bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐Resolution Mg/Ca Measurements of Foraminifer Shells Using Femtosecond LA‐ICP‐MS for Paleoclimate Proxy Development
Authors: Jochum K. P. , Jentzen A. , Schiebel R. , Stoll B. , Weis U. , Leitner J. , Repschläger J. , Nürnberg D. , Haug G. H. 
Published: April 2019

AbstractDetermination of Mg/Ca in foraminifer shells as a proxy of seawater temperature is of particular interest in paleoclimate reconstruction. Here we show that femtosecond–200 nm–laser ablation–inductively coupled plasma–mass spectrometry is a suitable technique to precisely and accurately determine Mg/Ca in the micrometer‐sized calcareous chambers of foraminifers. At low fluence (0.3–0.6 J/cm2) the double‐charged 44Ca++ and the single‐charged 25Mg+ ions are measured nearly simultaneously. Integrated single‐shot measurements using a pulse repetition rate of 1 Hz enable precise analyses at a depth resolution of about 50–100 nm/pulse corresponding to an ablated material of 0.3–0.6 ng calcite/pulse for a spot size of 55 μm. High‐resolution analyses can be performed until a depth of 10–20 μm and thus particularly suitable for thin‐shelled foraminifers. Reproducibility (relative standard deviation) is about 5% as approved by homogeneous reference materials. Calibration is performed with the microanalytical synthetic reference material MACS‐3. Magnesium and Ca data of different carbonate and silicate reference materials agree within uncertainties with reference values. The procedure has been successfully applied for detailed analyses of single chambers and shell‐depth profiles of live individuals and empty planktic and benthic foraminifer tests from different ocean basins.
Polarization Electric Field Inside Auroral Patches: Simultaneous Experiment of EISCAT Radars and KAIRA
Authors: Takahashi Toru , Virtanen Ilkka I. , Hosokawa Keisuke , Ogawa Yasunobu , Aikio Anita , Miyaoka Hiroshi , Kero Antti 
Published: April 2019

AbstractThe primary focus of this study was the motion of auroral patches and the polarization electric field generated therein observed on 9 November 2015 in an experiment using the European incoherent scatter (EISCAT) radars, Kilpisjärvi Atmospheric Imaging Receiver Array (KAIRA), and an all‐sky imager simultaneously. Based on the all‐sky imager data, the drift speed of the auroral patches corresponded to a southward electric field of 14.1( ± 3.7)–17.2( ± 4.5) mV/m. The convective electric field derived from the EISCAT radars and KAIRA observation was approximately 14.6 mV/m in the southward direction. This suggest that the spatial distribution of the auroral patches reflects the distribution of the cold plasma in the magnetosphere. The electron density and the height‐integrated Hall conductance between 80 and 120 km were enhanced by a factor of 2–4 inside the auroral patches. In this situation, a polarization electric field was generated therein. Enhanced ion velocities due to the polarization electric field was observed at up to 200‐km altitude; however, the absolute values of the ion velocities were approximately 40% of what was expected from the polarization electric field. A field‐aligned current (FAC) from 5 to 10 μA/m−2 in the edges of the auroral patches could explain the weakening of the polarization electric field. Since a FAC of that order of magnitude corresponded with that observed by the Swarm satellite, it was suggested that the polarization electric field was weakened by the FAC. Furthermore, the polarization electric field propagated upward from the dynamo region to at least 200 km.
AERONET Remotely Sensed Measurements and Retrievals of Biomass Burning Aerosol Optical Properties During the 2015 Indonesian Burning Season
Authors: Eck T. F. , Holben B. N. , Giles D. M. , Slutsker I. , Sinyuk A. , Schafer J. S. , Smirnov A. , Sorokin M. , Reid J. S. , Sayer A. M. , Hsu N. C. , Shi Y. R. , Levy R. C. , Lyapustin A. , Rahman Muhammad Arif , Liew Soo‐Chin , Salinas Cortijo Santo V. , Li Tan , Kalbermatter Daniel , Keong Kwoh Leong , Yuggotomo Muhammad Elifant , Aditya Fanni , Mohamad Maznorizan , Mahmud Mastura , Chong Tan Kok , Lim Hwee‐San , Choon Yeap Eng , Deranadyan Gumilang , Kusumaningtyas Sheila D. A. , Aldrian Edvin 
Published: April 2019

