PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identifying the critical state of cancers by single-sample Markov flow entropy
items: Oleanolic acid and moderate drinking increase the pancreatic GLP-1R expression of the β-cell mass deficiency induced hyperglycemia
items: Comparison of dental anesthetic efficacy between the periodontal intraligamentary anesthesia and other infiltration anesthesia: a systematic review and meta-analysis
items: Impact of climate change on the geographical distribution and niche dynamics of Gastrodia elata
items: Effects of hydraulic retention time and influent nitrate concentration on solid-phase denitrification system using wheat husk as carbon source
items: Development of a video camera-type kayak motion capture system to measure water kayaking
items: Evaluation of the reliability and quality of YouTube videos as a source of information for transcutaneous electrical nerve stimulation
items: Protein family neighborhood analyzer—ProFaNA
items: Human disturbances and the daytime activity of sympatric otters along equatorial Amazonian rivers
items: Confirmatory digital subtraction angiography after clinical brain death/death by neurological criteria: impact on number of donors and organ transplants

Identifying the critical state of cancers by single-sample Markov flow entropy
type: item
type: AcademicArticle
description: Background The progression of complex diseases sometimes undergoes a drastic critical transition, at which the biological system abruptly shifts from a relatively healthy state (before-transition stage) to a disease state (after-transition stage). Searching for such a critical transition or critical state is crucial to provide timely and effective scientific treatment to patients. However, in most conditions where only a small sample size of clinical data is available, resulting in failure when detecting the critical states of complex diseases, particularly only single-sample data. Methods In this study, different from traditional methods that require multiple samples at each time, a model-free computational method, single-sample Markov flow entropy (sMFE), provides a solution to the identification problem of critical states/pre-disease states of complex diseases, solely based on a single-sample. Our proposed method was employed to characterize the dynamic changes of complex diseases from the perspective of network entropy. Results The proposed approach was verified by unmistakably identifying the critical state just before the occurrence of disease deterioration for four tumor datasets from The Cancer Genome Atlas (TCGA) database. In addition, two new prognostic biomarkers, optimistic sMFE (O-sMFE) and pessimistic sMFE (P-sMFE) biomarkers, were identified by our method and enable the prognosis evaluation of tumors. Conclusions The proposed method has shown its capability to accurately detect pre-disease states of four cancers and provide two novel prognostic biomarkers, O-sMFE and P-sMFE biomarkers, to facilitate the personalized prognosis of patients. This is a remarkable achievement that could have a major impact on the diagnosis and treatment of complex diseases.
format: application/pdf
format: text/html
creator: Juntan Liu
creator: Yuan Tao
creator: Ruoqi Lan
creator: Jiayuan Zhong
creator: Rui Liu
creator: Pei Chen
subject: Bioinformatics
subject: Computational Biology
subject: Oncology
description: doi:10.7717/peerj.15695
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Background The progression of complex diseases sometimes undergoes a drastic critical transition, at which the biological system abruptly shifts from a relatively healthy state (before-transition stage) to a disease state (after-transition stage). Searching for such a critical transition or critical state is crucial to provide timely and effective scientific treatment to patients. However, in most conditions where only a small sample size of clinical data is available, resulting in failure when detecting the critical states of complex diseases, particularly only single-sample data. Methods In this study, different from traditional methods that require multiple samples at each time, a model-free computational method, single-sample Markov flow entropy (sMFE), provides a solution to the identification problem of critical states/pre-disease states of complex diseases, solely based on a single-sample. Our proposed method was employed to characterize the dynamic changes of complex diseases from the perspective of network entropy. Results The proposed approach was verified by unmistakably identifying the critical state just before the occurrence of disease deterioration for four tumor datasets from The Cancer Genome Atlas (TCGA) database. In addition, two new prognostic biomarkers, optimistic sMFE (O-sMFE) and pessimistic sMFE (P-sMFE) biomarkers, were identified by our method and enable the prognosis evaluation of tumors. Conclusions The proposed method has shown its capability to accurately detect pre-disease states of four cancers and provide two novel prognostic biomarkers, O-sMFE and P-sMFE biomarkers, to facilitate the personalized prognosis of patients. This is a remarkable achievement that could have a major impact on the diagnosis and treatment of complex diseases.
bibliographic citation: Liu et al. (2023) Identifying the critical state of cancers by single-sample Markov flow entropy. PeerJ 11:e15695 https://doi.org/10.7717/peerj.15695
date submitted: 2023-03-13
date accepted: 2023-06-14
issued: 2023-07-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Juntan
author list: Agent
  family name: Tao
  given name: Yuan
author list: Agent
  family name: Lan
  given name: Ruoqi
author list: Agent
  family name: Zhong
  given name: Jiayuan
author list: Agent
  family name: Liu
  given name: Rui
author list: Agent
  family name: Chen
  given name: Pei
doi: 10.7717/peerj.15695
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-24
copyright: © 2023 Liu et al.
attribution name: Liu et al.

