PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Study on soil-water characteristic curves in the profiles of collapsing walls of typical granite Benggang in southeast China
items: The effect of listening to preferred music after a stressful task on performance and psychophysiological responses in collegiate golfers
items: High gene flow in the silverlip pearl oyster Pinctada maxima between inshore and offshore sites near Eighty Mile Beach in Western Australia
items: Ferulic acid attenuates high glucose-induced apoptosis in retinal pigment epithelium cells and protects retina in db/db mice
items: The application of plant growth-promoting rhizobacteria in Solanum lycopersicum production in the agricultural system: a review
items: Epidemiology of Helicobacter pylori in Australia: a scoping review
items: Population genetics and demography of the coral-killing cyanobacteriosponge, Terpios hoshinota, in the Indo-West Pacific
items: Spain is not different: teaching quantitative courses can also be hazardous to one’s career (at least in undergraduate courses)
items: Dramatic impact of future climate change on the genetic diversity and distribution of ecologically relevant Western Mediterranean Carex (Cyperaceae)
items: A comparative metabolomics study of anthocyanins and taste components in Chinese bayberry (Morella rubra) with different flesh colors

Study on soil-water characteristic curves in the profiles of collapsing walls of typical granite Benggang in southeast China
type: item
type: AcademicArticle
description: Benggang with steep collapsing walls is one of the worst soil erosion problems in South China. The collapse of walls is the most critical process in Benggang development. This is mainly due to the soil water properties. The soil water characteristic curve (SWCC) is a key indicator for analyzing soil moisture, but the SWCC and its mechanism of influence in collapsing walls remain obscure. A pressure plate meter was used for drying experiments to research the SWCCs of undisturbed soils of five layers (from top to bottom: red soil layer, transition layer I, sand soil layer, transition layer II and detrital layer) of two typical collapsing walls. The van Genuchten (VG) model can be fitted to the SWCCs for different layers (NSE ≥ 0.90). With increasing soil depth, the parameters a and θs first decreased and then increased, the parameters n first increased and then decreased, θr declined as the soil depth increased. These findings illustrate that soil water holding capacity decreases with increasing soil depth. The bottom of the soil is weak in water retention and water can easily reach saturation, resulting in a decline in soil stability, thus promoting soil collapse and finally inducing upper soil collapse. Furthermore, gravel content and particle morphology are factors that should not be neglected for SWCCs. The results of this study provide a theoretical basis for understanding the process of wall collapse in Benggang landforms in South China.
format: application/pdf
format: text/html
creator: Liting Zhang
creator: Shujun Sun
creator: Mengqi Lin
creator: Kaijun Feng
creator: Yue Zhang
creator: Jinshi Lin
creator: Hongli Ge
creator: Yanhe Huang
creator: Fangshi Jiang
subject: Soil Science
subject: Natural Resource Management
description: doi:10.7717/peerj.13526
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Benggang with steep collapsing walls is one of the worst soil erosion problems in South China. The collapse of walls is the most critical process in Benggang development. This is mainly due to the soil water properties. The soil water characteristic curve (SWCC) is a key indicator for analyzing soil moisture, but the SWCC and its mechanism of influence in collapsing walls remain obscure. A pressure plate meter was used for drying experiments to research the SWCCs of undisturbed soils of five layers (from top to bottom: red soil layer, transition layer I, sand soil layer, transition layer II and detrital layer) of two typical collapsing walls. The van Genuchten (VG) model can be fitted to the SWCCs for different layers (NSE ≥ 0.90). With increasing soil depth, the parameters a and θs first decreased and then increased, the parameters n first increased and then decreased, θr declined as the soil depth increased. These findings illustrate that soil water holding capacity decreases with increasing soil depth. The bottom of the soil is weak in water retention and water can easily reach saturation, resulting in a decline in soil stability, thus promoting soil collapse and finally inducing upper soil collapse. Furthermore, gravel content and particle morphology are factors that should not be neglected for SWCCs. The results of this study provide a theoretical basis for understanding the process of wall collapse in Benggang landforms in South China.
bibliographic citation: Zhang et al. (2022) Study on soil-water characteristic curves in the profiles of collapsing walls of typical granite Benggang in southeast China. PeerJ 10:e13526 https://doi.org/10.7717/peerj.13526
date submitted: 2022-01-20
date accepted: 2022-05-11
issued: 2022-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Liting
author list: Agent
  family name: Sun
  given name: Shujun
author list: Agent
  family name: Lin
  given name: Mengqi
author list: Agent
  family name: Feng
  given name: Kaijun
author list: Agent
  family name: Zhang
  given name: Yue
author list: Agent
  family name: Lin
  given name: Jinshi
author list: Agent
  family name: Ge
  given name: Hongli
author list: Agent
  family name: Huang
  given name: Yanhe
author list: Agent
  family name: Jiang
  given name: Fangshi
doi: 10.7717/peerj.13526
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-01
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

The effect of listening to preferred music after a stressful task on performance and psychophysiological responses in collegiate golfers
type: item
type: AcademicArticle
description: Background This study explores whether listening to preferred music after a stressful situation affects putting and swinging performance, heart rate (HR), HR variability (HRV), and anxiety among amateur golfers. Methods Twenty healthy amateur collegiate golfers voluntarily participated in this study (age 20.1 ± 1.17 yrs., height = 173.8 ± 7.74 cm, body weight = 72.35 ± 12.67 kg). Pre- and post-intervention HR and HRV measurements were taken, along with a self-report of the State-Trait Anxiety Inventory (STAI-S) and Triple Factor Anxiety Inventory (TFAI). Participants were exposed to a stressful situation through the Stroop Colour and Word Test (SCWT) and then instructed to perform three golf-practice sessions in a golf simulator, separated by 48–72 hours of recovery, under different conditions: control, pre-task music, and synchronised music. Results No significant difference was identified between the experimental conditions for swinging (in terms of total distance (p = 0.116), carry distance (p = 0.608), speed of the ball (p = 0.819), and launch angle (p = 0.550) and putting performance (the number of successful putts on target (p > 0.05) and distance error between the target and ball (p = 0.122). No main effect for condition and time of intervention, as well as no interaction between these two factors was found for HR, HRV, and STAI-S (p = 0.116). However, the pre and post-intervention percentages of physiological items of the TFAI indicated a large, significant difference in synchronised music trial (p = 0.012, pre-task trial = −1.92% < control trial = 0% < synchronised trial = 4.58%). Conclusions The results imply that following a stressful situation, listening to preferred music before and/or during golf has no immediate effect on golf performance, anxiety, and psychophysiological responses in collegiate golfers.
