PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Paleomass for R—bracketing body volume of marine vertebrates with 3D models
items: Effects of drought and salt stress on seed germination and seedling growth of Elymus nutans
items: Understanding mental fatigue and its detection: a comparative analysis of assessments and tools
items: Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD)
items: Calcification detection on upper extremity arteries: a comparison of ultrasonic and X-ray methods
items: Evaluation of the validity of the HPV viral load compared to conventional techniques for the detection of high-grade anal intraepithelial lesions in men with HIV who have sex with men
items: CTRP3 attenuates inflammation, oxidative and cell death in cisplatin induced HK-2 cells
items: No genetic causal association between dental caries and Alzheimer’s disease: a bidirectional two-sample Mendelian randomization analysis
items: Farmers’ perception of the ecosystem services provided by diurnal raptors in arid Rajasthan
items: Comparative genomics of bacteria from amphibian skin associated with inhibition of an amphibian fungal pathogen, Batrachochytrium dendrobatidis

Paleomass for R—bracketing body volume of marine vertebrates with 3D models
type: item
type: AcademicArticle
description: Body mass is arguably the most important characteristic of an organism, yet it is often not available in biological samples that have been skeletonized, liquid-preserved, or fossilized. The lack of information is especially problematic for fossil species, for which individuals with body mass information are not available anywhere. Multiple methods are available for estimating the body mass of fossil terrestrial vertebrates but those for their marine counterparts are limited. Paleomass is a software tool for estimating the body mass of marine vertebrates from their orthogonal silhouettes through bracketing. It generates a set of two 3D models from these silhouettes, assuming superelliptical body cross-sections with different exponent values. By setting the exponents appropriately, it is possible to bracket the true volume of the animal between those of the two models. The original version phased out together with the language platform it used. A new version is reported here as an open-source package based on the R scripting language. It inherits the underlying principles of the original version but has been completely rewritten with a new architecture. For example, it first produces 3D mesh models of the animal and then measures their volumes and areas with the VCG library, unlike the original version that did not produce a 3D model but instead computed the volume and area segment by segment using parametric equations. The new version also exports 3D models in polygon meshes, allowing later tests by other software. Other improvements include the use of NACA foil sections for hydrofoils such as flippers, and optional interpolation with local regression. The software has a high accuracy, with the mean absolute errors of 1.33% when the silhouettes of the animals are known.
format: application/pdf
format: text/html
creator: Ryosuke Motani
subject: Bioinformatics
subject: Ecology
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
description: doi:10.7717/peerj.15957
publisher: PeerJ Inc.
rights: © 2023 Motani
abstract: Body mass is arguably the most important characteristic of an organism, yet it is often not available in biological samples that have been skeletonized, liquid-preserved, or fossilized. The lack of information is especially problematic for fossil species, for which individuals with body mass information are not available anywhere. Multiple methods are available for estimating the body mass of fossil terrestrial vertebrates but those for their marine counterparts are limited. Paleomass is a software tool for estimating the body mass of marine vertebrates from their orthogonal silhouettes through bracketing. It generates a set of two 3D models from these silhouettes, assuming superelliptical body cross-sections with different exponent values. By setting the exponents appropriately, it is possible to bracket the true volume of the animal between those of the two models. The original version phased out together with the language platform it used. A new version is reported here as an open-source package based on the R scripting language. It inherits the underlying principles of the original version but has been completely rewritten with a new architecture. For example, it first produces 3D mesh models of the animal and then measures their volumes and areas with the VCG library, unlike the original version that did not produce a 3D model but instead computed the volume and area segment by segment using parametric equations. The new version also exports 3D models in polygon meshes, allowing later tests by other software. Other improvements include the use of NACA foil sections for hydrofoils such as flippers, and optional interpolation with local regression. The software has a high accuracy, with the mean absolute errors of 1.33% when the silhouettes of the animals are known.
bibliographic citation: Motani (2023) Paleomass for R—bracketing body volume of marine vertebrates with 3D models. PeerJ 11:e15957 https://doi.org/10.7717/peerj.15957
date submitted: 2023-06-23
date accepted: 2023-08-03
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Motani
  given name: Ryosuke
doi: 10.7717/peerj.15957
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: © 2023 Motani
attribution name: Motani

Effects of drought and salt stress on seed germination and seedling growth of Elymus nutans
type: item
type: AcademicArticle
description: Drought and soil salinization are global environmental issues, and Elymus nutans play an important role in vegetation restoration in arid and saline environments due to their excellent stress resistance. In the process of vegetation restoration, the stage from germination to seedling growth of forage is crucial. This experiment studied the effects of PEG-6000 simulated drought stress and NaCl simulated salinization stress on the germination of E. nutans seeds, and explored the growth of forage seedlings from sowing to 28 days under drought and salinization stress conditions. The results showed that under the same environmental water potential, there were significant differences in responses of seed germination, seedling growth, organic carbon, total nitrogen and total phosphorus of above-ground and underground parts of E. nutans to drought stress and salinization stress. Using the membership function method to comprehensively evaluate the seed germination and seedling indicators of E. nutans, it was found that under the same environmental water potential, E. nutans was more severely affected by drought stress during both the seed germination and seedling growth stages. E. nutans showed better salt tolerance than drought resistance.
