PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Reference evapotranspiration estimate with missing climatic data and multiple linear regression models
items: Out of thin air: surveying tropical bat roosts through air sampling of eDNA
items: Differential expression of some termite neuropeptides and insulin/IGF-related hormones and their plausible functions in growth, reproduction and caste determination
items: Effects of different soil types on gas exhange parameters and fruits of Hippophae rhamnoides ssp. mongolica “Ulanshalin” plants
items: Bacterial coinfection and antibiotic resistance in hospitalized COVID-19 patients: a systematic review and meta-analysis
items: Evaluation of morpho-physiological responses and genotoxicity in Eruca sativa (Mill.) grown in hydroponics from seeds exposed to X-rays
items: Discovery of grey matter lesion-related immune genes for diagnostic prediction in multiple sclerosis
items: Advances in the diagnosis of non-occlusive mesenteric ischemia and challenges in intra-abdominal sepsis patients: a narrative review
items: Association between Vitamin D receptor (VDR) gene polymorphisms and hypertensive disorders of pregnancy: a systematic review and meta-analysis
items: Pyrus calleryana extracts reduce germination of native grassland species, suggesting the potential for allelopathic effects during ecological invasion

Reference evapotranspiration estimate with missing climatic data and multiple linear regression models
type: item
type: AcademicArticle
description: The reference evapotranspiration (ETo) is considered one of the primary variables for water resource management, irrigation practices, agricultural and hydro-meteorological studies, and modeling different hydrological processes. Therefore, an accurate prediction of ETo is essential. A large number of empirical methods have been developed by numerous scientists and specialists worldwide to estimate ETo from different climatic variables. The FAO56 Penman-Monteith (PM) is the most accepted and accurate model to estimate ETo in various environments and climatic conditions. However, the FAO56-PM method requires radiation, air temperature, air humidity, and wind speed data. In this study in Adana Plain, which has a Mediterranean climate for the summer growing season, using 22-year daily climatic data, the performance of the FAO56-PM method was evaluated with different combinations of climatic variables when climatic data were missing. Additionally, the performances of Hargreaves-Samani (HS) and HS (A&G) equations were assessed, and multiple linear regression models (MLR) were developed using different combinations of climatic variables. The FAO56-PM method could accurately estimate daily ETo when wind speed (U) and relative humidity (RH) data were unavailable, using the procedures suggested by FAO56 Paper (RMSEs were smaller than 0.4 mm d−1, and percent relative errors (REs) were smaller than 9%). Hargreaves-Samani (A&G) and HS equations could not estimate daily ETo accurately according to the statistical indices (RMSEs = 0.772-0.957 mm d−1; REs (%) = 18.2–22.6; R2 = 0.604–0.686, respectively). On the other hand, MLR models’ performance varied according to a combination of different climatic variables. According to t-stat and p values of independent variables for MLR models, solar radiation (Rs) and sunshine hours (n) variables had more effect on estimating ETo than other variables. Therefore, the models that used Rs and n data estimated daily ETo more accurately than the…
format: application/pdf
format: text/html
creator: Deniz Levent Koç
creator: Müge Erkan Can
subject: Agricultural Science
subject: Environmental Sciences
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.15252
publisher: PeerJ Inc.
rights: © 2023 Koç et al.
abstract: The reference evapotranspiration (ETo) is considered one of the primary variables for water resource management, irrigation practices, agricultural and hydro-meteorological studies, and modeling different hydrological processes. Therefore, an accurate prediction of ETo is essential. A large number of empirical methods have been developed by numerous scientists and specialists worldwide to estimate ETo from different climatic variables. The FAO56 Penman-Monteith (PM) is the most accepted and accurate model to estimate ETo in various environments and climatic conditions. However, the FAO56-PM method requires radiation, air temperature, air humidity, and wind speed data. In this study in Adana Plain, which has a Mediterranean climate for the summer growing season, using 22-year daily climatic data, the performance of the FAO56-PM method was evaluated with different combinations of climatic variables when climatic data were missing. Additionally, the performances of Hargreaves-Samani (HS) and HS (A&G) equations were assessed, and multiple linear regression models (MLR) were developed using different combinations of climatic variables. The FAO56-PM method could accurately estimate daily ETo when wind speed (U) and relative humidity (RH) data were unavailable, using the procedures suggested by FAO56 Paper (RMSEs were smaller than 0.4 mm d−1, and percent relative errors (REs) were smaller than 9%). Hargreaves-Samani (A&G) and HS equations could not estimate daily ETo accurately according to the statistical indices (RMSEs = 0.772-0.957 mm d−1; REs (%) = 18.2–22.6; R2 = 0.604–0.686, respectively). On the other hand, MLR models’ performance varied according to a combination of different climatic variables. According to t-stat and p values of independent variables for MLR models, solar radiation (Rs) and sunshine hours (n) variables had more effect on estimating ETo than other variables. Therefore, the models that used Rs and n data estimated daily ETo more accurately than the…
bibliographic citation: Koç et al. (2023) Reference evapotranspiration estimate with missing climatic data and multiple linear regression models. PeerJ 11:e15252 https://doi.org/10.7717/peerj.15252
date submitted: 2023-01-11
date accepted: 2023-03-28
issued: 2023-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Koç
  given name: Deniz Levent
author list: Agent
  family name: Erkan Can
  given name: Müge
doi: 10.7717/peerj.15252
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-27
copyright: ©2023 Koç et al.
attribution name: Koç et al.

