PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: High LYRM4-AS1 predicts poor prognosis in patients with glioma and correlates with immune infiltration
items: Characterization of macroalgal-associated microbial communities from shallow to mesophotic depths at Manawai, Papahānaumokuākea Marine National Monument, Hawai‘i
items: Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics
items: Effect of body mass index on soft tissues in adolescents with skeletal class I and normal facial height
items: 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
items: Epiperipatus puri sp. nov., a new velvet worm from Atlantic Forest in Southeastern Brazil (Onychophora, Peripatidae)
items: Prediction models of macro-nutrient content in plant organs of Cucumis melo in response to soil elements using support vector regression
items: Mitochondrial sequence data reveal population structure within Pustulosa pustulosa
items: Assessing the magnitude of changes from protocol to publication—a survey on Cochrane and non-Cochrane Systematic Reviews
items: Integration of exome-seq and mRNA-seq using DawnRank, identified genes involved in innate immunity as drivers of breast cancer in the Indian cohort

High LYRM4-AS1 predicts poor prognosis in patients with glioma and correlates with immune infiltration
type: item
type: AcademicArticle
description: 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 demonstra…
format: application/pdf
format: text/html
creator: Hai yue Wang
creator: Ying Xie
creator: Hongzhen Du
creator: Bin Luo
creator: Zengning Li
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.16104
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: 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 demonstra…
bibliographic citation: 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
date submitted: 2023-04-21
date accepted: 2023-08-25
issued: 2023-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Hai yue
author list: Agent
  family name: Xie
  given name: Ying
author list: Agent
  family name: Du
  given name: Hongzhen
author list: Agent
  family name: Luo
  given name: Bin
author list: Agent
  family name: Li
  given name: Zengning
doi: 10.7717/peerj.16104
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-03
copyright: © 2023 Wang et al.
attribution name: Wang et al.

Characterization of macroalgal-associated microbial communities from shallow to mesophotic depths at Manawai, Papahānaumokuākea Marine National Monument, Hawai‘i
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Gabrielle M. Kuba
creator: Heather L. Spalding
creator: Kristina M. Hill-Spanik
creator: Taylor M. Williams
creator: Monica O. Paiano
creator: Alison R. Sherwood
creator: Brian B. Hauk
creator: Randall K. Kosaki
creator: Heather Fullerton
subject: Ecology
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.16114
publisher: PeerJ Inc.
rights: © 2023
abstract: 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.
bibliographic citation: 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
date submitted: 2023-01-17
date accepted: 2023-08-27
issued: 2023-10-03
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Kuba
  given name: Gabrielle M.
author list: Agent
  family name: Spalding
  given name: Heather L.
author list: Agent
  family name: Hill-Spanik
  given name: Kristina M.
author list: Agent
  family name: Williams
  given name: Taylor M.
author list: Agent
  family name: Paiano
  given name: Monica O.
author list: Agent
  family name: Sherwood
  given name: Alison R.
author list: Agent
  family name: Hauk
  given name: Brian B.
author list: Agent
  family name: Kosaki
  given name: Randall K.
author list: Agent
  family name: Fullerton
  given name: Heather
doi: 10.7717/peerj.16114
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-03

Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Da Teng
creator: Hongping Chen
creator: Wenjuan Jia
creator: Qingmiao Ren
creator: Xiaoning Ding
creator: Lihui Zhang
creator: Lei Gong
creator: Hua Wang
creator: Lin Zhong
creator: Jun Yang
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Cardiology
subject: Pathology
description: doi:10.7717/peerj.16122
publisher: PeerJ Inc.
rights: © 2023 Teng et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2023-06-08
date accepted: 2023-08-27
issued: 2023-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Teng
  given name: Da
author list: Agent
  family name: Chen
  given name: Hongping
author list: Agent
  family name: Jia
  given name: Wenjuan
author list: Agent
  family name: Ren
  given name: Qingmiao
author list: Agent
  family name: Ding
  given name: Xiaoning
author list: Agent
  family name: Zhang
  given name: Lihui
author list: Agent
  family name: Gong
  given name: Lei
author list: Agent
  family name: Wang
  given name: Hua
author list: Agent
  family name: Zhong
  given name: Lin
author list: Agent
  family name: Yang
  given name: Jun
doi: 10.7717/peerj.16122
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-03
copyright: ©2023 Teng et al.
attribution name: Teng et al.

