PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Demographic history and population genetic analysis of Decapterus maruadsi from the northern South China Sea based on mitochondrial control region sequence
items: Evaluation of ultrasound-guided lateral thoracolumbar interfascial plane block for postoperative analgesia in lumbar spine fusion surgery: a prospective, randomized, and controlled clinical trial
items: The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA
items: Predicting the potential distribution of the endemic seabird Pelecanus thagus in the Humboldt Current Large Marine Ecosystem under different climate change scenarios
items: Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV
items: Identification of hub genes and small-molecule compounds related to intracerebral hemorrhage with bioinformatics analysis
items: New Bohaiornis-like bird from the Early Cretaceous of China: enantiornithine interrelationships and flight performance
items: Strategies of elite Chinese gymnasts in coping with landing impact from backward somersault
items: Investigating the significance of tumor-infiltrating immune cells for the prognosis of lung squamous cell carcinoma
items: Combined effect of the entomopathogenic fungus Metarhizium robertsii and avermectins on the survival and immune response of Aedes aegypti larvae

Demographic history and population genetic analysis of Decapterus maruadsi from the northern South China Sea based on mitochondrial control region sequence
type: item
type: AcademicArticle
description: Late Pleistocene climate oscillations are believed to have greatly influenced the distribution, population dynamics, and genetic variation of many marine organisms in the western Pacific. However, the impact of the late Pleistocene climate cycles on the demographic history and population genetics of pelagic fish in the northern South China Sea (SCS) remains largely unexplored. In this study, we explored the demographic history, genetic structure, and genetic diversity of Decapterus maruadsi, a typical pelagic fish, over most of its range in the northern SCS. A 828–832 bp fragment of mitochondrial control region were sequenced in 241 individuals from 11 locations. High haplotype diversity (0.905–0.980) and low nucleotide diversity (0.00269–0.00849) was detected, revealing low levels of genetic diversity. Demographic history analysis revealed a pattern of decline and subsequent rapid growth in the effective population size during deglaciation, which showed that D. maruadsi experienced recent demographic expansion after a period of low effective population size. Genetic diversity, genetic structure, and phylogenetic relationship analysis all demonstrated that no significant genetic differentiation existed among the populations, indicating that D. maruadsi was panmictic throughout the northern SCS. Periodic sea-level changes, fluctuation of the East Asian Monsoon, and Kuroshio variability were responsible for the population decline and expansion of D. maruadsi. The demographic history was the primary reason for the low levels of genetic diversity and the lack of significant genetic structure. The life history characteristics and ocean currents also had a strong correlation with the genetic homogeneity of D. maruadsi. However, the genetic structure of the population (genetic homogeneity) is inconsistent with biological characteristics (significant difference), which is an important reminder to identify and manage the D. maruadsi population carefully.
format: application/pdf
format: text/html
creator: Su-Fang Niu
creator: Ren-Xie Wu
creator: Yun Zhai
creator: Hao-Ran Zhang
creator: Zhong-Lu Li
creator: Zhen-Bang Liang
creator: Yu-Hang Chen
subject: Biodiversity
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.7953
publisher: PeerJ Inc.
rights: © 2019 Niu et al.
abstract: Late Pleistocene climate oscillations are believed to have greatly influenced the distribution, population dynamics, and genetic variation of many marine organisms in the western Pacific. However, the impact of the late Pleistocene climate cycles on the demographic history and population genetics of pelagic fish in the northern South China Sea (SCS) remains largely unexplored. In this study, we explored the demographic history, genetic structure, and genetic diversity of Decapterus maruadsi, a typical pelagic fish, over most of its range in the northern SCS. A 828–832 bp fragment of mitochondrial control region were sequenced in 241 individuals from 11 locations. High haplotype diversity (0.905–0.980) and low nucleotide diversity (0.00269–0.00849) was detected, revealing low levels of genetic diversity. Demographic history analysis revealed a pattern of decline and subsequent rapid growth in the effective population size during deglaciation, which showed that D. maruadsi experienced recent demographic expansion after a period of low effective population size. Genetic diversity, genetic structure, and phylogenetic relationship analysis all demonstrated that no significant genetic differentiation existed among the populations, indicating that D. maruadsi was panmictic throughout the northern SCS. Periodic sea-level changes, fluctuation of the East Asian Monsoon, and Kuroshio variability were responsible for the population decline and expansion of D. maruadsi. The demographic history was the primary reason for the low levels of genetic diversity and the lack of significant genetic structure. The life history characteristics and ocean currents also had a strong correlation with the genetic homogeneity of D. maruadsi. However, the genetic structure of the population (genetic homogeneity) is inconsistent with biological characteristics (significant difference), which is an important reminder to identify and manage the D. maruadsi population carefully.
bibliographic citation: Niu et al. (2019) Demographic history and population genetic analysis of Decapterus maruadsi from the northern South China Sea based on mitochondrial control region sequence. PeerJ 7:e7953 https://doi.org/10.7717/peerj.7953
date submitted: 2019-01-02
date accepted: 2019-09-26
issued: 2019-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niu
  given name: Su-Fang
author list: Agent
  family name: Wu
  given name: Ren-Xie
author list: Agent
  family name: Zhai
  given name: Yun
author list: Agent
  family name: Zhang
  given name: Hao-Ran
author list: Agent
  family name: Li
  given name: Zhong-Lu
author list: Agent
  family name: Liang
  given name: Zhen-Bang
author list: Agent
  family name: Chen
  given name: Yu-Hang
doi: 10.7717/peerj.7953
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-28
copyright: ©2019 Niu et al.
attribution name: Niu et al.

