PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Combined effects of dietary faba bean water extract and vitamin K3 on growth performance, textural quality, intestinal characteristics, oxidative and immune responses in grass carp
items: mRNA sequencing reveals the distinct gene expression and biological functions in cardiac fibroblasts regulated by recombinant fibroblast growth factor 2
items: Leaf nutrient resorption of two life-form tree species in urban gardens and their response to soil nutrient availability
items: Optimal tillage depths for enhancing rice yield, quality and lodging resistance in the rice production systems of northeast China
items: Prediction of sea ice area based on the CEEMDAN-SO-BiLSTM model
items: Recent research progress on the correlation between metabolic syndrome and Helicobacter pylori infection
items: Putative causal inference for the relationship between obesity and sex hormones in males: a bidirectional Mendelian randomization study
items: Why can people with developmental prosopagnosia recognise some familiar faces? Insights from subjective experience
items: Functional trait diversity of Cyclanthaceae and its convergent evolution with Araceae in Neotropical forests
items: Pogonias courbina sperm characteristcs in its first reproductive season

Combined effects of dietary faba bean water extract and vitamin K3 on growth performance, textural quality, intestinal characteristics, oxidative and immune responses in grass carp
type: item
type: AcademicArticle
description: Faba bean water extract (FBW) and vitamin K3 (VK3) have been demonstrated to improve the muscle textural quality of fish. To better apply these two feed additives in commercial aquaculture setting, four experimental diets (control, commercial feed group; 15% FBW, 15% faba bean water extract group; 2.5% VK3, 2.5% vitamin K3 group; combined group, 15% faba bean water extract + 2.5% vitamin K3 group) were formulated to explore their combined effects of FBW and VK3 on the growth, health status, and muscle textural quality of grass carp. The growth performance, textural quality, intestinal characteristics, and oxidative and immune responses were analyzed on days 40, 80 and 120. The results showed that supplementation with higher doses of FBW and VK3 have no influence on growth-related parameters and immune parameters of grass carp. Notably, compared with the control, fish in the combined group had the highest textural qualities (hardness, chewiness and adhesiveness), followed by those in 15% FBW and 2.5% VK3 groups (P < 0.05). Also, FBW and VK3, to some extent, may lower antioxidative ability of grass carp, as illustrated by lower levels of GSH and CAT in 15% FBW, 2.5% VK3, and combined groups on day 120 (P < 0.05). In addition, enhanced lipase activity was observed in the 15% FBW group. Taken together, the combined supplementation of FBW and VK3 was demonstrated to be a more advanced option than their individual supplementation in a commercial setting owing to the resulting combined effects on both the textural quality and health status of grass carp.
format: application/pdf
format: text/html
creator: Yichao Li
creator: Bin Chen
creator: Junming Zhang
creator: Guangjun Wang
creator: Wangbao Gong
creator: Jingjing Tian
creator: Hongyan Li
creator: Kai Zhang
creator: Yun Xia
creator: Zhifei Li
creator: Jun Xie
creator: Ermeng Yu
subject: Aquaculture, Fisheries and Fish Science
subject: Food Science and Technology
subject: Zoology
subject: Histology
subject: Freshwater Biology
description: doi:10.7717/peerj.15733
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Faba bean water extract (FBW) and vitamin K3 (VK3) have been demonstrated to improve the muscle textural quality of fish. To better apply these two feed additives in commercial aquaculture setting, four experimental diets (control, commercial feed group; 15% FBW, 15% faba bean water extract group; 2.5% VK3, 2.5% vitamin K3 group; combined group, 15% faba bean water extract + 2.5% vitamin K3 group) were formulated to explore their combined effects of FBW and VK3 on the growth, health status, and muscle textural quality of grass carp. The growth performance, textural quality, intestinal characteristics, and oxidative and immune responses were analyzed on days 40, 80 and 120. The results showed that supplementation with higher doses of FBW and VK3 have no influence on growth-related parameters and immune parameters of grass carp. Notably, compared with the control, fish in the combined group had the highest textural qualities (hardness, chewiness and adhesiveness), followed by those in 15% FBW and 2.5% VK3 groups (P < 0.05). Also, FBW and VK3, to some extent, may lower antioxidative ability of grass carp, as illustrated by lower levels of GSH and CAT in 15% FBW, 2.5% VK3, and combined groups on day 120 (P < 0.05). In addition, enhanced lipase activity was observed in the 15% FBW group. Taken together, the combined supplementation of FBW and VK3 was demonstrated to be a more advanced option than their individual supplementation in a commercial setting owing to the resulting combined effects on both the textural quality and health status of grass carp.
bibliographic citation: Li et al. (2023) Combined effects of dietary faba bean water extract and vitamin K3 on growth performance, textural quality, intestinal characteristics, oxidative and immune responses in grass carp. PeerJ 11:e15733 https://doi.org/10.7717/peerj.15733
date submitted: 2023-03-20
date accepted: 2023-06-19
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yichao
author list: Agent
  family name: Chen
  given name: Bin
author list: Agent
  family name: Zhang
  given name: Junming
author list: Agent
  family name: Wang
  given name: Guangjun
author list: Agent
  family name: Gong
  given name: Wangbao
author list: Agent
  family name: Tian
  given name: Jingjing
author list: Agent
  family name: Li
  given name: Hongyan
author list: Agent
  family name: Zhang
  given name: Kai
author list: Agent
  family name: Xia
  given name: Yun
author list: Agent
  family name: Li
  given name: Zhifei
author list: Agent
  family name: Xie
  given name: Jun
author list: Agent
  family name: Yu
  given name: Ermeng
doi: 10.7717/peerj.15733
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: © 2023 Li et al.
attribution name: Li et al.

