bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea
Authors: Yamamoto Satoshi , Masuda Reiji , Sato Yukuto , Sado Tetsuya , Araki Hitoshi , Kondoh Michio , Minamoto Toshifumi , Miya Masaki 
Published: January 2017

AbstractEnvironmental DNA (eDNA) metabarcoding has emerged as a potentially powerful tool to assess aquatic community structures. However, the method has hitherto lacked field tests that evaluate its effectiveness and practical properties as a biodiversity monitoring tool. Here, we evaluated the ability of eDNA metabarcoding to reveal fish community structures in species-rich coastal waters. High-performance fish-universal primers and systematic spatial water sampling at 47 stations covering ~11 km2 revealed the fish community structure at a species resolution. The eDNA metabarcoding based on a 6-h collection of water samples detected 128 fish species, of which 62.5% (40 species) were also observed by underwater visual censuses conducted over a 14-year period. This method also detected other local fishes (≥23 species) that were not observed by the visual censuses. These eDNA metabarcoding features will enhance marine ecosystem-related research, and the method will potentially become a standard tool for surveying fish communities.
Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities
Authors: Jing Gongchao , Sun Zheng , Wang Honglei , Gong Yanhai , Huang Shi , Ning Kang , Xu Jian , Su Xiaoquan 
Published: January 2017

AbstractThe number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing. Application of Parallel-META 3 on 5,337 samples with 1,117,555,208 sequences from diverse studies and platforms showed it could produce similar results as QIIME and PICRUSt with much faster speed and lower memory usage, which demonstrates its ability to unravel the taxonomical and functional dynamics patterns across large datasets and elucidate ecological links between microbiome and the environment. Parallel-META 3 is implemented in C/C++ and R, and integrated into an executive package for rapid installation and easy access under Linux and Mac OS X. Both binary and source code packages are available at http://bioinfo.single-cell.cn/parallel-meta.html.
The prognostic role of EGFR-TKIs for patients with advanced non-small cell lung cancer
Authors: Zhao Dan , Chen Xuejing , Qin Na , Su Dan , Zhou Lijuan , Zhang Quan , Li Xi , Zhang Xinyong , Jin Mulan , Wang Jinghui 
Published: January 2017

AbstractClinical trials have shown that epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) did not improve the survival of patients with EGFR-mutated non-small cell lung cancer (NSCLC) because of the high crossover of treatments. Realistically, the role of EGFR-TKIs in NSCLC with mutated EGFR is not well known. We retrospectively analysed data from patients with recurrent or metastatic NSCLC. Clinical prognostic factors were identified by Cox proportional hazards modelling. Among 503 patients, the median overall survival (OS) for all of patients was 11.7 months. Cox analysis showed that PS 0–1, recurrent disease, EGFR mutations, or EGFR-TKI treatment were associated with improved OS. In patients with EGFR-activating mutations, Cox analysis showed that patients with adenocarcinoma, recurrent disease, or EGFR-TKI treatment had significantly longer survival. Patients with EGFR-activating mutations who received EGFR-TKI therapy had a median OS of 24.3 months, which was significantly longer than those who had not received EGFR-TKI therapy (10.8 months). Patients with wild-type EGFR had a median OS of 9.7 months and Cox analysis showed that PS score and disease type were independent predictors. EGFR-TKI therapy is an independently prognostic factor for NSCLC with mutated EGFR. A more effective therapy is needed for patients with wild-type EGFR.
Methionine residues around phosphorylation sites are preferentially oxidized in vivo under stress conditions
Authors: Veredas Francisco J. , Cantón Francisco R. , Aledo J. Carlos 
Published: January 2017

