bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photo-induced enhanced Raman spectroscopy for universal ultra-trace detection of explosives, pollutants and biomolecules
Authors: Ben-Jaber Sultan , Peveler William J. , Quesada-Cabrera Raul , Cortés Emiliano , Sotelo-Vazquez Carlos , Abdul-Karim Nadia , Maier Stefan A. , Parkin Ivan P. 
Published: July 2016

AbstractSurface-enhanced Raman spectroscopy is one of the most sensitive spectroscopic techniques available, with single-molecule detection possible on a range of noble-metal substrates. It is widely used to detect molecules that have a strong Raman response at very low concentrations. Here we present photo-induced-enhanced Raman spectroscopy, where the combination of plasmonic nanoparticles with a photo-activated substrate gives rise to large signal enhancement (an order of magnitude) for a wide range of small molecules, even those with a typically low Raman cross-section. We show that the induced chemical enhancement is due to increased electron density at the noble-metal nanoparticles, and demonstrate the universality of this system with explosives, biomolecules and organic dyes, at trace levels. Our substrates are also easy to fabricate, self-cleaning and reusable.
Quantum gate learning in qubit networks: Toffoli gate without time-dependent control
Authors: Banchi Leonardo , Pancotti Nicola , Bose Sougato 
Published: July 2016

AbstractWe put forward a strategy to encode a quantum operation into the unmodulated dynamics of a quantum network without the need for external control pulses, measurements or active feedback. Our optimisation scheme, inspired by supervised machine learning, consists in engineering the pairwise couplings between the network qubits so that the target quantum operation is encoded in the natural reduced dynamics of a network section. The efficacy of the proposed scheme is demonstrated by the finding of uncontrolled four-qubit networks that implement either the Toffoli gate, the Fredkin gate or remote logic operations. The proposed Toffoli gate is stable against imperfections, has a high fidelity for fault-tolerant quantum computation and is fast, being based on the non-equilibrium dynamics.
G-protein-coupled receptor kinase 2 terminates G-protein-coupled receptor function in steroid hormone 20-hydroxyecdysone signaling
Authors: Zhao Wen-Li , Wang Di , Liu Chun-Yan , Zhao Xiao-Fan 
Published: July 2016

AbstractG-protein-coupled receptors (GPCRs) transmit extracellular signals across the cell membrane. GPCR kinases (GRKs) desensitize GPCR signals in the cell membrane. However, the role and mechanism of GRKs in the desensitization of steroid hormone signaling are unclear. In this study, we propose that GRK2 is phosphorylated by protein kinase C (PKC) in response to induction by the steroid hormone 20-hydroxyecdysone (20E), which determines its translocation to the cell membrane of the lepidopteran Helicoverpa armigera. GRK2 protein expression is increased during the metamorphic stage because of induction by 20E. Knockdown of GRK2 in larvae causes accelerated pupation, an increase in 20E-response gene expression and advanced apoptosis and metamorphosis. 20E induces translocation of GRK2 from the cytoplasm to the cell membrane via steroid hormone ecdysone-responsive GPCR (ErGPCR-2). GRK2 is phosphorylated by PKC on serine 680 after induction by 20E, which leads to the translocation of GRK2 to the cell membrane. GRK2 interacts with ErGPCR-2. These data indicate that GRK2 terminates the ErGPCR-2 function in 20E signaling in the cell membrane by a negative feedback mechanism.
Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness
Authors: Walsh Christopher J. , Batt Jane , Herridge Margaret S. , Mathur Sunita , Bader Gary D. , Hu Pingzhao , dos Santos Claudia C. 
Published: July 2016

AbstractICU acquired weakness (ICUAW) is a common complication of critical illness characterized by structural and functional impairment of skeletal muscle. The resulting physical impairment may persist for years after ICU discharge, with few patients regaining functional independence. Elucidating molecular mechanisms underscoring sustained ICUAW is crucial to understanding outcomes linked to different morbidity trajectories as well as for the development of novel therapies. Quadriceps muscle biopsies and functional measures of muscle strength and mass were obtained at 7 days and 6 months post-ICU discharge from a cohort of ICUAW patients. Unsupervised co-expression network analysis of transcriptomic profiles identified discrete modules of co-expressed genes associated with the degree of muscle weakness and atrophy in early and sustained ICUAW. Modules were enriched for genes involved in skeletal muscle regeneration and extracellular matrix deposition. Collagen deposition in persistent ICUAW was confirmed by histochemical stain. Modules were further validated in an independent cohort of critically ill patients with sepsis-induced multi-organ failure and a porcine model of ICUAW, demonstrating disease-associated conservation across species and peripheral muscle type. Our findings provide a pathomolecular basis for sustained ICUAW, implicating aberrant expression of distinct skeletal muscle structural and regenerative genes in early and persistent ICUAW.
Breeding signature of combining ability improvement revealed by a genomic variation map from recurrent selection population in Brassica napus
Authors: Zhao Xinwang , Li Bao , Zhang Ka , Hu Kaining , Yi Bin , Wen Jing , Ma Chaozhi , Shen Jinxiong , Fu Tingdong , Tu Jinxing 
Published: July 2016

