bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and agro-morphological characterization of new barley genotypes in arid environments
Authors: Elshafei Adel A. , Ibrahim Eid I. , Abdellatif Kamal F. , Salem Abd El-Azeem K. , Moustafa Khaled A. , Al-Doss Abdullah A. , Migdadi Hussein M. , Hussien Amal M. , Soufan Walid , Abd El Rahman Taha , Eldemery Samah M. 
Published: June 2024

Abstract
Background
Genetic diversity, population structure, agro-morphological traits, and molecular characteristics, are crucial for either preserving genetic resources or developing new cultivars. Due to climate change, water availability for agricultural use is progressively diminishing. This study used 100 molecular markers (25 TRAP, 22 SRAP, 23 ISTR, and 30 SSR). Additionally, 15 morphological characteristics were utilized to evaluate the optimal agronomic traits of 12 different barley genotypes under arid conditions.

Results
Substantial variations, ranging from significant to highly significant, were observed in the 15 agromorphological parameters evaluated among the 12 genotypes. The KSU-B101 barley genotype demonstrated superior performance in five specific traits: spike number per plant, 100-grain weight, spike number per square meter, harvest index, and grain yield. These results indicate its potential for achieving high yields in arid regions.
The Sahrawy barley genotype exhibited the highest values across five parameters, namely leaf area, spike weight per plant, spike length, spike weight per square meter, and biological yield, making it a promising candidate for animal feed. The KSU-B105 genotype exhibited early maturity and a high grain count per spike, which reflects its early maturity and ability to produce a high number of grains per spike. This suggests its suitability for both animal feed and human food in arid areas. Based on marker data, the molecular study found that the similarity coefficients between the barley genotypes ranged from 0.48 to 0.80, with an average of 0.64. The dendrogram constructed from these data revealed three distinct clusters with a similarity coefficient of 0.80. Notably, the correlation between the dendrogram and its similarity matrix was high (0.903), indicating its accuracy in depicting the genetic relationships. The combined analysis revealed a moderate correlation between the morphological and molecular analysis, suggesting alignment between the two characterization methods.

Conclusions
The morphological and molecular analyses of the 12 barley genotypes in this study effectively revealed the varied genetic characteristics of their agro-performance in arid conditions. KSU-B101, Sahrawy, and KSU-B105 have emerged as promising candidates for different agricultural applications in arid regions. Further research on these genotypes could reveal their full potential for breeding programs.
The relationship between ambulance team’s professional commitment, occupational anxiety, and resilience levels
Authors: Uysal İbrahim , Korkmaz Güneş , Toraman Çetin 
Published: June 2024

AbstractBackgroundIndividuals who have the ability to bounce back from stressful events, to recover from their troubles and adverse environmental conditions by getting stronger each time are known as resilient people. Some professions may cause more occupational anxiety than others due to their characteristics and working conditions. In this research, we aimed to develop a professional commitment scale for the ambulance team. Another aim was to analyze the relationships between professional commitment, occupational anxiety, resilience, gender, job, seniority and working unit variables.MethodsIn the study, data were collected from a total of 1142 emergency ambulance workers working in Emergency Ambulance and Emergency Call Centers in 34 different cities in Turkey. Data were collected using the “Professional Commitment of Ambulance Team Scale (PCATS), Occupational Anxiety Scale for Emergency Medical Service Professionals (OASEMSP), and Resilience Scale for Adults (RSA). Scale development analyses were carried out using Classical Test Theory (CTT) and Item Response Theory (IRT). Regression analysis were used to examine the relationships between professional commitment, occupational anxiety, resilience, gender, job, seniority and working unit.ResultsAs a result of the exploratory factor analysis (EFA), it was determined that 8 items remaining in the professional commitment scale formed a single-factor structure, explaining 46% of the variance of professional commitment of the team. The Cronbach’s Alpha reliability value was 0.867. Confirmatory factor analysis (CFA) confirmed the results of exploratory factor analysis. The Cronbach’s Alpha reliability coefficient obtained through CTT was 0.868, and the marginal reliability coefficient within the scope of IRT was 0.877. The test-retest reliability coefficient was calculated as 0.832, which indicates that the scale is valid and reliable.ConclusionsThe study revealed that resilience has a positive effect for professional commitment while occupational anxiety has a negative effect for professional commitment. In addition, having a moderate seniority has a negative (reducing) effect for professional commitment. Other variables (gender, job, and working unit) was found to have no significant impact on professional commitment.
Mechanism of ERBB2 gene overexpression by the formation of super-enhancer with genomic structural abnormalities in lung adenocarcinoma without clinically actionable genetic alterations
Authors: Kaneko Syuzo , Takasawa Ken , Asada Ken , Shiraishi Kouya , Ikawa Noriko , Machino Hidenori , Shinkai Norio , Matsuda Maiko , Masuda Mari , Adachi Shungo , Takahashi Satoshi , Kobayashi Kazuma , Kouno Nobuji , Bolatkan Amina , Komatsu Masaaki , Yamada Masayoshi , Miyake Mototaka , Watanabe Hirokazu , Tateishi Akiko , Mizuno Takaaki , Okubo Yu , Mukai Masami , Yoshida Tatsuya , Yoshida Yukihiro , Horinouchi Hidehito , Watanabe Shun-Ichi , Ohe Yuichiro , Yatabe Yasushi , Saloura Vassiliki , Kohno Takashi , Hamamoto Ryuji 
Published: June 2024

