bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression profiles and bioinformatics analysis in lung samples from ovalbumin-induced asthmatic mice
Authors: Song Yilan , Jiang Jingzhi , Bai Qiaoyun , Liu Siqi , Zhang Yalin , Xu Chang , Piao Hongmei , Li Liangchang , Yan Guanghai 
Published: February 2023

Abstract
Background
Asthma is characterized by chronic inflammation and airway remodeling. However, limited study is conducted on the gene expression profiles of ovalbumin (OVA) induced asthma in mice. Here, we explored the gene expression profiles in lung tissues from mice with OVA-induced asthma using microarray and bioinformatics analysis.

Methods
For establishment of OVA-induced asthma model, mice first received intraperitoneal sensitization with OVA on day 0, 7 and 14, followed by atomizing inhalation of OVA 3 times a week for 8 weeks. The lung tissues were collected and subjected to microarray analysis, bioinformatics analysis and expression validation.

Results
Microarray data of lung tissues suggested that 3754 lncRNAs and 2976 mRNAs were differentially expressed in lung tissues between control and asthmatic mice, including 1647 up-regulated and 2106 down-regulated lncRNAs, and 1201 up-regulated and 1766 down-regulated mRNAs. GO analysis displayed that the up-regulated genes were enriched in inflammatory response, leukocyte migration involved in inflammatory response, and Notch signaling pathway. KEGG pathway analysis indicated that the enriched pathway terms of the up-regulated gene included Toll-like receptor signaling pathway and Th17 cell differentiation signaling pathway. Additionally, based on the previously published literatures on asthma and inflammation, we screened out down-regulated genes, such as Smg7, Sumo2, and Stat5a, and up-regulated genes, such as Myl9, Fos and Tlr4. According to the mRNA-lncRNA co-expression network, we selected lncRNAs associated with above genes, including the down-regulated lncRNAs of NONMMUT032848, NONMMUT008873, NONMMUT009478, and NONMMUT006807, and the up-regulated lncRNAs of NONMMUT052633, NONMMUT05340 and NONMMUT042325. The expression changes of the above genes were validated in lung tissues by real-time quantitaive PCR and Western blot.

Conclusions
Overall, we performed gene microarray on lung samples from OVA-induced asthmatic mice and summarized core mRNAs and their related lncRNAs. This study may provide evidence for further research on the therapeutic targets of asthma.
A time-dependent subdistribution hazard model for major dental treatment events in cancer patients: a nationwide cohort study
Authors: Han Areum , Park Eun-Gee , Yoon Jeong-Hwa , Choi Ji-Yeob , Park Hee-Kyung , Hahn Seokyung 
Published: February 2023

AbstractBackgroundDental care in cancer patients tends to be less prioritized. However, limited research has focused on major dental treatment events in cancer patients after the diagnosis. This study aimed to examine dental treatment delays in cancer patients compared to the general population using a national claims database in South Korea.MethodThe Korea National Health Insurance Service-National Sample Cohort version 2.0, collected from 2002 to 2015, was analyzed. Treatment events were considered for stomatitis, tooth loss, dental caries/pulp disease, and gingivitis/periodontal disease. For each considered event, time-dependent hazard ratios and associated 95% confidence intervals were calculated by applying a subdistribution hazard model with time-varying covariates. Mortality was treated as a competing event. Subgroup analyses were conducted by type of cancer.ResultsThe time-dependent subdistribution hazard ratios (SHRs) of stomatitis treatment were greater than 1 in cancer patients in all time intervals, 2.04 within 30 days after cancer diagnosis, and gradually decreased to 1.15 after 5 years. The SHR for tooth loss was less than 0.70 within 3 months after cancer diagnosis and increased to 1 after 5 years. The trends in SHRs of treatment events for other dental diseases were similar to those observed for tooth loss. Subgroup analyses by cancer type suggested that probability of all dental treatment event occurrence was higher in head and neck cancer patients, particularly in the early phase after cancer diagnosis.ConclusionApart from treatments that are associated with cancer therapy, dental treatments in cancer patients are generally delayed and cancer patients tend to refrain from dental treatments. Consideration should be given to seeking more active and effective means for oral health promotion in cancer patients.
The link between different infection forms of Porphyromonas gingivalis and acute myocardial infarction: a cross-sectional study
Authors: Wu Yingle , Wang Yanyu , Du Laijing , Wang Ke , Wang Shaoxin , Li Guangping 
Published: February 2023

Abstract
Background
Porphyromonas gingivalis (Pg) is one of the keystone pathogens involved in periodontitis. The present study aimed to observe the relationship among different infection forms of Pg, systemic inflammation, and acute myocardial infarction (AMI).