Out of thin air: surveying tropical bat roosts through air sampling of eDNA
type: item
type: AcademicArticle
description: Understanding roosting behaviour is essential to bat conservation and biomonitoring, often providing the most accurate methods of assessing bat population size and health. However, roosts can be challenging to survey, e.g., physically impossible to access or presenting risks for researchers. Disturbance during monitoring can also disrupt natural bat behaviour and present material risks to the population such as disrupting hibernation cycles. One solution to this is the use of non-invasive monitoring approaches. Environmental (e)DNA has proven especially effective at detecting rare and elusive species particularly in hard-to-reach locations. It has recently been demonstrated that eDNA from vertebrates is carried in air. When collected in semi-confined spaces, this airborne eDNA can provide remarkably accurate profiles of biodiversity, even in complex tropical communities. In this study, we deploy novel airborne eDNA collection for the first time in a natural setting and use this approach to survey difficult to access potential roosts in the neotropics. Using airborne eDNA, we confirmed the presence of bats in nine out of 12 roosts. The identified species matched previous records of roost use obtained from photographic and live capture methods, thus demonstrating the utility of this approach. We also detected the presence of the white-winged vampire bat (Diaemus youngi) which had never been confirmed in the area but was long suspected based on range maps. In addition to the bats, we detected several non-bat vertebrates, including the big-eared climbing rat (Ototylomys phyllotis), which has previously been observed in and around bat roosts in our study area. We also detected eDNA from other local species known to be in the vicinity. Using airborne eDNA to detect new roosts and monitor known populations, particularly when species turnover is rapid, could maximize efficiency for surveyors while minimizing disturbance to the animals. This study presents the first applied …
format: application/pdf
format: text/html
creator: Nina R. Garrett
creator: Jonathan Watkins
creator: Charles M. Francis
creator: Nancy B. Simmons
creator: Natalia Ivanova
creator: Amanda Naaum
creator: Andrew Briscoe
creator: Rosie Drinkwater
creator: Elizabeth L. Clare
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.14772
publisher: PeerJ Inc.
rights: © 2023 Garrett et al.
abstract: Understanding roosting behaviour is essential to bat conservation and biomonitoring, often providing the most accurate methods of assessing bat population size and health. However, roosts can be challenging to survey, e.g., physically impossible to access or presenting risks for researchers. Disturbance during monitoring can also disrupt natural bat behaviour and present material risks to the population such as disrupting hibernation cycles. One solution to this is the use of non-invasive monitoring approaches. Environmental (e)DNA has proven especially effective at detecting rare and elusive species particularly in hard-to-reach locations. It has recently been demonstrated that eDNA from vertebrates is carried in air. When collected in semi-confined spaces, this airborne eDNA can provide remarkably accurate profiles of biodiversity, even in complex tropical communities. In this study, we deploy novel airborne eDNA collection for the first time in a natural setting and use this approach to survey difficult to access potential roosts in the neotropics. Using airborne eDNA, we confirmed the presence of bats in nine out of 12 roosts. The identified species matched previous records of roost use obtained from photographic and live capture methods, thus demonstrating the utility of this approach. We also detected the presence of the white-winged vampire bat (Diaemus youngi) which had never been confirmed in the area but was long suspected based on range maps. In addition to the bats, we detected several non-bat vertebrates, including the big-eared climbing rat (Ototylomys phyllotis), which has previously been observed in and around bat roosts in our study area. We also detected eDNA from other local species known to be in the vicinity. Using airborne eDNA to detect new roosts and monitor known populations, particularly when species turnover is rapid, could maximize efficiency for surveyors while minimizing disturbance to the animals. This study presents the first applied …
bibliographic citation: Garrett et al. (2023) Out of thin air: surveying tropical bat roosts through air sampling of eDNA. PeerJ 11:e14772 https://doi.org/10.7717/peerj.14772
date submitted: 2022-11-18
date accepted: 2023-01-03
issued: 2023-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garrett
  given name: Nina R.
author list: Agent
  family name: Watkins
  given name: Jonathan
author list: Agent
  family name: Francis
  given name: Charles M.
author list: Agent
  family name: Simmons
  given name: Nancy B.
author list: Agent
  family name: Ivanova
  given name: Natalia
author list: Agent
  family name: Naaum
  given name: Amanda
author list: Agent
  family name: Briscoe
  given name: Andrew
author list: Agent
  family name: Drinkwater
  given name: Rosie
author list: Agent
  family name: Clare
  given name: Elizabeth L.
doi: 10.7717/peerj.14772
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-26
copyright: © 2023 Garrett et al.
attribution name: Garrett et al.

