bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endocidal Regulation of Secondary Metabolites in the Producing Organisms
Authors: Li Shiyou , Wang Ping , Yuan Wei , Su Zushang , Bullard Steven H. 
Published: July 2016

AbstractSecondary metabolites are defined as organic compounds that are not directly involved in the normal growth, development, and reproduction of an organism. They are widely believed to be responsible for interactions between the producing organism and its environment, with the producer avoiding their toxicities. In our experiments, however, none of the randomly selected 44 species representing different groups of plants and insects can avoid autotoxicity by its endogenous metabolites once made available. We coined the term endocides (endogenous biocides) to describe such metabolites that can poison or inhibit the parent via induced biosynthesis or external applications. Dosage-dependent endocides can selectively induce morphological mutations in the parent organism (e.g., shrubbiness/dwarfism, pleiocotyly, abnormal leaf morphogenesis, disturbed phyllotaxis, fasciated stems, and variegation in plants), inhibit its growth, development, and reproduction and cause death than non-closely related species. The propagule, as well as the organism itself contains or produces adequate endocides to kill itself.
Exome Array Analysis of Susceptibility to Pneumococcal Meningitis
Authors: Kloek Anne T. , van Setten Jessica , van der Ende Arie , Bots Michiel L. , Asselbergs Folkert W. , Serón Mercedes Valls , Brouwer Matthijs C. , van de Beek Diederik , Ferwerda Bart 
Published: July 2016

AbstractHost genetic variability may contribute to susceptibility of bacterial meningitis, but which genes contribute to the susceptibility to this complex disease remains undefined. We performed a genetic association study in 469 community-acquired pneumococcal meningitis cases and 2072 population-based controls from the Utrecht Health Project in order to find genetic variants associated with pneumococcal meningitis susceptibility. A HumanExome BeadChip was used to genotype 102,097 SNPs in the collected DNA samples. Associations were tested with the Fisher exact test. None of the genetic variants tested reached Bonferroni corrected significance (p-value <5 × 10−7). Our strongest signals associated with susceptibility to pneumococcal meningitis were rs139064549 on chromosome 1 in the COL11A1 gene (p = 1.51 × 10−6; G allele OR 3.21 [95% CI 2.05–5.02]) and rs9309464 in the EXOC6B gene on chromosome 2 (p = 6.01 × 10−5; G allele OR 0.66 [95% CI 0.54–0.81]). The sequence kernel association test (SKAT) tests for associations between multiple variants in a gene region and pneumococcal meningitis susceptibility yielded one significant associated gene namely COL11A1 (p = 1.03 × 10−7). Replication studies are needed to validate these results. If replicated, the functionality of these genetic variations should be further studied to identify by which means they influence the pathophysiology of pneumococcal meningitis.
Human induced pluripotent stem cell-derived hepatic cell lines as a new model for host interaction with hepatitis B virus
Authors: Kaneko Shun , Kakinuma Sei , Asahina Yasuhiro , Kamiya Akihide , Miyoshi Masato , Tsunoda Tomoyuki , Nitta Sayuri , Asano Yu , Nagata Hiroko , Otani Satoshi , Kawai-Kitahata Fukiko , Murakawa Miyako , Itsui Yasuhiro , Nakagawa Mina , Azuma Seishin , Nakauchi Hiromitsu , Nishitsuji Hironori , Ujino Saneyuki , Shimotohno Kunitada , Iwamoto Masashi , Watashi Koichi , Wakita Takaji , Watanabe Mamoru 
Published: July 2016

AbstractHepatitis B virus (HBV) is not eradicated by current antiviral therapies due to persistence of HBV covalently closed circular DNA (cccDNA) in host cells and thus development of novel culture models for productive HBV infection is urgently needed, which will allow the study of HBV cccDNA eradication. To meet this need, we developed culture models of HBV infection using human induced pluripotent stem cell-derived hepatocyte lineages, including immature proliferating hepatic progenitor-like cell lines (iPS-HPCs) and differentiated hepatocyte-like cells (iPS-Heps). These cells were susceptible to HBV infection, produced HBV particles and maintained innate immune responses. The infection efficiency of HBV in iPS-HPCs predominantly depended on the expression levels of sodium taurocholate cotransporting polypeptide (NTCP) and was low relative to iPS-Heps: however, long-term culture of iPS-Heps was difficult. To provide a model for HBV persistence, iPS-HPCs overexpressing NTCP were established. The long-term persistence of HBV cccDNA was detected in iPS-HPCs overexpressing NTCP and depended on the inhibition of the Janus-kinase signaling pathway. In conclusion, this study provides evidence that iPS-derived hepatic cell lines can be utilized for novel HBV culture models with genetic variation to investigate the interactions between HBV and host cells and the development of anti-HBV strategies.
Arabidopsis thaliana extracts optimized for polyphenols production as potential therapeutics for the APOE-modulated neuroinflammation characteristic of Alzheimer’s disease in vitro
Authors: Ghura Shivesh , Tai Leon , Zhao Ming , Collins Nicole , Che Chun-Tao , Warpeha Katherine M. , LaDu Mary Jo 
Published: July 2016