AbstractAn extreme biomass burning event occurred in Indonesia from September through October 2015 due to severe drought conditions, partially caused by a major El Niño event, thereby allowing for significant burning of peatland that had been previously drained. This event had the highest sustained aerosol optical depths (AODs) ever monitored by the global Aerosol Robotic Network (AERONET). The newly developed AERONET Version 3 algorithms retain high AOD at the longer wavelengths when associated with high Ångström exponents (AEs), which thereby allowed for measurements of AOD at 675 nm as high as approximately 7, the upper limit of Sun photometry. Measured AEs at the highest monitored AOD levels were subsequently utilized to estimate instantaneous values of AOD at 550 nm in the range of 11 to 13, well beyond the upper measurement limit. Additionally, retrievals of complex refractive indices, size distributions, and single scattering albedos (SSAs) were obtained at much higher AOD levels than possible from almucantar scans due to the ability to perform retrievals at smaller solar zenith angles with new hybrid sky radiance scans. For retrievals made at the highest AOD levels the fine‐mode volume median radii were ~0.25–0.30 micron, which are very large particles for biomass burning. Very high SSA values (~0.975 from 440 to 1,020 nm) are consistent with the domination by smoldering combustion of peat burning. Estimates of the percentage peat contribution to total biomass burning aerosol based on retrieved SSA and laboratory measured peat SSA were ~80–85%, in excellent agreement with independent estimates.
Using Ghost Fronts Within STEREO Heliospheric Imager Data to Infer the Evolution in Longitudinal Structure of a Coronal Mass Ejection
Authors: Scott C. J. , Owens M. J. , de Koning C. A. , Barnard L. A. , Jones S. R. , Wilkinson J. 
Published: April 2019

AbstractImages of coronal mass ejections (CMEs) from the Heliospheric Imager instruments on board the Solar Terrestrial Relations Observatory (STEREO) spacecraft frequently contain rich structure. Here, we present analysis of the Earth‐directed CME launched on 12 December 2008 in which we interpret the revealed structure as projections of separate discrete sections of the physical boundary of the CME. By comparing the relative position of the outer and inner “ghost” fronts seen in the STEREO Heliospheric Imager 1 cameras with the positions of features determined from three CME models, we show that the two fronts seen in the images correspond to the expected position of the flank and nose of the CME where the background solar wind is uniform. In contrast, the flank of the CME observed expanding into a structured background solar wind results in the elongation between the two fronts being greater than expected. This is consistent with the CME flank distorting in the presence of a high‐speed solar wind stream. Further work is required to consolidate these results. The presence of a shock for this event was ruled out by consideration of the low CME speed and by studying in situ spacecraft data. The CME flank crossing the Thomson sphere was also ruled out as a cause of the ghost fronts. Ghost fronts could provide information about the longitudinal shape of the CME independent of geometric models. This technique could subsequently be used to improve space weather forecast models through techniques such as data assimilation.
Hypomethylation at non-CpG/CpG sites in the promoter of HIF-1α gene combined with enhanced H3K9Ac modification contribute to maintain higher HIF-1α expression in breast cancer
Authors: Li Chun , Xiong Wei , Liu Xiong , Xiao Wenjun , Guo Yuxian , Tan Junyu , Li Yaochen 
Published: April 2019

AbstractHIF-1α has a broad impact on tumors, including enhanced utilization of glucose, tumor cell stemness, migration, metastasis and so on. In pilot study, we found that the expression of HIF-1α significantly increased in breast cancer cell lines and tissue samples with higher malignant behaviors and decreased in luminal subtype breast cancer cells and tissue samples. We analyzed and found there is one large CpG island in HIF-1α promoter around transcription start site, and the hypermethylation occurred at these CpGs and their surrounding non-CpGs sites. Epigenetic events driving tumorigenesis has been characterized. However, knowledge is lacking on the non-CpGs methylation of HIF-1α promoter in breast cancer cells. We validated that non-CpGs methylation can directly regulate HIF-1α expression by luciferase activity assay. We also found DNMT3a and Mecp2 play vital role in methylation at non-CpGs and CpGs sites. In addition, we noticed that H3K9ac modification could promote the transcription of HIF-1α in MDA-MB-231 cells by binding to the region contained hypomethylated non-CpG and CpG sites. Taken together, the hypomethylation status at non-CpG and CpG loci in HIF-1α promoter and H3K9ac modification together contribute to maintain higher HIF-1αactivity in invasive breast cancer cells when compared with the non-invasive breast cancer cells, which may establish a tissue-specific epigenetic modification pattern and point to the new directions for future understanding breast cancer therapy.
Decoupling tRNA promoter and processing activities enables specific Pol-II Cas9 guide RNA expression
Authors: Knapp David J. H. F. , Michaels Yale S. , Jamilly Max , Ferry Quentin R. V. , Barbosa Hector , Milne Thomas A. , Fulga Tudor A. 
Published: April 2019