Differential expression of some termite neuropeptides and insulin/IGF-related hormones and their plausible functions in growth, reproduction and caste determination
type: item
type: AcademicArticle
description: Background Insulin-like growth factor (IGF) and other insulin-like peptides (ilps) are important hormones regulating growth and development in animals. Whereas most animals have a single female and male adult phenotype, in some insect species the same genome may lead to different final forms. Perhaps the best known example is the honeybee where females can either develop into queens or workers. More extreme forms of such polyphenism occur in termites, where queens, kings, workers and soldiers coexist. Both juvenile hormone and insulin-like peptides are known to regulate growth and reproduction as well as polyphenism. In termites the role of juvenile hormone in reproduction and the induction of the soldier caste is well known, but the role of IGF and other ilps in these processes remains largely unknown. Here the various termite ilps are identified and hypotheses regarding their functions suggested. Methods Genome assemblies and transcriptome short read archives (SRAs) were used to identify insulin-like peptides and neuropeptides in termites and to determine their expression in different species, tissues and castes. Results and Discussion Termites have seven different ilps, i.e. gonadulin, IGF and an ortholog of Drosophila insulin-like peptide 7 (dilp7), which are commonly present in insects, and four smaller peptides, that have collectively been called short IGF-related peptides (sirps) and individually atirpin, birpin, cirpin and brovirpin. Gonadulin is lost from the higher termites which have however amplified the brovirpin gene, of which they often have two or three paralogs. Based on differential expression of these genes it seems likely that IGF is a growth hormone and atirpin an autocrine tissue factor that is released when a tissue faces metabolic stress. Birpin seems to be responsible for growth and in the absence of juvenile hormone this may lead to reproductive adults or, when juvenile hormone is present, to soldiers. Brovirpin is expressed both by the bra…
format: application/pdf
format: text/html
creator: Jan A. Veenstra
subject: Bioinformatics
subject: Developmental Biology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.15259
publisher: PeerJ Inc.
rights: © 2023 Veenstra
abstract: Background Insulin-like growth factor (IGF) and other insulin-like peptides (ilps) are important hormones regulating growth and development in animals. Whereas most animals have a single female and male adult phenotype, in some insect species the same genome may lead to different final forms. Perhaps the best known example is the honeybee where females can either develop into queens or workers. More extreme forms of such polyphenism occur in termites, where queens, kings, workers and soldiers coexist. Both juvenile hormone and insulin-like peptides are known to regulate growth and reproduction as well as polyphenism. In termites the role of juvenile hormone in reproduction and the induction of the soldier caste is well known, but the role of IGF and other ilps in these processes remains largely unknown. Here the various termite ilps are identified and hypotheses regarding their functions suggested. Methods Genome assemblies and transcriptome short read archives (SRAs) were used to identify insulin-like peptides and neuropeptides in termites and to determine their expression in different species, tissues and castes. Results and Discussion Termites have seven different ilps, i.e. gonadulin, IGF and an ortholog of Drosophila insulin-like peptide 7 (dilp7), which are commonly present in insects, and four smaller peptides, that have collectively been called short IGF-related peptides (sirps) and individually atirpin, birpin, cirpin and brovirpin. Gonadulin is lost from the higher termites which have however amplified the brovirpin gene, of which they often have two or three paralogs. Based on differential expression of these genes it seems likely that IGF is a growth hormone and atirpin an autocrine tissue factor that is released when a tissue faces metabolic stress. Birpin seems to be responsible for growth and in the absence of juvenile hormone this may lead to reproductive adults or, when juvenile hormone is present, to soldiers. Brovirpin is expressed both by the bra…
bibliographic citation: Veenstra (2023) Differential expression of some termite neuropeptides and insulin/IGF-related hormones and their plausible functions in growth, reproduction and caste determination. PeerJ 11:e15259 https://doi.org/10.7717/peerj.15259
date submitted: 2022-11-25
date accepted: 2023-03-28
issued: 2023-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Veenstra
  given name: Jan A.
doi: 10.7717/peerj.15259
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-26
copyright: ©2023 Veenstra
attribution name: Veenstra

Effects of different soil types on gas exhange parameters and fruits of Hippophae rhamnoides ssp. mongolica “Ulanshalin” plants
type: item
type: AcademicArticle
description: Background This study aims to explore the growth and production potential of Hippophae rhamnoides ssp. mongolica “Ulanshalin,” a pioneer species of soil and water conservation, after being planted in the Yellow River Basin area with serious soil erosion. An analysis of the differences in photosynthesis and fruit yield of H. rhamnoides plants grown in two typical soils in the watershed is key to understanding whether local conditions are suitable for the growth and yield of H. rhamnoides, as well as the impact of the plants on soil and water conservation. Methods During the growing season, diurnal changes in the gas exchange parameters of Hippophae rhamnoides-like plants growing in Loess soil and Aeolian soil were continuously monitored, and the effects of total nitrogen (TN) and other elements on the net photosynthetic rate (PN) of the plants were analyzed and compared in the two different soil types. The morphological and quality differences of Hippophae rhamnoides fruits were also compared after reaching the ripening stage. Results (1) There was a significant difference in the composition of Loess soil and of Aeolian soil. The organic matter content and AK content of the Loess soil was significantly higher than in the Aeolian soil, and the pH was closer to neutral. However, the TK content, TP content, and AP content of the Aeolian soil were slightly higher than in the Loess soil, the pH was higher, and it was alkaline. (2) After controlling the light and temperature, with all other external factors consistent, the daily variation trend of PN, Tr, and Gs in the leaves of H. rhamnoides plants growing in the two different soils were basically the same. There were differences, however, in when these factors reached their peaks. Soil composition had an impact on the photosynthetic characteristics of H. rhamnoides, with TN, TP, AP, and SOM being the main factors promoting the photosynthetic rate of H. rhamnoides PN. The peaks of PN, Tr, and Gs of H. rhamnoides plants gr…
format: application/pdf
format: text/html
creator: Fanjing Bu
creator: Yuefeng Guo
creator: Wei Qi
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.15264
publisher: PeerJ Inc.
rights: © 2023 Bu et al.