Oleanolic acid and moderate drinking increase the pancreatic GLP-1R expression of the β-cell mass deficiency induced hyperglycemia
type: item
type: AcademicArticle
description: Background Oleanolic acid (OA) and moderate drinking have been reported to attenuate diabetes. However, the underlying mechanism of OA and moderate drinking alone or in combination on the islet β-cell deficiency induced diabetes is not fully elucidated. Methods Male Sprague Dawley (SD) rats were intraperitoneally injected with 55 mg/kg streptozotocin (STZ) to induce β-cell deficiency. OA, 5% ethanol (EtOH), or a mixture of OA in 5% ethanol (OA+EtOH) were applied to three treatment groups of hyperglycemia rats for 6 weeks. Results STZ caused the increase of fast blood glucose (FBG) level.OA and EtOH treatment alone or in combination decreased the STZ increased FBG level during the 6 weeks of treatment. In addition, OA treatment also significantly increased the β-cell to total islet cell ratio. Both EtOH and OA+EtOH treatments promoted the increase of total islet cell number and α-cell to β-cell ratio when compared to OA group. STZ induced hyperglycemia dramatically reduced the glucagon-like peptide-1 receptor (GLP-1R) positive cells in islets, all the three treatments significantly increased the pancreatic GLP-1R positive cell number. In the meantime, STZ induced hyperglycemia suppressed the insulin mRNA expression and boosted the glucagon mRNA expression. EtOH and OA+EtOH treatments increased the insulin mRNA expression, but none of the 3 treatments altered the elevated glucagon level. Conclusion GLP-1R positive cell ratio in islets is crucial for the blood glucose level of diabetes. OA and 5% ethanol alone or in combination suppresses the blood glucose level of β-cell deficiency induced diabetes by increasing islet GLP-1R expression.
format: application/pdf
format: text/html
creator: Li Xu
creator: Ruibin Hu
creator: Shreyas Venkataraman Jois
creator: Lei Zhang
subject: Biochemistry
subject: Toxicology
subject: Diabetes and Endocrinology
subject: Pharmacology
subject: Histology
description: doi:10.7717/peerj.15705
publisher: PeerJ Inc.
rights: © 2023 Xu et al.
abstract: Background Oleanolic acid (OA) and moderate drinking have been reported to attenuate diabetes. However, the underlying mechanism of OA and moderate drinking alone or in combination on the islet β-cell deficiency induced diabetes is not fully elucidated. Methods Male Sprague Dawley (SD) rats were intraperitoneally injected with 55 mg/kg streptozotocin (STZ) to induce β-cell deficiency. OA, 5% ethanol (EtOH), or a mixture of OA in 5% ethanol (OA+EtOH) were applied to three treatment groups of hyperglycemia rats for 6 weeks. Results STZ caused the increase of fast blood glucose (FBG) level.OA and EtOH treatment alone or in combination decreased the STZ increased FBG level during the 6 weeks of treatment. In addition, OA treatment also significantly increased the β-cell to total islet cell ratio. Both EtOH and OA+EtOH treatments promoted the increase of total islet cell number and α-cell to β-cell ratio when compared to OA group. STZ induced hyperglycemia dramatically reduced the glucagon-like peptide-1 receptor (GLP-1R) positive cells in islets, all the three treatments significantly increased the pancreatic GLP-1R positive cell number. In the meantime, STZ induced hyperglycemia suppressed the insulin mRNA expression and boosted the glucagon mRNA expression. EtOH and OA+EtOH treatments increased the insulin mRNA expression, but none of the 3 treatments altered the elevated glucagon level. Conclusion GLP-1R positive cell ratio in islets is crucial for the blood glucose level of diabetes. OA and 5% ethanol alone or in combination suppresses the blood glucose level of β-cell deficiency induced diabetes by increasing islet GLP-1R expression.
bibliographic citation: Xu et al. (2023) Oleanolic acid and moderate drinking increase the pancreatic GLP-1R expression of the β-cell mass deficiency induced hyperglycemia. PeerJ 11:e15705 https://doi.org/10.7717/peerj.15705
date submitted: 2023-02-16
date accepted: 2023-06-15
issued: 2023-07-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Li
author list: Agent
  family name: Hu
  given name: Ruibin
author list: Agent
  family name: Jois
  given name: Shreyas Venkataraman
author list: Agent
  family name: Zhang
  given name: Lei
doi: 10.7717/peerj.15705
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-24
copyright: ©2023 Xu et al.
attribution name: Xu et al.

Comparison of dental anesthetic efficacy between the periodontal intraligamentary anesthesia and other infiltration anesthesia: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Uncertainty exists regarding the pain scores and the success rate of intraligamentary anesthesia compared to other infiltration anesthesia. Based on the conditions of clinical anesthesia techniques, we conducted a systematic review and meta-analysis to compare the efficacy of intraligamentary anesthesia with other infiltration anesthesia. Methods The search was carried out in PubMed Central, Cochrane Central Register of Controlled Trials, MEDLINE (via OVID), Embase (via OVID), and Scopus from the inception to March 26, 2023. Results Seven eligible randomized controlled trials were included in the meta-analysis. The results indicated no significant difference in the success rate (RR = 0.96; 95% CI [0.81–1.14]; p = 0.65; I2= 73%) and visual analog scale (VAS) during dental procedures (MD = 3.81; 95% CI [−0.54–8.16]; p = 0.09; I2= 97%) between intraligamentary anesthesia and other infiltration anesthesia. However, intraligamentary anesthesia exhibited a higher VAS score during injection than other infiltration anesthesia (MD = 8.83; 95% CI [4.86–12.79]; p < 0.0001; I2= 90%). A subgroup analysis according to infiltration techniques showed that supraperiosteal anesthesia had a lower VAS score during dental procedures than intraligamentary anesthesia. Conclusions Intraligamentary anesthesia and other infiltration anesthesias have the same success rate and pain during dental procedures. However, the pain during injection of intraligamentary anesthesia is heavier than that of other infiltration anesthesia.
