title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=400 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: Microbiota plasticity in tilapia gut revealed by meta-analysis evaluating the effect of probiotics, prebiotics, and biofloc link: https://peerj.com/articles/16213 last-modified: 2023-10-11 description: Tilapia species are among the most cultivated fish worldwide due to their biological advantages but face several challenges, including environmental impact and disease outbreaks. Feed additives, such as probiotics, prebiotics, and other microorganisms, have emerged as strategies to protect against pathogens and promote immune system activation and other host responses, with consequent reductions in antibiotic use. Because these additives also influence tilapia’s gut microbiota and positively affect the tilapia culture, we assume it is a flexible annex organ capable of being subject to significant modifications without affecting the biological performance of the host. Therefore, we evaluated the effect of probiotics and other additives ingested by tilapia on its gut microbiota through a meta-analysis of several bioprojects studying the tilapia gut microbiota exposed to feed additives (probiotic, prebiotic, biofloc). A total of 221 tilapia gut microbiota samples from 14 bioprojects were evaluated. Alpha and beta diversity metrics showed no differentiation patterns in relation to the control group, either comparing additives as a group or individually. Results also revealed a control group with a wide dispersion pattern even when these fish did not receive additives. After concatenating the information, the tilapia gut core microbiota was represented by four enriched phyla including Proteobacteria (31%), Fusobacteria (23%), Actinobacteria (19%), and Firmicutes (16%), and seven minor phyla Planctomycetes (1%), Chlamydiae (1%), Chloroflexi (1%), Cyanobacteria (1%), Spirochaetes (1%), Deinococcus Thermus (1%), and Verrucomicrobia (1%). Finally, results suggest that the tilapia gut microbiota is a dynamic microbial community that can plastically respond to feed additives exposure with the potential to influence its taxonomic profile allowing a considerable optimal range of variation, probably guaranteeing its physiological function under different circumstances. creator: Marcel Martinez-Porchas creator: Aranza Preciado-Álvarez creator: Francisco Vargas-Albores creator: Martina Hilda Gracia-Valenzuela creator: Francesco Cicala creator: Luis Rafael Martinez-Cordova creator: Diana Medina-Félix creator: Estefania Garibay-Valdez uri: https://doi.org/10.7717/peerj.16213 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Martinez-Porchas et al. title: Mitochondrial genome characteristics of six Phylloscopus species and their phylogenetic implication link: https://peerj.com/articles/16233 last-modified: 2023-10-11 description: The mitochondrial genomes of six Phylloscopus species—small insectivores belonging to the Phylloscopidae family—were obtained using the Illumina sequencing platform. The mitogenomes were closed circular molecules 16,922–17,007 bp in size, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two control regions (CR1 and remnant CR2). The gene orders were conserved in 35 sampled Phylloscopus mitogenomes in the GenBank database, with a gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. The average base compositions of the six Phylloscopus mitogenomes were 29.43% A, 32.75% C, 14.68% G, and 23.10% T, with the A+T content slightly higher than that of G+C. ATG and TAA were the most frequent initiating and terminating codons, respectively. Several conserved boxes were identified in CR1, including C-string in domain I; F, E, D, and C boxes, as well as bird similarity and B boxes, in domain II; and CSB1 in domain III. Tandem repeats were observed in remnant CR2 of the Phylloscopus fuscatus and Phylloscopus proregulus mitogenomes. A phylogenetic analysis with maximum likelihood (ML) and Bayesian inference (BI) methods, based on 13 protein-coding genes and two rRNA genes, indicated that the Phylloscopus species was divided into two larger clades, with a splitting time approximately 11.06 million years ago (mya). The taxa of Phylloscopus coronatus/Phylloscopus burkii and Phylloscopus inornatus/P. proregulus were located at the basal position of the different clades. The phylogenetic result of the cox1 gene showed that Seicercus was nested within Phylloscopus. The complete set of mitogenomes of the Phylloscopus species provides potentially useful resources for the further exploration of the taxonomic status and phylogenetic history of Phylloscopidae. creator: Chao Yang creator: Xiaomei Dong creator: Qingxiong Wang creator: Xiang Hou creator: Hao Yuan creator: Xuejuan Li uri: https://doi.org/10.7717/peerj.16233 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yang et al. title: Bridging the gap between sustainability and profitability: unveiling the untapped potential of sea cucumber viscera link: https://peerj.com/articles/16252 last-modified: 2023-10-11 description: Sea cucumbers have high economic value, and in most forms of trade, their body wall is typically the only part that is harvested and sold. The organs of the sea cucumber, collectively known as the viscera, are frequently discarded, contributing to land and water pollution. However, discarded sea cucumber viscera contain various nutrients that can be used in many applications. Therefore, this review highlights the biological and economic