PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Clostridioides difficile infection after cardiac surgery: Assessment of prevalence, risk factors and clinical outcomes—retrospective study
items: The predisposing factors of AKI for prophylactic strategies in burn care
items: Coral reefs as a source of climate-active aerosols
items: The mechanism of the plant roots’ soil-reinforcement based on generalized equivalent confining pressure
items: Hydrological and soil physiochemical variables determine the rhizospheric microbiota in subtropical lakeshore areas
items: Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast
items: Expression of collagen type 1 alpha 1 indicates lymph node metastasis and poor outcomes in squamous cell carcinomas of the lung
items: The role of m6A-related genes in the prognosis and immune microenvironment of pancreatic adenocarcinoma
items: No one-size-fits-all solution to clean GBIF
items: Identification of an 8-miRNA signature as a potential prognostic biomarker for glioma

Clostridioides difficile infection after cardiac surgery: Assessment of prevalence, risk factors and clinical outcomes—retrospective study
type: item
type: AcademicArticle
description: Background Clostridioides difficile infection (CDI) is the most common cause of hospital-acquired diarrhea. There is little available data regarding risk factors of CDI for patients who undergo cardiac surgery. The study evaluated the course of CDI in patients after cardiac surgery. Methods Of 6,198 patients studied, 70 (1.1%) developed CDI. The control group consisted of 73 patients in whom CDI was excluded. Perioperative data and clinical outcomes were analyzed. Results Patients with CDI were significantly older in comparison to the control group (median age 73.0 vs 67.0, P = 0.005) and more frequently received proton pump inhibitors, statins, β-blockers and acetylsalicylic acid before surgery (P = 0.008, P = 0.012, P = 0.004, and P = 0.001, respectively). In addition, the presence of atherosclerosis, coronary disease and history of malignant neoplasms correlated positively with the development of CDI (P = 0.012, P = 0.036 and P = 0.05, respectively). There were no differences in the type or timing of surgery, aortic cross-clamp and cardiopulmonary bypass time, volume of postoperative drainage and administration of blood products between the studied groups. Relapse was more common among overweight patients with high postoperative plasma glucose or patients with higher C-reactive protein during the first episode of CDI, as well as those with a history of coronary disease or diabetes mellitus (P = 0.005, P = 0.030, P = 0.009, P = 0.049, and P = 0.025, respectively). Fifteen patients died (21.4%) from the CDI group and 7 (9.6%) from the control group (P = 0.050). Emergent procedures, prolonged stay in the intensive care unit, longer mechanical ventilation and high white blood cell count during the diarrhea were associated with higher mortality among patients with CDI (P = 0.05, P = 0.041, P = 0.004 and P = 0.007, respectively). Conclusions The study did not reveal any specific cardiac surgery-related risk factors for development of CDI.
format: application/pdf
format: text/html
creator: Anna Rzucidło-Hymczak
creator: Hubert Hymczak
creator: Aldona Olechowska-Jarząb
creator: Anna Gorczyca
creator: Boguslaw Kapelak
creator: Rafał Drwiła
creator: Dariusz Plicner
subject: Cardiology
subject: Epidemiology
subject: Infectious Diseases
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.9972
publisher: PeerJ Inc.
rights: © 2020 Rzucidło-Hymczak et al.
abstract: Background Clostridioides difficile infection (CDI) is the most common cause of hospital-acquired diarrhea. There is little available data regarding risk factors of CDI for patients who undergo cardiac surgery. The study evaluated the course of CDI in patients after cardiac surgery. Methods Of 6,198 patients studied, 70 (1.1%) developed CDI. The control group consisted of 73 patients in whom CDI was excluded. Perioperative data and clinical outcomes were analyzed. Results Patients with CDI were significantly older in comparison to the control group (median age 73.0 vs 67.0, P = 0.005) and more frequently received proton pump inhibitors, statins, β-blockers and acetylsalicylic acid before surgery (P = 0.008, P = 0.012, P = 0.004, and P = 0.001, respectively). In addition, the presence of atherosclerosis, coronary disease and history of malignant neoplasms correlated positively with the development of CDI (P = 0.012, P = 0.036 and P = 0.05, respectively). There were no differences in the type or timing of surgery, aortic cross-clamp and cardiopulmonary bypass time, volume of postoperative drainage and administration of blood products between the studied groups. Relapse was more common among overweight patients with high postoperative plasma glucose or patients with higher C-reactive protein during the first episode of CDI, as well as those with a history of coronary disease or diabetes mellitus (P = 0.005, P = 0.030, P = 0.009, P = 0.049, and P = 0.025, respectively). Fifteen patients died (21.4%) from the CDI group and 7 (9.6%) from the control group (P = 0.050). Emergent procedures, prolonged stay in the intensive care unit, longer mechanical ventilation and high white blood cell count during the diarrhea were associated with higher mortality among patients with CDI (P = 0.05, P = 0.041, P = 0.004 and P = 0.007, respectively). Conclusions The study did not reveal any specific cardiac surgery-related risk factors for development of CDI.
bibliographic citation: Rzucidło-Hymczak et al. (2020) Clostridioides difficile infection after cardiac surgery: Assessment of prevalence, risk factors and clinical outcomes—retrospective study. PeerJ 8:e9972 https://doi.org/10.7717/peerj.9972
date submitted: 2020-06-12
date accepted: 2020-08-26
issued: 2020-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rzucidło-Hymczak
  given name: Anna
author list: Agent
  family name: Hymczak
  given name: Hubert
author list: Agent
  family name: Olechowska-Jarząb
  given name: Aldona
author list: Agent
  family name: Gorczyca
  given name: Anna
author list: Agent
  family name: Kapelak
  given name: Boguslaw
author list: Agent
  family name: Drwiła
  given name: Rafał
author list: Agent
  family name: Plicner
  given name: Dariusz
doi: 10.7717/peerj.9972
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-29
copyright: ©2020 Rzucidło-Hymczak et al.
attribution name: Rzucidło-Hymczak et al.

