bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide identification and expression analysis of the Eriobotrya japonica TIFY gene family reveals its functional diversity under abiotic stress conditions
Authors: Li Xulin , Wen Ke , Zhu Ling , Chen Chaoying , Yin Tuo , Yang Xiuyao , Zhao Ke , Zi Yinqiang , Zhang Huiyun , Luo Xinping , Zhang Hanyao 
Published: May 2024

Abstract
Background
Plant-specific TIFY proteins are widely found in terrestrial plants and play important roles in plant adversity responses. Although the genome of loquat at the chromosome level has been published, studies on the TIFY family in loquat are lacking. Therefore, the EjTIFY gene family was bioinformatically analyzed by constructing a phylogenetic tree, chromosomal localization, gene structure, and adversity expression profiling in this study.

Results
Twenty-six EjTIFY genes were identified and categorized into four subfamilies (ZML, JAZ, PPD, and TIFY) based on their structural domains. Twenty-four EjTIFY genes were irregularly distributed on 11 of the 17 chromosomes, and the remaining two genes were distributed in fragments. We identified 15 covariate TIFY gene pairs in the loquat genome, 13 of which were involved in large-scale interchromosomal segmental duplication events, and two of which were involved in tandem duplication events. Many abiotic stress cis-elements were widely present in the promoter region. Analysis of the Ka/Ks ratio showed that the paralogous homologs of the EjTIFY family were mainly subjected to purifying selection. Analysis of the RNA-seq data revealed that a total of five differentially expressed genes (DEGs) were expressed in the shoots under gibberellin treatment, whereas only one gene was significantly differentially expressed in the leaves; under both low-temperature and high-temperature stresses, there were significantly differentially expressed genes, and the EjJAZ15 gene was significantly upregulated under both low- and high-temperature stress. RNA-seq and qRT-PCR expression analysis under salt stress conditions revealed that EjJAZ2, EjJAZ4, and EjJAZ9 responded to salt stress in loquat plants, which promoted resistance to salt stress through the JA pathway. The response model of the TIFY genes in the jasmonic acid pathway under salt stress in loquat was systematically summarized.

Conclusions
These results provide a theoretical basis for exploring the characteristics and functions of additional EjTIFY genes in the future. This study also provides a theoretical basis for further research on breeding for salt stress resistance in loquat. RT-qPCR analysis revealed that the expression of one of the three EjTIFY genes increased and the expression of two decreased under salt stress conditions, suggesting that EjTIFY exhibited different expression patterns under salt stress conditions.
Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis
Authors: Qian Weiye , Ma Nan , Zeng Xi , Shi Mai , Wang Mingqiang , Yang Zhiyuan , Tsui Stephen Kwok-Wing 
Published: May 2024

Abstract
Background
Tuberculosis (TB) represents a major global health challenge. Drug resistance in Mycobacterium tuberculosis (MTB) poses a substantial obstacle to effective TB treatment. Identifying genomic mutations in MTB isolates holds promise for unraveling the underlying mechanisms of drug resistance in this bacterium.

Methods
In this study, we investigated the roles of single nucleotide variants (SNVs) in MTB isolates resistant to four antibiotics (moxifloxacin, ofloxacin, amikacin, and capreomycin) through whole-genome analysis. We identified the drug-resistance-associated SNVs by comparing the genomes of MTB isolates with reference genomes using the MuMmer4 tool.

Results
We observed a strikingly high proportion (94.2%) of MTB isolates resistant to ofloxacin, underscoring the current prevalence of drug resistance in MTB. An average of 3529 SNVs were detected in a single ofloxacin-resistant isolate, indicating a mutation rate of approximately 0.08% under the selective pressure of ofloxacin exposure. We identified a set of 60 SNVs associated with extensively drug-resistant tuberculosis (XDR-TB), among which 42 SNVs were non-synonymous mutations located in the coding regions of nine key genes (ctpI, desA3, mce1R, moeB1, ndhA, PE_PGRS4, PPE18, rpsA, secF). Protein structure modeling revealed that SNVs of three genes (PE_PGRS4, desA3, secF) are close to the critical catalytic active sites in the three-dimensional structure of the coding proteins.

