title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=277 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Stress induced on permanent mandible first molar and space maintainer under normal masticatory forces: a finite element study link: https://peerj.com/articles/17456 last-modified: 2024-07-26 description: BackgroundThe band and loop space maintainer is used to maintain the missing space of deciduous molars which are lost early. When the second deciduous molar is lost prematurely, the stress on the first permanent molar during different degrees of development may vary when it is the abutment. The design and use of the space maintainer may also lead to damage of the loop. The purpose of this article is to use the finite element method to study the stress on the first permanent molar and the loop with or without occlusal contact, with the first permanent molar of four different degrees of development serving as the abutment. We aimed to guide the clinical design and use of the space maintainer.MethodsWe developed finite element models of the mandibular first permanent molar and the band and loop space maintainer, and simulated alveolar bone, periodontal ligament (PDL), enamel and dentin. The four developmental stages were 1/2 (I), 2/3 (II), 3/4 (III) and full development (IV). Ansys Workbench was used to analyze the effects of root development and occlusal contact between the loop and the opposite jaw on abutment teeth and the loop. Abutment teeth were statically loaded vertically and obliquely with a force of 70 N. The loop was statically loaded vertically with a force of 14 N. The stress on all structures and the displacement trends of the loop were calculated.ResultsThe stress on enamel, dentin, PDL and alveolar bone were similar, and the concentration was consistent. But if there was occlusal contact, the loop produced maximum displacement at the near middle edge of contact with the anterior teeth. When the loop was in occlusal contact with the opposing occlusal tooth, the peak value of the equivalent stress on the space maintainer under vertical load was: group I > group IV > group III > group II, and the maximum principal stress peak change was: group I > group III > group II > group IV. The change of the equivalent stress peak value of the loop under oblique load was: group I > group III > group IV > group II, and the maximum principal stress peak change was: group III > group I > group II > group IV. When the loop was not in occlusal contact with the opposing occlusal tooth, the peak value of the equivalent stress on the space maintainer under vertical load was: group IV > group I > group II > group III, and the maximum principal stress peak change was: group IV > group I > group II > group III. The change of the equivalent stress peak value of the space maintainer under oblique load was: group I > group IV > group II > group III, and the maximum principal stress peak change was: group I > group IV > group II > group III.ConclusionsOur results suggested that whenever possible, choosing the teeth with nearly complete root development as the abutment of the space maintainer is advisable. The design and use of the band and loop space maintainer should avoid occlusal contact with the occlusal teeth to prevent deformation of the loop. creator: Hui Shi creator: Fang Fang Kang creator: Qian Liu uri: https://doi.org/10.7717/peerj.17456 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Shi et al. title: Curcumin improves atrial fibrillation susceptibility by regulating tsRNA expression in aging mouse atrium link: https://peerj.com/articles/17495 last-modified: 2024-07-26 description: Age is an independent risk factor for atrial fibrillation (AF), and curcumin can delay aging related disease through reducing oxidative stress and inflammation. However, its target in aging-related AF remains unclear. Transfer RNA-derived small RNA (tsRNA) is a novel short non-coding RNA (sncRNA), and exerts a potential regulatory function in aging. This study was to explore the therapeutic targets of curcumin in atrium of aged mice by PANDORA-seq. Aged mice (18 month) were treated with curcumin (100 mg/kg). Rapid transjugular atrial pacing was performed to observe AF inducibility. SA-β-gal staining, reactive oxygen species (ROS) detection and qRT-PCR were used to assess the degree of aging and oxidative stress/inflammation levels. PANDORA-seq was performed to reveal the differentially expressed sncRNAs in the atrium of mice. The results showed that curcumin reduced the susceptibility AF of aged mice by improving aging-related atrial fibrosis. Compared to young mice (5 month) group, aged mice yielded 473 significantly altered tsRNA sequences, while 947 tsRNA sequences were significantly altered after