bluuebunny/crossref_metadata_2025_split huggingface dataset:
PRMD: an integrated database for plant RNA modifications
Authors: Lang Xiaoqiang , Yu Chunyan , Shen Mengyuan , Gu Lei , Qian Qian , Zhou Degui , Tan Jiantao , Li Yiliang , Peng Xin , Diao Shu , Deng Zhujun , Ruan Zhaohui , Xu Zhi , Xing Junlian , Li Chen , Wang Runfeng , Ding Changjun , Cao Yi , Liu Qi 
Published: October 2023

Abstract
The scope and function of RNA modifications in model plant systems have been extensively studied, resulting in the identification of an increasing number of novel RNA modifications in recent years. Researchers have gradually revealed that RNA modifications, especially N6-methyladenosine (m6A), which is one of the most abundant and commonly studied RNA modifications in plants, have important roles in physiological and pathological processes. These modifications alter the structure of RNA, which affects its molecular complementarity and binding to specific proteins, thereby resulting in various of physiological effects. The increasing interest in plant RNA modifications has necessitated research into RNA modifications and associated datasets. However, there is a lack of a convenient and integrated database with comprehensive annotations and intuitive visualization of plant RNA modifications. Here, we developed the Plant RNA Modification Database (PRMD; http://bioinformatics.sc.cn/PRMD and http://rnainformatics.org.cn/PRMD) to facilitate RNA modification research. This database contains information regarding 20 plant species and provides an intuitive interface for displaying information. Moreover, PRMD offers multiple tools, including RMlevelDiff, RMplantVar, RNAmodNet and Blast (for functional analyses), and mRNAbrowse, RNAlollipop, JBrowse and Integrative Genomics Viewer (for displaying data). Furthermore, PRMD is freely available, making it useful for the rapid development and promotion of research on plant RNA modifications.
RAVAR: a curated repository for rare variant–trait associations
Authors: Cao Chen , Shao Mengting , Zuo Chunman , Kwok Devin , Liu Lin , Ge Yuli , Zhang Zilong , Cui Feifei , Chen Mingshuai , Fan Rui , Ding Yijie , Jiang Hangjin , Wang Guishen , Zou Quan 
Published: October 2023

Abstract
Rare variants contribute significantly to the genetic causes of complex traits, as they can have much larger effects than common variants and account for much of the missing heritability in genome-wide association studies. The emergence of UK Biobank scale datasets and accurate gene-level rare variant–trait association testing methods have dramatically increased the number of rare variant associations that have been detected. However, no systematic collection of these associations has been carried out to date, especially at the gene level. To address the issue, we present the Rare Variant Association Repository (RAVAR), a comprehensive collection of rare variant associations. RAVAR includes 95 047 high-quality rare variant associations (76186 gene-level and 18 861 variant-level associations) for 4429 reported traits which are manually curated from 245 publications. RAVAR is the first resource to collect and curate published rare variant associations in an interactive web interface with integrated visualization, search, and download features. Detailed gene and SNP information are provided for each association, and users can conveniently search for related studies by exploring the EFO tree structure and interactive Manhattan plots. RAVAR could vastly improve the accessibility of rare variant studies. RAVAR is freely available for all users without login requirement at http://www.ravar.bio.
mHapBrowser: a comprehensive database for visualization and analysis of DNA methylation haplotypes
Authors: Hong Yuyang , Liu Leiqin , Feng Yan , Zhang Zhiqiang , Hou Rui , Xu Qiong , Shi Jiantao 
Published: October 2023

