bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytokine profiling in 128 patients with transient abnormal myelopoiesis: a report from the JPLSG TAM-10 trial
Authors: Yamato Genki , Tsumura Yusuke , Muramatsu Hideki , Shimada Akira , Imaizumi Takahiro , Tsukagoshi Hiroyuki , Kaburagi Taeko , Shiba Norio , Yamada Yoshiyuki , Deguchi Takao , Kawai Tomoko , Terui Kiminori , Ito Etsuro , Watanabe Kenichiro , Hayashi Yasuhide 
Published: May 2024

Abstract
Transient abnormal myelopoiesis (TAM) occurs in 10% of neonates with Down syndrome (DS). Although most patients show spontaneous resolution of TAM, early death occurs in ∼20% of cases. Therefore, new biomarkers are needed to predict early death and determine therapeutic interventions. This study aimed to determine the association between clinical characteristics and cytokine levels in patients with TAM. A total of 128 patients with DS with TAM enrolled in the TAM-10 study conducted by the Japanese Pediatric Leukemia/Lymphoma Study Group were included in this study. Five cytokine levels (interleukin-1b [IL-1b], IL-1 receptor agonist, IL-6, IL-8, and IL-13) were significantly higher in patients with early death than in those with nonearly death. Cumulative incidence rates (CIRs) of early death were significantly associated with high levels of the 5 cytokines. Based on unsupervised consensus clustering, patients were classified into 3 cytokine groups: hot-1 (n = 37), hot-2 (n = 42), and cold (n = 49). The CIR of early death was significantly different between the cytokine groups (hot-1/2, n = 79; cold, n = 49; hot-1/2 CIR, 16.5% [95% confidence interval (CI), 7.9-24.2]; cold CIR, 2.0% [95% CI, 0.0-5.9]; P = .013). Furthermore, cytokine groups (hot-1/2 vs cold) were independent poor prognostic factors in the multivariable analysis for early death (hazard ratio, 15.53; 95% CI, 1.434-168.3; P = .024). These results provide valuable information that cytokine level measurement was useful in predicting early death in patients with TAM and might help to determine the need for therapeutic interventions. This trial was registered at UMIN Clinical Trials Registry as #UMIN000005418.
Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus)
Authors: Lu Yan , Liu Dongqi , Kong Xiangjiu , Song Yang , Jing Lan 
Published: May 2024

Abstract
Background
Sunflower (Helianthusannuus) is one of the most important economic crops in oilseed production worldwide. The different cultivars exhibit variability in their resistance genes. The NAC transcription factor (TF) family plays diverse roles in plant development and stress responses. With the completion of the H. annuus genome sequence, the entire complement of genes coding for NACs has been identified. However, the reference genome of a single individual cannot cover all the genetic information of the species.

Results
Considering only a single reference genome to study gene families will miss many meaningful genes. A pangenome-wide survey and characterization of the NAC genes in sunflower species were conducted. In total, 139 HaNAC genes are identified, of which 114 are core and 25 are variable. Phylogenetic analysis of sunflower NAC proteins categorizes these proteins into 16 subgroups. 138 HaNACs are randomly distributed on 17 chromosomes. SNP-based haplotype analysis shows haplotype diversity of the HaNAC genes in wild accessions is richer than in landraces and modern cultivars. Ten HaNAC genes in the basal stalk rot (BSR) resistance quantitative trait loci (QTL) are found. A total of 26 HaNAC genes are differentially expressed in response to Sclerotinia head rot (SHR). A total of 137 HaNAC genes are annotated in Gene Ontology (GO) and are classified into 24 functional groups. GO functional enrichment analysis reveals that HaNAC genes are involved in various functions of the biological process.

