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Cancers Jun 2024Early diagnosis of lung cancer can significantly improve patient outcomes. We developed a Growth Predictive model based on the Wasserstein Generative Adversarial Network...
Early diagnosis of lung cancer can significantly improve patient outcomes. We developed a Growth Predictive model based on the Wasserstein Generative Adversarial Network framework (GP-WGAN) to predict the nodule growth patterns in the follow-up LDCT scans. The GP-WGAN was trained with a training set (N = 776) containing 1121 pairs of nodule images with about 1-year intervals and deployed to an independent test set of 450 nodules on baseline LDCT scans to predict nodule images (GP-nodules) in their 1-year follow-up scans. The 450 GP-nodules were finally classified as malignant or benign by a lung cancer risk prediction (LCRP) model, achieving a test AUC of 0.827 ± 0.028, which was comparable to the AUC of 0.862 ± 0.028 achieved by the same LCRP model classifying real follow-up nodule images ( = 0.071). The net reclassification index yielded consistent outcomes (NRI = 0.04; = 0.62). Other baseline methods, including Lung-RADS and the Brock model, achieved significantly lower performance ( < 0.05). The results demonstrated that the GP-nodules predicted by our GP-WGAN model achieved comparable performance with the nodules in the real follow-up scans for lung cancer diagnosis, indicating the potential to detect lung cancer earlier when coupled with accelerated clinical management versus the current approach of waiting until the next screening exam.
PubMed: 38927934
DOI: 10.3390/cancers16122229 -
Genes Jun 2024Eggshell color plays important biological roles and attracts the attention of both egg retailers and researchers. However, whether non-coding RNAs are involved in...
Eggshell color plays important biological roles and attracts the attention of both egg retailers and researchers. However, whether non-coding RNAs are involved in pigment deposition among different eggshell colors remains unknown. In this study, RNA sequencing was used to analyse the uterine gland transcriptome (CircRNA and miRNA) of Changshun chicken blue-shell hens producing four different eggshell color eggs including dark blue PK(DB) and light blue (LB), dark brown and greenish (between blue and pink, DP) and pink (p). We found that , targeting , was expressed in DB, DP, and LB groups compared with the PK group, which indicates that may play a role in the blue eggshell color. KEGG and GO analyses showed that the "metabolic pathways" with targeted genes such and were detected in dark and light blue color eggshell chickens, which confirms the different ratios of biliverdin and involved in the deposition of blue color. As annotated by connectivity analysis, and , belonging to the family, are involved in the signaling pathway, which plays an important role in cell growth, differentiation, metastasis and apoptosis. Our findings enrich the database of circRNA, miRNAs and genes for chicken uterine tissue, which will be useful in accelerating molecular selection for blue eggshell color layers.
Topics: Animals; Chickens; MicroRNAs; Egg Shell; RNA, Circular; Female; Pigmentation; Transcriptome; Sequence Analysis, RNA; Gene Regulatory Networks
PubMed: 38927747
DOI: 10.3390/genes15060812 -
Genes Jun 2024Egg production plays a pivotal role in the economic viability of hens. To analyze the genetic rules of egg production, a total of 3151 Luhua chickens were selected, the...
Egg production plays a pivotal role in the economic viability of hens. To analyze the genetic rules of egg production, a total of 3151 Luhua chickens were selected, the egg production traits including egg weight at first laying (Start-EW), egg weight at 43 weeks (EW-43), egg number at 43 weeks (EN-43), and total egg number (EN-All) were recorded. Then, the effects of related factors on egg production traits were explored, using a multi-trait animal model for genetic parameter estimation and a genome-wide association study (GWAS). The results showed that body weight at first egg (BWFE), body weight at 43 weeks (BW-43), age at first egg (AFE), and seasons had significant effects on the egg production traits. Start-EW and EW-43 had moderate heritability of 0.30 and 0.21, while EN-43 and EN-All had low heritability of 0.13 and 0.16, respectively. Start-EW exhibited a robust positive correlation with EW-43, while Start-EW was negatively correlated with EN-43 and EN-All. Furthermore, gene ontology (GO) results indicated that Annexin A2 (ANXA2) and Frizzled family receptor 7 (FZD7) related to EW-43, Cyclin D1 (CCND1) and A2B adenosine receptor (ADORA2B) related to EN-All, and have been found to be mainly involved in metabolism and growth processes, and deserve more attention and further study. This study contributes to accelerating genetic progress in improving low heritability egg production traits in layers, especially in Luhua chickens.