AbstractProtein phosphorylation is one of the most prevalent and well-understood protein modifications. Oxidation of protein-bound methionine, which has been traditionally perceived as an inevitable damage derived from oxidative stress, is now emerging as another modification capable of regulating protein activity during stress conditions. However, the mechanism coupling oxidative signals to changes in protein function remains unknown. An appealing hypothesis is that methionine oxidation might serve as a rheostat to control phosphorylation. To investigate this potential crosstalk between phosphorylation and methionine oxidation, we have addressed the co-occurrence of these two types of modifications within the human proteome. Here, we show that nearly all (98%) proteins containing oxidized methionine were also phosphoproteins. Furthermore, phosphorylation sites were much closer to oxidized methionines when compared to non-oxidized methionines. This proximity between modification sites cannot be accounted for by their co-localization within unstructured clusters because it was faithfully reproduced in a smaller sample of structured proteins. We also provide evidence that the oxidation of methionine located within phosphorylation motifs is a highly selective process among stress-related proteins, which supports the hypothesis of crosstalk between methionine oxidation and phosphorylation as part of the cellular defence against oxidative stress.
Comfortable, high-efficiency heat pump with desiccant-coated, water-sorbing heat exchangers
Authors: Tu Y. D. , Wang R. Z. , Ge T. S. , Zheng X. 
Published: January 2017

AbstractComfortable, efficient, and affordable heating, ventilation, and air conditioning systems in buildings are highly desirable due to the demands of energy efficiency and environmental friendliness. Traditional vapor-compression air conditioners exhibit a lower coefficient of performance (COP) (typically 2.8–3.8) owing to the cooling-based dehumidification methods that handle both sensible and latent loads together. Temperature- and humidity-independent control or desiccant systems have been proposed to overcome these challenges; however, the COP of current desiccant systems is quite small and additional heat sources are usually needed. Here, we report on a desiccant-enhanced, direct expansion heat pump based on a water-sorbing heat exchanger with a desiccant coating that exhibits an ultrahigh COP value of more than 7 without sacrificing any comfort or compactness. The pump’s efficiency is doubled compared to that of pumps currently used in conventional room air conditioners, which is a revolutionary HVAC breakthrough. Our proposed water-sorbing heat exchanger can independently handle sensible and latent loads at the same time. The desiccants adsorb moisture almost isothermally and can be regenerated by condensation heat. This new approach opens up the possibility of achieving ultrahigh efficiency for a broad range of temperature- and humidity-control applications.
Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota
Authors: Davis Jasmine C. C. , Lewis Zachery T. , Krishnan Sridevi , Bernstein Robin M. , Moore Sophie E. , Prentice Andrew M. , Mills David A. , Lebrilla Carlito B. , Zivkovic Angela M. 
Published: January 2017

AbstractHuman milk oligosaccharides (HMOs) play an important role in the health of an infant as substrate for beneficial gut bacteria. Little is known about the effects of HMO composition and its changes on the morbidity and growth outcomes of infants living in areas with high infection rates. Mother’s HMO composition and infant gut microbiota from 33 Gambian mother/infant pairs at 4, 16, and 20 weeks postpartum were analyzed for relationships between HMOs, microbiota, and infant morbidity and growth. The data indicate that lacto-N-fucopentaose I was associated with decreased infant morbidity, and 3′-sialyllactose was found to be a good indicator of infant weight-for-age. Because HMOs, gut microbiota, and infant health are interrelated, the relationship between infant health and their microbiome were analyzed. While bifidobacteria were the dominant genus in the infant gut overall, Dialister and Prevotella were negatively correlated with morbidity, and Bacteroides was increased in infants with abnormal calprotectin. Mothers nursing in the wet season (July to October) produced significantly less oligosaccharides compared to those nursing in the dry season (November to June). These results suggest that specific types and structures of HMOs are sensitive to environmental conditions, protective of morbidity, predictive of growth, and correlated with specific microbiota.
The Herbivore-Induced Plant Volatiles Methyl Salicylate and Menthol Positively affect Growth and Pathogenicity of Entomopathogenic Fungi
Authors: Lin Yongwen , Qasim Muhammad , Hussain Mubasher , Akutse Komivi Senyo , Avery Pasco Bruce , Dash Chandra Kanta , Wang Liande 
Published: January 2017

