PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Biomarkers of non-communicable chronic disease: an update on contemporary methods
items: Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard
items: Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy
items: Spatial patterns in the contribution of biotic and abiotic factors to the population dynamics of three freshwater fish species
items: Synovial fluid proteome profile of surgical versus chemical induced osteoarthritis in rabbits
items: Efficacy of brain natriuretic peptide vs. nicorandil in preventing contrast-induced nephropathy: a network meta-analysis
items: Disentangling bias for non-destructive insect metabarcoding
items: Microbial biogeography of the wombat gastrointestinal tract
items: A noninvasive and comprehensive method for continuous assessment of cerebral blood flow pulsation based on magnetic induction phase shift
items: Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum

Biomarkers of non-communicable chronic disease: an update on contemporary methods
type: item
type: AcademicArticle
description: Chronic diseases constitute a major global burden with significant impact on health systems, economies, and quality of life. Chronic diseases include a broad range of diseases that can be communicable or non-communicable. Chronic diseases are often associated with modifications of normal physiological levels of various analytes that are routinely measured in serum and other body fluids, as well as pathological findings, such as chronic inflammation, oxidative stress, and mitochondrial dysfunction. Identification of at-risk populations, early diagnosis, and prediction of prognosis play a major role in preventing or reducing the burden of chronic diseases. Biomarkers are tools that are used by health professionals to aid in the identification and management of chronic diseases. Biomarkers can be diagnostic, predictive, or prognostic. Several individual or grouped biomarkers have been used successfully in the diagnosis and prediction of certain chronic diseases, however, it is generally accepted that a more sophisticated approach to link and interpret various biomarkers involved in chronic disease is necessary to improve our current procedures. In order to ensure a comprehensive and unbiased coverage of the literature, first a primary frame of the manuscript (title, headings and subheadings) was drafted by the authors working on this paper. Second, based on the components drafted in the preliminary skeleton a comprehensive search of the literature was performed using the PubMed and Google Scholar search engines. Multiple keywords related to the topic were used. Out of screened papers, only 190 papers, which are the most relevant, and recent articles were selected to cover the topic in relation to etiological mechanisms of different chronic diseases, the most recently used biomarkers of chronic diseases and finally the advances in the applications of multivariate biomarkers of chronic diseases as statistical and clinically applied tool for the early diagnosis of chronic…
format: application/pdf
format: text/html
creator: Solaiman M. Al-hadlaq
creator: Hanan A. Balto
creator: Wail M. Hassan
creator: Najat A. Marraiki
creator: Afaf K. El-Ansary
subject: Cardiology
subject: Diabetes and Endocrinology
subject: Evidence Based Medicine
subject: Statistics
description: doi:10.7717/peerj.12977
publisher: PeerJ Inc.
rights: © 2022 Al-hadlaq et al.
abstract: Chronic diseases constitute a major global burden with significant impact on health systems, economies, and quality of life. Chronic diseases include a broad range of diseases that can be communicable or non-communicable. Chronic diseases are often associated with modifications of normal physiological levels of various analytes that are routinely measured in serum and other body fluids, as well as pathological findings, such as chronic inflammation, oxidative stress, and mitochondrial dysfunction. Identification of at-risk populations, early diagnosis, and prediction of prognosis play a major role in preventing or reducing the burden of chronic diseases. Biomarkers are tools that are used by health professionals to aid in the identification and management of chronic diseases. Biomarkers can be diagnostic, predictive, or prognostic. Several individual or grouped biomarkers have been used successfully in the diagnosis and prediction of certain chronic diseases, however, it is generally accepted that a more sophisticated approach to link and interpret various biomarkers involved in chronic disease is necessary to improve our current procedures. In order to ensure a comprehensive and unbiased coverage of the literature, first a primary frame of the manuscript (title, headings and subheadings) was drafted by the authors working on this paper. Second, based on the components drafted in the preliminary skeleton a comprehensive search of the literature was performed using the PubMed and Google Scholar search engines. Multiple keywords related to the topic were used. Out of screened papers, only 190 papers, which are the most relevant, and recent articles were selected to cover the topic in relation to etiological mechanisms of different chronic diseases, the most recently used biomarkers of chronic diseases and finally the advances in the applications of multivariate biomarkers of chronic diseases as statistical and clinically applied tool for the early diagnosis of chronic…
bibliographic citation: Al-hadlaq et al. (2022) Biomarkers of non-communicable chronic disease: an update on contemporary methods. PeerJ 10:e12977 https://doi.org/10.7717/peerj.12977
date submitted: 2021-07-15
date accepted: 2022-01-31
issued: 2022-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al-hadlaq
  given name: Solaiman M.
author list: Agent
  family name: Balto
  given name: Hanan A.
author list: Agent
  family name: Hassan
  given name: Wail M.
author list: Agent
  family name: Marraiki
  given name: Najat A.
author list: Agent
  family name: El-Ansary
  given name: Afaf K.
doi: 10.7717/peerj.12977
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-24
copyright: ©2022 Al-hadlaq et al.
attribution name: Al-hadlaq et al.

Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard
type: item
type: AcademicArticle
description: High levels of within-individual variation (WIV) in reiterative components in plants such as leaves, flowers, and fruits have been shown to increase individual fitness by multiple mechanisms including mediating interactions with natural enemies. This relationship between WIV and fitness has been studied almost exclusively in plant systems. While animals do not exhibit conspicuous reiterative components, they have traits that can vary at the individual level such as erythrocyte size. It is currently unknown if WIV in animals can influence individual fitness by mediating the outcome of interactions with natural enemies as it has been shown in plants. To address this issue, we tested for a relationship between WIV in erythrocyte size, hemoparasite infection status, and body condition (a proxy for fitness) in a Caribbean anole lizard. We quantified the coefficient of variation of adult erythrocytes size in $n = 95$ infected and $n = 107$ non-infected lizards. We found higher degrees of erythrocyte size variation in infected lizards than in non-infected individuals. However, we found no significant relationship between infection status or erythrocyte size variation, and lizard body condition. These results suggest that higher WIV in erythrocyte size in infected lizards is not necessarily adaptive but likely a consequence of the host response to infection. Many hemoparasites destroy their host cells as part of their life cycle. To compensate, the host lizard may respond by increasing production of erythrocytes resulting in higher WIV. Our results emphasize the need to better understand the role of within-animal variation as a neglected driver or consequence of ecological and evolutionary interactions.
format: application/pdf
format: text/html
creator: Virnaliz Cruz
creator: Omar Cruz-Pantoja
creator: Raymond Tremblay
creator: Miguel Acevedo
subject: Ecology
subject: Parasitology
subject: Zoology
subject: Hematology
description: doi:10.7717/peerj.12761
publisher: PeerJ Inc.
rights: © 2022 Cruz et al.
abstract: High levels of within-individual variation (WIV) in reiterative components in plants such as leaves, flowers, and fruits have been shown to increase individual fitness by multiple mechanisms including mediating interactions with natural enemies. This relationship between WIV and fitness has been studied almost exclusively in plant systems. While animals do not exhibit conspicuous reiterative components, they have traits that can vary at the individual level such as erythrocyte size. It is currently unknown if WIV in animals can influence individual fitness by mediating the outcome of interactions with natural enemies as it has been shown in plants. To address this issue, we tested for a relationship between WIV in erythrocyte size, hemoparasite infection status, and body condition (a proxy for fitness) in a Caribbean anole lizard. We quantified the coefficient of variation of adult erythrocytes size in $n = 95$ infected and $n = 107$ non-infected lizards. We found higher degrees of erythrocyte size variation in infected lizards than in non-infected individuals. However, we found no significant relationship between infection status or erythrocyte size variation, and lizard body condition. These results suggest that higher WIV in erythrocyte size in infected lizards is not necessarily adaptive but likely a consequence of the host response to infection. Many hemoparasites destroy their host cells as part of their life cycle. To compensate, the host lizard may respond by increasing production of erythrocytes resulting in higher WIV. Our results emphasize the need to better understand the role of within-animal variation as a neglected driver or consequence of ecological and evolutionary interactions.
bibliographic citation: Cruz et al. (2022) Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard. PeerJ 10:e12761 https://doi.org/10.7717/peerj.12761
date submitted: 2019-07-15
date accepted: 2021-12-16
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cruz
  given name: Virnaliz
author list: Agent
  family name: Cruz-Pantoja
  given name: Omar
author list: Agent
  family name: Tremblay
  given name: Raymond
author list: Agent
  family name: Acevedo
  given name: Miguel
doi: 10.7717/peerj.12761
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Cruz et al.
attribution name: Cruz et al.

Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy
type: item
type: AcademicArticle
description: Background Holothuriophilus trapeziformis Nauck, 1880 is a holothurian-dweller pinnotherid crab representing one of the two species of the genus distributed along the Pacific coast of Mexico and Chile, respectively. While the parasitic ecological interaction with its host is well established, the morphology of the male remains unknown, and DNA information for the species is not available. Furthermore, the only morphological trait separating both species of the genus is subjective and corresponds to the presence or absence of a gap between the fingers of the chelae. Our goal is to complete and clarify the taxonomic status of H. trapeziformis and describe the male morphology with the use of the integrative taxonomy, providing additional characters to differentiate this species. Methods We collected new biological material in the Pacific coast of Mexico including the topotypes. We also reviewed material from national collections to integrate morphology (based on a complete and detailed description and illustration of the species using light microscopy), ecological data (based on the identification of the host and the place where it was located within the host), and the mtCOI gene information (commonly known as DNA barcode) to differentiate Holothuriophilus trapeziformis from other related crabs. Results This species presents marked sexual dimorphism only in the primary sexual characters. For the first time we describe morphological variability of traditionally stable characters. In addition to the gap between the fingers of the chelae, Holothuriophilus trapeziformis differs from H. pacificus (Poeppig, 1836) by their ornamentation, the shape of the male abdomen, and the gonopod. Cytocrome Oxidase 1 gene (COI) distance divergence was >3% between both Holothuriophilus species forming a clear clade. DNA barcoding indicates only one taxon, with a maximum divergence of 2.2%. All the specimens have the same Barcode Index Number (BIN; BOLD: ADE9974). All the hosts for H. trape…
format: application/pdf
format: text/html
creator: Fernando Cortés-Carrasco
creator: Manuel Elías-Gutiérrez
creator: María del Socorro García-Madrigal
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12774
publisher: PeerJ Inc.
