title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=279 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Applicability and perspectives for DNA barcoding of soil invertebrates link: https://peerj.com/articles/17709 last-modified: 2024-07-24 description: Belowground invertebrate communities are dominated by species-rich and very small microarthropods that require long handling times and high taxonomic expertise for species determination. Molecular based methods like metabarcoding circumvent the morphological determination process by assigning taxa bioinformatically based on sequence information. The potential to analyse diverse and cryptic communities in short time at high taxonomic resolution is promising. However, metabarcoding studies revealed that taxonomic assignment below family-level in Collembola (Hexapoda) and Oribatida (Acariformes) is difficult and often fails. These are the most abundant and species-rich soil-living microarthropods, and the application of molecular-based, automated species determination would be most beneficial in these taxa. In this study, we analysed the presence of a barcoding gap in the standard barcoding gene cytochrome oxidase I (COI) in Collembola and Oribatida. The barcoding gap describes a significant difference between intra- and interspecific genetic distances among taxa and is essential for bioinformatic taxa assignment. We collected COI sequences of Collembola and Oribatida from BOLD and NCBI and focused on species with a wide geographic sampling to capture the range of their intraspecific variance. Our results show that intra- and interspecific genetic distances in COI overlapped in most species, impeding accurate assignment. When a barcoding gap was present, it exceeded the standard threshold of 3% intraspecific distances and also differed between species. Automatic specimen assignments also showed that most species comprised of multiple genetic lineages that caused ambiguous taxon assignments in distance-based methods. Character-based taxonomic assignment using phylogenetic trees and monophyletic clades as criteria worked for some species of Oribatida but failed completely for Collembola. Notably, parthenogenetic species showed lower genetic variance in COI and more accurate species assignment than sexual species. The different patterns in genetic diversity among species suggest that the different degrees of genetic variance result from deep evolutionary distances. This indicates that a single genetic threshold, or a single standard gene, will probably not be sufficient for the molecular species identification of many Collembola and Oribatida taxa. Our results also show that haplotype diversity in some of the investigated taxa was not even nearly covered, but coverage was better for Collembola than for Oribatida. Additional use of secondary barcoding genes and long-read sequencing of marker genes can improve metabarcoding studies. We also recommend the construction of pan-genomes and pan-barcodes of species lacking a barcoding gap. This will allow both to identify species boundaries, and to cover the full range of variability in the marker genes, making molecular identification also possible for species with highly diverse barcode sequences. creator: Jéhan Le Cadre creator: Finn Luca Klemp creator: Miklós Bálint creator: Stefan Scheu creator: Ina Schaefer uri: https://doi.org/10.7717/peerj.17709 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Le Cadre et al. title: Evaluation of the facial profile of skeletal Class III patients undergoing camouflage orthodontic treatment: a retrospective study link: https://peerj.com/articles/17733 last-modified: 2024-07-24 description: ObjectiveTo identify objective metrics for evaluating the esthetics of facial profiles in skeletal Class III patients undergoing camouflage orthodontic treatment.MethodsEighty Asian–Chinese patients classified as skeletal Class III were included. Thirty cephalometric measurements of pre- and posttreatment cephalograms were analyzed. Ten orthodontists assigned visual analog scale (VAS) scores to the pre- and posttreatment profiles based on standardized lateral photographs. Correlations between subjective VAS scores and objective measurements were assessed using Pearson correlation and stepwise multiple linear regression analysis.ResultsLower incisor (L1) protrusion, nasolabial angle, lower lip-E line distance, SNB angle, and L1 to AP plane were significantly correlated with VAS scores of pretreatment profiles of skeletal Class III patients. Factors such as retraction of the lower incisor, increased interincisal angle and overjet, reduction of lower lip-E line distance, as well as augmentation of the Z angle and nasolabial angle were significantly correlated with the changes