bluuebunny/crossref_metadata_2025_split huggingface dataset:
What we know about Turkey oak (Quercus cerris L.) — from evolutionary history to species ecology
Authors: Lados Botond B , Benke Attila , Borovics Attila , Köbölkuti Zoltán A , Molnár Csilla É , Nagy László , Tóth Endre Gy , Cseke Klára 
Published: July 2024

Abstract
Turkey oak (Quercus cerris L.) is a deciduous tree species of the genus Quercus section Cerris (Fagaceae), widely distributed in Europe and Asia Minor. Throughout its vast distribution range, the species carries high phenotypic and genetic variability. Due to its high drought tolerance, Turkey oak may have great potential to be a key tree species in Central and Western Europe under climate change conditions. However, more detailed information on its phylogeny, phylogeography, phenotypic, and genetic variability is still needed for a more careful and reliable assessment of the species’ adaptation potential. To this end, based on 41 reviewed articles, we collected detailed information to support the evaluation of Turkey oak’s adaptation potential under climate change. In the reviewed articles, we observed a significantly lower number of genetic studies of the members of the section Cerris (especially the Euro-Mediterranean species) relative to the subgenus Quercus. We also identified research gaps with respect to the functional and population genetics of the species that should be addressed in the future. Nevertheless, the different evolutionary background and adaptation strategies of Turkey oak as compared to Central European white oaks, as well as its high phenotypic and genetic variability, may indeed represent a great potential for this species to support the climate adaptation of forestry in Central and Western Europe.
Dominant suppressor genes of p53-induced apoptosis in Drosophila melanogaster
Authors: Szlanka Tamás , Lukacsovich Tamás , Bálint Éva , Virágh Erika , Szabó Kornélia , Hajdu Ildikó , Molnár Enikő , Lin Yu-Hsien , Zvara Ágnes , Kelemen-Valkony Ildikó , Méhi Orsolya , Török István , Hegedűs Zoltán , Kiss Brigitta , Ramasz Beáta , Magdalena Laura M , Puskás László , Mechler Bernard M , Fónagy Adrien , Asztalos Zoltán , Steinbach Gábor , Žurovec Michal , Boros Imre , Kiss István 
Published: July 2024

Abstract
One of the major functions of programmed cell death (apoptosis) is the removal of cells that suffered oncogenic mutations, thereby preventing cancerous transformation. By making use of a Double-Headed-EP (DEP) transposon, a P element derivative made in our laboratory, we made an insertional mutagenesis screen in Drosophila melanogaster to identify genes that, when overexpressed, suppress the p53-activated apoptosis. The DEP element has Gal4-activatable, outward-directed UAS promoters at both ends, which can be deleted separately in vivo. In the DEP insertion mutants, we used the GMR-Gal4 driver to induce transcription from both UAS promoters and tested the suppression effect on the apoptotic rough eye phenotype generated by an activated UAS-p53 transgene. By DEP insertions, 7 genes were identified, which suppressed the p53-induced apoptosis. In 4 mutants, the suppression effect resulted from single genes activated by 1 UAS promoter (Pka-R2, Rga, crol, and Spt5). In the other 3 (Orct2, Polr2M, and stg), deleting either UAS promoter eliminated the suppression effect. In qPCR experiments, we found that the genes in the vicinity of the DEP insertion also showed an elevated expression level. This suggested an additive effect of the nearby genes on suppressing apoptosis. In the eukaryotic genomes, there are coexpressed gene clusters. Three of the DEP insertion mutants are included, and 2 are in close vicinity of separate coexpressed gene clusters. This raises the possibility that the activity of some of the genes in these clusters may help the suppression of the apoptotic cell death.
The core competencies of a health education teacher
Authors: Paakkari Olli , Kulmala Markus , Lyyra Nelli , Saaranen Terhi , Lindfors Pirjo , Tyrväinen Heli 
Published: July 2024