AbstractSome herbivore-induced-plant volatiles (HIPVs) compounds are vital for the functioning of an ecosystem, by triggering multi-trophic interactions for natural enemies, plants and herbivores. However, the effect of these chemicals, which play a crucial role in regulating the multi-trophic interactions between plant-herbivore-entomopathogenic fungi, is still unknown. To fill this scientific gap, we therefore investigated how these chemicals influence the entomopathogenic fungi growth and efficacy. In this study, Lipaphis erysimi induced Arabidopsis thaliana HIPVs were collected using headspace system and detected with GC-MS, and then analyzed the effects of these HIPVs chemicals on Lecanicillium lecanii strain V3450. We found that the HIPVs menthol and methyl salicylate at 1 and 10 nmol·ml−1 improved many performance aspects of the fungus, such as germination, sporulation, appressorial formation as well as its pathogenicity and virulence. These findings are not only important for understanding the multi-trophic interactions in an ecosystem, but also would contribute for developing new and easier procedures for conidial mass production as well as improve the pathogenicity and virulence of entomopathogenic fungi in biological pest management strategies.
Modulation of snow reflectance and snowmelt from Central Asian glaciers by anthropogenic black carbon
Authors: Schmale Julia , Flanner Mark , Kang Shichang , Sprenger Michael , Zhang Qianggong , Guo Junming , Li Yang , Schwikowski Margit , Farinotti Daniel 
Published: January 2017

AbstractDeposited mineral dust and black carbon are known to reduce the albedo of snow and enhance melt. Here we estimate the contribution of anthropogenic black carbon (BC) to snowmelt in glacier accumulation zones of Central Asia based on in-situ measurements and modelling. Source apportionment suggests that more than 94% of the BC is emitted from mostly regional anthropogenic sources while the remaining contribution comes from natural biomass burning. Even though the annual deposition flux of mineral dust can be up to 20 times higher than that of BC, we find that anthropogenic BC causes the majority (60% on average) of snow darkening. This leads to summer snowmelt rate increases of up to 6.3% (7 cm a−1) on glaciers in three different mountain environments in Kyrgyzstan, based on albedo reduction and snowmelt models.
Feeling Touched: Emotional Modulation of Somatosensory Potentials to Interpersonal Touch
Authors: Ravaja N. , Harjunen V. , Ahmed I. , Jacucci G. , Spapé M. M. 
Published: January 2017

AbstractAlthough the previous studies have shown that an emotional context may alter touch processing, it is not clear how visual contextual information modulates the sensory signals, and at what levels does this modulation take place. Therefore, we investigated how a toucher’s emotional expressions (anger, happiness, fear, and sadness) modulate touchee’s somatosensory-evoked potentials (SEPs) in different temporal ranges. Participants were presented with tactile stimulation appearing to originate from expressive characters in virtual reality. Touch processing was indexed using SEPs, and self-reports of touch experience were collected. Early potentials were found to be amplified after angry, happy and sad facial expressions, while late potentials were amplified after anger but attenuated after happiness. These effects were related to two stages of emotional modulation of tactile perception: anticipation and interpretation. The findings show that not only does touch affect emotion, but also emotional expressions affect touch perception. The affective modulation of touch was initially obtained as early as 25 ms after the touch onset suggesting that emotional context is integrated to the tactile sensation at a very early stage.
Tempo of magma degassing and the genesis of porphyry copper deposits
Authors: Chelle-Michou Cyril , Rottier Bertrand , Caricchi Luca , Simpson Guy 
Published: January 2017