mRNA sequencing reveals the distinct gene expression and biological functions in cardiac fibroblasts regulated by recombinant fibroblast growth factor 2
type: item
type: AcademicArticle
description: After myocardial injury, cardiac fibroblasts (CFs) differentiate into myofibroblasts, which express and secrete extracellular matrix (ECM) components for myocardial repair, but also promote myocardial fibrosis. Recombinant fibroblast growth factor 2 (FGF2) protein drug with low molecular weight can promote cell survival and angiogenesis, and it was found that FGF2 could inhibit the activation of CFs, suggesting FGF2 has great potential in myocardial repair. However, the regulatory role of FGF2 on CFs has not been fully elucidated. Here, we found that recombinant FGF2 significantly suppressed the expression of alpha smooth muscle actin (α-SMA) in CFs. Through RNA sequencing, we analyzed mRNA expression in CFs and the differently expressed genes regulated by FGF2, including 430 up-regulated genes and 391 down-regulated genes. Gene ontology analysis revealed that the differentially expressed genes were strongly enriched in multiple biological functions, including ECM organization, cell adhesion, actin filament organization and axon guidance. The results of gene set enrichment analysis (GSEA) show that ECM organization and actin filament organization are down-regulated, while axon guidance is up-regulated. Further cellular experiments indicate that the regulatory functions of FGF2 are consistent with the findings of the gene enrichment analysis. This study provides valuable insights into the potential therapeutic role of FGF2 in treating cardiac fibrosis and establishes a foundation for further research to uncover the underlying mechanisms of CFs gene expression regulated by FGF2.
format: application/pdf
format: text/html
creator: Changye Sun
creator: Mengru Bai
creator: Yangyang Jia
creator: Xiangqin Tian
creator: Yonglong Guo
creator: Xinhui Xu
creator: Zhikun Guo
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Cardiology
description: doi:10.7717/peerj.15736
publisher: PeerJ Inc.
rights: © 2023 Sun et al.
abstract: After myocardial injury, cardiac fibroblasts (CFs) differentiate into myofibroblasts, which express and secrete extracellular matrix (ECM) components for myocardial repair, but also promote myocardial fibrosis. Recombinant fibroblast growth factor 2 (FGF2) protein drug with low molecular weight can promote cell survival and angiogenesis, and it was found that FGF2 could inhibit the activation of CFs, suggesting FGF2 has great potential in myocardial repair. However, the regulatory role of FGF2 on CFs has not been fully elucidated. Here, we found that recombinant FGF2 significantly suppressed the expression of alpha smooth muscle actin (α-SMA) in CFs. Through RNA sequencing, we analyzed mRNA expression in CFs and the differently expressed genes regulated by FGF2, including 430 up-regulated genes and 391 down-regulated genes. Gene ontology analysis revealed that the differentially expressed genes were strongly enriched in multiple biological functions, including ECM organization, cell adhesion, actin filament organization and axon guidance. The results of gene set enrichment analysis (GSEA) show that ECM organization and actin filament organization are down-regulated, while axon guidance is up-regulated. Further cellular experiments indicate that the regulatory functions of FGF2 are consistent with the findings of the gene enrichment analysis. This study provides valuable insights into the potential therapeutic role of FGF2 in treating cardiac fibrosis and establishes a foundation for further research to uncover the underlying mechanisms of CFs gene expression regulated by FGF2.
bibliographic citation: Sun et al. (2023) mRNA sequencing reveals the distinct gene expression and biological functions in cardiac fibroblasts regulated by recombinant fibroblast growth factor 2. PeerJ 11:e15736 https://doi.org/10.7717/peerj.15736
date submitted: 2023-02-09
date accepted: 2023-06-20
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Changye
author list: Agent
  family name: Bai
  given name: Mengru
author list: Agent
  family name: Jia
  given name: Yangyang
author list: Agent
  family name: Tian
  given name: Xiangqin
author list: Agent
  family name: Guo
  given name: Yonglong
author list: Agent
  family name: Xu
  given name: Xinhui
author list: Agent
  family name: Guo
  given name: Zhikun
doi: 10.7717/peerj.15736
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: © 2023 Sun et al.
attribution name: Sun et al.

Leaf nutrient resorption of two life-form tree species in urban gardens and their response to soil nutrient availability
type: item
type: AcademicArticle
description: Background Leaf nutrient resorption is a key strategy in plant conservation that minimizes nutrient loss and enhances productivity. However, the differences of the nutrient resorption among garden tree species in urban ecosystems were not clearly understood, especially the differences of nitrogen resorption efficiency (NRE) and phosphorous resorption efficiency (PRE) between evergreen and deciduous trees. Methods We selected 40 most generally used garden tree specie belonged two life forms (evergreen and deciduous) and investigated the nitrogen (N) and phosphorus (P) concentrations in green and senesced leaves and soil nutrient concentrations of nine samples trees for each species. Then, the nutrient concentrations and resorption efficiency were compared, and the soil nutrients utilization strategies were further analyzed. Results The results showed that the N concentration was significantly higher in the green and senesced leaves of deciduous trees than in the leaves of evergreen trees. The two life-form trees were both N limited and evergreen trees were more sensitive to N limitation. The NRE and PRE in the deciduous trees were significantly higher than those in the evergreen trees. The NRE was significantly positively correlated with the PRE in the deciduous trees. As the soil N and P concentrations increased, the nutrient resorption efficiency (NuRE) of the evergreen trees increased, but that of the deciduous trees decreased. Compared with the deciduous trees, the evergreen trees were more sensitive to the feedback of soil N and P concentrations. These findings reveal the N and P nutrient resorption mechanism of evergreen and deciduous trees and fill a gap in the understanding of nutrient resorption in urban ecosystems.