Abstract
Background
In an extensive genomic analysis of lung adenocarcinomas (LUADs), driver mutations have been recognized as potential targets for molecular therapy. However, there remain cases where target genes are not identified. Super-enhancers and structural variants are frequently identified in several hundred loci per case. Despite this, most cancer research has approached the analysis of these data sets separately, without merging and comparing the data, and there are no examples of integrated analysis in LUAD.

Methods
We performed an integrated analysis of super-enhancers and structural variants in a cohort of 174 LUAD cases that lacked clinically actionable genetic alterations. To achieve this, we conducted both WGS and H3K27Ac ChIP-seq analyses using samples with driver gene mutations and those without, allowing for a comprehensive investigation of the potential roles of super-enhancer in LUAD cases.

Results
We demonstrate that most genes situated in these overlapped regions were associated with known and previously unknown driver genes and aberrant expression resulting from the formation of super-enhancers accompanied by genomic structural abnormalities. Hi-C and long-read sequencing data further corroborated this insight. When we employed CRISPR-Cas9 to induce structural abnormalities that mimicked cases with outlier ERBB2 gene expression, we observed an elevation in ERBB2 expression. These abnormalities are associated with a higher risk of recurrence after surgery, irrespective of the presence or absence of driver mutations.

Conclusions
Our findings suggest that aberrant gene expression linked to structural polymorphisms can significantly impact personalized cancer treatment by facilitating the identification of driver mutations and prognostic factors, contributing to a more comprehensive understanding of LUAD pathogenesis.
Efficiency of hospitals in COVID-19 era: a case study of an affected country
Authors: Hamdollahzadeh Anita , Nabilou Bahram , Yusefzadeh Hasan 
Published: June 2024

Abstract
Background
The COVID-19 pandemic has affected all aspects of human life and society and has damaged the global economy. Health systems and hospitals were not exempted from this situation. The performance of hospitals during the COVID-19 pandemic was affected by policies related to the pandemic and other factors. This study aimed to investigate hospital performance indicators such as admissions and revenue.

Methods
The medical records of patients with selected orthopedic and general surgical diseases were studied in two government hospitals in the capital city of Urmia in the second quarter of 2019, with the same period in 2020. Data were extracted based on the number of medical records, including length of stay, hospitalization type, sex, age, insurance, number of deaths, and readmissions from the medical records department. Payment amounts were collected from the revenue department and Hospital Information System. Two performance indicators, two result indicators, and two control indicators were used. Mean disease-specific revenue, total revenue, length of stay, and bed occupancy rate were calculated for both periods. Data were analyzed using SPSS (version 16) and the Mann-Whitney statistical test.

Results
2140 cases were studied in the two disease groups. An increase was observed in the number of hospitalizations and average length of stay during the pandemic. The mean disease-specific revenue in the quarter of 2020 was higher than in 2019. However, total revenue decreased, and the difference in the mean of total revenue was significant for the two years (P = 0.00) in teaching center. The number of readmissions remained unchanged throughout in the pandemic. The number of deaths due to general surgery diseases in 2020 compared to the same period in 2019 was associated with a relative increase.

