bluuebunny/crossref_metadata_2025_split huggingface dataset:
Socio-economic factors associated with a healthy diet: results from the E3N study
Authors: Affret Aurélie , Severi Gianluca , Dow Courtney , Rey Grégoire , Delpierre Cyrille , Boutron-Ruault Marie-Christine , Clavel-Chapelon Françoise , Fagherazzi Guy 
Published: March 2017

AbstractObjectiveTo identify individual and contextual socio-economic factors associated with a healthy diet.DesignDietary data from a large cohort study were used to derive two mutually exclusive dietary patterns through a latent class analysis. Associations between dietary patterns and socio-economic factors were studied with logistic regression.SettingE3N, a French prospective cohort study composed of women recruited from a national health insurance plan covering people working in the national education system.SubjectsE3N participants (n 73 031) with dietary and socio-economic data available.ResultsThe ‘Healthy’ pattern was characterized by a large consumption of fruits and vegetables and the ‘Less Healthy’ pattern by a large consumption of pizza and processed meat. When all socio-economic factors were analysed together, all of the individual factors considered were associated with a healthy diet (e.g. women with three or more children were less likely to follow a healthy diet v. women with no children, OR (95 % CI): 0·70 (0·66, 0·75)) while the contextual factors associated with a healthy diet included the size of the agglomeration of residence and the area of birth and residence (e.g. women living in the West of France were less likely to follow a healthy diet v. those living in the South of France: 0·78 (0·72, 0·83)).ConclusionsWe demonstrated that individual and contextual factors are both associated with diet. Rather than focusing only on individual factors, we recommend future studies or public health and nutritional strategies on diet to consider both types of factors.
Efficient Simulation of Secondary Fluorescence Via NIST DTSA-II Monte Carlo
Authors: Ritchie Nicholas W. M. 
Published: March 2017

AbstractSecondary fluorescence, the final term in the familiar matrix correction triumvirate Z·A·F, is the most challenging for Monte Carlo models to simulate. In fact, only two implementations of Monte Carlo models commonly used to simulate electron probe X-ray spectra can calculate secondary fluorescence—PENEPMA and NIST DTSA-IIa (DTSA-II is discussed herein). These two models share many physical models but there are some important differences in the way each implements X-ray emission including secondary fluorescence. PENEPMA is based on PENELOPE, a general purpose software package for simulation of both relativistic and subrelativistic electron/positron interactions with matter. On the other hand, NIST DTSA-II was designed exclusively for simulation of X-ray spectra generated by subrelativistic electrons. NIST DTSA-II uses variance reduction techniques unsuited to general purpose code. These optimizations help NIST DTSA-II to be orders of magnitude more computationally efficient while retaining detector position sensitivity. Simulations execute in minutes rather than hours and can model differences that result from detector position. Both PENEPMA and NIST DTSA-II are capable of handling complex sample geometries and we will demonstrate that both are of similar accuracy when modeling experimental secondary fluorescence data from the literature.
Accurate nanoelectrode recording of human pluripotent stem cell-derived cardiomyocytes for assaying drugs and modeling disease
Authors: Lin Ziliang Carter , McGuire Allister F. , Burridge Paul W. , Matsa Elena , Lou Hsin-Ya , Wu Joseph C. , Cui Bianxiao 
Published: March 2017

AbstractThe measurement of the electrophysiology of human pluripotent stem cell-derived cardiomyocytes is critical for their biomedical applications, from disease modeling to drug screening. Yet, a method that enables the high-throughput intracellular electrophysiology measurement of single cardiomyocytes in adherent culture is not available. To address this area, we have fabricated vertical nanopillar electrodes that can record intracellular action potentials from up to 60 single beating cardiomyocytes. Intracellular access is achieved by highly localized electroporation, which allows for low impedance electrical access to the intracellular voltage. Herein, we demonstrate that this method provides the accurate measurement of the shape and duration of intracellular action potentials, validated by patch clamp, and can facilitate cellular drug screening and disease modeling using human pluripotent stem cells. This study validates the use of nanopillar electrodes for myriad further applications of human pluripotent stem cell-derived cardiomyocytes such as cardiomyocyte maturation monitoring and electrophysiology-contractile force correlation.
Self-amplified Amazon forest loss due to vegetation-atmosphere feedbacks
Authors: Zemp Delphine Clara , Schleussner Carl-Friedrich , Barbosa Henrique M. J. , Hirota Marina , Montade Vincent , Sampaio Gilvan , Staal Arie , Wang-Erlandsson Lan , Rammig Anja 
Published: March 2017