format: application/pdf
format: text/html
creator: Ruyuan Hu
creator: Tairui Liu
creator: Yunxiang Zhang
creator: Rongrong Zheng
creator: Jinping Guo
subject: Ecology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15738
publisher: PeerJ Inc.
rights: © 2023 Hu et al.
abstract: Background Leaf nutrient resorption is a key strategy in plant conservation that minimizes nutrient loss and enhances productivity. However, the differences of the nutrient resorption among garden tree species in urban ecosystems were not clearly understood, especially the differences of nitrogen resorption efficiency (NRE) and phosphorous resorption efficiency (PRE) between evergreen and deciduous trees. Methods We selected 40 most generally used garden tree specie belonged two life forms (evergreen and deciduous) and investigated the nitrogen (N) and phosphorus (P) concentrations in green and senesced leaves and soil nutrient concentrations of nine samples trees for each species. Then, the nutrient concentrations and resorption efficiency were compared, and the soil nutrients utilization strategies were further analyzed. Results The results showed that the N concentration was significantly higher in the green and senesced leaves of deciduous trees than in the leaves of evergreen trees. The two life-form trees were both N limited and evergreen trees were more sensitive to N limitation. The NRE and PRE in the deciduous trees were significantly higher than those in the evergreen trees. The NRE was significantly positively correlated with the PRE in the deciduous trees. As the soil N and P concentrations increased, the nutrient resorption efficiency (NuRE) of the evergreen trees increased, but that of the deciduous trees decreased. Compared with the deciduous trees, the evergreen trees were more sensitive to the feedback of soil N and P concentrations. These findings reveal the N and P nutrient resorption mechanism of evergreen and deciduous trees and fill a gap in the understanding of nutrient resorption in urban ecosystems.
bibliographic citation: Hu et al. (2023) Leaf nutrient resorption of two life-form tree species in urban gardens and their response to soil nutrient availability. PeerJ 11:e15738 https://doi.org/10.7717/peerj.15738
date submitted: 2023-02-01
date accepted: 2023-06-20
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Ruyuan
author list: Agent
  family name: Liu
  given name: Tairui
author list: Agent
  family name: Zhang
  given name: Yunxiang
author list: Agent
  family name: Zheng
  given name: Rongrong
author list: Agent
  family name: Guo
  given name: Jinping
doi: 10.7717/peerj.15738
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: ©2023 Hu et al.
attribution name: Hu et al.

Optimal tillage depths for enhancing rice yield, quality and lodging resistance in the rice production systems of northeast China
type: item
type: AcademicArticle
description: Long-term shallow tillage leads to poor development of root system and deterioration of soil quality. Field experiments were conducted during 2019–2021 to explore the effects of different tillage depths on rice root system, stem lodging resistance, rice yield and quality. The experimental treatments were comprised of four tillage depths i.e., 14 cm (TD 14) as the control, 17 cm (TD17), 20 cm (TD20), and 23 cm (TD23) by using a tractor- mounted hydraulic-adjustable. Results indicated that the TD17 treatment substantially improved the breaking resistance by 39.45–72.37% and decreased the lodging index by 11.73–29.94% of first to third node attribute, increased the stem diameter and unit length dry weight and decreased the internode length, compared with control. The TD17 treatment also reduced the chalkiness, chalkiness rate by 26.23% and 32.30%, respectively. Moreover, the viscosity value and cooking and eating quality of rice in TD17 treatment were improved 27.30% and 12.33%, respectively, compared to control. Moreover, the TD20 treatment enhanced the grain yield by 9.18% owing to the higher panicle number and grain number per panicle. The highest photosynthetic rate was also found in the TD20 treatment, which was significant higher 15.57% than TD14 treatment. Overall, the 17–20 cm was found the optimum tillage depth and therefore recommended to the farmers to get improved rice yield with minimum lodging in the rice production systems of the Northeast China.
format: application/pdf
format: text/html
creator: Diankai Gong
creator: Guijin Dai
creator: Ying Chen
creator: Guangxing Yu
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15739
publisher: PeerJ Inc.
rights: © 2023 Gong et al.
