bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Minimal Hybrid Sterility Genome Assembled by Chromosome Swapping Between Mouse Subspecies (Mus musculus)
Authors: Fotopulosova Vladana , Tanieli Giordano , Fusek Karel , Jansa Petr , Forejt Jiri 
Published: October 2024

Abstract
Hybrid sterility is a reproductive isolation barrier between diverging taxa securing the early steps of speciation. Hybrid sterility is ubiquitous in the animal and plant kingdoms, but its genetic control is poorly understood. In our previous studies, we have uncovered the sterility of hybrids between musculus and domesticus subspecies of the house mouse, which is controlled by the Prdm9 gene, the X-linked Hstx2 locus, and subspecific heterozygosity for genetic background. To further investigate this form of genic-driven chromosomal sterility, we constructed a simplified hybrid sterility model within the genome of the domesticus subspecies by swapping domesticus autosomes with their homologous partners from the musculus subspecies. We show that the “sterility” allelic combination of Prdm9 and Hstx2 can be activated by a musculus/domesticus heterozygosity of as few as two autosomes, Chromosome 17 (Chr 17) and Chr 18 and is further enhanced when another heterosubspecific autosomal pair is present, whereas it has no effect on meiotic progression in the pure domesticus genome. In addition, we identify a new X-linked hybrid sterility locus, Hstx3, at the centromeric end of Chr X, which modulates the incompatibility between Prdm9 and Hstx2. These results further support our concept of chromosomal hybrid sterility based on evolutionarily accumulated divergence between homologous sequences. Based on these and previous results, we believe that future studies should include more information on the mutual recognition of homologous chromosomes at or before the first meiotic prophase in interspecific hybrids, as this may serve as a general reproductive isolation checkpoint in mice and other species.
The genus Kelliella (Bivalvia) in the Atlantic Ocean
Authors: Utrilla Olga , Gofas Serge , Salas Carmen 
Published: October 2024

ABSTRACT
Kelliella M. Sars, 1870 is a genus of small epibenthic bivalves inhabiting muddy bottoms of the outer shelf and slope worldwide, commonly in habitats that are oxygen-poor or enriched in organic carbon. Currently, there are five accepted species of Kelliella with an Atlantic type locality, and six more Atlantic species, including Vesicomya atlantica (Smith, 1885), the type species of Vesicomya Dall, 1886, were at some time placed in Kelliella. In this work, we revise the genus Kelliella from the North Atlantic waters, based on large amounts of new material from both sides, and describe a new species from Martinique (Kelliella madininae n. sp.). We here propose, after revision of the shell morphology, the synonymy of K. biscayensis Allen, 2001 with K. miliaris (Philippi, 1844), and consider a single West European and Mediterranean species of Kelliella. The fossil “Kelliella” barbara is also excluded from the genus Kelliella and reallocated as Coralliophaga barbara (Studencka, 1987) n. comb. In the Atlantic margin of America, we consider that Diplodonta pilula Dall, 1881 remains a nomen dubium. The type material of K. concentrica Allen, 2001 is figured, and this species considered a member of the Vesicomyinae. The new Caribbean species, K. madininae, resemble K. brasuca Passos, Machado & Fantinatti, 2017 from southeastern Brazil. We recorded new localities for Kelliella goesi Odhner, 1960, so far known only from its original description. Diagnostic characters discriminating Vesicomya from Kelliella, stated by Krylova et al. (2018), Journal of Molluscan Studies, 84: 69–91, are discussed, and we consider the hinge architecture as the most robust.
Re-appraising the evidence for the source, regulation and function of p53-family isoforms
Authors: López Ignacio , Valdivia Irene Larghero , Vojtesek Borivoj , Fåhraeus Robin , Coates Philip J 
Published: October 2024

