bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do editorial board members publish in their own journal? – Review of editorial board members as authors in the main foot and ankle journals
Authors: Fa-Binefa Manel , Fontanellas Fes Albert , González Lucena Gemma , Ginés Cespedosa Albert , Gamba Carlo 
Published: September 2024

ABSTRACTBackgroundScientific publications by editorial board members in their own journals raise questions about potential biases in the peer-review process. This study investigates the prevalence of self-publishing in high-impact factor foot and ankle focused journals.MethodsA review was performed of the highest impact factor foot and ankle focused journals/:Foot and Ankle International,Foot and Ankle SurgeryyJournal of Foot and Ankle Surgery.In January 2023, the editorial board members were identified, and their names, roles, academic backgrounds, and regions were obtained. For each board member, the number of total published articles listed in PubMed and those for each corresponding journal over their entire history, during the last 5 years and during the last 3 years were compiled. Descriptive statistics analyses were performed using IBM SPSS Statistics v26.0.ResultsThe study included 196 editorial board members from the 3 selected journals. Editorial board members have published 1694 articles in their own journals (9.17% of all the articles published in those 3 journals). Editorial board members published 23.4% (SD 23.6) of their overall production in their affiliated journals. Of that production, 39.0% (SD 38.6) have been published in the last 5 years, considering this 5-year period as the baseline for their role on the editorial board in question. Some 10% of editorial board members have published more than 50% of their scientific production in their own affiliated journal in the last 5 years. European editors (51%) have published more in their own journal over the last 5-year period than North Americans (29%) (p<0.001). Being a surgeon is related to greater publication rates in one’s own affiliated journal when compared to other specialist profiles (p=0.003).ConclusionThe publication scientific articles by editorial board members as authors in journals with which they are affiliated is a present-day phenomenon in the highest impact factor journals with a focus on the foot & ankle. Knowledge of this data could be the key to understanding the prevalence of this phenomenon, and lead to making this data more accessible.
Effectiveness of a booster dose of aerosolized or intramuscular adenovirus type 5 vectored COVID-19 vaccine in adults with hybrid immunity against COVID-19: a multicenter, partially randomized, platform trial in China
Authors: Jia Si-Yue , Liu Yuan-Bao , He Qian , Pan Hong-Xing , Liang Zheng-Lun , Zhou Juan , Pan Ying-Zi , Liu Sheng , Wu Jing-Jing , Yang Kun , Zhang Xuan-Xuan , Zhao Yang , Li Si-Min , Zhang Lei , Chen Li , Yao Ai-Hua , Lu Meng-Yi , Mao Qun-Ying , Zhu Feng-Cai , Li Jing-Xin 
Published: September 2024

AbstractBackgroundThe primary objective of this research was to assess if a booster dose with COVID-19 vaccines containing ancestral strain could still provide significant protection against symptomatic SARS-CoV-2 infection in a predominantly hybrid-immune population during the period of omicron variant dominance.MethodsWe did a multicenter, partially randomized, platform trial to evaluate the effectiveness of a booster dose of an aerosolized or intramuscular adenovirus type 5 vectored COVID-19 vaccine (Ad5-nCoV) in adults, after the national-wide omicron circulating at the end of year 2022 in China. Participants who were willing to receive a COVID-19 booster dose were randomly assigned to receive one of the booster doses. While, those participants who refused to take a booster dose but consented to participate COVID-19 surveillance were included in a control group. Both participants receiving a booster dose or not were monitored for symptomatic COVID-19 during a six-month surveillance period.ResultsBetween May 23, 2023, and August 28, 2023, 4089 eligible participants were equally randomized to receive a booster dose of aerosolized Ad5-nCoV through oral inhalation at 0.1mL (IH Ad5-nCoV, n=2039) or intramuscular injection of Ad5-nCoV at 0.5 mL (IM Ad5-nCoV, n=2050). While, 2008 participants were enrolled in the blank-control group. A total of 79 COVID-19 cases were confirmed, with 22 (0.006%) in the IH Ad5-nCoV group, 23 (0.007%) in the IM Ad5-nCoV group, and 34 (0.01%) in the control group. Adjusted effectiveness of IH Ad5-nCoV and IM Ad5-nCoV from 14 days after the vaccination were 51.6% (95% CI 9.0 to 74.3) and 38.1% (95% CI - 9.6 to 65.1), respectively.InterpretationSignificant protection against symptomatic COVID-19 caused by the Omicron variant, during the ongoing pandemic of evolving COVID-19 variants, was found to be provided by boosting with the ancestral strain-containing vaccine IH Ad5-nCoV, but not by boosting with IM Ad5-nCoV.
easybio: an R Package for Single-Cell Annotation with CellMarker2.0
Authors: Cui Wei 
Published: September 2024

