title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=439 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: An application of topological data analysis in predicting sumoylation sites link: https://peerj.com/articles/16204 last-modified: 2023-10-12 description: Sumoylation is a reversible post-translational modification that regulates certain significant biochemical functions in proteins. The protein alterations caused by sumoylation are associated with the incidence of some human diseases. Therefore, identifying the sites of sumoylation in proteins may provide a direction for mechanistic research and drug development. Here, we propose a new computational approach for identifying sumoylation sites using an encoding method based on topological data analysis. The features of our model captured the key physical and biological properties of proteins at multiple scales. In a 10-fold cross validation, the outcomes of our model showed 96.45% of sensitivity (Sn), 94.65% of accuracy (Acc), 0.8946 of Matthew’s correlation coefficient (MCC), and 0.99 of area under curve (AUC). The proposed predictor with only topological features achieves the best MCC and AUC in comparison to the other released methods. Our results suggest that topological information is an additional parameter that can assist in the prediction of sumoylation sites and provide a novel perspective for further research in protein sumoylation. creator: Xiaoxi Lin creator: Yaru Gao creator: Fengchun Lei uri: https://doi.org/10.7717/peerj.16204 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lin et al. title: Nomogram model for predicting the risk of post-stroke depression based on clinical characteristics and DNA methylation link: https://peerj.com/articles/16240 last-modified: 2023-10-12 description: ObjectiveTo construct a comprehensive nomogram model for predicting the risk of post-stroke depression (PSD) by using clinical data that are easily collected in the early stages, and the level of DNA methylation, so as to help doctors and patients prevent the occurrence of PSD as soon as possible.MethodsWe continuously recruited 226 patients with a history of acute ischemic stroke and followed up for three months. Socio-demographic indicators, vascular-risk factors, and clinical data were collected at admission, and the outcome of depression was evaluated at the third month after stroke. At the same time, a DNA-methylation-related sequencing test was performed on the fasting peripheral blood of the hospitalized patients which was taken the morning after admission.ResultsA total of 206 samples were randomly divided into training dataset and validation set according to the ratio of 7:3. We screened 24 potentially-predictive factors by Univariate logistic regression and least absolute shrinkage and selection operator (LASSO) regression analysis, and 10 of the factors were found to have predictive ability in the training set. The PSD nomogram model was established based on seven significant variables in multivariate logistic regression. The consistency statistic (C-index) was as high as 0.937, and the area under curve (AUC) in the ROC analysis was 0.933. Replication analysis results in the validation set suggest the C-index was 0.953 and AUC was 0.926. This shows that the model has excellent calibration and differentiating abilities.ConclusionGender, Rankin score, history of hyperlipidemia, time from onset to hospitalization, location of stroke, National Institutes of Health Stroke scale (NIHSS) score, and the methylation level of the cg02550950 site are all related to the occurrence of PSD. Using this information, we developed a prediction model based on methylation characteristics. creator: Shihang Luo creator: Fan Liu creator: Qiao Liao creator: Hengshu Chen creator: Tongtong Zhang creator: Rui Mao uri: https://doi.org/10.7717/peerj.16240 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Luo et al. title: Spatial effects of trade, foreign direct investment (FDI), and natural resource rents on carbon productivity in the GCC region link: https://peerj.com/articles/16281 last-modified: 2023-10-12 description: BackgroundNatural resource rents (NRRs) may determine the environment and economic growth of the GCC countries due to their over-reliance on the natural resource sector. NRRs are the source of income in resource-abundant GCC countries. So, increasing income of these countries could pollute the environment by increasing overall economic activities. Consequently, NRRs could determine carbon productivity in the GCC region through increasing income and carbon emissions.MethodsThe effects of trade openness (TO), foreign direct investment (FDI), urbanization, and oil and natural gas rents on carbon productivity (CP) are examined in the GCC region from 1980–2021 using the spatial Durbin model.ResultsThe CP of the GCC countries has spillovers in their neighboring countries. Oil rent reduces carbon productivity in domestic economies and the entire GCC region. Natural gas rent, TO, and FDI increase, and urbanization reduces carbon productivity in neighboring economies and the entire GCC region. Moreover, urbanization reduces carbon productivity in domestic economies as well. The study recommends the GCC countries to reduce reliance on oil rent and increase globalization in terms of TO and FDI in the region to promote carbon productivity. Moreover, GCC countries should also focus more on natural gas rent instead of oil rent to raise carbon productivity. creator: Haider Mahmood uri: https://doi.org/10.7717/peerj.16281 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mahmood title: Prognostic analyses of genes associated with anoikis in breast cancer link: https://peerj.com/articles/15475 last-modified: 2023-10-11 description: Breast cancer (BRCA) is the most diagnosed cancer worldwide and is responsible for the highest cancer-associated mortality among women. It is evident that anoikis resistance contributes to tumour cell metastasis, and this is the primary cause of treatment failure for BRCA. However, anoikis-related gene (ARG) expression profiles and their prognostic value in BRCA remain unclear. In this study, a prognostic model of ARGs based on The Cancer Genome Atlas (TCGA) database was established using a least absolute shrinkage and selection operator analysis to evaluate the prognostic value of ARGs in BRCA. The risk factor graph demonstrated that the low-risk group had longer survival than the high-risk group, implying that the prognostic model had a good performance. We identified 11 ARGs that exhibited differential expression between the two risk groups in TCGA and Gene Expression Omnibus databases. Through Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes enrichment analyses, we revealed that the screened ARGs were associated with tumour progression and metastasis. In addition, a protein–protein interaction network showed potential interactions among these ARGs. Furthermore, gene set enrichment analysis suggested that the Notch and Wnt signalling pathways were overexpressed in the high-risk group, and gene set variation analysis revealed that 38 hallmark genes differed between the two groups. Moreover, Kaplan–Meier survival curves and receiver operating characteristic curves were used to identify five ARGs (CD24, KRT15, MIA, NDRG1, TP63), and quantitative polymerase chain reaction was employed to assess the differential expression of these ARGs. Univariate and multivariate Cox regression analyses were then performed for the key ARGs, with the best prediction of 3 year survival. In conclusion, ARGs might play a crucial role in tumour progression and serve as indicators of prognosis in BRCA. creator: Jingyu Cao creator: Xinyi Ma creator: Guijuan Zhang creator: Shouyi Hong creator: Ruirui Ma creator: Yanqiu Wang creator: Xianxin Yan creator: Min Ma uri: https://doi.org/10.7717/peerj.15475 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cao et al. title: Evaluation of drought stress level in Sargent’s cherry (Prunus sargentii Rehder) using photosynthesis and chlorophyll fluorescence parameters and proline content analysis link: https://peerj.com/articles/15954 last-modified: 2023-10-11 description: Sargent’s cherry trees (Prunus sargentiiRehder) are widely planted as an ornamental, climate change-sensing species. This study investigated changes in the soil moisture content, fresh weight, photosynthesis and chlorophyll fluorescence properties, and the chlorophyll and proline content of four-year-old P. sargentii seedlings after 30 days of drought stress. In the trees subjected to drought stress treatment, soil moisture content decreased, and the fresh weight of the aboveground part of the plant decreased. However, there was no significant difference in the root growth of the dried plants. Among the photosynthesis parameters, Pn MAX, E and gs showed a significant (p  <  0.001) decrease after 15 days in dry-stressed seedlings, but there was no difference between treatments in WUE until 20 days, and there was a significant (p  <  0.001) difference after 24 days. Chlorophyll fluorescence parameters, Fv/Fm, ΦPSII, Rfd, NPQ, and Pn MAX, also increased after 10 days in dry-stressed seedlings, but these changes did not reach statistical significance compared to the control treatment. These results may suggest that drought stress highly correlates with photosynthesis and chlorophyll fluorescence parameters. Chlorophyll content also significantly decreased in the seedlings under drought stress compared with the control treatment. The proline content decreased until the 10th day of drought stress treatment and increased after the 15th day, showing an increase of 10.9% on the 15th day and 57.1% on the 30th day, compared to the control treatment. These results suggest that photosynthesis, chlorophyll fluorescence parameters, and proline content can be used to evaluate drought stress in trees. The results of this study can contribute to the management of forests, such as the irrigation of trees when pore control ability and photosynthesis ability decrease. creator: Eon Ju Jin creator: Jun-Hyuk Yoon creator: Hyeok Lee creator: Eun Ji Bae creator: Seong Hyeon Yong creator: Myung Suk Choi uri: https://doi.org/10.7717/peerj.15954 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jin et al. title: Dead but not forgotten: complexity of Acropora palmata colonies increases with greater composition of dead coral link: https://peerj.com/articles/16101 last-modified: 2023-10-11 description: Coral reefs are highly biodiverse ecosystems that have declined due to natural and anthropogenic stressors. Researchers often attribute reef ecological processes to corals’ complex structure, but effective conservation requires disentangling the contributions of coral versus reef structures. Many studies assessing the relationships between reef structure and ecological dynamics commonly use live coral as a proxy for reef complexity, disregarding the contribution of dead coral skeletons to reef habitat provision or other biogeochemical reef dynamics. This study aimed to assess the contribution of dead coral to reef complexity by examining structural variations in live and dead Acropora palmata colonies. We used photogrammetry to reconstruct digital elevation models (DEMs) and orthomosaics of the benthic region immediately surrounding 10 A. palmata colonies. These reconstructions were used to quantify