bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends and factors associated with influenza vaccination in subjects with asthma: analysis of the Korea National Health and Nutrition Examination Survey between 2010 and 2019
Authors: Kim Sang Hyuk , Park Hye Yun , Jung Hwasik , Zo Sungmin , Kim Saerom , Park Dong Won , Park Tai Sun , Moon Ji-Yong , Kim Sang-Heon , Kim Tae-Hyung , Sohn Jang Won , Yoon Ho Joo , Lee Hyun , Shin Sun Hye 
Published: October 2022

Background: Despite the importance of influenza vaccination, its rates in subjects with asthma are suboptimal, especially in the young population. Methods: Among 72,843 adults aged ⩾18 years from the Korea National Health and Nutrition Examination Survey conducted between 2010 and 2019, 1643 with asthma were included. The yearly trends and factors associated with influenza vaccination were analyzed in subjects with asthma. In addition, stratified analyses were performed by age group (<65 versus ⩾65 years). Results: During the study period, the overall influenza vaccination rate among subjects with asthma fluctuated from 51.0% to 64.3%, with a consistently higher vaccination rate in elderly subjects than in young subjects. Among young subjects with asthma, factors positively associated with influenza vaccination were female sex [adjusted odds ratio (aOR) = 1.66, 95% confidence interval (CI) = 1.11–2.49], current asthma being treated (aOR = 1.69, 95% CI = 1.14–2.50), history of pulmonary tuberculosis (aOR = 2.01, 95% CI = 1.04–3.87), and dyslipidemia (aOR = 1.86, 95% CI = 1.05–3.30). However, unmarried subjects showed an inverse relationship (aOR = 0.50, 95% CI = 0.34–0.75). In elderly subjects, unmarried status (aOR = 0.52, 95% CI = 0.29–0.94), being underweight (aOR = 0.29, 95% CI = 0.09–0.97), and having a low income (aOR = 0.42, 95% CI = 0.18–0.97) were factors negatively associated with influenza vaccination. Conclusion: In the last 10 years, influenza vaccination rates have still been insufficient in subjects with asthma, particularly in young subjects. Considering the factors that are influencing the vaccination rates of young subjects, public policies to increase influenza vaccination rates in subjects with asthma need to be established urgently.
Prognostic value of echocardiography-derived right ventricular dysfunction in haemodynamically stable pulmonary embolism: a systematic review and meta-analysis
Authors: Prosperi-Porta Graeme , Ronksley Paul , Kiamanesh Omid , Solverson Kevin , Motazedian Pouya , Weatherald Jason 
Published: October 2022

BackgroundWe sought to determine the prognostic value of transthoracic echocardiography (TTE)-derived right ventricular dysfunction (RVD) in haemodynamically stable and intermediate-risk patients with acute pulmonary embolism (PE), evaluate continuous RVD parameters, and assess the literature quality.MethodsWe searched MEDLINE, Embase and the Cochrane Central Register of Controlled Trials for studies assessing TTE-derived RVD in haemodynamically stable PE that reported in-hospital adverse events within 30 days. We determined pooled odds ratios (ORs) using a random-effects model, created funnel plots, evaluated the Newcastle–Ottawa scale and performed Grading of Recommendations, Assessment, Development and Evaluation.ResultsBased on 55 studies (17 090 patients, 37.8% RVD), RVD was associated with combined adverse events (AEs) (OR 3.29, 95% confidence interval (CI) 2.59–4.18), mortality (OR 2.00, CI 1.66–2.40) and PE-related mortality (OR 4.01, CI 2.79–5.78). In intermediate-risk patients, RVD was associated with AEs (OR 1.99, CI 1.17–3.37) and PE-related mortality (OR 6.16, CI 1.33–28.40), but not mortality (OR 1.63, CI 0.76–3.48). Continuous RVD parameters provide a greater spectrum of risk compared to categorical RVD. We identified publication bias, poor methodological quality in 34/55 studies and overall low certainty of evidence.ConclusionsRVD is frequent in PE and associated with adverse outcomes. However, data quality and publication bias are limitations of existing evidence.
Benchmark study of feature selection strategies for multi-omics data
Authors: Li Yingxia , Mansmann Ulrich , Du Shangming , Hornung Roman 
Published: October 2022