Conclusions
We identified NAC genes in H. annuus (HaNAC) on a pangenome-wide scale and analyzed S. sclerotiorum resistance-related NACs. This study provided a theoretical basis for further genomic improvement targeting resistance-related NAC genes in sunflowers.
Annotations of four high-quality indigenous chicken genomes identify more than one thousand missing genes in subtelomeric regions and micro-chromosomes with high G/C contents
Authors: Wu Siwen , Dou Tengfei , Yuan Sisi , Yan Shixiong , Xu Zhiqiang , Liu Yong , Jian Zonghui , Zhao Jingying , Zhao Rouhan , Zi Xiannian , Gu Dahai , Liu Lixian , Li Qihua , Wu Dong-Dong , Jia Junjing , Ge Changrong , Su Zhengchang , Wang Kun 
Published: May 2024

Abstract
Background
Although multiple chicken genomes have been assembled and annotated, the numbers of protein-coding genes in chicken genomes and their variation among breeds are still uncertain due to the low quality of these genome assemblies and limited resources used in their gene annotations. To fill these gaps, we recently assembled genomes of four indigenous chicken breeds with distinct traits at chromosome-level. In this study, we annotated genes in each of these assembled genomes using a combination of RNA-seq- and homology-based approaches.

Results
We identified varying numbers (17,497–17,718) of protein-coding genes in the four indigenous chicken genomes, while recovering 51 of the 274 “missing” genes in birds in general, and 36 of the 174 “missing” genes in chickens in particular. Intriguingly, based on deeply sequenced RNA-seq data collected in multiple tissues in the four breeds, we found 571 ~ 627 protein-coding genes in each genome, which were missing in the annotations of the reference chicken genomes (GRCg6a and GRCg7b/w). After removing redundancy, we ended up with a total of 1,420 newly annotated genes (NAGs). The NAGs tend to be found in subtelomeric regions of macro-chromosomes (chr1 to chr5, plus chrZ) and middle chromosomes (chr6 to chr13, plus chrW), as well as in micro-chromosomes (chr14 to chr39) and unplaced contigs, where G/C contents are high. Moreover, the NAGs have elevated quadruplexes G frequencies, while both G/C contents and quadruplexes G frequencies in their surrounding regions are also high. The NAGs showed tissue-specific expression, and we were able to verify 39 (92.9%) of 42 randomly selected ones in various tissues of the four chicken breeds using RT-qPCR experiments. Most of the NAGs were also encoded in the reference chicken genomes, thus, these genomes might harbor more genes than previously thought.

Conclusion
The NAGs are widely distributed in wild, indigenous and commercial chickens, and they might play critical roles in chicken physiology. Counting these new genes, chicken genomes harbor more genes than originally thought.
Ocular A-to-I RNA editing signatures associated with SARS-CoV-2 infection
Authors: Jin Yun-Yun , Liang Ya-Ping , Huang Wen-Hao , Guo Liang , Cheng Li-Li , Ran Tian-Tian , Yao Jin-Ping , Zhu Lin , Chen Jian-Huan 
Published: May 2024

AbstractOphthalmic manifestations have recently been observed in acute and post-acute complications of COVID-19 caused by SARS-CoV-2 infection. Our precious study has shown that host RNA editing is linked to RNA viral infection, yet ocular adenosine to inosine (A-to-I) RNA editing during SARS-CoV-2 infection remains uninvestigated in COVID-19. Herein we used an epitranscriptomic pipeline to analyze 37 samples and investigate A-to-I editing associated with SARS-CoV-2 infection, in five ocular tissue types including the conjunctiva, limbus, cornea, sclera, and retinal organoids. Our results revealed dramatically altered A-to-I RNA editing across the five ocular tissues. Notably, the transcriptome-wide average level of RNA editing was increased in the cornea but generally decreased in the other four ocular tissues. Functional enrichment analysis showed that differential RNA editing (DRE) was mainly in genes related to ubiquitin-dependent protein catabolic process, transcriptional regulation, and RNA splicing. In addition to tissue-specific RNA editing found in each tissue, common RNA editing was observed across different tissues, especially in the innate antiviral immune gene MAVS and the E3 ubiquitin-protein ligase MDM2. Analysis in retinal organoids further revealed highly dynamic RNA editing alterations over time during SARS-CoV-2 infection. Our study thus suggested the potential role played by RNA editing in ophthalmic manifestations of COVID-19, and highlighted its potential transcriptome impact, especially on innate immunity.
Cis-eQTLs in seven duck tissues identify novel candidate genes for growth and carcass traits
Authors: Cai Wentao , Hu Jian , Zhang Yunsheng , Guo Zhanbao , Zhou Zhengkui , Hou Shuisheng 
Published: May 2024