format: application/pdf
format: text/html
creator: Jianting Long
creator: Mengjie Dong
creator: Chuanqi Wang
creator: Yanjun Miao
subject: Agricultural Science
subject: Plant Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.15968
publisher: PeerJ Inc.
rights: © 2023 Long et al.
abstract: Drought and soil salinization are global environmental issues, and Elymus nutans play an important role in vegetation restoration in arid and saline environments due to their excellent stress resistance. In the process of vegetation restoration, the stage from germination to seedling growth of forage is crucial. This experiment studied the effects of PEG-6000 simulated drought stress and NaCl simulated salinization stress on the germination of E. nutans seeds, and explored the growth of forage seedlings from sowing to 28 days under drought and salinization stress conditions. The results showed that under the same environmental water potential, there were significant differences in responses of seed germination, seedling growth, organic carbon, total nitrogen and total phosphorus of above-ground and underground parts of E. nutans to drought stress and salinization stress. Using the membership function method to comprehensively evaluate the seed germination and seedling indicators of E. nutans, it was found that under the same environmental water potential, E. nutans was more severely affected by drought stress during both the seed germination and seedling growth stages. E. nutans showed better salt tolerance than drought resistance.
bibliographic citation: Long et al. (2023) Effects of drought and salt stress on seed germination and seedling growth of Elymus nutans. PeerJ 11:e15968 https://doi.org/10.7717/peerj.15968
date submitted: 2023-03-14
date accepted: 2023-08-04
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Long
  given name: Jianting
author list: Agent
  family name: Dong
  given name: Mengjie
author list: Agent
  family name: Wang
  given name: Chuanqi
author list: Agent
  family name: Miao
  given name: Yanjun
doi: 10.7717/peerj.15968
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: © 2023 Long et al.
attribution name: Long et al.

Understanding mental fatigue and its detection: a comparative analysis of assessments and tools
type: item
type: AcademicArticle
description: Mental fatigue has shown to be one of the root causes of decreased productivity and overall cognitive performance, by decreasing an individual’s ability to inhibit responses, process information and concentrate. The effects of mental fatigue have led to occupational errors and motorway accidents. Early detection of mental fatigue can prevent the escalation of symptoms that may lead to chronic fatigue syndrome and other disorders. To date, in clinical settings, the assessment of mental fatigue and stress is done through self-reported questionnaires. The validity of these questionnaires is questionable, as they are highly subjective measurement tools and are not immune to response biases. This review examines the wider presence of mental fatigue in the general population and critically compares its various detection techniques (i.e., self-reporting questionnaires, heart rate variability, salivary cortisol levels, electroencephalogram, and saccadic eye movements). The ability of these detection tools to assess inhibition responses (which are sensitive enough to be manifested in a fatigue state) is specifically evaluated for a reliable marker in identifying mentally fatigued individuals. In laboratory settings, antisaccade tasks have been long used to assess inhibitory control and this technique can potentially serve as the most promising assessment tool to objectively detect mental fatigue. However, more studies need to be conducted in the future to validate and correlate this assessment with other existing measures of mental fatigue detection. This review is intended for, but not limited to, mental health professionals, digital health scientists, vision researchers, and behavioral scientists.
format: application/pdf
format: text/html
creator: Kaveena Kunasegaran
creator: Ahamed Miflah Hussain Ismail
creator: Shamala Ramasamy
creator: Justin Vijay Gnanou
creator: Brinnell Annette Caszo
creator: Po Ling Chen
subject: Neuroscience
subject: Ophthalmology
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.15744
publisher: PeerJ Inc.
rights: © 2023 Kunasegaran et al.
abstract: Mental fatigue has shown to be one of the root causes of decreased productivity and overall cognitive performance, by decreasing an individual’s ability to inhibit responses, process information and concentrate. The effects of mental fatigue have led to occupational errors and motorway accidents. Early detection of mental fatigue can prevent the escalation of symptoms that may lead to chronic fatigue syndrome and other disorders. To date, in clinical settings, the assessment of mental fatigue and stress is done through self-reported questionnaires. The validity of these questionnaires is questionable, as they are highly subjective measurement tools and are not immune to response biases. This review examines the wider presence of mental fatigue in the general population and critically compares its various detection techniques (i.e., self-reporting questionnaires, heart rate variability, salivary cortisol levels, electroencephalogram, and saccadic eye movements). The ability of these detection tools to assess inhibition responses (which are sensitive enough to be manifested in a fatigue state) is specifically evaluated for a reliable marker in identifying mentally fatigued individuals. In laboratory settings, antisaccade tasks have been long used to assess inhibitory control and this technique can potentially serve as the most promising assessment tool to objectively detect mental fatigue. However, more studies need to be conducted in the future to validate and correlate this assessment with other existing measures of mental fatigue detection. This review is intended for, but not limited to, mental health professionals, digital health scientists, vision researchers, and behavioral scientists.
bibliographic citation: Kunasegaran et al. (2023) Understanding mental fatigue and its detection: a comparative analysis of assessments and tools. PeerJ 11:e15744 https://doi.org/10.7717/peerj.15744
date submitted: 2023-02-09
date accepted: 2023-06-21
issued: 2023-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kunasegaran
  given name: Kaveena
author list: Agent
  family name: Ismail
  given name: Ahamed Miflah Hussain
author list: Agent
  family name: Ramasamy
  given name: Shamala
author list: Agent
  family name: Gnanou
  given name: Justin Vijay
author list: Agent
  family name: Caszo
  given name: Brinnell Annette
author list: Agent
  family name: Chen
  given name: Po Ling
doi: 10.7717/peerj.15744
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-23
copyright: © 2023 Kunasegaran et al.
attribution name: Kunasegaran et al.

Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD)
type: item
type: AcademicArticle
description: Effective treatment and prevention of any disease necessitates knowledge of the causative agent, yet the causative agents of most coral diseases remain unknown, in part due to the difficulty of distinguishing the pathogenic microbe(s) among the complex microbial backdrop of coral hosts. Stony coral tissue loss disease (SCTLD) is a particularly destructive disease of unknown etiology, capable of transmitting through the water column and killing entire colonies within a matter of weeks. Here we used a previously described method to (i) isolate diseased and apparently healthy coral colonies within individual mesocosms containing filtered seawater with low microbial background levels; (ii) incubate for several days to enrich the water with coral-shed microbes; (iii) use tangential-flow filtration to concentrate the microbial community in the mesocosm water; and then (iv) filter the resulting concentrate through a sequential series of different pore-sized filters. To investigate the size class of microorganism(s) associated with SCTLD transmission, we used 0.8 µm pore size filters to capture microeukaryotes and expelled zooxanthellae, 0.22 µm pore size filters to capture bacteria and large viruses, and 0.025 µm pore size filters to capture smaller viruses. In an attempt to further refine which size fraction(s) contained the transmissible element of SCTLD, we then applied these filters to healthy “receiver” coral fragments and monitored them for the onset of SCTLD signs over three separate experimental runs. However, several factors outside of our control confounded the transmission results, rendering them inconclusive. As the bulk of prior studies of SCTLD in coral tissues have primarily investigated the associated bacterial community, we chose to characterize the prokaryotic community associated with all mesocosm 0.22 µm pore size filters using Illumina sequencing of the V4 region of the 16S rRNA gene. We identified overlaps with prior SCTLD studies, including the prese…
format: application/pdf
format: text/html
creator: James S. Evans
creator: Valerie J. Paul
creator: Blake Ushijima
creator: Kelly A. Pitts
creator: Christina A. Kellogg
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.15836
publisher: PeerJ Inc.
rights: © 2023
abstract: Effective treatment and prevention of any disease necessitates knowledge of the causative agent, yet the causative agents of most coral diseases remain unknown, in part due to the difficulty of distinguishing the pathogenic microbe(s) among the complex microbial backdrop of coral hosts. Stony coral tissue loss disease (SCTLD) is a particularly destructive disease of unknown etiology, capable of transmitting through the water column and killing entire colonies within a matter of weeks. Here we used a previously described method to (i) isolate diseased and apparently healthy coral colonies within individual mesocosms containing filtered seawater with low microbial background levels; (ii) incubate for several days to enrich the water with coral-shed microbes; (iii) use tangential-flow filtration to concentrate the microbial community in the mesocosm water; and then (iv) filter the resulting concentrate through a sequential series of different pore-sized filters. To investigate the size class of microorganism(s) associated with SCTLD transmission, we used 0.8 µm pore size filters to capture microeukaryotes and expelled zooxanthellae, 0.22 µm pore size filters to capture bacteria and large viruses, and 0.025 µm pore size filters to capture smaller viruses. In an attempt to further refine which size fraction(s) contained the transmissible element of SCTLD, we then applied these filters to healthy “receiver” coral fragments and monitored them for the onset of SCTLD signs over three separate experimental runs. However, several factors outside of our control confounded the transmission results, rendering them inconclusive. As the bulk of prior studies of SCTLD in coral tissues have primarily investigated the associated bacterial community, we chose to characterize the prokaryotic community associated with all mesocosm 0.22 µm pore size filters using Illumina sequencing of the V4 region of the 16S rRNA gene. We identified overlaps with prior SCTLD studies, including the prese…
bibliographic citation: Evans et al. (2023) Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD). PeerJ 11:e15836 https://doi.org/10.7717/peerj.15836
date submitted: 2023-01-26
date accepted: 2023-07-11
issued: 2023-08-23
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Evans
  given name: James S.
author list: Agent
  family name: Paul
  given name: Valerie J.
author list: Agent
  family name: Ushijima
  given name: Blake
author list: Agent
  family name: Pitts
  given name: Kelly A.
author list: Agent
  family name: Kellogg
  given name: Christina A.