Abstract
DNA methylation acts as a vital epigenetic regulatory mechanism involved in controlling gene expression. Advances in sequencing technologies have enabled characterization of methylation patterns at single-base resolution using bisulfite sequencing approaches. However, existing methylation databases have primarily focused on mean methylation levels, overlooking phased methylation patterns. The methylation status of CpGs on individual sequencing reads represents discrete DNA methylation haplotypes (mHaps). Here, we present mHapBrowser, a comprehensive database for visualizing and analyzing mHaps. We systematically processed data of diverse tissues in human, mouse and rat from public repositories, generating mHap format files for 6366 samples. mHapBrowser enables users to visualize eight mHap metrics across the genome through an integrated WashU Epigenome Browser. It also provides an online server for comparing mHap patterns across samples. Additionally, mHap files for all samples can be downloaded to facilitate local processing using downstream analysis toolkits. The utilities of mHapBrowser were demonstrated through three case studies: (i) mHap patterns are associated with gene expression; (ii) changes in mHap patterns independent of mean methylation correlate with differential expression between lung cancer subtypes; and (iii) the mHap metric MHL outperforms mean methylation for classifying tumor and normal samples from cell-free DNA. The database is freely accessible at http://mhap.sibcb.ac.cn/.
Comparing Adult Smokers Who Switched to JUUL versus Continuing Smokers: Biomarkers of Exposure and of Potential Harm and Respiratory Symptoms
Authors: Shiffman Saul , Oliveri Douglas R , Goldenson Nicholas I , Liang Qiwei , Black Ryan A , Mishra Snigdha 
Published: October 2023

Abstract

Objectives
Real-world evidence on exposure to harmful and potentially harmful constituents (HPHCs) and on biological effects in cigarette smokers who switch to electronic nicotine delivery systems (ENDS) can inform the health effects of switching.

Aims and Methods
This cross-sectional, observational study assessed adults who had smoked ≥10 cigarettes/day for ≥10 years, comparing 124 continuing cigarette smokers (Smokers) to 140 former smokers who switched to JUUL-brand ENDS exclusively for ≥6 months (Switchers). Assessments included biomarkers of exposure (BOEs) to select HPHCs, biomarkers of potential harm (BOPHs) related to smoking-related diseases, psychometric assessments of dependence on cigarettes and ENDS, respectively, and respiratory symptoms. Planned analyses compared geometric means, adjusted for demographic covariates; further analyses adjusted for additional lifestyle and smoking history covariates.

Results
Nicotine levels were significantly higher in Switchers (median time switched = 3 years), who were unusually heavy users of JUUL. All other BOEs, including NNAL and HPMA3 (primary endpoints), were significantly lower in Switchers than Smokers. Most BOPHs (sICAM-1 [primary], and eg, white blood cell count, MCP1, HbA1c) were significantly lower in Switchers than Smokers; HDL was significantly higher. Switchers reported significantly lower dependence on JUUL than Smokers did on cigarettes, and respiratory symptom scores were significantly lower among Switchers than Smokers.

Conclusions
Compared to continuing smokers, smokers who switched to JUUL had substantially lower exposures to multiple HPHCs, favorable differences in markers of inflammation, endothelial function, oxidative stress, and cardiovascular risk, and fewer respiratory symptoms. These findings suggest that switching from cigarettes to JUUL likely reduces smokers’ health risks.

Implications
Short-term confinement studies and randomized clinical trials demonstrate that adult smokers who switch completely to ENDS experience substantial reductions in exposure to many smoking-related toxicants. This study extends those findings to longer periods of switching to JUUL-brand ENDS (almost 3 years on average) under naturalistic use conditions in real-world settings and also found that switching to JUUL resulted in favorable differences in BOPHs more proximally related to smoking-induced disease, as well as in respiratory symptoms. Smokers who switch to ENDS reduce their exposure to toxicants, likely reducing their disease risk.
“If You Just Tell Me You’re 18, I’ll Still Sell to You”: A Qualitative Study of Underage Tobacco Product Purchasing Experiences in a Tobacco 21 Compliance Study
Authors: West Tyler A , Awadalla Josephine , Ackerman Christopher , Sesay Mahdi , Hrywna Mary , Giovenco Daniel P , Kong Amanda Y , Lee Joseph G L 
Published: October 2023

Abstract

Background
Tens of thousands of underage tobacco buy attempts are conducted each year for research, compliance, and public health surveillance. However, little research has qualitatively examined the perceptions and experiences of underage buyers participating in these programs. We sought to understand underage buyers’ experiences and gather recommendations for protocol improvements.

