PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Retrospective study of intrapartum fever in term pregnancies and adverse obstetric and neonatal outcomes
items: Rediscovery and redescription of the only known mosasaur bone from the Turonian (Upper Cretaceous) of Poland
items: Distressed (Type D) personality is predicted by avoidance: evidence from a computer-based avatar task
items: Five-year LDL-cholesterol trend and its predictors among type 2 diabetes patients in an upper-middle-income country: a retrospective open cohort study
items: Determining the hip joint isokinetic muscle strength and range of motion of professional soccer players based on their field position
items: Benthic ecosystem functioning under climate change: modelling the bioturbation potential for benthic key species in the southern North Sea
items: A retrospective study of immunoglobulin E as a biomarker for the diagnosis of acute ischemic stroke with carotid atherosclerotic plaques
items: De novo transcriptome assembly using Illumina sequencing and development of EST-SSR markers in a monoecious herb Sagittaria trifolia Linn
items: 2FAST2Q: a general-purpose sequence search and counting program for FASTQ files
items: Icariside II induces rapid phosphorylation of endothelial nitric oxide synthase via multiple signaling pathways

Retrospective study of intrapartum fever in term pregnancies and adverse obstetric and neonatal outcomes
type: item
type: AcademicArticle
description: Background Intrapartum fever is a well-known predisposing factor for severe perinatal outcomes. Herein, we explored the intrapartum features, obstetric outcomes, and neonatal outcomes in relation to the extent of intrapartum fever via three group analyses. Methods A retrospective cohort analysis consisting of 575 term, singleton live births in one medical center from January 1st to December 31st, 2020 was carried out. Parturients who had experienced a maximal intrapartum fever of <38.0 °C were compared with two sub-groups of parturients who had experienced respective maximal fevers of 38.0–38.9 °C and ≥39.0 °C. We computed the adjusted risks for adverse perinatal outcomes via multiple logistic regression models to control for confounders. Results There were statistically remarkable differences among the three groups in 13 items including body mass index, epidural, and WBC before delivery (p < 0.05). In contrast with intrapartum fevers of 37.5–37.9 °C, intrapartum fevers of 38.0–38.9 °C were linked to an elevated risk of neonatal sepsis and neonatal intensive care unit admission with an odds ratio (OR) of 4.28 (95% CI 2.162–8.479) and 1.73 (95% CI 1.125–2.666), nonetheless, the relationship was remarkably higher for intrapartum fever ≥39.0 °C, with an OR of 6.40 (95% CI 2.450–16.725) and 2.23 (95% CI 1.021–4.854). Additionally, intrapartum fevers of 38.0-38.9 °C and ≥39.0 °C were related to remarkably higher risk for operative deliveries (OR 2.24, 95% CI 1.373–3.648; OR 3.59, 95% CI 1.398–9.226; respectively) and histological chorioamnionitis (OR 3.77, 95% CI 2.261-6.271; OR 19.24, 95% CI 7.385–50.111, respectively). Conclusions Intrapartum fever is an important indicator of adverse perinatal outcomes. The higher the temperature, the higher risk of histological chorioamnionitis, as well as the risk of neonatal sepsis and neonatal intensive care unit admission.
format: application/pdf
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creator: Hongmin An
creator: Wei Zheng
creator: Qinghua Zhu
creator: Haiyan Wen
subject: Gynecology and Obstetrics
subject: Infectious Diseases
subject: Women’s Health
description: doi:10.7717/peerj.14242
publisher: PeerJ Inc.
rights: © 2022 An et al.
abstract: Background Intrapartum fever is a well-known predisposing factor for severe perinatal outcomes. Herein, we explored the intrapartum features, obstetric outcomes, and neonatal outcomes in relation to the extent of intrapartum fever via three group analyses. Methods A retrospective cohort analysis consisting of 575 term, singleton live births in one medical center from January 1st to December 31st, 2020 was carried out. Parturients who had experienced a maximal intrapartum fever of <38.0 °C were compared with two sub-groups of parturients who had experienced respective maximal fevers of 38.0–38.9 °C and ≥39.0 °C. We computed the adjusted risks for adverse perinatal outcomes via multiple logistic regression models to control for confounders. Results There were statistically remarkable differences among the three groups in 13 items including body mass index, epidural, and WBC before delivery (p < 0.05). In contrast with intrapartum fevers of 37.5–37.9 °C, intrapartum fevers of 38.0–38.9 °C were linked to an elevated risk of neonatal sepsis and neonatal intensive care unit admission with an odds ratio (OR) of 4.28 (95% CI 2.162–8.479) and 1.73 (95% CI 1.125–2.666), nonetheless, the relationship was remarkably higher for intrapartum fever ≥39.0 °C, with an OR of 6.40 (95% CI 2.450–16.725) and 2.23 (95% CI 1.021–4.854). Additionally, intrapartum fevers of 38.0-38.9 °C and ≥39.0 °C were related to remarkably higher risk for operative deliveries (OR 2.24, 95% CI 1.373–3.648; OR 3.59, 95% CI 1.398–9.226; respectively) and histological chorioamnionitis (OR 3.77, 95% CI 2.261-6.271; OR 19.24, 95% CI 7.385–50.111, respectively). Conclusions Intrapartum fever is an important indicator of adverse perinatal outcomes. The higher the temperature, the higher risk of histological chorioamnionitis, as well as the risk of neonatal sepsis and neonatal intensive care unit admission.
bibliographic citation: An et al. (2022) Retrospective study of intrapartum fever in term pregnancies and adverse obstetric and neonatal outcomes. PeerJ 10:e14242 https://doi.org/10.7717/peerj.14242
date submitted: 2022-03-11
date accepted: 2022-09-23
issued: 2022-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: An
  given name: Hongmin
author list: Agent
  family name: Zheng
  given name: Wei
author list: Agent
  family name: Zhu
  given name: Qinghua
author list: Agent
  family name: Wen
  given name: Haiyan
doi: 10.7717/peerj.14242
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-27
copyright: ©2022 An et al.
attribution name: An et al.