treated with curcumin. Enrichment analysis revealed that the target genes were mainly related to DNA damage and protein modification. Compared with the 5 month group, the expression levels of mature-mt_tRNA-Val-TAC_CCA_end, mature-mt_tRNA-Glu-TTC_CCA_end, and mature-tRNA-Asp-GTC_CCA_end were up-regulated in the 18 month group, while the expression of mature-mt_tRNA-Thr-TGT_5_end was down-regulated. This trend was reversed in the 18 month + curcumin group. Increased cellular ROS levels, inflammation expression and senescence in aged mice atrium were improved by the down-regulation of mature-mt_tRNA-Val-TAC_CCA_end. In conclusion, our findings identified mature-mt_tRNA-Val-TAC_CCA_end participated in the mechanism of aging-related atrial fibrosis, providing new intervention target of aging-related AF. creator: Xueshan Luo creator: Panyue Liu creator: Xingdong Ye creator: Jintao He creator: Yingyu Lai creator: Yidong Lv creator: Xiongbin Wu creator: Yang Liu creator: Qianhuan Zhang creator: Hui Yang creator: Wei Wei creator: Chunyu Deng creator: Sujuan Kuang creator: Shulin Wu creator: Yumei Xue creator: Fang Rao uri: https://doi.org/10.7717/peerj.17495 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Luo et al. title: Identification of the RRM1 gene family in rice (Oryza sativa) and its response to rice blast link: https://peerj.com/articles/17668 last-modified: 2024-07-26 description: To better understand RNA-binding proteins in rice, a comprehensive investigation was conducted on the RRM1 gene family of rice. It encompassed genome-wide identification and exploration of its role in rice blast resistance. The physicochemical properties of the rice OsRRM1 gene family were analyzed. There genes were also analyzed for their conserved domains, motifs, location information, gene structure, phylogenetic trees, collinearity, and cis-acting elements. Furthermore, alterations in the expression patterns of selected OsRRM1 genes were assessed using quantitative real-time PCR (qRT-PCR). A total of 212 members of the OsRRM1 gene family were identified, which were dispersed across 12 chromosomes. These genes all exhibit multiple exons and introns, all of which encompass the conserved RRM1 domain and share analogous motifs. This observation suggests a high degree of conservation within the encoded sequence domain of these genes. Phylogenetic analysis revealed the existence of five subfamilies within the OsRRM1 gene family. Furthermore, investigation of the promoter region identified cis-regulatory elements that are involved in nucleic acid binding and interaction with multiple transcription factors. By employing GO and KEGG analyses, four RRM1 genes were tentatively identified as crucial contributors to plant immunity, while the RRM1 gene family was also found to have a significant involvement in the complex of alternative splicing. The qRT-PCR results revealed distinct temporal changes in the expression patterns of OsRRM1 genes following rice blast infection. Additionally, gene expression analysis indicates that the majority of OsRRM1 genes exhibited constitutive expressions. These findings enrich our understanding of the OsRRM1 gene family. They also provide a foundation for further research on immune mechanisms rice and the management of rice blast. creator: Xinlei Jiang creator: Shangwei Yu creator: Yuhan Huang creator: Junying Huang creator: Shaochun Liu creator: Dewei Yang creator: Junru Fu creator: Haohua He creator: Haihui Fu uri: https://doi.org/10.7717/peerj.17668 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Jiang et al. title: Psycho-physio-neurological correlates of qualitative attention, emotion and flow experiences in a close-to-real-life extreme sports situation: low- and high-altitude slackline walking link: https://peerj.com/articles/17743 last-modified: 2024-07-26 description: It has been indicated that extreme sport activities result in a highly rewarding experience, despite also providing fear, stress and anxiety. Studies have related this experience to the concept of flow, a positive feeling that individuals undergo when they are completely immersed in an activity. However, little is known about the exact nature of these experiences, and, there are still no empirical results to characterize the brain dynamics during extreme sport practice. This work aimed at investigating changes in psychological responses while recording physiological (heart rate–HR, and breathing rate–BR) and neural (electroencephalographic–EEG) data of eight volunteers, during outdoors slackline walking in a mountainous environment at two different altitude conditions (1 m–low-walk– and 45 m–high-walk–from the ground). Low-walk showed a higher score on flow scale, while high-walk displayed a higher score