Abstract
Background
In the last few years, multi-omics data, that is, datasets containing different types of high-dimensional molecular variables for the same samples, have become increasingly available. To date, several comparison studies focused on feature selection methods for omics data, but to our knowledge, none compared these methods for the special case of multi-omics data. Given that these data have specific structures that differentiate them from single-omics data, it is unclear whether different feature selection strategies may be optimal for such data. In this paper, using 15 cancer multi-omics datasets we compared four filter methods, two embedded methods, and two wrapper methods with respect to their performance in the prediction of a binary outcome in several situations that may affect the prediction results. As classifiers, we used support vector machines and random forests. The methods were compared using repeated fivefold cross-validation. The accuracy, the AUC, and the Brier score served as performance metrics.

Results
The results suggested that, first, the chosen number of selected features affects the predictive performance for many feature selection methods but not all. Second, whether the features were selected by data type or from all data types concurrently did not considerably affect the predictive performance, but for some methods, concurrent selection took more time. Third, regardless of which performance measure was considered, the feature selection methods mRMR, the permutation importance of random forests, and the Lasso tended to outperform the other considered methods. Here, mRMR and the permutation importance of random forests already delivered strong predictive performance when considering only a few selected features. Finally, the wrapper methods were computationally much more expensive than the filter and embedded methods.

Conclusions
We recommend the permutation importance of random forests and the filter method mRMR for feature selection using multi-omics data, where, however, mRMR is considerably more computationally costly.
High-throughput detection of T-DNA insertion sites for multiple transgenes in complex genomes
Authors: Edwards Brianne , Hornstein Eli D. , Wilson Nathan J. , Sederoff Heike 
Published: October 2022

Abstract
Background
Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency.

Results
We have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T1 generation of any crop transformed via Agrobacterium. We present an example using the allohexaploid oil-seed plant Camelina sativa to determine insertion site location of two transgenes.

Conclusion
This new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations.
Evolutionary origin and functional specialization of Dormancy-Associated MADS box (DAM) proteins in perennial crops
Authors: Quesada-Traver Carles , Lloret Alba , Carretero-Paulet Lorenzo , Badenes María Luisa , Ríos Gabino 
Published: October 2022

Abstract
Background
Bud dormancy is a phenological adaptation of temperate perennials that ensures survival under winter temperature conditions by ceasing growth and increasing cold hardiness. SHORT VEGETATIVE PHASE (SVP)-like factors, and particularly a subset of them named DORMANCY-ASSOCIATED MADS-BOX (DAM), are master regulators of bud dormancy in perennials, prominently Rosaceae crops widely adapted to varying environmental conditions.

Results
SVP-like proteins from recently sequenced Rosaceae genomes were identified and characterized using sequence, phylogenetic and synteny analysis tools. SVP-like proteins clustered in three clades (SVP1–3), with known DAM proteins located within SVP2 clade, which also included Arabidopsis AGAMOUS-LIKE 24 (AthAGL24). A more detailed study on these protein sequences led to the identification of a 15-amino acid long motif specific to DAM proteins, which affected protein heteromerization properties by yeast two-hybrid system in peach PpeDAM6, and the unexpected finding of predicted DAM-like genes in loquat, an evergreen species lacking winter dormancy. DAM gene expression in loquat trees was studied by quantitative PCR, associating with inflorescence development and growth in varieties with contrasting flowering behaviour.

Conclusions
Phylogenetic, synteny analyses and heterologous overexpression in the model plant Arabidopsis thaliana supported three major conclusions: 1) DAM proteins might have emerged from the SVP2 clade in the Amygdaloideae subfamily of Rosaceae; 2) a short DAM-specific motif affects protein heteromerization, with a likely effect on DAM transcriptional targets and other functional features, providing a sequence signature for the DAM group of dormancy factors; 3) in agreement with other recent studies, DAM associates with inflorescence development and growth, independently of the dormancy habit.
The case against censoring of progression-free survival in cancer clinical trials – A pandemic shutdown as an illustration
Authors: Jamoul Corinne , Collette Laurence , Coart Elisabeth , D’Hollander Koenraad , Burzykowski Tomasz , Saad Everardo D. , Buyse Marc 
Published: October 2022

Abstract
Background
Missing data may lead to loss of statistical power and introduce bias in clinical trials. The Covid-19 pandemic has had a profound impact on patient health care and on the conduct of cancer clinical trials. Although several endpoints may be affected, progression-free survival (PFS) is of major concern, given its frequent use as primary endpoint in advanced cancer and the fact that missed radiographic assessments are to be expected. The recent introduction of the estimand framework creates an opportunity to define more precisely the target of estimation and ensure alignment between the scientific question and the statistical analysis.

