bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overnight desaturation in interstitial lung diseases: links to pulmonary vasculopathy and mortality
Authors: Margaritopoulos George A. , Proklou Athanasia , Trachalaki Athina , Badenes Bonet Diana , Kokosi Maria , Kouranos Vasilis , Chua Felix , George Peter M. , Renzoni Elisabetta A. , Devaraj Anand , Desai Sujal , Nicholson Andrew G. , Antoniou Katerina M. , Wells Athol U. 
Published: December 2023

BackgroundOvernight desaturation predicts poor prognosis across interstitial lung diseases (ILDs). The aim of the present study was to investigate whether nocturnal desaturation is associated with pulmonary vasculopathy and mortality.MethodsA retrospective single centre study of 397 new ILD patients was carried out including patients with idiopathic pulmonary fibrosis (IPF) (n=107) and patients with non-IPF fibrotic ILD (n=290). This is the largest study to date of the effect of significant nocturnal desaturation (SND) (≥10% of total sleep time with oxygen saturation ≤90% measured by pulse oximetry).ResultsThe prevalence of SND was 28/107 (26.2%) in IPF and 80/290 (27.6%) in non-IPF ILD. The prevalence of SND was higher in non-IPF ILDs than in IPF (p=0.025) in multivariate analysis. SND was associated with noninvasive markers of pulmonary hypertension (PH): tricuspid regurgitation velocity (TRV) (p<0.0001), brain natriuretic peptide (p<0.007), carbon monoxide transfer coefficient (p<0.0001), A–a gradient (p<0.0001), desaturation >4% in 6-min walking test (p<0.03) and pulmonary artery diameter (p<0.005). SND was independently associated with high echocardiographic PH probability in the entire cohort (OR 2.865, 95% CI 1.486–5.522, p<0.002) and in non-IPF fibrotic ILD (OR 3.492, 95% CI 1.597–7.636, p<0.002) in multivariate analysis. In multivariate analysis, SND was associated with mortality in the entire cohort (OR 1.734, 95% CI 1.202–2.499, p=0.003) and in IPF (OR 1.908, 95% CI 1.120–3.251, p=0.017) and non-IPF fibrotic ILD (OR 1.663, 95% CI 1.000–2.819, p=0.041). Separate models with exclusion of each one of the diagnostic subgroups showed that no subgroup was responsible for this finding in non-IPF ILDs. SND was a stronger marker of 5-year mortality than markers of PH.ConclusionSND was associated with high echocardiographic probability and mortality and was a stronger predictor of mortality in IPF and non-IPF ILDs grouped together to power the study.
Bronchial reactivity and asthma at school age after early-life metapneumovirus infection
Authors: Myklebust Åsne , Rae Simpson Melanie , Valand Jonas , Stenhaug Langaas Vibeke , Jartti Tuomas , Døllner Henrik , Risnes Kari 
Published: December 2023

BackgroundThe association between early-life lower respiratory tract infection (LRTI) and asthma is well established. Knowledge about bronchial hyperresponsiveness (BHR) and asthma after metapneumovirus (MPV) LRTI is scarce. The aim of this study was to assess BHR and current asthma in school-aged children after hospital admission for early-life LRTI with MPV, and to compare with more well-known viruses, rhinovirus (RV) and respiratory syncytial virus (RSV), and with controls.MethodsA cohort consisting of children admitted for LRTI and controls was followed-up at school age with a clinical research assessment and lung function tests, including a methacholine provocation test. Current asthma was defined based on objective variable airway obstruction and clinical symptoms. BHR and asthma were compared according to viral groups.Results135 children (median age 9.3 years) were included (16 MPV, 34 RV, 51 RSV, 13 mixed infections and 21 controls). Compared with controls there was increased BHR after MPV and RV LRTI (provocative dose causing a 20% fall in forced expiratory volume in 1 s and dose–response slope; p<0.05). Using Kaplan–Meier statistics, BHR was increased for MPV compared with both controls and RSV (p=0.02 and p=0.01). The proportion of children with current asthma at follow-up was higher in the LRTI children compared with the controls (46% versus 24%; p=0.06). Among children who had undergone MPV and RV infection, 50% fulfilled the asthma criteria compared with 43% in the RSV group (p=0.37).ConclusionWe found increased BHR and a high prevalence of asthma in school-aged children after early-life MPV infection, and findings were similar to RV, and less to RSV, compared with controls.
The impact of clinical pharmacists’ medication reconciliation upon patients’ admission to reduce medication discrepancies in the emergency department: a prospective quasi-interventional study
Authors: Shaker Heba Othman , Sabry Ahmed Abdel Fattah , Salah Asmaa , Ragab Gilan Mohamed , Sedik Nahla Ahmed , Ali Zahraa , Magdy Doha , Alkafafy Asmaa Mohamed 
Published: December 2023