in the negative affect aspects, which together point to some level of flow restriction during high-walk. The order of task performance was shown to be relevant for the physiological and neural variables. The brain behavior during flow, mainly considering attention networks, displayed the stimulus-driven ventral attention network–VAN, regionally prevailing (mainly at the frontal lobe), over the goal-directed dorsal attention network–DAN. Therefore, we suggest an interpretation of flow experiences as an opened attention to more changing details in the surroundings, i.e., configured as a ‘task-constantly-opened-to-subtle-information experience’, rather than a ‘task-focused experience’. creator: Marcelo Felipe de Sampaio Barros creator: Carlos Alberto Stefano Filho creator: Lucas Toffoli de Menezes creator: Fernando Manuel Araújo-Moreira creator: Luis Carlos Trevelin creator: Rafael Pimentel Maia creator: Rémi Radel creator: Gabriela Castellano uri: https://doi.org/10.7717/peerj.17743 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 de Sampaio Barros et al. title: DTDHM: detection of tandem duplications based on hybrid methods using next-generation sequencing data link: https://peerj.com/articles/17748 last-modified: 2024-07-26 description: BackgroundTandem duplication (TD) is a common and important type of structural variation in the human genome. TDs have been shown to play an essential role in many diseases, including cancer. However, it is difficult to accurately detect TDs due to the uneven distribution of reads and the inherent complexity of next-generation sequencing (NGS) data.MethodsThis article proposes a method called DTDHM (detection of tandem duplications based on hybrid methods), which utilizes NGS data to detect TDs in a single sample. DTDHM builds a pipeline that integrates read depth (RD), split read (SR), and paired-end mapping (PEM) signals. To solve the problem of uneven distribution of normal and abnormal samples, DTDHM uses the K-nearest neighbor (KNN) algorithm for multi-feature classification prediction. Then, the qualified split reads and discordant reads are extracted and analyzed to achieve accurate localization of variation sites. This article compares DTDHM with three other methods on 450 simulated datasets and five real datasets.ResultsIn 450 simulated data samples, DTDHM consistently maintained the highest F1-score. The average F1-score of DTDHM, SVIM, TARDIS, and TIDDIT were 80.0%, 56.2%, 43.4%, and 67.1%, respectively. The F1-score of DTDHM had a small variation range and its detection effect was the most stable and 1.2 times that of the suboptimal method. Most of the boundary biases of DTDHM fluctuated around 20 bp, and its boundary deviation detection ability was better than TARDIS and TIDDIT. In real data experiments, five real sequencing samples (NA19238, NA19239, NA19240, HG00266, and NA12891) were used to test DTDHM. The results showed that DTDHM had the highest overlap density score (ODS) and F1-score of the four methods.ConclusionsCompared with the other three methods, DTDHM achieved excellent results in terms of sensitivity, precision, F1-score, and boundary bias. These results indicate that DTDHM can be used as a reliable tool for detecting TDs from NGS data, especially in the case of low coverage depth and tumor purity samples. creator: Tianting Yuan creator: Jinxin Dong creator: Baoxian Jia creator: Hua Jiang creator: Zuyao Zhao creator: Mengjiao Zhou uri: https://doi.org/10.7717/peerj.17748 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yuan et al. title: Gene synthesis design: a pythonic approach link: https://peerj.com/articles/17750 last-modified: 2024-07-26 description: Researchers often need to synthesize genes of interest in this era of synthetic biology. Gene synthesis by PCR assembly of multiple DNA fragments is a quick and economical method that is widely applied. Up to now, there have been a few software solutions for designing fragments in gene synthesis. However, some of these software solutions use programming languages that are not popular now, other software products are commercial or require users to visit servers. In this study, we propose a Python program to design DNA fragments for gene synthesis. The algorithm is designed to meet the experimental needs. Also, the source code with detailed annotation is freely available for all users. Furthermore, the feasibility of the algorithm and the program is validated by experiments. Our program can be useful for the design of gene synthesis in the labs and help the study of gene structure and function. creator: Yunzhuo Hu creator: Danni Pan creator: Fei Xu creator: Bifang Huang creator: Xuanyang Chen creator: Shiqiang Lin uri: https://doi.org/10.7717/peerj.17750 