PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effectiveness of specific stabilization exercise compared with traditional trunk exercise in women with non-specific low back pain: a pilot randomized controlled trial
items: Eco-morphological diversity of larvae of soldier flies and their closest relatives in deep time
items: A diverse global fungal library for drug discovery
items: Data quantity is more important than its spatial bias for predictive species distribution modelling
items: Identification and prognostic value of DLGAP5 in endometrial cancer
items: The mRNA landscape profiling reveals potential biomarkers associated with acute kidney injury AKI after kidney transplantation
items: Adaptive evolution at mRNA editing sites in soft-bodied cephalopods
items: Invasion history of Harmonia axyridis (Pallas, 1773) (Coleoptera: Coccinellidae) in Ecuador
items: Cumulative oxygen deficit is a novel predictor for the timing of invasive mechanical ventilation in COVID-19 patients with respiratory distress
items: Early abolition of cough reflex predicts mortality in deeply sedated brain-injured patients

Effectiveness of specific stabilization exercise compared with traditional trunk exercise in women with non-specific low back pain: a pilot randomized controlled trial
type: item
type: AcademicArticle
description: Background Non-specific low back pain (LBP) is the leading cause of disability worldwide. The primary physiotherapeutic treatment for LBP is physical exercise, but evidence suggesting a specific exercise as most appropriate for any given case is limited. Objective To determine if specific stabilization exercise (SSE) is more effective than traditional trunk exercise (TTE) in reducing levels of pain, disability and inflammation in women with non-specific low back pain (LBP). Design A pilot randomized controlled trial was conducted in Rovira i Virgili University, Catalonia. Methods Thirty-nine females experiencing non-specific LBP were included in two groups: the TTE program and SSE program, both were conducted by a physiotherapist during twenty sessions. The primary outcome was pain intensity (10-cm Visual Analogue Scale). Secondary outcomes were disability (Roland Morris Disability Questionnaire), and inflammation (IL-6 and TNF-α plasma levels). Measurements were taken at baseline, at half intervention, at post-intervention, and a month later. Results Mean group differences in change from baseline to post-intervention for TTE were: −4.5 points (CI 3.3 to 5.6) for pain, −5.1 points (CI 3.0 to 7.3) for disability, 0.19 pg/mL (95% CI [−1.6–1.2]) for IL-6 levels, and 46.2 pg/mL (CI 13.0 to 85.3) for TNF-α levels. For SSE, differences were: −4.3 points (CI 3.1 to 5.6) for pain, −6.1 points (CI 3.7 to 8.6) for disability, 1.1 pg/mL (CI 0.0 to 2.1) for IL-6 levels , and 12.8 pg/mL (95% CI [−42.3–16.7]) for TNF-α levels. There were an insignificant effect size and no statistically significant overall mean differences between both groups. Conclusion This study suggests that both interventions (traditional trunk and specific stabilization exercises) are effective in reducing pain and disability in non-specific LBP patients, but the two programs produce different degrees of inflammation change. Clinical trial registration number NCT02103036.
format: application/pdf
format: text/html
creator: Eduard Minobes-Molina
creator: Maria Rosa Nogués
creator: Montse Giralt
creator: Carme Casajuana
creator: Dyego Leandro Bezerra de Souza
creator: Javier Jerez-Roig
creator: Marta Romeu
subject: Anesthesiology and Pain Management
subject: Clinical Trials
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.10304
publisher: PeerJ Inc.
rights: © 2020 Minobes-Molina et al.
abstract: Background Non-specific low back pain (LBP) is the leading cause of disability worldwide. The primary physiotherapeutic treatment for LBP is physical exercise, but evidence suggesting a specific exercise as most appropriate for any given case is limited. Objective To determine if specific stabilization exercise (SSE) is more effective than traditional trunk exercise (TTE) in reducing levels of pain, disability and inflammation in women with non-specific low back pain (LBP). Design A pilot randomized controlled trial was conducted in Rovira i Virgili University, Catalonia. Methods Thirty-nine females experiencing non-specific LBP were included in two groups: the TTE program and SSE program, both were conducted by a physiotherapist during twenty sessions. The primary outcome was pain intensity (10-cm Visual Analogue Scale). Secondary outcomes were disability (Roland Morris Disability Questionnaire), and inflammation (IL-6 and TNF-α plasma levels). Measurements were taken at baseline, at half intervention, at post-intervention, and a month later. Results Mean group differences in change from baseline to post-intervention for TTE were: −4.5 points (CI 3.3 to 5.6) for pain, −5.1 points (CI 3.0 to 7.3) for disability, 0.19 pg/mL (95% CI [−1.6–1.2]) for IL-6 levels, and 46.2 pg/mL (CI 13.0 to 85.3) for TNF-α levels. For SSE, differences were: −4.3 points (CI 3.1 to 5.6) for pain, −6.1 points (CI 3.7 to 8.6) for disability, 1.1 pg/mL (CI 0.0 to 2.1) for IL-6 levels , and 12.8 pg/mL (95% CI [−42.3–16.7]) for TNF-α levels. There were an insignificant effect size and no statistically significant overall mean differences between both groups. Conclusion This study suggests that both interventions (traditional trunk and specific stabilization exercises) are effective in reducing pain and disability in non-specific LBP patients, but the two programs produce different degrees of inflammation change. Clinical trial registration number NCT02103036.