abstract: Long-term shallow tillage leads to poor development of root system and deterioration of soil quality. Field experiments were conducted during 2019–2021 to explore the effects of different tillage depths on rice root system, stem lodging resistance, rice yield and quality. The experimental treatments were comprised of four tillage depths i.e., 14 cm (TD 14) as the control, 17 cm (TD17), 20 cm (TD20), and 23 cm (TD23) by using a tractor- mounted hydraulic-adjustable. Results indicated that the TD17 treatment substantially improved the breaking resistance by 39.45–72.37% and decreased the lodging index by 11.73–29.94% of first to third node attribute, increased the stem diameter and unit length dry weight and decreased the internode length, compared with control. The TD17 treatment also reduced the chalkiness, chalkiness rate by 26.23% and 32.30%, respectively. Moreover, the viscosity value and cooking and eating quality of rice in TD17 treatment were improved 27.30% and 12.33%, respectively, compared to control. Moreover, the TD20 treatment enhanced the grain yield by 9.18% owing to the higher panicle number and grain number per panicle. The highest photosynthetic rate was also found in the TD20 treatment, which was significant higher 15.57% than TD14 treatment. Overall, the 17–20 cm was found the optimum tillage depth and therefore recommended to the farmers to get improved rice yield with minimum lodging in the rice production systems of the Northeast China.
bibliographic citation: Gong et al. (2023) Optimal tillage depths for enhancing rice yield, quality and lodging resistance in the rice production systems of northeast China. PeerJ 11:e15739 https://doi.org/10.7717/peerj.15739
date submitted: 2023-02-20
date accepted: 2023-06-20
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gong
  given name: Diankai
author list: Agent
  family name: Dai
  given name: Guijin
author list: Agent
  family name: Chen
  given name: Ying
author list: Agent
  family name: Yu
  given name: Guangxing
doi: 10.7717/peerj.15739
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: © 2023 Gong et al.
attribution name: Gong et al.

Prediction of sea ice area based on the CEEMDAN-SO-BiLSTM model
type: item
type: AcademicArticle
description: This article proposes a combined prediction model based on a bidirectional long short-term memory (BiLSTM) neural network optimized by the snake optimizer (SO) under complete ensemble empirical mode decomposition with adaptive noise. First, complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) was used to decompose the sea ice area time series data into a series of eigenmodes and perform noise reduction to enhance the stationarity and smoothness of the time series. Second, this article used a bidirectional long short-term memory neural network optimized by the snake optimizer to fully exploit the characteristics of each eigenmode of the time series to achieve the prediction of each. Finally, the predicted values of each mode are superimposed and reconstructed as the final prediction values. Our model achieves a good score of RMSE: 1.047, MAE: 0.815, and SMAPE: 3.938 on the test set.
format: application/pdf
format: text/html
creator: Qiao Guo
creator: Haoyu Zhang
creator: Yuhao Zhang
creator: Xuchu Jiang
subject: Computational Science
subject: Data Mining and Machine Learning
subject: Aquatic and Marine Chemistry
subject: Environmental Impacts
subject: Biological Oceanography
description: doi:10.7717/peerj.15748
publisher: PeerJ Inc.
rights: © 2023 Guo et al.
abstract: This article proposes a combined prediction model based on a bidirectional long short-term memory (BiLSTM) neural network optimized by the snake optimizer (SO) under complete ensemble empirical mode decomposition with adaptive noise. First, complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) was used to decompose the sea ice area time series data into a series of eigenmodes and perform noise reduction to enhance the stationarity and smoothness of the time series. Second, this article used a bidirectional long short-term memory neural network optimized by the snake optimizer to fully exploit the characteristics of each eigenmode of the time series to achieve the prediction of each. Finally, the predicted values of each mode are superimposed and reconstructed as the final prediction values. Our model achieves a good score of RMSE: 1.047, MAE: 0.815, and SMAPE: 3.938 on the test set.
bibliographic citation: Guo et al. (2023) Prediction of sea ice area based on the CEEMDAN-SO-BiLSTM model. PeerJ 11:e15748 https://doi.org/10.7717/peerj.15748
date submitted: 2023-03-10
date accepted: 2023-06-22
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Qiao
author list: Agent
  family name: Zhang
  given name: Haoyu
author list: Agent
  family name: Zhang
  given name: Yuhao
author list: Agent
  family name: Jiang
  given name: Xuchu
doi: 10.7717/peerj.15748
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: ©2023 Guo et al.
attribution name: Guo et al.

Recent research progress on the correlation between metabolic syndrome and Helicobacter pylori infection
type: item
type: AcademicArticle
description: Background Globally, metabolic syndrome (MS) and Helicobacter pylori (HP) infection, which have gained an epidemic status, are major challenges to human health, society, and medical professionals. Recent studies have demonstrated that MS is closely related to HP infection. Additionally, HP is an important risk factor for gastric cancer. However, systematic reviews on HP are lacking. This review aimed to summarize and analyze the potential correlation of HP infection with MS and its components, as well as the underlying mechanism, to provide reference and strategies for clinical prevention and treatment. Methodology Previous studies examining the correlation between HP and MS since 1990 were retrieved from the PubMed, Web of Science, and Embase databases. The potential correlation between HP infection and MS and its components was comprehensively analyzed. The keywords “Helicobacter pylori,” “HP,” “metabolic syndrome,” “hypertension,” “obesity,” “diabetes,” or “dyslipidemia” were used in all fields. No language restrictions were imposed. Results MS was strongly correlated to HP infection. The inflammatory response and inflammatory factors produced during HP infection are important etiological factors for insulin resistance and MS. The co-occurrence of long-term chronic inflammation and immune dysfunction with MS may be the predisposing factor for HP infection. MS components, such as diabetes, hypertension, dyslipidemia, and obesity were also correlated with HP infection in one or both directions. Conclusions HP infection and MS may promote the pathogenesis of each other. The contribution of HP infection and MS to gastric cancer cannot be ruled out based on co-occurrence. The MS components diabetes and obesity may be bidirectionally correlated with HP infection.
