bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Absorption and Evolution Mechanisms of PM2.5Brown Carbon Revealed by Electrospray Ionization Fourier Transform–Ion Cyclotron Resonance Mass Spectrometry During a Severe Winter Pollution Episode in Xi'an, China
Authors: Zeng Yaling , Shen Zhenxing , Takahama Satoshi , Zhang Leiming , Zhang Tian , Lei Yali , Zhang Qian , Xu Hongmei , Ning Yanli , Huang Yu , Cao Junji , Rudolf Höhn 
Published: April 2020

AbstractKnowledge of the molecular‐level chemistry of brown carbon (BrC) is important in reducing the uncertainties in aerosol radiative forcing. Time‐resolved ambient PM2.5samples were collected during a severe pollution episode in January 2017 over Xi'an, China for a comprehensive nontarget and full scanning of BrC molecules and their absorption properties using electrospray ionization Fourier transform–ion cyclotron resonance mass spectrometry combined with partial least squares regression analysis, which apportioned the overall ultraviolet absorption to individual molecules. The estimated absorption of CHNO and CHNOS molecules exhibited nighttime prevalence, whereas CHOS, CHNS, CHN, CHO, CHS, and CH molecules presented a dynamic trend. Carbon conjugation was positively correlated with estimated absorption by CHO and CHNO molecules, while exhibiting a mixed relationship with CHNOS. Higher nitrogen content was associated with enhanced light‐absorption properties of BrC molecules, while higher oxygen and sulfur content appeared to be associated with photobleaching during secondary transformation.
Numerical Simulation of Ionospheric Depletions Resulting From Rocket Launches Using a General Circulation Model
Authors: Bowden George William , Lorrain Philippe , Brown Melrose 
Published: April 2020

AbstractRocket exhaust plumes have been observed to cause large‐scale depletions of ionospheric plasmas (“ionospheric holes”). In the F region, charge exchange reactions occur between O+ ions and exhaust species such as H2O, H2, and CO2 to form ions, which then undergo rapid dissociative recombination. The Global Ionosphere‐Thermosphere Model (GITM) was extended to include these chemical reactions and appropriate source terms to represent rocket exhaust plumes. The resulting model allowed for the detailed simulation of advection, diffusion, and chemical interactions of rocket exhaust gasses in the upper atmosphere. This model was applied to ionospheric depletions resulting from the launches of Jason‐3 and FORMOSAT‐5 on SpaceX Falcon 9 rockets from Vandenberg Air Force Base. Outputs from the model were compared with GNSS, ionosonde, and satellite Langmuir probe measurements. Simulation indicated that the FORMOSAT‐5 launch resulted in a far larger and longer‐lived ionospheric depletion than the Jason‐3 launch, consistent with observations. These differences resulted primarily from the deposition of exhaust gasses at higher altitudes in the former case, which resulted in longer residence times in the upper F region where ionospheric plasma was replenished more slowly. Simulation of the FORMOSAT‐5 launch reproduced the approximate size, shape, and motion of the observed ionospheric depletion, which reflected the advection and diffusion of the rocket exhaust gasses through the thermosphere.
Layering in Shales Controls Microfracturing at the Onset of Primary Migration in Source Rocks
Authors: Chauve Thomas , Scholtès Luc , Donzé Frédéric‐Victor , Haque Mondol Nazmul , Renard François 
Published: April 2020

AbstractThe process of primary migration, which controls the transfer of hydrocarbons from source to reservoir rocks, necessitates the existence of fluid pathways in low permeability sedimentary formations. Primary migration starts with the maturation of organic matter which produces fluids that increase the effective stress locally. The interactions between local fluid production, microfracturing, stress conditions, and transport remain difficult to apprehend in shale source rocks. Here, we analyze these interactions using a coupled hydro‐mechanical numerical model based on the discrete element method. The model is used to simulate the effects of fluid production emanating from kerogen patches contained within a shale rock alternating kerogen‐poor and kerogen‐rich layers. We identify two microfracturing mechanisms that control fluid migration: (i) propagation of hydraulically driven fractures induced by kerogen maturation in kerogen‐rich layers and (ii) compression‐induced fracturing in kerogen‐poor layers caused by fluid overpressurization of the surrounding kerogen‐rich layers. The relative importance of these two mechanisms is discussed considering different elastic properties contrasts between the shale layers, as well as various stress conditions encountered in sedimentary basins, from normal to reverse faulting regimes. The layering in shales causes local stress redistribution that controls the prevalence of each mechanism over the other and the onset of microfracturing during kerogen maturation. The approach is applied to the Draupne formation, a major source rock in the Norwegian continental shelf in the North Sea.
Apolipoprotein E4 and meningeal lymphatics in Alzheimer disease: a conceptual framework
Authors: Mentis Alexios-Fotios A. , Dardiotis Efthimios , Chrousos George P. 
Published: April 2020

