bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays
Authors: Blombach Fabian , Sýkora Michal , Case Jo , Feng Xu , Baquero Diana P. , Fouqueau Thomas , Phung Duy Khanh , Barker Declan , Krupovic Mart , She Qunxin , Werner Finn 
Published: February 2024

AbstractCRISPR arrays form the physical memory of CRISPR adaptive immune systems by incorporating foreign DNA as spacers that are often AT-rich and derived from viruses. As promoter elements such as the TATA-box are AT-rich, CRISPR arrays are prone to harbouring cryptic promoters. Sulfolobales harbour extremely long CRISPR arrays spanning several kilobases, a feature that is accompanied by the CRISPR-specific transcription factor Cbp1. Aberrant Cbp1 expression modulates CRISPR array transcription, but the molecular mechanisms underlying this regulation are unknown. Here, we characterise the genome-wide Cbp1 binding at nucleotide resolution and characterise the binding motifs on distinct CRISPR arrays, as well as on unexpected non-canonical binding sites associated with transposons. Cbp1 recruits Cren7 forming together ‘chimeric’ chromatin-like structures at CRISPR arrays. We dissect Cbp1 function in vitro and in vivo and show that the third helix-turn-helix domain is responsible for Cren7 recruitment, and that Cbp1-Cren7 chromatinization plays a dual role in the transcription of CRISPR arrays. It suppresses spurious transcription from cryptic promoters within CRISPR arrays but enhances CRISPR RNA transcription directed from their cognate promoters in their leader region. Our results show that Cbp1-Cren7 chromatinization drives the productive expression of long CRISPR arrays.
Noncanonical function of folate through folate receptor 1 during neural tube formation
Authors: Balashova Olga A. , Panoutsopoulos Alexios A. , Visina Olesya , Selhub Jacob , Knoepfler Paul S. , Borodinsky Laura N. 
Published: February 2024

AbstractFolate supplementation reduces the occurrence of neural tube defects (NTDs), birth defects consisting in the failure of the neural tube to form and close. The mechanisms underlying NTDs and their prevention by folate remain unclear. Here we show that folate receptor 1 (FOLR1) is necessary for the formation of neural tube-like structures in human-cell derived neural organoids. FOLR1 knockdown in neural organoids and inXenopus laevisembryos leads to NTDs that are rescued by pteroate, a folate precursor that is unable to participate in metabolism. We demonstrate that FOLR1 interacts with and opposes the function of CD2-associated protein, molecule essential for apical endocytosis and turnover of C-cadherin in neural plate cells. In addition, folates increase Ca2+transient frequency, suggesting that folate and FOLR1 signal intracellularly to regulate neural plate folding. This study identifies a mechanism of action of folate distinct from its vitamin function during neural tube formation.
Unveiling the nature of Pt-induced anti-deactivation of Ru for alkaline hydrogen oxidation reaction
Authors: Fang Yanyan , Wei Cong , Bian Zenan , Yin Xuanwei , Liu Bo , Liu Zhaohui , Chi Peng , Xiao Junxin , Song Wanjie , Niu Shuwen , Tang Chongyang , Liu Jun , Ge Xiaolin , Xu Tongwen , Wang Gongming 
Published: February 2024

AbstractWhile Ru owns superior catalytic activity toward hydrogen oxidation reaction and cost advantages, the catalyst deactivation under high anodic potential range severely limits its potential to replace the Pt benchmark catalyst. Unveiling the deactivation mechanism of Ru and correspondingly developing protection strategies remain a great challenge. Herein, we develop atomic Pt-functioned Ru nanoparticles with excellent anti-deactivation feature and meanwhile employ advanced operando characterization tools to probe the underlying roles of Pt in the anti-deactivation. Our studies reveal the introduced Pt single atoms effectively prevent Ru from oxidative passivation and consequently preserve the interfacial water network for the critical H* oxidative release during catalysis. Clearly understanding the deactivation nature of Ru and Pt-induced anti-deactivation under atomic levels could provide valuable insights for rationally designing stable Ru-based catalysts for hydrogen oxidation reaction and beyond.
Reactive aldehyde chemistry explains the missing source of hydroxyl radicals
Authors: Yang Xinping , Wang Haichao , Lu Keding , Ma Xuefei , Tan Zhaofeng , Long Bo , Chen Xiaorui , Li Chunmeng , Zhai Tianyu , Li Yang , Qu Kun , Xia Yu , Zhang Yuqiong , Li Xin , Chen Shiyi , Dong Huabin , Zeng Limin , Zhang Yuanhang 
Published: February 2024

