bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early‐to‐Late Winter 20th Century North Atlantic Multidecadal Atmospheric Variability in Observations, CMIP5 and CMIP6
Authors: Bracegirdle Thomas J. 
Published: May 2022

AbstractThe strong multidecadal variability in North Atlantic (NA) winter atmospheric circulation is poorly understood and appears too weak in climate models. Recent research has shown peak atmospheric multidecadal variability over the NA in late winter, particularly March, linked to Atlantic multidecadal variability (AMV) of the ocean. Here a range of NA atmospheric circulation indices are assessed to provide a comprehensive picture of early‐to‐late winter low‐frequency variability and its representation in the latest generation of climate models (Coupled Model Intercomparison Project Phase 6 [CMIP6]). As found for CMIP5, CMIP6 models exhibit too‐weak multidecadal NA atmospheric variability compared to reanalysis data over the period 1862–2005. Consistent with previous research, the eastern part of the NA westerly jet (U700NA) exhibits peak low‐frequency variability in March. However, for NA‐wide jet speed and the NAO, low‐frequency variability and model‐reanalysis discrepancies are strongest in January and February, associated with too‐weak NA ocean‐atmosphere linkages.
Present‐Day Strike‐Slip Faulting and Thrusting of the Kepingtage Fold‐and‐Thrust Belt in Southern Tianshan: Constraints From GPS Observations
Authors: Li Jie , Yao Yuan , Li Rui , Yusan Sulitan , Li Guirong , Freymueller Jeffrey T. , Wang Qi 
Published: May 2022

AbstractAcross inherited complex fold‐and‐thrust belts (FTBs), shortening may be accommodated at different rates depending on structural style variations; such cases have rarely been documented We present the example of the Kepingtage FTB in southern Tianshan, which is bisected by the NNW‐trending left‐lateral strike‐slip Piqiang Fault (PQF) into eastern and western segments. The 1.45 ± 0.31–2.10 ± 0.42 mm/a shortening rate of the eastern segment is accommodated in a diffuse‐deformation pattern within the five‐row thrust‐anticlinal zone and the 2.36 ± 0.23–3.70 ± 0.59 mm/a shortening rate of the western segment is accommodated within the two‐row thrust‐anticlinal zone at the FTB front. To accommodate the latitudinal variability, the PQF exhibits a 2.30 ± 0.20–4.10 ± 0.40 mm/a segmentation strike‐slip rate. The 2.35 ± 0.33–4.20 ± 0.45 mm/a shortening rate of the Kepingtage FTB and southern Tianshan Fault is one‐third of the total convergence rate between the Tarim Basin and Kazakh Platform at 77°–79°E; hence, the complex Tianshan deformation occurred mainly at the FTB.
Elucidating the importance and regulation of key enhancers for human MEIS1 expression
Authors: Xiang Ping , Yang Xining , Escano Leo , Dhillon Ishpreet , Schneider Edith , Clemans-Gibbon Jack , Wei Wei , Wong Jasper , Wang Simon Xufeng , Tam Derek , Deng Yu , Yung Eric , Morin Gregg B. , Hoodless Pamela A. , Hirst Martin , Karsan Aly , Kuchenbauer Florian , Humphries R. Keith , Rouhi Arefeh 
Published: May 2022

AbstractMyeloid ecotropic virus insertion site 1 (MEIS1) is essential for normal hematopoiesis and is a critical factor in the pathogenesis of a large subset of acute myeloid leukemia (AML). Despite the clinical relevance of MEIS1, its regulation is largely unknown. To understand the transcriptional regulatory mechanisms contributing to human MEIS1 expression, we created a knock-in green florescent protein (GFP) reporter system at the endogenous MEIS1 locus in a human AML cell line. Using this model, we have delineated and dissected a critical enhancer region of the MEIS1 locus for transcription factor (TF) binding through in silico prediction in combination with oligo pull-down, mass-spectrometry and knockout analysis leading to the identification of FLI1, an E-twenty-six (ETS) transcription factor, as an important regulator of MEIS1 transcription. We further show direct binding of FLI1 to the MEIS1 locus in human AML cell lines as well as enrichment of histone acetylation in MEIS1-high healthy and leukemic cells. We also observe a positive correlation between high FLI1 transcript levels and worse overall survival in AML patients. Our study expands the role of ETS factors in AML and our model constitutes a feasible tool for a more detailed understanding of transcriptional regulatory elements and their interactome.
Regulation of proton partitioning in kinase-activating acute myeloid leukemia and its therapeutic implication
Authors: Man Cheuk-Him , Zeng Xiaoyuan , Lam Wing , Ng Timothy C. C. , Kwok Tsz-Ho , Dang Kenny C. C. , Leung Thomas W. Y. , Ng Nelson K. L. , Lam Stephen S. Y. , Cher Chae-Yin , Leung Anskar Y. H. 
Published: May 2022

