High LYRM4-AS1 predicts poor prognosis in patients with glioma and correlates with immune infiltration
Background Many researches proved that non-coding RNAs are important in glioma development. We screened the differentially expressed genes through The Cancer Genome Atlas (TCGA) database and identified the molecule LYRM4-AS1 associated with prognosis. As a lncRNA, the expression level and role of LYRM4-AS1 in glioma are inconclusive. Therefore, we attempted to assess the clinical significance, expression and related mechanisms of LYRM4-AS1 in glioma by employing cell experiments and an integrative in silico methodology. Methods RNA-seq data were obtained from UCSC XENA and TCGA datasets. The Gene Expression Omnibus (GEO) database was used to download glioma-related expression profile data. The LYRM4-AS1 expression level was evaluated. Survival curves were constructed by the Kaplan–Meier method. Cox regression analysis was used to analyze independent variables. Patients were divided into high and low expression group base on the median LYRM4-AS1 expression value in glioma tissues. The DESeq2 R package was used to identify differentially expressed genes (DEGs) between two different expression LYRM4-AS1 groups. Gene set enrichment analysis (GSEA) was conducted. Next, the single-sample Gene Set Enrichment Analysis (ssGSEA) was done to quantify the immune infiltration of immune cells in glioma tissues. Gene expression profiles for glioma tumor tissues were used to quantify the relative enrichment score for each immune cell. Spearman correlation analysis was used to analyze the correlation between LYRM4-AS1 and biomarkers of immune cells as well as immune checkpoints in glioma. Finally, assays for cell apoptosis, cell viability and wound healing were conducted to evaluate the function on U87 MG and U251 cells after knocking down LYRM4-AS1. Results We found that LYRM4-AS1 was upregulated and related to the grade and malignancy of glioma. Survival analyses showed that high expression LYRM4-AS1 patients had poor clinical outcomes (P < 0.01). Cox regression analyses demonstrated that LYRM4-AS1 was an independent risk factor for overall survival (OS) in glioma (HR: 274 1.836; CI [1.278–2.639]; P = 0.001). Enrichment and immune infiltration analysis showed interferon signaling and cytokine-cytokine receptor interaction enriched in the LYRM4-AS1 high-expression phenotype, and LYRM4-AS1 showed significantly positively related to immune infiltration as well as immune checkpoints (P < 0.01). The knockdown of LYRM4-AS1 in U87 MG and U251 cells can inhibit migration and proliferation of cells (P < 0.05). Conclusions These findings indicated that the increased LYRM4-AS1 may be useful for the diagnosis and prognosis of glioma and might participate in the immune infiltration.
Wang et al. (2023) High LYRM4-AS1 predicts poor prognosis in patients with glioma and correlates with immune infiltration. PeerJ 11:e16104 https://doi.org/10.7717/peerj.16104
Characterization of macroalgal-associated microbial communities from shallow to mesophotic depths at Manawai, Papahānaumokuākea Marine National Monument, Hawai‘i
The Papahānaumokuākea Marine National Monument, Hawai‘i, is one of the most isolated and protected archipelagos in the world, making it a natural laboratory to examine macroalgal-microbial diversity because of limited direct anthropogenic impacts. We collected the most abundant macroalgae from nine sites ranging from shallow subtidal (1.5 m) to mesophotic (75 m) depths around Manawai (Pearl and Hermes Atoll). We characterized the macroalgal bacterial communities via high-throughput amplicon sequencing and compared the influence of host phylum, species, site, and depth on these relationships at a single atoll. Ochrophyta species had the lowest bacterial diversity compared to Chlorophyta and Rhodophyta. Site and/or depth may influence the microbial community structure associated with Microdictyon setchellianum, indicating a possible disconnect of these microbial communities among habitats. Chondria tumulosa, a cryptogenic species with invasive traits, differed in associated microbiota compared to the native Laurencia galtsoffii, an alga from the same family collected at the same site and depth. While there was overlap of bacterial communities across sites for some algal species, the majority had minimal macroalgal-microbial community connectivity across Manawai. This mesophotic system, therefore, did not appear to be refugia for shallow water coral reefs at microscopic scales. Additional studies are required to identify other significant influences on microbial community variation.
