Analysis of technical characteristics of typical lower limb balance movements in Tai Chi: a cross-sectional study based on AnyBody bone muscle modeling
Background Tai Chi is an excellent traditional Chinese physical fitness exercise, and its unique balancing movements are very important for improving human balance. In this study, the two most representative Tai Chi balance movements, “knee lift balance” and “leg stirrup balance”, were selected to establish the lower limb bone muscle model of Tai Chi balance movements by using computer simulation modeling technology, aiming to analyze the characteristics of the lower limb movement mechanisms of typical balance movements, to provide a quantitative theoretical basis for improving the scientific level of Tai Chi. Method A total of 16 subjects were recruited for this study. the BTS three-dimensional motion capture system and three-dimensional force platform were used for motion data acquisition, the physiological electromyographic signals were collected using BTS surface electromyography, and the lower limb bone muscle model of Tai Chi balance movements was established by AnyBody human simulation. Result In the knee lift balancing movement, the balance leg hip abduction/adduction angle, hip flexion/extension moment, and the strength of the rectus femoris muscle, biceps femoris short capitis, and iliacus muscle of the amateur group was significantly smaller than that of the professional group (P < 0.01). In the leg stirrup balance movement, the knee flexion/extension angle of the balancing leg in the amateur group was significantly greater than that in the professional group (P < 0.01), and the hip flexion/extension angle, hip inversion/abduction angle, knee flexion/extension moment, hip flexion/extension moment, the strength iliacus, gluteus maximus, and obturator internus were significantly smaller than those in the professional group (P < 0.01). The integral EMG of the biceps femoris of the support leg in the amateur group was significantly smaller than that of the professional group (P < 0.01). The integral EMG of the lateral femoral muscle of the balance leg was significantly smaller than that of the professional group (P < 0.01). Conclusion In this study, we found that the balancing leg of the balancing movement has a larger hip joint angle, the stirrup balancing knee joint angle is smaller, and the hip and knee joint moments are larger. This is related to joint activity and muscle activation, and amateurs should pay attention to increasing the range of motion of the hip joint and decreasing the range of motion of the knee joint when practicing to better stimulate exercise of the lower limb joints. In addition, the practice of balancing movements should strengthen the iliacus muscle, which plays an important role in maintaining the stable balance of the lower limbs, and strengthen the knee flexor and extensor muscles and hip adductor/abductor muscles of the balancing leg, thus promoting the stability of the balancing leg movements.
Li et al. (2023) Analysis of technical characteristics of typical lower limb balance movements in Tai Chi: a cross-sectional study based on AnyBody bone muscle modeling. PeerJ 11:e15817 https://doi.org/10.7717/peerj.15817
Development of a novel prediction model based on protein structure for identifying RPE65-associated inherited retinal disease (IRDs) of missense variants
Purpose This study aimed to develop a prediction model to classify RPE65-mediated inherited retinal disease (IRDs) based on protein secondary structure and to analyze phenotype-protein structure correlations of RPE65 missense variants in a Chinese cohort. Methods Pathogenic or likely pathogenic missense variants of RPE65 were obtained from UniProt, ClinVar, and HGMD databases. The three-dimensional structure of RPE65 was retrieved from the Protein Data Bank (PDB) and modified with Pymol software. A novel prediction model was developed using LASSO regression and multivariate logistic regression to identify RPE65-associated IRDs. A total of 21 Chinese probands with RPE65 variants were collected to analyze phenotype-protein structure correlations of RPE65 missense variants. Results The study found that both pathogenic and population missense variants were associated with structural features of RPE65. Pathogenic variants were linked to sheet, β-sheet, strands, β-hairpins, Fe2+ (iron center), and active site cavity, while population variants were related to helix, loop, helices, and helix–helix interactions. The novel prediction model showed accuracy and confidence in predicting the disease type of RPE65 variants (AUC = 0.7531). The study identified 25 missense variants in Chinese patients, accounting for 72.4% of total mutations. A significant correlation was observed between clinical characteristics of RPE65-associated IRDs and changes in amino acid type, specifically for missense variants of F8 (H68Y, P419S). Conclusion The study developed a novel prediction model based on the protein structure of RPE65 and investigated phenotype-protein structure correlations of RPE65 missense variants in a Chinese cohort. The findings provide insights into the precise diagnosis of RPE65-mutated IRDs.
