PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants
items: Fast, low-memory detection and localization of large, polymorphic inversions from SNPs
items: Exploring the relationship between ADHD, its common comorbidities, and their relationship to organizational skills
items: Effect of fire on the palatability of plants in an African woodland savanna: varying impacts depending on plant functional groups
items: Effective asexual reproduction of a widespread soft coral: comparative assessment of four different fragmentation methods
items: A novel nutritional index as a predictor of mortality in dilated cardiomyopathy: a retrospective study
items: Plasma FGF21 concentrations are regulated by glucose independently of insulin and GLP-1 in lean, healthy humans
items: DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
items: Optimized nitrogen rate, plant density, and irrigation level reduced ammonia emission and nitrate leaching on maize farmland in the oasis area of China
items: Reconstructing the transmission dynamics of varicella in Japan: an elevation of age at infection

Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants
type: item
type: AcademicArticle
description: Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C4 photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C4 and CAM plants and shed light on the adaptation of plants in dry, hot environments.
format: application/pdf
format: text/html
creator: Jiang-Ping Shu
creator: Yue-Hong Yan
creator: Rui-Jiang Wang
subject: Agricultural Science
subject: Bioinformatics
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.12828
publisher: PeerJ Inc.
rights: © 2022 Shu et al.
abstract: Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C4 photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C4 and CAM plants and shed light on the adaptation of plants in dry, hot environments.
bibliographic citation: Shu et al. (2022) Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants. PeerJ 10:e12828 https://doi.org/10.7717/peerj.12828
date submitted: 2021-07-08
date accepted: 2022-01-03
issued: 2022-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shu
  given name: Jiang-Ping
author list: Agent
  family name: Yan
  given name: Yue-Hong
author list: Agent
  family name: Wang
  given name: Rui-Jiang
doi: 10.7717/peerj.12828
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-20
copyright: ©2022 Shu et al.
attribution name: Shu et al.

Fast, low-memory detection and localization of large, polymorphic inversions from SNPs
type: item
type: AcademicArticle
description: Background Large (>1 Mb), polymorphic inversions have substantial impacts on population structure and maintenance of genotypes. These large inversions can be detected from single nucleotide polymorphism (SNP) data using unsupervised learning techniques like PCA. Construction and analysis of a feature matrix from millions of SNPs requires large amount of memory and limits the sizes of data sets that can be analyzed. Methods We propose using feature hashing construct a feature matrix from a VCF file of SNPs for reducing memory usage. The matrix is constructed in a streaming fashion such that the entire VCF file is never loaded into memory at one time. Results When evaluated on Anopheles mosquito and Drosophila fly data sets, our approach reduced memory usage by 97% with minimal reductions in accuracy for inversion detection and localization tasks. Conclusion With these changes, inversions in larger data sets can be analyzed easily and efficiently on common laptop and desktop computers. Our method is publicly available through our open-source inversion analysis software, Asaph.
format: application/pdf
format: text/html
creator: Ronald J. Nowling
creator: Fabian Fallas-Moya
creator: Amir Sadovnik
creator: Scott Emrich
creator: Matthew Aleck
creator: Daniel Leskiewicz
creator: John G. Peters
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.12831
publisher: PeerJ Inc.
rights: © 2022 Nowling et al.
abstract: Background Large (>1 Mb), polymorphic inversions have substantial impacts on population structure and maintenance of genotypes. These large inversions can be detected from single nucleotide polymorphism (SNP) data using unsupervised learning techniques like PCA. Construction and analysis of a feature matrix from millions of SNPs requires large amount of memory and limits the sizes of data sets that can be analyzed. Methods We propose using feature hashing construct a feature matrix from a VCF file of SNPs for reducing memory usage. The matrix is constructed in a streaming fashion such that the entire VCF file is never loaded into memory at one time. Results When evaluated on Anopheles mosquito and Drosophila fly data sets, our approach reduced memory usage by 97% with minimal reductions in accuracy for inversion detection and localization tasks. Conclusion With these changes, inversions in larger data sets can be analyzed easily and efficiently on common laptop and desktop computers. Our method is publicly available through our open-source inversion analysis software, Asaph.
bibliographic citation: Nowling et al. (2022) Fast, low-memory detection and localization of large, polymorphic inversions from SNPs. PeerJ 10:e12831 https://doi.org/10.7717/peerj.12831
date submitted: 2021-09-02
date accepted: 2022-01-04
issued: 2022-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nowling
  given name: Ronald J.
author list: Agent
  family name: Fallas-Moya
  given name: Fabian
author list: Agent
  family name: Sadovnik
  given name: Amir
author list: Agent
  family name: Emrich
  given name: Scott
author list: Agent
  family name: Aleck
  given name: Matthew
author list: Agent
  family name: Leskiewicz
  given name: Daniel
author list: Agent
  family name: Peters
  given name: John G.
doi: 10.7717/peerj.12831
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-20
copyright: © 2022 Nowling et al.
attribution name: Nowling et al.