Evaluation of ultrasound-guided lateral thoracolumbar interfascial plane block for postoperative analgesia in lumbar spine fusion surgery: a prospective, randomized, and controlled clinical trial
type: item
type: AcademicArticle
description: Objective Ultrasound-guided lateral thoracolumbar interfascial plane block (US-TLIP block) is a novel regional technique for anesthesia or analgesia. However, there has been no prospective, randomized and controlled clinical trial investigating the perioperative analgesic effect of US-TLIP block on lumbar spinal fusion surgery. The aim of this study was to investigate the analgesic effect of bilateral single-shot US-TLIP in patients undergoing lumbar spinal fusion surgery. Methods A prospective and randomized comparative clinical study was conducted. A total of 60 patients (ASA classes: I–II), aged 21–74 years who were scheduled for lumbar spinal fusion surgery were randomized and divided into the TLIP group (Group T, n = 30) and control group (Group C, n = 30). The patients in Group T received preoperative bilateral single-shot US-TLIP with 30 ml of 0.375% ropivacaine at the third lumbar spine (L3) vertebral level, and the patients in Group C received an injection of 30 ml 0.9% saline through same technique. All patients received patient-controlled analgesia (PCA) after their operation. The frequency of PCA compressions and rescue analgesic administrations were recorded. Opioids (sufentanil and remifentanil), anesthetic consumption, the number of postoperative days spent in a hospital bed, overall hospital stay time and postoperative complications were recorded. The Visual Analogue Scale (VAS) and Bruggemann Comfort Scale (BCS) scores for pain and comfort assessment were recorded at 1, 12, 24, 36, and 48 hours postoperatively. Results Opioids and anesthetic consumption in the perioperative period decreased significantly in the TLIP group compared to the control group (P < 0.05). The VAS and BCS scores in the TLIP group were lower at 12, 24, and 36 hours postoperatively (P < 0.05). US-TLIP block has been shown to shorten postoperative hospital stays (P < 0.05). There was no significant difference in postoperative complications between the two groups. Conclusion Our …
format: application/pdf
format: text/html
creator: Ke Chen
creator: Lizhen Wang
creator: Meng Ning
creator: Lianjie Dou
creator: Wei Li
creator: Yuanhai Li
subject: Anesthesiology and Pain Management
subject: Clinical Trials
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.7967
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Objective Ultrasound-guided lateral thoracolumbar interfascial plane block (US-TLIP block) is a novel regional technique for anesthesia or analgesia. However, there has been no prospective, randomized and controlled clinical trial investigating the perioperative analgesic effect of US-TLIP block on lumbar spinal fusion surgery. The aim of this study was to investigate the analgesic effect of bilateral single-shot US-TLIP in patients undergoing lumbar spinal fusion surgery. Methods A prospective and randomized comparative clinical study was conducted. A total of 60 patients (ASA classes: I–II), aged 21–74 years who were scheduled for lumbar spinal fusion surgery were randomized and divided into the TLIP group (Group T, n = 30) and control group (Group C, n = 30). The patients in Group T received preoperative bilateral single-shot US-TLIP with 30 ml of 0.375% ropivacaine at the third lumbar spine (L3) vertebral level, and the patients in Group C received an injection of 30 ml 0.9% saline through same technique. All patients received patient-controlled analgesia (PCA) after their operation. The frequency of PCA compressions and rescue analgesic administrations were recorded. Opioids (sufentanil and remifentanil), anesthetic consumption, the number of postoperative days spent in a hospital bed, overall hospital stay time and postoperative complications were recorded. The Visual Analogue Scale (VAS) and Bruggemann Comfort Scale (BCS) scores for pain and comfort assessment were recorded at 1, 12, 24, 36, and 48 hours postoperatively. Results Opioids and anesthetic consumption in the perioperative period decreased significantly in the TLIP group compared to the control group (P < 0.05). The VAS and BCS scores in the TLIP group were lower at 12, 24, and 36 hours postoperatively (P < 0.05). US-TLIP block has been shown to shorten postoperative hospital stays (P < 0.05). There was no significant difference in postoperative complications between the two groups. Conclusion Our …
bibliographic citation: Chen et al. (2019) Evaluation of ultrasound-guided lateral thoracolumbar interfascial plane block for postoperative analgesia in lumbar spine fusion surgery: a prospective, randomized, and controlled clinical trial. PeerJ 7:e7967 https://doi.org/10.7717/peerj.7967
date submitted: 2019-06-25
date accepted: 2019-09-30
issued: 2019-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Ke
author list: Agent
  family name: Wang
  given name: Lizhen
author list: Agent
  family name: Ning
  given name: Meng
author list: Agent
  family name: Dou
  given name: Lianjie
author list: Agent
  family name: Li
  given name: Wei
author list: Agent
  family name: Li
  given name: Yuanhai
doi: 10.7717/peerj.7967
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-28
copyright: ©2019 Chen et al.
attribution name: Chen et al.