AbstractHydroxyl radicals (OH) determine the tropospheric self-cleansing capacity, thus regulating air quality and climate. However, the state-of-the-art mechanisms still underestimate OH at low nitrogen oxide and high volatile organic compound regimes even considering the latest isoprene chemistry. Here we propose that the reactive aldehyde chemistry, especially the autoxidation of carbonyl organic peroxy radicals (R(CO)O2) derived from higher aldehydes, is a noteworthy OH regeneration mechanism that overwhelms the contribution of the isoprene autoxidation, the latter has been proved to largely contribute to the missing OH source under high isoprene condition. As diagnosed by the quantum chemical calculations, the R(CO)O2 radicals undergo fast H-migration to produce unsaturated hydroperoxyl-carbonyls that generate OH through rapid photolysis. This chemistry could explain almost all unknown OH sources in areas rich in both natural and anthropogenic emissions in the warm seasons, and may increasingly impact the global self-cleansing capacity in a future low nitrogen oxide society under carbon neutrality scenarios.
Euglena’s atypical respiratory chain adapts to the discoidal cristae and flexible metabolism
Authors: He Zhaoxiang , Wu Mengchen , Tian Hongtao , Wang Liangdong , Hu Yiqi , Han Fangzhu , Zhou Jiancang , Wang Yong , Zhou Long 
Published: February 2024

AbstractEuglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron transport chain. While structures of the electron transport chain complexes and supercomplexes of most other eukaryotic clades have been reported, no similar structure is currently available for Discoba, limiting the understandings of its core metabolism and leaving a gap in the evolutionary tree of eukaryotic bioenergetics. Here, we report high-resolution cryo-EM structures of Euglena’s respirasome I + III2 + IV and supercomplex III2 + IV2. A previously unreported fatty acid synthesis domain locates on the tip of complex I’s peripheral arm, providing a clear picture of its atypical subunit composition identified previously. Individual complexes are re-arranged in the respirasome to adapt to the non-uniform membrane curvature of the discoidal cristae. Furthermore, Euglena’s conformationally rigid complex I is deactivated by restricting ubiquinone’s access to its substrate tunnel. Our findings provide structural insights for therapeutic developments against euglenozoan parasite infections.
Hyperbolic photonic topological insulators
Authors: Huang Lei , He Lu , Zhang Weixuan , Zhang Huizhen , Liu Dongning , Feng Xue , Liu Fang , Cui Kaiyu , Huang Yidong , Zhang Wei , Zhang Xiangdong 
Published: February 2024

AbstractTopological photonics provides a new degree of freedom to robustly control electromagnetic fields. To date, most of established topological states in photonics have been employed in Euclidean space. Motivated by unique properties of hyperbolic lattices, which are regular tessellations in non-Euclidean space with a constant negative curvature, the boundary-dominated hyperbolic topological states have been proposed. However, limited by highly crowded boundary resonators and complicated site couplings, the hyperbolic topological insulator has only been experimentally constructed in electric circuits. How to achieve hyperbolic photonic topological insulators is still an open question. Here, we report the experimental realization of hyperbolic photonic topological insulators using coupled ring resonators on silicon chips. Boundary-dominated one-way edge states with pseudospin-dependent propagation directions have been observed. Furthermore, the robustness of edge states in hyperbolic photonic topological insulators is also verified. Our findings have potential applications in the field of designing high-efficient topological photonic devices with enhanced boundary responses.
scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data
Authors: Tang Songming , Cui Xuejian , Wang Rongxiang , Li Sijie , Li Siyu , Huang Xin , Chen Shengquan 
Published: February 2024

