PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Exogenous hydrogen sulfide improves salt stress tolerance of Reaumuria soongorica seedlings by regulating active oxygen metabolism
items: Neighborhood-based inference and restricted Boltzmann machine for small molecule-miRNA associations prediction
items: Genetic diversity analysis and molecular characteristics of wild centipedegrass using sequence-related amplified polymorphism (SRAP) markers
items: Characteristics of water jump for better performance in collegiate male 3000 m steeplechase
items: Bacillus amyloliquefaciens 11B91 inoculation enhances the growth of quinoa (Chenopodium quinoa Willd.) under salt stress
items: A decision tree model to predict liver cirrhosis in hepatocellular carcinoma patients: a retrospective study
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)

Exogenous hydrogen sulfide improves salt stress tolerance of Reaumuria soongorica seedlings by regulating active oxygen metabolism
type: item
type: AcademicArticle
description: Hydrogen sulfide (H2S), as an endogenous gas signaling molecule, plays an important role in plant growth regulation and resistance to abiotic stress. This study aims to investigate the mechanism of exogenous H2S on the growth and development of Reaumuria soongorica seedlings under salt stress and to determine the optimal concentration for foliar application. To investigate the regulatory effects of exogenous H2S (donor sodium hydrosulfide, NaHS) at concentrations ranging from 0 to 1 mM on reactive oxygen species (ROS), antioxidant system, and osmoregulation in R. soongorica seedlings under 300 mM NaCl stress. The growth of R. soongorica seedlings was inhibited by salt stress, which resulted in a decrease in the leaf relative water content (LRWC), specific leaf area (SLA), and soluble sugar content in leaves, elevated activity levels of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT); and accumulated superoxide anion (O2–), proline, malondialdehyde (MDA), and soluble protein content in leaves; and increased L-cysteine desulfhydrase (LCD) activity and endogenous H2S content. This indicated that a high level of ROS was produced in the leaves of R. soongorica seedlings and seriously affected the growth and development of R. soongorica seedlings. The exogenous application of different concentrations of NaHS reduced the content of O 2–, proline and MDA, increased the activity of antioxidant enzymes and the content of osmoregulators (soluble sugars and soluble proteins), while the LCD enzyme activity and the content of endogenous H2S were further increased with the continuous application of exogenous H2S. The inhibitory effects of salt stress on the growth rate of plant height and ground diameter, the LRWC, biomass, and SLA were effectively alleviated. A comprehensive analysis showed that the LRWC, POD, and proline could be used as the main indicators to evaluate the alleviating effect of exogenous H2S on R. soongorica seedlings under salt stress. The opti…
format: application/pdf
format: text/html
creator: Hanghang Liu
creator: Peifang Chong
creator: Zehua Liu
creator: Xinguang Bao
creator: Bingbing Tan
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.15881
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Hydrogen sulfide (H2S), as an endogenous gas signaling molecule, plays an important role in plant growth regulation and resistance to abiotic stress. This study aims to investigate the mechanism of exogenous H2S on the growth and development of Reaumuria soongorica seedlings under salt stress and to determine the optimal concentration for foliar application. To investigate the regulatory effects of exogenous H2S (donor sodium hydrosulfide, NaHS) at concentrations ranging from 0 to 1 mM on reactive oxygen species (ROS), antioxidant system, and osmoregulation in R. soongorica seedlings under 300 mM NaCl stress. The growth of R. soongorica seedlings was inhibited by salt stress, which resulted in a decrease in the leaf relative water content (LRWC), specific leaf area (SLA), and soluble sugar content in leaves, elevated activity levels of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT); and accumulated superoxide anion (O2–), proline, malondialdehyde (MDA), and soluble protein content in leaves; and increased L-cysteine desulfhydrase (LCD) activity and endogenous H2S content. This indicated that a high level of ROS was produced in the leaves of R. soongorica seedlings and seriously affected the growth and development of R. soongorica seedlings. The exogenous application of different concentrations of NaHS reduced the content of O 2–, proline and MDA, increased the activity of antioxidant enzymes and the content of osmoregulators (soluble sugars and soluble proteins), while the LCD enzyme activity and the content of endogenous H2S were further increased with the continuous application of exogenous H2S. The inhibitory effects of salt stress on the growth rate of plant height and ground diameter, the LRWC, biomass, and SLA were effectively alleviated. A comprehensive analysis showed that the LRWC, POD, and proline could be used as the main indicators to evaluate the alleviating effect of exogenous H2S on R. soongorica seedlings under salt stress. The opti…
bibliographic citation: Liu et al. (2023) Exogenous hydrogen sulfide improves salt stress tolerance of Reaumuria soongorica seedlings by regulating active oxygen metabolism. PeerJ 11:e15881 https://doi.org/10.7717/peerj.15881
date submitted: 2023-03-31
date accepted: 2023-07-20
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Hanghang
author list: Agent
  family name: Chong
  given name: Peifang
author list: Agent
  family name: Liu
  given name: Zehua
author list: Agent
  family name: Bao
  given name: Xinguang
author list: Agent
  family name: Tan
  given name: Bingbing
doi: 10.7717/peerj.15881
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: ©2023 Liu et al.
