PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: https://peerj.com/articles/15975
items: Analysis of the rhizosphere bacterial diversity of Angelica dahurica var. formosana from different experimental sites and varieties (strains)
items: D-DI/PLT can be a prognostic indicator for sepsis
items: Genetic structure of Trifolium pratense populations in a cityscape
items: Genetic structure and relatedness of brown trout (Salmo trutta) populations in the drainage basin of the Ölfusá river, South-Western Iceland
items: Relationship between vertical facial morphology and dental arch measurements in class II malocclusion: a retrospective study
items: Interaction of Val66Met BDNF and 5-HTTLPR polymorphisms with prevalence of post-earthquake 27-F PTSD in Chilean population
items: A novel signaling transduction pathway of melatonin on lactose synthesis in cows via melatonin receptor 1 (MT1) and prolactin receptor (PRLR)
items: Vertical contact forces affect vibration perception in human hairy skin
items: Identification of a pathogen causing fruiting body rot of Sanghuangporus vaninii

https://peerj.com/articles/15975
type: item
type: AcademicArticle
title: Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences
description: The spotted pond turtle (Geoclemys hamiltonii) is a threatened and less explored species endemic to Bangladesh, India, Nepal, and Pakistan. To infer structural variation and matrilineal phylogenetic interpretation, the present research decoded the mitogenome of G. hamiltonii (16,509 bp) using next-generation sequencing technology. The mitogenome comprises 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one AT-rich control region (CR) with similar strand symmetry in vertebrates. The ATG was identified as a start codon in most of the PCGs except Cytochrome oxidase subunit 1 (cox1), which started with the GTG codon. The non-coding CR of G. hamiltonii was determined to have a unique structure and variation in different domains and stem-loop secondary structure as compared with other Batagurinae species. The PCGs-based Bayesian phylogeny inferred strong monophyletic support for all Batagurinae species and confirmed the sister relationship of G. hamiltonii with Pangshura and Batagur taxa. We recommend generating more mitogenomic data for other Batagurinae species to confirm their population structure and evolutionary relationships. In addition, the present study aims to infer the habitat suitability and habitat quality of G. hamiltonii in its global distribution, both in the present and future climatic scenarios. We identify that only 58,542 km2 (7.16%) of the total range extent (817,341 km2) is suitable for this species, along with the fragmented habitats in both the eastern and western ranges. Comparative habitat quality assessment suggests the level of patch shape in the western range is higher (71.3%) compared to the eastern range. Our results suggest a massive decline of approximately 65.73% to 70.31% and 70.53% to 75.30% under ssp245 and ssp585 future scenarios, respectively, for the years between 2021–2040 and 2061–2080 compared with the current distribution. The present study indicates that proper conservation management r…
format: application/pdf
format: text/html
creator: Shantanu Kundu
creator: Tanoy Mukherjee
creator: Manokaran Kamalakannan
creator: Gaurav Barhadiya
creator: Chirashree Ghosh
creator: Hyun-Woo Kim
subject: Biogeography
subject: Conservation Biology
subject: Genomics
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.15975
publisher: PeerJ Inc.
rights: © 2023 Kundu et al.
abstract: The spotted pond turtle (Geoclemys hamiltonii) is a threatened and less explored species endemic to Bangladesh, India, Nepal, and Pakistan. To infer structural variation and matrilineal phylogenetic interpretation, the present research decoded the mitogenome of G. hamiltonii (16,509 bp) using next-generation sequencing technology. The mitogenome comprises 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one AT-rich control region (CR) with similar strand symmetry in vertebrates. The ATG was identified as a start codon in most of the PCGs except Cytochrome oxidase subunit 1 (cox1), which started with the GTG codon. The non-coding CR of G. hamiltonii was determined to have a unique structure and variation in different domains and stem-loop secondary structure as compared with other Batagurinae species. The PCGs-based Bayesian phylogeny inferred strong monophyletic support for all Batagurinae species and confirmed the sister relationship of G. hamiltonii with Pangshura and Batagur taxa. We recommend generating more mitogenomic data for other Batagurinae species to confirm their population structure and evolutionary relationships. In addition, the present study aims to infer the habitat suitability and habitat quality of G. hamiltonii in its global distribution, both in the present and future climatic scenarios. We identify that only 58,542 km2 (7.16%) of the total range extent (817,341 km2) is suitable for this species, along with the fragmented habitats in both the eastern and western ranges. Comparative habitat quality assessment suggests the level of patch shape in the western range is higher (71.3%) compared to the eastern range. Our results suggest a massive decline of approximately 65.73% to 70.31% and 70.53% to 75.30% under ssp245 and ssp585 future scenarios, respectively, for the years between 2021–2040 and 2061–2080 compared with the current distribution. The present study indicates that proper conservation management r…
bibliographic citation: Kundu et al. (2023) Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences. PeerJ 11:e15975 https://doi.org/10.7717/peerj.15975
date submitted: 2023-03-03
date accepted: 2023-08-07
issued: 2023-09-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kundu
  given name: Shantanu
author list: Agent
  family name: Mukherjee
  given name: Tanoy
author list: Agent
  family name: Kamalakannan
  given name: Manokaran
author list: Agent
  family name: Barhadiya
  given name: Gaurav
author list: Agent
  family name: Ghosh
  given name: Chirashree
author list: Agent
  family name: Kim
  given name: Hyun-Woo
doi: 10.7717/peerj.15975
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-06
copyright: © 2023 Kundu et al.
attribution name: Kundu et al.

