title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=534 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Change the direction: 3D optimal control simulation by directly tracking marker and ground reaction force data link: https://peerj.com/articles/14852 last-modified: 2023-02-07 description: Optimal control simulations of musculoskeletal models can be used to reconstruct motions measured with optical motion capture to estimate joint and muscle kinematics and kinetics. These simulations are mutually and dynamically consistent, in contrast to traditional inverse methods. Commonly, optimal control simulations are generated by tracking generalized coordinates in combination with ground reaction forces. The generalized coordinates are estimated from marker positions using, for example, inverse kinematics. Hence, inaccuracies in the estimated coordinates are tracked in the simulation. We developed an approach to reconstruct arbitrary motions, such as change of direction motions, using optimal control simulations of 3D full-body musculoskeletal models by directly tracking marker and ground reaction force data. For evaluation, we recorded three trials each of straight running, curved running, and a v-cut for 10 participants. We reconstructed the recordings with marker tracking simulations, coordinate tracking simulations, and inverse kinematics and dynamics. First, we analyzed the convergence of the simulations and found that the wall time increased three to four times when using marker tracking compared to coordinate tracking. Then, we compared the marker trajectories, ground reaction forces, pelvis translations, joint angles, and joint moments between the three reconstruction methods. Root mean squared deviations between measured and estimated marker positions were smallest for inverse kinematics (e.g., 7.6 ± 5.1 mm for v-cut). However, measurement noise and soft tissue artifacts are likely also tracked in inverse kinematics, meaning that this approach does not reflect a gold standard. Marker tracking simulations resulted in slightly higher root mean squared marker deviations (e.g., 9.5 ± 6.2 mm for v-cut) than inverse kinematics. In contrast, coordinate tracking resulted in deviations that were nearly twice as high (e.g., 16.8 ± 10.5 mm for v-cut). Joint angles from coordinate tracking followed the estimated joint angles from inverse kinematics more closely than marker tracking (e.g., root mean squared deviation of 1.4 ± 1.8 deg vs. 3.5 ± 4.0 deg for v-cut). However, we did not have a gold standard measurement of the joint angles, so it is unknown if this larger deviation means the solution is less accurate. In conclusion, we showed that optimal control simulations of change of direction running motions can be created by tracking marker and ground reaction force data. Marker tracking considerably improved marker accuracy compared to coordinate tracking. Therefore, we recommend reconstructing movements by directly tracking marker data in the optimal control simulation when precise marker tracking is required. creator: Marlies Nitschke creator: Robert Marzilger creator: Sigrid Leyendecker creator: Bjoern M. Eskofier creator: Anne D. Koelewijn uri: https://doi.org/10.7717/peerj.14852 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Nitschke et al. title: CG4968 positively regulates the immune deficiency pathway by targeting Imd protein in Drosophila link: https://peerj.com/articles/14870 last-modified: 2023-02-07 description: Drosophila melanogaster relies solely on innate immunity to defend against various microbial pathogens. Although it is well-known that the adaptor protein Imd undergoes K63-linked ubiquitination to activate the downstream signaling cascades, its involvement with K48-linked ubiquitination and what is responsible for controlling this modification remain largely unknown. In this study, we explored the immunological function of CG4968, which encodes a typical ovarian tumour-associated protease (OTU)-type deubiquitinase (Dub) in flies. Our in vitro and vivo evidence demonstrated that CG4968 plays a positive role in governing the immune deficiency (IMD), but not the Toll innate immune response in an OTU domain-dependent manner. Mechanistically, we found that CG4968 is associated with Imd to restrict its K48-linked ubiquitination, thereby contributing to its turnover. Collectively, our study uncovered a novel regulatory mechanism involving the K48-linked ubiquitination of Imd in Drosophila innate immunity. creator: Qingyang Li creator: Chao Zhang creator: Chuchu Zhang creator: Renjie Duan creator: Yongzhi Hua uri: https://doi.org/10.7717/peerj.14870 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: The imbalance of liver resident macrophages polarization promotes chronic autoimmune hepatitis development in mice link: https://peerj.com/articles/14871 last-modified: 2023-02-07 description: BackgroundAutoimmune hepatitis (AIH) is a chronic immune-mediated inflammatory liver disease. At present, it is largely unknown how the innate immune cells influence AIH development.ObjectiveTo