Effect of body mass index on soft tissues in adolescents with skeletal class I and normal facial height
type: item
type: AcademicArticle
description: 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).
format: application/pdf
format: text/html
creator: Nurver Karsli
creator: Esra Tuhan Kutlu
subject: Anatomy and Physiology
subject: Dentistry
subject: Nutrition
subject: Otorhinolaryngology
description: doi:10.7717/peerj.16196
publisher: PeerJ Inc.
rights: © 2023 Karsli and Tuhan Kutlu
abstract: 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).
bibliographic citation: 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
date submitted: 2023-04-26
date accepted: 2023-09-06
issued: 2023-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karsli
  given name: Nurver
author list: Agent
  family name: Tuhan Kutlu
  given name: Esra
doi: 10.7717/peerj.16196
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-03
copyright: © 2023 Karsli and Tuhan Kutlu
attribution name: Karsli and Tuhan Kutlu

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
type: item
type: AcademicArticle
description: 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…
format: application/pdf
format: text/html
creator: Alison Bard
creator: Lars Forsberg
creator: Hans Wickström
creator: Ulf Emanuelson
creator: Kristen Reyher
creator: Catarina Svensson
subject: Veterinary Medicine
subject: Psychiatry and Psychology
subject: Science and Medical Education
subject: Healthcare Services
description: doi:10.7717/peerj.14634
publisher: PeerJ Inc.
rights: © 2023 Bard et al.
abstract: 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…
bibliographic citation: 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
date submitted: 2022-04-14
date accepted: 2022-12-04
issued: 2023-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bard
  given name: Alison
author list: Agent
  family name: Forsberg
  given name: Lars
author list: Agent
  family name: Wickström
  given name: Hans
author list: Agent
  family name: Emanuelson
  given name: Ulf
author list: Agent
  family name: Reyher
  given name: Kristen
author list: Agent
  family name: Svensson
  given name: Catarina
doi: 10.7717/peerj.14634
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-02
copyright: © 2023 Bard et al.
attribution name: Bard et al.

Epiperipatus puri sp. nov., a new velvet worm from Atlantic Forest in Southeastern Brazil (Onychophora, Peripatidae)
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Cristiano Sampaio Costa
creator: Amanda Cruz Mendes
creator: Alessandro Ponce de Leão Giupponi
subject: Biodiversity
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15384
publisher: PeerJ Inc.
rights: © 2023 Costa et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-03-10
date accepted: 2023-04-18
issued: 2023-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Costa
  given name: Cristiano Sampaio
author list: Agent
  family name: Mendes
  given name: Amanda Cruz
author list: Agent
  family name: Giupponi
  given name: Alessandro Ponce de Leão
doi: 10.7717/peerj.15384
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-02
copyright: © 2023 Costa et al.
attribution name: Costa et al.

Prediction models of macro-nutrient content in plant organs of Cucumis melo in response to soil elements using support vector regression
type: item
type: AcademicArticle
description: 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 rang…
format: application/pdf
format: text/html
creator: Abbas Keshtehgar
creator: Mahdi Dahmardeh
creator: Ahmad Ghanbari
creator: Issa Khammari
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Data Mining and Machine Learning
subject: Natural Resource Management
description: doi:10.7717/peerj.15417
publisher: PeerJ Inc.
rights: © 2023 Keshtehgar et al.
abstract: 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 rang…
bibliographic citation: 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
date submitted: 2022-09-26
date accepted: 2023-04-24
issued: 2023-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Keshtehgar
  given name: Abbas
author list: Agent
  family name: Dahmardeh
  given name: Mahdi
author list: Agent
  family name: Ghanbari
  given name: Ahmad
author list: Agent
  family name: Khammari
  given name: Issa
doi: 10.7717/peerj.15417
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-02
copyright: ©2023 Keshtehgar et al.
attribution name: Keshtehgar et al.

