bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revised estimates of ocean-atmosphere CO2 flux are consistent with ocean carbon inventory
Authors: Watson Andrew J. , Schuster Ute , Shutler Jamie D. , Holding Thomas , Ashton Ian G. C. , Landschützer Peter , Woolf David K. , Goddijn-Murphy Lonneke 
Published: September 2020

AbstractThe ocean is a sink for ~25% of the atmospheric CO2 emitted by human activities, an amount in excess of 2 petagrams of carbon per year (PgC yr−1). Time-resolved estimates of global ocean-atmosphere CO2 flux provide an important constraint on the global carbon budget. However, previous estimates of this flux, derived from surface ocean CO2 concentrations, have not corrected the data for temperature gradients between the surface and sampling at a few meters depth, or for the effect of the cool ocean surface skin. Here we calculate a time history of ocean-atmosphere CO2 fluxes from 1992 to 2018, corrected for these effects. These increase the calculated net flux into the oceans by 0.8–0.9  PgC yr−1, at times doubling uncorrected values. We estimate uncertainties using multiple interpolation methods, finding convergent results for fluxes globally after 2000, or over the Northern Hemisphere throughout the period. Our corrections reconcile surface uptake with independent estimates of the increase in ocean CO2 inventory, and suggest most ocean models underestimate uptake.
Repertoire-scale determination of class II MHC peptide binding via yeast display improves antigen prediction
Authors: Rappazzo C. Garrett , Huisman Brooke D. , Birnbaum Michael E. 
Published: September 2020

AbstractCD4+helper T cells contribute important functions to the immune response during pathogen infection and tumor formation by recognizing antigenic peptides presented by class II major histocompatibility complexes (MHC-II). While many computational algorithms for predicting peptide binding to MHC-II proteins have been reported, their performance varies greatly. Here we present a yeast-display-based platform that allows the identification of over an order of magnitude more unique MHC-II binders than comparable approaches. These peptides contain previously identified motifs, but also reveal new motifs that are validated by in vitro binding assays. Training of prediction algorithms with yeast-display library data improves the prediction of peptide-binding affinity and the identification of pathogen-associated and tumor-associated peptides. In summary, our yeast-display-based platform yields high-quality MHC-II-binding peptide datasets that can be used to improve the accuracy of MHC-II binding prediction algorithms, and potentially enhance our understanding of CD4+T cell recognition.
Synthetic band-structure engineering in polariton crystals with non-Hermitian topological phases
Authors: Pickup L. , Sigurdsson H. , Ruostekoski J. , Lagoudakis P. G. 
Published: September 2020

AbstractSynthetic crystal lattices provide ideal environments for simulating and exploring the band structure of solid-state materials in clean and controlled experimental settings. Physical realisations have, so far, dominantly focused on implementing irreversible patterning of the system, or interference techniques such as optical lattices of cold atoms. Here, we realise reprogrammable synthetic band-structure engineering in an all optical exciton-polariton lattice. We demonstrate polariton condensation into excited states of linear one-dimensional lattices, periodic rings, dimerised non-trivial topological phases, and defect modes utilising malleable optically imprinted non-Hermitian potential landscapes. The stable excited nature of the condensate lattice with strong interactions between sites results in an actively tuneable non-Hermitian analogue of the Su-Schrieffer-Heeger system.
Marker aided introgression of ‘Saltol’, a major QTL for seedling stage salinity tolerance into an elite Basmati rice variety ‘Pusa Basmati 1509’
Authors: Yadav Ashutosh Kumar , Kumar Aruna , Grover Nitasha , Ellur Ranjith Kumar , Krishnan S. Gopala , Bollinedi Haritha , Bhowmick Prolay Kumar , Vinod K. K. , Nagarajan M. , Krishnamurthy S. L. , Singh Ashok Kumar 
Published: September 2020

