PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A novel nomogram based on the patient’s clinical data and CT signs to predict poor outcomes in AIS patients
items: Comparative analysis of volume growth processes of Masson pine and Chinese fir forests in different regions of southern China
items: Responses of fungal communities at different soil depths to grazing intensity in a desert steppe
items: Exploring the phenotypic and molecular diversity of Calendula officinalis L. cultivars featuring varying flower types
items: Construction and validation of prognosis and treatment outcome models based on plasma membrane tension characteristics in bladder cancer
items: Coral histology reveals consistent declines in tissue integrity during a marine heatwave despite differences in bleaching severity
items: The non-indigenous dung beetle (Onthophagus nuchicornis) can effectively reproduce using the dung of indigenous eastern North American mammals
items: The effect of the Wnt pathway on the osteogenic differentiation of periodontal ligament stem cells in different environments
items: The status quo and influencing factors of breastfeeding social support in China based on LASSO regression model
items: Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers

A novel nomogram based on the patient’s clinical data and CT signs to predict poor outcomes in AIS patients
type: item
type: AcademicArticle
description: Background The 2019 American Heart Association/American Stroke Association (AHA/ASA) guidelines strongly advise using non-contrast CT (NCCT) of the head as a mandatory test for all patients with suspected acute ischemic stroke (AIS) due to CT’s advantages of affordability and speed of imaging. Therefore, our objective was to combine patient clinical data with head CT signs to create a nomogram to predict poor outcomes in AIS patients. Methods A retrospective analysis was conducted on 161 patients with acute ischemic stroke who underwent mechanical thrombectomy at the Guangzhou Hospital of Integrated Traditional and Western Medicine from January 2019 to June 2023. All patients were randomly assigned to either the training cohort (n = 113) or the validation cohort (n = 48) at a 7:3 ratio. According to the National Institute of Health Stroke Scale (NIHSS) score 7 days after mechanical thrombectomy, the patients were divided into the good outcome group (<15) and the poor outcome group (≥15). Predictive factors were selected through univariate analyses, LASSO regression analysis, and multivariate logistic regression analysis, followed by the construction of a nomogram predictive model. The receiver operating characteristic (ROC) curve was used to evaluate the predictive performance of the model, and bootstrapped ROC area under the curve (AUC) estimates were calculated to provide a more stable evaluation of the model’s accuracy. The model’s calibration performance was evaluated through the Hosmer-Lemeshow goodness-of-fit test and calibration plot, and the clinical effectiveness of the model was analyzed through decision curve analysis (DCA). Results Multivariate logistic regression analysis showed that hyperdense middle cerebral artery sign (HMCAS) (OR 9.113; 95% CI [1.945–42.708]; P = 0.005), the Alberta Stroke Program Early Computed Tomography Score (ASPECTS) > 6 (OR 7.707; 95% CI [2.201–26.991]; P = 0.001), NIHSS score (OR 1.085; 95% CI [1.009–1.166]; P = 0.027), age (…
format: application/pdf
format: text/html
creator: Jingyao Yang
creator: Fangfang Deng
creator: Qian Zhang
creator: Zhuyin Zhang
creator: Qinghua Luo
creator: Yeyu Xiao
subject: Epidemiology
subject: Neurology
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.18662
publisher: PeerJ Inc.
rights: © 2025 Yang et al.
abstract: Background The 2019 American Heart Association/American Stroke Association (AHA/ASA) guidelines strongly advise using non-contrast CT (NCCT) of the head as a mandatory test for all patients with suspected acute ischemic stroke (AIS) due to CT’s advantages of affordability and speed of imaging. Therefore, our objective was to combine patient clinical data with head CT signs to create a nomogram to predict poor outcomes in AIS patients. Methods A retrospective analysis was conducted on 161 patients with acute ischemic stroke who underwent mechanical thrombectomy at the Guangzhou Hospital of Integrated Traditional and Western Medicine from January 2019 to June 2023. All patients were randomly assigned to either the training cohort (n = 113) or the validation cohort (n = 48) at a 7:3 ratio. According to the National Institute of Health Stroke Scale (NIHSS) score 7 days after mechanical thrombectomy, the patients were divided into the good outcome group (<15) and the poor outcome group (≥15). Predictive factors were selected through univariate analyses, LASSO regression analysis, and multivariate logistic regression analysis, followed by the construction of a nomogram predictive model. The receiver operating characteristic (ROC) curve was used to evaluate the predictive performance of the model, and bootstrapped ROC area under the curve (AUC) estimates were calculated to provide a more stable evaluation of the model’s accuracy. The model’s calibration performance was evaluated through the Hosmer-Lemeshow goodness-of-fit test and calibration plot, and the clinical effectiveness of the model was analyzed through decision curve analysis (DCA). Results Multivariate logistic regression analysis showed that hyperdense middle cerebral artery sign (HMCAS) (OR 9.113; 95% CI [1.945–42.708]; P = 0.005), the Alberta Stroke Program Early Computed Tomography Score (ASPECTS) > 6 (OR 7.707; 95% CI [2.201–26.991]; P = 0.001), NIHSS score (OR 1.085; 95% CI [1.009–1.166]; P = 0.027), age (…
bibliographic citation: Yang et al. (2025) A novel nomogram based on the patient’s clinical data and CT signs to predict poor outcomes in AIS patients. PeerJ 13:e18662 https://doi.org/10.7717/peerj.18662
date submitted: 2024-07-05
date accepted: 2024-11-18
issued: 2025-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Jingyao
author list: Agent
  family name: Deng
  given name: Fangfang
author list: Agent
  family name: Zhang
  given name: Qian
author list: Agent
  family name: Zhang
  given name: Zhuyin
author list: Agent
  family name: Luo
  given name: Qinghua
author list: Agent
  family name: Xiao
  given name: Yeyu
doi: 10.7717/peerj.18662
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-06
copyright: © 2025 Yang et al.
