bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examining young people’s views and understanding of traffic light and physical activity calorie equivalent (PACE) food labels
Authors: Iris Natalia , Munir Fehmidah , Daley Amanda J. 
Published: June 2023

Abstract
Background
Childhood obesity is a public health challenge in many countries. Food labelling may help children make healthier food choices. Food is typically labelled using the traffic light label system but this is complex to understand. Physical activity calorie equivalent (PACE) labelling may be easier for children to understand and more appealing because it contextualises the energy content of food/drinks.

Methods
A cross-sectional online questionnaire was completed by 808 adolescents aged 12–18 years in England. The questionnaire investigated participants’ views and understanding of traffic light and PACE labels. Participants were also asked about their understanding of the meaning of calories. The questionnaire explored participants’ views about the potential frequency of use of PACE labels and their perceived usefulness in influencing purchasing and consumption decisions. Questions that explored participants’ views about the possible implementation of PACE labelling, preferences for food settings and types of food/drinks they may like such labelling implemented, and whether PACE labels would encourage physical activity were included. Descriptive statistics were explored. Analyses assessed associations between variables and tested differences in the proportions of views about the labels.

Results
More participants reported PACE labels as easier to understand than traffic light labels (69% vs 31%). Of participants who had seen traffic light labels, 19% looked at them often/always. Forty-two percent of participants would look at PACE labels often/always. The most common reason why participants never/would never look at food labels is because they are not interested in making healthy choices. Fifty-two percent of participants said PACE labels would make it easier for them to choose healthy food and drinks. Fifty percent of participants reported PACE labels would encourage them to be physically active. It was perceived that PACE labels could be useful in a range of food settings and on a range of food/drinks.

Conclusions
PACE labelling may be easier for young people to understand and more appealing/useful to them than traffic light labelling. PACE labelling may help young people choose healthier food/drinks and reduce excess energy consumption. Research is now needed to understand the impact of PACE labelling on food choice among adolescents in real eating settings.
Safety and utility of Endoscopic Ultrasound with Bronchoscope-guided Fine Needle Aspiration (EUS-B-FNA) in suspected lung cancer patients with poor respiratory or general conditions: a prospective three-center observational study
Authors: Nakashima Koki , Umeda Yukihiro , Demura Yoshiki , Takeda Toshihiro , Tada Toshihiko , Sato Masayuki , Jikuya Norihiro , Kurokawa Kosuke , Sonoda Tomoaki , Yamaguchi Makiko , Mitsui Miho , Oi Masahiro , Chikazawa Ryo , Waseda Yuko , Anzai Masaki , Akai Masaya , Ishizuka Tamotsu 
Published: June 2023

Abstract
Background
Although transbronchial diagnostic procedures are sometimes difficult to perform because of the patient’s respiratory or general conditions, endoscopic ultrasound with bronchoscope-guided fine-needle aspiration (EUS-B-FNA), a known transesophageal diagnostic procedure, might be useful for such cases. We conducted this prospective three-center observational study to evaluate the safety and efficacy of EUS-B-FNA in suspected lung cancer patients with poor respiratory or general conditions.

Methods
Patients with suspected lung cancer with respiratory failure, Eastern Cooperative Oncology Group performance status of 2 or higher, or severe respiratory symptoms, were enrolled. The primary endpoints were the diagnostic yield of lung cancer and its safety, and the secondary endpoints were the success rate of molecular and programmed death ligand 1 (PD-L1) analyses, and the 6-month survival rate in patients with lung cancer.

Results
We enrolled 30 patients, of which 29 were included in the analysis. Among them, 26 were eventually diagnosed with lung cancer. The diagnostic yield for lung cancer was 100% (26/26). There were no adverse events associated with EUS-B-FNA requiring procedure discontinuation. The success rates of molecular analysis for EGFR, ALK, ROS-1, and BRAF were 100% (14/14), 100% (11/11), 100% (9/9), and 75% (6/8), respectively. The success rate of the PD-L1 analysis was 100% (15/15). The 6-month survival rate in patients with lung cancer was 53.8% (95% confidence interval [CI]: 33.4–76.4), and the median overall survival (OS) was 196 days (95% CI: 142–446).