Methods
We conducted semi-structured interviews in the fall of 2022 to assess experiences with underage tobacco product purchasing. Participants (N = 19, 58% male, 42% White) were research assistants aged 18–20 in New Jersey, New York, or North Carolina. Interviews examined purchasing experiences in relation to store characteristics, clerk interactions, and buyer identities. We used deductive and inductive thematic coding to explore key themes related to buyer experiences.

Results
We identified four themes: (1) non-chain stores lacked consistency in verifying age; (2) female data collectors experienced uncomfortable situations more frequently than male data collectors; (3) not identifying with the store’s typical demographics impacted purchase attempts; and (4) participants suggested improvements for inspections and research during training.

Discussion
Retailer education, widespread adoption of ID scanners, and enforcement could increase standardization of ID requests and verification. Male and female buyers can be trained on what they might expect based on their gender, as well as how to maneuver through unwanted situations. Consideration of shared identity is important for future waves of data collection and research. Efforts to improve training include more extensive mock purchase training with supervisors well-versed in this area.

Implications
Electronic ID verification and promoting compliance at non-chain retailers could impact access to tobacco products for underage buyers. Training for underage buyers in research and compliance assessments should focus on ways to enhance data collectors’ confidence when making a purchase attempt, which may improve the validity of the rate of sales to individuals under 21.
Alcohol dehydrogenases regulated by a MYB44 transcription factor underlie Lauraceae citral biosynthesis
Authors: Zhao Yunxiao , Chen Yicun , Gao Ming , Wang Yangdong 
Published: October 2023

Abstract
Lineage-specific terpenoids have arisen throughout the evolution of land plants and are believed to play a role in interactions between plants and the environment. Species-specific gene clusters in plants have provided insight on the evolution of secondary metabolism. Lauraceae is an ecologically important plant family whose members are also of considerable economic value given their monoterpene contents. However, the gene cluster responsible for the biosynthesis of monoterpenes remains yet to be elucidated. Here, a Lauraceae-specific citral biosynthetic gene cluster (CGC) was identified and investigated using a multifaceted approach that combined phylogenetic, collinearity, and biochemical analyses. The CGC comprises MYB44 as a regulator and 2 alcohol dehydrogenases (ADHs) as modifying enzymes, which derived from species-specific tandem and proximal duplication events. Activity and substrate divergence of the ADHs has resulted in the fruit of mountain pepper (Litsea cubeba), a core Lauraceae species, consisting of more than 80% citral. In addition, MYB44 negatively regulates citral biosynthesis by directly binding to the promoters of the ADH-encoding genes. The aggregation of citral biosynthetic pathways suggests that they may form the basis of important characteristics that enhance adaptability. The findings of this study provide insights into the evolution of and the regulatory mechanisms involved in plant terpene biosynthesis.
Suicidal ideation in female individuals with fibromyalgia and comorbid obesity: prevalence and association with clinical, pain-related, and psychological factors
Authors: Varallo Giorgia , Scarpina Federica , Arnison Tor , Giusti Emanuele Maria , Tenti Micheal , Rapelli Giada , Cattivelli Roberto , Landi Giulia , Tossani Eliana , Grandi Silvana , Franceschini Christian , Baldini Valentina , Plazzi Giuseppe , Capodaglio Paolo , Castelnuovo Gianluca 
Published: October 2023

Abstract

Objective
Individuals with fibromyalgia report alarming levels of suicidal ideation, and comorbidity with other chronic health conditions such as obesity—a risk factor for suicidal ideation per se—could further complicate the clinical picture. The aim of this study is to determine, in a sample of women with fibromyalgia and comorbid obesity, the prevalence of suicidal ideation and to evaluate clinical, pain-related and psychological factors associated with suicidal ideation.

Methods
In total, 156 female individuals with fibromyalgia and obesity were recruited and completed a series of self-report measures that assessed (i) the level of pain intensity, (ii) depressive symptomatology, (iii) sleep quality, and (iv) pain catastrophizing. Suicidal ideation was evaluated by item #9 of the Beck Depression Inventory. In addition, information regarding previous suicide attempts and current opioid use was collected.