Exploring the relationship between ADHD, its common comorbidities, and their relationship to organizational skills
type: item
type: AcademicArticle
description: Background Attention Deficit Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder affecting numerous executive functioning skills, such as organizational skills. While the relationship between the inattention aspect of ADHD and poor organizational skills is well documented, it is still unclear if lower organizational skills are only associated with ADHD or if they are also associated with other comorbid disorders commonly diagnosed in conjunction with ADHD. The purpose of the present study is to investigate the relationship between organizational skills and ADHD in adults, as well as the impact of comorbid disorders on ADHD in relation to organizational skills. Methods Four hundred seven (n = 201 with a diagnosis of ADHD) adults from the general population were recruited online. Participants completed a measure of organizational skills, measures assessing levels of ADHD, depression, and anxiety, and extensive demographic information related to their diagnosis of ADHD or other possible diagnosis. Results Participants with a diagnosis of ADHD were significantly more likely to have a comorbid diagnosis of depression and/or anxiety. Organizational skills were significantly lower in individuals who reported having received a diagnosis of ADHD, but not in those with a past diagnosis of depression and anxiety. However, organizational skills were lower in individuals currently experiencing higher levels of depression and anxiety. The results of regression analyses suggest that levels of organizational skills are most strongly predicted by inattention and more weakly predicted by comorbid disorders. Discussion These results highlight the centrality of organizational skills deficit in ADHD as well as the influence of the inattention component over other components commonly observed in ADHD on organizational skills. Suggestions for treatment of ADHD in adults are discussed.
format: application/pdf
format: text/html
creator: Guillaume Durand
creator: Ioana-Smarandita Arbone
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.12836
publisher: PeerJ Inc.
rights: © 2022 Durand and Arbone
abstract: Background Attention Deficit Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder affecting numerous executive functioning skills, such as organizational skills. While the relationship between the inattention aspect of ADHD and poor organizational skills is well documented, it is still unclear if lower organizational skills are only associated with ADHD or if they are also associated with other comorbid disorders commonly diagnosed in conjunction with ADHD. The purpose of the present study is to investigate the relationship between organizational skills and ADHD in adults, as well as the impact of comorbid disorders on ADHD in relation to organizational skills. Methods Four hundred seven (n = 201 with a diagnosis of ADHD) adults from the general population were recruited online. Participants completed a measure of organizational skills, measures assessing levels of ADHD, depression, and anxiety, and extensive demographic information related to their diagnosis of ADHD or other possible diagnosis. Results Participants with a diagnosis of ADHD were significantly more likely to have a comorbid diagnosis of depression and/or anxiety. Organizational skills were significantly lower in individuals who reported having received a diagnosis of ADHD, but not in those with a past diagnosis of depression and anxiety. However, organizational skills were lower in individuals currently experiencing higher levels of depression and anxiety. The results of regression analyses suggest that levels of organizational skills are most strongly predicted by inattention and more weakly predicted by comorbid disorders. Discussion These results highlight the centrality of organizational skills deficit in ADHD as well as the influence of the inattention component over other components commonly observed in ADHD on organizational skills. Suggestions for treatment of ADHD in adults are discussed.