attribution name: Yang et al.

Comparative analysis of volume growth processes of Masson pine and Chinese fir forests in different regions of southern China
type: item
type: AcademicArticle
description: Masson pine (Pinus massoniana Lamb.) and Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) are important coniferous species commonly found in southern China and play crucial ecological and economic roles. Understanding how regionally variable conditions influence their growth patterns can support effective forest management strategies and conservation efforts. Here, we used the Richards growth equation to comprehensively analyze their volumetric growth processes through multiple diverse regions in southern China, representing a pioneering large-scale application of unified modeling techniques. This work provides theoretical and technical knowledge to support the sustainable stewardship of these vital forest ecosystems. We found that: (1) The highest per-hectare volume accumulation occurs in southwestern China, at 97.455 m3 hm−2 for P. massoniana and 85.288 m3 hm−2 for C. lanceolata. These values are higher than in the southeastern (71.424 m3 hm−2 and 79.520 m3 hm−2, respectively) or south-central regions (70.697 m3 hm−2 and 65.647 m3 hm−2), predominantly due to varying stand maturity across these regions. (2) Both species exhibit age-dependent growth patterns in the first 100 years of forest development, characterized by rapid early growth and transitioning into slower, stable phases. The highest total volume growth for P. massoniana occurred in the southwest, followed by the southeast and south-central regions. Conversely, C. lanceolata growth is highest in the southeast, followed by south-central and the southwest. (3) Quantitative maturity for P. massoniana ranges from 27 to 29 years (average: 30 years) whereas C. lanceolata matures earlier, between 16 to 19 years (average: 20 years). Climate and soil factors significantly influence their growth dynamics, with precipitation, temperature variation, and soil characteristics driving differences in suitability and growth potential across distinct regions in southern China. Tailored management practices that align w…
format: application/pdf
format: text/html
creator: YuHui Chen
creator: Zongzheng Chai
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Natural Resource Management
subject: Forestry
description: doi:10.7717/peerj.18706
publisher: PeerJ Inc.
rights: © 2025 Chen and Chai
abstract: Masson pine (Pinus massoniana Lamb.) and Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) are important coniferous species commonly found in southern China and play crucial ecological and economic roles. Understanding how regionally variable conditions influence their growth patterns can support effective forest management strategies and conservation efforts. Here, we used the Richards growth equation to comprehensively analyze their volumetric growth processes through multiple diverse regions in southern China, representing a pioneering large-scale application of unified modeling techniques. This work provides theoretical and technical knowledge to support the sustainable stewardship of these vital forest ecosystems. We found that: (1) The highest per-hectare volume accumulation occurs in southwestern China, at 97.455 m3 hm−2 for P. massoniana and 85.288 m3 hm−2 for C. lanceolata. These values are higher than in the southeastern (71.424 m3 hm−2 and 79.520 m3 hm−2, respectively) or south-central regions (70.697 m3 hm−2 and 65.647 m3 hm−2), predominantly due to varying stand maturity across these regions. (2) Both species exhibit age-dependent growth patterns in the first 100 years of forest development, characterized by rapid early growth and transitioning into slower, stable phases. The highest total volume growth for P. massoniana occurred in the southwest, followed by the southeast and south-central regions. Conversely, C. lanceolata growth is highest in the southeast, followed by south-central and the southwest. (3) Quantitative maturity for P. massoniana ranges from 27 to 29 years (average: 30 years) whereas C. lanceolata matures earlier, between 16 to 19 years (average: 20 years). Climate and soil factors significantly influence their growth dynamics, with precipitation, temperature variation, and soil characteristics driving differences in suitability and growth potential across distinct regions in southern China. Tailored management practices that align w…
bibliographic citation: Chen et al. (2025) Comparative analysis of volume growth processes of Masson pine and Chinese fir forests in different regions of southern China. PeerJ 13:e18706 https://doi.org/10.7717/peerj.18706
date submitted: 2024-09-27
date accepted: 2024-11-22
issued: 2025-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: YuHui
author list: Agent
  family name: Chai
  given name: Zongzheng
doi: 10.7717/peerj.18706
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-06
copyright: ©2025 Chen and Chai