abstract: Background This study aims to explore the growth and production potential of Hippophae rhamnoides ssp. mongolica “Ulanshalin,” a pioneer species of soil and water conservation, after being planted in the Yellow River Basin area with serious soil erosion. An analysis of the differences in photosynthesis and fruit yield of H. rhamnoides plants grown in two typical soils in the watershed is key to understanding whether local conditions are suitable for the growth and yield of H. rhamnoides, as well as the impact of the plants on soil and water conservation. Methods During the growing season, diurnal changes in the gas exchange parameters of Hippophae rhamnoides-like plants growing in Loess soil and Aeolian soil were continuously monitored, and the effects of total nitrogen (TN) and other elements on the net photosynthetic rate (PN) of the plants were analyzed and compared in the two different soil types. The morphological and quality differences of Hippophae rhamnoides fruits were also compared after reaching the ripening stage. Results (1) There was a significant difference in the composition of Loess soil and of Aeolian soil. The organic matter content and AK content of the Loess soil was significantly higher than in the Aeolian soil, and the pH was closer to neutral. However, the TK content, TP content, and AP content of the Aeolian soil were slightly higher than in the Loess soil, the pH was higher, and it was alkaline. (2) After controlling the light and temperature, with all other external factors consistent, the daily variation trend of PN, Tr, and Gs in the leaves of H. rhamnoides plants growing in the two different soils were basically the same. There were differences, however, in when these factors reached their peaks. Soil composition had an impact on the photosynthetic characteristics of H. rhamnoides, with TN, TP, AP, and SOM being the main factors promoting the photosynthetic rate of H. rhamnoides PN. The peaks of PN, Tr, and Gs of H. rhamnoides plants gr…
bibliographic citation: Bu et al. (2023) Effects of different soil types on gas exhange parameters and fruits of Hippophae rhamnoides ssp. mongolica “Ulanshalin” plants. PeerJ 11:e15264 https://doi.org/10.7717/peerj.15264
date submitted: 2023-01-06
date accepted: 2023-03-28
issued: 2023-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bu
  given name: Fanjing
author list: Agent
  family name: Guo
  given name: Yuefeng
author list: Agent
  family name: Qi
  given name: Wei
doi: 10.7717/peerj.15264
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-26
copyright: ©2023 Bu et al.
attribution name: Bu et al.

Bacterial coinfection and antibiotic resistance in hospitalized COVID-19 patients: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background There were a few studies on bacterial coinfection in hospitalized COVID-19 patients worldwide. This systematic review aimed to provide the pooled prevalence of bacterial coinfection from published studies from 2020 to 2022. Methods Three databases were used to search the studies, and 49 studies from 2,451 identified studies involving 212,605 COVID-19 patients were included in this review. Results The random-effects inverse-variance model determined that the pooled prevalence of bacterial coinfection in hospitalized COVID-19 patients was 26.84% (95% CI [23.85–29.83]). The pooled prevalence of isolated bacteria for Acinetobacter baumannii was 23.25% (95% CI [19.27–27.24]), Escherichia coli was 10.51% (95% CI [8.90–12.12]), Klebsiella pneumoniae was 15.24% (95% CI [7.84–22.64]), Pseudomonas aeruginosa was 11.09% (95% CI [8.92–13.27]) and Staphylococcus aureus (11.59% (95% CI [9.71–13.46])). Meanwhile, the pooled prevalence of antibiotic-resistant bacteria for extended-spectrum beta-lactamases producing Enterobacteriaceae was 15.24% (95% CI [7.84–22.64]) followed by carbapenem-resistant Acinetobacter baumannii (14.55% (95% CI [9.59–19.52%])), carbapenem-resistant Pseudomonas aeruginosa (6.95% (95% CI [2.61–11.29])), methicillin-resistant Staphylococcus aureus (5.05% (95% CI [3.49–6.60])), carbapenem-resistant Enterobacteriaceae (4.95% (95% CI [3.10–6.79])), and vancomycin-resistant Enterococcus (1.26% (95% CI [0.46–2.05])). Conclusion All the prevalences were considered as low. However, effective management and prevention of the infection should be considered since these coinfections have a bad impact on the morbidity and mortality of patients.
format: application/pdf
format: text/html
creator: Ruhana Che Yusof
creator: Mohd Noor Norhayati
creator: Yacob Mohd Azman
subject: Microbiology
subject: Drugs and Devices
subject: Infectious Diseases
subject: Respiratory Medicine
subject: COVID-19
description: doi:10.7717/peerj.15265
publisher: PeerJ Inc.
rights: © 2023 Che Yusof et al.
abstract: Background There were a few studies on bacterial coinfection in hospitalized COVID-19 patients worldwide. This systematic review aimed to provide the pooled prevalence of bacterial coinfection from published studies from 2020 to 2022. Methods Three databases were used to search the studies, and 49 studies from 2,451 identified studies involving 212,605 COVID-19 patients were included in this review. Results The random-effects inverse-variance model determined that the pooled prevalence of bacterial coinfection in hospitalized COVID-19 patients was 26.84% (95% CI [23.85–29.83]). The pooled prevalence of isolated bacteria for Acinetobacter baumannii was 23.25% (95% CI [19.27–27.24]), Escherichia coli was 10.51% (95% CI [8.90–12.12]), Klebsiella pneumoniae was 15.24% (95% CI [7.84–22.64]), Pseudomonas aeruginosa was 11.09% (95% CI [8.92–13.27]) and Staphylococcus aureus (11.59% (95% CI [9.71–13.46])). Meanwhile, the pooled prevalence of antibiotic-resistant bacteria for extended-spectrum beta-lactamases producing Enterobacteriaceae was 15.24% (95% CI [7.84–22.64]) followed by carbapenem-resistant Acinetobacter baumannii (14.55% (95% CI [9.59–19.52%])), carbapenem-resistant Pseudomonas aeruginosa (6.95% (95% CI [2.61–11.29])), methicillin-resistant Staphylococcus aureus (5.05% (95% CI [3.49–6.60])), carbapenem-resistant Enterobacteriaceae (4.95% (95% CI [3.10–6.79])), and vancomycin-resistant Enterococcus (1.26% (95% CI [0.46–2.05])). Conclusion All the prevalences were considered as low. However, effective management and prevention of the infection should be considered since these coinfections have a bad impact on the morbidity and mortality of patients.