in VAS scores post-camouflage orthodontic treatment. Stepwise multiple linear regression analysis revealed that pretreatment nasolabial angle, changes in the lower lip-E line distance, and pretreatment Pog-NB distance were the key factors influencing the posttreatment facial profile esthetics of skeletal Class III patients with camouflage orthodontic treatment.ConclusionSeveral cephalometric measurements correlate with subjective facial esthetic evaluations of skeletal Class III patients. Changes in lower lip prominence, the pretreatment nasolabial angle, and Pog-NB distance are the main factors related to facial esthetics in skeletal Class III patients after camouflage orthodontic treatment. creator: Xiaobei Li creator: Yuan Tian creator: Runzhi Guo creator: Weiran Li creator: Danqing He creator: Yannan Sun uri: https://doi.org/10.7717/peerj.17733 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Evaluation of in-house dengue real-time PCR assays in West Java, Indonesia link: https://peerj.com/articles/17758 last-modified: 2024-07-24 description: Dengue is an infectious disease caused by infection of dengue virus (DENV) transmitted by Aedes aegypti and Aedes albopictus. In Indonesia, dengue commonly occurs with an increasing incidence rate annually. It is known that early detection of dengue infection is one of the keys to controlling this disease outbreak. Rapid and accurate early detection to diagnose dengue can be achieved by molecular tests, one of which is through a real-time PCR method. However, real-time PCR assay for dengue developed based on Indonesian DENV sequences has not been available. Therefore, we developed in-house dengue real-time PCR (SYBR- and TaqMan-based) assays and evaluated those assays in routine clinical testing in the community. These assays target the 3′ UTR region of the four DENV serotypes and was found to be specific for DENV. The most sensitive assay was the TaqMan assay with the LOD95% of 482 copy/ml, followed by the SYBR assay with the LOD95% of 14,398 copy/ml. We recruited dengue suspected patients from three primary health care services in West Java, Indonesia to represent the community testing setting. Dengue infection was examined using the two in-house real-time PCR assays along with NS1, IgM, and IgG rapid diagnostic tests (RDT). In total, as many as 74 clinical specimens of dengue suspected patients were included in this study. Among those patients, 21 were positive for TaqMan assay, 17 were positive for SYBR assay, nine were positive for NS1 test, six were positive for both IgG and IgM tests, and 22 were positive for IgG test only. Compared with our in-house TaqMan assay, the sensitivity of NS1 test, IgM test, and IgG test were 42.86%, 14.29%, and 28.57% respectively. Among these three RDT tests, NS1 showed 100% specificity. Thus, our study confirmed that NS1 test showed high specificity, indicating that a positive result of NS1 can be confidently considered a dengue case. However, NS1, IgM, and IgG tests with RDT are not enough to diagnose a dengue case. We suggest applying the high sensitivity and specificity rRT-PCR test as the gold standard for early detection and antibody test as a follow-up test for rRT-PCR negative cases. creator: Denti R. Kinanti creator: Intan Ahmad creator: Ramadhani Putra creator: Sri Yusmalinar creator: Indra Wibowo creator: Tjandra Anggraeni creator: Angga Dwiartama creator: Tommy Octavianus Soetrisno Tjia creator: Putri Cahya Destiani creator: Karimatu Khoirunnisa creator: Wu-Chun Tu creator: Kok-Boon Neoh creator: Rosye Arosdiani Apip creator: Ahyani Raksanagara creator: Ira Dewi Jani creator: Yeppi Tisnawati creator: Aan Warisman creator: Tita Rostiana creator: Azzania Fibriani uri: https://doi.org/10.7717/peerj.17758 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Kinanti et al. title: A methodological and reporting quality assessment of systematic reviews/meta-analyses on exercise interventions for cognitive function in older adults with mild cognitive impairment link: https://peerj.com/articles/17773 last-modified: 2024-07-24 description: ObjectiveTo assess the methodological quality of meta-analytic literature on exercise interventions for cognitive function in patients with mild cognitive impairment (MCI) and the certainty of evidence for its outcome indicators, and to provide clinicians and researchers with more reliable data for making decisions.MethodsMeta-analytic literature related to the effect of exercise intervention on cognitive function in patients with mild cognitive impairment was searched through PubMed, Cochrane Library, Embase, Scopus, Physiotherapy Evidence Database and Web of Science, all with a search period frame of each database until June 1, 2024. The AMSTAR2 scale was used to evaluate the