rights: © 2022 Cortés-Carrasco et al.
abstract: Background Holothuriophilus trapeziformis Nauck, 1880 is a holothurian-dweller pinnotherid crab representing one of the two species of the genus distributed along the Pacific coast of Mexico and Chile, respectively. While the parasitic ecological interaction with its host is well established, the morphology of the male remains unknown, and DNA information for the species is not available. Furthermore, the only morphological trait separating both species of the genus is subjective and corresponds to the presence or absence of a gap between the fingers of the chelae. Our goal is to complete and clarify the taxonomic status of H. trapeziformis and describe the male morphology with the use of the integrative taxonomy, providing additional characters to differentiate this species. Methods We collected new biological material in the Pacific coast of Mexico including the topotypes. We also reviewed material from national collections to integrate morphology (based on a complete and detailed description and illustration of the species using light microscopy), ecological data (based on the identification of the host and the place where it was located within the host), and the mtCOI gene information (commonly known as DNA barcode) to differentiate Holothuriophilus trapeziformis from other related crabs. Results This species presents marked sexual dimorphism only in the primary sexual characters. For the first time we describe morphological variability of traditionally stable characters. In addition to the gap between the fingers of the chelae, Holothuriophilus trapeziformis differs from H. pacificus (Poeppig, 1836) by their ornamentation, the shape of the male abdomen, and the gonopod. Cytocrome Oxidase 1 gene (COI) distance divergence was >3% between both Holothuriophilus species forming a clear clade. DNA barcoding indicates only one taxon, with a maximum divergence of 2.2%. All the specimens have the same Barcode Index Number (BIN; BOLD: ADE9974). All the hosts for H. trape…
bibliographic citation: Cortés-Carrasco et al. (2022) Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy. PeerJ 10:e12774 https://doi.org/10.7717/peerj.12774
date submitted: 2021-02-19
date accepted: 2021-12-20
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cortés-Carrasco
  given name: Fernando
author list: Agent
  family name: Elías-Gutiérrez
  given name: Manuel
author list: Agent
  family name: García-Madrigal
  given name: María del Socorro
doi: 10.7717/peerj.12774
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: © 2022 Cortés-Carrasco et al.
attribution name: Cortés-Carrasco et al.

Spatial patterns in the contribution of biotic and abiotic factors to the population dynamics of three freshwater fish species
type: item
type: AcademicArticle
description: Background Population dynamics are driven by a number of biotic (e.g., density-dependence) and abiotic (e.g., climate) factors whose contribution can greatly vary across study systems (i.e., populations). Yet, the extent to which the contribution of these factors varies across populations and between species and whether spatial patterns can be identified has received little attention. Methods Here, we used a long-term (1982–2011), broad scale (182 sites distributed across metropolitan France) dataset to study spatial patterns in the population’s dynamics of three freshwater fish species presenting contrasted life-histories and patterns of elevation range shifts in recent decades. We used a hierarchical Bayesian approach together with an elasticity analysis to estimate the relative contribution of a set of biotic (e.g., strength of density dependence, recruitment rate) and abiotic (mean and variability of water temperature) factors affecting the site-specific dynamic of two different size classes (0+ and >0+ individuals) for the three species. We then tested whether the local contribution of each factor presented evidence for biogeographical patterns by confronting two non-mutually exclusive hypotheses: the “range-shift” hypothesis that predicts a gradient along elevation or latitude and the “abundant-center” hypothesis that predicts a gradient from the center to the edge of the species’ distributional range. Results Despite contrasted life-histories, the three species displayed similar large-scale patterns in population dynamics with a much stronger contribution of biotic factors over abiotic ones. Yet, the contribution of the different factors strongly varied within distributional ranges and followed distinct spatial patterns. Indeed, while abiotic factors mostly varied along elevation, biotic factors—which disproportionately contributed to population dynamics—varied along both elevation and latitude. Conclusions Overall while our results provide stronger support f…
format: application/pdf
format: text/html
creator: Mathieu Chevalier
creator: Pablo Tedesco
creator: Gael Grenouillet
subject: Aquaculture, Fisheries and Fish Science
subject: Biogeography
subject: Ecology
subject: Freshwater Biology
subject: Population Biology
description: doi:10.7717/peerj.12857
publisher: PeerJ Inc.
rights: © 2022 Chevalier et al.