AbstractSingle-cell RNA sequencing (scRNA-seq) allows researchers to study biological activities at the cellular level, enabling the discovery of new cell types and the analysis of intercellular interactions. However, annotating cell types in scRNA-seq data is a crucial and time-consuming process, with its quality significantly influencing downstream analyses. Accurate identification of potential cell types provides valuable insights for discovering new cell populations or identifying novel markers for known cells, which may be utilized in future research. While various methods exist for single-cell annotation, one of the most common approaches is to use known cell markers. The CellMarker2.0 database, a human-curated repository of cell markers extracted from published articles, is widely used for this purpose. However, it currently offers only a web-based tool for usage, which can be inconvenient when integrating with workflows like Seurat. To address this limitation, we introduceeasybio, an R package designed to streamline single-cell annotation using the CellMarker2.0 database in conjunction with Seurat.easybioprovides a suite of functions for querying the CellMarker2.0 database locally, offering insights into potential cell types for each cluster. In addition to single-cell annotation, the package also supports various bioinformatics workflows, including RNA-seq analysis, making it a versatile tool for transcriptomic research.
Cell cycle-dependent S-sulfenyl proteomics uncover a redox switch in p21-CDK feedback governing the proliferation-senescence decision
Authors: Vorhauser Julia , Roumeliotis Theodoros I. , Leung Jacky K. , Coupe David , Yu Lu , Böhlig Kristin , Nadler André , Choudhary Jyoti S. , Mansfeld Jörg 
Published: September 2024

SUMMARYCells are constantly exposed to reactive oxygen species (ROS) from both intrinsic and extrinsic sources. ROS influence proliferation and cell fate through cysteine oxidation (S-sulfenylation), but specific targets and mechanisms remain unclear. Here, we use redox proteomics to identify cell cycle-coordinated S-sulfenylation and investigate its role in cell cycle decision-making. We find that oxidation of a single cysteine (C41) on the CDK inhibitor p21 during G2 phase determines whether cells continue to proliferate. Preventing C41 oxidation redirects p21 from CDK4-Cyclin D to CDK2-Cyclin A, affecting a negative feedback loop that regulates p21 stability. When C41 cannot be oxidized in G2, daughter cells inherit more p21 from their mother, which decreases proliferation and induces senescence upon irradiation. We therefore identify a redox switch in a core cell cycle regulator that governs the decision to proliferate or exit the cell cycle and present a cell cycle-resolved S-sulfenyl proteome as a valuable resource.
Maltodextrin Transport in the Extremely Thermophilic, Lignocellulose Degrading BacteriumAnaerocellum bescii (f. Caldicellulosiruptor bescii)
Authors: Tjo Hansen , Jiang Virginia , Joseph Jerelle A. , Conway Jonathan M. 
Published: September 2024