AbstractAlthough the cause of Alzheimer’s disease (AD) is unknown, glial-induced neuroinflammation is an early symptom. Familial AD is caused by increases in amyloid-beta (Aβ) peptide, particularly soluble oligomeric (oAβ), considered a proximal neurotoxin and neuroinflammatory stimuli. APOE4, a naturally occurring genotype of APOE, is the greatest genetic risk factor for AD; increasing risk up to 12-fold compared to APOE3 and APOE2. oAβ-induced neuroinflammation is greater with APOE4 compared to APOE3 and APOE2. As sinapates and flavonoids have anti-inflammatory properties, a protocol was developed for optimizing polyphenol production in seedlings of Arabidopsis thaliana (A. thaliana). Three mutants (cop1, prn1, xpf3) were identified and the extracts treated with liver microsomes to mimic physiological metabolism, with HPLC and MS performed on the resulting metabolites for peak identification. These extracts were used to treat primary glial cells isolated from human APOE-targeted-replacement (APOE-TR) and APOE-knock-out (KO) mice, with neuroinflammation induced by lipopolysaccharide (LPS) or oAβ. The dose-response data for TNFα secretion demonstrate the followed the order: APOE-KO > APOE4 > APOE3 > APOE2, with xpf3 the most effective anti-neuroinflammatory across APOE genotypes. Thus, the plant-based approach described herein may be particularly valuable in treating the APOE4-induced neuroinflammatory component of AD risk.
From Ewald sphere to Ewald shell in nonlinear optics
Authors: Huang Huang , Huang Cheng-Ping , Zhang Chao , Hong Xu-Hao , Zhang Xue-Jin , Qin Yi-Qiang , Zhu Yong-Yuan 
Published: July 2016

AbstractEwald sphere is a simple vector scheme to depict the X-ray Bragg diffraction in a crystal. A similar method, known as the nonlinear Ewald sphere, was employed to illustrate optical frequency conversion processes. We extend the nonlinear Ewald sphere to the Ewald shell construction. With the Ewald shell, a variety of quasi-phase-matching (QPM) effects, such as the collective envelope effect associated with multiple QPM resonances, the enhanced second- harmonic generation due to multiple reciprocal vectors etc., are suggested theoretically and verified experimentally. By rotating the nonlinear photonic crystal sample, the dynamic evolution of these QPM effects has also been observed, which agreed well with the Ewald shell model.
Characterization of two PEBP genes, SrFT and SrMFT, in thermogenic skunk cabbage (Symplocarpus renifolius)
Authors: Ito-Inaba Yasuko , Masuko-Suzuki Hiromi , Maekawa Haruhiko , Watanabe Masao , Inaba Takehito 
Published: July 2016

AbstractFloral thermogenesis has been found in dozens of primitive seed plants and the reproductive organs in these plants produce heat during anthesis. Thus, characterization of the molecular mechanisms underlying flowering is required to fully understand the role of thermogenesis, but this aspect of thermogenic plant development is largely unknown. In this study, extensive database searches and cloning experiments suggest that thermogenic skunk cabbage (Symplocarpus renifolius), which is a member of the family Araceae, possesses two genes encoding phosphatidyl ethanolamine-binding proteins (PEBP), FLOWERING LOCUS T (SrFT) and MOTHER OF FT AND TFL1 (SrMFT). Functional analyses of SrFT and SrMFT in Arabidopsis indicate that SrFT promotes flowering, whereas SrMFT does not. In S. renifolius, the stage- and tissue-specific expression of SrFT was more evident than that of SrMFT. SrFT was highly expressed in flowers and leaves and was mainly localized in fibrovascular tissues. In addition, microarray analysis revealed that, within floral tissues, SrFT was co-regulated with the genes associated with cellular respiration and mitochondrial function, including ALTERNATIVE OXIDASE gene proposed to play a major role in floral thermogenesis. Taken together, these data suggest that, among the PEBP genes, SrFT plays a role in flowering and floral development in the thermogenic skunk cabbage.
Polarity control in WSe2 double-gate transistors
Authors: Resta Giovanni V. , Sutar Surajit , Balaji Yashwanth , Lin Dennis , Raghavan Praveen , Radu Iuliana , Catthoor Francky , Thean Aaron , Gaillardon Pierre-Emmanuel , de Micheli Giovanni 
Published: July 2016

