bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wave Attenuation Through an Arctic Marginal Ice Zone on 12 October 2015: 1. Measurement of Wave Spectra and Ice Features From Sentinel 1A
Authors: Stopa J. E. , Ardhuin F. , Thomson Jim , Smith Madison M. , Kohout Alison , Doble Martin , Wadhams Peter 
Published: April 2018

AbstractA storm with significant wave heights exceeding 4 m occurred in the Beaufort Sea on 11–13 October 2015. The waves and ice were captured on 12 October by the Synthetic Aperture Radar (SAR) on board Sentinel‐1A, with Interferometric Wide swath images covering 400 × 1,100 km at 10 m resolution. This data set allows the estimation of wave spectra across the marginal ice zone (MIZ) every 5 km, over 400 km of sea ice. Since ice attenuates waves with wavelengths shorter than 50 m in a few kilometers, the longer waves are clearly imaged by SAR in sea ice. Obtaining wave spectra from the image requires a careful estimation of the blurring effect produced by unresolved wavelengths in the azimuthal direction. Using in situ wave buoy measurements as reference, we establish that this azimuth cutoff can be estimated in mixed ocean‐ice conditions. Wave spectra could not be estimated where ice features such as leads contribute to a large fraction of the radar backscatter variance. The resulting wave height map exhibits a steep decay in the first 100 km of ice, with a transition into a weaker decay further away. This unique wave decay pattern transitions where large‐scale ice features such as leads become visible. As in situ ice information is limited, it is not known whether the decay is caused by a difference in ice properties or a wave dissipation mechanism. The implications of the observed wave patterns are discussed in the context of other observations.
Water Mass Analysis of the East China Sea and Interannual Variation of Kuroshio Subsurface Water Intrusion Through an Optimum Multiparameter Method
Authors: Zhou Peng , Song Xiuxian , Yuan Yongquan , Cao Xihua , Wang Wentao , Chi Lianbao , Yu Zhiming 
Published: April 2018

AbstractThe Optimum Multiparameter (OMP) method was used to determine the relative contribution of water masses in the East China Sea (ECS) based on their measured temperature, salinity, and dissolved inorganic iodine species (DIIS, iodate and iodide) from recent oceanographic cruises in June 2014, 2015, and 2016. DIIS (as quasi‐conservative parameters) were added first into the OMP analysis, which enabled us to quantitatively estimate the water composition in the extremely dynamic and productive ECS. The OMP results indicate that seawater in the ECS mainly consisted of Changjiang Diluted Water (CDW), Taiwan Strait Warm Water (TSWW), Kuroshio Surface Water (KSW), and Kuroshio Subsurface Water (KSSW). In June 2014, 2015, and 2016, the KSSW dominated in the deep water, intruded into the ECS shelf from the northeast of Taiwan and bifurcated into a nearshore branch and offshore branch. The nearshore branch could reach north of 29°N off the Zhejiang coast. When comparing the KSSW intrusion in June 2014, 2015, and 2016, the average KSSW contribution of the bottom KSSW area in June 2016 (78.9%) was greater than in the previous 2 years (67.9% and 64.5%). In the northern transects (north of 28°N), the KSSW intrusion in June 2016 also contained the greatest average KSSW contribution and the maximum coverage area. Thus, the KSSW intrusion was strongest in June 2016 and may be comparable in June 2014 and 2015. This interannual variability of the KSSW intrusion is likely related to the El Niño‐Southern Oscillation (ENSO) rather than the Pacific Decadal Oscillation (PDO).
Climate-driven shifts in sediment chemistry enhance methane production in northern lakes
Authors: Emilson E. J. S. , Carson M. A. , Yakimovich K. M. , Osterholz H. , Dittmar T. , Gunn J. M. , Mykytczuk N. C. S. , Basiliko N. , Tanentzap A. J. 
Published: April 2018

AbstractFreshwater ecosystems are a major source of methane (CH4), contributing 0.65 Pg (in CO2 equivalents) yr−1 towards global carbon emissions and offsetting ~25% of the terrestrial carbon sink. Most freshwater CH4 emissions come from littoral sediments, where large quantities of plant material are decomposed. Climate change is predicted to shift plant community composition, and thus change the quality of inputs into detrital food webs, with the potential to affect CH4 production. Here we find that variation in phenol availability from decomposing organic matter underlies large differences in CH4 production in lake sediments. Production is at least 400-times higher from sediments composed of macrophyte litter compared to terrestrial sources because of inhibition of methanogenesis by phenol leachates. Our results now suggest that earth system models and carbon budgets should consider the effects of plant communities on sediment chemistry and ultimately CH4 emissions at a global scale.
Bayesian model selection for complex dynamic systems
Authors: Mark Christoph , Metzner Claus , Lautscham Lena , Strissel Pamela L. , Strick Reiner , Fabry Ben 
Published: April 2018