bibliographic citation: Durand et al. (2022) Exploring the relationship between ADHD, its common comorbidities, and their relationship to organizational skills. PeerJ 10:e12836 https://doi.org/10.7717/peerj.12836
date submitted: 2021-06-26
date accepted: 2022-01-05
issued: 2022-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Durand
  given name: Guillaume
author list: Agent
  family name: Arbone
  given name: Ioana-Smarandita
doi: 10.7717/peerj.12836
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-20
copyright: ©2022 Durand and Arbone
attribution name: Durand and Arbone

Effect of fire on the palatability of plants in an African woodland savanna: varying impacts depending on plant functional groups
type: item
type: AcademicArticle
description: Fire and herbivores are two important drivers of changes in vegetation composition, quality and dynamics and both are highly related to each other. Herbivores are known to respond to fire both in terms of foraging decisions and distribution. However, little is known about the actual changes in plant chemistry following a fire event and how long these changes will last. We investigated the effect of fire on two different plant functional groups (grasses and woody species) in a woodland savanna of southern Africa. We studied chemical compounds known to be important for palatability of five perennial grass and seven woody species (trees and shrubs) common in the woodland savanna and known to be utilized by herbivores. We wanted to know if plant chemistry differs between a recently burned site (burned 2 years ago) and a control site, burned 16 years ago, and if grasses and woody species show similar relative differences between sites (i.e., the plants’ response to fire). We found a clear difference in chemical composition patterns between the plant functional groups, with an almost homogenous response to fire among woody species, but higher variability in response among grass species. Furthermore, we found that woody species maintained a higher nutritional value even 2 years after burning, whereas grasses did not show clear differences among the two investigated sites. Hence, few years after burning, woody plants might still serve as an attraction for herbivores, especially browsers, in contrast to grasses. The knowledge about these differences between the two functional groups in response to fire is beneficial for the development of management strategies for large herbivores whether domestic or wild.
format: application/pdf
format: text/html
creator: Caroline Stolter
creator: David F. Joubert
creator: Nekulilo Uunona
creator: Elise Nghalipo
creator: Vistorina Amputu
creator: Annika M. Felton
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.12721
publisher: PeerJ Inc.
rights: © 2022 Stolter et al.
abstract: Fire and herbivores are two important drivers of changes in vegetation composition, quality and dynamics and both are highly related to each other. Herbivores are known to respond to fire both in terms of foraging decisions and distribution. However, little is known about the actual changes in plant chemistry following a fire event and how long these changes will last. We investigated the effect of fire on two different plant functional groups (grasses and woody species) in a woodland savanna of southern Africa. We studied chemical compounds known to be important for palatability of five perennial grass and seven woody species (trees and shrubs) common in the woodland savanna and known to be utilized by herbivores. We wanted to know if plant chemistry differs between a recently burned site (burned 2 years ago) and a control site, burned 16 years ago, and if grasses and woody species show similar relative differences between sites (i.e., the plants’ response to fire). We found a clear difference in chemical composition patterns between the plant functional groups, with an almost homogenous response to fire among woody species, but higher variability in response among grass species. Furthermore, we found that woody species maintained a higher nutritional value even 2 years after burning, whereas grasses did not show clear differences among the two investigated sites. Hence, few years after burning, woody plants might still serve as an attraction for herbivores, especially browsers, in contrast to grasses. The knowledge about these differences between the two functional groups in response to fire is beneficial for the development of management strategies for large herbivores whether domestic or wild.
bibliographic citation: Stolter et al. (2022) Effect of fire on the palatability of plants in an African woodland savanna: varying impacts depending on plant functional groups. PeerJ 10:e12721 https://doi.org/10.7717/peerj.12721
date submitted: 2021-07-27
date accepted: 2021-12-09
issued: 2022-01-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stolter
  given name: Caroline
author list: Agent
  family name: Joubert
  given name: David F.
author list: Agent
  family name: Uunona
  given name: Nekulilo
author list: Agent
  family name: Nghalipo
  given name: Elise
author list: Agent
  family name: Amputu
  given name: Vistorina
author list: Agent
  family name: Felton
  given name: Annika M.
doi: 10.7717/peerj.12721
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-19
copyright: © 2022 Stolter et al.
attribution name: Stolter et al.

Effective asexual reproduction of a widespread soft coral: comparative assessment of four different fragmentation methods
type: item
type: AcademicArticle
description: Background Many coral reefs worldwide are experiencing declines in hard corals, resulting in other benthic organisms, e.g., soft corals, becoming more dominant. As such, more studies on the ecophysiology of soft corals are needed. Despite many methods for asexual reproduction of hard corals, effective methods for soft corals, i.e., without a hard skeleton, are scarce. This study, thus, assessed four fragmentation methods, the glue, rubber band, tunnel mesh, and plug mesh method for the pulsating soft coral Xenia umbellata that is widely distributed in the tropical Indo-Pacific. Methods Methods were comparatively assessed by determining the required time and labor for the fragmentation plus the health status of the fragmented corals by measuring their oxygen fluxes and pulsation rates, i.e., a special feature of this soft coral that can be used as a proxy for its health. Results There were no significant health status differences between methods. This was indicated by similar gross photosynthesis (between 7.4 to 9.7 μg O2 polyp−1 h−1) and pulsating rates (between 35 and 44 pulses min−1) among methods. In terms of time/labor intensity and success rates, i.e., the percentage of fragments attached to the desired surface, the plug mesh method was the most efficient method with a significantly higher success rate (95 ± 5%), while the others had a success rate between 5 ± 5 and 45 ± 15%. The time needed for fragmentation, though not significant, was also the shortest (78 ± 11 s fragment−1), while other methods required between 84 ± 14 and 126 ± 8 s frag−1. The plug mesh method may thus be a valuable tool related to the reproduction of soft corals for use in subsequent experimental work.