bibliographic citation: Minobes-Molina et al. (2020) Effectiveness of specific stabilization exercise compared with traditional trunk exercise in women with non-specific low back pain: a pilot randomized controlled trial. PeerJ 8:e10304 https://doi.org/10.7717/peerj.10304
date submitted: 2020-05-14
date accepted: 2020-10-15
issued: 2020-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Minobes-Molina
  given name: Eduard
author list: Agent
  family name: Nogués
  given name: Maria Rosa
author list: Agent
  family name: Giralt
  given name: Montse
author list: Agent
  family name: Casajuana
  given name: Carme
author list: Agent
  family name: de Souza
  given name: Dyego Leandro Bezerra
author list: Agent
  family name: Jerez-Roig
  given name: Javier
author list: Agent
  family name: Romeu
  given name: Marta
doi: 10.7717/peerj.10304
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-27
copyright: ©2020 Minobes-Molina et al.
attribution name: Minobes-Molina et al.

Eco-morphological diversity of larvae of soldier flies and their closest relatives in deep time
type: item
type: AcademicArticle
description: Stratiomyomorpha (soldier flies and allies) is an ingroup of Diptera, with a fossil record stretching back to the Early Cretaceous (the Barremian, about 125 MYA). Stratiomyomorpha includes at least 3,000 species in the modern fauna, with many species being crucial for ecosystem functions, especially as saprophages. Larvae of many stratiomyomorphans are especially important as scavengers and saproxyls in modern ecosystems. Yet, fossil larvae of the group are extremely scarce. Here we present 23 new records of fossil stratiomyomorphan larvae, representing six discrete morphotypes. Specimens originate from Cretaceous amber from Myanmar, Eocene Baltic amber, Miocene Dominican amber, and compression fossils from the Eocene of Messel (Germany) and the Miocene of Slovenia. We discuss the implications of these new records for our understanding of stratiomyomorphan ecomorphology in deep time as well as their palaeoecology.
format: application/pdf
format: text/html
creator: Viktor A. Baranov
creator: Yinan Wang
creator: Rok Gašparič
creator: Sonja Wedmann
creator: Joachim T. Haug
subject: Developmental Biology
subject: Entomology
subject: Paleontology
description: doi:10.7717/peerj.10356
publisher: PeerJ Inc.
rights: © 2020 Baranov et al.
abstract: Stratiomyomorpha (soldier flies and allies) is an ingroup of Diptera, with a fossil record stretching back to the Early Cretaceous (the Barremian, about 125 MYA). Stratiomyomorpha includes at least 3,000 species in the modern fauna, with many species being crucial for ecosystem functions, especially as saprophages. Larvae of many stratiomyomorphans are especially important as scavengers and saproxyls in modern ecosystems. Yet, fossil larvae of the group are extremely scarce. Here we present 23 new records of fossil stratiomyomorphan larvae, representing six discrete morphotypes. Specimens originate from Cretaceous amber from Myanmar, Eocene Baltic amber, Miocene Dominican amber, and compression fossils from the Eocene of Messel (Germany) and the Miocene of Slovenia. We discuss the implications of these new records for our understanding of stratiomyomorphan ecomorphology in deep time as well as their palaeoecology.
bibliographic citation: Baranov et al. (2020) Eco-morphological diversity of larvae of soldier flies and their closest relatives in deep time. PeerJ 8:e10356 https://doi.org/10.7717/peerj.10356
date submitted: 2019-12-21
date accepted: 2020-10-23
issued: 2020-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baranov
  given name: Viktor A.
author list: Agent
  family name: Wang
  given name: Yinan
author list: Agent
  family name: Gašparič
  given name: Rok
author list: Agent
  family name: Wedmann
  given name: Sonja
author list: Agent
  family name: Haug
  given name: Joachim T.
doi: 10.7717/peerj.10356
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-27
copyright: © 2020 Baranov et al.
attribution name: Baranov et al.

A diverse global fungal library for drug discovery
type: item
type: AcademicArticle
description: Background Secondary fungal metabolites are important sources for new drugs against infectious diseases and cancers. Methods To obtain a library with enough diversity, we collected about 2,395 soil samples and 2,324 plant samples from 36 regions in Africa, Asia, and North America. The collection areas covered various climate zones in the world. We examined the usability of the global fungal extract library (GFEL) against parasitic malaria transmission, Gram-positive and negative bacterial pathogens, and leukemia cells. Results Nearly ten thousand fungal strains were isolated. Sequences of nuclear ribosomal internal transcribed spacer (ITS) from 40 randomly selected strains showed that over 80% were unique. Screening GFEL, we found that the fungal extract from Penicillium thomii was able to block Plasmodium falciparum transmission to Anopheles gambiae, and the fungal extract from Tolypocladium album was able to kill myelogenous leukemia cell line K562. We also identified a set of candidate fungal extracts against bacterial pathogens.