abstract: Background Population dynamics are driven by a number of biotic (e.g., density-dependence) and abiotic (e.g., climate) factors whose contribution can greatly vary across study systems (i.e., populations). Yet, the extent to which the contribution of these factors varies across populations and between species and whether spatial patterns can be identified has received little attention. Methods Here, we used a long-term (1982–2011), broad scale (182 sites distributed across metropolitan France) dataset to study spatial patterns in the population’s dynamics of three freshwater fish species presenting contrasted life-histories and patterns of elevation range shifts in recent decades. We used a hierarchical Bayesian approach together with an elasticity analysis to estimate the relative contribution of a set of biotic (e.g., strength of density dependence, recruitment rate) and abiotic (mean and variability of water temperature) factors affecting the site-specific dynamic of two different size classes (0+ and >0+ individuals) for the three species. We then tested whether the local contribution of each factor presented evidence for biogeographical patterns by confronting two non-mutually exclusive hypotheses: the “range-shift” hypothesis that predicts a gradient along elevation or latitude and the “abundant-center” hypothesis that predicts a gradient from the center to the edge of the species’ distributional range. Results Despite contrasted life-histories, the three species displayed similar large-scale patterns in population dynamics with a much stronger contribution of biotic factors over abiotic ones. Yet, the contribution of the different factors strongly varied within distributional ranges and followed distinct spatial patterns. Indeed, while abiotic factors mostly varied along elevation, biotic factors—which disproportionately contributed to population dynamics—varied along both elevation and latitude. Conclusions Overall while our results provide stronger support f…
bibliographic citation: Chevalier et al. (2022) Spatial patterns in the contribution of biotic and abiotic factors to the population dynamics of three freshwater fish species. PeerJ 10:e12857 https://doi.org/10.7717/peerj.12857
date submitted: 2021-07-15
date accepted: 2022-01-09
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chevalier
  given name: Mathieu
author list: Agent
  family name: Tedesco
  given name: Pablo
author list: Agent
  family name: Grenouillet
  given name: Gael
doi: 10.7717/peerj.12857
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Chevalier et al.
attribution name: Chevalier et al.

Synovial fluid proteome profile of surgical versus chemical induced osteoarthritis in rabbits
type: item
type: AcademicArticle
description: Background Animal models are significant for understanding human osteoarthritis (OA). This study compared the synovial fluid proteomics changes in surgical and chemical induced OA models. Methods Thirty rabbits either had anterior cruciate ligament transection (ACLT) procedure or injected intra-articularly with monosodium iodoacetate (MIA, 8 mg) into the right knee. The joints were anatomically assessed, and the synovial fluid proteins analyzed using two-dimensional polyacrylamide gel electrophoresis (2DGE) and MALDI TOF/TOF mass spectrometry analysis at 4, 8 and 12 weeks. The proteins’ upregulation and downregulation were compared with control healthy knees. Results Seven proteins (histidine-rich glycoprotein, beta-actin-like protein 2 isoform X1, retinol-binding protein-4, alpha-1-antiproteinase, gelsolin isoform, serotransferrin, immunoglobulin kappa-b4 chain-C-region) were significantly expressed by the surgical induction. They characterized cellular process (27%), organization of cellular components or biogenesis (27%), localization (27%) and biological regulation (18%), which related to synovitis, increased cellularity, and subsequently cartilage damage. Three proteins (apolipoprotein I-IV precursor, serpin peptidase inhibitor and haptoglobin precursor) were significantly modified by the chemical induction. They characterized stimulus responses (23%), immune responses (15%), biological regulations (15%), metabolism (15%), organization of cellular components or biogenesis (8%), cellular process (8%), biological adhesions (8%) and localization (8%), which related to chondrocytes glycolysis/death, neovascularization, subchondral bone necrosis/collapse and inflammation. Conclusions The surgical induced OA model showed a wider range of protein changes, which were most upregulated at week 12. The biological process proteins expressions showed the chemical induced joints had slower OA progression compared to surgical induced joints. The chemical induced OA joints sho…
format: application/pdf
format: text/html
creator: Sharifah Zakiah Syed Sulaiman
creator: Wei Miao Tan
creator: Rozanaliza Radzi
creator: Intan Nur Fatiha Shafie
creator: Mokrish Ajat
creator: Rozaihan Mansor
creator: Suhaila Mohamed
creator: Norasfaliza Rahmad
creator: Angela Min Hwei Ng
creator: Seng Fong Lau
subject: Biochemistry
subject: Molecular Biology
subject: Orthopedics
subject: Rheumatology
description: doi:10.7717/peerj.12897
publisher: PeerJ Inc.
rights: © 2022 Syed Sulaiman et al.