methodological quality of the included studies.ResultsSeventeen meta-analyses were included. The AMSTAR2 scale evaluation results showed that there was one medium-quality studies (5.55%), seven low-quality studies (38.88%), and 10 very low-quality studies (55.55%). Methodological deficiencies included failure to prepare a plan and provide a registration number, literature screening, data extraction, reasons for exclusion not described in detail, poor implementation process for systematic evaluation, and failure to describe the source of funding for the included studies or relevant conflicts of interest.ConclusionThe overall methodological quality of the meta-analytic literature is low, and the certainty of evidence is low. We encourage the conduction of high-quality randomized trials to generate stronger evidence. Subsequent systematic reviews can then synthesize this evidence to inform future research and clinical guidelines. creator: Wanli Zang creator: Qinghai Zou creator: Ningkun Xiao creator: Mingqing Fang creator: Su Wang creator: Jingjing Chen uri: https://doi.org/10.7717/peerj.17773 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zang et al. title: Validation of a commercially available mobile application for velocity-based resistance training link: https://peerj.com/articles/17789 last-modified: 2024-07-24 description: BackgroundVelocity-based training (VBT) is commonly used for programming and autoregulation of resistance training. Velocity may also be measured during resistance training to estimate one repetition maximum and monitor fatigue. This study quantifies the validity of Metric VBT, a mobile application that uses camera-vision for measuring barbell range of motion (RoM) and mean velocity during resistance exercises.MethodsTwenty-four participants completed back squat and bench press repetitions across various loads. Five mobile devices were placed at varying angles (0, ±10, and ±20°) perpendicular to the participant. The validity of Metric VBT was assessed in comparison to Vicon motion analysis using precision and recall, Lin’s concordance correlation coefficient, and Bland-Altman plots. Proportional bias was assessed using linear regression.ResultsMetric VBT accurately detected over 95% of repetitions. It showed moderate to substantial agreement with the Vicon system for measuring RoM in both exercises. The average Limits of Agreement (LoA) for RoM across all camera positions were −5.45 to 4.94 cm for squats and −5.80 to 3.55 cm for bench presses. Metric VBT exhibited poor to moderate agreement with the Vicon system for measuring mean velocity. The average LoA for mean velocity were 0.03 to 0.25 m/s for squats and −5.80 to 3.55 m/s for bench presses. A proportional bias was observed, with bias increasing as repetition velocity increased.ConclusionsMetric VBT’s wide LoA for measuring RoM and mean velocity highlights significant accuracy concerns, exceeding acceptable levels for practical use. However, for users prioritizing repetition counts over precise RoM or mean velocity data, the application can still provide useful information for monitoring workout volume. creator: Danielle Anne Trowell creator: Angus G. Carruthers Collins creator: Ashlee M. Hendy creator: Eric James Drinkwater creator: Claire Kenneally-Dabrowski uri: https://doi.org/10.7717/peerj.17789 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Trowell et al. title: Application of combined teaching method of case-based-learning and clinical pathway in practical gynecological teaching link: https://peerj.com/articles/17813 last-modified: 2024-07-24 description: BackgroundTo train highly qualified medical talent in 5-year programs and improve students’ analytical and problem-solving abilities, it is necessary to change the traditional teaching method. This study introduces the combined teaching method of case-based learning (CBL) and clinical pathway and evaluates its role in practical gynecological teaching.MethodsMedical students in a 5-year program who were enrolled in the fourth year were selected as the research subjects; these students were randomized into two groups that separately received either the traditional teaching method or the combined teaching method of CBL and clinical pathway. Before the internship, a questionnaire was administered to explore students’ views of internship in gynecology, and after the internship, the questionnaire was administered to assess the two teaching methods. Furthermore, theoretical and skill tests were performed both before and after the internship.ResultsA total of 206 medical students in a 5-year program who were in their fourth year were enrolled in the study. Students in the experimental group performed significantly better than those in the control group. They