AbstractMarker assisted backcross breeding was used to transferSaltol, a major QTL for seedling stage salinity tolerance from the donor FL478 to Pusa Basmati 1509 (PB 1509), a high yielding and early maturing Basmati rice variety. Foreground selection was carried out using three markers namely, AP3206f, RM3412b and RM10793, linked toSaltol. In addition, 105 genome-wide SSR markers polymorphic between FL478 and PB 1509 were used in background selection. Among the BC3F4near isogenic lines (NILs) developed, recurrent parent genome recovery ranged from 96.67 to 98.57%. Multi-season evaluation identified some of the NILs showing significantly higher yield with grain and cooking quality comparable to PB 1509. All the NILs exhibited tolerance to salinity with significantly higher relative water content, membrane stability index and proline content as compared to PB 1509. The root and shoot concentration of Na+, K+and Na+/K+in NILs was at par with FL478 under stress conditions. The geneOsHKT1;5 located in theSaltolregion showed higher expression levels under stress indicating its role in conferring salinity tolerance. Salt tolerant NILs of PB 1509 will be useful in stabilizing production in salt affected areas.
Changes of central noradrenaline transporter availability in immunotherapy-naïve multiple sclerosis patients
Authors: Schmidt Elisa , Schinke Christian , Rullmann Michael , Luthardt Julia , Becker Georg-Alexander , Haars Sarah , Stoppe Muriel , Lobsien Donald , Hoffmann Karl-Titus , Sabri Osama , Hesse Swen , Then Bergh Florian 
Published: September 2020

AbstractThe neurotransmitter noradrenaline (NA) mediates arousal, attention and mood, and exerts anti-inflammatory and neuroprotective effects. Alterations of monoamine signalling were reported in multiple sclerosis (MS) and psychiatric illness and may account for the high prevalence of comorbid depression and fatigue in MS patients. We assessed central noradrenaline transporter (NAT) availability using positron emission tomography (PET) and the NAT selective radiotracer S,S-[11C]O-methylreboxetine in immunotherapy-naïve patients with relapsing–remitting MS (RRMS; n = 11) compared to healthy controls (HC; n = 12), and its association to lesion load, time since manifestation, the expanded disability status scale (EDSS), the fatigue scale Würzburger Erschöpfungsinventar bei MS (WEIMuS) and Beck Depression Inventory (BDI). We found NAT availability to be increased in the thalamus, amygdala, putamen and pons/midbrain of MS patients. No relation to clinical or psychometric variables was found. These first data indicate higher NAT availability in subcortical brain regions of immunotherapy-naïve RRMS patients. If these changes of noradrenergic neurotransmission predispose to psychiatric symptoms or associate with disease activity needs to be investigated in longitudinal studies or a larger sample which allows subgroup analyses.
Diversity and pathogenicity of Colletotrichum species causing strawberry anthracnose in Taiwan and description of a new species, Colletotrichum miaoliense sp. nov.
Authors: Chung Pei-Che , Wu Hung-Yi , Wang Yen-Wen , Ariyawansa Hiran A. , Hu Hsien-Pin , Hung Ting-Hsuan , Tzean Shean-Shong , Chung Chia-Lin 
Published: September 2020

AbstractStrawberry is a small fruit crop with high economic value. Anthracnose caused byColletotrichumspp. poses a serious threat to strawberry production, particularly in warm and humid climates, but knowledge of pathogen populations in tropical and subtropical regions is limited. To investigate the diversity of infectious agents causing strawberry anthracnose in Taiwan, a disease survey was conducted from 2010 to 2018, andColletotrichumspp. were identified through morphological characterization and multilocus phylogenetic analysis with internal transcribed spacer, glyceraldehyde 3-phosphate dehydrogenase, chitin synthase, actin, beta-tubulin, calmodulin, and the intergenic region betweenApn2andMAT1-2-1(ApMAT). Among 52 isolates collected from 24 farms/nurseries in Taiwan, a new species,Colletotrichum miaoliensesp. nov. (6% of all isolates), a species not previously known to be associated with strawberry,Colletotrichum karstii(6%), and three known species,Colletotrichum siamense(75%),Colletotrichum fructicola(11%), andColletotrichum boninense(2%), were identified. The predominant speciesC.siamenseandC.fructicolaexhibited higher mycelial growth rates on potato dextrose agar and caused larger lesions on wounded and non-wounded detached strawberry leaves.Colletotrichum boninense,C. karstii, andC. miaolienseonly caused lesions on wounded leaves. Understanding the composition and biology of the pathogen population will help in disease management and resistance breeding.
A novel protocol to detect green fluorescent protein in unfixed, snap-frozen tissue
Authors: Scandella Valentina , Paolicelli Rosa Chiara , Knobloch Marlen 
Published: September 2020