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hu et al. title: An intense 60-day weight-loss course leads to an 18 kg body weight reduction and metabolic reprogramming of soldiers with obesity link: https://peerj.com/articles/17757 last-modified: 2024-07-26 description: Soldiers of the Mexican Army with obesity were subjected to an intense 60-day weight-loss course consisting of a controlled diet, daily physical training, and psychological sessions. The nutritional treatment followed the European Society of Cardiology (ESC) recommendations, incorporating elements of the traditional milpa diet in the nutritional intervention. The total energy intake was reduced by 200 kcal every 20 days, starting with 1,800 kcal and ending with 1,400 kcal daily. On average, the participants reduced their body weight by 18 kg. We employed an innovative approach to monitor the progress of the twelve soldiers who completed the entire program. We compared the untargeted metabolomics profiles of their urine samples, taken before and after the course. The data obtained through liquid chromatography and high-resolution mass spectrometry (LC-MS) provided insightful results. Classification models perfectly separated the profiles pre and post-course, indicating a significant reprogramming of the participants’ metabolism. The changes were observed in the C1-, vitamin, amino acid, and energy metabolism pathways, primarily affecting the liver, biliary system, and mitochondria. This study not only demonstrates the potential of rapid weight loss and metabolic pathway modification but also introduces a non-invasive method for monitoring the metabolic state of individuals through urine mass spectrometry data. creator: Exsal M. Albores-Méndez creator: Humberto Carrasco-Vargas creator: Samary Alaniz Monreal creator: Rodolfo David Mayen Quinto creator: Ernesto Diderot López García creator: Gabriela Gutierrez Salmean creator: Karen Medina-Quero creator: Marco A. Vargas-Hernández creator: Cesar Vicente Ferreira Batista creator: Yamilé López-Hernández creator: Robert Winkler uri: https://doi.org/10.7717/peerj.17757 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Albores-Méndez et al. title: Genotypes and phenotypes in a Wolbachia-ant symbiosis link: https://peerj.com/articles/17781 last-modified: 2024-07-26 description: The fitness effects of overt parasites, and host resistance to them, are well documented. Most symbionts, however, are more covert and their interactions with their hosts are less well understood. Wolbachia, an intracellular symbiont of insects, is particularly interesting because it is thought to be unaffected by the host immune response and to have fitness effects mostly focussed on sex ratio manipulation. Here, we use quantitative PCR to investigate whether host genotype affects Wolbachia infection density in the leaf-cutting ant Acromyrmex echinatior, and whether Wolbachia infection density may affect host morphology or caste determination. We found significant differences between host colonies in the density of Wolbachia infections, and also smaller intracolonial differences in infection density between host patrilines. However, the density of Wolbachia infections did not appear to affect the morphology of adult queens or likelihood of ants developing as queens. The results suggest that both host genotype and environment influence the host-Wolbachia relationship, but that Wolbachia infections carry little or no physiological effect on the development of larvae in this system. creator: Crystal L. Frost creator: Rowena Mitchell creator: Judith Elizabeth Smith creator: William O.H. Hughes uri: https://doi.org/10.7717/peerj.17781 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Frost et al. title: Negative effects of agricultural open-channel irrigation system on vertebrate populations in central Mexico link: https://peerj.com/articles/17818 last-modified: 2024-07-26 description: Linear infrastructures such as agricultural irrigation channels produce physical changes and negative impacts to habitats, wildlife populations, communities, and ecosystems. Open irrigation channels act as a pitfall for wildlife and can affect vertebrates of all sizes. Nonetheless, small channels have received relatively little attention by conservation biologists. The objective of this study was to analyze vertebrate species richness and mortality in relation to different sections of an irrigation channel system and the surrounding landscape characteristics. For two years, we conducted monthly surveys along an open-channel irrigation system to estimate its effect on vertebrates through records of dead and alive individuals. We examined the spatial relation of species richness and mortality with transects using a canonical correspondence