AbstractTime series generated by complex systems like financial markets and the earth’s atmosphere often represent superstatistical random walks: on short time scales, the data follow a simple low-level model, but the model parameters are not constant and can fluctuate on longer time scales according to a high-level model. While the low-level model is often dictated by the type of the data, the high-level model, which describes how the parameters change, is unknown in most cases. Here we present a computationally efficient method to infer the time course of the parameter variations from time-series with short-range correlations. Importantly, this method evaluates the model evidence to objectively select between competing high-level models. We apply this method to detect anomalous price movements in financial markets, characterize cancer cell invasiveness, identify historical policies relevant for working safety in coal mines, and compare different climate change scenarios to forecast global warming.
Retinal microcirculation and leukocyte telomere length in the general population
Authors: Martens Dries S. , Wei Fang-Fei , Cox Bianca , Plusquin Michelle , Thijs Lutgarde , Winckelmans Ellen , Zhang Zhen-Yu , Nawrot Tim S. , Staessen Jan A. 
Published: April 2018

AbstractRetinal arteriolar narrowing increases with age and predict adverse cardiovascular outcomes. Telomere length keeps track of the division of somatic cells and is a biomarker of biological age. We investigated to what extent retinal arteriolar diameters are associated with biological age, as captured by leukocyte telomere length (LTL). In 168 randomly selected Flemish participants from the family-based population study FLEMENGHO (mean age, 46.2 years) at baseline, of whom 85 underwent a follow-up examination (median, 4.1 years), we post-processed nonmydriatic retinal photographs and measured LTL. In men only, central retinal arteriolar equivalents (CRAE) and arteriole-to-venule ratio (AVR) were associated with LTL with stronger associations at higher age and body mass index. In men aged 57.6 years (75th percentile) a 20% shorter LTL was associated with a decrease in CRAE of 4.57 µm. A 20% shorter LTL was associated with a decrease of 5.88 µm in CRAE at a BMI of 29.9 kg/m2 (75th percentile). Similar associations were observed between AVR and LTL. In women, no retinal microvascular traits were associated with LTL. Retinal arteriolar narrowing in men but not in women is associated with biological age. Our findings support the idea that avoiding overweight contributes to maintaining a healthier microcirculation.
Identification of the effector domain of biglycan that facilitates BMP-2 osteogenic function
Authors: Jongwattanapisan Prapaporn , Terajima Masahiko , Miguez Patricia A. , Querido William , Nagaoka Hideaki , Sumida Noriko , Gurysh Elizabeth Grace , Ainslie Kristy M. , Pleshko Nancy , Perera Lalith , Yamauchi Mitsuo 
Published: April 2018

AbstractWe have reported that recombinant biglycan (BGN) core protein accelerates bone formation in vivo by enhancing bone morphogenetic protein (BMP)-2 function. The purpose of the present study was to identify the specific domain (“effector”) within the BGN core protein that facilitates BMP-2 osteogenic function. Thus, we generated various recombinant and synthetic peptides corresponding to several domains of BGN, and tested their effects on BMP-2 functions in vitro. The results demonstrated that the leucine-rich repeats 2–3 domain (LRR2-3) of BGN significantly enhanced the BMP-2 induced Smad1/5/9 phosphorylation, osteogenic gene expression, and alkaline phosphatase activity in myogenic C2C12 cells. Furthermore, addition of LRR2-3 to osteoblastic MC3T3-E1 cells accelerated in vitro mineralization without compromising the quality of the mineral and matrix. These data indicate that LRR2-3 is, at least in part, responsible for BGN’s ability to enhance BMP-2 osteogenic function, and it could be useful for bone tissue regeneration.
Migratory Whooper Swans Cygnus cygnus Transmit H5N1 Virus between China and Mongolia: Combination Evidence from Satellite Tracking and Phylogenetics Analysis
Authors: Li Shuhong , Meng Weiyue , Liu Dongping , Yang Qiqi , Chen Lixia , Dai Qiang , Ma Tian , Gao Ruyi , Ru Wendong , Li Yunfeng , Yu Pengbo , Lu Jun , Zhang Guogang , Tian Huaiyu , Chai Hongliang , Li Yanbing 
Published: April 2018

