bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid clonal expansion and somatic hypermutation contribute to the fate of SARS-CoV-2 broadly neutralizing antibodies
Authors: Wang Miao , Liu Congcong , Fan Qing , Sun Yuehong , Tang Shilong , Guo Huimin , Zhou Bing , Wang Haiyan , Ge Xiangyang , Zhang Zheng , Ju Bin 
Published: February 2025

Abstract
Several vaccines and immunization strategies, including inactivated vaccines, have proven effective in eliciting antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), providing an opportunity to characterize the antibody response. In this study, we investigated the monoclonal antibody responses elicited by wild-type SARS-CoV-2 inactivated vaccination compared to those elicited by natural infection and mRNA vaccination. The analysis showed that antibodies encoded by biased germline genes were shared between SARS-CoV-2 vaccinated and naturally infected individuals. Among the 35 shared clonotypes identified, besides the well-known IGHV3-53 and IGHV1-58, we identified a class of IGHV4-59 antibodies characterized by rapid response and neutralizing activity, elicited by 3 doses of inactivated vaccine. Members of this lineage exhibited similar sensitivity against wild-type SARS-CoV-2, whereas different neutralizing activities against SARS-CoV-2 variants, especially against various Omicron subvariants, BA.1, BA.2, BA.2.12.1, BA.4/5, and BA.2.75. Structural analysis of BA.1 spike complexed with VacBB-639 revealed that the IGHV4-59-lineage antibodies belonged to the Class 2/3 group. Using sequence alignment, site-mutation assays, and functional verification, we identified two substitutions, N60K in HFR3 and S56G in HCDR2, contributing to opposite neutralization changes of IGHV4-59-lineage antibodies against these Omicron subvariants. These results demonstrate the importance of somatic hypermutation in the evolution of prototypical antigen-elicited antibodies in terms of their neutralization breadth and potency against SARS-CoV-2 Omicron variants.
Practical design considerations for cluster randomized controlled trials: lessons learned in community oncology research
Authors: Dressler Emily V , Pugh Stephanie L , Gunn Heather J , Unger Joseph M , Zahrieh David M , Snavely Anna C 
Published: February 2025

Abstract
Cancer care delivery research trials conducted within the National Cancer Institute (NCI) Community Oncology Research Program (NCORP) routinely implement interventions at the practice or provider level, necessitating the use of cluster randomized controlled trials (cRCTs). The intervention delivery requires cluster-level randomization instead of participant-level, affecting sample size calculation and statistical analyses to incorporate correlation between participants within a practice. Practical challenges exist in the conduct of these cRCTs due to unique trial network infrastructures, including the possibility of unequal participant accrual totals and rates and staggered study initiation by clusters, potentially with differences between randomized arms. Execution of cRCT designs can be complex, ie, if some clusters do not accrue participants, unintended cluster-level crossover occurs, how best to identify appropriate cluster-level stratification, timing of randomization, and multilevel eligibility criteria considerations. This article shares lessons learned with potential mitigation strategies from 3 NCORP cRCTs.
Carbon-based pedicle screw fixation for lumbar fusion for degenerative pathologies in a cancer patient requiring radiotherapy
Authors: Mobbs Ralph Jasper , Liu Daniel 
Published: February 2025

Abstract
Spinal instability due to degenerative pathologies in patients with metastatic cancer presents significant challenges when spinal fusion and post-operative imaging and radiotherapy are required. Traditional metallic hardware hinders imaging quality and radiotherapy precision due to metal artefact. Carbon-fiber-reinforced polymer (CFRP) implants offer a novel solution, combining mechanical stability with radiolucency to enhance post-operative multidisciplinary care. We present the case of a patient with metastatic cancer requiring spinal stabilization and fusion. To address the dual needs of spinal stabilization and radiotherapy planning, CFRP pedicle screws and rods were used. Postoperative imaging and radiotherapy planning benefited from the radiolucent properties of the implants, enabling precise tumor targeting and disease monitoring. This case highlights the advantages of CFRP implants in managing cancer-associated spinal instability. The radiolucent nature of these implants allows for high-quality imaging and optimal radiotherapy delivery, addressing limitations associated with metallic implants.
More than a passive barrier: algal cell walls play an active role in determining cell shape, cell size, and organelle morphology
Authors: Hoffmann Natalie 
Published: February 2025