Abstract
Background
The role of the clinical pharmacist in medication reconciliation is well established. Upon patients’ admission, the reconciliation service mainly focuses on achieving an accurate and full drug history. This will achieve the best treatment plan and reduce medication discrepancies.
Upon the recent implementation of clinical pharmacy services in the emergency department at Alexandria Main University Hospital, medication reconciliation was one of the most important duties that needed to be focused on.
We hypothesized that clinical pharmacists are able to achieve patients’ drug history lists with higher accuracy than emergency physicians.

Results
A total number of 161 patients were included. Age was 58.59 ± (13.78) years, number of comorbidities was 2.39 ± (1.22) and number of home medications was 4.51 ± (2.72). Clinical pharmacists’ fulfillment of patients’ drug history was significantly more accurate than the emergency physicians (75.16% and 50.3% of the total number of revised patients’ profiles respectively). The clinical pharmacists could put a written copy of the accurate patients’ drug history list in only 50.93% of the revised patients’ profiles. Five hundred eighty-five medication discrepancies were detected which represent an average of 3.63 discrepancies/medication sheet. Medications at Transitions and Clinical Handoffs (MATCH) Toolkit for medication reconciliation and the National Coordinating Council for Medication Error Reporting and Prevention (NCC MERP) index were used to categorize discrepancies. Categories A, B, and C represented (66.5%), while categories D, E, and F represented (33.5%) of the total discrepancies. There was a significant direct relationship between the total number of discrepancies and both the number of comorbidities and the number of drugs administered before hospital admission.

Conclusion
The clinical pharmacists are the main members of the emergency health care team. One of their fundamental services is medication reconciliation. The establishment of a complete drug history list and physicians’ discussion about the current treatment plan can obviously detect and reduce medication errors.

Trial registration
NCT04395443. Registered 16 May 2020.
Machine learning-based donor permission extraction from informed consent documents
Authors: Zhang Meng , Sankaranarayanapillai Madhuri , Du Jingcheng , Xiang Yang , Manion Frank J. , Harris Marcelline R. , Stansbury Cooper , Pham Huy Anh , Tao Cui 
Published: December 2023

Abstract
Background
With more clinical trials are offering optional participation in the collection of bio-specimens for biobanking comes the increasing complexity of requirements of informed consent forms. The aim of this study is to develop an automatic natural language processing (NLP) tool to annotate informed consent documents to promote biorepository data regulation, sharing, and decision support. We collected informed consent documents from several publicly available sources, then manually annotated them, covering sentences containing permission information about the sharing of either bio-specimens or donor data, or conducting genetic research or future research using bio-specimens or donor data.

Results
We evaluated a variety of machine learning algorithms including random forest (RF) and support vector machine (SVM) for the automatic identification of these sentences. 120 informed consent documents containing 29,204 sentences were annotated, of which 1250 sentences (4.28%) provide answers to a permission question. A support vector machine (SVM) model achieved a F-1 score of 0.95 on classifying the sentences when using a gold standard, which is a prefiltered corpus containing all relevant sentences.

Conclusions
This study provides the feasibility of using machine learning tools to classify permission-related sentences in informed consent documents.
Integrated metabolome and transcriptome analyses of anthocyanin biosynthesis reveal key candidate genes involved in colour variation of Scutellaria baicalensis flowers
Authors: Guo Fengdan , Guan Renwei , Sun Xinru , Zhang Cuicui , Shan Chenggang , Liu Mengyu , Cui Ning , Wang Ping , Lin Huibin 
Published: December 2023

Abstract
Background
Bright flower colour assists plants attract insects to complete pollination and provides distinct ornamental values. In some medicinal plants, diverse flower colour variations usually imply differences in active ingredients. Compared to the common bluish purple of Scutellaria baicalensis flower (SB), the natural variants present rose red (SR) and white (SW) flowers were screened out under the same growing conditions in the genuine producing area Shandong Province, China. However, the mechanism of flower colour variation in S. baicalensis was remain unclear. In the present study, we conducted integrated transcriptome and metabolome analyses to uncover the metabolic difference and regulation mechanism in three S. baicalensis flowers.

