bluuebunny/crossref_metadata_2025_split huggingface dataset:
When is prostate cancer really cancer?
Authors: Cooperberg Matthew R , Braun Avery E , Berlin Alejandro , Kibel Adam S , Eggener Scott E ,   CANCER-GG1 Writing Group, Paner Gladell P , Nikiforov Yuri E , Esserman Laura J , van der Kwast Theo , Simko Jeff , Lamb Alastair D , Klotz Laurence , Murphy Declan G , Moore Caroline M , Etzioni Ruth , Vickers Andrew , Tilki Derya , Jalloh Mohamed , Trinh Quoc , Yamoah Kosj , Wolinsky Howard , Izdebski Leszek , Stimpson C J , Ryan Charles J , Wilt Timothy J , Ahmed Hashim U , Feng Felix Y 
Published: October 2024

Abstract
Prostate cancer (PC) is a major cause of cancer-related deaths worldwide, with far more diagnoses than deaths annually. Recent discussions have challenged whether Grade Group 1 (GG1) PC should be labeled “cancer” due to its indolent nature. To address this question, an international symposium convened stakeholders from various fields. We summarize key discussion points: autopsy studies reveal GG1 is so common in aging males as to be perhaps a normal aspect of aging. Pure GG1 has no capacity to metastasize. Modern diagnostic pathways focus on detecting higher-grade disease, explicitly omitting biopsy if GG 2 or higher is not suspected, so GG1 has effectively become an “incidentaloma.” Recent spatial transcriptomics of prostate sections identifies a continuum of genomic changes—including alterations characteristic of malignancy in histologically normal regions, so the designation of cancer based entirely on conventional pathology findings increasingly seems arbitrary at least to an extent. Pathologists discussed heterogeneity and diagnostic challenges, suggesting “acinar neoplasm” as one possible alternative label. GG1 should not be considered “normal,” and absolutely requires ongoing active surveillance; whether patients would adhere to surveillance absent a cancer diagnosis is unknown. Patient perspectives highlighted the adverse effects of overtreatment and the burden of a cancer diagnosis. The anticipated impact on screening and treatment varies across health-care systems, but many believe public health would on balance greatly improve if GG1—along with lesions in other organs with no capacity to cause symptoms or threaten life—were labeled something other than “cancer.” Ultimately, our goal is to reduce PC mortality while minimizing harms associated with both overdiagnosis and overtreatment.
Unexpected intraoperative finding of a hyalinizing cholecystitis in a patient with gallbladder calculi
Authors: Gjinoska Klaudia , Nikolovski Andrej , Stoicovski Emil , Mitrev Zan 
Published: October 2024

Abstract
Hyalinizing cholecystitis is a rare subtype of chronic cholecystitis in which the gallbladder tissue is replaced with hyaline sclerosis, more or less, and has a characteristic intraoperative appearance. Preoperative diagnosis is hard to establish. The entity is strongly associated with gallbladder carcinoma. Therefore, the pathologist should perform a thorough microscopic analysis. We present a case of an unusual intraoperative finding in a male patient with chronic cholecystitis which was proved to be a hyalinizing cholecystitis.
The PAU survey: photometric redshift estimation in deep wide fields
Authors: Navarro-Gironés D , Gaztañaga E , Crocce M , Wittje A , Hildebrandt H , Wright A H , Siudek M , Eriksen M , Serrano S , Renard P , Gonzalez E J , Baugh C M , Cabayol L , Carretero J , Casas R , Castander F J , Daza-Perilla I V , De Vicente J , Fernandez E , García-Bellido J , Hoekstra H , Manzoni G , Miquel R , Padilla C , Sánchez E , Sevilla-Noarbe I , Tallada-Crespí P 
Published: October 2024