Analysis of the rhizosphere bacterial diversity of Angelica dahurica var. formosana from different experimental sites and varieties (strains)
type: item
type: AcademicArticle
description: Background Rhizosphere bacteria play important roles in plant growth and secondary metabolite accumulation. Moreover, only with favorable production areas and desirable germplasm can high-yield and high-quality medicinal materials be produced. However, whether origin and germplasm indirectly affect the yield and quality of Angelica dahurica var. formosana through rhizosphere bacterial effects are not known. Methods In this study, a high-throughput sequencing strategy was used to explore the relationship between the rhizosphere bacterial community and the cultivation of A. dahurica var. formosana from different production areas and germplasm for the first time. Results (1) Proteobacteria was the dominant bacterial phylum in the rhizosphere soil of A. dahurica var. formosana, and these bacteria were stable and conserved to a certain extent. (2) High abundance of Proteobacteria was an important rhizospheric indicator of high yield, and high abundance of Firmicutes was an important indicator of high quality. Proteobacteria and Firmicutes might have an important relationship with the yield and quality of A. dahurica var. formosana, respectively. (3) PCoA cluster analysis demonstrated that both production area and germplasm affected the bacterial community structure in the rhizosphere of A. dahurica var. formosana to a certain extent, and production area had the greatest effect. In addition to available potassium, the rhizosphere soil nutrient levels of different production areas strongly affected the bacterial diversity and community. These findings provide a theoretical basis for the exploitation and utilization of rhizosphere microbial resources of A. dahurica var. formosana and offer a novel approach for increasing the yield and quality of this crop.
format: application/pdf
format: text/html
creator: Meiyan Jiang
creator: Fei Yao
creator: Yunshu Yang
creator: Yang Zhou
creator: Kai Hou
creator: Yinyin Chen
creator: Dongju Feng
creator: Wei Wu
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15997
publisher: PeerJ Inc.
rights: © 2023 Jiang et al.
abstract: Background Rhizosphere bacteria play important roles in plant growth and secondary metabolite accumulation. Moreover, only with favorable production areas and desirable germplasm can high-yield and high-quality medicinal materials be produced. However, whether origin and germplasm indirectly affect the yield and quality of Angelica dahurica var. formosana through rhizosphere bacterial effects are not known. Methods In this study, a high-throughput sequencing strategy was used to explore the relationship between the rhizosphere bacterial community and the cultivation of A. dahurica var. formosana from different production areas and germplasm for the first time. Results (1) Proteobacteria was the dominant bacterial phylum in the rhizosphere soil of A. dahurica var. formosana, and these bacteria were stable and conserved to a certain extent. (2) High abundance of Proteobacteria was an important rhizospheric indicator of high yield, and high abundance of Firmicutes was an important indicator of high quality. Proteobacteria and Firmicutes might have an important relationship with the yield and quality of A. dahurica var. formosana, respectively. (3) PCoA cluster analysis demonstrated that both production area and germplasm affected the bacterial community structure in the rhizosphere of A. dahurica var. formosana to a certain extent, and production area had the greatest effect. In addition to available potassium, the rhizosphere soil nutrient levels of different production areas strongly affected the bacterial diversity and community. These findings provide a theoretical basis for the exploitation and utilization of rhizosphere microbial resources of A. dahurica var. formosana and offer a novel approach for increasing the yield and quality of this crop.
bibliographic citation: Jiang et al. (2023) Analysis of the rhizosphere bacterial diversity of Angelica dahurica var. formosana from different experimental sites and varieties (strains). PeerJ 11:e15997 https://doi.org/10.7717/peerj.15997
date submitted: 2023-02-22
date accepted: 2023-08-08
issued: 2023-09-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Meiyan
author list: Agent
  family name: Yao
  given name: Fei
author list: Agent
  family name: Yang
  given name: Yunshu
author list: Agent
  family name: Zhou
  given name: Yang
author list: Agent
  family name: Hou
  given name: Kai
author list: Agent
  family name: Chen
  given name: Yinyin
author list: Agent
  family name: Feng
  given name: Dongju
author list: Agent
  family name: Wu
  given name: Wei
doi: 10.7717/peerj.15997
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-06
copyright: © 2023 Jiang et al.
attribution name: Jiang et al.

D-DI/PLT can be a prognostic indicator for sepsis
type: item
type: AcademicArticle
description: Aims To investigate the indicators affecting the early outcome of patients with sepsis and to explore its prognostic efficacy for sepsis. Methods We collected clinical data from 201 patients with sepsis admitted to the emergency department of Xijing Hospital between June 2019 and June 2022. The patients were categorized into groups (survival or fatality) based on their 28-day prognosis. The clinical characteristics, biochemical indexes, organ function-related indicators, and disease scores of the patients were analyzed for both groups. Risk factor analysis was conducted for the indicators with significant differences. Results Among the indicators with significant differences between the deceased and survival groups, D-dimer (D-DI), Sequential Organ Failure Assessment (SOFA) score, platelet (PLT), international normalized ratio (INR), and D-DI/PLT were identified as independent risk factors affecting the prognosis of sepsis patients. Receiver operating characteristic (ROC) curves showed that D-DI/PLT (area under the curve (AUC) = 93.9), D-DI (AUC = 89.6), PLT (AUC = 81.3), and SOFA (AUC = 78.4) had good judgment efficacy. Further, Kaplan Meier (K-M) survival analysis indicated that the 28-day survival rates of sepsis patients were significantly decreased when they had high levels of D-DI/PLT, D-DI, and SOFA as well as low PLTs. The hazard ratio (HR) of D-DI/PLT between the two groups was the largest (HR = 16.19). Conclusions D-DI/PLT may be an independent risk factor for poor prognosis in sepsis as well as a clinical predictor of patient prognosis.