format: application/pdf
format: text/html
creator: Qinli Xie
creator: Yangjun He
creator: Danni Zhou
creator: Yi Jiang
creator: Ying Deng
creator: Ruoqing Li
subject: Microbiology
subject: Epidemiology
subject: Gastroenterology and Hepatology
subject: Metabolic Sciences
subject: Obesity
description: doi:10.7717/peerj.15755
publisher: PeerJ Inc.
rights: © 2023 Xie et al.
abstract: Background Globally, metabolic syndrome (MS) and Helicobacter pylori (HP) infection, which have gained an epidemic status, are major challenges to human health, society, and medical professionals. Recent studies have demonstrated that MS is closely related to HP infection. Additionally, HP is an important risk factor for gastric cancer. However, systematic reviews on HP are lacking. This review aimed to summarize and analyze the potential correlation of HP infection with MS and its components, as well as the underlying mechanism, to provide reference and strategies for clinical prevention and treatment. Methodology Previous studies examining the correlation between HP and MS since 1990 were retrieved from the PubMed, Web of Science, and Embase databases. The potential correlation between HP infection and MS and its components was comprehensively analyzed. The keywords “Helicobacter pylori,” “HP,” “metabolic syndrome,” “hypertension,” “obesity,” “diabetes,” or “dyslipidemia” were used in all fields. No language restrictions were imposed. Results MS was strongly correlated to HP infection. The inflammatory response and inflammatory factors produced during HP infection are important etiological factors for insulin resistance and MS. The co-occurrence of long-term chronic inflammation and immune dysfunction with MS may be the predisposing factor for HP infection. MS components, such as diabetes, hypertension, dyslipidemia, and obesity were also correlated with HP infection in one or both directions. Conclusions HP infection and MS may promote the pathogenesis of each other. The contribution of HP infection and MS to gastric cancer cannot be ruled out based on co-occurrence. The MS components diabetes and obesity may be bidirectionally correlated with HP infection.
bibliographic citation: Xie et al. (2023) Recent research progress on the correlation between metabolic syndrome and Helicobacter pylori infection. PeerJ 11:e15755 https://doi.org/10.7717/peerj.15755
date submitted: 2023-05-04
date accepted: 2023-06-26
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Qinli
author list: Agent
  family name: He
  given name: Yangjun
author list: Agent
  family name: Zhou
  given name: Danni
author list: Agent
  family name: Jiang
  given name: Yi
author list: Agent
  family name: Deng
  given name: Ying
author list: Agent
  family name: Li
  given name: Ruoqing
doi: 10.7717/peerj.15755
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: © 2023 Xie et al.
attribution name: Xie et al.

Putative causal inference for the relationship between obesity and sex hormones in males: a bidirectional Mendelian randomization study
type: item
type: AcademicArticle
description: Background Obesity is a chronic disease with a high prevalence rate and is an established risk factor for human health. Body mass index (BMI) is a common and primary indicator used in assessing obesity. This work aims to investigate the putative causal relationship among BMI, sex hormone-binding globulin (SHBG), bioavailable testosterone (BioT), and estradiol levels. Materials and Methods We conducted a bidirectional Mendelian randomization study, using single-nucleotide polymorphisms (SNPs) strongly associated with BMI, SHBG, BioT, and estradiol as instrumental variables. All SNPs were identified from the genome-wide association study (GWAS) summary data of large sample studies recruiting more than 150,000 European adult male individuals. The inverse-variance-weighted (IVW) approach was used as a primary algorithm for putative causal estimation. Results Genetically predicted elevated BMI was associated with decreased SHBG (IVW, β = −0.103, 95% confidence interval [CI] [−0.113 to −0.092], P = 1.50 × 10−77) and BioT levels (IVW, β = −0.139, 95% CI [−0.165 to −0.113], P = 9.54 × 10−26) and high estradiol levels (IVW, β = 0.014, 95% CI [0.009–0.019], P = 2.19 × 10−7). Increased SHBG levels were causally associated with low BMI (IVW, β = −0.051, 95% CI [−0.098 to −0.005], P = 0.030) and BioT (IVW, β = −0.126, 95% CI [−0.175 to −0.077], P = 5.97 × 10−7) and high estradiol levels (IVW, β = 0.046, 95% CI [0.035–0.056], P = 6.51 × 10−17). Conversely, no evidence of an effect of estradiol imbalance on SHBG levels (IVW, β = 1.035, 95% CI [−0.854 to 2.926], P = 0.283) and BMI (IVW, β = 0.091, 95% CI [−0.094 to 0.276], P = 0.336) was obtained. However, increased BioT levels were causally associated with lower SHBG levels (IVW, β = −0.044, 95% CI [−0.061 to −0.026], P = 8.76 × 10−7), not BMI (IVW, β = −0.006, 95% CI [−0.035 to 0.023], P = 0.679). Conclusions The findings support a network putative causal relationship among BMI, SHBG, BioT, and estradiol. SHBG, BioT, and estradio…
format: application/pdf
format: text/html
creator: Bangbei Wan
creator: Ning Ma
creator: Zhi Zhou
creator: Cai Lv
subject: Bioinformatics
subject: Genomics
subject: Andrology
subject: Medical Genetics
subject: Obesity
description: doi:10.7717/peerj.15760
publisher: PeerJ Inc.
rights: © 2023 Wan et al.