format: application/pdf
format: text/html
creator: Jialei Pan
creator: Yan Wang
creator: Yuran Qian
creator: Jing Zou
creator: Qiong Zhang
subject: Anesthesiology and Pain Management
subject: Dentistry
description: doi:10.7717/peerj.15734
publisher: PeerJ Inc.
rights: © 2023 Pan et al.
abstract: Background Uncertainty exists regarding the pain scores and the success rate of intraligamentary anesthesia compared to other infiltration anesthesia. Based on the conditions of clinical anesthesia techniques, we conducted a systematic review and meta-analysis to compare the efficacy of intraligamentary anesthesia with other infiltration anesthesia. Methods The search was carried out in PubMed Central, Cochrane Central Register of Controlled Trials, MEDLINE (via OVID), Embase (via OVID), and Scopus from the inception to March 26, 2023. Results Seven eligible randomized controlled trials were included in the meta-analysis. The results indicated no significant difference in the success rate (RR = 0.96; 95% CI [0.81–1.14]; p = 0.65; I2= 73%) and visual analog scale (VAS) during dental procedures (MD = 3.81; 95% CI [−0.54–8.16]; p = 0.09; I2= 97%) between intraligamentary anesthesia and other infiltration anesthesia. However, intraligamentary anesthesia exhibited a higher VAS score during injection than other infiltration anesthesia (MD = 8.83; 95% CI [4.86–12.79]; p < 0.0001; I2= 90%). A subgroup analysis according to infiltration techniques showed that supraperiosteal anesthesia had a lower VAS score during dental procedures than intraligamentary anesthesia. Conclusions Intraligamentary anesthesia and other infiltration anesthesias have the same success rate and pain during dental procedures. However, the pain during injection of intraligamentary anesthesia is heavier than that of other infiltration anesthesia.
bibliographic citation: Pan et al. (2023) Comparison of dental anesthetic efficacy between the periodontal intraligamentary anesthesia and other infiltration anesthesia: a systematic review and meta-analysis. PeerJ 11:e15734 https://doi.org/10.7717/peerj.15734
date submitted: 2022-11-29
date accepted: 2023-06-19
issued: 2023-07-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Jialei
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Qian
  given name: Yuran
author list: Agent
  family name: Zou
  given name: Jing
author list: Agent
  family name: Zhang
  given name: Qiong
doi: 10.7717/peerj.15734
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-24
copyright: ©2023 Pan et al.
attribution name: Pan et al.

Impact of climate change on the geographical distribution and niche dynamics of Gastrodia elata
type: item
type: AcademicArticle
description: Background Gastrodia elata is widely used in China as a valuable herbal medicine. Owing to its high medicinal and nutrient value, wild resources of G. elata have been overexploited and its native areas have been severely damaged. Understanding the impacts of climate change on the distribution of this endangered species is important for the conservation and sustainable use of G. elata. Methods We used the optimized maximum entropy model to simulate the potential distribution of G. elata under contemporary and future time periods (1970–2000, 2050s, 2070s, and 2090s) and different climate change scenarios (SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5). Under these conditions, we investigated the key environmental factors influencing the distribution of G. elata as well as the spatial and temporal characteristics of its niche dynamics. Results With high Maxent model accuracy (AUCmean = 0.947 ± 0.012, and the Kappa value is 0.817), our analysis revealed that annual precipitation, altitude, and mean temperature of driest quarter are the most important environmental factors influencing the distribution of G. elata. Under current bioclimatic conditions, the potentially suitable area for G. elata in China is 71.98 × 104 km2, while the highly suitable region for G. elata growth is 7.28 × 104 km2. Our models for three future periods under four climate change scenarios indicate that G. elata can maintain stable distributions in southern Shaanxi, southwestern Hubei, and around the Sichuan basin, as these areas are highly suitable for its growth. However, the center of the highly suitable areas of G. elata shift depending on different climatic scenarios. The values of niche overlap for G. elata show a decreasing trend over the forecasted periods, of which the niche overlap under the SSP3-7.0 scenario shows the greatest decrease. Discussions Under the condition of global climate change in the future, our study provides basic reference data for the conservation and sustainable utiliz…
format: application/pdf
format: text/html
creator: Juan Hu
creator: Ying Feng
creator: Haotian Zhong
creator: Wei Liu
creator: Xufang Tian
creator: Yehong Wang
creator: Tao Tan
creator: Zhigang Hu
creator: Yifei Liu
subject: Agricultural Science
subject: Biogeography
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.15741
publisher: PeerJ Inc.
rights: © 2023 Hu et al.