AbstractSugar transport into microbial cells is a critical, yet understudied step in the conversion of lignocellulosic biomass to metabolic products.Anaerocellum bescii(formerlyCaldicellulosiruptor bescii) is an extremely thermophilic, anaerobic bacterium that readily degrades the cellulose and hemicellulose components of lignocellulosic biomass into a diversity of oligosaccharide substrates. Despite significant understanding of how this microorganism degrades lignocellulose, the mechanisms underlying its highly efficient transport of the resulting oligosaccharides into the cell are comparatively underexplored. Here, we identify and characterize the ATP-Binding Cassette (ABC) transporters inA. besciigoverning maltodextrin transport. Utilizing past transcriptomic studies onAnaerocellumandCaldicellulosiruptorspecies, we identify two maltodextrin transporters inA. besciiand express and purify their substrate-binding proteins (Athe_2310 and Athe_2574) for characterization. Using differential scanning calorimetry and isothermal titration calorimetry, we show that Athe_2310 strongly interacts with shorter maltodextrins such as maltose and trehalose with dissociation constants in the micromolar range, while Athe_2574 binds longer maltodextrins, with dissociation constants in the sub-micro molar range. Using a sequence-structure-function comparison approach combined with molecular modeling we provide context for the specificity of each of these substrate-binding proteins. We propose thatA. besciiutilizes orthogonal ABC transporters to uptake malto-oligosaccharides of different lengths to maximize transport efficiency.ImportanceHere, we reveal the biophysical and structural basis for oligosaccharide transport by two maltodextrin ABC transporters inA. bescii. This is the first biophysical characterization of carbohydrate uptake in this organism and establishes a workflow for characterizing other oligosaccharide transporters inA. besciiand similar lignocellulosic thermophiles of interest for lignocellulosic bioprocessing. By deciphering the mechanisms underlying high affinity sugar uptake inA. bescii, we shed light on an underexplored step between extracellular lignocellulose degradation and intracellular conversion of sugars to metabolic products. This understanding will expand opportunities for harnessing sugar transport in thermophiles to reshape lignocellulose bioprocessing as part of a renewable bioeconomy.
NuRD chromatin remodeling is required to repair exogenous DSBs in theCaenorhabditis elegansgermline
Authors: Ananthaswamy Deepshikha , Funes Kelin , Borges Thiago , Roques Scott , Fassnacht Nina , El Jamal Sereen , Checchi Paula M. , Lee Teresa Wei-sy 
Published: September 2024

ABSTRACTOrganisms rely on coordinated networks of DNA repair pathways to protect genomes against toxic double-strand breaks (DSBs), particularly in germ cells. All repair mechanisms must successfully negotiate the local chromatin environment in order to access DNA. For example, nucleosomes can be repositioned by the highly conserved Nucleosome Remodeling and Deacetylase (NuRD) complex. InCaenorhabditis elegans, NuRD functions in the germline to repair DSBs – the loss of NuRD’s ATPase subunit, LET-418/CHD4, prevents DSB resolution and therefore reduces fertility. In this study, we challenge germlines with exogenous DNA damage to better understand NuRD’s role in repairing DSBs. We find thatlet-418mutants are hypersensitive to cisplatin and hydroxyurea: exposure to either mutagen impedes DSB repair, generates aneuploid oocytes, and severely reduces fertility and embryonic survival. These defects resemble those seen when the Fanconi anemia (FA) DNA repair pathway is compromised, and we find that LET-418’s activity is epistatic to that of the FA component FCD-2/FANCD2. We propose a model in which NuRD is recruited to the site of DNA lesions to remodel chromatin and allow access for FA pathway components. Together, these results implicate NuRD in the repair of both endogenous DSBs and exogenous DNA lesions to preserve genome integrity in developing germ cells.ARTICLE SUMMARYPreserving genome integrity in germ cells is critical for the survival of individuals and species. Our previous work shows that nucleosome remodeling plays an important role in repairing meiotic DNA damage. Here, we further challenge genomes with toxic DNA damaging agents to test the requirement for remodeling in the germline. We find that DNA damage accumulates in the absence of remodeling, which drastically reduces oocyte quality, and also show that the requirement for remodeling is epistatic to the Fanconi anemia DNA repair pathway. These findings demonstrate that local chromatin environments must be remodeled in response to DNA damage to maintain oocyte quality.
Extracellular condensates (ECs) are endogenous modulators of HIV transcription and latency reactivation
Authors: Naushad Wasifa , Premadasa Lakmini S , Okeoma Bryson C. , Mohan Mahesh , Okeoma Chioma M. 
Published: September 2024

