PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Carbon content and other soil properties of near-surface peats before and after peatland restoration
items: COVID-19 and malaria co-infection: a systematic review of clinical outcomes in endemic areas
items: Hand grab or noose pole? Evaluating the least stressful practice for capture of endangered Turks and Caicos Rock Iguanas Cyclura carinata
items: Preliminary study on the protective effect of remazolam against sepsis-induced acute respiratory distress syndrome (ARDS)
items: Novel monoclonal antibodies against house dust mite allergen Der p 21 and their application to analyze allergen extracts
items: Transcriptome analysis during 4-vinylcyclohexene diepoxide exposure-induced premature ovarian insufficiency in mice
items: Cytokine profiles of mild-to-moderate SARS-CoV-2 infected and recovered pre-vaccinated individuals residing in Indonesia
items: Citizen science initiatives document biodiversity baselines at an urban lake
items: Gene expression profiles of Japanese precious coral Corallium japonicum during gametogenesis
items: Bidirectional correlation between gastroesophageal reflux disease and sleep problems: a systematic review and meta-analysis

Carbon content and other soil properties of near-surface peats before and after peatland restoration
type: item
type: AcademicArticle
description: Peatland restoration usually aims at restarting the peatlands’ function to store carbon within peat. The soil properties of the near-surface peat can give a first understanding of this process. Therefore, we sampled pH value, total organic carbon content (TOC), total nitrogen content (TN), C/N ratio as well as dry bulk density (BD), and describe the structure of near-surface peats in six restored fens in North-East Germany before (2002–2004) and after (2019–2021) restoration. Before restoration, the study sites showed peat degradation to various extents in their near-surface peats. pH values remained relatively stable over time. Comparing the degraded peat horizons, TOC increased significantly in four study sites, ranging from 35.7% to 47.8% in 2002–2004 and from 42.5% to 54.0% in 2019–2021. TN varied from 1.5% to 3.5% in 2002–2004 and from 1.8% to 3.2% in 2019–2021, but changes were only significant in one site, showing a slight decrease. In three sites, the increase in C/N ratio was significant, indicating lower nutrient availability. BD ranged from 0.08 to 0.48 g/cm3 in 2002–2004 and from 0.10 to 0.16 g/cm3 in 2019–2021, decreasing significantly in four sites. The structure of the degraded peat horizons changed after restoration to a more homogenous, sludge mass with larger re-aggregates. In three sites, new peat moss peat layers above the degraded soil horizon were present in 2019–2021, with a mean thickness of 6.8 to 36.1 cm. The structure was comparable to typical, slightly decomposed peat moss peat. Our findings suggest that within about 17 years after fen restoration, and thereby a water table rise close to surface, TOC of the near-surface peats increased to values that are typical for undisturbed peatlands. This indicates that restoration can lead to the re-establishment of peatlands as potential carbon sinks, with TOC within the near-surface peat as one key factor in this process. Further, we assume that the decrease in nutrient availability, decrease of B…
format: application/pdf
format: text/html
creator: Jenny Hammerich
creator: Corinna Schulz
creator: Robert Probst
creator: Thomas Lüdicke
creator: Vera Luthardt
subject: Ecosystem Science
subject: Soil Science
description: doi:10.7717/peerj.17113
publisher: PeerJ Inc.
rights: © 2024 Hammerich et al.
abstract: Peatland restoration usually aims at restarting the peatlands’ function to store carbon within peat. The soil properties of the near-surface peat can give a first understanding of this process. Therefore, we sampled pH value, total organic carbon content (TOC), total nitrogen content (TN), C/N ratio as well as dry bulk density (BD), and describe the structure of near-surface peats in six restored fens in North-East Germany before (2002–2004) and after (2019–2021) restoration. Before restoration, the study sites showed peat degradation to various extents in their near-surface peats. pH values remained relatively stable over time. Comparing the degraded peat horizons, TOC increased significantly in four study sites, ranging from 35.7% to 47.8% in 2002–2004 and from 42.5% to 54.0% in 2019–2021. TN varied from 1.5% to 3.5% in 2002–2004 and from 1.8% to 3.2% in 2019–2021, but changes were only significant in one site, showing a slight decrease. In three sites, the increase in C/N ratio was significant, indicating lower nutrient availability. BD ranged from 0.08 to 0.48 g/cm3 in 2002–2004 and from 0.10 to 0.16 g/cm3 in 2019–2021, decreasing significantly in four sites. The structure of the degraded peat horizons changed after restoration to a more homogenous, sludge mass with larger re-aggregates. In three sites, new peat moss peat layers above the degraded soil horizon were present in 2019–2021, with a mean thickness of 6.8 to 36.1 cm. The structure was comparable to typical, slightly decomposed peat moss peat. Our findings suggest that within about 17 years after fen restoration, and thereby a water table rise close to surface, TOC of the near-surface peats increased to values that are typical for undisturbed peatlands. This indicates that restoration can lead to the re-establishment of peatlands as potential carbon sinks, with TOC within the near-surface peat as one key factor in this process. Further, we assume that the decrease in nutrient availability, decrease of B…
bibliographic citation: Hammerich et al. (2024) Carbon content and other soil properties of near-surface peats before and after peatland restoration. PeerJ 12:e17113 https://doi.org/10.7717/peerj.17113
date submitted: 2023-05-22
date accepted: 2024-02-26
issued: 2024-04-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hammerich
  given name: Jenny
author list: Agent
  family name: Schulz
  given name: Corinna
author list: Agent
  family name: Probst
  given name: Robert
author list: Agent
  family name: Lüdicke
  given name: Thomas
author list: Agent
  family name: Luthardt
  given name: Vera
doi: 10.7717/peerj.17113
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-18
copyright: © 2024 Hammerich et al.
attribution name: Hammerich et al.