doi: 10.7717/peerj.15836
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-23

Calcification detection on upper extremity arteries: a comparison of ultrasonic and X-ray methods
type: item
type: AcademicArticle
description: Background Vascular calcification (VC) has been observed in patients with hemodialysis, whereas few studies have investigated calcification in the upper extremity vasculature. Both ultrasound and X-ray are used to investigate the calcification of arteries in patients. However, there is a lack of data on the consistency between these two methods. The aim of this study was to investigate the occurrence of VC in the radial and ulnar arteries of hemodialysis patients and investigate the detection consistency in VC between ultrasound and X-ray. Methods Ultrasound and X-ray examinations were performed in the radial and ulnar arteries of both the left and right upper extremities of 40 patients on hemodialysis. The calcification status of arteries was evaluated by the calcification index from ultrasound and X-ray respectively. Clinical variables of patients were collected from all the involved patients. Results Of the 40 patients, VC was detected in 31 patients by ultrasound, while X-ray detected VC in 22 patients. Compared to ultrasound assessment, X-ray assessment was 73.21% sensitive but only 66.35% specific with a positive predictive value of 53.95% for detecting calcifications in the radial or ulnar artery. The level of agreement between ultrasound and X-ray results was fair. In addition, our data showed that more ulnar arteries had VCs than the corresponding radial arteries. Conclusion Ultrasound is more sensitive in detecting the presence of calcified atherosclerotic lesions. Ultrasound and X-ray exhibited fair consistency. Ultrasound screening for upper extremity radial and ulnar arteries in hemodialysis patients may deserve attention to explore its clinical significance.
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creator: Yanli Yang
creator: Na Lin
creator: Yuankai Xu
creator: Zheli Niu
creator: Fulei Meng
creator: Kaidi Zhang
creator: Yuhuan Wang
creator: Lin Ruan
creator: Lihong Zhang
subject: Cardiology
subject: Internal Medicine
subject: Nephrology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.15855
publisher: PeerJ Inc.
rights: © 2023 Yang et al.
abstract: Background Vascular calcification (VC) has been observed in patients with hemodialysis, whereas few studies have investigated calcification in the upper extremity vasculature. Both ultrasound and X-ray are used to investigate the calcification of arteries in patients. However, there is a lack of data on the consistency between these two methods. The aim of this study was to investigate the occurrence of VC in the radial and ulnar arteries of hemodialysis patients and investigate the detection consistency in VC between ultrasound and X-ray. Methods Ultrasound and X-ray examinations were performed in the radial and ulnar arteries of both the left and right upper extremities of 40 patients on hemodialysis. The calcification status of arteries was evaluated by the calcification index from ultrasound and X-ray respectively. Clinical variables of patients were collected from all the involved patients. Results Of the 40 patients, VC was detected in 31 patients by ultrasound, while X-ray detected VC in 22 patients. Compared to ultrasound assessment, X-ray assessment was 73.21% sensitive but only 66.35% specific with a positive predictive value of 53.95% for detecting calcifications in the radial or ulnar artery. The level of agreement between ultrasound and X-ray results was fair. In addition, our data showed that more ulnar arteries had VCs than the corresponding radial arteries. Conclusion Ultrasound is more sensitive in detecting the presence of calcified atherosclerotic lesions. Ultrasound and X-ray exhibited fair consistency. Ultrasound screening for upper extremity radial and ulnar arteries in hemodialysis patients may deserve attention to explore its clinical significance.
bibliographic citation: Yang et al. (2023) Calcification detection on upper extremity arteries: a comparison of ultrasonic and X-ray methods. PeerJ 11:e15855 https://doi.org/10.7717/peerj.15855
date submitted: 2023-03-20
date accepted: 2023-07-16
issued: 2023-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yanli
author list: Agent
  family name: Lin
  given name: Na
author list: Agent
  family name: Xu
  given name: Yuankai
author list: Agent
  family name: Niu
  given name: Zheli
author list: Agent
  family name: Meng
  given name: Fulei
author list: Agent
  family name: Zhang
  given name: Kaidi
author list: Agent
  family name: Wang
  given name: Yuhuan
author list: Agent
  family name: Ruan
  given name: Lin
author list: Agent
  family name: Zhang
  given name: Lihong
doi: 10.7717/peerj.15855
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-23
copyright: ©2023 Yang et al.
attribution name: Yang et al.

Evaluation of the validity of the HPV viral load compared to conventional techniques for the detection of high-grade anal intraepithelial lesions in men with HIV who have sex with men
type: item
type: AcademicArticle
description: Background The incidence of high-grade anal intraepithelial lesions (HSILs) has increased in recent years among men who have sex with men with human immunodeficiency virus (HIV). This work evaluated the validity of the human papilloma virus viral load (HPV-VL) versus cytological and qualitative HPV results to detect HSILs. Methods From May 2017 to January 2020, 93 men who have sex with men and HIV were included in an anal cancer screening program from the Infectious Diseases Unit at a tertiary-care hospital in Alicante (Spain). The gold-standard for the screening of anal HSILs is the anal biopsy using high-resolution anoscopy. The diagnostic methods compared against gold-standard were HPV-16-VL, HPV-18-VL, and HPV-16-18-VL co-testing, anal cytology, and qualitative HPV detection. The receiver operating characteristic (ROC) curve and cut-off points for HPV-VL were calculated. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and Cohen’s Kappa coefficient (κ) were also calculated. Results The mean patient age was 44.6 ± 9.5 years. All of them received antiretroviral treatment, 96.8% had an HIV viral load of <50 copies/mL and 17.2% had a previous diagnosis of AIDS. The diagnosis of the anal biopsies were: 19.4% (n = 18) HSIL, 29.1% (n = 27) LSIL, and 51.6% (n = 48) negative. An HPV-16-VL >6.2 copies/cell was detected in the HSIL biopsy samples (p = 0.007), showing a sensitivity of 100% and a specificity of 46.2%. HPV-18-VL and HPV16-18-VL co-testing showed a sensitivity of 75% and 76.9% and a specificity of 72.7% and 61.3%, respectively. The highest PPV was 50% obtained with the cytology and HPV-18-VL. The HPV-16-VL showed a NPV of 100%, followed by 88.9% in the HPV-18-VL and 87% in the abnormal cytology. Cohen’s Kappa coefficient were: HPV-18-VL (κ = 0.412), abnormal cytology (κ = 0.353) and HPV-16-VL (κ = 0.338). Conclusions HPV-VL testing improved the detection sensitivity but not the specificity for HSIL biopsies compar…
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format: text/html
creator: Marcos Díez-Martínez
creator: Juana Perpiñá-Galvañ
creator: Joaquín Ferri
creator: Maripaz Ventero
creator: Joaquin Portilla
creator: María José Cabañero-Martínez
subject: Gastroenterology and Hepatology
subject: HIV
subject: Infectious Diseases
subject: Oncology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.15878
publisher: PeerJ Inc.