attribution name: Chen and Chai

Responses of fungal communities at different soil depths to grazing intensity in a desert steppe
type: item
type: AcademicArticle
description: Grazing can alter the physicochemical properties of soil and quickly influence the composition of microbial communities. However, the effects of grazing intensity on fungal community composition in different soil depth remain unclear. On the Inner Mongolia Plateau, we studied the effects of grazing intensity treatments including no grazing (NG), light grazing (LG), moderate grazing (MG), heavy grazing (HG), and over grazing (OG) on the physicochemical properties and fungal community composition of surface (0–20 cm) and subsurface (20–40 cm) soil layers. The α-diversity of fungi in subsurface soil decreased under the influence of grazing. The relative abundance of Ascomycota in the subsoil was higher than that in the topsoil, while the situation of Basidiomycota was the opposite. This was caused by the differences in the soil carbon (C) environment for the growth of oligotrophic and copiotrophic fungi. In the subsoil, grazing affected nutrient contents such as soil organic matter (SOM) and total nitrogen (TN), resulting in significantly lower relative abundance of Ortierellomycota under LG, HG, and OG than in the NG. HG showed much higher relative abundance of Glomeromycota. Results of a multiple regression tree (MRT) analysis revealed that TN and nitrate nitrogen affected the fungal α-diversity in top- and subsoils, respectively; the main driving factor regulating fungal community changes was soil water content (SWC) in the topsoil, while it was ammonium nitrogen and nitrate nitrogen in the subsoil. The results of our study indicate that grazing changes the soil environment by changing TN, SWC, nitrate nitrogen, ammonium nitrogen, and affects the diversity and community structure of soil fungi. This provides empirical support for coping with the impact of grazing on soil microbiomes in desert steppes.
format: application/pdf
format: text/html
creator: Xiangjian Tu
creator: Paul C. Struik
creator: Shixian Sun
creator: Zhang Wenbo
creator: Yong Zhang
creator: Ke Jin
creator: Zhen Wang
subject: Agricultural Science
subject: Ecology
subject: Mycology
subject: Soil Science
description: doi:10.7717/peerj.18791
publisher: PeerJ Inc.
rights: © 2025 Tu et al.
abstract: Grazing can alter the physicochemical properties of soil and quickly influence the composition of microbial communities. However, the effects of grazing intensity on fungal community composition in different soil depth remain unclear. On the Inner Mongolia Plateau, we studied the effects of grazing intensity treatments including no grazing (NG), light grazing (LG), moderate grazing (MG), heavy grazing (HG), and over grazing (OG) on the physicochemical properties and fungal community composition of surface (0–20 cm) and subsurface (20–40 cm) soil layers. The α-diversity of fungi in subsurface soil decreased under the influence of grazing. The relative abundance of Ascomycota in the subsoil was higher than that in the topsoil, while the situation of Basidiomycota was the opposite. This was caused by the differences in the soil carbon (C) environment for the growth of oligotrophic and copiotrophic fungi. In the subsoil, grazing affected nutrient contents such as soil organic matter (SOM) and total nitrogen (TN), resulting in significantly lower relative abundance of Ortierellomycota under LG, HG, and OG than in the NG. HG showed much higher relative abundance of Glomeromycota. Results of a multiple regression tree (MRT) analysis revealed that TN and nitrate nitrogen affected the fungal α-diversity in top- and subsoils, respectively; the main driving factor regulating fungal community changes was soil water content (SWC) in the topsoil, while it was ammonium nitrogen and nitrate nitrogen in the subsoil. The results of our study indicate that grazing changes the soil environment by changing TN, SWC, nitrate nitrogen, ammonium nitrogen, and affects the diversity and community structure of soil fungi. This provides empirical support for coping with the impact of grazing on soil microbiomes in desert steppes.
bibliographic citation: Tu et al. (2025) Responses of fungal communities at different soil depths to grazing intensity in a desert steppe. PeerJ 13:e18791 https://doi.org/10.7717/peerj.18791
date submitted: 2024-07-16
date accepted: 2024-12-10
issued: 2025-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tu
  given name: Xiangjian
author list: Agent
  family name: Struik
  given name: Paul C.
author list: Agent
  family name: Sun
  given name: Shixian
author list: Agent
  family name: Wenbo
  given name: Zhang
author list: Agent
  family name: Zhang
  given name: Yong
author list: Agent
  family name: Jin
  given name: Ke
author list: Agent
  family name: Wang
  given name: Zhen
doi: 10.7717/peerj.18791
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-06
copyright: ©2025 Tu et al.
attribution name: Tu et al.