Methods
A total of 382 patients diagnosed with AMI and 78 patients without coronary heart disease (CHD) were included in the study. DNA from exfoliated oral cells, circulating cell-free DNA (cfDNA), and genomic DNA (gDNA) from blood samples were extracted. The qPCR method was employed to detect Pg infection. Clinical characteristics, inflammatory parameters, and severity of coronary artery lesions of the patients were analyzed and compared.

Results
Both the oral colonization and distant invasion of Pg correlated positively with systemic inflammation. Multivariate logistic regression analysis suggested that Pg positivity in gDNA was correlated with the risk of AMI [Model 1 (odds ratio (OR) = 1.917, 95% confidence interval (CI) 1.108–3.315), Model 2 (OR = 1.863, 95% CI 1.064–3.262), and Model 3 (OR = 1.853, 95% CI 1.042–3.295); p < 0.05]. Pg positivity in cfDNA and gDNA was related to the severity of coronary artery lesions (cfDNA-positive cases, adjusted OR = 1.577, p < 0.05; gDNA-positive cases, adjusted OR = 1.976, p < 0.01).

Conclusions
The distant invasion and colonization of Pg were the risk factors of AMI. They also affected the severity of CHD, indicating that periodontitis severity and distant invasion of periodontal pathogens were related to CHD. The presence of Pg was likely able to drive systemic inflammation, suggesting that there was an inflammatory relationship between periodontitis and AMI.
What are the ways in which social media is used in the context of complementary and alternative medicine in the health and medical scholarly literature? a scoping review
Authors: Ng Jeremy Y. , Verhoeff Natasha , Steen Jeremy 
Published: February 2023

Abstract
Background
Despite the increased use of social media to share health-related information and the substantial impact that complementary and alternative medicine (CAM) can have on individuals’ health and wellbeing, currently, to our knowledge, there is no review that compiles research on how social media is used in the context of CAM. The objective of this study was to summarize what are the ways in which social media is used in the context of CAM.

Methods
A scoping review was conducted, following Arksey and O’Malley’s five-stage methodological framework. MEDLINE, EMBASE, PsycINFO, AMED, and CINAHL databases were systematically searched from inception until October 3, 2020, in addition to the Canadian Agency for Drugs and Technology in Health (CADTH) website. Eligible studies had to have investigated how at least one social media platform is used in the context of a single or multiple types of CAM treatments.

Results
Searches retrieved 1714 items following deduplication, of which 1687 titles and abstracts were eliminated, leaving 94 full-text articles to be considered. Of those, 65 were not eligible, leaving a total of 29 articles eligible for review. Three themes emerged from our analysis: 1) social media is used to share user/practitioner beliefs, attitudes, and experiences about CAM, 2) social media acts as a vehicle for the spread of misinformation about CAM, and 3) there are unique challenges with social media research in the context of CAM.

Conclusions
In addition to social media being a useful tool to share user/practitioner beliefs, attitudes, and experiences about CAM, it has shown to be accessible, effective, and a viable option in delivering CAM therapies and information. Social media has also been shown to spread a large amount of misleading and false information in the context of CAM. Additionally, this review highlights the challenges with conducting social media research in the context of CAM, particularly in collecting a representative sample.
Terminally ill patients’ and their relatives’ experiences and behaviors regarding complementary and alternative medicine utilization in hospice palliative inpatient care units: a cross-sectional, multicenter survey
Authors: Lin Yu-Jia , Chang Hsiao-Ting , Lin Ming-Hwai , Chen Ru-Yih , Chen Ping-Jen , Lin Wen-Yuan , Hsieh Jyh-Gang , Wang Ying-Wei , Hu Chung-Chieh , Liou Yi-Sheng , Chiu Tai-Yuan , Tu Chun-Yi , Cheng Bo-Ren , Chen Tzeng-Ji , Chen Fang-Pey , Hwang Shinn-Jang 
Published: February 2023

Abstract
Background
Terminally ill patients often experience exacerbations of diseases that render mainstream medicine ineffective in relieving symptoms, prompting attempts at complementary and alternative medicine (CAM). This study collected data from terminally ill patients and their relatives to determine differences between CAM use, behavioral patterns, and perceptions of health information about CAM.

Methods
A cross-sectional design using a self-administered questionnaire was adopted. Eight medical institutions in Taiwan with inpatient hospice palliative care units were chosen. Ninety-two terminally ill patients and 267 relatives met the inclusion criteria. The questions concerned the experience of CAM use, the kinds of products/services CAM provided, the purpose of CAM use, the source of CAM information, and the perceptions and attitudes toward CAM.