COVID-19 and malaria co-infection: a systematic review of clinical outcomes in endemic areas
type: item
type: AcademicArticle
description: Background COVID-19 and malaria cause significant morbidity and mortality globally. Co-infection of these diseases can worsen their impact on public health. This review aims to synthesize literature on the clinical outcomes of COVID-19 and malaria co-infection to develop effective prevention and treatment strategies. Methods A comprehensive literature search was conducted using MeSH terms and keywords from the start of the COVID-19 pandemic to January 2023. The review included original articles on COVID-19 and malaria co-infection, evaluating their methodological quality and certainty of evidence. It was registered in PROSPERO (CRD42023393562). Results Out of 1,596 screened articles, 19 met the inclusion criteria. These studies involved 2,810 patients, 618 of whom had COVID-19 and malaria co-infection. Plasmodium falciparum and vivax were identified as causative organisms in six studies. Hospital admission ranged from three to 18 days. Nine studies associated co-infection with severe disease, ICU admission, assisted ventilation, and related complications. One study reported 6% ICU admission, and mortality rates of 3%, 9.4%, and 40.4% were observed in four studies. Estimated crude mortality rates were 10.71 and 5.87 per 1,000 person-days for patients with and without concurrent malaria, respectively. Common co-morbidities included Diabetes mellitus, hypertension, cardiovascular diseases, and respiratory disorders. Conclusion Most patients with COVID-19 and malaria co-infection experienced short-term hospitalization and mild to moderate disease severity. However, at presentation, co-morbidities and severe malaria were significantly associated with higher mortality or worse clinical outcomes. These findings emphasize the importance of early detection, prompt treatment, and close monitoring of patients with COVID-19 and malaria co-infection.
format: application/pdf
format: text/html
creator: Amal H. Mohamed
creator: Ebtihal Eltyeb
creator: Badria Said
creator: Raga Eltayeb
creator: Abdullah Algaissi
creator: Didier Hober
creator: Abdulaziz H. Alhazmi
subject: Global Health
subject: Infectious Diseases
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.17160
publisher: PeerJ Inc.
rights: © 2024 Mohamed et al.
abstract: Background COVID-19 and malaria cause significant morbidity and mortality globally. Co-infection of these diseases can worsen their impact on public health. This review aims to synthesize literature on the clinical outcomes of COVID-19 and malaria co-infection to develop effective prevention and treatment strategies. Methods A comprehensive literature search was conducted using MeSH terms and keywords from the start of the COVID-19 pandemic to January 2023. The review included original articles on COVID-19 and malaria co-infection, evaluating their methodological quality and certainty of evidence. It was registered in PROSPERO (CRD42023393562). Results Out of 1,596 screened articles, 19 met the inclusion criteria. These studies involved 2,810 patients, 618 of whom had COVID-19 and malaria co-infection. Plasmodium falciparum and vivax were identified as causative organisms in six studies. Hospital admission ranged from three to 18 days. Nine studies associated co-infection with severe disease, ICU admission, assisted ventilation, and related complications. One study reported 6% ICU admission, and mortality rates of 3%, 9.4%, and 40.4% were observed in four studies. Estimated crude mortality rates were 10.71 and 5.87 per 1,000 person-days for patients with and without concurrent malaria, respectively. Common co-morbidities included Diabetes mellitus, hypertension, cardiovascular diseases, and respiratory disorders. Conclusion Most patients with COVID-19 and malaria co-infection experienced short-term hospitalization and mild to moderate disease severity. However, at presentation, co-morbidities and severe malaria were significantly associated with higher mortality or worse clinical outcomes. These findings emphasize the importance of early detection, prompt treatment, and close monitoring of patients with COVID-19 and malaria co-infection.
bibliographic citation: Mohamed et al. (2024) COVID-19 and malaria co-infection: a systematic review of clinical outcomes in endemic areas. PeerJ 12:e17160 https://doi.org/10.7717/peerj.17160
date submitted: 2023-07-27
date accepted: 2024-03-04
issued: 2024-04-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohamed
  given name: Amal H.
author list: Agent
  family name: Eltyeb
  given name: Ebtihal
author list: Agent
  family name: Said
  given name: Badria
author list: Agent
  family name: Eltayeb
  given name: Raga
author list: Agent
  family name: Algaissi
  given name: Abdullah
author list: Agent
  family name: Hober
  given name: Didier
author list: Agent
  family name: Alhazmi
  given name: Abdulaziz H.
doi: 10.7717/peerj.17160
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-18
copyright: © 2024 Mohamed et al.
attribution name: Mohamed et al.