rights: © 2023 Díez-Martínez et al.
abstract: Background The incidence of high-grade anal intraepithelial lesions (HSILs) has increased in recent years among men who have sex with men with human immunodeficiency virus (HIV). This work evaluated the validity of the human papilloma virus viral load (HPV-VL) versus cytological and qualitative HPV results to detect HSILs. Methods From May 2017 to January 2020, 93 men who have sex with men and HIV were included in an anal cancer screening program from the Infectious Diseases Unit at a tertiary-care hospital in Alicante (Spain). The gold-standard for the screening of anal HSILs is the anal biopsy using high-resolution anoscopy. The diagnostic methods compared against gold-standard were HPV-16-VL, HPV-18-VL, and HPV-16-18-VL co-testing, anal cytology, and qualitative HPV detection. The receiver operating characteristic (ROC) curve and cut-off points for HPV-VL were calculated. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and Cohen’s Kappa coefficient (κ) were also calculated. Results The mean patient age was 44.6 ± 9.5 years. All of them received antiretroviral treatment, 96.8% had an HIV viral load of <50 copies/mL and 17.2% had a previous diagnosis of AIDS. The diagnosis of the anal biopsies were: 19.4% (n = 18) HSIL, 29.1% (n = 27) LSIL, and 51.6% (n = 48) negative. An HPV-16-VL >6.2 copies/cell was detected in the HSIL biopsy samples (p = 0.007), showing a sensitivity of 100% and a specificity of 46.2%. HPV-18-VL and HPV16-18-VL co-testing showed a sensitivity of 75% and 76.9% and a specificity of 72.7% and 61.3%, respectively. The highest PPV was 50% obtained with the cytology and HPV-18-VL. The HPV-16-VL showed a NPV of 100%, followed by 88.9% in the HPV-18-VL and 87% in the abnormal cytology. Cohen’s Kappa coefficient were: HPV-18-VL (κ = 0.412), abnormal cytology (κ = 0.353) and HPV-16-VL (κ = 0.338). Conclusions HPV-VL testing improved the detection sensitivity but not the specificity for HSIL biopsies compar…
bibliographic citation: Díez-Martínez et al. (2023) Evaluation of the validity of the HPV viral load compared to conventional techniques for the detection of high-grade anal intraepithelial lesions in men with HIV who have sex with men. PeerJ 11:e15878 https://doi.org/10.7717/peerj.15878
date submitted: 2023-05-15
date accepted: 2023-07-18
issued: 2023-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Díez-Martínez
  given name: Marcos
author list: Agent
  family name: Perpiñá-Galvañ
  given name: Juana
author list: Agent
  family name: Ferri
  given name: Joaquín
author list: Agent
  family name: Ventero
  given name: Maripaz
author list: Agent
  family name: Portilla
  given name: Joaquin
author list: Agent
  family name: Cabañero-Martínez
  given name: María José
doi: 10.7717/peerj.15878
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-23
copyright: ©2023 Díez-Martínez et al.
attribution name: Díez-Martínez et al.

