bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Field Evaluation and Transcriptome Analysis Reveals that Chromosome Doubling Enhances Sheath Blight Resistance in Rice
Authors: Liu Sanglin , Liu Jiahao , Wang Wei , Yan Yugang , Wang Tianya , Wu Jinwen , Liu Xiangdong , Wu Jian , Zeng Yuxiang 
Published: July 2024

AbstractRice sheath blight, caused by Rhizoctonia solani Kihn (R. solani), poses a significant threat to rice production and quality. Autotetraploid rice, developed through chromosome doubling of diploid rice, holds great potential for enhancing biological and yield traits. However, its resistance to sheath blight in the field has remained unclear. In this study, the field resistance of 35 autotetraploid genotypes and corresponding diploids was evaluated across three environments from 2020 to 2021. The booting stage was optimal for inoculating period based on the inoculation and analysis of R. solani at five rice growth stages. We found autotetraploids generally exhibited lower disease scores than diploids, indicating enhanced resistance after chromosome doubling. Among the 35 genotypes, 16 (45.71%) displayed increased resistance, 2 (5.71%) showed decreased resistance, and 17 (48.57%) displayed unstable resistance in different sowing dates. All combinations of the genotype, environment and ploidy, including the genotype-environment-ploidy interaction, contributed significantly to field resistance. Chromosome doubling increased sheath blight resistance in most genotypes, but was also dependent on the genotype-environment interaction. To elucidate the enhanced resistance mechanism, RNA-seq revealed autotetraploid recruited more down-regulated differentially expressed genes (DEGs), additionally, more resistance-related DEGs, were down-regulated at 24 h post inoculation in autotetraploid versus diploid. The ubiquinone/terpenoid quinone and diterpenoid biosynthesis pathways may play key roles in ploidy-specific resistance mechanisms. In summary, our findings shed light on the understanding of sheath blight resistance mechanisms in autotetraploid rice.
Key gene modules and hub genes associated with pyrethroid and organophosphate resistance in Anopheles mosquitoes: a systems biology approach
Authors: Odhiambo Cynthia Awuor , Derilus Dieunel , Impoinvil Lucy Mackenzie , Omoke Diana , Saizonou Helga , Okeyo Stephen , Dada Nsa , Mulder Nicola , Nyamai Dorothy , Nyanjom Steven , Lenhart Audrey , Djogbénou Luc S. , Ochomo Eric 
Published: July 2024

AbstractIndoor residual spraying (IRS) and insecticide-treated nets (ITNs) are the main methods used to control mosquito populations for malaria prevention. The efficacy of these strategies is threatened by the spread of insecticide resistance (IR), limiting the success of malaria control. Studies of the genetic evolution leading to insecticide resistance could enable the identification of molecular markers that can be used for IR surveillance and an improved understanding of the molecular mechanisms associated with IR. This study used a weighted gene co-expression network analysis (WGCNA) algorithm, a systems biology approach, to identify genes with similar co-expression patterns (modules) and hub genes that are potential molecular markers for insecticide resistance surveillance in Kenya and Benin. A total of 20 and 26 gene co-expression modules were identified via average linkage hierarchical clustering from Anopheles arabiensis and An. gambiae, respectively, and hub genes (highly connected genes) were identified within each module. Three specific genes stood out: serine protease, E3 ubiquitin-protein ligase, and cuticular proteins, which were top hub genes in both species and could serve as potential markers and targets for monitoring IR in these malaria vectors. In addition to the identified markers, we explored molecular mechanisms using enrichment maps that revealed a complex process involving multiple steps, from odorant binding and neuronal signaling to cellular responses, immune modulation, cellular metabolism, and gene regulation. Incorporation of these dynamics into the development of new insecticides and the tracking of insecticide resistance could improve the sustainable and cost-effective deployment of interventions.
Genetic factors explaining anthocyanin pigmentation differences
Authors: Marin-Recinos Maria F. , Pucker Boas 
Published: July 2024

Abstract
Background
Anthocyanins are important contributors to coloration across a wide phylogenetic range of plants. Biological functions of anthocyanins span from reproduction to protection against biotic and abiotic stressors. Owing to a clearly visible phenotype of mutants, the anthocyanin biosynthesis and its sophisticated regulation have been studied in numerous plant species. Genes encoding the anthocyanin biosynthesis enzymes are regulated by a transcription factor complex comprising MYB, bHLH and WD40 proteins.