This article comments on:
LoRicco JG, Malone S, Becker A, Xue N, Bagdan K, Eastman A, Sgambettera G, Winegrad A, Gibeau. B, Bauer L, Epstein R, Domozych DS. 2025. Aberrant growth and expansion in Penium margaritaceum triggered by disruption of microtubules and the cell wall. Journal of Experimental Botany75, 961–979. https://doi.org/10.1093/jxb/erae387
High-throughput screening of wheat leaf dark respiration identifies significant genetic control
Authors: Vicente Rubén , Fernie Alisdair R , Uberegui Estefanía 
Published: February 2025

This article comments on:
Gaju O, Bloomfield KJ, Negrini ACA, Bowerman AF, Cullerne D, Posch BC, Bryant C, Fan Y, Spence M, Stone B, Gilliham M, Furbank RT, Molero G, Pogson BJ, Mathews K, Millar AH, Pearson AL, Reynolds MP, Stroeher E, Taylor NL, Turnbull MH, Atkin OK. 2025. Accounting for the impact of genotype and environment on variation in leaf respiration of wheat in Mexico and Australia. Journal of Experimental Botany 76, 1099–1115. https://doi.org/10.1093/jxb/erae449.
Root sweet root: how date palm uses osmotic adjustment to thrive in arid climates
Authors: Hernandez-Santana Virginia , Pichaco Javier 
Published: February 2025

This article comments on:
Franzisky BL, Mueller HM, Du B, Lux T, White PJ, Carpentier SC, Winkler JB, Schnitzler JP, Kudla J, Kangasjärvi J, Reichelt M, Mithöfer A, Mayer KFX, Rennenberg H, Ache P, Hedrich R, Messerer M, Geilfus CM. 2025. Date palm diverts organic solutes for root osmotic adjustment and protects leaves from oxidative damage in early drought acclimation. Journal of Experimental Botany 76, 1244–1265 https://doi.org/10.1093/jxb/erae456.
Real-world treatment persistence in csDMARD-IR and bDMARD-IR patients with rheumatoid arthritis in Japan: A large claims database study
Authors: Takeuchi Tsutomu , Pfeifer Craig , Zhong Yan , Piao Yi , Kaise Toshihiko , Tani Mahiro 
Published: February 2025

Abstract
Objectives: To investigate treatment persistence for biologic disease-modifying antirheumatic drugs (bDMARDs) and Janus kinase inhibitors (JAKis), including filgotinib, in Japanese patients with rheumatoid arthritis (RA) with inadequate response (IR) to conventional synthetic DMARDs (csDMARD-IR) and bDMARDs (bDMARD-IR) and identify characteristics associated with treatment discontinuation.
Methods: We analyzed 2020–2023 health claims data from adults with RA who received ≥1 prescription for bDMARDs or JAKis during the study period and ≥1 prescription for csDMARDs over 6 previous months. Persistence rates were estimated for the csDMARD-IR (patients naïve to bDMARDs/JAKis switching from csDMARDs to bDMARDs or JAKis) and bDMARD-IR (patients switching to bDMARDs or JAKis from an initial bDMARD) cohorts using the Kaplan-Meier method.
Results: Overall, 7208 and 1581 patients were identified in the csDMARD-IR and bDMARD-IR cohorts, respectively. In the csDMARD-IR cohort, 1-year persistence rates were 59%–70% for JAKis (67% for filgotinib) and 53%–69% for bDMARDs. In the bDMARD-IR cohort, 1-year persistence rates were 57%–66% for JAKis (66% for filgotinib) and 19%–91% for bDMARDs. No clinical characteristics were consistently associated with persistence of JAKi or bDMARD treatment.
Conclusions: Rates of persistence among patients taking JAKis, including filgotinib, were approximately 60% or higher in csDMARD-IR and bDMARD-IR cohorts.
NAIL-MS reveals tRNA and rRNA hypomodification as a consequence of 5-fluorouracil treatment
Authors: Berg Maximilian , Li Chengkang , Kaiser Stefanie 
Published: February 2025