AbstractPersistence of human immunodeficiency virus (HIV) latent reservoir is the major challenge to HIV cure because the latent reservoir is not eliminated by antiretroviral therapy (ART), and they serve as sources for viral rebound upon cessation of ART. Mechanisms regulating viral persistence are not well understood. This study used model systems of post-integration latency to explore the role of basal ganglia (BG) isolated extracellular condensates (ECs) in reprogramming HIV latent cells. We found that BG ECs from uninfected macaques (VEH) and SIV infected macaques (VEH|SIV) activate latent HIV transcription in various model systems. VEH and VEH|SIV ECs significantly increased expression of viral antigen in latently infected cells. Activation of viral transcription, antigen expression, and latency reactivation was inhibited by ECs from the brain of macaques treated with Delta-9-tetrahydrocannabinol (THC) and infected with SIV (THC|SIV). Virus produced by latently infected cells treated with VEH|SIV ECs potentiated cell-cell and cell-free HIV transmission. VEH|SIV ECs also reversed dexamethasone-mediated inhibition of HIV transcription while TNFα-mediated reactivation of latency was reversed by THC|SIV ECs. Transcriptome and secretome analyses of total RNA and supernatants from latently infected cells treated with ECs revealed significant alteration in gene expression and cytokine secretion. THC|SIV ECs increased secretion of Th2 and decreased secretion of proinflammatory cytokines. Most strikingly, while VEH/SIV ECs robustly induced HIV RNA in latently HIV-infected cells, long-term low-dose THC administration enriched ECs for anti-inflammatory cargo that significantly diminished their ability to reactivate latent HIV, an indication that ECs are endogenous host factors that may regulate HIV persistence.HighlightsECs isolated from SIV infected macaques (VEH|SIV ECs) is a positive regulator of LTR-dependent HIV transcription and production of infectious viral particles in vitro.ECs isolated from THC treated SIV infected macaques (THC|SIV ECs) prevents the transcription and reactivation of HIV in latently infected cells and prevents production of viral particles in vitro.ECs reprogram host transcriptome and secretome in manners that or suppress promote reactivation of latent HIV reservoir.The above highlights led to the conclusion that while VEH/SIV ECs robustly induced HIV RNA in latently HIV-infected cells, long-term low-dose THC administration enriched ECs for anti-inflammatory cargo that significantly diminished their ability to reactivate latent HIV.
Comparative study on the effects of different types of acute exercise on cortisol levels and cognitive functions
Authors: shao Zhongshu , Zikereya Talifu , Peng Jiazheng , Luo Minggang , Chen Jinliang , Shi Kaixuan 
Published: September 2024

AbstractThis study examines the different effects of dual-task and single-task exercises on cortisol levels and cognitive performance. Seventeen male college students participated, performing each exercise on separate days. Salivary samples were taken before and after exercise to assess cortisol levels. Cognitive functions were measured using the 2-Back Test, Bells Test, and Mental Rotation Test. Results showed that both exercises significantly improved reaction times across cognitive tests. However, dual-task exercise caused a more notable increase in cortisol levels (p=0.002) than the single-task. A negative correlation between post-exercise cortisol levels and reaction times suggests that higher cortisol levels might enhance cognitive processing speed. Cognitive performance ac-curacy remained unchanged across both exercises. These findings indicate that while both exercise types enhance cognitive speed, dual-task exercise triggers a greater cortisol response, potentially offering more benefits for cognitive processing speed without affecting accuracy. This research highlights the complex interaction between acute exercise, stress hormones, and cognitive function, providing insights into how different exercise types influence cognitive performance through hormonal pathways.
Engineering a Cell-Based Orthogonal Ubiquitin Transfer Cascade for Profiling the Substrates of RBR E3 Parkin
Authors: Fang Shuai , Zhou Li , Chen Geng , Wang Xiaoyu , Jeong In Ho , Jacobs Savannah E , Kossmann Bradley R. , Wei Wei , Zhang Jing , Jeong Geon H. , Ivanov Ivaylo , Mabb Angela M. , Kiyokawa Hiroaki , Zhao Bo , Yin Jun 
Published: September 2024

AbstractThe E3 ubiquitin (UB) ligase Parkin utilizes a Ring-Between-Ring (RBR) domain to mediate the transfer of UB to its substrates to regulate diverse cellular functions, including mitochondrial quality control, cell cycle progression, metabolism programming, and the establishment of synaptic functions. Mutations affecting the E3 ligase activity of Parkin are associated with cancer and Parkinson’s disease (PD). An essential role of Parkin is to synthesize UB chains on the surface of damaged mitochondria to initiate mitophagy. Still, it is not clear how Parkin carries out other biological functions through the ubiquitination of its downstream targets in the cell. We hypothesized that a comprehensive substrate profile of Parkin would facilitate the discovery of ubiquitination pathways underpinning its multifaceted roles in cell regulation and reveal mechanistic linkages between Parkin malfunction and disease development. Here, we used phage display to assemble an orthogonal ubiquitin transfer (OUT) cascade of Parkin that can exclusively deliver an engineered UB mutant (xUB) to Parkin and its substrates in living cells. We then generated a substrate profile of Parkin by purifying xUB-conjugated proteins from cells and identifying them by proteomics. The OUT screen identified Parkin substrates involved in DNA replication, protein translation, intracellular protein transport, and rhythmic regulation. Based on previous literature implicating alterations in membrane vesicle trafficking in PD, we verified Parkin-catalyzed ubiquitination of Rab GTPases (Rab1a, Rab5a, Rab5c, Rab7a, Rab8a, Rab10, an Rab13) as well as CDK5, with reconstituted ubiquitination reactions in vitro and in cells. We also found chemical-induced stimulation of mitophagy enhanced Parkin-mediated ubiquitination of Rab proteins. These findings demonstrate that the OUT cascade of Parkin can serve as an empowering tool for identifying Parkin substrates to elucidate its cellular functions.
De novo Design of A Fusion Protein Tool for GPCR Research
Authors: Gao Kaixuan , Zhang Xin , Nie Jia , Meng Hengyu , Zhang Weishe , Tian Boxue , Liu Xiangyu 
Published: September 2024