bibliographic citation: Che Yusof et al. (2023) Bacterial coinfection and antibiotic resistance in hospitalized COVID-19 patients: a systematic review and meta-analysis. PeerJ 11:e15265 https://doi.org/10.7717/peerj.15265
date submitted: 2023-01-27
date accepted: 2023-03-29
issued: 2023-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Che Yusof
  given name: Ruhana
author list: Agent
  family name: Norhayati
  given name: Mohd Noor
author list: Agent
  family name: Mohd Azman
  given name: Yacob
doi: 10.7717/peerj.15265
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-26
copyright: © 2023 Che Yusof et al.
attribution name: Che Yusof et al.

Evaluation of morpho-physiological responses and genotoxicity in Eruca sativa (Mill.) grown in hydroponics from seeds exposed to X-rays
type: item
type: AcademicArticle
description: Due to its potential applications in cultivated plants, ionizing radiation (IR) and its effect on organisms is increasingly studied. Here we measured the effects of ionizing radiation on Eruca sativa by analyzing plants from irradiated seeds (1 and 10 Gy) grown in hydroponics. We measured several morpho-physiological traits and genotoxicity. Radiation stress induced a noticeable variability of the morpho-physiological traits highlighting decreased plant vigor. Shoot length and leaf number were significantly higher in 1 Gy-treated samples, whereas root length was significantly higher in 10 Gy treated plants. Stomata number significantly increased with IR dose, whereas both pigment and Rubisco content decreased under radiation stress. Phenol content significantly increased in 1 Gy treated samples, otherwise from total antioxidants, which were not different from control. Most results could find a feasible explanation in a hormesis-like pattern and in a decreased plant vigor under radiation stress. IR induced genotoxic damage, evaluated by ISSR markers, in 15 day old leaves; specifically, a severe decrease in the genome template stability was observed. However, a partial recovery occurred after 2 weeks, especially under the lowest dose (i.e., 1 Gy), suggesting that DNA damage detection and repair mechanisms are active. Pigment content and genotoxic damage may serve as proxies for evaluating plant responses to IR stress, since they show univocal dose-dependent trends. The use of more checkpoints for analyses and more doses over a wider range, as well as the focus on different metabolites, could help elucidate plant response in terms of morpho-physiological changes.
format: application/pdf
format: text/html
creator: Maria Cristina Sorrentino
creator: Angelo Granata
creator: Mariagabriella Pugliese
creator: Lorenzo Manti
creator: Simonetta Giordano
creator: Fiore Capozzi
creator: Valeria Spagnuolo
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.15281
publisher: PeerJ Inc.
rights: © 2023 Sorrentino et al.
abstract: Due to its potential applications in cultivated plants, ionizing radiation (IR) and its effect on organisms is increasingly studied. Here we measured the effects of ionizing radiation on Eruca sativa by analyzing plants from irradiated seeds (1 and 10 Gy) grown in hydroponics. We measured several morpho-physiological traits and genotoxicity. Radiation stress induced a noticeable variability of the morpho-physiological traits highlighting decreased plant vigor. Shoot length and leaf number were significantly higher in 1 Gy-treated samples, whereas root length was significantly higher in 10 Gy treated plants. Stomata number significantly increased with IR dose, whereas both pigment and Rubisco content decreased under radiation stress. Phenol content significantly increased in 1 Gy treated samples, otherwise from total antioxidants, which were not different from control. Most results could find a feasible explanation in a hormesis-like pattern and in a decreased plant vigor under radiation stress. IR induced genotoxic damage, evaluated by ISSR markers, in 15 day old leaves; specifically, a severe decrease in the genome template stability was observed. However, a partial recovery occurred after 2 weeks, especially under the lowest dose (i.e., 1 Gy), suggesting that DNA damage detection and repair mechanisms are active. Pigment content and genotoxic damage may serve as proxies for evaluating plant responses to IR stress, since they show univocal dose-dependent trends. The use of more checkpoints for analyses and more doses over a wider range, as well as the focus on different metabolites, could help elucidate plant response in terms of morpho-physiological changes.
bibliographic citation: Sorrentino et al. (2023) Evaluation of morpho-physiological responses and genotoxicity in Eruca sativa (Mill.) grown in hydroponics from seeds exposed to X-rays. PeerJ 11:e15281 https://doi.org/10.7717/peerj.15281
date submitted: 2023-01-12
date accepted: 2023-04-03
issued: 2023-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sorrentino
  given name: Maria Cristina
author list: Agent
  family name: Granata
  given name: Angelo
author list: Agent
  family name: Pugliese
  given name: Mariagabriella
author list: Agent
  family name: Manti
  given name: Lorenzo
author list: Agent
  family name: Giordano
  given name: Simonetta
author list: Agent
  family name: Capozzi
  given name: Fiore
author list: Agent
  family name: Spagnuolo
  given name: Valeria
doi: 10.7717/peerj.15281
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-26
copyright: © 2023 Sorrentino et al.
attribution name: Sorrentino et al.