Wu et al. (2023) Development of a novel prediction model based on protein structure for identifying RPE65-associated inherited retinal disease (IRDs) of missense variants. PeerJ 11:e15702 https://doi.org/10.7717/peerj.15702
Estimating plant biomass in agroecosystems using a drop-plate meter
Reason for doing the work Plant biomass is a commonly used metric to assess agricultural health and productivity. Removing plant material is the most accurate method to estimate plant biomass, but this approach is time consuming, labor intensive, and destructive. Previous attempts to use indirect methods to estimate plant biomass have been limited in breadth and/or have added complexity in data collection and/or modeling. A cost-effective, quick, accurate, and easy to use and understand approach is desirable for use by scientists and growers. Objectives An indirect method for estimating plant biomass using a drop-plate meter was explored for use in broad array of crop systems. Methods Drop-plate data collected by more than 20 individuals from 16 crop types on 312 farms across 15 states were used to generate models to estimate plant biomass among and within crop types. Results A linear model using data from all crop types explained approximately 67% of the variation in plant biomass overall. This model performed differently among crop types and stand heights, which was owed to differences among sample sizes and farming between annual and perennial systems. Comparatively, the model using the combined dataset explained more variance in biomass than models generated with commodity specific data, with the exception of wheat. Conclusions The drop-plate approach described here was inexpensive, quick, simple, and easy to interpret, and the model generated was robust to error and accurate across multiple crop types. The methods met all expectations for a broad-use approach to estimating plant biomass and are recommended for use across all agroecosystems included in this study. While it may be useful in crops beyond those included, validation is suggested before application.
Robertson et al. (2023) Estimating plant biomass in agroecosystems using a drop-plate meter. PeerJ 11:e15740 https://doi.org/10.7717/peerj.15740
Transcriptomic characterization revealed that METTL7A inhibits melanoma progression via the p53 signaling pathway and immunomodulatory pathway
METTL7A is a protein-coding gene expected to be associated with methylation, and its expression disorder is associated with a range of diseases. However, few research have been carried out to explore the relationship between METTL7A and tumor malignant phenotype as well as the involvement potential mechanism. We conducted our research via a combination of silico analysis and molecular biology techniques to investigate the biological function of METTL7A in the progression of cancer. Gene expression and clinical information were extracted from the TCGA database to explore expression variation and prognostic value of METTL7A. In vitro, CCK8, transwell, wound healing and colony formation assays were conducted to explore the biological functions of METT7A in cancer cell. GSEA was performed to explore the signaling pathway involved in METTL7A and validated via western blotting. In conclusion, METTL7A was downregulated in most cancer tissues and its low expression was associated with shorter overall survival. In melanoma, METTL7A downregulation was associated with poorer clinical staging, lower levels of TIL infiltration, higher IC50 levels of chemotherapeutic agents, and poorer immunotherapy outcomes. QPCR results confirm that METTL7A is down-regulated in melanoma cells. Cell function assays showed that METTL7A knockdown promoted proliferation, invasion, migration and clone formation of melanoma cells. Mechanistic studies showed that METTL7A inhibits tumorigenicity through the p53 signaling pathway. Meanwhile, METTL7A is also a potential immune regulatory factor.
Zhang et al. (2023) Transcriptomic characterization revealed that METTL7A inhibits melanoma progression via the p53 signaling pathway and immunomodulatory pathway. PeerJ 11:e15799 https://doi.org/10.7717/peerj.15799
Mutation-derived, genomic instability-associated lncRNAs are prognostic markers in gliomas
Background Gliomas are the most commonly-detected malignant tumors of the brain. They contain abundant long non-coding RNAs (lncRNAs), which are valuable cancer biomarkers. LncRNAs may be involved in genomic instability; however, their specific role and mechanism in gliomas remains unclear. LncRNAs that are related to genomic instability have not been reported in gliomas. Methods The transcriptome data from The Cancer Genome Atlas (TCGA) database were analyzed. The co-expression network of genomic instability-related lncRNAs and mRNA was established, and the model of genomic instability-related lncRNA was identified by univariate Cox regression and LASSO analyses. Based on the median risk score obtained in the training set, we divided the samples into high-risk and low-risk groups and proved the survival prediction ability of genomic instability-related lncRNA signatures. The results were verified in the external data set. Finally, a real-time quantitative polymerase chain reaction assay was performed to validate the signature. Results The signatures of 17 lncRNAs (LINC01579, AL022344.1, AC025171.5, LINC01116, MIR155HG, AC131097.3, LINC00906, CYTOR, AC015540.1, SLC25A21.AS1, H19, AL133415.1, SNHG18, FOXD3.AS1, LINC02593, AL354919.2 and CRNDE) related to genomic instability were identified. In the internal data set and Gene Expression Omnibus (GEO) external data set, the low-risk group showed better survival than the high-risk group (P < 0.001). In addition, this feature was identified as an independent risk factor, showing its independent prognostic value with different clinical stratifications. The majority of patients in the low-risk group had isocitrate dehydrogenase 1 (IDH1) mutations. The expression levels of these lncRNAs were significantly higher in glioblastoma cell lines than in normal cells. Conclusions Our study shows that the signature of 17 lncRNAs related to genomic instability has prognostic value for gliomas and could provide a potential therapeutic method for glioblastoma.