Hand grab or noose pole? Evaluating the least stressful practice for capture of endangered Turks and Caicos Rock Iguanas Cyclura carinata
type: item
type: AcademicArticle
description: As the analysis of blood metabolites has become more readily accessible thanks to the use of point-of-care analyzers, it is now possible to evaluate stress level of wild animals directly in the field. Lactate is receiving much attention as a good stress level proxy in individuals subjected to capture, manual restraint, and data sampling in the wild, and appropriate protocols to maintain lactate values low should be preferred. In this study we compare how two different capture methodologies, hand grab vs. noose pole, affect the variation of blood lactate values in Cyclura carinata iguanas when captured for sampling. We used blood lactate concentration, measured immediately upon- and 15 min after-capture, as a proxy for stress level. While the primary goal of this work is to determine the least stressful capture methodology to be favored when sampling this and other wild iguanas, we also evaluated additional baseline physiological parameters relevant to the health and disease monitoring for this species. Our results show that while initial lactate values level-out in sampled individuals after 15 min in captivity, regardless of the capture methodology, rock iguanas captured by noose pole showed significantly higher lactate concentration and increased heartbeat rate immediately after capture. While the overall health evaluation determined that all analyzed individuals were in good health, based on our results we recommend that, when possible, hand capture should be preferred over noose pole when sampling wild individuals.
format: application/pdf
format: text/html
creator: Giuliano Colosimo
creator: Gwyneth Montemuro
creator: Gregory A. Lewbart
creator: Gabriele Gentile
creator: Glenn P. Gerber
subject: Conservation Biology
subject: Veterinary Medicine
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.17171
publisher: PeerJ Inc.
rights: © 2024 Colosimo et al.
abstract: As the analysis of blood metabolites has become more readily accessible thanks to the use of point-of-care analyzers, it is now possible to evaluate stress level of wild animals directly in the field. Lactate is receiving much attention as a good stress level proxy in individuals subjected to capture, manual restraint, and data sampling in the wild, and appropriate protocols to maintain lactate values low should be preferred. In this study we compare how two different capture methodologies, hand grab vs. noose pole, affect the variation of blood lactate values in Cyclura carinata iguanas when captured for sampling. We used blood lactate concentration, measured immediately upon- and 15 min after-capture, as a proxy for stress level. While the primary goal of this work is to determine the least stressful capture methodology to be favored when sampling this and other wild iguanas, we also evaluated additional baseline physiological parameters relevant to the health and disease monitoring for this species. Our results show that while initial lactate values level-out in sampled individuals after 15 min in captivity, regardless of the capture methodology, rock iguanas captured by noose pole showed significantly higher lactate concentration and increased heartbeat rate immediately after capture. While the overall health evaluation determined that all analyzed individuals were in good health, based on our results we recommend that, when possible, hand capture should be preferred over noose pole when sampling wild individuals.
bibliographic citation: Colosimo et al. (2024) Hand grab or noose pole? Evaluating the least stressful practice for capture of endangered Turks and Caicos Rock Iguanas Cyclura carinata. PeerJ 12:e17171 https://doi.org/10.7717/peerj.17171
date submitted: 2023-10-08
date accepted: 2024-03-07
issued: 2024-04-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Colosimo
  given name: Giuliano
author list: Agent
  family name: Montemuro
  given name: Gwyneth
author list: Agent
  family name: Lewbart
  given name: Gregory A.
author list: Agent
  family name: Gentile
  given name: Gabriele
author list: Agent
  family name: Gerber
  given name: Glenn P.
doi: 10.7717/peerj.17171
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-18
copyright: © 2024 Colosimo et al.
attribution name: Colosimo et al.

Preliminary study on the protective effect of remazolam against sepsis-induced acute respiratory distress syndrome (ARDS)
type: item
type: AcademicArticle
description: Background Sepsis can disrupt immune regulation and lead to acute respiratory distress syndrome (ARDS) frequently. Remazolam, a fast-acting hypnotic drug with superior qualities compared to other drugs, was investigated for its potential protective effects against sepsis-induced ARDS. Methods Forty Sprague-Dawley rats were randomly divided into four groups, including the sepsis + saline group, sham operation + saline group, sham operation + remazolam group and the sepsis + remazolam group. Lung tissues of rats were extracted for HE staining to assess lung damage, and the wet weight to dry weight (W/D) ratio was calculated. The levels of proinflammatory factors, anti-inflammatory factors, CD4+ and CD8+ T cells in peripheral blood, MDA, MPO, and ATP in the lung tissue were measured by using ELISA. Western blotting was performed to determine the protein expression of HMGB1 in lung tissues. Results In comparison to the sham operation + saline and sham operation + remazolam groups, the sepsis + saline group exhibited significantly higher values for W/D ratio, lung damage score, IL-1β, IL-6, TNF-α, PCT, CRP, MDP and MPO, while exhibiting lower levels of CD4+ and CD8+ T lymphocytes, PaO2, PCO2, and ATP. The rats in the sepsis + saline group displayed ruptured alveolar walls and evident interstitial lung edema. However, the rats in the sepsis + remazolam group showed improved alveolar structure. Furthermore, the HMGB1 protein expression in the sepsis + remazolam group was lower than the sepsis + saline group. Conclusion Remazolam can alleviate the inflammatory response in infected rats, thereby alleviating lung injury and improving immune function, which may be attributed to the reduction in HMGB1 protein expression.