AbstractThe green fluorescent protein (GFP) is a powerful reporter protein that allows labeling of specific proteins or entire cells. However, as GFP is a small soluble protein, it easily crosses membranes if cell integrity is disrupted, and GFP signal is lost or diffuse if the specimen is not fixed beforehand. While pre-fixation is often feasible for histological analyses, many molecular biology procedures and new imaging techniques, such as imaging mass spectrometry, require unfixed specimens. To be able to use GFP labeling in tissues prepared for such applications, we have tested various protocols to minimize the loss of GFP signal. Here we show that, in cryocut sections of snap-frozen brain tissue from two GFP reporter mouse lines, leaking of the GFP signal is prevented by omitting the commonly performed drying of the cryosections, and by direct post-fixation with 4% paraformaldehyde pre-warmed at 30–37 °C. Although the GFP staining does not reach the same quality as obtained with pre-fixed tissue, GFP localization within the cells that express it is preserved with this method. This protocol can thus be used to identify GFP positive cells on sections originating from unfixed, cryosectioned tissue.
Kinship analysis on single cells after whole genome amplification
Authors: Weymaere Jana , Vander Plaetsen Ann-Sophie , Tilleman Laurentijn , Tytgat Olivier , Rubben Kaat , Geeraert Sofie , Deforce Dieter , Van Nieuwerburgh Filip 
Published: September 2020

AbstractShort Tandem Repeat (STR-) and Single Nucleotide Polymorphism (SNP-) genotyping have been extensively studied within forensic kinship analysis. Nevertheless, no results have been reported on kinship analysis after whole genome amplification (WGA) of single cells. This WGA step is a necessary procedure in several applications, such as cell-based non-invasive prenatal testing (cbNIPT) and pre-implantation genetic diagnosis (PGD). In cbNIPT, all putative fetal cells must be discriminated from maternal cells after enrichment from whole blood. This study investigates the efficacy and evidential value of STR- and SNP-genotyping methods for the discrimination of 24 single cells after WGA, within three families. Formaldehyde-fixed and unfixed cells are assessed in offspring-parent duos and offspring-mother-father trios. Results demonstrate that both genotyping methods can be used in all tested conditions and scenarios with 100% sensitivity and 100% specificity, with a similar evidential value for fixed and unfixed cells. Moreover, sequence-based SNP-genotyping results in a higher evidential value than length-based STR-genotyping after WGA, which is not observed using high-quality offspring bulk DNA samples. Finally, it is also demonstrated that the availability of the DNA genotypes of both parents strongly increases the evidential value of the results.
Piceatannol inhibits pyroptosis and suppresses oxLDL-induced lipid storage in macrophages by regulating miR-200a/Nrf2/GSDMD axis
Authors: Mu Zhongyuan , Zhang Hongling , Lei Peng 
Published: September 2020

Abstract
As a major bioactive compound from grapes, piceatannol (PIC) has been reported to exert anti-atherosclerotic activity in various studies. Nevertheless, the mechanism underlying the effect of piceatannol against atherosclerosis (AS) is elusive. Our study identified miR-200a/Nrf2/GSDMD signaling pathway as critical mediators in the effect of piceatannol on macrophages. In the present study, we confirmed that treatment of piceatannol repressed the oxLDL-induced lipid storage in macrophages. Compared with control group, piceatannol inhibited TG storage and the activity of caspase1. It is noting that in response to oxLDL challenge, piceatannol abated the pyroptosis in RAW264.7 cells, with a decreased expression of caspase1, gasdermin D (GSDMD), IL-18, IL-1β and NLRP3. Moreover, we investigated the role of microRNA (miR)-200a/Nrf2 signaling pathway in the effect of piceatannol. The results declared that after transfection of si-miR-200a or si-Nrf2 plasmids, the effects of piceatannol on macrophages were converted, including lipid storage and pyroptosis. Importantly, si-miR-200a plasmid reduced the expression of nuclear factor erythroid 2-related factor 2 (Nrf2), indicating that miR-200a acted as an enhancer of Nrf2 in macrophages. Collectively, our findings demonstrate that piceatannol exerts anti-atherosclerotic activity on RAW264.7 cells by regulating miR-200a/Nrf2/GSDMD signaling. The present study is the first time to identify miR-200a as a candidate target in AS and declared an association between miR-200a and pyroptosis, which provides a novel therapy for the treatment of AS.
MicroRNA-132 attenuated cardiac fibrosis in myocardial infarction-induced heart failure rats
Authors: Wang Guoyu , Wang Ruzhu , Ruan Zhongbao , Liu Ling , Li Yong , Zhu Li 
Published: September 2020