Li et al. (2023) Mutation-derived, genomic instability-associated lncRNAs are prognostic markers in gliomas. PeerJ 11:e15810 https://doi.org/10.7717/peerj.15810
Extraction and characterisation of pigment from Yanzhiguo [Prunus napaulensis (Ser.) Steud.]
Yanzhiguo [Prunus napaulensis (Ser.) Steud] belongs to Rosaceae family and is consumed as wild fruit, pulp and juice. However, its potential for extracting natural pigment has not yet been explored. Herein, the components in the fresh Yanzhiguo pulp were preliminarily analyzed by liquid chromatography coupled to mass spectrometry. And, the optimal pre-treatment conditions were established for further extraction of Yanzhiguo pigment based on the a* value. Then, by combining the data from single-factor experiments and response surface methodology, the optimal extraction process was established as: 35% EtOH, a liquid-solid ratio of 200:1 mL g−1, an extraction time of 65 min, and an extraction temperature of 100 °C. Moreover, it was found that the a* value and yield had high fitness except when extracted into ethanol (EtOH) with different concentrations. Meanwhile, our result demonstrated Yanzhiguo pigment had high stability in general environments with carmine (a synthetic pigment) as control, except for extreme environments such as direct (hot) sunlight, high temperature (75 °C) and strong alkaline (pH $\geq$≥ 11). Also, Yanzhiguo pigment exhibited good antioxidant activity. Our results contribute to more information on Yanzhiguo pigment and promote its application by providing efficient extraction technology.
Shi et al. (2023) Extraction and characterisation of pigment from Yanzhiguo [Prunus napaulensis (Ser.) Steud.]. PeerJ 11:e15517 https://doi.org/10.7717/peerj.15517
The novel role of LDHA/LDHB in the prognostic value and tumor-immune infiltration in clear cell renal cell carcinoma
Lactate dehydrogenase (LDH) is a crucial glycolytic enzyme which mediates the metabolic plasticity of cancer cells, however its clinical significance in renal cell carcinoma (RCC) is poorly understood. Herein, we examined the prognostic significance of the two primary components of LDH, i.e., LDHA and LDHB, in clear cell RCC (ccRCC) patients and further explored their association with immune infiltration in ccRCC. In this study, the expression levels of LDHA and LDHB were examined in ccRCC and adjacent normal tissues by Gene Expression Profiling Interactive Analysis 2 (GEPIA2), UALCAN, and western blotting (WB) analyses, and their prognostic values were estimated in 150 ccRCC and 30 adjacent normal tissues by immunohistochemistry (IHC) analysis. The relationship to immune infiltration of LDHA and LDHB genes was further investigated using tumor immune estimation resource 2 (TIMER2) and Tumor-Immune System Interactions and DrugBank (TISIDB) databases, respectively. Public databases and WB analyses demonstrated higher LDHA and lower LDHB in ccRCC than in non-tumor tissues. IHC analysis revealed that LDHA and LDHB expression profiles were significantly associated with tumor grade, stage, size, and overall survival (OS). Univariate survival analysis displayed that high grade, advanced stage, large tumor, metastasis, high LDHA, and low LDHB expression were significantly associated with a poorer OS, and multivariate analysis revealed tumor stage and LDHB were identified as independent predictors for OS in patients with ccRCC. Further TIMER2 and TISIDB analyses demonstrated that LDHA and LDHB expression was significantly related to multiple immune cells and immune inhibitors in over 500 ccRCC patients. These findings revealed that LDHB was an independent favorable predictor, and LDHA and LDHB correlated with tumor immune infiltrates in ccRCC patients, which indicated LDHA/LDHB could be implicated in the tumorigenesis of ccRCC and might be potential therapeutic targets for patients with ccRCC.