The predisposing factors of AKI for prophylactic strategies in burn care
type: item
type: AcademicArticle
description: Background Acute kidney injury (AKI) is one of the most severe complications of burn injury. AKI with severe burn injury causes high mortality. This study aims to investigate the incidence of and predisposing factors for AKI in burn patients. Methods This is a single-center, retrospective, descriptive criterion standard study conducted from June 27, 2015, to March 8, 2016. We used Kidney Disease Improving Global Outcomes criteria to define and select patients with AKI. The study was conducted by recruiting in hospital patients who suffered from the flammable cornstarch-based powder explosion and were treated under primary care procedures. A total of 49 patients who suffered from flammable dust explosion-related burn injury were enrolled and admitted on June 27, 2015. The patients with more than 20% total body surface area of burn were transferred to the intensive care unit. Patients received fluid resuscitation in the first 24 hours based on the Parkland formula. The primary measurements were the incidence of and predisposing factors for AKI in these patients. Demographic characteristics, laboratory data, and inpatient outcomes were also evaluated. The incidence of AKI in this cohort was 61.2% (n = 30). The mortality rate was 2.0% (n = 1) during a 59-day follow-up period. The multivariate analysis revealed inhalation injury (adjusted OR = 22.0; 95% CI [1.4–358.2]) and meeting ≥3 American Burn Association (ABA) sepsis criteria (adjusted OR = 13.7; 95% CI [1.7–110.5]) as independent risk factors for early advanced AKI. Conclusions The incidence rate of AKI was higher in this cohort than in previous studies, possibly due to the flammable dust explosion-related burn injury. However, the mortality was lower than that expected. In clinical practice, indicators of inflammation, including ABA sepsis criteria may help in predicting the risk of AKI in patients with burn injury.
format: application/pdf
format: text/html
creator: Shin-Yi Tsai
creator: Chon-Fu Lio
creator: Shou-Chuan Shih
creator: Cheng-Jui Lin
creator: Yu-Tien Chen
creator: Chia-Meng Yu
creator: Fang-ju Sun
creator: Chien-Feng Kuo
creator: Xiaofeng Jia
subject: Emergency and Critical Care
subject: Health Policy
subject: Internal Medicine
subject: Public Health
subject: Translational Medicine
description: doi:10.7717/peerj.9984
publisher: PeerJ Inc.
rights: © 2020 Tsai et al.
abstract: Background Acute kidney injury (AKI) is one of the most severe complications of burn injury. AKI with severe burn injury causes high mortality. This study aims to investigate the incidence of and predisposing factors for AKI in burn patients. Methods This is a single-center, retrospective, descriptive criterion standard study conducted from June 27, 2015, to March 8, 2016. We used Kidney Disease Improving Global Outcomes criteria to define and select patients with AKI. The study was conducted by recruiting in hospital patients who suffered from the flammable cornstarch-based powder explosion and were treated under primary care procedures. A total of 49 patients who suffered from flammable dust explosion-related burn injury were enrolled and admitted on June 27, 2015. The patients with more than 20% total body surface area of burn were transferred to the intensive care unit. Patients received fluid resuscitation in the first 24 hours based on the Parkland formula. The primary measurements were the incidence of and predisposing factors for AKI in these patients. Demographic characteristics, laboratory data, and inpatient outcomes were also evaluated. The incidence of AKI in this cohort was 61.2% (n = 30). The mortality rate was 2.0% (n = 1) during a 59-day follow-up period. The multivariate analysis revealed inhalation injury (adjusted OR = 22.0; 95% CI [1.4–358.2]) and meeting ≥3 American Burn Association (ABA) sepsis criteria (adjusted OR = 13.7; 95% CI [1.7–110.5]) as independent risk factors for early advanced AKI. Conclusions The incidence rate of AKI was higher in this cohort than in previous studies, possibly due to the flammable dust explosion-related burn injury. However, the mortality was lower than that expected. In clinical practice, indicators of inflammation, including ABA sepsis criteria may help in predicting the risk of AKI in patients with burn injury.
bibliographic citation: Tsai et al. (2020) The predisposing factors of AKI for prophylactic strategies in burn care. PeerJ 8:e9984 https://doi.org/10.7717/peerj.9984
date submitted: 2019-09-19
date accepted: 2020-08-27
issued: 2020-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tsai
  given name: Shin-Yi
author list: Agent
  family name: Lio
  given name: Chon-Fu
author list: Agent
  family name: Shih
  given name: Shou-Chuan
author list: Agent
  family name: Lin
  given name: Cheng-Jui
author list: Agent
  family name: Chen
  given name: Yu-Tien
author list: Agent
  family name: Yu
  given name: Chia-Meng
author list: Agent
  family name: Sun
  given name: Fang-ju
author list: Agent
  family name: Kuo
  given name: Chien-Feng
author list: Agent
  family name: Jia
  given name: Xiaofeng
doi: 10.7717/peerj.9984
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-29
copyright: ©2020 Tsai et al.
attribution name: Tsai et al.