Results
A systematic comparison of anthocyanin-pigmented vs. non-pigmented varieties was performed within numerous plant species covering the taxonomic diversity of flowering plants. The literature was screened for cases in which genetic factors causing anthocyanin loss were reported. Additionally, transcriptomic data sets from four previous studies were reanalyzed to determine the genes possibly responsible for color variation based on their expression pattern. The contribution of different structural and regulatory genes to the intraspecific pigmentation differences was quantified. Differences concerning transcription factors are by far the most frequent explanation for pigmentation differences observed between two varieties of the same species. Among the transcription factors in the analyzed cases, MYB genes are significantly more prone to account for pigmentation differences compared to bHLH or WD40 genes. Among the structural genes, DFR genes are most often associated with anthocyanin loss.

Conclusions
These findings support previous assumptions about the susceptibility of transcriptional regulation to evolutionary changes and its importance for the evolution of novel coloration phenotypes. Our findings underline the particular significance of MYBs and their apparent prevalent role in the specificity of the MBW complex.
Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance
Authors: Miao Xiaorong , Yang Wenwen , Li Donghai , Wang Aiqin , Li Juanyun , Deng Xu , He Longfei , Niu Junqi 
Published: July 2024

Abstract
Background
Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes.

Results
We assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection.

Conclusion
We assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.
Physical enhancement of older adults using hyperbaric oxygen: a randomized controlled trial
Authors: Hadanny Amir , Sasson Efrat , Copel Laurian , Daniel-Kotovsky Malka , Yaakobi Eldad , Lang Erez , Fishlev Gregory , Polak Nir , Friedman Mony , Doenyas Keren , Finci Shachar , Zemel Yonatan , Bechor Yair , Efrati Shai 
Published: July 2024

Abstract
Introduction
Aging is associated with a progressive decline in the capacity for physical activity. The objective of the current study was to evaluate the effect of an intermittent hyperbaric oxygen therapy (HBOT) protocol on maximal physical performance and cardiac perfusion in sedentary older adults.

Methods
A randomized controlled clinical trial randomized 63 adults (> 64yrs) either to HBOT (n = 30) or control arms (n = 33) for three months. Primary endpoint included the maximal oxygen consumption (VO2Max) and VO2Max/Kg, on an E100 cycle ergometer. Secondary endpoints included cardiac perfusion, evaluated by magnetic resonance imaging and pulmonary function. The HBOT protocol comprised of 60 sessions administered on a daily basis, for 12 consecutive weeks, breathing 100% oxygen at 2 absolute atmospheres (ATA) for 90 min with 5-minute air breaks every 20 min.

Results
Following HBOT, improvements were observed in VO2Max/kg, with a significant increase of 1.91 ± 3.29 ml/kg/min indicated by a net effect size of 0.455 (p = 0.0034). Additionally, oxygen consumption measured at the first ventilatory threshold (VO2VT1) showed a significant increase by 160.03 ± 155.35 ml/min (p < 0.001) with a net effect size of 0.617. Furthermore, both cardiac blood flow (MBF) and cardiac blood volume (MBV) exhibited significant increases when compared to the control group. The net effect size for MBF was large at 0.797 (p = 0.008), while the net effect size for MBV was even larger at 0.896 (p = 0.009).

Conclusion
The findings of the study indicate that HBOT has the potential to improve physical performance in aging adults. The enhancements observed encompass improvements in key factors including VO2Max, and VO2VT1. An important mechanism contributing to these improvements is the heightened cardiac perfusion induced by HBOT.

