PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Bite force data suggests relationship between acrodont tooth implantation and strong bite force
items: Comparative metabolomic analyses of Dendrobium officinale Kimura et Migo responding to UV-B radiation reveal variations in the metabolisms associated with its bioactive ingredients
items: https://peerj.com/articles/9265
items: https://peerj.com/articles/9370
items: Shannon diversity index: a call to replace the original Shannon’s formula with unbiased estimator in the population genetics studies
items: Using Bumble Bee Watch to investigate the accuracy and perception of bumble bee (Bombus spp.) identification by community scientists
items: A preoperative nomogram for sepsis in percutaneous nephrolithotomy treating solitary, unilateral and proximal ureteral stones
items: Integrative analysis of competitive endogenous RNA network reveals the regulatory role of non-coding RNAs in high-glucose-induced human retinal endothelial cells
items: Gait characteristics in individuals with Parkinson’s disease during 1-minute treadmill walking
items: Hemogram data as a tool for decision-making in COVID-19 management: applications to resource scarcity scenarios

Bite force data suggests relationship between acrodont tooth implantation and strong bite force
type: item
type: AcademicArticle
description: Extant and extinct reptiles exhibit numerous combinations of tooth implantation and attachment. Tooth implantation ranges from those possessing roots and lying within a socket (thecodonty), to teeth lying against the lingual wall of the jawbone (pleurodonty), to teeth without roots or sockets that are attached to the apex of the marginal jawbones (acrodonty). Attachment may be ligamentous (gomphosis) or via fusion (ankylosis). Generally speaking, adaptative reasonings are proposed as an underlying driver for evolutionary changes in some forms of tooth implantation and attachment. However, a substantiated adaptive hypothesis is lacking for the state of acrodont ankylosis that is seen in several lineages of Lepidosauria, a clade that is plesiomorphically pleurodont. The convergent evolution of acrodont ankylosis in several clades of lepidosaurs suggests a selective pressure shaped the evolution of the trait. We hypothesize that acrodont ankylosis as seen in Acrodonta and Sphenodon punctatus, is an adaptation either resulting from or allowing for a stronger bite force. We analyzed bite force data gathered from the literature to show that those taxa possessing acrodont dentition possess a stronger bite force on average than those taxa with pleurodont dentition. Dietary specialists with pleurodont dentition may also possess relatively high bite forces, though body size may also play a role in their ability to bite hard. Furthermore, our results have implications for the evolution of acrodont ankylosis and potential behaviors related to strong bite force that influenced the evolution of acrodonty within Acrodonta and Rhynchocephalia.
format: application/pdf
format: text/html
creator: Kelsey M. Jenkins
creator: Jack O. Shaw
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.9468
publisher: PeerJ Inc.
rights: © 2020 Jenkins and Shaw
abstract: Extant and extinct reptiles exhibit numerous combinations of tooth implantation and attachment. Tooth implantation ranges from those possessing roots and lying within a socket (thecodonty), to teeth lying against the lingual wall of the jawbone (pleurodonty), to teeth without roots or sockets that are attached to the apex of the marginal jawbones (acrodonty). Attachment may be ligamentous (gomphosis) or via fusion (ankylosis). Generally speaking, adaptative reasonings are proposed as an underlying driver for evolutionary changes in some forms of tooth implantation and attachment. However, a substantiated adaptive hypothesis is lacking for the state of acrodont ankylosis that is seen in several lineages of Lepidosauria, a clade that is plesiomorphically pleurodont. The convergent evolution of acrodont ankylosis in several clades of lepidosaurs suggests a selective pressure shaped the evolution of the trait. We hypothesize that acrodont ankylosis as seen in Acrodonta and Sphenodon punctatus, is an adaptation either resulting from or allowing for a stronger bite force. We analyzed bite force data gathered from the literature to show that those taxa possessing acrodont dentition possess a stronger bite force on average than those taxa with pleurodont dentition. Dietary specialists with pleurodont dentition may also possess relatively high bite forces, though body size may also play a role in their ability to bite hard. Furthermore, our results have implications for the evolution of acrodont ankylosis and potential behaviors related to strong bite force that influenced the evolution of acrodonty within Acrodonta and Rhynchocephalia.
bibliographic citation: Jenkins et al. (2020) Bite force data suggests relationship between acrodont tooth implantation and strong bite force. PeerJ 8:e9468 https://doi.org/10.7717/peerj.9468
date submitted: 2020-02-17
date accepted: 2020-06-11
issued: 2020-06-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jenkins
  given name: Kelsey M.
author list: Agent
  family name: Shaw
  given name: Jack O.