AbstractSpatial/temporal control of Cas9 guide RNA expression could considerably expand the utility of CRISPR-based technologies. Current approaches based on tRNA processing offer a promising strategy but suffer from high background. Here, to address this limitation, we present a screening platform which allows simultaneous measurements of the promoter strength, 5′, and 3′ processing efficiencies across a library of tRNA variants. This analysis reveals that the sequence determinants underlying these activities, while overlapping, are dissociable. Rational design based on the ensuing principles allowed us to engineer an improved tRNA scaffold that enables highly specific guide RNA production from a Pol-II promoter. When benchmarked against other reported systems this tRNA scaffold is superior to most alternatives, and is equivalent in function to an optimized version of the Csy4-based guide RNA release system. The results and methods described in this manuscript enable avenues of research both in genome engineering and basic tRNA biology.
Structural and biochemical evidence supporting poly ADP-ribosylation in the bacterium Deinococcus radiodurans
Authors: Cho Chao-Cheng , Chien Chia-Yu , Chiu Yi-Chih , Lin Meng-Hsuan , Hsu Chun-Hua 
Published: April 2019

AbstractPoly-ADP-ribosylation, a post-translational modification involved in various cellular processes, is well characterized in eukaryotes but thought to be devoid in bacteria. Here, we solve crystal structures of ADP-ribose–bound poly(ADP-ribose)glycohydrolase from the radioresistant bacterium Deinococcus radiodurans (DrPARG), revealing a solvent-accessible 2’-hydroxy group of ADP-ribose, which suggests that DrPARG may possess endo-glycohydrolase activity toward poly-ADP-ribose (PAR). We confirm the existence of PAR in D. radiodurans and show that disruption of DrPARG expression causes accumulation of endogenous PAR and compromises recovery from UV radiation damage. Moreover, endogenous PAR levels in D. radiodurans are elevated after UV irradiation, indicating that PARylation may be involved in resistance to genotoxic stresses. These findings provide structural insights into a bacterial-type PARG and suggest the existence of a prokaryotic PARylation machinery that may be involved in stress responses.
The computational and neural substrates of moral strategies in social decision-making
Authors: van Baar Jeroen M. , Chang Luke J. , Sanfey Alan G. 
Published: April 2019

AbstractIndividuals employ different moral principles to guide their social decision-making, thus expressing a specific ‘moral strategy’. Which computations characterize different moral strategies, and how might they be instantiated in the brain? Here, we tackle these questions in the context of decisions about reciprocity using a modified Trust Game. We show that different participants spontaneously and consistently employ different moral strategies. By mapping an integrative computational model of reciprocity decisions onto brain activity using inter-subject representational similarity analysis of fMRI data, we find markedly different neural substrates for the strategies of ‘guilt aversion’ and ‘inequity aversion’, even under conditions where the two strategies produce the same choices. We also identify a new strategy, ‘moral opportunism’, in which participants adaptively switch between guilt and inequity aversion, with a corresponding switch observed in their neural activation patterns. These findings provide a valuable view into understanding how different individuals may utilize different moral principles.
Crizotinib-induced immunogenic cell death in non-small cell lung cancer
Authors: Liu Peng , Zhao Liwei , Pol Jonathan , Levesque Sarah , Petrazzuolo Adriana , Pfirschke Christina , Engblom Camilla , Rickelt Steffen , Yamazaki Takahiro , Iribarren Kristina , Senovilla Laura , Bezu Lucillia , Vacchelli Erika , Sica Valentina , Melis Andréa , Martin Tiffany , Xia Lin , Yang Heng , Li Qingqing , Chen Jinfeng , Durand Sylvère , Aprahamian Fanny , Lefevre Deborah , Broutin Sophie , Paci Angelo , Bongers Amaury , Minard-Colin Veronique , Tartour Eric , Zitvogel Laurence , Apetoh Lionel , Ma Yuting , Pittet Mikael J. , Kepp Oliver , Kroemer Guido 
Published: April 2019