structural metrics, including surface rugosity, fractal dimension, slope, planform curvature, and profile curvature, as a function of benthic composition (i.e., live A. palmata, dead A. palmata, or non-A. palmata substrate). The results revealed that dead coral maintained more varied profile curvatures and higher fractal dimensions than live or non-coral substrate. Conversely, A. palmata colonies with a higher proportion of live coral displayed more uniform structure, with lower fractal dimensions and less variability in profile curvature measures. Other metrics showed no significant difference among substrate types. These findings provide novel insights into the structural differences between live and dead coral, and an alternative perspective on the mechanisms driving the observed structural complexity on reefs. Overall, our results highlight the overlooked potential contributions of dead coral to reef habitat provision, ecological processes, and other biogeochemical reef dynamics, and could have important implications for coral reef conservation. creator: Abigail Engleman creator: Kieran Cox creator: Sandra Brooke uri: https://doi.org/10.7717/peerj.16101 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Engleman et al. title: 24-hour movement behaviours and self-rated health in Chinese adolescents: a questionnaire-based survey in Eastern China link: https://peerj.com/articles/16174 last-modified: 2023-10-11 description: ObjectiveAlthough much evidence has demonstrated the benefits of adhering to the 24-hour movement guidelines, little is known about their association with self-rated health in adolescents. The objective of this study was to explore the association between adherence to the 24-hour movement guidelines (i.e., physical activity, screen time, and sleep) and self-rated health among Chinese adolescents aged 10–17 ages.MethodsA convenient sample of 12 schools and their students were recruited for this cross-sectional study. Physical activity and screen time were assessed using a questionnaire based on the Health Behaviour in School-aged Children questionnaire, while sleep duration was used measured using the Pittsburgh Sleep Scale. Ordinal logistic regression was performed to examine the association between adherence to the 24-hour movement guidelines and self-rated health.ResultsAdolescents who adhered to more guidelines contained in the 24-hour movement guidelines reported better self-rated health. A dose-response association was observed, with the odds ratio (OR) for adhering to all three = 11.26, 95% CI [4.82–26.35]; OR for meeting two = 1.62, 95% CI [1.25–2.12]; OR for meeting one = 1.16, 95% CI [0.98–1.38]) indicating a higher probability of better self-rated health with increasing adherence. Regarding adherence to specific combination of 24-hour movement guidelines, positive associations were found for adhering to all three recommendations (OR = 11.95, 95% CI [5.06–28.19]), only MVPA (OR = 4.96, 95% CI [2.82–8.72]), MVPA + screen time (OR = 5.50, 95% CI [3.02–9.99]), and MVPA + sleep (OR = 4.63, 95% CI [2.52–8.51]).ConclusionThis study provides evidence supporting the association between adherence to the 24-hour movement guidelines and better self-rated health among Chinese adolescents. Sufficient physical activity may be particularly important for promoting self-rated health in this population. creator: Guanghui Shi creator: Chaomei Liang creator: Wanli Zang creator: Ran Bao creator: Jin Yan creator: Li Zhou creator: Lei Wang uri: https://doi.org/10.7717/peerj.16174 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Shi et al. title: Computer simulation on the cueing movements in cue sports: a validation study link: https://peerj.com/articles/16180 last-modified: 2023-10-11 description: BackgroundSimulation models have been applied to analyze daily living activities and some sports movements. However, it is unknown whether the current upper extremity musculoskeletal models can be utilized for investigating cue sports movements to generate corresponding kinematic and muscle activation profiles. This study aimed to test the feasibility of applying simulation models to investigate cue sports players’ cueing movements with OpenSim. Preliminary muscle forces would be calculated once the model is validated.MethodsA previously customized and validated unimanual upper extremity musculoskeletal model with six degrees of freedom at the scapula, shoulder, elbow, and wrist, as well as muscles was used in this study. Two types of cueing movements were simulated: (1) the back spin shot, and (2) 9-ball break shot. Firstly, kinematic data of the upper extremity joints were collected with a 3D motion capture system. Using the experimental marker trajectories of the back spin shot on 10 male cue sports players, the simulation on the cueing movements was executed. The model was then validated by comparing the model-generated joint angles against the experimental results using statistical parametric mapping (SPM1D) to examine the entire angle-time waveform as well as t-tests to compare the discrete variables (e.g., joint range of motion). Secondly, simulation of the break shot was run with the experimental marker trajectories and electromyographic (EMG) data of two male cue sports players as the model inputs. A model-estimated muscle activation calculation was performed accordingly for the upper extremity muscles.ResultsThe OpenSim-generated joint angles for the back spin shot corresponded well with the experimental results for the elbow, while the model outputs of the shoulder deviated from the experimental data. The discrepancy in shoulder joint angles could be due to the insufficient kinematic inputs for the shoulder joint. In