Chen et al. (2023) The novel role of LDHA/LDHB in the prognostic value and tumor-immune infiltration in clear cell renal cell carcinoma. PeerJ 11:e15749 https://doi.org/10.7717/peerj.15749
Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest
The Brazilian Atlantic Forest and its associated ecosystems are highly biodiverse but still understudied, especially with respect to eukaryotic microbes. Protists represent the largest proportion of eukaryotic diversity and play important roles in nutrient cycling and maintenance of the ecosystems in which they occur. However, much of protist diversity remains unknown, particularly in the Neotropics. Understanding the taxonomic and functional diversity of these organisms is urgently needed, not only to fill this gap in our knowledge, but also to enable the development of public policies for biological conservation. This is the first study to investigate the taxonomic and trophic diversity of the major protist groups in freshwater systems and brackish coastal lagoons located in fragments of the Brazilian Atlantic Forest by DNA metabarcoding, using high-throughput sequencing of the gene coding for the V4 region of the 18S rRNA gene. We compared α and β diversity for all protist communities and assessed the relative abundance of phototrophic, consumer, and parasitic taxa. We found that the protist communities of coastal lagoons are as diverse as the freshwater systems studied in terms of α diversity, although differed significantly in terms of taxonomic composition. Our results still showed a notable functional homogeneity between the trophic groups in freshwater environments. Beta diversity was higher among freshwater samples, suggesting a greater level of heterogeneity within this group of samples concerning the composition and abundance of OTUs.Ciliophora was the most represented group in freshwater, while Diatomea dominated diversity in coastal lagoons.
Carvalho da Silva et al. (2023) Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest. PeerJ 11:e15762 https://doi.org/10.7717/peerj.15762
The impact of containment policy and mobility on COVID-19 cases through structural equation model in Chile, Singapore, South Korea and Israel
Objectives The study aims to understand the impact of containment policy and mobility on COVID-19 cases in Chile, Singapore, South Korea and Israel. To provide experience in epidemic prevention and control. Methods Structural equation modeling (SEM) of containment policies, mobility, and COVID-19 cases were used to test and analyze the proposed hypotheses. Results Chile, Israel and Singapore adopted containment strategies, focusing on closure measures. South Korea adopted a mitigation strategy with fewer closure measures, focusing on vaccination and severe case management. There was a significant negative relationship among containment policies, mobility, and COVID-19 cases. Conclusion To control the COVID-19 and slow down the increase of COVID-19 cases, countries can increase the stringency of containment policies when COVID-19 epidemic is more severe. Thus, countries can take measures from the following three aspects: strengthen the risk monitoring, and keep abreast of the COVID-19 risk; adjust closure measures in time and reduce mobility; and strengthen public education on COVID-19 prevention to motivate citizen to consciously adhere to preventive measures.
Jiao et al. (2023) The impact of containment policy and mobility on COVID-19 cases through structural equation model in Chile, Singapore, South Korea and Israel. PeerJ 11:e15769 https://doi.org/10.7717/peerj.15769
Long-term survival, growth, and reproduction of Acropora palmata sexual recruits outplanted onto Mexican Caribbean reefs
Acropora palmata is a foundational yet endangered Caribbean reef-building coral species. The lack of recovery after a disease outbreak and low recruitment has led to widespread use of fragmentation to restore populations. Another option is the production of sexual recruits (settlers) via assisted reproduction to improve the genetic diversity of depleted populations; however, the viability of this approach has not been tested over the long term. In 2011 and 2012, A. palmata larvae were cultured, settled, and the sexual recruits raised in an ex-situ nursery. Survival and growth were monitored over time. In 2014, these two F1 cohorts were moved to an in-situ nursery and after one year, a subset (29 colonies) was outplanted onto Cuevones Reef in the Mexican Caribbean. Growth and survival of these colonies were monitored periodically and compared to colonies that remained in the in-situ nursery. In 2019, samples were collected and analyzed for fertility and fecundity. 53% of the colonies were gravid and fecundity was 5.61 ± 1.91 oocytes and 3.04 ± 0.26 spermaries per polyp. A further 14 colonies from these two cohorts were outplanted in 2020 onto Picudas Reef and monitored during the subsequent spawning seasons. Two years after outplanting onto Picudas Reef, all colonies were alive and spawning of three of these colonies was recorded in 2022 in synchrony with the wild population. Gametes were collected from two colonies and crossed, with 15% fertilization success. Spermatozoa from wild colonies were then added and fertilization success increased to 95%. The resultant larvae followed normal development and symbiont uptake was visible within two weeks. The F2 generation was settled, maintained in an ex-situ nursery, and monitored for survival and growth. Both F1 and F2 generations followed a Type III survival curve with high initial mortality while in the ex-situ nursery and low later-stage mortality. The growth rates of these colonies increased three-fold after outplanting when compared to their growth rates in the ex-situ and in-situ nurseries. All colonies survived while in the in-situ nursery and for an additional nine years after outplanting onto Cuevones Reef. Overall, our results show that colonies produced by assisted breeding, once outplanted, may contribute to the genetic diversity and establishment of self-sustaining sexually-reproducing populations, which is an overarching goal of coral restoration programs.
Mendoza Quiroz et al. (2023) Long-term survival, growth, and reproduction of Acropora palmata sexual recruits outplanted onto Mexican Caribbean reefs. PeerJ 11:e15813 https://doi.org/10.7717/peerj.15813