Abstract
The p53 family of proteins evolved from a common ancestor into three separate genes encoding proteins that act as transcription factors with distinct cellular roles. Isoforms of each member that lack specific regions or domains are suggested to result from alternative transcription start sites, alternative splicing or alternative translation initiation, and have the potential to exponentially increase the functional repertoire of each gene. However, evidence supporting the presence of individual protein variants at functional levels is often limited and is inferred by mRNA detection using highly sensitive amplification techniques. We provide a critical appraisal of the current evidence for the origins, expression, functions and regulation of p53-family isoforms. We conclude that despite the wealth of publications, several putative isoforms remain poorly established. Future research with improved technical approaches and the generation of isoform-specific protein detection reagents is required to establish the physiological relevance of p53-family isoforms in health and disease. In addition, our analyses suggest that p53-family variants evolved partly through convergent rather than divergent evolution from the ancestral gene.
Probing the mechanism of nick searching by LIG1 at the single-molecule level
Authors: Chatterjee Surajit , Chaubet Loïc , van den Berg Aafke , Mukhortava Ann , Almohdar Danah , Ratcliffe Jacob , Gulkis Mitchell , Çağlayan Melike 
Published: October 2024

Abstract
DNA ligase 1 (LIG1) joins Okazaki fragments during the nuclear replication and completes DNA repair pathways by joining 3′-OH and 5′-PO4 ends of nick at the final step. Yet, the mechanism of how LIG1 searches for a nick at single-molecule level is unknown. Here, we combine single-molecule fluorescence microscopy approaches, C-Trap and total internal reflection fluorescence (TIRF), to investigate the dynamics of LIG1-nick DNA binding. Our C-Trap data reveal that DNA binding by LIG1 full-length is enriched near the nick sites and the protein exhibits diffusive behavior to form a long-lived ligase/nick complex after binding to a non-nick region. However, LIG1 C-terminal mutant, containing the catalytic core and DNA-binding domain, predominantly binds throughout DNA non-specifically to the regions lacking nick site for shorter time. These results are further supported by TIRF data for LIG1 binding to DNA with a single nick site and demonstrate that a fraction of LIG1 full-length binds significantly longer period compared to the C-terminal mutant. Overall comparison of DNA binding modes provides a mechanistic model where the N-terminal domain promotes 1D diffusion and the enrichment of LIG1 binding at nick sites with longer binding lifetime, thereby facilitating an efficient nick search process.
RNALocate v3.0: Advancing the Repository of RNA Subcellular Localization with Dynamic Analysis and Prediction
Authors: Wu Le , Wang Luqi , Hu Shijie , Tang Guangjue , Chen Jia , Yi Ying , Xie Hailong , Lin Jiahao , Wang Mei , Wang Dong , Yang Bin , Huang Yan 
Published: October 2024

Abstract
Subcellular localization of RNA is a crucial mechanism for regulating diverse biological processes within cells. Dynamic RNA subcellular localizations are essential for maintaining cellular homeostasis; however, their distribution and changes during development and differentiation remain largely unexplored. To elucidate the dynamic patterns of RNA distribution within cells, we have upgraded RNALocate to version 3.0, a repository for RNA-subcellular localization (http://www.rnalocate.org/ or http://www.rna-society.org/rnalocate/). RNALocate v3.0 incorporates and analyzes RNA subcellular localization sequencing data from over 850 samples, with a specific focus on the dynamic changes in subcellular localizations under various conditions. The species coverage has also been expanded to encompass mammals, non-mammals, plants and microbes. Additionally, we provide an integrated prediction algorithm for the subcellular localization of seven RNA types across eleven subcellular compartments, utilizing convolutional neural networks (CNNs) and transformer models. Overall, RNALocate v3.0 contains a total of 1 844 013 RNA-localization entries covering 26 RNA types, 242 species and 177 subcellular localizations. It serves as a comprehensive and readily accessible data resource for RNA-subcellular localization, facilitating the elucidation of cellular function and disease pathogenesis.
Pipolins are bimodular platforms that maintain a reservoir of defense systems exchangeable with various bacterial genetic mobile elements
Authors: Mateo-Cáceres Víctor , Redrejo-Rodríguez Modesto 
Published: October 2024

