bluuebunny/crossref_metadata_2025_split huggingface dataset:
County-level racial disparities in prostate cancer–specific mortality from 2005 to 2020
Authors: Washington III Samuel L , Fakunle Mary , Wang Lufan , Braun Avery E , Leapman Michael , Cowan Janet E , Cooperberg Matthew R 
Published: November 2024

Abstract

Background
Local conditions where people live continue to influence prostate cancer outcomes. By examining local characteristics associated with trends in Black-White differences in prostate cancer–specific mortality over time, we aim to identify factors driving county-level prostate cancer–specific mortality disparities over a 15-year period.

Methods
We linked county-level data (Area Health Resource File) with clinicodemographic data of men with prostate cancer (Surveillance, Epidemiology, and End Results registry) from 2005 to 2020. Generalized linear mixed models evaluated associations between race and county-level age-standardized prostate cancer–specific mortality, adjusting for age; year of death; rurality; county-level education; income; uninsured rates; and densities of urologists, radiologists, primary care practitioners, and hospital beds.

Results
In 1085 counties, 185 390 patients were identified of which 15.8% were non-Hispanic Black. Racial disparities in prostate cancer–specific mortality narrowed from 2005 to 2020 (25.4 per 100 000 to 19.2 per 100 000 overall, 57.9 per 100 000 to 38 per 100 000 for non-Hispanic Black patients, and 23.4 per 100 000 to 18.3 per 100 000 for non-Hispanic White patients). For non-Hispanic Black and non-Hispanic White patients, county prostate cancer–specific mortality changes varied greatly (-65% to +77% and -61% to +112%, respectively). From 2016 to 2020, non-Hispanic Black patients harbored greater prostate cancer–specific mortality risk (relative risk = 2.09, 95% confidence interval [CI] = 2.01 to 2.18); higher radiation oncologist density was associated with lower mortality risk (relative risk = 0.93, 95% CI = 0.89 to 0.98), while other practitioner densities were not.

Conclusion
Although overall rates improved, specific counties experienced worsening race-based disparities over time. Identifying locations of highest (and lowest) mortality disparities remains critical to development of location-specific solutions to racial disparities in prostate cancer outcomes.
Predictors of duty sex frequency in women
Authors: Metcalfe Kate B , Kilimnik Chelsea D , Meston Cindy M 
Published: November 2024

Abstract

Background
Duty Sex—the act of engaging in sex out of a sense of duty or obligation to a partner—is a commonly reported reason why women have sex, with studies indicating associations between Duty Sex and sexual dysfunction, as well as nonconsensual sexual experiences (NSEs).

Aim
This study sought to examine the associations between Duty Sex frequency, sexual function, and NSEs using comprehensive, validated measures of sexual function and NSE histories in a large community sample of women.

Methods
Six hundred and fifty-eight women with (n = 293) and without (n = 365) NSE histories completed measures of sexual function and sexual motivations.

Results
Women with NSE histories reported more sexual pain, lower sexual satisfaction, and more frequent Duty Sex. The relation between NSE history and Duty Sex remained after controlling for the variance in sexual function. The type of NSE behavior, but not the timing of the first NSE nor the perceived impact of the experience, predicted Duty Sex frequency.

Clinical implications
Clinicians should consider sexual motivations, particularly Duty Sex, when treating women with NSE histories or who experience sexual dysfunction.

Strengths and Limitations
To our knowledge, this was the first study to examine how NSEs relate to all domains of sexual function and sexual motives, revealing a link between NSEs, sexual function, and Duty Sex. However, we were unable to account for what percentage of sexual encounters are considered Duty Sex. Therefore, our measurement of Duty Sex lacks specificity, which may explain the relatively low variance accounted for by the models in our analyses.