format: application/pdf
format: text/html
creator: Hung-Tsung Wang
creator: Yung-Sheng Chen
creator: Ghazi Rekik
creator: Chia-Chen Yang
creator: Mao-Sheng Lai
creator: Hsia-Ling Tai
subject: Cardiology
subject: Kinesiology
subject: Mental Health
description: doi:10.7717/peerj.13557
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background This study explores whether listening to preferred music after a stressful situation affects putting and swinging performance, heart rate (HR), HR variability (HRV), and anxiety among amateur golfers. Methods Twenty healthy amateur collegiate golfers voluntarily participated in this study (age 20.1 ± 1.17 yrs., height = 173.8 ± 7.74 cm, body weight = 72.35 ± 12.67 kg). Pre- and post-intervention HR and HRV measurements were taken, along with a self-report of the State-Trait Anxiety Inventory (STAI-S) and Triple Factor Anxiety Inventory (TFAI). Participants were exposed to a stressful situation through the Stroop Colour and Word Test (SCWT) and then instructed to perform three golf-practice sessions in a golf simulator, separated by 48–72 hours of recovery, under different conditions: control, pre-task music, and synchronised music. Results No significant difference was identified between the experimental conditions for swinging (in terms of total distance (p = 0.116), carry distance (p = 0.608), speed of the ball (p = 0.819), and launch angle (p = 0.550) and putting performance (the number of successful putts on target (p > 0.05) and distance error between the target and ball (p = 0.122). No main effect for condition and time of intervention, as well as no interaction between these two factors was found for HR, HRV, and STAI-S (p = 0.116). However, the pre and post-intervention percentages of physiological items of the TFAI indicated a large, significant difference in synchronised music trial (p = 0.012, pre-task trial = −1.92% < control trial = 0% < synchronised trial = 4.58%). Conclusions The results imply that following a stressful situation, listening to preferred music before and/or during golf has no immediate effect on golf performance, anxiety, and psychophysiological responses in collegiate golfers.
bibliographic citation: Wang et al. (2022) The effect of listening to preferred music after a stressful task on performance and psychophysiological responses in collegiate golfers. PeerJ 10:e13557 https://doi.org/10.7717/peerj.13557
date submitted: 2022-02-09
date accepted: 2022-05-18
issued: 2022-06-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Hung-Tsung
author list: Agent
  family name: Chen
  given name: Yung-Sheng
author list: Agent
  family name: Rekik
  given name: Ghazi
author list: Agent
  family name: Yang
  given name: Chia-Chen
author list: Agent
  family name: Lai
  given name: Mao-Sheng
author list: Agent
  family name: Tai
  given name: Hsia-Ling
doi: 10.7717/peerj.13557
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-01
copyright: ©2022 Wang et al.
attribution name: Wang et al.

High gene flow in the silverlip pearl oyster Pinctada maxima between inshore and offshore sites near Eighty Mile Beach in Western Australia
type: item
type: AcademicArticle
description: An understanding of stock recruitment dynamics in fisheries is fundamental to successful management. Pinctada maxima is a bivalve mollusc widely distributed throughout the Indo-Pacific and is the main species targeted for cultured pearl and pearl shell production in Australia. Pearl production in Australia relies heavily on wild-caught individuals, the majority of which come from the Eighty Mile Beach region near Broome in Western Australia. In this study, we used a genotyping by sequencing approach to explore fine-scale patterns of genetic connectivity among inshore shallow and offshore deep populations of P. maxima near Eighty Mile Beach. Our results revealed high-levels of gene flow among inshore and offshore sites and no differences in genetic diversity between depths. Global estimates of genetic differentiation were low (FST = 0.006) but significantly different from zero, and pairwise estimates of genetic differentiation among sites were significant in only 3% of comparisons. Moreover, Bayesian clustering detected no separation of inshore and offshore sample sites, and instead showed all samples to be admixed among sites, locations and depths. Despite an absence of any clear spatial clustering among sites, we identified a significant pattern of isolation by distance. In a dynamic environment like Eighty Mile Beach, genetic structure can change from year-to-year and successive dispersal and recruitment events over generations likely act to homogenize the population. Although we cannot rule out the null hypothesis of panmixia, our data indicate high levels of dispersal and connectivity among inshore and offshore fishing grounds.
