bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-density migratory beekeeping induces intermediate disturbance effects on native bee communities in Tibetan Plateau alpine meadows
Authors: Vaudo Anthony D , Orr Michael C , Zhou Qing-Song , Zhu Chao-Dong , Mu Junpeng , López-Uribe Margarita M 
Published: November 2024

Abstract
Ecological disturbance can promote or reduce community biodiversity depending on its severity. Beekeeping activities represent a type of ecological disturbance when large numbers of honey bees are introduced to a landscape and interact with the local plant and pollinator community. In this study, we characterized the effect of immediate and long-term low-density migratory beekeeping on the diversity and abundance of native bees in the Qinghai-Tibet Plateau (China). We found that the presence of apiaries and the number of honey bees reduced native bee abundances in the local bee community, likely through displacement from floral resources. However, in locations where apiaries were previously kept for decades but are not currently present, native bee abundances recovered, and phylogenetic diversity increased; yet community relative abundances and dominant species were distinct from those that had never been stocked. Our results suggest that the presence of a transient, intermediate number of migratory honey bee colonies (60–100 colonies spaced ≥15 km from each other) may represent an intermediate ecological disturbance and not permanently reduce native bee abundances past a critical threshold that may lead to local extirpation. Yet, our study demonstrates the potential for even intermediate-scale low-density beekeeping to alter native bee communities in the long-term.
The tumor–neutrophil interactions in the microenvironment of brain metastases with different primary sites
Authors: Kaya Tamer A , Stein Klaus-Peter , Schaufler Anna , Neyazi Belal , Rashidi Ali , Kahlert Ulf D , Mawrin Christian , Sandalcioglu I Erol , Dumitru Claudia A 
Published: November 2024

Abstract
Brain metastases originating from lung and breast cancer can recruit and activate neutrophils to acquire a tumor-promoting phenotype. It is currently unclear if this phenomenon also occurs in brain metastases arising from other primary sites. Here, we investigated the effect of tumor cells isolated from melanoma, lung cancer, and gastrointestinal cancer brain metastases on neutrophil biology and functions. We found that lung and gastrointestinal but not melanoma brain metastasis cells produced CXCL8/IL-8 and promoted neutrophil recruitment. Similarly, lung and gastrointestinal but not melanoma brain metastasis cells prolonged the survival of neutrophils and stimulated them to release MMP9 and CCL4/MIP1β. In situ, lung and gastrointestinal brain metastasis tissues contained significantly higher numbers of tumor-infiltrating neutrophils compared to melanoma brain metastases. The levels of neutrophil infiltration significantly correlated with the proliferation index of these tumors. Our findings identify variabilities in the immune microenvironment of brain metastases with different primary sites, which may ultimately affect their pathophysiology and progression.
TORquing chromatin: the regulatory role of TOR kinase in chromatin function
Authors: Dong Yihan , Aflaki Fatemeh , Mozgova Iva , Berr Alexandre 
Published: November 2024

Abstract
The target of rapamycin (TOR) kinase is a critical regulator of plant growth and development, integrating environmental and internal signals to modulate cellular processes. This review explores the emerging role of TOR in chromatin regulation, focusing on its nuclear activities and interactions with chromatin remodeling factors. We highlight the mechanisms by which TOR influences chromatin structure and gene expression, including its involvement in histone modifications and DNA methylation. Additionally, we discuss the interplay between TOR signaling, the cytoskeleton, and nuclear functions, emphasizing the potential of TOR to act as a bridge between cytoskeletal dynamics and chromatin regulation. Finally, besides TOR-mediated cyto-nuclear shuttling and metabolic regulation, we address the translational control of chromatin components by TOR as additional layers impacting the chromatin landscape. We also propose future research directions to further elucidate the complex regulatory network governed by TOR in plant cells.
Correlation of the abundance of MDSCs, Tregs, PD-1, and PD-L1 with the efficacy of chemotherapy and prognosis in gastric cancer
Authors: Li Na , Li Yun , Li Jing , Tang Shimin , Gao Hongbo , Li Yong 
Published: November 2024

Abstract

Objective
The aim of this study was to investigate the relationship between tumor microenvironment markers (myeloid-derived suppressor cells [MDSCs], regulatory T cells [Tregs], programmed cell death 1 [PD-1], and programmed death ligand 1 [PD-L1]) and chemotherapy efficacy and prognosis in advanced gastric cancer, identifying potential monitoring indicators.

