bluuebunny/crossref_metadata_2025_split huggingface dataset:
The contribution of Saccharomyces cerevisiae replicative age to the variations in the levels of Trx2p, Pdr5p, Can1p and Idh isoforms
Authors: Azbarova Aglaia V. , Galkina Kseniia V. , Sorokin Maxim I. , Severin Fedor F. , Knorre Dmitry A. 
Published: October 2017

AbstractAsymmetrical division can be a reason for microbial populations heterogeneity. In particular, budding yeast daughter cells are more vulnerable to stresses than the mothers. It was suggested that yeast mother cells could also differ from each other depending on their replicative age. To test this, we measured the levels of Idh1-GFP, Idh2-GFP, Trx2-GFP, Pdr5-GFP and Can1-GFP proteins in cells of the few first, most represented, age cohorts. Pdr5p and Can1p were selected because of the pronounced mother-bud asymmetry for these proteins distributions, Trx2p as indicator of oxidative stress. Isocitrate dehydrogenase subunits Idh1p and Idh2p were assessed because their levels are regulated by mitochondria. We found a small negative correlation between yeast replicative age and Idh1-GFP or Idh2-GFP but not Trx2-GFP levels. Mitochondrial network fragmentation was also confirmed as an early event of replicative aging. No significant difference in the membrane proteins levels Pdr5p and Can1p was found. Moreover, the elder mother cells showed lower coefficient of variation for Pdr5p levels compared to the younger ones and the daughters. Our data suggest that the levels of stress-response proteins Pdr5p and Trx2p in the mother cells are stable during the first few cell cycles regardless of their mother-bud asymmetry.
Replacing conventional decontamination of hatching eggs with a natural defense strategy based on antimicrobial, volatile pyrazines
Authors: Kusstatscher Peter , Cernava Tomislav , Liebminger Stefan , Berg Gabriele 
Published: October 2017

AbstractThe treatment of hatching eggs relies on classic yet environmentally harmful decontamination methods such as formaldehyde fumigation. We evaluated bacteria-derived volatiles as a replacement within a fundamentally novel approach based on volatile organic compounds (VOCs), which are naturally involved in microbial communication and antagonism due to their high antimicrobial efficiency. Pyrazine (5-isobutyl-2,3-dimethylpyrazine) was applied passively and actively in prototypes of a pre-industry-scale utilization. Altogether, pyrazine decontamination rates of up to 99.6% were observed, which is comparable to formaldehyde fumigation. While active evaporation was highly efficient in all experiments, passive treatment showed reducing effects in two of four tested groups only. These results were confirmed by visualization using LIVE/DEAD staining microscopy. The natural egg shell microbiome was characterized by an unexpected bacterial diversity of Pseudomonadales, Enterobacteriales, Sphingomonadales, Streptophyta, Burkholderiales, Actinomycetales, Xanthomonadales, Rhizobiales, Bacillales, Clostridiales, Lactobacillales, and Flavobacteriales members. Interestingly, we found that especially low pyrazine concentrations lead to a microbiome shift, which can be explained by varying antimicrobial effects on different microorganisms. Micrococcus spp., which are linked to embryonic death and reduced hatchability, was found to be highly sensitive to pyrazines. Taken together, pyrazine application was shown to be a promising, environmentally friendly alternative for fumigation treatments of hatchery eggs.
Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts
Authors: Duff Aoife M. , Zhang Li-Mei , Smith Cindy J. 
Published: October 2017

