title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=219 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Potential molecular mechanisms of ETV6-RUNX1-positive B progenitor cell cluster in acute lymphoblastic leukemia revealed by single-cell RNA sequencing link: https://peerj.com/articles/18445 last-modified: 2024-11-01 description: AimThis study was to explore role of immune landscape and the immune cells in acute lymphoblastic leukemia (ALL) progression.BackgroundThe most prevalent genetic alteration in childhood ALL is the ETV6-RUNX1 fusion. The increased proliferation of B progenitor cells could expedite the disease’s progression due to irregularities in the cell cycle. Nevertheless, the mechanisms by which particular cell clusters influence the cell cycle and promote the advancement of ALL are still not well understood.ObjectiveThis study was to explore role of immune landscape and the immune cells in ALL progression.MethodsSingle-cell RNA sequencing (scRNA-seq) data of ETV6-RUNX1 and healthy pediatric samples obtained from GSE132509 were clustered and annotated using the Seurat package, and differentially highly expressed genes identified in each cluster were analyzed using DAVID for pathway annotation. Chromosome amplification and deletion were analyzed using the inferCNV package. SCENIC evaluated the regulation of transcription factors and target gene formation in cells. cellphoneDB and CellChat were served to infer ligand-receptor pairs that mediate interactions between subpopulations. The role of the target gene in regulating ALL progression was assessed using RT-qPCR, Transwell and scratch healing assays.ResultsThe bone marrow mononuclear cells (BMMCs) from ETV6-RUNX1 and healthy pediatric samples in GSE132509 were divided into 11 clusters, and B cell cluster 1 was identified as B progenitor cell, which was amplified on chromosome 6p. B progenitor cells were divided into seven clusters. Expression levels of amplified genes in chromosome 6p of B progenitor cell cluster 5 were the highest, and its specific highly expressed genes were annotated to pathways promoting cell cycle progression. Regulons formed in B progenitor cell cluster 5 were all involved in promoting cell cycle progression, so it was regarded as the B progenitor cell cluster that drives cell cycle progression. The key regulator of the B progenitor cell is E2F1, which promotes the migration and invasion ability of the cell line HAP1. The major ligand-receptor pairs that mediate the communication of B progenitor cell cluster 5 with cytotoxic NK/T cells or naive T cells included FAM3C−CLEC2D, CD47−SIRPG, HLAE−KLRC2, and CD47−KLRC2. HLAE−KLRC1 and TGFB1−(TGFBR1+TGFBR2).ConclusionThis study outlined the immune cell landscape of ETV6-RUNX1 ALL and identified chromosome 6p amplification in B progenitor cells, described the major B progenitor cell cluster driving cell cycle progression and its potential regulatory mechanisms on NK cells and T cells, providing cellular and molecular insights into ETV6-RUNX1 ALL. creator: Ning Qu creator: Yue Wan creator: Xin Sui creator: Tianyi Sui creator: Yang Yang uri: https://doi.org/10.7717/peerj.18445 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Qu et al. title: Prognosis of hepatitis B virus reactivation in newly diagnosed multiple myeloma in modern era therapy: a retrospective study link: https://peerj.com/articles/18475 last-modified: 2024-11-01 description: Studies on the prognosis of hepatitis B virus (HBV) reactivation following modern therapies for newly diagnosed MM (NDMM) are lacking. In this retrospective study, we aimed to assess the incidence, risk factors and prognosis of HBV reactivation in NDMM. A total of 33 of 355 patients with NDMM and HBV reactivation were included in this study. Multivariable analysis showed that hepatitis B surface antigen-positivity, hepatitis B core antibody-positivity, bortezomib-containing regimens, autologous stem cell transplantation, and gain of 1q21 were identified as independent risk factors of HBV reactivation in NDMM patients. The NDMM patients with HBV reactivation had poorer 3-year overall survival (OS) and progression-free survival (PFS) than did those without HBV reactivation, as confirmed by multivariate analysis. In conclusion, HBV reactivation in patients with NDMM constitutes a significant complication, correlating with reduced OS and PFS, and emerges as a potential adverse prognostic factor in the contemporary era of treatment. creator: Weiran Lv creator: Xiaojin Li creator: Jingbo Xu creator: Yun Wang creator: Hanying Huang creator: Fang Hu creator: Yingying Cui creator: Yuanbin Song creator: Lezong Chen creator: Bingyi Wu creator: Yang Liang uri: https://doi.org/10.7717/peerj.18475 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Lv et al. title: A novel nomogram to predict the risk of requiring mechanical ventilation in patients with sepsis within 48 hours of admission: a retrospective analysis link: https://peerj.com/articles/18500 last-modified: 2024-11-01 description: ObjectiveTo establish a model that can predict the risk of requiring mechanical ventilation within 48 h after admission in patients with sepsis.MethodsData for patients with sepsis admitted to Dongyang People’s Hospital from October 2011 to October 2023 were collected and divided into a modeling group and a validation group. Independent risk factors in the modeling group were analyzed, and a corresponding predictive nomogram was established. The model was evaluated for discriminative power (the area under the curve of the receiver operating characteristic curve, AUC), calibration degree (Hosmer-Lemeshow test), and clinical benefit (decision curve analysis, DCA). Models based on the Sequential Organ Failure Assessment (SOFA) scores, the National Early Warning Score (NEWS) scores and multiple machine learning methods were also established.ResultsThe independent factors related to the risk of requiring mechanical ventilation in patients with sepsis within 48 h included lactic acid, pro-brain natriuretic peptide (PRO-BNP), and albumin levels, as well as prothrombin time, the presence of lung infection, and D-dimer levels. The AUC values of nomogram model in the modeling group and validation group were 0.820 and 0.837, respectively. The nomogram model had a good fit and clinical value. The AUC values of the models constructed using SOFA scores and NEWSs were significantly lower than those of the nomogram (P < 0.01). The AUC value of the integrated machine-learning model for the validation group was 0.849, comparable to that of the nomogram model (P = 0.791).ConclusionThe established nomogram could effectively predict the risk of requiring mechanical ventilation within 48 h of admission by patients with sepsis. Thus, the model can be used for the treatment and management of sepsis. creator: Bin Wang creator: Jian Ouyang creator: Rui Xing creator: Jiyuan Jiang creator: Manzhen Ying uri: https://doi.org/10.7717/peerj.18500 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: The behavior patterns of giraffes (Giraffa camelopardalis) housed across 18 US zoos link: https://peerj.com/articles/18164 last-modified: 2024-10-31 description: Interpreting animal behavior in the context of welfare can be inherently challenging given the limited behavior data available for many species housed in zoos. Describing common behavior patterns may help animal managers by providing additional background when assessing the individuals in their care. Although valuable, these efforts require a large, collaborative approach and have, consequently, been rare. Here, we share the behavior patterns of zoo-housed giraffes, an iconic and commonly housed megafauna in zoos. Behavior data were evaluated for 66 giraffes living across 18 AZA-accredited zoos using the ZooMonitor Community platform. Data were recorded during 10-minute observation sessions. Observations were conducted during daytime hours over the course of approximately one year at each zoo (mean total observed time per individual = 23.2 hr). The most common behaviors observed were feeding/ foraging behaviors, which accounted for 38.6% of the mean visible time budget across giraffes. Time spent in these behaviors varied by individual and ranged from 14.3% to 69.3% of visible time. Stereotypic behaviors occurred in all study individuals, with oral stereotypic behaviors being most common. Although prevalent, stereotypic behaviors varied considerably across giraffes, with some individuals exhibiting these behaviors only on a few occasions to an individual that exhibited these behaviors once every few minutes. This study provides a robust evaluation of giraffe behavior across zoos to present a picture of their common behavior patterns in managed care. We hope these multi-institutional behavior patterns can provide perspective to aid animal managers in evaluating giraffes in their care. creator: Jason D. Wark creator: Katherine A. Cronin uri: https://doi.org/10.7717/peerj.18164 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wark and Cronin title: Phylogenetic and taxonomic revisions of Jurassic sea stars support a delayed evolutionary origin of the Asteriidae link: https://peerj.com/articles/18169 last-modified: 2024-10-31 description: BackgroundThe superorder Forcipulatacea is a major clade of sea stars with approximately 400 extant species across three orders (Forcipulatida, Brisingida, Zorocallida). Over the past century, the systematics of Forcipulatacea have undergone multiple revisions by various authors, with some considering numerous families such as Asteriidae, Zoroasteridae, Pedicellasteridae, Stichasteridae, Heliasteridae, Labidiasteridae, and Neomorphasteridae, while others recognized only two families (i.e., Asteriidae and Zoroasteridae). Recent molecular analyses have shown the artificial nature of some of these groupings. Notably, four well-supported clades (Zorocallida, Brisingida, Stichasteridae, and Asteriidae) emerged from a synthesis of morphological and molecular evidence. The majority of extinct forcipulatacean