AbstractReduced rainfall increases the risk of forest dieback, while in return forest loss might intensify regional droughts. The consequences of this vegetation–atmosphere feedback for the stability of the Amazon forest are still unclear. Here we show that the risk of self-amplified Amazon forest loss increases nonlinearly with dry-season intensification. We apply a novel complex-network approach, in which Amazon forest patches are linked by observation-based atmospheric water fluxes. Our results suggest that the risk of self-amplified forest loss is reduced with increasing heterogeneity in the response of forest patches to reduced rainfall. Under dry-season Amazonian rainfall reductions, comparable to Last Glacial Maximum conditions, additional forest loss due to self-amplified effects occurs in 10–13% of the Amazon basin. Although our findings do not indicate that the projected rainfall changes for the end of the twenty-first century will lead to complete Amazon dieback, they suggest that frequent extreme drought events have the potential to destabilize large parts of the Amazon forest.
Pre-plaque conformational changes in Alzheimer’s disease-linked Aβ and APP
Authors: Klementieva O. , Willén K. , Martinsson I. , Israelsson B. , Engdahl A. , Cladera J. , Uvdal P. , Gouras G. K. 
Published: March 2017

AbstractReducing levels of the aggregation-prone Aβ peptide that accumulates in the brain with Alzheimer’s disease (AD) has been a major target of experimental therapies. An alternative approach may be to stabilize the physiological conformation of Aβ. To date, the physiological state of Aβ in brain remains unclear, since the available methods used to process brain tissue for determination of Aβ aggregate conformation can in themselves alter the structure and/or composition of the aggregates. Here, using synchrotron-based Fourier transform infrared micro-spectroscopy, non-denaturing gel electrophoresis and conformational specific antibodies we show that the physiological conformations of Aβ and amyloid precursor protein (APP) in brain of transgenic mouse models of AD are altered before formation of amyloid plaques. Furthermore, focal Aβ aggregates in brain that precede amyloid plaque formation localize to synaptic terminals. These changes in the states of Aβ and APP that occur prior to plaque formation may provide novel targets for AD therapy.
Identification of common non-coding variants at 1p22 that are functional for non-syndromic orofacial clefting
Authors: Liu Huan , Leslie Elizabeth J. , Carlson Jenna C. , Beaty Terri H. , Marazita Mary L. , Lidral Andrew C. , Cornell Robert A. 
Published: March 2017

AbstractGenome-wide association studies (GWAS) do not distinguish between single nucleotide polymorphisms (SNPs) that are causal and those that are merely in linkage-disequilibrium with causal mutations. Here we describe a versatile, functional pipeline and apply it to SNPs at 1p22, a locus identified in several GWAS for non-syndromic cleft lip with or without cleft palate (NS CL/P). First we amplified DNA elements containing the ten most-highly risk-associated SNPs and tested their enhancer activityin vitro, identifying three SNPs with allele-dependent effects on such activity. We then usedin vivoreporter assays to test the tissue-specificity of these enhancers, chromatin configuration capture to test enhancer–promoter interactions, and genome editingin vitroto show allele-specific effects on ARHGAP29 expression and cell migration. Our results further indicate that two SNPs affect binding of CL/P-associated transcription factors, and one affects chromatin configuration. These results translate risk into potential mechanisms of pathogenesis.
Double-stranded RNA virus outer shell assembly by bona fide domain-swapping
Authors: Sun Zhaoyang , El Omari Kamel , Sun Xiaoyu , Ilca Serban L. , Kotecha Abhay , Stuart David I. , Poranen Minna M. , Huiskonen Juha T. 
Published: March 2017

AbstractCorrect outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by calcium ions but its biomechanics remain poorly understood. Here, we describe the near-atomic resolution structure of the φ6 double-shelled particle. The outer T=13 shell protein P8 consists of two alpha-helical domains joined by a linker, which allows the trimer to adopt either a closed or an open conformation. The trimers in an open conformation swap domains with each other. Our observations allow us to propose a mechanistic model for calcium concentration regulated outer shell assembly. Furthermore, the structure provides a prime exemplar of bona fide domain-swapping. This leads us to extend the theory of domain-swapping from the level of monomeric subunits and multimers to closed spherical shells, and to hypothesize a mechanism by which closed protein shells may arise in evolution.
Negative association between acrylamide exposure and body composition in adults: NHANES, 2003–2004
Authors: Chu P-L , Lin L-Y , Chen P-C , Su T-C , Lin C-Y 
Published: March 2017