Abstract
Defense genes gather in diverse types of genomic islands in bacteria and provide immunity against viruses and other genetic mobile elements. Here, we disclose pipolins, previously found in diverse bacterial phyla and encoding a primer-independent PolB, as a new category of widespread defense islands. The analysis of the occurrence and structure of pipolins revealed that they are commonly integrative elements flanked by direct repeats in Gammaproteobacteria genomes, mainly Escherichia, Vibrio or Aeromonas, often taking up known mobile elements integration hotspots. Remarkably, integrase dynamics correlates with alternative integration spots and enables diverse lifestyles, from integrative to mobilizable and plasmid pipolins, such as in members of the genera Limosilactobacillus, Pseudosulfitobacter or Staphylococcus. Pipolins harbor a minimal core and a large cargo module enriched for defense factors. In addition, analysis of the weighted gene repertoire relatedness revealed that many of these defense factors are actively exchanged with other mobile elements. These findings indicate pipolins and, potentially other defense islands, act as orthogonal reservoirs of defense genes, potentially transferable to immune autonomous MGEs, suggesting complementary exchange mechanisms for defense genes in bacterial populations.
Risk of Reinfection and Incidence of Chronic Symptoms After SARS-CoV-2 Infections
Authors: Golding Liam , Watts Allison W , Pitblado Mark , Clemens Felicity , Viñeta Paramo Marina , Shew Jacob , Irvine Michael A , Abu-Raya Bahaa , Goldfarb David M , Mâsse Louise C , Lavoie Pascal M 
Published: October 2024

Abstract
This study showed that a severe acute respiratory syndrome coronavirus 2 infection reduced the risk of reinfection among vaccinated individuals by 0.50 (95% CI, 0.39–0.64) over a 1-year period, after accounting for unreported infections using avidity-based serology. Reciprocally, chronic symptoms increased from a baseline of 21% (95% CI, 16%–28%) among infection-naïve individuals to 43% (95% CI, 30%–61%) in reinfected individuals.
Phytochrome B promotes blast disease resistance and enhances yield in rice
Authors: Li Xinrui , Chen Huan , Yang Shuo , Kumar Vikranth , Xuan Yuan Hu 
Published: October 2024

Abstract
Phytochromes are red/far-red light receptors that regulate various aspects of plant growth, development, and stress responses. The precise mechanism by which phytochrome B (PhyB)-mediated light signaling influences plant defense and development remains unclear. In this study, we showed that PhyB enhances rice (Oryza sativa) blast disease resistance, tillering, and grain size compared to wild-type plants. Notably, PhyB interacted with and degraded grassy tiller 1 (GT1), a negative regulator of tiller development. Knockdown of GT1 in a phyB background partially rescued the diminished tillering of phyB. However, GT1 negatively regulates rice resistance to blast, suggesting that PhyB degradation of GT1 promotes tillering but not blast resistance. Previously, PhyB was found to interact with and degrade phytochrome-interacting factor 15 (PIL15), a key regulator of seed development that reduces rice resistance to blast and seed size. pil15 mutation in phyB mutants rescued phyB seed size and blast resistance, suggesting that PhyB might interact with and degrade PIL15 to negatively regulate blast resistance and seed size. PIL15 directly activated sugar will be eventually exported transporter 2a (SWEET2a). sweet2a mutants were less susceptible to blast disease compared to wild type. Collectively, these data demonstrate that PhyB promotes rice yield and blast resistance by inhibiting the transcription factors GT1 and PIL15 and downstream signaling.
Anarchy, Evolution, and Ethics in International Relations
Authors: Davis James W 
Published: October 2024

Abstract
Challenging the Realist claim that international anarchy produces an amoral sphere of political action, Brian C. Rathbun argues that anarchy has selected for individuals with a particular moral sense. Flipping Realist arguments around, he claims that individuals would have never survived the hardships of anarchy if they were completely amoral. Rather, morality is a precondition for survival in anarchy. But unlike Constructivists, who maintain that socially constructed norms over time have civilized international politics, Rathbun claims that a morality is part of our human nature, and thus, a material feature of the world. To substantiate his claims, Rathbun adeptly applies insights from multiple disciplines, marshalling empirical evidence generated through a variety of natural and social scientific methods.
Current and future advances in practice: SAPHO syndrome and chronic non-bacterial osteitis (CNO)
Authors: Furer Victoria , Kishimoto Mitsumasa , Tomita Tetsuya , Elkayam Ori , Helliwell Philip S 
Published: October 2024