Kuba et al. (2023) Characterization of macroalgal-associated microbial communities from shallow to mesophotic depths at Manawai, Papahānaumokuākea Marine National Monument, Hawai‘i. PeerJ 11:e16114 https://doi.org/10.7717/peerj.16114
Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics
Background Foam cells play crucial roles in all phases of atherosclerosis. However, until now, the specific mechanisms by which these foam cells contribute to atherosclerosis remain unclear. We aimed to identify novel foam cell biomarkers and interventional targets for atherosclerosis, characterizing their potential mechanisms in the progression of atherosclerosis. Methods Microarray data of atherosclerosis and foam cells were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expression genes (DEGs) were screened using the “LIMMA” package in R software. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Ontology (GO) annotation were both carried out. Hub genes were found in Cytoscape after a protein-protein interaction (PPI) enrichment analysis was carried out. Validation of important genes in the GSE41571 dataset, cellular assays, and tissue samples. Results A total of 407 DEGs in atherosclerosis and 219 DEGs in foam cells were identified, and the DEGs in atherosclerosis were mainly involved in cell proliferation and differentiation. CSF1R and PLAUR were identified as common hub genes and validated in GSE41571. In addition, we also found that the expression of CSF1R and PLAUR gradually increased with the accumulation of lipids and disease progression in cell and tissue experiments. Conclusion CSF1R and PLAUR are key hub genes of foam cells and may play an important role in the biological process of atherosclerosis. These results advance our understanding of the mechanism behind atherosclerosis and potential therapeutic targets for future development.
Teng et al. (2023) Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics. PeerJ 11:e16122 https://doi.org/10.7717/peerj.16122
Effect of body mass index on soft tissues in adolescents with skeletal class I and normal facial height
Background The evaluation of soft tissues in patients undergoing orthodontic treatment plays a critical role in diagnosis and treatment planning. This study aims to evaluate the effect of body mass index (BMI) on facial soft tissues in skeletal Class I patients with normal vertical growth. Methods The study included 72 patients with a normal vertical growth pattern (SN-GoGn 26–38°) and skeletal Class I (ANB 2‒4°) malocclusion. According to their BMI (kg/m2) values, the patients were divided into three groups of 24 individuals each: underweight (>5th percentile) (13 females, 11 males; mean age, 11.58 ± 1.95 years), normal weight (5‒85th percentile) (12 females, 12 males; mean age, 11.54 ± 1.95 years), overweight (85‒95th percentile) (12 females, 12 males; mean age, 11.62 ± 2.01 years). Soft tissue thickness and height measurements were made on lateral cephalometric radiographs. Results In all soft tissue thickness measurements, except for the nasion, the overweight weight group had higher values. In comparing the underweight and normal weight groups, statistically significant differences were found in the thickness measurements at the nasion and gnathion (p < 0.05). The differences in thickness measurements at the glabella, labiale superius, stomion, labiale inferius, pogonion, gnathion, and menton are statistically significant between the underweight and overweight groups (p < 0.005). Comparing the normal and overweight groups revealed statistically significant differences the thickness measurements at the glabella, labiale superius, stomion, pogonion and menton (p < 0.05).