AbstractImmunogenic cell death (ICD) converts dying cancer cells into a therapeutic vaccine and stimulates antitumor immune responses. Here we unravel the results of an unbiased screen identifying high-dose (10 µM) crizotinib as an ICD-inducing tyrosine kinase inhibitor that has exceptional antineoplastic activity when combined with non-ICD inducing chemotherapeutics like cisplatin. The combination of cisplatin and high-dose crizotinib induces ICD in non-small cell lung carcinoma (NSCLC) cells and effectively controls the growth of distinct (transplantable, carcinogen- or oncogene induced) orthotopic NSCLC models. These anticancer effects are linked to increased T lymphocyte infiltration and are abolished by T cell depletion or interferon-γ neutralization. Crizotinib plus cisplatin leads to an increase in the expression of PD-1 and PD-L1 in tumors, coupled to a strong sensitization of NSCLC to immunotherapy with PD-1 antibodies. Hence, a sequential combination treatment consisting in conventional chemotherapy together with crizotinib, followed by immune checkpoint blockade may be active against NSCLC.
Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes
Authors: Liu Yang , Johnson Matthew G. , Cox Cymon J. , Medina Rafael , Devos Nicolas , Vanderpoorten Alain , Hedenäs Lars , Bell Neil E. , Shevock James R. , Aguero Blanka , Quandt Dietmar , Wickett Norman J. , Shaw A. Jonathan , Goffinet Bernard 
Published: April 2019

AbstractMosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30 moss orders reveals that relative average rates of non-synonymous substitutions in nuclear versus plastid genes are much higher in mosses than in seed plants, consistent with the emerging concept of evolutionary dynamism in mosses. Our results highlight the evolutionary significance of taxa with reduced morphologies, shed light on the relative tempo and mechanisms underlying major cladogenic events, and suggest hypotheses for the relationships and delineation of moss orders.
Genome-wide association study of alcohol consumption and use disorder in 274,424 individuals from multiple populations
Authors: Kranzler Henry R. , Zhou Hang , Kember Rachel L. , Vickers Smith Rachel , Justice Amy C. , Damrauer Scott , Tsao Philip S. , Klarin Derek , Baras Aris , Reid Jeffrey , Overton John , Rader Daniel J. , Cheng Zhongshan , Tate Janet P. , Becker William C. , Concato John , Xu Ke , Polimanti Renato , Zhao Hongyu , Gelernter Joel 
Published: April 2019

AbstractAlcohol consumption level and alcohol use disorder (AUD) diagnosis are moderately heritable traits. We conduct genome-wide association studies of these traits using longitudinal Alcohol Use Disorder Identification Test-Consumption (AUDIT-C) scores and AUD diagnoses in a multi-ancestry Million Veteran Program sample (N = 274,424). We identify 18 genome-wide significant loci: 5 associated with both traits, 8 associated with AUDIT-C only, and 5 associated with AUD diagnosis only. Polygenic Risk Scores (PRS) for both traits are associated with alcohol-related disorders in two independent samples. Although a significant genetic correlation reflects the overlap between the traits, genetic correlations for 188 non-alcohol-related traits differ significantly for the two traits, as do the phenotypes associated with the traits’ PRS. Cell type group partitioning heritability enrichment analyses also differentiate the two traits. We conclude that, although heavy drinking is a key risk factor for AUD, it is not a sufficient cause of the disorder.
The lncRNA Neat1 promotes activation of inflammasomes in macrophages
Authors: Zhang Pengfei , Cao Limian , Zhou Rongbin , Yang Xiaolu , Wu Mian 
Published: April 2019