AbstractAs scaling of conventional silicon-based electronics is reaching its ultimate limit, considerable effort has been devoted to find new materials and new device concepts that could ultimately outperform standard silicon transistors. In this perspective two-dimensional transition metal dichalcogenides, such as MoS2 and WSe2, have recently attracted considerable interest thanks to their electrical properties. Here, we report the first experimental demonstration of a doping-free, polarity-controllable device fabricated on few-layer WSe2. We show how modulation of the Schottky barriers at drain and source by a separate gate, named program gate, can enable the selection of the carriers injected in the channel and achieved controllable polarity behaviour with ON/OFF current ratios >106 for both electrons and holes conduction. Polarity-controlled WSe2 transistors enable the design of compact logic gates, leading to higher computational densities in 2D-flatronics.
Areca Nut Chewing and an Impaired Estimated Glomerular Filtration Rate as Significant Risk Factors for Non-Muscle-Invasive Bladder Cancer Recurrence
Authors: Cao Jian , Xu Ran , Zhao Xiaokun , Zhong Zhaohui , Zhang Lei , Zhu Xuan , Wu Shuiqing , Ai Kai 
Published: July 2016

AbstractThe present study sought to investigate the predictive value of preoperative clinicopathological variables, with a special focus on areca nut chewing, on disease recurrence and progression in patients with non-muscle-invasive bladder cancer (NMIBC). Data from 242 patients diagnosed with NMIBC between 2008 and 2013 were analyzed retrospectively. Fifteen clinicopathological variables were analyzed to evaluate their prognostic value. During a mean observation period of 21 months, disease recurrence occurred in 140 patients (57.9%). On multivariate analysis, heavy-areca nut chewing (HR = 2.18, 95% CI: 1.37–3.47), current smoking (HR = 3.09, 95% CI: 1.99–4.80), moderately impaired estimated glomerular filtration rate (eGFR) (HR = 1.76, 95% CI: 1.09–2.83), severely impaired eGFR (HR = 3.32, 95% CI: 1.70–6.48) and tumor grade (HR = 1.94, 95% CI: 1.36–2.77) were independent factors for recurrence, based on which a risk factor model was developed to stratify patients into high, medium and low risk groups. In conclusion, our study suggests that in addition to quitting smoking, quitting areca nut chewing may also reduce the risk of first recurrence in NMBIC patients, monitoring and preserving their renal function may be beneficial as well. Further prospective studies are needed to verify the prognostic significance of these factors and the risk stratification model in this population.
The role of membrane ERα signaling in bone and other major estrogen responsive tissues
Authors: Gustafsson K. L. , Farman H. , Henning P. , Lionikaite V. , Movérare-Skrtic S. , Wu J. , Ryberg H. , Koskela A. , Gustafsson J.-Å. , Tuukkanen J. , Levin E. R. , Ohlsson C. , Lagerquist M. K. 
Published: July 2016

AbstractEstrogen receptor α (ERα) signaling leads to cellular responses in several tissues and in addition to nuclear ERα-mediated effects, membrane ERα (mERα) signaling may be of importance. To elucidate the significance, in vivo, of mERα signaling in multiple estrogen-responsive tissues, we have used female mice lacking the ability to localize ERα to the membrane due to a point mutation in the palmitoylation site (C451A), so called Nuclear-Only-ER (NOER) mice. Interestingly, the role of mERα signaling for the estrogen response was highly tissue-dependent, with trabecular bone in the axial skeleton being strongly dependent (>80% reduction in estrogen response in NOER mice), cortical and trabecular bone in long bones, as well as uterus and thymus being partly dependent (40–70% reduction in estrogen response in NOER mice) and effects on liver weight and total body fat mass being essentially independent of mERα (<35% reduction in estrogen response in NOER mice). In conclusion, mERα signaling is important for the estrogenic response in female mice in a tissue-dependent manner. Increased knowledge regarding membrane initiated ERα actions may provide means to develop new selective estrogen receptor modulators with improved profiles.
The integrative role of orexin/hypocretin neurons in nociceptive perception and analgesic regulation
Authors: Inutsuka Ayumu , Yamashita Akira , Chowdhury Srikanta , Nakai Junichi , Ohkura Masamichi , Taguchi Toru , Yamanaka Akihiro 
Published: July 2016