abstract: Background Gastrodia elata is widely used in China as a valuable herbal medicine. Owing to its high medicinal and nutrient value, wild resources of G. elata have been overexploited and its native areas have been severely damaged. Understanding the impacts of climate change on the distribution of this endangered species is important for the conservation and sustainable use of G. elata. Methods We used the optimized maximum entropy model to simulate the potential distribution of G. elata under contemporary and future time periods (1970–2000, 2050s, 2070s, and 2090s) and different climate change scenarios (SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5). Under these conditions, we investigated the key environmental factors influencing the distribution of G. elata as well as the spatial and temporal characteristics of its niche dynamics. Results With high Maxent model accuracy (AUCmean = 0.947 ± 0.012, and the Kappa value is 0.817), our analysis revealed that annual precipitation, altitude, and mean temperature of driest quarter are the most important environmental factors influencing the distribution of G. elata. Under current bioclimatic conditions, the potentially suitable area for G. elata in China is 71.98 × 104 km2, while the highly suitable region for G. elata growth is 7.28 × 104 km2. Our models for three future periods under four climate change scenarios indicate that G. elata can maintain stable distributions in southern Shaanxi, southwestern Hubei, and around the Sichuan basin, as these areas are highly suitable for its growth. However, the center of the highly suitable areas of G. elata shift depending on different climatic scenarios. The values of niche overlap for G. elata show a decreasing trend over the forecasted periods, of which the niche overlap under the SSP3-7.0 scenario shows the greatest decrease. Discussions Under the condition of global climate change in the future, our study provides basic reference data for the conservation and sustainable utiliz…
bibliographic citation: Hu et al. (2023) Impact of climate change on the geographical distribution and niche dynamics of Gastrodia elata. PeerJ 11:e15741 https://doi.org/10.7717/peerj.15741
date submitted: 2022-11-15
date accepted: 2023-06-20
issued: 2023-07-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Juan
author list: Agent
  family name: Feng
  given name: Ying
author list: Agent
  family name: Zhong
  given name: Haotian
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Tian
  given name: Xufang
author list: Agent
  family name: Wang
  given name: Yehong
author list: Agent
  family name: Tan
  given name: Tao
author list: Agent
  family name: Hu
  given name: Zhigang
author list: Agent
  family name: Liu
  given name: Yifei
doi: 10.7717/peerj.15741
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-24
copyright: ©2023 Hu et al.
attribution name: Hu et al.

Effects of hydraulic retention time and influent nitrate concentration on solid-phase denitrification system using wheat husk as carbon source
type: item
type: AcademicArticle
description: Solid-phase denitrification shows promise for removing nitrate (NO3−-N) from water. Biological denitrification uses external carbon sources to remove nitrogen from wastewater, among which agriculture waste is considered the most promising source due to its economic and efficiency advantages. Hydraulic retention time (HRT) and influent nitrate concentration (INC) are the main factors influencing biological denitrification. This study explored the effects of HRT and INC on solid-phase denitrification using wheat husk (WH) as a carbon source. A solid-phase denitrification system with WH carbon source was constructed to explore denitrification performance with differing HRT and INC. The optimal HRT and INC of the wheat husk-denitrification reactor (WH-DR) were 32 h and 50 mg/L, respectively. Under these conditions, NO3−-N and total nitrogen removal rates were 97.37 ± 2.68% and 94.08 ± 4.01%, respectively. High-throughput sequencing revealed that the dominant phyla in the WH-DR operation were Proteobacteria, Bacteroidetes, and Campilobacterota. Among the dominant genera, Diaphorobacter (0.85%), Ideonella (0.38%), Thiobacillus (4.22%), and Sulfurifustis (0.60%) have denitrification functions; Spirochaeta (0.47%) is mainly involved in the degradation of WH; and Acidovorax (0.37%) and Azospira (0.86%) can both denitrify and degrade WH. This study determined the optimal HRT and INC for WH-DR and provides a reference for the development and application of WH as a novel, slow-release carbon source in treating aquaculture wastewater.
format: application/pdf
format: text/html
creator: Shuhui Niu
creator: Shuwei Gao
creator: Kai Zhang
creator: Zhifei Li
creator: Guangjun Wang
creator: Hongyan Li
creator: Yun Xia
creator: Jingjing Tian
creator: Ermeng Yu
creator: Jun Xie
creator: Minting Zhang
creator: Wangbao Gong
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Aquatic and Marine Chemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.15756
publisher: PeerJ Inc.
rights: © 2023 Niu et al.
abstract: Solid-phase denitrification shows promise for removing nitrate (NO3−-N) from water. Biological denitrification uses external carbon sources to remove nitrogen from wastewater, among which agriculture waste is considered the most promising source due to its economic and efficiency advantages. Hydraulic retention time (HRT) and influent nitrate concentration (INC) are the main factors influencing biological denitrification. This study explored the effects of HRT and INC on solid-phase denitrification using wheat husk (WH) as a carbon source. A solid-phase denitrification system with WH carbon source was constructed to explore denitrification performance with differing HRT and INC. The optimal HRT and INC of the wheat husk-denitrification reactor (WH-DR) were 32 h and 50 mg/L, respectively. Under these conditions, NO3−-N and total nitrogen removal rates were 97.37 ± 2.68% and 94.08 ± 4.01%, respectively. High-throughput sequencing revealed that the dominant phyla in the WH-DR operation were Proteobacteria, Bacteroidetes, and Campilobacterota. Among the dominant genera, Diaphorobacter (0.85%), Ideonella (0.38%), Thiobacillus (4.22%), and Sulfurifustis (0.60%) have denitrification functions; Spirochaeta (0.47%) is mainly involved in the degradation of WH; and Acidovorax (0.37%) and Azospira (0.86%) can both denitrify and degrade WH. This study determined the optimal HRT and INC for WH-DR and provides a reference for the development and application of WH as a novel, slow-release carbon source in treating aquaculture wastewater.
bibliographic citation: Niu et al. (2023) Effects of hydraulic retention time and influent nitrate concentration on solid-phase denitrification system using wheat husk as carbon source. PeerJ 11:e15756 https://doi.org/10.7717/peerj.15756
date submitted: 2023-03-31
date accepted: 2023-06-26
issued: 2023-07-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niu
  given name: Shuhui
author list: Agent
  family name: Gao
  given name: Shuwei
author list: Agent
  family name: Zhang
  given name: Kai
author list: Agent
  family name: Li
  given name: Zhifei
author list: Agent
  family name: Wang
  given name: Guangjun
author list: Agent
  family name: Li
  given name: Hongyan
author list: Agent
  family name: Xia
  given name: Yun
author list: Agent
  family name: Tian
  given name: Jingjing
author list: Agent
  family name: Yu
  given name: Ermeng
author list: Agent
  family name: Xie
  given name: Jun
author list: Agent
  family name: Zhang
  given name: Minting
author list: Agent
  family name: Gong
  given name: Wangbao
doi: 10.7717/peerj.15756
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-24
copyright: © 2023 Niu et al.
attribution name: Niu et al.