AbstractThe potential existence and roles of the meningeal lymphatic system in normal and pathological brain function have been a long-standing enigma. Recent evidence suggests that meningeal lymphatic vessels are present in both the mouse and human brain; in mice, they seem to play a role in clearing toxic amyloid-beta peptides, which have been connected with Alzheimer disease (AD). Here, we review the evidence linking the meningeal lymphatic system with human AD. Novel findings suggest that the recently described meningeal lymphatic vessels could be linked to, and possibly drain, the efferent paravascular glial lymphatic (glymphatic) system carrying cerebrospinal fluid, after solute and immune cell exchange with brain interstitial fluid. In so doing, the glymphatic system could contribute to the export of toxic solutes and immune cells from the brain (an exported fluid we wish to describe as glymph, similarly to lymph) to the meningeal lymphatic system; the latter, by being connected with downstream anatomic regions, carries the glymph to the conventional cervical lymphatic vessels and nodes. Thus, abnormal function in the meningeal lymphatic system could, in theory, lead to the accumulation, in the brain, of amyloid-beta, cellular debris, and inflammatory mediators, as well as immune cells, resulting in damage of the brain parenchyma and, in turn, cognitive and other neurologic dysfunctions. In addition, we provide novel insights into APOE4—the leading genetic risk factor for AD—and its relation to the meningeal lymphatic system. In this regard, we have reanalyzed previously published RNA-Seq data to show that induced pluripotent stem cells (iPSCs) carrying theAPOE4allele (either asAPOE4knock-in or stemming fromAPOE4patients) express lower levels of (a) genes associated with lymphatic markers, and (b) genes for which well-characterized missense mutations have been linked to peripheral lymphedema. Taking into account this evidence, we propose a new conceptual framework, according to which APOE4 could play a novel role in the premature shrinkage of meningeal lymphatic vessels (meningeal lymphosclerosis), leading to abnormal meningeal lymphatic functions (meningeal lymphedema), and, in turn, reduction in the clearance of amyloid-beta and other macromolecules and inflammatory mediators, as well as immune cells, from the brain, exacerbation of AD manifestations, and progression of the disease. Altogether, these findings and their potential interpretations may herald novel diagnostic tools and therapeutic approaches in patients with AD.
Genetic diversity, population structure, and relationships of apricot (Prunus) based on restriction site-associated DNA sequencing
Authors: Li Wenwen , Liu Liqiang , Wang Yanan , Zhang Qiuping , Fan Guoquan , Zhang Shikui , Wang Yatong , Liao Kang 
Published: April 2020

AbstractSingle-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. Here, high-throughput sequencing was used to examine the genome-level diversity, population structure, and relationships of apricot, which are important for germplasm conservation and molecular breeding. Restriction site-associated DNA sequencing (RAD-seq) was adopted to sequence 168Prunusspp. accessions distributed in five ecological groups, including 74 accessions of cultivatedPrunus armeniacaL. and 94 accessions of wild apricots (P. armeniacaL. andPrunus sibiricaL.), which generated 417,961 high-quality SNPs. We used cluster, genetic structure, and principal component analyses to examine the genetic diversities and genetic relationships of the 168 accessions. The Dzhungar-Ili ecological group accessions showed the highest genetic diversity in terms of private allele number, observed heterozygosity, and nucleotide diversity. We speculate that the Central Asian ecological group accessions were domesticated from the Dzhungar-Ili ecological group accessions. The population structure and gene flow of the North China and European ecological group accessions suggested a genetic background ofP. sibirica. We argue that the two groups should be considered hybrid swarms connected toP. sibiricaby continuous and extensive gene flow.P. armeniacaoriginated in Northwest China (Ili Valley), subsequently spread throughout Central Asia, and eventually spread to Europe. In addition, selective sweep signatures inP. armeniacaduring domestication from wild to cultivated apricots, combined with differentially expressed genes, underlie distinct fruit traits, including sugars, aromas, organic acids, and carotenoids. This study provides substantive and valuable genomic resources that will significantly advance apricot improvement and effective utilization.
Downstream changes in river avulsion style are related to channel morphology
Authors: Valenza J. M. , Edmonds D. A. , Hwang T. , Roy S. 
Published: April 2020