Karsli et al. (2023) Effect of body mass index on soft tissues in adolescents with skeletal class I and normal facial height. PeerJ 11:e16196 https://doi.org/10.7717/peerj.16196
Clinician motivational interviewing skills in ‘simulated’ and ‘real-life’ consultations differ and show predictive validity for ‘real life’ client change talk under differing integrity thresholds
Background Accurate and reliable assessment of clinician integrity in the delivery of empirically supported treatments is critical to effective research and training interventions. Assessment of clinician integrity can be performed through recording simulated (SI) or real-life (RL) consultations, yet research examining the equivalence of these data is in its infancy. To explore the strength of integrity assessment between SI and RL samples in Motivational Interviewing (MI) consultations, this article examines whether Motivational Interviewing Treatment Integrity (MITI) assessments differ between SI and RL consultations and reviews the predictive validity of SI and RL MI skills categorisations for RL client response language. Methods This study first compared MITI coding obtained in SI and RL consultations for 36 veterinary clinicians. Multilevel models of 10 MITI behaviour counts and four MITI global scores were run using MLwiN 3.02 to assess if a significant difference existed between SI and RL MITI data, with consultation within clinician within cohort (A and B) as nested random effects. Second, we investigated the effect of SI and RL MI skills groupings on rate of RL client response talk using three multivariable regression models. Two Poisson regression models, with random intercepts for farm and veterinarian and offset for number of minutes of the recordings, were estimated in the statistical software R using the package glmmTMB for the two response variables Change Talk and Sustain Talk. A logistic regression model, with the same random intercepts, with the response variable Proportion Change Talk was also estimated using the same package. Results Veterinary clinicians were less MI consistent in RL consultations, evidenced through significantly lower global MITI Cultivating Change Talk (p < 0.001), Partnership (p < 0.001) and Empathy (p = 0.003) measures. Despite lower objective MI skills groupings in RL consultations, ranking order of veterinary clinicians by MI skills was similar between contexts. The predictive validity of SI and RL MI skills groupings for RL client Change Talk was therefore similar, with significantly more RL client Change Talk associated with veterinarians categorised in the highest grouping (‘moderate’) in both SI (p = 0.01) and RL (p = 0.02) compared to untrained veterinarians in each respective context. Conclusions Findings suggest SI and RL data may not be interchangeable. Whilst both data offer useful insights for specific research and training purposes, differing contextual MI skills thresholds may offer a more equitable assessment of clinician RL client-facing MI integrity. Further research is needed to explore the applicability of these findings across health contexts.
Bard et al. (2023) Clinician motivational interviewing skills in ‘simulated’ and ‘real-life’ consultations differ and show predictive validity for ‘real life’ client change talk under differing integrity thresholds. PeerJ 11:e14634 https://doi.org/10.7717/peerj.14634
Epiperipatus puri sp. nov., a new velvet worm from Atlantic Forest in Southeastern Brazil (Onychophora, Peripatidae)
Epiperipatus ohausi (Bouvier, 1900) is the first species known from Rio de Janeiro, and more than 120 years later a new species is described in the state of Rio de Janeiro (RJ). In this study, we describe the second species in the state of Rio de Janeiro, which we are naming in honor of the indigenous population called puri who resided in southeastern coastal Brazil. The species can be diagnosed mainly by large dorsal primary papillae close to the insertion of the legs drawing a light band from the anterior to the posterior region of the body, and large dorsal primary papillae alternating on the dorsal plicae. Moreover, they are recognized in vivo by the color of the diamond-shaped marks brownish orange on the dorsal portion of the body. Epiperipatus puri sp. nov. morphologically seems to be related to Epiperipatus acacioi (Marcus & Marcus, 1995) by the shape of the primary papillae apical piece and to E. ohausi by the resemblance of dorsal papillae. The phylogeny shows a close relationship between the new species and E. ohausi in a clade with a still undescribed species from Rio de Janeiro, Brazil located within the Atlantic Forest, one of the most threatened biomes in the world.