ABSTRACT
We present photometric redshifts (photo-z) for the deep wide fields of the Physics of the Accelerating Universe Survey (PAUS), covering an area of $\sim$50 deg$^{2}$, for $\sim$1.8 million objects up to $i_{\rm {AB}}\lt 23$. The PAUS deep wide fields overlap with the W1 and W3 fields from CFHTLenS and the G09 field from KiDS/GAMA. Photo-z are estimated using the 40 narrow bands (NB) of PAUS and the broad-bands (BB) of CFHTLenS and KiDS. We compute the redshifts with the SED template-fitting code bcnz, with a modification in the calibration technique of the zero-point between the observed and the modelled fluxes, that removes any dependence on spectroscopic redshift samples. We enhance the redshift accuracy by introducing an additional photo-z estimate ($z_{\textrm {b}}$), obtained through the combination of the bcnz and the BB-only photo-z. Comparing with spectroscopic redshift estimates ($z_{\textrm {s}}$), we obtain a $\sigma _{68} \simeq 0.020$ for all galaxies with $i_{\rm {AB}}\lt 23$ and a typical bias $|z_{\textrm {b}}\!-\!z_{\textrm {s}}|$ smaller than 0.01. For $z_{\textrm {b}} \sim (0.10\!-\!0.75)$, we find $\sigma _{68} \simeq (0.003\!-\!0.02)$, this is a factor of $10\!-\!2$ higher accuracy than the corresponding BB-only results. We obtain similar performance when we split the samples into red (passive) and blue (active) galaxies. We validate the redshift probability $p(z)$ obtained by bcnz and compare its performance with that of $z_{\textrm {b}}$. These photo-z catalogues will facilitate important science cases, such as the study of galaxy clustering and intrinsic alignment at high redshifts ($z \lesssim 1$) and faint magnitudes.
Nuclease-induced stepwise photodropping (NISP) to precisely investigate single-stranded DNA degradation behaviors of exonucleases and endonucleases
Authors: Chiu Hui-Pin , Shen Chung-Han , Wu Jan-Kai , Mao Eric Y C , Yen Han-Yi , Chang Yuan-Pin , Wu Chyuan-Chuan , Fan Hsiu-Fang 
Published: October 2024

Abstract
Here, we employed a fluorescence-based single molecule method called nuclease-induced stepwise photodropping (NISP) to measure in real time the DNA degradation mediated by mitochondrial genome maintenance exonuclease 1 (MGME1), a bidirectional single-stranded DNA (ssDNA)-specific exonuclease. The method detects a stepwise decrease in fluorescence signals from Cy3 fluorophores labeled on an immobilized DNA substrate. Using NISP, we successfully determined the DNA degradation rates of 6.3 ± 0.4 and 2.0 ± 0.1 nucleotides (nt) s–1 for MGME1 in the 5′-to-3′ and 3′-to-5′ directions, respectively. These results provide direct evidence of the stronger 5′ directionality of MGME1, consistent with its established role in mitochondrial DNA maintenance. Importantly, when we employed NISP to investigate mung bean nuclease, an ss-specific endonuclease, we observed a markedly different NISP pattern, suggesting a distributive cleavage activity of the enzyme. Furthermore, we applied NISP to determine the ssDNA degradation behavior of the double-stranded-specific exonuclease, λ exonuclease. These findings underscore the capability of NISP to accurately and reliably measure the degradation of ssDNA by both exo- and endonucleases. Here, we demonstrate NISP as a powerful tool for investigating the ssDNA degradation behavior of nucleases at the single-molecule level.
Protein–RNA interactions mediated by silvestrol—insight into a unique molecular clamp
Authors: Naineni Sai Kiran , Bhatt Garvit , Jiramongkolsiri Ekkanat , Robert Francis , Cencic Regina , Huang Sidong , Nagar Bhushan , Pelletier Jerry 
Published: October 2024