Exploring the phenotypic and molecular diversity of Calendula officinalis L. cultivars featuring varying flower types
type: item
type: AcademicArticle
description: Pot marigold is an ornamental plant of great importance in pharmacy and cosmetology. However, there is limited published information on the diversity of the species at both the morphological and genetic levels. This paper aimed to determine the morphological and genetic diversity of selected marigold varieties. The research focused on varieties with different flower colours, and the most important morphological features of flowers and plant height were analysed. Genetic diversity analyses were performed using start codon target (SCoT) markers. The correlation coefficients between the analysed morphological features of the studied marigold varieties showed a significant positive relationship between plant height, the number of inflorescences per plant and inflorescence diameter. Genetic analyses grouped the studied varieties according to the colour of their flowers. The results obtained in our work indicate that, despite the variability observed in morphological features, the gene pool of the analysed marigold varieties is limited. This information can be valuable for marigold breeders, particularly for selecting varieties suitable for crossbreeding in breeding programs. Additionally, it offers insights into the genetic resources of the species and highlights the importance of their bioconservation.
format: application/pdf
format: text/html
creator: Aleksandra Nucia
creator: Tomasz Ociepa
creator: Beata Król
creator: Sylwia Okoń
subject: Agricultural Science
subject: Biodiversity
subject: Plant Science
description: doi:10.7717/peerj.18814
publisher: PeerJ Inc.
rights: © 2025 Nucia et al.
abstract: Pot marigold is an ornamental plant of great importance in pharmacy and cosmetology. However, there is limited published information on the diversity of the species at both the morphological and genetic levels. This paper aimed to determine the morphological and genetic diversity of selected marigold varieties. The research focused on varieties with different flower colours, and the most important morphological features of flowers and plant height were analysed. Genetic diversity analyses were performed using start codon target (SCoT) markers. The correlation coefficients between the analysed morphological features of the studied marigold varieties showed a significant positive relationship between plant height, the number of inflorescences per plant and inflorescence diameter. Genetic analyses grouped the studied varieties according to the colour of their flowers. The results obtained in our work indicate that, despite the variability observed in morphological features, the gene pool of the analysed marigold varieties is limited. This information can be valuable for marigold breeders, particularly for selecting varieties suitable for crossbreeding in breeding programs. Additionally, it offers insights into the genetic resources of the species and highlights the importance of their bioconservation.
bibliographic citation: Nucia et al. (2025) Exploring the phenotypic and molecular diversity of Calendula officinalis L. cultivars featuring varying flower types. PeerJ 13:e18814 https://doi.org/10.7717/peerj.18814
date submitted: 2024-10-02
date accepted: 2024-12-13
issued: 2025-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nucia
  given name: Aleksandra
author list: Agent
  family name: Ociepa
  given name: Tomasz
author list: Agent
  family name: Król
  given name: Beata
author list: Agent
  family name: Okoń
  given name: Sylwia
doi: 10.7717/peerj.18814
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-06
copyright: ©2025 Nucia et al.
attribution name: Nucia et al.

Construction and validation of prognosis and treatment outcome models based on plasma membrane tension characteristics in bladder cancer
type: item
type: AcademicArticle
description: Background Plasma membrane tension-related genes (MTRGs) are known to play a crucial role in tumor progression by influencing cell migration and adhesion. However, their specific mechanisms in bladder cancer (BLCA) remain unclear. Methods Transcriptomic, clinical and mutation data from BLCA patients were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Clusters associated with MTRGs were identified by consensus unsupervised cluster analysis. The genes of different clusters were analyzed by GO and KEGG gene enrichment analysis. Differentially expressed genes (DEGs) were screened from different clusters. Consensus cluster analysis of prognostic DEGs was performed to identify gene subtypes. Patients were then randomly divided into training and validation groups, and MTRG scores were constructed by logistic minimum absolute contraction and selection operator (LASSO) and Cox regression analysis. We assessed changes in clinical outcomes and immune-related factors between different patient groups. The single-cell RNA sequencing (scRNA-seq) dataset for BLCA was collected and analyzed from the Tumor Immune Single-cell Hub (TISCH) database. Biological functions were investigated using a series of experiments including quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), wound healing, transwell, etc. Results Our MTRG score is based on eight genes (HTRA1, GOLT1A, DCBLD2, UGT1A1, FOSL1, DSC2, IGFBP3 and TAC3). Higher scores were characterized by lower cancer stem cell (CSC) indices, as well as higher tumor microenvironment (TME) stromal and immune scores, suggesting that high scores were associated with poorer prognosis. In addition, some drugs such as cisplatin, paclitaxel, doxorubicin, and docetaxel exhibited lower IC50 values in the high MTRG score group. Functional experiments have demonstrated that downregulation of DCBLD2 affects tumor cell migration, but not proliferation. Conclusions Our study sheds light on t…