abstract: Background Obesity is a chronic disease with a high prevalence rate and is an established risk factor for human health. Body mass index (BMI) is a common and primary indicator used in assessing obesity. This work aims to investigate the putative causal relationship among BMI, sex hormone-binding globulin (SHBG), bioavailable testosterone (BioT), and estradiol levels. Materials and Methods We conducted a bidirectional Mendelian randomization study, using single-nucleotide polymorphisms (SNPs) strongly associated with BMI, SHBG, BioT, and estradiol as instrumental variables. All SNPs were identified from the genome-wide association study (GWAS) summary data of large sample studies recruiting more than 150,000 European adult male individuals. The inverse-variance-weighted (IVW) approach was used as a primary algorithm for putative causal estimation. Results Genetically predicted elevated BMI was associated with decreased SHBG (IVW, β = −0.103, 95% confidence interval [CI] [−0.113 to −0.092], P = 1.50 × 10−77) and BioT levels (IVW, β = −0.139, 95% CI [−0.165 to −0.113], P = 9.54 × 10−26) and high estradiol levels (IVW, β = 0.014, 95% CI [0.009–0.019], P = 2.19 × 10−7). Increased SHBG levels were causally associated with low BMI (IVW, β = −0.051, 95% CI [−0.098 to −0.005], P = 0.030) and BioT (IVW, β = −0.126, 95% CI [−0.175 to −0.077], P = 5.97 × 10−7) and high estradiol levels (IVW, β = 0.046, 95% CI [0.035–0.056], P = 6.51 × 10−17). Conversely, no evidence of an effect of estradiol imbalance on SHBG levels (IVW, β = 1.035, 95% CI [−0.854 to 2.926], P = 0.283) and BMI (IVW, β = 0.091, 95% CI [−0.094 to 0.276], P = 0.336) was obtained. However, increased BioT levels were causally associated with lower SHBG levels (IVW, β = −0.044, 95% CI [−0.061 to −0.026], P = 8.76 × 10−7), not BMI (IVW, β = −0.006, 95% CI [−0.035 to 0.023], P = 0.679). Conclusions The findings support a network putative causal relationship among BMI, SHBG, BioT, and estradiol. SHBG, BioT, and estradio…
bibliographic citation: Wan et al. (2023) Putative causal inference for the relationship between obesity and sex hormones in males: a bidirectional Mendelian randomization study. PeerJ 11:e15760 https://doi.org/10.7717/peerj.15760
date submitted: 2023-02-06
date accepted: 2023-06-27
issued: 2023-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wan
  given name: Bangbei
author list: Agent
  family name: Ma
  given name: Ning
author list: Agent
  family name: Zhou
  given name: Zhi
author list: Agent
  family name: Lv
  given name: Cai
doi: 10.7717/peerj.15760
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-19
copyright: © 2023 Wan et al.
attribution name: Wan et al.

Why can people with developmental prosopagnosia recognise some familiar faces? Insights from subjective experience
type: item
type: AcademicArticle
description: Developmental prosopagnosia is a relatively common visuo-cognitive condition, characterised by impaired facial identity recognition. Impairment severity appears to reside on a continuum, however, it is unknown whether instances of milder deficits reflect the successful use of spontaneous (typical) face recognition strategies, or the application of extraneous compensatory cues to recognition. Here, we explore this issue in two studies. First, 23 adults with developmental prosopagnosia were asked about their use of spontaneous versus compensatory face recognition techniques in everyday life, using a series of closed- and open-ended questions. Second, the same participants performed a computerised famous face recognition task where they were asked to provide reasons why they could make any successful identifications. Findings from both studies suggest that people with developmental prosopagnosia can successfully, and quite frequently, use compensatory strategies to recognition, and that these cues support the majority of instances of preserved familiar face recognition. In contrast, 16 of the 23 participants were able to spontaneously recognise familiar faces on at least some occasions, but there were vast individual differences in frequencies of success. These findings have important implications for our conceptualisation of the condition, as well as for diagnostic practice.
format: application/pdf
format: text/html
creator: Emma Portch
creator: Liam Wignall
creator: Sarah Bate
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.15497
publisher: PeerJ Inc.
rights: © 2023 Portch et al.
abstract: Developmental prosopagnosia is a relatively common visuo-cognitive condition, characterised by impaired facial identity recognition. Impairment severity appears to reside on a continuum, however, it is unknown whether instances of milder deficits reflect the successful use of spontaneous (typical) face recognition strategies, or the application of extraneous compensatory cues to recognition. Here, we explore this issue in two studies. First, 23 adults with developmental prosopagnosia were asked about their use of spontaneous versus compensatory face recognition techniques in everyday life, using a series of closed- and open-ended questions. Second, the same participants performed a computerised famous face recognition task where they were asked to provide reasons why they could make any successful identifications. Findings from both studies suggest that people with developmental prosopagnosia can successfully, and quite frequently, use compensatory strategies to recognition, and that these cues support the majority of instances of preserved familiar face recognition. In contrast, 16 of the 23 participants were able to spontaneously recognise familiar faces on at least some occasions, but there were vast individual differences in frequencies of success. These findings have important implications for our conceptualisation of the condition, as well as for diagnostic practice.
bibliographic citation: Portch et al. (2023) Why can people with developmental prosopagnosia recognise some familiar faces? Insights from subjective experience. PeerJ 11:e15497 https://doi.org/10.7717/peerj.15497
date submitted: 2022-11-25
date accepted: 2023-05-12
issued: 2023-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Portch
  given name: Emma
author list: Agent
  family name: Wignall
  given name: Liam
author list: Agent
  family name: Bate
  given name: Sarah
doi: 10.7717/peerj.15497
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-18
copyright: ©2023 Portch et al.
attribution name: Portch et al.

