bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genetic admixture and evolutionary history in the Shandong Peninsula inferred from integrative modern and ancient genomic resources
Authors: Su Haoran , Wang Mengge , Li Xiangping , Duan Shuhan , Sun Qiuxia , Sun Yuntao , Wang Zhiyong , Yang Qingxin , Huang Yuguo , Zhong Jie , Chen Jing , Jiang Xiucheng , Ma Jinyue , Yang Ting , Liu Yunhui , Luo Lintao , Liu Yan , Yang Junbao , Chen Gang , Liu Chao , Cai Yan , He Guanglin 
Published: June 2024

AbstractBackgroundAncient northern East Asians (ANEA) from the Yellow River region, who pioneered millet cultivation, play a crucial role in understanding the origins of ethnolinguistically diverse populations in modern China and the entire landscape of deep genetic structure and variation discovery in modern East Asians. However, the direct links between ANEA and geographically proximate modern populations, as well as the biological adaptive processes involved, remain poorly understood.ResultsHere, we generated genome-wide SNP data for 264 individuals from geographically different Han populations in Shandong. An integrated genomic resource encompassing both modern and ancient East Asians was compiled to examine fine-scale population admixture scenarios and adaptive traits. The reconstruction of demographic history and hierarchical clustering patterns revealed that individuals from the Shandong Peninsula share a close genetic affinity with ANEA, indicating long-term genetic continuity and mobility in the lower Yellow River basin since the early Neolithic period. Biological adaptive signatures, including those related to immune and metabolic pathways, were identified through analyses of haplotype homozygosity and allele frequency spectra. These signatures are linked to complex traits such as height and body mass index, which may be associated with adaptations to cold environments, dietary practices, and pathogen exposure. Additionally, allele frequency trajectories over time and a haplotype network of two highly differentiated genes,ABCC11andSLC10A1, were delineated. These genes, which are associated with axillary odor and bilirubin metabolism, respectively, illustrate how local adaptations can influence the diversification of traits in East Asians.ConclusionsOur findings provide a comprehensive genomic dataset that elucidates the fine-scale genetic history and evolutionary trajectory of natural selection signals and disease susceptibility in Han Chinese populations. This study serves as a paradigm for integrating spatiotemporally diverse ancient genomes in the era of population genomic medicine.
Tissue- and time-dependent metabolite profiles during early grain development under normal and high night-time temperature conditions
Authors: Abshire Nathan , Hauck Andrew L. , Walia Harkamal , Obata Toshihiro 
Published: June 2024

Abstract
Background
Wheat grain development in the first few days after pollination determines the number of endosperm cells that influence grain yield potential and is susceptible to various environmental conditions, including high night temperatures (HNTs). Flag leaves and seed-associated bracts (glumes, awn, palea, and lemma) provide nutrients to the developing seed. However, the specific metabolic roles of these tissues are uncertain, especially their dynamics at different developmental stages and the time in a day. Tissue- and time-dependent metabolite profiling may hint at the metabolic roles of tissues and the mechanisms of how HNTs affect daytime metabolic status in early grain development.

Results
The metabolite profiles of flag leaf, bract, seed (embryo and endosperm), and entire spike were analyzed at 12:00 (day) and 23:00 (night) on 2, 4, and 6 days after fertilization under control and HNT conditions. The metabolite levels in flag leaves and bracts showed day/night oscillations, while their behaviors were distinct between the tissues. Some metabolites, such as sucrose, cellobiose, and succinic acid, showed contrasting oscillations in the two photosynthetic tissues. In contrast, seed metabolite levels differed due to the days after fertilization rather than the time in a day. The seed metabolite profile altered earlier in the HNT than in the control condition, likely associated with accelerated grain development caused by HNT. HNT also disrupted the day/night oscillation of sugar accumulation in flag leaves and bracts.