The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA
type: item
type: AcademicArticle
description: It is assumed that the sequencing of ribosomes better reflects the active microbial community than the sequencing of the ribosomal RNA encoding genes. Yet, many studies exploring microbial communities in various environments, ranging from the human gut to deep oceans, questioned the validity of this paradigm due to the discrepancies between the DNA and RNA based communities. Here, we focus on an often neglected key step in the analysis, the reverse transcription (RT) reaction. Previous studies showed that RT may introduce biases when expressed genes and ribosmal rRNA are quantified, yet its effect on microbial diversity and community composition was never tested. High throughput sequencing of ribosomal RNA is a valuable tool to understand microbial communities as it better describes the active population than DNA analysis. However, the necessary step of RT may introduce biases that have so far been poorly described. In this manuscript, we compare three RT enzymes, commonly used in soil microbiology, in two temperature modes to determine a potential source of bias due to non-standardized RT conditions. In our comparisons, we have observed up to six fold differences in bacterial class abundance. A temperature induced bias can be partially explained by G-C content of the affected bacterial groups, thus pointing toward a need for higher reaction temperatures. However, another source of bias was due to enzyme processivity differences. This bias is potentially hard to overcome and thus mitigating it might require the use of one enzyme for the sake of cross-study comparison.
format: application/pdf
format: text/html
creator: Adam Šťovíček
creator: Smadar Cohen-Chalamish
creator: Osnat Gillor
subject: Microbiology
subject: Molecular Biology
subject: Soil Science
subject: Population Biology
description: doi:10.7717/peerj.7608
publisher: PeerJ Inc.
rights: © 2019 Šťovíček et al.
abstract: It is assumed that the sequencing of ribosomes better reflects the active microbial community than the sequencing of the ribosomal RNA encoding genes. Yet, many studies exploring microbial communities in various environments, ranging from the human gut to deep oceans, questioned the validity of this paradigm due to the discrepancies between the DNA and RNA based communities. Here, we focus on an often neglected key step in the analysis, the reverse transcription (RT) reaction. Previous studies showed that RT may introduce biases when expressed genes and ribosmal rRNA are quantified, yet its effect on microbial diversity and community composition was never tested. High throughput sequencing of ribosomal RNA is a valuable tool to understand microbial communities as it better describes the active population than DNA analysis. However, the necessary step of RT may introduce biases that have so far been poorly described. In this manuscript, we compare three RT enzymes, commonly used in soil microbiology, in two temperature modes to determine a potential source of bias due to non-standardized RT conditions. In our comparisons, we have observed up to six fold differences in bacterial class abundance. A temperature induced bias can be partially explained by G-C content of the affected bacterial groups, thus pointing toward a need for higher reaction temperatures. However, another source of bias was due to enzyme processivity differences. This bias is potentially hard to overcome and thus mitigating it might require the use of one enzyme for the sake of cross-study comparison.
bibliographic citation: Šťovíček et al. (2019) The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA. PeerJ 7:e7608 https://doi.org/10.7717/peerj.7608
date submitted: 2019-06-03
date accepted: 2019-08-05
issued: 2019-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Šťovíček
  given name: Adam
author list: Agent
  family name: Cohen-Chalamish
  given name: Smadar
author list: Agent
  family name: Gillor
  given name: Osnat
doi: 10.7717/peerj.7608
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-25
copyright: © 2019 Šťovíček et al.
attribution name: Šťovíček et al.

Predicting the potential distribution of the endemic seabird Pelecanus thagus in the Humboldt Current Large Marine Ecosystem under different climate change scenarios
type: item
type: AcademicArticle
description: Background The effects of global climate change on species inhabiting marine ecosystems are of growing concern, especially for endemic species that are sensitive due to restricted distribution. One method employed for determining the effects of climate change on the distribution of these organisms is species distribution modeling. Methods We generated a model to evaluate the potential geographic distribution and breeding distribution of the Peruvian pelican (Pelecanus thagus). Based on maximum entropy modeling (MaxEnt), we identified the environmental factors that currently affect its geographic distribution and breeding. Then we predicted its future distribution range under two climate change scenarios: moderate (rcp 2.6) and severe (rcp 8.5). Results The mean daytime temperature range and marine primary productivity explain the current potential distribution and breeding of the pelican. Under the future climate change scenarios, the spatial distribution of the pelican is predicted to slightly change. While the breeding distribution of the pelican can benefit in the moderate scenario, it is predicted to decrease (near −20 %) in the severe scenario. Discussion The current potential geographic distribution of the pelican is influenced to a large extent by thermal conditions and primary productivity. Under the moderate scenario, a slight increase in pelican breeding distribution is predicted. This increase in habitable area is explained by the climatic conditions in southern Chile, and those climatic conditions will likely be similar to the current conditions of the central coast of Chile. We predict that the coasts of southern Chile will constitute an important refuge for the conservation of the Peruvian pelican under future climate change scenarios.