Methods
We used simulations to investigate the impact of two basic approaches for handling missing tumor scans due to the pandemic: a “treatment policy” strategy, which consisted in ascribing events to the time they are observed, and a “hypothetical” approach of censoring patients with events during the shutdown period at the last assessment prior to that period. We computed the power of the logrank test, estimated hazard ratios (HR) using Cox models, and estimated median PFS times without and with a hypothetical 6-month shutdown period with no patient enrollment or tumor scans being performed, varying the shutdown starting times.

Results
Compared with the results in the absence of shutdown, the “treatment policy” strategy slightly overestimated median PFS proportionally to the timing of the shutdown period, but power was not affected. Except for one specific scenario, there was no impact on the estimated HR. In general, the pandemic had a greater impact on the analyses using the “hypothetical” strategy, which led to decreased power and overestimated median PFS times to a greater extent than the “treatment policy” strategy.

Conclusion
As a rule, we suggest that the treatment policy approach, which conforms with the intent-to-treat principle, should be the primary analysis to avoid unnecessary loss of power and minimize bias in median PFS estimates.
Acute kidney injury in Turkey: epidemiological characteristics, etiology, clinical course, and prognosis
Authors: Gursu Meltem , Yegenaga Itir , Tuglular Serhan , Dursun Belda , Bek Sibel Gokcay , Bardak Simge , Onan Engin , Demir Serap , Derici Ulver , Dogukan Ayhan , Sevinc Mustafa , Kocyigit Ismail , Altun Eda , Haras Ali Burak , Altiparmak Mehmet Riza , Tonbul Halil Zeki 
Published: October 2022

AbstractBackgroundThis study aimed to evaluate the etiologies, comorbidities, and outcomes of acute kidney injury (AKI) in Turkey and determine any potential differences among different geographical parts of the country.MethodsThis prospective observational study was conducted by the Acute Kidney Injury Working Group of the Turkish Society of Nephrology. Demographical and clinical data of patients with AKI at the time of diagnosis and at the 1stweek and 1st, 3rd, and 6thmonths of diagnosis were evaluated to determine patient and renal survival and factors associated with patient prognosis.ResultsA total of 776 patients were included (54.7% male, median age: 67 years). Prerenal etiologies, including dehydration, heart failure, and sepsis, were more frequent than other etiologies. 58.9% of the patients had at least one renal etiology, with nephrotoxic agent exposure as the most common etiology. The etiologic factors were mostly similar throughout the country. 33.6% of the patients needed kidney replacement therapy. At the 6thmonth of diagnosis, 29.5% of the patients had complete recovery; 34.1% had partial recovery; 9.5% developed end-stage kidney disease; and 24.1% died. The mortality rate was higher in the patients from the Eastern Anatolian region; those admitted to the intensive care unit; those with prerenal, renal, and postrenal etiologies together, stage 3 AKI, sepsis, cirrhosis, heart failure, and malignancy; those who need kidney replacement therapy; and those without chronic kidney disease than in the other patients.ConclusionPhysicians managing patients with AKI should be alert against dehydration, heart failure, sepsis, and nephrotoxic agent exposure. Understanding the characteristics and outcomes of patients with AKI in their countries would help prevent AKI and improve treatment strategies.
Significant associations between bone mineral density and vascular calcification in patients with different stages of chronic kidney disease
Authors: Uhlinova Jana , Kuudeberg Anne , Metsküla Kaja , Lember Margus , Rosenberg Mai 
Published: October 2022

Abstract
Introduction
Chronic kidney disease—mineral and bone disorders (CKD-MBD) is characterised by generalised vascular calcification (VC) and impaired bone health. We aimed to investigate the relationship between VC and bone mineral density (BMD) in CKD patients.

Methods
We performed a cross-sectional study of patients with different stages of CKD. For assessment of VC of abdominal aorta lateral lumbar X-rays (Kauppila score), the ankle-brachial index (ABI) and echocardiography were used. Total body densitometry provided BMD.