Conclusions
These results highlight distinct metabolic roles of flag leaves and bracts during wheat early seed development. The seed metabolite levels are related to the developmental stages. The early metabolic events in the seeds and the disruption of the day/night metabolic cycle in photosynthetic tissues may partly explain the adverse effects of HNT on grain yield.
Comprehensive analysis of little leaf disease incidence and resistance in eggplant
Authors: Karthikeyan Muthusamy , Yogiraj Gawande Priya , Elaiyabharathi Thiyagarajan , Jesu Bonipas Antony John , Johnson Iruthayasamy , Jaffer Shajith Basha , Dhanabalan Shanmuga Priya , Boopathi Narayanan Manikanda , Marimuthu Subbaiyan , Nejad Hamid Shobeiri , Adorada Dante L. , Periyannan Sambasivam 
Published: June 2024

AbstractBackgroundLittle leaf disease caused by phytoplasma infection is a significant threat to eggplant (also known as brinjal) cultivation in India. This study focused on the molecular characterisation of the phytoplasma strains and insect vectors responsible for its transmission and screening of brinjal germplasm for resistance to little leaf disease.ResultsSurveys conducted across districts in the Tamil Nadu state of India during 2021–2022 showed a higher incidence of phytoplasma during the Zaid (March to June), followed by Kharif (June to November) and Rabi (November to March) seasons with mean incidence ranging from 22 to 27%. As the name indicates, phytoplasma infection results in little leaf (reduction in leaf size), excessive growth of axillary shoots, virescence, phyllody, stunted growth, leaf chlorosis and witches’ broom symptoms. PCR amplification with phytoplasma-specific primers confirmed the presence of this pathogen in all symptomatic brinjal plants and inHishimonus phycitis(leafhopper), providing valuable insights into the role of leafhoppers in disease transmission. BLAST search and phylogenetic analysis revealed the phytoplasma strain as “Candidatus Phytoplasma trifolii”. Insect population and disease dynamics are highly influenced by environmental factors such as temperature, relative humidity and rainfall. Further, the evaluation of 22 eggplant accessions revealed immune to highly susceptible responses where over 50% of the entries were highly susceptible. Finally, additive main effect and multiplicative interaction (AMMI) and won-where biplot analyses identified G18 as a best-performing accession for little leaf resistance due to its consistent responses across multiple environments.ConclusionsThis research contributes essential information on little leaf incidence, symptoms, transmission and resistance profiles of different brinjal genotypes, which together ensure effective and sustainable management of this important disease of eggplants.
Metabolomic and transcriptomic analyses highlight metabolic regulatory networks of Salvia miltiorrhiza in response to replant disease
Authors: Jiang Mei , Yan YaXing , Zhou BingQian , Li Jian , Cui Li , Guo LanPing , Liu Wei 
Published: June 2024

AbstractBackgroundSalvia miltiorrhiza, a well-known traditional Chinese medicine, frequently suffers from replant diseases that adversely affect its quality and yield. To elucidateS. miltiorrhiza’s metabolic adaptations to replant disease, we analyzed its metabolome and transcriptome, comparing normal and replant diseased plants for the first time.ResultsWe identified 1,269 metabolites, 257 of which were differentially accumulated metabolites, and identified 217 differentially expressed genes. Integrated transcriptomic and metabolomic analyses revealed a significant up-regulation and co-expression of metabolites and genes associated with plant hormone signal transduction and flavonoid biosynthesis pathways in replant diseases. Within plant hormone signal transduction pathway, plants afflicted with replant disease markedly accumulated indole-3-acetic acid and abscisic acid, correlating with high expression of their biosynthesis-related genes (SmAmidase,SmALDH,SmNCED, andSmAAOX3). Simultaneously, changes in hormone concentrations activated plant hormone signal transduction pathways. Moreover, under replant disease, metabolites in the local flavonoid metabolite biosynthetic pathway were significantly accumulated, consistent with the up-regulated gene (SmHTC1andSmHTC2). The qRT-PCR analysis largely aligned with the transcriptomic results, confirming the trends in gene expression. Moreover, we identified 10 transcription factors co-expressed with differentially accumulated metabolites.ConclusionsOverall, we revealed the key genes and metabolites ofS. miltiorrhizaunder replant disease, establishing a robust foundation for future inquiries into the molecular responses to combat replant stress.
Predicting severity of acute appendicitis with machine learning methods: a simple and promising approach for clinicians
Authors: Yazici Hilmi , Ugurlu Onur , Aygul Yesim , Ugur Mehmet Alperen , Sen Yigit Kaan , Yildirim Mehmet 
Published: June 2024

