material encloses the circuits design and the leakage problem occurs due to the gap in such conductive material, non-contact RF shielding at a distance is very promising but still impossible to achieve so far. In this paper, a multi-folded transformation optics method is proposed to design a non-contact device for RF shielding. This “open-shielded” device can shield any object at a distance from the electromagnetic waves at the operating frequency, while the object is still physically open to the outer space. Based on this, an open-carpet cloak is proposed and the functionality of the open-carpet cloak is demonstrated. Furthermore, we investigate a scheme of non-contact wave guiding to remotely control the propagation of surface waves over any obstacles. The flexibilities of such multi-folded transformation optics method demonstrate the powerfulness of the method in the design of novel remote devices with impressive new functionalities.
Fastest Formation Routes of Nanocarbons in Solution Plasma Processes
Authors: Morishita Tetsunori , Ueno Tomonaga , Panomsuwan Gasidit , Hieda Junko , Yoshida Akihito , Bratescu Maria Antoaneta , Saito Nagahiro 
Published: November 2016

AbstractAlthough solution-plasma processing enables room-temperature synthesis of nanocarbons, the underlying mechanisms are not well understood. We investigated the routes of solution-plasma-induced nanocarbon formation from hexane, hexadecane, cyclohexane, and benzene. The synthesis rate from benzene was the highest. However, the nanocarbons from linear molecules were more crystalline than those from ring molecules. Linear molecules decomposed into shorter olefins, whereas ring molecules were reconstructed in the plasma. In the saturated ring molecules, C–H dissociation proceeded, followed by conversion into unsaturated ring molecules. However, unsaturated ring molecules were directly polymerized through cation radicals, such as benzene radical cation, and were converted into two- and three-ring molecules at the plasma–solution interface. The nanocarbons from linear molecules were synthesized in plasma from small molecules such as C2under heat; the obtained products were the same as those obtained via pyrolysis synthesis. Conversely, the nanocarbons obtained from ring molecules were directly synthesized through an intermediate, such as benzene radical cation, at the interface between plasma and solution, resulting in the same products as those obtained via polymerization. These two different reaction fields provide a reasonable explanation for the fastest synthesis rate observed in the case of benzene.
High Hepsin expression predicts poor prognosis in Gastric Cancer
Authors: Zhang Mingming , Zhao Junjie , Tang Wenyi , Wang Yanru , Peng Peike , Li Lili , Song Shushu , Wu Hao , Li Can , Yang Caiting , Wang Xuefei , Zhang Chunyi , Gu Jianxin 
Published: November 2016

AbstractHepsin, a membrane-associated serine protease, is frequently upregulated in epithelial cancers and involved in cancer progression. Our study aims to describe the expression pattern and evaluate the clinical implication of hepsin in gastric cancer patients. The mRNA expression of hepsin was analyzed in 50 gastric cancer and matched non-tumor tissues, which was downregulated in 78% (39/50) of gastric cancer. By searching and analyzing four independent datasets from Oncomine, we obtained the similar results. Furthermore, we evaluated the hepsin expression by IHC in tissue microarray (TMA) containing 220 Gastric Cancer specimens. More importantly, Kaplan-Meier survival and Cox regression analyses were taken to access the prognosis of gastric cancer and predicted that hepsin protein expression was one of the significant and independent prognostic factors for overall survival of Gastric Cancer.
Chip-scale cavity optomechanics in lithium niobate
Authors: Jiang Wei C. , Lin Qiang 
Published: November 2016

AbstractWe develop a chip-scale cavity optomechanical system in single-crystal lithium niobate that exhibits high optical quality factors and a large frequency-quality product as high as 3.6 × 1012 Hz at room temperature and atmosphere. The excellent optical and mechanical properties together with the strong optomechanical coupling allow us to efficiently excite the coherent regenerative optomechanical oscillation operating at 375 MHz with a threshold power of 174 μW in the air. The demonstrated lithium niobate optomechanical device enables great potential for achieving electro-optic-mechanical hybrid systems for broad applications in sensing, metrology, and quantum physics.
PD-L1 expression on immune cells, but not on tumor cells, is a favorable prognostic factor for head and neck cancer patients
Authors: Kim Hye Ryun , Ha Sang-Jun , Hong Min Hee , Heo Su Jin , Koh Yoon Woo , Choi Eun Chang , Kim Eun Kyung , Pyo Kyoung Ho , Jung Inkyung , Seo Daekwan , Choi Jaewoo , Cho Byoung Chul , Yoon Sun Och 
Published: November 2016

AbstractTo investigate the expression of programmed death-ligand 1 (PD-L1) and immune checkpoints and their prognostic value for resected head and neck squamous cell cancer (HNSCC). PD-L1 expression on tumor cells (TC) and tumor-infiltrating immune cells (IC), abundance of tumor-infiltrating lymphocytes (TILs), and expression of the immune checkpoints were investigated in 402 HNSCC patients. PD-L1 expression on TC and IC was categorized into four groups according to the percentage of PD-L1-positive cells. PD-L1 positivity was defined as ≥5% of cells based on immunohistochemistry. High PD-L1 expression on IC, but not TC, was an independent favorable prognostic factor for RFS and OS adjusted for age, gender, smoking, stage, and HPV. High frequencies of CD3+ or CD8+ TILs, Foxp3+ Tregs, and PD-1+ TILs were strongly associated with favorable prognosis. PD-L1 was exclusively expressed on either TC or IC. Transcriptome analysis demonstrated that IC3 expressed higher levels of the effector T cell markers than TC3, suggesting that PD-L1 expression is regulated via an adaptive IFNγ-mediated mechanism. High PD-L1 expression on IC, but not TC, and high abundance of PD-1+ T cells and Foxp3+ Tregs are favorable prognostic factors for resected HNSCC. This study highlights the importance of comprehensive assessment of both TC and IC.