format: application/pdf
format: text/html
creator: Luke Thomas
creator: Karen J. Miller
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
subject: Population Biology
description: doi:10.7717/peerj.13323
publisher: PeerJ Inc.
rights: © 2022 Thomas and Miller
abstract: An understanding of stock recruitment dynamics in fisheries is fundamental to successful management. Pinctada maxima is a bivalve mollusc widely distributed throughout the Indo-Pacific and is the main species targeted for cultured pearl and pearl shell production in Australia. Pearl production in Australia relies heavily on wild-caught individuals, the majority of which come from the Eighty Mile Beach region near Broome in Western Australia. In this study, we used a genotyping by sequencing approach to explore fine-scale patterns of genetic connectivity among inshore shallow and offshore deep populations of P. maxima near Eighty Mile Beach. Our results revealed high-levels of gene flow among inshore and offshore sites and no differences in genetic diversity between depths. Global estimates of genetic differentiation were low (FST = 0.006) but significantly different from zero, and pairwise estimates of genetic differentiation among sites were significant in only 3% of comparisons. Moreover, Bayesian clustering detected no separation of inshore and offshore sample sites, and instead showed all samples to be admixed among sites, locations and depths. Despite an absence of any clear spatial clustering among sites, we identified a significant pattern of isolation by distance. In a dynamic environment like Eighty Mile Beach, genetic structure can change from year-to-year and successive dispersal and recruitment events over generations likely act to homogenize the population. Although we cannot rule out the null hypothesis of panmixia, our data indicate high levels of dispersal and connectivity among inshore and offshore fishing grounds.
bibliographic citation: Thomas et al. (2022) High gene flow in the silverlip pearl oyster Pinctada maxima between inshore and offshore sites near Eighty Mile Beach in Western Australia. PeerJ 10:e13323 https://doi.org/10.7717/peerj.13323
date submitted: 2021-04-19
date accepted: 2022-04-01
issued: 2022-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thomas
  given name: Luke
author list: Agent
  family name: Miller
  given name: Karen J.
doi: 10.7717/peerj.13323
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-31
copyright: © 2022 Thomas and Miller
attribution name: Thomas and Miller

Ferulic acid attenuates high glucose-induced apoptosis in retinal pigment epithelium cells and protects retina in db/db mice
type: item
type: AcademicArticle
description: Background Herein, we aimed to present evidence that Ferulic acid (FA), a phenolic acid, can alleviate high glucose (HG)-induced retinal pigment epithelium (RPE) cell apoptosis and protect retina in db/db mice. Methods ARPE-19 cells (a human RPE cell line) were divided into four groups: control group; HG group (30 mmol/L glucose); HG+FA group (30 mmol/L glucose and 10 mmol/L FA). Cell viability and apoptosis were detected using CCK-8 and Annexin-5 staining, respectively. Apoptosis-related markers including P53, BAX and Bcl2 were examined by RT-qPCR, western blot and immunohistochemistry. Totally, 30 male db/db mice were randomly divided into db/db group (5 ml/kg saline) and FA group (0.05 g/kg FA). After treatment for 2 months, retinal samples were subjected to hematoxylin and eosin (H&E) and Masson staining. Moreover, immunofluorescence was used to detect apoptosis-related markers. Blood samples were collected for measuring cholesterol, triglyceride (TG), low-density lipoprotein (LDL) and high-density lipoprotein (HDL) levels. Results FA treatment markedly increased cell viability and suppressed cell apoptosis of ARPE-19 cells compared to the HG-exposed group. Furthermore, FA ameliorated the abnormal expression levels of P53, BAX and Bcl2 in HG-induced ARPE-19 cells. In animal models, FA attenuated pathological changes in the retina tissues of diabetic mice. Consistent with in vitro models, FA significantly ameliorated the expression of apoptosis-related markers in retina tissues. Biochemical test results showed that FA reduced hyperlipidemia in diabetic mice. Conclusion Our findings suggest that FA alleviates HG-induced apoptosis in RPE cells and protects retina in db/db mice, which can be associated with P53 and BAX inactivation and Bcl2 activation.
format: application/pdf
format: text/html
creator: Dejun Zhu
creator: Wenqing Zou
creator: Xiangmei Cao
creator: Weigang Xu
creator: Zhaogang Lu
creator: Yan Zhu
creator: Xiaowen Hu
creator: Jin Hu
creator: Qing Zhu
subject: Cell Biology
subject: Molecular Biology
subject: Diabetes and Endocrinology
subject: Ophthalmology
subject: Pharmacology
description: doi:10.7717/peerj.13375
publisher: PeerJ Inc.
rights: © 2022 Zhu et al.