Abstract
Background
Expression quantitative trait loci (eQTL) studies aim to understand the influence of genetic variants on gene expression. The colocalization of eQTL mapping and GWAS strategy could help identify essential candidate genes and causal DNA variants vital to complex traits in human and many farm animals. However, eQTL mapping has not been conducted in ducks. It is desirable to know whether eQTLs within GWAS signals contributed to duck economic traits.

Results
In this study, we conducted an eQTL analysis using publicly available RNA sequencing data from 820 samples, focusing on liver, muscle, blood, adipose, ovary, spleen, and lung tissues. We identified 113,374 cis-eQTLs for 12,266 genes, a substantial fraction 39.1% of which were discovered in at least two tissues. The cis-eQTLs of blood were less conserved across tissues, while cis-eQTLs from any tissue exhibit a strong sharing pattern to liver tissue. Colocalization between cis-eQTLs and genome-wide association studies (GWAS) of 50 traits uncovered new associations between gene expression and potential loci influencing growth and carcass traits. SRSF4, GSS, and IGF2BP1 in liver, NDUFC2 in muscle, ELF3 in adipose, and RUNDC1 in blood could serve as the candidate genes for duck growth and carcass traits.

Conclusions
Our findings highlight substantial differences in genetic regulation of gene expression across duck primary tissues, shedding light on potential mechanisms through which candidate genes may impact growth and carcass traits. Furthermore, this availability of eQTL data offers a valuable resource for deciphering further genetic association signals that may arise from ongoing extensive endeavors aimed at enhancing duck production traits.
Myrosinase isogenes in wasabi (Wasabia japonica Matsum) and their putative roles in glucosinolate metabolism
Authors: Truong To Quyen , Park Yun Ji , Jeon Je-Seung , Choi Jaeyoung , Koo Song Yi , Choi Yeong Bin , Huynh Phuong Kim , Moon Jinyoung , Kim Sang Min 
Published: May 2024

Abstract
Background
Wasabi, a Brassicaceae member, is well-known for its unique pungent and hot flavor which is produced from glucosinolate (GSL) degradation. Myrosinase (MYR) is a principle enzyme catalyzing the primary conversion of GSLs to GSL hydrolysis products (GHPs) which is responsible for plant defense system and food quality. Due to the limited information in relation to MYRs present in wasabi (Wasabia japonica M.), this study aimed to identify the MYR isogenes in W. japonica and analyze their roles in relation to GSL metabolism.

Results
In results, WjMYRI-1 was abundantly expressed in all organs, whereas WjMYRI-2 showed only trace expression levels. WjMYRII was highly expressed in the aboveground tissues. Interestingly, WjMYRII expression was significantly upregulated by certain abiotic factors, such as methyl jasmonate (more than 40-fold in petioles and 15-fold in leaves) and salt (tenfold in leaves). Young leaves and roots contained 97.89 and 91.17 µmol‧g−1 of GSL, whereas less GSL was produced in mature leaves and petioles (38.36 and 44.79 µmol‧g−1, respectively). Similar pattern was observed in the accumulation of GHPs in various plant organs. Notably, despite the non-significant changes in GSL production, abiotic factors treated samples enhanced significantly GHP content. Pearson’s correlation analysis revealed that WjMYRI-1 expression significantly correlated with GSL accumulation and GHP formation, suggesting the primary role of WjMYRI-1-encoding putative protein in GSL degradation. In contrast, WjMYRII expression level showed no correlation with GSL or GHP content, suggesting another physiological role of WjMYRII in stress-induced response.