Rediscovery and redescription of the only known mosasaur bone from the Turonian (Upper Cretaceous) of Poland
type: item
type: AcademicArticle
description: Mosasaur remains from Poland are very rare and are restricted mostly to the Campanian and Maastrichtian. The only currently known pre-Campanian records come from the Turonian strata in the Opole area, southwestern Poland. One of them is a single tooth which probably belongs to a yaguarasaurine while the other is an incomplete vertebra, for many years considered lost. The latter specimen has recently been found and is redescribed in this article. Its most characteristic feature is a strong dorsoventral compression of the articular surfaces. This is similar to the condition observed in basal mosasauroids such as halisaurines and tethysaurines. Unfortunately, due to its incompleteness, the rediscovered specimen cannot be confidently referred to any of these clades and can only be described as a probable non-mosasaurine, non-plioplatecarpine, non-tylosaurine mosasauroid. Despite its uncertain phylogenetic position, it is important from a historical point of view and as only the second record (and the only bone record) of mosasauroids from the Turonian of Poland.
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creator: Tomasz Skawiński
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.14278
publisher: PeerJ Inc.
rights: © 2022 Skawiński
abstract: Mosasaur remains from Poland are very rare and are restricted mostly to the Campanian and Maastrichtian. The only currently known pre-Campanian records come from the Turonian strata in the Opole area, southwestern Poland. One of them is a single tooth which probably belongs to a yaguarasaurine while the other is an incomplete vertebra, for many years considered lost. The latter specimen has recently been found and is redescribed in this article. Its most characteristic feature is a strong dorsoventral compression of the articular surfaces. This is similar to the condition observed in basal mosasauroids such as halisaurines and tethysaurines. Unfortunately, due to its incompleteness, the rediscovered specimen cannot be confidently referred to any of these clades and can only be described as a probable non-mosasaurine, non-plioplatecarpine, non-tylosaurine mosasauroid. Despite its uncertain phylogenetic position, it is important from a historical point of view and as only the second record (and the only bone record) of mosasauroids from the Turonian of Poland.
bibliographic citation: Skawiński (2022) Rediscovery and redescription of the only known mosasaur bone from the Turonian (Upper Cretaceous) of Poland. PeerJ 10:e14278 https://doi.org/10.7717/peerj.14278
date submitted: 2022-07-19
date accepted: 2022-09-29
issued: 2022-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Skawiński
  given name: Tomasz
doi: 10.7717/peerj.14278
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-27
copyright: ©2022 Skawiński
attribution name: Skawiński

Distressed (Type D) personality is predicted by avoidance: evidence from a computer-based avatar task
type: item
type: AcademicArticle
description: Background One personality type associated with poor health outcomes is distressed (Type D) personality which involves high levels of both social inhibition (SI) and negative affectivity (NA). Type D is also linked to psychopathologies such as post-traumatic stress disorder (PTSD), anxiety disorders, and depression. One mechanism through which personality temperament may result in these psychopathologies is avoidance. Recently, a computer-based measure designed to assess avoidant behaviors, in which the participant guides the behavior of an avatar interacting with strangers in social situations, has been found to be related to various forms of avoidance. In the current study, we extended this work with the avatar avoidance task to determine its relationship to distressed (Type D) personality. We hypothesized that Type D personality, along with SI, but not NA, would be positively related to avatar avoidance scores. We also hypothesized that avatar avoidance scores would be higher in Type D individuals than non-Type D individuals. Methods A total of 302 undergraduates completed the Distressed Type D Personality Scale (DS-14), and a computer-based avatar avoidance task. Results Type D and SI, and NA to a lesser degree, were positively correlated with avoidance scores on the avatar task. Furthermore, regression analyses revealed that Type D and SI scores were best predicted by a model including avoidance scores and education level while NA scores were best predicted by a model including avoidance scores. Standard cut-off scores on the DS-14 scale resulted in four groups (i.e., low SI and NA, high SI, high NA, and Type D) which significantly differed in avoidance scores. Specifically, Type D individuals had higher avoidance scores than the other three groups. Taken together these findings support a role for avoidance in Type D personality. The computer-based avatar avoidance task may be particularly relevant as an ecologically valid measure to identify avoidance in a vir…
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creator: M. Todd Allen
creator: Michelle M. Shields
creator: Catherine E. Myers
subject: Psychiatry and Psychology
subject: Human-Computer Interaction
subject: Mental Health
description: doi:10.7717/peerj.14302
publisher: PeerJ Inc.
rights: © 2022 Allen et al.