Functional trait diversity of Cyclanthaceae and its convergent evolution with Araceae in Neotropical forests
type: item
type: AcademicArticle
description: The Cyclanthaceae comprise a relatively small family of about 230 species and 12 genera in the Pandanales that is widespread in wet Neotropical forests. The great majority of species can be divided into three growth forms (understory herbs, epiphytes, and root-climbing hemiepiphytes) that share functional traits with similar growth forms present in the Araceae, a member of the Alismatales and not closely related. Our objectives were first to characterize the diversity, functional growth forms, and ecological traits of Cyclanthaceae at the La Selva Biological Station. Specific functional leaf and canopy traits of terrestrial herbs and epiphytes are very similar and associated with ecological success in both families. We further examined the functional traits of root-climbing hemiepiphytes, a specialized growth form that links the two families but rare in other families and argue that their specialized functional traits allow them to be considered as a distinct functional growth form. A key trait in distinguishing hemiepiphytes which are rare outside of the Cyclanthaceae and Araceae is the severance of the main stem hydraulic connection to the soil early in plant development. We used field data to examine the possible evolutionary pathways of developmental and ecological transition from terrestrial to hemiepiphyte growth forms. The broader ecological success of hemiepiphytic Araceae compared to Cyclanthaceae is hypothesized to result from the presence of heteroblasty in developing stems and leaves which allows more efficient utilization of complex canopy light environments of wet tropical forests.
format: application/pdf
format: text/html
creator: Erin C. Riordan
creator: Orlando Vargas Ramirez
creator: Philip W. Rundel
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.15557
publisher: PeerJ Inc.
rights: © 2023 Riordan et al.
abstract: The Cyclanthaceae comprise a relatively small family of about 230 species and 12 genera in the Pandanales that is widespread in wet Neotropical forests. The great majority of species can be divided into three growth forms (understory herbs, epiphytes, and root-climbing hemiepiphytes) that share functional traits with similar growth forms present in the Araceae, a member of the Alismatales and not closely related. Our objectives were first to characterize the diversity, functional growth forms, and ecological traits of Cyclanthaceae at the La Selva Biological Station. Specific functional leaf and canopy traits of terrestrial herbs and epiphytes are very similar and associated with ecological success in both families. We further examined the functional traits of root-climbing hemiepiphytes, a specialized growth form that links the two families but rare in other families and argue that their specialized functional traits allow them to be considered as a distinct functional growth form. A key trait in distinguishing hemiepiphytes which are rare outside of the Cyclanthaceae and Araceae is the severance of the main stem hydraulic connection to the soil early in plant development. We used field data to examine the possible evolutionary pathways of developmental and ecological transition from terrestrial to hemiepiphyte growth forms. The broader ecological success of hemiepiphytic Araceae compared to Cyclanthaceae is hypothesized to result from the presence of heteroblasty in developing stems and leaves which allows more efficient utilization of complex canopy light environments of wet tropical forests.
bibliographic citation: Riordan et al. (2023) Functional trait diversity of Cyclanthaceae and its convergent evolution with Araceae in Neotropical forests. PeerJ 11:e15557 https://doi.org/10.7717/peerj.15557
date submitted: 2022-12-21
date accepted: 2023-05-23
issued: 2023-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Riordan
  given name: Erin C.
author list: Agent
  family name: Vargas Ramirez
  given name: Orlando
author list: Agent
  family name: Rundel
  given name: Philip W.
doi: 10.7717/peerj.15557
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-18
copyright: © 2023 Riordan et al.
attribution name: Riordan et al.