format: application/pdf
format: text/html
creator: Xiaojun Zhao
creator: Xiuhua Wu
creator: Yi Si
creator: Jiangang Xie
creator: Linxiao Wang
creator: Shanshou Liu
creator: Chujun Duan
creator: Qianmei Wang
creator: Dan Wu
creator: Yifan Wang
creator: Jijun Chen
creator: Jing Yang
creator: Shanbo Hu
creator: Wen Yin
creator: Junjie Li
subject: Emergency and Critical Care
subject: Epidemiology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.15910
publisher: PeerJ Inc.
rights: © 2023 Zhao et al.
abstract: Aims To investigate the indicators affecting the early outcome of patients with sepsis and to explore its prognostic efficacy for sepsis. Methods We collected clinical data from 201 patients with sepsis admitted to the emergency department of Xijing Hospital between June 2019 and June 2022. The patients were categorized into groups (survival or fatality) based on their 28-day prognosis. The clinical characteristics, biochemical indexes, organ function-related indicators, and disease scores of the patients were analyzed for both groups. Risk factor analysis was conducted for the indicators with significant differences. Results Among the indicators with significant differences between the deceased and survival groups, D-dimer (D-DI), Sequential Organ Failure Assessment (SOFA) score, platelet (PLT), international normalized ratio (INR), and D-DI/PLT were identified as independent risk factors affecting the prognosis of sepsis patients. Receiver operating characteristic (ROC) curves showed that D-DI/PLT (area under the curve (AUC) = 93.9), D-DI (AUC = 89.6), PLT (AUC = 81.3), and SOFA (AUC = 78.4) had good judgment efficacy. Further, Kaplan Meier (K-M) survival analysis indicated that the 28-day survival rates of sepsis patients were significantly decreased when they had high levels of D-DI/PLT, D-DI, and SOFA as well as low PLTs. The hazard ratio (HR) of D-DI/PLT between the two groups was the largest (HR = 16.19). Conclusions D-DI/PLT may be an independent risk factor for poor prognosis in sepsis as well as a clinical predictor of patient prognosis.
bibliographic citation: Zhao et al. (2023) D-DI/PLT can be a prognostic indicator for sepsis. PeerJ 11:e15910 https://doi.org/10.7717/peerj.15910
date submitted: 2023-03-20
date accepted: 2023-07-26
issued: 2023-09-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Xiaojun
author list: Agent
  family name: Wu
  given name: Xiuhua
author list: Agent
  family name: Si
  given name: Yi
author list: Agent
  family name: Xie
  given name: Jiangang
author list: Agent
  family name: Wang
  given name: Linxiao
author list: Agent
  family name: Liu
  given name: Shanshou
author list: Agent
  family name: Duan
  given name: Chujun
author list: Agent
  family name: Wang
  given name: Qianmei
author list: Agent
  family name: Wu
  given name: Dan
author list: Agent
  family name: Wang
  given name: Yifan
author list: Agent
  family name: Chen
  given name: Jijun
author list: Agent
  family name: Yang
  given name: Jing
author list: Agent
  family name: Hu
  given name: Shanbo
author list: Agent
  family name: Yin
  given name: Wen
author list: Agent
  family name: Li
  given name: Junjie
doi: 10.7717/peerj.15910
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-05
copyright: © 2023 Zhao et al.
attribution name: Zhao et al.

Genetic structure of Trifolium pratense populations in a cityscape
type: item
type: AcademicArticle
description: Urban grasslands provide numerous ecosystem services, and their maintenance should be based on naturally regenerating plant populations. However, the urban environment is challenging for preserving viable populations, mostly because of their high fragmentation and small size, which can lead to genetic drift. We examined red clover (Trifolium pratense) in a medium-size city in Central Europe to test the cityscape effect on within- and among-population genetic diversity. We used eight inter-simple sequence repeat markers to examine the genetic structure of 16 populations, each represented by eight individuals. The isolation by resistance was analysed using a least cost patch approach, focusing on gene flow via pollinators. We found great variation among T. pratense populations, with no discernible geographic pattern in genetic diversity. We linked the diversity to the long history of the city and high stochasticity of land use changes that occurred with city development. In particular, we did not find that the Odra River (ca. 100 m wide) was a strong barrier to gene transfer. However, notable isolation was present due to resistance and distance, indicating that the populations are threatened by genetic drift. Therefore, gene movement between populations should be increased by appropriate management of urban green areas. We also found that small urban grassland (UG) patches with small populations can still hold rare alleles which significantly contribute to the overall genetic variation of T. pratense in the city.
format: application/pdf
format: text/html
creator: Hassanali Mollashahi
creator: Jacek Urbaniak
creator: Tomasz H. Szymura
creator: Magdalena Szymura
subject: Agricultural Science
subject: Genetics
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.15927
publisher: PeerJ Inc.
rights: © 2023 Mollashahi et al.
