bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathophysiology and genomics of bronchiectasis
Authors: Perea Lidia , Faner Rosa , Chalmers James D. , Sibila Oriol 
Published: July 2024

Bronchiectasis is a complex and heterogeneous inflammatory chronic respiratory disease with an unknown cause in around 30–40% of patients. The presence of airway infection together with chronic inflammation, airway mucociliary dysfunction and lung damage are key components of the vicious vortex model that better describes its pathophysiology. Although bronchiectasis research has significantly increased over the past years and different endotypes have been identified, there are still major gaps in the understanding of the pathophysiology. Genomic approaches may help to identify new endotypes, as has been shown in other chronic airway diseases, such as COPD.Different studies have started to work in this direction, and significant contributions to the understanding of the microbiome and proteome diversity have been made in bronchiectasis in recent years. However, the systematic application of omics approaches to identify new molecular insights into the pathophysiology of bronchiectasis (endotypes) is still limited compared with other respiratory diseases.Given the complexity and diversity of these technologies, this review describes the key components of the pathophysiology of bronchiectasis and how genomics can be applied to increase our knowledge, including the study of new techniques such as proteomics, metabolomics and epigenomics. Furthermore, we propose that the novel concept of trained innate immunity, which is driven by microbiome exposures leading to epigenetic modifications, can complement our current understanding of the vicious vortex. Finally, we discuss the challenges, opportunities and implications of genomics application in clinical practice for better patient stratification into new therapies.
Formic acid sandwich method is well-suited for filamentous fungi identification and improves turn around time using Zybio EXS2600 mass spectrometry
Authors: Wu Chongyang , Ao Keping , Zheng Yue , Jin Ying , Liu Ya , Chen Zhixing , Li Dongdong 
Published: July 2024

Abstract
Objectives
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is extensively employed for the identification of filamentous fungi on MALDI Biotyper (Bruker Daltonics) and Vitek MS (biomerieux), but the performance of fungi identification on new EXS2600 (Zybio) is still unknow. Our study aims to evaluate the new EXS2600 system's (Zybio) ability to rapidly identify filamentous fungi and determine its effect on turnaround time (TAT) in our laboratory.

Methods
We tested 117 filamentous fungi using two pretreatment methods: the formic acid sandwich (FA-sandwich) and a commercial mold extraction kit (MEK, Zybio). All isolates were confirmed via sequence analysis. Laboratory data were extracted from our laboratory information system over two 9-month periods: pre-EXS (April to December 2022) and post-EXS (April to December 2023), respectively.

Results
The total correct identification (at the species, genus, or complex/group level) rate of fungi was high, FA-sandwich (95.73%, 112/117), followed by MEK (94.02%, 110/117). Excluding 6 isolates not in the database, species-level identification accuracy was 92.79% (103/111) for FA-sandwich and 91.89% (102/111) for MEK; genus-level accuracy was 97.29% (108/111) and 96.39% (107/111), respectively. Both methods attained a 100% correct identification rate for Aspergillus, Lichtheimia, Rhizopus Mucor and Talaromyces species, and were able to differentiate between Fusarium verticillioides and Fusarium proliferatum within the Fusarium fujikuroi species complex. Notably, high confidence was observed in the species-level identification of uncommon fungi such as Trichothecium roseum and Geotrichum candidum. The TAT for all positive cultures decreased from pre EXS2600 to post (108.379 VS 102.438, P < 0.05), and the TAT for tissue decreased most (451.538 VS 222.304, P < 0.001).

Conclusions
The FA-sandwich method is more efficient and accurate for identifying filamentous fungi with EXS2600 than the MEK. Our study firstly evaluated the performance of fungi identification on EXS2600 and showed it is suitable for clinical microbiology laboratories use.
A case report and literature review: Mycobacterium leprae infection diagnosed by metagenomic next-generation sequencing of cerebrospinal fluid
Authors: Zhao Conglin , Liu Zhenzhen 
Published: July 2024

Abstract
Background
Leprosy is a chronic infectious disease caused by Mycobacterium leprae (M. leprae) that is responsible for deformities and irreversible peripheral nerve damage and has a broad spectrum of clinical and serological manifestations. Leprosy primarily affects the peripheral nerves and rarely presents with central nervous system involvement. Diagnosing leprosy can still be difficult in some cases, especially when the infection involves uncommon clinical manifestations and extracutaneous sites. Delayed diagnosis and treatment of leprosy may lead to irreversible damage and death.