inquiry about mechanism of liver resident macrophages in AIH development, thus offering a new direction for AIH targeted treatment.MethodsThe liver resident macrophages were eliminated by clodronate liposomes in AIH liver tissues, followed by HE and Picrosirius assay to detect liver fibrosis and lymphocyte infiltration. The liver resident macrophages polarization was detected by Immunohistochemistry and qPCR. The collagenase digestion was used to isolate Kupffer cells from AIH mice liver tissues and pro-/anti-inflammatory cytokines were determined by qPCR.ResultsM2 macrophages were the dominant phenotype at early immune response stage and hepatic inflammation was progressively aggravated after depletion of liver resident macrophages. M2 macrophages could effectively delay the development of AIH and could be polarized to M1 macrophages at the disease progresses. TLR2 ligands could promote M2 macrophages producing anti-inflammatory cytokines, whereas TLR4 ligands could promote M1 macrophages producing proinflammatory cytokines. The change of TLR2 and TLR4 ligands could lead to continuous high expression of TLR4 and decreased expression of TLR2 in macrophages to further affect liver resident macrophages polarization state.ConclusionTLR2 and TLR4 ligands mediated liver resident macrophages polarization to favor chronic autoimmune hepatitis development. creator: Gang Chi creator: Jinhong Pei creator: Xueqing Li uri: https://doi.org/10.7717/peerj.14871 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Chi et al. title: Molecular identification of critically endangered European eels (Anguilla anguilla) in US retail outlets link: https://peerj.com/articles/14531 last-modified: 2023-02-06 description: The European eel (Anguilla anguilla) has declined by over 90% since the early 1980s and has been listed as critically endangered. Yet, despite strict export bans from the European Union, the European eel is still sold illegally in many countries. Efforts to monitor the trade of European eels have been primarily concentrated in Asian markets where concerningly high rates of European eel have been reported. Comparably fewer studies have assessed the identities of eel samples from the United States (US), despite the obvious implications for eel conservation. To address this knowledge gap, we purchased 137 eel products (134 freshwater eels and three saltwater eels) from grocers, sushi bars, and restaurants in nine states across the US from 2019 to 2021. Seven samples (5.2%) labeled as freshwater eels (or “unagi”) were identified as European eels using a combination of mitochondrial (cytochrome b) and nuclear (18S rRNA) restriction digestion assays, a fast and inexpensive molecular tool for seafood identification that can identify hybrids between European eels (A. anguilla) and American eels (A. rostrata). No hybrids between European and American eels were found and all seven samples identified with restriction digestion as European eels were confirmed by sequencing of cytochrome b and 18S rRNA. Frequency of European eels in US markets did not significantly correlate with state or retail type. Although illegal eel exports are likely reaching US consumers, the frequency of European eel samples in this study of the US market is much lower than found in other non-European countries. creator: Taylor Ely creator: Nathaniel Patten creator: Lewis C. Naisbett-Jones creator: Erin T. Spencer creator: Demian A. Willette creator: Peter B. Marko uri: https://doi.org/10.7717/peerj.14531 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ely et al. title: Remote sensing technology for rapid extraction of burned areas and ecosystem environmental assessment link: https://peerj.com/articles/14557 last-modified: 2023-02-06 description: Forest fires are one of the significant disturbances in forest ecosystems. It is essential to extract burned areas rapidly and accurately to formulate forest restoration strategies and plan restoration plans. In this work, we constructed decision trees and used a combination of differential normalized burn ratio (dNBR) index and OTSU threshold method to extract the heavily and mildly burned areas. The applicability of this method was evaluated with three fires in Muli County, Sichuan, China, and we concluded that the extraction accuracy of this method could reach 97.69% and 96.37% for small area forest fires, while the extraction accuracy was lower for large area fires, only 89.32%. In addition, the remote sensing environment index (RSEI) was used to evaluate the ecological environment changes. It analyzed the change of the RSEI level through the transition matrix, and all three fires showed that the changes in RSEI were stronger for heavily burned areas than for mildly burned areas, after the forest fire the ecological environment (RSEI) was reduced from good to moderate. These results realized the quantitative evaluation and dynamic evaluation of the ecological environment condition, providing an essential basis for the restoration, decision making and management of the affected forests. creator: Shiqi Zhang creator: Maoyang Bai creator: Xiao Wang creator: Xuefeng Peng creator: Ailin Chen creator: Peihao Peng uri: https://doi.org/10.7717/peerj.14557 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhang et al. title: Putative source and niche shift pattern of a new alien ant species (Odontomachus troglodytes) in Taiwan link: https://peerj.com/articles/14718 last-modified: 2023-02-06 description: Alien species may pose substantial impacts on biodiversity around the globe through international trade and travel. A niche shift hypothesis was proposed to explain the adaptive change of alien or invasive species in new habitats. However, whether niche shifts occur in alien species likely depends on both characteristics inherent to the species itself and its original distribution. Here we identified a newly exotic trap-jaw ant (Odontomachus troglodytes) in Taiwan by morphological and phylogenetic analyses. The possible distribution range and the niche shift pattern were evaluated using ecological niche modelling. The results indicated that exotic O. troglodytes in the newly distributed area displayed a significant niche shift with low niche overlap and high niche expansion. This study reveals a long-distance invasive event from central Africa to Southeast Asia (more than 10,000 km) and predicts the potential distribution range of this new alien species in Taiwan. creator: Tzong-Han Lin creator: Kai-Wei Chan creator: Feng-Chuan Hsu creator: Chung-Chi Lin creator: Hui-Yun Tseng uri: https://doi.org/10.7717/peerj.14718 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lin et al. title: Cross-sectional associations between body mass index, waist circumference, and multimorbidity: Pró-Saúde study link: https://peerj.com/articles/14744 last-modified: 2023-02-06 description: BackgroundThis study aimed (1) To investigate the association between the Body Mass Index (BMI) and waist circumference (WC) with multimorbidity (MM), and (2) To identify patterns of MM and investigate the relationship between BMI and WC with specific combinations of MM (patterns of MM).MethodsA cross-sectional study was conducted with 2,698 participants of the fourth phase of the Brazilian Longitudinal Study of Adult Health (Pró-Saúde Study). MM was defined by the presence of two or more morbidities. MM patterns were identified by exploratory factor analysis based on tetrachoric correlations. Logistic regression models were used to assess associations (odds ratios (OR) with the respective confidence intervals (CI)).ResultsOf the total number of participants, 39.5% were overweight and 30.0% were obese; 89.0% (n = 1,468) of women and 77.0% (n = 952) of men were abdominally obese. Indeed, 60.7% (n = 1,635) was identified with MM. For the category four or more morbidities, OR values of 5.98 (95% CI 4.84–7.13) and 7.48 (95% CI 6.14–8.18) were found for each point of increase in BMI, and 6.74 (95% CI 5.48–7.99) and 8.48 (95% CI 7.64–9.29) for each additional centimeter in the WC, for female and male, respectively. Five patterns of MM were identified: respiratory, osteoarticular, cardiometabolic, gastric, and thyroid diseases (56.4% of the total variance). Positive associations were found between BMI and patterns of cardiometabolic, osteoarticular, thyroid and gastric diseases (higher OR of 1.09 [95% CI 1.04–1.14]) and less pronounced between WC and patterns of cardiometabolic and osteoarticular (higher OR of 1.04 [95% CI 1.03–1.04]).ConclusionsThe results showed that an increase of both BMI and WC was associated with a higher number of morbidities and with patterns of cardiometabolic and osteoarticular diseases. creator: Fernanda Muniz de Macedo Stumpf creator: Alessandra Silva Dias de Oliveira creator: Eduardo Faerstein creator: Cintia Chaves Curioni uri: https://doi.org/10.7717/peerj.14744 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Stumpf et al. title: Efficacy of Saccharothrix algeriensis NRRL B-24137 to suppress Fusarium oxysporum f.sp. vasinfectum induced wilt disease in cotton link: https://peerj.com/articles/14754 last-modified: 2023-02-06 description: Fusarium cotton wilt is a devastating disease of the cotton crop throughout the world, caused by Fusarium oxysporum f.sp. vasinfectum (FOV). Chemical control has many side effects, so, biological controls have been widely used for the management of Fusarium wilt. This study aimed to investigate the possible use of an actinomycetes Saccharothrix algeriensis (SA) NRRL B-24137 to control FOV. To access in-vitro anti-Fusarium ability of SA NRRL B-24137, dual culture assay, spore germination and seed germination tests were carried out. Following in-vitro investigations, several pot tests in a greenhouse environment were used to evaluate the biological control potential of SA NRRL B-24137 against FOV. Dual culture assay and spore germination revealed that SA NRRL B-24137 showed significant anti-Fusarium activity.During spore germination 87.77% inhibition of spore germination were observed. In pot experiments, SA NRRL B-24137 primed cotton seeds resulted in a 74.0% reduction in