Coral reefs as a source of climate-active aerosols
type: item
type: AcademicArticle
description: We review the evidence for bio-regulation by coral reefs of local climate through stress-induced emissions of aerosol precursors, such as dimethylsulfide. This is an issue that goes to the core of the coral ecosystem’s ability to maintain homeostasis in the face of increasing climate change impacts and other anthropogenic pressures. We examine this through an analysis of data on aerosol emissions by corals of the Great Barrier Reef, Australia. We focus on the relationship with local stressors, such as surface irradiance levels and sea surface temperature, both before and after notable coral bleaching events. We conclude that coral reefs may be able to regulate their exposure to environmental stressors through modification of the optical properties of the atmosphere, however this ability may be impaired as climate change intensifies.
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format: text/html
creator: Rebecca L. Jackson
creator: Albert J. Gabric
creator: Roger Cropp
subject: Biosphere Interactions
subject: Climate Change Biology
subject: Atmospheric Chemistry
subject: Biogeochemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.10023
publisher: PeerJ Inc.
rights: © 2020 Jackson et al.
abstract: We review the evidence for bio-regulation by coral reefs of local climate through stress-induced emissions of aerosol precursors, such as dimethylsulfide. This is an issue that goes to the core of the coral ecosystem’s ability to maintain homeostasis in the face of increasing climate change impacts and other anthropogenic pressures. We examine this through an analysis of data on aerosol emissions by corals of the Great Barrier Reef, Australia. We focus on the relationship with local stressors, such as surface irradiance levels and sea surface temperature, both before and after notable coral bleaching events. We conclude that coral reefs may be able to regulate their exposure to environmental stressors through modification of the optical properties of the atmosphere, however this ability may be impaired as climate change intensifies.
bibliographic citation: Jackson et al. (2020) Coral reefs as a source of climate-active aerosols. PeerJ 8:e10023 https://doi.org/10.7717/peerj.10023
date submitted: 2020-03-10
date accepted: 2020-09-02
issued: 2020-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jackson
  given name: Rebecca L.
author list: Agent
  family name: Gabric
  given name: Albert J.
author list: Agent
  family name: Cropp
  given name: Roger
doi: 10.7717/peerj.10023
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-29
copyright: © 2020 Jackson et al.
attribution name: Jackson et al.

The mechanism of the plant roots’ soil-reinforcement based on generalized equivalent confining pressure
type: item
type: AcademicArticle
description: Background To quantitatively evaluate the contribution of plant roots to soil shear strength, the generalized equivalent confining pressure (GECP), which is the difference in confining pressure between the reinforced and un-reinforced soil specimens at the same shear strength, was proposed and considered in terms of the function of plant roots in soil reinforcement. Methods In this paper, silt loam soil was selected as the test soil, and the roots of Indigofera amblyantha were chosen as the reinforcing material. Different drainage conditions (consolidation drained (CD), consolidation undrained (CU), and unconsolidated undrained (UU)) were used to analyse the influences of different root distribution patterns (horizontal root (HR), vertical root (VR), and complex root (CR)) and root contents (0.25%, 0.50%, and 0.75%) on the shear strength of soil-root composites. Results The cohesion (c) values of the soil-root composites varied under different drainage conditions and root contents, while the internal friction angle (φ ) values remain basically stable under different drainage conditions. Under the same root content and drainage conditions, the shear strength indexes ranked in order of lower to higher were HR, VR and CR. The GECP of the soil-root composites with a 0.75% root content was 1.5–2.0 times that with a 0.50% root content and more than 5 times that with a 0.25% root content under the CD and CU conditions. The GECP in reinforced soil followed the sequence of CD > CU > UU. The GECP of the plant roots increased as confining pressure increased under CD and CU conditions while showed a complex change to the confining pressure under the UU condition. Conclusion It was concluded that the evaluation of plant root reinforcing soil based on GECP can be used to measure effectively the influences of roots on soil under different drainage conditions and root distribution patterns.
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format: text/html
creator: Ping Guo
creator: Zhenyao Xia
creator: Qi Liu
creator: Hai Xiao
creator: Feng Gao
creator: Lun Zhang
creator: Mingyi Li
creator: Yueshu Yang
creator: Wennian Xu
subject: Plant Science
subject: Soil Science
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.10064
publisher: PeerJ Inc.
rights: © 2020 Guo et al.
abstract: Background To quantitatively evaluate the contribution of plant roots to soil shear strength, the generalized equivalent confining pressure (GECP), which is the difference in confining pressure between the reinforced and un-reinforced soil specimens at the same shear strength, was proposed and considered in terms of the function of plant roots in soil reinforcement. Methods In this paper, silt loam soil was selected as the test soil, and the roots of Indigofera amblyantha were chosen as the reinforcing material. Different drainage conditions (consolidation drained (CD), consolidation undrained (CU), and unconsolidated undrained (UU)) were used to analyse the influences of different root distribution patterns (horizontal root (HR), vertical root (VR), and complex root (CR)) and root contents (0.25%, 0.50%, and 0.75%) on the shear strength of soil-root composites. Results The cohesion (c) values of the soil-root composites varied under different drainage conditions and root contents, while the internal friction angle (φ ) values remain basically stable under different drainage conditions. Under the same root content and drainage conditions, the shear strength indexes ranked in order of lower to higher were HR, VR and CR. The GECP of the soil-root composites with a 0.75% root content was 1.5–2.0 times that with a 0.50% root content and more than 5 times that with a 0.25% root content under the CD and CU conditions. The GECP in reinforced soil followed the sequence of CD > CU > UU. The GECP of the plant roots increased as confining pressure increased under CD and CU conditions while showed a complex change to the confining pressure under the UU condition. Conclusion It was concluded that the evaluation of plant root reinforcing soil based on GECP can be used to measure effectively the influences of roots on soil under different drainage conditions and root distribution patterns.