Discovery of grey matter lesion-related immune genes for diagnostic prediction in multiple sclerosis
type: item
type: AcademicArticle
description: Background Multiple sclerosis (MS) is a chronic debilitating disease characterized by inflammatory demyelination of the central nervous system. Grey matter (GM) lesions have been shown to be closely related to MS motor deficits and cognitive impairment. In this study, GM lesion-related genes for diagnosis and immune status in MS were investigated. Methods Gene Expression Omnibus (GEO) databases were utilized to analyze RNA-seq data for GM lesions in MS. Differentially expressed genes (DEGs) were identified. Weighted gene co-expression network analysis (WGCNA), least absolute shrinkage and selection operator (LASSO) algorithm and protein-protein interaction (PPI) network were used to screen related gene modules and candidate genes. The abundance of immune cell infiltration was analyzed by the CIBERSORT algorithm. Candidate genes with strong correlation with immune cell types were determined to be hub genes. A diagnosis model of nomogram was constructed based on the hub genes. Gene set enrichment analysis (GSEA) was performed to identify the biological functions of hub genes. Finally, an MS mouse model was induced to verify the expression levels of immune hub genes. Results Nine genes were identified by WGCNA, LASSO regression and PPI network. The infiltration of immune cells was significantly different between the MS and control groups. Four genes were identified as GM lesion-related hub genes. A reliable prediction model was established by nomogram and verified by calibration, decision curve analysis and receiver operating characteristic curves. GSEA indicated that the hub genes were mainly enriched in cell adhesion molecules, cytokine-cytokine receptor interaction and the JAK-STAT signaling pathway, etc. Conclusions TLR9, CCL5, CXCL8 and PDGFRB were identified as potential biomarkers for GM injury in MS. The effectively predicted diagnosis model will provide guidance for therapeutic intervention of MS.
format: application/pdf
format: text/html
creator: Peiyuan Zhao
creator: Xihong Liu
creator: Yunqian Wang
creator: Xinyan Zhang
creator: Han Wang
creator: Xiaodan Du
creator: Zhixin Du
creator: Liping Yang
creator: Junlin Hou
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Neurology
description: doi:10.7717/peerj.15299
publisher: PeerJ Inc.
rights: © 2023 Zhao et al.
abstract: Background Multiple sclerosis (MS) is a chronic debilitating disease characterized by inflammatory demyelination of the central nervous system. Grey matter (GM) lesions have been shown to be closely related to MS motor deficits and cognitive impairment. In this study, GM lesion-related genes for diagnosis and immune status in MS were investigated. Methods Gene Expression Omnibus (GEO) databases were utilized to analyze RNA-seq data for GM lesions in MS. Differentially expressed genes (DEGs) were identified. Weighted gene co-expression network analysis (WGCNA), least absolute shrinkage and selection operator (LASSO) algorithm and protein-protein interaction (PPI) network were used to screen related gene modules and candidate genes. The abundance of immune cell infiltration was analyzed by the CIBERSORT algorithm. Candidate genes with strong correlation with immune cell types were determined to be hub genes. A diagnosis model of nomogram was constructed based on the hub genes. Gene set enrichment analysis (GSEA) was performed to identify the biological functions of hub genes. Finally, an MS mouse model was induced to verify the expression levels of immune hub genes. Results Nine genes were identified by WGCNA, LASSO regression and PPI network. The infiltration of immune cells was significantly different between the MS and control groups. Four genes were identified as GM lesion-related hub genes. A reliable prediction model was established by nomogram and verified by calibration, decision curve analysis and receiver operating characteristic curves. GSEA indicated that the hub genes were mainly enriched in cell adhesion molecules, cytokine-cytokine receptor interaction and the JAK-STAT signaling pathway, etc. Conclusions TLR9, CCL5, CXCL8 and PDGFRB were identified as potential biomarkers for GM injury in MS. The effectively predicted diagnosis model will provide guidance for therapeutic intervention of MS.
bibliographic citation: Zhao et al. (2023) Discovery of grey matter lesion-related immune genes for diagnostic prediction in multiple sclerosis. PeerJ 11:e15299 https://doi.org/10.7717/peerj.15299
date submitted: 2023-01-17
date accepted: 2023-04-05
issued: 2023-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Peiyuan
author list: Agent
  family name: Liu
  given name: Xihong
author list: Agent
  family name: Wang
  given name: Yunqian
author list: Agent
  family name: Zhang
  given name: Xinyan
author list: Agent
  family name: Wang
  given name: Han
author list: Agent
  family name: Du
  given name: Xiaodan
author list: Agent
  family name: Du
  given name: Zhixin
author list: Agent
  family name: Yang
  given name: Liping
author list: Agent
  family name: Hou
  given name: Junlin
doi: 10.7717/peerj.15299
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-26
copyright: © 2023 Zhao et al.
attribution name: Zhao et al.