AbstractOne of the most dramatic events in river environments is the natural diversion, or avulsion, of a channel across its floodplain. Though rarely witnessed, avulsions can cause massive floods, and over geologic time they create most of the fluvial stratigraphic record. Avulsions exhibit behavior ranging from reoccupying abandoned channels to constructing new channels and splay complexes. To quantify avulsion behavior, or style, we measure avulsion-related floodplain disturbance in modern environments. We show that for 63 avulsions from Andean, Himalayan, and New Guinean basins, avulsion style correlates with channel morphology and changes systematically downstream. Avulsions in braided rivers reoccupy abandoned channels, whereas avulsions in meandering rivers often produce flooding and sediment deposition during channel construction. These downstream changes in avulsion style can explain the abrupt transition from channel-dominated to floodplain-dominated facies commonly observed in foreland basin stratigraphy. These dynamics also explain why some avulsions are more hazardous than others.
Selection and Validation of Reference Genes for Normalisation of Gene Expression in Glehnia littoralis
Authors: Li Li , Li Naiwei , Fang Hailing , Qi Xiwu , Zhou Yifeng 
Published: April 2020

AbstractGlehnia littoralisis an important medicinal halophyte—the dried root of which is used as Chinese herbal medicine. However, the use, selection and stability of reference genes are rarely verified in studies ofG. littoralis, which hampers investigation of its salt tolerance and metabolism. In this study, we selected 13 candidate reference genes from the transcriptome data ofG. littoralis—serine/threonine-protein phosphatase PP2A (PP2A), polyubiquitin 10 (UBQ10), actin (ACT), elongation factor 1-α (EF1-α), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), α-tubulin (α-TUB), β-tubulin (β-TUB), polypyrimidine tract-binding protein 1 (PTBP1), expressed protein 1 (EXP1), expressed protein 2 (EXP2), TIP41-like (TIP41), SAND family (SAND), and cyclophilin 2 (CYP2), and used qRT-PCR to analyse their expression levels in roots ofG. littoralistreated with NaCl, polyethylene glycol (PEG), abscisic acid (ABA), and methyl jasmonate (MeJA), as well as in various organs ofG. littoralis. The ΔCt, geNorm, NormFinder, and BestKeeper algorithms were used to assess the expression stability of the candidate reference genes and the results were then used to generate a comprehensive rank list with the RankAggreg R package. The most stable reference genes for normalisation wereEXP1andPP2Ain response to NaCl,EXP2andPP2Ain response to ABA,CYP2andα-TUBin response to MeJA, andACTandEXP1in the PEG and the organ subsets.GAPDH,β-TUB, andUBQ10exhibited low stability and so were unsuitable for normalisation. This study is the first systematic analysis of candidate reference genes inG. littoralisand will facilitate further investigation of normalisation of gene expression inG. littoralis.
Intranasal immunization with outer membrane vesicle pertussis vaccine confers broad protection through mucosal IgA and Th17 responses
Authors: Raeven René H. M. , Rockx-Brouwer Dedeke , Kanojia Gaurav , van der Maas Larissa , Bindels Tim H. E. , ten Have Rimko , van Riet Elly , Metz Bernard , Kersten Gideon F. A. 
Published: April 2020