doi: 10.7717/peerj.9468
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-30
copyright: ©2020 Jenkins and Shaw
attribution name: Jenkins and Shaw

Comparative metabolomic analyses of Dendrobium officinale Kimura et Migo responding to UV-B radiation reveal variations in the metabolisms associated with its bioactive ingredients
type: item
type: AcademicArticle
description: Background Dendrobium officinale Kimura et Migo, a member of the genus Dendrobium, is a traditional Chinese medicine with high commercial value. The positive roles of UV-B radiation on active ingredient metabolism in various medicinal plants have been studied. However, the metabolic responses of D. officinale stems to UV-B treatment is largely unknown. Methods An untargeted metabolomics method was used to investigate the metabolic variations in D. officinale stems between the control and UV-B treatments. Results In total, 3,655 annotated metabolites, including 640 up- and 783 down-regulated metabolites, were identified and grouped into various primary metabolic categories. Then, a number of metabolites involved in the polysaccharide, alkaloid and flavonoid biosynthesis pathways were identified. For polysaccharide biosynthesis, several intermediate products, such as pyruvate, secologanate, tryptophan and secologanin, were significantly up-regulated by the UV-B treatment. For polysaccharide biosynthesis, many key fundamental building blocks, from the glycolysis, starch and sucrose metabolism, and fructose and mannose metabolism pathways, were induced by the UV-B treatment. For flavonoid metabolism, accumulations of several intermediate products of chalcone synthase, chalcone isomerase and flavanone 3-hydroxylase were affected by the UV-B treatment, indicating an involvement of UV-B in flavonoid biosynthesis. The UV-B induced accumulation of polysaccharides, alkaloids and flavonoids was confirmed by HPLC analysis. Our study will help to understand the effects of UV-B on the accumulation of active ingredients in D. officinale.
format: application/pdf
format: text/html
creator: Yue Chen
creator: Qi Shen
creator: Ping Lv
creator: Chongbo Sun
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.9107
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Background Dendrobium officinale Kimura et Migo, a member of the genus Dendrobium, is a traditional Chinese medicine with high commercial value. The positive roles of UV-B radiation on active ingredient metabolism in various medicinal plants have been studied. However, the metabolic responses of D. officinale stems to UV-B treatment is largely unknown. Methods An untargeted metabolomics method was used to investigate the metabolic variations in D. officinale stems between the control and UV-B treatments. Results In total, 3,655 annotated metabolites, including 640 up- and 783 down-regulated metabolites, were identified and grouped into various primary metabolic categories. Then, a number of metabolites involved in the polysaccharide, alkaloid and flavonoid biosynthesis pathways were identified. For polysaccharide biosynthesis, several intermediate products, such as pyruvate, secologanate, tryptophan and secologanin, were significantly up-regulated by the UV-B treatment. For polysaccharide biosynthesis, many key fundamental building blocks, from the glycolysis, starch and sucrose metabolism, and fructose and mannose metabolism pathways, were induced by the UV-B treatment. For flavonoid metabolism, accumulations of several intermediate products of chalcone synthase, chalcone isomerase and flavanone 3-hydroxylase were affected by the UV-B treatment, indicating an involvement of UV-B in flavonoid biosynthesis. The UV-B induced accumulation of polysaccharides, alkaloids and flavonoids was confirmed by HPLC analysis. Our study will help to understand the effects of UV-B on the accumulation of active ingredients in D. officinale.
bibliographic citation: Chen et al. (2020) Comparative metabolomic analyses of Dendrobium officinale Kimura et Migo responding to UV-B radiation reveal variations in the metabolisms associated with its bioactive ingredients. PeerJ 8:e9107 https://doi.org/10.7717/peerj.9107
date submitted: 2019-12-31
date accepted: 2020-04-10
issued: 2020-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yue
author list: Agent
  family name: Shen
  given name: Qi
author list: Agent
  family name: Lv
  given name: Ping
author list: Agent
  family name: Sun
  given name: Chongbo
doi: 10.7717/peerj.9107
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-29
copyright: ©2020 Chen et al.
attribution name: Chen et al.

https://peerj.com/articles/9265
type: item
type: AcademicArticle
title: The genome of the butternut canker pathogen, Ophiognomonia clavigignenti-juglandacearum shows an elevated number of genes associated with secondary metabolism and protection from host resistance responses
description: Ophiognomonia clavigignenti-juglandacearum (Oc-j) is a plant pathogenic fungus that causes canker and branch dieback diseases in the hardwood tree butternut, Juglans cinerea. Oc-j is a member of the order of Diaporthales, which includes many other plant pathogenic species, several of which also infect hardwood tree species. In this study, we sequenced the genome of Oc-j and achieved a high-quality assembly and delineated its phylogeny within the Diaporthales order using a genome-wide multi-gene approach. We also further examined multiple gene families that might be involved in plant pathogenicity and degradation of complex biomass, which are relevant to a pathogenic life-style in a tree host. We found that the Oc-j genome contains a greater number of genes in these gene families compared to other species in the Diaporthales. These gene families include secreted CAZymes, kinases, cytochrome P450, efflux pumps, and secondary metabolism gene clusters. The large numbers of these genes provide Oc-j with an arsenal to cope with the specific ecological niche as a pathogen of the butternut tree.
format: application/pdf
format: text/html
creator: Guangxi Wu
creator: Taruna A. Schuelke
creator: Gloria Iriarte
creator: Kirk Broders
subject: Genomics
subject: Mycology
description: doi:10.7717/peerj.9265
publisher: PeerJ Inc.
rights: © 2020 Wu et al.
