bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversification of flowering plants in space and time
Authors: Dimitrov Dimitar , Xu Xiaoting , Su Xiangyan , Shrestha Nawal , Liu Yunpeng , Kennedy Jonathan D. , Lyu Lisha , Nogués-Bravo David , Rosindell James , Yang Yong , Fjeldså Jon , Liu Jianquan , Schmid Bernhard , Fang Jingyun , Rahbek Carsten , Wang Zhiheng 
Published: November 2023

AbstractThe rapid diversification and high species richness of flowering plants is regarded as ‘Darwin’s second abominable mystery’. Today the global spatiotemporal pattern of plant diversification remains elusive. Using a newly generated genus-level phylogeny and global distribution data for 14,244 flowering plant genera, we describe the diversification dynamics of angiosperms through space and time. Our analyses show that diversification rates increased throughout the early Cretaceous and then slightly decreased or remained mostly stable until the end of the Cretaceous–Paleogene mass extinction event 66 million years ago. After that, diversification rates increased again towards the present. Younger genera with high diversification rates dominate temperate and dryland regions, whereas old genera with low diversification dominate the tropics. This leads to a negative correlation between spatial patterns of diversification and genus diversity. Our findings suggest that global changes since the Cenozoic shaped the patterns of flowering plant diversity and support an emerging consensus that diversification rates are higher outside the tropics.
Four-dimensional hydrogel dressing adaptable to the urethral microenvironment for scarless urethral reconstruction
Authors: Hua Yujie , Wang Kai , Huo Yingying , Zhuang Yaping , Wang Yuhui , Fang Wenzhuo , Sun Yuyan , Zhou Guangdong , Fu Qiang , Cui Wenguo , Zhang Kaile 
Published: November 2023

AbstractThe harsh urethral microenvironment (UME) after trauma severely hinders the current hydrogel-based urethral repair. In fact, four-dimensional (4D) consideration to mimic time-dependent physiological processes is essential for scarless urethral reconstruction, which requires balancing extracellular matrix (ECM) deposition and remodeling at different healing stages. In this study, we develop a UME-adaptable 4D hydrogel dressing to sequentially provide an early-vascularized microenvironment and later-antifibrogenic microenvironment for scarless urethral reconstruction. With the combination of dynamic boronic ester crosslinking and covalent photopolymerization, the resultant gelatin methacryloyl phenylboronic acid/cis-diol-crosslinked (GMPD) hydrogels exhibit mussel-mimetic viscoelasticity, satisfactory adhesion, and acid-reinforced stability, which can adapt to harsh UME. In addition, a temporally on-demand regulatory (TOR) technical platform is introduced into GMPD hydrogels to create a time-dependent 4D microenvironment. As a result, physiological urethral recovery is successfully mimicked by means of an early-vascularized microenvironment to promote wound healing by activating the vascular endothelial growth factor (VEGF) signaling pathway, as well as a later-antifibrogenic microenvironment to prevent hypertrophic scar formation by timing transforming growth factor-β (TGFβ) signaling pathway inhibition. Both in vitro molecular mechanisms of the physiological healing process and in vivo scarless urethral reconstruction in a rabbit model are effectively verified, providing a promising alternative for urethral injury treatment.
Structure of the N-RNA/P interface indicates mode of L/P recruitment to the nucleocapsid of human metapneumovirus
Authors: Whitehead Jack D. , Decool Hortense , Leyrat Cédric , Carrique Loic , Fix Jenna , Eléouët Jean-François , Galloux Marie , Renner Max 
Published: November 2023

AbstractHuman metapneumovirus (HMPV) is a major cause of respiratory illness in young children. The HMPV polymerase (L) binds an obligate cofactor, the phosphoprotein (P). During replication and transcription, the L/P complex traverses the viral RNA genome, which is encapsidated within nucleoproteins (N). An essential interaction between N and a C-terminal region of P tethers the L/P polymerase to the template. This N-P interaction is also involved in the formation of cytoplasmic viral factories in infected cells, called inclusion bodies. To define how the polymerase component P recognizes N-encapsidated RNA (N-RNA) we employed cryogenic electron microscopy (cryo-EM) and molecular dynamics simulations, coupled to activity assays and imaging of inclusion bodies in cells. We report a 2.9 Å resolution structure of a triple-complex between multimeric N, bound to both RNA and the C-terminal region of P. Furthermore, we also present cryo-EM structures of assembled N in different oligomeric states, highlighting the plasticity of N. Combined with our functional assays, these structural data delineate in molecular detail how P attaches to N-RNA whilst retaining substantial conformational dynamics. Moreover, the N-RNA-P triple complex structure provides a molecular blueprint for the design of therapeutics to potentially disrupt the attachment of L/P to its template.
Taxonomic and environmental distribution of bacterial amino acid auxotrophies
Authors: Ramoneda Josep , Jensen Thomas B. N. , Price Morgan N. , Casamayor Emilio O. , Fierer Noah 
Published: November 2023