Case Presentation
We report a case of a 30-year-old female presenting with “repeated high fever with symptoms of headache for 14 days”. On the day of admission, physical signs of lost eyebrows and scattered red induration patches all over her body were observed. The patient’s diagnosis was based on the clinical characteristics using a combination of metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) and slit-skin smear. After confirming Listeria meningitis and multibacillary leprosy with erythema nodosum leprosum (ENL), a type 2 reaction, she was treated with ampicillin sodium, dapsone, rifampicin, clofazimine, methylprednisolone, and thalidomide. At the 1-year follow-up, the frequency and severity of headaches have significantly decreased and a good clinical response with improved skin lesions was found.

Conclusion
This case highlights the importance of considering leprosy, which is a rare and underrecognized disease, in the differential diagnosis of skin rashes with rheumatic manifestations, even in areas where the disease is not endemic, and physicians should be alerted about the possibility of central nervous system infections. In addition, mNGS can be used as a complementary diagnostic tool to traditional diagnostic methods to enhance the diagnostic accuracy of leprosy.
Image features and clinical analysis of retroperitoneal pelvic schwannoma: a case report
Authors: Wu Xining , Meng Hua , Fan Qingbo , Qi Zhenhong , Pan Weidong 
Published: July 2024

Abstract
Background
Schwannomas are benign usually encapsulated nerve sheath tumors derived from the Schwann cells, and affecting single or multiple nerves. The tumors commonly arise from the cranial nerves as acoustic neurinomas but they are extremely rare in the pelvis and the retroperitoneal area. Retroperitoneal pelvic schwannomas often present with non-specific symptoms leading to misdiagnosis and prolonged morbidity.

Case presentation
We report the case of a 59-year-old woman presenting with a feeling of heaviness in the lower abdomen who was found to have a retroperitoneal pelvic schwannoma originating from the right femoral nerve. She had a history of two resections of peripheral schwannomas at four different sites of limbs. After conducting magnetic resonance imaging, this pelvic schwannoma was misdiagnosed as a gynecological malignancy. The tumor was successfully removed by laparoscopic surgery. Pathological analysis of the mass revealed a benign schwannoma of the femoral nerve sheath with demonstrating strong, diffuse positivity for S-100 protein.

Conclusions
Although retroperitoneal pelvic schwannoma is rare, it should be considered in the differential diagnosis of pelvic masses, especially in patients with a history of neurogenic mass or the presence of neurogenic mass elsewhere.
Comparison of pregnancy outcomes between 4th day morula and 5th day blastocyst after embryo transfer: a retrospective cohort study
Authors: Sun Yiqun , Shen Qi , Xi Haitao , Sui Liucai , Fu Yanghua , Zhao Junzhao 
Published: July 2024

Abstract
Background
This study was designed to evaluate pregnancy outcomes between morulae transferred on day 4 (D4) and blastocysts transferred on day 5 (D5).

Methods
From September 2017 to September 2020, 1963 fresh transfer cycles underwent early follicular phase extra-long protocol for assisted conception in our fertility center were divided into D4 (324 cases) and D5 (1639 cases) groups, and the general situation and other differences of patients in both groups were compared. To compare the differences in pregnancy outcomes, the D4 and D5 groups were further divided into groups A and B based on single and double embryo transfers. Furthermore, the cohort was divided into two groups: those with live births (1116 cases) and those without (847 cases), enabling a deeper evaluation of the effects of D4 or D5 transplantation on assisted reproductive outcomes.