Abstract
The aim of the present study was to determine the effect of microRNA (miR)-132 on cardiac fibrosis in myocardial infarction (MI)-induced heart failure and angiotensin (Ang) II-treated cardiac fibroblasts (CFs). Experiments were carried out in Sprague-Dawley rat treatment with ligation of left coronary artery to induce heart failure, and in CFs administration of Ang II to induce fibrosis. The level of miR-132 was increased in the heart of rats with MI-induced heart failure and the Ang II-treated CFs. In MI rats, left ventricle (LV) ejection fraction, fractional shortening, the maximum of the first differentiation of LV pressure (LV +dp/dtmax) and decline (LV -dp/dtmax) and LV systolic pressure (LVSP) were reduced, and LV end-systolic diameter (LVESD), LV end-diastolic diameter (LVEDD), LV volumes in systole (LVVS) and LV volumes in diastole (LVVD) were increased, which were reversed by miR-132 agomiR but deteriorated by miR-132 antagomiR. The expression levels of collagen I, collagen III, transforming growth factor-β (TGF-β), and α-smooth muscle actin (α-SMA) were increased in the heart of rat with MI-induced heart failure and CFs administration of Ang II. These increases were inhibited by miR-132 agomiR but enhanced by miR-132 antagomiR treatment. MiR-132 inhibited PTEN expression, and attenuated PI3K/Akt signal pathway in CFs. These results indicated that the up-regulation of miR-132 improved the cardiac dysfunction, attenuated cardiac fibrosis in heart failure via inhibiting PTEN expression, and attenuating PI3K/Akt signal pathway. Up-regulation of miR-132 may be a strategy for the treatment of heart failure and cardiac fibrosis.
Identification of novel biomarkers involved in pulmonary arterial hypertension based on multiple-microarray analysis
Authors: Ma Yi , Chen Shu-Shu , Feng Yan-Yan , Wang Huan-Liang 
Published: September 2020

Abstract
Pulmonary arterial hypertension (PAH) is a life-threatening chronic cardiopulmonary disorder. However, studies providing PAH-related gene expression profiles are scarce. To identify hub genes involved in PAH, we investigate two microarray data sets from gene expression omnibus (GEO). A total of 150 differentially expressed genes (DEGs) were identified by limma package. Enriched Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of DEGs mostly included mitotic nuclear division, ATPase activity, and Herpes simplex virus one infection. Ten hub genes from three significant modules were ascertained by Cytoscape (CytoHubba). Gene set enrichment analysis (GSEA) plots showed that transcription elongation factor complex was the most significantly enriched gene set positively correlated with the PAH group. At the same time, solute proton symporter activity was the most significantly enriched gene set positively correlated with the control group. Correlation analysis between hub genes suggested that SMC4, TOP2A, SMC2, KIF11, KIF23, ANLN, ARHGAP11A, SMC3, SMC6 and RAD50 may involve in the pathogenesis of PAH. Then, the miRNA-target genes regulation network was performed to unveil the underlying complex association among them. Finally, RNA extracted from monocrotaline (MCT)-induced Rat-PAH model lung artery tissues were to conduct quantitative real-time PCR (qRT-PCR) to validate these hub genes. In conclusion, our study offers new evidence for the underlying molecular mechanisms of PAH as well as attractive targets for diagnosis and treatment of PAH.
Specialized pro-resolving mediator network: an update on production and actions
Authors: Chiang Nan , Serhan Charles N. 
Published: September 2020