Abstract
Teachers play a crucial role in students’ learning and in the development of health literacy. Hence, the aim of this study was to identify the core competencies needed for teachers of health education in supporting student learning. A three-round Delphi study was carried out over an 8-week period, through consultation with 25 Finnish experts in health education. An open-ended question was used to identify the core competencies for school health educators. The data were analysed using inductive content analysis. In subsequent rounds, experts were asked to assess the importance of the identified competencies on a 7-point Likert scale, and finally to rank the most important competencies. In total, 52 competencies were identified and categorized into eight core competence domains. Thereafter, 40 competencies were assessed and selected for the third round, in which the experts ranked the 15 most important competencies, encompassing four core domains, i.e. pedagogic and subject-specific didactic, social and emotional, content knowledge and continuous professional development. Other domains of competence identified in the present study were ethical competence, competence in school health promotion, contextual competence and professional well-being competence. The study defines health education teacher core competencies and domains, and the information can be used in teacher education programmes, for developing teaching and for teachers’ self-evaluation.
Joint models reveal genetic architecture of pubertal stage transitions and their association with BMI in admixed Chilean population
Authors: Vicuña Lucas , Barrientos Esteban , Leiva-Yamaguchi Valeria , Alvares Danilo , Mericq Veronica , Pereira Anita , Eyheramendy Susana 
Published: July 2024

Abstract
Early or late pubertal onset can lead to disease in adulthood, including cancer, obesity, type 2 diabetes, metabolic disorders, bone fractures, and psychopathologies. Thus, knowing the age at which puberty is attained is crucial as it can serve as a risk factor for future diseases. Pubertal development is divided into five stages of sexual maturation in boys and girls according to the standardized Tanner scale. We performed genome-wide association studies (GWAS) on the “Growth and Obesity Chilean Cohort Study” cohort composed of admixed children with mainly European and Native American ancestry. Using joint models that integrate time-to-event data with longitudinal trajectories of body mass index (BMI), we identified genetic variants associated with phenotypic transitions between pairs of Tanner stages. We identified $42$ novel significant associations, most of them in boys. The GWAS on Tanner $3\rightarrow 4$ transition in boys captured an association peak around the growth-related genes LARS2 and LIMD1 genes, the former of which causes ovarian dysfunction when mutated. The associated variants are expression and splicing Quantitative Trait Loci regulating gene expression and alternative splicing in multiple tissues. Further, higher individual Native American genetic ancestry proportions predicted a significantly earlier puberty onset in boys but not in girls. Finally, the joint models identified a longitudinal BMI parameter significantly associated with several Tanner stages’ transitions, confirming the association of BMI with pubertal timing.
SlTrxh functions downstream of SlMYB86 and positively regulates nitrate stress tolerance via S-nitrosation in tomato seedling
Authors: Zeng Senlin , Sun Xudong , Zhai Jiali , Li Xixian , Pedro García-Caparrós , Nian Hongjuan , Li Kunzhi , Xu Huini 
Published: July 2024

Abstract
Nitric oxide (NO) is a redox-dependent signaling molecule that plays a crucial role in regulating a wide range of biological processes in plants. It functions by post-translationally modifying proteins, primarily through S-nitrosation. Thioredoxin (Trx), a small and ubiquitous protein with multifunctional properties, plays a pivotal role in the antioxidant defense system. However, the regulatory mechanism governing the response of tomato Trxh (SlTrxh) to excessive nitrate stress remains unknown. In this study, overexpression or silencing of SlTrxh in tomato led to increased or decreased nitrate stress tolerance, respectively. The overexpression of SlTrxh resulted in a reduction in levels of reactive oxygen species (ROS) and an increase in S-nitrosothiol (SNO) contents; conversely, silencing SlTrxh exhibited the opposite trend. The level of S-nitrosated SlTrxh was increased and decreased in SlTrxh overexpression and RNAi plants after nitrate treatment, respectively. SlTrxh was found to be susceptible to S-nitrosation both in vivo and in vitro, with Cysteine 54 potentially being the key site for S-nitrosation. Protein interaction assays revealed that SlTrxh physically interacts with SlGrx9, and this interaction is strengthened by S-nitrosation. Moreover, a combination of yeast one-hybrid (Y1H), electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR), and transient expression assays confirmed the direct binding of SlMYB86 to the SlTrxh promoter, thereby enhancing its expression. SlMYB86 is located in the nucleus and SlMYB86 overexpressed and knockout tomato lines showed enhanced and decreased nitrate stress tolerance, respectively. Our findings indicate that SlTrxh functions downstream of SlMYB86 and highlight the potential significance of S-nitrosation of SlTrxh in modulating its function under nitrate stress.
Development of super-infective ternary vector systems for enhancing the Agrobacterium-mediated plant transformation and genome editing efficiency
Authors: Jeong Jin-hee , Jeon Eun-young , Hwang Min Ki , Song Young Jong , Kim Jae-Yean 
Published: July 2024