Results
In single embryo transfer, there was no significant difference between groups D4A and D5A (P > 0.05). In double embryo transfer, group D4B had a lower newborn birthweight and a larger proportion of low birthweight infants (P < 0.05). The preterm delivery rate, twin delivery rate, cesarean delivery rate, and percentage of low birthweight infants were lower in the D5A group than in the D5B group (P < 0.05). Analysis of factors influencing live birth outcomes further confirmed the absence of a significant difference between D4 and D5 transplantation in achieving live birth (P > 0.05).

Conclusion
When factors such as working life and hospital holidays are being considered, D4 morula transfer may be a good alternative to D5 blastocyst transfer. Given the in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) success rate and risk of twin pregnancy, D4 morula transfer requires an adapted decision between single and double embryo transfer, although a single blastocyst transfer is recommended for the D5 transfer in order to decrease the twin pregnancy rate. In addition, age, endometrial thickness and other factors need to be taken into account to personalize the IVF program and optimize pregnancy outcomes.
Early change of plasma Epstein-Barr virus DNA load and the viral lytic genome level could positively predict clinical outcome in recurrent or metastatic nasopharyngeal carcinoma receiving anti-programmed cell death 1 monotherapy
Authors: Lin Shaoyan , Zhou Huaqiang , Chen Gang , Xue Jinhui , Liu Qianwen , Li Jianing , Yang Yanhua , Zhao Yuanyuan , Bao Hua , Huang Yan , Ma Yuxiang , Zhao Hongyun 
Published: July 2024

Abstract
Purpose
Patients with recurrent or metastatic nasopharyngeal carcinoma (RM-NPC) have proven benefit from anti-programmed cell death 1 (anti-PD-1) monotherapy. Here, we retrospectively analyze the association of plasma Epstein-Barr virus (EBV) DNA load and tumor viral lytic genome with clinical outcome from 2 registered phase I trials.

Methods
Patients with RM-NPC from Checkmate 077 (nivolumab phase I trial in China) and Camrelizumab phase I trial between March 2016 and January 2018 were enrolled. Baseline EBV DNA titers were tested in 68 patients and EBV assessment was performed in 60 patients who had at least 3 post-baseline timepoints of EBV data and at least 1 post-baseline timepoint of radiographic assessment. We defined “EBV response” as 3 consecutive timepoints of load below 50% of baseline, and “EBV progression” as 3 consecutive timepoints of load above 150% of baseline. Whole-exome sequencing was performed in 60 patients with available tumor samples.

Results
We found that the baseline EBV DNA load was positively correlated with tumor size (spearman p < 0.001). Both partial response (PR) and stable disease (SD) patients had significantly lower EBV load than progression disease (PD) patients. EBV assessment was highly consistent with radiographic evaluation. Patients with EBV response had significantly improved overall survival (OS) than patients with EBV progression (log-rank p = 0.004, HR = 0.351 [95% CI: 0.171–0.720], median 22.5 vs. 11.9 months). The median time to initial EBV response and progression were 25 and 36 days prior to initial radiographic response and progression, respectively. Patients with high levels of EBV lytic genomes at baseline, including BKRF2, BKRF3 and BKRF4, had better progression-free survival (PFS) and OS.

Conclusion
In summary, early clearance of plasma EBV DNA load and high levels of lytic EBV genes were associated with better clinical outcome in patients with RM-NPC receiving anti-PD-1 monotherapy.
The association between shift work, shift work sleep disorders and premature ejaculation in male workers
Authors: Zheng Zhenming , Pan Jiashan , Chen Zhimin , Gao Pan , Gao Jingjing , Jiang Hui , Zhang Xiansheng 
Published: July 2024

Abstract
Objective
Shift work and Shift Work Sleep Disorder (SWSD) are known to affect the secretion of several neurotransmitters and hormones associated with premature ejaculation (PE). However, their specific influence on the regulation of male ejaculation remains unclear. This study explores the relationship between shift work, SWSD, and PE.

Methods
From April to October 2023, a cross-sectional survey was conducted across five regions of China to explore the work schedules, sleep quality, and sexual function of male workers. Participants' sleep quality was evaluated using a validated SWSD questionnaire, and their erectile function and ejaculatory control were assessed with the International Inventory of Erectile Function (IIEF-5) scores and Premature Ejaculation Diagnostic Tool (PEDT) scores, respectively. Univariate and multivariate linear regression analyses were employed to identify risk factors associated with PE. Confounders were controlled using multiple regression models, and clinical prediction models were developed to predict PE onset and assess the contribution of risk factors.