Conclusions
EUS-B-FNA is a safe and effective diagnostic method, even in patients with suspected lung cancer with poor respiratory or general conditions.

Trial registration
This clinical trial was registered at https://www.umin.ac.jp/ctr/index.htm (UMIN000041235, approved on 28/07/2020).
Implementing a cirrhosis order set in a tertiary healthcare system: a theory-informed formative evaluation
Authors: Hyde A. M. , Johnson E. , Luig T. , Schroeder D. , Carbonneau M. , Campbell-Scherer D. , Tandon P. 
Published: June 2023

Abstract
Background
Standardized order sets are a means of increasing adherence to clinical practice guidelines and improving the quality of patient care. Implementation of novel quality improvement initiatives like order sets can be challenging. Before the COVID-19 pandemic, we conducted a formative evaluation to understand healthcare providers’ perspectives on implementing clinical changes and the individual, collective and organizational contextual factors that might impact implementation at eight hospital sites in Alberta, Canada.

Methods
We utilized concepts from the Consolidated Framework for Implementation Research (CFIR) and Normalisation Process Theory (NPT) to understand the context, past implementation experiences, and perceptions of the cirrhosis order set. Eight focus groups were held with healthcare professionals caring for patients with cirrhosis. Data were coded deductively using relevant constructs of NPT and CFIR. A total of 54 healthcare professionals, including physicians, nurses, nurse practitioners, social workers and pharmacists and a physiotherapist, participated in the focus groups.

Results
Key findings revealed that participants recognized the value of the cirrhosis order set and its potential to improve the quality of care. Participants highlighted potential implementation challenges, including multiple competing quality improvement initiatives, feelings of burnout, lack of communication between healthcare provider groups, and a lack of dedicated resources to support implementation.

Conclusions
Implementing a complex improvement initiative across clinician groups and acute care sites presents challenges. This work yielded insights into the significant influence of past implementation of similar interventions and highlighted the importance of communication between clinician groups and resources to support implementation. However, by using multiple theoretical lenses to illuminate what and how contextual and social processes will influence uptake, we can better anticipate challenges during the implementation process.
Signature construction and molecular subtype identification based on immune-related genes for better prediction of prognosis in hepatocellular carcinoma
Authors: Sun Liang , Wu Zhengyi , Dong Cairong , Yu Shian , Huang He , Chen Zhendong , Wu Zhipeng , Yin Xiangbao 
Published: June 2023

Abstract
Objective
Hepatocellular carcinoma (HCC) immunotherapy is a focus of current research. We established a model that can effectively predict the prognosis and efficacy of HCC immunotherapy by analyzing the immune genes of HCC.

Methods
Through the data mining of hepatocellular carcinoma in The Cancer Genome Atlas (TCGA), the immune genes with differences in tumor and normal tissues are screened, and then the univariate regression analysis is carried out to screen the immune genes with differences related to prognosis. The prognosis model of immune related genes is constructed by using the minimum absolute contraction and selection operator (lasso) Cox regression model in the TCGA training set data, The risk score of each sample was calculated, and the survival was compared with the Kaplan Meier curve and the receiver operating characteristic (ROC) curve to evaluate the predictive ability. Data sets from ICGC and TCGA were used to verify the reliability of signatures. The correlation between clinicopathological features, immune infiltration, immune escape and risk score was analyzed.

Results
Seven immune genes were finally determined as the prognostic model of liver cancer. According to these 7 genes, the samples were divided into the high and low risk groups, and the results suggested that the high-risk group had a poorer prognosis, lower risk of immune escape, and better immunotherapy effect. In addition, the expression of TP53 and MSI was positively correlated in the high-risk group. Consensus clustering was performed to identify two main molecular subtypes (named clusters 1 and 2) based on the signature. It was found that compared with cluster 1, better survival outcome was observed in cluster 2.