Trial registration
ClinicalTrials.gov Identifier NCT02790541 (registration date 06/06/2016).
Mammary fat globules as a source of mRNA to model alterations in the expression of some milk component genes during lactation in bovines
Authors: Shaban Samar M. , Hassan Rania A. , Hassanin Abeer A. I. , Fathy Ahmed , El Nabtiti Adel A. S. 
Published: July 2024

Abstract
Background
The milk's nutritional value is determined by its constituents, including fat, protein, carbohydrates, and minerals. The mammary gland's ability to produce milk is controlled by a complex network of genes.
Thereby, the fat, protein, and lactose synthesis must be boost in milk to increase milk production efficiency. This can be accomplished by fusing genetic advancements with proper management practices. Therefore, this study aimed to investigate the association between the Lipoprotein lipase (LPL), kappa casein CSN3, and Glucose transporter 1 (GLUT1) genes expression levels and such milk components as fat, protein, and lactose in different dairy breeds during different stages of lactation.

Methods
To achieve such a purpose, 94 milk samples were collected (72 samples from 36 multiparous black-white and red-white Holstein–Friesian (HF) cows and 22 milk samples from 11 Egyptian buffaloes) during the early and peak lactation stages. The milk samples were utilized for milk analysis and genes expressions analyses using non- invasive approach in obtaining milk fat globules (MFGs) as a source of Ribonucleic acid (RNA).

Results
LPL and CSN3 genes expressions levels were found to be significantly higher in Egyptian buffalo than Holstein–Friesian (HF) cows as well as fat and protein percentages. On the other hand, GLUT1 gene expression level was shown to be significantly higher during peak lactation than early lactation. Moreover, lactose % showed a significant difference in peak lactation phase compared to early lactation phase. Also, fat and protein percentages were significantly higher in early lactation period than peak lactation period but lactose% showed the opposite pattern of Egyptian buffalo.

Conclusion
Total RNA can be successfully obtained from MFGs. The results suggest that these genes play a role in glucose absorption and lactose synthesis in bovine mammary epithelial cells during lactation. Also, these results provide light on the differential expression of these genes among distinct Holstein–Friesian cow breeds and Egyptian buffalo subspecies throughout various lactation phases.
More than sleep problems? Testing five key health behaviors as reasons for quality of life issues among shift workers
Authors: Chen Yuxin , Deng Kaiyi , Hughes Ian M. , Smith Claire E. , Meng Hongdao , Le Minh Quan , Sun Min , Zhang Xianyan , Liu Danping 
Published: July 2024

Abstract
Background
The shift work schedule is a common work arrangement that can disrupt typical sleep-wake rhythms and lead to negative health consequences. The present study aims to examine the effect of shift work on health-related quality of life (QoL) and explore potential behaviorial mediators (i.e., sleep, eating, exercise, smoking, drinking).

Methods
A cross-sectional survey was conducted among 4,449 petroleum workers in southwest China. Data on shift work status, health behaviors, and physical and mental health QoL were collected. We tested our model using path analysis and the Monte Carlo approach among 2,129 included participants.

Results
After adjusting for covariates, shift work did not exhibit a significant direct association with QoL. However, shift work indirectly related to poorer physical health quality of life via less frequent healthy food consumption; shift work also indirectly related to poorer mental health QoL via both less frequent healthy food consumption and physical exercise. No significant indirect effects were found via sleeping, smoking, or drinking.

Conclusions
Results suggest that shift work presents a challenge for QoL among Chinese petroleum workers due to their lesser engagement in two specific health behaviors: healthy eating and physical exercise. Healthy eating and exercise may present an even more prominent threat to shift workers’ QoL than sleep and substance use. Strategies targeting shift work schedule as well as eating and exercise behaviors may help protect against poor QoL and adverse physical and mental health outcomes in this vulnerable group.
Is the burden of metastatic lymph node stations a prognostic factor in patients with resected lung cancer?
Authors: Çitak Necati , Erdogu Volkan , Aksoy Yunus , Ciftci Ayşegül , Yildiz Nisa , İsgörücü Özgür , Ozdemir Servet , Kose Selçuk , Ceylan Kenan Can , Metin Muzaffer 
Published: July 2024

Abstract
Objectives
The burden of metastatic lymph node (LN) stations might reflect a distinct N subcategory with a more aggressive biology and behaviour than the traditional N classification.