abstract: Background Herein, we aimed to present evidence that Ferulic acid (FA), a phenolic acid, can alleviate high glucose (HG)-induced retinal pigment epithelium (RPE) cell apoptosis and protect retina in db/db mice. Methods ARPE-19 cells (a human RPE cell line) were divided into four groups: control group; HG group (30 mmol/L glucose); HG+FA group (30 mmol/L glucose and 10 mmol/L FA). Cell viability and apoptosis were detected using CCK-8 and Annexin-5 staining, respectively. Apoptosis-related markers including P53, BAX and Bcl2 were examined by RT-qPCR, western blot and immunohistochemistry. Totally, 30 male db/db mice were randomly divided into db/db group (5 ml/kg saline) and FA group (0.05 g/kg FA). After treatment for 2 months, retinal samples were subjected to hematoxylin and eosin (H&E) and Masson staining. Moreover, immunofluorescence was used to detect apoptosis-related markers. Blood samples were collected for measuring cholesterol, triglyceride (TG), low-density lipoprotein (LDL) and high-density lipoprotein (HDL) levels. Results FA treatment markedly increased cell viability and suppressed cell apoptosis of ARPE-19 cells compared to the HG-exposed group. Furthermore, FA ameliorated the abnormal expression levels of P53, BAX and Bcl2 in HG-induced ARPE-19 cells. In animal models, FA attenuated pathological changes in the retina tissues of diabetic mice. Consistent with in vitro models, FA significantly ameliorated the expression of apoptosis-related markers in retina tissues. Biochemical test results showed that FA reduced hyperlipidemia in diabetic mice. Conclusion Our findings suggest that FA alleviates HG-induced apoptosis in RPE cells and protects retina in db/db mice, which can be associated with P53 and BAX inactivation and Bcl2 activation.
bibliographic citation: Zhu et al. (2022) Ferulic acid attenuates high glucose-induced apoptosis in retinal pigment epithelium cells and protects retina in db/db mice. PeerJ 10:e13375 https://doi.org/10.7717/peerj.13375
date submitted: 2020-05-14
date accepted: 2022-04-13
issued: 2022-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Dejun
author list: Agent
  family name: Zou
  given name: Wenqing
author list: Agent
  family name: Cao
  given name: Xiangmei
author list: Agent
  family name: Xu
  given name: Weigang
author list: Agent
  family name: Lu
  given name: Zhaogang
author list: Agent
  family name: Zhu
  given name: Yan
author list: Agent
  family name: Hu
  given name: Xiaowen
author list: Agent
  family name: Hu
  given name: Jin
author list: Agent
  family name: Zhu
  given name: Qing
doi: 10.7717/peerj.13375
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-31
copyright: © 2022 Zhu et al.
attribution name: Zhu et al.

The application of plant growth-promoting rhizobacteria in Solanum lycopersicum production in the agricultural system: a review
type: item
type: AcademicArticle
description: Food safety is a significant challenge worldwide, from plantation to cultivation, especially for perishable products such as tomatoes. New eco-friendly strategies are needed, and beneficial microorganisms might be a sustainable solution. This study demonstrates bacteria activity in the tomato plant rhizosphere. Further, it investigates the rhizobacteria’s structure, function, and diversity in soil. Rhizobacteria that promote the growth and development of tomato plants are referred to as plant growth-promoting bacteria (PGPR). They form a series of associations with plants and other organisms in the soil through a mutualistic relationship where both parties benefit from living together. It implies the antagonistic activities of the rhizobacteria to deter pathogens from invading tomato plants through their roots. Some PGPR are regarded as biological control agents that hinder the development of spoilage organisms and can act as an alternative for agricultural chemicals that may be detrimental to the health of humans, animals, and some of the beneficial microbes in the rhizosphere soil. These bacteria also help tomato plants acquire essential nutrients like potassium (K), magnesium (Mg), phosphorus (P), and nitrogen (N). Some rhizobacteria may offer a solution to low tomato production and help tackle food insecurity and farming problems. In this review, an overview of soil-inhabiting rhizobacteria focused on improving the sustainable production of Solanum lycopersicum.
format: application/pdf
format: text/html
creator: Afeez Adesina Adedayo
creator: Olubukola Oluranti Babalola
creator: Claire Prigent-Combaret
creator: Cristina Cruz
creator: Marius Stefan
creator: Funso Kutu
creator: Bernard R. Glick
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.13405
publisher: PeerJ Inc.
rights: © 2022 Adedayo et al.
abstract: Food safety is a significant challenge worldwide, from plantation to cultivation, especially for perishable products such as tomatoes. New eco-friendly strategies are needed, and beneficial microorganisms might be a sustainable solution. This study demonstrates bacteria activity in the tomato plant rhizosphere. Further, it investigates the rhizobacteria’s structure, function, and diversity in soil. Rhizobacteria that promote the growth and development of tomato plants are referred to as plant growth-promoting bacteria (PGPR). They form a series of associations with plants and other organisms in the soil through a mutualistic relationship where both parties benefit from living together. It implies the antagonistic activities of the rhizobacteria to deter pathogens from invading tomato plants through their roots. Some PGPR are regarded as biological control agents that hinder the development of spoilage organisms and can act as an alternative for agricultural chemicals that may be detrimental to the health of humans, animals, and some of the beneficial microbes in the rhizosphere soil. These bacteria also help tomato plants acquire essential nutrients like potassium (K), magnesium (Mg), phosphorus (P), and nitrogen (N). Some rhizobacteria may offer a solution to low tomato production and help tackle food insecurity and farming problems. In this review, an overview of soil-inhabiting rhizobacteria focused on improving the sustainable production of Solanum lycopersicum.
bibliographic citation: Adedayo et al. (2022) The application of plant growth-promoting rhizobacteria in Solanum lycopersicum production in the agricultural system: a review. PeerJ 10:e13405 https://doi.org/10.7717/peerj.13405
date submitted: 2022-02-21
date accepted: 2022-04-18
issued: 2022-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Adedayo
  given name: Afeez Adesina
author list: Agent
  family name: Babalola
  given name: Olubukola Oluranti
author list: Agent
  family name: Prigent-Combaret
  given name: Claire
author list: Agent
  family name: Cruz
  given name: Cristina
author list: Agent
  family name: Stefan
  given name: Marius
author list: Agent
  family name: Kutu
  given name: Funso
author list: Agent
  family name: Glick
  given name: Bernard R.
doi: 10.7717/peerj.13405
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-31
copyright: ©2022 Adedayo et al.
attribution name: Adedayo et al.

