bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Expanding Universe of Mutational Signatures and Its Rapid Evolution in Single-Stranded RNA Viruses
Authors: Yang Yue , Zhang Xinyi , Chen Tingting , Wu Fengyuan , Huang Yu S , Qu Yanhua , Xu Miao , Ma Liang , Liu Mo , Zhai Weiwei 
Published: January 2025

Abstract
The study of mutational processes in somatic genomes has gained recent momentum, uncovering a wide array of endogenous and exogenous factors associated with somatic changes. However, the overall landscape of mutational processes in germline mutations across the tree of life and associated evolutionary driving forces are rather unclear. In this study, we analyzed mutational processes in single-stranded RNA (ssRNA) viruses which are known to jump between different hosts with divergent exogenous environments. We found that mutational spectra in different ssRNA viruses differ significantly and are mainly associated with their genetic divergence. Surprisingly, host environments contribute much less significantly to the mutational spectrum, challenging the prevailing view that the exogenous cellular environment is a major determinant of the mutational spectrum in viruses. To dissect the evolutionary forces shaping viral spectra, we selected two important scenarios, namely the inter-host evolution between different viral strains as well as the intra-host evolution. In both scenarios, we found mutational spectra change significantly through space and time, strongly correlating with levels of natural selection. Combining the mutations across all ssRNA viruses, we identified a suite of mutational signatures with varying degrees of similarity to somatic signatures in humans, indicating universal and divergent mutational processes across the tree of life. Taken together, we unraveled an unprecedented dynamic landscape of mutational processes in ssRNA viruses, pinpointing important evolutionary forces shaping fast evolution of mutational spectra in different species.
The serum amyloid A to C-reactive protein ratio is lower in men than in women because of higher C-reactive protein concentrations in men
Authors: Uda Hiroshi , Katayama Michihito , Maeda Keiji , Saiki Osamu 
Published: January 2025

ABSTRACT

Objectives
We previously found that discrepancy between serum amyloid A (SAA) and C-reactive protein (CRP) levels linked to the difference of SAA/CRP ratio in patients with early rheumatoid arthritis, and the ratio varied among different patients. This study aimed to determine why the SAA/CRP ratio differed among different patients.

Methods
The patients (n = 466) with most of inflammatory diseases were enrolled. After examined CRP and SAA concentrations, we compared the SAA/CRP ratio, and SAA and CRP concentrations in men and women.

Results
The SAA/CRP ratio varied dramatically among different patients (33.6–0.140). The 10 highest SAA/CRP ratios were all in women, and half of the 10 lowest ratios were found in men. The loge SAA/CRP ratio was significantly higher in women than in men (P &lt; .0001). The loge SAA concentration was not different between women and men (P = .174), but the loge CRP concentration was significantly higher in men (P &lt; .0001).

Conclusions
The SAA/CRP ratio varies considerably among different patients. The SAA/CRP ratio in women is higher than in men because loge CRP but not SAA concentrations in men are higher than in women. The finding is against the conventional view and suggests that the reference range of CRP concentrations in women should be assessed lower than in men.
Trends in Mental Health Symptoms, Nicotine Product Use, and their Association Over Time Among Adolescents in Canada, England, and the US: Findings from the ITC Adolescents Tobacco and Vaping Survey, 2020-2023
Authors: Hackworth Emily E , Vidaña-Pérez Desiree , O’Neal Riley , Kim Minji , Fillo Jennifer , Hammond David , Thrasher James F 
Published: January 2025

Abstract

Introduction
There is a well-established bi-directional relationship between cigarette smoking and internalizing mental health (IMH) symptoms (e.g., symptoms of depression, symptoms of anxiety). However, it is unclear whether IMH symptoms are associated with using different types or combinations of nicotine products (e.g., combustible, non-combustible, exclusive product use or multi-product use). The purpose of this study is to improve our understanding of the relationship between adolescent IMH symptoms and use of a wide variety of nicotine products by examining the association between IMH symptoms and current nicotine use from 2020-2023.

Methods
Data come from the 2020-2023 waves of the International Tobacco Control (ITC) Adolescents Tobacco and Vaping Survey, an online repeat cross-sectional survey of adolescents aged 16-19 in Canada, England, and the US (n=80,427). Current nicotine use was examined in four categories: 1) no use, 2) exclusive non-combustible product use, 3) exclusive combustible product use, and 4) use of both product types. Respondents reported current symptoms of depression or anxiety, and we generated a dichotomous IMH symptoms variable (yes vs. no). We examined the association between IMH symptoms and current nicotine use using multinomial logistic regression models that adjusted for covariates.