Abstract
Agrobacterium-mediated transformation remains a cornerstone of plant biology, fueling advancements in molecular genetics, new genomic techniques (NGTs), and the biotech industry. However, recalcitrant crops and technical hurdles persist as bottlenecks. The goal was to develop super-infective ternary vector systems that integrate a novel salicylic acid-degrading enzyme, GABA, and ethylene-degrading enzymes, targeting the transformation of crops by neutralizing plant defense system on Agrobacterium. Firstly, both the effect and activity of introducing enzymes were validated in EHA105, an important Agrobacterium strain. Our study demonstrates that all ternary vector (Tv) system variants significantly enhance reporter expression in transient assays with Nicotiana benthamiana and Cannabis sativa. Specifically, incorporating a constitutive virG mutation with novel enzyme combinations increased GFP and RUBY expression in C. sativa by &gt;5-fold and 13-fold, respectively. The Tv system, combined with a geminivirus replicon, markedly boosted GUS gene expression in tomato, enhancing genome editing efficiency. Notably, compared to controls, Tv-VS demonstrated up to 18-fold and 4.5-fold increases in genome editing efficiency in C. sativa and tomato, respectively. Additionally, stable transformation rates in tomato and Arabidopsis improved significantly, with Tv-VS showing a remarkable 2.5-fold increase in transformation efficiency compared to control strains. The research marks notable progress in Agrobacterium-mediated plant transformation. The innovative ternary vectors overcome plant defense mechanisms, enabling genetic manipulation in previously challenging plant species. This development is anticipated to broaden the applications of plant genetic engineering, contributing to advancements in crop genome editing.
Single-cell RNA sequencing reveals a high-resolution cell atlas of petals in Prunus mume at different flowering development stages
Authors: Guo Yuhong , Chen Xiling , Li Jinhong , Wang Qi , Zhang Shuangyu , Liu Nuoxuan , Zhang Yanlong , Zhang Tengxun 
Published: July 2024

Abstract
Prunus mume (mei), a traditional ornamental plant in China, is renowned for its fragrant flowers, primarily emitted by its petals. However, the cell types of mei petals and where floral volatile synthesis occurs are rarely reported. The study used single-cell RNA sequencing to characterize the gene expression landscape in petals of P. mume ‘Fenhong Zhusha’ at budding stage (BS) and full-blooming stage (FS). Six major cell types of petals were identified: epidermal cells (ECs), parenchyma cells (PCs), xylem parenchyma cells, phloem parenchyma cells, xylem vessels and fibers, and sieve elements and companion cells complex. Cell-specific marker genes in each cell type were provided. Floral volatiles from mei petals were measured at four flowering development stages, and their emissions increased from BS to FS, and decreased at the withering stage. Fifty-eight differentially expressed genes (DEGs) in benzenoid/phenylpropanoid pathway were screened using bulk RNA-seq data. Twenty-eight DEGs expression increased from BS to FS, indicating that they might play roles in floral volatile synthesis in P. mume, among which PmBAHD3 would participate in benzyl acetate synthesis. ScRNA-seq data showed that 27 DEGs mentioned above were expressed variously in different cell types. In situ hybridization confirmed that PmPAL2, PmCAD1, PmBAHD3,5, and PmEGS1 involved in floral volatile synthesis in mei petals are mainly expressed in EC, PC, and most vascular tissues, consistent with scRNA-seq data. The result indicates that benzyl acetate and eugenol, the characteristic volatiles in mei, are mostly synthesized in these cell types. The first petal single-cell atlas was constructed, offering new insights into the molecular mechanism of floral volatile synthesis.
Association analysis of BSA-seq, BSR-seq, and RNA-seq reveals key genes involved in purple leaf formation in a tea population (Camellia sinensis)
Authors: Wang Yueqi , Jin Ji-Qiang , Zhang Rui , He Mengdi , Wang Liubin , Mao Zhuozhuo , Gan Min , Wu Liyun , Chen Liang , Wang Liyuan , Wei Kang 
Published: July 2024