AbstractMany microorganisms are auxotrophic—unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino acid biosynthetic capabilities of 26,277 unique bacterial genomes spanning 12 phyla using a metabolic pathway model validated with empirical data. Amino acid auxotrophy is widespread across bacterial phyla, but we conservatively estimate that the majority of taxa (78.4%) are able to synthesize all amino acids. Our estimates indicate that amino acid auxotrophies are more prevalent among obligate intracellular parasites and in free-living taxa with genomic attributes characteristic of ‘streamlined’ life history strategies. We predicted the amino acid biosynthetic capabilities of bacterial communities found in 12 unique habitats to investigate environmental associations with auxotrophy, using data compiled from 3813 samples spanning major aquatic, terrestrial, and engineered environments. Auxotrophic taxa were more abundant in host-associated environments (including the human oral cavity and gut) and in fermented food products, with auxotrophic taxa being relatively rare in soil and aquatic systems. Overall, this work contributes to a more complete understanding of amino acid auxotrophy across the bacterial tree of life and the ecological contexts in which auxotrophy can be a successful strategy.
Design principles for sodium superionic conductors
Authors: Wang Shuo , Fu Jiamin , Liu Yunsheng , Saravanan Ramanuja Srinivasan , Luo Jing , Deng Sixu , Sham Tsun-Kong , Sun Xueliang , Mo Yifei 
Published: November 2023

AbstractMotivated by the high-performance solid-state lithium batteries enabled by lithium superionic conductors, sodium superionic conductor materials have great potential to empower sodium batteries with high energy, low cost, and sustainability. A critical challenge lies in designing and discovering sodium superionic conductors with high ionic conductivities to enable the development of solid-state sodium batteries. Here, by studying the structures and diffusion mechanisms of Li-ion versus Na-ion conducting solids, we reveal the structural feature of face-sharing high-coordination sites for fast sodium-ion conductors. By applying this feature as a design principle, we discover a number of Na-ion conductors in oxides, sulfides, and halides. Notably, we discover a chloride-based family of Na-ion conductors NaxMyCl6 (M = La–Sm) with UCl3-type structure and experimentally validate with the highest reported ionic conductivity. Our findings not only pave the way for the future development of sodium-ion conductors for sodium batteries, but also consolidate design principles of fast ion-conducting materials for a variety of energy applications.
Risk to rely on soil carbon sequestration to offset global ruminant emissions
Authors: Wang Yue , de Boer Imke J. M. , Persson U. Martin , Ripoll-Bosch Raimon , Cederberg Christel , Gerber Pierre J. , Smith Pete , van Middelaar Corina E. 
Published: November 2023

AbstractCarbon sequestration in grasslands has been proposed as an important means to offset greenhouse gas emissions from ruminant systems. To understand the potential and limitations of this strategy, we need to acknowledge that soil carbon sequestration is a time-limited benefit, and there are intrinsic differences between short- and long-lived greenhouse gases. Here, our analysis shows that one tonne of carbon sequestrated can offset radiative forcing of a continuous emission of 0.99 kg methane or 0.1 kg nitrous oxide per year over 100 years. About 135 gigatonnes of carbon is required to offset the continuous methane and nitrous oxide emissions from ruminant sector worldwide, nearly twice the current global carbon stock in managed grasslands. For various regions, grassland carbon stocks would need to increase by approximately 25% − 2,000%, indicating that solely relying on carbon sequestration in grasslands to offset warming effect of emissions from current ruminant systems is not feasible.
Mid-old cells are a potential target for anti-aging interventions in the elderly
Authors: Kim Young Hwa , Lee Young-Kyoung , Park Soon Sang , Park So Hyun , Eom So Yeong , Lee Young-Sam , Lee Wonhee John , Jang Juhee , Seo Daeha , Kang Hee Young , Kim Jin Cheol , Lim Su Bin , Yoon Gyesoon , Kim Hong Seok , Kim Jang-Hee , Park Tae Jun 
Published: November 2023