AbstractThe inflammasome has an essential function in innate immune, responding to a wide variety of stimuli. Here we show that the lncRNANeat1promotes the activation of several inflammasomes.Neat1associates with the NLRP3, NLRC4, and AIM2 inflammasomes in mouse macrophages to enhance their assembly and subsequent pro-caspase-1 processing.Neat1also stabilizes the mature caspase-1 to promote interleukin-1β production and pyroptosis. Upon stimulation with inflammasome-activating signals,Neat1, which normally resides in the paraspeckles, disassociates from these nuclear bodies and translocates to the cytoplasm to modulate inflammasome activation using above mechanism.Neat1is also up-regulated under hypoxic conditions in a HIF-2α-dependent manner, mediating the effect of hypoxia on inflammasomes. Moreover, in the mouse models of peritonitis and pneumonia,Neat1deficiency significantly reduces inflammatory responses. These results reveal a previously unrecognized role of lncRNAs in innate immunity, and suggest thatNeat1is a common mediator for inflammasome stimuli.
Cortex-wide neural interfacing via transparent polymer skulls
Authors: Ghanbari Leila , Carter Russell E. , Rynes Mathew L. , Dominguez Judith , Chen Gang , Naik Anant , Hu Jia , Sagar Md Abdul Kader , Haltom Lenora , Mossazghi Nahom , Gray Madelyn M. , West Sarah L. , Eliceiri Kevin W. , Ebner Timothy J. , Kodandaramaiah Suhasa B. 
Published: April 2019

AbstractNeural computations occurring simultaneously in multiple cerebral cortical regions are critical for mediating behaviors. Progress has been made in understanding how neural activity in specific cortical regions contributes to behavior. However, there is a lack of tools that allow simultaneous monitoring and perturbing neural activity from multiple cortical regions. We engineered ‘See-Shells’—digitally designed, morphologically realistic, transparent polymer skulls that allow long-term (>300 days) optical access to 45 mm2 of the dorsal cerebral cortex in the mouse. We demonstrate the ability to perform mesoscopic imaging, as well as cellular and subcellular resolution two-photon imaging of neural structures up to 600 µm deep. See-Shells allow calcium imaging from multiple, non-contiguous regions across the cortex. Perforated See-Shells enable introducing penetrating neural probes to perturb or record neural activity simultaneously with whole cortex imaging. See-Shells are constructed using common desktop fabrication tools, providing a powerful tool for investigating brain structure and function.
A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour
Authors: Zhang Liyi , Hu Jiang , Han Xiaolei , Li Jingjing , Gao Yuan , Richards Christopher M. , Zhang Caixia , Tian Yi , Liu Guiming , Gul Hera , Wang Dajiang , Tian Yu , Yang Chuanxin , Meng Minghui , Yuan Gaopeng , Kang Guodong , Wu Yonglong , Wang Kun , Zhang Hengtao , Wang Depeng , Cong Peihua 
Published: April 2019

AbstractA complete and accurate genome sequence provides a fundamental tool for functional genomics and DNA-informed breeding. Here, we assemble a high-quality genome (contig N50 of 6.99 Mb) of the apple anther-derived homozygous line HFTH1, including 22 telomere sequences, using a combination of PacBio single-molecule real-time (SMRT) sequencing, chromosome conformation capture (Hi-C) sequencing, and optical mapping. In comparison to the Golden Delicious reference genome, we identify 18,047 deletions, 12,101 insertions and 14 large inversions. We reveal that these extensive genomic variations are largely attributable to activity of transposable elements. Interestingly, we find that a long terminal repeat (LTR) retrotransposon insertion upstream of MdMYB1, a core transcriptional activator of anthocyanin biosynthesis, is associated with red-skinned phenotype. This finding provides insights into the molecular mechanisms underlying red fruit coloration, and highlights the utility of this high-quality genome assembly in deciphering agriculturally important trait in apple.
Transcriptomic Diversification of Granulosa Cells during Follicular Development in Chicken
Authors: Zhu Guoqiang , Fang Chao , Li Jing , Mo Chunheng , Wang Yajun , Li Juan 
Published: April 2019

AbstractGranulosa cells play important roles in ovarian follicular development. To better understand the molecular mechanisms involved in this physiological process in chicken, high-throughput transcriptome analyses were performed to study the expression profiles of granulosa cells harvested from 6 mm white follicles, F5 follicles and F1 follicles. The analyses elucidated a clear tendency of granulosa cells in shifting its expression profile from proliferation to differentiation during follicular development. Transcripts down-regulated during this process were mainly associated with cell division, cell cycle and DNA replication while the up-regulated transcripts were related to ribosomal function, lipid metabolism and protein synthesis. Our study for the first time provides the complete gene expression profiles along follicular development supporting the active involvement of many genes characterized in cell signaling (AMH, Inhibins, Activins, BMPs) and transcription factors (SMAD3, SMAD5, ID1, ID2, ID3). Their temporal expression profiles support the notion of continual cross-talk between granulosa cells and its neighboring cells and shed light on the mechanisms behind avian follicular selection and pave the way to the better understanding of reproductive efficiency.