bluuebunny/crossref_metadata_2025_split huggingface dataset:
International validation of a health-related quality-of-life questionnaire for Hodgkin lymphoma: the EORTC QLQ-HL27
Authors: Oerlemans Simone , Efficace Fabio , Shamieh Omar , Cardoso Borges Fabio , de Jong Corine , Dong Dong , Lehmann Jens , Malak Sandra , Petranovic Duska , Scholz Christian W. , Caocci Giovanni , Molica Stefano , Griskevicius Laimonas , Nagele Eva , Bredart Anne , Carvalho Elisabete , Xochelli Aliki , Agelink van Rentergem Joost , Alrjoob Waleed , Mueller Anja , Freitas Ana Carolina , Cocks Kim , Creutzberg Carien , Kyriakou Charalampia , van de Poll-Franse Lonneke 
Published: September 2023

Abstract
Hodgkin lymphoma (HL) has become 1 of the most curable cancers. Therefore, rigorous assessment of health-related quality of life (HRQoL) and symptom burden of these patients is essential to support informed clinical decisions. The European Organisation for Research and Treatment of Cancer (EORTC) Quality of Life Group previously developed the EORTC Quality of Life Questionnaire (QLQ) Hodgkin Lymphoma 27. This paper reports the final results of an international study by the EORTC group to develop a HRQoL disease-specific measure for these patients: the EORTC QLQ-HL27. Patients with a confirmed diagnosis of HL (N = 381) were enrolled from 12 countries and completed the EORTC QLQ-C30, QLQ-HL27, and a debriefing questionnaire at baseline (any time after diagnosis). A subset completed a retest (n = 126) or responsiveness-to-change analyses (RCA) second measurement (n = 98). Psychometrics were evaluated. Confirmatory factor analysis showed an acceptable fit of the 27 items of the QLQ-HL27 on its 4 scales (symptom burden, physical condition/fatigue, emotional impact, and worries about health/functioning). Test–retest reliability, convergent validity, known-group comparisons, and RCA find satisfactory results. Symptom burden and fatigue was higher among patients on treatment (with 36%-83% reporting at least a few problems) compared with those who had completed treatment (19%-61% reporting at least a few problems). Prevalence of worries about health and functioning (reporting at least some worry) was similar for patients on treatment (51%-81%) vs those who had completed treatment (52%-78%). Implementation of the EORTC QLQ-HL27 in research and clinical applications will increase sensitivity of HRQoL assessment in patients with HL. High quality data generated through use of this questionnaire are expected to facilitate clinical decision making in the HL setting.
Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing
Authors: Padilla Juan-Carlos A. , Barutcu Seda , Malet Ludovic , Deschamps-Francoeur Gabrielle , Calderon Virginie , Kwon Eunjeong , Lécuyer Eric 
Published: September 2023

Abstract
Background
While numerous studies have described the transcriptomes of extracellular vesicles (EVs) in different cellular contexts, these efforts have typically relied on sequencing methods requiring RNA fragmentation, which limits interpretations on the integrity and isoform diversity of EV-targeted RNA populations. It has been assumed that mRNA signatures in EVs are likely to be fragmentation products of the cellular mRNA material, and the extent to which full-length mRNAs are present within EVs remains to be clarified.

Results
Using long-read nanopore RNA sequencing, we sought to characterize the full-length polyadenylated (poly-A) transcriptome of EVs released by human chronic myelogenous leukemia K562 cells. We detected 443 and 280 RNAs that were respectively enriched or depleted in EVs. EV-enriched poly-A transcripts consist of a variety of biotypes, including mRNAs, long non-coding RNAs, and pseudogenes. Our analysis revealed that 10.58% of all EV reads, and 18.67% of all cellular (WC) reads, corresponded to known full-length transcripts, with mRNAs representing the largest biotype for each group (EV = 58.13%, WC = 43.93%). We also observed that for many well-represented coding and non-coding genes, diverse full-length transcript isoforms were present in EV specimens, and these isoforms were reflective-of but often in different ratio compared to cellular samples.