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format: text/html
creator: Xiaoxin Gao
creator: Rujun Zhang
creator: Zhenzhou Wang
creator: Qingan Chen
creator: Zhenlin Lei
creator: Yanan Yang
creator: Jia Tian
subject: Biochemistry
subject: Molecular Biology
subject: Pathology
subject: Histology
description: doi:10.7717/peerj.17205
publisher: PeerJ Inc.
rights: © 2024 Gao et al.
abstract: Background Sepsis can disrupt immune regulation and lead to acute respiratory distress syndrome (ARDS) frequently. Remazolam, a fast-acting hypnotic drug with superior qualities compared to other drugs, was investigated for its potential protective effects against sepsis-induced ARDS. Methods Forty Sprague-Dawley rats were randomly divided into four groups, including the sepsis + saline group, sham operation + saline group, sham operation + remazolam group and the sepsis + remazolam group. Lung tissues of rats were extracted for HE staining to assess lung damage, and the wet weight to dry weight (W/D) ratio was calculated. The levels of proinflammatory factors, anti-inflammatory factors, CD4+ and CD8+ T cells in peripheral blood, MDA, MPO, and ATP in the lung tissue were measured by using ELISA. Western blotting was performed to determine the protein expression of HMGB1 in lung tissues. Results In comparison to the sham operation + saline and sham operation + remazolam groups, the sepsis + saline group exhibited significantly higher values for W/D ratio, lung damage score, IL-1β, IL-6, TNF-α, PCT, CRP, MDP and MPO, while exhibiting lower levels of CD4+ and CD8+ T lymphocytes, PaO2, PCO2, and ATP. The rats in the sepsis + saline group displayed ruptured alveolar walls and evident interstitial lung edema. However, the rats in the sepsis + remazolam group showed improved alveolar structure. Furthermore, the HMGB1 protein expression in the sepsis + remazolam group was lower than the sepsis + saline group. Conclusion Remazolam can alleviate the inflammatory response in infected rats, thereby alleviating lung injury and improving immune function, which may be attributed to the reduction in HMGB1 protein expression.
bibliographic citation: Gao et al. (2024) Preliminary study on the protective effect of remazolam against sepsis-induced acute respiratory distress syndrome (ARDS). PeerJ 12:e17205 https://doi.org/10.7717/peerj.17205
date submitted: 2023-01-05
date accepted: 2024-03-15
issued: 2024-04-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Xiaoxin
author list: Agent
  family name: Zhang
  given name: Rujun
author list: Agent
  family name: Wang
  given name: Zhenzhou
author list: Agent
  family name: Chen
  given name: Qingan
author list: Agent
  family name: Lei
  given name: Zhenlin
author list: Agent
  family name: Yang
  given name: Yanan
author list: Agent
  family name: Tian
  given name: Jia
doi: 10.7717/peerj.17205
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-18
copyright: ©2024 Gao et al.
attribution name: Gao et al.

Novel monoclonal antibodies against house dust mite allergen Der p 21 and their application to analyze allergen extracts
type: item
type: AcademicArticle
description: Background Allergen extracts and recombinant allergens are used in allergy diagnostics and immunotherapy. Since allergen extracts from different manufacturers lack proper standardization regarding their composition, monoclonal antibodies (MAbs) against specific allergen components can be used for their identification and quantification in allergen extracts. This study aimed to generate MAbs against allergen Der p 21 of Dermatophagoides pteronyssinus for the analysis of allergen extracts. Methods Recombinant Der p 21 was expressed in E. coli and purified using affinity chromatography. MAbs against Der p 21 were generated using hybridoma technology. House dust mite (HDM) allergen extracts were analyzed using the newly developed sandwich enzyme-linked immunosorbent assay, Western blotting and microarray immunoassay. Results MAbs raised against recombinant Der p 21 were characterized in detail and proven to be reactive with natural Der p 21. Highly specific sandwich enzyme-linked immunosorbent assay for the quantification of Der p 21 was developed and optimized. The allergen was detected and its concentration was determined in only three of six analyzed HDM allergen extracts from different manufacturers. Conclusion HDM analysis by MAb-based immunoassays shows their differences in allergen composition. The results demonstrate the importance of allergen-specific MAbs as a tool for the characterization of allergen extracts and the need for their appropriate standardization before their use for allergy diagnostics or immunotherapy.
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format: text/html
creator: Vytautas Rudokas
creator: Laimis Silimavicius
creator: Indre Kucinskaite-Kodze
creator: Aiste Sliziene
creator: Milda Pleckaityte
creator: Aurelija Zvirbliene
subject: Biotechnology
subject: Allergy and Clinical Immunology
subject: Immunology
description: doi:10.7717/peerj.17233
publisher: PeerJ Inc.
rights: © 2024 Rudokas et al.
abstract: Background Allergen extracts and recombinant allergens are used in allergy diagnostics and immunotherapy. Since allergen extracts from different manufacturers lack proper standardization regarding their composition, monoclonal antibodies (MAbs) against specific allergen components can be used for their identification and quantification in allergen extracts. This study aimed to generate MAbs against allergen Der p 21 of Dermatophagoides pteronyssinus for the analysis of allergen extracts. Methods Recombinant Der p 21 was expressed in E. coli and purified using affinity chromatography. MAbs against Der p 21 were generated using hybridoma technology. House dust mite (HDM) allergen extracts were analyzed using the newly developed sandwich enzyme-linked immunosorbent assay, Western blotting and microarray immunoassay. Results MAbs raised against recombinant Der p 21 were characterized in detail and proven to be reactive with natural Der p 21. Highly specific sandwich enzyme-linked immunosorbent assay for the quantification of Der p 21 was developed and optimized. The allergen was detected and its concentration was determined in only three of six analyzed HDM allergen extracts from different manufacturers. Conclusion HDM analysis by MAb-based immunoassays shows their differences in allergen composition. The results demonstrate the importance of allergen-specific MAbs as a tool for the characterization of allergen extracts and the need for their appropriate standardization before their use for allergy diagnostics or immunotherapy.