Abstract
Backgrounds
Acute Appendicitis (AA) is one of the most common surgical emergencies worldwide. This study aims to investigate the predictive performances of 6 different Machine Learning (ML) algorithms for simple and complicated AA.

Methods
Data regarding operated AA patients between 2012 and 2022 were analyzed retrospectively. Based on operative findings, patients were evaluated under two groups: perforated AA and none-perforated AA. The features that showed statistical significance (p < 0.05) in both univariate and multivariate analysis were included in the prediction models as input features. Five different error metrics and the area under the receiver operating characteristic curve (AUC) were used for model comparison.

Results
A total number of 1132 patients were included in the study. Patients were divided into training (932 samples), testing (100 samples), and validation (100 samples) sets. Age, gender, neutrophil count, lymphocyte count, Neutrophil to Lymphocyte ratio, total bilirubin, C-Reactive Protein (CRP), Appendix Diameter, and PeriAppendicular Liquid Collection (PALC) were significantly different between the two groups. In the multivariate analysis, age, CRP, and PALC continued to show a significant difference in the perforated AA group. According to univariate and multivariate analysis, two data sets were used in the prediction model. K-Nearest Neighbors and Logistic Regression algorithms achieved the best prediction performance in the validation group with an accuracy of 96%.

Conclusion
The results showed that using only three input features (age, CRP, and PALC), the severity of AA can be predicted with high accuracy. The developed prediction model can be useful in clinical practice.
Treatment strategies for insomnia in Japanese primary care physicians’ practice: A Web-based questionnaire survey
Authors: Takeshima Masahiro , Sakurai Hitoshi , Inada Ken , Aoki Yumi , Ie Kenya , Kise Morito , Yoshida Eriko , Matsui Kentaro , Utsumi Tomohiro , Shimura Akiyoshi , Okajima Isa , Kotorii Nozomu , Yamashita Hidehisa , Suzuki Masahiro , Kuriyama Kenichi , Shimizu Eiji , Mishima Kazuo , Watanabe Koichiro , Takaesu Yoshikazu 
Published: June 2024

AbstractBackgroundIt is unclear how primary care physicians manage insomnia after the introduction of novel hypnotics such as orexin receptor antagonists and melatonin receptor agonists. This Web-based questionnaire survey aimed to examine treatment strategies for insomnia in Japanese primary care practice.MethodsOne-hundred-and-seventeen primary care physicians were surveyed on the familiarity of each management option for insomnia on a binary response scale (0 = “unfamiliar”; 1 = “familiar”) and how they managed insomnia using a nine-point Likert scale (1 = “I never prescribe/perform it”; 9 = “I often prescribe/perform it”). Physicians who were unfamiliar with a management option were deemed to have never prescribed or performed it.ResultsRegarding medication, most physicians were familiar with novel hypnotics. Suvorexant was the most used hypnotic, followed by lemborexant and ramelteon. These novel hypnotics averaged 4.8–5.4 points and 4.0–4.7 points for sleep onset and sleep maintenance insomnia, respectively. By contrast, most benzodiazepines were seldom used below two points. Regarding psychotherapy, only approximately 40% of the physicians were familiar with cognitive behavioral therapy for insomnia (CBT-I) and they rarely implemented it, at an average of 1.5–1.6 points. More physicians were familiar with single-component psychotherapies (i.e., relaxation, sleep restriction therapy, and stimulus control) compared to CBT-I, and 48–74% of them implemented it slightly more often, with scores ranging from 2.6 to 3.4 points.ConclusionThis study suggests that Japanese primary care physicians seldom use CBT-I to treat insomnia. In addition, they use novel sleep medications more frequently than benzodiazepines in terms of pharmacotherapy. The use and availability of CBT-I in Japanese primary care might be facilitated by: educating primary care physicians, implementing brief or digital CBT-I, and/or developing collaborations between primary care physicians and CBT-I specialists.
Finding key genes (UBE2T, KIF4A, CDCA3, and CDCA5) co-expressed in hepatitis, cirrhosis and hepatocellular carcinoma based on multiple bioinformatics techniques
Authors: Zhang Yingai , Yu Weiling , Zhou Shuai , Xiao Jingchuan , Zhang Xiaoyu , Yang Haoliang , Zhang Jianquan 
Published: June 2024