attribution name: Liu et al.

Neighborhood-based inference and restricted Boltzmann machine for small molecule-miRNA associations prediction
type: item
type: AcademicArticle
description: Background A growing number of experiments have shown that microRNAs (miRNAs) can be used as target of small molecules (SMs) to regulate gene expression for treating diseases. Therefore, identifying SM-related miRNAs is helpful for the treatment of diseases in the domain of medical investigation. Methods This article presents a new computational model, called NIRBMSMMA (neighborhood-based inference (NI) and restricted Boltzmann machine (RBM)), which we developed to identify potential small molecule-miRNA associations (NIRBMSMMA). First, grounded on known SM-miRNAs associations, SM similarity and miRNA similarity, NI was used to predict score of an unknown SM-miRNA pair by reckoning the sum of known associations between neighbors of the SM (miRNA) and the miRNA (SM). Second, utilizing a two-layered generative stochastic artificial neural network, RBM was used to predict SM-miRNA association by learning potential probability distribution from known SM-miRNA associations. At last, an ensemble learning model was conducted to combine NI and RBM for identifying potential SM-miRNA associations. Results Furthermore, we conducted global leave one out cross validation (LOOCV), miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation to assess performance of NIRBMSMMA based on three datasets. Results showed that NIRBMSMMA obtained areas under the curve (AUC) of 0.9912, 0.9875, 0.8376 and 0.9898 ± 0.0009 under global LOOCV, miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation based on dataset 1, respectively. For dataset 2, the AUCs are 0.8645, 0.8720, 0.7066 and 0.8547 ± 0.0046 in turn. For dataset 3, the AUCs are 0.9884, 0.9802, 0.8239 and 0.9870 ± 0.0015 in turn. Also, we conducted case studies to further assess the predictive performance of NIRBMSMMA. These results illustrated the proposed model is a useful tool in predicting potential SM-miRNA associations.
format: application/pdf
format: text/html
creator: Jia Qu
creator: Zihao Song
creator: Xiaolong Cheng
creator: Zhibin Jiang
creator: Jie Zhou
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.15889
publisher: PeerJ Inc.
rights: © 2023 Qu et al.
abstract: Background A growing number of experiments have shown that microRNAs (miRNAs) can be used as target of small molecules (SMs) to regulate gene expression for treating diseases. Therefore, identifying SM-related miRNAs is helpful for the treatment of diseases in the domain of medical investigation. Methods This article presents a new computational model, called NIRBMSMMA (neighborhood-based inference (NI) and restricted Boltzmann machine (RBM)), which we developed to identify potential small molecule-miRNA associations (NIRBMSMMA). First, grounded on known SM-miRNAs associations, SM similarity and miRNA similarity, NI was used to predict score of an unknown SM-miRNA pair by reckoning the sum of known associations between neighbors of the SM (miRNA) and the miRNA (SM). Second, utilizing a two-layered generative stochastic artificial neural network, RBM was used to predict SM-miRNA association by learning potential probability distribution from known SM-miRNA associations. At last, an ensemble learning model was conducted to combine NI and RBM for identifying potential SM-miRNA associations. Results Furthermore, we conducted global leave one out cross validation (LOOCV), miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation to assess performance of NIRBMSMMA based on three datasets. Results showed that NIRBMSMMA obtained areas under the curve (AUC) of 0.9912, 0.9875, 0.8376 and 0.9898 ± 0.0009 under global LOOCV, miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation based on dataset 1, respectively. For dataset 2, the AUCs are 0.8645, 0.8720, 0.7066 and 0.8547 ± 0.0046 in turn. For dataset 3, the AUCs are 0.9884, 0.9802, 0.8239 and 0.9870 ± 0.0015 in turn. Also, we conducted case studies to further assess the predictive performance of NIRBMSMMA. These results illustrated the proposed model is a useful tool in predicting potential SM-miRNA associations.