abstract: Ophiognomonia clavigignenti-juglandacearum (Oc-j) is a plant pathogenic fungus that causes canker and branch dieback diseases in the hardwood tree butternut, Juglans cinerea. Oc-j is a member of the order of Diaporthales, which includes many other plant pathogenic species, several of which also infect hardwood tree species. In this study, we sequenced the genome of Oc-j and achieved a high-quality assembly and delineated its phylogeny within the Diaporthales order using a genome-wide multi-gene approach. We also further examined multiple gene families that might be involved in plant pathogenicity and degradation of complex biomass, which are relevant to a pathogenic life-style in a tree host. We found that the Oc-j genome contains a greater number of genes in these gene families compared to other species in the Diaporthales. These gene families include secreted CAZymes, kinases, cytochrome P450, efflux pumps, and secondary metabolism gene clusters. The large numbers of these genes provide Oc-j with an arsenal to cope with the specific ecological niche as a pathogen of the butternut tree.
bibliographic citation: Wu et al. (2020) The genome of the butternut canker pathogen, Ophiognomonia clavigignenti-juglandacearum shows an elevated number of genes associated with secondary metabolism and protection from host resistance responses. PeerJ 8:e9265 https://doi.org/10.7717/peerj.9265
date submitted: 2019-11-04
date accepted: 2020-05-10
issued: 2020-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Guangxi
author list: Agent
  family name: Schuelke
  given name: Taruna A.
author list: Agent
  family name: Iriarte
  given name: Gloria
author list: Agent
  family name: Broders
  given name: Kirk
doi: 10.7717/peerj.9265
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-29
copyright: © 2020 Wu et al.
attribution name: Wu et al.

https://peerj.com/articles/9370
type: item
type: AcademicArticle
title: A new species of freshwater crab genus Fredius Pretzmann, 1967 (Crustacea: Brachyura: Pseudothelphusidae) from a naturally isolated orographic forest enclave within the semiarid Caatinga in Ceará, northeastern Brazil
description: A new species of freshwater crab, Fredius ibiapaba, is described and illustrated from a mid-altitude forested patch in Ipú (Ibiapaba plateau, Ceará, northeastern Brazil), between 635 to 782 m. The new species can be separated from its congeners by the morphology of its first gonopod: proximal half remarkably swollen, sloping abruptly downwards distally to a nearly right-angular shoulder; mesial lobe much smaller than cephalic spine; cephalic lobe moderately developed; auxiliary lobe lip, delimiting field of apical spines, protruded all the way to distal margin of auxiliary lobe. Comparative 16S rDNA sequencing used to infer the phylogenetic placement of Fredius ibiapaba n. sp. revealed that it is the sister taxon of F. reflexifrons, a species which occurs allopatrically in the Amazon and Atlantic basin’s lowlands (<100 m). Fredius ibiapaba n. sp. and F. reflexifrons are highly dependent upon humidity and most probably were once part of an ancestral population living in a wide humid territory. Shrinking humid forests during several dry periods of the Tertiary and Quaternary likely have resulted in the fragmentation of the ancestral humid area and hence of the ancestral crab population. Fredius reflexifrons evolved and spread in a lowland, humid river basin (Amazon and Atlantic basins), whilst F. ibiapaba n. sp. evolved isolated on the top of a humid plateau. The two species are now separated by a vast intervening area occupied by the semiarid Caatinga
format: application/pdf
format: text/html
creator: Livanio C. Santos
creator: Marcos Tavares
creator: José R.F. Silva
creator: Marcelo Cervini
creator: Allysson P. Pinheiro
creator: William Santana
subject: Biodiversity
subject: Taxonomy
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.9370
publisher: PeerJ Inc.
rights: © 2020 Santos et al.
abstract: A new species of freshwater crab, Fredius ibiapaba, is described and illustrated from a mid-altitude forested patch in Ipú (Ibiapaba plateau, Ceará, northeastern Brazil), between 635 to 782 m. The new species can be separated from its congeners by the morphology of its first gonopod: proximal half remarkably swollen, sloping abruptly downwards distally to a nearly right-angular shoulder; mesial lobe much smaller than cephalic spine; cephalic lobe moderately developed; auxiliary lobe lip, delimiting field of apical spines, protruded all the way to distal margin of auxiliary lobe. Comparative 16S rDNA sequencing used to infer the phylogenetic placement of Fredius ibiapaba n. sp. revealed that it is the sister taxon of F. reflexifrons, a species which occurs allopatrically in the Amazon and Atlantic basin’s lowlands (<100 m). Fredius ibiapaba n. sp. and F. reflexifrons are highly dependent upon humidity and most probably were once part of an ancestral population living in a wide humid territory. Shrinking humid forests during several dry periods of the Tertiary and Quaternary likely have resulted in the fragmentation of the ancestral humid area and hence of the ancestral crab population. Fredius reflexifrons evolved and spread in a lowland, humid river basin (Amazon and Atlantic basins), whilst F. ibiapaba n. sp. evolved isolated on the top of a humid plateau. The two species are now separated by a vast intervening area occupied by the semiarid Caatinga
bibliographic citation: Santos et al. (2020) A new species of freshwater crab genus Fredius Pretzmann, 1967 (Crustacea: Brachyura: Pseudothelphusidae) from a naturally isolated orographic forest enclave within the semiarid Caatinga in Ceará, northeastern Brazil. PeerJ 8:e9370 https://doi.org/10.7717/peerj.9370
date submitted: 2019-12-06
date accepted: 2020-05-27
issued: 2020-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santos
  given name: Livanio C.
author list: Agent
  family name: Tavares
  given name: Marcos
author list: Agent
  family name: Silva
  given name: José R.F.
author list: Agent
  family name: Cervini
  given name: Marcelo
author list: Agent
  family name: Pinheiro
  given name: Allysson P.
author list: Agent
  family name: Santana
  given name: William
doi: 10.7717/peerj.9370
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-29
copyright: ©2020 Santos et al.
attribution name: Santos et al.