Conclusions
The COVID-19 pandemic increased the slope of health care costs. The analysis of the studied variables as performance, result, and control indicators showed that hospitalization rate, bed occupancy rate, and total revenue followed a similar and decreasing pattern in the selected hospitals during the COVID-19 pandemic. Hospitals should adopt appropriate strategies so that, in conditions identical to the COVID-19 pandemic, their performance is accompanied by proper management of resources, efficiency, and minimal reduction in revenue.
Co-evolution of vaginal microbiome and cervical cancer
Authors: Hu Menglu , Yang Wentao , Yan Ruiyi , Chi Jiayu , Xia Qi , Yang Yilin , Wang Yinhan , Sun Lejia , Li Ping 
Published: June 2024

Abstract
Background
Exploration of adaptive evolutionary changes at the genetic level in vaginal microbial communities during different stages of cervical cancer remains limited. This study aimed to elucidate the mutational profile of the vaginal microbiota throughout the progression of cervical disease and subsequently establish diagnostic models.

Methods
This study utilized a metagenomic dataset consisting of 151 subjects classified into four categories: invasive cervical cancer (CC) (n = 42), cervical intraepithelial neoplasia (CIN) (n = 43), HPV-infected (HPVi) patients without cervical lesions (n = 34), and healthy controls (n = 32). The analysis focused on changes in microbiome abundance and extracted information on genetic variation. Consequently, comprehensive multimodal microbial signatures associated with CC, encompassing taxonomic alterations, mutation signatures, and enriched metabolic functional pathways, were identified. Diagnostic models for predicting CC were established considering gene characteristics based on single nucleotide variants (SNVs).

Results
In this study, we screened and analyzed the abundances of 18 key microbial strains during CC progression. Additionally, 71,6358 non-redundant mutations were identified, predominantly consisting of SNVs that were further annotated into 25,773 genes. Altered abundances of SNVs and mutation types were observed across the four groups. Specifically, there were 9847 SNVs in the HPV-infected group and 14,892 in the CC group. Furthermore, two distinct mutation signatures corresponding to the benign and malignant groups were identified. The enriched metabolic pathways showed limited similarity with only two overlapping pathways among the four groups. HPVi patients exhibited active nucleotide biosynthesis, whereas patients with CC demonstrated a significantly higher abundance of signaling and cellular-associated protein families. In contrast, healthy controls showed a distinct enrichment in sugar metabolism. Moreover, biomarkers based on microbial SNV abundance displayed stronger diagnostic capability (cc.AUC = 0.87) than the species-level biomarkers (cc.AUC = 0.78). Ultimately, the integration of multimodal biomarkers demonstrated optimal performance for accurately identifying different cervical statuses (cc.AUC = 0.86), with an acceptable performance (AUC = 0.79) in the external testing set.

Conclusions
The vaginal microbiome exhibits specific SNV evolution in conjunction with the progression of CC, and serves as a specific biomarker for distinguishing between different statuses of cervical disease.
Entomophagy and entomo-therapeutic practices in a mountainous territory in southeast Guangxi Zhuang Autonomous Region, China
Authors: Luo Huimin , Dai Chuanyin , Feng Ping 
Published: June 2024

Abstract
Background
Although China has a long history of using insects as food and medicine and has developed numerous associated knowledge and practices, especially in its rural and mountainous areas, systematic surveys concerning this subject are limited. In-depth ethnobiological research is needed to compile a comprehensive database of edible and medicinal insects and record the associated knowledge of these food and medicinal resources.

Methods
Data on edible and medicinal insects and associated knowledge about them were collected by interviewing 216 local villagers in a mountainous territory in southeast Guangxi Zhuang Autonomous Region, China.

Results
Local villagers used at least 16 edible and 9 medicinal insects, of which 4 wasp species were used in both entomophagy and medicinal practices. Parapolybia varia, Polistes olivaceus, and Anomala chamaeleon were newly recorded edible insects in China. The wasps, Euconocephalus sp., Gryllotalpa orientalis, and Cyrtotrachelus longimanus, were preferred and culturally important edible insects. Populations of Euconocephalus sp. and G. orientalis were reported to have substantially decreased in recent years. Wasps and a bamboo bee were used to treat rheumatism, while cockroaches and antlions were used to treat common cold symptoms in infants. Insect-related knowledge was positively correlated with the interviewees’ age.