AbstractWhile numerous studies have investigated the abundance of ammonia oxidising bacteria and archaea (AOB/AOA) via the ammonia monooxygenase gene amoA, less is known about their small-scale variation and if amoA gene abundance equates to activity. Here we present a spatial and temporal study of ammonia oxidation in two small intertidal bays, Rusheen and Clew bay, Ireland. Potential Nitrification Rate (PNR) was ten-fold higher in Rusheen bay (Clew: 0.27 ± SD 0.55; Rusheen: 2.46 ± SD 3.4 NO2− µg−1 g−1 day−1, P < 0.001) than in Clew bay but amoA gene abundances were similar between bays, and comparable to those in other coastal ecosystems. Within bays AOB genes increased towards the muddy sediments and were positively correlated with PNR and pH. Less spatial variation was observed in AOA abundances which nevertheless positively correlated with pH and temperature and negatively with salinity and ammonia. Transcriptionally active AOB and AOA were quantified from all sites in Rusheen bay, February 2014, following the general trends observed at DNA level. AOB phylotypes predominantly from the known Nitrosomonas group were distributed across the bay, while Nitrosomonas group B phylotypes were absent from low salinity sites. AOA genes and transcripts were primarily affiliated with Thaumarchaeota group I.1a.
Bacteriome genetic structures of urban deposits are indicative of their origin and impacted by chemical pollutants
Authors: Marti Romain , Bécouze-Lareure Céline , Ribun Sébastien , Marjolet Laurence , Bernardin Souibgui Claire , Aubin Jean-Baptiste , Lipeme Kouyi Gislain , Wiest Laure , Blaha Didier , Cournoyer Benoit 
Published: October 2017

AbstractUrban activities generate surface deposits over impervious surfaces that can represent ecological and health hazards. Bacteriome genetic structures of deposits washed off during rainfall events, over an urban industrial watershed, were inferred from 16 S rRNA gene (rrs) sequences generated by high throughput sequencing. Deposits were sampled over a 4 year-period from a detention basin (DB). Major shifts, matching key management practices, in the structure of these urban bacteriomes, were recorded. Correlation analyses of rrs similarities between samples and their respective concentrations in chemical pollutants, markers of human fecal contaminations (HF183) and antimicrobial resistances (integrons), were performed. Harsher environmental constraints building up in the older deposits led to an increase number of rrs reads from extremophiles such as Acidibacter and Haliangium. Deposits accumulating in the decantation pit of the DB showed an increase in rrs reads from warm blooded intestinal tract bacteria such as Bacteroides and Prevotella. This enrichment matched higher concentrations of Bacteroides HF183 genotypes normally restricted to humans. Bacteriomes of urban deposits appeared good indicators of human-driven environmental changes. Their composition was found representative of their origin. Soil particles and rain appeared to be major contributors of the inferred bacterial taxa recovered from recent deposits.
Higher-order Network Analysis of Fine Particulate Matter (PM
2.5) Transport in China at City Level
Authors: Wang Yufang , Wang Haiyan , Chang Shuhua , Liu Maoxing 
Published: October 2017

AbstractSpecification of PM2.5 transmission characteristics is important for pollution control and policymaking. We apply higher-order organization of complex networks to identify major potential PM2.5 contributors and PM2.5 transport pathways of a network of 189 cities in China. The network we create in this paper consists of major cities in China and contains information on meteorological conditions of wind speed and wind direction, data on geographic distance, mountains, and PM2.5 concentrations. We aim to reveal PM2.5 mobility between cities in China. Two major conclusions are revealed through motif analysis of complex networks. First, major potential PM2.5 pollution contributors are identified for each cluster by one motif, which reflects movements from source to target. Second, transport pathways of PM2.5 are revealed by another motif, which reflects transmission routes. To our knowledge, this is the first work to apply higher-order network analysis to study PM2.5 transport.
Size effect on the deformation mechanisms of nanocrystalline platinum thin films
Authors: Shu Xinyu , Kong Deli , Lu Yan , Long Haibo , Sun Shiduo , Sha Xuechao , Zhou Hao , Chen Yanhui , Mao Shengcheng , Liu Yinong 
Published: October 2017

AbstractThis paper reports a study of time-resolved deformation process at the atomic scale of a nanocrystalline Pt thin film captured in situ under a transmission electron microscope. The main mechanism of plastic deformation was found to evolve from full dislocation activity-enabled plasticity in large grains (with grain size d > 10 nm), to partial dislocation plasticity in smaller grains (with grain size 10 nm < d < 6 nm), and grain boundary-mediated plasticity in the matrix with grain sizes d < 6 nm. The critical grain size for the transition from full dislocation activity to partial dislocation activity was estimated based on consideration of stacking fault energy. For grain boundary-mediated plasticity, the possible contributions to strain rate of grain creep, grain sliding and grain rotation to plastic deformation were estimated using established models. The contribution of grain creep is found to be negligible, the contribution of grain rotation is effective but limited in magnitude, and grain sliding is suggested to be the dominant deformation mechanism in nanocrystalline Pt thin films. This study provided the direct evidence of these deformation processes at the atomic scale.
Patterns and underlying mechanisms of non-volant small mammal richness along two contrasting mountain slopes in southwestern China
Authors: Chen Zhongzheng , He Kai , Cheng Feng , Khanal Laxman , Jiang Xuelong 
Published: October 2017