format: application/pdf
format: text/html
creator: Guodong Niu
creator: Thirunavukkarasu Annamalai
creator: Xiaohong Wang
creator: Sheng Li
creator: Stephen Munga
creator: Guomin Niu
creator: Yuk-Ching Tse-Dinh
creator: Jun Li
subject: Molecular Biology
subject: Mycology
subject: Drugs and Devices
subject: Infectious Diseases
description: doi:10.7717/peerj.10392
publisher: PeerJ Inc.
rights: © 2020 Niu et al.
abstract: Background Secondary fungal metabolites are important sources for new drugs against infectious diseases and cancers. Methods To obtain a library with enough diversity, we collected about 2,395 soil samples and 2,324 plant samples from 36 regions in Africa, Asia, and North America. The collection areas covered various climate zones in the world. We examined the usability of the global fungal extract library (GFEL) against parasitic malaria transmission, Gram-positive and negative bacterial pathogens, and leukemia cells. Results Nearly ten thousand fungal strains were isolated. Sequences of nuclear ribosomal internal transcribed spacer (ITS) from 40 randomly selected strains showed that over 80% were unique. Screening GFEL, we found that the fungal extract from Penicillium thomii was able to block Plasmodium falciparum transmission to Anopheles gambiae, and the fungal extract from Tolypocladium album was able to kill myelogenous leukemia cell line K562. We also identified a set of candidate fungal extracts against bacterial pathogens.
bibliographic citation: Niu et al. (2020) A diverse global fungal library for drug discovery. PeerJ 8:e10392 https://doi.org/10.7717/peerj.10392
date submitted: 2020-06-25
date accepted: 2020-10-28
issued: 2020-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niu
  given name: Guodong
author list: Agent
  family name: Annamalai
  given name: Thirunavukkarasu
author list: Agent
  family name: Wang
  given name: Xiaohong
author list: Agent
  family name: Li
  given name: Sheng
author list: Agent
  family name: Munga
  given name: Stephen
author list: Agent
  family name: Niu
  given name: Guomin
author list: Agent
  family name: Tse-Dinh
  given name: Yuk-Ching
author list: Agent
  family name: Li
  given name: Jun
doi: 10.7717/peerj.10392
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-27
copyright: ©2020 Niu et al.
attribution name: Niu et al.

Data quantity is more important than its spatial bias for predictive species distribution modelling
type: item
type: AcademicArticle
description: Biological records are often the data of choice for training predictive species distribution models (SDMs), but spatial sampling bias is pervasive in biological records data at multiple spatial scales and is thought to impair the performance of SDMs. We simulated presences and absences of virtual species as well as the process of recording these species to evaluate the effect on species distribution model prediction performance of (1) spatial bias in training data, (2) sample size (the average number of observations per species), and (3) the choice of species distribution modelling method. Our approach is novel in quantifying and applying real-world spatial sampling biases to simulated data. Spatial bias in training data decreased species distribution model prediction performance, but sample size and the choice of modelling method were more important than spatial bias in determining the prediction performance of species distribution models.
format: application/pdf
format: text/html
creator: Willson Gaul
creator: Dinara Sadykova
creator: Hannah J. White
creator: Lupe Leon-Sanchez
creator: Paul Caplat
creator: Mark C. Emmerson
creator: Jon M. Yearsley
subject: Biogeography
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.10411
publisher: PeerJ Inc.
rights: © 2020 Gaul et al.
abstract: Biological records are often the data of choice for training predictive species distribution models (SDMs), but spatial sampling bias is pervasive in biological records data at multiple spatial scales and is thought to impair the performance of SDMs. We simulated presences and absences of virtual species as well as the process of recording these species to evaluate the effect on species distribution model prediction performance of (1) spatial bias in training data, (2) sample size (the average number of observations per species), and (3) the choice of species distribution modelling method. Our approach is novel in quantifying and applying real-world spatial sampling biases to simulated data. Spatial bias in training data decreased species distribution model prediction performance, but sample size and the choice of modelling method were more important than spatial bias in determining the prediction performance of species distribution models.
bibliographic citation: Gaul et al. (2020) Data quantity is more important than its spatial bias for predictive species distribution modelling. PeerJ 8:e10411 https://doi.org/10.7717/peerj.10411
date submitted: 2020-06-09
date accepted: 2020-11-02
issued: 2020-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gaul
  given name: Willson
author list: Agent
  family name: Sadykova
  given name: Dinara
author list: Agent
  family name: White
  given name: Hannah J.
author list: Agent
  family name: Leon-Sanchez
  given name: Lupe
author list: Agent
  family name: Caplat
  given name: Paul
author list: Agent
  family name: Emmerson
  given name: Mark C.
author list: Agent
  family name: Yearsley
  given name: Jon M.
doi: 10.7717/peerj.10411
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-27
copyright: ©2020 Gaul et al.
attribution name: Gaul et al.