Conclusion
This work provides novel insights into the compositional diversity of poly-A transcript isoforms enriched within EVs, while also underscoring the potential usefulness of nanopore sequencing to interrogate secreted RNA transcriptomes.
Harmonization of supervised machine learning practices for efficient source attribution of Listeria monocytogenes based on genomic data
Authors: Castelli Pierluigi , De Ruvo Andrea , Bucciacchio Andrea , D’Alterio Nicola , Cammà Cesare , Di Pasquale Adriano , Radomski Nicolas 
Published: September 2023

Abstract
Background
Genomic data-based machine learning tools are promising for real-time surveillance activities performing source attribution of foodborne bacteria such as Listeria monocytogenes. Given the heterogeneity of machine learning practices, our aim was to identify those influencing the source prediction performance of the usual holdout method combined with the repeated k-fold cross-validation method.

Methods
A large collection of 1 100 L. monocytogenes genomes with known sources was built according to several genomic metrics to ensure authenticity and completeness of genomic profiles. Based on these genomic profiles (i.e. 7-locus alleles, core alleles, accessory genes, core SNPs and pan kmers), we developed a versatile workflow assessing prediction performance of different combinations of training dataset splitting (i.e. 50, 60, 70, 80 and 90%), data preprocessing (i.e. with or without near-zero variance removal), and learning models (i.e. BLR, ERT, RF, SGB, SVM and XGB). The performance metrics included accuracy, Cohen’s kappa, F1-score, area under the curves from receiver operating characteristic curve, precision recall curve or precision recall gain curve, and execution time.

Results
The testing average accuracies from accessory genes and pan kmers were significantly higher than accuracies from core alleles or SNPs. While the accuracies from 70 and 80% of training dataset splitting were not significantly different, those from 80% were significantly higher than the other tested proportions. The near-zero variance removal did not allow to produce results for 7-locus alleles, did not impact significantly the accuracy for core alleles, accessory genes and pan kmers, and decreased significantly accuracy for core SNPs. The SVM and XGB models did not present significant differences in accuracy between each other and reached significantly higher accuracies than BLR, SGB, ERT and RF, in this order of magnitude. However, the SVM model required more computing power than the XGB model, especially for high amount of descriptors such like core SNPs and pan kmers.

Conclusions
In addition to recommendations about machine learning practices for L. monocytogenes source attribution based on genomic data, the present study also provides a freely available workflow to solve other balanced or unbalanced multiclass phenotypes from binary and categorical genomic profiles of other microorganisms without source code modifications.
The mitoepigenome responds to stress, suggesting novel mito-nuclear interactions in vertebrates
Authors: Lees John , Pèrtille Fábio , Løtvedt Pia , Jensen Per , Bosagna Carlos Guerrero 
Published: September 2023

AbstractThe mitochondria are central in the cellular response to changing environmental conditions resulting from disease states, environmental exposures or normal physiological processes. Although the influences of environmental stressors upon the nuclear epigenome are well characterized, the existence and role of the mitochondrial epigenome remains contentious. Here, by quantifying the mitochondrial epigenomic response of pineal gland cells to circadian stress, we confirm the presence of extensive cytosine methylation within the mitochondrial genome. Furthermore, we identify distinct epigenetically plastic regions (mtDMRs) which vary in cytosinic methylation, primarily in a non CpG context, in response to stress and in a sex-specific manner. Motifs enriched in mtDMRs contain recognition sites for nuclear-derived DNA-binding factors (ATF4, HNF4A) important in the cellular metabolic stress response, which we found to be conserved across diverse vertebrate taxa. Together, these findings suggest a new layer of mito-nuclear interaction in which the nuclear metabolic stress response could alter mitochondrial transcriptional dynamics through the binding of nuclear-derived transcription factors in a methylation-dependent context.
Combined oral intake of short and long fructans alters the gut microbiota in food allergy model mice and contributes to food allergy prevention
Authors: Takahashi Hideaki , Fujii Tadashi , Yamakawa Saki , Yamada Chikako , Fujiki Kotoyo , Kondo Nobuhiro , Funasaka Kohei , Hirooka Yoshiki , Tochio Takumi 
Published: September 2023

Abstract
Background
It has become clear that the intestinal microbiota plays a role in food allergies. The objective of this study was to assess the food allergy-preventive effects of combined intake of a short fructan (1-kestose [Kes]) and a long fructan (inulin ([Inu]) in an ovalbumin (OVA)-induced food allergy mouse model.