Conclusions
Villagers have accumulated considerable local and traditional knowledge of entomophagy and entomo-therapeutic practices. However, this knowledge is in danger of being lost, which highlights the urgent need to document this information. Edible insects enrich local diets, and a more sustainable supply (such as through insect farming) could maintain local entomophagy practices. Medicinal insects are a part of local folk medicine, and pharmacological and chemical techniques could be applied to identify various biologically active substances in these insects.
Internal initiation of reverse transcription in a Penelope-like retrotransposon
Authors: Frangieh Chris J. , Wilkinson Max E. , Strebinger Daniel , Strecker Jonathan , Walsh Michelle L. , Faure Guilhem , Yushenova Irina A. , Macrae Rhiannon K. , Arkhipova Irina R. , Zhang Feng 
Published: June 2024

AbstractEukaryotic retroelements are generally divided into two classes: long terminal repeat (LTR) retrotransposons and non-LTR retrotransposons. A third class of eukaryotic retroelement, the Penelope-like elements (PLEs), has been well-characterized bioinformatically, but relatively little is known about the transposition mechanism of these elements. PLEs share some features with the R2 retrotransposon from Bombyx mori, which uses a target-primed reverse transcription (TPRT) mechanism, but their distinct phylogeny suggests PLEs may utilize a novel mechanism of mobilization. Using protein purified from E. coli, we report unique in vitro properties of a PLE from the green anole (Anolis carolinensis), revealing mechanistic aspects not shared by other retrotransposons. We found that reverse transcription is initiated at two adjacent sites within the transposon RNA that is not homologous to the cleaved DNA, a feature that is reflected in the genomic “tail” signature shared between and unique to PLEs. Our results for the first active PLE in vitro provide a starting point for understanding PLE mobilization and biology.
Evaluation of bovine coronavirus in Korean native calves challenged through different inoculation routes
Authors: Cho Hyung-Chul , Kim Youngjun , Cho Yong-Il , Park Jinho , Choi Kyoung-Seong 
Published: June 2024

AbstractBovine coronavirus (BCoV) is a pneumoenteric virus that can infect the digestive and respiratory tracts of cattle, resulting in economic losses. Despite its significance, information regarding BCoV pathogenesis is limited. Hence, we investigated clinical signs, patterns of viral shedding, changes in antibody abundance, and cytokine/chemokine production in calves inoculated with BCoV via intranasal and oral. Six clinically healthy Korean native calves (< 30 days old), initially negative for BCoV, were divided into intranasal and oral groups and monitored for 15 days post-infection (dpi). BCoV-infected calves exhibited clinical signs such as nasal discharge and diarrhea, starting at 3 dpi and recovering by 12 dpi, with nasal discharge being the most common symptoms. Viral RNA was detected in nasal and fecal samples from all infected calves. Nasal shedding occurred before fecal shedding regardless of the inoculation route; however, fecal shedding persisted longer. Although the number of partitions was very few, viral RNA was identified in the blood of two calves in the oral group at 7 dpi and 9 dpi using digital RT-PCR analysis. The effectiveness of maternal antibodies in preventing viral replication and shedding appeared limited. Our results showed interleukin (IL)-8 as the most common and highly induced chemokine. During BCoV infection, the levels of IL-8, monocyte chemoattractant protein-1, and macrophage inflammatory protein-1β were significantly affected, suggesting that these emerge as potential and reliable biomarkers for predicting BCoV infection. This study underscores the importance of BCoV as a major pathogen causing diarrhea and respiratory disease.
Stress drops of intermediate-depth intraslab earthquakes beneath Tohoku, northern Japan
Authors: Kita Saeko , Shiina Takahiro , Houston Heidi , Shiomi Katsuhiko 
Published: June 2024