Results
Ninety patients (41% male, median age 64 years (range 29–87)) were included, of whom 41.1% had a Kauppila score > 1. Evidence of peripheral VC as measured by ABI was detected in 23.3% of cases. Lesions of the heart valves were found in 46.7% of patients. There was a significant association between high ABI and lesions of the heart valves. In the multivariate regression model to analyse the independent determinants of abdominal aorta calcification (AAC) and ABI, the BMD of the femoral neck was identified as significant for both (p = 0.001, p = 0.001). The total spine BMD was found to be significant for AAC (p = 0.001), and the BMD of spine L1-L4 and the ribs were found to be significant for ABI (p = 0.01, p = 0.002 respectively). In factorial regression analysis, where BMD was independent determinant, valvular calcification was significant for BMD of femur, femoral neck and total BMD. Age and tALP were inversely correlated with the BMD of femur and femoral neck.

Conclusions
Our work highlighted clinically important relationships between VC and bone mineral density (BMD) in CKD patients. We detected inverse relationships between AAC, high ABI and BMD. Secondly, BMD at certain bone sites (femur, femoral neck) and total BMD were associated with important lesions of heart valves. Thirdly, a significant association between a high ABI and lesions of the heart valves. We believe that the results of our study will help in the planning of future research and in current clinical practice for the early diagnosis, further monitoring and management of CKD-MBD. Additionally, these results may have treatment implications on use of different CKD-MBD medications.
Lnc-SELPLG-2:1 enhanced osteosarcoma oncogenesis via hsa-miR-10a-5p and the BTRC cascade
Authors: Li Shiyuan , Zeng Ming , Yang Lin , Tan Jianshao , Yang Jianqi , Guan Hongye , Kuang Manyuan , Li Jiaying 
Published: October 2022

Abstract
Background
To investigate the potential role of Long Non-coding RNAs (lncRNAs) in the progression of osteosarcoma.

Methods
The candidate lncRNAs were screened with RNA-seq and confirmed with quantitative real-time PCR. Using MTS, transwell assay, and flow cytometric analysis, the effects of overexpressed lnc-SELPLG-2:1 on cell functions were determined. Immunohistochemical staining, fluorescence in situ hybridization, and luciferase reporter assay were used to evaluate the potential mechanism of lnc-SELPLG-2:1 in vivo and in vitro using a tumor model. Moreover, the effects of overexpression of hsa-miR-10a-5p on the functions of SaOS2 cells were determined using functional cell analysis. A response test was used to confirm the mechanism by which lnc-SELPLG-2:1 sponge hsa-miR-10a-5p promotes the expression of BTRC to regulate osteosarcoma.

Results
Lnc-SELPLG-2:1 was highly expressed in osteosarcoma compared to normal cells and bone and marrow samples. Inhibition of lnc-SELPLG-2:1 accelerated cell apoptosis and suppressed cell proliferation, migration, and invasion, whereas lnc-SELPLG-2:1 overexpression had the opposite effect. Moreover, inhibiting lnc-SELPLG-2:1 in an in vivo model decreased tumor size and suppressed the expression of cell migration-related proteins. The prediction, dual luciferase assay, and response test results indicated that hsa-miR-10-5p and BTRC were involved in the lnc-SELPLG-2:1 cascade. Unlike lnc-SELPLG-2:1, hsa-hsa-miR-10a-5p had opposite expression and function. Competitive binding of lnc-SELPLG-2:1 to hsa-hsa-miR-10a-5p prevented BTRC from miRNA-mediated degradation, thereby activating the expression of VIM, MMP9, and MMP2, promoting osteosarcoma cell proliferation, migration, and invasion, and inhibiting apoptosis.

Conclusion
Lnc-SELPLG-2:1 is an oncogenesis activator in osteosarcoma, and its functions are performed via hsa-miR-10a-5p /BTRC cascade.
Are health promoting lifestyles associated with pain intensity and menstrual distress among Iranian adolescent girls?
Authors: Cholbeigi Elahe , Rezaienik Shaghayegh , Safari Narges , Lissack Kerrie , Griffiths Mark D , Alimoradi Zainab 
Published: October 2022

Abstract
Objective
The present study investigated the relationship between a health-promoting lifestyle and menstrual pain intensity and distress among adolescent girls in Qazvin.