abstract: Background One personality type associated with poor health outcomes is distressed (Type D) personality which involves high levels of both social inhibition (SI) and negative affectivity (NA). Type D is also linked to psychopathologies such as post-traumatic stress disorder (PTSD), anxiety disorders, and depression. One mechanism through which personality temperament may result in these psychopathologies is avoidance. Recently, a computer-based measure designed to assess avoidant behaviors, in which the participant guides the behavior of an avatar interacting with strangers in social situations, has been found to be related to various forms of avoidance. In the current study, we extended this work with the avatar avoidance task to determine its relationship to distressed (Type D) personality. We hypothesized that Type D personality, along with SI, but not NA, would be positively related to avatar avoidance scores. We also hypothesized that avatar avoidance scores would be higher in Type D individuals than non-Type D individuals. Methods A total of 302 undergraduates completed the Distressed Type D Personality Scale (DS-14), and a computer-based avatar avoidance task. Results Type D and SI, and NA to a lesser degree, were positively correlated with avoidance scores on the avatar task. Furthermore, regression analyses revealed that Type D and SI scores were best predicted by a model including avoidance scores and education level while NA scores were best predicted by a model including avoidance scores. Standard cut-off scores on the DS-14 scale resulted in four groups (i.e., low SI and NA, high SI, high NA, and Type D) which significantly differed in avoidance scores. Specifically, Type D individuals had higher avoidance scores than the other three groups. Taken together these findings support a role for avoidance in Type D personality. The computer-based avatar avoidance task may be particularly relevant as an ecologically valid measure to identify avoidance in a vir…
bibliographic citation: Allen et al. (2022) Distressed (Type D) personality is predicted by avoidance: evidence from a computer-based avatar task. PeerJ 10:e14302 https://doi.org/10.7717/peerj.14302
date submitted: 2022-07-07
date accepted: 2022-10-05
issued: 2022-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Allen
  given name: M. Todd
author list: Agent
  family name: Shields
  given name: Michelle M.
author list: Agent
  family name: Myers
  given name: Catherine E.
doi: 10.7717/peerj.14302
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-27
copyright: © 2022 Allen et al.
attribution name: Allen et al.

Five-year LDL-cholesterol trend and its predictors among type 2 diabetes patients in an upper-middle-income country: a retrospective open cohort study
type: item
type: AcademicArticle
description: Background Patients with diabetes have increased risks of cardiovascular diseases (CVD), and their LDL-cholesterol (LDL-C) has to be treated to target to prevent complications. We aim to determine the LDL-C trend and its predictors among patients with type 2 diabetes (T2D) in Malaysia. Methods This was a retrospective open cohort study from 2013 to 2017 among T2D patients in public primary health care clinics in Negeri Sembilan state, Malaysia. Linear mixed-effects modelling was conducted to determine the LDL-C trend and its predictors. The LDL-C target for patients without CVD was <2.6 mmol/L, whereas <1.8 mmol/L was targeted for those with CVD. Results Among 18,312 patients, there were more females (55.9%), adults ≥60 years (49.4%), Malays (64.7%), non-smokers (93.6%), and 45.3% had diabetes for <5 years. The overall LDL-C trend reduced by 6.8% from 2.96 to 2.76 mmol/L. In 2017, 16.8% (95% CI: 13.2–21.0) of patients without CVD and 45.8% (95% CI: 44.8–46.8) of patients with CVD achieved their respective LDL-C targets. The predictors for a higher LDL-C trend were younger adults, Malay and Indian ethnicities, females, dyslipidemia, and diabetes treatment with lifestyle modification and insulin. Longer diabetes duration, obesity, hypertension, retinopathy, statin therapy, achievement of HbA1c target and achievement of BP target were independent predictors for a lower LDL-C trend. Conclusions The LDL-C trend has improved, but there are still gaps between actual results and clinical targets. Interventions should be planned and targeted at the high-risk populations to control their LDL-C.
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creator: Kim Sui Wan
creator: Noran Naqiah Hairi
creator: Feisul Mustapha
creator: Mastura Ismail
creator: Muhammad Fadhli Mohd Yusoff
creator: Foong Ming Moy
subject: Diabetes and Endocrinology
subject: Epidemiology
description: doi:10.7717/peerj.13816
publisher: PeerJ Inc.
rights: © 2022 Wan et al.
abstract: Background Patients with diabetes have increased risks of cardiovascular diseases (CVD), and their LDL-cholesterol (LDL-C) has to be treated to target to prevent complications. We aim to determine the LDL-C trend and its predictors among patients with type 2 diabetes (T2D) in Malaysia. Methods This was a retrospective open cohort study from 2013 to 2017 among T2D patients in public primary health care clinics in Negeri Sembilan state, Malaysia. Linear mixed-effects modelling was conducted to determine the LDL-C trend and its predictors. The LDL-C target for patients without CVD was <2.6 mmol/L, whereas <1.8 mmol/L was targeted for those with CVD. Results Among 18,312 patients, there were more females (55.9%), adults ≥60 years (49.4%), Malays (64.7%), non-smokers (93.6%), and 45.3% had diabetes for <5 years. The overall LDL-C trend reduced by 6.8% from 2.96 to 2.76 mmol/L. In 2017, 16.8% (95% CI: 13.2–21.0) of patients without CVD and 45.8% (95% CI: 44.8–46.8) of patients with CVD achieved their respective LDL-C targets. The predictors for a higher LDL-C trend were younger adults, Malay and Indian ethnicities, females, dyslipidemia, and diabetes treatment with lifestyle modification and insulin. Longer diabetes duration, obesity, hypertension, retinopathy, statin therapy, achievement of HbA1c target and achievement of BP target were independent predictors for a lower LDL-C trend. Conclusions The LDL-C trend has improved, but there are still gaps between actual results and clinical targets. Interventions should be planned and targeted at the high-risk populations to control their LDL-C.
bibliographic citation: Wan et al. (2022) Five-year LDL-cholesterol trend and its predictors among type 2 diabetes patients in an upper-middle-income country: a retrospective open cohort study. PeerJ 10:e13816 https://doi.org/10.7717/peerj.13816
date submitted: 2022-05-16
date accepted: 2022-07-08
issued: 2022-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wan
  given name: Kim Sui
author list: Agent
  family name: Hairi
  given name: Noran Naqiah
author list: Agent
  family name: Mustapha
  given name: Feisul
author list: Agent
  family name: Ismail
  given name: Mastura
author list: Agent
  family name: Mohd Yusoff
  given name: Muhammad Fadhli
author list: Agent
  family name: Moy
  given name: Foong Ming
doi: 10.7717/peerj.13816
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-26
copyright: ©2022 Wan et al.
attribution name: Wan et al.