AbstractIn late 2014, a highly pathogenic avian influenza (hereafter HPAI) H5N1 outbreak infected whooper swans Cygnus cygnus wintering at the Sanmenxia Reservoir area, China, and raised concerns about migratory linkages between wintering and breeding grounds of whooper swans. In this study, 61 swans were satellite tracked from 2013 to 2016 to determine the spatial association of their migration routes and H5N1 outbreaks, and 3596 fecal samples were collected along the migration routes for virology testing. Swans departed the wintering grounds and migrated along the Yellow River, and flew over the Yin Mountains in China. The Brownian bridge movement model showed there was a high degree of spatiotemporal overlap between the core use area along the spring migration pathway and historical H5N1 events in China and Mongolia from 2005 to 2015. The H5N1 strain was isolated and phylogenetic analyses confirmed that the HA gene sequence generated is genetically similar to that of the epidemic strain at a previous wintering site (the Sanmenxia Reservoir area) along its flyway. Our results identified a previously unknown migratory link of whooper swans in central China with Mongolia and confirmed that the swans could carry the HPAI H5N1 virus during migration, resulting in long-distance transmission.
Egr2-independent, Klf1-mediated induction of PD-L1 in CD4+ T cells
Authors: Teruya Shuzo , Okamura Tomohisa , Komai Toshihiko , Inoue Mariko , Iwasaki Yukiko , Sumitomo Shuji , Shoda Hirofumi , Yamamoto Kazuhiko , Fujio Keishi 
Published: April 2018

AbstractProgrammed death ligand 1 (PD-L1)-mediated induction of immune tolerance has been vigorously investigated in autoimmunity and anti-tumor immunity. However, details of the mechanism by which PD-L1 is induced in CD4+ T cells are unknown. Here, we revealed the potential function of Klf1 and Egr2-mediated induction of PD-L1 in CD4+ T cells. We focused on the molecules specifically expressed in CD4+CD25−LAG3+ regulatory T cells (LAG3+ Tregs) highly express of PD-L1 and transcription factor Egr2. Although ectopic expression of Egr2 induced PD-L1, a deficiency of Egr2 did not affect its expression, indicating the involvement of another PD-L1 induction mechanism. Comprehensive gene expression analysis of LAG3+ Tregs and in silico binding predictions revealed that Krüppel-like factor 1 (Klf1) is a candidate inducer of the PD-L1 gene (Cd274). Klf1 is a transcription factor that promotes β-globin synthesis in erythroid progenitors, and its role in immunological homeostasis is unknown. Ectopic expression of Klf1 induced PD-L1 in CD4+ T cells through activation of the PI3K-mTOR signaling pathway, independent of STATs signaling and Egr2 expression. Our findings indicate that Klf1 and Egr2 are modulators of PD-L1-mediated immune suppression in CD4+ T cells and might provide new insights into therapeutic targets for autoimmune diseases and malignancies.
Photoluminescent Cationic Carbon Dots as efficient Non-Viral Delivery of Plasmid SOX9 and Chondrogenesis of Fibroblasts
Authors: Cao Xia , Wang Jianping , Deng Wenwen , Chen Jingjing , Wang Yan , Zhou Jie , Du Pan , Xu Wenqian , Wang Qiang , Wang Qilong , Yu Qingtong , Spector Myron , Yu Jiangnan , Xu Ximing 
Published: April 2018

AbstractWith the increasing demand for higher gene carrier performance, a multifunctional vector could immensely simplify gene delivery for disease treatment; nevertheless, the current non- viral vectors lack self-tracking ability. Here, a type of novel, dual-functional cationic carbon dots (CDs), produced through one-step, microwave-assisted pyrolysis of arginine and glucose, have been utilized as both a self-imaging agent and a non-viral gene vector for chondrogenesis from fibroblasts. The cationic CDs could condense the model gene plasmid SOX9 (pSOX9) to form ultra-small (10–30 nm) nanoparticles which possessed several favorable properties, including high solubility, tunable fluorescence, high yield, low cytotoxicity and outstanding biocompatibility. The MTT assay indicated that CDs/pSOX9 nanoparticles had little cytotoxicity against mouse embryonic fibroblasts (MEFs) compared to Lipofectamine2000 and PEI (25 kDa). Importantly, the CDs/pSOX9 nanoparticles with tunable fluorescence not only enabled the intracellular tracking of the nanoparticles, but also could successfully deliver the pSOX9 into MEFs with significantly high efficiency. Furthermore, the CDs/pSOX9 nanoparticles-mediated transfection of MEFs showed obvious chondrogenic differentiation. Altogether, these findings demonstrated that the CDs prepared in this study could serve as a paradigmatic example of the dual-functional reagent for both self-imaging and effective non-viral gene delivery.
Dual extraction of mRNA and lipids from a single biological sample
Authors: Podechard Normand , Ducheix Simon , Polizzi Arnaud , Lasserre Frédéric , Montagner Alexandra , Legagneux Vincent , Fouché Edwin , Saez Fabrice , Lobaccaro Jean-Marc , Lakhal Laila , Ellero-Simatos Sandrine , Martin Pascal. G. , Loiseau Nicolas , Bertrand-Michel Justine , Guillou Hervé 
Published: April 2018