Mitochondrial sequence data reveal population structure within Pustulosa pustulosa
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: David Rodriguez
creator: Stephen F. Harding
creator: Shashwat Sirsi
creator: Kelly McNichols-O’Rourke
creator: Todd Morris
creator: Michael R. J. Forstner
creator: Astrid N. Schwalb
subject: Biodiversity
subject: Genetics
subject: Zoology
subject: Freshwater Biology
subject: Population Biology
description: doi:10.7717/peerj.15974
publisher: PeerJ Inc.
rights: © 2023 Rodriguez et al.
abstract: 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.
bibliographic citation: Rodriguez et al. (2023) Mitochondrial sequence data reveal population structure within Pustulosa pustulosa. PeerJ 11:e15974 https://doi.org/10.7717/peerj.15974
date submitted: 2023-03-23
date accepted: 2023-08-06
issued: 2023-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodriguez
  given name: David
author list: Agent
  family name: Harding
  given name: Stephen F.
author list: Agent
  family name: Sirsi
  given name: Shashwat
author list: Agent
  family name: McNichols-O’Rourke
  given name: Kelly
author list: Agent
  family name: Morris
  given name: Todd
author list: Agent
  family name: Forstner
  given name: Michael R. J.
author list: Agent
  family name: Schwalb
  given name: Astrid N.
doi: 10.7717/peerj.15974
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-02
copyright: © 2023 Rodriguez et al.
attribution name: Rodriguez et al.

Assessing the magnitude of changes from protocol to publication—a survey on Cochrane and non-Cochrane Systematic Reviews
type: item
type: AcademicArticle
description: 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/.
format: application/pdf
format: text/html
creator: Maximilian Siebert
creator: Laura Caquelin
creator: Meisser Madera
creator: Roberto Acosta-Dighero
creator: Florian Naudet
creator: Marta Roqué
subject: Clinical Trials
subject: Evidence Based Medicine
subject: Public Health
description: doi:10.7717/peerj.16016
publisher: PeerJ Inc.
rights: © 2023 Siebert et al.
abstract: 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/.
bibliographic citation: 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
date submitted: 2023-03-04
date accepted: 2023-08-10
issued: 2023-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Siebert
  given name: Maximilian
author list: Agent
  family name: Caquelin
  given name: Laura
author list: Agent
  family name: Madera
  given name: Meisser
author list: Agent
  family name: Acosta-Dighero
  given name: Roberto
author list: Agent
  family name: Naudet
  given name: Florian
author list: Agent
  family name: Roqué
  given name: Marta
doi: 10.7717/peerj.16016
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-02
copyright: ©2023 Siebert et al.
attribution name: Siebert et al.

Integration of exome-seq and mRNA-seq using DawnRank, identified genes involved in innate immunity as drivers of breast cancer in the Indian cohort
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Snehal Nirgude
creator: Sagar Desai
creator: Vartika Khanchandani
creator: Vidhyavathy Nagarajan
creator: Jayanti Thumsi
creator: Bibha Choudhary
subject: Bioinformatics
subject: Genomics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.16033
publisher: PeerJ Inc.
rights: © 2023 Nirgude et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2023-04-25
date accepted: 2023-08-14
issued: 2023-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nirgude
  given name: Snehal
author list: Agent
  family name: Desai
  given name: Sagar
author list: Agent
  family name: Khanchandani
  given name: Vartika
author list: Agent
  family name: Nagarajan
  given name: Vidhyavathy
author list: Agent
  family name: Thumsi
  given name: Jayanti
author list: Agent
  family name: Choudhary
  given name: Bibha
doi: 10.7717/peerj.16033
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-02
copyright: © 2023 Nirgude et al.
attribution name: Nirgude et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359