format: application/pdf
format: text/html
creator: Jaime A. Cursach
creator: Aldo Arriagada
creator: Jaime R. Rau
creator: Jaime Ojeda
creator: Gustavo Bizama
creator: Anderson Becerra
subject: Biogeography
subject: Conservation Biology
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.7642
publisher: PeerJ Inc.
rights: © 2019 Cursach et al.
abstract: Background The effects of global climate change on species inhabiting marine ecosystems are of growing concern, especially for endemic species that are sensitive due to restricted distribution. One method employed for determining the effects of climate change on the distribution of these organisms is species distribution modeling. Methods We generated a model to evaluate the potential geographic distribution and breeding distribution of the Peruvian pelican (Pelecanus thagus). Based on maximum entropy modeling (MaxEnt), we identified the environmental factors that currently affect its geographic distribution and breeding. Then we predicted its future distribution range under two climate change scenarios: moderate (rcp 2.6) and severe (rcp 8.5). Results The mean daytime temperature range and marine primary productivity explain the current potential distribution and breeding of the pelican. Under the future climate change scenarios, the spatial distribution of the pelican is predicted to slightly change. While the breeding distribution of the pelican can benefit in the moderate scenario, it is predicted to decrease (near −20 %) in the severe scenario. Discussion The current potential geographic distribution of the pelican is influenced to a large extent by thermal conditions and primary productivity. Under the moderate scenario, a slight increase in pelican breeding distribution is predicted. This increase in habitable area is explained by the climatic conditions in southern Chile, and those climatic conditions will likely be similar to the current conditions of the central coast of Chile. We predict that the coasts of southern Chile will constitute an important refuge for the conservation of the Peruvian pelican under future climate change scenarios.
bibliographic citation: Cursach et al. (2019) Predicting the potential distribution of the endemic seabird Pelecanus thagus in the Humboldt Current Large Marine Ecosystem under different climate change scenarios. PeerJ 7:e7642 https://doi.org/10.7717/peerj.7642
date submitted: 2019-03-04
date accepted: 2019-08-07
issued: 2019-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cursach
  given name: Jaime A.
author list: Agent
  family name: Arriagada
  given name: Aldo
author list: Agent
  family name: Rau
  given name: Jaime R.
author list: Agent
  family name: Ojeda
  given name: Jaime
author list: Agent
  family name: Bizama
  given name: Gustavo
author list: Agent
  family name: Becerra
  given name: Anderson
doi: 10.7717/peerj.7642
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-25
copyright: ©2019 Cursach et al.
attribution name: Cursach et al.

Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV
type: item
type: AcademicArticle
description: Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.
format: application/pdf
format: text/html
creator: Dora Serdari
creator: Evangelia-Georgia Kostaki
creator: Dimitrios Paraskevis
creator: Alexandros Stamatakis
creator: Paschalia Kapli
subject: Biodiversity
subject: Computational Biology
subject: Taxonomy
subject: Virology
subject: Infectious Diseases
description: doi:10.7717/peerj.7754
publisher: PeerJ Inc.
rights: © 2019 Serdari et al.
abstract: Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.
bibliographic citation: Serdari et al. (2019) Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV. PeerJ 7:e7754 https://doi.org/10.7717/peerj.7754
date submitted: 2019-04-17
date accepted: 2019-08-26
issued: 2019-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Serdari
  given name: Dora
author list: Agent
  family name: Kostaki
  given name: Evangelia-Georgia
author list: Agent
  family name: Paraskevis
  given name: Dimitrios
author list: Agent
  family name: Stamatakis
  given name: Alexandros
author list: Agent
  family name: Kapli
  given name: Paschalia
doi: 10.7717/peerj.7754
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-25
copyright: ©2019 Serdari et al.
attribution name: Serdari et al.