Shannon diversity index: a call to replace the original Shannon’s formula with unbiased estimator in the population genetics studies
type: item
type: AcademicArticle
description: Background The Shannon diversity index has been widely used in population genetics studies. Recently, it was proposed as a unifying measure of diversity at different levels—from genes and populations to whole species and ecosystems. The index, however, was proven to be negatively biased at small sample sizes. Modifications to the original Shannon’s formula have been proposed to obtain an unbiased estimator. Methods In this study, the performance of four different estimators of Shannon index—the original Shannon’s formula and those of Zahl, Chao and Shen and Chao et al.—was tested on simulated microsatellite data. Both the simulation and analysis of the results were performed in the R language environment. A new R function was created for the calculation of all four indices from the genind data format. Results Sample size dependence was detected in all the estimators analysed; however, the deviation from parametric values was substantially smaller in the derived measures than in the original Shannon’s formula. Error rate was negatively associated with population heterozygosity. Comparisons among loci showed that fast-mutating loci were less affected by the error, except for the original Shannon’s estimator which, in the smallest sample, was more strongly affected by loci with a higher number of alleles. The Zahl and Chao et al. estimators performed notably better than the original Shannon’s formula. Conclusion The results of this study show that the original Shannon index should no longer be used as a measure of genetic diversity and should be replaced by Zahl’s unbiased estimator.
format: application/pdf
format: text/html
creator: Maciej K. Konopiński
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Population Biology
description: doi:10.7717/peerj.9391
publisher: PeerJ Inc.
rights: © 2020 Konopiński
abstract: Background The Shannon diversity index has been widely used in population genetics studies. Recently, it was proposed as a unifying measure of diversity at different levels—from genes and populations to whole species and ecosystems. The index, however, was proven to be negatively biased at small sample sizes. Modifications to the original Shannon’s formula have been proposed to obtain an unbiased estimator. Methods In this study, the performance of four different estimators of Shannon index—the original Shannon’s formula and those of Zahl, Chao and Shen and Chao et al.—was tested on simulated microsatellite data. Both the simulation and analysis of the results were performed in the R language environment. A new R function was created for the calculation of all four indices from the genind data format. Results Sample size dependence was detected in all the estimators analysed; however, the deviation from parametric values was substantially smaller in the derived measures than in the original Shannon’s formula. Error rate was negatively associated with population heterozygosity. Comparisons among loci showed that fast-mutating loci were less affected by the error, except for the original Shannon’s estimator which, in the smallest sample, was more strongly affected by loci with a higher number of alleles. The Zahl and Chao et al. estimators performed notably better than the original Shannon’s formula. Conclusion The results of this study show that the original Shannon index should no longer be used as a measure of genetic diversity and should be replaced by Zahl’s unbiased estimator.
bibliographic citation: Konopiński (2020) Shannon diversity index: a call to replace the original Shannon’s formula with unbiased estimator in the population genetics studies. PeerJ 8:e9391 https://doi.org/10.7717/peerj.9391
date submitted: 2019-12-17
date accepted: 2020-05-29
issued: 2020-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Konopiński
  given name: Maciej K.
doi: 10.7717/peerj.9391
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-29
copyright: ©2020 Konopiński
attribution name: Konopiński

Using Bumble Bee Watch to investigate the accuracy and perception of bumble bee (Bombus spp.) identification by community scientists
type: item
type: AcademicArticle
description: Community science programs provide an opportunity to gather scientific data to inform conservation policy and management. This study examines the accuracy of community science identifications submitted to the North American Bumble Bee Watch program on a per species level and as compared to each species’ conservation status, as well as users (members of the public) and experts (those with expertise in the field of bumble bee biology) perceived ease of species identification. Photos of bumble bees (Hymenoptera: Apidae: Bombus) are submitted to the program by users and verified (species name corrected or assigned as necessary) by an expert. Over 22,000 records from over 4,900 users were used in the analyses. Accuracy was measured in two ways: percent agreement (percent of all records submitted correctly by users) and veracity (percent of all verified records submitted correctly by the users). Users generally perceived it harder to identify species than experts. User perceptions were not significantly different from the observed percent agreement or veracity, while expert perceptions were significantly different (overly optimistic) from the observed percent agreement but not the veracity. We compared user submitted names to final expert verified names and found that, for all species combined, the average percent agreement was 53.20% while the average veracity was 55.86%. There was a wide range in percent agreement values per species, although sample size and the role of chance did affect some species agreements. As the conservation status of species increased to higher levels of extinction risk, species were increasingly more likely to have a lower percent agreement but higher levels of veracity than species of least concern. For each species name submitted, the number of different species verified by experts varied from 1 to 32. Future research may investigate which factors relate to success in user identification through community science. These findings could play a …
format: application/pdf
format: text/html
creator: Victoria J. MacPhail
creator: Shelby D. Gibson
creator: Richard Hatfield
creator: Sheila R. Colla
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.9412
publisher: PeerJ Inc.