bibliographic citation: Qu et al. (2023) Neighborhood-based inference and restricted Boltzmann machine for small molecule-miRNA associations prediction. PeerJ 11:e15889 https://doi.org/10.7717/peerj.15889
date submitted: 2023-05-16
date accepted: 2023-07-21
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qu
  given name: Jia
author list: Agent
  family name: Song
  given name: Zihao
author list: Agent
  family name: Cheng
  given name: Xiaolong
author list: Agent
  family name: Jiang
  given name: Zhibin
author list: Agent
  family name: Zhou
  given name: Jie
doi: 10.7717/peerj.15889
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: ©2023 Qu et al.
attribution name: Qu et al.

Genetic diversity analysis and molecular characteristics of wild centipedegrass using sequence-related amplified polymorphism (SRAP) markers
type: item
type: AcademicArticle
description: Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is commonly used as a low-maintenance warm-season turfgrass owing to its excellent adaptation to various soil types. A better understanding of the genetic diversity pattern of centipedegrass is essential for the efficient development and utilization of accessions. This study used fifty-five pairs of primers to detect the genetic variation and genetic structure of twenty-three wild centipedegrass accessions by Sequence-related amplified polymorphism (SRAP) markers. A total of 919 reliable bands were amplified, among which 606 (65.80%) were polymorphic and 160 (2.91%) were the monomorphic loci. The average polymorphic information content (PIC) value was 0.228. The unweighted pair group method with arithmetic mean (UPGMA) clustering analysis grouped the twenty-three accessions into two clusters. Meanwhile, the structure analysis showed that the tested accessions possessed two main genetic memberships (K = 2). The Mantel test significantly correlated the genetic and geographic distance matrices (r = 0.3854, p = 0.000140). Furthermore, geographical groups showed moderate genetic differentiation, and the highest intragroup genetic diversity was found in the Sichuan group (He = 0.201). Overall, the present research findings could promote the protection and collection of centipedegrass and provide comprehensive information to develop novel breeding strategies.
format: application/pdf
format: text/html
creator: Xiaoyun Wang
creator: Wenlong Gou
creator: Ting Wang
creator: Yanli Xiong
creator: Yi Xiong
creator: Qingqing Yu
creator: Zhixiao Dong
creator: Xiao Ma
creator: Nanqing Liu
creator: Junming Zhao
subject: Biodiversity
subject: Genetics
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.15900
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is commonly used as a low-maintenance warm-season turfgrass owing to its excellent adaptation to various soil types. A better understanding of the genetic diversity pattern of centipedegrass is essential for the efficient development and utilization of accessions. This study used fifty-five pairs of primers to detect the genetic variation and genetic structure of twenty-three wild centipedegrass accessions by Sequence-related amplified polymorphism (SRAP) markers. A total of 919 reliable bands were amplified, among which 606 (65.80%) were polymorphic and 160 (2.91%) were the monomorphic loci. The average polymorphic information content (PIC) value was 0.228. The unweighted pair group method with arithmetic mean (UPGMA) clustering analysis grouped the twenty-three accessions into two clusters. Meanwhile, the structure analysis showed that the tested accessions possessed two main genetic memberships (K = 2). The Mantel test significantly correlated the genetic and geographic distance matrices (r = 0.3854, p = 0.000140). Furthermore, geographical groups showed moderate genetic differentiation, and the highest intragroup genetic diversity was found in the Sichuan group (He = 0.201). Overall, the present research findings could promote the protection and collection of centipedegrass and provide comprehensive information to develop novel breeding strategies.