AbstractCombining ability is crucial for parent selection in crop hybrid breeding. The present investigation and results had revealed the underlying genetic factors which might contribute in adequate combining ability, further assisting in enhancing heterosis and stability. Here, we conducted a large-scale analysis of genomic variation in order to define genomic regions affecting the combining ability in recurrent selection population of rapeseed. A population of 175 individuals was genotyped with the Brassica60K SNP chip. 525 hybrids were assembled with three different testers and used to evaluate the general combining ability (GCA) in three environments. By detecting the changes of the genomic variation, we identified 376 potential genome regions, spanning 3.03% of rapeseed genome which provided QTL-level resolution on potentially selected variants. More than 96% of these regions were located in the C subgenome, indicating that C subgenome had sustained stronger selection pressure in the breeding program than the A subgenome. In addition, a high level of linkage disequilibrium in rapeseed genome was detected, suggesting that marker-assisted selection for the population improvement might be easily implemented. This study outlines the evidence for high GCA on a genomic level and provided underlying molecular mechanism for recurrent selection improvement in B. napus.
The Synthetic Elicitor DPMP (2,4-dichloro-6-{(E)-[(3-methoxyphenyl)imino]methyl}phenol) Triggers Strong Immunity in Arabidopsis thaliana and Tomato
Authors: Bektas Yasemin , Rodriguez-Salus Melinda , Schroeder Mercedes , Gomez Adilene , Kaloshian Isgouhi , Eulgem Thomas 
Published: July 2016

AbstractSynthetic elicitors are drug-like compounds that are structurally distinct from natural defense elicitors. They can protect plants from diseases by activating host immune responses and can serve as tools for the dissection of the plant immune system as well as leads for the development of environmentally-safe pesticide alternatives. By high-throughput screening, we previously identified 114 synthetic elicitors that activate expression of the pathogen-responsive CaBP22−333::GUS reporter gene in Arabidopsis thaliana (Arabidopsis), 33 of which are [(phenylimino)methyl]phenol (PMP) derivatives or PMP-related compounds. Here we report on the characterization of one of these compounds, 2,4-dichloro-6-{(E)-[(3-methoxyphenyl)imino]methyl}phenol (DPMP). DPMP strongly triggers disease resistance of Arabidopsis against bacterial and oomycete pathogens. By mRNA-seq analysis we found transcriptional profiles triggered by DPMP to resemble typical defense-related responses.
Uncovering the Relationship between Sulphation Patterns and Conformation of Iduronic Acid in Heparan Sulphate
Authors: Hsieh Po-Hung , Thieker David F. , Guerrini Marco , Woods Robert J. , Liu Jian 
Published: July 2016

AbstractThe L-iduronic acid (IdoA) residue is a critically important structural component in heparan sulphate polysaccharide for the biological functions. The pyranose ring of IdoA is present in 1C4-chair, 2SO-skew boat and less frequently, in 4C1-chair conformations. Here, we analyzed the conformation of IdoA residue in eight hexasaccharides by NMR. The data demonstrate a correlation between the conformation of IdoA and sulphations in the surrounding saccharide residues. For the 2-O-sulpho IdoA residue, a high degree of sulphation on neighboring residues drives ring dynamics towards the 2SO-skew boat conformer. In contrast, the nonsulphated IdoA residue is pushed towards the 1C4-chair conformer when the neighboring residues are highly sulphated. Our data suggest that the conformation of IdoA is regulated by the sulphation pattern of nearby saccharides that is genetically controlled by the heparan sulphate biosynthetic pathway.
Neonicotinoid-contaminated pollinator strips adjacent to cropland reduce honey bee nutritional status
Authors: Mogren Christina L. , Lundgren Jonathan G. 
Published: July 2016