rights: © 2020 MacPhail et al.
abstract: Community science programs provide an opportunity to gather scientific data to inform conservation policy and management. This study examines the accuracy of community science identifications submitted to the North American Bumble Bee Watch program on a per species level and as compared to each species’ conservation status, as well as users (members of the public) and experts (those with expertise in the field of bumble bee biology) perceived ease of species identification. Photos of bumble bees (Hymenoptera: Apidae: Bombus) are submitted to the program by users and verified (species name corrected or assigned as necessary) by an expert. Over 22,000 records from over 4,900 users were used in the analyses. Accuracy was measured in two ways: percent agreement (percent of all records submitted correctly by users) and veracity (percent of all verified records submitted correctly by the users). Users generally perceived it harder to identify species than experts. User perceptions were not significantly different from the observed percent agreement or veracity, while expert perceptions were significantly different (overly optimistic) from the observed percent agreement but not the veracity. We compared user submitted names to final expert verified names and found that, for all species combined, the average percent agreement was 53.20% while the average veracity was 55.86%. There was a wide range in percent agreement values per species, although sample size and the role of chance did affect some species agreements. As the conservation status of species increased to higher levels of extinction risk, species were increasingly more likely to have a lower percent agreement but higher levels of veracity than species of least concern. For each species name submitted, the number of different species verified by experts varied from 1 to 32. Future research may investigate which factors relate to success in user identification through community science. These findings could play a …
bibliographic citation: MacPhail et al. (2020) Using Bumble Bee Watch to investigate the accuracy and perception of bumble bee (Bombus spp.) identification by community scientists. PeerJ 8:e9412 https://doi.org/10.7717/peerj.9412
date submitted: 2020-03-05
date accepted: 2020-06-03
issued: 2020-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: MacPhail
  given name: Victoria J.
author list: Agent
  family name: Gibson
  given name: Shelby D.
author list: Agent
  family name: Hatfield
  given name: Richard
author list: Agent
  family name: Colla
  given name: Sheila R.
doi: 10.7717/peerj.9412
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-29
copyright: © 2020 MacPhail et al.
attribution name: MacPhail et al.

A preoperative nomogram for sepsis in percutaneous nephrolithotomy treating solitary, unilateral and proximal ureteral stones
type: item
type: AcademicArticle
description: Background Postoperative sepsis is a lethal complication for percutaneous nephrolithotomy (PCNL). An early predictive model combined local and systemic conditions is urgently needed to predict infectious events. We aim to determine the preoperative predictors of sepsis after PCNL in patients with unilateral, solitary, and proximal ureteral stones. Methods A total of 745 patients who underwent PCNL between January 2012 and December 2018 were retrospectively enrolled. Sepsis was defined based on the International Sepsis Definitions in 2001, and the preoperative factors were compared between the non-sepsis and sepsis groups. Univariable analysis and multivariable logistic regression analysis were conducted to determine the predictors for sepsis after PCNL. A nomogram was generated using the predictors. Results In this study, 35 patients (4.7%) developed sepsis after PCNL. Univariate analysis showed that post-PCNL sepsis was associated with the female, lower albumin, higher globulin, lower albumin globulin ratio (AGR < 1.5), preoperative fever, leukocytosis (WBC ≥ 10,000 cells/μL), positive urine culture, leukocyturia (≥50 cells/μL) and positive urine nitrite. Multivariate logistic regression analysis suggested that AGR < 1.5 (odds ratio [OR] = 5.068, 95% confidence interval [CI] [1.135–22.624], P = 0.033), positive urine culture (OR = 3.243, 95% CI [1.162–9.047], P = 0.025), leukocytosis (OR = 3.706, 95% CI [1.444–9.512], P = 0.006) and female (OR = 2.529, 95% CI [1.127–5.672], P = 0.024) were independent risk factors for sepsis. A nomogram was generated and displayed favorable fitting (Hosmer–Lemeshow test P = 0.797), discrimination (area under receiver operating characteristic curve was 0.807), and clinical usefulness by decision curve analysis. Conclusions Patients with certain preoperative characteristics, such as female, lower AGR, positive urine culture, and leukocytosis, who undergo PCNL may have a higher risk of developing sepsis. A cautious preoperative evalua…
format: application/pdf
format: text/html
creator: Yang Xun
creator: Yuanyuan Yang
creator: Xiao Yu
creator: Cong Li
creator: Junlin Lu
creator: Shaogang Wang
subject: Infectious Diseases
subject: Nephrology
subject: Surgery and Surgical Specialties
subject: Urology
description: doi:10.7717/peerj.9435
publisher: PeerJ Inc.
rights: © 2020 Xun et al.