abstract: Background Animal models are significant for understanding human osteoarthritis (OA). This study compared the synovial fluid proteomics changes in surgical and chemical induced OA models. Methods Thirty rabbits either had anterior cruciate ligament transection (ACLT) procedure or injected intra-articularly with monosodium iodoacetate (MIA, 8 mg) into the right knee. The joints were anatomically assessed, and the synovial fluid proteins analyzed using two-dimensional polyacrylamide gel electrophoresis (2DGE) and MALDI TOF/TOF mass spectrometry analysis at 4, 8 and 12 weeks. The proteins’ upregulation and downregulation were compared with control healthy knees. Results Seven proteins (histidine-rich glycoprotein, beta-actin-like protein 2 isoform X1, retinol-binding protein-4, alpha-1-antiproteinase, gelsolin isoform, serotransferrin, immunoglobulin kappa-b4 chain-C-region) were significantly expressed by the surgical induction. They characterized cellular process (27%), organization of cellular components or biogenesis (27%), localization (27%) and biological regulation (18%), which related to synovitis, increased cellularity, and subsequently cartilage damage. Three proteins (apolipoprotein I-IV precursor, serpin peptidase inhibitor and haptoglobin precursor) were significantly modified by the chemical induction. They characterized stimulus responses (23%), immune responses (15%), biological regulations (15%), metabolism (15%), organization of cellular components or biogenesis (8%), cellular process (8%), biological adhesions (8%) and localization (8%), which related to chondrocytes glycolysis/death, neovascularization, subchondral bone necrosis/collapse and inflammation. Conclusions The surgical induced OA model showed a wider range of protein changes, which were most upregulated at week 12. The biological process proteins expressions showed the chemical induced joints had slower OA progression compared to surgical induced joints. The chemical induced OA joints sho…
bibliographic citation: Syed Sulaiman et al. (2022) Synovial fluid proteome profile of surgical versus chemical induced osteoarthritis in rabbits. PeerJ 10:e12897 https://doi.org/10.7717/peerj.12897
date submitted: 2021-06-04
date accepted: 2022-01-16
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Syed Sulaiman
  given name: Sharifah Zakiah
author list: Agent
  family name: Tan
  given name: Wei Miao
author list: Agent
  family name: Radzi
  given name: Rozanaliza
author list: Agent
  family name: Shafie
  given name: Intan Nur Fatiha
author list: Agent
  family name: Ajat
  given name: Mokrish
author list: Agent
  family name: Mansor
  given name: Rozaihan
author list: Agent
  family name: Mohamed
  given name: Suhaila
author list: Agent
  family name: Rahmad
  given name: Norasfaliza
author list: Agent
  family name: Ng
  given name: Angela Min Hwei
author list: Agent
  family name: Lau
  given name: Seng Fong
doi: 10.7717/peerj.12897
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Syed Sulaiman et al.
attribution name: Syed Sulaiman et al.

Efficacy of brain natriuretic peptide vs. nicorandil in preventing contrast-induced nephropathy: a network meta-analysis
type: item
type: AcademicArticle
description: This study aimed to conduct a network meta-analysis (NMA) to compare the efficacy of brain natriuretic peptide (BNP) vs nicorandil for preventing contrast-induced nephropathy (CIN). Databases of Pubmed, Cochrane, Embase, Web of Science were searched by keywords for eligible studies of randomized controlled trials investigating different agents (BNP, nicorandil, nitroglycerin, intravenous saline) for preventing CIN. The outcomes included a change in serum creatinine level at 48 h and the incidence of CIN after percutaneous coronary intervention (PCI) or coronary angiography (CAG). A total of 13 studies with 3,462 patients were included. Compared with intravenous saline alone, except for nitroglycerin (odds ratio [OR]: 1.02, 95% CI [0.36–2.88]), the other drugs significantly reduced the CIN incidence with OR of 0.35 (95% CI [0.24–0.51]) for BNP, 0.52 (0.29, 0.94) for usual-dose nicorandil, 0.28 (0.19, 0.43) for double-dose nicorandil. BNP and double-dose nicorandil significantly decreased the change of serum creatinine (SCr) levels with mean difference (MD) of −6.98, (−10.01, −3.95) for BNP, −8.78, (−11.63, −5.93) for double-dose nicorandil. No significant differences were observed in the change of SCr levels for nitroglycerin (−4.97, [−11.46, 1.52]) and usual-dose nicorandil (−2.32, [−5.52, 0.89]) compared with intravenous saline alone. For double-dose nicorandil, the CIN incidence and the change of SCr level in group of 4–5 days treatment course were more than group of less than or equal to 24 h treatment course (OR of 1.48, [0.63–3.46] and MD of 2.48, [−1.96, 6.91]). In conclusion, BNP and double-dose nicorandil can have effects on preventing the incidence of CIN and double-dose nicorandil performed better than BNP. In double-dose nicorandil groups, a course of less than or equal to 24 h before and after procedure performed with better efficacy than a course of 4–5 days.
format: application/pdf
format: text/html
creator: Ziwei Mei
creator: Songmei Luo
creator: Peipei Chen
creator: Qiankun Zhang
creator: Limei Zhou
creator: Chaoyong Zhu
creator: Hong Zhu
creator: Lie Jin
subject: Biochemistry
subject: Diabetes and Endocrinology
subject: Nephrology
subject: Pharmacology
description: doi:10.7717/peerj.12975
publisher: PeerJ Inc.
rights: © 2022 Mei et al.
abstract: This study aimed to conduct a network meta-analysis (NMA) to compare the efficacy of brain natriuretic peptide (BNP) vs nicorandil for preventing contrast-induced nephropathy (CIN). Databases of Pubmed, Cochrane, Embase, Web of Science were searched by keywords for eligible studies of randomized controlled trials investigating different agents (BNP, nicorandil, nitroglycerin, intravenous saline) for preventing CIN. The outcomes included a change in serum creatinine level at 48 h and the incidence of CIN after percutaneous coronary intervention (PCI) or coronary angiography (CAG). A total of 13 studies with 3,462 patients were included. Compared with intravenous saline alone, except for nitroglycerin (odds ratio [OR]: 1.02, 95% CI [0.36–2.88]), the other drugs significantly reduced the CIN incidence with OR of 0.35 (95% CI [0.24–0.51]) for BNP, 0.52 (0.29, 0.94) for usual-dose nicorandil, 0.28 (0.19, 0.43) for double-dose nicorandil. BNP and double-dose nicorandil significantly decreased the change of serum creatinine (SCr) levels with mean difference (MD) of −6.98, (−10.01, −3.95) for BNP, −8.78, (−11.63, −5.93) for double-dose nicorandil. No significant differences were observed in the change of SCr levels for nitroglycerin (−4.97, [−11.46, 1.52]) and usual-dose nicorandil (−2.32, [−5.52, 0.89]) compared with intravenous saline alone. For double-dose nicorandil, the CIN incidence and the change of SCr level in group of 4–5 days treatment course were more than group of less than or equal to 24 h treatment course (OR of 1.48, [0.63–3.46] and MD of 2.48, [−1.96, 6.91]). In conclusion, BNP and double-dose nicorandil can have effects on preventing the incidence of CIN and double-dose nicorandil performed better than BNP. In double-dose nicorandil groups, a course of less than or equal to 24 h before and after procedure performed with better efficacy than a course of 4–5 days.