Determining the hip joint isokinetic muscle strength and range of motion of professional soccer players based on their field position
type: item
type: AcademicArticle
description: Background Soccer players’ physical and physiological demands vary based on their field position. Although the hip joint has an important role in soccer, little information is available about the strength and flexibility of the hip joint based on player positions. Therefore, this study aims to investigate the differences in muscle strength and flexibility of the hip joint of professional soccer players based on their field position. Methods Ninety-six professional soccer players from Saudi Arabia were divided into four groups (goalkeepers, defenders, midfielders, and attackers), with 24 participants in each group based on their field position. The Modified Thomas test was used to measure the hip extension range of motion (ROM), and muscle strength was assessed by an Isokinetic dynamometer. Results There were no statistically significant differences in the isokinetic strength at the hip joint movements between goalkeepers, defenders, midfielders, and attackers (p ≥ 0.05). At the same time, there was a significant difference between groups in the hip extension ROM (p ≤ 0.05). according to different player positions. Post hoc tests reported significant differences between goalkeepers and defenders (p ≤ 0.05), midfielders (p ≤ 0.05), and attackers p ≤ 0.05). At the same time, there were no significant differences between defenders and midfielders (p ≥ 0.05), defenders and attackers (p ≥ 0.05), and midfielders and attackers (p ≥ 0.05). Conclusion Even though there was no significant difference in isokinetic strength, there was a significant difference in hip extension ROM among players based on field position. This study may help coaches and trainers to recognize the strengths and weaknesses of players and design training programs to rectify the weaker components and improve players’ performance in different playing positions.
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format: text/html
creator: Ali AlTaweel
creator: Shibili Nuhmani
creator: Mohammad Ahsan
creator: Turki Abualait
creator: Qassim Muaidi
subject: Kinesiology
subject: Orthopedics
subject: Sports Injury
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.14000
publisher: PeerJ Inc.
rights: © 2022 AlTaweel et al.
abstract: Background Soccer players’ physical and physiological demands vary based on their field position. Although the hip joint has an important role in soccer, little information is available about the strength and flexibility of the hip joint based on player positions. Therefore, this study aims to investigate the differences in muscle strength and flexibility of the hip joint of professional soccer players based on their field position. Methods Ninety-six professional soccer players from Saudi Arabia were divided into four groups (goalkeepers, defenders, midfielders, and attackers), with 24 participants in each group based on their field position. The Modified Thomas test was used to measure the hip extension range of motion (ROM), and muscle strength was assessed by an Isokinetic dynamometer. Results There were no statistically significant differences in the isokinetic strength at the hip joint movements between goalkeepers, defenders, midfielders, and attackers (p ≥ 0.05). At the same time, there was a significant difference between groups in the hip extension ROM (p ≤ 0.05). according to different player positions. Post hoc tests reported significant differences between goalkeepers and defenders (p ≤ 0.05), midfielders (p ≤ 0.05), and attackers p ≤ 0.05). At the same time, there were no significant differences between defenders and midfielders (p ≥ 0.05), defenders and attackers (p ≥ 0.05), and midfielders and attackers (p ≥ 0.05). Conclusion Even though there was no significant difference in isokinetic strength, there was a significant difference in hip extension ROM among players based on field position. This study may help coaches and trainers to recognize the strengths and weaknesses of players and design training programs to rectify the weaker components and improve players’ performance in different playing positions.
bibliographic citation: AlTaweel et al. (2022) Determining the hip joint isokinetic muscle strength and range of motion of professional soccer players based on their field position. PeerJ 10:e14000 https://doi.org/10.7717/peerj.14000
date submitted: 2022-06-13
date accepted: 2022-08-13
issued: 2022-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: AlTaweel
  given name: Ali
author list: Agent
  family name: Nuhmani
  given name: Shibili
author list: Agent
  family name: Ahsan
  given name: Mohammad
author list: Agent
  family name: Abualait
  given name: Turki
author list: Agent
  family name: Muaidi
  given name: Qassim
doi: 10.7717/peerj.14000
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-26
copyright: ©2022 AlTaweel et al.
attribution name: AlTaweel et al.

Benthic ecosystem functioning under climate change: modelling the bioturbation potential for benthic key species in the southern North Sea
type: item
type: AcademicArticle
description: Climate change affects the marine environment on many levels with profound consequences for numerous biological, chemical, and physical processes. Benthic bioturbation is one of the most relevant and significant processes for benthic-pelagic coupling and biogeochemical fluxes in marine sediments, such as the uptake, transport, and remineralisation of organic carbon. However, only little is known about how climate change affects the distribution and intensity of benthic bioturbation of a shallow temperate shelf sea system such as the southern North Sea. In this study, we modelled and projected changes in bioturbation potential (BPp) under a continuous global warming scenario for seven southern North Sea key bioturbators: Abra alba, Amphiura filiformis, Callianassa subterranea, Echinocardium cordatum, Goniada maculata, Nephtys hombergii, and Nucula nitidosa. Spatial changes in species bioturbation intensity are simulated for the years 2050 and 2099 based on one species distribution model per species driven by bottom temperature and salinity changes using the IPCC SRES scenario A1B. Local mean bottom temperature was projected to increase between 0.15 and 5.4 °C, while mean bottom salinity was projected to moderately decrease by 1.7. Our results show that the considered benthic species are strongly influenced by the temperature increase. Although the total BP remained rather constant in the southern North Sea, the BPp for four out of seven species was projected to increase, mainly due to a simultaneous northward range expansion, while the BPp in the core area of the southern North Sea declined for the same species. Bioturbation of the most important species, Amphiura filiformis and Echinocardium cordatum, showed no substantial change in the spatial distribution, but over time. The BPp of E. cordatum remained almost constant until 2099, while the BPp of A. filiformis decreased by 41%. The northward expansion of some species and the decline of most species in the south le…
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format: text/html
creator: Michael Weinert
creator: Ingrid Kröncke
creator: Julia Meyer
creator: Moritz Mathis
creator: Thomas Pohlmann
creator: Henning Reiss
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Climate Change Biology
description: doi:10.7717/peerj.14105
publisher: PeerJ Inc.