Abstract
Today, persistent and uncontrolled inflammation is appreciated to play a pivotal role in many diseases, such as cardiovascular diseases, neurodegenerative diseases, metabolic syndrome and many other diseases of public health concern (e.g. Coronavirus Disease 2019 (COVID-19) and periodontal disease). The ideal response to initial challenge in humans is a self-limited inflammatory response leading to complete resolution. The resolution phase is now widely recognized as a biosynthetically active process, governed by a superfamily of endogenous chemical mediators that stimulate resolution of inflammatory responses, namely specialized proresolving mediators (SPMs). Because resolution is the natural ideal response, the SPMs have gained attention. SPMs are mediators that include ω-6 arachidonic acid-derived lipoxins, ω-3 eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)-derived resolvins, protectins and maresins, cysteinyl-SPMs, as well as n-3 docosapentaenoic acid (DPA)-derived SPMs. These novel immunoresolvents, their biosynthetic pathways and receptors have proven to promote resolution of inflammation, clearance of microbes, reduce pain and promote tissue regeneration via specific cellular and molecular mechanisms. As of 17 August, 2020, PubMed.gov reported &gt;1170 publications for resolvins, confirming their potent protective actions from many laboratories worldwide. Since this field is rapidly expanding, we provide a short update of advances within 2–3 years from human and preclinical animal studies, together with the structural–functional elucidation of SPMs and identification of novel SPM receptors. These new discoveries indicate that SPMs, their pathways and receptors could provide a basis for new approaches for treating inflammation-associated diseases and for stimulating tissue regeneration via resolution pharmacology and precision nutrition.
The ARCiS framework for exoplanet atmospheres
Authors: Min Michiel , Ormel Chris W. , Chubb Katy , Helling Christiane , Kawashima Yui 
Published: September 2020

Aims.We present ARCiS, a novel code for the analysis of exoplanet transmission and emission spectra. The aim of the modelling framework is to provide a tool able to link observations to physical models of exoplanet atmospheres.Methods.The modelling philosophy chosen in this paper is to use physical and chemical models to constrain certain parameters while leaving certain parts of the model, where our physical understanding remains limited, free to vary. This approach, in between full physical modelling and full parameterisation, allows us to use the processes we understand well and parameterise those less understood. We implemented a Bayesian retrieval framework and applied it to the transit spectra of a set of ten hot Jupiters. The code contains chemistry and cloud formation and has the option for self-consistent temperature structure computations.Results.The code presented is fast and flexible enough to be used for retrieval and for target list simulations for JWST or the ESA Ariel missions for example. We present results for the retrieval of elemental abundance ratios using the physical retrieval framework and compare this to results obtained using a parameterised retrieval setup.Conclusions.We conclude that for most of the targets considered, their elemental abundance ratios cannot be reliably constrained based on the current dataset. We find no significant correlations between different physical parameters. We confirm that planets in our sample with a strong slope in the optical transmission spectrum are those for which we find cloud formation to be most active. Finally, we conclude that with ARCiS we have a computationally efficient tool to analyse exoplanet observations in the context of physical and chemical models.
Diffusion of radial action in a galactic disc
Authors: Wozniak Hervé 
Published: September 2020

Context. The stellar migration of the galactic disc stars has been invoked to explain the dispersion of stellar metallicity observed in the solar neighbourhood.
Aims. We seek to identify the dynamical mechanisms underlying stellar migration in an isolated galaxy disc under the influence of a bar. Our approach is to analyse the diffusion of dynamical quantities.
Methods. We extend our previous work by exploring Chirikov’s diffusion rate (and derived timescale) of the radial action JR in an idealised N-body simulation of an isolated disc galaxy. We limit our study to the evolution of the disc region well after the formation of the bar, in a regime of adiabatic evolution.
Results. The JR diffusion timescale TD(JR) is less than 3 Gyr for roughly half the galaxy mass. It is always much shorter than the angular momentum diffusion timescale TD(Lz) outside the stellar bar. In the disc, ⟨TD(JR)⟩ ∼ 1 Gyr. All non-axisymmetric morphological structures that are characteristic of resonances and waves in the disc are associated to particles with TD(JR) < 3 Gyr and TD(Lz) > 10 Gyr. Short TD(JR) can be explained by the gradual de-circularisation of initially circular orbits (JR = 0) under the effect of intermittent. Inner Linblad resonance scattering by wave trains propagating in the disc, well beyond the outer Lindblad resonance of the bar (OLR). This leads to a moderate secular heating of the disc beyond the bar’s OLR for 7 Gyr, which is comparable to solar neighbourhood observations. The complex multi-wave structure, mixing permanent and intermittent modes, allows for multiple resonance overlaps.