title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=236 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Assessment of genetic diversity by phenological traits, field performance, and Start Codon Targeted (SCoT) polymorphism marker of seventeen soybean genotypes (Glycine max L.) link: https://peerj.com/articles/17868 last-modified: 2024-10-09 description: The Egyptian-farmed soybeans have a wide range of genetic diversity which is most important in plant improvement programs in order to develop new higher yielding soybean genotypes. The present study is designed to determine the genetic variability among seventeen genotypes of cultivated soybean (Glycine max L.) by examining the phenotypic level at the seedling stage, field performance over two years 2022/2023 and genetically using Start Codon Targeted (SCoT) markers. Results indicated that the SCoT markers, 100 seed weight, and tip angle (TA) traits were positively correlated with H2L12, DR 101, H15L5, and H117 genotypes. In addition, the number of branches per plant and plant height were associated with H113, H32, Crowford, H129, and D7512035. Furthermore, the length of the first internode (LFI), root width (RW), root length (RL), and shoot length (SL) were more associated with Giza 111, NC105, and Hutcheson. The hierarchical cluster analysis (HCA) and its associated heatmap explored the differences among the genotypes. It showed that all examined parameters were clustered into four distinct clusters. The obtained results showed that genotypes NC105, H30, D75_12035, and H2L12 have promising phenological and morphological traits besides tracking the inheritance of nearby genes surrounding the ATG translation start codon since they are in a monoclades. The obtained results will help the breeder plan appropriate selection strategies for improving seed yield in soybeans through hybridization from divergent clusters. creator: Mahmoud Abdel-Sattar creator: Ehab M. Zayed creator: Mohamed K. Abou-Shlell creator: Hail Z. Rihan creator: Ahmed A. Helal creator: Nabil E.G. Mekhaile creator: Ghada E. El-Badan uri: https://doi.org/10.7717/peerj.17868 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Abdel-Sattar et al. title: Dynamic perspectives on biodiversity quantification: beyond conventional metrics link: https://peerj.com/articles/17924 last-modified: 2024-10-09 description: Our research addresses the pressing need to assess biodiversity in the face of increasing habitat destruction and species extinctions. Several researchers have modelled conventional measures to assess biodiversity. Every measure evaluates biodiversity by considering different properties. Among them Simpson and Shannon indices are widely used, they primarily focus on species richness and abundance, overlooking the importance of rare or unique species. This limitation makes it challenging to identify which species drive changes in biodiversity and hampers conservation efforts. Moreover, these measures are sensitive to sample size and biased towards dominant species, leading to inaccurate estimations. To overcome these challenges, we propose a novel mathematical model that provides a comprehensive assessment of biodiversity. Our model accounts for species dominance, addresses sample size sensitivity, and highlights the significance of rare species within a community. By applying our measure to real-time scenarios and comparing it with traditional methods using the same dataset, proposed measure demonstrated its efficacy in capturing biodiversity dynamics over time. creator: Manjula Josephine Bollarapu creator: Swarna Kuchibhotla creator: Ramarao Kvsn creator: Harshita Patel uri: https://doi.org/10.7717/peerj.17924 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bollarapu et al. title: The relationship between virtual simulation, critical thinking, and self-directed learning abilities of nursing students in Riyadh, Saudi Arabia link: https://peerj.com/articles/18150 last-modified: 2024-10-09 description: ObjectiveThe use of virtual simulation in nursing education is an effective approach for improving nursing critical thinking and self-learning abilities, but the previous studies were limited to providing the required evidence that supports the association. This study aimed to assess the relationship between virtual simulation and critical thinking disposition and self-directed learning abilities among nursing students.MethodsThis is a descriptive correlational, non-experimental study. It was conducted among 201 third- and fourth-year nursing students at the Academic Institution, Saudi Arabia. A non-probability convenience sampling technique was used to select the participants; then, an online, adapted questionnaire was sent to the participants, the data from which was analyzed by SPSS.ResultsThe study findings showed that virtual simulation benefited nursing students. Most participants (56%) agreed that it helped them to think critically, and approximately 27% strongly agreed. It also enhanced their self-directed learning abilities, and the majority of the students agreed that they often review the way nursing practice is conducted. Furthermore, the results showed a