bibliographic citation: Wang et al. (2023) Genetic diversity analysis and molecular characteristics of wild centipedegrass using sequence-related amplified polymorphism (SRAP) markers. PeerJ 11:e15900 https://doi.org/10.7717/peerj.15900
date submitted: 2023-03-29
date accepted: 2023-07-25
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xiaoyun
author list: Agent
  family name: Gou
  given name: Wenlong
author list: Agent
  family name: Wang
  given name: Ting
author list: Agent
  family name: Xiong
  given name: Yanli
author list: Agent
  family name: Xiong
  given name: Yi
author list: Agent
  family name: Yu
  given name: Qingqing
author list: Agent
  family name: Dong
  given name: Zhixiao
author list: Agent
  family name: Ma
  given name: Xiao
author list: Agent
  family name: Liu
  given name: Nanqing
author list: Agent
  family name: Zhao
  given name: Junming
doi: 10.7717/peerj.15900
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: ©2023 Wang et al.
attribution name: Wang et al.

Characteristics of water jump for better performance in collegiate male 3000 m steeplechase
type: item
type: AcademicArticle
description: Background The 3000 m steeplechase consists of 28 barriers and seven water-jumping obstacles. The water jump in the 3000 m steeplechase makes it different from the sprint hurdle events. It is important for coaches and athletes to understand how to clear the water jump successfully. I aimed to investigate whether the takeoff and landing distances for the water jump per lap differ between participants with good and worse records. Methods Data were collected from the men’s 3000 m steeplechase races (heats) at Kanto Intercollegiate race. A total of 48 men’s performances were analyzed (24 upper group, 24 lower group). Takeoff distance, landing distance and clearance time were analyzed. Takeoff distance, landing distance, total water jump distance and clearance time were subjected to mixed two-way ANOVAs with repeated factors of Lap (lap 1/lap 2/lap 3/lap 4/lap 5/lap 6/lap 7) with Group (upper group/lower group) as a between group factor. Results Takeoff distance was longer for upper group (1.43 m) than lower group (1.34 m) (p = .01). Landing distance was longer for upper group (2.95 m) than for lower group (2.74 m) (p = .01) and was longer for lap 1 (2.95 m) than last three laps (lap 5: 2.83 m, lap 6: 2.82 m, lap 7: 2.76 m) (p = .01). Discussion Individuals who were faster in 3000 m steeplechase exhibited longer water jump distance. The effect of fatigue might be greater for landing distance than for takeoff distance. Because the landing distance becomes shorter in the second half of the 3000 m steeplechase, it is important to note that athletes should aim to land as far away from the water pit as possible.
format: application/pdf
format: text/html
creator: Yuya Maruo
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.15918
publisher: PeerJ Inc.
rights: © 2023 Maruo
abstract: Background The 3000 m steeplechase consists of 28 barriers and seven water-jumping obstacles. The water jump in the 3000 m steeplechase makes it different from the sprint hurdle events. It is important for coaches and athletes to understand how to clear the water jump successfully. I aimed to investigate whether the takeoff and landing distances for the water jump per lap differ between participants with good and worse records. Methods Data were collected from the men’s 3000 m steeplechase races (heats) at Kanto Intercollegiate race. A total of 48 men’s performances were analyzed (24 upper group, 24 lower group). Takeoff distance, landing distance and clearance time were analyzed. Takeoff distance, landing distance, total water jump distance and clearance time were subjected to mixed two-way ANOVAs with repeated factors of Lap (lap 1/lap 2/lap 3/lap 4/lap 5/lap 6/lap 7) with Group (upper group/lower group) as a between group factor. Results Takeoff distance was longer for upper group (1.43 m) than lower group (1.34 m) (p = .01). Landing distance was longer for upper group (2.95 m) than for lower group (2.74 m) (p = .01) and was longer for lap 1 (2.95 m) than last three laps (lap 5: 2.83 m, lap 6: 2.82 m, lap 7: 2.76 m) (p = .01). Discussion Individuals who were faster in 3000 m steeplechase exhibited longer water jump distance. The effect of fatigue might be greater for landing distance than for takeoff distance. Because the landing distance becomes shorter in the second half of the 3000 m steeplechase, it is important to note that athletes should aim to land as far away from the water pit as possible.