Abstract
Purple tea, rich in anthocyanins, has a variety of health benefits and is attracting global interest. However, the regulation mechanism of anthocyanin in purple tea populations has not been extensively studied. In this experiment, RNA-seq, BSA-seq, and BSR-seq were performed using 30 individuals with extreme colors (dark-purple and green) in an F1 population of ‘Zijuan’ and ‘Jinxuan’. The results show that 459 genes were differentially expressed in purple and green leaves, among which genes involved in the anthocyanin synthesis and transport pathway, such as CHS, F3H, ANS, MYB75, GST, MATE, and ABCC, were highly expressed in purple leaves. Moreover, there were multiple SNP/InDel variation sites on chromosomes 2 and 14 of the tea plant, as identified by BSA-seq. The integrated analysis identified two highly expressed genes (CsANS and CsMYB75) with SNP/InDel site variations in the purple tea plants. By silencing leaves, we proved that CsMYB75 could positively regulate anthocyanin accumulation and expression of related structural genes in tea plants. A 181-bp InDel in the CsMYB75 promoter was also found to be co-segregating with leaf color. The results of this study provide a theoretical reference for the molecular mechanism of anthocyanin accumulation in purple tea plants and contribute to the creation of new tea cultivars with high anthocyanin content.
Extended remdesivir administration in haematological patients with malignancies and COVID-19 during the Omicron era: safety and outcomes
Authors: Gras Emmanuelle , Aiello Tommaso Francesco , Chumbita Mariana , Gallardo-Pizarro Antonio , Monzó-Gallo Patricia , Teijón-Lumbreras Christian , Suárez-Lledó Maria , Magnano Laura , Tuset Montse , Marcos Maria Ángeles , Soriano Alex , Garcia-Vidal Carolina 
Published: July 2024

Abstract

Objectives
To describe the management of haematological patients experiencing prolonged SARS-CoV-2 viral shedding, as the optimal management strategy for this condition remains undetermined.

Methods
We conducted a retrospective evaluation of our prospectively followed cohort of haematological patients treated with remdesivir for more than 10 days. Starting January 2023, upon COVID-19 diagnosis, the treatment strategy was based on symptoms and PCR cycle threshold (Ct) as follows: (i) when Ct was 25 or less or if the patient had symptoms, a course of remdesivir for at least 10 days, nirmatrelvir/ritonavir for 5 days (whenever possible) and convalescent plasma was administered; and (ii) when the patient was asymptomatic and had a PCR Ct of more than 25, when possible, a course of 5 days of nirmatrelvir/ritonavir was administered. The patient was considered to have achieved viral clearance and, thus, remdesivir was stopped, in either of these cases: (i) PCR negativity, or (ii) subgenomic RNA negativity.

Results
From January to November 2023, 18 patients benefited from a safe extended remdesivir administration, resulting in detection of SARS-CoV-2 viral clearance in a median time of 3.5 weeks (IQR 2.6–3.9) (min–max 1.6–8.0). No clinical or biological side effects were detected. No patient died or needed further treatment for their COVID-19 episode.

Conclusions
The extended course of remdesivir, combined with other active therapies for COVID-19 infection, was well tolerated. Cure and virus negativity were obtained in all these high-risk patients.
The bacterial and fungal profiles of patients hospitalized with non-COVID-19 lower respiratory tract infections in Wuhan, China, 2019–2021
Authors: Li Liangyu , Zhang Haiyue , Liu Chan , Wan Lu , Liu Mengling , Li Ruiyun , Liu Hailing , Yin Jing , Shang Min , Luo Yuchuan , Wang Ming , Wu Xiaojun 
Published: July 2024

Abstract

Aims
A severe lockdown occurred in Wuhan during the COVID-19 pandemic, followed by a remission phase in the pandemic’s aftermath. This study analyzed the bacterial and fungal profiles of respiratory pathogens in patients hospitalized with non-COVID-19 lower respiratory tract infections (LRTIs) during this period to determine the pathogen profile distributions in different age groups and hospital departments in Wuhan.

Methods and results
We collected reports of pathogen testing in the medical records of patients hospitalized with non-COVID-19 LRTI between 2019 and 2021. These cases were tested for bacterial and fungal pathogens using 16S and internal transcribed spacer sequencing methods on bronchoalveolar lavage fluid samples. The study included 1368 cases. The bacteria most commonly identified were Streptococcus pneumoniae (12.50%) and Mycoplasma pneumoniae (8.33%). The most commonly identified fungi were Aspergillus fumigatus (2.49%) and Pneumocystis jirovecii (1.75%). Compared to 2019, the S. pneumoniae detection rates increased significantly in 2021, and those of M. pneumoniae decreased. Streptococcus pneumoniae was detected mainly in children. The detection rates of almost all fungi were greater in the respiratory Intensive Care Unit compared to respiratory medicine. Streptococcus pneumoniae and M. pneumoniae were detected more frequently in the pediatric department.