Identification of hub genes and small-molecule compounds related to intracerebral hemorrhage with bioinformatics analysis
type: item
type: AcademicArticle
description: Background Because of the complex mechanisms of injury, conventional surgical treatment and early blood pressure control does not significantly reduce mortality or improve patient prognosis in cases of intracerebral hemorrhage (ICH). We aimed to identify the hub genes associated with intracerebral hemorrhage, to act as therapeutic targets, and to identify potential small-molecule compounds for treating ICH. Methods The GSE24265 dataset, consisting of data from four perihematomal brain tissues and seven contralateral brain tissues, was downloaded from the Gene Expression Omnibus (GEO) database and screened for differentially expressed genes (DEGs) in ICH, with a fold change (FC) value of (|log2FC|) > 2 and a P-value of <0.05 set as cut-offs. The functional annotation of DEGs was performed using Gene Ontology (GO) resources, and the cell signaling pathway analysis of DEGs was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG), with a P-value of <0.05 set as the cut-off. We constructed a protein-protein interaction (PPI) network to clarify the interrelationships between the different DEGs and to select the hub genes with significant interactions. Next, the DEGs were analyzed using the CMap tool to identify small-molecule compounds with potential therapeutic effects. Finally, we verified the expression levels of the hub genes by RT-qPCR on the rat ICH model. Result A total of 59 up-regulated genes and eight down-regulated genes associated with ICH were identified. The biological functions of DEGs associated with ICH are mainly involved in the inflammatory response, chemokine activity, and immune response. The KEGG analysis identified several pathways significantly associated with ICH, including but not limited to HIF-1, TNF, toll-like receptor, cytokine-cytokine receptor interaction, and chemokine molecules. A PPI network consisting of 57 nodes and 373 edges was constructed using STRING, and 10 hub genes were identified with Cytoscape software. These hub…
format: application/pdf
format: text/html
creator: Zhendong Liu
creator: Ruotian Zhang
creator: Xin Chen
creator: Penglei Yao
creator: Tao Yan
creator: Wenwu Liu
creator: Jiawei Yao
creator: Andrei Sokhatskii
creator: Ilgiz Gareev
creator: Shiguang Zhao
subject: Bioinformatics
subject: Molecular Biology
subject: Neurology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.7782
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Background Because of the complex mechanisms of injury, conventional surgical treatment and early blood pressure control does not significantly reduce mortality or improve patient prognosis in cases of intracerebral hemorrhage (ICH). We aimed to identify the hub genes associated with intracerebral hemorrhage, to act as therapeutic targets, and to identify potential small-molecule compounds for treating ICH. Methods The GSE24265 dataset, consisting of data from four perihematomal brain tissues and seven contralateral brain tissues, was downloaded from the Gene Expression Omnibus (GEO) database and screened for differentially expressed genes (DEGs) in ICH, with a fold change (FC) value of (|log2FC|) > 2 and a P-value of <0.05 set as cut-offs. The functional annotation of DEGs was performed using Gene Ontology (GO) resources, and the cell signaling pathway analysis of DEGs was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG), with a P-value of <0.05 set as the cut-off. We constructed a protein-protein interaction (PPI) network to clarify the interrelationships between the different DEGs and to select the hub genes with significant interactions. Next, the DEGs were analyzed using the CMap tool to identify small-molecule compounds with potential therapeutic effects. Finally, we verified the expression levels of the hub genes by RT-qPCR on the rat ICH model. Result A total of 59 up-regulated genes and eight down-regulated genes associated with ICH were identified. The biological functions of DEGs associated with ICH are mainly involved in the inflammatory response, chemokine activity, and immune response. The KEGG analysis identified several pathways significantly associated with ICH, including but not limited to HIF-1, TNF, toll-like receptor, cytokine-cytokine receptor interaction, and chemokine molecules. A PPI network consisting of 57 nodes and 373 edges was constructed using STRING, and 10 hub genes were identified with Cytoscape software. These hub…
bibliographic citation: Liu et al. (2019) Identification of hub genes and small-molecule compounds related to intracerebral hemorrhage with bioinformatics analysis. PeerJ 7:e7782 https://doi.org/10.7717/peerj.7782
date submitted: 2019-04-19
date accepted: 2019-08-28
issued: 2019-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Zhendong
author list: Agent
  family name: Zhang
  given name: Ruotian
author list: Agent
  family name: Chen
  given name: Xin
author list: Agent
  family name: Yao
  given name: Penglei
author list: Agent
  family name: Yan
  given name: Tao
author list: Agent
  family name: Liu
  given name: Wenwu
author list: Agent
  family name: Yao
  given name: Jiawei
author list: Agent
  family name: Sokhatskii
  given name: Andrei
author list: Agent
  family name: Gareev
  given name: Ilgiz
author list: Agent
  family name: Zhao
  given name: Shiguang
doi: 10.7717/peerj.7782
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-25
copyright: ©2019 Liu et al.
attribution name: Liu et al.

New Bohaiornis-like bird from the Early Cretaceous of China: enantiornithine interrelationships and flight performance
type: item
type: AcademicArticle
description: During the last decade, several Bohaiornis-like enantiornithine species—and numerous specimens—have been recognized from the celebrated Jehol Biota of northwestern China. In this paper, we describe the anatomy of another “bohaiornithid” species from the 125 million-year-old Yixian Formation of Liaoning Province, China. The new taxon differs from previously recognized “bohaiornithids” on a number of characters from the forelimb and shoulder girdle. We also provide a new phylogenetic framework for enantiornithine birds, which questions the monophyly of the previously recognized bohaiornithid clade and highlights ongoing challenges for resolving enantiornithine interrelationships. Additionally, we offer the first assessment of the flight properties of Bohaiornis-like enantiornithines. Our results indicate that while “bohaiornithids” were morphologically suited for flying through continuous flapping, they would have been unable to sustain prolonged flights. Such findings expand the flight strategies previously known for enantiornithines and other early birds.