bibliographic citation: Guo et al. (2020) The mechanism of the plant roots’ soil-reinforcement based on generalized equivalent confining pressure. PeerJ 8:e10064 https://doi.org/10.7717/peerj.10064
date submitted: 2020-03-11
date accepted: 2020-09-08
issued: 2020-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Ping
author list: Agent
  family name: Xia
  given name: Zhenyao
author list: Agent
  family name: Liu
  given name: Qi
author list: Agent
  family name: Xiao
  given name: Hai
author list: Agent
  family name: Gao
  given name: Feng
author list: Agent
  family name: Zhang
  given name: Lun
author list: Agent
  family name: Li
  given name: Mingyi
author list: Agent
  family name: Yang
  given name: Yueshu
author list: Agent
  family name: Xu
  given name: Wennian
doi: 10.7717/peerj.10064
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-29
copyright: ©2020 Guo et al.
attribution name: Guo et al.

Hydrological and soil physiochemical variables determine the rhizospheric microbiota in subtropical lakeshore areas
type: item
type: AcademicArticle
description: Background Due to intensive sluice construction and other human disturbances, lakeshore vegetation has been destroyed and ecosystems greatly changed. Rhizospheric microbiota constitute a key part of a functioning rhizosphere ecosystem. Maintaining rhizosphere microbial diversity is a central, critical issue for sustaining these rhizospheric microbiota functions and associated ecosystem services. However, the community composition and abiotic factors influencing rhizospheric microbiota in lakeshore remain largely understudied. Methods The spatiotemporal composition of lakeshore rhizospheric microbiota and the factors shaping them were seasonally investigated in three subtropical floodplain lakes (Lake Chaohu, Lake Wuchang, and Lake Dahuchi) along the Yangtze River in China through 16S rRNA amplicon high-throughput sequencing. Results Our results showed that four archaeal and 21 bacterial phyla (97.04 ± 0.25% of total sequences) dominated the rhizospheric microbiota communities of three lakeshore areas. Moreover, we uncovered significant differences among rhizospheric microbiota among the lakes, seasons, and average submerged depths. The Acidobacteria, Actinobacteria, Bacteroidetes, Bathyarchaeota, Gemmatimonadetes, and Proteobacteria differed significantly among the three lakes, with more than half of these dominant phyla showing significant changes in abundance between seasons, while the DHVEG-6, Ignavibacteriae, Nitrospirae, Spirochaetes, and Zixibacteria varied considerably across the average submerged depths (n = 58 sites in total). Canonical correspondence analyses revealed that the fluctuation range of water level and pH were the most important factors influencing the microbial communities and their dominant microbiota, followed by total nitrogen, moisture, and total phosphorus in soil. These results suggest a suite of hydrological and soil physiochemical variables together governed the differential structuring of rhizospheric microbiota composition among diffe…
format: application/pdf
format: text/html
creator: Xiaoke Zhang
creator: Huili Wang
creator: Zhifei Li
creator: Jun Xie
creator: Jiajia Ni
subject: Ecosystem Science
subject: Microbiology
subject: Soil Science
subject: Ecohydrology
subject: Environmental Impacts
description: doi:10.7717/peerj.10078
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Background Due to intensive sluice construction and other human disturbances, lakeshore vegetation has been destroyed and ecosystems greatly changed. Rhizospheric microbiota constitute a key part of a functioning rhizosphere ecosystem. Maintaining rhizosphere microbial diversity is a central, critical issue for sustaining these rhizospheric microbiota functions and associated ecosystem services. However, the community composition and abiotic factors influencing rhizospheric microbiota in lakeshore remain largely understudied. Methods The spatiotemporal composition of lakeshore rhizospheric microbiota and the factors shaping them were seasonally investigated in three subtropical floodplain lakes (Lake Chaohu, Lake Wuchang, and Lake Dahuchi) along the Yangtze River in China through 16S rRNA amplicon high-throughput sequencing. Results Our results showed that four archaeal and 21 bacterial phyla (97.04 ± 0.25% of total sequences) dominated the rhizospheric microbiota communities of three lakeshore areas. Moreover, we uncovered significant differences among rhizospheric microbiota among the lakes, seasons, and average submerged depths. The Acidobacteria, Actinobacteria, Bacteroidetes, Bathyarchaeota, Gemmatimonadetes, and Proteobacteria differed significantly among the three lakes, with more than half of these dominant phyla showing significant changes in abundance between seasons, while the DHVEG-6, Ignavibacteriae, Nitrospirae, Spirochaetes, and Zixibacteria varied considerably across the average submerged depths (n = 58 sites in total). Canonical correspondence analyses revealed that the fluctuation range of water level and pH were the most important factors influencing the microbial communities and their dominant microbiota, followed by total nitrogen, moisture, and total phosphorus in soil. These results suggest a suite of hydrological and soil physiochemical variables together governed the differential structuring of rhizospheric microbiota composition among diffe…
bibliographic citation: Zhang et al. (2020) Hydrological and soil physiochemical variables determine the rhizospheric microbiota in subtropical lakeshore areas. PeerJ 8:e10078 https://doi.org/10.7717/peerj.10078
date submitted: 2020-05-06
date accepted: 2020-09-10
issued: 2020-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiaoke
author list: Agent
  family name: Wang
  given name: Huili
author list: Agent
  family name: Li
  given name: Zhifei
author list: Agent
  family name: Xie
  given name: Jun
author list: Agent
  family name: Ni
  given name: Jiajia
doi: 10.7717/peerj.10078
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-29
copyright: ©2020 Zhang et al.
attribution name: Zhang et al.

Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast
type: item
type: AcademicArticle
description: Background The genomic sequences of centromeres, as well as the set of proteins that recognize and interact with centromeres, are known to quickly diverge between lineages potentially contributing to post-zygotic reproductive isolation. However, the actual sequence of events and processes involved in the divergence of the kinetochore machinery is not known. The patterns of gene loss that occur during evolution concomitant with phenotypic changes have been used to understand the timing and order of molecular changes. Methods I screened the high-quality genomes of twenty budding yeast species for the presence of well-studied kinetochore genes. Based on the conserved gene order and complete genome assemblies, I identified gene loss events. Subsequently, I searched the intergenic regions to identify any un-annotated genes or gene remnants to obtain additional evidence of gene loss. Results My analysis identified the loss of four genes (NKP1, NKP2, CENPL/IML3 and CENPN/CHL4) of the inner kinetochore constitutive centromere-associated network (CCAN/also known as CTF19 complex in yeast) in both the Naumovozyma species for which genome assemblies are available. Surprisingly, this collective loss of four genes of the CCAN/CTF19 complex coincides with the emergence of unconventional centromeres in N. castellii and N. dairenensis. My study suggests a tentative link between the emergence of unconventional point centromeres and the turnover of kinetochore genes in budding yeast.
format: application/pdf
format: text/html
creator: Nagarjun Vijay
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Mycology
description: doi:10.7717/peerj.10085
publisher: PeerJ Inc.
rights: © 2020 Vijay
abstract: Background The genomic sequences of centromeres, as well as the set of proteins that recognize and interact with centromeres, are known to quickly diverge between lineages potentially contributing to post-zygotic reproductive isolation. However, the actual sequence of events and processes involved in the divergence of the kinetochore machinery is not known. The patterns of gene loss that occur during evolution concomitant with phenotypic changes have been used to understand the timing and order of molecular changes. Methods I screened the high-quality genomes of twenty budding yeast species for the presence of well-studied kinetochore genes. Based on the conserved gene order and complete genome assemblies, I identified gene loss events. Subsequently, I searched the intergenic regions to identify any un-annotated genes or gene remnants to obtain additional evidence of gene loss. Results My analysis identified the loss of four genes (NKP1, NKP2, CENPL/IML3 and CENPN/CHL4) of the inner kinetochore constitutive centromere-associated network (CCAN/also known as CTF19 complex in yeast) in both the Naumovozyma species for which genome assemblies are available. Surprisingly, this collective loss of four genes of the CCAN/CTF19 complex coincides with the emergence of unconventional centromeres in N. castellii and N. dairenensis. My study suggests a tentative link between the emergence of unconventional point centromeres and the turnover of kinetochore genes in budding yeast.
bibliographic citation: Vijay (2020) Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast. PeerJ 8:e10085 https://doi.org/10.7717/peerj.10085
date submitted: 2020-06-18
date accepted: 2020-09-11
issued: 2020-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vijay
  given name: Nagarjun
doi: 10.7717/peerj.10085
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-29
copyright: © 2020 Vijay
attribution name: Vijay

Expression of collagen type 1 alpha 1 indicates lymph node metastasis and poor outcomes in squamous cell carcinomas of the lung
type: item
type: AcademicArticle
description: Background Squamous cell carcinomas of the lung are an extremely common and deadly form of non-small cell lung cancers. Clinical management of the disease is dependent on staging and metastatic status. Metastasis to the lymph node is especially crucial to diagnose as it occurs at an earlier stage. However, lymphadenectomies are invasive and tumor cells may be overlooked during evaluation.There are limited approved biomarkers for predicting lymph node metastasis with squamous cell carcinomas of the lung (LSCC). Methods Genome data of 60 tumor-adjacent samples were downloaded from Genome Expression Omnibus. We identified over-expressed HUB genes using Cytoscape as key prognostic markers. The selected markers were further evaluated based on gene ontology and overall expression levels compared to normal tissue using The Cancer Genome Atlas. We further validated these results using clinical biopsy tissue taken from squamous cell carcinoma patients. Results Analysis of the genome expression data resulted in 13 relevant hub genes that were differentially expressed in cancerous samples. All of these genes are associated with collagen biosynthesis within the tumor microenvironment. We chose Collagen Type 1 Alpha 1 (COL1A1) as the most relevant prognostic marker due to its high number of pathway connections and over expression in the tumor microenvironment compared to the other 12 genes. Additionally, based on analysis of The Cancer Genome Atlas, tumors with higher levels of COL1A1 expression are associated with poorer overall survival. Finally, evaluation of clinical biopsy samples suggests that overexpression of COL1A1 in the LSCC microenvironment highly correlates with lymph node metastasis. These results suggest COL1A1 is a clinically relevant marker that should be used to justify lymphadenectomies.
format: application/pdf
format: text/html
creator: Siyuan Dong
creator: Peiyao Zhu
creator: Shuguang Zhang
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
subject: Surgery and Surgical Specialties
subject: Medical Genetics
description: doi:10.7717/peerj.10089
publisher: PeerJ Inc.
rights: © 2020 Dong et al.