bibliographic citation: Mei et al. (2022) Efficacy of brain natriuretic peptide vs. nicorandil in preventing contrast-induced nephropathy: a network meta-analysis. PeerJ 10:e12975 https://doi.org/10.7717/peerj.12975
date submitted: 2021-11-23
date accepted: 2022-01-31
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mei
  given name: Ziwei
author list: Agent
  family name: Luo
  given name: Songmei
author list: Agent
  family name: Chen
  given name: Peipei
author list: Agent
  family name: Zhang
  given name: Qiankun
author list: Agent
  family name: Zhou
  given name: Limei
author list: Agent
  family name: Zhu
  given name: Chaoyong
author list: Agent
  family name: Zhu
  given name: Hong
author list: Agent
  family name: Jin
  given name: Lie
doi: 10.7717/peerj.12975
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Mei et al.
attribution name: Mei et al.

Disentangling bias for non-destructive insect metabarcoding
type: item
type: AcademicArticle
description: A fast and reliable method for obtaining a species-level identification is a fundamental requirement for a wide range of activities, from plant protection and invasive species management to biodiversity assessments and ecological studies. For insects, novel molecular techniques such as DNA metabarcoding have emerged as a rapid alternative to traditional morphological identification, reducing the dependence on limited taxonomic experts. Until recently, molecular techniques have required a destructive DNA extraction, precluding the possibility of preserving voucher specimens for future studies, or species descriptions. Here we paired insect metabarcoding with two recent non-destructive DNA extraction protocols, to obtain a rapid and high-throughput taxonomic identification of diverse insect taxa while retaining a physical voucher specimen. The aim of this work was to explore how non-destructive extraction protocols impact the semi-quantitative nature of metabarcoding, which alongside species presence/absence also provides a quantitative, but biased, representation of their relative abundances. By using a series of mock communities representing each stage of a typical metabarcoding workflow we were able to determine how different morphological (i.e., insect biomass and exoskeleton hardness) and molecular traits (i.e., primer mismatch and amplicon GC%), interact with different protocol steps to introduce quantitative bias into non-destructive metabarcoding results. We discuss the relevance of taxonomic bias to metabarcoding identification of insects and potential approaches to account for it.
format: application/pdf
format: text/html
creator: Francesco Martoni
creator: Alexander M. Piper
creator: Brendan C. Rodoni
creator: Mark J. Blacket
subject: Bioinformatics
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.12981
publisher: PeerJ Inc.
rights: © 2022 Martoni et al.
abstract: A fast and reliable method for obtaining a species-level identification is a fundamental requirement for a wide range of activities, from plant protection and invasive species management to biodiversity assessments and ecological studies. For insects, novel molecular techniques such as DNA metabarcoding have emerged as a rapid alternative to traditional morphological identification, reducing the dependence on limited taxonomic experts. Until recently, molecular techniques have required a destructive DNA extraction, precluding the possibility of preserving voucher specimens for future studies, or species descriptions. Here we paired insect metabarcoding with two recent non-destructive DNA extraction protocols, to obtain a rapid and high-throughput taxonomic identification of diverse insect taxa while retaining a physical voucher specimen. The aim of this work was to explore how non-destructive extraction protocols impact the semi-quantitative nature of metabarcoding, which alongside species presence/absence also provides a quantitative, but biased, representation of their relative abundances. By using a series of mock communities representing each stage of a typical metabarcoding workflow we were able to determine how different morphological (i.e., insect biomass and exoskeleton hardness) and molecular traits (i.e., primer mismatch and amplicon GC%), interact with different protocol steps to introduce quantitative bias into non-destructive metabarcoding results. We discuss the relevance of taxonomic bias to metabarcoding identification of insects and potential approaches to account for it.
bibliographic citation: Martoni et al. (2022) Disentangling bias for non-destructive insect metabarcoding. PeerJ 10:e12981 https://doi.org/10.7717/peerj.12981
date submitted: 2021-10-01
date accepted: 2022-02-01
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martoni
  given name: Francesco
author list: Agent
  family name: Piper
  given name: Alexander M.
author list: Agent
  family name: Rodoni
  given name: Brendan C.
author list: Agent
  family name: Blacket
  given name: Mark J.
doi: 10.7717/peerj.12981
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: © 2022 Martoni et al.
attribution name: Martoni et al.