Identification and prognostic value of DLGAP5 in endometrial cancer
type: item
type: AcademicArticle
description: Background Endometrial cancer poses a serious threat to women’s health worldwide, and its pathogenesis, although actively explored, is not fully understood. DLGAP5 is a recently identified cell cycle-regulation gene not reported in endometrial cancer. This study was aiming to analyze the role of DLGAP5 in tumorigenesis and development and to investigate its prognostic significance of patients with endometrial cancer. Methodology Microarray datasets (GSE17025, GSE39099 and GSE63678) from the GEO database were used for comparative analysis, and their intersection was obtained by applying the Venn diagram, and DLGAP5 was selected as the target gene. Next, transcriptome data (n = 578) was downloaded from TCGA-UCEC to analyze the mRNA expression profile of DLGAP5. Then, immunohistochemical data provided by HPA were used to identify the different protein expression levels of DLGAP5 in tumor tissues and normal tissues. Subsequently, the prognostic meaning of DLGAP5 in patients with endometrial cancer was explored based on survival data from TCGA-UCEC (n = 541). Finally, the reliability of DLGAP5 expression was verified by RT-qPCR. Results Transcriptome data from TCGA-UCEC, immunohistochemical data from HPA, and RT-qPCR results from clinical samples were used for triple validation to confirm that the expression of DLGAP5 in endometrial cancer tissues was significantly higher than that in normal endometrial tissues. Kaplan–Meier survival analysis announced that the expression level of DLGAP5 was negatively correlated with the overall survival of patients with endometrial cancer. Conclusions DLGAP5 is a potential oncogene with cell cycle regulation, and its overexpression can predict the poor prognosis of patients with endometrial cancer. As a candidate target for the diagnosis and treatment of endometrial cancer, it is worthwhile to make further study to reveal the carcinogenicity of DLGAP5 and the mechanism of its resistance of organisms.
format: application/pdf
format: text/html
creator: Ruoyi Zheng
creator: Zhengzheng Shi
creator: Wenzhi Li
creator: Jianqin Yu
creator: Yuli Wang
creator: Qing Zhou
subject: Bioinformatics
subject: Gynecology and Obstetrics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.10433
publisher: PeerJ Inc.
rights: © 2020 Zheng et al.
abstract: Background Endometrial cancer poses a serious threat to women’s health worldwide, and its pathogenesis, although actively explored, is not fully understood. DLGAP5 is a recently identified cell cycle-regulation gene not reported in endometrial cancer. This study was aiming to analyze the role of DLGAP5 in tumorigenesis and development and to investigate its prognostic significance of patients with endometrial cancer. Methodology Microarray datasets (GSE17025, GSE39099 and GSE63678) from the GEO database were used for comparative analysis, and their intersection was obtained by applying the Venn diagram, and DLGAP5 was selected as the target gene. Next, transcriptome data (n = 578) was downloaded from TCGA-UCEC to analyze the mRNA expression profile of DLGAP5. Then, immunohistochemical data provided by HPA were used to identify the different protein expression levels of DLGAP5 in tumor tissues and normal tissues. Subsequently, the prognostic meaning of DLGAP5 in patients with endometrial cancer was explored based on survival data from TCGA-UCEC (n = 541). Finally, the reliability of DLGAP5 expression was verified by RT-qPCR. Results Transcriptome data from TCGA-UCEC, immunohistochemical data from HPA, and RT-qPCR results from clinical samples were used for triple validation to confirm that the expression of DLGAP5 in endometrial cancer tissues was significantly higher than that in normal endometrial tissues. Kaplan–Meier survival analysis announced that the expression level of DLGAP5 was negatively correlated with the overall survival of patients with endometrial cancer. Conclusions DLGAP5 is a potential oncogene with cell cycle regulation, and its overexpression can predict the poor prognosis of patients with endometrial cancer. As a candidate target for the diagnosis and treatment of endometrial cancer, it is worthwhile to make further study to reveal the carcinogenicity of DLGAP5 and the mechanism of its resistance of organisms.
bibliographic citation: Zheng et al. (2020) Identification and prognostic value of DLGAP5 in endometrial cancer. PeerJ 8:e10433 https://doi.org/10.7717/peerj.10433
date submitted: 2020-05-19
date accepted: 2020-11-05
issued: 2020-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Ruoyi
author list: Agent
  family name: Shi
  given name: Zhengzheng
author list: Agent
  family name: Li
  given name: Wenzhi
author list: Agent
  family name: Yu
  given name: Jianqin
author list: Agent
  family name: Wang
  given name: Yuli
author list: Agent
  family name: Zhou
  given name: Qing
doi: 10.7717/peerj.10433
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-27
copyright: ©2020 Zheng et al.
attribution name: Zheng et al.