abstract: Urban grasslands provide numerous ecosystem services, and their maintenance should be based on naturally regenerating plant populations. However, the urban environment is challenging for preserving viable populations, mostly because of their high fragmentation and small size, which can lead to genetic drift. We examined red clover (Trifolium pratense) in a medium-size city in Central Europe to test the cityscape effect on within- and among-population genetic diversity. We used eight inter-simple sequence repeat markers to examine the genetic structure of 16 populations, each represented by eight individuals. The isolation by resistance was analysed using a least cost patch approach, focusing on gene flow via pollinators. We found great variation among T. pratense populations, with no discernible geographic pattern in genetic diversity. We linked the diversity to the long history of the city and high stochasticity of land use changes that occurred with city development. In particular, we did not find that the Odra River (ca. 100 m wide) was a strong barrier to gene transfer. However, notable isolation was present due to resistance and distance, indicating that the populations are threatened by genetic drift. Therefore, gene movement between populations should be increased by appropriate management of urban green areas. We also found that small urban grassland (UG) patches with small populations can still hold rare alleles which significantly contribute to the overall genetic variation of T. pratense in the city.
bibliographic citation: Mollashahi et al. (2023) Genetic structure of Trifolium pratense populations in a cityscape. PeerJ 11:e15927 https://doi.org/10.7717/peerj.15927
date submitted: 2023-02-22
date accepted: 2023-07-30
issued: 2023-09-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mollashahi
  given name: Hassanali
author list: Agent
  family name: Urbaniak
  given name: Jacek
author list: Agent
  family name: Szymura
  given name: Tomasz H.
author list: Agent
  family name: Szymura
  given name: Magdalena
doi: 10.7717/peerj.15927
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-05
copyright: ©2023 Mollashahi et al.
attribution name: Mollashahi et al.

Genetic structure and relatedness of brown trout (Salmo trutta) populations in the drainage basin of the Ölfusá river, South-Western Iceland
type: item
type: AcademicArticle
description: Background Lake Þingvallavatn in Iceland, a part of the river Ölfusá drainage basin, was presumably populated by brown trout soon after it formed at the end of the last Ice Age. The genetic relatedness of the brown trout in Þingvallavatn to other populations in the Ölfusá drainage basin is unknown. After the building of a dam at the outlet of the lake in 1959 brown trout catches declined, though numbers have now increased. The aim of this study was to assess effects of geographic isolation and potential downstream gene flow on the genetic structure and diversity in brown trout sampled in several locations in the western side of the watershed of River Ölfusá. We hypothesized that brown trout in Lake Þingvallavatn constituted several local spawning populations connected by occasional gene flow before the damming of the lake. We also estimated the effective population size (NE) of some of these populations and tested for signs of a recent population bottleneck in Lake Þingvallavatn. Methods We sampled brown trout inhabiting four lakes and 12 rivers within and near the watershed of River Ölfusá by means of electro- and net- fishing. After stringent data filtering, 2,597 polymorphic loci obtained from ddRADseq data from 317 individuals were ascertained as putative neutral markers. Results Overall, the genetic relatedness of brown trout in the Ölfusá watershed reflected the connectivity and topography of the waterways. Ancestry proportion analyses and a phylogenetic tree revealed seven distinct clusters, some of which corresponded to small populations with reduced genetic diversity. There was no evidence of downstream gene flow from Lake Þingvallavatn, although gene flow was observed from much smaller mountain populations. Most locations showed low NE values (i.e., ~14.6 on average) while the putative anadromous trout from River Sog and the spawning population from River Öxará, that flows into Lake Þingvallavatn, showed notably higher NE values (i.e., 71.2 and 56.5, respe…
format: application/pdf
format: text/html
creator: Marcos Lagunas
creator: Arnar Pálsson
creator: Benóný Jónsson
creator: Magnús Jóhannsson
creator: Zophonías O. Jónsson
creator: Sigurður S. Snorrason
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Freshwater Biology
description: doi:10.7717/peerj.15985
publisher: PeerJ Inc.
rights: © 2023 Lagunas et al.
abstract: Background Lake Þingvallavatn in Iceland, a part of the river Ölfusá drainage basin, was presumably populated by brown trout soon after it formed at the end of the last Ice Age. The genetic relatedness of the brown trout in Þingvallavatn to other populations in the Ölfusá drainage basin is unknown. After the building of a dam at the outlet of the lake in 1959 brown trout catches declined, though numbers have now increased. The aim of this study was to assess effects of geographic isolation and potential downstream gene flow on the genetic structure and diversity in brown trout sampled in several locations in the western side of the watershed of River Ölfusá. We hypothesized that brown trout in Lake Þingvallavatn constituted several local spawning populations connected by occasional gene flow before the damming of the lake. We also estimated the effective population size (NE) of some of these populations and tested for signs of a recent population bottleneck in Lake Þingvallavatn. Methods We sampled brown trout inhabiting four lakes and 12 rivers within and near the watershed of River Ölfusá by means of electro- and net- fishing. After stringent data filtering, 2,597 polymorphic loci obtained from ddRADseq data from 317 individuals were ascertained as putative neutral markers. Results Overall, the genetic relatedness of brown trout in the Ölfusá watershed reflected the connectivity and topography of the waterways. Ancestry proportion analyses and a phylogenetic tree revealed seven distinct clusters, some of which corresponded to small populations with reduced genetic diversity. There was no evidence of downstream gene flow from Lake Þingvallavatn, although gene flow was observed from much smaller mountain populations. Most locations showed low NE values (i.e., ~14.6 on average) while the putative anadromous trout from River Sog and the spawning population from River Öxará, that flows into Lake Þingvallavatn, showed notably higher NE values (i.e., 71.2 and 56.5, respe…
bibliographic citation: Lagunas et al. (2023) Genetic structure and relatedness of brown trout (Salmo trutta) populations in the drainage basin of the Ölfusá river, South-Western Iceland. PeerJ 11:e15985 https://doi.org/10.7717/peerj.15985
date submitted: 2021-12-15
date accepted: 2023-08-08
issued: 2023-09-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lagunas
  given name: Marcos
author list: Agent
  family name: Pálsson
  given name: Arnar
author list: Agent
  family name: Jónsson
  given name: Benóný
author list: Agent
  family name: Jóhannsson
  given name: Magnús
author list: Agent
  family name: Jónsson
  given name: Zophonías O.
author list: Agent
  family name: Snorrason
  given name: Sigurður S.
doi: 10.7717/peerj.15985
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-05
copyright: © 2023 Lagunas et al.
attribution name: Lagunas et al.