CTRP3 attenuates inflammation, oxidative and cell death in cisplatin induced HK-2 cells
type: item
type: AcademicArticle
description: Cisplatin has been widely studied and found to be a highly effective anti-tumor drug. It has several side effects, including acute kidney injury (AKI). Cisplatin-induced AKI can be primarily attributed to oxidative stress, inflammation, and apoptosis. The CTRP3 adipokine is a new adipokine that exhibits antioxidant, anti-inflammatory, and antiapoptotic properties. Despite this, the role of CTRP3 in AKI remain unclear. In cisplatin-induced AKI models, our findings demonstrated that CTRP3 expression was decreased in human proximal tubule epithelial cells (HK-2). In the in vitro experiments, HK-2 cells were first transfected with an overexpression plasmid of CTRP3 (pcDNA-CTRP3) or a small interfering RNA for CTRP3 (si-CTRP3) and induced by cisplatin; and cell oxidative stress, inflammation, proliferation, and apoptosis were found to be present. Overexpressing CTRP3 inhibited oxidative stress through decreasing malondialdehyde (MDA) levels and increasing the activity of SOD and CAT. The mRNA levels of SOD1 and SOD2 were increased in response to CTRP3 overexpression. Additionally, CTRP3 decreased TNF-α and MCP-1 levels. Moreover, CTRP3 overexpression increased cisplatin-induced cell activity and decreased cell apoptosis, as indicated by the elevated numbers of EdU positive cells and decreased numbers of apoptotic cells. Consistent with these results, the overexpression of CTRP3 effectively elevated the mRNA levels of Bcl-2 and reduced the mRNA levels of Bax. In contrast, inhibition of CTRP3 expression by si-CTRP3 reversed the cisplatin-induced indices. Mechanistically, we found that the overexpression of CTRP3 can increase expression of Nrf2 and inhibit the activation of MAPK phosphorylation (ERK, JNK, and p38). Furthermore, inhibition of ERK, JNK and p38 activity eliminated aggravation of cisplatin-induced inflammation and apoptosis caused by CTRP3 knockdown. Additionally, the cisplatin-induced oxidative stress and activation of MAPK phosphorylation (ERK, JNK, and p38) …
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format: text/html
creator: Chenglin Zou
creator: Xun Tang
creator: Tingting Guo
creator: Tingting Jiang
creator: Wenying Zhang
creator: Jun Zhang
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.15890
publisher: PeerJ Inc.
rights: © 2023 Zou et al.
abstract: Cisplatin has been widely studied and found to be a highly effective anti-tumor drug. It has several side effects, including acute kidney injury (AKI). Cisplatin-induced AKI can be primarily attributed to oxidative stress, inflammation, and apoptosis. The CTRP3 adipokine is a new adipokine that exhibits antioxidant, anti-inflammatory, and antiapoptotic properties. Despite this, the role of CTRP3 in AKI remain unclear. In cisplatin-induced AKI models, our findings demonstrated that CTRP3 expression was decreased in human proximal tubule epithelial cells (HK-2). In the in vitro experiments, HK-2 cells were first transfected with an overexpression plasmid of CTRP3 (pcDNA-CTRP3) or a small interfering RNA for CTRP3 (si-CTRP3) and induced by cisplatin; and cell oxidative stress, inflammation, proliferation, and apoptosis were found to be present. Overexpressing CTRP3 inhibited oxidative stress through decreasing malondialdehyde (MDA) levels and increasing the activity of SOD and CAT. The mRNA levels of SOD1 and SOD2 were increased in response to CTRP3 overexpression. Additionally, CTRP3 decreased TNF-α and MCP-1 levels. Moreover, CTRP3 overexpression increased cisplatin-induced cell activity and decreased cell apoptosis, as indicated by the elevated numbers of EdU positive cells and decreased numbers of apoptotic cells. Consistent with these results, the overexpression of CTRP3 effectively elevated the mRNA levels of Bcl-2 and reduced the mRNA levels of Bax. In contrast, inhibition of CTRP3 expression by si-CTRP3 reversed the cisplatin-induced indices. Mechanistically, we found that the overexpression of CTRP3 can increase expression of Nrf2 and inhibit the activation of MAPK phosphorylation (ERK, JNK, and p38). Furthermore, inhibition of ERK, JNK and p38 activity eliminated aggravation of cisplatin-induced inflammation and apoptosis caused by CTRP3 knockdown. Additionally, the cisplatin-induced oxidative stress and activation of MAPK phosphorylation (ERK, JNK, and p38) …
bibliographic citation: Zou et al. (2023) CTRP3 attenuates inflammation, oxidative and cell death in cisplatin induced HK-2 cells. PeerJ 11:e15890 https://doi.org/10.7717/peerj.15890
date submitted: 2023-02-20
date accepted: 2023-07-21
issued: 2023-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zou
  given name: Chenglin
author list: Agent
  family name: Tang
  given name: Xun
author list: Agent
  family name: Guo
  given name: Tingting
author list: Agent
  family name: Jiang
  given name: Tingting
author list: Agent
  family name: Zhang
  given name: Wenying
author list: Agent
  family name: Zhang
  given name: Jun
doi: 10.7717/peerj.15890
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-23
copyright: ©2023 Zou et al.
attribution name: Zou et al.

No genetic causal association between dental caries and Alzheimer’s disease: a bidirectional two-sample Mendelian randomization analysis
type: item
type: AcademicArticle
description: Background An increasing number of observational studies have suggested an association between dental caries and Alzheimer’s disease (AD). The association between dental caries and Alzheimer’s disease may be mediated by confounders or reverse causality. In this study, we conducted bidirectional two-sample Mendelian randomization (MR) to estimate the bidirectional causality between dental caries and AD. Materials and Methods Genome-wide association study (GWAS) summary statistics of dental caries were extracted from a published meta-analysis which included a total of 487,823 participants. GWAS datasets of AD and AD onset age were obtained from the FinnGen bank. A bidirectional two-sample analysis was performed to explore the causality between dental caries and AD. Results For the dental caries-AD causality estimation, there was no significant association between dental caries and AD, neither with the AD GWASs from the FinnGen database (OR: 1.041, p = 0.874) nor with those from the International Genomics of Alzheimer’s Project (OR: 1.162, p = 0.409). In addition, the genetic susceptibility to dental caries was not related to the onset age of AD. No causality existed between dental caries and early-onset AD (OR: 0.515, p = 0.302) or late-onset AD (OR: 1.329, p = 0.347). For the AD-dental caries relationship, no causality was detected by the IVW method (OR: 1.000, p = 0.717). Findings from other MR methods were consistent. The pleiotropy test and sensitivity analysis confirmed the validity of these MR results. Conclusions In this bidirectional MR study, robust evidence to support a bidirectional causal effect between dental caries and AD from the GWAS results within large-scale European-descent populations was absent. Having dental caries would not alter the onset age of AD.