AbstractBackgroundHepatocellular carcinoma (HCC) is one of the most common cancers worldwide. Hepatitis B virus (HBV) is one of the major causes of liver cirrhosis (LC) and HCC. Therefore, the discovery of common markers for hepatitis B or LC and HCC is crucial for the prevention of HCC.MethodsExpressed genes for to chronic active hepaititis B (CAH-B), LC and HCC were obtained from the GEO and TCGA databases, and co-expressed genes were screened using Protein-protein interaction (PPI) networks, least absolute shrinkage and selection operator (LASSO), random forest (RF) and support vector machine - recursive feature elimination (SVM-RFE). The prognostic value of genes was assessed using Kaplan-Meier (KM) survival curves. Columnar line plots, calibration curves and receiver operating characteristic (ROC) curves of individual genes were used for evaluation. Validation was performed using GEO datasets. The association of these key genes with HCC clinical features was explored using the UALCAN database (https://ualcan.path.uab.edu/index.html).ResultsBased on WGCNA analysis and TCGA database, the co-expressed genes (565) were screened. Moreover, the five algorithms of MCODE (ClusteringCoefficient, MCC, Degree, MNC, and DMNC) was used to select one of the most important and most closely linked clusters (the top 50 genes ranked). Using, LASSO regression model, RF model and SVM-RFE model, four key genes (UBE2T, KIF4A, CDCA3, and CDCA5) were identified for subsequent research analysis. These 4 genes were highly expressed and associated with poor prognosis and clinical features in HCC patients.ConclusionThese four key genes (UBE2T, KIF4A, CDCA3, and CDCA5) may be common biomarkers for CAH-B and HCC or LC and HCC, promising to advance our understanding of the molecular basis of CAH-B/LC/HCC progression.
Association between standing height and physical disability among U.S. adults aged 60 years and older: findings from NHANES 2015–2018
Authors: Wang Shihong , Yang Zihua , Tan Xiwei , Lai Fengxia , Luo Ling , Ding Yuanlin 
Published: June 2024

Abstract
Background
Physical disability is an important cause of affecting the quality of life in the elderly. The association between standing height and physical disability is less studied.

Purpose
The purpose of this study is to investigate the possible link between standing height and physical disability among U.S. adults aged 60 years and older.

Methods
The cross-sectional data were obtained from the US National Health and Nutrition Examination Survey (NHANES) 2015–2018. Physical disability was assessed by six questions: “Have serious difficulty hearing (SDH)?”, “Have serious difficulty seeing (SDS)?”, “Have serious difficulty concentrating (SDC)?”, “Have serious difficulty walking (SDW)?”, “Have difficulty dressing or bathing (DDB)?” and “Have difficulty doing errands alone (DDEA)?”. Responses to these questions were “yes” or “no”. Answer yes to one of the above six questions was identified as physical disability. Standing height (cm) was measured with an altimeter. Multivariate logistic regression was performed to examine the possible link between standing height and physical disability after adjustment for all covariates.