rights: © 2022 Weinert et al.
abstract: Climate change affects the marine environment on many levels with profound consequences for numerous biological, chemical, and physical processes. Benthic bioturbation is one of the most relevant and significant processes for benthic-pelagic coupling and biogeochemical fluxes in marine sediments, such as the uptake, transport, and remineralisation of organic carbon. However, only little is known about how climate change affects the distribution and intensity of benthic bioturbation of a shallow temperate shelf sea system such as the southern North Sea. In this study, we modelled and projected changes in bioturbation potential (BPp) under a continuous global warming scenario for seven southern North Sea key bioturbators: Abra alba, Amphiura filiformis, Callianassa subterranea, Echinocardium cordatum, Goniada maculata, Nephtys hombergii, and Nucula nitidosa. Spatial changes in species bioturbation intensity are simulated for the years 2050 and 2099 based on one species distribution model per species driven by bottom temperature and salinity changes using the IPCC SRES scenario A1B. Local mean bottom temperature was projected to increase between 0.15 and 5.4 °C, while mean bottom salinity was projected to moderately decrease by 1.7. Our results show that the considered benthic species are strongly influenced by the temperature increase. Although the total BP remained rather constant in the southern North Sea, the BPp for four out of seven species was projected to increase, mainly due to a simultaneous northward range expansion, while the BPp in the core area of the southern North Sea declined for the same species. Bioturbation of the most important species, Amphiura filiformis and Echinocardium cordatum, showed no substantial change in the spatial distribution, but over time. The BPp of E. cordatum remained almost constant until 2099, while the BPp of A. filiformis decreased by 41%. The northward expansion of some species and the decline of most species in the south le…
bibliographic citation: Weinert et al. (2022) Benthic ecosystem functioning under climate change: modelling the bioturbation potential for benthic key species in the southern North Sea. PeerJ 10:e14105 https://doi.org/10.7717/peerj.14105
date submitted: 2021-12-20
date accepted: 2022-09-01
issued: 2022-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weinert
  given name: Michael
author list: Agent
  family name: Kröncke
  given name: Ingrid
author list: Agent
  family name: Meyer
  given name: Julia
author list: Agent
  family name: Mathis
  given name: Moritz
author list: Agent
  family name: Pohlmann
  given name: Thomas
author list: Agent
  family name: Reiss
  given name: Henning
doi: 10.7717/peerj.14105
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-26
copyright: © 2022 Weinert et al.
attribution name: Weinert et al.

A retrospective study of immunoglobulin E as a biomarker for the diagnosis of acute ischemic stroke with carotid atherosclerotic plaques
type: item
type: AcademicArticle
description: Objective In this study, serum markers of acute ischemic stroke (AICS) with carotid artery plaque were retrospectively evaluated to establish a basis for discovering serological indicators for early warning of acute ischemic stroke (AICS). Methods A total of 248 patients with AICS were enrolled in Lanzhou University Second Hospital from January 2019 to December 2020. The study population included 136 males and 112 females, 64 ± 11 years of age. Of these, there were 90 patients with a transient ischemic attack (TIA), including 60 males and 30 females, aged 64 ± 8 years old. Patients with AICS were stratified by carotid ultrasound into a plaque group (n = 154) and a non-plaque group (n = 94). A total of 160 healthy subjects were selected as the control group. Serum lipoprotein-associated phospholipase A2 (Lp-PLA2), amyloid A (SAA), immunoglobulin E (IgE), D-dimer (D-D), total cholesterol (TC), triglyceride (TG), and low-density lipoprotein cholesterol (LDL-C) were collected from all subjects. Multivariate logistic regression was used to analyze the risk factors of AICS with carotid plaque. ROC curve was used to analyze the diagnostic efficacy of AICS with carotid plaque. Results The IgE, Lp-PLA2, SAA, LDL-C, TC, TG, and D-D levels in the AICS group were higher than those in the TIA group and healthy control group (P < 0.05). The IgE level was significantly higher than that in the healthy control group and TIA group. The IgE level in the AICS plaque group was significantly higher than that in the AICS non-plaque group (P < 0.01), and the Lp-PLA2 level was also different (P < 0.05). The incidence of AICS was positively correlated with Lp-PLA2, TC, IgE, TG, D-D, SAA and LDL-C (r = 0.611, 0.499, 0.478, 0.431, 0.386, 0.332, 0.280, all P < 0.05). The incidence of AICS with plaque was only positively correlated with IgE and Lp-PLA2 (r = 0.588, 0.246, P < 0.05). Logistic regression analysis showed that IgE and Lp-PLA2 were independent risk factors for predicting the occurrenc…
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format: text/html
creator: Wenwen Jiang
creator: Jindou Niu
creator: Hongwei Gao
creator: Yingqiang Dang
creator: Meijiao Qi
creator: Yumei Liu
subject: Cardiology
subject: Epidemiology
subject: Immunology
subject: Neurology
subject: Metabolic Sciences
description: doi:10.7717/peerj.14235
publisher: PeerJ Inc.
rights: © 2022 Jiang et al.