aspects of sea cucumbers, followed by a critical discussion of the nutritional value of their internal organs and possible applications, including as functional feed additives in the aquaculture industry, sources of natural testosterone for application in sex reversal and production of monosex population, of neuroprotective agents against central nervous system disorders and of cosmetic ingredients, especially for skin whitening and anti-ageing products. The review further highlights the valorisation potential of viscera to maximize their economic potential, thus providing an enormous prospect for reusing sea cucumber waste, thereby reducing the negative impact of the sea cucumber fishery sector on the environment. creator: Muhammad Fatratullah Muhsin creator: Yushinta Fujaya creator: Andi Aliah Hidayani creator: Hanafiah Fazhan creator: Wan Adibah Wan Mahari creator: Su Shiung Lam creator: Alexander Chong Shu-Chien creator: Youji Wang creator: Nor Afiqah-Aleng creator: Nita Rukminasari creator: Khor Waiho uri: https://doi.org/10.7717/peerj.16252 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Muhsin et al. title: Beneficial effects of upgrading to His-Purkinje system pacing in patients with pacing-induced cardiomyopathy: a systematic review and meta-analysis link: https://peerj.com/articles/16268 last-modified: 2023-10-11 description: BackgroundThe purpose of this study was to evaluate the effectiveness of His-Purkinje system pacing (HPSP) in the management of patients with pace-induced cardiomyopathy (PICM).MethodsPubMed, Embase, Web of Science, and the Cochrane Library were searched comprehensively to collect related studies published from the inception of databases to June 1, 2022. R 4.04 software, including the Metafor package, matrix package, and the Meta package, was utilized to conduct the singe-arm meta-analysis. The methodology index for non-randomized studies (MINORS) was used to assess the methodological quality of the included studies.ResultsA total of seven studies were included, involving 164 PICM patients. The meta-analysis showed that HPSP ameliorated the left ventricular ejection fraction (LVEF) by 13.41% (95% CI [11.21–15.61]), improved the New York Heart Association (NYHA) classification by 1.02 (95% CI [−1.41 to −0.63]), and shortened the QRS duration (QRSd) by 60.85 ms (95% CI [−63.94 to −57.75]), resulting in improved cardiac functions in PICM patients. Besides, HPSP reversed the ventricular remodeling, with a 32.46 ml (95% CI [−53.18 to −11.75]) decrease in left ventricular end systolic volume (LVESV) and a 5.93 mm (95% CI [−7.68 to −4.19]) decrease in left ventricular end-diastolic dimension (LVEDD). HPSP also showed stable electrical parameters of pacemakers, with a 0.07 V (95% CI [0.01–0.13]) increase in pacing threshold, a 0.02 mV (95% CI [−0.85 to 0.90]) increase in sensed R-wave amplitude, and a 31.12 Ω reduction in impedance (95% CI [−69.62 to 7.39]). Compared with LBBP, HBP improved LVEF by 13.28% (95% CI [−11.64 to 14.92]) vs 14.43% (95% CI [−13.01 to 15.85]), ameliorated NHYA classification by 1.18 (95% CI [−1.97 to −0.39]) vs 0.95 (95% CI [−1.33 to −0.58]), shortened QRSd by 63.16 ms (95% CI [−67.00 to −59.32]) vs 57.98 ms (95% CI [−62.52 to −53.25]), and decreased LVEDD by 4.12 mm (95% CI [−5.79 to −2.45]) vs 6.26 mm (95% CI [−62.52 to −53.25]). The electrical parameters of the pacemaker were stable in both groups.ConclusionsThis meta-analysis showed that HPSP could significantly improve cardiac function, promote reverse remodeling, and provide stable electrical parameters of pacemakers for PICM patients. creator: Nian Tang creator: Xiaoxiao Chen creator: Hongfei Li creator: Denghong Zhang uri: https://doi.org/10.7717/peerj.16268 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Tang et al. title: Physical activity, problematic smartphone use, and burnout among Chinese college students link: https://peerj.com/articles/16270 last-modified: 2023-10-11 description: The aim of this study was to investigate the association between physical activity (PA), problematic smartphone use (PSU), and burnout, as well as to identify whether there is a mediating role for PSU. We recruited 823 college students (Mage = 18.55, SD = 0.83) from Wuhan, China, in December 2022, including 499 males and 324 females. Demographic information, the International Physical Activity Questionnaire-Short Form (IPAQ-SF), the Smartphone Addiction Scale-Short Version (SAS-SV), and the Maslach Burnout Inventory-Student Survey (MBI-SS) were used for assessments. Pearson correlation analysis showed that PA was significantly associated with PSU (r = −0.151, p < 0.001), PSU was significantly associated with burnout (r = 0.421, p < 0.001), and the association between PA and burnout was not statistically significant (r = −0.046, p > 0.05). The results of the mediation model test showed that PA could not predict burnout directly; it instead predicted burnout entirely indirectly through PSU. Furthermore, PSU mediated the predictive effect of PA on exhaustion and cynicism. In conclusion, there is no direct connection between PA levels and burnout. PA indirectly affects burnout through PSU, but does not fully apply to the three different dimensions of exhaustion, cynicism, and professional efficacy. creator: Lianghao Zhu creator: Junli Hou creator: Bojun Zhou creator: Xi Xiao creator: Jingqiang Wang creator: Wanping Jia uri: https://doi.org/10.7717/peerj.16270 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhu et al.