Results
3n sum, 7.8% of participants reported presence of suicidal ideation. According to the results of the multiple logistic regression, depressive symptomatology, sleep quality, and pain catastrophizing were associated with the presence of suicidal ideation.

Discussion
The presence of suicidal ideation in our sample was significantly associated with depressive symptomatology, sleep quality, and pain catastrophizing. Our findings are the first to suggest a unique (ie, independent of depressive symptomatology, and sleep quality) association between pain catastrophizing and suicidal ideation in the context of fibromyalgia and comorbid obesity. In order to prevent and reduce suicidal ideation, these factors should be assessed and targeted in interventions for pain management. Future research should investigate the extent to which addressing depressive symptoms, sleep quality, and pain catastrophizing reduces suicidal ideation.
Exchange Rate Dynamics and Monetary Spillovers with Imperfect Financial Markets
Authors: Akinci Özge , Queralto Albert 
Published: October 2023

Abstract
We develop a quantitative model with imperfections in domestic and international financial markets that generates strong effects of U.S. monetary policy on emerging markets (EMs). Financial imperfections prevent arbitrage both between local EM lending and borrowing rates, and between local-currency and dollar borrowing rates. An adverse feedback effect between financial health and external conditions amplifies the domestic “financial accelerator,” leading to large cross-border spillovers of U.S. monetary policy shocks. The model implies a link between uncovered interest parity violations and local credit spreads, a prediction we show the data strongly supports.
Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Prognostic value and predictors of the alteration of the diffusing capacity of the lungs for carbon monoxide in systemic lupus erythematosus
Authors: Le Tallec Erwan , Bourg Corentin , Bouzillé Guillaume , Belhomme Nicolas , Le Pabic Estelle , Guillot Stéphanie , Droitcourt Catherine , Perlat Antoinette , Jouneau Stéphane , Donal Erwan , Lescoat Alain 
Published: October 2023

Abstract

Objectives
SLE is a systemic autoimmune disease characterized by heterogeneous manifestations and severity, with frequent lung involvement. Among pulmonary function tests, the measure of the diffusing capacity of the lungs for carbon monoxide (DLCO) is a noninvasive and sensitive tool assessing pulmonary microcirculation. Asymptomatic and isolated DLCO alteration has frequently been reported in SLE, but its clinical relevance has not been established.

Methods
This retrospective study focused on 232 SLE patients fulfilling the 2019 EULAR/ACR classification criteria for SLE. Data were collected from the patient’s medical record, including demographic, clinical and immunological characteristics, while DLCO was measured when performing pulmonary function tests as part of routine patient follow-up.

Results
At the end of follow-up, DLCO alteration (&lt;70% of predicted value) was measured at least once in 154 patients (66.4%), and was associated with a history of smoking as well as interstitial lung disease, but was also associated with renal and neurological involvement. History of smoking, detection of anti-nucleosome autoantibodies and clinical lymphadenopathy at diagnosis were independent predictors of DLCO alteration, while early cutaneous involvement with photosensitivity was a protective factor. DLCO alteration, at baseline or any time during follow-up, was predictive of admission in intensive care unit and/or of all-cause death, both mainly due to severe disease flares and premature cardiovascular complications.

Conclusion
This study suggests a link between DLCO alteration and disease damage, potentially related to SLE vasculopathy, and a prognostic value of DLCO on death or intensive care unit admission in SLE.
The lncRNA H19/miR-29a-3p/SNIP1/c-myc regulatory axis is involved in pulmonary fibrosis induced by Nd2O3
Authors: Bu Ning , Wang Shurui , Ma Yupeng , Xia Haibo , Zhao Yuhang , Shi Xuemin , Liu Qizhan , Wang Suhua , Gao Yanrong 
Published: October 2023