Results
IMH symptoms were most strongly associated with use of both product types (adjusted relative risk ratio [ARRR]: 1.91, 95% confidence interval [CI] 1.80-2.03), followed by exclusive non-combustible use (ARRR: 1.70, 95% CI=1.61-1.80), and then exclusive combustible use (ARRR: 1.29, 95% CI=1.21-1.37).

Conclusions
Adolescents with IMH symptoms are more likely to use nicotine products in general than adolescents without IMH symptoms. Specifically, non-combustible product use may have a particularly strong relationship with poor mental health among adolescents. Longitudinal research is needed to better understand directionality.

Implications
This study provides an up-to-date understanding of how mental health and nicotine use are related among adolescents, particularly during the COVID-19 pandemic and its aftermath. Results indicate that youth mental health may be related to nicotine use, particularly non-combustible use, which is largely driven by e-cigarette use. Efforts to reduce youth e-cigarette use may consider emphasizing its relationship with mental health. Efforts to promote e-cigarette use as a less harmful alternative to cigarette smoking should be aware of the association between vaping and youth mental health.
Strong inorganic acid mists and respiratory tract cancers: a meta-analysis
Authors: Seyyedsalehi M S , Di Lorenzo A , Vimercati L , Boffetta P 
Published: January 2025

Abstract

Background
Exposure to strong inorganic acid mists (SIAMs) in the workplace has been linked to respiratory tract cancers.

Aims
We conducted a meta-analysis of cohort and case–control studies examining the association between occupational SIAMs and respiratory tract cancers other than laryngeal cancer, which is already established.

Methods
Studies mentioned in the 1992 IARC Monograph on carcinogenicity of SIAMs were combined with later studies identified from a systematic search of Scopus, PubMed and Embase. Forest plots of relative risks (RR) and odds ratios were constructed for the 34 identified studies. A random-effects model was used to address heterogeneity.

Results
An association between the roles associated with occupational SIAMs exposure and risk of lung (RR = 1.17; 95% confidence interval [CI] = 1.05–1.32), and nasal cancers (RR = 3.30, 95% CI = 1.16–9.41) was found. The risk of oral and pharyngeal cancer was also associated with SIAMs exposure-related roles (RR = 1.59, 95% CI = 0.98–2.57). Results did not differ by study design, gender or outcome for all three cancers. A positive association for lung cancer was found with chemical (RR = 1.25, 95% CI = 1.13–1.38), and metal and steel industries (RR = 1.19, 95% CI = 1.04–1.37), as well as for oral and pharyngeal cancer with chemical industry (RR = 1.72, 95% CI = 1.57–1.89). We checked publication bias for lung (p = 0.35), oral and pharyngeal (p = 0.02) and nasal cancer (p = 0.40).

Conclusions
Our study showed an association between occupational SIAM exposure and risk of lung, nasal, and possibly oral and pharyngeal cancers. However, weaknesses in the recording of confounding and exposure data in the currently available literature were found.
Breakthrough Invasive Mold Infections in Hematologic Cases: Relevance of the Host's Factors
Authors: Rodríguez-Goncer Isabel , Boán Jorge , Carrero-Arribas Riansares , Sanchez-Pina José María , Lizasoaín Manuel , Fernández-Ruiz Mario , San-Juan Rafael , López-Medrano Francisco , Pérez-Ayala Ana , Caro-Teller José Manuel , Martínez-López Joaquín , Aguado José María , Calbacho María 
Published: January 2025

Abstract

Background
Breakthrough invasive mold infections (bIMIs) are life-threatening complications in hematologic cases. Most previous studies in this field covered the whole spectrum of fungal pathogens, including yeasts, and antifungal agents.

Methods
We conducted a retrospective study including all hematologic cases of patients diagnosed with a bIMI while receiving a mold-active antifungal agent at our center between January 2017 and June 2022.