Conclusions
Before and after the COVID-19 outbreak, a change in the common pathogen spectrum was detected in patients with non-COVID-19 in Wuhan, with the greatest change occurring among children. The major pathogens varied by the patient’s age and the hospital department.
Period circadian regulator 2-mediated steroid hormone synthesis by regulating transcription of steroidogenic acute regulatory protein in porcine granulosa cells
Authors: Zhang Zelin , Cheng Jianyong , Yang Li , Li Xiaoya , Li Qingwang 
Published: July 2024

Abstract
Steroidogenesis is associated with circadian clock genes. However, the regulation of steroid hormone production in sow granulosal cells by Per2, a crucial circadian regulator, remains unexplored. In this study, we have identified the presence of Per2 in ovarian granulosa cells and have observed its circadian expression pattern. Employing siRNA to interfere with Per2 expression, our investigation revealed that Per2 knockdown notably elevated progesterone (P4) levels along with increasing the expression of StAR but interference of Per2 did not alter the rhythm of clock-related gene (Bmal1, Clock, Per1, and Cry1) in granulosa cells. Subsequent mechanistic analysis showed that Per2 formed complexes with PPARγ and interference with Per2 promoted the formation of the PPARγ:RXRα heterodimer. Importantly, we uncovered that PPARγ:RXRα heterodimer could control the expression of StAR via direct peroxisome proliferator response element binding to its promoter to regulate its activity, and knockdown of Per2 promoted the transcription of StAR via increasing the binding of PPARγ:RXRα ligands. Altogether, these findings indicated a noncanonical role of Per2 in controlling PPARγ:RXRα binding to regulate transcription of StAR and progesterone synthesis, thus revealing potential avenues of pharmacological and therapeutic intervention.
Sex chromosome cycle as a mechanism of stable sex determination
Authors: Hayashi Shun , Abe Takuya , Igawa Takeshi , Katsura Yukako , Kazama Yusuke , Nozawa Masafumi 
Published: July 2024

Abstract
Recent advances in DNA sequencing technology have enabled the precise decoding of genomes in non-model organisms, providing a basis for unraveling the patterns and mechanisms of sex chromosome evolution. Studies of different species have yielded conflicting results regarding the traditional theory that sex chromosomes evolve from autosomes via the accumulation of deleterious mutations and degeneration of the Y (or W) chromosome. The concept of the ‘sex chromosome cycle,’ emerging from this context, posits that at any stage of the cycle (i.e., differentiation, degeneration, or loss), sex chromosome turnover can occur while maintaining stable sex determination. Thus, understanding the mechanisms that drive both the persistence and turnover of sex chromosomes at each stage of the cycle is crucial. In this review, we integrate recent findings on the mechanisms underlying maintenance and turnover, with a special focus on several organisms having unique sex chromosomes. Our review suggests that the diversity of sex chromosomes in the maintenance of stable sex determination is underappreciated and emphasizes the need for more research on the sex chromosome cycle.
Utility of the Severity-of-Illness Score for Toxic Epidermal Necrolysis (SCORTEN) in Pediatric Stevens-Johnson Syndrome Patients
Authors: Gust Nina K B , Adams Rebecca M , Frei Ashley , Coughlin Michelle , Klein Justin , Ridelman Elika , Shanti Christina 
Published: July 2024

Abstract
The Severity-of-Illness Score for Toxic Epidermal Necrolysis (SCORTEN) is a system that predicts in-hospital mortality for Stevens-Johnson Syndrome/Toxic Epidermal Necrolysis (SJS/TEN). The system is widely utilized in adults but not in pediatrics. We aim to determine the accuracy of the SCORTEN in pediatrics. A retrospective review of pediatric patients admitted to a verified pediatric burn center with SJS/TEN from 2008 to 2022 was performed. Twenty-four patients were analyzed. Ten patients had 0-1 SCORTEN risk factor, 13 had 2 risk factors, and 1 had 3 risk factors. There was no relationship between initial blood urea nitrogen, bicarbonate, glucose, or initial heart rate on the length of an intensive care unit (ICU) stay or ventilator days. Hospital length of stay and feeding tube days were positively related (P &lt; .001) along with length of stay and maximum total body surface areas (P &lt; .05). Hospital length of stay, ICU length of stay, and ventilator days were not statistically significant between those having 0-1 and 2 risk factors. This study suggests that the SCORTEN system is not useful for pediatrics and a different scoring system is needed, as SCORTEN overestimates mortality and does not have a relationship to outcome measures.