Abstract
Background/Objectives:
Acrylamide is present in mainstream cigarette smoke and in some food prepared at high temperature. Animal studies have shown that acrylamide exposure reduces body weight. Prenatal exposure to acrylamide also has been linked to reduced birth weight in human. Whether acrylamide exposure is associated with altered body compositions in adults is not clear.

Subjects/Methods:
We selected 3623 subjects (aged ⩾20 years) from a National Health and Nutrition Examination Survey (NHANES) in 2003–2004 to determine the relationship among hemoglobin adducts of acrylamide (HbAA), hemoglobin adducts of glycidamide (HbGA) and body composition (body measures, bioelectrical impedance analysis (BIA), dual energy x-ray absorptiometry (DXA)). Data were adjusted for potential confounding variables.

Results:
The geometric means and 95% CI concentrations of HbAA and HbGA were 60.48 (59.32–61.65) pmol/g Hb and 55.64 (54.40–56.92) pmol/g Hb, respectively. After weighting for sampling strategy, we identified that one-unit increase in natural log-HbAA, but not HbGA, was associated with reduction in body measures (body weight, body mass index (BMI), subscapular/triceps skinfold), parameters of BIA (fat-free mass, fat mass, percent body fat, total body water) and parameters of DXA (android fat mass, android percent fat, gynoid fat/lean mass, gynoid percent mass, android to gynoid ratio). Subgroup analysis showed that these associations were more evident in subjects at younger age, male gender, whites, lower education level, active smokers and those with lower BMI.

Conclusions:
Higher concentrations of HbAA are associated with a decrease in body composition in the US general population. Further studies are warranted to clarify this association.
Overweight and obesity in Mexican children and adolescents during the last 25 years
Authors: Hernández-Cordero S , Cuevas-Nasu L , Morales-Ruán M C , Méndez-Gómez Humarán I , Ávila-Arcos M A , Rivera-Dommarco J A 
Published: March 2017

Abstract
Background/Objective:
The objective of the study was to provide current estimates of the prevalence and trends of overweight and obesity (OW+OB) in Mexican children and adolescents.

Subjects/Methods:
Body mass index objectively measured was analyzed for 37 147 children and adolescents aged 0–19 years obtained in 2012 as part of the National Health and Nutrition Survey (ENSANUT-2012), a nationally representative sample of the Mexican population. In addition, data from previous National Nutrition Surveys obtained in 1988, 1999 and 2006 were compared with analyze trends over a 24-year period (1988–2012) for children <5 years of age and adolescents and over a 13-year period (1999–2012) for school-age children. World Health Organization Child Growth Standard was used to define OW+OB.

Results:
In 2012, 33.5% of children <5 years of age (both sexes) were at risk of overweight or were overweight (OW); 32% and 36.9% of girls and boys 5–11 years of age were OW+OB, respectively, and 35.8% and 34.1% of female and male adolescents were OW+OB, respectively. Statistically significant trends were documented for all age groups during the study period. Overall change in the combined prevalence in preschool children was 6.3±1.0 percentage points (pp; P<0.001; 0.26 pp per year) in the last 24 years, showing the highest increase between 1988 and 1999, whereas for school-age girls (from 1999 to 2012) and adolescent females (from 1988 to 2012), OW+OB increased across all periods at a declining trend, with an overall change of 0.5 and 1.0 pp per year, respectively. Changes in the prevalence of OW+OB were highest among children and adolescents in the lowest quintile of the household living condition index.