Results
Both terminally ill patients and their relatives have a high proportion of lifetime and one-year prevalence of CAM use (88.0% vs. 88.4%; p = 0.929). CAM use for musculoskeletal and neurological discomfort is higher among terminally ill patients than among their relatives. Relatives/friends are the most frequent sources of information on CAM (53.3% vs. 62.2%; p = 0.133). The percentage of terminally ill patients who discontinued mainstream medical treatment because of CAM use was higher than that of their relatives (18.5% vs. 9.3%; p = 0.026). More than half the terminally ill patients and their relatives had never been asked about CAM by medical staff (64.1% vs. 66.7%), nor had they informed medical professionals about the use of CAM products and services (63% vs. 66.9%). Random inquiries by medical professionals may be associated with increased disclosure of CAM use (terminally ill patients: odds ratio, 9.75; 95% confidence interval, 1.97–48.35 vs. relatives: odds ratio, 5.61; 95% confidence interval, 2.66–11.83).

Conclusions
The high prevalence and concealment of CAM use in terminally ill patients should be considered. Medical professionals should establish a friendly and barrier-free communication model, encourage patients to share CAM experiences, and provide evidence-based information on the use of CAM products and services, to reduce the potential damage caused by harmful use.
Clinical pharmacy undergraduate education in China: a comparative analysis based on ten universities’ training programs
Authors: Li Jiakai , Xiao Chenlin , Hou Jingjing , Zhao Yichang , Gong Hui , Zhang Bikui , Yan Miao 
Published: February 2023

Abstract
Background
In recent years, the scale of personnel training for clinical pharmacy professionals in China has expanded increasingly, however, the shortage of clinical pharmacists is still prominent. In 2018, the Ministry of Education of China released national standards for the teaching quality of undergraduate majors at regular colleges and universities, which has developed a core policy for undergraduate clinical pharmacy training. To explore the training methods for clinical pharmacy professionals in China and to promote the healthy and sustainable development of the clinical pharmacy education system. This study comparatively analyzed the training programs for clinical pharmacy undergraduates in China’s ten universities, discussed training programs suitable for clinical pharmacy professionals in China.

Methods
The clinical pharmacy education programs in these ten universities were obtained through official school websites or by interviewing relevant people, and then compared and analyzed.

Results
The school with the largest number of courses and the most class hours in general courses is University A1 (34 courses, 1316 class hours), and the school with the most credits is University B1 (75.5 credits). The schools with the largest number of courses and the most class hours in the basic courses are University A1 (50 courses, 1997 class hours), and the schools with the most credits are University B3 and University B1 (105.5 credits). The schools with the largest number of courses in the core courses are University C1 (23 courses), and the school with the most credits and class hours is University B2 (51 credits, 914 class hours). The school with the most class hours in practical teaching is University B6 (1406 class hours), and the schools with the longest internship time are University A1 and University B6 (52 weeks).

Conclusions
There was substantial variation in programs. There remains a gap between the existing educational model and clinical training in pharmacy in China and developed countries. China should explore the most appropriate method for undergraduate education in clinical pharmacy based on studying foreign excellent educational models and the experience of China.
Looking back to inform the future: a review of published paramedicine research
Authors: Cavanagh N. , Blanchard I. E. , Weiss D. , Tavares W. 
Published: February 2023

AbstractObjectiveParamedicine has evolved in ways that may outpace the science informing these changes. Examining the scholarly pursuits of paramedicine may provide insights into the historical academic focus, which may inform future endeavors and evolution of paramedicine. The objective of this study was to explore the existing discourse in paramedicine research to reflect on the academic pursuits of this community.MethodsWe searched Medline, Embase, CINAHL, Google Scholar and Web of Science from January, 2006 to April, 2019. We further refined the yield using a ranking formula that prioritized journals most relevant to paramedicine, then sampled randomly in two-year clusters for full text review. We extracted literature type, study topic and context, then used elements of qualitative content, thematic, and discourse analysis to further describe the sample.ResultsThe initial search yielded 99,124 citations, leaving 54,638 after removing duplicates and 7084 relevant articles from nine journals after ranking. Subsequently, 2058 articles were included for topic categorization, and 241 papers were included for full text analysis after random sampling. Overall, this literature reveals: 1) a relatively narrow topic focus, given the majority of research has concentrated on general operational activities and specific clinical conditions and interventions (e.g., resuscitation, airway management, etc.); 2) a limited methodological (and possibly philosophical) focus, given that most were observational studies (e.g., cohort, case control, and case series) or editorial/commentary; 3) a variety of observed trajectories of academic attention, indicating where the evolution of paramedicine is evident, areas where scope of practice is uncertain, and areas that aim to improve skills historically considered core to paramedic clinical practice.ConclusionsIncluded articles suggest a relatively narrow topic focus, a limited methodological focus, and observed trajectories of academic attention indicating where research pursuits and priorities are shifting. We have highlighted that the academic focus may require an alignment with aspirational and direction setting documents aimed at developing paramedicine. This review may be a snapshot of scholarly activity that reflects a young medically directed profession and systems focusing on a few high acuity conditions, with aspirations of professional autonomy contributing to the health and social well-being of communities.
Lost genome segments associate with trait diversity during rice domestication
Authors: Zheng Xiaoming , Zhong Limei , Pang Hongbo , Wen Siyu , Li Fei , Lou Danjing , Ge Jinyue , Fan Weiya , Wang Tianyi , Han Zhenyun , Qiao Weihua , Pan Xiaowu , Zhu Yebao , Wang Jilin , Tang Cuifeng , Wang Xinhua , Zhang Jing , Xu Zhijian , Kim Sung Ryul , Kohli Ajay , Ye Guoyou , Olsen Kenneth M. , Fang Wei , Yang Qingwen 
Published: February 2023