Results
The results showed that 9 anthocyanins were identified. Among which, 4 delphinidin-based anthocyanins were only detected in SB, 4 cyanidin-based anthocyanins (without cyanidin-3-O-glucoside) mainly accumulated in SR, and no anthocyanin but high level of flavanone, naringenin, was detected in SW. The gene expression profile indicated that the key structural genes in the flavonoid and anthocyanin biosynthesis pathway differentially expressed in flowers with different colours. Compared to SB, the down-regulated expression of F3’5’H, ANS, and 3GT gene in SR might influence the anthocyanin composition. Especially the InDel site with deletion of 7 nucleotides (AATAGAG) in F3’5’H in SR might be the determinant for lack of delphinidin-based anthocyanins in rose red flowers. In SW, the lower expression levels of DFR and two F3H genes might reduce the anthocyanin accumulation. Notably the SNP site of G > A mutation in the splicing site of DFR in SW might block anthocyanin biosynthesis from flavanones and thus cause white flowers. In addition, several key transcription factors, including MYB, bHLH, and NAC, which highly correlated with structural gene expression and anthocyanin contents were also identified.

Conclusions
These results provide clues to uncover the molecular regulatory mechanism of flower colour variation in S. baicalensis and promote novel insights into understanding the anthocyanin biosynthesis and regulation.
Genome-wide analysis of long noncoding RNAs in response to salt stress in Nicotiana tabacum
Authors: Li Zefeng , Zhou Huina , Xu Guoyun , Zhang Peipei , Zhai Niu , Zheng Qingxia , Liu Pingping , Jin Lifeng , Bai Ge , Zhang Hui 
Published: December 2023

Abstract
Background
Long noncoding RNAs (lncRNAs) have been shown to play important roles in the response of plants to various abiotic stresses, including drought, heat and salt stress. However, the identification and characterization of genome-wide salt-responsive lncRNAs in tobacco (Nicotiana tabacum L.) have been limited. Therefore, this study aimed to identify tobacco lncRNAs in roots and leaves in response to different durations of salt stress treatment.

Results
A total of 5,831 lncRNAs were discovered, with 2,428 classified as differentially expressed lncRNAs (DElncRNAs) in response to salt stress. Among these, only 214 DElncRNAs were shared between the 2,147 DElncRNAs in roots and the 495 DElncRNAs in leaves. KEGG pathway enrichment analysis revealed that these DElncRNAs were primarily associated with pathways involved in starch and sucrose metabolism in roots and cysteine and methionine metabolism pathway in leaves. Furthermore, weighted gene co-expression network analysis (WGCNA) identified 15 co-expression modules, with four modules strongly linked to salt stress across different treatment durations (MEsalmon, MElightgreen, MEgreenyellow and MEdarkred). Additionally, an lncRNA-miRNA-mRNA network was constructed, incorporating several known salt-associated miRNAs such as miR156, miR169 and miR396.

Conclusions
This study enhances our understanding of the role of lncRNAs in the response of tobacco to salt stress. It provides valuable information on co-expression networks of lncRNA and mRNAs, as well as networks of lncRNAs-miRNAs-mRNAs. These findings identify important candidate lncRNAs that warrant further investigation in the study of plant-environment interactions.
"We are still tired": staff and administrators’ experiences during the COVID-19 pandemic within California residential care facilities for older adults
Authors: Bahr Kaitlin O. , Bhavsar Grishma P. , Zhao David 
Published: December 2023

Abstract
Background
Extensive research has been conducted on the impacts of the COVID-19 pandemic on long-term care workers in specialized care facilities. However, little is known about the impacts faced by facilities that provide generalized long-term support and care, such as residential care facilities for older adults (RCFs). This study describes the challenges experienced by staff and administrators of RCFs during the COVID-19 pandemic.