AbstractThe level of wakefulness is one of the major factors affecting nociception and pain. Stress-induced analgesia supports an animal’s survival via prompt defensive responses against predators or competitors. Previous studies have shown the pharmacological effects of orexin peptides on analgesia. However, orexin neurons contain not only orexin but also other co-transmitters such as dynorphin, neurotensin and glutamate. Thus, the physiological importance of orexin neuronal activity in nociception is unknown. Here we show that adult-stage selective ablation of orexin neurons enhances pain-related behaviors, while pharmacogenetic activation of orexin neurons induces analgesia. Additionally, we found correlative activation of orexin neurons during nociception using fiber photometry recordings of orexin neurons in conscious animals. These findings suggest an integrative role for orexin neurons in nociceptive perception and pain regulation.
Analysis of temporal evolution of quantum dot surface chemistry by surface-enhanced Raman scattering
Authors: Doğan İlker , Gresback Ryan , Nozaki Tomohiro , van de Sanden Mauritius C. M. 
Published: July 2016

AbstractTemporal evolution of surface chemistry during oxidation of silicon quantum dot (Si-QD) surfaces were probed using surface-enhanced Raman scattering (SERS). A monolayer of hydrogen and chlorine terminated plasma-synthesized Si-QDs were spin-coated on silver oxide thin films. A clearly enhanced signal of surface modes, including Si-Clx and Si-Hx modes were observed from as-synthesized Si-QDs as a result of the plasmonic enhancement of the Raman signal at Si-QD/silver oxide interface. Upon oxidation, a gradual decrease of Si-Clx and Si-Hx modes and an emergence of Si-Ox and Si-O-Hx modes have been observed. In addition, first, second and third transverse optical modes of Si-QDs were also observed in the SERS spectra, revealing information on the crystalline morphology of Si-QDs. An absence of any of the abovementioned spectral features, but only the first transverse optical mode of Si-QDs from thick Si-QD films validated that the spectral features observed from Si-QDs on silver oxide thin films are originated from the SERS effect. These results indicate that real-time SERS is a powerful diagnostic tool and a novel approach to probe the dynamic surface/interface chemistry of quantum dots, especially when they involve in oxidative, catalytic and electrochemical surface/interface reactions.
Quantifying mammalian genomic DNA hydroxymethylcytosine content using solid-state nanopores
Authors: Zahid Osama K. , Zhao Boxuan Simen , He Chuan , Hall Adam R. 
Published: July 2016

Abstract5-hydroxymethylcytosine (5 hmC), the oxidized form of 5-methylcytosine (5 mC), is a base modification with emerging importance in biology and disease. However, like most epigenetic elements, it is transparent to many conventional genetic techniques and is thus challenging to probe. Here, we report a rapid solid-state nanopore assay that is capable of resolving 5 hmC with high specificity and sensitivity and demonstrate its utility in assessing global modification abundance in genomic DNA.
Evaluation of treadmill exercise effect on muscular lipid profiles of diabetic fatty rats by nanoflow liquid chromatography–tandem mass spectrometry
Authors: Lee Jong Cheol , Kim Il Yong , Son Yeri , Byeon Seul Kee , Yoon Dong Hyun , Son Jun Seok , Song Han Sol , Song Wook , Seong Je Kyung , Moon Myeong Hee 
Published: July 2016

AbstractWe compare comprehensive quantitative profiling of lipids at the molecular level from skeletal muscle tissues (gastrocnemius and soleus) of Zucker diabetic fatty rats and Zucker lean control rats during treadmill exercise by nanoflow liquid chromatography–tandem mass spectrometry. Because type II diabetes is caused by decreased insulin sensitivity due to excess lipids accumulated in skeletal muscle tissue, lipidomic analysis of muscle tissues under treadmill exercise can help unveil the mechanism of lipid-associated insulin resistance. In total, 314 lipid species, including phospholipids, sphingolipids, ceramides, diacylglycerols (DAGs), and triacylglycerols (TAGs), were analyzed to examine diabetes-related lipid species and responses to treadmill exercise. Most lysophospholipid levels increased with diabetes. While DAG levels (10 from the gastrocnemius and 13 from the soleus) were >3-fold higher in diabetic rats, levels of most of these decreased after exercise in soleus but not in gastrocnemius. Levels of 5 highly abundant TAGs (52:1 and 54:3 in the gastrocnemius and 48:2, 50:2, and 52:4 in the soleus) displaying 2-fold increases in diabetic rats decreased after exercise in the soleus but not in the gastrocnemius in most cases. Thus, aerobic exercise has a stronger influence on lipid levels in the soleus than in the gastrocnemius in type 2 diabetic rats.
Use of Atmospheric Budget to Reduce Uncertainty in Estimated Water Availability over South Asia from Different Reanalyses
Authors: Sebastian Dawn Emil , Pathak Amey , Ghosh Subimal 
Published: July 2016