Relationship between vertical facial morphology and dental arch measurements in class II malocclusion: a retrospective study
type: item
type: AcademicArticle
description: Background To evaluate the relationship between dental arch measurements and the vertical facial pattern determined in skeletal Class II untreated patients. Methods Lateral cephalograms and plaster models were obtained from 124 untreated female adults (average age: 17.6 ± 3.8 years). Class I (CI), Class II Division 1 (CII/1) and Class II Division 2 (CII/2) malocclusions were divided into three subgroups according to their vertical morphology as hypodivergent, normodivergent and hyperdivergent. The multivariate variance analysis (MANOVA) method was used in the comparison of measurement values according to vertical and sagittal morphology. The relationship between both A point-Nasion-B point (ANB) and Frankfurt-mandibular plane (FMA) angles and dental arch measurements was examined by Pearson correlation analysis. The significance level was received as p < 0.05. Results While vertical morphology has a statistically significant effect on mandibular arch length, sagittal morphology affects maxillary arch depth. The parameters influenced by both morphologies are maxillary and mandibular arch length, as well as maxillary intermolar width. The mandibular arch length was significantly shorter in hyperdivergent-CII-2 malocclusion (50.5 ± 7.4 mm). Larger values were obtained in both mandibular arch length and maxillary arch depth measurements in CII-1 malocclusion compared to CII-2 malocclusion. The maxillary intermolar width was significantly shorter in hypodivergent-CII-1 malocclusion (46.8 ± 3.4 mm), while it was higher in hypodivergent-CI malocclusion (51.1 ± 3.4 mm). The maxillary arch length was the lowest in hyperdivergent-CI malocclusion (63.1 ± 13.3 mm) and the highest in hypodivergent-CI malocclusion (72.8 ± 7.6 mm). Additionally, a positive but weak correlation was found between ANB and FMA angles. Conclusion Dental arch measurements have been found to be affected by both vertical facial morphology and skeletal sagittal relationship. A positive correlation was foun…
format: application/pdf
format: text/html
creator: Irmak Ocak
creator: Nurver Karsli
creator: Ayse Tuba Altug
creator: Muge Aksu
subject: Anatomy and Physiology
subject: Dentistry
description: doi:10.7717/peerj.16031
publisher: PeerJ Inc.
rights: © 2023 Ocak et al.
abstract: Background To evaluate the relationship between dental arch measurements and the vertical facial pattern determined in skeletal Class II untreated patients. Methods Lateral cephalograms and plaster models were obtained from 124 untreated female adults (average age: 17.6 ± 3.8 years). Class I (CI), Class II Division 1 (CII/1) and Class II Division 2 (CII/2) malocclusions were divided into three subgroups according to their vertical morphology as hypodivergent, normodivergent and hyperdivergent. The multivariate variance analysis (MANOVA) method was used in the comparison of measurement values according to vertical and sagittal morphology. The relationship between both A point-Nasion-B point (ANB) and Frankfurt-mandibular plane (FMA) angles and dental arch measurements was examined by Pearson correlation analysis. The significance level was received as p < 0.05. Results While vertical morphology has a statistically significant effect on mandibular arch length, sagittal morphology affects maxillary arch depth. The parameters influenced by both morphologies are maxillary and mandibular arch length, as well as maxillary intermolar width. The mandibular arch length was significantly shorter in hyperdivergent-CII-2 malocclusion (50.5 ± 7.4 mm). Larger values were obtained in both mandibular arch length and maxillary arch depth measurements in CII-1 malocclusion compared to CII-2 malocclusion. The maxillary intermolar width was significantly shorter in hypodivergent-CII-1 malocclusion (46.8 ± 3.4 mm), while it was higher in hypodivergent-CI malocclusion (51.1 ± 3.4 mm). The maxillary arch length was the lowest in hyperdivergent-CI malocclusion (63.1 ± 13.3 mm) and the highest in hypodivergent-CI malocclusion (72.8 ± 7.6 mm). Additionally, a positive but weak correlation was found between ANB and FMA angles. Conclusion Dental arch measurements have been found to be affected by both vertical facial morphology and skeletal sagittal relationship. A positive correlation was foun…
bibliographic citation: Ocak et al. (2023) Relationship between vertical facial morphology and dental arch measurements in class II malocclusion: a retrospective study. PeerJ 11:e16031 https://doi.org/10.7717/peerj.16031
date submitted: 2023-03-30
date accepted: 2023-08-13
issued: 2023-09-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ocak
  given name: Irmak
author list: Agent
  family name: Karsli
  given name: Nurver
author list: Agent
  family name: Altug
  given name: Ayse Tuba
author list: Agent
  family name: Aksu
  given name: Muge
doi: 10.7717/peerj.16031
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-05
copyright: © 2023 Ocak et al.
attribution name: Ocak et al.