Results
A total of 2624 participants aged ≥ 60 years were included in our study, including 1279 (48.7%) females and 1345 (51.3%) males. The mean age of participants was 69.41 ± 6.82 years. After adjusting for all potential confounders, the inverse relationship between standing height and all physical disability (APD) was statistically significant (OR = 0.976, 95%CI:0.957–0.995). In addition, among six types of physical disability (SDH, SDS, SDC, SDW, DDB, DDEA), standing height was also a protective factor for SDW (OR = 0.961, 95%CI:0.939–0.983) and DDEA (OR = 0.944, 95%CI:0.915–0.975) in the full-adjusted model.

Conclusion
The cross-sectional population based study demonstrates that standing height is a protective factor for physical disability among U.S. adults aged 60 years and older.
Patient-centered outcomes and outcome measurements for people aged 65 years and older—a scoping review
Authors: Andersson Åsa G. , Dahlkvist Lisabet , Kurland Lisa 
Published: June 2024

Abstract
Introduction
The aging population is a challenge for the healthcare system that must identify strategies that meet their needs. Practicing patient-centered care has been shown beneficial for this patient-group. The effect of patient-centered care is called patient-centered outcomes and can be appraised using outcomes measurements.

Objectives
The main aim was to review and map existing knowledge related to patient-centered outcomes and patient-centered outcomes measurements for older people, as well as identify key-concepts and knowledge-gaps. The research questions were: How can patient-centered outcomes for older people be measured, and which patient-centered outcomes matters the most for the older people?

Study design
Scoping review.

Methods
Search for relevant publications in electronical databases, grey literature databases and websites from year 2000 to 2021. Two reviewers independently screened titles and abstracts, followed by full text review and extraction of data using a data extraction framework.

Results
Eighteen studies were included, of which six with involvement of patients and/or experts in the process on determine the outcomes. Outcomes that matter the most to older people was interpreted as: access to- and experience of care, autonomy and control, cognition, daily living, emotional health, falls, general health, medications, overall survival, pain, participation in decision making, physical function, physical health, place of death, social role function, symptom burden, and time spent in hospital. The most frequently mentioned/used outcomes measurements tools were the Adult Social Care Outcomes Toolkit (ASCOT), EQ-5D, Gait Speed, Katz- ADL index, Patient Health Questionnaire (PHQ9), SF/RAND-36 and 4-Item Screening Zarit Burden Interview.

Conclusions
Few studies have investigated the older people’s opinion of what matters the most to them, which forms a knowledge-gap in the field. Future research should focus on providing older people a stronger voice in what they think matters the most to them.
Experiences of family caregivers taking care getting lost of persons with dementia: a qualitative study
Authors: Li Shu-Hui , Wu Shu-Fang Vivienne , Liu Chieh-Yu , Lin Chiou-Fen , Lin Hung-Ru 
Published: June 2024

Abstract
Background
Getting lost with family members who have dementia is a significant source of stress for family caregivers. In Taiwan, family caregivers develop strategies to deal with dementia persons who may get lost. This study aimed to explore the experiences of family caregivers caring for persons with dementia who have been lost outside the home.

Methods
A descriptive phenomenological method was used. The COREQ checklist was used to ensure the explicit reporting of data. A total of 20 family caregivers caring for persons with dementia who were lost outside their homes were selected from hospital outpatient clinics and a day care center in northern Taiwan using purposive sampling. Data were analyzed using the Giorgi analysis method.

Results
Five main themes emerged: (i) surprised persons with dementia lost outside, (ii) using strategies to prevent persons with dementia from getting lost, (iii) using strategies to find lost persons with dementia, (iv) exhaustion in long-term care persons with dementia, and (v) coping with the care load. It was found that family caregivers were surprised, nervous, and worried about persons with dementia being lost outside. They used the first strategy to supervise persons with dementia to prevent external losses. In addition, long-term supervision of persons with dementia led to mental exhaustion in the family caregivers. Finally, the family caregivers learned about loss prevention strategies and obtained family support and care replacement workers to reduce the care burden.

Conclusions
It is essential to teach family caregivers early to prevent persons with dementia from losing external strategies. Nurses also provide long-term care services to reduce the care burden on family caregivers.