Pogonias courbina sperm characteristcs in its first reproductive season
type: item
type: AcademicArticle
description: Southern black drum (Pogonias courbina) is a species distributed along the western Atlantic Ocean, and it is the largest Sciaenidae observed in the coast of Rio Grande do Sul state, Brazil. However, it is listed as a vulnerable species at The IUCN Red List of Threatened Species™, and their fishing is prohibited. The objective of this study was to determine the sperm characteristics of P. courbina. Sperm samples of five young males (two-year-old fish) were collected through abdominal pressure. The sperm kinetics parameters were sperm motility (MOT) 10.7 ± 5.6%, curvilinear velocity (VCL) 120.07 ± 16.16 mm s ± 1, average path velocity (VAP) 75.64 ± 23.78 mm s ± 1, straight-line velocity (VSL) 62.49 ± 15.83 mm s ± 1, straightness (STR) 83.9 ± 5.3%, wobble (WOB) 61.9 ± 12.7%, beat cross frequency (BCF) 42.981 ± 4.627 Hz and progression (PRG) 1,805.4 ± 564.5 µm. The proportion of normal spermatozoa was 35.6 ± 6.1%. About the abnormalities observed, 22.7% occurred in the tail (short tail = 0.6 ± 0.5%, distally curled tail = 2.4 ± 1.6%, strongly curled tail = 1.9 ± 1.3%, broken tail = 7.9 ± 5.1%, folded tail = 5.5 ± 0.8%, loose tail = 4.4 ± 1.9%); 14.2% occurred in the head (degenerate head = 4.2 ± 1.6%, microcephaly = 1.8 ± 2.5%, loose head = 8.2 ± 2.1%) and 27.5% of the spermatozoa showed cytoplasmatic gouts (proximal gout = 20.0 ± 8.4%, distal gout = 7.5 ± 2.8%). Besides that, a correlation analysis was performed between sperm morphology and kinetics parameters, and the spermatozoa were measured for the morphometric parameters. There was a positive correlation between BCF and normal spermatozoa (r = 0.9269). A negative correlation occurred between BCF and loose head (r = −0.9047); WOB and strongly curled tail (r = −0.8911); and PROG and strongly curled tail (r = −0.9191). The morphometric measures found for the head were length of 2.50 ± 0.21 µm and width of 2.12 ± 0.22 µm, and for the tail it was length of 37.97 ± 2.01 µm. It was possible to verify that the animals hav…
format: application/pdf
format: text/html
creator: Jhony Lisboa Benato
creator: Danilo Streit Jr
creator: Nathalia Dos Santos Teixeira
creator: Rômulo Batista Rodrigues
creator: Thaiza Rodrigues de Freitas
creator: Marcelo Okamoto
creator: Ricardo Rodrigues
creator: Raquel Santos dos Santos
creator: Renata Villar Dantas
creator: Ana Paula de Abreu Balbinot
creator: Rodrigo Ribeiro Bezerra de Oliveira
creator: Lucas Campos Maltez
creator: Olivia Menossi
creator: Luis Andre Sampaio
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.15600
publisher: PeerJ Inc.
rights: © 2023 Benato et al.
abstract: Southern black drum (Pogonias courbina) is a species distributed along the western Atlantic Ocean, and it is the largest Sciaenidae observed in the coast of Rio Grande do Sul state, Brazil. However, it is listed as a vulnerable species at The IUCN Red List of Threatened Species™, and their fishing is prohibited. The objective of this study was to determine the sperm characteristics of P. courbina. Sperm samples of five young males (two-year-old fish) were collected through abdominal pressure. The sperm kinetics parameters were sperm motility (MOT) 10.7 ± 5.6%, curvilinear velocity (VCL) 120.07 ± 16.16 mm s ± 1, average path velocity (VAP) 75.64 ± 23.78 mm s ± 1, straight-line velocity (VSL) 62.49 ± 15.83 mm s ± 1, straightness (STR) 83.9 ± 5.3%, wobble (WOB) 61.9 ± 12.7%, beat cross frequency (BCF) 42.981 ± 4.627 Hz and progression (PRG) 1,805.4 ± 564.5 µm. The proportion of normal spermatozoa was 35.6 ± 6.1%. About the abnormalities observed, 22.7% occurred in the tail (short tail = 0.6 ± 0.5%, distally curled tail = 2.4 ± 1.6%, strongly curled tail = 1.9 ± 1.3%, broken tail = 7.9 ± 5.1%, folded tail = 5.5 ± 0.8%, loose tail = 4.4 ± 1.9%); 14.2% occurred in the head (degenerate head = 4.2 ± 1.6%, microcephaly = 1.8 ± 2.5%, loose head = 8.2 ± 2.1%) and 27.5% of the spermatozoa showed cytoplasmatic gouts (proximal gout = 20.0 ± 8.4%, distal gout = 7.5 ± 2.8%). Besides that, a correlation analysis was performed between sperm morphology and kinetics parameters, and the spermatozoa were measured for the morphometric parameters. There was a positive correlation between BCF and normal spermatozoa (r = 0.9269). A negative correlation occurred between BCF and loose head (r = −0.9047); WOB and strongly curled tail (r = −0.8911); and PROG and strongly curled tail (r = −0.9191). The morphometric measures found for the head were length of 2.50 ± 0.21 µm and width of 2.12 ± 0.22 µm, and for the tail it was length of 37.97 ± 2.01 µm. It was possible to verify that the animals hav…
bibliographic citation: Benato et al. (2023) Pogonias courbina sperm characteristcs in its first reproductive season. PeerJ 11:e15600 https://doi.org/10.7717/peerj.15600
date submitted: 2023-01-26
date accepted: 2023-05-30
issued: 2023-07-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Benato
  given name: Jhony Lisboa
author list: Agent
  family name: Streit Jr
  given name: Danilo
author list: Agent
  family name: Teixeira
  given name: Nathalia Dos Santos
author list: Agent
  family name: Rodrigues
  given name: Rômulo Batista
author list: Agent
  family name: de Freitas
  given name: Thaiza Rodrigues
author list: Agent
  family name: Okamoto
  given name: Marcelo
author list: Agent
  family name: Rodrigues
  given name: Ricardo
author list: Agent
  family name: dos Santos
  given name: Raquel Santos
author list: Agent
  family name: Dantas
  given name: Renata Villar
author list: Agent
  family name: Balbinot
  given name: Ana Paula de Abreu
author list: Agent
  family name: de Oliveira
  given name: Rodrigo Ribeiro Bezerra
author list: Agent
  family name: Maltez
  given name: Lucas Campos
author list: Agent
  family name: Menossi
  given name: Olivia
author list: Agent
  family name: Sampaio
  given name: Luis Andre
doi: 10.7717/peerj.15600
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-18
copyright: ©2023 Benato et al.
attribution name: Benato et al.

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