The mRNA landscape profiling reveals potential biomarkers associated with acute kidney injury AKI after kidney transplantation
type: item
type: AcademicArticle
description: Background This study aims to identify potential biomarkers associated with acute kidney injury (AKI) post kidney transplantation. Material and Methods Two mRNA expression profiles from Gene Expression Omnibus repertory were downloaded, including 20 delayed graft function (DGF) and 68 immediate graft function (IGF) samples. Differentially expressed genes (DEGs) were identified between DGF and IGF group. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis of DEGs were performed. Then, a protein-protein interaction analysis was performed to extract hub genes. The key genes were searched by literature retrieval and cross-validated based on the training dataset. An external dataset was used to validate the expression levels of key genes. Receiver operating characteristic curve analyses were performed to evaluate diagnostic performance of key genes for AKI. Results A total of 330 DEGs were identified between DGF and IGF samples, including 179 up-regulated and 151 down-regulated genes. Of these, OLIG3, EBF3 and ETV1 were transcription factor genes. Moreover, LEP, EIF4A3, WDR3, MC4R, PPP2CB, DDX21 and GPT served as hub genes in PPI network. EBF3 was significantly up-regulated in validation GSE139061 dataset, which was consistently with our initial gene differential expression analysis. Finally, we found that LEP had a great diagnostic value for AKI (AUC = 0.740). Conclusion EBF3 may be associated with the development of AKI following kidney transplantation. Furthermore, LEP had a good diagnostic value for AKI. These findings provide deeper insights into the diagnosis and management of AKI post renal transplantation.
format: application/pdf
format: text/html
creator: Hui Bi
creator: Min Zhang
creator: Jialin Wang
creator: Gang Long
subject: Bioinformatics
subject: Biotechnology
subject: Nephrology
subject: Surgery and Surgical Specialties
subject: Medical Genetics
description: doi:10.7717/peerj.10441
publisher: PeerJ Inc.
rights: © 2020 Bi et al.
abstract: Background This study aims to identify potential biomarkers associated with acute kidney injury (AKI) post kidney transplantation. Material and Methods Two mRNA expression profiles from Gene Expression Omnibus repertory were downloaded, including 20 delayed graft function (DGF) and 68 immediate graft function (IGF) samples. Differentially expressed genes (DEGs) were identified between DGF and IGF group. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis of DEGs were performed. Then, a protein-protein interaction analysis was performed to extract hub genes. The key genes were searched by literature retrieval and cross-validated based on the training dataset. An external dataset was used to validate the expression levels of key genes. Receiver operating characteristic curve analyses were performed to evaluate diagnostic performance of key genes for AKI. Results A total of 330 DEGs were identified between DGF and IGF samples, including 179 up-regulated and 151 down-regulated genes. Of these, OLIG3, EBF3 and ETV1 were transcription factor genes. Moreover, LEP, EIF4A3, WDR3, MC4R, PPP2CB, DDX21 and GPT served as hub genes in PPI network. EBF3 was significantly up-regulated in validation GSE139061 dataset, which was consistently with our initial gene differential expression analysis. Finally, we found that LEP had a great diagnostic value for AKI (AUC = 0.740). Conclusion EBF3 may be associated with the development of AKI following kidney transplantation. Furthermore, LEP had a good diagnostic value for AKI. These findings provide deeper insights into the diagnosis and management of AKI post renal transplantation.
bibliographic citation: Bi et al. (2020) The mRNA landscape profiling reveals potential biomarkers associated with acute kidney injury AKI after kidney transplantation. PeerJ 8:e10441 https://doi.org/10.7717/peerj.10441
date submitted: 2020-06-08
date accepted: 2020-11-06
issued: 2020-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Bi
  given name: Hui
author list: Agent
  family name: Zhang
  given name: Min
author list: Agent
  family name: Wang
  given name: Jialin
author list: Agent
  family name: Long
  given name: Gang
doi: 10.7717/peerj.10441
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-27
copyright: ©2020 Bi et al.
attribution name: Bi et al.

Adaptive evolution at mRNA editing sites in soft-bodied cephalopods
type: item
type: AcademicArticle
description: Background The bulk of variability in mRNA sequence arises due to mutation—change in DNA sequence which is heritable if it occurs in the germline. However, variation in mRNA can also be achieved by post-transcriptional modification including mRNA editing, changes in mRNA nucleotide sequence that mimic the effect of mutations. Such modifications are not inherited directly; however, as the processes affecting them are encoded in the genome, they have a heritable component, and therefore can be shaped by selection. In soft-bodied cephalopods, adenine-to-inosine RNA editing is very frequent, and much of it occurs at nonsynonymous sites, affecting the sequence of the encoded protein. Methods We study selection regimes at coleoid A-to-I editing sites, estimate the prevalence of positive selection, and analyze interdependencies between the editing level and contextual characteristics of editing site. Results Here, we show that mRNA editing of individual nonsynonymous sites in cephalopods originates in evolution through substitutions at regions adjacent to these sites. As such substitutions mimic the effect of the substitution at the edited site itself, we hypothesize that they are favored by selection if the inosine is selectively advantageous to adenine at the edited position. Consistent with this hypothesis, we show that edited adenines are more frequently substituted with guanine, an informational analog of inosine, in the course of evolution than their unedited counterparts, and for heavily edited adenines, these transitions are favored by positive selection. Our study shows that coleoid editing sites may enhance adaptation, which, together with recent observations on Drosophila and human editing sites, points at a general role of RNA editing in the molecular evolution of metazoans.