species have been placed in modern families. However, many of these fossil species are in need of revision, especially those species placed within the Asteriidae, the largest of all forcipulatacean families.MethodsIn light of recent advancements in forcipulatacean systematics, we comprehensively reassess six well-preserved Jurassic forcipulatacean taxa, including the earliest crown-group members from the Hettangian (∼201.4 Ma), and also describe two new Jurassic genera, Forbesasterias gen. nov. and Marbleaster gen. nov. We assembled the largest and most comprehensive phylogenetic matrix for this group, sampling 42 fossil and extant forcipulatacean species for 120 morphological characters. To infer phylogenetic relationships and construct an evolutionary timeline for the diversification of major clades, we conducted a Bayesian tip-dating analysis incorporating the fossilized birth-death process. A total of 13 fossil species were sampled in our analysis, including six taxonomically revaluated herein, two recently reappraised species from the Jurassic, and five additional species from the Cretaceous and Miocene.ResultsContrary to prior assumptions, our results indicate that none of the Jurassic taxa investigated belong to Asteriidae or any other modern families, and instead represent stem-forcipulatids. Furthermore, our phylogenetic results suggest that Asteriidae likely originated during the late Cretaceous. Our findings highlight a greater early diversity within the Forcipulatacea than previously presumed, challenging existing perceptions of the evolutionary history of this significant clade of marine invertebrates. creator: Marine Fau creator: David F. Wright creator: Timothy A.M. Ewin creator: Andrew S. Gale creator: Loïc Villier uri: https://doi.org/10.7717/peerj.18169 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Fau et al. title: Effect of bioceramic-based and resin-based sealers on postoperative discomfort following root canal therapy: a systematic review and meta-analysis link: https://peerj.com/articles/18198 last-modified: 2024-10-31 description: BackgroundThe aim of this systematic review and meta-analysis was to furnish evidence-based recommendations for the utilization of bioceramic-based and resin-based sealers in clinical endodontics, with a focus on reducing postoperative discomfort.MethodsThe investigation’s methodology was registered on the International Prospective Database of Systematic Reviews (PROSPERO: CRD42022355506) and executed using the 2020 PRISMA protocol. Articles were selected utilizing the PICO technique and applying specific inclusion and exclusion criteria. Articles published between January 2000 and August 2022, PubMed, MEDLINE, and DOAJ were utilized as primary data sources. After the identification of studies, two autonomous reviewers evaluated the titles and abstracts, and data from qualifying studies were extracted.ResultsNine published studies were included in this analysis. The findings indicate that there were no significant differences in the Visual Analog Scale (VAS) scores between resin-based and bioceramic root canal sealers at intervals of 6 hours, 12 hours, 24 hours, and 48 hours after treatment.ConclusionThe findings of this systematic review and meta-analysis suggest that after the utilization of bioceramic sealers during root canal therapy, the pain and discomfort levels were not significantly different from those experienced pain after the use of resin-based sealers. creator: Mansi Supare creator: Ajinkya M. Pawar creator: Kashmira Sawant creator: Dian Agustin Wahjuningrum creator: Suraj Arora creator: Firas Elmsmari creator: Mohmed Isaqali Karobari creator: Bhagyashree Thakur uri: https://doi.org/10.7717/peerj.18198 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Supare et al. title: Assessing population structure and morpho-molecular characterization of sunflower (Helianthus annuus L.) for elite germplasm identification link: https://peerj.com/articles/18205 last-modified: 2024-10-31 description: Sunflower (Helianthus annuus L.), known for its adaptability and high yield potential, is vital in global edible oil production. Estimating genetic diversity is a key pre-breeding activity in crop breeding. The current study comprised of 48 genotypes which were assessed for their biometrical traits at department of Oilseeds, Tamil Nadu Agricultural University, during the rainy season of 2022. The lines were subsequently characterised using 103 simple sequence repeat (SSR) markers for molecular diversity analysis. The results indicated that the net nucleotide distances indicated varying genetic divergence, with subpopulations II and V showing the highest (0.056) and I and IV the lowest (0.014). Subpopulation IV exhibited the highest heterozygosity (0.352), while subpopulation III had the lowest heterozygosity and a low Fst (0.173). Principal components analysis (PCA) and hierarchical cluster analysis were employed for assessing the morphological diversity, facilitating genotype grouping and parent selection