title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=275 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Evaluation of in vitro osteoblast and osteoclast differentiation from stem cell: a systematic review of morphological assays and staining techniques link: https://peerj.com/articles/17790 last-modified: 2024-07-25 description: BackgroundUnderstanding human stem cell differentiation into osteoblasts and osteoclasts is crucial for bone regeneration and disease modeling. Numerous morphological techniques have been employed to assess this differentiation, but a comprehensive review of their application and effectiveness is lacking.MethodsGuided by the PRISMA framework, we conducted a rigorous search through the PubMed, Web of Science and Scopus databases, analyzing 254 articles. Each article was scrutinized against pre-defined inclusion criteria, yielding a refined selection of 14 studies worthy of in-depth analysis.ResultsThe trends in using morphological approaches were identified for analyzing osteoblast and osteoclast differentiation. The three most used techniques for osteoblasts were Alizarin Red S (mineralization; six articles), von Kossa (mineralization; three articles) and alkaline phosphatase (ALP; two articles) followed by one article on Giemsa staining (cell morphology) and finally immunochemistry (three articles involved Vinculin, F-actin and Col1 biomarkers). For osteoclasts, tartrate-resistant acid phosphatase (TRAP staining) has the highest number of articles (six articles), followed by two articles on DAPI staining (cell morphology), and immunochemistry (two articles with VNR, Cathepsin K and TROP2. The study involved four stem cell types: peripheral blood monocyte, mesenchymal, dental pulp, and periodontal ligament.ConclusionThis review offers a valuable resource for researchers, with Alizarin Red S and TRAP staining being the most utilized morphological procedures for osteoblasts and osteoclasts, respectively. This understanding provides a foundation for future research in this rapidly changing field. creator: Shahrul Hisham Zainal Ariffin creator: Rohaya Megat Abdul Wahab creator: Muhammad Abdul Razak creator: Muhammad Dain Yazid creator: Muhammad Ashraf Shahidan creator: Azizi Miskon creator: Intan Zarina Zainol Abidin uri: https://doi.org/10.7717/peerj.17790 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zainal Ariffin et al. title: Identification of pre-flexion fish larvae from the western South Atlantic using DNA barcoding and morphological characters link: https://peerj.com/articles/17791 last-modified: 2024-07-25 description: Knowledge on species composition is the first step necessary for the proper conservation and management of biological resources and ecologically relevant species. High species diversity and a lack of diagnostic characters for some groups can impose difficulties for taxonomic identification through traditional methodologies, and ichthyoplankton (fish larvae and eggs) are a good example of such a scenario. With more than 35.000 valid species of fishes worldwide and overall similar anatomies in early developmental stages in closely related groups, fish larvae are often hard to be identified at the species or even more encompassing taxonomic levels. To overcome this situation, molecular techniques have been applied, with different markers tested over the years. Cytochrome c oxidase I (COI) is the most commonly used marker and now has the broadest public reference libraries, providing consistent results for species identification in different metazoan studies. Here we sequenced the mitochondrial COI-5P fragment of 89 fish larvae collected in the Campos Basin, coastal southeastern Brazil, and compared these sequences with references deposited in public databases to obtain taxonomic identifications. Most specimens identified are species of the Blenniiformes, with Parablennius and Labrisomus the most frequently identified genera. Parablennius included two species (P. marmoreus and P. pilicornis), while Labrisomus included three species (L. cricota, L. conditus and L. nuchipinnis). Anatomy of these molecularly identified specimens were then analyzed with the intention of finding anatomical characters that might be diagnostically informative amongst the early development stage (pre-flexion) larvae. Ventral pigmentation patterns are proposed as useful markers to identify Labrisomus species. However, additional specimens are needed to confirm if the character holds stability through the geographic distribution of the species. creator: Allan Pierre Bonetti Pozzobon creator: Jonathan Stuart Ready creator: Fabio Di Dario creator: Rodrigo Nunes-da-Fonseca uri: https://doi.org/10.7717/peerj.17791 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Pozzobon et al. title: Effect of bioceramic intracanal medication on the dentinal bond strength of bioceramic cements: an ex-vivo study link: https://peerj.com/articles/17826 last-modified: 2024-07-25 description: BackgroundThe present study evaluated the effect of a bioceramic intracanal medicament (Bio-C Temp) on the push-out bond strength of bioceramic cements.MethodsForty-eight human single-canaled premolars were prepared and randomly divided into three groups: Group (A) received no intracanal medicament; Group (B) calcium hydroxide (CH); and Group (C) Bio-C Temp. After medicament removal, the roots were sectioned transversely. The slices in each group were separated into two subgroups (n = 16): in Subgroup (1), mineral trioxide