abstract: Background Postoperative sepsis is a lethal complication for percutaneous nephrolithotomy (PCNL). An early predictive model combined local and systemic conditions is urgently needed to predict infectious events. We aim to determine the preoperative predictors of sepsis after PCNL in patients with unilateral, solitary, and proximal ureteral stones. Methods A total of 745 patients who underwent PCNL between January 2012 and December 2018 were retrospectively enrolled. Sepsis was defined based on the International Sepsis Definitions in 2001, and the preoperative factors were compared between the non-sepsis and sepsis groups. Univariable analysis and multivariable logistic regression analysis were conducted to determine the predictors for sepsis after PCNL. A nomogram was generated using the predictors. Results In this study, 35 patients (4.7%) developed sepsis after PCNL. Univariate analysis showed that post-PCNL sepsis was associated with the female, lower albumin, higher globulin, lower albumin globulin ratio (AGR < 1.5), preoperative fever, leukocytosis (WBC ≥ 10,000 cells/μL), positive urine culture, leukocyturia (≥50 cells/μL) and positive urine nitrite. Multivariate logistic regression analysis suggested that AGR < 1.5 (odds ratio [OR] = 5.068, 95% confidence interval [CI] [1.135–22.624], P = 0.033), positive urine culture (OR = 3.243, 95% CI [1.162–9.047], P = 0.025), leukocytosis (OR = 3.706, 95% CI [1.444–9.512], P = 0.006) and female (OR = 2.529, 95% CI [1.127–5.672], P = 0.024) were independent risk factors for sepsis. A nomogram was generated and displayed favorable fitting (Hosmer–Lemeshow test P = 0.797), discrimination (area under receiver operating characteristic curve was 0.807), and clinical usefulness by decision curve analysis. Conclusions Patients with certain preoperative characteristics, such as female, lower AGR, positive urine culture, and leukocytosis, who undergo PCNL may have a higher risk of developing sepsis. A cautious preoperative evalua…
bibliographic citation: Xun et al. (2020) A preoperative nomogram for sepsis in percutaneous nephrolithotomy treating solitary, unilateral and proximal ureteral stones. PeerJ 8:e9435 https://doi.org/10.7717/peerj.9435
date submitted: 2020-03-13
date accepted: 2020-06-06
issued: 2020-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xun
  given name: Yang
author list: Agent
  family name: Yang
  given name: Yuanyuan
author list: Agent
  family name: Yu
  given name: Xiao
author list: Agent
  family name: Li
  given name: Cong
author list: Agent
  family name: Lu
  given name: Junlin
author list: Agent
  family name: Wang
  given name: Shaogang
doi: 10.7717/peerj.9435
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-29
copyright: © 2020 Xun et al.
attribution name: Xun et al.

Integrative analysis of competitive endogenous RNA network reveals the regulatory role of non-coding RNAs in high-glucose-induced human retinal endothelial cells
type: item
type: AcademicArticle
description: Background Increasing evidence has suggested that non-coding RNAs (ncRNAs) play critical roles in the pathogenesis of diabetic retinopathy (DR), but their underlying mechanisms remain unclear. The purpose of this study was to determine latent key genes and to structure a competing endogenous RNA (ceRNA) regulatory network to discover the potential molecular mechanisms governing the effects of high glucose on human retinal endothelial cells (HRECs). Methods We obtained microarray data for long non-coding RNA (lncRNA) and mRNA of high-glucose-induced HREC samples from NCBI GEO datasets. The ceRNA network was screened using intersecting prediction results from miRcode, TargetScan, miRTarBase and miRDB. The protein–protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes and hub genes were obtained using the cytoHubba app. The ClusterProfiler package was applied for performing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The expression of key RNAs was verified using the qRT-PCR method. A key ceRNA subnetwork was constructed based on the criticality of the genes and its binding sites were verified by luciferase reporter assay. The viability and apoptosis of HRECs were tested using the transfection of the miR-449c inhibitor. Results A total of 3,328 lncRNAs and 2,017 mRNAs were screened for differentially expressed (DE) profiles. The newly constructed ceRNA network was composed of 410 lncRNAs, 35 miRNAs and 122 mRNAs. The 10 hub genes were identified through the PPI network. GO and KEGG analysis revealed that DE mRNAs were mainly related to the positive regulation of the mRNA catabolic process, cell polarity, and the G1/S transition of mitotic and cell cycle signaling pathways. QRT-PCR was used to verify RNAs and the most important genes were screened out. A key ceRNA subnetwork OIP5-AS1/miR-449c/MYC was established. The binding site was verified by luciferase reporter assay. …
format: application/pdf
format: text/html
creator: Nan-Jue Cao
creator: He-Nan Liu
creator: Feng Dong
creator: Wei Wang
creator: Wei Sun
creator: Gang Wang
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Ophthalmology
description: doi:10.7717/peerj.9452
publisher: PeerJ Inc.
rights: © 2020 Cao et al.