AbstractWorldwide pollinator declines are attributed to a number of factors, including pesticide exposures. Neonicotinoid insecticides specifically have been detected in surface waters, non-target vegetation, and bee products, but the risks posed by environmental exposures are still not well understood. Pollinator strips were tested for clothianidin contamination in plant tissues, and the risks to honey bees assessed. An enzyme-linked immunosorbent assay (ELISA) quantified clothianidin in leaf, nectar, honey, and bee bread at organic and seed-treated farms. Total glycogen, lipids, and protein from honey bee workers were quantified. The proportion of plants testing positive for clothianidin were the same between treatments. Leaf tissue and honey had similar concentrations of clothianidin between organic and seed-treated farms. Honey (mean±SE: 6.61 ± 0.88 ppb clothianidin per hive) had seven times greater concentrations than nectar collected by bees (0.94 ± 0.09 ppb). Bee bread collected from organic sites (25.8 ± 3.0 ppb) had significantly less clothianidin than those at seed treated locations (41.6 ± 2.9 ppb). Increasing concentrations of clothianidin in bee bread were correlated with decreased glycogen, lipid, and protein in workers. This study shows that small, isolated areas set aside for conservation do not provide spatial or temporal relief from neonicotinoid exposures in agricultural regions where their use is largely prophylactic.
Interferon regulatory factor 3 is a key regulation factor for inducing the expression of SAMHD1 in antiviral innate immunity
Authors: Yang Shen , Zhan Yuan , Zhou Yanjun , Jiang Yifeng , Zheng Xuchen , Yu Lingxue , Tong Wu , Gao Fei , Li Liwei , Huang Qinfeng , Ma Zhiyong , Tong Guangzhi 
Published: July 2016

AbstractSAMHD1 is a type I interferon (IFN) inducible host innate immunity restriction factor that inhibits an early step of the viral life cycle. The underlying mechanisms of SAMHD1 transcriptional regulation remains elusive. Here, we report that inducing SAMHD1 upregulation is part of an early intrinsic immune response via TLR3 and RIG-I/MDA5 agonists that ultimately induce the nuclear translocation of the interferon regulation factor 3 (IRF3) protein. Further studies show that IRF3 plays a major role in upregulating endogenous SAMHD1 expression in a mechanism that is independent of the classical IFN-induced JAK-STAT pathway. Both overexpression and activation of IRF3 enhanced the SAMHD1 promoter luciferase activity, and activated IRF3 was necessary for upregulating SAMHD1 expression in a type I IFN cascade. We also show that the SAMHD1 promoter is a direct target of IRF3 and an IRF3 binding site is sufficient to render this promoter responsive to stimulation. Collectively, these findings indicate that upregulation of endogenous SAMHD1 expression is attributed to the phosphorylation and nuclear translocation of IRF3 and we suggest that type I IFN induction and induced SAMHD1 expression are coordinated.
Zwitterionic chitosan for the systemic treatment of sepsis
Authors: Cho Eun Jung , Doh Kyung-Oh , Park Jinho , Hyun Hyesun , Wilson Erin M. , Snyder Paul W. , Tsifansky Michael D. , Yeo Yoon 
Published: July 2016

AbstractSevere sepsis and septic shock are life-threatening conditions, with Gram-negative organisms responsible for most sepsis mortality. Systemic administration of compounds that block the action of lipopolysaccharide (LPS), a constituent of the Gram-negative outer cell membrane, is hampered by their hydrophobicity and cationic charge, the very properties responsible for their interactions with LPS. We hypothesize that a chitosan derivative zwitterionic chitosan (ZWC), previously shown to suppress the production of pro-inflammatory cellular mediators in LPS-challenged macrophages, will have protective effects in an animal model of sepsis induced by systemic injection of LPS. In this study, we evaluate whether ZWC attenuates the fatal effect of LPS in C57BL/6 mice and investigate the mechanism by which ZWC counteracts the LPS effect using a PMJ2-PC peritoneal macrophage cell line. Unlike its parent compound with low water solubility, intraperitoneally administered ZWC is readily absorbed with no local residue or adverse tissue reaction at the injection site. Whether administered at or prior to the LPS challenge, ZWC more than doubles the animals’ median survival time. ZWC appears to protect the LPS-challenged organisms by forming a complex with LPS and thus attenuating pro-inflammatory signaling pathways. These findings suggest that ZWC have utility as a systemic anti-LPS agent.
Persisting and Increasing Neutrophil Infiltration Associates with Gastric Carcinogenesis and E-cadherin Downregulation
Authors: Fu Hualin , Ma Yue , Yang Meng , Zhang Chunlei , Huang Hai , Xia Ying , Lu Lungen , Jin Weilin , Cui Daxiang 
Published: July 2016