AbstractPorphyry deposits are copper-rich orebodies formed by precipitation of metal sulphides from hydrothermal fluids released from magmatic intrusions that cooled at depth within the Earth’s crust. Finding new porphyry deposits is essential because they are our largest source of copper and they also contain other strategic metals including gold and molybdenum. However, the discovery of giant porphyry deposits is hindered by a lack of understanding of the factors governing their size. Here, we use thermal modelling and statistical simulations to quantify the tempo and the chemistry of fluids released from cooling magmatic systems. We confirm that typical arc magmas produce fluids similar in composition to those that form porphyry deposits and conclude that the volume and duration of magmatic activity exert a first order control on the endowment (total mass of deposited copper) of economic porphyry copper deposits. Therefore, initial magma enrichment in copper and sulphur, although adding to the metallogenic potential, is not necessary to form a giant deposit. Our results link the respective durations of magmatic and hydrothermal activity from well-known large to supergiant deposits to their metal endowment. This novel approach can readily be implemented as an additional exploration tool that can help assess the economic potential of magmatic-hydrothermal systems.
Dietary phytochemical PEITC restricts tumor development via modulation of epigenetic writers and erasers
Authors: Park Jung Eun , Sun Yang , Lim Sai Kiang , Tam James P. , Dekker Matthijs , Chen Hong , Sze Siu Kwan 
Published: January 2017

AbstractDietary intake of bioactive phytochemicals including the cruciferous vegetable derivative phenethyl isothiocyanate (PEITC) can reduce risk of human cancers, but possible epigenetic mechanisms of these effects are yet unknown. We therefore sought to identify the molecular basis of PEITC-mediated epigenetic tumor restriction. Colon cancer cells treated with low-dose PEITC for >1 month exhibited stable alterations in expression profile of epigenetic writers/erasers and chromatin-binding of histone deacetylases (HDACs) and Polycomb-group (PcG) proteins. Sustained PEITC exposure not only blocked HDAC binding to euchromatin but was also associated with hypomethylation of PcG target genes that are typically hypermethylated in cancer. Furthermore, PEITC treatment induced expression of pro-apoptotic genes in tumor cells, which was partially reversed by overexpression of PcG member BMI-1, suggesting opposing roles for PEITC and PcG proteins in control of tumor progression. These data demonstrate that PEITC regulates chromatin binding of key epigenetic writers/erasers and PcG complexes to restrict tumor development.
Oxytocin biases men but not women to restore social connections with individuals who socially exclude them
Authors: Xu Xiaolei , Yao Shuxia , Xu Lei , Geng Yayuan , Zhao Weihua , Ma Xiaole , Kou Juan , Luo Ruixue , Kendrick Keith M. 
Published: January 2017

AbstractWe normally react to individuals who exclude us socially by either avoiding them or increasing our attempts to interact with them. The neuropeptide oxytocin can promote social bonds and reduce social conflict and we therefore investigated whether it facilitates more positive social responses towards individuals who exclude or include us. In a double-blind, placebo-controlled, between-subject design 77 healthy Chinese male and female participants received intranasal oxytocin (40 IU) or placebo before playing a modified virtual ball-tossing game with three fictitious partners who either showed exclusion, inclusion or neutral behavioral interactions with them. Results showed that both male and female subjects threw the ball more often to individuals who excluded rather than included them, although oxytocin did not alter this or awareness/feelings of exclusion or inclusion. However, when subjects returned a week later males, but not females, in the oxytocin group exhibited an increased liking for, and preference for playing again with, players who had previously excluded them. This oxytocin effect was positively associated with independent traits. Our findings suggest that in a collectivist culture oxytocin may promote the desire of males, but not females, with a stronger independent orientation to rebuild social connections with individuals who have previously excluded them.
Spatiotemporal Pattern of PM2.5 Concentrations in Mainland China and Analysis of Its Influencing Factors using Geographically Weighted Regression
Authors: Luo Jieqiong , Du Peijun , Samat Alim , Xia Junshi , Che Meiqin , Xue Zhaohui 
Published: January 2017