Microbial biogeography of the wombat gastrointestinal tract
type: item
type: AcademicArticle
description: Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on samples collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat (Vombatus ursinus) and a single southern hairy-nosed wombat (Lasiorhinus latifrons). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat individuals, we observed a trend of increasing microbial diversity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal samples). Surprisingly, only 10.6% (98) and 18.8% (206) of amplicon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region—the putative site of primary plant fermentation in wombats—are distinct from the distal colon, and that faecal sample…
format: application/pdf
format: text/html
creator: Raphael Eisenhofer
creator: Erin D’Agnese
creator: David Taggart
creator: Scott Carver
creator: Beth Penrose
subject: Biodiversity
subject: Biogeography
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.12982
publisher: PeerJ Inc.
rights: © 2022 Eisenhofer et al.
abstract: Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on samples collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat (Vombatus ursinus) and a single southern hairy-nosed wombat (Lasiorhinus latifrons). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat individuals, we observed a trend of increasing microbial diversity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal samples). Surprisingly, only 10.6% (98) and 18.8% (206) of amplicon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region—the putative site of primary plant fermentation in wombats—are distinct from the distal colon, and that faecal sample…
bibliographic citation: Eisenhofer et al. (2022) Microbial biogeography of the wombat gastrointestinal tract. PeerJ 10:e12982 https://doi.org/10.7717/peerj.12982
date submitted: 2021-09-15
date accepted: 2022-02-01
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eisenhofer
  given name: Raphael
author list: Agent
  family name: D’Agnese
  given name: Erin
author list: Agent
  family name: Taggart
  given name: David
author list: Agent
  family name: Carver
  given name: Scott
author list: Agent
  family name: Penrose
  given name: Beth
doi: 10.7717/peerj.12982
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Eisenhofer et al.
attribution name: Eisenhofer et al.

A noninvasive and comprehensive method for continuous assessment of cerebral blood flow pulsation based on magnetic induction phase shift
type: item
type: AcademicArticle
description: Cerebral blood flow (CBF) monitoring is of great significance for treating and preventing strokes. However, there has not been a fully accepted method targeting continuous assessment in clinical practice. In this work, we built a noninvasive continuous assessment system for cerebral blood flow pulsation (CBFP) that is based on magnetic induction phase shift (MIPS) technology and designed a physical model of the middle cerebral artery (MCA). Physical experiments were carried out through different simulations of CBF states. Four healthy volunteers were enrolled to perform the MIPS and ECG synchronously monitoring trials. Then, the components of MIPS related to the blood supply level and CBFP were investigated by signal analysis in time and frequency domain, wavelet decomposition and band-pass filtering. The results show that the time-domain baseline of MIPS increases with blood supply level. A pulse signal was identified in the spectrum (0.2–2 Hz in 200–2,000 ml/h groups, respectively) of MIPS when the simulated blood flow rate was not zero. The pulsation frequency with different simulated blood flow rates is the same as the squeezing frequency of the feeding pump. Similar to pulse waves, the MIPS signals on four healthy volunteers all had periodic change trends with obvious peaks and valleys. Its frequency is close to that of the ECG signal and there is a certain time delay between them. These results indicate that the CBFP component can effectively be extracted from MIPS, through which different blood supply levels can be distinguished. This method has the potential to become a new solution for non-invasive and comprehensive monitoring of CBFP.
format: application/pdf
format: text/html
creator: Lingxi Zeng
creator: Gen Li
creator: Maoting Zhang
creator: Rui Zhu
creator: Jingbo Chen
creator: Mingyan Li
creator: Shengtong Yin
creator: Zelin Bai
creator: Wei Zhuang
creator: Jian Sun
subject: Bioengineering
subject: Biophysics
subject: Neuroscience
subject: Neurology
description: doi:10.7717/peerj.13002
publisher: PeerJ Inc.
rights: © 2022 Zeng et al.
abstract: Cerebral blood flow (CBF) monitoring is of great significance for treating and preventing strokes. However, there has not been a fully accepted method targeting continuous assessment in clinical practice. In this work, we built a noninvasive continuous assessment system for cerebral blood flow pulsation (CBFP) that is based on magnetic induction phase shift (MIPS) technology and designed a physical model of the middle cerebral artery (MCA). Physical experiments were carried out through different simulations of CBF states. Four healthy volunteers were enrolled to perform the MIPS and ECG synchronously monitoring trials. Then, the components of MIPS related to the blood supply level and CBFP were investigated by signal analysis in time and frequency domain, wavelet decomposition and band-pass filtering. The results show that the time-domain baseline of MIPS increases with blood supply level. A pulse signal was identified in the spectrum (0.2–2 Hz in 200–2,000 ml/h groups, respectively) of MIPS when the simulated blood flow rate was not zero. The pulsation frequency with different simulated blood flow rates is the same as the squeezing frequency of the feeding pump. Similar to pulse waves, the MIPS signals on four healthy volunteers all had periodic change trends with obvious peaks and valleys. Its frequency is close to that of the ECG signal and there is a certain time delay between them. These results indicate that the CBFP component can effectively be extracted from MIPS, through which different blood supply levels can be distinguished. This method has the potential to become a new solution for non-invasive and comprehensive monitoring of CBFP.