the break shot simulation, the preliminary findings suggested that great shoulder muscle forces could primarily contribute to the forward swing in a break shot. This suggests that strengthening the shoulder muscles may be a viable strategy to improve the break shot performance.ConclusionIt is feasible to cater simulation modeling in OpenSim for biomechanical investigations of the upper extremity movements in cue sports. Model outputs can help better understand the contributions of individual muscle forces when performing cueing movements. creator: Jing Wen Pan creator: Qichang Mei creator: Justin Fernandez creator: Hesheng Song creator: John Komar creator: Pui Wah Kong uri: https://doi.org/10.7717/peerj.16180 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Pan et al. title: Automatic identification and morphological comparison of bivalve and brachiopod fossils based on deep learning link: https://peerj.com/articles/16200 last-modified: 2023-10-11 description: Fossil identification is an essential and fundamental task for conducting palaeontological research. Because the manual identification of fossils requires extensive experience and is time-consuming, automatic identification methods are proposed. However, these studies are limited to a few or dozens of species, which is hardly adequate for the needs of research. This study enabled the automatic identification of hundreds of species based on a newly established fossil dataset. An available “bivalve and brachiopod fossil image dataset” (BBFID, containing >16,000 “image-label” data pairs, taxonomic determination completed) was created. The bivalves and brachiopods contained in BBFID are closely related in morphology, ecology and evolution that have long attracted the interest of researchers. We achieved >80% identification accuracy at 22 genera and ∼64% accuracy at 343 species using EfficientNetV2s architecture. The intermediate output of the model was extracted and downscaled to obtain the morphological feature space of fossils using t-distributed stochastic neighbor embedding (t-SNE). We found a distinctive boundary between the morphological feature points of bivalves and brachiopods in fossil morphological feature distribution maps. This study provides a possible method for studying the morphological evolution of fossil clades using computer vision in the future. creator: Jiarui Sun creator: Xiaokang Liu creator: Yunfei Huang creator: Fengyu Wang creator: Yongfang Sun creator: Jing Chen creator: Daoliang Chu creator: Haijun Song uri: https://doi.org/10.7717/peerj.16200 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sun et al. title: Impacts of land use change on native plant-butterfly interaction networks from central Mexico link: https://peerj.com/articles/16205 last-modified: 2023-10-11 description: BackgroundLand use change is a key catalyst of global biodiversity loss and ecosystem degradation. Deforestation and conversion of natural habitats to agricultural or urban areas can profoundly disrupt plant-flower visitor interactions by altering their abundances and distribution. Yet, specific studies analyzing the effects of land use change on the structure of networks of the interactions between particular groups of flower visitors and their plants are still scarce. Here, we aimed to analyze how converting native habitats affects the species composition of butterfly communities and their plants, and whether this, in turn, leads to changes in the structure of interaction networks in the modified habitats.MethodsWe performed bi-monthly censuses for a year to record plant-butterfly interactions and assess species diversity across three habitat types, reflecting a land-use change gradient. From original native juniper forest to urban and agricultural zones in central Mexico, one site per land use type was surveyed. Interactions were summarized in matrices on which we calculated network descriptors: connectance, nestedness and modularity.ResultsWe found highest butterfly diversity in native forest, with the most unique species (i.e., species not shared with the other two sites). Agricultural and urban sites had similar diversity, yet the urban site featured more unique species. The plant species richness was highest in the urban site, and the native forest site had the lowest plant species richness, with most of the plants being unique to this site. Butterfly and plant compositions contrasted most between native forest and modified sites. Network analysis showed differences between sites in the mean number of links and interactions. The urban network surpassed agriculture and native forest networks in links, while the native forest network had more interactions than the agriculture and urban networks. Native plants had more interactions than alien species. All networks exhibited low connectance and significant nestedness and modularity, with the urban network featuring the most modules (i.e., 10 modules).ConclusionsConverting native habitats to urban or agricultural areas reshapes species composition, diversity and interaction network structure for butterfly communities and plants. The urban network showed more links and modules, suggesting intricate urban ecosystems due to diverse species, enhanced resources, and ecological niches encouraging interactions and coexistence. These findings emphasize the impacts of land use change on plant-butterfly interactions and the structure of their interaction networks. creator: Deysi Muñoz-Galicia creator: Carlos Lara creator: Citlalli Castillo-Guevara creator: Mariana Cuautle creator: Claudia Rodríguez-Flores uri: https://doi.org/10.7717/peerj.16205 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Muñoz-Galicia et al.