Methods
A cross-sectional survey study using a two-stage sampling method was conducted. The participants (n = 986) were female high school students aged 14–19 years living in Qazvin. Random cluster sampling was used to recruit participants from schools and classes from each grade. An online survey was provided to all participants to complete. Data were collected using a Demographic and Menstrual Characteristics Checklist, the Visual Analogue Scale (VAS) to assess dysmenorrhea intensity, the Andresh Milsom Scale (AMS) to assess dysmenorrhea severity, the Moos Menstrual Distress Questionnaire (MMDS) to assess menstrual distress, and the Health-Promoting Lifestyle Profile (HPLP) to assess a health promoting lifestyle. Data were analyzed using an univariable linear regression model at a significance level of 0.05.

Results
The findings indicated that 421 participants (42.7%) experienced dysmenorrhea with a mean duration of 2.24 days (SD = 1.57) and a mean pain intensity of 4.62 on the VAS (SD = 2.87). The mean score on the menstrual distress on the MDDS was 13.55 (SD = 8.88) and the mean score on the HPLP was 2.55 (SD = 0.50). Based on the results of univariable linear regression, nutrition (β=-0.18, p < 0.001) and exercise (β=-0.17, p < 0.001) had the most significant effect on the severity of dysmenorrhea pain. Also, self-actualization (β=-0.29, p < 0.001), stress management (β=-0.25, p < 0.001) and nutrition (β=-0.25, p < 0.001) had the most significant effect on menstrual distress.

Conclusion
Based on these findings, it is suggested that (i) improving nutrition and exercise might reduce the severity of dysmenorrhea pain and (ii) improving self-actualization, stress management and nutrition might reduce the severity of menstrual distress. Overall, it seems that improving health-promoting lifestyle behaviors can help improve the severity of dysmenorrhea pain and menstrual distress among adolescent girls.
Violence against women from partners and other household members during COVID-19 in Burkina Faso and Kenya
Authors: Decker Michele R. , Wood Shannon N. , Thomas Haley L. , Thiongo Mary , Guiella Georges , Fiacre Bazie , Onadja Yentéma , Gichangi Peter 
Published: October 2022

Abstract
Background
Global evidence indicates increases in gender-based violence (GBV) during the COVID-19 pandemic following mitigation measures, such as stay at home orders. Indirect effects of the pandemic, including income loss, strained social support, and closed or inaccessible violence response services, may further exacerbate GBV and undermine help-seeking. In Kenya and Burkina Faso, as in many settings, GBV was prevalent prior to the COVID-19 pandemic. Studies specific to COVID-impact on GBV in Kenya indicate mixed results and there remains a lack of evidence from Burkina Faso. Our study takes a comprehensive lens by addressing both intimate partner violence (IPV) and non-partner household abuse through the COVID-19 pandemic in two priority settings.

Methods
Annual, national cross-sections of women ages 15–49 completed survey data collection in November–December 2020 and December 2020–March 2021; the GBV module was limited to one woman per household [Kenya n = 6715; Burkina n = 4065]. Descriptive statistics, Venn diagrams, and logistic and multinomial regression characterized prevalence of IPV and other household abuse, frequency relative to the COVID-19 pandemic, help-seeking behaviors, and predictors of IPV and household abuse across the socioecological framework.

Results
In both settings, past-year IPV prevalence exceeded non-partner household abuse (Kenya: 23.5%IPV, 11.0%household; Burkina Faso: 25.7%IPV, 16.2%household). Over half of those affected in each setting did not seek help; those that did turned first to family. Among those with past-year experiences, increased frequency since COVID-19 was noted for IPV (16.0%Burkina Faso; 33.6%Kenya) and household violence (14.3%Burkina Faso; 26.2%Kenya). Both context-specific (i.e., financial autonomy in Burkina Faso) and universal (i.e., COVID-related income loss) risk factors emerged.

Conclusion
Past-year IPV and household violence against women in Kenya and Burkina Faso were prevalent, and in some cases, intensified during the COVID-19 pandemic. Across settings, help-seeking from formal services was notably low, likely reflecting shame, blame, and stigmatization identified as barriers in pre-COVID literature. Both primary prevention and survivor-centered support services, including those related to economic empowerment, should be integrated within COVID-recovery efforts, and extended into the post-pandemic period to fully meet women’s safety needs.