Methods
Between 2008 and 2018, we analyzed 1236 patients with pN1/2 lung cancer. Survival was analyzed based on LN station metastasis, determining the optimal threshold for the number of metastatic LN stations that provided additional prognostic information. N prognostic subgrouping was performed using thresholds for the number of metastatic LN stations with the maximum chi-square log-rank value, and validated at each pT-stage.

Results
Survival showed stepwise statistical deterioration with an increase in the number of metastatic LN stations., Threshold values for the number of metastatic LN stations were determined and N prognostic subgroupswas created as sN-alpha; one LN station metastases (n = 632), sN-beta; two-three LN stations metastases (n = 505), and sN-gamma; ≥4 LN stations metastasis (n = 99). The 5-year survival rate was 57.7% for sN-alpha, 39.2% for sN-beta, and 12.7% for sN-gamma (chi-square log rank = 97.906, p < 0.001). A clear tendency of survival deterioration was observed from sN-alpha to sN-gamma in the same pT stage, except for pT4 stage. Multivariate analysis showed that age (p < 0.001), sex (p = 0.002), tumour histology (p < 0.001), IASLC-proposed N subclassification (p < 0.001), and sN prognostic subgroups (p < 0.001) were independent risk factors for survival.

Conclusion
The burden of metastatic LN stations is an independent prognostic factor for survival in patients with lung cancer. It could provide additional prognostic information to the N classification.
A critically prolonged avalanche burial with recorded cardiac electrical activity and complete recovery - a case report
Authors: Bracco C. , Strapazzon G. , Sciolla A. , Dupuis A. , Lauria G. , Fenoglio L. 
Published: July 2024

AbstractThe probability of survival in avalanche accidents is time-dependent. Critically buried victims who undergo a long burial duration (over 60 min) face a possible mortality rate of over 80%. Understanding the physiological response during critical avalanche burial is crucial for improving rescue strategies and outcomes. We present the case of a 55-year-old male skier buried under an avalanche for 4 h and 51 min in the Italian Alps. Continuous heart rate monitoring revealed distinct phases of cardiac activity during burial. Despite severe hypothermia, the victim survived without extracorporeal rewarming. This case highlights the importance of continuous monitoring and appropriate on-site management in avalanche accidents. Factors such as the presence of an air pocket may positively influence survival. This case underscores the importance of comprehensive resuscitative measures and guidelines for managing avalanche victims with prolonged burial durations.
Extracorporeal cardiopulmonary resuscitation versus standard treatment for refractory out-of-hospital cardiac arrest: a Bayesian meta-analysis
Authors: Heuts Samuel , Ubben Johannes F. H. , Kawczynski Michal J. , Gabrio Andrea , Suverein Martje M. , Delnoij Thijs S. R. , Kavalkova Petra , Rob Daniel , Komárek Arnošt , van der Horst Iwan C. C. , Maessen Jos G. , Yannopoulos Demetris , Bělohlávek Jan , Lorusso Roberto , van de Poll Marcel C. G. 
Published: July 2024

Abstract
Background
The outcomes of several randomized trials on extracorporeal cardiopulmonary resuscitation (ECPR) in patients with refractory out-of-hospital cardiac arrest were examined using frequentist methods, resulting in a dichotomous interpretation of results based on p-values rather than in the probability of clinically relevant treatment effects. To determine such a probability of a clinically relevant ECPR-based treatment effect on neurological outcomes, the authors of these trials performed a Bayesian meta-analysis of the totality of randomized ECPR evidence.

Methods
A systematic search was applied to three electronic databases. Randomized trials that compared ECPR-based treatment with conventional CPR for refractory out-of-hospital cardiac arrest were included. The study was preregistered in INPLASY (INPLASY2023120060). The primary Bayesian hierarchical meta-analysis estimated the difference in 6-month neurologically favorable survival in patients with all rhythms, and a secondary analysis assessed this difference in patients with shockable rhythms (Bayesian hierarchical random-effects model). Primary Bayesian analyses were performed under vague priors. Outcomes were formulated as estimated median relative risks, mean absolute risk differences, and numbers needed to treat with corresponding 95% credible intervals (CrIs). The posterior probabilities of various clinically relevant absolute risk difference thresholds were estimated.