Results
Overall 37 patients were diagnosed with bIMI: 6 (16.2%) proven, 18 (48.6%) probable, and 13 (35.1%) possible. The highest incidence rate was found for micafungin (1.31 bIMI episodes per 1000 treatment-days), although with no significant differences across antifungal agents. Most patients (90.9%) for whom therapeutic drug monitoring was performed exhibited adequate through levels. Ten (27.0%) patients had undergone allogeneic hematopoietic stem cell transplantation. Aspergillus species was the most common pathogen in cases with microbiological identification. Regarding risk factors, 67.6% had severe neutropenia at diagnosis and 40.5% had received high-intensity chemotherapy. Rates of clinical response and attributable mortality by day +30 were 64.9% and 23.3%, respectively. Poorer performance status, higher Charlson Comorbidity index, older age, and higher C-reactive protein by day +7 were associated with 30-day attributable mortality.

Conclusions
Aspergillus was the predominant pathogen in our cohort of bIMIs, with a significant proportion of episodes occurring despite adequate triazole levels. Thirty-day attributable mortality was lower than previously reported. Poorer performance status, higher comorbidity burden, and older age had a relevant role in the outcome of bIMI.
Real-world Rollout of Injectable Antiretrovirals for HIV Prevention and Treatment: Correlates of Early Adoption
Authors: Koshy Liza , Payne Erika , Barakat Lydia , Hao Ritche , Sureshanand Soundhari , Cedillo Ornelas Andrea , Dewan Andrew , Meyer Jaimie P 
Published: January 2025

Abstract

Background
Data are limited on implementation of long-acting injectable (LAI) HIV treatment (ART) and preexposure prophylaxis (PrEP). We characterized “early adopters” of LAI ART and PrEP in terms of social determinants of health using a health equity lens.

Methods
Our retrospective cohort included patients prescribed ART or PrEP through a large urban health system (January 2021–September 2023) in the Northeastern United States. We used electronic health record data for PrEP and ART to examine group differences between those on LAI or oral medications using analysis of variance, chi-square tests, or Fisher exact tests. Bivariate logistic regression modeled associations between LAI ART or LAI PrEP and social determinants of health.

Results
In the PrEP group, 238 patients were prescribed LAI (n = 63) or oral (n = 193) PrEP. Most PrEP patients were men (80.7%), non-Hispanic (79.5%), and White (60.7%) and had public insurance (83.1%). Compared with patients on oral PrEP, those on LAI less often experienced food insecurity, financial strain, depression, anxiety, or substance use disorders. In bivariate models, LAI PrEP inversely correlated with female sex, current smoking, depression, anxiety, and substance use disorders. In the treatment group, 1194 patients were prescribed LAI (n = 76) or oral (n = 1118) ART, with a median age of 57.0 years; 63.6% were from minoritized groups. Only age was significantly associated with LAI ART (odds ratio, 0.97; 95% CI, 0.961–0.993; P = .005).

Conclusions
In this large retrospective cohort of patients on LAI PrEP and ART, patients receiving LAI less often experienced social barriers to accessing care. Public health interventions are needed to overcome health inequities tied to access of LAI ART for HIV prevention and treatment.
Contribution of nebulized budesonide before bronchoscopy, a prospective clinical study
Authors: Zhang Guoxin , Yu Hu , Zhang Li , Zhao Xiaoyun 
Published: January 2025

Abstract

Purpose
This study evaluated the efficacy of adding budesonide to nebulized lidocaine in patients undergoing flexible bronchoscopy (FB) under topical anaesthesia.

Study design
Patients aged ≥18 years, scheduled for FB under topical anaesthesia were randomized into two groups: the combination group received a pre-treatment of 2 ml 1 mg budesonide with 5 ml 2% lidocaine, whilst the lidocaine group received 5 ml 2% lidocaine with 2 ml saline solution, both administered via nebulization. Blood pressure (BP), heart rate, and percutaneous oxygen saturation were recorded before, during, and 10 min after FB. The Visual Analogue Scale (VAS) and Wong-Baker FACES Pain Rating Scale (FPS-R) were used to evaluate cough severity, discomfort, willingness to accept reoperation, and the operator’s satisfaction with patient cooperation. In addition, the duration of the procedure, total lidocaine dosage instilled through the bronchoscope during the procedure, and types of procedures performed were documented.

Results
Compared to the lidocaine group, the combination group showed lower maximum systolic and diastolic BP, higher minimum percutaneous oxygen saturation, and lower cough and discomfort severity scores. Operator’s satisfaction, as measured via the VAS or FPS-R, was greater in the combination group, which also exhibited shorter procedure times and required lower lidocaine dosages. There were no significant differences between the groups in terms of willingness to accept reoperation or types of procedures performed.

