PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The complete mitochondrial genome and gene rearrangements in a gall wasp species, Dryocosmus liui (Hymenoptera: Cynipoidea: Cynipidae)
items: An acoustic-based method for locating maternity colonies of rare woodland bats
items: Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project
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

The complete mitochondrial genome and gene rearrangements in a gall wasp species, Dryocosmus liui (Hymenoptera: Cynipoidea: Cynipidae)
type: item
type: AcademicArticle
description: Mitochondrial genomes (mitogenomes) have been widely used in comparative and evolutionary genomics, molecular evolution, phylogenetics, and population genetics, but very limited information is available for the family Cynipidae. In this report, we describe the mitogenome of Dryocosmus liui Pang, Su et Zhu, providing the first complete mitogenomic data for a cynipid gall wasp species. The mitogenome of D. liui is 16,819 bp in length, and contains the typical set of 37 genes. Two control regions were detected, with the second being a perfect inverted repeat of the major portion of the first. Gene rearrangements were found in transfer RNA (tRNA) genes, protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes, compared with the putative ancestral mitogenome. Similar to two other Cynipidae species with mitogenome data available, D. liui has a novel tRNA gene cluster trnL1–trnI–trnL2–trnW–trnM–trnQ between nad1 and nad2. Phylogenetic analysis based on sequences of PCGs and rRNA genes with D. liui included obtained topologies identical to previous studies supporting the a relationship of (Cynipoidea , (Platygastroidea, Proctotrupoidea)) within the monophyletic Proctotrupomorpha and (Cynipidae, Figitidae), Ibaliidae) within the Cynipoidea.
format: application/pdf
format: text/html
creator: Cheng-Yuan Su
creator: Dao-Hong Zhu
creator: Yoshihisa Abe
creator: Tatsuya Ide
creator: Zhiwei Liu
subject: Entomology
description: doi:10.7717/peerj.15865
publisher: PeerJ Inc.
rights: © 2023 Su et al.
abstract: Mitochondrial genomes (mitogenomes) have been widely used in comparative and evolutionary genomics, molecular evolution, phylogenetics, and population genetics, but very limited information is available for the family Cynipidae. In this report, we describe the mitogenome of Dryocosmus liui Pang, Su et Zhu, providing the first complete mitogenomic data for a cynipid gall wasp species. The mitogenome of D. liui is 16,819 bp in length, and contains the typical set of 37 genes. Two control regions were detected, with the second being a perfect inverted repeat of the major portion of the first. Gene rearrangements were found in transfer RNA (tRNA) genes, protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes, compared with the putative ancestral mitogenome. Similar to two other Cynipidae species with mitogenome data available, D. liui has a novel tRNA gene cluster trnL1–trnI–trnL2–trnW–trnM–trnQ between nad1 and nad2. Phylogenetic analysis based on sequences of PCGs and rRNA genes with D. liui included obtained topologies identical to previous studies supporting the a relationship of (Cynipoidea , (Platygastroidea, Proctotrupoidea)) within the monophyletic Proctotrupomorpha and (Cynipidae, Figitidae), Ibaliidae) within the Cynipoidea.
bibliographic citation: Su et al. (2023) The complete mitochondrial genome and gene rearrangements in a gall wasp species, Dryocosmus liui (Hymenoptera: Cynipoidea: Cynipidae). PeerJ 11:e15865 https://doi.org/10.7717/peerj.15865
date submitted: 2021-03-29
date accepted: 2023-07-17
issued: 2023-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Cheng-Yuan
author list: Agent
  family name: Zhu
  given name: Dao-Hong
author list: Agent
  family name: Abe
  given name: Yoshihisa
author list: Agent
  family name: Ide
  given name: Tatsuya
author list: Agent
  family name: Liu
  given name: Zhiwei
doi: 10.7717/peerj.15865
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-03
copyright: ©2023 Su et al.
attribution name: Su et al.