significant, positive relationship between virtual simulation and the critical thinking disposition of nursing students (p-value = 0.03; correlation coefficient = 0.65), a strong positive relationship with self-directed learning abilities of nursing students (p-value = 0.004; correlation coefficient = 0.78), and a strong positive relationship between critical thinking disposition with self-directed learning abilities of nursing students (p-value = 0.01; correlation coefficient = 0.72).ConclusionThere are significant relationships between virtual simulation and the critical thinking disposition and self-directed learning abilities of nursing students. Furthermore, virtual simulation made the students practice critical thinking and self-learning, so, they simulate events and try to seek out and solve the problems. creator: Hanan F. Alharbi creator: Amjad Alsubaie creator: Rahaf Gharawi creator: Rawan Ba Mazroo creator: Shaikhah Alajaleen creator: Munerah Alsultan creator: Munira Alsaleem creator: Nora Alsubihi creator: Norah Alsahli creator: Nashwa Alqahtani creator: Raghad Rayzah uri: https://doi.org/10.7717/peerj.18150 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Alharbi et al. title: Health perceptions of patients with forgotten double-J stent link: https://peerj.com/articles/18156 last-modified: 2024-10-09 description: AimIn this article, we aimed to determine the health perceptions of the patients who did not apply for double-J stent (DJS) removal on time and evaluate whether health perceptions impact this behavior.Materials and MethodsHealth perceptions of 22 patients who were treated for forgotten double-J stent (FDJS) between January 2017–October 2020 and 25 patients who applied for DJS removal during the given appointment time in the urology department of Elazig Training and Research Hospital and Elazig Fethi Sekin City Hospital were compared using the “Health Perception Scale”.ResultsHealth perception scale scores in the FDJS group and control group were 62-68 (mean = 64.27 ± 1.75) and 63-68 (mean = 65.36 ± 1.55), respectively. With regard to the sub-factors of the scale, control center scores were 21.86 ± 0.77 and 22.08 ± 1.15; precision scores were 16.54 ± 0.80 and 16.56 ± 0.82; importance of health scores were 12.77 ± 0, 92 and 13.32 ± 0.74; and self-awareness points were 13.04  ± 0.72 and 13.48 ± 0.58, respectively. There was a statistically significant difference between the health perception scale in total, importance of health, and self-awareness scores between the two groups. At the same time, there was no difference in terms of the control center and precision scores (p∗ = 0.029, p∗ = 0.030, p∗ = 0.028, p = 0.460, p = 0.951).ConclusionPatients’ and their families’ educational status, income levels and lack of follow-up by healthcare professionals play an important role in forgotten DJS cases and patients’ perception of health may also have an impact on this behavior. creator: Mehmet Sezai Ogras creator: Kadir Yildirim uri: https://doi.org/10.7717/peerj.18156 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ogras and Yildirim title: Effects of video game immersion and task interference on cognitive performance: a study on immediate and delayed recall and recognition accuracy link: https://peerj.com/articles/18195 last-modified: 2024-10-09 description: This study investigates the cognitive impacts of video game immersion and task interference on immediate and delayed recall as well as recognition tasks. We enrolled 160 subjects aged 18 to 29, who were regular players of “shoot-em-up” video games for at least 3 years. Participants were assigned to one of three experimental groups or a control group. The experimental conditions varied in the timing and type of tasks: the first group performed a video game session between recall tasks, the second group multitasked with video games and recall tasks simultaneously, and the third group engaged in task switching from video games to recall tasks. Using the Rey Auditory Verbal Learning Test, we measured the effects of these conditions on cognitive performance, focusing on error types and recall accuracy. Results indicated that multitasking and task switching significantly affected the subjects’ performance, with notable decrements in recall and recognition accuracy in conditions of high task interference. The study highlights the cognitive costs associated with multitasking in immersive digital games and provides insights into how task similarity and interference might increase error rates and affect memory performance. creator: Stefania Mancone creator: Beatrice Tosti creator: Stefano Corrado creator: Pierluigi Diotaiuti uri: https://doi.org/10.7717/peerj.18195 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mancone et al. title: Integrating whole genome sequencing and machine learning for predicting antimicrobial resistance in critical pathogens: a systematic review of antimicrobial susceptibility tests link: https://peerj.com/articles/18213 last-modified: 2024-10-09 description: BackgroundInfections caused by antibiotic-resistant bacteria pose a major challenge to modern healthcare. This systematic review evaluates the efficacy of machine