abstract: Objective In this study, serum markers of acute ischemic stroke (AICS) with carotid artery plaque were retrospectively evaluated to establish a basis for discovering serological indicators for early warning of acute ischemic stroke (AICS). Methods A total of 248 patients with AICS were enrolled in Lanzhou University Second Hospital from January 2019 to December 2020. The study population included 136 males and 112 females, 64 ± 11 years of age. Of these, there were 90 patients with a transient ischemic attack (TIA), including 60 males and 30 females, aged 64 ± 8 years old. Patients with AICS were stratified by carotid ultrasound into a plaque group (n = 154) and a non-plaque group (n = 94). A total of 160 healthy subjects were selected as the control group. Serum lipoprotein-associated phospholipase A2 (Lp-PLA2), amyloid A (SAA), immunoglobulin E (IgE), D-dimer (D-D), total cholesterol (TC), triglyceride (TG), and low-density lipoprotein cholesterol (LDL-C) were collected from all subjects. Multivariate logistic regression was used to analyze the risk factors of AICS with carotid plaque. ROC curve was used to analyze the diagnostic efficacy of AICS with carotid plaque. Results The IgE, Lp-PLA2, SAA, LDL-C, TC, TG, and D-D levels in the AICS group were higher than those in the TIA group and healthy control group (P < 0.05). The IgE level was significantly higher than that in the healthy control group and TIA group. The IgE level in the AICS plaque group was significantly higher than that in the AICS non-plaque group (P < 0.01), and the Lp-PLA2 level was also different (P < 0.05). The incidence of AICS was positively correlated with Lp-PLA2, TC, IgE, TG, D-D, SAA and LDL-C (r = 0.611, 0.499, 0.478, 0.431, 0.386, 0.332, 0.280, all P < 0.05). The incidence of AICS with plaque was only positively correlated with IgE and Lp-PLA2 (r = 0.588, 0.246, P < 0.05). Logistic regression analysis showed that IgE and Lp-PLA2 were independent risk factors for predicting the occurrenc…
bibliographic citation: Jiang et al. (2022) A retrospective study of immunoglobulin E as a biomarker for the diagnosis of acute ischemic stroke with carotid atherosclerotic plaques. PeerJ 10:e14235 https://doi.org/10.7717/peerj.14235
date submitted: 2022-05-12
date accepted: 2022-09-22
issued: 2022-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Wenwen
author list: Agent
  family name: Niu
  given name: Jindou
author list: Agent
  family name: Gao
  given name: Hongwei
author list: Agent
  family name: Dang
  given name: Yingqiang
author list: Agent
  family name: Qi
  given name: Meijiao
author list: Agent
  family name: Liu
  given name: Yumei
doi: 10.7717/peerj.14235
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-26
copyright: ©2022 Jiang et al.
attribution name: Jiang et al.

De novo transcriptome assembly using Illumina sequencing and development of EST-SSR markers in a monoecious herb Sagittaria trifolia Linn
type: item
type: AcademicArticle
description: Background Sagittaria trifolia Linn. is a widespread macrophyte in Asia and southeast Europe and cultivated in parts of Asia. Although a few genomic studies have been conducted for S. trifolia var. sinensis, a crop breed, there is limited genomic information on the wild species of S. trifolia. Effective microsatellite markers are also lacking. Objective To assemble transcriptome sequence and develop effective EST-SSR markers for S. trifolia. Methods Here we developed microsatellite markers based on tri-, tetra-, penta-, and hexa-nucleotide repeat sequences by comparatively screening multiple transcriptome sequences of eleven individuals from ten natural populations of S. trifolia. Results A total of 107,022 unigenes were de novo assembled, with a mean length of 730 bp and an N50 length of 1,378 bp. The main repeat types were mononucleotide, trinucleotide, and dinucleotide, accounting for 55.83%, 23.51%, and 17.56% of the total repeats, respectively. A total of 86 microsatellite loci were identified with repeats of tri-, tetra-, penta-, and hexa-nucleotide. For SSR verification, 28 polymorphic loci from 41 randomly picked markers were found to produce stable and polymorphic bands, with the number of alleles per locus ranging from 2 to 11 and a mean of 5.2. The range of polymorphic information content (PIC) of each SSR locus varied from 0.25 to 0.80, with an average of 0.58. The expected heterozygosity ranged from 0.29 to 0.82, whereas the observed heterozygosity ranged from 0.25 to 0.90. Conclusion The assembled transcriptome and annotated unigenes of S. trifolia provide a basis for future studies on gene functions, pathways, and molecular mechanisms associated with this species and other related. The newly developed EST-SSR markers could be effective in examining population genetic structure, differentiation, and parentage analyses in ecological and evolutionary studies of S. trifolia.
format: application/pdf
format: text/html
creator: Hanqing Tang
creator: Josphat K. Saina
creator: Zhi-Cheng Long
creator: Jinming Chen
creator: Can Dai
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14268
publisher: PeerJ Inc.
rights: © 2022 Tang et al.