Abstract
Recent studies have investigated RNA modifications in response to stressors like chemical agents, including the anticancer drug 5-fluorouracil (5-FU). Traditionally, 5-FU’s mechanism of action was believed to involve inhibition of thymidylate synthase, leading to thymidine depletion and cancer cell death. However, recent findings suggest that ribosome collisions and defects in ribosomal RNA (rRNA) processing drive 5-FU toxicity, potentially through RNA writer inhibition. To explore the effects of 5-FU on rRNA and transfer RNA (tRNA) modifications, we exposed HEK293T cells to 5-FU and quantified key RNA modifications. We found 55% and 40% reduction in 5-methyluridine and pseudouridine (Ψ), respectively, in tRNAs, but only minor changes in rRNA. Using nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS), we identified that pre-existing tRNA and rRNA retained their modification profiles, while newly synthesized RNAs lost various modifications. In addition, new tRNAs exhibited modification reprogramming, particularly important for cell survival after 5-FU removal. In rRNA, we observed reduced levels of mature rRNA, with hypomodification in newly transcribed mature rRNA, particularly in Ψ and ribose methylations. In summary, we observe RNA hypomodification in both tRNA and rRNA due to 5-FU, which might be the molecular basis of 5-FU’s mechanism of action.
Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms
Authors: Kubota Naoto , Chen Liang , Zheng Sika 
Published: February 2025

Abstract
Alternative pre-mRNA splicing (AS) is a fundamental regulatory process that generates transcript diversity and cell type variation. We developed Shiba, a comprehensive method that integrates transcript assembly, splicing event identification, read counting, and differential splicing analysis across RNA-seq platforms. Shiba excels in capturing annotated and unannotated AS events with superior accuracy, sensitivity, and reproducibility. It addresses the often-overlooked issue of junction read imbalance, significantly reducing false positives to aid target prioritization and downstream analyses. Unlike other tools that require large numbers of biological replicates or resulting in low sensitivity and high false positives, Shiba's statistics framework is agnostic to sample size, as demonstrated by simulated data and its effective application to real n= 1 RNA-seq datasets. To extend its utility to single-cell RNA-seq, we developed scShiba, which applies Shiba's pseudobulk approach to analyze splicing at the cluster level. scShiba successfully revealed AS regulation in developmental dopaminergic neurons and differences between excitatory and inhibitory neurons. Both Shiba and scShiba are available in Docker/Singularity containers and Snakemake pipelines, ensuring reproducibility. With their comprehensive capabilities, Shiba and scShiba enable systematic quantification of alternative splicing events across various platforms, laying a solid foundation for mechanistic exploration of the functional complexity in RNA splicing.
Protein bL38 facilitates incorporation of uL6 during assembly of the 50S subunit in Flavobacterium johnsoniae
Authors: Alom Md Siddik , Arpin Dominic , Zhu Haojun , Hay Brenna N , Foster Leonard J , Ortega Joaquin , Fredrick Kurt 
Published: February 2025

Abstract
Previous studies of the 70S ribosome from Flavobacterium johnsoniae revealed a novel ribosomal protein, bL38, which interacts with uL6 on the 50S subunit. This 5.6 kDa protein is conserved across the Bacteroidia and encoded downstream of bL28 and bL33 in a three-gene operon. Here, we show that bL38 is critical for the growth of F. johnsoniae, and depletion of bL38 leads to accumulation of immature 50S particles, which lack uL6 and retain precursor rRNA sequences. Cryo-EM analysis of these particles reveals several putative assembly intermediates, all showing an absence of electron density for uL6 and the entire uL12 stalk region and additional densities corresponding to the unprocessed ends of the pre-23S rRNA. Extra copies of the uL6 gene can rescue the phenotypes caused by bL38 depletion, suggesting that bL38 facilitates uL6 incorporation during 50S subunit biogenesis. Cryo-EM analysis of 50S particles from this rescued strain reveals nearly twice as many intermediates, suggesting a broader and more robust assembly landscape. Differential scanning fluorimetry shows that uL6 of F. johnsoniae is intrinsically unstable, and bL38 increases the melting temperature of uL6 by 12°C. Collectively, these data suggest that bL38 binds and stabilizes uL6, thereby promoting 50S biogenesis in the Bacteroidia.
The IGF2BP1 oncogene is a druggable m6A-dependent enhancer of YAP1-driven gene expression in ovarian cancer
Authors: Schott Annekatrin , Simon Theresa , Müller Simon , Rausch Alexander , Busch Bianca , Glaß Markus , Misiak Danny , Dipto Mohammad , Elrewany Hend , Peters Lara Meret , Tripathee Sunita , Ghazy Ehab , Müller Florian , Rolnik Robin Benedikt , Lederer Marcell , Hmedat Ali , Vetter Martina , Wallwiener Markus , Sippl Wolfgang , Hüttelmaier Stefan , Bley Nadine 
Published: February 2025

