bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modification of Microphysical Parameterization Schemes and Their Application in the Simulation of an Extremely Heavy Rainfall Event in Zhengzhou
Authors: Yin Lei , Ping Fan , Cheng Rui , Mao Jiahua 
Published: January 2024

AbstractIn the present study, the Morrison and Thompson microphysics schemes in the Weather Research and Forecasting model were improved and used to simulate a record‐breaking heavy rainfall event occurred in Henan Province over central China during 19–21 July 2021. In the modified schemes, the terminal velocity of graupel and initial cloud droplet concentration were adjusted based on sensitivity tests. Results showed that the modified Morrison scheme (MORR_MOD) better captured the spatial distribution and temporal evolution of precipitation than the original scheme (MORR). Specifically, it produced a 40‐hr cumulative rainfall amount of 963 mm and an extreme hourly rainfall rate of 157.7 mm, which were closer to observations than MORR. Analysis of the dynamic and microphysical structures of the extreme‐rain‐producing convective clusters revealed that MORR_MOD predicted stronger updrafts, higher rain mass content and larger mean mass diameter of raindrops than MORR. By analyzing the tendencies of rain mass and number concentration, it was found that MORR_MOD predicted stronger accretion rates of cloud droplets by rain and weaker auto‐conversion rates of cloud droplets than MORR, which contributed to the high rain mixing ratio and low number concentration, respectively. In addition, MORR_MOD predicted stronger diabatic heating rates than MORR, which were primarily attributed to stronger condensation of water vapor, and may have been the reason why MORR_MOD simulated stronger updrafts.
Dune Geometry and the Associated Hydraulic Roughness in the Fluvial to Tidal Transition Zone of the Fraser River at Low River Flow
Authors: de Lange S. I. , Bradley R. , Schrijvershof R. A. , Murphy D. , Waldschläger K. , Kostaschuk R. , Venditti J. G. , Hoitink A. J. F. 
Published: January 2024

AbstractIn deltas and estuaries throughout the world, a fluvial‐to‐tidal transition zone (FTTZ) exists where both the river discharge and the tidal motion drive the flow. It is unclear how dune characteristics are impacted by changes in tidal flow strength, and how this is reflected in the hydraulic roughness. To understand dune geometry and variability in the FTTZ and possible impacts on hydraulic roughness, we assess dune variability from multibeam bathymetric surveys, and we use a calibrated 2D hydrodynamic model (Delft3D‐FM) of a sand‐bedded lowland river (Fraser River, Canada). We focus on a period of low river discharge during which tidal impact is strong. We find that the fluvial‐tidal to tidal regime change is not directly reflected in dune height, but local patterns of increasing and decreasing dune height are present. The fluvial‐to‐tidal regime change is reflected in dune shape, where dunes have lower leeside angles and are more symmetrical in the tidal regime. The calibrated model allows to estimate local patterns of dune heights using tidally averaged values of bed shear stress. However, the spatially variable dune morphology hampers local dune height estimation. Changes in dune shape do not significantly impact the reach‐scale roughness, and estimated dune roughness using dune height and length is similar to the dune roughness inferred from model calibration. Hydraulic model performance with a calibrated, constant roughness is not improved by implementing dune‐derived bed roughness. Instead, the data analysis revealed that large‐scale river morphology may explain differences in model roughness and corresponding estimates from dune predictors.
RUNX1/NPM1/H3K4me3 complex contributes to extracellular matrix remodeling via enhancing FOSL2 transcriptional activation in glioblastoma
Authors: Cui Xiaoteng , Huo Dawei , Wang Qixue , Wang Yunfei , Liu Xiaomin , Zhao Kai , You Yongping , Zhang Junxia , Kang Chunsheng 
Published: January 2024