Conclusion
Signature construction and molecular subtype identification of immune-related genes could be used to predict the prognosis of HCC, which may provide a specific reference for the development of novel biomarkers for HCC immunotherapy.
Neutralizing antibodies targeting a novel epitope on envelope protein exhibited broad protection against flavivirus without risk of disease enhancement
Authors: Yen Li-Chen , Chen Hsin-Wei , Ho Chia-Lo , Lin Chang-Chi , Lin Yi-Ling , Yang Qiao-Wen , Chiu Kuo-Chou , Lien Shu-Pei , Lin Ren-Jye , Liao Ching-Len 
Published: June 2023

Abstract
Background
Flavivirus causes many serious public health problems worldwide. However, licensed DENV vaccine has restrictions on its use, and there is currently no approved ZIKV vaccine. Development of a potent and safe flavivirus vaccine is urgently needed. As a previous study revealed the epitope, RCPTQGE, located on the bc loop in the E protein domain II of DENV, in this study, we rationally designed and synthesized a series of peptides based on the sequence of JEV epitope RCPTTGE and DENV/ZIKV epitope RCPTQGE.

Methods
Immune sera were generated by immunization with the peptides which were synthesized by using five copies of RCPTTGE or RCPTQGE and named as JEV-NTE and DV/ZV-NTE. Immunogenicity and neutralizing abilities of JEV-NTE or DV/ZV-NTE-immune sera against flavivirus were evaluated by ELISA and neutralization tests, respectively. Protective efficacy in vivo were determined by passive transfer the immune sera into JEV-infected ICR or DENV- and ZIKV-challenged AG129 mice. In vitro and in vivo ADE assays were used to examine whether JEV-NTE or DV/ZV-NTE-immune sera would induce ADE.

Results
Passive immunization with JEV-NTE-immunized sera or DV/ZV-NTE-immunized sera could increase the survival rate or prolong the survival time in JEV-challenged ICR mice and reduce the viremia levels significantly in DENV- or ZIKV-infected AG129 mice. Furthermore, neither JEV -NTE- nor DV/ZV-NTE-immune sera induced antibody-dependent enhancement (ADE) as compared with the control mAb 4G2 both in vitro and in vivo.

Conclusions
We showed for the first time that novel bc loop epitope RCPTQGE located on the amino acids 73 to 79 of DENV/ZIKV E protein could elicit cross-neutralizing antibodies and reduced the viremia level in DENV- and ZIKV-challenged AG129 mice. Our results highlighted that the bc loop epitope could be a promising target for flavivirus vaccine development.
Machine learning-based models to predict one-year mortality among Chinese older patients with coronary artery disease combined with impaired glucose tolerance or diabetes mellitus
Authors: Li Yan , Guan Lixun , Ning Chaoxue , Zhang Pei , Zhao Yali , Liu Qiong , Ping Ping , Fu Shihui 
Published: June 2023

Abstract
Purpose
An accurate prediction of survival prognosis is beneficial to guide clinical decision-making. This prospective study aimed to develop a model to predict one-year mortality among older patients with coronary artery disease (CAD) combined with impaired glucose tolerance (IGT) or diabetes mellitus (DM) using machine learning techniques.

Methods
A total of 451 patients with CAD combined with IGT and DM were finally enrolled, and those patients randomly split 70:30 into training cohort (n = 308) and validation cohort (n = 143).

Results
The one-year mortality was 26.83%. The least absolute shrinkage and selection operator (LASSO) method and ten-fold cross-validation identified that seven characteristics were significantly associated with one-year mortality with creatine, N-terminal pro-B-type natriuretic peptide (NT-proBNP), and chronic heart failure being risk factors and hemoglobin, high density lipoprotein cholesterol, albumin, and statins being protective factors. The gradient boosting machine model outperformed other models in terms of Brier score (0.114) and area under the curve (0.836). The gradient boosting machine model also showed favorable calibration and clinical usefulness based on calibration curve and clinical decision curve. The Shapley Additive exPlanations (SHAP) found that the top three features associated with one-year mortality were NT-proBNP, albumin, and statins. The web-based application could be available at https://starxueshu-online-application1-year-mortality-main-49cye8.streamlitapp.com/.