Conclusion
This comprehensive study elucidates novel resistance mechanisms in MTB against antibiotics, paving the way for future design and development of anti-tuberculosis drugs.
Genomic identification and expression analysis of acid invertase (AINV) gene family in Dendrobium officinale Kimura et Migo
Authors: Liu Yujia , Liu Boting , Luo Kefa , Yu Baiyin , Li Xiang , Zeng Jian , Chen Jie , Xia Rui , Xu Jing , Liu Yuanlong 
Published: May 2024

Abstract
Background
Dendrobium officinale Kimura et Migo, a renowned traditional Chinese orchid herb esteemed for its significant horticultural and medicinal value, thrives in adverse habitats and contends with various abiotic or biotic stresses. Acid invertases (AINV) are widely considered enzymes involved in regulating sucrose metabolism and have been revealed to participate in plant responses to environmental stress. Although members of AINV gene family have been identified and characterized in multiple plant genomes, detailed information regarding this gene family and its expression patterns remains unknown in D. officinale, despite their significance in polysaccharide biosynthesis.

Results
This study systematically analyzed the D. officinale genome and identified four DoAINV genes, which were classified into two subfamilies based on subcellular prediction and phylogenetic analysis. Comparison of gene structures and conserved motifs in DoAINV genes indicated a high-level conservation during their evolution history. The conserved amino acids and domains of DoAINV proteins were identified as pivotal for their functional roles. Additionally, cis-elements associated with responses to abiotic and biotic stress were found to be the most prevalent motif in all DoAINV genes, indicating their responsiveness to stress. Furthermore, bioinformatics analysis of transcriptome data, validated by quantitative real-time reverse transcription PCR (qRT-PCR), revealed distinct organ-specific expression patterns of DoAINV genes across various tissues and in response to abiotic stress. Examination of soluble sugar content and interaction networks provided insights into stress release and sucrose metabolism.

Conclusions
DoAINV genes are implicated in various activities including growth and development, stress response, and polysaccharide biosynthesis. These findings provide valuable insights into the AINV gene amily of D. officinale and will aid in further elucidating the functions of DoAINV genes.
Serum levels of lipoprotein-associated phospholipase A2 are associated with coronary atherosclerotic plaque progression in diabetic and non-diabetic patients
Authors: Zhang Shudong , Wang Jiangang , Chen Shuai , Zhang Ying , He Ruming , Wang Xiaoqun , Ding Fenghua , Hu Wenbo , Dai Yang , Lu Lin , Zhang Ruiyan , Ni Jingwei , Chen Qiujing 
Published: May 2024

Abstract
Background
Lp-PLA2 is linked to cardiovascular diseases and poor outcomes, especially in diabetes, as it functions as a pro-inflammatory and oxidative mediator.

Objectives
This research aimed to explore if there is a connection between the serum levels of Lp-PLA2 and the progression of coronary plaques (PP) in individuals with type 2 diabetes mellitus (T2DM) and those without the condition.

Materials and methods
Serum Lp-PLA2 levels were measured in 137 T2DM patients with PP and 137 T2DM patients with no PP, and in 205 non-diabetic patients with PP and 205 non-diabetic patients with no PP. These individuals met the criteria for eligibility and underwent quantitative coronary angiography at the outset and again after about one year of follow-up. The attributes and parameters of the participants at the outset were recorded.

Results
Increased serum levels of Lp-PLA2 were closely associated with coronary artery PP, and also significantly correlated with change of MLD, change of diameter stenosis and change of cumulative coronary obstruction in both diabetic and non-diabetic groups, with higher correlation coefficients in diabetic patients as compared with non-diabetic patients. Moreover, multivariate logistic regression analysis showed that serum Lp-PLA2 level was an independent determinant of PP in both groups, with OR values more significant in diabetic patients than in non-diabetic patients.

Conclusions
Levels of serum Lp-PLA2 show a significant association with the progression of coronary atherosclerotic plaque in patients with T2DM and those without, especially among individuals with diabetes.
Long-term prognosis after endoscopic submucosal dissection for esophageal cancer in older adult patients
Authors: Konishi Hirona , Urabe Yuji , Nakamura Takeo , Ishibashi Kazuki , Mizuno Junichi , Fukuhara Motomitsu , Takasago Takeshi , Tanaka Hidenori , Tsuboi Akiyoshi , Yamashita Ken , Hiyama Yuichi , Takigawa Hidehiko , Kotachi Takahiro , Yuge Ryo , Ishikawa Akira , Oka Shiro 
Published: May 2024

Abstract
Background
The validity of endoscopic submucosal dissection (ESD) for esophageal squamous cell carcinoma (ESCC) in older individuals with comorbidities remains unclear. Therefore, this study evaluated the safety and efficacy of ESD and additional treatment for ESCC in older adult patients.