format: application/pdf
format: text/html
creator: Sohyoung Kim
creator: Christian Wild
creator: Arjen Tilstra
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12589
publisher: PeerJ Inc.
rights: © 2022 Kim et al.
abstract: Background Many coral reefs worldwide are experiencing declines in hard corals, resulting in other benthic organisms, e.g., soft corals, becoming more dominant. As such, more studies on the ecophysiology of soft corals are needed. Despite many methods for asexual reproduction of hard corals, effective methods for soft corals, i.e., without a hard skeleton, are scarce. This study, thus, assessed four fragmentation methods, the glue, rubber band, tunnel mesh, and plug mesh method for the pulsating soft coral Xenia umbellata that is widely distributed in the tropical Indo-Pacific. Methods Methods were comparatively assessed by determining the required time and labor for the fragmentation plus the health status of the fragmented corals by measuring their oxygen fluxes and pulsation rates, i.e., a special feature of this soft coral that can be used as a proxy for its health. Results There were no significant health status differences between methods. This was indicated by similar gross photosynthesis (between 7.4 to 9.7 μg O2 polyp−1 h−1) and pulsating rates (between 35 and 44 pulses min−1) among methods. In terms of time/labor intensity and success rates, i.e., the percentage of fragments attached to the desired surface, the plug mesh method was the most efficient method with a significantly higher success rate (95 ± 5%), while the others had a success rate between 5 ± 5 and 45 ± 15%. The time needed for fragmentation, though not significant, was also the shortest (78 ± 11 s fragment−1), while other methods required between 84 ± 14 and 126 ± 8 s frag−1. The plug mesh method may thus be a valuable tool related to the reproduction of soft corals for use in subsequent experimental work.
bibliographic citation: Kim et al. (2022) Effective asexual reproduction of a widespread soft coral: comparative assessment of four different fragmentation methods. PeerJ 10:e12589 https://doi.org/10.7717/peerj.12589
date submitted: 2021-06-04
date accepted: 2021-11-12
issued: 2022-01-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Sohyoung
author list: Agent
  family name: Wild
  given name: Christian
author list: Agent
  family name: Tilstra
  given name: Arjen
doi: 10.7717/peerj.12589
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-19
copyright: © 2022 Kim et al.
attribution name: Kim et al.

A novel nutritional index as a predictor of mortality in dilated cardiomyopathy: a retrospective study
type: item
type: AcademicArticle
description: Background Research has associated nutritional status with the prognosis of cardiovascular diseases. This study aimed to investigate the prognostic value of a novel nutritional index, triglycerides × total cholesterol × body weight index (TCBI), in patients with dilated cardiomyopathy (DCM). Methods This retrospective cohort study enrolled 445 patients with DCM. The median follow-up period was 2.8 years, and the primary endpoint was all-cause death. Results During follow-up, the all-cause mortality was observed in 135 out of 445 patients (30.3%). In Kaplan–Meier survival analysis, the third TCBI tertile had a lower mortality risk (T3 vs. T2 vs. T1: 16.9% vs. 35.1% vs. 38.9%; log-rank P < 0.001). In the multivariable Cox regression analysis, patients in the third tertile were associated with a decreased mortality, whereas there was no significant difference between the T2 and T1 groups. Moreover, TCBI could significantly improve risk stratification (continuous net reclassification improvement and integrated discrimination improvement) over the Geriatric Nutritional Risk Index (GNRI) and N-terminal pro-brain natriuretic peptide (NT-proBNP). Conclusions TCBI is independently associated with long-term survival in patients with DCM. Combination of TCBI and other biomarkers, such as GNRI and NT-proBNP, can significantly improve prognostic prediction. Further studies with larger sample size are required to validate our results.