AbstractA vaccine based on outer membrane vesicles of pertussis (omvPV) is protective in a mouse-challenge model and induces a broad antibody and mixed Th1/Th2/Th17 response against multiple antigens following subcutaneous immunization. However, this route did not result in mucosal immunity and did not prevent nasopharyngeal colonization. In this study, we explored the potential of intranasal immunization with omvPV. Only intranasal immunization induced strong mucosal immune responses that encompasses enhanced pulmonary and nasal IgA antibody levels, mainly directed against Vag8 and LPS. Furthermore, high numbers of IgA- and IgG-producing plasma cells were detected as well as lung-resident IgA memory B-cells. Finally, only intranasal immunization induced pulmonary Th1/Th17-related cytokine responses. The magnitude and type of systemic immunity was comparable between both routes and included high systemic IgG antibody levels, strong IgG-producing plasma cell responses, memory B-cells residing in the spleen and systemic Th1/Th2/Th17-related cytokine responses. Importantly, only intranasal immunization prevented colonization in both the lungs and the nasal cavity. In conclusion, intranasal omvPV immunization induces mucosal IgA and Th17-mediated responses without influencing the systemic immunity profile. These responses resulted in prevention of Bordetella pertussis colonization in the respiratory tract, including the nasal cavity, thereby potentially preventing transmission.
Volcanic related methylmercury poisoning as the possible driver of the end-Devonian Mass Extinction
Authors: Rakociński Michał , Marynowski Leszek , Pisarzowska Agnieszka , Bełdowski Jacek , Siedlewicz Grzegorz , Zatoń Michał , Perri Maria Cristina , Spalletta Claudia , Schönlaub Hans Peter 
Published: April 2020

AbstractThe end-Devonian global Hangenberg event (359 Ma) is among the most devastating mass extinction events in Earth’s history, albeit not one of the “Big Five”. This extinction is linked to worldwide anoxia caused by global climatic changes. These changes could have been driven by astronomical forcing and volcanic cataclysm, but ultimate causes of the extinction still remain unclear. Here we report anomalously high mercury (Hg) concentration in marine deposits encompassing the Hangenberg event from Italy and Austria (Carnic Alps). The Hangenberg event recorded in the sections investigated can be here interpreted as caused by extensive volcanic activity of large igneous provinces (LIPs), arc volcanism and/or hydrothermal activity. Our results (very large Hg anomalies) imply volcanism as a most possible cause of the Hangenberg event, similar to other first order mass extinctions during the Phanerozoic. For the first time we show that apart from anoxia, proximate kill mechanism of aquatic life during the event could have been methylmercury formed by biomethylation of a volcanically derived, huge concentration of inorganic Hg supplied to the ocean. Methylmercury as a much more toxic Hg form, potentially could have had a devastating impact on end-Devonian biodiversity, causing the extinction of many pelagic species.
The spatial non-stationary effect of urban landscape pattern on urban waterlogging: a case study of Shenzhen City
Authors: Wu Jiansheng , Sha Wei , Zhang Puhua , Wang Zhenyu 
Published: April 2020

AbstractThe problem of urban waterlogging has consistently affected areas of southern China, and has generated widespread concerns among the public and professionals. The geographically weighted regression model (GWR) is widely used to reflect the spatial non-stationarity of parameters in different locations, with the relationship between variables able to change with spatial position. In this research, Shenzhen City, which has a serious waterlogging problem, was used as a case study. Several key results were obtained. (1) The spatial autocorrelation of flood spot density in Shenzhen was significant at the 5% level, but because the Z value was not large it was not very obvious. (2) The degree of impact on flood disasters from large to small was: Built up_ DIVISION > SHDI > Built up_ COHESION > CONTAG > Built up_ LPI. (3) The degree of waterlogging disasters in higher altitude regions was less affected by the landscape pattern. The results of this study highlight the important role of the landscape pattern on waterlogging disasters and also indicate the different impacts of different regional landscape patterns on waterlogging disasters, which provides useful information for planning the landscape pattern and controlling waterlogging.
Crystal structure of Type IX secretion system PorE C-terminal domain from Porphyromonas gingivalis in complex with a peptidoglycan fragment
Authors: Trinh Nhung Thi Trang , Tran Hieu Quang , Van Dong Quyen , Cambillau Christian , Roussel Alain , Leone Philippe 
Published: April 2020

AbstractPorphyromonas gingivalis, the major human pathogen associated to periodontal diseases, utilizes the Bacteroidetes-specific type IX secretion system (T9SS) to export virulence factors. PorE is a periplasmic multi-domain lipoprotein associated to the outer membrane that was recently identified as essential for T9SS function. Little is known on T9SS at the structural level, and in particular its interaction with peptidoglycan. This prompted us to carry out structural studies on PorE full length as well as on its four isolated domains. Here we report the crystal structure of the C-terminal OmpA_C-like putative peptidoglycan-binding domain at 1.55 Å resolution. An electron density volume was identified in the protein cleft, making it possible to build a naturally-occurring peptidoglycan fragment. This result suggests that PorE interacts with peptidoglycan and that PorE could anchor T9SS to the cell wall.
J-CKD-DB: a nationwide multicentre electronic health record-based chronic kidney disease database in Japan
Authors: Nakagawa Naoki , Sofue Tadashi , Kanda Eiichiro , Nagasu Hajime , Matsushita Kunihiro , Nangaku Masaomi , Maruyama Shoichi , Wada Takashi , Terada Yoshio , Yamagata Kunihiro , Narita Ichiei , Yanagita Motoko , Sugiyama Hitoshi , Shigematsu Takashi , Ito Takafumi , Tamura Kouichi , Isaka Yoshitaka , Okada Hirokazu , Tsuruya Kazuhiko , Yokoyama Hitoshi , Nakashima Naoki , Kataoka Hiromi , Ohe Kazuhiko , Okada Mihoko , Kashihara Naoki 
Published: April 2020