AbstractExtracellular matrix (ECM) remodeling has been implicated in the tumor malignant progression and immune escape in glioblastoma (GBM). Runt-related transcription factor 1 (RUNX1) is a vital transcriptional factor for promoting tumorigenesis and invasion in mesenchymal subtype of GBM. But the correlation between RUNX1 and ECM genes expression and regulatory mechanism of RUNX1 on ECM genes expression remain poorly understood to date. In this study, by using integral analysis of chromatin immunoprecipitation-sequencing and RNA sequencing, we reported that RUNX1 positively regulated the expression of various ECM-related genes, including Fibronectin 1 (FN1), Collagen type IV alpha 1 chain (COL4A1), and Lumican (LUM), in GBM. Mechanistically, we demonstrated that RUNX1 interacted with Nucleophosmin 1 (NPM1) to maintain the chromatin accessibility and facilitate FOS Like 2, AP-1 Transcription Factor Subunit (FOSL2)-mediated transcriptional activation of ECM-related genes, which was independent of RUNX1’s transcriptional function. ECM remodeling driven by RUNX1 promoted immunosuppressive microenvironment in GBM. In conclusion, this study provides a novel mechanism of RUNX1 binding to NPM1 in driving the ECM remodeling and GBM progression.
Id2 epigenetically controls CD8+ T-cell exhaustion by disrupting the assembly of the Tcf3-LSD1 complex
Authors: Li Yiming , Han Mingwei , Wei Haolin , Huang Wan , Chen Zhinan , Zhang Tianjiao , Qian Meirui , Jing Lin , Nan Gang , Sun Xiuxuan , Dai Shuhui , Wang Kun , Jiang Jianli , Zhu Ping , Chen Liang 
Published: January 2024

AbstractCD8+ T-cell exhaustion is a state of dysfunction that promotes tumor progression and is marked by the generation of Slamf6+ progenitor exhausted (Texprog) and Tim-3+ terminally exhausted (Texterm) subpopulations. Inhibitor of DNA binding protein 2 (Id2) has been shown to play important roles in T-cell development and CD8+ T-cell immunity. However, the role of Id2 in CD8+ T-cell exhaustion is unclear. Here, we found that Id2 transcriptionally and epigenetically regulates the generation of Texprog cells and their conversion to Texterm cells. Genetic deletion of Id2 dampens CD8+ T-cell-mediated immune responses and the maintenance of stem-like CD8+ T-cell subpopulations, suppresses PD-1 blockade and increases tumor susceptibility. Mechanistically, through its HLH domain, Id2 binds and disrupts the assembly of the Tcf3-Tal1 transcriptional regulatory complex, and thus modulates chromatin accessibility at the Slamf6 promoter by preventing the interaction of Tcf3 with the histone lysine demethylase LSD1. Therefore, Id2 increases the abundance of the permissive H3K4me2 mark on the Tcf3-occupied E-boxes in the Slamf6 promoter, modulates chromatin accessibility at the Slamf6 promoter and epigenetically regulates the generation of Slamf6+ Texprog cells. An LSD1 inhibitor GSK2879552 can rescue the Id2 knockout phenotype in tumor-bearing mice. Inhibition of LSD1 increases the abundance of Slamf6+Tim-3− Texprog cells in tumors and the expression level of Tcf1 in Id2-deleted CD8+ T cells. This study demonstrates that Id2-mediated transcriptional and epigenetic modification drives hierarchical CD8+ T-cell exhaustion, and the mechanistic insights gained may have implications for therapeutic intervention with tumor immune evasion.
IMA peptides regulate root nodulation and nitrogen homeostasis by providing iron according to internal nitrogen status
Authors: Ito Momoyo , Tajima Yuri , Ogawa-Ohnishi Mari , Nishida Hanna , Nosaki Shohei , Noda Momona , Sotta Naoyuki , Kawade Kensuke , Kamiya Takehiro , Fujiwara Toru , Matsubayashi Yoshikatsu , Suzaki Takuya 
Published: January 2024

AbstractLegumes control root nodule symbiosis (RNS) in response to environmental nitrogen availability. Despite the recent understanding of the molecular basis of external nitrate-mediated control of RNS, it remains mostly elusive how plants regulate physiological processes depending on internal nitrogen status. In addition, iron (Fe) acts as an essential element that enables symbiotic nitrogen fixation; however, the mechanism of Fe accumulation in nodules is poorly understood. Here, we focus on the transcriptome in response to internal nitrogen status during RNS in Lotus japonicus and identify that IRON MAN (IMA) peptide genes are expressed during symbiotic nitrogen fixation. We show that LjIMA1 and LjIMA2 expressed in the shoot and root play systemic and local roles in concentrating internal Fe to the nodule. Furthermore, IMA peptides have conserved roles in regulating nitrogen homeostasis by adjusting nitrogen-Fe balance in L. japonicus and Arabidopsis thaliana. These findings indicate that IMA-mediated Fe provision plays an essential role in regulating nitrogen-related physiological processes.
Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction
Authors: Sun Haofan , Fu Bin , Qian Xiaohong , Xu Ping , Qin Weijie 
Published: January 2024