format: application/pdf
format: text/html
creator: Mikhail Moldovan
creator: Zoe Chervontseva
creator: Georgii Bazykin
creator: Mikhail S. Gelfand
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.10456
publisher: PeerJ Inc.
rights: © 2020 Moldovan et al.
abstract: Background The bulk of variability in mRNA sequence arises due to mutation—change in DNA sequence which is heritable if it occurs in the germline. However, variation in mRNA can also be achieved by post-transcriptional modification including mRNA editing, changes in mRNA nucleotide sequence that mimic the effect of mutations. Such modifications are not inherited directly; however, as the processes affecting them are encoded in the genome, they have a heritable component, and therefore can be shaped by selection. In soft-bodied cephalopods, adenine-to-inosine RNA editing is very frequent, and much of it occurs at nonsynonymous sites, affecting the sequence of the encoded protein. Methods We study selection regimes at coleoid A-to-I editing sites, estimate the prevalence of positive selection, and analyze interdependencies between the editing level and contextual characteristics of editing site. Results Here, we show that mRNA editing of individual nonsynonymous sites in cephalopods originates in evolution through substitutions at regions adjacent to these sites. As such substitutions mimic the effect of the substitution at the edited site itself, we hypothesize that they are favored by selection if the inosine is selectively advantageous to adenine at the edited position. Consistent with this hypothesis, we show that edited adenines are more frequently substituted with guanine, an informational analog of inosine, in the course of evolution than their unedited counterparts, and for heavily edited adenines, these transitions are favored by positive selection. Our study shows that coleoid editing sites may enhance adaptation, which, together with recent observations on Drosophila and human editing sites, points at a general role of RNA editing in the molecular evolution of metazoans.
bibliographic citation: Moldovan et al. (2020) Adaptive evolution at mRNA editing sites in soft-bodied cephalopods. PeerJ 8:e10456 https://doi.org/10.7717/peerj.10456
date submitted: 2020-10-01
date accepted: 2020-11-09
issued: 2020-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moldovan
  given name: Mikhail
author list: Agent
  family name: Chervontseva
  given name: Zoe
author list: Agent
  family name: Bazykin
  given name: Georgii
author list: Agent
  family name: Gelfand
  given name: Mikhail S.
doi: 10.7717/peerj.10456
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-27
copyright: © 2020 Moldovan et al.
attribution name: Moldovan et al.

Invasion history of Harmonia axyridis (Pallas, 1773) (Coleoptera: Coccinellidae) in Ecuador
type: item
type: AcademicArticle
description: Harmonia axyridis is a ladybird extensively used around the world for biological control of agricultural pests. However, it has become invasive in several countries, producing negative ecological and socio-economic impacts. Herein, we review the invasion history of the Harlequin Ladybird Harmonia axyridis (Pallas, 1773) in Ecuador. Although first reported in Ecuador in 2012, museum specimens date back to 2004 and it is currently established across the country, especially along the Andean region. Due to its invasive nature, further studies are urgently needed to evaluate possible impacts of H. axyridis on the Ecuadorian biodiversity and agroindustry.
format: application/pdf
format: text/html
creator: Diego F. Cisneros-Heredia
creator: Emilia Peñaherrera-Romero
subject: Biodiversity
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.10461
publisher: PeerJ Inc.
rights: © 2020 Cisneros-Heredia and Peñaherrera-Romero
abstract: Harmonia axyridis is a ladybird extensively used around the world for biological control of agricultural pests. However, it has become invasive in several countries, producing negative ecological and socio-economic impacts. Herein, we review the invasion history of the Harlequin Ladybird Harmonia axyridis (Pallas, 1773) in Ecuador. Although first reported in Ecuador in 2012, museum specimens date back to 2004 and it is currently established across the country, especially along the Andean region. Due to its invasive nature, further studies are urgently needed to evaluate possible impacts of H. axyridis on the Ecuadorian biodiversity and agroindustry.
bibliographic citation: Cisneros-Heredia et al. (2020) Invasion history of Harmonia axyridis (Pallas, 1773) (Coleoptera: Coccinellidae) in Ecuador. PeerJ 8:e10461 https://doi.org/10.7717/peerj.10461
date submitted: 2019-02-28
date accepted: 2020-11-10
issued: 2020-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cisneros-Heredia
  given name: Diego F.