Methods
The clinicopathological characteristics and clinical outcomes of 398 consecutive older adult patients (≥ 65 years) with 505 lesions who underwent ESD for ESCC at the Hiroshima University Hospital between September 2007 and December 2019 were retrospectively evaluated. Additionally, the prognoses of 381 patients who were followed up for > 3 years were assessed.

Results
The mean patient age and procedure time were 73.1 ± 5.8 years and 77.1 ± 43.5 min, respectively. The histological en bloc resection rate was 98% (496/505). Postoperative stenosis, perforation, pneumonia, and delayed bleeding were conservatively treated in 82 (16%), 19 (4%), 15 (3%), and 5 (1%) patients, respectively. The 5-year overall and disease-specific survival rates were 78.9% and 98.0%, respectively (mean follow-up time: 71.1 ± 37.3 months). Multivariate analysis showed that age and the American Society of Anesthesiologists classification of physical status class ≥III (hazard ratio: 1.27; 95% confidence interval: 1.01–1.59, p = 0.0392) were independently associated with overall survival. A significantly lower overall survival rate was observed in the high-risk follow-up group than in the low-risk follow-up and high-risk additional treatment groups (p < 0.01). However, no significant difference in disease-specific survival was observed among the three groups.

Conclusions
ESD is safe for ESCC treatment in patients aged ≥ 65 years. However, additional treatments should be considered based on the patient’s general condition.
Diagnostic accuracy of cognitive screening tools validated for older adults in Iran: a systematic review and meta-analysis
Authors: Kamalzadeh Leila , Tayyebi Gooya , Shariati Behnam , Shati Mohsen , Saeedi Vahid , Malakouti Seyed Kazem 
Published: May 2024

Abstract
Background
This systematic review aims to comprehensively assess the diagnostic accuracy of cognitive screening tools validated for older adults in Iran, providing evidence-based recommendations for clinicians and researchers.

Methods
A comprehensive search in March 2023 across Web of Science, PubMed, Scopus, ScienceDirect, SID, IranMedex, and IranDoc, enhanced by hand-searching references and Google Scholar, identified cross-sectional studies on cognitive screening in Iranian seniors. We assessed diagnostic accuracy, cognitive domains, and test strengths and weaknesses. A bivariate random-effects meta-analysis provided summary estimates and 95% confidence intervals, illustrated in forest plots.

Results
Our review, derived from an initial screening of 38 articles, focused on 17 studies involving 14 cognitive screening tools and participant counts from 60 to 350, mostly from specialized clinics. The MMSE was the only tool examined in at least three studies, prompting a meta-analysis revealing its sensitivity at 0.89 and specificity at 0.77 for dementia detection, albeit amidst significant heterogeneity (I^2 > 80%). ACE-III demonstrated the highest diagnostic accuracy for MCI and dementia, while MoCA’s performance was deemed adequate for MCI and excellent for dementia. High bias risk in studies limits interpretation.

Conclusion
This review identifies key cognitive tools for dementia and MCI in Iranian older adults, tailored to educational levels for use in primary and specialized care. It emphasizes the need for further validation to enhance diagnostic precision across diverse settings, within a concise framework prioritizing brevity and accuracy for clinical applicability.
Association of serum total IgE and allergen-specific IgE with insulin resistance in adolescents: an analysis of the NHANES database
Authors: Liu Yaping , Wang Xiaoxia , Liu Yong 
Published: May 2024

Abstract
Background
Recent studies have found that total immunoglobulin E (IgE) and allergen-specific IgE were associated with some metabolic diseases. However, the role of IgE in metabolism among adolescents is still unclear. Herein, this study aims to investigate the associations of serum total IgE and allergen-specific IgE with insulin resistance (IR) in adolescents, in order to provide some reference for the prevention and treatment of metabolic diseases in a young age.

Methods
Data of 870 adolescents were extracted from the National Health and Nutrition Examination Survey (NHANES) database in 2005–2006 in this cross-sectional study. Weighted univariate and multivariate logistic regression analyses were utilized to screen covariates and explore the relationships of serum total IgE and allergen-specific IgE with IR. The evaluation indexes were odds ratios (ORs) and 95% confidence intervals (CIs). In addition, these relationships were also assessed in subgroups of allergy history, asthma history, and number of allergens.