Conclusions:
Prevalence of OW+OB among children and adolescents increased significantly during the last 13–24 years. The rate of increase has declined in the last 6 years in all age groups. Changes in prevalence of OW+OB presented here suggest that, in Mexico, the burden of obesity is shifting toward the groups with lower socioeconomic level.
Knockdown of long non-coding RNA XIST increases blood–tumor barrier permeability and inhibits glioma angiogenesis by targeting miR-137
Authors: Yu H , Xue Y , Wang P , Liu X , Ma J , Zheng J , Li Z , Li Z , Cai H , Liu Y 
Published: March 2017

AbstractAntiangiogenic therapy plays a significant role in combined glioma treatment. However, poor permeability of the blood–tumor barrier (BTB) limits the transport of chemotherapeutic agents, including antiangiogenic drugs, into tumor tissues. Long non-coding RNAs (lncRNAs) have been implicated in various diseases, especially malignant tumors. The present study found that lncRNA X-inactive-specific transcript (XIST) was upregulated in endothelial cells that were obtained in a BTB model in vitro. XIST knockdown increased BTB permeability and inhibited glioma angiogenesis. The analysis of the mechanism of action revealed that the reduction of XIST inhibited the expression of the transcription factor forkhead box C1 (FOXC1) and zonula occludens 2 (ZO-2) by upregulating miR-137. FOXC1 decreased BTB permeability by increasing the promoter activity and expression of ZO-1 and occludin, and promoted glioma angiogenesis by increasing the promoter activity and expression of chemokine (C–X–C motif) receptor 7b (CXCR7). Overall, the present study demonstrates that XIST plays a pivotal role in BTB permeability and glioma angiogenesis, and the inhibition of XIST may be a potential target for the clinical management of glioma.
Development of Customized [18F]Fluoride Elution Techniques for the Enhancement of Copper-Mediated Late-Stage Radiofluorination
Authors: Mossine Andrew V. , Brooks Allen F. , Ichiishi Naoko , Makaravage Katarina J. , Sanford Melanie S. , Scott Peter J. H. 
Published: March 2017

AbstractIn a relatively short period of time, transition metal-mediated radiofluorination reactions have changed the PET radiochemistry landscape. These reactions have enabled the radiofluorination of a wide range of substrates, facilitating access to radiopharmaceuticals that were challenging to synthesize using traditional fluorine-18 radiochemistry. However, the process of adapting these new reactions for automated radiopharmaceutical production has revealed limitations in fitting them into the confines of traditional radiochemistry systems. In particular, the presence of bases (e.g. K2CO3) and/or phase transfer catalysts (PTC) (e.g. kryptofix 2.2.2) associated with fluorine-18 preparation has been found to be detrimental to reaction yields. We hypothesized that these limitations could be addressed through the development of alternate techniques for preparing [18F]fluoride. This approach also opens the possibility that an eluent can be individually tailored to meet the specific needs of a metal-catalyzed reaction of interest. In this communication, we demonstrate that various solutions of copper salts, bases, and ancillary ligands can be utilized to elute [18F]fluoride from ion exchange cartridges. The new procedures are effective for fluorine-18 radiochemistry and, as proof of concept, have been used to optimize an otherwise base-sensitive copper-mediated radiofluorination reaction.
Cockles, barnacles and ascidians compose a subtidal facilitation cascade with multiple hierarchical levels of foundation species
Authors: Yakovis Eugeniy , Artemieva Anna 
Published: March 2017

AbstractFacilitation cascades occur when multiple foundation species in a community are involved in a hierarchy of positive interactions, and consist of a primary facilitator which positively affects secondary facilitators, each supporting a suit of dependent species. There is no theoretical limit to the number of levels in a facilitation cascade, yet the existence of more than two has rarely been examined. We manipulated biogenic substrate produced by a primary facilitator (cockle shells) and a secondary facilitator (barnacles and their empty tests) in a space-limited subtidal community to test the hypothesis that solitary ascidians would be the third-level facilitator. In the field, most ascidians were found on barnacles, and most barnacles occupied cockle shells. To produce this pattern, barnacles could nurse ascidians (a longer ‘facilitation chain’) or outcompete them from cockle shells (a shorter chain). Experimental results clearly supported the nursing hypothesis providing evidence for a facilitation cascade with three hierarchical levels of foundation species. Our findings confirm that like predation and competition, positive interspecific interactions nest into multi-tier hierarchies with numerous levels. While the number of foundation species should increase community stability and resilience as it increases diversity and reduces environmental stress, facilitation chain length may have the opposite effect.
Geographic distribution of cadmium and its interaction with the microbial community in the Longjiang River: risk evaluation after a shocking pollution accident
Authors: Zhang MingJiang , Huang FuKe , Wang GuangYuan , Liu XingYu , Wen JianKang , Zhang XiaoSheng , Huang YaoSi , Xia Yu 
Published: March 2017

