Identification of pre-flexion fish larvae from the western South Atlantic using DNA barcoding and morphological characters
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.
Pozzobon et al. (2024) Identification of pre-flexion fish larvae from the western South Atlantic using DNA barcoding and morphological characters. PeerJ 12:e17791 https://doi.org/10.7717/peerj.17791
Effect of bioceramic intracanal medication on the dentinal bond strength of bioceramic cements: an ex-vivo study
Background The present study evaluated the effect of a bioceramic intracanal medicament (Bio-C Temp) on the push-out bond strength of bioceramic cements. Methods Forty-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%. Results The 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). Conclusion Bio-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.
Almohareb et al. (2024) Effect of bioceramic intracanal medication on the dentinal bond strength of bioceramic cements: an ex-vivo study. PeerJ 12:e17826 https://doi.org/10.7717/peerj.17826
Cognitive-behavioral treatment for insomnia and mindfulness-based stress reduction in nurses with insomnia: a non-inferiority internet delivered randomized controlled trial
Background Insomnia 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). Objective The 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. Method Among 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). Results The 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. Conclusion Overall, 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.
Guo et al. (2024) Cognitive-behavioral treatment for insomnia and mindfulness-based stress reduction in nurses with insomnia: a non-inferiority internet delivered randomized controlled trial. PeerJ 12:e17491 https://doi.org/10.7717/peerj.17491
Systematic review assessing the effects of amendments on acidic soils pH in tea plantations
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.
Yang et al. (2024) Systematic review assessing the effects of amendments on acidic soils pH in tea plantations. PeerJ 12:e17653 https://doi.org/10.7717/peerj.17653
Applicability and perspectives for DNA barcoding of soil invertebrates
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.
Le Cadre et al. (2024) Applicability and perspectives for DNA barcoding of soil invertebrates. PeerJ 12:e17709 https://doi.org/10.7717/peerj.17709
Evaluation of the facial profile of skeletal Class III patients undergoing camouflage orthodontic treatment: a retrospective study
Objective To identify objective metrics for evaluating the esthetics of facial profiles in skeletal Class III patients undergoing camouflage orthodontic treatment. Methods Eighty 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. Results Lower 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. Conclusion Several 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.
Li et al. (2024) Evaluation of the facial profile of skeletal Class III patients undergoing camouflage orthodontic treatment: a retrospective study. PeerJ 12:e17733 https://doi.org/10.7717/peerj.17733
Evaluation of in-house dengue real-time PCR assays in West Java, Indonesia
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.
Kinanti et al. (2024) Evaluation of in-house dengue real-time PCR assays in West Java, Indonesia. PeerJ 12:e17758 https://doi.org/10.7717/peerj.17758
A methodological and reporting quality assessment of systematic reviews/meta-analyses on exercise interventions for cognitive function in older adults with mild cognitive impairment
Objective To 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. Methods Meta-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. Results Seventeen 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. Conclusion The 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.
Zang et al. (2024) A methodological and reporting quality assessment of systematic reviews/meta-analyses on exercise interventions for cognitive function in older adults with mild cognitive impairment. PeerJ 12:e17773 https://doi.org/10.7717/peerj.17773
Validation of a commercially available mobile application for velocity-based resistance training
Background Velocity-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. Methods Twenty-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. Results Metric 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. Conclusions Metric 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.
Trowell et al. (2024) Validation of a commercially available mobile application for velocity-based resistance training. PeerJ 12:e17789 https://doi.org/10.7717/peerj.17789
Application of combined teaching method of case-based-learning and clinical pathway in practical gynecological teaching
Background To 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. Methods Medical 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. Results A 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). Discussion Compared 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.
Wang et al. (2024) Application of combined teaching method of case-based-learning and clinical pathway in practical gynecological teaching. PeerJ 12:e17813 https://doi.org/10.7717/peerj.17813