AbstractSingle-cell chromatin accessibility sequencing (scCAS) has emerged as a valuable tool for interrogating and elucidating epigenomic heterogeneity and gene regulation. However, scCAS data inherently suffers from limitations such as high sparsity and dimensionality, which pose significant challenges for downstream analyses. Although several methods are proposed to enhance scCAS data, there are still challenges and limitations that hinder the effectiveness of these methods. Here, we propose scCASE, a scCAS data enhancement method based on non-negative matrix factorization which incorporates an iteratively updating cell-to-cell similarity matrix. Through comprehensive experiments on multiple datasets, we demonstrate the advantages of scCASE over existing methods for scCAS data enhancement. The interpretable cell type-specific peaks identified by scCASE can provide valuable biological insights into cell subpopulations. Moreover, to leverage the large compendia of available omics data as a reference, we further expand scCASE to scCASER, which enables the incorporation of external reference data to improve enhancement performance.
Non-volatile rippled-assisted optoelectronic array for all-day motion detection and recognition
Authors: Pang Xingchen , Wang Yang , Zhu Yuyan , Zhang Zhenhan , Xiang Du , Ge Xun , Wu Haoqi , Jiang Yongbo , Liu Zizheng , Liu Xiaoxian , Liu Chunsen , Hu Weida , Zhou Peng 
Published: February 2024

AbstractIn-sensor processing has the potential to reduce the energy consumption and hardware complexity of motion detection and recognition. However, the state-of-the-art all-in-one array integration technologies with simultaneous broadband spectrum image capture (sensory), image memory (storage) and image processing (computation) functions are still insufficient. Here, macroscale (2 × 2 mm2) integration of a rippled-assisted optoelectronic array (18 × 18 pixels) for all-day motion detection and recognition. The rippled-assisted optoelectronic array exhibits remarkable uniformity in the memory window, optically stimulated non-volatile positive and negative photoconductance. Importantly, the array achieves an extensive optical storage dynamic range exceeding 106, and exceptionally high room-temperature mobility up to 406.7 cm2 V−1 s−1, four times higher than the International Roadmap for Device and Systems 2028 target. Additionally, the spectral range of each rippled-assisted optoelectronic processor covers visible to near-infrared (405 nm–940 nm), achieving function of motion detection and recognition.
Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication
Authors: Feng Xiao , Chen Qipian , Wu Weihong , Wang Jiexin , Li Guohong , Xu Shaohua , Shao Shao , Liu Min , Zhong Cairong , Wu Chung-I , Shi Suhua , He Ziwen 
Published: February 2024

AbstractWhole-genome duplication (WGD), or polyploidy, events are widespread and significant in the evolutionary history of angiosperms. However, empirical evidence for rediploidization, the major process where polyploids give rise to diploid descendants, is still lacking at the genomic level. Here we present chromosome-scale genomes of the mangrove tree Sonneratia alba and the related inland plant Lagerstroemia speciosa. Their common ancestor has experienced a whole-genome triplication (WGT) approximately 64 million years ago coinciding with a period of dramatic global climate change. Sonneratia, adapting mangrove habitats, experienced extensive chromosome rearrangements post-WGT. We observe the WGT retentions display sequence and expression divergence, suggesting potential neo- and sub-functionalization. Strong selection acting on three-copy retentions indicates adaptive value in response to new environments. To elucidate the role of ploidy changes in genome evolution, we improve a model of the polyploidization–rediploidization process based on genomic evidence, contributing to the understanding of adaptive evolution during climate change.
Nature’s contribution to poverty alleviation, human wellbeing and the SDGs
Authors: Poudyal Mahesh , Kraft Franziska , Wells Geoff , Das Anamika , Attiwilli Suman , Schreckenberg Kate , Lele Sharachchandra , Daw Tim , Torres-Vitolas Carlos , Setty Siddappa , Adams Helen , Ahmad Sate , Ryan Casey , Fisher Janet , Robinson Brian , Jones Julia P. G. , Homewood Katherine , Bluwstein Jevgeniy , Keane Aidan , Macamo Celia , Mugi Lilian Mwihaki 
Published: February 2024