AbstractThe key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221 nuclear RBPs and 1333 cytoplasmic RBPs were enriched and identified using nuclear/cytoplasm targeting enrichment probes, representing an increase of 54.4% and 85.7% compared with previous reports. The probes were further applied in the omics-level investigation of subcellular-specific RBP-RNA interactions upon ferroptosis induction. Interestingly, large-scale RBPs display enhanced interaction with RNAs in nucleus but reduced association with RNAs in cytoplasm during ferroptosis process. Furthermore, we discovered dozens of nucleoplasmic translocation candidate RBPs upon ferroptosis induction and validated representative ones by immunofluorescence imaging. The enrichment of Tricarboxylic acid cycle in the translocation candidate RBPs may provide insights for investigating their possible roles in ferroptosis induced metabolism dysregulation.
Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies
Authors: Medina-Munoz Hugo C. , Kofman Eric , Jagannatha Pratibha , Boyle Evan A. , Yu Tao , Jones Krysten L. , Mueller Jasmine R. , Lykins Grace D. , Doudna Andrew T. , Park Samuel S. , Blue Steven M. , Ranzau Brodie L. , Kohli Rahul M. , Komor Alexis C. , Yeo Gene W. 
Published: January 2024

AbstractRNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.
Strain-restricted transfer of ferromagnetic electrodes for constructing reproducibly superior-quality spintronic devices
Authors: Guo Lidan , Gu Xianrong , Hu Shunhua , Sun Wenchao , Zhang Rui , Qin Yang , Meng Ke , Lu Xiangqian , Liu Yayun , Wang Jiaxing , Ma Peijie , Zhang Cheng , Guo Ankang , Yang Tingting , Yang Xueli , Wang Guorui , Liu Yaling , Wang Kai , Mi Wenbo , Zhang Chuang , Jiang Lang , Liu Luqi , Zheng Kun , Qin Wei , Yan Wenjing , Sun Xiangnan 
Published: January 2024

AbstractSpintronic device is the fundamental platform for spin-related academic and practical studies. However, conventional techniques with energetic deposition or boorish transfer of ferromagnetic metal inevitably introduce uncontrollable damage and undesired contamination in various spin-transport-channel materials, leading to partially attenuated and widely distributed spintronic device performances. These issues will eventually confuse the conclusions of academic studies and limit the practical applications of spintronics. Here we propose a polymer-assistant strain-restricted transfer technique that allows perfectly transferring the pre-patterned ferromagnetic electrodes onto channel materials without any damage and change on the properties of magnetism, interface, and channel. This technique is found productive for pursuing superior-quality spintronic devices with high controllability and reproducibility. It can also apply to various-kind (organic, inorganic, organic-inorganic hybrid, or carbon-based) and diverse-morphology (smooth, rough, even discontinuous) channel materials. This technique can be very useful for reliable device construction and will facilitate the technological transition of spintronic study.
Accurate additive manufacturing of lightweight and elastic carbons using plastic precursors
Authors: Smith Paul , Hu Jiayue , Griffin Anthony , Robertson Mark , Güillen Obando Alejandro , Bounds Ethan , Dunn Carmen B. , Ye Changhuai , Liu Ling , Qiang Zhe 
Published: January 2024

AbstractDespite groundbreaking advances in the additive manufacturing of polymers, metals, and ceramics, scaled and accurate production of structured carbons remains largely underdeveloped. This work reports a simple method to produce complex carbon materials with very low dimensional shrinkage from printed to carbonized state (less than 4%), using commercially available polypropylene precursors and a fused filament fabrication-based process. The control of macrostructural retention is enabled by the inclusion of fiber fillers regardless of the crosslinking degree of the polypropylene matrix, providing a significant advantage to directly control the density, porosity, and mechanical properties of 3D printed carbons. Using the same printed plastic precursors, different mechanical responses of derived carbons can be obtained, notably from stiff to highly compressible. This report harnesses the power of additive manufacturing for producing carbons with accurately controlled structure and properties, while enabling great opportunities for various applications.
Defect passivation in methylammonium/bromine free inverted perovskite solar cells using charge-modulated molecular bonding
Authors: Khadka Dhruba B. , Shirai Yasuhiro , Yanagida Masatoshi , Ota Hitoshi , Lyalin Andrey , Taketsugu Tetsuya , Miyano Kenjiro 
Published: January 2024