bibliographic citation: Rudokas et al. (2024) Novel monoclonal antibodies against house dust mite allergen Der p 21 and their application to analyze allergen extracts. PeerJ 12:e17233 https://doi.org/10.7717/peerj.17233
date submitted: 2024-01-10
date accepted: 2024-03-22
issued: 2024-04-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rudokas
  given name: Vytautas
author list: Agent
  family name: Silimavicius
  given name: Laimis
author list: Agent
  family name: Kucinskaite-Kodze
  given name: Indre
author list: Agent
  family name: Sliziene
  given name: Aiste
author list: Agent
  family name: Pleckaityte
  given name: Milda
author list: Agent
  family name: Zvirbliene
  given name: Aurelija
doi: 10.7717/peerj.17233
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-18
copyright: ©2024 Rudokas et al.
attribution name: Rudokas et al.

Transcriptome analysis during 4-vinylcyclohexene diepoxide exposure-induced premature ovarian insufficiency in mice
type: item
type: AcademicArticle
description: The occupational chemical 4-Vinylcyclohexene diepoxide (VCD) is a reproductively toxic environmental pollutant that causes follicular failure, leading to premature ovarian insufficiency (POI), which significantly impacts a woman’s physical health and fertility. Investigating VCD’s pathogenic mechanisms can offer insights for the prevention of ovarian impairment and the treatment of POI. This study established a mouse model of POI through intraperitoneal injection of VCD into female C57BL/6 mice for 15 days. The results were then compared with those of the control group, including a comparison of phenotypic characteristics and transcriptome differences, at two time points: day 15 and day 30. Through a comprehensive analysis of differentially expressed genes (DEGs), key genes were identified and validated some using RT-PCR. The results revealed significant impacts on sex hormone levels, follicle number, and the estrous cycle in VCD-induced POI mice on both day 15 and day 30. The DEGs and enrichment results obtained on day 15 were not as significant as those obtained on day 30. The results of this study provide a preliminary indication that steroid hormone synthesis, DNA damage repair, and impaired oocyte mitosis are pivotal in VCD-mediated ovarian dysfunction. This dysfunction may have been caused by VCD damage to the primordial follicular pool, impairing follicular development and aggravating ovarian damage over time, making it gradually difficult for the ovaries to perform their normal functions.
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format: text/html
creator: Yi Li
creator: Ruifen He
creator: Xue Qin
creator: Qinying Zhu
creator: Liangjian Ma
creator: Xiaolei Liang
subject: Biochemistry
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Toxicology
description: doi:10.7717/peerj.17251
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: The occupational chemical 4-Vinylcyclohexene diepoxide (VCD) is a reproductively toxic environmental pollutant that causes follicular failure, leading to premature ovarian insufficiency (POI), which significantly impacts a woman’s physical health and fertility. Investigating VCD’s pathogenic mechanisms can offer insights for the prevention of ovarian impairment and the treatment of POI. This study established a mouse model of POI through intraperitoneal injection of VCD into female C57BL/6 mice for 15 days. The results were then compared with those of the control group, including a comparison of phenotypic characteristics and transcriptome differences, at two time points: day 15 and day 30. Through a comprehensive analysis of differentially expressed genes (DEGs), key genes were identified and validated some using RT-PCR. The results revealed significant impacts on sex hormone levels, follicle number, and the estrous cycle in VCD-induced POI mice on both day 15 and day 30. The DEGs and enrichment results obtained on day 15 were not as significant as those obtained on day 30. The results of this study provide a preliminary indication that steroid hormone synthesis, DNA damage repair, and impaired oocyte mitosis are pivotal in VCD-mediated ovarian dysfunction. This dysfunction may have been caused by VCD damage to the primordial follicular pool, impairing follicular development and aggravating ovarian damage over time, making it gradually difficult for the ovaries to perform their normal functions.
bibliographic citation: Li et al. (2024) Transcriptome analysis during 4-vinylcyclohexene diepoxide exposure-induced premature ovarian insufficiency in mice. PeerJ 12:e17251 https://doi.org/10.7717/peerj.17251
date submitted: 2023-12-04
date accepted: 2024-03-26
issued: 2024-04-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yi
author list: Agent
  family name: He
  given name: Ruifen
author list: Agent
  family name: Qin
  given name: Xue
author list: Agent
  family name: Zhu
  given name: Qinying
author list: Agent
  family name: Ma
  given name: Liangjian
author list: Agent
  family name: Liang
  given name: Xiaolei
doi: 10.7717/peerj.17251
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-18
copyright: ©2024 Li et al.
attribution name: Li et al.