Epidemiology of Helicobacter pylori in Australia: a scoping review
type: item
type: AcademicArticle
description: Background Helicobacter pylori (H. pylori), a bacterium implicated in the development of peptic ulcer and gastric cancer, is estimated to infect around half the world’s population. Its prevalence in Australia is unclear. This scoping review aimed to evaluate all Australian literature providing estimates of the prevalence of H. pylori. Methods Australian studies examining H. pylori prevalence from 1982 onwards were eligible for inclusion. Medline, Embase and Scopus databases, and grey literature sources, were searched. Two independent reviewers undertook a two-stage screening process. Data were extracted by two independent reviewers using a pre-specified template. Results Of 444 identified studies, 75 were included in the review. H. pylori prevalence in Australian population-based studies (n = 8) ranged from 38.0% in 1991 to 15.1% in 2002; however, estimated prevalence across all non-clinical population studies in diverse sub-groups (n = 29) has varied dramatically. Decreased prevalence has been more marked in populations with gastrointestinal symptoms and conditions compared to non-clinical populations. Data on H. pyloriprevalence in vulnerable populations are lacking. Conclusions This is the first scoping review of Australian studies reporting H. pylori prevalence. A wide range of study designs, population groups, geographic regions, and diagnostic methods was included, involving data collected over a 50-year period (1969 to 2018). The summary of H. pylori prevalence estimates over time in this review points to a decrease in prevalence in Australia, particularly among populations with gastrointestinal symptoms and illnesses; however, it is unknown whether there is inequity in prevalence trends across vulnerable sub-groups of the Australian population. Future research and interventions supporting the health and wellbeing of vulnerable populations is required to ensure equitable health gains are made for all.
format: application/pdf
format: text/html
creator: Jillian Congedi
creator: Craig Williams
creator: Katherine L. Baldock
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.13430
publisher: PeerJ Inc.
rights: © 2022 Congedi et al.
abstract: Background Helicobacter pylori (H. pylori), a bacterium implicated in the development of peptic ulcer and gastric cancer, is estimated to infect around half the world’s population. Its prevalence in Australia is unclear. This scoping review aimed to evaluate all Australian literature providing estimates of the prevalence of H. pylori. Methods Australian studies examining H. pylori prevalence from 1982 onwards were eligible for inclusion. Medline, Embase and Scopus databases, and grey literature sources, were searched. Two independent reviewers undertook a two-stage screening process. Data were extracted by two independent reviewers using a pre-specified template. Results Of 444 identified studies, 75 were included in the review. H. pylori prevalence in Australian population-based studies (n = 8) ranged from 38.0% in 1991 to 15.1% in 2002; however, estimated prevalence across all non-clinical population studies in diverse sub-groups (n = 29) has varied dramatically. Decreased prevalence has been more marked in populations with gastrointestinal symptoms and conditions compared to non-clinical populations. Data on H. pyloriprevalence in vulnerable populations are lacking. Conclusions This is the first scoping review of Australian studies reporting H. pylori prevalence. A wide range of study designs, population groups, geographic regions, and diagnostic methods was included, involving data collected over a 50-year period (1969 to 2018). The summary of H. pylori prevalence estimates over time in this review points to a decrease in prevalence in Australia, particularly among populations with gastrointestinal symptoms and illnesses; however, it is unknown whether there is inequity in prevalence trends across vulnerable sub-groups of the Australian population. Future research and interventions supporting the health and wellbeing of vulnerable populations is required to ensure equitable health gains are made for all.
bibliographic citation: Congedi et al. (2022) Epidemiology of Helicobacter pylori in Australia: a scoping review. PeerJ 10:e13430 https://doi.org/10.7717/peerj.13430
date submitted: 2021-12-22
date accepted: 2022-04-21
issued: 2022-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Congedi
  given name: Jillian
author list: Agent
  family name: Williams
  given name: Craig
author list: Agent
  family name: Baldock
  given name: Katherine L.
doi: 10.7717/peerj.13430
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-31
copyright: ©2022 Congedi et al.
attribution name: Congedi et al.

Population genetics and demography of the coral-killing cyanobacteriosponge, Terpios hoshinota, in the Indo-West Pacific
type: item
type: AcademicArticle
description: The first occurrence of the cyanobacteriosponge Terpios hoshinota was reported from coral reefs in Guam in 1973, but was only formally described in 1993. Since then, the invasive behavior of this encrusting, coral-killing sponge has been observed in many coral reefs in the West Pacific. From 2015, its occurrence has expanded westward to the Indian Ocean. Although many studies have investigated the morphology, ecology, and symbiotic cyanobacteria of this sponge, little is known of its population genetics and demography. In this study, a mitochondrial cytochrome oxidase I (COI) fragment and nuclear ribosomal internal transcribed spacer 2 (ITS2) were sequenced to reveal the genetic variation of T. hoshinota collected from 11 marine ecoregions throughout the Indo-West Pacific. Both of the statistical parsimony networks based on the COI and nuclear ITS2 were dominated by a common haplotype. Pairwise FST and Isolation-by-distance by Mantel test of ITS2 showed moderate gene flow existed among most populations in the marine ecoregions of West Pacific, Coral Triangle, and Eastern Indian Ocean, but with a restricted gene flow between these regions and Maldives in the Central Indian Ocean. Demographic analyses of most T. hoshinota populations were consistent with the mutation-drift equilibrium, except for the Sulawesi Sea and Maldives, which showed bottlenecks following recent expansion. Our results suggest that while long-range dispersal might explain the capability of T. hoshinota to spread in the IWP, stable population demography might account for the long-term persistence of T. hoshinota outbreaks on local reefs.