for breeding programs. The first four components cumulatively accounted for 86.72% of the total variation. Cluster Analysis grouped 48 sunflower genotypes into three clusters based on genetic diversity. COSF 13B stands out for its high head diameter, oil content, seed yield, and oil yield based on mean performance of morphological data. Principal coordinate analysis (PCoA) mirrored the groupings from the Neighbor Joining method, with the first three components explaining 27.24% of the total variation. Molecular data analysis identified five distinct clusters among the germplasm. By integrating morphological and molecular marker data with genetic distance analysis, substantial diversity was revealed with the genotypes RHA 273 and GMU 325 consistently demonstrated high oil yield per plant. The genotypes GMU 477, GMU 450, COSF 13B, RHA 102, CMS 1103B, and RHA GPR 58 have been identified as suitable parents for enhancing oil content in sunflower breeding programs. These findings also aid in selecting SSR markers for genotype characterization and in choosing diverse parents for breeding programs. creator: Sampath Lavudya creator: Kalaimagal Thiyagarajan creator: Sasikala Ramasamy creator: Harish Sankarasubramanian creator: Senthivelu Muniyandi creator: Anita Bellie creator: Sushil Kumar creator: Susmitha Dhanapal uri: https://doi.org/10.7717/peerj.18205 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lavudya et al. title: Study on the effect of chlorogenic acid on the antimicrobial effect, physical properties and model accuracy of alginate impression materials link: https://peerj.com/articles/18228 last-modified: 2024-10-31 description: BackgroundDental impressions are essential for accurately capturing the detailed anatomy of teeth and surrounding oral structures. However, these impressions often become contaminated with saliva and blood, making proper disinfection necessary. The application of chemical disinfectants has been associated with negative side effects, leading to suboptimal disinfection practices in clinical settings.ObjectiveThe purpose of this study was to evaluate the effectiveness of chlorogenic acid (CA) as a disinfectant for alginate impression materials, the impact of CA disinfection on the physical properties and dimensional accuracy of alginate impressions was also investigated.MethodsThe physical properties of alginate impression materials, such as elastic recovery, strain-in-compression, initial setting time, and fluidity, were assessed after mixing the alginate impression materials with three different concentrations of CA solution (10 mg/mL, 15 mg/mL, 20 mg/mL). To evaluate the antimicrobial effect of CA, alginate impressions mixed with a 10 mg/mL CA solution and impressions mixed with distilled water (control group) were contaminated with four types of microorganism: Escherichia coli, Staphylococcus aureus, Candida albicans, and Streptococcus pneumoniae. Following a five-minute incubation period, a CA solution at a concentration of either 50 mg/mL, 55 mg/mL, or 60 mg/mL was sprayed on the samples for disinfection. Samples were collected at different time intervals (10 min, 20 min, 30 min) and cultured to determine the number of colony-forming units (CFU/mL), providing insight into the antimicrobial efficacy of these CA solutions. The dimensional accuracy of alginate impressions was assessed in three groups: one with alginate impressions mixed with distilled water, another with alginate impressions sterilized with available chlorine (2,000 mg/L) mixed with distilled water, and the last group consisting of alginate impressions mixed with 10 mg/mL CA solution and sprayed with 60 mg/mL CA solution. Both the standard model and the plaster model underwent 3D scanning, and the data were processed and compared by software. The root mean square (RMS) was used as a parameter to evaluate the deviation between models.ResultsAll alginate impression materials mixed with either 10 mg/mL, 15 mg/mL, or 20 mg/mL concentrations of CA solution met the ISO 21563 standard for elastic recovery, strain-in-compression, and fluidity. However, only the material mixed with a concentration of 10 mg/mL CA had an initial setting time within the range specified by the T-6505 Japanese industrial standard. The application of CA solution by mixing or spraying showed significant antimicrobial effects on Staphylococcus aureus, Escherichia coli, Candida albicans, and Streptococcus pneumoniae. There was no significant difference in the dimensional accuracy of the alginate impressions between the group of the CA solution applied, the blank group, or the chlorine intervention group. creator: Shuling Jiang creator: Fu-Qing Chen creator: Qiao-qiao Hu creator: Fen Yang creator: Niya Hu creator: Xi Nan Luo creator: Yewen Zhang creator: Nuodan Wu creator: Na Li uri: https://doi.org/10.7717/peerj.18228 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Jiang et al. title: Identification and validation of a prognostic model based on immune-related genes in ovarian carcinoma