format: application/pdf
format: text/html
creator: Can Wang
creator: Yali Qing
creator: Wuxian Chen
creator: Gaoye Li
subject: Cardiology
subject: Nutrition
description: doi:10.7717/peerj.12704
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Research has associated nutritional status with the prognosis of cardiovascular diseases. This study aimed to investigate the prognostic value of a novel nutritional index, triglycerides × total cholesterol × body weight index (TCBI), in patients with dilated cardiomyopathy (DCM). Methods This retrospective cohort study enrolled 445 patients with DCM. The median follow-up period was 2.8 years, and the primary endpoint was all-cause death. Results During follow-up, the all-cause mortality was observed in 135 out of 445 patients (30.3%). In Kaplan–Meier survival analysis, the third TCBI tertile had a lower mortality risk (T3 vs. T2 vs. T1: 16.9% vs. 35.1% vs. 38.9%; log-rank P < 0.001). In the multivariable Cox regression analysis, patients in the third tertile were associated with a decreased mortality, whereas there was no significant difference between the T2 and T1 groups. Moreover, TCBI could significantly improve risk stratification (continuous net reclassification improvement and integrated discrimination improvement) over the Geriatric Nutritional Risk Index (GNRI) and N-terminal pro-brain natriuretic peptide (NT-proBNP). Conclusions TCBI is independently associated with long-term survival in patients with DCM. Combination of TCBI and other biomarkers, such as GNRI and NT-proBNP, can significantly improve prognostic prediction. Further studies with larger sample size are required to validate our results.
bibliographic citation: Wang et al. (2022) A novel nutritional index as a predictor of mortality in dilated cardiomyopathy: a retrospective study. PeerJ 10:e12704 https://doi.org/10.7717/peerj.12704
date submitted: 2021-08-18
date accepted: 2021-12-07
issued: 2022-01-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Can
author list: Agent
  family name: Qing
  given name: Yali
author list: Agent
  family name: Chen
  given name: Wuxian
author list: Agent
  family name: Li
  given name: Gaoye
doi: 10.7717/peerj.12704
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-19
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Plasma FGF21 concentrations are regulated by glucose independently of insulin and GLP-1 in lean, healthy humans
type: item
type: AcademicArticle
description: Background Fibroblast growth factor 21 (FGF21) treatment improves metabolic homeostasis in diverse species, including humans. Physiologically, plasma FGF21 levels increase modestly after glucose ingestion, but it is unclear whether this is mediated by glucose itself or due to a secondary effect of postprandial endocrine responses. A refined understanding of the mechanisms that control FGF21 release in humans may accelerate the development of small-molecule FGF21 secretagogues to treat metabolic disease. This study aimed to determine whether FGF21 secretion is stimulated by elevations in plasma glucose, insulin, or glucagon-like peptide-1 (GLP-1) in humans. Methods Three groups of ten healthy participants were included in a parallel-group observational study. Group A underwent a hyperglycemic infusion; Group B underwent a 40 mU/m2/min hyperinsulinemic euglycemic clamp; Group C underwent two pancreatic clamps (to suppress endogenous insulin secretion) with euglycemic and hyperglycemic stages with an infusion of either saline or 0.5 pmol/kg/min GLP-1. Plasma FGF21 concentrations were measured at baseline and during each clamp stage by ELISA. Results Plasma FGF21 was unaltered during hyperglycemic infusion and hyperinsulinemic euglycemic clamps, compared to baseline. FGF21 was, however, increased by hyperglycemia under pancreatic clamp conditions (P < 0.05), while GLP-1 infusion under pancreatic clamp conditions did not change circulating FGF21 levels. Conclusion Increases in plasma FGF21 are likely driven directly by changes in plasma glucose independent of changes in insulin or GLP-1 secretion. Ecologically valid postprandial investigations are now needed to confirm our observations from basic science infusion models.
format: application/pdf
format: text/html
creator: Thomas P.J. Solomon
creator: Steven Carter
creator: Jacob M. Haus
creator: Kristian Karstoft
creator: Stephanie von Holstein-Rathlou
creator: Mette S. Nielsen
creator: Matthew P. Gillum
subject: Clinical Trials
subject: Diabetes and Endocrinology
subject: Hematology
subject: Metabolic Sciences
description: doi:10.7717/peerj.12755
publisher: PeerJ Inc.