disease incidence. In soil there was a significant reduction in FOV spores in the presence of SA NRRL B-24137. Positive correlation was also observed on different concentrations of SA NRRL B-24137 towards FOV reduction. The results of this study showed that SA NRRL B-24137 has the potential to be employed as a biocontrol agent against Fusarium cotton wilt, improving cotton growth characteristics and yield. creator: Rizwan Asif creator: Muhammad Hussnain Siddique creator: Sumreen Hayat creator: Ijaz Rasul creator: Habibullah Nadeem creator: Muhammad Faisal creator: Muhammad Waseem creator: Shahbaz Ahmad Zakki creator: Abdelghani Zitouni creator: Saima Muzammil uri: https://doi.org/10.7717/peerj.14754 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Asif et al. title: Prohexadione calcium enhances rice growth and tillering under NaCl stress link: https://peerj.com/articles/14804 last-modified: 2023-02-06 description: Salt stress affects crop quality and reduces crop yields, and growth regulators enhance salt tolerance of crop plants. In this report, we examined the effects of prohexadione-calcium (Pro-Ca) on improving rice (Oryza sativa L.) growth and tillering under salt stress. We found that NaCl stress inhibited the growth of two rice varieties and increased malondialdehyde (MDA) levels, electrolyte leakage, and the activities of the antioxidant enzymes. Foliar application of Pro-Ca reduced seedling height and increased stem base width and lodging resistance of rice. Further analyses showed that Pro-Ca application reduced MDA content, electrolyte leakage, and membrane damage in rice leaves under NaCl stress. Pro-Ca enhanced the net photosynthetic rate (Pn), stomatal conductance (Gs), and intercellular CO2 concentration (Ci) of rice seedlings, while increasing the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbic acid peroxidase (APX) at the tillering stage under salt stress. Overall, Pro-Ca improves salt tolerance of rice seedlings at the tillering stage by enhancing lodging resistance, reducing membrane damages, and enhancing photosynthesis and antioxidant capacities of rice seedlings. creator: Rongjun Zhang creator: Dianfeng Zheng creator: Naijie Feng creator: Quan-Sheng Qiu creator: Hang Zhou creator: Meiling Liu creator: Yao Li creator: Fengyan Meng creator: XiXin Huang creator: Anqi Huang creator: Yixiang Li uri: https://doi.org/10.7717/peerj.14804 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Influence of resin modified glass ionomer cement incorporating protein-repellent and antimicrobial agents on supragingival microbiome around brackets: an in-vivo split-mouth 3-month study link: https://peerj.com/articles/14820 last-modified: 2023-02-06 description: ObjectiveTo explore the influence of resin modified glass ionomer cement (RMGIC) adhesives containing protein-repellent and quaternary ammonium salt agents on supragingival microbiome, enamel and gingival health around brackets.Materials and MethodsTen patients (21.4 ± 3.5 years) about to receive fixed orthodontics were enrolled in this study. Unilateral upper teeth bonded with RMGIC incorporating 2-Methacryloyloxyethyl phosphorylcholine (MPC) and Dimethylaminohexadecyl methacrylate (DMAHDM) were regarded as experimental group (RMD), while contralateral upper teeth bonded with RMGIC were control group (RMGIC), using a split-mouth design. Supragingival plaque was collected from both groups before treatment (T0), and at 1 month (T1) and 3 months (T2) of treatment. High-throughput sequencing was performed targeting v3–v4 of 16S rRNA gene. Streptococcus mutans and Fusobacterium nucleatum quantification was done by qPCR analysis. Bracket failures, enamel decalcification index (EDI), DIAGNODent scores (Dd), plaque index (PI) and gingival index (GI) were monitored at indicated time points.ResultsWithin 3 months, alpha and beta diversity of supragingival plaque had no difference between RMGIC and RMD groups. From T0 to T2, the relative abundance of Streptococcus depleted in RMD but remained steady in RMGIC group. Streptococcus, Prevotella, and Fusobacterium became depleted in RMD, Haemophilus and Capnocytophaga became depleted in RMGIC group but Prevotella enriched. Quantification of Fusbacterium nucleatum and Streptococcus mutans showed significant difference between RMGIC and RMD groups at T2. Teeth bonded with RMD had significant lower plaque index (PI) and DIAGNODent (Dd) score at T2, compared with teeth bonded with RMGIC (p < 0.05). No difference in bracket failure rate was examined between both groups (p > 0.05).ConclusionBy incorporating MPC and DMAHDM into RMGIC, the material could affect the supragingival microbial composition, inhibit the progress of plaque accumulation as well as the key pathogens S. mutans and F. nucleatum in the early stage of orthodontic treatment. creator: Yansong Ma creator: Chengjun Su creator: Hao Yang creator: Hockin H.K. Xu creator: Yuxing Bai creator: Yan Xu creator: Xiaoxia Che creator: Ning Zhang uri: https://doi.org/10.7717/peerj.14820 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ma et al.