bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new broom sweeps clean: CLDN16 surpasses the BRAF-V600E mutation as an unrivaled biomarker in papillary thyroid cancer
Authors: Cai Yefeng , Guo Yawen , Ma Wenli , Cheng Pu , Jiang Liehao , Shen Shuyan , Song Fahuan , Zhu Lei , Hu Yiqun , Chen Yao , Duan Yanting , Cai Xiujun , Li Quan , Zheng Guowan , Ge Minghua 
Published: February 2025

Abstract

Objective
This study assessed CLDN16 as a potential replacement or improvement biomarker for papillary thyroid cancer (PTC), addressing the limitations associated with the prevalently used BRAF-V600E mutation.

Design
Database analyses, tissue validation, RNA sequencing, and functional assays were conducted to evaluate CLDN16 as a PTC biomarker and its clinical application.

Methods
CLDN16 expression was examined in PTC and normal thyroid/para-tumor tissues and compared across various cancer types. We evaluated diagnostic accuracy, stability in primary and metastatic sites, and associations with aggressive features. Knockdown experiments were performed to investigate the impact on PTC cell behavior. Additionally, we developed a support vector machine model for diagnosing malignant and high-risk PTCs.

Results
CLDN16 demonstrated high specificity for PTC, with positive detection rates (88.0% in The Cancer Genome Atlas [TCGA] and 88.3% in our center) significantly surpassing BRAF-V600E (47.5% in TCGA and 74.3% in our center). This resulted in superior diagnostic accuracy (ROC-CLDN16 = 0.922 vs ROC-BRAF-V600E = 0.742 in TCGA). CLDN16 exhibited stable expression across primary and metastatic sites and was associated with aggressive features, including extrathyroidal extension and lymph node metastasis. CLDN16 knockdown inhibited migration, invasion, and iodine uptake in PTC cells. Clinically, CLDN16 effectively identified malignancy in BRAF wild patients (94.2%), and combined with BRAF-V600E, achieved 96.9% accuracy. The incorporation of CLDN16 into PTC molecular typing facilitated precise high-risk identification (92.0% accuracy in the training set and 100% in the validation set).

Conclusions
CLDN16 presents a promising biomarker that could surpass BRAF-V600E, offering effective clinical utility and revolutionizing PTC molecular typing for precise high-risk identification.
The Global Scope of Competitive Legalities in the Early 19th-Century South China Sea: The Topaz Incident
Authors: Kroncke Jedidiah J , Li Haimo 
Published: February 2025

Abstract
This article examines the 1807 capture of the American merchant vessel Topaz by the British cutter HMS Diana in waters outside of Macau. By unearthing the full transnational context of this event, the article establishes the under-appreciated global scope of post-colonial American foreign policy as well as the early 19th-century Anglo-American rivalry that culminated in the War of 1812. Moreover, explicating the transnational dynamics of the Topaz incident demonstrates the similarly under-appreciated centrality of the China trade to this growing geopolitical rivalry. This trade was materially critical to the resolution of British ambitions in Europe during the Napoleonic Wars, and such importance drove aggressive British reactions to the rapid success of the USA as a re-exporter of Chinese goods. Similarly, Sino-American trade relations were a symbolically charged arena for American ambitions to establish a distinct post-colonial identity as a true adherent to the law of nations. Herein, recovering the full diplomatic and legal aftermath of the Topaz incident also reveals the importance of prize law as a global forum for this era of Anglo-American rivalry as well as how prize law’s particular form of quasi-privatized legality played into often opportunistic American invocations of ‘commercial empire’. The article’s mapping of the local and transnational reactions to the Topaz incident also challenges extant scholarship’s focus on Opium War-era treaty negotiations as the primary driver of Qing understandings of Western legalities by highlighting the neglected importance of pre-Opium War legal interactions, especially commercial interactions and conflicts.
How I became the man I had always been: Narrating the self in recent English and German life writing by trans men
Authors: Gratzke Michael 
Published: February 2025