format: application/pdf
format: text/html
creator: Zhipeng Wang
creator: Sheng Li
creator: Fuchun Zheng
creator: Situ Xiong
creator: Lei Zhang
creator: Liangwei Wan
creator: Chen Wang
creator: Xiaoqiang Liu
creator: Jun Deng
subject: Biogeography
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.18816
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Background Plasma membrane tension-related genes (MTRGs) are known to play a crucial role in tumor progression by influencing cell migration and adhesion. However, their specific mechanisms in bladder cancer (BLCA) remain unclear. Methods Transcriptomic, clinical and mutation data from BLCA patients were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Clusters associated with MTRGs were identified by consensus unsupervised cluster analysis. The genes of different clusters were analyzed by GO and KEGG gene enrichment analysis. Differentially expressed genes (DEGs) were screened from different clusters. Consensus cluster analysis of prognostic DEGs was performed to identify gene subtypes. Patients were then randomly divided into training and validation groups, and MTRG scores were constructed by logistic minimum absolute contraction and selection operator (LASSO) and Cox regression analysis. We assessed changes in clinical outcomes and immune-related factors between different patient groups. The single-cell RNA sequencing (scRNA-seq) dataset for BLCA was collected and analyzed from the Tumor Immune Single-cell Hub (TISCH) database. Biological functions were investigated using a series of experiments including quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), wound healing, transwell, etc. Results Our MTRG score is based on eight genes (HTRA1, GOLT1A, DCBLD2, UGT1A1, FOSL1, DSC2, IGFBP3 and TAC3). Higher scores were characterized by lower cancer stem cell (CSC) indices, as well as higher tumor microenvironment (TME) stromal and immune scores, suggesting that high scores were associated with poorer prognosis. In addition, some drugs such as cisplatin, paclitaxel, doxorubicin, and docetaxel exhibited lower IC50 values in the high MTRG score group. Functional experiments have demonstrated that downregulation of DCBLD2 affects tumor cell migration, but not proliferation. Conclusions Our study sheds light on t…
bibliographic citation: Wang et al. (2025) Construction and validation of prognosis and treatment outcome models based on plasma membrane tension characteristics in bladder cancer. PeerJ 13:e18816 https://doi.org/10.7717/peerj.18816
date submitted: 2024-09-11
date accepted: 2024-12-14
issued: 2025-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhipeng
author list: Agent
  family name: Li
  given name: Sheng
author list: Agent
  family name: Zheng
  given name: Fuchun
author list: Agent
  family name: Xiong
  given name: Situ
author list: Agent
  family name: Zhang
  given name: Lei
author list: Agent
  family name: Wan
  given name: Liangwei
author list: Agent
  family name: Wang
  given name: Chen
author list: Agent
  family name: Liu
  given name: Xiaoqiang
author list: Agent
  family name: Deng
  given name: Jun
doi: 10.7717/peerj.18816
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-06
copyright: ©2025 Wang et al.
attribution name: Wang et al.

Coral histology reveals consistent declines in tissue integrity during a marine heatwave despite differences in bleaching severity
type: item
type: AcademicArticle
description: Marine heatwaves are starting to occur several times a decade, yet we do not understand the effect this has on corals across biological scales. This study combines tissue-, organism-, and community-level analyses to investigate the effects of a marine heatwave on reef-building corals. Adjacent conspecific pairs of coral colonies of Montipora capitata and Porites compressa that showed contrasting phenotypic responses (i.e., bleached vs. not bleached) were first identified during a marine heatwave that occurred in 2015 in Kāne’ohe Bay, Hawai‘ i. These conspecific pairs of bleaching-resistant and bleaching-susceptible colonies were sampled for histology and photographed before, during, and after a subsequent marine heatwave that occurred in 2019. Histology samples were quantified for: (i) abundance of mesenterial filaments, (ii) tissue structural integrity, (iii) clarity of epidermis, and (iv) cellular integrity (lack of necrosis/granulation) on a 1–5 scale and averaged for an overall tissue integrity score. Tissue integrity scores revealed a significant decline in overall tissue health during the 2019 heatwave relative to the months prior to the heatwave for individuals of both species, regardless of past bleaching history in 2015 or bleaching severity during the 2019 heatwave. Coral tissue integrity scores were then compared to concurrent colony bleaching severity, which revealed that tissue integrity was significantly correlated with colony bleaching severity and suggests that the stability of the symbiosis is related to host tissue health. Colony partial mortality was also quantified as the cumulative proportion of each colony that appeared dead 2.5 years following the 2019 bleaching event, and tissue integrity during the heatwave was found to be strongly predictive of the extent of partial mortality following the heatwave for M. capitata but not P. compressa, the latter of which suffered little to no mortality. Surprisingly, bleaching severity and partial mortalit…
format: application/pdf
format: text/html
creator: Elisa Kruse
creator: Kristen T. Brown
creator: Katie L. Barott
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Histology
subject: Climate Change Biology
description: doi:10.7717/peerj.18654
publisher: PeerJ Inc.
rights: © 2025 Kruse et al.