Abstract
Some rare earth elements are occupational and environmental toxicants and can cause organ and systemic damage; therefore, they have attracted global attention. Neodymium oxide (Nd2O3) is a rare earth element that is refined and significantly utilized in China. The long noncoding RNA (lncRNA) H19 is encoded by the H19/IGF2 imprinted gene cluster located on human chromosome 11p15.5. H19 has become a research focus due to its ectopic expression leading to the promotion of fibrosis. However, the mechanisms by which it causes pulmonary fibrosis are elusive. This investigation indicates that biologically active Nd2O3 increases H19, SNIP1, and c-myc, decreases miR-29a-3p, accelerates macrophage M2 polarization, and causes pulmonary fibrosis in mice lung tissues. In macrophage-differentiated THP-1 cells, Nd2O3 (25 μg/ml) enhanced H19, SNIP1, and c-myc, reduced miR-29a-3p, accelerated macrophages M2 polarization, and stimulated fibrogenic cytokine (TGF-β1) secretion. Furthermore, the coculturing of Nd2O3-treated macrophage-differentiated THP-1 cells. And human embryonic lung fibroblast cells activated lung fibroblast, which increases the levels of collagen I, α-SMA, p-Smad2/3, and Smad4, whereas H19 knockdown or miR-29a-3p upregulation in macrophages had opposite effects. Moreover, it was revealed that H19/miR-29a-3p/SNIP1/c-myc regulatory axis is involved in pulmonary fibrosis induced by Nd2O3. Therefore, this study provides new molecular insights into the mechanism of pulmonary fibrosis by Nd2O3.
Long-term Outcomes with Spinal versus General Anesthesia for Hip Fracture Surgery: A Randomized Trial
Authors: Vail Emily A. , Feng Rui , Sieber Frederick , Carson Jeffrey L. , Ellenberg Susan S. , Magaziner Jay , Dillane Derek , Marcantonio Edward R. , Sessler Daniel I. , Ayad Sabry , Stone Trevor , Papp Steven , Donegan Derek , Mehta Samir , Schwenk Eric S. , Marshall Mitchell , Jaffe J. Douglas , Luke Charles , Sharma Balram , Azim Syed , Hymes Robert , Chin Ki-Jinn , Sheppard Richard , Perlman Barry , Sappenfield Joshua , Hauck Ellen , Tierney Ann , Horan Annamarie D. , Neuman Mark D. ,   for the REGAIN (Regional versus General Anesthesia for Promoting Independence after Hip Fracture) Investigators
Published: October 2023

Background
The effects of spinal versus general anesthesia on long-term outcomes have not been well studied. This study tested the hypothesis that spinal anesthesia is associated with better long-term survival and functional recovery than general anesthesia.

Methods
A prespecified analysis was conducted of long-term outcomes of a completed randomized superiority trial that compared spinal anesthesia versus general anesthesia for hip fracture repair. Participants included previously ambulatory patients 50 yr of age or older at 46 U.S. and Canadian hospitals. Patients were randomized 1:1 to spinal or general anesthesia, stratified by sex, fracture type, and study site. Outcome assessors and investigators involved in the data analysis were masked to the treatment arm. Outcomes included survival at up to 365 days after randomization (primary); recovery of ambulation among 365-day survivors; and composite endpoints for death or new inability to ambulate and death or new nursing home residence at 365 days. Patients were included in the analysis as randomized.

Results
A total of 1,600 patients were enrolled between February 12, 2016, and February 18, 2021; 795 were assigned to spinal anesthesia, and 805 were assigned to general anesthesia. Among 1,599 patients who underwent surgery, vital status information at or beyond the final study interview (conducted at approximately 365 days after randomization) was available for 1,427 (89.2%). Survival did not differ by treatment arm; at 365 days after randomization, there were 98 deaths in patients assigned to spinal anesthesia versus 92 deaths in patients assigned to general anesthesia (hazard ratio, 1.08; 95% CI, 0.81 to 1.44, P = 0.59). Recovery of ambulation among patients who survived a year did not differ by type of anesthesia (adjusted odds ratio for spinal vs. general, 0.87; 95% CI, 0.67 to 1.14; P = 0.31). Other outcomes did not differ by treatment arm.

Conclusions
Long-term outcomes were similar with spinal versus general anesthesia.

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