Abstract
The literary corpus of this article consists of twenty-first-century life writing by trans men in the United States, Canada and Germany. The books fall broadly into two categories in line with Ruth Pearce’s distinction between trans-as-condition and trans-as-movement. A series of close readings uses Christa Binswanger and Andrea Zimmermann’s notion of palimpsestic queer subjectivity and Paul B. Preciado’s somatheque (trans body-as-archive) to highlight the commonalities of and differences between these two groups. This article concludes that any interpretation of trans people’s narratives needs to account for the position that the transition narrative is assigned in the text. Some writers go into great detail to create a coherent and comprehensive lifespan account, others focus on key episodes and yet another group, more commonly on the side of trans-as-movement, avoid autobiographical depth in favour of a focus on the near present in its social and political contexts.
Suppression of meiotic crossovers in pericentromeric heterochromatin requires synaptonemal complex and meiotic recombination factors in Drosophila melanogaster
Authors: Pazhayam Nila M , Sagar Sasha , Sekelsky Jeff 
Published: February 2025

Abstract
The centromere effect (CE) is a meiotic phenomenon that ensures meiotic crossover suppression in pericentromeric regions. Despite being a critical safeguard against nondisjunction, the mechanisms behind the CE remain unknown. Previous studies found that different regions of the Drosophila pericentromere, encompassing proximal euchromatin, beta and alpha heterochromatin, undergo varying levels of crossover suppression, raising the question of whether distinct mechanisms establish the CE in different regions. We asked whether different pericentromeric regions respond differently to mutations that impair features that may play a role in the CE. In flies with a mutation that affects the synaptonemal complex (SC), a structure is hypothesized to have roles in recombination and crossover patterning, we observed a redistribution of pericentromeric crossovers from proximal euchromatin towards beta heterochromatin but not alpha heterochromatin, indicating a role for the SC in suppressing crossovers in beta heterochromatin. In flies mutant for mei-218 or rec, which encode components of a critical pro-crossover complex, there was a more extreme redistribution of pericentromeric crossovers towards both beta and alpha heterochromatin, suggesting an important role for these meiotic recombination factors in suppressing heterochromatic crossovers. We mapped crossovers in flies mutant for Su(var)3-9, which encodes histone H3-lysine-9 methyltransferase. Although we expected strong alleviation of crossover suppression in heterochromatin, no changes in pericentromeric crossover distribution were observed in this mutant, indicating that this vital heterochromatin factor is dispensable for preventing crossovers in heterochromatin. Thus, in D. melanogaster the meiotic machinery seems to play a more significant role in suppressing centromere-proximal crossovers than chromatin state.
The Divergence of Mean Phenotypes Under Persistent Gaussian Selection
Authors: Lynch Michael , Menor Scott 
Published: February 2025

Abstract
Although multigenic traits are often assumed to be under some form of stabilizing selection, numerous aspects of the population-genetic environment can cause mean phenotypes to deviate from presumed optima, often in ways that effectively transform the fitness landscape to one of directional selection. Focusing on an asexual population, we consider the ways in which such deviations scale with the relative power of selection and genetic drift, number of linked genomic sites, magnitude of mutation bias, and the location of optima with respect to possible genotypic space. Even in the absence of mutation bias, mutation will influence evolved mean phenotypes unless the optimum happens to coincide exactly with the mean expected under neutrality. In the case of directional mutation bias and large numbers of selected sites, effective population sizes (Ne) can be dramatically reduced by selective-interference effects, leading to further mismatches between phenotypic means and optima. Situations in which the optimum is outside or near the limits of possible genotypic space (e.g., a half-Gaussian fitness function) can lead to particularly pronounced gradients of phenotypic means with respect to Ne, but such gradients can also occur when optima are well within the bounds of attainable phenotypes. These results help clarify the degree to which mean phenotypes can vary among populations experiencing identical mutation and selection pressures but differing in Ne, and yield insight into how the expected scaling relationships depend on the underlying features of the genetic system.
Topography Prediction from Marine Gravity and Satellite Imagery and Ship Soundings
Authors: Xu Huan , Wanga Qiuyu , Yu Jinhai , Anderson Ole Baltazar , Tian Yuwei , Xu Nan 
Published: February 2025