performed significantly better in the postinternship test than in the preinternship test (P < 0.001). The questionnaire showed that more students in the experimental group thought that their learning interests, clinical skills, case analysis ability, clinical communication ability, understanding of theoretical knowledge and clinical thinking ability had improved and significantly differed between the two groups (P < 0.05).DiscussionCompared to traditional teaching methods, combined teaching method of CBL and clinical pathway can elevate students’ academic performance, improve their learning enthusiasm and help promote clinical teachers’ teaching quality. Additionally, this novel method is effective in facilitating the achievement of teaching objectives and improving the quality of talent training. Therefore, the combined teaching method of CBL and clinical pathway should be popularized and applied in gynecological practice. creator: Xiaoxia Wang creator: Xuan Che creator: Xuedong Tang creator: Zhengfen Xu uri: https://doi.org/10.7717/peerj.17813 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Wang et al. title: Reliability of dynamic and isometric upper muscle strength testing in breast cancer survivors link: https://peerj.com/articles/17576 last-modified: 2024-07-23 description: Breast cancer is the most common cancer in women worldwide, and its treatment usually involves a combination of many medical procedures, including surgery, chemotherapy, radiotherapy, and hormonal therapy. One of the detrimental effects on physical function is reduced upper limb muscle strength. This study aimed to evaluate upper body strength intra-day and inter-day (test-retest) reliability using the handgrip strength test (HGS) and the bilateral isometric bench press (BIBP) and the test-retest reliability of the one repetition maximum on the bench press (BP-1RM) in breast cancer survivors (BCS). Thirty-two (52.94 ± 8.99 yrs) BCS participated in this study. The muscle strength tests were performed in two different moments, three to seven days apart. Intraclass coefficient correlation (ICC) and coefficient of variation (CV) were used to assess the reliability. Standard error of measurement (SEM), typical error of measurement (TEM), and minimally detectable change (MDC) analyses were performed. The Bland-Altman analysis was used to assess the agreement between test-retest. We found a reliability that can be described as “high” to “very high” (ICC ≥ 0.88; CV ≤ 10%) for intra-day and test-retest. SEM% and MDC% were lower than 5% and 11%, respectively, for all intra-day testing. SEM% and TEM% ranged from 3% to 11%, and MDC% ranged from 9% to 23% in the test-retest reliability. The agreement demonstrated a systematic bias ranging from 2.3% to 6.0% for all testing, and a lower systematic bias may be presented in the non-treated side assessed by HGS and BIBP. HGS, BIBP, and BP-1RM assessments are reliable for measuring upper-body muscle strength in BCS. creator: Wanderson Santos creator: Vitor Marques creator: Claudio Andre B. de Lira creator: Wagner Martins creator: Amilton Vieira creator: Diba Mani creator: Claudio Battaglini creator: Carlos Vieira uri: https://doi.org/10.7717/peerj.17576 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Santos et al. title: Genetic variation for tolerance to pre-harvest sprouting in mungbean (Vigna radiata) genotypes link: https://peerj.com/articles/17609 last-modified: 2024-07-23 description: Pre-harvest sprouting (PHS) is one of the important abiotic stresses in mungbean which significantly reduces yield and quality of the produce. This study was conducted to evaluate the genetic variability for tolerance to pre-harvest sprouting in diverse mungbean genotypes while simultaneously deciphering the association of yield contributing traits with PHS. Eighty-three diverse mungbean genotypes (23 released varieties, 23 advanced breeding lines and 37 exotic germplasm lines) were investigated for tolerance to PHS, water imbibition capacities by pods, pod and seed physical traits. Wide variation in PHS was recorded which ranged between 17.8% to 81% (mean value 54.34%). Germplasm lines exhibited higher tolerance to PHS than the high-yielding released varieties. Correlation analysis revealed PHS to be positively associated with water imbibition capacity by pods (r = 0.21) and germinated pod % (r = 0.78). Pod length (r = −0.13) and seeds per pod (r = −0.13) were negatively influencing PHS. Positive associations between PHS and water imbibition capacity by pods, germinated pod % and 100-seed weight was further confirmed by multivariate analysis. Small-seeded genotypes having 100-seed weight <3 g exhibited higher tolerance to PHS compared to bold-seeded genotypes having 100-seed weight more than 3.5 