AbstractMolecular passivation is a prominent approach for improving the performance and operation stability of halide perovskite solar cells (HPSCs). Herein, we reveal discernible effects of diammonium molecules with either an aryl or alkyl core onto Methylammonium-free perovskites. Piperazine dihydriodide (PZDI), characterized by an alkyl core-electron cloud-rich-NH terminal, proves effective in mitigating surface and bulk defects and modifying surface chemistry or interfacial energy band, ultimately leading to improved carrier extraction. Benefiting from superior PZDI passivation, the device achieves an impressive efficiency of 23.17% (area ~1 cm2) (low open circuit voltage deficit ~0.327 V) along with superior operational stability. We achieve a certified efficiency of ~21.47% (area ~1.024 cm2) for inverted HPSC. PZDI strengthens adhesion to the perovskite via -NH2I and Mulliken charge distribution. Device analysis corroborates that stronger bonding interaction attenuates the defect densities and suppresses ion migration. This work underscores the crucial role of bifunctional molecules with stronger surface adsorption in defect mitigation, setting the stage for the design of charge-regulated molecular passivation to enhance the performance and stability of HPSC.
Nanoscale visualization and spectral fingerprints of the charge order in ScV6Sn6 distinct from other kagome metals
Authors: Cheng Siyu , Ren Zheng , Li Hong , Oh Ji Seop , Tan Hengxin , Pokharel Ganesh , DeStefano Jonathan M. , Rosenberg Elliott , Guo Yucheng , Zhang Yichen , Yue Ziqin , Lee Yongbin , Gorovikov Sergey , Zonno Marta , Hashimoto Makoto , Lu Donghui , Ke Liqin , Mazzola Federico , Kono Junichiro , Birgeneau R. J. , Chu Jiun-Haw , Wilson Stephen D. , Wang Ziqiang , Yan Binghai , Yi Ming , Zeljkovic Ilija 
Published: January 2024

AbstractCharge density waves (CDWs) in kagome metals have been tied to many exotic phenomena. Here, using spectroscopic-imaging scanning tunneling microscopy and angle-resolved photoemission spectroscopy, we study the charge order in kagome metal ScV6Sn6. The similarity of electronic band structures of ScV6Sn6 and TbV6Sn6 (where charge ordering is absent) suggests that charge ordering in ScV6Sn6 is unlikely to be primarily driven by Fermi surface nesting of the Van Hove singularities. In contrast to the CDW state of cousin kagome metals, we find no evidence supporting rotation symmetry breaking. Differential conductance dI/dV spectra show a partial gap Δ1CO ≈ 20 meV at the Fermi level. Interestingly, dI/dV maps reveal that charge modulations exhibit an abrupt phase shift as a function of energy at energy much higher than Δ1CO, which we attribute to another spectral gap. Our experiments reveal a distinctive nature of the charge order in ScV6Sn6 with fundamental differences compared to other kagome metals.
An architecture for collaboration in systems biology at the age of the Metaverse
Authors: Jacopin Eliott , Sakamoto Yuki , Nishida Kozo , Kaizu Kazunari , Takahashi Koichi 
Published: January 2024

AbstractAs the current state of the Metaverse is largely driven by corporate interests, which may not align with scientific goals and values, academia should play a more active role in its development. Here, we present the challenges and solutions for building a Metaverse that supports systems biology research and collaboration. Our solution consists of two components: Kosmogora, a server ensuring biological data access, traceability, and integrity in the context of a highly collaborative environment such as a metaverse; and ECellDive, a virtual reality application to explore, interact, and build upon the data managed by Kosmogora. We illustrate the synergy between the two components by visualizing a metabolic network and its flux balance analysis. We also argue that the Metaverse of systems biology will foster closer communication and cooperation between experimentalists and modelers in the field.
Geographical location influence ‘Cabernet Franc’ fruit quality in Shandong province
Authors: Wang Chaoping , Chen Xueqin , Ren Yanhua , Xuan Xuxian , Pervaiz Tariq , Shangguan Lingfei , Fang Jinggui 
Published: January 2024