An acoustic-based method for locating maternity colonies of rare woodland bats
type: item
type: AcademicArticle
description: Locating colonies of rare bats can be a time consuming process, as it is often difficult to know where to focus survey effort. However, identifying peaks of bat activity via acoustic monitoring may provide insights into whether a colony is locally present, and help screen out sites with low potential. Using a triage approach, we developed a survey methodology for locating colonies of the woodland-specialist barbastelle bat (Barbastella barbastellus). We investigated whether woodland occupancy by a colony could be predicted by acoustic data, and assessed the influence of survey effort (number of acoustic detectors deployed) on detectability. The methodology was then trialled in citizen science surveys of 77 woodlands, with follow-up radio-tracking surveys by specialists being used to confirm presence or absence. Using Receiver Operating Characteristic (ROC) curve analysis, we found that a threshold of four barbastelle passes recorded by at least one detector within one hour of sunset optimised the balance between the true- and false-positive rates. Subsequently, we found that a minimum survey effort of one detector per 6.25 hectares of woodland was needed to ensure a colony would be detected using this threshold, based on a survey sensitivity of 90%. Radio-tracking surveys in a subset of the woodlands, identified as having a high probability of being occupied by a colony based on acoustic monitoring, confirmed the presence of five previously unknown barbastelle maternity colonies. These results demonstrate that a triage system, in which high probability woodland sites are identified based on acoustic survey data, can be used to prioritise sites for future specialist surveys and conservation action.
format: application/pdf
format: text/html
creator: Kieran D. O’Malley
creator: Henry Schofield
creator: Patrick G.R. Wright
creator: Daniel Hargreaves
creator: Tom Kitching
creator: Marina Bollo Palacios
creator: Fiona Mathews
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.15951
publisher: PeerJ Inc.
rights: © 2023 O’Malley et al.
abstract: Locating colonies of rare bats can be a time consuming process, as it is often difficult to know where to focus survey effort. However, identifying peaks of bat activity via acoustic monitoring may provide insights into whether a colony is locally present, and help screen out sites with low potential. Using a triage approach, we developed a survey methodology for locating colonies of the woodland-specialist barbastelle bat (Barbastella barbastellus). We investigated whether woodland occupancy by a colony could be predicted by acoustic data, and assessed the influence of survey effort (number of acoustic detectors deployed) on detectability. The methodology was then trialled in citizen science surveys of 77 woodlands, with follow-up radio-tracking surveys by specialists being used to confirm presence or absence. Using Receiver Operating Characteristic (ROC) curve analysis, we found that a threshold of four barbastelle passes recorded by at least one detector within one hour of sunset optimised the balance between the true- and false-positive rates. Subsequently, we found that a minimum survey effort of one detector per 6.25 hectares of woodland was needed to ensure a colony would be detected using this threshold, based on a survey sensitivity of 90%. Radio-tracking surveys in a subset of the woodlands, identified as having a high probability of being occupied by a colony based on acoustic monitoring, confirmed the presence of five previously unknown barbastelle maternity colonies. These results demonstrate that a triage system, in which high probability woodland sites are identified based on acoustic survey data, can be used to prioritise sites for future specialist surveys and conservation action.
bibliographic citation: O’Malley et al. (2023) An acoustic-based method for locating maternity colonies of rare woodland bats. PeerJ 11:e15951 https://doi.org/10.7717/peerj.15951
date submitted: 2023-06-01
date accepted: 2023-08-01
issued: 2023-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: O’Malley
  given name: Kieran D.
author list: Agent
  family name: Schofield
  given name: Henry
author list: Agent
  family name: Wright
  given name: Patrick G.R.
author list: Agent
  family name: Hargreaves
  given name: Daniel
author list: Agent
  family name: Kitching
  given name: Tom
author list: Agent
  family name: Bollo Palacios
  given name: Marina
author list: Agent
  family name: Mathews
  given name: Fiona
doi: 10.7717/peerj.15951
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-03
copyright: ©2023 O’Malley et al.
attribution name: O’Malley et al.

Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project
type: item
type: AcademicArticle
description: Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as “microbial gardening”. In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species …
format: application/pdf
format: text/html
creator: Manuel Ochoa-Sánchez
creator: Eliana Paola Acuña Gomez
creator: Lia Ramírez-Fenández
creator: Luis E. Eguiarte
creator: Valeria Souza
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.15978
publisher: PeerJ Inc.
rights: © 2023 Ochoa-Sánchez et al.
abstract: Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as “microbial gardening”. In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species …
bibliographic citation: Ochoa-Sánchez et al. (2023) Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project. PeerJ 11:e15978 https://doi.org/10.7717/peerj.15978
date submitted: 2023-03-28
date accepted: 2023-08-07
issued: 2023-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ochoa-Sánchez
  given name: Manuel
author list: Agent
  family name: Acuña Gomez
  given name: Eliana Paola
author list: Agent
  family name: Ramírez-Fenández
  given name: Lia
author list: Agent
  family name: Eguiarte
  given name: Luis E.
author list: Agent
  family name: Souza
  given name: Valeria
doi: 10.7717/peerj.15978
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-03
copyright: © 2023 Ochoa-Sánchez et al.
attribution name: Ochoa-Sánchez et al.

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.

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