abstract: Marine heatwaves are starting to occur several times a decade, yet we do not understand the effect this has on corals across biological scales. This study combines tissue-, organism-, and community-level analyses to investigate the effects of a marine heatwave on reef-building corals. Adjacent conspecific pairs of coral colonies of Montipora capitata and Porites compressa that showed contrasting phenotypic responses (i.e., bleached vs. not bleached) were first identified during a marine heatwave that occurred in 2015 in Kāne’ohe Bay, Hawai‘ i. These conspecific pairs of bleaching-resistant and bleaching-susceptible colonies were sampled for histology and photographed before, during, and after a subsequent marine heatwave that occurred in 2019. Histology samples were quantified for: (i) abundance of mesenterial filaments, (ii) tissue structural integrity, (iii) clarity of epidermis, and (iv) cellular integrity (lack of necrosis/granulation) on a 1–5 scale and averaged for an overall tissue integrity score. Tissue integrity scores revealed a significant decline in overall tissue health during the 2019 heatwave relative to the months prior to the heatwave for individuals of both species, regardless of past bleaching history in 2015 or bleaching severity during the 2019 heatwave. Coral tissue integrity scores were then compared to concurrent colony bleaching severity, which revealed that tissue integrity was significantly correlated with colony bleaching severity and suggests that the stability of the symbiosis is related to host tissue health. Colony partial mortality was also quantified as the cumulative proportion of each colony that appeared dead 2.5 years following the 2019 bleaching event, and tissue integrity during the heatwave was found to be strongly predictive of the extent of partial mortality following the heatwave for M. capitata but not P. compressa, the latter of which suffered little to no mortality. Surprisingly, bleaching severity and partial mortalit…
bibliographic citation: Kruse et al. (2025) Coral histology reveals consistent declines in tissue integrity during a marine heatwave despite differences in bleaching severity. PeerJ 13:e18654 https://doi.org/10.7717/peerj.18654
date submitted: 2024-07-18
date accepted: 2024-11-17
issued: 2025-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kruse
  given name: Elisa
author list: Agent
  family name: Brown
  given name: Kristen T.
author list: Agent
  family name: Barott
  given name: Katie L.
doi: 10.7717/peerj.18654
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-03
copyright: ©2025 Kruse et al.
attribution name: Kruse et al.

The non-indigenous dung beetle (Onthophagus nuchicornis) can effectively reproduce using the dung of indigenous eastern North American mammals
type: item
type: AcademicArticle
description: Non-indigenous dung beetle (Coleoptera: Scarabaeoidea) species in North America are important contributors to ecosystem functions, particularly in pasture-based livestock systems. Despite the significant body of research surrounding non-indigenous (and often invasive) dung beetles in agricultural contexts, there has been minimal study concerning the impact that these species may have on indigenous dung beetle populations in natural environments. Here we examine the possible impact of the introduced dung beetle Onthophagus nuchicornis on indigenous dung beetle populations via use of indigenous mammal dung. Using a controlled laboratory experiment, we quantified how readily beetles could use dung from bobcat (Lynx rufus), red fox (Vulpes vulpes), moose (Alces alces), raccoon (Procyon lotor), and domestic sheep (Ovis aries). To determine the suitability of each dung type for reproduction, we measured offspring abundance and fitness. While the number of developed offspring was significantly different among treatments, offspring fitness did not vary significantly across dung types. Our results demonstrate the generalist feeding habits of the non-indigenous dung beetle O. nuchicornis can allow this species to use the dung of various wild animals indigenous to eastern North America.
format: application/pdf
format: text/html
creator: Alexe Indigo
creator: Katelyn Stokes
creator: Olivia Burchell
creator: Paul Manning
subject: Agricultural Science
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.18674
publisher: PeerJ Inc.
rights: © 2025 Indigo et al.
abstract: Non-indigenous dung beetle (Coleoptera: Scarabaeoidea) species in North America are important contributors to ecosystem functions, particularly in pasture-based livestock systems. Despite the significant body of research surrounding non-indigenous (and often invasive) dung beetles in agricultural contexts, there has been minimal study concerning the impact that these species may have on indigenous dung beetle populations in natural environments. Here we examine the possible impact of the introduced dung beetle Onthophagus nuchicornis on indigenous dung beetle populations via use of indigenous mammal dung. Using a controlled laboratory experiment, we quantified how readily beetles could use dung from bobcat (Lynx rufus), red fox (Vulpes vulpes), moose (Alces alces), raccoon (Procyon lotor), and domestic sheep (Ovis aries). To determine the suitability of each dung type for reproduction, we measured offspring abundance and fitness. While the number of developed offspring was significantly different among treatments, offspring fitness did not vary significantly across dung types. Our results demonstrate the generalist feeding habits of the non-indigenous dung beetle O. nuchicornis can allow this species to use the dung of various wild animals indigenous to eastern North America.
bibliographic citation: Indigo et al. (2025) The non-indigenous dung beetle (Onthophagus nuchicornis) can effectively reproduce using the dung of indigenous eastern North American mammals. PeerJ 13:e18674 https://doi.org/10.7717/peerj.18674
date submitted: 2024-07-05
date accepted: 2024-11-19
issued: 2025-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Indigo
  given name: Alexe
author list: Agent
  family name: Stokes
  given name: Katelyn
author list: Agent
  family name: Burchell
  given name: Olivia
author list: Agent
  family name: Manning
  given name: Paul
doi: 10.7717/peerj.18674
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-03
copyright: ©2025 Indigo et al.
attribution name: Indigo et al.