format: application/pdf
format: text/html
creator: Savanna Wenhua Chow
creator: Shashank Keshavmurthy
creator: James Davis Reimer
creator: Nicole de Voogd
creator: Hui Huang
creator: Jih-Terng Wang
creator: Sen-Lin Tang
creator: Peter J. Schupp
creator: Chun Hong Tan
creator: Hock-Chark Liew
creator: Keryea Soong
creator: Beginer Subhan
creator: Hawis Madduppa
creator: Chaolun Allen Chen
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Molecular Biology
subject: Population Biology
description: doi:10.7717/peerj.13451
publisher: PeerJ Inc.
rights: © 2022 Chow et al.
abstract: The first occurrence of the cyanobacteriosponge Terpios hoshinota was reported from coral reefs in Guam in 1973, but was only formally described in 1993. Since then, the invasive behavior of this encrusting, coral-killing sponge has been observed in many coral reefs in the West Pacific. From 2015, its occurrence has expanded westward to the Indian Ocean. Although many studies have investigated the morphology, ecology, and symbiotic cyanobacteria of this sponge, little is known of its population genetics and demography. In this study, a mitochondrial cytochrome oxidase I (COI) fragment and nuclear ribosomal internal transcribed spacer 2 (ITS2) were sequenced to reveal the genetic variation of T. hoshinota collected from 11 marine ecoregions throughout the Indo-West Pacific. Both of the statistical parsimony networks based on the COI and nuclear ITS2 were dominated by a common haplotype. Pairwise FST and Isolation-by-distance by Mantel test of ITS2 showed moderate gene flow existed among most populations in the marine ecoregions of West Pacific, Coral Triangle, and Eastern Indian Ocean, but with a restricted gene flow between these regions and Maldives in the Central Indian Ocean. Demographic analyses of most T. hoshinota populations were consistent with the mutation-drift equilibrium, except for the Sulawesi Sea and Maldives, which showed bottlenecks following recent expansion. Our results suggest that while long-range dispersal might explain the capability of T. hoshinota to spread in the IWP, stable population demography might account for the long-term persistence of T. hoshinota outbreaks on local reefs.
bibliographic citation: Chow et al. (2022) Population genetics and demography of the coral-killing cyanobacteriosponge, Terpios hoshinota, in the Indo-West Pacific. PeerJ 10:e13451 https://doi.org/10.7717/peerj.13451
date submitted: 2021-06-23
date accepted: 2022-04-26
issued: 2022-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chow
  given name: Savanna Wenhua
author list: Agent
  family name: Keshavmurthy
  given name: Shashank
author list: Agent
  family name: Reimer
  given name: James Davis
author list: Agent
  family name: de Voogd
  given name: Nicole
author list: Agent
  family name: Huang
  given name: Hui
author list: Agent
  family name: Wang
  given name: Jih-Terng
author list: Agent
  family name: Tang
  given name: Sen-Lin
author list: Agent
  family name: Schupp
  given name: Peter J.
author list: Agent
  family name: Tan
  given name: Chun Hong
author list: Agent
  family name: Liew
  given name: Hock-Chark
author list: Agent
  family name: Soong
  given name: Keryea
author list: Agent
  family name: Subhan
  given name: Beginer
author list: Agent
  family name: Madduppa
  given name: Hawis
author list: Agent
  family name: Chen
  given name: Chaolun Allen
doi: 10.7717/peerj.13451
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-31
copyright: ©2022 Chow et al.
attribution name: Chow et al.

Spain is not different: teaching quantitative courses can also be hazardous to one’s career (at least in undergraduate courses)
type: item
type: AcademicArticle
description: Student evaluations of teaching (SETs) have become a widely used tool for assessing teaching in higher education. However, numerous investigations have shown that SETs are subject to multiple biases, one of which is particularly relevant, namely, the area of knowledge to which the subject belongs. This article aims to replicate the article by Uttl & Smibert (2017, https://doi.org/10.7717/peerj.3299) in a different educational context to verify whether the negative bias toward instructors who teach quantitative courses found by the authors in the US also appears in the Spanish university system. The study was conducted at the Business and Law School of the Universidad Pontificia Comillas, a private Spanish university, using two different samples. First, we analyzed undergraduate courses using a sample of 80,667 SETs in which 2,885 classes (defined as a single semester-long course taught by an individual instructor to a specific group of students), 488 instructors, and 322 different courses were evaluated over a time period of four academic years (2016/2017–2019/2020). Second, in the same period, 16,083 SETs corresponding to master’s degree courses were analyzed, which involved the study of 871 classes, 275 instructors, and 155 different courses. All the data included in the analysis were obtained from official university surveys developed by a team of professionals specialized in teaching quality responsible for ensuring the reliability of the information. At the degree level, the results show that despite the considerable cultural and temporal difference between the samples, the results are very similar to those obtained by Uttl & Smibert (2017, https://doi.org/10.7717/peerj.3299); i.e., professors teaching quantitative courses are far more likely to obtain worse SETs than instructors in other areas. There are hardly any differences at the master’s degree level, regardless of whether nearly 75% of master’s degree instructors also teach at the undergraduate level. Th…
format: application/pdf
format: text/html
creator: Jose Luis Arroyo-Barrigüete
creator: Antonio Obregón
creator: José María Ortiz-Lozano
creator: Antonio Rua-Vieites
subject: Psychiatry and Psychology
subject: Science and Medical Education
description: doi:10.7717/peerj.13456
publisher: PeerJ Inc.