AbstractG protein-coupled receptors (GPCRs) play pivotal roles in cellular signaling and represent prominent drug targets. Structural elucidation of GPCRs is crucial for drug discovery efforts. However, structural studies of GPCRs remain challenging, particularly for inactive state structures, which often require extensive protein engineering. Here, we present a de novo design strategy termed “click fusion” for generating fusion proteins to facilitate GPCR structural studies. Our method involves the rational design of structurally stable protein domains rigidly linked to GPCRs. The resulting fusion protein enhances the thermostability of the target GPCR and aids in determining GPCR structures via cryo-electron microscopy (cryo-EM). We further demonstrate that the designed fusion protein can be transferred among structurally similar GPCRs with minor adjustments to the linker region. Our study introduces a promising approach for facilitating GPCR structural studies and advancing drug discovery efforts.
Ca2+-evoked sperm cessation determines embryo number in mammals
Authors: Watanabe Hitomi , Ohara Daiya , Chuma Shinichiro , Takeuchi Yusuke , Takano Tomoatsu , Katanaya Ami , Nakao Satohiro , Kaneko Akihisa , Oida Takatoku , Katsuno Tatsuya , Uehata Takuya , Takeo Toru , Okamoto Munehiro , Hirota Keiji , Kondoh Gen 
Published: September 2024

AbstractIn mammals, fertilization takes place followed by fetus development in the maternal body, so the number of fetuses that exceeds the mother’s capacity increases the frequency of stunted growth and stillbirths, while an excessive number of pups increases postnatal stunting and maternal child-rearing stress, which is detrimental to offspring procreation and species maintenance. Therefore, various control mechanisms are thought to be at work to ensure that fertilization occurs in appropriate numbers. Sperm are not capable of fertilization immediately after they are produced in the testis, and must undergo a stepwise activation process including capacitation, hyper motility activation or acrosome reaction before they meet the egg in the oviduct, where fertilization takes place, contributing positively on fertilization, which in turn ensures the number of fetuses for the maintenance of species. In contrast, in this study, we found that a subpopulation of sperm is derived in a Ca2+-dependent manner during the process for sperm to acquire fertility, which may regulate the number of fetuses. When sperm were harvested from the epididymis of mice and activatedin vitro, a subpopulation of sperm emerged from the sperm population in which Lypd4 was expressed on the sperm surface at a ratio up to 30%. The sperm in this subpopulation were rather small in size, more permeable to dyes, and had already ceased motility. We further characterized this sperm population by surface antigen screening using various monoclonal antibodies and found the expression of several proteins, such as CD55, ICOS or Ccr3, specific to this population. The emergence of this sperm population was induced at a concentration of about 4% of Ca2+in body fluids and was independent of capacitation or acrosome reaction, and also apoptotic process. This subpopulation also appeared over time in sperm ejaculated into the female body, accounting for about 50% of the sperm that reached the oviduct in an hour. When this sperm subpopulation was then removed from the entire population using anti-Lypd4 antibody followed byin uteroinsemination, the fertilization rate of the oocytes collected from the oviducts doubled. Such a sperm subpopulation was also observed in macaque monkeys, and removal of this subpopulation increased the egg penetration rate of sperm, suggesting that this sperm subpopulation exists commonly in mammals and that the mother’s acceptable fetal number is adjusted by systematically sterilizing a certain number of sperm.