rights: © 2022 Solomon et al.
abstract: Background Fibroblast growth factor 21 (FGF21) treatment improves metabolic homeostasis in diverse species, including humans. Physiologically, plasma FGF21 levels increase modestly after glucose ingestion, but it is unclear whether this is mediated by glucose itself or due to a secondary effect of postprandial endocrine responses. A refined understanding of the mechanisms that control FGF21 release in humans may accelerate the development of small-molecule FGF21 secretagogues to treat metabolic disease. This study aimed to determine whether FGF21 secretion is stimulated by elevations in plasma glucose, insulin, or glucagon-like peptide-1 (GLP-1) in humans. Methods Three groups of ten healthy participants were included in a parallel-group observational study. Group A underwent a hyperglycemic infusion; Group B underwent a 40 mU/m2/min hyperinsulinemic euglycemic clamp; Group C underwent two pancreatic clamps (to suppress endogenous insulin secretion) with euglycemic and hyperglycemic stages with an infusion of either saline or 0.5 pmol/kg/min GLP-1. Plasma FGF21 concentrations were measured at baseline and during each clamp stage by ELISA. Results Plasma FGF21 was unaltered during hyperglycemic infusion and hyperinsulinemic euglycemic clamps, compared to baseline. FGF21 was, however, increased by hyperglycemia under pancreatic clamp conditions (P < 0.05), while GLP-1 infusion under pancreatic clamp conditions did not change circulating FGF21 levels. Conclusion Increases in plasma FGF21 are likely driven directly by changes in plasma glucose independent of changes in insulin or GLP-1 secretion. Ecologically valid postprandial investigations are now needed to confirm our observations from basic science infusion models.
bibliographic citation: Solomon et al. (2022) Plasma FGF21 concentrations are regulated by glucose independently of insulin and GLP-1 in lean, healthy humans. PeerJ 10:e12755 https://doi.org/10.7717/peerj.12755
date submitted: 2021-06-25
date accepted: 2021-12-15
issued: 2022-01-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Solomon
  given name: Thomas P.J.
author list: Agent
  family name: Carter
  given name: Steven
author list: Agent
  family name: Haus
  given name: Jacob M.
author list: Agent
  family name: Karstoft
  given name: Kristian
author list: Agent
  family name: von Holstein-Rathlou
  given name: Stephanie
author list: Agent
  family name: Nielsen
  given name: Mette S.
author list: Agent
  family name: Gillum
  given name: Matthew P.
doi: 10.7717/peerj.12755
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-19
copyright: ©2022 Solomon et al.
attribution name: Solomon et al.

DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
type: item
type: AcademicArticle
description: DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.
format: application/pdf
format: text/html
creator: Adrià Antich
creator: Creu Palacín
creator: Xavier Turon
creator: Owen S. Wangensteen
subject: Biodiversity
subject: Bioinformatics
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.12758
publisher: PeerJ Inc.
rights: © 2022 Antich et al.
abstract: DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.
bibliographic citation: Antich et al. (2022) DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets. PeerJ 10:e12758 https://doi.org/10.7717/peerj.12758
date submitted: 2021-07-13
date accepted: 2021-12-16
issued: 2022-01-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Antich
  given name: Adrià
author list: Agent
  family name: Palacín
  given name: Creu
author list: Agent
  family name: Turon
  given name: Xavier
author list: Agent
  family name: Wangensteen
  given name: Owen S.
doi: 10.7717/peerj.12758
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-19
copyright: ©2022 Antich et al.
attribution name: Antich et al.