Abstract
Molecular staples or interfacial inhibitors are small molecules that exert their activity through co-association with macromolecules leading to various effects on target functions. Some molecules inhibit target activity, while others generate gain-of-function complexes. We and others have previously identified two structurally distinct classes of molecular staples, pateamine A and rocaglates. These molecules inhibit eukaryotic initiation factor (eIF) 4A, a critical RNA helicase required for translation initiation, by simultaneously interacting with both RNA and protein components. Structural insights from members of these two families indicate that they wedge themselves between RNA bases during engagement. To extend our understanding of rocaglates, we investigated the RNA-binding properties of silvestrol, a natural rocaglate distinguished by the presence of a unique dioxanyloxy ring. Our study demonstrates that silvestrol expands the RNA-binding repertoire of rocaglates due to this structural characteristic, providing a rationale for improving synthetic molecular staples targeting eIF4A.
Haplotype-resolved de novo assembly revealed unique characteristics of alternative lengthening of telomeres in mouse embryonic stem cells
Authors: Lee Hyunji , Niida Hiroyuki , Sung Sanghyun , Lee Junho 
Published: October 2024

Abstract
Telomeres protect chromosome ends from DNA damage responses, and their dysfunction triggers genomic alterations like chromosome fusion and rearrangement, which can lead to cellular death. Certain cells, including specific cancer cells, adopt alternative lengthening of telomere (ALT) to counteract dysfunctional telomeres and proliferate indefinitely. While telomere instability and ALT activity are likely major sources of genomic alteration, the patterns and consequences of such changes at the nucleotide level in ALT cells remain unexplored. Here we generated haplotype-resolved genome assemblies for type I ALT mouse embryonic stem cells, facilitated by highly accurate or ultra-long reads and Hi-C reads. High-quality genome revealed ALT-specific complex chromosome end structures and various genomic alterations including over 1000 structural variants (SVs). The unique sequence (mTALT) used as a template for type I ALT telomeres showed traces of being recruited into the genome, with mTALT being replicated with remarkably high accuracy. Subtelomeric regions exhibited distinct characteristics: resistance to the accumulation of SVs and small variants. We genotyped SVs at allele resolution, identifying genes (Rgs6, Dpf3 and Tacc2) crucial for maintaining ALT telomere stability. Our genome assembly-based approach elucidated the unique characteristics of ALT genome, offering insights into the genome evolution of cells surviving telomere-derived crisis.
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2-Alkyl-dG lesions elicit R-loop accumulation in the genome
Authors: Wang Yinan , Tang Feng , Zhao Ting , Yuan Jun , Kellum Andrew H , Wang Yinsheng 
Published: October 2024

Abstract
Humans are exposed to DNA alkylating agents through endogenous metabolism, environmental exposure and cancer chemotherapy. The resulting alkylated DNA adducts may elicit genome instability by perturbing DNA replication and transcription. R-loops regulate various cellular processes, including transcription, DNA repair, and telomere maintenance. However, unscheduled R-loops are also recognized as potential sources of DNA damage and genome instability. In this study, by employing fluorescence microscopy and R-loop sequencing approaches, we uncovered, for the first time, that minor-groove N2-alkyl-dG lesions elicit elevated R-loop accumulation in chromatin and in plasmid DNA in cells. We also demonstrated that the N2-alkyl-dG-induced R-loops impede transcription elongation and compromise genome integrity. Moreover, genetic depletion of DDX23, a R-loop helicase, renders cells more sensitive toward benzo[a]pyrene diolepoxide, a carcinogen that induces mainly the minor-groove N2-dG adduct. Together, our work unveiled that unrepaired minor-groove N2-alkyl-dG lesions may perturb genome integrity through augmenting R-loop levels in chromatin. Our findings suggest a potential therapeutic strategy involving the combination of R-loop helicase inhibitors with DNA alkylating drugs.
Ribosome Quality Control mitigates the cytotoxicity of ribosome collisions induced by 5-Fluorouracil
Authors: Chatterjee Susanta , Naeli Parisa , Onar Okan , Simms Nicole , Garzia Aitor , Hackett Angela , Coyle Kelsey , Harris Snell Patric , McGirr Tom , Sawant Tanvi Nitin , Dang Kexin , Stoichkova Zornitsa Vasileva , Azam Yumna , Saunders Mark P , Braun Michael , Alain Tommy , Tuschl Thomas , McDade Simon S , Longley Daniel B , Gkogkas Christos G , Adrain Colin , Knight John R P , Jafarnejad Seyed Mehdi 
Published: October 2024