Conclusions
In patients undergoing FB with topical anaesthesia, pre-treatment with a combination of nebulized lidocaine and budesonide is more effective than nebulized lidocaine alone.
Key message What is already known on this topic? Flexible bronchoscopy (FB) with topical anaesthesia remains a common practice in many settings, although it can cause significant discomfort for patients. What this study adds? Pre-treatment with a combination of nebulized budesonide and lidocaine was more effective and safer than nebulized lidocaine alone for improving patient tolerance during FB. How this study might affect research, practice, or policy? In settings where conscious sedation is not feasible, the combined nebulization of lidocaine and budesonide may offer an optimized approach for FB, enhancing patient comfort and procedural efficiency.
Prediction of scleroderma renal crisis in patients of SSc: insight from the CRDC cohort study
Authors: Huang Haochen , Xu Shihan , Li Hongbin , Duan Xinwang , Hui Min , Zhou Jiaxin , Zhang Ling-ling , Li Mengtao , Zeng Xiaofeng , Xu Dong 
Published: January 2025

Abstract

Objective
Early personalized identification of SSc patients at risk of scleroderma renal crisis (SRC) can help provide better treatment and improve outcomes. This study aimed to create and validate a new multi-predictor Nomogram to predict SRC risk and compare it to an existing model.

Methods
A retrospective multicentre observational study was conducted using clinical data from SSc patients with SRC registered in the Chinese Rheumatism Data Center (CRDC) database. Each SSc patient with SRC was matched with four SSc patients without SRC, registered consecutively afterward, as controls. Differences between the two groups were analysed using Student’s t-test, Mann–Whitney U test, χ2 test, or Fisher’s exact test. Key risk factors were identified using univariate and multivariate logistic regression, as well as LASSO regression. The Nomogram’s performance was assessed with receiver operating characteristic curves, calibration plots, decision curve analysis (DCA), and bootstrap resampling for internal and external validation. Net reclassification improvement (NRI) and integrated discrimination improvement (IDI) were used to compare models.

Results
The Nomogram incorporated predictive factors such as myocardial involvement, SSc subtype, anaemia, platelet count, and disease duration. The area under the ROC curve showed strong discrimination in both the training and validation datasets. Calibration curves and the Hosmer–Lemeshow test indicated good agreement between predicted and actual outcomes. DCA demonstrated greater clinical net benefit. The NRI and IDI results showed significant improvement over the previous model.

Conclusion
A Nomogram with improved predictive performance compared with the previous one was developed in a larger sample size in China.
Polysomnographic endotypes of successful multilevel upper airway surgery for obstructive sleep apnea
Authors: Wang Xiaoting , Zhang Jingyu , Zou Jianyin , Zhou Tianjiao , Zhou Enhui , Shen Li , Yang Siyu , Huang Weijun , Zhu Huaming , Guan Jian , Yi Hongliang , Yin Shankai 
Published: January 2025

Abstract

Study Objectives
Multilevel upper airway surgery is effective for some patients with obstructive sleep apnea (OSA), but predicting the response to surgery remains a challenge. The underlying endotypes of OSA include upper airway collapsibility, muscle compensation, loop gain, and the arousal threshold. This study aimed to explore the effect of surgery on polysomnography (PSG)-derived OSA endotypes and establish a surgical response prediction model.

Methods
Our study included 54 Chinese patients with OSA who underwent multilevel upper airway surgery. Participants underwent PSG before and after surgery with a median follow-up time of 6.5 months. Using AHIBaseline/AHIpost-surgery ≥ 2 and AHIpost-surgery &lt; 10 events/h as criteria, participants were classified as surgery responders and non-responders. The surgical success rate was 26%. These endotypic traits were derived from a standard PSG data by validated methods.