link: https://peerj.com/articles/18235 last-modified: 2024-10-31 description: BackgroundA novel valuable prognostic model has been developed on the basis of immune-related genes (IRGs), which could be used to estimate overall survival (OS) in ovarian cancer (OC) patients in The Cancer Genome Atlas (TCGA) dataset and the International Cancer Genome Consortium (ICGC) dataset.MethodsThis prognostic model was engineered by employing LASSO regression in training cohort (TCGA dataset). The corresponding growth predictive values of this model for individualized survival was evaluated using survival analysis, receiver operating characteristic curve (ROC curve), and risk curve analysis. Combined with clinical characteristics, a model risk score nomogram for OS was well built. Thereafter, depended on the model risk score, patients were divided into high and low risk subgroups. The survival difference between these subgroups was measured using Kaplan-Meier survival method. In addition, correlations containing pathway enrichment, treatment, immune cell infiltration and the prognostic model were also analyzed. We established the ovarian cancer cell line W038 for this study and identified the performances of GBP1P1 knockdown on a series of activities including cellular proliferation, apoptosis, migration, and invasion of W038 cells in vitro.ResultsWe constructed a 25-genes prognostic model (TNFAIP8L3, PI3, TMEM181, GBP1P1 (LOC400759), STX18, KIF26B, MRPS11, CACNA1C, PACSIN3, GMPR, MANF, PYGB, SNRPA1, ST7L, ZBP1, BMPR1B-DT, STAC2, LINC02585, LYPD6, NSG1, ACOT13, FAM120B, LEFTY1, SULT1A2, FZD3). The areas under the curves (AUC) of 1, 2 and 3 years were 0.806, 0.773 and 0.762, in the TCGA cohort, respectively. Besides, the effectiveness of the model was verified using ICGC testing data. Univariate and multivariate Cox regression analysis exposes the risk score as an independent prognosis predictor for OS both in the TCGA and ICGC cohort. In summary, we utilized comprehensive bioinformatics analysis to build an effective prognostic gene model for OC patients. These bioinformatic results suggested that GBP1P1 could act as a novel biomarker for OC. GBP1P1 knockdown substantially inhibited the proliferation, migration, and invasion of W038 cells in vitro, and increased the percentage of apoptotic W038 cells.ConclusionsThe analyses of genetic status of patients with 25-genes model might improve the ability to predict the prognosis of patients with OC and help to select patients suit able to therapies. Immune-related gene GBP1P1 might serve as prognostic biomarker for OC. creator: Min Yu creator: Dan Li creator: Li Zhang creator: Ke Wang uri: https://doi.org/10.7717/peerj.18235 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yu et al. title: The significance of biowaste drying analysis as a key pre-treatment for transforming it into a sustainable biomass feedstock link: https://peerj.com/articles/18248 last-modified: 2024-10-31 description: The objective of this study is to investigate the drying kinetics of fruit and vegetable peel biowaste using a sustainable technique as a key-pretreatment for its conversion into useful feedstock. Biowaste represents a missed potential source of bioenergy and bioproducts, but moisture removal is required, and conventional drying methods are expensive since they require great quantity of energy supplied, almost always, by a non-renewable energy. In this study six batches with the same quantity of biowaste, and heterogeneous physical composition were dried under open-sun conditions. We evaluated the influence of the interaction between drying area and the initial moisture content on drying rate. Eight semi-theoretical models were fitted using Levenberg–Marquardt algorithm to predict drying rate, and their accuracy was assessed through goodness-of-fit tests. Maximum moisture content to preserve biomass (10%) was reached on 5th day and the equilibrium on 16th day of drying. According to goodness-of-fit test (R2 = 0.999, χ2 = 4.666 × 10−5, RMSE = 0.00683) the best model to predict drying rate was Two-term model. The mathematical model obtained from Fick’s second law is reliable to predict drying kinetics, R2 (0.9648 ± 0.0106); despite the variation between drying area and initial moisture content. Kruskal-Wallis test showed that drying rates between batches are not significantly different (p = 0.639; 0.05); nor effective diffusion coefficient (Deff = 4.97 × 10−11  ±  0.3491 × 10−11), (p = 0.723; 0.05). The study of drying kinetics is crucial for selecting the optimal biowaste treatment based on its generation context. This could enable its use as feedstock for bioproduct or bioenergy production, thereby reducing waste accumulation in landfills and environmental impact. creator: Fernando Damián Barajas Godoy creator: Marco A. Martínez-Cinco creator: José G. Rutiaga-Quiñones creator: Otoniel Buenrostro-Delgado creator: Jose Mendoza uri: https://doi.org/10.7717/peerj.18248 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Barajas Godoy et al.