abstract: Background Increasing evidence has suggested that non-coding RNAs (ncRNAs) play critical roles in the pathogenesis of diabetic retinopathy (DR), but their underlying mechanisms remain unclear. The purpose of this study was to determine latent key genes and to structure a competing endogenous RNA (ceRNA) regulatory network to discover the potential molecular mechanisms governing the effects of high glucose on human retinal endothelial cells (HRECs). Methods We obtained microarray data for long non-coding RNA (lncRNA) and mRNA of high-glucose-induced HREC samples from NCBI GEO datasets. The ceRNA network was screened using intersecting prediction results from miRcode, TargetScan, miRTarBase and miRDB. The protein–protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes and hub genes were obtained using the cytoHubba app. The ClusterProfiler package was applied for performing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The expression of key RNAs was verified using the qRT-PCR method. A key ceRNA subnetwork was constructed based on the criticality of the genes and its binding sites were verified by luciferase reporter assay. The viability and apoptosis of HRECs were tested using the transfection of the miR-449c inhibitor. Results A total of 3,328 lncRNAs and 2,017 mRNAs were screened for differentially expressed (DE) profiles. The newly constructed ceRNA network was composed of 410 lncRNAs, 35 miRNAs and 122 mRNAs. The 10 hub genes were identified through the PPI network. GO and KEGG analysis revealed that DE mRNAs were mainly related to the positive regulation of the mRNA catabolic process, cell polarity, and the G1/S transition of mitotic and cell cycle signaling pathways. QRT-PCR was used to verify RNAs and the most important genes were screened out. A key ceRNA subnetwork OIP5-AS1/miR-449c/MYC was established. The binding site was verified by luciferase reporter assay. …
bibliographic citation: Cao et al. (2020) Integrative analysis of competitive endogenous RNA network reveals the regulatory role of non-coding RNAs in high-glucose-induced human retinal endothelial cells. PeerJ 8:e9452 https://doi.org/10.7717/peerj.9452
date submitted: 2020-02-04
date accepted: 2020-06-09
issued: 2020-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Nan-Jue
author list: Agent
  family name: Liu
  given name: He-Nan
author list: Agent
  family name: Dong
  given name: Feng
author list: Agent
  family name: Wang
  given name: Wei
author list: Agent
  family name: Sun
  given name: Wei
author list: Agent
  family name: Wang
  given name: Gang
doi: 10.7717/peerj.9452
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-29
copyright: © 2020 Cao et al.
attribution name: Cao et al.

Gait characteristics in individuals with Parkinson’s disease during 1-minute treadmill walking
type: item
type: AcademicArticle
description: Background No previous study has examined the age-dependent characteristics of gait in individuals between 50 and 79 years simultaneously in healthy individuals and individuals with Parkinson’s disease (PD) over continuous gait cycles. This study aimed to investigate age-related differences in gait characteristics on individuals age ranged 50–79 years, including individuals with PD, during a 1-minute treadmill walking session. Additionally, we aimed to investigate the differences associated with spatiotemporal gait parameters and PD compared in age-matched individuals. Methods This study included 26 individuals with PD and 90 participants age ranged 50–79 years. The treadmill walking test at a self-preferred speed was performed for 1 min. The embedded inertial measurement unit sensor in the left and right outsoles-based system was used to collect gait characteristics based on tri-axial acceleration and tri-axial angular velocities. Results Participants aged >60 years had a decreased gait speed and shortened stride and step, which may demonstrate a distinct shift in aging (all p < 0.005). Individuals with PD showed more of a decrease in variables with a loss of consistency, including gait asymmetry (GA), phase coordination index (PCI) and coefficient of variation (CV) of all variables, than age-matched individuals (all p < 0.001). Gait speed, stride and step length, stance phase, variability, GA and PCI were the variables that highly depended on age and PD. Discussion Older adults could be considered those older than 60 years of age when gait alterations begin, such as a decreased gait speed as well as shortened stride and step length. On the other hand, a loss of consistency in spatiotemporal parameters and a higher GA and PCI could be used to identify individuals with PD. Thus, the CV of all spatiotemporal parameters, GA and PCI during walking could play an important role and be useful in identifying individuals with PD. Conclusion This study provided the notable a…
format: application/pdf
format: text/html
creator: Byungjoo Noh
creator: Changhong Youm
creator: Myeounggon Lee
creator: Sang-Myung Cheon
subject: Geriatrics
subject: Kinesiology
subject: Neurology
description: doi:10.7717/peerj.9463
publisher: PeerJ Inc.
rights: © 2020 Noh et al.
abstract: Background No previous study has examined the age-dependent characteristics of gait in individuals between 50 and 79 years simultaneously in healthy individuals and individuals with Parkinson’s disease (PD) over continuous gait cycles. This study aimed to investigate age-related differences in gait characteristics on individuals age ranged 50–79 years, including individuals with PD, during a 1-minute treadmill walking session. Additionally, we aimed to investigate the differences associated with spatiotemporal gait parameters and PD compared in age-matched individuals. Methods This study included 26 individuals with PD and 90 participants age ranged 50–79 years. The treadmill walking test at a self-preferred speed was performed for 1 min. The embedded inertial measurement unit sensor in the left and right outsoles-based system was used to collect gait characteristics based on tri-axial acceleration and tri-axial angular velocities. Results Participants aged >60 years had a decreased gait speed and shortened stride and step, which may demonstrate a distinct shift in aging (all p < 0.005). Individuals with PD showed more of a decrease in variables with a loss of consistency, including gait asymmetry (GA), phase coordination index (PCI) and coefficient of variation (CV) of all variables, than age-matched individuals (all p < 0.001). Gait speed, stride and step length, stance phase, variability, GA and PCI were the variables that highly depended on age and PD. Discussion Older adults could be considered those older than 60 years of age when gait alterations begin, such as a decreased gait speed as well as shortened stride and step length. On the other hand, a loss of consistency in spatiotemporal parameters and a higher GA and PCI could be used to identify individuals with PD. Thus, the CV of all spatiotemporal parameters, GA and PCI during walking could play an important role and be useful in identifying individuals with PD. Conclusion This study provided the notable a…
bibliographic citation: Noh et al. (2020) Gait characteristics in individuals with Parkinson’s disease during 1-minute treadmill walking. PeerJ 8:e9463 https://doi.org/10.7717/peerj.9463
date submitted: 2020-02-17
date accepted: 2020-06-10
issued: 2020-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Noh
  given name: Byungjoo
author list: Agent
  family name: Youm
  given name: Changhong
author list: Agent
  family name: Lee
  given name: Myeounggon
author list: Agent
  family name: Cheon
  given name: Sang-Myung
doi: 10.7717/peerj.9463
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-29
copyright: © 2020 Noh et al.