AbstractThe extraction of RNA and lipids from a large number of biological samples is time-consuming and costly with steps required for both transcriptomic and lipidomic approaches. Most protocols rely on independent extraction of nucleic acids and lipids from a single sample, thereby increasing the need for biological material and inducing variability in data analysis. We investigated whether it is possible to use a standard RNA extraction procedure to analyze not only RNA levels, but also lipids in a single liver sample. We show that the organic phase obtained when using standard reagents for RNA extraction can be used to analyze lipids, including neutral lipids and fatty acids, by gas chromatography. We applied this technique to an analysis of lipids and the associated gene expression pattern in mice with hepatic steatosis induced by pharmacological activation of nuclear receptor LXR.
Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae)
Authors: Chen Long , Chen Peng-Yan , Xue Xiao-Feng , Hua Hai-Qing , Li Yuan-Xi , Zhang Fan , Wei Shu-Jun 
Published: April 2018

AbstractAnimal mitochondrial genomes usually exhibit conserved gene arrangement across major lineages, while those in the Hymenoptera are known to possess frequent rearrangements, as are those of several other orders of insects. Here, we sequenced two complete mitochondrial genomes of Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). In total, 37 mitochondrial genes were identified in both species. The same gene arrangement pattern was found in the two species, with extensive gene rearrangement compared with the ancestral insect mitochondrial genome. Most tRNA genes and all protein-coding genes were encoded on the minority strand. In total, 15 tRNA genes and seven protein-coding genes were rearranged. The rearrangements of cox1 and nad2 as well as most tRNA genes were novel. Phylogenetic analysis based on nucleotide sequences of protein-coding genes and on gene arrangement patterns produced identical topologies that support the relationship of (Agaonidae + Pteromalidae) + Trichogrammatidae in Chalcidoidea. CREx analysis revealed eight rearrangement operations occurred from presumed ancestral gene order of Chalcidoidea to form the derived gene order of Trichogramma. Our study shows that gene rearrangement information in Chalcidoidea can potentially contribute to the phylogeny of Chalcidoidea when more mitochondrial genome sequences are available.
Climate deteriorations and Neanderthal demise in interior Iberia
Authors: Wolf D. , Kolb T. , Alcaraz-Castaño M. , Heinrich S. , Baumgart P. , Calvo R. , Sánchez J. , Ryborz K. , Schäfer I. , Bliedtner M. , Zech R. , Zöller L. , Faust D. 
Published: April 2018

AbstractTime and circumstances for the disappearance of Neanderthals and its relationship with the advent of Modern Humans are not yet sufficiently resolved, especially in case of the Iberian Peninsula. Reconstructing palaeoenvironmental conditions during the last glacial period is crucial to clarifying whether climate deteriorations or competition and contacts with Modern Humans played the pivotal role in driving Neanderthals to extinction. A high-resolution loess record from the Upper Tagus Basin in central Spain demonstrates that the Neanderthal abandonment of inner Iberian territories 42 kyr ago coincided with the evolvement of hostile environmental conditions, while archaeological evidence testifies that this desertion took place regardless of modern humans’ activities. According to stratigraphic findings and stable isotope analyses, this period corresponded to the driest environmental conditions of the last glacial apart from an even drier period linked to Heinrich Stadial 3. Our results show that during Marine Isotope Stages (MIS) 4 and 2 climate deteriorations in interior Iberia temporally coincided with northern hemisphere cold periods (Heinrich stadials). Solely during the middle MIS 3, in a period surrounding 42 kyr ago, this relation seems not straightforward, which may demonstrate the complexity of terrestrial climate conditions during glacial periods.
Abundance of impacted forest patches less than 5 km2 is a key driver of the incidence of malaria in Amazonian Brazil
Authors: Chaves Leonardo Suveges Moreira , Conn Jan E. , López Rossana Verónica Mendoza , Sallum Maria Anice Mureb 
Published: April 2018