Conclusions
In conclusions, three potential isogenes (WjMYRI-1, WjMYRI-2, and WjMYRII) encoding for different MYR isoforms in W. japonica were identified. Our results provided new insights related to MYR and GSL metabolism which are important for the implications of wasabi in agriculture, food and pharmaceutical industry. Particularly, WjMYRI-1 may be primarily responsible for GSL degradation, whereas WjMYRII (clade II) may be involved in other regulatory pathways induced by abiotic factors.
Association between plasma metal exposure and health span in very elderly adults: a prospective cohort study with mixture statistical approach
Authors: Ye Xiaoying , Xu Tingting , Yang Le , Hu Xiangju , Xie Xiaowei , Lan Guohui , Lu Xiaoli , Huang Zelin , Wang Tinggui , Wu Jieyu , Lan Jieli , Zhang Qian , Zhan Zhiying , Guo Yansong , Xie Xiaoxu 
Published: May 2024

Abstract
Background
Metals have been linked to a diverse spectrum of age-related diseases; however, the effects of metal exposure on health span remains largely unknown. This cohort study aims to determine the association between plasma metal and health span in elder adults aged ≥ 90 years.

Methods
The plasma concentrations of seven metals were measured at baseline in 300 elder adults. The end of the health span (EHS) was identified as the occurrence of one of eight major morbidities or mortality events. We used Cox regression to assess hazard ratios (HR). The combined effects of multiple metal mixtures were estimated using grouped-weighted quantile sum (GWQS), quantile g-computation (Q-gcomp), and Bayesian kernel machine regression (BKMR) methods.

Results
The estimated HR for EHS with an inter-quartile range (IQR) increment for selenium (Se) was 0.826 (95% confidence interval [CI]: 0.737–0.926); magnesium (Mg), 0.806 (95% CI: 0.691–0.941); iron (Fe), 0.756 (95% CI: 0.623–0.917), and copper (Cu), 0.856 (95% CI: 0.750–0.976). The P for trend of Se, Mg, and Fe were all < 0.05. In the mixture analyses, Q-gcomp showed a negative correlation with EHS (P = 0.904), with the sum of the negative coefficients being -0.211.

Conclusion
Higher plasma Se, Mg, and Fe reduced the risk of premature end of health span, suggesting that essential metal elements played a role in health maintenance in elder adults.
Association of serum 25-hydroxy-vitamin D concentration and risk of mortality in cancer survivors in the United States
Authors: Mo Xiaofei , He Chen , Han Fengfeng , Yan Hui , Chen Xueqin , Wang Yuetao , Zhou Mingge 
Published: May 2024

Abstract
Purpose
Cancer survivors have a high risk of mortality, and vitamin D (VD) is associated with the risk of mortality. This study is aim to examine the impact of VD on mortality in cancer survivors.

Methods
A prospective study was conducted using data from the National Health and Nutrition Examination Survey. Participants were obtained information on their baseline characteristics, dietary habits, comorbidities, lifestyle, and serum 25-hydroxy VD [25(OH)D] concentrations. The weighted Cox proportional hazard and competing risk regression models were used to estimate the hazard ratio and 95% confidence intervals (HR, 95% CI) of mortality for different serum 25(OH)D concentrations. Restricted cubic spline (RCS) curves were utilized to illustrate the dose–response relationship between serum 25(OH)D concentrations and mortality.

Results
The study encompassed 2,495 participants with cancer diagnoses. Multivariate models indicated that, compared to serum 25(OH)D concentrations below 58.5 nmol/L, concentrations exceeding 81.6 nmol/L were associated with reduced HRs for all-cause mortality (HR = 0.70; 95% CI: 0.56–0.87), cardiovascular mortality (HR = 0.53; 95% CI: 0.32–0.86), and cancer-specific mortality (HR = 0.66; 95% CI: 0.45–0.99). RCS curves revealed “L-shaped” associations between serum 25(OH)D concentration and both all-cause and cancer-specific mortality, with threshold effects at 87.9 nmol/L and 84.6 nmol/L, respectively. Conversely, the relationship between serum 25(OH)D concentration and cardiovascular mortality exhibited a more linear pattern, with a threshold at 88.7 nmol/L. Subgroup analyses highlighted a gender-specific interaction that elevated serum 25(OH)D concentrations were significantly more protective against mortality in males than in females, especially regarding cancer-specific mortality (P-interaction = 0.009).