AbstractA shocking Longjiang River cadmium pollution accident occurred in 2012, the effects of which on microbial communities remain unclear. Alkaline precipitation technology was applied for remediation, but concerns rose about the stability of this technology. To understand the geographic distribution of cadmium and its correlation with microbes, in this study, 39 water samples and 39 sludge samples from this river and 2 soil samples from the nearby farmland were collected for chemical and microbial analyses. The Cd concentrations of all water samples were lower than 0.005 mg/L and reached the quality standards for Chinese surface water. A ranking of sludge samples based on Cd contents showed sewage outfall > dosing sites > farmland, all of which were higher than the quality standard for soil. Alkaline precipitation technology was effective for Cd precipitation. Cd was unstable; it was constantly dissolving and being released from the sludge. The Cd content of each phase was mainly influenced by the total Cd content. Over 40,000 effective sequences were detected in each sample, and a total of 59,833 OTUs and 1,273 genera were found using Illumina MiSeq sequencing. Two phyla and 39 genera were notably positively correlated with the Cd distribution, while the cases of 10 phyla and 6 genera were the opposite.
Two LEAFY homologs ILFY1 and ILFY2 control reproductive and vegetative developments in Isoetes L.
Authors: Yang Tao , Du Ming-fang , Guo You-hao , Liu Xing 
Published: March 2017

AbstractLEAFY (LFY) is a plant-specific transcription factor, which is found in algae and all land plants. LFY homologs exert ancestral roles in regulating cell division and obtain novel functions to control floral identity. Isoetes L. is an ancient genus of heterosporous lycophytes. However, characters about LFY homologs in lycophytes remain poorly investigated. In this study, two LFY homologs, ILFY1 and ILFY2, were cloned from five Isoetes species, including I. hypsophila, I. yunguiensis, I. sinensis, I. orientalis, and I. taiwanensis. The full length of ILFY1 was 1449–1456 bp with an open reading frame (ORF) of 927–936 bp. The full length of ILFY2 was 1768 bp with ORF of 726 bp. Phylogenetic tree revealed that ILFY1 and ILFY2 were separated into two clades, and I. hypsophila were separated with the others. Expression analysis demonstrated that IsLFY1 and IsLFY2 for I. sinensis did not show functional diversity. The two transcripts were similarly accumulated in both vegetative and reproductive tissues and highly expressed in juvenile tissues. In addition, the IsLFY1 and IsLFY2 transgenic Arabidopsis similarly did not promote precocious flowering, and they were inactive to rescue lfy mutants. The results facilitate general understandings about the characteristics of LFY in Isoetes and evolutionary process.
Multi-walled carbon nanotubes act as a chemokine and recruit macrophages by activating the PLC/IP3/CRAC channel signaling pathway
Authors: Li Hui , Tan Xiao-Qiu , Yan Li , Zeng Bo , Meng Jie , Xu Hai-Yan , Cao Ji-Min 
Published: March 2017

AbstractThe impact of nanomaterials on immune cells is gaining attention but is not well documented. Here, we report a novel stimulating effect of carboxylated multi-walled carbon nanotubes (c-MWCNTs) on the migration of macrophages and uncover the underlying mechanisms, especially the upstream signaling, using a series of techniques including transwell migration assay, patch clamp, ELISA and confocal microscopy. c-MWCNTs dramatically stimulated the migration of RAW264.7 macrophages when endocytosed, and this effect was abolished by inhibiting phospholipase C (PLC) with U-73122, antagonizing the IP3 receptor with 2-APB, and blocking calcium release-activated calcium (CRAC) channels with SK&F96365. c-MWCNTs directly activated PLC and increased the IP3 level and [Ca2+]i level in RAW264.7 cells, promoted the translocation of the ER-resident stromal interaction molecule 1 (STIM1) towards the membranous calcium release-activated calcium channel modulator 1 (Orai1), and increased CRAC current densities in both RAW264.7 cells and HEK293 cells stably expressing the CRAC channel subunits Orai1 and STIM1. c-MWCNTs also induced dramatic spatial polarization of KCa3.1 channels in the RAW264.7 cells. We conclude that c-MWCNT is an activator of PLC and strongly recruits macrophages via the PLC/IP3/CRAC channel signaling cascade. These novel findings may provide a fundamental basis for the impact of MWCNTs on the immune system.