Results
Among eligible adolescents, 168 had IR. No significant association between serum total IgE level and IR was found. However, adolescents with higher level of allergen-specific IgE to rye grass [OR = 0.47, 95%CI: (0.25–0.91)], white oak [OR = 0.57, 95%CI: (0.37–0.88)], or peanut [OR = 0.38, 95%CI: (0.15–0.97)] seemed to have lower odds of IR, whereas those had higher level of shrimp-specific IgE [OR = 2.65, 95%CI: (1.21–5.84)] have increased odds of IR. In addition, these associations between allergen-specific IgE and IR were also discovered in adolescents who had allergy history or asthma history, or had different numbers of allergens.

Conclusion
Paying attention to different allergens in adolescents may be important in the early identification of IR among this high-risk population. The study results relatively provided some reference for further exploration on IR prevention.
Knowledge and attitude towards home quarantine instructions and associations with history of Covid-19 infection in Malaysia
Authors: Choo Shea Jiun , Chang Chee Tao , Chan Huan-Keat , Abu Hassan Muhammad Radzi , Hamdan Muhammad Hazmi , Cheong Ai Ting , Mat Noh Fatin Nadhirah , Uzma Mustafa Nur Syahmina 
Published: May 2024

Abstract
Introduction
Although COVID-19 has entered the endemic phase, individuals infected with COVID-19 are required to adhere to home quarantine measures. By exploring the public’s knowledge and attitude towards recommended home quarantine measures, their readiness in containing potential COVID-19 outbreak can be determined. This study aimed to assess the public knowledge and attitude towards home quarantine instructions and their association with history of COVID-19 infections.

Methods
This was a web-based cross-sectional study conducted among the public in Malaysia between August to October 2022. All Malaysian adults over 18 years of age were included. Knowledge on home quarantine instructions and COVID-19 warning signs were measured using “True,” “False,” or “I’m not sure”, while attitude towards home quarantine instructions was measured using a five-point Likert Scale. The questionnaire was initially constructed in English and then translated into the national language, Bahasa Malaysia. Face and content validation were performed. The internal consistency of the questionnaire was found to be satisfactory.

Results
1,036 respondents were analyzed, comprised mostly of females (743, 71.6%) with a history of COVID-19 (673, 64.9%). In the knowledge domain, more than 80% of the respondents answered 9 out of 11 home quarantine instructions statements correctly. 457 (44.1%) were unaware or unsure about the minimum distance of the infected individual’s bed from the rest of the occupants in a shared bedroom. The respondents reported relatively weaker knowledge in identifying uncommon warning signs of COVID-19 deterioration, including anuria (162, 44.5%), ingestion problems (191, 52.5%), and immobility (195, 53.6%). In the attitude domain, more than 90% of respondents answered correctly in 8 out of 9 questions. Respondents with a previous history of COVID-19 infections had better knowledge than COVID-19 infection-naïve individuals towards both home quarantine instructions and COVID-19 warning signs.

Conclusion
Most respondents had good knowledge and attitude towards home quarantine instructions, with those previously infected with COVID-19 showing greater awareness of uncommon warning signs. However, there was a notable lack of awareness regarding physical distancing within shared rooms, appropriate disinfectant use and mobility limitation within the household. This study highlights the knowledge gaps to be improved in future educational campaigns.
Analysis of the relationship between shorter sleep duration and wrist fractures: based on NHANES
Authors: Wu Lang , Han Shaoyu , Cui Bingjun , Wang Chuangong , Zhang Zhenqing , Chen Zhixiang 
Published: May 2024

Abstract
Background
Wrist fracture is one of the common limb fractures. Its incidence rate increases with age and osteoporosis. Nowadays, Sleep health is increasingly valued, but the relationship between wrist fractures and sleep time is not yet clear.

Methods
Data in this study were collected and screened from the NHANES from 2005 to 2010 and 2013 to 2014. The variables were extracted from interviews and compared between the wrist fractures and the sleep duration. The data was analyzed by weighted multivariate logistic regression.

Results
After excluding individuals who were not eligible and had invalid data, we finally identified 1835 participants for inclusion in this study. We found a negative association between the sleep duration and the fractured of the wrist (OR = 1.027,95% CI (1.027, 1.028), P < 0.00001).