Conclusions
There are consequences of NSEs, including difficulties with communicating sexual boundaries and impairment of sexual function, that may contribute to the increased likelihood of engaging in Duty Sex.
β-Aminobutyric acid-induced resistance in postharvest peach fruit involves interaction between the MAPK cascade and SNARE13 protein in the salicylic acid-dependent pathway
Authors: Li Chunhong , Wang Kaituo , Lei Changyi , Zou Yanyu , Yang Sisi , Xiang Fei , Li Meilin , Zheng Yonghua 
Published: November 2024

Abstract
The inducer β-aminobutyric acid (BABA) participates in the immune response in various plants. However, the specific mitogen-activated protein kinase (MAPK) cascade involved in BABA-induced resistance (BABA-IR) has not yet been elucidated. Here, peach (Prunus persica) fruits treated with the BABA exhibited pattern-triggered immunity defense against Rhizopus stolonifer, accompanied by the generation of reactive oxygen species and activation of a MAPK cascade. Transcriptome sequencing suggested that a total of 15 MAPK kinase kinase (PpMAPKKK)/MAPK kinase (PpMAPKK)/PpMAPK genes were involved in BABA-IR in peach fruit. Further qRT-PCR analysis showed that the transcript profiles of PpMAPKKK3, PpMAPKK5, and PpMAPK1 were elevated. Subsequently, yeast two-hybrid, luciferase complementation imaging, pull-down, and in vitro phosphorylation assays were conducted to characterize the complete MAPK cascade (PpMAPKKK3–PpMAPKK5–PpMAPK1) involved in peach fruit. Moreover, the downstream events of MAPK1 include the involvement of SNARE13 and the corresponding NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1)-responsive defense. Single silencing of MAPKKK3, MAPKK5, or MAPK1 and double silencing of MAPKKK3 and MAPKK5 or MAPKK5 and MAPK1 resulted in enhanced susceptibility to the fungus R. stolonifer in mutants and attenuated salicylic acid (SA)-dependent defense gene expression. In contrast, the homologous or heterologous overexpression of PpSNARE13 in peach fruit or Arabidopsis led to an enhanced SA pool and elevated expression of pathogenesis related (PR) genes. Reciprocally, the ppsnare13cas9 mutants were generally compromised in the priming of SA-dependent resistance. Therefore, the MAPKKK3–MAPKK5–MAPK1 cascade contributed to pattern-triggered immunity signal transduction in BABA-elicited peach fruit, by combination with downstream events such as SNARE13, NPR1, and SA-dependent signaling.
Wave Optical Modeling of the SEM Column From Source to Specimen
Authors: Kamal Surya , Zhou Yongjian , Gong Zizhou 
Published: November 2024

Abstract
Probe formation in scanning electron microscope (SEM) is often reduced to objective lens action modeling based on a point-spread function or Fourier transforms. In this study, we present the first complete wave optical modeling of the whole SEM column based on plane-by-plane propagation of the electron beam wavefunction without simplifying the optical system. We identify the challenges in plane-by-plane beam propagation and show how sampling limitations produce aliased results. Through a careful selection and combination of propagators, we have developed a general wave optical propagation method that is able to overcome the aliasing problem to achieve the appropriate probe widths. Using a two-step propagator, we show that it is possible to model the electron beam distribution throughout the column from the virtual source plane to the specimen plane. We also show that our results from the wave optical simulations are consistent with the geometrical theory of probe formation. Finally, as a direct application of this method, we demonstrated that the combined effect of aberrations in the condenser lens and the probe forming objective lens cannot be accurately represented using only the objective lens. Designing beam shaping experiments and studying the effect of partial coherence can be some novel applications.
Variations of flare energy release behaviour and magnetic loop characteristics versus absolute stellar parameters
Authors: Yoldaş E , Dal H A 
Published: November 2024

ABSTRACT
In this paper, we examine how stellar flare activity varies with evolution stage, rotation period, and spectral type. To do this, we examine the distributions of the flare equivalent duration on a logarithmic scale, which we consider as an indicator of the maximum energy level that a star can reach in white-light flares. We conduct these analyses using two distinct statistical models of data obtained from white-light flare patrols of 33 stars. These models are the one-phase exponential association (OPEA) and cumulative flare frequency models. The results show that the value of the OPEA model parameter Plateau has a linear relationship with the stellar B – V colour index and the rotation period. In addition, it is shown that flare time-scales, and therefore the maximum magnetic loop height that stars can have, vary according to the evolutionary stage of the star. Finally, it is concluded that the cumulative flare frequency parameters of the stars are not as effective as the OPEA parameters at exhibiting these variations.
The PRIDE database at 20 years: 2025 update
Authors: Perez-Riverol Yasset , Bandla Chakradhar , Kundu Deepti J , Kamatchinathan Selvakumar , Bai Jingwen , Hewapathirana Suresh , John Nithu Sara , Prakash Ananth , Walzer Mathias , Wang Shengbo , Vizcaíno Juan Antonio 
Published: November 2024