Conclusions
This study proposes an accurate model to stratify patients with a high risk of one-year mortality. The gradient boosting machine model demonstrates promising prediction performance. Some interventions to affect NT-proBNP and albumin levels, and statins, are beneficial to improve survival outcome among patients with CAD combined with IGT or DM.
5-Methylcytosine-related lncRNAs: predicting prognosis and identifying hot and cold tumor subtypes in head and neck squamous cell carcinoma
Authors: Huang Juntao , Xu Ziqian , Zhou Chongchang , Cheng Lixin , Zeng Hong , Shen Yi 
Published: June 2023

Abstract
Background
5-Methylcytosine (m5C) methylation is recognized as an mRNA modification that participates in biological progression by regulating related lncRNAs. In this research, we explored the relationship between m5C-related lncRNAs (mrlncRNAs) and head and neck squamous cell carcinoma (HNSCC) to establish a predictive model.

Methods
RNA sequencing and related information were obtained from the TCGA database, and patients were divided into two sets to establish and verify the risk model while identifying prognostic mrlncRNAs. Areas under the ROC curves were assessed to evaluate the predictive effectiveness, and a predictive nomogram was constructed for further prediction. Subsequently, the tumor mutation burden (TMB), stemness, functional enrichment analysis, tumor microenvironment, and immunotherapeutic and chemotherapeutic responses were also assessed based on this novel risk model. Moreover, patients were regrouped into subtypes according to the expression of model mrlncRNAs.

Results
Assessed by the predictive risk model, patients were distinguished into the low-MLRS and high-MLRS groups, showing satisfactory predictive effects with AUCs of 0.673, 0.712, and 0.681 for the ROCs, respectively. Patients in the low-MLRS groups exhibited better survival status, lower mutated frequency, and lower stemness but were more sensitive to immunotherapeutic response, whereas the high-MLRS group appeared to have higher sensitivity to chemotherapy. Subsequently, patients were regrouped into two clusters: cluster 1 displayed immunosuppressive status, but cluster 2 behaved as a hot tumor with a better immunotherapeutic response.

Conclusions
Referring to the above results, we established a m5C-related lncRNA model to evaluate the prognosis, TME, TMB, and clinical treatments for HNSCC patients. This novel assessment system is able to precisely predict the patients’ prognosis and identify hot and cold tumor subtypes clearly for HNSCC patients, providing ideas for clinical treatment.
It is the time for quorum sensing inhibition as alternative strategy of antimicrobial therapy
Authors: Naga Nourhan G. , El-Badan Dalia E. , Ghanem Khaled M. , Shaaban Mona I. 
Published: June 2023

AbstractMultiple drug resistance poses a significant threat to public health worldwide, with a substantial increase in morbidity and mortality rates. Consequently, searching for novel strategies to control microbial pathogenicity is necessary. With the aid of auto-inducers (AIs), quorum sensing (QS) regulates bacterial virulence factors through cell-to-cell signaling networks. AIs are small signaling molecules produced during the stationary phase. When bacterial cultures reach a certain level of growth, these molecules regulate the expression of the bound genes by acting as mirrors that reflect the inoculum density.Gram-positive bacteria use the peptide derivatives of these signaling molecules, whereas Gram-negative bacteria use the fatty acid derivatives, and the majority of bacteria can use both types to modulate the expression of the target gene. Numerous natural and synthetic QS inhibitors (QSIs) have been developed to reduce microbial pathogenesis. Applications of QSI are vital to human health, as well as fisheries and aquaculture, agriculture, and water treatment.
Effect of fortification on the osmolality of human milk
Authors: Elia Serena , Ciarcià Martina , Cini Nicoletta , Luceri Francesca , Mattei Mauro Leucio , Miselli Francesca , Perugi Silvia , Fanelli Alessandra , Dani Carlo 
Published: June 2023

Abstract
Background
It is known that human milk fortifiers (HMF) increases osmolality of human milk (HM) but some aspects of fortification have not been deeply investigated. Our aim was to evaluate the effect of fortification on the osmolality of donor human milk (DHM) and mother’s own milk (MOM) over 72 h of storage using two commercial fortifiers and medium-chain triglycerides (MCT) supplementation.

Methods
Pasteurized DHM and unpasteurized preterm MOM were fortified with 4% PreNAN FM85, 4% PreNAN FM85 plus 2% MCT, or 4% Aptamil BMF. Osmolality was measured in unfortified DHM and MOM and, moreover, just after fortification (T0), and after 6 (T6), 24 (T24) and 72 h (T72) to determine the effect of mixing and storage.