AbstractGain-of-function kinase mutations are common in AML and usually portend an inferior prognosis. We reported a novel mechanism whereby kinase mutants induced intracellular alkalization characteristic in oncogenesis. Thirteen kinases were found to activate sodium/hydrogen exchanger (NHE1) in normal hematopoietic progenitors, of which FLT3-ITD, KRASG12D, and BTK phosphorylated NHE1 maintained alkaline intracellular pH (pHi) and supported survival of AML cells. Primary AML samples with kinase mutations also showed increased NHE1 phosphorylation and evidence of NHE1 addiction. Amiloride enhanced anti-leukemic effects and intracellular distribution of kinase inhibitors and chemotherapy. Co-inhibition of NHE1 and kinase synergistically acidified pHi in leukemia and inhibited its growth in vivo. Plasma from patients taking amiloride for diuresis reduced pHi of leukemia and enhanced cytotoxic effects of kinase inhibitors and chemotherapy in vitro. NHE1-mediated intracellular alkalization played a key pathogenetic role in transmitting the proliferative signal from mutated-kinase and could be exploited for therapeutic intervention in AML.
FANCD2 maintains replication fork stability during misincorporation of the DNA demethylation products 5-hydroxymethyl-2’-deoxycytidine and 5-hydroxymethyl-2’-deoxyuridine
Authors: Peña-Gómez María José , Moreno-Gordillo Paula , Narmontė Milda , García-Calderón Clara B. , Rukšėnaitė Audronė , Klimašauskas Saulius , Rosado Iván V. 
Published: May 2022

AbstractFanconi anemia (FA) is a rare hereditary disorder caused by mutations in any one of the FANC genes. FA cells are mainly characterized by extreme hypersensitivity to interstrand crosslink (ICL) agents. Additionally, the FA proteins play a crucial role in concert with homologous recombination (HR) factors to protect stalled replication forks. Here, we report that the 5-methyl-2’-deoxycytidine (5mdC) demethylation (pathway) intermediate 5-hydroxymethyl-2’-deoxycytidine (5hmdC) and its deamination product 5-hydroxymethyl-2’-deoxyuridine (5hmdU) elicit a DNA damage response, chromosome aberrations, replication fork impairment and cell viability loss in the absence of FANCD2. Interestingly, replication fork instability by 5hmdC or 5hmdU was associated to the presence of Poly(ADP-ribose) polymerase 1 (PARP1) on chromatin, being both phenotypes exacerbated by olaparib treatment. Remarkably, Parp1−/− cells did not show any replication fork defects or sensitivity to 5hmdC or 5hmdU, suggesting that retained PARP1 at base excision repair (BER) intermediates accounts for the observed replication fork defects upon 5hmdC or 5hmdU incorporation in the absence of FANCD2. We therefore conclude that 5hmdC is deaminated in vivo to 5hmdU, whose fixation by PARP1 during BER, hinders replication fork progression and contributes to genomic instability in FA cells.
Rewritable two-dimensional DNA-based data storage with machine learning reconstruction
Authors: Pan Chao , Tabatabaei S. Kasra , Tabatabaei Yazdi S. M. Hossein , Hernandez Alvaro G. , Schroeder Charles M. , Milenkovic Olgica 
Published: May 2022

AbstractDNA-based data storage platforms traditionally encode information only in the nucleotide sequence of the molecule. Here we report on a two-dimensional molecular data storage system that records information in both the sequence and the backbone structure of DNA and performs nontrivial joint data encoding, decoding and processing. Our 2DDNA method efficiently stores images in synthetic DNA and embeds pertinent metadata as nicks in the DNA backbone. To avoid costly worst-case redundancy for correcting sequencing/rewriting errors and to mitigate issues associated with mismatched decoding parameters, we develop machine learning techniques for automatic discoloration detection and image inpainting. The 2DDNA platform is experimentally tested by reconstructing a library of images with undetectable or small visual degradation after readout processing, and by erasing and rewriting copyright metadata encoded in nicks. Our results demonstrate that DNA can serve both as a write-once and rewritable memory for heterogenous data and that data can be erased in a permanent, privacy-preserving manner. Moreover, the storage system can be made robust to degrading channel qualities while avoiding global error-correction redundancy.
PI(18:1/18:1) is a SCD1-derived lipokine that limits stress signaling
Authors: Thürmer Maria , Gollowitzer André , Pein Helmut , Neukirch Konstantin , Gelmez Elif , Waltl Lorenz , Wielsch Natalie , Winkler René , Löser Konstantin , Grander Julia , Hotze Madlen , Harder Sönke , Döding Annika , Meßner Martina , Troisi Fabiana , Ardelt Maximilian , Schlüter Hartmut , Pachmayr Johanna , Gutiérrez-Gutiérrez Óscar , Rudolph Karl Lenhard , Thedieck Kathrin , Schulze-Späte Ulrike , González-Estévez Cristina , Kosan Christian , Svatoš Aleš , Kwiatkowski Marcel , Koeberle Andreas 
Published: May 2022

