bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time scales for pluton growth, magma chamber formation and super-eruptions
Authors: Sparks Stephen , Zalinge Marit van , Mark Darren , Tremblay Marissa , Keller Brenhin , Cooper Francis , Rust Alison 
Published: May 2021

Abstract
Generation of silicic magmas leads to emplacement of granite plutons, huge explosive volcanic eruptions and physical and chemical zoning of continental and arc crust1-7. While the time scales for silicic magma generation in the deep and middle crust are prolonged8 magma transfer into the upper crust followed by eruption is episodic and can be rapid9-12. Ages of inherited zircons and sanidines from four Miocene ignimbrites in the Central Andes indicate a gap of 4.6 Myr between the start of pluton emplacement and onset of super-eruptions, with a 1 Myr cyclicity. Here we show that inherited sanidine crystals were stored at temperatures <470oC prior to incorporation in the magma. Our observations are explained by silicic melt segregation in a middle crustal hot zone with episodic melt ascent from an unstable layer at the top of the zone with a time scale governed by the rheology of the upper crust. After thermal incubation of the growing batholith, large magma chambers formed in only a few thousand years or less by dyke transport from the hot zone melt layer. Instability and disruption of earlier plutonic rock occurred in a few decades or less just prior to or during super-eruptions.
Investigation of Long Term Hazards of Chemical Weapon Agents in the Environment of Sardasht Area, Iran
Authors: Vaezihir Abdorreza , Pirkhezranian Asra , Sehati Negar , Hosseinzadeh Mohammad Reza , Salehi-Lisar Seyed Yahya , Sanderson Hans 
Published: May 2021

Abstract
The present study aimed to was to investigate the persistence and existence of chemical warfare agents (CWAs) and related dissipation products in the environment. The study area is Sardasht district located in the western borderline of Iran and Iraq in which was subjected to attack with chemical weapons in July 1987 during the Iran-Iraq war. Three types of environmental samples including water, soil and native local plant materials were collected and analyzed. Gas chromatography-mass spectrometry in the electron impact ionization mode has been developed for the separation, screening, identification and qualification of chemicals after the sample preparation methods. In order to validate the applied extraction procedures, ethylene glycol was spiked to some of the samples including groundwater, surface soil, grape and alfalfa plants. All the recoveries were in the range of 83.6–107.4% with the relative standard deviations varying from 4.9–12.4% (n = 3) successfully. The initial results revealed that no trace of related compounds or CWAs was detected in the soil and water samples. However, trace amounts of some degradation products of blistering agents like Mustard gas (HD) and Lewisite were found in a tree wood from a house subjected to chemical attack as well as in barley samples (a mixture of leaves and root) collected from an agricultural field in the area indicating chronic low exposure to the environment and people.
Organogenesis and Sonication-Assisted Agrobacterium-Mediated Transformation of Poplar Roots
Authors: Giovanella Thais Salete , Degenhardt Juliana , Zanella Laudiane Bruna , Filho João Carlos Bespalhok 
Published: May 2021

Abstract
Functional genomics along with genetic transformation and plant regeneration are used to identify genes of interest, comprising essential tools to obtain plants with desired characteristics. In this study, we described an organogenesis and a genetic transformation protocol for Populus tremula x Populus alba clone 717-1B4 using roots. In the organogenesis experiments the PGRs zeatin, BA and kinetin at different concentrations were evaluated. The effect of explant age was evaluated and at 30 days “old” roots (6 months old) showed a higher regeneration rate when compared to “young” roots (2 months old). In the genetic transformation experiments kanamycin concentration, the use of sonication (SAAT), co-cultivation period and explant age were evaluated. Sonication positively affected transformation, while co-cultivation time did not interfere. Regarding explant age, no statistical differences were observed. Quantitative real-time PCR (qPCR) data showed that among the six transgenic plants evaluated, two presented two copies and the others only one copy of the gene. In this study, efficient protocols of organogenesis and genetic transformation for poplar roots are presented with a transformation efficiency of 58%.
Effects of Haze Pollution on Pesticide use by Rice Farmers: Fresh Evidence from Rural Area of China
Authors: Guo Lili , Cao Andi , Huang Minjun , Li Houjian 
Published: May 2021