aggregate (MTA) was placed, and in Subgroup (2) Bio-C Repair. Push-out bond strength was determined using a universal testing machine, applying a constant compressive force on the cement until bond failure. The failure mode was also evaluated. Data were analyzed using the Chi-square test and two-way ANOVA followed by Tukey’s post hoc tests. The level of significance was set at 5%.ResultsThe pushout bond strength of Bio-C Repair was significantly higher than that of MTA irrespective of intracanal medication (p = 0.005). The placement of Bio-C Temp was associated with significantly lower bond strength (p = 0.002, p = 0.001).ConclusionBio-C Repair showed better bond strength compared to MTA, irrespective of intracanal medication. Bio-C Temp intracanal medicament, however, decreased the bond strength of both these cements. creator: Rahaf A. Almohareb creator: Reem M. Barakat creator: Fahda N. Algahtani creator: Mshael Ahmed Almohaimel creator: Denah Alaraj creator: Norah Alotaibi uri: https://doi.org/10.7717/peerj.17826 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Almohareb et al. title: Cognitive-behavioral treatment for insomnia and mindfulness-based stress reduction in nurses with insomnia: a non-inferiority internet delivered randomized controlled trial link: https://peerj.com/articles/17491 last-modified: 2024-07-24 description: BackgroundInsomnia is a highly prevalent sleep disorder frequently comorbid with mental health conditions in nurses. Despite the effectiveness of evidence-based cognitive behavioral therapy for insomnia (CBT-I), there is a critical need for alternative approaches. This study investigated whether internet-delivered mindfulness-based stress reduction (IMBSR) for insomnia could be an alternative to internet-delivered CBT-I (ICBT-I).ObjectiveThe hypothesis was that the IMBSR would be noninferior to the ICBT-I in reducing the severity of insomnia among nurses with insomnia. Additionally, it was expected that ICBT-I would produce a greater reduction in the severity of insomnia and depression than IMBSR.MethodAmong 240 screened nurses, 134 with insomnia were randomly allocated (IMBSR, n = 67; ICBT-I, n = 67). The assessment protocol comprised clinical interviews and self-reported outcome measures, including the Insomnia Severity Index (ISI), Patient Health Questionnaire-9 (PHQ-9), the 15-item Five Facet Mindfulness Questionnaire (FFMQ), and the Client Satisfaction Questionnaire (CSQ-I).ResultsThe retention rate was 55% with 77.6% (n = 104) of participants completing the study. At post-intervention, the noninferiority analysis of the ISI score showed that the upper limit of the 95% confidence interval was 4.88 (P = 0.46), surpassing the pre-specified noninferiority margin of 4 points. Analysis of covariance revealed that the ICBT-I group had significantly lower ISI (Cohen’s d = 1.37) and PHQ-9 (Cohen’s d = 0.71) scores than did the IMBSR group. In contrast, the IMBSR group showed a statistically significant increase in the FFMQ-15 score (Cohen’s d = 0.67). Within-group differences showed that both the IMBSR and ICBT-I were effective at reducing insomnia severity and depression severity and improving mindfulness.ConclusionOverall, nurses demonstrated high levels of satisfaction and adherence to both interventions. The IMBSR significantly reduced insomnia severity and depression, but the findings of this study do not provide strong evidence that the IMBSR is at least as effective as the ICBT-I in reducing insomnia symptoms among nurses with insomnia. The ICBT-I was found to be significantly superior to the IMBSR in reducing insomnia severity, making it a recommended treatment option for nurses with insomnia. creator: Wanran Guo creator: Nabi Nazari creator: Masoud Sadeghi uri: https://doi.org/10.7717/peerj.17491 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Guo et al. title: Systematic review assessing the effects of amendments on acidic soils pH in tea plantations link: https://peerj.com/articles/17653 last-modified: 2024-07-24 description: Soil acidification has emerged as a critical limiting factor for the sustainable development of the tea industry. In this article, a comprehensive review of 63 original research articles focusing on the impact of amendments on the pH in tea plantations soil was conducted. Through meta-analysis, the effect of applying soil amendments to increase the pH of tea plantation soil and its influencing factors were investigated. The results revealed that lime had a significant impact, increasing the pH by 18% in tea plantation soil, while rapeseed cake had a minimal (2%) effect. It was observed that as the quantity of amendments and pH levels increased, so did their impact on the pH of tea plantation soil. Subgroup analysis within biochar showed varying effects, depending on soil pH, with an 11% increase in acidic soil. Among these amendments, biochar produced at pyrolysis temperature ranging from 501–600 °C and derived from animal waste demonstrated significant effect on increasing soil pH in tea plantations by 9% and 12%, respectively. This study offers valuable insights into improving and ensuring the health and sustainability of tea plantations. creator: Zhenyu Yang creator: Bo Yao creator: Ronghui Li creator: Wenyan Yang creator: Dubin Dong creator: Zhengqian Ye creator: Yuchun Wang creator: Jiawei Ma uri: https://doi.org/10.7717/peerj.17653 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Yang et al. 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.