learning (ML) approaches in predicting antimicrobial resistance (AMR) in critical pathogens (CP), considering Whole Genome Sequencing (WGS) and antimicrobial susceptibility testing (AST).MethodsThe search covered databases including PubMed/MEDLINE, EMBASE, Web of Science, SCOPUS, and SCIELO, from their inception until June 2024. The review protocol was officially registered on PROSPERO (CRD42024543099).ResultsThe review included 26 papers, analyzing data from 104,141 microbial samples. Random Forest (RF), XGBoost, and logistic regression (LR) emerged as the top-performing models, with mean Area Under the Receiver Operating Characteristic (AUC) values of 0.89, 0.87, and 0.87, respectively. RF showed superior performance with AUC values ranging from 0.66 to 0.97, while XGBoost and LR showed similar performance with AUC values ranging from 0.83 to 0.91 and 0.76 to 0.96, respectively. Most studies indicate that integrating WGS and AST data into ML models enhances predictive performance, improves antibiotic stewardship, and provides valuable clinical decision support. ML shows significant promise for predicting AMR by integrating WGS and AST data in CP. Standardized guidelines are needed to ensure consistency in future research. creator: Carlos M. Ardila creator: Pradeep K. Yadalam creator: Daniel González-Arroyave uri: https://doi.org/10.7717/peerj.18213 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ardila et al. title: Pdk3’s role in RANKL-induced osteoclast differentiation: insights from a bone marrow macrophage model link: https://peerj.com/articles/18222 last-modified: 2024-10-09 description: BackgroundOsteoporosis (OP) is a chronic disease characterized by decreased bone mass, loss of skeletal structural integrity and increased susceptibility to fracture. Available studies have shown that the pyruvate dehydrogenase kinase (PDK) family is associated with osteoclastogenesis and bone loss, but the specific role of Pdk3 in bone pathology has not been systematically investigated. MethodsA cell OP model was established in receptor activator for nuclear factor-κB Ligand (RANKL)-induced bone marrow macrophages (BMMs). Hereafter, the expression levels of Pdk3 and osteoclastogenesis feature genes including nuclear factor of activated T cells 1 (Nfatc1), Cathepsin K (Ctsk), osteoclast associated Ig-like receptor (Oscar) in BMMs-derived osteoclasts were examined based on real-time quantitative PCR and western blotting methods. Further, the phosphorylation of ERK, P65 and JAK/STAT and their correlation was Pdk3 was gauged. In particular, changes in the activity of these signaling pathways were observed by silencing experiments of the Pdk3 gene (using small interfering RNA). Finally, the effects of Pdk3 gene silencing on signaling pathway activity, osteoclastogenesis, and related inflammatory and apoptotic indicators were observed by transfection with PDK3-specific siRNA.ResultsFollowing RANKL exposure, the levels of Pdk3 and osteoclastogenesis feature genes were all elevated, and a positive correlation between Pdk3 and osteoclastogenesis feature genes was seen. Meanwhile, ERK, P65 and JAK/STAT phosphorylation was increased by RANKL, and Pdk3 was confirmed to be positively correlated with the phosphorylation of ERK, P65 and JAK/STAT. Additionally, in RANKL-exposed osteoclasts, Pdk3 knockdown diminished the phosphorylation of ERK, P65 and JAK/STAT, reduced the expressions of osteoclastogenesis feature genes. Importantly, knockdown of Pdk3 also reduced the expression of inflammatory cytokines and resulted in elevated levels of Bax and Casp3 expression, as well as downregulation of Bcl2 expression.ConclusionThis study reveals for the first time the role of Pdk3 in RANKL-induced osteoclastogenesis and OP. These findings provide a foundation for future studies on the role of Pdk3 in other bone diseases and provide new ideas for the development of OP therapeutics targeting Pdk3. creator: Nan Zhang creator: Lingting Wang creator: Xuxin Ye uri: https://doi.org/10.7717/peerj.18222 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: The impact of three thioxothiazolidin compounds on trehalase activity and development of Spodoptera frugiperda larvae link: https://peerj.com/articles/18233 last-modified: 2024-10-09 description: Trehalases (TREs), serving as crucial enzymes regulating trehalose and chitin metabolism in insects, represent prime targets for pest control strategies. We investigated the impact of three thioxothiazolidin compounds (1G, 2G, and 11G) on TRE activity and summarized their effects on the growth and development of Spodoptera frugiperda (Lepidoptera, Noctuidae). The experimental larvae of S. frugiperda were injected with the three thioxothiazolidin compounds (1G, 2G, and 11G), while the control group received an equivalent volume of 2% DMSO as a control. All three compounds had a strong effect on inhibiting TRE activity, significantly prolonging the pre-pupal development stage. However, compared with the 11G-treated group, the survival rate of larvae treated with 1G and 2G was significantly reduced by 31.11% and 27.78% respectively, while the occurrence of phenotypic abnormalities related to growth