Summary
Marine observation data are plentiful for constructing seafloor topography, and the integration of multi-sources data to construct a more accurate topography model remains a significant subject that continues to be explored and studied. In this study, we use geoid height (GH), Gravity (VG) and Vertical Gravity Gradient (VGG) derived from a single rectangular prism to establish the foundational observation equations for predicting topography. The effectiveness of the foundational observation equations is verified through study cases without the use of the ship measurement depth data. Additionally, the single- and multi-beam soundings data are employed as control points to integrate into the foundational observation equations for predicting topography. The prediction results demonstrate that the prediction accuracy of combined VG anomalies with ship soundings is better than GH and VGG anomalies, which is primarily because VG anomalies are effective than GH amplify high frequency signals of topography and stronger than VGG anomalies in suppressing high frequency errors. Additionally, considering the limited accuracy of marine gravity in sea region with islands and reefs, this study incorporates satellite imagery data to identify the location and size of the islands. Then, the topography of the islands is introduced and the control equations is established to jointly predict topography. The prediction results reveal the RMS errors between prediction results and single- and multi-beam sounding data are 67.4 m, which is 37.4%, 57.8% and 62.8% higher than that of SRTM 15+, DTU and ETOPO-1 models respectively. Notably, compared with the STRM 15+ model, the algorithm improves the topography accuracy of the sea area near the islands by nearly 60.8%.
In silico analysis of pressure distribution and flow profiles across an experimental left ventricular assist device accessory
Authors: Osypka Anna , Meissner Florian , Ozturk Deniz , Windisch Roxane , Vestner Heiko , Galbas Michelle Costa , Czerny Martin , Bothe Wolfgang 
Published: February 2025

Abstract

OBJECTIVES
Implantation of left ventricular assist devices conventionally requires a sternotomy and cardiopulmonary bypass. An experimental accessory was designed to redirect the device’s outflow graft through the left ventricle into the ascending aorta. This design allows for implantation via left thoracotomy only but resulted in significant pressure loss both in vitro and in vivo. We evaluated the reasons for the pressure loss of the experimental accessory by quantifying pressure distribution and flow profiles using computational fluid dynamics simulation tools.

METHODS
A computational fluid dynamics model based on the accessory’s geometry was used to simulate nominal blood flow through the model. Quantities of interest included pressure and flow velocity. Pressure differences between the pump inlet and outlet were calculated at different rotational speeds (4000, 5200, 6400 rpm) and pump flow rates (1, 5, 8.4 L/min). Results were compared with simulations of a generic left ventricular assist device to determine the accessory's impact.

RESULTS
Natural pump characteristics were observed, as increased rotational speed caused an increase in pressure head with a constant flow rate. For all cases, a greater decrease in pressure head was seen between 5 and 8.4 L/min than between 1 and 5 L/min. Curvature intensity and channel bifurcation in the outflow were the main contributors to downstream pressure loss.

CONCLUSIONS
The next iteration of the LVAD accessory should focus on minimizing curvatures and avoiding bifurcations in the outflow. Further development may allow for less invasive left ventricular assist device implantation with negligible alterations in pump performance.
Microbiota contribute to regulation of the gut-testis axis in seasonal spermatogenesis
Authors: Wu Zifang , Li Long , Chen Shaoxian , Gong Ye , Liu Yuyan , Jin Tianqi , Wang Yang , Tang Jie , Dong Qian , Yang Bangzhu , Yang Fangxia , Dong Wuzi 
Published: February 2025