AbstractWe calculated stress drops for 2875 small intraslab earthquakes at intermediate depths beneath Tohoku, Japan. We applied an S-coda-wave spectral ratio method to almost 900,000 event pairs. Detailed velocity values for the oceanic crust (OC) were adopted from previous observational studies. The median stress drops in the OC are about half those in the oceanic mantle (OM). The median stress drop for earthquakes in the OC decreases from depths of 70 to 120 km and increases from 120 to 170 km. Our preferred interpretation is that the rigidity in the OC decreases and then increases with depth due to combined effects of the dehydration associated with the eclogite formation and the increasing temperature with depth. These depth variations are consistent with results of a similar study beneath Hokkaido. The median stress drops in the oceanic plate beneath Tohoku are generally smaller than those beneath Hokkaido. Previous studies imaging the seismic structure at shallow depths and b-value analyses of intraslab earthquakes indicate that the near-trench region of the oceanic plate off Tohoku is more hydrated than that off Hokkaido. Taken together, these results suggest that differences in the degree of hydration of the oceanic plate in the near-trench regions could produce the different behaviors of stress drops of intermediate-depth earthquakes observed in Tohoku and Hokkaido.
Graphical Abstract
Genome-wide enhancer RNA profiling adds molecular links between genetic variation and human cancers
Authors: Cai Yi-Min , Lu Ze-Qun , Li Bin , Huang Jin-Yu , Zhang Ming , Chen Can , Fan Lin-Yun , Ma Qian-Ying , He Chun-Yi , Chen Shuo-Ni , Jiang Yuan , Li Yan-Min , Ning Cai-Bo , Zhang Fu-Wei , Wang Wen-Zhuo , Liu Yi-Zhuo , Zhang Heng , Jin Meng , Wang Xiao-Yang , Han Jin-Xin , Xiong Zhen , Cai Ming , Huang Chao-Qun , Yang Xiao-Jun , Zhu Xu , Zhu Ying , Miao Xiao-Ping , Zhang Shao-Kai , Wei Yong-Chang , Tian Jian-Bo 
Published: June 2024

Abstract
Background
Dysregulation of enhancer transcription occurs in multiple cancers. Enhancer RNAs (eRNAs) are transcribed products from enhancers that play critical roles in transcriptional control. Characterizing the genetic basis of eRNA expression may elucidate the molecular mechanisms underlying cancers.

Methods
Initially, a comprehensive analysis of eRNA quantitative trait loci (eRNAQTLs) was performed in The Cancer Genome Atlas (TCGA), and functional features were characterized using multi-omics data. To establish the first eRNAQTL profiles for colorectal cancer (CRC) in China, epigenomic data were used to define active enhancers, which were subsequently integrated with transcription and genotyping data from 154 paired CRC samples. Finally, large-scale case-control studies (34,585 cases and 69,544 controls) were conducted along with multipronged experiments to investigate the potential mechanisms by which candidate eRNAQTLs affect CRC risk.

Results
A total of 300,112 eRNAQTLs were identified across 30 different cancer types, which exert their influence on eRNA transcription by modulating chromatin status, binding affinity to transcription factors and RNA-binding proteins. These eRNAQTLs were found to be significantly enriched in cancer risk loci, explaining a substantial proportion of cancer heritability. Additionally, tumor-specific eRNAQTLs exhibited high responsiveness to the development of cancer. Moreover, the target genes of these eRNAs were associated with dysregulated signaling pathways and immune cell infiltration in cancer, highlighting their potential as therapeutic targets. Furthermore, multiple ethnic population studies have confirmed that an eRNAQTL rs3094296-T variant decreases the risk of CRC in populations from China (OR = 0.91, 95%CI 0.88–0.95, P = 2.92 × 10−7) and Europe (OR = 0.92, 95%CI 0.88–0.95, P = 4.61 × 10−6). Mechanistically, rs3094296 had an allele-specific effect on the transcription of the eRNA ENSR00000155786, which functioned as a transcriptional activator promoting the expression of its target gene SENP7. These two genes synergistically suppressed tumor cell proliferation. Our curated list of variants, genes, and drugs has been made available in CancereRNAQTL (http://canernaqtl.whu.edu.cn/#/) to serve as an informative resource for advancing this field.

Conclusion
Our findings underscore the significance of eRNAQTLs in transcriptional regulation and disease heritability, pinpointing the potential of eRNA-based therapeutic strategies in cancers.