Cytokine profiles of mild-to-moderate SARS-CoV-2 infected and recovered pre-vaccinated individuals residing in Indonesia
type: item
type: AcademicArticle
description: Background Accumulating evidence suggests the involvement of cytokine-mediated inflammation, in clinical severity and death related to SARS-CoV-2 infection, especially among pre-vaccinated individuals. An increased risk of death was also described among SARS-CoV-2 recovered individuals, which might be correlated with prolonged inflammatory responses. Despite being among the countries with the highest cumulative deaths due to COVID-19, evidence regarding cytokine profiles among SARS-CoV-2 infected and recovered pre-vaccinated individuals in Indonesia is scarce. Thus, this study aimed to describe the cytokines profiles of pre-vaccinated individuals residing in Indonesia, with mild-to-moderate SARS-CoV-2 infection and those who recovered. Methods Sixty-one sera from 24 hospitalized patients with mild-to-moderate SARS-CoV-2 infection, 24 individuals recovered from asymptomatic-to-moderate SARS-CoV-2 infection, and 13 healthy controls unexposed to SARS-CoV-2 were used in this study. Quantification of serum cytokine levels, including IL-6, IL-8, IP-10, TNF-α, CCL-2, CCL-3, CCL-4, and CXCL-13, was performed using a Luminex multi-analyte-profiling (xMAP)-based assay. Results The levels of IL-8 along with CCL-2 and CCL-4, were significantly higher (p ≤ 0.01) in hospitalized patients with mild-to-moderate SARS-CoV-2 infection and recovered individuals compared to healthy controls. However, no significant difference was observed in these cytokine levels between infected and recovered individuals. On the other hand, there were no significant differences in several other cytokine levels, including IL-6, IL-10, TNF-α, CCL-3, and CXCL-13, among all groups. Conclusion IL-8, CCL-2, and CCL-4 were significantly elevated in pre-vaccinated Indonesian individuals with mild-to-moderate SARS-CoV-2 infection and those who recovered. The cytokine profiles described in this study might indicate inflammatory responses not only among SARS-CoV-2 infected, but also recovered individuals.
format: application/pdf
format: text/html
creator: Ni Luh Ayu Megasari
creator: Siti Qamariyah Khairunisa
creator: Radita Yuniar Arizandy
creator: I. Komang Evan Wijaksana
creator: Citrawati Dyah Kencono Wungu
subject: Biochemistry
subject: Immunology
subject: Infectious Diseases
subject: COVID-19
description: doi:10.7717/peerj.17257
publisher: PeerJ Inc.
rights: © 2024 Megasari et al.
abstract: Background Accumulating evidence suggests the involvement of cytokine-mediated inflammation, in clinical severity and death related to SARS-CoV-2 infection, especially among pre-vaccinated individuals. An increased risk of death was also described among SARS-CoV-2 recovered individuals, which might be correlated with prolonged inflammatory responses. Despite being among the countries with the highest cumulative deaths due to COVID-19, evidence regarding cytokine profiles among SARS-CoV-2 infected and recovered pre-vaccinated individuals in Indonesia is scarce. Thus, this study aimed to describe the cytokines profiles of pre-vaccinated individuals residing in Indonesia, with mild-to-moderate SARS-CoV-2 infection and those who recovered. Methods Sixty-one sera from 24 hospitalized patients with mild-to-moderate SARS-CoV-2 infection, 24 individuals recovered from asymptomatic-to-moderate SARS-CoV-2 infection, and 13 healthy controls unexposed to SARS-CoV-2 were used in this study. Quantification of serum cytokine levels, including IL-6, IL-8, IP-10, TNF-α, CCL-2, CCL-3, CCL-4, and CXCL-13, was performed using a Luminex multi-analyte-profiling (xMAP)-based assay. Results The levels of IL-8 along with CCL-2 and CCL-4, were significantly higher (p ≤ 0.01) in hospitalized patients with mild-to-moderate SARS-CoV-2 infection and recovered individuals compared to healthy controls. However, no significant difference was observed in these cytokine levels between infected and recovered individuals. On the other hand, there were no significant differences in several other cytokine levels, including IL-6, IL-10, TNF-α, CCL-3, and CXCL-13, among all groups. Conclusion IL-8, CCL-2, and CCL-4 were significantly elevated in pre-vaccinated Indonesian individuals with mild-to-moderate SARS-CoV-2 infection and those who recovered. The cytokine profiles described in this study might indicate inflammatory responses not only among SARS-CoV-2 infected, but also recovered individuals.
bibliographic citation: Megasari et al. (2024) Cytokine profiles of mild-to-moderate SARS-CoV-2 infected and recovered pre-vaccinated individuals residing in Indonesia. PeerJ 12:e17257 https://doi.org/10.7717/peerj.17257
date submitted: 2023-10-19
date accepted: 2024-03-27
issued: 2024-04-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Megasari
  given name: Ni Luh Ayu
author list: Agent
  family name: Khairunisa
  given name: Siti Qamariyah
author list: Agent
  family name: Arizandy
  given name: Radita Yuniar
author list: Agent
  family name: Wijaksana
  given name: I. Komang Evan
author list: Agent
  family name: Wungu
  given name: Citrawati Dyah Kencono
doi: 10.7717/peerj.17257
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-18
copyright: ©2024 Megasari et al.
attribution name: Megasari et al.