Methods
An electronic questionnaire collecting data using both closed- and open-ended questions on staff experiences was sent to 5,721 unique RCF administrator emails within the state of California between June-December 2021. Email addresses were obtained from the public database of RCFs available through the California Health and Human Services Open Data Portal. Descriptive statistics were calculated on quantitative data regarding staff preparedness training, access to resources, and administrators’ confidence in meeting recommended guidelines during the pandemic. Inductive thematic analysis was conducted on qualitative data regarding the confidence levels in meeting pandemic guidelines and challenges faced related to staff stress and morale.

Results
A total of 150 RCF administrators across California (response rate of 2.6%) completed the survey. Over three-fourths of respondents indicated their facilities had a designated staff member to train other staff members on emergency preparedness plans and the most frequently used resources during the COVID-19 pandemic were the Department of Social Services Community Care Licensing Division (88.7%), the county health department (86.7%), and the Centers for Disease Control and Prevention (80.7%). Administrators felt least confident in their facilities’ ability to maintain adequate staffing (52.0%), communication with nearby hospitals (62.1%) and communication with state and local public health officials (69.8%) during the pandemic. Three central themes emerged from the thematic analysis on staff stress and morale: (1) physical safety, mental and emotional impact of the COVID-19 pandemic; (2) staffing issues; and (3) challenges with guidelines in managing the ongoing pandemic.

Conclusions
Findings from this research study can be used to actively target training resources for facility administrators and staff that have been identified as most frequently used and relevant for emergency preparedness in these understudied facilities. Additionally, developing a better understanding of the staffing stress and morale difficulties in RCFs can provide insight on how policymakers can assist these critical facilities in better preparing for future crises.
Multi-omics integrative modelling for stereotactic body radiotherapy in early-stage non-small cell lung cancer: clinical trial protocol of the MONDRIAN study
Authors: Volpe Stefania , Zaffaroni Mattia , Piperno Gaia , Vincini Maria Giulia , Zerella Maria Alessia , Mastroleo Federico , Cattani Federica , Fodor Cristiana Iuliana , Bellerba Federica , Bonaldi Tiziana , Bonizzi Giuseppina , Ceci Francesco , Cremonesi Marta , Fusco Nicola , Gandini Sara , Garibaldi Cristina , Torre Davide La , Noberini Roberta , Petralia Giuseppe , Spaggiari Lorenzo , Venetis Konstantinos , Orecchia Roberto , Casiraghi Monica , Jereczek-Fossa Barbara Alicja 
Published: December 2023

Abstract
Background
Currently, main treatment strategies for early-stage non-small cell lung cancer (ES-NSCLC) disease are surgery or stereotactic body radiation therapy (SBRT), with successful local control rates for both approaches. However, regional and distant failure remain critical in SBRT, and it is paramount to identify predictive factors of response to identify high-risk patients who may benefit from more aggressive approaches. The main endpoint of the MONDRIAN trial is to identify multi-omic biomarkers of SBRT response integrating information from the individual fields of radiomics, genomics and proteomics.

Methods
MONDRIAN is a prospective observational explorative cohort clinical study, with a data-driven, bottom-up approach. It is expected to enroll 100 ES-NSCLC SBRT candidates treated at an Italian tertiary cancer center with well-recognized expertise in SBRT and thoracic surgery. To identify predictors specific to SBRT, MONDRIAN will include data from 200 patients treated with surgery, in a 1:2 ratio, with comparable clinical characteristics. The project will have an overall expected duration of 60 months, and will be structured into five main tasks: (i) Clinical Study; (ii) Imaging/ Radiomic Study, (iii) Gene Expression Study, (iv) Proteomic Study, (v) Integrative Model Building.

Discussion
Thanks to its multi-disciplinary nature, MONDRIAN is expected to provide the opportunity to characterize ES-NSCLC from a multi-omic perspective, with a Radiation Oncology-oriented focus. Other than contributing to a mechanistic understanding of the disease, the study will assist the identification of high-risk patients in a largely unexplored clinical setting. Ultimately, this would orient further clinical research efforts on the combination of SBRT and systemic treatments, such as immunotherapy, with the perspective of improving oncological outcomes in this subset of patients.