abstract: Background Sagittaria trifolia Linn. is a widespread macrophyte in Asia and southeast Europe and cultivated in parts of Asia. Although a few genomic studies have been conducted for S. trifolia var. sinensis, a crop breed, there is limited genomic information on the wild species of S. trifolia. Effective microsatellite markers are also lacking. Objective To assemble transcriptome sequence and develop effective EST-SSR markers for S. trifolia. Methods Here we developed microsatellite markers based on tri-, tetra-, penta-, and hexa-nucleotide repeat sequences by comparatively screening multiple transcriptome sequences of eleven individuals from ten natural populations of S. trifolia. Results A total of 107,022 unigenes were de novo assembled, with a mean length of 730 bp and an N50 length of 1,378 bp. The main repeat types were mononucleotide, trinucleotide, and dinucleotide, accounting for 55.83%, 23.51%, and 17.56% of the total repeats, respectively. A total of 86 microsatellite loci were identified with repeats of tri-, tetra-, penta-, and hexa-nucleotide. For SSR verification, 28 polymorphic loci from 41 randomly picked markers were found to produce stable and polymorphic bands, with the number of alleles per locus ranging from 2 to 11 and a mean of 5.2. The range of polymorphic information content (PIC) of each SSR locus varied from 0.25 to 0.80, with an average of 0.58. The expected heterozygosity ranged from 0.29 to 0.82, whereas the observed heterozygosity ranged from 0.25 to 0.90. Conclusion The assembled transcriptome and annotated unigenes of S. trifolia provide a basis for future studies on gene functions, pathways, and molecular mechanisms associated with this species and other related. The newly developed EST-SSR markers could be effective in examining population genetic structure, differentiation, and parentage analyses in ecological and evolutionary studies of S. trifolia.
bibliographic citation: Tang et al. (2022) De novo transcriptome assembly using Illumina sequencing and development of EST-SSR markers in a monoecious herb Sagittaria trifolia Linn. PeerJ 10:e14268 https://doi.org/10.7717/peerj.14268
date submitted: 2022-07-31
date accepted: 2022-09-28
issued: 2022-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Hanqing
author list: Agent
  family name: Saina
  given name: Josphat K.
author list: Agent
  family name: Long
  given name: Zhi-Cheng
author list: Agent
  family name: Chen
  given name: Jinming
author list: Agent
  family name: Dai
  given name: Can
doi: 10.7717/peerj.14268
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-26
copyright: ©2022 Tang et al.
attribution name: Tang et al.

2FAST2Q: a general-purpose sequence search and counting program for FASTQ files
type: item
type: AcademicArticle
description: Background The increasingly widespread use of next generation sequencing protocols has brought the need for the development of user-friendly raw data processing tools. Here, we explore 2FAST2Q, a versatile and intuitive standalone program capable of extracting and counting feature occurrences in FASTQ files. Despite 2FAST2Q being previously described as part of a CRISPRi-seq analysis pipeline, in here we further elaborate on the program’s functionality, and its broader applicability and functions. Methods 2FAST2Q is built in Python, with published standalone executables in Windows MS, MacOS, and Linux. It has a familiar user interface, and uses an advanced custom sequence searching algorithm. Results Using published CRISPRi datasets in which Escherichia coli and Mycobacterium tuberculosis gene essentiality, as well as host-cell sensitivity towards SARS-CoV2 infectivity were tested, we demonstrate that 2FAST2Q efficiently recapitulates published output in read counts per provided feature. We further show that 2FAST2Q can be used in any experimental setup that requires feature extraction from raw reads, being able to quickly handle Hamming distance based mismatch alignments, nucleotide wise Phred score filtering, custom read trimming, and sequence searching within a single program. Moreover, we exemplify how different FASTQ read filtering parameters impact downstream analysis, and suggest a default usage protocol. 2FAST2Q is easier to use and faster than currently available tools, efficiently processing not only CRISPRi-seq / random-barcode sequencing datasets on any up-to-date laptop, but also handling the advanced extraction of de novo features from FASTQ files. We expect that 2FAST2Q will not only be useful for people working in microbiology but also for other fields in which amplicon sequencing data is generated. 2FAST2Q is available as an executable file for all current operating systems without installation and as a Python3 module on the PyPI repository (availab…
format: application/pdf
format: text/html
creator: Afonso M. Bravo
creator: Athanasios Typas
creator: Jan-Willem Veening
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.14041
publisher: PeerJ Inc.
rights: © 2022 Bravo et al.
abstract: Background The increasingly widespread use of next generation sequencing protocols has brought the need for the development of user-friendly raw data processing tools. Here, we explore 2FAST2Q, a versatile and intuitive standalone program capable of extracting and counting feature occurrences in FASTQ files. Despite 2FAST2Q being previously described as part of a CRISPRi-seq analysis pipeline, in here we further elaborate on the program’s functionality, and its broader applicability and functions. Methods 2FAST2Q is built in Python, with published standalone executables in Windows MS, MacOS, and Linux. It has a familiar user interface, and uses an advanced custom sequence searching algorithm. Results Using published CRISPRi datasets in which Escherichia coli and Mycobacterium tuberculosis gene essentiality, as well as host-cell sensitivity towards SARS-CoV2 infectivity were tested, we demonstrate that 2FAST2Q efficiently recapitulates published output in read counts per provided feature. We further show that 2FAST2Q can be used in any experimental setup that requires feature extraction from raw reads, being able to quickly handle Hamming distance based mismatch alignments, nucleotide wise Phred score filtering, custom read trimming, and sequence searching within a single program. Moreover, we exemplify how different FASTQ read filtering parameters impact downstream analysis, and suggest a default usage protocol. 2FAST2Q is easier to use and faster than currently available tools, efficiently processing not only CRISPRi-seq / random-barcode sequencing datasets on any up-to-date laptop, but also handling the advanced extraction of de novo features from FASTQ files. We expect that 2FAST2Q will not only be useful for people working in microbiology but also for other fields in which amplicon sequencing data is generated. 2FAST2Q is available as an executable file for all current operating systems without installation and as a Python3 module on the PyPI repository (availab…
bibliographic citation: Bravo et al. (2022) 2FAST2Q: a general-purpose sequence search and counting program for FASTQ files. PeerJ 10:e14041 https://doi.org/10.7717/peerj.14041
date submitted: 2022-06-14
date accepted: 2022-08-19
issued: 2022-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bravo
  given name: Afonso M.
author list: Agent
  family name: Typas
  given name: Athanasios
author list: Agent
  family name: Veening
  given name: Jan-Willem
doi: 10.7717/peerj.14041
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-25
copyright: ©2022 Bravo et al.
attribution name: Bravo et al.