Costa et al. (2023) Epiperipatus puri sp. nov., a new velvet worm from Atlantic Forest in Southeastern Brazil (Onychophora, Peripatidae). PeerJ 11:e15384 https://doi.org/10.7717/peerj.15384
Prediction models of macro-nutrient content in plant organs of Cucumis melo in response to soil elements using support vector regression
Background Undoubtedly, the importance of food and food security as one of the present and future challenges is not invisible to anyone. Nowadays, the development of methods for monitoring the nutrient content in crop products is an essential issue for implementing reasonable and logical soil properties management. The modeling technique can evaluate the soil properties of fields and study the subject of crop yield through soil management. This study aims to predict fruit yield and macro-nutrient content in plant organs of Cucumis melo in response to soil elements using support vector regression (SVR). Methodology In the spring of 2020, this study was done as a factorial test in a randomized complete block design with three replications. The first factor was the use of fertilizers in six levels: no fertilizer (control), cow manure (30 t ha−1), sheep manure (30 t ha−1), nanobiomic foliar application (2 l ha−1), silicone foliar application (3 l ha−1), and chemical fertilizer from urea, triple superphosphate, and potassium sulfate sources (200, 100, and 150 kg ha−1). In addition, four levels of vermicompost considering as the second factor: no vermicompost (control), 5, 10, and 15 t ha−1. Input data sets such as fruit yield and nitrogen, phosphorus, and potassium levels in the seeds, fruits, leaves, and roots are used to calibrate the probabilistic model of SP using SVR. Results According to the results, when the data sets of the nitrogen, phosphorus, and potassium in the fruit uses as input, the accuracy of these models was higher than 80.0% (R2 = 0.807 for predicting fruit nitrogen; R2 = 0.999 for fruit phosphorus; R2 = 0.968 for fruit potassium). Also, the results of the prediction models in response to soil elements showed that the soil nitrogen content ranged from 0.05 to 1.1%, soil phosphorus from 10 to 59 mg kg−1, and soil potassium from 180 to 320 mg kg−1, which offers a suitable macro-nutrient content in the soil. Likewise, the best fruit nitrogen content ranged from 1.27 to 4.33%, fruit phosphorus from 15.74 to 26.19%, fruit potassium from 15.19 to 19.67%, and fruit yield from 2.16 to 5.95 kg per plant obtained under NPK chemical fertilizers and using 15 t ha−1 of vermicompost. Conclusions Because the fruit values had the highest contribution in prediction than observed values, thus identified as the best plant organs in response to soil elements. Based on our findings, the importance of fruit phosphorus identifies as a determinant that strongly influenced melon prediction models. More significant values of soil elements do not affect increasing fruit yield and macro-nutrient content in plant organs, and excessive application may not be economical. Therefore, our studies provide an efficient approach with potentially high accuracy to estimate fruit yield and macro-nutrient in the fruits of Cucumis melo in response to soil elements and cause a saving in the amount of fertilizer during the growing season.
Keshtehgar et al. (2023) Prediction models of macro-nutrient content in plant organs of Cucumis melo in response to soil elements using support vector regression. PeerJ 11:e15417 https://doi.org/10.7717/peerj.15417
Mitochondrial sequence data reveal population structure within Pustulosa pustulosa
Unionid mussels are among the most imperiled group of organisms in North America, and Pustulosa pustulosa is a freshwater species with a relatively wide latitudinal distribution that extends from southern Ontario, Canada, to Texas, USA. Considerable morphological and geographic variation in the genus Pustulosa (formerly Cyclonaias) has led to uncertainty over species boundaries, and recent studies have suggested revisions to species-level classifications by synonymizing C. aurea, C. houstonensis, C. mortoni, and C. refulgens with C. pustulosa (currently P. pustulosa). Owing to its wide range and shallow phylogenetic differentiation, we analyzed individuals of P. pustulosa using mitochondrial DNA sequence data under a population genetics framework. We included 496 individuals, which were comprised of 166 samples collected during this study and 330 additional sequences retrieved from GenBank. Pairwise ΦST measures based on ND1 data suggested there may be up to five major geographic groups present within P. pustulosa. Genetic differentiation between regions within Texas was higher compared to populations from the Mississippi and Great Lakes populations, which may reflect differences in historical connectivity. Mitochondrial sequence data also revealed varying demographic histories for each major group suggesting each geographic region has also experienced differential population dynamics in the past. Future surveys should consider exploring variation within species after phylogeographic delimitation has been performed. In this study, we begin to address this need for freshwater mussels via the P. pustulosa system.