AbstractCytotoxic stress activates stress-activated kinases, initiates adaptive mechanisms, including the unfolded protein response (UPR) and autophagy, and induces programmed cell death. Fatty acid unsaturation, controlled by stearoyl-CoA desaturase (SCD)1, prevents cytotoxic stress but the mechanisms are diffuse. Here, we show that 1,2-dioleoyl-sn-glycero-3-phospho-(1’-myo-inositol) [PI(18:1/18:1)] is a SCD1-derived signaling lipid, which inhibits p38 mitogen-activated protein kinase activation, counteracts UPR, endoplasmic reticulum-associated protein degradation, and apoptosis, regulates autophagy, and maintains cell morphology and proliferation. SCD1 expression and the cellular PI(18:1/18:1) proportion decrease during the onset of cell death, thereby repressing protein phosphatase 2 A and enhancing stress signaling. This counter-regulation applies to mechanistically diverse death-inducing conditions and is found in multiple human and mouse cell lines and tissues of Scd1-defective mice. PI(18:1/18:1) ratios reflect stress tolerance in tumorigenesis, chemoresistance, infection, high-fat diet, and immune aging. Together, PI(18:1/18:1) is a lipokine that links fatty acid unsaturation with stress responses, and its depletion evokes stress signaling.
Nitrogen represses haustoria formation through abscisic acid in the parasitic plant Phtheirospermum japonicum
Authors: Kokla Anna , Leso Martina , Zhang Xiang , Simura Jan , Serivichyaswat Phanu T. , Cui Songkui , Ljung Karin , Yoshida Satoko , Melnyk Charles W. 
Published: May 2022

AbstractParasitic plants are globally prevalent pathogens that withdraw nutrients from their host plants using an organ known as the haustorium. The external environment including nutrient availability affects the extent of parasitism and to understand this phenomenon, we investigated the role of nutrients and found that nitrogen is sufficient to repress haustoria formation in the root parasite Phtheirospermum japonicum. Nitrogen increases levels of abscisic acid (ABA) in P. japonicum and prevents the activation of hundreds of genes including cell cycle and xylem development genes. Blocking ABA signaling overcomes nitrogen’s inhibitory effects indicating that nitrogen represses haustoria formation by increasing ABA. The effect of nitrogen appears more widespread since nitrogen also inhibits haustoria in the obligate root parasite Striga hermonthica. Together, our data show that nitrogen acts as a haustoria repressing factor and suggests a mechanism whereby parasitic plants use nitrogen availability in the external environment to regulate the extent of parasitism.
SpotClean adjusts for spot swapping in spatial transcriptomics data
Authors: Ni Zijian , Prasad Aman , Chen Shuyang , Halberg Richard B. , Arkin Lisa M. , Drolet Beth A. , Newton Michael A. , Kendziorski Christina 
Published: May 2022

AbstractSpatial transcriptomics is a powerful and widely used approach for profiling the gene expression landscape across a tissue with emerging applications in molecular medicine and tumor diagnostics. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind RNA. Ideally, unique molecular identifiers (UMIs) at a spot measure spot-specific expression, but this is often not the case in practice due to bleed from nearby spots, an artifact we refer to as spot swapping. To improve the power and precision of downstream analyses in spatial transcriptomics experiments, we propose SpotClean, a probabilistic model that adjusts for spot swapping to provide more accurate estimates of gene-specific UMI counts. SpotClean provides substantial improvements in marker gene analyses and in clustering, especially when tissue regions are not easily separated. As demonstrated in multiple studies of cancer, SpotClean improves tumor versus normal tissue delineation and improves tumor burden estimation thus increasing the potential for clinical and diagnostic applications of spatial transcriptomics technologies.
Histone functions as a cell-surface receptor for AGEs
Authors: Itakura Masanori , Yamaguchi Kosuke , Kitazawa Roma , Lim Sei-Young , Anan Yusuke , Yoshitake Jun , Shibata Takahiro , Negishi Lumi , Sugawa Hikari , Nagai Ryoji , Uchida Koji 
Published: May 2022