Citizen science initiatives document biodiversity baselines at an urban lake
type: item
type: AcademicArticle
description: Changes to biodiversity from urbanization are occurring worldwide, and baseline data is vital to document the magnitude and direction of these alterations. We set out to document the biodiversity of an urban lake in Eastern Iowa that was devoid of baseline data prior to a renovation project that will convert the site into a major area for human recreation. Throughout the course of one year, we studied the biodiversity at Cedar Lake utilizing the citizen-science application iNaturalist coupled with semi-structured BioBlitz events, which we compared to previous opportunistic observations at the site. From a semi-structured approach to document biodiversity with citizen science, our analyses revealed more diverse community metrics over a shorter period compared to more than a decade of prior observations.
format: application/pdf
format: text/html
creator: Alyssah Ahern
creator: Daniel F. Hughes
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.17209
publisher: PeerJ Inc.
rights: © 2024 Ahern and Hughes
abstract: Changes to biodiversity from urbanization are occurring worldwide, and baseline data is vital to document the magnitude and direction of these alterations. We set out to document the biodiversity of an urban lake in Eastern Iowa that was devoid of baseline data prior to a renovation project that will convert the site into a major area for human recreation. Throughout the course of one year, we studied the biodiversity at Cedar Lake utilizing the citizen-science application iNaturalist coupled with semi-structured BioBlitz events, which we compared to previous opportunistic observations at the site. From a semi-structured approach to document biodiversity with citizen science, our analyses revealed more diverse community metrics over a shorter period compared to more than a decade of prior observations.
bibliographic citation: Ahern et al. (2024) Citizen science initiatives document biodiversity baselines at an urban lake. PeerJ 12:e17209 https://doi.org/10.7717/peerj.17209
date submitted: 2023-09-25
date accepted: 2024-03-18
issued: 2024-04-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahern
  given name: Alyssah
author list: Agent
  family name: Hughes
  given name: Daniel F.
doi: 10.7717/peerj.17209
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-17
copyright: ©2024 Ahern and Hughes
attribution name: Ahern and Hughes

Gene expression profiles of Japanese precious coral Corallium japonicum during gametogenesis
type: item
type: AcademicArticle
description: Background Corallium japonicum, a prized resource in Japan, plays a vital role in traditional arts and fishing industries. Because of diminished stock due to overexploitation, ongoing efforts are focused on restoration through transplantation. This study aimed to enhance our understanding of the reproductive biology of these valuable corals and find more efficient methods for sex determination, which may significantly contribute to conservation initiatives. Methods We used 12 three-month aquarium reared C. japonicum colony fragments, conducted histological analysis for maturity and sex verification, and performed transcriptome analysis via de novo assembly and mapping using the C. rubrum transcriptome to explore gene expression differences between female and male C. japonicum. Results Our histological observations enabled sex identification in 33% of incompletely mature samples. However, the sex of the remaining 67% of samples, classified as immature, could not be identified. RNA-seq yielded approximately 21–31 million short reads from 12 samples. De novo assembly yielded 404,439 highly expressed transcripts. Among them, 855 showed significant differential expression, with 786 differentially expressed transcripts between females and males. Heatmap analysis highlighted 283 female-specific and 525 male-specific upregulated transcripts. Transcriptome assembly mapped to C. rubrum yielded 28,092 contigs, leading to the identification of 190 highly differentially expressed genes, with 113 upregulated exclusively in females and 70 upregulated exclusively in males. Blastp analysis provided putative protein annotations for 83 female and 72 male transcripts. Annotation analysis revealed that female biological processes were related to oocyte proliferation and reproduction, whereas those in males were associated with cell adhesion. Discussion Transcriptome analysis revealed sex-specific gene upregulation in incompletely mature C. japonicum and shared transcripts with C. rubrum…
format: application/pdf
format: text/html
creator: Ma. Marivic Capitle Pepino
creator: Sam Edward Manalili
creator: Satoko Sekida
creator: Takuma Mezaki
creator: Tomoyo Okumura
creator: Satoshi Kubota
subject: Ecology
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.17182
publisher: PeerJ Inc.
rights: © 2024 Pepino et al.
abstract: Background Corallium japonicum, a prized resource in Japan, plays a vital role in traditional arts and fishing industries. Because of diminished stock due to overexploitation, ongoing efforts are focused on restoration through transplantation. This study aimed to enhance our understanding of the reproductive biology of these valuable corals and find more efficient methods for sex determination, which may significantly contribute to conservation initiatives. Methods We used 12 three-month aquarium reared C. japonicum colony fragments, conducted histological analysis for maturity and sex verification, and performed transcriptome analysis via de novo assembly and mapping using the C. rubrum transcriptome to explore gene expression differences between female and male C. japonicum. Results Our histological observations enabled sex identification in 33% of incompletely mature samples. However, the sex of the remaining 67% of samples, classified as immature, could not be identified. RNA-seq yielded approximately 21–31 million short reads from 12 samples. De novo assembly yielded 404,439 highly expressed transcripts. Among them, 855 showed significant differential expression, with 786 differentially expressed transcripts between females and males. Heatmap analysis highlighted 283 female-specific and 525 male-specific upregulated transcripts. Transcriptome assembly mapped to C. rubrum yielded 28,092 contigs, leading to the identification of 190 highly differentially expressed genes, with 113 upregulated exclusively in females and 70 upregulated exclusively in males. Blastp analysis provided putative protein annotations for 83 female and 72 male transcripts. Annotation analysis revealed that female biological processes were related to oocyte proliferation and reproduction, whereas those in males were associated with cell adhesion. Discussion Transcriptome analysis revealed sex-specific gene upregulation in incompletely mature C. japonicum and shared transcripts with C. rubrum…
bibliographic citation: Pepino et al. (2024) Gene expression profiles of Japanese precious coral Corallium japonicum during gametogenesis. PeerJ 12:e17182 https://doi.org/10.7717/peerj.17182
date submitted: 2023-08-17
date accepted: 2024-03-11
issued: 2024-04-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pepino
  given name: Ma. Marivic Capitle
author list: Agent
  family name: Manalili
  given name: Sam Edward
author list: Agent
  family name: Sekida
  given name: Satoko
author list: Agent
  family name: Mezaki
  given name: Takuma
author list: Agent
  family name: Okumura
  given name: Tomoyo
author list: Agent
  family name: Kubota
  given name: Satoshi
doi: 10.7717/peerj.17182
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-16
copyright: ©2024 Pepino et al.
attribution name: Pepino et al.