AbstractThe biological process of aging is thought to result in part from accumulation of senescent cells in organs. However, the present study identified a subset of fibroblasts and smooth muscle cells which are the major constituents of organ stroma neither proliferative nor senescent in tissues of the elderly, which we termed “mid-old status” cells. Upregulation of pro-inflammatory genes (IL1B and SAA1) and downregulation of anti-inflammatory genes (SLIT2 and CXCL12) were detected in mid-old cells. In the stroma, SAA1 promotes development of the inflammatory microenvironment via upregulation of MMP9, which decreases the stability of epithelial cells present on the basement membrane, decreasing epithelial cell function. Remarkably, the microenvironmental change and the functional decline of mid-old cells could be reversed by a young cell-originated protein, SLIT2. Our data identify functional reversion of mid-old cells as a potential method to prevent or ameliorate aspects of aging-related tissue dysfunction.
Fear extinction is regulated by the activity of long noncoding RNAs at the synapse
Authors: Liau Wei-Siang , Zhao Qiongyi , Bademosi Adekunle , Gormal Rachel S. , Gong Hao , Marshall Paul R. , Periyakaruppiah Ambika , Madugalle Sachithrani U. , Zajaczkowski Esmi L. , Leighton Laura J. , Ren Haobin , Musgrove Mason , Davies Joshua , Rauch Simone , He Chuan , Dickinson Bryan C. , Li Xiang , Wei Wei , Meunier Frédéric A. , Fernández-Moya Sandra M. , Kiebler Michael A. , Srinivasan Balakumar , Banerjee Sourav , Clark Michael , Spitale Robert C. , Bredy Timothy W. 
Published: November 2023

AbstractLong noncoding RNAs (lncRNAs) represent a multidimensional class of regulatory molecules that are involved in many aspects of brain function. Emerging evidence indicates that lncRNAs are localized to the synapse; however, a direct role for their activity in this subcellular compartment in memory formation has yet to be demonstrated. Using lncRNA capture-seq, we identified a specific set of lncRNAs that accumulate in the synaptic compartment within the infralimbic prefrontal cortex of adult male C57/Bl6 mice. Among these was a splice variant related to the stress-associated lncRNA, Gas5. RNA immunoprecipitation followed by mass spectrometry and single-molecule imaging revealed that this Gas5 isoform, in association with the RNA binding proteins G3BP2 and CAPRIN1, regulates the activity-dependent trafficking and clustering of RNA granules. In addition, we found that cell-type-specific, activity-dependent, and synapse-specific knockdown of the Gas5 variant led to impaired fear extinction memory. These findings identify a new mechanism of fear extinction that involves the dynamic interaction between local lncRNA activity and RNA condensates in the synaptic compartment.
Orthosteric and allosteric modulation of human HCAR2 signaling complex
Authors: Mao Chunyou , Gao Mengru , Zang Shao-Kun , Zhu Yanqing , Shen Dan-Dan , Chen Li-Nan , Yang Liu , Wang Zhiwei , Zhang Huibing , Wang Wei-Wei , Shen Qingya , Lu Yanhui , Ma Xin , Zhang Yan 
Published: November 2023