Abstract
Recently, serious haze pollution has not only threatened the human health and food security, but also seems to have aggravated the unscientific use of pesticides by rice farmers in rural area of China. Using original data on haze pollution across China, combined with rural household survey data collected from 2014 to 2018, we conducted a detailed empirical study on the effects of haze pollution on pesticide use by rice farmers based on the theory of risk aversion. The empirical results revealed that haze pollution with higher levels of PM2.5 positively impacted the use of chemical pesticides in the rice cultivation. More precisely, with 1% increases in PM2.5 concentration, the amount of pesticide application per mu increased by 7.9%, and the average pesticide fee per mu increased by 2.3%, respectively. The results were robust to a series of tests that addressed potential endogeneity concerns, including omitted variable bias, measurement error and reverse causality. We then examined the heterogeneous effects of haze pollution increase on the use of chemical pesticides and found that the effects of haze pollution on the use of chemical pesticides to be weaker for rice farmer with more rice-planting experience, those with smaller cultivated area of rice, however, the effects on the amount of chemical pesticide application per mu to be weaker for those with rice insurance, but the effects on the average chemical pesticide fee per mu to be stronger for those with rice insurance. Our findings provide important policy implications for pesticide risk management in rural areas of developing countries.
Oyster As, Cd, Cu, Hg, Pb and Zn Levels in the Northern South China Sea: Long-term Spatiotemporal Distributions, Interacting Effects, and Risk Assessment to Human Health
Authors: Wang Lifei , Wang Xuefeng , Chen Haigang , Wang Zenghuan , Jia Xiaoping 
Published: May 2021

Abstract
Estuarine and coastal ecosystems are often considered vulnerable due to the complex biogeochemical processes and the human disturbances through a variety of pollution. Among environmental contaminants, heavy metals in estuarine and coastal ecosystems have been of increasing concern in environmental conservation. Long-term exposure to heavy metal contamination, mainly through food and water, could be harmful to human health. It is therefore critical to understand the quantitative comparisons and interacting effects of different heavy metals in common seafood species, such as oysters. This work studied the long-term spatiotemporal trends and health risk assessment of oyster arsenic (As), cadmium (Cd), copper (Cu), mercury (Hg), lead (Pb) and zinc (Zn) levels in the coastal waters of northern South China Sea. Cultured oysters (Crassostrea rivularis) from 23 estuaries and harbors in the coastal areas of northern South China Sea in 1989–2015 were analyzed for the spatiotemporal trends of the six heavy metal levels. Metal pollution index (MPI), target hazard quotient (THQ) and hazard index (HI) were used for quantifying the exposure of the six heavy metals to human health through oyster consumption. Principal component analysis (PCA) was used for assessing the relative importance of the six metals in oyster heavy metal distribution patterns in the northern South China Sea. Overall, the As, Cd, Cu, Hg, Pb and Zn levels in oysters from the northern South China Sea generally declined from 1989 to 2015, stayed relatively high (MPI = 2.42–3.68) during 1989–2000, gradually decreased since 2000, and slightly increased after 2010. Oyster heavy metal levels were highest in the Pearl River Estuary (MPI = 1.20–5.52), followed by west Guangdong and east Guangdong, Guangxi, and Hainan coastal waters. This pattern is probably because economics and industry around the Pearl River Estuary have been growing faster than the other areas of this work in the recent two decades, and it should be taken as a hotspot for the monitoring of seafood safety in southern China. Principal component analysis indicated that Cu, Zn and Cd were the most important metals in the long-term distributions of oyster heavy metal levels in the northern South China Sea. Health risk assessment suggested that the risk of the six heavy metals exposure through oyster consumption were relatively high during 1989–2005 (THQ = 1.01–5.82), significantly decreased since 2005 (THQ < 1), and slightly increased after 2010.
The synergistic coordination of DNA 5-hydroxylmethylcytosine and RNA 5-methycytosine regulates human foetal development
Authors: Han Xiao , Guo Jia , Wang Mengke , Zhang Nan , Ren Jie , Yang Ying , Chi Xu , Chen Yusheng , Yao Huan , Zhao Yongliang , Yang Yun-Gui , Sun Yingpu , Xu Jiawei 
Published: May 2021