Abstract
Ribosome quality control (RQC) resolves collided ribosomes, thus preventing their cytotoxic effects. The chemotherapeutic agent 5-Fluorouracil (5FU) is best known for its misincorporation into DNA and inhibition of thymidylate synthase. However, while a major determinant of 5FU’s anticancer activity is its misincorporation into RNAs, the mechanisms by which cancer cells overcome the RNA-dependent 5FU toxicity remain ill-defined. Here, we report a role for RQC in mitigating the cytotoxic effects of 5FU. We show that 5FU treatment results in rapid induction of the mTOR signalling pathway, enhanced rate of mRNA translation initiation, and increased ribosome collisions. Consistently, a defective RQC exacerbates the 5FU-induced cell death, which is mitigated by blocking mTOR pathway or mRNA translation initiation. Furthermore, 5FU treatment enhances the expression of the key RQC factors ZNF598 and GIGYF2 via an mTOR-dependent post-translational mechanism. This adaptation likely mitigates the cytotoxic consequences of increased ribosome collisions upon 5FU treatment.
PerturbAtlas: a comprehensive atlas of public genetic perturbation bulk RNA-seq datasets
Authors: Zhang Yiming , Zhang Ting , Yang Gaoxia , Pan Zhenzhong , Tang Min , Wen Yue , He Ping , Wang Yuan , Zhou Ran 
Published: October 2024

Abstract
Manipulating gene expression is crucial for understanding gene function, with high-throughput sequencing techniques such as RNA-seq elucidating the downstream mechanisms involved. However, the lack of a standardized metadata format for small-scale perturbation expression datasets in public repositories hinders their reuse. To address this issue, we developed PerturbAtlas, an add-value resource that re-analyzes publicly archived RNA-seq libraries to provide quantitative data on gene expression, transcript profiles, and alternative splicing events following genetic perturbation. PerturbAtlas assists users in identifying trends at the gene and isoform levels in perturbation assays by re-analyzing a curated set of 122 801 RNA-seq libraries across 13 species. This resource is freely available at https://perturbatlas.kratoss.site as both raw data tables and an interactive browser, allowing searches by species, tissue or genomic features. The results provide detailed information on alterations following perturbations, accessible through both forward and reverse approaches, thereby enabling the exploration of perturbation consequences and the identification of potential causal perturbations.
Trajectories of Adherence to Oral Pre-exposure Prophylaxis and Risks of HIV and Sexually Transmitted Infections
Authors: Unigwe Ikenna F , Goodin Amie , Lo-Ciganic Wei-Hsuan , Cook Robert L , Janelle Jennifer , Park Haesuk 
Published: October 2024

Abstract

Background
Pre-exposure prophylaxis (PrEP) effectiveness is highly dependent on medication adherence, which is associated with differential HIV risks and possibly sexually transmitted infection (STI).

Methods
This retrospective cohort study of PrEP users (01/01/2012–12/31/2021) used the MarketScan database of commercially insured enrollees to examine PrEP adherence trajectory groups’ associations with HIV and STI acquisition risks. Distinct PrEP adherence trajectories were identified by group-based trajectory modeling among individuals who used oral PrEP. The primary outcome was HIV acquisition incidence, and secondary was STI rate, compared among trajectory groups. Inverse probability treatment weighting time-varying Cox proportional hazards models assessed HIV acquisition, and Poisson regression models assessed STI.