AbstractThe species richness patterns of small mammals and the processes shaping them in two gradients of a mountain with different spatial and climatic characteristics were examined using standard sampling scheme. We trapped 2,006 small mammals representing 37 species, along elevational gradients on both western and eastern slopes of the Ailao Mountains, Southwest China. Using mid-domain effect model, model selection and model averaging, we examined the effects of slope, area, mean annual temperature (MAT), mean annual humidity (MAH), productivity, plant species richness (PSR) and the mid-domain effect (MDE) on the patterns of small mammal diversity. The hump-shaped patterns were favored along the elevational gradient, but shapes of diversity curves were different on the contrasting slopes. Area and productivity were the most important factors in explaining the variation of total species richness. However, for each specific group of small mammals (i.e. insectivores vs. rodents, large-ranged vs. small-ranged species, endemic vs. non-endemic species), the peaks of species richness and their primary drivers varied. The major explanatory factors for richness pattern of each small mammal group were not significantly different between the slopes, suggesting the existence of the general underlying mechanisms on two slopes of a mountain.
Genomics alterations of metastatic and primary tissues across 15 cancer types
Authors: Liu Gang , Zhan Xiaohui , Dong Chuanpeng , Liu Lei 
Published: October 2017

AbstractMetastasis is an important event for cancer evolution and prognosis. In this article, we analyzed the differences in genomic alterations between primary and metastatic tissues at hotspot regions in 15 cancer types and 10,456 samples. Differential somatic mutations at the amino acid, protein domain and gene levels, mutational exclusiveness, and copy number variations were identified in these cancers, while no significant nucleotide and gene fusion differences were detected. The homogeneity and heterogeneity of these differences in cancers were also detected. By characterizing the genomic alterations of these genes, important signaling pathways during metastasis were also identified. In summary, the metastatic cancer tissues retained most genomic features of the primary tumor at the biological level and acquired new signatures during cancer cell migration.
Climate and permafrost effects on the chemistry and ecosystems of High Arctic Lakes
Authors: Roberts K. E. , Lamoureux S. F. , Kyser T. K. , Muir D. C. G. , Lafrenière M. J. , Iqaluk D. , Pieńkowski A. J. , Normandeau A. 
Published: October 2017

AbstractPermafrost exerts an important control over hydrological processes in Arctic landscapes and lakes. Recent warming and summer precipitation has the potential to alter water availability and quality in this environment through thermal perturbation of near surface permafrost and increased mobility of previously frozen solutes to Arctic freshwaters. We present a unique thirteen-year record (2003–16) of the physiochemical properties of two High Arctic lakes and show that the concentration of major ions, especially SO42−, has rapidly increased up to 500% since 2008. This hydrochemical change has occurred synchronously in both lakes and ionic ratio changes in the lakes indicate that the source for the SO42− is compositionally similar to terrestrial sources arising from permafrost thaw. Record summer temperatures during this period (2003–16) following over 100 years of warming and summer precipitation in this polar desert environment provide likely mechanisms for this rapid chemical change. An abrupt limnological change is also reflected in the otolith chemistry and improved relative condition of resident Arctic char (Salvelinus alpinus) and increased diatom diversity point to a positive ecosystem response during the same period.
Advanced Silicon-on-Insulator: Crystalline Silicon on Atomic Layer Deposited Beryllium Oxide
Authors: Min Lee Seung , Hwan Yum Jung , Larsen Eric S. , Chul Lee Woo , Keun Kim Seong , Bielawski Christopher W. , Oh Jungwoo 
Published: October 2017