bibliographic citation: Zeng et al. (2022) A noninvasive and comprehensive method for continuous assessment of cerebral blood flow pulsation based on magnetic induction phase shift. PeerJ 10:e13002 https://doi.org/10.7717/peerj.13002
date submitted: 2021-11-08
date accepted: 2022-02-03
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zeng
  given name: Lingxi
author list: Agent
  family name: Li
  given name: Gen
author list: Agent
  family name: Zhang
  given name: Maoting
author list: Agent
  family name: Zhu
  given name: Rui
author list: Agent
  family name: Chen
  given name: Jingbo
author list: Agent
  family name: Li
  given name: Mingyan
author list: Agent
  family name: Yin
  given name: Shengtong
author list: Agent
  family name: Bai
  given name: Zelin
author list: Agent
  family name: Zhuang
  given name: Wei
author list: Agent
  family name: Sun
  given name: Jian
doi: 10.7717/peerj.13002
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: © 2022 Zeng et al.
attribution name: Zeng et al.

Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum
type: item
type: AcademicArticle
description: Fusarium oxysporum f. sp. cubense (FOC4) is a pathogen of banana fusarium wilt, which is a serious problem that has plagued the tropical banana industry for many years. The pathogenic mechanism is complex and unclear, so the prevention and control in agricultural production applications is ineffective. SNP-D4, an artificial peptide aptamer, was identified and specifically inhibited FOC4. To evaluate the efficacy of SNP-D4, FoC4 spores were treated with purified SNP-D4 to calculate the germination and fungicide rates. Damage of FOC4 spores was observed by staining with propidium iodide (PI). Eight proteins of FOC4 were identified to have high affinity for SNP-D4 by a pull-down method combined with Q-Exactive mass spectrometry. Of these eight proteins, A0A5C6SPC6, the aldehyde dehydrogenase of FOC4, was selected as an example to scrutinize the interaction sites with SNP-D4. Molecular docking revealed that Thr66 on the peptide loop of SNP-D4 bound with Tyr437 near the catalytic center of A0A5C6SPC6. Subsequently 42 spore proteins which exhibited associations with the eight proteins were retrieved for protein-protein interaction analysis, demonstrating that SNP-D4 interfered with pathways including ‘translation’, ‘folding, sorting and degradation’, ‘transcription’, ‘signal transduction’ and ‘cell growth and death’, eventually causing the inhibition of growth of FOC4. This study not only investigated the possible pathogenic mechanism of FOC4, but also provided a potential antifungal agent SNP-D4 for use in the control of banana wilt disease.
format: application/pdf
format: text/html
creator: Junjun Huang
creator: Dan Wang
creator: Hong Li
creator: Yanqiong Tang
creator: Xiang Ma
creator: Hongqian Tang
creator: Min Lin
creator: Zhu Liu
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.12756
publisher: PeerJ Inc.
rights: © 2022 Huang et al.
abstract: Fusarium oxysporum f. sp. cubense (FOC4) is a pathogen of banana fusarium wilt, which is a serious problem that has plagued the tropical banana industry for many years. The pathogenic mechanism is complex and unclear, so the prevention and control in agricultural production applications is ineffective. SNP-D4, an artificial peptide aptamer, was identified and specifically inhibited FOC4. To evaluate the efficacy of SNP-D4, FoC4 spores were treated with purified SNP-D4 to calculate the germination and fungicide rates. Damage of FOC4 spores was observed by staining with propidium iodide (PI). Eight proteins of FOC4 were identified to have high affinity for SNP-D4 by a pull-down method combined with Q-Exactive mass spectrometry. Of these eight proteins, A0A5C6SPC6, the aldehyde dehydrogenase of FOC4, was selected as an example to scrutinize the interaction sites with SNP-D4. Molecular docking revealed that Thr66 on the peptide loop of SNP-D4 bound with Tyr437 near the catalytic center of A0A5C6SPC6. Subsequently 42 spore proteins which exhibited associations with the eight proteins were retrieved for protein-protein interaction analysis, demonstrating that SNP-D4 interfered with pathways including ‘translation’, ‘folding, sorting and degradation’, ‘transcription’, ‘signal transduction’ and ‘cell growth and death’, eventually causing the inhibition of growth of FOC4. This study not only investigated the possible pathogenic mechanism of FOC4, but also provided a potential antifungal agent SNP-D4 for use in the control of banana wilt disease.
bibliographic citation: Huang et al. (2022) Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum. PeerJ 10:e12756 https://doi.org/10.7717/peerj.12756
date submitted: 2021-08-30
date accepted: 2021-12-16
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Junjun
author list: Agent
  family name: Wang
  given name: Dan
author list: Agent
  family name: Li
  given name: Hong
author list: Agent
  family name: Tang
  given name: Yanqiong
author list: Agent
  family name: Ma
  given name: Xiang
author list: Agent
  family name: Tang
  given name: Hongqian
author list: Agent
  family name: Lin
  given name: Min
author list: Agent
  family name: Liu
  given name: Zhu
doi: 10.7717/peerj.12756
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: © 2022 Huang et al.
attribution name: Huang et al.

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