AbstractMillions of households globally rely on uncultivated ecosystems for their livelihoods. However, much of the understanding about the broader contribution of uncultivated ecosystems to human wellbeing is still based on a series of small-scale studies due to limited availability of large-scale datasets. We pooled together 11 comparable datasets comprising 232 settlements and 10,971 households in ten low-and middle-income countries, representing forest, savanna and coastal ecosystems to analyse how uncultivated nature contributes to multi-dimensional wellbeing and how benefits from nature are distributed between households. The resulting dataset integrates secondary data on rural livelihoods, multidimensional human wellbeing, household demographics, resource tenure and social-ecological context, primarily drawing on nine existing household surveys and their associated contextual information together with selected variables, such as travel time to cities, population density, local area GDP and land use and land cover from existing global datasets. This integrated dataset has been archived with ReShare (UK Data Service) and will be useful for further analyses on nature-wellbeing relationships on its own or in combination with similar datasets.
Ground far-red sun-induced chlorophyll fluorescence and vegetation indices in the US Midwestern agroecosystems
Authors: Wu Genghong , Guan Kaiyu , Kimm Hyungsuk , Miao Guofang , Yang Xi , Jiang Chongya 
Published: February 2024

AbstractSun-induced chlorophyll fluorescence (SIF) provides an opportunity to study terrestrial ecosystem photosynthesis dynamics. However, the current coarse spatiotemporal satellite SIF products are challenging for mechanistic interpretations of SIF signals. Long-term ground SIF and vegetation indices (VIs) are important for satellite SIF validation and mechanistic understanding of the relationship between SIF and photosynthesis when combined with leaf- and canopy-level auxiliary measurements. In this study, we present and analyze a total of 15 site-years of ground far-red SIF (SIF at 760 nm, SIF760) and VIs datasets from soybean, corn, and miscanthus grown in the U.S. Corn Belt from 2016 to 2021. We introduce a comprehensive data processing protocol, including different retrieval methods, calibration coefficient adjustment, and nadir SIF footprint upscaling to match the eddy covariance footprint. This long-term ground far-red SIF and VIs dataset provides important and first-hand data for far-red SIF interpretation and understanding the mechanistic relationship between far-red SIF and canopy photosynthesis across various crop species and environmental conditions.
Plaque heterogeneity and the spatial distributions of its components dictate drug-coated balloon therapy
Authors: Sarifuddin  , Mandal Prashanta Kumar 
Published: February 2024

AbstractDrug-coated balloon (DCB) angioplasty is one of the potential approaches to alleviating in-stent restenosis and treating peripheral artery disease. An in-silico model has been developed for sirolimus drug eluted from an inflated balloon in a patient-specific arterial cross-section consisting of fibrous tissue, fibrofatty tissue, dense calcium, necrotic core, and healthy tissue. The convection-diffusion-reaction equation represents the transport of drug, while drug binding, both specific and non-specific, can be modelled as a reaction process. The Brinkman equations describe the interstitial flow in porous tissue. An image processing technique is leveraged for reconstructing the computational domain. The Marker and Cell, and Immersed Boundary Methods are used to solve the set of governing equations. The no-flux interface condition and convection do amplify the tissue content, and the regions of dense calcium and necrotic core limited to or extremely close to the interface pose a clinical threat to DCB therapy. Simulations predict the effects of the positioning and clustering of plaque components in the domain. This study demands extensive intravascular ultrasound-derived virtual histology (VH-IVUS) imaging to understand the plaque morphology and determine the relative positions of different plaque compositions about the lumen-tissue interface, which have a significant impact on arterial pharmacokinetics.
Optimization and characterization of silver nanoparticle-modified luffa for the adsorption of ketoprofen and reactive yellow 15 from aqueous solutions
Authors: Tavassoli Soheil , Cheraghi Setareh , Etemadifar Pardis , Mollahosseini Afsaneh , joodaki Shirin , Sedighi Niloofar 
Published: February 2024