format: application/pdf
format: text/html
creator: Luis M. Chiappe
creator: Meng Qingjin
creator: Francisco Serrano
creator: Trond Sigurdsen
creator: Wang Min
creator: Alyssa Bell
creator: Liu Di
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.7846
publisher: PeerJ Inc.
rights: © 2019 Chiappe et al.
abstract: During the last decade, several Bohaiornis-like enantiornithine species—and numerous specimens—have been recognized from the celebrated Jehol Biota of northwestern China. In this paper, we describe the anatomy of another “bohaiornithid” species from the 125 million-year-old Yixian Formation of Liaoning Province, China. The new taxon differs from previously recognized “bohaiornithids” on a number of characters from the forelimb and shoulder girdle. We also provide a new phylogenetic framework for enantiornithine birds, which questions the monophyly of the previously recognized bohaiornithid clade and highlights ongoing challenges for resolving enantiornithine interrelationships. Additionally, we offer the first assessment of the flight properties of Bohaiornis-like enantiornithines. Our results indicate that while “bohaiornithids” were morphologically suited for flying through continuous flapping, they would have been unable to sustain prolonged flights. Such findings expand the flight strategies previously known for enantiornithines and other early birds.
bibliographic citation: Chiappe et al. (2019) New Bohaiornis-like bird from the Early Cretaceous of China: enantiornithine interrelationships and flight performance. PeerJ 7:e7846 https://doi.org/10.7717/peerj.7846
date submitted: 2019-03-08
date accepted: 2019-09-08
issued: 2019-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chiappe
  given name: Luis M.
author list: Agent
  family name: Qingjin
  given name: Meng
author list: Agent
  family name: Serrano
  given name: Francisco
author list: Agent
  family name: Sigurdsen
  given name: Trond
author list: Agent
  family name: Min
  given name: Wang
author list: Agent
  family name: Bell
  given name: Alyssa
author list: Agent
  family name: Di
  given name: Liu
doi: 10.7717/peerj.7846
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-25
copyright: © 2019 Chiappe et al.
attribution name: Chiappe et al.

Strategies of elite Chinese gymnasts in coping with landing impact from backward somersault
type: item
type: AcademicArticle
description: This study aimed to investigate how elite Chinese gymnasts manage the landing impact from a backward somersault. Six international-level male gymnasts performed backward somersault tests with a synchronous collection of kinematics (250 Hz), ground reaction forces (1,000 Hz), and surface electromyography (EMG) (2,000 Hz). A 19-segment human model was developed and lower extremity joints torques were calculated by means of a computer simulation. The angles of the lower extremity joints initially extended and then flexed. These angular velocities of extension continued to decrease and the joint torques changed from extensor to flexor within 100 ms before touchdown. The angles of the hips, knees, and ankles flexed rapidly by 12°, 36°, and 29°, respectively, and the angular velocities of flexion, flexor torque, and EMG peaked sharply during the initial impact phase of the landing. The angles of the hips, knees, and ankles flexed at approximately 90°, 100°, and 80°, respectively. The torques were reversed with the extensor torques, showing a relatively high level of muscle activation during the terminal impact phase of the landing. The results showed that the international-level gymnasts first extended their lower extremity joints, then flexed just before touchdown. They continued flexing actively and rapidly in the initial impact phase and then extended to resist the landing impact and maintain body posture during the terminal impact phase of the landing. The information gained from this study could improve our understanding of the landings of elite gymnasts and assist in injury prevention.
format: application/pdf
format: text/html
creator: Chengliang Wu
creator: Weiya Hao
creator: Qichang Mei
creator: Xiaofei Xiao
creator: Xuhong Li
creator: Wei Sun
subject: Kinesiology
description: doi:10.7717/peerj.7914
publisher: PeerJ Inc.
rights: © 2019 Wu et al.
abstract: This study aimed to investigate how elite Chinese gymnasts manage the landing impact from a backward somersault. Six international-level male gymnasts performed backward somersault tests with a synchronous collection of kinematics (250 Hz), ground reaction forces (1,000 Hz), and surface electromyography (EMG) (2,000 Hz). A 19-segment human model was developed and lower extremity joints torques were calculated by means of a computer simulation. The angles of the lower extremity joints initially extended and then flexed. These angular velocities of extension continued to decrease and the joint torques changed from extensor to flexor within 100 ms before touchdown. The angles of the hips, knees, and ankles flexed rapidly by 12°, 36°, and 29°, respectively, and the angular velocities of flexion, flexor torque, and EMG peaked sharply during the initial impact phase of the landing. The angles of the hips, knees, and ankles flexed at approximately 90°, 100°, and 80°, respectively. The torques were reversed with the extensor torques, showing a relatively high level of muscle activation during the terminal impact phase of the landing. The results showed that the international-level gymnasts first extended their lower extremity joints, then flexed just before touchdown. They continued flexing actively and rapidly in the initial impact phase and then extended to resist the landing impact and maintain body posture during the terminal impact phase of the landing. The information gained from this study could improve our understanding of the landings of elite gymnasts and assist in injury prevention.
bibliographic citation: Wu et al. (2019) Strategies of elite Chinese gymnasts in coping with landing impact from backward somersault. PeerJ 7:e7914 https://doi.org/10.7717/peerj.7914
date submitted: 2019-04-19
date accepted: 2019-09-17
issued: 2019-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Chengliang
author list: Agent
  family name: Hao
  given name: Weiya
author list: Agent
  family name: Mei
  given name: Qichang
author list: Agent
  family name: Xiao
  given name: Xiaofei
author list: Agent
  family name: Li
  given name: Xuhong
author list: Agent
  family name: Sun
  given name: Wei
doi: 10.7717/peerj.7914
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-25
copyright: © 2019 Wu et al.
attribution name: Wu et al.