Abstract
The Hippo/YAP1 signaling pathway regulates normal development by controlling contact inhibition of growth. In cancer, YAP1 activation is often dysregulated, leading to excessive tumor growth and metastasis. SRC kinase can cross talk to Hippo signaling by disrupting adherens junctions, repressing the Hippo cascade, or activating YAP1 to promote proliferation. Here, we demonstrate that the IGF2 messenger RNA-binding protein 1 (IGF2BP1) impedes the repression of YAP1 by Hippo signaling in carcinomas. IGF2BP1 stabilizes the YAP1 messenger RNA (mRNA) and enhances YAP1 protein synthesis through an m6A-dependent interaction with the 3′ untranslated region of the YAP1 mRNA, thereby increasing YAP1/TAZ-driven transcription to bypass contact inhibition of tumor cell growth. Inhibiting IGF2BP1–mRNA binding using BTYNB reduces YAP1 levels and transcriptional activity, leading to significant growth inhibition in carcinoma cells and ovarian cancer organoids. In contrast, SRC inhibition with Saracatinib fails to inhibit YAP1/TAZ-driven transcription and cell growth in general. This is particularly significant in de-differentiated, rather mesenchymal carcinoma-derived cells, which exhibit high IGF2BP1 and YAP1 expression, rendering them less reliant on SRC-directed growth stimulation. In such invasive carcinoma models, the combined inhibition of SRC, IGF2BP1, and YAP1/TAZ proved superior over monotherapies. These findings highlight the therapeutic potential of targeting IGF2BP1, a key regulator of oncogenic transcription networks.
Comprehensive analysis of RNA–chromatin, RNA–, and DNA–protein interactions
Authors: Khlebnikov Daniil A , Nikolskaya Arina I , Zharikova Anastasia A , Mironov Andrey A 
Published: February 2025

Abstract
RNA–chromatin interactome data are considered to be one of the noisiest types of data in biology. This is due to protein-coding RNA contacts and nonspecific interactions between RNA and chromatin caused by protocol specifics. Therefore, finding regulatory interactions between certain transcripts and genome loci requires a wide range of filtering techniques to obtain significant results. Using data on pairwise interactions between these molecules, we propose a concept of triad interaction involving RNA, protein, and a DNA locus. The constructed triads show significantly less noise contacts and are more significant when compared to a background model for generating pairwise interactions. RNA–chromatin contacts data can be used to validate the proposed triad object as positive (Red-ChIP experiment) or negative (RADICL-seq NPM) controls. Our approach also filters RNA–chromatin contacts in chromatin regions associated with protein functions based on ChromHMM annotation.
The enduring effects of early life adversity on the dysregulation of the stress awakening response among dependent tobacco users
Authors: Anker Justin J , Nakajima Motohiro , Hatsukami Dorothy , Allen Sharon S , al’Absi Mustafa 
Published: February 2025

Abstract

Introduction
Adults with early life adversity (ELA) often exhibit stress system dysregulation and are prone to smoke for stress relief. This study, conducted as part of a larger project examining psychobiological stress responses in smokers, specifically focuses on the a priori research question of how ELA influences the cortisol awakening response (CAR) during acute tobacco withdrawal.

Methods
Using quasi-experimental design, adult daily (heavy) smokers were randomly assigned to either regular smoking (ad-lib) (N=37) or 24-hour withdrawal (N=55), and categorized into low or high ELA. CO levels verified smoking status, and CAR was assessed through salivary cortisol upon awakening and at 30 and 60 post-wakening. CAR was evaluated using mean cortisol levels, peak reactivity, and area under the curve with respect to increase (AUCi) and ground (AUCg) while controlling for possible covariates. Self-reported measures of mood, craving, and withdrawal were also analyzed.

Results
Smoking status X ELA interaction on peak cortisol and AUCi. High ELA ad-lib smokers (vs. high ELA withdrawal) had elevated peak and AUCi levels and were higher than low ELA ad-lib smokers with respect to peak (ps &lt; 0.05). Withdrawal (vs. ad-lib smokers) had lower positive affect and higher negative affect, craving, and withdrawal (ps &lt; 0.05). Adult smokers with a history of ELA exhibit heightened stress response dysregulation, as evidenced by altered CAR, compared to those without ELA or in smoking withdrawal.

Conclusions
These findings demonstrate that early life adversity significantly exacerbates stress system dysregulation among adult smokers, as evidenced by alterations in the cortisol awakening response. Identifying ELA experiences in smokers may inform the development of more targeted interventions for stress management and tobacco cessation.