format: application/pdf
format: text/html
creator: Qiao Liao
creator: Si-Zhuo Li
creator: Fa-Fa Tian
creator: Kun Huang
creator: Fang-Fang Bi
subject: Cognitive Disorders
subject: Dentistry
subject: Epidemiology
subject: Neurology
description: doi:10.7717/peerj.15936
publisher: PeerJ Inc.
rights: © 2023 Liao et al.
abstract: Background An increasing number of observational studies have suggested an association between dental caries and Alzheimer’s disease (AD). The association between dental caries and Alzheimer’s disease may be mediated by confounders or reverse causality. In this study, we conducted bidirectional two-sample Mendelian randomization (MR) to estimate the bidirectional causality between dental caries and AD. Materials and Methods Genome-wide association study (GWAS) summary statistics of dental caries were extracted from a published meta-analysis which included a total of 487,823 participants. GWAS datasets of AD and AD onset age were obtained from the FinnGen bank. A bidirectional two-sample analysis was performed to explore the causality between dental caries and AD. Results For the dental caries-AD causality estimation, there was no significant association between dental caries and AD, neither with the AD GWASs from the FinnGen database (OR: 1.041, p = 0.874) nor with those from the International Genomics of Alzheimer’s Project (OR: 1.162, p = 0.409). In addition, the genetic susceptibility to dental caries was not related to the onset age of AD. No causality existed between dental caries and early-onset AD (OR: 0.515, p = 0.302) or late-onset AD (OR: 1.329, p = 0.347). For the AD-dental caries relationship, no causality was detected by the IVW method (OR: 1.000, p = 0.717). Findings from other MR methods were consistent. The pleiotropy test and sensitivity analysis confirmed the validity of these MR results. Conclusions In this bidirectional MR study, robust evidence to support a bidirectional causal effect between dental caries and AD from the GWAS results within large-scale European-descent populations was absent. Having dental caries would not alter the onset age of AD.
bibliographic citation: Liao et al. (2023) No genetic causal association between dental caries and Alzheimer’s disease: a bidirectional two-sample Mendelian randomization analysis. PeerJ 11:e15936 https://doi.org/10.7717/peerj.15936
date submitted: 2023-01-30
date accepted: 2023-07-31
issued: 2023-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liao
  given name: Qiao
author list: Agent
  family name: Li
  given name: Si-Zhuo
author list: Agent
  family name: Tian
  given name: Fa-Fa
author list: Agent
  family name: Huang
  given name: Kun
author list: Agent
  family name: Bi
  given name: Fang-Fang
doi: 10.7717/peerj.15936
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-23
copyright: © 2023 Liao et al.
attribution name: Liao et al.

Farmers’ perception of the ecosystem services provided by diurnal raptors in arid Rajasthan
type: item
type: AcademicArticle
description: Farmers are the most important stakeholders in wildlife conservation in the agricultural landscape. Understanding the farmer’s perceptions, attitude, behaviour, and knowledge toward conservation is critical in developing an effective conservation programme in human-dominated landscapes. We conducted semi-structured face-to-face interviews with 373 farmers to understand the farmer’s perception of ecosystem services provided by diurnal raptors in the arid region of Rajasthan from July 2020 to February 2021 and from August 2021 to January 2022. We grouped ecosystem services and disservices into larger categories and estimated the correlation between them, finding that disservices are negatively correlated with benefits. Raptors were perceived as beneficial for their role in controlling rodents and pests, but negatively for poultry predation. In addition, we built a binomial generalised linear model with a logit function to better understand the factors that influence farmers’ perceptions of raptors (positive or negative). We observed that males and females have different attitudes toward the ecosystem services provided by raptors. It is critical to understand social perceptions in order to conserve species that are rare on a global scale but may face negative perceptions on a local scale. Our study connects ecological information with socio-demographic factors, which can be useful in developing policy measures for raptor conservation.
format: application/pdf
format: text/html
creator: Govind Tiwari
creator: Puneet Pandey
creator: Rahul Kaul
creator: Randeep Singh
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.15996
publisher: PeerJ Inc.
rights: © 2023 Tiwari et al.