and development was higher. These results manifest that only the TRE inhibitors, 1G and 2G, modulate trehalose and chitin metabolism pathways of larvae, ultimately resulting in the failure molting and reduction of survival rates. Consequently, the thioxothiazolidin compounds, 1G and 2G, hold potential as environmentally friendly insecticides. creator: Yan Wu creator: Shangrong Hu creator: Qixuan Mao creator: Dongmei Shi creator: Xiangyu Liu creator: Busheng Liu creator: Liyuhan Hua creator: Gao Hu creator: Can Li creator: Hongxia Duan creator: Bin Tang uri: https://doi.org/10.7717/peerj.18233 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wu et al. title: Enhancement of loop-mediated isothermal amplification (LAMP) with guanidine hydrochloride for the detection of Streptococcus equi subspecies equi (Strangles) link: https://peerj.com/articles/17955 last-modified: 2024-10-08 description: Streptococcus equi subspecies equi, commonly referred to as “strangles”, poses a significant biosecurity challenge across equine farms worldwide. The continuous prevalence and highly transmissibility of strangles necessitates a rapid and accurate diagnostic procedure. However, current “gold-standard” techniques, such as cultures and quantitative polymerase chain reaction (qPCR), are unreliable or inaccessible, and require lengthy periods between sample collection and results. Moreover, the lack of a standardized detection protocol can lead to variations in results. This study aimed to develop a reproducible and field-deployable diagnostic assay to detect strangles in real-time. Utilising the rapid technique loop-mediated isothermal amplification (LAMP), we developed an assay targeting a conserved region of the S. equi-specific M gene (SeM). Additionally, we optimised our assay with guanidine hydrochloride (GuHCl) to enhance the assay’s performance and detection capabilities. The Str-LAMP was able to detect S. equi within 13 minutes and 20 seconds for both synthetic DNA and clinical isolates, with a limit of detection (LOD) of  53 copies/µl. Our assay demonstrated high repeatability with the inter-coefficient of variation ranging from 0.17% to 3.93%. Furthermore, the clinical sensitivity and specificity was calculated at 91.3% and 93.3%, respectively, with a correct classification rate of 91.8%. The implementation of this newly developed strangles assay can be employed as an efficient aid for in-field surveillance programs. The assay’s reproducibility can allow for equine managers to undertake routine self-surveillance on their properties, without the requirement of specialised training. The Str-LAMP assay has the potential to be a valuable tool to help mitigate potential strangles outbreaks. creator: Alexandra Knox creator: Travis Beddoe uri: https://doi.org/10.7717/peerj.17955 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Knox and Beddoe title: Adaptation and validation of the Spanish version of the Being a Mother scale link: https://peerj.com/articles/18015 last-modified: 2024-10-08 description: BackgroundBecoming a mother is a very important process because of the impact it can have on women and their families. Currently, there is no validated questionnaire that evaluates the process of becoming a mother in the Spanish population. Moreover, no consistent results have been obtained to identify significant differences between primiparous and multiparous mothers.Aim(1) Linguistic and metric validation of the Being a Mother scale (BaM-13) in the Spanish population, (2) analysis of possible differences between primiparous and multiparous mothers’ experience of motherhood.MethodsInstrumental design. In 2016–2017, a sample of 579 mothers with children between 6 and 11 months of age completed the Spanish version of BaM-13. The instrument was translated using forward and back translation. Construct validity, internal consistency, and criterion validity were empirically analyzed.ResultsFactorial analyses showed that the scale presented two adequate factors. Internal consistency of the global scale (α = 0.818, ω = 0.861), the Postnatal bonding factor (α = 0.773, ω = 0.784), and the Adult’s experience factor (α = 0.710, ω = 0.721) was adequate. Significant associations were found with postpartum depression (r = 0.560), parental competence (r =  − 0.584) and postnatal bonding (r =  − 0.327). In terms of parity, primiparous mothers have greater difficulty in postnatal bonding, compared to multiparous mothers (p = 0.006).ConclusionsThe Spanish version of the BaM-13 scale is valid for measuring mothers’ experience of motherhood in a wide range of domains. The findings of the study show the importance of considering parity in the experience of becoming a mother, highlighting the approach to postnatal bonding in primiparous mothers. Additionally, we underline that it should not be assumed that multiparous mothers experience fewer difficulties in their motherhood process. creator: Anna Riera-Martín creator: Antonio Oliver-Roig creator: Susana Cormenzana creator: Miguel Richart-Martínez creator: Ana Martínez-Pampliega uri: https://doi.org/10.7717/peerj.18015 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Riera-Martín et al.