AbstractThe precise role that deforestation for agricultural settlements and commercial forest products plays in promoting or inhibiting malaria incidence in Amazonian Brazil is controversial. Using publically available databases, we analyzed temporal malaria incidence (2009–2015) in municipalities of nine Amazonian states in relation to ecologically defined variables: (i) deforestation (rate of forest clearing over time); (ii) degraded forest (degree of human disturbance and openness of forest canopy for logging) and (iii) impacted forest (sum of deforested and degraded forest patches). We found that areas affected by one kilometer square of deforestation produced 27 new malaria cases (r² = 0.78; F1,10 = 35.81; P < 0.001). Unexpectedly, we found both a highly significant positive correlation between number of impacted forest patches less than 5 km2 and malaria cases, and that these patch sizes accounted for greater than ~95% of all patches in the study area. There was a significantly negative correlation between extraction forestry economic indices and malaria cases. Our results emphasize not only that deforestation promotes malaria incidence, but also that it directly or indirectly results in a low Human Development Index, and favors environmental conditions that promote malaria vector proliferation.
Genome-wide analysis of the SPL/miR156 module and its interaction with the AP2/miR172 unit in barley
Authors: Tripathi Rajiv K. , Bregitzer Phil , Singh Jaswinder 
Published: April 2018

AbstractThe SQUAMOSA-promoter binding like (SPL) gene family encodes transcription factors that have been shown in many species to influence plant growth and development, but information about these genes in barley (Hordeum vulgare L.) is limited. This study identified 17 barley SPL genes, within eight distinct groups, that are orthologs of SPL genes described in Arabidopsis, wheat, and rice. Sixteen barley SPLs undergo alternative splicing. Seven SPLs contain a putative miR156 target site and the transcript levels of the miR156-targeted HvSPLs (HvSPL3, 13 and 23) were lower in vegetative than in reproductive phase but this was true also for some SPL genes such as HvSPL6 that were not regulated by miR156. Because SPL gene products regulate miR172, which is also involved in floral development, the expression of miR172 was studied. An antagonistic expression pattern of miR156 and miR172b during the vegetative and the reproductive phases signifies their apparent function in barley growth phase transition. Characterization of a barley mir172 mutant having an abnormal, indeterminate spikelet phenotype suggests the possible feedback role of AP2/miR172 module on HvSPL genes. This is the first comprehensive analysis of the miR156/SPL/miR172 axis in barley that provides a basis to elucidate their roles in various biological processes.
Molecular characterization of mesenchymal stem cells in human osteoarthritis cartilage reveals contribution to the OA phenotype
Authors: Jayasuriya Chathuraka T. , Hu Nan , Li Jing , Lemme Nicholas , Terek Richard , Ehrlich Michael G. , Chen Qian 
Published: April 2018

AbstractAdult human articular cartilage harbors a population of CD166+ mesenchymal stem cell-like progenitors that become more numerous during osteoarthritis (OA). While their role is not well understood, here we report that they are indeed part of cellular clusters formed in OA cartilage, which is a pathological hallmark of this disease. We hypothesize that these cells, termed OA mesenchymal stem cells (OA-MSCs), contribute to OA pathogenesis. To test this hypothesis, we generated and characterized multiple clonally derived stable/immortalized human OA-MSC cell lines, which exhibited the following properties. Firstly, two mesenchymal stem cell populations exist in human OA cartilage. While both populations are multi-potent, one preferentially undergoes chondrogenesis while the other exhibits higher osteogenesis potential. Secondly, both OA-MSCs exhibit significantly higher expression of hypertrophic OA cartilage markers COL10A1 and RUNX2, compared to OA chondrocytes. Induction of chondrogenesis in OA-MSCs further stimulated COL10A1 expression and MMP-13 release, suggesting that they contribute to OA phenotypes. Finally, knocking down RUNX2 is insufficient to inhibit COL10A1 in OA-MSCs and also requires simultaneous knockdown of NOTCH1 thereby suggesting altered gene regulation in OA stem cells in comparison to chondrocytes. Overall, our findings suggest that OA-MSCs may drive pathogenesis of cartilage degeneration and should therefore be a novel cell target for OA therapy.