AbstractHydroxycarboxylic acids are crucial metabolic intermediates involved in various physiological and pathological processes, some of which are recognized by specific hydroxycarboxylic acid receptors (HCARs). HCAR2 is one such receptor, activated by endogenous β-hydroxybutyrate (3-HB) and butyrate, and is the target for Niacin. Interest in HCAR2 has been driven by its potential as a therapeutic target in cardiovascular and neuroinflammatory diseases. However, the limited understanding of how ligands bind to this receptor has hindered the development of alternative drugs able to avoid the common flushing side-effects associated with Niacin therapy. Here, we present three high-resolution structures of HCAR2-Gi1 complexes bound to four different ligands, one potent synthetic agonist (MK-6892) bound alone, and the two structures bound to the allosteric agonist compound 9n in conjunction with either the endogenous ligand 3-HB or niacin. These structures coupled with our functional and computational analyses further our understanding of ligand recognition, allosteric modulation, and activation of HCAR2 and pave the way for the development of high-efficiency drugs with reduced side-effects.
HIV-1 Env trimers asymmetrically engage CD4 receptors in membranes
Authors: Li Wenwei , Qin Zhuan , Nand Elizabeth , Grunst Michael W. , Grover Jonathan R. , Bess Julian W. , Lifson Jeffrey D. , Zwick Michael B. , Tagare Hemant D. , Uchil Pradeep D. , Mothes Walther 
Published: November 2023

Abstract
Human immunodeficiency virus 1 (HIV-1) infection is initiated by binding of the viral envelope glycoprotein (Env) to the cell-surface receptor CD41–4. Although high-resolution structures of Env in a complex with the soluble domains of CD4 have been determined, the binding process is less understood in native membranes5–13. Here we used cryo-electron tomography to monitor Env–CD4 interactions at the membrane–membrane interfaces formed between HIV-1 and CD4-presenting virus-like particles. Env–CD4 complexes organized into clusters and rings, bringing the opposing membranes closer together. Env–CD4 clustering was dependent on capsid maturation. Subtomogram averaging and classification revealed that Env bound to one, two and finally three CD4 molecules, after which Env adopted an open state. Our data indicate that asymmetric HIV-1 Env trimers bound to one and two CD4 molecules are detectable intermediates during virus binding to host cell membranes, which probably has consequences for antibody-mediated immune responses and vaccine immunogen design.
Venom-gland transcriptomics and venom proteomics of the Tibellus oblongus spider
Authors: Korolkova Yuliya , Mikov Alexander , Lobas Anna , Solovyeva Elizaveta , Surin Alexey , Andreev Yaroslav , Gorshkov Mikhail , Kozlov Sergey 
Published: November 2023

AbstractThe Tibellus oblongus spider is an active hunter that does not spin webs and remains highly underinvestigated in terms of the venom composition. Here, we describe venom glands transcriptome and venom proteome analysis for unveiling the polypeptide composition of Tibellus oblongus spider venom. The resulting EST database includes 1733 records, including 1263 nucleotide sequences with ORFs, of these 942 have been identified as toxin-coding. The database of peptide sequences was built based on of the transcriptomics results. It contains 217 new toxins, 212 of them were detected in the T. oblongus venom by the proteomics.
Investigation of erosion-corrosion failure of API X52 carbon steel pipeline
Authors: Abdu Mahmoud T. , Khalifa Waleed , Abdelrahman Maiada S. 
Published: November 2023

AbstractA failure analysis of API X52 steel pipeline was conducted. The investigation included complete material characterizations using tensile and hardness testing, optical microscope, SEM, and EDS. The main failure occurred in the downstream pipe located near the welded joint at the elbow outlet instead of elbow which was interesting. The main mechanism of failure was found to be erosion-corrosion mechanism that caused breakdown of the protective FeCO3 film, thinning of the downstream pipe, and finally failure. It is believed that the erosion-corrosion was induced by sand impingement due to turbulent flow that was promoted by sudden change in the flow cross section between the elbow inlet and upstream pipe and poor welding quality of joint at the elbow outlet.
A novel chaotic and neighborhood search-based artificial bee colony algorithm for solving optimization problems
Authors: Xiao Wen-sheng , Li Guang-xin , Liu Chao , Tan Li-ping 
Published: November 2023