Results
The surgery altered both anatomical and non-anatomical endotypic traits, including increased Vpassive (baseline vs post-surgery: 51.5 [18.7–84.2] vs 86.8 [67.4–93.7] %Veupnea, p &lt; .001), decreased loop gain (baseline vs post-surgery: 0.7 [0.7–0.8] vs 0.6 [0.5–0.6]; p &lt; .001), and a higher arousal threshold (baseline vs post-surgery: 202.9 [183.7–222.0] vs 160.7 [143.9–177.4] %Veupnea; p &lt; .001). However, it did not significantly affect muscle compensation. Fully adjusted logistic regression analyses indicated that a favorable response to surgery was independently associated with a lower LG (OR [CI 95%], 0.1 [0.0–0.5], p = .032). In patients with improved muscle compensation or a more collapsible airway (lower Vpassive), a lower loop gain was more strongly indicative of success. However, when muscle compensation was lower or collapsibility was less severe (higher Vpassive), a lower loop gain was less predictive of success.

Conclusions
This study demonstrated that multilevel upper airway surgery altered both anatomical and non-anatomical endotypes in Chinese patients with OSA. An endotype based regression model may meaningfully predict surgical success.
Impact of prior SARS-CoV-2 infection on perioperative cardiac, pulmonary and neurocognitive complications in elderly patients: study protocol for an observative cohort study
Authors: Abramova Dayana , Haase Paula Marie , Just Anne-Marie , Frank Sandra , Saller Thomas 
Published: January 2025

AbstractBackgroundPostoperative delirium is considered a serious complication in elderly patients. Elderly patients often suffer from several concomitant diseases. The reduced physical condition can increase the risk of cardiac, pulmonary and neurocognitive complications during and after surgery. SARS-CoV-2 infection primarily affects the respiratory tract but can also damage other organ systems such as the heart and brain. Given the wide range of pulmonary, cardiac and neurocognitive complications caused by SARS-CoV-2, these risks must be given special consideration during planned surgical procedures. Both surgical procedures and anesthesia are risk factors for postoperative complications in themselves. The specific impact of prior SARS-CoV-2 infection on perioperative complications in elderly patients has not been sufficiently researched. The aim of this study is to understand how a previous SARS-CoV-2 infection influences the occurrence of perioperative complications.MethodsIn this case-control study, the data of patients over 60 years of age undergoing elective surgery are analyzed. Subjects are divided into two groups based on their SARS-CoV-2 infection status: those with a documented previous infection and those without. Confirmation of infection will be based on written evidence and anamnestic information. The primary endpoint of the examination is the occurrence of delirium within the first five postoperative days. In addition, further cardiac, pulmonary and neurocognitive complications are recorded in the perioperative period.The occurrence of postoperative delirium is recorded during the daily ward round in the first five days after the operation. The 3DCAM test and the 4AT are used for this purpose. In addition, the CAM-ICU will be used in the intensive care unit. The recruitment will include 266 patients. Statistical analyses will be performed to determine the correlation between a previous SARS-CoV-2 infection and the observed clinical outcomes.DiscussionThe results of this study will provide new insights into the impact of prior SARS-CoV-2 infection on perioperative complications in elderly patients undergoing elective surgery.Trial registration:Deutsches Register Klinischer Studien DRKS00034861
In vivoMorphological Dynamics of Single Laser-Axotomized Corneal Nerve Fibers in Sarm1-Null Adult Mice
Authors: Íñigo-Portugués Almudena , Aleixandre-Carrera Fernando , Sala Salvador , Borrás Fernando , Gomez-Sanchez Jose A. , Arthur-Farraj Peter , Carmen Acosta M. , Belmonte Carlos , Gallar Juana , Meseguer Víctor 
Published: January 2025

AbstractAxonal regeneration represents a pivotal aspect of the adult peripheral nervous system (PNS). When an injury occurs, peripheral axons are able to regenerate and reestablish connections with their original targets. Although several precision techniques for severing axons in various non-mammalian model organisms have allowed to study the dynamics of regeneration after injury, similar axonal injury models have yet to be fully developed in mammals. In this study, we introduced a novel experimental method for laser-induced axotomy of single corneal sensory subbasal nerve fibers. This method enables thein vivomonitoring and quantification of axonal degeneration and regeneration morphological dynamics in adult mice. Results revealed that the degeneration of the distal stump of the subbasal fiber was delayed in mice lacking the protein SARM1, which promotes degenerative process after injury. Meanwhile, the proximal stump maintained the regenerative dynamics of the subbasal fiber, but regeneration of its nerve terminals was impaired. The present study introduces a valuable model for thein vivostudy of the morphological plasticity dynamics of peripheral axons after injury in genetically tractable adult mammals.