Interaction of Val66Met BDNF and 5-HTTLPR polymorphisms with prevalence of post-earthquake 27-F PTSD in Chilean population
type: item
type: AcademicArticle
description: Post-traumatic stress (PTSD) disorder is a mental health condition that can occur after experiencing or witnessing a traumatic event. The 27-F earthquake that struck Chile in 2010 was one such event that had a significant impact on the mental health of the population. A study was conducted to investigate the prevalence of PTSD and its associated factors among survivors of this earthquake. The study was a longitudinal design, involving a sample of 913 patients aged 18 to 75 years who attended 10 Primary Care Centers in Concepción, Chile. The Composite International Diagnostic Interview (CIDI) was used to assess both depressive episodes (DE) and PTSD before and after the earthquake. The study also involved genotyping studies using saliva samples from the participants, specifically focusing on the Val66Met and 5-HTTLPR polymorphisms. Statistical analysis was performed to examine the association between different variables and the presence of PTSD. These variables included demographic factors, family history of psychiatric disorders, DE, childhood maltreatment experiences, and critical traumatic events related to the earthquake. The results showed that the incidence of post-earthquake PTSD was 11.06%. No significant differences were found between the groups of participants who developed post-earthquake PTSD regarding the Val66Met or 5-HTTLPR polymorphisms. However, a significant association was found between the concomitant diagnosis of DE and the development of post-earthquake PTSD. The presence of DE doubled the risk of developing post-earthquake PTSD. The number of traumatic events experienced also had a statistically significant association with an increased risk of developing post-earthquake PTSD. The study’s limitations include the potential interference of different DE subtypes, the complexity of quantifying the degree of earthquake exposure experienced by each individual, and events entailing social disruption, such as looting, that can profoundly influence dist…
format: application/pdf
format: text/html
creator: Juan-Luis Castillo-Navarrete
creator: Benjamin Vicente
creator: Kristin Schmidt
creator: Esteban Moraga-Escobar
creator: Romina Rojas-Ponce
creator: Paola Lagos
creator: Ximena Macaya
creator: Alejandra Guzman-Castillo
subject: Genetics
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.15870
publisher: PeerJ Inc.
rights: © 2023 Castillo-Navarrete et al.
abstract: Post-traumatic stress (PTSD) disorder is a mental health condition that can occur after experiencing or witnessing a traumatic event. The 27-F earthquake that struck Chile in 2010 was one such event that had a significant impact on the mental health of the population. A study was conducted to investigate the prevalence of PTSD and its associated factors among survivors of this earthquake. The study was a longitudinal design, involving a sample of 913 patients aged 18 to 75 years who attended 10 Primary Care Centers in Concepción, Chile. The Composite International Diagnostic Interview (CIDI) was used to assess both depressive episodes (DE) and PTSD before and after the earthquake. The study also involved genotyping studies using saliva samples from the participants, specifically focusing on the Val66Met and 5-HTTLPR polymorphisms. Statistical analysis was performed to examine the association between different variables and the presence of PTSD. These variables included demographic factors, family history of psychiatric disorders, DE, childhood maltreatment experiences, and critical traumatic events related to the earthquake. The results showed that the incidence of post-earthquake PTSD was 11.06%. No significant differences were found between the groups of participants who developed post-earthquake PTSD regarding the Val66Met or 5-HTTLPR polymorphisms. However, a significant association was found between the concomitant diagnosis of DE and the development of post-earthquake PTSD. The presence of DE doubled the risk of developing post-earthquake PTSD. The number of traumatic events experienced also had a statistically significant association with an increased risk of developing post-earthquake PTSD. The study’s limitations include the potential interference of different DE subtypes, the complexity of quantifying the degree of earthquake exposure experienced by each individual, and events entailing social disruption, such as looting, that can profoundly influence dist…
bibliographic citation: Castillo-Navarrete et al. (2023) Interaction of Val66Met BDNF and 5-HTTLPR polymorphisms with prevalence of post-earthquake 27-F PTSD in Chilean population. PeerJ 11:e15870 https://doi.org/10.7717/peerj.15870
date submitted: 2022-12-23
date accepted: 2023-07-18
issued: 2023-09-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Castillo-Navarrete
  given name: Juan-Luis
author list: Agent
  family name: Vicente
  given name: Benjamin
author list: Agent
  family name: Schmidt
  given name: Kristin
author list: Agent
  family name: Moraga-Escobar
  given name: Esteban
author list: Agent
  family name: Rojas-Ponce
  given name: Romina
author list: Agent
  family name: Lagos
  given name: Paola
author list: Agent
  family name: Macaya
  given name: Ximena
author list: Agent
  family name: Guzman-Castillo
  given name: Alejandra
doi: 10.7717/peerj.15870
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-04
copyright: ©2023 Castillo-Navarrete et al.
attribution name: Castillo-Navarrete et al.