Abstract
The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s leading mass spectrometry (MS)-based proteomics data repository and one of the founding members of the ProteomeXchange consortium. This manuscript summarizes the developments in PRIDE resources and related tools for the last three years. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 534 datasets per month. This has been possible thanks to continuous improvements in infrastructure such as a new file transfer protocol for very large datasets (Globus), a new data resubmission pipeline and an automatic dataset validation process. Additionally, we will highlight novel activities such as the availability of the PRIDE chatbot (based on the use of open-source Large Language Models), and our work to improve support for MS crosslinking datasets. Furthermore, we will describe how we have increased our efforts to reuse, reanalyze and disseminate high-quality proteomics data into added-value resources such as UniProt, Ensembl and Expression Atlas.
RNA G-quadruplex formation in biologically important transcribed regions: can two-tetrad intramolecular RNA quadruplexes be formed?
Authors: Basu Pritha , Kejnovská Iva , Gajarský Martin , Šubert Denis , Mikešová Tereza , Renčiuk Daniel , Trantírek Lukáš , Mergny Jean-Louis , Vorlíčková Michaela 
Published: November 2024

Abstract
G-quadruplexes (G4s) formed within RNA are emerging as promising targets for therapeutic intervention in cancer, neurodegenerative disorders and infectious diseases. Sequences containing a succession of short GG blocks, or uneven G-tract lengths unable to form three-tetrad G4s (GG motifs), are overwhelmingly more frequent than canonical motifs involving multiple GGG blocks. We recently showed that DNA is not able to form stable two-tetrad intramolecular parallel G4s. Whether RNA GG motifs can form intramolecular G4s under physiological conditions and play regulatory roles remains a burning question. In this study, we performed a systematic analysis and experimental evaluation of a number of biologically important RNA regions involving RNA GG motifs. We show that most of these motifs do not form stable intramolecular G4s but need to dimerize to form stable G4 structures. The strong tendency of RNA GG motif G4s to associate may participate in RNA-based aggregation under conditions of cellular stress.
The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes
Authors: Krasikova Alla , Kulikova Tatiana , Schelkunov Mikhail , Makarova Nadezhda , Fedotova Anna , Plotnikov Vladimir , Berngardt Valeria , Maslova Antonina , Fedorov Anton 
Published: November 2024

Abstract
Lampbrush chromosomes, with their unusually high rate of nascent RNA synthesis, provide a valuable model for studying mechanisms of global transcriptome up-regulation. Here, we obtained a whole-genomic profile of transcription along the entire length of all lampbrush chromosomes in the chicken karyotype. With nuclear RNA-seq, we obtained information about a wider set of transcripts, including long non-coding RNAs retained in the nucleus and stable intronic sequence RNAs. For a number of protein-coding genes, we visualized their nascent transcripts on the lateral loops of lampbrush chromosomes by RNA-FISH. The set of genes transcribed on the lampbrush chromosomes is required for basic cellular processes and is characterized by a broad expression pattern. We also present the first high-throughput transcriptome characterization of miRNAs and piRNAs in chicken oocytes at the lampbrush chromosome stage. Major targets of predicted piRNAs include CR1 and long terminal repeat (LTR) containing retrotransposable elements. Transcription of tandem repeat arrays was demonstrated by alignment against the whole telomere-to-telomere chromosome assemblies. We show that transcription of telomere-derived RNAs is initiated at adjacent LTR elements. We conclude that hypertranscription on the lateral loops of giant lampbrush chromosomes is required for synthesizing large amounts of transferred to the embryo maternal RNA for thousands of genes.
Recruitment of homodimeric proneural factors by conserved CAT–CAT E-boxes drives major epigenetic reconfiguration in cortical neurogenesis
Authors: de Martin Xabier , Oliva Baldomero , Santpere Gabriel 
Published: November 2024