AbstractSilicon-on-insulator (SOI) technology improves the performance of devices by reducing parasitic capacitance. Devices based on SOI or silicon-on-sapphire technology are primarily used in high-performance radio frequency (RF) and radiation sensitive applications as well as for reducing the short channel effects in microelectronic devices. Despite their advantages, the high substrate cost and overheating problems associated with complexities in substrate fabrication as well as the low thermal conductivity of silicon oxide prevent broad applications of this technology. To overcome these challenges, we describe a new approach of using beryllium oxide (BeO). The use of atomic layer deposition (ALD) for producing this material results in lowering the SOI wafer production cost. Furthermore, the use of BeO exhibiting a high thermal conductivity might minimize the self-heating issues. We show that crystalline Si can be grown on ALD BeO and the resultant devices exhibit potential for use in advanced SOI technology applications.
Li2MnO3 domain size and current rate dependence on the electrochemical properties of 0.5Li2MnO3·0.5LiCoO2 cathode material
Authors: Kaewmala Songyoot , Chantrasuwan Patcharapohn , Wiriya Narinthron , Srilomsak Sutham , Limphirat Wanwisa , Limthongkul Pimpa , Meethong Nonglak 
Published: October 2017

AbstractLayered-layered composite oxides of the form xLi2MnO3·(1−x) LiMO2 (M = Mn, Co, Ni) have received much attention as candidate cathode materials for lithium ion batteries due to their high specific capacity (>250mAh/g) and wide operating voltage range of 2.0–4.8 V. However, the cathode materials of this class generally exhibit large capacity fade upon cycling and poor rate performance caused by structural transformations. Since electrochemical properties of the cathode materials are strongly dependent on their structural characteristics, the roles of these components in 0.5Li2MnO3·0.5LiCoO2 cathode material was the focus of this work. In this work, the influences of Li2MnO3 domain size and current rate on electrochemical properties of 0.5Li2MnO3·0.5LiCoO2 cathodes were studied. Experimental results obtained showed that a large domain size provided higher cycling stability. Furthermore, fast cycling rate was also found to help reduce possible structural changes from layered structure to spinel structure that takes place in continuous cycling.
Angiotensin II type 2 receptor (AT2R) as a novel modulator of inflammation in rheumatoid arthritis synovium
Authors: Terenzi Riccardo , Manetti Mirko , Rosa Irene , Romano Eloisa , Galluccio Felice , Guiducci Serena , Ibba-Manneschi Lidia , Matucci-Cerinic Marco 
Published: October 2017

AbstractDespite increasing evidence suggesting that angiotensin II type 2 receptor (AT2R) may regulate tissue inflammation, no study has yet analyzed its possible implication in rheumatoid arthritis (RA) synovitis. In this study, we investigated the expression and function of AT2R in synovial tissue and cultured fibroblast-like synoviocytes (FLS) from RA patients. AT2R expression was strongly increased in RA compared with osteoarthritis (OA) synovium, as well as in in cultured RA-FLS respect to OA-FLS and healthy FLS. Treatment with pro-inflammatory cytokines was able not only to boost AT2R expression in RA-FLS and OA-FLS, but also to induce its de novo expression in healthy FLS. The stimulation of AT2R with the specific agonist CGP42112A significantly reduced gene expression of interleukin (IL)-1β and IL-6 and activation of NF-κB in RA-FLS, while opposite effects were elicited by AT2R small interfering RNA. Moreover, AT2R agonism efficiently decreased RA-FLS proliferation and migration either at baseline or under pro-inflammatory cytokine challenge. In conclusion, AT2R is strongly expressed in key effector cells of rheumatoid synovitis, namely RA-FLS, and the activation of AT2R with a specific agonist may effectively dampen their pro-inflammatory and aggressive behavior. AT2R agonism might represent a novel therapeutic strategy for patients with RA.
Punctate White Matter Lesions Associated With Altered Brain Development And Adverse Motor Outcome In Preterm Infants
Authors: Tusor Nora , Benders Manon J. , Counsell Serena J. , Nongena Phumza , Ederies Moegamad A. , Falconer Shona , Chew Andrew , Gonzalez-Cinca Nuria , Hajnal Joseph V. , Gangadharan Sunay , Chatzi Vasiliki , Kersbergen Karina J. , Kennea Nigel , Azzopardi Denis V. , Edwards A. David 
Published: October 2017