Bidirectional correlation between gastroesophageal reflux disease and sleep problems: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objectives Gastroesophageal reflux disease (GERD) and sleep problems are highly prevalent among the general population. Both them are associated with a variety of psychiatric disorders such as depression and anxiety, which is highlighting an underexplored connection between them. This meta-analysis aims to explore the association between sleep problems and GERD. Methods We conducted a comprehensive search on PubMed, Cochrane Library, Embase, and Web of Science, using Medical Subject Headings (MeSH) and keywords, covering articles from the inception of the databases until August 2023. Stata statistical software, version 14.0, was utilized for all statistical analyses. A fixed-effects model was applied when p > 0.1 and I2 ≤ 50%, while a random-effects model was employed for high heterogeneity (p < 0.1 and I2 > 50%). Funnel plots and Egger’s test were used to assess publication bias. Results Involving 22 studies, our meta-analysis revealed that insomnia, sleep disturbance, or short sleep duration significantly increased the risk of GERD (OR = 2.02, 95% CI [1.64–2.49], p < 0.001; I2 = 66.4%; OR = 1.98, 95% CI [1.58–2.50], p < 0.001, I2 = 50.1%; OR = 2.66, 95% CI [2.02–3.15], p < 0.001; I2 = 62.5%, respectively). GERD was associated with an elevated risk of poor sleep quality (OR = 1.47, 95% CI [1.47–1.79], p < 0.001, I2 = 72.4%), sleep disturbance (OR = 1.47, 95% CI [1.24–1.74], p < 0.001, I2 = 71.6%), or short sleep duration (OR = 1.17, 95% CI [1.12–1.21], p < 0.001, I2 = 0). Conclusion This meta-analysis establishes a bidirectional relationship between four distinct types of sleep problems and GERD. The findings offer insights for the development of innovative approaches in the treatment of both GERD and sleep problems.
format: application/pdf
format: text/html
creator: Xiaolong Tan
creator: Shasha Wang
creator: Fengjie Wu
creator: Jun Zhu
subject: Evidence Based Medicine
subject: Gastroenterology and Hepatology
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.17202
publisher: PeerJ Inc.
rights: © 2024 Tan et al.
abstract: Objectives Gastroesophageal reflux disease (GERD) and sleep problems are highly prevalent among the general population. Both them are associated with a variety of psychiatric disorders such as depression and anxiety, which is highlighting an underexplored connection between them. This meta-analysis aims to explore the association between sleep problems and GERD. Methods We conducted a comprehensive search on PubMed, Cochrane Library, Embase, and Web of Science, using Medical Subject Headings (MeSH) and keywords, covering articles from the inception of the databases until August 2023. Stata statistical software, version 14.0, was utilized for all statistical analyses. A fixed-effects model was applied when p > 0.1 and I2 ≤ 50%, while a random-effects model was employed for high heterogeneity (p < 0.1 and I2 > 50%). Funnel plots and Egger’s test were used to assess publication bias. Results Involving 22 studies, our meta-analysis revealed that insomnia, sleep disturbance, or short sleep duration significantly increased the risk of GERD (OR = 2.02, 95% CI [1.64–2.49], p < 0.001; I2 = 66.4%; OR = 1.98, 95% CI [1.58–2.50], p < 0.001, I2 = 50.1%; OR = 2.66, 95% CI [2.02–3.15], p < 0.001; I2 = 62.5%, respectively). GERD was associated with an elevated risk of poor sleep quality (OR = 1.47, 95% CI [1.47–1.79], p < 0.001, I2 = 72.4%), sleep disturbance (OR = 1.47, 95% CI [1.24–1.74], p < 0.001, I2 = 71.6%), or short sleep duration (OR = 1.17, 95% CI [1.12–1.21], p < 0.001, I2 = 0). Conclusion This meta-analysis establishes a bidirectional relationship between four distinct types of sleep problems and GERD. The findings offer insights for the development of innovative approaches in the treatment of both GERD and sleep problems.
bibliographic citation: Tan et al. (2024) Bidirectional correlation between gastroesophageal reflux disease and sleep problems: a systematic review and meta-analysis. PeerJ 12:e17202 https://doi.org/10.7717/peerj.17202
date submitted: 2023-12-10
date accepted: 2024-03-15
issued: 2024-04-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Xiaolong
author list: Agent
  family name: Wang
  given name: Shasha
author list: Agent
  family name: Wu
  given name: Fengjie
author list: Agent
  family name: Zhu
  given name: Jun
doi: 10.7717/peerj.17202
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-16
copyright: © 2024 Tan et al.
attribution name: Tan et al.

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