Results
Three randomized trials were included in the analysis (ECPR, n = 209 patients; conventional CPR, n = 211 patients). The estimated median relative risk of ECPR for 6-month neurologically favorable survival was 1.47 (95%CrI 0.73–3.32) with a mean absolute risk difference of 8.7% (− 5.0; 42.7%) in patients with all rhythms, and the median relative risk was 1.54 (95%CrI 0.79–3.71) with a mean absolute risk difference of 10.8% (95%CrI − 4.2; 73.9%) in patients with shockable rhythms. The posterior probabilities of an absolute risk difference > 0% and > 5% were 91.0% and 71.1% in patients with all rhythms and 92.4% and 75.8% in patients with shockable rhythms, respectively.

Conclusion
The current Bayesian meta-analysis found a 71.1% and 75.8% posterior probability of a clinically relevant ECPR-based treatment effect on 6-month neurologically favorable survival in patients with all rhythms and shockable rhythms. These results must be interpreted within the context of the reported credible intervals and varying designs of the randomized trials.

Registration
INPLASY (INPLASY2023120060, December 14th, 2023, https://doi.org/10.37766/inplasy2023.12.0060).
A hybrid digital parenting programme to prevent abuse of adolescents in Tanzania: statistical analysis plan for a pragmatic cluster randomised controlled trial
Authors: Klapwijk Jonathan , Melendez-Torres G. J. , Ornellas Abigail , Wambura Mwita , Chetty Angelique N. , Baerecke Lauren , Wamoyi Joyce , Cluver Lucie D. 
Published: July 2024

Abstract
Background
Globally, violence against children poses substantial health and economic challenges, with estimated costs nearing USD 7 trillion. This prompts the urgent call for effective evidence-based interventions in preventing and mitigating violence against children. ParentApp is a mobile, open-source application designed to offer a remote version of the Parenting for Lifelong Health (PLH) programme. ParentApp is the first digital parenting intervention for caregivers of adolescents aged 10–17 years to be tested in low- and middle-income settings.

Methods
This study is a pragmatic, two-arm, cluster-randomised trial in Mwanza, Tanzania’s urban and peri-urban areas. Assessments are set for baseline, 1 month post-intervention, and 12 months post-intervention. We randomised 80 clusters, each with about 30 caregiver-adolescent dyads, with a 1:1 ratio stratified by urban or peri-urban location. Both arms receive an entry-level smartphone preloaded with Kiswahili apps—ParentApp for intervention and WashApp control.
The primary method of analysis will be generalised linear mixed-effects models with adjustment for person-level characteristics and multiple imputation. In three-level models, measurement waves are nested within a person, nested within a sub-ward. Regressions will constrain groups to be equal at baseline and include covariates for stratification, percentage of male caregivers, and individual-level characteristics.

Discussions
Preparations for the trial began in December 2022, including community mobilisation and sensitisation. Rolling recruitment, baseline data collection, and implementation onboarding took place between April and September 2023. One-month post-test data collection began in August 2023 and thus far achieved 97% and 94% retention rates for caregivers and adolescents respectively. Final post-test data collection will begin in September 2024, anticipated to run until April 2025. This SAP was submitted to the journal before the interim analysis to preserve scientific integrity under a superiority hypothesis testing framework.

Trial registration
The trial was registered on the Open Science Framework on 14 March 2023: https://doi.org/10.17605/OSF.IO/T9FXZ.

The trial protocol was published in Trials 25, 119 (2024): Baerecke, L., Ornellas, A., Wamoyi, J. et al. A hybrid digital parenting programme to prevent abuse of adolescents in Tanzania: study protocol for a pragmatic cluster-randomised controlled trial. Trials 25, 119 (2024). https://doi.org/10.1186/s13063-023-07893-x.