AbstractH. pylori-induced chronic inflammation is considered the most important cause of gastric cancer. The actual process how chronic inflammation triggers gastric carcinogenesis is still not clear. In this study, neutrophils and relative markers in gastric cancer development were examined with immunohistochemistry and fluorescence RNA in situ hybridization methods. On average, 24 times more neutrophils were found in gastric cancer tissues and about 9 times more neutrophils were found in gastric intestinal metaplasia tissues comparing to normal gastric tissue controls. CagA+ H. pylori infection in cancer adjacent tissues or EBV infection in cancer tissues did not increase neutrophil infiltration into gastric cancer tissues significantly. Neutrophil density was positively correlated with cell proliferation while negatively correlated with E-cadherin intensity. E-cadherin is also transcriptionally downregulated in gastric cancer tissues comparing to adjacent tissue controls. The increased neutrophils in the gastric cancer tissues appear to be related to increased chemoattractant IL-8 levels. In gastric cancers, neutrophil numbers were higher comparing to cancer adjacent tissues and not associated with patient ages, tumor invasion depth, tumor staging, metastasis or cancer types. The conclusion is that persisting and increasing neutrophil infiltration is associated with E-cadherin downregulation, cell proliferation and gastric carcinogenesis.
Intra-amniotic Candida albicans infection induces mucosal injury and inflammation in the ovine fetal intestine
Authors: Nikiforou Maria , Jacobs Esmee M.R. , Kemp Matthew W. , Hornef Mathias W. , Payne Matthew S. , Saito Masatoshi , Newnham John P. , Janssen Leon E.W. , Jobe Alan H. , Kallapur Suhas G. , Kramer Boris W. , Wolfs Tim G.A.M. 
Published: July 2016

AbstractChorioamnionitis is caused by intrauterine infection with microorganisms including Candida albicans (C.albicans). Chorioamnionitis is associated with postnatal intestinal pathologies including necrotizing enterocolitis. The underlying mechanisms by which intra-amnioticC.albicansinfection adversely affects the fetal gut remain unknown. Therefore, we assessed whether intra-amnioticC.albicansinfection would cause intestinal inflammation and mucosal injury in an ovine model. Additionally, we tested whether treatment with the fungistatic fluconazole ameliorated the adverse intestinal outcome of intra-amnioticC.albicansinfection. Pregnant sheep received intra-amniotic injections with 107colony-forming unitsC.albicansor saline at 3 or 5 days before preterm delivery at 122 days of gestation. Fetuses were given intra-amniotic and intra-peritoneal fluconazole treatments 2 days after intra-amniotic administration ofC.albicans. Intra-amnioticC.albicanscaused intestinal colonization and invasive growth within the fetal gut with mucosal injury and intestinal inflammation, characterized by increased CD3+lymphocytes, MPO+cells and elevated TNF-α and IL-17 mRNA levels. Fluconazole treatmentin uterodecreased intestinalC.albicanscolonization, mucosal injury but failed to attenuate intestinal inflammation. Intra-amnioticC.albicanscaused intestinal infection, injury and inflammation. Fluconazole treatment decreased mucosal injury but failed to ameliorateC.albicans-mediated mucosal inflammation emphasizing the need to optimize the applied antifungal therapeutic strategy.
Acetylome analysis reveals the involvement of lysine acetylation in diverse biological processes in Phytophthora sojae
Authors: Li Delong , Lv Binna , Tan Lingling , Yang Qianqian , Liang Wenxing 
Published: July 2016

AbstractLysine acetylation is a dynamic and highly conserved post-translational modification that plays an important regulatory role in almost every aspects of cell metabolism in both eukaryotes and prokaryotes. Phytophthora sojae is one of the most important plant pathogens due to its huge economic impact. However, to date, little is known about the functions of lysine acetylation in this Phytopthora. Here, we conducted a lysine acetylome in P. sojae. Overall, 2197 lysine acetylation sites in 1150 proteins were identified. The modified proteins are involved in diverse biological processes and are localized to multiple cellular compartments. Importantly, 7 proteins involved in the pathogenicity or the secretion pathway of P. sojae were found to be acetylated. These data provide the first comprehensive view of the acetylome of P. sojae and serve as an important resource for functional analysis of lysine acetylation in plant pathogens.
Environmental Exposure to Cadmium: Health Risk Assessment and its Associations with Hypertension and Impaired Kidney Function
Authors: Wu Haiyun , Liao Qilin , Chillrud Steven N. , Yang Qiang , Huang Lei , Bi Jun , Yan Beizhan 
Published: July 2016