AbstractWith the development of artificial intelligence, numerous researchers are attracted to study new heuristic algorithms and improve traditional algorithms. Artificial bee colony (ABC) algorithm is a swarm intelligence optimization algorithm inspired by the foraging behavior of honeybees, which is one of the most widely applied methods to solve optimization problems. However, the traditional ABC has some shortcomings such as under-exploitation and slow convergence, etc. In this study, a novel variant of ABC named chaotic and neighborhood search-based ABC algorithm (CNSABC) is proposed. The CNSABC contains three improved mechanisms, including Bernoulli chaotic mapping with mutual exclusion mechanism, neighborhood search mechanism with compression factor, and sustained bees. In detail, Bernoulli chaotic mapping with mutual exclusion mechanism is introduced to enhance the diversity and the exploration ability. To enhance the convergence efficiency and exploitation capability of the algorithm, the neighborhood search mechanism with compression factor and sustained bees are presented. Subsequently, a series of experiments are conducted to verify the effectiveness of the three presented mechanisms and the superiority of the proposed CNSABC, the results demonstrate that the proposed CNSABC has better convergence efficiency and search ability. Finally, the CNSABC is applied to solve two engineering optimization problems, experimental results show that CNSABC can produce satisfactory solutions.
Unraveling the molecular links between benzopyrene exposure, NASH, and HCC: an integrated bioinformatics and experimental study
Authors: Yang Zheming , Li Jiayin , Song Haixu , Mei Zhu , Jia Xiaodong , Tian Xiaoxiang , Yan Chenghui , Han Yaling 
Published: November 2023

AbstractBenzopyrene (B[a]P) is a well-known carcinogen that can induce chronic inflammation and fibrosis in the liver, leading to liver disease upon chronic exposure. Nonalcoholic steatohepatitis (NASH) is a chronic liver condition characterized by fat accumulation, inflammation, and fibrosis, often resulting in hepatocellular carcinoma (HCC). In this study, we aimed to investigate the intricate connections between B[a]P exposure, NASH, and HCC. Through comprehensive bioinformatics analysis of publicly available gene expression profiles, we identified differentially expressed genes (DEGs) associated with B[a]P exposure, NASH, and liver cancer. Furthermore, network analysis revealed hub genes and protein–protein interactions, highlighting cellular metabolic dysfunction and disruption of DNA damage repair in the B[a]P-NASH-HCC process. Notably, HSPA1A and PPARGC1A emerged as significant genes in this pathway. To validate their involvement, we conducted qPCR analysis on cell lines and NASH mouse liver tissues and performed immunohistochemistry labeling in mouse and human HCC liver sections. These findings provide crucial insights into the potential regulatory mechanisms underlying benzopyrene-induced hepatotoxicity, shedding light on the pathogenesis of B[a]P-associated NASH and HCC. Moreover, our study suggests that HSPA1A and PPARGC1A could serve as promising therapeutic targets. Enhancing our understanding of their regulatory roles may facilitate the development of targeted therapies, leading to improved patient outcomes.
Bioinformatics analysis and machine learning approach applied to the identification of novel key genes involved in non-alcoholic fatty liver disease
Authors: Nazari Elham , Khalili-Tanha Ghazaleh , Asadnia Alireza , Pourali Ghazaleh , Maftooh Mina , Khazaei Majid , Nasiri Mohammadreza , Hassanian Seyed Mahdi , Ghayour-Mobarhan Majid , Ferns Gordon A. , Kiani Mohammad Ali , Avan Amir 
Published: November 2023

AbstractNon-alcoholic fatty liver disease (NAFLD) comprises a range of chronic liver diseases that result from the accumulation of excess triglycerides in the liver, and which, in its early phases, is categorized NAFLD, or hepato-steatosis with pure fatty liver. The mortality rate of non-alcoholic steatohepatitis (NASH) is more than NAFLD; therefore, diagnosing the disease in its early stages may decrease liver damage and increase the survival rate. In the current study, we screened the gene expression data of NAFLD patients and control samples from the public dataset GEO to detect DEGs. Then, the correlation betweenbetween the top selected DEGs and clinical data was evaluated. In the present study, two GEO datasets (GSE48452, GSE126848) were downloaded. The dysregulated expressed genes (DEGs) were identified by machine learning methods (Penalize regression models). Then, the shared DEGs between the two training datasets were validated using validation datasets. ROC-curve analysis was used to identify diagnostic markers. R software analyzed the interactions between DEGs, clinical data, and fatty liver. Ten novel genes, including ABCF1, SART3, APC5, NONO, KAT7, ZPR1, RABGAP1, SLC7A8, SPAG9, and KAT6A were found to have a differential expression between NAFLD and healthy individuals. Based on validation results and ROC analysis, NR4A2 and IGFBP1b were identified as diagnostic markers. These key genes may be predictive markers for the development of fatty liver. It is recommended that these key genes are assessed further as possible predictive markers during the development of fatty liver.