Topics: Animals; Chickens; Genome-Wide Association Study; Female; Eggs; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Phenotype
PubMed: 38927732
DOI: 10.3390/genes15060796 -
Biology Jun 2024Rice ( L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages,... (Review)
Review
Rice ( L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages, resulting in a dramatic loss of grain yield. Over the past century, substantial efforts have been undertaken to investigate the physiological, biochemical, and molecular mechanisms of cold stress tolerance in rice. This review aims to provide a comprehensive overview of the recent developments and trends in this field. We summarized the previous advancements and methodologies used for identifying cold-responsive genes and the molecular mechanisms of cold tolerance in rice. Integration of new technologies has significantly improved studies in this era, facilitating the identification of essential genes, QTLs, and molecular modules in rice. These findings have accelerated the molecular breeding of cold-resistant rice varieties. In addition, functional genomics, including the investigation of natural variations in alleles and artificially developed mutants, is emerging as an exciting new approach to investigating cold tolerance. Looking ahead, it is imperative for scientists to evaluate the collective impacts of these novel genes to develop rice cultivars resilient to global climate change.
PubMed: 38927322
DOI: 10.3390/biology13060442 -
Journal of Perinatal Medicine Jun 2024A recent European randomized trial - Tracheal Occlusion To Accelerate Lung Growth - demonstrated that fetoscopic endoluminal tracheal occlusion (FETO) is associated...
OBJECTIVES
A recent European randomized trial - Tracheal Occlusion To Accelerate Lung Growth - demonstrated that fetoscopic endoluminal tracheal occlusion (FETO) is associated with increased postnatal survival among infants with severe congenital diaphragmatic hernia (CDH). However, this differs in middle-income countries such as Brazil, where abortion is illegal and neonatal intensive care is inadequate. This study evaluated the effects of FETO on improving the survival of infants with moderate-to-severe CDH in isolated and non-isolated cases.
METHODS
This retrospective cohort study selected 49 fetuses with CDH, a normal karyotype, and a lung-to-head ratio (LHR) of <1 from a single national referral center for fetal surgery in São Paulo, Brazil, between January 2016 and November 2019. FETO was performed between 26 and 29 weeks of gestation. The primary outcomes were infant survival until discharge from the neonatal intensive care unit and survival until six months of age.
RESULTS
Forty-six women with singleton fetuses having severe CDH underwent prenatal intervention with FETO. Infant survival rates until discharge and at six months of age were both 38 %. The observed-to-expected LHR increased by 25 % after FETO in neonates who survived until discharge. Spontaneous intrauterine death occurred in four growth-restricted fetuses after FETO. Preterm birth in <37 weeks and preterm rupture of membranes in <34 weeks occurred in 56.5 % (26) and 26 % (12) cases, respectively.
CONCLUSIONS
FETO may increase neonatal survival in fetuses with severe CDH, particularly in countries with limited neonatal intensive care.
PubMed: 38926929
DOI: 10.1515/jpm-2024-0070 -
BMC Plant Biology Jun 2024Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate...
BACKGROUND
Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate industry. However, the long generation time and difficulties associated with breeding a tropical tree crop have limited the progress of breeders to develop high-yielding disease-resistant varieties. Development of marker-assisted breeding methods for cacao requires discovery of genomic regions and specific alleles of genes encoding important traits of interest. To accelerate gene discovery, we developed a gene atlas composed of a large dataset of replicated transcriptomes with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao.