bibliographic citation: Maruo (2023) Characteristics of water jump for better performance in collegiate male 3000 m steeplechase. PeerJ 11:e15918 https://doi.org/10.7717/peerj.15918
date submitted: 2023-06-01
date accepted: 2023-07-27
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maruo
  given name: Yuya
doi: 10.7717/peerj.15918
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: ©2023 Maruo
attribution name: Maruo

Bacillus amyloliquefaciens 11B91 inoculation enhances the growth of quinoa (Chenopodium quinoa Willd.) under salt stress
type: item
type: AcademicArticle
description: Quinoa (Chenopodium quinoa Willd.) is a highly nutritious food product with a comprehensive development prospect. Here, we discussed the effect of Bacillus amyloliquefaciens 11B91 on the growth, development and salt tolerance (salt concentrations: 0, 150, 300 mmol·L−1) of quinoa and highlighted a positive role for the application of plant growth-promoting rhizobacteria bacteria in quinoa. In this artical, the growth-promoting effect of Bacillus amyloliquefaciens 11B91 on quinoa (Longli No.1) and the changes in biomass, chlorophyll content, root activity and total phosphorus content under salt stress were measured. The results revealed that plants inoculated with 11B91 exhibited increased maximum shoot fresh weight (73.95%), root fresh weight (75.36%), root dry weight (136%), chlorophyll a (65.32%) contents and chlorophyll b (58.5%) contents, root activity (54.44%) and total phosphorus content (16.66%). Additionally, plants inoculated with 11B91 under salt stress plants showed significantly improved, fresh weight (107%), dry weight (133%), chlorophyll a (162%) contents and chlorophyll b (76.37%) contents, root activity (33.07%), and total phosphorus content (42.73%).
format: application/pdf
format: text/html
creator: Jing Li
creator: Xiaonong Guo
creator: Deyu Cai
creator: Ying Xu
creator: Yaling Wang
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15925
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Quinoa (Chenopodium quinoa Willd.) is a highly nutritious food product with a comprehensive development prospect. Here, we discussed the effect of Bacillus amyloliquefaciens 11B91 on the growth, development and salt tolerance (salt concentrations: 0, 150, 300 mmol·L−1) of quinoa and highlighted a positive role for the application of plant growth-promoting rhizobacteria bacteria in quinoa. In this artical, the growth-promoting effect of Bacillus amyloliquefaciens 11B91 on quinoa (Longli No.1) and the changes in biomass, chlorophyll content, root activity and total phosphorus content under salt stress were measured. The results revealed that plants inoculated with 11B91 exhibited increased maximum shoot fresh weight (73.95%), root fresh weight (75.36%), root dry weight (136%), chlorophyll a (65.32%) contents and chlorophyll b (58.5%) contents, root activity (54.44%) and total phosphorus content (16.66%). Additionally, plants inoculated with 11B91 under salt stress plants showed significantly improved, fresh weight (107%), dry weight (133%), chlorophyll a (162%) contents and chlorophyll b (76.37%) contents, root activity (33.07%), and total phosphorus content (42.73%).
bibliographic citation: Li et al. (2023) Bacillus amyloliquefaciens 11B91 inoculation enhances the growth of quinoa (Chenopodium quinoa Willd.) under salt stress. PeerJ 11:e15925 https://doi.org/10.7717/peerj.15925
date submitted: 2023-03-31
date accepted: 2023-07-30
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Guo
  given name: Xiaonong
author list: Agent
  family name: Cai
  given name: Deyu
author list: Agent
  family name: Xu
  given name: Ying
author list: Agent
  family name: Wang
  given name: Yaling
doi: 10.7717/peerj.15925
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: © 2023 Li et al.
attribution name: Li et al.