Development of a video camera-type kayak motion capture system to measure water kayaking
type: item
type: AcademicArticle
description: Background In kayaking, trunk motion is one of the important factors that prevent injury and improve performance. Kinematic studies in kayaking have been reported in laboratory settings using paddling simulators and ergometers. However, such studies do not reflect kayaking on water, the actual competitive environment. Therefore, we developed a video camera-type kayak motion capture system (KMCS) wherein action cameras were fixed to a kayak to capture images of markers attached to an athlete’s body. This study aimed to compare the kinematic data between KMCS and an optical motion capture system (OMCS) in kayaking and to determine the accuracy of the KMCS analysis. Methods In a competition, five elite junior female kayak athletes performed kayak paddling under the unloaded condition using a kayak. The kayak was secured using a tri-folding bench and a towel, and twenty strokes were recorded during maximal paddling. One stroke was defined as the period from right catch to left catch, and the first six strokes were used to evaluate the accuracy. Trunk angles (tilting, turning, and rotation) were examined with the simultaneous use of KMCS and OMCS, and the differences between these systems were evaluated. To ensure reliability, intraclass correlation coefficient (ICC; a two-way mixed model for absolute agreement) was calculated for each angle. Furthermore, Bland–Altman analysis was performed to understand the agreement between the two systems. Results Root mean square errors (RMSEs) were 1.42° and 3.94° for turning and rotation, respectively, and mean absolute errors (MAEs) were 1.08° and 3.00° for turning and rotation, respectively. The RMSE and MAE for tilting were 2.43° and 1.76°, respectively, which indicated that the validity was comparable to that of other angles. However, the range of motion in tilting was lower than that in turning and rotation. Bland–Altman analysis showed good agreement in the total range of motion, with mean bias values of −0.84°, −0.07°, and −…
format: application/pdf
format: text/html
creator: Shigeaki Miyazaki
creator: Go Yamako
creator: Ryo Kimura
creator: Niroshan G. Punchihewa
creator: Tsubasa Kawaguchi
creator: Hideki Arakawa
creator: Etsuo Chosa
subject: Kinesiology
subject: Biomechanics
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.15227
publisher: PeerJ Inc.
rights: © 2023 Miyazaki et al.
abstract: Background In kayaking, trunk motion is one of the important factors that prevent injury and improve performance. Kinematic studies in kayaking have been reported in laboratory settings using paddling simulators and ergometers. However, such studies do not reflect kayaking on water, the actual competitive environment. Therefore, we developed a video camera-type kayak motion capture system (KMCS) wherein action cameras were fixed to a kayak to capture images of markers attached to an athlete’s body. This study aimed to compare the kinematic data between KMCS and an optical motion capture system (OMCS) in kayaking and to determine the accuracy of the KMCS analysis. Methods In a competition, five elite junior female kayak athletes performed kayak paddling under the unloaded condition using a kayak. The kayak was secured using a tri-folding bench and a towel, and twenty strokes were recorded during maximal paddling. One stroke was defined as the period from right catch to left catch, and the first six strokes were used to evaluate the accuracy. Trunk angles (tilting, turning, and rotation) were examined with the simultaneous use of KMCS and OMCS, and the differences between these systems were evaluated. To ensure reliability, intraclass correlation coefficient (ICC; a two-way mixed model for absolute agreement) was calculated for each angle. Furthermore, Bland–Altman analysis was performed to understand the agreement between the two systems. Results Root mean square errors (RMSEs) were 1.42° and 3.94° for turning and rotation, respectively, and mean absolute errors (MAEs) were 1.08° and 3.00° for turning and rotation, respectively. The RMSE and MAE for tilting were 2.43° and 1.76°, respectively, which indicated that the validity was comparable to that of other angles. However, the range of motion in tilting was lower than that in turning and rotation. Bland–Altman analysis showed good agreement in the total range of motion, with mean bias values of −0.84°, −0.07°, and −…
bibliographic citation: Miyazaki et al. (2023) Development of a video camera-type kayak motion capture system to measure water kayaking. PeerJ 11:e15227 https://doi.org/10.7717/peerj.15227
date submitted: 2022-10-28
date accepted: 2023-06-12
issued: 2023-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miyazaki
  given name: Shigeaki
author list: Agent
  family name: Yamako
  given name: Go
author list: Agent
  family name: Kimura
  given name: Ryo
author list: Agent
  family name: Punchihewa
  given name: Niroshan G.
author list: Agent
  family name: Kawaguchi
  given name: Tsubasa
author list: Agent
  family name: Arakawa
  given name: Hideki
author list: Agent
  family name: Chosa
  given name: Etsuo
doi: 10.7717/peerj.15227
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-21
copyright: © 2023 Miyazaki et al.
attribution name: Miyazaki et al.