author list: Agent
  family name: Peñaherrera-Romero
  given name: Emilia
doi: 10.7717/peerj.10461
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-27
copyright: © 2020 Cisneros-Heredia and Peñaherrera-Romero
attribution name: Cisneros-Heredia and Peñaherrera-Romero

Cumulative oxygen deficit is a novel predictor for the timing of invasive mechanical ventilation in COVID-19 patients with respiratory distress
type: item
type: AcademicArticle
description: Background and objectives The timing of invasive mechanical ventilation (IMV) is controversial in COVID-19 patients with acute respiratory hypoxemia. The study aimed to develop a novel predictor called cumulative oxygen deficit (COD) for the risk stratification. Methods The study was conducted in four designated hospitals for treating COVID-19 patients in Jingmen, Wuhan, from January to March 2020. COD was defined to account for both the magnitude and duration of hypoxemia. A higher value of COD indicated more oxygen deficit. The predictive performance of COD was calculated in multivariable Cox regression models. Results A number of 111 patients including 80 in the non-IMV group and 31 in the IMV group were included. Patients with IMV had substantially lower PaO2 (62 (49, 89) vs. 90.5 (68, 125.25) mmHg; p < 0.001), and higher COD (−6.87 (−29.36, 52.38) vs. −231.68 (−1040.78, 119.83) mmHg·day) than patients without IMV. As compared to patients with COD < 0, patients with COD > 30 mmHg·day had higher risk of fatality (HR: 3.79, 95% CI [2.57–16.93]; p = 0.037), and those with COD > 50 mmHg·day were 10 times more likely to die (HR: 10.45, 95% CI [1.28–85.37]; p = 0.029). Conclusions The study developed a novel predictor COD which considered both magnitude and duration of hypoxemia, to assist risk stratification of COVID-19 patients with acute respiratory distress.
format: application/pdf
format: text/html
creator: Huiqing Ge
creator: Jian-cang Zhou
creator: FangFang Lv
creator: Junli Zhang
creator: Jun Yi
creator: Changming Yang
creator: Lingwei Zhang
creator: Yuhan Zhou
creator: Binbin Ren
creator: Qing Pan
creator: Zhongheng Zhang
subject: Emergency and Critical Care
subject: Respiratory Medicine
description: doi:10.7717/peerj.10497
publisher: PeerJ Inc.
rights: © 2020 Ge et al.
abstract: Background and objectives The timing of invasive mechanical ventilation (IMV) is controversial in COVID-19 patients with acute respiratory hypoxemia. The study aimed to develop a novel predictor called cumulative oxygen deficit (COD) for the risk stratification. Methods The study was conducted in four designated hospitals for treating COVID-19 patients in Jingmen, Wuhan, from January to March 2020. COD was defined to account for both the magnitude and duration of hypoxemia. A higher value of COD indicated more oxygen deficit. The predictive performance of COD was calculated in multivariable Cox regression models. Results A number of 111 patients including 80 in the non-IMV group and 31 in the IMV group were included. Patients with IMV had substantially lower PaO2 (62 (49, 89) vs. 90.5 (68, 125.25) mmHg; p < 0.001), and higher COD (−6.87 (−29.36, 52.38) vs. −231.68 (−1040.78, 119.83) mmHg·day) than patients without IMV. As compared to patients with COD < 0, patients with COD > 30 mmHg·day had higher risk of fatality (HR: 3.79, 95% CI [2.57–16.93]; p = 0.037), and those with COD > 50 mmHg·day were 10 times more likely to die (HR: 10.45, 95% CI [1.28–85.37]; p = 0.029). Conclusions The study developed a novel predictor COD which considered both magnitude and duration of hypoxemia, to assist risk stratification of COVID-19 patients with acute respiratory distress.
bibliographic citation: Ge et al. (2020) Cumulative oxygen deficit is a novel predictor for the timing of invasive mechanical ventilation in COVID-19 patients with respiratory distress. PeerJ 8:e10497 https://doi.org/10.7717/peerj.10497
date submitted: 2020-09-20
date accepted: 2020-11-14
issued: 2020-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ge
  given name: Huiqing
author list: Agent
  family name: Zhou
  given name: Jian-cang
author list: Agent
  family name: Lv
  given name: FangFang
author list: Agent
  family name: Zhang
  given name: Junli
author list: Agent
  family name: Yi
  given name: Jun
author list: Agent
  family name: Yang
  given name: Changming
author list: Agent
  family name: Zhang
  given name: Lingwei
author list: Agent
  family name: Zhou
  given name: Yuhan
author list: Agent
  family name: Ren
  given name: Binbin
author list: Agent
  family name: Pan
  given name: Qing
author list: Agent
  family name: Zhang
  given name: Zhongheng
doi: 10.7717/peerj.10497
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-27
copyright: © 2020 Ge et al.
attribution name: Ge et al.