Results
Among 23 258 oral PrEP users, 4 distinct PrEP adherence patterns were identified: minimal use (10.5% of the cohort), rapidly declining (25.4%), gradually declining (24.3%), and consistently high (39.8%). Compared with the minimal use group, the gradually declining (adjusted hazard ratio [AHR], 0.53; 95% CI, 0.31–0.90) and consistently high (AHR, 0.50; 95% CI, 0.30–0.84) PrEP adherence groups showed decreased HIV incidence risks. Compared with the minimal use group, the rapidly declining (adjusted incidence rate ratio [AIRR], 1.35; 95% CI, 1.07–1.72), gradually declining (AIRR, 1.73; 95% CI, 1.38–2.18), and consistently high (AIRR, 2.06; 95% CI, 1.64–2.58) groups were associated with increased STI risk.

Conclusions
These findings underscore the benefits of continuing and remaining adherent to PrEP and may also inform public health strategies, clinical guidelines, and interventions aimed at maximizing the effectiveness of PrEP in reducing new HIV infections while developing targeted strategies to prevent STIs with PrEP use.
Functional diversification of Sec13 isoforms for storage protein trafficking in rice endosperm cells
Authors: Wang Yongfei , Ren Yulong , Teng Xuan , Wang Fan , Chen Yanyu , Duan Erchao , Wang Xin , Pan Tian , Zhang Binglei , Wan Gexing , Zhang Yu , Zhang Pengcheng , Sun Xiejun , Yang Wenkun , Zhu Yun , Chen Yu , Zhao Wenjie , Han Xiaohang , Lei Cailin , Zhu Shanshan , Liu Shijia , Wang Yihua , Wan Jianmin 
Published: October 2024

Abstract
Coat protein complex II (COPII) vesicles play crucial roles in mediating the endoplasmic reticulum (ER) exit of newly synthesized proteins to the Golgi in eukaryotic cells. However, the molecular functions of COPII components and their functional diversifications in plant seeds remain obscure. Here, we showed that the rice (Oryza sativa) glutelin precursor accumulation12 (gpa12) mutant is defective in storage protein export from the ER, resulting in the formation of aggregated protein bodies. Map-based cloning revealed that GPA12 encodes a COPII outer layer protein, Sec13a, that mainly localizes to endoplasmic reticulum exit sites (ERES) and partially localizes to the Golgi. Biochemical experiments verified that Sec13a physically interacts with Sec31 and Sec16, and mutation in Sec13 compromises its interaction with Sec31 and Sec16, thereby affecting the membrane association of the inner complex components Sar1b and Sec23c. Apart from Sec13a, the rice genome encodes 2 other Sec13 isoforms, Sec13b and Sec13c. Notably, we observed an abnormal accumulation of globular ER structures in the sec13bc double mutant but not in the single mutants, suggesting a functional redundancy of Sec13b and Sec13c in modulating ER morphology. Taken together, our results substantiated that Sec13a plays an important role in regulating storage protein export from the ER, while Sec13b and Sec13c are required for maintaining ER morphology in rice endosperm cells. Our findings provide insights into the functional diversification of COPII components in plants.
Effectiveness and possible brain mechanisms of cervical invasive vagus nerve stimulation (iVNS) intervention for avoidant/restrictive food intake disorder: a case report
Authors: Cai Suping , Wang Yihan , Zhao Bofeng , Li Xiaoliang , He Huan , Yuan Kai , Zhao Qingchuan , Huang Qinxian , Yang Bin , Ji Gang 
Published: October 2024

Abstract

Background
We reported a case of cervical invasive vagus nerve stimulation (iVNS) treatment for avoidant/restrictive food intake disorder (ARFID) in a patient with severe anxiety and depression. This patient was even given a critical illness notice during his hospitalization and all treatment efforts were failed.

Objective
We aimed to verfiy the effectiveness of iVNS in a patient with ARFID.

Methods
We first attempted to perform cervical iVNS in this case and then observed the changes in clinical scores. We also analyzed the alterations in brain magnetic resonance imaging characteristics before and after iVNS using multi-modal neuroimagings.