AbstractReducing sugars can covalently react with proteins to generate a heterogeneous and complex group of compounds called advanced glycation end products (AGEs). AGEs are generally considered as pathogenic molecules, mediating a pro-inflammatory response and contributing to the development of a number of human diseases. However, the intrinsic function of AGEs remains to be elucidated. We now provide multiple lines of evidence showing that AGEs can specifically bind histone localized on the cell surface as an AGE-binding protein, regulate the function of histone as a plasminogen receptor, and result in the regulation of monocytes/macrophage recruitment to the site of inflammation. Our finding of histone as a cell-surface receptor for AGEs suggests that, beside our common concept of AGEs as danger-associated molecular patterns mediating a pro-inflammatory response, they may also be involved in the homeostatic response via binding to histone.
Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints
Authors: Li Feiran , Chen Yu , Qi Qi , Wang Yanyan , Yuan Le , Huang Mingtao , Elsemman Ibrahim E. , Feizi Amir , Kerkhoven Eduard J. , Nielsen Jens 
Published: May 2022

AbstractEukaryotic cells are used as cell factories to produce and secrete multitudes of recombinant pharmaceutical proteins, including several of the current top-selling drugs. Due to the essential role and complexity of the secretory pathway, improvement for recombinant protein production through metabolic engineering has traditionally been relatively ad-hoc; and a more systematic approach is required to generate novel design principles. Here, we present the proteome-constrained genome-scale protein secretory model of yeast Saccharomyces cerevisiae (pcSecYeast), which enables us to simulate and explain phenotypes caused by limited secretory capacity. We further apply the pcSecYeast model to predict overexpression targets for the production of several recombinant proteins. We experimentally validate many of the predicted targets for α-amylase production to demonstrate pcSecYeast application as a computational tool in guiding yeast engineering and improving recombinant protein production.
Ag9GaSe6: high-pressure-induced Ag migration causes thermoelectric performance irreproducibility and elimination of such instability
Authors: Liu Jing-Yuan , Chen Ling , Wu Li-Ming 
Published: May 2022

AbstractThe argyrodite Ag9GaSe6 is a newly recognized high-efficiency thermoelectric material with an ultralow thermal conductivity; however, liquid-like Ag atoms are believed to cause poor stability and performance irreproducibility, which was evidenced even after the 1st measurement run. Herein, we demonstrate the abovementioned instability and irreproducibility are caused by standard thermoelectric sample hot-pressing procedure, during which high pressure promotes the 3-fold-coordinated Ag atoms migrate to 4-fold-coordinated sites with higher-chemical potentials. Such instability can be eliminated by a simple annealing treatment, driving the metastable Ag atoms back to the original sites with lower-chemical potentials as revealed by the valence band X-ray photoelectron chemical potential spectra and single crystal X-ray diffraction data. Furthermore, the hot-pressed-annealed samples exhibit great stability and TE property repeatability. Such a stability and repeatability has never been reported before. This discovery will give liquid-like materials great application potential.
Pressured-induced superconducting phase with large upper critical field and concomitant enhancement of antiferromagnetic transition in EuTe2
Authors: Yang P. T. , Liu Z. Y. , Chen K. Y. , Liu X. L. , Zhang X. , Yu Z. H. , Zhang H. , Sun J. P. , Uwatoko Y. , Dong X. L. , Jiang K. , Hu J. P. , Guo Y. F. , Wang B. S. , Cheng J.-G. 
Published: May 2022