Implications
Findings from this study suggest ELA not only leads to an earlier initiation of smoking but also worsens stress system dysregulation in adult smokers. These insights highlight the importance of developing early prevention strategies aimed at adolescents with ELA to prevent smoking initiation and reduce its impact on stress regulation. Additionally, the findings support the need for customized, trauma-informed smoking cessation programs for adults with ELA, emphasizing the necessity to address the distinct challenges related to stress regulation and nicotine withdrawal they face.
Climatic Variability and Associated Changes in a Nigerian Nature Forest Reserve
Authors: Olanipon Damilola Grace , Adewoyin Adelowo Adefisayo , Eludoyin Adebayo Oluwole 
Published: February 2025

Abstract
Climate variability and its impact have become of serious interest to environmentalists worldwide, but reports from many sub-Saharan African countries are still relatively more uncertain than many parts, mostly due to challenges with datasets and methodology. In this study, the daily rainfall and temperature records for 34 years (1984–2018; for which data were available at the time of study) were examined alongside changes in the land cover at a natural forest reserve in the Ife area of southwestern Nigeria. The specific objective was to examine climate variability with changes in the land cover of the nature reserve. Data used included archival records of rainfall and temperature and open-access Landsat satellite imageries of the area. Results showed that area experienced rainfall fluctuations, significant monthly decrease and temperature rise in many months increase. The Normalized Difference Vegetation Index and supervised classification of land cover also revealed a decline in vegetation health and loss of forested land to non-forest uses such as farmlands and built-up lands over time. The study could not establish a direct link between forest loss and climate change in the study area but detected a complex implication of urban pressure through human activities and urbanization, and thus concluded that the impact of climate change on the forest environment has been exacerbated by pressure for urban growth and probably a poorly monitored quest for land resource.
Overstatement of GDP growth in autocracies and the recent decline in global inequality
Authors: Pandian Roshan K 
Published: February 2025

Abstract
After rising for almost two centuries, global income inequality declined substantially after 2000. While past scholarship on global inequality has explored several causes for this recent decline in inequality, these studies take for granted the official GDP figures released by national governments. A parallel social science literature has documented the manipulation of official data to exaggerate economic performance in autocratic countries, but this work has stopped short of examining the broader implications of this phenomenon. In this study, I explore the overstatement of GDP growth figures in autocracies as another contributor to the recent decline in estimates of global inequality based on officially reported GDP figures. Drawing on satellite-based night-time lights data and an empirical strategy from recent research, I compute model-based estimates of GDP overstatement in autocracies. I then combine this information with data on within-country income inequality to arrive at adjusted estimates of global income inequality in a sample of 109 countries constituting 92 percent of the world’s population. I find that between 1995 and 2014, ~20 percent of the decline in global inequality can be explained by the overstatement of GDP growth in less democratic countries. I conclude by discussing the broader implications of these findings for our understanding of global inequality and its political economy.
Amoxicillin-induced linear IgA bullous dermatosis mimicking erythema multiforme: a case report
Authors: Silagy Marion , Carvalho Priscille , Tedbirt Billal , Tamarit Clémence , Carrette Marion , Tétart Florence , Lefebvre Alexis 
Published: February 2025

Abstract
A 77-year-old man presented with a cutaneous rash of 3 days. Seven days before the onset, the patient reported a bronchopulmonary infection treated with amoxicillin. Physical examination revealed multiforme cutaneous lesions, involving the armpits, pubis, genitals, and lower back. In the lower back area, lesions were erythematous, purplish targetoid-like with multiple concentric circles. In places, bullae and post-blistering erosions could be seen. In places, a ‘string of pearls’ pattern could be observed. The Nikolsky sign was negative. Herpes simplex virus polymerase chain reaction (PCR) on mucosal erosions was negative. Multiplex nasopharyngeal PCR was negative for influenza virus, COVID-19, and mycoplasma pneumoniae. Histopathological examination revealed spontaneous subepithelial cleavage with neutrophilic micro-abscesses. Direct immunofluorescence showed linear immunoglobulin A (IgA) deposit on the dermal–epidermal junction affirming the diagnosis of linear IgA bullous dermatosis. As for therapeutic management, skin lesions were treated with topical clobetasol propionate cream and oral mucosa with corticosteroid mouth rinses. The disease course was marked by complete remission 7 days after amoxicillin discontinuation. There was no relapse after 4 months of follow-up.