Investigating the significance of tumor-infiltrating immune cells for the prognosis of lung squamous cell carcinoma
type: item
type: AcademicArticle
description: Objective Increasing evidence has indicated an association between immune cells infiltration in LSCC and clinical outcome. The aim of this research was tantamount to comprehensively investigate the effect of 22 tumor infiltrating immune cells (TIICs) on the prognosis of LSCC patients. Methods In our research, the CIBERSORT algorithm was utilized to calculate the proportion of 22 TIICs in 502 cases from the TCGA cohort. Cases with a CIBERSORT P-value of <0.05 were kept for further study. Using the CIBERSORT algorithm, we first investigated the difference of immune infiltration between normal tissue and LSCC in 22 subpopulations of immune cells. Kaplan-Meier analysis was used to analyze the effect of 22 TIICs on the prognosis of LSCC. An immune risk score model was constructed based on TIICs correlated with LSCC-related recurrence. Multivariate cox regression analysis was used to investigate whether the immune risk score was an independent factor for prognosis prediction of LSCC. Nomogram was under construction to comprehensively predict the survival rate of LSCC. Results The results of the different analysis showed that except of memory B cells, naive CD4+T cells, T cells and activated NK cells, the remaining immune cells all had differential infiltration in normal tissues and LSCC (p < 0.05). Kaplan-Meier analysis revealed two immune cells statistically related to LSCC-related recurrence, including activated mast cells and follicular helper T cells. Immune risk score model was constructed based on three immune cells including resting memory CD4+T cells, activated mast cells and follicular helper T cells retained by forward stepwise regression analysis. The Kaplan-Meier curve indicated that patients in the high-risk group linked to poor outcome (P = 8.277e−03). ROC curve indicated that the immune risk score model was reliable in predicting recurrence risk (AUC = 0.614). Multivariate cox regression analysis showed that the immune risk score model was just an independe…
format: application/pdf
format: text/html
creator: Yueyan Zhu
creator: Xiaoqin Zhang
subject: Bioinformatics
subject: Oncology
description: doi:10.7717/peerj.7918
publisher: PeerJ Inc.
rights: © 2019 Zhu and Zhang
abstract: Objective Increasing evidence has indicated an association between immune cells infiltration in LSCC and clinical outcome. The aim of this research was tantamount to comprehensively investigate the effect of 22 tumor infiltrating immune cells (TIICs) on the prognosis of LSCC patients. Methods In our research, the CIBERSORT algorithm was utilized to calculate the proportion of 22 TIICs in 502 cases from the TCGA cohort. Cases with a CIBERSORT P-value of <0.05 were kept for further study. Using the CIBERSORT algorithm, we first investigated the difference of immune infiltration between normal tissue and LSCC in 22 subpopulations of immune cells. Kaplan-Meier analysis was used to analyze the effect of 22 TIICs on the prognosis of LSCC. An immune risk score model was constructed based on TIICs correlated with LSCC-related recurrence. Multivariate cox regression analysis was used to investigate whether the immune risk score was an independent factor for prognosis prediction of LSCC. Nomogram was under construction to comprehensively predict the survival rate of LSCC. Results The results of the different analysis showed that except of memory B cells, naive CD4+T cells, T cells and activated NK cells, the remaining immune cells all had differential infiltration in normal tissues and LSCC (p < 0.05). Kaplan-Meier analysis revealed two immune cells statistically related to LSCC-related recurrence, including activated mast cells and follicular helper T cells. Immune risk score model was constructed based on three immune cells including resting memory CD4+T cells, activated mast cells and follicular helper T cells retained by forward stepwise regression analysis. The Kaplan-Meier curve indicated that patients in the high-risk group linked to poor outcome (P = 8.277e−03). ROC curve indicated that the immune risk score model was reliable in predicting recurrence risk (AUC = 0.614). Multivariate cox regression analysis showed that the immune risk score model was just an independe…
bibliographic citation: Zhu et al. (2019) Investigating the significance of tumor-infiltrating immune cells for the prognosis of lung squamous cell carcinoma. PeerJ 7:e7918 https://doi.org/10.7717/peerj.7918
date submitted: 2019-06-21
date accepted: 2019-09-18
issued: 2019-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Yueyan
author list: Agent
  family name: Zhang
  given name: Xiaoqin
doi: 10.7717/peerj.7918
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-25
copyright: ©2019 Zhu and Zhang
attribution name: Zhu and Zhang

Combined effect of the entomopathogenic fungus Metarhizium robertsii and avermectins on the survival and immune response of Aedes aegypti larvae
type: item
type: AcademicArticle