Advances in the diagnosis of non-occlusive mesenteric ischemia and challenges in intra-abdominal sepsis patients: a narrative review
type: item
type: AcademicArticle
description: Non-occlusive mesenteric ischemia (NOMI) is a type of acute mesenteric ischemia (AMI) with a high mortality rate mainly because of a delayed or misdiagnosis. Intra-abdominal sepsis is one of the risk factors for developing NOMI, and its presence makes early diagnosis much more difficult. An increase in routine abdominal surgeries carries a corresponding risk of abdominal infection, which is a complication that should not be overlooked. It is critical that physicians are aware of the possibility for intestinal necrosis in abdominal sepsis patients due to the poor survival rate of NOMI. This review aims to summarize advances in the diagnosis of NOMI, and focuses on the diagnostic challenges of mesenteric ischemia in patients with intra-abdominal sepsis.
format: application/pdf
format: text/html
creator: Zhou Chen
creator: Xiaosun Liu
creator: Chunhui Shou
creator: Weili Yang
creator: Jiren Yu
subject: Emergency and Critical Care
subject: Infectious Diseases
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.15307
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Non-occlusive mesenteric ischemia (NOMI) is a type of acute mesenteric ischemia (AMI) with a high mortality rate mainly because of a delayed or misdiagnosis. Intra-abdominal sepsis is one of the risk factors for developing NOMI, and its presence makes early diagnosis much more difficult. An increase in routine abdominal surgeries carries a corresponding risk of abdominal infection, which is a complication that should not be overlooked. It is critical that physicians are aware of the possibility for intestinal necrosis in abdominal sepsis patients due to the poor survival rate of NOMI. This review aims to summarize advances in the diagnosis of NOMI, and focuses on the diagnostic challenges of mesenteric ischemia in patients with intra-abdominal sepsis.
bibliographic citation: Chen et al. (2023) Advances in the diagnosis of non-occlusive mesenteric ischemia and challenges in intra-abdominal sepsis patients: a narrative review. PeerJ 11:e15307 https://doi.org/10.7717/peerj.15307
date submitted: 2022-12-27
date accepted: 2023-04-06
issued: 2023-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Zhou
author list: Agent
  family name: Liu
  given name: Xiaosun
author list: Agent
  family name: Shou
  given name: Chunhui
author list: Agent
  family name: Yang
  given name: Weili
author list: Agent
  family name: Yu
  given name: Jiren
doi: 10.7717/peerj.15307
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-26
copyright: © 2023 Chen et al.
attribution name: Chen et al.

Association between Vitamin D receptor (VDR) gene polymorphisms and hypertensive disorders of pregnancy: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Hypertensive disorders of pregnancy (HDP) are currently one of the major causes of pregnancy-related maternal and fetal morbidity and mortality worldwide. Recent studies provide evidence that maternal Vitamin D receptor (VDR) gene polymorphisms probably play a key role by affecting the biological function of vitamin D in some adverse pregnancy outcomes, while the relationship between the VDR gene polymorphisms and the risk of HDP remains controversial in current studies. This systematic review and meta-analysis aimed to comprehensively evaluate the association of the VDR gene polymorphisms with HDP susceptibility. Methods This meta-analysis follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement and a protocol has been registered in the PROSPERO (ID: CRD42022344383) before commencing this review. PubMed, Web of Science, Embase, and the Cochrane Library databases were searched until January 21, 2023. Case-control and cohort studies that reported the association of the VDR gene polymorphisms with HDP were included. The quality of the included studies was assessed using the Newcastle-Ottawa Scale (NOS) for non-randomized studies. The odds ratios (ORs) with corresponding 95% confidence intervals (CIs) of the five models (allele model, dominant model, recessive model, homozygous model, heterozygous model) were pooled respectively, and subgroup analysis was performed based on ethnicity. Results A total of ten studies were included. The VDR gene ApaI polymorphism was associated with HDP susceptibility in the dominant model (OR: 1.38; 95% CI [1.07–1.79]; P = 0.014) and the heterozygote model (OR: 1.48; 95% CI [1.12–1.95]; P = 0.006). In subgroup analysis, the heterozygote model (OR: 2.06; 95% CI [1.21–3.52]; P = 0.008) of the ApaI polymorphism was associated with HDP in Asians, but not in Caucasians. Conclusion The VDR gene ApaI polymorphism may be associated with HDP susceptibility. Insufficient evidence to support the e…
format: application/pdf
format: text/html
creator: Yicong Guo
creator: Yu Zhang
creator: Xiangling Tang
creator: Xionghao Liu
creator: Huilan Xu
subject: Cardiology
subject: Gynecology and Obstetrics
subject: Public Health
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.15181
publisher: PeerJ Inc.
rights: © 2023 Guo et al.