AbstractThe Japan Chronic Kidney Disease (CKD) Database (J-CKD-DB) is a large-scale, nation-wide registry based on electronic health record (EHR) data from participating university hospitals. Using a standardized exchangeable information storage, the J-CKD-DB succeeded to efficiently collect clinical data of CKD patients across hospitals despite their different EHR systems. CKD was defined as dipstick proteinuria ≥1+ and/or estimated glomerular filtration rate <60 mL/min/1.73 m2 base on both out- and inpatient laboratory data. As an initial analysis, we analyzed 39,121 CKD outpatients (median age was 71 years, 54.7% were men, median eGFR was 51.3 mL/min/1.73 m2) and observed that the number of patients with a CKD stage G1, G2, G3a, G3b, G4 and G5 were 1,001 (2.6%), 2,612 (6.7%), 23,333 (59.6%), 8,357 (21.4%), 2,710 (6.9%) and 1,108 (2.8%), respectively. According to the KDIGO risk classification, there were 30.1% and 25.5% of male and female patients with CKD at very high-risk, respectively. As the information from every clinical encounter from those participating hospitals will be continuously updated with an anonymized patient ID, the J-CKD-DB will be a dynamic registry of Japanese CKD patients by expanding and linking with other existing databases and a platform for a number of cross-sectional and prospective analyses to answer important clinical questions in CKD care.
Reconfiguration of magnetic domain structures of ErFeO3 by intense terahertz free electron laser pulses
Authors: Kurihara Takayuki , Hirota Kazumasa , Qiu Hongsong , Phan Khoa Thanh Nhat , Kato Kosaku , Isoyama Goro , Nakajima Makoto 
Published: April 2020

AbstractUnderstanding the interaction between intense terahertz (THz) electromagnetic fields and spin systems has been gaining importance in modern spintronics research as a unique pathway to realize ultrafast macroscopic magnetization control. In this work, we used intense THz pulses with pulse energies in the order of 10 mJ/pulse generated from the terahertz free electron laser (THz-FEL) to irradiate the ferromagnetic domains of ErFeO3 single crystal. It was found that the domain shape can be locally reconfigured by irradiating the THz − FEL pulses near the domain boundary. Observed domain reconfiguration mechanism can be phenomenologically understood by the combination of depinning effect and the entropic force due to local thermal gradient exerted by terahertz irradiation. Our finding opens up a new possibility of realizing thermal-spin effects at THz frequency ranges by using THz-FEL pulses.
Using an unbiased symbolic movement representation to characterize Parkinson’s disease states
Authors: Abrami Avner , Heisig Stephen , Ramos Vesper , Thomas Kevin C. , Ho Bryan K. , Caggiano Vittorio 
Published: April 2020

AbstractUnconstrained human movement can be broken down into a series of stereotyped motifs or ‘syllables’ in an unsupervised fashion. Sequences of these syllables can be represented by symbols and characterized by a statistical grammar which varies with external situational context and internal neurological state. By first constructing a Markov chain from the transitions between these syllables then calculating the stationary distribution of this chain, we estimate the overall severity of Parkinson’s symptoms by capturing the increasingly disorganized transitions between syllables as motor impairment increases. Comparing stationary distributions of movement syllables has several advantages over traditional neurologist administered in-clinic assessments. This technique can be used on unconstrained at-home behavior as well as scripted in-clinic exercises, it avoids differences across human evaluators, and can be used continuously without requiring scripted tasks be performed. We demonstrate the effectiveness of this technique using movement data captured with commercially available wrist worn sensors in 35 participants with Parkinson’s disease in-clinic and 25 participants monitored at home.