rights: © 2022 Arroyo-Barrigüete et al.
abstract: Student evaluations of teaching (SETs) have become a widely used tool for assessing teaching in higher education. However, numerous investigations have shown that SETs are subject to multiple biases, one of which is particularly relevant, namely, the area of knowledge to which the subject belongs. This article aims to replicate the article by Uttl & Smibert (2017, https://doi.org/10.7717/peerj.3299) in a different educational context to verify whether the negative bias toward instructors who teach quantitative courses found by the authors in the US also appears in the Spanish university system. The study was conducted at the Business and Law School of the Universidad Pontificia Comillas, a private Spanish university, using two different samples. First, we analyzed undergraduate courses using a sample of 80,667 SETs in which 2,885 classes (defined as a single semester-long course taught by an individual instructor to a specific group of students), 488 instructors, and 322 different courses were evaluated over a time period of four academic years (2016/2017–2019/2020). Second, in the same period, 16,083 SETs corresponding to master’s degree courses were analyzed, which involved the study of 871 classes, 275 instructors, and 155 different courses. All the data included in the analysis were obtained from official university surveys developed by a team of professionals specialized in teaching quality responsible for ensuring the reliability of the information. At the degree level, the results show that despite the considerable cultural and temporal difference between the samples, the results are very similar to those obtained by Uttl & Smibert (2017, https://doi.org/10.7717/peerj.3299); i.e., professors teaching quantitative courses are far more likely to obtain worse SETs than instructors in other areas. There are hardly any differences at the master’s degree level, regardless of whether nearly 75% of master’s degree instructors also teach at the undergraduate level. Th…
bibliographic citation: Arroyo-Barrigüete et al. (2022) Spain is not different: teaching quantitative courses can also be hazardous to one’s career (at least in undergraduate courses). PeerJ 10:e13456 https://doi.org/10.7717/peerj.13456
date submitted: 2021-12-13
date accepted: 2022-04-27
issued: 2022-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arroyo-Barrigüete
  given name: Jose Luis
author list: Agent
  family name: Obregón
  given name: Antonio
author list: Agent
  family name: Ortiz-Lozano
  given name: José María
author list: Agent
  family name: Rua-Vieites
  given name: Antonio
doi: 10.7717/peerj.13456
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-31
copyright: © 2022 Arroyo-Barrigüete et al.
attribution name: Arroyo-Barrigüete et al.

Dramatic impact of future climate change on the genetic diversity and distribution of ecologically relevant Western Mediterranean Carex (Cyperaceae)
type: item
type: AcademicArticle
description: Anticipating the evolutionary responses of species to ongoing climate change is essential to propose effective management and conservation measures. The Western Mediterranean Basin constitutes one of the hotspots of biodiversity where the effects of climate change are expected to be more dramatic. Plant species with ecological relevance constitute ideal models to evaluate and predict the impact of climate change on ecosystems. Here we investigate these impacts through the spatio-temporal comparison of genetic diversity/structure (AFLPs), potential distribution under different future scenarios of climate change, and ecological space in two Western Mediterranean sister species of genus Carex. Both species are ecologically key in their riparian habitats, but display contrasting distribution patterns, with one widespread in the Iberian Peninsula and North Africa (C. reuteriana), while the other (C. panormitana) is a restricted, probably endangered, Central Mediterranean endemic. At present, we found a strong genetic structure driven by geography in both species, and lower values of genetic diversity and a narrower ecological space in C. panormitana than in C. reuteriana, while the allelic rarity was higher in the former than in C. reuteriana subspecies. Future projections predict an overall dramatic reduction of suitable areas for both species under all climate change scenarios, which could be almost total for C. panormitana. In addition, gene diversity was inferred to decrease in all taxa, with genetic structure reinforcing in C. reuteriana by the loss of admixture among populations. Our findings stress the need for a reassessment of C. panormitana conservation status under IUCN Red List criteria and the implementation of conservation measures.
format: application/pdf
format: text/html
creator: Carmen Benítez-Benítez
creator: María Sanz-Arnal
creator: Malvina Urbani
creator: Pedro Jiménez-Mejías
creator: Santiago Martín-Bravo
subject: Biodiversity
subject: Bioinformatics
subject: Conservation Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13464
publisher: PeerJ Inc.
rights: © 2022 Benítez-Benítez et al.