The effect of the Wnt pathway on the osteogenic differentiation of periodontal ligament stem cells in different environments
type: item
type: AcademicArticle
description: Alveolar bone defects have always been an urgent problem in the oral cavity. For some patients with periodontal disease or undergoing orthodontic treatment or implant restoration, alveolar bone defects can greatly inconvenience clinical diagnosis and treatment. Periodontal ligament stem cells (PDLSCs) are considered a promising source for stem cell therapy due to their high osteogenic differentiation capability. The osteogenic differentiation of PDLSCs is influenced by various cytokines mediating signaling pathways, as well as a range of biochemical, physical, and chemical factors. Different environments typically impact the Wnt signaling pathway and consequently affect the osteogenic differentiation of PDLSCs. Understanding the effects of the Wnt signaling pathway on the osteogenic differentiation of periodontal ligament stem cells in various environments contributes to addressing the diverse clinical scenarios encountered in the oral environment. This knowledge aids in influencing the pathway through bioengineering or the development of novel materials, thereby enhancing the osteogenic potential of stem cells and providing new diagnostic and therapeutic strategies for clinical practice.
format: application/pdf
format: text/html
creator: Qi Su
creator: Fengqiong Huang
creator: XiuLei Fang
creator: Qiang Lin
subject: Cell Biology
subject: Molecular Biology
subject: Dentistry
description: doi:10.7717/peerj.18770
publisher: PeerJ Inc.
rights: © 2025 Su et al.
abstract: Alveolar bone defects have always been an urgent problem in the oral cavity. For some patients with periodontal disease or undergoing orthodontic treatment or implant restoration, alveolar bone defects can greatly inconvenience clinical diagnosis and treatment. Periodontal ligament stem cells (PDLSCs) are considered a promising source for stem cell therapy due to their high osteogenic differentiation capability. The osteogenic differentiation of PDLSCs is influenced by various cytokines mediating signaling pathways, as well as a range of biochemical, physical, and chemical factors. Different environments typically impact the Wnt signaling pathway and consequently affect the osteogenic differentiation of PDLSCs. Understanding the effects of the Wnt signaling pathway on the osteogenic differentiation of periodontal ligament stem cells in various environments contributes to addressing the diverse clinical scenarios encountered in the oral environment. This knowledge aids in influencing the pathway through bioengineering or the development of novel materials, thereby enhancing the osteogenic potential of stem cells and providing new diagnostic and therapeutic strategies for clinical practice.
bibliographic citation: Su et al. (2025) The effect of the Wnt pathway on the osteogenic differentiation of periodontal ligament stem cells in different environments. PeerJ 13:e18770 https://doi.org/10.7717/peerj.18770
date submitted: 2024-08-12
date accepted: 2024-12-05
issued: 2025-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Qi
author list: Agent
  family name: Huang
  given name: Fengqiong
author list: Agent
  family name: Fang
  given name: XiuLei
author list: Agent
  family name: Lin
  given name: Qiang
doi: 10.7717/peerj.18770
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-03
copyright: © 2025 Su et al.
attribution name: Su et al.

The status quo and influencing factors of breastfeeding social support in China based on LASSO regression model
type: item
type: AcademicArticle
description: Background In China, the rate of exclusive breastfeeding at 6 months is only 29.2%, well below the global breastfeeding collective target of at least 50% by 2025. This study explores the status quo of breastfeeding social support among puerpera and analyses its influencing factors, in order to provide a basis for improving breastfeeding rate in China. Methods A total of 251 puerpera were selected to fill in the general information questionnaire and the Breastfeeding Social Support Scale from three community health service centers in the city of Chengde, Hebei province, China, from September to November 2023 by completed random cluster sampling method. And the LASSO regression was used to screen and order the influencing factors of breastfeeding social support. Results The total score of the Breastfeeding Social Support Scale was (48.95 ± 7.93). The results of LASSO regression showed that when the lambda (λ) value was 0.7428, the error was the smallest, and the corresponding number of influencing factors was four, and the top four independent variables in importance ranking were whether or not breastfeeding at night, employment status, the feeding mode of the youngest baby, partner attended school/lecture for pregnant women. Conclusion The level of breastfeeding social support remains to be improved; health care providers were suggested to develop targeted intervention according to the influencing factors.
format: application/pdf
format: text/html
creator: Tian Sun
creator: Chanzhi Duan
creator: Yan Wang
creator: Qing Li
subject: Global Health
subject: Gynecology and Obstetrics
subject: Health Policy
subject: Nursing
subject: Healthcare Services
description: doi:10.7717/peerj.18779
publisher: PeerJ Inc.
rights: © 2025 Sun et al.
abstract: Background In China, the rate of exclusive breastfeeding at 6 months is only 29.2%, well below the global breastfeeding collective target of at least 50% by 2025. This study explores the status quo of breastfeeding social support among puerpera and analyses its influencing factors, in order to provide a basis for improving breastfeeding rate in China. Methods A total of 251 puerpera were selected to fill in the general information questionnaire and the Breastfeeding Social Support Scale from three community health service centers in the city of Chengde, Hebei province, China, from September to November 2023 by completed random cluster sampling method. And the LASSO regression was used to screen and order the influencing factors of breastfeeding social support. Results The total score of the Breastfeeding Social Support Scale was (48.95 ± 7.93). The results of LASSO regression showed that when the lambda (λ) value was 0.7428, the error was the smallest, and the corresponding number of influencing factors was four, and the top four independent variables in importance ranking were whether or not breastfeeding at night, employment status, the feeding mode of the youngest baby, partner attended school/lecture for pregnant women. Conclusion The level of breastfeeding social support remains to be improved; health care providers were suggested to develop targeted intervention according to the influencing factors.