A novel signaling transduction pathway of melatonin on lactose synthesis in cows via melatonin receptor 1 (MT1) and prolactin receptor (PRLR)
type: item
type: AcademicArticle
description: In the current study, we explored the relationship between melatonin and lactose synthesis in in vivo and in vitro conditions. We found that long-term melatonin feeding to the dairy cows significantly reduced the milk lactose content in a dose dependent manner. This lactose reduction was not associated with a negative energy balance, since melatonin treatment did not alter the fat, glucose, or protein metabolisms of the cows. To identify the potential molecular mechanisms, the cow’s mammary epithelial cells were cultured for gene expression analysis. The results showed that the effect of melatonin on lactose reduction was mediated by its receptor MT1. MT1 activation downregulated the mRNA expression of the prolactin receptor gene (PRLR), which then suppressed the gene expression of SLC35B1. SLC35B1 is a galactose transporter and is responsible for the transportation of galactose to Golgi apparatus for lactose synthesis. Its suppression reduced the lactose synthesis and the milk lactose content. The discovery of this signal transduction pathway of melatonin on lactose synthesis provides a novel aspect of melatonin’s effect on carbohydrate metabolism in cows and maybe also in other mammals, including humans.
format: application/pdf
format: text/html
creator: Yunjie Liu
creator: Songyang Yao
creator: Qinggeng Meng
creator: Xuening Liu
creator: Huigang Han
creator: Chunli Kan
creator: Tiankun Wang
creator: Wenjuan Wei
creator: Shujing Li
creator: Wenli Yu
creator: Zengyuan Zhao
creator: Changwang He
creator: Guoshi Liu
subject: Agricultural Science
subject: Biochemistry
subject: Food Science and Technology
subject: Zoology
subject: Nutrition
description: doi:10.7717/peerj.15932
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: In the current study, we explored the relationship between melatonin and lactose synthesis in in vivo and in vitro conditions. We found that long-term melatonin feeding to the dairy cows significantly reduced the milk lactose content in a dose dependent manner. This lactose reduction was not associated with a negative energy balance, since melatonin treatment did not alter the fat, glucose, or protein metabolisms of the cows. To identify the potential molecular mechanisms, the cow’s mammary epithelial cells were cultured for gene expression analysis. The results showed that the effect of melatonin on lactose reduction was mediated by its receptor MT1. MT1 activation downregulated the mRNA expression of the prolactin receptor gene (PRLR), which then suppressed the gene expression of SLC35B1. SLC35B1 is a galactose transporter and is responsible for the transportation of galactose to Golgi apparatus for lactose synthesis. Its suppression reduced the lactose synthesis and the milk lactose content. The discovery of this signal transduction pathway of melatonin on lactose synthesis provides a novel aspect of melatonin’s effect on carbohydrate metabolism in cows and maybe also in other mammals, including humans.
bibliographic citation: Liu et al. (2023) A novel signaling transduction pathway of melatonin on lactose synthesis in cows via melatonin receptor 1 (MT1) and prolactin receptor (PRLR). PeerJ 11:e15932 https://doi.org/10.7717/peerj.15932
date submitted: 2023-03-02
date accepted: 2023-07-30
issued: 2023-09-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yunjie
author list: Agent
  family name: Yao
  given name: Songyang
author list: Agent
  family name: Meng
  given name: Qinggeng
author list: Agent
  family name: Liu
  given name: Xuening
author list: Agent
  family name: Han
  given name: Huigang
author list: Agent
  family name: Kan
  given name: Chunli
author list: Agent
  family name: Wang
  given name: Tiankun
author list: Agent
  family name: Wei
  given name: Wenjuan
author list: Agent
  family name: Li
  given name: Shujing
author list: Agent
  family name: Yu
  given name: Wenli
author list: Agent
  family name: Zhao
  given name: Zengyuan
author list: Agent
  family name: He
  given name: Changwang
author list: Agent
  family name: Liu
  given name: Guoshi
doi: 10.7717/peerj.15932
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-04
copyright: ©2023 Liu et al.
attribution name: Liu et al.

Vertical contact forces affect vibration perception in human hairy skin
type: item
type: AcademicArticle
description: Background Skin is the largest organ of the human body and fulfills many important functions, like detecting mechanical stimuli. Skin can be divided into glabrous (non-hairy) and hairy skin. These two skin types differ with regard to their mechanical properties and in the distribution of mechanoreceptors. Although many investigations focus on glabrous skin, hairy skin still plays a fundamental role in various activities, e.g., with regard to the perception of pleasantness or for developing wearable vibrotactile devices for pattern recognition in persons with disabilities. Unfortunately, investigations on influencing factors, like vertical contactor force, are scarce for hairy skin. Similarly, it would also be interesting to investigate whether regional vibratory sensitivity differences are present across the human torso. Hence, this study investigated the effects of vertical contactor forces and different anatomical locations on vibration perception. Four anatomical torso regions were studied. Based on findings in glabrous skin, we generally hypothesized improved vibration perception with increasing contactor forces and regional sensitivity differences between the anatomical locations. Methods Forty young and healthy individuals participated (23.0 ± 2.0 yrs), and vibration perception thresholds (VPTs) were determined at 30 Hz for three vertical force levels (0.6, 2.4, and 4.8 N) at four torso locations (sternum, deltoid/shoulder, lower back, middle lateral torso side). Results Higher contactor forces resulted in lower VPTs corresponding to improved vibration perception, regardless of anatomical location. In addition, the sternum region was more sensitive than the remaining three regions, regardless of force level. The reasons for these findings may be a varying number and activation pattern of afferents activated under the different conditions. The findings of this study complement the understanding of vibrotactile sensitivity in hairy skin and may offer implication…
format: application/pdf
format: text/html
creator: Daniel Schmidt
creator: Guenther Schlee
creator: Thomas L. Milani
creator: Andresa M. C. Germano
subject: Neuroscience
subject: Dermatology
description: doi:10.7717/peerj.15952
publisher: PeerJ Inc.
rights: © 2023 Schmidt et al.