Evaluation of the reliability and quality of YouTube videos as a source of information for transcutaneous electrical nerve stimulation
type: item
type: AcademicArticle
description: Background YouTube plays an influential role in disseminating health-related information in the digital age. This study aimed to evaluate YouTube videos on transcutaneous electrical nerve stimulation (TENS) in terms of their information value and quality. Methods In this descriptive study, we ranked the first 100 videos that met the inclusion criteria using the search term “transcutaneous electrical nerve stimulation” on October 30, 2022. These videos were classified according to the number of views, likes, dislikes, comments, duration, popularity and content categories. Reliability, quality, and accuracy of the videos were assessed using the Journal of American Medical Association (JAMA) Benchmark Criteria and Modified DISCERN Questionnaire and Global Quality Score (GQS). Video popularity were calculated by the Video Power Index (VPI). Results Based on the GQS results, we found that 59, 27, and 14 videos had low, intermediate, and high quality, respectively. In addition, based on the JAMA results, 79 and 21 videos had poor and high reliability, respectively. No statistically significant difference was found between the JAMA, modified DISCERN and GQS scores in terms of the sources of videos (p = 0.226, p = 0.115, p = 0.812). Notably, there was a weak positive correlation between the JAMA scores and the number of views (r = 0.204, p = 0.041). Conclusion According to our study results, most YouTube videos on TENS were of low quality and reliability. Additionally, most videos were uploaded from sources created by doctors; the most frequently found content was about the TENS procedure, and content on complications of the procedure became less frequent as the videos became more recent. In particular, it was found that videos uploaded by academics have longer duration. It has been found that reliable videos with high JAMA scores also have high number of views. Accordingly, it can be concluded that videos with higher quality and more reliability that are created by healthc…
format: application/pdf
format: text/html
creator: Yüksel Erkin
creator: Volkan Hanci
creator: Erkan Ozduran
subject: Anesthesiology and Pain Management
subject: Drugs and Devices
subject: Neurology
description: doi:10.7717/peerj.15412
publisher: PeerJ Inc.
rights: © 2023 Erkin et al.
abstract: Background YouTube plays an influential role in disseminating health-related information in the digital age. This study aimed to evaluate YouTube videos on transcutaneous electrical nerve stimulation (TENS) in terms of their information value and quality. Methods In this descriptive study, we ranked the first 100 videos that met the inclusion criteria using the search term “transcutaneous electrical nerve stimulation” on October 30, 2022. These videos were classified according to the number of views, likes, dislikes, comments, duration, popularity and content categories. Reliability, quality, and accuracy of the videos were assessed using the Journal of American Medical Association (JAMA) Benchmark Criteria and Modified DISCERN Questionnaire and Global Quality Score (GQS). Video popularity were calculated by the Video Power Index (VPI). Results Based on the GQS results, we found that 59, 27, and 14 videos had low, intermediate, and high quality, respectively. In addition, based on the JAMA results, 79 and 21 videos had poor and high reliability, respectively. No statistically significant difference was found between the JAMA, modified DISCERN and GQS scores in terms of the sources of videos (p = 0.226, p = 0.115, p = 0.812). Notably, there was a weak positive correlation between the JAMA scores and the number of views (r = 0.204, p = 0.041). Conclusion According to our study results, most YouTube videos on TENS were of low quality and reliability. Additionally, most videos were uploaded from sources created by doctors; the most frequently found content was about the TENS procedure, and content on complications of the procedure became less frequent as the videos became more recent. In particular, it was found that videos uploaded by academics have longer duration. It has been found that reliable videos with high JAMA scores also have high number of views. Accordingly, it can be concluded that videos with higher quality and more reliability that are created by healthc…
bibliographic citation: Erkin et al. (2023) Evaluation of the reliability and quality of YouTube videos as a source of information for transcutaneous electrical nerve stimulation. PeerJ 11:e15412 https://doi.org/10.7717/peerj.15412
date submitted: 2022-12-21
date accepted: 2023-04-24
issued: 2023-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Erkin
  given name: Yüksel
author list: Agent
  family name: Hanci
  given name: Volkan
author list: Agent
  family name: Ozduran
  given name: Erkan
doi: 10.7717/peerj.15412
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-21
copyright: ©2023 Erkin et al.
attribution name: Erkin et al.

Protein family neighborhood analyzer—ProFaNA
type: item
type: AcademicArticle
description: Background Functionally related genes are well known to be often grouped in close vicinity in the genomes, particularly in prokaryotes. Notwithstanding the diverse evolutionary mechanisms leading to this phenomenon, it can be used to predict functions of uncharacterized genes. Methods Here, we provide a simple but robust statistical approach that leverages the vast amounts of genomic data available today. Considering a protein domain as a functional unit, one can explore other functional units (domains) that significantly often occur within the genomic neighborhoods of the queried domain. This analysis can be performed across different taxonomic levels. Provisions can also be made to correct for the uneven sampling of the taxonomic space by genomic sequencing projects that often focus on large numbers of very closely related strains, e.g., pathogenic ones. To this end, an optional procedure for averaging occurrences within subtaxa is available. Results Several examples show this approach can provide useful functional predictions for uncharacterized gene families, and how to combine this information with other approaches. The method is made available as a web server at http://bioinfo.sggw.edu.pl/neighborhood_analysis.