Abstract
Proneural factors of the basic helix–loop–helix family coordinate neurogenesis and neurodifferentiation. Among them, NEUROG2 and NEUROD2 subsequently act to specify neurons of the glutamatergic lineage. Disruption of these factors, their target genes and binding DNA motifs has been linked to various neuropsychiatric disorders. Proneural factors bind to specific DNA motifs called E-boxes (hexanucleotides of the form CANNTG, composed of two CAN half sites on opposed strands). While corticogenesis heavily relies on E-box activity, the collaboration of proneural factors on different E-box types and their chromatin remodeling mechanisms remain largely unknown. Here, we conducted a comprehensive analysis using chromatin immunoprecipitation followed by sequencing (ChIP-seq) data for NEUROG2 and NEUROD2, along with time-matched single-cell RNA-seq, ATAC-seq and DNA methylation data from the developing mouse cortex. Our findings show that these factors are highly enriched in transiently active genomic regions during intermediate stages of neuronal differentiation. Although they primarily bind CAG-containing E-boxes, their binding in dynamic regions is notably enriched in CAT–CAT E-boxes (i.e. CATATG, denoted as 5′3′ half sites for dimers), which undergo significant DNA demethylation and exhibit the highest levels of evolutionary constraint. Aided by HT-SELEX data reanalysis, structural modeling and DNA footprinting, we propose that these proneural factors exert maximal chromatin remodeling influence during intermediate stages of neurogenesis by binding as homodimers to CAT–CAT motifs. This study provides an in-depth integrative analysis of the dynamic regulation of E-boxes during neuronal development, enhancing our understanding of the mechanisms underlying the binding specificity of critical proneural factors.
Pairpot: a database with real-time lasso-based analysis tailored for paired single-cell and spatial transcriptomics
Authors: Ruan Zhihan , Lin Fan , Zhang Zhenjie , Cao Jiayue , Xiang Wenting , Wei Xiaoyi , Liu Jian 
Published: November 2024

Abstract
Paired single-cell and spatially resolved transcriptomics (SRT) data supplement each other, providing in-depth insights into biological processes and disease mechanisms. Previous SRT databases have limitations in curating sufficient single-cell and SRT pairs (SC–SP pairs) and providing real-time heuristic analysis, which hinder the effort to uncover potential biological insights. Here, we developed Pairpot (http://pairpot.bioxai.cn), a database tailored for paired single-cell and SRT data with real-time heuristic analysis. Pairpot curates 99 high-quality pairs including 1,425,656 spots from 299 datasets, and creates the association networks. It constructs the curated pairs by integrating multiple slices and establishing potential associations between single-cell and SRT data. On this basis, Pairpot adopts semi-supervised learning that enables real-time heuristic analysis for SC–SP pairs where Lasso-View refines the user-selected SRT domains within milliseconds, Pair-View infers cell proportions of spots based on user-selected cell types in real-time and Layer-View displays SRT slices using a 3D hierarchical layout. Experiments demonstrated Pairpot’s efficiency in identifying heterogeneous domains and cell proportions.
Diverse intrinsic properties shape transcript stability and stabilization in Mycolicibacterium smegmatis
Authors: Sun Huaming , Vargas-Blanco Diego A , Zhou Ying , Masiello Catherine S , Kelly Jessica M , Moy Justin K , Korkin Dmitry , Shell Scarlet S 
Published: November 2024

Abstract
Mycobacteria regulate transcript degradation to facilitate adaptation to environmental stress. However, the mechanisms underlying this regulation are unknown. Here we sought to gain understanding of the mechanisms controlling mRNA stability by investigating the transcript properties associated with variance in transcript stability and stress-induced transcript stabilization. We measured mRNA half-lives transcriptome-wide in Mycolicibacterium smegmatis in log phase growth and hypoxia-induced growth arrest. The transcriptome was globally stabilized in response to hypoxia, but transcripts of essential genes were generally stabilized more than those of non-essential genes. We then developed machine learning models that enabled us to identify the non-linear collective effect of a compendium of transcript properties on transcript stability and stabilization. We identified properties that were more predictive of half-life in log phase as well as properties that were more predictive in hypoxia, and many of these varied between leadered and leaderless transcripts. In summary, we found that transcript properties are differentially associated with transcript stability depending on both the transcript type and the growth condition. Our results reveal the complex interplay between transcript features and microenvironment that shapes transcript stability in mycobacteria.
Phase II trial of pathology-based tripartite treatment stratification for patients with CNS germ cell tumors: A long-term follow-up study
Authors: Takami Hirokazu , Matsutani Masao , Suzuki Tomonari , Takabatake Kazuhiko , Fujimaki Takamitsu , Okamoto Michinari , Yamaguchi Shigeru , Kanamori Masayuki , Matsuda Kenichiro , Sonoda Yukihiko , Natsumeda Manabu , Ichinose Toshiya , Nakada Mitsutoshi , Muroi Ai , Ishikawa Eiichi , Takahashi Masamichi , Narita Yoshitaka , Tanaka Shota , Saito Nobuhito , Higuchi Fumi , Shin Masahiro , Mineharu Yohei , Arakawa Yoshiki , Kagawa Naoki , Kawabata Shinji , Wanibuchi Masahiko , Takayasu Takeshi , Yamasaki Fumiyuki , Fujii Kentaro , Ishida Joji , Date Isao , Miyake Keisuke , Fujioka Yutaka , Kuga Daisuke , Yamashita Shinji , Takeshima Hideo , Shinojima Naoki , Mukasa Akitake , Asai Akio , Nishikawa Ryo 
Published: November 2024