Methods
Advanced gastric cancer patients’ MDSC and Treg expression was measured by flow cytometry pre- and postchemotherapy; PD-1 and PD-L1 expression in cancer tissues was assessed by immunohistochemistry. Correlations with chemotherapy outcomes and prognosis were analyzed.

Results
Postchemotherapy reductions in MDSC and Treg levels correlated with chemotherapy efficacy (P &lt;.01). Negative PD-1 and PD-L1 expression in cancer tissues predicted better chemotherapy responses (P &lt;.01). Patients with lower MDSC and Treg levels and negative PD-1 and PD-L1 had significantly longer median progression-free survival (PFS) and overall survival (OS) (P &lt;.05).

Conclusion
In advanced gastric cancer, reduced peripheral blood MDSC and Treg levels postchemotherapy and negative PD-1 and PD-L1 expression in tissues are associated with improved chemotherapy efficacy and are independent prognostic factors for PFS and OS.
GENCODE 2025: reference gene annotation for human and mouse
Authors: Mudge Jonathan M , Carbonell-Sala Sílvia , Diekhans Mark , Martinez Jose Gonzalez , Hunt Toby , Jungreis Irwin , Loveland Jane E , Arnan Carme , Barnes If , Bennett Ruth , Berry Andrew , Bignell Alexandra , Cerdán-Vélez Daniel , Cochran Kelly , Cortés Lucas T , Davidson Claire , Donaldson Sarah , Dursun Cagatay , Fatima Reham , Hardy Matthew , Hebbar Prajna , Hollis Zoe , James Benjamin T , Jiang Yunzhe , Johnson Rory , Kaur Gazaldeep , Kay Mike , Mangan Riley J , Maquedano Miguel , Gómez Laura Martínez , Mathlouthi Nourhen , Merritt Ryan , Ni Pengyu , Palumbo Emilio , Perteghella Tamara , Pozo Fernando , Raj Shriya , Sisu Cristina , Steed Emily , Sumathipala Dulika , Suner Marie-Marthe , Uszczynska-Ratajczak Barbara , Wass Elizabeth , Yang Yucheng T , Zhang Dingyao , Finn Robert D , Gerstein Mark , Guigó Roderic , Hubbard Tim J P , Kellis Manolis , Kundaje Anshul , Paten Benedict , Tress Michael L , Birney Ewan , Martin Fergal J , Frankish Adam 
Published: November 2024

Abstract
GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables us to identify large numbers of missing transcripts and to substantially improve existing models, and our long non-coding RNA catalogs have undergone a dramatic expansion and reconfiguration as a result. Meanwhile, we are incorporating data from state-of-the-art proteomics and Ribo-seq experiments to fine-tune our annotation of translated sequences, while further insights into function can be gained from multi-genome alignments that grow richer as more species’ genomes are sequenced. Such methodologies are combined into a fully integrated annotation workflow. However, the increasing complexity of our resources can present usability challenges, and we are resolving these with the creation of filtered genesets such as MANE Select and GENCODE Primary. The next challenge is to propagate annotations throughout multiple human and mouse genomes, as we enter the pangenome era. Our resources are freely available at our web portal www.gencodegenes.org, and via the Ensembl and UCSC genome browsers.
L1-ORF1p nucleoprotein can rapidly assume distinct conformations and simultaneously bind more than one nucleic acid
Authors: Cashen Ben A , Naufer M Nabuan , Morse Michael , McCauley Micah J , Rouzina Ioulia , Jones Charles E , Furano Anthony V , Williams Mark C 
Published: November 2024