analysis and chi-squared tests to determine possible variations in the different structures of the channel and seasonality. Further, a landscape diversity index was used to analyze the importance of surrounding habitat structure and composition on these parameters. Most vertebrates (61%) were found dead, small mammals and reptiles were the most affected. Our results indicate that mortality of small vertebrates varies depending on species, structures of the open-channel agricultural irrigation system (i.e., concrete channel and floodgates), seasonality (i.e., wet, and dry), and landscape heterogeneity (i.e., high, medium, and low landscape diversity). The open-channel irrigation system is a threat to populations of small vertebrates in anthropized landscapes, conservation efforts should be directed at protecting water bodies and restructuring the open-channel agricultural irrigation system to avoid mortality of species such as small rodents (M. mexicanus) and reptiles (C. triseriatus, B. imbricata, and Thamnophis spp.). creator: Yuriana Gómez-Ortiz creator: Hublester Domínguez-Vega creator: Leroy Soria-Díaz creator: Tamara Rubio-Blanco creator: Claudia C. Astudillo-Sánchez creator: Victor Mundo creator: Armando Sunny uri: https://doi.org/10.7717/peerj.17818 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gómez-Ortiz et al. title: Occurrence and abundance of microplastics in surface water of Songkhla Lagoon link: https://peerj.com/articles/17822 last-modified: 2024-07-26 description: BackgroundMicroplastic (MP) pollution is now a global critical issue and has been the subject of considerable worry for multiple various types of habitats, notably in lagoons which are coastal areas connected to the ocean. MPs are of concern, particularly because floating MP in surface water can be ingested by a number of marine organisms. There are several lagoons along Southeast Asia’s coastline, but Songkhla Lagoon is Thailand’s only exit with a rich biodiversity. To date, there has been little research undertaken on MP in this lagoon, so there is a pressing need to learn more about the presence of MP in the lagoon’s water.MethodsWe investigate MPs in the surface water of Songkhla Lagoon, Thailand. Sampling took place at ten stations in the lagoon during the wet season in December 2022 and the dry season in February 2023. Samples were digested with hydrogen peroxide to remove organic matter followed by density separation using saturated sodium chloride. MPs were visually examined under a stereo microscope to describe and determine the shape, size, and color. Polymer type was identified using a micro Fourier transform infrared (FTIR) spectrometer. Moreover, the in-situ of water quality of the surface water was measured using a multi-parameter probe. A Mann-Whitney U test was performed to investigate the variations in MP levels and water quality parameters between the wet and dry seasons. Correlation analysis (Spearman rho) was used to determine the significance of correlations between MP and water quality (p < 0.05).ResultsMPs were detected at all ten of the sites sampled. The most abundant MPs were small size class (<500 µm, primarily consisting of fibers). Five types of polymers were seen in surface water, including polyethylene terephthalate, rayon, polypropylene, polyester, and poly (ethylene:propylene). Rayon and polyester were the dominant polymers. Additionally, the most dominant color of MPs in the wet and dry season was black and blue, respectively. The mean contents of MPs in the wet and dry season were 0.43 ± 0.18 and 0.34 ± 0.08 items/L, respectively. The Mann-Whitney U test suggested a significant difference between water quality in the wet and dry seasons (p < 0.05). Correlation analysis (Spearman rho) indicated a negative significant difference relationship between the MPs and the values of total dissolved solid (TDS) in the wet season (r = −0.821, p = <0.05), revealing that the large amounts of MPs may possibly be dispersed within surface water bodies with low TDS concentrations. Based on the overall findings, MP pollution in the surface water of the lagoon is not found to be influenced by the seasonal context. Rivers flowing into the lagoon, especially the U-Taphao River, may be a principal pathway contributing to increased MP pollution loading in the lagoon. The results can be used as baseline data to undertake further research work relevant to sources, fates, distribution, and impacts of MPs in other coastal lagoons. creator: Siriporn Pradit creator: Prakrit Noppradit creator: Kittiwara Sornplang creator: Preyanuch Jitkaew creator: Thanakorn Jiwarungrueangkul creator: Dudsadee Muenhor uri: https://doi.org/10.7717/peerj.17822 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Pradit et al.