Results
Oral administration of fructans lowered the allergenic symptom score and alleviated the decreases in rectal temperature and total IgA levels and increases in OVA-specific IgE and IgA levels induced by high-dose OVA challenge, and in particular, combined intake of Kes and Inu significantly suppressed the changes in all these parameters. The expression of the pro-inflammatory cytokine IL-4, which was increased in the allergy model group, was significantly suppressed by fructan administration, and the expression of the anti-inflammatory cytokine IL-10 was significantly increased upon Kes administration. 16 S rRNA amplicon sequencing of the gut microbiota and beta diversity analysis revealed that fructan administration may induce gut microbiota resistance to food allergy sensitization, rather than returning the gut microbiota to a non-sensitized state. The relative abundances of the genera Parabacteroides B 862,066 and Alloprevotella, which were significantly reduced by food allergy sensitization, were restored by fructan administration. In Parabacteroides, the relative abundances of Parabacteroides distasonis, Parabacteroides goldsteinii, and their fructan-degrading glycoside hydrolase family 32 gene copy numbers were increased upon Kes or Inu administration. The concentrations of short-chain fatty acids (acetate and propionate) and lactate were increased by fructan administration, especially significantly in the Kes + Inu, Kes, and Inu-fed (Inu, Kes + Inu) groups.

Conclusion
Combined intake of Kes and Inu suppressed allergy scores more effectively than single intake, suggesting that Kes and Inu have different allergy-preventive mechanisms. This indicates that the combined intake of these short and long fructans may have an allergy-preventive benefit.
Health-related quality of life in stroke survivors: a 5-year follow-up of The Fall Study of Gothenburg (FallsGOT)
Authors: Segerdahl Mårten , Hansson Per-Olof , Samuelsson Carina M. , Persson Carina U. 
Published: September 2023

Abstract
Background
There are limited data on long-term prevalence and predictors of health-related quality of life (HRQoL) in stroke survivors. Therefore, the aim was to describe the prevalence of impaired HRQoL, and to identify factors in acute stroke that are associated with impaired HRQoL, 5 years after stroke.

Methods
The 305 (60.5%) stroke survivors of the original 504 participants from The Fall Study of Gothenburg were invited to participate in a 5-year follow-up including assessment of HRQoL using the EuroQol 5 Dimensions 3 Levels questionnaire (EQ-5D-3L). To identify baseline predictors of impaired HRQoL, based on the EQ-5D-3L’s five dimensions, univariate and multivariate logistic regression analyses were performed.

Results
A total of 129 participants (42.3% of the survivors) completed the questionnaire at a median follow-up time of 58 months. At baseline, their mean age was 70.6 years, and they had a median NIHSS score of 1. The median (interquartile range [IQR]) EQ-5D-3L index score was 0.87 (0.71–0.93) and the median (IQR) EQ-visual analogue scale was 70 (49.8–88). In total, 102 (79%) participants were classified as having impaired HRQoL, stated primarily (among 68.5%) related to Pain/Discomfort. Higher age was identified as a predictor of impaired HRQoL related to Mobility (Odds ratio (OR) 1.05, 95% confidence interval (CI) 1.01–1.10) and Self-Care (OR 1.09, 95% CI 1.02–1.17), and longer hospital stay at baseline was identified as a predictor related to Mobility (OR 1.09, 95% CI 1.01–1.18), Self-Care (OR 1.10, 95% CI 1.02–1.18)) and Usual Activities. (OR 1.10, 95% CI 1.03–1.18).

Conclusion
At 5 years after stroke, four out of five participants (79%) reported impaired HRQoL related to any of the five dimensions assessed by using the EQ-5D-3L. Most reported, impaired HRQoL was related to Pain/Discomfort. Higher age and longer hospital care period at index stroke were associated with impaired HRQoL. The findings could assist to identify individuals at high risk of low HRQoL, who might benefit from special attention and psychological support.
Added value of CE-CT radiomics to predict high Ki-67 expression in hepatocellular carcinoma
Authors: Zhao Yu-meng , Xie Shuang-shuang , Wang Jian , Zhang Ya-min ,  Li Wen-Cui , Ye Zhao-Xiang , Shen Wen 
Published: September 2023

Abstract
Background
This study aimed to develop a computed tomography (CT) model to predict Ki-67 expression in hepatocellular carcinoma (HCC) and to examine the added value of radiomics to clinico-radiological features.