Abstract
LINE-1 (L1) is a parasitic retrotransposable DNA element, active in primates for the last 80–120 Myr. L1 has generated nearly one-third of the human genome by copying its transcripts, and those of other genetic elements (e.g. Alu and SVA), into genomic DNA by target site-primed reverse transcription (TPRT) and remains active in modern humans. L1 encodes two proteins that bind their encoding transcript (cis preference) to form an L1 ribonucleoprotein (RNP) that mediates retrotransposition. ORF2p provides reverse transcriptase and endonuclease activity. ORF1p, its major component, is a homo-trimeric phospho-protein that binds single-stranded nucleic acid (ssNA) with high affinity and exhibits nucleic acid (NA) chaperone activity. We used optical tweezers to examine ORF1p binding to individual single-stranded DNA (ssDNA) molecules and found that the arrangement of ORF1p on the ssDNA depends on their molar ratio. When the concentration of ORF1p is just sufficient to saturate the entire NA molecule, the nucleoprotein (NP) is compact and stable. However, additional ORF1p binds and destabilizes the compacted NP, allowing it to engage a second ssDNA. Our results suggest that ORF1p displaced from its RNA template during TPRT could bind and destabilize remaining downstream L1 RNP, making them susceptible to hijacking by non-L1 templates, and thereby enable retrotransposition of non-L1 transcripts.
Interrogation of the interplay between DNA N6-methyladenosine (6mA) and hypoxia-induced chromatin accessibility by a randomized empirical model (EnrichShuf)
Authors: Lai Joseph Chieh-Yu , Hsu Kai-Wen , Wu Kou-Juey 
Published: November 2024

Abstract
N 6-Methyladenosine (6mA) is an epigenetic mark in eukaryotes regulating development, stress response and tumor progression. METTL4 has been reported as a 6mA methyltransferase induced by hypoxia. The detection and annotation of 6mA signals in mammalian cells have been hampered by the techniques and analytical methods developed so far. Here we developed a 6mA-ChIP-exo-5.1-seq to improve the sensitivity of detecting 6mAs in human cell lines. Furthermore, an EnrichShuf analysis tool for comprehensively comparing 6mA-ChIP-exo-5.1-seq, ATAC-seq, ChIP-seq and RNA-seq has been developed to annotate the functional relevance of 6mA in relation to chromatin accessibility and histone marks. Using a hypoxia-induced 6mA induction system as a model, we showed that hypoxic 6mA signals positively correlated with accessible chromatin regions. These 6mA signals correlate with their regulation by METTL4 under hypoxia, consistent with previous results. 6mAs also co-exist with H3K4me1, a histone mark for enhancers. Further analysis of enhancers using an ABC (active-by-contact) model shows that hypoxia-inducible factor-1α-induced H3K4me3 surrounds the 6mA/H3K4me1 site to augment active enhancers. These results suggest that correlation between 6mA and accessible chromatin regions plays a significant role in enhancer–promoter interactions during hypoxia-induced gene expression.
The use of wearable technology in studies in older adults with cancer: a systematic review
Authors: Duin Jan J , Baltussen Joosje C , Albalak Gali , van Dam van Isselt Eléonore F , Portielje Johanneke E A , Mooijaart Simon P , Soto-Perez-de-Celis Enrique , van den Bos Frederiek 
Published: November 2024

Abstract

Background
Despite the increasing integration of wearable technology in oncology, its application in the care of older adults, representing most patients with cancer, is poorly defined.

Objective
This systematic review aimed to summarize the current use of wearables in studies in older adults with cancer.

Methods
This systematic review was conducted following the PRISMA guidelines. A systematic search was conducted in PubMed, Embase, Emcare, Web of Science, and Cochrane Library on May 1, 2024. Studies involving wearable devices and patients aged ≥60 years diagnosed with cancer were included. Outcomes reported were study characteristics, wearable outcomes, feasibility and adherence. The mixed method appraisal tool was used to assess the quality of included studies.

Results
A total of 31 publications were included, comprising 1298 older patients. Of these, 12 were pilot/feasibility studies, 12 were observational studies, 6 were randomized controlled trials, and 1 was a cross-sectional study. Most studies used wearable data to measure recovery (19 studies, 61%). Physical activity was the most studied wearable outcome (27 studies, 87%). Adherence to the wearable device was documented in 11 of the 31 studies (35%), with adherence ranging from 74% to 100%.