abstract: Background Skin is the largest organ of the human body and fulfills many important functions, like detecting mechanical stimuli. Skin can be divided into glabrous (non-hairy) and hairy skin. These two skin types differ with regard to their mechanical properties and in the distribution of mechanoreceptors. Although many investigations focus on glabrous skin, hairy skin still plays a fundamental role in various activities, e.g., with regard to the perception of pleasantness or for developing wearable vibrotactile devices for pattern recognition in persons with disabilities. Unfortunately, investigations on influencing factors, like vertical contactor force, are scarce for hairy skin. Similarly, it would also be interesting to investigate whether regional vibratory sensitivity differences are present across the human torso. Hence, this study investigated the effects of vertical contactor forces and different anatomical locations on vibration perception. Four anatomical torso regions were studied. Based on findings in glabrous skin, we generally hypothesized improved vibration perception with increasing contactor forces and regional sensitivity differences between the anatomical locations. Methods Forty young and healthy individuals participated (23.0 ± 2.0 yrs), and vibration perception thresholds (VPTs) were determined at 30 Hz for three vertical force levels (0.6, 2.4, and 4.8 N) at four torso locations (sternum, deltoid/shoulder, lower back, middle lateral torso side). Results Higher contactor forces resulted in lower VPTs corresponding to improved vibration perception, regardless of anatomical location. In addition, the sternum region was more sensitive than the remaining three regions, regardless of force level. The reasons for these findings may be a varying number and activation pattern of afferents activated under the different conditions. The findings of this study complement the understanding of vibrotactile sensitivity in hairy skin and may offer implication…
bibliographic citation: Schmidt et al. (2023) Vertical contact forces affect vibration perception in human hairy skin. PeerJ 11:e15952 https://doi.org/10.7717/peerj.15952
date submitted: 2022-12-13
date accepted: 2023-08-01
issued: 2023-09-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schmidt
  given name: Daniel
author list: Agent
  family name: Schlee
  given name: Guenther
author list: Agent
  family name: Milani
  given name: Thomas L.
author list: Agent
  family name: Germano
  given name: Andresa M. C.
doi: 10.7717/peerj.15952
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-04
copyright: © 2023 Schmidt et al.
attribution name: Schmidt et al.

Identification of a pathogen causing fruiting body rot of Sanghuangporus vaninii
type: item
type: AcademicArticle
description: Sanghuangporus vaninii is a medicinal macrofungus that is increasingly cultivated in China. During cultivation, it was found that the fruiting body of S. vaninii was susceptible to pathogenic fungi, resulting in significant economic losses to the industry. The symptoms of the disease occur in the initial stage of fruiting body development. The isolate YZB-1 was obtained from the junction of the diseased and healthy areas of the fruiting body. In order to verify the pathogenicity of YZB-1, its purified spore suspension was inoculated into the exposed area nearby the developing fruiting body of S. vaninii. After 10 days, the same disease symptoms appeared in the inoculated area. Morphological identification and molecular analysis of rDNA ITS region confirmed that the isolate YZB-1 was identified as Trichoderma virens. The temperature stability assay revealed that the mycelia of YZB-1 grew the fastest at 25 °C, with growth slowing down gradually as the temperature increased or decreased. Dual-culture tests of T. virens and S. vaninii showed that the inhibition rate of T. virens on S. vaninii mycelium was the highest (79.01 ± 2.79%) at 25 °C, and more green spores were produced at the intersection of T. virens and S. vaninii.
format: application/pdf
format: text/html
creator: Weidong Yuan
creator: Lin Ma
creator: Xingkun Chen
creator: Jiling Song
creator: Qing Chen
subject: Agricultural Science
subject: Microbiology
subject: Mycology
description: doi:10.7717/peerj.15983
publisher: PeerJ Inc.
rights: © 2023 Yuan et al.
abstract: Sanghuangporus vaninii is a medicinal macrofungus that is increasingly cultivated in China. During cultivation, it was found that the fruiting body of S. vaninii was susceptible to pathogenic fungi, resulting in significant economic losses to the industry. The symptoms of the disease occur in the initial stage of fruiting body development. The isolate YZB-1 was obtained from the junction of the diseased and healthy areas of the fruiting body. In order to verify the pathogenicity of YZB-1, its purified spore suspension was inoculated into the exposed area nearby the developing fruiting body of S. vaninii. After 10 days, the same disease symptoms appeared in the inoculated area. Morphological identification and molecular analysis of rDNA ITS region confirmed that the isolate YZB-1 was identified as Trichoderma virens. The temperature stability assay revealed that the mycelia of YZB-1 grew the fastest at 25 °C, with growth slowing down gradually as the temperature increased or decreased. Dual-culture tests of T. virens and S. vaninii showed that the inhibition rate of T. virens on S. vaninii mycelium was the highest (79.01 ± 2.79%) at 25 °C, and more green spores were produced at the intersection of T. virens and S. vaninii.
bibliographic citation: Yuan et al. (2023) Identification of a pathogen causing fruiting body rot of Sanghuangporus vaninii. PeerJ 11:e15983 https://doi.org/10.7717/peerj.15983
date submitted: 2023-04-05
date accepted: 2023-08-08
issued: 2023-09-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Weidong
author list: Agent
  family name: Ma
  given name: Lin
author list: Agent
  family name: Chen
  given name: Xingkun
author list: Agent
  family name: Song
  given name: Jiling
author list: Agent
  family name: Chen
  given name: Qing
doi: 10.7717/peerj.15983
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-04
copyright: © 2023 Yuan et al.
attribution name: Yuan et al.

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