abstract: Background Hypertensive disorders of pregnancy (HDP) are currently one of the major causes of pregnancy-related maternal and fetal morbidity and mortality worldwide. Recent studies provide evidence that maternal Vitamin D receptor (VDR) gene polymorphisms probably play a key role by affecting the biological function of vitamin D in some adverse pregnancy outcomes, while the relationship between the VDR gene polymorphisms and the risk of HDP remains controversial in current studies. This systematic review and meta-analysis aimed to comprehensively evaluate the association of the VDR gene polymorphisms with HDP susceptibility. Methods This meta-analysis follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement and a protocol has been registered in the PROSPERO (ID: CRD42022344383) before commencing this review. PubMed, Web of Science, Embase, and the Cochrane Library databases were searched until January 21, 2023. Case-control and cohort studies that reported the association of the VDR gene polymorphisms with HDP were included. The quality of the included studies was assessed using the Newcastle-Ottawa Scale (NOS) for non-randomized studies. The odds ratios (ORs) with corresponding 95% confidence intervals (CIs) of the five models (allele model, dominant model, recessive model, homozygous model, heterozygous model) were pooled respectively, and subgroup analysis was performed based on ethnicity. Results A total of ten studies were included. The VDR gene ApaI polymorphism was associated with HDP susceptibility in the dominant model (OR: 1.38; 95% CI [1.07–1.79]; P = 0.014) and the heterozygote model (OR: 1.48; 95% CI [1.12–1.95]; P = 0.006). In subgroup analysis, the heterozygote model (OR: 2.06; 95% CI [1.21–3.52]; P = 0.008) of the ApaI polymorphism was associated with HDP in Asians, but not in Caucasians. Conclusion The VDR gene ApaI polymorphism may be associated with HDP susceptibility. Insufficient evidence to support the e…
bibliographic citation: Guo et al. (2023) Association between Vitamin D receptor (VDR) gene polymorphisms and hypertensive disorders of pregnancy: a systematic review and meta-analysis. PeerJ 11:e15181 https://doi.org/10.7717/peerj.15181
date submitted: 2022-12-27
date accepted: 2023-03-14
issued: 2023-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Yicong
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Tang
  given name: Xiangling
author list: Agent
  family name: Liu
  given name: Xionghao
author list: Agent
  family name: Xu
  given name: Huilan
doi: 10.7717/peerj.15181
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-25
copyright: ©2023 Guo et al.
attribution name: Guo et al.

Pyrus calleryana extracts reduce germination of native grassland species, suggesting the potential for allelopathic effects during ecological invasion
type: item
type: AcademicArticle
description: Invasive plant species’ success may be a result of allelopathy, or the release of secondary metabolites that are harmful for surrounding plant species. Allelopathy can be mediated through the abiotic environment by chemical sorption or transformation, so the substrate on which interactions occur can lead to differential outcomes in allelopathic potential. One aggressive invader, Pyrus calleryana, has become dominant in many ecosystems throughout Eastern US, and has reduced the abundance of native species where it invades. Thus, our goal was to identify if P. calleryana had allelopathic potential by testing the impact of leaf and flower leachate on gemination of six common grassland species (three grasses and three forbs) in either sterilized sand or field collected soils. Germination of five out of six tested species was reduced by P. calleryana leaf litter, with weaker impacts from flower leachate. This suggests that allelopathy is one mechanism driving the success of P. calleryana and that allelopathic effects may change with plant phenology. For instance, P. calleryana has late leaf senescence in the fall and copious blooming in the spring that may elongate the timeframe that allelopathic inhibition can occur. Further, germination was higher in sand than in soil, suggesting that the context of the abiotic environment can mediate this relationship. In our study, two grass species that could be overabundant in restored grasslands had higher germination rates in soil than sand and one was not altered by P. calleryana suggesting that this relationship could further promote the overabundance of grass species. Taken together, P. calleryana likely inhibits the germination of native species where it invades, but there is context dependency of this relationship with both soil chemistry and seasonality.
format: application/pdf
format: text/html
creator: Michaela J. Woods
creator: Jonathan T. Bauer
creator: Dena Schaeffer
creator: Ryan W. McEwan
subject: Ecology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.15189
publisher: PeerJ Inc.
rights: © 2023 Woods et al.
abstract: Invasive plant species’ success may be a result of allelopathy, or the release of secondary metabolites that are harmful for surrounding plant species. Allelopathy can be mediated through the abiotic environment by chemical sorption or transformation, so the substrate on which interactions occur can lead to differential outcomes in allelopathic potential. One aggressive invader, Pyrus calleryana, has become dominant in many ecosystems throughout Eastern US, and has reduced the abundance of native species where it invades. Thus, our goal was to identify if P. calleryana had allelopathic potential by testing the impact of leaf and flower leachate on gemination of six common grassland species (three grasses and three forbs) in either sterilized sand or field collected soils. Germination of five out of six tested species was reduced by P. calleryana leaf litter, with weaker impacts from flower leachate. This suggests that allelopathy is one mechanism driving the success of P. calleryana and that allelopathic effects may change with plant phenology. For instance, P. calleryana has late leaf senescence in the fall and copious blooming in the spring that may elongate the timeframe that allelopathic inhibition can occur. Further, germination was higher in sand than in soil, suggesting that the context of the abiotic environment can mediate this relationship. In our study, two grass species that could be overabundant in restored grasslands had higher germination rates in soil than sand and one was not altered by P. calleryana suggesting that this relationship could further promote the overabundance of grass species. Taken together, P. calleryana likely inhibits the germination of native species where it invades, but there is context dependency of this relationship with both soil chemistry and seasonality.
bibliographic citation: Woods et al. (2023) Pyrus calleryana extracts reduce germination of native grassland species, suggesting the potential for allelopathic effects during ecological invasion. PeerJ 11:e15189 https://doi.org/10.7717/peerj.15189
date submitted: 2022-12-09
date accepted: 2023-03-15
issued: 2023-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Woods
  given name: Michaela J.
author list: Agent
  family name: Bauer
  given name: Jonathan T.
author list: Agent
  family name: Schaeffer
  given name: Dena
author list: Agent
  family name: McEwan
  given name: Ryan W.
doi: 10.7717/peerj.15189
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-25
copyright: ©2023 Woods et al.
attribution name: Woods et al.

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