Conclusions
Our systematic review found wearables were mostly used to measure physical activity, with the most common primary aim of measuring recovery. Most studies reported high adherence, although definitions of adherence were diverse. Our results highlight the need for more and larger studies on wearable technology in older cancer patients, the use of standardized reporting frameworks, and increased participation in research in low- and middle-income countries.
Roman Catholic Exegesis from the Spirituali to the Jesuits
Authors: Roldán-Figueroa Rady 
Published: November 2024

Abstract
The exegetical habits of the spirituali and the Jesuits are explored in this case study through a focused examination of the exegetical theory and practice of Cardinal Gasparo Contarini (1483–1542) and Juan Maldonado, SJ (1533–83). A comparative approach to these figures illuminates the ways that the spirituali’s irenicism and Jesuit’s Counter-Reformation militancy shaped corresponding exegetical practices. Contarini’s exegetical method is gleaned from his Scholia in epistolas divi Pauli (1571). Discussion of Maldonado’s theory of exegesis, on the other hand, is based on his De ratione theologiae docendae (1573). The chapter concludes by pointing out that the contrast between these two exegetical approaches underscores an intra-confessional tendency in early modern Catholicism towards post-Tridentine regulation and normalization of exegetical practices.
Thomas Müntzer (1489–1525)
Authors: Martinuzzi Christopher 
Published: November 2024

Abstract
Thomas Müntzer was primarily a humanist theologian, scholar, and pastor active in the dawning years of the Reformation. He developed a theology of the Spirit that centered around the notion of direct divine revelation. God spoke directly to all human beings through a fragment of the Holy Spirit present in the abyss of the soul, rendering the Bible’s supposed revelatory nature void. Müntzer’s thought collided with the historical course that was rushing fast toward the Peasants’ War, the 1525 massacre of Frankenhausen, his execution, and the inevitable failure of his theological program. Müntzer’s death represented a momentary disappearance of radical spiritualism within the context of the Reformation; one that ultimately undermined the revelatory role of Scripture (though not its authority and example) in favor of a form of revelation that was direct and present a priori in all human hearts. Nevertheless, the reformer remains an important early Reformation exegete.
Martin Bucer (1491–1551)
Authors: Noblesse-Rocher Annie 
Published: November 2024

Abstract
Martin Bucer is one of the most important exegetes of the Reformation of the sixteenth century. He authored numerous biblical commentaries that influenced Reformed exegesis in the next generation. In his work, he used medieval Jewish authors to ascertain the literal meaning of the text and, as a result, renewed the four medieval scriptural meanings by developing a new anagogical approach that contributed to the updating of the Bible for the readers of his time. His commentaries were also a way for him to defend Reformation theology against the Anabaptists. In particular, the commentary on Zephaniah and the commentary on John are reflective of the confrontation that took place with some of the dissidents residing in Strasbourg in the 1530s. The French and English translations of his work indicate that influence. His skill as a Christian Hebraist made him something of a Nicholas of Lyra during the Reformation.
Marie Dentière (c.1495–1561)
Authors: Pak G. Sujin 
Published: November 2024

Abstract
Marie Dentière was converted to the Protestant faith in the early to mid-1520s. This chapter explores her life and the historical circumstances to which her writings responded, with a particular focus on Marie’s uses of Scripture in her Very Useful Epistle (1539). This text illuminates not only her scriptural themes and exegetical strategies. Dentière aimed to apply biblical histories and scriptural signs to interpret the events of her time, rebuke worship practices that she deemed contrary to God’s Word, and expound a vision for Protestant unity for which she argued that women had a distinct and crucial role to play. She also offered more than just a defense of women reading Scripture; she provided one of the first examples of an early modern Reformed woman’s extensive engagement with Scripture around themes of right worship and a vision for Protestant unity rooted in God’s Word alone.
Jean Calvin (1509–1564)
Authors: Holder R. Ward 
Published: November 2024