Results
The study included 1239 eligible participants, comprising 840 non-shift workers and 399 shift workers (148 with SWSD and 251 without SWSD). Compared to non-shift working males, those involved in shift work (β 1.58, 95% CI 0.75 – 2.42, p < 0.001) and those suffering from SWSD (β 2.86, 95% CI 1.86 – 3.85, p < 0.001) they had significantly higher PEDT scores. Additionally, we identified daily sleep of less than six hours, depression, anxiety, diabetes, hyperlipidemia, frequent alcohol consumption (more than twice a week), and erectile dysfunction as risk factors for PE. The predictive model for PE demonstrated commendable efficacy.

Conclusion
Both shift work and SWSD significantly increase the risk of premature ejaculation, with the risk magnifying in tandem with the duration of shift work. This study reveals the potential impact of shift work and SWSD on PE and provides new theoretical foundations for the risk assessment and prevention of this condition.
Reallocating just 10 min to moderate-to-vigorous physical activity from other components of 24-hour movement behaviors improves cardiovascular health in adults
Authors: Ji Yemeng , Atakan Muhammed M. , Yan Xu , Wu Jinlong , Kuang Jujiao , Peng Li 
Published: July 2024

Abstract
Background
As components of a 24-hour day, sedentary behavior (SB), physical activity (PA), and sleep are all independently linked to cardiovascular health (CVH). However, insufficient understanding of components’ mutual exclusion limits the exploration of the associations between all movement behaviors and health outcomes. The aim of this study was to employ compositional data analysis (CoDA) approach to investigate the associations between 24-hour movement behaviors and overall CVH.

Methods
Data from 581 participants, including 230 women, were collected from the 2005–2006 wave of the US National Health and Nutrition Examination Survey (NHANES). This dataset included information on the duration of SB and PA, derived from ActiGraph accelerometers, as well as self-reported sleep duration. The assessment of CVH was conducted in accordance with the criteria outlined in Life’s Simple 7, encompassing the evaluation of both health behaviors and health factors. Compositional linear regression was utilized to examine the cross-sectional associations of 24-hour movement behaviors and each component with CVH score. Furthermore, the study predicted the potential differences in CVH score that would occur by reallocating 10 to 60 min among different movement behaviors.

Results
A significant association was observed between 24-hour movement behaviors and overall CVH (p < 0.001) after adjusting for potential confounders. Substituting moderate-to-vigorous physical activity (MVPA) for other components was strongly associated with favorable differences in CVH score (p < 0.05), whether in one-for-one reallocations or one-for-remaining reallocations. Allocating time away from MVPA consistently resulted in larger negative differences in CVH score (p < 0.05). For instance, replacing 10 min of light physical activity (LPA) with MVPA was related to an increase of 0.21 in CVH score (95% confidence interval (95% CI) 0.11 to 0.31). Conversely, when the same duration of MVPA was replaced with LPA, CVH score decreased by 0.67 (95% CI -0.99 to -0.35). No such significance was discovered for all duration reallocations involving only LPA, SB, and sleep (p > 0.05).

Conclusions
MVPA seems to be as a pivotal determinant for enhancing CVH among general adult population, relative to other movement behaviors. Consequently, optimization of MVPA duration is an essential element in promoting overall health and well-being.
Measurement properties of the Regular Physical Exercise Adherence Scale (REPEAS) in individuals with chronic pain
Authors: Pinheiro Cezar Augusto Brito , Bassi-Dibai Daniela , Pontes-Silva André , Pereira Fábio Henrique Ferreira , Pinheiro Jocassia Silva , Fidelis-de-Paula-Gomes Cid André , Dibai-Filho Almir Vieira 
Published: July 2024

Abstract
Objective
To examine the measurement properties of the Regular Physical Exercise Adherence Scale (REPEAS) in Brazilians with chronic pain.