g. Fresh seed germination among the selected PHS tolerant and susceptible genotypes ranged from 42% (M 204) to 98% (Pusa 1131). A positive association (r = 0.79) was recorded between fresh seed germination and PHS. Genotypes M 1255, M 145, M 422, M 1421 identified as potential genetic donors against PHS could be utilized in mungbean breeding programs. creator: Soma Gupta creator: Muraleedhar Aski creator: Gyan Prakash Mishra creator: Prachi S. Yadav creator: Kuldeep Tripathi creator: Sandeep Kumar Lal creator: Simran Jain creator: Ramakrishnan Madhavan Nair creator: Harsh Kumar Dikshit uri: https://doi.org/10.7717/peerj.17609 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gupta et al. title: Comparison of selective laser melting and stereolithography etching templates for guided endodontics link: https://peerj.com/articles/17646 last-modified: 2024-07-23 description: BackgroundWith the increasing application of guided endodontics to treat complex root canal treatment, the entire process of root canal treatment has become more precise, reducing damage to tooth structure and improving success rates. However, due to the limitations of the operating space, the use of guided endodontic templates in posterior root canal treatment is less common. This study aims to compare the accuracy and reliability of selective laser melting (SLM) and traditional stereolithography etching (SLA) guided endodontic templates for posterior root canals, providing better treatment strategies for posterior root canal treatment.MethodsThe teeth were randomly assigned to either SLM or SLA group. Preoperative cone-beam computed tomography (CBCT) and a three-dimensional (3D) scanner were used to establish the 3D root canal system and the accurate occlusal models of the teeth. The virtual access to the canal access was designed using Mimics 19.0 and 3-Matic 11.0. The endodontic access was performed based on either SLM or SLA templates. The accuracy of endodontic preparation was measured in three-dimensions by calculating deviations from planned accesses. The template height and tooth substance loss rates in each group were measured.ResultsSLM-guided templates have a low average deviation at the entry point and apical portion of the bur of total posterior teeth (including premolars and molars) and individual molars (P < 0.05). Moreover, there was a significant difference in angular deviations and height of template in total posterior teeth and individual molars (P < 0.05). The mean substance loss rate of the SLA group was slightly greater than that of the SLM group, but the difference was not statistically (P > 0.05).ConclusionsSLM-guided endodontics provides a more predictable and precise location of root canal orifice for the treatment of posterior teeth. creator: Ting Zhang creator: Du Chen creator: Fei Zhang creator: Sijing Xie creator: Guofeng Wu creator: Qingang Hu creator: Fuhua Yan creator: Xuna Tang uri: https://doi.org/10.7717/peerj.17646 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Tomato yellow leaf curl virus manipulates Bemisia tabaci, MEAM1 both directly and indirectly through changes in visual and volatile cues link: https://peerj.com/articles/17665 last-modified: 2024-07-23 description: The sweetpotato whitefly, Bemisia tabaci MEAM1, is one of the most devastating pests of row-crop vegetables worldwide, damaging crops directly through feeding and indirectly through the transmission of many different viruses, including the geminivirus Tomato yellow leaf curl virus (TYLCV). Y-tube olfactometer tests were conducted at different stages of TYLCV infection in tomatoes to understand how TYLCV affects B. tabaci behavior. We also recorded changes in tomato hosts’ color and volatile profiles using color spectrophotometry and gas chromatography-mass spectrometry (GC-MS). We found that the infection status of B. tabaci and the infection stage of TYLCV influenced host selection, with uninfected whiteflies showing a preference for TYLCV-infected hosts, especially during the late stages of infection. Viruliferous B. tabaci attraction to visual targets significantly differed from non-viruliferous B. tabaci. Late-stage infected hosts had larger surface areas reflecting yellow-green wavelengths and higher emissions of methyl salicylate in their volatile profiles. These findings shed new light on several critical mechanisms involved in the viral manipulation of an insect vector and its economically important host. creator: Thomson M. Paris creator: Nicholas Johnston creator: Iris Strzyzewski creator: Jessica L. Griesheimer creator: Benjamin Reimer creator: Kathi Malfa creator: Sandra A. Allan creator: Xavier Martini uri: https://doi.org/10.7717/peerj.17665 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Paris et al.