Abstract
After implantation, complex and highly specialized molecular events render functionally distinct organ formation, whereas how the epigenome shapes organ-specific development remains to be fully elucidated. Here, Nano-hmC-Seal and RNA bisulfite sequencing (RNA-BisSeq) were performed and the first multilayer landscapes of both DNA 5hmC and RNA m5C epigenome, as well as the accompanying transcriptome were obtained, in the heart, kidney, liver and lung of the human foetuses at 13 − 28 weeks with 123 samples in total. DNA 5hmC plays a consistently leading role, while RNA m5C acts as a dynamic downstream regulatory valve in regulating gene expression with a turning point of 18–19 weeks. Although, these modifications appear to coordinate in general, they also play different roles with regard to specific functions. Our integrated studies illustrate the epigenetic maps during different stages of human foetal organogenesis, which provide a foundation for understanding the in-depth epigenetic mechanisms for early development and birth defects.
Global Disparities of Greenhouse Gases Emission in Agriculture Sector: Panel Club Convergence Analysis
Authors: Akram Vaseem , Ali Jabir 
Published: May 2021

Abstract
A lot has been discussed about the greenhouse gases (GHGs) emissions in the existing studies, the study on the club convergence of GHGs emissions is limited particularly for the agriculture sector. This study tries to investigate the convergence hypothesis across 93 countries spanning 1980–2017. To examine the convergence hypothesis, we implement the novel Phillips and Sul test. Results obtained from this test show the evidence of divergence when we consider all 93 countries as a group. This implies that GHGs across the countries are following different convergence paths. To capture this, we further apply clustering algorithms and results show the existence of five clubs of convergence and one group stating the need for altered the polices at the club level to achieve a single steady-state in GHGs emission. Moreover, our findings recommend that the mitigation policies would be considered the presence of different clubs of regions with different convergence paths in terms of GHGs emissions and account for the distributional effect of transfers across countries.
Altered cfDNA Fragmentation Profile in Hypomethylated Regions as Diagnostic Marker in Breast Cancer
Authors: Wang Jun , Yang Ming , Su Mingyang , Shu Lirong , Wang Hongxian , Wu Xiaoqian , Zhong Guocheng , Tang Zhixiong , Chen Peng , Zhang Shasha , Wang Yun , Yu Li , Gou Deming 
Published: May 2021

Abstract
Backgroud: Breast cancer, the most common malignancy in women, has been proved to have both altered plasma cell-free DNA (cfDNA) methylation and fragmentation profiles, nevertheless, simultaneously detecting both of them for breast cancer diagnosis has never been reported. Moreover, although fragmentation pattern of cfDNA is determined by nuclease digestion of chromatin, structure of which may be affected by DNA methylation, whether cfDNA methylation and fragmentation are biologically related or not still remains unclear.Methods: Improved cfMeDIP-seq were utilized to characterize both cfDNA methylation and fragmentation profiles in 25 plasma samples from both healthy individuals and patients with breast cancer. The feasibility of using cfDNA fragmentation profile in hypo- and hyper- methylated regions as diagnostic markers for breast cancer was evaluated. Results: Mean size of cfDNA fragments ranging from 100 to 220 base pairs (bp) was found to increase from 170.06 (Input libraries) to 173.04 (IP libraries) bp in healthy individuals, which was not observed in patients with breast cancer (170.51 to 170.71 bp). Furthermore, mean size of cfDNA fragments mapped to hypomethylated regions decreased more win patients with breast cancer (4.60 bp, 172.33 bp in hypermethylated regions to 167.73 bp in hypomethylated regions) than healthy individuals (2.87 bp, 174.54 bp in hypermethylated regions to 171.67 bp in hypomethylated regions). The feasibility of using abnormality of short cfDNA fragments ratio in hypomethylated genomic regions for diagnosis of breast cancer in validation cohort was evaluated. 7 out of 11 patients were detected as having breast cancer (63.6% sensitivity), whereas no healthy individuals were mis-detected (100% specificity). Conclusion: We identified enriched short cfDNA fragments after 5mC-immunoprecipitation (IP) in patients with breast cancer, and demonstrated the enriched short cfDNA fragments might originated from hypomethylated genomic regions. Furthermore, we proved the feasibility of using differentially methylated regions (DMRs)-dependent cfDNA fragmentation profile for breast cancer diagnosis.
Cretaceous fire-resistant angiosperms
Authors: Wang Shuo , Shi Chao , Cai Hao-hong , Zhang Hong-rui , Long Xiao-xuan , Tihelka Erik , Song Wei-cai , Feng Qi , Jiang Ri-xin , Cai Chenyang , Lombard Natasha , Li Xiong , Yuan Ji , Zhu Jian-ping , Yang Hui-yu , Liu Xiao-fan , Xiang Qiao-Ping , Zhao Zun-tian , Long Chunlin , Zhang Xianchun , Peng Hua , Li De-Zhu , Schneider Harald , Engel Michael , Wang Yongdong , Spicer Robert 
Published: May 2021