Conclusion
Elevated serum 25(OH)D concentrations were correlated with decreased risks of all-cause, cardiovascular, and cancer-specific mortality in cancer survivors, with benefit thresholds at 87.9, 88.7, and 84.6 nmol/L, respectively. These findings suggested that cancer survivors might benefit from higher vitamin D recommendations than the general population.
Addressing loneliness and social isolation in 52 countries: a scoping review of National policies
Authors: Goldman Nina , Khanna Devi , El Asmar Marie Line , Qualter Pamela , El-Osta Austen 
Published: May 2024

AbstractBackgroundEven prior to the advent of the COVID-19 pandemic, there was ample evidence that loneliness and social isolation negatively impacted physical and mental health, employability, and are a financial burden on the state. In response, there has been significant policy-level attention on tackling loneliness. The objective of this scoping review was to conduct a loneliness policy landscape analysis across 52 countries of the UN European country groups. Our policy analysis sought to highlight commonalities and differences between the different national approaches to manage loneliness, with the goal to provide actionable recommendations for the consideration of policymakers wishing to develop, expand or review existing loneliness policies.MethodsWe searched governmental websites using the Google search engine for publicly available documents related to loneliness and social isolation. Seventy-eight documents were identified in total, from which 23 documents were retained. Exclusion of documents was based on predetermined criteria. A structured content analysis approach was used to capture key information from the policy documents. Contextual data were captured in a configuration matrix to highlight common and unique themes.ResultsWe could show that most policies describe loneliness as a phenomenon that was addressed to varying degrees in different domains such as social, health, geographical, economic and political. Limited evidence was found regarding funding for suggested interventions. We synthesised actionable recommendations for the consideration of policy makers focusing on the use of language, prioritisation of interventions, revisiting previous campaigns, sharing best practice across borders, setting out a vision, evaluating interventions, and the need for the rapid and sustainable scalability of interventions.ConclusionsOur study provides the first overview of the national loneliness policy landscape, highlighting the increasing prioritisation of loneliness and social isolation as a major public health and societal issue. Our findings suggest that policymakers can sustain this momentum and strengthen their strategies by incorporating rigorous, evidence-based intervention evaluations and fostering international collaborations for knowledge sharing. We believe that policymakers can more effectively address loneliness by directing funds to develop and implement interventions that impact the individual, the community and society.
Exploring pre-pandemic patterns of vaccine decision-making with the 5C model: results from representative surveys in 2016 and 2018
Authors: Eitze Sarah , Felgendreff Lisa , Horstkötter Nina , Seefeld Linda , Betsch Cornelia 
Published: May 2024

Abstract
Background
The 5C psychological antecedents of vaccination (Confidence, Complacency, Constraints, Calculation, and Collective Responsibility) facilitate understanding vaccination decisions in specific target groups as well as the general public’s informational needs. This study aims to explain pre-pandemic vaccination behaviour (a) in general, (b) for specific vaccines such as influenza, and (c) for certain target groups (e.g. people over the age of 59 years, parents, healthcare workers), using the 5C model and sociodemographic variables. The intention to get an influenza vaccination was also analysed for target groups.

Methods
The 5C, self-reported vaccination behaviour and the intention to vaccinate were collected in two representative telephone surveys in Germany – one in 2016 (n1 = 5,012) and another in 2018 (n2 = 5,054). Parents, people over the age of 59 years, chronically ill people, people with a migratory background, pregnant women and healthcare workers were target groups.

Results
Overall, the 5C model had higher explanatory power than sociodemographic variables. The pattern of vaccine hesitancy slightly differed between vaccinations and target groups. Confidence in safety and effectiveness was always a significant predictor. Complacency (the underestimation of disease risks) and Constraints were significant predictors as well. Calculation (of risks and benefits) was important for influenza vaccination intentions.

Conclusions
This work builds an important benchmark for understanding potential changes in vaccine acceptance due to the pandemic. The benchmark can be used in research on potential effects of the pandemic on vaccination behaviours. Intervention designers can also use the results to understand specific audiences and their vaccination decisions.