Trial registration
The study was prospectively registered at clinicaltrials.gov (NCT05974475).
The state of clinical education and factors affecting effective clinical education: the point of view of nursing and midwifery students
Authors: Asadi Mohammadreza , Noorian Sajad , Motefakker Sanaz , Heydari Fatemeh , Shahsavari Neda , Senmar Mojtaba 
Published: December 2023

AbstractBackgroundClinical education is the basis of education in medical sciences. Clinical education, as the essence of education in nursing and midwifery, promotes social health, improves health care, and reduces mortality. Considering the position of nursing and midwifery, investigating the views of students in this field can be an effective step in improving clinical education. Therefore, the present study was conducted to investigate the status of clinical education and the factors affecting effective clinical education from the point of view of nursing and midwifery students.MethodsA descriptive-analytical study was conducted among nursing and midwifery students at Qazvin University of Medical Sciences in 2022–2023. Using available sampling, 242 students were included in the study. Students were included in the study if they completed at least one unit of in-person internship. Refusing to continue the study for any reason and having a practical nurse certificate were the criteria for exclusion from the study. The data collection tools included a demographic information questionnaire, a questionnaire to assess the status of clinical education, and a questionnaire on factors affecting effective clinical education. The data were analysed with descriptive and inferential statistics and SPSS 20 software.ResultsThe mean age of the participants in this study was 21.66 ± 2.25. A total of 180 (74.4%) of the participants were women, and the rest were men. The results showed that the general condition of clinical education is at an average level (103.16 ± 19.21). It was also found that the clinical education status of midwifery students was better than that of nursing students, and this difference was significant (p = 0.003). Among the fields of clinical education, the highest score belonging to the field of objectives and planning was reported on the average level (34.39 ± 6.66). Among the factors affecting effective clinical education, the highest score was given to the field of personal characteristics of the student (33.97 ± 5.99). The results showed that there is a significant relationship between the grades of the general state of clinical education with the academic semester (p = 0.001) and interest in the field of study (p < 0.040).ConclusionsBased on the findings of the present study, clinical education is at an average level. Among the factors affecting effective clinical training, the field of personal characteristics of the student is more effective in clinical training. Providing educational facilities according to the number of students, using modern teaching methods, and determining and communicating the duties of professors and students can help to improve clinical education.
Genetic and observational associations of lung function with gastrointestinal tract diseases: pleiotropic and mendelian randomization analysis
Authors: Jiang Minghui , Hao Xingjie , Jiang Yi , Li Si , Wang Chaolong , Cheng Shanshan 
Published: December 2023

Abstract
Background
The two-way communications along the gut-lung axis influence the immune function in both gut and lung. However, the shared genetic characteristics of lung function with gastrointestinal tract (GIT) diseases remain to be investigated.

Methods
We first investigated the genetic correlations between three lung function traits and four GIT diseases. Second, we illustrated the genetic overlap by genome-wide pleiotropic analysis (PLACO) and further pinpointed the relevant tissue and cell types by partitioning heritability. Furthermore, we proposed pleiotropic genes as potential drug targets by drug database mining. Finally, we evaluated the causal relationships by epidemiologic observational study and Mendelian randomization (MR) analysis.

Results
We found lung function and GIT diseases were genetically correlated. We identified 258 pleiotropic loci, which were enriched in gut- and lung-specific regions marked by H3K4me1. Among these, 16 pleiotropic genes were targets of drugs, such as tofacitinib and baricitinib targeting TYK2 for the treatment of ulcer colitis and COVID-19, respectively. We identified a missense variant in TYK2, exhibiting a shared causal effect on FEV1/FVC and inflammatory bowel disease (rs12720356, PPLACO=1.38 × 10− 8). These findings suggested TYK2 as a promising drug target. Although the epidemiologic observational study suggested the protective role of lung function in the development of GIT diseases, no causalities were found by MR analysis.

Conclusions
Our study suggested the shared genetic characteristics between lung function and GIT diseases. The pleiotropic variants could exert their effects by modulating gene expression marked by histone modifications. Finally, we highlighted the potential of pleiotropic analyses in drug repurposing.