Abstract
Background: Flowering plants (angiosperms) dominate most global ecosystems today, but their rapid Cretaceous diversification has remained poorly understood ever since Darwin referred to it as an ‘abominable mystery’. Although numerous Cretaceous fossil flowers have been discovered in recent years, most are represented by incomplete charcoalified fragments that do not preserve delicate structures such as complete petals and surface textures, which means that their similarity to living forms is often difficult to discern. The scarcity of information about the ecology of early angiosperms makes it difficult to test hypotheses about the drivers of their diversification. Among other factors, frequent fires in the Cretaceous have been postulated as having possibly facilitated the rise of angiosperms. However, to date no early fossil angiosperms displaying fire-adapted traits have been known, making the role of fire in shaping Cretaceous floras uncertain.Results: We report the discovery of two exquisitely preserved fossil flower species, one identical to the inflorescences of the extant crown eudicot genus Phylica and the other recovered as a sister group to Phylica, both preserved as inclusions in Cretaceous amber from northern Myanmar (~99 Ma). These specialized flower structures, named Phylica piloburmensis sp. nov. and Eophylica priscastellata gen. et sp. nov., were adapted to surviving frequent wildfires, providing the earliest evidence of fire-resistance in angiosperms. The fossils suggest that fire was a significant selective force in Cretaceous angiosperm floras and that adaptations to fire resistance in some eudicot clades have been conserved for at least 99 Ma. This morphological stasis encompasses a range of floral characters, including the production of ‘pseudo-flowers’, and characteristic fruit and pollen architecture. Given its morphological distinctiveness, the Eophylica-Phylica clade represents one of the first well-documented angiosperm ‘living fossil’ genera from the Cretaceous. Conclusion: Our study suggests that core eudicots with specialised flower morphology displaying hallmarks of fire resistance and identical to those of the extant south African genus Phylica, had originated by the mid-Cretaceous (~99 Ma). Palaeoenvironmental reconstructions indicate that these plants lived in conditions similar to those of present-day southern Africa where 70% of taxa survive frequent burning, and that fire resistance was probably widespread in the fire-prone Cretaceous. The results also provide new insights into the biogeographic origin of at least one element of the highly endemic Greater Cape Region biodiversity hotspot flora biota.
Quantum Structured Light: Non-classical Spin Texture of Twisted Single-photon Pulses
Authors: Yang Li-Ping , Jacob Zubin 
Published: May 2021

Abstract
Classical structured light with controlled polarization and orbital angular momentum (OAM) of electromagnetic waves has varied applications in optical trapping, bio-sensing, optical communications and quantum simulations. The classical electromagnetic theory of such structured light beams and pulses have advanced significantly over the last two decades. However, a framework for the quantum density of spin and OAM for single-photons remains elusive. Here, we develop a theoretical framework and put forth the concept of quantum structured light for space-time wavepackets at the single-photon level. Our work marks a paradigm shift beyond scalar-field theory as well as the paraxial approximation and can be utilized to study the quantum properties of the spin and OAM of all classes of twisted quantum light pulses. We capture the uncertainty in full three-dimensional (3D) projections of vector spin demonstrating their quantum behavior beyond the conventional concept of classical polarization. Even in laser beams with high OAM along the propagation direction, we predict the existence of large OAM quantum fluctuations in the transverse plane which can be verified experimentally. We show that the spin density generates modulated helical texture beyond the paraxial limit and exhibits distinct statistics for Fock-state vs. coherent-state twisted pulses. We introduce the quantum correlator of photon spin density to characterize the nonlocal spin noise providing a rigorous parallel with fermionic spin noise operators. Our work paves the way for quantum spin-OAM physics in twisted single photon pulses and also opens explorations for new phases of light with long-range spin order.
In Vivo Imaging of Cannabinoid Type 2 Receptors, Functional and Structural Alterations in Mouse Model of Cerebral Ischemia by PET and MRI
Authors: Ni Ruiqing , Herde Adrienne Müller , Haider Ahmed , Keller Claudia , Louloudis Georgios , Vaas Markus , Schibli Roger , Ametamey Simon M. , Klohs Jan , Mu Linjing 
Published: May 2021