AbstractCadmium (Cd) is a toxic metal. This study was aimed to estimate the potential health risks in a Cd-polluted district in China, and examine the relationship between urinary cadmium(UCd) and hypertension and impaired kidney function at low exposure levels (UCd: GM 1.3 μg/g creatinine). Blood pressure measurement, questionnaires, and collection of urinary samples were conducted from 217 residents. Environmental samples, food, and cigarette samples were collected and detected to estimate the risks posed by Cd and the contribution of inhalation, ingestion, and dermal contact pathways to these risks. A logistic regression model was used in examining associations between exposure and hypertension and impaired kidney function. Results show that this population is at high risk. For non-smokers, incremental lifetime cancer risk (ILCR) and hazard quotient (HQ) are 1.74E-04 and 2.96, and for smokers, they are 1.07E-03 and 52.5, respectively. Among all exposure pathways, smoking and foods cause the major increases in ILCR and HQ. UCd is significantly associated with hypertension (odds ratio (OR) = 1.468; 95% confidence interval (CI): 1.104, 1.953; P = 0.008) and impaired kidney function (OR = 1.902, 95% CI: 1.054, 3.432; P = 0.033). The results demonstrate that Cd can potentially lead to adverse health effects.
Two constructions of binary sequences with optimal autocorrelation magnitude
Authors: Krengel E.I. , Ivanov P.V. 
Published: July 2016

In this Letter, two constructions of new binary sequences with optimal autocorrelation magnitude of length 4N derived from binary sequences with optimal autocorrelation of length N = 2 (mod 4) and almost‐perfect binary sequences of length 2N using N × 2 interleaved structure is presented. The first construction is to use binary Sidelnikov sequences of length N = pn−1 whereas the second one is to use binary Ding–Helleseth–Martinsen sequences of length N = 2p. The obtained sequences have large linear complexity and can be used in communication and cryptography.
Mode Effect and Response Rate Issues in Mixed-Mode Survey Research: Implications for Recreational Fisheries Management
Authors: Wallen Kenneth E. , Landon Adam C. , Kyle Gerard T. , Schuett Michael A. , Leitz Jeremy , Kurzawski Ken 
Published: July 2016

Abstract
While the social, economic, and ecological impact of recreational fisheries is well established, the inherent diversity of both fisheries resources and resource users, particularly anglers, continues to present a challenge for management agencies. To better understand the diversity of recreational anglers, agencies often utilize survey methods to collect data on angler characteristics and preferences. However, obtaining necessary and representative data is becoming more challenging, exacerbated by declining response rates and an increase in the number of single and mixed-mode survey designs researchers can choose to collect data. We examined three survey designs—surface mail with a Web push, e-mail, and mixed mode—each with varying modes of solicitation and response, in the context of a statewide survey of licensed Texas anglers. Our findings illustrated that response rates varied considerably among these three survey designs. We also observed significant variation in terms of anglers’ sociodemographic characteristics based on solicitation and response modes of each survey design. Interestingly, we observed limited variation in terms of anglers’ behaviors, preferences, and motivations. Our results highlight the need for researchers and managers to be aware of the various survey designs available and the variability that particular survey designs can introduce into data.
Received August 1, 2014; accepted March 2, 2016 Published online July 13, 2016
Patient portals and personal health information online: perception, access, and use by US adults
Authors: Peacock Sue , Reddy Ashok , Leveille Suzanne G , Walker Jan , Payne Thomas H , Oster Natalia V , Elmore Joann G 
Published: July 2016

Background: Access to online patient portals is key to improving care, but we have limited understanding of patient perceptions of online portals and the characteristics of people who use them.
Methods: Using a national survey of 3677 respondents, we describe perceptions and utilization of online personal health information (PHI) portals.
Results: Most respondents (92%) considered online PHI access important, yet only 34% were offered access to online PHI by a health care provider, and just 28% accessed online PHI in the past year. While there were no differences across race or ethnicity in importance of access, black and Hispanic respondents were significantly less likely to be offered access (P = .006 and &lt;.001, respectively) and less likely to access their online PHI (P = .041 and &lt;.001, respectively) compared to white and non-Hispanic respondents.
Conclusion: Health care providers are crucial to the adoption and use of online patient portals and should be encouraged to offer consistent access regardless of patient race and ethnicity.