Optimized nitrogen rate, plant density, and irrigation level reduced ammonia emission and nitrate leaching on maize farmland in the oasis area of China
type: item
type: AcademicArticle
description: Nitrogen fertilizers play a key role in crop production to meet global food demand. Inappropriate application of nitrogen fertilizer coupled with poor irrigation and other crop management practices threaten agriculture and environmental sustainability. Over application of nitrogen fertilizer increases nitrogen gas emission and nitrate leaching. A field experiment was conducted in China’s oasis irrigation area in 2018 and 2019 to determine which nitrogen rate, plant density, and irrigation level in sole maize (Zea mays L.) cropping system reduce ammonia emission and nitrate leaching. Three nitrogen rates of urea (46-0-0 of N-P2O5-K2O), at (N0 = 0 kg N ha−1, N1 = 270 kg N ha−1, and N2 = 360 kg N ha−1) were combined with three plant densities (D1 = 75,000 plants/ha−1, D2 = 97,500 plants/ha−1, and D3 = 120,000 plants/ha−1) with two irrigation levels (W1 = 5,250 m3/hm2 and W2 = 4,740 m3/hm2) using a randomized complete block design. The results showed that, both the main and interaction effects of nitrogen rate, plant density, and irrigation level reduced nitrate leaching (p < 0.05). In addition, irrigation level × nitrogen rate significantly (p < 0.05) reduced ammonia emission. Nitrate leaching and ammonia emission decreased with higher irrigation level and higher plant density. However, high nitrogen rates increased both nitrate leaching and ammonia emission. The study found lowest leaching (0.35 mg kg−1) occurring at the interaction of 270 kg N ha−1 × 120,000 plants/ha−1 × 4,740 m3/hm2, and higher plant density of 120,000 plants/ha−1 combined with 0 kg N ha−1 and irrigation level of 5,250 m3/hm2 recorded the lowest ammonia emission (0.001 kg N)−1. Overall, ammonia emission increased as days after planting increased while nitrate leaching decreased in deeper soil depths. These findings show that, though the contributory roles of days after planting, soil depth, amount of nitrogen fertilizer applied and year of cultivation cannot be undermined, it is possible to reduce …
format: application/pdf
format: text/html
creator: Aziiba Emmanuel Asibi
creator: Wen Yin
creator: Falong Hu
creator: Zhilong Fan
creator: Zhiwen Gou
creator: Hongwei Yang
creator: Yao Guo
creator: Qiang Chai
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Natural Resource Management
description: doi:10.7717/peerj.12762
publisher: PeerJ Inc.
rights: © 2022 Asibi et al.
abstract: Nitrogen fertilizers play a key role in crop production to meet global food demand. Inappropriate application of nitrogen fertilizer coupled with poor irrigation and other crop management practices threaten agriculture and environmental sustainability. Over application of nitrogen fertilizer increases nitrogen gas emission and nitrate leaching. A field experiment was conducted in China’s oasis irrigation area in 2018 and 2019 to determine which nitrogen rate, plant density, and irrigation level in sole maize (Zea mays L.) cropping system reduce ammonia emission and nitrate leaching. Three nitrogen rates of urea (46-0-0 of N-P2O5-K2O), at (N0 = 0 kg N ha−1, N1 = 270 kg N ha−1, and N2 = 360 kg N ha−1) were combined with three plant densities (D1 = 75,000 plants/ha−1, D2 = 97,500 plants/ha−1, and D3 = 120,000 plants/ha−1) with two irrigation levels (W1 = 5,250 m3/hm2 and W2 = 4,740 m3/hm2) using a randomized complete block design. The results showed that, both the main and interaction effects of nitrogen rate, plant density, and irrigation level reduced nitrate leaching (p < 0.05). In addition, irrigation level × nitrogen rate significantly (p < 0.05) reduced ammonia emission. Nitrate leaching and ammonia emission decreased with higher irrigation level and higher plant density. However, high nitrogen rates increased both nitrate leaching and ammonia emission. The study found lowest leaching (0.35 mg kg−1) occurring at the interaction of 270 kg N ha−1 × 120,000 plants/ha−1 × 4,740 m3/hm2, and higher plant density of 120,000 plants/ha−1 combined with 0 kg N ha−1 and irrigation level of 5,250 m3/hm2 recorded the lowest ammonia emission (0.001 kg N)−1. Overall, ammonia emission increased as days after planting increased while nitrate leaching decreased in deeper soil depths. These findings show that, though the contributory roles of days after planting, soil depth, amount of nitrogen fertilizer applied and year of cultivation cannot be undermined, it is possible to reduce …
bibliographic citation: Asibi et al. (2022) Optimized nitrogen rate, plant density, and irrigation level reduced ammonia emission and nitrate leaching on maize farmland in the oasis area of China. PeerJ 10:e12762 https://doi.org/10.7717/peerj.12762
date submitted: 2021-07-22
date accepted: 2021-12-17
issued: 2022-01-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Asibi
  given name: Aziiba Emmanuel
author list: Agent
  family name: Yin
  given name: Wen
author list: Agent
  family name: Hu
  given name: Falong
author list: Agent
  family name: Fan
  given name: Zhilong
author list: Agent
  family name: Gou
  given name: Zhiwen
author list: Agent
  family name: Yang
  given name: Hongwei
author list: Agent
  family name: Guo
  given name: Yao
author list: Agent
  family name: Chai
  given name: Qiang
doi: 10.7717/peerj.12762
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-19
copyright: © 2022 Asibi et al.
attribution name: Asibi et al.