Abstract
Synovitis, acne, pustulosis, hyperostosis and osteitis (SAPHO) syndrome is a rare, underdiagnosed disease with a wide clinical spectrum. Sterile bone inflammation, predominantly of the anterior chest, and skin manifestations (palmoplantar pustulosis, psoriasis vulgaris and acne) are the key features of SAPHO, which shares certain similarities with SpA. SAPHO is closely related to paediatric chronic non-bacterial osteitis (CNO), a spectrum of autoinflammatory bone diseases. The aetiology of SAPHO is considered multifactorial based on a complex interplay of genetic, immune and infectious factors. Despite the increasing awareness of SAPHO/CNO, diagnostic delay is common, as validated classification and diagnostic criteria are lacking. Treatment of SAPHO represents a challenge and includes anti-inflammatory drugs, antibiotics, bisphosphonates, synthetic conventional DMARDs and off-label use of anti-cytokine biologics and Janus kinase inhibitors. This review summarizes the current diagnostic and practical treatment approach to SAPHO/CNO and highlights the ongoing research endeavours concerning the definition and validation of diagnostic criteria, core domains and treatment.
Inflammation of the temporalis muscle and adjacent nerve tissue in giant cell arteritis: expanding the spectrum of inflammatory lesions
Authors: Ruffer Nikolas , Holzer Marie-Therese , Kawelke Leona , Goebel Hans-Hilmar , Poddubnyy Denis , Schänzer Anne , Preuße Corinna , Krusche Martin , Schneider Udo , Stenzel Werner 
Published: October 2024

Abstract

Objective
The objective of this study was to investigate the histopathological features of the temporalis muscle (TM) and adjacent nerve tissue in active cranial giant cell arteritis (C-GCA).

Methods
Temporal artery biopsy (TAB) specimens containing fragments of the TM from patients with active C-GCA fulfilling the 2022 ACR/EULAR classification criteria (n = 11) were assessed by conventional histology and immunohistochemistry in comparison with non-GCA controls (n = 3). Clinical, laboratory and imaging features based on patient charts at time of biopsy were retrospectively recorded.

Results
The majority of the studied TAB specimens showed inflammation of the TM (10/11) and adjacent nerve fascicles (7/11) that was characterized by prominent endomysial lymphomonocytic infiltrates, whereas controls showed no inflammatory lesions and no disruption of the local architecture. The association of active C-GCA with sarcolemmal MHC class I (8/8) and MHC class II (6/11) upregulation suggests primary inflammation of the TM in a subset of patients. αB-Crystallin positivity (10/11) highlights areas of pre-necrotic myofibres within the TM. The presence of endomysial fibrosis, signs of atrophy and variations in muscle fibre size suggest a rather longstanding and potentially subclinical process of myoinflammation.

Conclusion
Our results expand the spectrum of inflammatory lesions known to be associated with active C-GCA. Specifically, inflammatory infiltration of the TM and adjacent nerve structures could contribute to localized symptoms of the temporomandibular region and may be included in future concepts of pathophysiology.
Arthralgia with risk of progression to psoriatic arthritis: role of clinical assessments and ultrasound as prognostic factors
Authors: Garcia-Salinas Rodrigo , Magri Sebastian , Mareco Jonatan , Jaldin Rosario , Perez Ronald , Ruta Santiago , Baraliakos Xenofon 
Published: October 2024

Abstract

Objectives
Referral of patients from dermatology to rheumatology practices due to psoriasis is unnecessary delayed. Many times musculoskeletal symptoms are the first reason for consultation. We aimed to estimate the proportion of ARP-PsA (arthralgia with risk to progression) defined by patients with arthralgia and the presence of psoriasis and/or a family history. Also, identify clinical, laboratory and imaging prognostic factors of PsA progression within the ARP-PsA group over a one year follow-up period.

Methods
Patients were included in a comprehensive arthralgia evaluation program, with the ARP-PsA criteria defined as arthralgia with Pso and/or a family history of Pso, not referred from dermatology. Baseline characteristics were analysed, and the progression to PsA at one year was assessed. Multivariate analysis identified predictor features for progression.

Results
Of the 1419 patients, 8.4% met ARP-PsA criteria, and 29% of this subgroup developed PsA at one year. Baseline differences between those who developed PsA and those who did not included family history, Pso duration, pain severity, joint count and imaging findings (X-ray and ultrasound). Multivariate analysis revealed the predictive significance of a combination of Pso plus family history of psoriasis disease, synovitis by Power Doppler ultrasound, ultrasound enthesopathy findings and low tender joint count.