format: application/pdf
format: text/html
creator: Bartosz Baranowski
creator: Krzysztof Pawłowski
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.15715
publisher: PeerJ Inc.
rights: © 2023 Baranowski and Pawłowski
abstract: Background Functionally related genes are well known to be often grouped in close vicinity in the genomes, particularly in prokaryotes. Notwithstanding the diverse evolutionary mechanisms leading to this phenomenon, it can be used to predict functions of uncharacterized genes. Methods Here, we provide a simple but robust statistical approach that leverages the vast amounts of genomic data available today. Considering a protein domain as a functional unit, one can explore other functional units (domains) that significantly often occur within the genomic neighborhoods of the queried domain. This analysis can be performed across different taxonomic levels. Provisions can also be made to correct for the uneven sampling of the taxonomic space by genomic sequencing projects that often focus on large numbers of very closely related strains, e.g., pathogenic ones. To this end, an optional procedure for averaging occurrences within subtaxa is available. Results Several examples show this approach can provide useful functional predictions for uncharacterized gene families, and how to combine this information with other approaches. The method is made available as a web server at http://bioinfo.sggw.edu.pl/neighborhood_analysis.
bibliographic citation: Baranowski et al. (2023) Protein family neighborhood analyzer—ProFaNA. PeerJ 11:e15715 https://doi.org/10.7717/peerj.15715
date submitted: 2023-02-03
date accepted: 2023-06-16
issued: 2023-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baranowski
  given name: Bartosz
author list: Agent
  family name: Pawłowski
  given name: Krzysztof
doi: 10.7717/peerj.15715
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-21
copyright: © 2023 Baranowski and Pawłowski
attribution name: Baranowski and Pawłowski

Human disturbances and the daytime activity of sympatric otters along equatorial Amazonian rivers
type: item
type: AcademicArticle
description: Background Previous studies suggest coexistence between sympatric neotropical (Lontra longicaudis) and giant otters (Pteronura brasiliensis) maybe facilitated by temporal and spatial differences in activity. Yet, to date there has been no systematic evaluation of activity of these species in sympatry. Here we use extensive multi-year field data to compare temporal and spatial patterns in the diurnal activity of sympatric giant and neotropical otters to answer three questions: Do temporal patterns in daytime river use change in relation to seasonal river levels (low, rising, high and declining river levels), do they change due to human disturbances (boats and fishing nets) and do patterns in neotropical otter activity change due to the presence of the larger sized giant otter? Methods Direct observations of both species were recorded using standardized boat surveys along 218 km of rivers over 53 months during nine years (2011–2013 and 2015–2020). Complementary techniques (Generalized Additive Models, Kernel density estimates and non-parametric tests,) were used to compare diurnal activity patterns along rivers subdivided into 41 river reaches. Results The presence of giant otters decreased threefold from 67% of the least disturbed reaches (few boats no fishing nets) to 18% of the most disturbed reaches with many boats and fishing nets. In contrast neotropical otter presence nearly doubled from 44% of the least disturbed to 73% of the most disturbed reaches with fewest giant otter detections. Both species were observed across all daytime hours but were observed rarely on the same day. There was no evidence to suggest simultaneous use of the same reach. When species were detected on the same day, they were separated spatially (median distance between species 12.5 km) and temporally (median time difference 3.0 hours). There was little change in activity of either species among seasons. Giant otters were less active in river reaches with fishing nets and boat use, wherea…
format: application/pdf
format: text/html
creator: Darren Norris
creator: Fernanda Michalski
subject: Biodiversity
subject: Conservation Biology
subject: Zoology
subject: Coupled Natural and Human Systems
subject: Freshwater Biology
description: doi:10.7717/peerj.15742
publisher: PeerJ Inc.
rights: © 2023 Norris and Michalski
abstract: Background Previous studies suggest coexistence between sympatric neotropical (Lontra longicaudis) and giant otters (Pteronura brasiliensis) maybe facilitated by temporal and spatial differences in activity. Yet, to date there has been no systematic evaluation of activity of these species in sympatry. Here we use extensive multi-year field data to compare temporal and spatial patterns in the diurnal activity of sympatric giant and neotropical otters to answer three questions: Do temporal patterns in daytime river use change in relation to seasonal river levels (low, rising, high and declining river levels), do they change due to human disturbances (boats and fishing nets) and do patterns in neotropical otter activity change due to the presence of the larger sized giant otter? Methods Direct observations of both species were recorded using standardized boat surveys along 218 km of rivers over 53 months during nine years (2011–2013 and 2015–2020). Complementary techniques (Generalized Additive Models, Kernel density estimates and non-parametric tests,) were used to compare diurnal activity patterns along rivers subdivided into 41 river reaches. Results The presence of giant otters decreased threefold from 67% of the least disturbed reaches (few boats no fishing nets) to 18% of the most disturbed reaches with many boats and fishing nets. In contrast neotropical otter presence nearly doubled from 44% of the least disturbed to 73% of the most disturbed reaches with fewest giant otter detections. Both species were observed across all daytime hours but were observed rarely on the same day. There was no evidence to suggest simultaneous use of the same reach. When species were detected on the same day, they were separated spatially (median distance between species 12.5 km) and temporally (median time difference 3.0 hours). There was little change in activity of either species among seasons. Giant otters were less active in river reaches with fishing nets and boat use, wherea…