Methods
A total of 208 patients (training set, n = 120; internal test set, n = 51; external validation set, n = 37) with pathologically confirmed HCC who underwent contrast-enhanced CT (CE-CT) within 1 month before surgery were retrospectively included from January 2014 to September 2021. Radiomics features were extracted and selected from three phases of CE-CT images, least absolute shrinkage and selection operator regression (LASSO) was used to select features, and the rad-score was calculated. CE-CT imaging and clinical features were selected using univariate and multivariate analyses, respectively. Three prediction models, including clinic-radiologic (CR) model, rad-score (R) model, and clinic-radiologic-radiomic (CRR) model, were developed and validated using logistic regression analysis. The performance of different models for predicting Ki-67 expression was evaluated using the area under the receiver operating characteristic curve (AUROC) and decision curve analysis (DCA).

Results
HCCs with high Ki-67 expression were more likely to have high serum α-fetoprotein levels (P = 0.041, odds ratio [OR] 2.54, 95% confidence interval [CI]: 1.04–6.21), non-rim arterial phase hyperenhancement (P = 0.001, OR 15.13, 95% CI 2.87–79.76), portal vein tumor thrombus (P = 0.035, OR 3.19, 95% CI: 1.08–9.37), and two-trait predictor of venous invasion (P = 0.026, OR 14.04, 95% CI: 1.39–144.32). The CR model achieved relatively good and stable performance compared with the R model (AUC, 0.805 [95% CI: 0.683–0.926] vs. 0.678 [95% CI: 0.536–0.839], P = 0.211; and 0.805 [95% CI: 0.657–0.953] vs. 0.667 [95% CI: 0.495–0.839], P = 0.135) in the internal and external validation sets. After combining the CR model with the R model, the AUC of the CRR model increased to 0.903 (95% CI: 0.849–0.956) in the training set, which was significantly higher than that of the CR model (P = 0.0148). However, no significant differences were found between the CRR and CR models in the internal and external validation sets (P = 0.264 and P = 0.084, respectively).

Conclusions
Preoperative models based on clinical and CE-CT imaging features can be used to predict HCC with high Ki-67 expression accurately. However, radiomics cannot provide added value.
Association of neighborhood-level sociodemographic factors with Direct-to-Consumer (DTC) distribution of COVID-19 rapid antigen tests in 5 US communities
Authors: Herbert Carly , Shi Qiming , Baek Jonggyu , Wang Biqi , Kheterpal Vik , Nowak Christopher , Suvarna Thejas , Singh Aditi , Hartin Paul , Durnam Basyl , Schrader Summer , Harman Emma , Gerber Ben , Barton Bruce , Zai Adrian , Cohen-Wolkowiez Michael , Corbie-Smith Giselle , Kibbe Warren , Marquez Juan , Hafer Nathaniel , Broach John , Lin Honghuang , Heetderks William , McManus David D , Soni Apurv 
Published: September 2023

Abstract
Background
Many interventions for widescale distribution of rapid antigen tests for COVID-19 have utilized online, direct-to-consumer (DTC) ordering systems; however, little is known about the sociodemographic characteristics of home-test users. We aimed to characterize the patterns of online orders for rapid antigen tests and determine geospatial and temporal associations with neighborhood characteristics and community incidence of COVID-19, respectively.

Methods
This observational study analyzed online, DTC orders for rapid antigen test kits from beneficiaries of the Say Yes! Covid Test program from March to November 2021 in five communities: Louisville, Kentucky; Indianapolis, Indiana; Fulton County, Georgia; O’ahu, Hawaii; and Ann Arbor/Ypsilanti, Michigan. Using spatial autoregressive models, we assessed the geospatial associations of test kit distribution with Census block-level education, income, age, population density, and racial distribution and Census tract-level Social Vulnerability Index. Lag association analyses were used to measure the association between online rapid antigen kit orders and community-level COVID-19 incidence.

Results
In total, 164,402 DTC test kits were ordered during the intervention. Distribution of tests at all sites were significantly geospatially clustered at the block-group level (Moran’s I: p < 0.001); however, education, income, age, population density, race, and social vulnerability index were inconsistently associated with test orders across sites. In Michigan, Georgia, and Kentucky, there were strong associations between same-day COVID-19 incidence and test kit orders (Michigan: r = 0.89, Georgia: r = 0.85, Kentucky: r = 0.75). The incidence of COVID-19 during the current day and the previous 6-days increased current DTC orders by 9.0 (95% CI = 1.7, 16.3), 3.0 (95% CI = 1.3, 4.6), and 6.8 (95% CI = 3.4, 10.2) in Michigan, Georgia, and Kentucky, respectively. There was no same-day or 6-day lagged correlation between test kit orders and COVID-19 incidence in Indiana.