AbstractIn the current work, luffa was modified with silver nanoparticles to prepare LF/AgNPs adsorbent for the elimination of ketoprofen and reactive yellow 15 (RY15) from aqueous media. Various characterization techniques, including FT-IR, XRD, BET, and SEM–EDS analysis, were employed to confirm the successful modification of LF/AgNPs. Several key parameters such as contact time, adsorbent dosage, concentration, pH, and agitation technique were fine-tuned to optimize the adsorption process. Ketoprofen removal was found to be most effective in weakly acidic conditions (pH = 5), while reactive yellow 15 adsorption was enhanced in an acidic environment (pH = 2). At 298 K, the highest adsorption capacities reached 56.88 mg/g for ketoprofen and 97.76 mg/g for reactive yellow 15. In both scenarios involving the elimination of ketoprofen and RY15, the Temkin isotherm exhibits higher R2 values, specifically 0.997 for ketoprofen and 0.963 for RY15, demonstrating a strong correlation with the observed adsorption data. Additionally, the kinetics of ketoprofen adsorption were best described by the Pseudo-first order model (R2 = 0.989), whereas the Pseudo-second order model provided the most accurate fit for reactive yellow 15 adsorption (R2 = 0.997). Importantly, the LF/AgNPs adsorbent displayed consistent performance over five consecutive reuse cycles, affirming its stability and efficacy in removing both contaminants. These findings underscore the exceptional potential of LF/AgNPs as a reliable adsorbent for the removal of reactive yellow 15 and ketoprofen from aqueous solutions.
Plasma membrane damage limits replicative lifespan in yeast and induces premature senescence in human fibroblasts
Authors: Suda Kojiro , Moriyama Yohsuke , Razali Nurhanani , Chiu Yatzu , Masukagami Yumiko , Nishimura Koutarou , Barbee Hunter , Takase Hiroshi , Sugiyama Shinju , Yamazaki Yuta , Sato Yoshikatsu , Higashiyama Tetsuya , Johmura Yoshikazu , Nakanishi Makoto , Kono Keiko 
Published: February 2024

AbstractPlasma membrane damage (PMD) occurs in all cell types due to environmental perturbation and cell-autonomous activities. However, cellular outcomes of PMD remain largely unknown except for recovery or death. In this study, using budding yeast and normal human fibroblasts, we found that cellular senescence—stable cell cycle arrest contributing to organismal aging—is the long-term outcome of PMD. Our genetic screening using budding yeast unexpectedly identified a close genetic association between PMD response and replicative lifespan regulations. Furthermore, PMD limits replicative lifespan in budding yeast; upregulation of membrane repair factors ESCRT-III (SNF7) and AAA-ATPase (VPS4) extends it. In normal human fibroblasts, PMD induces premature senescence via the Ca2+–p53 axis but not the major senescence pathway, DNA damage response pathway. Transient upregulation of ESCRT-III (CHMP4B) suppressed PMD-dependent senescence. Together with mRNA sequencing results, our study highlights an underappreciated but ubiquitous senescent cell subtype: PMD-dependent senescent cells.
Estimating the risk of brain metastasis for patients newly diagnosed with cancer
Authors: Miccio Joseph A. , Tian Zizhong , Mahase Sean S. , Lin Christine , Choi Serah , Zacharia Brad E. , Sheehan Jason P. , Brown Paul D. , Trifiletti Daniel M. , Palmer Joshua D. , Wang Ming , Zaorsky Nicholas G. 
Published: February 2024

Abstract
Background
Brain metastases (BM) affect clinical management and prognosis but limited resources exist to estimate BM risk in newly diagnosed cancer patients. Additionally, guidelines for brain MRI screening are limited. We aimed to develop and validate models to predict risk of BM at diagnosis for the most common cancer types that spread to the brain.

Methods
Breast cancer, melanoma, kidney cancer, colorectal cancer (CRC), small cell lung cancer (SCLC), and non-small cell lung cancer (NSCLC) data were extracted from the National Cancer Database to evaluate for the variables associated with the presence of BM at diagnosis. Multivariable logistic regression (LR) models were developed and performance was evaluated with Area Under the Receiver Operating Characteristic Curve (AUC) and random-split training and testing datasets. Nomograms and a Webtool were created for each cancer type.

Results
We identify 4,828,305 patients from 2010-2018 (2,095,339 breast cancer, 472,611 melanoma, 407,627 kidney cancer, 627,090 CRC, 164,864 SCLC, and 1,060,774 NSCLC). The proportion of patients with BM at diagnosis is 0.3%, 1.5%, 1.3%, 0.3%, 16.0%, and 10.3% for breast cancer, melanoma, kidney cancer, CRC, SCLC, and NSCLC, respectively. The average AUC over 100 random splitting for the LR models is 0.9534 for breast cancer, 0.9420 for melanoma, 0.8785 for CRC, 0.9054 for kidney cancer, 0.7759 for NSCLC, and 0.6180 for SCLC.

Conclusions
We develop accurate models that predict the BM risk at diagnosis for multiple cancer types. The nomograms and Webtool may aid clinicians in considering brain MRI at the time of initial cancer diagnosis.