abstract: Anticipating the evolutionary responses of species to ongoing climate change is essential to propose effective management and conservation measures. The Western Mediterranean Basin constitutes one of the hotspots of biodiversity where the effects of climate change are expected to be more dramatic. Plant species with ecological relevance constitute ideal models to evaluate and predict the impact of climate change on ecosystems. Here we investigate these impacts through the spatio-temporal comparison of genetic diversity/structure (AFLPs), potential distribution under different future scenarios of climate change, and ecological space in two Western Mediterranean sister species of genus Carex. Both species are ecologically key in their riparian habitats, but display contrasting distribution patterns, with one widespread in the Iberian Peninsula and North Africa (C. reuteriana), while the other (C. panormitana) is a restricted, probably endangered, Central Mediterranean endemic. At present, we found a strong genetic structure driven by geography in both species, and lower values of genetic diversity and a narrower ecological space in C. panormitana than in C. reuteriana, while the allelic rarity was higher in the former than in C. reuteriana subspecies. Future projections predict an overall dramatic reduction of suitable areas for both species under all climate change scenarios, which could be almost total for C. panormitana. In addition, gene diversity was inferred to decrease in all taxa, with genetic structure reinforcing in C. reuteriana by the loss of admixture among populations. Our findings stress the need for a reassessment of C. panormitana conservation status under IUCN Red List criteria and the implementation of conservation measures.
bibliographic citation: Benítez-Benítez et al. (2022) Dramatic impact of future climate change on the genetic diversity and distribution of ecologically relevant Western Mediterranean Carex (Cyperaceae). PeerJ 10:e13464 https://doi.org/10.7717/peerj.13464
date submitted: 2022-03-09
date accepted: 2022-04-28
issued: 2022-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Benítez-Benítez
  given name: Carmen
author list: Agent
  family name: Sanz-Arnal
  given name: María
author list: Agent
  family name: Urbani
  given name: Malvina
author list: Agent
  family name: Jiménez-Mejías
  given name: Pedro
author list: Agent
  family name: Martín-Bravo
  given name: Santiago
doi: 10.7717/peerj.13464
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-31
copyright: © 2022 Benítez-Benítez et al.
attribution name: Benítez-Benítez et al.

A comparative metabolomics study of anthocyanins and taste components in Chinese bayberry (Morella rubra) with different flesh colors
type: item
type: AcademicArticle
description: The Chinese bayberry (Morella rubra Sieb. et Zucc.) is grown commercially in China and other Asian countries for its flavorful and appealing fruit. Here, two bayberry varieties differing in both color and flavor, namely, BDK (‘Baidongkui’) and DK (‘Dongkui’), in China were compared. A total of 18 anthocyanins, three proanthocyanidins, and 229 primary metabolites were identified in the pulp of the two varieties; these were analyzed and compared using ultra-performance liquid chromatography-tandem mass spectrometry. The DK pulp showed higher concentrations of all 18 anthocyanins compared with BDK, apart from peonidin-3,5-O-diglucoside which was not detected in BDK and which was responsible for the formation of pink pulp in BDK. Principal component analysis and cluster analysis of the primary metabolites indicated that the two bayberry varieties had distinct metabolite profiles with approximately 37% (85/229) of the primary metabolome being significantly different. Of these, 62 metabolites were down-regulated and 23 metabolites were up-regulated in BDK relative to DK. Our results suggested that the flavor of the BDK fruit was different from DK, which could be explained by the reduced saccharide, organic acid, amino acid, and proanthocyanidin contents. These findings enhance our understanding of the metabolites responsible for color and taste differences in the Chinese bayberry.
format: application/pdf
format: text/html
creator: Qihua Lin
creator: Qiuzhen Zhong
creator: Zehuang Zhang
subject: Agricultural Science
subject: Biochemistry
subject: Biotechnology
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.13466
publisher: PeerJ Inc.
rights: © 2022 Lin et al.
abstract: The Chinese bayberry (Morella rubra Sieb. et Zucc.) is grown commercially in China and other Asian countries for its flavorful and appealing fruit. Here, two bayberry varieties differing in both color and flavor, namely, BDK (‘Baidongkui’) and DK (‘Dongkui’), in China were compared. A total of 18 anthocyanins, three proanthocyanidins, and 229 primary metabolites were identified in the pulp of the two varieties; these were analyzed and compared using ultra-performance liquid chromatography-tandem mass spectrometry. The DK pulp showed higher concentrations of all 18 anthocyanins compared with BDK, apart from peonidin-3,5-O-diglucoside which was not detected in BDK and which was responsible for the formation of pink pulp in BDK. Principal component analysis and cluster analysis of the primary metabolites indicated that the two bayberry varieties had distinct metabolite profiles with approximately 37% (85/229) of the primary metabolome being significantly different. Of these, 62 metabolites were down-regulated and 23 metabolites were up-regulated in BDK relative to DK. Our results suggested that the flavor of the BDK fruit was different from DK, which could be explained by the reduced saccharide, organic acid, amino acid, and proanthocyanidin contents. These findings enhance our understanding of the metabolites responsible for color and taste differences in the Chinese bayberry.
bibliographic citation: Lin et al. (2022) A comparative metabolomics study of anthocyanins and taste components in Chinese bayberry (Morella rubra) with different flesh colors. PeerJ 10:e13466 https://doi.org/10.7717/peerj.13466
date submitted: 2021-12-27
date accepted: 2022-04-28
issued: 2022-05-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Qihua
author list: Agent
  family name: Zhong
  given name: Qiuzhen
author list: Agent
  family name: Zhang
  given name: Zehuang
doi: 10.7717/peerj.13466
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-31
copyright: © 2022 Lin et al.
attribution name: Lin et al.

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