AbstractPreterm infants who develop neurodevelopmental impairment do not always have recognized abnormalities on cerebral ultrasound, a modality routinely used to assess prognosis. In a high proportion of infants, MRI detects punctate white matter lesions that are not seen on ultrasonography. To determine the relation of punctate lesions to brain development and early neurodevelopmental outcome we used multimodal brain MRI to study a large cohort of preterm infants. Punctate lesions without other focal cerebral or cerebellar lesions were detected at term equivalent age in 123 (24.3%) (59 male) of the 506 infants, predominantly in the centrum semiovale and corona radiata. Infants with lesions had higher gestational age, birth weight, and less chronic lung disease. Punctate lesions showed a dose dependent relation to abnormalities in white matter microstructure, assessed with tract-based spatial statistics, and reduced thalamic volume (p < 0.0001), and predicted unfavourable motor outcome at a median (range) corrected age of 20.2 (18.4–26.3) months with sensitivity (95% confidence intervals) 71 (43–88) and specificity 72 (69–77). Punctate white matter lesions without associated cerebral lesions are common in preterm infants currently not regarded as at highest risk for cerebral injury, and are associated with widespread neuroanatomical abnormalities and adverse early neurodevelopmental outcome.
Development of an athyroid mouse model using 131I ablation after preparation with a low-iodine diet
Authors: Oh Ji Min , Lee Ho Won , Kalimuthu Senthilkumar , Gangadaran Prakash , Baek Se Hwan , Han Man-Hoon , Hong Chae Moon , Jeong Shin Young , Lee Sang-Woo , Lee Jaetae , Ahn Byeong-Cheol 
Published: October 2017

AbstractWe optimized the protocol for thyroid ablation in living mice using radioactive iodine (RAI) and a low-iodine diet (LID). To examine the effect of LID on thyroid ablation, mice were randomly divided into 4 groups: Vehicle, 131I 2.775 MBq, 131I 5.55 MBq, and LID + 131I 2.775 MBq. The LID group was fed a LID for up to 7 days and then mice in the 131I 2.775, 131I 5.55, and LID + 131I 2.775 MBq groups were intravenously administrated with 131I, respectively. Scintigraphy imaging with 99mTc pertechnetate was performed once in 2 weeks for 4 weeks. After establishment of athyroid mice, control or athyroid mice were injected with human anaplastic thyroid cancer cells co-expressing sodium iodine symporter and enhanced firefly luciferase (ARO/NF) to evaluate RAI uptake. Scintigraphy imaging with 99mTc pertechnetate was performed with ARO/NF tumor-bearing mice. Scintigraphy imaging showed decreased thyroid uptake in the LID + 131I 2.775 MBq group compared to other groups. Scintigraphy images showed that tumor uptake was statically higher in athyroid mice than in control mice. These data suggest that these optimized conditions for thyroid ablation could be helpful to establish an in vivo mouse model.
The Bacteroidales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolytic activity
Authors: Lynch Alli , Crowley Elaine , Casey Eoghan , Cano Rafael , Shanahan Rachel , McGlacken Ger , Marchesi Julian R. , Clarke David J. 
Published: October 2017

AbstractThe contribution of the gut microbiota to the metabolism of cholesterol is not well understood. In this study, we identify 21 fosmid clones from a human gut microbiome metagenomic library that, when expressed in Escherichia coli, produce halos on LB agar supplemented with 0.01% (w/v) cholesterol (LBC agar). Analysis of 14 of these clones revealed that they all share a fragment of DNA with homology to the genome of Bacteroides vulgatus. The gene responsible for halo production on LBC agar, named choA, was identified as an N-acyltransferase known to produce an acylated glycine molecule called commendamide. In this study we show that commendamide is capable of producing a halo on LBC agar suggesting that this molecule is solubilizing the cholesterol micelles in LBC agar. We also show that commendamide is responsible for the previously described hemolytic activity associated with the choA orthologue in Bacteroides fragilis. A functional analysis of ChoA identified 2 amino acids that are important for commendamide biosynthesis and we present phylogenetic and functional data showing that orthologues of choA are found only in the order Bacteroidales. Therefore, the production of commendamide may be an adaptation to the environments colonized by the Bacteroidales, including the mammalian gut.