RESULTS
We describe the creation of the Cacao Transcriptome Atlas, its global characterization and define sets of genes co-regulated in highly organ- and temporally-specific manners. RNAs were extracted and transcriptomes sequenced from 123 different tissues and stages of development representing major organs and developmental stages of the cacao lifecycle. In addition, several experimental treatments and time courses were performed to measure gene expression in tissues responding to biotic and abiotic stressors. Samples were collected in replicates (3-5) to enable statistical analysis of gene expression levels for a total of 390 transcriptomes. To promote wide use of these data, all raw sequencing data, expression read mapping matrices, scripts, and other information used to create the resource are freely available online. We verified our atlas by analyzing the expression of genes with known functions and expression patterns in Arabidopsis (ACT7, LEA19, AGL16, TIP13, LHY, MYB2) and found their expression profiles to be generally similar between both species. We also successfully identified tissue-specific genes at two thresholds in many tissue types represented and a set of genes highly conserved across all tissues.
CONCLUSION
The Cacao Gene Atlas consists of a gene expression browser with graphical user interface and open access to raw sequencing data files as well as the unnormalized and CPM normalized read count data mapped to several cacao genomes. The gene atlas is a publicly available resource to allow rapid mining of cacao gene expression profiles. We hope this resource will be used to help accelerate the discovery of important genes for key cacao traits such as disease resistance and contribute to the breeding of elite varieties to help farmers increase yields.
Topics: Cacao; Transcriptome; Gene Regulatory Networks; Gene Expression Regulation, Plant; Genes, Plant; Gene Expression Profiling; Organ Specificity
PubMed: 38926852
DOI: 10.1186/s12870-024-05171-9 -
Pediatric Obesity Jun 2024Executive control and temperament have been associated with pediatric obesity. However, interactions between these constructs in relation to future weight outcomes have...
BACKGROUND
Executive control and temperament have been associated with pediatric obesity. However, interactions between these constructs in relation to future weight outcomes have not been investigated.
OBJECTIVE
This longitudinal study examined early childhood executive control, early temperament (negative affectivity and surgency), and their interactions as predictors of adolescent BMI trajectories.
METHODS
At age 5.25, children (N = 229) completed executive control tasks, and parents completed the Child Behavior Questionnaire to assess temperament. BMI was calculated annually between ages 14-17.
RESULTS
Greater early negative affectivity predicted more positive BMI growth. Although early childhood executive control was not associated with BMI growth, greater negative affectivity predicted greater BMI escalation at average and below average executive control abilities.
CONCLUSIONS
For children without robust executive control abilities early in development, negative affectivity may be a risk factor for accelerated adolescent BMI growth. Targeted assessment of early risk factors may be useful for childhood obesity prevention efforts.
PubMed: 38926799
DOI: 10.1111/ijpo.13144 -
Radiation Oncology (London, England) Jun 2024At present, it has been found that many patients have acquired resistance to radiotherapy, which greatly reduces the effect of radiotherapy and further affects the...
BACKGROUND
At present, it has been found that many patients have acquired resistance to radiotherapy, which greatly reduces the effect of radiotherapy and further affects the prognosis. CircRNAs is involved in the regulation of radiosensitivity of many kinds of tumor cells. Therefore, the main purpose of this study is to explore the regulatory effect of CircRNA_101491 on radiosensitivity of ESCC and its related mechanism.
METHODS
We established ESCC radiation-resistant cell line (KYSE150R cell) by gradient dose method, and tested the difference of KYSE150 between KYSE150R cell and parent cell in vitro. Then, after knocking down the expression of CircRNA_101491, a series of in vitro experiments were conducted to verify the effects of CircRNA_101491 on the phenotype and radiosensitivity of KYSE150R cells, and further analyzed the related regulatory mechanism. In addition, we also used the model of transplanted tumor in nude mice to investigate the effect of CircRNA_101491 on the radiosensitivity of ESCC in vivo.
RESULTS
According to a series of in vitro experiments, we confirmed that KYSE150R cells lost the epithelial phenotype and obtained interstitial cell-like phenotype, and found that CircRNA_101491 was highly expressed in KYSE150R cells. In addition, we found that knocking down the expression of CircRNA_101491 will lift the inhibition of miR-125a-5p, and then reverse the process of EMT, accelerate the process of apoptosis, thus play a role in radiosensitization. The in vivo experiment of transplanted tumor in nude mice also showed that knocking down the expression of CircRNA_101491 could enhance the radiosensitivity of ESCC.