bibliographic citation: Sun et al. (2025) The status quo and influencing factors of breastfeeding social support in China based on LASSO regression model. PeerJ 13:e18779 https://doi.org/10.7717/peerj.18779
date submitted: 2024-07-23
date accepted: 2024-12-09
issued: 2025-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Sun
  given name: Tian
author list: Agent
  family name: Duan
  given name: Chanzhi
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Li
  given name: Qing
doi: 10.7717/peerj.18779
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-03
copyright: ©2025 Sun et al.
attribution name: Sun et al.

Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers
type: item
type: AcademicArticle
description: Background Understanding the diversity and distribution of fungal communities at a regional scale is important since fungi play a crucial role in ecosystem functioning. Our study used environmental metagenomics to determine fungal communities in mountainous forest soils in the central highlands of Mexico. Methods We used four different bioinformatic workflows to profile fungal assemblages, i.e., Geneious+UNITE, single- and paired-end microbial community profiling (MiCoP), and Kraken2. Results The workflows yielded different results; one detected a higher abundance of ectomycorrhizal (EcM) and saprophytic fungi, while the other identified more saprophytic and pathogenic fungi. Environmental, vegetation, and geographical factors determined the spatial distribution of soil fungi at a regional scale. Potential hydrogen (pH), calcium (Ca), magnesium (Mg), and silt content were detected as common drivers of fungal communities across different datasets enriched towards a functional guild. Vegetation traits were found to be more influential in shaping symbiotrophic fungi composition than saprotrophic and pathogenic fungi. This highlights the importance of considering vegetation traits when studying fungal community diversity and distribution. Clustering patterns of sampling points near the volcanoes indicated shared environmental and vegetation characteristics. A weak but significant distance decay in taxonomic similarity revealed that dispersal limitation contributed to fungal community composition, although it was not the primary factor in this study. Overall, this study provides important insights into the challenges and opportunities of studying fungal communities at a regional scale using metagenomic data.
format: application/pdf
format: text/html
creator: Stephanie Hereira-Pacheco
creator: Itzel Arias-Del Razo
creator: Alejandra Miranda-Carrazco
creator: Luc Dendooven
creator: Arturo Estrada-Torres
creator: Yendi E. Navarro-Noya
subject: Bioinformatics
subject: Ecology
subject: Ecosystem Science
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.18323
publisher: PeerJ Inc.
rights: © 2025 Hereira-Pacheco et al.
abstract: Background Understanding the diversity and distribution of fungal communities at a regional scale is important since fungi play a crucial role in ecosystem functioning. Our study used environmental metagenomics to determine fungal communities in mountainous forest soils in the central highlands of Mexico. Methods We used four different bioinformatic workflows to profile fungal assemblages, i.e., Geneious+UNITE, single- and paired-end microbial community profiling (MiCoP), and Kraken2. Results The workflows yielded different results; one detected a higher abundance of ectomycorrhizal (EcM) and saprophytic fungi, while the other identified more saprophytic and pathogenic fungi. Environmental, vegetation, and geographical factors determined the spatial distribution of soil fungi at a regional scale. Potential hydrogen (pH), calcium (Ca), magnesium (Mg), and silt content were detected as common drivers of fungal communities across different datasets enriched towards a functional guild. Vegetation traits were found to be more influential in shaping symbiotrophic fungi composition than saprotrophic and pathogenic fungi. This highlights the importance of considering vegetation traits when studying fungal community diversity and distribution. Clustering patterns of sampling points near the volcanoes indicated shared environmental and vegetation characteristics. A weak but significant distance decay in taxonomic similarity revealed that dispersal limitation contributed to fungal community composition, although it was not the primary factor in this study. Overall, this study provides important insights into the challenges and opportunities of studying fungal communities at a regional scale using metagenomic data.
bibliographic citation: Hereira-Pacheco et al. (2025) Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers. PeerJ 13:e18323 https://doi.org/10.7717/peerj.18323
date submitted: 2024-05-30
date accepted: 2024-09-25
issued: 2025-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hereira-Pacheco
  given name: Stephanie
author list: Agent
  family name: Arias-Del Razo
  given name: Itzel
author list: Agent
  family name: Miranda-Carrazco
  given name: Alejandra
author list: Agent
  family name: Dendooven
  given name: Luc
author list: Agent
  family name: Estrada-Torres
  given name: Arturo
author list: Agent
  family name: Navarro-Noya
  given name: Yendi E.
doi: 10.7717/peerj.18323
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-02
copyright: © 2025 Hereira-Pacheco et al.
attribution name: Hereira-Pacheco et al.

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