Conclusion
This study demons that the association between the sleep duration and the fractures of the wrist is significant. Our findings provide a better understanding of the relationship between sleep duration and wrist fractures. This study may help us reducing the incidence of wrist fractures in the population based on healthy sleep management in the future, and improve the quality of life of middle-aged and elderly patients. Provide evidence for clinical patients to manage healthy sleep.
Incidence and risk factors of postoperative delirium following hepatic resection: a retrospective national inpatient sample database study
Authors: Liu Rui , Liu Ningyuan , Suo Shanlian , Yang Qinfeng , Deng Zhen , Fu Wei , Wang Min 
Published: May 2024

Abstract
Background
Postoperative delirium (POD) is a common complication after major surgery and can cause a variety of adverse effects. However, no large-scale national database was used to assess the occurrence and factors associated with postoperative delirium (POD) following hepatic resection.

Methods
Patients who underwent hepatic resection from 2015 to 2019 were screened using the International Classification of Diseases (ICD) 10th edition clinical modification code from the National Inpatient Sample (NIS) Database. Peri-operative factors associated with delirium were screened and underwent statistical analysis to identify independent predictors for delirium following hepatic resection.

Results
A total of 80,070 patients underwent hepatic resection over a five-year period from 2015 to 2019. The overall occurrence of POD after hepatic resection was 1.46% (1039 cases), with a slight upward trend every year. The incidence of elective admission was 6.66% lower (88.60% vs. 81.94%) than that of patients without POD after hepatic resection and 2.34% (45.53% vs. 43.19%) higher than that of patients without POD in teaching hospitals (P < 0.001). In addition, POD patients were 6 years older (67 vs. 61 years) and comprised 9.27% (56.69% vs. 47.42%) more male patients (P < 0.001) compared to the unaffected population. In addition, the occurrence of POD was associated with longer hospitalization duration (13 vs. 5 days; P < 0.001), higher total cost ($1,481,89 vs. $683,90; P < 0.001), and higher in-hospital mortality (12.61% vs. 4.11%; P < 0.001). Multivariate logistic regression identified hepatic resection-independent risk factors for POD, including non-elective hospital admission, teaching hospital, older age, male sex, depression, fluid and electrolyte disorders, coagulopathy, other neurological disorders, psychoses, and weight loss. In addition, the POD after hepatic resection has been associated with sepsis, dementia, urinary retention, gastrointestinal complications, acute renal failure, pneumonia, continuous invasive mechanical ventilation, blood transfusion, respiratory failure, and wound dehiscence / non-healing.

Conclusion
Although the occurrence of POD after hepatic resection is relatively low, it is beneficial to investigate factors predisposing to POD to allow optimal care management and improve the outcomes of this patient population.
Risk factors for postoperative pulmonary complications in elderly patients undergoing video-assisted thoracoscopic surgery lobectomy under general anesthesia: a retrospective study
Authors: Feng Guang , Jia Yitong , Zhao Guanxu , Meng Fanqi , Wang Tianlong 
Published: May 2024

Abstract
Background
The objective of this study is to identify and evaluate the risk factors associated with the development of postoperative pulmonary complications (PPCs) in elderly patients undergoing video-assisted thoracoscopic surgery lobectomy under general anesthesia.

Methods
The retrospective study consecutively included elderly patients (≥ 70 years old) who underwent thoracoscopic lobectomy at Xuanwu Hospital of Capital Medical University from January 1, 2018 to August 31, 2023. The demographic characteristics, the preoperative, intraoperative and postoperative parameters were collected and analyzed using multivariate logistic regression to identify the prediction of risk factors for PPCs.

Results
322 patients were included for analysis, and 115 patients (35.7%) developed PPCs. Multifactorial regression analysis showed that ASA ≥ III (P = 0.006, 95% CI: 1.230 ∼ 3.532), duration of one-lung ventilation (P = 0.033, 95% CI: 1.069 ∼ 4.867), smoking (P = 0.027, 95% CI: 1.072 ∼ 3.194) and COPD (P = 0.015, 95% CI: 1.332 ∼ 13.716) are independent risk factors for PPCs after thoracoscopic lobectomy in elderly patients.

Conclusion
Risk factors for PPCs are ASA ≥ III, duration of one-lung ventilation, smoking and COPD in elderly patients over 70 years old undergoing thoracoscopic lobectomy. It is necessary to pay special attention to these patients to help optimize the allocation of resources and enhance preventive efforts.