Abstract
This chapter summarizes Calvin’s engagement with the Bible. It provides a brief biographical sketch keyed to Calvin’s education in the Bible and biblical languages, and the influences that contributed to his formation. The chapter then considers the genres of his engagement with Scripture, especially commentaries, lectures, sermons, the congrégations, and the manner that his theological masterwork, the Institutes of the Christian Religion, worked with his biblical-interpretive works to edify the church of Geneva. That effort, in concert with the work of the Genevan Consistory, the sermons, the work of explicating Scripture in the Genevan Academy and the catechetical training, effected the creation of a biblical community in Geneva.
Church and State (Rom. 13)
Authors: Brown Allison M. 
Published: November 2024

Abstract
Structured around significant moments of political crisis, this chapter explores the use of Romans 13 in the sixteenth century. Through peasant rebellions, war, exile, and persecution, Romans 13 provided a foundation for understanding the Christian’s relationship to the state. In this era, debates over the role and authority of rulers and the extent to which they should be obeyed by Christians erupted as Protestants attempted to survive, grow, and establish legitimacy. Some Protestant writers emphasized obedience to civil rulers and bolstered the rulers’ authority, while others advocated for resistance, rebellion, and even regicide. Intertwined in these interpretations and rhetoric are complex questions on how one can be both a faithful Christian and faithful subject of the realm.
Improving senior medical workforce retention at a large teaching hospital trust
Authors: Longwell Sarah , McLure Hamish , Jain Sunjay 
Published: November 2024

Abstract

Purpose
To understand senior clinicians’ current thinking regarding retirement at a large teaching hospital trust, the reasons behind it, and what the trust can do to improve retention of these valuable staff.

Methods
An anonymized survey followed by qualitative study from a focus group. Data from these were analysed using a thematic analysis. Participants were senior clinicians currently employed or who had taken retirement from the trust in the preceding 12 months. In total 140 respondents completed the survey, giving a response rate of 65%; 8 senior clinicians attended the focus group.

Results
The commonest reasons for taking retirement were wanting to pursue leisure interests, reaching a pensionable age, and feeling unable to sustain their workloads. A significant proportion, 29%, also cited that they did not feel valued. The commonest factors that would encourage respondents to remain at work included increased flexibility, reduced hours, and ability to come off on-call rotas. The main themes from the focus group were focusing on well-being, personalized conversations, and better/more accessible information.

Conclusion
Our project identified a number of reasons why clinicians are considering taking retirement, with a major theme of feeling valued underpinning decisions. This could influence strategies to help retain these experienced members of staff. We made a series of recommendations. If enacted, these would have a wider-reaching impact on more junior medical staff, aiding them to consider their own late-stage careers. They are also applicable and could easily be adapted when considering retention of other valued professionals within the trust.
Key messages What is already known on this topic—We know that there is currently a medical workforce crisis at a time of greatest patient need, with an ageing workforce and senior staff who are choosing to retire early. Previous studies have reviewed the reasons behind these decisions but not specifically looked at changes that can be implemented at a local level to improve retention. What this study adds—We combined both quantitative and qualitative data from senior clinicians at a large teaching hospital trust in the North of England to understand current thinking regarding retirement and what the trust could do to improve their retention. How this study might affect research, practice, or policy—From our study we were able to make a series of recommendations that can be implemented at a local level to inform medical retention policies. These will also have wider impacts on junior medical staff and could be expanded to other healthcare professionals.
What must a medical student learn?
Authors: Franklin Gustavo L 
Published: November 2024

Abstract
Studying medicine is not a passive activity; it demands dedication, curiosity, and continuous learning through observation, reading, and repetition. The Latin root of “student” reflects eagerness, and similarly, “aluno” derives from “alere,” meaning “to nourish,” symbolizing the nourishment of knowledge. As students, it is crucial to understand not just the scientific knowledge but also the human side of medicine. Learning goes beyond textbooks. Patients themselves are the greatest source of wisdom. Medicine is the art of care, offering comfort and understanding of what is hidden beneath the surface. Growth in this field requires seeing beyond the obvious and developing strategies to understand patients’ stories. The medical student may develop strategies to know how to listen, build trust, and empathize with patients, guiding them through their fears. Carrying their burdens and interpreting their unspoken words is essential for providing both medical care and comfort.