attribution name: Noh et al.

Hemogram data as a tool for decision-making in COVID-19 management: applications to resource scarcity scenarios
type: item
type: AcademicArticle
description: Background COVID-19 pandemics has challenged emergency response systems worldwide, with widespread reports of essential services breakdown and collapse of health care structure. A critical element involves essential workforce management since current protocols recommend release from duty for symptomatic individuals, including essential personnel. Testing capacity is also problematic in several countries, where diagnosis demand outnumbers available local testing capacity. Purpose This work describes a machine learning model derived from hemogram exam data performed in symptomatic patients and how they can be used to predict qRT-PCR test results. Methods Hemogram exams data from 510 symptomatic patients (73 positives and 437 negatives) were used to model and predict qRT-PCR results through Naïve-Bayes algorithms. Different scarcity scenarios were simulated, including symptomatic essential workforce management and absence of diagnostic tests. Adjusts in assumed prior probabilities allow fine-tuning of the model, according to actual prediction context. Results Proposed models can predict COVID-19 qRT-PCR results in symptomatic individuals with high accuracy, sensitivity and specificity, yielding a 100% sensitivity and 22.6% specificity with a prior of 0.9999; 76.7% for both sensitivity and specificity with a prior of 0.2933; and 0% sensitivity and 100% specificity with a prior of 0.001. Regarding background scarcity context, resources allocation can be significantly improved when model-based patient selection is observed, compared to random choice. Conclusions Machine learning models can be derived from widely available, quick, and inexpensive exam data in order to predict qRT-PCR results used in COVID-19 diagnosis. These models can be used to assist strategic decision-making in resource scarcity scenarios, including personnel shortage, lack of medical resources, and testing insufficiency.
format: application/pdf
format: text/html
creator: Eduardo Avila
creator: Alessandro Kahmann
creator: Clarice Alho
creator: Marcio Dorn
subject: Hematology
subject: Infectious Diseases
subject: Public Health
subject: Statistics
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.9482
publisher: PeerJ Inc.
rights: © 2020 Avila et al.
abstract: Background COVID-19 pandemics has challenged emergency response systems worldwide, with widespread reports of essential services breakdown and collapse of health care structure. A critical element involves essential workforce management since current protocols recommend release from duty for symptomatic individuals, including essential personnel. Testing capacity is also problematic in several countries, where diagnosis demand outnumbers available local testing capacity. Purpose This work describes a machine learning model derived from hemogram exam data performed in symptomatic patients and how they can be used to predict qRT-PCR test results. Methods Hemogram exams data from 510 symptomatic patients (73 positives and 437 negatives) were used to model and predict qRT-PCR results through Naïve-Bayes algorithms. Different scarcity scenarios were simulated, including symptomatic essential workforce management and absence of diagnostic tests. Adjusts in assumed prior probabilities allow fine-tuning of the model, according to actual prediction context. Results Proposed models can predict COVID-19 qRT-PCR results in symptomatic individuals with high accuracy, sensitivity and specificity, yielding a 100% sensitivity and 22.6% specificity with a prior of 0.9999; 76.7% for both sensitivity and specificity with a prior of 0.2933; and 0% sensitivity and 100% specificity with a prior of 0.001. Regarding background scarcity context, resources allocation can be significantly improved when model-based patient selection is observed, compared to random choice. Conclusions Machine learning models can be derived from widely available, quick, and inexpensive exam data in order to predict qRT-PCR results used in COVID-19 diagnosis. These models can be used to assist strategic decision-making in resource scarcity scenarios, including personnel shortage, lack of medical resources, and testing insufficiency.
bibliographic citation: Avila et al. (2020) Hemogram data as a tool for decision-making in COVID-19 management: applications to resource scarcity scenarios. PeerJ 8:e9482 https://doi.org/10.7717/peerj.9482
date submitted: 2020-05-10
date accepted: 2020-06-15
issued: 2020-06-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Avila
  given name: Eduardo
author list: Agent
  family name: Kahmann
  given name: Alessandro
author list: Agent
  family name: Alho
  given name: Clarice
author list: Agent
  family name: Dorn
  given name: Marcio
doi: 10.7717/peerj.9482
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-29
copyright: © 2020 Avila et al.
attribution name: Avila et al.

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