Methods
Cross-sectional and longitudinal design (washout period for reliability). The study was conducted in two Brazilian states, Maranhão and São Paulo, and included Brazilian adults, irregular exercisers, former exercisers or non-exercise practitioners, aged 18 to 59 years and with chronic pain. The instruments used in this study were: the REPEAS, the Numerical Pain Rating Scale (NPRS), the Baecke Habitual Physical Activity Questionnaire (BHPAQ), the Pain Self-Efficacy Questionnaire (PSEQ), and the Roland-Morris Disability Questionnaire for general pain (RMDQ-g). The evaluation focused on structural validity, construct validity, reliability (with standard error of measurement and minimum detectable change), internal consistency, and floor and ceiling effects.

Results
The two-dimensional structure was tested through confirmatory factor analysis, which resulted in adequate fit indeces: chi-square values/degrees of freedom = 1.541, Tucker-Lewis Index = 0.966, comparative fit index = 0.974, root mean square error of approximation = 0.074, and standardized root mean square residual = 0.068. Additionally, satisfactory factor loadings (> 0.40) were obtained. Test-retest reliability and internal consistency were adequate for the environmental factors domain (intraclass correlation coefficient [ICC] = 0.79, Cronbach’s alpha = 0.88) and the personal factors domain (ICC = 0.97, Cronbach’s alpha = 0.93). In hypothesis testing for construct validity, we observed a significant correlation with magnitude below 0.30 of the environmental factors domain of the REPEAS with RMDQ-g, PSEQ and sport domain of the BHPAQ. For the personal factors domain, we observed a significant correlation with a magnitude of 0.30 to 0.50 with RMDQ-g, PSEQ, and sport domain of the BHPAQ, and below 0.30 with leisure domain of the BHPAQ. No floor or ceiling effects were found for the REPEAS domains.

Conclusion
The REPEAS is a valid instrument with a two-dimensional internal structure consisting of 12 items. It has a reliable construct and is suitable for use in the clinical and epidemiological context for adults with chronic pain in Brazil.
Influence of lifestyle patterns on depression among adults with diabetes: a mediation effect of dietary inflammatory index
Authors: Wang Baoping , Fan Yuxin , Wang Xin , Zeng Xiangru , Zeng Sha , Jia Hongwei , Li Yin , Dai Chenlin 
Published: July 2024

Abstract
Background
Lifestyle has become a crucial modulator in the management of diabetes and is intimately linked with the development and exacerbation of comorbid depression. The study aimed to analyze lifestyle patterns and their impact on depression in individuals with diabetes and to explore the role of the Dietary Inflammatory Index (DII) in the relationship between lifestyle patterns and depression.

Methods
Data was attained from the National Health and Nutrition Examination Survey (NHANES) between 2009 and 2020. A latent class analysis (LCA) was performed on 3,009 diabetic adults based on lifestyle behaviors. A generalised linear model (GLM) was employed to analyse the effects of different lifestyle patterns on depression. The mediation effect model was utilised to examine the relationship between lifestyle patterns, DII and Patient Health Questionnaire-9 (PHQ-9) scores.

Results
The cohort was divided through LCA into unhealthy lifestyle (44.53%), unhealthy but non-alcohol use (48.06%) and healthy but smoking (7.41%) groups of lifestyle behaviors, the unhealthy but non-alcohol use group was identified as a risk factor for depression (OR = 1.379, 95%CI = 1.095 ~ 1.735, P = 0.006). The DII partially mediated the relationship between the unhealthy but non-alcohol use group and PHQ-9, and fully mediated the relationship between the healthy but smoking group and PHQ-9, with effect coefficients of − 0.018 (95%CI: −0.044 ~ − 0.001) and − 0.035 (95%CI: −0.083 ~ − 0.001).

Conclusions
Lifestyle patterns significantly influence the occurrence of depression among diabetes patients. The dietary inflammation plays a varying mediating role between different lifestyle patterns and depression. Restricting pro-inflammatory diets or encouraging anti-inflammatory diets, combined with the promotion of healthy lifestyle practices, may be an effective method for preventing and alleviating symptoms of depression among patients with diabetes.