abstract: Farmers are the most important stakeholders in wildlife conservation in the agricultural landscape. Understanding the farmer’s perceptions, attitude, behaviour, and knowledge toward conservation is critical in developing an effective conservation programme in human-dominated landscapes. We conducted semi-structured face-to-face interviews with 373 farmers to understand the farmer’s perception of ecosystem services provided by diurnal raptors in the arid region of Rajasthan from July 2020 to February 2021 and from August 2021 to January 2022. We grouped ecosystem services and disservices into larger categories and estimated the correlation between them, finding that disservices are negatively correlated with benefits. Raptors were perceived as beneficial for their role in controlling rodents and pests, but negatively for poultry predation. In addition, we built a binomial generalised linear model with a logit function to better understand the factors that influence farmers’ perceptions of raptors (positive or negative). We observed that males and females have different attitudes toward the ecosystem services provided by raptors. It is critical to understand social perceptions in order to conserve species that are rare on a global scale but may face negative perceptions on a local scale. Our study connects ecological information with socio-demographic factors, which can be useful in developing policy measures for raptor conservation.
bibliographic citation: Tiwari et al. (2023) Farmers’ perception of the ecosystem services provided by diurnal raptors in arid Rajasthan. PeerJ 11:e15996 https://doi.org/10.7717/peerj.15996
date submitted: 2022-10-11
date accepted: 2023-08-08
issued: 2023-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tiwari
  given name: Govind
author list: Agent
  family name: Pandey
  given name: Puneet
author list: Agent
  family name: Kaul
  given name: Rahul
author list: Agent
  family name: Singh
  given name: Randeep
doi: 10.7717/peerj.15996
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-23
copyright: © 2023 Tiwari et al.
attribution name: Tiwari et al.

Comparative genomics of bacteria from amphibian skin associated with inhibition of an amphibian fungal pathogen, Batrachochytrium dendrobatidis
type: item
type: AcademicArticle
description: Chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), is a skin disease associated with worldwide amphibian declines. Symbiotic microbes living on amphibian skin interact with Bd and may alter infection outcomes. We completed whole genome sequencing of 40 bacterial isolates cultured from the skin of four amphibian species in the Eastern US. Each isolate was tested in vitro for the ability to inhibit Bd growth. The aim of this study was to identify genomic differences among the isolates and generate hypotheses about the genomic underpinnings of Bd growth inhibition. We identified sixty-five gene families that were present in all 40 isolates. Screening for common biosynthetic gene clusters revealed that this set of isolates contained a wide variety of clusters; the two most abundant clusters with potential antifungal activity were siderophores (N=17 isolates) and Type III polyketide synthases (N=22 isolates). We then examined various subsets of the 22 isolates in the phylum Proteobacteria for genes encoding specific compounds that may inhibit fungal growth, including chitinase and violacein. We identified differences in Agrobacterium and Sphingomonas isolates in the chitinase genes that showed some association with anti-Bd activity, as well as variation in the violacein genes in the Janthinobacterium isolates. Using a comparative genomics approach, we generated several testable hypotheses about differences among bacterial isolates from amphibian skin communities that could contribute to variation in the ability to inhibit Bd growth. Further work is necessary to explore and uncover the various mechanisms utilized by amphibian skin bacterial isolates to inhibit Bd.
format: application/pdf
format: text/html
creator: Noah Wax
creator: Jenifer B. Walke
creator: David C. Haak
creator: Lisa K. Belden
subject: Bioinformatics
subject: Ecology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.15714
publisher: PeerJ Inc.
rights: © 2023 Wax et al.
abstract: Chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), is a skin disease associated with worldwide amphibian declines. Symbiotic microbes living on amphibian skin interact with Bd and may alter infection outcomes. We completed whole genome sequencing of 40 bacterial isolates cultured from the skin of four amphibian species in the Eastern US. Each isolate was tested in vitro for the ability to inhibit Bd growth. The aim of this study was to identify genomic differences among the isolates and generate hypotheses about the genomic underpinnings of Bd growth inhibition. We identified sixty-five gene families that were present in all 40 isolates. Screening for common biosynthetic gene clusters revealed that this set of isolates contained a wide variety of clusters; the two most abundant clusters with potential antifungal activity were siderophores (N=17 isolates) and Type III polyketide synthases (N=22 isolates). We then examined various subsets of the 22 isolates in the phylum Proteobacteria for genes encoding specific compounds that may inhibit fungal growth, including chitinase and violacein. We identified differences in Agrobacterium and Sphingomonas isolates in the chitinase genes that showed some association with anti-Bd activity, as well as variation in the violacein genes in the Janthinobacterium isolates. Using a comparative genomics approach, we generated several testable hypotheses about differences among bacterial isolates from amphibian skin communities that could contribute to variation in the ability to inhibit Bd growth. Further work is necessary to explore and uncover the various mechanisms utilized by amphibian skin bacterial isolates to inhibit Bd.
bibliographic citation: Wax et al. (2023) Comparative genomics of bacteria from amphibian skin associated with inhibition of an amphibian fungal pathogen, Batrachochytrium dendrobatidis. PeerJ 11:e15714 https://doi.org/10.7717/peerj.15714
date submitted: 2023-01-26
date accepted: 2023-06-16
issued: 2023-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wax
  given name: Noah
author list: Agent
  family name: Walke
  given name: Jenifer B.
author list: Agent
  family name: Haak
  given name: David C.
author list: Agent
  family name: Belden
  given name: Lisa K.
doi: 10.7717/peerj.15714
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-22
copyright: ©2023 Wax et al.
attribution name: Wax et al.

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