Abstract
Seasonal breeding is an important adaptive strategy for animals. Recent studies have highlighted the potential role of the gut microbiota in reproductive health. However, the relationship between the gut microbiota and reproduction in seasonal breeders remains unclear. In this study, we selected a unique single food source animal, the flying squirrel (Trogopterus xanthipes), as a model organism for studying seasonal breeding. By integrating transcriptomic, metabolomic, and microbiome data, we comprehensively investigated the regulation of the gut-metabolism-testis axis in seasonal breeding. Here, we demonstrated a significant spermatogenic phenotype and highly active spermatogenic transcriptional characteristics in the testes of flying squirrels during the breeding season, which were associated with increased polyamine metabolism, primarily involving spermine and γ-amino butyric acid. Moreover, an enrichment of Ruminococcus was observed in the large intestine during the BS and may contribute to enhanced methionine biosynthesis in the gut. Similar changes in Ruminococcus abundance were also observed in several other seasonal breeders. These findings innovatively revealed that reshaping the gut microbiota regulates spermatogenesis in seasonal breeders through polyamine metabolism, highlighting the great potential of the gut-testis axis in livestock animal breeding and human health management.
Duration of antibiotic treatment for respiratory tract infections in primary care
Authors: Llor Carl , Hansen Malene Plejdrup , Lykkegaard Jesper , Olsen Jonas , Lindberg Bent Håkan , Rebnord Ingrid Keilegavlen , Touboul Lundgren Pia , Bruno Pascale , Kowalczyk Anna , Lionis Christos , Radzeviciene Ruta , Jaruseviciene Lina , Bjerrum Lars , García-Sangenís Ana ,   HAPPY PATIENT Study Group, Mally Stella , Modena Daniela , Bjerrum Anders , Monfà Ramon , Pedrós Rosa Morros , Moragas Ana , Søndergaard Jens , Munck Anders , Berntsen Susanne Døssing , Nexøe Jørgen , Døssing-Poulsen Nina Camilla , Sebjørnsen Isabel , Lesage Vanessa , Godycki-Cwirko Maciek , Karkana Maria-Nefeli , Anastasaki Marilena , López-Valcárcel Beatriz González , Floriano Fabiana Raynal , Vallejo-Torres Laura , Chalkidou Athina , Jensen Jette Nygaard , Hansen Matilde Bøgelund , Cordoba Gloria , Taxis Katja , Lambert Maarten , Vilanova Pere , Álvarez Laura , Ricart Marta , Briones Sergi , Bandzaite Auste , Trečiokienė Indrė , Marquet Pierre , Benkő Ria , Tattevin Pierre , Cailleaux Marine , Ruppe Georg , Balint Andras 
Published: February 2025

Abstract

Objectives
The primary driver of antimicrobial resistance is excessive antibiotic use, posing a global threat to public health. Reducing individual exposure to antibiotics is a key to addressing the problem. This study aimed to assess the duration of antibiotic courses administered to patients with acute respiratory tract infections (RTIs) in primary care.

Methods
Consecutive patients presenting with RTI symptoms were prospectively included from general practices and out-of-hours services in France, Greece, Lithuania, Poland and Spain for two winter periods (February to April 2022 and 2023). Data were collected using a paper-based Audit Project Odense template, with clinicians recording patient age, gender, RTI diagnosis, type of antibiotic prescribed and treatment duration.

Results
A total of 196 doctors (133 in general practice and 63 in out-of-hours services) registered 11 270 cases, with 34.0% (3835) receiving antibiotics. The mean antibiotic course duration was 7.52 days (SD 2.11), which was significantly longer for pneumonia, COVID-19 infection and pharyngotonsillitis (8.01, 8.00 and 7.74 days, respectively), and lowest for predominantly viral infections, such as the common cold and flu infection, laryngitis and acute bronchitis (6.32, 6.48 and 6.98 days, respectively; P &lt; 0.001). A total of 26.7% of the courses were prescribed for 10 days or longer.