Results
Unfortified DHM and MOM did not show changes of osmolality. Fortification increased osmolality of DHM and MOM without changes during the study period, except for Aptamil BMF which increased osmolality of MOM. The addition of MCT to fortified human milk (FHM) did not affect its osmolality.

Conclusions
Changes of osmolality in the 72 h following fortification of both DHM and MOM did not exceed the safety values supporting the theoretically possibility of preparing 72 h volumes of FHM. Supplementation with MCT of FHM does not change osmolality suggesting that increasing energy intake in preterm infants via this approach is safe.
Non-BRCA1/BRCA2 high-risk familial breast cancers are not associated with a high prevalence of BRCAness
Authors: Andersen Lars v. B. , Larsen Martin J. , Davies Helen , Degasperi Andrea , Nielsen Henriette Roed , Jensen Louise A. , Kroeldrup Lone , Gerdes Anne-Marie , Lænkholm Anne-Vibeke , Kruse Torben A. , Nik-Zainal Serena , Thomassen Mads 
Published: June 2023

Abstract
Background
Familial breast cancer is in most cases unexplained due to the lack of identifiable pathogenic variants in the BRCA1 and BRCA2 genes. The somatic mutational landscape and in particular the extent of BRCA-like tumour features (BRCAness) in these familial breast cancers where germline BRCA1 or BRCA2 mutations have not been identified is to a large extent unknown.

Methods
We performed whole-genome sequencing on matched tumour and normal samples from high-risk non-BRCA1/BRCA2 breast cancer families to understand the germline and somatic mutational landscape and mutational signatures. We measured BRCAness using HRDetect. As a comparator, we also analysed samples from BRCA1 and BRCA2 germline mutation carriers.

Results
We noted for non-BRCA1/BRCA2 tumours, only a small proportion displayed high HRDetect scores and were characterized by concomitant promoter hypermethylation or in one case a RAD51D splice variant previously reported as having unknown significance to potentially explain their BRCAness. Another small proportion showed no features of BRCAness but had mutationally active tumours. The remaining tumours lacked features of BRCAness and were mutationally quiescent.

Conclusions
A limited fraction of high-risk familial non-BRCA1/BRCA2 breast cancer patients is expected to benefit from treatment strategies against homologue repair deficient cancer cells.
Var∣Decrypt: a novel and user-friendly tool to explore and prioritize variants in whole-exome sequencing data
Authors: Salma Mohammad , Alaterre Elina , Moreaux Jérôme , Soler Eric 
Published: June 2023

Abstract
Background
High-throughput sequencing (HTS) offers unprecedented opportunities for the discovery of causative gene variants in multiple human disorders including cancers, and has revolutionized clinical diagnostics. However, despite more than a decade of use of HTS-based assays, extracting relevant functional information from whole-exome sequencing (WES) data remains challenging, especially for non-specialists lacking in-depth bioinformatic skills.

Results
To address this limitation, we developed Var∣Decrypt, a web-based tool designed to greatly facilitate WES data browsing and analysis. Var∣Decrypt offers a wide range of gene and variant filtering possibilities, clustering and enrichment tools, providing an efficient way to derive patient-specific functional information and to prioritize gene variants for functional analyses. We applied Var∣Decrypt on WES datasets of 10 acute erythroid leukemia patients, a rare and aggressive form of leukemia, and recovered known disease oncogenes in addition to novel putative drivers. We additionally validated the performance of Var∣Decrypt using an independent dataset of ~ 90 multiple myeloma WES, recapitulating the identified deregulated genes and pathways, showing the general applicability and versatility of Var∣Decrypt for WES analysis.

Conclusion
Despite years of use of WES in human health for diagnosis and discovery of disease drivers, WES data analysis still remains a complex task requiring advanced bioinformatic skills. In that context, there is a need for user-friendly all-in-one dedicated tools for data analysis, to allow biologists and clinicians to extract relevant biological information from patient datasets. Here, we provide Var∣Decrypt (trial version accessible here: https://vardecrypt.com/app/vardecrypt), a simple and intuitive Rshiny application created to fill this gap. Source code and detailed user tutorial are available at https://gitlab.com/mohammadsalma/vardecrypt.