AbstractDisagreements across different reanalyses over South Asia result into uncertainty in assessment of water availability, which is computed as the difference between Precipitation and Evapotranspiration (P–E). Here, we compute P–E directly from atmospheric budget with divergence of moisture flux for different reanalyses and find improved correlation with observed values of P–E, acquired from station and satellite data. We also find reduced closure terms for water cycle computed with atmospheric budget, analysed over South Asian landmass, when compared to that obtained with individual values of P and E. The P–E value derived with atmospheric budget is more consistent with energy budget, when we use top-of-atmosphere radiation for the same. For analysing water cycle, we use runoff from Global Land Data Assimilation System and water storage from Gravity Recovery and Climate Experiment. We find improvements in agreements across different reanalyses, in terms of inter-annual cross correlation when atmospheric budget is used to estimate P–E and hence, emphasize to use the same for estimations of water availability in South Asia to reduce uncertainty. Our results on water availability with reduced uncertainty over highly populated monsoon driven South Asia will be useful for water management and agricultural decision making.
A nanometric Rh overlayer on a metal foil surface as a highly efficient three-way catalyst
Authors: Misumi Satoshi , Yoshida Hiroshi , Hinokuma Satoshi , Sato Tetsuya , Machida Masato 
Published: July 2016

AbstractPulsed arc-plasma (AP) deposition of an Rh overlayer on an Fe–Cr–Al stainless steel foil produced a composite material that exhibited high activity for automotive three-way catalysis (TWC). The AP pulses deposited metallic Rh nanoparticles 1–3 nm in size, whose density on the surface increased with the number of pulses. This led to coalescence and grain growth on the foil surface and the eventual formation of a uniform two-dimensional Rh overlayer. Full coverage of the 51 μm-thick flat foil by a 3.2 nm-thick Rh overlayer was achieved after 1,000 pulses. A simulated TWC reaction using a miniature honeycomb fabricated using flat and corrugated foils with the Rh overlayers exhibited successful light-off at a practical gaseous hourly space velocity of 1.2 × 105 h−1. The turnover frequency for the NO–CO reaction over the metallic honeycomb catalyst was ca. 80-fold greater than that achieved with a reference Rh/ZrO2-coated cordierite honeycomb prepared using a conventional wet impregnation and slurry coating procedure. Despite the nonporosity and low surface area of the foil-supported Rh overlayer compared with conventional powder catalysts (Rh/ZrO2), it is a promising alternative design for more efficient automotive catalysts that use less Rh loading.
Acoustic–Phonetic Versus Lexical Processing in Nonnative Listeners Differing in Their Dominant Language
Authors: Shi Lu-Feng , Koenig Laura L. 
Published: July 2016

Purpose

Nonnative listeners have difficulty recognizing English words due to underdeveloped acoustic–phonetic and/or lexical skills. The present study used Boothroyd and Nittrouer's (1988)
j
factor to tease apart these two components of word recognition.

Method

Participants included 15 native English and 29 native Russian listeners. Fourteen and 15 of the Russian listeners reported English (ED) and Russian (RD) to be their dominant language, respectively. Listeners were presented 119 consonant–vowel–consonant real and nonsense words in speech-spectrum noise at +6 dB SNR. Responses were scored for word and phoneme recognition, the logarithmic quotient of which yielded
j
.

Results

Word and phoneme recognition was comparable between native and ED listeners but poorer in RD listeners. Analysis of
j
indicated less effective use of lexical information in RD than in native and ED listeners. Lexical processing was strongly correlated with the length of residence in the United States.

Conclusions
Language background is important for nonnative word recognition. Lexical skills can be regarded as nativelike in ED nonnative listeners. Compromised word recognition in ED listeners is unlikely a result of poor lexical processing. Performance should be interpreted with caution for listeners dominant in their first language, whose word recognition is affected by both lexical and acoustic–phonetic factors.