AbstractGrape quality is a key factor in determining wine quality, and it depends not only on management skills, but also on the geographic location of the producing area. In China, Shandong is the province with the largest wine production, and ‘Cabernet Franc’ is widely planted. This study evaluated the ‘Cabernet Franc’ fruit quality in relation to geographical conditions in five ‘Cabernet Franc’ producing districts of Shandong province, China, including Dezhou Aodeman Winery (DZ), Tai’an Zhongqingsongshi Winery (TA), Penglai Longhu Winery (PL), Rushan Taiyihu Winery (RS), and Rizhao Taiyangcheng Winery (RZ). At the time of veraison and maturity, fruit was harvested from five areas, and compared for cosmetic and internal fruit quality. The soluble sugar content in the Rizhao area was rich, and the weight and volume of single fruit were relatively large. The titratable acid of the berries in Tai'an area was high. RNA-seq analysis showed that the number of genes in the véraison stage was 19,571–20,750, and the number of genes in the mature stage was 19,176–20,735. The analysis found that areas with multiple high-quality characteristics tended to have more DEGs (differential expressed genes). And the DEGs in different areas were mainly distributed on chromosome 7, and at least on chromosome 15. DEGs in 5 areas were enriched on 855 GO terms and 116 KEGG pathways during berries development. Among them, it was found that the up/down-regulation of DEGs was related to the formation of berry quality, which helps to explain the impact of environment on grape quality components. In summary, this study is helpful to understand the influence of cultivation location on the quality of 'Cabernet Franc' in different production areas in Shandong province, and further provide a reference for the production of high-quality wine grapes and winemaking.
Assessing perceptual chromatic equiluminance using a reflexive pupillary response
Authors: Liu Ye , Mahony Bridget W. , Wang Xiaochun , Daye Pierre M. , Wang Wei , Cavanagh Patrick , Pouget Pierre , Andolina Ian Max 
Published: January 2024

AbstractEquiluminant stimuli help assess the integrity of colour perception and the relationship of colour to other visual features. As a result of individual variation, it is necessary to calibrate experimental visual stimuli to suit each individual’s unique equiluminant ratio. Most traditional methods rely on training observers to report their subjective equiluminance point. Such paradigms cannot easily be implemented on pre-verbal or non-verbal observers. Here, we present a novel Pupil Frequency-Tagging Method (PFTM) for detecting a participant’s unique equiluminance point without verbal instruction and with minimal training. PFTM analyses reflexive pupil oscillations induced by slow (< 2 Hz) temporal alternations between coloured stimuli. Two equiluminant stimuli will induce a similar pupil dilation response regardless of colour; therefore, an observer’s equiluminant point can be identified as the luminance ratio between two colours for which the oscillatory amplitude of the pupil at the tagged frequency is minimal. We compared pupillometry-based equiluminance ratios to those obtained with two established techniques in humans: minimum flicker and minimum motion. In addition, we estimated the equiluminance point in non-human primates, demonstrating that this new technique can be successfully employed in non-verbal subjects.
A cost-effective RNA extraction and RT-qPCR approach to detect California serogroup viruses from pooled mosquito samples
Authors: Avramov Marc , Gallo Vanessa , Gross Antonia , Lapen David R. , Ludwig Antoinette , Cullingham Catherine I. 
Published: January 2024

AbstractMosquito-borne diseases pose ongoing global health concerns, demanding more cost-efficient methods to detect pathogens to support enhanced surveillance efforts. This study introduces an adapted TRIzol-based high-throughput RNA extraction protocol, tailored for the detection of California serogroup viruses in pooled mosquito samples in a rapid and cost-effective manner. This approach provided consistent RNA yields and sensitive viral detection relative to two commercial extraction kits (QIAGEN RNeasy Mini Kit and MACHEREY–NAGEL NucleoSpin RNA Plus Kit). The incorporation of a user-friendly and non-spiking-based RT-qPCR internal control designed for the 18S rRNA gene in mosquitoes minimizes potential false positives/negatives, improving the fidelity of viral detection outcomes. Effective RNA yields, purity, and successful target amplification across 25 mosquito species and varied pool sizes (1–50 mosquitoes per tube) affirm the reliability of our approach. The extraction method is cost-effective, with an incurred cost of $0.58 CAD per sample, in contrast to the $5.25 CAD cost per sample of the two kits, rendering it promising for mosquito-borne disease surveillance initiatives.