Rodriguez et al. (2023) Mitochondrial sequence data reveal population structure within Pustulosa pustulosa. PeerJ 11:e15974 https://doi.org/10.7717/peerj.15974
Assessing the magnitude of changes from protocol to publication—a survey on Cochrane and non-Cochrane Systematic Reviews
Objective To explore differences between published reviews and their respective protocols in a sample of 97 non-Cochrane Systematic Reviews (non-CSRs) and 97 Cochrane Systematic Reviews (CSRs) in terms of PICOS (Patients/Population, Intervention, Comparison/Control, Outcome, Study type) elements and the extent to which they were reported. Study Design and Setting We searched PubMed and Cochrane databases to identify non-CSRs and CSRs that were published in 2018. We then searched for their corresponding Cochrane or PROSPERO protocols. The published reviews were compared to their protocols. The primary outcome was changes from protocol to review in terms of PICOS elements. Results We identified a total of 227 changes from protocol to review in PICOS elements, 1.11 (Standard Deviation (SD), 1.22) changes per review for CSRs and 1.23 (SD, 1.12) for non-CSRs per review. More than half of each sub-sample (54.6% of CSRs and 67.0% of non-CSRs) (Absolute Risk Reduction (ARR) 12.4% [−1.3%; 26.0%]) had changes in PICOS elements. For both subsamples, approximately a third of all changes corresponded to changes related to primary outcomes. Marked differences were found between the sub-samples for the reporting of changes. 95.8% of the changes in PICOS items were not reported in the non-CSRs compared to 42.6% in the CSRs (ARR 53.2% [43.2%; 63.2%]). Conclusion CSRs showed better results than non-CSRs in terms of the reporting of changes. Reporting of changes from protocol needs to be promoted and requires general improvement. The limitations of this study lie in its observational design. Registration: https://osf.io/6j8gd/.
Siebert et al. (2023) Assessing the magnitude of changes from protocol to publication—a survey on Cochrane and non-Cochrane Systematic Reviews. PeerJ 11:e16016 https://doi.org/10.7717/peerj.16016
Integration of exome-seq and mRNA-seq using DawnRank, identified genes involved in innate immunity as drivers of breast cancer in the Indian cohort
Genetic heterogeneity influences the prognosis and therapy of breast cancer. The cause of disease progression varies and can be addressed individually. To identify the mutations and their impact on disease progression at an individual level, we sequenced exome and transcriptome from matched normal-tumor samples. We utilised DawnRank to prioritise driver genes and identify specific mutations in Indian patients. Mutations in the C3 and HLA genes were identified as drivers of disease progression, indicating the involvement of the innate immune system. We performed immune profiling on 16 matched normal/tumor samples using CIBERSORTx. We identified CD8+ve T cells, M2 macrophages, and neutrophils to be enriched in luminal A and T cells CD4+naïve, natural killer (NK) cells activated, T follicular helper (Tfh) cells, dendritic cells activated, and neutrophils in triple-negative breast cancer (TNBC) subtypes. Weighted gene co-expression network analysis (WGCNA) revealed activation of T cell-mediated response in ER positive samples and Interleukin and Interferons in ER negative samples. WGCNA analysis also identified unique pathways for each individual, suggesting that rare mutations/expression signatures can be used to design personalised treatment.
Nirgude et al. (2023) Integration of exome-seq and mRNA-seq using DawnRank, identified genes involved in innate immunity as drivers of breast cancer in the Indian cohort. PeerJ 11:e16033 https://doi.org/10.7717/peerj.16033