AbstractBased on annual average PM2.5 gridded dataset, this study first analyzed the spatiotemporal pattern of PM2.5 across Mainland China during 1998–2012. Then facilitated with meteorological site data, land cover data, population and Gross Domestic Product (GDP) data, etc., the contributions of latent geographic factors, including socioeconomic factors (e.g., road, agriculture, population, industry) and natural geographical factors (e.g., topography, climate, vegetation) to PM2.5 were explored through Geographically Weighted Regression (GWR) model. The results revealed that PM2.5 concentrations increased while the spatial pattern remained stable, and the proportion of areas with PM2.5 concentrations greater than 35 μg/m3 significantly increased from 23.08% to 29.89%. Moreover, road, agriculture, population and vegetation showed the most significant impacts on PM2.5. Additionally, the Moran’s I for the residuals of GWR was 0.025 (not significant at a 0.01 level), indicating that the GWR model was properly specified. The local coefficient estimates of GDP in some cities were negative, suggesting the existence of the inverted-U shaped Environmental Kuznets Curve (EKC) for PM2.5 in Mainland China. The effects of each latent factor on PM2.5 in various regions were different. Therefore, regional measures and strategies for controlling PM2.5 should be formulated in terms of the local impacts of specific factors.
Proteome Response of Chicken Embryo Fibroblast Cells to Recombinant H5N1 Avian Influenza Viruses with Different Neuraminidase Stalk Lengths
Authors: Li Yongtao , Ming Fan , Huang Huimin , Guo Kelei , Chen Huanchun , Jin Meilin , Zhou Hongbo 
Published: January 2017

AbstractThe variation on neuraminidase (NA) stalk region of highly pathogenic avian influenza H5N1 virus results in virulence change in animals. In our previous studies, the special NA stalk-motif of H5N1 viruses has been demonstrated to play a significant role in the high virulence and pathogenicity in chickens. However, the molecular mechanisms underlying the pathogenicity of viruses with different NA stalk remain poorly understood. This study presents a comprehensive characterization of the proteome response of chicken cells to recombinant H5N1 virus with stalk-short NA (rNA-wt) and the stalkless NA mutant virus (rSD20). 208 proteins with differential abundance profiles were identified differentially expressed (DE), and these proteins were mainly related to stress response, transcription regulation, transport, metabolic process, cellular component and cytoskeleton. Through Ingenuity Pathways Analysis (IPA), the significant biological functions of DE proteins represented included Post-Translational Modification, Protein Folding, DNA Replication, Recombination and Repair. It was interesting to find that most DE proteins were involved in the TGF-β mediated functional network. Moreover, the specific DE proteins may play important roles in the innate immune responses and H5N1 virus replication. Our data provide important information regarding the comparable host response to H5N1 influenza virus infection with different NA stalk lengths.
Oriented and Ordered Biomimetic Remineralization of the Surface of Demineralized Dental Enamel Using HAP@ACP Nanoparticles Guided by Glycine
Authors: Wang Haorong , Xiao Zuohui , Yang Jie , Lu Danyang , Kishen Anil , Li Yanqiu , Chen Zhen , Que Kehua , Zhang Qian , Deng Xuliang , Yang Xiaoping , Cai Qing , Chen Ning , Cong Changhong , Guan Binbin , Li Ting , Zhang Xu 
Published: January 2017

AbstractAchieving oriented and ordered remineralization on the surface of demineralized dental enamel, thereby restoring the satisfactory mechanical properties approaching those of sound enamel, is still a challenge for dentists. To mimic the natural biomineralization approach for enamel remineralization, the biological process of enamel development proteins, such as amelogenin, was simulated in this study. In this work, carboxymethyl chitosan (CMC) conjugated with alendronate (ALN) was applied to stabilize amorphous calcium phosphate (ACP) to form CMC/ACP nanoparticles. Sodium hypochlorite (NaClO) functioned as the protease which decompose amelogenin in vivo to degrade the CMC-ALN matrix and generate HAP@ACP core-shell nanoparticles. Finally, when guided by 10 mM glycine (Gly), HAP@ACP nanoparticles can arrange orderly and subsequently transform from an amorphous phase to well-ordered rod-like apatite crystals to achieve oriented and ordered biomimetic remineralization on acid-etched enamel surfaces. This biomimetic remineralization process is achieved through the oriented attachment (OA) of nanoparticles based on non-classical crystallization theory. These results indicate that finding and developing analogues of natural proteins such as amelogenin involved in the biomineralization by natural macromolecular polymers and imitating the process of biomineralization would be an effective strategy for enamel remineralization. Furthermore, this method represents a promising method for the management of early caries in minimal invasive dentistry (MID).