bibliographic citation: Norris et al. (2023) Human disturbances and the daytime activity of sympatric otters along equatorial Amazonian rivers. PeerJ 11:e15742 https://doi.org/10.7717/peerj.15742
date submitted: 2022-07-13
date accepted: 2023-06-21
issued: 2023-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Norris
  given name: Darren
author list: Agent
  family name: Michalski
  given name: Fernanda
doi: 10.7717/peerj.15742
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-21
copyright: ©2023 Norris and Michalski
attribution name: Norris and Michalski

Confirmatory digital subtraction angiography after clinical brain death/death by neurological criteria: impact on number of donors and organ transplants
type: item
type: AcademicArticle
description: Background Demand for organs exceeds the number of transplants available, underscoring the need to optimize organ donation procedures. However, protocols for determining brain death (BD)/death by neurological criteria (DNC) vary considerably worldwide. In Denmark, digital subtraction angiography (DSA) is the only legally approved confirmatory test for diagnosing BD/DNC. We investigated the effect of the time delay caused by (repeat) confirmatory DSA on the number of organs donated by patients meeting clinical criteria for BD/DNC. We hypothesized that, first, patients investigated with ≥2 DSAs donate fewer organs than those investigated with a single DSA; second, radiological interpretation of DSA is subject to interrater variability; and third, residual intracranial circulation is inversely correlated with inotropic blood pressure support. Methods All DSAs performed over a 7-year period as part of BD/DNC protocols at Rigshospitalet, Copenhagen University Hospital, Denmark, were included. Clinical data were extracted from electronic health records. DSAs were reinterpreted by an independent neurinterventionist blinded to the original radiological reports. Results We identified 130 DSAs in 100 eligible patients. Patients with ≥2 DSAs (n = 20) donated fewer organs (1.7 +/− 1.6 SD) than patients undergoing a single DSA (n = 80, 2.6 +/− 1.7 organs, p = 0.03), and they became less often donors (n = 12, 60%) than patients with just 1 DSA (n = 65, 81.3%; p = 0.04). Interrater agreement of radiological DSA interpretation was 88.5% (Cohen’s kappa = 0.76). Patients with self-maintained blood pressure had more often residual intracranial circulation (n = 13/26, 50%) than patients requiring inotropic support (n = 14/74, 18.9%; OR = 0.23, 95% CI [0.09–0.61]; p = 0.002). Discussion In potential donors who fulfill clinical BD/DNC criteria, delays caused by repetition of confirmatory DSA result in lost donors and organ transplants. Self-maintained blood pressure at the time of clinic…
format: application/pdf
format: text/html
creator: Karen Irgens Tanderup Hansen
creator: Jesper Kelsen
creator: Marwan H. Othman
creator: Trine Stavngaard
creator: Daniel Kondziella
subject: Anesthesiology and Pain Management
subject: Emergency and Critical Care
subject: Neurology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.15759
publisher: PeerJ Inc.
rights: © 2023 Hansen et al.
abstract: Background Demand for organs exceeds the number of transplants available, underscoring the need to optimize organ donation procedures. However, protocols for determining brain death (BD)/death by neurological criteria (DNC) vary considerably worldwide. In Denmark, digital subtraction angiography (DSA) is the only legally approved confirmatory test for diagnosing BD/DNC. We investigated the effect of the time delay caused by (repeat) confirmatory DSA on the number of organs donated by patients meeting clinical criteria for BD/DNC. We hypothesized that, first, patients investigated with ≥2 DSAs donate fewer organs than those investigated with a single DSA; second, radiological interpretation of DSA is subject to interrater variability; and third, residual intracranial circulation is inversely correlated with inotropic blood pressure support. Methods All DSAs performed over a 7-year period as part of BD/DNC protocols at Rigshospitalet, Copenhagen University Hospital, Denmark, were included. Clinical data were extracted from electronic health records. DSAs were reinterpreted by an independent neurinterventionist blinded to the original radiological reports. Results We identified 130 DSAs in 100 eligible patients. Patients with ≥2 DSAs (n = 20) donated fewer organs (1.7 +/− 1.6 SD) than patients undergoing a single DSA (n = 80, 2.6 +/− 1.7 organs, p = 0.03), and they became less often donors (n = 12, 60%) than patients with just 1 DSA (n = 65, 81.3%; p = 0.04). Interrater agreement of radiological DSA interpretation was 88.5% (Cohen’s kappa = 0.76). Patients with self-maintained blood pressure had more often residual intracranial circulation (n = 13/26, 50%) than patients requiring inotropic support (n = 14/74, 18.9%; OR = 0.23, 95% CI [0.09–0.61]; p = 0.002). Discussion In potential donors who fulfill clinical BD/DNC criteria, delays caused by repetition of confirmatory DSA result in lost donors and organ transplants. Self-maintained blood pressure at the time of clinic…
bibliographic citation: Hansen et al. (2023) Confirmatory digital subtraction angiography after clinical brain death/death by neurological criteria: impact on number of donors and organ transplants. PeerJ 11:e15759 https://doi.org/10.7717/peerj.15759
date submitted: 2023-05-04
date accepted: 2023-06-26
issued: 2023-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hansen
  given name: Karen Irgens Tanderup
author list: Agent
  family name: Kelsen
  given name: Jesper
author list: Agent
  family name: Othman
  given name: Marwan H.
author list: Agent
  family name: Stavngaard
  given name: Trine
author list: Agent
  family name: Kondziella
  given name: Daniel
doi: 10.7717/peerj.15759
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-21
copyright: © 2023 Hansen et al.
attribution name: Hansen et al.

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