Abstract
Background
DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication.

Results
In this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length.

Conclusions
We provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice.
Lung Inflammation in alpha-1-antitrypsin deficient individuals with normal lung function
Authors: Kokturk Nurdan , Khodayari Nazli , Lascano Jorge , Riley E. Leonard , Brantly Mark L. 
Published: February 2023

Abstract
Background
Alpha-1-antitrypsin deficient (AATD) individuals are prone to develop early age of onset chronic obstructive pulmonary disease (COPD) more severe than non-genetic COPD. Here, we investigated the characteristics of lower respiratory tract of AATD individuals prior to the onset of clinically significant COPD.

Methods
Bronchoalveolar lavage was performed on 22 AATD with normal lung function and 14 healthy individuals. Cell counts and concentrations of proteases, alpha-1-antitrypsin and proinflammatory mediators were determined in the bronchoalveolar lavage fluid from study subjects. In order to determine the airway inflammation, we also analyzed immune cell components of the large airways from bronchial biopsies using immunohistochemistry in both study subjects. Finally, we made comparisons between airway inflammation and lung function rate of decline using four repeated lung function tests over one year in AATD individuals.

Results
AATD individuals with normal lung function had 3 folds higher neutrophil counts, 2 folds increase in the proteases levels, and 2–4 folds higher levels of IL-8, IL-6, IL-1β, and leukotriene B4 in their epithelial lining fluid compared to controls. Neutrophil elastase levels showed a positive correlation with the levels of IL-8 and neutrophils in AATD epithelial lining fluid. AATD individuals also showed a negative correlation of baseline FEV1 with neutrophil count, neutrophil elastase, and cytokine levels in epithelial lining fluid (p < 0.05). In addition, we observed twofold increase in the number of lymphocytes, macrophages, neutrophils, and mast cells of AATD epithelial lining fluid as compared to controls.

Conclusion
Mild inflammation is present in the lower respiratory tract and airways of AATD individuals despite having normal lung function. A declining trend was also noticed in the lung function of AATD individuals which was correlated with pro-inflammatory phenotype of their lower respiratory tract. This results suggest the presence of proinflammatory phenotype in AATD lungs. Therefore, early anti-inflammatory therapies may be a potential strategy to prevent progression of lung disease in AATD individuals.
Insights into the susceptibility of Pseudomonas putida to industrially relevant aromatic hydrocarbons that it can synthesize from sugars
Authors: García-Franco Ana , Godoy Patricia , Duque Estrella , Ramos Juan Luis 
Published: February 2023

AbstractPseudomonas putida DOT-T1E is a highly solvent tolerant strain for which many genetic tools have been developed. The strain represents a promising candidate host for the synthesis of aromatic compounds—opening a path towards a green alternative to petrol-derived chemicals. We have engineered this strain to produce phenylalanine, which can then be used as a raw material for the synthesis of styrene via trans-cinnamic acid. To understand the response of this strain to the bioproducts of interest, we have analyzed the in-depth physiological and genetic response of the strain to these compounds. We found that in response to the exposure to the toxic compounds that the strain can produce, the cell launches a multifactorial response to enhance membrane impermeabilization. This process occurs via the activation of a cis to trans isomerase that converts cis unsaturated fatty acids to their corresponding trans isomers. In addition, the bacterial cells initiate a stress response program that involves the synthesis of a number of chaperones and ROS removing enzymes, such as peroxidases and superoxide dismutases. The strain also responds by enhancing the metabolism of glucose through the specific induction of the glucose phosphorylative pathway, Entner-Doudoroff enzymes, Krebs cycle enzymes and Nuo. In step with these changes, the cells induce two efflux pumps to extrude the toxic chemicals. Through analyzing a wide collection of efflux pump mutants, we found that the most relevant pump is TtgGHI, which is controlled by the TtgV regulator.
Graphical Abstract