Conclusions
Antibiotic courses for common RTIs are often prolonged, which does not align with current recommendations for course duration. Antibiotics should be avoided in cases of predominantly viral infections and most mixed infections; however, if deemed necessary, the courses should be substantially reduced to minimize unnecessary exposure.
Increased sulfate-reducing bacteria can drive microbial dysbiosis in bleached corals
Authors: Sajid Sumbal , Xiao Baohua , Zhang Guoqiang , Zhang Zongyao , Chen Lianguo , Fang James Kar-Hei , Lu Yishan , Cai Lin 
Published: February 2025

Abstract

Aims
Coral bleaching occurs when coral colonies lose their Symbiodiniaceae partner and turn pale or white. Although this event is generally temperature-induced, there is also the possibility of holobiont microbial infection and dysbiosis. To address this issue, this study was conducted to investigate the diversity and composition of Symbiodiniaceae and bacteria in healthy and bleached colonies of Porites lutea collected from eastern Shenzhen.

Methods and results
Internal transcribed spacer 2 (ITS2) and 16S amplicon sequencing analysis were used to explore the diversity and composition of Symbiodiniaceae and bacteria in healthy and bleached colonies of P. lutea. Bacterial diversity and richness were significantly higher in bleached colonies than in healthy colonies (P &lt; 0.05), whereas the diversity and richness of Symbiodiniaceae showed no significant changes. The bleaching event exerted a more significant impact on Symbiodiniaceae composition, which differed between healthy and bleached colonies (PERMANOVA, F = 8.246, P &lt; 0.05). In terms of composition, Clade C (Cladocopium) was the predominant Symbiodiniaceae, whereas subclade C116 and C2r were significantly less abundant in bleached colonies than in healthy colonies (P &lt; 0.05). The phyla Bacteroidetes, Acidobacteria, and Actinobacteria were significantly more abundant in bleached colonies than in healthy colonies (P &lt; 0.05). The sulfate-reducing bacteria (SRB) Desulfobulbus and Desulfobacter at the genus level and Desulfobacterales and Desulfuromonadales at the order level were significantly more abundant in bleached colonies than in healthy colonies (P &lt; 0.05). The co-occurrence patterns of Symbiodiniaceae and bacteria revealed a negative correlation of Desulfofaba, Desulfovibrio, Desulfarculus, and Desulfobulbus with Endozoicomonas, a very common symbiotic bacterial genus found in corals.

Conclusion
Coral bleaching may be associated with significant shifts in microbial communities, including increased SRB abundance, which may disrupt microbial balance and contribute to bleaching.
Deciphering genomic codes using advanced natural language processing techniques: a scoping review
Authors: Cheng Shuyan , Wei Yishu , Zhou Yiliang , Xu Zihan , Wright Drew N , Liu Jinze , Peng Yifan 
Published: February 2025

Abstract

Objectives
The vast and complex nature of human genomic sequencing data presents challenges for effective analysis. This review aims to investigate the application of natural language processing (NLP) techniques, particularly large language models (LLMs) and transformer architectures, in deciphering genomic codes, focusing on tokenization, transformer models, and regulatory annotation prediction. The goal of this review is to assess data and model accessibility in the most recent literature, gaining a better understanding of the existing capabilities and constraints of these tools in processing genomic sequencing data.

Materials and Methods
Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, our scoping review was conducted across PubMed, Medline, Scopus, Web of Science, Embase, and ACM Digital Library. Studies were included if they focused on NLP methodologies applied to genomic sequencing data analysis, without restrictions on publication date or article type.

Results
A total of 26 studies published between 2021 and April 2024 were selected for review. The review highlights that tokenization and transformer models enhance the processing and understanding of genomic data, with applications in predicting regulatory annotations like transcription-factor binding sites and chromatin accessibility.

Discussion
The application of NLP and LLMs to genomic sequencing data interpretation is a promising field that can help streamline the processing of large-scale genomic data while also providing a better understanding of its complex structures. It has the potential to drive advancements in personalized medicine by offering more efficient and scalable solutions for genomic analysis. Further research is also needed to discuss and overcome current limitations, enhancing model transparency and applicability.

Conclusion
This review highlights the growing role of NLP, particularly LLMs, in genomic sequencing data analysis. While these models improve data processing and regulatory annotation prediction, challenges remain in accessibility and interpretability. Further research is needed to refine their application in genomics.