Results
After 18 days of iVNS (from 1 to 19 July 2023), the patient's clinical symptoms improved significantly and he rapidly gained 5 kg in weight. The brain functional characteristics of this patient tended toward those of the normal group. Functional connectivities of the medial of orbitalis prefrontal cortex returned to the normal range after iVNS.

Conclusion
This is a precedent for performing cervical iVNS in an ARFID patient. Brain neural activity can be modulated through iVNS. The observed improvements in clinical scores and positive changes in brain function validated the effectiveness of iVNS. This case study provides evidence that this intervention technique could be used to reduce the burden on more similar ARFID patients.
Clinical case of 45,X/46,XY mosaic male with ejaculatory disorder associated with seminal vesicle dysplasia: a case report
Authors: Karibe Jurii , Takeshima Teppei , Takamoto Daiji , Kawahara Takashi , Osaka Kimito , Teranishi Jun-ichi , Makiyama Kazuhide , Uemura Hiroji , Yumura Yasushi 
Published: October 2024

Abstract

Introduction
45,X/46,XY mosaicism is a rare anomaly in sexual differentiation, presenting with diverse phenotypes and often leading to infertility due to abnormal gonadal development.

Aims
This report aims to present a case study of a 45,X/46,XY mosaic male patient with an ejaculatory disorder attributed to seminal vesicle dysplasia.

Methods
In this case study, diagnostic procedures encompassed blood tests, semen analysis, chromosomal examination, and imaging studies to assess gonadal morphology. Treatment strategies included attempted varicocelectomy, pharmacological intervention with amoxapine, and surgical testicular sperm extraction. Additionally, the patient underwent assisted reproductive techniques, specifically intracytoplasmic sperm injection (ICSI), to facilitate pregnancy for his wife.

Results
A 32-year-old man could not ejaculate, with post-orgasmic urinalysis revealing minimal sperm presence. Chromosomal analysis confirmed 45,X/46,XY mosaicism. Despite undergoing microsurgical varicocelectomy for clinical varicocele and receiving tricyclic antidepressants, no improvement in semen volume occurred. Imaging studies indicated ejaculatory disorder due to prostate and seminal vesicle aplasia. Consequently, surgical retrieval of testicular sperm was performed, leading to successful pregnancy via ICSI for his wife.

Conclusion
Our approach has effectively addressed ejaculatory disorder in 45,X/46,XY mosaic men, resulting in successful pregnancy.
Cardiovascular procedures in ambulatory cardiac procedures: really?
Authors: Davila Victor R. , Saklayen Samiya , Tang Jonathan 
Published: October 2024

Purpose of review
To evaluate the current trends, safety, and feasibility of same-day discharge (SDD) in ambulatory cardiac procedures, with a focus on percutaneous coronary interventions (PCI). This review also discusses the impact of technological advancements and explores future directions for expanding the scope of SDD in more complex cardiac procedures.

Recent findings
Recent studies have demonstrated that SDD after PCI is both well tolerated and effective for appropriately selected patients, with outcomes comparable with those of patients who remain hospitalized overnight. Advancements in PCI technology, including improved stent designs, smaller sheath sizes, and the adoption of the transradial approach, have significantly enhanced the feasibility of SDD. Enhanced recovery after surgery (ERAS) pathways, adapted for ambulatory settings, further improve patient safety, particularly as more complex procedures are attempted. However, challenges remain in determining SDD eligibility, particularly in settings with limited emergency care capabilities.

Summary
SDD is a viable and cost-effective option for low-risk patients undergoing PCI and other ambulatory cardiac procedures. The successful implementation of SDD requires careful patient selection, adherence to standardized protocols, and vigilant postprocedural monitoring. Future research should focus on refining patient selection tools, expanding the scope of SDD to include more complex procedures, and enhancing postdischarge monitoring through advanced technologies. Multidisciplinary collaboration and ongoing education are essential to support the well tolerated and effective adoption of SDD in ambulatory cardiac care.