AbstractWe report an unusual pressure-induced superconducting state that coexists with an antiferromagnetic ordering of Eu2+ moments and shows a large upper critical field comparable to the Pauli paramagnetic limit in EuTe2. In concomitant with the emergence of superconductivity with Tc ≈ 3–5 K above Pc ≈ 6 GPa, the antiferromagnetic transition temperature TN(P) experiences a quicker rise with the slope increased dramatically from dTN/dP = 0.85(14) K/GPa for P ≤ Pc to 3.7(2) K/GPa for P ≥ Pc. Moreover, the superconducting state can survive in the spin-flop state with a net ferromagnetic component of the Eu2+ sublattice under moderate magnetic fields μ0H ≥ 2 T. Our findings establish the pressurized EuTe2 as a rare magnetic superconductor possessing an intimated interplay between magnetism and superconductivity.
Hypoxia shapes the immune landscape in lung injury and promotes the persistence of inflammation
Authors: Mirchandani Ananda S. , Jenkins Stephen J. , Bain Calum C. , Sanchez-Garcia Manuel A. , Lawson Hannah , Coelho Patricia , Murphy Fiona , Griffith David M. , Zhang Ailiang , Morrison Tyler , Ly Tony , Arienti Simone , Sadiku Pranvera , Watts Emily R. , Dickinson Rebecca. S. , Reyes Leila , Cooper George , Clark Sarah , Lewis David , Kelly Van , Spanos Christos , Musgrave Kathryn M. , Delaney Liam , Harper Isla , Scott Jonathan , Parkinson Nicholas J. , Rostron Anthony J. , Baillie J. Kenneth , Clohisey Sara , Pridans Clare , Campana Lara , Lewis Philip Starkey , Simpson A. John , Dockrell David H. , Schwarze Jürgen , Hirani Nikhil , Ratcliffe Peter J. , Pugh Christopher W. , Kranc Kamil , Forbes Stuart J. , Whyte Moira K. B. , Walmsley Sarah R. 
Published: May 2022

AbstractHypoxemia is a defining feature of acute respiratory distress syndrome (ARDS), an often-fatal complication of pulmonary or systemic inflammation, yet the resulting tissue hypoxia, and its impact on immune responses, is often neglected. In the present study, we have shown that ARDS patients were hypoxemic and monocytopenic within the first 48 h of ventilation. Monocytopenia was also observed in mouse models of hypoxic acute lung injury, in which hypoxemia drove the suppression of type I interferon signaling in the bone marrow. This impaired monopoiesis resulted in reduced accumulation of monocyte-derived macrophages and enhanced neutrophil-mediated inflammation in the lung. Administration of colony-stimulating factor 1 in mice with hypoxic lung injury rescued the monocytopenia, altered the phenotype of circulating monocytes, increased monocyte-derived macrophages in the lung and limited injury. Thus, tissue hypoxia altered the dynamics of the immune response to the detriment of the host and interventions to address the aberrant response offer new therapeutic strategies for ARDS.
A high-speed railway network dataset from train operation records and weather data
Authors: Zhang Dalin , Peng Yunjuan , Xu Yi , Du Chenyue , Zhang Yumei , Wang Nan , Chong Yunhao , Wang Hongwei , Wu Daohua , Liu Jintao , Zhang Hailong , Lu Lingyun , Liu Jiqiang 
Published: May 2022

AbstractHigh-speed train operation data are reliable and rich resources in data-driven research. However, the data released by railway companies are poorly organized and not comprehensive enough to be applied directly and effectively. A public high-speed railway network dataset suitable for research is still lacking. To support the research in large-scale complex network, complex dynamic system and intelligent transportation, we develop a high-speed railway network dataset, containing the train operation data in different directions from October 8, 2019 to January 27, 2020, the train delay data of the railway stations, the junction stations data, and the mileage data of adjacent stations. In the dataset, weather, temperature, wind power and major holidays are considered as factors affecting train operation. Potential research values of the dataset include but are not limited to complex dynamic system pattern mining, community detection and discovery, and train delay analysis. Besides, the dataset can be used to solve various railway operation and management problems, such as passenger service network improvement, train real-time dispatching and intelligent driving assistance.
Underwater image restoration with Haar wavelet transform and ensemble of triple correction algorithms using Bootstrap aggregation and random forests
Authors: Rowghanian Vahid 
Published: May 2022

AbstractThis paper presents both a new strategy for traditional underwater image restoration using Haar wavelet transform as well as a new learned model that generates an ensemble of triple correction algorithm labels based on histogram quadrants’ cumulative distribution feature instead of generating pixel intensities. The Haar wavelet transform is our tentative dynamic stretching plan that is applied on the input image and its contrast stretched image to generate the degraded wavelet coefficients which are blended using Gaussian pyramid of the saliency weights to restore the original image. The ensemble of triple corrections exerts three color correction algorithms sequentially on the degraded image for restoration. The ensemble of algorithms entails the superposition effect of the red channel mean shifting, global RGB adaptation, global luminance adaptation, global saturation adaptation, luminance stretching, saturation stretching, contrast stretching, adaptive Gamma correction for red spectrum, even to odd middle intensity transference using look-up table, green to red spectrum transference using histogram equalization, local brightening, Dark Channel Prior, fusion restoration, and our Haar wavelet transform restoration. The source is available at https://github.com/vahidr213/Underwater-Image-Restoration-And-Enhancement-Collection.