abstract: Background Squamous cell carcinomas of the lung are an extremely common and deadly form of non-small cell lung cancers. Clinical management of the disease is dependent on staging and metastatic status. Metastasis to the lymph node is especially crucial to diagnose as it occurs at an earlier stage. However, lymphadenectomies are invasive and tumor cells may be overlooked during evaluation.There are limited approved biomarkers for predicting lymph node metastasis with squamous cell carcinomas of the lung (LSCC). Methods Genome data of 60 tumor-adjacent samples were downloaded from Genome Expression Omnibus. We identified over-expressed HUB genes using Cytoscape as key prognostic markers. The selected markers were further evaluated based on gene ontology and overall expression levels compared to normal tissue using The Cancer Genome Atlas. We further validated these results using clinical biopsy tissue taken from squamous cell carcinoma patients. Results Analysis of the genome expression data resulted in 13 relevant hub genes that were differentially expressed in cancerous samples. All of these genes are associated with collagen biosynthesis within the tumor microenvironment. We chose Collagen Type 1 Alpha 1 (COL1A1) as the most relevant prognostic marker due to its high number of pathway connections and over expression in the tumor microenvironment compared to the other 12 genes. Additionally, based on analysis of The Cancer Genome Atlas, tumors with higher levels of COL1A1 expression are associated with poorer overall survival. Finally, evaluation of clinical biopsy samples suggests that overexpression of COL1A1 in the LSCC microenvironment highly correlates with lymph node metastasis. These results suggest COL1A1 is a clinically relevant marker that should be used to justify lymphadenectomies.
bibliographic citation: Dong et al. (2020) Expression of collagen type 1 alpha 1 indicates lymph node metastasis and poor outcomes in squamous cell carcinomas of the lung. PeerJ 8:e10089 https://doi.org/10.7717/peerj.10089
date submitted: 2020-04-20
date accepted: 2020-09-13
issued: 2020-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Siyuan
author list: Agent
  family name: Zhu
  given name: Peiyao
author list: Agent
  family name: Zhang
  given name: Shuguang
doi: 10.7717/peerj.10089
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-29
copyright: ©2020 Dong et al.
attribution name: Dong et al.

The role of m6A-related genes in the prognosis and immune microenvironment of pancreatic adenocarcinoma
type: item
type: AcademicArticle
description: Background Pancreatic adenocarcinoma (PAAD) is among the most lethal diseases and has a dismal prognosis; however, efficient treatment is currently limited. Several studies have observed epigenetic variation during tumorigenesis, suggesting the potential role of RNA methylation, especially N6-methyladenosine (m6A) modification, as a novel epigenetic modification mediating PAAD prognosis. Methods The expression levels of m6A-related genes were downloaded from The Cancer Genome Atlas-Pancreatic Adenocarcinoma (TCGA) and Genotype-Tissue Expression (GTEx) projects, and the findings were validated in four Expression Omnibus (GEO) datasets. A predictive model was constructed using a lasso regression and evaluated by a survival analysis and receiver operating characteristic curve. Consensus clustering identified two distinct subgroups with different immune activity signatures based on the expression pattern of m6A-related genes. The relationship between the mutation state of m6A-related genes and infiltration of immune cells was established and visualized using Tumor Immune Estimation Resource (https://cistrome.shinyapps.io/timer/). Results Fourteen of twenty-one m6A-related genes were differentially expressed between PAAD and normal tissues in TCGA-GTEx cohort. Among these genes, HNRNPC, IGF2BP2 and YTHDF1 were further validated in four GEO datasets. Moreover, an m6A-based model exhibited moderate accuracy in predicting overall survival in PAAD samples. Additionally, potential m6A modification targets were screened by selecting genes from a set of 23,391 genes that not only harbored the most m6A-modified sites but also showed a robust correlation with PAAD survival. Moreover, we correlated the expression level of m6A-related genes with the immune microenvironment of pancreatic cancer for the first time. Specifically, both arm-level gain and deletion of ALKBH5 decreased the infiltration of CD8+T cells (P < 0.05 and P < 0.01, respectively). Conclusion Collectively, our find…
format: application/pdf
format: text/html
creator: Rong Tang
creator: Yiyin Zhang
creator: Chen Liang
creator: Jin Xu
creator: Qingcai Meng
creator: Jie Hua
creator: Jiang Liu
creator: Bo Zhang
creator: Xianjun Yu
creator: Si Shi
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.9602
publisher: PeerJ Inc.
rights: © 2020 Tang et al.
abstract: Background Pancreatic adenocarcinoma (PAAD) is among the most lethal diseases and has a dismal prognosis; however, efficient treatment is currently limited. Several studies have observed epigenetic variation during tumorigenesis, suggesting the potential role of RNA methylation, especially N6-methyladenosine (m6A) modification, as a novel epigenetic modification mediating PAAD prognosis. Methods The expression levels of m6A-related genes were downloaded from The Cancer Genome Atlas-Pancreatic Adenocarcinoma (TCGA) and Genotype-Tissue Expression (GTEx) projects, and the findings were validated in four Expression Omnibus (GEO) datasets. A predictive model was constructed using a lasso regression and evaluated by a survival analysis and receiver operating characteristic curve. Consensus clustering identified two distinct subgroups with different immune activity signatures based on the expression pattern of m6A-related genes. The relationship between the mutation state of m6A-related genes and infiltration of immune cells was established and visualized using Tumor Immune Estimation Resource (https://cistrome.shinyapps.io/timer/). Results Fourteen of twenty-one m6A-related genes were differentially expressed between PAAD and normal tissues in TCGA-GTEx cohort. Among these genes, HNRNPC, IGF2BP2 and YTHDF1 were further validated in four GEO datasets. Moreover, an m6A-based model exhibited moderate accuracy in predicting overall survival in PAAD samples. Additionally, potential m6A modification targets were screened by selecting genes from a set of 23,391 genes that not only harbored the most m6A-modified sites but also showed a robust correlation with PAAD survival. Moreover, we correlated the expression level of m6A-related genes with the immune microenvironment of pancreatic cancer for the first time. Specifically, both arm-level gain and deletion of ALKBH5 decreased the infiltration of CD8+T cells (P < 0.05 and P < 0.01, respectively). Conclusion Collectively, our find…
bibliographic citation: Tang et al. (2020) The role of m6A-related genes in the prognosis and immune microenvironment of pancreatic adenocarcinoma. PeerJ 8:e9602 https://doi.org/10.7717/peerj.9602
date submitted: 2020-03-30
date accepted: 2020-07-03
issued: 2020-09-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Rong
author list: Agent
  family name: Zhang
  given name: Yiyin
author list: Agent
  family name: Liang
  given name: Chen
author list: Agent
  family name: Xu
  given name: Jin
author list: Agent
  family name: Meng
  given name: Qingcai
author list: Agent
  family name: Hua
  given name: Jie
author list: Agent
  family name: Liu
  given name: Jiang
author list: Agent
  family name: Zhang
  given name: Bo
author list: Agent
  family name: Yu
  given name: Xianjun
author list: Agent
  family name: Shi
  given name: Si
doi: 10.7717/peerj.9602
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-28
copyright: ©2020 Tang et al.