CONCLUSION
In conclusion, we confirmed that interfering with the expression of CircRNA_101491 can relieve the inhibition of miR-125a-5p, thus reverse the process of interstitial phenotype, accelerate the process of apoptosis, and enhance the radiosensitivity of ESCC.
Topics: MicroRNAs; Radiation Tolerance; Animals; RNA, Circular; Humans; Mice; Esophageal Neoplasms; Mice, Nude; Esophageal Squamous Cell Carcinoma; Apoptosis; Cell Proliferation; Gene Expression Regulation, Neoplastic; Mice, Inbred BALB C; Cell Line, Tumor; Xenograft Model Antitumor Assays; Tumor Cells, Cultured
PubMed: 38926729
DOI: 10.1186/s13014-024-02478-7 -
Journal of Nanobiotechnology Jun 2024Hypoxia-activated prodrugs present new opportunities for safe and effective tumor drug resistance therapy due to their high selectivity for hypoxic cells. However, the...
BACKGROUND
Hypoxia-activated prodrugs present new opportunities for safe and effective tumor drug resistance therapy due to their high selectivity for hypoxic cells. However, the uneven distribution of oxygen in solid tumor and insufficient hypoxia in the tumor microenvironment greatly limit its therapeutic efficacy.
RESULTS
In this paper, a novel AQ4N-Mn(II)@PDA coordination nanoplatform was designed and functionalized with GMBP1 to target drug-resistant tumor cells. Its excellent photothermal conversion efficiency could achieve local high-temperature photothermal therapy in tumors, which could not only effectively exacerbate tumor hypoxia and thus improve the efficacy of hypoxia-activated chemotherapy of AQ4N but also significantly accelerate Mn-mediated Fenton-like activity to enhance chemodynamic therapy. Moreover, real-time monitoring of blood oxygen saturation through photoacoustic imaging could reflect the hypoxic status of tumors during treatment. Furthermore, synergistic treatment effectively inhibited tumor growth and improved the survival rate of mice bearing orthotopic drug-resistant tumors.
CONCLUSIONS
This study not only provided a new idea for PTT combined with hypoxia-activated chemotherapy and CDT for drug-resistant tumors but also explored a vital theory for real-time monitoring of hypoxia during treatment.
Topics: Animals; Mice; Drug Resistance, Neoplasm; Cell Line, Tumor; Humans; Photothermal Therapy; Mice, Inbred BALB C; Nanoparticles; Antineoplastic Agents; Tumor Microenvironment; Mice, Nude; Prodrugs; Tumor Hypoxia; Manganese; Female; Neoplasms; Anthraquinones
PubMed: 38926723
DOI: 10.1186/s12951-024-02653-8 -
Nature Communications Jun 2024Phage predation is generally assumed to reduce microbial proliferation while not contributing to the spread of antibiotic resistance. However, this assumption does not...
Phage predation is generally assumed to reduce microbial proliferation while not contributing to the spread of antibiotic resistance. However, this assumption does not consider the effect of phage predation on the spatial organization of different microbial populations. Here, we show that phage predation can increase the spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth by reshaping spatial organization. Using two strains of the bacterium Escherichia coli, we demonstrate that phage predation slows the spatial segregation of the strains during growth. This increases the number of cell-cell contacts and the extent of conjugation-mediated plasmid transfer between them. The underlying mechanism is that phage predation shifts the location of fastest growth from the biomass periphery to the interior where cells are densely packed and aligned closer to parallel with each other. This creates straighter interfaces between the strains that are less likely to merge together during growth, consequently slowing the spatial segregation of the strains and enhancing plasmid transfer between them. Our results have implications for the design and application of phage therapy and reveal a mechanism for how microbial functions that are deleterious to human and environmental health can proliferate in the absence of positive selection.
Topics: Plasmids; Escherichia coli; Bacteriophages; Drug Resistance, Bacterial; Anti-Bacterial Agents; Conjugation, Genetic
PubMed: 38926498
DOI: 10.1038/s41467-024-49840-7