A decision tree model to predict liver cirrhosis in hepatocellular carcinoma patients: a retrospective study
type: item
type: AcademicArticle
description: Background The severity of liver cirrhosis in hepatocellular carcinoma (HCC) patients is essential for determining the scope of surgical resection. It also affects the long-term efficacy of systemic anti-tumor therapy and transcatheter arterial chemoembolization (TACE). Non-invasive tools, including aspartate aminotransferase to platelet ratio index (APRI), fibrosis-4 (FIB-4), and γ-glutamyl transferase to platelet ratio (GPR), are less accurate in predicting cirrhosis in HCC patients. We aimed to build a novel decision tree model to improve diagnostic accuracy of liver cirrhosis. Patients and Methods The Mann-Whitney U test, χ2 test, and multivariate logistic regression analysis were used to identify independent cirrhosis predictors. A decision tree model was developed using machine learning algorithms in a training cohort of 141 HCC patients. Internal validation was conducted in 99 HCC patients. The diagnostic accuracy and calibration of the established model were evaluated using receiver operating characteristic (ROC) and calibration curves, respectively. Results Sex and platelet count were identified as independent cirrhosis predictors. A decision tree model integrating imaging-reported cirrhosis, APRI, FIB-4, and GPR was established. The novel model had an excellent diagnostic performance in the training and validation cohorts, with area under the curve (AUC) values of 0.853 and 0.817, respectively. Calibration curves and the Hosmer-Lemeshow test showed good calibration of the novel model. The decision curve analysis (DCA) indicated that the decision tree model could provide a larger net benefit to predict liver cirrhosis. Conclusion Our developed decision tree model could successfully predict liver cirrhosis in HCC patients, which may be helpful in clinical decision-making.
format: application/pdf
format: text/html
creator: Zheyu Zhou
creator: Chaobo Chen
creator: Meiling Sun
creator: Xiaoliang Xu
creator: Yang Liu
creator: Qiaoyu Liu
creator: Jincheng Wang
creator: Yin Yin
creator: Beicheng Sun
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Pathology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.15950
publisher: PeerJ Inc.
rights: © 2023 Zhou et al.
abstract: Background The severity of liver cirrhosis in hepatocellular carcinoma (HCC) patients is essential for determining the scope of surgical resection. It also affects the long-term efficacy of systemic anti-tumor therapy and transcatheter arterial chemoembolization (TACE). Non-invasive tools, including aspartate aminotransferase to platelet ratio index (APRI), fibrosis-4 (FIB-4), and γ-glutamyl transferase to platelet ratio (GPR), are less accurate in predicting cirrhosis in HCC patients. We aimed to build a novel decision tree model to improve diagnostic accuracy of liver cirrhosis. Patients and Methods The Mann-Whitney U test, χ2 test, and multivariate logistic regression analysis were used to identify independent cirrhosis predictors. A decision tree model was developed using machine learning algorithms in a training cohort of 141 HCC patients. Internal validation was conducted in 99 HCC patients. The diagnostic accuracy and calibration of the established model were evaluated using receiver operating characteristic (ROC) and calibration curves, respectively. Results Sex and platelet count were identified as independent cirrhosis predictors. A decision tree model integrating imaging-reported cirrhosis, APRI, FIB-4, and GPR was established. The novel model had an excellent diagnostic performance in the training and validation cohorts, with area under the curve (AUC) values of 0.853 and 0.817, respectively. Calibration curves and the Hosmer-Lemeshow test showed good calibration of the novel model. The decision curve analysis (DCA) indicated that the decision tree model could provide a larger net benefit to predict liver cirrhosis. Conclusion Our developed decision tree model could successfully predict liver cirrhosis in HCC patients, which may be helpful in clinical decision-making.
bibliographic citation: Zhou et al. (2023) A decision tree model to predict liver cirrhosis in hepatocellular carcinoma patients: a retrospective study. PeerJ 11:e15950 https://doi.org/10.7717/peerj.15950
date submitted: 2023-06-16
date accepted: 2023-08-01
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Zheyu
author list: Agent
  family name: Chen
  given name: Chaobo
author list: Agent
  family name: Sun
  given name: Meiling
author list: Agent
  family name: Xu
  given name: Xiaoliang
author list: Agent
  family name: Liu
  given name: Yang
author list: Agent
  family name: Liu
  given name: Qiaoyu
author list: Agent
  family name: Wang
  given name: Jincheng
author list: Agent
  family name: Yin
  given name: Yin
author list: Agent
  family name: Sun
  given name: Beicheng
doi: 10.7717/peerj.15950
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: © 2023 Zhou et al.
attribution name: Zhou et al.

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

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