attribution name: Tang et al.

No one-size-fits-all solution to clean GBIF
type: item
type: AcademicArticle
description: Species occurrence records provide the basis for many biodiversity studies. They derive from georeferenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accuracy constitutes a particular concern. Automatic filtering is a scalable and reproducible means to identify potentially problematic records and tailor datasets from public databases such as the Global Biodiversity Information Facility (GBIF; http://www.gbif.org), for biodiversity analyses. However, it is unclear how much data may be lost by filtering, whether the same filters should be applied across all taxonomic groups, and what the effect of filtering is on common downstream analyses. Here, we evaluate the effect of 13 recently proposed filters on the inference of species richness patterns and automated conservation assessments for 18 Neotropical taxa, including terrestrial and marine animals, fungi, and plants downloaded from GBIF. We find that a total of 44.3% of the records are potentially problematic, with large variation across taxonomic groups (25–90%). A small fraction of records was identified as erroneous in the strict sense (4.2%), and a much larger proportion as unfit for most downstream analyses (41.7%). Filters of duplicated information, collection year, and basis of record, as well as coordinates in urban areas, or for terrestrial taxa in the sea or marine taxa on land, have the greatest effect. Automated filtering can help in identifying problematic records, but requires customization of which tests and thresholds should be applied to the taxonomic group and geographic area under focus. Our results stress the importance of thorough recording and exploration of the meta-data associated with species records for biodiversity research.
format: application/pdf
format: text/html
creator: Alexander Zizka
creator: Fernanda Antunes Carvalho
creator: Alice Calvente
creator: Mabel Rocio Baez-Lizarazo
creator: Andressa Cabral
creator: Jéssica Fernanda Ramos Coelho
creator: Matheus Colli-Silva
creator: Mariana Ramos Fantinati
creator: Moabe F. Fernandes
creator: Thais Ferreira-Araújo
creator: Fernanda Gondim Lambert Moreira
creator: Nathália Michellyda Cunha Santos
creator: Tiago Andrade Borges Santos
creator: Renata Clicia dos Santos-Costa
creator: Filipe C. Serrano
creator: Ana Paula Alves da Silva
creator: Arthur de Souza Soares
creator: Paolla Gabryelle Cavalcante de Souza
creator: Eduardo Calisto Tomaz
creator: Valéria Fonseca Vale
creator: Tiago Luiz Vieira
creator: Alexandre Antonelli
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.9916
publisher: PeerJ Inc.
rights: © 2020 Zizka et al.
abstract: Species occurrence records provide the basis for many biodiversity studies. They derive from georeferenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accuracy constitutes a particular concern. Automatic filtering is a scalable and reproducible means to identify potentially problematic records and tailor datasets from public databases such as the Global Biodiversity Information Facility (GBIF; http://www.gbif.org), for biodiversity analyses. However, it is unclear how much data may be lost by filtering, whether the same filters should be applied across all taxonomic groups, and what the effect of filtering is on common downstream analyses. Here, we evaluate the effect of 13 recently proposed filters on the inference of species richness patterns and automated conservation assessments for 18 Neotropical taxa, including terrestrial and marine animals, fungi, and plants downloaded from GBIF. We find that a total of 44.3% of the records are potentially problematic, with large variation across taxonomic groups (25–90%). A small fraction of records was identified as erroneous in the strict sense (4.2%), and a much larger proportion as unfit for most downstream analyses (41.7%). Filters of duplicated information, collection year, and basis of record, as well as coordinates in urban areas, or for terrestrial taxa in the sea or marine taxa on land, have the greatest effect. Automated filtering can help in identifying problematic records, but requires customization of which tests and thresholds should be applied to the taxonomic group and geographic area under focus. Our results stress the importance of thorough recording and exploration of the meta-data associated with species records for biodiversity research.
bibliographic citation: Zizka et al. (2020) No one-size-fits-all solution to clean GBIF. PeerJ 8:e9916 https://doi.org/10.7717/peerj.9916
date submitted: 2020-03-17
date accepted: 2020-08-20
issued: 2020-09-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zizka
  given name: Alexander
author list: Agent
  family name: Antunes Carvalho
  given name: Fernanda
author list: Agent
  family name: Calvente
  given name: Alice
author list: Agent
  family name: Rocio Baez-Lizarazo
  given name: Mabel
author list: Agent
  family name: Cabral
  given name: Andressa
author list: Agent
  family name: Coelho
  given name: Jéssica Fernanda Ramos
author list: Agent
  family name: Colli-Silva
  given name: Matheus
author list: Agent
  family name: Fantinati
  given name: Mariana Ramos
author list: Agent
  family name: Fernandes
  given name: Moabe F.