Conclusion
The frequency of patients ARP-PsA was 8.4%, of whom 29% developed PsA at one year. The main predictor variables for this progression were identified.
Associations Between Noise Exposure Level, Noise Kurtosis, and Distortion Product Otoacoustic Emissions in Young Workers With Normal Hearing
Authors: Wei Fang , Zhao Wulan , Gao Xiangjing , Xue Panqi , Xu Fei , Xie Hongwei , Yang Ning , Zou Hua , Qiu Wei 
Published: October 2024

Objectives:
Growing evidence has suggested that, in addition to noise exposure level, noise temporal structure (i.e., kurtosis) plays an important role in the development of noise-induced hearing loss, while most of the relevant research has been on the results of pure-tone audiometry. This study focuses on the combined effect of noise exposure level and noise kurtosis on distortion product otoacoustic emissions (DPOAEs) in young workers with normal hearing.

Design:
A cross-sectional study among young workers in manufacturing industries was conducted in Zhejiang Province, China. Individual noise exposure measurements were performed on participants to obtain an A-weighted noise exposure level normalized to 8 hr (L
Aeq, 8hr), cumulative noise exposure (CNE), kurtosis, and kurtosis-adjusted CNE (CNE-K). The DPOAE test was performed on the participants and DPOAE levels were obtained. The relationships between noise exposure level, kurtosis, and DPOAE levels were explored by univariate analyses. Furthermore, multivariate regression models were conducted to estimate the combined effects of exposure level and kurtosis after adjusting for age, gender, and use of hearing protection devices.

Results:
The overall DPOAE curves across frequency bands presented a fluctuating downward trend with increasing frequency. Both exposure level and kurtosis were found to be associated with decreases in DPOAE levels. The multivariate regression model including CNE-K as a joint indicator of complex noise showed an increased R
2 compared with the model including CNE. After adjustment for age, gender, and the use of hearing protection devices, significant effects of CNE-K on DPOAE levels were observed at 3, 4, and 5 kHz frequencies, with maximum effect presented at 4 kHz.

Conclusions:
DPOAE is a sensitive test that can detect cochlear damage in limited areas that cannot be detected by conventional audiometry. The present study provided a more comprehensive understanding of the impact of complex noise on the DPOAE levels. It also suggested that CNE-K was an effective metric in assessing DPOAE levels associated with complex noise.
Erector Spinae Plane Block with Liposomal Bupivacaine for Adolescent Idiopathic Scoliosis Surgery
Authors: Young Ernest Y. , Gurd David , Kuivila Thomas , Seif John , Bess Leah , Goodwin Ryan 
Published: October 2024

Study Design:
Retrospective Controlled Cohort

Objective:
To evaluate the effect of intraoperative liposomal bupivacaine (LB) via Erector Spinae Plane Block (ESPB) on postoperative adolescent idiopathic scoliosis (AIS) patients with and without patient-controlled analgesia (PCA).

Summary of Background Data:
Pain control after posterior spinal fusion (PSF) for AIS includes opioids and other modalities. The goal of these modalities is to reduce pain and opioid consumption. Two new modalities for pain control include LB and ESPB. There are scant studies on these modalities tested in concert on patients undergoing PSF for AIS

Methods:
72 consecutive patients with AIS who underwent PSF separated into patients who had a PCA (Group A) as part of their postoperative pain management and those who did not (Group B). Opioid consumption was measured via Morphine Milligram Equivalents (MME). Pain scores were measured via the Visual Acuity Score (VAS). Patient mobility was measured by steps taken. These were measured by function of postoperative day from surgery (POD).

Results:
Group B had significant lower MME at every point after surgery, most notably throughout the entire hospital stay (99.8 vs. 200.7). Postoperative pain scores in Group B were the same if not better than Group A. There was no difference in mobility between the cohorts. The Group B had lower LOS (3.7 s 4.1).

Conclusion:
In postoperative PSF for AIS patients receiving LB via ESPB, those who did not receive a PCA had lower opioid consumption without worse pain scores or mobility and had a lower LOS. Adding LB via ESPB to postoperative pain regimens effectively replaces a PCA by providing the same pain control and reducing overall opioid consumption and LOS.