description: Combination of insect pathogenic fungi and microbial metabolites is a prospective method for mosquito control. The effect of the entomopathogenic fungus Metarhizium robertsii J.F. Bischoff, S.A. Rehner & Humber and avermectins on the survival and physiological parameters of Aedes aegypti (Linnaeus, 1762) larvae (dopamine concentration, glutathione S-transferase (GST), nonspecific esterases (EST), acid proteases, lysozyme-like, phenoloxidase (PO) activities) was studied. It is shown that the combination of these agents leads to a synergistic effect on mosquito mortality. Colonization of Ae. aegypti larvae by hyphal bodies following water inoculation with conidia is shown for the first time. The larvae affected by fungi are characterized by a decrease in PO and dopamine levels. In the initial stages of toxicosis and/or fungal infection (12 h posttreatment), increases in the activity of insect detoxifying enzymes (GST and EST) and acid proteases are observed after monotreatments, and these increases are suppressed after combined treatment with the fungus and avermectins. Lysozyme-like activity is also most strongly suppressed under combined treatment with the fungus and avermectins in the early stages posttreatment (12 h). Forty-eight hours posttreatment, we observe increases in GST, EST, acid proteases, and lysozyme-like activities under the influence of the fungus and/or avermectins. The larvae affected by avermectins accumulate lower levels of conidia than avermectin-free larvae. On the other hand, a burst of bacterial CFUs is observed under treatment with both the fungus and avermectins. We suggest that disturbance of the responses of the immune and detoxifying systems under the combined treatment and the development of opportunistic bacteria may be among the causes of the synergistic effect.
format: application/pdf
format: text/html
creator: Yuriy A. Noskov
creator: Olga V. Polenogova
creator: Olga N. Yaroslavtseva
creator: Olga E. Belevich
creator: Yuriy A. Yurchenko
creator: Ekaterina A. Chertkova
creator: Natalya A. Kryukova
creator: Vadim Yu Kryukov
creator: Viktor V. Glupov
subject: Ecology
subject: Entomology
subject: Parasitology
subject: Toxicology
description: doi:10.7717/peerj.7931
publisher: PeerJ Inc.
rights: © 2019 Noskov et al.
abstract: Combination of insect pathogenic fungi and microbial metabolites is a prospective method for mosquito control. The effect of the entomopathogenic fungus Metarhizium robertsii J.F. Bischoff, S.A. Rehner & Humber and avermectins on the survival and physiological parameters of Aedes aegypti (Linnaeus, 1762) larvae (dopamine concentration, glutathione S-transferase (GST), nonspecific esterases (EST), acid proteases, lysozyme-like, phenoloxidase (PO) activities) was studied. It is shown that the combination of these agents leads to a synergistic effect on mosquito mortality. Colonization of Ae. aegypti larvae by hyphal bodies following water inoculation with conidia is shown for the first time. The larvae affected by fungi are characterized by a decrease in PO and dopamine levels. In the initial stages of toxicosis and/or fungal infection (12 h posttreatment), increases in the activity of insect detoxifying enzymes (GST and EST) and acid proteases are observed after monotreatments, and these increases are suppressed after combined treatment with the fungus and avermectins. Lysozyme-like activity is also most strongly suppressed under combined treatment with the fungus and avermectins in the early stages posttreatment (12 h). Forty-eight hours posttreatment, we observe increases in GST, EST, acid proteases, and lysozyme-like activities under the influence of the fungus and/or avermectins. The larvae affected by avermectins accumulate lower levels of conidia than avermectin-free larvae. On the other hand, a burst of bacterial CFUs is observed under treatment with both the fungus and avermectins. We suggest that disturbance of the responses of the immune and detoxifying systems under the combined treatment and the development of opportunistic bacteria may be among the causes of the synergistic effect.
bibliographic citation: Noskov et al. (2019) Combined effect of the entomopathogenic fungus Metarhizium robertsii and avermectins on the survival and immune response of Aedes aegypti larvae. PeerJ 7:e7931 https://doi.org/10.7717/peerj.7931
date submitted: 2019-07-10
date accepted: 2019-09-23
issued: 2019-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Noskov
  given name: Yuriy A.
author list: Agent
  family name: Polenogova
  given name: Olga V.
author list: Agent
  family name: Yaroslavtseva
  given name: Olga N.
author list: Agent
  family name: Belevich
  given name: Olga E.
author list: Agent
  family name: Yurchenko
  given name: Yuriy A.
author list: Agent
  family name: Chertkova
  given name: Ekaterina A.
author list: Agent
  family name: Kryukova
  given name: Natalya A.
author list: Agent
  family name: Kryukov
  given name: Vadim Yu
author list: Agent
  family name: Glupov
  given name: Viktor V.
doi: 10.7717/peerj.7931
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-25
copyright: ©2019 Noskov et al.
attribution name: Noskov et al.

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