author list: Agent
  family name: Ferreira-Araújo
  given name: Thais
author list: Agent
  family name: Gondim Lambert Moreira
  given name: Fernanda
author list: Agent
  family name: Santos
  given name: Nathália Michellyda Cunha
author list: Agent
  family name: Santos
  given name: Tiago Andrade Borges
author list: Agent
  family name: dos Santos-Costa
  given name: Renata Clicia
author list: Agent
  family name: Serrano
  given name: Filipe C.
author list: Agent
  family name: Alves da Silva
  given name: Ana Paula
author list: Agent
  family name: de Souza Soares
  given name: Arthur
author list: Agent
  family name: Cavalcante de Souza
  given name: Paolla Gabryelle
author list: Agent
  family name: Calisto Tomaz
  given name: Eduardo
author list: Agent
  family name: Vale
  given name: Valéria Fonseca
author list: Agent
  family name: Vieira
  given name: Tiago Luiz
author list: Agent
  family name: Antonelli
  given name: Alexandre
doi: 10.7717/peerj.9916
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-28
copyright: ©2020 Zizka et al.
attribution name: Zizka et al.

Identification of an 8-miRNA signature as a potential prognostic biomarker for glioma
type: item
type: AcademicArticle
description: Background Glioma is the most common form of primary malignant intracranial tumor. Methods In the current study, miRNA matrix were obtained from the Chinese Glioma Genome Atlas (CGGA), and then univariate Cox regression analysis and Lasso regression analysis were utilized to select candidate miRNAs and multivariate Cox regression analysis was applied to establish a miRNA signature for predicting overall survival (OS) of glioma. The signature was assessed with the area under the curve (AUC) of the receiver operating characteristic curve (ROC) and validated by data from Gene Expression Omnibus (GEO). Results Eight miRNAs (miR-1246, miR-148a, miR-150, miR-196a, miR-338-3p, miR-342-5p, miR-548h and miR-645) were included in the miRNA signature. The AUC of ROC analysis for 1- and 3-year OS in the CGGA dataset was 0.747 and 0.905, respectively. In the GEO dataset, The AUC for 1- and 3-year was 0.736 and 0.809, respectively. The AUC in both the CGGA and GEO datasets was similar to that based on WHO 2007 classification (0.736 and 0.799) and WHO 2016 classification (0.663 and 0.807). Additionally, Kaplan–Meier plot revealed that high-risk score patients had a poorer clinical outcome. Multivariate Cox regression analysis suggested that the miRNA signature was an independent prognosis-related factor [HR: 6.579, 95% CI [1.227−35.268], p = 0.028]. Conclusion On the whole, in the present study, based on eight miRNAs, a novel prognostic signature was developed for predicting the 1- and 3- year survival rate in glioma. The results may be conducive to predict the precise prognosis of glioma and to elucidate the underlying molecular mechanisms. However, further experimental researches of miRNAs are needed to validate the findings of this study.
format: application/pdf
format: text/html
creator: Baowei Ji
creator: Lihua Chen
creator: Qiang Cai
creator: Qiao Guo
creator: Zhibiao Chen
creator: Du He
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.9943
publisher: PeerJ Inc.
rights: © 2020 Ji et al.
abstract: Background Glioma is the most common form of primary malignant intracranial tumor. Methods In the current study, miRNA matrix were obtained from the Chinese Glioma Genome Atlas (CGGA), and then univariate Cox regression analysis and Lasso regression analysis were utilized to select candidate miRNAs and multivariate Cox regression analysis was applied to establish a miRNA signature for predicting overall survival (OS) of glioma. The signature was assessed with the area under the curve (AUC) of the receiver operating characteristic curve (ROC) and validated by data from Gene Expression Omnibus (GEO). Results Eight miRNAs (miR-1246, miR-148a, miR-150, miR-196a, miR-338-3p, miR-342-5p, miR-548h and miR-645) were included in the miRNA signature. The AUC of ROC analysis for 1- and 3-year OS in the CGGA dataset was 0.747 and 0.905, respectively. In the GEO dataset, The AUC for 1- and 3-year was 0.736 and 0.809, respectively. The AUC in both the CGGA and GEO datasets was similar to that based on WHO 2007 classification (0.736 and 0.799) and WHO 2016 classification (0.663 and 0.807). Additionally, Kaplan–Meier plot revealed that high-risk score patients had a poorer clinical outcome. Multivariate Cox regression analysis suggested that the miRNA signature was an independent prognosis-related factor [HR: 6.579, 95% CI [1.227−35.268], p = 0.028]. Conclusion On the whole, in the present study, based on eight miRNAs, a novel prognostic signature was developed for predicting the 1- and 3- year survival rate in glioma. The results may be conducive to predict the precise prognosis of glioma and to elucidate the underlying molecular mechanisms. However, further experimental researches of miRNAs are needed to validate the findings of this study.
bibliographic citation: Ji et al. (2020) Identification of an 8-miRNA signature as a potential prognostic biomarker for glioma. PeerJ 8:e9943 https://doi.org/10.7717/peerj.9943
date submitted: 2020-04-03
date accepted: 2020-08-24
issued: 2020-09-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ji
  given name: Baowei
author list: Agent
  family name: Chen
  given name: Lihua
author list: Agent
  family name: Cai
  given name: Qiang
author list: Agent
  family name: Guo
  given name: Qiao
author list: Agent
  family name: Chen
  given name: Zhibiao
author list: Agent
  family name: He
  given name: Du
doi: 10.7717/peerj.9943
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-28
copyright: ©2020 Ji et al.
attribution name: Ji et al.

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