Conclusions
Our findings suggest that online ordering is not associated with geospatial clustering based on sociodemographic characteristics. Observed temporal preferences for DTC ordering can guide public health messaging around DTC testing programs.
A network meta-analysis of different acupuncture modalities in the treatment of bronchial asthma
Authors: Wang Xingyi , Zeng Shuyun , Li Zhuying , Li Yue , Jia Hongtao 
Published: September 2023

Abstract
Background
Glucocorticoids and Beta-2 receptor agonists are commonly used for the treatment of asthma in clinical practice, while these agents are accompanied by adverse reactions of different kinds. Studies have shown that acupuncture is effective in treating bronchial asthma. However, different acupuncture modalities have different costs and skill requirements, and there remains a lack of comparisons between different acupuncture modalities. This study aims to assess the efficacy of various acupuncture modalities in the treatment of asthma.

Methods
The following databases were searched for randomized controlled trials (RCTs) on acupuncture for the treatment of bronchial asthma from database inception to August 26, 2022: PubMed, Embase, The Cochrane Library, Web of Science, Chinese Journal Full-text Database (CNKI), Wanfang Database (Wanfang Date), VIP Database (VIP), China Biology Medicine disc (CBM). Stata 15.1 software was used to conduct network meta-analysis. The risk of bias in the included studies was evaluated using the Cochrane Risk of Bias Assessment Tool 2 (RoB2).

Results
A total of 8,693 relevant studies were found, and 30 RCTs were included, involving 2,722 patients with bronchial asthma and eight acupuncture modalities: manual acupuncture, moxibustion, electroacupuncture, ignipuncture, flying needle acupuncture, acupoint catgut embedding, acupoint application, and warm-needle moxibustion. The other 29 studies had certain risks, with the quality graded as “moderate”. Among the pair-wise comparisons of statistical significance (p < 0.05), acupoint application was the most effective in improving pulmonary function (FEV1: Traditional medicine therapy-acupoint application [-7.29 (-12.11,-2.47)]; acupoint application-moxibustion [7.20 (0.28,14.11)]; FVC: acupoint application-Traditional medicine therapy [8.02 (2.54,13.50)]). Acupoint catgut embedding was the most effective in improving the ACT score of the patients (Traditional medicine therapy-acupoint catgut embedding [-4.29 (-7.94, -0.65)]; acupoint catgut embedding-moxibustion [5.52 (1.05,9.99)]).

Conclusion
Acupoint application has evident merits in improving the clinical response rate and pulmonary function, while acupoint catgut embedding can improve other secondary indicators. For the clinical treatment of asthma, acupoint application can be selected as a complementary and alternative therapy, while the other acupuncture therapies can also be considered according to the examination results of the patients.
Subtrochanteric fracture after femoral neck system of femoral neck fractures: a report of four cases
Authors: Fisher John C. , Gerzina Christopher , Rush Kaitlin , Caroom Cyrus 
Published: September 2023

Abstract
Background
The femoral neck system (FNS) is commonly used for internal fixation of femoral neck fractures and has shown promising results. However, we have observed cases of peri-implant subtrochanteric femur fractures associated with the use of FNS at our institution. This case series aims to investigate four cases of peri-implant subtrochanteric fractures in patients treated with the FNS implant for femoral neck fractures.

Case presentation
We reviewed 35 patients who underwent treatment with FNS for femoral neck fractures between January 2017 and December 2021 at our level 1 trauma institution. Among these patients, four cases of peri-implant subtrochanteric femur fractures were identified. In contrast, no such fractures occurred in patients treated with cannulated screws or dynamic hip screws (DHS). Interestingly, all four cases of peri-implant fractures were seen in patients with incomplete nondisplaced femoral neck fractures. Only one case involved an identifiable technical error.

Conclusions
This case series sheds light on peri-implant subtrochanteric femur fractures as a previously unreported complication associated with the use of FNS for femoral neck fractures. These fractures were observed exclusively in patients with incomplete nondisplaced fractures who received FNS fixation. No similar complications were observed in patients treated with other types of fixation. This finding suggests the need for caution and further investigation when considering FNS as a treatment option for this specific fracture pattern.
The identification of peri-implant subtrochanteric femur fractures as a potential complication of FNS usage in incomplete nondisplaced femoral neck fractures raises important considerations for clinical decision-making and patient management in orthopedic trauma.