Early abolition of cough reflex predicts mortality in deeply sedated brain-injured patients
type: item
type: AcademicArticle
description: Background Deep sedation may hamper the detection of neurological deterioration in brain-injured patients. Impaired brainstem reflexes within the first 24 h of deep sedation are associated with increased mortality in non-brain-injured patients. Our objective was to confirm this association in brain-injured patients. Methods This was an observational prospective multicenter cohort study involving four neuro-intensive care units. We included acute brain-injured patients requiring deep sedation, defined by a Richmond Assessment Sedation Scale (RASS) < −3. Neurological assessment was performed at day 1 and included pupillary diameter, pupillary light, corneal and cough reflexes, and grimace and motor response to noxious stimuli. Pre-sedation Glasgow Coma Scale (GCS) and Simplified Acute Physiology Score (SAPS-II) were collected, as well as the cause of death in the Intensive Care Unit (ICU). Results A total of 137 brain-injured patients were recruited, including 70 (51%) traumatic brain-injured patients, 40 (29%) vascular (subarachnoid hemorrhage or intracerebral hemorrhage). Thirty patients (22%) died in the ICU. At day 1, the corneal (OR 2.69, p = 0.034) and cough reflexes (OR 5.12, p = 0.0003) were more frequently abolished in patients that died in the ICU. In a multivariate analysis, abolished cough reflex was associated with ICU mortality after adjustment to pre-sedation GCS, SAPS-II, RASS (OR: 5.19, 95% CI [1.92–14.1], p = 0.001) or dose of sedatives (OR: 8.89, 95% CI [2.64–30.0], p = 0.0004). Conclusion Early (day 1) cough reflex abolition is an independent predictor of mortality in deeply sedated brain-injured patients. Abolished cough reflex likely reflects a brainstem dysfunction that might result from the combination of primary and secondary neuro-inflammatory cerebral insults revealed and/or worsened by sedation.
format: application/pdf
format: text/html
creator: Stanislas Kandelman
creator: Jérémy Allary
creator: Raphael Porcher
creator: Cássia Righy
creator: Clarissa Francisca Valdez
creator: Frank Rasulo
creator: Nicholas Heming
creator: Guy Moneger
creator: Eric Azabou
creator: Guillaume Savary
creator: Djillali Annane
creator: Fabrice Chretien
creator: Nicola Latronico
creator: Fernando Augusto Bozza
creator: Benjamin Rohaut
creator: Tarek Sharshar
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Emergency and Critical Care
subject: Neurology
subject: Respiratory Medicine
description: doi:10.7717/peerj.10326
publisher: PeerJ Inc.
rights: © 2020 Kandelman et al.
abstract: Background Deep sedation may hamper the detection of neurological deterioration in brain-injured patients. Impaired brainstem reflexes within the first 24 h of deep sedation are associated with increased mortality in non-brain-injured patients. Our objective was to confirm this association in brain-injured patients. Methods This was an observational prospective multicenter cohort study involving four neuro-intensive care units. We included acute brain-injured patients requiring deep sedation, defined by a Richmond Assessment Sedation Scale (RASS) < −3. Neurological assessment was performed at day 1 and included pupillary diameter, pupillary light, corneal and cough reflexes, and grimace and motor response to noxious stimuli. Pre-sedation Glasgow Coma Scale (GCS) and Simplified Acute Physiology Score (SAPS-II) were collected, as well as the cause of death in the Intensive Care Unit (ICU). Results A total of 137 brain-injured patients were recruited, including 70 (51%) traumatic brain-injured patients, 40 (29%) vascular (subarachnoid hemorrhage or intracerebral hemorrhage). Thirty patients (22%) died in the ICU. At day 1, the corneal (OR 2.69, p = 0.034) and cough reflexes (OR 5.12, p = 0.0003) were more frequently abolished in patients that died in the ICU. In a multivariate analysis, abolished cough reflex was associated with ICU mortality after adjustment to pre-sedation GCS, SAPS-II, RASS (OR: 5.19, 95% CI [1.92–14.1], p = 0.001) or dose of sedatives (OR: 8.89, 95% CI [2.64–30.0], p = 0.0004). Conclusion Early (day 1) cough reflex abolition is an independent predictor of mortality in deeply sedated brain-injured patients. Abolished cough reflex likely reflects a brainstem dysfunction that might result from the combination of primary and secondary neuro-inflammatory cerebral insults revealed and/or worsened by sedation.
bibliographic citation: Kandelman et al. (2020) Early abolition of cough reflex predicts mortality in deeply sedated brain-injured patients. PeerJ 8:e10326 https://doi.org/10.7717/peerj.10326
date submitted: 2020-05-06
date accepted: 2020-10-19
issued: 2020-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kandelman
  given name: Stanislas
author list: Agent
  family name: Allary
  given name: Jérémy
author list: Agent
  family name: Porcher
  given name: Raphael
author list: Agent
  family name: Righy
  given name: Cássia
author list: Agent
  family name: Valdez
  given name: Clarissa Francisca
author list: Agent
  family name: Rasulo
  given name: Frank
author list: Agent
  family name: Heming
  given name: Nicholas
author list: Agent
  family name: Moneger
  given name: Guy
author list: Agent
  family name: Azabou
  given name: Eric
author list: Agent
  family name: Savary
  given name: Guillaume
author list: Agent
  family name: Annane
  given name: Djillali
author list: Agent
  family name: Chretien
  given name: Fabrice
author list: Agent
  family name: Latronico
  given name: Nicola
author list: Agent
  family name: Bozza
  given name: Fernando Augusto
author list: Agent
  family name: Rohaut
  given name: Benjamin
author list: Agent
  family name: Sharshar
  given name: Tarek
doi: 10.7717/peerj.10326
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-26
copyright: © 2020 Kandelman et al.
attribution name: Kandelman et al.

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