Icariside II induces rapid phosphorylation of endothelial nitric oxide synthase via multiple signaling pathways
type: item
type: AcademicArticle
description: Icariside II, as a favonoid compound derived from epimedium, has been proved to involed in a variety of biological and pharmacological effects such as anti-inflammatory, anti-osteoporosis, anti-oxidation, anti-aging, and anti-cancer but its mechanism is unclear, especially in terms of its effect on post-transcriptional modification of endothelial nitric oxide synthase (eNOS). Phosphorylation of eNOS plays an important role in the synthesis of nitric oxide in endothelial cells, which is closely related to erectile dysfunction, atherosclerosis, Alzheimer’s disease, and other diseases. Our study aims to investigate the effect and mechanism of Icariside II on the rapid phosphorylation of eNOS. In this study, human umbilical vein endothelial cells (HUVECs) were stimulated with Icariside II in the presence or absence of multiple inhibitors (1 µM), including LY294002 (PI3K-inhibitor), MK-2206 (AKT-inhibitor), Bisindolylmaleimide X (AMPK-inhibitor), H-89 (CaMKII-inhibitor), KN-62 (PKA-inhibitor), Dorsomorphin (PKC-inhibitor). The proliferation of HUVECs was assessed using cell counting kit-8 (CCK-8). The release of nitric oxide (NO) within HUVECs was detected via fluorescence probe (DAF-FM). Western blot was used to examine the effect of Icariside II on the expression of eNOS, phosphorylation of eNOS, and common signaling pathways proteins. In this study, Icariside II was found to promote the cell proliferation and rapid NO release in HUVECs. The phosphorylation of eNOS-Ser1177 was significantly increased after Icariside II stimulation and reached a peak at 10 min (p < 0.05). Meanwhile, the phosphorylation of eNOS-Thr495 was significantly decreased after 45 min of stimulation (p < 0.05). Following the intervention with multiple inhibitors, it was found that MK-2206 (AKT inhibitor), LY294002 (PI3K inhibitor), KN-62 (AMPK inhibitor), and Bisindolylmaleimide X (PKC inhibitor) could significantly inhibit the phosphorylation of eNOS-Ser1177 caused by Icariside II (p < 0.05), whi…
format: application/pdf
format: text/html
creator: Wenpeng Song
creator: Yiming Yuan
creator: Xiaohui Tan
creator: Yangyang Gu
creator: Jianyu Zeng
creator: Weidong Song
creator: Zhongcheng Xin
creator: Dong Fang
creator: Ruili Guan
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.14192
publisher: PeerJ Inc.
rights: © 2022 Song et al.
abstract: Icariside II, as a favonoid compound derived from epimedium, has been proved to involed in a variety of biological and pharmacological effects such as anti-inflammatory, anti-osteoporosis, anti-oxidation, anti-aging, and anti-cancer but its mechanism is unclear, especially in terms of its effect on post-transcriptional modification of endothelial nitric oxide synthase (eNOS). Phosphorylation of eNOS plays an important role in the synthesis of nitric oxide in endothelial cells, which is closely related to erectile dysfunction, atherosclerosis, Alzheimer’s disease, and other diseases. Our study aims to investigate the effect and mechanism of Icariside II on the rapid phosphorylation of eNOS. In this study, human umbilical vein endothelial cells (HUVECs) were stimulated with Icariside II in the presence or absence of multiple inhibitors (1 µM), including LY294002 (PI3K-inhibitor), MK-2206 (AKT-inhibitor), Bisindolylmaleimide X (AMPK-inhibitor), H-89 (CaMKII-inhibitor), KN-62 (PKA-inhibitor), Dorsomorphin (PKC-inhibitor). The proliferation of HUVECs was assessed using cell counting kit-8 (CCK-8). The release of nitric oxide (NO) within HUVECs was detected via fluorescence probe (DAF-FM). Western blot was used to examine the effect of Icariside II on the expression of eNOS, phosphorylation of eNOS, and common signaling pathways proteins. In this study, Icariside II was found to promote the cell proliferation and rapid NO release in HUVECs. The phosphorylation of eNOS-Ser1177 was significantly increased after Icariside II stimulation and reached a peak at 10 min (p < 0.05). Meanwhile, the phosphorylation of eNOS-Thr495 was significantly decreased after 45 min of stimulation (p < 0.05). Following the intervention with multiple inhibitors, it was found that MK-2206 (AKT inhibitor), LY294002 (PI3K inhibitor), KN-62 (AMPK inhibitor), and Bisindolylmaleimide X (PKC inhibitor) could significantly inhibit the phosphorylation of eNOS-Ser1177 caused by Icariside II (p < 0.05), whi…
bibliographic citation: Song et al. (2022) Icariside II induces rapid phosphorylation of endothelial nitric oxide synthase via multiple signaling pathways. PeerJ 10:e14192 https://doi.org/10.7717/peerj.14192
date submitted: 2022-05-24
date accepted: 2022-09-15
issued: 2022-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Wenpeng
author list: Agent
  family name: Yuan
  given name: Yiming
author list: Agent
  family name: Tan
  given name: Xiaohui
author list: Agent
  family name: Gu
  given name: Yangyang
author list: Agent
  family name: Zeng
  given name: Jianyu
author list: Agent
  family name: Song
  given name: Weidong
author list: Agent
  family name: Xin
  given name: Zhongcheng
author list: Agent
  family name: Fang
  given name: Dong
author list: Agent
  family name: Guan
  given name: Ruili
doi: 10.7717/peerj.14192
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-25
copyright: ©2022 Song et al.
attribution name: Song et al.

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