Abstract
Background and purposeBrain ischemia is one of the most important pathologies of the central nervous system. Non-invasive molecular imaging methods have the potential to provide critical insights into the temporal dynamics and follow alterations of receptor expression and metabolism in ischemic stroke. The aim of this study was to assess the cannabinoid type 2 receptors (CB2R) levels in transient middle cerebral artery occlusion (tMCAO) mouse models at subacute stage using positron emission tomography (PET) with our novel tracer [18F]RoSMA-18-d6, and structural imaging by magnetic resonance imaging (MRI). MethodsOur recently developed CB2R PET tracer [18F]RoSMA-18-d6 was used for imaging the neuroinflammation at 24 h after reperfusion in tMCAO mice. The RNA expression levels of CB2R and other inflammatory markers were analyzed by quantitative real-time polymerase chain reaction using brain tissues from tMCAO (1 h occlusion) and sham-operated mice. [18F]fluorodeoxyglucose (FDG) was included for evaluation of the cerebral metabolic rate of glucose (CMRglc). In addition, diffusion-weighted imaging and T2-weighted imaging were performed for anatomical reference and delineating the lesion in tMCAO mice. ResultsmRNA expressions of inflammatory markers TNF-a, Iba1, MMP9 and GFAP, CNR2 were increased at 24 h after reperfusion in the ipsilateral compared to contralateral hemisphere of tMCAO mice, while mRNA expression of the neuronal marker MAP-2 was markedly reduced. Reduced [18F]FDG uptake was observed in the ischemic striatum of tMCAO mouse brain at 24 h after reperfusion. Although higher activity of [18F]RoSMA-18-d6 in ex-vivo biodistribution studies and higher standard uptake value ratio (SUVR) were detected in the ischemic ipsilateral compared to contralateral striatum in tMCAO mice, the in-vivo specificity of [18F]RoSMA-18-d6 was confirmed only in the CB2R-rich spleen. ConclusionsThis study revealed an increased [18F]RoSMA-18-d6 measure of CB2R and a reduced [18F]FDG measure of CMRglc in ischemic striatum of tMCAO mice at subacute stage. [18F]RoSMA-18-d6 might be a promising PET tracer for detecting CB2R alterations in animal models of neuroinflammation without neuronal loss.
Identification of Differentially Expressed Genes for Disc Degeneration Using Gene Expression Profiling and Bioinformatics Analysis
Authors: Fan Ning , Yuan Shuo , Hai Yong , Du Peng , Li Jian , Kong Xiaochuan , Zhu Wenyi , Liu Yuzeng , Zang Lei 
Published: May 2021

Abstract
BackgroundInflammatory processes exacerbated by IL-1β are believed to be key mediators of disc degeneration and low back pain. However, the underlying mechanism remains unclear. We performed a bioinformatics analysis to identify the key genes that were differentially expressed between degenerative intervertebral disc cells with and without exposure to interleukin (IL)-1β, and explore the related signaling pathways and interaction networks.MethodsThe microarray data were downloaded from the Gene Expression Omnibus (GSE 27494). Then, analyses of the gene ontology, signaling pathways, and interaction networks for the differentially expressed genes (DEGs) were conducted using tools including the Database for Annotation, Visualization, and Integrated Discovery (DAVID), Metascape, Gene Set Enrichment Analysis (GSEA), Search Tool for the Retrieval of Interacting Genes (STRING), Cytoscape, the Venn method, and packages of the R computing language.ResultsA total of 260 DEGs were identified, including 161 upregulated genes and 99 down-regulated genes. Gene Ontology (GO) annotation analysis showed that these DEGs were mainly associated with the extracellular region, chemotaxis, taxis, cytokine activity, and cytokine receptor binding. A Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analysis showed that these DEGs were mainly involved in the interactions of cytokine-cytokine receptor interaction, rheumatoid arthritis, tumor necrosis factor (TNF) signaling pathway, salmonella infection, and chemokine signaling pathway. The interaction network analysis indicated that 10 hub genes, including CXCL8, CXCL1, CCL20, CXCL2, CXCL5, CXCL3, CXCL6, C3, PF4, and GPER1 may play key roles in intervertebral disc degeneration.ConclusionsBioinformatic analysis showed that CXCL8 and other 9 key genes may play a role in the development of disc degeneration induced by inflammatory reactions, and can be used to identify the potential therapeutic target genes.