Abstract

Background
A previous Phase II clinical trial, conducted from 1995 to 2003, evaluated CNS germ cell tumors (GCTs) using a three-group treatment stratification based on histopathology. The primary objective of the study was to assess the long-term efficacy of standardized treatment regimens, while the secondary objective focused on identifying associated long-term complications.

Methods
A total of 228 patients were classified into 3 groups for treatment: germinoma (n = 161), intermediate prognosis (n = 38), and poor prognosis (n = 28), excluding one mature teratoma case. Treatment involved stratified chemotherapy regimens and varied radiation doses/coverage. Clinical data was retrospectively analyzed at a median follow-up of 18.5 years.

Results
The treatment outcomes for germinoma, with or without syncytiotrophoblastic giant cells, were similar. The 10- and 20-year event-free survival rates for the germinoma, intermediate, and poor prognosis groups were 82/76/49% and 73/66/49%, respectively. Overall survival (OS) rates were 97/87/61% at 10 years and 92/70/53% at 20 years. Germinomas in the basal ganglia, treated without whole-brain radiation therapy (WBRT), frequently relapsed but were effectively managed with subsequent WBRT. Deaths in germinoma cases had varied causes, whereas deaths in the poor prognosis group were predominantly disease-related. Nineteen treatment-related complications were identified in 16 patients, with cumulative event rates of 1.9% at 10 years and 11.3% at 20 years. OS rates at 1 and 2 years post-relapse for tumors initially classified as germinoma, intermediate, and poor prognosis were 94/88/18% and 91/50/9%, respectively.

Conclusions
Initial treatment intensity is crucial for managing non-germinomatous GCTs, while long-term follow-up for relapse and complications is imperative in germinomas. Irradiation extending beyond the immediate tumor site is essential for basal ganglia germinomas. Addressing relapse in non-germinomatous GCT remains a significant challenge.
Systematic review and meta-analysis on the mental health of emergency and urgent call-handlers and dispatchers
Authors: Osório C , Talwar S , Stevelink S A M , Sihre H K , Lamb D , Billings J 
Published: November 2024

Abstract

Background
Call-handlers and dispatchers (CHDs) working in specialized emergency and urgent communication centres are essential in supporting public safety and health. Evidence suggests that these professionals are at increased risk of mental health conditions, including post-traumatic stress disorder (PTSD), depression, anxiety and alcohol abuse among other conditions; however, reliable prevalence estimates remain undetermined.

Aims
We provide the estimated pooled prevalence for PTSD, depression, anxiety and hazardous drinking among emergency and urgent CHDs globally.

Methods
We searched 10 electronic databases, grey literature and the Annals of Emergency Dispatch and Response. Eligible studies reported original quantitative data and used validated self-reported measures on the prevalence of mental health conditions of interest (i.e. PTSD, depression, anxiety and alcohol use) within CHD professionals. Three reviewers independently screened results for eligibility. Prevalence estimates were pooled using random-effects meta-analyses.

Results
In total, 16 857 references were retrieved. From these, 183 full-text articles were assessed for eligibility, of which 37 articles were included in this systematic review, and 13 articles provided necessary quantitative information for meta-analyses. In total, 7759 CHDs were considered across nine different countries. The overall pooled prevalence for PTSD was 17.8% (95% confidence interval [CI] 12.4−24.0%), depression was 28.2% (95% CI 20.7–36.2%), anxiety was 17.2% (95% CI 6.6–31.5%) and hazardous drinking was 17.8% (95% CI 6.9–32.2%).

Conclusions
These findings indicate CHDs are at significant risk of mental health problems. Further quantitative and qualitative research is warranted to help understand the psychological risks of working as a CHD and guide appropriate psychological support.