Reconstructing the transmission dynamics of varicella in Japan: an elevation of age at infection
type: item
type: AcademicArticle
description: Background In Japan, routine two-dose immunization against varicella has been conducted among children at ages of 12 and 36 months since 2014, and the vaccination coverage has reached around 90%. To understand the impact of routine varicella vaccination, we reconstructed the epidemiological dynamics of varicella in Japan. Methods Epidemiological and demographic datasets over the past three decades were analyzed to reconstruct the number of susceptible individuals by age and year. To estimate the annual risk of varicella infection, we fitted a balance equation model to the annual number of cases from 1990 to 2019. Using parameter estimates, we reconstructed varicella dynamics starting from 1990 and modeled future dynamics until 2033. Results Overall varicella incidence declined over time and the annual risk of infection among children younger than 10 years old decreased monotonically starting in 2014. Conversely, varicella incidence among teenagers (age 10 to 14 years) has increased each year since 2014. A substantial number of unvaccinated individuals born before the routine immunization era remained susceptible and aged without contracting varicella, while the annual risk of infection among teenagers aged 10 to 14 years increased starting in 2011 despite gradual expansion of varicella vaccine coverage. The number of susceptible individuals decreased over time in all age groups. Modeling indicated that susceptibility rates among pre-school children aged 1 to 4 years will remain low. Conclusion Routine varicella vaccination has successfully reduced infections in pre-school and early primary school age children, but has also resulted in increased infection rates among adolescents. This temporary increase was caused both by the increased age of susceptible individuals and increased transmission risk among adolescents resulting from the dynamic nature of varicella transmission. Monitoring susceptibility among adolescents will be important to prevent outbreaks over the n…
format: application/pdf
format: text/html
creator: Ayako Suzuki
creator: Hiroshi Nishiura
subject: Computational Biology
subject: Epidemiology
subject: Infectious Diseases
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.12767
publisher: PeerJ Inc.
rights: © 2022 Suzuki and Nishiura
abstract: Background In Japan, routine two-dose immunization against varicella has been conducted among children at ages of 12 and 36 months since 2014, and the vaccination coverage has reached around 90%. To understand the impact of routine varicella vaccination, we reconstructed the epidemiological dynamics of varicella in Japan. Methods Epidemiological and demographic datasets over the past three decades were analyzed to reconstruct the number of susceptible individuals by age and year. To estimate the annual risk of varicella infection, we fitted a balance equation model to the annual number of cases from 1990 to 2019. Using parameter estimates, we reconstructed varicella dynamics starting from 1990 and modeled future dynamics until 2033. Results Overall varicella incidence declined over time and the annual risk of infection among children younger than 10 years old decreased monotonically starting in 2014. Conversely, varicella incidence among teenagers (age 10 to 14 years) has increased each year since 2014. A substantial number of unvaccinated individuals born before the routine immunization era remained susceptible and aged without contracting varicella, while the annual risk of infection among teenagers aged 10 to 14 years increased starting in 2011 despite gradual expansion of varicella vaccine coverage. The number of susceptible individuals decreased over time in all age groups. Modeling indicated that susceptibility rates among pre-school children aged 1 to 4 years will remain low. Conclusion Routine varicella vaccination has successfully reduced infections in pre-school and early primary school age children, but has also resulted in increased infection rates among adolescents. This temporary increase was caused both by the increased age of susceptible individuals and increased transmission risk among adolescents resulting from the dynamic nature of varicella transmission. Monitoring susceptibility among adolescents will be important to prevent outbreaks over the n…
bibliographic citation: Suzuki et al. (2022) Reconstructing the transmission dynamics of varicella in Japan: an elevation of age at infection. PeerJ 10:e12767 https://doi.org/10.7717/peerj.12767
date submitted: 2021-10-01
date accepted: 2021-12-17
issued: 2022-01-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Suzuki
  given name: Ayako
author list: Agent
  family name: Nishiura
  given name: Hiroshi
doi: 10.7717/peerj.12767
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-19
copyright: © 2022 Suzuki and Nishiura
attribution name: Suzuki and Nishiura

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